Mutation of the amyloid precursor protein (APP), presenilin-1, or presenilin-2 results in the development of early onset autosomal dominant forms of Alzheimer disease (AD). These mutations lead to an increased A42/A40 ratio that correlates with the onset of disease. However, it remains unknown how these mutations affect ␥-secretase, a protease that generates the termini of A40 and A42. Here we have determined the reaction mechanism of ␥-secretase with wild type and three mutated APP substrates. Our findings indicate that despite the overall outcome of an increased A42/A40 ratio, these mutations each display rather distinct reactivity to ␥-secretase. Intriguingly, we found that the ratio of A42/A40 is variable with substrate concentration; increased substrate concentrations result in higher ratios of A42/A40. Moreover, we demonstrated that reduction of ␥-secretase substrate concentration by BACE1 inhibition in cells decreased the A42/A40 ratio. This study indicates that biological factors affecting targets such as BACE1 and APP, which ultimately cause an increased concentration of ␥-secretase substrate, can augment the A42/A40 ratio and may play a causative role in sporadic AD. Therefore, strategies lowering the A42/A40 ratio through partial reduction of ␥-secretase substrate production may introduce a practical therapeutic modality for treatment of AD.␥-Secretase cleaves the amyloid precursor protein (APP) to generate the C termini of -amyloid (A) 2 peptides, generally 40 or 42 amino acids in length (A40 and A42, respectively). A peptides are believed to be a major causative factor in the pathogenesis of Alzheimer disease (AD) (1). A42 is more prone to aggregation than A40 (2), and therefore biological or environmental factors that promote increased A42 production accelerate the pathological cascade leading to AD. Expression of A42, rather than A40, in Drosophila and mice leads to the formation of A plaques (3, 4). Furthermore, mouse model studies suggest that the ratio of A42/A40, rather than total amount of A, correlates with the load of characteristic AD plaques in the brain (5, 6). Moreover, evidence suggests A40 may play a beneficial role in that it antagonizes A42 aggregation (5, 6). Therefore, inhibition of ␥-secretase activity that specifically generates A42 or reduction of the Ab42/A40 ratio would be an appealing strategy for treatment of AD. However, despite intensive studies on ␥-secretase, the mechanism of cleavage specificity for ␥-secretase is still unknown.APP was the first gene found to be linked with inherited AD (7). Each mutation surrounding the ␥-secretase cleavage site appears to alter the production of A40 and A42. Suzuki et al. (8) demonstrated that mutating APP at Val-46 to Phe or Ile increased the ratio of secreted A42 to A40 in transfected cells. An increased ratio of A42/A40 was also observed with other mutations (9 -11). De Jonghe et al. (9) found certain mutations enhanced the stability of the ␥-secretase substrates known as C-terminal fragm...