Plasma ApoE proteotyping for ApoE ε4 stratification in the anti-amyloid therapies era

Background: Apolipoprotein E (ApoE) ε4 status informs risk stratification and safety management for anti-amyloid therapies, but genotyping typically requires dedicated procedures, longer turnaround times, and higher costs compared with automated laboratory assays. We evaluated an automated plasma approach for ε4 stratification based on proteotyping, the quantification of isoform-specific ApoE proteins to infer ApoE genotype. Methods: We retrospectively included 110 patients (mean age 67.82 ± 10.11 years, 49.1% female) of European ancestry with cognitive impairment across a broad diagnostic spectrum, including 68 AD-spectrum cases, 29 with subjective symptoms, and 16 with other etiologies. ApoE genotyping identified 57 ε4 non-carriers (51.8%), 44 heterozygous carriers (40.0%), and 9 homozygous carriers (8.2%). ApoE4 and total ApoE (PanApoE) were measured on Lumipulse and the ApoE4/PanApoE ratio (ApoE ratio) was derived. Results: The ratio showed excellent separation across genotypes in our cohort. For ε4 carrier identification, both the ratio and ApoE4 achieved an AUC of 1.00 (95% CI 1.00-1.00), whereas PanApoE showed poor discrimination (AUC 0.30, 95% CI 0.20-0.40), reflecting lower PanApoE levels in ε4 carriers. The ratio also accurately distinguished heterozygotes from homozygotes (AUC 1.00, 95% CI 1.00-1.00). Conclusions: Automated plasma ApoE proteotyping mirrored genetic ε4 status. The ApoE ratio provided complete genotype separation, supporting its use for individual-level stratification. These findings should be interpreted cautiously considering the retrospective single-center design and the limited number of ApoE ε4 homozygotes, and require validation in larger, independent cohorts.