Multi-component immunoaffinity subtraction chromatography: an innovative step towards a comprehensive survey of the human plasma proteome

In order to discover novel protein markers indicative of disease processes or drug effects, the proteomics technology platform most commonly used consists of high resolution protein separation by two-dimensional electrophoresis (2-DE), mass spectrometric identification of proteins from stained gel spots and a bioinformatic data analysis process supported by statistics. This approach has been more successful in profiling proteins and their disease- or treatment-related quantitative changes in tissue homogenates than in plasma samples. Plasma protein display and quantitation suffer from several disadvantages: very high abundance of a few proteins; high heterogeneity of many proteins resulting in long charge trains; crowding of 2-DE separated protein spots in the molecular mass range between 45-80 kD and in the isoelectric point range between 4.5 and 6. Therefore, proteomic technologies are needed that address these problems and particularly allow accurate quantitation of a larger number of less abundant proteins in plasma and other body fluids. The immunoaffinity-based protein subtraction chromatography (IASC) described here removes multiple proteins present in plasma and serum in high concentrations effectively and reproducibly. Applying IASC as an upfront plasma sample preparation process for 2-DE, the protein spot pattern observed in gels changes dramatically and at least 350 additional lower abundance proteins are visualized. Affinity-purified polyclonal antibodies (pAbs) are the immunoaffinity reagents used to specifically remove the abundant proteins such as albumin, immunoglobulin G, immunoglobulin A, transferrin, haptoglobin, alpha-1-antitrypsin, hemopexin, transthyretin, alpha-2-HS glycoprotein, alpha-1-acid glycoprotein, alpha-2-macroglobulin and fibrinogen from human plasma samples. To render the immunoaffinity subtraction procedure recyclable, the pAbs are immobilized and cross-linked on chromatographic matrices. Antibody-coupled matrices specific for one protein each can be pooled to form mixed-bed IASC columns. We show that up to ten affinity-bound plasma proteins with similar solubility characteristics are eluted from a mixed-bed column in one step. This facilitates automated chromatographic processing of plasma samples in high throughput, which is desirable in proteomic disease marker discovery projects.     

Recombinant antibodies for the depletion of abundant proteins from human serum

The identification of biomarkers from serum or plasma is often hindered by a few proteins present at high concentrations, which may obscure less abundant proteins. Ideal serum depletion strategies would be flexible as regards the proteins to be removed, and would feature the use of reagents with long shelf-lives. In this article, we describe a novel protein depletion methodology based on the incubation of serum samples with phage-derived recombinant antibody fragments, which are able to bind to staphylococcal Protein A, and which carry a C-terminal peptide tag capable of streptavidin binding. The resulting protein-antibody complexes can be removed by simultaneous capture on Protein A and/or streptavidin resin. The depletion methodology was exemplified by the isolation of recombinant human mAb fragments specific to abundant human serum Ags and by the simultaneous depletion of albumin, immunoglobulins, alpha2-macroglobulin, hemoglobin, transferrin and haptoglobin. The depleted serum samples were analyzed by 2-DE and by gel-free MS-based methodologies, confirming the efficiency and selectivity of the depletion process. The methodology presented is modular in nature, since several recombinant antibodies can be combined in a single depletion experiment. Furthermore, antibodies do not have to be covalently coupled to a solid support facilitating long-term storage.     

Comparison of protein enrichment strategies for proteome analysis of plasma

Efforts to discover protein biomarkers in plasma are hampered by the high abundance of few proteins, which interfere with the detection of low‐abundant proteins. Different commercially available protein‐partitioning products were tested for their ability to lower the detection limit of proteins in 2‐D gels. Immuno‐depletion using polyclonal antibodies raised against the proteins of highest abundance (Seppro IgY14 System) was compared with a two‐step immuno‐depletion strategy, where depletion with the Seppro IgY14 column was followed by depletion with the Seppro IgY‐SuperMix system. The third strategy tested was protein pre‐fractionation using the ProteoMiner kit, where proteins compete for binding sites on bead‐bound peptide hexamers with different binding properties. The pre‐fractionated protein samples were analyzed using 2‐DE, which revealed stunning differences in protein patterns. However, detectable protein spots in the different plasma fractions contained exclusively high‐abundant proteins normally present in plasma at concentrations between 1 μg and 40 mg/mL.     

A Depletion Strategy for Improved Detection of Human Proteins from Urine

With rapidly growing interest in the urine proteome, methods for reducing sample complexity are becoming increasingly important. Depletion strategies for removal of high-abundance proteins from human urine have not been reported. A commercial kit designed for depletion of abundant proteins from plasma was evaluated for removing top proteins from urine of patients with proteinuria. The number of low-abundance proteins identified in urine after depletion increased nearly 2.5-fold.     

Evaluation and optimization of IgY spin column technology in the depletion of abundant proteins from human serum

Serum depletion strategies are commonly implemented in order to remove abundant proteins, increasing the number of proteins detected in a biomarker study. The IgY spin columns used in this study bind 12 and 14 primate proteins, respectively. 1‐D SDS‐PAGE and 2‐DE revealed a suboptimal performance of the IgY spin columns. However, modification of the manufacturer's protocol, subjecting samples to two rounds of depletion, improved the number of proteins resolved by 2‐DE. With alteration of the manufacturer protocol, the Seppro^® IgY14 spin column can produce depleted serum with an increased number of spots resolved by 2‐DE compared to untreated serum.     

The HUPO Plasma Proteome Project: a report from the Munich congress

The Human Proteome Organization has several major collaborative research initiatives, including the Plasma Proteome Project. A major feature of the HUPO World Congress in Munich in August 2005 was the release of the special issue of PROTEOMICS with 28 articles from the pilot phase of the Plasma Proteome Project. An open Workshop and a presentation in the closing plenary session of the congress focused on next phases for the Plasma Proteome Project.     

Recent Workshops of the HUPO Human Plasma Proteome Project (HPPP): a bridge with the HUPO CardioVascular Initiative and the emergence of SRM targeted proteomics

We hereby provide a two-year update on the HUPO Human Plasma Proteome Project (HPPP) informed by advances presented at the HPPP sessions at the HUPO World Congresses in Toronto in September 2009 and in Sydney in September 2010.     

Immunoaffinity chromatographic isolation of a high molecular weight seroreactive protein from Mycobacterium leprae cell sonicate

Abstract The purpose of this study was to isolate Mycobacterium leprae antigen(s) by immunoaffinity chromatography using immunoglobulins from leprosy patients and from rabbit anti- M. leprae hyperimmune serum coupled to CNBr-Sepharose 4B. A high molecular weigh ( M _r) M. leprae protein (MLP) with a subunit M _r of 22000 was isolated. MLP was recognized by monoclonal antibody MMPII1G4 which is known to react with MMPII, a 22 kDa protein of M. leprae . The N-terminal sequence of the 22 kDa subunit (Met-gln-gly-asp-pro-asp-val-leu-arg-leu-leu-asn-glu-gln-leu-thr) was identical to MMPII and to antigen D (bacterioferritin) of M. paratuberculosis . It showed 44% homology with N-terminal end of E. coli bacterioferritin. In ELISA, MLP showed 100% and 60% positivity with leprosy and TB sera respectively as compared to normal healthy sera. The role of bacterioferritin in M. leprae and the importance of MLP as an immunogen has been discussed.     

Depletion of the high-abundance plasma proteins

Summary. Body fluids, like plasma and urine, are comparatively easy to obtain and are useful for the detection of novel diagnostic markers by applying new technologies, like proteomics. However, in plasma, several high-abundance proteins are dominant and repress the signals of the lower-abundance proteins, which then become undetectable either by two-dimensional gels or chromatography. Therefore, depletion of the abundant proteins is a prerequisite for the detection of the low-abundance components. We applied affinity chromatography on blue matrix and Protein G and removed the most abundant human plasma proteins, albumin and the immunoglobulin chains. The plasma proteins, prior to albumin and immunoglobulin depletion, as well the eluates from the two chromatography steps were analyzed by two-dimensional electrophoresis and the proteins were identified by MALDI-TOF-MS. The analysis resulted in the identification of 83 different gene products in the untreated plasma. Removal of the high-abundance proteins resulted in the visualization of new protein signals. In the eluate of the two affinity steps, mostly albumin and immunoglobulin spots were detected but also spots representing several other abundant plasma proteins. The methodology is easy to perform and is useful as a first step in the detection of diagnostic markers in body fluids by applying proteomics technologies.Current address: Foundation for Biomedical Research of the Academy of Athens, Greece     

Depletion and recovery of ATP in V79 cells with exposure to inhibitors of glycolysis and oxidative phosphorylation

Summary Cells of the cultured hamster cell line V79 were labeled with tritiated adenosine and incubated for up to 30 min in the presence of inhibitors of glycolysis and oxidative phosphorylation. These inhibitors were (a) 5 mM KCN plus 5 mM iodoacetate, (b) 5 mM KCN plus 5 mM KF, and (c) 15 mM KCN plus 15 mM KF. The fate of the tritium label was examined during incubation with inhibitors and also during subsequent incubation in growth medium in the absence of inhibitors. The tritiated ATP pool was found to decrease in cells incubated in the presence of any of the inhibitor combinations, but only in the presence of 15 mM KCN plus 15 mM KF was this pool decreased below the level of detection. After cells were incubated with KCN plus KF, a high level of ATP was recovered when the inhibitors were removed. Cells incubated with KCN plus iodoacetate retained depletion levels of ATP. Plating efficiency and trypan blue staining showed that KCN-KF treated cells retained viability, whereas KCN-iodoacetate treated cells did not. Cells were examined for ability to take up tritiated uridine before, during, and after depletion of ATP by incubation in the presence of 15 mM KCN plus 15 mM KF. These cells were found to have a variation in uridine uptake that was related directly to intracellular ATP level. Cells in which the ATP was very low exhibited little or no uridine uptake, whereas cells in which the ATP level was near normal exhibited normal uridine uptake. This work was supported in part by Grant GM24271 from the National Institutes of Health, Bethesda, Maryland.     

Effective elution of antibodies by arginine and arginine derivatives in affinity column chromatography

It has been shown that the recovery of monomeric antibodies from protein A affinity chromatography is enhanced significantly by using arginine as an eluent. To extend the applications of arginine to antibody purification and obtain an insight into the mechanism of arginine elution, we compared arginine with citrate, guanidine hydrochloride (GdnHCl), arginine derivatives, and other amino acids in protein A chromatography. We also applied arginine to elution of polyclonal antibodies (pAbs) in antigen affinity chromatography. As described previously, arginine was effective in eluting monoclonal antibodies IgG1 and IgG4. Two arginine derivatives, acetyl-arginine and agmatine, resulted in efficient elution at pH 4.0 or higher, and this was comparable to arginine. On the other hand, other amino acids, such as glycine, proline, lysine, and histidine, are much less effective than arginine under identical pH conditions. Whereas elution increased with arginine concentration, elution with citrate was insignificant in excess of 1 M at pH 4.3. Arginine was also effective in fractionation of pAbs using antigen-conjugated affinity columns. Although GdnHCl was also effective under similar conditions, the eluted material showed more aggregation than did the protein eluted by arginine.     

An integrated quantification method to increase the precision,robustness, and resolution of protein measurement in human plasma samples

Background

Current quantification methods for mass spectrometry (MS)-based proteomics either do not provide sufficient control of variability or are difficult to implement for routine clinical testing.

Results

We present here an integrated quantification (InteQuan) method that better controls pre-analytical and analytical variability than the popular quantification method using stable isotope-labeled standard peptides (SISQuan). We quantified 16 lung cancer biomarker candidates in human plasma samples in three assessment studies, using immunoaffinity depletion coupled with multiple reaction monitoring (MRM) MS. InteQuan outperformed SISQuan in precision in all three studies and tolerated a two-fold difference in sample loading. The three studies lasted over six months and encountered major changes in experimental settings. Nevertheless, plasma proteins in low ng/ml to low μg/ml concentrations were measured with a median technical coefficient of variation (CV) of 11.9% using InteQuan. The corresponding median CV using SISQuan was 15.3% after linear fitting. Furthermore, InteQuan surpassed SISQuan in measuring biological difference among clinical samples and in distinguishing benign versus cancer plasma samples.

Conclusions

We demonstrated that InteQuan is a simple yet robust quantification method for MS-based quantitative proteomics, especially for applications in biomarker research and in routine clinical testing.

Electronic supplementary material

The online version of this article (doi:10.1186/1559-0275-12-3) contains supplementary material, which is available to authorized users.     

Isolation, Characterization, and Synthesis of AlphaFetoprotein from Neonatal Rat Brain

Monospecific anti-rat serum alpha-fetoprotein (AFP) IgG was coupled to cyanogen bromide-activated Sepharose-4B (4.5 mg/ml packed volume of gel) to yield an immunoaffinity matrix. The immunoaffinity column was used to isolate AFP from feto-neonatal rat brain. The purified AFP was immunologically and electrophoretically similar to serum AFP. It yielded a single band with a molecular weight of 70,000 on sodium dodecyl sulphate polyacrylamide gel electrophoresis. Polyacrylamide gel electrophoresis of the protein under nondenaturing conditions yielded two charge variants of AFP, reminiscent of AFP from feto-neonatal rat serum. The AFP was observed to bind estradiol with Ka = 5.8 X 10(8) M -1 and 1.3 X 10(8) M -1 by dextran-coated charcoal adsorption and Sephadex gel filtration techniques, respectively. Newborn rat brain cells linearly incorporated [14C]leucine into immunoprecipitable AFP during 6 h in culture. It is, therefore, concluded that feto-neonatal rat brain contains AFP similar to that present in fetal serum and that it may arise in brain as a result of its in situ synthesis.     

Prediction of reversible IgG1 aggregation occurring in a size exclusion chromatography column is enabled through a model based approach

One important aspect of antibody separation being studied today is aggregation, as this not only leads to a loss in yield, but aggregates can also be hazardous if injected into the body. The aim of this study was to determine whether the methodology applied in the previous study could be used to predict the aggregation of a different batch of IgG1, and to model the aggregation occurring in a SEC column. Aggregation was found to be reversible. The equilibrium parameter was found to be 272 M^‐1 and the reaction kinetic parameter 1.33 × 10^‐5 s^‐1, both within the 95% confidence interval of the results obtained in the previous work. The effective diffusivities were estimated to be 1.45 × 10^‐13 and 1.90 10^‐14 m²/s for the monomers and dimers, respectively. Good agreement was found between the new model and the chromatograms obtained in the SEC experiments. The model was also able to predict the decrease of dimers due to the dilution and separation in the SEC column during long retention times.     

The Isolation of Plasma Membrane from Vicia faba Leaves and Pollen Tubes of Luffs cylindrica by the Two-Polymer Phase System

A method for the isolation of plasma membrane enriched fraction from plant sources is described. An aqueous two-phase system is suitable for the isolation of plasma membrane. Purified plasma membrane fractions have been prepared from Vicia faba leaves and pollen tubes of Luffa cylindrica. The determination of marker enzymes shows that the plasma membrane has a high affinity for the polyethylene glycol-rich upper phase, whereas those membranes from mitochondria, chloroplasts and other organelles prefer the dextran-rich lower phase and the interface. The plasma membrane was identified with the aid of silicotungstic acid-chromic acid staining. In the upper phase there are mainly stained elliptical vesicles, whereas in the lower phase there are many differnet kind of unstained vesicles. This result is coincident with the marker enzyme examination. The two-phase method for the isolation of plasma membrane may be widely applied not only to nongreen tissues but also to green tissues of plants.     

Characterization of the human urinary proteome: a method for high-resolution display of urinary proteins on two-dimensional electrophoresis gels with a yield of nearly 1400 distinct protein spots

The abundance profile of the human urinary proteome is known to change as a result of diseases or drug toxicities, particularly of those affecting the kidney and the urogenital tract. A consequence of such insults is the ability to identify proteins in urine, which may be useful as quantitative biomarkers. To succeed in discovering them, reproducible urine sample preparation methods and good protein resolution in two-dimensional electrophoresis (2-DE) gels for parallel semiquantitative protein measurements are desirable. Here, we describe a protein fractionation strategy enriching proteins of molecular masses (M(r)) lower than 30 kDa in a fraction separate from larger proteins. The fraction containing proteins with M(r)s higher than 30 kDa was subsequently subjected to immunoaffinity subtraction chromatography removing most of the highly abundant albumin and immunoglobulin G. Following 2-DE display, superior protein spot resolution was observed. Subsequent high-throughput mass spectrometry analysis of ca. 1400 distinct spots using matrix-assisted laser desorption/ionization-time of flight peptide mass fingerprinting and liquid chromatography-electrospray ionization tandem mass spectrometry lead to the successful identification of 30% of the proteins. As expected from high levels of post-translational modifications in most urinary proteins and the presence of proteolytic products, ca. 420 identified spots collapsed into 150 unique protein annotations. Only a third of the proteins identified in this study are described as classical plasma proteins in circulation, which are known to be relatively abundant in urine despite their retention to a large extent in the glomerular blood filtration process. As a proof of principle that our urinary proteome display effort holds promise for biomarker discovery, proteins isolated from the urine of a renal cell carcinoma patient were profiled prior to and after nephrectomy. Particularly, the decrease in abundance of the kininogen 2-DE gel spot train in urine after surgery was striking.     

Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat

The growing availability of EST sequences from a range of crop plantsprovides a potentially valuable source of new DNA markers. We have examined theInternational Triticeae EST Cooperative database for the presence ofdinucleotide and trinucleotide simple sequence repeats. Analysis of 24,344 ESTsidentified 388 dinucleotide repeats and 978 trinucleotide repeats in ESTs,representing 1.6% and 4.0% of the total number of ESTs, respectively. To testthe utility and cross-species transferability of EST-derived SSR markers,primers were designed to the flanking regions of 41 barley SSRs and used toscreen 11 barley and 15 wheat varieties. Sixteen of the barley SSR markers werepolymorphic in barley and five were polymorphic in wheat. This represents arelatively high level of transferability of SSR markers between barley andwheat, which has important implications for the development of new markers andcomparative mapping of barley, wheat and other cereals. An additional 56 SSRsfrom wheat ESTs were tested in the same barley and wheat varieties. Four wheatEST SSR markers were polymorphic in wheat and one in barley. Chromosomallocations in barley and wheat were determined for the majority of polymorphicmarkers.     

Comparison of batch and continuous multi‐column protein A capture processes by optimal design

Multi‐column capture processes show several advantages compared to batch capture. It is however not evident how many columns one should use exactly. To investigate this issue, twin‐column CaptureSMB, 3‐ and 4‐column periodic counter‐current chromatography (PCC) and single column batch capture are numerically optimized and compared in terms of process performance for capturing a monoclonal antibody using protein A chromatography. Optimization is carried out with respect to productivity and capacity utilization (amount of product loaded per cycle compared to the maximum amount possible), while keeping yield and purity constant. For a wide range of process parameters, all three multi‐column processes show similar maximum capacity utilization and performed significantly better than batch. When maximizing productivity, the CaptureSMB process shows optimal performance, except at high feed titers, where batch chromatography can reach higher productivity values than the multi‐column processes due to the complete decoupling of the loading and elution steps, albeit at a large cost in terms of capacity utilization. In terms of trade‐off, i.e. how much the capacity utilization decreases with increasing productivity, CaptureSMB is optimal for low and high feed titers, whereas the 3‐column process is optimal in an intermediate region. Using these findings, the most suitable process can be chosen for different production scenarios.     

Control of photosynthesis during nitrogen depletion and recovery in a non-nitrogen-fixing cyanobacterium

When cells of Synechocystis strain PCC 6308 are starved for nitrogen, the amount of stored carbohydrate increases, the phycocyanin to chlorophyll a ratio decreases, and the rates of oxygen evolution and of carbon dioxide fixation decrease. When nitrate-nitrogen is replenished, the amount of carbohydrate decreases, the rate of oxygen evolution increases immediately, preceeding the increase in phycocyanin or carbon dioxide fixation. The rate of respiration first increases and then decreases upon nitrogen addition. Nitrogen-starved cells show no variable fluorescence; variable fluorescence recovered in parallel with oxygen evolution. This suggests that photosystem II is inactive in nitrogen depleted cells and not blocked by a build up of metabolic endproducts. Since carbon dioxide fixation does not increase until two to four hours after nitrate is replenished to nitrogen starved cells, it is suggested that reducing power may first be needed within the cell for some other process than photosynthesis, such as nitrate reduction.     

Depletion of T-cell receptor alpha/beta and CD19 positive cells from apheresis products with the CliniMACS device

Background aimsThe CliniMACS device (Miltenyi Biotec, Bergisch Gladbach, Germany) was used for depletion of T-cell receptor alpha/beta positive (TCRαβ⁺) and CD19 positive (CD19⁺) cells from apheresis products.MethodsInvestigators performed 102 separations. Apheresis products with a median 5.8 (minimum to maximum, 1.2–10.4) × 10¹⁰ mononuclear cells were used with a median 358 (92–1432) × 10⁶ CD34⁺ cells. There were 24.8% (6.1–45.7%) median TCRαβ⁺ cells and 4.4% (1.2–11.7%) median B cells in the apheresis product.ResultsAfter depletion, a median 0.00097% (0.00025–0.0048%) of TCRαβ⁺ cells could be detected, and B cells, as determined as CD20⁺ cells, were reduced to 0.0072% (0.0008–0.072%). TCRαβ⁺ cells were depleted by log 4.7 (3.8–5.5), and B cells were depleted by log 4.1 (3.0–4.7). Recovery of mononuclear cells was 55% (33–77%), and recovery of CD34⁺ cells was 73% (43–98%). Recovery of CD56⁺/3^? natural killer cells was 80% (35–142%), recovery of TCR gamma/delta positive (TCRγδ⁺) T cells was 83% (39–173%) and recovery of CD14⁺ cells was 79% (22–141%). Viability of cells was 98% (93–99%) after separation (all values median).ConclusionsProfound depletion of TCRαβ⁺ T cells can be achieved with the CliniMACS system. Recovery of CD34⁺ stem cells is in the same range than after CD34⁺ enrichment and CD3/CD19 depletion. Transplantation with >4 × 10⁶ CD34⁺ cells/kg can be performed for every patient with 1–5 × 10⁴ TCRαβ⁺ cells/kg and about 5–10 × 10⁶ TCRγδ⁺ cells/kg with two rounds of apheresis.