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Almagro JC, Pedraza-Escalona M, Arrieta HI, Pérez-Tapia SM. Phage Display Libraries for Antibody Therapeutic Discovery and Development. Antibodies (Basel) 2019; 8:antib8030044. [PMID: 31544850 PMCID: PMC6784186 DOI: 10.3390/antib8030044] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 01/24/2023] Open
Abstract
Phage display technology has played a key role in the remarkable progress of discovering and optimizing antibodies for diverse applications, particularly antibody-based drugs. This technology was initially developed by George Smith in the mid-1980s and applied by John McCafferty and Gregory Winter to antibody engineering at the beginning of 1990s. Here, we compare nine phage display antibody libraries published in the last decade, which represent the state of the art in the discovery and development of therapeutic antibodies using phage display. We first discuss the quality of the libraries and the diverse types of antibody repertoires used as substrates to build the libraries, i.e., naïve, synthetic, and semisynthetic. Second, we review the performance of the libraries in terms of the number of positive clones per panning, hit rate, affinity, and developability of the selected antibodies. Finally, we highlight current opportunities and challenges pertaining to phage display platforms and related display technologies.
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Affiliation(s)
- Juan C Almagro
- GlobalBio, Inc., 320, Cambridge, MA 02138, USA.
- UDIBI, ENCB, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Casco de Santo Tomas, Delegación Miguel Hidalgo, Ciudad de Mexico 11340, Mexico.
| | - Martha Pedraza-Escalona
- CONACyT-UDIBI, ENCB, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Casco de Santo Tomas, Delegación Miguel Hidalgo, Ciudad de Mexico 11340, Mexico
| | - Hugo Iván Arrieta
- CONACyT-UDIBI, ENCB, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Casco de Santo Tomas, Delegación Miguel Hidalgo, Ciudad de Mexico 11340, Mexico
| | - Sonia Mayra Pérez-Tapia
- CONACyT-UDIBI, ENCB, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Colonia Casco de Santo Tomas, Delegación Miguel Hidalgo, Ciudad de Mexico 11340, Mexico
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102
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Lua WH, Su CTT, Yeo JY, Poh JJ, Ling WL, Phua SX, Gan SKE. Role of the IgE variable heavy chain in FcεRIα and superantigen binding in allergy and immunotherapy. J Allergy Clin Immunol 2019; 144:514-523.e5. [DOI: 10.1016/j.jaci.2019.03.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/25/2019] [Accepted: 03/29/2019] [Indexed: 01/17/2023]
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103
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Sewid AH, Hassan MN, Ammar AM, Bemis DA, Kania SA. Staphylococcus pseudintermedius Sbi paralogs inhibit complement and bind IgM, IgG Fc and Fab. PLoS One 2019; 14:e0219817. [PMID: 31335868 PMCID: PMC6650138 DOI: 10.1371/journal.pone.0219817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 07/03/2019] [Indexed: 12/30/2022] Open
Abstract
The success of staphylococci as pathogens has been attributed, in part, to their ability to evade their hosts’ immune systems. Although the proteins involved in evasion have been extensively studied in staphylococci affecting humans little characterization has been done with Staphylococcus pseudintermedius, an important cause of pyoderma in dogs. Staphylococcus aureus binder of immunoglobulin (Sbi) interferes with innate immune recognition by interacting with multiple host proteins. In this study, a S. pseudintermedius gene that shares 38% similarity to S. aureus Sbi was cloned from S. pseudintermedius strains representative of major clonal lineages bearing two paralogs of the protein. Binding of immunoglobulins and Fab and Fc fragments as well as interaction with complement was measured. S. pseudintermedius Sbi protein bound IgG from multiple species and canine complement C3, neutralized complement activity and bound to canine IgM and B cells. Evidence from this work suggests Sbi may play an important role in S. pseudintermedius immune evasion.
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Affiliation(s)
- Alaa H. Sewid
- Department of Biomedical and Diagnostic Sciences, University of Tennessee, Knoxville, Tennessee, United States of America
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - M. Nabil Hassan
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - A. M. Ammar
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - David A. Bemis
- Department of Biomedical and Diagnostic Sciences, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Stephen A. Kania
- Department of Biomedical and Diagnostic Sciences, University of Tennessee, Knoxville, Tennessee, United States of America
- * E-mail:
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104
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Yao Q, Weaver SJ, Mock JY, Jensen GJ. Fusion of DARPin to Aldolase Enables Visualization of Small Protein by Cryo-EM. Structure 2019; 27:1148-1155.e3. [PMID: 31080120 PMCID: PMC6610650 DOI: 10.1016/j.str.2019.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 03/04/2019] [Accepted: 04/05/2019] [Indexed: 12/21/2022]
Abstract
Solving protein structures by single-particle cryoelectron microscopy (cryo-EM) has become a crucial tool in structural biology. While exciting progress is being made toward the visualization of small macromolecules, the median protein size in both eukaryotes and bacteria is still beyond the reach of cryo-EM. To overcome this problem, we implemented a platform strategy in which a small protein target was rigidly attached to a large, symmetric base via a selectable adapter. Of our seven designs, the best construct used a designed ankyrin repeat protein (DARPin) rigidly fused to tetrameric rabbit muscle aldolase through a helical linker. The DARPin retained its ability to bind its target: GFP. We solved the structure of this complex to 3.0 Å resolution overall, with 5-8 Å resolution in the GFP region. As flexibility in the DARPin position limited the overall resolution of the target, we describe strategies to rigidify this element.
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Affiliation(s)
- Qing Yao
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Sara J Weaver
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Jee-Young Mock
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, 1200 E. California Boulevard, Pasadena, CA 91125, USA.
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105
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Foster TJ. Surface Proteins of Staphylococcus aureus. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0046-2018. [PMID: 31267926 PMCID: PMC10957221 DOI: 10.1128/microbiolspec.gpp3-0046-2018] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Indexed: 12/20/2022] Open
Abstract
The surface of Staphylococcus aureus is decorated with over 20 proteins that are covalently anchored to peptidoglycan by the action of sortase A. These cell wall-anchored (CWA) proteins can be classified into several structural and functional groups. The largest is the MSCRAMM family, which is characterized by tandemly repeated IgG-like folded domains that bind peptide ligands by the dock lock latch mechanism or the collagen triple helix by the collagen hug. Several CWA proteins comprise modules that have different functions, and some individual domains can bind different ligands, sometimes by different mechanisms. For example, the N-terminus of the fibronectin binding proteins comprises an MSCRAMM domain which binds several ligands, while the C-terminus is composed of tandem fibronectin binding repeats. Surface proteins promote adhesion to host cells and tissue, including components of the extracellular matrix, contribute to biofilm formation by stimulating attachment to the host or indwelling medical devices followed by cell-cell accumulation via homophilic interactions between proteins on neighboring cells, help bacteria evade host innate immune responses, participate in iron acquisition from host hemoglobin, and trigger invasion of bacteria into cells that are not normally phagocytic. The study of genetically manipulated strains using animal infection models has shown that many CWA proteins contribute to pathogenesis. Fragments of CWA proteins have the potential to be used in multicomponent vaccines to prevent S. aureus infections.
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106
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Maso K, Montagner IM, Grigoletto A, Schiavon O, Rosato A, Pasut G. A non-covalent antibody complex for the delivery of anti-cancer drugs. Eur J Pharm Biopharm 2019; 142:49-60. [PMID: 31201855 DOI: 10.1016/j.ejpb.2019.06.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 10/26/2022]
Abstract
Antibody drug conjugates (ADCs), which are obtained by coupling a potent cytotoxic agent to a monoclonal antibody (mAb), are traditionally bound in a random way to lysine or cysteine residues, with the final product's heterogeneity having an important impact on their activity, characterization, and manufacturing. A new antibody drug delivery system (ADS) based on a non-covalent linkage between a Fc-binding protein, in this case Protein A or Protein G, and a mAb was investigated in the effort to achieve greater homogeneity and to create a versatile and adaptable drug delivery system. Recombinant staphylococcal Protein A and streptococcal Protein G were chemically PEGylated at the N-terminus with a 5 kDa and a 20 kDa PEG, respectively, yielding two monoconjugates with a mass of ≈50 and ≈45 kDa. Circular dichroism studies showed that both conjugates preserved secondary structures of the protein, and isothermal titration calorimetry experiments demonstrated that their affinity for mAb was approximately 107 M-1. Upon complexation with a mAb (Trastuzumab or Rituximab), in vitro flow-cytometry analysis of the new ADSs showed high selectivity for the specific antigen expressing cells. In addition, the ADS complex based on Trastuzumab and Protein G, conjugated with a heterobifunctional 20 kDa PEG carrying the toxin Tubulysin A, had a marked cytotoxic effect on the cancer cell line overexpressing the HER2/neu receptor, thus supporting its application in cancer therapy.
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Affiliation(s)
- Katia Maso
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | | | - Antonella Grigoletto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Oddone Schiavon
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy
| | - Antonio Rosato
- Veneto Institute of Oncology IOV-IRCCS, Padua, Italy; Department of Surgery, Oncology and Gastroenterology, University of Padova, Via Gattamelata 64, 35128 Padova, Italy.
| | - Gianfranco Pasut
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via F. Marzolo 5, 35131 Padova, Italy; Veneto Institute of Oncology IOV-IRCCS, Padua, Italy.
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107
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Zhang Y, Wang Y, Li Y. A method for improving protein A chromatography's aggregate removal capability. Protein Expr Purif 2019; 158:65-73. [DOI: 10.1016/j.pep.2019.02.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 02/19/2019] [Accepted: 02/27/2019] [Indexed: 11/29/2022]
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108
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Insights into IgM-mediated complement activation based on in situ structures of IgM-C1-C4b. Proc Natl Acad Sci U S A 2019; 116:11900-11905. [PMID: 31147461 PMCID: PMC6575175 DOI: 10.1073/pnas.1901841116] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
IgM antibodies protect mammals against humoral microbial infection and mediate clearance of cellular debris. IgM activates the immune complement system only after binding to cell-surface antigens. Here we report the in situ 3D structures of surface-antigen–bound IgM antibodies in complex with both C1 and C4b complement components. The data indicate the structural arrangement of pentameric and hexameric IgM upon antigen binding, exposing the C1q-binding sites with both adopting hexagonal symmetry. The structures reveal the entire C1qr2s2 complex and elucidate several protein–protein interactions with C4b and IgM. Based on the structural data, we hypothesize a C1q-transmitted surface trigger that activates C1, leading to C4 cleavage and C4b deposition on membranes. Antigen binding by serum Ig-M (IgM) protects against microbial infections and helps to prevent autoimmunity, but causes life-threatening diseases when mistargeted. How antigen-bound IgM activates complement-immune responses remains unclear. We present cryoelectron tomography structures of IgM, C1, and C4b complexes formed on antigen-bearing lipid membranes by normal human serum at 4 °C. The IgM-C1-C4b complexes revealed C4b product release as the temperature-limiting step in complement activation. Both IgM hexamers and pentamers adopted hexagonal, dome-shaped structures with Fab pairs, dimerized by hinge domains, bound to surface antigens that support a platform of Fc regions. C1 binds IgM through widely spread C1q-collagen helices, with C1r proteases pointing outward and C1s bending downward and interacting with surface-attached C4b, which further interacts with the adjacent IgM-Fab2 and globular C1q-recognition unit. Based on these data, we present mechanistic models for antibody-mediated, C1q-transmitted activation of C1 and for C4b deposition, while further conformational rearrangements are required to form C3 convertases.
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109
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Rigi G, Ghaedmohammadi S, Ahmadian G. A comprehensive review on staphylococcal protein A (SpA): Its production and applications. Biotechnol Appl Biochem 2019; 66:454-464. [PMID: 30869160 DOI: 10.1002/bab.1742] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/13/2019] [Indexed: 01/09/2023]
Abstract
The Staphylococcus aureus protein A (SpA) can be obtained through the culture of wild-type S. aureus and also as a recombinant protein in safe bacterial hosts. Several methods have been used to purify SpA among which ion-exchange chromatography, affinity chromatography, gel filtration, and per aqueous liquid chromatography (PALC) are common. SpA has a wide range of biochemical, biotechnological, and medical applications and is most commonly used in test methods such as immunoprecipitation, enzyme-linked immunosorbent assay, and Western blotting. SpA has also been widely utilized in pharmaceutical applications to bind to immune complexes and serum immunoglobulins. SpA also directly binds to the B-cells preventing initiation of infectious diseases as well as having a role in the development of various autoimmune diseases. This review considers different applications of SpA in biotechnology and its novel clinical application for effective treatment of autoimmune diseases. It also discusses various strategies for expression and purification of the SpA including types of column chromatography that are commonly used in protein purification and developing SpA surface display technologies. Finally, this review highlights the potential and novel applications of SpA immobilization, SpA typing, protein engineering for further development of immunological and biochemical research, and also application of SpA as a diagnostic biosensor.
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Affiliation(s)
- Garshasb Rigi
- Department of Genetics, Faculty of Basic Science, Shahrekord University, Shahrekord, 881 863 4141, Iran.,Department of Industrial Biotechnology, Research Institute of Biotechnology, Shahrekord University, Shahrekord, Iran
| | - Samira Ghaedmohammadi
- Department of Cellular and Molecular Biology, Estahban Higher Education Center, Estahban, Iran
| | - Gholamreza Ahmadian
- Associate Professor, Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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110
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Tam K, Torres VJ. Staphylococcus aureus Secreted Toxins and Extracellular Enzymes. Microbiol Spectr 2019; 7:10.1128/microbiolspec.GPP3-0039-2018. [PMID: 30873936 PMCID: PMC6422052 DOI: 10.1128/microbiolspec.gpp3-0039-2018] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 02/06/2023] Open
Abstract
Staphylococcus aureus is a formidable pathogen capable of causing infections in different sites of the body in a variety of vertebrate animals, including humans and livestock. A major contribution to the success of S. aureus as a pathogen is the plethora of virulence factors that manipulate the host's innate and adaptive immune responses. Many of these immune modulating virulence factors are secreted toxins, cofactors for activating host zymogens, and exoenzymes. Secreted toxins such as pore-forming toxins and superantigens are highly inflammatory and can cause leukocyte cell death by cytolysis and clonal deletion, respectively. Coagulases and staphylokinases are cofactors that hijack the host's coagulation system. Exoenzymes, including nucleases and proteases, cleave and inactivate various immune defense and surveillance molecules, such as complement factors, antimicrobial peptides, and surface receptors that are important for leukocyte chemotaxis. Additionally, some of these secreted toxins and exoenzymes can cause disruption of endothelial and epithelial barriers through cell lysis and cleavage of junction proteins. A unique feature when examining the repertoire of S. aureus secreted virulence factors is the apparent functional redundancy exhibited by the majority of the toxins and exoenzymes. However, closer examination of each virulence factor revealed that each has unique properties that have important functional consequences. This chapter provides a brief overview of our current understanding of the major secreted virulence factors critical for S. aureus pathogenesis.
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Affiliation(s)
- Kayan Tam
- Department of Microbiology, New York University School of Medicine, Alexandria Center for Life Science, New York, NY 10016
| | - Victor J Torres
- Department of Microbiology, New York University School of Medicine, Alexandria Center for Life Science, New York, NY 10016
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111
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Mueller GA, Min J, Foo ACY, Pomés A, Pedersen LC. Structural Analysis of Recent Allergen-Antibody Complexes and Future Directions. Curr Allergy Asthma Rep 2019; 19:17. [PMID: 30815753 DOI: 10.1007/s11882-019-0848-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
PURPOSE OF REVIEW Allergen-antibody complexes are extremely valuable in describing the detailed molecular features of epitopes. This review summarizes insights gained from recently published co-structures and what obstacles impede the acquisition of further data. RECENT FINDINGS Structural epitope data helped define the epitopes of two anti-Fel d 1 antibodies undergoing phase I clinical trials, providing a greater level of detail than was possible through hydrogen-deuterium exchange protection studies. Separately, a human camelid-like antibody structure with lysozyme described several unique features in a long variable loop that interacted with the active site cleft of Gal d 4. Finally, a co-structure conclusively demonstrated that Phl p 7 could function as a superantigen and that an antibody could simultaneously recognize two epitopes. These remarkable assertions would not have been possible without visualization of the complex. Only three new complexes have appeared in the last few years, suggesting that there are major impediments to traditional production and crystallization. The structural data was extremely valuable in describing epitopes. New techniques like cryo-EM may provide an alternative to crystallography.
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Affiliation(s)
- Geoffrey A Mueller
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive MD-MR-01, Research Triangle Park, NC, 27709, USA.
| | - Jungki Min
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive MD-MR-01, Research Triangle Park, NC, 27709, USA
| | - Alexander C Y Foo
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive MD-MR-01, Research Triangle Park, NC, 27709, USA
| | - Anna Pomés
- Indoor Biotechnologies, Inc., Charlottesville, VA, USA
| | - Lars C Pedersen
- National Institute of Environmental Health Sciences, 111 T.W. Alexander Drive MD-MR-01, Research Triangle Park, NC, 27709, USA
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112
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Valadon P, Pérez-Tapia SM, Nelson RS, Guzmán-Bringas OU, Arrieta-Oliva HI, Gómez-Castellano KM, Pohl MA, Almagro JC. ALTHEA Gold Libraries™: antibody libraries for therapeutic antibody discovery. MAbs 2019; 11:516-531. [PMID: 30663541 PMCID: PMC6512909 DOI: 10.1080/19420862.2019.1571879] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We describe here the design, construction and validation of ALTHEA Gold Libraries™. These single-chain variable fragment (scFv), semisynthetic libraries are built on synthetic human well-known IGHV and IGKV germline genes combined with natural human complementarity-determining region (CDR)-H3/JH (H3J) fragments. One IGHV gene provided a universal VH scaffold and was paired with two IGKV scaffolds to furnish different topographies for binding distinct epitopes. The scaffolds were diversified at positions identified as in contact with antigens in the known antigen-antibody complex structures. The diversification regime consisted of high-usage amino acids found at those positions in human antibody sequences. Functionality, stability and diversity of the libraries were improved throughout a three-step construction process. In a first step, fully synthetic primary libraries were generated by combining the diversified scaffolds with a set of synthetic neutral H3J germline gene fragments. The second step consisted of selecting the primary libraries for enhanced thermostability based on the natural capacity of Protein A to bind the universal VH scaffold. In the third and final step, the resultant stable synthetic antibody fragments were combined with natural H3J fragments obtained from peripheral blood mononuclear cells of a large pool of 200 donors. Validation of ALTHEA Gold Libraries™ with seven targets yielded specific antibodies in all the cases. Further characterization of the isolated antibodies indicated KD values as human IgG1 molecules in the single-digit and sub-nM range. The thermal stability (Tm) of all the antigen-binding fragments was 75°C–80°C, demonstrating that ALTHEA Gold Libraries™ are a valuable source of specific, high affinity and highly stable antibodies.
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Affiliation(s)
| | | | | | | | | | | | - Mary Ann Pohl
- c Tri-Institutional Therapeutics Discovery Institute , New York , NY , USA
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113
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Buchan KD, Foster SJ, Renshaw SA. Staphylococcus aureus: setting its sights on the human innate immune system. MICROBIOLOGY-SGM 2019; 165:367-385. [PMID: 30625113 DOI: 10.1099/mic.0.000759] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Staphylococcus aureus has colonized humans for at least 10 000 years, and today inhabits roughly a third of the population. In addition, S. aureus is a major pathogen that is responsible for a significant disease burden, ranging in severity from mild skin and soft-tissue infections to life-threatening endocarditis and necrotizing pneumonia, with treatment often hampered by resistance to commonly available antibiotics. Underpinning its versatility as a pathogen is its ability to evade the innate immune system. S. aureus specifically targets innate immunity to establish and sustain infection, utilizing a large repertoire of virulence factors to do so. Using these factors, S. aureus can resist phagosomal killing, impair complement activity, disrupt cytokine signalling and target phagocytes directly using proteolytic enzymes and cytolytic toxins. Although most of these virulence factors are well characterized, their importance during infection is less clear, as many display species-specific activity against humans or against animal hosts, including cows, horses and chickens. Several staphylococcal virulence factors display species specificity for components of the human innate immune system, with as few as two amino acid changes reducing binding affinity by as much as 100-fold. This represents a major issue for studying their roles during infection, which cannot be examined without the use of humanized infection models. This review summarizes the major factors S. aureus uses to impair the innate immune system, and provides an in-depth look into the host specificity of S. aureus and how this problem is being approached.
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Affiliation(s)
- Kyle D Buchan
- 1The Bateson Centre and Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Simon J Foster
- 2Department of Molecular Biology and Biotechnology, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Stephen A Renshaw
- 1The Bateson Centre and Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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114
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Schneewind O, Missiakas D. Sortases, Surface Proteins, and Their Roles in Staphylococcus aureus Disease and Vaccine Development. Microbiol Spectr 2019; 7:10.1128/microbiolspec.PSIB-0004-2018. [PMID: 30737913 PMCID: PMC6386163 DOI: 10.1128/microbiolspec.psib-0004-2018] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Indexed: 12/27/2022] Open
Abstract
Sortases cleave short peptide motif sequences at the C-terminal end of secreted surface protein precursors and either attach these polypeptides to the peptidoglycan of Gram-positive bacteria or promote their assembly into pilus structures that are also attached to peptidoglycan. Sortase A, the enzyme first identified in the human pathogen Staphylococcus aureus, binds LPXTG motif sorting signals, cleaves between threonine (T) and glycine (G) residues, and forms an acyl enzyme between its active-site cysteine thiol and the carboxyl group of threonine (T). Sortase A acyl enzyme is relieved by the nucleophilic attack of the cross bridge amino group within lipid II, thereby generating surface protein linked to peptidoglycan precursor. Such products are subsequently incorporated into the cell wall envelope by enzymes of the peptidoglycan synthesis pathway. Surface proteins linked to peptidoglycan may be released from the bacterial envelope to diffuse into host tissues and fulfill specific biological functions. S. aureus sortase A is essential for host colonization and for the pathogenesis of invasive diseases. Staphylococcal sortase-anchored surface proteins fulfill key functions during the infectious process, and vaccine-induced antibodies targeting surface proteins may provide protection against S. aureus. Alternatively, small-molecule inhibitors of sortase may be useful agents for the prevention of S. aureus colonization and invasive disease.
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Affiliation(s)
- Olaf Schneewind
- Department of Microbiology, University of Chicago, Chicago, IL 60637
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115
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Yang XH, Huan LM, Chu XS, Sun Y, Shi QH. A comparative investigation of random and oriented immobilization of protein A ligands on the binding of immunoglobulin G. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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116
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Plewka J, Silva GL, Tscheließnig R, Rennhofer H, Dias‐Cabral C, Jungbauer A, Lichtenegger HC. Antibody adsorption in protein-A affinity chromatography - in situ measurement of nanoscale structure by small-angle X-ray scattering. J Sep Sci 2018; 41:4122-4132. [PMID: 30240534 PMCID: PMC6282589 DOI: 10.1002/jssc.201800776] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 09/14/2018] [Accepted: 09/14/2018] [Indexed: 02/02/2023]
Abstract
Protein-A chromatography is the most widely used chromatography step in downstream processing of antibodies. A deeper understanding of the influence of the surface topology on a molecular/nanoscale level on adsorption is essential for further improvement. It is not clear if the binding is homogenous throughout the entire bead network. We followed the protein absorption process and observed the formation of a protein layer on fibers of chromatography resin in a time-resolved manner in nanoscale. To characterize the changes in the antibody-protein-A ligand complex, small angle X-ray scattering was employed using a miniaturized X-ray-transparent chromatography column packed with a MabSelect SuRe resin. Antibody-free MabSelect SuRe resin fiber had an average radius of 12 nm and the protein layer thickness resulting from antibody adsorption was 5.5 and 10.4 nm for fiber and junctions, respectively under applied native conditions. We hypothesize that an average of 1.2 antibodies were adsorbed per protein-A ligand tetramer bound to the outermost units. In contrast to previous studies, it was therefore possible for the first time to directly correlate the nanostructure changes inside the column, which is otherwise a black box, with the adsorption and elution process.
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Affiliation(s)
- Jacek Plewka
- Department of Material Science and Process EngineeringUniversity of Natural Resources and LifeSciencesViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Gonçalo L. Silva
- Austrian Centre of Industrial BiotechnologyViennaAustria
- CICS‐UBI – Health Sciences Research CentreUniversity of Beira Interior
CovilhãPortugal
- Department of ChemistryUniversity of Beira InteriorCovilhãPortugal
| | - Rupert Tscheließnig
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences
ViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Harald Rennhofer
- Department of Material Science and Process EngineeringUniversity of Natural Resources and LifeSciencesViennaAustria
| | - Cristina Dias‐Cabral
- CICS‐UBI – Health Sciences Research CentreUniversity of Beira Interior
CovilhãPortugal
- Department of ChemistryUniversity of Beira InteriorCovilhãPortugal
| | - Alois Jungbauer
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences
ViennaAustria
- Austrian Centre of Industrial BiotechnologyViennaAustria
| | - Helga C. Lichtenegger
- Department of Material Science and Process EngineeringUniversity of Natural Resources and LifeSciencesViennaAustria
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117
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L Silva G, Plewka J, Lichtenegger H, Dias-Cabral AC, Jungbauer A, Tscheließnig R. The pearl necklace model in protein A chromatography: Molecular mechanisms at the resin interface. Biotechnol Bioeng 2018; 116:76-86. [PMID: 30252938 PMCID: PMC6587469 DOI: 10.1002/bit.26843] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/17/2018] [Accepted: 09/21/2018] [Indexed: 01/08/2023]
Abstract
Staphylococcal protein A chromatography is an established core technology for monoclonal antibody purification and capture in the downstream processing. MabSelect SuRe involves a tetrameric chain of a recombinant form of the B domain of staphylococcal protein A, called the Z-domain. Little is known about the stoichiometry, binding orientation, or preferred binding. We analyzed small-angle X-ray scattering data of the antibody-protein A complex immobilized in an industrial highly relevant chromatographic resin at different antibody concentrations. From scattering data, we computed the normalized radial density distributions. We designed three-dimensional (3D) models with protein data bank crystallographic structures of an IgG1 (the isoform of trastuzumab, used here; Protein Data Bank: 1HZH) and the staphylococcal protein A B domain (the native form of the recombinant structure contained in MabSelect SuRe resin; Protein Data Bank: 1BDD). We computed different binding conformations for different antibody to protein A stoichiometries (1:1, 2:1, and 3:1) and compared the normalized radial density distributions computed from 3D models with those obtained from the experimental data. In the linear range of the isotherm we favor a 1:1 ratio, with the antibody binding to the outer domains in the protein A chain at very low and high concentrations. In the saturation region, a 2:1 ratio is more likely to occur. A 3:1 stoichiometry is excluded because of steric effects.
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Affiliation(s)
- Goncalo L Silva
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal.,Department of Chemistry, University of Beira Interior, Covilhã, Portugal.,Department of Biotechnology, Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Jacek Plewka
- Department of Biotechnology, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Material Science and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Helga Lichtenegger
- Department of Biotechnology, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Material Science and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ana C Dias-Cabral
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal.,Department of Chemistry, University of Beira Interior, Covilhã, Portugal
| | - Alois Jungbauer
- Department of Biotechnology, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Rupert Tscheließnig
- Department of Biotechnology, Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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118
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Abouelkhair MA, Bemis DA, Kania SA. Characterization of recombinant wild-type and nontoxigenic protein A from Staphylococcus pseudintermedius. Virulence 2018; 9:1050-1061. [PMID: 30052123 PMCID: PMC6086296 DOI: 10.1080/21505594.2018.1489199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background:Staphylococcus pseudintermedius is an opportunistic pathogen that is the major cause of pyoderma affecting dogs. Conventional antimicrobial treatment for infections caused by this organism have failed in recent years due to widespread resistance and alternative treatment strategies are a high priority. Protein A encoded in Staphylococcus aureus by spa protects the bacterium by binding IgG and acts as a superantigen. Staphylococcus pseudintermedius possess two genes orthologous to S. aureus spa, spsP, and spsQ. Methods: SpsQ and SpsQ-M, a non-toxigenic SpsQ, were cloned and expressed as recombinant proteins and their cytotoxic effect on canine B cells was measured. The neutralizing ability of antibody raised against them in clinically healthy dogs was evaluated. Results:S. pseudintermedius SpsQ induced apoptosis of canine B cells. Specific amino acid substitutions diminished SpsQ-M binding to immunoglobulin and its super-antigenic activity, while its antigenicity was maintained. This recombinant, non-toxigenic S. pseudintermedius SpsQ stimulated the production of antibodies in dogs that specifically reacted with SpsQ and greatly diminished its cytotoxic effect on canine B cells. Conclusions: The production of neutralizing antibody suggests that attenuated, non-toxic SpsQ produced in this study is a good candidate for inclusion in a vaccine for use in the treatment and prevention of S. pseudintermedius infections. Abbreviations: SpA: Staphylococcus aureus protein A; SpsP: Staphylococcus pseudintermedius protein A; SpsQ: Staphylococcus pseudintermedius protein A; SpsQ-M: attenuated Staphylococcus pseudintermedius protein A; MRSP: methicillin resistant Staphylococcus pseudintermedius; IgA: immunoglobulin A; IgG: immunoglobulin G; IgM: immunoglobulin M; VH: variable region of immunoglobulin heavy chain; IgBD: immunoglobulin binding domains; MFI: mean fluorescent intensity; SEM: standard error of the mean; PBMC: Peripheral blood mononuclear cells; CD21: complement receptor type 2; ST: Sequence type; OD: Optical density; ORF: open reading frame; PBS: Phosphate buffered saline; Tween 20: Polyethylene glycol sorbitan monolaurate 20; HRP: horseradish peroxidase; TMB- 3,3',5,5'-Tetramethylbenzidine
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Affiliation(s)
- Mohamed A Abouelkhair
- a Department of Biomedical and Diagnostic Sciences , University of Tennessee, College of Veterinary Medicine , Knoxville , TN , USA.,b Faculty of Veterinary Medicine , University of Sadat City , Menoufia , Egypt
| | - David A Bemis
- a Department of Biomedical and Diagnostic Sciences , University of Tennessee, College of Veterinary Medicine , Knoxville , TN , USA
| | - Stephen A Kania
- a Department of Biomedical and Diagnostic Sciences , University of Tennessee, College of Veterinary Medicine , Knoxville , TN , USA
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119
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Oliveira GS, Ierich JCM, Moraes AS, Silva GBRF, Liu Y, de S Neto LR, Faria RR, Franca EF, Freitas LCG, Briggs JM, Leite FL. Immobilization and unbinding investigation of the antigen-antibody complex using theoretical and experimental techniques. J Mol Graph Model 2018; 86:219-227. [PMID: 30388696 DOI: 10.1016/j.jmgm.2018.10.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 09/24/2018] [Accepted: 10/10/2018] [Indexed: 12/11/2022]
Abstract
Experimental results for the antibody known as immunoglobulin G - IgG interacting with phenobarbital were obtained via atomic force microscopy (AFM) and thereafter investigated using computer simulation modeling tools. Using molecular dynamics simulation and docking calculations, the energetically stable configurations of an immobilized antibody over a silicon surface were searched. Six stable configurations of the immobilized antibody over the silicon nitride surface covered by linker molecules were found. Although, only three of them (P1, P2, P5) maintained the Fragment antigen binding available for antigen interaction. Therefore, these configurations were equilibrated after reaching 100 ns molecular dynamics trajectory. The average interaction energy between the surface and the immunoglobulin G - IgG antibody in the P1, P2 and P5 configurations were -62.4 ± 2.4 kcal/mol; -54.3 ± 5.7 kcal/mol, and -360.9 ± 4.2 kcal/mol respectively. Phenobarbital was docked within the Fab domain of P1, P2, and P5 immobilized configurations and equilibrated with molecular dynamics for binding energy estimation. Then, steered molecular dynamics was performed to evaluate unbinding energy pathway between phenobarbital and IgG in each of the three-oriented IgG configurations. No significant differences were observed in the rupture force values (EP1 = 591 ± 13 pN, EP2 = 605 ± 18 pN, and EP5 = 610 ± 45 pN). In comparison, the average AFM experimental results were (641.6 ± 363.3 pN). Therefore, it is worth noting that P5 is the configuration with highest protein-surface interaction. Therefore, the force value calculated for the P5 orientation is statistically more favorable and it is the one to be compared to the experimental data. The agreement between experimental and theoretical results indicates a favorable presented for this study opening new perspectives for antigen-antibody evaluation.
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Affiliation(s)
- Guedmiller S Oliveira
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, MG, 38400-902, Brazil.
| | - Jéssica C M Ierich
- Grupo de Nanoneurobiofísica, Departamento de Física, Química e Matemática, Universidade Federal de São Carlos, Sorocaba, SP, 18052-780, Brazil
| | - Ariana S Moraes
- Grupo de Nanoneurobiofísica, Departamento de Física, Química e Matemática, Universidade Federal de São Carlos, Sorocaba, SP, 18052-780, Brazil
| | - Gisela B R F Silva
- Grupo de Nanoneurobiofísica, Departamento de Física, Química e Matemática, Universidade Federal de São Carlos, Sorocaba, SP, 18052-780, Brazil
| | - Yanyun Liu
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Lourival R de S Neto
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, MG, 38400-902, Brazil
| | - Roberto R Faria
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, MG, 38400-902, Brazil
| | - Eduardo F Franca
- Instituto de Química, Universidade Federal de Uberlândia, Uberlândia, MG, 38400-902, Brazil
| | - Luiz C G Freitas
- Departmento de Química, Universidade Federal de São Carlos, São Carlos, SP, 13565-905, Brazil
| | - James M Briggs
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Fabio L Leite
- Grupo de Nanoneurobiofísica, Departamento de Física, Química e Matemática, Universidade Federal de São Carlos, Sorocaba, SP, 18052-780, Brazil
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120
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Ferdous S, Martin ACR. AbDb: antibody structure database-a database of PDB-derived antibody structures. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:4989324. [PMID: 29718130 PMCID: PMC5925428 DOI: 10.1093/database/bay040] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/26/2018] [Indexed: 11/14/2022]
Abstract
In order to analyse structures of proteins of a particular class, these need to be extracted from Protein Data Bank (PDB) files. In the case of antibodies, there are a number of special considerations: (i) identifying antibodies in the PDB is not trivial, (ii) they may be crystallized with or without antigen, (iii) for analysis purposes, one is normally only interested in the Fv region of the antibody, (iv) structural analysis of epitopes, in particular, requires individual antibody–antigen complexes from a PDB file which may contain multiple copies of the same, or different, antibodies and (v) standard numbering schemes should be applied. Consequently, there is a need for a specialist resource containing pre-numbered non-redundant antibody Fv structures with their cognate antigens. We have created an automatically updated resource, AbDb, which collects the Fv regions from antibody structures using information from our SACS database which summarizes antibody structures from the PDB. PDB files containing multiple structures are split and numbered and each antibody structure is associated with its antigen where available. Antibody structures with only light or heavy chains have also been processed and sequences of antibodies are compared to identify multiple structures of the same antibody. The data may be queried on the basis of PDB code, or the name or species of the antibody or antigen, and the complete datasets may be downloaded. Database URL: www.bioinf.org.uk/abs/abdb/
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Affiliation(s)
- Saba Ferdous
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Andrew C R Martin
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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121
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Ulloa-Morales AJ, Goodyear CS, Silverman GJ. Essential Domain-Dependent Roles Within Soluble IgG for in vivo Superantigen Properties of Staphylococcal Protein A: Resolving the B-Cell Superantigen Paradox. Front Immunol 2018; 9:2011. [PMID: 30283436 PMCID: PMC6156153 DOI: 10.3389/fimmu.2018.02011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/15/2018] [Indexed: 12/20/2022] Open
Abstract
Staphylococcus aureus is a common commensal and frequent opportunistic pathogen that causes invasive infections that often recur. Co-evolution with the host has led to the development of toxins that affect diverse immune cell types. Recent reports have highlighted the contributions of staphylococcal protein A (SpA). This small oligomeric secreted protein contains 4–5 homologous domains with two distinct immunoglobulin-binding sites; one for IgG Fc domains, while a separate site binds an evolutionarily conserved surface on Fab encoded by VHIII clan related genes. The Fab-binding site has been implicated in in vivo supraclonal VHIII-BCR targeted B-cell depletion by an activation induced death pathway. Yet the concept of a superantigen for B lymphocytes poses a seeming paradox. Unlike TCR that are expressed only in a membrane-associated form, BCR are expressed in both a membrane BCR form and in secreted Ig forms, which permeate virtually every part of the body at high levels. We therefore asked, why circulating immunoglobulin do not block the superantigen properties of SpA? Herein, we show that soluble IgG molecules are not in vivo inhibitors of these B-cell superantigen effects but are instead essential for potentiating these properties. We also show that the Fc subclass of circulating IgG is an indirect critical determinant of the B-cell superantigen effect. In contrast, host FcγR and complement are not required for SpA mediated in vivo B-cell depletion. Unexpectedly, after VHIII-IgG2a pretreatment SpA challenge resulted in fatal anaphylactic reactions, which we speculate may have involved FcγR interactions with mast cells and basophils. Cumulatively, our findings illuminate a cunning and potent molecular strategy by which a bacterial toxin effectively confounds the contributions of host B-lymphocytes to immune defenses.
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Affiliation(s)
- Alejandro J Ulloa-Morales
- Laboratory of B-cell Immunobiology, Department of Medicine, New York University School of Medicine, New York, NY, United States
| | - Carl S Goodyear
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gregg J Silverman
- Laboratory of B-cell Immunobiology, Department of Medicine, New York University School of Medicine, New York, NY, United States
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122
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Structure of a patient-derived antibody in complex with allergen reveals simultaneous conventional and superantigen-like recognition. Proc Natl Acad Sci U S A 2018; 115:E8707-E8716. [PMID: 30150373 PMCID: PMC6140506 DOI: 10.1073/pnas.1806840115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antibodies classically bind antigens via their complementarity-determining regions, but an alternative mode of interaction involving V-domain framework regions has been observed for some B cell "superantigens." We report the crystal structure of an antibody employing both modes of interaction simultaneously and binding two antigen molecules. This human antibody from an allergic individual binds to the grass pollen allergen Phl p 7. Not only are two allergen molecules bound to each antibody fragment (Fab) but also each allergen molecule is bound by two Fabs: One epitope is recognized classically, the other in a superantigen-like manner. A single allergen molecule thus cross-links two identical Fabs, contrary to the one-antibody-one-epitope dogma, which dictates that a dimeric allergen at least is required for this to occur. Allergens trigger immediate hypersensitivity reactions by cross-linking receptor-bound IgE molecules on effector cells. We found that monomeric Phl p 7 induced degranulation of basophils sensitized solely with this monoclonal antibody expressed as an IgE, demonstrating that the dual specificity has functional consequences. The monomeric state of Phl p 7 and two structurally related allergens was confirmed by size-exclusion chromatography and multiangle laser light scattering, and the results were supported by degranulation studies with the related allergens, a second patient-derived allergen-specific antibody lacking the nonclassical binding site, and mutagenesis of the nonclassically recognized allergen epitope. The antibody dual reactivity and cross-linking mechanism not only have implications for understanding allergenicity and allergen potency but, importantly, also have broader relevance to antigen recognition by membrane Ig and cross-linking of the B cell receptor.
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123
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Covalent Immobilization of Protein A on Chitosan and Aldehyde Double-Branched Chitosan as Biocompatible Carriers for Immunoglobulin G (Igg) Purification. J Chromatogr Sci 2018; 56:933-940. [DOI: 10.1093/chromsci/bmy070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 06/16/2018] [Indexed: 11/14/2022]
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124
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Weppner G, Ohlei O, Hammers CM, Holl-Ulrich K, Voswinkel J, Bischof J, Hasselbacher K, Riemekasten G, Lamprecht P, Ibrahim S, Iking-Konert C, Recke A, Müller A. In situ detection of PR3-ANCA + B cells and alterations in the variable region of immunoglobulin genes support a role of inflamed tissue in the emergence of auto-reactivity in granulomatosis with polyangiitis. J Autoimmun 2018; 93:89-103. [PMID: 30054207 DOI: 10.1016/j.jaut.2018.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 07/01/2018] [Indexed: 10/28/2022]
Abstract
Circulating anti-neutrophilic cytoplasmic autoantibodies targeting proteinase 3 (PR3-ANCA) are a diagnostic and pathogenic hallmark of granulomatosis with polyangiitis (GPA). It is, however, incompletely understood if inflamed tissue supports presence or emergence of PR3-ANCA+ B cells. In search of such cells in inflamed tissue of GPA, immunofluorescence staining for IgG and a common PR3-ANCA idiotype (5/7 Id) was undertaken. Few 5/7 Id+/IgG+ B cells were detected in respiratory and kidney tissue of GPA. To gain more insight into surrogate markers possibly indicative of an anti-PR3-response, a meta-analysis comprising IGVH and IGVL genes derived from respiratory tract tissue of GPA (231 clones) was performed. Next generation sequencing-based IGHV genes derived from peripheral blood of healthy donors (244.353 clones) and previously published IGLV genes (148 clones) served as controls. Additionally, Ig genes of three murine and five known human monoclonal anti-PR3 antibodies were analyzed. Primary and probably secondary rearrangements led to altered VDJ usage and an extended complementarity determining region 3 (CDR3) of IGHV clones from GPA tissue. Selection against amino acid exchanges was prominent in the framework region of IGHV clones from GPA tissue. The comparison of V(D)J rearrangements and deduced amino acid sequences of the CDR3 yielded no identities and few similarities between clones derived from respiratory tissue of GPA and anti-PR3 antibodies, arguing against a presence of B cells that carry PR3-ANCA-prone Ig genes among the clones. In line with the scarcity of 5/7 Id+ B lymphocytes in GPA tissue, the results suggest that with respect to a local anti-PR3 response, methods detecting rare clones are required.
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Affiliation(s)
- Gesche Weppner
- Dept. of Rheumatology & Clinical Immunology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | - Olena Ohlei
- Lübeck Interdisciplinary Platform for Genome Analytics, Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christoph M Hammers
- Dept. of Dermatology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | | | - Jan Voswinkel
- Medical Faculty, University of Saarland, Saarbrücken, Germany
| | - Julia Bischof
- Dept. of Dermatology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | - Katrin Hasselbacher
- Dept. of Otorhinolaryngology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | - Gabriela Riemekasten
- Dept. of Rheumatology & Clinical Immunology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | - Peter Lamprecht
- Dept. of Rheumatology & Clinical Immunology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | - Saleh Ibrahim
- Dept. of Dermatology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | | | - Andreas Recke
- Dept. of Dermatology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany
| | - Antje Müller
- Dept. of Rheumatology & Clinical Immunology, University Hospital of Schleswig-Holstein, Campus Lübeck & University of Lübeck, Lübeck, Germany.
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125
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Ricciardi BF, Muthukrishnan G, Masters E, Ninomiya M, Lee CC, Schwarz EM. Staphylococcus aureus Evasion of Host Immunity in the Setting of Prosthetic Joint Infection: Biofilm and Beyond. Curr Rev Musculoskelet Med 2018; 11:389-400. [PMID: 29987645 DOI: 10.1007/s12178-018-9501-4] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
PURPOSE OF REVIEW The incidence of complications from prosthetic joint infection (PJI) is increasing, and treatment failure remains high. We review the current literature with a focus on Staphylococcus aureus pathogenesis and biofilm, as well as treatment challenges, and novel therapeutic strategies. RECENT FINDINGS S. aureus biofilm creates a favorable environment that increases antibiotic resistance, impairs host immunity, and increases tolerance to nutritional deprivation. Secreted proteins from bacterial cells within the biofilm and the quorum-sensing agr system contribute to immune evasion. Additional immunoevasive properties of S. aureus include the formation of staphylococcal abscess communities (SACs) and canalicular invasion. Novel approaches to target biofilm and increase resistance to implant colonization include novel antibiotic therapy, immunotherapy, and local implant treatments. Challenges remain given the diverse mechanisms developed by S. aureus to alter the host immune responses. Further understanding of these processes should provide novel therapeutic mechanisms to enhance eradication after PJI.
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Affiliation(s)
- Benjamin F Ricciardi
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester School of Medicine, 601 Elmwood Avenue, Box 665, Rochester, NY, 14642, USA
| | - Gowrishankar Muthukrishnan
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester School of Medicine, 601 Elmwood Avenue, Box 665, Rochester, NY, 14642, USA
| | - Elysia Masters
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester School of Medicine, 601 Elmwood Avenue, Box 665, Rochester, NY, 14642, USA
| | - Mark Ninomiya
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester School of Medicine, 601 Elmwood Avenue, Box 665, Rochester, NY, 14642, USA
| | - Charles C Lee
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester School of Medicine, 601 Elmwood Avenue, Box 665, Rochester, NY, 14642, USA
| | - Edward M Schwarz
- Center for Musculoskeletal Research, Department of Orthopaedics, University of Rochester School of Medicine, 601 Elmwood Avenue, Box 665, Rochester, NY, 14642, USA.
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Trastoy B, Klontz E, Orwenyo J, Marina A, Wang LX, Sundberg EJ, Guerin ME. Structural basis for the recognition of complex-type N-glycans by Endoglycosidase S. Nat Commun 2018; 9:1874. [PMID: 29760474 PMCID: PMC5951799 DOI: 10.1038/s41467-018-04300-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 04/18/2018] [Indexed: 11/09/2022] Open
Abstract
Endoglycosidase S (EndoS) is a bacterial endo-β-N-acetylglucosaminidase that specifically catalyzes the hydrolysis of the β-1,4 linkage between the first two N-acetylglucosamine residues of the biantennary complex-type N-linked glycans of IgG Fc regions. It is used for the chemoenzymatic synthesis of homogeneously glycosylated antibodies with improved therapeutic properties, but the molecular basis for its substrate specificity is unknown. Here, we report the crystal structure of the full-length EndoS in complex with its oligosaccharide G2 product. The glycoside hydrolase domain contains two well-defined asymmetric grooves that accommodate the complex-type N-linked glycan antennae near the active site. Several loops shape the glycan binding site, thereby governing the strict substrate specificity of EndoS. Comparing the arrangement of these loops within EndoS and related endoglycosidases, reveals distinct-binding site architectures that correlate with the respective glycan specificities, providing a basis for the bioengineering of endoglycosidases to tailor the chemoenzymatic synthesis of monoclonal antibodies. Endoglycosidase S only recognizes one particular type of glycan within IgG antibodies but the molecular basis for this high specificity is not fully understood. Here, the authors present the crystal structure of product-bound Endoglycosidase S, revealing the determinants for its glycan specificity.
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Affiliation(s)
- Beatriz Trastoy
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Erik Klontz
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jared Orwenyo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Alberto Marina
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160, Derio, Spain
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
| | - Eric J Sundberg
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Marcelo E Guerin
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160, Derio, Spain. .,Unidad de Biofísica, Centro Mixto Consejo Superior de Investigaciones Científicas-Universidad del País Vasco/Euskal Herriko Unibertsitatea (CSIC,UPV/EHU), Barrio Sarriena s/n Leioa, Bizkaia, 48940, Spain. .,Departamento de Bioquímica, Universidad del País Vasco, Leioa, 48940, Spain. .,IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
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127
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Huang G, Zhong Z, Miersch S, Sidhu SS, Hou SC, Wu D. Construction of Synthetic Phage Displayed Fab Library with Tailored Diversity. J Vis Exp 2018:57357. [PMID: 29782009 PMCID: PMC6101057 DOI: 10.3791/57357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Demand for monoclonal antibodies (mAbs) in basic research and medicine is increasing yearly. Hybridoma technology has been the dominant method for mAb development since its first report in 1975. As an alternative technology, phage display methods for mAb development are increasingly attractive since Humira, the first phage-derived antibody and one of the best-selling mAbs, was approved for clinical treatment of rheumatoid arthritis in 2002. As a non-animal based mAb development technology, phage display bypasses antigen immunogenicity, humanization, and animal maintenance that are required from traditional hybridoma technology based antibody development. In this protocol, we describe a method for construction of synthetic phage-displayed Fab libraries with diversities of 109-1010 obtainable with a single electroporation. This protocol consists of: 1) high-efficiency electro-competent cell preparation; 2) extraction of uracil-containing single-stranded DNA (dU-ssDNA); 3) Kunkel's method based oligonucleotide-directed mutagenesis; 4) electroporation and calculation of library size; 5) protein A/L-based enzyme-linked immunosorbent assay (ELISA) for folding and functional diversity evaluation; and 6) DNA sequence analysis of diversity.
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Affiliation(s)
- Ganggang Huang
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University
| | - Zhenwei Zhong
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University
| | - Shane Miersch
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto; Department of Molecular Genetics, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto
| | - Sachdev S Sidhu
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University; Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto; Department of Molecular Genetics, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto
| | - Shin-Chen Hou
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University;
| | - Donghui Wu
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University;
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128
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Faccio G. From Protein Features to Sensing Surfaces. SENSORS (BASEL, SWITZERLAND) 2018; 18:E1204. [PMID: 29662030 PMCID: PMC5948494 DOI: 10.3390/s18041204] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/08/2018] [Accepted: 04/12/2018] [Indexed: 12/25/2022]
Abstract
Proteins play a major role in biosensors in which they provide catalytic activity and specificity in molecular recognition. However, the immobilization process is far from straightforward as it often affects the protein functionality. Extensive interaction of the protein with the surface or significant surface crowding can lead to changes in the mobility and conformation of the protein structure. This review will provide insights as to how an analysis of the physico-chemical features of the protein surface before the immobilization process can help to identify the optimal immobilization approach. Such an analysis can help to preserve the functionality of the protein when on a biosensor surface.
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Affiliation(s)
- Greta Faccio
- Independent Scientist, St. Gallen 9000, Switzerland.
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129
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Sadana P, Geyer R, Pezoldt J, Helmsing S, Huehn J, Hust M, Dersch P, Scrima A. The invasin D protein from Yersinia pseudotuberculosis selectively binds the Fab region of host antibodies and affects colonization of the intestine. J Biol Chem 2018. [PMID: 29535184 DOI: 10.1074/jbc.ra117.001068] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Yersinia pseudotuberculosis is a Gram-negative bacterium and zoonotic pathogen responsible for a wide range of diseases, ranging from mild diarrhea, enterocolitis, lymphatic adenitis to persistent local inflammation. The Y. pseudotuberculosis invasin D (InvD) molecule belongs to the invasin (InvA)-type autotransporter proteins, but its structure and function remain unknown. In this study, we present the first crystal structure of InvD, analyzed its expression and function in a murine infection model, and identified its target molecule in the host. We found that InvD is induced at 37 °C and expressed in vivo 2-4 days after infection, indicating that InvD is a virulence factor. During infection, InvD was expressed in all parts of the intestinal tract, but not in deeper lymphoid tissues. The crystal structure of the C-terminal adhesion domain of InvD revealed a distinct Ig-related fold that, apart from the canonical β-sheets, comprises various modifications of and insertions into the Ig-core structure. We identified the Fab fragment of host-derived IgG/IgA antibodies as the target of the adhesion domain. Phage display panning and flow cytometry data further revealed that InvD exhibits a preferential binding specificity toward antibodies with VH3/VK1 variable domains and that it is specifically recruited to a subset of B cells. This finding suggests that InvD modulates Ig functions in the intestine and affects direct interactions with a subset of cell surface-exposed B-cell receptors. In summary, our results provide extensive insights into the structure of InvD and its specific interaction with the target molecule in the host.
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Affiliation(s)
- Pooja Sadana
- From the Young Investigator Group Structural Biology of Autophagy, Department of Structure and Function of Proteins
| | | | - Joern Pezoldt
- Experimental Immunology, Helmholtz-Centre for Infection Research, 38124 Braunschweig and
| | - Saskia Helmsing
- the Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität, 38106 Braunschweig, Germany
| | - Jochen Huehn
- Experimental Immunology, Helmholtz-Centre for Infection Research, 38124 Braunschweig and
| | - Michael Hust
- the Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität, 38106 Braunschweig, Germany
| | - Petra Dersch
- the Departments of Molecular Infection Biology and
| | - Andrea Scrima
- From the Young Investigator Group Structural Biology of Autophagy, Department of Structure and Function of Proteins,
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130
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Su X, Wang M, Wu Y, He Y, Fu Z. Specific chemiluminescent protocol for dual-site recognition of Streptococcus mutans utilizing strong affinity between teicoplanin and Gram-positive bacteria. Talanta 2018; 179:350-355. [DOI: 10.1016/j.talanta.2017.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 10/27/2017] [Accepted: 11/03/2017] [Indexed: 12/11/2022]
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131
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Yang L, Zhou H, Cheng P, Yang Y, Tong Y, Zuo Q, Feng Q, Zou Q, Zeng H. A novel bivalent fusion vaccine induces broad immunoprotection against Staphylococcus aureus infection in different murine models. Clin Immunol 2018; 188:85-93. [DOI: 10.1016/j.clim.2017.12.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 12/16/2017] [Accepted: 12/27/2017] [Indexed: 12/22/2022]
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132
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Fichtner M, Spies E, Seismann H, Riecken K, Engels N, Gösch B, Dierlamm J, Gerull H, Nollau P, Klapper W, Dreyling M, Binder M, Trepel M. Complementarity determining region-independent recognition of a superantigen by B-cell antigen receptors of mantle cell lymphoma. Haematologica 2018; 101:e378-81. [PMID: 27582571 DOI: 10.3324/haematol.2016.141929] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Michael Fichtner
- Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elmar Spies
- Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Henning Seismann
- Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kristoffer Riecken
- Research Department Cell and Gene Therapy, Clinic for Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Niklas Engels
- Institute of Cellular and Molecular Immunology, Georg-August-University of Göttingen, Medical Faculty, Germany
| | - Barbara Gösch
- Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Judith Dierlamm
- Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Helwe Gerull
- Research Institute Children's Cancer Center and Dept. of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Nollau
- Research Institute Children's Cancer Center and Dept. of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Wolfram Klapper
- Institute of Pathology, Division of Hematopathology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Martin Dreyling
- Department of Hematology and Oncology, University of Munich Medical Center (LMU), Munich, Germany
| | - Mascha Binder
- Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Trepel
- Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany Department of Hematology and Oncology, Augsburg Medical Center, Germany
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133
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Asadollahi P, Farahani NN, Mirzaii M, Khoramrooz SS, van Belkum A, Asadollahi K, Dadashi M, Darban-Sarokhalil D. Distribution of the Most Prevalent Spa Types among Clinical Isolates of Methicillin-Resistant and -Susceptible Staphylococcus aureus around the World: A Review. Front Microbiol 2018; 9:163. [PMID: 29487578 PMCID: PMC5816571 DOI: 10.3389/fmicb.2018.00163] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/24/2018] [Indexed: 12/25/2022] Open
Abstract
Background:Staphylococcus aureus, a leading cause of community-acquired and nosocomial infections, remains a major health problem worldwide. Molecular typing methods, such as spa typing, are vital for the control and, when typing can be made more timely, prevention of S. aureus spread around healthcare settings. The current study aims to review the literature to report the most common clinical spa types around the world, which is important for epidemiological surveys and nosocomial infection control policies. Methods: A search via PubMed, Google Scholar, Web of Science, Embase, the Cochrane library, and Scopus was conducted for original articles reporting the most prevalent spa types among S. aureus isolates. The search terms were “Staphylococcus aureus, spa typing.” Results: The most prevalent spa types were t032, t008 and t002 in Europe; t037 and t002 in Asia; t008, t002, and t242 in America; t037, t084, and t064 in Africa; and t020 in Australia. In Europe, all the isolates related to spa type t032 were MRSA. In addition, spa type t037 in Africa and t037and t437 in Australia also consisted exclusively of MRSA isolates. Given the fact that more than 95% of the papers we studied originated in the past decade there was no option to study the dynamics of regional clone emergence. Conclusion: This review documents the presence of the most prevalent spa types in countries, continents and worldwide and shows big local differences in clonal distribution.
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Affiliation(s)
- Parisa Asadollahi
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Narges Nodeh Farahani
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Mirzaii
- Department of Microbiology, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Seyed Sajjad Khoramrooz
- Department of Microbiology, Faculty of Medicine, Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Alex van Belkum
- Data Analytics Unit, bioMérieux 3, La Balme Les Grottes, France
| | - Khairollah Asadollahi
- Department of Social Medicine, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran.,Faculty of Medicine, Biotechnology and Medicinal Plants Researches Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Masoud Dadashi
- Department of Microbiology, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Darban-Sarokhalil
- Department of Microbiology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
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134
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Kane TL, Carothers KE, Lee SW. Virulence Factor Targeting of the Bacterial Pathogen Staphylococcus aureus for Vaccine and Therapeutics. Curr Drug Targets 2018; 19:111-127. [PMID: 27894236 PMCID: PMC5957279 DOI: 10.2174/1389450117666161128123536] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/12/2016] [Accepted: 10/27/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND Staphylococcus aureus is a major bacterial pathogen capable of causing a range of infections in humans from gastrointestinal disease, skin and soft tissue infections, to severe outcomes such as sepsis. Staphylococcal infections in humans can be frequent and recurring, with treatments becoming less effective due to the growing persistence of antibiotic resistant S. aureus strains. Due to the prevalence of antibiotic resistance, and the current limitations on antibiotic development, an active and highly promising avenue of research has been to develop strategies to specifically inhibit the activity of virulence factors produced S. aureus as an alternative means to treat disease. OBJECTIVE In this review we specifically highlight several major virulence factors produced by S. aureus for which recent advances in antivirulence approaches may hold promise as an alternative means to treating diseases caused by this pathogen. Strategies to inhibit virulence factors can range from small molecule inhibitors, to antibodies, to mutant and toxoid forms of the virulence proteins. CONCLUSION The major prevalence of antibiotic resistant strains of S. aureus combined with the lack of new antibiotic discoveries highlight the need for vigorous research into alternative strategies to combat diseases caused by this highly successful pathogen. Current efforts to develop specific antivirulence strategies, vaccine approaches, and alternative therapies for treating severe disease caused by S. aureus have the potential to stem the tide against the limitations that we face in the post-antibiotic era.
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Affiliation(s)
- Trevor L. Kane
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Katelyn E. Carothers
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shaun W. Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
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135
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Park KS, Ki MR, Yeo KB, Choi JH, Pack SP. Design of bio-inspired silica-encapsulated protein A for improved immunoprecipitation assays. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.08.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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136
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Vaziri-Sani F, Brundin C, Agardh D. Osteoprotegerin autoantibodies do not predict low bone mineral density in middle-aged women. Bone Rep 2017; 7:132-136. [PMID: 29124083 PMCID: PMC5671386 DOI: 10.1016/j.bonr.2017.10.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/16/2017] [Accepted: 10/22/2017] [Indexed: 11/20/2022] Open
Abstract
Purpose Autoantibodies against osteoprotegerin (OPG) have been associated with osteoporosis. The aim was to develop an immunoassay for OPG autoantibodies and test their diagnostic usefulness of identifying women general population with low bone mineral density. Methods Included were 698 women at mean age 55.1 years (range 50.4–60.6) randomly selected from the general population. Measurement of wrist bone mineral density (g/cm2) was performed of the non-dominant wrist by dual-energy X-ray absorptiometry (DXA). A T-score < − 2.5 was defined as having a low bone mineral density. Measurements of OPG autoantibodies were carried by radiobinding assays. Cut-off levels for a positive value were determined from the deviation from normality in the distribution of 398 healthy blood donors representing the 99.7th percentile. Results Forty-five of the 698 (6.6%) women were IgG-OPG positive compared with 2 of 398 (0.5%) controls (p < 0.0001) and 35 of the 698 (5.0%) women had a T-score < − 2.5. There was no difference in bone mineral density between IgG-OPG positive (median 0.439 (range 0.315–0.547) g/cm2) women and IgG-OPG negative (median 0.435 (range 0.176–0.652) g/cm2) women (p = 0.3956). Furthermore, there was neither a correlation between IgG-OPG levels and bone mineral density (rs = 0.1896; p = 0.2068) nor T-score (rs = 0.1889; p = 0.2086). Diagnostic sensitivity and specificity of IgG-OPG for low bone mineral density were 5.7% and 92.9%, and positive and negative predictive values were 7.4% and 90.8%, respectively. Conclusion Elevated OPG autoantibody levels do not predict low bone mineral density in middle-aged women selected from the general population.
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Affiliation(s)
- Fariba Vaziri-Sani
- Kristianstad University, Kristianstad, Sweden
- Diabetes and Celiac Disease Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Charlotte Brundin
- Diabetes and Celiac Disease Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Daniel Agardh
- Diabetes and Celiac Disease Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden
- Corresponding author at: Lund University, CRC 91:10, Jan Waldenströms gata 35, Skåne University Hospital, 205 02 Malmö, Sweden.Lund UniversitySkåne University HospitalCRC 91:10, Jan Waldenströms gata 35Malmö205 02Sweden
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137
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Paloni M, Cavallotti C. Molecular Modeling of the Interaction of Protein L with Antibodies. ACS OMEGA 2017; 2:6464-6472. [PMID: 31457247 PMCID: PMC6645367 DOI: 10.1021/acsomega.7b01123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 09/27/2017] [Indexed: 06/10/2023]
Abstract
Protein L (PpL) is a bacterial protein which is used in the affinity chromatography stage of the production of monoclonal antibodies because of its ability to form high affinity complexes with the light chains of immunoglobulins. In the present work, the binding interfaces between one domain of PpL and antigen-binding fragments (Fab) have been investigated adopting molecular dynamics with the aim of determining the binding contribution of the residues located at the Fab-PpL interface. Because it is known that PpL binds antibodies through two distinct binding sites with different affinities, simulations were performed for both sites to determine interaction free energies to assess the relative binding contribution of the two sites. Mutational studies were then performed only on the dominant binding site. The binding free energy was evaluated with the molecular mechanics Poisson-Boltzmann surface area (MMPBSA) and umbrella sampling/weighted histogram analysis methods. Key residues for the formation of the dominant binding site complex were identified by means of alanine scanning performed both for the Fab and PpL domains. Residues of the light chain of the antibody that contribute most to binding were found to be located between SER7 and VAL13. Four residues from PpL are important for the stability of the complex: PHE839, LYS840, GLU849, and TYR853. Three residues of PpL that do not contribute to the interaction were mutated to histidine (HIS), which changes its protonation state as a function of pH, to find whether this could allow us to control the binding interaction energy. This can be useful in the elution stage of the affinity chromatography purification of antibodies if PpL is used as a ligand. These residues are GLN835, THR836, and ALA837. Molecular dynamics simulations with both protonated and unprotonated HIS were performed to mimic how changing pH may reflect on protein-ligand interaction energies. The MMPBSA approach was used to evaluate the variation of the affinity of the mutated systems with reference to the wild type. Our results show that these mutations could help in disrupting the complex under acidic conditions without impairing the affinity of PpL for the light chains at higher pHs.
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138
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Fichtner M, Dreyling M, Binder M, Trepel M. The role of B cell antigen receptors in mantle cell lymphoma. J Hematol Oncol 2017; 10:164. [PMID: 29041946 PMCID: PMC5646121 DOI: 10.1186/s13045-017-0533-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/09/2017] [Indexed: 12/15/2022] Open
Abstract
Mantle cell lymphoma (MCL) is characterized by an aggressive clinical course and secondary resistance to currently available therapies in most cases. Therefore, despite recent advances in the treatment of this disease, it is still considered to be incurable in the majority of cases. MCL B cells retain their B cell antigen receptor (BCR) expression during and after neoplastic transformation. BCRs in MCL show distinct patterns of antigen selection and ongoing BCR signaling. However, little is known about the involved antigens and the mechanisms leading to lymphomagenesis and lymphoma progression in MCL. Recent preclinical and clinical studies have established a crucial role of the BCR and the potential of inhibiting its signaling in this disease. This has established the B cell antigen receptor signaling cascade as a very promising therapeutic target to improve outcome in MCL alone or in combination with chemo-immunotherapy in recent years.
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Affiliation(s)
- Michael Fichtner
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, St. Stephen's Green, Dublin 2, Ireland.,Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Martin Dreyling
- Department of Medicine III, University Hospital LMU Munich, Marchioninistr. 15, 81377, Munich, Germany
| | - Mascha Binder
- Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Martin Trepel
- Department of Oncology and Hematology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany. .,Department of Hematology and Oncology, Augsburg Medical Center, Stenglinstr. 2, 86156, Augsburg, Germany.
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139
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Per Aqueous Liquid Chromatography (PALC) as a Simple Method for Native Separation of Protein A. Chromatographia 2017. [DOI: 10.1007/s10337-017-3412-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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140
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Seyfi Abad Shapouri MR, Mahmoodi P, Gharibi D, Ghorbanpoor M, Yaghoubi S, Rezaei E, Rashno M, Mehravar N. Molecular Cloning, Expression and Peroxidase Conjugation of Staphylococcus aureus Protein A. IRANIAN JOURNAL OF BIOTECHNOLOGY 2017; 14:230-235. [PMID: 28959340 PMCID: PMC5434992 DOI: 10.15171/ijb.1267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Background
Staphylococcal protein A (SPA) is a cell wall component of Staphylococcus aureus that binds to different IgG subclasses of human and several animal species. This bacterial protein can be used as an antibody detector in various immunological assays or as an isolation reagent for the purification of antibody molecules via immuno-chromatography procedures.
Objectives
Molecular cloning and expression of SPA followed by the purification and conjugation of the recombinant protein to peroxidase enzyme.
Material and Methods
Encoding DNA fragment of SPA was amplified and inserted into a prokaryotic plasmid vector for the expression of recombinant SPA fused to a maltose binding protein (MBP). The recombinant protein was purified using amylose resin column chromatography and conjugated to horseradish peroxidase (HRP) enzyme. Finally, the reactivity of the recombinant SPA was examined against human IgG molecules in ELISA.
Results
The results indicated that the recombinant peroxidase-conjugated SPA has a good recognition capacity for human IgG molecules and it was able to produce significant OD values after reacting with human IgG molecules at a concentration up to 0.06 μg.well-1.
Conclusions
This recombinant protein can be very useful in all research laboratories and may decrease some of the expenses, e.g. those for preparing conjugated anti-antibodies.
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Affiliation(s)
| | - Pezhman Mahmoodi
- Department of Pathobiology, Faculty of Veterinary Science, Bu-Ali Sina University, Hamedan, Iran
| | - Dariush Gharibi
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Masoud Ghorbanpoor
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Sara Yaghoubi
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Elham Rezaei
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohammad Rashno
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Neda Mehravar
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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141
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Herold EM, John C, Weber B, Kremser S, Eras J, Berner C, Deubler S, Zacharias M, Buchner J. Determinants of the assembly and function of antibody variable domains. Sci Rep 2017; 7:12276. [PMID: 28947772 PMCID: PMC5613017 DOI: 10.1038/s41598-017-12519-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/12/2017] [Indexed: 01/17/2023] Open
Abstract
The antibody Fv module which binds antigen consists of the variable domains VL and VH. These exhibit a conserved ß-sheet structure and comprise highly variable loops (CDRs). Little is known about the contributions of the framework residues and CDRs to their association. We exchanged conserved interface residues as well as CDR loops and tested the effects on two Fvs interacting with moderate affinities (KDs of ~2.5 µM and ~6 µM). While for the rather instable domains, almost all mutations had a negative effect, the more stable domains tolerated a number of mutations of conserved interface residues. Of particular importance for Fv association are VLP44 and VHL45. In general, the exchange of conserved residues in the VL/VH interface did not have uniform effects on domain stability. Furthermore, the effects on association and antigen binding do not strictly correlate. In addition to the interface, the CDRs modulate the variable domain framework to a significant extent as shown by swap experiments. Our study reveals a complex interplay of domain stability, association and antigen binding including an unexpected strong mutual influence of the domain framework and the CDRs on stability/association on the one side and antigen binding on the other side.
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Affiliation(s)
- Eva Maria Herold
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany.,Sanofi-Aventis GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Christine John
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany
| | - Benedikt Weber
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany
| | - Stephan Kremser
- Center for Integrated Protein Science Munich (CIPSM) at the Physics Department, Technische Universität München, 85747, Garching, Germany
| | - Jonathan Eras
- ETH Zürich, Otto-Stern-Weg 5, 8093, Zuerich, Switzerland
| | - Carolin Berner
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany
| | - Sabrina Deubler
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany
| | - Martin Zacharias
- Center for Integrated Protein Science Munich (CIPSM) at the Physics Department, Technische Universität München, 85747, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science Munich (CIPSM) at the Department Chemie, Technische Universität München, 85747, Garching, Germany.
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142
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Goldmann O, Medina E. Staphylococcus aureus strategies to evade the host acquired immune response. Int J Med Microbiol 2017; 308:625-630. [PMID: 28939437 DOI: 10.1016/j.ijmm.2017.09.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/01/2017] [Accepted: 09/13/2017] [Indexed: 12/13/2022] Open
Abstract
Staphylococcus aureus poses a significant public-health problem. Infection caused by S. aureus can manifest as acute or long-lasting persistent diseases that are often refractory to antibiotic and are associated with significant morbidity and mortality. To develop more effective strategies for preventing or treating these infections, it is crucial to understand why the immune response is incapable to eradicate the bacterium. When S. aureus first infect the host, there is a robust activation of the host innate immune responses. Generally, S. aureus can survive this initial interaction due to the expression of a wide array of virulence factors that interfere with the host innate immune defenses. After this initial interaction the acquired immune response is the arm of the host defenses that will try to clear the pathogen. However, S. aureus is capable of maintaining infection in the host even in the presence of a robust antigen-specific immune response. Thus, understanding the mechanisms underlying the ability of S. aureus to escape immune surveillance by the acquired immune response will help uncover potentially important targets for the development of immune-based adjunctive therapies and more efficient vaccines. There are several lines of evidence that lead us to believe that S. aureus can directly or indirectly disable the acquired immune response. This review will discuss the different immune evasion strategies used by S. aureus to modulate the different components of the acquired immune defenses.
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Affiliation(s)
- Oliver Goldmann
- Infection Immunology Research Group, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany.
| | - Eva Medina
- Infection Immunology Research Group, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany.
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143
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Artificial DnaJ Protein for protein production and conformational diseases. Sci Rep 2017; 7:8531. [PMID: 28819167 PMCID: PMC5561034 DOI: 10.1038/s41598-017-09067-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/21/2017] [Indexed: 11/20/2022] Open
Abstract
For secreted proteins, proper protein folding is essential not only for biological function but also for secretion itself. Proteins with folding problems are trapped in the endoplasmic reticulum (ER) and are eventually degraded in the cytoplasm. In this study, we exploited co-expression of an artificial fusion protein, based on the sequence of a DnaJ protein, which could interact as co-chaperones in the Hsp70-based protein-folding system, with target recombinant secreted proteins to enhance their production and secretion. The J-domain sequence or a fragment thereof was conjugated to a target protein–binding domain that was capable of binding to a portion of the target-protein sequence. Production of many of the target proteins was significantly upregulated when co-expressed with the J-domain fusion protein. Surprisingly, the enhancement of secretion was observed even when the J-domain had a mutation in the HPD motif, which is necessary for J-protein–Hsp70 interactions, suggesting the phenomenon observed is independent on functional J-protein–Hsp70 interactions. This technology has great potential for not only enhancing the production of recombinant proteins, but also to treat conformational diseases such as cystic fibrosis, and Alpha-1 antitrypsin deficiency.
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144
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Pham-Ledard A, Prochazkova-Carlotti M, Deveza M, Laforet MP, Beylot-Barry M, Vergier B, Parrens M, Feuillard J, Merlio JP, Gachard N. Molecular analysis of immunoglobulin variable genes supports a germinal center experienced normal counterpart in primary cutaneous diffuse large B-cell lymphoma, leg-type. J Dermatol Sci 2017; 88:238-246. [PMID: 28838616 DOI: 10.1016/j.jdermsci.2017.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/09/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Immunophenotype of primary cutaneous diffuse large B-cell lymphoma, leg-type (PCLBCL-LT) suggests a germinal center-experienced B lymphocyte (BCL2+ MUM1+ BCL6+/-). OBJECTIVES As maturation history of B-cell is "imprinted" during B-cell development on the immunoglobulin gene sequence, we studied the structure and sequence of the variable part of the genes (IGHV, IGLV, IGKV), immunoglobulin surface expression and features of class switching in order to determine the PCLBCL-LT cell of origin. METHODS Clonality analysis with BIOMED2 protocol and VH leader primers was done on DNA extracted from frozen skin biopsies on retrospective samples from 14 patients. The clonal DNA IGHV sequence of the tumor was aligned and compared with the closest germline sequence and homology percentage was calculated. Superantigen binding sites were studied. Features of selection pressure were evaluated with the multinomial Lossos model. RESULTS A functional monoclonal sequence was observed in 14 cases as determined for IGHV (10), IGLV (2) or IGKV (3). IGV mutation rates were high (>5%) in all cases but one (median:15.5%), with superantigen binding sites conservation. Features of selection pressure were identified in 11/12 interpretable cases, more frequently negative (75%) than positive (25%). Intraclonal variation was detected in 3 of 8 tumor specimens with a low rate of mutations. Surface immunoglobulin was an IgM in 12/12 cases. FISH analysis of IGHM locus, deleted during class switching, showed heterozygous IGHM gene deletion in half of cases. The genomic PCR analysis confirmed the deletions within the switch μ region. IGV sequences were highly mutated but functional, with negative features of selection pressure suggesting one or more germinal center passage(s) with somatic hypermutation, but superantigen (SpA) binding sites conservation. Genetic features of class switch were observed, but on the non functional allele and co-existing with primary isotype IgM expression. CONCLUSION These data suggest that cell-of origin is germinal center experienced and superantigen driven selected B-cell, in a stage between germinal center B-cell and plasma cell.
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Affiliation(s)
- Anne Pham-Ledard
- INSERM U1053, Team 3 Oncogenesis of Cutaneous Lymphomas, Univ. Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France; Dermatology Department, CHU Bordeaux,1 avenue Jean Burguet, 33000 Bordeaux, France.
| | - Martina Prochazkova-Carlotti
- INSERM U1053, Team 3 Oncogenesis of Cutaneous Lymphomas, Univ. Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Mélanie Deveza
- UMR CNRS 7276, Univ. Limoges,2 avenue Martin Luther King, 87042 Limoges, France
| | | | - Marie Beylot-Barry
- INSERM U1053, Team 3 Oncogenesis of Cutaneous Lymphomas, Univ. Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France; Dermatology Department, CHU Bordeaux,1 avenue Jean Burguet, 33000 Bordeaux, France
| | - Béatrice Vergier
- INSERM U1053, Team 3 Oncogenesis of Cutaneous Lymphomas, Univ. Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France; Pathology Department, CHU Bordeaux,Avenue de Magellan, 33604 Pessac, France
| | - Marie Parrens
- INSERM U1053, Team 3 Oncogenesis of Cutaneous Lymphomas, Univ. Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France; Pathology Department, CHU Bordeaux,Avenue de Magellan, 33604 Pessac, France
| | - Jean Feuillard
- UMR CNRS 7276, Univ. Limoges,2 avenue Martin Luther King, 87042 Limoges, France
| | - Jean-Philippe Merlio
- INSERM U1053, Team 3 Oncogenesis of Cutaneous Lymphomas, Univ. Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France; Tumor Bank and Tumor Biology Laboratory,Avenue de Magellan, CHU Bordeaux, 33604 Pessac, France
| | - Nathalie Gachard
- UMR CNRS 7276, Univ. Limoges,2 avenue Martin Luther King, 87042 Limoges, France
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145
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Affiliation(s)
- Nika Kruljec
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Tomaž Bratkovič
- Faculty
of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
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146
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TalebiFard S, Schmidt S, Shi W, Wu W, Jaeger NAF, Kwok E, Ratner DM, Chrostowski L. Optimized sensitivity of Silicon-on-Insulator (SOI) strip waveguide resonator sensor. BIOMEDICAL OPTICS EXPRESS 2017; 8:500-511. [PMID: 28270963 PMCID: PMC5330585 DOI: 10.1364/boe.8.000500] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/26/2016] [Accepted: 11/16/2016] [Indexed: 05/24/2023]
Abstract
Evanescent field sensors have shown promise for biological sensing applications. In particular, Silicon-on-Insulator (SOI)-nano-photonic based resonator sensors have many advantages for lab-on-chip diagnostics, including high sensitivity for molecular detection and compatibility with CMOS foundries for high volume manufacturing. We have investigated the optimum design parameters within the fabrication constraints of Multi-Project Wafer (MPW) foundries that result in the highest sensitivity for a resonator sensor. We have demonstrated the optimum waveguide thickness needed to achieve the maximum bulk sensitivity with SOI-based resonator sensors to be 165 nm using the quasi-TM guided mode. The closest thickness offered by MPW foundry services is 150 nm. Therefore, resonators with 150 nm thick silicon waveguides were fabricated resulting in sensitivities as high as 270 nm/RIU, whereas a similar resonator sensor with a 220 nm thick waveguide demonstrated sensitivities of approximately 200 nm/RIU.
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Affiliation(s)
- Sahba TalebiFard
- Department of Electrical and Computer Engineering, University of British Columbia, 2332 Main Mall, Vancouver, BC, V6T 1Z4,
Canada
| | - Shon Schmidt
- Department of Bioengineering, University of Washington, Box 355061 Seattle, WA 98195,
USA
| | - Wei Shi
- University of Laval 2325 Rue de l’Universite, Ville de Quebec, QC G1V 0A6,
Canada
| | - WenXuan Wu
- Department of Bioengineering, University of Washington, Box 355061 Seattle, WA 98195,
USA
| | - Nicolas A. F. Jaeger
- Department of Electrical and Computer Engineering, University of British Columbia, 2332 Main Mall, Vancouver, BC, V6T 1Z4,
Canada
| | - Ezra Kwok
- Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC V6T 1Z3,
Canada
| | - Daniel M. Ratner
- Department of Bioengineering, University of Washington, Box 355061 Seattle, WA 98195,
USA
| | - Lukas Chrostowski
- Department of Electrical and Computer Engineering, University of British Columbia, 2332 Main Mall, Vancouver, BC, V6T 1Z4,
Canada
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147
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Fc-Binding Ligands of Immunoglobulin G: An Overview of High Affinity Proteins and Peptides. MATERIALS 2016; 9:ma9120994. [PMID: 28774114 PMCID: PMC5456964 DOI: 10.3390/ma9120994] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/26/2016] [Accepted: 11/29/2016] [Indexed: 01/20/2023]
Abstract
The rapidly increasing application of antibodies has inspired the development of several novel methods to isolate and target antibodies using smart biomaterials that mimic the binding of Fc-receptors to antibodies. The Fc-binding domain of antibodies is the primary binding site for e.g., effector proteins and secondary antibodies, whereas antigens bind to the Fab region. Protein A, G, and L, surface proteins expressed by pathogenic bacteria, are well known to bind immunoglobulin and have been widely exploited in antibody purification strategies. Several difficulties are encountered when bacterial proteins are used in antibody research and application. One of the major obstacles hampering the use of bacterial proteins is sample contamination with trace amounts of these proteins, which can invoke an immune response in the host. Many research groups actively develop synthetic ligands that are able to selectively and strongly bind to antibodies. Among the reported ligands, peptides that bind to the Fc-domain of antibodies are attractive tools in antibody research. Besides their use as high affinity ligands in antibody purification chromatography, Fc-binding peptides are applied e.g., to localize antibodies on nanomaterials and to increase the half-life of proteins in serum. In this review, recent developments of Fc-binding peptides are presented and their binding characteristics and diverse applications are discussed.
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148
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Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire. Nat Commun 2016; 7:13376. [PMID: 27857134 PMCID: PMC5120205 DOI: 10.1038/ncomms13376] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 09/28/2016] [Indexed: 11/08/2022] Open
Abstract
Staphylococcus aureus is both an important pathogen and a human commensal. To explore this ambivalent relationship between host and microbe, we analysed the memory humoral response against IsdB, a protein involved in iron acquisition, in four healthy donors. Here we show that in all donors a heavily biased use of two immunoglobulin heavy chain germlines generated high affinity (pM) antibodies that neutralize the two IsdB NEAT domains, IGHV4-39 for NEAT1 and IGHV1-69 for NEAT2. In contrast to the typical antibody/antigen interactions, the binding is primarily driven by the germline-encoded hydrophobic CDRH-2 motifs of IGHV1-69 and IGHV4-39, with a binding mechanism nearly identical for each antibody derived from different donors. Our results suggest that IGHV1-69 and IGHV4-39, while part of the adaptive immune system, may have evolved under selection pressure to encode a binding motif innately capable of recognizing and neutralizing a structurally conserved protein domain involved in pathogen iron acquisition.
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149
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Geddie ML, Kohli N, Kirpotin DB, Razlog M, Jiao Y, Kornaga T, Rennard R, Xu L, Schoerberl B, Marks JD, Drummond DC, Lugovskoy AA. Improving the developability of an anti-EphA2 single-chain variable fragment for nanoparticle targeting. MAbs 2016; 9:58-67. [PMID: 27854147 DOI: 10.1080/19420862.2016.1259047] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Antibody-targeted nanoparticles have great promise as anti-cancer drugs; however, substantial developmental challenges of antibody modules prevent many candidates from reaching the clinic. Here, we describe a robust strategy for developing an EphA2-targeting antibody fragment for immunoliposomal drug delivery. A highly bioactive single-chain variable fragment (scFv) was engineered to overcome developmental liabilities, including low thermostability and weak binding to affinity purification resins. Improved thermostability was achieved by modifying the framework of the scFv, and complementarity-determining region (CDR)-H2 was modified to increase binding to protein A resins. The results of our engineering campaigns demonstrate that it is possible, using focused design strategies, to rapidly improve the stability and manufacturing characteristics of an antibody fragment for use as a component of a novel therapeutic construct.
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Affiliation(s)
| | | | | | | | - Yang Jiao
- a Merrimack, Inc. , Cambridge , MA , USA
| | | | | | - Lihui Xu
- a Merrimack, Inc. , Cambridge , MA , USA
| | | | - James D Marks
- a Merrimack, Inc. , Cambridge , MA , USA.,b Department of Anesthesia and Pharmaceutical Chemistry , University of California San Francisco , San Francisco , CA , USA
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150
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Development of an immunoFET biosensor for the detection of biotinylated PCR product. Heliyon 2016; 2:e00188. [PMID: 27822563 PMCID: PMC5090196 DOI: 10.1016/j.heliyon.2016.e00188] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/01/2016] [Accepted: 10/21/2016] [Indexed: 12/19/2022] Open
Abstract
ImmunoFET (IMFET) biosensor is a simple platform for the detection of biotinylated products of polymerase chain reaction (PCR). Construction of the IMFET biosensor started with adsorption of 1.5 mg/mL of protein A (PA) onto the insulated gate surface of ISFET for 90 min. Next, the immobilized 1/500 dilution of anti-biotin antibody was adsorbed onto the PA layer for 60 min. The IMFET biosensor was subsequently ready for detection of the biotinylated amplicon. The IMFET biosensor showed highly specific binding to the biotinylated PCR product of the phaE gene of Haloquadratum walsbyi DSM 16854. The phaE gene is a biomarker of polyhydroxyalkanoate (PHA) producers that contain PHA synthase class III. The lowest amount of DNA template of H. walsbyi DSM 16854 that the IMFET biosensor could detect was 125 fg. The IMFET biosensor has a lower amount of detection compared with a DNA lateral flow biosensor from our previous study. The degree of linearity of the biosensor signal was influenced by the concentration of the biotinylated amplicon. The IMFET biosensor also has a short response time (approximately 30 times) to detect the phaE amplicon compared to an agarose gel electrophoresis. The IMFET biosensor is a promising tool for the detection of the biotinylated PCR product, and it can be integrated into a micro total analysis system (μTAS).
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