Discovery and validation of autosomal dominant Alzheimer's disease mutations

Abstract

Background: Alzheimer's disease (AD) is a neurodegenerative disease that is clinically characterized by progressive cognitive decline. Mutations in amyloid-β precursor protein (APP), presenilin 1 (PSEN1), and presenilin 2 (PSEN2) are the pathogenic cause of autosomal dominant AD (ADAD). However, polymorphisms also exist within these genes.

Methods: In order to distinguish polymorphisms from pathogenic mutations, the DIAN Expanded Registry has implemented an algorithm for determining ADAD pathogenicity using available information from multiple domains, including genetic, bioinformatic, clinical, imaging, and biofluid measures and in vitro analyses.

Results: We propose that PSEN1 M84V, PSEN1 A396T, PSEN2 R284G, and APP T719N are likely pathogenic mutations, whereas PSEN1 c.379_382delXXXXinsG and PSEN2 L238F have uncertain pathogenicity.

Conclusions: In defining a subset of these variants as pathogenic, individuals from these families can now be enrolled in observational and clinical trials. This study outlines a critical approach for translating genetic data into meaningful clinical outcomes.

Keywords: APP; Autosomal dominant Alzheimer’s disease; Cell-based assays; PSEN1; PSEN2; Pathogenicity algorithm.

Fig. 1

Identification of APP, PSEN1, and PSEN2 variants in densely affected Alzheimer’s disease (AD) pedigrees. a–e Pedigrees. Half-shaded triangles represent individuals with a clinical diagnosis of symptomatic AD. Fully shaded triangles represent individuals with autopsy-confirmed symptomatic AD. Diagonal lines represent deceased individuals. Arrows indicate those individuals with DNA, all of whom are mutation/variant carriers. Pedigrees have been masked to maintain anonymity. The pedigree of the PSEN1 M84V family was excluded to prevent potential disclosure of mutation status in asymptomatic mutation carriers

Fig. 2

Pittsburgh compound B (PiB) uptake in the brain of a presymptomatic PSEN1 M84V carrier is consistent with presymptomatic autosomal dominant Alzheimer’s disease mutation carriers. ¹¹C-PiB positron emission tomographic scans were performed longitudinally in a PSEN1 M84V noncarrier and carrier. The color scale for standardized uptake values (SUV) indicate red (high), yellow (medium), and blue (low) PiB retention. EYO Estimated years of onset

Fig. 3

Amyloid-β 1–42 peptide (Aβ₄₂) and Aβ₄₀ in cells expressing APP, PSEN1, and PSEN2 variants of unknown pathogenicity. N2A695 cells were transfected with vectors expressing presenilin 1 or 2. Media was replaced 24 hours posttransfection and incubated for an additional 24 hours. Media were collected, and Aβ₄₂ and Aβ₄₀ were measured by enzyme-linked immunosorbent assay (ELISA) (pg/ml). Total intracellular protein was measured by bicinchoninic acid assay and used to normalize to ELISA Aβ values, resulting in a value represented as pg/μg (see the Methods section of text). a–c PSEN1 wild type (WT), pathogenic mutation A79V, and variants with unknown pathogenicity. a Aβ₄₂. b Aβ₄₀. c Aβ₄₂/Aβ₄₀ ratio. d–f PSEN2 WT, pathogenic mutation N141I, and variants with unknown pathogenicity. d Aβ₄₂. e Aβ₄₀. f Aβ₄₂/Aβ₄₀ ratio. g–i APP WT, pathogenic mutation KM670/671NL(Swe), and APP T719N. Graphs represent the mean (±SEM) of four replicate experiments. * p < 0.05. PSEN1 QR127G is the amino acid representation for PSEN1 c.379_382delXXXXinsG

Fig. 4

Algorithm to classify the benign or pathogenic nature of APP, PSEN1, and PSEN2 variants. This model is modified from the algorithm previously proposed by Guerreiro et al. in 2010 [4]. The modifications include the evaluation of variants in the Exome Variant Server and Exome Aggregation Consortium databases and a tiered approach to evaluating functional studies that more heavily weighs the impact of the variant on amyloid-β 1–42 peptide (Aβ₄₂) and Aβ₄₀ levels on pathogenicity