Background Why are autoantibodies in systemic autoimmunity directed against only ~5% of the proteome? It has recently been discovered that many intracellular proteins, rather than being evenly distributed throughout the cell, instead form assemblages (also known as Membraneless Organelles and Biological Condensates) that arise from phase separation of their protein components, akin to partitioning of oil droplets in water. Such a conformation might be potentially more immunogenic than that of proteins with a diffuse presence in cells. We wondered if lupus autoantigens might preferentially exist as assemblages and thereby provoke autoantibody production.

Methods We obtained from an assemblage prediction algorithm (Vernon et al., elife 7, 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. We used the European Molecular Biology Laboratory ‘InTact’ Molecular Interactions Database to assess the potential for interactions of autoantigens compared with non-autoantigens.

Results 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 observed for non-autoantigens. When potential interactions were compared using InTact, autoantigens had at least a ten-fold greater tendency to interact with themselves and other proteins.

Conclusions We suggest that assemblage formation and certain protein structural features are key factors in determining the spectrum of lupus autoantibodies. Assemblages may promote autoantibody formation by concentrating certain intracellular proteins, as concentrations may be ~100x or more that of the intracellular proteins not contained in assemblages or organelles. Assemblages also foster protein-protein interactions, which could lead to changes in conformation of one or both partners, resulting in novel conformations to which the immune system might not be tolerized.