Overview

Pathogenicity: Alzheimer's Disease : Pathogenic, ALS-FTD : Not Classified
ACMG/AMP Pathogenicity Criteria: PS3, PM1, PM2, PM5, PM6, PP2, PP3
Clinical Phenotype: Alzheimer's Disease, Spastic Paraparesis
Reference Assembly: GRCh37/hg19
Position: Chr14:73653577 T>C
dbSNP ID: rs63750265
Coding/Non-Coding: Coding
DNA Change: Substitution
Expected RNA Consequence: Substitution
Expected Protein Consequence: Missense
Codon Change: CTT to CCT
Reference Isoform: PSEN1 Isoform 1 (467 aa)
Genomic Region: Exon 6
Research Models: 4

Findings

This mutation is associated with very early disease onset and a variable phenotype. It was first reported in a woman with familial Alzheimer's disease (AD) who developed secondary generalized seizures at age 15, major depression at age 19, and memory impairment by age 24. Ataxia and spastic paraparesis were recorded by age 27, and moderate-stage dementia by 28. Dementia, ataxia, and spasticity progressed until death at age 35. Family history details were not reported (Moehlmann et al., 2002). The mutation was also found in a Korean man who developed a variant of AD with progressive memory impairment, dysarthria, and spastic paraparesis at age 23 (Lyoo et al., 2016). The mutation was suspected to have arisen de novo, although paternity was not confirmed. 

In addition, this variant was reported in three members of a family with primary lateral sclerosis (PLS), a progressive upper motor disorder sometimes classified as a form of amyotrophic lateral sclerosis (ALS) (Vázquez-Costa et al., 2021). Mild cognitive and behavioral symptoms appeared years after the motor symptoms. The proband progressed toward akinetic mutism, suggesting that severe dementia might appear late in the disease course. Both of the proband's children were affected, but his parents were healthy, suggesting the mutation might have arisen de novo in the proband. The father was not genotyped, however. 

The variant was absent from the gnomAD variant database (gnomAD v2.1.1, June 2021).

Neuropathology

Postmortem examination of the original proband’s brain revealed numerous Aβ-positive neuritic and cotton-wool plaques throughout the cerebral cortex. Aβ-positive amyloid cores were abundant in the cerebellar cortex (Moehlmann et al., 2002). In the second individual, robust amyloid pathology was observed in the striatum and cerebellum, and asymmetric tau pathology in the primary sensorimotor cortex contralateral to the side most affected by spasticity (Lyoo et al., 2016).

In one patient with PLS, FDG-PET showed hypometabolism in both anterior temporal lobes, pre- and post-central gyri, and cerebellum, a pattern that was not characteristic of either AD or PLS (Vázquez-Costa et al., 2021). MRI revealed microbleeds suggestive of amyloid angiopathy. Of note, 18F-flutemetamol PET showed widespread amyloid deposition in the brain, except in hypometabolic areas, suggesting amyloid may not be responsible for the observed symptoms.

Biological Effect

When expressed in different types of cultured cells, this mutation impaired the carboxypeptidase-like γ-cleavage, but spared the endoproteolytic ε-cleavage of APP. This resulted in reduced intracellular and secreted levels of Aβ40 and an increased Aβ42/Aβ40 ratio (Bentahir 2006; Koch et al., 2012;Li et al., 2016; Sannerud et al., 2016). An elevated Aβ42/Aβ40 ratio was also reported in neurons derived from induced pluripotent stem cells (iPSCs), which showed decreased total Aβ production and elevated levels of Aβ42 and Aβ43 in culture supernatants (Kwart et al., 2019, Aug 2019 news). Increased levels of Aβ42 and Aβ43 were also reported in HEK293 cells stably overexpressing Swedish (sw) mutant APP in combination with the mutant protein (Trambauer et al., 2020). In vitro experiments using isolated proteins are mostly consistent with these findings, revealing an increased Aβ42/Aβ40 ratio and  decreased production of Aβ42, Aβ40 and the APP intracellular domain (Winkler et al., 2009; Cacquevel et al., 2012; Sun et al., 2017). The mutation also reduced the endoproteolytic ε-cleavage of N-cadherin and Notch (Moehlmann et al., 2002; Bentahir et al., 2006; Sannerud et al., 2016), but not that of presenilin (Trambauer et al., 2020). 

A more detailed assesment of the activity of this mutant showed it decreases γ-secretase efficiency by 75 percent for both Notch and APP, reducing global production of Aβ38, Aβ40, Aβ42, and Aβ43 peptides (Chávez-Gutiérrez et al., 2012).  Sizeable reductions in the Aβ38/Aβ42 and Aβ40/Aβ43 ratios were observed, both in cells and in vitro. Interestingly, the levels of the shorter peptides, Aβ40 and Aβ38, were particularly decreased, while those of longer peptides, greater than Aβ42, were increased. These data suggest impairment of the fourth γ-secretase cleavage in the Aβ production lines that sequentially digest Aβ49 and Aβ48 into shorter peptides. Moreover, in vitro experiments testing the mutant’s γ-secretase activity at different temperatures showed it increases enzyme-Aβn complex dissociation rates, enhancing the release of longer Aβ peptides (Szaruga et al., 2017). A mass spectrometry analysis of the tri- and tetra-peptides released by the mutant revealed decreased activity of the Aβ49 production line in particular (Li et al 2016). Moreover, another study suggested that a switch in Aβ43 generation from the Aβ49 to the Aβ48 production line may contribute to increasing Aβ43 levels which, together with decreasing Aβ40 production, may be key to determining AD age at onset (Kakuda et al., 2021). 

In addition to affecting Aβ peptide production, L166P promotes the accumulation of APP β-C-terminal fragments (β-CTFs) which appears to disrupt endosomes (Kwart et al., 2019, Aug 2019 news). Enlarged endosomes and altered expression of genes involved in endocytic vesicle pathways were observed in iPSC-derived neurons. This phenotype correlated with β-CTF, but not Aβ, levels.

Insight into how the mutant disrupts PSEN1 conformation has been obtained from fluorescence lifetime imaging microscopy (Berezovska et al., 2005) and Förster resonance energy transfer experiments (Uemura et al., 2009). In addition, studies using APP substrates with photosensitive cross-linkable amino acids revealed the mutant causes mispositioning of the APP C99 cleavage domain (Fukumori and Steiner, 2016; Trambauer et al., 2020). In particular, altered cross-linking at T48 and L49, the initial substrate cleavage sites of C99, was observed. The authors suggested this could affect interactions whose strength play a key role in the carboxy‐terminal trimming pathway and the generation of pathogenic longer Aβ species. Also of note, a cryo-electron microscopy study of the atomic structure of γ-secretase bound to an APP fragment indicates this residue is apposed to the APP transmembrane helix, with its side-chain reaching towards the interior of the substrate-binding pore (Zhou et al., 2019; Jan 2019 news).

PSEN1 L166P may also have a dominant-negative effect on wild-type PSEN1 as suggested by the suppression of Aβ production by wild-type PSEN1 in the presence of the mutant protein in vitro. The effect was specifically sensitive to a detergent that disrupts PSEN1 oligomerization, indicating the mutant may disrupt wild-type activity via hetero-oligomerization (Zhou et al., 2017).

L166P may also disrupt other cellular functions relevant to AD. Interestingly, PSEN1 was reported to play a key role in ApoE secretion and cytosolic localization. In experiments with PSEN-deficient fibroblasts, L166P transfection was less able to rescue these functions compared with transfection of wildtype PSEN1 (Islam et al., 2022). This mutant was also reported to abolish PSEN1's activity as a calcium leak channel in the endoplasmic reticulum (Nelson et al., 2007), and caused PSEN1 to localize to endolysosomal compartments, similar to the distribution of PSEN2 (Sannerud et al., 2016; see May 2016 news).

Several in silico algorithms (SIFT, Polyphen-2, LRT, MutationTaster, MutationAssessor, FATHMM, PROVEAN, CADD, REVEL, and Reve in the VarCards database) predicted this variant is damaging (Xiao et al., 2021).

Pathogenicity

Alzheimer's Disease : Pathogenic

This variant fulfilled the following criteria based on the ACMG/AMP guidelines. See a full list of the criteria in the Methods page.

Research Models

This mutation has been introduced into mouse models including the double transgenic model, APPPS1, which also expresses APP with the Swedish mutation, and the APP+PS1 transgenic rat, which expresses human APP with the Swedish and Indiana mutations. In addition, the mutation has been inserted in mice expressing the APP Swedish mutation and lacking the Trem2 gene, Trem2 KO (KOMP) x APPPS1, as well as in mice expressing the APP Swedish mutation and a R47H variant of the Trem2 gene, Trem2 R47H KI (Lamb/Landreth) X APPPS1-21.

An iPSC line carrying this mutation has been created using CRISPR technology (Kwart et al., 2019). It is part of a collection of isogenic iPSCs carrying familial AD mutations.

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References

Research Models Citations

1. APPPS1
2. APP+PS1
3. Trem2 KO (KOMP) x APPPS1
4. Trem2 R47H KI (Lamb/Landreth) X APPPS1-21

News Citations

1. Familial AD Mutations, β-CTF, Spell Trouble for Endosomes 16 Aug 2019
2. CryoEM γ-Secretase Structures Nail APP, Notch Binding 11 Jan 2019
3. Lodged in Late Endosomes, Presenilin 2 Churns Out Intraneuronal Aβ 10 Jun 2016

Paper Citations

1. Kwart D, Gregg A, Scheckel C, Murphy EA, Paquet D, Duffield M, Fak J, Olsen O, Darnell RB, Tessier-Lavigne M. A Large Panel of Isogenic APP and PSEN1 Mutant Human iPSC Neurons Reveals Shared Endosomal Abnormalities Mediated by APP β-CTFs, Not Aβ. Neuron. 2019 Oct 23;104(2):256-270.e5. Epub 2019 Aug 12 PubMed.
2. Moehlmann T, Winkler E, Xia X, Edbauer D, Murrell J, Capell A, Kaether C, Zheng H, Ghetti B, Haass C, Steiner H. Presenilin-1 mutations of leucine 166 equally affect the generation of the Notch and APP intracellular domains independent of their effect on Abeta 42 production. Proc Natl Acad Sci U S A. 2002 Jun 11;99(12):8025-30. PubMed.
3. Lyoo CH, Cho H, Choi JY, Hwang MS, Hong SK, Kim YJ, Ryu YH, Lee MS. Tau Accumulation in Primary Motor Cortex of Variant Alzheimer's Disease with Spastic Paraparesis. J Alzheimers Dis. 2016;51(3):671-5. PubMed.
4. Bentahir M, Nyabi O, Verhamme J, Tolia A, Horré K, Wiltfang J, Esselmann H, De Strooper B. Presenilin clinical mutations can affect gamma-secretase activity by different mechanisms. J Neurochem. 2006 Feb;96(3):732-42. PubMed.
5. Koch P, Tamboli IY, Mertens J, Wunderlich P, Ladewig J, Stüber K, Esselmann H, Wiltfang J, Brüstle O, Walter J. Presenilin-1 L166P mutant human pluripotent stem cell-derived neurons exhibit partial loss of γ-secretase activity in endogenous amyloid-β generation. Am J Pathol. 2012 Jun;180(6):2404-16. PubMed.
6. Li N, Liu K, Qiu Y, Ren Z, Dai R, Deng Y, Qing H. Effect of Presenilin Mutations on APP Cleavage; Insights into the Pathogenesis of FAD. Front Aging Neurosci. 2016;8:51. Epub 2016 Mar 11 PubMed.
7. Sannerud R, Esselens C, Ejsmont P, Mattera R, Rochin L, Tharkeshwar AK, De Baets G, De Wever V, Habets R, Baert V, Vermeire W, Michiels C, Groot AJ, Wouters R, Dillen K, Vints K, Baatsen P, Munck S, Derua R, Waelkens E, Basi GS, Mercken M, Vooijs M, Bollen M, Schymkowitz J, Rousseau F, Bonifacino JS, Van Niel G, De Strooper B, Annaert W. Restricted Location of PSEN2/γ-Secretase Determines Substrate Specificity and Generates an Intracellular Aβ Pool. Cell. 2016 Jun 30;166(1):193-208. Epub 2016 Jun 9 PubMed.
8. Trambauer J, Rodríguez Sarmiento RM, Fukumori A, Feederle R, Baumann K, Steiner H. Aβ43-producing PS1 FAD mutants cause altered substrate interactions and respond to γ-secretase modulation. EMBO Rep. 2020 Jan 7;21(1):e47996. Epub 2019 Nov 25 PubMed.
9. Winkler E, Hobson S, Fukumori A, Dümpelfeld B, Luebbers T, Baumann K, Haass C, Hopf C, Steiner H. Purification, pharmacological modulation, and biochemical characterization of interactors of endogenous human gamma-secretase. Biochemistry. 2009 Feb 17;48(6):1183-97. PubMed.
10. Cacquevel M, Aeschbach L, Houacine J, Fraering PC. Alzheimer's disease-linked mutations in presenilin-1 result in a drastic loss of activity in purified γ-secretase complexes. PLoS One. 2012;7(4):e35133. PubMed.
11. Sun L, Zhou R, Yang G, Shi Y. Analysis of 138 pathogenic mutations in presenilin-1 on the in vitro production of Aβ42 and Aβ40 peptides by γ-secretase. Proc Natl Acad Sci U S A. 2017 Jan 24;114(4):E476-E485. Epub 2016 Dec 5 PubMed.
12. Chávez-Gutiérrez L, Bammens L, Benilova I, Vandersteen A, Benurwar M, Borgers M, Lismont S, Zhou L, Van Cleynenbreugel S, Esselmann H, Wiltfang J, Serneels L, Karran E, Gijsen H, Schymkowitz J, Rousseau F, Broersen K, De Strooper B. The mechanism of γ-Secretase dysfunction in familial Alzheimer disease. EMBO J. 2012 May 16;31(10):2261-74. Epub 2012 Apr 13 PubMed.
13. Szaruga M, Munteanu B, Lismont S, Veugelen S, Horré K, Mercken M, Saido TC, Ryan NS, De Vos T, Savvides SN, Gallardo R, Schymkowitz J, Rousseau F, Fox NC, Hopf C, De Strooper B, Chávez-Gutiérrez L. Alzheimer's-Causing Mutations Shift Aβ Length by Destabilizing γ-Secretase-Aβn Interactions. Cell. 2017 Jul 27;170(3):443-456.e14. PubMed. Correction.
14. Kakuda N, Takami M, Okochi M, Kasuga K, Ihara Y, Ikeuchi T. Switched Aβ43 generation in familial Alzheimer's disease with presenilin 1 mutation. Transl Psychiatry. 2021 Nov 3;11(1):558. PubMed.
15. Berezovska O, Lleo A, Herl LD, Frosch MP, Stern EA, Bacskai BJ, Hyman BT. Familial Alzheimer's disease presenilin 1 mutations cause alterations in the conformation of presenilin and interactions with amyloid precursor protein. J Neurosci. 2005 Mar 16;25(11):3009-17. PubMed.
16. Uemura K, Lill CM, Li X, Peters JA, Ivanov A, Fan Z, Destrooper B, Bacskai BJ, Hyman BT, Berezovska O. Allosteric modulation of PS1/gamma-secretase conformation correlates with amyloid beta(42/40) ratio. PLoS One. 2009;4(11):e7893. PubMed.
17. Fukumori A, Steiner H. Substrate recruitment of γ-secretase and mechanism of clinical presenilin mutations revealed by photoaffinity mapping. EMBO J. 2016 Aug 1;35(15):1628-43. Epub 2016 May 23 PubMed.
18. Zhou R, Yang G, Guo X, Zhou Q, Lei J, Shi Y. Recognition of the amyloid precursor protein by human γ-secretase. Science. 2019 Feb 15;363(6428) Epub 2019 Jan 10 PubMed.
19. Zhou R, Yang G, Shi Y. Dominant negative effect of the loss-of-function γ-secretase mutants on the wild-type enzyme through heterooligomerization. Proc Natl Acad Sci U S A. 2017 Nov 28;114(48):12731-12736. Epub 2017 Oct 9 PubMed.
20. Nelson O, Tu H, Lei T, Bentahir M, de Strooper B, Bezprozvanny I. Familial Alzheimer disease-linked mutations specifically disrupt Ca2+ leak function of presenilin 1. J Clin Invest. 2007 May;117(5):1230-9. Epub 2007 Apr 12 PubMed.
21. Xiao X, Liu H, Liu X, Zhang W, Zhang S, Jiao B. APP, PSEN1, and PSEN2 Variants in Alzheimer's Disease: Systematic Re-evaluation According to ACMG Guidelines. Front Aging Neurosci. 2021;13:695808. Epub 2021 Jun 18 PubMed.

External Citations

1. gnomAD v2.1.1
2. Aug 2019 news
3. Islam et al., 2022

Further Reading