Overview

Pathogenicity: Alzheimer's Disease : Pathogenic
ACMG/AMP Pathogenicity Criteria: PS3, PM1, PM2, PM4, PP1
Clinical Phenotype: Alzheimer's Disease
Position: (GRCh38/hg38):Chr21:25891856_25891854 GAA>---
Position: (GRCh37/hg19):Chr21:27264168_27264166 GAA>---
dbSNP ID: NA
Coding/Non-Coding: Coding
DNA Change: Deletion
Expected RNA Consequence: Deletion
Expected Protein Consequence: Deletion
Codon Change: GAA to ---
Reference Isoform: APP Isoform APP770 (770 aa)
Genomic Region: Exon 17
Research Models: 1

Findings

This in-frame microdeletion has been identified in at least three families from Japan. It appears to be recessive and pathogenic only in the homozygous state. However, it is also possible that the absence of disease in the relatively small number of known heterozygous carriers is due to incomplete penetrance.

The largest pedigree consists of seven affected individuals over two generations (Tomiyama et al., 2008). DNA was available from two affected family members and both were homozygous for the deletion. The proband of this kindred was a 62-year-old woman who developed memory impairment at age 55. She later developed cerebellar ataxia, gait disturbance, and pyramidal signs, such as an abnormal Babinski reflex. She was diagnosed with AD at age 59 and had severe dementia by age 62. Her sister developed AD at age 59. DNA was not available from a third affected sister. Two heterozygous sisters were unaffected at age 56 and 65. No mutations were found in PSEN1 or PSEN2.

The authors subsequently screened 5,310 Japanese people with and without AD and found another homozygous individual who had developed AD at age 36. Unlike the proband in the previously described kindred, this individual did not have cerebellar ataxia or pyramidal signs, suggesting these may not be obligatory phenotypes of E693del. The screen also turned up two individuals who were heterozygous carriers. One individual had mild cognitive impairment at age 81 and the other was cognitively healthy at age 64. 

More recently, three siblings from an isolated island in Japan were found to be homozygous for this microdeletion (Kutoku et al., 2015). Their parents were first-degree cousins and cognitively healthy. The proband developed short-term memory impairment at age 35. She was diagnosed with AD at age 42 based on progressive cognitive impairment and spatial disorientation. Later she developed difficulty walking due to spastic paraparesis in her lower limbs. Her brother and sister developed similar symptoms but had a slightly milder clinical course. They developed symptoms at age 59 and 44 respectively, with spastic paraparesis setting in at ages 66 and 58. All three affected siblings ultimately became mute. An unaffected sibling was found to be a heterozygous carrier of the deletion.

This mutation was absent from the gnomAD variant database (v2.1.1, Oct 2021).

Neuropathology

Postmortem analysis is not available for affected individuals carrying the E693Δ mutation; however, imaging studies have shown an unusually low amyloid signal by PiB-PET, and only mild atrophy considering the degree of cognitive impairment (Tomiyama et al., 2008; Shimada et al., 2011). In a putative unrelated kindred, a similar absence of amyloid deposition was revealed by PiB-PET, despite severe dementia. MRI showed generalized brain atrophy and FDG-PET showed severe impairment of glucose uptake. Analysis of cerebral spinal fluid showed low levels of overall Aβ, but elevated levels of high molecular weight species, presumably Aβ oligomers (Kutoku et al., 2015). Whether the low amyloid PET signal is due to a lack of amyloid fibrils, or to fibrils with an unusual structure poorly detected by PET remains uncertain (see Biological Effects below).

In contrast to the low Aβ signal, tau PET signal was high, at least in one carrier (Shimada et al., 2020). Increased tau accumulation was found in the cerebellum and latero-temporal and parietal cortices compared with patients suffering from sporadic AD. Tau was also elevated in the frontal cortex, posterior cingulate gyrus, and precuneus compared with healthy controls.

Biological Effect

This mutation involves the deletion of the entire 693 codon, which is located within the Aβ sequence of APP. The Aβ peptides produced from this mutant APP lack glutamate at position 22, and are therefore called E22delta or E22Δ. 

Multiple alterations have been associated with this mutation. Initial studies found that mutant Aβ42 injected intraventricularly into rat brains inhibited hippocampal LTP more potently than wild-type Aβ42 (Tomiyama et al., 2008) and the presynaptic marker synaptophysin was decreased in hippocampal slices exposed to the mutant peptide (Takuma et al., 2008). Subsequently, mice expressing E693Δ were reported to develop cognitive impairment, synaptic deficits, neuronal loss, glial activation, and tau hyperphosphorylation (Tomiyama et al., 2010, Apr 2010 news, Umeda et al., 2014 , Kulic et al., 2012, Umeda et al., 2017). One study examining transgenic hippocampal slices failed to identify damaging effects (Tackenberg et al., 2020), but the authors noted this may be due to the slices being derived from very young animals.

Loss of APP function resulting in decreased GABAergic neurons has been proposed as an explanation for this mutation’s recessive pattern of inheritance (Umeda et al., 2017, Tomiyama and Shimada, 2020). Decreased inhibitory activity in the dentate gyrus was hypothesized as triggering a cascade of alterations, including accelerated Aβ oligomerization.

Multiple studies in cultured cells have shed light on the mutation’s damaging effects. Some studies have shown that although E22Δ Aβ peptides are not cytotoxic to human and rodent cultured neurons, they induce synaptic alterations and toxic radical formation (Takuma et al., 2008, Suzuki et al., 2010), Another study reported Aβ40 E22Δ was neurotoxic in rat primary neuron compared with wildtype Aβ40, while Aβ42 E22Δ was less toxic than wildtype Aβ42, but decreased neurite outgrowth (Ovchinnikova et al., 2011). 

Furthermore, the Osaka mutation has been reported to alter the production, secretion, localization, and clearance of Aβ peptides. Experiments in transfected cells indicate this mutation increases both β- and γ-cleavage of APP, but Aβ secretion is reduced, with the cells accumulating Aβ peptides intracellularly (Tomiyama et al., 2008, Nishitsuji et al., 2009). The accumulation of oligomers in the endoplasmic reticulum (ER), Golgi apparatus, endosomes, lysosomes, autophagosomes, and mitochondria suggests an impairment of APP/Aβ trafficking which may result in ER stress, endosomal/lysosomal impairment, and mitochondrial dysfunction leading to apoptosis (Nishitsuji et al., 2009, Umeda et al., 2011). Also, studies using patient iPSC-derived neurons showed intracellular accumulation of Aβ oligomers, ER and oxidative stress, as well as upregulation of autophagy-related protein ATG4A, with reduced autophagosome formation (Kondo et al., 2013, Feb 2013 news, Shirotani et al., 2023). The mutation also seems to confer increased molecular stability (Kassler et al., 2010, Inayathullah and Teplow 2011), as well as enhanced resistance to degradation by neprilysin and insulin-degrading enzyme (Tomiyama et al., 2008).

Insertion into, and destabilization of, cell membranes may contribute to E22Δ’s toxic effects (Jang et al., 2013, McKnelly et al., 2022). Of note, E693 lies within a cholesterol-binding site as determined by NMR resonance spectroscopy and site-directed mutagenesis (Barrett et al., 2012) and the Osaka mutation has been shown to impair intracellular cholesterol transport and efflux (Nomura et al., 2013).

Whether E22Δ forms extracellular amyloid fibrils in vivo like other APP familial mutants do and, if so, whether they are involved in mediating E22Δ toxicity, remains controversial. Tomiyama and colleagues first reported that E22Δ accelerates oligomerization, without causing fibrillization, in vitro (Tomiyama et al., 2008). They subsequently reported that transgenic mice expressing E693del accumulated toxic intraneuronal Aβ oligomers starting at eight months, without developing amyloid deposits, even at 24 months of age (Tomiyama et al., 2010). The authors proposed that the Osaka mutation supported the hypothesis that Aβ oligomers alone, in the absence of amyloid fibrils, disrupt synaptic function and cause cognitive impairment (Nov 2007 conference news, Tomiyama and Shimada, 2020). Moreover, in transgenic mice expressing the Osaka mutation together with the K670_M671delinsNL (Swedish), Kulic and colleagues also found intraneuronal accumulation of Aβ oligomers associated with cognitive impairment and no amyloid plaque deposition up to 15 months of age (Kulic et al., 2012). 

In juxtaposition to these findings, E22Δ peptides have been observed to readily assemble into amyloid fibrils in multiple in vitro studies (Inayathullah and Teplow 2011, Ovchinnikova et al., 2011, Cloe et al., 2011, Schütz et al., 2015, Poduslo and Howell, 2015, Huber et al., 2015, Elkins et al., 2016, Hatami et al., 2017, Murakami et al., 2020, Hayward and Kitao, 2021, Seuma et al., 2022). These studies have shown E22Δ aggregates very rapidly, forming fibrils rich in β-sheet structure that are distinct from wildtype Aβ fibrils, as well as from aggregates formed by Aβ peptides carrying other familial AD mutations. Although in some studies the E22Δ structures had a particularly high affinity for thioflavin T, an indicator of β-sheet conformation in amyloid fibrils (e.g., Suzuki et al., 2010, Ovchinnikova et al., 2011, Inayathullah and Teplow 2011), in others the affinity was very low (Tomiyama et al., 2008, Hatami et al., 2017). Tomiyama and colleagues found no amyloid fibrils upon examination under the electron microscope, but Hatami and colleagues reported fibrillar bundles forming dense networks, as well as individual amyloid fibrils and amorphous structures, despite their negative thioflavin T findings (Hatami et al., 2017). 

An NMR study of the structure of E22Δ Aβ40 revealed highly ordered, structurally stable fibrils (Schütz et al., 2015, Amyloid Atlas). Although a computational model of fibril formation did not resemble this structure, it suggested a mechanism by which E22Δ Aβ exposes amino acids that are buried in the wildtype peptide, enabling the interlocking of side chains to bring protofilaments together and form protofibrils (Hayward and Kitao, 2021).

How in vitro generated fibrils compare to in vivo structures remains uncertain. It is possible they are similar or identical, but are poorly detected by amyloid PET because of their unusual structure (e.g., Hatami et al., 2017). Alternatively, the in vitro fibrils may be artifactual due to non-physiological conditions, including the use of synthetic peptides (Tomiyama and Shimada, 2020). Adding to the difficulty of discerning between these possibilities, mutant Aβ oligomers have been reported to have some of the same characteristics as fibrils, including insolubility, β-sheet conformation, and fibrillar structure (Suzuki et al., 2010, Tomiyama and Shimada, 2020). Also of note, one of the transgenic mouse models which had intracellular oligomers but no amyloid deposits, did eventually develop CAA-like extracellular amyloid fibrils surrounding blood vessels, as assessed at 24 months of age (Kulic et al., 2012).

Interestingly, some studies have suggested E22Δ peptides may affect the aggregation of other Aβ peptides. Cloe and colleagues, for example, reported mutant Aβ40 induced the prion-like conversion of wildtype Aβ40 into atypical fibrils (Cloe et al., 2011). Another study suggested E22Δ Aβ42 is deficient at seeding wild-type Aβ aggregation (Kulic et al., 2012). This study also reported an inhibitory effect of E22Δ Aβ42 on E22Δ Aβ40 fibrillogenesis. On its own, E22Δ Aβ42 had minimal ability to mediate nucleation and fibril growth.

Pathogenicity

Alzheimer's Disease : Pathogenic*

*This variant appears to be recessive or have incomplete penetrance.

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

A transgenic mouse model containing APP with the E693del mutation has been developed. APP(OSK)-Tg mice exhibit intraneuronal Aβ oligomers and memory impairment as early as 8 months of age (Tomiyama et al., 2010; Umeda et al., 2012, Takano et al., 2012). In addition, mice expressing wildtype human tau in addition to the APP E693del mutation have been generated (Umeda et al., 2014), a transgenic mouse model expressing the Osaka mutation together with the K670_M671delinsNL (Swedish) (Kulic et al., 2012), and a knockin mouse (Umeda et al., 2017).

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References

News Citations

1. New APP Model: No Plaques—Plenty of Pathology 9 Apr 2010
2. Aβ Oligomers Linked to ER Stress in Patient-Derived Neurons 22 Feb 2013
3. San Diego: Oligomers Live Up to Bad Reputation, Part 2 19 Nov 2007

Paper Citations

1. Tomiyama T, Matsuyama S, Iso H, Umeda T, Takuma H, Ohnishi K, Ishibashi K, Teraoka R, Sakama N, Yamashita T, Nishitsuji K, Ito K, Shimada H, Lambert MP, Klein WL, Mori H. A mouse model of amyloid beta oligomers: their contribution to synaptic alteration, abnormal tau phosphorylation, glial activation, and neuronal loss in vivo. J Neurosci. 2010 Apr 7;30(14):4845-56. PubMed.
2. Umeda T, Tomiyama T, Kitajima E, Idomoto T, Nomura S, Lambert MP, Klein WL, Mori H. Hypercholesterolemia accelerates intraneuronal accumulation of Aβ oligomers resulting in memory impairment in Alzheimer's disease model mice. Life Sci. 2012 Jan 17; PubMed.
3. Takano M, Maekura K, Otani M, Sano K, Nakamura-Hirota T, Tokuyama S, Min KS, Tomiyama T, Mori H, Matsuyama S. Proteomic analysis of the brain tissues from a transgenic mouse model of amyloid β oligomers. Neurochem Int. 2012 Aug;61(3):347-55. Epub 2012 May 23 PubMed.
4. Umeda T, Maekawa S, Kimura T, Takashima A, Tomiyama T, Mori H. Neurofibrillary tangle formation by introducing wild-type human tau into APP transgenic mice. Acta Neuropathol. 2014 May;127(5):685-98. Epub 2014 Feb 15 PubMed.
5. Kulic L, McAfoose J, Welt T, Tackenberg C, Späni C, Wirth F, Finder V, Konietzko U, Giese M, Eckert A, Noriaki K, Shimizu T, Murakami K, Irie K, Rasool S, Glabe C, Hock C, Nitsch RM. Early accumulation of intracellular fibrillar oligomers and late congophilic amyloid angiopathy in mice expressing the Osaka intra-Aβ APP mutation. Transl Psychiatry. 2012 Nov 13;2(11):e183. PubMed.
6. Umeda T, Kimura T, Yoshida K, Takao K, Fujita Y, Matsuyama S, Sakai A, Yamashita M, Yamashita Y, Ohnishi K, Suzuki M, Takuma H, Miyakawa T, Takashima A, Morita T, Mori H, Tomiyama T. Mutation-induced loss of APP function causes GABAergic depletion in recessive familial Alzheimer's disease: analysis of Osaka mutation-knockin mice. Acta Neuropathol Commun. 2017 Jul 31;5(1):59. PubMed.
7. Tomiyama T, Nagata T, Shimada H, Teraoka R, Fukushima A, Kanemitsu H, Takuma H, Kuwano R, Imagawa M, Ataka S, Wada Y, Yoshioka E, Nishizaki T, Watanabe Y, Mori H. A new amyloid beta variant favoring oligomerization in Alzheimer's-type dementia. Ann Neurol. 2008 Mar;63(3):377-87. PubMed.
8. Kutoku Y, Ohsawa Y, Kuwano R, Ikeuchi T, Inoue H, Ataka S, Shimada H, Mori H, Sunada Y. A second pedigree with amyloid-less familial Alzheimer's disease harboring an identical mutation in the amyloid precursor protein gene (E693delta). Intern Med. 2015;54(2):205-8. Epub 2015 Jan 15 PubMed.
9. Shimada H, Ataka S, Tomiyama T, Takechi H, Mori H, Miki T. Clinical course of patients with familial early-onset Alzheimer's disease potentially lacking senile plaques bearing the E693Δ mutation in amyloid precursor protein. Dement Geriatr Cogn Disord. 2011;32(1):45-54. PubMed.
10. Shimada H, Minatani S, Takeuchi J, Takeda A, Kawabe J, Wada Y, Mawatari A, Watanabe Y, Shimada H, Higuchi M, Suhara T, Tomiyama T, Itoh Y. Heavy Tau Burden with Subtle Amyloid β Accumulation in the Cerebral Cortex and Cerebellum in a Case of Familial Alzheimer's Disease with APP Osaka Mutation. Int J Mol Sci. 2020 Jun 22;21(12) PubMed.
11. Takuma H, Teraoka R, Mori H, Tomiyama T. Amyloid-beta E22Delta variant induces synaptic alteration in mouse hippocampal slices. Neuroreport. 2008 Apr 16;19(6):615-9. PubMed.
12. Tackenberg C, Kulic L, Nitsch RM. Familial Alzheimer's disease mutations at position 22 of the amyloid β-peptide sequence differentially affect synaptic loss, tau phosphorylation and neuronal cell death in an ex vivo system. PLoS One. 2020;15(9):e0239584. Epub 2020 Sep 23 PubMed.
13. Tomiyama T, Shimada H. APP Osaka Mutation in Familial Alzheimer's Disease-Its Discovery, Phenotypes, and Mechanism of Recessive Inheritance. Int J Mol Sci. 2020 Feb 19;21(4) PubMed.
14. Suzuki T, Murakami K, Izuo N, Kume T, Akaike A, Nagata T, Nishizaki T, Tomiyama T, Takuma H, Mori H, Irie K. E22Δ Mutation in Amyloid β-Protein Promotes β-Sheet Transformation, Radical Production, and Synaptotoxicity, But Not Neurotoxicity. Int J Alzheimers Dis. 2010 Dec 19;2011:431320. PubMed.
15. Ovchinnikova OY, Finder VH, Vodopivec I, Nitsch RM, Glockshuber R. The Osaka FAD mutation E22Δ leads to the formation of a previously unknown type of amyloid β fibrils and modulates Aβ neurotoxicity. J Mol Biol. 2011 May 13;408(4):780-91. Epub 2011 Mar 21 PubMed.
16. Nishitsuji K, Tomiyama T, Ishibashi K, Ito K, Teraoka R, Lambert MP, Klein WL, Mori H. The E693Delta mutation in amyloid precursor protein increases intracellular accumulation of amyloid beta oligomers and causes endoplasmic reticulum stress-induced apoptosis in cultured cells. Am J Pathol. 2009 Mar;174(3):957-69. Epub 2009 Jan 22 PubMed.
17. Umeda T, Tomiyama T, Sakama N, Tanaka S, Lambert MP, Klein WL, Mori H. Intraneuronal amyloid β oligomers cause cell death via endoplasmic reticulum stress, endosomal/lysosomal leakage, and mitochondrial dysfunction in vivo. J Neurosci Res. 2011 Jul;89(7):1031-42. Epub 2011 Apr 12 PubMed.
18. Kondo T, Asai M, Tsukita K, Kutoku Y, Ohsawa Y, Sunada Y, Imamura K, Egawa N, Yahata N, Okita K, Takahashi K, Asaka I, Aoi T, Watanabe A, Watanabe K, Kadoya C, Nakano R, Watanabe D, Maruyama K, Hori O, Hibino S, Choshi T, Nakahata T, Hioki H, Kaneko T, Naitoh M, Yoshikawa K, Yamawaki S, Suzuki S, Hata R, Ueno S, Seki T, Kobayashi K, Toda T, Murakami K, Irie K, Klein WL, Mori H, Asada T, Takahashi R, Iwata N, Yamanaka S, Inoue H. Modeling Alzheimer's disease with iPSCs reveals stress phenotypes associated with intracellular Aβ and differential drug responsiveness. Cell Stem Cell. 2013 Apr 4;12(4):487-96. Epub 2013 Feb 21 PubMed.
19. Shirotani K, Watanabe K, Hatta D, Kutoku Y, Ohsawa Y, Sunada Y, Kondo T, Inoue H, Iwata N. Alterations of ATG4A and LC3B in neurons derived from Alzheimer's disease patients. Genes Cells. 2023 Apr;28(4):319-325. Epub 2023 Feb 14 PubMed.
20. Kassler K, Horn AH, Sticht H. Effect of pathogenic mutations on the structure and dynamics of Alzheimer's A beta 42-amyloid oligomers. J Mol Model. 2010 May;16(5):1011-20. Epub 2009 Nov 12 PubMed.
21. Inayathullah M, Teplow DB. Structural dynamics of the ΔE22 (Osaka) familial Alzheimer's disease-linked amyloid β-protein. Amyloid. 2011 Sep;18(3):98-107. Epub 2011 Jun 13 PubMed.
23. McKnelly KJ, Kreutzer AG, Howitz WJ, Haduong K, Yoo S, Hart C, Nowick JS. Effects of Familial Alzheimer's Disease Mutations on the Assembly of a β-Hairpin Peptide Derived from Aβ16-36. Biochemistry. 2022 Mar 15;61(6):446-454. Epub 2022 Feb 25 PubMed.
24. Barrett PJ, Song Y, Van Horn WD, Hustedt EJ, Schafer JM, Hadziselimovic A, Beel AJ, Sanders CR. The amyloid precursor protein has a flexible transmembrane domain and binds cholesterol. Science. 2012 Jun 1;336(6085):1168-71. PubMed.
25. Nomura S, Umeda T, Tomiyama T, Mori H. The E693Δ (Osaka) mutation in amyloid precursor protein potentiates cholesterol-mediated intracellular amyloid β toxicity via its impaired cholesterol efflux. J Neurosci Res. 2013 Dec;91(12):1541-50. Epub 2013 Sep 16 PubMed.
26. Cloe AL, Orgel JP, Sachleben JR, Tycko R, Meredith SC. The Japanese mutant Aβ (ΔE22-Aβ(1-39)) forms fibrils instantaneously, with low-thioflavin T fluorescence: seeding of wild-type Aβ(1-40) into atypical fibrils by ΔE22-Aβ(1-39). Biochemistry. 2011 Mar 29;50(12):2026-39. Epub 2011 Feb 24 PubMed.
27. Schütz AK, Vagt T, Huber M, Ovchinnikova OY, Cadalbert R, Wall J, Güntert P, Böckmann A, Glockshuber R, Meier BH. Atomic-resolution three-dimensional structure of amyloid β fibrils bearing the Osaka mutation. Angew Chem Int Ed Engl. 2015 Jan 2;54(1):331-5. Epub 2014 Nov 13 PubMed.
28. Poduslo JF, Howell KG. Unique molecular signatures of Alzheimer's disease amyloid β peptide mutations and deletion during aggregate/oligomer/fibril formation. J Neurosci Res. 2015 Mar;93(3):410-23. Epub 2014 Nov 6 PubMed.
29. Huber M, Ovchinnikova OY, Schütz AK, Glockshuber R, Meier BH, Böckmann A. Solid-state NMR sequential assignment of Osaka-mutant amyloid-beta (Aβ1-40 E22Δ) fibrils. Biomol NMR Assign. 2015 Apr;9(1):7-14. Epub 2014 Jan 7 PubMed.
30. Elkins MR, Wang T, Nick M, Jo H, Lemmin T, Prusiner SB, DeGrado WF, Stöhr J, Hong M. Structural Polymorphism of Alzheimer's β-Amyloid Fibrils as Controlled by an E22 Switch: A Solid-State NMR Study. J Am Chem Soc. 2016 Aug 10;138(31):9840-52. Epub 2016 Jul 28 PubMed.
31. Hatami A, Monjazeb S, Milton S, Glabe CG. Familial Alzheimer's Disease Mutations within the Amyloid Precursor Protein Alter the Aggregation and Conformation of the Amyloid-β Peptide. J Biol Chem. 2017 Feb 24;292(8):3172-3185. Epub 2017 Jan 3 PubMed.
32. Murakami K, Yamaguchi T, Izuo N, Kume T, Hara H, Irie K. Synthetic and Biophysical Studies on the Toxic Conformer in Amyloid β with the E22Δ Mutation in Alzheimer Pathology. ACS Chem Neurosci. 2020 Oct 7;11(19):3017-3024. Epub 2020 Sep 16 PubMed.
33. Hayward S, Kitao A. The role of the half-turn in determining structures of Alzheimer's Aβ wild-type and mutants. J Struct Biol. 2021 Dec;213(4):107792. Epub 2021 Sep 2 PubMed.
34. Seuma M, Lehner B, Bolognesi B. An atlas of amyloid aggregation: the impact of substitutions, insertions, deletions and truncations on amyloid beta fibril nucleation. Nat Commun. 2022 Nov 18;13(1):7084. PubMed.

Other Citations

1. APP(OSK)-Tg

External Citations

1. Amyloid Atlas

Further Reading