A comprehensive study of the genetic impact of rare variants in SORL1 in European early-onset Alzheimer's disease

Abstract

The sortilin-related receptor 1 (SORL1) gene has been associated with increased risk for Alzheimer's disease (AD). Rare genetic variants in the SORL1 gene have also been implicated in autosomal dominant early-onset AD (EOAD). Here we report a large-scale investigation of the contribution of genetic variability in SORL1 to EOAD in a European EOAD cohort. We performed massive parallel amplicon-based re-sequencing of the full coding region of SORL1 in 1255 EOAD patients and 1938 age- and origin-matched control individuals in the context of the European Early-Onset Dementia (EOD) consortium, originating from Belgium, Spain, Portugal, Italy, Sweden, Germany, and Czech Republic. We identified six frameshift variants and two nonsense variants that were exclusively present in patients. These mutations are predicted to result in haploinsufficiency through nonsense-mediated mRNA decay, which could be confirmed experimentally for SORL1 p.Gly447Argfs*22 observed in a Belgian EOAD patient. We observed a 1.5-fold enrichment of rare non-synonymous variants in patients (carrier frequency 8.8 %; SkatOMeta p value 0.0001). Of the 84 non-synonymous rare variants detected in the full patient/control cohort, 36 were only detected in patients. Our findings underscore a role of rare SORL1 variants in EOAD, but also show a non-negligible frequency of these variants in healthy individuals, necessitating the need for pathogenicity assays. Premature stop codons due to frameshift and nonsense variants, have so far exclusively been found in patients, and their predicted mode of action corresponds with evidence from in vitro functional studies of SORL1 in AD.

Keywords: Alzheimer; Early onset; Haploinsufficiency; Loss-of-function; Meta-analysis; Rare variants; SORL1.

Fig. 1

Non-synonymous rare SORL1 variants identified in EOAD patients and control individuals. Patient-only variants denote variant present in patient cohort. Shared variants denote variants present in both the patient and control cohort. Control-only variants denote variants present in the control cohort. Functional domains are adapted from [37], and based on uniprot information. Protein-level variant position was based on NP_003096. Vps10p vacuolar protein sorting 10 domain, LDLR low-density lipoprotein receptor domain, TM transmembrane domain

Fig. 2

SORL1 expression and investigation of NMD. a SORL1 expression in lymphoblast cell lines of AD patient carrying SORL1 frameshift variant p.Gly447Argfs*22 and non-carrying control individuals. Measurements per sample were conducted in triplicate, with three measurements per experiment in two separate experiments. Y-axis indicates the relative expression quantities of SORL1. Error bars correspond to the standard error of the mean (SEM). Normalization was carried out against the housekeeping gene YWHAZ. Unpaired nonparametric Mann–Whitney test was performed to compare SORL1 expression of the p.Gly447Argfs*22 variant carrier with the control individuals. b SORL1 expression in lymphoblast cell lines of AD patient carrying SORL1 frameshift variant p.Gly447Argfs*22 and non-carrying controls. Black bars represent SORL1 expression in untreated samples (reference, set to 1); grey bars represent SORL1 expression after cycloheximide (CHX) treatment (relative to the non-treated sample). Error bars correspond to the standard error of the mean (SEM). Unpaired nonparametric Mann–Whitney test was performed to compare the effect of CHX incubation on SORL1 expression of the p.Gly447Argfs*22 variant with the control individuals

Fig. 3

Clinical characteristics of mutation carriers. a Scatter plot showing the onset ages for the SORL1 PTC and patient exclusive missense carriers versus those of PSEN1, PSEN2 and APP carriers. Mann–Whitney U test p value 0.016. b The proportion of SORL1 PTC, SORL1 missense and PSEN1, PSEN2 and APP carriers with a sporadic, unknown or positive familial history for AD

Fig. 4

Neuropathology of SORL1 missense carrier CS540. Neuropathological brain examination of a SORL1 missense carrier showing cortical thinning and superficial spongiosis in the frontal cortex, where pyramidal neurons contain very large tangles and abundant lipofuscin (a). Frequent mature and in a lesser extent diffuse beta-amyloid plaques are observed in the neocortical regions (b), as well as the cingulum and hippocampus. Frequent hyperphosphorylated tau immunoreactive (AT8) threads and large globose neurofibrillary tangles are present in neocortical areas (c) and cingulum