Apolipoprotein E

Evolution

Apolipoproteins are not unique to mammals. Many terrestrial and marine vertebrates have versions of them. It is believed that APOE arose via gene duplications of APOC1 before the fish–tetrapod split ca. 400 million years ago. Proteins similar in function have been found in choanoflagellates, suggesting that they are a very old class of proteins predating the dawn of all living animals.

The three major human alleles (E4, E3, E2) arose after the primate–human split around 7.5 million years ago. These alleles are the by-product of non-synonymous mutations which led to changes in functionality. The first allele to emerge was E4. After the primate–human split, there were four amino acid changes in the human lineage, three of which had no effect on protein function (V174L, A18T, A135V). The fourth substitution (T61R) traded a threonine for an arginine altering the protein's functionality. This substitution occurred somewhere in the 6 million year gap between the primate–human split and the Denisovan–human split, since exactly the same substitutions were found in Denisovan APOE.

About 220,000 years ago, a cysteine to arginine substitution took place at amino acid 112 (Cys112Arg) of the APOE4 gene, and this resulted in the E3 allele. Finally, 80,000 years ago, an arginine to cysteine substitution at amino acid 158 (Arg158Cys) of the APOE3 gene created the E2 allele.

Structure

Gene

The gene, APOE, is mapped to chromosome 19 in a cluster with the apolipoprotein C1 (APOC1) gene and the apolipoprotein C2 (APOC2) gene. The APOE gene consists of four exons and three introns, totaling 3597 base pairs. APOE is transcriptionally activated by the liver X receptor (an important regulator of cholesterol, fatty acid, and glucose homeostasis) and peroxisome proliferator-activated receptor γ, nuclear receptors that form heterodimers with retinoid X receptors. In melanocytic cells APOE gene expression may be regulated by MITF.

Protein

Apoe-E is 299 amino acids long and contains multiple amphipathic α-helices. According to crystallography studies, a hinge region connects the N- and C-terminal regions of the protein. The N-terminal region (residues 1–167) forms an anti-parallel four-helix bundle such that the non-polar sides face inside the protein. Meanwhile, the C-terminal domain (residues 206–299) contains three α-helices which form a large exposed hydrophobic surface and interact with those in the N-terminal helix bundle domain through hydrogen bonds and salt-bridges. The C-terminal region also contains a low density lipoprotein receptor (LDLR)-binding site.

Polymorphisms

APOE is polymorphic, with three major alleles (epsilon 2, epsilon 3, and epsilon 4): APOE-ε2 (cys112, cys158), APOE-ε3 (cys112, arg158), and APOE-ε4 (arg112, arg158). Although these allelic forms differ from each other by only one or two amino acids at positions 112 and 158, these differences alter APOE structure and function.

There are several low-frequency polymorphisms of APOE. APOE5 comes in two subtypes E5f and E5s, based on migration rates. APOE5 E5f and APOE7 combined were found in 2.8% of Japanese males. APOE7 is a mutation of APOE3 with two lysine residues replacing glutamic acid residues at positions 244 and 245.

Much remains to be learned about the APOE isoforms, including the interaction of other protective genes. so caution is advised before making determinant statements about the influence of APOE polymorphisms on cognition, development of Alzheimer's disease, cardiovascular disease, telomere shortening, etc. Many of the studies cited that purport these adverse outcomes are from single studies that have not been replicated and the research is based on unchecked assumptions about this isoform. As of 2007, there was no evidence that APOE polymorphisms influence cognition in younger age groups (other than possible better visual working memory in younger APOE4 age groups), nor that the APOE4 isoform places individuals at increased risk for any infectious disease.

However, the association between the APOE4 allele and Alzheimer's disease has been shown to be weaker in minority groups differently compared to their Caucasian counterparts. Hispanics/Latinos and African Americans who were homozygous for the APOE4 allele had 2.2 and 5.7 times the odds, respectively of developing Alzheimer's disease. The homozygous APOE4 allele has an even stronger effect in East Asian populations, with Japanese populations have 33 times the odds compared to the heterozygous population. Caucasians who were homozygous for the allele had 12.5 times the odds.

Function

As a component of the lipoprotein lipid transport system, APOE facilitates the transport of lipids, fat-soluble vitamins, and cholesterol via the blood. It interacts with the LDL receptor to facilitate endocytosis of VLDL remnants. It is synthesized principally in the liver, but has also been found in other tissues such as the brain, kidneys, and spleen. APOE synthesized in the liver associates with HDL which can then distribute it to newly formed VLDL or chylomicron particles to facilitate their eventual uptake by the liver.

In the nervous system, non-neuronal cell types, most notably astroglia and microglia, are the primary producers of APOE, while neurons preferentially express the receptors for APOE. There are seven currently identified mammalian receptors for APOE which belong to the evolutionarily conserved LDLR family.

APOE was initially recognized for its importance in lipoprotein metabolism and cardiovascular disease. Defects in APOE result in familial dysbetalipoproteinemia aka type III hyperlipoproteinemia (HLP III), in which increased plasma cholesterol and triglycerides are the consequence of impaired clearance of chylomicron, VLDL and LDL. More recently, it has been studied for its role in several biological processes not directly related to lipoprotein transport, including Alzheimer's disease (AD), immunoregulation, and cognition. Though the exact mechanisms remain to be elucidated, isoform 4 of APOE, encoded by an APOE allele, has been associated with increased calcium ion levels and apoptosis following mechanical injury.

In the field of immune regulation, a growing number of studies point to APOE's interaction with many immunological processes, including suppressing T cell proliferation, macrophage functioning regulation, lipid antigen presentation facilitation (by CD1) to natural killer T cell as well as modulation of inflammation and oxidation. APOE is produced by macrophages and APOE secretion has been shown to be restricted to classical monocytes in PBMC, and the secretion of APOE by monocytes is down regulated by inflammatory cytokines and upregulated by TGF-beta.

Clinical significance

Alzheimer's disease

As of 2012, the E4 variant was the largest known genetic risk factor for late-onset sporadic Alzheimer's disease (AD) in a variety of ethnic groups. However, the E4 variant does not correlate with risk in every population. Nigerian people have the highest observed frequency of the APOE4 allele in world populations, but AD is rare among them. This may be due to their low cholesterol levels. Caucasian and Japanese carriers of two E4 alleles have between 10 and 30 times the risk of developing AD by 75 years of age, as compared to those not carrying any E4 alleles. This may be caused by an interaction with amyloid. There is a sex specific effect, as presence of APOE4 increases AD risk more in women than in men. Alzheimer's disease is characterized by build-ups of aggregates of the peptide beta-amyloid, the breakdown of which Apolipoprotein E enhances, both within and between cells. The isoform APOE-ε4 is not as effective as the others at promoting this breakdown, resulting in increased vulnerability to AD in individuals with that gene variation.

The amyloid hypothesis of Alzheimer's disease has been questioned, and a 2021 article in Science claimed that "Just as removing smoke does not extinguish a fire, reducing amyloid plaques may not affect the course of Alzheimer's disease." The role that the E4 variant carries can still be fully explained even in the absence of a valid amyloid hypothesis given the fact that reelin signaling emerges to be one of the key processes involved in Alzheimer's disease and the E4 variant is shown to interact with ApoER2, one of the neuronal reelin receptors, thereby obstructing reelin signaling.

Although 40–65% of AD patients have at least one copy of the ε4 allele, APOE4 is not a determinant of the disease. At least one-third of patients with AD are APOE4 negative and some APOE4 homozygotes never develop the disease. Yet those with two ε4 alleles have up to 20 times the risk of developing AD. There is also evidence that the APOE2 allele may serve a protective role in AD. Thus, the genotype most at risk for Alzheimer's disease and at an earlier age is APOE4,4. Using genotype APOE3,3 as a benchmark (with the persons who have this genotype regarded as having a risk level of 1.0) and for white populations only, individuals with genotype APOE4,4 have an odds ratio of 14.9 of developing Alzheimer's disease. Individuals with the APOE3,4 genotype face an odds ratio of 3.2, and people with a copy of the 2 allele and the 4 allele (APOE2,4), have an odds ratio of 2.6. Persons with one copy each of the 2 allele and the 3 allele (APOE2,3) have an odds ratio of 0.6. Persons with two copies of the 2 allele (APOE2,2) also have an odds ratio of 0.6.

While ApoE4 has been found to greatly increase the odds that an individual will develop Alzheimer's, a 2002 study concluded, that in persons with any combination of APOE alleles, high serum total cholesterol and high blood pressure in mid-life are independent risk factors which together can nearly triple the risk that the individual will later develop AD. Projecting from their data, some researchers have suggested that lowering serum cholesterol levels may reduce a person's risk for Alzheimer's disease, even if they have two ApoE4 alleles, thus reducing the risk from nine or ten times the odds of getting AD down to just two times the odds.

Women are more likely to develop AD than men across most ages and APOE genotypes. Premorbid women with the ε4 allele have significantly more neurological dysfunction than men.

APOE-ε4 increases the risk not only for AD but also for dementia in pure alpha-synucleinopathies. The influence of APOE-ε4 on hippocampal atrophy was suggested to be more predominant early in the course of AD at milder stages prior to more widespread neurodegeneration.

With the approval of the first disease-modifying therapies for Alzheimer's disease based on monoclonal antibodies against amyloid-beta, which delay disease progression, APOE genotyping has also become important in assessing a patient's risk of side effects under therapy. In November 2024, the Committee for Medicinal Products for Human Use of the European Medicines Agency following a re-examination procedure, adopted a positive opinion, recommending the granting of a marketing authorization for the medicinal product Leqembi, intended for the treatment of early Alzheimer's disease in apolipoprotein E ε4 (ApoE ε4) non-carriers or heterozygotes. The applicant for this medicinal product is Eisai GmbH.

References

References

1. (2010). "Encyclopedia of Psychopharmacology". Springer.
2. (April 2009). "Apolipoprotein E: structure determines function, from atherosclerosis to Alzheimer's disease to AIDS". Journal of Lipid Research.
3. "Entrez Gene: APOE apolipoprotein E".
4. (August 2021). "Regulation of beta-amyloid production in neurons by astrocyte-derived cholesterol". Proceedings of the National Academy of Sciences of the United States of America.
5. (April 2003). "Alzheimer's disease: the cholesterol connection". Nature Neuroscience.
6. (March 2019). "ApoE attenuates unresolvable inflammation by complex formation with activated C1q". Nature Medicine.
7. (August 1997). "Both apolipoprotein E and A-I genes are present in a nonmammalian vertebrate and are highly expressed during embryonic development". Proceedings of the National Academy of Sciences of the United States of America.
8. (August 2017). "Evolution of human apolipoprotein E (APOE) isoforms: Gene structure, protein function and interaction with dietary factors". Ageing Research Reviews.
9. (2012). "The apolipoprotein E (APOE) gene appears functionally monomorphic in chimpanzees (Pan troglodytes)". PLOS ONE.
10. (March 2004). "Meat-adaptive genes and the evolution of slower aging in humans". The Quarterly Review of Biology.
11. (January 2001). "A PPAR gamma-LXR-ABCA1 pathway in macrophages is involved in cholesterol efflux and atherogenesis". Molecular Cell.
12. (December 2008). "Novel MITF targets identified using a two-step DNA microarray strategy". Pigment Cell & Melanoma Research.
13. (September 2014). "Apolipoprotein E isoforms and lipoprotein metabolism". IUBMB Life.
14. (2006). "APOE distribution in world populations with new data from India and the UK". Annals of Human Biology.
15. (September 2010). "Worldwide allele frequencies of the human apolipoprotein E gene: climate, local adaptations, and evolutionary history". American Journal of Physical Anthropology.
16. (October 2005). "Detection of ApoE E2, E3 and E4 alleles using MALDI-TOF mass spectrometry and the homogeneous mass-extend technology". Nucleic Acids Research.
17. {{OMIM. 107741#0015. APOE3 isoform, hyperlipoproteinemia, type III, autosomal recessive
18. {{OMIM. 107741#0001. APOE3 isoform, APOE, CYS112 and ARG158
19. (April 2006). "Variation at APOE and STH loci and Alzheimer's disease". Behavioral and Brain Functions.
20. (September 1994). "Apolipoprotein E5 and E7 in apparently healthy Japanese males: frequencies and relation to plasma lipid levels". The Japanese Journal of Human Genetics.
21. (November 2000). "Human apolipoprotein E7:lysine mutations in the carboxy-terminal domain are directly responsible for preferential binding to very low density lipoproteins". Journal of Lipid Research.
22. (February 2013). "Apolipoprotein E and Alzheimer disease: risk, mechanisms and therapy". Nature Reviews. Neurology.
23. (March 1982). "Abnormal lipoprotein receptor-binding activity of the human E apoprotein due to cysteine-arginine interchange at a single site". The Journal of Biological Chemistry.
24. (November 1982). "Studies of familial type III hyperlipoproteinemia using as a genetic marker the apoE phenotype E2/2". Journal of Lipid Research.
25. (1998). "Molecular basis of type III hyperlipoproteinemia in Germany". Human Mutation.
26. (December 1996). "Apo E variants in patients with type III hyperlipoproteinemia". Atherosclerosis.
27. (June 2004). "APOE-[epsilon]2 allele associated with higher prevalence of sporadic Parkinson disease". Neurology.
28. (May 2012). "A large study reveals no association between APOE and Parkinson's disease". Neurobiology of Disease.
29. (2021-03-16). "APOE4 Promotes Tonic-Clonic Seizures, an Effect Modified by Familial Alzheimer's Disease Mutations". Frontiers in Cell and Developmental Biology.
30. (September 2020). "Presence of the apolipoprotein E-ε4 allele is associated with an increased risk of sepsis progression". Scientific Reports.
31. (2015). "Association between Apolipoprotein E polymorphism and myocardial infarction risk: A systematic review and meta-analysis". FEBS Open Bio.
32. (2014). "Is apolipoprotein E4 an important risk factor for vascular dementia?". International Journal of Clinical and Experimental Pathology.
33. (September 2023). "Apolipoprotein E and viral infection: Risks and Mechanisms". Molecular Therapy. Nucleic Acids.
34. (September 2005). "Impact of hypertension and apolipoprotein E4 on poststroke cognition in subjects >75 years of age". Stroke.
35. (September 2014). "Apolipoprotein E isoforms and lipoprotein metabolism". IUBMB Life.
36. (2000). "Apolipoprotein E: far more than a lipid transport protein". Annual Review of Genomics and Human Genetics.
37. (August 1993). "Gene dose of apolipoprotein E type 4 allele and the risk of Alzheimer's disease in late onset families". Science.
38. (March 1993). "Apolipoprotein E: high-avidity binding to beta-amyloid and increased frequency of type 4 allele in late-onset familial Alzheimer disease". Proceedings of the National Academy of Sciences of the United States of America.
39. (August 2002). "Cognitive change and the APOE epsilon 4 allele". Nature.
40. (November 2004). "Impact of APOE in mild cognitive impairment". Neurology.
41. (August 2021). "The APOE ε4 variant and hippocampal atrophy in Alzheimer's disease and Lewy body dementia: a systematic review of magnetic resonance imaging studies and therapeutic relevance". Expert Review of Neurotherapeutics.
42. (June 2008). "Apolipoprotein (apo) E4 enhances HIV-1 cell entry in vitro, and the APOE epsilon4/epsilon4 genotype accelerates HIV disease progression". Proceedings of the National Academy of Sciences of the United States of America.
43. (February 2001). "APOE genotype is a major predictor of long-term progression of disability in MS". Neurology.
44. (March 2002). "Association of polymorphisms in the apolipoprotein E region with susceptibility to and progression of multiple sclerosis". American Journal of Human Genetics.
45. (January 1999). "Apolipoprotein E-epsilon4 genotype predicts a poor outcome in survivors of traumatic brain injury". Neurology.
46. (October 1999). "APOE genotype as a risk factor for ischemic cerebrovascular disease: a meta-analysis". Neurology.
47. (June 2001). "Association between apolipoprotein E epsilon4 and sleep-disordered breathing in adults". JAMA.
48. (August 2004). "APOE epsilon4 is associated with obstructive sleep apnea/hypopnea: the Sleep Heart Health Study". Neurology.
49. (February 2013). "Accelerated cell aging in female APOE-ε4 carriers: implications for hormone therapy use". PLOS ONE.
50. (February 2012). "APOE ε4 is associated with longer telomeres, and longer telomeres among ε4 carriers predicts worse episodic memory". Neurobiology of Aging.
51. (August 2006). "Shorter telomeres are associated with mortality in those with APOE epsilon4 and dementia". Annals of Neurology.
52. (September 2020). "Shorter Telomere Length in Carriers of APOE-ε4 and High Plasma Concentration of Glucose, Glyoxal and Other Advanced Glycation End Products (AGEs)". The Journals of Gerontology. Series A, Biological Sciences and Medical Sciences.
53. (May 2008). "AR, apoE, and cognitive function". Hormones and Behavior.
54. (2022-10-19). "Tumor Apolipoprotein E is a key checkpoint blocking anti-tumor immunity in mouse melanoma". Frontiers in Immunology.
55. (October 2015). "APOE Isoforms Control Pathogenic Subretinal Inflammation in Age-Related Macular Degeneration". The Journal of Neuroscience.
56. (September 2022). "Apolipoprotein E4 impairs the response of neurodegenerative retinal microglia and prevents neuronal loss in glaucoma". Immunity.
57. (September 2011). "APOE ε4 is associated with higher vitamin D levels in targeted replacement mice and humans". FASEB Journal.
58. (March 2015). "Apolipoprotein E (ApoE) polymorphism is related to differences in potential fertility in women: a case of antagonistic pleiotropy?". Proceedings. Biological Sciences.
59. (March 2010). "ApoE polymorphisms and diarrheal outcomes in Brazilian shanty town children". Brazilian Journal of Medical and Biological Research = Revista Brasileira de Pesquisas Medicas e Biologicas.
60. (August 2008). "Apolipoprotein E e4 and its prevalence in early childhood death due to sudden infant death syndrome or to recognised causes". Early Human Development.
61. (2016). "Cholesteryl ester transfer protein genotype modifies the effect of apolipoprotein ε4 on memory decline in older adults". Neurobiol Aging.
62. (August 2007). "Better memory and neural efficiency in young apolipoprotein E epsilon4 carriers". Cerebral Cortex.
63. (2017). "Alzheimer's Disease: Biomarkers in the Genome, Blood, and Cerebrospinal Fluid". Frontiers in Neurology.
64. (March 2023). "Genetics of Alzheimer's disease: an East Asian perspective". Journal of Human Genetics.
65. (2011). "Clinical Cardiogenetics". Springer.
66. (January 2013). "Aberrant apolipoprotein E expression and cognitive dysfunction in patients with poststroke depression". Genetic Testing and Molecular Biomarkers.
67. (August 2008). "Reelin and apoE actions on signal transduction, synaptic function and memory formation". Neuron Glia Biology.
68. (February 2015). "The crucial roles of apolipoproteins E and C-III in apoB lipoprotein metabolism in normolipidemia and hypertriglyceridemia". Current Opinion in Lipidology.
69. (August 2015). "Effects of ApoE on intracellular calcium levels and apoptosis of neurons after mechanical injury". Neuroscience.
70. (October 2005). "Apolipoprotein-mediated pathways of lipid antigen presentation". Nature.
71. (2010). "The role of apolipoprotein E in Guillain-Barré syndrome and experimental autoimmune neuritis". Journal of Biomedicine & Biotechnology.
72. (2013). "ApoE production in human monocytes and its regulation by inflammatory cytokines". PLOS ONE.
73. (October 2012). "Association of apolipoprotein E epsilon 4 allele with sporadic late onset Alzheimer's disease. A meta-analysis". Neurosciences.
74. (October 1989). "Genetic studies of human apolipoproteins. X. The effect of the apolipoprotein E polymorphism on quantitative levels of lipoproteins in Nigerian blacks". American Journal of Human Genetics.
75. (1998-01-01). "Serum total cholesterol, apolipoprotein E epsilon 4 allele, and Alzheimer's disease". Neuroepidemiology.
76. (2003-01-01). "Changes in apolipoprotein E expression in response to dietary and pharmacological modulation of cholesterol". Journal of Molecular Neuroscience.
77. (August 2002). "Apolipoprotein E epsilon4 allele, elevated midlife total cholesterol level, and high midlife systolic blood pressure are independent risk factors for late-life Alzheimer disease". Annals of Internal Medicine.
78. (February 1992). "Apolipoprotein E: a pathological chaperone protein in patients with cerebral and systemic amyloid". Neuroscience Letters.
79. (April 2025). "Disentangling the effects of sex and gender on APOE ɛ4-related neurocognitive impairment". Alzheimer's & Dementia.
80. (October 2021). "Alzheimer's drugs: Does reducing amyloid work?". Science.
81. (December 2021). "Relevance of a Novel Circuit-Level Model of Episodic Memories to Alzheimer's Disease". International Journal of Molecular Sciences.
82. (October 2013). "Impact of apolipoprotein E on Alzheimer's disease". Current Alzheimer Research.
83. (June 1994). "Protective effect of apolipoprotein E type 2 allele for late onset Alzheimer disease". Nature Genetics.
84. (1997). "Effects of age, sex, and ethnicity on the association between apolipoprotein E genotype and Alzheimer disease. A meta-analysis. APOE and Alzheimer Disease Meta Analysis Consortium". JAMA.
85. (June 2012). "Gender modulates the APOE ε4 effect in healthy older adults: convergent evidence from functional brain connectivity and spinal fluid tau levels". The Journal of Neuroscience.
86. (February 2013). "APOE ε4 increases risk for dementia in pure synucleinopathies". JAMA Neurology.
87. (27 February 2025). "Leqembi EPAR".
88. (14 November 2024). "Leqembi recommended for treatment of early Alzheimer's disease".