Analysis of cerebrospinal fluid from patients with psychiatric and neurological disorders by two-dimensional electrophoresis: identification of disease-associated polypeptides as fibrin fragments

Açaí (Euterpe oleracea Mart.) presents anti-neuroinflammatory capacity in LPS-activated microglia cells

INTRODUCTION

Neuropsychiatric diseases are responsible for one of the highest burden of morbidity and mortality worldwide. These illnesses include schizophrenia, bipolar disorder, and major depression. Individuals affected by these diseases may present mitochondrial dysfunction and oxidative stress. Additionally, patients also have increased peripheral and neural chronic inflammation. The Brazilian fruit, açaí, has been demonstrated to be a neuroprotective agent through its recovery of mitochondrial complex I activity. This extract has previously shown anti-inflammatory effects in inflammatory cells. However, there is a lack of understanding of potential anti-neuroinflammatory mechanisms, such as cell cycle involvement.

OBJECTIVE

The objective of this study is to evaluate the anti-neuroinflammatory potential of an açaí extract in lipopolysaccharide-activated BV-2 microglia cells.

METHODS

Açaí extract was produced and characterized through high performance liquid chromatography. Following açaí extraction and characterization, BV-2 microglia cells were activated with LPS and a dose-response curve was generated to select the most effective açaí dose to reduce cellular proliferation. This dose was then used to assess reactive oxygen species (ROS) production, double-strand DNA release, cell cycle modulation, and cytokine and caspase protein expression.

RESULTS

Characterization of the açaí extract revealed 10 bioactive molecules. The extract reduced cellular proliferation, ROS production, and reduced pro-inflammatory cytokines and caspase 1 protein expression under 1 μg/mL in LPS-activated BV-2 microglia cells but had no effect on double strand DNA release. Additionally, açaí treatment caused cell cycle arrest, specifically within synthesis and G2/Mitosis phases.

CONCLUSION

These results suggest that the freeze-dried hydroalcoholic açaí extract presents high anti-neuroinflammatory potential.

A Panel of Exosome-Derived miRNAs of Cerebrospinal Fluid for the Diagnosis of Moyamoya Disease

Background

Moyamoya disease (MMD) is an important cause of stroke in children and young adults in Asia. To date, diagnosis remains challenging due to varying clinical manifestations and unknown pathogenesis. The study aims to identify cerebrospinal fluid (CSF) exosomal microRNAs (exomiRs) that can serve as a novel diagnostic biomarker for diagnosis and assess its clinical applications.

Methods

CSF samples were taken from 31 MMD patients and 31 healthy controls. Initial screening of miRNA expression was performed on samples pooled from MMD patients and controls using microarray and validated using quantitative reverse transcription polymerase chain reaction (qRT-PCR). The diagnostic accuracy of the potential exosomal miRNAs was evaluated using receiver operating characteristic curve analyses in an independent patient cohort. The potential pathways regulated by the miRNAs was also determined using bioinformatics analysis.

Results

The microarray results demonstrated that six exomiRs were dysregulated in the MMD patients compared to the controls. Using qRT-PCR, we validated four of the miRNAs (miR-3679-5p, miR-6165, miR-6760-5p, and miR-574-5p) as a biomarker for MMD diagnosis. The four exomiRs showed enhanced sensitivity (75%) and specificity (93.75%) in terms of differentiating MMD patients from healthy subjects [area under the curve (AUC) = 0.9453]. Pathway enrichment analysis for potential targets of six exomiRs identified proteins involved in cell adhesion and junction formation in the brain.

Conclusions

We identified a novel and highly sensitive exomiRs signature for MMD detection and explored its potential targets using bioinformatics analysis.

Kynurenines and the Endocannabinoid System in Schizophrenia: Common Points and Potential Interactions

Schizophrenia, which affects around 1% of the world’s population, has been described as a complex set of symptoms triggered by multiple factors. However, the exact background mechanisms remain to be explored, whereas therapeutic agents with excellent effectivity and safety profiles have yet to be developed. Kynurenines and the endocannabinoid system (ECS) play significant roles in both the development and manifestation of schizophrenia, which have been extensively studied and reviewed previously. Accordingly, kynurenines and the ECS share multiple features and mechanisms in schizophrenia, which have yet to be reviewed. Thus, the present study focuses on the main common points and potential interactions between kynurenines and the ECS in schizophrenia, which include (i) the regulation of glutamatergic/dopaminergic/γ-aminobutyric acidergic neurotransmission, (ii) their presence in astrocytes, and (iii) their role in inflammatory mechanisms. Additionally, promising pharmaceutical approaches involving the kynurenine pathway and the ECS will be reviewed herein.

Coagulation Pathways in Neurological Diseases: Multiple Sclerosis

Significant progress has been made in understanding the complex interactions between the coagulation system and inflammation and autoimmunity. Increased blood-brain-barrier (BBB) permeability, a key event in the pathophysiology of multiple sclerosis (MS), leads to the irruption into the central nervous system of blood components that include virtually all coagulation/hemostasis factors. Besides their cytotoxic deposition and role as a possible trigger of the coagulation cascade, hemostasis components cause inflammatory response and immune activation, sustaining neurodegenerative events in MS. Early studies showing the contribution of altered hemostasis in the complex pathophysiology of MS have been strengthened by recent studies using methodologies that permitted deeper investigation. Fibrin(ogen), an abundant protein in plasma, has been identified as a key contributor to neuroinflammation. Perturbed fibrinolysis was found to be a hallmark of progressive MS with abundant cortical fibrin(ogen) deposition. The immune-modulatory function of the intrinsic coagulation pathway still remains to be elucidated in MS. New molecular details in key hemostasis components participating in MS pathophysiology, and particularly involved in inflammatory and immune responses, could favor the development of novel therapeutic targets to ameliorate the evolution of MS. This review article introduces essential information on coagulation factors, inhibitors, and the fibrinolytic pathway, and highlights key aspects of their involvement in the immune system and inflammatory response. It discusses how hemostasis components are (dys)regulated in MS, and summarizes histopathological post-mortem human brain evidence, as well as cerebrospinal fluid, plasma, and serum studies of hemostasis and fibrinolytic pathways in MS. Studies of disease-modifying treatments as potential modifiers of coagulation factor levels, and case reports of autoimmunity affecting hemostasis in MS are also discussed.

Inflammation in Schizophrenia: Pathogenetic Aspects and Therapeutic Considerations

This paper discusses the current evidence from animal and human studies for a central role of inflammation in schizophrenia. In animal models, pre- or perinatal elicitation of the immune response may increase immune reactivity throughout life, and similar findings have been described in humans. Levels of pro-inflammatory markers, such as cytokines, have been found to be increased in the blood and cerebrospinal fluid of patients with schizophrenia. Numerous epidemiological and clinical studies have provided evidence that various infectious agents are risk factors for schizophrenia and other psychoses. For example, a large-scale epidemiological study performed in Denmark clearly showed that severe infections and autoimmune disorders are such risk factors. The vulnerability-stress-inflammation model may help to explain the role of inflammation in schizophrenia because stress can increase pro-inflammatory cytokines and may even contribute to a chronic pro-inflammatory state. Schizophrenia is characterized by risk genes that promote inflammation and by environmental stress factors and alterations of the immune system. Typical alterations of dopaminergic, serotonergic, noradrenergic, and glutamatergic neurotransmission described in schizophrenia have also been found in low-level neuroinflammation and consequently may be key factors in the generation of schizophrenia symptoms. Further support for the relevance of a low-level neuroinflammatory process in schizophrenia is provided by the loss of central nervous system volume and microglial activation demonstrated in neuroimaging studies. Last but not least, the benefit of anti-inflammatory medications found in some studies and the intrinsic anti-inflammatory and immunomodulatory effects of antipsychotics provide further support for the role of inflammation in this debilitating disease.

Variations in the cerebrospinal fluid proteome following traumatic brain injury and subarachnoid hemorrhage

BACKGROUND

Proteomic analysis of cerebrospinal fluid (CSF) has shown great promise in identifying potential markers of injury in neurodegenerative diseases [1-13]. Here we compared CSF proteomes in healthy individuals, with patients diagnosed with traumatic brain injury (TBI) and subarachnoid hemorrhage (SAH) in order to characterize molecular biomarkers which might identify these different clinical states and describe different molecular mechanisms active in each disease state.

METHODS

Patients presenting to the Neurosurgery service at the Louisiana State University Hospital-Shreveport with an admitting diagnosis of TBI or SAH were prospectively enrolled. Patients undergoing CSF sampling for diagnostic procedures were also enrolled as controls. CSF aliquots were subjected to 2-dimensional gel electrophoresis (2D GE) and spot percentage densities analyzed. Increased or decreased spot expression (compared to controls) was defined in terms of in spot percentages, with spots showing consistent expression change across TBI or SAH specimens being followed up by Matrix-Assisted Laser Desorption/Ionization mass spectrometry (MALDI-MS). Polypeptide masses generated were matched to known standards using a search of the NCBI and/or GenPept databases for protein matches. Eight hundred fifteen separately identifiable polypeptide migration spots were identified on 2D GE gels. MALDI-MS successfully identified 13 of 22 selected 2D GE spots as recognizable polypeptides.

RESULTS

Statistically significant changes were noted in the expression of fibrinogen, carbonic anhydrase-I (CA-I), peroxiredoxin-2 (Prx-2), both α and β chains of hemoglobin, serotransferrin (Tf) and N-terminal haptoglobin (Hp) in TBI and SAH specimens, as compared to controls. The greatest mean fold change among all specimens was seen in CA-I and Hp at 30.7 and -25.7, respectively. TBI specimens trended toward greater mean increases in CA-I and Prx-2 and greater mean decreases in Hp and Tf.

CONCLUSIONS

Consistent CSF elevation of CA-I and Prx-2 with concurrent depletion of Hp and Tf may represent a useful combination of biomarkers for the prediction of severity and prognosis following brain injury.

The role of inflammation in schizophrenia

High levels of pro-inflammatory substances such as cytokines have been described in the blood and cerebrospinal fluid of schizophrenia patients. Animal models of schizophrenia show that under certain conditions an immune disturbance during early life, such as an infection-triggered immune activation, might trigger lifelong increased immune reactivity. A large epidemiological study clearly demonstrated that severe infections and autoimmune disorders are risk factors for schizophrenia. Genetic studies have shown a strong signal for schizophrenia on chromosome 6p22.1, in a region related to the human leucocyte antigen (HLA) system and other immune functions. Another line of evidence demonstrates that chronic (dis)stress is associated with immune activation. The vulnerability-stress-inflammation model of schizophrenia includes the contribution of stress on the basis of increased genetic vulnerability for the pathogenesis of schizophrenia, because stress may increase pro-inflammatory cytokines and even contribute to a lasting pro-inflammatory state. Immune alterations influence the dopaminergic, serotonergic, noradrenergic, and glutamatergic neurotransmission. The activated immune system in turn activates the enzyme indoleamine 2,3-dioxygenase (IDO) of the tryptophan/kynurenine metabolism which influences the serotonergic and glutamatergic neurotransmission via neuroactive metabolites such as kynurenic acid. The described loss of central nervous system volume and the activation of microglia, both of which have been clearly demonstrated in neuroimaging studies of schizophrenia patients, match the assumption of a (low level) inflammatory neurotoxic process. Further support for the inflammatory hypothesis comes from the therapeutic benefit of anti-inflammatory medication. Metaanalyses have shown an advantageous effect of cyclo-oxygenase-2 inhibitors in early stages of schizophrenia. Moreover, intrinsic anti-inflammatory, and immunomodulatory effects of antipsychotic drugs are known since a long time. Anti-inflammatory effects of antipsychotics, therapeutic effects of anti-inflammtory compounds, genetic, biochemical, and immunological findings point to a major role of inflammation in schizophrenia.

Comparative Proteomics for the Evaluation of Protein Expression and Modifications in Neurodegenerative Diseases

Together with hypothesis-driven approaches, high-throughput differential proteomic analysis performed primarily not only in human cerebrospinal fluid and serum but also on protein content of other tissues (blood cells, muscles, peripheral nerves, etc.) has been used in the last years to investigate neurodegenerative diseases. Even if the goal for these analyses was mainly the discovery of neurodegenerative disorders biomarkers, the characterization of specific posttranslational modifications (PTMs) and the differential protein expression resulted in being very informative to better define the pathological mechanisms. In this chapter are presented and discussed the positive aspects and challenges of the outcomes of some of our investigations on neurological and neurodegenerative disease, in order to highlight the important role of protein PTMs studies in proteomics-based approaches.

CSF proteome: a protein repository for potential biomarker identification

Proteomic analysis is not limited to the analysis of serum or tissues. Synovial, peritoneal, pericardial and cerebrospinal fluid represent unique proteomes for disease diagnosis and prognosis. In particular, cerebrospinal fluid serves as a rich source of putative biomarkers that are not solely limited to neurologic disorders. Peptides, proteolytic fragments and antibodies are capable of crossing the blood-brain barrier, thus providing a repository of pathologic information. Proteomic technologies such as immunoblotting, isoelectric focusing, 2D gel electrophoresis and mass spectrometry have proven useful for deciphering this unique proteome. Cerebrospinal fluid proteins are generally less abundant than their corresponding serum counterparts, necessitating the development and use of sensitive analytical techniques. This review highlights some of the promising areas of cerebrospinal fluid proteomic research and their clinical applications.

Immunology of schizophrenia

Increased proinflammatory markers like cytokines have been described in the blood and cerebrospinal fluid of patients suffering from schizophrenia. Animal models have shown that a hit in early life to the immune system might trigger a lifelong increased immune reactivity. Many epidemiological and clinical studies show the role of various infectious agents as risk factors for schizophrenia with overlap to other psychoses. The first large-scale epidemiological study in psychiatry from Denmark clearly demonstrates severe infections and autoimmune disorders during lifetime to be risk factors for schizophrenia. Genetic studies have shown the strongest signal for schizophrenia on chromosome 6p22.1, in a region related to the major histocompatibility complex and other immune functions. The vulnerability-stress-inflammation model is important as stress may increase proinflammatory cytokines and even contribute to a lasting proinflammatory state. The immune system itself is considered an important further piece in the puzzle, as in autoimmune disorders in general, which are always linked to three factors: genes, the environment and the immune system. Alterations of dopaminergic, serotonergic, noradrenergic and glutamatergic neurotransmission have been shown with low-level neuroinflammation and may directly be involved in the generation of schizophrenic symptoms. Loss of central nervous system volume and microglial activation has been demonstrated in schizophrenia in neuroimaging studies, which supports the assumption of a low-level neuroinflammatory process. Further support comes from the therapeutic benefit of anti-inflammatory medications in specific studies and the anti-inflammatory and immunomodulatory intrinsic effects of antipsychotics.

Two-dimensional fluorescence difference gel electrophoresis for comparative proteomics profiling

Quantitative proteomics is the workhorse of the modern proteomics initiative. The gel-based and MuDPIT approaches have facilitated vital advances in the measurement of protein expression alterations in normal and disease phenotypic states. The methodological advance in two-dimensional gel electrophoresis (2DGE) has been the multiplexing fluorescent two-dimensional fluorescence difference gel electrophoresis (2D-DIGE). 2D-DIGE is based on direct labeling of lysine groups on proteins with cyanine CyDye DIGE Fluor minimal dyes before isoelectric focusing, enabling the labeling of 2-3 samples with different dyes and electrophoresis of all the samples on the same 2D gel. This capability minimizes spot pattern variability and the number of gels in an experiment while providing simple, accurate and reproducible spot matching. This protocol can be completed in 3-5 weeks depending on the sample size of the experiment and the level of expertise of the investigator.

Methods for proteomics in neuroscience

Proteomics reveals complex protein expression, function, interactions and localization in different phenotypes of neuron. As proteomics, regarded as a highly complex screening technology, moves from a theoretical approach to practical reality, neuroscientists have to determine the most-appropriate applications for this technology. Even though proteomics compliments genomics, it is in sheer contrast to the basically constant genome due to its dynamic nature. Neuroscientists have to surmount difficulties particular to the research in neuroscience; such as limited sample amounts, heterogeneous cellular compositions in samples and the fact that many proteins of interest are hydrophobic proteins. The necessity of exclusive technology, sophisticated software and skilled manpower tops the challenge. This review examines subcellular organelle isolation, protein fractionation and separation using two-dimensional gel electrophoresis (2-DGE) as well as multi-dimensional liquid chromatography (LC) followed by mass spectrometry (MS). The methods for quantifying relative gene product expression between samples (e.g., two-dimensional difference in gel electrophoresis (2D-DIGE), isotope-coded affinity tag (ICAT) and iTRAQ) are elaborated. An overview of the techniques used currently to assign post-translational modification status on a proteomics scale is also evaluated. The feasible coverage of the proteome, ability to detect unique cell components such as post-synaptic densities and membrane proteins, resource requirements and quantitative as well as qualitative reliability of different approaches is also discussed. While there are many challenges in neuroproteomics, this field promises many returns in the future.

Proteome Study of Human Cerebrospinal Fluid following Traumatic Brain Injury Indicates Fibrin(ogen) Degradation Products as Trauma-Associated Markers

Traumatic brain injury (TBI), like other central nervous system pathologies, causes changes in the composition of cerebrospinal fluid (CSF). Consequently analysis of the CSF components is important to better understand the pathological processes involved in such diseases. The aim of this work was to identify specific markers of severe TBI. Proteomic analysis including two-dimensional gel electrophoresis combined with mass spectrometry analysis was used to compare the CSF protein profile of severe TBI patients and controls. Proteins (alpha 1 antitrypsin, haptoglobin 1 alpha1, alpha2, and beta) belonging to the acute phase response showed an increased expression in severe TBI patients. Two other proteins, identified as proteolytic degradation products of the carboxyl-terminal portion of the fibrinogen beta, were present only in TBI patients. The presence of these markers could correlate with a post-traumatic local increase in fibrinolysis as well as to an inflammatory event following CNS tissue injury.

The proteome of human brain microdialysate

Background

Cerebral microdialysis has been established as a monitoring tool in neurocritically ill patients suffering from severe stroke. The technique allows to sample small molecules in the brain tissue for subsequent biochemical analysis. In this study, we investigated the proteomic profile of human cerebral microdialysate and if the identified proteins might be useful predictors for disease characteristics in stroke for tissue at risk in the contralateral hemisphere. We analysed cerebral protein expression in microdialysate from three stroke patients sampled from the hemisphere contralateral to the lesion. Using a proteomic approach based on two-dimensional gel electrophoresis and subsequent mass spectrometry, we created a protein map for the global protein expression pattern of human microdialyste.

Results

We found an average of 158 ± 24 (N = 18) protein spots in the human cerebral microdialysate and could identify 95 spots, representing 27 individual proteins. Most of these have been detected in human cerebrospinal fluid before, but 10 additional proteins mainly of cerebral intracellular origin were identified exclusively in the microdialysate.

Conclusions

The 10 proteins found exclusively in human cerebral microdialysate, but not in cerebrospinal fluid, indicate the possibility to monitor the progression of the disease towards deterioration. The correlation of protein composition in the human cerebral microdialysate with the patients' clinical condition and results of cerebral imaging may be a useful approach to future applications for neurological stroke diagnosis, prognosis, and treatment.

Disease-specific alterations in frontal cortex brain proteins in schizophrenia, bipolar disorder, and major depressive disorder. The Stanley Neuropathology Consortium

Severe psychiatric disorders such as schizophrenia, bipolar disorder and major depressive disorder are brain diseases of unknown origin. No biological marker has been documented at the pathological, cellular, or molecular level, suggesting that a number of complex but subtle changes underlie these illnesses. We have used proteomic technology to survey postmortem tissue to identify changes linked to the various diseases. Proteomics uses two-dimensional gel electrophoresis and mass spectrometric sequencing of proteins to allow the comparison of subsets of expressed proteins among a large number of samples. This form of analysis was combined with a multivariate statistical model to study changes in protein levels in 89 frontal cortices obtained postmortem from individuals with schizophrenia, bipolar disorder, major depressive disorder, and non-psychiatric controls. We identified eight protein species that display disease-specific alterations in level in the frontal cortex. Six show decreases compared with the non-psychiatric controls for one or more diseases. Four of these are forms of glial fibrillary acidic protein (GFAP), one is dihydropyrimidinase-related protein 2, and the sixth is ubiquinone cytochrome c reductase core protein 1. Two spots, carbonic anhydrase 1 and fructose biphosphate aldolase C, show increase in one or more diseases compared to controls. Proteomic analysis may identify novel pathogenic mechanisms of human neuropsychiatric diseases.

A cerebrospinal fluid protein associated with moyamoya disease: report of three cases

OBJECTIVE

The pathogenesis of moyamoya disease is unknown. The purpose of this study was to detect proteins associated with the pathogenesis of moyamoya disease.

CLINICAL PRESENTATION

Cerebrospinal fluid (CSF) samples from three patients with moyamoya disease and four control patients who had cervical lesions but no intracranial lesion were studied.

INTERVENTION

CSF proteins separated by two-dimensional polyacrylamide gel electrophoresis were analyzed with the SWISS-2DPAGE and SWISS-PROT databases. In the CSF samples from all three patients with moyamoya disease, a polypeptide spot (Mr = 12,000, pI = 5.35) was observed. This spot was not evident in samples from the four control patients and has not been reported in the SWISS-2DPAGE and SWISS-PROT databases.

CONCLUSION

A CSF protein, which is possibly novel and associated with moyamoya disease, has been detected. The analysis of CSF by two-dimensional polyacrylamide gel electrophoresis may reveal a clue by which the molecular mechanism of moyamoya disease may be elucidated.

Acute phase proteins in male Chinese schizophrenic patients in Singapore

Changes in the concentration of some serum acute phase proteins (alpha 1-antitrypsin, alpha 2-macroglobulin, complement C3, haptoglobin, ceruloplasmin, transferrin, albumin and hemopexin), thyroxine-binding globulin, retinol-binding globulin, plasminogen and Gc-globulin are reported in two separate series of Chinese, male schizophrenic patients and healthy controls. In the first series, 41 healthy blood donors and 98 schizophrenic patients in different stages of the disease were investigated. The second series consists of a random sample of 50 acutely ill schizophrenic patients and a second group of healthy subjects. The concentrations of these serum proteins were measured by rocket immunoelectrophoresis in agarose gel. Increased levels of serum alpha 1-antitrypsin, alpha 2-macroglobulin, haptoglobin, ceruloplasmin, and thyroxine-binding globulin were observed in both series of patients when compared to their respective controls. Albumin, transferrin and retinol-binding protein levels were reduced in patients in both series. Hemopexin levels were increased only in the acutely ill patients while complement C3 was decreased in the chronically ill patients. No changes were observed in the Gc-globulin levels of all groups of patients. With the exception of complement C3, the changes observed in the levels of these serum proteins were appropriate for that of an acute phase response.

Plasma protein variations in monozygotic twins discordant for schizophrenia

Monozygotic twins discordant for schizophrenia were analyzed by two-dimensional (2-D) gel electrophoresis to identify extrahereditary factors important in the development of schizophrenia. Plasma protein patterns in 2-D gels of monozygotic twins discordant for schizophrenia were found to be significantly less alike than those of normal control monozygotic twins. Several polypeptide spots were found to be elevated in the plasma of the schizophrenic twin. One of these polypeptides, spot 782, was also found to be significantly (p < .001) elevated when schizophrenic patients were compared to unrelated normal control individuals. Spot 782 may be an isoform of haptoglobin. Quantitative variations in some plasma haptoglobin levels were seen between discordant twins, but not between unrelated schizophrenic and normal control individuals.

Fibrin degradation products in post mortem brain tissue of schizophrenics: a possible marker for underlying inflammatory processes

Alterations in protein composition are often present in diseases of the central nervous system (CNS). Inflammatory processes causing these alterations have been suggested by many authors to underlie the cerebral disturbance in some cases of schizophrenia. In a previous study, two disease-associated additional polypeptides P1 and P2 could be detected in the cerebrospinal fluid (CSF) of 60 out of 123 (49%) schizophrenic patients. These polypeptides were identified as cleavage products of the beta-chain of fibrin(ogen), an acute-phase protein which is increased in inflammatory processes. Because investigations of brain tissue might better reflect the disease process than cerebrospinal fluid, we examined 6 post mortem brains (3 schizophrenics, 3 normal controls) for the presence of fibrin(ogen) and its cleavage products by two dimensional gel electrophoresis followed by immunoblotting. We detected fibrin(ogen) and its degradation products P1 and P2 in all schizophrenic brain tissue samples, but not in that from controls. These results are consistent with previous CSF observations and suggest that a CNS inflammatory process may be occurring in a subgroup of schizophrenic patients.

The yeast SWISS-2DPAGE database

The systematic sequencing of the yeast genome will soon be completed. A new challenge has been launched by the EUROFAN (European Functional Analysis) project whose goal is to elucidate the physiological and biochemical function of newly discovered open reading frames (ORF) from yeast. One of the approaches is to use protein-based technologies such as two-dimensional gel electrophoresis and protein identification in order to establish a yeast reference map. Modified protein patterns can be compared to the reference map which hopefully will help identify changes related, for example, to growth processes or developmental events. This paper describes the yeast SWISS-2DPAGE database in which charge separation was obtained using immobilized pH gradient (IPG). Proteins identified by gel comparison, amino acid composition analysis and/or microsequencing are recorded and described in an accessible uniform format. We have identified more than one hundred polypeptides, several of which were newly mapped. In addition, the yeast SWISS-2DPAGE database can be freely accessed through the World Wide Web (WWW) network on the ExPASy molecular biology server.

Inside SWISS-2DPAGE database

Several two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) databases have been established and updated for more than 15 years. Only recently have developments of computer networks and high-speed transfer protocols provided the required tools for sharing comprehensive and hypermedia 2-D PAGE databases. This publication describes the SWISS-2DPAGE database structure. Proteins present in samples of human tissue, cells, cell lines and body fluids are assembled and described in an accessible uniform format. SWISS-2DPAGE can be freely accessed through the World-Wide Web (WWW) network on the ExPASy molecular biology server.

Clinical applications of two-dimensional electrophoresis

Two-dimensional electrophoresis is increasingly being used as an important tool for biological research although it continues to have few direct clinical applications. In the absence of simple systems to identify and quantify individual proteins or groups of proteins it is unlikely that clinical applications will increase. Measurement of some individual proteins, for example a single acute phase reactant, often yields as much clinically useful information as could be currently expected from quantitation of several proteins with the same physiological role. Cost-containment pressures within the clinical laboratory will prevent the technique from becoming widely used in the clinical laboratory until it can clearly demonstrate that it can produce clinically important and necessary information that can not be obtained by other means. We continue to believe that the technique's greatest potential lies in identifying a protein or proteins whose concentration can be correlated with a disease and whose concentration varies with the progress of the disease. Antibodies to such proteins can then be produced and used to quantify the disease-associated proteins by a simple procedure, such as nephelometry. In spite of our belief of the likely clinical application of the technique there appears to be no systematic use of two-dimensional electrophoresis for this purpose. With clinical specimens a few investigators still run gels of serum or urine from patients with apparently unusual disorders and compare them visually with gels from healthy individuals. Nevertheless, the technique continues to have considerable unmet promise for clinical applications.

Human liver protein map: update 1993

This publication updates the reference human liver protein map. By microsequencing, 27 spots or 34 polypeptide chains were identified. The most abundant polypeptides detected on the silver stained liver map were key elements in major hepatic biochemical pathways. The new polypeptides and previously known proteins are listed in a table and/or labeled on the protein map, thus providing the 1993 reference human liver SWISS-2DPAGE database. SWISS-2DPAGE and the SWISS-PROT protein sequence databases are closely linked together through the use of common accession numbers.

Plasma and red blood cell protein maps: update 1993

This publication updates the reference plasma and red blood cell protein maps obtained with immobilized pH gradients. Seventeen polypeptide spots or chains were partially characterized by direct N-terminal sequencing or by sequencing of peptides obtained from enzymatic digestion. Additional new polypeptides and previously known proteins are listed in a table and/or labeled on the protein maps, thus providing the 1993 update of the human plasma and red blood cell two-dimensional gel SWISS-2DPAGE database. SWISS-2DPAGE and the SWISS-PROT protein sequence databases are closely linked together through the use of common accession numbers.

Human liver protein map: a reference database established by microsequencing and gel comparison

This publication establishes a reference human liver protein map obtained with immobilized pH gradients. By microsequencing, 57 spots or 42 polypeptide chains were identified. By protein map comparison and matching (liver, red blood cell and plasma sample maps), 8 additional proteins were identified. The new polypeptides and previously known proteins are listed in a table and/or labeled on the protein map, thus providing a human liver two-dimensional gel database. This reference map can be used to identify protein spots on other samples such as rectal cancer biopsies.

Human cerebrospinal fluid protein database: edition 1992

Two-dimensional electrophoresis maps of human cerebrospinal fluid proteins are presented in the form of labeled images. 931 protein spots are identified in spinal fluid from a normal volunteer. Distinct spots that represent variants of the same protein, especially posttranslational modifications, are estimated to reduce the 931 different spots to < 200 different proteins. 248 spots of 29 protein groups have been identified and are indicated on enlargements of specific gel regions. The distribution of protein abundance, mass, charge and shape characteristics of these normal 931 spinal fluid spots are graphically profiled. Analysis of the shape parameter "vertical height: width ratio" reveals that a ratio > 3.5 correlates with glycoproteins, enabling their identification simply by image analysis. Proteins that are not present on the normal map, but appear in spinal fluid in patients with schizophrenia and Creutzfeldt-Jakob disease are illustrated on additional maps.

Polypeptide marker and disease patterns found while mapping proteins in ascitis

To assess the protein composition of ascitis, 28 samples of ascitic fluid were obtained from patients admitted to Geneva University Hospital. The samples were analysed randomly and blindly by high-resolution two-dimensional polyacrylamide gel electrophoresis. The final visual evaluation was compared with the discharged summary and diagnosis. The protein pattern of ascitis was, as expected, very similar to normal or diseased plasma, with the exception of two spots which were present in ascitic fluids but not in the 200 plasma samples analyzed in parallel. After microsequencing, they proved to be beta-fibrinogen fragments. Several diseases showed distinct patterns, especially acute pancreatitis. A group of intense spots with an apparent molecular mass between those of alpha 1-antitrypsin and beta-haptoglobin were found in all ascitic fluid from pancreatitis cases (six patients). These spots had isoelectric points similar to those of alpha 1-antitrypsin and beta-haptoglobin and microsequencing revealed that they were three different fragments of alpha 1-antitrypsin.

Plasma protein map: an update by microsequencing

The reference plasma protein map, obtained with immobilized pH gradients in the first dimension of two-dimensional electrophoresis, is presented. By microsequencing, more than 40 polypeptide chains were identified. The new polypeptides and previously known proteins are listed in a table and labeled on the protein map, thus providing an update of the human plasma two-dimensional gel database.