CM-TRAP: A chemoproteomic workflow for profiling circulating metabolites and their protein targets in Alzheimer's disease.

Abstract

BACKGROUND: Metabolites serve not only as metabolic intermediates but also as potent signaling molecules that orchestrate cell fate. However, decoding the specific "metabolite-target-phenotype" axis within complex pathophysiological environment remains a major challenge due to the lack of systematic target deconvolution strategies. Here, we developed Circulating Metabolite-Target Responsive Accessibility Profiling (CM-TRAP), an integrated multi-omics workflow that couples untargeted metabolomic screening with TRAP-based chemical proteomic target discovery. This analytical framework enables the direct linkage of disease characteristic metabolic alterations to their molecular targets. RESULTS: To investigate the signaling role of circulating metabolites during Alzheimer's disease (AD) progression, we performed comprehensive metabolomic profiling of cerebrospinal fluid (CSF) and serum from 3- and 12-month-old 5 × FAD transgenic mice, a well-established mouse model of AD, and identified an early disruption in purine metabolism and late alterations in amino acid and glycolytic pathways within the CSF. Specifically, xanthine emerged as a key stage-dependent metabolite significantly elevated in AD CSF. Functionally, xanthine acts as a pro-inflammatory modulator, potentiating the LPS-induced IL-6 secretion in a dose-dependent manner in BV2 microglial cells. To mechanistically link this pro-inflammatory phenotype with molecular function, we applied TRAP-based chemical proteomics to delineate the dose-dependent structural profiling of xanthine, which led to the identification of peptidase D (PEPD) and prosaposin (PSAP) as candidate targets with potential roles in neuroinflammatory regulation. SIGNIFICANCE: CM-TRAP establishes an effective analytical strategy for functionally linking metabolic alterations to candidate protein targets, providing a framework for understanding metabolite-associated neuroinflammation. The identification of xanthine as a pro-inflammatory mediator and its engagement with PEPD and PSAP offers site-resolved insights into how a stage-specific metabolite may reshape the microglial proteome to propagate inflammatory signaling. With further validation, this platform could be broadly applicable for discovering bioactive metabolites and their cognate targets across diverse disease contexts.