Overview

Pathogenicity: Alzheimer's Disease : Pathogenic
ACMG/AMP Pathogenicity Criteria: PS3, PM1, PM2, PM4, PP1
Clinical Phenotype: Alzheimer's Disease
Reference Assembly: GRCh37/hg19
Position: Chr21:27264160_27264177 TTCTTTGCAGAAGATGTG>------------------
dbSNP ID: NA
Coding/Non-Coding: Coding
DNA Change: Deletion
Expected RNA Consequence: Deletion
Expected Protein Consequence: Deletion
Codon Change: TTC to ---, TTT to ---, GCA to ---, GAA to ---, GAT to ---, GTG to ---
Reference Isoform: APP Isoform APP770 (770 aa)
Genomic Region: Exon 17

Findings

This six-amino-acid deletion within the mid-region of Aβ was found to segregate with disease in a Swedish family with a multigeneration history of early onset Alzheimer’s disease (Pagnon de la Vega et al., 2021). The mutation appears to largely eliminate non-amyloidogenic, α-secretase processing of APP, and leads to the generation of rapidly aggregating Aβ peptides lacking amino acids 19-24.

The “Uppsala deletion” was identified in three affected family members—two siblings and their cousin —from a three-generation pedigree showing an autosomal-dominant pattern of inheritance of disease. Affected family members suffered from severe dementia, with symptom onset in their 40s, and death occurring five to 15 years later. The mutation was absent in older, unaffected family members and more than 500 Swedish healthy controls and patients with sporadic AD. A subsequent study reported two additional Swedish carriers with familial AD and ages at onset of 40 and 44 years (Pagnon de la Vega et al., 2022). They both also carried a risk modifier for AD, the TREM2 R62H variant.

Biomarkers

Core AD biomarkers in cerebrospinal fluid—Aβ42, total tau, and phospho-tau—were measured in the three index cases (Pagnon de la Vega et al., 2021): While levels of total tau and phospho-tau were elevated, as seen in sporadic AD, levels of Aβ42 were within the normal range (i.e., the carriers did not exhibit the drop in CSF Aβ42 characteristic of sporadic AD). These relatively high levels of Aβ42 may reflect elevations in Aβ generated from the mutant allele, as discussed below.

Amyloid-PET imaging with Pittsburgh Compound B in two of the mutation carriers revealed only mild elevations of tracer uptake in the cerebral cortex. (Paradoxically, when one of these subjects came to autopsy, abundant amyloid plaques were seen in tissue sections stained with Thioflavin-S or antibodies directed against Aβ.)

CT scans showed medial temporal lobe atrophy in one of the siblings, while the other two carriers exhibited moderate global cortical atrophy with sparing of the temporal lobes.

FDG-PET revealed hypometabolism in the temporal and parietal lobes of all three carriers.

Neuropathology

One carrier of the Uppsala deletion—one of the siblings mentioned above—is deceased, and his or her brain has been examined (Pagnon de la Vega et al., 2021). Autopsy confirmed AD pathology, with dilated ventricles, abundant amyloid plaques (Thal stage 5) and neurofibrillary tangles (Braak Stage 6),and gliosis in limbic regions and neocortex.

Mass spectrometric analysis showed that plaques were composed primarily of Aβ42 generated from the mutant APP allele and thus lacking amino acids 19-24 (AβUpp42_Δ19–24). In addition to full-length AβUpp42_Δ19–24, several N-terminally truncated forms were detected, including peptides starting at positions 3 (pyroglutamate), 4, 5, or 8.

Biological Effects

Compared with brains from subjects with sporadic AD, the level of Aβ42 in the brain of the carrier was elevated, while the amount of Aβ40 was decreased (Pagnon de la Vega et al., 2021), a feature also observed in mice. carrying human APP with the Uppsala and Swedish mutations (Pagnon de la Vega et al., 2024; Feb 2024 news).

In vitro studies showed that the mutation largely eliminates non-amyloidogenic processing of APP, with an accompanying increase in amyloidogenic processing: Levels of sAPPα in the culture media of HEK293 cells transfected with mutant APP (APPUpp) were at background levels, in contrast to the elevated levels found in the media of cells transfected with wild-type APP, while more sAPPβ was released by the cells transfected with APPUpp than by cells carrying wild-type APP (Pagnon de la Vega et al., 2021). Consistent with these findings, levels of CTFα were lower and CTFβ were higher in cells transfected with APPUpp, compared with cells transfected with wild-type APP. Levels of Aβ peptides were also elevated in the media of APPUpp-transfected cells.

The Uppsala deletion also seems to create a new major cleavage site in APP, between amino acids 4 and 5 of the Aβ sequence. In media from cells transfected with wild-type APP, the most prevalent APP metabolites were Aβ1–40 and the p3 peptide generated by sequential α- and γ-secretase cleavages. In cells transfected with APPUpp, the predominant APP metabolites were AβUpp1–40_Δ19–24 (Aβ40 missing amino acids 19-24) and an N-terminally truncated peptide, AβUpp5–40_Δ19–24. The latter peptide is not merely a cell culture artifact, as AβUpp5–40_Δ19–24 was found in the CSF of APP Uppsala mutation carriers.

Cleavage at the β' site in APP (between amino acids 10 and 11 of Aβ) was also increased by the Uppsala deletion: Aβ11–40_Δ19–24 and Aβ11– 42_Δ19–24 were found in culture media from HEK29 cells transfected with APPUpp and in CSF from mutation carriers. Aβp11– 42_Δ19–24 was also detected in plaques from the brain of the deceased carrier.

The propensity of AβUpp1–42_Δ19-24 to aggregate was evaluated using synthetic peptides. AβUpp1–42_Δ19-24 formed fibrils more quickly than did wild-type Aβ42, at a rate similar to Aβ42 with the Arctic mutation (Aβ42Arc). While the amounts of soluble Aβ oligomers and protofibrils formed by wild-type Aβ42 and Aβ42Arc increased over time, these species decreased for AβUpp1–42_Δ19-24, possibly because they represent intermediates that are quickly consumed on the way to fibril formation. Findings from biochemical analyses of the brain of the deceased mutation carrier were consistent with increased generation of insoluble fibrils at the expense of soluble aggregates: Although levels of insoluble Aβ42 were elevated in the mutation carrier, compared with sporadic AD, levels of soluble oligomers and protofibrils were lower. Consistent with these findings, a subsequent study revealed that a large number of experimental multi-amino acid deletions in a region centered around the Uppsala mutation accelerate the nucleation of Aβ aggregates (Seuma et al., 2022).

Electron microscopy of fibrils formed by synthetic AβUpp1–42_Δ19-24 showed at least four morphologies (Pagnon de la Vega et al., 2021). Cryo-EM structural analyses of the two most prominent polymorphs revealed unique structures that differed from previously described Aβ42 fibrils. Consistent with these findings and with observations in human carriers, mice expressing human APP with the Uppsala and Swedish mutations had amyloid deposits that were undetectable by PiB-PET and stained positive only with certain antibodies (Pagnon de la Vega et al., 2024; Feb 2024 news).  The aggregates were detectable by mAb3D6, the murine precursor to bapineuzumab, which binds the Aβ N-terminus, but undetectable by mAb158, the mouse equivalent of lecanemab, which specifically binds Aβ protofibrils. The Aβ peptides might change conformation when they become insoluble.

Also of note, the Aβ fibrils in this mouse model evoked only a minimal response from microglia and astrocytes. The authors hypothesized that the dampened response may be due to low levels of soluble Aβ oligomers.

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

As mentioned above, a mouse model that expresses human APP with both the Uppsala deletion and the Swedish mutation has been generated (Pagnon de la Vega et al., 2024; Feb 2024 news).  The mice recapitulate several pathological features observed in the carrier who was examined at autopsy, including plaques composed of Aβ42 generated from the mutant APP allele, with nearly no Aβ40 found in either soluble form or plaques.  Immunostaining revealed small, diffuse plaques surfacing initially in the frontal cortex at 4 months of age, followed by staining of the hippocampus, cerebral cortex, and eventually, at 18 months, the thalamus. Synapses were less dense around plaques and, as noted above, gliosis was minimal. No tau pathology was detected.

Mice carrying only the Uppsala mutation died for unknown reasons.

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References

Mutations Citations

1. APP K670_M671delinsNL (Swedish)
2. TREM2 R62H
3. APP E693G (Arctic)

News Citations

1. Under the Radar: APP Uppsala Fibrils Evade Microglia, PiB, Leqembi 16 Feb 2024

Therapeutics Citations

1. Bapineuzumab
2. Leqembi

Paper Citations

1. Pagnon de la Vega M, Syvänen S, Giedraitis V, Hooley M, Konstantinidis E, Meier SR, Rokka J, Eriksson J, Aguilar X, Spires-Jones TL, Lannfelt L, Nilsson LN, Erlandsson A, Hultqvist G, Ingelsson M, Sehlin D. Altered amyloid-β structure markedly reduces gliosis in the brain of mice harboring the Uppsala APP deletion. Acta Neuropathol Commun. 2024 Feb 5;12(1):22. PubMed.
2. Pagnon de la Vega M, Giedraitis V, Michno W, Kilander L, Güner G, Zielinski M, Löwenmark M, Brundin R, Danfors T, Söderberg L, Alafuzoff I, Nilsson LN, Erlandsson A, Willbold D, Müller SA, Schröder GF, Hanrieder J, Lichtenthaler SF, Lannfelt L, Sehlin D, Ingelsson M. The Uppsala APP deletion causes early onset autosomal dominant Alzheimer's disease by altering APP processing and increasing amyloid β fibril formation. Sci Transl Med. 2021 Aug 11;13(606) PubMed. Correction.
3. Pagnon de la Vega M, Näslund C, Brundin R, Lannfelt L, Löwenmark M, Kilander L, Ingelsson M, Giedraitis V. Mutation analysis of disease causing genes in patients with early onset or familial forms of Alzheimer's disease and frontotemporal dementia. BMC Genomics. 2022 Feb 4;23(1):99. PubMed.
4. 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. Pagnon de la Vega et al., 2021

Further Reading