Proteomics analysis of prefractionated human lumbar cerebrospinal fluid

Cerebrospinal fluid (CSF) is produced by the chorioid plexus in the ventricles. It surrounds the brain and bone marrow, and reflects several different disorders of the central nervous system (CNS). Proteomics has been used to analyze CSF in order to discover disease-associated proteins and to elucidate the basic molecular mechanisms that either cause, or result from, CNS disorders. However, some disease-associated proteins are of low-abundance and are difficult to detect. A low total-protein concentration, a high amount of albumin and immunoglobins, and a wide dynamic range (several orders of magnitude) of protein concentration cause several difficulties in the identification of low-abundance CSF proteins. In this study, advantage was taken of the range of different hydrophobic properties of CSF proteins, and a reversed-phase solid-phase extraction (SPE) cartridge was used to prefractionate human lumbar CSF proteins into three separate fractions prior to two-dimensional gel electrophoresis resolution of the proteome. A portion of the high-abundance CSF proteins were removed from two (eluted with 35% and 50% acetonitrile) of the three fractions. Some trace CSF proteins were preferentially enriched in the two fractions, and many proteins were detected in the two-dimensional (2-D) gels of the two fractions. Among the novel proteins identified, sixty-two protein spots that represent forty-two proteins were characterized. Most of the proteins have not been annotated in any previous 2-D map of human CSF, and several have been implicated in CNS diseases. The prefractionation of CSF proteins with SPE, followed by proteomics analysis, provides a new method to explore low-abundance, disease-specific CSF proteins.     

Proteomics analysis of human cerebrospinal fluid

Cerebrospinal fluid (CSF) is secreted from several different central nervous system (CNS) structures, and any changes in the CSF composition will accurately reflect pathological processes. Proteomics offers a comprehensive bird's eye view to analyze CSF proteins at a systems level. This paper reviews the variety of analytical methods that have been used for proteomics analysis of CSF, including sample preparation, two-dimensional liquid and gel electrophoresis, mass spectrometry, bioinformatics, and non-gel methods. The differentially expressed CSF proteins that have been identified by proteomics methods are discussed.     

Serotonin in human lumbar cerebrospinal fluid: a reassessment

An inter-laboratory comparison study was carried out in order to ascertain mean levels of serotonin (5-HT) in human lumbar cerebrospinal fluid (CSF). Analyses were performed using high performance liquid chromatography (HPLC) coupled with either electrochemical (LC-EC) or fluorometric (LC-F) detection. With the detection limits obtained (7-8 pg/ml for LC-EC, 7-15 pg/ml for LC-F) 5-HT was not usually detected in human lumbar CSF. The findings indicate that the true mean concentration of CSF 5-HT is less than 10 pg/ml. This upper limit is substantially lower than all previous reports of 5-HT concentrations in normal human lumbar CSF. The extremely low concentrations of 5-HT present in CSF make it unlikely that CSF 5-HT will be of clinical utility in assessing central serotonergic function.     

Proteomic analysis of the cerebrospinal fluid of patients with lumbar disk herniation

To better understand the pathophysiologic mechanisms underlying spinal nerve root injury induced by lumbar disk herniation (LDH), comparative proteomic analysis of cerebrospinal fluid (CSF) between patients with LDH (the experiment group) and the otherwise healthy patients who had had implants removed from healed fractures in the lower limbs (the control group) was carried out using 2-DE followed by LC-IT-MS and database searching. Image analysis of silver-stained 2-DE gels revealed that 15 protein spots showed significant differential expression between the two groups of CSF samples (p < 0.05). After searching the database we found that in CSF of LDH patients, the expression of cystatin C, apolipoprotein A-IV, vitamin D-binding protein, neurofilament triplet L protein, IgG, tetranectin, and hemoglobin were elevated. However, ProSAAS, prostagladin D2 synthase, creatine kinase B, superoxide dismutase 1 and peroxiredoxin 2 were decreased. The subsequent ELISA measured the concentration of tetranectin, vitamin D-binding protein and cystatin C and confirmed the results of proteomic analysis. These identified proteins are involved in the pathophysiological process of spinal nerve root injury caused by herniated lumbar disk. The functional implications of the alterations in the levels of these proteins are discussed in this paper.     

Endorphins in human cerebrospinal fluid

Opiate activity in CSF samples drawn from patients with suspected intracranial hydrodynamic dysfunction has been fractionated on Sephadex G-10 and separated by column electrophoresis in agarose suspension. From the Sephadex G-10 chromatography two receptor active fractions (FI and FII) were recovered. Both FI and FII were further resolved by the electrophoresis. FI separated into at least four components and FII into two components. The study also includes a comparison of the endorphin concentrations in CSF (samples drawn from healthy volunteers) measured by receptorassay with those detected by radioimmunoassay of beta-endorphin, [Met]enkephalin and dynorphin, respectively. The data obtained indicated negligible quantities of the radioimmunoassayable endorphins in the total CSF opiate activity.     

Neuropeptides in human cerebrospinal fluid

Ten neuropeptides were measured by RIA in human cerebrospinal fluid obtained from 30 normal volunteers. The levels of seven peptides (corticotropin releasing factor, adrenocorticotropin, vasoactive intestinal peptide, somatostatin, beta-endorphin, beta-lipotropin, and the N-terminal fragment of proopiomelanocortin) were highly, positively correlated with one another. This result is consistent with the hypothesis that cerebrospinal fluid levels of these seven peptides are a function of some common regulatory factor, such as shared release into the cerebrospinal fluid.     

Beta-endorphin-immunoreactive components in human cerebrospinal fluid

Cerebrospinal fluid (CSF) from patients without neurological disorder was analyzed after Sep-Pak extraction for beta-endorphin (beta-EP)-immunoreactive components by combined reversed-phase high-performance liquid chromatography (HPLC) and radioimmunoassay. A C-terminal directed antibody detected one major immunoreactive component, probably identical with beta-EP1-31. An N-terminal directed antibody detected several immunoreactive components. One co-eluted with beta-EP1-31 but the others are probably C-terminal truncated or otherwise modified forms of beta-EP1-31. However, they eluted differently from beta-EP1-16 (alpha-endorphin), beta-EP1-26, 1-27 and alpha,N-acetyl-beta-EP1-31. Alternatively, some of the fragments may represent C-terminal extended forms of pro-enkephalin A-derived Met-enkephalin. A Met-enkephalin antiserum detected several immunoreactive components probably representing N-terminal extended forms; neither of them were identical with the beta-EP-immunoreactive components. The results illustrate the heterogeneity of the beta-EP-immunoreactive components in CSF and the need to characterize the beta-EP radioimmunoassay before its application to biological extracts.     

Proteomics of human cerebrospinal fluid: discovery and verification of biomarker candidates in neurodegenerative diseases using quantitative proteomics

There is an urgent need for novel biomarkers that can be used to improve the diagnosis, predict the disease progression, improve our understanding of the pathology or serve as therapeutic targets for neurodegenerative diseases. Cerebrospinal fluid (CSF) is in direct contact with the CNS and reflects the biochemical state of the CNS under different physiological and pathological settings. Because of this, CSF is regarded as an excellent source for identifying biomarkers for neurological diseases and other diseases affecting the CNS. Quantitative proteomics and sophisticated computational software applied to analyze the protein content of CSF has been fronted as an attractive approach to find novel biomarkers for neurological diseases. This review will focus on some of the potential pitfalls in biomarker studies using CSF, summarize the status of the field of CSF proteomics in general, and discuss some of the most promising proteomics biomarker study approaches. A brief status of the biomarker discovery efforts in multiple sclerosis, Alzheimer's disease, and Parkinson's disease is also given.     

Selected ion monitoring assay for biogenic amine metabolites and probenecid in human lumbar cerebrospinal fluid

Details are presented of an improved selected ion monitoring assay for the major biogenic amine metabolites and probenecid in human lumbar cerebrospinal fluid (CSF). The metabolites and probenecid are simultaneously extracted with ethyl acetate from an acidified aqueous phase, and are simultaneously converted to pentafluoropropionyl esters by reaction with pentafluoropropionic anhydride and pentafluoropropanol. The esters of the metabolites are analyzed following a single injection of the derivatized sample onto the gas chromatographic column, while the ester of probenecid is analyzed following a separate injection onto the gas chromatographic column. Quantitation is achieved using for internal standards deuterated analogues of the metabolites and a chemical analogue of probenecid. Data are presented on the concentration of free and conjugated forms of the metabolites in lumbar CSF taken from healthy volunteers.     

The human cerebrospinal fluid metabolome

With continuing improvements in analytical technology and an increased interest in comprehensive metabolic profiling of biofluids and tissues, there is a growing need to develop comprehensive reference resources for certain clinically important biofluids, such as blood, urine and cerebrospinal fluid (CSF). As part of our effort to systematically characterize the human metabolome we have chosen to characterize CSF as the first biofluid to be intensively scrutinized. In doing so, we combined comprehensive NMR, gas chromatography-mass spectrometry (GC-MS) and liquid chromatography (LC) Fourier transform-mass spectrometry (FTMS) methods with computer-aided literature mining to identify and quantify essentially all of the metabolites that can be commonly detected (with today's technology) in the human CSF metabolome. Tables containing the compounds, concentrations, spectra, protocols and links to disease associations that we have found for the human CSF metabolome are freely available at http://www.csfmetabolome.ca.     

Phosphotyrosine profiling of human cerebrospinal fluid

Background

Cerebrospinal fluid (CSF) is an important source of potential biomarkers that affect the brain. Biomarkers for neurodegenerative disorders are needed to assist in diagnosis, monitoring disease progression and evaluating efficacy of therapies. Recent studies have demonstrated the involvement of tyrosine kinases in neuronal cell death. Thus, neurodegeneration in the brain is related to altered tyrosine phosphorylation of proteins in the brain and identification of abnormally phosphorylated tyrosine peptides in CSF has the potential to ascertain candidate biomarkers for neurodegenerative disorders.

Methods

In this study, we used an antibody-based tyrosine phosphopeptide enrichment method coupled with high resolution Orbitrap Fusion Tribrid Lumos Fourier transform mass spectrometer to catalog tyrosine phosphorylated peptides from cerebrospinal fluid. The subset of identified tyrosine phosphorylated peptides was also validated using parallel reaction monitoring (PRM)-based targeted approach.

Results

To date, there are no published studies on global profiling of phosphotyrosine modifications of CSF proteins. We carried out phosphotyrosine profiling of CSF using an anti-phosphotyrosine antibody-based enrichment and analysis using high resolution Orbitrap Fusion Lumos mass spectrometer. We identified 111 phosphotyrosine peptides mapping to 66 proteins, which included 24 proteins which have not been identified in CSF previously. We then validated a set of 5 tyrosine phosphorylated peptides in an independent set of CSF samples from cognitively normal subjects, using a PRM-based targeted approach.

Conclusions

The findings from this deep phosphotyrosine profiling of CSF samples have the potential to identify novel disease-related phosphotyrosine-containing peptides in CSF.

     

A comparative proteomic analysis of human and rat embryonic cerebrospinal fluid

During vertebrate central nervous system development, the apical neuroepithelium is bathed with embryonic Cerebrospinal Fluid (e-CSF) which plays regulatory roles in cortical cell proliferation and maintenance. Here, we report the first proteomic analysis of human e-CSF and compare it to an extensive proteomic analysis of rat e-CSF. As expected, we identified a large collection of protease inhibitors, extracellular matrix proteins, and transport proteins in CSF. However, we also found a surprising suite of signaling and intracellular proteins not predicted by previous proteomic analysis. Some of the intracellular proteins are likely to represent the contents of microvesicles recently described within the CSF (Marzesco, A. M., et al. J. Cell Sci. 2005, 118 (Pt. 13), 2849-2858). Defining the rich composition of e-CSF will enable a greater understanding of its concerted actions during critical stages of brain development.     

Substance P-like immunoreactivity in human cerebrospinal fluid

In a study to elucidate molecular mechanisms in pain, substance P-like immunoreactivity (SP-LI) was measured in lumbar CSF from 75 patients with lower back pain. Two samples--one before and one after lidocaine treatment--were obtained from each patient, and total SP-LI was measured in unfractionated (no HPLC) samples. SP-LI data were separated into three categories: placebo responders, pharmacological responders, and pharmacological non-responders. A significant difference was observed between the total SP-LI measurement of first and second samples of pharmacological non-responders. Distribution of SP-LI immunoreactive molecular species in two CSF patient samples (no ODS) was analyzed with a combination of reversed phase (RP) HPLC and RIA. Immunoreactivity in collected HPLC fractions was measured at calibrated retention times of synthetic SP-sulfoxide (SP-O), SP, and SP. Qualitative and quantitative differences in those HPLC-RIA metabolic profiles were observed within and between those two patients' samples. These data indicate that the type and amount of SP metabolism and SP precursor-processing differs in CSF between these two representative patients and within the short amount of time elapsed between acquiring these two samples.     

Zinc and copper in human cerebrospinal fluid

Zinc and copper have been estimated in CSF of 14 normal volunteers, nine men and five women. Zinc was analyzed by limited-aspiration flame atomic absorption spectrophotometry using a deuterium continuum light source. Copper was analyzed in 0.1% HNO₃ by flameless atomic absorption spectrophotometry with a graphite cuvette on a flameless atomizer. Recovery of added zinc varied less than 5% and that of the added copper varied less than 8%. CSF zinc was 31.5±19.8 μg/L (mean ± 1 SD); CSF copper, 7.5±3.1 μ/L. Values obtained for CSF zinc are about 1/2 those we and others obtained previously, the decrease related almost exclusively to removal of interference by the CSF matrix, which produced spuriously elevated values without use of the deuterium light source. Values obtained for CSF copper were approximately one-tenth those we and others had obtained previously. The decrease related, in part, to the removal of matrix effects, but also to improvement of the signal-to-noise ratio present in other techniques.     

Endogenous benzodiazepine ligands in human cerebrospinal fluid

Human cerebrospinal fluid was chromatographed on Bio-Gel P-4. Fractions containing material with molecular weights less than 4000 Dalton were pooled and further fractionated by high pressure liquid chromatography on an UltroPack TSK column G 2000 SW. At least three peaks, which were free of salt and GABA, were shown to displace (3H)-diazepam in the receptor-binding assay. Two of these peaks inhibited diazepam-binding competitively as shown by Lineweaver-Burke and displacement analysis. Their activity could be enhanced by the addition of GABA to the assay mixture. Incubation of these two peaks with various enzymes indicated that at least part of the activity of the second peak is due to a peptide.     

Diurnal beta-endorphin changes in human cerebrospinal fluid

Plasma and cerebrospinal fluid (CSF) beta-endorphin levels were determined by a RIA method in seven hydrocephalic male patients. The samples were simultaneously collected every two hours from 8 AM to 12 midnight and every hour from 1 AM to 7 AM. In both plasma and CSF beta-endorphin levels showed significant time-related variations during the 24 hour period. These results suggest the existence of diurnal CSF beta-endorphin variations analogous to those observed in plasma.     

Homogeneous distribution of prolactin in human cerebrospinal fluid

Concentrations of prolactin were assayed from human cerebrospinal fluid (CSF). Samples were taken from lumbar CSF space (n=105 neurological patients) and from lateral ventricles (n=31 neurosurgical patients). Ventricular CSF samples were taken from operatively treated subarachnoidal hemorrhage (SAH) patients during the monitoring of intraventricular pressure. More voluminous and frequent sampling was obtained from six patients undergoing diagnostic pneumoencephalography (PEG) procedure. Prolactin concentrations in lumbar CSF ranged between undetectable and 2.8 ng/ml with a mean value of 0.78±0.54 (SD) ng/ml. Some fluctuation was seen in the fractionated samples taken at PEG, but no definitive gradient was noticed. Ventricular CSF concentrations of prolactin (n=18) were 0.85±0.67 (SD) ng/ml at operation (range : undetectable ? 2.5 ng/ml). Somewhat lower values were recorded in the 3-day postoperative period, prolactin mean concentrations being 0.3 ? 0.6 ng/ml. The CSF prolactin concentrations in the lateral ventricles and lumbar sac are practically identical with no concentration gradient between these compartments.