Characterization of effective, simple, and low-cost precipitation methods for depleting abundant plasma proteins to enhance the depth and breadth of plasma proteomics.

Plasma is an abundant source of proteins and potential biomarkers to aid in the detection, diagnosis, and prognosis of human diseases. These proteins are often present at low levels in the blood and difficult to identify and measure due to the large dynamic range of proteins. The goal of this work was to characterize and compare various protein precipitation methods related to how they affect the depth and breadth of plasma proteomic studies. Abundant protein precipitation with perchloric acid (PerCA) can increase protein identifications and depth of plasma proteomic studies. Three acid- and four solvent-based precipitation methods were evaluated. All methods tested provided excellent plasma proteomic coverage (>600 identified protein groups) and detected protein in the low pg/mL range. Functional enrichment analysis revealed subtle differences within and larger changes between the precipitant groups. Methanol-based precipitation outperformed the other methods based on identifications and reproducibility. The methods' performance was verified using eight lung cancer patient samples, where >700 protein groups were measured and proteins with an estimated plasma concentration of ∼10 pg/mL were detected. Various protein precipitation agents are amenable to extending the depth and breadth of plasma proteomes. These data can guide investigators to implement inexpensive, high-throughput methods for their plasma proteomic workflows.

The contested market of plasma.

Voluntary, anonymous free gift-giving has become the dominant norm for blood donation for transfusion purposes, in view of its established ability to satisfy the needs for labile blood products that meet satisfactory conditions of safety and cost. But the economy of blood products is also the place for one of the main exceptions to the principle of non-commercialization of body parts. I show that there exists a genuine international plasma market, which provides the raw materials to produce blood protein products by pharmaceutical industries. The recent years have seen a considerable strengthening of the massive and globalized features of this market. I briefly describe the issues that this evolution raises, and I sketch some directions for a partial resolution of these issues. I explain why the development of contract fractionation appears both possible and desirable from an economic perspective in the present context.

Systematic evaluation of species-independent serum pre-fractionation strategies revealed cost-effective methods to reduce proteome complexity.

In this study, the efficiency of one commercial (ProteoMiner™ -PM) and five simple and cost-effective laboratory chemicals (Acetone, TCA/acetone, DTT, ACN and DTT-ACN) based serum protein pre-fractionation strategies was compared in pig model by label-free quantitation based mass spectrometric approach to find out the most suitable strategy for reducing the complexity of serum proteome for subsequent proteomic studies. The highest serum protein depletion percentage and highest depletion of albumin, the most abundant serum protein, was observed in DTT-ACN method. The maximum number of serum proteins was identified in ACN followed by DTT-ACN method and importantly, detection of more number of low-abundant proteins (LAPs) could also be achieved by these two methods. Although PM method resulted into lowest dynamic range of protein abundance, quite a less number of proteins were identified by this method. Overall, sequential depletion using DTT-ACN and ACN methods provided advantage of simultaneous detection of more number of proteins along with LAPs with a reasonably high dynamic range of protein abundances over other methods and thus emerged as cheaper and effective alternatives to the commercial methods. Further, these methods are species-independent and hence can be applied in human and in any livestock species to simplify the serum proteome.

Assessment of glutathione/glutathione disulphide ratio and S-glutathionylated proteins in human blood, solid tissues, and cultured cells.

Glutathione (GSH) is the major non-protein thiol in humans and other mammals, which is present in millimolar concentrations within cells, but at much lower concentrations in the blood plasma. GSH and GSH-related enzymes act both to prevent oxidative damage and to detoxify electrophiles. Under oxidative stress, two GSH molecules become linked by a disulphide bridge to form glutathione disulphide (GSSG). Therefore, assessment of the GSH/GSSG ratio may provide an estimation of cellular redox metabolism. Current evidence resulting from studies in human blood, solid tissues, and cultured cells suggests that GSH also plays a prominent role in protein redox regulation via S -glutathionylation, i.e., the conjugation of GSH to reactive protein cysteine residues. A number of methodologies that enable quantitative analysis of GSH/GSSG ratio and S-glutathionylated proteins (PSSG), as well as identification and visualization of PSSG in tissue sections or cultured cells are currently available. Here, we have considered the main methodologies applied for GSH, GSSG and PSSG detection in biological samples. This review paper provides an up-to-date critical overview of the application of the most relevant analytical, morphological, and proteomics approaches to detect and analyse GSH, GSSG and PSSG in mammalian samples as well as discusses their current limitations.

Deproteinization assessment using isotopically enriched compounds to trace the coprecipitation of low-molecular-weight selenium species with proteins.

Studies have shown that information related to the presence of low-molecular-weight metabolites is frequently lost after deproteinization of complex matrices, such as blood and plasma, during sample preparation. Therefore, the effect of several deproteinization reagents on low-molecular-weight selenium species has been compared by species-specific isotope labeling. Two isotopically enriched selenium tracers were used to mimic models of small inorganic anionic (77Se-selenite) and organic zwitterionic (76Se-selenomethionine) species. The results presented here show that the use of a methanol-acetonitrile-acetone (1:1:1 v/v/v) mixture provided approximately two times less tracer loss from plasma samples in comparison with the classic procedure using acetonitrile, which may not be optimal as it leads to important losses of low-molecular-weight selenium species. In addition, the possible interactions between selenium tracers and proteins were investigated, revealing that both coprecipitation phenomena and association with proteins were potentially responsible for selenite tracer losses during protein precipitation in blood samples. However, coprecipitation phenomena were found to be fully responsible for losses of both tracers observed in plasma samples and of the selenomethionine tracer in blood samples. This successfully applied strategy is anticipated to be useful for more extensive future studies in selenometabolomics.

The dynamics of contract plasma fractionation.

Plasma Derived Medicinal Products (PMDPs) are an essential component of the modern therapeutic armamentarium. They are differentiated from most other medicines in several ways, particularly the unique nature of the raw material used for their manufacture. Human plasma has been fractionated to PDMPs for the past 75 years, and the economics of manufacturing requires currently that as many products are harvested from each litre as is feasible and reflective of clinical needs. PDMPs may be purchased on the open market from the various commercial and not-for-profit (NFP) manufacturers. They may also be manufactured under contract (CM) from plasma supplied by government and similar agencies as a product of blood transfusion services. Clients for CM aspire to make full use of donated plasma, hence maximizing the donors' gift after the standard components of transfusion have been harvested. Many such countries also aspire to making their national clinical needs self-sufficient in PDMPs, attempting to acquire strategic independence from the vagaries of the commercial open market. The increasing commercial imperatives operating in the PMDP sector generate a tension with such ethical aspirations which are not easily resolved. In particular, the need to harvest as many proteins as possible may generate products which are surplus to national needs, necessitating an ethical paradigm for the optimal provision of such products. In addition, traditional relationships between blood services and domestic fractionation agencies may come under stress as a result of the competitive processes underpinning such transactions, which are now subject to international norms of free trade. Blood services engaged in the supply of hospital transfusion components are detached from the pharmaceutical Good Manufacturing Practices (GMP) culture needed for the production of plasma for CM, while the generation of such plasma through extraction from whole blood donations deflects the focus from that of a dedicated raw material for CM to a byproduct of the donation process. We review the field of CM, assess the current tensions within the sector, and offer suggestions for the strategic positioning of governments and other clients to ensure optimal outcomes for all the stakeholders involved.

[Blood components: Are they drugs or special medicines?]. / Les produits sanguins thérapeutiques : des médicaments ou des produits de santé à part ?

Blood transfusion and plasma derived-drugs significantly differ from other medicines in that their availability strictly depends on blood and plasma collected from healthy donors. Blood collection must comply with a double objective: to maintain donor heath safety, and to avoid any transmitted infections in recipients. This raises several ethical concerns that appear to be different from usual ethical and deontological issues linked to other pharmaceutical and industrial processes. The main concern is the non-commercialization of the human body. Words and concept are of major importance in this context. This short review aims at presenting the main issues relevant to those questions with respect to the various stakeholders.

Quantitative In Vitro Assessment of Liposome Stability and Drug Transfer Employing Asymmetrical Flow Field-Flow Fractionation (AF4).

PURPOSE: In the present study we introduce an efficient approach for a size-based separation of liposomes from plasma proteins employing AF4. We investigated vesicle stability and release behavior of the strongly lipophilic drug temoporfin from liposomes in human plasma for various incubation times at 37°C. METHODS: We used the radioactive tracer cholesteryl oleyl ether (COE) or dipalmitoyl-phosphocholine (DPPC) as lipid markers and (14)C-labeled temoporfin. First, both lipid labels were examined for their suitability as liposome markers. Furthermore, the influence of plasma origin on liposome stability and drug transfer was investigated. The effect of membrane fluidity and PEGylation on vesicle stability and drug release characteristics was also analyzed. RESULTS: Surprisingly, we observed an enzymatic transfer of (3)H-COE to lipoproteins due to the cholesterol ester transfer protein (CETP) in human plasma in dependence on membrane rigidity and were able to inhibit this transfer by plasma preincubation with the CETP inhibitor torcetrapib. This effect was not seen when liposomes were incubated in rat plasma. DPPC labels suffered from hydrolysis effects during preparation and/or storage. Fluid liposomes were less stable in human plasma than their PEGylated analogues or a rigid formulation. In contrast, the transfer of the incorporated drug to lipoproteins was higher for the rigid formulations. CONCLUSIONS: The observed effects render COE-labels questionable for in vivo studies using CEPT-rich species. Here, choline labelled (14)C-DPPC was found to be the most promising alternative. Bilayer composition has a high influence on stability and drug release of a liposomal formulation in human plasma.

"Go no Go" in plasma fractionation in the world's emerging economies: still a question asked 70 years after the COHN process was developed!

In the late 1980s, following the human immunodeficiency virus (HIV) epidemic and transfusion-transmitted infections from plasma-derived coagulation factor concentrates to hemophiliacs, many "advanced thinkers" claimed that plasma-derived products would be completely replaced by the year 2000 by safe recombinant products in most developed countries. However, things have not turned out that way, due to both the continual progress witnessed in plasma fractionation and viral-reduction technologies and technical difficulties still being encountered in developing more cost-effective non-immunogenic, fully active recombinant therapeutic proteins. Accordingly, plasma fractionation remains a reasonably healthy industry worldwide, with an ever-increasing volume of plasma fractionated each year to meet the demands for safe and effective plasma-derived medicines at the global level. While high-income countries currently have generally good access to a panel of plasma-derived and recombinant products, desperate shortages of fractionated plasma products remain in developing economies,and patients still have to be treated inadequately. The steady development of the collection of whole blood in developing economies, to gradually cover the recognized needs for red blood cell concentrates, generates an increasing volume of recovered plasma that is currently wasted. Incentives are therefore high for those countries to consider fractionating such plasma as a means of enhancing their supply of products to treat patients, thereby also decreasing the level of dependence on imported products. Challenges of local plasma fractionation in developing economies are high, in a context where the technological and regulatory sophistication of the plasma fractionation industry is often underestimated, and the blood supply may be exposed to emerging infectious agents. In parallel, plasma product quality requirements and drivers are evolving in developed economies as is the awareness of clinicians to newer uses of products such as intravenous immunoglobulins, somewhat deviating from what currently remain the basic needs of developing countries in terms of affordable safe plasma products. Global market trends for plasma-derived products, through plasma fractionation, are still increasing, despite increasing use of recombinant products, and attention is being focused on the five Ws of the fractionation field: which products; where; when; what and how much; and who will be the main suppliers?

Assessment of reproducibility in depletion and enrichment workflows for plasma proteomics using label-free quantitative data-independent LC-MS.

Quantitation in plasma-based proteomics necessitates the reproducible removal of highly abundant proteins to enable the less abundant proteins to be visible to the mass spectrometer. We have evaluated immunodepletion (proteoprep20) and enrichment (Bio-Rad beads), as the current predominant approaches. Label-free analysis offers an opportunity to estimate the effectiveness of this approach without incorporating chemical labels. Human plasma samples were used to quantitatively assess the reproducibility of these two methods using nano-LC-data-independent acquisition MS. We have selected 18 candidate proteins and a comparison of both methodologies showed that both of the methods were reproducible and fell below 20% residual SD. With the same candidate proteins, individual inter-day variability for the samples was also processed, allowing us to monitor instrument reproducibility. Overall, a total of 131 proteins were identified by both methods with 272 proteins identified by enrichment and 200 identified by immunodepletion. Reproducibility of measurements of the amount of protein in the processed sample for individual proteins is within analytically acceptable standards for both methodologies. This enables both methods to be used for biomarker studies. However, when sample is limited, enrichment is not suitable as larger volumes (>1.0 mL) are required. In experiments where sample is not limited then a greater number of proteins can be reliably identified using enrichment.

Development of chromatofocusing techniques employing mixed-mode column packings for protein separations.

Recent studies reported in the literature using mixed-mode chromatography (MMC) column packings have shown that multiple modes of interactions between the column packing and proteins can be usefully exploited to yield excellent resolution as well as salt-tolerant adsorption of the target protein. In this study, a mixed-mode separation method using commercially available column packings was explored which combines the techniques of hydrophobic-interaction chromatography and chromatofocusing. Two different column packings, one based on mercapto-ethyl-pyridine (MEP) and the other based on hexylamine (HEA) were investigated with regard to their ability to separate proteins when using internally generated, retained pH gradients. The effects of added salt and urea on the behavior of the retained pH gradient and the protein separation achieved when using MMC column packings for chromatofocusing were also investigated. Numerical simulations using methods developed in previous work were shown to agree with experimental results when using reasonable physical parameters. These numerical simulations were also shown to be a useful qualitative method to select the compositions of the starting and elution buffers in order to achieve desired shapes for the pH and ionic strength gradients. The use of the method to fractionate blood serum was explored as a prototype example application.

Developing a strong anion exchange/RP (SAX/RP) 2D LC system for high-abundance proteins depletion in human plasma.

Human plasma is dominated by high-abundance proteins which severely impede the detection of low-abundance proteins. Unfortunately, now there is no efficient method for large-scale depletion of high-abundance proteins in human plasma. In this study, we developed a new strategy, strong anion exchange (SAX)/RP 2D LC system, which has potential for large-scale depletion of high-abundance proteins in human plasma. Separation gradients of the system were optimized to ensure an extensive separation of plasma proteins. Plasma was fractionated into 67 fractions by SAX. All these fractions were subjected a thorough separation by the 2D RPLC and 66 peaks with high UV absorption (>20 mAU) at 215 nm were collected. Proteins in these peaks were identified by LC-MS/MS analysis. Results showed that 83 proteins could be identified in these peaks, 68 among them were reported to be high- or middle-abundance proteins in plasma. All these proteins had definite retention times and were mapped in the 2D SAX-RP system, which resulted in accurate depletion of high-abundance proteins with ease. Our studies provide a convenient and effective method for large-scale depletion of high-abundance proteins and in-depth research in human plasma proteomics.

An assessment of peptide enrichment methods employing mTRAQ quantification approaches.

The human plasma peptidome has potential in biomarker discovery not least because the plasma proteome is a challenging matrix due to its complexity and dynamic range. However, methods to significantly reduce the amount of protein present in plasma while retaining the less abundant peptides present in plasma samples has been a major issue. Here, we present a novel strategy which has been employed to assess the effectiveness of removing interfering proteins while retaining peptides of interest. To monitor peptide retention, a spiked in digested protein, in this case a synthetic QconCAT protein, was employed. This enabled a variety of target analytes (peptides) to be monitored for their retention in liquid phase, providing a broader picture of peptide loss from each method assessed. The incorporation of mTRAQ labeling allowed the presence of each peptide to be monitored, and accurate peptide losses to be determined in a Selected Reaction Monitoring (SRM) assay, thus, enabling an objective semiquantitative conclusion to be drawn regarding the suitability of each method for protein removal and peptide retention. We also assessed a range of methods for retaining nontryptic peptides in a plasma peptidomics workflow. From these data, we determined an optimal workflow for removing intact protein, while retaining peptides for MS-based analyses.

Assessment of protein entrapment in hydroxyapatite scaffolds by size exclusion chromatography.

Although it is well known that the textural properties of scaffolds play an important role in the process of tissue regeneration, the investigation of such effects remain difficult especially at the micro/nano level. Texture confers the material the additional ability to entrap/concentrate molecules circulating in the body fluid regardless of their binding affinity to the material. The goal of the present work is to isolate protein entrapment from protein adsorption phenomena in two macroporous hydroxyapatite scaffolds with identical chemical structure, similar macroporosity but different micro/nanoporosity using proteins of different sizes. This was achieved implementing size exclusion chromatography and using the scaffolds as chromatographic columns. The results showed that the larger the crystal size and the lower the packing density of the crystals composing the scaffold increased protein retention but decreased the protein dwelling time in the column. Differences in the amount of protein retained depended on the protein type.

A simple method for large-scale purification of plasma-derived apo-transferrin.

We investigated and optimized a purification process, suitable for industrial scale, to obtain pharmaceutical grade apo-Tf (apo-transferrin), preserving its physiological properties and functions. Apo-Tf was obtained from fraction IV subfraction 1 and IV subfraction 4 (fraction IV-1,4), a waste product of the Cohn fractionation process, performing a single chromatographic run and two viral inactivation/removal steps. The structural integrity and the biological activity of the final product were extensively tested. The yield of apo-Tf produced was 80% on laboratory scale and 90% in scale-up lots, and the purity was higher than 95%. The purified protein preserves iron- and receptor-binding activities and shows a normal glycosylation pattern. The single chromatographic step process presented here provides an efficient means to prepare commercial quantities of the protein. The final product is sterile and two viral inactivation/removal steps were introduced into the process.

Imatinib assay by HPLC with photodiode-array UV detection in plasma from patients with chronic myeloid leukemia: Comparison with LC-MS/MS.

BACKGROUND: Imatinib, a competitive inhibitor of BCR-ABL tyrosine kinase, is now the first-line treatment for chronic myelogenous leukemia (CML). Therapeutic drug monitoring targeting trough plasma levels of about 1000ng/mL may help to optimize the therapeutic effect. METHODS: We developed a high-performance liquid chromatography (HPLC) method with UV/Diode Array Detection (DAD) for trough imatinib concentration determination in human plasma. Imatinib trough levels were measured in plasma from 65 CML patients using our method and LC-MS/MS as the reference method. Results with these two methods were compared using Deming regression, chi-square test, and sign test. RESULTS: The calibration curve was prepared in blank human plasma. HPLC-UV/DAD calibration curves were linear from 80 to 4000ng/mL, and the limit of quantification was set at 80ng/mL. The between-day variation was 6.1% with greater than 96% recovery after direct plasma deproteinization and greater than 98% recovery from the column. No significant differences in imatinib plasma levels were found between HPLC-UV/DAD and LC-MS/MS. CONCLUSIONS: This HPLC-UV/DAD method was sufficiently specific and sensitive for imatinib TDM, with no evidence of interference. Our rapid inexpensive HPLC-UV/DAD method that requires only widely available equipment performs well for plasma imatinib assays.

Optimization of a direct analysis in real time/time-of-flight mass spectrometry method for rapid serum metabolomic fingerprinting.

Metabolomic fingerprinting of bodily fluids can reveal the underlying causes of metabolic disorders associated with many diseases, and has thus been recognized as a potential tool for disease diagnosis and prognosis following therapy. Here we report a rapid approach in which direct analysis in real time (DART) coupled with time-of-flight (TOF) mass spectrometry (MS) and hybrid quadrupole TOF (Q-TOF) MS is used as a means for metabolomic fingerprinting of human serum. In this approach, serum samples are first treated to precipitate proteins, and the volatility of the remaining metabolites increased by derivatization, followed by DART MS analysis. Maximum DART MS performance was obtained by optimizing instrumental parameters such as ionizing gas temperature and flow rate for the analysis of identical aliquots of a healthy human serum samples. These variables were observed to have a significant effect on the overall mass range of the metabolites detected as well as the signal-to-noise ratios in DART mass spectra. Each DART run requires only 1.2 min, during which more than 1500 different spectral features are observed in a time-dependent fashion. A repeatability of 4.1% to 4.5% was obtained for the total ion signal using a manual sampling arm. With the appealing features of high-throughput, lack of memory effects, and simplicity, DART MS has shown potential to become an invaluable tool for metabolomic fingerprinting.

Economical impact of plasma fractionation project in Iran on affordability of plasma-derived medicines.

In Iran all transfusion services are concentrated under authority of one public and centralized transfusion organization which has created the opportunity of using plasma produced in its blood centers for fractionation. In 2008 voluntary and non remunerated Iranian donors donated 1.8 million units of blood. This indicates a 25/1000 donation index. After responding to the needs for fresh plasma and cryoprecipitate each year about 150000 L of recovered plasma are reserved for fractionation. In an attempt to improve both blood safety profile and availability and affordability of plasma derived medicines, Iran's national transfusion service has entered into a contract fractionation agreement for surplus of plasma produced from donated blood by voluntary non remunerated donors. In order to ensure safety of product produced, Iran has chosen to collaborate with international fractionators based in highly regulated countries. The main objective of this study was to evaluate the impact of contract plasma fractionation on the affordability of the plasma derived medicines in Iran. During 2006-2008, Iran's contract fractionation project was able to produce 46%, 18% and 6% of IVIG, Albumin and FVIII consumed in Iran's market, respectively. In contrary to IVIG and Albumin, due to fairly high consumption of FVIII in Iran, the role of fractionation project in meeting the needs to FVIII was not substantial. However, Iran's experience has shown that contract plasma fractionation, through direct and indirect effects on price of plasma derived medicines, could substantially improve availability and affordability of such products in national health care system.

Assessment of sample collection and storage methods for multicenter immunologic research in children.

Multicenter studies involving both large and small centers separated by significant distances pose unique challenges to biological sample collection. The objective of this study was to evaluate protocols for determining inflammatory biomarkers that are cost and manpower efficient for handling blood destined for a sample repository. Tempus (Applied Biosystems) and Paxgene (Qiagen) blood collection systems were evaluated for RNA isolation. P100 tubes (BD), containing propriety stabilizers for preservation of plasma proteins, were evaluated for protein content and compared with plasma collected in conventional tubes. Blood for plasma separation was spiked with recombinant TNF-alpha and IL-2 prior to being processed and stored under various conditions. The Tempus RNA system produced a significantly greater yield of RNA at comparable quality when stored at 4 degrees C and shipped at ambient temperature than any other condition tested. The Tempus system was 20% less expensive and required approximately 40% less processing time thereby reducing costs. The P100 system preserved recombinant TNF-alpha in blood shipped at ambient temperature significantly better than conventionally collected plasma that was shipped on dry ice. There was no significant difference in IL-2 levels between the two collection methods and shipping temperatures. The Tempus RNA blood collection tubes and the P100 protein stabilization system provide the opportunity for reliable collection and ambient temperature transport of samples in multicenter studies. This cost-effective, standardized protocol for a large multicenter trial ensures the integrity of biological samples and maximizes study participation by both large and small centers.

A rapid, economical, and reproducible method for human serum delipidation and albumin and IgG removal for proteomic analysis.

Serum is a readily available source for diagnostic assays, but the identification of disease-specific serum biomarkers has been impeded by the dominance of human serum albumin (HSA) and immunoglobulin G (IgG) in the serum proteome. Therefore, in order to observe lower-abundance serum proteins, removal or depletion of at least these two proteins is required. However, the depletion method needs to be inexpensive and reproducible. We describe such a protocol that combines delipidation by centrifugation, IgG removal with Protein G Sepharose, and HSA depletion with sodium chloride/ethanol precipitation. The protocol is streamlined to increase reproducibility and is compatible with many proteomic platforms, including two-dimensional gel electrophoresis, and high-performance liquid chromatography either offline or coupled online with a mass spectrometer. The reproducible depletion of lipids, IgG, and HSA permits a higher load of the remaining serum proteins, facilitating the identification of disease biomarkers.