scholarly journals Age-Dependent Hippocampal Proteomics in the APP/PS1 Alzheimer Mouse Model: A Comparative Analysis with Classical SWATH/DIA and directDIA Approaches

Cells ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1588
Author(s):  
Sophie J. F. van der Spek ◽  
Miguel A. Gonzalez-Lozano ◽  
Frank Koopmans ◽  
Suzanne S. M. Miedema ◽  
Iryna Paliukhovich ◽  
...  
Keyword(s):  
Mouse Model ◽  
Neurodegenerative Disorder ◽  
Differential Expression Analysis ◽  
Amyloid Β ◽  
Label Free ◽  
Proteomics Data ◽  
Protein Levels ◽  
Data Independent Acquisition ◽  
Downstream Analysis ◽  
Synaptic Pruning

Alzheimer’s disease (AD) is the most common neurodegenerative disorder in the human population, for which there is currently no cure. The cause of AD is unknown; however, the toxic effects of amyloid-β (Aβ) are believed to play a role in its onset. To investigate this, we examined changes in global protein levels in a hippocampal synaptosome fraction of the Amyloid Precursor Protein swe/Presenelin 1 dE9 (APP/PS1) mouse model of AD at 6 and 12 months of age (moa). Data independent acquisition (DIA), or Sequential Window Acquisition of all THeoretical fragment-ion (SWATH), was used for a quantitative label-free proteomics analysis. We first assessed the usefulness of a recently improved directDIA workflow as an alternative to conventional DIA data analysis using a project-specific spectral library. Subsequently, we applied directDIA to the 6- and 12-moa APP/PS1 datasets and applied the Mass Spectrometry Downstream Analysis Pipeline (MS-DAP) for differential expression analysis and candidate discovery. We observed most regulation at 12-moa, in particular of proteins involved in Aβ homeostasis and microglial-dependent processes, like synaptic pruning and the immune response, such as APOE, CLU and C1QA-C. All proteomics data are available via ProteomeXchange with identifier PXD025777.

scholarly journals obaDIA: one-step biological analysis pipeline for data-independent acquisition and other quantitative proteomics data

2020 ◽  
Author(s):  
Jun Yan ◽  
Hongning Zhai ◽  
Ling Zhu ◽  
Sasha Sa ◽  
Xiaojun Ding
Keyword(s):  
Protein Level ◽  
Quantitative Proteomics ◽  
Differential Expression Analysis ◽  
Biological Significance ◽  
Enrichment Analysis ◽  
Supplementary Information ◽  
Proteomics Data ◽  
Data Independent Acquisition ◽  
One Step ◽  
Automatic Tool

Abstract Motivation Data mining and data quality evaluation are indispensable constituents of quantitative proteomics, but few integrated tools available. Results We introduced obaDIA, a one-step pipeline to generate visualizable and comprehensive results for quantitative proteomics data. obaDIA supports fragment-level, peptide-level and protein-level abundance matrices from DIA technique, as well as protein-level abundance matrices from other quantitative proteomic techniques. The result contains abundance matrix statistics, differential expression analysis, protein functional annotation and enrichment analysis. Additionally, enrichment strategies which use total proteins or expressed proteins as background are optional, and HTML based interactive visualization for differentially expressed proteins in the KEGG pathway is offered, which helps biological significance mining. In short, obaDIA is an automatic tool for bioinformatics analysis for quantitative proteomics. Availability and implementation obaDIA is freely available from https://github.com/yjthu/obaDIA.git. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals FLEXIQuant-LF to quantify protein modification extent in label-free proteomics data

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Christoph N Schlaffner ◽  
Konstantin Kahnert ◽  
Jan Muntel ◽  
Ruchi Chauhan ◽  
Bernhard Y Renard ◽  
...  
Keyword(s):  
Protein Modification ◽  
Large Scale ◽  
Software Tool ◽  
Label Free ◽  
Anaphase Promoting Complex ◽  
Proteomics Data ◽  
Single Experiment ◽  
Post Translational Modifications ◽  
Data Independent Acquisition ◽  
Modified Peptides

Improvements in LC-MS/MS methods and technology have enabled the identification of thousands of modified peptides in a single experiment. However, protein regulation by post-translational modifications (PTMs) is not binary, making methods to quantify the modification extent crucial to understanding the role of PTMs. Here, we introduce FLEXIQuant-LF, a software tool for large-scale identification of differentially modified peptides and quantification of their modification extent without knowledge of the types of modifications involved. We developed FLEXIQuant-LF using label-free quantification of unmodified peptides and robust linear regression to quantify the modification extent of peptides. As proof of concept, we applied FLEXIQuant-LF to data-independent-acquisition (DIA) data of the anaphase promoting complex/cyclosome (APC/C) during mitosis. The unbiased FLEXIQuant-LF approach to assess the modification extent in quantitative proteomics data provides a better understanding of the function and regulation of PTMs. The software is available at https://github.com/SteenOmicsLab/FLEXIQuantLF.

scholarly journals Fluorescent indolizine derivative YI-13 detects amyloid-β monomers, dimers, and plaques in the brain of 5XFAD Alzheimer transgenic mouse model

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243041
Author(s):  
DaWon Kim ◽  
Jeong Hwa Lee ◽  
Hye Yun Kim ◽  
Jisu Shin ◽  
Kyeonghwan Kim ◽  
...  
Keyword(s):  
Mouse Model ◽  
Transgenic Mouse ◽  
Neurodegenerative Disorder ◽  
Amyloid Β ◽  
Transgenic Mouse Model ◽  
Aβ Oligomers ◽  
Aβ Peptides ◽  
Soluble Aβ Oligomers ◽  
The Brain

Alzheimer disease (AD) is a neurodegenerative disorder characterized by the aberrant production and accumulation of amyloid-β (Aβ) peptides in the brain. Accumulated Aβ in soluble oligomer and insoluble plaque forms are considered to be a pathological culprit and biomarker of the disorder. Here, we report a fluorescent universal Aβ-indicator YI-13, 5-(4-fluorobenzoyl)-7,8-dihydropyrrolo[1,2-b]isoquinolin-9(6H)-one, which detects Aβ monomers, dimers, and plaques. We synthesized a library of 26 fluorescence chemicals with the indolizine core and screen them through a series of in vitro tests utilizing Aβ as a target and YI-13 was selected as the final imaging candidate. YI-13 was found to stain and visualize insoluble Aβ plaques in the brain tissue, of a transgenic mouse model with five familial AD mutations (5XFAD), by a histochemical approach and to label soluble Aβ oligomers within brain lysates of the mouse model under a fluorescence plate reader. Among oligomers aggregated from monomers and synthetic dimers from chemically conjugated monomers, YI-13 preferred the dimeric Aβ.

scholarly journals Caspase-6 Knockout in the 5xFAD Model of Alzheimer’s Disease Reveals Favorable Outcome on Memory and Neurological Hallmarks

2020 ◽  
Vol 21 (3) ◽  
pp. 1144
Author(s):  
Ariel Angel ◽  
Rotem Volkman ◽  
Tabitha Grace Royal ◽  
Daniel Offen
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Mouse Model ◽  
Neurodegenerative Disorder ◽  
Amyloid Β ◽  
Cysteine Proteases ◽  
Knock Out ◽  
Model Of Alzheimer’S Disease ◽  
Caspase 6 ◽  
5Xfad Mice

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder and is the most common form of dementia in the elderly. Caspases, a family of cysteine proteases, are major mediators of apoptosis and inflammation. Caspase-6 is considered to be an up-stream modulator of AD pathogenesis as active caspase-6 is abundant in neuropil threads, neuritic plaques, and neurofibrillary tangles of AD brains. In order to further elucidate the role of caspase-6 activity in the pathogenesis of AD, we produced a double transgenic mouse model, combining the 5xFAD mouse model of AD with caspase-6 knock out (C6-KO) mice. Behavioral examinations of 5xFAD/C6-KO double transgenic mice showed improved performance in spatial learning, memory, and anxiety/risk assessment behavior, as compared to 5xFAD mice. Hippocampal mRNA expression analyses showed significantly reduced levels of inflammatory mediator TNF-α, while the anti-inflammatory cytokine IL-10 was increased in 5xFAD/C6-KO mice. A significant reduction in amyloid-β plaques could be observed and immunohistochemistry analyses showed reduced levels of activated microglia and astrocytes in 5xFAD/C6-KO, compared to 5xFAD mice. Together, these results indicate a substantial role for caspase-6 in the pathology of the 5xFAD model of AD and suggest further validation of caspase-6 as a potential therapeutic target for AD.

scholarly journals Sex-Specific Effects of Chronic Creatine Supplementation on Hippocampal-Mediated Spatial Cognition in the 3xTg Mouse Model of Alzheimer’s Disease

Nutrients ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 3589
Author(s):  
Wanda M. Snow ◽  
Chris Cadonic ◽  
Claudia Cortes-Perez ◽  
Aida Adlimoghaddam ◽  
Subir K. Roy Chowdhury ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Mouse Model ◽  
Spatial Cognition ◽  
Creatine Supplementation ◽  
Amyloid Β ◽  
Western Blots ◽  
Protein Levels ◽  
Spatial Search ◽  
Model Of Alzheimer’S Disease

The creatine (Cr) energy system has been implicated in Alzheimer’s disease (AD), including reductions in brain phosphoCr and Cr kinase, yet no studies have examined the neurobehavioral effects of Cr supplementation in AD, including the 3xTg mouse model. This studied investigated the effects of Cr supplementation on spatial cognition, plasticity- and disease-related protein levels, and mitochondrial function in the 3xTg hippocampus. Here, 3xTg mice were fed a control or Cr-supplemented (3% Cr (w/w)) diet for 8–9 weeks and tested in the Morris water maze. Mitochondrial oxygen consumption (Seahorse) and protein levels (Western blots) were measured in the hippocampus in subsets of mice. Overall, 3xTg females exhibited impaired memory as compared to males. In females, Cr supplementation decreased escape latency and was associated with increased spatial search strategy use. In males, Cr supplementation decreased the use of spatial search strategies. Pilot data indicated mitochondrial enhancements with Cr supplementation in both sexes. In females, Cr supplementation increased CREB phosphorylation and levels of IκB (NF-κB suppressor), CaMKII, PSD-95, and high-molecular-weight amyloid β (Aβ) species, whereas Aβ trimers were reduced. These data suggest a beneficial preventative effect of Cr supplementation in females and warrant caution against Cr supplementation in males in the AD-like brain.

scholarly journals MaxDIA enables library-based and library-free data-independent acquisition proteomics

2021 ◽  
Author(s):  
Pavel Sinitcyn ◽  
Hamid Hamzeiy ◽  
Favio Salinas Soto ◽  
Daniel Itzhak ◽  
Frank McCarthy ◽  
...  
Keyword(s):  
Feature Detection ◽  
New Technologies ◽  
Protein Quantification ◽  
Proteomics Data ◽  
Software Environment ◽  
Protein Levels ◽  
Data Independent Acquisition ◽  
Coefficients Of Variation ◽  
Free Data ◽  
Spectral Libraries

AbstractMaxDIA is a software platform for analyzing data-independent acquisition (DIA) proteomics data within the MaxQuant software environment. Using spectral libraries, MaxDIA achieves deep proteome coverage with substantially better coefficients of variation in protein quantification than other software. MaxDIA is equipped with accurate false discovery rate (FDR) estimates on both library-to-DIA match and protein levels, including when using whole-proteome predicted spectral libraries. This is the foundation of discovery DIA—hypothesis-free analysis of DIA samples without library and with reliable FDR control. MaxDIA performs three- or four-dimensional feature detection of fragment data, and scoring of matches is augmented by machine learning on the features of an identification. MaxDIA’s bootstrap DIA workflow performs multiple rounds of matching with increasing quality of recalibration and stringency of matching to the library. Combining MaxDIA with two new technologies—BoxCar acquisition and trapped ion mobility spectrometry—both lead to deep and accurate proteome quantification.

scholarly journals Distinguishing Amyloid β-Protein in a Mouse Model of Alzheimer’s Disease by Label-Free Vibrational Imaging

Biosensors ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 365
Author(s):  
Shaowei Li ◽  
Ziyi Luo ◽  
Renlong Zhang ◽  
Hao Xu ◽  
Ting Zhou ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Mouse Model ◽  
Amyloid Β ◽  
Basic Research ◽  
Amyloid Β Protein ◽  
Label Free ◽  
Model Of Alzheimer’S Disease ◽  
Β Protein ◽  
Anti Stokes

Due to the increase in the average age of humans, Alzheimer’s disease (AD) has become one of the disorders with the highest incidence worldwide. Abnormal amyloid β protein (Aβ) accumulation is believed to be the most common cause of AD. Therefore, distinguishing the lesion areas can provide clues for AD diagnosis. Here, we present an optical spectroscopy and imaging approach based on coherent anti-Stokes Raman scattering (CARS). Label-free vibrational imaging of Aβ in a mouse model of AD was performed to distinguish the lesion areas by studying the spectra of regions with and without Aβ plaques. Raman spectra in Aβ and non-Aβ regions exhibited a specific difference in the intensity ratio of the wave peaks detected at 2850 and 2930 cm–1. In the non-Aβ region, the ratio of the peak intensity at 2850 cm–1 to that at 2930 cm–1 was approximately 1, whereas that in the Aβ region was 0.8. This label-free vibrational imaging may provide a new method for the clinical diagnosis and basic research of AD.

scholarly journals Proteus: an R package for downstream analysis of MaxQuant output

2018 ◽  
Author(s):  
Marek Gierlinski ◽  
Francesco Gastaldello ◽  
Chris Cole ◽  
Geoffrey J. Barton
Keyword(s):  
Mass Spectrometry ◽  
Differential Expression Analysis ◽  
Simulated Data ◽  
R Package ◽  
Data Exploration ◽  
Label Free ◽  
Interactive Analysis ◽  
Quality Checks ◽  
Downstream Analysis ◽  
Selection Of

AbstractProteus is a package for downstream analysis of MaxQuant evidence data in the R environment. It provides tools for peptide and protein aggregation, quality checks, data exploration and visualisation. Interactive analysis is implemented in the Shiny framework, where individual peptides or protein may be examined in the context of a volcano plot. Proteus performs differential expression analysis with the well-established tool limma, which offers robust treatment of missing data, frequently encountered in label-free mass-spectrometry experiments. We demonstrate on real and simulated data that limma results in improved sensitivity over random imputation combined with a t-test as implemented in the popular package Perseus. Embedding Proteus in R provides access to a wide selection of statistical and graphical tools for further analysis and reproducibility by scripting. Availability and implementation: The open-source R package, including example data and tutorials, is available to install from GitHub (https://github.com/bartongroup/proteus).

scholarly journals obaDIA: one-step biological analysis pipeline for data-independent acquisition and other quantitative proteomics data

2020 ◽  
Author(s):  
Jun Yan ◽  
Hongning Zhai ◽  
Ling Zhu ◽  
Sasha Sa ◽  
Xiaojun Ding
Keyword(s):  
Protein Level ◽  
Quantitative Proteomics ◽  
Differential Expression Analysis ◽  
Biological Significance ◽  
Enrichment Analysis ◽  
Proteomics Data ◽  
Analysis Pipeline ◽  
Data Independent Acquisition ◽  
One Step ◽  
Automatic Tool

AbstractMotivationData mining and data quality evaluation are indispensable constituents of quantitative proteomics, but few integrated tools available.ResultsWe introduced obaDIA, a one-step pipeline to generate visualizable and comprehensive results for quantitative proteomics data. obaDIA supports fragment-level, peptide-level and protein-level abundance matrices from DIA technique, as well as protein-level abundance matrices from other quantitative proteomic techniques. The result contains abundance matrix statistics, differential expression analysis, protein functional annotation and enrichment analysis. Additionally, enrichment strategies which use total proteins or expressed proteins as background are optional, and HTML based interactive visualization for differentially expressed proteins in the KEGG pathway is offered, which helps biological significance mining. In short, obaDIA is an automatic tool for bioinformatics analysis for quantitative proteomics.AvailabilityobaDIA is freely available from https://github.com/yjthu/[email protected]

scholarly journals Unraveling the Role of Inwardly Rectifying Potassium Channels in the Hippocampus of an Aβ(1–42)-Infused Rat Model of Alzheimer’s Disease

Biomedicines ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 58
Author(s):  
Enes Akyuz ◽  
Chiara Villa ◽  
Merve Beker ◽  
Birsen Elibol
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Rat Model ◽  
Neurodegenerative Disorder ◽  
Amyloid Β ◽  
Kir Channels ◽  
Protein Levels ◽  
Model Of Alzheimer’S Disease ◽  
Inwardly Rectifying

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder with a complex etiology and characterized by cognitive deficits and memory loss. The pathogenesis of AD is not yet completely elucidated, and no curative treatment is currently available. Inwardly rectifying potassium (Kir) channels are important for playing a key role in maintaining the resting membrane potential and controlling cell excitability, being largely expressed in both excitable and non-excitable tissues, including neurons. Accordingly, the aim of the study is to investigate the role of neuronal Kir channels in AD pathophysiology. The mRNA and protein levels of neuronal Kir2.1, Kir3.1, and Kir6.2 were evaluated by real-time PCR and Western blot analysis from the hippocampus of an amyloid-β(Aβ)(1-42)-infused rat model of AD. Extracellular deposition of Aβ was confirmed by both histological Congo red staining and immunofluorescence analysis. Significant decreased mRNA and protein levels of Kir2.1 and Kir6.2 channels were observed in the rat model of AD, whereas no differences were found in Kir3.1 channel levels as compared with controls. Our results provide in vivo evidence that Aβ can modulate the expression of these channels, which may represent novel potential therapeutic targets in the treatment of AD.

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