1
|
van Rijswijck DMH, Bondt A, de Kat N, Lood R, Heck AJR. Direct Comparison of the Hinge-Cleaving Proteases IgdE and BdpK for LC-MS-Based IgG1 Clonal Profiling. Anal Chem 2024; 96:23-27. [PMID: 38105593 PMCID: PMC10782413 DOI: 10.1021/acs.analchem.3c03712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/19/2023]
Abstract
Human antibodies are heterogeneous molecules primarily due to clonal sequence variations. Analytical techniques to assess antibody levels quantitatively, such as ELISA, lack the power to resolve abundances at the clonal level. Recently, we introduced an LC-MS-based approach that can distinguish and quantify antibody clones using the mass and retention time of their corresponding Fab-fragments. We used specific hinge-cleaving protease IgdE (FabALACTICA) to release the Fab-fragments from the constant Fc region of the antibody. Here, we explore an alternative IgG1 hinge-cleaving protease, BdpK (FabDELLO), and compare it directly to IgdE for use in IgG1 repertoire profiling. We used IgdE and BdpK in parallel to digest all IgG1s from the same set of plasma samples. Both proteases cleave IgG1 specifically in the hinge, albeit via different mechanisms and at two distinct cleavage sites. Notwithstanding these differences, the Fab fragments generated by IgdE or BdpK produced highly similar clonal repertoires. However, IgdE required ∼16 h of incubation to digest plasma IgG1s, while BdpK required ∼2 h. We authenticated the similarity of the clones by top-down proteomics using electron transfer dissociation. We conclude that BdpK performs very well in digesting polyclonal plasma IgG1s and that neither BdpK nor IgdE displays detectable biases in cleaving IgG1s. We anticipate that BdpK may emerge as the preferred protease for IgG1 hinge-digestion because it offers a shorter digestion time compared to IgdE, an equally specific digestion site, and no bias against any IgG1 present in plasma.
Collapse
Affiliation(s)
- Danique M H van Rijswijck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Albert Bondt
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Naomi de Kat
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| | - Rolf Lood
- Genovis AB, Scheelevägen 2, 223 63 Lund, Sweden
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, Utrecht 3584 CH, The Netherlands
- Netherlands Proteomics Center, Padualaan 8, Utrecht 3584 CH, The Netherlands
| |
Collapse
|
2
|
Blöchl C, Gstöttner C, Sénard T, Stork EM, Scherer HU, Toes REM, Wuhrer M, Domínguez-Vega E. A robust nanoscale RP HPLC-MS approach for sensitive Fc proteoform profiling of IgG allotypes. Anal Chim Acta 2023; 1279:341795. [PMID: 37827688 DOI: 10.1016/j.aca.2023.341795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/30/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023]
Abstract
The conserved region (Fc) of IgG antibodies dictates the interactions with designated receptors thus defining the immunological effector functions of IgG. Amino acid sequence variations in the Fc, recognized as subclasses and allotypes, as well as post-translational modifications (PTMs) modulate these interactions. Yet, the high similarity of Fc sequences hinders allotype-specific PTM analysis by state-of-the-art bottom-up methods and current subunit approaches lack sensitivity and face co-elution of near-isobaric allotypes. To circumvent these shortcomings, we present a nanoscale reversed-phase (RP) HPLC-MS workflow of intact Fc subunits for comprehensive characterization of Fc proteoforms in an allotype- and subclass-specific manner. Polyclonal IgGs were purified from individuals followed by enzymatic digestion releasing single chain Fc subunits (Fc/2) that were directly subjected to analysis. Chromatographic conditions were optimized to separate Fc/2 subunits of near-isobaric allotypes and subclasses allowing allotype and proteoform identification and quantification across all four IgG subclasses. The workflow was complemented by a semi-automated data analysis pipeline based on the open-source software Skyline followed by post-processing in R. The approach revealed pronounced differences in Fc glycosylation between donors, besides inter-subclass and inter-allotype variability within donors. Notably, partial occupancy of the N-glycosylation site in the CH3 domain of IgG3 was observed that is generally neglected by established approaches. The described method was benchmarked across several hundred runs and showed good precision and robustness. This methodology represents a first mature Fc subunit profiling approach allowing truly subclass- and allotype-specific Fc proteoform characterization beyond established approaches. The comprehensive information obtained paired with the high sensitivity provided by the miniaturization of the approach guarantees applicability to a broad range of research questions including clinically relevant (auto)antibody characterization or pharmacokinetics assessment of therapeutic IgGs.
Collapse
Affiliation(s)
- Constantin Blöchl
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, the Netherlands
| | - Christoph Gstöttner
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, the Netherlands
| | - Thomas Sénard
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, the Netherlands
| | - Eva Maria Stork
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, the Netherlands
| | - Hans Ulrich Scherer
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, the Netherlands
| | - Rene E M Toes
- Department of Rheumatology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, the Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, the Netherlands
| | - Elena Domínguez-Vega
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, the Netherlands.
| |
Collapse
|
3
|
Holzner C, Böttinger K, Blöchl C, Huber CG, Dahms SO, Dall E, Brandstetter H. Legumain Functions as a Transient TrkB Sheddase. Int J Mol Sci 2023; 24:ijms24065394. [PMID: 36982466 PMCID: PMC10049731 DOI: 10.3390/ijms24065394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
While primarily found in endo-lysosomal compartments, the cysteine protease legumain can also translocate to the cell surface if stabilized by the interaction with the RGD-dependent integrin receptor αVβ3. Previously, it has been shown that legumain expression is inversely related to BDNF-TrkB activity. Here we show that legumain can conversely act on TrkB-BDNF by processing the C-terminal linker region of the TrkB ectodomain in vitro. Importantly, when in complex with BDNF, TrkB was not cleaved by legumain. Legumain-processed TrkB was still able to bind BDNF, suggesting a potential scavenger function of soluble TrkB towards BDNF. The work thus presents another mechanistic link explaining the reciprocal TrkB signaling and δ-secretase activity of legumain, with relevance for neurodegeneration.
Collapse
|
4
|
Alhayek A, Abdelsamie AS, Schönauer E, Camberlein V, Hutterer E, Posselt G, Serwanja J, Blöchl C, Huber CG, Haupenthal J, Brandstetter H, Wessler S, Hirsch AKH. Discovery and Characterization of Synthesized and FDA-Approved Inhibitors of Clostridial and Bacillary Collagenases. J Med Chem 2022; 65:12933-12955. [PMID: 36154055 PMCID: PMC9574867 DOI: 10.1021/acs.jmedchem.2c00785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Indexed: 12/04/2022]
Abstract
In view of the worldwide antimicrobial resistance (AMR) threat, new bacterial targets and anti-infective agents are needed. Since important roles in bacterial pathogenesis have been demonstrated for the collagenase H and G (ColH and ColG) from Clostridium histolyticum, collagenase Q1 and A (ColQ1 and ColA) from Bacillus cereus represent attractive antivirulence targets. Furthermore, repurposing FDA-approved drugs may assist to tackle the AMR crisis and was addressed in this work. Here, we report on the discovery of two potent and chemically stable bacterial collagenase inhibitors: synthesized and FDA-approved diphosphonates and hydroxamates. Both classes showed high in vitro activity against the clostridial and bacillary collagenases. The potent diphosphonates reduced B. cereus-mediated detachment and death of cells and Galleria mellonella larvae. The hydroxamates were also tested in a similar manner; they did not have an effect in infection models. This might be due to their fast binding kinetics to bacterial collagenases.
Collapse
Affiliation(s)
- Alaa Alhayek
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
- Department
of Pharmacy, Saarland University, Campus Building C2. 3, 66123 Saarbrücken, Germany
| | - Ahmed S. Abdelsamie
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
- Department
of Chemistry of Natural and Microbial Products, Institute of Pharmaceutical and Drug Industries Research, National
Research Centre, El-Buhouth
St., Dokki, 12622 Cairo, Egypt
| | - Esther Schönauer
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Virgyl Camberlein
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Evelyn Hutterer
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Gernot Posselt
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Jamil Serwanja
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Constantin Blöchl
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Christian G. Huber
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Jörg Haupenthal
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
| | - Hans Brandstetter
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Silja Wessler
- Department
of Biosciences and Medical Biology, University
of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Anna K. H. Hirsch
- Helmholtz
Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI), Campus Building E8.1, 66123 Saarbrücken, Germany
- Department
of Pharmacy, Saarland University, Campus Building C2. 3, 66123 Saarbrücken, Germany
| |
Collapse
|
5
|
Ramírez-Larrota JS, Eckhard U. An Introduction to Bacterial Biofilms and Their Proteases, and Their Roles in Host Infection and Immune Evasion. Biomolecules 2022; 12:306. [PMID: 35204806 PMCID: PMC8869686 DOI: 10.3390/biom12020306] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/03/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
Bacterial biofilms represent multicellular communities embedded in a matrix of extracellular polymeric substances, conveying increased resistance against environmental stress factors but also antibiotics. They are shaped by secreted enzymes such as proteases, which can aid pathogenicity by degrading host proteins of the connective tissue or the immune system. Importantly, both secreted proteases and the capability of biofilm formation are considered key virulence factors. In this review, we focus on the basic aspects of proteolysis and protein secretion, and highlight various secreted bacterial proteases involved in biofilm establishment and dispersal, and how they aid bacteria in immune evasion by degrading immunoglobulins and components of the complement system. Thus, secreted proteases represent not only prominent antimicrobial targets but also enzymes that can be used for dedicated applications in biotechnology and biomedicine, including their use as laundry detergents, in mass spectrometry for the glycoprofiling of antibodies, and the desensitization of donor organs intended for positive crossmatch patients.
Collapse
Affiliation(s)
| | - Ulrich Eckhard
- Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Baldiri Reixac, 15-21, 08028 Barcelona, Spain;
| |
Collapse
|
6
|
Proteolytic Profiling of Streptococcal Pyrogenic Exotoxin B (SpeB) by Complementary HPLC-MS Approaches. Int J Mol Sci 2021; 23:ijms23010412. [PMID: 35008838 PMCID: PMC8745752 DOI: 10.3390/ijms23010412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 01/25/2023] Open
Abstract
Streptococcal pyrogenic exotoxin B (SpeB) is a cysteine protease expressed during group A streptococcal infection that represents a major virulence factor. Although subject to several studies, its role during infection is still under debate, and its proteolytic properties remain insufficiently characterized. Here, we revisited this protease through a set of complementary approaches relying on state of-the-art HPLC-MS methods. After conceiving an efficient protocol to recombinantly express SpeB, the zymogen of the protease and its activation were characterized. Employing proteome-derived peptide libraries, a strong preference for hydrophobic and aromatic residues at P2 alongside negatively charged amino acids at P3′ to P6′ was revealed. To identify relevant in vivo substrates, native proteins were obtained from monocytic secretome and plasma to assess their cleavage under physiological conditions. Besides corroborating our findings concerning specificity, more than 200 cleaved proteins were identified, including proteins of the extracellular matrix, proteins of the immune system, and proteins involved in inflammation. Finally, the cleavage of IgG subclasses was studied in detail. This study precisely depicts the proteolytic properties of SpeB and provides a library of potential host substrates, including their exact cleavage positions, as a valuable source for further research to unravel the role of SpeB during streptococcal infection.
Collapse
|
7
|
Morgan TE, Jakes C, Brouwer HJ, Millán-Martín S, Chervet JP, Cook K, Carillo S, Bones J. Inline electrochemical reduction of NISTmAb for middle-up subunit liquid chromatography-mass spectrometry analysis. Analyst 2021; 146:6547-6555. [PMID: 34585175 DOI: 10.1039/d1an01184g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Disulfide bond reduction within antibody mass spectrometry workflows is typically carried out using chemical reducing agents to produce antibody subunits for middle-down and middle-up analysis. In this contribution we offer an online electrochemical reduction method for the reduction of antibodies coupled with liquid chromatography (LC) and mass spectrometry (MS), reducing the disulfide bonds present in the antibody without the need for chemical reducing agents. An electrochemical cell placed before the analytical column and mass spectrometer facilitated complete reduction of NISTmAb inter- and intrachain disulfide bonds. Reduction and analysis were carried out under optimal solvent conditions using a trapping column and switching valve to facilitate solvent exchange during analysis. The level of reduction was shown to be affected by electrochemical potential, temperature and solvent organic content, but with optimization, complete disulfide bond cleavage was achieved. The use of an inline electrochemical cell offers a simple, rapid, workflow solution for liquid chromatography mass spectrometry analysis of antibody subunits.
Collapse
Affiliation(s)
- Tomos E Morgan
- Characterisation and Comparability Laboratory, NIBRT - the National Institute for bioprocessing research and training, Foster Avenue, Mount Merrion, Blackrock, Co., Dublin, A94 X099, Ireland.
| | - Craig Jakes
- Characterisation and Comparability Laboratory, NIBRT - the National Institute for bioprocessing research and training, Foster Avenue, Mount Merrion, Blackrock, Co., Dublin, A94 X099, Ireland. .,School of Chemical Engineering and Bioprocessing, University College of Dublin, Belfield, Dublin 4, Ireland
| | | | - Silvia Millán-Martín
- Characterisation and Comparability Laboratory, NIBRT - the National Institute for bioprocessing research and training, Foster Avenue, Mount Merrion, Blackrock, Co., Dublin, A94 X099, Ireland.
| | | | - Ken Cook
- Thermo Fisher Scientific, Hemel Hempstead, Herts, HP2 7GE, UK
| | - Sara Carillo
- Characterisation and Comparability Laboratory, NIBRT - the National Institute for bioprocessing research and training, Foster Avenue, Mount Merrion, Blackrock, Co., Dublin, A94 X099, Ireland.
| | - Jonathan Bones
- Characterisation and Comparability Laboratory, NIBRT - the National Institute for bioprocessing research and training, Foster Avenue, Mount Merrion, Blackrock, Co., Dublin, A94 X099, Ireland. .,School of Chemical Engineering and Bioprocessing, University College of Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|