Characterization of the porcine synovial fluid proteome and a comparison to the plasma proteome

AbstractSynovial fluid is present in all joint cavities, and protects the articular cartilage surfaces in large by lubricating the joint, thus reducing friction. Several studies have described changes in the protein composition of synovial fluid in patients with joint disease. However, the protein concentration, content, and synovial fluid volume change dramatically during active joint diseases and inflammation, and the proteome composition of healthy synovial fluid is incompletely characterized.We performed a normative proteomics analysis of porcine synovial fluid, and report data from optimizing proteomic methods to investigate the proteome of healthy porcine synovial fluid (Bennike et al., 2014 [1]). We included an evaluation of different proteolytic sample preparation techniques, and an analysis of posttranslational modifications with a focus on glycosylation. We used pig (Sus Scrofa) as a model organism, as the porcine immune system is highly similar to human and the pig genome is sequenced. Furthermore, porcine model systems are commonly used large animal models to study several human diseases.In addition, we analyzed the proteome of human plasma, and compared the proteomes to the obtained porcine synovial fluid proteome. The proteome of the two body fluids were found highly similar, underlining the detected plasma derived nature of many synovial fluid components. The healthy porcine synovial fluid proteomics data, human rheumatoid arthritis synovial fluid proteomics data used in the method optimization, human plasma proteomics data, and search results, have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier http://www.ebi.ac.uk/pride/archive/projects/PXD000935

COMPARISON OF MODIFICATION SITES FORMED ON HUMAN SERUM ALBUMIN AT VARIOUS STAGES OF GLYCATION

Background—Many of the complications encountered during diabetes can be linked to the nonenzymatic glycation of proteins, including human serum albumin (HSA). However, there is little information regarding how the glycation pattern of HSA changes as the total extent of glycation is varied. The goal of this study was to identify and conduct a semi-quantitative comparison of the glycation products on HSA that are produced in the presence of various levels of glycation. Methods—Three glycated HSA samples were prepared in vitro by incubating physiological concentrations of HSA with 15 mmol/l glucose for 2 or 5 weeks, or with 30 mmol/l glucose for 4 weeks. These samples were then digested and examined by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify the glycation products that were formed. Results—It was found that the glycation pattern of HSA changed with its overall extent of total glycation. Many modifications including previously-reported primary glycation sites (e.g., K199, K281, and the N-terminus) were consistently found in the tested samples. Lysines 199 and 281, as well as arginine 428, contained the most consistently identified and abundant glycation products. Lysines 93, 276, 286, 414, 439, and 524/525, as well as the N-terminus and arginines 98, 197, and 521, were also found to be modified at various degrees of HSA glycation. Conclusions—The glycation pattern of HSA was found to vary with different levels of total glycation and included modifications at the 2 major drug binding sites on this protein. This result suggests that different modified forms of HSA, both in terms of the total extent of glycation and glycation pattern, may be found at various stages of diabetes. The clinical implication of these results is that the binding of HSA to some drug may be altered at various stages of diabetes as the extent of glycation and types of modifications in this protein are varied

Meta-analysis of published cerebrospinal fluid proteomics data identifies and validates metabolic enzyme panel as Alzheimer's disease biomarkers

To develop therapies for Alzheimer's disease, we need accurate in vivo diagnostics. Multiple proteomic studies mapping biomarker candidates in cerebrospinal fluid (CSF) resulted in little overlap. To overcome this shortcoming, we apply the rarely used concept of proteomics meta-analysis to identify an effective biomarker panel. We combine ten independent datasets for biomarker identification: seven datasets from 150 patients/controls for discovery, one dataset with 20 patients/controls for down-selection, and two datasets with 494 patients/controls for validation. The discovery results in 21 biomarker candidates and down-selection in three, to be validated in the two additional large-scale proteomics datasets with 228 diseased and 266 control samples. This resulting 3-protein biomarker panel differentiates Alzheimer's disease (AD) from controls in the two validation cohorts with areas under the receiver operating characteristic curve (AUROCs) of 0.83 and 0.87, respectively. This study highlights the value of systematically re-analyzing previously published proteomics data and the need for more stringent data deposition

Characterization Of Drug Interactions With Serum Proteins by Using High-Performance Affinity Chromatography

The binding of drugs with serum proteins can affect the activity, distribution, rate of excretion, and toxicity of pharmaceutical agents in the body. One tool that can be used to quickly analyze and characterize these interactions is high-performance affinity chromatography (HPAC). This review shows how HPAC can be used to study drug-protein binding and describes the various applications of this approach when examining drug interactions with serum proteins. Methods for determining binding constants, characterizing binding sites, examining drug-drug interactions, and studying drug-protein dissociation rates will be discussed. Applications that illustrate the use of HPAC with serum binding agents such as human serum albumin, α1-acid glycoprotein, and lipoproteins will be presented. Recent developments will also be examined, such as new methods for immobilizing serum proteins in HPAC columns, the utilization of HPAC as a tool in personalized medicine, and HPAC methods for the high-throughput screening and characterization of drug-protein binding

Characterization Of Drug Interactions With Serum Proteins by Using High-Performance Affinity Chromatography

The binding of drugs with serum proteins can affect the activity, distribution, rate of excretion, and toxicity of pharmaceutical agents in the body. One tool that can be used to quickly analyze and characterize these interactions is high-performance affinity chromatography (HPAC). This review shows how HPAC can be used to study drug-protein binding and describes the various applications of this approach when examining drug interactions with serum proteins. Methods for determining binding constants, characterizing binding sites, examining drug-drug interactions, and studying drug-protein dissociation rates will be discussed. Applications that illustrate the use of HPAC with serum binding agents such as human serum albumin, α1-acid glycoprotein, and lipoproteins will be presented. Recent developments will also be examined, such as new methods for immobilizing serum proteins in HPAC columns, the utilization of HPAC as a tool in personalized medicine, and HPAC methods for the high-throughput screening and characterization of drug-protein binding

COMPARISON OF MODIFICATION SITES FORMED ON HUMAN SERUM ALBUMIN AT VARIOUS STAGES OF GLYCATION

Background—Many of the complications encountered during diabetes can be linked to the nonenzymatic glycation of proteins, including human serum albumin (HSA). However, there is little information regarding how the glycation pattern of HSA changes as the total extent of glycation is varied. The goal of this study was to identify and conduct a semi-quantitative comparison of the glycation products on HSA that are produced in the presence of various levels of glycation. Methods—Three glycated HSA samples were prepared in vitro by incubating physiological concentrations of HSA with 15 mmol/l glucose for 2 or 5 weeks, or with 30 mmol/l glucose for 4 weeks. These samples were then digested and examined by matrix-assisted laser desorption/ ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify the glycation products that were formed. Results—It was found that the glycation pattern of HSA changed with its overall extent of total glycation. Many modifications including previously-reported primary glycation sites (e.g., K199, K281, and the N-terminus) were consistently found in the tested samples. Lysines 199 and 281, as well as arginine 428, contained the most consistently identified and abundant glycation products. Lysines 93, 276, 286, 414, 439, and 524/525, as well as the N-terminus and arginines 98, 197, and 521, were also found to be modified at various degrees of HSA glycation. Conclusions—The glycation pattern of HSA was found to vary with different levels of total glycation and included modifications at the 2 major drug binding sites on this protein. This result suggests that different modified forms of HSA, both in terms of the total extent of glycation and glycation pattern, may be found at various stages of diabetes. The clinical implication of these results is that the binding of HSA to some drug may be altered at various stages of diabetes as the extent of glycation and types of modifications in this protein are varied

Characterization of Glycation Sites on Human Serum Albumin using Mass Spectrometry

The modification of proteins by reducing sugars is a process that occurs naturally in the body. This process, which is known as glycation, has been linked to many of the chronic complications encountered during diabetes. Glycation has also been linked to changes in the binding of human serum albumin (HSA) to several drugs and small solutes in the body. While these effects are known, there is little information that explains why these changes in binding occur. The goal of this project was to obtain qualitative and quantitative information about glycation that occurs on HSA. The first section of this dissertation examined methods that could be used to quantify and identify glycation that occurs on HSA. The extent of glycation that occurred on HSA was quantified using oxygen-18 labeling mass spectrometry and the glycation sites were identified by observing the mass-to-charge (m/z) shifts that occurred in glycated HSA. This initial investigation revealed that oxygen-18 labeling based quantitation can be improved over previous methods if a relative comparison is done with oxygen-18 labeled peptides in a control HSA sample. Similarly, the process of making m/z shift-based assignments could be improved if only the peptides that were unique to the glycated HSA samples were used with internal calibration. These techniques were used in subsequent chapters for the assignment of early and late-stage glycation products on HSA. The regions of HSA that contained the highest amount of modification were identified, quantified, and ranked in order of their relative abundance. Of the commonly reported glycation sites, the N-terminus was found to have the highest extent of modification, followed by lysines 525, 199, and 439. The relative amount of modification on lysine 281, with respect to the aforementioned residues, varied with different degrees of glycation. The oxygen-18 labeling approach used for this analysis was novel because it allowed for the simultaneous quantification of all glycation-related modifications that were occurring on HSA. As such, several arginine residues were also found to have high amounts of modification on glycated HSA

Determination of Free Catecholamines in Urine By Tandem Affinity/Ion-Pair Chromatography and Flow Injection Analysis

Background—A system was developed for the simultaneous measurement in urine of free catecholamines (i.e., dopamine, norepinephrine, epinephrine) and creatinine (i.e., an indicator of urine output and volume). This method was based on the use of tandem affinity/ion-pair HPLC and flow injection analysis. Methods—The free catecholamines were extracted directly from urine by using an on-line phenylboronic acid affinity column. The extracted solutes were then separated and measured by ionpair chromatography followed by amperometric detection. Creatinine was measured by an on-line flow injection analysis system based on the Jaffe reaction, which analyzed creatinine as it eluted nonretained from the phenylboronic acid column. Results—Various factors were considered in the design and optimization of the phenylboronic acid column, the tandem affinity/ion-pair HPLC columns and the flow injection analysis system. The total analysis time for the final combined system was approximately 16 min per injection at 1 ml/min. This method was found to have good agreement with the expected results for control urine samples. The limits of detection for 20 μl samples (S/N = 3.0) were 1.8, 1.0 and 4.3 μg/l for norepinephrine, epinephrine and dopamine, respectively, while the limit of detection of creatinine was 5.0 mg/l. The linear response of this method extended over a 450 to 930-fold range in concentration for the catecholamines and covered the range of clinical interest. The within-day precision of this method was ±2.0−2.7%. Conclusions—The ability of this method to simultaneously monitor both creatinine and other analytes makes this HPLC/FIA system an attractive method for use in monitoring urinary compounds. With this approach it was possible to provide fast results for small volumes of random urine samples that were collected as part of a psychological study. The same method could also be utilized with 12 or 24 h urine specimens

QUANTITATIVE ANALYSIS OF GLYCATION SITES ON HUMAN SERUM ALBUMIN USING 16O/18O-LABELING AND MATRIXASSISTED LASER DESORPTION/IONIZATION TIME-OF-FLIGHT MASS SPECTROMETRY

Background—One of the long term complications of diabetes is the non-enzymatic addition of glucose to proteins in blood, such as human serum albumin (HSA), which leads to the formation of an Amadori product and advanced glycation end products (AGEs). This study uses 16O/18O-labeling and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to provide quantitative data on the extent of modification that occurs in the presence of glucose at various regions in the structure of minimally glycated HSA. Methods—Normal HSA, with no significant levels of glycation, was digested by various proteolytic enzymes in the presence of water, while a similar sample containing in vitro glycated HSA was digested in 18O-enriched water. These samples were then mixed and the 16O/18O ratios were measured for peptides in each digest. The values obtained for the 16O/18O ratios of the detected peptides for the mixed sample were used to determine the degree of modification that occurred in various regions of glycated HSA. Results—Peptides containing arginines 114, 81, or 218 and lysines 413, 432, 159, 212, or 323 were found to have 16O/18O ratios greater than a cut off value of 2.0 (i.e., a cut off value based on results noted when using only normal HSA as a reference). A qualitative comparison of the 16O- and 18Olabeled digests indicated that lysines 525 and 439 also had significant degrees of modification. The modifications that occurred at these sites were variations of fructosyl-lysine and AGEs which included 1-alkyl-2-formyl-3,4-glycoyl-pyrole, and pyrraline. Conclusions—Peptides containing arginine 218 and lysines 212, 413, 432, and 439 contained high levels of modification and are also present near the major drug binding sites on HSA. This result is clinically relevant because it suggests the glycation of HSA may alter its ability to bind various drugs and small solutes in blood