To assess whether the APOE ε4-associated immune phenotype extended into the brain, we analysed TMT-based proteomic data from the Accelerating Medicine Partnerships in AD (AMP-AD) Diverse Cohorts study in the dorsolateral prefrontal cortex (dlPFC; n = 530 AD, n = 190 non-impaired controls) and superior temporal gyrus (STG; n = 161 AD, n = 49 non-impaired controls; Supplementary Table 5). Here, APOE is linked to Alzheimer disease.