NMR probing of in silico identification of anti-HPV16 E7 mAb linear peptide epitope

Oligopeptides for Immunotherapy Approaches in Ovarian Cancer Treatment

BACKGROUND

Anti-ovarian cancer vaccines based on minimal immune determinants uniquely expressed in ovarian cancer biomarkers appear to promise a high level of sensitivity and specificity for ovarian cancer immunodiagnostics, immunoprevention, and immunotherapy.

METHODS

Using the Pir Peptide Match program, three ovarian cancer biomarkers - namely, sperm surface protein Sp17, WAP four-disulfide core domain protein 2, and müllerian-inhibiting substance - were searched for unique peptide segments not shared with other human proteins. Then, the unique peptide segments were assembled to define oligopeptides potentially usable as synthetic ovarian cancer antigens.

RESULTS AND CONCLUSION

This study describes a methodology for constructing ovarian cancer biomarkerderived oligopeptide constructs that might induce powerful, specific, and non-crossreactive immune responses against ovarian cancer.

The comparative biochemistry of viruses and humans: an evolutionary path towards autoimmunity

Analyses of the peptide sharing between five common human viruses (Borna disease virus, influenza A virus, measles virus, mumps virus and rubella virus) and the human proteome highlight a massive viral vs. human peptide overlap that is mathematically unexpected. Evolutionarily, the data underscore a strict relationship between viruses and the origin of eukaryotic cells. Indeed, according to the viral eukaryogenesis hypothesis and in light of the endosymbiotic theory, the first eukaryotic cell (our lineage) originated as a consortium consisting of an archaeal ancestor of the eukaryotic cytoplasm, a bacterial ancestor of the mitochondria and a viral ancestor of the nucleus. From a pathologic point of view, the peptide sequence similarity between viruses and humans may provide a molecular platform for autoimmune crossreactions during immune responses following viral infections/immunizations.

Streptococcus mutans antigen I/II and autoimmunity in cardiovascular diseases

Infectious pathogens from the oral cavity cause oral diseases such as caries, gingivitis, periodontitis, endodontic infections, and alveolar osteitis, and often are also concomitant to systemic diseases, including cardiovascular disorders, stroke, preterm birth, diabetes, and pneumonia, among others. The relationship(s) between oral infections and systemic diseases are still unclear. Using the bacterial cell surface antigen I/II from S. mutans and cardiovascular diseases as a model, this study analyzes peptide commonalities that might underlie autoimmune crossreactions between the bacterial antigen and human proteins associated with cardiovascular disorders. The study outlines a vast peptide sharing that calls attention on autoimmune crossreactivity as a possible mechanism by which S. mutans infection might contribute to induce cardiovascular diseases, and, more in general, offers a new approach to investigate the still elusive molecular links between focal oral infections and human systemic diseases.

Ovarian cancer: designing effective vaccines and specific diagnostic tools

Aim: Notwithstanding a renewed interest in the application of immunotherapy as an alternative to chemotherapy and radiotherapy for the treatment of ovarian cancer (OC), and in spite of the available knowledge about ovarian tumor-associated-antigens, the search for a vaccine against OC remains a scientific and clinical challenge. Likewise, immunodiagnostics can detect only a late stage of the disease. Thus, the development of new therapeutic and diagnostic options is highly desirable. Methods: Based on the low-similarity hypothesis, which supports the concept that immunogenicity is preferentially associated to sequences with no/low-similarity to the host proteome, and using Protein Information Resource peptide match program, we searched the ovarian tumor antigen CA125 for amino acid sequences unique to CA125 and absent in the remaining human proteins. Results & conclusion: We identified a set of 159 pentapeptides unique to CA125 that might be used to design specific and effective immunological tools for diagnosis and treatment of OC.

The self/nonself issue: A confrontation between proteomes

Defining self and nonself is the most compelling challenge in science today, at the basis of the numerous questions that remain unanswered in the immunology-pathology-therapy debate. The generation of the antibody repertoire, the complicated scenario offered by tolerance and autoimmunity, natural auto-antibodies and their relationship to autoimmune diseases, and positive and negative selection are only a few examples of the unresolved immunological questions. In this context, we proposed that sequence similarity to the host proteome modulates antigen peptide recognition and immunogenicity. Using the available proteome assemblies of viruses, bacteria and higher vertebrates, and applying the low-similarity criterion, we are systematically defining the proteomic similarity of B-cell epitopes already validated experimentally. Here, we report further data documenting that a low similarity to the host proteome is the common property that defines the immunological "nonself" nature of antigenic sequences in cancer, autoimmunity, infectious diseases and allergy.

Immunogenicity in peptide-immunotherapy: from self/nonself to similar/dissimilar sequences

The nature of the relationship between an antigenic amino acid sequence and its capability to evoke an immune response is still an unsolved problem. Although experiments indicate that specific (dis)continuous amino acid sequences may determine specific immune responses, how immunogenic properties and recognition informations are mapped onto a non-linear sequence is not understood. Immunology has invoked the concept of self/nonself discrimination in order to explain the capability of the organism to selectively immunoreact. However, no clear, logical and rational pathway has emerged to relate a structure and its immuno-nonreactivity. It cannot yet be dismissed what Koshland wrote in 1990: "Of all the mysteries of modern science, the mechanism of self versus nonself recognition in the immune system ranks at or near the top". This chapter reviews the concept of self/nonself discrimination in the immune system starting from the historical perspective and the conceptual framework that underlie immune reaction pattern. It also introduces future research directions based on a proteomic dissection of the immune unit, qualitatively defined as a low-similarity sequence and quantitatively delimitated by the minimum amino acid requisite able to evoke an immune response, independently ofany, microbial or viral, "foreignness".

Non-redundant Peptidomes from DAPs: Towards “The Vaccine”?

Experimental analyses and literature survey reveal low-redundancy to the host proteins as a common denominator of immunogenic sequences mapped along tumor-, autoimmune-, and infectious disease-associated-proteins. The hypothesis that immunogenicity of peptide sequences is linked to proteomic redundancy is discussed.

Preliminary data on Pemphigus vulgaris treatment by a proteomics-defined peptide: a case report

Background

Although described by Hippocrates in 400 B.C., pemphigus disease still needs a safe therapeutical approach, given that the currently used therapies (i.e. corticosteroids and immunosuppressive drugs) often provoke collateral effects. Here we present preliminary data on the possible use of a proteomics derived desmoglein peptide which appears promising in halting disease progression without adverse effects.

Methods

The low-similarity Dsg3_49–60REWVKFAKPCRE peptide was topically applied for 1 wk onto a lesion in a patient with a late-stage Pemphigus vulgaris (PV) complicated by diabetes and cataract disease. The peptide was applied as an adjuvant in combination with the standard corticosteroid-based immunosuppressive treatment.

Results

After 1 wk, the treated PV eroded lesion appeared dimensionally reduced and with an increased rate of re-epithelization when compared to adjacent non-treated lesions. Short-term benefits were: decrease of anti-Dsg antibody titer and reduction of the corticosteroid dosage. Long-term benefits: after two years following the unique 1-wk topical treatment, the decrease of anti-Dsg antibody titer persists. The patient is still at the low cortisone dosage. Adverse effects: no adverse effect could be monitored.

Conclusion

With the limits inherent to any preliminary study, this case report indicates that topical treatment with Dsg3_49–60REWVKFAKPCRE peptide may represent a feasible first step in the search for a simple, effective and safe treatment of PV.

Proteomic definition of a desmoglein linear determinant common to Pemphigus vulgaris and Pemphigus foliaceous

Background

A number of autoimmune diseases have been clinically and pathologically characterized. In contrast, target antigens have been identified only in a few cases and, in these few cases, the knowledge of the exact epitopic antigenic sequence is still lacking. Thus the major objective of current work in the autoimmunity field is the identification of the epitopic sequences that are related to autoimmune reactions. Our labs propose that autoantigen peptide epitopes able to evoke humoral (auto)immune response are defined by the sequence similarity to the host proteome. The underlying scientific rationale is that antigen peptides acquire immunoreactivity in the context of their proteomic similarity level. Sequences uniquely owned by a protein will have high potential to evoke an immune reaction, whereas motifs with high proteomic redundancy should be immunogenically silenced by the tolerance phenomenon. The relationship between sequence redundancy and peptide immunoreactivity has been successfully validated in a number of experimental models. Here the hypothesis has been applied to pemphigus diseases and the corresponding desmoglein autoantigens.

Methods

Desmoglein 3 sequence similarity analysis to the human proteome followed by dot-blot/NMR immunoassays were carried out to identify and validate possible epitopic sequences.

Results

Computational analysis led to identifying a linear immunodominant desmoglein-3 epitope highly reactive with the sera from Pemphigus vulgaris as well as Pemphigus foliaceous. The epitopic peptide corresponded to the amino acid REWVKFAKPCRE sequence, was located in the extreme N-terminal region (residues 49 to 60), and had low redundancy to the human proteome. Sequence alignment showed that human desmoglein 1 and 3 share the REW-KFAK–RE sequence as a common motif with 75% residue identity.

Conclusion

This study 1) validates sequence redundancy to autoproteome as a main factor in shaping desmoglein peptide immunogenicity; 2) offers a molecular mechanicistic basis in analyzing the commonality of autoimmune responses exhibited by the two forms of pemphigus; 3) indicates possible peptide-immunotherapeutical approaches for pemphigus diseases.

Proteomic Scan for Tyrosinase Peptide Antigenic Pattern in Vitiligo and Melanoma: Role of Sequence Similarity and HLA-DR1 Affinity

Immune responses contribute to the pathogenesis of vitiligo and target melanoma sometimes associated with vitiligo-like depigmentation in some melanoma patients. We analyzed the sera from patients with vitiligo and cutaneous melanoma for reactivity toward tyrosinase peptide sequences 1) endowed with low level of similarity to human proteome, and 2) potentially able to bind HLA-DR1 Ags. We report that the tyrosinase autoantigen was immunorecognized with the same molecular pattern by sera from vitiligo and melanoma patients. Five autoantigen peptides composed the immunodominant anti-tyrosinase response: aa95-104FMGFNCGNCK; aa175-182 LFVWMHYY; aa176-190FVWMHYYVSMDALLG; aa222-236IQKLTGDENFTIPYW, and aa233-247 IPYWDWRDAEKCDIC. All of the five antigenic peptides were characterized by being (or containing) a sequence with low similarity level to the self proteome. Sera from healthy subjects were responsive to aa95-104FMGFNCGNCK, aa222-236IQKLTGDENFTIPYW, and aa233-247 IPYWDWRDAEKCDIC, but did not react with the aa175-182LFVWMHYY and aa176-190FVWMHYYVSMDALLG peptide sequences containing the copper-binding His180 and the oculocutaneous albinism I-A variant position F176. Our results indicate a clear-cut link between peptide immunogenicity and low similarity level of the corresponding amino acid sequence, and are an example of a comparative analysis that might allow to comprehensively distinguish the epitopic peptide sequences within a disease from those associated to natural autoantibodies. In particular, these data, for the first time, delineate the linear B epitope pattern on tyrosinase autoantigen and provide definitive evidence of humoral immune responses against tyrosinase.

Definition of anti-tyrosinase MAb T311 linear determinant by proteome-based similarity analysis

Using non-self discrimination as a driving force in generating peptide immunogenicity, we have developed a computer-assisted proteomic analysis in order to identify the protein antigenic regions that have evoked humoral response. The purpose of this study was to further validate the computational analysis for melanoma-associated antigens and, at the same time, to assess the efficacy of the methodology in defining antigenic regions of autoantigens associated to autoimmune diseases. To achieve this two-fold objective, we have examined the enzyme tyrosinase, a protein that represents an important autoantigen in patients with vitiligo or melanoma. Here, we report that the antigenic linear determinant of the monoclonal antibody (Mab) T311 raised against the melanoma/vitiligo tyrosinase autoantigen is located in the low similarity 15-mer amino acid sequence tyrosinase 233-247 IPYWDWRDAEKCDIC, within the fragment 237-247. These data confirm non-similarity to the host proteome as a factor that participates in shaping peptide immune reactivity and may be a first step towards designing tyrosinase antigenic peptides to be used for (i) direct neutralization of harmful melanocytes-attacking autoantibodies in vitiligo, or (ii) production of antibodies against tyrosinase-positive melanomas. Moreover tyrosinase peptide antigens might be used as key tools in studying the boundaries between self-tolerance and autoimmunity phenomena.