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It was recently suggested that beta-site amyloid precursor protein (APP)-cleaving enzyme 2 (BACE2) functions as an amyloid beta (Aβ)-degrading enzyme; in addition to its better understood role as an APP secretase. Due to this finding we sought to understand the possible genetic risk contributed by the  BACE2  locus to the development of late-onset Alzheimer’s disease (AD). In this study, we report that common single nucleotide polymorphism (SNP) variation in  BACE2  is associated with altered AD risk in apolipoprotein E gene (APOE) epsilon 4 variant (ε4) non-carriers. In addition, in ε4 non-carriers diagnosed with AD or mild cognitive impairment (MCI), SNPs within the  BACE2  locus are associated with cerebrospinal fluid (CSF) levels of Aβ1-42. Further, SNP variants in  BACE2  are also associated with BACE2 RNA expression levels suggesting a potential mechanism for the CSF Aβ1-42 findings. Lastly, overexpression of BACE2  in vitro  resulted in decreased Aβ1-40 and Aβ1-42 fragments in a cell line model of Aβ production. These findings suggest that genetic variation at the  BACE2  locus modifies AD risk for those individuals who don’t carry the ε4 variant of APOE. Further, our data indicate that the biological mechanism associated with this altered risk is linked to amyloid generation or clearance possibly through BACE2 expression changes.

Common BACE2 Polymorphisms are Associated with Altered Risk for Alzheimer’s Disease and CSF Amyloid Biomarkers in APOE ε4 Non-Carriers