Limitations of current proteomics technologies

Application of proteomics technologies in the investigation of biological systems creates new possibilities in the elucidation of biopathomechanisms and the discovery of novel drug targets and early disease markers. A proteomic analysis involves protein separation and protein identification as well as characterization of the post-translational modifications. Proteomics has been applied in the investigation of various disorders, like neurological diseases, and the application has resulted in the detection of a large number of differences in the levels and the modifications of proteins between healthy and diseased states. However, the current proteomics technologies are still under development and show certain limitations. In this article, we discuss the major drawbacks and pitfalls of proteomics we have observed in our laboratory and in particular during the application of proteomics technologies in the investigation of the brain.     

Prostaglandin D2 synthase and its post-translational modifications in neurological disorders

Prostaglandin D2 synthase (PGDS) (beta-trace protein) is a highly abundant cerebrospinal fluid (CSF) glycoprotein. A number of studies have been performed to determine the potential value of this protein for the diagnosis of various neurological disorders. The measurement of total PGDS levels in CSF has proved marginally useful for this purpose, but promising results were obtained while investigating changes in the posttranslational modifications (PTM) pattern. Using 2-DE analysis, we previously showed that PGDS is differentially expressed in ante- and post mortem CSF samples. In the present study, we examined whether the PGDS isoforms may help to distinguish stroke and neurodegenerative disease patients from healthy subjects. The pattern of PGDS PTM was analyzed in CSF from patients with various neurological disorders (n = 44) using IEF/immunoblotting techniques. Strong alterations of this pattern were detected in patients with different forms of degenerative dementia. These findings are consistent with PGDS being altered in some neurological diseases and provide new opportunities for clinical applications.     

基于质谱的蛋白质组学技术在神经退行性疾病生物标志物研究中的应用

蛋白质组学是在整体水平上研究细胞、组织或生物体蛋白质组成及变化规律的科学.与传统的生物学研究相比,蛋白质组学具有快速、灵敏、高通量的优点.神经退行性疾病是一类由神经系统内特定神经细胞的进程性病变或丢失而导致神经功能障碍的疾病,严重危害人类健康.近年来,基于质谱的蛋白质组学技术在神经退行性疾病的研究中得到了广泛应用.本文简要介绍了蛋白质组学在样品分离、多肽定量、质谱检测及生物标志物临床验证等方面的技术发展,并结合实例综述了基于质谱的蛋白质组学在神经退行性疾病生物标志物发现与验证中的研究进展.     

Analysis of cerebrospinal fluid proteins by electrophoresis

The cerebrospinal fluid (CSF) is a specific ultrafiltrate of plasma, which surrounds the brain and spinal cord. The study of its proteins and their alteration may yield useful information on several neurological diseases. By using various electrophoretic separation techniques, several CSF proteins have been identified derived from plasma or from brain. Different one-dimensional methods, such as agarose gel electrophoresis and isoelectric focusing, are of similar value in identifying the non-specific oligoclonal bands, which are mainly helpful in the diagnosis of multiple sclerosis and other inflammatory diseases. Isoelectric focusing has a greater resolution than other one-dimensional methods, and it yields additional data about disease-associated proteins occurring in Alzheimer's disease, Huntington's chorea and amyotrophic lateral sclerosis. Silver-stained two-dimensional gels provide more information about the complex protein composition of CSF, particularly about proteins produced in the brain, such as apolipoprotein E and neuron-specific enolase. For the detection of oligoclonal antibodies, the investigation of protein changes revealed by Parkinson's disease, schizophrenia and Creutzfeldt-Jakob disease, and the analysis of CSF immune complexes, two-dimensional electrophoresis has a greater sensitivity.     

Promising therapeutics with natural bioactive compounds for improving learning and memory - a review of randomized trials

Cognitive disorders can be associated with brain trauma, neurodegenerative disease or as a part of physiological aging. Aging in humans is generally associated with deterioration of cognitive performance and, in particular, learning and memory. Different therapeutic approaches are available to treat cognitive impairment during physiological aging and neurodegenerative or psychiatric disorders. Traditional herbal medicine and numerous plants, either directly as supplements or indirectly in the form of food, improve brain functions including memory and attention. More than a hundred herbal medicinal plants have been traditionally used for learning and memory improvement, but only a few have been tested in randomized clinical trials. Here, we will enumerate those medicinal plants that show positive effects on various cognitive functions in learning and memory clinical trials. Moreover, besides natural products that show promising effects in clinical trials, we briefly discuss medicinal plants that have promising experimental data or initial clinical data and might have potential to reach a clinical trial in the near future.     

Tau蛋白的翻译后修饰与阿尔茨海默病

阿尔茨海默病（Alzheimer disease,AD）是一种常见的神经退行性疾病,由过度磷酸化Tau蛋白聚集形成的神经纤维缠结是该病主要的病理特征之一,Tau蛋白的异常磷酸化与Tau蛋白的聚集及AD的进程相关.越来越多的证据表明,Tau蛋白的异常聚集与Tau蛋白相关神经退行性疾病的发生和发展及Tau蛋白的其他翻译后修饰有一定的关系,如糖基化、乙酰化、截断、肽脯氨酸异构化、泛素化等.本文重点综述Tau蛋白翻译后修饰与AD相互关系的研究进展.     

Urological malignancies and the proteomic-genomic interface

The urological malignancies, renal, bladder and prostate cancer, account for approximately 16% of all cancer cases. Unfortunately 5-year survival rates are relatively poor, largely a result of many cases not being diagnosed before the tumour has metastasised. There is a clear need for the identification of markers which will allow earlier detection of disease, and predict prognosis and response to therapy. In addition, they may be of use as therapeutic targets. Current advances in molecular biology are allowing the identification of a number of tumour-associated changes which could be of clinical use in the future. However, with the rapid technological advances being made in the field of proteomics, this approach could be integrated with genomics providing a complementary alternative, overcoming disparities between mRNA levels and protein production, and additionally allowing the identification of tumour-associated post-translational modifications. These approaches have already been used to identify novel genes and other cancer-related changes involved in the pathogenesis of urological malignancies. This review describes current progress in the genomic and proteomic study of urological malignancies, and highlights the potential of using proteomic technologies in the study of this group of diseases.     

Clinical perspectives of high-resolution mass spectrometry-based proteomics in neuroscience: exemplified in amyotrophic lateral sclerosis biomarker discovery research

Biomarker discovery is a central application in today's proteomic research. There is an urgent need for valid biomarkers to improve diagnostic tools and treatment in many disorders, such as the rapidly progressing neurodegenerative disorder amyotrophic lateral sclerosis (ALS) that has a fatal outcome in about 3 years and yet no curative treatment. Screening for clinically relevant biomarkers puts high demands on high-throughput, rapid and precise proteomic techniques. There is a large variety in the methods of choice involving mainly gel-based approaches as well as chromatographic techniques for multi-dimensional protein and peptide separations followed by mass spectrometry (MS) analysis. This special feature article will discuss some important aspects of MS-based clinical proteomics and biomarker discovery in the field of neurodegenerative diseases and ALS research respectively, with the aim to provide a prospective view on current and future research aspects in the field. Furthermore, examples for application of high-resolution MS-based proteomic strategies for ALS biomarker discovery will be demonstrated with two studies previously reported by our group. These studies include among others, utilization of capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR-MS) for advanced protein pattern classification in cerebrospinal fluid (CSF) samples of ALS patients as well as highly sensitive protein identification in minimal amounts of postmortem spinal cord tissue and laser micro-dissected motor neurons using FT-ICR-MS in conjunction with nanoflow LC coupled to matrix-assisted laser desorption ionization time-of-flight tandem mass spectrometry (LC-MALDI-TOF-TOF-MS).     

Nano-HPLC–MS analysis of phospholipids in cerebrospinal fluid of Alzheimer’s disease patients—a pilot study

There is emerging evidence that lipids play an important role in many neurodegenerative processes, for example in Alzheimer's disease (AD). Although different lipid alterations in the AD brain have been reported, there have only been very few investigations of lipid changes in the cerebrospinal fluid (CSF). Recent developments in mass spectrometry (MS) have enabled fast and sensitive detection of lipid species in different biological matrixes. In this study we developed an on-line HPLC-MS method for phospholipid profiling in the CSF based on nano-HPLC separation using an Amide column and detection with electrospray (ESI) quadrupole-time of flight (QTOF) MS. We achieved good separation, reproducibility, and sensitivity in monitoring of the major phospholipid classes, phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylinositol (PI), and sphingomyelin (SM) in CSF. To emphasize the applicability of the method, a pilot study was performed on a group of CSF samples (N = 16) from individuals with probable AD and non-demented controls. We observed a statistically significant increase of SM levels (24.3 ± 2.4%) in CSF from probable AD individuals vs. controls. Our findings indicate that SM levels in the CSF could potentially provide a new lead in AD biomarker research, and show the potential of the method for disease-associated CSF phospholipid screening.     

Identification of synaptic vesicle, pre- and postsynaptic proteins in human cerebrospinal fluid using liquid-phase isoelectric focusing

Synaptic pathology is central in the pathogenesis of several psychiatric disorders, for example in Alzheimer's disease (AD) and schizophrenia. Quantification of specific synaptic proteins has proved to be a useful method to estimate synapitc density in the brain. Using this approach, several synaptic proteins have been demonstrated to be altered in both AD and schizophrenia. Until recently, the analysis of synaptic pathology has been limited to postmortem tissue. In living subjects, these synaptic proteins may be studied through analysis of cerebrospinal fluid (CSF). In an earlier study performed by us, one synaptic vesicle specific protein, synaptotagmin, was detected in CSF for the first time using a procedure based on affinity chromatography, reversed-phase chromatography, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and chemiluminescence immunoblotting. However, other synaptic proteins were not detectable with this procedure. Therefore, we have developed a procedure including precipitation of CSF proteins with trichloroacetic acid, followed by liquid-phase isoelectric focusing using the Rotofor Cell, and finally analysis of Rotofor fractions by Western blotting for identification of synaptic proteins in CSF. Five synaptic proteins, rab3a, synaptotagmin, growth-associated protein (GAP-43), synaptosomal-associated protein (SNAP-25) and neurogranin, have been demonstrated in CSF using this method. The major advantage of liquid-phase isoelectric focusing (IEF) using the Rotofor cell is that it provides synaptic proteins from CSF in sufficient quantities for identification. This method may also be suitable for identification of other types of trace amounts of brain-specific proteins in CSF. These results demonstrate that several synaptic proteins can be identified and measured in CSF to study synaptic function and pathology in degenerative disorders.     

Recent advances in metabolomics in neurological disease, and future perspectives

Discovery of clinically relevant biomarkers for diseases has revealed metabolomics has potential advantages that classical diagnostic approaches do not. The great asset of metabolomics is that it enables assessment of global metabolic profiles of biofluids and discovery of biomarkers distinguishing disease status, with the possibility of enhancing clinical diagnostics. Most current clinical chemistry tests rely on old technology, and are neither sensitive nor specific for a particular disease. Clinical diagnosis of major neurological disorders, for example Alzheimer’s disease and Parkinson’s disease, on the basis of current clinical criteria is unsatisfactory. Emerging metabolomics is a powerful technique for discovering novel biomarkers and biochemical pathways to improve diagnosis, and for determination of prognosis and therapy. Identifying multiple novel biomarkers for neurological diseases has been greatly enhanced with recent advances in metabolomics that are more accurate than routine clinical practice. Cerebrospinal fluid (CSF), which is known to be a rich source of small-molecule biomarkers for neurological and neurodegenerative diseases, and is in close contact with diseased areas in neurological disorders, could potentially be used for disease diagnosis. Metabolomics will drive CSF analysis, facilitate and improve the development of disease treatment, and result in great benefits to public health in the long-term. This review covers different aspects of CSF metabolomics and discusses their significance in the postgenomic era, emphasizing the potential importance of endogenous small-molecule metabolites in this emerging field.     

Identification of proteins in human cerebrospinal fluid using liquid-phase isoelectric focusing as a prefractionation step followed by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionisation mass spectrometry

Cerebrospinal fluid (CSF) is in close proximity to the brain and changes in the protein composition of CSF may be indicative of altered brain protein expression in neurodegenerative disorders. Analysis of brain-specific proteins in CSF is complicated by the fact that most CSF proteins are derived from the plasma and tend to obscure less abundant proteins. By adopting a prefractionation step prior to two-dimensional gel electrophoresis (2-DE), less abundant proteins are enriched and can be detected in complex proteomes such as CSF. We have developed a method in which liquid-phase isoelectric focusing (IEF) is used to prefractionate individual CSF samples; selected IEF fractions are then analysed on SYPRO-Ruby-stained 2-D gels, with final protein identification by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS). To optimise the focusing of the protein spots on the 2-D gel, the ampholyte concentration in liquid-phase IEF was minimised and the focusing time in the first dimension was increased. When comparing 2-D gels from individual prefractionated and unfractionated CSF samples it is evident that individual protein spots are larger and contain more protein after prefractionation of CSF. Generally, more protein spots were also detected in the 2-D gels from prefractionated CSF compared with direct 2-DE separations of CSF. Several proteins, including cystatin C, IgM-kappa, hemopexin, acetyl-coenzyme A carboxylase-alpha, and alpha-1-acid glycoprotein, were identified in prefractionated CSF but not in unfractionated CSF. Low abundant forms of posttranslationally modified proteins, e.g. alpha-1-acid glycoprotein and alpha-2-HS glycoprotein, can be enriched, thus better resolved and detected on the 2-D gel. Liquid-phase IEF, as a prefractionation step prior to 2-DE, reduce sample complexity, facilitate detection of less abundant protein components, increases the protein loads and the protein amount in each gel spot for MALDI-MS analysis.     

Bioelectrochemical analysis of neurodegeneration: Refocusing efforts

Since 1970s, electrochemistry is enthusiastically used for studies of severe neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, or prion-associated transmissible spongiform encephalopathies, associated with the neuronal death in the brain. The existing electrochemical sensors can be used both for direct neurotransmitter analysis in the brain and for detection of both proteins/amyloid peptides and the extent of their aggregation/oligomerisation. However, these sensors' application in body fluids or certain brain areas of interest may be restricted by the presence of structurally or electrochemically related species interfering with electroanalysis. Thus, recent efforts are refocusing on bioelectroanalysis with the apatmer- and antibody-modified electrodes, enabling obtaining more specific, interference-free results that allow better correlations with the disease state. In this opinion, I consider these recent efforts aimed at deeper studies and better understanding of neurotransmitter and protein/peptide patterns linked to neurodegenerative disorders.     

MSQ: a tool for quantification of proteomics data generated by a liquid chromatography/matrix‐assisted laser desorption/ionization time‐of‐flight tandem mass spectrometry based targeted quantitative proteomics platform

Mass spectrometry (MS)‐based quantitative proteomics has become a critical component of biological and clinical research for identification of biomarkers that can be used for early detection of diseases. In particular, MS‐based targeted quantitative proteomics has been recently developed for the detection and validation of biomarker candidates in complex biological samples. In such approaches, synthetic reference peptides that are the stable isotope labeled version of proteotypic peptides of proteins to be quantitated are used as internal standards enabling specific identification and absolute quantification of targeted peptides. The quantification of targeted peptides is achieved using the intensity ratio of a native peptide to the corresponding reference peptide whose spike‐in amount is known. However, a manual calculation of the ratios can be time‐consuming and labor‐intensive, especially when the number of peptides to be tested is large. To establish a liquid chromatography/matrix‐assisted laser desorption/ionization time‐of‐flight tandem mass spectrometry (LC/MALDI TOF/TOF)‐based targeted quantitative proteomics pipeline, we have developed a software named Mass Spectrometry based Quantification (MSQ). This software can be used to automate the quantification and identification of targeted peptides/proteins by the MALDI TOF/TOF platform. MSQ was applied to the detection of a selected group of targeted peptides in pooled human cerebrospinal spinal fluid (CSF) from patients with Alzheimer's disease (AD) in comparison with age‐matched control (OC). The results for the automated quantification and identification of targeted peptides/proteins in CSF were in good agreement with results calculated manually. Copyright © 2010 John Wiley & Sons, Ltd.     

Biochemical and immunological aspects of protein aggregation in neurodegenerative diseases

Protein aggregation is commonly associated with a large number of neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and other types of pathological conditions. Misfolding and aggregation of a number of peptides and proteins have been found to occur under these conditions. In the present review, some mechanistic features of the events related to the type of structure–function relationships which may define the outcome of the abnormal conditions are discussed. The immunological responses to the aggregates and possible therapeutic strategies for prevention or control of the diseases are also reviewed. Protein aggregation and its effect on human body have become an important issue over the last two decades. Many diseases in human are related to aggregation and misfolding of different kinds of proteins; therefore, diagnosis of causes of the aggregation and their mechanisms which provoke it are important. This review describes the relations between structures and functions of already aggregated proteins, as well as proteins, which only enter initial stages of aggregation. The consequences of aggregations, which provoke many kinds of neurodegenerative disorders, are explained in details and some factors that may influence their severity are described. In addition, the immunologic responses to these aggregates are discussed. Suggestions of plausible therapies of preventing or slowing down the protein condensation diseases are presented.     

Advances in electrochemical detection for study of neurodegenerative disorders

Several severe neurodegenerative disorders, including Alzheimer’s disease, Parkinson’s disease, and prion-associated transmissible spongiform encephalopathies, have been linked to dysregulation of specific proteins capable of self-assembly into deleterious fibrillar aggregates termed amyloids. A wide range of analytical techniques has been used to clarify the mechanisms of these protein-misfolding processes, in the hope of developing effective therapeutic treatment. Most of these studies have relied heavily on conventional methods of protein characterization, notably circular dichroism spectroscopy, thioflavin T fluorescence, transmission electron microscopy, and atomic force microscopy, which are particularly suitable for monitoring later-stage aggregate formation. Although electrochemical methods of protein detection have existed for some time, they have only recently gained prominence as a powerful tool for studying the early stages of protein aggregation during which the more toxic soluble amyloid species form. Electrochemical detection methods include direct detection of intrinsic redox-active amino acid residues, protein-catalyzed hydrogen evolution, use of extrinsic β-sheet binding mediators, and impedance spectroscopy. In this review, we evaluate the use of electrochemistry for study of protein aggregation related to neurodegenerative disorders.

Advances in Detection Methods of β-Amyloid Protein

Alzheimer's disease (AD) is a neurodegenerative disease with unknown etiology. β-amyloid protein (Aβ) is one of the specific biomarkers of AD, and many clinical studies suggest that abnormal levels of Aβ in blood, cerebrospinal fluid and brain tissue are closely related to the progression of AD. The analysis and evaluation of Aβ are important for early detection, tracking, prevention, and treatment of AD. In this paper, the present situations of the commonly used detection methods of Aβ at home and abroad were summarized and compared. Specifically, the latest application of new electrochemical biosensor in Aβ detection was mainly described, and the summary of its future directions and the potential applications was given.     

The Therapeutic Potential of Celastrol in Central Nervous System Disorders: Highlights from In Vitro and In Vivo Approaches

Celastrol, the most abundant compound derived from the root of Tripterygium wilfordii, largely used in traditional Chinese medicine, has shown preclinical and clinical efficacy for a broad range of disorders, acting via numerous mechanisms, including the induction of the expression of several neuroprotective factors, the inhibition of cellular apoptosis, and the decrease of reactive oxygen species (ROS). Given the crucial implication of these pathways in the pathogenesis of Central Nervous System disorders, both in vitro and in vivo studies have focused their attention on the possible use of this compound in these diseases. However, although most of the available studies have reported significant neuroprotective effects of celastrol in cellular and animal models of these pathological conditions, some of these data could not be replicated. This review aims to discuss current in vitro and in vivo lines of evidence on the therapeutic potential of celastrol in neurodegenerative diseases, including Alzheimer’s and Parkinson’s diseases, amyotrophic lateral sclerosis, Huntington’s disease, multiple sclerosis, and cadmium-induced neurodegeneration, as well as in psychiatric disorders, such as psychosis and depression. In vitro and in vivo studies focused on celastrol effects in cerebral ischemia, ischemic stroke, traumatic brain injury, and epilepsy are also described.     

朊病毒和疯牛病中蛋白自由基化学问题的探讨

２０年来,人们一直认为朊蛋白病变是导致疯牛病的原因,但对其致病机制却一直未得出公认的结论。其中的“蛋白错折叠”学说被多数人所接受,然而无法解释病中的多菌株现象,在以往的研究中,朊蛋白病变从来没有与任何化学问题有过联系。近年,我们对哺乳动物所具有的此类脑神经疾病进行分析,认为蛋白氧化损伤所形成的序列专一的长寿命朊蛋白自由基所催化下的蛋白氧化交联,可能是致病的根本原因。