Andreas Chrambach and René Descartes: Plutarch's parallel lives?
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Chemistry, Analytic↗
Biomedical subjects
Pier Giorgio Righetti
Publications and source records attributed to Pier Giorgio Righetti.
Proteomic analysis of rat cortical neurons after fluoxetine treatment.
The known neurochemical effect of most currently available antidepressants is the enhancement of the synaptic levels of monoamine neurotransmitters. However, the existence of other mechanisms has been suggested to justify the significant delay between the modulation of the monoaminergic system and the clinical effects. In order to investigate the effects of the antidepressant fluoxetine (a prototypical serotonin selective re-uptake inhibitor) and to improve the understanding of its mechanism of action, we performed a proteomic investigation in rat primary cortical neurons exposed sub-chronically to this antidepressant. Cortical neurons were treated for 3 days with 1 microM fluoxetine or vehicle. Protein extracts were processed for 2D gel characterization. Image analysis allowed the identification of six proteins differently expressed by more than 100% and seven proteins differently expressed by more than 50% (P<0.05). Nine proteins were identified by mass spectrometry. Among them, cyclophilin A, 14-3-3 protein z/delta and GRP78 are involved in neuroprotection, in serotonin biosynthesis and in axonal transport, respectively. This study showed that the primary culture of cortical neurons is a suitable system for studying the effects of fluoxetine action and may contribute to improve the understanding of fluoxetine psychotherapeutic action and the mechanisms mediating the long-term effects of this antidepressant treatment.
Analysis of Variance↗
Real and imaginary artefacts in proteome analysis via two-dimensional maps.
The present review touches on a long-lasting debate on possible artefacts (i.e. generation of spurious spots, not belonging to the biological sample under analysis) induced by the separation technique (in this case, two-dimensional mapping) per se. It is shown here that some of the biggest offenders, always blamed in the past (at least since 1970, i.e. since the inception of gel-base isoelectric focusing protocols), namely deamidation (of Asn and Gln residues) and carbamylation (due to cyanate produced in urea solution), simply do not occur in properly handled samples and have never indeed been demonstrated in real samples, except when forced in purpose. Conversely, two unexpected major artefacts have been recently shown to plague 2D mapping. One is formation of homo- and hetero-oligomers in samples that have been reduced but not alkylated prior to entering the electric field. The phenomenon is highly aggravated in alkaline pH regions and can lead to an impressive number of spurious spots not existing in the original sample. Thus, alkylation (best if performed with acrylamide or vinylpyridines) is a must for avoiding such spurious spots, as well as sample streaking and smearing in the alkaline gel region, and for maintaining sample integrity. In fact, the other unexpected artefact is desulfuration (beta-elimination) by which, upon prolonged electrophoresis, the sample looses an -SH group fro Cys residues. This loss, in the long run, is accompanied by massive protein degradation due to lysis of a C-N bond along the polypeptide chain. Here too, alkylation of -SH groups of Cys almost completely prevents this noxious degradation phenomenon.
Alkylation↗
Reducing protein concentration range of biological samples using solid-phase ligand libraries.
The discovery of specific polypeptides of diagnostic relevance from a biological liquid is complicated by the overall vast number and the large concentration range of all polypeptides/proteins in the sample. Depletion or fractionation methodologies have been used for selectively removing abundant proteins; however, they failed to significantly enrich trace proteins. Here we expand upon a new method that allows the reduction of the protein concentration range within a complex mixture, like neat serum, through the simultaneous dilution of high abundance proteins and the concentration of low abundance ones in a single, simple step. This methodology utilizes solid-phase ligand libraries of large diversity. With a controlled sample-to-ligand ratio it is possible to modulate the relative concentration of proteins such that a large number of peptides or proteins that are normally not detectable by classical analytical methods become, easily detectable. Application of this method for reducing the dynamic range of unfractionated serum is specifically described along with treatment of other biological extracts. Analytical surface enhanced laser desorption/ionization mass spectrometry (SELDI-MS) technology and mono- and two-dimensional electrophoresis (1-DE and 2-DE) demonstrate the increase in the number of proteins detected. Examples linking this approach with additional fractionation methods demonstrate a further increase in the number of detectable species using either the so-called "top down" or "bottom up" approaches for proteomics analysis. By enabling the detection of a greater proportion of polypeptides/proteins within a sample, this method may contribute significantly towards the discovery of new biomarkers of diagnostic relevance.
Chromatography, Ion Exchange↗
Decoding 2D-PAGE complex maps: relevance to proteomics.
This review describes two mathematical approaches useful for decoding the complex signal of 2D-PAGE maps of protein mixtures. These methods are helpful for interpreting the large amount of data of each 2D-PAGE map by extracting all the analytical information hidden therein by spot overlapping. Here the basic theory and application to 2D-PAGE maps are reviewed: the means for extracting information from the experimental data and their relevance to proteomics are discussed. One method is based on the quantitative theory of statistical model of peak overlapping (SMO) using the spot experimental data (intensity and spatial coordinates). The second method is based on the study of the 2D-autocovariance function (2D-ACVF) computed on the experimental digitised map. They are two independent methods that are able to extract equal and complementary information from the 2D-PAGE map. Both methods permit to obtain fundamental information on the sample complexity and the separation performance and to single out ordered patterns present in spot positions: the availability of two independent procedures to compute the same separation parameters is a powerful tool to estimate the reliability of the obtained results. The SMO procedure is an unique tool to quantitatively estimate the degree of spot overlapping present in the map, while the 2D-ACVF method is particularly powerful in simply singling out the presence of order in the spot position from the complexity of the whole 2D map, i.e., spot trains. The procedures were validated by extensive numerical computation on computer-generated maps describing experimental 2D-PAGE gels of protein mixtures. Their applicability to real samples was tested on reference maps obtained from literature sources. The review describes the most relevant information for proteomics: sample complexity, separation performance, overlapping extent, identification of spot trains related to post-translational modifications (PTMs).
Electrophoresis, Gel, Two-Dimensional↗
Multivariate statistical tools applied to the characterization of the proteomic profiles of two human lymphoma cell lines by two-dimensional gel electrophoresis.
Mantle cell lymphoma (MCL) cell lines have been difficult to generate, since only few have been described so far and even fewer have been thoroughly characterized. Among them, there is only one cell line, called GRANTA-519, which is well established and universally adopted for most lymphoma studies. We succeeded in establishing a new MCL cell line, called MAVER-1, from a leukemic MCL, and performed a thorough phenotypical, cytogenetical and molecular characterization of the cell line. In the present report, the phenotypic expression of GRANTA-519 and MAVER-1 cell lines has been compared and evaluated by a proteomic approach, exploiting 2-D map analysis. By univariate statistical analysis (Student's t-test, as commonly used in most commercial software packages), most of the protein spots were found to be identical between the two cell lines. Thirty spots were found to be unique for the GRANTA-519, whereas another 11 polypeptides appeared to be expressed only by the MAVER-1 cell line. A number of these spots could be identified by MS. These data were confirmed and expanded by multivariate statistical tools (principal component analysis and soft-independent model of class analogy) that allowed identification of a larger number of differently expressed spots. Multivariate statistical tools have the advantage of reducing the risk of false positives and of identifying spots that are significantly altered in terms of correlated expression rather than absolute expression values. It is thus suggested that, in future work in differential proteomic profiling, both univariate and multivariate statistical tools should be adopted.
Cell Line, Tumor↗
The Alpher, Bethe, Gamow of isoelectric focusing, the alpha-Centaury of electrokinetic methodologies. Part I.
The birth and evolution of IEF in conventional carrier ampholyte buffers is reviewed here, from a shaky start during World War II, via desperate attempts of Svensson to create pH gradients by stationary electrolysis of salts, to the development of the IEF theory and the solution of the steady-state equation. The remarkable synthetic process of Ampholines, as ingeniously devised by Vesterberg, is additionally recalled, with a thorough description of the fundamental properties of these amphoteric buffers, creating and maintaining the pH gradient under strong electric fields. The review ends with a mention of the major contributions of B. J. Radola to this field, namely analytical and preparative IEF in granulated Sephadex layers and the development of ultrathin IEF, in polyacrylamide gels as thin as 20-100 mum. The latter technique paved the way to DNA sequencing gels and to CZE. The symptoms of decay are here presented through the simulations of Mosher and Thormann, clearly indicating an isotachophoretic mechanism for pH gradient decay with time. The decay of IEF was the birth of IPGs.
Acrylic Resins↗
Organic and inorganic di-cations for capillary silica coating and EOF modulation in CE: Example of application in PEG analysis.
EOF measurements, by using 1,4-di-(4-aza-1-azonia-bicyclo[2.2.2]octane)butane diiodide, barium and strontium tetraborate as silica wall modifiers, are reported and, as an example of application, analysis of PEG (PEG 400-2000) polydisperse preparations in free solution CZE is shown. PEGs have been derivatized with phthalic anhydride so as to form singly or doubly charged derivatives with strong UV absorbance at 214 nm. Whereas separations in plain tetraborate buffer, pH 9.0, without any EOF control, did not lead to good resolution of all-size oligomers and suffered from long analysis times, excellent resolution of all oligomers up to 40 ethylene oxide (EO) units could be obtained under EOF control. Such EOF modulation was engendered by addition of 1 mM M7C4M7, a doubly charged organic cation able to stick tenaciously to the silica wall. Further modulation of EOF and silica surface modification could be achieved also by addition of inorganic cations, notably those of group II, whereas monovalent cations did not seem to affect much the EOF flux. Among the doubly charged cations investigated, Ca++, Mg++, Sr++ and Ba++, the latter did seem to offer best EOF control and reproducible runs. A judicious blend of M7C4M7 (0.33-1 mM range) with barium (10-20 mM range) allowed baseline resolution of all PEG oligomers investigated up to PEG 2000 and >40 EO units in length. In this last case, best results in terms of reproducibility and separation efficiency of the more heavy homologues were obtained using Li+ salt in small amounts.
Aza Compounds↗
A new approach for the removal of protein impurities from purified biologicals using combinatorial solid-phase ligand libraries.
The removal of last impurity traces from a purified protein is generally called polishing. It is an important step in downstream processing since protein impurities may generate undesirable side effects when the preparation is intended for research, diagnostic and more importantly therapeutic applications. Polishing is generally achieved by using orthogonal separation methods to previous steps, the most common being gel permeation chromatography. In spite of its polishing effectiveness, this technique suffers from a poor separation capacity and modest productivity as a result of low speed. Other approaches, for instance, based on anion exchange or on hydrophobic chromatography, that may be optimized for a given process cannot be used as generic methods. This document reports for the first time the use of a combinatorial solid-phase peptide library as a general method for the removal of impurity traces. Several examples of impurity trace removal are reported; starting material is either a pure protein spiked with serum proteins or with Escherichia coli extracts or current purified proteins still containing a small percentage of impurities. Among polished proteins are recombinant human albumin expressed in Pichia pastoris and human transferrin purified from whole plasma. This new method is used in neutral or even physiological pH and ionic strength conditions, with a remarkable capability to remove impurities. The process is as rapid as current adsorption chromatography procedures usable for the removal of a large number of protein impurities, with each one present in small amounts, such as host cell proteins.
Biological Products↗
Effect of barium tetraborate on the separation of tryptic digests of proteins by zone electrophoresis in uncoated capillaries.
A simple, fast, efficient and reproducible method for peptide separations in CZE is reported. It consists in running tryptic digests of peptides in an uncoated capillary, in a BGE composed of tetraborate as a buffering ion, in which the typical sodium counterion is substituted with barium. Efficient absorption of this divalent cation to ionized silanols and barium silicate precipitation seem to be able to shield effectively the silica surface from separands. This is demonstrated by the fact that, when tBa(2+) ions are present in solution (from pH 8.5 up to pH 11.0), the electroendoosmotic flow is reversed; such reversal being progressively higher at higher pH values, by up to a four-fold. Separations become progressively better at higher pH values, whereas at pH 11 in sodium tetraborate they are dramatically worsened. It is further hypothesized that the barium silicate layer further protects the silica surface against dissolution and corrosion which is quite substantial at pH 11.
Barium↗
Mass distribution and focusing properties of carrier ampholytes for isoelectric focusing: I. Novel and unexpected results.
In an attempt to prepare quasi-isoelectric buffers as BGEs for CE, carrier ampholytes (CAs) (Ampholine, pH 7-9; Servalyt, pH 7-9; Bio-Lyte, pH 8-10 and Pharmalyte, pH 8-10.5) have been subdivided with the Rotofor into 20 fractions, of ca. 0.1 pH unit span, whose composition has been studied by CZE-MS. The results have allowed identifying the number of different molecular mass compounds present in every commercial brand, as well as the number of isoforms (having identical mass, but representing positional isomers) associated with a given M(r) value. Ampholine is composed of 29 species, for a total of 85 different isoforms; Bio-Lyte is made of 43 compounds, for a total of 136 isoforms; Pharmalyte comprises 58 different M(r) chemicals, for a total of 102 isoforms and Servalyt is constituted by 65 species, for a total of 306 compounds (all of these values to be considered as minimum numbers, as detected by the present methodology). Surprisingly, and contrary to theory, a very large proportion (up to 70%) of these species are 'poor carrier ampholytes', in that they are unable to focus and are evenly distributed along the generated pH gradient in the electric field. Paradoxically, the pH gradient is created and sustained by the minority of species (30% for three brands, up to 50% for Pharmalyte) that appear to focus at their pI position into reasonably sharp zones. Even in the narrowest pI fraction, up to 20 different compounds can be detected. It is concluded that very few amines with different useful pK values are utilized for the synthesis and that a new generation of CAs with a more diversified population of amines with proper pK values within the given pH intervals should be sought. Ampholine, the poorest of the commercial brands, appears to be still made with the original synthesis devised by Vesterberg, i.e. by reacting a concoction of oligoamines with alpha,beta-unsaturated acids.
Ampholyte Mixtures↗
Mass distribution, polydispersity and focusing properties of carrier ampholytes for IEF II: pH 4-6 intervals.
For studying the M(r) distribution and number of species in narrow-range (2 pH-unit wide, in the nominal pI 4-6 interval) carrier ampholytes from four commercial sources (Bio-Lyte, Servalyt, Ampholine and Pharmalyte), a 2-D technique was adopted consisting of a focusing step in a liquid phase (Rotofor, yielding 20 fractions) followed by orthogonal CE in both, acidic and basic buffers. As a final step, every other fraction was analyzed by CE-MS. The findings: Ampholine contains 80 different M(r) compounds, in the M(r) interval 203 to 893 Da, for a total of 325 isoforms. Bio-Lyte consists of 66 different M(r) species, in the M(r) range 388 to 835 Da, for a total of 436 isoforms. Servalyt is made of 199 different M(r) compounds, in the M(r) interval 204 to 907 Da, for a total of 1302 isoforms. Pharmalyte pH 4-6.5, comprises 217 amphoteres, in the M(r) range 150 to 1179 Da, for a total of 812 isoforms. Pharmalyte appears to be the best brand, with the vast majority of species focusing sharply at their pI position and <5% "poor" species, distributed along the entire pH gradient, denoting an extremely shallow pH/mobility curve across the pI value.
Ampholyte Mixtures↗
Searching for markers of Creutzfeldt-Jakob disease in cerebrospinal fluid by two-dimensional mapping.
Differential proteomic analysis has been performed on the cerebrospinal fluid (CSF) of six healthy and six patients suffering form sporadic Creutzfeldt-Jakob disease (sCJD), age- and sex-matched, after immuno-subtraction of albumin and immunoglobulins. These maps have revealed 28 polypeptide chains differentially modulated in the sCJD samples, of which 10 appeared to be up-regulated, the remaining 18 being down-regulated. Among those, 13 could be identified upon digestion and MALDI-TOF, MS analysis. In addition, the strong modulation of cystatin C was also confirmed by immunoblot analysis and the highly altered level of the 14-3-3 proteins that escaped detection by 2-D mapping, could be assessed by Western blots and immuno-detection of monomeric and homo- and hetero-dimeric 14-3-3 isotypes. In search for a panel of potential markers for sCJD, we highlight cystatin C, 14-3-3 proteins, transferrin, ubiquitin, Apoliprotein J and perhaps some of the still unidentified, but strongly modulated polypeptide chains detected in the differential map.
14-3-3 Proteins↗
Protein Equalizer Technology : the quest for a "democratic proteome".
No proteome can be considered "democratic", but rather "oligarchic", since a few proteins dominate the landscape and often obliterate the signal of the rare ones. This is the reason why most scientists lament that, in proteome analysis, the same set of abundant proteins is seen again and again. A host of pre-fractionation techniques have been described, but all of them, one way or another, are besieged by problems, in that they are based on a "depletion principle", i.e. getting rid of the unwanted species. Yet "democracy" calls not for killing the enemy, but for giving "equal rights" to all people. One way to achieve that would be the use of "Protein Equalizer Technology" for reducing protein concentration differences. This comprises a diverse library of combinatorial ligands coupled to spherical porous beads. When these beads come into contact with complex proteomes (e.g. human urine and serum, egg white, and any cell lysate, for that matter) of widely differing protein composition and relative abundances, they are able to "equalize" the protein population, by sharply reducing the concentration of the most abundant components, while simultaneously enhancing the concentration of the most dilute species. It is felt that this novel method could offer a strong step forward in bringing the "unseen proteome" (due to either low abundance and/or presence of interference) within the detection capabilities of current proteomics detection methods. Examples are given of equalization of human urine and serum samples, resulting in the discovery of a host of proteins never reported before. Additionally, these beads can be used to remove host cell proteins from purified recombinant proteins or protein purified from natural sources that are intended for human consumption. These proteins typically reach purities of the order of 98%: higher purities often become prohibitively expensive. Yet, if incubated with "equalizer beads", these last impurities can be effectively removed at a small cost and with minute losses of the main, valuable product.
Biomarkers↗
Proteomic analysis of anti-angiogenic effects by a combined treatment with vinblastine and rapamycin in an endothelial cell line.
Angiogenesis controls the new blood supply routes into the tumor mass via the host endothelial cells (ECs). In this study, the EA.hy926 endothelial cell line has been treated with vinblastine (VBL) and rapamycin (RAP), both separately and in combination at low doses. Recently, we demonstrated the synergistic antiangiogenic effects of a combination of VBL and RAP at very low doses in vitro and in vivo. Herein, we confirm the ability of this combined treatment to statistically inhibit the proliferation of ECs, in a synergistic manner, by inducing apoptosis. The aim of this study was to substantiate these findings at the protein level. Differential proteomic analysis was performed on untreated control cells, treated with VBL, incubated with RAP, or subjected to a drug combination. Differentially expressed 113 polypeptide chains were visualized and 65 were identified via MALDI-TOF analysis. Some of the regulated proteins are involved in the processes of angiogenesis, proliferation, migration, and apoptosis. The down-modulation of ATP synthase, annexin A2, heat shock p70, glucose-6-phosphate dehydrogenase, vasodilator-stimulated phosphoprotein, proteasome 26S, tryptophanyl-tRNA synthetase, and stathmin/OP18, as well as the up-modulation of carbonyl reductase, Rho-GDI, and histone H1.0 correlates with the synergistic antiangiogenic activity of VBL and RAP.
Angiogenesis Inhibitors↗
A new approach for the detection and identification of protein impurities using combinatorial solid phase ligand libraries.
We propose a novel method for detection of protein impurities present in plasma-derived and recombinant purified injectable biopharmaceuticals by enhancing the concentration of protein impurities, in essence "amplifying" their presence to detectable levels. The method is based on the capture of proteins using a combinatorial solid-phase hexapeptides ligand library previously described for the reduction of protein concentration difference in biological fluids. Three proteins have been investigated: Staphylococcus aureus Protein A, expressed in Escherichia coli and supplied as 99% pure, recombinant human albumin, expressed in Pichia pastoris and certified as 95% pure, and therapeutic albumin supplied as 96-98% pure injectable solution. In all cases, after treatment with the ligand libraries, a number of additional polypeptide chains, not visible in the control, could be detected and obtained in sufficient amounts for MS analysis. In the cases of the two recombinant proteins, it could be demonstrated that a number of these polypeptide chains were host cell proteins still present in the purified product. In addition, a substantial number of these spots were found to be cleavage products of the original recombinant DNA species. Such cleavage products were particularly abundant in the recombinant human albumin preparation. From pure injectable serum albumin, a number of human plasma protein impurities were also identified by LC-MS/MS analysis. Treatment with ligand libraries of purified proteins is thus seen as a very powerful method of capture and concentration of host proteins and cleaved products for further analysis to control better the quality of industrial biotechnology products.
Albumins↗
Quasi-isoelectric buffers for protein analysis in a fast alternative to conventional capillary zone electrophoresis.
Two different approaches are here reported for obtaining ultra-narrow pI cuts from 2-pH unit wide carrier ampholyte ranges, as commercially available, for use as quasi-isoelectric buffers in capillary electrophoresis separations of proteins. One of them uses multicompartment electrolyzers endowed with isoelectric membranes (Immobiline technology); the other employs the Rotofor equipment. Although the first approach results in more precise pI cuts, the latter technique is much faster, easier to handle and permits the immediate collection of 20 fractions in a single run. This results in ultra-narrow, ca. 0.1-pH unit intervals, uniformly spaced apart along the original wider gradient utilized for the fractionation. It is here shown that such quasi-isoelectric buffers, especially those in the pH 8-9 interval, have the unique property of coating the silica wall, thus preventing interaction of the proteins with the silica surface, that would otherwise totally disrupt the separation. On the contrary, such a shielding is not obtained in control, non isoelectric buffers (such as phosphate), that give very poor separations in uncoated capillaries. It is hypothesized that such a unique shielding effect is due to the oligo-amino backbone of the carrier ampholytes, typically composed (in the Vesterberg's synthetic approach) of 4-6 nitrogens spaced apart by ethylene moieties. Although such oligoprotic buffers should bear, in the isoelectric state, just one positive and one negative charge, they might be transiently ionized upon contact with the silanols, thus inducing a cooperative binding to the silica wall.
Buffers↗
Urinary prostasin: a candidate marker of epithelial sodium channel activation in humans.
Prostasin is a serine peptidase hypothesized to regulate epithelial sodium channel (ENaC) activity in animals or on in vitro cultured cells. We investigated whether urinary prostasin may be a candidate marker of ENaC activation in humans. We studied 10 healthy volunteers and 8 hypertensive patients with raised aldosterone-to-renin ratio before and after spironolactone or saline/Florinef suppression test, respectively. Four healthy subjects were also studied before and after saline. Urinary prostasin was evaluated by SDS-PAGE, 2D maps, and Western blotting. Every sample of normotensive individuals was compared with the corresponding sample of urine collected after spironolactone or saline; every sample of hypertensive patients was compared with the corresponding sample of urine collected after saline or Florinef. Prostasin was detectable in all subjects regardless of gender, dietary sodium intake, and spironolactone treatment. Spironolactone (100 mg) increased urinary Na+/K+ ratio and decreased urinary prostasin in normotensives in whom the renin/aldosterone axis was activated by a low Na+ intake, but it was ineffective in individuals with high Na+ intake. Saline infusion also reduced prostasin in normotensive subjects. In contrast, prostasin paradoxically increased in urine of patients affected by primary aldosteronism after volume expansion. By 2D immunoblotting, several protein isoforms were observed, some of them being overexpressed after inhibition tests in patients with primary aldosteronism. In addition to a "basal" aliquot of prostasin, constitutively released in human urine regardless of sodium balance and aldosterone activation, there exists a second "aldosterone-responsive" aliquot modulated by Na+ intake and potentially suitable as candidate marker of ENaC activation.
Adult↗