Methods for proteomics in neuroscience

Vibrio deploys type 2 secreted lipase to esterify cholesterol with host fatty acids and mediate cell egress

Pathogens find diverse niches for survival including inside a host cell where replication occurs in a relatively protective environment. Vibrio parahaemolyticus is a facultative intracellular pathogen that uses its type 3 secretion system 2 (T3SS2) to invade and replicate inside host cells. Analysis of the T3SS2 pathogenicity island encoding the T3SS2 appeared to lack a mechanism for egress of this bacterium from the invaded host cell. Using a combination of molecular tools, we found that VPA0226, a constitutively secreted lipase, is required for escape of V. parahaemolyticus from the host cells. This lipase must be delivered into the host cytoplasm where it preferentially uses fatty acids associated with innate immune response to esterify cholesterol, weakening the plasma membrane and allowing egress of the bacteria. This study reveals the resourcefulness of microbes and the interplay between virulence systems and host cell resources to evolve an ingenious scheme for survival and escape.

Haploinsufficiency of X-linked intellectual disability gene CASK induces post-transcriptional changes in synaptic and cellular metabolic pathways

Heterozygous mutations in the X-linked gene CASK are associated with intellectual disability, microcephaly, pontocerebellar hypoplasia, optic nerve hypoplasia and partially penetrant seizures in girls. The Cask^+/- heterozygous knockout female mouse phenocopies the human disorder and exhibits postnatal microencephaly, cerebellar hypoplasia and optic nerve hypoplasia. It is not known if Cask^+/- mice also display seizures, nor is known the molecular mechanism by which CASK haploinsufficiency produces the numerous documented phenotypes. 24-h video electroencephalography demonstrates that despite sporadic seizure activity, the overall electrographic patterns remain unaltered in Cask^+/- mice. Additionally, seizure threshold to the commonly used kindling agent, pentylenetetrazol, remains unaltered in Cask^+/- mice, indicating that even in mice the seizure phenotype is only partially penetrant and may have an indirect mechanism. RNA sequencing experiments on Cask^+/- mouse brain uncovers a very limited number of changes, with most differences arising in the transcripts of extracellular matrix proteins and the transcripts of a group of nuclear proteins. In contrast to limited changes at the transcript level, quantitative whole-brain proteomics using iTRAQ quantitative mass-spectrometry reveals major changes in synaptic, metabolic/mitochondrial, cytoskeletal, and protein metabolic pathways. Unbiased protein-protein interaction mapping using affinity chromatography demonstrates that CASK may form complexes with proteins belonging to the same functional groups in which altered protein levels are observed. We discuss the mechanism of the observed changes in the context of known molecular function/s of CASK. Overall, our data indicate that the phenotypic spectrum of female Cask^+/- mice includes sporadic seizures and thus closely parallels that of CASK haploinsufficient girls; the Cask^+/- mouse is thus a face-validated model for CASK-related pathologies. We therefore surmise that CASK haploinsufficiency is likely to affect brain structure and function due to dysregulation of several cellular pathways including synaptic signaling and cellular metabolism.

iTRAQ-based quantitative proteomic analysis and bioinformatics study of proteins in retinoblastoma

The aim of the present study was to analyze proteins in the aqueous humor (AH) of patients' retinoblastoma (RB), and investigate their potential role in RB using the comparative proteomic technique of isobaric tags for relative and absolute quantitation (iTRAQ) coupled with offline two-dimensional liquid chromatography-tandem mass spectrometry. A total of 0.1 ml AH was collected from 10 children with RB (mean age, 3.8 years; range, 2-5 years) and patients with senile cataracts (mean age, 70.4 years; range, 65-79 years), which was used as the control. iTRAQ was used to analyze proteins in the AH of patients and controls. Proteins with a fold change of >1.20 or <0.83 were considered to be significantly differentially expressed (with corrected P<0.05). The identified proteins were subjected to subsequent gene ontology (GO) analysis using the DAVID database. A total of 83 proteins that were expressed differently between the controls and patients' AH samples were identified using iTRAQ analysis. Of these proteins, 44 were upregulated and 39 were downregulated. On the basis of biological processes in GO, the identified proteins were primarily involved in glycoprotein, amyloid acute-inflammatory and defensive responses. Among these proteins, pigment epithelium-derived factor serves a potential role in the treatment of RB, and stimulated by retinoic acid 6 may serve as a potential protein involved in RB development. To the best of our knowledge, the present study is the first to identify 83 proteins associated with RB using iTRAQ technology. The results of the present study will aid in furthering the understanding of RB and developing novel therapy targets in the future.

Active and Repressive Chromatin-Associated Proteome after MPA Treatment and the Role of Midkine in Epithelial Monolayer Permeability

Mycophenolic acid (MPA) is prescribed to maintain allografts in organ-transplanted patients. However, gastrointestinal (GI) complications, particularly diarrhea, are frequently observed as a side effect following MPA therapy. We recently reported that MPA altered the tight junction (TJ)-mediated barrier function in a Caco-2 cell monolayer model system. This study investigates whether MPA induces epigenetic changes which lead to GI complications, especially diarrhea.

METHODS

We employed a Chromatin Immunoprecipitation-O-Proteomics (ChIP-O-Proteomics) approach to identify proteins associated with active (H3K4me3) as well as repressive (H3K27me3) chromatin histone modifications in MPA-treated cells, and further characterized the role of midkine, a H3K4me3-associated protein, in the context of epithelial monolayer permeability.

RESULTS

We identified a total of 333 and 306 proteins associated with active and repressive histone modification marks, respectively. Among them, 241 proteins were common both in active and repressive chromatin, 92 proteins were associated exclusively with the active histone modification mark, while 65 proteins remained specific to repressive chromatin. Our results show that 45 proteins which bind to the active and seven proteins which bind to the repressive chromatin region exhibited significantly altered abundance in MPA-treated cells as compared to DMSO control cells. A number of novel proteins whose function is not known in bowel barrier regulation were among the identified proteins, including midkine. Our functional integrity assays on the Caco-2 cell monolayer showed that the inhibition of midkine expression prior to MPA treatment could completely block the MPA-mediated increase in barrier permeability.

CONCLUSIONS

The ChIP-O-Proteomics approach delivered a number of novel proteins with potential implications in MPA toxicity. Consequently, it can be proposed that midkine inhibition could be a potent therapeutic approach to prevent the MPA-mediated increase in TJ permeability and leak flux diarrhea in organ transplant patients.

Quantification of the brain proteome in Alzheimer's disease using multiplexed mass spectrometry

We have compared the brain proteome in the temporal neocortex between Alzheimer's disease (AD) patients and non-AD individuals by using shotgun mass spectrometry based on a stable isotope dimethyl labeling. A total of 827 unique proteins were identified and quantitated. Of these, 227 proteins were found in at least 9 out of 10 AD/control pairs and were further subjected to statistical analysis. A total of 69 proteins showed different levels (p-value < 0.05) in AD versus control brain samples. Of these proteins, 37 were increased and 32 were decreased as compared to the non-AD subjects. Twenty-three proteins comprise novel proteins that have not previously been reported as related to AD, e.g., neuronal-specific septin-3, septin-2, septin-5, dihydropteridine reductase, and clathrin heavy chain 1. The proteins with altered levels in the AD brain represent a wide variety of pathways suggested to be involved in the disease pathogenesis, including energy metabolism, glycolysis, oxidative stress, apoptosis, signal transduction, and synaptic functioning. Apart from leading to new insights into the molecular mechanisms in AD, the findings provide us with possible novel candidates for future diagnostic and prognostic disease markers.

Identification of differentially expressed proteins in fresh and frozen–thawed boar spermatozoa by iTRAQ-coupled 2D LC–MS/MS

Cryodamage is a major problem in semen cryopreservation, causing changes in the levels of proteins that influence the function and motility of spermatozoa. In this study, protein samples prepared from fresh and frozen–thawed boar spermatozoa were compared using the isobaric tags for relative and absolute quantification (iTRAQ) labeling technique coupled to 2D LC–MS/MS analysis. A total of 41 differentially expressed proteins were identified and quantified, including 35 proteins that were present at higher levels and six proteins that were present at lower levels in frozen–thawed spermatozoa by at least a mean of 1.79-fold (P<0.05). On classifying into ten distinct categories using bioinformatic analysis, most of the 41 differentially expressed proteins were found to be closely relevant to sperm premature capacitation, adhesions, energy supply, and sperm–oocyte binding and fusion. The expression of four of these proteins, SOD1, TPI1, ODF2, and AKAP3, was verified by western blot analysis. We propose that alterations in these identified proteins affect the quality of cryopreserved semen and ultimately lower its fertilizing capacity. This is the first study to compare protein levels in fresh and frozen–thawed spermatozoa using the iTRAQ technology. Our preliminary results provide an overview of the molecular mechanisms of cryodamage in frozen–thawed spermatozoa and theoretical guidance to improve the cryopreservation of boar semen.

Proteomic analysis of vascular smooth muscle cells with S- and R-enantiomers of atenolol by iTRAQ and LC-MS/MS

The term "proteome" was first introduced by referring to the complete determination of proteins expressed in a given cell, tissue, or organism. In HPLC-based proteomics technique, the mixture of the cleaved peptides are bonded, separated sequentially on the multidimensional columns based on charge or hydrophobicity of the ionized analytes, and then eluted into the MS for identification. Among the developed stable isotope-based quantification methods, iTRAQ has recently gained popularity as its simple iTRAQ labeling procedures and up to eight labeled samples examined in a single experiment.

Exploring the nicotinic acetylcholine receptor-associated proteome with iTRAQ and transgenic mice

Neuronal nicotinic acetylcholine receptors (nAChRs) containing α4 and β2 subunits are the principal receptors in the mammalian central nervous system that bind nicotine with high affinity. These nAChRs are involved in nicotine dependence, mood disorders, neurodegeneration and neuroprotection. However, our understanding of the interactions between α4β2-containing (α4β2(∗)) nAChRs and other proteins remains limited. In this study, we identified proteins that interact with α4β2(∗) nAChRs in a genedose dependent pattern by immunopurifying β2(∗) nAChRs from mice that differ in α4 and β2 subunit expression and performing proteomic analysis using isobaric tags for relative and absolute quantitation (iTRAQ). Reduced expression of either the α4 or the β2 subunit results in a correlated decline in the expression of a number of putative interacting proteins. We identified 208 proteins co-immunoprecipitated with these nAChRs. Furthermore, stratified linear regression analysis indicated that levels of 17 proteins was correlated significantly with expression of α4β2 nAChRs, including proteins involved in cytoskeletal rearrangement and calcium signaling. These findings represent the first application of quantitative proteomics to produce a β2(∗) nAChR interactome and describe a novel technique used to discover potential targets for pharmacological manipulation of α4β2 nAChRs and their downstream signaling mechanisms.

Recent advances in quantitative neuroproteomics

The field of proteomics is undergoing rapid development in a number of different areas including improvements in mass spectrometric platforms, peptide identification algorithms and bioinformatics. In particular, new and/or improved approaches have established robust methods that not only allow for in-depth and accurate peptide and protein identification and modification, but also allow for sensitive measurement of relative or absolute quantitation. These methods are beginning to be applied to the area of neuroproteomics, but the central nervous system poses many specific challenges in terms of quantitative proteomics, given the large number of different neuronal cell types that are intermixed and that exhibit distinct patterns of gene and protein expression. This review highlights the recent advances that have been made in quantitative neuroproteomics, with a focus on work published over the last five years that applies emerging methods to normal brain function as well as to various neuropsychiatric disorders including schizophrenia and drug addiction as well as of neurodegenerative diseases including Parkinson's disease and Alzheimer's disease. While older methods such as two-dimensional polyacrylamide electrophoresis continued to be used, a variety of more in-depth MS-based approaches including both label (ICAT, iTRAQ, TMT, SILAC, SILAM), label-free (label-free, MRM, SWATH) and absolute quantification methods, are rapidly being applied to neurobiological investigations of normal and diseased brain tissue as well as of cerebrospinal fluid (CSF). While the biological implications of many of these studies remain to be clearly established, that there is a clear need for standardization of experimental design and data analysis, and that the analysis of protein changes in specific neuronal cell types in the central nervous system remains a serious challenge, it appears that the quality and depth of the more recent quantitative proteomics studies is beginning to shed light on a number of aspects of neuroscience that relates to normal brain function as well as of the changes in protein expression and regulation that occurs in neuropsychiatric and neurodegenerative disorders.

Monomeric synucleins generate membrane curvature

Synucleins are a family of presynaptic membrane binding proteins. α-Synuclein, the principal member of this family, is mutated in familial Parkinson disease. To gain insight into the molecular functions of synucleins, we performed an unbiased proteomic screen and identified synaptic protein changes in αβγ-synuclein knock-out brains. We observed increases in the levels of select membrane curvature sensing/generating proteins. One of the most prominent changes was for the N-BAR protein endophilin A1. Here we demonstrate that the levels of synucleins and endophilin A1 are reciprocally regulated and that they are functionally related. We show that all synucleins can robustly generate membrane curvature similar to endophilins. However, only monomeric but not tetrameric α-synuclein can bend membranes. Further, A30P α-synuclein, a Parkinson disease mutant that disrupts protein folding, is also deficient in this activity. This suggests that synucleins generate membrane curvature through the asymmetric insertion of their N-terminal amphipathic helix. Based on our findings, we propose to include synucleins in the class of amphipathic helix-containing proteins that sense and generate membrane curvature. These results advance our understanding of the physiological function of synucleins.

Genomic analysis of sleep deprivation reveals translational regulation in the hippocampus

Sleep deprivation is a common problem of considerable health and economic impact in today's society. Sleep loss is associated with deleterious effects on cognitive functions such as memory and has a high comorbidity with many neurodegenerative and neuropsychiatric disorders. Therefore, it is crucial to understand the molecular basis of the effect of sleep deprivation in the brain. In this study, we combined genome-wide and traditional molecular biological approaches to determine the cellular and molecular impacts of sleep deprivation in the mouse hippocampus, a brain area crucial for many forms of memory. Microarray analysis examining the effects of 5 h of sleep deprivation on gene expression in the mouse hippocampus found 533 genes with altered expression. Bioinformatic analysis revealed that a prominent effect of sleep deprivation was to downregulate translation, potentially mediated through components of the insulin signaling pathway such as the mammalian target of rapamycin (mTOR), a key regulator of protein synthesis. Consistent with this analysis, sleep deprivation reduced levels of total and phosphorylated mTOR, and levels returned to baseline after 2.5 h of recovery sleep. Our findings represent the first genome-wide analysis of the effects of sleep deprivation on the mouse hippocampus, and they suggest that the detrimental effects of sleep deprivation may be mediated by reductions in protein synthesis via downregulation of mTOR. Because protein synthesis and mTOR activation are required for long-term memory formation, our study improves our understanding of the molecular mechanisms underlying the memory impairments induced by sleep deprivation.

Systems biology approaches to finding novel pain mediators

Chronic pain represents a major health burden; this maladaptive pain state occurs as a consequence of hypersensitivity within the peripheral and central components of the somatosensory system. High throughput technologies (genomics, transciptomics, lipidomics, and proteomics) are now being applied to tissue derived from pain patients as well as experimental pain models to discover novel pain mediators. The use of clustering, meta-analysis and other techniques can help refine potential candidates. Of particular importance are systems biology methods, such as co-expression network generating algorithms, which infer potential associations/interactions between molecules and build networks based on these interactions. Protein-protein interaction networks allow the lists of potential targets generated by these different platforms to be analyzed in their biological context. Outputs from these different methods must also be related to the clinical pain phenotype. The improved and standardized phenotyping of pain symptoms and sensory signs enables much better subject stratification. Our hope is that, in the future, the use of computational approaches to integrate datasets including sensory phenotype as well as the outputs of high throughput technologies will help define novel pain mediators and provide insights into the pathogenesis of chronic pain.

Retinal proteome analysis in a mouse model of oxygen-induced retinopathy

To identify proteins that are involved in the molecular mechanisms of oxygen-induced retinopathy (OIR), a well-established model of blinding ischemic retinopathy, we quantitatively analyzed the retinal proteome in a mouse model of OIR. OIR was induced by exposing C57BL/6 mice on postnatal day 7 (P7) to 75% hyperoxia for 5 days, followed by 5 days in room air. Retinas from mice on P12 and P17, the hyperoxic and hypoxic phases, respectively, and control groups were examined using isobaric tags for relative and absolute quantitation (iTRAQ) and nano-LC-ESI-MS/MS. In total, 1422 retinal proteins were identified: 699 from the iTRAQ experiment and 1074 by nano-LC-ESI-MS/MS. Compared with control retinas in the iTRAQ study, OIR retinas upregulated and downregulated 21 and 17 proteins, respectively, in P17 retinas and 25 and 14 proteins, respectively, in P12 retinas. Of the differentially expressed proteins, the retinal expression of crystallin proteins, Müller cell-associated proteins, neurodegeneration-associated proteins, and angiogenesis-associated proteins, such as 150-kDa oxygen-regulated protein (ORP150), were analyzed. ORP150 colocalized to the neovascular tufts, and knockdown of ORP150 by siRNA decreased the levels of secreted VEGF in cultured retinal pigment epithelial cells. Moreover, intravitreal administration of siRNA targeting ORP150 significantly reduced the retinal neovascularization in OIR. In conclusion, our proteomic discovery method, coupled with targeted approaches, revealed many proteins that were differentially regulated in the mouse model of OIR. These proteins, including ORP150, are potential novel therapeutic targets for the treatment of proliferative ischemic retinopathy.

Identification of CSPα clients reveals a role in dynamin 1 regulation

Cysteine string protein α (CSPα), a presynaptic cochaperone for Hsc70, is required for synapse maintenance. Deletion of CSPα leads to neuronal dysfunction, synapse loss, and neurodegeneration. We utilized unbiased, systematic proteomics to identify putative CSPα protein clients. We found 22 such proteins whose levels are selectively decreased in CSPα knockout synapses. Of these putative CSPα protein clients, two directly bind to the CSPα chaperone complex and are bona fide clients. They are the t-SNARE SNAP-25 and the GTPase dynamin 1, which are necessary for synaptic vesicle fusion and fission, respectively. Using hippocampal cultures, we show that CSPα regulates the stability of client proteins and synaptic vesicle number. Our analysis of CSPα-dynamin 1 interactions reveals unexpectedly that CSPα regulates the polymerization of dynamin 1. CSPα, therefore, participates in synaptic vesicle endocytosis and may facilitate exo- and endocytic coupling. These findings advance the understanding of how synapses are functionally and structurally maintained.

Quantitative iTRAQ analysis of retinal ganglion cell degeneration after optic nerve crush

Retinal ganglion cells (RGCs) are central nervous system (CNS) neurons that transmit visual information from the retina to the brain. Apoptotic RGC degeneration causes visual impairment that can be modeled by optic nerve crush. Neuronal apoptosis is also a salient feature of CNS trauma, ischemia (stroke), and diseases of the CNS such as Alzheimer's, Parkinson's, multiple sclerosis, and amyotrophic lateral sclerosis. Optic nerve crush induces the apoptotic cell death of ∼ 70% of RGCs within the first 14 days after injury. This model is particularly attractive for studying adult neuron apoptosis because the time-course of RGC death is well established and axon regeneration within the myelinated optic nerve can be concurrently evaluated. Here, we performed a large scale iTRAQ proteomic study to identify and quantify proteins of the rat retina at 1, 3, 4, 7, 14, and 21 days after optic nerve crush. In total, 337 proteins were identified, and 110 were differentially regulated after injury. Of these, 58 proteins were upregulated (>1.3 ×), 46 were downregulated (<0.7 ×), and 6 showed both positive and negative regulation over 21 days, relative to normal retinas. Among the differentially expressed proteins, Thymosin-β4 showed an early upregulation at 3 days, the time-point that immediately precedes the induction of RGC apoptosis after injury. We examined the effect of exogenous Thymosin-β4 administration on RGC death after optic nerve injury. Intraocular injections of Thymosin-β4 significantly increased RGC survival by ∼ 3-fold compared to controls and enhanced axon regeneration after crush, demonstrating therapeutic potential for CNS insults. Overall, our study identified numerous proteins that are differentially regulated at key time-points after optic nerve crush, and how the temporal profiles of their expression parallel RGC death. This data will aid in the future development of novel therapeutics to promote neuronal survival and regeneration in the adult CNS.

AKAP signaling in reinstated cocaine seeking revealed by iTRAQ proteomic analysis

To identify candidate proteins in the nucleus accumbens (NAc) as potential pharmacotherapeutic targets for treating cocaine addition, an 8-plex iTRAQ (isobaric tag for relative and absolute quantitation) proteomic screen was performed using NAc tissue obtained from rats trained to self-administer cocaine followed by extinction training. Compared with yoked-saline controls, 42 proteins in a postsynaptic density (PSD)-enriched subfraction of the NAc from cocaine-trained animals were identified as significantly changed. Among proteins of interest whose levels were identified as increased was AKAP79/150, the rat ortholog of human AKAP5, a PSD scaffolding protein that localizes signaling molecules to the synapse. Functional downregulation of AKAP79/150 by microinjecting a cell-permeable synthetic AKAP (A-kinase anchor protein) peptide into the NAc to disrupt AKAP-dependent signaling revealed that inhibition of AKAP signaling impaired the reinstatement of cocaine seeking. Reinstatement of cocaine seeking is thought to require upregulated surface expression of AMPA glutamate receptors, and the inhibitory AKAP peptide reduced the PSD content of protein kinase A (PKA) as well as surface expression of GluR1 in NAc. However, reduced surface expression was not associated with changes in PKA phosphorylation of GluR1. This series of experiments demonstrates that proteomic analysis provides a useful tool for identifying proteins that can regulate cocaine relapse and that AKAP proteins may contribute to relapse vulnerability by promoting increased surface expression of AMPA receptors in the NAc.

Proteomic research in psychiatry

Psychiatric disorders such as Alzheimer's disease, schizophrenia and mood disorders are severe and disabling conditions of largely unknown origin and poorly understood pathophysiology. An accurate diagnosis and treatment of these disorders is often complicated by their aetiological and clinical heterogeneity. In recent years proteomic technologies based on mass spectrometry have been increasingly used, especially in the search for diagnostic and prognostic biomarkers in neuropsychiatric disorders. Proteomics enable an automated high-throughput protein determination revealing expression levels, post-translational modifications and complex protein-interaction networks. In contrast to other methods such as molecular genetics, proteomics provide the opportunity to determine modifications at the protein level thereby possibly being more closely related to pathophysiological processes underlying the clinical phenomenology of specific psychiatric conditions. In this article we review the theoretical background of proteomics and its most commonly utilized techniques. Furthermore the current impact of proteomic research on diverse psychiatric diseases, such as Alzheimer's disease, schizophrenia, mood and anxiety disorders, drug abuse and autism, is discussed. Proteomic methods are expected to gain crucial significance in psychiatric research and neuropharmacology over the coming decade.

Germline competency of parthenogenetic embryonic stem cells from immature oocytes of adult mouse ovary

Parthenogenetic embryonic stem cells (pESCs) have been generated in several mammalian species from parthenogenetic embryos that would otherwise die around mid-gestation. However, previous reports suggest that pESCs derived from in vivo ovulated (IVO) mature oocytes show limited pluripotency, as evidenced by low chimera production, high tissue preference and especially deficiency in germline competence, a critical test for genetic integrity and pluripotency of ESCs. Here, we report efficient generation of germline-competent pESC lines (named as IVM pESCs) from parthenogenetic embryos developed from immature oocytes of adult mouse ovaries following in vitro maturation (IVM) and artificial activation. In contrast, pESCs derived from IVO oocytes show defective germline competence, consistent with previous reports. Further, IVM pESCs resemble more ESCs from fertilized embryos (fESCs) than do IVO pESCs on genome-wide DNA methylation and global protein profiles. In addition, IVM pESCs express higher levels of Blimp1, Lin28 and Stella, relative to fESCs, and in their embryoid bodies following differentiation. This may indicate differences in differentiation potentially to the germline. The mechanisms for acquisition of pluripotency and germline competency of IVM pESCs from immature oocytes remain to be determined.

Quantitative phosphoproteomic analysis of neuronal intermediate filament proteins (NF-M/H) in Alzheimer's disease by iTRAQ

Aberrant hyperphosphorylation of neuronal cytoskeletal proteins is one of the major pathological hallmarks of neurodegenerative disorders such as Alzheimer disease (AD), amyotrophic lateral sclerosis (ALS), and Parkinson's disease (PD). Human NF-M/H display a large number of multiple KSP repeats in the carboxy-terminal tail domain, which are phosphorylation sites of proline-directed serine/threonine (pSer/Thr-Pro, KS/T-P) kinases. The phosphorylation sites of NF-M/H have not been characterized in AD brain. Here, we use quantitative phosphoproteomic methodology, isobaric tag for relative and absolute quantitation (iTRAQ), for the characterization of NF-M/H phosphorylation sites in AD brain. We identified 13 hyperphosphorylated sites of NF-M; 9 Lys-Ser-Pro (KSP) sites; 2 variant motifs, Glu-Ser-Pro (ESP) Ser-736 and Leu-Ser-Pro (LSP) Ser-837; and 2 non-S/T-P motifs, Ser-783 and Ser-788. All the Ser/Thr residues are phosphorylated at significantly greater abundance in AD brain compared with control brain. Ten hyperphosphorylated KSP sites have been identified on the C-terminal tail domain of NF-H, with greater abundance of phosphorylation in AD brain compared with control brain. Our data provide the direct evidence that NF-M/H are hyperphosphorylated in AD compared with control brain and suggest the role of both proline-directed and non-proline-directed protein kinases in AD. This study represents the first comprehensive iTRAQ analyses and quantification of phosphorylation sites of human NF-M and NF-H from AD brain and suggests that aberrant hyperphosphorylation of neuronal intermediate filament proteins is involved in AD.

Towards a better understanding of nuclear processes based on proteomics

The complex structural and functional organisation of the brain warrants the application of high-throughput approaches to study its functional alterations in physiological and pathological conditions. Such approaches have greatly benefited from advances in proteomics and genomics, and from their combination with computational modelling. They have been particularly instrumental for the analysis of processes such as the post-translational modification (PTM) of proteins, a critical biological process in the nervous system that remains not well studied. Protein PTMs are dynamic covalent marks that can be induced by activity and allow the maintenance of a trace of this activity. In the nucleus, they can modulate histone proteins and the components of the transcriptional machinery, and thereby contribute to regulating gene expression. PTMs do however need to be tightly controlled for proper chromatin functions. This review provides a synopsis of methods available to study PTMs and protein expression based on high-throughput mass spectrometry (MS), and covers basic concepts of traditional 'shot-gun'-based MS. It describes classical and emerging proteomic approaches such as multiple reaction monitoring and electron transfer dissociation, and their application to the analyses of nuclear processes in the brain.

Differential Human Plasma Proteomics Based on AniBal Quantification and Peptide-level Off-Gel Isoelectric Focussing

Despite its enormous complexity, human plasma is still one of the most frequently used body fluids for identification and quantification of health and disease biomarkers. We have developed a new workflow for qualitative and quantitative analysis of human plasma proteins. The first step was to remove the seven most abundant plasma proteins (MARS). Moreover, in order to reduce the complexity of the sample and to increase protein and proteome coverage, Off-Gel fractionation was performed at peptide level. Our own stable isotope-based quantitative proteomics approach termed AniBAL was chosen for relative quantification of proteins between conditions. The method was developed with commercial human plasma and resulted in the identification of 85 proteins, of which 68 revealed quantitative information (Mascot database search combined with Peptide-/ProteinProphet validation). The combined methods consisting of MARS, AniBAL, Off-Gel and nano-LC-MS/MS on a Bruker HCT ion trap represent a new and efficient platform to quantify human plasma proteome differences between conditions. The method was also found technically compatible to a pair of human plasma pilot samples from the European FP6 project “DiOGenes”. Many of the identifiable/quantifiable proteins are relevant to obesity, diabetes and inflammation, which form the context of investigation within “DiOGenes”.

Integrative proteomic analysis of the nucleus accumbens in rhesus monkeys following cocaine self-administration

The reinforcing effects and long-term consequences of cocaine self-administration have been associated with brain regions of the mesolimbic dopamine pathway, namely the nucleus accumbens (NAc). Studies of cocaine-induced biochemical adaptations in rodent models have advanced our knowledge; however, unbiased detailed assessments of intracellular alterations in the primate brain are scarce, yet essential, to develop a comprehensive understanding of cocaine addiction. To this end, two-dimensional difference in gel electrophoresis (2D-DIGE) was used to compare changes in cytosolic protein abundance in the NAc between rhesus monkeys self-administering cocaine and controls. Following image normalization, spots with significantly differential image intensities (P<0.05) were identified, excised, trypsin digested and analyzed by matrix-assisted laser-desorption ionization time-of-flight time-of-flight (MALDI-TOF-TOF). In total, 1098 spots were subjected to statistical analysis with 22 spots found to be differentially abundant of which 18 proteins were positively identified by mass spectrometry. In addition, approximately 1000 protein spots were constitutively expressed of which 21 proteins were positively identified by mass spectrometry. Increased levels of proteins in the cocaine-exposed monkeys include glial fibrillary acidic protein, syntaxin-binding protein 3, protein kinase C isoform, adenylate kinase isoenzyme 5 and mitochondrial-related proteins, whereas decreased levels of proteins included beta-soluble N-ethylmaleimide-sensitive factor attachment protein and neural and non-neural enolase. Using a complimentary proteomics approach, the differential expression of phosphorylated proteins in the cytosolic fraction of these subjects was examined. Two-dimensional gel electrophoresis (2DGE) was followed by gel staining with Pro-Q Diamond phosphoprotein gel stain, enabling differentiation of approximately 150 phosphoprotein spots between the groups. Following excision and trypsin digestions, MALDI-TOF-TOF was used to confirm the identity of 15 cocaine-altered phosphoproteins. Significant increased levels were detected for gamma-aminobutyric acid type A receptor-associated protein 1, 14-3-3 gamma-protein, glutathione S-transferase and brain-type aldolase, whereas significant decreases were observed for beta-actin, Rab GDP-dissociation inhibitor, guanine deaminase, peroxiredoxin 2 isoform b and several mitochondrial proteins. Results from these studies indicate coordinated dysregulation of proteins related to cell structure, signaling, metabolism and mitochondrial function. These data extend and compliment previous studies of cocaine-induced biochemical alterations in human postmortem brain tissue, using an animal model that closely recapitulates the human condition and provide new insight into the molecular basis of the disease and potential targets for pharmacotherapeutic intervention.

Ocular proteomics with emphasis on two-dimensional gel electrophoresis and mass spectrometry

The intention of this review is to provide an overview of current methodologies employed in the rapidly developing field of ocular proteomics with emphasis on sample preparation, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Appropriate sample preparation for the diverse range of cells and tissues of the eye is essential to ensure reliable results. Current methods of protein staining for 2D-PAGE, protein labelling for two-dimensional difference gel electrophoresis, gel-based expression analysis and protein identification by MS are summarised. The uses of gel-free MS-based strategies (MuDPIT, iTRAQ, ICAT and SILAC) are also discussed. Proteomic technologies promise to shed new light onto ocular disease processes that could lead to the discovery of strong novel biomarkers and therapeutic targets useful in many ophthalmic conditions.

Axonal transport proteomics reveals mobilization of translation machinery to the lesion site in injured sciatic nerve

Investigations of the molecular mechanisms underlying responses to nerve injury have highlighted the importance of axonal transport systems. To obtain a comprehensive view of the protein ensembles associated with axonal transport in injured axons, we analyzed the protein compositions of axoplasm concentrated at ligatures following crush injury of rat sciatic nerve. LC-MS/MS analyses of iTRAQ-labeled peptides from axoplasm distal and proximal to the ligation sites revealed protein ensembles transported in both anterograde and retrograde directions. Variability of replicates did not allow straightforward assignment of proteins to functional transport categories; hence, we performed principal component analysis and factor analysis with subsequent clustering to determine the most prominent injury-related transported proteins. This strategy circumvented experimental variability and allowed the extraction of biologically meaningful information from the quantitative neuroproteomics experiments. 299 proteins were highlighted by principal component analysis and factor analysis, 145 of which correlate with retrograde and 154 of which correlate with anterograde transport after injury. The analyses reveal extensive changes in both anterograde and retrograde transport proteomes in injured peripheral axons and emphasize the importance of RNA binding and translational machineries in the axonal response to injury.

Shotgun proteomics in neuroscience

Mass spectrometry-based proteomics is increasingly used to address basic and clinical questions in biomedical research through studies of differential protein expression, protein-protein interactions, and posttranslational modifications. The complex structural and functional organization of the human brain warrants the application of high-throughput, systematic approaches to understand the functional alterations under normal physiological conditions and the perturbations of neurological diseases. This primer focuses on shotgun-proteomics-based tandem mass spectrometry for the identification of proteins in a complex mixture. It describes the basic concepts of protein differential expression analysis and posttranslational modification analysis and discusses several strategies to improve the coverage of the proteome.

Proteomic Profiling of Cerebrospinal Fluid by 8-Plex iTRAQ Reveals Potential Biomarker Candidates of Alzheimer’s Disease

Introduction

Alzheimer’s disease (AD) poses specific challenges for drug development. It has a slow and variable clinical course, an insidious onset, and symptom expression is only observed when a significant proportion of neurons are already lost.

Discussion

Determinants of clinical course, such as molecular biomarkers, are urgently needed for early detection and diagnosis, or for prognosis and monitoring disease-modifying therapies in stratified patient populations. Due to its proximity to the brain and clinical availability, cerebrospinal fluid (CSF) is likely to have the highest yield of biomarker potential for neurodegenerative diseases. In this study, we examined the feasibility of using of an 8-plex isobaric tagging approach, coupled to two-dimensional liquid chromatography and tandem mass spectrometry using the matrix-assisted laser desorption/ionization time-of-flight/time-of-flight platform, for the discovery of potential biomarker candidates in CSF. Comparative analysis identified a number of statistically significant differences in the level of proteins when comparing AD to nondemented controls. Although the study is statistically underpowered to represent the disease population, the regulation of proteins with involvement in processes such as neuronal loss, synaptic dysfunction, neuroinflammation, and tissue degeneration and remodeling reflects the ability of our method in providing biologically meaningful CSF biomarkers as candidates for larger scale biomarker verification and validation studies.

Modeling substance abuse for applications in proteomics

The ability to model aspects of human addictive behaviors in laboratory animals provides an important avenue for gaining insight into the biochemical alterations associated with drug intake and the identification of targets for medication development to treat addictive disorders. The intravenous self-administration procedure provides the means to model the reinforcing effects of abused drugs and to correlate biochemical alterations with drug reinforcement. In this chapter, we provide a detailed methodology for rodent intravenous self-administration and the isolation and preparation of proteins from dissected brain regions for Western blot analysis and high-throughput proteomic analysis. Examples of cocaine-induced alterations in the abundances of ionotropic glutamate receptor subunits in reinforcement-related brain regions are provided.

The methodology of neuroproteomics

The human central nervous system (CNS) is the most complex organ in nature, composed of ten trillion cells forming complex neural networks using a quadrillion synaptic connections. Proteins, their modifications, and their interactions are integral to CNS function. The emerging field of neuroproteomics provides us with a wide-scope view of posttranslation protein dynamics within the CNS to better our understanding of its function, and more often, its dysfunction consequent to neurodegenerative disorders. This chapter reviews methodology employed in the neurosciences to study the neuroproteome in health and disease. The chapter layout parallels this volume's four parts. Part I focuses on modeling human neuropathology in animals as surrogate, accessible, and controllable platforms in our research. Part II discusses methodology used to focus analysis onto a subneuroproteome. Part III reviews analytical and bioinformatic technologies applied in neuroproteomics. Part IV discusses clinical neuroproteomics, from processing of human biofluids to translation in biomarkers research. Neuroproteomics continues to mature as a discipline, confronting the extreme complexity of the CNS proteome and its dynamics, and providing insight into the molecular mechanisms underlying how our nervous system works and how it is compromised by injury and disease.

Complementary methods to assist subcellular fractionation in organellar proteomics

Organellar proteomics aims to describe the full complement of proteins of subcellular structures and organelles. When compared with whole-cell or whole-tissue proteomes, the more focused results from subcellular proteomic studies have yielded relatively simpler datasets from which biologically relevant information can be more easily extracted. In every proteomic study, the quality and purity of the biological sample to be investigated is of the utmost importance for a successful analysis. In organellar proteomics, one of the most crucial steps in sample preparation is the initial subcellular fractionation procedure by which the enriched preparation of the sought-after organelle is obtained. In nearly all available organellar proteomic studies, the method of choice relies on one or several rounds of density-based gradient centrifugation. Although this method has been recognized for decades as yielding relatively pure preparations of organelles, recent technological advances in protein separation and identification can now reveal even minute amounts of contamination, which in turn can greatly complicate data interpretation. The scope of this review focuses on recently published innovative complementary or alternative methods to perform subcellular fractionation, which can further refine the way in which sample preparation is accomplished in organellar proteomics.

Proteomics in the study of hippocampal plasticity

Synaptic plasticity is the dynamic regulation of the strength of synaptic communication between nerve cells. It is central to neuronal development as well as experience-dependent remodeling of the adult nervous system as occurs during memory formation. Aberrant forms of synaptic plasticity also accompany a variety of neurological and psychiatric diseases, and unraveling the biological basis of synaptic plasticity has been a major goal in neurobiology research. The biochemical and structural mechanisms underlying different forms of synaptic plasticity are complex, involving multiple signaling cascades, reconfigurations of structural proteins and the trafficking of synaptic proteins. As such, proteomics should be a valuable tool in dissecting the molecular events underlying normal and disease-related forms of plasticity. In fact, progress in this area has been disappointingly slow. We discuss the particular challenges associated with proteomic interrogation of synaptic plasticity processes and outline ways in which we believe proteomics may advance the field over the next few years. We pay particular attention to technical advances being made in small sample proteomics and the advent of proteomic imaging in studying brain plasticity.

Genomic and Proteomic Biomarker Discovery in Neurological Disease

Technology for high-throughout scanning of the human genome and its encoded proteins have rapidly developed to allow systematic analyses of human disease. Application of these technologies is becoming an increasingly effective approach for identifying the biological basis of genetically complex neurological diseases. This review will highlight significant findings resulting from the use of a multitude of genomic and proteomic technologies toward biomarker discovery in neurological disorders. Though substantial discoveries have been made, there is clearly significant promise and potential remaining to be fully realized through increasing use of and further development of -omic technologies.

Moving forward in colorectal cancer research, what proteomics has to tell

Colorectal cancer is the third most common cancer and is highly fatal. During the last several years, research has been primarily based on the study of expression profiles using microarray technology. But now, investigators are putting into practice proteomic analyses of cancer tissues and cells to identify new diagnostic or therapeutic biomarkers for this cancer. Because the proteome reflects the state of a cell, tissue or organism more accurately, much is expected from proteomics to yield better tumor markers for disease diagnosis and therapy monitoring. This review summarizes the most relevant applications of proteomics the biomarker discovery for colorectal cancer.

The significance of organellar proteomics for the nervous system

Organellar proteomics is a useful tool for gaining biological insights about structures in the cell. Here, we discuss the tools used in organellar proteomics and the impact of this technique in understanding nervous system function. We will review insights gained from the proteomes of nervous system-specific organelles such as synaptic vesicles and the postsynaptic density. Moreover, we will show how comparison of proteomes between organelles isolated from the nervous system and from other tissues highlight nervous system-specific functions using the examples of clathrin-coated vesicles and RNA granules.

Proteomic strategies in multiple sclerosis and its animal models

The early and precise diagnosis, the prognosis, and the clinical management of multiple sclerosis, remain a considerable challenge. In recent years, the development of novel and powerful proteomic techniques prompted the use of these approaches for the search of unique biomarkers in the cerebrospinal fluid of multiple sclerosis patients. A few studies have also utilized proteomics to delineate the profile of differentially expressed proteins in animal models of the human disease in order to gain global insights into affected pathways. The identification of differentially expressed proteins may be an initial step in the discovery of novel targets and mechanisms that play critical roles in the pathology of multiple sclerosis. Based on these findings, future investigations may elucidate the events leading to demyelination, axonal damage, and neurodegeneration, providing better insights into mechanisms governing the onset and progression of the disease. Although these proteomic studies provide valuable information, they are also faced with a number of challenges. The present review discusses some of the strengths and limitations of proteomic investigations as applied to multiple sclerosis.

Clinical proteomics in neurodegenerative diseases

Investigation of the human specimens is an essential element for understanding the pathogenesis of neurodegenerative disorders, such as Alzheimer's disease, Parkinson's disease, and multiple sclerosis. The studies hold promise for identifying biomarkers for diagnosis and prognosis, elucidating disease mechanisms, and accelerating the development of new strategies for therapeutic intervention. Here, we review proteomics studies of human brain samples in light of recent advances of mass spectrometry, focusing on the general strategies for experimental design and analysis (e.g., sample pooling and replication, selection of proteomics platforms, and false discovery rate in data processing), because quantitative analysis of clinical samples is confounded by a number of variables, including genetic differences, antemortem and postmortem factors, and experimental errors. Diverse proteomics platforms are also discussed with respect to sensitivity, throughput, and accuracy. Regarding the enormous complexity of the human brain and the limitation of current proteomics technologies, it may be more practical to analyze a subset of proteome in a functional context, in order to facilitate the identification of important disease-related proteins in the substantial noise reflecting biological and technical variances.

The synaptic vesicle proteome

Synaptic vesicles are key organelles in neurotransmission. Vesicle integral or membrane-associated proteins mediate the various functions the organelle fulfills during its life cycle. These include organelle transport, interaction with the nerve terminal cytoskeleton, uptake and storage of low molecular weight constituents, and the regulated interaction with the pre-synaptic plasma membrane during exo- and endocytosis. Within the past two decades, converging work from several laboratories resulted in the molecular and functional characterization of the proteinaceous inventory of the synaptic vesicle compartment. However, up until recently and due to technical difficulties, it was impossible to screen the entire organelle thoroughly. Recent advances in membrane protein identification and mass spectrometry (MS) have dramatically promoted this field. A comparison of different techniques for elucidating the proteinaceous composition of synaptic vesicles revealed numerous overlaps but also remarkable differences in the protein constituents of the synaptic vesicle compartment, indicating that several protein separation techniques in combination with differing MS approaches are required to identify and characterize the synaptic vesicle proteome. This review highlights the power of various gel separation techniques and MS analyses for the characterization of the proteome of highly purified synaptic vesicles. Furthermore, the newly detected protein assignments to synaptic vesicles, especially those proteins which are new to the inventory of the synaptic vesicle proteome, are critically discussed.