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1.
Proc Natl Acad Sci U S A ; 117(23): 12693-12699, 2020 06 09.
Article in English | MEDLINE | ID: mdl-32457160

ABSTRACT

Natural environments can present diverse challenges, but some genotypes remain fit across many environments. Such "generalists" can be hard to evolve, outcompeted by specialists fitter in any particular environment. Here, inspired by the search for broadly neutralizing antibodies during B cell affinity maturation, we demonstrate that environmental changes on an intermediate timescale can reliably evolve generalists, even when faster or slower environmental changes are unable to do so. We find that changing environments on timescales comparable with evolutionary transients in a population enhance the rate of evolving generalists from specialists, without enhancing the reverse process. The yield of generalists is further increased in more complex dynamic environments, such as a "chirp" of increasing frequency. Our work offers design principles for how nonequilibrium fitness "seascapes" can dynamically funnel populations to genotypes unobtainable in static environments.


Subject(s)
Antibodies, Neutralizing/immunology , Antibody Specificity/genetics , Environment , Evolution, Molecular , Models, Genetic , Animals , Antibodies, Neutralizing/genetics , Antibody Specificity/immunology , B-Lymphocytes/cytology , B-Lymphocytes/immunology , Cell Differentiation , Genotype , Humans
2.
Proc Natl Acad Sci U S A ; 116(14): 6812-6817, 2019 04 02.
Article in English | MEDLINE | ID: mdl-30894493

ABSTRACT

Aberrant activation of Wnt/Ɵ-catenin signaling occurs frequently in cancer. However, therapeutic targeting of this pathway is complicated by the role of Wnt in stem cell maintenance and tissue homeostasis. Here, we evaluated antibodies blocking 6 of the 10 human Wnt/Frizzled (FZD) receptors as potential therapeutics. Crystal structures revealed a common binding site for these monoclonal antibodies (mAbs) on FZD, blocking the interaction with the Wnt palmitoleic acid moiety. However, these mAbs displayed gastrointestinal toxicity or poor plasma exposure in vivo. Structure-guided engineering was used to refine the binding of each mAb for FZD receptors, resulting in antibody variants with improved in vivo tolerability and developability. Importantly, the lead variant mAb significantly inhibited tumor growth in the HPAF-II pancreatic tumor xenograft model. Taken together, our data demonstrate that anti-FZD cancer therapeutic antibodies with broad specificity can be fine-tuned to navigate in vivo exposure and tolerability while driving therapeutic efficacy.


Subject(s)
Antibody Specificity , Antineoplastic Agents, Immunological , Frizzled Receptors/antagonists & inhibitors , Pancreatic Neoplasms , Protein Engineering , Animals , Antibody Specificity/genetics , Antibody Specificity/immunology , Antineoplastic Agents, Immunological/immunology , Antineoplastic Agents, Immunological/pharmacokinetics , Antineoplastic Agents, Immunological/pharmacology , Cell Line, Tumor , Female , Frizzled Receptors/genetics , Frizzled Receptors/immunology , HEK293 Cells , Humans , Mice , Mice, Nude , Pancreatic Neoplasms/drug therapy , Pancreatic Neoplasms/genetics , Pancreatic Neoplasms/immunology , Pancreatic Neoplasms/pathology , Xenograft Model Antitumor Assays
3.
Int J Mol Sci ; 22(3)2021 Jan 26.
Article in English | MEDLINE | ID: mdl-33530489

ABSTRACT

Since the first description of nuclear autoantigens in the late 1960s and early 1970s, researchers, including ourselves, have found it difficult to establish monoclonal antibodies (mabs) against nuclear antigens, including the La/SS-B (Sjƶgrens' syndrome associated antigen B) autoantigen. To date, only a few anti-La mabs have been derived by conventional hybridoma technology; however, those anti-La mabs were not bona fide autoantibodies as they recognize either human La specific, cryptic, or post-translationally modified epitopes which are not accessible on native mouse La protein. Herein, we present a series of novel murine anti-La mabs including truly autoreactive ones. These mabs were elicited from a human La transgenic animal through adoptive transfer of T cells from non-transgenic mice immunized with human La antigen. Detailed epitope and paratope analyses experimentally confirm the hypothesis that somatic hypermutations that occur during T cell dependent maturation can lead to autoreactivity to the nuclear La/SS-B autoantigen.


Subject(s)
Autoantigens/immunology , Autoimmunity/genetics , B-Lymphocytes/immunology , B-Lymphocytes/metabolism , Cell Communication/immunology , Ribonucleoproteins/immunology , Somatic Hypermutation, Immunoglobulin , T-Lymphocytes/immunology , 3T3 Cells , Adoptive Transfer , Amino Acid Sequence , Animals , Antibody Specificity/genetics , Autoantibodies/chemistry , Autoantibodies/genetics , Autoantibodies/immunology , Autoantigens/chemistry , Autoimmune Diseases/genetics , Autoimmune Diseases/immunology , Autoimmune Diseases/metabolism , Disease Models, Animal , Epitope Mapping , Epitopes/chemistry , Epitopes/immunology , Fluorescent Antibody Technique , Germ Cells/metabolism , Humans , Immunization , Mice , Mice, Transgenic , Models, Molecular , Protein Conformation , Ribonucleoproteins/chemistry , T-Lymphocytes/metabolism , SS-B Antigen
4.
Mol Biol Rep ; 46(4): 3865-3876, 2019 Aug.
Article in English | MEDLINE | ID: mdl-31016614

ABSTRACT

Classical swine fever virus (CSFV), a member of the Pestivirus genus within the Flaviviridae family causes contagious fatal disease in swine. Antibodies against E2, Erns and NS3 proteins of virus can be detected in infected animals. Development of an ELISA coating antigen to improve the sensitivity of detecting Erns-specific antibodies in pig sera is always desirable for diagnosis as well as for differentiation of infected from vaccinated animals. In present study, a lentivirus-based gene delivery system was used to develop a stable PK-15 cell line expressing Erns (PK-Erns) for production of diagnostic antigen. The Lenti-Erns virus was purified from the supernatant of co-transfected 293LTV cells and used to transduce PK-15 cells. The homogenous PK-Erns cell line was produced by single cell cloning by monitoring eGFP expression. The Erns gene in the genomic DNA and RNA transcripts in total RNA isolated from PK-Erns cells were detected by PCR and RT-PCR, respectively. Expression of 45Ā kDa Erns glycoprotein was detected in western blot using CSFV-specific hyperimmune sera. The use of PK-Erns cell lysate as antigen in serial dilution and single dilution ELISAs with known positive and negative pig sera was investigated. The PK-Erns ELISA revealed sensitivity equivalent to commercial HerdChek ELISA kit. The sensitivity, specificity and accuracy of the PK-Erns ELISA was 95%, 100% and 96.66%, respectively compared to ELISA using purified CSFV as coating antigen. When field pig sera (n = 69) were tested in PK-Erns ELISA, a significant correlation between the titers from serial dilution and single dilution ELISA was observed. This indicated that PK-Erns cell line can serve as continuous source of ELISA diagnostic antigen for detection of CSFV-specific antibodies in pig sera.


Subject(s)
Classical Swine Fever Virus/genetics , Molecular Diagnostic Techniques/methods , Viral Structural Proteins/immunology , Animals , Antibody Specificity/genetics , Antibody-Producing Cells/metabolism , Cell Line , Classical Swine Fever Virus/immunology , Enzyme-Linked Immunosorbent Assay , Gene Transfer Techniques , Lentivirus/metabolism , Proteins , Recombinant Proteins , Sensitivity and Specificity , Swine/genetics , Swine/metabolism , Viral Envelope Proteins/immunology , Viral Structural Proteins/genetics
5.
PLoS Genet ; 12(5): e1006035, 2016 05.
Article in English | MEDLINE | ID: mdl-27171438

ABSTRACT

During postnatal life the cerebral cortex passes through critical periods of plasticity allowing its physiological adaptation to the environment. In the visual cortex, critical period onset and closure are influenced by the non-cell autonomous activity of the Otx2 homeoprotein transcription factor, which regulates the maturation of parvalbumin-expressing inhibitory interneurons (PV cells). In adult mice, the maintenance of a non-plastic adult state requires continuous Otx2 import by PV cells. An important source of extra-cortical Otx2 is the choroid plexus, which secretes Otx2 into the cerebrospinal fluid. Otx2 secretion and internalization requires two small peptidic domains that are part of the DNA-binding domain. Thus, mutating these "transfer" sequences also modifies cell autonomous transcription, precluding this approach to obtain a cell autonomous-only mouse. Here, we develop a mouse model with inducible secretion of an anti-Otx2 single-chain antibody to trap Otx2 in the extracellular milieu. Postnatal secretion of this single-chain antibody by PV cells delays PV maturation and reduces plasticity gene expression. Induced adult expression of this single-chain antibody in cerebrospinal fluid decreases Otx2 internalization by PV cells, strongly induces plasticity gene expression and reopens physiological plasticity. We provide the first mammalian genetic evidence for a signaling mechanism involving intercellular transfer of a homeoprotein transcription factor. Our single-chain antibody mouse model is a valid strategy for extracellular neutralization that could be applied to other homeoproteins and signaling molecules within and beyond the nervous system.


Subject(s)
Antibody Specificity/immunology , Interneurons/immunology , Otx Transcription Factors/immunology , Single-Chain Antibodies/immunology , Animals , Antibody Specificity/genetics , Cerebral Cortex/immunology , Cerebral Cortex/metabolism , Disease Models, Animal , Gene Expression Regulation , Humans , Mice , Neuronal Plasticity/immunology , Otx Transcription Factors/genetics , Parvalbumins/biosynthesis , Signal Transduction , Single-Chain Antibodies/genetics , Visual Cortex/immunology , Visual Cortex/metabolism
6.
Clin Exp Immunol ; 194(2): 153-165, 2018 11.
Article in English | MEDLINE | ID: mdl-30076785

ABSTRACT

Ubiquitin is highly conserved across eukaryotes and is essential for normal eukaryotic cell function. The bacterium Bacteroides fragilis is a member of the normal human gut microbiota, and the only bacterium known to encode a homologue of eukaryotic ubiquitin. The B. fragilis gene sequence indicates a past horizontal gene transfer event from a eukaryotic source. It encodes a protein (BfUbb) with 63% identity to human ubiquitin which is exported from the bacterial cell. The aim of this study was (i) to determine if there was antigenic cross-reactivity between B. fragilis ubiquitin and human ubiquitin and (ii) to determine if humans produced antibodies to BfUbb. Molecular model comparisons of BfUbb and human ubiquitin predicted a high level (99Ā·8% confidence) of structural similarity. Linear epitope mapping identified epitopes in BfUbb and human ubiquitin that cross-react. BfUbb also has epitope(s) that do not cross-react with human ubiquitin. The reaction of human serum (n = 474) to BfUbb and human ubiquitin from the following four groups of subjects was compared by enzyme-linked immunosorbent assay (ELISA): (1) newly autoantibody-positive patients, (2) allergen-specific immunoglobulin (Ig)E-negative patients, (3) ulcerative colitis patients and (4) healthy volunteers. We show that the immune system of some individuals has been exposed to BfUbb which has resulted in the generation of IgG antibodies. Serum from patients referred for first-time testing to an immunology laboratory for autoimmune disease are more likely to have a high level of antibodies to BfUbb than healthy volunteers. Molecular mimicry of human ubiquitin by BfUbb could be a trigger for autoimmune disease.


Subject(s)
Antibody Specificity/immunology , Antigens, Bacterial/immunology , Autoimmune Diseases/immunology , Bacteroides fragilis/immunology , Gastrointestinal Microbiome/immunology , Ubiquitin/immunology , Adult , Antibody Specificity/genetics , Antigens, Bacterial/chemistry , Antigens, Bacterial/genetics , Autoantibodies/blood , Autoimmune Diseases/microbiology , Autoimmunity , Cross Reactions , Gene Transfer, Horizontal , Humans , Middle Aged , Models, Molecular , Molecular Conformation , Molecular Mimicry , Structure-Activity Relationship , Ubiquitin/chemistry , Ubiquitin/genetics
7.
Hepatology ; 65(4): 1117-1131, 2017 04.
Article in English | MEDLINE | ID: mdl-27997681

ABSTRACT

A vaccine that prevents hepatitis C virus (HCV) infection is urgently needed to support an emerging global elimination program. However, vaccine development has been confounded because of HCV's high degree of antigenic variability and the preferential induction of type-specific immune responses with limited potency against heterologous viral strains and genotypes. We showed previously that deletion of the three variable regions from the E2 receptor-binding domain (Δ123) increases the ability of human broadly neutralizing antibodies (bNAbs) to inhibit E2-CD81 receptor interactions, suggesting improved bNAb epitope exposure. In this study, the immunogenicity of Δ123 was examined. We show that high-molecular-weight forms of Δ123 elicit distinct antibody specificities with potent and broad neutralizing activity against all seven HCV genotypes. Antibody competition studies revealed that immune sera raised to high-molecular-weight Δ123 was poly specific, given that it inhibited the binding of human bNAbs directed to three major neutralization epitopes on E2. By contrast, the immune sera raised to monomeric Δ123 predominantly blocked the binding of a non-neutralizing antibody to Δ123, while having reduced ability to block bNAb binding to E2, and neutralization was largely toward the homologous genotype. This increased ability of oligomeric Δ123 to generate bNAbs correlates with occlusion of the non-neutralizing face of E2 in this glycoprotein form. CONCLUSION: The results from this study reveal new information on the antigenic and immunogenic potential of E2-based immunogens and provide a pathway for the development of a simple, recombinant protein-based prophylactic vaccine for HCV with potential for universal protection. (Hepatology 2017;65:1117-1131).


Subject(s)
Hepacivirus/genetics , Hepatitis C/genetics , Viral Envelope Proteins/genetics , Viral Hepatitis Vaccines/pharmacology , Animals , Antibodies, Neutralizing/immunology , Antibody Specificity/genetics , Disease Models, Animal , Enzyme-Linked Immunosorbent Assay , Epitopes/genetics , Genotype , Guinea Pigs , Hepacivirus/immunology , Hepatitis C/immunology , Hepatitis C Antibodies/immunology , Random Allocation , Statistics, Nonparametric , Viral Envelope Proteins/immunology
8.
Anal Biochem ; 555: 81-93, 2018 08 15.
Article in English | MEDLINE | ID: mdl-29775561

ABSTRACT

Anti-salbutamol antibodies remain as important tools for the detection of salbutamol abuse in athletic doping. This study evaluated the feasibility and efficiency of the chicken (Gallus gallus domesticus) as an immunization host to generate anti-salbutamol scFv antibodies by phage display. A phage display antibody library was constructed from a single chicken immunized against salbutamol-KLH conjugate. After a stringent biopanning strategy, a novel scFv clone which was inhibited by free salbutamol recorded the highest affinity. This scFv was expressed as soluble and functional protein in Escherichia coli T7 SHuffle Express B (DE3) strain. Cross-reactivity studies of the scFv towards other relevant Ɵ2-agonists revealed that the scFv cross-reacted significantly towards clenbuterol. The determined IC50 of the scFv towards the two Ɵ2-agonists were; IC50 salbutamolĆ¢Ā€ĀÆ=Ć¢Ā€ĀÆĆ¢ĀˆĀ¼0.310Ć¢Ā€ĀÆĀµg/ml, IC50 clenbuterolĆ¢Ā€ĀÆ=Ć¢Ā€ĀÆĆ¢ĀˆĀ¼0.076Ć¢Ā€ĀÆĀµg/ml. The generated scFv demonstrated poor stability based on accelerated stability studies. The scFv was used to develop an competitive indirect ELISA (LODĆ¢Ā€ĀÆ=Ć¢Ā€ĀÆ0.125Ć¢Ā€ĀÆĀµg/ml) for detection of parent salbutamol in spiked human urine (nĆ¢Ā€ĀÆ=Ć¢Ā€ĀÆ18) with Ć¢ĀˆĀ¼83.4% reliability at the cut-off of 1Ć¢Ā€ĀÆĀµg/ml currently implemented by WADA and may be of potential use in human doping urinalysis.


Subject(s)
Albuterol/urine , Avian Proteins/chemistry , Clenbuterol/urine , Doping in Sports , Single-Chain Antibodies/chemistry , Animals , Antibody Specificity/genetics , Avian Proteins/genetics , Chickens , Humans , Single-Chain Antibodies/genetics , Urinalysis
9.
Nature ; 489(7417): 526-32, 2012 Sep 27.
Article in English | MEDLINE | ID: mdl-22982990

ABSTRACT

Immune recognition of protein antigens relies on the combined interaction of multiple antibody loops, which provide a fairly large footprint and constrain the size and shape of protein surfaces that can be targeted. Single protein loops can mediate extremely high-affinity binding, but it is unclear whether such a mechanism is available to antibodies. Here we report the isolation and characterization of an antibody called C05, which neutralizes strains from multiple subtypes of influenza A virus, including H1, H2 and H3. X-ray and electron microscopy structures show that C05 recognizes conserved elements of the receptor-binding site on the haemagglutinin surface glycoprotein. Recognition of the haemagglutinin receptor-binding site is dominated by a single heavy-chain complementarity-determining region 3 loop, with minor contacts from heavy-chain complementarity-determining region 1, and is sufficient to achieve nanomolar binding with a minimal footprint. Thus, binding predominantly with a single loop can allow antibodies to target small, conserved functional sites on otherwise hypervariable antigens.


Subject(s)
Antibodies, Neutralizing/chemistry , Antibodies, Neutralizing/immunology , Antibodies, Viral/chemistry , Antibodies, Viral/immunology , Antibody Specificity/immunology , Influenza A virus/classification , Influenza A virus/immunology , Animals , Antibodies, Neutralizing/genetics , Antibodies, Viral/genetics , Antibody Specificity/genetics , Antigens, Viral/chemistry , Antigens, Viral/immunology , Binding Sites , Complementarity Determining Regions/chemistry , Complementarity Determining Regions/genetics , Complementarity Determining Regions/immunology , Conserved Sequence , Cross Reactions/genetics , Cross Reactions/immunology , Crystallography, X-Ray , Enzyme-Linked Immunosorbent Assay , Epitopes/chemistry , Epitopes/immunology , Hemagglutinin Glycoproteins, Influenza Virus/chemistry , Hemagglutinin Glycoproteins, Influenza Virus/immunology , Influenza A Virus, H1N1 Subtype/chemistry , Influenza A Virus, H1N1 Subtype/immunology , Influenza A Virus, H3N2 Subtype/chemistry , Influenza A Virus, H3N2 Subtype/immunology , Influenza A virus/chemistry , Influenza Vaccines/immunology , Mice , Models, Molecular , Molecular Sequence Data , Mutation/genetics , Orthomyxoviridae Infections/immunology , Orthomyxoviridae Infections/prevention & control , Orthomyxoviridae Infections/virology , Protein Conformation
10.
Bioinformatics ; 31(3): 434-5, 2015 Feb 01.
Article in English | MEDLINE | ID: mdl-25304777

ABSTRACT

SUMMARY: Antibodies are rapidly becoming essential tools in the clinical practice, given their ability to recognize their cognate antigens with high specificity and affinity, and a high yield at reasonable costs in model animals. Unfortunately, when administered to human patients, xenogeneic antibodies can elicit unwanted and dangerous immunogenic responses. Antibody humanization methods are designed to produce molecules with a better safety profile still maintaining their ability to bind the antigen. This can be accomplished by grafting the non-human regions determining the antigen specificity into a suitable human template. Unfortunately, this procedure may results in a partial or complete loss of affinity of the grafted molecule that can be restored by back-mutating some of the residues of human origin to the corresponding murine ones. This trial-and-error procedure is hard and involves expensive and time-consuming experiments. Here we present tools for antibody humanization (Tabhu) a web server for antibody humanization. Tabhu includes tools for human template selection, grafting, back-mutation evaluation, antibody modelling and structural analysis, helping the user in all the critical steps of the humanization experiment protocol. AVAILABILITY: http://www.biocomputing.it/tabhu CONTACT: anna.tramontano@uniroma1.it, pierpaolo.olimpieri@uniroma1.it SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Antibodies, Monoclonal/immunology , Antibody Specificity/genetics , Antigen-Antibody Complex/chemistry , Antigens/immunology , Protein Engineering/methods , Software , Animals , Antibodies, Monoclonal/genetics , Humans , Mice
11.
Int J Immunogenet ; 43(4): 200-8, 2016 Aug.
Article in English | MEDLINE | ID: mdl-27312793

ABSTRACT

The determination of HLA mismatch acceptability at the epitope level can be best performed with epitopes that have been verified experimentally with informative antibodies. The website-based International Registry of HLA Epitopes (http://www.epregistry.com.br) has a list of 81 antibody-verified HLA-ABC epitopes but more epitopes need to be added. Pregnancy offers an attractive model to study antibody responses to mismatched HLA epitopes which can be readily determined from the HLA types of child and mother. This report describes a HLAMatchmaker-based analysis of 16 postpregnancy sera tested in single HLA-ABC allele binding assays. Most sera reacted with alleles carrying epitopes that have been antibody-verified, and this study focused on the reactivity of additional alleles that share other epitopes corresponding to eplets and other amino acid residue configurations. This analysis led in the identification of 16 newly antibody-defined epitopes, seven are equivalent to eplets and nine correspond to combinations of eplets in combination with other nearby residue configurations. These epitopes will be added to the repertoire of antibody-verified epitopes in the HLA Epitope Registry.


Subject(s)
Antibody Specificity/genetics , Epitopes/genetics , HLA Antigens/genetics , Adult , Alleles , Amino Acid Sequence/genetics , Antibody Specificity/immunology , Epitopes/blood , Epitopes/immunology , Female , HLA Antigens/blood , HLA Antigens/immunology , Histocompatibility Testing , Humans , Pregnancy
12.
Proc Natl Acad Sci U S A ; 110(11): 4261-6, 2013 Mar 12.
Article in English | MEDLINE | ID: mdl-23440204

ABSTRACT

Somatic hypermutation and clonal selection lead to B cells expressing high-affinity antibodies. Here we show that somatic mutations not only play a critical role in antigen binding, they also affect the thermodynamic stability of the antibody molecule. Somatic mutations directly involved in antigen recognition by antibody 93F3, which binds a relatively small hapten, reduce the melting temperature compared with its germ-line precursor by up to 9 Ā°C. The destabilizing effects of these mutations are compensated by additional somatic mutations located on surface loops distal to the antigen binding site. Similarly, somatic mutations enhance both the affinity and thermodynamic stability of antibody OKT3, which binds the large protein antigen CD3. Analysis of the crystal structures of 93F3 and OKT3 indicates that these somatic mutations modulate antibody stability primarily through the interface of the heavy and light chain variable domains. The historical view of antibody maturation has been that somatic hypermutation and subsequent clonal selection increase antigen-antibody specificity and binding energy. Our results suggest that this process also optimizes protein stability, and that many peripheral mutations that were considered to be neutral are required to offset deleterious effects of mutations that increase affinity. Thus, the immunological evolution of antibodies recapitulates on a much shorter timescale the natural evolution of enzymes in which function and thermodynamic stability are simultaneously enhanced through mutation and selection.


Subject(s)
Antibodies, Monoclonal, Murine-Derived/immunology , Antibody Affinity/physiology , Antibody Specificity/immunology , Binding Sites, Antibody/immunology , Immunoglobulin Variable Region/immunology , Somatic Hypermutation, Immunoglobulin/physiology , Animals , Antibodies, Monoclonal, Murine-Derived/genetics , Antibody Specificity/genetics , Binding Sites, Antibody/genetics , HEK293 Cells , Humans , Immunoglobulin Variable Region/genetics , Mice , Mutation , Protein Stability
13.
Immunol Rev ; 248(1): 56-67, 2012 Jul.
Article in English | MEDLINE | ID: mdl-22725954

ABSTRACT

Systemic lupus erythematosus is an autoimmune disease characterized by antibodies that bind target autoantigens in multiple organs in the body. In peripheral organs, immune complexes engage the complement cascade, recruiting blood-borne inflammatory cells and initiating tissue inflammation. Immune complex-mediated activation of Fc receptors on infiltrating blood-borne cells and tissue resident cells amplifies an inflammatory cascade with resulting damage to tissue function, ultimately leading to tissue destruction. This pathophysiology appears to explain tissue injury throughout the body, except in the central nervous system. This review addresses a paradigm we have developed for autoantibody-mediated brain damage. This paradigm suggests that antibody-mediated brain disease does not depend on immune complex formation but rather on antibody-mediated alterations in neuronal activation and survival. Moreover, antibodies only access brain tissue when blood-brain barrier integrity is impaired, leading to a lack of concurrence of brain disease and tissue injury in other organs. We discuss the implications of this model for lupus and for identifying other antibodies that may contribute to brain disease.


Subject(s)
Brain Diseases/immunology , Lupus Erythematosus, Systemic/immunology , Amygdala/immunology , Amygdala/metabolism , Animals , Antibodies, Antinuclear/chemistry , Antibodies, Antinuclear/immunology , Antibodies, Antinuclear/metabolism , Antibody Specificity/genetics , Antibody Specificity/immunology , Autoantibodies/immunology , Autoantibodies/metabolism , Blood-Brain Barrier/metabolism , Brain/immunology , Brain/metabolism , Brain Diseases/drug therapy , Brain Diseases/etiology , Brain Diseases/metabolism , Hippocampus/immunology , Hippocampus/metabolism , Humans , Lupus Erythematosus, Systemic/complications , Lupus Erythematosus, Systemic/drug therapy , Lupus Erythematosus, Systemic/metabolism , Models, Immunological , Neurons/immunology , Neurons/metabolism , Peptides/immunology , Peptides/metabolism , Peptides/therapeutic use , Protein Binding , Receptors, N-Methyl-D-Aspartate/metabolism
14.
Proc Natl Acad Sci U S A ; 109(39): 15728-33, 2012 Sep 25.
Article in English | MEDLINE | ID: mdl-23019357

ABSTRACT

A method is presented that uses combinatorial antibody libraries to endow cells with new binding energy landscapes for the purpose of regulating their phenotypes. Antibodies that are expressed in cells infected with a lentiviral combinatorial antibody library are selected directly for function rather than only for binding. The potential diversity space can be very large because more than one lentivirus can infect a single cell. Thus, the initial combinatorial diversity of ~1.0 Ɨ 10(11) members generated by the random association of antibody heavy and light chains is greatly increased by the reassortment of the antibody Fv domains themselves inside cells. The power of the system is illustrated by its ability to select unusual antibodies. Here, the selected antibodies are potent erythropoietin agonists whose ontogeny depends on recombination at the protein level of pairs of antibodies expressed in the same cell to generate heterodimeric bispecific antibodies. The obligate synergy between the different binding specificities of the antibody's monomeric subunits appears to replicate the asymmetric binding mechanism of authentic erythropoietin.


Subject(s)
Antibody Specificity/genetics , Binding Sites, Antibody , Erythropoietin/immunology , Gene Library , Single-Chain Antibodies , Binding Sites, Antibody/genetics , Binding Sites, Antibody/immunology , Erythropoietin/genetics , HEK293 Cells , Humans , Single-Chain Antibodies/genetics , Single-Chain Antibodies/immunology
15.
Plant J ; 76(4): 709-17, 2013 Nov.
Article in English | MEDLINE | ID: mdl-23980604

ABSTRACT

Single-domain antibodies (sdAbs) are powerful tools for the detection, quantification, purification and subcellular localization of proteins of interest in biological research. We have generated camelid (Lama pacos) heavy chain-only variable VH domain (VH H) libraries against antigens in total cell lysates from Chlamydomonas reinhardtii. The sdAbs in the sera from immunized animals and VH H antibody domains isolated from the library show specificity to C. reinhardtii and lack of reactivity to antigens from four other algae: Chlorella variabilis, Coccomyxa subellipsoidea, Nannochloropsis oceanica and Thalassiosira pseudonana. Antibodies were produced against a diverse representation of antigens as evidenced by sera ELISA and protein-blot analyses. A phage-display library consisting of the VH H region contained at least 10(6) individual transformants, and thus should represent a wide range of C. reinhardtii antigens. The utility of the phage library was demonstrated by using live C. reinhardtii cells to pan for VH H clones with specific recognition of cell-surface epitopes. The lead candidate VH H clones (designated B11 and H10) bound to C. reinhardtii with EC50 values ≤ 0.5 nm. Treatment of cells with VH H B11 fused to the mCherry or green fluorescent proteins allowed brilliant and specific staining of the C. reinhardtii cell wall and analysis of cell-wall genesis during cell division. Such high-complexity VH H antibody libraries for algae will be valuable tools for algal researchers and biotechnologists.


Subject(s)
Antigens, Plant/immunology , Camelids, New World/immunology , Chlamydomonas reinhardtii/immunology , Immunoglobulin Heavy Chains/biosynthesis , Immunoglobulin Variable Region/biosynthesis , Peptide Library , Animals , Antibody Formation/genetics , Antibody Specificity/genetics , Antigens, Plant/genetics , Camelids, New World/genetics , Cell Division/genetics , Cell Division/immunology , Cell Membrane/genetics , Cell Membrane/immunology , Chlamydomonas reinhardtii/genetics , Immunoglobulin Heavy Chains/genetics , Immunoglobulin Variable Region/chemistry , Immunoglobulin Variable Region/genetics , Plantibodies/chemistry , Plantibodies/genetics , Protein Structure, Tertiary/genetics
16.
J Immunol ; 189(12): 5667-81, 2012 Dec 15.
Article in English | MEDLINE | ID: mdl-23144494

ABSTRACT

C57BL/6 (B6) mice carrying the Sle1b sublocus (named B6.Sle1b), which harbors the lupus-associated NZM2410/NZW SLAM family genes, produce antinuclear Abs (ANAs). However, the role and mechanism(s) involved in the alteration of the germinal center (GC) tolerance checkpoint in the development of ANAs in these mice is not defined. In this study, we show significantly higher spontaneously formed GCs (Spt-GCs) in B6.Sle1b female mice compared with B6 controls. We also found a significant increase in CD4(+)CXCR5(hi)PD-1(hi) spontaneously activated follicular Th cells in B6.Sle1b female mice. Compared with B6 controls, B6.Sle1b female mice had increased numbers of proliferating B cells predominantly located in Spt-GCs. The elevated Spt-GCs in B6.Sle1b female mice were strongly associated with increased ANA-specific Ab-forming cells and ANA titers. The increased numbers of Spt-GCs and spontaneously activated follicular Th cells in B6.Sle1b mice were not the result of a generalized defect in B cells expressing Sle1b. Consistent with the elevated spontaneous response in B6.Sle1b mice, the attenuated GC response characteristic of DNA and p-azophenylarsonate reactive B cells from Ig V(H) knock-in mice (termed HKIR) were relieved in adoptively transferred recipients in the presence of Sle1b. Finally, by generating mixed bone marrow chimeras, we showed that the effect of Sle1b on Spt-GC, follicular Th cell, and autoantibody responses in B6.Sle1b mice was B cell autonomous. These data indicate that the NZM2410/NZW-derived Sle1b sublocus in conjunction with the female sex primarily affects B cells, leading to the alteration of the GC tolerance checkpoint and the generation of ANA-specific Ab-forming cells.


Subject(s)
B-Lymphocyte Subsets/immunology , B-Lymphocyte Subsets/pathology , Genetic Predisposition to Disease , Germinal Center/immunology , Germinal Center/pathology , Lupus Erythematosus, Systemic/genetics , Lupus Erythematosus, Systemic/immunology , Animals , Antibodies, Antinuclear/biosynthesis , Antibody Specificity/genetics , B-Lymphocyte Subsets/metabolism , Female , Gene Knock-In Techniques , Genetic Loci/immunology , Germinal Center/metabolism , Immune Tolerance/genetics , Lupus Erythematosus, Systemic/pathology , Mice , Mice, 129 Strain , Mice, Inbred C57BL , Mice, Inbred NZB , Mice, Knockout , Radiation Chimera/immunology
17.
Biochem J ; 456(3): 385-95, 2013 Dec 15.
Article in English | MEDLINE | ID: mdl-24040933

ABSTRACT

Monobodies are small recombinant proteins designed to bind with high affinity to target proteins. Monobodies have been generated to mimic the SIM [SUMO (small ubiquitin-like modifier)-interacting motif] present in many SUMO target proteins, but their properties have not been determined in cells. In the present study we characterize the properties of two SUMO1-specific monobodies (hS1MB4 and hS1MB5) in HEK (human embyronic kidney)-293 and HeLa cells and examine their ability to purify SUMO substrates from cell lines and rat brain. Both hS1MB4 and hS1MB5 compared favourably with commercially available antibodies and were highly selective for binding to SUMO1 over SUMO2/3 in pull-down assays against endogenous and overexpressed SUMO and SUMOylated proteins. Monobodies expressed in HeLa cells displayed a nuclear and cytosolic distribution that overlaps with SUMO1. Expression of the monobodies effectively inhibited protein SUMOylation by SUMO1 and, surprisingly, by SUMO2/3, but were not cytotoxic for at least 36 h. We attribute the effects on SUMO2/3 to the role of SUMO1 in chain termination and/or monobody inhibition of the SUMO-conjugating E1 enzyme complex. Taken together, these data provide the first demonstration that monobodies represent useful new tools both to isolate SUMO conjugates and to probe cell SUMOylation pathways in vivo.


Subject(s)
Gene Expression , SUMO-1 Protein/antagonists & inhibitors , SUMO-1 Protein/metabolism , Single-Chain Antibodies/biosynthesis , Sumoylation , Animals , Antibody Specificity/genetics , Cell Nucleus/genetics , Cell Nucleus/metabolism , Cytosol/metabolism , HEK293 Cells , HeLa Cells , Humans , Rats , SUMO-1 Protein/genetics , Single-Chain Antibodies/genetics
18.
BMC Biotechnol ; 13: 55, 2013 Jul 05.
Article in English | MEDLINE | ID: mdl-23826749

ABSTRACT

BACKGROUND: Monoclonal antibody therapeutics are rapidly gaining in popularity for the treatment of a myriad of diseases, ranging from cancer to autoimmune diseases and neurological diseases. Multiple forms of antibody therapeutics are in use today that differ in the amount of human sequence present in both the constant and variable regions, where antibodies that are more human-like usually have reduced immunogenicity in clinical trials. RESULTS: Here we present a method to quantify the humanness of the variable region of monoclonal antibodies and show that this method is able to clearly distinguish human and non-human antibodies with excellent specificity. After creating and analyzing a database of human antibody sequences, we conducted an in-depth analysis of the humanness of therapeutic antibodies, and found that increased humanness score is correlated with decreased immunogenicity of antibodies. We further discovered a surprisingly similarity in the immunogenicity of fully human antibodies and humanized antibodies that are more human-like based on their humanness score. CONCLUSIONS: Our results reveal that in most cases humanizing an antibody and confirming the humanness of the final form may be sufficient to eliminate immunogenicity issues to the same extent as using fully human antibodies. We created a public website to calculate the humanness score of any input antibody sequence based on our human antibody database. This tool will be of great value during the preclinical drug development process for new monoclonal antibody therapeutics.


Subject(s)
Antibodies, Monoclonal, Humanized/chemistry , Antibodies, Monoclonal, Humanized/immunology , Antibody Specificity/genetics , Animals , Antibodies, Monoclonal, Humanized/therapeutic use , Databases, Factual , Humans , Immunogenetic Phenomena/genetics , Immunoglobulin Variable Region/chemistry , Immunoglobulin Variable Region/genetics , Mice , Rats
19.
J Immunol ; 187(7): 3704-11, 2011 Oct 01.
Article in English | MEDLINE | ID: mdl-21880983

ABSTRACT

We generated from a single blood sample five independent human mAbs that recognized the Sa antigenic site on the head of influenza hemagglutinin and exhibited inhibitory activity against a broad panel of H1N1 strains. All five Abs used the V(H)3-7 and J(H)6 gene segments, but at least four independent clones were identified by junctional analysis. High-throughput sequence analysis of circulating B cells revealed that each of the independent clones were members of complex phylogenetic lineages that had diversified widely using a pattern of progressive diversification through somatic mutation. Unexpectedly, B cells encoding multiple diverging lineages of these clones, including many containing very few mutations in the Ab genes, persisted in the circulation. Conversely, we noted frequent instances of amino acid sequence convergence in the Ag combining sites exhibited by members of independent clones, suggesting a strong selection for optimal binding sites. We suggest that maintenance in circulation of a wide diversity of somatic variants of dominant clones may facilitate recognition of drift variant virus epitopes that occur in rapidly mutating virus Ags, such as influenza hemagglutinin. In fact, these Ab clones recognize an epitope that acquired three glycosylation sites mediating escape from previously isolated human Abs.


Subject(s)
Antibodies, Monoclonal/immunology , Antibody Specificity/immunology , B-Lymphocytes/immunology , Epitopes, B-Lymphocyte/immunology , Hemagglutinin Glycoproteins, Influenza Virus/immunology , Amino Acid Sequence , Animals , Antibodies, Monoclonal/genetics , Antibody Specificity/genetics , Antigens, Viral/genetics , Antigens, Viral/immunology , B-Lymphocytes/cytology , Cell Lineage , Clone Cells , Epitopes, B-Lymphocyte/genetics , Female , Genes, Immunoglobulin , Hemagglutinin Glycoproteins, Influenza Virus/genetics , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H1N1 Subtype/immunology , Mice , Mice, Inbred BALB C , Molecular Sequence Data , Reverse Transcriptase Polymerase Chain Reaction
20.
J Immunol ; 186(1): 614-20, 2011 Jan 01.
Article in English | MEDLINE | ID: mdl-21084661

ABSTRACT

A major obstacle to transplantation tolerance is humoral immunity. In this paper, we demonstrate that the intrinsic developmental propensity of the B lymphocyte compartment for acquisition of self-tolerance can be harnessed to induce humoral unresponsiveness to transplanted alloantigens. In the current study, when transitional B cells developed in the presence of donor lymphoid cells, the mature B lymphocyte compartment failed to mount a donor-specific alloantibody response to an organ transplant--despite unrestrained acute T cell-mediated allograft rejection. Specifically, we generated an experimental system wherein a B6 strain B cell compartment developed de novo in the presence of F1 (B6xBALB/c) lymphoid cells and in a T cell-deficient setting. Following establishment of a steady-state B cell compartment, these B6 mice were transplanted with heterotopic cardiac allografts from allogeneic BALB/c donors. The mice were then inoculated with purified syngeneic B6 T cells. As expected, all cardiac allografts were acutely rejected. However, the B lymphocyte compartment of these mice was completely inert in its capacity to form a BALB/c-specific alloantibody response. Using an alloantigen-specific Ig transgenic system, we demonstrated that this profound degree of humoral tolerance was caused by clonal deletion of alloreactive specificities from the primary B cell repertoire. Thus, de novo B cell compartment development at the time of transplantation is of critical importance in recipient repertoire "remodeling" to a humoral tolerant state.


Subject(s)
B-Lymphocyte Subsets/cytology , B-Lymphocyte Subsets/immunology , Cell Differentiation/immunology , Isoantibodies/biosynthesis , Transplantation Tolerance , Adoptive Transfer , Animals , Antibody Specificity/genetics , B-Lymphocyte Subsets/transplantation , Bone Marrow Transplantation/immunology , Cell Differentiation/genetics , Clone Cells , Heart Transplantation/immunology , Hematopoietic Stem Cell Transplantation , Isoantigens/genetics , Isoantigens/immunology , Lymphocyte Depletion , Lymphocyte Transfusion , Lymphopenia/genetics , Lymphopenia/immunology , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Mice, Knockout , Mice, SCID , Mice, Transgenic , Skin Transplantation/immunology , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/transplantation , Transplantation Tolerance/genetics
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