Cross-Regional Trajectory Analysis Reveals Distinct Temporal Progression of Shared Proteomic Programs in Alzheimer's Disease

Alzheimer's pathology progresses through anatomically distinct brain regions, yet how molecular programs are temporally organized across vulnerable regions remains poorly understood. Here, we reconstructed continuous proteomic trajectories from matched dorsolateral prefrontal cortex (DLPFC) and superior temporal gyrus (STG) proteomes to investigate cross-regional molecular progression in AD. The inferred trajectories closely recapitulated established neuropathological staging while remaining independent of age, sex, and race. Across regions, a mitochondrial bioenergetic protein subset declined substantially earlier in the STG than in the DLPFC, revealing a previously unrecognized regional temporal offset in metabolic dysfunction. In parallel, a broadly shared proteomic program progressed in both regions but more rapidly in the STG, indicating that shared molecular responses differ in their temporal progression despite overall coordination. Together, these findings demonstrate that regional vulnerability in AD is reflected not only by the molecular programs involved but also by their temporal organization during disease progression.