Levels of Intersectin1 are increased in trisomic IPS cells relative to euploid cells harvested from DS patients. Whereas, Intersectin1 levels are decreased in the Superior Temporal Cortex of female AD patients, compared to controls, offering the first evidence that Intersectin1 protein levels differ significantly between cases and controls in AD. In transgenic mice, loss Intersectin1 expression was sufficient to alter the levels of key pathogenic proteins including APP, BACE1, and GSK3. For the first time, we demonstrate that (1) Intersectin1 co-localizes with APP and BACE1, (2) Intersectin1/Arf6/BACE1 and Intersectin1/Arfaptin2/BACE1 form complexes at distinct vesicle compartments, (3) and identify PI3KC2β as a novel Arf6 effector.