lerlic-msms-for-depth-characterization-quantification-glutamine

LERLIC-MS/MS for In-depth Characterization and Quantification of Glutamine and Asparagine Deamidation in Shotgun Proteomics

Characterization of protein deamidation is imperative to decipher the role(s) and potentialities of this protein posttranslational modification (PTM) in ...

Nanyang Technological University

C boutons are large, cholinergic, synaptic terminals that arise from local interneurons and specifically contact spinal α-motoneurons (MNs). C boutons characteristically display a postsynaptic specialization consisting of an endoplasmic reticulum-related subsurface cistern (SSC) of unknown function. In the present work, by using confocal microscopy and ultrastructural immunolabeling, we demonstrate that neuregulin-1 (NRG1) accumulates in the SSC of mouse spinal MNs. We also show that the NRG1 receptors erbB2 and erbB4 are presynaptically localized within C boutons, suggesting that NRG1-based retrograde signaling may occur in this type of synapse. In most of the cranial nuclei, MNs display the same pattern of NRG1 distribution as that observed in spinal cord MNs. Conversely, MNs in oculomotor nuclei, which are spared in amyotrophic lateral sclerosis (ALS), lack both C boutons and SSC-associated NRG1. NRG1 in spinal MNs is developmentally regulated and depends on the maintenance of nerve-muscle interactions, as we show after nerve transection experiments. Changes in NRG1 in C boutons were also investigated in mouse models of MN diseases: i.e., spinal muscular atrophy (SMNΔ7) and ALS (SOD1(G93A)). In both models, a transient increase in NRG1 in C boutons occurs during disease progression. These data increase our understanding of the role of C boutons in MN physiology and pathology.

Neuregulin-1 is concentrated in the postsynaptic subsurface cistern of C-bouton inputs to α-motoneurons and altered during motoneuron diseases.

Progressive synaptic failure precedes the loss of neurons and decline in cognitive function in neurodegenerative disorders, but the specific proteins and posttranslational modifications that promote synaptic failure in vascular dementia (VaD) remain largely unknown. We therefore used an isobaric tag for relative and absolute proteomic quantitation (iTRAQ) to profile the synapse-associated proteome of post-mortem human cortex from vascular dementia patients and age-matched controls. Brain tissue from VaD patients exhibited significant down-regulation of critical synaptic proteins including clathrin (0.29; p < 1.0⋅10(-3)) and GDI1 (0.51; p = 3.0⋅10(-3)), whereas SNAP25 (1.6; p = 5.5⋅10(-3)), bassoon (1.4; p = 1.3⋅10(-3)), excitatory amino acid transporter 2 (2.6; p = 9.2⋅10(-3)) and Ca(2+)/calmodulin dependent kinase II (1.6; p = 3.0⋅10(-2)) were substantially up-regulated. Our analyses further revealed divergent patterns of protein modification in the dementia patient samples, including a specific deamidation of synapsin1 predicted to compromise protein structure. Our results reveal potential molecular targets for intervention in synaptic failure and prevention of cognitive decline in VaD.

Temporal lobe proteins implicated in synaptic failure exhibit differential expression and deamidation in vascular dementia.

Individuals with Parkinson's disease (PD) with symptom onset on the left side of the body (LPD) show a mild type of left-sided visuospatial neglect, whereas those with right-onset (RPD) generally do not. The functional mechanisms underlying these observations are unknown. Two hypotheses are that the representation of left-space in LPD is either compressed or reduced in salience. We tested these hypotheses psychophysically. Participants were 31 non-demented adults with PD (15 LPD, 16 RPD) and 17 normal control adults (NC). The spatial compression hypothesis was tested by showing two sinusoidal gratings, side by side. One grating's spatial frequency (SF) was varied across trials, following a staircase procedure, whereas the comparison grating was held at a constant SF. While fixating on a central target, participants estimated the point at which they perceived the two gratings to be equal in SF. The reduced salience hypothesis was tested in a similar way, but by manipulating the contrast of the test grating rather than its SF. There were no significant differences between groups in the degree of bias across hemifields for SF discrimination or for contrast discrimination. Results did not support either the spatial compression hypothesis or the reduced salience hypothesis. Instead, they suggest that at this perceptual level, LPD do not have a systematically biased way of representing space in the left hemifield that differs from healthy individuals, nor do they perceive stimuli on the left as less salient than stimuli on the right. Neglect-like syndrome in LPD instead presumably arises from dysfunction of higher-order attention.

Normal discrimination of spatial frequency and contrast across visual hemifields in left-onset Parkinson's disease: evidence against perceptual hemifield biases.

Degenerative protein modifications (DPMs) are caused by nonenzymatic chemical reactions that induce changes in protein structure and function which promote disease initiation, pathological progression and also natural aging. These undesirable DPMs include oxidation, carbonylation, carbamylation, glycation, deamidation, isomerization, nitration, and racemization, which impart deleterious structural and functional changes on extracellular matrix proteins and long-lived cell types such as cardiomyocytes and neurons, leading to impaired overall organ function. Despite the obvious clinical importance of understanding DPM biology, the molecular mechanisms that mediate these modifications remain poorly understood largely due to the technical challenges associated with their study. However, recent advances in mass spectrometry-based proteomics technologies now permit global quantitative proteomic profiling of cell lines, animal models, and human clinical samples from a variety of different patient types. These new methods have not only uncovered changes in global protein expression levels but have also identified specific modifications of particular amino acid residues in protein backbones that are associated with disease progression. The nonenzymatic induction of DPMs as revealed by proteomic profiling can help us to better understand the underlying molecular pathology of protein dysfunction in human diseases and natural aging. This chapter discusses recent progress in understanding how proteomic profiling of patient samples derived from the central nervous system can elucidate the DPM biology of human neurodegenerative diseases.

Uncovering Neurodegenerative Protein Modifications via Proteomic Profiling.

Extracellular vesicles (EVs) such as exosomes and microvesicles mediate intercellular communication and regulate a diverse range of crucial biological processes. Host cells that are damaged, infected or transformed release biomarker-containing EVs into the peripheral circulation, where they can be readily accessed for use in diagnostic or prognostic testing. However, current methods of EV isolation from blood plasma are complex and often require relatively large sample volumes, hence are inefficient for widespread use in clinical settings. Here, we report a novel and inexpensive method of rapidly isolating EVs from small volumes of human blood plasma by PRotein Organic Solvent PRecipitation (PROSPR). PROSPR encompasses a rapid three-step protocol to remove soluble proteins from plasma via precipitation in cold acetone, leaving the lipid-encapsulated EVs behind in suspension. This generates higher purity EVs that can then be obtained from filtration or classical ultracentrifugation methods. We foresee that PROSPR-based purification of EVs will significantly accelerate the discovery of new disease biomarkers and the characterization of EVs with potential for clinical applications.

Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR).

Protein deamidation has been proposed to represent a "molecular clock" that progressively disrupts protein structure and function in human degenerative diseases and natural aging. Importantly, this spontaneous process can also modify therapeutic proteins by altering their purity, stability, bioactivity, and antigenicity during drug synthesis and storage. Deamidation occurs non-enzymatically in vivo, but can also take place spontaneously in vitro, hence artificial deamidation during proteomic sample preparation can hamper efforts to identify and quantify endogenous deamidation of complex proteomes. To overcome this, mass spectrometry (MS) can be used to conduct rigorous site-specific characterization of protein deamidation due to the high sensitivity, speed, and specificity offered by this technique. This article reviews recent progress in MS analysis of protein deamidation and discusses the strengths and limitations of common "top-down" and "bottom-up" approaches. Recent advances in sample preparation methods, chromatographic separation, MS technology, and data processing have for the first time enabled the accurate and reliable characterization of protein modifications in complex biological samples, yielding important new data on how deamidation occurs across the entire proteome of human cells and tissues. These technological advances will lead to a better understanding of how deamidation contributes to the pathology of biological aging and major degenerative diseases. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 9999: XX-XX, 2016.

Recent advances in mass spectrometric analysis of protein deamidation.

The ionic detergent sodium deoxycholate (SDC) is compatible with in-solution tryptic digestion and LC-MS/MS-based shotgun proteomics by virtue of being easy to separate from the peptide products via precipitation in acidic buffers. However, it remains unclear whether unique human peptides co-precipitate with SDC during acid treatment of complex biological samples. In this study, we demonstrate for the first time that a large quantity of unique peptides in human blood plasma can be co-precipitated with SDC using an optimized sample preparation method prior to shotgun proteomic analysis. We show that the plasma peptides co-precipitated with SDC can be successfully recovered using a sequential re-solubilization and precipitation procedure, and that this approach is particularly efficient at the extraction of long peptides. Recovery of peptides from the SDC pellet dramatically increased overall proteome coverage (>60 %), thereby improving the identification of low-abundance proteins and enhancing the identification of protein components of membrane-bound organelles. In addition, when we analyzed the physiochemical properties of the co-precipitated peptides, we observed that SDC-based sample preparation improved the identification of mildly hydrophilic/hydrophobic proteins that would otherwise be lost upon discarding the pellet. These data demonstrate that the optimized SDC protocol is superior to sodium dodecyl sulfate (SDS)/urea treatment for identifying plasma biomarkers by shotgun proteomics.

Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate.

Aggregation of malformed proteins is a key feature of many neurodegenerative diseases, but the mechanisms that drive proteinopathy in the brain are poorly understood. We aimed to characterize aggregated proteins in human brain tissues affected by dementia.

Dementia-linked amyloidosis is associated with brain protein deamidation as revealed by proteomic profiling of human brain tissues.

Dementia risk in women is higher than in men, but the molecular neuropathology of this gender difference remains poorly defined. In this study, we used unbiased, discovery-driven quantitative proteomics to assess the molecular basis of gender influences on risk of Alzheimer's disease with cerebrovascular disease (AD + CVD).

Gender differences in white matter pathology and mitochondrial dysfunction in Alzheimer's disease with cerebrovascular disease.

Mitochondrial pathology is a seminal pathogenic hallmark of familial amyotrophic lateral sclerosis (FALS) which is extensively manifested by human patients and mutant SOD1(G93A) mammalian models. Rodents expressing human FALS-associated mutations successfully mimic several human disease features; although they are not as amenable to genetic and therapeutic compound screenings as non-mammalian models. In this study, we report a newly generated and characterized Drosophila model that expresses human SOD1(G93A) in muscle fibers. Presence of SOD1(G93A) in thoracic muscles causes mitochondrial pathology and impairs normal motor behavior in these flies. Use of this new FALS-24B-SOD1(G93A) fly model holds promise for better understanding of the mitochondrial affectation process in FALS and for the discovery of novel therapeutic compounds able to reverse mitochondrial dysfunction in this fatal disease.

Drosophila expressing human SOD1 successfully recapitulates mitochondrial phenotypic features of familial amyotrophic lateral sclerosis.

Nutraceuticals have been proposed to exert positive effects on human health and confer protection against many chronic diseases. A major bioactive component of soy-based foods is lunasin peptide, which has potential to exert a major impact on the health of human consumers worldwide, but the biochemical features of dietary lunasin still remain poorly characterized. In this study, lunasin was purified from a soy-based food product via strong anion exchange solid phase extraction and then subjected to top-down mass spectrometry analysis that revealed in detail the molecular diversity of lunasin in processed soybean foods. We detected multiple glycated proteoforms together with potentially toxic advanced glycation end products (AGEs) derived from lunasin. In both cases, modification sites were Lys24 and Lys29 located at the helical region that shows structural homology with a conserved region of chromatin-binding proteins. The identified post-translational modifications may have an important repercussion on lunasin epigenetic regulatory capacity. Taking together, our results demonstrate the importance of proper chemical characterization of commercial processed food products to assess their impact on consumer's health and risk of chronic diseases.

Commercial processed soy-based food product contains glycated and glycoxidated lunasin proteoforms.

Extracellular vesicles (EVs) act as key mediators of intercellular communication and are secreted and taken up by all cell types in the central nervous system (CNS). While detailed study of EV-based signaling is likely to significantly advance our understanding of human neurobiology, the technical challenges of isolating EVs from CNS tissues have limited their characterization using 'omics' technologies. We therefore developed a new Protein Organic Solvent Precipitation (PROSPR) method that can efficiently isolate the EV repertoire from human biological samples.

Enrichment of extracellular vesicles from tissues of the central nervous system by PROSPR.

The tumour suppressor p53 is a central player in transcription regulation and cell fate determination. By interacting with p53 and altering its sequence-specific binding to the response elements, the hepatitis B virus X protein (HBx) was reported to re-direct p53 regulation of some genes.

Global re-wiring of p53 transcription regulation by the hepatitis B virus X protein.

Deamidation of glutamine (Gln) residues is a spontaneous or enzymatic process with significant implications in aging and human pathology. Although some methods are available to identify the γ/α-glutamyl products of deamidation, none of these methods allows the characterization of this post-translational modification (PTM) from complex biological samples by shotgun proteomics. Here we present LERLIC-MS/MS, a chromatographic strategy that uses a long (50 cm) anion-exchange capillary column operating in the electrostatic repulsion-hydrophilic interaction mode (ERLIC) and coupled directly to tandem mass spectrometry (MS/MS) for proteome analysis in a single injection. Profiling of soluble extracts of brain tissues by LERLIC-MS/MS distinguished for the first time γ/α-glutamyl isomers of deamidation, encountering a 1.7 γ/α-glutamyl ratio for most Gln deamidation products. A detailed analysis of any deviation from that observed ratio allowed the identification of transglutaminase-mediated γ-glutamyl isomers as intermediate products of transamidation. Furthermore, LERLIC-MS/MS was able to simultaneously separate Gln and asparagine (Asn) deamidation products even for those peptides showing multiple deamidated proteoforms. The characterization of Asn deamidated residues by LERLIC-MS/MS also uncovered novel PIMT (protein L-isoaspartyl methyltransferase) substrate proteins in human brain tissues that deviated from the expected 3:1 isoAsp/Asp ratio. Taken together, our results demonstrate that LERLIC-MS/MS can be used to perform an in-depth study of protein deamidation on a global proteome scale. This new strategy should help to elucidate the biological implications of deamidation in aging and disease conditions.

Characterization of Glutamine Deamidation by Long-Length Electrostatic Repulsion-Hydrophilic Interaction Chromatography-Tandem Mass Spectrometry (LERLIC-MS/MS) in Shotgun Proteomics.

Article	Year
Neuregulin-1 is concentrated in the postsynaptic subsurface cistern of C-bouton inputs to α-motoneurons and altered during motoneuron diseases. FASEB journal : official publication of the Federation of American Societies for Experimental Biology\| PubMed ID: 24803543	2014
Temporal lobe proteins implicated in synaptic failure exhibit differential expression and deamidation in vascular dementia. Neurochemistry international\| PubMed ID: 25497727	2015
Normal discrimination of spatial frequency and contrast across visual hemifields in left-onset Parkinson's disease: evidence against perceptual hemifield biases. Vision research\| PubMed ID: 25498374	2015
Uncovering Neurodegenerative Protein Modifications via Proteomic Profiling. International review of neurobiology\| PubMed ID: 26315763	2015
Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR). Scientific reports\| PubMed ID: 26419333	2015
Recent advances in mass spectrometric analysis of protein deamidation. Mass spectrometry reviews\| PubMed ID: 26763661	2016
Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate. Analytical and bioanalytical chemistry\| PubMed ID: 26804737	2016
Dementia-linked amyloidosis is associated with brain protein deamidation as revealed by proteomic profiling of human brain tissues. Molecular brain\| PubMed ID: 26892330	2016
Gender differences in white matter pathology and mitochondrial dysfunction in Alzheimer's disease with cerebrovascular disease. Molecular brain\| PubMed ID: 26983404	2016
Drosophila expressing human SOD1 successfully recapitulates mitochondrial phenotypic features of familial amyotrophic lateral sclerosis. Neuroscience letters\| PubMed ID: 27163198	2016
Commercial processed soy-based food product contains glycated and glycoxidated lunasin proteoforms. Scientific reports\| PubMed ID: 27189269	2016
Enrichment of extracellular vesicles from tissues of the central nervous system by PROSPR. Molecular neurodegeneration\| PubMed ID: 27216497	2016
Global re-wiring of p53 transcription regulation by the hepatitis B virus X protein. Molecular oncology\| PubMed ID: 27302019	2016
Characterization of Glutamine Deamidation by Long-Length Electrostatic Repulsion-Hydrophilic Interaction Chromatography-Tandem Mass Spectrometry (LERLIC-MS/MS) in Shotgun Proteomics. Analytical chemistry\| PubMed ID: 27689507	2016

Xavier Gallart-Palau

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