The epitopes for natural polyreactive antibodies are rich in proline

Compromising the immunogenicity of diphtheria toxin-based immunotoxins through epitope engineering: An in silico approach

Immunotoxins are genetically engineered recombinant proteins consisting of a targeting moiety, such as an antibody, and a cytotoxic toxin moiety of microbial origin. Pseudomonas exotoxin A and diphtheria toxin (DT) have been abundantly used in immunotoxins, with the latter applied as the toxin moiety of the FDA-approved drug Denileukin diftitox (ONTAK®). However, the use of immunotoxins provokes an adverse immune response in the host body against the toxin moiety, limiting their efficacy. In silico approaches have received increasing attention in protein engineering. In this study, the epitopes responsible for immunogenicity were identified through multiple platforms. By subtracting conserved and ligand-binding residues, K33, T111, and E112 were identified as common epitopes across all platforms. Substitution analysis evaluated alternative residues regarding their impact on protein stability, considering 19 different amino acid substitutions. Among the mutants explored, the T111A-E112G mutant exhibited the most destabilizing substitution for DT, thereby reducing immunogenicity. Finally, a 3D model of the mutant was generated and verified. The model was then docked with its native ligand NADH, and the complex's molecular behavior was simulated using molecular dynamics.

PSMA-Targeting Imprinted Nanogels for Prostate Tumor Localization and Imaging

Prostate-specific membrane antigen (PSMA) is overexpressed in prostate cancer cells and tumor vasculature, making it an important biomarker. However, conventional PSMA-targeting agents like antibodies and small molecules have limitations. Antibodies exhibit instability and complex production, while small molecules show lower specificity and higher toxicity. Herein, this work develops a novel PSMA-targeting synthetic antibody to address prior limitations. This work synthesizes fluorescently labelled, N-isopropylacrylamide-based epitope imprinted nanogels (MIP-M) using a dispersion of magnetic nanoparticles as template carriers with a linear epitope from PSMA's extracellular apical domain as the template. MIP-M demonstrates high binding affinities for both the epitope template (apparent KD = 6 × 10-10 м) and PSMA (apparent KD = 2.5 × 10-9 м). Compared to reference peptides and human serum albumin, MIP-M indicates high specificity. Flow cytometry and confocal laser scanning microscopy comparing cell lines displaying normal (PC3) and enhanced (LNCaP) PSMA expression levels, revealed that MIP-M and a PSMA antibody exhibits comparable binding preferences for the latter cell line. Moreover, MIP-M demonstrates selectivity on par with the PSMA antibody for targeting PSMA-positive prostate tumor over normal tissue, enabling discrimination. This MIP-M addresses stability, production, specificity and toxicity limitations of prior targeting agents and offer a promising alternative for PSMA-directed cancer diagnosis and treatment.

Identification of amino acid residue in the Cronobacter sakazakii LamB responsible for the receptor compatibility of polyvalent coliphage CSP1

Polyvalent bacteriophages show the feature of infecting bacteria across multiple species or even orders. Infectivity of a polyvalent phage is variable depending on the host bacteria, which can disclose differential inhibition of bacteria by the phage. In this study, a polyvalent phage CSP1 infecting both Cronobacter sakazakii ATCC 29544 and Escherichia coli MG1655 was isolated. CSP1 showed higher growth inhibition and adsorption rate in E. coli compared to C. sakazakii, and identification of host receptors revealed that CSP1 uses E. coli LamB (LamBE) as a receptor but that CSP1 requires both C. sakazakii LamB (LamBC) and lipopolysaccharide (LPS) core for C. sakazakii infection. The substitution of LamBC with LamBE in C. sakazakii enhanced CSP1 susceptibility and made C. sakazakii LPS core no more essential for CSP1 infection. Comparative analysis of LamBC and LamBE disclosed that the extra proline at amino acid residue 284 in LamBC made a structural distinction by forming a longer loop and that the deletion of 284P in LamBC aligns its structure and makes LamBC function like LamBE, enhancing CSP1 adsorption and growth inhibition of C. sakazakii. These results suggest that 284P of LamBC plays a critical role in determining the CSP1-host bacteria interaction. These findings could provide insight into the elucidation of molecular determinants in the interaction between polyvalent phages and host bacteria and help us to understand the phage infectivity for efficient phage application.

IMPORTANCE

Polyvalent phages have the advantage of a broader host range, overcoming the limitation of the narrow host range of phages. However, the limited molecular biological understanding on the host bacteria-polyvalent phage interaction hinders its effective application. Here, we revealed that the ability of the polyvalent phage CSP1 to infect Cronobacter sakazakii ATCC 29544 is disturbed by a single proline residue in the LamB protein and that lipopolysaccharide is used as an auxiliary receptor for CSP1 to support the adsorption and the subsequent infection of C. sakazakii. These results can contribute to a better understanding of the interaction between polyvalent phages and host bacteria for efficient phage application.

Understanding the Specific Implications of Amino Acids in the Antibody Development

As the demand for immunotherapy to treat and manage cancers, infectious diseases and other disorders grows, a comprehensive understanding of amino acids and their intricate role in antibody engineering has become a prime requirement. Naturally produced antibodies may not have the most suitable amino acids at the complementarity determining regions (CDR) and framework regions, for therapeutic purposes. Therefore, to enhance the binding affinity and therapeutic properties of an antibody, the specific impact of certain amino acids on the antibody's architecture must be thoroughly studied. In antibody engineering, it is crucial to identify the key amino acid residues that significantly contribute to improving antibody properties. Therapeutic antibodies with higher binding affinity and improved functionality can be achieved through modifications or substitutions with highly suitable amino acid residues. Here, we have indicated the frequency of amino acids and their association with the binding free energy in CDRs. The review also analyzes the experimental outcome of two studies that reveal the frequency of amino acids in CDRs and provides their significant correlation between the outcomes. Additionally, it discusses the various bond interactions within the antibody structure and antigen binding. A detailed understanding of these amino acid properties should assist in the analysis of antibody sequences and structures needed for designing and enhancing the overall performance of therapeutic antibodies.

Prediction of polyspecificity from antibody sequence data by machine learning

Antibodies are generated with great diversity in nature resulting in a set of molecules, each optimized to bind a specific target. Taking advantage of their diversity and specificity, antibodies make up for a large part of recently developed biologic drugs. For therapeutic use antibodies need to fulfill several criteria to be safe and efficient. Polyspecific antibodies can bind structurally unrelated molecules in addition to their main target, which can lead to side effects and decreased efficacy in a therapeutic setting, for example via reduction of effective drug levels. Therefore, we created a neural-network-based model to predict polyspecificity of antibodies using the heavy chain variable region sequence as input. We devised a strategy for enriching antibodies from an immunization campaign either for antigen-specific or polyspecific binding properties, followed by generation of a large sequencing data set for training and cross-validation of the model. We identified important physico-chemical features influencing polyspecificity by investigating the behaviour of this model. This work is a machine-learning-based approach to polyspecificity prediction and, besides increasing our understanding of polyspecificity, it might contribute to therapeutic antibody development.

A review on the effect of prolyl isomerization on immune response aberration and hypersensitivity reactions: A unifying hypothesis

Little is known about the causes and mechanisms of ectopic immune responses, including different types of hypersensitivity, superantigens, and cytokine storms. Two of the most questionable phenomena observed in immunology are why the intensity and extent of immune responses to different antigens are different, and why some self-antigens are attacked as foreign. The secondary structure of the peptides involved in the immune system, such as the epitope-paratope interfaces plays a pivotal role in the resulting immune responses. Prolyl cis/trans isomerization plays a fundamental role in the form of the secondary structure and the folding of proteins. This review covers some of the emerging evidence indicating the impact of prolyl isomerization on protein conformation, aberration of immune responses, and the development of hypersensitivity reactions.

Combination of Biodata Mining and Computational Modelling in Identification and Characterization of ORF1ab Polyprotein of SARS-CoV-2 Isolated from Oronasopharynx of an Iranian Patient

Background

Coronavirus disease 2019 (COVID-19) is an emerging zoonotic viral infection, which was started in Wuhan, China, in December 2019 and transmitted to other countries worldwide as a pandemic outbreak. Iran is one of the top ranked countries in the tables of COVID-19-infected and -mortality cases that make the Iranian patients as the potential targets for diversity of studies including epidemiology, biomedical, biodata, and viral proteins computational modelling studies.

Results

In this study, we applied bioinformatic biodata mining methods to detect CDS and protein sequences of ORF1ab polyprotein of SARS-CoV-2 isolated from oronasopharynx of an Iranian patient. Then through the computational modelling and antigenicity prediction approaches, the identified polyprotein sequence was analyzed. The results revealed that the identified ORF1ab polyprotein belongs to a part of nonstructural protein 1 (nsp1) with the high antigenicity residues in a glycine-proline or hydrophobic amino acid rich domain.

Conclusions

The results revealed that nsp1 as a virulence factor and crucial agent in spreading of the COVID-19 among the society can be a potential target for the future epidemiology, drug, and vaccine studies.

Diagnostic Profiling of the Human Public IgM Repertoire With Scalable Mimotope Libraries

Specific antibody reactivities are routinely used as biomarkers, but the antibody repertoire reactivity (igome) profiles are still neglected. Here, we propose rationally designed peptide arrays as efficient probes for these system level biomarkers. Most IgM antibodies are characterized by few somatic mutations, polyspecificity, and physiological autoreactivity with housekeeping function. Previously, probing this repertoire with a set of immunodominant self-proteins provided a coarse analysis of the respective repertoire profiles. In contrast, here, we describe the generation of a peptide mimotope library that reflects the common IgM repertoire of 10,000 healthy donors. In addition, an appropriately sized subset of this quasi-complete mimotope library was further designed as a potential diagnostic tool. A 7-mer random peptide phage display library was panned on pooled human IgM. Next-generation sequencing of the selected phage yielded 224,087 sequences, which clustered in 790 sequence clusters. A set of 594 mimotopes, representative of the most significant sequence clusters, was shown to probe symmetrically the space of IgM reactivities in patients' sera. This set of mimotopes can be easily scaled including a greater proportion of the mimotope library. The trade-off between the array size and the resolution can be explored while preserving the symmetric sampling of the mimotope sequence and reactivity spaces. BLAST search of the non-redundant protein database with the mimotopes sequences yielded significantly more immunoglobulin J region hits than random peptides, indicating a considerable idiotypic connectivity of the targeted igome. The proof of principle predictors for random diagnoses was represented by profiles of mimotopes. The number of potential reactivity profiles that can be extracted from this library is estimated at more than 10⁷⁰. Thus, a quasi-complete IgM mimotope library and a scalable representative subset thereof are found to address very efficiently the dynamic diversity of the human public IgM repertoire, providing informationally dense and structurally interpretable IgM reactivity profiles.

Natural antibodies and their relationship with total immunoglobulins and acquired antibody response in goat kid (Capra hircus, L. 1758) serum

Natural antibodies (NAb) are antibodies that can bind to a particular antigen without any apparent antigenic stimulation. In this paper, a careful analysis has been carried out on NAb levels in goat kid serum; possible correlations with the total immunoglobulin (tot-Ig) levels and specific antibody (SpAb) response were considered. Twenty randomly chosen kids were submitted to a first blood sampling (day 0). After 60 and 100 days, new blood samplings were carried out in the same animals. On day 0, after blood collection, all animals were immunized with a commercial vaccine; the immunization was repeated 30 days apart. Some exogenous antigens were tested to verify their immunoreactivity to NAb. Among them, the synthetic hapten 2,4,6-trinitrophenyl (TNP) conjugated with bovine serum albumin, resulted as the antigen with the higher immunoreactivity to NAb. Tot-Ig levels increased over time (p < 0.001). On the contrary, NAb levels, both IgG- and IgM-isotypes, significantly decreased during the experimental period (p < 0.001 and <0.05, respectively). Linear regression analyses showed a high correlation between IgM-NAb and tot-IgM levels (p < 0.001) at all the evaluated sampling times. However, a significant correlation between IgG-NAb and IgM-NAb was found only at the 1^st (p < 0.01) and at the 2^nd sampling (p < 0.05). No significant correlations were found between SpAb response and the other assessed humoral immune parameters. The obtained results are discussed in the light of the possible use of NAb assessment for the evaluation of the immune system activity in goat.

Identification of a Novel Autoimmune Peptide Epitope of Prostein in Prostate Cancer

There is a demand for novel targets and approaches to diagnose and treat prostate cancer (PCA). In this context, serum and plasma samples from a total of 609 individuals from two independent patient cohorts were screened for IgG reactivity against a sum of 3833 human protein fragments. Starting from planar protein arrays with 3786 protein fragments to screen 80 patients with and without PCA diagnosis, 161 fragments (4%) were chosen for further analysis based on their reactivity profiles. Adding 71 antigens from literature, the selection of antigens was corroborated for their reactivity in a set of 550 samples using suspension bead arrays. The antigens prostein (SLC45A3), TATA-box binding protein (TBP), and insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) showed higher reactivity in PCA patients with late disease compared with early disease. Because of its prostate tissue specificity, we focused on prostein and continued with mapping epitopes of the 66-mer protein fragment using patient samples. Using bead-based assays and 15-mer peptides, a minimal peptide epitope was identified and refined by alanine scanning to the KPxAPFP. Further sequence alignment of this motif revealed homology to transmembrane protein 79 (TMEM79) and TGF-beta-induced factor 2 (TGIF2), thus providing a reasoning for cross-reactivity found in females. A comprehensive workflow to discover and validate IgG reactivity against prostein and homologous targets in human serum and plasma was applied. This study provides useful information when searching for novel biomarkers or drug targets that are guided by the reactivity of the immune system against autoantigens.

Evaluation of the effects of dexamethasone-induced stress on levels of natural antibodies in immunized laying hens

Natural antibodies (NAb) are an important humoral component of innate immunity, playing a pivotal role as first line of defence against pathogens even without prior antigen-specific activation or antigen-driven selection. The levels of NAb in plasma of young laying hens were explored in more detail and identified 2,4,6-trinitrophenyl bovine serum albumin (TNP-BSA), as the non-self antigen showing the highest levels of IgΥ- and IgM-NAb. Subsequently, the relation between specific antibody (SpAb) levels and NAb levels, and the effect of dexamethasone (DEX)-induced stress on the acquired Ab response and on NAb levels were examined. According to obtained results, the affinity of NAb and SpAb, measured using the thiocyanate elution method, resulted higher in SpAb than in NAb. After stress induction, IgM-NAb and SpAb levels showed a transient decrease, whereas the levels of IgΥ-NAb were not changed. Moreover, statistical analysis showed positive correlations between IgΥ- and IgM-NAb levels and between IgM-NAb and SpAb levels that are lost as stress has been induced, whereas no correlation was observed between IgΥ-NAb and SpAb levels, neither before nor after the DEX-administration. This indicates that IgM-NAb assessment could be a valid tool to estimate the potential of the acquired Ab response and that the dexamethasone-induced stress condition causes depression of IgM-NAb levels and the acquired Ab response, but it has no evaluable effects on IgΥ-NAb levels.

Protective activity of the CnaBE3 domain conserved among Staphylococcus aureus Sdr proteins

Staphylococcus aureus is an opportunistic pathogen, commensal of the human skin and nares, but also responsible for invasive nosocomial as well as community acquired infections. Staphylococcus aureus adheres to the host tissues by means of surface adhesins, such as SdrC, SdrD, and SdrE proteins. The Sdr family of proteins together with a functional A domain, contain respectively two, three or five repeated sequences called B motifs which comprise the CnaB domains. SdrD and SdrE proteins were reported to be protective in animal models against invasive diseases or lethal challenge with human clinical S. aureus isolates. In this study we identified a 126 amino acid sequence containing a CnaB domain, conserved among the three Sdr proteins. The three fragments defined here as CnaBC2, D5 and E3 domains even though belonging to phylogenetically distinct strains, displayed high sequence similarity. Based on the sequence conservation data, we selected the CnaBE3 domain for further analysis and characterization. Polyclonal antibodies raised against the recombinant CnaBE3 domain recognized SdrE, SdrC and SdrD proteins of different S. aureus lineages. Moreover, we demonstrated that the CnaBE3 domain was expressed in vivo during S. aureus infections, and that immunization of this domain alone significantly reduces the bacterial load in mice challenged with S. aureus. Furthermore, we show that the reduction of bacteria by CnaBE3 vaccination is due to functional antibodies. Finally, we demonstrated that the region of the SdrE protein containing the CnaBE3 domain was resistant to trypsin digestion, a characteristic often associated with the presence of an isopeptide bond.

The immune effects of multiple antigen peptides containing the mimic epitopes of the adhesion protein of Mycoplasma genitalium

The purpose of this study was to investigate the humoral and cellular immune responses stimulated by multiple antigen peptides (MAPs) containing the mimic epitopes of Mycoplasma genitalium adhesion protein (MgPa). Three MAPs containing the mimic epitopes of MgPa were synthesized on a branched polylysine matrix. After purification and characterization, these MAPs were used to immunize BALB/c mice. The immunoglobulin G (IgG) antibody and the subtype of IgG antibody in the serum of the immunized mice were detected by indirect ELISA (enzyme-linked immunosorbent assay). The proliferation of the spleen lymphocyte was detected using the MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl tetrazolium bromide) assay. The gamma interferon (IFN-γ) and interleukin-4 (IL-4) levels in the cultured supernatant of spleen lymphocytes were measured by ELISA. The 3 different MAPs were prepared with high purity. Levels of IgG, IgG1, and IgG2a antibodies were elevated in the mice serum immunized by all 3 MAPs. The major antibody isotype was IgG2a. Importantly, mice immunized with a mixture of the 3 MAPs produced significantly more antibodies than those immunized with a single MAP (p < 0.05). Moreover, these MAPs could stimulate the proliferation of spleen lymphocytes of immunized mice and induce the production of IFN-γ and IL-4. The IFN-γ and IL-4 levels stimulated by the mixed MAPs were significantly higher than those stimulated by a single MAP (p < 0.01). The 3 different MAPs could induce strong cellular and humoral immune responses. The immunoreactivity of the mixed MAPs was stronger than that of the single MAP.

Plasmodium riboprotein PfP0 induces a deviant humoral immune response in Balb/c mice

Passive immunization with antibodies to recombinant Plasmodium falciparum P0 riboprotein (rPfP0, 61–316 amino acids) provides protection against malaria. Carboxy-terminal 16 amino acids of the protein (PfP0C0) are conserved and show 69% identity to human and mouse P0. Antibodies to this domain are found in 10–15% of systemic lupus erythematosus patients. We probed the nature of humoral response to PfP0C0 by repeatedly immunizing mice with rPfP0. We failed to raise stable anti-PfP0C0 hybridomas from any of the 21 mice. The average serum anti-PfP0C0 titer remained low (5.1 ± 1.3 × 10⁴). Pathological changes were observed in the mice after seven boosts. Adsorption with dinitrophenyl hapten revealed that the anti-PfP0C0 response was largely polyreactive. This polyreactivity was distributed across all isotypes. Similar polyreactive responses to PfP0 and PfP0C0 were observed in sera from malaria patients. Our data suggests that PfP0 induces a deviant humoral response, and this may contribute to immune evasion mechanisms of the parasite.

Applying bioinformatics for antibody epitope prediction using affinity-selected mimotopes - relevance for vaccine design

To properly characterize protective polyclonal antibody responses, it is necessary to examine epitope specificity. Most antibody epitopes are conformational in nature and, thus, cannot be identified using synthetic linear peptides. Cyclic peptides can function as mimetics of conformational epitopes (termed mimotopes), thereby providing targets, which can be selected by immunoaffinity purification. However, the management of large collections of random cyclic peptides is cumbersome. Filamentous bacteriophage provides a useful scaffold for the expression of random peptides (termed phage display) facilitating both the production and manipulation of complex peptide libraries. Immunoaffinity selection of phage displaying random cyclic peptides is an effective strategy for isolating mimotopes with specificity for a given antiserum. Further epitope prediction based on mimotope sequence is not trivial since mimotopes generally display only small homologies with the target protein. Large numbers of unique mimotopes are required to provide sufficient sequence coverage to elucidate the target epitope. We have developed a method based on pattern recognition theory to deal with the complexity of large collections of conformational mimotopes. The analysis consists of two phases: 1) The learning phase where a large collection of epitope-specific mimotopes is analyzed to identify epitope specific “signs” and 2) The identification phase where immunoaffinity-selected mimotopes are interrogated for the presence of the epitope specific “signs” and assigned to specific epitopes. We are currently using computational methods to define epitope “signs” without the need for prior knowledge of specific mimotopes. This technology provides an important tool for characterizing the breadth of antibody specificities within polyclonal antisera.

Studies of the anti-platelet factor 4/heparin immune response: adapting the enzyme-linked immunosorbent spot assay for detection of memory B cells against complex antigens

BACKGROUND

The anti-platelet factor 4 (PF4)/heparin immune response, which underlies heparin-induced thrombocytopenia (HIT), has several atypical features: relatively rapid onset even without previous heparin exposure, lack of immune anamnesis, and transience of antibody production.

STUDY DESIGN AND METHODS

We modified the enzyme-linked immunosorbent spot (ELISPOT) assay to investigate for PF4/heparin-specific memory B cells in cardiac surgery patients, in whom the high anti-PF4/heparin immunization rate made a prospective study feasible. The PF4-containing antigen complexes were attached to microtiter plates via a spacer, rather than using nitrocellulose, and the final reaction enzyme substrate was added in melted agarose which, after rapid hardening, localized color development of enzyme-tagged anti-immunoglobulin G (IgG) probes to single PF4/heparin-specific B cells. This modified ELISPOT assay was applied to 58 consecutive patients (testing blood from preoperative baseline and Postoperative Days 6 and 10), in which we compared detectability of PF4/heparin-specific B cells to tetanus toxin-specific B cells (comparator group with presumed vaccination).

RESULTS

No patient had detectable PF4/heparin-specific memory B cells at baseline. In 2 of 30 patients (6.7%) who formed anti-PF4/heparin IgG, PF4/heparin-specific memory B cells (three to four spots/well) were detected by Postoperative Day 10, whereas tetanus toxin-specific memory B cells were found in 12 of 24 (50.0%) patients tested (3-25 spots/well; p < 0.001).

CONCLUSIONS

HIT lacks a strong memory B-cell response, perhaps explaining transience and lack of anamnesis of the anti-PF4/heparin immune response. The technical modifications we describe for the ELISPOT assay, which permit detection of B-cell reactions to complex antigens, could be useful for studying other immunohematologic disorders, for example, drug-dependent thrombocytopenia and acquired hemophilia.

Deciphering epitope specificities within polyserum using affinity selection of random peptides and a novel algorithm based on pattern recognition theory

While numerous strategies have been developed to map epitope specificities for monoclonal antibodies, few have been designed for elucidating epitope specificity within complex polysera. We have developed a novel algorithm based on pattern recognition theory that can be used to characterize the breadth of epitope specificities within a polyserum based on affinity selection of random peptides. To attribute these random peptides to a specific epitope, the sequences of the affinity-selected peptides were matched against a database of random peptides selected using well-described monoclonal antibodies. To test this novel algorithm, we employed polyserum from patients infected with West Nile virus and isolated 109 unique sequences which were recognized selectively by serum from West Nile virus-infected patients but not uninfected patients. Through application of our algorithm, it was possible to match 20% of the polyserum-selected peptides to the database of peptides isolated by affinity selection using monoclonal antibodies against the virus envelope protein. Statistical analysis demonstrated that the peptides selected with the polyserum could not be attributed to the peptide database by chance. This novel algorithm provides the basis for further development of methods to characterize the breadth of epitope recognition within a complex pool of antibodies.

Lupus-like autoantibody development in rabbits and mice after immunization with EBNA-1 fragments

Epstein-Barr virus has been implicated in the etiology of systemic lupus erythematosus (SLE) through serologic and immunologic studies. A potential mechanism for this influence is through molecular mimicry. The EBV nuclear antigen EBNA-1 contains a region, PPPGRRP, with considerable homology to the initial sequence targeted by antibodies in Sm B' autoimmunity, PPPGMRPP. This study examined whether immunization of rabbits and mice with peptides containing the PPPGRRP sequence from EBNA-1 constructed on a poly-lysine backbone was able to drive the development of autoantibodies against the Smith antigen (Sm) and the related antigenic complex, the U1 nuclear ribonucleoproteins (nRNPs). PPPGRRP immunization, and immunization with an EBNA-1 fragment containing PPPGRRP, led to autoantibodies in both rabbits and mice at high frequency (83% of rabbits and 43% of mice). Five out of six immunized rabbits developed either leucopenia or lymphopenia or both. The fine specificity of antibody binding against the lupus-associated autoantigens Sm B', nRNP A, and nRNP C after immunization with the EBNA-1-derived peptides was very similar to the early antibody binding patterns against these proteins in human SLE. This similarity, as well as the prevalence of autoimmunity after immunization with these peptides, identifies PPPGRRP as a strong candidate for molecular mimicry in SLE etiology.

The innate immune response of finfish--a review of current knowledge

The decline in the fisheries of traditional marine species has been an incentive for the diversification of today's aquaculture sector into the intensive rearing of many finfish species. The increasing interest in commercial farming of different finfish species is expected to result in similar environmental and husbandry-related problems as have been experienced in the development of the salmonid farming industry. An understanding of the biology of the fish species being cultured, in particular the immune response is important for improved husbandry and health management of the species. The innate immune system of fish has generated increasing interest in recent years and is now thought to be of key importance in primary defence and in driving adaptive immunity. This review focuses on key components (cellular and humoral) of the innate immune responses of different fish species of commercial importance.

One day is enough: rapid and specific host-parasite interactions in a stickleback-trematode system

Red Queen models of host-parasite coevolution are based on genotype by genotype host-parasite interactions. Such interactions require a genotype specific host defence and, simultaneously, a genotype specific parasite infectivity. Specificity is defined here as defence or infection ability successful against only a subset of genotypes of the same species. A specific defence depends on detectable genotypic variation on the parasite side and on a host defence mechanism that differentiates between parasite genotypes. In vertebrates, the MHC-based adaptive immune system can provide such a defence mechanism, but it needs at least several days to get fully mounted. In contrast, the innate immune system is immediately ready. The trematode parasite species used here reaches the immunologically protected eye lens of its three-spined stickleback (Gasterosteus aculeatus) host within 24 h. Thus, it disappears too fast for the fully mounted MHC-based adaptive immune system. In a complete cross-infection experiment using five fish-families and five parasite-clones, we found for the first time fish-family by parasite-clone interactions in vertebrates, although the parasite was only exposed to the immune system for maximally one day. Such interactions require a fast genotype specific defence, suggesting the importance of other defence mechanisms than the too slow, fully mounted adaptive immune system in vertebrates.

Characterization of proline-serine-rich carboxyl terminus in human sulfotransferase 2B1b: immunogenicity, subcellular localization, kinetic properties, and phosphorylation

The human sulfotransferase (SULT) 2B1 gene is a member of the SULT2 gene family and encodes two isoforms, SULT2B1a and SULT2B1b. Although messages for both SULT2B1a and SULT2B1b are detectable in human tissues, only SULT2B1b has been identified immunologically. Compared with other human SULTs, SULT2B1b has an extension at the proline- and serine-rich carboxyl (PSC) end of about 53 amino acids. The structure and function of this unique PSC extension were investigated. Constructs of full-length SULT2B1b as well as truncated SULT2B1b without the PSC extension were expressed in Escherichia coli. Removal of the PSC extension significantly decreased the thermostability of the expressed enzyme as well as decreasing the rate of dehydroepiandrosterone sulfation. Rabbit polyclonal antibodies were raised against both the full-length and truncated SULT2B1b proteins. Immunoblot analysis showed that antibodies raised to full-length SULT2B1b immunoreact only with full-length SULT2B1b, whereas antibodies raised to truncated SULT2B1b react with both full-length and truncated SULT2B1b. Unlike full-length SULT2B1b, truncated SULT2B1b was incapable of translocation to nuclei in transfected human BeWo choriocarcinoma cells. Phosphorylated serines were detected in the PSC extension of full-length SULT2B1b expressed in BeWo cells but not in truncated SULT2B1b. At least one phosphorylated serine was detected in expressed SULT2B1b via two-dimensional gel electrophoresis, immunoblot analysis, and mass spectroscopic analysis. Bacterially expressed full-length SULT2B1b but not truncated SULT2B1b was phosphorylated by casein kinase or Cdc2 protein kinase in vitro. This study suggests that the PSC extension of SULT2B1b is an important site in the immunogenicity, nuclear translocation, kinetic activity, and thermostability of this SULT isoform.

Innate immunity of fish (overview)

The innate immune system is the only defence weapon of invertebrates and a fundamental defence mechanism of fish. The innate system also plays an instructive role in the acquired immune response and homeostasis and is therefore equally important in higher vertebrates. The innate system's recognition of non-self and danger signals is served by a limited number of germ-line encoded pattern recognition receptors/proteins, which recognise pathogen associated molecular patterns like bacterial and fungal glycoproteins and lipopolysaccharides and intracellular components released through injury or infection. The innate immune system is divided into physical barriers, cellular and humoral components. Humoral parameters include growth inhibitors, various lytic enzymes and components of the complement pathways, agglutinins and precipitins (opsonins, primarily lectins), natural antibodies, cytokines, chemokines and antibacterial peptides. Several external and internal factors can influence the activity of innate immune parameters. Temperature changes, handling and crowding stress can have suppressive effects on innate parameters, whereas several food additives and immunostimulants can enhance different innate factors. There is limited data available about the ontogenic development of the innate immunological system in fish. Active phagocytes, complement components and enzyme activity, like lysozyme and cathepsins, are present early in the development, before or soon after hatching.

Characterization of BoHV-1 gE envelope glycoprotein mimotopes obtained by phage display

A phage-displayed peptide library was screened using four mAbs directed against bovine herpesvirus 1 (BoHV-1) gE glycoprotein to identify peptides mimicking this glycoprotein. The selected mimotopes allowed us to characterize the epitopes corresponding to the mAbs as continuous and proteinic and to consider using these peptides in further studies. One epitope has been clearly located at the C-terminus of the protein (amino-acids 561-569). The three other mAbs enabled us to stress the immunogenic relevance of the proline-rich motifs of gE. Selected peptides showed no clear sequence identity with gE, but there is a clear link between gE proline-rich regions and the amino-acid composition of the mimotopes. The proline-rich motifs of gE are potentially located in flanking regions involved in the gE/gl glycoprotein complex formation. N-terminal fusion to pill or pVIII filamentous phage protein, C-terminal fusion to the T7 phage capsid protein, biotinylated synthetic peptides and insertion between the non-cleaved CX leader sequence and the C-terminal part of Caulobacter crescentus RsaA protein have been tested in order to increase the valency of a model peptide. We have diverted the C. crescentus expression system and proven its usefulness using the RsaA protein as a scaffold displaying the peptides of interest. Comparison between these different display systems in an indirect ELISA, indicates that the C. crescentus expression and the T7 phage display systems have some major advantages.

Epitope mapping of a protective monoclonal antibody against Pneumocystis carinii with shared reactivity to Streptococcus pneumoniae surface antigen PspA

Pneumocystis carinii is an opportunistic fungal pathogen that causes pneumonia in the immunocompromised host. A protective monoclonal antibody (MAb) termed 4F11 generated against mouse-derived P. carinii was shown by indirect immunofluorescence assay (IFA) to bind surface antigens of P. carinii derived from multiple host species, including humans. We have identified multiple epitopes recognized by MAb 4F11 in two recombinant mouse P. carinii antigens. The epitopes mapped have similar proline content and positive charge distribution. The consensus 8-mer epitope recognized by MAb 4F11 is K/RPA/RPK/QPA/TP. Immune sera raised against intact mouse P. carinii recognized native antigens affinity purified with MAb 4F11 and a recombinant antigen reactive with MAb 4F11. Database searches for short, nearly exact matches to the mapped MAb 4F11 epitopes identified a bacterial surface antigen, Streptococcus pneumoniae PspA, with a similar proline-rich region. In an IFA, MAb 4F11 detected antigens on the S. pneumoniae surface, and Western blotting identified a protein in S. pneumoniae lysates consistent with the M(r) of PspA. A fragment of the S. pneumoniae PspA gene was cloned and sequenced, and the deduced amino acid sequence contained a region with strong similarity to the MAb 4F11 epitopes identified in P. carinii. The PspA recombinant polypeptide was recognized by MAb 4F11 in a Western blot. The ability of MAb 4F11 to recognize similar proline-rich epitopes may explain its ability to recognize P. carinii derived from multiple hosts and will permit testing of the epitopes recognized by this antibody in immunization against P. carinii.

A proline-rich region with a highly periodic sequence in Streptococcal beta protein adopts the polyproline II structure and is exposed on the bacterial surface

Proline-rich regions have been identified in many surface proteins of pathogenic streptococci and staphylococci. These regions have been suggested to be located in cell wall-spanning domains and/or to be required for surface expression of the protein. Because little is known about these regions, which are found in extensively studied and biologically important surface proteins, we characterized the proline-rich region in one such protein, the beta protein of group B streptococci. The proline-rich region in beta, designated the XPZ region, has a proline at every third position, and the sequence is highly periodic in other respects. Immunochemical analysis showed that the XPZ region was not associated with the cell wall but was exposed on the bacterial surface. Moreover, characterization of a beta mutant lacking the XPZ region demonstrated that this region was not required for surface expression of the beta protein. Comparison of the XPZ region in different beta proteins showed that it varied in size but always retained the typical sequence periodicity. Circular dichroism spectroscopy indicated that the XPZ region had the structure of a polyproline II helix, an extended and solvent-exposed structure with exactly three residues per turn. Because of the three-residue sequence periodicity in the XPZ region, it is expected to be amphipathic and to have distinct nonpolar and polar surfaces. This study identified a proline-rich structure with unique properties that is exposed on the surface of an important human pathogen.

Autoantibodies to heat shock protein 90 in the human natural antibody repertoire

The present study demonstrates the presence of natural autoantibodies of the IgG isotype directed against heat shock protein 90 (HSP90). The binding properties of affinity-purified anti-HSP antibodies were compared with those of natural antibodies specific for other self antigens, including anti-thyroglobulin and anti-myoglobin autoantibodies, by using semiquantitative immunoblotting, with solubilized proteins from normal liver tissue as antigens, and cross-blot analysis using purified self proteins. Affinity-purified anti-HSP90 antibodies were polyreactive and the non-HSP90-specific fraction of normal IgG was depleted in its natural autoantibody content. We further observed that self antigens including HSP, myosin, tubulin and aldolase with highly conserved structures show similar patterns of binding with natural antibodies, and form a well-defined cluster as demonstrated by cluster analysis of immunoreactivity data, whereas the less-conserved self and non-self antigens remained unclustered. The results favor the hypothesis that HSP90 belongs to a subset of highly conserved and immunodominant self antigens that are the primary target for natural autoantibodies in normal human IgG.

DiSSiMiL: Diverse Small Size Mini-Libraries applied to simple and rapid epitope mapping of a monoclonal antibody

Methods for screening protein-protein interactions are useful in protein science and for the generation of drug leads. We set out to develop a simplified assay to rapidly test protein-protein interactions, with a library of 400 pentapeptides comprising the 20 natural amino acids at two variable positions followed by three glycines (NH2-X1X2GGG). The library was used to identify the epitope of monoclonal antibody (mAb) 10D11 directed against the HOXD4 protein. Three pentapeptide 'hits' were selected (VYGGG, PWGGG and WKGGG) from direct binding assays screening for pentapeptide-mAb interactions; and from assays using pentapeptides in solution to competitively block HOXD4-mAb interactions. Alignment of the three 'hit' pentapeptides to the HOXD4 sequence predicts the mAb 10D11 epitope as NH2-VYPWMK. Synthesis of NH2-VYPWMK hexapeptide confirmed this prediction; and an alanine scan of HOXD4 ablated binding by mAb 10D11 when amino acids in the putative epitope were mutated. We propose that these simplified but diverse libraries can be used for rapid epitope mapping of some mAbs, and for generating lead small peptide analogs that interfere with receptor-ligand or other protein-protein interactions, or with enzymatic activity.

Molecular analysis of cross-reactive anti-myosin/anti-streptococcal mouse monoclonal antibodies

Nucleotide sequences of VH- and VL-genes of anti-myosin/anti-streptococcal monoclonal antibodies (mAbs) were analyzed and compared with their highly detailed antigen binding reactivities. Antigen-specificities of the cross-reactive mAbs included myosin, streptococcal M-protein, actin, keratin, N-acetyl-beta-D-glucosamine, vimentin, DNA, tropomyosin, troponin, and laminin as previously described. After nucleotide sequence analysis, homology indicated that some of the V gene sequences aligned with antibodies recognizing gangliosides and blood group antigens glycophorin M and N. Therefore, mAb reactivity with gangliosides and glycophorin M and N was identified. The cross-reactive mAbs utilized a heterogeneous group of germline V-heavy genes comprised of nine J558-, four 7183- and two Q52-family VH-genes. Germline V-light genes utilized by the mAbs included six Vkappa4/5-, three Vkappa8-, two Vkappa10-, three Vkappa19- and one Vkappa23-family VL-genes. No preferential VH/VL-chains correlated with any of the 12 different antigen reactivities, even for mAbs with nearly identical cross-reactivities. However, we did find that the cross-reactive mAb germline genes within a V gene family shared more homology among themselves than with other germline genes within their V gene families, suggesting convergent mutation. Cross-reactive mAbs with the highest relative avidity for myosin were found in the VH7183 family which contained two cytotoxic mAbs. Antibodies with V gene sequences most homologous to those of our cross-reactive anti-myosin/anti-streptococcal mAbs had specificities for laminin, DNA, carbohydrates, or blood group antigens and were reported to cause autoimmune disease in mice.

Polyreactivity of disease-associated anti-RBC IgG autoantibodies of patients with warm autoimmune haemolytic anaemia and natural anti-RBC IgG autoantibodies of healthy individuals

Anti-red blood cell (RBC) immunoglobulin G (IgG) autoantibodies are present in patients with warm autoimmune haemolytic anaemia (WAIHA), and, as natural autoantibodies, in healthy individuals. This study investigated whether the feature of polyreactivity discriminates disease-associated from natural anti-RBC IgG autoantibodies. The patterns of reactivity of purified anti-RBC IgG eluted from the RBC of WAIHA patients and from the RBC of healthy individuals were analysed using quantitative immunoblotting on a panel of whole human tissue or bacterial cell extracts as antigen sources. In parallel, the reactivity patterns of IgG purified from plasma were analysed. Anti-RBC IgG of WAIHA patients and of healthy individuals recognized a wide range of self- and nonself-antigens. The reactivity patterns of anti-RBC IgG were homogeneous among patients and controls, did not differ between patients and controls, and were similar to those of IgG purified from plasma in the case of both patients and healthy individuals. The data demonstrate that the anti-RBC IgG autoantibodies of WAIHA patients share extensive similarity with those of healthy individuals. Polyreactivity is a common feature of both disease-associated and natural anti-RBC IgG autoantibodies.

Sequential determination of ligands binding to discrete components in heterogeneous mixtures by iterative panning and blocking (IPAB)

Biopanning has been used extensively in conjunction with purified components, but there are also examples in which mixtures of targets have been investigated. This study introduces a methodological innovation, termed iterative panning and blocking (IPAB), to extend the range of specific interactions that can be probed in mixtures. Here this procedure is used to probe a mixture of high molecular mass components of human cord blood with phage-peptide display libraries. The initial panning recovered phage that bore the consensus motif Gly-Pro-Arg-Pro, a known fibrinogen-binding motif. These phage bound specifically to purified fibrinogen. A series of peptides containing the Gly-Pro-Arg-Pro motif efficiently blocked the binding of phage having the same motif, presumably by binding to their common target. A second round of panning was performed against the same target mixture in the presence of this blocking peptide. Phage recovered from this second panning exhibited a motif (Ser-His-Tyr) that was subsequently shown to bind specifically to complement component C1q. A second peptide containing this motif specifically blocked the interaction of the phage with C1q. A third round of panning performed in the presence of both the fibrinogen- and the C1q- blocking peptides yielded phage with a new peptide motif (Asn-Pro-Phe) that also bound specifically to C1q, apparently at a new site. The three motifs isolated through this iterative process were distinct in that each was blocked only by its corresponding peptide. This IPAB strategy can be applied to many high diversity selection procedures that target complex mixtures.

Natural antibodies against alliinase in human serum and polyclonal antibodies elicited in rabbit share the same immunogenic determinants

Human serum contains natural antibodies against alliinase, a protein abundantly found in garlic (Allium sativum) cloves. In order to study the epitope(s) of this protein recognized by anti-alliinase antibodies, we used a random hexapeptide library displayed on filamentous M13 phage. Analysis of the phagotopes selected on rabbit anti-alliinase antibodies revealed that the motif-GKXVXX- was common for all peptides. The most frequent phage displaying -GKHVAV- sequence has a 50% identity with the original alliinase sequence (amino acid residues 156-161). The position of this epitope is only nine amino acids apart from the oligosaccharide chain attached to the N146. The rabbit anti-alliinase immunoglobulin G (IgG), which bound the phages displaying this phagotope, also bound the corresponding peptide derived from the alliinase sequence. Affinity-purified natural antibodies against alliinase, present in normal human serum (which can specifically recognize the native and denaturated protein) also bound the selected phagotope. Thus, our results indicate that specific natural anti-dietary protein antibodies presented in human serum can have the same. or overlapping. epitopes with the IgG evoked during the active (experimental) immunization in animals.

Phosphorylation of Bcl-2 and mitochondrial changes are associated with apoptosis of lymphoblastoid cells induced by normal immunoglobulin G

Normal human immunoglobulin G induces apoptosis in human lymphoblastoid cells which involves antibody-mediated Fas ligation and the activation of caspases. Here, we show that Bcl-2 is phosphorylated on serine upon treatment of CEM T cells with normal IgG and that the overexpression of Bcl-2 in stable transfectants of CEM T cells prevents IgG-induced cell death. Treatment of CEM cells with normal IgG also results in a reduction in mitochondrial transmembrane potential and in the release of cytochrome c (Cyt c) into cytosol. The findings are concordant with earlier observations that apoptosis induced by IgG is associated with the activation of caspases. Our results demonstrate that Bcl-2 controls apoptosis induced by normal IgG and support a central role for Bcl-2 and mitochondria in antibody-mediated selection of lymphocyte repertoires.

Natural human antibodies retrieved by phage display libraries from healthy donors: polyreactivity and recognition of human immunodeficiency virus type 1gp120 epitopes

We have characterized the human natural antibody repertoire that contains antibodies recognizing the human immunodeficiency virus type 1 (HIV-1) gp120. A panel of monovalent antigen-binding fragments (Fab) selected from IgM and IgG isotype libraries generated from peripheral blood mononuclear cells (PBMC) of a healthy, HIV-1 noninfected individual was analysed, reflecting that only IgM, but not IgG, Fab were able to recognize HIV-1 gp120. The IgM Fab antibodies were not restricted to any particular heavy chain variable region (VH) germ line gene. However, the recognition of gp120 is associated to polyreactive antibodies and all display low-affinity interaction. This correlates with the absence of any maturation process as somatic mutation or isotype switch as the nucleotide sequence analysis of the variable regions reveals they are expressed near to germline configuration. In addition, none of the antibodies showed any neutralizing activity on HIV-1-infected lymphocytes, reflecting that the natural anti-gp120 repertoire is not sufficient to neutralize HIV infection.

Phage-displayed T-cell epitope grafted into immunoglobulin heavy-chain complementarity-determining regions: an effective vaccine design tested in murine cysticercosis

A new type of immunogenic molecule was engineered by replacing all three complementarity-determining-region (CDR) loops of the human immunoglobulin (Ig) heavy-chain variable (V(H)) domain with the Taenia crassiceps epitope PT1 (PPPVDYLYQT) and by displaying this construct on the surfaces of M13 bacteriophage. When BALB/c mice were immunized with such phage particles (PIgphage), a strong protection against challenge infection in very susceptible female hosts was obtained. When specifically stimulated, the in vivo-primed CD4(+) and CD8(+) T cells isolated from mice immunized with PT1, both as a free peptide and as the PIgphage construct, proliferated in vitro, indicating efficient epitope presentation by both major histocompatibility complex class II and class I molecules in the specifically antigen-pulsed macrophages used as antigen-presenting cells. These data demonstrate the immunogenic potential of recombinant phage particles displaying CDR epitope-grafted Ig V(H) domains and establish an alternative approach to the design of an effective subunit vaccine for prevention of cysticercosis. The key advantage of this type of immunogen is that no adjuvant is required for its application. The proposed strategy for immunogen construction is potentially suitable for use in any host-pathogen interaction.

Selection of phage-display peptides that bind to cucumber mosaic virus coat protein

Several discrete peptides that bind specifically to the coat protein of cucumber mosaic virus (CMV) were isolated from a diverse phage library displaying random nonapeptides on the major coat protein VIII. Enrichment was shown by polyclonal phage enzyme linked immunosorbent assay (ELISA) after three rounds of selection. Sequencing of the genes encoding 10 of these peptides revealed an absence of any conserved motifs, although nine of them contained a high proportion of proline residues. Some of the selected peptides were displayed at the N-terminus of thioredoxin and expressed in the cytoplasm of Escherichia coli. Both the phage-displayed and thioredoxin-fusion versions of the peptides could detect purified CMV and CMV present in crude leaf extracts from infected plants. By dot blot analysis, a thioredoxin-peptide fusion could readily detect as little as 5 ng of CMV. The peptides did not bind to other plant viruses. These peptides have been shown to be specific and highly sensitive tools in the detection of CMV and, as well as their diagnostic potential, they could form the basis for a novel disease resistance strategy.