Clinical and functional evidence supporting the pathogenicity of the novel PSEN1 p.R358P variant in early-onset Alzheimer's disease

Abstract

Background

Pathogenic variants in PSEN1, PSEN2, or AβPP cause early-onset Alzheimer's disease (EOAD). Several novel variants remain of uncertain significance (VUS) due to limited evidence. The PSEN1 p.R358P variant has not been previously characterized or reported in EOAD cases.

Objective

To determine the pathogenicity of the PSEN1 p.R358P variant in a patient with EOAD and assess its effect on amyloid-β (Aβ) processing using a human cellular model.

Methods

We present the case of a 62-year-old female of Western European descent with memory impairment starting at 59 and a positive family history of Alzheimer's disease (AD). To evaluate the variant, a PSEN1 knockout HEK293T line was generated using CRISPR/Cas9. Cells were co-transfected with AβPP and either wild-type or mutant PSEN1, and Aβ₄₂/Aβ₄₀ levels were measured by ELISA in culture supernatants.

Results

The proband exhibited multidomain cognitive impairment and imaging biomarkers (PiB-PET and FDG-PET) consistent with AD. Whole-exome sequencing revealed a PSEN1 (NM_000021.4:c.1073G > C:p.Arg358Pro) variant, classified as VUS by ACMG guidelines, together with a SORL1 p.G1536D variant and APOE ε4/ε4 genotype. Cells expressing PSEN1 p.R358P showed an increased Aβ₄₂/Aβ₄₀ ratio compared to wild-type, mainly due to reduced Aβ₄₀ levels. This profile partially mimicked the pathogenic PSEN1 p.A246E variant. In silico analyses predicted deleterious effects for PSEN1 p.R358P.

Conclusions

Our results support a likely pathogenic role for the PSEN1 p.R358P variant in EOAD. Nonetheless, in the absence of segregation data, the variant should be considered a hot VUS.