Proximity labeling reveals unique and shared interactomes of unmodified and pyroglutamate amyloid beta in human hippocampus in Alzheimers disease

Amyloid plaques are a hallmark neuropathological feature of Alzheimers disease (AD), composed of insoluble amyloid beta (A{beta}) peptide. A{beta} undergoes post-translational modifications that alter their biophysical properties, aggregation kinetics, and neurotoxicity, creating a heterogeneous pool of species that differentially affect AD pathogenesis. Pyroglutamate-modified A{beta} (pEA{beta}) is a particularly aggregation-prone and proteolytically resistant variant that preferentially accumulates within plaque cores, is implicated in early plaque seeding, and is a major target of emerging anti-amyloid immunotherapies. However, the molecular environment surrounding pEA{beta} versus unmodified A{beta} (pan-A{beta}) in the human hippocampus remains incompletely defined. Here, we used Biotinylation by Antibody Recognition (BAR), an in-situ proximity labeling approach, to map and compare the protein-protein interactions (proteomes) of pEA{beta} and pan-A{beta} in formalin-fixed postmortem human hippocampal tissue from pathologically confirmed AD cases and cognitively normal (CN) controls. Differential proteomic analysis identified 48 significantly enriched proteins in AD pEA{beta} captures, 28 in AD pan-A{beta} captures, and 15 in CN pan-A{beta} captures. Whereas no significant enrichment was detected in CN pEA{beta} captures, supporting pEA{beta} as a pathology-associated species. pEA{beta} in AD demonstrated the largest variant-specific signature with 31 unique proteins, pan-A{beta} showed 11 unique proteins in AD, and 14 unique proteins in CN, 16 proteins were shared between AD pEA{beta} and AD pan-A{beta}, with PCSK1N shared across AD pEA{beta}, and AD/CN pan-A{beta}. Pathway enrichment analysis revealed broader biological disruptions linked to pEA{beta}, including synaptogenesis signaling, clathrin-mediated endocytosis, mitochondrial division signaling, and neurotransmitter release. Shared pathways included SNARE signaling, glutamatergic receptor signaling, and netrin signaling. These findings demonstrate that pEA{beta} engages an expanded, variant-specific interactome in human AD hippocampus and designate intracellular trafficking, synaptic signaling, and mitochondrial pathways as network-level vulnerabilities relevant to pEA{beta} pathology in AD. Notably, comparison of CN versus AD pan-A{beta} further distinguished protein networks associated with physiological A{beta} engagement versus pathological pan-A{beta} deposition.