APOE loss-of-function variants: Compatible with longevity and associated with resistance to Alzheimer's disease pathology

Abstract

The ε4 allele of apolipoprotein E (APOE) is the strongest genetic risk factor for sporadic Alzheimer's disease (AD). Knockdown of ε4 may provide a therapeutic strategy for AD, but the effect of APOE loss of function (LoF) on AD pathogenesis is unknown. We searched for APOE LoF variants in a large cohort of controls and patients with AD and identified seven heterozygote carriers of APOE LoF variants. Five carriers were controls (aged 71-90 years), one carrier was affected by progressive supranuclear palsy, and one carrier was affected by AD with an unremarkable age at onset of 75 years. Two APOE ε3/ε4 controls carried a stop-gain affecting ε4: one was cognitively normal at 90 years and had no neuritic plaques at autopsy; the other was cognitively healthy at 79 years, and lumbar puncture at 76 years showed normal levels of amyloid. These results suggest that ε4 drives AD risk through the gain of abnormal function and support ε4 knockdown as a viable therapeutic option.

Keywords: Alzheimer’s disease; apolipoprotein E; dementia; human genetics; long-read sequencing; loss of function; neurodegenerative disorders; structural variant.

Figure 1.. APOE loss-of-function carrier demographics and variant positions

(a) Carrier demographics. Seven carriers of high-confidence APOE loss-of-function variants were identified among 26,605 older controls and 20,856 AD cases sequenced as part of the Alzheimer’s Disease Sequencing Project. (b) Four distinct single nucleotide variants and one structural variant were identified. Genomic coordinates are based on hg38.

Figure 2.. Early truncation of APOE ε4 in a 90-year-old ε3/ε4 control is associated with absent amyloid pathology and reduced tau pathology

Subject 1 is a neuropathological outlier among age-matched ε3/ε4 individuals in their (a) CERAD staging of amyloid plaque density; (b) Thal staging of amyloid plaque regional distribution; (c) Cerebral amyloid angiopathy staging; and (d) Braak staging of neurofibrillary tangles (tau pathology). The data distributions for neuropathological staging and age at death in ε3/ε4 individuals were derived from the National Alzheimer’s Coordinating Center uniform data set.

Figure 3.. Subject 7 APOE genotyping, deletion phasing, and expression analysis

(a) Sanger sequencing was used to confirm the start and end positions of the deletion. (b) Primer sets were designed to phase the 1798 base pair deletion with ε3/4. (c) Sanger sequencing of PCR products establishes that both ε3 and ε4 alleles are present in post-mortem brain tissue and that the deletion is in phase with ε3. (d) Sanger sequencing of reverse transcribed mRNA from post-mortem frontal cortex tissue establishes that only the ε4 allele is expressed in Subject 7.