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Wagner TR, Blaess S, Leske IB, Frecot DI, Gramlich M, Traenkle B, Kaiser PD, Seyfried D, Maier S, Rezza A, Sônego F, Thiam K, Pezzana S, Zeck A, Gouttefangeas C, Scholz AM, Nueske S, Maurer A, Kneilling M, Pichler BJ, Sonanini D, Rothbauer U. Two birds with one stone: human SIRPα nanobodies for functional modulation and in vivo imaging of myeloid cells. Front Immunol 2023; 14:1264179. [PMID: 38164132 PMCID: PMC10757926 DOI: 10.3389/fimmu.2023.1264179] [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: 07/20/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
Signal-regulatory protein α (SIRPα) expressed by myeloid cells is of particular interest for therapeutic strategies targeting the interaction between SIRPα and the "don't eat me" ligand CD47 and as a marker to monitor macrophage infiltration into tumor lesions. To address both approaches, we developed a set of novel human SIRPα (hSIRPα)-specific nanobodies (Nbs). We identified high-affinity Nbs targeting the hSIRPα/hCD47 interface, thereby enhancing antibody-dependent cellular phagocytosis. For non-invasive in vivo imaging, we chose S36 Nb as a non-modulating binder. By quantitative positron emission tomography in novel hSIRPα/hCD47 knock-in mice, we demonstrated the applicability of 64Cu-hSIRPα-S36 Nb to visualize tumor infiltration of myeloid cells. We envision that the hSIRPα-Nbs presented in this study have potential as versatile theranostic probes, including novel myeloid-specific checkpoint inhibitors for combinatorial treatment approaches and for in vivo stratification and monitoring of individual responses during cancer immunotherapies.
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Affiliation(s)
- Teresa R. Wagner
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Simone Blaess
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany
| | - Inga B. Leske
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Desiree I. Frecot
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Marius Gramlich
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Philipp D. Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Dominik Seyfried
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Tübingen, Germany
| | - Sandra Maier
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Amélie Rezza
- Preclinical Models & Services, genOway, Lyon, France
| | | | - Kader Thiam
- Preclinical Models & Services, genOway, Lyon, France
| | - Stefania Pezzana
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany
| | - Anne Zeck
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Cécile Gouttefangeas
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Tübingen, Germany
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Armin M. Scholz
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig Maximilians University Munich, Oberschleissheim, Germany
| | - Stefan Nueske
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig Maximilians University Munich, Oberschleissheim, Germany
| | - Andreas Maurer
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Manfred Kneilling
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
- Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Bernd J. Pichler
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
| | - Dominik Sonanini
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany
- Department of Medical Oncology and Pneumology, University of Tübingen, Tübingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, Tübingen, Germany
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Lambert T, Gramlich M, Stutzke L, Smith L, Deng D, Kaiser PD, Rothbauer U, Benesch JLP, Wagner C, Koenig M, Pompach P, Novak P, Zeck A, Rand KD. Development of a PNGase Rc Column for Online Deglycosylation of Complex Glycoproteins during HDX-MS. J Am Soc Mass Spectrom 2023; 34:2556-2566. [PMID: 37756257 PMCID: PMC10623573 DOI: 10.1021/jasms.3c00268] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
Protein glycosylation is one of the most common PTMs and many cell surface receptors, extracellular proteins, and biopharmaceuticals are glycosylated. However, HDX-MS analysis of such important glycoproteins has so far been limited by difficulties in determining the HDX of the protein segments that contain glycans. We have developed a column containing immobilized PNGase Rc (from Rudaea cellulosilytica) that can readily be implemented into a conventional HDX-MS setup to allow improved analysis of glycoproteins. We show that HDX-MS with the PNGase Rc column enables efficient online removal of N-linked glycans and the determination of the HDX of glycosylated regions in several complex glycoproteins. Additionally, we use the PNGase Rc column to perform a comprehensive HDX-MS mapping of the binding epitope of a mAb to c-Met, a complex glycoprotein drug target. Importantly, the column retains high activity in the presence of common quench-buffer additives like TCEP and urea and performed consistent across 114 days of extensive use. Overall, our work shows that HDX-MS with the integrated PNGase Rc column can enable fast and efficient online deglycosylation at harsh quench conditions to provide comprehensive analysis of complex glycoproteins.
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Affiliation(s)
- Thomas Lambert
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Marius Gramlich
- NMI
Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Luisa Stutzke
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Luke Smith
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, England
| | - Dingyu Deng
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Philipp D. Kaiser
- NMI
Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI
Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
- Pharmaceutical
Biotechnology, Eberhard Karls University, 72074 Tübingen, Germany
| | - Justin L. P. Benesch
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, England
| | - Cornelia Wagner
- Roche
Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Maximiliane Koenig
- Roche
Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Petr Pompach
- BioCev,
Institute of Biotechnology of the CAS, 252 50 Prumyslova, Czech Republic
| | - Petr Novak
- BioCeV,
Institute of Microbiology of the CAS, 142 20 Prumyslova, Czech Republic
| | - Anne Zeck
- NMI
Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Kasper D. Rand
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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3
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Abstract
A milestone in the field of recombinant binding molecules was achieved 30 years ago with the discovery of single-domain antibodies from which antigen-binding variable domains, better known as nanobodies (Nbs), can be derived. Being only one tenth the size of conventional antibodies, Nbs feature high affinity and specificity, while being highly stable and soluble. In addition, they display accessibility to cryptic sites, low off-target accumulation and deep tissue penetration. Efficient selection methods, such as (semi-)synthetic/naïve or immunized cDNA libraries and display technologies, have facilitated the isolation of Nbs against diverse targets, and their single-gene format enables easy functionalization and high-yield production. This Review highlights recent advances in Nb applications in various areas of biological research, including structural biology, proteomics and high-resolution and in vivo imaging. In addition, we provide insights into intracellular applications of Nbs, such as live-cell imaging, biosensors and targeted protein degradation.
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Affiliation(s)
- Desiree I Frecot
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Reutlingen, Germany
| | - Theresa Froehlich
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
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4
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Wagner TR, Burgstaller S, Frecot DI, Lukowski R, Rothbauer U. 30 Jahre Nanobodies: Neues von kleinen Helfern mit großem Potenzial. Biospektrum (Heidelb) 2023; 29:145-149. [PMID: 37073321 PMCID: PMC10101533 DOI: 10.1007/s12268-023-1900-4] [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] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
2023 marks the 30th anniversary of the discovery of single-domain antibody fragments in camelids, better known as nanobodies. This was the starting point for their tremendous success story in biomedicine. Here we highlight recent advances in the development of nanobodies for the detection of neutralizing SARS-CoV-2 antibodies, as biosensors for monitoring extracellular metabolites and as tracer molecules for non-invasive imaging of immune cells.
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Affiliation(s)
- Teresa R. Wagner
- Pharmazeutische Biotechnologie, Universität Tübingen, Tübingen, Deutschland
- NMI Naturwissenschaftliches und Medizinisches Institut an der Universität Tübingen Pharmazeutische Biotechnologie, Markwiesenstraße 55, D-72770 Reutlingen, Deutschland
| | - Sandra Burgstaller
- Pharmazeutische Biotechnologie, Universität Tübingen, Tübingen, Deutschland
- Pharmakologie, Toxikologie und Klinische Pharmazie, Universität Tübingen, Tübingen, Deutschland
| | - Desiree I. Frecot
- Pharmazeutische Biotechnologie, Universität Tübingen, Tübingen, Deutschland
- NMI Naturwissenschaftliches und Medizinisches Institut an der Universität Tübingen Pharmazeutische Biotechnologie, Markwiesenstraße 55, D-72770 Reutlingen, Deutschland
| | - Robert Lukowski
- Pharmakologie, Toxikologie und Klinische Pharmazie, Universität Tübingen, Tübingen, Deutschland
| | - Ulrich Rothbauer
- Pharmazeutische Biotechnologie, Universität Tübingen, Tübingen, Deutschland
- NMI Naturwissenschaftliches und Medizinisches Institut an der Universität Tübingen Pharmazeutische Biotechnologie, Markwiesenstraße 55, D-72770 Reutlingen, Deutschland
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5
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Becker M, Cossmann A, Lürken K, Junker D, Gruber J, Juengling J, Ramos GM, Beigel A, Wrenger E, Lonnemann G, Stankov MV, Dopfer-Jablonka A, Kaiser PD, Traenkle B, Rothbauer U, Krause G, Schneiderhan-Marra N, Strengert M, Dulovic A, Behrens GMN. Longitudinal cellular and humoral immune responses after triple BNT162b2 and fourth full-dose mRNA-1273 vaccination in haemodialysis patients. Front Immunol 2022; 13:1004045. [PMID: 36275672 PMCID: PMC9582343 DOI: 10.3389/fimmu.2022.1004045] [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: 07/26/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
Abstract
Haemodialysis patients respond poorly to vaccination and continue to be at-risk for severe COVID-19. Therefore, dialysis patients were among the first for which a fourth COVID-19 vaccination was recommended. However, targeted information on how to best maintain immune protection after SARS-CoV-2 vaccinations in at-risk groups for severe COVID-19 remains limited. We provide, to the best of our knowledge, for the first time longitudinal vaccination response data in dialysis patients and controls after a triple BNT162b2 vaccination and in the latter after a subsequent fourth full-dose of mRNA-1273. We analysed systemic and mucosal humoral IgG responses against the receptor-binding domain (RBD) and ACE2-binding inhibition towards variants of concern including Omicron and Delta with multiplex-based immunoassays. In addition, we assessed Spike S1-specific T-cell responses by interferon γ release assay. After triple BNT162b2 vaccination, anti-RBD B.1 IgG and ACE2 binding inhibition reached peak levels in dialysis patients, but remained inferior compared to controls. Whilst we detected B.1-specific ACE2 binding inhibition in 84% of dialysis patients after three BNT162b2 doses, binding inhibition towards the Omicron variant was only detectable in 38% of samples and declining to 16% before the fourth vaccination. By using mRNA-1273 as fourth dose, humoral immunity against all SARS-CoV-2 variants tested was strongly augmented with 80% of dialysis patients having Omicron-specific ACE2 binding inhibition. Modest declines in T-cell responses in dialysis patients and controls after the second vaccination were restored by the third BNT162b2 dose and significantly increased by the fourth vaccination. Our data support current advice for a four-dose COVID-19 immunisation scheme for at-risk individuals such as haemodialysis patients. We conclude that administration of a fourth full-dose of mRNA-1273 as part of a mixed mRNA vaccination scheme to boost immunity and to prevent severe COVID-19 could also be beneficial in other immune impaired individuals. Additionally, strategic application of such mixed vaccine regimens may be an immediate response against SARS-CoV-2 variants with increased immune evasion potential.
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Affiliation(s)
- Matthias Becker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Anne Cossmann
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Karsten Lürken
- Department of Internal Medicine and Nephrology, Dialysis Centre Eickenhof, Langenhagen, Germany
| | - Daniel Junker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Jens Gruber
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Jennifer Juengling
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Gema Morillas Ramos
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Andrea Beigel
- Department of Internal Medicine and Nephrology, Dialysis Centre Eickenhof, Langenhagen, Germany
| | - Eike Wrenger
- Department of Internal Medicine and Nephrology, Dialysis Centre Eickenhof, Langenhagen, Germany
| | - Gerhard Lonnemann
- Department of Internal Medicine and Nephrology, Dialysis Centre Eickenhof, Langenhagen, Germany
| | - Metodi V. Stankov
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Alexandra Dopfer-Jablonka
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Philipp D. Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
- Pharmaceutical Biotechnology, University of Tübingen, Tübingen, Germany
| | - Gérard Krause
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
- Department Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | | | - Monika Strengert
- Department Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- *Correspondence: Monika Strengert, ; Alex Dulovic, ; Georg M. N. Behrens,
| | - Alex Dulovic
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
- *Correspondence: Monika Strengert, ; Alex Dulovic, ; Georg M. N. Behrens,
| | - Georg M. N. Behrens
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
- German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
- CiiM - Centre for Individualized Infection Medicine, Hannover, Germany
- *Correspondence: Monika Strengert, ; Alex Dulovic, ; Georg M. N. Behrens,
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6
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Burgstaller S, Wagner TR, Bischof H, Bueckle S, Padamsey A, Frecot D, Kaiser PD, Skrabak D, Malli R, Lukowski R, Rothbauer U. Monitoring extracellular ion and metabolite dynamics with recombinant nanobody-fused biosensors. iScience 2022; 25:104907. [PMID: 36046190 PMCID: PMC9421384 DOI: 10.1016/j.isci.2022.104907] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/29/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022] Open
Abstract
Ion and analyte changes in the tumor microenvironment (TME) alter the metabolic activity of cancer cells, promote tumor cell growth, and impair anti-tumor immunity. Consequently, accurate determination and visualization of extracellular changes of analytes in real time is desired. In this study, we genetically combined FRET-based biosensors with nanobodies (Nbs) to specifically visualize and monitor extracellular changes in K+, pH, and glucose on cell surfaces. We demonstrated that these Nb-fused biosensors quantitatively visualized K+ alterations on cancer and non-cancer cell lines and primary neurons. By implementing a HER2-specific Nb, we generated functional K+ and pH sensors, which specifically stained HER2-positive breast cancer cells. Based on the successful development of several Nb-fused biosensor combinations, we anticipate that this approach can be readily extended to other biosensors and will open new opportunities for the study of extracellular analytes in advanced experimental settings. Generation of recombinant nanobody-fused FRET biosensors Nb-fused biosensors specifically bind targets on the outer surface of various cells Cellular bound Nb-biosensors visualize extracellular analyte changes in real time
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Affiliation(s)
- Sandra Burgstaller
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany.,Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Teresa R Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany.,NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Helmut Bischof
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Sarah Bueckle
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Aman Padamsey
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Desiree Frecot
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany.,NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
| | - David Skrabak
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Roland Malli
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria.,BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Robert Lukowski
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Auf der Morgenstelle 8, 72076 Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany.,NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770 Reutlingen, Germany
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7
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Junker D, Becker M, Wagner TR, Kaiser PD, Maier S, Grimm TM, Griesbaum J, Marsall P, Gruber J, Traenkle B, Heinzel C, Pinilla YT, Held J, Fendel R, Kreidenweiss A, Nelde A, Maringer Y, Schroeder S, Walz JS, Althaus K, Uzun G, Mikus M, Bakchoul T, Schenke-Layland K, Bunk S, Haeberle H, Göpel S, Bitzer M, Renk H, Remppis J, Engel C, Franz AR, Harries M, Kessel B, Lange B, Strengert M, Krause G, Zeck A, Rothbauer U, Dulovic A, Schneiderhan-Marra N. Antibody Binding and Angiotensin-Converting Enzyme 2 Binding Inhibition Is Significantly Reduced for Both the BA.1 and BA.2 Omicron Variants. Clin Infect Dis 2022; 76:e240-e249. [PMID: 35717657 PMCID: PMC9384292 DOI: 10.1093/cid/ciac498] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 06/07/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The rapid emergence of the Omicron variant and its large number of mutations led to its classification as a variant of concern (VOC) by the World Health Organization. Subsequently, Omicron evolved into distinct sublineages (eg, BA.1 and BA.2), which currently represent the majority of global infections. Initial studies of the neutralizing response toward BA.1 in convalescent and vaccinated individuals showed a substantial reduction. METHODS We assessed antibody (immunoglobulin G [IgG]) binding, ACE2 (angiotensin-converting enzyme 2) binding inhibition, and IgG binding dynamics for the Omicron BA.1 and BA.2 variants compared to a panel of VOCs/variants of interest, in a large cohort (N = 352) of convalescent, vaccinated, and infected and subsequently vaccinated individuals. RESULTS While Omicron was capable of efficiently binding to ACE2, antibodies elicited by infection or immunization showed reduced binding capacities and ACE2 binding inhibition compared to wild type. Whereas BA.1 exhibited less IgG binding compared to BA.2, BA.2 showed reduced inhibition of ACE2 binding. Among vaccinated samples, antibody binding to Omicron only improved after administration of a third dose. CONCLUSIONS Omicron BA.1 and BA.2 can still efficiently bind to ACE2, while vaccine/infection-derived antibodies can bind to Omicron. The extent of the mutations within both variants prevents a strong inhibitory binding response. As a result, both Omicron variants are able to evade control by preexisting antibodies.
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Affiliation(s)
| | | | | | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Sandra Maier
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Tanja M Grimm
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Johanna Griesbaum
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Patrick Marsall
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Jens Gruber
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Constanze Heinzel
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Yudi T Pinilla
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Jana Held
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Rolf Fendel
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany,German Center for Infection Research, partner site Tuebingen, Tuebingen, Germany,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Andrea Kreidenweiss
- Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany,German Center for Infection Research, partner site Tuebingen, Tuebingen, Germany,Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Annika Nelde
- Department of Peptide-Based Immunotherapy, University of Tuebingen and University Hospital Tuebingen, Tuebingen, Germany,Department of Internal Medicine, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium, University Hospital Tuebingen, Tuebingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tuebingen, Tuebingen, Germany
| | - Yacine Maringer
- Department of Peptide-Based Immunotherapy, University of Tuebingen and University Hospital Tuebingen, Tuebingen, Germany,Department of Internal Medicine, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium, University Hospital Tuebingen, Tuebingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tuebingen, Tuebingen, Germany
| | - Sarah Schroeder
- Department of Peptide-Based Immunotherapy, University of Tuebingen and University Hospital Tuebingen, Tuebingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Department of Otorhinolaryngology, Head and Neck Surgery, University of Tuebingen, Tuebingen, Germany
| | - Juliane S Walz
- Department of Peptide-Based Immunotherapy, University of Tuebingen and University Hospital Tuebingen, Tuebingen, Germany,Department of Internal Medicine, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium, University Hospital Tuebingen, Tuebingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies,” University of Tuebingen, Tuebingen, Germany
| | - Karina Althaus
- Center for Clinical Transfusion Medicine, Tuebingen, Germany,Institute of Clinical and Experimental Transfusion Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Gunalp Uzun
- Center for Clinical Transfusion Medicine, Tuebingen, Germany
| | - Marco Mikus
- Center for Clinical Transfusion Medicine, Tuebingen, Germany
| | - Tamam Bakchoul
- Center for Clinical Transfusion Medicine, Tuebingen, Germany,Institute of Clinical and Experimental Transfusion Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Katja Schenke-Layland
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany,Department of Immunology, Institute for Cell Biology, University of Tuebingen, Tuebingen, Germany,Department for Medical Technologies and Regenerative Medicine, Institute of Biomedical Engineering, University of Tuebingen, Tuebingen, Germany,Division of Cardiology, Department of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Stefanie Bunk
- Infectious Diseases, Department of Internal Medicine I, University Hospital Tuebingen, Tuebingen, Germany
| | - Helene Haeberle
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Siri Göpel
- German Center for Infection Research, partner site Tuebingen, Tuebingen, Germany,Infectious Diseases, Department of Internal Medicine I, University Hospital Tuebingen, Tuebingen, Germany
| | - Michael Bitzer
- Infectious Diseases, Department of Internal Medicine I, University Hospital Tuebingen, Tuebingen, Germany,Center for Personalized Medicine, University of Tuebingen, Tuebingen, Germany
| | - Hanna Renk
- University Children’s Hospital, Tuebingen, Germany
| | | | - Corinna Engel
- University Children’s Hospital, Tuebingen, Germany,Center for Pediatric Clinical Studies, University Hospital Tuebingen, Tuebingen, Germany
| | - Axel R Franz
- University Children’s Hospital, Tuebingen, Germany,Center for Pediatric Clinical Studies, University Hospital Tuebingen, Tuebingen, Germany
| | - Manuela Harries
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Barbora Kessel
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Berit Lange
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Monika Strengert
- Helmholtz Centre for Infection Research, Braunschweig, Germany,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture of Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Gerard Krause
- Helmholtz Centre for Infection Research, Braunschweig, Germany,TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture of Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Anne Zeck
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany,Pharmaceutical Biotechnology, University of Tuebingen, Tuebingen, Germany
| | - Alex Dulovic
- Correspondence: A. Dulovic, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, Reutlingen, 72770 Germany ()
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8
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Gramlich M, Maier S, Kaiser PD, Traenkle B, Wagner TR, Voglmeir J, Stoll D, Rothbauer U, Zeck A. A Novel PNGase Rc for Improved Protein N-Deglycosylation in Bioanalytics and Hydrogen-Deuterium Exchange Coupled With Mass Spectrometry Epitope Mapping under Challenging Conditions. Anal Chem 2022; 94:9863-9871. [PMID: 35749695 DOI: 10.1021/acs.analchem.2c01748] [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] [Indexed: 11/29/2022]
Abstract
N-linked glycosylation is a ubiquitous posttranslational modification of proteins. While it plays an important role in the biological function of proteins, it often poses a major challenge for their analytical characterization. Currently available peptide N-glycanases (PNGases) are often inefficient at deglycosylating proteins due to sterically inaccessible N-glycosylation sites. This usually leads to poor sequence coverage in bottom-up analysis using liquid chromatography with tandem mass spectrometry and makes it impossible to obtain an intact mass signal in top-down MS analysis. In addition, most PNGases operate optimally only in the neutral to slightly acidic pH range and are severely compromised in the presence of reducing and denaturing substances, which limits their use for advanced bioanalysis based on hydrogen-deuterium exchange in combination with mass spectrometry (HDX-MS). Here, we present a novel peptide N-glycanase from Rudaea cellulosilytica (PNGase Rc) for which we demonstrate broad substrate specificity for N-glycan hydrolysis from multiply occupied and natively folded proteins. Our results show that PNGase Rc is functional even under challenging, HDX quenching conditions (pH 2.5, 0 °C) and in the presence of 0.4 M tris(2-carboxyethyl)phosphine, 4 M urea, and 1 M guanidinium chloride. Most importantly, we successfully applied the PNGase Rc in an HDX-MS workflow to determine the epitope of a nanobody targeting the extracellular domain of human signal-regulating protein alpha (SIRPα).
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Affiliation(s)
- Marius Gramlich
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
| | - Sandra Maier
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
| | - Teresa R Wagner
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen 72076, Germany
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Dieter Stoll
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany.,Department of Life Sciences, University of Applied Sciences Albstadt-Sigmaringen, Sigmaringen 72488, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen 72076, Germany
| | - Anne Zeck
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
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9
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Junker D, Dulovic A, Becker M, Wagner TR, Kaiser PD, Traenkle B, Kienzle K, Bunk S, Struemper C, Haeberle H, Schmauder K, Ruetalo N, Malek N, Althaus K, Koeppen M, Rothbauer U, Walz JS, Schindler M, Bitzer M, Göpel S, Schneiderhan-Marra N. COVID-19 patient serum less potently inhibits ACE2-RBD binding for various SARS-CoV-2 RBD mutants. Sci Rep 2022; 12:7168. [PMID: 35505068 PMCID: PMC9062870 DOI: 10.1038/s41598-022-10987-2] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/22/2022] [Indexed: 12/12/2022] Open
Abstract
As global vaccination campaigns against SARS-CoV-2 proceed, there is particular interest in the longevity of immune protection, especially with regard to increasingly infectious virus variants. Neutralizing antibodies (Nabs) targeting the receptor binding domain (RBD) of SARS-CoV-2 are promising correlates of protective immunity and have been successfully used for prevention and therapy. As SARS-CoV-2 variants of concern (VOCs) are known to affect binding to the ACE2 receptor and by extension neutralizing activity, we developed a bead-based multiplex ACE2-RBD inhibition assay (RBDCoV-ACE2) as a highly scalable, time-, cost-, and material-saving alternative to infectious live-virus neutralization tests. By mimicking the interaction between ACE2 and the RBD, this serological multiplex assay allows the simultaneous analysis of ACE2 binding inhibition to the RBDs of all SARS-CoV-2 VOCs and variants of interest (VOIs) in a single well. Following validation against a classical virus neutralization test and comparison of performance against a commercially available assay, we analyzed 266 serum samples from 168 COVID-19 patients of varying severity. ACE2 binding inhibition was reduced for ten out of eleven variants examined compared to wild-type, especially for those displaying the E484K mutation such as VOCs beta and gamma. ACE2 binding inhibition, while highly individualistic, positively correlated with IgG levels. ACE2 binding inhibition also correlated with disease severity up to WHO grade 7, after which it reduced.
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Affiliation(s)
- Daniel Junker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Alex Dulovic
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Matthias Becker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Teresa R Wagner
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Katharina Kienzle
- Department Internal Medicine I, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076, Tübingen, Germany
| | - Stefanie Bunk
- Department Internal Medicine I, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076, Tübingen, Germany
| | - Carlotta Struemper
- Department Internal Medicine I, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076, Tübingen, Germany
| | - Helene Haeberle
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Kristina Schmauder
- Institute for Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany.,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Natalia Ruetalo
- Institute for Medical Virology and Epidemiology, University Hospital Tübingen, Tübingen, Germany
| | - Nisar Malek
- Department Internal Medicine I, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076, Tübingen, Germany.,Center for Personalized Medicine, Eberhard Karls University, Tübingen, Germany
| | - Karina Althaus
- Institute for Clinical and Experimental Transfusion Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Michael Koeppen
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany
| | - Juliane S Walz
- Department of Internal Medicine, Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital Tübingen, Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Dr. Margarete Fischer-Bosch-Institute for Clinical Pharmacology, Robert Bosch Center for Tumor Diseases (RBCT), Stuttgart, Germany
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology, University Hospital Tübingen, Tübingen, Germany
| | - Michael Bitzer
- Department Internal Medicine I, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076, Tübingen, Germany.,Center for Personalized Medicine, Eberhard Karls University, Tübingen, Germany
| | - Siri Göpel
- Department Internal Medicine I, University Hospital Tübingen, Otfried-Müller-Strasse 10, 72076, Tübingen, Germany. .,German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
| | - Nicole Schneiderhan-Marra
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany.
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10
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Feuerer N, Carvajal Berrio DA, Billing F, Segan S, Weiss M, Rothbauer U, Marzi J, Schenke-Layland K. Raman Microspectroscopy Identifies Biochemical Activation Fingerprints in THP-1- and PBMC-Derived Macrophages. Biomedicines 2022; 10:biomedicines10050989. [PMID: 35625726 PMCID: PMC9139061 DOI: 10.3390/biomedicines10050989] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/18/2022] [Accepted: 04/23/2022] [Indexed: 11/24/2022] Open
Abstract
(1) The monocytic leukemia cell line THP-1 and primary monocyte-derived macrophages (MDMs) are popular in vitro model systems to study human innate immunity, wound healing, and tissue regeneration. However, both cell types differ significantly in their origin and response to activation stimuli. (2) Resting THP-1 and MDMs were stimulated with lipopolysaccharide (LPS) and interferon γ (IFNγ) and analyzed by Raman microspectroscopy (RM) before and 48 h after activation. Raman data were subsequently analyzed using principal component analysis. (3) We were able to resolve and analyze the spatial distribution and molecular composition of proteins, nucleic acids, and lipids in resting and activated THP-1 and MDMs. Our findings reveal that proinflammatory activation-induced significant spectral alterations at protein and phospholipid levels in THP-1. In MDMs, we identified that nucleic acid and non-membrane-associated intracellular lipid composition were also affected. (4) Our results show that it is crucial to carefully choose the right cell type for an in vitro model as the nature of the cells itself may impact immune cell polarization or activation results. Moreover, we demonstrated that RM is a sensitive tool for investigating cell-specific responses to activation stimuli and monitoring molecular changes in subcellular structures.
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Affiliation(s)
- Nora Feuerer
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; (N.F.); (D.A.C.B.); (K.S.-L.)
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany; (F.B.); (S.S.); (M.W.); (U.R.)
| | - Daniel A. Carvajal Berrio
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; (N.F.); (D.A.C.B.); (K.S.-L.)
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Florian Billing
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany; (F.B.); (S.S.); (M.W.); (U.R.)
| | - Sören Segan
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany; (F.B.); (S.S.); (M.W.); (U.R.)
| | - Martin Weiss
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany; (F.B.); (S.S.); (M.W.); (U.R.)
- Department of Women’s Health, Research Institute of Women’s Health, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany; (F.B.); (S.S.); (M.W.); (U.R.)
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
| | - Julia Marzi
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; (N.F.); (D.A.C.B.); (K.S.-L.)
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany; (F.B.); (S.S.); (M.W.); (U.R.)
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- Correspondence: ; Tel.: +49-707-1298-5204
| | - Katja Schenke-Layland
- Institute of Biomedical Engineering, Department for Medical Technologies and Regenerative Medicine, Eberhard Karls University Tübingen, 72076 Tübingen, Germany; (N.F.); (D.A.C.B.); (K.S.-L.)
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany; (F.B.); (S.S.); (M.W.); (U.R.)
- Cluster of Excellence iFIT (EXC 2180) “Image-Guided and Functionally Instructed Tumor Therapies”, Eberhard Karls University Tübingen, 72076 Tübingen, Germany
- Department of Medicine/Cardiology, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
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11
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Fagbadebo FO, Kaiser PD, Zittlau K, Bartlick N, Wagner TR, Froehlich T, Jarjour G, Nueske S, Scholz A, Traenkle B, Macek B, Rothbauer U. A Nanobody-Based Toolset to Monitor and Modify the Mitochondrial GTPase Miro1. Front Mol Biosci 2022; 9:835302. [PMID: 35359597 PMCID: PMC8960383 DOI: 10.3389/fmolb.2022.835302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/14/2021] [Accepted: 02/08/2022] [Indexed: 12/24/2022] Open
Abstract
The mitochondrial outer membrane (MOM)-anchored GTPase Miro1, is a central player in mitochondrial transport and homeostasis. The dysregulation of Miro1 in amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD) suggests that Miro1 may be a potential biomarker or drug target in neuronal disorders. However, the molecular functionality of Miro1 under (patho-) physiological conditions is poorly known. For a more comprehensive understanding of the molecular functions of Miro1, we have developed Miro1-specific nanobodies (Nbs) as novel research tools. We identified seven Nbs that bind either the N- or C-terminal GTPase domain of Miro1 and demonstrate their application as research tools for proteomic and imaging approaches. To visualize the dynamics of Miro1 in real time, we selected intracellularly functional Nbs, which we reformatted into chromobodies (Cbs) for time-lapse imaging of Miro1. By genetic fusion to an Fbox domain, these Nbs were further converted into Miro1-specific degrons and applied for targeted degradation of Miro1 in live cells. In summary, this study presents a collection of novel Nbs that serve as a toolkit for advanced biochemical and intracellular studies and modulations of Miro1, thereby contributing to the understanding of the functional role of Miro1 in disease-derived model systems.
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Affiliation(s)
| | - Philipp D. Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Katharina Zittlau
- Quantitative Proteomics, Department of Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Natascha Bartlick
- Interfaculty Institute of Biochemistry, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Teresa R. Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Tübingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Theresa Froehlich
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Grace Jarjour
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Stefan Nueske
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig Maximilians University Munich, Oberschleissheim, Germany
| | - Armin Scholz
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig Maximilians University Munich, Oberschleissheim, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Boris Macek
- Quantitative Proteomics, Department of Biology, Interfaculty Institute of Cell Biology, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Tübingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
- *Correspondence: Ulrich Rothbauer,
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12
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Sotolongo Bellón J, Birkholz O, Richter CP, Eull F, Kenneweg H, Wilmes S, Rothbauer U, You C, Walter MR, Kurre R, Piehler J. Four-color single-molecule imaging with engineered tags resolves the molecular architecture of signaling complexes in the plasma membrane. Cell Rep Methods 2022; 2:100165. [PMID: 35474965 PMCID: PMC9017138 DOI: 10.1016/j.crmeth.2022.100165] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/19/2021] [Accepted: 01/13/2022] [Indexed: 12/22/2022]
Abstract
Localization and tracking of individual receptors by single-molecule imaging opens unique possibilities to unravel the assembly and dynamics of signaling complexes in the plasma membrane. We present a comprehensive workflow for imaging and analyzing receptor diffusion and interaction in live cells at single molecule level with up to four colors. Two engineered, monomeric GFP variants, which are orthogonally recognized by anti-GFP nanobodies, are employed for efficient and selective labeling of target proteins in the plasma membrane with photostable fluorescence dyes. This labeling technique enables us to quantitatively resolve the stoichiometry and dynamics of the interferon-γ (IFNγ) receptor signaling complex in the plasma membrane of living cells by multicolor single-molecule imaging. Based on versatile spatial and spatiotemporal correlation analyses, we identify ligand-induced receptor homo- and heterodimerization. Multicolor single-molecule co-tracking and quantitative single-molecule Förster resonance energy transfer moreover reveals transient assembly of IFNγ receptor heterotetramers and confirms its structural architecture.
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Affiliation(s)
- Junel Sotolongo Bellón
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Oliver Birkholz
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Christian P. Richter
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Florian Eull
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Hella Kenneweg
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Stephan Wilmes
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
- Division of Cell Signalling and Immunology, University of Dundee, School of Life Sciences, Dundee, UK
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard-Karls-University, Tübingen, Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Changjiang You
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Mark R. Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Rainer Kurre
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
| | - Jacob Piehler
- Department of Biology and Center for Cellular Nanoanalytics (CellNanOs), Osnabrück University, Osnabrück, Germany
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13
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Dulovic A, Strengert M, Ramos GM, Becker M, Griesbaum J, Junker D, Lürken K, Beigel A, Wrenger E, Lonnemann G, Cossmann A, Stankov MV, Dopfer-Jablonka A, Kaiser PD, Traenkle B, Rothbauer U, Krause G, Schneiderhan-Marra N, Behrens GM. Diminishing Immune Responses against Variants of Concern in Dialysis Patients 4 Months after SARS-CoV-2 mRNA Vaccination. Emerg Infect Dis 2022; 28:743-750. [PMID: 35203113 PMCID: PMC8962909 DOI: 10.3201/eid2804.211907] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Patients undergoing chronic hemodialysis were among the first to receive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccinations because of their increased risk for severe coronavirus disease and high case-fatality rates. By using a previously reported cohort from Germany of at-risk hemodialysis patients and healthy donors, where antibody responses were examined 3 weeks after the second vaccination, we assessed systemic cellular and humoral immune responses in serum and saliva 4 months after vaccination with the Pfizer-BioNTech BNT162b2 vaccine using an interferon-γ release assay and multiplex-based IgG measurements. We further compared neutralization capacity of vaccination-induced IgG against 4 SARS-CoV-2 variants of concern (Alpha, Beta, Gamma, and Delta) by angiotensin-converting enzyme 2 receptor-binding domain competition assay. Sixteen weeks after second vaccination, compared with 3 weeks after, cellular and humoral responses against the original SARS-CoV-2 isolate and variants of concern were substantially reduced. Some dialysis patients even had no detectable B- or T-cell responses.
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14
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Walter RJ, Sonnentag SJ, Munoz-Sagredo L, Merkel M, Richert L, Bunert F, Heneka YM, Loustau T, Hodder M, Ridgway RA, Sansom OJ, Mely Y, Rothbauer U, Schmitt M, Orian-Rousseau V. Wnt signaling is boosted during intestinal regeneration by a CD44-positive feedback loop. Cell Death Dis 2022; 13:168. [PMID: 35190527 PMCID: PMC8861016 DOI: 10.1038/s41419-022-04607-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 07/06/2021] [Revised: 01/17/2022] [Accepted: 02/04/2022] [Indexed: 12/24/2022]
Abstract
Enhancement of Wnt signaling is fundamental for stem cell function during intestinal regeneration. Molecular modules control Wnt activity by regulating signal transduction. CD44 is such a positive regulator and a Wnt target gene. While highly expressed in intestinal crypts and used as a stem cell marker, its role during intestinal homeostasis and regeneration remains unknown. Here we propose a CD44 positive-feedback loop that boosts Wnt signal transduction, thus impacting intestinal regeneration. Excision of Cd44 in Cd44fl/fl;VillinCreERT2 mice reduced Wnt target gene expression in intestinal crypts and affected stem cell functionality in organoids. Although the integrity of the intestinal epithelium was conserved in mice lacking CD44, they were hypersensitive to dextran sulfate sodium, and showed more severe inflammation and delayed regeneration. We localized the molecular function of CD44 at the Wnt signalosome, and identified novel DVL/CD44 and AXIN/CD44 complexes. CD44 thus promotes optimal Wnt signaling during intestinal regeneration.
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Affiliation(s)
- Romina J Walter
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Steffen J Sonnentag
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Leonel Munoz-Sagredo
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.,Faculty of Medicine, Universidad de Valparaiso, Angamos 655, 2540064, Vina del Mar, Chile
| | - Melanie Merkel
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Ludovic Richert
- UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Felix Bunert
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Yvonne M Heneka
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Thomas Loustau
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Michael Hodder
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.,Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Rachel A Ridgway
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.,Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow, G61 1BD, UK.,Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow, G61 1QH, UK
| | - Yves Mely
- UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Faculté de Pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Mark Schmitt
- Institute of Pharmacology, University of Marburg, Karl-von-Frisch-Strasse 2, 35043, Marburg, Germany
| | - Véronique Orian-Rousseau
- Institute of Biological and Chemical Systems - Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany.
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15
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Dulovic A, Kessel B, Harries M, Becker M, Ortmann J, Griesbaum J, Jüngling J, Junker D, Hernandez P, Gornyk D, Glöckner S, Melhorn V, Castell S, Heise JK, Kemmling Y, Tonn T, Frank K, Illig T, Klopp N, Warikoo N, Rath A, Suckel C, Marzian AU, Grupe N, Kaiser PD, Traenkle B, Rothbauer U, Kerrinnes T, Krause G, Lange B, Schneiderhan-Marra N, Strengert M. Comparative Magnitude and Persistence of Humoral SARS-CoV-2 Vaccination Responses in the Adult Population in Germany. Front Immunol 2022; 13:828053. [PMID: 35251012 PMCID: PMC8888837 DOI: 10.3389/fimmu.2022.828053] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 12/02/2021] [Accepted: 01/17/2022] [Indexed: 12/01/2022] Open
Abstract
Recent increases in SARS-CoV-2 infections have led to questions about duration and quality of vaccine-induced immune protection. While numerous studies have been published on immune responses triggered by vaccination, these often focus on studying the impact of one or two immunisation schemes within subpopulations such as immunocompromised individuals or healthcare workers. To provide information on the duration and quality of vaccine-induced immune responses against SARS-CoV-2, we analyzed antibody titres against various SARS-CoV-2 antigens and ACE2 binding inhibition against SARS-CoV-2 wild-type and variants of concern in samples from a large German population-based seroprevalence study (MuSPAD) who had received all currently available immunisation schemes. We found that homologous mRNA-based or heterologous prime-boost vaccination produced significantly higher antibody responses than vector-based homologous vaccination. Ad26.CoV2S.2 performance was particularly concerning with reduced titres and 91.7% of samples classified as non-responsive for ACE2 binding inhibition, suggesting that recipients require a booster mRNA vaccination. While mRNA vaccination induced a higher ratio of RBD- and S1-targeting antibodies, vector-based vaccines resulted in an increased proportion of S2-targeting antibodies. Given the role of RBD- and S1-specific antibodies in neutralizing SARS-CoV-2, their relative over-representation after mRNA vaccination may explain why these vaccines have increased efficacy compared to vector-based formulations. Previously infected individuals had a robust immune response once vaccinated, regardless of which vaccine they received, which could aid future dose allocation should shortages arise for certain manufacturers. Overall, both titres and ACE2 binding inhibition peaked approximately 28 days post-second vaccination and then decreased.
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Affiliation(s)
- Alex Dulovic
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Barbora Kessel
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Manuela Harries
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Matthias Becker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Julia Ortmann
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Johanna Griesbaum
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Jennifer Jüngling
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Daniel Junker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Pilar Hernandez
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Daniela Gornyk
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stephan Glöckner
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Vanessa Melhorn
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefanie Castell
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Jana-Kristin Heise
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Yvonne Kemmling
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Torsten Tonn
- German Red Cross Blood Donation Service North East, Dresden, Germany
| | - Kerstin Frank
- German Red Cross Blood Donation Service North East, Dresden, Germany
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Norman Klopp
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Neha Warikoo
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Angelika Rath
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Christina Suckel
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Anne Ulrike Marzian
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Nicole Grupe
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Philipp D. Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
- Pharmaceutical Biotechnology, Department of Pharmacy and Biochemistry, University of Tübingen, Tübingen, Germany
| | - Tobias Kerrinnes
- Department of RNA-Biology of Bacterial Infections, Helmholtz Institute for RNA-Based Infection Research, Würzburg, Germany
| | - Gérard Krause
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Berit Lange
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | | | - Monika Strengert
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
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16
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Pantsar T, Kaiser PD, Kudolo M, Forster M, Rothbauer U, Laufer SA. Decisive role of water and protein dynamics in residence time of p38α MAP kinase inhibitors. Nat Commun 2022; 13:569. [PMID: 35091547 PMCID: PMC8799644 DOI: 10.1038/s41467-022-28164-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [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: 03/02/2021] [Accepted: 01/06/2022] [Indexed: 12/31/2022] Open
Abstract
Target residence time plays a crucial role in the pharmacological activity of small molecule inhibitors. Little is known, however, about the underlying causes of inhibitor residence time at the molecular level, which complicates drug optimization processes. Here, we employ all-atom molecular dynamics simulations (~400 μs in total) to gain insight into the binding modes of two structurally similar p38α MAPK inhibitors (type I and type I½) with short and long residence times that otherwise show nearly identical inhibitory activities in the low nanomolar IC50 range. Our results highlight the importance of protein conformational stability and solvent exposure, buried surface area of the ligand and binding site resolvation energy for residence time. These findings are further confirmed by simulations with a structurally diverse short residence time inhibitor SB203580. In summary, our data provide guidance in compound design when aiming for inhibitors with improved target residence time. The molecular determinants of the residence time of a small molecule inhibitor at its target protein are not well understood. Here, Pantsar et al. show that the target protein’s conformational stability and solvent exposure are key factors governing the target residence time of kinase inhibitors.
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Affiliation(s)
- Tatu Pantsar
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1, 70210, Kuopio, Finland
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Mark Kudolo
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Michael Forster
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, 72076, Tuebingen, Germany
| | - Stefan A Laufer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, 72076, Tuebingen, Germany. .,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tuebingen, 72076, Tuebingen, Germany. .,Tuebingen Center for Academic Drug Discovery & Development (TüCAD2), 72076, Tuebingen, Germany.
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17
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Renk H, Dulovic A, Seidel A, Becker M, Fabricius D, Zernickel M, Junker D, Groß R, Müller J, Hilger A, Bode SFN, Fritsch L, Frieh P, Haddad A, Görne T, Remppis J, Ganzemueller T, Dietz A, Huzly D, Hengel H, Kaier K, Weber S, Jacobsen EM, Kaiser PD, Traenkle B, Rothbauer U, Stich M, Tönshoff B, Hoffmann GF, Müller B, Ludwig C, Jahrsdörfer B, Schrezenmeier H, Peter A, Hörber S, Iftner T, Münch J, Stamminger T, Groß HJ, Wolkewitz M, Engel C, Liu W, Rizzi M, Hahn BH, Henneke P, Franz AR, Debatin KM, Schneiderhan-Marra N, Janda A, Elling R. Robust and durable serological response following pediatric SARS-CoV-2 infection. Nat Commun 2022; 13:128. [PMID: 35013206 PMCID: PMC8748910 DOI: 10.1038/s41467-021-27595-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [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: 08/26/2021] [Accepted: 11/22/2021] [Indexed: 02/07/2023] Open
Abstract
The quality and persistence of children's humoral immune response following SARS-CoV-2 infection remains largely unknown but will be crucial to guide pediatric SARS-CoV-2 vaccination programs. Here, we examine 548 children and 717 adults within 328 households with at least one member with a previous laboratory-confirmed SARS-CoV-2 infection. We assess serological response at 3-4 months and 11-12 months after infection using a bead-based multiplex immunoassay for 23 human coronavirus antigens including SARS-CoV-2 and its Variants of Concern (VOC) and endemic human coronaviruses (HCoVs), and additionally by three commercial SARS-CoV-2 antibody assays. Neutralization against wild type SARS-CoV-2 and the Delta VOC are analysed in a pseudotyped virus assay. Children, compared to adults, are five times more likely to be asymptomatic, and have higher specific antibody levels which persist longer (96.2% versus 82.9% still seropositive 11-12 months post infection). Of note, symptomatic and asymptomatic infections induce similar humoral responses in all age groups. SARS-CoV-2 infection occurs independent of HCoV serostatus. Neutralization responses of children and adults are similar, although neutralization is reduced for both against the Delta VOC. Overall, the long-term humoral immune response to SARS-CoV-2 infection in children is of longer duration than in adults even after asymptomatic infection.
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Affiliation(s)
- Hanna Renk
- University Children's Hospital Tübingen, Tübingen, Germany
| | - Alex Dulovic
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Alina Seidel
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Matthias Becker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Dorit Fabricius
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm University, Ulm, Germany
| | - Maria Zernickel
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm University, Ulm, Germany
| | - Daniel Junker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Rüdiger Groß
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Janis Müller
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Alexander Hilger
- Center for Pediatrics and Adolescent Medicine, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian F N Bode
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm University, Ulm, Germany
| | - Linus Fritsch
- Center for Pediatrics and Adolescent Medicine, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Pauline Frieh
- Center for Pediatrics and Adolescent Medicine, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anneke Haddad
- Center for Pediatrics and Adolescent Medicine, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tessa Görne
- Center for Pediatrics and Adolescent Medicine, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | | | - Tina Ganzemueller
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Andrea Dietz
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Daniela Huzly
- Institute of Virology, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hartmut Hengel
- Institute of Virology, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klaus Kaier
- Institute of Medical Biometry and Statistics, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Susanne Weber
- Institute of Medical Biometry and Statistics, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Eva-Maria Jacobsen
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm University, Ulm, Germany
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Maximilian Stich
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
| | - Burkhard Tönshoff
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
| | - Georg F Hoffmann
- Department of Pediatrics I, University Children's Hospital Heidelberg, Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, Heidelberg University Hospital, Heidelberg, Germany
| | - Carolin Ludwig
- Institute of Transfusion Medicine, Ulm University, Ulm, Germany
- Institute for Clinical Transfusion Medicine and Immunogenetics, Ulm, Germany
- German Red Cross Blood Transfusion Service, Baden-Württemberg-Hessen, Germany
| | - Bernd Jahrsdörfer
- Institute of Transfusion Medicine, Ulm University, Ulm, Germany
- Institute for Clinical Transfusion Medicine and Immunogenetics, Ulm, Germany
- German Red Cross Blood Transfusion Service, Baden-Württemberg-Hessen, Germany
| | - Hubert Schrezenmeier
- Institute of Transfusion Medicine, Ulm University, Ulm, Germany
- Institute for Clinical Transfusion Medicine and Immunogenetics, Ulm, Germany
- German Red Cross Blood Transfusion Service, Baden-Württemberg-Hessen, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, Tübingen, Germany
| | - Sebastian Hörber
- Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, Tübingen, Germany
| | - Thomas Iftner
- Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | | | - Martin Wolkewitz
- Institute of Medical Biometry and Statistics, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Corinna Engel
- University Children's Hospital Tübingen, Tübingen, Germany
- Center for Pediatric Clinical Studies, University Hospital Tübingen, Tübingen, Germany
| | - Weimin Liu
- Department of Microbiology and Department of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Marta Rizzi
- Department of Rheumatology and Clinical Immunology, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Beatrice H Hahn
- Department of Microbiology and Department of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Philipp Henneke
- Center for Pediatrics and Adolescent Medicine, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Institute for Immunodeficiency, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Axel R Franz
- University Children's Hospital Tübingen, Tübingen, Germany
- Center for Pediatric Clinical Studies, University Hospital Tübingen, Tübingen, Germany
| | - Klaus-Michael Debatin
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm University, Ulm, Germany
| | | | - Ales Janda
- Department of Pediatrics and Adolescent Medicine, Ulm University Medical Center, Ulm University, Ulm, Germany
| | - Roland Elling
- Center for Pediatrics and Adolescent Medicine, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Institute for Immunodeficiency, Medical Center Freiburg, Germany and Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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18
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Fagbadebo FO, Rothbauer U. Peptide-Tag Specific Nanobodies for Studying Proteins in Live Cells. Methods Mol Biol 2022; 2446:555-579. [PMID: 35157294 DOI: 10.1007/978-1-0716-2075-5_29] [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] [Indexed: 06/14/2023]
Abstract
Single-domain antibodies such as nanobodies (Nbs) have substantially expanded the possibilities of advanced cellular imaging. In comparison to conventional antibodies, Nbs are characterized by small size, high stability, and solubility in many environments, including the cytoplasm. Nbs can be efficiently functionalized or modified according to the needs of the imaging approach. Target-specific Nbs can be easily converted into genetically encoded fluorescently labeled intrabodies, also known as chromobodies (CBs), which represent powerful tools to study the dynamics of different proteins of interest within living cells. In this context, CBs specific for a short peptide epitope provide a versatile alternative to bypass the limitations observed with larger fluorescent protein fusions and can be readily used to visualize and monitor peptide-tagged proteins for which specific Nbs are not available. Here, we present our novel detection system comprising a 15 amino acid peptide-tag (PepTag) in combination with a peptide-tag specific CB (PepCB). We provide protocols for adding the PepTag to different proteins of interest, reformatting the peptide-specific Nb (PepNb) into a CB for expression in mammalian cells, and establishment of stable cell lines expressing the PepCB for protein interaction assays and compound screenings.
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Affiliation(s)
- Funmilayo O Fagbadebo
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen, Germany.
- Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany.
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19
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Wratil PR, Schmacke NA, Karakoc B, Dulovic A, Junker D, Becker M, Rothbauer U, Osterman A, Spaeth PM, Ruhle A, Gapp M, Schneider S, Muenchhoff M, Hellmuth JC, Scherer C, Mayerle J, Reincke M, Behr J, Kääb S, Zwissler B, von Bergwelt-Baildon M, Eberle J, Kaderali L, Schneiderhan-Marra N, Hornung V, Keppler OT. Evidence for increased SARS-CoV-2 susceptibility and COVID-19 severity related to pre-existing immunity to seasonal coronaviruses. Cell Rep 2021; 37:110169. [PMID: 34932974 PMCID: PMC8648802 DOI: 10.1016/j.celrep.2021.110169] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 05/14/2021] [Revised: 10/27/2021] [Accepted: 12/03/2021] [Indexed: 11/30/2022] Open
Abstract
The importance of pre-existing immune responses to seasonal endemic coronaviruses (HCoVs) for the susceptibility to SARS-CoV-2 infection and the course of COVID-19 is the subject of an ongoing scientific debate. Recent studies postulate that immune responses to previous HCoV infections can either have a slightly protective or no effect on SARS-CoV-2 pathogenesis and, consequently, be neglected for COVID-19 risk stratification. Challenging this notion, we provide evidence that pre-existing, anti-nucleocapsid antibodies against endemic α-coronaviruses and S2 domain-specific anti-spike antibodies against β-coronavirus HCoV-OC43 are elevated in patients with COVID-19 compared to pre-pandemic donors. This finding is particularly pronounced in males and in critically ill patients. Longitudinal evaluation reveals that antibody cross-reactivity or polyclonal stimulation by SARS-CoV-2 infection are unlikely to be confounders. Thus, specific pre-existing immunity to seasonal coronaviruses may increase susceptibility to SARS-CoV-2 and predispose individuals to an adverse COVID-19 outcome, guiding risk management and supporting the development of universal coronavirus vaccines.
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Affiliation(s)
- Paul R Wratil
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany; German Center for Infection Research (DZIF), partner site Munich, 80802 Munich, Bavaria, Germany
| | - Niklas A Schmacke
- Department of Biochemistry and Gene Center, LMU München, 81377 Munich, Bavaria, Germany
| | - Burak Karakoc
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany
| | - Alex Dulovic
- Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Baden-Württemberg, Germany
| | - Daniel Junker
- Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Baden-Württemberg, Germany
| | - Matthias Becker
- Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Baden-Württemberg, Germany
| | - Ulrich Rothbauer
- Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Baden-Württemberg, Germany; Pharmaceutical Biotechnology, University of Tübingen, 72770 Reutlingen, Baden-Württemberg, Germany
| | - Andreas Osterman
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany
| | - Patricia M Spaeth
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany
| | - Adrian Ruhle
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany
| | - Madeleine Gapp
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany
| | - Stephanie Schneider
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany
| | - Maximilian Muenchhoff
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany; German Center for Infection Research (DZIF), partner site Munich, 80802 Munich, Bavaria, Germany; COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany
| | - Johannes C Hellmuth
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Department of Medicine III, Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; German Cancer Consortium (DKTK), 81377 Munich, Bavaria, Germany
| | - Clemens Scherer
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Medizinische Klinik und Poliklinik I, Klinikum der Universität München, LMU München, 80336 Munich, Bavaria, Germany; Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, 85764 Neuherberg, Bavaria, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 81377 Munich, Bavaria, Germany
| | - Julia Mayerle
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Department of Medicine II, Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany
| | - Martin Reincke
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, LMU München, 80336 Munich, Bavaria, Germany
| | - Juergen Behr
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, 85764 Neuherberg, Bavaria, Germany; Department of Medicine V, Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany
| | - Stefan Kääb
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Medizinische Klinik und Poliklinik I, Klinikum der Universität München, LMU München, 80336 Munich, Bavaria, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, 81377 Munich, Bavaria, Germany
| | - Bernhard Zwissler
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, 85764 Neuherberg, Bavaria, Germany; Department of Anaesthesiology, Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany
| | - Michael von Bergwelt-Baildon
- COVID-19 Registry of the LMU Munich (CORKUM), Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; Department of Medicine III, Klinikum der Universität München, LMU München, 81377 Munich, Bavaria, Germany; German Cancer Consortium (DKTK), 81377 Munich, Bavaria, Germany
| | - Josef Eberle
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany
| | - Lars Kaderali
- Institute of Bioinformatics, University Medicine Greifswald, 17475 Greifswald, Mecklenburg-Vorpommern, Germany
| | - Nicole Schneiderhan-Marra
- Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Baden-Württemberg, Germany
| | - Veit Hornung
- Department of Biochemistry and Gene Center, LMU München, 81377 Munich, Bavaria, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute & Gene Center, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Pettenkoferstr. 9a, 80336 Munich, Bavaria, Germany; German Center for Infection Research (DZIF), partner site Munich, 80802 Munich, Bavaria, Germany.
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20
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Traenkle B, Kaiser PD, Pezzana S, Richardson J, Gramlich M, Wagner TR, Seyfried D, Weldle M, Holz S, Parfyonova Y, Nueske S, Scholz AM, Zeck A, Jakobi M, Schneiderhan-Marra N, Schaller M, Maurer A, Gouttefangeas C, Kneilling M, Pichler BJ, Sonanini D, Rothbauer U. Single-Domain Antibodies for Targeting, Detection, and In Vivo Imaging of Human CD4 + Cells. Front Immunol 2021; 12:799910. [PMID: 34956237 PMCID: PMC8696186 DOI: 10.3389/fimmu.2021.799910] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/17/2021] [Indexed: 12/23/2022] Open
Abstract
The advancement of new immunotherapies necessitates appropriate probes to monitor the presence and distribution of distinct immune cell populations. Considering the key role of CD4+ cells in regulating immunological processes, we generated novel single-domain antibodies [nanobodies (Nbs)] that specifically recognize human CD4. After in-depth analysis of their binding properties, recognized epitopes, and effects on T-cell proliferation, activation, and cytokine release, we selected CD4-specific Nbs that did not interfere with crucial T-cell processes in vitro and converted them into immune tracers for noninvasive molecular imaging. By optical imaging, we demonstrated the ability of a high-affinity CD4-Nb to specifically visualize CD4+ cells in vivo using a xenograft model. Furthermore, quantitative high-resolution immune positron emission tomography (immunoPET)/MR of a human CD4 knock-in mouse model showed rapid accumulation of 64Cu-radiolabeled CD4-Nb1 in CD4+ T cell-rich tissues. We propose that the CD4-Nbs presented here could serve as versatile probes for stratifying patients and monitoring individual immune responses during personalized immunotherapy in both cancer and inflammatory diseases.
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Affiliation(s)
- Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Stefania Pezzana
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany
| | - Jennifer Richardson
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen, Germany
| | - Marius Gramlich
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Teresa R Wagner
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany.,Pharmaceutical Biotechnology, University of Tübingen, Tübingen, Germany
| | - Dominik Seyfried
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Tübingen, Germany
| | - Melissa Weldle
- Pharmaceutical Biotechnology, University of Tübingen, Tübingen, Germany
| | - Stefanie Holz
- Pharmaceutical Biotechnology, University of Tübingen, Tübingen, Germany
| | - Yana Parfyonova
- Pharmaceutical Biotechnology, University of Tübingen, Tübingen, Germany
| | - Stefan Nueske
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig Maximilians University Munich, Oberschleissheim, Germany
| | - Armin M Scholz
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig Maximilians University Munich, Oberschleissheim, Germany
| | - Anne Zeck
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Meike Jakobi
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | | | - Martin Schaller
- Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Andreas Maurer
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Cécile Gouttefangeas
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Manfred Kneilling
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany.,Department of Dermatology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Bernd J Pichler
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
| | - Dominik Sonanini
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany.,Department of Medical Oncology and Pneumology, University of Tübingen, Tübingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany.,Pharmaceutical Biotechnology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen, Germany
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21
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Hamann MV, Beschorner N, Vu XK, Hauber I, Lange UC, Traenkle B, Kaiser PD, Foth D, Schneider C, Büning H, Rothbauer U, Hauber J. Improved targeting of human CD4+ T cells by nanobody-modified AAV2 gene therapy vectors. PLoS One 2021; 16:e0261269. [PMID: 34928979 PMCID: PMC8687595 DOI: 10.1371/journal.pone.0261269] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
Adeno-associated viruses (AAV) are considered non-pathogenic in humans, and thus have been developed into powerful vector platforms for in vivo gene therapy. Although the various AAV serotypes display broad tropism, frequently infecting multiple tissues and cell types, vectors for specific and efficient targeting of human CD4+ T lymphocytes are largely missing. In fact, a substantial translational bottleneck exists in the field of therapeutic gene transfer that would require in vivo delivery into peripheral disease-related lymphocytes for subsequent genome editing. To solve this issue, capsid modification for retargeting AAV tropism, and in turn improving vector potency, is considered a promising strategy. Here, we genetically modified the minor AAV2 capsid proteins, VP1 and VP2, with a set of novel nanobodies with high-affinity for the human CD4 receptor. These novel vector variants demonstrated improved targeting of human CD4+ cells, including primary human peripheral blood mononuclear cells (PBMC) and purified human CD4+ T lymphocytes. Thus, the technical approach presented here provides a promising strategy for developing specific gene therapy vectors, particularly targeting disease-related peripheral blood CD4+ leukocytes.
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Affiliation(s)
- Martin V. Hamann
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
| | - Niklas Beschorner
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
| | - Xuan-Khang Vu
- Institute of Experimental Haematology, Hannover Medical School, Hannover, Germany
| | - Ilona Hauber
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
| | - Ulrike C. Lange
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
- Department of Anaesthesiology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Bjoern Traenkle
- Natural and Medical Science Institute at the University Tübingen (NMI), Reutlingen, Germany
| | - Philipp D. Kaiser
- Natural and Medical Science Institute at the University Tübingen (NMI), Reutlingen, Germany
| | - Daniel Foth
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
| | - Carola Schneider
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
| | - Hildegard Büning
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
- Institute of Experimental Haematology, Hannover Medical School, Hannover, Germany
| | - Ulrich Rothbauer
- Natural and Medical Science Institute at the University Tübingen (NMI), Reutlingen, Germany
- Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Reutlingen, Germany
| | - Joachim Hauber
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology (HPI), Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg – Lübeck – Borstel – Riems, Hamburg, Germany
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22
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Wagner TR, Schnepf D, Beer J, Ruetalo N, Klingel K, Kaiser PD, Junker D, Sauter M, Traenkle B, Frecot DI, Becker M, Schneiderhan‐Marra N, Ohnemus A, Schwemmle M, Schindler M, Rothbauer U. Biparatopic nanobodies protect mice from lethal challenge with SARS‐CoV‐2 variants of concern. EMBO Rep 2021; 23:e53865. [PMID: 34927793 PMCID: PMC8811630 DOI: 10.15252/embr.202153865] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 10/13/2021] [Revised: 11/30/2021] [Accepted: 12/06/2021] [Indexed: 11/09/2022] Open
Abstract
The ongoing COVID‐19 pandemic and the emergence of new SARS‐CoV‐2 variants of concern (VOCs) requires continued development of effective therapeutics. Recently, we identified high‐affinity neutralizing nanobodies (Nbs) specific for the receptor‐binding domain (RBD) of SARS‐CoV‐2. Taking advantage of detailed epitope mapping, we generate two biparatopic Nbs (bipNbs) targeting a conserved epitope outside and two different epitopes inside the RBD:ACE2 interface. Both bipNbs bind all currently circulating VOCs with high affinities and are capable to neutralize cellular infection with VOC B.1.351 (Beta) and B.1.617.2 (Delta) in vitro. To assess if the bipNbs NM1267 and NM1268 confer protection against SARS‐CoV‐2 infection in vivo, human ACE2 transgenic mice are treated intranasally before infection with a lethal dose of SARS‐CoV‐2 B.1, B.1.351 (Beta) or B.1.617.2 (Delta). Nb‐treated mice show significantly reduced disease progression and increased survival rates. Histopathological analyses further reveal a drastically reduced viral load and inflammatory response in lungs. These data suggest that both bipNbs are broadly active against a variety of emerging SARS‐CoV‐2 VOCs and represent easily applicable drug candidates.
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Affiliation(s)
- Teresa R Wagner
- Pharmaceutical Biotechnology Eberhard Karls University Tübingen Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen Reutlingen Germany
| | - Daniel Schnepf
- Institute of Virology Medical Center University Freiburg Freiburg Germany
| | - Julius Beer
- Institute of Virology Medical Center University Freiburg Freiburg Germany
| | - Natalia Ruetalo
- Institute for Medical Virology and Epidemiology of Viral Diseases University Hospital Tübingen Tübingen Germany
| | - Karin Klingel
- Institute for Pathology and Neuropathology University Hospital Tübingen Tübingen Germany
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen Reutlingen Germany
| | - Daniel Junker
- NMI Natural and Medical Sciences Institute at the University of Tübingen Reutlingen Germany
| | - Martina Sauter
- Institute for Pathology and Neuropathology University Hospital Tübingen Tübingen Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tübingen Reutlingen Germany
| | - Desiree I Frecot
- Pharmaceutical Biotechnology Eberhard Karls University Tübingen Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen Reutlingen Germany
| | - Matthias Becker
- NMI Natural and Medical Sciences Institute at the University of Tübingen Reutlingen Germany
| | | | - Annette Ohnemus
- Institute of Virology Medical Center University Freiburg Freiburg Germany
| | - Martin Schwemmle
- Institute of Virology Medical Center University Freiburg Freiburg Germany
- Faculty of Medicine University of Freiburg Freiburg Germany
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral Diseases University Hospital Tübingen Tübingen Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology Eberhard Karls University Tübingen Germany
- NMI Natural and Medical Sciences Institute at the University of Tübingen Reutlingen Germany
- Cluster of Excellence iFIT (EXC2180) “Image‐Guided and Functionally Instructed Tumor Therapies” Eberhard Karls University Tübingen Germany
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23
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Abstract
The identification of diagnostic and therapeutic targets requires a comprehensive understanding of cellular processes, for which advanced technologies in biomedical research are needed. The emergence of nanobodies (Nbs) derived from antibody fragments of camelid heavy chain-only antibodies as intracellular research tools offers new possibilities to study and modulate target antigens in living cells. Here we summarize this rapidly changing field, beginning with a brief introduction of Nbs, followed by an overview of how target-specific Nbs can be generated, and introduce the selection of intrabodies as research tools. Intrabodies, by definition, are intracellular functional Nbs that target ectopic or endogenous intracellular antigens within living cells. Such binders can be applied in various formats, e.g. as chromobodies for live cell microscopy or as biosensors to decipher complex intracellular signaling pathways. In addition, protein knockouts can be achieved by target-specific Nbs, while modulating Nbs have the potential as future therapeutics. The development of fine-tunable and switchable Nb-based systems that simultaneously provide spatial and temporal control has recently taken the application of these binders to the next level.
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Affiliation(s)
- Teresa R Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University, Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany; Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany.
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24
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Kratzer U, Sommersdorf C, Maier S, Wagner TR, Templin M, Joos TO, Rothbauer U, Zeck A, Poetz O. Tris(hydroxymethyl)aminomethane Compatibility with N-Hydroxysuccinimide Ester Chemistry: Biotinylation of Peptides and Proteins in TRIS Buffer. Bioconjug Chem 2021; 32:1960-1965. [PMID: 34406760 DOI: 10.1021/acs.bioconjchem.1c00283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
N-Hydroxysuccinimide esters of small molecules are widely used to modify biomolecules such as antibodies or proteins. Primary amine groups preferably react with the ester to form covalent amide bonds. Currently, protocols strongly recommend replacing the buffer reagent tris(hydroxymethyl)aminomethane, and it has even been proposed as a stop reagent. Here, we show that TRIS indeed does not interfere with biotinylation of biomolecules with NHS chemistry.
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Affiliation(s)
- Ulrich Kratzer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | | | - Sandra Maier
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Teresa R Wagner
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Markus Templin
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Thomas O Joos
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany.,Pharmaceutical Biotechnology, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Anne Zeck
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Oliver Poetz
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany.,SIGNATOPE GmbH, 72770 Reutlingen, Germany
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25
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Strengert M, Becker M, Ramos GM, Dulovic A, Gruber J, Juengling J, Lürken K, Beigel A, Wrenger E, Lonnemann G, Cossmann A, Stankov MV, Dopfer-Jablonka A, Kaiser PD, Traenkle B, Rothbauer U, Krause G, Schneiderhan-Marra N, Behrens GMN. Cellular and humoral immunogenicity of a SARS-CoV-2 mRNA vaccine in patients on haemodialysis. EBioMedicine 2021; 70:103524. [PMID: 34391096 PMCID: PMC8357427 DOI: 10.1016/j.ebiom.2021.103524] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Patients with chronic renal insufficiency on maintenance haemodialysis face an increased risk of COVID-19 induced mortality and impaired vaccine responses. To date, only a few studies have addressed SARS-CoV-2 vaccine elicited immunity in this immunocompromised population. METHODS We assessed immunogenicity of the mRNA vaccine BNT162b2 in at-risk dialysis patients and characterised systemic cellular and humoral immune responses in serum and saliva using interferon γ release assay and multiplex-based cytokine and immunoglobulin measurements. We further compared binding capacity and neutralization efficacy of vaccination-induced immunoglobulins against emerging SARS-CoV-2 variants Alpha, Beta, Epsilon and Cluster 5 by ACE2-RBD competition assay. FINDINGS Patients on maintenance haemodialysis exhibit detectable but variable cellular and humoral immune responses against SARS-CoV-2 and variants of concern after a two-dose regimen of BNT162b2. Although vaccination-induced immunoglobulins were detectable in saliva and plasma, both anti-SARS-CoV-2 IgG and neutralization efficacy was reduced compared to a vaccinated non-dialysed control population. Similarly, T-cell mediated interferon γ release after stimulation with SARS-CoV-2 spike peptides was significantly diminished. INTERPRETATION Quantifiable humoral and cellular immune responses after BNT162b2 vaccination in individuals on maintenance haemodialysis are encouraging, but urge for longitudinal follow-up to assess longevity of immunity. Diminished virus neutralization and interferon γ responses in the face of emerging variants of concern may favour this at-risk population for re-vaccination using modified vaccines at the earliest opportunity. FUNDING Initiative and Networking Fund of the Helmholtz Association of German Research Centres, EU Horizon 2020 research and innovation program, State Ministry of Baden-Württemberg for Economic Affairs, Labour and Tourism.
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Affiliation(s)
- Monika Strengert
- Helmholtz Centre for Infection Research, Braunschweig, Germany; TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Matthias Becker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Gema Morillas Ramos
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Alex Dulovic
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Jens Gruber
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Jennifer Juengling
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | | | | | | | | | - Anne Cossmann
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Metodi V Stankov
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany
| | - Alexandra Dopfer-Jablonka
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany; Pharmaceutical Biotechnology, University of Tübingen, Germany
| | - Gérard Krause
- Helmholtz Centre for Infection Research, Braunschweig, Germany; TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | | | - Georg M N Behrens
- Department for Rheumatology and Immunology, Hannover Medical School, Hannover, Germany; German Centre for Infection Research (DZIF), partner site Hannover-Braunschweig, Germany; CiiM - Centre for Individualized Infection Medicine, Hannover, Germany.
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26
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Fink S, Ruoff F, Stahl A, Becker M, Kaiser P, Traenkle B, Junker D, Weise F, Ruetalo N, Hörber S, Peter A, Nelde A, Walz J, Krause G, Baillot A, Schenke-Layland K, Joos TO, Rothbauer U, Schneiderhan-Marra N, Schindler M, Templin MF. Multiplexed Serum Antibody Screening Platform Using Virus Extracts from Endemic Coronaviridae and SARS-CoV-2. ACS Infect Dis 2021; 7:1596-1606. [PMID: 33724771 PMCID: PMC8101008 DOI: 10.1021/acsinfecdis.0c00725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Indexed: 02/04/2023]
Abstract
The presence of antibodies against endemic coronaviruses has been linked to disease severity after SARS-CoV-2 infection. Assays capable of concomitantly detecting antibodies against endemic coronaviridae such as OC43, 229E, NL63, and SARS-CoV-2 may help to elucidate this question. We developed a serum screening platform using a bead-based Western blot system called DigiWest, capable of running hundreds of assays using microgram amounts of protein prepared directly from different viruses. Characterization of the immunoassay for detection of SARS-CoV-2 specific antibodies revealed a sensitivity of 90.3% and a diagnostic specificity of 98.1%. Concordance analysis with the SARS-CoV-2 immunoassays available by Roche, Siemens, and Euroimmun indicates comparable assay performances (Cohen's κ ranging from 0.8874 to 0.9508). Analogous assays for OC43, 229E, and NL63 were established and combined into one multiplex with the SARS-CoV-2 assay. Seroreactivity for different coronaviruses was detected with high incidence, and the multiplex assay was adapted for serum screening.
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Affiliation(s)
- Simon Fink
- NMI Natural and Medical
Sciences Institute at the University of
Tübingen, 72770 Reutlingen,
Germany
| | - Felix Ruoff
- NMI Natural and Medical
Sciences Institute at the University of
Tübingen, 72770 Reutlingen,
Germany
| | - Aaron Stahl
- NMI Natural and Medical
Sciences Institute at the University of
Tübingen, 72770 Reutlingen,
Germany
| | - Matthias Becker
- NMI Natural and Medical
Sciences Institute at the University of
Tübingen, 72770 Reutlingen,
Germany
| | - Philipp Kaiser
- NMI Natural and Medical
Sciences Institute at the University of
Tübingen, 72770 Reutlingen,
Germany
| | - Bjoern Traenkle
- Pharmaceutical Biotechnology,
Eberhard-Karls-University, 72076
Tübingen, Germany
| | - Daniel Junker
- NMI Natural and Medical
Sciences Institute at the University of
Tübingen, 72770 Reutlingen,
Germany
| | - Frank Weise
- NMI Natural and Medical
Sciences Institute at the University of
Tübingen, 72770 Reutlingen,
Germany
| | - Natalia Ruetalo
- Institute for Medical Virology and
Epidemiology of Viral Diseases, University Hospital
Tübingen, 72076 Tübingen,
Germany
| | - Sebastian Hörber
- Central Laboratory, Institute for
Clinical Chemistry and Pathobiochemistry, University
Hospital Tübingen, Tübingen 72076,
Germany
- Institute for Diabetes
Research and Metabolic Diseases of the Helmholtz Center Munich
at the University of Tübingen, 72076
Tübingen, Germany
- German Center for Diabetes
Research (DZD), München-Neuherberg 85764,
Germany
| | - Andreas Peter
- Central Laboratory, Institute for
Clinical Chemistry and Pathobiochemistry, University
Hospital Tübingen, Tübingen 72076,
Germany
- Institute for Diabetes
Research and Metabolic Diseases of the Helmholtz Center Munich
at the University of Tübingen, 72076
Tübingen, Germany
- German Center for Diabetes
Research (DZD), München-Neuherberg 85764,
Germany
| | - Annika Nelde
- Clinical Collaboration Unit
Translational Immunology, German Cancer Consortium (DKTK), Department
of Internal Medicine, University Hospital
Tübingen, 72076 Tübingen,
Germany
- Department of Immunology, Institute
for Cell Biology, University of
Tübingen, 72076 Tübingen,
Germany
- Cluster of Excellence iFIT (EXC2180)
“Image-Guided and Functionally Instructed Tumor
Therapies”, University of
Tübingen, 72076 Tübingen,
Germany
| | - Juliane Walz
- Clinical Collaboration Unit
Translational Immunology, German Cancer Consortium (DKTK), Department
of Internal Medicine, University Hospital
Tübingen, 72076 Tübingen,
Germany
- Department of Immunology, Institute
for Cell Biology, University of
Tübingen, 72076 Tübingen,
Germany
- Cluster of Excellence iFIT (EXC2180)
“Image-Guided and Functionally Instructed Tumor
Therapies”, University of
Tübingen, 72076 Tübingen,
Germany
- Department of Hematology, Oncology,
Clinical Immunology and Rheumatology, University Hospital
Tübingen, 72076 Tübingen,
Germany
| | - Gérard Krause
- Department of Epidemiology,
Helmholtz Centre for Infection
Research, 38124 Braunschweig,
Germany
- TWINCORE GmbH, Centre
for Experimental and Clinical Infection Research, a joint
venture of the Hannover Medical School and the Helmholtz Centre
for Infection Research, 30625 Hannover,
Germany
| | - Armin Baillot
- Department of Virology/Serology,
Niedersächsisches
Landesgesundheitsamt, 30449 Hannover,
Germany
| | - Katja Schenke-Layland
- NMI Natural and Medical
Sciences Institute at the University of
Tübingen, 72770 Reutlingen,
Germany
- Cluster of Excellence iFIT (EXC2180)
“Image-Guided and Functionally Instructed Tumor
Therapies”, University of
Tübingen, 72076 Tübingen,
Germany
- Department of Women’s Health,
Research Institute for Women’s Health,
Eberhard-Karls-University, 72076
Tübingen, Germany
- Department of Medicine/Cardiology,
Cardiovascular Research Laboratories, David Geffen School
of Medicine at UCLA, Los Angeles, California
90095, United States
| | - Thomas O. Joos
- NMI Natural and Medical
Sciences Institute at the University of
Tübingen, 72770 Reutlingen,
Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical
Sciences Institute at the University of
Tübingen, 72770 Reutlingen,
Germany
- Pharmaceutical Biotechnology,
Eberhard-Karls-University, 72076
Tübingen, Germany
| | | | - Michael Schindler
- Institute for Medical Virology and
Epidemiology of Viral Diseases, University Hospital
Tübingen, 72076 Tübingen,
Germany
| | - Markus F. Templin
- NMI Natural and Medical
Sciences Institute at the University of
Tübingen, 72770 Reutlingen,
Germany
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27
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Becker M, Dulovic A, Junker D, Ruetalo N, Kaiser PD, Pinilla YT, Heinzel C, Haering J, Traenkle B, Wagner TR, Layer M, Mehrlaender M, Mirakaj V, Held J, Planatscher H, Schenke-Layland K, Krause G, Strengert M, Bakchoul T, Althaus K, Fendel R, Kreidenweiss A, Koeppen M, Rothbauer U, Schindler M, Schneiderhan-Marra N. Immune response to SARS-CoV-2 variants of concern in vaccinated individuals. Nat Commun 2021; 12:3109. [PMID: 34035301 PMCID: PMC8149389 DOI: 10.1038/s41467-021-23473-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [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: 03/08/2021] [Accepted: 04/28/2021] [Indexed: 12/20/2022] Open
Abstract
SARS-CoV-2 is evolving with mutations in the receptor binding domain (RBD) being of particular concern. It is important to know how much cross-protection is offered between strains following vaccination or infection. Here, we obtain serum and saliva samples from groups of vaccinated (Pfizer BNT-162b2), infected and uninfected individuals and characterize the antibody response to RBD mutant strains. Vaccinated individuals have a robust humoral response after the second dose and have high IgG antibody titers in the saliva. Antibody responses however show considerable differences in binding to RBD mutants of emerging variants of concern and substantial reduction in RBD binding and neutralization is observed against a patient-isolated South African variant. Taken together our data reinforce the importance of the second dose of Pfizer BNT-162b2 to acquire high levels of neutralizing antibodies and high antibody titers in saliva suggest that vaccinated individuals may have reduced transmission potential. Substantially reduced neutralization for the South African variant further highlights the importance of surveillance strategies to detect new variants and targeting these in future vaccines.
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Affiliation(s)
- Matthias Becker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Alex Dulovic
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Daniel Junker
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Natalia Ruetalo
- Institute for Medical Virology and Epidemiology, University Hospital Tübingen, Tübingen, Germany
| | - Philipp D Kaiser
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Yudi T Pinilla
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Constanze Heinzel
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Julia Haering
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Bjoern Traenkle
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Teresa R Wagner
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
- Pharmaceutical Biotechnology, University of Tübingen, Tübingen, Germany
| | - Mirjam Layer
- Institute for Medical Virology and Epidemiology, University Hospital Tübingen, Tübingen, Germany
| | - Martin Mehrlaender
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Valbona Mirakaj
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Jana Held
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | | | - Katja Schenke-Layland
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
- Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Department of Women's Health, Research Institute for Women's Health, University of Tübingen, Tübingen, Germany
- Department of Medicine/Cardiology, Cardiovascular Research Laboratories, David Geffen School of Medicine at UCLA, Los Angeles, USA
| | - Gérard Krause
- Helmholtz Centre for Infection Research, Braunschweig, Germany
- TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Monika Strengert
- Helmholtz Centre for Infection Research, Braunschweig, Germany
- TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Tamam Bakchoul
- Institute for Clinical and Experimental Transfusion Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Karina Althaus
- Institute for Clinical and Experimental Transfusion Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Rolf Fendel
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Andrea Kreidenweiss
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Michael Koeppen
- Department of Anaesthesiology and Intensive Care Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Ulrich Rothbauer
- NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany.
- Pharmaceutical Biotechnology, University of Tübingen, Tübingen, Germany.
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology, University Hospital Tübingen, Tübingen, Germany.
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28
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Wagner TR, Ostertag E, Kaiser PD, Gramlich M, Ruetalo N, Junker D, Haering J, Traenkle B, Becker M, Dulovic A, Schweizer H, Nueske S, Scholz A, Zeck A, Schenke‐Layland K, Nelde A, Strengert M, Walz JS, Zocher G, Stehle T, Schindler M, Schneiderhan‐Marra N, Rothbauer U. NeutrobodyPlex-monitoring SARS-CoV-2 neutralizing immune responses using nanobodies. EMBO Rep 2021; 22:e52325. [PMID: 33904225 PMCID: PMC8097376 DOI: 10.15252/embr.202052325] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [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: 12/21/2020] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/23/2022] Open
Abstract
In light of the COVID-19 pandemic, there is an ongoing need for diagnostic tools to monitor the immune status of large patient cohorts and the effectiveness of vaccination campaigns. Here, we present 11 unique nanobodies (Nbs) specific for the SARS-CoV-2 spike receptor-binding domain (RBD), of which 8 Nbs potently inhibit the interaction of RBD with angiotensin-converting enzyme 2 (ACE2) as the major viral docking site. Following detailed epitope mapping and structural analysis, we select two inhibitory Nbs, one of which binds an epitope inside and one of which binds an epitope outside the RBD:ACE2 interface. Based on these, we generate a biparatopic nanobody (bipNb) with viral neutralization efficacy in the picomolar range. Using bipNb as a surrogate, we establish a competitive multiplex binding assay ("NeutrobodyPlex") for detailed analysis of the presence and performance of neutralizing RBD-binding antibodies in serum of convalescent or vaccinated patients. We demonstrate that NeutrobodyPlex enables high-throughput screening and detailed analysis of neutralizing immune responses in infected or vaccinated individuals, to monitor immune status or to guide vaccine design.
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Affiliation(s)
- Teresa R Wagner
- Pharmaceutical BiotechnologyEberhard Karls UniversityTuebingenGermany
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Elena Ostertag
- Interfaculty Institute of BiochemistryEberhard Karls UniversityTuebingenGermany
| | - Philipp D Kaiser
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Marius Gramlich
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Natalia Ruetalo
- Institute for Medical Virology and Epidemiology of Viral DiseasesUniversity Hospital TuebingenTuebingenGermany
| | - Daniel Junker
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Julia Haering
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Bjoern Traenkle
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Matthias Becker
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Alex Dulovic
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Helen Schweizer
- Livestock Center of the Faculty of Veterinary MedicineLudwig Maximilians UniversityOberschleissheimGermany
| | - Stefan Nueske
- Livestock Center of the Faculty of Veterinary MedicineLudwig Maximilians UniversityOberschleissheimGermany
| | - Armin Scholz
- Livestock Center of the Faculty of Veterinary MedicineLudwig Maximilians UniversityOberschleissheimGermany
| | - Anne Zeck
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
| | - Katja Schenke‐Layland
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
- Cluster of Excellence iFIT (EXC2180) “Image‐Guided and Functionally Instructed Tumor Therapies”Eberhard Karls UniversityTuebingenGermany
- Department of Women’s HealthResearch Institute for Women’s HealthEberhard Karls UniversityTuebingenGermany
- Department of Medicine/CardiologyCardiovascular Research LaboratoriesDavid Geffen School of Medicine at UCLALos AngelesCAUSA
| | - Annika Nelde
- Cluster of Excellence iFIT (EXC2180) “Image‐Guided and Functionally Instructed Tumor Therapies”Eberhard Karls UniversityTuebingenGermany
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TuebingenTuebingenGermany
- Institute for Cell BiologyDepartment of ImmunologyEberhard Karls UniversityTuebingenGermany
| | - Monika Strengert
- Department of EpidemiologyHelmholtz Centre for Infection ResearchBraunschweigGermany
- TWINCORE GmbHCentre for Experimental and Clinical Infection ResearchA Joint venture of the Hannover Medical School and the Helmholtz Centre for Infection ResearchHannoverGermany
| | - Juliane S Walz
- Cluster of Excellence iFIT (EXC2180) “Image‐Guided and Functionally Instructed Tumor Therapies”Eberhard Karls UniversityTuebingenGermany
- Clinical Collaboration Unit Translational ImmunologyGerman Cancer Consortium (DKTK)Department of Internal MedicineUniversity Hospital TuebingenTuebingenGermany
- Institute for Cell BiologyDepartment of ImmunologyEberhard Karls UniversityTuebingenGermany
- Dr. Margarete Fischer‐Bosch Institute of Clinical Pharmacology and Robert Bosch Center for Tumor DiseaseRBCTStuttgartGermany
| | - Georg Zocher
- Interfaculty Institute of BiochemistryEberhard Karls UniversityTuebingenGermany
| | - Thilo Stehle
- Interfaculty Institute of BiochemistryEberhard Karls UniversityTuebingenGermany
- Vanderbilt University School of MedicineNashvilleTNUSA
| | - Michael Schindler
- Institute for Medical Virology and Epidemiology of Viral DiseasesUniversity Hospital TuebingenTuebingenGermany
| | | | - Ulrich Rothbauer
- Pharmaceutical BiotechnologyEberhard Karls UniversityTuebingenGermany
- Natural and Medical Sciences InstituteUniversity of TuebingenReutlingenGermany
- Cluster of Excellence iFIT (EXC2180) “Image‐Guided and Functionally Instructed Tumor Therapies”Eberhard Karls UniversityTuebingenGermany
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29
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Huergo LF, Selim KA, Conzentino MS, Gerhardt ECM, Santos ARS, Wagner B, Alford JT, Deobald N, Pedrosa FO, de Souza EM, Nogueira MB, Raboni SM, Souto D, Rego FGM, Zanette DL, Aoki MN, Nardin JM, Fornazari B, Morales HMP, Borges VA, Nelde A, Walz JS, Becker M, Schneiderhan-Marra N, Rothbauer U, Reis RA, Forchhammer K. Magnetic Bead-Based Immunoassay Allows Rapid, Inexpensive, and Quantitative Detection of Human SARS-CoV-2 Antibodies. ACS Sens 2021; 6:703-708. [PMID: 33496577 PMCID: PMC7860136 DOI: 10.1021/acssensors.0c02544] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
Immunological methods to detect SARS-CoV-2 seroconversion in humans are important to track COVID-19 cases and the humoral response to SARS-CoV-2 infections and immunization to future vaccines. The aim of this work was to develop a simple chromogenic magnetic bead-based immunoassay which allows rapid, inexpensive, and quantitative detection of human antibodies against SARS-CoV-2 in serum, plasma, or blood. Recombinant 6xHis-tagged SARS-CoV-2 Nucleocapsid protein was mobilized on the surface of Ni2+ magnetic beads and challenged with serum or blood samples obtained from controls or COVID-19 cases. The beads were washed, incubated with anti-human IgG-HPR conjugate, and immersed into a solution containing a chromogenic HPR substrate. Bead transfer and homogenization between solutions was aided by a simple low-cost device. The method was validated by two independent laboratories, and the performance to detect SARS-CoV-2 seroconversion in humans was in the same range as obtained using the gold standard immunoassays ELISA and Luminex, though requiring only a fraction of consumables, instrumentation, time to deliver results, and volume of sample. Furthermore, the results obtained with the method described can be visually interpreted without compromising accuracy as demonstrated by validation at a point-of-care unit. The magnetic bead immunoassay throughput can be customized on demand and is readily adapted to be used with any other 6xHis tagged protein or peptide as antigen to track other diseases.
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Affiliation(s)
- Luciano F. Huergo
- Setor Litoral, Federal University of
Paraná (UFPR) Matinhos, PR 83260-000,
Brazil
| | - Khaled A. Selim
- Interfaculty Institute for Microbiology and Infection
Medicine, Eberhard Karls University of Tübingen, 72074
Tübingen,Germany
| | | | - Edileusa C. M. Gerhardt
- Biochemistry and Molecular Biology Department,
Federal University of Paraná (UFPR) Curitiba, PR
80060-000, Brazil
| | - Adrian R. S. Santos
- Biochemistry and Molecular Biology Department,
Federal University of Paraná (UFPR) Curitiba, PR
80060-000, Brazil
| | - Berenike Wagner
- Interfaculty Institute for Microbiology and Infection
Medicine, Eberhard Karls University of Tübingen, 72074
Tübingen,Germany
| | - Janette T. Alford
- Interfaculty Institute for Microbiology and Infection
Medicine, Eberhard Karls University of Tübingen, 72074
Tübingen,Germany
| | - Nelli Deobald
- Interfaculty Institute for Microbiology and Infection
Medicine, Eberhard Karls University of Tübingen, 72074
Tübingen,Germany
| | - Fabio O. Pedrosa
- Biochemistry and Molecular Biology Department,
Federal University of Paraná (UFPR) Curitiba, PR
80060-000, Brazil
| | - Emanuel M. de Souza
- Biochemistry and Molecular Biology Department,
Federal University of Paraná (UFPR) Curitiba, PR
80060-000, Brazil
| | - Meri B. Nogueira
- Complexo Hospital das Clínicas,
Federal University of Paraná (UFPR) Curitiba, PR
80060-000, Brazil
| | - Sônia M. Raboni
- Complexo Hospital das Clínicas,
Federal University of Paraná (UFPR) Curitiba, PR
80060-000, Brazil
| | - Dênio Souto
- Chemistry Departament, Federal University
of Paraná (UFPR), Curitiba, PR 80060-000,
Brazil
| | - Fabiane G. M. Rego
- Post-Graduation Program in Pharmaceutical Sciences,
Federal University of Paraná (UFPR), Curitiba, PR
80060-000, Brazil
| | | | - Mateus N. Aoki
- Instituto Carlos Chagas -
FioCruz, Curitiba, PR 81310-020, Brazil
| | | | | | | | - Vânia A. Borges
- Secretaria Municipal de Saúde de
Guaratuba, Guaratuba, PR 83280-000, Brazil
| | - Annika Nelde
- Clinical Collaboration Unit Translational Immunology,
German Cancer Consortium (DKTK), Department of Internal Medicine, University
Hospital Tübingen, 72076 Tübingen,
Germany
- Department of Immunology, Institute for Cell Biology,
Tübingen University, 72076 Tübingen,
Germany
- Cluster of Excellence iFIT (EXC2180)
“Image-Guided and Functionally Instructed Tumor Therapies”,
Tübingen University, 72076 Tübingen,
Germany
| | - Juliane S. Walz
- Clinical Collaboration Unit Translational Immunology,
German Cancer Consortium (DKTK), Department of Internal Medicine, University
Hospital Tübingen, 72076 Tübingen,
Germany
- Department of Immunology, Institute for Cell Biology,
Tübingen University, 72076 Tübingen,
Germany
- Cluster of Excellence iFIT (EXC2180)
“Image-Guided and Functionally Instructed Tumor Therapies”,
Tübingen University, 72076 Tübingen,
Germany
- Department of Hematology, Oncology, Clinical
Immunology and Rheumatology, University Hospital
Tübingen, 72076 Tübingen, Germany
| | - Matthias Becker
- NMI Natural and Medical Sciences
Institute at the University of Tübingen, 72770 Tübingen,
Germany
| | | | - Ulrich Rothbauer
- NMI Natural and Medical Sciences
Institute at the University of Tübingen, 72770 Tübingen,
Germany
- Pharmaceutical Biotechnology,
Tübingen University, 72076 Tübingen,
Germany
| | - Rodrigo A. Reis
- Setor Litoral, Federal University of
Paraná (UFPR) Matinhos, PR 83260-000,
Brazil
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection
Medicine, Eberhard Karls University of Tübingen, 72074
Tübingen,Germany
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30
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Gramlich M, Hays HCW, Crichton S, Kaiser PD, Heine A, Schneiderhan-Marra N, Rothbauer U, Stoll D, Maier S, Zeck A. HDX-MS for Epitope Characterization of a Therapeutic ANTIBODY Candidate on the Calcium-Binding Protein Annexin-A1. Antibodies (Basel) 2021; 10:11. [PMID: 33808657 PMCID: PMC8006148 DOI: 10.3390/antib10010011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 12/24/2020] [Revised: 01/15/2021] [Accepted: 03/02/2021] [Indexed: 12/25/2022] Open
Abstract
Annexin-A1 (ANXA1) belongs to a class of highly homologous Ca2+-dependent phospholipid-binding proteins. Its structure consists of a core region composed of four homologous repeats arranged in a compact, hydrolysis-resistant structure and an N-terminal region with a Ca2+-dependent conformation. ANXA1 is involved in several processes, including cell proliferation, apoptosis, metastasis, and the inflammatory response. Therefore, the development of antibodies blocking selected regions on ANXA1 holds great potential for the development of novel therapeutics treating inflammatory and cancer diseases. Here, we report the interaction site between an ANXA1-specific antibody known to inhibit T cell activation without adverse cytotoxic effects and ANXA1 using amide hydrogen-deuterium exchange mass spectrometry (HDX-MS). For the epitope determination, we applied two bottom-up HDX-MS approaches with pepsin digestion in solution and immobilized on beads. Both strategies revealed the interaction region within domain III of ANXA1 in Ca2+-bound conformation. The antibody-binding region correlates with the hydrophobic binding pocket of the N-terminal domain formed in the absence of calcium. This study demonstrates that even cryptic and flexible binding regions can be studied by HDX-MS, allowing a fast and efficient determination of the binding sites of antibodies which will help to define a mode of action profile for their use in therapy.
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Affiliation(s)
- Marius Gramlich
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Henry C. W. Hays
- Medannex Ltd., 1 Lochrin Square, Fountainbridge, Edinburgh EH3 9QA, UK; (H.C.W.H.); (S.C.)
| | - Scott Crichton
- Medannex Ltd., 1 Lochrin Square, Fountainbridge, Edinburgh EH3 9QA, UK; (H.C.W.H.); (S.C.)
| | - Philipp D. Kaiser
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Anne Heine
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Nicole Schneiderhan-Marra
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Ulrich Rothbauer
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Geschwister-Scholl-Platz, 72074 Tuebingen, Germany
| | - Dieter Stoll
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
- Department of Life Sciences, University of Applied Sciences Albstadt-Sigmaringen, Anton-Guentherstr. 51, 72488 Sigmaringen, Germany
| | - Sandra Maier
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
| | - Anne Zeck
- NMI, Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstr. 55, 72770 Reutlingen, Germany; (M.G.); (P.D.K.); (A.H.); (N.S.-M.); (U.R.); (D.S.); (S.M.)
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Wagner TR, Rothbauer U. Nanobodies Right in the Middle: Intrabodies as Toolbox to Visualize and Modulate Antigens in the Living Cell. Biomolecules 2020; 10:biom10121701. [PMID: 33371447 PMCID: PMC7767433 DOI: 10.3390/biom10121701] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/15/2020] [Accepted: 12/18/2020] [Indexed: 01/01/2023] Open
Abstract
In biomedical research, there is an ongoing demand for new technologies to elucidate disease mechanisms and develop novel therapeutics. This requires comprehensive understanding of cellular processes and their pathophysiology based on reliable information on abundance, localization, post-translational modifications and dynamic interactions of cellular components. Traceable intracellular binding molecules provide new opportunities for real-time cellular diagnostics. Most prominently, intrabodies derived from antibody fragments of heavy-chain only antibodies of camelids (nanobodies) have emerged as highly versatile and attractive probes to study and manipulate antigens within the context of living cells. In this review, we provide an overview on the selection, delivery and usage of intrabodies to visualize and monitor cellular antigens in living cells and organisms. Additionally, we summarize recent advances in the development of intrabodies as cellular biosensors and their application to manipulate disease-related cellular processes. Finally, we highlight switchable intrabodies, which open entirely new possibilities for real-time cell-based diagnostics including live-cell imaging, target validation and generation of precisely controllable binding reagents for future therapeutic applications.
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Affiliation(s)
- Teresa R. Wagner
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany;
- Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, 72076 Tuebingen, Germany;
- Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany
- Correspondence: ; Tel.: +49-7121-5153-0415; Fax: +49-7121-5153-0816
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32
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Nelde A, Bilich T, Heitmann JS, Maringer Y, Salih HR, Roerden M, Lübke M, Bauer J, Rieth J, Wacker M, Peter A, Hörber S, Traenkle B, Kaiser PD, Rothbauer U, Becker M, Junker D, Krause G, Strengert M, Schneiderhan-Marra N, Templin MF, Joos TO, Kowalewski DJ, Stos-Zweifel V, Fehr M, Rabsteyn A, Mirakaj V, Karbach J, Jäger E, Graf M, Gruber LC, Rachfalski D, Preuß B, Hagelstein I, Märklin M, Bakchoul T, Gouttefangeas C, Kohlbacher O, Klein R, Stevanović S, Rammensee HG, Walz JS. SARS-CoV-2-derived peptides define heterologous and COVID-19-induced T cell recognition. Nat Immunol 2020; 22:74-85. [PMID: 32999467 DOI: 10.1038/s41590-020-00808-x] [Citation(s) in RCA: 383] [Impact Index Per Article: 95.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/11/2020] [Indexed: 12/14/2022]
Abstract
T cell immunity is central for the control of viral infections. To characterize T cell immunity, but also for the development of vaccines, identification of exact viral T cell epitopes is fundamental. Here we identify and characterize multiple dominant and subdominant SARS-CoV-2 HLA class I and HLA-DR peptides as potential T cell epitopes in COVID-19 convalescent and unexposed individuals. SARS-CoV-2-specific peptides enabled detection of post-infectious T cell immunity, even in seronegative convalescent individuals. Cross-reactive SARS-CoV-2 peptides revealed pre-existing T cell responses in 81% of unexposed individuals and validated similarity with common cold coronaviruses, providing a functional basis for heterologous immunity in SARS-CoV-2 infection. Diversity of SARS-CoV-2 T cell responses was associated with mild symptoms of COVID-19, providing evidence that immunity requires recognition of multiple epitopes. Together, the proposed SARS-CoV-2 T cell epitopes enable identification of heterologous and post-infectious T cell immunity and facilitate development of diagnostic, preventive and therapeutic measures for COVID-19.
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Affiliation(s)
- Annika Nelde
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Tatjana Bilich
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Yacine Maringer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Malte Roerden
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Maren Lübke
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Jens Bauer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Jonas Rieth
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Marcel Wacker
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Andreas Peter
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Sebastian Hörber
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Bjoern Traenkle
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Philipp D Kaiser
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany.,Pharmaceutical Biotechnology, University of Tübingen, Tübingen, Germany
| | - Matthias Becker
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Daniel Junker
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Gérard Krause
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany.,German Center for Infection Research, Braunschweig, Germany
| | - Monika Strengert
- Department of Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,TWINCORE GmbH, Centre for Experimental and Clinical Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Centre for Infection Research, Hannover, Germany
| | | | - Markus F Templin
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | - Thomas O Joos
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, Germany
| | | | | | - Michael Fehr
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany
| | - Armin Rabsteyn
- Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,Department of General Pediatrics, Oncology/Hematology, University Children's Hospital Tübingen, Tübingen, Germany
| | - Valbona Mirakaj
- Department of Anesthesia and Intensive Care Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Julia Karbach
- Department of Oncology and Hematology, Krankenhaus Nordwest, Frankfurt, Germany
| | - Elke Jäger
- Department of Oncology and Hematology, Krankenhaus Nordwest, Frankfurt, Germany
| | - Michael Graf
- Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Lena-Christin Gruber
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - David Rachfalski
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Beate Preuß
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Ilona Hagelstein
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Melanie Märklin
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany
| | - Tamam Bakchoul
- Institute for Clinical and Experimental Transfusion Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Cécile Gouttefangeas
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Center for Bioinformatics and Department of Computer Science, University of Tübingen, Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.,Biomolecular Interactions, Max-Planck-Institute for Developmental Biology, Tübingen, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany. .,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen, Germany. .,Cluster of Excellence iFIT (EXC2180) 'Image-Guided and Functionally Instructed Tumor Therapies', University of Tübingen, Tübingen, Germany.
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33
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Tiwari A, Iida M, Kosnopfel C, Abbariki M, Menegakis A, Fehrenbacher B, Maier J, Schaller M, Brucker SY, Wheeler DL, Harari PM, Rothbauer U, Schittek B, Zips D, Toulany M. Blocking Y-Box Binding Protein-1 through Simultaneous Targeting of PI3K and MAPK in Triple Negative Breast Cancers. Cancers (Basel) 2020; 12:cancers12102795. [PMID: 33003386 PMCID: PMC7601769 DOI: 10.3390/cancers12102795] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 09/08/2020] [Accepted: 09/25/2020] [Indexed: 12/22/2022] Open
Abstract
Simple Summary Triple-negative breast cancer (TNBC) is associated with the high rates of relapse and metastasis and poor survival. YB-1 is overexpressed in TNBC tumor tissues. In the present study, we demonstrated that S102 phosphorylation of YB-1 in TNBC cell lines depend on the mutation status of the components of the MAPK/ERK and PI3K/Akt pathways. Simultaneous targeting of MEK and PI3K was found to be the most effective approach to block YB-1 phosphorylation and to inhibit YB-1 dependent cell proliferation. YBX1 knockout was sufficient to block TNBC tumor growth. Abstract The multifunctional protein Y-box binding protein-1 (YB-1) regulates all the so far described cancer hallmarks including cell proliferation and survival. The MAPK/ERK and PI3K/Akt pathways are also the major pathways involved in cell growth, proliferation, and survival, and are the frequently hyperactivated pathways in human cancers. A gain of function mutation in KRAS mainly leads to the constitutive activation of the MAPK pathway, while the activation of the PI3K/Akt pathway occurs either through the loss of PTEN or a gain of function mutation of the catalytic subunit alpha of PI3K (PIK3CA). In this study, we investigated the underlying signaling pathway involved in YB-1 phosphorylation at serine 102 (S102) in KRAS(G13D)-mutated triple-negative breast cancer (TNBC) MDA-MB-231 cells versus PIK3CA(H1047R)/PTEN(E307K) mutated TNBC MDA-MB-453 cells. Our data demonstrate that S102 phosphorylation of YB-1 in KRAS-mutated cells is mainly dependent on the MAPK/ERK pathway, while in PIK3CA/PTEN-mutated cells, YB-1 S102 phosphorylation is entirely dependent on the PI3K/Akt pathway. Independent of the individual dominant pathway regulating YB-1 phosphorylation, dual targeting of MEK and PI3K efficiently inhibited YB-1 phosphorylation and blocked cell proliferation. This represents functional crosstalk between the two pathways. Our data obtained from the experiments, applying pharmacological inhibitors and genetic approaches, shows that YB-1 is a key player in cell proliferation, clonogenic activity, and tumor growth of TNBC cells through the MAPK and PI3K pathways. Therefore, dual inhibition of these two pathways or single targeting of YB-1 may be an effective strategy to treat TNBC.
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Affiliation(s)
- Aadhya Tiwari
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, 72076 Tuebingen, Germany; (A.T.); (D.Z.)
- Department of Radiation Oncology, University of Tuebingen, 72076 Tuebingen, Germany;
- German Cancer Consortium (DKTK), Partner Site Tuebingen and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Mari Iida
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA; (M.I.); (M.A.); (D.L.W.); (P.M.H.)
| | - Corinna Kosnopfel
- Department of Dermatology, University of Tuebingen, 72076 Tuebingen, Germany; (C.K.); (B.F.); (M.S.); (B.S.)
| | - Mahyar Abbariki
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA; (M.I.); (M.A.); (D.L.W.); (P.M.H.)
| | - Apostolos Menegakis
- Department of Radiation Oncology, University of Tuebingen, 72076 Tuebingen, Germany;
- German Cancer Consortium (DKTK), Partner Site Tuebingen and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Birgit Fehrenbacher
- Department of Dermatology, University of Tuebingen, 72076 Tuebingen, Germany; (C.K.); (B.F.); (M.S.); (B.S.)
| | - Julia Maier
- Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany; (J.M.); (U.R.)
- Pharmaceutical Biotechnology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Martin Schaller
- Department of Dermatology, University of Tuebingen, 72076 Tuebingen, Germany; (C.K.); (B.F.); (M.S.); (B.S.)
| | - Sara Y. Brucker
- Department of Women’s Health, University of Tuebingen, 72076 Tuebingen, Germany;
| | - Deric L. Wheeler
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA; (M.I.); (M.A.); (D.L.W.); (P.M.H.)
| | - Paul M. Harari
- Department of Human Oncology, University of Wisconsin, Madison, WI 53705, USA; (M.I.); (M.A.); (D.L.W.); (P.M.H.)
| | - Ulrich Rothbauer
- Natural and Medical Sciences Institute, University of Tuebingen, 72770 Reutlingen, Germany; (J.M.); (U.R.)
- Pharmaceutical Biotechnology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Birgit Schittek
- Department of Dermatology, University of Tuebingen, 72076 Tuebingen, Germany; (C.K.); (B.F.); (M.S.); (B.S.)
| | - Daniel Zips
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, 72076 Tuebingen, Germany; (A.T.); (D.Z.)
- Department of Radiation Oncology, University of Tuebingen, 72076 Tuebingen, Germany;
- German Cancer Consortium (DKTK), Partner Site Tuebingen and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Mahmoud Toulany
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, 72076 Tuebingen, Germany; (A.T.); (D.Z.)
- Department of Radiation Oncology, University of Tuebingen, 72076 Tuebingen, Germany;
- German Cancer Consortium (DKTK), Partner Site Tuebingen and German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-7071-29-85832
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34
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Traenkle B, Segan S, Fagbadebo FO, Kaiser PD, Rothbauer U. A novel epitope tagging system to visualize and monitor antigens in live cells with chromobodies. Sci Rep 2020; 10:14267. [PMID: 32868807 PMCID: PMC7459311 DOI: 10.1038/s41598-020-71091-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [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: 06/08/2020] [Accepted: 08/06/2020] [Indexed: 11/09/2022] Open
Abstract
Epitope tagging is a versatile approach to study different proteins using a well-defined and established methodology. To date, most epitope tags such as myc, HA, V5 and FLAG tags are recognized by antibodies, which limits their use to fixed cells, tissues or protein samples. Here we introduce a broadly applicable tagging strategy utilizing a short peptide tag (PepTag) which is specifically recognized by a nanobody (PepNB). We demonstrated that the PepNB can be easily functionalized for immunoprecipitation or direct immunofluorescence staining of Pep-tagged proteins in vitro. For in cellulo studies we converted the PepNB into a fluorescently labeled Pep-chromobody (PepCB) which is functionally expressed in living cells. The addition of the small PepTag does not interfere with the examined structures in different cellular compartments and its detection with the PepCB enables optical antigen tracing in real time. By employing the phenomenon of antigen-mediated chromobody stabilization (AMCBS) using a turnover-accelerated PepCB we demonstrated that the system is suitable to visualize and quantify changes in Pep-tagged antigen concentration by quantitative live-cell imaging. We expect that this novel tagging strategy offers new opportunities to study the dynamic regulation of proteins, e.g. during cellular signaling, cell differentiation, or upon drug action.
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Affiliation(s)
- Bjoern Traenkle
- Pharmaceutical Biotechnology, Eberhard Karls University, Tuebingen, Germany.,Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Sören Segan
- Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | | | - Philipp D Kaiser
- Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University, Tuebingen, Germany. .,Natural and Medical Sciences Institute, University of Tuebingen, Markwiesenstr. 55, 72770, Reutlingen, Germany.
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35
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Segan S, Jakobi M, Khokhani P, Klimosch S, Billing F, Schneider M, Martin D, Metzger U, Biesemeier A, Xiong X, Mukherjee A, Steuer H, Keller BM, Joos T, Schmolz M, Rothbauer U, Hartmann H, Burkhardt C, Lorenz G, Schneiderhan-Marra N, Shipp C. Systematic Investigation of Polyurethane Biomaterial Surface Roughness on Human Immune Responses in vitro. Biomed Res Int 2020; 2020:3481549. [PMID: 32461979 PMCID: PMC7240656 DOI: 10.1155/2020/3481549] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/29/2020] [Accepted: 03/04/2020] [Indexed: 01/06/2023]
Abstract
It has been widely shown that biomaterial surface topography can modulate host immune response, but a fundamental understanding of how different topographies contribute to pro-inflammatory or anti-inflammatory responses is still lacking. To investigate the impact of surface topography on immune response, we undertook a systematic approach by analyzing immune response to eight grades of medical grade polyurethane of increasing surface roughness in three in vitro models of the human immune system. Polyurethane specimens were produced with defined roughness values by injection molding according to the VDI 3400 industrial standard. Specimens ranged from 0.1 μm to 18 μm in average roughness (Ra), which was confirmed by confocal scanning microscopy. Immunological responses were assessed with THP-1-derived macrophages, human peripheral blood mononuclear cells (PBMCs), and whole blood following culture on polyurethane specimens. As shown by the release of pro-inflammatory and anti-inflammatory cytokines in all three models, a mild immune response to polyurethane was observed, however, this was not associated with the degree of surface roughness. Likewise, the cell morphology (cell spreading, circularity, and elongation) in THP-1-derived macrophages and the expression of CD molecules in the PBMC model on T cells (HLA-DR and CD16), NK cells (HLA-DR), and monocytes (HLA-DR, CD16, CD86, and CD163) showed no influence of surface roughness. In summary, this study shows that modifying surface roughness in the micrometer range on polyurethane has no impact on the pro-inflammatory immune response. Therefore, we propose that such modifications do not affect the immunocompatibility of polyurethane, thereby supporting the notion of polyurethane as a biocompatible material.
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Affiliation(s)
- Sören Segan
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Meike Jakobi
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Paree Khokhani
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Sascha Klimosch
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
- HOT Screen GmbH, Aspenhaustraße 25, 72770 Reutlingen, Germany
| | - Florian Billing
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Markus Schneider
- University of Applied Sciences, Reutlingen, Alteburgstr. 150, 72762 Reutlingen, Germany
| | - Dagmar Martin
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Ute Metzger
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Antje Biesemeier
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
- Center for Ophthalmology, University Hospital Tübingen, Schleichstr. 12/1, 72076 Tübingen, Germany
| | - Xin Xiong
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Ashutosh Mukherjee
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Heiko Steuer
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | | | - Thomas Joos
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Manfred Schmolz
- HOT Screen GmbH, Aspenhaustraße 25, 72770 Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
- University of Tübingen, Geschwister-Scholl-Platz, 72074 Tübingen, Germany
| | - Hanna Hartmann
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Claus Burkhardt
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Günter Lorenz
- University of Applied Sciences, Reutlingen, Alteburgstr. 150, 72762 Reutlingen, Germany
| | - Nicole Schneiderhan-Marra
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Christopher Shipp
- NMI, Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
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Affiliation(s)
- Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Reutlingen, Germany. .,Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany.
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Keller BM, Maier J, Secker KA, Egetemaier SM, Parfyonova Y, Rothbauer U, Traenkle B. Chromobodies to Quantify Changes of Endogenous Protein Concentration in Living Cells. Mol Cell Proteomics 2018; 17:2518-2533. [PMID: 30228193 DOI: 10.1074/mcp.tir118.000914] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 06/12/2018] [Revised: 09/04/2018] [Indexed: 11/06/2022] Open
Abstract
Understanding cellular processes requires the determination of dynamic changes in the concentration of genetically nonmodified, endogenous proteins, which, to date, is commonly accomplished by end-point assays in vitro Molecular probes such as fluorescently labeled nanobodies (chromobodies, CBs) are powerful tools to visualize the dynamic subcellular localization of endogenous proteins in living cells. Here, we employed the dependence of intracellular levels of chromobodies on the amount of their endogenous antigens, a phenomenon, which we termed antigen-mediated CB stabilization (AMCBS), for simultaneous monitoring of time-resolved changes in the concentration and localization of native proteins. To improve the dynamic range of AMCBS we generated turnover-accelerated CBs and demonstrated their application in visualization and quantification of fast reversible changes in antigen concentration upon compound treatment by quantitative live-cell imaging. We expect that this broadly applicable strategy will enable unprecedented insights into the dynamic regulation of proteins, e.g. during cellular signaling, cell differentiation, or upon drug action.
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Affiliation(s)
| | - Julia Maier
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany
| | - Kathy-Ann Secker
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany
| | | | - Yana Parfyonova
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany; Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany.
| | - Bjoern Traenkle
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Germany.
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Sannino G, Armbruster N, Bodenhöfer M, Haerle U, Behrens D, Buchholz M, Rothbauer U, Sipos B, Schmees C. Role of BCL9L in transforming growth factor-β (TGF-β)-induced epithelial-to-mesenchymal-transition (EMT) and metastasis of pancreatic cancer. Oncotarget 2018; 7:73725-73738. [PMID: 27713160 PMCID: PMC5342010 DOI: 10.18632/oncotarget.12455] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 08/20/2015] [Accepted: 09/24/2016] [Indexed: 12/19/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has a low overall survival rate, which is approximately 20% during the first year and decreases to less than 6% within five years of the disease. This is due to premature dissemination accompanied by a lack of disease-specific symptoms during the initial stages. Additionally, to date there are no biomarkers for an early prognosis available.A growing number of studies indicate that epithelial to mesenchymal transition (EMT), triggered by WNT-, TGF-β- and other signaling pathways is crucial for the initiation of the metastatic process in PDAC. Here we show, that BCL9L is up-regulated in PDAC cell lines and patient tissue compared to non-cancer controls. RNAi-induced BCL9L knockdown negatively affected proliferation, migration and invasion of pancreatic cancer cells. On a molecular basis, BCL9L depletion provoked an increment of E-cadherin protein levels, with concomitant increase of β-catenin retention at the plasma membrane. This is linked to the induction of a strong epithelial phenotype in pancreatic cancer cells upon BCL9L knockdown even in the presence of the EMT-inducer TGF-β. Finally, xenograft mouse models of pancreatic cancer revealed a highly significant reduction in the number of liver metastases upon BCL9L knockdown. Taken together, our findings underline the key importance of BCL9L for EMT and thus progression and metastasis of pancreatic cancer cells. Direct targeting of this protein might be a valuable approach to effectively antagonize invasion and metastasis of PDAC.
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Affiliation(s)
- Giuseppina Sannino
- Natural and Medical Sciences Institute (NMI) at the University of Tuebingen, Tumor Biology Group, Reutlingen, Germany.,Current address: Institute of Pathology, Laboratory of Pediatric Sarcoma Biology, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Nicole Armbruster
- Natural and Medical Sciences Institute (NMI) at the University of Tuebingen, Tumor Biology Group, Reutlingen, Germany.,Current address: Department of Internal Medicine II, University of Tuebingen, Tuebingen, Germany
| | - Mona Bodenhöfer
- Natural and Medical Sciences Institute (NMI) at the University of Tuebingen, Tumor Biology Group, Reutlingen, Germany
| | - Ursula Haerle
- Natural and Medical Sciences Institute (NMI) at the University of Tuebingen, Tumor Biology Group, Reutlingen, Germany
| | - Diana Behrens
- Experimental Pharmacology and Oncology GmbH, Berlin, Germany
| | - Malte Buchholz
- Department of Medicine, Division of Gastroenterology, Endocrinology and Metabolism, Philipps University Marburg, Marburg, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, University of Tuebingen, Tuebingen, Germany
| | - Bence Sipos
- Institute of Pathology, University of Tuebingen, Tuebingen, Germany
| | - Christian Schmees
- Natural and Medical Sciences Institute (NMI) at the University of Tuebingen, Tumor Biology Group, Reutlingen, Germany
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Traenkle B, Rothbauer U. Under the Microscope: Single-Domain Antibodies for Live-Cell Imaging and Super-Resolution Microscopy. Front Immunol 2017; 8:1030. [PMID: 28883823 PMCID: PMC5573807 DOI: 10.3389/fimmu.2017.01030] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [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: 06/19/2017] [Accepted: 08/09/2017] [Indexed: 12/12/2022] Open
Abstract
Single-domain antibodies (sdAbs) have substantially expanded the possibilities of advanced cellular imaging such as live-cell or super-resolution microscopy to visualize cellular antigens and their dynamics. In addition to their unique properties including small size, high stability, and solubility in many environments, sdAbs can be efficiently functionalized according to the needs of the respective imaging approach. Genetically encoded intrabodies fused to fluorescent proteins (chromobodies) have become versatile tools to study dynamics of endogenous proteins in living cells. Additionally, sdAbs conjugated to organic dyes were shown to label cellular structures with high density and minimal fluorophore displacement making them highly attractive probes for super-resolution microscopy. Here, we review recent advances of the chromobody technology to visualize localization and dynamics of cellular targets and the application of chromobody-based cell models for compound screening. Acknowledging the emerging importance of super-resolution microscopy in cell biology, we further discuss advantages and challenges of sdAbs for this technology.
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Affiliation(s)
- Bjoern Traenkle
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen, Germany.,Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
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Maier J, Plaga T, Egetemaier S, Traenkle B, Rothbauer U. Abstract 3054: Tracing EMT with fluorescent biosensors (chromobodies) in living cancer cells. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3054] [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] [Indexed: 11/16/2022]
Abstract
Abstract
Epithelial-mesenchymal transition (EMT) is a complex cellular program, involved in the progression of epithelial cancers to a metastatic stage. During this process characteristic epithelial marker proteins are repressed in favor of mesenchymal biomarkers, such as the intermediate filament protein vimentin. There is an ongoing need for reliable cell-based EMT model systems, which can be adapted to screening campaigns for novel anti-metastatic therapies. Imaging-based screening systems are restricted to endpoint immunofluorescence studies that provide only little information about the dynamics of the process, or to ectopic expression of EMT markers, fused to fluorescent proteins. However, overexpression of EMT marker proteins, particularly vimentin, have been shown to influence the EMT phenotype of the cells.
Here we introduce chromobodies as an innovative technology to monitor EMT in living non-small lung cancer cells. Chromobodies are fluorescently-labeled single-domain-antibodies that are functional within in living cells and directly target endogenous proteins. We generated chromobodies against the EMT biomarkers vimentin, actin and β-catenin and stably introduced them into the genome of A549 cells. Upon induction of EMT with transforming growth factor β (TGF- β), we could visualize the dynamic reorganization of endogenous vimentin, actin and β-catenin in the established EMT chromobody models in 2D as well as 3D cell culture. By means of these chromobody cell lines we further developed a 2D high content analysis system to visualize and quantify spatiotemporal changes of the endogenous biomarkers vimentin and actin during the EMT process. In a proof-of-principle screen, using known EMT-affecting reagents (e.g. TGF receptor I inhibitors LY364947 and SB505124) as well as EMT-unrelated agents, we were able to show that this high content analysis system can be applied to select compounds that inhibit TGF-β-induced EMT.
In summary, live cell imaging of EMT markers with chromobodies provides a novel versatile approach to study EMT in real time and allows the identification of EMT inhibitors as potential candidates for anti-metastatic therapies by high content screening.
Citation Format: Julia Maier, Theresa Plaga, Stefanie Egetemaier, Bjoern Traenkle, Ulrich Rothbauer. Tracing EMT with fluorescent biosensors (chromobodies) in living cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3054. doi:10.1158/1538-7445.AM2017-3054
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Affiliation(s)
- Julia Maier
- University of Tuebingen, Reutlingen, Germany
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Maier J, Traenkle B, Rothbauer U. Visualizing Epithelial-Mesenchymal Transition Using the Chromobody Technology. Cancer Res 2016; 76:5592-5596. [PMID: 27634766 DOI: 10.1158/0008-5472.can-15-3419] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 06/15/2016] [Indexed: 11/16/2022]
Abstract
The epithelial-mesenchymal transition (EMT) is a complex cellular program involved in the progression of epithelial cancers to a metastatic stage. Along this process, epithelial traits are repressed in favor of a motile mesenchymal phenotype. A detailed characterization and monitoring of EMT-related processes is required for the design of screening strategies needed to develop novel antimetastatic therapies. Overexpression of the canonical EMT biomarker vimentin correlates with increased tumor growth and invasiveness, as well as with reduced patient survival across various epithelial cancers. Moreover, recent findings have demonstrated an active role of vimentin in regulating and reorganizing the cellular architecture toward a migratory and invasive phenotype. However, current studies suffer from a lack of appropriate methods to trace the induction and dynamics of vimentin in cell-based assays. Recently, we have reported a novel intrabody (chromobody)-based approach to study the spatiotemporal organization of endogenous vimentin upon induction of EMT by high-content imaging. In this review, we discuss the relevance of the chromobody technology with regard to the visualization of EMT-related processes in living systems. Cancer Res; 76(19); 5592-6. ©2016 AACR.
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Affiliation(s)
- Julia Maier
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Bjoern Traenkle
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard Karls University Tuebingen, Tuebingen, Germany. Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany.
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Buchfellner A, Yurlova L, Dennison S, Ruf B, Rothbauer U, Romer T. Abstract 2754: Antibody-based tools for in vitro and live cell analysis of endogenous PARP1, an essential human DNA repair enzyme. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2754] [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] [Indexed: 11/16/2022]
Abstract
Abstract
DNA damage caused by normal cell activity or exogenous genotoxic agents is a constant threat to the genome. The nuclear enzyme Poly(ADP-ribose) polymerase 1 (PARP1) is rapidly activated by DNA lesions such as single-strand breaks and signals their presence by attaching ADP-ribose units to chromatin-associated proteins. To improve our understanding of PARP1 within a disease context, there is an ongoing need to develop novel PARP1 detection systems.
Here we describe the development of a VHH directed against human PARP1. The variable domain of single chain antibodies (VHH or nanobody) is a versatile research tool for a variety of applications. The high binding affinity of VHHs, their small size (15 kDa) and their robust expression in various cellular systems make them preferable to conventional antibodies. Moreover, VHH domains can be selected to recognize and bind their target structures within living cells.
This highly specific PARP1 VHH was selected by phage display using a VHH library from an immunized alpaca. We characterized its affinity, selectivity and activity both in vitro and in live cells.
To validate the in vitro interactions of this PARP1-specific VHH, we developed a PARP1 immunoprecipitation reagent by conjugating the PARP1-specific VHH to an immobilizing matrix (termed PARP1-Trap). This PARP1-Trap was shown to bind with high specificity to human PARP1 and not to other members of the PARP family. Importantly, the binding of the PARP1-Trap to PARP1 leaves the enzymatic activity of PARP1 unaffected. The epitope of the PARP1-Trap was localized to the N-terminal domain of PARP1 and consists of the three-dimensional motif of zinc fingers 2 and 3 together.
To determine whether the PARP1 VHH recognizes its target structure also in a cellular environment, the VHH was genetically fused to a fluorescent protein and expressed in living cells (termed Chromobody). The interaction of the PARP1 Chromobody with PARP1 was visualized using a protein-protein interaction assay called fluorescent two-hybrid (F2H). The F2H principle is based on a tethering strategy: a GFP-tagged protein (here GFP-PARP1) is enriched at a protein interaction platform engineered into F2H-BHK cells and serves as bait, whereas the RFP-tagged PARP1 VHH serves as a prey. Using the F2H assay, we could show that the PARP1 Chromobody is functional within living cells and specifically recognizes its antigen in a cellular environment. Moreover, by monitoring the PARP1 Chromobody signal after microirradiation, we were for the first time able to follow the recruitment of endogenous PARP1 to sites of DNA damage in living cells.
In summary, we developed a novel PARP1 VHH for both biochemical and live cell analysis of human PARP1. We anticipate that PARP1-VHH based reagents will provide new insights into the PARP1 enzyme. For example, the use of the PARP1-Trap coupled with mass spectrometry analysis may lead to the identification of hitherto unknown PARP1 interaction partners.
Citation Format: Andrea Buchfellner, Larisa Yurlova, Stephanie Dennison, Benjamin Ruf, Ulrich Rothbauer, Tina Romer. Antibody-based tools for in vitro and live cell analysis of endogenous PARP1, an essential human DNA repair enzyme. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2754.
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Groll N, Petrikat T, Vetter S, Colnot S, Weiss F, Poetz O, Joos TO, Rothbauer U, Schwarz M, Braeuning A. Coordinate regulation of Cyp2e1 by β-catenin- and hepatocyte nuclear factor 1α-dependent signaling. Toxicology 2016; 350-352:40-8. [PMID: 27153753 DOI: 10.1016/j.tox.2016.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/02/2016] [Accepted: 05/02/2016] [Indexed: 01/14/2023]
Abstract
Depending on their position within the liver lobule, hepatocytes fulfill different metabolic functions. Cytochrome P450 (CYP) 2E1 is a drug-metabolizing enzyme which is exclusively expressed in hepatocytes surrounding branches of the hepatic central vein. Previous publications have shown that signaling through the Wnt/β-catenin pathway, a major determinant of liver zonation, and the hepatocyte-enriched transcription factor HNF (hepatocyte nuclear factor) 1α participate in the regulation of the gene. This study was aimed to decipher the molecular mechanisms by which the two transcription factors, β-catenin and HNF1α, jointly regulate CYP2E1 at the gene promoter level. Chromatin immunoprecipitation identified a conserved Wnt/β-catenin-responsive site (WRE) in the murine Cyp2e1 promoter adjacent to a known HNF1α response element (HNF1-RE). In vitro analyses demonstrated that both, activated β-catenin and HNF1α, are needed for the full response of the promoter. The WRE was dispensable for β-catenin-mediated effects on the Cyp2e1 promoter, while activity of β-catenin was integrated into the promoter response via the HNF1-RE. Physical interaction of β-catenin and HNF1α was demonstrated by co-immunoprecipitation. In conclusion, present data the first time identify and characterize the interplay of HNF1α and β-catenin and elucidate molecular determinants of CYP2E1 expression in the liver.
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Affiliation(s)
- Nicola Groll
- Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Tamara Petrikat
- University of Tübingen, Dept. of Toxicology, Wilhelmstr. 56, 72074 Tübingen, Germany
| | - Silvia Vetter
- University of Tübingen, Dept. of Toxicology, Wilhelmstr. 56, 72074 Tübingen, Germany
| | - Sabine Colnot
- Institut Cochin, INSERM U1016, CNRS, UMR8104, Equipe labellisée Ligue Nationale Contre le Cancer, Université Paris Descartes, 24 rue du Faubourg Saint-Jacques, 75014 Paris, France
| | - Frederik Weiss
- Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Oliver Poetz
- Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Thomas O Joos
- Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Ulrich Rothbauer
- Natural and Medical Sciences Institute at the University of Tübingen, Markwiesenstr. 55, 72770 Reutlingen, Germany
| | - Michael Schwarz
- University of Tübingen, Dept. of Toxicology, Wilhelmstr. 56, 72074 Tübingen, Germany
| | - Albert Braeuning
- University of Tübingen, Dept. of Toxicology, Wilhelmstr. 56, 72074 Tübingen, Germany; Federal Institute for Risk Assessment, Dept. Food Safety, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany.
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Schorpp K, Rothenaigner I, Maier J, Traenkle B, Rothbauer U, Hadian K. A Multiplexed High-Content Screening Approach Using the Chromobody Technology to Identify Cell Cycle Modulators in Living Cells. ACTA ACUST UNITED AC 2016; 21:965-77. [PMID: 27044685 DOI: 10.1177/1087057116641935] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 11/04/2015] [Accepted: 03/08/2016] [Indexed: 02/05/2023]
Abstract
Many screening hits show relatively poor quality regarding later efficacy and safety. Therefore, small-molecule screening efforts shift toward high-content analysis providing more detailed information. Here, we describe a novel screening approach to identify cell cycle modulators with low toxicity by combining the Cell Cycle Chromobody (CCC) technology with the CytoTox-Glo (CTG) cytotoxicity assay. The CCC technology employs intracellularly functional single-domain antibodies coupled to a fluorescent protein (chromobodies) to visualize the cell cycle-dependent redistribution of the proliferating cell nuclear antigen (PCNA) in living cells. This image-based cell cycle analysis was combined with determination of dead-cell protease activity in cell culture supernatants by the CTG assay. We adopted this multiplex approach to high-throughput format and screened 960 Food and Drug Administration (FDA)-approved drugs. By this, we identified nontoxic compounds, which modulate different cell cycle stages, and validated selected hits in diverse cell lines stably expressing CCC. Additionally, we independently validated these hits by flow cytometry as the current state-of-the-art format for cell cycle analysis. This study demonstrates that CCC imaging is a versatile high-content screening approach to identify cell cycle modulators, which can be multiplexed with cytotoxicity assays for early elimination of toxic compounds during screening.
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Affiliation(s)
- Kenji Schorpp
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
| | - Ina Rothenaigner
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
| | - Julia Maier
- Pharmaceutical Biotechnology, University of Tuebingen, Tuebingen, Germany
| | - Bjoern Traenkle
- Pharmaceutical Biotechnology, University of Tuebingen, Tuebingen, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, University of Tuebingen, Tuebingen, Germany Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Kamyar Hadian
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Bavaria, Germany
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Toulany M, Maier J, Rothbauer U, Rodemann H. OC-0238: Akt1 facilitates DNA double-strand breaks repair through a direct physical interaction with DNA-PKcs. Radiother Oncol 2016. [DOI: 10.1016/s0167-8140(16)31487-6] [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: 11/27/2022]
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Buchfellner A, Yurlova L, Nüske S, Scholz AM, Bogner J, Ruf B, Zolghadr K, Drexler SE, Drexler GA, Girst S, Greubel C, Reindl J, Siebenwirth C, Romer T, Friedl AA, Rothbauer U. A New Nanobody-Based Biosensor to Study Endogenous PARP1 In Vitro and in Live Human Cells. PLoS One 2016; 11:e0151041. [PMID: 26950694 PMCID: PMC4780744 DOI: 10.1371/journal.pone.0151041] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [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: 07/08/2015] [Accepted: 02/23/2016] [Indexed: 11/22/2022] Open
Abstract
Poly(ADP-ribose) polymerase 1 (PARP1) is a key player in DNA repair, genomic stability and cell survival and it emerges as a highly relevant target for cancer therapies. To deepen our understanding of PARP biology and mechanisms of action of PARP1-targeting anti-cancer compounds, we generated a novel PARP1-affinity reagent, active both in vitro and in live cells. This PARP1-biosensor is based on a PARP1-specific single-domain antibody fragment (~ 15 kDa), termed nanobody, which recognizes the N-terminus of human PARP1 with nanomolar affinity. In proteomic approaches, immobilized PARP1 nanobody facilitates quantitative immunoprecipitation of functional, endogenous PARP1 from cellular lysates. For cellular studies, we engineered an intracellularly functional PARP1 chromobody by combining the nanobody coding sequence with a fluorescent protein sequence. By following the chromobody signal, we were for the first time able to monitor the recruitment of endogenous PARP1 to DNA damage sites in live cells. Moreover, tracing of the sub-nuclear translocation of the chromobody signal upon treatment of human cells with chemical substances enables real-time profiling of active compounds in high content imaging. Due to its ability to perform as a biosensor at the endogenous level of the PARP1 enzyme, the novel PARP1 nanobody is a unique and versatile tool for basic and applied studies of PARP1 biology and DNA repair.
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Affiliation(s)
| | | | - Stefan Nüske
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig Maximilians University, Munich, Germany
| | - Armin M. Scholz
- Livestock Center of the Faculty of Veterinary Medicine, Ludwig Maximilians University, Munich, Germany
| | | | - Benjamin Ruf
- ChromoTek GmbH, IZB, Planegg, Martinsried, Germany
| | | | - Sophie E. Drexler
- Department of Radiation Oncology, Ludwig Maximilians University, Munich, Germany
| | - Guido A. Drexler
- Department of Radiation Oncology, Ludwig Maximilians University, Munich, Germany
| | - Stefanie Girst
- Institute for Applied Physics and Metrology, Bundeswehr University Munich, Neubiberg, Germany
| | - Christoph Greubel
- Institute for Applied Physics and Metrology, Bundeswehr University Munich, Neubiberg, Germany
| | - Judith Reindl
- Institute for Applied Physics and Metrology, Bundeswehr University Munich, Neubiberg, Germany
| | - Christian Siebenwirth
- Department of Radiation Oncology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Tina Romer
- ChromoTek GmbH, IZB, Planegg, Martinsried, Germany
- * E-mail:
| | - Anna A. Friedl
- Department of Radiation Oncology, Ludwig Maximilians University, Munich, Germany
- Clinical Cooperation Group ‘Personalized Radiotherapy of Head and Neck Cancer’, Helmholtz Center Munich, Neuherberg, Germany
| | - Ulrich Rothbauer
- Natural and Medical Institute at the University of Tuebingen, Reutlingen, Germany
- Pharmaceutical Biotechnology, University of Tuebingen, Tuebingen, Germany
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Rajan M, Mortusewicz O, Rothbauer U, Hastert FD, Schmidthals K, Rapp A, Leonhardt H, Cardoso MC. Generation of an alpaca-derived nanobody recognizing γ-H2AX. FEBS Open Bio 2015; 5:779-88. [PMID: 26500838 PMCID: PMC4588710 DOI: 10.1016/j.fob.2015.09.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 07/11/2015] [Revised: 09/09/2015] [Accepted: 09/16/2015] [Indexed: 12/31/2022] Open
Abstract
Post-translational modifications are difficult to visualize in living cells and are conveniently analyzed using antibodies. Single-chain antibody fragments derived from alpacas and called nanobodies can be expressed and bind to the target antigenic sites in living cells. As a proof of concept, we generated and characterized nanobodies against the commonly used biomarker for DNA double strand breaks γ-H2AX. In vitro and in vivo characterization showed the specificity of the γ-H2AX nanobody. Mammalian cells were transfected with fluorescent fusions called chromobodies and DNA breaks induced by laser microirradiation. We found that alternative epitope recognition and masking of the epitope in living cells compromised the chromobody function. These pitfalls should be considered in the future development and screening of intracellular antibody biomarkers.
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Key Words
- Alpaca heavy chain antibodies
- CKM, casein kinase 2 mutant
- Chromobodies
- DNA repair
- ELISA, enzyme linked immunosorbent assay
- FRAP, fluorescence recovery after photobleaching
- GFP, green fluorescent protein
- H2AX, histone H2AX
- HEK293, human embryonic kidney 293 cells
- KLH, keyhole limpet hemocyanin
- Laser microirradiation
- Live cell microscopy
- MDC1, mediator of DNA damage checkpoint-1
- MEF, mouse embryonic fibroblast
- Post-translational modifications
- RFP, red fluorescent protein
- VHH, variable domain of heavy-chain antibody
- XRCC1, X-ray repair cross-complementing protein 1
- siRNA, short interfering RNA
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Affiliation(s)
- Malini Rajan
- Department of Biology, Technische Universitaet Darmstadt, Germany
| | - Oliver Mortusewicz
- Biozentrum, Department of Biology II, Ludwig Maximilians Universitaet Munich, Germany
| | - Ulrich Rothbauer
- Pharmaceutical Biotechnology, Eberhard-Karls University Tuebingen, Germany
| | | | | | - Alexander Rapp
- Department of Biology, Technische Universitaet Darmstadt, Germany
| | - Heinrich Leonhardt
- Biozentrum, Department of Biology II, Ludwig Maximilians Universitaet Munich, Germany
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Abstract
Chromobodies are intracellular nanoprobes that combine the specificity of antibodies with the convenience of live fluorescence imaging in a flexible, DNA-encoded reagent. Here, we present the first application of this technique to an intact living vertebrate organism. We generated zebrafish lines expressing chromobodies that trace the major cytoskeletal component actin and the cell cycle marker PCNA with spatial and temporal specificity. Using these chromobodies, we captured full localization dynamics of the endogenous antigens in different cell types and at different stages of development. For the first time, the chromobody technology enables live imaging of endogenous subcellular structures in an animal, with the remarkable advantage of avoiding target protein overexpression or tagging. In combination with improved chromobody selection systems, we anticipate a rapid adaptation of this technique to new intracellular antigens and model organisms, allowing the faithful description of cellular and molecular processes in their dynamic state. SUMMARY: Chromobodies - small, intracellular fluorescent antibodies - are used to trace endogenous antigens, without the need for direct protein tagging, in zebrafish embryos.
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Affiliation(s)
- Paolo Panza
- Max-Planck-Institut für Entwicklungsbiologie, Abteilung Genetik, Spemannstraße 35, Tübingen 72076, Germany
| | - Julia Maier
- Naturwissenschaftliches und Medizinisches Institut der Universität Tübingen, Markwiesenstraße 55, Reutlingen 72770, Germany Pharmazeutische Biotechnologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Christian Schmees
- Naturwissenschaftliches und Medizinisches Institut der Universität Tübingen, Markwiesenstraße 55, Reutlingen 72770, Germany
| | - Ulrich Rothbauer
- Naturwissenschaftliches und Medizinisches Institut der Universität Tübingen, Markwiesenstraße 55, Reutlingen 72770, Germany Pharmazeutische Biotechnologie, Eberhard Karls Universität Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
| | - Christian Söllner
- Max-Planck-Institut für Entwicklungsbiologie, Abteilung Genetik, Spemannstraße 35, Tübingen 72076, Germany
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Groll N, Emele F, Poetz O, Rothbauer U. Towards multiplexed protein-protein interaction analysis using protein tag-specific nanobodies. J Proteomics 2015; 127:289-99. [PMID: 25937269 DOI: 10.1016/j.jprot.2015.04.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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: 01/31/2015] [Revised: 03/27/2015] [Accepted: 04/14/2015] [Indexed: 01/28/2023]
Abstract
UNLABELLED Dynamic protein-protein interactions (PPIs) are an integral part of cellular processes. The discovery of modulators that disrupt or stabilize such interactions is highly important to understand PPIs and address correlating diseases. Bead-based protein assays analyzing PPIs between bait- and prey-proteins exemplify emerging methodologies. To date, most studies employ purified bait-proteins from bacteria. Such proteins are of limited use as they do not undergo eukaryotic folding and lack posttranslational modifications. Here, we present a novel method to generate bead-based protein arrays combining μ-scale purification of bait-proteins combined with site-directed immobilization. First, we express individual bait-proteins as GST- or GFP-fusion constructs in bacterial and mammalian cells. Next, we purify and immobilize these bait-proteins from crude lysates using high affinity tag-specific nanobodies coupled to color-coded beads. Finally, we combined those bait-coupled beads in a protein-array for miniaturized multiplexed GST- and GFP pulldown studies. In a proof-of-principle we study dynamic changes of the endogenous prey-protein β-catenin following proteasomal inhibition or signaling pathway perturbation. Our strategy enables a fast isolation of highly pure and stable bait-proteins derived from small-scale expression cultures. We propose that this approach enables the generation of bead-based protein arrays comprising hundreds of bait-proteins from different expression systems to study complex PPIs. BIOLOGICAL SIGNIFICANCE Protein arrays and multiplexed sandwich immunoassays, are widely applied to study protein-protein interaction or to investigate the signaling status of stimulated cells. This study describes for the first time the application of tag-specific nanobodies for site directed immobilization of bait-proteins from different expression systems to generate bead based protein arrays. The analysis of the Wnt-pathway activation by multiplexed μ-scale pulldowns demonstrated the advantages of eukaryotic expression systems regarding the stability and binding properties of individual bait proteins. This article is part of a Special Issue entitled: HUPO 2014.
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Affiliation(s)
- Nicola Groll
- Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany
| | - Felix Emele
- Pharmaceutical Biotechnology, Eberhard Karls University, Tuebingen, Germany
| | - Oliver Poetz
- Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany.
| | - Ulrich Rothbauer
- Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany; Pharmaceutical Biotechnology, Eberhard Karls University, Tuebingen, Germany.
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Muth F, Günther M, Bauer SM, Döring E, Fischer S, Maier J, Drückes P, Köppler J, Trappe J, Rothbauer U, Koch P, Laufer SA. Correction to Tetra-Substituted Pyridinylimidazoles As Dual Inhibitors of p38α Mitogen-Activated Protein Kinase and c-Jun N-Terminal Kinase 3 for Potential Treatment of Neurodegenerative Diseases. J Med Chem 2015; 58:2567. [DOI: 10.1021/acs.jmedchem.5b00235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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