Overview

Clinical Phenotype: Kidney Disorder: Lipoprotein Glomerulopathy
Position: (GRCh38/hg38):Chr19:44908784 G>C
Position: (GRCh37/hg19):Chr19:45412041 G>C
Transcript: NM_000041; ENSG00000130203
dbSNP ID: rs121918397
Coding/Non-Coding: Coding
DNA Change: Substitution
Expected RNA Consequence: Substitution
Expected Protein Consequence: Missense
Codon Change: CGT to CCT
Reference Isoform: APOE Isoform 1
Genomic Region: Exon 4

Findings

This variant is one of two major risk factors for lipoprotein glomerulopathy (LPG), a rare kidney disorder in which the glomerular capillaries of the kidney dilate and accumulate layered, lipoprotein-rich aggregates (Saito et al., 2020).

It was first identified in a father, son, and an unrelated individual, all suffering from LPG in Sendai, Japan (Oikawa et al., 1997). Their symptoms and pathology included lipoprotein clumps in the enlarged lumina of their kidneys’ glomerular capillaries, protein in urine, and elevated ApoE in blood (Oikawa et al., 1991, Oikawa et al., 1997). All carriers had ApoE proteins that migrated to the position of the common ApoE isoform R176C (ApoE2) upon isoelectric focusing. One had a pattern consistent with the APOE2/E4 genotype and the other two had patterns consistent with the APOE2/E3 genotype. However, upon sequencing, it was revealed that the ApoE2-migrating protein was R163P rather than ApoE2.

At least 28 LPG patients have been reported to carry this mutation (Saito et al., 2014, Saito et al., 2020, Li et al., 2022, Tanimizu et al., 2023). Not all carriers develop LPG, however. In a study of 13 LPG patients and their families, for example, all affected members had the mutation, as did four asymptomatic individuals (Toyota et al., 2013). Moreover, incomplete penetrance has been reported in APOE knockout mice expressing human APOE R163P (Ishimura et al., 2009). Factors that may influence disease expression include the presence of other genetic variants and comorbid conditions (e.g., Takasaki et al., 2018; see E21K).

Also of note, at least in some cases, this variant appears to disrupt regions in the nephron, the functional unit of the kidney, beyond the glomeruli. Examination of a renal biopsy of the proband of a family carrying this variant revealed lipoprotein deposits, not only in glomerular capillaries, but in the peritubular capillaries in the tubulointerstitium (Tanimizu et al., 2023).

Interestingly, all R163P carriers identified to date are from Eastern Japan where the mutation is relatively common in LPG patients (Toyota et al., 2013, Saito et al., 2020). Genetic analysis of the families studied by Toyota and colleagues, including nine ostensibly unrelated pedigrees, indicated R163P may have been inherited from a common ancestor. The authors found that the APOE sequences of mutation carriers were identical at 26 single nucleotide polymorphisms; in other words, all carriers had the same APOE haplotype, including the common APOE3 allele. This suggests a “founder effect” in which the R163P mutation has been passed along in a population derived from a small ancestral group. Indeed, even in a nearby region west of Sendai, R163P was absent from 418 patients with kidney disease and 2,023 controls. In addition, the variant was absent from the gnomAD variant database (v2.1.1, May 2022).

Biological Effect

The low penetrance of several LPG-associated variants has often made it difficult to establish their contribution to disease. For R163P, mouse models have provided informative clues. Ishigaki and colleagues showed that expressing R163 in mice produced LPG-like deposits in kidney glomeruli (Ishigaki et al., 2000). Six days after injecting viral vectors carrying the mutant human gene into Apoe knockout mice, the authors observed characteristic LPG aggregates which lasted at least 60 days. Although a subsequent report showed that Apoe knockout mice spontaneously develop an LPG-like phenotype with age (Wen et al., 2002), a detailed comparison between the two pathologies revealed important differences (Ishimura et al., 2009). The enlarged lumina of mice expressing the mutant protein contained mostly lipids and lipoproteins appearing as round droplets in electron micrographs, whereas those of aged knockout mice were fibrillar and protein-rich.

Although some studies have provided clues on the effects of R163P on renal and vascular homeostasis, and the interaction between the two, open questions remain. Some studies have reported alterations in lipid blood levels that could lead to glomerular lesions, while others have reported local alterations in the glomeruli mediated by macrophages. It is possible that the combined effects explain the observed pathology (Saito et al., 2002).

The size of LPG deposits in R163P carriers appears to be influenced by plasma triglyceride levels; particularly by triglycerides in very low-density lipoprotein (VLDL) and high-density lipoprotein (HDL) particles (Saito et al., 1999). The authors suggested LPG aggregates may be smaller when these triglylceride-rich species are elevated and exacerbate protein leakage into the urine. In Ishigaki and co-workers’ viral mouse model, expression of the mutant protein resulted in high triglyceride levels in plasma, in addition to a partial correction of the hypercholesterolemia of Apoe knockout mice (Ishigaki et al., 2000). However, Wu and colleagues observed no triglyceride surge in a similar viral mouse model suggesting it is not required for LPG pathology (Wu et al., 2021). Also, Ito and colleagues reported that in mice that develop LPG-like pathology due to lack of the macrophage Fcγ receptors, expression of R163P actually reduced pathology compared with wildtype ApoE3 (Ito et al., 2012). Triglyceride levels were much higher in mice expressing wildtype ApoE3 than in those expressing R163P.

As reviewed by Saito and colleagues, ApoE expression by macrophages may be an important piece of the puzzle (Saito et al., 2020). In experiments in which mouse bone marrow was transduced with either APOE2, APOE3, or R163P on an APOE3 backbone, and transplanted into irradiated Apoe knockout mice, R163P reduced atherosclerosis better than ApoE2 and similarly to wildtype ApoE3 (Tavori et al., 2014). The authors concluded that macrophage expression of R163P protects against atherosclerosis while causing LPG. Other studies have shown that macrophages produce a small amount of ApoE, which may be important for the suppression of hyperlipidemia and atherosclerosis (Fazio et al., 2002, Dove et al., 2005).

ApoE3 carrying the R163P binds less effectively to low-density lipoprotein (LDL) receptors than wildtype ApoE3 (Ishigaki et al., 2000, Hoffman et al., 2001). Using recombinant ApoE complexed to phospholipid vesicles and VLDL particles from a patient with an ApoE deficiency, Hoffman and colleagues found that the mutant protein’s binding was less than 5 percent that of ApoE3. Interestingly, heparin binding was 66 percent that of ApoE3. This relatively moderate effect is unexpected because R163 is thought to be critical for heparin binding in the receptor-binding region (Weisgraber et al., 1986, Libeu et al., 2001, Dong et al., 2001). Hoffman and colleagues suggested this may explain the mutation’s incomplete penetrance (Hoffman et al., 2001). Of note, the distribution of the mutant protein among the major plasma lipoprotein fractions was similar to that of ApoE3 and ApoE2. 

R163P has long been suspected to alter ApoE structure by disrupting the fourth α-helix of the N-terminal domain where it resides (Oikawa et al., 1997). Proline residues kink the helix axis, acting as helix breakers in globular proteins. A detailed biochemical analysis indicated that, indeed, R163P appears to reduce helical content (Georgiadou et al., 2013). In addition, it was reported to increase exposure of hydrophobic residues to the surrounding solvent, and thermodynamically destabilize ApoE’s structure, likely disrupting its oligomerization properties, and making it prone to aggregation and more susceptible to proteases (Georgiadou et al., 2013, Stratikos and Chroni 2013). Although the mutant protein is able to form discoidal particles that appear normal, a subpopulation was larger and misshapen. The authors hypothesized the mutation induces a generalized unfolding of the N-terminal domain.

Also of note, R163 has been predicted to engage in several long-range interactions that may be important to ApoE's' 3D structure. An NMR study of an ApoE3-like construct harboring five mutations to keep it from aggregating, suggested R163 interacts with Q59 (Chen et al., 2011), and a study using FRET and computational simulations to analyze monomeric ApoE4 predicted interactions with E27 and E45 when the C-terminal domain is undocked from the N-terminal helix bundle, a form suspected to enable lipid binding (Stuchell-Brereton et al., 2023).

R163 may also play a role in the formation of ApoE dimers which adopt different conformations in an isoform-dependent manner (Nemergut et al., 2023). Interestingly, a metabolite of the AD drug candidate ALZ-801 was observed to interact with several amino acids involved in dimerization, including R163, possibly decreasing the stability of ApoE4 V-shaped dimers.

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).

Research models

As described above, R163P has been introduced via viral transduction into Apoe knockout mice. Within a few days, these mice develop LPG-like pathology (Ishigaki et al., 2000, Wu et al., 2021).

Note on nomenclature

This variant is sometimes referred to as ApoE2 Sendai because it was identified in Sendai, Japan and its migration pattern upon isoelectric focusing is similar to that of the common ApoE2 isoform.

Comments

No Available Comments

Make a Comment

To make a comment you must login or register.

References

Mutations Citations

1. APOE R176C (ApoE2)
2. APOE E21K
3. APOE C130R (ApoE4)

Therapeutics Citations

1. ALZ-801

Paper Citations

1. Saito T, Matsunaga A, Fukunaga M, Nagahama K, Hara S, Muso E. Apolipoprotein E-related glomerular disorders. Kidney Int. 2020 Feb;97(2):279-288. Epub 2019 Nov 22 PubMed.
2. Oikawa S, Matsunaga A, Saito T, Sato H, Seki T, Hoshi K, Hayasaka K, Kotake H, Midorikawa H, Sekikawa A, Hara S, Abe K, Toyota T, Jingami H, Nakamura H, Sasaki J. Apolipoprotein E Sendai (arginine 145-->proline): a new variant associated with lipoprotein glomerulopathy. J Am Soc Nephrol. 1997 May;8(5):820-3. PubMed.
3. Oikawa S, Suzuki N, Sakuma E, Saito T, Namai K, Kotake H, Fujii Y, Toyota T. Abnormal lipoprotein and apolipoprotein pattern in lipoprotein glomerulopathy. Am J Kidney Dis. 1991 Nov;18(5):553-8. PubMed.
4. Saito T, Matsunaga A, Ito K, Nakashima H. Topics in lipoprotein glomerulopathy: an overview. Clin Exp Nephrol. 2014 Apr;18(2):214-7. Epub 2013 Oct 23 PubMed.
5. Li MS, Li Y, Liu Y, Zhou XJ, Zhang H. An Updated Review and Meta Analysis of Lipoprotein Glomerulopathy. Front Med (Lausanne). 2022;9:905007. Epub 2022 May 6 PubMed.
6. Tanimizu H, Hara R, Sekine A, Inoue N, Hasegawa E, Tanaka K, Kono K, Kinowaki K, Ohashi K, Okubo M, Yamaguchi Y, Kang D, Honda K, Saito T, Sawa N, Ubara Y, Hoshino J. Apolipoprotein E-associated Lipoprotein Glomerulo-tubulopathy. Intern Med. 2023;62(15):2209-2214. Epub 2023 Aug 1 PubMed.
7. Toyota K, Hashimoto T, Ogino D, Matsunaga A, Ito M, Masakane I, Degawa N, Sato H, Shirai S, Umetsu K, Tamiya G, Saito T, Hayasaka K. A founder haplotype of APOE-Sendai mutation associated with lipoprotein glomerulopathy. J Hum Genet. 2013 May;58(5):254-8. Epub 2013 Feb 14 PubMed.
8. Ishimura A, Watanabe M, Nakashima H, Ito K, Miyake K, Mochizuki S, Ishigaki Y, Saito T. Lipoprotein glomerulopathy induced by ApoE-Sendai is different from glomerular lesions in aged apoE-deficient mice. Clin Exp Nephrol. 2009 Oct;13(5):430-437. Epub 2009 May 21 PubMed.
9. Takasaki S, Matsunaga A, Joh K, Saito T. A case of lipoprotein glomerulopathy with a rare apolipoprotein E isoform combined with neurofibromatosis type I. CEN Case Rep. 2018 May;7(1):127-131. Epub 2018 Jan 22 PubMed.
10. Ishigaki Y, Oikawa S, Suzuki T, Usui S, Magoori K, Kim DH, Suzuki H, Sasaki J, Sasano H, Okazaki M, Toyota T, Saito T, Yamamoto TT. Virus-mediated transduction of apolipoprotein E (ApoE)-sendai develops lipoprotein glomerulopathy in ApoE-deficient mice. J Biol Chem. 2000 Oct 6;275(40):31269-73. PubMed.
11. Wen M, Segerer S, Dantas M, Brown PA, Hudkins KL, Goodpaster T, Kirk E, LeBoeuf RC, Alpers CE. Renal injury in apolipoprotein E-deficient mice. Lab Invest. 2002 Aug;82(8):999-1006. PubMed.
12. Saito T, Ishigaki Y, Oikawa S, Yamamoto TT. Etiological significance of apolipoprotein E mutations in lipoprotein glomerulopathy. Trends Cardiovasc Med. 2002 Feb;12(2):67-70. PubMed.
13. Saito T, Oikawa S, Sato H, Sato T, Ito S, Sasaki J. Lipoprotein glomerulopathy: significance of lipoprotein and ultrastructural features. Kidney Int Suppl. 1999 Jul;71:S37-41. PubMed.
14. Wu H, Yang J, Liu YQ, Lei S, Yang M, Yang Z, Yang Y, Hu Z. Lipoprotein glomerulopathy induced by ApoE Kyoto mutation in ApoE-deficient mice. J Transl Med. 2021 Mar 4;19(1):97. PubMed.
15. Ito K, Nakashima H, Watanabe M, Ishimura A, Miyahara Y, Abe Y, Yasuno T, Ifuku M, Sasatomi Y, Saito T. Macrophage impairment produced by Fc receptor gamma deficiency plays a principal role in the development of lipoprotein glomerulopathy in concert with apoE abnormalities. Nephrol Dial Transplant. 2012 Oct;27(10):3899-907. Epub 2012 Aug 3 PubMed.
16. Tavori H, Fan D, Giunzioni I, Zhu L, Linton MF, Fogo AB, Fazio S. Macrophage-derived apoESendai suppresses atherosclerosis while causing lipoprotein glomerulopathy in hyperlipidemic mice. J Lipid Res. 2014 Oct;55(10):2073-81. Epub 2014 Sep 2 PubMed.
17. Fazio S, Babaev VR, Burleigh ME, Major AS, Hasty AH, Linton MF. Physiological expression of macrophage apoE in the artery wall reduces atherosclerosis in severely hyperlipidemic mice. J Lipid Res. 2002 Oct;43(10):1602-9. PubMed.
18. Dove DE, Linton MF, Fazio S. ApoE-mediated cholesterol efflux from macrophages: separation of autocrine and paracrine effects. Am J Physiol Cell Physiol. 2005 Mar;288(3):C586-92. Epub 2004 Oct 27 PubMed.
19. Hoffmann MM, Scharnagl H, Panagiotou E, Banghard WT, Wieland H, März W. Diminished LDL receptor and high heparin binding of apolipoprotein E2 Sendai associated with lipoprotein glomerulopathy. J Am Soc Nephrol. 2001 Mar;12(3):524-530. PubMed.
20. Weisgraber KH, Rall SC Jr, Mahley RW, Milne RW, Marcel YL, Sparrow JT. Human apolipoprotein E. Determination of the heparin binding sites of apolipoprotein E3. J Biol Chem. 1986 Feb 15;261(5):2068-76. PubMed.
21. 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.
22. Dong J, Peters-Libeu CA, Weisgraber KH, Segelke BW, Rupp B, Capila I, Hernáiz MJ, LeBrun LA, Linhardt RJ. Interaction of the N-terminal domain of apolipoprotein E4 with heparin. Biochemistry. 2001 Mar 6;40(9):2826-34. PubMed.
23. Georgiadou D, Stamatakis K, Efthimiadou EK, Kordas G, Gantz D, Chroni A, Stratikos E. Thermodynamic and structural destabilization of apoE3 by hereditary mutations associated with the development of lipoprotein glomerulopathy. J Lipid Res. 2013 Jan;54(1):164-76. Epub 2012 Oct 30 PubMed.
24. Stratikos E, Chroni A. A possible structural basis behind the pathogenic role of apolipoprotein E hereditary mutations associated with lipoprotein glomerulopathy. Clin Exp Nephrol. 2014 Apr;18(2):225-9. Epub 2013 Oct 23 PubMed.
25. Chen J, Li Q, Wang J. Topology of human apolipoprotein E3 uniquely regulates its diverse biological functions. Proc Natl Acad Sci U S A. 2011 Sep 6;108(36):14813-8. Epub 2011 Aug 22 PubMed.
26. Stuchell-Brereton MD, Zimmerman MI, Miller JJ, Mallimadugula UL, Incicco JJ, Roy D, Smith LG, Cubuk J, Baban B, DeKoster GT, Frieden C, Bowman GR, Soranno A. Apolipoprotein E4 has extensive conformational heterogeneity in lipid-free and lipid-bound forms. Proc Natl Acad Sci U S A. 2023 Feb 14;120(7):e2215371120. Epub 2023 Feb 7 PubMed.
27. Nemergut M, Marques SM, Uhrik L, Vanova T, Nezvedova M, Gadara DC, Jha D, Tulis J, Novakova V, Planas-Iglesias J, Kunka A, Legrand A, Hribkova H, Pospisilova V, Sedmik J, Raska J, Prokop Z, Damborsky J, Bohaciakova D, Spacil Z, Hernychova L, Bednar D, Marek M. Domino-like effect of C112R mutation on ApoE4 aggregation and its reduction by Alzheimer's Disease drug candidate. Mol Neurodegener. 2023 Jun 6;18(1):38. PubMed.

Further Reading

No Available Further Reading