1
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Pettersson L, Frischknecht L, Westerling S, Ramezanali H, Weidmann L, Lopez KC, Schachtner T, Nilsson J. Detection of donor-derived cell-free DNA in the setting of multiple kidney transplantations. Front Immunol 2024; 15:1282521. [PMID: 38455037 PMCID: PMC10917974 DOI: 10.3389/fimmu.2024.1282521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/30/2024] [Indexed: 03/09/2024] Open
Abstract
Background The routine use of donor-derived cell-free DNA (dd-cfDNA) assays to monitor graft damage in patients after kidney transplantation is being implemented in many transplant centers worldwide. The interpretation of the results can be complicated in the setting of multiple sequential kidney transplantations where accurate donor assignment of the detected dd-cfDNA can be methodologically challenging. Methods We investigated the ability of a new next-generation sequencing (NGS)-based dd-cfDNA assay to accurately identify the source of the detected dd-cfDNA in artificially generated samples as well as clinical samples from 31 patients who had undergone two sequential kidney transplantations. Results The assay showed a high accuracy in quantifying and correctly assigning dd-cfDNA in our artificially generated chimeric sample experiments over a clinically meaningful quantitative range. In our clinical samples, we were able to detect dd-cfDNA from the first transplanted (nonfunctioning) graft in 20% of the analyzed patients. The amount of dd-cfDNA detected from the first graft was consistently in the range of 0.1%-0.6% and showed a fluctuation over time in patients where we analyzed sequential samples. Conclusion This is the first report on the use of a dd-cfDNA assay to detect dd-cfDNA from multiple kidney transplants. Our data show that a clinically relevant fraction of the transplanted patients have detectable dd-cfDNA from the first donor graft and that the amount of detected dd-cfDNA is in a range where it could influence clinical decision-making.
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Affiliation(s)
| | - Lukas Frischknecht
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | | | | | - Lukas Weidmann
- Division of Nephrology, University Hospital Zurich (USZ), Zurich, Switzerland
| | | | - Thomas Schachtner
- Division of Nephrology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
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2
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Kruse T, Garvanska DH, Varga J, Garland W, McEwan B, Hein JB, Weisser MB, Puy IB, Chan CB, Parrila PS, Mendez BL, Arulanandam J, Schueler-Furman O, Jensen TH, Kettenbach A, Nilsson J. Substrate recognition principles for the PP2A-B55 protein phosphatase. bioRxiv 2024:2024.02.10.579793. [PMID: 38370611 PMCID: PMC10871369 DOI: 10.1101/2024.02.10.579793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The PP2A-B55 phosphatase regulates a plethora of signaling pathways throughout eukaryotes. How PP2A-B55 selects its substrates presents a severe knowledge gap. By integrating AlphaFold modelling with comprehensive high resolution mutational scanning, we show that α-helices in substrates bind B55 through an evolutionary conserved mechanism. Despite a large diversity in sequence and composition, these α-helices share key amino acid determinants that engage discrete hydrophobic and electrostatic patches. Using deep learning protein design, we generate a specific and potent competitive peptide inhibitor of PP2A-B55 substrate interactions. With this inhibitor, we uncover that PP2A-B55 regulates the nuclear exosome targeting complex by binding to an α-helical recruitment module in RBM7. Collectively, our findings provide a framework for the understanding and interrogation of PP2A-B55 in health and disease.
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Affiliation(s)
- Thomas Kruse
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Dimitriya H Garvanska
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Julia Varga
- Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - William Garland
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Brennan McEwan
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Jamin B Hein
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- Current address: Amgen Research Copenhagen, Rønnegade 8, 5, 2100 Copenhagen, Denmark
| | - Melanie Bianca Weisser
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Iker Benavides Puy
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Camilla Bachman Chan
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Paula Sotelo Parrila
- Gene Center Munich, Ludwig-Maximilians- Universität München, Munich, 81377, Germany
| | - Blanca Lopez Mendez
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jeyaprakash Arulanandam
- Gene Center Munich, Ludwig-Maximilians- Universität München, Munich, 81377, Germany
- Wellcome Centre for Cell Biology, University of Edinburg, Edinburgh, EH9 3BF, UK
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Biomedical Research Israel-Canada, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, 9112001, Israel
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Arminja Kettenbach
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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3
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Zhang Y, Young R, Garvanska DH, Song C, Zhai Y, Wang Y, Jiang H, Fang J, Nilsson J, Alfieri C, Zhang G. Functional analysis of Cdc20 reveals a critical role of CRY box in mitotic checkpoint signaling. Commun Biol 2024; 7:164. [PMID: 38337031 PMCID: PMC10858191 DOI: 10.1038/s42003-024-05859-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/26/2024] [Indexed: 02/12/2024] Open
Abstract
Accurate mitosis is coordinated by the spindle assembly checkpoint (SAC) through the mitotic checkpoint complex (MCC), which inhibits the anaphase-promoting complex or cyclosome (APC/C). As an essential regulator, Cdc20 promotes mitotic exit through activating APC/C and monitors kinetochore-microtubule attachment through activating SAC. Cdc20 requires multiple interactions with APC/C and MCC subunits to elicit these functions. Functionally assessing these interactions within cells requires efficient depletion of endogenous Cdc20, which is highly difficult to achieve by RNA interference (RNAi). Here we generated Cdc20 RNAi-sensitive cell lines which display a penetrant metaphase arrest by a single RNAi treatment. In this null background, we accurately measured the contribution of each known motif of Cdc20 on APC/C and SAC activation. The CRY box, a previously identified degron, was found critical for SAC by promoting MCC formation and its interaction with APC/C. These data reveal additional regulation within the SAC and establish a novel method to interrogate Cdc20.
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Affiliation(s)
- Yuqing Zhang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Rose Young
- Chester Beatty Laboratories, Structural Biology Division, Institute of Cancer Research, London, UK
| | | | - Chunlin Song
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Yujing Zhai
- School of Public Health, Qingdao University, Qingdao, China
| | - Ying Wang
- School of Public Health, Qingdao University, Qingdao, China
| | - Hongfei Jiang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Jing Fang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Jakob Nilsson
- The NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Claudio Alfieri
- Chester Beatty Laboratories, Structural Biology Division, Institute of Cancer Research, London, UK.
| | - Gang Zhang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China.
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4
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Súkeníková L, Mallone A, Schreiner B, Ripellino P, Nilsson J, Stoffel M, Ulbrich SE, Sallusto F, Latorre D. Autoreactive T cells target peripheral nerves in Guillain-Barré syndrome. Nature 2024; 626:160-168. [PMID: 38233524 PMCID: PMC10830418 DOI: 10.1038/s41586-023-06916-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 11/30/2023] [Indexed: 01/19/2024]
Abstract
Guillain-Barré syndrome (GBS) is a rare heterogenous disorder of the peripheral nervous system, which is usually triggered by a preceding infection, and causes a potentially life-threatening progressive muscle weakness1. Although GBS is considered an autoimmune disease, the mechanisms that underlie its distinct clinical subtypes remain largely unknown. Here, by combining in vitro T cell screening, single-cell RNA sequencing and T cell receptor (TCR) sequencing, we identify autoreactive memory CD4+ cells, that show a cytotoxic T helper 1 (TH1)-like phenotype, and rare CD8+ T cells that target myelin antigens of the peripheral nerves in patients with the demyelinating disease variant. We characterized more than 1,000 autoreactive single T cell clones, which revealed a polyclonal TCR repertoire, short CDR3β lengths, preferential HLA-DR restrictions and recognition of immunodominant epitopes. We found that autoreactive TCRβ clonotypes were expanded in the blood of the same patient at distinct disease stages and, notably, that they were shared in the blood and the cerebrospinal fluid across different patients with GBS, but not in control individuals. Finally, we identified myelin-reactive T cells in the nerve biopsy from one patient, which indicates that these cells contribute directly to disease pathophysiology. Collectively, our data provide clear evidence of autoreactive T cell immunity in a subset of patients with GBS, and open new perspectives in the field of inflammatory peripheral neuropathies, with potential impact for biomedical applications.
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Affiliation(s)
- L Súkeníková
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - A Mallone
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - B Schreiner
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - P Ripellino
- Department of Neurology, Neurocenter of Southern Switzerland EOC, Lugano, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - J Nilsson
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - M Stoffel
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
- Medical Faculty, University of Zurich, Zurich, Switzerland
| | - S E Ulbrich
- Animal Physiology, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - F Sallusto
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - D Latorre
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
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Garvanska DH, Alvarado RE, Mundt FO, Lindqvist R, Duel JK, Coscia F, Nilsson E, Lokugamage K, Johnson BA, Plante JA, Morris DR, Vu MN, Estes LK, McLeland AM, Walker J, Crocquet-Valdes PA, Mendez BL, Plante KS, Walker DH, Weisser MB, Överby AK, Mann M, Menachery VD, Nilsson J. The NSP3 protein of SARS-CoV-2 binds fragile X mental retardation proteins to disrupt UBAP2L interactions. EMBO Rep 2024; 25:902-926. [PMID: 38177924 PMCID: PMC10897489 DOI: 10.1038/s44319-023-00043-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
Viruses interact with numerous host factors to facilitate viral replication and to dampen antiviral defense mechanisms. We currently have a limited mechanistic understanding of how SARS-CoV-2 binds host factors and the functional role of these interactions. Here, we uncover a novel interaction between the viral NSP3 protein and the fragile X mental retardation proteins (FMRPs: FMR1, FXR1-2). SARS-CoV-2 NSP3 mutant viruses preventing FMRP binding have attenuated replication in vitro and reduced levels of viral antigen in lungs during the early stages of infection. We show that a unique peptide motif in NSP3 binds directly to the two central KH domains of FMRPs and that this interaction is disrupted by the I304N mutation found in a patient with fragile X syndrome. NSP3 binding to FMRPs disrupts their interaction with the stress granule component UBAP2L through direct competition with a peptide motif in UBAP2L to prevent FMRP incorporation into stress granules. Collectively, our results provide novel insight into how SARS-CoV-2 hijacks host cell proteins and provides molecular insight into the possible underlying molecular defects in fragile X syndrome.
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Affiliation(s)
- Dimitriya H Garvanska
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - R Elias Alvarado
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Filip Oskar Mundt
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Josephine Kerzel Duel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabian Coscia
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emma Nilsson
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Kumari Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Bryan A Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Dorothea R Morris
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Michelle N Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Leah K Estes
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Alyssa M McLeland
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jordyn Walker
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Blanca Lopez Mendez
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - David H Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Melanie Bianca Weisser
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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6
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Deng Y, Frischnknecht L, Wehmeier C, de Rougemont O, Villard J, Ferrari-Lacraz S, Golshayan D, Gannagé M, Binet I, Wirthmueller U, Sidler D, Schachtner T, Schaub S, Nilsson J. Pre-transplant donor specific antibodies in ABO incompatible kidney transplantation - data from the Swiss transplant cohort study. Front Immunol 2024; 15:1355128. [PMID: 38361942 PMCID: PMC10867099 DOI: 10.3389/fimmu.2024.1355128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024] Open
Abstract
Background Living donor (LD) kidney transplantation in the setting of ABO blood group incompatibility (ABOi) has been previously reported to be associated with increased risk for antibody-mediated rejection (ABMR). It is however unclear if the presence of pre-transplant donor specific antibodies (DSA) works as an additive risk factor in the setting of ABOi and if DSA positive ABOi transplants have a significantly worse long-term outcome as compared with ABO compatible (ABOc) DSA positive transplants. Methods We investigated the effect of pre-transplant DSA in the ABOi and ABOc setting on the risk of antibody-mediated rejection (ABMR) and graft loss in a cohort of 952 LD kidney transplants. Results We found a higher incidence of ABMR in ABOi transplants as compared to ABOc transplants but this did not significantly affect graft survival or overall survival which was similar in both groups. The presence of pre-transplant DSA was associated with a significantly increased risk of ABMR and graft loss both in the ABOi and ABOc setting. We could not detect an additional risk of DSA in the ABOi setting and outcomes were comparable between DSA positive ABOi and ABOc recipients. Furthermore, a combination of DSA directed at both Class I and Class II, as well as DSA with a high mean fluorescence intensity (MFI) showed the strongest relation to ABMR development and graft loss. Conclusion The presence of pre-transplant DSA was associated with a significantly worse long-term outcome in both ABOi and ABOc LD kidney transplants and our results suggests that the risk associated with pre-transplant DSA is perhaps not augmented in the ABOi setting. Our study is the first to investigate the long-term effects of DSA in the ABOi setting and argues that pre-transplant DSA risk could potentially be evaluated similarly regardless of ABO compatibility status.
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Affiliation(s)
- Yun Deng
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Lukas Frischnknecht
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Caroline Wehmeier
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Olivier de Rougemont
- Department of Surgery and Transplantation, University Hospital Zurich, Zurich, Switzerland
| | - Jean Villard
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Diagnostic, Geneva University Hospitals, Geneva, Switzerland
| | - Sylvie Ferrari-Lacraz
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Diagnostic, Geneva University Hospitals, Geneva, Switzerland
| | - Déla Golshayan
- Transplantation Center, Lausanne University Hospital, Lausanne, Switzerland
| | - Monique Gannagé
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Isabelle Binet
- Nephrology & Transplantation Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Urs Wirthmueller
- Department of Laboratory Medicine, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Daniel Sidler
- Department of Nephrology and Hypertension, Inselspital, Berne University Hospital and University of Berne, Berne, Switzerland
| | - Thomas Schachtner
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Stefan Schaub
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
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7
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Cervia-Hasler C, Brüningk SC, Hoch T, Fan B, Muzio G, Thompson RC, Ceglarek L, Meledin R, Westermann P, Emmenegger M, Taeschler P, Zurbuchen Y, Pons M, Menges D, Ballouz T, Cervia-Hasler S, Adamo S, Merad M, Charney AW, Puhan M, Brodin P, Nilsson J, Aguzzi A, Raeber ME, Messner CB, Beckmann ND, Borgwardt K, Boyman O. Persistent complement dysregulation with signs of thromboinflammation in active Long Covid. Science 2024; 383:eadg7942. [PMID: 38236961 DOI: 10.1126/science.adg7942] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 11/24/2023] [Indexed: 01/23/2024]
Abstract
Long Covid is a debilitating condition of unknown etiology. We performed multimodal proteomics analyses of blood serum from COVID-19 patients followed up to 12 months after confirmed severe acute respiratory syndrome coronavirus 2 infection. Analysis of >6500 proteins in 268 longitudinal samples revealed dysregulated activation of the complement system, an innate immune protection and homeostasis mechanism, in individuals experiencing Long Covid. Thus, active Long Covid was characterized by terminal complement system dysregulation and ongoing activation of the alternative and classical complement pathways, the latter associated with increased antibody titers against several herpesviruses possibly stimulating this pathway. Moreover, markers of hemolysis, tissue injury, platelet activation, and monocyte-platelet aggregates were increased in Long Covid. Machine learning confirmed complement and thromboinflammatory proteins as top biomarkers, warranting diagnostic and therapeutic interrogation of these systems.
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Affiliation(s)
- Carlo Cervia-Hasler
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Sarah C Brüningk
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Tobias Hoch
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Bowen Fan
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Giulia Muzio
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Ryan C Thompson
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Ceglarek
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Roman Meledin
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Patrick Westermann
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research, University of Zurich, 7265 Davos, Switzerland
| | - Marc Emmenegger
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Patrick Taeschler
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Yves Zurbuchen
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Michele Pons
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Dominik Menges
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Tala Ballouz
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Sara Cervia-Hasler
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Sarah Adamo
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Miriam Merad
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander W Charney
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Milo Puhan
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, 8001 Zurich, Switzerland
| | - Petter Brodin
- Unit for Clinical Pediatrics, Department of Women's and Children's Health, Karolinska Institute, 17165 Solna, Sweden
- Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Miro E Raeber
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Christoph B Messner
- Precision Proteomics Center, Swiss Institute of Allergy and Asthma Research, University of Zurich, 7265 Davos, Switzerland
| | - Noam D Beckmann
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Data Driven and Digital Medicine (D3M), Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karsten Borgwardt
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
- Faculty of Medicine and Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
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8
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Shih NR, Nong T, Murphey C, Lopez-Cepero M, Nickerson PW, Taupin JL, Devriese M, Nilsson J, Matignon MB, Bray RA, Lee JH. HLA class I peptide polymorphisms contribute to class II DQβ0603:DQα0103 antibody specificity. Nat Commun 2024; 15:609. [PMID: 38242876 PMCID: PMC10798988 DOI: 10.1038/s41467-024-44912-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/03/2024] [Indexed: 01/21/2024] Open
Abstract
Antibodies reactive to human leukocyte antigens (HLA) represent a barrier for patients awaiting transplantation. Based on reactivity patterns in single-antigen bead (SAB) assays, various epitope matching algorithms have been proposed to improve transplant outcomes. However, some antibody reactivities cannot be explained by amino acid motifs, leading to uncertainty about their clinical relevance. Antibodies against the HLA class II molecule, DQβ0603:DQα0103, present in some candidates, represent one such example. Here, we show that peptides derived from amino acids 119-148 of the HLA class I heavy chain are bound to DQβ0603:DQα0103 proteins and contribute to antibody reactivity through an HLA-DM-dependent process. Moreover, antibody reactivity is impacted by the specific amino acid sequence presented. In summary, we demonstrate that polymorphic HLA class I peptides, bound to HLA class II proteins, can directly or indirectly be part of the antibody binding epitope. Our findings have potential important implications for the field of transplant immunology and for our understanding of adaptive immunity.
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Affiliation(s)
- N Remi Shih
- Terasaki Innovation Center, Los Angeles, CA, USA
| | - Thoa Nong
- Terasaki Innovation Center, Los Angeles, CA, USA
| | - Cathi Murphey
- Southwest Immunodiagnostics, Inc., San Antonio, TX, USA
| | | | - Peter W Nickerson
- Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada
| | - Jean-Luc Taupin
- Laboratoire d'Immunologie et Histocompatibilité and INSERM U976 IRSL, Hôpital Saint-Louis APHP, Paris, France
| | - Magali Devriese
- Laboratoire d'Immunologie et Histocompatibilité and INSERM U976 IRSL, Hôpital Saint-Louis APHP, Paris, France
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | | | - Robert A Bray
- Department of Pathology, Emory University, Atlanta, GA, USA
| | - Jar-How Lee
- Terasaki Innovation Center, Los Angeles, CA, USA.
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9
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Padi SKR, Vos MR, Godek RJ, Fuller JR, Kruse T, Hein JB, Nilsson J, Kelker MS, Page R, Peti W. Cryo-EM structures of PP2A:B55-FAM122A and PP2A:B55-ARPP19. Nature 2024; 625:195-203. [PMID: 38123684 PMCID: PMC10765524 DOI: 10.1038/s41586-023-06870-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023]
Abstract
Progression through the cell cycle is controlled by regulated and abrupt changes in phosphorylation1. Mitotic entry is initiated by increased phosphorylation of mitotic proteins, a process driven by kinases2, whereas mitotic exit is achieved by counteracting dephosphorylation, a process driven by phosphatases, especially PP2A:B553. Although the role of kinases in mitotic entry is well established, recent data have shown that mitosis is only successfully initiated when the counterbalancing phosphatases are also inhibited4. Inhibition of PP2A:B55 is achieved by the intrinsically disordered proteins ARPP195,6 and FAM122A7. Despite their critical roles in mitosis, the mechanisms by which they achieve PP2A:B55 inhibition is unknown. Here, we report the single-particle cryo-electron microscopy structures of PP2A:B55 bound to phosphorylated ARPP19 and FAM122A. Consistent with our complementary NMR spectroscopy studies, both intrinsically disordered proteins bind PP2A:B55, but do so in highly distinct manners, leveraging multiple distinct binding sites on B55. Our extensive structural, biophysical and biochemical data explain how substrates and inhibitors are recruited to PP2A:B55 and provide a molecular roadmap for the development of therapeutic interventions for PP2A:B55-related diseases.
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Affiliation(s)
- Sathish K R Padi
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA
| | - Margaret R Vos
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Rachel J Godek
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | | | - Thomas Kruse
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jamin B Hein
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Rebecca Page
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA.
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA.
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10
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Hein JB, Nguyen HT, Garvanska DH, Nasa I, Kruse T, Feng Y, Lopez Mendez B, Davey N, Kettenbach AN, Fordyce PM, Nilsson J. Phosphatase specificity principles uncovered by MRBLE:Dephos and global substrate identification. Mol Syst Biol 2023; 19:e11782. [PMID: 37916966 PMCID: PMC10698503 DOI: 10.15252/msb.202311782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023] Open
Abstract
Phosphoprotein phosphatases (PPPs) regulate major signaling pathways, but the determinants of phosphatase specificity are poorly understood. This is because methods to investigate this at scale are lacking. Here, we develop a novel in vitro assay, MRBLE:Dephos, that allows multiplexing of dephosphorylation reactions to determine phosphatase preferences. Using MRBLE:Dephos, we establish amino acid preferences of the residues surrounding the dephosphorylation site for PP1 and PP2A-B55, which reveals common and unique preferences. To compare the MRBLE:Dephos results to cellular substrates, we focused on mitotic exit that requires extensive dephosphorylation by PP1 and PP2A-B55. We use specific inhibition of PP1 and PP2A-B55 in mitotic exit lysates coupled with phosphoproteomics to identify more than 2,000 regulated sites. Importantly, the sites dephosphorylated during mitotic exit reveal key signatures that are consistent with MRBLE:Dephos. Furthermore, integration of our phosphoproteomic data with mitotic interactomes of PP1 and PP2A-B55 provides insight into how binding of phosphatases to substrates shapes dephosphorylation. Collectively, we develop novel approaches to investigate protein phosphatases that provide insight into mitotic exit regulation.
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Affiliation(s)
- Jamin B Hein
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
- Department of BioengineeringStanford UniversityStanfordCAUSA
| | - Hieu T Nguyen
- Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Dimitriya H Garvanska
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Isha Nasa
- Department of BioengineeringStanford UniversityStanfordCAUSA
| | - Thomas Kruse
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Yinnian Feng
- Department of GeneticsStanford UniversityStanfordCAUSA
| | - Blanca Lopez Mendez
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Norman Davey
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
| | - Arminja N Kettenbach
- Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Polly M Fordyce
- Department of BioengineeringStanford UniversityStanfordCAUSA
- Department of GeneticsStanford UniversityStanfordCAUSA
- Sarafan ChEM‐HStanford UniversityStanfordCAUSA
- Chan Zuckerberg BiohubSan FranciscoCAUSA
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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11
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Frischknecht L, Schaab J, Schmauch E, Yalamanoglu A, Arnold DD, Schwaiger J, Gruner C, Buechel RR, Franzen DP, Kolios AG, Nilsson J. Assessment of treatment response in cardiac sarcoidosis based on myocardial 18F-FDG uptake. Front Immunol 2023; 14:1286684. [PMID: 38077350 PMCID: PMC10704456 DOI: 10.3389/fimmu.2023.1286684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
Objective Immunosuppressive therapy for cardiac sarcoidosis (CS) still largely consists of corticosteroid monotherapy. However, high relapse rates after tapering and insufficient efficacy are significant problems. The objective of this study was to investigate the efficacy and safety of non-biological and biological disease-modifying anti-rheumatic drugs (nb/bDMARDs) considering control of myocardial inflammation assessed by 18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) of the heart. Methods We conducted a retrospective analysis of treatment response to nb/bDMARDs of all CS patients seen in the sarcoidosis center of the University Hospital Zurich between January 2016 and December 2020. Results We identified 50 patients with CS. Forty-five patients with at least one follow-up PET/CT scan were followed up for a mean of 20.5 ± 12.8 months. Most of the patients were treated with prednisone and concomitant nb/bDMARDs. At the first follow-up PET/CT scan after approximately 6.7 ± 3 months, only adalimumab showed a significant reduction in cardiac metabolic activity. Furthermore, comparing all serial follow-up PET/CT scans (143), tumor necrosis factor inhibitor (TNFi)-based therapies showed statistically significant better suppression of myocardial 18F-FDG uptake compared to other treatment regimens. On the last follow-up, most adalimumab-treated patients were inactive (n = 15, 48%) or remitting (n = 11, 35%), and only five patients (16%) were progressive. TNFi was safe even in patients with severely reduced left ventricular ejection fraction (LVEF), and a significant improvement in LVEF under TNFi treatment was observed. Conclusion TNFi shows better control of myocardial inflammation compared to nbDMARDs and corticosteroid monotherapies in patients with CS. TNFi was efficient and safe even in patients with severely reduced LVEF.
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Affiliation(s)
- Lukas Frischknecht
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Jan Schaab
- Department of Nuclear Medicine, Cardiac Imaging, University Hospital Zurich, Zurich, Switzerland
| | - Eloi Schmauch
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Artturi Ilmari (A.I) Virtanen Institute, University of Eastern Finland, Kuopio, Finland
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Ayla Yalamanoglu
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Dennis D. Arnold
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Judith Schwaiger
- Department of Cardiology, University Hospital Zurich, Zurich, Switzerland
| | - Christiane Gruner
- Department of Cardiology, University Hospital Zurich, Zurich, Switzerland
| | - Ronny R. Buechel
- Department of Nuclear Medicine, Cardiac Imaging, University Hospital Zurich, Zurich, Switzerland
| | - Daniel P. Franzen
- Department of Pulmonology, University Hospital Zurich, Zurich, Switzerland
| | - Antonios G.A. Kolios
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
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12
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Zurbuchen Y, Michler J, Taeschler P, Adamo S, Cervia C, Raeber ME, Acar IE, Nilsson J, Warnatz K, Soyka MB, Moor AE, Boyman O. Publisher Correction: Human memory B cells show plasticity and adopt multiple fates upon recall response to SARS-CoV-2. Nat Immunol 2023; 24:1961. [PMID: 37604946 PMCID: PMC10602848 DOI: 10.1038/s41590-023-01628-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Affiliation(s)
- Yves Zurbuchen
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Jan Michler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Patrick Taeschler
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Sarah Adamo
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Carlo Cervia
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Miro E Raeber
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Ilhan E Acar
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Klaus Warnatz
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael B Soyka
- Department of Otorhinolaryngology, Head and Neck Surgery, University and University Hospital Zurich, Zurich, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland.
- Faculty of Medicine and Faculty of Science, University of Zurich, Zurich, Switzerland.
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13
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Garvanska DH, Alvarado RE, Mundt FO, Nilsson E, Duel JK, Coscia F, Lindqvist R, Lokugamage K, Johnson BA, Plante JA, Morris DR, Vu MN, Estes LK, McLeland AM, Walker J, Crocquet-Valdes PA, Mendez BL, Plante KS, Walker DH, Weisser MB, Overby AK, Mann M, Menachery VD, Nilsson J. SARS-CoV-2 hijacks fragile X mental retardation proteins for efficient infection. bioRxiv 2023:2023.09.01.555899. [PMID: 37693415 PMCID: PMC10491247 DOI: 10.1101/2023.09.01.555899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Viruses interact with numerous host factors to facilitate viral replication and to dampen antiviral defense mechanisms. We currently have a limited mechanistic understanding of how SARS-CoV-2 binds host factors and the functional role of these interactions. Here, we uncover a novel interaction between the viral NSP3 protein and the fragile X mental retardation proteins (FMRPs: FMR1 and FXR1-2). SARS-CoV-2 NSP3 mutant viruses preventing FMRP binding have attenuated replication in vitro and have delayed disease onset in vivo. We show that a unique peptide motif in NSP3 binds directly to the two central KH domains of FMRPs and that this interaction is disrupted by the I304N mutation found in a patient with fragile X syndrome. NSP3 binding to FMRPs disrupts their interaction with the stress granule component UBAP2L through direct competition with a peptide motif in UBAP2L to prevent FMRP incorporation into stress granules. Collectively, our results provide novel insight into how SARS-CoV-2 hijacks host cell proteins for efficient infection and provides molecular insight to the possible underlying molecular defects in fragile X syndrome.
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Affiliation(s)
- Dimitriya H Garvanska
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rojelio E Alvarado
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, United States
| | - Filip Oskar Mundt
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emma Nilsson
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Josephine Kerzel Duel
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabian Coscia
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Kumari Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Bryan A Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jessica A Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, United States
| | - Dorothea R Morris
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, United States
| | - Michelle N Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Leah K Estes
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Alyssa M McLeland
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jordyn Walker
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, United States
| | | | - Blanca Lopez Mendez
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kenneth S Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, United States
| | - David H Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, United States
| | - Melanie Bianca Weisser
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anna K Overby
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, United States
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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14
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Hertz EPT, Vega IAD, Kruse T, Wang Y, Hendriks IA, Bizard AH, Eugui-Anta A, Hay RT, Nielsen ML, Nilsson J, Hickson ID, Mailand N. The SUMO-NIP45 pathway processes toxic DNA catenanes to prevent mitotic failure. Nat Struct Mol Biol 2023; 30:1303-1313. [PMID: 37474739 PMCID: PMC10497417 DOI: 10.1038/s41594-023-01045-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 06/26/2023] [Indexed: 07/22/2023]
Abstract
SUMOylation regulates numerous cellular processes, but what represents the essential functions of this protein modification remains unclear. To address this, we performed genome-scale CRISPR-Cas9-based screens, revealing that the BLM-TOP3A-RMI1-RMI2 (BTRR)-PICH pathway, which resolves ultrafine anaphase DNA bridges (UFBs) arising from catenated DNA structures, and the poorly characterized protein NIP45/NFATC2IP become indispensable for cell proliferation when SUMOylation is inhibited. We demonstrate that NIP45 and SUMOylation orchestrate an interphase pathway for converting DNA catenanes into double-strand breaks (DSBs) that activate the G2 DNA-damage checkpoint, thereby preventing cytokinesis failure and binucleation when BTRR-PICH-dependent UFB resolution is defective. NIP45 mediates this new TOP2-independent DNA catenane resolution process via its SUMO-like domains, promoting SUMOylation of specific factors including the SLX4 multi-nuclease complex, which contributes to catenane conversion into DSBs. Our findings establish that SUMOylation exerts its essential role in cell proliferation by enabling resolution of toxic DNA catenanes via nonepistatic NIP45- and BTRR-PICH-dependent pathways to prevent mitotic failure.
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Affiliation(s)
- Emil P T Hertz
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | - Ignacio Alonso-de Vega
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Kruse
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Yiqing Wang
- Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Anna H Bizard
- Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ania Eugui-Anta
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Nilsson
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Niels Mailand
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
- Center for Chromosome Stability, University of Copenhagen, Copenhagen, Denmark.
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15
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Padi SK, Vos MR, Godek RJ, Fuller JR, Kruse T, Hein JB, Nilsson J, Kelker MS, Page R, Peti W. Cryo-EM structures of PP2A:B55-FAM122A and PP2A:B55-ARPP19. bioRxiv 2023:2023.08.31.555365. [PMID: 37693408 PMCID: PMC10491220 DOI: 10.1101/2023.08.31.555365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Progression through the cell cycle is controlled by regulated and abrupt changes in phosphorylation.1 Mitotic entry is initiated by increased phosphorylation of mitotic proteins, a process driven by kinases,2 while mitotic exit is achieved by counteracting dephosphorylation, a process driven by phosphatases, especially PP2A:B55.3 While the role of kinases in mitotic entry is well-established, recent data have shown that mitosis is only successfully initiated when the counterbalancing phosphatases are also inhibited.4 For PP2A:B55, inhibition is achieved by the two intrinsically disordered proteins (IDPs), ARPP19 (phosphorylation-dependent)6,7 and FAM122A5 (inhibition is phosphorylation-independent). Despite their critical roles in mitosis, the mechanisms by which they achieve PP2A:B55 inhibition is unknown. Here, we report the cryo-electron microscopy structures of PP2A:B55 bound to phosphorylated ARPP19 and FAM122A. Consistent with our complementary NMR spectroscopy studies both IDPs bind PP2A:B55, but do so in highly distinct manners, unexpectedly leveraging multiple distinct binding sites on B55. Our extensive structural, biophysical and biochemical data explain how substrates and inhibitors are recruited to PP2A:B55 and provides a molecular roadmap for the development of therapeutic interventions for PP2A:B55 related diseases.
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Affiliation(s)
- Sathish K.R. Padi
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, USA
| | - Margaret R. Vos
- Department of Cell Biology, University of Connecticut Health Center, Farmington, USA
| | - Rachel J. Godek
- Department of Cell Biology, University of Connecticut Health Center, Farmington, USA
| | | | - Thomas Kruse
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jamin B. Hein
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | - Rebecca Page
- Department of Cell Biology, University of Connecticut Health Center, Farmington, USA
| | - Wolfgang Peti
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, USA
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16
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Kliche J, Garvanska DH, Simonetti L, Badgujar D, Dobritzsch D, Nilsson J, Davey NE, Ivarsson Y. Large-scale phosphomimetic screening identifies phospho-modulated motif-based protein interactions. Mol Syst Biol 2023; 19:e11164. [PMID: 37219487 PMCID: PMC10333884 DOI: 10.15252/msb.202211164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
Phosphorylation is a ubiquitous post-translation modification that regulates protein function by promoting, inhibiting or modulating protein-protein interactions. Hundreds of thousands of phosphosites have been identified but the vast majority have not been functionally characterised and it remains a challenge to decipher phosphorylation events modulating interactions. We generated a phosphomimetic proteomic peptide-phage display library to screen for phosphosites that modulate short linear motif-based interactions. The peptidome covers ~13,500 phospho-serine/threonine sites found in the intrinsically disordered regions of the human proteome. Each phosphosite is represented as wild-type and phosphomimetic variant. We screened 71 protein domains to identify 248 phosphosites that modulate motif-mediated interactions. Affinity measurements confirmed the phospho-modulation of 14 out of 18 tested interactions. We performed a detailed follow-up on a phospho-dependent interaction between clathrin and the mitotic spindle protein hepatoma-upregulated protein (HURP), demonstrating the essentiality of the phospho-dependency to the mitotic function of HURP. Structural characterisation of the clathrin-HURP complex elucidated the molecular basis for the phospho-dependency. Our work showcases the power of phosphomimetic ProP-PD to discover novel phospho-modulated interactions required for cellular function.
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Affiliation(s)
- Johanna Kliche
- Department of Chemistry, BMCUppsala UniversityUppsalaSweden
| | - Dimitriya Hristoforova Garvanska
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | | | - Dilip Badgujar
- Department of Chemistry, BMCUppsala UniversityUppsalaSweden
| | | | - Jakob Nilsson
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Norman E Davey
- Division of Cancer BiologyThe Institute of Cancer ResearchLondonUK
| | - Ylva Ivarsson
- Department of Chemistry, BMCUppsala UniversityUppsalaSweden
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17
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Zurbuchen Y, Michler J, Taeschler P, Adamo S, Cervia C, Raeber ME, Acar IE, Nilsson J, Warnatz K, Soyka MB, Moor AE, Boyman O. Human memory B cells show plasticity and adopt multiple fates upon recall response to SARS-CoV-2. Nat Immunol 2023; 24:955-965. [PMID: 37106039 PMCID: PMC10232369 DOI: 10.1038/s41590-023-01497-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/21/2023] [Indexed: 04/29/2023]
Abstract
The B cell response to different pathogens uses tailored effector mechanisms and results in functionally specialized memory B (Bm) cell subsets, including CD21+ resting, CD21-CD27+ activated and CD21-CD27- Bm cells. The interrelatedness between these Bm cell subsets remains unknown. Here we showed that single severe acute respiratory syndrome coronavirus 2-specific Bm cell clones showed plasticity upon antigen rechallenge in previously exposed individuals. CD21- Bm cells were the predominant subsets during acute infection and early after severe acute respiratory syndrome coronavirus 2-specific immunization. At months 6 and 12 post-infection, CD21+ resting Bm cells were the major Bm cell subset in the circulation and were also detected in peripheral lymphoid organs, where they carried tissue residency markers. Tracking of individual B cell clones by B cell receptor sequencing revealed that previously fated Bm cell clones could redifferentiate upon antigen rechallenge into other Bm cell subsets, including CD21-CD27- Bm cells, demonstrating that single Bm cell clones can adopt functionally different trajectories.
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Affiliation(s)
- Yves Zurbuchen
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Jan Michler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Patrick Taeschler
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Sarah Adamo
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Carlo Cervia
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Miro E Raeber
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Ilhan E Acar
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Klaus Warnatz
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michael B Soyka
- Department of Otorhinolaryngology, Head and Neck Surgery, University and University Hospital Zurich, Zurich, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland.
- Faculty of Medicine and Faculty of Science, University of Zurich, Zurich, Switzerland.
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18
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Simonetti L, Nilsson J, McInerney G, Ivarsson Y, Davey NE. SLiM-binding pockets: an attractive target for broad-spectrum antivirals. Trends Biochem Sci 2023; 48:420-427. [PMID: 36623987 DOI: 10.1016/j.tibs.2022.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 12/09/2022] [Accepted: 12/15/2022] [Indexed: 01/08/2023]
Abstract
Short linear motif (SLiM)-mediated interactions offer a unique strategy for viral intervention due to their compact interfaces, ease of convergent evolution, and key functional roles. Consequently, many viruses extensively mimic host SLiMs to hijack or deregulate cellular pathways and the same motif-binding pocket is often targeted by numerous unrelated viruses. A toolkit of therapeutics targeting commonly mimicked SLiMs could provide prophylactic and therapeutic broad-spectrum antivirals and vastly improve our ability to treat ongoing and future viral outbreaks. In this opinion article, we discuss the therapeutic relevance of SLiMs, advocating their suitability as targets for broad-spectrum antiviral inhibitors.
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Affiliation(s)
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Husargatan 3, 751 23 Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
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19
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Castrezana-Lopez K, Malchow R, Nilsson J, Kokkonen SM, Rho E, von Moos S, Mueller TF, Schachtner T. Association between PIRCHE-II scores and de novo allosensitization after reduction of immunosuppression during SARS-CoV-2 infection in kidney transplant recipients. Transpl Infect Dis 2023; 25:e14052. [PMID: 36884207 DOI: 10.1111/tid.14052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023]
Abstract
BACKGROUND Before the availability of mRNA vaccines, many transplant centers chose to significantly reduce maintenance immunosuppression in kidney transplant recipients (KTRs) with SARS-CoV-2 infection. The extent to which this increases the risk of allosensitization is unclear. METHODS In this observational cohort study, we analyzed 47 KTRs from March 2020 to February 2021 who underwent substantial reduction of maintenance immunosuppression during SARS-CoV-2 infection. KTRs were followed at 6 and 18 months concerning the development of de novo donor-specific anti-HLA (human leukocyte antigen) antibodies (DSA). The HLA-derived epitope mismatches were calculated using the predicted indirectly recognizable HLA-epitopes (PIRCHE-II) algorithm. RESULTS In total, 14 of 47 KTRs (30%) developed de novo HLA antibodies after the reduction of maintenance immunosuppression. KTRs with higher total PIRCHE-II scores and higher PIRCHE-II scores for the HLA-DR locus were more likely to develop de novo HLA antibodies (p = .023, p = .009). Furthermore, 4 of the 47 KTRs (9%) developed de novo DSA after reduction of maintenance immunosuppression, which were exclusively directed against HLA-class II antigens and also showed higher PIRCHE-II scores for HLA-class II. The cumulative mean fluorescence intensity of 40 KTRs with preexisting anti-HLA antibodies and 13 KTRs with preexisting DSA at the time of SARS-CoV-2 infection remained stable after the reduction of maintenance immunosuppression (p = .141; p = .529). CONCLUSIONS Our data show that the HLA-derived epitope mismatch load between donor and recipient influences the risk of de novo DSA development when immunosuppression is temporarily reduced. Our data further suggest that reduction in immunosuppression should be made more cautiously in KTRs with high PIRCHE-II scores for HLA-class II antigens.
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Affiliation(s)
| | - Ronja Malchow
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Sanna M Kokkonen
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Elena Rho
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Seraina von Moos
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Thomas F Mueller
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Thomas Schachtner
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
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20
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Pavic K, Gupta N, Omella JD, Derua R, Aakula A, Huhtaniemi R, Määttä JA, Höfflin N, Okkeri J, Wang Z, Kauko O, Varjus R, Honkanen H, Abankwa D, Köhn M, Hytönen VP, Xu W, Nilsson J, Page R, Janssens V, Leitner A, Westermarck J. Structural mechanism for inhibition of PP2A-B56α and oncogenicity by CIP2A. Nat Commun 2023; 14:1143. [PMID: 36854761 PMCID: PMC9974998 DOI: 10.1038/s41467-023-36693-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/09/2023] [Indexed: 03/02/2023] Open
Abstract
The protein phosphatase 2A (PP2A) heterotrimer PP2A-B56α is a human tumour suppressor. However, the molecular mechanisms inhibiting PP2A-B56α in cancer are poorly understood. Here, we report molecular level details and structural mechanisms of PP2A-B56α inhibition by an oncoprotein CIP2A. Upon direct binding to PP2A-B56α trimer, CIP2A displaces the PP2A-A subunit and thereby hijacks both the B56α, and the catalytic PP2Ac subunit to form a CIP2A-B56α-PP2Ac pseudotrimer. Further, CIP2A competes with B56α substrate binding by blocking the LxxIxE-motif substrate binding pocket on B56α. Relevant to oncogenic activity of CIP2A across human cancers, the N-terminal head domain-mediated interaction with B56α stabilizes CIP2A protein. Functionally, CRISPR/Cas9-mediated single amino acid mutagenesis of the head domain blunted MYC expression and MEK phosphorylation, and abrogated triple-negative breast cancer in vivo tumour growth. Collectively, we discover a unique multi-step hijack and mute protein complex regulation mechanism resulting in tumour suppressor PP2A-B56α inhibition. Further, the results unfold a structural determinant for the oncogenic activity of CIP2A, potentially facilitating therapeutic modulation of CIP2A in cancer and other diseases.
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Affiliation(s)
- Karolina Pavic
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Nikhil Gupta
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Judit Domènech Omella
- Laboratory of Protein Phosphorylation & Proteomics, Department of Cellular & Molecular Medicine, University of Leuven (KU Leuven), B-3000, Leuven, Belgium
| | - Rita Derua
- Laboratory of Protein Phosphorylation & Proteomics, Department of Cellular & Molecular Medicine, University of Leuven (KU Leuven), B-3000, Leuven, Belgium
- SyBioMa, University of Leuven (KU Leuven), B-3000, Leuven, Belgium
| | - Anna Aakula
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Riikka Huhtaniemi
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Juha A Määttä
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland and Fimlab Laboratories, 33520, Tampere, Finland
| | - Nico Höfflin
- Faculty of Biology, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
| | - Juha Okkeri
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Zhizhi Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Otto Kauko
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Roosa Varjus
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Henrik Honkanen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland
| | - Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Maja Köhn
- Faculty of Biology, Institute of Biology III, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Vesa P Hytönen
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland and Fimlab Laboratories, 33520, Tampere, Finland
| | - Wenqing Xu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Rebecca Page
- Department of Chemistry and Biochemistry University of Arizona, Tucson, AZ, USA
| | - Veerle Janssens
- Laboratory of Protein Phosphorylation & Proteomics, Department of Cellular & Molecular Medicine, University of Leuven (KU Leuven), B-3000, Leuven, Belgium
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093, Zurich, Switzerland
| | - Jukka Westermarck
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520, Turku, Finland.
- Institute of Biomedicine, University of Turku, 20520, Turku, Finland.
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21
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Emmenegger M, De Cecco E, Lamparter D, Jacquat RP, Riou J, Menges D, Ballouz T, Ebner D, Schneider MM, Morales IC, Doğançay B, Guo J, Wiedmer A, Domange J, Imeri M, Moos R, Zografou C, Batkitar L, Madrigal L, Schneider D, Trevisan C, Gonzalez-Guerra A, Carrella A, Dubach IL, Xu CK, Meisl G, Kosmoliaptsis V, Malinauskas T, Burgess-Brown N, Owens R, Hatch S, Mongkolsapaya J, Screaton GR, Schubert K, Huck JD, Liu F, Pojer F, Lau K, Hacker D, Probst-Müller E, Cervia C, Nilsson J, Boyman O, Saleh L, Spanaus K, von Eckardstein A, Schaer DJ, Ban N, Tsai CJ, Marino J, Schertler GF, Ebert N, Thiel V, Gottschalk J, Frey BM, Reimann RR, Hornemann S, Ring AM, Knowles TP, Puhan MA, Althaus CL, Xenarios I, Stuart DI, Aguzzi A. Continuous population-level monitoring of SARS-CoV-2 seroprevalence in a large European metropolitan region. iScience 2023; 26:105928. [PMID: 36619367 PMCID: PMC9811913 DOI: 10.1016/j.isci.2023.105928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 12/18/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Effective public health measures against SARS-CoV-2 require granular knowledge of population-level immune responses. We developed a Tripartite Automated Blood Immunoassay (TRABI) to assess the IgG response against three SARS-CoV-2 proteins. We used TRABI for continuous seromonitoring of hospital patients and blood donors (n = 72'250) in the canton of Zurich from December 2019 to December 2020 (pre-vaccine period). We found that antibodies waned with a half-life of 75 days, whereas the cumulative incidence rose from 2.3% in June 2020 to 12.2% in mid-December 2020. A follow-up health survey indicated that about 10% of patients infected with wildtype SARS-CoV-2 sustained some symptoms at least twelve months post COVID-19. Crucially, we found no evidence of a difference in long-term complications between those whose infection was symptomatic and those with asymptomatic acute infection. The cohort of asymptomatic SARS-CoV-2-infected subjects represents a resource for the study of chronic and possibly unexpected sequelae.
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Affiliation(s)
- Marc Emmenegger
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Elena De Cecco
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - David Lamparter
- Health2030 Genome Center, 9 Chemin des Mines, 1202 Geneva, Switzerland
| | - Raphaël P.B. Jacquat
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland
| | - Dominik Menges
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zürich, Switzerland
| | - Tala Ballouz
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zürich, Switzerland
| | - Daniel Ebner
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, England
| | - Matthias M. Schneider
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | | - Berre Doğançay
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Jingjing Guo
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Anne Wiedmer
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Julie Domange
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Marigona Imeri
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Rita Moos
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Chryssa Zografou
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Leyla Batkitar
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Lidia Madrigal
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Dezirae Schneider
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Chiara Trevisan
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | | | | | - Irina L. Dubach
- Division of Internal Medicine, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Catherine K. Xu
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Georg Meisl
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Vasilis Kosmoliaptsis
- Department of Surgery, Addenbrooke’s Hospital, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
- NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Tomas Malinauskas
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | | | - Ray Owens
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
- The Rosalind Franklin Institute, Harwell Campus, Oxford OX11 0FA, UK
| | - Stephanie Hatch
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, England
| | - Juthathip Mongkolsapaya
- Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Gavin R. Screaton
- Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Katharina Schubert
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - John D. Huck
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Florence Pojer
- Protein Production and Structure Core Facility, EPFL SV PTECH PTPSP, 1015 Lausanne, Switzerland
| | - Kelvin Lau
- Protein Production and Structure Core Facility, EPFL SV PTECH PTPSP, 1015 Lausanne, Switzerland
| | - David Hacker
- Protein Production and Structure Core Facility, EPFL SV PTECH PTPSP, 1015 Lausanne, Switzerland
| | | | - Carlo Cervia
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, 8091 Zurich, Switzerland
- Faculty of Medicine, University of Zurich, 8006 Zurich, Switzerland
| | - Lanja Saleh
- Institute of Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Katharina Spanaus
- Institute of Clinical Chemistry, University Hospital Zurich, 8091 Zurich, Switzerland
| | | | - Dominik J. Schaer
- Division of Internal Medicine, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Ching-Ju Tsai
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
| | - Jacopo Marino
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
| | - Gebhard F.X. Schertler
- Department of Biology and Chemistry, Laboratory of Biomolecular Research, Paul Scherrer Institute, 5303 Villigen-PSI, Switzerland
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology, 3012 Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Volker Thiel
- Institute of Virology and Immunology, 3012 Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Jochen Gottschalk
- Regional Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland
| | - Beat M. Frey
- Regional Blood Transfusion Service Zurich, Swiss Red Cross, 8952 Schlieren, Switzerland
| | - Regina R. Reimann
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Simone Hornemann
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
| | - Aaron M. Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tuomas P.J. Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Milo A. Puhan
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zürich, Switzerland
| | - Christian L. Althaus
- Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland
| | - Ioannis Xenarios
- Health2030 Genome Center, 9 Chemin des Mines, 1202 Geneva, Switzerland
- Agora Center, University of Lausanne, 25 Avenue du Bugnon, 1005 Lausanne, Switzerland
| | - David I. Stuart
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Headington, Oxford OX3 7BN, UK
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland
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22
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de Rougemont O, Deng Y, Frischknecht L, Wehmeier C, Villard J, Ferrari-Lacraz S, Golshayan D, Gannagé M, Binet I, Wirthmueller U, Sidler D, Schachtner T, Schaub S, Nilsson J. Donation type and the effect of pre-transplant donor specific antibodies - Data from the Swiss Transplant Cohort Study. Front Immunol 2023; 14:1104371. [PMID: 36875145 PMCID: PMC9974644 DOI: 10.3389/fimmu.2023.1104371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/30/2023] [Indexed: 02/19/2023] Open
Abstract
Introduction The type of donation may affect how susceptible a donor kidney is to injury from pre-existing alloimmunity. Many centers are, therefore, reluctant to perform donor specific antibody (DSA) positive transplantations in the setting of donation after circulatory death (DCD). There are, however, no large studies comparing the impact of pre-transplant DSA stratified on donation type in a cohort with a complete virtual cross-match and long-term follow-up of transplant outcome. Methods We investigated the effect of pre-transplant DSA on the risk of rejection, graft loss, and the rate of eGFR decline in 1282 donation after brain death (DBD) transplants and compared it to 130 (DCD) and 803 living donor (LD) transplants. Results There was a significant worse outcome associated with pre-transplant DSA in all of the studied donation types. DSA directed against Class II HLA antigens as well as a high cumulative mean fluorescent intensity (MFI) of the detected DSA showed the strongest association with worse transplant outcome. We could not detect a significant additive negative effect of DSA in DCD transplantations in our cohort. Conversely, DSA positive DCD transplants appeared to have a slightly better outcome, possibly in part due to the lower mean fluorescent intensity (MFI) of the pre-transplant DSA. Indeed when DCD transplants were compared to DBD transplants with similar MFI (<6.5k), graft survival was not significantly different. Discussion Our results suggest that the negative impact of pre-transplant DSA on graft outcome could be similar between all donation types. This suggests that immunological risk assessment could be performed in a similar way regardless of the type of donor kidney transplantation.
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Affiliation(s)
- Olivier de Rougemont
- Department of Surgery and Transplantation, University Hospital Zurich, Zurich, Switzerland
| | - Yun Deng
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Lukas Frischknecht
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Caroline Wehmeier
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Jean Villard
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Diagnostic, Geneva University Hospitals, Geneva, Switzerland
| | - Sylvie Ferrari-Lacraz
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Diagnostic, Geneva University Hospitals, Geneva, Switzerland
| | - Déla Golshayan
- Transplantation Center, Lausanne University Hospital, Lausanne, Switzerland
| | - Monique Gannagé
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Isabelle Binet
- Nephrology & Transplantation Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Urs Wirthmueller
- Department of Laboratory Medicine, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Daniel Sidler
- Department of Nephrology and Hypertension, Inselspital, Berne University Hospital and University of Berne, Berne, Switzerland
| | - Thomas Schachtner
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Stefan Schaub
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
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23
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Vit G, Hirth A, Neugebauer N, Kraft BN, Sigismondo G, Cazzola A, Tessmer C, Duro J, Krijgsveld J, Hofmann I, Berger M, Klüter H, Niehrs C, Nilsson J, Krämer A. Human SLFN5 and its Xenopus Laevis ortholog regulate entry into mitosis and oocyte meiotic resumption. Cell Death Dis 2022; 8:484. [PMID: 36477080 PMCID: PMC9729291 DOI: 10.1038/s41420-022-01274-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022]
Abstract
The Schlafen gene family was first described in mice as a regulator of thymocyte development. Further studies showed involvement of human orthologs in different processes related with viral replication, cellular proliferation, and differentiation. In recent years, a new role for human Slfn11 in DNA replication and chromatin remodeling was described. As commonly observed in many gene families, Slfn paralogs show a tissue-specific expression. This made it difficult to reach conclusions which can be valid in different biological models regarding the function of the different Schlafen proteins. In the present study, we investigate the involvement of SLFN5 in cell-cycle regulation and cell proliferation. A careful analysis of SLFN5 expression revealed that SLFN5 is highly expressed in proliferating tissues and that the protein is ubiquitously present in all the tissues and cell line models we analyzed. Very interestingly, SLFN5 expression oscillates during cell cycle, peaking during S phase. The fact that SLFN5 interacts with protein phosphatase 2A and that SLFN5 depletion causes cell cycle arrest and cellular apoptosis, suggests a direct involvement of this human paralog in cell cycle progression and cellular proliferation. We substantiated our in vitro and in cellulo results using Xenopus laevis oocytes to show that mRNA depletion of the unique Slfn gene present in Xenopus, whose protein sequence shares 80% of homology with SLFN5, recapitulates the phenotype observed in human cells preventing the resumption of meiosis during oocyte development.
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Affiliation(s)
- Gianmatteo Vit
- grid.7700.00000 0001 2190 4373Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Medical Faculty Mannheim, Institute for Transfusion Medicine and Immunology, Ruprecht-Karls University of Heidelberg, Mannheim, Germany ,grid.5254.60000 0001 0674 042XThe Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alexander Hirth
- grid.424631.60000 0004 1794 1771Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany, and Institute of Molecular Biology (IMB), Mainz, Germany
| | - Nicolas Neugebauer
- grid.7700.00000 0001 2190 4373Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Bianca N. Kraft
- grid.7700.00000 0001 2190 4373Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Gianluca Sigismondo
- grid.7497.d0000 0004 0492 0584Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna Cazzola
- grid.7700.00000 0001 2190 4373Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Claudia Tessmer
- grid.7497.d0000 0004 0492 0584Genomics and Proteomics Core Facility, Unit Antibodies, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Joana Duro
- grid.5254.60000 0001 0674 042XThe Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeroen Krijgsveld
- grid.7497.d0000 0004 0492 0584Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ilse Hofmann
- grid.7497.d0000 0004 0492 0584Genomics and Proteomics Core Facility, Unit Antibodies, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Berger
- grid.9619.70000 0004 1937 0538The Lautenberg Center for General and Tumor Immunology, The Hebrew University of Jerusalem, Hadassah Medical School, Jerusalem, Israel
| | - Harald Klüter
- grid.7700.00000 0001 2190 4373Medical Faculty Mannheim, Institute for Transfusion Medicine and Immunology, Ruprecht-Karls University of Heidelberg, Mannheim, Germany
| | - Christof Niehrs
- grid.424631.60000 0004 1794 1771Division of Molecular Embryology, DKFZ-ZMBH Alliance, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany, and Institute of Molecular Biology (IMB), Mainz, Germany
| | - Jakob Nilsson
- grid.5254.60000 0001 0674 042XThe Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alwin Krämer
- grid.7700.00000 0001 2190 4373Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
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Wang L, Kruse T, López-Méndez B, Zhang Y, Song C, Zhu L, Li B, Fang J, Lu Z, Nilsson J, Zhang G. Spatial separation of phosphatase and kinase activity within the Bub complex is required for proper mitosis. J Mol Cell Biol 2022; 14:6849558. [PMID: 36441015 PMCID: PMC10155811 DOI: 10.1093/jmcb/mjac062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/29/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
Abstract
Abstract
The Bub1 and BubR1 kinetochore proteins support proper chromosome segregation and mitotic checkpoint activity. Bub1 and BubR1 are paralogues with Bub1 being a kinase while BubR1 localizes the PP2A-B56 protein phosphatase to kinetochores in humans. Whether this spatial separation of kinase and phosphatase activity is important is unclear as some organisms integrate both activities into one Bub protein. Here we engineer human Bub1 and BubR1 proteins integrating kinase and phosphatase activities into one protein and show that these do not support normal mitotic progression. A Bub1–PP2A-B56 complex can supports chromosome alignment but results in impairment of the checkpoint due to dephosphorylation of the Mad1 binding site in Bub1. Furthermore, a chimeric BubR1 protein containing the Bub1 kinase domain induces delocalized H2ApT120 phosphorylation, resulting in reduction of centromeric hSgo2 and chromosome segregation errors. Collectively, these results argue that the spatial separation of kinase and phosphatase activities within the Bub complex is required for balancing its functions in the checkpoint and chromosome alignment.
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Affiliation(s)
- Lei Wang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University , Qingdao 266061 , China
| | - Thomas Kruse
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen, DK-2200, Denmark
| | - Blanca López-Méndez
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen, DK-2200, Denmark
| | - Yuqing Zhang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University , Qingdao 266061 , China
| | - Chunlin Song
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University , Qingdao 266061 , China
| | - Lei Zhu
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University , Qingdao 266061 , China
| | - Bing Li
- The Department of Genetics and Cell Biology, Basic Medical College, Qingdao University , Qingdao 266061 , China
| | - Jing Fang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University , Qingdao 266061 , China
| | - Zhimin Lu
- Institute of Translational Medicine, Zhejiang University School of Medicine , Hangzhou 310029 , China
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen, DK-2200, Denmark
| | - Gang Zhang
- The Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao University , Qingdao 266061 , China
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen , Copenhagen, DK-2200, Denmark
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Bankova AK, Pasin C, Huang A, Cicin‐Sain C, Epp S, Audige A, Mueller NJ, Nilsson J, Vilinovszki O, Nair G, Wolfensberger N, Hockl P, Schanz U, Trkola A, Kouyos R, Hasse B, Zinkernagel AS, Manz MG, Abela IA, Müller AMS. Antibody response to a third SARS‐CoV‐2 vaccine dose in recipients of an allogeneic haematopoietic cell transplantation. Br J Haematol 2022; 201:58-63. [PMID: 36382698 DOI: 10.1111/bjh.18562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/29/2022] [Accepted: 11/01/2022] [Indexed: 11/17/2022]
Abstract
Allogeneic haematopoietic cell transplantation (allo-HCT) recipients show impaired antibody (Ab) response to a standard two-dose vaccination against severe acute respiratory syndrome coronavirus-2 and currently a third dose is recommended as part of the primary vaccination regimen. By assessing Ab titres 1 month after a third mRNA vaccine dose in 74 allo-HCT recipients we show sufficient neutralisation activity in 77% of the patients. Discontinuation of immunosuppression before the third vaccine led to serological responses in 50% of low responders to two vaccinations. Identifying factors that might contribute to better vaccine responses in allo-HCT recipients is critical to optimise current vaccination strategies.
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Affiliation(s)
- Andriyana K. Bankova
- Department of Medical Oncology and Hematology University Hospital Zürich Zürich Switzerland
| | - Chloé Pasin
- Institute of Medical Virology University of Zürich Zürich Switzerland
- Department of Infectious Diseases and Hospital Epidemiology University Hospital Zurich, University of Zürich Zürich Switzerland
| | - Alice Huang
- Department of Medical Oncology and Hematology University Hospital Zürich Zürich Switzerland
| | - Caroline Cicin‐Sain
- Department of Medical Oncology and Hematology University Hospital Zürich Zürich Switzerland
| | - Selina Epp
- Institute of Medical Virology University of Zürich Zürich Switzerland
| | - Annette Audige
- Institute of Medical Virology University of Zürich Zürich Switzerland
| | - Nicolas J. Mueller
- Department of Infectious Diseases and Hospital Epidemiology University Hospital Zurich, University of Zürich Zürich Switzerland
| | - Jakob Nilsson
- Department of Immunology University Hospital Zürich Zürich Switzerland
| | - Oliver Vilinovszki
- Department of Medical Oncology and Hematology University Hospital Zürich Zürich Switzerland
- Department of Internal Medicine University Hospital Zürich Zürich Switzerland
| | - Gayathri Nair
- Department of Medical Oncology and Hematology University Hospital Zürich Zürich Switzerland
| | - Nathan Wolfensberger
- Department of Medical Oncology and Hematology University Hospital Zürich Zürich Switzerland
| | - Philipp Hockl
- Department of Medical Oncology and Hematology University Hospital Zürich Zürich Switzerland
| | - Urs Schanz
- Department of Medical Oncology and Hematology University Hospital Zürich Zürich Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology University of Zürich Zürich Switzerland
| | - Roger Kouyos
- Institute of Medical Virology University of Zürich Zürich Switzerland
- Department of Infectious Diseases and Hospital Epidemiology University Hospital Zurich, University of Zürich Zürich Switzerland
| | - Barbara Hasse
- Department of Infectious Diseases and Hospital Epidemiology University Hospital Zurich, University of Zürich Zürich Switzerland
| | - Annelies S. Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology University Hospital Zurich, University of Zürich Zürich Switzerland
| | - Markus G. Manz
- Department of Medical Oncology and Hematology University Hospital Zürich Zürich Switzerland
| | - Irene A. Abela
- Institute of Medical Virology University of Zürich Zürich Switzerland
- Department of Infectious Diseases and Hospital Epidemiology University Hospital Zurich, University of Zürich Zürich Switzerland
| | - Antonia M. S. Müller
- Department of Medical Oncology and Hematology University Hospital Zürich Zürich Switzerland
- Department of Blood Group Serology and Transfusion Medicine Medical University of Vienna Vienna Austria
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Reimann AV, Nilsson J, Wuethrich RP, Mueller TF, Schachtner T. Entering the Third Decade After Kidney Transplantation: Excellent Graft Function Refers to Superior Graft but Not Patient Survival. Transpl Int 2022; 35:10675. [DOI: 10.3389/ti.2022.10675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/18/2022] [Indexed: 11/07/2022]
Abstract
Kidney transplant recipients (KTRs) with ultralong-term survival represent a growing, yet insufficiently studied patient cohort. In this single-center retrospective study, we analyzed 248 ultralong-term survivors (≥20 years). KTRs were classified into those with superior graft function (defined as eGFR ≥45 ml/min + proteinuria ≤300 mg/day + eGFR-slope ≤ 2 ml/min/1.73 m2/year) and inferior graft function regarding the risk of CKD progression. 20 years post-transplant, median eGFR was 54 ml/min (11–114), proteinuria 200 mg/24 h (0–7,620), eGFR decline 0.45 ml/min/1.73 m2/year (11.7 6.5) and DSA had been detected in 19.7% of KTRs. We identified 96 KTRs (38.7%) with superior (group 1) and 152 KTRs (61.3%) with inferior graft function (group 2). Donation after cardiac death, female sex, glomerulonephritis as primary disease, and early TCMR were independently associated with inferior graft function. Graft survival was significantly better in group 1 compared to group 2 (LogRank, p < 0.001). Besides group affiliation (HR 20.515, p = 0.003), multivariable analysis identified DSA development (HR 3.081, p = 0.023) and donor age (HR 1.032, p = 0.024) as independent factors. Interestingly, there was no significant difference in patient survival (LogRank, p = 0.350). In ultralong-term survivors, excellent graft function refers to superior graft survival but does not extend ultimate patient survival. DSA-formation should be taken seriously even in the ultralong-term.
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Sah V, Karlsson J, Bucher V, Olofsson Bagge R, Ny L, Nilsson L, Nilsson J. Using patient-derived xenografts as sources of 3D tumor sphere cultures to study autologous tumor-infiltrating lymphocytes in metastatic uveal melanoma. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)00922-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Roeder M, Sievi NA, Schneider A, Osswald M, Malesevic S, Kolios A, Nilsson J, Kohler M, Franzen D. The prevalence of obstructive sleep apnea in sarcoidosis and its impact on sleepiness, fatigue, and sleep-associated quality of life: a cross-sectional study with matched controls (the OSASA study). J Clin Sleep Med 2022; 18:2415-2422. [PMID: 35855534 PMCID: PMC9516590 DOI: 10.5664/jcsm.10140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/30/2022] [Accepted: 06/02/2022] [Indexed: 11/13/2022]
Abstract
STUDY OBJECTIVES Patients with sarcoidosis experience fatigue and excessive daytime sleepiness (EDS). However, the underlying pathomechanism is unclear. Studies suggested undiagnosed obstructive sleep apnea (OSA) to be an important contributor, but reliable data on prevalence and impact of OSA in sarcoidosis are scarce. METHODS 71 adult patients with sarcoidosis, 1-to-1 matched to 71 adult controls according to sex, age, and body mass index were included. Participants underwent structured interviews (including Epworth Sleepiness Scale [ESS], Fatigue Assessment Scale [FAS], and Functional Outcome of Sleep Questionnaire [FOSQ-30]) and level-3 respiratory polygraphy. OSA was defined as apnea-hypopnea index ≥ 5 events/h. Prevalence of OSA was assessed and possible risk factors for OSA in sarcoidosis were investigated. RESULTS Mild OSA (AHI ≥ 5 events/h) was prevalent in 32 (45%) sarcoidosis patients vs 22 (31%) controls (P = .040). Sarcoidosis patients presented higher ESS compared with matched controls (P = .037). FAS scores (median [quartile] of 21.5 [16, 27.5]) indicated fatigue in sarcoidosis patients. Patients with EDS (ESS ≥ 11) presented reduced FOSQ-30 results (median [quartile] of 16.7 [15.2, 17.8]). ESS, FAS, and FOSQ were not associated with AHI in sarcoidosis patients. Body mass index, sex, neck circumference, and NoSAS score were predictors for OSA in sarcoidosis. CONCLUSIONS The risk for mild OSA is 2.5-fold higher in sarcoidosis patients compared with matched controls. OSA seems not to be the reason for increased sleepiness or fatigue in sarcoidosis. Risk factors such as body mass index, sex, neck circumference, and NoSAS score can be used to screen for OSA in sarcoidosis patients. CLINICAL TRIAL REGISTRATION Registry: ClinicalTrials.gov; Name: Obstructive Sleep Apnoea in Sarcoidosis (OSASA); URL: https://clinicaltrials.gov/ct2/history/NCT04156789?V_2=View; Identifier: NCT04156789. CITATION Roeder M, Sievi NA, Schneider A, et al. The prevalence of obstructive sleep apnea in sarcoidosis and its impact on sleepiness, fatigue, and sleep-associated quality of life: a cross-sectional study with matched controls (the OSASA study). J Clin Sleep Med. 2022;18(10):2415-2422.
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Affiliation(s)
- Maurice Roeder
- Department of Pulmonology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Noriane A. Sievi
- Department of Pulmonology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Alexandra Schneider
- Department of Pulmonology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Martin Osswald
- Department of Pulmonology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Stefan Malesevic
- Department of Pulmonology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Antonios Kolios
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
| | - Jakob Nilsson
- Department of Clinical Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Malcolm Kohler
- Department of Pulmonology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Zurich Centre for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Daniel Franzen
- Department of Pulmonology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Frischknecht L, Deng Y, Wehmeier C, de Rougemont O, Villard J, Ferrari-Lacraz S, Golshayan D, Gannagé M, Binet I, Wirthmueller U, Sidler D, Schachtner T, Schaub S, Nilsson J. The impact of pre-transplant donor specific antibodies on the outcome of kidney transplantation – Data from the Swiss transplant cohort study. Front Immunol 2022; 13:1005790. [PMID: 36211367 PMCID: PMC9532952 DOI: 10.3389/fimmu.2022.1005790] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Background Pre-transplant donor specific antibodies (DSA), directed at non-self human leukocyte antigen (HLA) protein variants present in the donor organ, have been associated with worse outcomes in kidney transplantation. The impact of the mean fluorescence intensity (MFI) and the target HLA antigen of the detected DSA has, however, not been conclusively studied in a large cohort with a complete virtual cross-match (vXM). Methods We investigated the effect of pre-transplant DSA on the risk of antibody-mediated rejection (ABMR), graft loss, and the rate of eGFR decline in 411 DSA positive transplants and 1804 DSA negative controls. Results Pre-transplant DSA were associated with a significantly increased risk of ABMR, graft loss, and accelerated eGFR decline. DSA directed at Class I and Class II HLA antigens were strongly associated with increased risk of ABMR, but only DSA directed at Class II associated with graft loss. DSA MFI markedly affected outcome, and Class II DSA were associated with ABMR already at 500-1000 MFI, whereas Class I DSA did not affect outcome at similar low MFI values. Furthermore, isolated DSA against HLA-DP carried comparable risks for ABMR, accelerated eGFR decline, and graft loss as DSA against HLA-DR. Conclusion Our results have important implications for the construction and optimization of vXM algorithms used within organ allocation systems. Our data suggest that both the HLA antigen target of the detected DSA as well as the cumulative MFI should be considered and that different MFI cut-offs could be considered for Class I and Class II directed DSA.
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Affiliation(s)
- Lukas Frischknecht
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Yun Deng
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Caroline Wehmeier
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Olivier de Rougemont
- Department of Surgery and Transplantation, University Hospital Zurich, Zurich, Switzerland
| | - Jean Villard
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Diagnostic, Geneva University Hospitals, Geneva, Switzerland
| | - Sylvie Ferrari-Lacraz
- Transplantation Immunology Unit and National Reference Laboratory for Histocompatibility, Department of Diagnostic, Geneva University Hospitals, Geneva, Switzerland
| | - Déla Golshayan
- Transplantation Center, Lausanne University Hospital, Lausanne, Switzerland
| | - Monique Gannagé
- Service of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Isabelle Binet
- Nephrology & Transplantation Medicine, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Urs Wirthmueller
- Department of Laboratory Medicine, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Daniel Sidler
- Department of Nephrology and Hypertension, Inselspital, Berne University Hospital and University of Berne, Berne, Switzerland
| | - Thomas Schachtner
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Stefan Schaub
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland
- *Correspondence: Jakob Nilsson,
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30
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Spitznagel T, Matter LS, Kaufmann YL, Nilsson J, von Moos S, Schachtner T. PIRCHE-II scores prove useful as a predictive biomarker among kidney transplant recipients with rejection: An analysis of indication and follow-up biopsies. Front Immunol 2022; 13:949933. [PMID: 36059499 PMCID: PMC9428698 DOI: 10.3389/fimmu.2022.949933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022] Open
Abstract
Background Indication biopsies for deterioration of kidney allograft function often require follow-up biopsies to assess treatment response or lack of improvement. Immune-mediated injury, namely borderline rejection (BLR), T-cell mediated rejection (TCMR), or antibody-mediated rejection (ABMR), results from preformed or de novo alloreactivity due to donor and recipient HLA-mismatches. The impact of HLA-mismatches on alloreactivity is determined by highly immunogenic HLA-epitopes. Methods We analyzed 123 kidney transplant recipients (KTRs) from 2009 to 2019 who underwent a first indication and a follow-up biopsy. KTRs were divided into three groups according to the first biopsy: No rejection (NR)/BLR (n=68); TCMR (n=21); ABMR (n=34). The HLA-derived epitope-mismatches were calculated using the Predicted Indirectly Recognizable HLA-Epitopes (PIRCHE-II) algorithm. Results Group NR/BLR: KTRs with higher total PIRCHE-II scores were more likely to develop TCMR in the follow-up biopsy (p=0.031). Interestingly, these differences were significant for both HLA-class I- (p=0.017) and HLA-class II-derived (p=0.017) PIRCHE-II scores. Group TCMR: KTRs with ongoing TCMR in the follow-up biopsy were more likely to show higher total PIRCHE-II scores (median 101.50 vs. 74.00). Group ABMR: KTRs with higher total PIRCHE-II scores were more likely to show an increase in the microvascular inflammation score in the follow-up biopsy. This difference was more pronounced for the HLA-class II-derived PIRCHE-II scores (median 70.00 vs. 31.76; p=0.086). Conclusions PIRCHE-II scores may prove useful as a biomarker to predict the histopathological changes of immune-related injury from a first indication to a follow-up biopsy. This immunological risk stratification may contribute to individualized treatment strategies.
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Affiliation(s)
- Tahm Spitznagel
- Division of Nephrology, University Hospital of Zurich (USZ), Zurich, Switzerland
| | - Laurenz S. Matter
- Division of Nephrology, University Hospital of Zurich (USZ), Zurich, Switzerland
| | - Yves L. Kaufmann
- Division of Nephrology, University Hospital of Zurich (USZ), Zurich, Switzerland
| | - Jakob Nilsson
- Division of Immunology, University Hospital of Zurich (USZ), Zurich, Switzerland
| | - Seraina von Moos
- Division of Nephrology, University Hospital of Zurich (USZ), Zurich, Switzerland
| | - Thomas Schachtner
- Division of Nephrology, University Hospital of Zurich (USZ), Zurich, Switzerland
- *Correspondence: Thomas Schachtner,
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31
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Taeschler P, Cervia C, Zurbuchen Y, Hasler S, Pou C, Tan Z, Adamo S, Raeber ME, Bächli E, Rudiger A, Stüssi‐Helbling M, Huber LC, Brodin P, Nilsson J, Probst‐Müller E, Boyman O. Autoantibodies in COVID-19 correlate with antiviral humoral responses and distinct immune signatures. Allergy 2022; 77:2415-2430. [PMID: 35364615 PMCID: PMC9111424 DOI: 10.1111/all.15302] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/08/2022] [Accepted: 03/20/2022] [Indexed: 01/08/2023]
Abstract
BACKGROUND Several autoimmune features occur during coronavirus disease 2019 (COVID-19), with possible implications for disease course, immunity, and autoimmune pathology. In this study, we longitudinally screened for clinically relevant systemic autoantibodies to assess their prevalence, temporal trajectory, and association with immunity, comorbidities, and severity of COVID-19. METHODS We performed highly sensitive indirect immunofluorescence assays to detect antinuclear antibodies (ANA) and antineutrophil cytoplasmic antibodies (ANCA), along with serum proteomics and virome-wide serological profiling in a multicentric cohort of 175 COVID-19 patients followed up to 1 year after infection, eleven vaccinated individuals, and 41 unexposed controls. RESULTS Compared with healthy controls, similar prevalence and patterns of ANA were present in patients during acute COVID-19 and recovery. However, the paired analysis revealed a subgroup of patients with transient presence of certain ANA patterns during acute COVID-19. Furthermore, patients with severe COVID-19 exhibited a high prevalence of ANCA during acute disease. These autoantibodies were quantitatively associated with higher SARS-CoV-2-specific antibody titers in COVID-19 patients and in vaccinated individuals, thus linking autoantibody production to increased antigen-specific humoral responses. Notably, the qualitative breadth of antibodies cross-reactive with other coronaviruses was comparable in ANA-positive and ANA-negative individuals during acute COVID-19. In autoantibody-positive patients, multiparametric characterization demonstrated an inflammatory signature during acute COVID-19 and alterations of the B-cell compartment after recovery. CONCLUSION Highly sensitive indirect immunofluorescence assays revealed transient autoantibody production during acute SARS-CoV-2 infection, while the presence of autoantibodies in COVID-19 patients correlated with increased antiviral humoral immune responses and inflammatory immune signatures.
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Affiliation(s)
| | - Carlo Cervia
- Department of ImmunologyUniversity Hospital ZurichZurichSwitzerland
| | - Yves Zurbuchen
- Department of ImmunologyUniversity Hospital ZurichZurichSwitzerland
| | - Sara Hasler
- Department of ImmunologyUniversity Hospital ZurichZurichSwitzerland
| | - Christian Pou
- Science for Life LaboratoryDepartment of Women's and Children's HealthKarolinska InstitutetSolnaSweden
| | - Ziyang Tan
- Science for Life LaboratoryDepartment of Women's and Children's HealthKarolinska InstitutetSolnaSweden
| | - Sarah Adamo
- Department of ImmunologyUniversity Hospital ZurichZurichSwitzerland
| | - Miro E. Raeber
- Department of ImmunologyUniversity Hospital ZurichZurichSwitzerland
| | - Esther Bächli
- Clinic for Internal MedicineHirslanden Klinik St. AnnaLucerneSwitzerland
| | - Alain Rudiger
- Department of MedicineLimmattal HospitalSchlierenSwitzerland
| | | | - Lars C. Huber
- Clinic for Internal MedicineCity Hospital Triemli ZurichZurichSwitzerland
| | - Petter Brodin
- Science for Life LaboratoryDepartment of Women's and Children's HealthKarolinska InstitutetSolnaSweden
- Pediatric RheumatologyKarolinska University HospitalSolnaSweden
- Department of Immunology and InflammationImperial College LondonLondonUK
| | - Jakob Nilsson
- Department of ImmunologyUniversity Hospital ZurichZurichSwitzerland
| | | | - Onur Boyman
- Department of ImmunologyUniversity Hospital ZurichZurichSwitzerland
- Faculty of MedicineUniversity of ZurichZurichSwitzerland
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Vit G, Duro J, Rajendraprasad G, Hertz EPT, Holland LKK, Weisser MB, McEwan BC, Lopez‐Mendez B, Sotelo‐Parrilla P, Jeyaprakash AA, Montoya G, Mailand N, Maeda K, Kettenbach A, Barisic M, Nilsson J. Chemogenetic profiling reveals PP2A-independent cytotoxicity of proposed PP2A activators iHAP1 and DT-061. EMBO J 2022; 41:e110611. [PMID: 35695070 PMCID: PMC9289710 DOI: 10.15252/embj.2022110611] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 01/01/2023] Open
Abstract
Protein phosphatase 2A (PP2A) is an abundant phosphoprotein phosphatase that acts as a tumor suppressor. For this reason, compounds able to activate PP2A are attractive anticancer agents. The compounds iHAP1 and DT-061 have recently been reported to selectively stabilize specific PP2A-B56 complexes to mediate cell killing. We were unable to detect direct effects of iHAP1 and DT-061 on PP2A-B56 activity in biochemical assays and composition of holoenzymes. Therefore, we undertook genome-wide CRISPR-Cas9 synthetic lethality screens to uncover biological pathways affected by these compounds. We found that knockout of mitotic regulators is synthetic lethal with iHAP1 while knockout of endoplasmic reticulum (ER) and Golgi components is synthetic lethal with DT-061. Indeed we showed that iHAP1 directly blocks microtubule assembly both in vitro and in vivo and thus acts as a microtubule poison. In contrast, DT-061 disrupts both the Golgi apparatus and the ER and lipid synthesis associated with these structures. Our work provides insight into the biological pathways perturbed by iHAP1 and DT-061 causing cellular toxicity and argues that these compounds cannot be used for dissecting PP2A-B56 biology.
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Affiliation(s)
- Gianmatteo Vit
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Joana Duro
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Girish Rajendraprasad
- Cell Division and CytoskeletonDanish Cancer Society Research CenterCopenhagenDenmark
| | - Emil P T Hertz
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Lya Katrine Kauffeldt Holland
- Cell Death and Metabolism UnitCenter for Autophagy, Recycling and Disease (CARD)Danish Cancer Society Research Center (DCRC)CopenhagenDenmark
| | - Melanie Bianca Weisser
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Brennan C McEwan
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA,Norris Cotton Cancer CenterLebanonNHUSA
| | - Blanca Lopez‐Mendez
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | | | | | - Guillermo Montoya
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Kenji Maeda
- Cell Death and Metabolism UnitCenter for Autophagy, Recycling and Disease (CARD)Danish Cancer Society Research Center (DCRC)CopenhagenDenmark
| | - Arminja Kettenbach
- Department of Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Marin Barisic
- Cell Division and CytoskeletonDanish Cancer Society Research CenterCopenhagenDenmark,Department of Cellular and Molecular MedicineFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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33
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Taeschler P, Adamo S, Deng Y, Cervia C, Zurbuchen Y, Chevrier S, Raeber ME, Hasler S, Bächli E, Rudiger A, Stüssi‐Helbling M, Huber LC, Bodenmiller B, Boyman O, Nilsson J. T-cell recovery and evidence of persistent immune activation 12 months after severe COVID-19. Allergy 2022; 77:2468-2481. [PMID: 35567391 PMCID: PMC9347640 DOI: 10.1111/all.15372] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 04/06/2022] [Accepted: 04/19/2022] [Indexed: 01/08/2023]
Abstract
BACKGROUND T-cell lymphopenia and functional impairment is a hallmark of severe acute coronavirus disease 2019 (COVID-19). How T-cell numbers and function evolve at later timepoints after clinical recovery remains poorly investigated. METHODS We prospectively enrolled and longitudinally sampled 173 individuals with asymptomatic to critical COVID-19 and analyzed phenotypic and functional characteristics of T cells using flow cytometry, 40-parameter mass cytometry, targeted proteomics, and functional assays. RESULTS The extensive T-cell lymphopenia observed particularly in patients with severe COVID-19 during acute infection had recovered 6 months after infection, which was accompanied by a normalization of functional T-cell responses to common viral antigens. We detected persisting CD4+ and CD8+ T-cell activation up to 12 months after infection, in patients with mild and severe COVID-19, as measured by increased HLA-DR and CD38 expression on these cells. Persistent T-cell activation after COVID-19 was independent of administration of a COVID-19 vaccine post-infection. Furthermore, we identified a subgroup of patients with severe COVID-19 that presented with persistently low CD8+ T-cell counts at follow-up and exhibited a distinct phenotype during acute infection consisting of a dysfunctional T-cell response and signs of excessive pro-inflammatory cytokine production. CONCLUSION Our study suggests that T-cell numbers and function recover in most patients after COVID-19. However, we find evidence of persistent T-cell activation up to 12 months after infection and describe a subgroup of severe COVID-19 patients with persistently low CD8+ T-cell counts exhibiting a dysregulated immune response during acute infection.
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Affiliation(s)
- Patrick Taeschler
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Sarah Adamo
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Yun Deng
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Carlo Cervia
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Yves Zurbuchen
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Stéphane Chevrier
- Department of Quantitative Biomedicine University of Zurich Zurich Switzerland
- Institute of Molecular Health Sciences ETH Zurich Zurich Switzerland
| | - Miro E. Raeber
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Sara Hasler
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Esther Bächli
- Clinic for Internal Medicine, Hirslanden Klinik St. Anna Lucerne Switzerland
| | - Alain Rudiger
- Department of Medicine Limmattal Hospital Schlieren Switzerland
| | | | - Lars C. Huber
- Clinic for Internal Medicine, City Hospital Triemli Zurich Zurich Switzerland
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine University of Zurich Zurich Switzerland
- Institute of Molecular Health Sciences ETH Zurich Zurich Switzerland
| | - Onur Boyman
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
- Faculty of Medicine University of Zurich Zurich Switzerland
| | - Jakob Nilsson
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
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34
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Lezoeva E, Nilsson J, Wüthrich R, Mueller TF, Schachtner T. High PIRCHE Scores May Allow Risk Stratification of Borderline Rejection in Kidney Transplant Recipients. Front Immunol 2022; 13:788818. [PMID: 35250973 PMCID: PMC8894244 DOI: 10.3389/fimmu.2022.788818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/31/2022] [Indexed: 12/11/2022] Open
Abstract
Background The diagnosis of borderline rejection (BLR) ranges from mild inflammation to clinically significant TCMR and is associated with an increased risk of allograft dysfunction. Currently, there is no consensus regarding its treatment due in part to a lack of biomarkers to identify cases with increased risk for immune-mediated injury. Methods We identified 60 of 924 kidney transplant recipients (KTRs) with isolated and untreated BLR. We analyzed the impact of predicted indirectly recognizable HLA epitopes (PIRCHE) score on future rejection, de novo DSA development, and recovery to baseline allograft function. Additionally, we compared the outcomes of different Banff rejection phenotypes. Results Total PIRCHE scores were significantly higher in KTRs with BLR compared to the entire study population (p=0.016). Among KTRs with BLR total PIRCHE scores were significantly higher in KTRs who developed TCMR/ABMR in follow-up biopsies (p=0.029). Notably, the most significant difference was found in PIRCHE scores for the HLA-A locus (p=0.010). PIRCHE scores were not associated with the development of de novo DSA or recovery to baseline allograft function among KTRs with BLR (p>0.05). However, KTRs under cyclosporine-based immunosuppression were more likely to develop de novo DSA (p=0.033) than those with tacrolimus, whereas KTRs undergoing retransplantation were less likely to recover to baseline allograft function (p=0.003). Conclusions High PIRCHE scores put KTRs with BLR at an increased risk for future TCMR/ABMR and contribute to improved immunological risk stratification. The benefit of anti-rejection treatment, however, needs to be evaluated in future studies.
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Affiliation(s)
- Ekaterina Lezoeva
- Department of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Rudolf Wüthrich
- Department of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Thomas F. Mueller
- Department of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Thomas Schachtner
- Department of Nephrology, University Hospital Zurich, Zurich, Switzerland
- *Correspondence: Thomas Schachtner, ; orcid.org/0000-0001-5549-4798
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35
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Kreutmair S, Unger S, Núñez NG, Ingelfinger F, Alberti C, De Feo D, Krishnarajah S, Kauffmann M, Friebel E, Babaei S, Gaborit B, Lutz M, Jurado NP, Malek NP, Goepel S, Rosenberger P, Häberle HA, Ayoub I, Al-Hajj S, Nilsson J, Claassen M, Liblau R, Martin-Blondel G, Bitzer M, Roquilly A, Becher B. Distinct immunological signatures discriminate severe COVID-19 from non-SARS-CoV-2-driven critical pneumonia. Immunity 2022; 55:366-375. [PMID: 35139354 PMCID: PMC8822770 DOI: 10.1016/j.immuni.2022.01.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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36
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Fehr T, Hübel K, de Rougemont O, Abela I, Gaspert A, Güngör T, Hauri M, Helmchen B, Linsenmeier C, Müller T, Nilsson J, Riesterer O, Scandling JD, Schanz U, Cippà PE. Successful Induction of Specific Immunological Tolerance by Combined Kidney and Hematopoietic Stem Cell Transplantation in HLA-Identical Siblings. Front Immunol 2022; 13:796456. [PMID: 35173720 PMCID: PMC8841472 DOI: 10.3389/fimmu.2022.796456] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 01/05/2022] [Indexed: 11/30/2022] Open
Abstract
Induction of immunological tolerance has been the holy grail of transplantation immunology for decades. The only successful approach to achieve it in patients has been a combined kidney and hematopoietic stem cell transplantation from an HLA-matched or -mismatched living donor. Here, we report the first three patients in Europe included in a clinical trial aiming at the induction of tolerance by mixed lymphohematopoietic chimerism after kidney transplantation. Two female and one male patient were transplanted with a kidney and peripherally mobilized hematopoietic stem cells from their HLA-identical sibling donor. The protocol followed previous studies at Stanford University: kidney transplantation was performed on day 0 including induction with anti-thymocyte globulin followed by conditioning with 10x 1.2 Gy total lymphoid irradiation and the transfusion of CD34+ cells together with a body weight-adjusted dose of donor T cells on day 11. Immunosuppression consisted of cyclosporine A and steroids for 10 days, cyclosporine A and mycophenolate mofetil for 1 month, and then cyclosporine A monotherapy with tapering over 9–20 months. The 3 patients have been off immunosuppression for 4 years, 19 months and 8 months, respectively. No rejection or graft-versus-host disease occurred. Hematological donor chimerism was stable in the first, but slowly declining in the other two patients. A molecular microscope analysis in patient 2 revealed the genetic profile of a normal kidney. No relevant infections were observed, and the quality of life in all three patients is excellent. During the SARS-CoV-2 pandemic, all three patients were vaccinated with the mRNA vaccine BNT162b2 (Comirnaty®), and they showed excellent humoral and in 2 out 3 patients also cellular SARS-CoV-2-specific immunity. Thus, combined kidney and hematopoietic stem cell transplantation is a feasible and successful approach to induce specific immunological tolerance in the setting of HLA-matched sibling living kidney donation while maintaining immune responsiveness to an mRNA vaccine (ClinicalTrials.gov: NCT00365846).
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Affiliation(s)
- Thomas Fehr
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
- Department of Internal Medicine, Cantonal Hospital Graubuenden, Chur, Switzerland
- *Correspondence: Thomas Fehr,
| | - Kerstin Hübel
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
- Department of Surgery and Transplantation, University Hospital Zurich, Zurich, Switzerland
| | - Olivier de Rougemont
- Department of Surgery and Transplantation, University Hospital Zurich, Zurich, Switzerland
| | - Irene Abela
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Ariana Gaspert
- Department of Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Tayfun Güngör
- Division of Stem Cell Transplantation, University Children’s Hospital Zurich – Eleonore Foundation & Children`s Research Center (CRC), Zurich, Switzerland
| | - Mathias Hauri
- Division of Stem Cell Transplantation, University Children’s Hospital Zurich – Eleonore Foundation & Children`s Research Center (CRC), Zurich, Switzerland
| | - Birgit Helmchen
- Department of Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Claudia Linsenmeier
- Department of Radiation Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Thomas Müller
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Jakob Nilsson
- Laboratory for Transplantation Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Oliver Riesterer
- Department of Radiation Oncology, University Hospital Zurich, Zurich, Switzerland
| | - John D. Scandling
- Division of Nephrology, Stanford University School of Medicine, Stanford, CA, United States
| | - Urs Schanz
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Pietro E. Cippà
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
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Huang A, Cicin-Sain C, Pasin C, Epp S, Audigé A, Müller NJ, Nilsson J, Bankova A, Wolfensberger N, Vilinovszki O, Nair G, Hockl P, Schanz U, Kouyos RD, Hasse B, Zinkernagel AS, Trkola A, Manz MG, Abela IA, Müller AMS. Antibody Response to SARS-CoV-2 Vaccination in Patients Following Allogeneic Hematopoietic Cell Transplantation. Transplant Cell Ther 2022; 28:214.e1-214.e11. [PMID: 35092892 PMCID: PMC8802693 DOI: 10.1016/j.jtct.2022.01.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 01/06/2023]
Abstract
Vaccines against SARS-CoV-2 have been rapidly approved. Although pivotal studies were conducted in healthy volunteers, little information is available on the safety and efficacy of mRNA vaccines in immunocompromised patients, including recipients of allogeneic hematopoietic cell transplantation (allo-HCT). Here we used a novel assay to analyze patient- and transplantation-related factors and their influence on immune responses to SARS-CoV-2 vaccination over an extended period (up to 6 months) in a large and homogenous group of allo-HCT recipients at a single center in Switzerland. We examined longitudinal antibody responses to SARS-CoV-2 vaccination with BNT162b2 (BioNTech/Pfizer) and mRNA-1273 (Moderna) in 110 allo-HCT recipients and 86 healthy controls. Seroprofiling recording IgG, IgA, and IgM reactivity against SARS-CoV-2 antigens (receptor-binding domain, spike glycoprotein subunits S1 and S2, and nucleocapsid protein) was performed before vaccination, before the second dose, and at 1, 3, and 6 months after the second dose. Patients were stratified to 3 groups: 3 to 6 months post-allo-HCT, 6 to 12 months post-allo-HCT, and >12 months post-allo-HCT. Patients in the 3 to 6 months and 6 to 12 months post-allo-HCT groups developed significantly lower antibody titers after vaccination compared with patients in the >12 months post-allo-HCT group and healthy controls (P < .001). Within the cohort of allo-HCT recipients, patients age >65 years (P = .030), those receiving immunosuppression for prevention or treatment of graft-versus-host disease (GVHD) (P = .033), and patients with relapsed disease (P = .014) displayed low humoral immune responses to the vaccine. In contrast, the intensity of the conditioning regimen, underlying disease (myeloid/lymphoid/other), and presence of chronic GVHD had no impact on antibody levels. Antibody titers achieved the highest levels at 1 month after the second dose of the vaccine but waned substantially in all transplantation groups and healthy controls over time. This analysis of long-term vaccine antibody response is of critical importance to allo-HCT recipients and transplant physicians to guide treatment decisions regarding revaccination and social behavior during the SARS-CoV-2 pandemic.
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Affiliation(s)
- Alice Huang
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Caroline Cicin-Sain
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Chloe Pasin
- Institute of Medical Virology, University of Zurich, Switzerland; Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland
| | - Selina Epp
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Annette Audigé
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Nicolas J Müller
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, Switzerland
| | - Andriyana Bankova
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Nathan Wolfensberger
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Oliver Vilinovszki
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Gayathri Nair
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Philipp Hockl
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Urs Schanz
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Roger D Kouyos
- Institute of Medical Virology, University of Zurich, Switzerland; Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland
| | - Barbara Hasse
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland
| | - Annelies S Zinkernagel
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Switzerland
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland
| | - Irene A Abela
- Institute of Medical Virology, University of Zurich, Switzerland; Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Switzerland
| | - Antonia M S Müller
- Department of Medical Oncology and Hematology, University Hospital Zurich, Switzerland.
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38
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DeLuca KF, Mick JE, Ide AH, Lima WC, Sherman L, Schaller KL, Anderson SM, Zhao N, Stasevich TJ, Varma D, Nilsson J, DeLuca JG. Generation and diversification of recombinant monoclonal antibodies. eLife 2021; 10:72093. [PMID: 34970967 PMCID: PMC8763395 DOI: 10.7554/elife.72093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Antibodies are indispensable tools used for a large number of applications in both foundational and translational bioscience research; however, there are drawbacks to using traditional antibodies generated in animals. These include a lack of standardization leading to problems with reproducibility, high costs of antibodies purchased from commercial sources, and ethical concerns regarding the large number of animals used to generate antibodies. To address these issues, we have developed practical methodologies and tools for generating low-cost, high-yield preparations of recombinant monoclonal antibodies and antibody fragments directed to protein epitopes from primary sequences. We describe these methods here, as well as approaches to diversify monoclonal antibodies, including customization of antibody species specificity, generation of genetically encoded small antibody fragments, and conversion of single chain antibody fragments (e.g. scFv) into full-length, bivalent antibodies. This study focuses on antibodies directed to epitopes important for mitosis and kinetochore function; however, the methods and reagents described here are applicable to antibodies and antibody fragments for use in any field.
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Affiliation(s)
- Keith F DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Jeanne E Mick
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Amy Hodges Ide
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Wanessa C Lima
- Geneva Antibody Facility, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Lori Sherman
- CU Cancer Center Cell Technologies Shared Resource, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Kristin L Schaller
- Department of Pediatric Hematology, Oncology and Bone Marrow Transplant, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Steven M Anderson
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, United States
| | - Ning Zhao
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Timothy J Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
| | - Dileep Varma
- Department of Cell and Developmental Biology, Northwestern University, Chicago, United States
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Germany
| | - Jennifer G DeLuca
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, United States
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39
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Kruse T, Benz C, Garvanska DH, Lindqvist R, Mihalic F, Coscia F, Inturi R, Sayadi A, Simonetti L, Nilsson E, Ali M, Kliche J, Moliner Morro A, Mund A, Andersson E, McInerney G, Mann M, Jemth P, Davey NE, Överby AK, Nilsson J, Ivarsson Y. Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities. Nat Commun 2021; 12:6761. [PMID: 34799561 PMCID: PMC8605023 DOI: 10.1038/s41467-021-26498-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
Viral proteins make extensive use of short peptide interaction motifs to hijack cellular host factors. However, most current large-scale methods do not identify this important class of protein-protein interactions. Uncovering peptide mediated interactions provides both a molecular understanding of viral interactions with their host and the foundation for developing novel antiviral reagents. Here we describe a viral peptide discovery approach covering 23 coronavirus strains that provides high resolution information on direct virus-host interactions. We identify 269 peptide-based interactions for 18 coronaviruses including a specific interaction between the human G3BP1/2 proteins and an ΦxFG peptide motif in the SARS-CoV-2 nucleocapsid (N) protein. This interaction supports viral replication and through its ΦxFG motif N rewires the G3BP1/2 interactome to disrupt stress granules. A peptide-based inhibitor disrupting the G3BP1/2-N interaction dampened SARS-CoV-2 infection showing that our results can be directly translated into novel specific antiviral reagents.
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Affiliation(s)
- Thomas Kruse
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Dimitriya H Garvanska
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Richard Lindqvist
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Filip Mihalic
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Fabian Coscia
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
- Spatial Proteomics Group, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Raviteja Inturi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ahmed Sayadi
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Emma Nilsson
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden
| | - Muhammad Ali
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Johanna Kliche
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ainhoa Moliner Morro
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Mund
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Gerald McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Matthias Mann
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC, Box 582, Husargatan 3, 751 23, Uppsala, Sweden
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Anna K Överby
- Department of Clinical Microbiology, Umeå University, 90185, Umeå, Sweden.
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, 90186, Umeå, Sweden.
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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Schiopu A, Svedlund S, Yndigegn T, Varma V, Ongstad EL, Collen A, George RT, Wang X, Goncalves I, Nilsson J, Gan LM. Elevated soluble lectin-like oxidised low-density lipoprotein receptor-1 (sLOX-1) associated with increased risk for heart failure and MACE after an acute coronary event. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.1129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background/Introduction
The lectin-like oxidised low-density lipoprotein receptor (LOX-1) is involved in atherosclerotic plaque inflammation and vulnerability. Plasma levels of soluble LOX-1 (sLOX-1) have previously been associated with increased risk for recurrent coronary events and mortality in patients with acute coronary syndrome (ACS).
Purpose
To assess the association of sLOX-1 with the development of heart failure (HF) post-ACS.
Methods
We measured sLOX-1 in 524 patients with ACS within 24 hours after the acute event. A subgroup of 97 of these patients completed a follow-up echocardiogram after one year. The incidence of HF-related hospitalisation and recurrent major adverse cardiovascular events (MACE), defined as recurrent ACS or cardiovascular death, was followed for a mean period of two years. In a separate cohort of 363 patients with ACS and percutaneous coronary intervention (PCI), we studied the correlations between sLOX-1, coronary flow reserve, left ventricular systolic function and systemic inflammation at two follow-up visits within four weeks and 16 weeks post-ACS, respectively.
Results
Baseline sLOX-1 was positively associated with the risk of HF and MACE, independently of traditional cardiovascular risk factors, revascularisation and medication. The hazard ratios and 95% confidence intervals were 1.57 (1.10–2.23), p=0.012 for HF and 1.36 (1.08–1.71), p=0.009 for MACE per standard deviation baseline sLOX-1 increase. Elevated sLOX-1 was also negatively associated with lower-left ventricular ejection fraction at one year (r=−0.263, p=0.009). In the second ACS cohort, we found that plasma sLOX-1 measured at the two follow-up visits was negatively associated with coronary flow reserve and left ventricular systolic function, and positively correlated with biomarkers of systemic inflammation and cardiac overload.
Conclusion
Elevated sLOX-1 is associated with the development of HF and recurrent cardiovascular events in patients with ACS. Although this association study cannot confirm causality, the results suggest LOX-1 as a potential biomarker and treatment target in patients with ACS.
Funding Acknowledgement
Type of funding sources: Foundation. Main funding source(s): • Swedish Research Council • The Swedish Heart and Lung foundation• Swedish Foundation for Strategic Research Dnr IRC15-0067 • Marianne and Marcus Wallenberg Foundation • Bundy Academy at Lund University
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Affiliation(s)
- A Schiopu
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - S Svedlund
- Department of Clinical Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - T Yndigegn
- Department of Cardiology, Skåne University Hospital, Lund, Sweden
| | - V Varma
- Translational Science and Experimental Medicine, Research and Early Development, CVRM, AstraZeneca, Gaithersburg, MD, United States of America
| | - E L Ongstad
- Bioscience Cardiovascular, Research and Early Development, CVRM, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States of America
| | - A Collen
- Projects, Research and Early Development, CVRM, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - R T George
- Early Clinical Development, Research and Early Development, CVRM, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, United States of America
| | - X Wang
- Translational Science and Experimental Medicine, Research and Early Development, CVRM, AstraZeneca, Gaithersburg, MD, United States of America
| | - I Goncalves
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - J Nilsson
- Department of Clinical Sciences Malmö, Lund University, Malmö, Sweden
| | - L M Gan
- Early Clinical Development, Research and Early Development, CVRM, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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Wehmeier C, Amico P, Sidler D, Wirthmüller U, Hadaya K, Ferrari-Lacraz S, Golshayan D, Aubert V, Schnyder A, Sunic K, Schachtner T, Nilsson J, Schaub S. Pre-transplant donor-specific HLA antibodies and risk for poor first-year renal transplant outcomes: results from the Swiss Transplant Cohort Study. Transpl Int 2021; 34:2755-2768. [PMID: 34561920 DOI: 10.1111/tri.14119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/11/2021] [Accepted: 09/21/2021] [Indexed: 12/30/2022]
Abstract
The aim of this study was to analyze first year renal outcomes in a nationwide prospective multicenter cohort comprising 2215 renal transplants, with a special emphasis on the presence of pre-transplant donor-specific HLA antibodies (DSA). All transplants had a complete virtual crossmatch and DSA were detected in 19% (411/2215). The investigated composite endpoint was a poor first-year outcome defined as (i) allograft failure or (ii) death or (iii) poor allograft function (eGFR ≤25 ml/min/1.73 m2 ) at one year. Two hundred and twenty-one (221/2215; 10%) transplants showed a poor first-year outcome. Rejection (24/70; 34%) was the most common reason for graft failure. First-year patient's death was rare (48/2215; 2%). There were no statistically significant differences between DSA-positive and DSA-negative transplants regarding composite and each individual endpoint, as well as reasons for graft failure and death. DSA-positive transplants experienced more frequently rejection episodes, mainly antibody-mediated rejection (both P < 0.0001). The combination of DSA and any first year rejection was associated with the overall poorest death-censored allograft survival (P < 0.0001). In conclusion, presence of pre-transplant DSA per se does not affect first year outcomes. However, DSA-positive transplants experiencing first year rejection are a high-risk population for poor allograft survival and may benefit from intense clinical surveillance.
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Affiliation(s)
- Caroline Wehmeier
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Patrizia Amico
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
| | - Daniel Sidler
- Department of Nephrology and Hypertension, Inselspital, Berne University Hospital and University of Berne, Berne, Switzerland
| | - Urs Wirthmüller
- Department of Laboratory Medicine, Inselspital, Berne University Hospital and University of Berne, Berne, Switzerland
| | - Karine Hadaya
- Divisions of Nephrology and Transplantation, Geneva University Hospitals, Geneva, Switzerland
| | - Sylvie Ferrari-Lacraz
- Transplantation Immunology Unit, Service of Immunology and Allergy and Service of Laboratory Medicine, Geneva University Hospital and Medical School, Geneva, Switzerland
| | - Déla Golshayan
- Transplantation Center, Lausanne University Hospital, Lausanne, Switzerland
| | - Vincent Aubert
- Division of Immunology and Allergy, Lausanne University Hospital, Lausanne, Switzerland
| | - Aurelia Schnyder
- Department of Nephrology and Transplantation Medicine, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Kata Sunic
- HLA Laboratory, Blutspende Schweizerisches Rotkreuz Ostschweiz, St. Gallen, Switzerland
| | - Thomas Schachtner
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, Zurich, Switzerland
| | - Stefan Schaub
- Clinic for Transplantation Immunology and Nephrology, University Hospital Basel, Basel, Switzerland
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Adamo S, Chevrier S, Cervia C, Zurbuchen Y, Raeber ME, Yang L, Sivapatham S, Jacobs A, Baechli E, Rudiger A, Stüssi‐Helbling M, Huber LC, Schaer DJ, Bodenmiller B, Boyman O, Nilsson J. Profound dysregulation of T cell homeostasis and function in patients with severe COVID-19. Allergy 2021; 76:2866-2881. [PMID: 33884644 PMCID: PMC8251365 DOI: 10.1111/all.14866] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/09/2021] [Accepted: 03/14/2021] [Indexed: 01/08/2023]
Abstract
Background Coronavirus disease 2019 (COVID‐19) is caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) and shows a broad clinical presentation ranging from asymptomatic infection to fatal disease. A very prominent feature associated with severe COVID‐19 is T cell lymphopenia. However, homeostatic and functional properties of T cells are ill‐defined in COVID‐19. Methods We prospectively enrolled individuals with mild and severe COVID‐19 into our multicenter cohort and performed a cross‐sectional analysis of phenotypic and functional characteristics of T cells using 40‐parameter mass cytometry, flow cytometry, targeted proteomics, and functional assays. Results Compared with mild disease, we observed strong perturbations of peripheral T cell homeostasis and function in severe COVID‐19. Individuals with severe COVID‐19 showed T cell lymphopenia and redistribution of T cell populations, including loss of naïve T cells, skewing toward CD4+T follicular helper cells and cytotoxic CD4+ T cells, and expansion of activated and exhausted T cells. Extensive T cell apoptosis was particularly evident with severe disease and T cell lymphopenia, which in turn was accompanied by impaired T cell responses to several common viral antigens. Patients with severe disease showed elevated interleukin‐7 and increased T cell proliferation. Furthermore, patients sampled at late time points after symptom onset had higher T cell counts and improved antiviral T cell responses. Conclusion Our study suggests that severe COVID‐19 is characterized by extensive T cell dysfunction and T cell apoptosis, which is associated with signs of homeostatic T cell proliferation and T cell recovery.
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Affiliation(s)
- Sarah Adamo
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Stéphane Chevrier
- Department of Quantitative Biomedicine University of Zurich Zurich Switzerland
- Institute of Molecular Health Sciences ETH Zurich Zurich Switzerland
| | - Carlo Cervia
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Yves Zurbuchen
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Miro E. Raeber
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Liliane Yang
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
| | - Sujana Sivapatham
- Department of Quantitative Biomedicine University of Zurich Zurich Switzerland
- Institute of Molecular Health Sciences ETH Zurich Zurich Switzerland
| | - Andrea Jacobs
- Department of Quantitative Biomedicine University of Zurich Zurich Switzerland
- Institute of Molecular Health Sciences ETH Zurich Zurich Switzerland
| | - Esther Baechli
- Clinic for Internal Medicine Uster Hospital Uster Switzerland
| | - Alain Rudiger
- Department of Medicine Limmattal Hospital Schlieren Switzerland
| | | | - Lars C. Huber
- Clinic for Internal Medicine City Hospital Triemli Zurich Zurich Switzerland
| | | | - Bernd Bodenmiller
- Department of Quantitative Biomedicine University of Zurich Zurich Switzerland
- Institute of Molecular Health Sciences ETH Zurich Zurich Switzerland
| | - Onur Boyman
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
- Faculty of Medicine University of Zurich Zurich Switzerland
| | - Jakob Nilsson
- Department of Immunology University Hospital Zurich (USZ) Zurich Switzerland
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Kreutmair S, Unger S, Núñez NG, Ingelfinger F, Alberti C, De Feo D, Krishnarajah S, Kauffmann M, Friebel E, Babaei S, Gaborit B, Lutz M, Jurado NP, Malek NP, Goepel S, Rosenberger P, Häberle HA, Ayoub I, Al-Hajj S, Nilsson J, Claassen M, Liblau R, Martin-Blondel G, Bitzer M, Roquilly A, Becher B. Distinct immunological signatures discriminate severe COVID-19 from non-SARS-CoV-2-driven critical pneumonia. Immunity 2021; 54:1578-1593.e5. [PMID: 34051147 PMCID: PMC8106882 DOI: 10.1016/j.immuni.2021.05.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/24/2021] [Accepted: 05/04/2021] [Indexed: 12/29/2022]
Abstract
Immune profiling of COVID-19 patients has identified numerous alterations in both innate and adaptive immunity. However, whether those changes are specific to SARS-CoV-2 or driven by a general inflammatory response shared across severely ill pneumonia patients remains unknown. Here, we compared the immune profile of severe COVID-19 with non-SARS-CoV-2 pneumonia ICU patients using longitudinal, high-dimensional single-cell spectral cytometry and algorithm-guided analysis. COVID-19 and non-SARS-CoV-2 pneumonia both showed increased emergency myelopoiesis and displayed features of adaptive immune paralysis. However, pathological immune signatures suggestive of T cell exhaustion were exclusive to COVID-19. The integration of single-cell profiling with a predicted binding capacity of SARS-CoV-2 peptides to the patients' HLA profile further linked the COVID-19 immunopathology to impaired virus recognition. Toward clinical translation, circulating NKT cell frequency was identified as a predictive biomarker for patient outcome. Our comparative immune map serves to delineate treatment strategies to interfere with the immunopathologic cascade exclusive to severe COVID-19.
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Affiliation(s)
- Stefanie Kreutmair
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland; German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Heidelberg, Partner Site Freiburg, 79106 Freiburg, Germany
| | - Susanne Unger
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland
| | - Nicolás Gonzalo Núñez
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland
| | - Florian Ingelfinger
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland
| | - Chiara Alberti
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland
| | - Donatella De Feo
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland
| | - Sinduya Krishnarajah
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland
| | - Manuel Kauffmann
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland
| | - Ekaterina Friebel
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland
| | - Sepideh Babaei
- Department Internal Medicine I, Eberhard-Karls University, 72076 Tuebingen, Germany
| | - Benjamin Gaborit
- Université de Nantes, CHU Nantes, Pôle Anesthésie Réanimations, Service d'Anesthésie Réanimation Chirurgicale, Hôtel Dieu, 44093 Nantes, France
| | - Mirjam Lutz
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland
| | - Nicole Puertas Jurado
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland
| | - Nisar P Malek
- Department Internal Medicine I, Eberhard-Karls University, 72076 Tuebingen, Germany
| | - Siri Goepel
- Department Internal Medicine I, Eberhard-Karls University, 72076 Tuebingen, Germany; German Centre for Infection Research (DZIF), Partner Site Tuebingen, 72076 Tuebingen, Germany
| | - Peter Rosenberger
- Department of Anesthesiology and Intensive Care Medicine, Eberhard-Karls University, 72076 Tuebingen, Germany
| | - Helene A Häberle
- Department of Anesthesiology and Intensive Care Medicine, Eberhard-Karls University, 72076 Tuebingen, Germany
| | - Ikram Ayoub
- Toulouse Institute for Infectious and Inflammatory Diseases, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, UPS, 31024 Toulouse, France
| | - Sally Al-Hajj
- Toulouse Institute for Infectious and Inflammatory Diseases, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, UPS, 31024 Toulouse, France
| | - Jakob Nilsson
- Department of Immunology, University Hospital Zurich, 8006 Zurich, Switzerland
| | - Manfred Claassen
- Department Internal Medicine I, Eberhard-Karls University, 72076 Tuebingen, Germany
| | - Roland Liblau
- Toulouse Institute for Infectious and Inflammatory Diseases, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, UPS, 31024 Toulouse, France
| | - Guillaume Martin-Blondel
- Toulouse Institute for Infectious and Inflammatory Diseases, Université de Toulouse, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, UPS, 31024 Toulouse, France; Department of Infectious and Tropical Diseases, Toulouse University Hospital, 31059 Toulouse, France
| | - Michael Bitzer
- Department Internal Medicine I, Eberhard-Karls University, 72076 Tuebingen, Germany
| | - Antoine Roquilly
- Université de Nantes, CHU Nantes, Pôle Anesthésie Réanimations, Service d'Anesthésie Réanimation Chirurgicale, Hôtel Dieu, 44093 Nantes, France
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland.
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44
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Ueki Y, Hadders MA, Weisser MB, Nasa I, Sotelo‐Parrilla P, Cressey LE, Gupta T, Hertz EPT, Kruse T, Montoya G, Jeyaprakash AA, Kettenbach A, Lens SMA, Nilsson J. A highly conserved pocket on PP2A-B56 is required for hSgo1 binding and cohesion protection during mitosis. EMBO Rep 2021; 22:e52295. [PMID: 33973335 PMCID: PMC8256288 DOI: 10.15252/embr.202052295] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/07/2021] [Accepted: 04/13/2021] [Indexed: 01/11/2023] Open
Abstract
The shugoshin proteins are universal protectors of centromeric cohesin during mitosis and meiosis. The binding of human hSgo1 to the PP2A-B56 phosphatase through a coiled-coil (CC) region mediates cohesion protection during mitosis. Here we undertook a structure function analysis of the PP2A-B56-hSgo1 complex, revealing unanticipated aspects of complex formation and function. We establish that a highly conserved pocket on the B56 regulatory subunit is required for hSgo1 binding and cohesion protection during mitosis in human somatic cells. Consistent with this, we show that hSgo1 blocks the binding of PP2A-B56 substrates containing a canonical B56 binding motif. We find that PP2A-B56 bound to hSgo1 dephosphorylates Cdk1 sites on hSgo1 itself to modulate cohesin interactions. Collectively our work provides important insight into cohesion protection during mitosis.
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Affiliation(s)
- Yumi Ueki
- The Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Michael A Hadders
- Oncode Institute and Center for Molecular MedicineUniversity Medical Center UtrechUtrecht UniversityUtrechtThe Netherlands
| | - Melanie B Weisser
- The Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Isha Nasa
- Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | | | - Lauren E Cressey
- Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Tanmay Gupta
- Wellcome Center for Cell BiologyUniversity of EdinburghEdinburghUK
| | - Emil P T Hertz
- The Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Thomas Kruse
- The Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Guillermo Montoya
- The Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical ScienceUniversity of CopenhagenCopenhagenDenmark
| | | | - Arminja Kettenbach
- Biochemistry and Cell BiologyGeisel School of Medicine at Dartmouth CollegeHanoverNHUSA
| | - Susanne M A Lens
- Oncode Institute and Center for Molecular MedicineUniversity Medical Center UtrechUtrecht UniversityUtrechtThe Netherlands
| | - Jakob Nilsson
- The Novo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical ScienceUniversity of CopenhagenCopenhagenDenmark
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45
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Holm Nielsen S, Edsfeldt A, Tengryd C, Gustafsson H, Shore AC, Natali A, Khan F, Genovese F, Bengtsson E, Karsdal M, Leeming DJ, Nilsson J, Goncalves I. The novel collagen matrikine, endotrophin, is associated with mortality and cardiovascular events in patients with atherosclerosis. J Intern Med 2021; 290:179-189. [PMID: 33951242 PMCID: PMC8359970 DOI: 10.1111/joim.13253] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/27/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Rupture of atherosclerotic plaques is the major cause of acute cardiovascular events. The biomarker PRO-C6 measuring Endotrophin, a matrikine of collagen type VI, may provide valuable information detecting subjects in need of intensified strategies for secondary prevention. OBJECTIVE In this study, we evaluate endotrophin in human atherosclerotic plaques and circulating levels of PRO-C6 in patients with atherosclerosis, to determine the predictive potential of the biomarker. METHODS Sections from the stenotic human carotid plaques were stained with the PRO-C6 antibody. PRO-C6 was measured in serum of patients enrolled in the Carotid Plaque Imagining Project (CPIP) (discovery cohort, n = 577) and the innovative medicines initiative surrogate markers for micro- and macrovascular hard end-points for innovative diabetes tools (IMI-SUMMIT, validation cohort, n = 1,378). Median follow-up was 43 months. Kaplan-Meier curves and log-rank tests were performed in the discovery cohort. Cox proportional hazard regression analysis (HR with 95% CI) was used in the discovery cohort and binary logistic regression (OR with 95% CI) in the validation cohort. RESULTS PRO-C6 was localized in the core and shoulder of the atherosclerotic plaque. In the discovery cohort, PRO-C6 independently predicted future cardiovascular events (HR 1.089 [95% CI 1.019 -1.164], p = 0.01), cardiovascular death (HR 1.118 [95% CI 1.008 -1.241], p = 0.04) and all-cause death (HR 1.087 [95% CI 1.008 -1.172], p = 0.03). In the validation cohort, PRO-C6 predicted future cardiovascular events (OR 1.063 [95% CI 1.011 -1.117], p = 0.017). CONCLUSION PRO-C6 is present in the atherosclerotic plaque and associated with future cardiovascular events, cardiovascular death and all-cause mortality in two large prospective cohorts.
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Affiliation(s)
- S Holm Nielsen
- Nordic Bioscience, Herlev, Denmark.,Department of Biomedicine and Biotechnology, Technical University of Denmark, Lyngby, Denmark
| | - A Edsfeldt
- Department of Cardiology, Skåne University Hospital, Malmö, Sweden.,Department of Clinical Sciences, Lund University, Malmö, Sweden.,Wallenberg Center for Molecular Medicine, Lund University, Malmö, Sweden
| | - C Tengryd
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - H Gustafsson
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - A C Shore
- Diabetes and Vascular Medicine, University of Exeter, Medical School, National Institute for Health Research Exeter Clinical Research Facility, Exeter, UK
| | - A Natali
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - F Khan
- Division of Molecular and Clinical medicine, University of Dundee, Dundee, UK
| | | | - E Bengtsson
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | | | | | - J Nilsson
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - I Goncalves
- Department of Cardiology, Skåne University Hospital, Malmö, Sweden.,Department of Clinical Sciences, Lund University, Malmö, Sweden
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Naef B, Nilsson J, Wuethrich RP, Mueller TF, Schachtner T. Intravenous immunoglobulins do not prove beneficial to reduce alloimmunity among kidney transplant recipients with BKV-associated nephropathy. Transpl Int 2021; 34:1481-1493. [PMID: 33872427 DOI: 10.1111/tri.13882] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/18/2021] [Accepted: 04/10/2021] [Indexed: 12/18/2022]
Abstract
Reduced immunosuppression during BKV-DNAemia has been associated with T-cell mediated rejection (TCMR), de novo donor-specific antibodies (DSA) and antibody-mediated rejection (ABMR). Intravenous immunoglobulins (IVIG) may reduce alloimmunity. We studied 860 kidney transplant recipients (KTRs) for the development of BKV-DNAuria and BKV-DNAemia (low-level <10 000 IE/ml, high-level >10 000 IE/ml). 52/131 KTRs with high-level BKV-DNAemia received IVIG. The HLA-related immunological risk was stratified by the Predicted Indirectly Recognizable HLA Epitopes (PIRCHE) algorithm. BKV-DNAuria only was observed in 86 KTRs (10.0%), low-level BKV-DNAemia in 180 KTRs (20.9%) and high-level BKV-DNAemia in 131 KTRs (15.2%). KTRs with low-level BKV-DNAemia showed significantly less TCMR compared to KTRs with high-level BKV-DNAemia (5.2% vs. 25.5%; P < 0.001) and no BKV-replication (13.2%; P = 0.014), lowest rates of de novo DSA (21.3%), ABMR (9.2%) and flattest glomerular filtration rate (GFR) slope (-0.8 ml/min). KTRs with low-level BKV-DNAemia showed significantly higher median (interquartile range) total PIRCHE if they developed TCMR [100.22 (72.6) vs. 69.52 (49.97); P = 0.020] or ABMR [128.86 (52.99) vs. 69.52 (49.96); P = 0.005]. Administration of IVIG did not shorten duration of BKV-DNAemia (P = 0.798) or reduce TCMR, de novo DSA and ABMR (P > 0.05). KTRs with low-level BKV-DNAemia showed best protection against alloimmunity, with a high number of PIRCHE co-determining the remaining risk. The administration of IVIG, however, was not beneficial in reducing alloimmunity.
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Affiliation(s)
- Bettina Naef
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Jakob Nilsson
- Division of Immunology, University Hospital Zurich, Zurich, Switzerland
| | | | - Thomas F Mueller
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
| | - Thomas Schachtner
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
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Folkedal O, Utskot SO, Nilsson J. Thermal delousing in anaesthetised small Atlantic salmon (Salmo salar) post-smolts: A case study showing the viability of anaesthesia prior to delousing for improved welfare during treatment for salmon lice. Anim Welf 2021. [DOI: 10.7120/09627286.30.2.117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Delousing treatment for salmon sea lice (Lepeophtheirus salmonis) is considered a significant welfare concern in farming of Atlantic salmon ( Salmo salar), where both industry and legislative bodies prompt for better methods. Currently, the most common method is thermal
delousing, where fish are crowded, pumped into a vessel and exposed to ∼28–34°C for ∼30 s. Physical collisions occurring as a result of a loss of behavioural control lead to acute stress. Crowding triggers vigorous escape behaviour as salmon respond not only to treatment
but also to being channeled to and from the treatment zone. A sequence of events considered to cause mortality and poor welfare. The present case study was motivated by an urgent need for delousing in groups of small salmon post-smolts in experimental research. For this purpose, a simple,
small-scale system for thermal delousing was constructed, including anaesthesia to alleviate behavioural responses. The anaesthetised fish showed little behavioural response to thermal treatment, strong appetite within hours, and negligible mortality. The described method is regarded as a
welfare-friendly alternative to industrial delousing in smaller fish groups, for example, in experimental research. We would encourage detailed research aimed towards gaining a deeper under-standing of the welfare effects of anaesthesia prior to treatment for delousing.
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Hein JB, Garvanska DH, Nasa I, Kettenbach AN, Nilsson J. Coupling of Cdc20 inhibition and activation by BubR1. J Cell Biol 2021; 220:211939. [PMID: 33819340 PMCID: PMC8025235 DOI: 10.1083/jcb.202012081] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/18/2021] [Accepted: 02/25/2021] [Indexed: 12/25/2022] Open
Abstract
Tight regulation of the APC/C-Cdc20 ubiquitin ligase that targets cyclin B1 for degradation is important for mitotic fidelity. The spindle assembly checkpoint (SAC) inhibits Cdc20 through the mitotic checkpoint complex (MCC). In addition, phosphorylation of Cdc20 by cyclin B1–Cdk1 independently inhibits APC/C–Cdc20 activation. This creates a conundrum for how Cdc20 is activated before cyclin B1 degradation. Here, we show that the MCC component BubR1 harbors both Cdc20 inhibition and activation activities, allowing for cross-talk between the two Cdc20 inhibition pathways. Specifically, BubR1 acts as a substrate specifier for PP2A-B56 to enable efficient Cdc20 dephosphorylation in the MCC. A mutant Cdc20 mimicking the dephosphorylated state escapes a mitotic checkpoint arrest, arguing that restricting Cdc20 dephosphorylation to the MCC is important. Collectively, our work reveals how Cdc20 can be dephosphorylated in the presence of cyclin B1-Cdk1 activity without causing premature anaphase onset.
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Affiliation(s)
- Jamin B Hein
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Science, Copenhagen, Denmark
| | - Dimitriya H Garvanska
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Science, Copenhagen, Denmark
| | - Isha Nasa
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH
| | - Arminja N Kettenbach
- Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth College, Hanover, NH
| | - Jakob Nilsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Science, Copenhagen, Denmark
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Ringdal M, Bergbom I, Nilsson J, Karlsson V. Older patients' recovery following intensive care: A follow-up study with the RAIN questionnaire. Intensive Crit Care Nurs 2021; 65:103038. [PMID: 33775549 DOI: 10.1016/j.iccn.2021.103038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 12/12/2022]
Abstract
The aim was to investigate older patient recovery (65 years+) up to two years following discharge from an intensive care unit (ICU) using the Recovery After Intensive Care (RAIN) instrument and to correlate RAIN with the Hospital Anxiety and Depression Scale (HAD). METHODS An explorative and descriptive longitudinal design was used. Eighty-two patients answered RAIN and HAD at least twice following discharge. Demographic and clinical data were collected from patient records. RESULTS Recovery after the ICU was relatively stable and good for older patients at the four data collection points. There was little variation on the RAIN subscales over time. The greatest recovery improvement was found in existential ruminations from 2 to 24 months. A patient that could look forward and those with supportive relatives had the highest scores at all four measurements. Having lower financial situation was correlated to poorer recovery and was significant at 24 months. The RAIN and HAD instruments showed significant correlations, except for the revaluation of life subscale, which is not an aspect in HAD. CONCLUSION The RAIN instrument shows to be a good measurement for all dimensions of recovery, including existential dimensions, which are not covered by any other instrument.
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Affiliation(s)
- M Ringdal
- Institute of Health and Care Sciences at Sahlgrenska Academy, University of Gothenburg, Kungälvs Hospital, Sweden.
| | - I Bergbom
- Institute of Health and Care Sciences at Sahlgrenska Academy, University of Gothenburg, Sweden, Professor Emerita, Honorary Doctor at Åbo Academy, Åbo, Finland
| | - J Nilsson
- Institute of Health and Care Sciences at Sahlgrenska Academy, University of Gothenburg, Sweden
| | - V Karlsson
- Department of Health Science, University West, Trollhättan, Sweden
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Nilsson J, Winfree K, Molife C, Bhattacharyya D, D'Yachova Y, Wang X, Malmenäs M, Taipale K. P10.04 A Budget Impact Analysis for Treatment with Ramucirumab Plus Erlotinib in Metastatic EGFR-Mutated NSCLC in the US. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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