Would carrying a muted version of APOE4, the strongest genetic risk factor of sporadic Alzheimer’s disease, protect against the disorder? Perhaps. Scientists led by Michael Greicius at Stanford University and Chang-En Yu at the VA Puget Sound Health Care System, Seattle, described two such cases in a medRxiv preprint uploaded July 24.

  • Scientists found two men with APOE4 loss-of-function variants.
  • At 70+ and 90+, both were cognitively sharp, with no signs of amyloid plaques.
  • This may bode well for future therapeutics aiming to knock down APOE4.

Both men, who were APOE3/4, had an aberrant stop codon in their E4 allele. One stayed sharp into his 90s, the other until his most recent doctor’s visit at 79. The former had no amyloid plaques in his brain postmortem and the latter had no amyloid markers in his cerebrospinal fluid. “The results provide the strongest human genetics evidence yet available suggesting that ε4 drives AD risk through a gain of abnormal function and support knockdown of APOE ε4 or its protein product as a viable therapeutic option,” the authors concluded. In contrast, a woman who was ApoE3/4 carried a deletion in her E3 allele, rendering it inactive. She developed AD at 75, about average for people with one copy of E4.

Loss-of-function (LoF) variants in APOE are rare. Eight have been reported, but only one, a frameshift in exon 4, was studied for its effects on cognition. A man in his early 40s with both copies of APOE silenced by the frameshift had blood choked with lipids, but his cerebrospinal fluid (CSF) was devoid of AD markers and he seemed cognitively normal, according to his global Mini-Mental State Exam score. Even so, he scored slightly below average for his age on verbal memory and language tasks, leaving it unclear whether the lack of APOE was helpful or harmful to his brain (Aug 2014 news).

To find others like him, co-first authors Augustine Chemparathy and Yann Le Guen, both at Stanford, analyzed whole-genome and whole-exome sequencing data from 20,850 people with AD and 26,600 controls ages 64 to 90 in the Alzheimer’s Disease Sequencing Project (ADSP), a compilation of genetic data from more than 40 cohorts worldwide. They looked for single nucleotide polymorphisms (SNPs) or structural variants in APOE predicted to quash protein levels. Four mutations fit the bill: two SNPs in exon 2, p.W5* and p.L8*, one in exon 3, p.Q39*, and a deletion. The SNPs create a premature stop codon leading to a truncated protein predicted to have no function. The 1,798bp deletion cuts out part of the promoter through to exon 2, preventing transcription (see image below).

Disrupting ApoE. The point mutations p.W5*, p.L8*, and pQ39* create premature stop codons, truncating ApoE. A deletion spanning the promoter to exon 2 silences transcription completely. The mutation p.W228* was more common, but left ApoE protein levels in human cells unchanged. [Courtesy of Chemparathy et al., medRxiv, 2023.]

In the whole ADSP cohort, five controls and one person with AD carried one of these LoF variants. One was the man who was cognitively healthy when he died in his 90s. He was APOE3/4 and had the p.W5* SNP in his E4 allele, rendering him effectively APOE3/-. Postmortem analysis revealed no amyloid plaques despite moderate neurofibrillary tangles at Braak stage IV. Still, he was an outlier for his age among other APOE3/4 carriers (see image below). This pattern of no plaques yet some tangles suggests primary age-related tauopathy, or PART (Nov 2014 news).

Healthy Outlier. Compared to age-related scores for amyloid plaques (top row), cerebral amyloid angiopathy (bottom left), and neurofibrillary tangles (bottom right) among APOE4 heterozygotes, a 90-year-old man with a loss-of-function variant in his APOE4 allele stood out for lack of amyloid and few tangles (red dot). [Courtesy of Chemparathy et al., medRxiv, 2023.]

Another man who was APOE3/4 with the same pW5* SNP, stayed sharp until age 79 and had normal levels of CSF Aβ42/40 and total tau. About two-thirds of APOE3/4 carriers test positive for amyloid by age 75 (Feb 2022 news).

The remaining controls were three cognitively normal women in their 70s and 80s. Two were effectively APOE3/- as the pW5* or pQ39* SNP knocked out their other E3 allele. The third woman was APOE3/4 and had the p.L8* SNP, but the scientists were unable to pinpoint which allele was silenced.

The sixth person was a woman diagnosed with AD at 75 who died in her late 80s. She was APOE3/4 and had the 1,1798 bp deletion in her E3 allele, leaving her with just an intact E4 allele. In ADSP, the mean age of AD onset for APOE4 heterozygotes is 73.5 years old, meaning she developed the disease at around the average age.

All told, these cases suggest that APOE3/4 carriers can lose an APOE4, dodge the risk for AD associated with that allele, and still live healthy lives.

Indeed, researchers are exploring therapeutically silencing the E4 allele. At the Alzheimer’s Association International Conference, held last month in Amsterdam, scientists led by Ornit Chiba-Falek of Duke University School of Medicine, Durham, North Carolina, reported a CRISPR-based epigenome targeting system that represses ApoE expression in human brain organoids and in mice carrying the human gene. The virally delivered CRISPR machinery reduced expression by 50 percent in the organoids and 70 percent in mice. It also slashed phospho-tau production in the organoids by 70 percent. For preclinical studies, others have developed a “switch” mouse to study the effects of knocking down E4 and adding E2 at any point during the AD continuum (see Part 13 of this series).—Chelsea Weidman Burke


  1. Congratulations on a very nice paper confirming in humans what Thomas Wisniewski's and our labs have been study for decades in vitro and in mice, that is, the catalytic activity of apoE4 on amyloid formation and consequent cognitive decline.

    We and colleagues have also used a repurposed drug screen to identify two human drugs, imipramine and olanzapine, that block the catalytic activity of apoE4 on Aβ polymerization into neurotoxic filaments. Both these drugs reversed cognitive decline and clinical diagnosis of AD patients in the NACC database, when they were prescribed for their normal indications. No other anti-depressant or antipsychotic was identified by our screen, or benefitted AD patients in the NACC database, confirming that the common beneficial function of imipramine and olanzapine is in blocking the effect of apoE4. Clinical trials are planned.


    . Amyloid-associated proteins alpha 1-antichymotrypsin and apolipoprotein E promote assembly of Alzheimer beta-protein into filaments. Nature. 1994 Nov 3;372(6501):92-4. PubMed.

    . Apolipoprotein e: essential catalyst of the Alzheimer amyloid cascade. Int J Alzheimers Dis. 2012;2012:489428. PubMed.

    . Imipramine and olanzapine block apoE4-catalyzed polymerization of Aβ and show evidence of improving Alzheimer's disease cognition. Alzheimers Res Ther. 2022 Jun 29;14(1):88. PubMed.

  2. I thoroughly enjoyed reading this elegant study. It nicely addresses the question of whether APOE4 exerts a gain-of-function role in the development of AD pathology and gives hope to the notion that therapeutically reducing APOE4 might be tolerated without significant metabolic or lipidomic side effects. The observation that the loss of functional APOE4 expression so remarkably affected the development of amyloid pathology or cognitive decline in APOE4/APOE3 individuals is a powerful indication that APOE4 protein exerts some deleterious gain-of-function relative to APOE3.

    Of course the role of APOE4 in promoting amyloid pathology is well established, and results from animal models suggest that reducing or removing APOE expression reduces amyloid deposition. Nonetheless, it is a pretty amazing, and very satisfying, result to see such a remarkable protection against amyloid in humans due to loss of APOE4 protein expression.

    Moreover, the fact that the individuals lived rather long lives with only one functional APOE allele suggests that at least reduction of APOE4 or partial reduction of APOE levels could both alleviate AD pathology and be well tolerated in regard to effects on systemic lipid metabolism.

    In our previous studies in mouse models of amyloid or tau pathology we found that about 50 percent reduction of APOE4 expression via anti-sense oligonucleotides could reduce amyloid pathology or tau pathology and tau-dependent neurodegeneration (Litvinchuk et al., 2021; Huynh et al., 2017). In the case of tauopathy, an assessment of plasma lipids found no significant differences resulting from CNS-delivery of ApoE ASOs. One caveat, translationally speaking, is that administration of APOE ASOs after amyloid pathology had begun to develop did not significantly impact amyloid burden in mouse models, although reductions in axonal dystrophy around plaques was noted. Other studies using divalent siRNA knockdown of mouse Apoe reported reductions in plaque burden both before and after the onset of pathology, perhaps due to the more robust level of knockdown reported (about 95 percent; Ferguson et al., 2022). Therapeutic efforts to target APOE4 for reduction will thus need to consider carefully the proper patient population in terms of pathology stage and level of APOE reduction that might yield a therapeutic effect.


    . Apolipoprotein E4 Reduction with Antisense Oligonucleotides Decreases Neurodegeneration in a Tauopathy Model. Ann Neurol. 2021 May;89(5):952-966. Epub 2021 Feb 24 PubMed.

    . Age-Dependent Effects of apoE Reduction Using Antisense Oligonucleotides in a Model of β-amyloidosis. Neuron. 2017 Dec 6;96(5):1013-1023.e4. PubMed.

    . Silencing of ApoE with Divalent siRNAs Drives Activation of Immune Clearance Pathways and Improves Amyloid Pathology in Mouse Models of Alzheimer's Disease. 2022 Jul 02 10.1101/2022.06.28.498012 (version 1) bioRxiv.

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Mutations Citations

  1. APOE E98Nfs
  2. APOE W5Ter
  3. APOE L8Ter
  4. APOE Q39Ter
  5. APOE g.45408560_45410359del

News Citations

  1. ApoE: One Man’s Brain Can Do Without It
  2. Scientists Propose a New Definition for Tau-Only Pathology
  3. Amyloid Lurks in a Third of Cognitively Normal People Over 70
  4. Meet the Switching Mice: They Flip Their Glia APOE4 to APOE2

External Citations

  1. Alzheimer’s Disease Sequencing Project (ADSP)

Further Reading

No Available Further Reading

Primary Papers

  1. . APOE loss-of-function variants: Compatible with longevity and associated with resistance to Alzheimer's Disease pathology. 2023 Jul 24 10.1101/2023.07.20.23292771 (version 1) medRxiv.