Detecting significant changes in protein abundance

Kammers, Kai; Cole, Robert N.; Tiengwe, Calvin; Ruczinski, Ingo

doi:10.1016/j.euprot.2015.02.002

Cited by 257 publications

(274 citation statements)

References 46 publications

(51 reference statements)

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“…Analogously, for the second analysis of six HDL2 and six control brain tissue samples, we fitted a similar regression model for each protein (here X 1 = 1 denotes HDL2 samples). Statistical inference for the slope parameters β was assessed with moderated test statistics and p values (developed by Smyth 34 and extended to quantitative proteomics experiments by Kammers et al 33 ). Here the observed protein samples variances were shrunk toward a pooled variance estimate to obtain more stable variability estimates.…”

Section: Methodsmentioning

confidence: 99%

Quantitative Proteomic Analysis Reveals Similarities between Huntington’s Disease (HD) and Huntington’s Disease-Like 2 (HDL2) Human Brains

et al. 2016

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The pathogenesis of HD and HDL2, similar progressive neurodegenerative disorders caused by expansion mutations, remains incompletely understood. No systematic quantitative proteomics studies, assessing global changes in HD or HDL2 human brain, were reported. To address this deficit, we used a stable isotope labeling-based approach to quantify the changes in protein abundances in the cortex of 12 HD and 12 control cases and, separately, of 6 HDL2 and 6 control cases. The quality of the tissues was assessed to minimize variability due to post mortem autolysis. We applied a robust median sweep algorithm to quantify protein abundance and performed statistical inference using moderated test statistics. 1211 proteins showed statistically significant fold changes between HD and control tissues; the differences in selected proteins were verified by Western blotting. Differentially abundant proteins were enriched in cellular pathways previously implicated in HD, including Rho-mediated, actin cytoskeleton and integrin signaling, mitochondrial dysfunction, endocytosis, axonal guidance, DNA/RNA processing, and protein transport. The abundance of 717 proteins significantly differed between control and HDL2 brain. Comparative analysis of the disease-associated changes in the HD and HDL2 proteomes revealed that similar pathways were altered, suggesting the commonality of pathogenesis between the two disorders.

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Section: Methodsmentioning

confidence: 99%

Quantitative Proteomic Analysis Reveals Similarities between Huntington’s Disease (HD) and Huntington’s Disease-Like 2 (HDL2) Human Brains

et al. 2016

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“…FDR was identified based on a concatenated decoy database search. Statistical calculations were performed using R version 3.4.3 (https://www.R-project.org/) as previously described (Foster et al, 2016;Herbrich et al, 2013;Kammers, Cole, Tiengwe, & Ruczinski, 2015;Ratovitski et al, 2016). In a first step, reporter ion spectra with isolation interference ≥30% were excluded.…”

Section: Protein Quantitationmentioning

confidence: 99%

Stimulus‐dependent modifications in astrocyte‐derived extracellular vesicle cargo regulate neuronal excitability

Chaudhuri

Dasgheyb

DeVine

et al. 2019

Glia

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Extracellular vesicles have now emerged as key players in cell‐to‐cell communication. This is particularly important in the central nervous system, where glia–neuron cross‐talk helps maintain normal neuronal function. Astrocyte‐derived extracellular vesicles (ADEVs) secreted constitutively promote neurite outgrowth and neuronal survival. However, extracellular stimuli can alter the cargo and downstream functions of ADEVs. For example, ADEVs secreted in response to inflammation contain cargo microRNAs and proteins that reduce neurite outgrowth, neuronal firing, and promote neuronal apoptosis. We performed a comprehensive quantitative proteomic analysis to enumerate the proteomic cargo of ADEVs secreted in response to multiple stimuli. Rat primary astrocytes were stimulated with a trophic stimulus (adenosine triphosphate, ATP), an inflammatory stimulus (IL‐1β) or an anti‐inflammatory stimulus (IL10) and extracellular vesicles secreted within a 2 hr time frame were collected using sequential ultracentrifugation method. ADEVs secreted constitutively without exposure to any stimulus were used a control. A tandem mass tag‐based proteomic platform was used to identify and quantify proteins in the ADEVs. Ingenuity pathway analysis was performed to predict the downstream signaling events regulated by ADEVs. We found that in response to ATP or IL10, ADEVs contain a set of proteins that are involved in increasing neurite outgrowth, dendritic branching, regulation of synaptic transmission, and promoting neuronal survival. In contrast, ADEVs secreted in response to IL‐1β contain proteins that regulate peripheral immune response and immune cell trafficking to the central nervous system.

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“…Tissue lysis, sample preparation, liquid chromatography‐tandem mass spectrometry (LC‐MS/MS), and data analysis were performed as described . Statistical analysis of proteomic data was performed using linear models for microarray data (limma) …”

Section: Methodsmentioning

confidence: 99%

Impact of left ventricular assist device therapy on the cardiac proteome and metabolome composition in ischemic cardiomyopathy

et al. 2019

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The changes in the myocardial proteome and metabolome associated with left ventricular assist device (LVAD) therapy in patients with ischemic cardiomyopathy (ICM) are poorly characterized. We investigated the impact of mechanical unloading following LVAD therapy on the myocardial proteome and metabolome. Matched samples of 5 patients’ myocardial tissue, harvested at the time of LVAD implant (“pre‐LVAD”) or heart transplant (“post‐LVAD”), were studied by quantitative proteomics and metabolomics as well as being probed for T‐tubule structure and connexin‐43 distribution. Moreover, pre‐LVAD proteome profiles of ICM context were bioinformatically compared to pre‐LVAD proteome profiles of dilated cardiac myopathy (DCM). More than 2120 proteins were reliably identified and quantified in paired patient samples. LVAD therapy led to proteomic remodeling, including reduced levels of α‐1‐antichymotrypsin together with an overall decrease of immune response proteins and an increase of proteins involved in membrane biology. Metabolomics highlighted increased glucose and glucose‐6‐phosphate levels in the left ventricle upon LVAD therapy. Wheat germ agglutinin staining demonstrated improved T‐tubule structure. Connexin‐43 displayed a trend for more pronounced intercalated disc localization. In comparing pre‐LVAD proteome profiles of ICM context with pre‐LVAD proteome profiles of dilated cardiac myopathy (DCM), we noticed an overrepresentation in ICM of proteins associated with humoral immune response. Our findings underline an impact of LVAD therapy on left ventricular biology in ICM. The proteomic, metabolomic, and structural alterations described here are typically associated with cardiac recovery. On the molecular level, our findings indicate the possibility of cardiac remodeling under LVAD therapy in ICM.

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Detecting significant changes in protein abundance

Cited by 257 publications

References 46 publications

Quantitative Proteomic Analysis Reveals Similarities between Huntington’s Disease (HD) and Huntington’s Disease-Like 2 (HDL2) Human Brains

Quantitative Proteomic Analysis Reveals Similarities between Huntington’s Disease (HD) and Huntington’s Disease-Like 2 (HDL2) Human Brains

Stimulus‐dependent modifications in astrocyte‐derived extracellular vesicle cargo regulate neuronal excitability

Impact of left ventricular assist device therapy on the cardiac proteome and metabolome composition in ischemic cardiomyopathy

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