The role of proteomics in defining autoimmunity.

Kanduc, Darja

IntroductionDuring the last two decades, proteomics ̶ i.e., the study of the set of proteins produced in a cell, tissue, organism, or biological entity ̶ made possible analyses and contextual comparisons of proteomes/proteins and biological functions among the most disparate entities, from viruses to the human being. In this way, proteomic scrutiny of tumor-associated proteins, autoantigens, and pathogen antigens offers the tools for fighting cancer, autoimmunity, and infections.Areas coveredComparative proteomics and immunoproteomics, the new scientific disciplines generated by proteomics, are main themes of the present review that describes how comparative analyses of pathogen and human proteomes led to re-modulate the molecular mimicry concept of the pre-proteomic era. In front of the immunological idea of a peptide epitope being an a priori selected amino acid sequence, immunoproteomics introduced the peptide epitope concept as mathematically defined by its frequency and physico-chemically characterized by hydrophobicity. I.e., before proteomics, molecular mimicry - the sharing of peptide sequences between two biological entities - was considered as intrinsically endowed with immunologic properties and was related to cross-reactivity. Proteomics allowed to redefine such an assumption using physico-chemical parameters according to which frequency and hydrophobicity preferentially confer an immunologic potential to shared peptide sequences.Expert opinionProteomics is outlining peptide platforms to be used for the diagnostics and management of human diseases. A Molecular Medicine targeted to obtain healing without paying the price of adverse events is on the horizon. The next step is to take up the challenge and operate the paradigm shift that the current proteomic era requires.