Overview

Clinical Phenotype: Blood Lipids/Lipoproteins, Cardiovascular Disease, Hyperlipoproteinemia Type III
Position: (GRCh38/hg38):Chr19:44908786 A>G
Position: (GRCh37/hg19):Chr19:45412043 A>G
Transcript: NM_000041; ENSG00000130203
dbSNP ID: rs121918394
Coding/Non-Coding: Coding
DNA Change: Substitution
Expected RNA Consequence: Substitution
Expected Protein Consequence: Missense
Codon Change: AAG to GAG
Reference Isoform: APOE Isoform 1
Genomic Region: Exon 4

Findings

This rare variant has been detected in one family and two unrelated individuals with hyperlipoproteinemia type III (HLPP3), also known as familial dysbetalipoproteinemia. HLPP3 is characterized by elevated cholesterol and triglyceride levels in blood, and early onset atherosclerosis and heart disease (Koopal et al., 2017). 

The variant was first described in a middle-aged American man with HLPP3 (Mann et al., 1989a, Mann et al., 1989b). The proband had a history of hyperlipidemia and coronary artery disease, as well as lipid deposits under his skin known as xanthomas. Compared with six healthy controls, he had elevated levels of triglycerides and total cholesterol, with high levels of cholesterol in very low-density lipoprotein (VLDL) particles, but normal levels of cholesterol in low-density lipoprotein (LDL) and high-density lipoprotein (HDL) particles (Mann et al., 1995a).

When analyzing his ApoE proteins by isoelectric focusing, the authors detected a band whose position differed from those of the common ApoE isoforms 2,3, and 4: it was shifted to a more negative position corresponding to ApoE1 (Mann et al., 1989a, Mann et al., 1989b). A genetic mutation was suspected given that neuraminidase treatment, which removes sialic acid residues, did not change the anomalous migration pattern. In addition, cysteamine treatment, which adds a positively charged group to cysteine, followed by electrophoresis, indicated that, like ApoE3, the unknown ApoE species had a single cysteine. The protein was named ApoE1 Harrisburg, and DNA sequence analysis ultimately revealed the underlying substitution, K164E, on an APOE3 backbone (Mann et al., 1995a). 

Examination of the family members of this original carrier revealed five additional heterozygote carriers, four with HLPP3 and the fifth with a similar disruption of lipid metabolism, suggesting dominant inheritance (Mann et al., 1989a). The mutation was also found in a Japanese family with HLPP3 (Moriyama et al., 1992), a Dutch HLPP3 patient (Visser et al., 2012), and a German patient with high triglyceride levels and a low ApoB/TC ratio (Evans et al., 2013).

This variant is very rare; it was absent from the gnomAD variant database (v2.1.1, May 2022).

Biological Effect

K164E has been reported to disrupt receptor and heparin binding, as well as ApoE turnover. In vitro experiments measuring the ability of K146E to displace labeled LDL from binding to receptors on human fibroblasts, revealed binding below 10 percent of that of wildtype ApoE3 (Moriyama et al., 1992, Mann et al., 1995a). In addition, binding of the mutant protein to cells lacking LDL receptors was 18 percent of ApoE3, suggesting deficient interactions with other cell surface proteins such as heparan sulfate proteoglycans (Mann et al., 1995b).  In these experiments, binding was assessed using β-VLDL particles, remnant lipoproteins that rely on ApoE for liver reuptake. Consistent with these findings, in vitro assays measuring binding to heparin-coated beads showed mutant binding was 21 percent of that of ApoE3. The authors noted that this deficiency may contribute to the mutation resulting in a dominant, high penetrance phenotype compared with the recessive, incomplete penetrance of ApoE2 which impairs receptor binding substantially, but has little effect on heparin binding.

The effect of the mutation on binding to other cell surface proteins, such as the lipoprotein receptor-related protein (LRP), remains uncertain. Crosslinking experiments showed that K164E is able to bind to LRP, but how this interaction compares quantitatively with that of ApoE3 is unknown (Mann et al., 1995b). 

The substantial effects on binding described above are perhaps not surprising considering the mutation involves the substitution of a positive charge for a negative charge in the middle of the ApoE receptor binding region, a sequence highly conserved across species (Frieden et al., 2015). Studies of ApoE structure suggest that K164, together with K161, interact directly with ligand-binding repeat domains found in members of the LDL receptor family (Guttman et al., 2010). Lipid binding may induce a conformational change that exposes K164 and K161 and provides a more positive electrostatic potential, both required for receptor binding (Lund-Katz et al., 2000).

Also of note, K164E’s effects on receptor binding may differ depending on its ApoE backbone. In vitro experiments with ApoE fragments bound to the artificial lipid DMPC suggest K164 has an increased PK(a) when it is on an ApoE2, versus ApoE3 or ApoE4, backbone, arising from a reduction in the positive electrostatic potential of its microenvironment (Lund-Katz et al., 2001). Moreover, the artificial substitution K164A substantially reduced binding of ApoE4 to the microglial leukocyte immunoglobulin-like receptor B3 (LilrB3), a receptor that binds to ApoE4 much more strongly than to ApoE3 or ApoE2 and activates pro-inflammatory pathways (Zhou et al., 2023).

K164 is also within the heparin-binding site of ApoE, lining the shallow groove that binds and makes direct contact with the sulfo groups of HSPGs (Libeu et al., 2001, Saito et al., 2003). Consistent with earlier findings, a more in-depth assessment of heparin binding revealed the mutation’s binding capacity, when lipid-free, is 34 percent of wildtype ApoE3’s, and 10 percent when bound to the artificial lipid DMPC. The reduction was pH-dependent, with 70 percent binding observed at pH 5, suggesting the ionization state of this glutamate is important. Indeed, nuclear magnetic resonance studies showed that, in lipid-laden wildtype ApoE3, K164 had an unusually low pK(a) value, indicating high positive electrostatic potential around this residue. The authors noted the potential importance of H158 and D172, as well as a heparin carboxyl group, in defining the ionic microenvironment. A subsequent study suggested heparin binding is a two-step process, with this mutation disrupting the first step which involves electrostatic interactions with rapid kinetics (Futamura et al., 2005).

K164E may also have farther-ranging effects. Biophysical analyses indicate that, although the mutation does not appear to significantly affect ApoE secondary structure, it is expected to perturb interactions between the protein’s N- and C-terminal domains (Georgiadou et al., 2011). In particular, it may stabilize an unfolding transition, affecting the dynamic coordination between receptor binding and lipid association.

Also of note, kinetic studies in vivo suggest K164E is catabolized more slowly than ApoE3 (Mann et al., 1995a). A mutation carrier and six healthy controls were injected with labeled wildtype ApoE3 and K164E, and plasma residence times of both proteins were monitored. In the controls, the mutant protein was catabolized slower than control ApoE3 and, in the proband, both protein species persisted longer and the production rate of total ApoE was about twice as high as in controls.

This variant's PHRED-scaled CADD score, which integrates diverse information in silico, was above 20, suggesting a deleterious effect (CADD v.1.6, May 2022).

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References

Paper Citations

1. Koopal C, Marais AD, Westerink J, Visseren FL. Autosomal dominant familial dysbetalipoproteinemia: A pathophysiological framework and practical approach to diagnosis and therapy. J Clin Lipidol. 2017 Jan - Feb;11(1):12-23.e1. Epub 2016 Oct 13 PubMed.
2. Mann WA, Gregg RE, Sprecher DL, Brewer HB Jr. Apolipoprotein E-1Harrisburg: a new variant of apolipoprotein E dominantly associated with type III hyperlipoproteinemia. Biochim Biophys Acta. 1989 Oct 17;1005(3):239-44. PubMed.
3. Mann AW, Gregg RE, Ronan R, Fairwell T, Hoeg JM, Brewer HB. Apolipoprotein E-1 Harrisburg, a mutation in the receptor binding domain, that is dominant for dysbetalipoproteinemia results in defective ligand-receptor interactions. Clin. Res. 37:520A. (Abstr.), 1989 National Library of Medicine
4. Mann WA, Lohse P, Gregg RE, Ronan R, Hoeg JM, Zech LA, Brewer HB Jr. Dominant expression of type III hyperlipoproteinemia. Pathophysiological insights derived from the structural and kinetic characteristics of ApoE-1 (Lys146-->Glu). J Clin Invest. 1995 Aug;96(2):1100-7. PubMed.
5. Moriyama K, Sasaki J, Matsunaga A, Arakawa F, Takada Y, Araki K, Kaneko S, Arakawa K. Apolipoprotein E1 Lys-146----Glu with type III hyperlipoproteinemia. Biochim Biophys Acta. 1992 Sep 22;1128(1):58-64. PubMed.
6. Visser ME, Dallinga-Thie GM, Pinto-Sietsma SJ, Defesche JC, Stroes ES, van der Valk PR. APOE1 mutation in a patient with type III hyperlipoproteinaemia: detailed genetic analysis required. Neth J Med. 2012 Aug;70(6):278-80. PubMed.
7. Evans D, Beil FU, Aberle J. Resequencing the APOE gene reveals that rare mutations are not significant contributory factors in the development of type III hyperlipidemia. J Clin Lipidol. 2013 Nov-Dec;7(6):671-4. Epub 2013 May 25 PubMed.
8. Mann WA, Meyer N, Weber W, Meyer S, Greten H, Beisiegel U. Apolipoprotein E isoforms and rare mutations: parallel reduction in binding to cells and to heparin reflects severity of associated type III hyperlipoproteinemia. J Lipid Res. 1995 Mar;36(3):517-25. PubMed.
9. Frieden C. ApoE: the role of conserved residues in defining function. Protein Sci. 2015 Jan;24(1):138-44. Epub 2014 Dec 9 PubMed.
10. Guttman M, Prieto JH, Handel TM, Domaille PJ, Komives EA. Structure of the minimal interface between ApoE and LRP. J Mol Biol. 2010 Apr 30;398(2):306-19. Epub 2010 Mar 19 PubMed.
11. Lund-Katz S, Zaiou M, Wehrli S, Dhanasekaran P, Baldwin F, Weisgraber KH, Phillips MC. Effects of lipid interaction on the lysine microenvironments in apolipoprotein E. J Biol Chem. 2000 Nov 3;275(44):34459-64. PubMed.
12. Lund-Katz S, Wehrli S, Zaiou M, Newhouse Y, Weisgraber KH, Phillips MC. Effects of polymorphism on the microenvironment of the LDL receptor-binding region of human apoE. J Lipid Res. 2001 Jun;42(6):894-901. PubMed.
13. Zhou J, Wang Y, Huang G, Yang M, Zhu Y, Jin C, Jing D, Ji K, Shi Y. LilrB3 is a putative cell surface receptor of APOE4. Cell Res. 2023 Feb;33(2):116-130. Epub 2023 Jan 2 PubMed.
14. Libeu CP, Lund-Katz S, Phillips MC, Wehrli S, Hernáiz MJ, Capila I, Linhardt RJ, Raffaï RL, Newhouse YM, Zhou F, Weisgraber KH. New insights into the heparan sulfate proteoglycan-binding activity of apolipoprotein E. J Biol Chem. 2001 Oct 19;276(42):39138-44. Epub 2001 Aug 10 PubMed.
15. Saito H, Dhanasekaran P, Nguyen D, Baldwin F, Weisgraber KH, Wehrli S, Phillips MC, Lund-Katz S. Characterization of the heparin binding sites in human apolipoprotein E. J Biol Chem. 2003 Apr 25;278(17):14782-7. Epub 2003 Feb 14 PubMed.
16. Futamura M, Dhanasekaran P, Handa T, Phillips MC, Lund-Katz S, Saito H. Two-step mechanism of binding of apolipoprotein E to heparin: implications for the kinetics of apolipoprotein E-heparan sulfate proteoglycan complex formation on cell surfaces. J Biol Chem. 2005 Feb 18;280(7):5414-22. Epub 2004 Dec 6 PubMed.
17. Georgiadou D, Chroni A, Vezeridis A, Zannis VI, Stratikos E. Biophysical analysis of apolipoprotein E3 variants linked with development of type III hyperlipoproteinemia. PLoS One. 2011;6(11):e27037. Epub 2011 Nov 1 PubMed.

Further Reading

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