Mass-Spectrometric Identification of Proteins and Pathways Responsible for Fouling on Poly(ethylene glycol) Methacrylate Polymer Brushes.

Prevention of fouling from proteins in blood plasma attracts significant efforts, and great progress is made in identifying surface coatings that display antifouling properties. In particular, poly(ethylene glycol) (PEG) is widely used and dense PEG-like cylindrical brushes of poly[oligo(ethylene glycol) methacrylate] (poly(OEGMA)) can drastically reduce blood plasma fouling. Herein, a comprehensive study of the variation of blood plasma fouling on this surface, including the analysis of the composition of protein deposits on poly(OEGMA) coatings after contact with blood plasma from many different donors, is reported. Correlation between the plasma fouling behavior and protein deposit composition points to the activation of the complement system as the main culprit of dramatically increased and accelerated deposition of blood plasma proteins on this type of antifouling coating, specifically through the classical pathway. These findings are consistent with observations on PEGylated drug carriers and highlight the importance of understanding the potential interactions between antifouling coatings and their environment.

The Relation Between Protein Adsorption and Hemocompatibility of Antifouling Polymer Brushes.

Whenever an artificial surface comes into contact with blood, proteins are rapidly adsorbed onto its surface. This phenomenon, termed fouling, is then followed by a series of undesired reactions involving activation of complement or the coagulation cascade and adhesion of leukocytes and platelets leading to thrombus formation. Thus, considerable efforts are directed towards the preparation of fouling-resistant surfaces with the best possible hemocompatibility. Herein, a comprehensive hemocompatibility study after heparinized blood contact with seven polymer brushes prepared by surface-initiated atom transfer radical polymerization is reported. The resistance to fouling is quantified and thrombus formation and deposition of blood cellular components on the coatings are analyzed. Moreover, identification of the remaining adsorbed proteins is performed via mass spectroscopy to elucidate their influence on the surface hemocompatibility. Compared with an unmodified glass surface, the grafting of polymer brushes minimizes the adhesion of platelets and leukocytes and prevents the thrombus formation. The fouling from undiluted blood plasma is reduced by up to 99%. Most of the identified proteins are connected with the initial events of foreign body reaction towards biomaterial (coagulation cascade proteins, complement component, and inflammatory proteins). In addition, several proteins that are not previously linked with blood-biomaterial interaction are presented and discussed.

Mass spectrometry, data re-analysis, and homology modelling predict posttranslational modifications of leucine-rich alpha-2-glycoprotein as a marker of myelodysplastic syndrome.

BACKGROUND: Leucine-rich alpha-2-glycoprotein (LRG) has been repeatedly proposed as a potential plasma biomarker for myelodysplastic syndrome (MDS). OBJECTIVE: The goal of our work was to establish the total LRG plasma level and LRG posttranslational modifications (PTMs) as a suitable MDS biomarker. METHODS: The total plasma LRG concentration was determined with ELISA, whilst the LRG-specific PTMs and their locations, were established using mass spectrometry and public mass spectrometry data re-analysis. Homology modelling and sequence analysis were used to establish the potential impact of PTMs on LRG functions via their impact on the LRG structure. RESULTS: While the results showed that the total LRG plasma concentration is not a suitable MDS marker, alterations within two LRG sites correlated with MDS diagnosis (p= 0.0011). Sequence analysis and the homology model suggest the influence of PTMs within the two LRG sites on the function of this protein. CONCLUSIONS: We report the presence of LRG proteoforms that correlate with diagnosis in the plasma of MDS patients. The combination of mass spectrometry, re-analysis of publicly available data, and homology modelling, represents an approach that can be used for any protein to predict clinically relevant protein sites for biomarker research despite the character of the PTMs being unknown.

Proteome changes of plasma-derived extracellular vesicles in patients with myelodysplastic syndrome.

BACKGROUND: Extracellular vesicles are released into body fluids from the majority of, if not all, cell types. Because their secretion and specific cargo (e.g., proteins) varies according to pathology, extracellular vesicles may prove a rich source of biomarkers. However, their biological and pathophysiological functions are poorly understood in hematological malignancies. OBJECTIVE: Here, we investigated proteome changes in the exosome-rich fraction of the plasma of myelodysplastic syndrome patients and healthy donors. METHODS: Exosome-rich fraction of the plasma was isolated using ExoQuick™: proteomes were compared and statistically processed; proteins were identified by nanoLC-MS/MS and verified using the ExoCarta and QuickGO databases. Mann-Whitney and Spearman analyses were used to statistically analyze the data. 2D western blot was used to monitor clusterin proteoforms. RESULTS: Statistical analyses of the data highlighted clusterin alterations as the most significant. 2D western blot showed that the clusterin changes were caused by posttranslational modifications. Moreover, there was a notable increase in the clusterin proteoform in the exosome-rich fraction of plasma of patients with more severe myelodysplastic syndrome; this corresponded with a simultaneous decrease in their plasma. CONCLUSIONS: This specific clusterin proteoform seems to be a promising biomarker for myelodysplastic syndrome progression.

Complement Activation Dramatically Accelerates Blood Plasma Fouling On Antifouling Poly(2-hydroxyethyl methacrylate) Brush Surfaces.

Non-specific protein adsorption (fouling) triggers a number of deleterious events in the application of biomaterials. Antifouling polymer brushes successfully suppress fouling, however for some coatings an extremely high variability of fouling for different donors remains unexplained. The authors report that in the case of poly(2-hydroxyethyl methacrylate) (poly(HEMA)) this variability is due to the complement system activation that causes massive acceleration in the fouling kinetics of blood plasma. Using plasma from various donors, the fouling kinetics on poly(HEMA) is analyzed and correlated with proteins identified in the deposits on the surface and with the biochemical compositions of the plasma. The presence of complement components in fouling deposits and concentrations of C3a in different plasmas indicate that the alternative complement pathway plays a significant role in the fouling on poly(HEMA) through the "tick-over" mechanism of spontaneous C3 activation. The generated C3b binds to the poly(HEMA) surface and amplifies complement activation locally. Heat-inactivated plasma prevents accelerated fouling kinetics, confirming the central role of complement activation. The results highlight the need to take into account the variability between individuals when assessing interactions between biomaterials and blood plasma, as well as the importance of the mechanistic insight that can be gained from protein identification.

Headspace study of chiral interconversion of N-acetyl-homocysteine thiolactones.

The rate constants for (L)-N-acetyl homocysteine thiolactone enantiomerization have been obtained from batch-wise studies and by dynamic gas chromatography of racemic mixtures. Results from the batch-wise experiments show that the kinetics of racemization at 150 °C is the same for vials made of glass, silanized glass or Teflon-coated glass so that the vial surface exhibited no effect on the kinetics of racemization. From the temperature dependence of the rate constants the preexponential factor, activation energy, the activation Gibbs energy and activation entropy have been obtained from transition state theory. The catalytic effect of G-DP, G-BP and B-DP GC chiral stationary phases on racemization has been observed and quantified by the values of rate constants; B-DP exhibited the greatest activity. The Eyring activation parameters obtained from batch-wise experiment were compared with theoretical values acquired from quantum chemical modelling. Agreement between the experimental and calculated values of activation Gibbs energy, activation enthalpy and activation entropy is good. The dynamic gas chromatography of racemic mixture on chiral B-DP, G-DP and G-BP capillary columns indicate that the rate constants of forward and reverse reactions are different in chiral environments. The greatest accelerating effect in the process of enantiomerization has been identified for G-BP both in the batch-wise experiments and by the dynamic gas chromatography.

Endothelialization of an ePTFE vessel prosthesis modified with an antithrombogenic fibrin/heparin coating enriched with bound growth factors.

Early and late thrombosis remain the most frequent reasons for the failure of synthetic cardiovascular grafts. Long-term hemocompatibility of implanted synthetic grafts can be achieved if a natural living endothelium is formed over its blood-contacting surface. Here we present a modification of a standard expanded polytetrafluorethylene (ePTFE) vessel prosthesis by a controlled preparation of a fibrin mesh enriched with covalently bound heparin and noncovalently bound vascular endothelial growth factor (VEGF) and fibroblast growth factor (FGF). Compared to a bare prosthesis, the coated prosthesis showed excellent antithrombogenic properties after contact with heparinized fresh human blood. Human umbilical vein endothelial cells seeded on the inner surface of the coated prosthesis formed a confluent layer in 5 days, whereas only small colonies of cells were scattered on the bare prosthesis. Viability of the cells was promoted mainly by FGF immobilized on the coating. These findings suggest that the coating may prevent acute thrombus formation and support the self-endothelialization of an implanted ePTFE vascular graft in vivo.

Extension of the Human Fibrinogen Database with Detailed Clinical Information-The αC-Connector Segment.

Fibrinogen, an abundant plasma glycoprotein, is involved in the final stage of blood coagulation. Decreased fibrinogen levels, which may be caused by mutations, are manifested mainly in bleeding and thrombotic disorders. Clinically relevant mutations of fibrinogen are listed in the Human Fibrinogen Database. For the αC-connector (amino acids Aα240-410, nascent chain numbering), we have extended this database, with detailed descriptions of the clinical manifestations among members of reported families. This includes the specification of bleeding and thrombotic events and results of coagulation assays. Where available, the impact of a mutation on clotting and fibrinolysis is reported. The collected data show that the Human Fibrinogen Database reports considerably fewer missense and synonymous mutations than the general COSMIC and dbSNP databases. Homozygous nonsense or frameshift mutations in the αC-connector are responsible for most clinically relevant symptoms, while heterozygous mutations are often asymptomatic. Symptomatic subjects suffer from bleeding and, less frequently, from thrombotic events. Miscarriages within the first trimester and prolonged wound healing were reported in a few subjects. All mutations inducing thrombotic phenotypes are located at the identical positions within the consensus sequence of the tandem repeats.

Impact of posttranslational modifications on atomistic structure of fibrinogen.

Oxidative stress in humans is related to various pathophysiological processes, which can manifest in numerous diseases including cancer, cardiovascular diseases, and Alzheimer's disease. On the atomistic level, oxidative stress causes posttranslational modifications, thus inducing structural and functional changes into the proteins structure. This study focuses on fibrinogen, a blood plasma protein that is frequently targeted by reagents causing posttranslational modifications in proteins. Fibrinogen was in vitro modified by three reagents, namely sodium hypochlorite, malondialdehyde, and 3-morpholinosydnonimine that mimic the oxidative stress in diseases. Newly induced posttranslational modifications were detected via mass spectrometry. Electron microscopy was used to visualize changes in the fibrin networks, which highlight the extent of disturbances in fibrinogen behavior after exposure to reagents. We used molecular dynamics simulations to observe the impact of selected posttranslational modifications on the fibrinogen structure at the atomistic level. In total, 154 posttranslational modifications were identified, 84 of them were in fibrinogen treated with hypochlorite, 51 resulted from a reaction of fibrinogen with malondialdehyde, and 19 were caused by 3-morpholinosydnonimine. Our data reveal that the stronger reagents induce more posttranslational modifications in the fibrinogen structure than the weaker ones, and they extensively alter the architecture of the fibrin network. Molecular dynamics simulations revealed that the effect of posttranslational modifications on fibrinogen secondary structure varies from negligible alternations to serious disruptions. Among the serious disruptions is the oxidation of γR375 resulting in the release of Ca2+ ion that is necessary for appropriate fibrin fiber formation. Folding of amino acids γE72-γN77 into a short α-helix is a result of oxidation of γP76 to glutamic acid. The study describes behaviour of fibrinogen coiled-coil connecter in the vicinity of plasmin and hementin cleavage sites.

Comparison of different fluorescence techniques in brandy classification by region of production.

Fluorescence spectrometry coupled with chemometrics was used to discriminate between 44 brandies originating from different countries. The kind of spectrum (emission, total luminescence and synchronous fluorescence), the geometry of sample illumination (front-face and right angle), and the sample type (bulk and diluted) were considered to compare the brandy classification. Firstly, the emission and synchronous fluorescence spectra (SFS) were processed by the principal component analysis (PCA) and the excitation-emission matrix (EEM) fluorescence spectra were modeled by unfolded PCA and parallel factor analysis (PARAFAC). Secondly, the scores of PCA/PARAFAC components were used in the linear discriminant analysis (LDA). Finally, the quality of the PCA-LDA and PARAFAC-LDA models was compared. Total correct classification using emission spectra was poor, regardless of the experimental conditions. The highest total correct classification (95.5%) was achieved by processing the SFS recorded at wavelength difference of 20 and 60nm on the diluted samples. However, 90.9% observed for bulk samples and their SFS at wavelength difference of 20nm in the right angle geometry as well as EEM fluorescence spectra in both geometries is still an acceptable result.

Alpha-2-HS-glycoprotein plasma level decrease correlates with age in patients with myelodysplastic syndromes.

BACKGOUND: It has been indicated in plasma proteomic studies on different myelodysplastic syndrome (MDS) cohorts that alpha-2-HS-glycoprotein could be a promising MDS biomarker candidate. OBJECTIVE: The goal of this work was to estimate alpha-2-HS-glycoprotein (AHSG) plasma levels and its biomarker value in the low- and high-risk subgroups of MDS patients. METHODS: The level of AHSG was estimated for 115 plasma samples using ELISA. RESULTS: The AHSG plasma level was found to be decreased significantly (p= 2.59 × 10-7) in MDS patients (515 ± 58 µg/ml) when compared to healthy controls (579 ± 64 µg/ml). Pearson and Spearman correlation analyses showed that age is the principal factor affecting the AHSG plasma level, rather than risk/diagnosis in MDS. CONCLUSIONS: In this work we demonstrate that although the total plasma level of AHSG is decreased in myelodysplastic syndrome patients, in particular in advanced MDS, that decrease correlates more strongly with age than with diagnosis within our studied cohort. Thus, according to the AHSG data gathered so far, AHSG total plasma level does not seem to be a suitable MDS biomarker, but its particular proteoforms should be considered for the next steps in MDS research.

Enhanced plasma protein carbonylation in patients with myelodysplastic syndromes.

Myelodysplastic syndromes (MDS) represent a heterogeneous group of pre-leukemic disorders, characterized by ineffective hematopoiesis and the abnormal blood cell development of one or more lineages. Oxidative stress, as an important factor in the carcinogenesis of onco-hematological diseases, is also one of the known factors involved in the pathogenesis of MDS. An increase of reactive oxygen species (ROS) may lead to the oxidation of DNA, lipids, and proteins, thereby causing cell damage. Protein carbonylation caused by ROS is defined as an irreversible post-translational oxidative modification of amino acid side chains, and could play an important role in signaling processes. The detection of protein carbonyl groups is a specific useful marker of oxidative stress. In this study, we examined 32 patients divided into three different subtypes of MDS according to the World Health Organization (WHO) classification criteria as refractory anemia with ringed sideroblasts (RARS), refractory cytopenia with multilineage dysplasia (RCMD), refractory anemia with excess blasts-1,2 (RAEB-1,2). We found significant differences in protein carbonylation between the group of all MDS patients and healthy controls (P=0.0078). Furthermore, carbonylated protein levels were significantly elevated in RARS patients compared to healthy donors (P=0.0013) and to RCMD patients (P=0.0277). We also found a significant difference in the total iron binding capacity (TIBC) between individual subgroups of MDS patients (P=0.0263). Moreover, TIBC was decreased in RARS patients compared to RCMD patients (P=0.0203). TIBC moderately negatively correlated with carbonyl levels (r=-0.5978, P=0.0054) in the MDS patients as a whole. Additionally we observed changes in the carbonylated proteins of RARS patients in comparison with healthy controls and their negative controls. Using tandem mass spectrometry (LC-MS/MS) we identified 27 uniquely carbonylated proteins of RARS patients, which were generated by ROS and could influence the pathophysiology of low-risk MDS. These data indicate that increased protein carbonylation is related with RARS as low-risk MDS subgroup. We suggest that this type of post-translational modification in MDS disease is not "only" a consequence of oxidative stress, but also plays an active role in the pathophysiology and iron metabolism within the RARS subgroup of MDS. Measurement of plasma carbonyl levels and the isolation of carbonylated plasma proteins, followed by their identification, could serve as a potential diagnostic and prognostic tool in MDS.

Determination of the interconversion energy barrier of three novel pentahelicene derivative enantiomers by dynamic high resolution liquid chromatography.

Dynamic high resolution liquid chromatography (DHPLC) was used to determine the kinetic and thermodynamic activation parameters of interconversion of three novel pentahelicene derivatives {3,5-bis(trifluoromethyl)benzo[i]pentahelicene, naphtho[1,2-i]pentahelicene and 4-methoxybenzo[i]pentahelicene}. DHPLC was performed on a chiral isopropyl - carbamate cyclofructan 6 (LARIHC CF6-P) column under normal phase conditions. Variation of the column temperature and flow rate was used to study the interconversion process. A computer assisted deconvolution method was employed to determine the individual peak areas and the retention times required for the calculation of apparent enantiomerization energy barriers, enthalphy and entropy of the interconvertion of above defined pentahelicene derivative enantiomers. An ab initio quantum chemistry method was used to estimate theoretical kinetic and thermodynamic interconversion parameters and to evaluate experimental data of these three novel pentahelicene derivative enantiomers.

Application of Fluorescence Spectrometry With Multivariate Calibration to the Enantiomeric Recognition of Fluoxetine in Pharmaceutical Preparations.

Fluoxetine is the most prescribed antidepressant chiral drug worldwide. Its enantiomers have a different duration of serotonin inhibition. A novel simple and rapid method for determination of the enantiomeric composition of fluoxetine in pharmaceutical pills is presented. Specifically, emission, excitation, and synchronous fluorescence techniques were employed to obtain the spectral data, which with multivariate calibration methods, namely, principal component regression (PCR) and partial least square (PLS), were investigated. The chiral recognition of fluoxetine enantiomers in the presence of ß-cyclodextrin was based on diastereomeric complexes. The results of the multivariate calibration modeling indicated good prediction abilities. The obtained results for tablets were compared with those from chiral HPLC and no significant differences are shown by Fisher's (F) test and Student's t-test. The smallest residuals between reference or nominal values and predicted values were achieved by multivariate calibration of synchronous fluorescence spectral data. This conclusion is supported by calculated values of the figure of merit.

Plasma Protein Biomarker Candidates for Myelodysplastic Syndrome Subgroups.

In recent years the plasma proteomes of several different myelodysplastic syndrome (MDS) subgroups have been investigated and compared with those of healthy donors. However, the resulting data do not facilitate a direct and statistical comparison of the changes among the different MDS subgroups that would be useful for the selection and proposal of diagnostic biomarker candidates. The aim of this work was to identify plasma protein biomarker candidates for different MDS subgroups by reanalyzing the proteomic data of four MDS subgroups: refractory cytopenia with multilineage dysplasia (RCMD), refractory anemia or refractory anemia with ringed sideroblasts (RA-RARS), refractory anemia with excess blasts subtype 1 (RAEB-1), and refractory anemia with excess blasts subtype 2 (RAEB-2). Reanalysis of a total of 47 MDS patients revealed biomarker candidates, with alpha-2-HS-glycoprotein and leucine-rich alpha-2-glycoprotein as the most promising candidates.

Peripheral blood mononuclear cell proteome changes in patients with myelodysplastic syndrome.

Our aim was to search for proteome changes in peripheral blood mononuclear cells (PBMCs) of MDS patients with refractory cytopenia with multilineage dysplasia. PBMCs were isolated from a total of 12 blood samples using a Histopaque-1077 solution. The proteins were fractioned, separated by 2D SDS-PAGE (pI 4-7), and double-stained. The proteomes were compared and statistically processed with Progenesis SameSpots; then proteins were identified by nano-LC-MS/MS. Protein functional association and expression profiles were analyzed using the EnrichNet application and Progenesis SameSpots hierarchical clustering software, respectively. By comparing the cytosolic, membrane, and nuclear fractions of the two groups, 178 significantly (P < 0.05, ANOVA) differing spots were found, corresponding to 139 unique proteins. Data mining of the Reactome and KEGG databases using EnrichNet highlighted the possible involvement of the identified protein alterations in apoptosis, proteasome protein degradation, heat shock protein action, and signal transduction. Western blot analysis revealed underexpression of vinculin and advanced fragmentation of fermitin-3 in MDS patients. To the best of our knowledge, this is the first time that proteome changes have been identified in the mononuclear cells of MDS patients. Vinculin and fermitin-3, the proteins involved in cell adhesion and integrin signaling, have been shown to be dysregulated in MDS.

Considerations on the determination of the limit of detection and the limit of quantification in one-dimensional and comprehensive two-dimensional gas chromatography.

Methods based on the blank signal as proposed by IUPAC procedure and on the signal to noise ratio (S/N) as listed in the ISO-11843-1 norm for determination of the limit of detection (LOD) and quantitation (LOQ) in one-dimensional capillary gas chromatography (1D-GC) and comprehensive two-dimensional capillary gas chromatography (CG×GC) are described in detail and compared for both techniques. Flame ionization detection was applied and variables were the data acquisition frequency and, for CG×GC, also the modulation time. It has been stated that LOD and LOQ estimated according to IUPAC might be successfully used for 1D-GC-FID method. Moreover, LOD and LOQ decrease with decrease of data acquisition frequency (DAF). For GC×GC-FID, estimation of LOD by IUPAC gave poor reproducibility of results while for LOQ reproducibility was acceptable (within ±10% rel.). The LOD and LOQ determined by the S/N concept both for 1D-GC-FID and GC×GC-FID methods are ca. three times higher than those values estimated by the standard deviation of the blank. Since the distribution pattern of modulated peaks for any analyte separated by GC×GC is random and cannot be predicted, LOQ and LOD may vary within 30% for 3s modulation time. Concerning sensitivity, 1D-GC-FID at 2Hz and of GC×GC-FID at 50Hz shows a ca. 5 times enhancement of sensitivity in the modulated signal output.

Fluorescence spectroscopy as a tool for determination of coumarins by multivariate calibration.

At present, it is necessary to check the quality of many food products in which the content of coumarins is limited. Since a rapid and simple method for the determination of coumarin (COU), 4-hydroxycoumarin (4HC) and dicoumarol (DC) in tea samples was needed, we developed an alternative option to chromatography, i.e., fluorescence spectroscopy with multivariate calibration. The synchronous fluorescence spectra were recorded at constant wavelength differences 70, 80 and 90 nm from 200 to 400 nm. The different experimental parameters affecting the synchronous fluorescence intensities of the analytes were carefully studied and optimized. Partial least squares (PLS) method and multi linear regression (MLR) were compared on determining the concentrations. The best results were obtained by the PLS method on synchronous fluorescence spectra at Δλ = 90 nm. The results from the analysis of herbal tea Melilotus officinalis by synchronous fluorescence spectroscopy with PLS model are equivalent with the results from HPLC. Fisher F-test and Student's t-test confirmed this finding.