An "epitomic" analysis of the specificity of conformation dependent, anti-Aß amyloid monoclonal antibodies

Abstract

Antibodies against Aß amyloid are indispensable research tools and potential therapeutics for Alzheimers disease. They display several unusual properties, such as specificity for aggregated forms of the peptide, the ability to distinguish polymorphic aggregate structures, and the ability to recognize generic aggregation-related epitopes formed by unrelated am yloid sequences. Understanding the mechanisms underlying these unusual properties and the structures of their corre sponding epitopes is crucial for the understanding why anti bodies display different therapeutic activities and for the development of more effective therapeutic agents. Here we employed a novel "epitomic"approach to map the fine struc ture of the epitopes of 28 monoclonal antibodies against amyloid-beta using immunoselection of random sequences from a phage display library, deep sequencing, and pattern analysis to define the critical sequence elements recognized by the antibodies. Although most of the antibodies map to major linear epitopes in the amino terminal 1 to 14 residues of Aß, the antibodies display differences in the target sequence resi dues that are critical for binding and in their individual pref erences for nontarget residues, indicating that the antibodies bind to alternative conformations of the sequence by different mechanisms. Epitomic analysis also identifies discontinuous, nonoverlapping sequence Aß segments that may constitute the conformational epitopes that underlie the aggregation speci ficity of antibodies. Aggregation-specific antibodies recognize sequences that display a significantly higher predicted pro pensity for forming amyloid than antibodies that recognize the monomer, indicating that the ability of random sequences to aggregate into amyloid is a critical element of their binding mechanism.