Apolipoprotein E
Apolipoprotein E (ApoE) is a class of proteins involved in the metabolism of fats in the body. It is important in Alzheimer's disease and cardiovascular disease.
Lipoproteins are molecules composed of fats and proteins. Apolipoprotein E is a fat-binding protein (apolipoprotein) that is part of the chylomicron and intermediate-density lipoprotein (IDLs). These are essential for the normal processing (catabolism) of triglyceride-rich lipoproteins. In peripheral tissues, ApoE is primarily produced by the liver and macrophages, and mediates cholesterol metabolism. In the central nervous system, ApoE is mainly produced by astrocytes and transports cholesterol to neurons via ApoE receptors, which are members of the low density lipoprotein receptor gene family. ApoE is the principal cholesterol carrier in the brain.

# Structure

## Gene
The gene, APOE, is mapped to chromosome 19 in a cluster with apolipoprotein C1 (APOC-I) and the apolipoprotein C2. 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 , nuclear receptors that form heterodimers with retinoid X receptors. In melanocytic cells APOE gene expression may be regulated by MITF.

## Protein
APOE is 299 amino acids long and contains multiple amphipathic -helices. According to crystallography studies, a hinge region connects the N- and C-terminal regions of the protein. The N-terminal region (residues 1167) forms an anti-parallel four-helix bundle such that the non-polar sides face inside the protein. Meanwhile, the C-terminal domain (residues 206299) contains three -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-2 (cys112, cys158), APOE-3 (cys112, arg158), and APOE-4 (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. These have physiological consequences:
- 2 (rs7412-T, rs429358-T) has an allele frequency of approximately 7 percent. This variant of the apoprotein binds poorly to cell surface receptors while E3 and E4 bind well. E2 is associated with both increased and decreased risk for atherosclerosis. Individuals with an E2/E2 combination may clear dietary fat slowly and be at greater risk for early vascular disease and the genetic disorder type III hyperlipoproteinemia94.4% of such patients are E2/E2, while only 2% of E2/E2 develop the disease, so other environmental and genetic factors are likely to be involved (such as cholesterol in the diet and age). E2 has also been implicated in Parkinson's disease, but this finding was not replicated in a larger population association study.
- 3 (rs7412-C, rs429358-T) has an allele frequency of approximately 79 percent. It is considered the "neutral" Apo E genotype.
- 4 (rs7412-C, rs429358-C) has an allele frequency of approximately 14 percent. E4 has been implicated in atherosclerosis, Alzheimer's disease, impaired cognitive function, reduced hippocampal volume, HIV, faster disease progression in multiple sclerosis, unfavorable outcome after traumatic brain injury, ischemic cerebrovascular disease, sleep apnea, accelerated telomere shortening  and reduced neurite outgrowth. A notable advantage of the E4 allele (relative to E2 and E3) is a positive association with higher levels of vitamin D, which may help explain its prevalence despite its seeming complicity in various diseases or disorders.
However, there is much to be learned about these APOE isoforms, including the interaction of other potentially protective genetic polymorphisms, so caution is advised before making determinant statements about the influence of APOE polymorphisms; this is particularly true as it relates to how APOE isoforms influence cognition and the development of Alzheimers Disease. In addition, there is no evidence that APOE polymorphisms influence cognition in younger age groups (other than possible increased episodic memory ability and neural efficiency in younger APOE4 age groups), nor is there evidence that the APOE4 isoform places individuals at increased risk for any infectious disease.

# Function
APOE transports lipids, fat-soluble vitamins, and cholesterol into the lymph system and then into the blood. It is synthesized principally in the liver, but has also been found in other tissues such as the brain, kidneys, and spleen. 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 remnants. 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
The E4 variant is 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 blacks have the highest observed frequency of the APO E*4 allele in world populations, but AD is rare among them. This may be due to their low cholesterol levels. Caucasian and Japanese carriers of 2 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. Alzheimer's disease is characterized by build-ups of aggregates of the peptide beta-amyloid. Apolipoprotein E enhances proteolytic break-down of this peptide, both within and between cells. The isoform ApoE-4 is not as effective as the others at promoting these reactions, resulting in increased vulnerability to AD in individuals with that gene variation.
Although 4065% of AD patients have at least one copy of the 4 allele, ApoE4 is not a determinant of the disease  at least a third of patients with AD are ApoE4 negative and some ApoE4 homozygotes never develop the disease. Yet those with two 4 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 ApoE 4,4.  Using  genotype ApoE 3,3 as a benchmark (with the persons who have this genotype regarded as having a risk level of 1.0), individuals with genotype ApoE4,4 have an odds ratio of 14.9 of developing Alzheimer's disease. Individuals with the ApoE 3,4 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 Alzheimers, 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 persons risk for Alzheimers 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 4 allele have significantly more neurological dysfunction than men.

## Atherosclerosis
Knockout mice that lack the apolipoprotein-E gene (ApoE/) develop extreme hypercholesterolemia when fed a high-fat diet.

## Malaria
ApoE/ knockout mice show marked attenuation of cerebral malaria and increased survival, as well as decreased sequestration of parasites and T cells within the brain, likely due to protection of the blood-brain barrier. Human studies have shown that the ApoE2 polymorphism correlates with earlier infection and ApoE3/4 polymorphisms increase likelihood of severe malaria.

# Interactions

## Interactive pathway map
Click on genes, proteins and metabolites below to link to respective articles. 
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# Evolution
Apolipoproteins are not unique to mammals. Many terrestrial and marine vertebrates have versions of them.  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.  It is believed that  the APOE arose via gene duplications of APOC-I before the fish-mammal split 400 million years ago.
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 those changes had no effect (V174L, A18T, A135V), but the fourth substitution 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 the exact same substitutions were found in Denisovan APOE.
About 220,000 years ago, an arginine to cysteine substitution took place at amino acid 112 (Arg112Cys) of the APOE4 gene and this resulted in the E3 allele.  Finally, 80,000 years ago another arginine to cysteine substitution at amino acid 158 (Arg158Cys) of the APOE3 gene created the E2 allele.