Alzheimer's disease (AD) is a progressive neurodegenerative disorder driven by complex, incompletely understood genetic and pathogenic factors. E3 ubiquitin ligases (E3s), crucial for protein degradation, are implicated in AD, but their specific contributions to its progression remain to be elucidated.
Objective
This study aimed to identify dysregulated E3s in AD and elucidate the role of a hub E3, FBXW7, in its pathogenesis and tau protein regulation.
Methods
We integrated four datasets to identify differentially expressed E3s (DE-E3s) in AD and performed functional enrichment and PPI network analyses. Machine learning identified hub E3s and stratified AD patients into molecular subtypes. Furthermore, we validated the expression and functional role of FBXW7 using western blot, immunoprecipitation-mass spectrometry (IP-MS), and co-immunoprecipitation (Co-IP).
Results
We identified 42 DE-E3s primarily enriched in protein ubiquitination and Notch signaling pathways. FBXW7 and ENC1 emerged as hub E3s, stratifying patients into two subtypes. Subtype I exhibited enrichment of inflammatory pathways, suggesting immune dysregulation. Conversely, subtype II displayed activation of pathways associated with synaptic dysfunction and neuronal loss, potentially representing distinct primary pathological features. Furthermore, we observed decreased FBXW7 expression in AD models compared to controls. Notably, FBXW7 interacted with Tau protein. Overexpression of FBXW7 reduced the levels of both total Tau and p-Tau Ser262, and this reduction in Tau levels was reversed by MG132 treatment.
Conclusions
This study comprehensively identified E3s associated with AD, with our findings highlighting FBXW7 as a potential key regulator of AD pathogenesis through its modulation of tau protein levels.
LongJMHoltzmanDM. Alzheimer disease: an update on pathobiology and treatment strategies. Cell2019; 179: 312–339.
2.
RajanKBWeuveJBarnesLL, et al.Population estimate of people with clinical Alzheimer’s disease and mild cognitive impairment in the United States (2020-2060). Alzheimers Dement2021; 17: 1966–1975.
KeppKP. Alzheimer’s disease due to loss of function: a new synthesis of the available data. Prog Neurobiol2016; 143: 36–60.
6.
IsraelLLGalstyanACoxA, et al.Signature effects of vector-guided systemic nano bioconjugate delivery across blood-brain barrier of normal, Alzheimer’s, and tumor mouse models. ACS Nano2022; 16: 11815–11832.
7.
BarthélemyNRLiYJoseph-MathurinN, et al.A soluble phosphorylated tau signature links tau, amyloid and the evolution of stages of dominantly inherited Alzheimer’s disease. Nature Med2020; 26: 398–407.
8.
ChoiJGaoJKimJ, et al.The E3 ubiquitin ligase Idol controls brain LDL receptor expression, ApoE clearance, and A amyloidosis. Sci Transl Med2015; 7: 314ra184.
9.
PerryGFriedmanRShawG, et al.Ubiquitin is detected in neurofibrillary tangles and senile plaque neurites of Alzheimer disease brains. Proc Natl Acad Sci U S A1987; 84: 3033–3036.
10.
ChocronESMunkácsyEKimHS, et al.Genetic and pharmacologic proteasome augmentation ameliorates Alzheimer’s-like pathology in mouse and fly APP overexpression models. Sci Adv2022; 8: eabk2252.
11.
KeckSNitschRGruneT, et al.Proteasome inhibition by paired helical filament-tau in brains of patients with Alzheimer’s disease. J Neurochem2003; 85: 115–122.
12.
CiechanoverABrundinP. The ubiquitin proteasome system in neurodegenerative diseases: sometimes the chicken, sometimes the egg. Neuron2003; 40: 427–446.
13.
DavidsonKPickeringAM. The proteasome: a key modulator of nervous system function, brain aging, and neurodegenerative disease. Front Cell Dev Biol2023; 11: 1124907.
14.
MalynnBAMaA. Ubiquitin makes its mark on immune regulation. Immunity2010; 33: 843–852.
15.
ShiPSuYLiR, et al.Dual regulation of host TRAIP post-translation and nuclear/plasma distribution by porcine reproductive and respiratory syndrome virus non-structural protein 1α promotes viral proliferation. Front Immunol2018; 9: 3023.
16.
MorrealeFEWaldenH. Types of ubiquitin ligases. Cell2016; 165: 248–248.e1.
17.
HarrisLDJasemSLicchesiJDF. The ubiquitin system in Alzheimer’s disease. Adv Exp Med Biol2020; 1233: 195–221.
18.
PotjewydFMAxtmanAD. Exploration of aberrant E3 ligases implicated in Alzheimer’s disease and development of chemical tools to modulate their function. Front Cell Neurosci2021; 15: 768655.
19.
WatanabeTHikichiYWilluweitA, et al.FBL2 Regulates amyloid precursor protein (APP) metabolism by promoting ubiquitination-dependent APP degradation and inhibition of APP endocytosis. J Neurosci2012; 32: 3352–3365.
20.
KanekoMKoikeHSaitoR, et al.Loss of HRD1-mediated protein degradation causes amyloid precursor protein accumulation and amyloid-beta generation. J Neurosci2010; 30: 3924–3932.
21.
SinghAKPatiU. CHIP Stabilizes amyloid precursor protein via proteasomal degradation and p53-mediated trans-repression of β-secretase. Aging Cell2015; 14: 595–604.
22.
SilvaMCFergusonFMCaiQ, et al.Targeted degradation of aberrant tau in frontotemporal dementia patient-derived neuronal cell models. Elife2019; 8: e45457.
23.
FlachKRammingerEHilbrichI, et al.Axotrophin/MARCH7 acts as an E3 ubiquitin ligase and ubiquitinates tau protein in vitro impairing microtubule binding. Biochim Biophys Acta2014; 1842: 1527–1538.
24.
DickeyCAYueMLinW-L, et al.Deletion of the ubiquitin ligase CHIP leads to the accumulation, but not the aggregation, of both endogenous phospho- and caspase-3-cleaved tau species. J Neurosci2006; 26: 6985–6996.
25.
ZhangY-JXuY-FLiuX-H, et al.Carboxyl terminus of heat-shock cognate 70-interacting protein degrades tau regardless its phosphorylation status without affecting the spatial memory of the rats. J Neural Transm (Vienna)2008; 115: 483–491.
26.
PettmannBKristiansenMRahmehR, et al.Trim17, a novel E3 ubiquitin-ligase, initiates neuronal apoptosis. Cell Death Differ2010; 17: 1928–1941.
27.
EspinozaSArredondoSBBarakeF, et al.Neuronal surface P antigen (NSPA) modulates postsynaptic NMDAR stability through ubiquitination of tyrosine phosphatase PTPMEG. BMC Biol2020; 18: 164.
28.
DongLLiYZAnHT, et al.The E3 ubiquitin ligase c-Cbl inhibits microglia-mediated CNS inflammation by regulating PI3K/Akt/NF-κB pathway. CNS Neurosci Ther2016; 22: 661.
29.
VenkatachalamNBakavayevSEngelD, et al.Primate Differential Redoxome (PDR) – a paradigm for understanding neurodegenerative diseases. Redox Biol2020; 36: 101683.
30.
WangWZhouQJiangT, et al.A novel small-molecule PROTAC selectively promotes tau clearance to improve cognitive functions in Alzheimer-like models. Theranostics2021; 11: 5279–5295.
31.
YangFZhangNOuGY, et al.Integrated bioinformatic analysis and validation identifies immune microenvironment-related potential biomarkers in Alzheimer’s disease. J Prev Alzheimers Dis2024; 11: 495–506.
32.
DongLShenYLiH, et al.Shared genes of PPARG and NOS2 in Alzheimer’s disease and ulcerative colitis drive macrophages and microglia polarization: evidence from bioinformatics analysis and following validation. Int J Mol Sci2023; 24: 5651.
33.
LiangWSDunckleyTBeachTG, et al.Gene expression profiles in anatomically and functionally distinct regions of the normal aged human brain. Physiol Genomics2007; 28: 311–322.
34.
HokamaMOkaSLeonJ, et al.Altered expression of diabetes-related genes in Alzheimer’s disease brains: the Hisayama study. Cereb Cortex2014; 24: 2476–2488.
35.
TanMGChuaW-TEsiriMM, et al.Genome wide profiling of altered gene expression in the neocortex of Alzheimer’s disease. J Neurosci Res2010; 88: 1157–1169.
36.
SimpsonJEIncePGShawPJ, et al.Microarray analysis of the astrocyte transcriptome in the aging brain: relationship to Alzheimer’s pathology and APOE genotype. Neurobiol Aging2011; 32: 1795–1807.
37.
NativioRDonahueGBersonA, et al.Dysregulation of the epigenetic landscape of normal aging in Alzheimer’s disease. Nat Neurosci2018; 21: 497–505.
38.
CloughEBarrettT. The gene expression omnibus database. Methods Mol Biol2016; 1418: 93.
39.
DavisSMeltzerPS. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics2007; 23: 1846–1847.
40.
RitchieMEPhipsonBWuD, et al.Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res2015; 43: e47.
41.
LeekJTJohnsonWEParkerHS, et al.The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics2012; 28: 882–883.
42.
WangXLiYHeM, et al.Ubibrowser 2.0: a comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species. Nucleic Acids Res2022; 50: D719–D728.
43.
ZhangHMeltzerPDavisS. RCircos: an R package for Circos 2D track plots. BMC Bioinformatics2013; 14: 244.
44.
WuTHuEXuS, et al.Clusterprofiler 4.0: a universal enrichment tool for interpreting omics data. Innovation (Camb)2021; 2: 100141.
45.
SzklarczykDKirschRKoutrouliM, et al.The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Res2023; 51: D638–D646.
46.
ShannonPMarkielAOzierO, et al.Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res2003; 13: 2498–2504.
TibshiraniR. Regression shrinkage and selection via the lasso: a retrospective. J R Stat Soc B Stat Methodol2011; 73: 267–288.
49.
RamendraPDeoRCYanL, et al.Soil moisture forecasting by a hybrid machine learning technique: ELM integrated with ensemble empirical mode decomposition. Geoderma2018; 330: 136–161.
50.
WilkersonMDHayesDN. Consensusclusterplus: a class discovery tool with confidence assessments and item tracking. Bioinformatics2010; 26: 1572–1573.
51.
LinNGaoX-YLiX, et al.Involvement of ubiquitination in Alzheimer’s disease. Front Neurol2024; 15: 1459678.
52.
GeZLeightonJSWangY, et al.Integrated genomic analysis of the ubiquitin pathway across cancer types. Cell Rep2018; 23: 213–226.e3.
53.
HoeckJDJandkeABlakeSM, et al.Fbw7 controls neural stem cell differentiation and progenitor apoptosis via Notch and c-Jun. Nat Neurosci2010; 13: 1365–1372.
54.
ChongZBaoCHeJ, et al.E3 ligase FBXW7 aggravates TMPD-induced systemic lupus erythematosus by promoting cell apoptosis. Cell Mol Immunol2018; 15: 1057–1070.
55.
YangYZhouXLiuX, et al.Implications of FBXW7 in neurodevelopment and neurodegeneration: molecular mechanisms and therapeutic potential. Front Cell Neurosci2021; 15: 736008.
56.
Ekholm-ReedSGoldbergMSSchlossmacherMG, et al.Parkin-dependent degradation of the F-box protein Fbw7β promotes neuronal survival in response to oxidative stress by stabilizing Mcl-1. Mol Cell Biol2013; 33: 3627–3643.
57.
LiJPauleyAMMyersRL, et al.SEL-10 interacts with presenilin 1, facilitates its ubiquitination, and alters A-beta peptide production: SEL-10 facilitates presenilin 1 ubiquitination. J Neurochem2002; 82: 1540–1548.
58.
WuGHubbardEJAKitajewskiJK, et al.Evidence for functional and physical association between Caenorhabditis elegans SEL-10, a Cdc4p-related protein, and SEL-12 presenilin. Proc Natl Acad Sci U S A1998; 95: 15787–15791.
59.
Haj-YahyaMGopinathPRajasekharK, et al.Site-specific hyperphosphorylation inhibits, rather than promotes, tau fibrillization, seeding capacity, and its microtubule binding. Angew Chem Int Ed Engl2020; 59: 4059–4067.
60.
KimJHLeeJChoiWH, et al.CHIP-mediated hyperubiquitylation of tau promotes its self-assembly into the insoluble tau filaments. Chem Sci2021; 12: 5599–5610.
61.
StephensonSEMCostainGBlokLER, et al.Germline variants in tumor suppressor FBXW7 lead to impaired ubiquitination and a neurodevelopmental syndrome. Am J Hum Genet2022; 109: 601–617.
62.
BarthélemyNRTothBManserPT, et al.Site-specific cerebrospinal fluid tau hyperphosphorylation in response to Alzheimer’s disease brain pathology: not all tau phospho-sites are hyperphosphorylated. J Alzheimers Dis2022; 85: 415–429.
63.
SanchezCGAckerCMGrayA, et al.Genome-wide CRISPR screen identifies protein pathways modulating tau protein levels in neurons. Commun Biol2021; 4: 736.
64.
KumarSEarnestTYangB, et al.Analyzing heterogeneity in Alzheimer disease using multimodal normative modeling on imaging-based ATN biomarkers. bioRxiv 2024; 2023.08.15.553412.
65.
CalsolaroVEdisonP. Neuroinflammation in Alzheimer’s disease: current evidence and future directions. Alzheimers Dement2016; 12: 719–732.
66.
CaiYLiuJWangB, et al.Microglia in the neuroinflammatory pathogenesis of Alzheimer’s disease and related therapeutic targets. Front Immunol2022; 13: 856376.
67.
Lopez-LeeCTorresERSCarlingG, et al.Mechanisms of sex differences in Alzheimer’s disease. Neuron2024; 112: 1208–1221.
ZhuQ-BBaoA-MSwaabD. Activation of the brain to postpone dementia: a concept originating from postmortem human brain studies. Neurosci Bull2019; 35: 253–266.
70.
WangRReddyPH. Role of glutamate and NMDA receptors in Alzheimer’s disease. J Alzheimers Dis2017; 57: 1041–1048.
71.
Corriveau-LecavalierNAdamsJNFischerL, et al.Cerebral hyperactivation across the Alzheimer’s disease pathological cascade. Brain Commun2024; 6: fcae376.
Supplementary Material
Please find the following supplemental material available below.
For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.
For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.
