Quantitative Analysis of the Brain Ubiquitylome in Alzheimer's Disease

Abreha, Measho; Dammer, Eric B.; Ping, Lingyan; Tian, Zhong; Duong, Duc M.; Gearing, Marla; Lah, James J.; Levey, Aĺlan I.; Seyfried, Nicholas T.

doi:10.1002/pmic.201800108

Cited by 58 publications

(56 citation statements)

References 75 publications

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“…Other recent studies have used proteomics to answer specific questions about which proteins are primarily affected by post-translational modifications in AD. Two recent studies have used enrichment strategies to identify all proteins that are phosphorylated and ubiquitinated in AD (38,39). These studies showed that the number of ubiquitinated proteins was much higher in AD brains than in control brains, which is consistent with the accumulation of insoluble and misfolded proteins during AD and reflects the proteolytic stress present in AD (38).…”

Section: Ad Proteomic Studies Using Bulk Tissue Homogenatesmentioning

confidence: 78%

“…Two recent studies have used enrichment strategies to identify all proteins that are phosphorylated and ubiquitinated in AD (38,39). These studies showed that the number of ubiquitinated proteins was much higher in AD brains than in control brains, which is consistent with the accumulation of insoluble and misfolded proteins during AD and reflects the proteolytic stress present in AD (38). Examination of phosphorylated proteins confirmed that tau was the most highly phosphorylated protein in AD in comparison to controls and also identified an additional 142 proteins that were phosphorylated to a greater extent in AD brains (39).…”

Section: Ad Proteomic Studies Using Bulk Tissue Homogenatesmentioning

confidence: 99%

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Using Proteomics to Understand Alzheimer’s Disease Pathogenesis

Drummond

Wısnıewskı

2019

Alzheimer’s Disease

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Our current understanding of the molecular changes that drive Alzheimer' s disease (AD) pathogenesis is incomplete. Unbiased, massspectrometry-based proteomic studies provide an efficient and comprehensive way to quantitatively examine thousands of proteins at once using microscopic amounts of human brain tissue. Recently, the number of proteomic studies that examine protein changes in AD brain tissue has been increasing. This chapter reviews the different proteomic approaches currently being used to identify pathological protein changes in AD brain tissue including bulk tissue studies that examine protein changes throughout the progression of AD, studies of the insoluble proteome in AD, studies using proteomics to examine selective vulnerability in AD, studies of the amyloid plaque and neurofibrillary tangle proteome, studies of the synaptic proteome, and studies of the interactome of beta amyloid and tau. Combined, these complementary proteomic approaches provide increased understanding about the protein changes that occur in the AD brain. Results from these proteomic studies provide an excellent resource for future hypothesisdriven targeted studies and will help identify new biomarkers of disease and new drug targets for AD.

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Section: Ad Proteomic Studies Using Bulk Tissue Homogenatesmentioning

confidence: 78%

Section: Ad Proteomic Studies Using Bulk Tissue Homogenatesmentioning

confidence: 99%

Using Proteomics to Understand Alzheimer’s Disease Pathogenesis

Drummond

Wısnıewskı

2019

Alzheimer’s Disease

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“…For mass spectrometry analyses the TBK1 kinase activity assay reaction was resuspended in 100 µL 50 µM NH4HCO3 buffer and subjected to standard tryptic digestion and MS analysis as described (76,77). MS raw files were searched using MaxQuant (78) (version 1.6.3.4) search platform for identification and quantification of tau phosphorylation sites (Table S2).…”

Section: Mass Spectrometry and Tau Phosphopeptide Quantificationmentioning

confidence: 99%

“…Functional enrichment of differentially expressed proteins was determined using the GO-Elite (v1.2.5) python package as previously described (76,80). Briefly, GO-Elite Hs (human) databases were downloaded on or after June 2016.…”

Section: Gene Ontology (Go) Enrichment and Hierarchical Clustering Anmentioning

confidence: 99%

TBK1 interacts with tau and enhances neurodegeneration in tauopathy

Abreha

Ojelade

Dammer

et al. 2020

Preprint

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Running title: TBK1 is a tau-directed kinase Key words: TANK-binding kinase 1 (TBK1), microtubule associated protein tau (MAPT), neurofibrillary tangles (NFTs), Alzheimer's disease (AD), familial frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17), co-immunoprecipitation (co-IP), mass spectrometry (MS), post-translational modification (PTM), Drosophila, IκB kinase (IKK) ABSTRACT One of the defining pathological features of Alzheimer's Disease (AD) is the deposition of neurofibrillary tangles (NFTs) composed of hyperphosphorylated tau in the brain. Aberrant activation of kinases in AD has been suggested to enhance phosphorylation and toxicity of tau, making the responsible taudirected kinases attractive therapeutic targets. The full complement of tau interacting kinases in AD brain and their activity in disease remains incompletely defined.Here, immunoaffinity enrichment coupled with mass spectrometry (MS) identified TANKbinding kinase 1 (TBK1) as a tau-interacting partner in human AD cortical brain tissues. We validated this interaction in both human AD and familial frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17) caused by mutations in MAPT (R406W) postmortem brain tissues as well as human cell lines. Further, we document increased TBK1 activity in both AD and FTDP-17 and map the predominant TBK1 phosphorylation sites on tau based on in vitro kinase assays coupled to MS. Lastly, in a Drosophila tauopathy model, activating expression of a conserved TBK1 ortholog triggers tau hyperphosphorylation and enhanced neurodegeneration, whereas knockdown had the reciprocal effect, suppressing tau toxicity. Collectively, our findings suggest that increased TBK1 activity may promote tau hyperphosphorylation and neuronal loss in AD and related tauopathies.

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“…In contrast, quantitative analysis of ubiquitylomes has proven to be a valuable tool for elucidating targets and mechanisms of the ubiquitin signaling systems, as well as gaining insights into many diseases, such as neuroblastoma, cancer, and Alzheimer's disease.…”

Section: Introductionmentioning

confidence: 99%

Ubiquitylomes Analysis of the Whole blood in Postmenopausal Osteoporosis Patients and healthy Postmenopausal Women

Yang

Wang

et al. 2019

Orthopaedic Surgery

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Objectives:To determine the mechanisms of ubiquitination in postmenopausal osteoporosis and investigate the ubiquitinated spectrum of novel targets between healthy postmenopausal women and postmenopausal osteoporosis patients, we performed ubiquitylome analysis of the whole blood of postmenopausal women and postmenopausal osteoporosis patients. Methods:To obtain a more comprehensive understanding of the postmenopausal osteoporosis mechanism, we performed a quantitative assessment of the ubiquitylome in whole blood from seven healthy postmenopausal women and seven postmenopausal osteoporosis patients using high-performance liquid chromatography fractionation, affinity enrichment, and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). To examine the ubiquitylome data, we performed enrichment analysis using an ubiquitylated amino acid motif, Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway.Results: Altogether, 133 ubiquitinated sites and 102 proteins were quantified. A difference of more than 1.2 times is considered significant upregulation and less than 0.83 significant downregulation; 32 ubiquitinated sites on 25 proteins were upregulated and 101 ubiquitinated sites on 77 proteins were downregulated. These quantified proteins, both with differently ubiquitinated sites, participated in various cellular processes, such as cellular processes, biological regulation processes, response to stimulus processes, single-organism and metabolic processes. Ubiquitin conjugating enzyme activity and ubiquitin-like protein conjugating enzyme activity were the most highly enriched in molecular function of upregulated sites with corresponding proteins, but they were not enriched in downregulated in sites with corresponding proteins. The KEGG pathways analysis of quantified proteins with differentiated ubiquitinated sites found 13 kinds of molecular interactions and functional pathways, such as glyoxylate and decarboxylate metabolism, dopaminergic synapse, ubiquitin-mediated proteolysis, salivary secretion, coagulation and complement cascades, Parkinson's disease, and hippo signaling pathway. In addition, hsa04120 ubiquitin-mediated proteolysis was the most highly enriched in proteins with upregulated sites, hsa04610 complement and coagulation cascades was the most highly enriched in proteins with downregulated ubiquitinated sites, and hsa04114 Oocyte meiosis was the most highly enriched among all differential proteins. Conclusion:Our study expands the understanding of the spectrum of novel targets that are differentially ubiquitinated in whole blood from healthy postmenopausal women and postmenopausal osteoporosis patients. The findings will contribute toward our understanding of the underlying proteostasis pathways in postmenopausal osteoporosis and the potential identification of diagnostic biomarkers in whole blood.

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Quantitative Analysis of the Brain Ubiquitylome in Alzheimer's Disease

Cited by 58 publications

References 75 publications

Using Proteomics to Understand Alzheimer’s Disease Pathogenesis

Using Proteomics to Understand Alzheimer’s Disease Pathogenesis

TBK1 interacts with tau and enhances neurodegeneration in tauopathy

Ubiquitylomes Analysis of the Whole blood in Postmenopausal Osteoporosis Patients and healthy Postmenopausal Women

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