Depletion and fractionation technologies in plasma proteomic analysis

Antibody-Based Affinity Capture Combined with LC-MS Analysis for Identification of COVID-19 Disease Serum Biomarkers

Blood serum or plasma proteins are potentially useful in COVID-19 research as biomarkers for risk prediction, diagnosis, stratification, and treatment monitoring. However, serum protein-based biomarker identification and validation is complicated due to the wide concentration range of these proteins, which spans more than ten orders of magnitude. Here we present a combined affinity purification-liquid chromatography mass spectrometry approach which allows identification and quantitation of the most abundant serum proteins along with the nonspecifically bound and interaction proteins. This led to the reproducible identification of more than 100 proteins that were not specifically targeted by the affinity column. Many of these have already been implicated in COVID-19 disease.

Dominin and Segon Form Multiprotein Particles in the Plasma of Eastern Oysters (Crassostrea virginica) and Are Likely Involved in Shell Formation

Dominin and segon are two proteins purified and characterized from the plasma of eastern oysters Crassostrea virginica, making up about 70% of the total plasma proteins. Their proposed functions are in host defense based on their pathogen binding properties and in metal metabolism based on their metal binding abilities. In the present study, the two proteins were further studied for their native states in circulation and extrapallial fluid and their possible involvement in shell formation. Two-dimensional electrophoresis confirmed that the oyster plasma was dominated by a few major proteins and size exclusion chromatography indicated that these proteins were present in circulation in a morphologically homogenous form. Density gradient ultracentrifugation in Cesium Chloride isolated morphologically homogenous particles of about 25 nm in diameter from the plasma and extrapallial fluids. Polyacrylamide gel electrophoresis identified dominin, segon and an unidentified protein as the principal components of the particles and the three proteins likely formed a multiprotein complex that associated to form the particle. Additionally, three major proteins extracted from shell organic matrix were identified based on the apparent molecular weight in SDS-PAGE to correspond to the three major proteins of plasma and protein particles. Moreover, the hemocyte expression of dominin and segon genes measured by real-time RT-PCR increased significantly upon the initiation of shell repair and were significantly greater in younger oysters. These findings suggest that dominin and segon form protein particles by association with each other and perhaps some other major plasma proteins and play a significant role in oyster shell formation.

Using systems biology approaches to understand cardiac inflammation and extracellular matrix remodeling in the setting of myocardial infarction

Inflammation and extracellular matrix (ECM) remodeling are important components regulating the response of the left ventricle to myocardial infarction (MI). Significant cellular- and molecular-level contributors can be identified by analyzing data acquired through high-throughput genomic and proteomic technologies that provide expression levels for thousands of genes and proteins. Large-scale data provide both temporal and spatial information that need to be analyzed and interpreted using systems biology approaches in order to integrate this information into dynamic models that predict and explain mechanisms of cardiac healing post-MI. In this review, we summarize the systems biology approaches needed to computationally simulate post-MI remodeling, including data acquisition, data analysis for biomarker classification and identification, data integration to build dynamic models, and data interpretation for biological functions. An example for applying a systems biology approach to ECM remodeling is presented as a reference illustration.

Mass spectrometry in cancer biomarker research: a case for immunodepletion of abundant blood-derived proteins from clinical tissue specimens

The discovery of clinically relevant cancer biomarkers using mass spectrometry (MS)-based proteomics has proven difficult, primarily because of the enormous dynamic range of blood-derived protein concentrations and the fact that the 22 most abundant blood-derived proteins constitute approximately 99% of the total plasma protein mass. Immunodepletion of clinical body fluid specimens (e.g., serum/plasma) for the removal of highly abundant proteins is a reasonable and reproducible solution. Often overlooked, clinical tissue specimens also contain a formidable amount of highly abundant blood-derived proteins present in tissue-embedded networks of blood/lymph capillaries and interstitial fluid. Hence, the dynamic range impediment to biomarker discovery remains a formidable obstacle, regardless of clinical sample type (solid tissue and/or body fluid). Thus, we optimized and applied simultaneous immunodepletion of blood-derived proteins from solid tissue and peripheral blood, using clear cell renal cell carcinoma as a model disease. Integrative analysis of data from this approach and genomic data obtained from the same type of tumor revealed concordant key pathways and protein targets germane to clear cell renal cell carcinoma. This includes the activation of the lipogenic pathway characterized by increased expression of adipophilin (PLIN2) along with 'cadherin switching', a phenomenon indicative of transcriptional reprogramming linked to renal epithelial dedifferentiation. We also applied immunodepletion of abundant blood-derived proteins to various tissue types (e.g., adipose tissue and breast tissue) showing unambiguously that the removal of abundant blood-derived proteins represents a powerful tool for the reproducible profiling of tissue proteomes. Herein, we show that the removal of abundant blood-derived proteins from solid tissue specimens is of equal importance to depletion of body fluids and recommend its routine use in the context of biological discovery and/or cancer biomarker research. Finally, this perspective presents the background, rationale and strategy for using tissue-directed high-resolution/accuracy MS-based shotgun proteomics to detect genuine tumor proteins in the peripheral blood of a patient diagnosed with nonmetastatic cancer, employing concurrent liquid chromatography-MS analysis of immunodepleted clinical tissue and blood specimens.

Solid-phase fractionation strategies applied to proteomics investigations

Methods for protein fractionation in the proteomics investigation field are relatively numerous. They apply to the prefractionation of the sample to obtain less complex protein mixtures for an easier analysis; they are also used as a means to evidence specific proteins or protein classes otherwise impossible to detect. They involve depletion of high-abundance proteins suppressing the signal of dilute species; they are also capable to enhance the detectability of low-abundance species while concomitantly decreasing the concentration of abundant proteins such as albumin in serum and hemoglobin in red blood cell lysates. Fractionation of proteomes is also used for the isolation of targeted species that are selected for their different expression under certain pathological conditions and that are detected by mass spectrometry. Two unconventional methods of large interest in proteomics due to the low level of protein redundancy between fractions are also reported.All these methods are reviewed and detailed method given to allow specialists of proteomics investigation to access selected separation methods generally dispersed on different technical reviews or books.

Using extracellular matrix proteomics to understand left ventricular remodeling

Survival following myocardial infarction (MI) has improved substantially over the last 40 years; however, the incidence of subsequent congestive heart failure has dramatically increased as a consequence. Discovering plasma markers that signify adverse cardiac remodeling may allow high-risk patients to be recognized earlier and may provide an improved way to assess treatment efficacy. Alterations in extracellular matrix (ECM) regulate cardiac remodeling following MI and potentially provide a large array of candidate indicators.

The field of cardiac proteomics has progressed rapidly over the past 20 years, since publication of the first two-dimensional electrophoretic gels of left ventricle proteins. Proteomic approaches are now routinely utilized to better understand how the left ventricle responds to injury.

In this review, we will discuss how methods have developed to allow comprehensive evaluation of the ECM proteome. We will explain how ECM proteomic data can be used to predict adverse remodeling for an individual patient and highlight future directions. Although this review will focus on the use of ECM proteomics to better understand post-MI remodeling responses, these approaches have applicability to a wide-range of cardiac pathologies, including pressure overload hypertrophy, viral myocarditis, and non-ischemic heart failure.

Differential Human Plasma Proteomics Based on AniBal Quantification and Peptide-level Off-Gel Isoelectric Focussing

Despite its enormous complexity, human plasma is still one of the most frequently used body fluids for identification and quantification of health and disease biomarkers. We have developed a new workflow for qualitative and quantitative analysis of human plasma proteins. The first step was to remove the seven most abundant plasma proteins (MARS). Moreover, in order to reduce the complexity of the sample and to increase protein and proteome coverage, Off-Gel fractionation was performed at peptide level. Our own stable isotope-based quantitative proteomics approach termed AniBAL was chosen for relative quantification of proteins between conditions. The method was developed with commercial human plasma and resulted in the identification of 85 proteins, of which 68 revealed quantitative information (Mascot database search combined with Peptide-/ProteinProphet validation). The combined methods consisting of MARS, AniBAL, Off-Gel and nano-LC-MS/MS on a Bruker HCT ion trap represent a new and efficient platform to quantify human plasma proteome differences between conditions. The method was also found technically compatible to a pair of human plasma pilot samples from the European FP6 project “DiOGenes”. Many of the identifiable/quantifiable proteins are relevant to obesity, diabetes and inflammation, which form the context of investigation within “DiOGenes”.

Isobaric labeling and tandem mass spectrometry: a novel approach for profiling and quantifying proteins differentially expressed in amniotic fluid in preterm labor with and without intra-amniotic infection/inflammation

OBJECTIVE

Examination of the amniotic fluid (AF) proteome has been previously attempted to identify useful biomarkers in predicting the outcome of preterm labor (PTL). Isobaric Tag for Relative and Absolute Quantitation (iTRAQ) labeling allows direct ratiometric comparison of relative abundance of identified protein species among multiplexed samples. The purpose of this study was to apply, for the first time, the combination of iTRAQ and tandem mass spectrometry to identify proteins differentially regulated in AF samples of women with spontaneous PTL and intact membranes with and without intra-amniotic infection/inflammation (IAI).

METHODS

A cross-sectional study was designed and included AF samples from patients with spontaneous PTL and intact membranes in the following groups: (1) patients without IAI who delivered at term (n = 26); (2) patients who delivered preterm without IAI (n = 25); and (3) patients with IAI (n = 24). Proteomic profiling of AF samples was performed using a workflow involving tryptic digestion, iTRAQ labeling and multiplexing, strong cation exchange fractionation, and liquid chromatography tandem mass spectrometry. Twenty-five separate 4-plex samples were prepared and analyzed.

RESULTS

Collectively, 123,011 MS(2) spectra were analyzed, and over 25,000 peptides were analyzed by database search (X!Tandem and Mascot), resulting in the identification of 309 unique high-confidence proteins. Analysis of differentially present iTRAQ reporter peaks revealed many proteins that have been previously reported to be associated with preterm delivery with IAI. Importantly, many novel proteins were found to be up-regulated in the AF of patients with PTL and IAI including leukocyte elastase precursor, Thymosin-like 3, and 14-3-3 protein isoforms. Moreover, we observed differential expression of proteins in AF of patients who delivered preterm in the absence of IAI in comparison with those with PTL who delivered at term including Mimecan precursor, latent-transforming growth factor beta-binding protein isoform 1L precursor, and Resistin. These findings have been confirmed for Resistin in an independent cohort of samples using ELISA. Gene ontology enrichment analysis was employed to reveal families of proteins participating in distinct biological processes. We identified enrichment for host defense, anti-apoptosis, metabolism/catabolism and cell and protein mobility, localization and targeting.

CONCLUSIONS

(1) Proteomics with iTRAQ labeling is a profiling tool capable of revealing differential expression of proteins in AF; (2) We discovered 82 proteins differentially expressed in three clinical subgroups of premature labor, 67 which were heretofore unknown. Of particular importance is the identification of proteins differentially expressed in AF from women who delivered preterm in the absence of IAI. This is the first report of the positive identification of biomarkers in this subgroup of patients.

Comparison of three methods for fractionation and enrichment of low molecular weight proteins for SELDI-TOF-MS differential analysis

In most diseases, the clinical need for serum/plasma markers has never been so crucial, not only for diagnosis, but also for the selection of the most efficient therapies, as well as exclusion of ineffective or toxic treatment. Due to the high sample complexity, prefractionation is essential for exploring the deep proteome and finding specific markers. In this study, three different sample preparation methods (i.e., highly abundant protein precipitation, restricted access materials (RAM) combined with IMAC chromatography and peptide ligand affinity beads) were investigated in order to select the best fractionation step for further differential proteomic experiments focusing on the LMW proteome (MW inferior to 40,000 Da). Indeed, the aim was not to cover the entire plasma/serum proteome, but to enrich potentially interesting tissue leakage proteins. These three methods were evaluated on their reproducibility, on the SELDI-TOF-MS peptide/protein peaks generated after fractionation and on the information supplied. The studied methods appeared to give complementary information and presented good reproducibility (below 20%). Peptide ligand affinity beads were found to provide efficient depletion of HMW proteins and peak enrichment in protein/peptide profiles.

Depletion of highly abundant proteins in blood plasma by hydrophobic interaction chromatography for proteomic analysis

The proteomic analysis of plasma is extremely complex due to the presence of few highly abundant proteins. These proteins have to be depleted in order to detect low abundance proteins, which are likely to be of biomedical interest. In this work it was investigated the applicability of hydrophobic interaction chromatography (HIC) as a plasma fractionation method prior to two-dimensional gel electrophoresis (2DGE). The average hydrophobicity of the 56 main plasma proteins was calculated. Plasma proteins were classified as low, medium and highly hydrophobic through a cluster analysis. The highly abundant proteins showed a medium hydrophobicity, and therefore a HIC step was designed to deplete them from plasma. HIC performance was assessed by 2DGE, and it was compared to that obtained by a commercial immuno-affinity (IA) column for albumin depletion. Both methods showed similar reproducibility. HIC allowed partially depleting alpha-1-antitrypsin and albumin, and permitted to detect twice the number of spots than IA. Since albumin depletion by HIC was incomplete, it should be further optimized for its use as a complementary or alternative method to IA.

Challenges for biomarker discovery in body fluids using SELDI-TOF-MS

Protein profiling using SELDI-TOF-MS has gained over the past few years an increasing interest in the field of biomarker discovery. The technology presents great potential if some parameters, such as sample handling, SELDI settings, and data analysis, are strictly controlled. Practical considerations to set up a robust and sensitive strategy for biomarker discovery are presented. This paper also reviews biological fluids generally available including a description of their peculiar properties and the preanalytical challenges inherent to sample collection and storage. Finally, some new insights for biomarker identification and validation challenges are provided.

Effect of separation dimensions on resolution and throughput using very narrow-range IEF for 2-DE after solution phase isoelectric fractionation of a complex proteome

This paper describes how the lengths of the first and second dimensions in narrow pH-range 2-DE affect the number of detected protein spots, by analysis of human breast carcinoma cell line lysates prefractionated by solution phase IEF. The aim is to maximize throughput while minimizing experimental costs. In this study, systematic evaluation of narrow-range IPG strip lengths showed that separation distances were very important, with dramatic increases in resolution when longer gels were used. Compared with 7 cm minigels, maximal resolution was obtained using 18 and 24 cm IPG strips. Systematic evaluation of SDS-PAGE gel length showed a far weaker influence of separation length on resolution in the second dimension compared with that observed for the IEF dimension. There was little benefit in using separation distances greater than 12-15 cm, at least with currently available electrophoresis units. The work shows that regions of the IPG strip not containing any proteins can be excised to fit a smaller gel if prefractionation using IEF in solution has been performed. As expected, larger 2-DE gel volumes resulting from the use of longer IPG strips and second dimension gels decreased detection sensitivity when equal protein loads were used. However, this effect could be readily eliminated by increasing the loads applied to IPG strips.

The application of proteomics technology to thrombosis research: the identification of potential therapeutic targets in cardiovascular disease

Thrombus formation underpins the development of cardiovascular diseases, including acute coronary syndromes and ischaemic stroke. A number of well-characterised cardiovascular risk factors which contribute to the development of the majority of cardiovascular events have been identified, including dyslipidaemia, hypertension and diabetes. Individuals with type 2 diabetes mellitus (T2DM) have a 3- to 5-fold increased risk for development of cardiovascular disease (CVD). They may have a cluster of haemostatic abnormalities, including elevated levels of plasminogen activator inhibitor-1 (PAI-1) and fibrinogen, which contribute to acute thrombotic events. It is clear that additional unidentified risk factors contribute to the pathogenesis of cardiovascular events, and so the search for novel biomarkers and effectors, particularly in individuals with T2DM, remains a major challenge of cardiovascular medicine. Plasma and cellular proteins which contribute to thrombus formation have the potential to confer a pro-thrombotic state and represent a link between genotype, environment and disease phenotype. The comprehensive analysis of these proteins is now increasingly facilitated through the continued development of proteomic technologies which provide multifaceted approaches to the identification of novel biomarkers and/or effectors of thrombus formation and on which future anticoagulant and thrombolytic therapies may be based. This review provides an overview of current proteomic technologies. It focuses on the recent studies in which these technologies have been applied in the search for novel proteins that may confer increased risk of acute cardiovascular diseases and therefore that may influence disease progression and therapy.

Lost in translation: five grand challenges for proteomic biomarker discovery

The biomedical community has the imperative to develop reliable, clinically relevant and generalizable bioassays that can be used to accurately recognize those individuals with early-stage disease or those patients who will respond to therapy, with the ultimate aim of achieving individualized medicine. In recent years, increasingly sophisticated proteomic screening technologies have been introduced, providing the biomedical community with a valuable new approach for the systematic discovery and validation of novel diagnostic, prognostic and therapeutic tools. Nevertheless, the complexity of the cellular milieu wherein a variety of macromolecules interact in dynamic fashion, combined with the complex clinical manifestation of chronic pathologies and widespread diversity of patient populations, mean that universal biomarkers will not be easily developed. In this review, the five key challenges that must be surmounted in order to advance the clinical impact of this nascent field are described, and plausible solutions based on the authors' own ongoing proteomic profiling of cardiovascular disease is outlined.

Proteomic analysis of human plasma proteins by two-dimensional gel electrophoresis and by antibody arrays following depletion of high-abundance proteins

Detecting proteins that are present at lower levels in human plasma, for the identification of potential disease biomarkers, is complicated by a few highly abundant proteins. One promising strategy is the removal of these abundant proteins interfering with the analysis of plasma content by proteomic techniques. This study compared three affinity-based methods to remove the most abundant proteins in human plasma. Two of them, based on antibodies, which depletes the six or the 12 most abundant proteins, demonstrated the highest efficiency in enriching less abundant plasma proteins. Comparison of two anticoagulant treatments for plasma preparation, EDTA and CTAD, showed that this treatment influenced the patterns of lower-abundance proteins visible on 2-dimensional (2-D) gels. Several staining procedures including two fluorescent dyes, Sypro Ruby and Deep Purple, were also compared with a very sensitive silver staining method for the visualization of lower-abundance proteins on 2-D gels. Furthermore, treatments of lower-abundance plasma proteins with hydroxyethyl disulfide enhanced protein sharpness and resolution. The purpose of all these systematic comparisons was to select the most reliable methods in different steps of plasma preparation and handling as well as in analysis of proteins by 2-D gels to obtain highly reproducible patterns of lower-abundance plasma proteins. Importantly, the lower-abundance plasma proteins enriched by these optimized conditions were further analyzed by antibody microarrays allowing the identification of 61 proteins using 350 antibodies directed against signalling proteins suggesting that this proteomic strategy is a valuable approach for detecting potential plasma biomarkers.

Functional identification of novel activities: Activity-based selection of proteins from complete proteomes

The identification of proteins with desired activities, especially from complex samples such as plasma and whole blood, is a continual challenge. We have developed a technology platform called Functional Identification of Novel Activities (FIoNA) to discover desired protein activities from complex biological samples. FIoNA uses immobilized libraries of combinatorial peptide ligands to purify and concentrate essentially all of the components of a complex mixture on ligands synthesized on individual beads. No depletion or prefractionation of the starting material is performed before it is incubated with the library, and no a priori knowledge of the active protein or of the ligand to which it binds is required. Instead, the protein-loaded beads are individually evaluated en masse in disease- relevant assays to identify proteins possessing a desired function. Beads associated with the activity are selected, and the ligand is sequenced and resynthesized in bulk on the original backbone for purification and characterization of the active component. Here we illustrate the use of FIoNA in a cell proliferation assay to detect a growth factor present in conditioned cell medium at nanogram/milliliter concentrations. We also have selected beads associated with hydrolysis of nerve agent analogs in assays performed in 100,000-well microtiter plates.

Human blood plasma preparation for two-dimensional gel electrophoresis

Human plasma consists of mainly large proteins, which vary in terms of both composition and concentration with the physiological state of the individual. Alterations in protein concentrations reflect the current state of the individual's health and thus may be utilized as valuable biomarkers for a specific biological process or disease. Two-dimensional gel electrophoresis (2-DE) has proven to be a valuable method for the separation and comparison of complex protein mixtures, for example, from disease and healthy states, as this method provides information regarding the variation, relative quantities, and structures of the intact proteins. The procedures utilized for the preparation of samples for 2-DE are critical to the acquisition of high-quality results for the discovery of biomarkers. The objective of this study was to review the preparation methods of plasma for 2-DE, particularly those designed to improve the detection of proteins in low abundance in plasma on 2-DE. The use of anticoagulants and protease inhibitors during the collection of blood, the removal of abundant proteins using multicomponent immunodepletion system, and desalting procedure allow us to compile profiles of proteins occurring in low concentrations in the plasma and to improve the pattern generated during 2-DE.

Proteome-based plasma biomarkers for Alzheimer's disease

Alzheimer's disease is a common and devastating disease for which there is no readily available biomarker to aid diagnosis or to monitor disease progression. Biomarkers have been sought in CSF but no previous study has used two-dimensional gel electrophoresis coupled with mass spectrometry to seek biomarkers in peripheral tissue. We performed a case-control study of plasma using this proteomics approach to identify proteins that differ in the disease state relative to aged controls. For discovery-phase proteomics analysis, 50 people with Alzheimer's dementia were recruited through secondary services and 50 normal elderly controls through primary care. For validation purposes a total of 511 subjects with Alzheimer's disease and other neurodegenerative diseases and normal elderly controls were examined. Image analysis of the protein distribution of the gels alone identifies disease cases with 56% sensitivity and 80% specificity. Mass spectrometric analysis of the changes observed in two-dimensional electrophoresis identified a number of proteins previously implicated in the disease pathology, including complement factor H (CFH) precursor and alpha-2-macroglobulin (alpha-2M). Using semi-quantitative immunoblotting, the elevation of CFH and alpha-2M was shown to be specific for Alzheimer's disease and to correlate with disease severity although alternative assays would be necessary to improve sensitivity and specificity. These findings suggest that blood may be a rich source for biomarkers of Alzheimer's disease and that CFH, together with other proteins such as alpha-2M may be a specific markers of this illness.

Substrate specificity of soluble and membrane-associated ADP-ribosyltransferase ART2.1

ADP-ribosyltransferases (ARTs) are a family of enzymes that catalyze the covalent transfer of an ADP-ribose moiety, derived from NAD, to an amino acid of an acceptor protein, thereby altering its function. To date, little information is available on the protein target specificity of different ART family members. ART2 is a T-cell-specific transferase, attached to the cell surface by a glycosylphosphatidylinositol (GPI) anchor, and also found in serum. Here we investigated the role of ART2 localization in serum or on the cell surface, or solubilized with detergents or enzymes, on its target protein specificity. We found that detergent solubilization of cell membranes, or release of ART2 by phosphoinositide-specific phospholipase C treatment, altered the ability of ART2 to ADP-ribosylate high or low molecular weight histone proteins. Similarly, soluble recombinant ART2 (lacking the GPI anchor) showed a different histone specificity than did cell-bound ART2. When soluble ART2 was incubated with serum proteins in the presence of [32P]-labeled NAD, several serum proteins were ADP-ribosylated in a thiol-specific manner. Mass spectrometry of labeled proteins identified albumin and transferrin as ADP-ribosylated proteins in serum. Collectively, these studies reveal that the membrane or solution environment of ART2 plays a pivotal role in determining its substrate specificity.

Rarity gives a charm: evaluation of trace proteins in plasma and serum

Since plasma potentially contacts every cell as it circulates through the body, it may carry clues both to diagnosis and treatment of disease. It is commonly expected that the growing ability to detect and characterize trace proteins will result in discovery of novel therapeutics and biomarkers; however, the familiar, super-abundant plasma proteins remain a fundamental stumbling block. Furthermore, robust validation of proteomic data is a sometimes overlooked but always necessary component for the eventual development of clinical reagents. This review surveys some of the uses of typical and atypical low-abundance proteins, current analytical methods, existing impediments to discovery, and some innovations that are overcoming the challenges to evaluation of trace proteins in plasma and serum.