Proteins in assemblages formed by phase separation possess properties that promote their transformation to...

Autoantibodies in systemic autoimmunity are directed against only ~5% of the proteome. The purpose of this study was to assess whether the properties of assemblages (also known as Membraneless Organelles and Biological Condensates) and their protein constituents partly explain the immunological selectivity of autoimmunity. Assemblages arise from phase separation of their protein components, akin to partitioning of oil droplets in water. We obtained from a prediction algorithm (Vernon et al., elife7, 2018) the propensity scores (PScores), i.e., likelihood, for phase separation of autoantigens and non-autoantigens. We then compared autoantigens with the highest PScores to identify shared structural properties. The mean PScores for autoantigens (n = 1050) and the entire human proteome of non-autoantigens (n = 17,532) were 1.46 and 1.09 (p = 1.2E-08). To varying extents, the 25 autoantigens with the highest phase separation propensities shared additional features such as compositional bias, repeated domains, coiled coil regions, nucleic acid binding, and disorder. Most of these properties were present with greater frequencies than their frequencies in the non-autoantigens. We conclude that, on average, autoantigens have a higher predisposition to undergo phase separation, thus, they are more likely to exist in assemblages compared with the average non-autoantigen. We suggest that assemblage formation and the greater than average presence of certain structural features are key factors in selection of a portion of the autoimmune repertoire. Other properties of assemblage proteins, such as high concentration and tendency to form novel complexes with other proteins, may partially explain why assemblages are potent sources of autoantigens.