Potential SARS-CoV-2 Preimmune IgM Epitopes.

While studying the human public IgM igome as represented by a library of 224,087 linear mimotopes, three exact matches to peptides in the proteins of SARS-CoV-2 were found: two in the open reading frame 1ab and one in the spike protein. Joining the efforts to fast track SARS-CoV-2 vaccine development, here we describe briefly these potential epitopes in comparison to mimotopes representing peptides of SARS-CoV, HCoV 229E and OC43.

Targeting tumor-associated carbohydrate antigens: a phase I study of a carbohydrate mimetic-peptide vaccine in stage IV breast cancer subjects.

Tumor-associated carbohydrate antigens (TACAs) support cell survival that could be interrupted by anti-TACA antibodies. Among TACAs that mediate cell survival signals are the neolactoseries antigen Lewis Y (LeY) and the ganglioside GD2. To induce sustained immunity against both LeY and GD2, we developed a carbohydrate mimicking peptide (CMP) as a surrogate pan-immunogen that mimics both. This CMP, referred to as P10s, is the N-terminal half of a peptide vaccine named P10s-PADRE, the C-terminal half of which (PADRE) is a Pan-T-cell epitope. A Phase I dose-escalation trial of P10s-PADRE plus adjuvant MONTANIDE™ ISA 51 VG was conducted in subjects with metastatic breast cancer to test 300 and 500 µg/injection in two cohorts of 3 subjects each. Doses of the P10s-PADRE vaccine were administered to research participants subcutaneously on weeks 1, 2, 3, 7 and 19. Antibody responses to P10s, GD2, and LeY were measured by ELISA. The P10s-PADRE vaccine induced antibodies specifically reactive with P10s, LeY and GD2 in all 6 subjects. Serum antibodies displayed Caspase-3-dependent apoptotic functionality against LeY or GD2 expressing breast cancer cell lines. Immunization with the P10s-PADRE vaccine was well-tolerated and induced functional antibodies, and the data suggest potential clinical benefit.

Impact of Antigen Density on the Binding Mechanism of IgG Antibodies.

The density and distribution pattern of epitopes at the surface of pathogens have a profound impact on immune responses. Although multiple lines of evidence highlight the significance of antigen surface density for antibody binding, a quantitative description of its effect on recognition mechanisms is missing. Here, we analyzed binding kinetics and thermodynamics of six HIV-1 neutralizing antibodies as a function of the surface density of envelope glycoprotein gp120. Antibodies that recognize gp120 with low to moderate binding affinity displayed the most pronounced sensitivity to variation in antigen density, with qualitative and substantial quantitative changes in the energetics of the binding process as revealed by non-equilibrium and equilibrium thermodynamic analyses. In contrast, the recognition of gp120 by the antibodies with the highest affinity was considerably less influenced by variations in antigen density. These data suggest that a lower affinity of antibodies permits higher dynamics during the antigen recognition process, which may have considerable functional repercussions. These findings contribute to a better understanding of the mechanisms of antigen recognition by antibodies. They are also of importance for apprehending the impact of antigen topology on immune-defense functions of antibodies.

The Patterns of Coevolution in Clade B HIV Envelope's N-Glycosylation Sites.

The co-evolution of the potential N-glycosylation sites of HIV Clade B gp120 was mapped onto the coevolution network of the protein structure using mean field direct coupling analysis (mfDCA). This was possible for 327 positions with suitable entropy and gap content. Indications of pressure to preserve the evolving glycan shield are seen as well as strong dependencies between the majority of the potential N-glycosylation sites and the rest of the structure. These findings indicate that although mainly an adaptation against antibody neutralization, the evolving glycan shield is structurally related to the core polypeptide, which, thus, is also under pressure to reflect the changes in the N-glycosylation. The map we propose fills the gap in previous attempts to tease out sequon evolution by providing a more general molecular context. Thus, it will help design strategies guiding HIV gp120 evolution in a rational way.

Prevalence and gene characteristics of antibodies with cofactor-induced HIV-1 specificity.

The healthy immune repertoire contains a fraction of antibodies that bind to various biologically relevant cofactors, including heme. Interaction of heme with some antibodies results in induction of new antigen binding specificities and acquisition of binding polyreactivity. In vivo, extracellular heme is released as a result of hemolysis or tissue damage; hence the post-translational acquisition of novel antigen specificities might play an important role in the diversification of the immunoglobulin repertoire and host defense. Here, we demonstrate that seronegative immune repertoires contain antibodies that gain reactivity to HIV-1 gp120 upon exposure to heme. Furthermore, a panel of human recombinant antibodies was cloned from different B cell subpopulations, and the prevalence of antibodies with cofactor-induced specificity for gp120 was determined. Our data reveal that upon exposure to heme, ∼24% of antibodies acquired binding specificity for divergent strains of HIV-1 gp120. Sequence analyses reveal that heme-sensitive antibodies do not differ in their repertoire of variable region genes and in most of the molecular features of their antigen-binding sites from antibodies that do not change their antigen binding specificity. However, antibodies with cofactor-induced gp120 specificity possess significantly lower numbers of somatic mutations in their variable region genes. This study contributes to the understanding of the significance of cofactor-binding antibodies in immunoglobulin repertoires and of the influence that the tissue microenvironment might have in shaping adaptive immune responses.

Antibody polyspecificity: what does it matter?

Polyspecificity (polyreactivity) is currently considered an intrinsic property of a subset of antibodies, primarily of naturally occurring autoantibodies. Polyspecificity is no longer viewed as a biologically irrelevant stickiness. Furthermore, the capacity to bind defined sets of unrelated antigens finds its structural explanation. What is most intriguing, the elucidation of the role of polyspecificity may promote a better understanding of specific recognition as a function of the entire immune system. The early events of immune recognition depend on polyspecific binding. Thus, the completeness of the naïve repertoires of antigen receptors is ensured. The process of immunologically-relevant antigen recognition that is initiated goes beyond simple molecular interaction with the antigenic determinants. It involves cellular cooperation and culminates in antibody response maturation. Recent findings also pave the way for the clinical application of posttranslationally induced polyspecificity.

Multiple antigenic mimotopes of HIV carbohydrate antigens: relating structure and antigenicity.

Carbohydrate mimetic peptides are designable, and they can carry T-cell epitopes and circumvent tolerance. A mimic-based human immunodeficiency virus (HIV) vaccine can be a viable alternative to carbohydrate-based antigens if the diversity of epitopes found on gp120 can be recapitulated. To improve existing mimics, an attempt was made to study the structural correlates of the observed polyspecificity of carbohydrate mimetic peptides based on the Y(P/R)Y motif in more detail. A carbohydrate mimetic peptide, D002 (RGGLCYCRYRYCVCVGR), bound a number of lectins with different specificities. Although this peptide reacted strongly with both lotus and concanavalin A (ConA) lectins, it bound to lotus stronger than ConA. By varying the central motif RYRY, five versions were produced in multiple antigen peptide format, and their avidity for lotus and ConA lectins was tested by surface plasmon resonance. Although the kinetic parameters were similar, the version based on the sequence YPYRY had an optimal affinity for both lectins as well as improved avidity for wheat germ agglutinin and phytohemagglutinin. Thus, as far as lectin specificity is concerned, YPYRY had improved multiple antigenic properties. Both RYRY and YPYRY precipitated antibodies from human IgG for intravenous use that bound to gp120 in vitro and immunoprecipitated gp120 from transfected CHO-PI cells. Thus, Y(P/R)Y motifs mimic multiple carbohydrate epitopes, many of which are found on HIV, and preimmune human IgG antibodies that bind to HIV carbohydrates cross-react to a comparable extent with both RYRY and YPYRY carbohydrate mimetic peptides.

Serum IgM, IgG and IgA block by F(ab')-dependent mechanism the binding of natural IgG autoantibodies from therapeutic immunoglobulin preparations to self-antigens.

Natural polyreactive IgG autoantibodies are present in the plasma of healthy individuals and as a result in pooled therapeutic intravenous immunoglobulin (i.v.Ig) preparations. The spectrum of self-antigens to which these autoantibodies bind, their fate after intravenous infusion and their biological activity are not well understood. The identity of serum proteins that mask binding of natural autoantibodies to self-proteins is a matter of controversy. The spectrum of native serum proteins bound by i.v.Ig was analyzed by two-dimensional electrophoresis. The reactivity of i.v.Ig was directed mainly to circulating immunoglobulins. The binding of the IgG autoantibodies from i.v.Ig to native human liver antigens was blocked not only by a F(ab')2-dependent mechanism by circulating IgM and IgG (as has been previously suggested), but also by serum IgA. This control of anti-self reactivity may be inefficient in some autoimmune diseases.