The impact of structural integrity and route of administration on the antibody specificity against three cow's milk allergens - a study in Brown Norway rats

Background

Characterisation of the specific antibody response, including the epitope binding pattern, is an essential task for understanding the molecular mechanisms of food allergy. Examination of antibody formation in a controlled environment requires animal models. The purpose of this study was to examine the amount and types of antibodies raised against three cow’s milk allergens; β-lactoglobulin (BLG), α-lactalbumin (ALA) and β-casein upon oral or intraperitoneal (i.p.) administration. A special focus was given to the relative amount of antibodies raised against linear versus conformational epitopes.

Methods

Specific antibodies were raised in Brown Norway (BN) rats. BN rats were dosed either (1) i.p. with the purified native cow’s milk allergens or (2) orally with skimmed milk powder (SMP) alone or together with gluten, without the use of adjuvants. The allergens were denatured by reduction and alkylation, resulting in unfolding of the primary structure and a consequential loss of conformational epitopes. The specific IgG1 and IgE responses were analysed against both the native and denatured form of the three cow’s milk allergens, thus allowing examination of the relative amount of linear versus conformational epitopes.

Results

The inherent capacity to induce specific IgG1 and IgE antibodies were rather similar upon i.p. administration for the three cow’s milk allergens, with BLG = ALA > β-casein. Larger differences were found between the allergens upon oral administration, with BLG > ALA > β-casein. Co-administration of SMP and gluten had a great impact on the specific antibody response, resulting in a significant reduced amount of antibodies. Together results indicated that most antibodies were raised against conformational epitopes irrespectively of the administration route, though the relative proportions between linear and conformational epitopes differed remarkably between the allergens.

Conclusions

This study showed that the three-dimensional (3D) structure has a significant impact on the antibodies raised for both systemic and orally administered allergens. A remarkable difference in the antibody binding patterns against linear and conformational epitope was seen between the allergens, indicating that the structural characteristics of proteins may heavily affect the induced antibody response.

Antigenic composition and immunoreactivity differences between HEV recombinant capsid proteins generated from different genotypes

Appreciable variability has been observed in hepatitis E virus (HEV) serological diagnostics. Four recombinant proteins (p166s) were generated from position 452 to 617 aa of ORF2 of different HEV genotypes and used in an indirect ELISA to detect anti-HEV IgMs and IgGs in serially diluted sera of patients infected with different HEV genotypes (genotype 1, n=15; genotype 3, n=12; genotype 4, n=17). To evaluate the differences at a conformational level, 3D-structure models of p166s were predicted, and different bioinformatics tools were used to analyze the antigenic composition. With both anti-HEV IgMs and IgGs antibodies, there was a considerable variability between the four antigens immunoreactivities. In silico results revealed the region 483-533 aa with the highest antigenic potential and contains six key aa at positions 488, 489, 512, 533, 483 and 530. This immunoreactivity variation could affect diagnosis results and seroprevalence estimations and the identification in silico of a region highly antigenic would guide the development of efficient serological assays and epitope-based vaccines.

Identification of B-cell linear epitopes in domains 1-3 of pyolysin of Trueperella pyogenes using polyclonal antibodies

Trueperella pyogenes is an important opportunistic pathogen. Pyolysin (PLO) makes important contributions to the pathogenicity of T. pyogenes. However, the structure and function of PLO has not been well documented. In the current study, epitopes in domain 1-3 of PLO have been mapped using rabbit anti-recombinant PLO (rPLO) polyclonal antibodies, and then the results were re-checked by using mouse and chicken anti-rPLO polyclonal antibodies, respectively. The results indicated that the region of aa 281-393 in PLO could not elicit antibodies against linear epitopes. A total of six B cell linear epitopes have been found in domain 1 of PLO. Two of the six epitopes (EP1 and EP2) were used to immunize mice and chicken. Chicken anti-EP1 and anti-EP2 serum and mouse anti-EP2 serum could react with rPLO and corresponding epitope polypeptide in western blot assay; however, only mouse anti-EP2 serum shows weak anti-hemolysis effect in the rPLO and sheep red blood system. Our results provide some new information to the research field of PLO structure and function.

Antibodies against linear epitopes on Goodpasture autoantigen in patients with anti-neutrophil cytoplasmic antibody-associated vasculitis

In a substantial number of patients with crescentic glomerulonephritis, both anti-glomerular basement membrane (GBM) antibodies and anti-neutrophil cytoplasmic antibodies (ANCA) are detected simultaneously. ANCA is presumed to be the initial event but the mechanism is unknown. In the present study, we investigated the antibodies against linear epitopes on Goodpasture autoantigen in sera from patients with ANCA-associated vasculitis, aiming to reveal the mechanisms of the coexistence of the two kinds of autoantibodies. Thirty-one patients with ANCA-associated vasculitis were enrolled in this study. Twenty-four overlapping linear peptides were synthesized across the whole sequence of Goodpasture autoantigen. Serum antibodies against linear peptides were detected by ELISA and their associations with clinical features were further analyzed. Twenty-five out of the thirty-one (80.6%) sera from patients with ANCA-associated vasculitis possessed antibodies against linear peptides on Goodpasture autoantigen. These antibodies could be detected in 50% of patients with normal renal function (Scr ≤ 133 μmol/L), 70% of patients with moderate renal dysfunction (133 μmol/L < Scr ≤ 600 μmol/L), and 94% of patients with renal failure (Scr > 600 μmol/L) (P = 0.032). The highest recognition frequencies were found for peptides P4 (51.6%), P14 (54.8%), and P24 (54.8%), which contained the sequences that constitute the conformational epitopes of E_A (P4) and E_B (P14) recognized by anti-GBM antibodies. The level of anti-P4 antibodies was positively correlated with the percentage of crescents in glomeruli (r = 0.764, P = 0.027). Patients with anti-P24 antibodies had a significantly higher prevalence of renal dysfunction on diagnosis (88.2 vs. 42.9%, P = 0.018). Antibodies against linear epitopes on Goodpasture autoantigen could be detected in sera of patients with ANCA-associated vasculitis, which might mediate the production of antibodies towards the conformational epitopes on Goodpasture autoantigen, namely, the anti-GBM antibodies.

Automated High-Throughput Mapping of Linear B-Cell Epitopes Using a Statistical Analysis of High-Density Peptide Microarray Data

Detailed information of antibodies' specificity is often missing or inadequate even for continuous (i.e., linear) epitopes. Recent developments in peptide microarray technology has enabled the synthesis of up to two million peptides per array thereby allowing linear peptide epitopes to be examined by a systematic amino acid substitution and positional scanning approach. This kind of analysis generates a very large body of data, which needs to be analyzed and interpreted in a robust and automated manner. Here, we describe a rational systematic approach to define linear antibody epitopes using ANOVA statistics to identify not only significant but also important residues involved in antibody recognition. This statistical approach can be used to perform a comprehensive linear epitope discovery. For polyclonal antibodies, this could be extended to entire proteins pinpointing critical residues for each epitope. We argue that the ANOVA analysis levels out issues of unknown peptide concentration/quality and unknown antibody titers leading to identification of epitopes that otherwise would be neglected if the evaluation was based merely on signal strength.

Sequence analysis of digestion-resistant peptides may be an efficient strategy for studying the linear epitopes of Jug r 1, the major walnut allergen

Jug r 1, the major allergen of walnut, triggers severe allergic reactions through epitopes. Hence, research on the efficient strategy for analyzing the linear epitopes of Jug r 1 are necessary. In this work, bioinformatics analysis was used to predict the linear epitopes of Jug r 1. Overlapping peptide synthesis was used to map linear epitopes. In vitro simulated gastrointestinal digestion and HPLC-MS/MS were used to identify digestion-resistant peptides. The results showed that six predicted linear epitopes were AA28-35, AA42-49, AA55-62, AA65-73, AA97-104, and AA109-121. AA16-30 and AA125-139 were identified by the sera of walnut allergic patients. Five digestion-resistant peptides were AA19-33, AA40-45, AA54-74, AA96-106, and AA117-137. The predicted results only included one of the linear epitopes identified by sera, while the digestion-resistant peptides covered all. Therefore, the digestion-resistant property of food allergens may be a promising direction for studying the linear epitopes of Jug r 1.

Cross-reactive immunogenicity of group A streptococcal vaccines designed using a recurrent neural network to identify conserved M protein linear epitopes

The M protein of group A streptococci (Strep A) is a major virulence determinant and protective antigen. The N-terminal sequence of the protein defines the more than 200 M types of Strep A and also contains epitopes that elicit opsonic antibodies, some of which cross-react with heterologous M types. Current efforts to develop broadly protective M protein-based vaccines are directed at identifying potential cross-protective epitopes located in the N-terminal regions of cluster-related M proteins for use as vaccine antigens. In this study, we have used a comprehensive approach using the recurrent neural network ABCpred and IEDB epitope conservancy analysis tools to predict 16 residue linear B-cell epitopes from 117 clinically relevant M types of Strep A (~88% of global Strep A infections). To examine the immunogenicity of these epitope-based vaccines, nine peptides that together shared ≥60% sequence identity with 37 heterologous M proteins were incorporated into two recombinant hybrid protein vaccines, in which the epitopes were repeated 2 or 3 times, respectively. The combined immune responses of immunized rabbits showed that the vaccines elicited significant levels of antibodies against all nine vaccine epitopes present in homologous N-terminal 1-50 amino acid synthetic M peptides, as well as cross-reactive antibodies against 16 of 37 heterologous M peptides predicted to contain similar epitopes. The epitope-specificity of the cross-reactive antibodies was confirmed by ELISA inhibition assays and functional opsonic activity was assayed in HL-60-based bactericidal assays. The results provide important information for the future design of broadly protective M protein-based Strep A vaccines.

High-resolution mapping of linear epitopes from LiNTPDase2: Advancing leishmaniasis detection using optimized protein and peptide antigens

Visceral Leishmaniasis, caused by Leishmania infantum, is a tropical neglected disease and the most dangerous form of Leishmaniasis. It occurs zoonotically, with domestic transmission posing risks to humans as dogs have high susceptibility and are natural reservoirs of the parasite. Given their epidemiological role, improvements are needed in diagnosing Canine Visceral Leishmaniasis (CVL). Thus, we mapped linear epitopes from the rLiNTPDase2 antigen through peptide microarray and identified six positive epitopes. Validation through peptide ELISA revealed three promising peptides with accuracies of 78.6%, 85.92%, and 79.59%. Their combination yielded 97.58% accuracy. Negative epitopes were also found, which interacted with CVL-negative and Chagas Disease positive samples. Their removal from the rLiNTPDase2 sequence resulted in the rNT2.neg, which obtained enhanced specificity over rLiNTPDase2. The rNT2.neg validation achieved 87.50% sensitivity, 90.55% specificity, and 93.5% accuracy within 127 CVL-positive and 96 CVL-negative samples. Therefore, three peptides and rNT2.neg show significant promise for CVL diagnosis.

Unveiling the regulatory mechanism of pulsed electric field modified instant soy milk powder: Exploring allergenicity, conformation, and epitopes

Glycinin and β-conglycinin are prominent allergens, limiting the safety of soy and soy products in a wide range of applications. The study investigated the effects of pulsed electric field (PEF) on allergenicity, conformation, and epitopes of instant soy milk powder (ISMP) and the simulated digestion products (SDP), and to preliminarily elucidate the regulatory mechanism using multispectroscopy and peptidomics. The allergenicity of SDP and ISMP treated at 20 and 30 kV/cm were reduced and conformations were altered, especially decrease or disappearance of α-helix, enhancement of random coil, and reduction of hydrogen and disulfide bonds in SDP (P < 0.05). Furthermore, their digestion-resistant linear epitopes (DRLE) were differed, such as RSQSDN, EEEEQRQQ, and SRNPIY, therein N and P might be critical amino acids affecting their allergenicity. Overall, PEF reduced the ISPM allergenicity by altering conformations, increasing sensitivities to gastrointestinal digestive enzymes, and modulating binding sites to IgE by covering or disrupting linear epitopes.

Linear and conformational determinants of visceral leishmaniasis diagnostic antigens rK28 and rK39

Background

Recombinant antigens rK39 (based on kinesin sequence) and rK28 (comprising kinesin and HASPB sequences) are a mainstay of serological diagnosis for visceral leishmaniasis (VL). However, their key epitopes and the significance of their structural conformation are not clearly defined, particularly in relation to reported cross-reactivity with sera from patients with malaria, schistosomiasis, and tuberculosis.

Methods

To assess the effect of conformation on antigenicity with Sudanese VL sera, antigens rK39 and rK28 were heat-denatured at 95 °C for 10 min and then assayed by enzyme-linked immunosorbent assay (ELISA). Amino acid sequences of rK39 and rK28 were submitted to NCBI BLASTp to assess homology with Plasmodium, Schistosoma, and Mycobacterium.

Results

Heat denaturation significantly diminished the antigenicity of rK39 compared to non-denatured antigen (P = 0.001), but not for rK28 (P = 0.275). In BLASTp searches, HASPB sequences from rK28 had similarities with sequences from Plasmodium, encompassing software-predicted B-cell epitopes.

Conclusions

The antigenicity of rK39 appears to be dependent on structural conformation, whereas that of rK28 depends on linear sequence. HASPB sequence homology with Plasmodium may be responsible for the reported cross-reactivity of rK28 with malaria sera. Further work is warranted to refine the specificity of these antigens.

Graphical Abstract

Performance of protein N linear epitopes in serodiagnosis of COVID-19 infection

Introduction

Despite the efforts to contain the spread of COVID-19, the virus remains in circulation, posing a considerable risk to populations across the globe. Hence, rapid and early detection of this infection is essential for effective disease control. The nucleocapsid (N) protein of the virus serves as a primary target for antibody response during CoV2 infections, making it a potential candidate for COVID-19 detection. This study aims to prepare and evaluate the linear epitopes of the N protein for serodiagnosis of COVID-19 infection.

Methods

The linear epitope of the N protein gene was identified using ABCpred, BCpred, and IEDB. These epitopes were subsequently amplified by RT-PCR, cloned, and expressed in soluble form in the E. coli BL21 strain. The recombinant protein was purified using the Ni-NTA column. The reactivity of purified N protein with sera from SARS-CoV-2 patients was analyzed using an ELISA assay.

Results

Sequencing analysis demonstrated the successful cloning of the linear epitopes of the N protein into the PET-28a vector, along with an n-terminal His-tag fusion. The recombinant protein was produced in E. coli BL21 and purified with a Ni-NTA column. The analysis demonstrated that the N protein linear epitopes were expressed in a soluble form and appeared as a 50 kDa band in the SDS-PAGE. Examination for the reactivity of the purified N protein with the COVID-19 patient's sera by ELISA revealed that the N protein recognizes the infection with high sensitivity and specificity.

Conclusion

The results of this study indicated that linear epitopes of the SARS-CoV-2 N protein are highly immunogenic and could be exploited for serodiagnosis of infection in patients suspected of COVID-19 infection.

A rapid approach for linear epitope vaccine profiling reveals unexpected epitope tag immunogenicity

Antibody epitope profiling is essential for assessing the robustness of vaccine-induced immune responses, particularly while in development. Despite advancements in computational tools, high throughput experimental epitope validation remains an important step. Here, we describe a readily accessible method for rapid linear epitope profiling using phage-displayed oligo pools in combination with Nanopore deep sequencing. We applied this approach to TeeVax3, a Group A Streptococcus vaccine candidate, to investigate the antibody response generated in a pre-clinical rabbit model and assess antigen immunogenicity. Surprisingly, we found a strong bias in antibody binding response towards the N-terminal epitope tag used for purification. These tags are widely reported to have low immunogenicity and are frequently left uncleaved in pre-clinical studies. We further confirmed that the observed immune response against the epitope tag dominated even the conformational binding response and, using synthetic peptides, narrowed the epitope down to a set of 10 residues inclusive of the Histidine residues. Our findings highlight the importance of epitope-tag removal in pre-clinical studies and demonstrate the utility of rapid Nanopore sequencing for early-stage vaccine evaluation.