1
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Benazza R, Koutsopetras I, Vaur V, Chaubet G, Hernandez-Alba O, Cianférani S. SEC-MS in denaturing conditions (dSEC-MS) for in-depth analysis of rebridged monoclonal antibody-based formats. Talanta 2024; 272:125727. [PMID: 38364570 DOI: 10.1016/j.talanta.2024.125727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/04/2023] [Accepted: 01/27/2024] [Indexed: 02/18/2024]
Abstract
Disulfide rebridging methods are emerging recently as new ways to specifically modify antibody-based entities and produce future conjugates. Briefly, the solvent-accessible disulfide bonds of antibodies or antigen-binding fragments (Fab) thereof are reduced under controlled conditions and further covalently attached with a rebridging agent allowing the incorporation of one payload per disulfide bond. There are many examples of successful rebridging cases providing homogeneous conjugates due to the use of symmetrical reagents, such as dibromomaleimides. However, partial rebridging due to the use of unsymmetrical ones, containing functional groups with different reactivity, usually leads to the development of heterogeneous species that cannot be identified by a simple sodium dodecyl sulfate-polyacrylamide gel eletrophoresis (SDS-PAGE) due to its lack of sensitivity, resolution and low mass accuracy. Mass spectrometry coupled to liquid chromatography (LC-MS) approaches have already been demonstrated as highly promising alternatives for the characterization of newly developed antibody-drug-conjugate (ADC) and monoclonal antibody (mAb)-based formats. We report here the in-depth characterization of covalently rebridged antibodies and Fab fragments in-development, using size-exclusion chromatography hyphenated to mass spectrometry in denaturing conditions (denaturing SEC-MS, dSEC-MS). DSEC-MS was used to monitor closely the rebridging reaction of a conjugated trastuzumab, in addition to conjugated Fab fragments, which allowed an unambiguous identification of the covalently rebridged products along with the unbound species. This all-in-one approach allowed a straightforward analysis of the studied samples with precise mass measurement; critical quality attributes (CQAs) assessment along with rebridging efficiency determination.
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Affiliation(s)
- Rania Benazza
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI-FR2048, 67087 Strasbourg, France
| | - Ilias Koutsopetras
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Valentine Vaur
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI-FR2048, 67087 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI-FR2048, 67087 Strasbourg, France.
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2
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Gizardin-Fredon H, Santo PE, Chagot ME, Charpentier B, Bandeiras TM, Manival X, Hernandez-Alba O, Cianférani S. Denaturing mass photometry for rapid optimization of chemical protein-protein cross-linking reactions. Nat Commun 2024; 15:3516. [PMID: 38664367 PMCID: PMC11045720 DOI: 10.1038/s41467-024-47732-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Chemical cross-linking reactions (XL) are an important strategy for studying protein-protein interactions (PPIs), including low abundant sub-complexes, in structural biology. However, choosing XL reagents and conditions is laborious and mostly limited to analysis of protein assemblies that can be resolved using SDS-PAGE. To overcome these limitations, we develop here a denaturing mass photometry (dMP) method for fast, reliable and user-friendly optimization and monitoring of chemical XL reactions. The dMP is a robust 2-step protocol that ensures 95% of irreversible denaturation within only 5 min. We show that dMP provides accurate mass identification across a broad mass range (30 kDa-5 MDa) along with direct label-free relative quantification of all coexisting XL species (sub-complexes and aggregates). We compare dMP with SDS-PAGE and observe that, unlike the benchmark, dMP is time-efficient (3 min/triplicate), requires significantly less material (20-100×) and affords single molecule sensitivity. To illustrate its utility for routine structural biology applications, we show that dMP affords screening of 20 XL conditions in 1 h, accurately identifying and quantifying all coexisting species. Taken together, we anticipate that dMP will have an impact on ability to structurally characterize more PPIs and macromolecular assemblies, expected final complexes but also sub-complexes that form en route.
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Affiliation(s)
- Hugo Gizardin-Fredon
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Paulo E Santo
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | | | | | - Tiago M Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157, Oeiras, Portugal
| | | | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg, France.
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France.
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3
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Iacobucci I, Monaco V, Hovasse A, Dupouy B, Keumoe R, Cichocki B, Elhabiri M, Meunier B, Strub JM, Monti M, Cianférani S, Blandin SA, Schaeffer-Reiss C, Davioud-Charvet E. Proteomic Profiling of Antimalarial Plasmodione Using 3-Benz(o)ylmenadione Affinity-Based Probes. Chembiochem 2024:e202400187. [PMID: 38639212 DOI: 10.1002/cbic.202400187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/20/2024]
Abstract
Understanding the mechanisms of drug action in malarial parasites is crucial for the development of new drugs to combat infection and to counteract drug resistance. Proteomics is a widely used approach to study host-pathogen systems and to identify drug protein targets. Plasmodione is an antiplasmodial early-lead drug exerting potent activities against young asexual and sexual blood stages in vitro with low toxicity to host cells. To elucidate its molecular mechanisms, an affinity-based protein profiling (AfBPP) approach was applied to yeast and P. falciparum proteomes. New (pro-)AfBPP probes based on the 3-benz(o)yl-6-fluoro-menadione scaffold were synthesized. With optimized conditions of both photoaffinity labeling and click reaction steps, the AfBPP protocol was then applied to a yeast proteome, yielding 11 putative drug-protein targets. Among these, we found four proteins associated with oxidoreductase activities, the hypothesized type of targets for plasmodione and its metabolites, and other proteins associated with the mitochondria. In Plasmodium parasites, the MS analysis revealed 44 potential plasmodione targets that need to be validated in further studies. Finally, the localization of a 3-benzyl-6-fluoromenadione AfBPP probe was studied in the subcellular structures of the parasite at the trophozoite stage.
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Affiliation(s)
- Ilaria Iacobucci
- National Centre for Scientific Research, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, Strasbourg, FRANCE
| | - Vittoria Monaco
- National Centre for Scientific Research, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, Strasbourg, FRANCE
| | - Agnès Hovasse
- National Centre for Scientific Research, IPHC UMR 7178 CNRS, Université de Strasbourg, Strasbourg, FRANCE
| | - Baptiste Dupouy
- National Centre for Scientific Research, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, Strasbourg, FRANCE
| | - Rodrigue Keumoe
- National Centre for Scientific Research, INSERM U1257 - CNRS UPR9022 - Université de Strasbourg, Strasbourg, FRANCE
| | - Bogdan Cichocki
- National Centre for Scientific Research, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, Strasbourg, FRANCE
| | - Mourad Elhabiri
- National Centre for Scientific Research, UMR7042 CNRS-Université de Strasbourg-Université Haute-Alsace, Strasbourg, FRANCE
| | - Brigitte Meunier
- National Centre for Scientific Research, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, FRANCE
| | - Jean-Marc Strub
- National Centre for Scientific Research, IPHC UMR 7178 CNRS, Université de Strasbourg, Strasbourg, FRANCE
| | - Maria Monti
- University of Naples Federico II, Department of Chemical Sciences, Naples, ITALY
| | - Sarah Cianférani
- National Centre for Scientific Research, IPHC UMR 7178 CNRS, Université de Strasbourg, Strasbourg, FRANCE
| | - Stéphanie A Blandin
- National Centre for Scientific Research, INSERM U1257 - CNRS UPR9022 - Université de Strasbourg, Strasbourg, FRANCE
| | - Christine Schaeffer-Reiss
- National Centre for Scientific Research, IPHC UMR 7178 CNRS, Université de Strasbourg, Strasbourg, FRANCE
| | - Elisabeth Davioud-Charvet
- Centre National de la Recherche Scientifique and Strasbourg University, European School of Chemistry, Polymers and Materials ECPM , UMR CNRS 7509,, 25, rue Becquerel, 67087, Strasbourg, FRANCE
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4
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Rady T, Erb S, Deddouche-Grass S, Morales R, Chaubet G, Cianférani S, Basse N, Wagner A. Targeted delivery of immune-stimulating bispecific RNA, inducing apoptosis and anti-tumor immunity in cancer cells. iScience 2024; 27:109068. [PMID: 38380254 PMCID: PMC10877685 DOI: 10.1016/j.isci.2024.109068] [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: 01/26/2023] [Revised: 07/18/2023] [Accepted: 01/25/2024] [Indexed: 02/22/2024] Open
Abstract
Double-stranded RNAs (dsRNA)-based strategies appeared as promising therapies to induce an inflammation in the tumor microenvironment. However, currently described systems generally lack active targeting of tissues, and their clinical translation is thus limited to intratumoral injection. Herein, we developed an antibody-siRNA-5'triphosphate conjugate with multiple modes of action, combining cell surface EphA2-specific internalization, leading to a simultaneous gene silencing and activation of the receptor retinoic acid-inducible gene I (RIG-I). Recognition of cytosolic siRNA-5'triphosphate by RIG-I triggers the expression of interferons and pro-inflammatory cytokines, inducing an inflammation of the tumor environment and activating neighboring immune cells. In addition, these RIG-I-specific effects synergized with siRNA-mediated PLK1 silencing to promote cancer cell death by apoptosis. Altogether, such immune-stimulating antibody-RNA conjugate opens a novel modality to overcome some limitations encountered by dsRNA molecules currently in clinical trials.
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Affiliation(s)
- Tony Rady
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
- Sanofi, 13 Quai Jules Guesde, 94400 Vitry-sur-Seine, France
| | - Stéphane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR2048, 67087 Strasbourg, France
| | | | - Renaud Morales
- Sanofi, 13 Quai Jules Guesde, 94400 Vitry-sur-Seine, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR2048, 67087 Strasbourg, France
| | - Nicolas Basse
- Sanofi, 13 Quai Jules Guesde, 94400 Vitry-sur-Seine, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
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Becharguia N, Nierengarten I, Strub JM, Cianférani S, Rémy M, Wasielewski E, Abidi R, Nierengarten JF. Solution and Solvent-Free Stopper Exchange Reactions for the Preparation of Pillar[5]arene-containing [2] and [3]Rotaxanes. Chemistry 2024; 30:e202304131. [PMID: 38165139 DOI: 10.1002/chem.202304131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/03/2024]
Abstract
Diamine reagents have been used to functionalize a [2]rotaxane building block bearing an activated pentafluorophenyl ester stopper. Upon a first acylation, an intermediate host-guest complex with a terminal amine function is obtained. Dissociation of the intermediate occurs in solution and acylation of the released axle generates a [2]rotaxane with an elongated axle subunit. In contrast, the corresponding [3]rotaxane can be obtained if the reaction conditions are appropriate to stabilize the inclusion complex of the mono-amine intermediate and the pillar[5]arene. This is the case when the stopper exchange is performed under mechanochemical solvent-free conditions. Alternatively, if the newly introduced terminal amide group is large enough to prevent the dissociation, the second acylation provides exclusively a [3]rotaxane. On the other hand, detailed conformational analysis has been also carried out by variable temperature NMR investigations. A complete understanding of the shuttling motions of the pillar[5]arene subunit along the axles of the rotaxanes reported therein has been achieved with the help of density functional theory calculations.
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Affiliation(s)
- Nihed Becharguia
- Laboratoire de Chimie des Matériaux Moléculaires, Université de Strasbourg et CNRS (UMR 7042, LIMA), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
- Laboratoire d'Applications de la Chimie aux Ressources et Substances Naturelles et l'Environnement, Faculté des Sciences de Bizerte, Université de Carthage, 7021, Zarzouna Bizerte, Tunisia
| | - Iwona Nierengarten
- Laboratoire de Chimie des Matériaux Moléculaires, Université de Strasbourg et CNRS (UMR 7042, LIMA), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
| | - Jean-Marc Strub
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg et CNRS (UMR 7178, IPHC), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg et CNRS (UMR 7178, IPHC), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
| | - Marine Rémy
- Laboratoire de Chimie des Matériaux Moléculaires, Université de Strasbourg et CNRS (UMR 7042, LIMA), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
| | - Emeric Wasielewski
- Plateforme RMN Cronenbourg, Université de Strasbourg et CNRS (UMR 7042, LIMA) Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
| | - Rym Abidi
- Laboratoire d'Applications de la Chimie aux Ressources et Substances Naturelles et l'Environnement, Faculté des Sciences de Bizerte, Université de Carthage, 7021, Zarzouna Bizerte, Tunisia
| | - Jean-François Nierengarten
- Laboratoire de Chimie des Matériaux Moléculaires, Université de Strasbourg et CNRS (UMR 7042, LIMA), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
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6
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Becharguia N, Nierengarten I, Strub JM, Cianférani S, Rémy M, Wasielewski E, Abidi R, Nierengarten JF. Solution and Solvent-Free Stopper Exchange Reactions for the Preparation of Pillar[5]arene-Containing [2] and [3]Rotaxanes. Chemistry 2024; 30:e202400246. [PMID: 38295139 DOI: 10.1002/chem.202400246] [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: 02/02/2024]
Abstract
Invited for the cover of this issue are the group of Iwona and Jean-François Nierengarten from the University of Strasbourg (LIMA, UMR 7042, CNRS) and collaborators from the University of Carthage and the IPHC (University of Strasbourg and CNRS, UMR 7178). The image illustrates the fast motions of a pillar[5]arene subunit along the axle of a rotaxane, reminiscent of those of a guitarist's hand along the neck allowing him to use random parts of a scale with certain sweet spots when improvising a solo. Read the full text of the article at 10.1002/chem.202304131.
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Affiliation(s)
- Nihed Becharguia
- Laboratoire de Chimie des Matériaux Moléculaires, Université de Strasbourg et CNRS (UMR 7042, LIMA), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
- Laboratoire d'Applications de la Chimie aux Ressources et Substances Naturelles et l'Environnement, Faculté des Sciences de Bizerte, Université de Carthage, 7021, Zarzouna Bizerte, Tunisia
| | - Iwona Nierengarten
- Laboratoire de Chimie des Matériaux Moléculaires, Université de Strasbourg et CNRS (UMR 7042, LIMA), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
| | - Jean-Marc Strub
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg et CNRS (UMR 7178, IPHC), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg et CNRS (UMR 7178, IPHC), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
| | - Marine Rémy
- Laboratoire de Chimie des Matériaux Moléculaires, Université de Strasbourg et CNRS (UMR 7042, LIMA), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
| | - Emeric Wasielewski
- Plateforme RMN Cronenbourg, Université de Strasbourg et CNRS (UMR 7042, LIMA) Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
| | - Rym Abidi
- Laboratoire d'Applications de la Chimie aux Ressources et Substances Naturelles et l'Environnement, Faculté des Sciences de Bizerte, Université de Carthage, 7021, Zarzouna Bizerte, Tunisia
| | - Jean-François Nierengarten
- Laboratoire de Chimie des Matériaux Moléculaires, Université de Strasbourg et CNRS (UMR 7042, LIMA), Ecole Européenne de Chimie, Polymères et Matériaux, 25 rue Becquerel, 67087, Strasbourg Cedex 2, France
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7
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Beaumal C, Deslignière E, Diemer H, Carapito C, Cianférani S, Hernandez-Alba O. Improved characterization of trastuzumab deruxtecan with PTCR and internal fragments implemented in middle-down MS workflows. Anal Bioanal Chem 2024; 416:519-532. [PMID: 38008785 DOI: 10.1007/s00216-023-05059-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/28/2023]
Abstract
Antibody-drug conjugates (ADCs) are highly complex proteins mainly due to the structural microvariability of the mAb, along with the additional heterogeneity afforded by the bioconjugation process. Top-down (TD) and middle-down (MD) strategies allow the straightforward fragmentation of proteins to elucidate the conjugated amino acid residues. Nevertheless, these spectra are very crowded with multiple overlapping and unassigned ion fragments. Here we report on the use of dedicated software (ClipsMS) and application of proton transfer charge reduction (PTCR), to respectively expand the fragment ion search space to internal fragments and improve the separation of overlapping fragment ions for a more comprehensive characterization of a recently approved ADC, trastuzumab deruxtecan (T-DXd). Subunit fragmentation allowed between 70 and 90% of sequence coverage to be obtained. Upon addition of internal fragment assignment, the three subunits were fully sequenced, although internal fragments did not contribute significantly to the localization of the payloads. Finally, the use of PTCR after subunit fragmentation provided a moderate sequence coverage increase between 2 and 13%. The reaction efficiently decluttered the fragmentation spectra allowing increasing the number of fragment ions characteristic of the conjugation site by 1.5- to 2.5-fold. Altogether, these results show the interest in the implementation of internal fragment ion searches and more particularly the use of PTCR reactions to increase the number of signature ions to elucidate the conjugation sites and enhance the overall sequence coverage of ADCs, making this approach particularly appealing for its implementation in R&D laboratories.
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Affiliation(s)
- Corentin Beaumal
- Laboratoire de Spectrométrie de Masse Bio Organique, IPHC UMR 7178, CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Evolène Deslignière
- Laboratoire de Spectrométrie de Masse Bio Organique, IPHC UMR 7178, CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse Bio Organique, IPHC UMR 7178, CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio Organique, IPHC UMR 7178, CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio Organique, IPHC UMR 7178, CNRS, Université de Strasbourg, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse Bio Organique, IPHC UMR 7178, CNRS, Université de Strasbourg, 67087, Strasbourg, France.
- Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg, France.
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8
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Shajan I, Rochet LNC, Tracey SR, Jackowska B, Benazza R, Hernandez-Alba O, Cianférani S, Scott CJ, van Delft FL, Chudasama V, Albada B. Rapid Access to Potent Bispecific T Cell Engagers Using Biogenic Tyrosine Click Chemistry. Bioconjug Chem 2023; 34:2215-2220. [PMID: 37962868 PMCID: PMC10739583 DOI: 10.1021/acs.bioconjchem.3c00357] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
Bispecific antibodies as T cell engagers designed to display binding capabilities to both tumor-associated antigens and antigens on T cells are considered promising agents in the fight against cancer. Even though chemical strategies to develop such constructs have emerged, a method that readily converts a therapeutically applied antibody into a bispecific construct by a fully non-genetic process is not yet available. Herein, we report the application of a biogenic, tyrosine-based click reaction utilizing chemoenzymatic modifications of native IgG1 antibodies to generate a synthetic bispecific antibody construct that exhibits tumor-killing capability at picomolar concentrations. Control experiments revealed that a covalent linkage of the different components is required for the observed biological activities. In view of the highly potent nature of the constructs and the modular approach that relies on convenient synthetic methods utilizing therapeutically approved biomolecules, our method expedites the production of potent bispecific antibody constructs with tunable cell killing efficacy with significant impact on therapeutic properties.
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Affiliation(s)
- Irene Shajan
- Laboratory
of Organic Chemistry, Wageningen University
& Research, Stippeneng 4, Wageningen 6807 WE, The Netherlands
| | - Léa N. C. Rochet
- Department
of Chemistry, University College London, 20 Gordon St, London WC1H 0AJ, U.K.
| | - Shannon R. Tracey
- Patrick
G Johnston Centre for Cancer Research, School of Medicine, Dentistry
and Biomedical Sciences, Queen’s
University Belfast, 97 Lisburn Road, Belfast BT9 7BL, U.K.
| | - Bianka Jackowska
- Patrick
G Johnston Centre for Cancer Research, School of Medicine, Dentistry
and Biomedical Sciences, Queen’s
University Belfast, 97 Lisburn Road, Belfast BT9 7BL, U.K.
| | - Rania Benazza
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France
- Infrastructure
Nationale de Protéomique ProFI − FR2048, Strasbourg 67087, France
| | - Oscar Hernandez-Alba
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France
- Infrastructure
Nationale de Protéomique ProFI − FR2048, Strasbourg 67087, France
| | - Sarah Cianférani
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France
- Infrastructure
Nationale de Protéomique ProFI − FR2048, Strasbourg 67087, France
| | - Christopher J. Scott
- Patrick
G Johnston Centre for Cancer Research, School of Medicine, Dentistry
and Biomedical Sciences, Queen’s
University Belfast, 97 Lisburn Road, Belfast BT9 7BL, U.K.
| | - Floris L. van Delft
- Laboratory
of Organic Chemistry, Wageningen University
& Research, Stippeneng 4, Wageningen 6807 WE, The Netherlands
- Synaffix
BV − A Lonza Company, Kloosterstraat 9, Oss 5349 AB, The Netherlands
| | - Vijay Chudasama
- Department
of Chemistry, University College London, 20 Gordon St, London WC1H 0AJ, U.K.
| | - Bauke Albada
- Laboratory
of Organic Chemistry, Wageningen University
& Research, Stippeneng 4, Wageningen 6807 WE, The Netherlands
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9
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Koutsopetras I, Mishra AK, Benazza R, Hernandez-Alba O, Cianférani S, Chaubet G, Nicolai S, Waser J. Cysteine-Cysteine Cross-Conjugation of both Peptides and Proteins with a Bifunctional Hypervalent Iodine-Electrophilic Reagent. Chemistry 2023; 29:e202302689. [PMID: 37712523 DOI: 10.1002/chem.202302689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
Peptide and protein bioconjugation sees ever-growing applications in the pharmaceutical sector. Novel strategies and reagents that can address the chemo- and regioselectivity issues inherent to these biomolecules, while delivering stable and functionalizable conjugates, are therefore needed. Herein, we introduce the crosslinking ethynylbenziodazolone (EBZ) reagent JW-AM-005 for the conjugation of peptides and proteins through the selective linkage of cysteine residues. This easily accessed compound gives access to peptide dimers or stapled peptides under mild and tuneable conditions. Applied to the antibody fragment of antigen binding (Fab) species, JW-AM-005 delivered rebridged proteins in a one-pot three-reaction process with high regioselectivity, outperforming the standard reagents commonly used for this transformation.
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Affiliation(s)
- Ilias Koutsopetras
- UMR 7199 CNRS-UdS, Chime Bio-Fonctionnelle, Faculté de Pharmacie, 74 route du Rhin, 67401, Illkirch cedex, France
| | - Abhaya Kumar Mishra
- Laboratory of Catalysis and Organic Synthesis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédéralede de Lausanne, 1015, Lausanne, Switzerland
| | - Rania Benazza
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg CNRS, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI-FR2048, 67087, Strasbourg, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg CNRS, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI-FR2048, 67087, Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg CNRS, 67087, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI-FR2048, 67087, Strasbourg, France
| | - Guilhem Chaubet
- UMR 7199 CNRS-UdS, Chime Bio-Fonctionnelle, Faculté de Pharmacie, 74 route du Rhin, 67401, Illkirch cedex, France
| | - Stefano Nicolai
- Laboratory of Catalysis and Organic Synthesis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédéralede de Lausanne, 1015, Lausanne, Switzerland
| | - Jérôme Waser
- Laboratory of Catalysis and Organic Synthesis, Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédéralede de Lausanne, 1015, Lausanne, Switzerland
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10
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Coliat P, Erb S, Diemer H, Karouby D, Martin T, Banerjee M, Zhu C, Demarchi M, Cianférani S, Detappe A, Pivot X. Influence of pneumatic transportation on the stability of monoclonal antibodies. Sci Rep 2023; 13:21875. [PMID: 38072852 PMCID: PMC10710995 DOI: 10.1038/s41598-023-49235-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023] Open
Abstract
Pneumatic transportation systems (PTS) were recently proposed as a method to carry ready-for-injection diluted monoclonal antibodies (mAbs) from the pharmacy to the bedside of patients. This method reduces transportation time and improves the efficiency of drug distribution process. However, mAbs are highly sensitive molecules for which subtle alterations may lead to deleterious clinical effects. These alterations can be caused by various external factors such as temperature, pH, pressure, and mechanical forces that may occur during transportation. Hence, it is essential to ensure that the mAbs transported by PTS remain stable and active throughout the transportation process. This study aims to determine the safety profile of PTS to transport 11 routinely used mAbs in a clinical setting through assessment of critical quality attributes (CQA) and orthogonal analysis. Hence, we performed aggregation/degradation profiling, post-translational modifications identification using complementary mass spectrometry-based methods, along with visible and subvisible particle formation determination by light absorbance and light obscuration analysis. Altogether, these results highlight that PTS can be safely used for this purpose when air is removed from the bags during preparation.
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Affiliation(s)
- Pierre Coliat
- Institut de Cancérologie Strasbourg Europe, ICANS, 17 Rue Albert Calmette, Strasbourg, France.
| | - Stéphane Erb
- Institut Pluridisciplinaire Hubert Curien, CNRS UMR7178, Université de Strasbourg, Strasbourg, France
- Institut du Médicament Strasbourg, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI-FR2048, Strasbourg, France
| | - Hélène Diemer
- Institut Pluridisciplinaire Hubert Curien, CNRS UMR7178, Université de Strasbourg, Strasbourg, France
- Institut du Médicament Strasbourg, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI-FR2048, Strasbourg, France
| | - Dan Karouby
- Institut de Cancérologie Strasbourg Europe, ICANS, 17 Rue Albert Calmette, Strasbourg, France
| | - Tristan Martin
- Institut de Cancérologie Strasbourg Europe, ICANS, 17 Rue Albert Calmette, Strasbourg, France
| | - Mainak Banerjee
- Institut de Cancérologie Strasbourg Europe, ICANS, 17 Rue Albert Calmette, Strasbourg, France
| | - Chen Zhu
- Institut de Cancérologie Strasbourg Europe, ICANS, 17 Rue Albert Calmette, Strasbourg, France
| | - Martin Demarchi
- Institut de Cancérologie Strasbourg Europe, ICANS, 17 Rue Albert Calmette, Strasbourg, France
| | - Sarah Cianférani
- Institut Pluridisciplinaire Hubert Curien, CNRS UMR7178, Université de Strasbourg, Strasbourg, France
- Institut du Médicament Strasbourg, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI-FR2048, Strasbourg, France
| | - Alexandre Detappe
- Institut de Cancérologie Strasbourg Europe, ICANS, 17 Rue Albert Calmette, Strasbourg, France
- Institut Pluridisciplinaire Hubert Curien, CNRS UMR7178, Université de Strasbourg, Strasbourg, France
- Institut du Médicament Strasbourg, Strasbourg, France
| | - Xavier Pivot
- Institut de Cancérologie Strasbourg Europe, ICANS, 17 Rue Albert Calmette, Strasbourg, France
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11
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Castel J, Delaux S, Hernandez-Alba O, Cianférani S. Recent advances in structural mass spectrometry methods in the context of biosimilarity assessment: from sequence heterogeneities to higher order structures. J Pharm Biomed Anal 2023; 236:115696. [PMID: 37713983 DOI: 10.1016/j.jpba.2023.115696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023]
Abstract
Biotherapeutics and their biosimilar versions have been flourishing in the biopharmaceutical market for several years. Structural and functional characterization is needed to achieve analytical biosimilarity through the assessment of critical quality attributes as required by regulatory authorities. The role of analytical strategies, particularly mass spectrometry-based methods, is pivotal to gathering valuable information for the in-depth characterization of biotherapeutics and biosimilarity assessment. Structural mass spectrometry methods (native MS, HDX-MS, top-down MS, etc.) provide information ranging from primary sequence assessment to higher order structure evaluation. This review focuses on recent developments and applications in structural mass spectrometry for biotherapeutic and biosimilar characterization.
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Affiliation(s)
- Jérôme Castel
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Delaux
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France.
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12
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Lehot V, Lidický O, Most J, Erb S, Dovgan I, Osypenko A, Koniev O, Kolodych S, Kotrchová L, Chaubet G, Cianférani S, Etrych T, Wagner A. Reinvestigation of the Automated Synthesis of Stoichiometrically Conjugated Antibodies to Access High Molecular Weight Payloads and Multiplexed Conjugation via an In-Solution Trans-Tagging Process. ACS Omega 2023; 8:40508-40516. [PMID: 37929096 PMCID: PMC10620776 DOI: 10.1021/acsomega.3c05206] [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] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/05/2023] [Indexed: 11/07/2023]
Abstract
Protein conjugates have found applications in a wide variety of fields, ranging from therapeutics to imaging and detection. However, robust control over the parameters of the conjugation process (such as sites and degree of conjugation) remains challenging. Previously, our group introduced Equimolar NAtive Chemical Tagging (ENACT), a method which allows for the monofunctionalization of proteins by combining an iterative low-conversion bioconjugation, an automated process, and a bioorthogonal trans-tagging reaction. However, while the automated ENACT was dimensioned to achieve monoconjugation at the mg scale, in early stage research, because of the rarity and cost of the starting materials, it is often necessary to prepare conjugates at the lower, μg, scale. Here, we introduce modified ENACT protocols, as well as a new ENACT conjugation reagent, which allow for the monofunctionalization of proteins on the micrograms scale, using minimal quantities of payload.
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Affiliation(s)
- Victor Lehot
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Ondřej Lidický
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Prague 6, Czechia
| | - Julien Most
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Stéphane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Institut du Médicament de Strasbourg, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Igor Dovgan
- Syndivia SAS, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Artem Osypenko
- Syndivia SAS, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | | | - Sergii Kolodych
- Syndivia SAS, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Lenka Kotrchová
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Prague 6, Czechia
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Institut du Médicament de Strasbourg, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Tomáš Etrych
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Heyrovského nám. 2, 162 06 Prague 6, Czechia
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
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13
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Arezki Y, Harmouch E, Delalande F, Rapp M, Schaeffer-Reiss C, Galli O, Cianférani S, Lebeau L, Pons F, Ronzani C. The interplay between lysosome, protein corona and biological effects of cationic carbon dots: Role of surface charge titratability. Int J Pharm 2023; 645:123388. [PMID: 37683981 DOI: 10.1016/j.ijpharm.2023.123388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/07/2023] [Accepted: 09/05/2023] [Indexed: 09/10/2023]
Abstract
Carbon dots (CDs) are nanoparticles (NPs) with potential applications in the biomedical field. When in contact with biological fluids, most NPs are covered by a protein corona. As well, upon cell entry, most NP are sequestered in the lysosome. However, the interplay between the lysosome, the protein corona and the biological effects of NPs is still poorly understood. In this context, we investigated the role of the lysosome in the toxicological responses evoked by four cationic CDs exhibiting protonatable or non-protonatable amine groups at their surface, and the associated changes in the CD protein corona. The four CDs accumulated in the lysosome and led to lysosomal swelling, loss lysosome integrity, cathepsin B activation, NLRP3 inflammasome activation, and cell death by pyroptosis in a human macrophage model, but with a stronger effect for CDs with titratable amino groups. The protein corona formed around CDs in contact with serum partially dissociated under lysosomal conditions with subsequent protein rearrangement, as assessed by quantitative proteomic analysis. The residual protein corona still contained binding proteins, catalytic proteins, and proteins involved in the proteasome, glycolysis, or PI3k-Akt KEGG pathways, but with again a more pronounced effect for CDs with titratable amino groups. These results demonstrate an interplay between lysosome, protein corona and biological effects of cationic NPs in link with the titratability of NP surface charges.
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Affiliation(s)
- Yasmin Arezki
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199, CNRS-Université de Strasbourg, Illkirch, France
| | - Ezeddine Harmouch
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199, CNRS-Université de Strasbourg, Illkirch, France
| | - François Delalande
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC, UMR 7178, CNRS-Université de Strasbourg, Strasbourg, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, Strasbourg, France
| | - Mickaël Rapp
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199, CNRS-Université de Strasbourg, Illkirch, France
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC, UMR 7178, CNRS-Université de Strasbourg, Strasbourg, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, Strasbourg, France
| | - Ophélie Galli
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199, CNRS-Université de Strasbourg, Illkirch, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC, UMR 7178, CNRS-Université de Strasbourg, Strasbourg, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, Strasbourg, France
| | - Luc Lebeau
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199, CNRS-Université de Strasbourg, Illkirch, France
| | - Françoise Pons
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199, CNRS-Université de Strasbourg, Illkirch, France
| | - Carole Ronzani
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199, CNRS-Université de Strasbourg, Illkirch, France.
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14
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Lehot V, Neuberg P, Ripoll M, Daubeuf F, Erb S, Dovgan I, Ursuegui S, Cianférani S, Kichler A, Chaubet G, Wagner A. Targeted Anticancer Agent with Original Mode of Action Prepared by Supramolecular Assembly of Antibody Oligonucleotide Conjugates and Cationic Nanoparticles. Pharmaceutics 2023; 15:1643. [PMID: 37376091 DOI: 10.3390/pharmaceutics15061643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Despite their clinical success, Antibody-Drug Conjugates (ADCs) are still limited to the delivery of a handful of cytotoxic small-molecule payloads. Adaptation of this successful format to the delivery of alternative types of cytotoxic payloads is of high interest in the search for novel anticancer treatments. Herein, we considered that the inherent toxicity of cationic nanoparticles (cNP), which limits their use as oligonucleotide delivery systems, could be turned into an opportunity to access a new family of toxic payloads. We complexed anti-HER2 antibody-oligonucleotide conjugates (AOC) with cytotoxic cationic polydiacetylenic micelles to obtain Antibody-Toxic-Nanoparticles Conjugates (ATNPs) and studied their physicochemical properties, as well as their bioactivity in both in vitro and in vivo HER2 models. After optimising their AOC/cNP ratio, the small (73 nm) HER2-targeting ATNPs were found to selectively kill antigen-positive SKBR-2 cells over antigen-negative MDA-MB-231 cells in serum-containing medium. Further in vivo anti-cancer activity was demonstrated in an SKBR-3 tumour xenograft model in BALB/c mice in which stable 60% tumour regression could be observed just after two injections of 45 pmol of ATNP. These results open interesting prospects in the use of such cationic nanoparticles as payloads for ADC-like strategies.
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Affiliation(s)
- Victor Lehot
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Patrick Neuberg
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Manon Ripoll
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - François Daubeuf
- UAR3286, Plate-Forme de Chimie Biologique Intégrative de Strasbourg, ESBS, CNRS-Strasbourg University, 67400 Illkirch-Graffenstaden, France
| | - Stéphane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Institut du Médicament de Strasbourg, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Igor Dovgan
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Sylvain Ursuegui
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Institut du Médicament de Strasbourg, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Antoine Kichler
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), Institut du Médicament de Strasbourg, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
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15
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Groysbeck N, Hanss V, Donzeau M, Strub JM, Cianférani S, Spehner D, Bahri M, Ersen O, Eltsov M, Schultz P, Zuber G. Bioactivated and PEG-Protected Circa 2 nm Gold Nanoparticles for in Cell Labelling and Cryo-Electron Microscopy. Small Methods 2023; 7:e2300098. [PMID: 37035956 DOI: 10.1002/smtd.202300098] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/09/2023] [Indexed: 06/09/2023]
Abstract
Advances in cryo-electron microscopy (EM) enable imaging of protein assemblies within mammalian cells in a near native state when samples are preserved by cryogenic vitrification. To accompany this progress, specialized EM labelling protocols must be developed. Gold nanoparticles (AuNPs) of 2 nm are synthesized and functionalized to bind selected intracellular targets inside living human cells and to be detected in vitreous sections. As a proof of concept, thioaminobenzoate-, thionitrobenzoate-coordinated gold nanoparticles are functionalized on their surface with SV40 Nuclear Localization Signal (NLS)-containing peptides and 2 kDa polyethyleneglycols (PEG) by thiolate exchange to target the importin-mediated nuclear machinery and facilitate cytosolic diffusion by shielding the AuNP surface from non-specific binding to cell components, respectively. After delivery by electroporation into the cytoplasm of living human cells, the PEG-coated AuNPs diffuse freely in the cytoplasm but do not enter the nucleus. Incorporation of NLS within the PEG coverage promotes a quick nuclear import of the nanoparticles in relation to the density of NLS onto the AuNPs. Cryo-EM of vitreous cell sections demonstrate the presence of 2 nm AuNPs as single entities in the nucleus. Biofunctionalized AuNPs combined with live-cell electroporation procedures are thus potent labeling tools for the identification of macromolecules in cellular cryo-EM.
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Affiliation(s)
- Nadja Groysbeck
- Université de Strasbourg - CNRS, UMR 7242, Biotechnologie et Signalisation Cellulaire, Boulevard Sebastien Brant, Illkirch, F-67400, France
| | - Victor Hanss
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, BP10142, Illkirch Cedex, F-67404, France
| | - Mariel Donzeau
- Université de Strasbourg - CNRS, UMR 7242, Biotechnologie et Signalisation Cellulaire, Boulevard Sebastien Brant, Illkirch, F-67400, France
| | - Jean-Marc Strub
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, F-67000, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, F-67000, France
| | - Danièle Spehner
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, BP10142, Illkirch Cedex, F-67404, France
| | - Mounib Bahri
- Albert Crewe Centre, University of Liverpool, 4. Waterhouse Building, Block C, 1-3 Brownlow Street, London, L69 3GL, UK
| | - Ovidiu Ersen
- Université de Strasbourg - CNRS, UMR 7504, Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS), 23 rue de Loess, Strasbourg, 67034, France
| | - Mikhael Eltsov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, BP10142, Illkirch Cedex, F-67404, France
| | - Patrick Schultz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 rue Laurent Fries, BP10142, Illkirch Cedex, F-67404, France
| | - Guy Zuber
- Université de Strasbourg - CNRS, UMR 7242, Biotechnologie et Signalisation Cellulaire, Boulevard Sebastien Brant, Illkirch, F-67400, France
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16
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Deslignière E, Ollivier S, Beck A, Ropartz D, Rogniaux H, Cianférani S. Benefits and Limitations of High-Resolution Cyclic IM-MS for Conformational Characterization of Native Therapeutic Monoclonal Antibodies. Anal Chem 2023; 95:4162-4171. [PMID: 36780376 DOI: 10.1021/acs.analchem.2c05265] [Citation(s) in RCA: 3] [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] [Indexed: 02/15/2023]
Abstract
Monoclonal antibodies (mAbs) currently represent the main class of therapeutic proteins. mAbs approved by regulatory agencies are selected from IgG1, IgG2, and IgG4 subclasses, which possess different interchain disulfide connectivities. Ion mobility coupled to native mass spectrometry (IM-MS) has emerged as a valuable approach to tackle the challenging characterization of mAbs' higher order structures. However, due to the limited resolution of first-generation IM-MS instruments, subtle conformational differences on large proteins have long been hard to capture. Recent technological developments have aimed at increasing available IM resolving powers and acquisition mode capabilities, namely, through the release of high-resolution IM-MS (HR-IM-MS) instruments, like cyclic IM-MS (cIM-MS). Here, we outline the advantages and drawbacks of cIM-MS for better conformational characterization of intact mAbs (∼150 kDa) in native conditions compared to first-generation instruments. We first assessed the extent to which multipass cIM-MS experiments could improve the separation of mAbs' conformers. These initial results evidenced some limitations of HR-IM-MS for large native biomolecules which possess rich conformational landscapes that remain challenging to decipher even with higher IM resolving powers. Conversely, for collision-induced unfolding (CIU) approaches, higher resolution proved to be particularly useful (i) to reveal new unfolding states and (ii) to enhance the separation of coexisting activated states, thus allowing one to apprehend gas-phase CIU behaviors of mAbs directly at the intact level. Altogether, this study offers a first panoramic overview of the capabilities of cIM-MS for therapeutic mAbs, paving the way for more widespread HR-IM-MS/CIU characterization of mAb-derived formats.
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Affiliation(s)
- Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67000, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg 67087, France
| | - Simon Ollivier
- UR BIA, INRAE, Nantes F-44316, France.,PROBE Research Infrastructure, BIBS Facility, INRAE, Nantes F-44316, France
| | - Alain Beck
- IRPF Centre d'Immunologie Pierre-Fabre (CIPF), Saint-Julien-en-Genevois 74160, France
| | - David Ropartz
- UR BIA, INRAE, Nantes F-44316, France.,PROBE Research Infrastructure, BIBS Facility, INRAE, Nantes F-44316, France
| | - Hélène Rogniaux
- UR BIA, INRAE, Nantes F-44316, France.,PROBE Research Infrastructure, BIBS Facility, INRAE, Nantes F-44316, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67000, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, Strasbourg 67087, France
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17
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van Schaick G, Domínguez-Vega E, Castel J, Wuhrer M, Hernandez-Alba O, Cianférani S. Online Collision-Induced Unfolding of Therapeutic Monoclonal Antibody Glyco-Variants through Direct Hyphenation of Cation Exchange Chromatography with Native Ion Mobility-Mass Spectrometry. Anal Chem 2023; 95:3932-3939. [PMID: 36791123 PMCID: PMC9979139 DOI: 10.1021/acs.analchem.2c03163] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Post-translational modifications (PTMs) not only substantially increase structural heterogeneity of proteins but can also alter the conformation or even biological functions. Monitoring of these PTMs is particularly important for therapeutic products, including monoclonal antibodies (mAbs), since their efficacy and safety may depend on the PTM profile. Innovative analytical strategies should be developed to map these PTMs as well as explore possible induced conformational changes. Cation-exchange chromatography (CEX) coupled with native mass spectrometry has already emerged as a valuable asset for the characterization of mAb charge variants. Nevertheless, questions regarding protein conformation cannot be explored using this approach. Thus, we have combined CEX separation with collision-induced unfolding (CIU) experiments to monitor the unfolding pattern of separated mAbs and thereby pick up subtle conformational differences without impairing the CEX resolution. Using this novel strategy, only four CEX-CIU runs had to be recorded for a complete CIU fingerprint either at the intact mAb level or after enzymatic digestion at the mAb subunit level. As a proof of concept, CEX-CIU was first used for an isobaric mAb mixture to highlight the possibility to acquire individual CIU fingerprints of CEX-separated species without compromising CEX separation performances. CEX-CIU was next successfully applied to conformational characterization of mAb glyco-variants, in order to derive glycoform-specific information on the gas-phase unfolding, and CIU patterns of Fc fragments, revealing increased resistance of sialylated glycoforms against gas-phase unfolding. Altogether, we demonstrated the possibilities and benefits of combining CEX with CIU for in-depth characterization of mAb glycoforms, paving the way for linking conformational changes and resistance to gas-phase unfolding charge variants.
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Affiliation(s)
- Guusje van Schaick
- 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
| | - Jérôme Castel
- Laboratoire
de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France,Infrastructure
Nationale de Protéomique ProFI, FR2048
CNRS CEA, Strasbourg 67087, France
| | - Manfred Wuhrer
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Oscar Hernandez-Alba
- Laboratoire
de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France,Infrastructure
Nationale de Protéomique ProFI, FR2048
CNRS CEA, Strasbourg 67087, France
| | - Sarah Cianférani
- Laboratoire
de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France,Infrastructure
Nationale de Protéomique ProFI, FR2048
CNRS CEA, Strasbourg 67087, France,
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18
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Vinod M, Berthier A, Maréchal X, Gheeraert C, Boutry R, Delhaye S, Annicotte JS, Duez H, Hovasse A, Cianférani S, Montaigne D, Eeckhoute J, Staels B, Lefebvre P. Timed use of digoxin prevents heart ischemia-reperfusion injury through a REV-ERBα-UPS signaling pathway. Nat Cardiovasc Res 2022; 1:990-1005. [PMID: 38229609 PMCID: PMC7615528 DOI: 10.1038/s44161-022-00148-z] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 09/16/2022] [Indexed: 01/18/2024]
Abstract
Myocardial ischemia-reperfusion injury (MIRI) induces life-threatening damages to the cardiac tissue and pharmacological means to achieve cardioprotection are sorely needed. MIRI severity varies along the day-night cycle and is molecularly linked to components of the cellular clock including the nuclear receptor REV-ERBα, a transcriptional repressor. Here we show that digoxin administration in mice is cardioprotective when timed to trigger REV-ERBα protein degradation. In cardiomyocytes, digoxin increases REV-ERBα ubiquitinylation and proteasomal degradation, which depend on REV-ERBα ability to bind its natural ligand, heme. Inhibition of the membrane-bound Src tyrosine-kinase partially alleviated digoxin-induced REV-ERBα degradation. In untreated cardiomyocytes, REV-ERBα proteolysis is controlled by known (HUWE1, FBXW7, SIAH2) or novel (CBL, UBE4B) E3 ubiquitin ligases and the proteasome subunit PSMB5. Only SIAH2 and PSMB5 contributed to digoxin-induced degradation of REV-ERBα. Thus, controlling REV-ERBα proteostasis through the ubiquitin-proteasome system is an appealing cardioprotective strategy. Our data support the timed use of clinically-approved cardiotonic steroids in prophylactic cardioprotection.
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Affiliation(s)
- Manjula Vinod
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Alexandre Berthier
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Xavier Maréchal
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Céline Gheeraert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Raphaёl Boutry
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 – RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000 Lille, France
| | - Stéphane Delhaye
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Jean-Sébastien Annicotte
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 – RID-AGE - Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, F-59000 Lille, France
| | - Hélène Duez
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Agnès Hovasse
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, F-67087 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS, UMR7178, 25 Rue Becquerel, F-67087 Strasbourg, France
| | - David Montaigne
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Jérôme Eeckhoute
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Bart Staels
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
| | - Philippe Lefebvre
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, F-59000 Lille, France
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19
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Deslignière E, Diemer H, Erb S, Coliat P, Pivot X, Detappe A, Hernandez-Alba O, Cianférani S. A Combination of Native LC-MS Approaches for the Comprehensive Characterization of the Antibody-Drug Conjugate Trastuzumab Deruxtecan. Front Biosci (Landmark Ed) 2022; 27:290. [PMID: 36336868 DOI: 10.31083/j.fbl2710290] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Native mass spectrometry (nMS) approaches appear attractive to complement bottom-up strategies traditionally used in biopharmaceutical industries thanks to their quite straightforward and rapid workflows, especially through online hyphenation of non-denaturing liquid chromatography (LC) to nMS. The present work provides an overview of the state-of-the-art chromatographic tools available for the detailed characterization of monoclonal antibody (mAb) formats, exemplified on the antibody-drug conjugate (ADC) trastuzumab deruxtecan (T-DXd). METHODS T-DXd was first characterized by conventional reversed phase LC (rpLC) and peptide mapping. Couplings of size exclusion chromatography (SEC), cation exchange chromatography (CEX), and hydrophobic interaction chromatography (HIC) to nMS were used to gain further insights into size, hydrophobic, and charge variants of T-DXd and its parental mAb trastuzumab, at intact and middle-up levels. RESULTS SEC-nMS first offered a direct snapshot of the homogeneous conjugation of T-DXd, with an average drug-to-antibody ratio (DAR) of 8 in agreement with a conjugation on cysteines after reduction of all interchain disulfide bonds. Moreover, SEC-nMS afforded precise identification and quantification of aggregates and fragments. Middle-up level experiments performed after IdeS digestion confirmed that drug conjugation occurs in the Fab region of the mAb, as seen with rpLC. HIC separated two DAR8 species that could not be differentiated by nMS. Although middle-up HIC-nMS proved to be more informative for oxidized forms, the identification of minor variants was still difficult because of poor MS signal quality, showing how the coupling of HIC to nMS remains challenging. Lastly, middle-up CEX-nMS provided accurate determination and localization of post-translational modifications, with several acidic/basic variants within Fab and Fc regions of T-DXd that were also identified by peptide mapping. CONCLUSIONS This study illustrates the strengths and drawbacks of each LC-nMS coupling. By combining SEC-, HIC-, and CEX-nMS, we were able to achieve a comprehensive characterization of T-DXd without extensive sample preparation prior to MS analysis.
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Affiliation(s)
- Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France.,Strasbourg Drug Discovery and Development Institute (IMS), University of Strasbourg, 67000 Strasbourg, France
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France.,Strasbourg Drug Discovery and Development Institute (IMS), University of Strasbourg, 67000 Strasbourg, France
| | - Stéphane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France.,Strasbourg Drug Discovery and Development Institute (IMS), University of Strasbourg, 67000 Strasbourg, France
| | - Pierre Coliat
- Strasbourg Drug Discovery and Development Institute (IMS), University of Strasbourg, 67000 Strasbourg, France.,Institut de Cancérologie Strasbourg Europe, 67000 Strasbourg, France
| | - Xavier Pivot
- Strasbourg Drug Discovery and Development Institute (IMS), University of Strasbourg, 67000 Strasbourg, France.,Institut de Cancérologie Strasbourg Europe, 67000 Strasbourg, France
| | - Alexandre Detappe
- Strasbourg Drug Discovery and Development Institute (IMS), University of Strasbourg, 67000 Strasbourg, France.,Institut de Cancérologie Strasbourg Europe, 67000 Strasbourg, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France.,Strasbourg Drug Discovery and Development Institute (IMS), University of Strasbourg, 67000 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France.,Strasbourg Drug Discovery and Development Institute (IMS), University of Strasbourg, 67000 Strasbourg, France
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20
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Arezki Y, Delalande F, Schaeffer-Reiss C, Cianférani S, Rapp M, Lebeau L, Pons F, Ronzani C. Surface charge influences protein corona, cell uptake and biological effects of carbon dots. Nanoscale 2022; 14:14695-14710. [PMID: 36168840 DOI: 10.1039/d2nr03611h] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Carbon dots are emerging nanoparticles (NPs) with tremendous applications, especially in the biomedical field. Herein is reported the first quantitative proteomic analysis of the protein corona formed on CDs with different surface charge properties. Four CDs were synthesized from citric acid and various amine group-containing passivation reagents, resulting in cationic NPs with increasing zeta (ζ)-potential and density of positive charges. After CD contact with serum, we show that protein corona identity is influenced by CD surface charge properties, which in turn impacts CD uptake and viability loss in macrophages. In particular, CDs with high ζ-potential (>+30 mV) and charge density (>2 μmol mg-1) are the most highly internalized, and their cell uptake is strongly correlated with a corona enriched in vitronectin, fibulin, fetuin, adiponectin and alpha-glycoprotein. On the contrary, CDs with a lower ζ-potential (+11 mV) and charge density (0.01 μmol mg-1) are poorly internalized, while having a corona with a very different protein signature characterized by a high abundance of apolipoproteins (APOA1, APOB and APOC), albumin and hemoglobin. These data illustrate how corona characterization may contribute to a better understanding of CD cellular fate and biological effects, and provide useful information for the development of CDs for biomedical applications.
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Affiliation(s)
- Yasmin Arezki
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS-Université de Strasbourg, 67400 Illkirch, France.
| | - François Delalande
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, CNRS-Université de Strasbourg, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, CNRS-Université de Strasbourg, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, CNRS-Université de Strasbourg, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | - Mickaël Rapp
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS-Université de Strasbourg, 67400 Illkirch, France.
| | - Luc Lebeau
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS-Université de Strasbourg, 67400 Illkirch, France.
| | - Françoise Pons
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS-Université de Strasbourg, 67400 Illkirch, France.
| | - Carole Ronzani
- Laboratoire de Conception et Application de Molécules Bioactives, UMR 7199 CNRS-Université de Strasbourg, 67400 Illkirch, France.
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21
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Beinsteiner B, Markov GV, Bourguet M, McEwen AG, Erb S, Patel AKM, El Khaloufi El Khaddar FZ, Lecroisey C, Holzer G, Essabri K, Hazemann I, Hamiche A, Cianférani S, Moras D, Laudet V, Billas IML. A novel nuclear receptor subfamily enlightens the origin of heterodimerization. BMC Biol 2022; 20:217. [PMID: 36199108 PMCID: PMC9535869 DOI: 10.1186/s12915-022-01413-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Background Nuclear receptors are transcription factors of central importance in human biology and associated diseases. Much of the knowledge related to their major functions, such as ligand and DNA binding or dimerization, derives from functional studies undertaken in classical model animals. It has become evident, however, that a deeper understanding of these molecular functions requires uncovering how these characteristics originated and diversified during evolution, by looking at more species. In particular, the comprehension of how dimerization evolved from ancestral homodimers to a more sophisticated state of heterodimers has been missing, due to a too narrow phylogenetic sampling. Here, we experimentally and phylogenetically define the evolutionary trajectory of nuclear receptor dimerization by analyzing a novel NR7 subgroup, present in various metazoan groups, including cnidarians, annelids, mollusks, sea urchins, and amphioxus, but lost in vertebrates, arthropods, and nematodes. Results We focused on NR7 of the cephalochordate amphioxus B. lanceolatum. We present a complementary set of functional, structural, and evolutionary analyses that establish that NR7 lies at a pivotal point in the evolutionary trajectory from homodimerizing to heterodimerizing nuclear receptors. The crystal structure of the NR7 ligand-binding domain suggests that the isolated domain is not capable of dimerizing with the ubiquitous dimerization partner RXR. In contrast, the full-length NR7 dimerizes with RXR in a DNA-dependent manner and acts as a constitutively active receptor. The phylogenetic and sequence analyses position NR7 at a pivotal point, just between the basal class I nuclear receptors that form monomers or homodimers on DNA and the derived class II nuclear receptors that exhibit the classical DNA-independent RXR heterodimers. Conclusions Our data suggest that NR7 represents the “missing link” in the transition between class I and class II nuclear receptors and that the DNA independency of heterodimer formation is a feature that was acquired during evolution. Our studies define a novel paradigm of nuclear receptor dimerization that evolved from DNA-dependent to DNA-independent requirements. This new concept emphasizes the importance of DNA in the dimerization of nuclear receptors, such as the glucocorticoid receptor and other members of this pharmacologically important oxosteroid receptor subfamily. Our studies further underline the importance of studying emerging model organisms for supporting cutting-edge research. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01413-0.
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Affiliation(s)
- Brice Beinsteiner
- IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Université de Strasbourg, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Gabriel V Markov
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), 29680, Roscoff, France
| | - Maxime Bourguet
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS CEA, 67087, Strasbourg, France
| | - Alastair G McEwen
- IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Université de Strasbourg, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Stéphane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS CEA, 67087, Strasbourg, France
| | - Abdul Kareem Mohideen Patel
- IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Université de Strasbourg, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Fatima Z El Khaloufi El Khaddar
- IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Université de Strasbourg, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Claire Lecroisey
- Ecole Normale Supérieure de Lyon, Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, UMR 5242 CNRS, Molecular Zoology Team, 46 allée d'Italie, 69364, Lyon, Cedex 07, France
| | - Guillaume Holzer
- Ecole Normale Supérieure de Lyon, Université de Lyon, Institut de Génomique Fonctionnelle de Lyon, UMR 5242 CNRS, Molecular Zoology Team, 46 allée d'Italie, 69364, Lyon, Cedex 07, France.,Present address: Uniklinikum RWTH Aachen, Pauwelsstraße 30, 52074, Aachen, Nordrhein-Westfalen, Germany
| | - Karim Essabri
- IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Université de Strasbourg, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Isabelle Hazemann
- IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Université de Strasbourg, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Ali Hamiche
- IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Université de Strasbourg, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000, Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS CEA, 67087, Strasbourg, France
| | - Dino Moras
- IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France.,Université de Strasbourg, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Vincent Laudet
- Marine Eco-Evo-Devo Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan. .,Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, 23-10, Dah-Uen Rd, Jiau Shi, I-Lan, 262, Taiwan.
| | - Isabelle M L Billas
- IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Illkirch, France. .,Université de Strasbourg, Illkirch, France. .,Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France. .,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.
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22
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Dos Santos Morais R, Santo PE, Ley M, Schelcher C, Abel Y, Plassart L, Deslignière E, Chagot ME, Quinternet M, Paiva ACF, Hessmann S, Morellet N, M F Sousa P, Vandermoere F, Bertrand E, Charpentier B, Bandeiras TM, Plisson-Chastang C, Verheggen C, Cianférani S, Manival X. Deciphering cellular and molecular determinants of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases. J Mol Biol 2022; 434:167760. [PMID: 35901867 DOI: 10.1016/j.jmb.2022.167760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/24/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022]
Abstract
DPCD is a protein that may play a role in cilia formation and whose absence leads to primary ciliary dyskinesia (PCD), a rare disease caused by impairment of ciliated cells. Except for high-throughput studies that identified DPCD as a possible RUVBL1 (R1) and RUVBL2 (R2) partner, no in-depth cellular, biochemical, and structural investigation involving DPCD have been reported so far. R1 and R2 proteins are ubiquitous highly conserved AAA+ family ATPases that assemble and mature a plethora of macromolecular complexes and are pivotal in numerous cellular processes, especially by guaranteeing a co-chaperoning function within R2TP or R2TP-like machineries. In the present study, we identified DPCD as a new R1R2 partner in vivo. We show that DPCD interacts directly with R1 and R2 in vitro and in cells. We characterized the physico-chemical properties of DPCD in solution and built a 3D model of DPCD. In addition, we used a variety of orthogonal biophysical techniques including small-angle X-ray scattering, structural mass spectrometry and electron microscopy to assess the molecular determinants of DPCD interaction with R1R2. Interestingly, DPCD disrupts the dodecameric state of R1R2 complex upon binding and this interaction occurs mainly via the DII domains of R1R2.
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Affiliation(s)
| | - Paulo E Santo
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Marie Ley
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | | | - Yoann Abel
- IGH, CNRS, Univ Montpellier, Montpellier, France; Equipe labélisée Ligue Nationale Contre le Cancer, 34293 Montpellier, France
| | - Laura Plassart
- MCD, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | | | - Marc Quinternet
- Université de Lorraine, CNRS, INSERM, IBSLor, Biophysics and Structural Biology Core Facility, F-54000, France
| | - Ana C F Paiva
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Steve Hessmann
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | - Nelly Morellet
- Très Grandes Infrastructures de Recherche, Institut de Chimie des Substances Naturelles - CNRS, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Pedro M F Sousa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | | | - Edouard Bertrand
- IGH, CNRS, Univ Montpellier, Montpellier, France; Equipe labélisée Ligue Nationale Contre le Cancer, 34293 Montpellier, France
| | | | - Tiago M Bandeiras
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901 Oeiras, Portugal; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Célia Plisson-Chastang
- MCD, Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Céline Verheggen
- IGH, CNRS, Univ Montpellier, Montpellier, France; Equipe labélisée Ligue Nationale Contre le Cancer, 34293 Montpellier, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg 67000, France; Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS, 67087 Strasbourg, France
| | - Xavier Manival
- IMoPA, CNRS, Université de Lorraine, Nancy F-54000, France
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23
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Sicoli G, Konijnenberg A, Guérin J, Hessmann S, Del Nero E, Hernandez-Alba O, Lecher S, Rouaut G, Müggenburg L, Vezin H, Cianférani S, Sobott F, Schneider R, Jacob-Dubuisson F. Large-Scale Conformational Changes of FhaC Provide Insights Into the Two-Partner Secretion Mechanism. Front Mol Biosci 2022; 9:950871. [PMID: 35936790 PMCID: PMC9355242 DOI: 10.3389/fmolb.2022.950871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/24/2022] [Indexed: 11/30/2022] Open
Abstract
The Two-Partner secretion pathway mediates protein transport across the outer membrane of Gram-negative bacteria. TpsB transporters belong to the Omp85 superfamily, whose members catalyze protein insertion into, or translocation across membranes without external energy sources. They are composed of a transmembrane β barrel preceded by two periplasmic POTRA domains that bind the incoming protein substrate. Here we used an integrative approach combining in vivo assays, mass spectrometry, nuclear magnetic resonance and electron paramagnetic resonance techniques suitable to detect minor states in heterogeneous populations, to explore transient conformers of the TpsB transporter FhaC. This revealed substantial, spontaneous conformational changes on a slow time scale, with parts of the POTRA2 domain approaching the lipid bilayer and the protein’s surface loops. Specifically, our data indicate that an amphipathic POTRA2 β hairpin can insert into the β barrel. We propose that these motions enlarge the channel and initiate substrate secretion. Our data propose a solution to the conundrum how TpsB transporters mediate protein secretion without the need for cofactors, by utilizing intrinsic protein dynamics.
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Affiliation(s)
- Giuseppe Sicoli
- Laboratoire Avancé de Spectroscopie pour les Interactions, la Réactivité et l’Environnement (LASIRE), UMR CNRS 8516, Université de Lille, Lille, France
| | | | - Jérémy Guérin
- CNRS, INSERM, Institut Pasteur de Lille, Université de Lille, U1019-UMR9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Steve Hessmann
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR 2048, Strasbourg, France
| | - Elise Del Nero
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR 2048, Strasbourg, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR 2048, Strasbourg, France
| | - Sophie Lecher
- CNRS, INSERM, Institut Pasteur de Lille, Université de Lille, U1019-UMR9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
| | - Guillaume Rouaut
- CNRS EMR9002 Integrative Structural Biology, Lille, France
- INSERM, CHU Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Linn Müggenburg
- CNRS EMR9002 Integrative Structural Biology, Lille, France
- INSERM, CHU Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Institut Pasteur de Lille, Université de Lille, Lille, France
| | - Hervé Vezin
- Laboratoire Avancé de Spectroscopie pour les Interactions, la Réactivité et l’Environnement (LASIRE), UMR CNRS 8516, Université de Lille, Lille, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI – FR 2048, Strasbourg, France
| | - Frank Sobott
- BAMS Research Group, University of Antwerp, Antwerp, Belgium
- Astbury Centre for Structural Molecular Biology and the School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Robert Schneider
- CNRS EMR9002 Integrative Structural Biology, Lille, France
- INSERM, CHU Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Institut Pasteur de Lille, Université de Lille, Lille, France
- *Correspondence: Robert Schneider, ; Françoise Jacob-Dubuisson,
| | - Françoise Jacob-Dubuisson
- CNRS, INSERM, Institut Pasteur de Lille, Université de Lille, U1019-UMR9017-CIIL-Center for Infection and Immunity of Lille, Lille, France
- *Correspondence: Robert Schneider, ; Françoise Jacob-Dubuisson,
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24
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Sebastiani M, Behrens C, Dörr S, Gerber HD, Benazza R, Hernandez-Alba O, Cianférani S, Klebe G, Heine A, Reuter K. Structural and Biochemical Investigation of the Heterodimeric Murine tRNA-Guanine Transglycosylase. ACS Chem Biol 2022; 17:2229-2247. [PMID: 35815944 DOI: 10.1021/acschembio.2c00368] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In tRNAAsp, tRNAAsn, tRNATyr, and tRNAHis of most bacteria and eukaryotes, the anticodon wobble position may be occupied by the modified nucleoside queuosine, which affects the speed and the accuracy of translation. Since eukaryotes are not able to synthesize queuosine de novo, they have to salvage queuine (the queuosine base) as a micronutrient from food and/or the gut microbiome. The heterodimeric Zn2+ containing enzyme tRNA-guanine transglycosylase (TGT) catalyzes the insertion of queuine into the above-named tRNAs in exchange for the genetically encoded guanine. This enzyme has attracted medical interest since it was shown to be potentially useful for the treatment of multiple sclerosis. In addition, TGT inactivation via gene knockout leads to the suppressed cell proliferation and migration of certain breast cancer cells, which may render this enzyme a potential target for the design of compounds supporting breast cancer therapy. As a prerequisite to fully exploit the medical potential of eukaryotic TGT, we have determined and analyzed a number of crystal structures of the functional murine TGT with and without bound queuine. In addition, we have investigated the importance of two residues of its non-catalytic subunit on dimer stability and determined the Michaelis-Menten parameters of murine TGT with respect to tRNA and several natural and artificial nucleobase substrates. Ultimately, on the basis of available TGT crystal structures, we provide an entirely conclusive reaction mechanism for this enzyme, which in detail explains why the TGT-catalyzed insertion of some nucleobases into tRNA occurs reversibly while that of others is irreversible.
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Affiliation(s)
- Maurice Sebastiani
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Christina Behrens
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Stefanie Dörr
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Hans-Dieter Gerber
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Rania Benazza
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI─FR2048, 67087 Strasbourg, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI─FR2048, 67087 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI─FR2048, 67087 Strasbourg, France
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
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25
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Knighton RC, Soro LK, Thor W, Strub JM, Cianférani S, Mély Y, Lenertz M, Wong KL, Platas-Iglesias C, Przybilla F, Charbonnière LJ. Upconversion in a d-f [RuYb 3] Supramolecular Assembly. J Am Chem Soc 2022; 144:13356-13365. [PMID: 35771602 DOI: 10.1021/jacs.2c05037] [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: 11/30/2022]
Abstract
We have prepared a hetero-tetrametallic assembly consisting of three ytterbium ions coordinated to a central [Ru(bpm)3]2+ (bpm = 2,2'-bipyrimidine) motif. Irradiation into the absorption band of the peripheral ytterbium ions at 980 nm engenders emission of the 3MLCT state of the central [Ru(bpm)3]2+ core at 636 nm, which represents the first example of f → d molecular upconversion (UC). Time-resolved measurements reveal a slow rise of the UC emission, which was modeled with a mathematical treatment of the observed kinetics according to a cooperative photosensitization mechanism using a virtual Yb centered doubly excited state followed by energy transfer to the Ru centered 1MLCT state.
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Affiliation(s)
- Richard C Knighton
- Equipe de Synthèse Pour L'Analyse (SynPA), Institut Pluridisciplinaire Hubert Curien (IPHC), UMR 7178, CNRS, Université de Strasbourg, ECPM, 25 rue Becquerel, 67087 Strasbourg Cedex, France
| | - Lohona K Soro
- Equipe de Synthèse Pour L'Analyse (SynPA), Institut Pluridisciplinaire Hubert Curien (IPHC), UMR 7178, CNRS, Université de Strasbourg, ECPM, 25 rue Becquerel, 67087 Strasbourg Cedex, France
| | - Waygen Thor
- Equipe de Synthèse Pour L'Analyse (SynPA), Institut Pluridisciplinaire Hubert Curien (IPHC), UMR 7178, CNRS, Université de Strasbourg, ECPM, 25 rue Becquerel, 67087 Strasbourg Cedex, France.,Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, China
| | - Jean-Marc Strub
- Laboratoire de Spectrometrie de Masse Bio-Organique, IPHC, UMR 7178, CNRS-Université de Strasbourg, ECPM, 25, rue Becquerel, 67087 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrometrie de Masse Bio-Organique, IPHC, UMR 7178, CNRS-Université de Strasbourg, ECPM, 25, rue Becquerel, 67087 Strasbourg, France
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Faculté de Pharmacie CS60024 74, Route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Marc Lenertz
- Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS), UMR 7504, CNRS/Université de Strasbourg, 23 rue du Lœss, BP 43, 67034 Strasbourg Cedex 2, France
| | - Ka-Leung Wong
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, China
| | - Carlos Platas-Iglesias
- Centro de Investigacións Científicas Avanzadas (CICA) and Departamento de Química, Universidade da Coruña, Campus da Zapateira-Rúa da Fraga 10, 15008 A Coruña, Spain
| | - Frédéric Przybilla
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Faculté de Pharmacie CS60024 74, Route du Rhin, 67401 Illkirch-Graffenstaden, France
| | - Loïc J Charbonnière
- Equipe de Synthèse Pour L'Analyse (SynPA), Institut Pluridisciplinaire Hubert Curien (IPHC), UMR 7178, CNRS, Université de Strasbourg, ECPM, 25 rue Becquerel, 67087 Strasbourg Cedex, France
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26
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Deslignière E, Ollivier S, Ehkirch A, Martelet A, Ropartz D, Lechat N, Hernandez-Alba O, Menet JM, Clavier S, Rogniaux H, Genet B, Cianférani S. Combination of IM-Based Approaches to Unravel the Coexistence of Two Conformers on a Therapeutic Multispecific mAb. Anal Chem 2022; 94:7981-7989. [PMID: 35604400 PMCID: PMC9178554 DOI: 10.1021/acs.analchem.2c00928] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Multispecific antibodies,
which target multiple antigens at once,
are emerging as promising therapeutic entities to offer more effective
treatment than conventional monoclonal antibodies (mAbs). However,
these highly complex mAb formats pose significant analytical challenges.
We report here on the characterization of a trispecific antibody (tsAb),
which presents two isomeric forms clearly separated and identified
with size exclusion chromatography coupled to native mass spectrometry
(SEC-nMS). Previous studies showed that these isomers might originate
from a proline cis/trans isomerization
in one Fab subunit of the tsAb. We combined several innovative ion
mobility (IM)-based approaches to confirm the isomeric nature of the
two species and to gain new insights into the conformational landscape
of both isomers. Preliminary SEC-nIM-MS measurements performed on
a low IM resolution instrument provided the first hints of the coexistence
of different conformers, while complementary collision-induced unfolding
(CIU) experiments evidenced distinct gas-phase unfolding behaviors
upon activation for the two isomers. As subtle conformational differences
remained poorly resolved on our early generation IM platform, we performed
high-resolution cyclic IM (cIM-MS) to unambiguously conclude on the
coexistence of two conformers. The cis/trans equilibrium was further tackled by exploiting the IMn slicing capabilities of the cIM-MS instrument. Altogether, our results
clearly illustrate the benefits of combining state-of-the-art nMS
and IM-MS approaches to address challenging issues encountered in
biopharma. As engineered antibody constructs become increasingly sophisticated,
CIU and cIM-MS methodologies undoubtedly have the potential to integrate
the drug development analytical toolbox to achieve in-depth conformational
characterization of these products.
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Affiliation(s)
- Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67087 Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Simon Ollivier
- INRAE, UR BIA, F-44316 Nantes, France.,INRAE, BIBS Facility, F-44316 Nantes, France
| | - Anthony Ehkirch
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67087 Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Armelle Martelet
- CMC Development, BioAnalytics department France, SANOFI R&D, 94400 Vitry-sur-Seine, France
| | - David Ropartz
- INRAE, UR BIA, F-44316 Nantes, France.,INRAE, BIBS Facility, F-44316 Nantes, France
| | - Nelly Lechat
- CMC Development, BioAnalytics department France, SANOFI R&D, 94400 Vitry-sur-Seine, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67087 Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Jean-Michel Menet
- CMC Development, BioAnalytics department France, SANOFI R&D, 94400 Vitry-sur-Seine, France
| | - Séverine Clavier
- CMC Development, BioAnalytics department France, SANOFI R&D, 94400 Vitry-sur-Seine, France
| | - Hélène Rogniaux
- INRAE, UR BIA, F-44316 Nantes, France.,INRAE, BIBS Facility, F-44316 Nantes, France
| | - Bruno Genet
- CMC Development, BioAnalytics department France, SANOFI R&D, 94400 Vitry-sur-Seine, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67087 Strasbourg, France.,Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
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27
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Beaussart A, Canonico F, Mazon H, Hidalgo J, Cianférani S, Le Cordier H, Kriznik A, Rahuel-Clermont S. Probing the mechanism of the peroxiredoxin decamer interaction with its reductase sulfiredoxin from the single molecule to the solution scale. Nanoscale Horiz 2022; 7:515-525. [PMID: 35234779 DOI: 10.1039/d2nh00037g] [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] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peroxiredoxins from the Prx1 subfamily (Prx) are highly regulated multifunctional proteins involved in oxidative stress response, redox signaling and cell protection. Prx is a homodimer that associates into a decamer. The monomer C-terminus plays intricate roles in Prx catalytic functions, decamer stability and interaction with its redox partner, the small reductase sulfiredoxin (Srx), that regulates the switching between Prx cellular functions. As only static structures of covalent Prx-Srx complexes have been reported, whether Srx binding dissociates the decameric assembly and how Prx subunit flexibility impacts complex formation are unknown. Here, we assessed the non-covalent interaction mechanism and dynamics in the solution of Saccharomyces cerevisiae Srx with the ten subunits of Prx Tsa1 at the decamer level via a combination of multiscale biophysical approaches including native mass spectrometry. We show that the ten subunits of the decamer can be saturated by ten Srx molecules and that the Tsa1 decamer in complex with Srx does not dissociate in solution. Furthermore, the binding events of atomic force microscopy (AFM) tip-grafted Srx molecules to Tsa1 individual subunits were relevant to the interactions between free molecules in solution. Combined with protein engineering and rapid kinetics, the observation of peculiar AFM force-distance signatures revealed that Tsa1 C-terminus flexibility controls Tsa1/Srx two-step binding and dynamics and determines the force-induced dissociation of Srx from each subunit of the decameric complex in a sequential or concerted mode. This combined approach from the solution to the single-molecule level offers promising prospects for understanding oligomeric protein interactions with their partners.
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Affiliation(s)
| | | | - Hortense Mazon
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Jorge Hidalgo
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048 CNRS CEA, 67087 Strasbourg, France
| | | | - Alexandre Kriznik
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Biophysics and Structural Biology core facility, F-54000 Nancy, France.
| | - Sophie Rahuel-Clermont
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Biophysics and Structural Biology core facility, F-54000 Nancy, France.
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28
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Cotin G, Heinrich B, Perton F, Kiefer C, Francius G, Mertz D, Freis B, Pichon B, Strub JM, Cianférani S, Ortiz Peña N, Ihiawakrim D, Portehault D, Ersen O, Khammari A, Picher M, Banhart F, Sanchez C, Begin-Colin S. A Confinement-Driven Nucleation Mechanism of Metal Oxide Nanoparticles Obtained via Thermal Decomposition in Organic Media. Small 2022; 18:e2200414. [PMID: 35426247 DOI: 10.1002/smll.202200414] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Thermal decomposition is a very efficient synthesis strategy to obtain nanosized metal oxides with controlled structures and properties. For the iron oxide nanoparticle synthesis, it allows an easy tuning of the nanoparticle's size, shape, and composition, which is often explained by the LaMer theory involving a clear separation between nucleation and growth steps. Here, the events before the nucleation of iron oxide nanocrystals are investigated by combining different complementary in situ characterization techniques. These characterizations are carried out not only on powdered iron stearate precursors but also on a preheated liquid reaction mixture. They reveal a new nucleation mechanism for the thermal decomposition method: instead of a homogeneous nucleation, the nucleation occurs within vesicle-like-nanoreactors confining the reactants. The different steps are: 1) the melting and coalescence of iron stearate particles, leading to "droplet-shaped nanostructures" acting as nanoreactors; 2) the formation of a hitherto unobserved iron stearate crystalline phase within the nucleation temperature range, simultaneously with stearate chains loss and Fe(III) to Fe(II) reduction; 3) the formation of iron oxide nuclei inside the nanoreactors, which are then ejected from them. This mechanism paves the way toward a better mastering of the metal oxide nanoparticles synthesis and the control of their properties.
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Affiliation(s)
- Geoffrey Cotin
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg, F-67034, France
- Labex CSC, Fondation IcFRC/Université de Strasbourg, 8 allée Gaspard Monge BP 70028, Strasbourg Cedex, F-67083, France
| | - Benoît Heinrich
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg, F-67034, France
| | - Francis Perton
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg, F-67034, France
- Labex CSC, Fondation IcFRC/Université de Strasbourg, 8 allée Gaspard Monge BP 70028, Strasbourg Cedex, F-67083, France
| | - Céline Kiefer
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg, F-67034, France
- Labex CSC, Fondation IcFRC/Université de Strasbourg, 8 allée Gaspard Monge BP 70028, Strasbourg Cedex, F-67083, France
| | - Gregory Francius
- Université de Lorraine and CNRS, LPCME UMR 7564, Nancy, F-54000, France
| | - Damien Mertz
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg, F-67034, France
- Labex CSC, Fondation IcFRC/Université de Strasbourg, 8 allée Gaspard Monge BP 70028, Strasbourg Cedex, F-67083, France
| | - Barbara Freis
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg, F-67034, France
| | - Benoit Pichon
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg, F-67034, France
- Labex CSC, Fondation IcFRC/Université de Strasbourg, 8 allée Gaspard Monge BP 70028, Strasbourg Cedex, F-67083, France
| | - Jean-Marc Strub
- Université Strasbourg, CNRS, IPHC, Laboratoire de Spectrométrie de Masse BioOrganique, UMR 7178, Strasbourg, F-67000, France
| | - Sarah Cianférani
- Université Strasbourg, CNRS, IPHC, Laboratoire de Spectrométrie de Masse BioOrganique, UMR 7178, Strasbourg, F-67000, France
| | - Nathalie Ortiz Peña
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg, F-67034, France
| | - Dris Ihiawakrim
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg, F-67034, France
| | - David Portehault
- Sorbonne Université, CNRS UMR 7574, Collège de France, LCMCP, 4 place Jussieu, Paris cedex 05, 75252, France
| | - Ovidiu Ersen
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg, F-67034, France
- Labex CSC, Fondation IcFRC/Université de Strasbourg, 8 allée Gaspard Monge BP 70028, Strasbourg Cedex, F-67083, France
| | - Amir Khammari
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg, F-67034, France
| | - Matthieu Picher
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg, F-67034, France
| | - Florian Banhart
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg, F-67034, France
| | - Clement Sanchez
- Sorbonne Université, CNRS UMR 7574, Collège de France, LCMCP, 4 place Jussieu, Paris cedex 05, 75252, France
- USIAS Chair of Chemistry of ultradivided matter, University of Strasbourg Institut of Advanced Study, Strasbourg, 67000, France
| | - Sylvie Begin-Colin
- Université de Strasbourg, CNRS, Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504, Strasbourg, F-67034, France
- Labex CSC, Fondation IcFRC/Université de Strasbourg, 8 allée Gaspard Monge BP 70028, Strasbourg Cedex, F-67083, France
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Torres A, Collin-Faure V, Diemer H, Moriscot C, Fenel D, Gallet B, Cianférani S, Sergent JA, Rabilloud T. Repeated Exposure of Macrophages to Synthetic Amorphous Silica Induces Adaptive Proteome Changes and a Moderate Cell Activation. Nanomaterials 2022; 12:nano12091424. [PMID: 35564134 PMCID: PMC9105884 DOI: 10.3390/nano12091424] [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] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 11/21/2022]
Abstract
Synthetic amorphous silica (SAS) is a nanomaterial used in a wide variety of applications, including the use as a food additive. Two types of SAS are commonly employed as a powder additive, precipitated silica and fumed silica. Numerous studies have investigated the effects of synthetic amorphous silica on mammalian cells. However, most of them have used an exposure scheme based on a single dose of SAS. In this study, we have used instead a repeated 10-day exposure scheme in an effort to better simulate the occupational exposure encountered in daily life by consumers and workers. As a biological model, we have used the murine macrophage cell line J774A.1, as macrophages are very important innate immune cells in the response to particulate materials. In order to obtain a better appraisal of the macrophage responses to this repeated exposure to SAS, we have used proteomics as a wide-scale approach. Furthermore, some of the biological pathways detected as modulated by the exposure to SAS by the proteomic experiments have been validated through targeted experiments. Overall, proteomics showed that precipitated SAS induced a more important macrophage response than fumed SAS at equal dose. Nevertheless, validation experiments showed that most of the responses detected by proteomics are indeed adaptive, as the cellular homeostasis appeared to be maintained at the end of the exposure. For example, the intracellular glutathione levels or the mitochondrial transmembrane potential at the end of the 10 days exposure were similar for SAS-exposed cells and for unexposed cells. Similarly, no gross lysosomal damage was observed after repeated exposure to SAS. Nevertheless, important functions of macrophages such as phagocytosis, TNFα, and interleukin-6 secretion were up-modulated after exposure, as was the expression of important membrane proteins such as the scavenger receptors, MHC-II, or the MAC-1 receptor. These results suggest that repeated exposure to low doses of SAS slightly modulates the immune functions of macrophages, which may alter the homeostasis of the immune system.
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Affiliation(s)
- Anaelle Torres
- Chemistry and Biology of Metals Laboratory, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Commissariat à l’Energie Atomique, Interdisciplinary Research Institute of Grenoble, 38054 Grenoble, France; (A.T.); (V.C.-F.)
| | - Véronique Collin-Faure
- Chemistry and Biology of Metals Laboratory, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Commissariat à l’Energie Atomique, Interdisciplinary Research Institute of Grenoble, 38054 Grenoble, France; (A.T.); (V.C.-F.)
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Centre National de la Rech erche Scientifique, Hubert Curien Pluridisciplinary Institute UMR 7178, Strasbourg University, 67087 Strasbourg, France; (H.D.); (S.C.)
- Infrastructure Nationale de Protéomique ProFI—FR2048, 67087 Strasbourg, France
| | - Christine Moriscot
- Integrated Structural Biology Grenoble (ISBG), European Molecular Biology Laboratory Université Grenoble Alpes, Centre National de la Recherche Scientifique, Commissariat à l’Energie Atomique, 71 Avenue des Martyrs, 38042 Grenoble, France;
| | - Daphna Fenel
- Institute of Structural Biology (IBS), Université Grenoble Alpes, Centre National de la Recherche Scientifique, Commissariat à l’Energie Atomique, Interdisciplinary Research Institute of Grenoble, 38044 Grenoble, France; (D.F.); (B.G.)
| | - Benoît Gallet
- Institute of Structural Biology (IBS), Université Grenoble Alpes, Centre National de la Recherche Scientifique, Commissariat à l’Energie Atomique, Interdisciplinary Research Institute of Grenoble, 38044 Grenoble, France; (D.F.); (B.G.)
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Centre National de la Rech erche Scientifique, Hubert Curien Pluridisciplinary Institute UMR 7178, Strasbourg University, 67087 Strasbourg, France; (H.D.); (S.C.)
- Infrastructure Nationale de Protéomique ProFI—FR2048, 67087 Strasbourg, France
| | | | - Thierry Rabilloud
- Chemistry and Biology of Metals Laboratory, Université Grenoble Alpes, Centre National de la Recherche Scientifique, Commissariat à l’Energie Atomique, Interdisciplinary Research Institute of Grenoble, 38054 Grenoble, France; (A.T.); (V.C.-F.)
- Correspondence: ; Tel.: +33-43-878-3212
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Cavazza C, Collin-Faure V, Pérard J, Diemer H, Cianférani S, Rabilloud T, Darrouzet E. Proteomic analysis of Rhodospirillum rubrum after carbon monoxide exposure reveals an important effect on metallic cofactor biosynthesis. J Proteomics 2022; 250:104389. [PMID: 34601154 DOI: 10.1016/j.jprot.2021.104389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/14/2022]
Abstract
Some carboxydotrophs like Rhodospirillum rubrum are able to grow with CO as their sole source of energy using a Carbone monoxide dehydrogenase (CODH) and an Energy conserving hydrogenase (ECH) to perform anaerobically the so called water-gas shift reaction (WGSR) (CO + H2O → CO2 + H2). Several studies have focused at the biochemical and biophysical level on this enzymatic system and a few OMICS studies on CO metabolism. Knowing that CO is toxic in particular due to its binding to heme iron atoms, and is even considered as a potential antibacterial agent, we decided to use a proteomic approach in order to analyze R. rubrum adaptation in term of metabolism and management of the toxic effect. In particular, this study allowed highlighting a set of proteins likely implicated in ECH maturation, and important perturbations in term of cofactor biosynthesis, especially metallic cofactors. This shows that even this CO tolerant microorganism cannot avoid completely CO toxic effects associated with its interaction with metallic ions. SIGNIFICANCE: This proteomic study highlights the fact that even in a microorganism able to handle carbon monoxide and in some way detoxifying it via the intrinsic action of the carbon monoxide dehydrogenase (CODH), CO has important effects on metal homeostasis, metal cofactors and metalloproteins. These effects are direct or indirect via transcription regulation, and amplified by the high interdependency of cofactors biosynthesis.
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Affiliation(s)
- Christine Cavazza
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
| | | | - Julien Pérard
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI - FR2048 (CNRS-CEA), 67087 Strasbourg, France.
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France; Infrastructure Nationale de Protéomique ProFI - FR2048 (CNRS-CEA), 67087 Strasbourg, France.
| | - Thierry Rabilloud
- Univ. Grenoble Alpes, CEA, CNRS, IRIG, CBM, F-38000 Grenoble, France.
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31
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Deslignière E, Botzanowski T, Diemer H, Cooper-Shepherd DA, Wagner-Rousset E, Colas O, Béchade G, Giles K, Hernandez-Alba O, Beck A, Cianférani S. High-Resolution IMS-MS to Assign Additional Disulfide Bridge Pairing in Complementarity-Determining Regions of an IgG4 Monoclonal Antibody. J Am Soc Mass Spectrom 2021; 32:2505-2512. [PMID: 34437803 DOI: 10.1021/jasms.1c00151] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Monoclonal antibodies (mAbs) have taken on an increasing importance for the treatment of various diseases, including cancers and immunological disorders. Disulfide bonds play a pivotal role in therapeutic antibody structure and activity relationships. Disulfide connectivity and cysteine-related variants are considered as critical quality attributes that must be monitored during mAb manufacturing and storage, as non-native disulfide bridges and aggregates might be responsible for loss of biological function and immunogenicity. The presence of cysteine residues in the complementarity-determining regions (CDRs) is rare in human antibodies but may be critical for the antigen-binding or deleterious for therapeutic antibody development. Consequently, in-depth characterization of their disulfide network is a prerequisite for mAb developability assessment. Mass spectrometry (MS) techniques represent powerful tools for accurate identification of disulfide connectivity. We report here on the MS-based characterization of an IgG4 comprising two additional cysteine residues in the CDR of its light chain. Classical bottom-up approaches after trypsin digestion first allowed identification of a dipeptide containing two disulfide bridges. To further investigate the conformational heterogeneity of the disulfide-bridged dipeptide, we performed ion mobility spectrometry-mass spectrometry (IMS-MS) experiments. Our results highlight benefits of high resolution IMS-MS to tackle the conformational landscape of disulfide peptides generated after trypsin digestion of a humanized IgG4 mAb under development. By comparing arrival time distributions of the mAb-collected and synthetic peptides, cyclic IMS afforded unambiguous assessment of disulfide bonds. In addition to classical peptide mapping, qualitative high-resolution IMS-MS can be of great interest to identify disulfide bonds within therapeutic mAbs.
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Affiliation(s)
- Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | | | - Elsa Wagner-Rousset
- IRPF - Centre d'Immunologie Pierre-Fabre (CIPF), 74160 Saint-Julien-en-Genevois, France
| | - Olivier Colas
- IRPF - Centre d'Immunologie Pierre-Fabre (CIPF), 74160 Saint-Julien-en-Genevois, France
| | - Guillaume Béchade
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, Cheshire SK9 4AX, U.K
| | - Kevin Giles
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, Cheshire SK9 4AX, U.K
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
| | - Alain Beck
- IRPF - Centre d'Immunologie Pierre-Fabre (CIPF), 74160 Saint-Julien-en-Genevois, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France
- Infrastructure Nationale de Protéomique ProFI - FR2048, 67087 Strasbourg, France
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32
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Delfosse V, Huet T, Harrus D, Granell M, Bourguet M, Gardia-Parège C, Chiavarina B, Grimaldi M, Le Mével S, Blanc P, Huang D, Gruszczyk J, Demeneix B, Cianférani S, Fini JB, Balaguer P, Bourguet W. Mechanistic insights into the synergistic activation ofthe RXR–PXR heterodimer by endocrinedisruptor mixtures. Acta Crystallogr A Found Adv 2021. [DOI: 10.1107/s0108767321092035] [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: 11/10/2022] Open
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Rady T, Erb S, Deddouche-Grass S, Morales R, Bouchard H, Chaubet G, Cianférani S, Wiederschain D, Basse N, Wagner A. Abstract 691: Antibody conjugated to a bispecific RNA molecule targeting RIG-I and PLK1. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-691] [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
Simultaneous access to several targets has become the subject of intense studies in immuno-oncology. In order to benefit from the synergies provided by the activation of different signaling pathways in immunology and the knockdown of proteins involved in cancer cell survival, we established a bispecific approach. The activation of the innate immune response by delivering agonists of pattern-recognition receptors (PRR) such as RIG-I (retinoic acid-inducible I) represents a promising strategy. RIG-I detects short double-stranded RNA molecules ended by a 5'-di/triphosphate moiety (5'ppp-dsRNA). RIG-I activation promotes type I IFN secretion and cancer-cell selective apoptosis. To obtain a bifunctional molecule, the 5'ppp-dsRNA sequence was designed to silence PLK1 (polo-like kinase 1). Suppressing PLK1 expression with small interfering RNAs (siRNA) leads to cell cycle arrest and retards cancer cell growth. This concept of bifunctional RNAs has been validated by using non-targeted systems.1
To enhance this synergy, we conjugated this 5'ppp-siPLK1 to an antibody for a specific delivery to cancerous cells that overexpress erythropoietin-producing hepatocellular receptor A2 (EphA2) at their surface. Upon binding to EphA2 receptor, the antibody is well internalized, thus making it a good vehicle to deliver the bispecific 5'ppp-siPLK1. After EphA2-positive cells treatment, we observed RIG-I specific activation as well as PLK1 depletion. Both effects were correlated with cellular apoptosis and the mode of action was further confirmed with mechanistic and kinetic studies. Finally, while non-modified unconjugated siRNA has a very short half-life in plasma, we observed an increase in stability for the antibody-5'ppp-siPLK1 conjugates. These data suggest that anti-EphA2 receptor antibody could be used to deliver a bispecific RNA molecule.
References:1H. Poeck, R. Besch, C. Maihoefer, M. Renn, D. Tormo, S. S. Morskaya, S. Kirschnek, E. Gaffal, J. Landsberg, J. Hellmuth, A. Schmidt, D. Anz, M. Bscheider, T. Schwerd, C. Berking, C. Bourquin, U. Kalinke, E. Kremmer, H. Kato, S. Akira, R. Meyers, G. Häcker, M. Neuenhahn, D. Busch, J. Ruland, S. Rothenfusser, M. Prinz, V. Hornung, S. Endres, T. Tüting and G. Hartmann, 5′-triphosphate-siRNA: turning gene silencing and Rig-I activation against melanoma, Nat. Med., 2008, 14, 1256-1263.
Citation Format: Tony Rady, Stéphane Erb, Safia Deddouche-Grass, Renaud Morales, Hervé Bouchard, Guilhem Chaubet, Sarah Cianférani, Dmitri Wiederschain, Nicolas Basse, Alain Wagner. Antibody conjugated to a bispecific RNA molecule targeting RIG-I and PLK1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 691.
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Affiliation(s)
- Tony Rady
- 1University of Strasbourg/Sanofi, Strasbourg, France
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Ramirez Rios S, Torres A, Diemer H, Collin-Faure V, Cianférani S, Lafanechère L, Rabilloud T. A proteomic-informed view of the changes induced by loss of cellular adherence: The example of mouse macrophages. PLoS One 2021; 16:e0252450. [PMID: 34048472 PMCID: PMC8162644 DOI: 10.1371/journal.pone.0252450] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 05/14/2021] [Indexed: 11/19/2022] Open
Abstract
Except cells circulating in the bloodstream, most cells in vertebrates are adherent. Studying the repercussions of adherence per se in cell physiology is thus very difficult to carry out, although it plays an important role in cancer biology, e.g. in the metastasis process. In order to study how adherence impacts major cell functions, we used a murine macrophage cell line. Opposite to the monocyte/macrophage system, where adherence is associated with the acquisition of differentiated functions, these cells can be grown in both adherent or suspension conditions without altering their differentiated functions (phagocytosis and inflammation signaling). We used a proteomic approach to cover a large panel of proteins potentially modified by the adherence status. Targeted experiments were carried out to validate the proteomic results, e.g. on metabolic enzymes, mitochondrial and cytoskeletal proteins. The mitochondrial activity was increased in non-adherent cells compared with adherent cells, without differences in glucose consumption. Concerning the cytoskeleton, a rearrangement of the actin organization (filopodia vs sub-cortical network) and of the microtubule network were observed between adherent and non-adherent cells. Taken together, these data show the mechanisms at play for the modification of the cytoskeleton and also modifications of the metabolic activity between adherent and non-adherent cells.
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Affiliation(s)
- Sacnite Ramirez Rios
- Institute for Advanced Biosciences, Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Grenoble, France
| | - Anaelle Torres
- Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS UMR5249, CEA, IRIG-DIESE-CBM-ProMD, Grenoble, France
| | - Hélène Diemer
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, France
- Infrastructure Nationale de Protéomique, FR2048 ProFI, Strasbourg, France
| | - Véronique Collin-Faure
- Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS UMR5249, CEA, IRIG-DIESE-CBM-ProMD, Grenoble, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, France
- Infrastructure Nationale de Protéomique, FR2048 ProFI, Strasbourg, France
| | - Laurence Lafanechère
- Institute for Advanced Biosciences, Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Grenoble, France
| | - Thierry Rabilloud
- Chemistry and Biology of Metals, Univ. Grenoble Alpes, CNRS UMR5249, CEA, IRIG-DIESE-CBM-ProMD, Grenoble, France
- * E-mail:
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Deslignière E, Ehkirch A, Duivelshof BL, Toftevall H, Sjögren J, Guillarme D, D’Atri V, Beck A, Hernandez-Alba O, Cianférani S. State-of-the-Art Native Mass Spectrometry and Ion Mobility Methods to Monitor Homogeneous Site-Specific Antibody-Drug Conjugates Synthesis. Pharmaceuticals (Basel) 2021; 14:ph14060498. [PMID: 34073805 PMCID: PMC8225019 DOI: 10.3390/ph14060498] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
Antibody-drug conjugates (ADCs) are biotherapeutics consisting of a tumor-targeting monoclonal antibody (mAb) linked covalently to a cytotoxic drug. Early generation ADCs were predominantly obtained through non-selective conjugation methods based on lysine and cysteine residues, resulting in heterogeneous populations with varying drug-to-antibody ratios (DAR). Site-specific conjugation is one of the current challenges in ADC development, allowing for controlled conjugation and production of homogeneous ADCs. We report here the characterization of a site-specific DAR2 ADC generated with the GlyCLICK three-step process, which involves glycan-based enzymatic remodeling and click chemistry, using state-of-the-art native mass spectrometry (nMS) methods. The conjugation process was monitored with size exclusion chromatography coupled to nMS (SEC-nMS), which offered a straightforward identification and quantification of all reaction products, providing a direct snapshot of the ADC homogeneity. Benefits of SEC-nMS were further demonstrated for forced degradation studies, for which fragments generated upon thermal stress were clearly identified, with no deconjugation of the drug linker observed for the T-GlyGLICK-DM1 ADC. Lastly, innovative ion mobility-based collision-induced unfolding (CIU) approaches were used to assess the gas-phase behavior of compounds along the conjugation process, highlighting an increased resistance of the mAb against gas-phase unfolding upon drug conjugation. Altogether, these state-of-the-art nMS methods represent innovative approaches to investigate drug loading and distribution of last generation ADCs, their evolution during the bioconjugation process and their impact on gas-phase stabilities. We envision nMS and CIU methods to improve the conformational characterization of next generation-empowered mAb-derived products such as engineered nanobodies, bispecific ADCs or immunocytokines.
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Affiliation(s)
- Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France; (E.D.); (A.E.); (O.H.-A.)
- Infrastructure Nationale de Protéomique ProFI—FR2048, 67087 Strasbourg, France
| | - Anthony Ehkirch
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France; (E.D.); (A.E.); (O.H.-A.)
- Infrastructure Nationale de Protéomique ProFI—FR2048, 67087 Strasbourg, France
| | - Bastiaan L. Duivelshof
- School of Pharmaceutical Sciences, University of Geneva, CMU—Rue Michel-Servet 1, 1211 Geneva, Switzerland; (B.L.D.); (D.G.); (V.D.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU—Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | | | | | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, CMU—Rue Michel-Servet 1, 1211 Geneva, Switzerland; (B.L.D.); (D.G.); (V.D.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU—Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Valentina D’Atri
- School of Pharmaceutical Sciences, University of Geneva, CMU—Rue Michel-Servet 1, 1211 Geneva, Switzerland; (B.L.D.); (D.G.); (V.D.)
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU—Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Alain Beck
- IRPF—Centre d’Immunologie Pierre-Fabre (CIPF), 74160 Saint-Julien-en-Genevois, France;
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France; (E.D.); (A.E.); (O.H.-A.)
- Infrastructure Nationale de Protéomique ProFI—FR2048, 67087 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR 7178, Université de Strasbourg, CNRS, 67087 Strasbourg, France; (E.D.); (A.E.); (O.H.-A.)
- Infrastructure Nationale de Protéomique ProFI—FR2048, 67087 Strasbourg, France
- Correspondence:
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36
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Cichocki B, Khobragade V, Donzel M, Cotos L, Blandin S, Schaeffer-Reiss C, Cianférani S, Strub JM, Elhabiri M, Davioud-Charvet E. A Class of Valuable (Pro-)Activity-Based Protein Profiling Probes: Application to the Redox-Active Antiplasmodial Agent, Plasmodione. JACS Au 2021; 1:669-689. [PMID: 34056636 PMCID: PMC8154199 DOI: 10.1021/jacsau.1c00025] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 05/03/2023]
Abstract
Plasmodione (PD) is a potent antimalarial redox-active drug acting at low nM range concentrations on different malaria parasite stages. In this study, in order to determine the precise PD protein interactome in parasites, we developed a class of (pro-)activity-based protein profiling probes (ABPP) as precursors of photoreactive benzophenone-like probes based on the skeleton of PD metabolites (PDO) generated in a cascade of redox reactions. Under UV-photoirradiation, we clearly demonstrate that benzylic oxidation of 3-benzylmenadione 11 produces the 3-benzoylmenadione probe 7, allowing investigation of the proof-of-concept of the ABPP strategy with 3-benzoylmenadiones 7-10. The synthesized 3-benzoylmenadiones, probe 7 with an alkyne group or probe 9 with -NO2 in para position of the benzoyl chain, were found to be the most efficient photoreactive and clickable probes. In the presence of various H-donor partners, the UV-irradiation of the photoreactive ABPP probes generates different adducts, the expected "benzophenone-like" adducts (pathway 1) in addition to "benzoxanthone" adducts (via two other pathways, 2 and 3). Using both human and Plasmodium falciparum glutathione reductases, three protein ligand binding sites were identified following photolabeling with probes 7 or 9. The photoreduction of 3-benzoylmenadiones (PDO and probe 9) promoting the formation of both the corresponding benzoxanthone and the derived enone could be replaced by the glutathione reductase-catalyzed reduction step. In particular, the electrophilic character of the benzoxanthone was evidenced by its ability to alkylate heme, as a relevant event supporting the antimalarial mode of action of PD. This work provides a proof-of-principle that (pro-)ABPP probes can generate benzophenone-like metabolites enabling optimized activity-based protein profiling conditions that will be instrumental to analyze the interactome of early lead antiplasmodial 3-benzylmenadiones displaying an original and innovative mode of action.
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Affiliation(s)
- Bogdan
Adam Cichocki
- Université
de Strasbourg−CNRS−UHA, UMR7042, Laboratoire d’Innovation Moléculaire
et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry,
European School of Chemistry, Polymers and
Materials (ECPM), 25
Rue Becquerel, 67087 Strasbourg, France
| | - Vrushali Khobragade
- Université
de Strasbourg−CNRS−UHA, UMR7042, Laboratoire d’Innovation Moléculaire
et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry,
European School of Chemistry, Polymers and
Materials (ECPM), 25
Rue Becquerel, 67087 Strasbourg, France
| | - Maxime Donzel
- Université
de Strasbourg−CNRS−UHA, UMR7042, Laboratoire d’Innovation Moléculaire
et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry,
European School of Chemistry, Polymers and
Materials (ECPM), 25
Rue Becquerel, 67087 Strasbourg, France
| | - Leandro Cotos
- Université
de Strasbourg−CNRS−UHA, UMR7042, Laboratoire d’Innovation Moléculaire
et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry,
European School of Chemistry, Polymers and
Materials (ECPM), 25
Rue Becquerel, 67087 Strasbourg, France
| | - Stephanie Blandin
- Université
de Strasbourg−CNRS−INSERM UPR9022/U1257, Mosquito Immune Responses (MIR), F-67000 Strasbourg, France
| | - Christine Schaeffer-Reiss
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Jean-Marc Strub
- Laboratoire
de Spectrométrie de Masse BioOrganique, Université Strasbourg, CNRS, IPHC UMR 7178, F-67000 Strasbourg, France
| | - Mourad Elhabiri
- Université
de Strasbourg−CNRS−UHA, UMR7042, Laboratoire d’Innovation Moléculaire
et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry,
European School of Chemistry, Polymers and
Materials (ECPM), 25
Rue Becquerel, 67087 Strasbourg, France
| | - Elisabeth Davioud-Charvet
- Université
de Strasbourg−CNRS−UHA, UMR7042, Laboratoire d’Innovation Moléculaire
et Applications (LIMA), Team Bio(IN)organic and Medicinal Chemistry,
European School of Chemistry, Polymers and
Materials (ECPM), 25
Rue Becquerel, 67087 Strasbourg, France
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37
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Bons J, Husson G, Chion M, Bonnet M, Maumy-Bertrand M, Delalande F, Cianférani S, Bertrand F, Picard B, Carapito C. Combining label-free and label-based accurate quantifications with SWATH-MS: Comparison with SRM and PRM for the evaluation of bovine muscle type effects. Proteomics 2021; 21:e2000214. [PMID: 33733615 DOI: 10.1002/pmic.202000214] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 11/11/2022]
Abstract
Mass spectrometry has proven to be a valuable tool for the accurate quantification of proteins. In this study, the performances of three targeted approaches, namely selected reaction monitoring (SRM), parallel reaction monitoring (PRM) and sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS), to accurately quantify ten potential biomarkers of beef meat tenderness or marbling in a cohort of 64 muscle samples were evaluated. So as to get the most benefit out of the complete MS2 maps that are acquired in SWATH-MS, an original label-free quantification method to estimate protein amounts using an I-spline regression model was developed. Overall, SWATH-MS outperformed SRM in terms of sensitivity and dynamic range, while PRM still performed the best, and all three strategies showed similar quantification accuracies and precisions for the absolute quantification of targets of interest. This targeted picture was extended by 585 additional proteins for which amounts were estimated using the label-free approach on SWATH-MS; thus, offering a more global profiling of muscle proteomes and further insights into muscle type effect on candidate biomarkers of beef meat qualities as well as muscle metabolism.
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Affiliation(s)
- Joanna Bons
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR7178, CNRS, Université de Strasbourg, Strasbourg, France
| | - Gauthier Husson
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR7178, CNRS, Université de Strasbourg, Strasbourg, France
| | - Marie Chion
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR7178, CNRS, Université de Strasbourg, Strasbourg, France.,Institut de Recherche Mathématique Avancée, Université de Strasbourg, Strasbourg, France
| | - Muriel Bonnet
- Université Clermont Auvergne, Saint-Genès-Champanelle, France
| | - Myriam Maumy-Bertrand
- Institut de Recherche Mathématique Avancée, Université de Strasbourg, Strasbourg, France
| | - François Delalande
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR7178, CNRS, Université de Strasbourg, Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR7178, CNRS, Université de Strasbourg, Strasbourg, France
| | - Frédéric Bertrand
- Laboratoire de Modélisation et Sûreté des Systèmes, Institut Charles Delaunay, Université de Technologie de Troyes, Troyes, France
| | - Brigitte Picard
- Université Clermont Auvergne, Saint-Genès-Champanelle, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, IPHC UMR7178, CNRS, Université de Strasbourg, Strasbourg, France
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38
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Lehot V, Kuhn I, Nothisen M, Erb S, Kolodych S, Cianférani S, Chaubet G, Wagner A. Non-specific interactions of antibody-oligonucleotide conjugates with living cells. Sci Rep 2021; 11:5881. [PMID: 33723336 PMCID: PMC7961061 DOI: 10.1038/s41598-021-85352-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/29/2021] [Indexed: 11/15/2022] Open
Abstract
Antibody-Oligonucleotide Conjugates (AOCs) represent an emerging class of functionalized antibodies that have already been used in a wide variety of applications. While the impact of dye and drug conjugation on antibodies' ability to bind their target has been extensively studied, little is known about the effect caused by the conjugation of hydrophilic and charged payloads such as oligonucleotides on the functions of an antibody. Previous observations of non-specific interactions of nucleic acids with untargeted cells prompted us to further investigate their impact on AOC binding abilities and cell selectivity. We synthesized a series of single- and double-stranded AOCs, as well as a human serum albumin-oligonucleotide conjugate, and studied their interactions with both targeted and non-targeted living cells using a time-resolved analysis of ligand binding assay. Our results indicate that conjugation of single strand oligonucleotides to proteins induce consistent non-specific interactions with cell surfaces while double strand oligonucleotides have little or no effect, depending on the preparation method.
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Affiliation(s)
- Victor Lehot
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Isabelle Kuhn
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Marc Nothisen
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Stéphane Erb
- BioOrganicMass Spectrometry Laboratory (LSMBO), IPHC, University of Strasbourg, 25 rue Becquerel, 67087, Strasbourg, France
| | - Sergii Kolodych
- Syndivia SAS, ISIS, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Sarah Cianférani
- BioOrganicMass Spectrometry Laboratory (LSMBO), IPHC, University of Strasbourg, 25 rue Becquerel, 67087, Strasbourg, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400, Illkirch-Graffenstaden, France.
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39
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Oerum S, Catala M, Bourguet M, Gilet L, Barraud P, Cianférani S, Condon C, Tisné C. Structural studies of RNase M5 reveal two-metal-ion supported two-step dsRNA cleavage for 5S rRNA maturation. RNA Biol 2021; 18:1996-2006. [PMID: 33541205 DOI: 10.1080/15476286.2021.1885896] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
All species transcribe ribosomal RNA in an immature form that requires several enzymes for processing into mature rRNA. The number and types of enzymes utilized for these processes vary greatly between different species. In low G + C Gram-positive bacteria including Bacillus subtilis and Geobacillus stearothermophilus, the endoribonuclease (RNase) M5 performs the final step in 5S rRNA maturation, by removing the 3'- and 5'-extensions from precursor (pre) 5S rRNA. This cleavage activity requires initial complex formation between the pre-rRNA and a ribosomal protein, uL18, making the full M5 substrate a ribonucleoprotein particle (RNP). M5 contains a catalytic N-terminal Toprim domain and an RNA-binding C-terminal domain, respectively, shown to assist in processing and binding of the RNP. Here, we present structural data that show how two Mg2+ ions are accommodated in the active site pocket of the catalytic Toprim domain and investigate the importance of these ions for catalysis. We further perform solution studies that support the previously proposed 3'-before-5' order of removal of the pre-5S rRNA extensions and map the corresponding M5 structural rearrangements during catalysis.
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Affiliation(s)
- Stephanie Oerum
- Expression Génétique Microbienne, UMR 8261, CNRS, Institut de Biologie Physico-Chimique (IBPC), Université de Paris, Paris, France
| | - Marjorie Catala
- Expression Génétique Microbienne, UMR 8261, CNRS, Institut de Biologie Physico-Chimique (IBPC), Université de Paris, Paris, France
| | - Maxime Bourguet
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, IPHC UMR 7178, Université de Strasbourg, Strasbourg, France
| | - Laetitia Gilet
- Expression Génétique Microbienne, UMR 8261, CNRS, Institut de Biologie Physico-Chimique (IBPC), Université de Paris, Paris, France
| | - Pierre Barraud
- Expression Génétique Microbienne, UMR 8261, CNRS, Institut de Biologie Physico-Chimique (IBPC), Université de Paris, Paris, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, CNRS, IPHC UMR 7178, Université de Strasbourg, Strasbourg, France
| | - Ciarán Condon
- Expression Génétique Microbienne, UMR 8261, CNRS, Institut de Biologie Physico-Chimique (IBPC), Université de Paris, Paris, France
| | - Carine Tisné
- Expression Génétique Microbienne, UMR 8261, CNRS, Institut de Biologie Physico-Chimique (IBPC), Université de Paris, Paris, France
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40
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Rady T, Mosser M, Nothisen M, Erb S, Dovgan I, Cianférani S, Wagner A, Chaubet G. Bicyclo[6.1.0]nonyne carboxylic acid for the production of stable molecular probes. RSC Adv 2021; 11:36777-36780. [PMID: 35494363 PMCID: PMC9043778 DOI: 10.1039/d1ra07905k] [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: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/24/2022] Open
Abstract
Bicyclo[6.1.0]non-4-yn-9-ylmethanol (BCN alcohol) is the most prominent strained-alkyne scaffold in chemical biology. Described herein is the synthesis of an oxidized analogue – BCN acid – whose facile functionalization via amide bond formation yields more stable derivatives than the classically encountered carbamates. We report a novel strained alkyne, coined BCN acid. This compound participates efficiently in diverse bioorthogonal reactions and allows the facile production of amide probes, which showed superior in vitro stability compared to carbamate analogues.![]()
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Affiliation(s)
- Tony Rady
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Michel Mosser
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Marc Nothisen
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Stephane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), LabEx Medalis, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Igor Dovgan
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), LabEx Medalis, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199), LabEx Medalis, University of Strasbourg, 74 Route du Rhin, 67400 Illkirch-Graffenstaden, France
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41
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Nguyen A, Nguyen D, Phong Nguyen TX, Sebastiani M, Dörr S, Hernandez-Alba O, Debaene F, Cianférani S, Heine A, Klebe G, Reuter K. The Importance of Charge in Perturbing the Aromatic Glue Stabilizing the Protein-Protein Interface of Homodimeric tRNA-Guanine Transglycosylase. ACS Chem Biol 2020; 15:3021-3029. [PMID: 33166460 DOI: 10.1021/acschembio.0c00700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Bacterial tRNA-guanine transglycosylase (Tgt) is involved in the biosynthesis of the modified tRNA nucleoside queuosine present in the anticodon wobble position of tRNAs specific for aspartate, asparagine, histidine, and tyrosine. Inactivation of the tgt gene leads to decreased pathogenicity of Shigella bacteria. Therefore, Tgt constitutes a putative target for Shigellosis drug therapy. Since it is only active as homodimer, interference with dimer-interface formation may, in addition to active-site inhibition, provide further means to disable this protein. A cluster of four aromatic residues seems important to stabilize the homodimer. We mutated residues of this aromatic cluster and analyzed each mutated variant with respect to the dimer and thermal stability or enzyme activity by applying native mass spectrometry, a thermal shift assay, enzyme kinetics, and X-ray crystallography. Our structural studies indicate a strong influence of pH on the homodimer stability. Apparently, protonation of a histidine within the aromatic cluster supports the collapse of an essential structural motif within the dimer interface at slightly acidic pH.
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Affiliation(s)
- Andreas Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Dzung Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Tran Xuan Phong Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Maurice Sebastiani
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Stefanie Dörr
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France
| | - François Debaene
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 F-Strasbourg, France
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
| | - Klaus Reuter
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 8, D-35037 Marburg, Germany
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42
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Belorusova AY, Bourguet M, Hessmann S, Chalhoub S, Kieffer B, Cianférani S, Rochel N. Molecular determinants of MED1 interaction with the DNA bound VDR-RXR heterodimer. Nucleic Acids Res 2020; 48:11199-11213. [PMID: 32990725 PMCID: PMC7641746 DOI: 10.1093/nar/gkaa775] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 06/29/2020] [Revised: 08/24/2020] [Accepted: 09/08/2020] [Indexed: 12/26/2022] Open
Abstract
The MED1 subunit of the Mediator complex is an essential coactivator of nuclear receptor-mediated transcriptional activation. While structural requirements for ligand-dependent binding of classical coactivator motifs of MED1 to numerous nuclear receptor ligand-binding domains have been fully elucidated, the recognition of the full-length or truncated coactivator by full nuclear receptor complexes remain unknown. Here we present structural details of the interaction between a large part of MED1 comprising its structured N-terminal and the flexible receptor-interacting domains and the mutual heterodimer of the vitamin D receptor (VDR) and the retinoid X receptor (RXR) bound to their cognate DNA response element. Using a combination of structural and biophysical methods we show that the ligand-dependent interaction between VDR and the second coactivator motif of MED1 is crucial for complex formation and we identify additional, previously unseen, interaction details. In particular, we identified RXR regions involved in the interaction with the structured N-terminal domain of MED1, as well as VDR regions outside the classical coactivator binding cleft affected by coactivator recruitment. These findings highlight important roles of each receptor within the heterodimer in selective recognition of MED1 and contribute to our understanding of the nuclear receptor-coregulator complexes.
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Affiliation(s)
- Anna Y Belorusova
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Maxime Bourguet
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR 7178, IPHC, Strasbourg, France
| | - Steve Hessmann
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR 7178, IPHC, Strasbourg, France
| | - Sandra Chalhoub
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Bruno Kieffer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR 7178, IPHC, Strasbourg, France
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Centre National de la Recherche Scientifique UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
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43
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Osz J, McEwen AG, Bourguet M, Przybilla F, Peluso-Iltis C, Poussin-Courmontagne P, Mély Y, Cianférani S, Jeffries CM, Svergun DI, Rochel N. Structural basis for DNA recognition and allosteric control of the retinoic acid receptors RAR-RXR. Nucleic Acids Res 2020; 48:9969-9985. [PMID: 32974652 PMCID: PMC7515732 DOI: 10.1093/nar/gkaa697] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 03/28/2020] [Revised: 07/16/2020] [Accepted: 08/12/2020] [Indexed: 12/14/2022] Open
Abstract
Retinoic acid receptors (RARs) as a functional heterodimer with retinoid X receptors (RXRs), bind a diverse series of RA-response elements (RAREs) in regulated genes. Among them, the non-canonical DR0 elements are bound by RXR–RAR with comparable affinities to DR5 elements but DR0 elements do not act transcriptionally as independent RAREs. In this work, we present structural insights for the recognition of DR5 and DR0 elements by RXR–RAR heterodimer using x-ray crystallography, small angle x-ray scattering, and hydrogen/deuterium exchange coupled to mass spectrometry. We solved the crystal structures of RXR–RAR DNA-binding domain in complex with the Rarb2 DR5 and RXR–RXR DNA-binding domain in complex with Hoxb13 DR0. While cooperative binding was observed on DR5, the two molecules bound non-cooperatively on DR0 on opposite sides of the DNA. In addition, our data unveil the structural organization and dynamics of the multi-domain RXR–RAR DNA complexes providing evidence for DNA-dependent allosteric communication between domains. Differential binding modes between DR0 and DR5 were observed leading to differences in conformation and structural dynamics of the multi-domain RXR–RAR DNA complexes. These results reveal that the topological organization of the RAR binding element confer regulatory information by modulating the overall topology and structural dynamics of the RXR–RAR heterodimers.
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Affiliation(s)
- Judit Osz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Alastair G McEwen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Maxime Bourguet
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR 7178, IPHC, Strasbourg, France
| | - Frédéric Przybilla
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Carole Peluso-Iltis
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Pierre Poussin-Courmontagne
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, CNRS UMR 7021, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS UMR 7178, IPHC, Strasbourg, France
| | - Cy M Jeffries
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Hamburg, Germany
| | - Natacha Rochel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Illkirch, France.,Institut National de La Santé et de La Recherche Médicale (INSERM) U1258, Illkirch, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Université de Strasbourg, Illkirch, France
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44
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Sornay C, Hessmann S, Erb S, Dovgan I, Ehkirch A, Botzanowski T, Cianférani S, Wagner A, Chaubet G. Frontispiece: Investigating Ugi/Passerini Multicomponent Reactions for the Site‐Selective Conjugation of Native Trastuzumab. Chemistry 2020. [DOI: 10.1002/chem.202086163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Charlotte Sornay
- Bio-Functional Chemistry (UMR 7199) LabEx Medalis University of Strasbourg 74 Route du Rhin 67400 Illkirch-Graffenstaden France
| | - Steve Hessmann
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO) LabEx Medalis Université de Strasbourg CNRS, IPHC UMR 7178 67000 Strasbourg France
| | - Stéphane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO) LabEx Medalis Université de Strasbourg CNRS, IPHC UMR 7178 67000 Strasbourg France
| | - Igor Dovgan
- Bio-Functional Chemistry (UMR 7199) LabEx Medalis University of Strasbourg 74 Route du Rhin 67400 Illkirch-Graffenstaden France
| | - Anthony Ehkirch
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO) LabEx Medalis Université de Strasbourg CNRS, IPHC UMR 7178 67000 Strasbourg France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO) LabEx Medalis Université de Strasbourg CNRS, IPHC UMR 7178 67000 Strasbourg France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO) LabEx Medalis Université de Strasbourg CNRS, IPHC UMR 7178 67000 Strasbourg France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199) LabEx Medalis University of Strasbourg 74 Route du Rhin 67400 Illkirch-Graffenstaden France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199) LabEx Medalis University of Strasbourg 74 Route du Rhin 67400 Illkirch-Graffenstaden France
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45
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Bouyssié D, Hesse AM, Mouton-Barbosa E, Rompais M, Macron C, Carapito C, Gonzalez de Peredo A, Couté Y, Dupierris V, Burel A, Menetrey JP, Kalaitzakis A, Poisat J, Romdhani A, Burlet-Schiltz O, Cianférani S, Garin J, Bruley C. Proline: an efficient and user-friendly software suite for large-scale proteomics. Bioinformatics 2020; 36:3148-3155. [PMID: 32096818 PMCID: PMC7214047 DOI: 10.1093/bioinformatics/btaa118] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [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: 07/20/2018] [Revised: 01/10/2020] [Accepted: 02/18/2020] [Indexed: 11/30/2022] Open
Abstract
Motivation The proteomics field requires the production and publication of reliable mass spectrometry-based identification and quantification results. Although many tools or algorithms exist, very few consider the importance of combining, in a unique software environment, efficient processing algorithms and a data management system to process and curate hundreds of datasets associated with a single proteomics study. Results Here, we present Proline, a robust software suite for analysis of MS-based proteomics data, which collects, processes and allows visualization and publication of proteomics datasets. We illustrate its ease of use for various steps in the validation and quantification workflow, its data curation capabilities and its computational efficiency. The DDA label-free quantification workflow efficiency was assessed by comparing results obtained with Proline to those obtained with a widely used software using a spiked-in sample. This assessment demonstrated Proline’s ability to provide high quantification accuracy in a user-friendly interface for datasets of any size. Availability and implementation Proline is available for Windows and Linux under CECILL open-source license. It can be deployed in client–server mode or in standalone mode at http://proline.profiproteomics.fr/#downloads. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David Bouyssié
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Anne-Marie Hesse
- Université Grenoble Alpes, Inserm, CEA, IRIG, BGE, Grenoble 38000, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Magali Rompais
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, Strasbourg 67087, UMR 7178, France
| | - Charlotte Macron
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, Strasbourg 67087, UMR 7178, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, Strasbourg 67087, UMR 7178, France
| | - Anne Gonzalez de Peredo
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Yohann Couté
- Université Grenoble Alpes, Inserm, CEA, IRIG, BGE, Grenoble 38000, France
| | | | - Alexandre Burel
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, Strasbourg 67087, UMR 7178, France
| | | | - Andrea Kalaitzakis
- Université Grenoble Alpes, Inserm, CEA, IRIG, BGE, Grenoble 38000, France
| | - Julie Poisat
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Aymen Romdhani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, Strasbourg 67087, UMR 7178, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, Strasbourg 67087, UMR 7178, France
| | - Jerome Garin
- Université Grenoble Alpes, Inserm, CEA, IRIG, BGE, Grenoble 38000, France
| | - Christophe Bruley
- Université Grenoble Alpes, Inserm, CEA, IRIG, BGE, Grenoble 38000, France
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46
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Pythoud N, Bons J, Mijola G, Beck A, Cianférani S, Carapito C. Optimized Sample Preparation and Data Processing of Data-Independent Acquisition Methods for the Robust Quantification of Trace-Level Host Cell Protein Impurities in Antibody Drug Products. J Proteome Res 2020; 20:923-931. [PMID: 33016074 DOI: 10.1021/acs.jproteome.0c00664] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Host cell proteins (HCPs) are a major class of bioprocess-related impurities generated by the host organism and are generally present at low levels in purified biopharmaceutical products. The monitoring of these impurities is identified as an important critical quality attribute of monoclonal antibody (mAb) formulations not only due to the potential risk for the product stability and efficacy but also concerns linked to the immunogenicity of some of them. While overall HCP levels are usually monitored by enzyme-linked immunosorbent assay (ELISA), mass spectrometry (MS)-based approaches have been emerging as powerful and promising alternatives providing qualitative and quantitative information. However, a major challenge for liquid chromatography (LC)-MS-based methods is to deal with the wide dynamic range of drug products and the extreme sensitivity required to detect trace-level HCPs. In this study, we developed powerful and reproducible MS-based analytical workflows coupling optimized and efficient sample preparations, the library-free data-independent acquisition (DIA) method, and stringent validation criteria. The performances of several preparation protocols and DIA versus classical data-dependent acquisition (DDA) were evaluated using a series of four commercially available drug products. Depending on the selected protocols, the user has access to different information: on the one hand, a deep profiling of tens of identified HCPs and on the other hand, accurate and reproducible (coefficients of variation (CVs) < 12%) quantification of major HCPs. Overall, a final global HCP amount of a few tens of ng/mg mAb in these mAb samples was measured, while reaching a sensitivity down to the sub-ng/mg mAb level. Thus, this straightforward and robust approach can be intended as a routine quality control for any drug product analysis.
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Affiliation(s)
- Nicolas Pythoud
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, UMR7178, F-67087 Strasbourg, France
| | - Joanna Bons
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, UMR7178, F-67087 Strasbourg, France
| | - Geoffroy Mijola
- IRPF, Centre d'Immunologie Pierre-Fabre (CIPF), F-74160 Saint-Julien-en-Genevois, France
| | - Alain Beck
- IRPF, Centre d'Immunologie Pierre-Fabre (CIPF), F-74160 Saint-Julien-en-Genevois, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, UMR7178, F-67087 Strasbourg, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC, UMR7178, F-67087 Strasbourg, France
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47
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Sornay C, Hessmann S, Erb S, Dovgan I, Ehkirch A, Botzanowski T, Cianférani S, Wagner A, Chaubet G. Investigating Ugi/Passerini Multicomponent Reactions for the Site‐Selective Conjugation of Native Trastuzumab**. Chemistry 2020; 26:13797-13805. [DOI: 10.1002/chem.202002432] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Charlotte Sornay
- Bio-Functional Chemistry (UMR 7199) LabEx Medalis University of Strasbourg 74 Route du Rhin 67400 Illkirch-Graffenstaden France
| | - Steve Hessmann
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO) LabEx Medalis Université de Strasbourg CNRS, IPHC UMR 7178 67000 Strasbourg France
| | - Stéphane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO) LabEx Medalis Université de Strasbourg CNRS, IPHC UMR 7178 67000 Strasbourg France
| | - Igor Dovgan
- Bio-Functional Chemistry (UMR 7199) LabEx Medalis University of Strasbourg 74 Route du Rhin 67400 Illkirch-Graffenstaden France
| | - Anthony Ehkirch
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO) LabEx Medalis Université de Strasbourg CNRS, IPHC UMR 7178 67000 Strasbourg France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO) LabEx Medalis Université de Strasbourg CNRS, IPHC UMR 7178 67000 Strasbourg France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO) LabEx Medalis Université de Strasbourg CNRS, IPHC UMR 7178 67000 Strasbourg France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199) LabEx Medalis University of Strasbourg 74 Route du Rhin 67400 Illkirch-Graffenstaden France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199) LabEx Medalis University of Strasbourg 74 Route du Rhin 67400 Illkirch-Graffenstaden France
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48
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Deslignière E, Ehkirch A, Botzanowski T, Beck A, Hernandez-Alba O, Cianférani S. Toward Automation of Collision-Induced Unfolding Experiments through Online Size Exclusion Chromatography Coupled to Native Mass Spectrometry. Anal Chem 2020; 92:12900-12908. [DOI: 10.1021/acs.analchem.0c01426] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Evolène Deslignière
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Anthony Ehkirch
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Alain Beck
- IRPF—Centre d’Immunologie Pierre-Fabre (CIPF), 74160 Saint-Julien-en-Genevois, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
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49
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Allison TM, Barran P, Cianférani S, Degiacomi MT, Gabelica V, Grandori R, Marklund EG, Menneteau T, Migas LG, Politis A, Sharon M, Sobott F, Thalassinos K, Benesch JLP. Computational Strategies and Challenges for Using Native Ion Mobility Mass Spectrometry in Biophysics and Structural Biology. Anal Chem 2020; 92:10872-10880. [DOI: 10.1021/acs.analchem.9b05791] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Timothy M. Allison
- School of Physical and Chemical Sciences, Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand
| | - Perdita Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), Université de Strasbourg, CNRS, IPHC UMR 7178, 67000 Strasbourg, France
| | - Matteo T. Degiacomi
- Department of Physics, Durham University, South Road, Durham, DH1 3LE, United Kingdom
| | - Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site, 2 Rue Robert Escarpit, 33600 Pessac, France
| | - Rita Grandori
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milan, Italy
| | - Erik G. Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123, Uppsala, Sweden
| | - Thomas Menneteau
- Division of Biosciences, Institute of Structural and Molecular Biology, University College of London, Gower Street, London WC1E 6BT, United Kingdom
| | - Lukasz G. Migas
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Argyris Politis
- Department of Chemistry, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry, Department of Chemistry, University of Antwerp, 2020 Antwerp, Belgium
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Konstantinos Thalassinos
- Department of Chemistry, King’s College London, 7 Trinity Street, London SE1 1DB, United Kingdom
- Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, Malet Street, London WC1E 7HX, United Kingdom
| | - Justin L. P. Benesch
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3TA, United Kingdom
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50
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Tessier R, Nandi RK, Dwyer BG, Abegg D, Sornay C, Ceballos J, Erb S, Cianférani S, Wagner A, Chaubet G, Adibekian A, Waser J. Frontispiz: Ethynylation of Cysteine Residues: From Peptides to Proteins in Vitro and in Living Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202082762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Romain Tessier
- Laboratory of Catalysis and Organic SynthesisEcole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 4306 1015 Lausanne Switzerland
- Present address: Department of Chemical BiologyMax Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Raj Kumar Nandi
- Laboratory of Catalysis and Organic SynthesisEcole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 4306 1015 Lausanne Switzerland
- Present address: Department of ChemistryDiamond Harbour Women's University Sarisha South 24 Parganas West Bengal 743368 India
| | - Brendan G. Dwyer
- Department of ChemistryThe Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Daniel Abegg
- Department of ChemistryThe Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Charlotte Sornay
- Bio-Functional Chemistry (UMR 7199)LabEx Medalis, University of Strasbourg 74 Route du Rhin 67400 Illkirch-Graffenstaden France
| | - Javier Ceballos
- Laboratory of Catalysis and Organic SynthesisEcole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 4306 1015 Lausanne Switzerland
| | - Stéphane Erb
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO)Université de StrasbourgCNRS, IPHC UMR 7178 67000 Strasbourg France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO)Université de StrasbourgCNRS, IPHC UMR 7178 67000 Strasbourg France
| | - Alain Wagner
- Bio-Functional Chemistry (UMR 7199)LabEx Medalis, University of Strasbourg 74 Route du Rhin 67400 Illkirch-Graffenstaden France
| | - Guilhem Chaubet
- Bio-Functional Chemistry (UMR 7199)LabEx Medalis, University of Strasbourg 74 Route du Rhin 67400 Illkirch-Graffenstaden France
| | - Alexander Adibekian
- Department of ChemistryThe Scripps Research Institute 130 Scripps Way Jupiter FL 33458 USA
| | - Jerome Waser
- Laboratory of Catalysis and Organic SynthesisEcole Polytechnique Fédérale de Lausanne EPFL SB ISIC LCSO, BCH 4306 1015 Lausanne Switzerland
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