US20090035849A1 - Depletion of plasma proteins - Google Patents

Depletion of plasma proteins Download PDF

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US20090035849A1
US20090035849A1 US11/983,203 US98320307A US2009035849A1 US 20090035849 A1 US20090035849 A1 US 20090035849A1 US 98320307 A US98320307 A US 98320307A US 2009035849 A1 US2009035849 A1 US 2009035849A1
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antibody
affinity
serum
abundance molecule
protein
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Gregory E. Rice
Mark S. Baker
Michael Quinn
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HealthLinx Ltd
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HealthLinx Ltd
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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N30/00—Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
    • G01N30/02—Column chromatography
    • G01N30/04—Preparation or injection of sample to be analysed
    • G01N30/06—Preparation
    • G01N30/14—Preparation by elimination of some components
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C07K1/14—Extraction; Separation; Purification
    • C07K1/16—Extraction; Separation; Purification by chromatography
    • C07K1/22—Affinity chromatography or related techniques based upon selective absorption processes
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6854—Immunoglobulins
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N30/00—Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
    • G01N2030/009—Extraction

Definitions

  • This invention relates to methods of analysis, and in particular to methods for the preliminary fractionation of samples in which low abundance molecules of interest, for example proteins, polysaccharides or fatty acids, are present together with more abundant molecules of little or no interest.
  • the invention relates to methods of depletion of high abundance proteins from biological samples.
  • the method is particularly applicable to samples of human biological fluids such as serum, plasma, tears, saliva, cerebrospinal fluid, uterine washings, amniotic fluid, cervico-vaginal fluid or urine. It is contemplated that the method of the invention will be especially useful for proteomic applications involving biomarker discovery. Products and kits for use in the method are also disclosed, and form part of the invention.
  • Proteomics is an area of research which seeks to define the function and relative expression profiles of subsets of proteins encoded by a given genome at a given time in a given cellular location. Proteomics separates, identifies, and characterizes the proteins expressed, retained, secreted or released by a cell or tissue in order to establish their function(s) and their potential relationship to the onset, type, stage and progression of diseases, as well as response to therapy and/or relapse.
  • Proteomics may be used to compare tissue samples from diseased and healthy people, in order to identify proteins whose expression is changed in disease. Proteins which are significantly altered in their expression, location or post-translational modification (PTM) in patients with a disease, compared to those in a group of healthy individuals, may represent protein targets for drug or discovery of biological markers, for example, endpoint and/or surrogate biomarkers.
  • PTM post-translational modification
  • One application of proteomics is in the search for biological markers of disease onset, progression and treatment in elements of the blood, such as serum or plasma.
  • Serum proteins are useful diagnostic tools, and alteration of the expression of some serum proteins is an early sign of an altered physiology, which may be indicative of disease.
  • identification of specific low abundant disease-associated proteins in serum relies heavily on time-consuming and expensive radiolabelled or enzyme-linked immunoassay methods (RIA or ELISA) which only have the ability to evaluate a single protein component at a time. Due to the heterogenous nature of most physiological disorders, it is generally considered that no single marker is likely to be sufficiently predictive of disease, so that there is a need for more than one candidate biomarker to enhance already available diagnostic or prognostic tests. It has been suggested that a panel of multiple diagnostic/prognostic markers in serum can be identified by utilizing proteomic approaches which have the capacity to profile multiple biomarkers (Daly and Ozols, 2002).
  • Two-dimensional gel electrophoresis 2DE
  • proteins are characterized and identified, usually using matrix-assisted laser desorption interferometery (MALDI) peptide mass fingerprinting or other forms of advanced mass spectrometry, for example, electrospray mass spectroscopy (MS) or time-of-flight (TOF)/TOF MS, or surface-enhanced (SELDI-TOF MS), laser desorption ionization time-of-flight mass spectrometry coupled to protein and genomic database searching.
  • MALDI matrix-assisted laser desorption interferometery
  • MS electrospray mass spectroscopy
  • TOF time-of-flight
  • SELDI-TOF MS surface-enhanced
  • proteomic technologies are limited by the presence of high abundance “housekeeping” proteins like albumin and immunoglobulins, which constitute approximately 60-97% of the total serum protein (Georgiou et al, 2001). Such proteins hinder the detection of hundreds of low abundance proteins, some of which might potentially be relevant to a particular disease state. Moreover, the widely spread pattern of albumin and immunoglobulin in the 2-DE gel can also obscure proteins with a similar pI and molecular weight. Theoretically, by removing albumin and immunoglobulin, which together constitute 60-97% of the total serum protein, 3-5-fold more protein can be analyzed. If proteomic technologies are to be used routinely for diagnostic purposes, a rapid, inexpensive and simple method is required to remove the high abundant proteins.
  • FIG. 1 shows the results of 2DE of a sample of unfractionated human plasma. This illustrates the problem presented by very abundant proteins, such as albumin, which comprises more than 80% of the total protein present in plasma; see the circle in FIG. 1 .
  • the maximum amount of “non-albumin” proteins which can be loaded is limited to approximately 36 mg, thus limiting the ability of this technique to visualize and identify putative clinically-relevant low abundance biomarker proteins. Rare proteins may be difficult if not impossible to detect. Similar, although less extreme, dynamic range problems are experienced with 2DE analyses of other types of biological samples, such as urine, tissue extracts, and cell lysates.
  • One approach to solving this problem is to develop methods for removing albumin and other highly abundant proteins from blood samples such as serum and plasma before analysis, thus increasing the sensitivity of the analysis and hence the likelihood of identifying low abundance protein biological markers.
  • a method of removal of the 50 to 100 most abundant proteins from plasma before analysis would be greatly advantageous, in order to permit the use of higher relative mass loading of samples.
  • the invention provides a method of depleting a high-abundance protein molecule from a biological sample, comprising the steps of
  • the antibody binds to a high abundance molecule.
  • the sample is subjected to both affinity depletion and immunodepletion. While it is possible to perform the steps in either order, we have found that by performing step (a) before step (b) much less antibody is required for substantially complete removal of high abundance molecules. Therefore this order is preferred.
  • the high abundance molecule is a protein. Even more preferably, the protein is albumin.
  • the antibody is an avian antibody.
  • the biological sample is a biological fluid, such as serum, plasma, lymph, cerebrospinal fluid, amniotic fluid, cervicovaginal fluid, uterine fluid, or seminal fluid.
  • the sample may be conditioned medium from a cell or tissue culture, or may be a tissue or cell extract, especially an extract of a highly vascularized tissue.
  • the biological sample may be obtained from any mammalian species, including humans, companion animals such as dogs and cats, domestic animals such as horses, cattle and sheep, or zoo animals such as non-human primates, felids, canids, bovids, and ungulates.
  • the sample is obtained from a human.
  • the mammal may be of either sex, may be of any age, and may be either healthy or suffering from any kind of pathological condition, including but not limited to infections, cancers, or chronic degenerative conditions.
  • the method of the invention is applicable to any situation where it is desired to perform analysis in order to detect a low abundance molecule, or to identify whether there is a change in the pattern of expression of such a molecule in a mammal.
  • the affinity support used in step (a) may be any such support which is known to have a high affinity for albumins, immunoglobulins or other highly abundant proteins.
  • the support will be a dye affinity chromatography resin, in which a solid support is coupled to a dye such as a chlorotriazine compound, including but not limited to Cibacron blue F3GA affinity supports such as Affi-gel Blue (Bio-Rad Laboratories), or Blue Sepharose (Amersham Biosciences).
  • dye-ligands which could also alternatively be employed to remove abundant blood proteins include Procion Red HE3B, Reactive Blue MRB, Reactive Green H4G, Reactive Green HE4BD, Reactive Green HE4BD, Reactive Yellow M8G, and Reactive Brown M4R, all of which can be coupled to supports such as Sepharose 4B and 6B. Dyes suitable for use in affinity chromatography are discussed in a review by Scawen (1991). Alternatively the support may be coupled to a protein such as Protein A, Protein G or Protein A/G fusions. Affinity chromotography techniques are well known in the art, and are reviewed in Hage (1999) and Larsson (1987).
  • the affinity depletion in step (a) may involve the use of magnetic beads such as agarose (Dynabead M-280) as a solid phase matrix support for an affinity ligand for the magnetic separation of high abundance molecules from low abundance molecules.
  • magnetic beads such as agarose (Dynabead M-280) as a solid phase matrix support for an affinity ligand for the magnetic separation of high abundance molecules from low abundance molecules.
  • any solid-phase support which can be coupled to an immunoglobulin to form an affinity support may be used in step (b); these include but are not limited to agarose gels such as Sepharose 4B or Sepharose 6B (Pharmacia), cross-linked agarose, or acrylamide-based and cellulose-based beads.
  • the antibody used in step (b) may be a first generation polyclonal antibody raised against whole serum or plasma, or against any fraction of these complex proteinaceous mixtures, and may suitably be raised using an immunization schedule comprising multiple booster injections.
  • the antibody may be raised in any convenient avian or mammalian species. Where the antibody is an avian antibody, this may be raised in any convenient species of bird, but most conveniently will be raised in a poultry species such as a chicken, turkey, duck or goose. Most preferably the avian antibody is a chicken antibody. In one embodiment the antibody is chicken IgY.
  • the high-abundance molecule may be conjugated to a carrier protein if necessary in order to increase immunogenicity.
  • the antibody is a second generation polyclonal antibody raised against plasma or serum which has already been subjected to at least one round of affinity depletion and immunodepletion IgY directed against homologous plasma or serum.
  • the antibody may be produced and purified using any conventional method. Suitable methods for preparation of IgY are disclosed in U.S. Pat. No. 5,367,054, No. 5,420,253, No. 4,550,019 and No. 4,056,737.
  • Suitable separation technologies include, but are not limited to, one-dimensional gel electrophoresis (1DE), 2DE, capillary electrophoresis, mass spectrometry, high-pressure liquid chromatography (HPLC), gas-chromatography, liquid chromatography (LC), multi-dimensional LC, or LC/MS.
  • the invention provides a method of separation or analysis of a low abundance molecule in a biological sample, comprising the step of depleting a high abundance molecule from the sample by the method of the first aspect of the invention, and then subjecting the thus-treated sample to a separation method, such as chromatography, electrophoresis or mass spectrometry.
  • a separation method such as chromatography, electrophoresis or mass spectrometry.
  • the invention provides a composition for immunodepletion of a high abundance molecule from a biological sample, comprising an antibody preparation directed against a high abundance molecule, coupled to an affinity support.
  • the antibody is an avian polyclonal antibody, more preferably a second generation avian polyclonal antibody, and the high abundance molecules are those present in serum or plasma.
  • the avian antibody is from chicken, and the serum or plasma molecules are serum or plasma proteins.
  • the antibody is chicken IgY.
  • the support may be any solid-phase support which may be coupled to immunoglobulin to form an affinity support.
  • suitable supports are known in the art, such as Sepharose and the like, as described above.
  • the invention provides a device for the rapid processing of biological samples in the method of the invention, comprising a generally cylindrical chamber having an opening at either end, in which each opening is adapted to fit sealingly to a receptacle, in which the sample can be transferred from one receptacle to the other via the chamber, and in which the chamber has transversely disposed within it multiple layers of an affinity support having a high affinity for high abundance molecule, separated by a layer of an affinity support coupled to one or more antibodies directed against a high abundance molecule.
  • the high abundance molecule(s) is/are albumin and/or immunoglobulins, the antibody is avian, and the abundant molecule(s) is/are plasma or serum proteins.
  • sealingly means that the chamber fits to the receptacle sufficiently tightly that substantially no fluid can escape when fluid is passed from one receptacle to another via the chamber.
  • the plane of each layer of the support is generally perpendicular to the axis of the chamber.
  • the chamber is connected at one end to a receptacle containing a fluid biological sample, and at the other end to an empty receptacle, and the sample is passed a number of times from one receptacle to the other through the chamber.
  • the receptacles are hypodermic syringes and the chamber is a Luer-type cartridge. More preferably both the chamber and the receptacles are made of plastics.
  • the chamber is adapted to be coupled directly to a separation or analytical apparatus such as an HPLC or LC column, or a mass spectrometry.
  • a separation or analytical apparatus such as an HPLC or LC column, or a mass spectrometry.
  • a Sep-Pale type cartridge would be suitable.
  • the invention provides a kit for removal of high-abundance molecules from a biological sample, comprising:
  • a) a first affinity support with high affinity for high abundance molecules such as albumin and/or other highly abundant proteins such as IgG;
  • the antibody binds to a high abundance molecule.
  • the antibody is an avian antibody, and is directed against the whole serum or whole plasma, or against high abundance serum or plasma proteins.
  • the kit also comprises a device according to the fourth aspect of the invention; optionally the kit may also comprise a diluent suitable for use with biological fluids.
  • the affinity supports are as described for the first aspect.
  • FIG. 1 shows the results of 2DE of a sample of human plasma.
  • the circle indicates spots representing albumin.
  • FIG. 2A is a schematic illustration of the process for production of first and second generation polyclonal antibodies in chickens.
  • FIG. 2B is a schematic illustration of the processes for affinity and immunodepletion of proteins from human plasma.
  • FIG. 3 is a Western blot of a 2DE of a sample of whole human plasma. The blot was probed with pooled first and second round chicken antibody raised against human plasma, and demonstrates the range of abundant protein antigens against which antibody responses have been mounted by the immunised chickens.
  • FIG. 4 shows the results of 2DE of a sample of human plasma subjected to 4-7 IPG isoelectric focusing and 10% acrylamide SDS-PAGE (Criterion gel Bio-Rad), and visualized by SYPRO Ruby®.
  • FIG. 4A is a display of proteins present in unfractionated human plasma.
  • FIG. 4B is a display of proteins present after treatment of human plasma with Affi-gel Blue.
  • FIG. 4C is a display of proteins present after treatment of human plasma with Affi-gel blue and then anti-human plasma (AHP)-Sepharose 4B.
  • FIG. 5 is a schematic representation of a cartridge device according to the invention for rapid processing of samples of biological fluids.
  • FIG. 6 is a 2-DE profile of (a) Untreated serum, (b) Affi-Gel Blue and (c) Aurum kit treated human serum. Human serum was treated with Affi-Gel Blue or Aurum kit for 16 h before analysis by 2-DE. 15 ⁇ g of protein was loaded on each gel. Results are representative of three independent experiments.
  • FIG. 7 is a depiction of the reference profile of all protein spots identified by 2-DE.
  • FIG. 8 is a depiction of the reference profile of all protein spots identified by 2-DE.
  • FIG. 9 shows time-dependent removal of albumin after treatment of human serum with Affi-Gel Blue or Aurum kit.
  • Serum sample was treated with Aurum kit for 0 min (untreated serum), 15 min, 1 h, 5 h and 16 h.
  • Serum sample was treated with Affi-Gel Blue for 0 min (untreated serum); 1 h and 16 h. 15 ⁇ g of protein was loaded on each gel.
  • finity depletion means the removal of components from a complex mixture based upon chemical or immunological characteristics by specific agents.
  • finity support refers to a matrix or support to which specific agents are bound or coupled and which is used to deplete components from a complex mixture.
  • Immunodepletion means the use of antibodies raised against specific components of a complex mixture to remove those components from the mixture.
  • Immunoaffinity refers to the association between an antibody and its corresponding antigen or epitope.
  • High affinity refers to the strength of binding between an antibody and its corresponding antigen or epitope, and the person skilled in the art will readily be able to determine whether a given antibody binds strongly enough to a high abundance protein to be useful for the purposes of the invention.
  • secondary antibodies have higher affinity than primary antibodies, so antibodies elicited by a series of two or more immunizations will be expected to have higher affinity than those obtained after a single immunization.
  • high abundance protein refers to a protein which is present at a concentration greater than 1 mg/ml in a biological sample.
  • depletion of albumin using a Cibacron Blue-based affinity support greatly reduces the number of protein spots detectable by SYPRO Ruby® staining of 2DE gels.
  • Using this step in conjunction with a second step of immunodepletion with an immuno-affinity support coupled to an IgY further reduces the number of spots, as well as enabling the detection of previously undetectable spots.
  • IgY The avian equivalent of IgG, usually referred to as IgY, is significantly different in its chemical and physical properties from IgG.
  • IgY has a much higher electrophoretic mobility, a much lower isoelectric pH, and a higher molecular weight than IgG, and has substantially different chemical stability.
  • IgY requires stabilization by non-ionic surfactants, whereas IgG is stable in the absence of surfactants.
  • Ionic detergents can inhibit the reaction of IgG with some antigens, but these agents have little effect on the ability of IgY to bind antigens.
  • IgY is monomeric in 0.15 M NaCl (low salt conditions), and is dimeric in 1.5 M NaCl (high salt conditions), while IgG is monomeric at both low and high salt conditions.
  • the properties of IgY are described in detail in U.S. Pat. No. 4,550,019.
  • the structural differences between the two molecules mean that the hinge region which is present in IgG between the Fab pieces is absent in IgY. This hinge region renders IgG less stable than IgY, and hence IgG is slightly less suitable than IgY for use in solid-phase extraction procedures.
  • the yolk of eggs laid by immunized chickens is an abundant source of polyclonal antibodies (pAb).
  • pAb polyclonal antibodies
  • Affi-gel Blue has been previously used to remove albumin and certain other proteins from serum samples. However, to our knowledge it has not hitherto been suggested that Affi-gel Blue could be useful in preparation of samples for 2DE analysis.
  • Affi-gel Blue and similar supports such as HiTrap Blue P (Amersham Biosciences) are agarose supports coupled to the dye Cibacron Blue F3G-A, which has a high affinity not only for albumin, but also for interferon, a broad range of nucleotide-requiring enzymes, ⁇ 2 -macroglobulin, coagulation factors, and nucleic acid-binding proteins. Thus it depletes not only albumin but also ⁇ 2 -macroglobulin and coagulation factors from plasma.
  • ligands based on synthetic dyes such as triazine or triphenylmethane compounds
  • specific ligands used in this method include Cibacron Blue F3G-A, Procion Blue MX-3G or MX-R, Procion Red HE-3B, and Thymol Blue or Phenol Red (Hage, 1998; Hermanson et al, 1992).
  • affinity ligands because they interact with and bind to many biomolecules such as proteins and enzymes by mimicking the structure of their substrates, cofactors, or binding agents.
  • Cibacron Blue F3G-A consists of a chlorotriazine ring which has several substituents, one of which is an anthraquinone which interacts with enzymes which have a binding site for NAD+, NADP+, or ATP.
  • dye ligands can be produced in large quantities and demonstrate a high degree of selectivity and reproducibility. These properties have made them useful for the large-scale purification of dehydrogenases, kinases, albumin, ⁇ -fetoprotein, CoA-dependent enzymes, hydrolases, IgG, lipoproteins, nucleases, polymerases, synthetases, and transferases (Hage, 1998; Hermanson et al, 1992; Jones, 1991; Scawen, 1991).
  • the binding characteristics of the extracted antibodies were determined by 2DE Western Blot analysis as described below. The antibodies were then coupled to Sepharose 4B according to the manufacturer's instructions.
  • PEG 6000 was dissolved in 2 ml IgY solution (17.3 mg protein/ml), incubated for 10 min at room temperature and then centrifuged at 2000 g for 1 h. The pellet was resuspended in coupling buffer (0.1M NaHCO 3 pH 8.3, containing 0.5M NaCl) to a final concentration of 7.5 mg protein/ml.
  • coupling buffer 0.1M NaHCO 3 pH 8.3, containing 0.5M NaCl
  • CNBr-activated Sepharose 4B (Pharmacia; 1 g) was suspended in 20 ml of 1 mM HCl. The suspension was then washed with 200 ml 1 mM HCl on a sintered glass filter. The washed gel was resuspended in the IgY solution, and mixed on a rotary mixer for 18 h at 4° C. The gel was then washed with 5 volumes of coupling buffer and incubated in 0.1M Tris-HCl buffer, pH8.0 for 2 h at 4° C.
  • the gel was washed 3 times alternately with 5 volumes 0.1M acetate buffer pH 4.0 containing 0.5M NaCl, and then 0.1M Tris HCl pH 8.0 containing 0.5M NaCl.
  • the anti-human plasma antibody-Sepharose 4B (AHP-Sepharose) gel was then stored at 4° C. in 0.01 M phosphate-buffered saline, pH7.4, containing 0.05% sodium azide as a preservative.
  • Affi-gel Blue (5 ml gel suspension per ml of plasma) was suspended in sealed 10 ml polypropylene columns (Econo-Columns; Bio-Rad) and eluted with 2 volumes of 20 mM phosphate buffer (pH7.1).
  • Plasma 500 ⁇ l
  • Plasma 500 ⁇ l
  • Plasma was mixed with an equal volume of 20 mM phosphate buffer (pH7.1) and mixed on a rotary mixer for 4 h at 4° C. ml.
  • This solution was then added to the Affi-gel Blue column.
  • the column was capped and mixed on a rotary mixer for 18 h at 4° C.
  • the column tip seal and cap were removed, and the flow-through collected.
  • the protein content was determined, and the aliquot was stored at ⁇ 80° C. for subsequent analysis.
  • Affi-gel Blue-treated plasma was then subjected to AHP-Sepharose immunodepletion as follows.
  • AHP-Sepharose 100 ⁇ l was washed with 4 volumes of 100 mM phosphate buffer (pH7.1) using a sintered glass filter.
  • the washed gel was resuspended in Affi-gel Blue-treated plasma (100 ⁇ l) in a 2 ml microcentrifuge tube, and mixed on a rotary mixer for 18 h at 4° C.
  • the suspension was centrifuged at 13,200 g for 5 min at room temperature and the supernatant collected, its protein content determined and the aliquot then stored at ⁇ 80° C. for subsequent analysis.
  • Affinity-depleted and immunodepleted plasma was then used as antigen to raise second-generation antibodies in chickens, using the same immunization schedule as in Example 1.
  • the antibodies raised were evaluated individually and pooled for evaluation of their effects on the removal of proteins from untreated and Affi-gel Blue-treated plasma respectively.
  • the process of antibody preparation is summarised in FIG. 2 .
  • Human serum samples were treated with Affi-gel Blue by the following process for the primary removal of albumin.
  • whole blood (2 ml) was collected by venepuncture into plain collection tubes, in which blood was allowed to clot at room temperature for 30 min and then processed. Samples were then centrifuged at 2000 g for 10 min, after which serum was collected.
  • whole blood was collected in the same way into EDTA anticoagulant tubes. An aliquot (100 ⁇ l) was removed for the determination of total protein. Serum and plasma samples were stored at ⁇ 80° C. until analysed.
  • Samples were thawed at room temperature and incubated with 5 volumes of Affi-gel Blue for 16 h at 4° C. room on a rotary platform. Samples were then centrifuged at 2000 g for 10 min. The supernatant was recovered, an aliquot (100 ⁇ l) was removed for the determination of total protein and 2DE analysis, and the remainder of the sample was incubated with either first or second generation anti-human plasma antibody coupled to Sepharose 4B for 4 h at 4° C. The samples were then centrifuged for 20 min at 2000 g at 4° C. The supernatant was recovered, an aliquot (50 ⁇ l) was removed for determination of total protein, and the remainder stored at ⁇ 80° C. until subjected to 2DE analysis.
  • This mixture was then applied to a Ready Strip (11 cm, pH 4-7, Bio-Rad) and actively rehydrated at 50V and 20° C. for 16 h.
  • Serum proteins were isoelectrically focused at 250V for 15 min and then 8000V for 150 min, and then maintained at 8000V for a total of 35000 Vh/gel, i.e. a total of 42000 Vh per gel.
  • Ready Strips were then stored at ⁇ 80° C. until second dimension processing.
  • Ready Strips from the first dimension separation were equilibrated in 6 ml of equilibration buffer (50 mM Tris-HCl pH 8.8, 6M urea, 30% glycerol, 2% SDS, 0.01% BPB, 5 mM TBP). Strips were rinsed in Tris-glycine SDS running buffer (25 mM Tris, 192 mM glycine, 0.1% w/v SDS, pH 8.3) and then applied to the top of a Ready Gel (10% or 8-16% acrylamide, Criterion Gel; Bio-Rad). Low melting point agarose (0.5% in running buffer containing BPB) was layered on top of the strip.
  • Tris-glycine SDS running buffer 25 mM Tris, 192 mM glycine, 0.1% w/v SDS, pH 8.3
  • FIG. 4 shows a comparison between the number of protein species identifiable by 2DE which can be detected using pooled
  • the process and product of the invention for the preparation of either serum or plasma samples for the display of a low abundance proteome may be used in the form of a sealed Luer-type cartridge suitable for use together with plastic syringes.
  • Anti-human plasma antibody resin 0.5 ml
  • Affi-gel Blue resin or other protein-binding resin, in a 1.5 ml cartridge.
  • a 2.5 ml syringe containing 1 ml of serum is connected to one end of the cartridge, and an empty 2.5 ml syringe is connected to the other end of the cartridge.
  • This device is illustrated in FIG. 6 .
  • the serum sample is refluxed through the cartridge 5 times, and then collected and stored for 2DE analysis.
  • the cartridge and syringe may be provided as a kit.
  • Total protein content was determined using a commercial protein assay kit with BSA standards according to the manufacturer's instruction (Pierce, Rockford, Ill., USA).
  • Serum samples were thawed at room temperature and incubated with 5 volumes of Affi-Gel Blue and incubated for 1 h or 16 h at 4° C. on a rotary platform. Samples were centrifuged at 2000 g for 10 min. The supernatants were recovered and aliquots (100 ⁇ l) were removed for the determination of total protein after correcting for dilution factors.
  • Aurum serum protein mini-kit Bio-Rad Laboratories, USA. This kit utilizes spin columns containing a mixture of Affi-Gel Blue and Affi-Gel Protein A to selectively bind and remove albumin and immunoglobulin.
  • the Aurum matrix Bio-Rad Laboratories, USA
  • a Micro Bio-Spin Column was washed twice with 1 ml of binding buffer (20 mM phosphate buffer, pH 7.0) by centrifugation for 20 sec at 1000 ⁇ g. Sixty ⁇ l of serum was added to 180 ⁇ l of binding buffer and mixed by vortexing. 200 ⁇ l was added to the Aurum matrix.
  • the column was centrifuged for 20 sec at 1000 ⁇ g to collect the eluate.
  • the column was washed with 200 ⁇ l of binding buffer and combined with the first eluate to form the depleted serum sample.
  • the total protein concentration of the combined eluate was determined after taking the dilution factors into account.
  • the eluate was stored at ⁇ 80° C. until further analysis.
  • First Dimension Separation Fifty ⁇ l of neat serum was diluted in sample preparation buffer and was incubated at 95° C. for 5 min. Fifteen ⁇ g of treated serum protein or diluted neat serum protein solubilization buffer was subjected to first-dimension separation as described in Example 6. Ready Strips were then stored at ⁇ 80° C. until second dimension processing. Second Dimension Separation: Ready Strips from the first dimension separation were subjected to second-dimension separation as described for Example 7, except that 10% Tris-HCl Precast Criterion Gels (Bio-Rad Laboratories, USA) were used. The gels were analyzed using PDQuest version 6. The computer program identified protein spots from the digitalized images of the gel. Each serum sample was repeated three times, and variability between the experiments was assessed on three different gels.
  • the serum protein yields obtained using untreated and Affi-Gel Blue or Aurum kit-treated specimens are summarized in Table 2. Both treatment methods removed 96-98% of total serum protein in 16 h, but with equal protein loading ( ⁇ 15 ⁇ g), there was no significant change in the total number of detectable protein spots by 2-DE analysis.
  • FIG. 6 a SYPRO Ruby-stained 2-DE gel of serum samples revealed a typical 2-DE serum profile ( FIG. 6 a ).
  • the albumin smear at around 68 kDa was present in the untreated control sample, but was absent in the 16 h Affi-Gel Blue and Aurum kit treated serum samples ( FIGS. 6 a, b and c ).
  • Affi-Gel Blue treatment resulted in the enhancement of 53 protein spots by 2-fold, 31 by 5-fold, 12 by 10-fold and 6 by 20-fold ( FIG. 7 a ).
  • 16 h Aurum kit treatment resulted in 2, 5, 10 and 20-fold enhancement of 30, 13, 8 and 5 protein spots respectively, as shown in Table 4 and FIG. 7 b .
  • Aurum kit treatment results in a greater depletion of protein, as its Protein A component also removes immunoglobulins.
  • the serum pattern of IgG (heavy chain) is apparent over a pI range of 6.5-8.3. As this range falls in the borderline of the pI range used in this study, a less defined pattern of IgG heavy chain was evident on the gels.
  • Sixteen h treatment with Affi-Gel Blue or the Aurum kit resulted in the removal of proteins other than albumin.
  • Affi-Gel Blue and the Aurum kit bind albumin with high affinity, but other proteins can also bind to the planar ring structure of the Cibracon Blue 3G dye, through a complex combination of electrostatic, hydrophobic and hydrogen bonding interactions.

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US9388243B2 (en) 2013-05-29 2016-07-12 Samsung Electronics Co., Ltd. Method of target membrane protein depletion
CN112485452A (zh) * 2020-12-08 2021-03-12 北京工业大学 金属团簇作为人工抗体定量蛋白丰度的方法
WO2023185840A1 (zh) * 2022-04-01 2023-10-05 清华大学 一种基于质谱检测体液样本里中低丰度蛋白的方法

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US20070048795A1 (en) * 2005-08-26 2007-03-01 Xiangming Fang Immunoaffinity separation and analysis compositions and methods
WO2008058325A1 (en) * 2006-11-13 2008-05-22 Healthlinx Limited Immunoaffinity compositions for immunodepletion of proteins
US20080227112A1 (en) * 2007-03-12 2008-09-18 Genetel Laboratories Llc Global polyclonal antibodies, process for depleting commonly shared proteins by same, devices using same
EP2918641A1 (en) * 2014-03-13 2015-09-16 Basf Se Method for purification of antibodies, antibody fragments or engineered variants thereof using specific anthraquinone dye-ligand structures
SG11201605954SA (en) * 2014-02-04 2016-08-30 Basf Se Method for purification of antibodies, antibody fragments or engineered variants thereof using specific anthraquinone dye-ligand structures
CN114585883A (zh) * 2019-10-01 2022-06-03 瑞普利金公司 流体中蛋白质浓度的测定

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WO2023185840A1 (zh) * 2022-04-01 2023-10-05 清华大学 一种基于质谱检测体液样本里中低丰度蛋白的方法

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