Overview

Clinical Phenotype: Hyperlipoproteinemia Type III
Position: (GRCh38/hg38):Chr19:44908788_44908789 GC>CT
Position: (GRCh37/hg19):Chr19:45412045_45412046 GC>CT
Transcript: NM_000041; ENSG00000130203
dbSNP ID: NA
Coding/Non-Coding: Coding
DNA Change: Deletion-Insertion
Expected RNA Consequence: Deletion-Insertion
Expected Protein Consequence: Deletion-Insertion
Codon Change: AAG to AAC, CGG to TGG
Reference Isoform: APOE Isoform 1
Genomic Region: Exon 4

Findings

This variant was identified in a 26-year-old woman suffering from hyperlipoproteinemia type III (HLPP3), also known as familial dysbetalipoproteinemia (Hoffer et al., 1996). The first sign of the condition surfaced very early, at age three, when she developed fat deposits under her skin known as tubero-eruptive xanthomas. She also had high levels of cholesterol and triglycerides in plasma typical of HLPP3. Isoelectric focusing revealed two ApoE species: one migrating to the position of the common isoform ApoE3, while the other migrated to a more negatively charged position corresponding to ApoE1. DNA sequencing revealed the ApoE1 species was encoded by a DNA variant with a dinucleotide substitution causing amino acid changes at positions 164 and 165. The mutation occurred on an APOE3 backbone.

The variant, named ApoE1-Hammersmith, was also found in the proband’s son and daughter. The daughter developed xanthomas at age seven. No clinical abnormalities were detected in the son, but he was only three years old when examined.

Of note, one of the substitutions in this mutation, R165W, was identified in a Spanish individual with HLPP3 and hyperlipoproteinemia type IIb (Bea et al., 2023).

K164_R165delinsNW was absent from the gnomAD variant database (v2.1.1, Nov 2021).

Biological Effect

This variant results in the replacement of two positively charged amino acids with two neutral ones in the middle of the receptor binding region, a sequence highly conserved across species (Hoffer et al., 1996; Frieden et al., 2015). Also, both amino acids are within ApoE’s main heparin-binding site and may be important for ApoE's interaction with the sulfo groups of heparan sulfate proteoglycans (Libeu et al., 2001; Saito et al., 2003), particularly R165 (Mah et al., 2023).

Experiments in mice transfected with adenovirus carrying the variant suggested this mutant may disrupt receptor binding and prevent the catabolism of triglyceride-rich ApoE-containing lipoprotein particles (Fotakis et al., 2014). The mice, which lacked endogenous Apoe, had severe hypercholesterolemia and hypertriglyceridemia, a reduced ratio of cholesteryl esters to total cholesterol, immature discoidal high density lipoprotein (HDL) particles, very high plasma ApoE levels, and accumulation of ApoE in particles of very-low, low, and intermediate densities (VLDL/IDL/LDL).

Fotakis and colleagues hypothesized these alterations reflect a lack of normal lipoprotein clearance by the LDL receptor, with the variant acting as a dominant-negative ligand. Consistent with this proposal, elevated cholesterol levels persisted even after deletion of the C-terminal portion of the variant (residues 221-317), a region that normally gates ligand binding and, when deleted from some loss-of-function mutants, rescues binding activity.

K164_R165delinsNW may also affect binding to other cell surface receptors. Individually introducing adenines at positions K164 or R165 substantially reduced binding of ApoE4 to the microglial leukocyte immunoglobulin-like receptor B3 (LilrB3), a receptor that binds to ApoE4 more strongly than to ApoE3 or ApoE2 and activates pro-inflammatory pathways (Zhou et al., 2023).

Moreover, K164_R165delinsNW appears to interfere with the activities of two enzymes: lipoprotein lipase (LPL) which releases triglycerides from lipoprotein particles, and lecithin-cholesterol acyltransferase (LCAT) which esterifies cholesterol enhancing the packaging efficiency in lipoprotein particles and enabling HDL maturation (Fotakis et al., 2014). The effect on LCAT appeared to be direct—it could only be corrected by elevating LCAT levels.

Physicochemical studies showed the mutant had decreased thermal stability and increased the exposure of hydrophobic residues on the surface of the protein (Fotakis et al., 2014).

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References

Mutations Citations

1. APOE R165W

Paper Citations

1. Hoffer MJ, Niththyananthan S, Naoumova RP, Kibirige MS, Frants RR, Havekes LM, Thompson GR. Apolipoprotein E1-Hammersmith (Lys146-->Asn;Arg147-->Trp), due to a dinucleotide substitution, is associated with early manifestation of dominant type III hyperlipoproteinaemia. Atherosclerosis. 1996 Aug 2;124(2):183-9. PubMed.
2. Libíková H, Pogády J, Wiedermann V, Breier S. Search for herpetic antibodies in the cerebrospinal fluid in senile dementia and mental retardation. Acta Virol. 1975 Nov;19(6):493-5. PubMed.
3. Frieden C. ApoE: the role of conserved residues in defining function. Protein Sci. 2015 Jan;24(1):138-44. Epub 2014 Dec 9 PubMed.
4. 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.
5. 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.
6. Mah D, Zhu Y, Su G, Zhao J, Canning A, Gibson J, Song X, Stancanelli E, Xu Y, Zhang F, Linhardt RJ, Liu J, Wang L, Wang C. Apolipoprotein E Recognizes Alzheimer's Disease Associated 3-O Sulfation of Heparan Sulfate. Angew Chem Int Ed Engl. 2023 Jun 5;62(23):e202212636. Epub 2023 Apr 28 PubMed.
7. Fotakis P, Vezeridis A, Dafnis I, Chroni A, Kardassis D, Zannis VI. apoE3[K146N/R147W] acts as a dominant negative apoE form that prevents remnant clearance and inhibits the biogenesis of HDL. J Lipid Res. 2014 Jul;55(7):1310-23. Epub 2014 Apr 28 PubMed.
8. 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.

Other Citations

1. Bea et al., 2023

Further Reading

No Available Further Reading