γ‐Secretase complexes (GSECs) are multimeric membrane proteases involved in a variety of physiological processes and linked to Alzheimer's disease (AD). Presenilin (PSEN, catalytic subunit), ...Nicastrin (NCT), Presenilin Enhancer 2 (PEN‐2), and Anterior Pharynx Defective 1 (APH1) are the essential subunits of GSECs. Mutations in PSEN and the Amyloid Precursor Protein (APP) cause early‐onset AD. GSECs successively cut APP to generate amyloid‐β (Aβ) peptides of various lengths. AD‐causing mutations destabilize GSEC‐APP/Aβn interactions and thus enhance the production of longer Aβs, which elicit neurotoxic events underlying pathogenesis. Here, we investigated the molecular strategies that anchor GSEC and APP/Aβn during the sequential proteolysis. Our studies reveal that a direct interaction between NCT ectodomain and APPC99 influences the stability of GSEC‐Aβn assemblies and thereby modulates Aβ length. The data suggest a potential link between single‐nucleotide variants in NCSTN and AD risk. Furthermore, our work indicates that an extracellular interface between the protease (NCT, PSEN) and the substrate (APP) represents the target for compounds (GSMs) modulating Aβ length. Our findings may guide future rationale‐based drug discovery efforts.
Synopsis
γ‐Secretase mediated cleavage of APP defines the length of Aβ peptides. Alzheimer's disease causing mutations destabilize γ‐secretase – APP interactions and thus promote the production of longer, amyloidogenic Aβs. Here, we investigated the molecular strategies securing γ‐secretase – APP interactions.
NCT ectodomain establishes a direct, short distance interaction with APP ectodomain.
NCT‐APP interface influences the stability of γ‐secretase – APP interactions and thereby modulates Aβ length.
NCT ectodomain influences the response towards compounds modulating Aβ length.
The data suggest a potential link between single nucleotide variants in NCSTN and AD risk.
A direct interaction between the gamma secretase subunit Nicastrin and APP regulates the stability and processivity of the γ‐secretase/substrate complex to affect Aβ length and Alzheimer disease pathogenicity.
Sequential proteolysis of the amyloid precursor protein (APP) by γ‐secretases generates amyloid‐β (Aβ) peptides and defines the proportion of short‐to‐long Aβ peptides, which is tightly connected to ...Alzheimer's disease (AD) pathogenesis. Here, we study the mechanism that controls substrate processing by γ‐secretases and Aβ peptide length. We found that polar interactions established by the APPC99 ectodomain (ECD), involving but not limited to its juxtamembrane region, restrain both the extent and degree of γ‐secretases processive cleavage by destabilizing enzyme–substrate interactions. We show that increasing hydrophobicity, via mutation or ligand binding, at APPC99‐ECD attenuates substrate‐driven product release and rescues the effects of Alzheimer's disease‐associated pathogenic γ‐secretase and APP variants on Aβ length. In addition, our study reveals that APPC99‐ECD facilitates the paradoxical production of longer Aβs caused by some γ‐secretase inhibitors, which act as high‐affinity competitors of the substrate. These findings assign a pivotal role to the substrate ECD in the sequential proteolysis by γ‐secretases and suggest it as a sweet spot for the potential design of APP‐targeting compounds selectively promoting its processing by these enzymes.
Synopsis
Sequential proteolysis of amyloid precursor protein (APP) by γ‐secretase generates various amyloid‐β (Aβ) peptides, whose length correlates with pathogenicity of Alzheimer's disease (AD)‐associated mutations. Here, the ectodomain of the APP substrate is found to define Aβ length by promoting product release and destabilizing enzyme–substrate interactions.
Polar residues in the APPC99 ectodomain (APPC99‐ECD) drive product release by destabilizing enzyme–substrate interactions.
Increased hydrophobicity in the substrate ECD increases both efficiency and extent of sequential γ‐secretase‐mediated proteolysis of APP and Notch.
γ‐Secretase inhibitors (GSIs) DAPT and semagacestat act as high‐affinity competitors of substrates.
GSI‐mediated displacement of partially digested Aβ peptides, facilitated by the APPC99‐ECD, explains paradoxical increases in longer Aβ peptides.
Mitigation of APPC99‐ECD‐driven product release rescues the increased production of longer Aβ peptides linked to pathogenic variants in γ‐secretase and APP.
How γ‐secretase cleaves and processes the amyloid precursor protein depends on the hydrophobicity of its ectodomain, with implications for disease mechanism and drug discovery.
Cerebral accumulation of amyloid-β (Aβ) initiates molecular and cellular cascades that lead to Alzheimer’s disease (AD). However, amyloid deposition does not invariably lead to dementia. ...Amyloid-positive but cognitively unaffected (AP-CU) individuals present widespread amyloid pathology, suggesting that molecular signatures more complex than the total amyloid burden are required to better differentiate AD from AP-CU cases. Motivated by the essential role of Aβ and the key lipid involvement in AD pathogenesis, we applied multimodal mass spectrometry imaging (MSI) and machine learning (ML) to investigate amyloid plaque heterogeneity, regarding Aβ and lipid composition, in AP-CU versus AD brain samples at the single-plaque level. Instead of focusing on a population mean, our analytical approach allowed the investigation of large populations of plaques at the single-plaque level. We found that different (sub)populations of amyloid plaques, differing in Aβ and lipid composition, coexist in the brain samples studied. The integration of MSI data with ML-based feature extraction further revealed that plaque-associated gangliosides GM2 and GM1, as well as Aβ1–38, but not Aβ1–42, are relevant differentiators between the investigated pathologies. The pinpointed differences may guide further fundamental research investigating the role of amyloid plaque heterogeneity in AD pathogenesis/progression and may provide molecular clues for further development of emerging immunotherapies to effectively target toxic amyloid assemblies in AD therapy. Our study exemplifies how an integrative analytical strategy facilitates the unraveling of complex biochemical phenomena, advancing our understanding of AD from an analytical perspective and offering potential avenues for the refinement of diagnostic tools.
Inhibition of γ-secretase, an intramembrane protease, to reduce secretion of Amyloid-β (Aβ) peptides has been considered for treating Alzheimer’s disease. However, γ-secretase inhibitors suffer from ...severe side effects. As an alternative, γ-secretase modulators (GSM) reduce the generation of toxic peptides by enhancing the cleavage processivity without diminishing the enzyme activity. Starting from a known γ-secretase structure without substrate but in complex with an E2012 GSM, we generated a structural model that included a bound Aβ43 peptide and studied interactions among enzyme, substrate, GSM, and lipids. Our result suggests that E2012 binding at the enzyme–substrate–membrane interface attenuates the membrane distortion by shielding the substrate–membrane interaction. The model predicts that the E2012 modulation is charge-dependent and explains the preserved hydrogen acceptor and the aromatic ring observed in many imidazole-based GSM. Predicted effects of γ-secretase mutations on E2012 modulation were confirmed experimentally. We anticipate that the study will facilitate the future development of effective GSMs.
The mechanisms by which mutations in the presenilins (PSEN) or the amyloid precursor protein (APP) genes cause familial Alzheimer disease (FAD) are controversial. FAD mutations increase the release ...of amyloid β (Aβ)42 relative to Aβ40 by an unknown, possibly gain‐of‐toxic‐function, mechanism. However, many PSEN mutations paradoxically impair γ‐secretase and ‘loss‐of‐function’ mechanisms have also been postulated. Here, we use kinetic studies to demonstrate that FAD mutations affect Aβ generation via three different mechanisms, resulting in qualitative changes in the Aβ profiles, which are not limited to Aβ42. Loss of ε‐cleavage function is not generally observed among FAD mutants. On the other hand, γ‐secretase inhibitors used in the clinic appear to block the initial ε‐cleavage step, but unexpectedly affect more selectively Notch than APP processing, while modulators act as activators of the carboxypeptidase‐like (γ) activity. Overall, we provide a coherent explanation for the effect of different FAD mutations, demonstrating the importance of qualitative rather than quantitative changes in the Aβ products, and suggest fundamental improvements for current drug development efforts.
Mutations in presenilin (PSEN) and amyloid precursor protein (APP) cause dominant early‐onset Alzheimer's disease (AD), but the mechanism involved is debated. Here, such mutations are shown to alter γ‐secretase activity, leading to changes in Aβ peptide cleavage patterns.
γ‐Secretases are a family of intramembrane cleaving aspartyl proteases and important drug targets in Alzheimer's disease. Here, we generated mice deficient for all γ‐secretases in the pyramidal ...neurons of the postnatal forebrain by deleting the three anterior pharynx defective 1 (Aph1) subunits (Aph1abc cKO Cre+). The mice show progressive cortical atrophy, neuronal loss, and gliosis. Interestingly, this is associated with more than 10‐fold accumulation of membrane‐bound fragments of App, Aplp1, Nrg1, and Dcc, while other known substrates of γ‐secretase such as Aplp2, Lrp1, and Sdc3 accumulate to lesser extents. Despite numerous reports linking neurodegeneration to accumulation of membrane‐bound App fragments, deletion of App expression in the combined Aph1 knockout does not rescue this phenotype. Importantly, knockout of only Aph1a‐ or Aph1bc‐secretases causes limited and differential accumulation of substrates. This was not associated with neurodegeneration. Further development of selective Aph1‐γ‐secretase inhibitors should be considered for treatment of Alzheimer's disease.
Synopsis
γ‐Secretases are proteases with central roles in Alzheimer's disease pathogenesis. The impact of partial and combined deficiencies of the Aph1‐γ‐secretase subunits on mouse brain was investigated at biochemical and morphological levels with a focus on potential neurodegenerative phenotypes.
Combined Aph1abc‐γ‐secretase cKO (conditional knock out) animals suffer from progressive neurodegeneration.
Neurodegeneration, characterized by strong accumulation of APP‐carboxyterminal fragments, is not modulated by decreased expression of APP.
Accumulation of APP and other substrates is much less outspoken in single Aph1a or Aph1bc knockout mice and these mice do not display neurodegeneration.
Aph1bc targeted animals display a significant effect on Aβ42 generation
The in vivo substrate selectivity of two different γ‐secretase subtypes is demonstrated.
γ‐Secretases are proteases with central roles in Alzheimer's disease pathogenesis. The impact of partial and combined deficiencies of the Aph1‐γ‐secretase subunits on mouse brain was investigated at biochemical and morphological levels with a focus on potential neurodegenerative phenotypes.
Inherited familial Alzheimer's disease (AD) is characterized by small increases in the ratio of Aβ42 versus Aβ40 peptide which is thought to drive the amyloid plaque formation in the brain of these ...patients. Little is known however whether ageing, the major risk factor for sporadic AD, affects amyloid beta‐peptide (Aβ) generation as well. Here we demonstrate that the secretion of Aβ is enhanced in an in vitro model of neuronal ageing, correlating with an increase in γ‐secretase complex formation. Moreover we found that peroxynitrite (ONOO−), produced by the reaction of superoxide anion with nitric oxide, promoted the nitrotyrosination of presenilin 1 (PS1), the catalytic subunit of γ‐secretase. This was associated with an increased association of the two PS1 fragments, PS1‐CTF and PS1‐NTF, which constitute the active catalytic centre. Furthermore, we found that peroxynitrite shifted the production of Aβ towards Aβ42 and increased the Aβ42/Aβ40 ratio. Our work identifies nitrosative stress as a potential mechanistic link between ageing and AD.
γ-Secretases are a group of widely expressed, intramembrane-cleaving proteases involved in many physiological processes. Their clinical relevance comes from their involvement in Alzheimer's disease, ...cancer, and other disorders. A clinical trial with the wide-spectrum γ-secretase inhibitor semagacestat has, however, demonstrated that global inhibition of all γ-secretases causes serious toxicity. Evolving insights suggest that selective inhibition of one of these proteases, or more subtle modulation of γ-secretases by stimulating their carboxypeptidase-like activity but sparing their endopeptidase activity, are potentially highly interesting approaches. The rapidly growing knowledge of regulation, assembly, and specificity of these intriguing protein complexes and the potential advent of high-resolution structural information could dramatically change the perspective on safe and efficacious γ-secretase inhibition in various disorders.
Introduction
We investigated the frequency, neuropathology, and phenotypic characteristics of spastic paraplegia (SP) that precedes dementia in presenilin 1 (PSEN1) related familial Alzheimer's ...disease (AD).
Methods
We performed whole exome sequencing (WES) in 60 probands with hereditary spastic paraplegia (HSP) phenotype that was negative for variants in known HSP‐related genes. Where PSEN1 mutation was identified, brain biopsy was performed. We investigated the link between HSP and AD with PSEN1 in silico pathway analysis and measured in vivo the stability of PSEN1 mutant γ‐secretase.
Results
We identified a PSEN1 variant (p.Thr291Pro) in an individual presenting with pure SP at 30 years of age. Three years later, SP was associated with severe, fast cognitive decline and amyloid deposition with diffuse cortical plaques on brain biopsy. Biochemical analysis of p.Thr291Pro PSEN1 revealed that although the mutation does not alter active γ‐secretase reconstitution, it destabilizes γ‐secretase‐amyloid precursor protein (APP)/amyloid beta (Aβn) interactions during proteolysis, enhancing the production of longer Aβ peptides. We then extended our analysis to all 226 PSEN1 pathogenic variants reported and show that 7.5% were associated with pure SP onset followed by cognitive decline later in the disease. We found that PSEN1 cases manifesting initially as SP have a later age of onset, are associated with mutations located beyond codon 200, and showed larger diffuse, cored plaques, amyloid‐ring arteries, and severe CAA.
Discussion
We show that pure SP can precede dementia onset in PSEN1‐related familial AD. We recommend PSEN1 genetic testing in patients presenting with SP with no variants in known HSP‐related genes, particularly when associated with a family history of cognitive decline.
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