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1. High-dimensional single-cell analysis of human natural killer cell heterogeneity.

Author

Rebuffet, Lucas, Melsen, Janine, Escalière, Bertrand, Basurto-Lozada, Daniela, Bhandoola, Avinash, Björkström, Niklas, Bryceson, Yenan, Castriconi, Roberta, Cichocki, Frank, Colonna, Marco, Davis, Daniel, Diefenbach, Andreas, Ding, Yi, Haniffa, Muzlifah, Horowitz, Amir, Lanier, Lewis, Malmberg, Karl-Johan, Miller, Jeffrey, Moretta, Lorenzo, Narni-Mancinelli, Emilie, ONeill, Luke, Romagnani, Chiara, Ryan, Dylan, Sivori, Simona, Sun, Dan, Vagne, Constance, and Vivier, Eric

Subjects
Humans, Single-Cell Analysis, Killer Cells, Natural, Transcriptome, Neoplasms, Lymphocyte Subsets, Palatine Tonsil, Gene Expression Profiling, Lung, Cytokines
Abstract

Natural killer (NK) cells are innate lymphoid cells (ILCs) contributing to immune responses to microbes and tumors. Historically, their classification hinged on a limited array of surface protein markers. Here, we used single-cell RNA sequencing (scRNA-seq) and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) to dissect the heterogeneity of NK cells. We identified three prominent NK cell subsets in healthy human blood: NK1, NK2 and NK3, further differentiated into six distinct subgroups. Our findings delineate the molecular characteristics, key transcription factors, biological functions, metabolic traits and cytokine responses of each subgroup. These data also suggest two separate ontogenetic origins for NK cells, leading to divergent transcriptional trajectories. Furthermore, we analyzed the distribution of NK cell subsets in the lung, tonsils and intraepithelial lymphocytes isolated from healthy individuals and in 22 tumor types. This standardized terminology aims at fostering clarity and consistency in future research, thereby improving cross-study comparisons.

Published
2024

2. Cross-regulation of antibody responses against the SARS-CoV-2 Spike protein and commensal microbiota via molecular mimicry

Author

Bondareva, Marina, Budzinski, Lisa, Durek, Pawel, Witkowski, Mario, Angermair, Stefan, Ninnemann, Justus, Kreye, Jakob, Letz, Philine, Ferreira-Gomes, Marta, Semin, Iaroslav, Guerra, Gabriela Maria, Momsen Reincke, S., Sánchez-Sendin, Elisa, Yilmaz, Selin, Sempert, Toni, Heinz, Gitta Anne, Tizian, Caroline, Raftery, Martin, Schönrich, Günther, Matyushkina, Daria, Smirnov, Ivan V., Govorun, Vadim M., Schrezenmeier, Eva, Stefanski, Anna-Luisa, Dörner, Thomas, Zocche, Silvia, Viviano, Edoardo, Klement, Nele, Sehmsdorf, Katharina Johanna, Lunin, Alexander, Chang, Hyun-Dong, Drutskaya, Marina, Kozlovskaya, Liubov, Treskatsch, Sascha, Radbruch, Andreas, Diefenbach, Andreas, Prüss, Harald, Enghard, Philipp, Mashreghi, Mir-Farzin, and Kruglov, Andrey A.

Published
2023
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4. Non-redundant functions of group 2 innate lymphoid cells

Author

Jarick, Katja J., Topczewska, Patrycja M., Jakob, Manuel O., Yano, Hiroshi, Arifuzzaman, Mohammad, Gao, Xuemei, Boulekou, Sotiria, Stokic-Trtica, Vladislava, Leclère, Pierre S., Preußer, Alexandra, Rompe, Zoe A., Stamm, Anton, Tsou, Amy M., Chu, Coco, Heinrich, Frederik R., Guerra, Gabriela M., Durek, Pawel, Ivanov, Andranik, Beule, Dieter, Helfrich, Sofia, Duerr, Claudia U., Kühl, Anja A., Stehle, Christina, Romagnani, Chiara, Mashreghi, Mir-Farzin, Diefenbach, Andreas, Artis, David, and Klose, Christoph S. N.

Published
2022
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5. 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

6. ILC3s restrict the dissemination of intestinal bacteria to safeguard liver regeneration after surgery

Author

Jakob, Manuel O., Spari, Daniel, Sànchez Taltavull, Daniel, Salm, Lilian, Yilmaz, Bahtiyar, Doucet Ladevèze, Rémi, Mooser, Catherine, Pereyra, David, Ouyang, Ye, Schmidt, Theresa, Mattiola, Irene, Starlinger, Patrick, Stroka, Deborah, Tschan, Franziska, Candinas, Daniel, Gasteiger, Georg, Klose, Christoph S.N., Diefenbach, Andreas, Gomez de Agüero, Mercedes, and Beldi, Guido

Published
2023
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7. Antigen-presenting innate lymphoid cells orchestrate neuroinflammation

Author

Grigg, John B., Shanmugavadivu, Arthi, Regen, Tommy, Parkhurst, Christopher N., Ahmed, Anees, Joseph, Ann M., Mazzucco, Michael, Gronke, Konrad, Diefenbach, Andreas, Eberi, Gerard, Vartanian, Timothy, Waisman, Ari, and Sonnnberg, Gregory F.

Subjects
Inflammation -- Development and progression, Antigens -- Physiological aspects, Lymphoid tissue -- Physiological aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Pro-inflammatory T cells in the central nervous system (CNS) are causally associated with multiple demyelinating and neurodegenerative diseases.sup.1-6, but the pathways that control these responses remain unclear. Here we define a population of inflammatory group 3 innate lymphoid cells (ILC3s) that infiltrate the CNS in a mouse model of multiple sclerosis. These ILC3s are derived from the circulation, localize in proximity to infiltrating T cells in the CNS, function as antigen-presenting cells that restimulate myelin-specific T cells, and are increased in individuals with multiple sclerosis. Notably, antigen presentation by inflammatory ILC3s is required to promote T cell responses in the CNS and the development of multiple-sclerosis-like disease in mouse models. By contrast, conventional and tissue-resident ILC3s in the periphery do not appear to contribute to disease induction, but instead limit autoimmune T cell responses and prevent multiple-sclerosis-like disease when experimentally targeted to present myelin antigen. Collectively, our data define a population of inflammatory ILC3s that is essential for directly promoting T-cell-dependent neuroinflammation in the CNS and reveal the potential of harnessing peripheral tissue-resident ILC3s for the prevention of autoimmune disease. A subset of inflammatory group 3 innate lymphoid cells, here termed iILC3s, infiltrate the central nervous system and promote neuroinflammation and disease progression in a mouse model of multiple sclerosis., Author(s): John B. Grigg [sup.1] [sup.2] [sup.3] , Arthi Shanmugavadivu [sup.4] , Tommy Regen [sup.4] , Christopher N. Parkhurst [sup.1] [sup.2] [sup.3] , Anees Ahmed [sup.1] [sup.2] [sup.3] , Ann [...]

Published
2021
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8. Untimely TGFβ responses in COVID-19 limit antiviral functions of NK cells

Author

Witkowski, Mario, Tizian, Caroline, Ferreira-Gomes, Marta, Niemeyer, Daniela, Jones, Terry C., Heinrich, Frederik, Frischbutter, Stefan, Angermair, Stefan, Hohnstein, Thordis, Mattiola, Irene, Nawrath, Philipp, McEwen, Sophie, Zocche, Silvia, Viviano, Edoardo, Heinz, Gitta Anne, Maurer, Marcus, Kölsch, Uwe, Chua, Robert Lorenz, Aschman, Tom, Meisel, Christian, Radke, Josefine, Sawitzki, Birgit, Roehmel, Jobst, Allers, Kristina, Moos, Verena, Schneider, Thomas, Hanitsch, Leif, Mall, Marcus A., Conrad, Christian, Radbruch, Helena, Duerr, Claudia U., Trapani, Joseph A., Marcenaro, Emanuela, Kallinich, Tilmann, Corman, Victor M., Kurth, Florian, Sander, Leif Erik, Drosten, Christian, Treskatsch, Sascha, Durek, Pawel, Kruglov, Andrey, Radbruch, Andreas, Mashreghi, Mir-Farzin, and Diefenbach, Andreas

Published
2021
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9. Thirty years of VRE in Germany – “expect the unexpected”: The view from the National Reference Centre for Staphylococci and Enterococci

Author

Becker, Karsten, Borgmann, Stefan, Diefenbach, Andreas, Hamprecht, Axel, Hogardt, Michael, Wichelhaus, Thomas, Kemp, Volkhard, Huebner, Nils-Olaf, Kaasch, Achim, Geginat, Gernot, Kohnen, Wolfgang, Menzer, Alexander, Krause, T., Miethke, Thomas, Pranada, Felix, Radojn, Florian, Tobisch, Steffen, Jansen, Verena, Regnath, Thomas, Bührlen, Uwe, Schneider-Brachert, Wulf, Schwarz, Roman, Luemen, Michaela, Skov, Robert, Thuermer, Alexander, Baum, Heike von, Weig, Michael, Uwe, Groß, Zabel, Lutz, Wulffen, Hinrik von, Döring, Stefanie, Werner, Guido, Neumann, Bernd, Weber, Robert E., Kresken, Michael, Wendt, Constanze, and Bender, Jennifer K.

Published
2020
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10. SARS-CoV-2 in severe COVID-19 induces a TGF-β-dominated chronic immune response that does not target itself

Author

Ferreira-Gomes, Marta, Kruglov, Andrey, Durek, Pawel, Heinrich, Frederik, Tizian, Caroline, Heinz, Gitta Anne, Pascual-Reguant, Anna, Du, Weijie, Mothes, Ronja, Fan, Chaofan, Frischbutter, Stefan, Habenicht, Katharina, Budzinski, Lisa, Ninnemann, Justus, Jani, Peter K., Guerra, Gabriela Maria, Lehmann, Katrin, Matz, Mareen, Ostendorf, Lennard, Heiberger, Lukas, Chang, Hyun-Dong, Bauherr, Sandy, Maurer, Marcus, Schönrich, Günther, Raftery, Martin, Kallinich, Tilmann, Mall, Marcus Alexander, Angermair, Stefan, Treskatsch, Sascha, Dörner, Thomas, Corman, Victor Max, Diefenbach, Andreas, Volk, Hans-Dieter, Elezkurtaj, Sefer, Winkler, Thomas H., Dong, Jun, Hauser, Anja Erika, Radbruch, Helena, Witkowski, Mario, Melchers, Fritz, Radbruch, Andreas, and Mashreghi, Mir-Farzin

Published
2021
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12. Divergent roles for STAT4 in shaping differentiation of cytotoxic ILC1 and NK cells during gut inflammation

Author

Scarno, Gianluca, primary, Mazej, Julija, additional, Laffranchi, Mattia, additional, Di Censo, Chiara, additional, Mattiola, Irene, additional, Candelotti, Arianna M., additional, Pietropaolo, Giuseppe, additional, Stabile, Helena, additional, Fionda, Cinzia, additional, Peruzzi, Giovanna, additional, Brooks, Stephen R., additional, Tsai, Wanxia Li, additional, Mikami, Yohei, additional, Bernardini, Giovanni, additional, Gismondi, Angela, additional, Sozzani, Silvano, additional, Di Santo, James P., additional, Vosshenrich, Christian A. J., additional, Diefenbach, Andreas, additional, Gadina, Massimo, additional, Santoni, Angela, additional, and Sciumè, Giuseppe, additional

Published
2023
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15. Impaired humoral and cellular immunity after SARS-CoV-2 BNT162b2 (tozinameran) prime-boost vaccination in kidney transplant recipients

Author

Sattler, Arne, Schrezenmeier, Eva, Weber, Ulrike A., Potekhin, Alexander, Bachmann, Friederike, Straub-Hohenbleicher, Henriette, Budde, Klemens, Storz, Elena, Pross, Vanessa, Bergmann, Yasmin, Thole, Linda M.L., Tizian, Caroline, Holsken, Oliver, Diefenbach, Andreas, Schrezenmeier, Hubert, Jahrsdorfer, Bernd, Zemojtel, Tomasz, Jechow, Katharina, Conrad, Christian, Lukassen, Soren, Stauch, Diana, Lachmann, Nils, Choi, Mira, Halleck, Fabian, and Kotsch, Katja

Subjects
Kidneys -- Transplantation, Cellular immunity -- Health aspects, Organ transplant recipients -- Drug therapy -- Physiological aspects, Health care industry
Abstract

Novel mRNA-based vaccines have been proven to be powerful tools in combating the global pandemic caused by SARS-CoV-2, with BNT162b2 (trade name: Comirnaty) efficiently protecting individuals from COVID-19 across a broad age range. Still, it remains largely unknown how renal insufficiency and immunosuppressive medication affect development of vaccine-induced immunity. We therefore comprehensively analyzed humoral and cellular responses in kidney transplant recipients after the standard second vaccination dose. As opposed to all healthy vaccinees and the majority of hemodialysis patients, only 4 of 39 and 1 of 39 transplanted individuals showed IgA and IgG seroconversion at day 8 [+ or -] 1 after booster immunization, with minor changes until day 23 [+ or -] 5, respectively. Although most transplanted patients mounted spike-specific T helper cell responses, frequencies were significantly reduced compared with those in controls and dialysis patients and this was accompanied by a broad impairment in effector cytokine production, memory differentiation, and activation-related signatures. Spike-specific [CD8.sup.+] T cell responses were less abundant than their [CD4.sup.+] counterparts in healthy controls and hemodialysis patients and almost undetectable in transplant patients. Promotion of anti-HLA antibodies or acute rejection was not detected after vaccination. In summary, our data strongly suggest revised vaccination approaches in immunosuppressed patients, including individual immune monitoring for protection of this vulnerable group at risk of developing severe COVID-19., Introduction Kidney transplant (KTx) recipients and patients suffering from kidney failure are imperiled by increased infection risks, either due to dialysis-associated (reviewed in ref. 1) or therapeutic immunosuppression (IS). This [...]

Published
2021
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20. Transcription Factors Controlling Innate Lymphoid Cell Fate Decisions

Author

Klose, Christoph S. N., Diefenbach, Andreas, Compans, Richard W, Series editor, Cooper, Max D., Series editor, Gleba, Yuri Y., Series editor, Honjo, Tasuku, Series editor, Oldstone, Michael B. A., Series editor, Vogt, Peter K., Series editor, Malissen, Bernard, Series editor, Aktories, Klaus, Series editor, Kawaoka, Yoshihiro, Series editor, Rappuoli, Rino, Series editor, Galan, Jorge E., Series editor, Ahmed, Rafi, Series editor, Ellmeier, Wilfried, editor, and Taniuchi, Ichiro, editor

Published
2014
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21. An interdisciplinary approach to characterize peanut‐allergic patients—First data from the FOOD@ consortium

Author

Worm, Margitta, primary, Alexiou, Aikaterina, additional, Höfer, Veronika, additional, Birkner, Till, additional, Jeanrenaud, Alexander C. S. N., additional, Fauchère, Florent, additional, Pazur, Kristijan, additional, Steinert, Carolin, additional, Arnau‐Soler, Aleix, additional, Banerjee, Priyanka, additional, Diefenbach, Andreas, additional, Dobbertin‐Welsch, Josefine, additional, Dölle‐Bierke, Sabine, additional, Francuzik, Wojciech, additional, Ghauri, Ahla, additional, Heller, Stephanie, additional, Kalb, Birgit, additional, Löber, Ulrike, additional, Marenholz, Ingo, additional, Markó, Lajos, additional, Scheffel, Jörg, additional, Potapenko, Olena, additional, Roll, Stephanie, additional, Lau, Susanne, additional, Lee, Young‐Ae, additional, Braun, Julian, additional, Thiel, Andreas, additional, Babina, Magda, additional, Altrichter, Sabine, additional, Forslund, Sofia Kirke, additional, and Beyer, Kirsten, additional

Published
2022
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22. An interdisciplinary approach to characterize peanut-allergic patients - first data from the FOOD@ consortium

Author

Worm, Margitta M., Alexiou, Aikaterina, Höfer, Veronika, Birkner, Till, Jeanrenaud, Alexander C.S.N., Fauchère, Florent, Pažur, Kristijan, Steinert, Carolin, Arnau-Soler, Aleix, Banerjee, Priyanka, Diefenbach, Andreas, Dobbertin-Welsch, Josefine, Dölle-Bierke, Sabine, Francuzik, W., Ghauri, Ahla, Heller, Stephanie, Kalb, Birgit, Löber, Ulrike, Marenholz, Ingo, Markó, Lajos, Scheffel, Jörg, Potapenko, Olena, Roll, Stephanie, Lau, Susanne, Lee, Young-ae, Braun, Julian, Thiel, Andreas, Babina, Magda, Altrichter, Sabine, Forslund, Sofia Kirke, Beyer, Kirsten, and Publica

Subjects
food allergy, epigenetics, Cardiovascular and Metabolic Diseases, biomarker, microbiome, peanut allergy
Abstract

Background: Peanut allergy is a frequent cause of food allergy and potentially life-threatening. Within this interdisciplinary research approach, we aim to unravel the complex mechanisms of peanut allergy. As a first step were applied in an exploratory manner the analysis of peanut allergic versus non-allergic controls. Methods: Biosamples were studied regarding DNA methylation signatures, gut microbiome, adaptive and innate immune cell populations, soluble signaling molecules and allergen-reactive antibody specificities. We applied a scalable systems medicine computational workflow to the assembled data. Results: We identified combined cellular and soluble biomarker signatures that stratify donors into peanut-allergic and non-allergic with high specificity. DNA methylation profiling revealed various genes of interest and stool microbiota differences in bacteria abundances. Conclusion: By extending our findings to a larger set of patients (e.g., children vs. adults), we will establish predictors for food allergy and tolerance and translate these as for example, indicators for interventional studies.

Published
2022

28. Natural killer cell activation enhances immune pathology and promotes chronic infection by limiting CD8⁺ T-cell immunity

Author

Lang, Philipp A., Lang, Karl S., Xu, Haifeng C., Grusdat, Melanie, Parish, Ian A., Recher, Mike, Elford, Alisha R., Dhanji, Salim, Shaabani, Namir, Tran, Charles W., Dissanayake, Dilan, Rahbar, Ramtin, Ghazarian, Magar, Brüstle, Anne, Fine, Jason, Chen, Peter, Weaver, Casey T., Klose, Christoph, Diefenbach, Andreas, Häussinger, Dieter, Carlyle, James R., Kaech, Susan M., Mak, Tak W., and Ohashi, Pamela S.

Published
2012

29. Type 1 innate lymphoid cells regulate the onset of Toxoplasma gondii-induced neuroinflammation

Author

Steffen, Johannes, primary, Ehrentraut, Stefanie, additional, Bank, Ute, additional, Biswas, Aindrila, additional, Figueiredo, Caio Andreeta, additional, Hölsken, Oliver, additional, Düsedau, Henning Peter, additional, Dovhan, Vladyslava, additional, Knop, Laura, additional, Thode, Jacqueline, additional, Romero-Suárez, Silvina, additional, Duarte, Carmen Infante, additional, Gigley, Jason, additional, Romagnani, Chiara, additional, Diefenbach, Andreas, additional, Klose, Christoph S.N., additional, Schüler, Thomas, additional, and Dunay, Ildiko Rita, additional

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

Author

Cossarizza, Andrea, primary, Chang, Hyun‐Dong, additional, Radbruch, Andreas, additional, Abrignani, Sergio, additional, Addo, Richard, additional, Akdis, Mübeccel, additional, Andrä, Immanuel, additional, Andreata, Francesco, additional, Annunziato, Francesco, additional, Arranz, Eduardo, additional, Bacher, Petra, additional, Bari, Sudipto, additional, Barnaba, Vincenzo, additional, Barros‐Martins, Joana, additional, Baumjohann, Dirk, additional, Beccaria, Cristian G., additional, Bernardo, David, additional, Boardman, Dominic A., additional, Borger, Jessica, additional, Böttcher, Chotima, additional, Brockmann, Leonie, additional, Burns, Marie, additional, Busch, Dirk H., additional, Cameron, Garth, additional, Cammarata, Ilenia, additional, Cassotta, Antonino, additional, Chang, Yinshui, additional, Chirdo, Fernando Gabriel, additional, Christakou, Eleni, additional, Čičin‐Šain, Luka, additional, Cook, Laura, additional, Corbett, Alexandra J., additional, Cornelis, Rebecca, additional, Cosmi, Lorenzo, additional, Davey, Martin S., additional, De Biasi, Sara, additional, De Simone, Gabriele, additional, del Zotto, Genny, additional, Delacher, Michael, additional, Di Rosa, Francesca, additional, Di Santo, James, additional, Diefenbach, Andreas, additional, Dong, Jun, additional, Dörner, Thomas, additional, Dress, Regine J., additional, Dutertre, Charles‐Antoine, additional, Eckle, Sidonia B. G., additional, Eede, Pascale, additional, Evrard, Maximilien, additional, Falk, Christine S., additional, Feuerer, Markus, additional, Fillatreau, Simon, additional, Fiz‐Lopez, Aida, additional, Follo, Marie, additional, Foulds, Gemma A., additional, Fröbel, Julia, additional, Gagliani, Nicola, additional, Galletti, Giovanni, additional, Gangaev, Anastasia, additional, Garbi, Natalio, additional, Garrote, José Antonio, additional, Geginat, Jens, additional, Gherardin, Nicholas A., additional, Gibellini, Lara, additional, Ginhoux, Florent, additional, Godfrey, Dale I., additional, Gruarin, Paola, additional, Haftmann, Claudia, additional, Hansmann, Leo, additional, Harpur, Christopher M., additional, Hayday, Adrian C., additional, Heine, Guido, additional, Hernández, Daniela Carolina, additional, Herrmann, Martin, additional, Hoelsken, Oliver, additional, Huang, Qing, additional, Huber, Samuel, additional, Huber, Johanna E., additional, Huehn, Jochen, additional, Hundemer, Michael, additional, Hwang, William Y. K., additional, Iannacone, Matteo, additional, Ivison, Sabine M., additional, Jäck, Hans‐Martin, additional, Jani, Peter K., additional, Keller, Baerbel, additional, Kessler, Nina, additional, Ketelaars, Steven, additional, Knop, Laura, additional, Knopf, Jasmin, additional, Koay, Hui‐Fern, additional, Kobow, Katja, additional, Kriegsmann, Katharina, additional, Kristyanto, H., additional, Krueger, Andreas, additional, Kuehne, Jenny F., additional, Kunze‐Schumacher, Heike, additional, Kvistborg, Pia, additional, Kwok, Immanuel, additional, Latorre, Daniela, additional, Lenz, Daniel, additional, Levings, Megan K., additional, Lino, Andreia C., additional, Liotta, Francesco, additional, Long, Heather M., additional, Lugli, Enrico, additional, MacDonald, Katherine N., additional, Maggi, Laura, additional, Maini, Mala K., additional, Mair, Florian, additional, Manta, Calin, additional, Manz, Rudolf Armin, additional, Mashreghi, Mir‐Farzin, additional, Mazzoni, Alessio, additional, McCluskey, James, additional, Mei, Henrik E., additional, Melchers, Fritz, additional, Melzer, Susanne, additional, Mielenz, Dirk, additional, Monin, Leticia, additional, Moretta, Lorenzo, additional, Multhoff, Gabriele, additional, Muñoz, Luis Enrique, additional, Muñoz‐Ruiz, Miguel, additional, Muscate, Franziska, additional, Natalini, Ambra, additional, Neumann, Katrin, additional, Ng, Lai Guan, additional, Niedobitek, Antonia, additional, Niemz, Jana, additional, Almeida, Larissa Nogueira, additional, Notarbartolo, Samuele, additional, Ostendorf, Lennard, additional, Pallett, Laura J., additional, Patel, Amit A., additional, Percin, Gulce Itir, additional, Peruzzi, Giovanna, additional, Pinti, Marcello, additional, Pockley, A. Graham, additional, Pracht, Katharina, additional, Prinz, Immo, additional, Pujol‐Autonell, Irma, additional, Pulvirenti, Nadia, additional, Quatrini, Linda, additional, Quinn, Kylie M., additional, Radbruch, Helena, additional, Rhys, Hefin, additional, Rodrigo, Maria B., additional, Romagnani, Chiara, additional, Saggau, Carina, additional, Sakaguchi, Shimon, additional, Sallusto, Federica, additional, Sanderink, Lieke, additional, Sandrock, Inga, additional, Schauer, Christine, additional, Scheffold, Alexander, additional, Scherer, Hans U., additional, Schiemann, Matthias, additional, Schildberg, Frank A., additional, Schober, Kilian, additional, Schoen, Janina, additional, Schuh, Wolfgang, additional, Schüler, Thomas, additional, Schulz, Axel R., additional, Schulz, Sebastian, additional, Schulze, Julia, additional, Simonetti, Sonia, additional, Singh, Jeeshan, additional, Sitnik, Katarzyna M., additional, Stark, Regina, additional, Starossom, Sarah, additional, Stehle, Christina, additional, Szelinski, Franziska, additional, Tan, Leonard, additional, Tarnok, Attila, additional, Tornack, Julia, additional, Tree, Timothy I. M., additional, van Beek, Jasper J. P., additional, van de Veen, Willem, additional, van Gisbergen, Klaas, additional, Vasco, Chiara, additional, Verheyden, Nikita A., additional, von Borstel, Anouk, additional, Ward‐Hartstonge, Kirsten A., additional, Warnatz, Klaus, additional, Waskow, Claudia, additional, Wiedemann, Annika, additional, Wilharm, Anneke, additional, Wing, James, additional, Wirz, Oliver, additional, Wittner, Jens, additional, Yang, Jennie H. M., additional, and Yang, Juhao, additional

Published
2021
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33. Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19

Author

Krämer, Benjamin, primary, Knoll, Rainer, additional, Bonaguro, Lorenzo, additional, ToVinh, Michael, additional, Raabe, Jan, additional, Astaburuaga-García, Rosario, additional, Schulte-Schrepping, Jonas, additional, Kaiser, Kim Melanie, additional, Rieke, Gereon J., additional, Bischoff, Jenny, additional, Monin, Malte B., additional, Hoffmeister, Christoph, additional, Schlabe, Stefan, additional, De Domenico, Elena, additional, Reusch, Nico, additional, Händler, Kristian, additional, Reynolds, Gary, additional, Blüthgen, Nils, additional, Hack, Gudrun, additional, Finnemann, Claudia, additional, Nischalke, Hans D., additional, Strassburg, Christian P., additional, Stephenson, Emily, additional, Su, Yapeng, additional, Gardner, Louis, additional, Yuan, Dan, additional, Chen, Daniel, additional, Goldman, Jason, additional, Rosenstiel, Philipp, additional, Schmidt, Susanne V., additional, Latz, Eicke, additional, Hrusovsky, Kevin, additional, Ball, Andrew J., additional, Johnson, Joe M., additional, Koenig, Paul-Albert, additional, Schmidt, Florian I., additional, Haniffa, Muzlifah, additional, Heath, James R., additional, Kümmerer, Beate M., additional, Keitel, Verena, additional, Jensen, Björn, additional, Stubbemann, Paula, additional, Kurth, Florian, additional, Sander, Leif E., additional, Sawitzki, Birgit, additional, Aschenbrenner, Anna C., additional, Schultze, Joachim L., additional, Nattermann, Jacob, additional, Altmüller, Janine, additional, Angelov, Angel, additional, Bals, Robert, additional, Bartholomäus, Alexander, additional, Becker, Anke, additional, Becker, Matthias, additional, Bezdan, Daniela, additional, Bitzer, Michael, additional, Blumert, Conny, additional, Bonifacio, Ezio, additional, Bork, Peer, additional, Boyke, Bunk, additional, Blum, Helmut, additional, Casadei, Nicolas, additional, Clavel, Thomas, additional, Colome-Tatche, Maria, additional, Cornberg, Markus, additional, De La Rosa Velázquez, Inti Alberto, additional, Diefenbach, Andreas, additional, Dilthey, Alexander, additional, Fischer, Nicole, additional, Förstner, Konrad, additional, Franzenburg, Sören, additional, Frick, Julia-Stefanie, additional, Gabernet, Gisela, additional, Gagneur, Julien, additional, Ganzenmueller, Tina, additional, Gauder, Marie, additional, Geißert, Janina, additional, Goesmann, Alexander, additional, Göpel, Siri, additional, Grundhoff, Adam, additional, Grundmann, Hajo, additional, Hain, Torsten, additional, Hanses, Frank, additional, Hehr, Ute, additional, Heimbach, André, additional, Hoeper, Marius, additional, Horn, Friedemann, additional, Hübschmann, Daniel, additional, Hummel, Michael, additional, Iftner, Thomas, additional, Iftner, Angelika, additional, Illig, Thomas, additional, Janssen, Stefan, additional, Kalinowski, Jörn, additional, Kallies, René, additional, Kehr, Birte, additional, Keller, Andreas, additional, Keppler, Oliver T., additional, Kim-Hellmuth, Sarah, additional, Klein, Christoph, additional, Knop, Michael, additional, Kohlbacher, Oliver, additional, Köhrer, Karl, additional, Korbel, Jan, additional, Kremsner, Peter G., additional, Kühnert, Denise, additional, Kurth, Ingo, additional, Landthaler, Markus, additional, Li, Yang, additional, Ludwig, Kerstin U., additional, Makarewicz, Oliwia, additional, Marini, Federico, additional, Marz, Manja, additional, McHardy, Alice C., additional, Mertes, Christian, additional, Münchhoff, Maximilian, additional, Nahnsen, Sven, additional, Nöthen, Markus, additional, Ntoumi, Francine, additional, Nürnberg, Peter, additional, Ossowski, Stephan, additional, Overmann, Jörg, additional, Peter, Silke, additional, Pfeffer, Klaus, additional, Pink, Isabell, additional, Poetsch, Anna R., additional, Protzer, Ulrike, additional, Pühler, Alfred, additional, Rajewsky, Nikolaus, additional, Ralser, Markus, additional, Reiche, Kristin, additional, Rieß, Olaf, additional, Ripke, Stephan, additional, Nunes da Rocha, Ulisses, additional, Rosenstiel, Philip, additional, Saliba, Antoine-Emmanuel, additional, Sander, Leif Erik, additional, Scheithauer, Simone, additional, Schiffer, Philipp, additional, Schmid-Burgk, Jonathan, additional, Schneider, Wulf, additional, Schulte, Eva-Christina, additional, Sczyrba, Alexander, additional, Sharaf, Mariam L., additional, Singh, Yogesh, additional, Sonnabend, Michael, additional, Stegle, Oliver, additional, Stoye, Jens, additional, Theis, Fabian, additional, Ulas, Thomas, additional, Vehreschild, Janne, additional, Velavan, Thirumalaisamy P., additional, Vogel, Jörg, additional, Volland, Sonja, additional, von Kleist, Max, additional, Walker, Andreas, additional, Walter, Jörn, additional, Wieczorek, Dagmar, additional, Winkler, Sylke, additional, and Ziebuhr, John, additional

Published
2021
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35. Contributors

Author

Abadie, Valérie, primary, Abraham, Clara, additional, Adams, David H., additional, Agace, William W., additional, Alexander-Brett, Jennifer, additional, Alkhairy, Omar, additional, Ambite, Ines, additional, Anderson, Deborah J., additional, Artis, David, additional, Atmar, Robert L., additional, Aymeric, Laetitia, additional, Bachert, Claus, additional, Bakema, Jantine E., additional, Baker, Kristi, additional, Beagley, Kenneth W., additional, Befus, A.D., additional, Bemark, Mats, additional, Berin, M. Cecilia, additional, Berings, Margot, additional, Berzofsky, Jay A., additional, Bilej, Martin, additional, Biswas, Nabanita, additional, Blumberg, Richard S., additional, Bienenstock, John, additional, Bogdanos, Dimitrios, additional, Boirivant, Monica, additional, Boonnak, Kobporn, additional, Bracke, Ken R., additional, Brandtzaeg, Per, additional, Braun, Jonathan, additional, Bringer, Marie-Agnès, additional, Broadbent, Andrew J., additional, Bronson, Richard, additional, Brusselle, Guy G., additional, Bulmer, Judith N., additional, Butler, J.E., additional, Cardenas, Paul A., additional, Cebra, John J., additional, Cella, Marina, additional, Cerutti, Andrea, additional, Challacombe, Stephen J., additional, Chattha, Kuldeep, additional, Cheroutre, Hilde, additional, Chiba, Tsutomu, additional, Chorny, Alejo, additional, Clements, John D., additional, Colonna, Marco, additional, Cookson, William O.C., additional, Corbeil, Lynette B., additional, Corthésy, Blaise, additional, Cripps, Allan W., additional, van Crombruggen, Koen, additional, Pires da Cunha, Andre, additional, Cunningham-Rundles, Susanna, additional, Curtiss, Roy, additional, Darfeuille-Michaud, Arlette, additional, de Jonge, Wouter J., additional, Deban, Livija, additional, Denning, Timothy L., additional, Di Santo, James P., additional, Diefenbach, Andreas, additional, DiRita, Victor J., additional, Downey, Jordan, additional, Du, Ming-Qing, additional, Edelblum, Karen L., additional, van Egmond, Marjolein, additional, Epple, H.-J., additional, Fagarasan, Sidonia, additional, Fahey, John V., additional, Ferris, Michael J., additional, Fichtner-Feigl, Stefan, additional, Fidel, Paul L., additional, Flach, Melanie, additional, Flavell, Richard, additional, Fleit, Howard B., additional, Franchini, Genoveffa, additional, Freytag, Lucy C., additional, Fuchs, Anja, additional, Fujihashi, kohtaro, additional, Fuss, Ivan J., additional, Gagliani, Nicola, additional, Garcia, Marta Rodriguez, additional, Garrett, Wendy S., additional, Gershwin, M. Eric, additional, Gevaert, Philippe, additional, Gleeson, Maree, additional, Godaly, Gabriela, additional, Goldblum, Randall M., additional, Gour, Naina, additional, Gursel, Mayda, additional, Hajishengallis, George, additional, Hammad, Hamida, additional, Hammarström, Lennart, additional, Hänninen, Arno, additional, Hanson, Lars Å., additional, Hayday, Adrian, additional, Herzog, Ronit, additional, Hodgins, Douglas C., additional, Holgate, Stephen T., additional, Holmgren, Jan, additional, Holtzman, Michael J., additional, Hook, Edward W., additional, Huber, Samuel, additional, Hurwitz, Julia L., additional, Ivanyi, Juraj, additional, Iwasaki, Akiko, additional, Jabri, Bana, additional, Jackson, Susan, additional, Jacobs, Jonathan, additional, Jalkanen, Sirpa, additional, Janoff, Edward N., additional, Jerse, Ann E., additional, Jeyanathan, Mangalakumari, additional, Julian, Bruce A., additional, Kacskovics, Imre, additional, Kaetzel, Charlotte S., additional, Kaushic, Charu, additional, Kelsall, Brian L., additional, Kessans, Sarah, additional, Kesselring, Rebecca, additional, Kilian, Mogens, additional, Kiyono, Hiroshi, additional, Klinman, Dennis M., additional, Korotkova, Marina, additional, Kronenberg, Mitchell, additional, Krysko, Olga, additional, Kurono, Yuichi, additional, Kverka, Miloslav, additional, Lambrecht, Bart N., additional, Lamm, Michael E., additional, Lantz, Olivier, additional, Lash, Gendie E., additional, Lavelle, E.C., additional, Lefrancois, Leo, additional, Leung, Patrick S.C., additional, Levine, Myron M., additional, Lim, David J., additional, Lippolis, John, additional, Louis, Nancy A., additional, Luster, Andrew D., additional, Lutay, Nataliya, additional, Lycke, Nils, additional, Macpherson, Andrew J., additional, Mantis, Nicholas J., additional, Marcotte, Harold, additional, Martin, David H., additional, Mason, Hugh S., additional, Massa, Helen M., additional, Matoba, Nobuyuki, additional, Mayer, Lloyd, additional, Maynard, Craig L., additional, McElrath, M. Juliana, additional, McEntee, C., additional, McGhee, Jerry R., additional, McGuckin, Michael A., additional, Mestecky, Jiri, additional, Mikhak, Zamaneh, additional, Miller, Robert D., additional, Moldoveanu, Zina, additional, Montgomery, Paul C., additional, Mor, Tsafrir, additional, Neurath, Markus F., additional, Neyt, Katrijn, additional, Nicholson, Lindsay K., additional, Novak, Jan, additional, Nowicki, Stella, additional, O’Hagan, D.T., additional, O’Sullivan, Nancy L., additional, Ogra, Pearay, additional, Orihuela, Carlos, additional, Ouellette, André J., additional, Owen, Robert L., additional, Pabst, Oliver, additional, Parkos, Charles A., additional, Parreño, Viviana, additional, Patel, Mickey V., additional, Perez-Novo, Claudina, additional, Perkins, Darren J., additional, Prussin, Calman, additional, Pudney, Jeffrey, additional, Raghavan, Sukanya, additional, Rainard, Pascal, additional, Ramani, Sasirekha, additional, Randall, Troy D., additional, Raska, Milan, additional, Renukaradhya, Gourapura J., additional, Rescigno, Maria, additional, Rosenthal, Kenneth L., additional, Rothenberg, Marc E., additional, Ruemmele, Frank M., additional, Russell, Michael W., additional, Saif, Linda J., additional, Salinas, Irene, additional, Salmi, Marko, additional, Salmon, Henri, additional, Sampson, Hugh A., additional, Sansonetti, Philippe, additional, Schneider, T., additional, Serafini, Nicolas, additional, Sharma, Dolly, additional, Shen, Zheng, additional, Shi, Hai Ning, additional, Shirlaw, Penelope J., additional, Shivhare, Sourima B., additional, Smith, Phillip D., additional, Smith, Patrick M., additional, Smith, Daniel J., additional, Smythies, Lesley E., additional, Spencer, Jo, additional, Strober, Warren, additional, Subbarao, Kanta, additional, Svanborg, Catharina, additional, Svennerholm, Ann-Mari, additional, Taubman, Martin A., additional, Telemo, Esbjörn, additional, Thornhill, Martin H., additional, Thornton, David J., additional, Thuenemann, Eva, additional, Tlaskalova-Hogenova, Helena, additional, Tristram, Debra, additional, Trivedi, Palak, additional, Tuomanen, Elaine, additional, Turanek, Jaroslav, additional, Turner, Jerrold R., additional, Underdown, Brian J., additional, van Helden, Mary J., additional, Veazey, Ronald S., additional, Verdu, Elena F., additional, Vlasova, Anastasia, additional, Vliagoftis, Harissios, additional, Vogel, Stefanie N., additional, Walker, W. Allan, additional, Wang, Xiaolei, additional, Watanabe, Tomohiro, additional, Weaver, Casey T., additional, Weiner, Howard L., additional, Wells, Jerry M., additional, Wen, Ting, additional, Whittum-Hudson, Judith, additional, Whitsett, Jeffrey A., additional, Williams, Ifor R., additional, Wills-Karp, Marsha, additional, Wira, Charles R., additional, Woof, Jenny M., additional, Wotherspoon, Andrew C., additional, Xing, Zhou, additional, Xu, Huanbin, additional, Zaph, Colby, additional, Zeissig, Sebastian, additional, and Zeitz, M., additional

Published
2015
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40. Swarm Learning for decentralized and confidential clinical machine learning

Author

Warnat-Herresthal, Stefanie, Schultze, Hartmut, Ktena, Sofia, Franzenburg, Sören, Frick, Julia-Stefanie, Gabernet, Gisela, Gagneur, Julien, Ganzenmueller, Tina, Gauder, Marie, Geißert, Janina, Goesmann, Alexander, Göpel, Siri, Grundhoff, Adam, Tran, Florian, Grundmann, Hajo, Hain, Torsten, Hanses, Frank, Hehr, Ute, Heimbach, André, Hoeper, Marius, Horn, Friedemann, Hübschmann, Daniel, Hummel, Michael, Iftner, Thomas, Bitzer, Michael, Iftner, Angelika, Illig, Thomas, Janssen, Stefan, Kalinowski, Jörn, Kallies, René, Kehr, Birte, Keppler, Oliver T, Klein, Christoph, Knop, Michael, Kohlbacher, Oliver, Ossowski, Stephan, Köhrer, Karl, Korbel, Jan, Kremsner, Peter G, Kühnert, Denise, Landthaler, Markus, Li, Yang, Ludwig, Kerstin U, Makarewicz, Oliwia, Marz, Manja, McHardy, Alice C, Casadei, Nicolas, Mertes, Christian, Münchhoff, Maximilian, Nahnsen, Sven, Nöthen, Markus M., Ntoumi, Francine, Overmann, Jörg, Peter, Silke, Pfeffer, Klaus, Pink, Isabell, Poetsch, Anna R, Herr, Christian, Protzer, Ulrike, Pühler, Alfred, Rajewsky, Nikolaus, Ralser, Markus, Reiche, Kristin, Ripke, Stephan, da Rocha, Ulisses Nunes, Saliba, Antoine-Emmanuel, Sander, Leif Erik, Sawitzki, Birgit, Petersheim, Daniel, Scheithauer, Simone, Schiffer, Philipp, Schmid-Burgk, Jonathan, Schneider, Wulf, Schulte, Eva-Christina, Sczyrba, Alexander, Sharaf, Mariam L, Singh, Yogesh, Sonnabend, Michael, Stegle, Oliver, Behrends, Uta, Stoye, Jens, Vehreschild, Janne, Velavan, Thirumalaisamy P, Vogel, Jörg, Volland, Sonja, von Kleist, Max, Walker, Andreas, Walter, Jörn, Wieczorek, Dagmar, Winkler, Sylke, Kern, Fabian, Ziebuhr, John, Fehlmann, Tobias, Shastry, Krishnaprasad Lingadahalli, Schommers, Philipp, Lehmann, Clara, Augustin, Max, Rybniker, Jan, Altmüller, Janine, Mishra, Neha, Bernardes, Joana P, Krämer, Benjamin, Bonaguro, Lorenzo, Schulte-Schrepping, Jonas, Manamohan, Sathyanarayanan, De Domenico, Elena, Siever, Christian, Kraut, Michael, Desai, Milind, Monnet, Bruno, Saridaki, Maria, Siegel, Charles Martin, Drews, Anna, Nuesch Germano, Melanie, Theis, Heidi, Mukherjee, Saikat, Heyckendorf, Jan, Schreiber, Stefan, Kim-Hellmuth, Sarah, Study, COVID-19 Aachen, Nattermann, Jacob, Skowasch, Dirk, Kurth, Ingo, Keller, Andreas, Bals, Robert, Nürnberg, Peter, Garg, Vishesh, Rieß, Olaf, Rosenstiel, Philip, Netea, Mihai G, Theis, Fabian, Mukherjee, Sach, Backes, Michael, Aschenbrenner, Anna C, Ulas, Thomas, Initiative, Deutsche COVID-19 Omics, Breteler, Monique, Sarveswara, Ravi, Giamarellos-Bourboulis, Evangelos J, Kox, Matthijs, Becker, Matthias, Cheran, Sorin, Woodacre, Michael S, Goh, Eng Lim, Schultze, Joachim L, Balfanz, Paul, Eggermann, Thomas, Boor, Peter, Händler, Kristian, Hausmann, Ralf, Kuhn, Hannah, Isfort, Susanne, Stingl, Julia Carolin, Schmalzing, Günther, Kuhl, Christiane K, Röhrig, Rainer, Marx, Gernot, Uhlig, Stefan, Dahl, Edgar, Pickkers, Peter, Müller-Wieland, Dirk, Dreher, Michael, Marx, Nikolaus, Angelov, Angel, Bartholomäus, Alexander, Becker, Anke, Bezdan, Daniela, Blumert, Conny, Bonifacio, Ezio, Bork, Peer, Aziz, Ahmad, Boyke, Bunk, Blum, Helmut, Clavel, Thomas, Colome-Tatche, Maria, Cornberg, Markus, De La Rosa Velázquez, Inti Alberto, Diefenbach, Andreas, Dilthey, Alexander, Fischer, Nicole, Förstner, Konrad, and Stem Cell Aging Leukemia and Lymphoma (SALL)

Subjects
Lung Diseases, Male, 0301 basic medicine, Cancer Research, Computer science, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Privacy laws of the United States, Datasets as Topic, computer.software_genre, Disease Outbreaks, 0302 clinical medicine, Software, diagnosis [Leukemia], pathology [Leukemia], Leukocytes, Computational models, Use case, Confidentiality, 030212 general & internal medicine, Precision Medicine, Edge computing, Leukemia, Multidisciplinary, Swarm behaviour, diagnosis [Lung Diseases], ddc, 3. Good health, diagnosis [Tuberculosis], Female, ddc:500, Clinical Decision-Making, Predictive medicine, methods [Clinical Decision-Making], pathology [Leukocytes], Machine learning, Article, 03 medical and health sciences, methods [Precision Medicine], Blockchain, Humans, Tuberculosis, trends [Machine Learning], business.industry, COVID-19, Diagnostic markers, diagnosis [COVID-19], epidemiology [COVID-19], Precision medicine, 030104 developmental biology, Cardiovascular and Metabolic Diseases, Viral infection, Artificial intelligence, business, computer
Abstract

Fast and reliable detection of patients with severe and heterogeneous illnesses is a major goal of precision medicine1,2. Patients with leukaemia can be identified using machine learning on the basis of their blood transcriptomes3. However, there is an increasing divide between what is technically possible and what is allowed, because of privacy legislation4,5. Here, to facilitate the integration of any medical data from any data owner worldwide without violating privacy laws, we introduce Swarm Learning—a decentralized machine-learning approach that unites edge computing, blockchain-based peer-to-peer networking and coordination while maintaining confidentiality without the need for a central coordinator, thereby going beyond federated learning. To illustrate the feasibility of using Swarm Learning to develop disease classifiers using distributed data, we chose four use cases of heterogeneous diseases (COVID-19, tuberculosis, leukaemia and lung pathologies). With more than 16,400 blood transcriptomes derived from 127 clinical studies with non-uniform distributions of cases and controls and substantial study biases, as well as more than 95,000 chest X-ray images, we show that Swarm Learning classifiers outperform those developed at individual sites. In addition, Swarm Learning completely fulfils local confidentiality regulations by design. We believe that this approach will notably accelerate the introduction of precision medicine., Swarm Learning is a decentralized machine learning approach that outperforms classifiers developed at individual sites for COVID-19 and other diseases while preserving confidentiality and privacy.

Published
2021

41. Granzyme A and CD160 expression delineates ILC1 with graded functions in the mouse liver

Author

Di Censo, Chiara, primary, Marotel, Marie, additional, Mattiola, Irene, additional, Müller, Lena, additional, Scarno, Gianluca, additional, Pietropaolo, Giuseppe, additional, Peruzzi, Giovanna, additional, Laffranchi, Mattia, additional, Mazej, Julija, additional, Hasim, Mohamed Shaad, additional, Asif, Sara, additional, Russo, Eleonora, additional, Tomaipitinca, Luana, additional, Stabile, Helena, additional, Lee, Seung‐Hwan, additional, Vian, Laura, additional, Gadina, Massimo, additional, Gismondi, Angela, additional, Shih, Han‐Yu, additional, Mikami, Yohei, additional, Capuano, Cristina, additional, Bernardini, Giovanni, additional, Bonelli, Michael, additional, Sozzani, Silvano, additional, Diefenbach, Andreas, additional, Ardolino, Michele, additional, Santoni, Angela, additional, and Sciumè, Giuseppe, additional

Published
2021
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42. Rotavirus susceptibility of antibiotic-treated mice ascribed to diminished expression of interleukin-22

Author

Schnepf, Daniel, primary, Hernandez, Pedro, additional, Mahlakõiv, Tanel, additional, Crotta, Stefania, additional, Sullender, Meagan E., additional, Peterson, Stefan T., additional, Ohnemus, Annette, additional, Michiels, Camille, additional, Gentle, Ian, additional, Dumoutier, Laure, additional, Reis, Celso A., additional, Diefenbach, Andreas, additional, Wack, Andreas, additional, Baldridge, Megan T., additional, and Staeheli, Peter, additional

Published
2021
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43. Induction of cross-reactive antibody responses against the RBD domain of the spike protein of SARS-CoV-2 by commensal microbiota

Author

Ninnemann, Justus, primary, Budzinski, Lisa, additional, Bondareva, Marina, additional, Witkowski, Mario, additional, Angermair, Stefan, additional, Kreye, Jakob, additional, Durek, Pawel, additional, Reincke, S. Momsen, additional, Sánchez-Sendin, Elisa, additional, Yilmaz, Selin, additional, Sempert, Toni, additional, Heinz, Gitta Anne, additional, Tizian, Caroline, additional, Raftery, Martin, additional, Schönrich, Günther, additional, Matyushkina, Daria, additional, Smirnov, Ivan V., additional, Govorun, Vadim M., additional, Schrezenmeier, Eva, additional, Dörner, Thomas, additional, Zocche, Silvia, additional, Viviano, Edoardo, additional, Sehmsdorf, Katharina Johanna, additional, Chang, Hyun-Dong, additional, Enghard, Philipp, additional, Treskatsch, Sascha, additional, Radbruch, Andreas, additional, Diefenbach, Andreas, additional, Prüss, Harald, additional, Mashreghi, Mir-Farzin, additional, and Kruglov, Andrey A., additional

Published
2021
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45. Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients

Author

Aschenbrenner, Anna C, Mouktaroudi, Maria, Saridaki, Maria, McHardy, Alice, Mertes, Christian, Nöthen, Markus, Nürnberg, Peter, Ohler, Uwe, Ossowski, Stephan, Overmann, Jörg, Pfeffer, Klaus, Poetsch, Anna R, Pühler, Alfred, Knoll, Rainer, Rajewsky, Nikolaus, Ralser, Markus, Rieß, Olaf, Ripke, Stephan, Nunes da Rocha, Ulisses, Rosenstiel, Philip, Saliba, Antoine-Emmanuel, Sander, Leif Erik, Sawitzki, Birgit, Schiffer, Philipp, Pecht, Tal, Schneider, Wulf, Schulte, Eva-Christina, Schultze, Joachim L, Sczyrba, Alexander, Singh, Yogesh, Sonnabend, Michael, Stegle, Oliver, Stoye, Jens, Theis, Fabian, Vehreschild, Janne, Kapellos, Theodore S, Vogel, Jörg, von Kleist, Max, Walker, Andreas, Walter, Jörn, Wieczorek, Dagmar, Winkler, Sylke, Ziebuhr, John, Doulou, Sarandia, Kröger, Charlotte, Herbert, Miriam, Holsten, Lisa, Horne, Arik, Gemünd, Ioanna D, Krämer, Benjamin, Rovina, Nikoletta, Agrawal, Shobhit, Dahm, Kilian, van Uelft, Martina, Drews, Anna, Lenkeit, Lena, Bruse, Niklas, Gerretsen, Jelle, Gierlich, Jannik, Becker, Matthias, Oestreich, Marie, Händler, Kristian, Kraut, Michael, Theis, Heidi, Mengiste, Simachew, De Domenico, Elena, Schulte-Schrepping, Jonas, Seep, Lea, Raabe, Jan, Hoffmeister, Christoph, ToVinh, Michael, Antonakos, Nikolaos, Keitel, Verena, Rieke, Gereon, Talevi, Valentina, Skowasch, Dirk, Aziz, N. Ahmad, Pickkers, Peter, van de Veerdonk, Frank L, Netea, Mihai G, Kox, Matthijs, Nuesch-Germano, Melanie, Breteler, Monique M B, Nattermann, Jacob, Koutsoukou, Antonia, Giamarellos-Bourboulis, Evangelos J, Ulas, Thomas, Initiative, German COVID-19 Omics, Altmüller, Janine, Angelov, Angel, Bals, Robert, Bartholomäus, Alexander, Gkizeli, Konstantina, Becker, Anke, Bitzer, Michael, Bonifacio, Ezio, Bork, Peer, Casadei, Nicolas, Clavel, Thomas, Colome-Tatche, Maria, Diefenbach, Andreas, Dilthey, Alexander, Fischer, Nicole, Bonaguro, Lorenzo, Förstner, Konrad, Franzenburg, Sören, Frick, Julia-Stefanie, Gabernet, Gisela, Gagneur, Julien, Ganzenmüller, Tina, Göpel, Siri, Goesmann, Alexander, Hain, Torsten, Heimbach, André, Reusch, Nico, Hummel, Michael, Iftner, Angelika, Iftner, Thomas, Janssen, Stefan, Kalinowski, Jörn, Kallies, René, Kehr, Birte, Keller, Andreas, Kim-Hellmuth, Sarah, Klein, Christoph, Baßler, Kevin, Kohlbacher, Oliver, Köhrer, Karl, Korbel, Jan, Kühnert, Denise, Kurth, Ingo, Landthaler, Markus, Li, Yang, Ludwig, Kerstin, Makarewicz, Oliwia, and Marz, Manja

Subjects
Cancer Research, Neutrophils, virology [COVID-19], cytology [Neutrophils], Drug repurposing, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], lcsh:Medicine, chemistry [RNA], Severity of Illness Index, pathology [COVID-19], Transcriptome, 0302 clinical medicine, Genetics (clinical), Whole blood, immunology [Neutrophils], Principal Component Analysis, 0303 health sciences, metabolism [Neutrophils], Up-Regulation, 3. Good health, Co-expression analysis, Phenotype, medicine.anatomical_structure, metabolism [RNA], 030220 oncology & carcinogenesis, Molecular disease phenotypes, Molecular Medicine, Technology Platforms, lcsh:QH426-470, blood [RNA], Down-Regulation, drug therapy [COVID-19], Granulocyte, Antiviral Agents, 03 medical and health sciences, Immune system, All institutes and research themes of the Radboud University Medical Center, Severity of illness, Genetics, medicine, Humans, ddc:610, Molecular Biology, 030304 developmental biology, Sequence Analysis, RNA, business.industry, Research, lcsh:R, Drug Repositioning, Case-control study, Blood transcriptomics, COVID-19, Human genetics, COVID-19 Drug Treatment, therapeutic use [Antiviral Agents], lcsh:Genetics, Respiratory failure, Cardiovascular and Metabolic Diseases, Case-Control Studies, Immunology, RNA, Stratification, business, Granulocytes
Abstract

Background The SARS-CoV-2 pandemic is currently leading to increasing numbers of COVID-19 patients all over the world. Clinical presentations range from asymptomatic, mild respiratory tract infection, to severe cases with acute respiratory distress syndrome, respiratory failure, and death. Reports on a dysregulated immune system in the severe cases call for a better characterization and understanding of the changes in the immune system. Methods In order to dissect COVID-19-driven immune host responses, we performed RNA-seq of whole blood cell transcriptomes and granulocyte preparations from mild and severe COVID-19 patients and analyzed the data using a combination of conventional and data-driven co-expression analysis. Additionally, publicly available data was used to show the distinction from COVID-19 to other diseases. Reverse drug target prediction was used to identify known or novel drug candidates based on finding from data-driven findings. Results Here, we profiled whole blood transcriptomes of 39 COVID-19 patients and 10 control donors enabling a data-driven stratification based on molecular phenotype. Neutrophil activation-associated signatures were prominently enriched in severe patient groups, which was corroborated in whole blood transcriptomes from an independent second cohort of 30 as well as in granulocyte samples from a third cohort of 16 COVID-19 patients (44 samples). Comparison of COVID-19 blood transcriptomes with those of a collection of over 3100 samples derived from 12 different viral infections, inflammatory diseases, and independent control samples revealed highly specific transcriptome signatures for COVID-19. Further, stratified transcriptomes predicted patient subgroup-specific drug candidates targeting the dysregulated systemic immune response of the host. Conclusions Our study provides novel insights in the distinct molecular subgroups or phenotypes that are not simply explained by clinical parameters. We show that whole blood transcriptomes are extremely informative for COVID-19 since they capture granulocytes which are major drivers of disease severity.

Published
2021

46. A T-bet gradient controls the fate and function of [CCR6.sup.-][RORγt.sup.+] innate lymphoid cells

Author

Klose, Christoph S.N., Kiss, Elina A., Schwierzeck, Vera, Ebert, Karolina, Hoyler, Thomas, d'Hargues, Yannick, Goppert, Nathalie, Croxford, Andrew L., Waisman, Ari, Tanriver, Yakup, and Diefenbach, Andreas

Subjects
Immune response -- Research, Host-bacteria relationships -- Observations, Transcription factors -- Properties, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

At mucosal surfaces, the immune system should not initiate inflammatory immune responses to the plethora of antigens constantly present in the environment, but should remain poised to unleash a potent [...]

Published
2013

50. List of Contributors

Author

Allen, Shannon A., primary, Anthony, Robert M., additional, Baruah, Kavitha, additional, Black, Carolyn M., additional, Bleeker, Wim K., additional, Bolland, Silvia, additional, Clatworthy, Menna R., additional, Collin, Mattias, additional, Crispin, Max, additional, Diefenbach, Andreas, additional, Román, Victor Raúl Gómez, additional, Halstead, Scott B., additional, Hessell, Ann J., additional, Hope, Thomas J., additional, Igietseme, Joseph U., additional, Jefferis, Roy, additional, Köhla, Jörg, additional, Kilian, Mogens, additional, Lindorfer, Margaret A., additional, Martinez-Pomares, Luisa, additional, Moldt, Brian, additional, Murray, Joseph C., additional, Nimmerjahn, Falk, additional, Overdijk, Marije B., additional, Oxenius, Annette, additional, Parren, Paul W.H.I., additional, Rispens, Theo, additional, Scanlan, Christopher N., additional, Sun, Peter, additional, Taylor, Ronald P., additional, Verploegen, Sandra, additional, Vidarsson, Gestur, additional, Walsh, Elizabeth R., additional, Weber, Stefan S., additional, Weiner, George J., additional, Weiner, Louis M., additional, Yu, Xiaojie, additional, and Zhu, Xiaoping, additional

Published
2014
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