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Schulz S, Boyer S, Smerlak M, Cocco S, Monasson R, Nizak C, Rivoire O. Parameters and determinants of responses to selection in antibody libraries. PLoS Comput Biol 2021; 17:e1008751. [PMID: 33765014 PMCID: PMC7993935 DOI: 10.1371/journal.pcbi.1008751] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 01/31/2021] [Indexed: 12/01/2022] Open
Abstract
The sequences of antibodies from a given repertoire are highly diverse at few sites located on the surface of a genome-encoded larger scaffold. The scaffold is often considered to play a lesser role than highly diverse, non-genome-encoded sites in controlling binding affinity and specificity. To gauge the impact of the scaffold, we carried out quantitative phage display experiments where we compare the response to selection for binding to four different targets of three different antibody libraries based on distinct scaffolds but harboring the same diversity at randomized sites. We first show that the response to selection of an antibody library may be captured by two measurable parameters. Second, we provide evidence that one of these parameters is determined by the degree of affinity maturation of the scaffold, affinity maturation being the process by which antibodies accumulate somatic mutations to evolve towards higher affinities during the natural immune response. In all cases, we find that libraries of antibodies built around maturated scaffolds have a lower response to selection to other arbitrary targets than libraries built around germline-based scaffolds. We thus propose that germline-encoded scaffolds have a higher selective potential than maturated ones as a consequence of a selection for this potential over the long-term evolution of germline antibody genes. Our results are a first step towards quantifying the evolutionary potential of biomolecules. Antibodies in the immune system consist of a genetically encoded scaffold that exposes a few highly diverse, non-genetically encoded sites. This focused diversity is sufficient to produce antibodies that bind to any target molecule. To understand the role of the scaffold, which acquires hypermutations during the immune response, over the selective response, we analyze quantitative in vitro experiments where large antibody populations based on different scaffolds are selected against different targets. We show that selective responses are described statistically by two parameters, one of which depends on prior evolution of the scaffold as part of a previous response. Our work provides methods to assay whether naïve antibody scaffolds are endowed with a distinctively high selective potential.
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Affiliation(s)
- Steven Schulz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050, PSL University, Paris, France
| | - Sébastien Boyer
- Département de biochimie, Faculté de Médecine, Université de Montréal, Montréal, Canada
| | - Matteo Smerlak
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
| | - Simona Cocco
- Laboratory of Physics of École Normale Supérieure, UMR 8023, CNRS & PSL University, Paris, France
| | - Rémi Monasson
- Laboratory of Physics of École Normale Supérieure, UMR 8023, CNRS & PSL University, Paris, France
| | - Clément Nizak
- Laboratory of Biochemistry, CBI, UMR 8231, ESPCI Paris, PSL University, CNRS, Paris, France
- * E-mail: (CN); (OR)
| | - Olivier Rivoire
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050, PSL University, Paris, France
- * E-mail: (CN); (OR)
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2
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Gérard A, Woolfe A, Mottet G, Reichen M, Castrillon C, Menrath V, Ellouze S, Poitou A, Doineau R, Briseno-Roa L, Canales-Herrerias P, Mary P, Rose G, Ortega C, Delincé M, Essono S, Jia B, Iannascoli B, Richard-Le Goff O, Kumar R, Stewart SN, Pousse Y, Shen B, Grosselin K, Saudemont B, Sautel-Caillé A, Godina A, McNamara S, Eyer K, Millot GA, Baudry J, England P, Nizak C, Jensen A, Griffiths AD, Bruhns P, Brenan C. Author Correction: High-throughput single-cell activity-based screening and sequencing of antibodies using droplet microfluidics. Nat Biotechnol 2020; 38:756. [PMID: 32444853 DOI: 10.1038/s41587-020-0563-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
| | | | - Guillaume Mottet
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France
| | | | - Carlos Castrillon
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France.,École Doctorale Frontières du Vivant (FdV), Centre de Recherches Interdisciplinaires, Paris, France.,Laboratoire de Biochimie (LBC), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, Paris, France
| | | | | | | | - Raphaël Doineau
- HiFiBiO Therapeutics SAS, Paris, France.,École Doctorale Frontières du Vivant (FdV), Centre de Recherches Interdisciplinaires, Paris, France.,Laboratoire de Biochimie (LBC), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, Paris, France.,Institute for Integrative Nanosciences, Leibniz IFW Dresden e.V., Dresden, Germany
| | - Luis Briseno-Roa
- HiFiBiO Therapeutics SAS, Paris, France.,Medetia Pharma, Institut Imagine, Paris, France
| | - Pablo Canales-Herrerias
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France.,École Doctorale Frontières du Vivant (FdV), Centre de Recherches Interdisciplinaires, Paris, France.,Laboratoire Colloïdes et Matériaux Divisés (LCMD), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, Paris, France
| | | | | | | | | | | | - Bin Jia
- Pfizer, Cambridge, MA, USA.,Abbvie Bioresearch Center, Worcester, MA, USA
| | - Bruno Iannascoli
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France
| | - Odile Richard-Le Goff
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France
| | | | | | | | | | - Kevin Grosselin
- HiFiBiO Therapeutics SAS, Paris, France.,Laboratoire de Biochimie (LBC), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, Paris, France
| | - Baptiste Saudemont
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France.,Laboratoire de Biochimie (LBC), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, Paris, France
| | - Antoine Sautel-Caillé
- Laboratoire de Biochimie (LBC), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, Paris, France
| | - Alexei Godina
- Laboratoire de Biochimie (LBC), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, Paris, France
| | | | - Klaus Eyer
- Laboratoire Colloïdes et Matériaux Divisés (LCMD), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, Paris, France.,Laboratory for Functional Immune Repertoire Analysis, Institute of Pharmaceutical Sciences, D-CHAB, ETH Zürich, Zurich, Switzerland
| | - Gaël A Millot
- Institut Pasteur, Hub Bioinformatique et Biostatistique, C3BI, USR 3756 IP CNRS, Paris, France
| | - Jean Baudry
- Laboratoire Colloïdes et Matériaux Divisés (LCMD), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, Paris, France
| | - Patrick England
- Plateforme de Biophysique Moléculaire, Institut Pasteur, CNRS UMR3528, Paris, France.,Centre d'Innovation et de Technologie, Plateforme de Biophysique des Macromolecules et de leurs Interactions, Institut Pasteur, Paris, France
| | - Clément Nizak
- Laboratoire de Biochimie (LBC), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, Paris, France
| | - Allan Jensen
- HiFiBiO Therapeutics SAS, Paris, France.,Lundbeck A/S, Valby, Denmark
| | - Andrew D Griffiths
- Laboratoire de Biochimie (LBC), ESPCI Paris, PSL Research University, CNRS UMR8231 Chimie Biologie Innovation, Paris, France.
| | - Pierre Bruhns
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 INSERM, Paris, France.
| | - Colin Brenan
- HiFiBiO Therapeutics SAS, Paris, France. .,HiFiBiO Therapeutics Inc., Cambridge, MA, USA. .,1CellBiO Inc., Watertown, MA, USA.
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3
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Fenneteau J, Chauvin D, Griffiths AD, Nizak C, Cossy J. Synthesis of new hydrophilic rhodamine based enzymatic substrates compatible with droplet-based microfluidic assays. Chem Commun (Camb) 2018; 53:5437-5440. [PMID: 28462964 DOI: 10.1039/c7cc01506b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Here we report the conception, synthesis and evaluation of new hydrophilic rhodamine-based enzymatic substrates for detection of peptidase activity compatible with high-throughput screening using droplet-based microfluidics.
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Affiliation(s)
- Johan Fenneteau
- Laboratoire de Chimie Organique, Institute of Chemistry, Biology and Innovation (CBI), UMR 8231, ESPCI Paris/CNRS, PSL Research University, 10 rue Vauquelin, 75231-Paris Cedex 05, France.
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4
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Boyer S, Biswas D, Kumar Soshee A, Scaramozzino N, Nizak C, Rivoire O. Hierarchy and extremes in selections from pools of randomized proteins. Proc Natl Acad Sci U S A 2016; 113:3482-7. [PMID: 26969726 PMCID: PMC4822605 DOI: 10.1073/pnas.1517813113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Variation and selection are the core principles of Darwinian evolution, but quantitatively relating the diversity of a population to its capacity to respond to selection is challenging. Here, we examine this problem at a molecular level in the context of populations of partially randomized proteins selected for binding to well-defined targets. We built several minimal protein libraries, screened them in vitro by phage display, and analyzed their response to selection by high-throughput sequencing. A statistical analysis of the results reveals two main findings. First, libraries with the same sequence diversity but built around different "frameworks" typically have vastly different responses; second, the distribution of responses of the best binders in a library follows a simple scaling law. We show how an elementary probabilistic model based on extreme value theory rationalizes the latter finding. Our results have implications for designing synthetic protein libraries, estimating the density of functional biomolecules in sequence space, characterizing diversity in natural populations, and experimentally investigating evolvability (i.e., the potential for future evolution).
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Affiliation(s)
- Sébastien Boyer
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, 38000 Grenoble, France
| | - Dipanwita Biswas
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, 38000 Grenoble, France
| | - Ananda Kumar Soshee
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, 38000 Grenoble, France
| | - Natale Scaramozzino
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, 38000 Grenoble, France
| | - Clément Nizak
- Laboratoire de Biochimie, Chimie-Biologie-Innovation UMR8231, CNRS and Ecole Supérieure de Physique et Chimie Industrielles ParisTech, Paris Sciences & Lettres Research University, 75005 Paris, France
| | - Olivier Rivoire
- Laboratoire Interdisciplinaire de Physique, CNRS and Université Grenoble Alpes, 38000 Grenoble, France;
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5
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Dubravcic D, van Baalen M, Nizak C. An evolutionarily significant unicellular strategy in response to starvation in Dictyostelium social amoebae. F1000Res 2014; 3:133. [PMID: 25309731 PMCID: PMC4184345 DOI: 10.12688/f1000research.4218.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/01/2014] [Indexed: 02/04/2024] Open
Abstract
The social amoeba Dictyostelium discoideum is widely studied for its multicellular development program as a response to starvation. Aggregates of up to 10 (6) cells form fruiting bodies containing (i) dormant spores (~80%) that can persist for months in the absence of nutrients, and (ii) dead stalk cells (~20%) that promote the dispersion of the spores towards nutrient-rich areas. It is often overlooked that not all cells aggregate upon starvation. Using a new quantitative approach based on time-lapse fluorescence microscopy and a low ratio of reporting cells, we have quantified this fraction of non-aggregating cells. In realistic starvation conditions, up to 15% of cells do not aggregate, which makes this third cell fate a significant component of the population-level response of social amoebae to starvation. Non-aggregating cells have an advantage over cells in aggregates since they resume growth earlier upon arrival of new nutrients, but have a shorter lifespan under prolonged starvation. We find that phenotypic heterogeneities linked to cell nutritional state bias the representation of cells in the aggregating vs. non-aggregating fractions, and thus affect population partitioning. Next, we report that the fraction of non-aggregating cells depends on genetic factors that regulate the timing of starvation, signal sensing efficiency and aggregation efficiency. In addition, interactions between clones in mixtures of non-isogenic cells affect the partitioning of each clone into both fractions. We further build a numerical model to test the evolutionary significance of the non-aggregating cell fraction. The partitioning of cells into aggregating and non-aggregating fractions is optimal in fluctuating environments with an unpredictable duration of starvation periods. Our study highlights the unicellular component of the response of social amoebae to starvation, and thus extends its evolutionary and ecological framework.
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Affiliation(s)
- Darja Dubravcic
- CNRS, LIPHY, F-38000 Grenoble, France
- Laboratory of Ecology and Evolution, CNRS UMR7625, Ecole Normale Supérieure, Université Pierre et Marie Curie, Paris Universitas, CNRS, Paris, France
| | - Minus van Baalen
- Laboratory of Ecology and Evolution, CNRS UMR7625, Ecole Normale Supérieure, Université Pierre et Marie Curie, Paris Universitas, CNRS, Paris, France
| | - Clément Nizak
- CNRS, LIPHY, F-38000 Grenoble, France
- Laboratory of Biochemistry, UMR 8231 ESPCI ParisTech/CNRS, PSL Research University, Paris, France
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6
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Abstract
The social amoeba Dictyostelium discoideum is widely studied for its multicellular development program as a response to starvation. Aggregates of up to 10 (6) cells form fruiting bodies containing (i) dormant spores (~80%) that can persist for months in the absence of nutrients, and (ii) dead stalk cells (~20%) that promote the dispersion of the spores towards nutrient-rich areas. It is often overlooked that not all cells aggregate upon starvation. Using a new quantitative approach based on time-lapse fluorescence microscopy and a low ratio of reporting cells, we have quantified this fraction of non-aggregating cells. In realistic starvation conditions, up to 15% of cells do not aggregate, which makes this third cell fate a significant component of the population-level response of social amoebae to starvation. Non-aggregating cells have an advantage over cells in aggregates since they resume growth earlier upon arrival of new nutrients, but have a shorter lifespan under prolonged starvation. We find that phenotypic heterogeneities linked to cell nutritional state bias the representation of cells in the aggregating vs. non-aggregating fractions, and thus affect population partitioning. Next, we report that the fraction of non-aggregating cells depends on genetic factors that regulate the timing of starvation, signal sensing efficiency and aggregation efficiency. In addition, interactions between clones in mixtures of non-isogenic cells affect the partitioning of each clone into both fractions. We further build a numerical model to test the evolutionary significance of the non-aggregating cell fraction. The partitioning of cells into aggregating and non-aggregating fractions is optimal in fluctuating environments with an unpredictable duration of starvation periods. Our study highlights the unicellular component of the response of social amoebae to starvation, and thus extends its evolutionary and ecological framework.
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Affiliation(s)
- Darja Dubravcic
- CNRS, LIPHY, F-38000 Grenoble, France ; Laboratory of Ecology and Evolution, CNRS UMR7625, Ecole Normale Supérieure, Université Pierre et Marie Curie, Paris Universitas, CNRS, Paris, France
| | - Minus van Baalen
- Laboratory of Ecology and Evolution, CNRS UMR7625, Ecole Normale Supérieure, Université Pierre et Marie Curie, Paris Universitas, CNRS, Paris, France
| | - Clément Nizak
- CNRS, LIPHY, F-38000 Grenoble, France ; Laboratory of Biochemistry, UMR 8231 ESPCI ParisTech/CNRS, PSL Research University, Paris, France
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7
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Modi S, Halder S, Nizak C, Krishnan Y. Recombinant antibody mediated delivery of organelle-specific DNA pH sensors along endocytic pathways. Nanoscale 2014; 6:1144-1152. [PMID: 24297098 DOI: 10.1039/c3nr03769j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
DNA has been used to build nanomachines with potential in cellulo and in vivo applications. However their different in cellulo applications are limited by the lack of generalizable strategies to deliver them to precise intracellular locations. Here we describe a new molecular design of DNA pH sensors with response times that are nearly 20 fold faster. Further, by changing the sequence of the pH sensitive domain of the DNA sensor, we have been able to tune their pH sensitive regimes and create a family of DNA sensors spanning ranges from pH 4 to 7.6. To enable a generalizable targeting methodology, this new sensor design also incorporates a 'handle' domain. We have identified, using a phage display screen, a set of three recombinant antibodies (scFv) that bind sequence specifically to the handle domain. Sequence analysis of these antibodies revealed several conserved residues that mediate specific interactions with the cognate DNA duplex. We also found that all three scFvs clustered into different branches indicating that their specificity arises from mutations in key residues. When one of these scFvs is fused to a membrane protein (furin) that traffics via the cell surface, the scFv-furin chimera binds the 'handle' and ferries a family of DNA pH sensors along the furin endocytic pathway. Post endocytosis, all DNA nanodevices retain their functionality in cellulo and provide spatiotemporal pH maps of retrogradely trafficking furin inside living cells. This new molecular technology of DNA-scFv-protein chimeras can be used to site-specifically complex DNA nanostructures for bioanalytical applications.
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Affiliation(s)
- Souvik Modi
- National Centre for Biological Sciences, TIFR, GKVK, Bellary Road, Bangalore 560 065, India.
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8
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Soshee A, Zürcher S, Spencer ND, Halperin A, Nizak C. General in vitro method to analyze the interactions of synthetic polymers with human antibody repertoires. Biomacromolecules 2013; 15:113-21. [PMID: 24328191 DOI: 10.1021/bm401360y] [Citation(s) in RCA: 9] [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: 01/01/2023]
Abstract
Recent reports on the hitherto underestimated antigenicity of poly(ethylene glycol) (PEG), which is widely used for pharmaceutical applications, highlight the need for efficient testing of polymer antigenicity and for a better understanding of its molecular origins. With this goal in mind, we have used the phage-display technique to screen large, recombinant antibody repertoires of human origin in vitro for antibodies that bind poly(vinylpyrrolidone) (PVP). PVP is a neutral synthetic polymer of industrial and clinical interest that is also a well-known model antigen in animal studies, thus allowing the comparison of in vitro and in vivo responses. We have identified 44 distinct antibodies that bind specifically to PVP. Competitive binding assays show that the PVP-antibody binding constant is proportional to the polymerization degree of PVP and that specific binding is detected down to the vinylpyrrolidone (VP) monomer level. Statistical analysis of anti-PVP antibody sequences identifies an amino-acid motif that is shared by many phage-display-selected anti-PVP antibodies that are similar to a previously described natural anti-PVP antibody. This suggests a role for this motif in specific antibody/PVP interactions. Interestingly, sequence analysis also suggests that only a single antibody chain containing this shared motif is responsible for antibody binding to PVP, as confirmed upon systematic deletion of either antibody chain for 90% of selected anti-PVP antibodies. Overall, a large number of antibodies in the human repertoires we have screened bind specifically to PVP through a small number of shared amino acid motifs, and preliminary comparison points to significant correlations between the sequences of phage-display-selected anti-PVP antibodies and their natural counterparts isolated from immunized mice in previous studies. This study pioneers the use of antibody phage-display to explore the antigenicity of biotechnologically relevant polymers. It also paves the way for a fast, cost-effective, and systematic in vitro analysis, thus reducing the need for animal immunization experiments. Moreover, identifying the encoding DNA sequence of polymer-binding antibodies via phage-display enables future applications of a molecular biology approach to protein-polymer conjugation, based on protein-antibody fusion.
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Affiliation(s)
- Anandakumar Soshee
- Laboratory of Interdisciplinary Physics, UMR5588 Grenoble Université 1/CNRS , Grenoble, France
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Modi S, Nizak C, Surana S, Halder S, Krishnan Y. Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell. Nat Nanotechnol 2013; 8:459-67. [PMID: 23708428 DOI: 10.1038/nnano.2013.92] [Citation(s) in RCA: 251] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 04/22/2013] [Indexed: 05/18/2023]
Abstract
DNA is a versatile scaffold for molecular sensing in living cells, and various cellular applications of DNA nanodevices have been demonstrated. However, the simultaneous use of different DNA nanodevices within the same living cell remains a challenge. Here, we show that two distinct DNA nanomachines can be used simultaneously to map pH gradients along two different but intersecting cellular entry pathways. The two nanomachines, which are molecularly programmed to enter cells via different pathways, can map pH changes within well-defined subcellular environments along both pathways inside the same cell. We applied these nanomachines to probe the pH of early endosomes and the trans-Golgi network, in real time. When delivered either sequentially or simultaneously, both nanomachines localized into and independently captured the pH of the organelles for which they were designed. The successful functioning of DNA nanodevices within living systems has important implications for sensing and therapies in a diverse range of contexts.
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Affiliation(s)
- Souvik Modi
- National Centre for Biological Sciences, TIFR, GKVK, Bellary Road, Bangalore 560065, India
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Vielemeyer O, Nizak C, Jimenez AJ, Echard A, Goud B, Camonis J, Rain JC, Perez F. Characterization of single chain antibody targets through yeast two hybrid. BMC Biotechnol 2010; 10:59. [PMID: 20727208 PMCID: PMC2936416 DOI: 10.1186/1472-6750-10-59] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [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: 04/26/2010] [Accepted: 08/22/2010] [Indexed: 05/12/2023] Open
Abstract
Background Due to their unique ability to bind their targets with high fidelity, antibodies are used widely not only in biomedical research, but also in many clinical applications. Recombinant antibodies, including single chain variable fragments (scFv), are gaining momentum because they allow powerful in vitro selection and manipulation without loss of function. Regardless of the ultimate application or type of antibody used, precise understanding of the interaction between the antibody's binding site and its specific target epitope(s) is of great importance. However, such data is frequently difficult to obtain. Results We describe an approach that allows detailed characterization of a given antibody's target(s) using the yeast two-hybrid system. Several recombinant scFv were used as bait and screened against highly complex cDNA libraries. Systematic sequencing of all retained clones and statistical analysis allowed efficient ranking of the prey fragments. Multiple alignment of the obtained cDNA fragments provided a selected interacting domain (SID), efficiently narrowing the epitope-containing region. Interactions between antibodies and their respective targets were characterized for several scFv. For AA2 and ROF7, two conformation-specific sensors that exclusively bind the activated forms of the small GTPases Rab6 and Rab1 respectively, only fragments expressing the entire target protein's core region were retained. This strongly suggested interaction with a non-linear epitope. For two other scFv, TA10 and SF9, which recognize the large proteins giantin and non-muscle myosin IIA, respectively, precise antibody-binding regions within the target were defined. Finally, for some antibodies, secondary targets within and across species could be revealed. Conclusions Our method, utilizing the yeast two-hybrid technology and scFv as bait, is a simple yet powerful approach for the detailed characterization of antibody targets. It allows precise domain mapping for linear epitopes, confirmation of non-linear epitopes for conformational sensors, and detection of secondary binding partners. This approach may thus prove to be an elegant and rapid method for the target characterization of newly obtained scFv antibodies. It may be considered prior to any research application and particularly before any use of such recombinant antibodies in clinical medicine.
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Affiliation(s)
- Ole Vielemeyer
- Institut Curie-Research Center, 26 rue d'Ulm, Paris cedex 05, France
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Adiba S, Nizak C, van Baalen M, Denamur E, Depaulis F. From grazing resistance to pathogenesis: the coincidental evolution of virulence factors. PLoS One 2010; 5:e11882. [PMID: 20711443 PMCID: PMC2920306 DOI: 10.1371/journal.pone.0011882] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Accepted: 07/09/2010] [Indexed: 11/29/2022] Open
Abstract
To many pathogenic bacteria, human hosts are an evolutionary dead end. This begs the question what evolutionary forces have shaped their virulence traits. Why are these bacteria so virulent? The coincidental evolution hypothesis suggests that such virulence factors result from adaptation to other ecological niches. In particular, virulence traits in bacteria might result from selective pressure exerted by protozoan predator. Thus, grazing resistance may be an evolutionarily exaptation for bacterial pathogenicity. This hypothesis was tested by subjecting a well characterized collection of 31 Escherichia coli strains (human commensal or extra-intestinal pathogenic) to grazing by the social haploid amoeba Dictyostelium discoideum. We then assessed how resistance to grazing correlates with some bacterial traits, such as the presence of virulence genes. Whatever the relative population size (bacteria/amoeba) for a non-pathogenic bacteria strain, D. discoideum was able to phagocytise, digest and grow. In contrast, a pathogenic bacterium strain killed D. discoideum above a certain bacteria/amoeba population size. A plating assay was then carried out using the E. coli collection faced to the grazing of D. discoideum. E. coli strains carrying virulence genes such as iroN, irp2, fyuA involved in iron uptake, belonging to the B2 phylogenetic group and being virulent in a mouse model of septicaemia were resistant to the grazing from D. discoideum. Experimental proof of the key role of the irp gene in the grazing resistance was evidenced with a mutant strain lacking this gene. Such determinant of virulence may well be originally selected and (or) further maintained for their role in natural habitat: resistance to digestion by free-living protozoa, rather than for virulence per se.
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Affiliation(s)
- Sandrine Adiba
- Laboratoire d'Ecologie, CNRS UMR7625, Université Pierre et Marie Curie, Paris Universitas, Paris, France.
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12
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Vielemeyer O, Yuan H, Moutel S, Saint-Fort R, Tang D, Nizak C, Goud B, Wang Y, Perez F. Direct selection of monoclonal phosphospecific antibodies without prior phosphoamino acid mapping. J Biol Chem 2009; 284:20791-5. [PMID: 19473967 DOI: 10.1074/jbc.m109.008730] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the current post-genomic era, large scale efforts are underway to functionally explore the proteome by assembling large antibody libraries. However, because many proteins are modified post-translationally to regulate their function, collections of modification-specific sensors are also needed. Here we applied a novel approach to select monoclonal phosphospecific antibodies directly from the full-length protein and without up-front phosphoamino acid identification. We chose as antigen GRASP65, a well studied Golgi phosphoprotein. Bacterially produced full-length protein was first incubated with mitotic cytosol, thus allowing modification by naturally occurring kinases, and then used directly for affinity-based antibody selection using a single chain variable fragment phagemid library. In less than 1 week, three distinct and highly functional monoclonal phosphospecific antibodies against two GRASP65 epitopes were obtained and subsequently characterized. The presented approach is carried out fully in vitro, requires no prior knowledge of the phosphoamino acid identity, and is fast and inexpensive. It therefore has great potential to be an attractive alternative to classic animal-based protocols for the selection of post-translation modification sensors and thus to become an invaluable tool in our quest to understand the proteome in all its complexity.
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Affiliation(s)
- Ole Vielemeyer
- Research Section, Translational Department, Institut Curie, 26 Rue d'Ulm, 75248 Paris Cedex 5, France
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Moutel S, El Marjou A, Vielemeyer O, Nizak C, Benaroch P, Dübel S, Perez F. A multi-Fc-species system for recombinant antibody production. BMC Biotechnol 2009; 9:14. [PMID: 19245715 PMCID: PMC2654441 DOI: 10.1186/1472-6750-9-14] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [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: 08/04/2008] [Accepted: 02/26/2009] [Indexed: 11/29/2022] Open
Abstract
Background Genomic, transcriptomic and proteomic projects often suffer from a lack of functional validation creating a strong demand for specific and versatile antibodies. Antibody phage display represents an attractive approach to select rapidly in vitro the equivalent of monoclonal antibodies, like single chain Fv antibodies, in an inexpensive and animal free way. However, so far, recombinant antibodies have not managed to impose themselves as efficient alternatives to natural antibodies. Results We developed a series of vectors that allow one to easily fuse single chain Fv antibodies to Fc domains of immunoglobulins, improving their sensitivity and facilitating their use. This series enables the fusion of single chain Fv antibodies with human, mouse or rabbit Fc so that a given antibody is no longer restricted to a particular species. This opens up unlimited multiplexing possibilities and gives additional value to recombinant antibodies. We also show that this multi-Fc species production system can be applied to natural monoclonal antibodies cloned as single chain Fv antibodies and we converted the widely used 9E10 mouse anti-Myc-tag antibody into a human and a rabbit antibody. Conclusion Altogether, this new expression system, that brings constant quality, sensitivity and unique versatility, will be important to broaden the use of recombinant and natural monoclonal antibodies both for laboratory and diagnosis use.
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Abstract
Dictyostelium amoebae faced with starvation trigger a developmental program during which many cells aggregate and form fruiting bodies that consist of a ball of spores held aloft by a thin stalk. This developmental strategy is open to several forms of exploitation, including the remarkable case of Dictyostelium caveatum, which, even when it constitutes 1/10(3) of the cells in an aggregate, can inhibit the development of the host and eventually devour it. We show that it accomplishes this feat by inhibiting a region of cells, called the tip, which organizes the development of the aggregate into a fruiting body. We use live-cell microscopy to define the D. caveatum developmental cycle and to show that D. caveatum amoebae have the capacity to ingest amoebae of other Dictyostelid species, but do not attack each other. The block in development induced by D. caveatum does not affect the expression of specific markers of prespore cell or prestalk cell differentiation, but does stop the coordinated cell movement leading to tip formation. The inhibition mechanism involves the constitutive secretion of a small molecule by D. caveatum and is reversible. Four Dictyostelid species were inhibited in their development, while D. caveatum is not inhibited by its own compound(s). D. caveatum has evolved a predation strategy to exploit other members of its genus, including mechanisms of developmental inhibition and specific phagocytosis.
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Affiliation(s)
- Clément Nizak
- Living Matter Laboratory, Center for Physics and Biology, Rockefeller University, New York, New York, United States of America.
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Abstract
The closely related Rab6 isoforms, Rab6A and Rab6A', have been shown to regulate vesicular trafficking within the Golgi and post-Golgi compartments, but studies using dominant active or negative mutant suggested conflicting models. Here, we report that reduction in the expression of Rab6 isoform using specific small interfering RNA reveals noticeable differences in the Rab6A and Rab6A' biological functions. Surprisingly, Rab6A seems to be largely dispensable in membrane trafficking events, whereas knocking down the expression of Rab6A' hampers the intracellular transport of the retrograde cargo marker, the Shiga Toxin B-subunit along the endocytic pathway, and causes defects in Golgi- associated protein recycling through the endoplasmic reticulum. We also showed that Rab6A' is required for cell cycle progression through mitosis and identify Ile(62) as a key residue for uncoupling Rab6A' functions in mitosis and retrograde trafficking. Thus, our work shows that Rab6A and Rab6A' perform different functions within the cell and suggests a novel role for Rab6A' as the major Rab6 isoform regulating previously described Rab6-dependent transport pathways.
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Affiliation(s)
- Elaine Del Nery
- Molecular Mechanisms of Intracellular Transport, UMR CNRS 144, Institut Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
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Sannerud R, Marie M, Nizak C, Dale HA, Pernet-Gallay K, Perez F, Goud B, Saraste J. Rab1 defines a novel pathway connecting the pre-Golgi intermediate compartment with the cell periphery. Mol Biol Cell 2006; 17:1514-26. [PMID: 16421253 PMCID: PMC1415313 DOI: 10.1091/mbc.e05-08-0792] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The function of the pre-Golgi intermediate compartment (IC) and its relationship with the endoplasmic reticulum (ER) and Golgi remain only partially understood. Here, we report striking segregation of IC domains in polarized PC12 cells that develop neurite-like processes. Differentiation involves expansion of the IC and movement of Rab1-containing tubules to the growth cones of the neurites, whereas p58- and COPI-positive IC elements, like rough ER and Golgi, remain in the cell body. Exclusion of Rab1 effectors p115 and GM130 from the neurites further indicated that the centrifugal, Rab1-mediated pathway has functions that are not directly related to ER-to-Golgi trafficking. Disassembly of COPI coats did not affect this pathway but resulted in missorting of p58 to the neurites. Live cell imaging showed that green fluorescent protein (GFP)-Rab1A-containing IC elements move bidirectionally both within the neurites and cell bodies, interconnecting different ER exit sites and the cis-Golgi region. Moreover, in nonpolarized cells GFP-Rab1A-positive tubules moved centrifugally towards the cell cortex. Hydroxymethylglutaryl-CoA reductase, the key enzyme of cholesterol biosynthesis, colocalized with slowly sedimenting, Rab1-enriched membranes when the IC subdomains were separated by velocity sedimentation. These results reveal a novel pathway directly connecting the IC with the cell periphery and suggest that this Rab1-mediated pathway is linked to the dynamics of smooth ER.
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Affiliation(s)
- Ragna Sannerud
- Section of Anatomy and Cell Biology, Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
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Abstract
The existence of a conformational switch of Rabs and other small GTPases involved in intracellular transport regulation has been known for many years. This switch is superimposed on the membrane association/dissociation cycle for most of these GTPases. While these processes are key features of the dynamics of intracellular transport events, surprisingly very few previous studies have focused on the dynamics of the GDP/GTP cycle of Rab proteins in time and space. The main reason for this is the lack of tools available to dynamically probe for Rab GTPases conformation switches and membrane association/dissociation, in particular in vivo. We recently reported the in vitro selection of conformation-specific recombinant antibodies specific to the GTP-bound conformation of Rab6 proteins. These antibodies were obtained in vitro by phage display, a rather simple, rapid, and cheap technique. We additionally showed that these conformation-specific antibodies can be expressed in living cells to follow endogenous Rab6 in its activated conformation in vivo. The same strategy could be used to study other conformation switching mechanisms and, in general, to study the switching between states that antibodies can distinguish (e.g., phosphorylation, ubiquitination).
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Abstract
In mitosis, the Golgi complex is inherited following its dispersion, equal partitioning and reformation in each daughter cell. The state of Golgi membranes during mitosis is controversial, and the role of Golgi-intersecting traffic in Golgi inheritance is unclear. We have used brefeldin A (BFA) to perturb Golgi-intersecting membrane traffic at different stages of the cell cycle and followed by live cell imaging the fate of Golgi membranes in those conditions. We observed that addition of the drug on cells in prometaphase prevents mitotic Golgi dispersion. Under continuous treatment, Golgi fragments persist throughout mitosis and accumulate in a Golgi-like structure at the end of mitosis. This structure localizes at microtubule minus ends and contains all classes of Golgi markers, but is not accessible to cargo from the endoplasmic reticulum or the plasma membrane because of the continuous BFA traffic block. However, it contains preaccumulated cargo, and intermixes with the reforming Golgi upon BFA washout. This structure also forms when BFA is added during metaphase, when the Golgi is not discernible by light microscopy. Together the data indicate that independent Golgi fragments that contain all classes of Golgi markers (and that can be isolated from other organelles by blocking anterograde and retrograde Golgi-intersecting traffic) persist throughout mitosis.
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Affiliation(s)
- Clément Nizak
- Institut Curie, CNRS UMR144, 26 rue d'Ulm 75248 Paris cedex 05, France
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Nizak C, Martin-Lluesma S, Moutel S, Roux A, Kreis TE, Goud B, Perez F. Recombinant Antibodies Against Subcellular Fractions Used to Track Endogenous Golgi Protein Dynamicsin Vivo. Traffic 2003; 4:739-53. [PMID: 14617357 DOI: 10.1034/j.1600-0854.2003.00132.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Generation of specific antibodies against enriched subcellular fractions is a powerful strategy to identify and characterize cellular components. We show that recombinant antibodies can be selected in vitro by phage display against complex subcellular fractions, namely microtubule-binding proteins and Golgi stacks. This technique has allowed us to overcome many limitations of the classical animal-based approach and generate cell biology-compliant antibodies. In addition, we show that intracellular expression of GFP-tagged recombinant antibodies can reveal the dynamics of endogenous proteins in vivo. Endogenous Giantin is very static and outlines the Golgi in living cells. It accumulates neither onto Golgi-derived tubules upon Brefeldin A treatment before Golgi disappearance, nor onto de novo formed Golgi mini-stacks upon microtubule depolymerization, and remains instead on the 'old' pericentriolar Golgi. This suggests that, in contrast to other Golgi matrix proteins, endogenous Giantin is very stably associated with the Golgi and does not efficiently recycle to the ER. Altogether, we show that the antibody phage display technique represents an efficient alternative to rapidly generate versatile antibodies that represent new tools to study protein function.
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Affiliation(s)
- Clément Nizak
- CNRS UMR144, Institut Curie, 26 rue d'Ulm 75248 Paris cedex 05 France
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Abstract
The microtubule cytoskeleton plays a fundamental role in cell organization and membrane traffic in higher eukaryotes. It is well established that molecular motors are involved in membrane-microtubule interactions, but it has also been proposed that nonmotor microtubule-binding (MTB) proteins known as CLIPs (cytoplasmic linker proteins) have basic roles in these processes. We report here the characterization of CLIPR-59, a CLIP-170-related protein localized to the trans-most part of the Golgi apparatus. CLIPR-59 contains an acidic region followed by three ankyrin-like repeats and two CLIP-170-related MTB motifs. We show that the 60-amino acid-long carboxy-terminal domain of CLIPR-59 is necessary and sufficient to achieve Golgi targeting, which represents the first identification of a membrane targeting domain in a CLIP-170-related protein. The MTB domain of CLIPR-59 is functional because it localizes to microtubules when expressed as a fragment in HeLa cells. However, our results suggest that this domain is normally inhibited by the presence of adjacent domains, because neither full-length CLIPR-59 nor a CLIPR-59 mutant missing its membrane-targeting region localize to microtubules. Consistent with this observation, overexpression of CLIPR-59 does not affect the microtubule network. However, CLIPR-59 overexpression strongly perturbs early/recycling endosome-TGN dynamics, implicating CLIPR-59 in the regulation of this pathway.
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Affiliation(s)
- Franck Perez
- Institut Curie, CNRS UMR144, 75248 Paris, France.
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