AU2007203524A1 - Depletion of plasma proteins - Google Patents

Description

P/00/011 Regulation 3.2

AUSTRALIA

Patents Act 1990 COMPLETE SPECIFICATION STANDARD PATENT

(ORIGINAL)

Name of Applicant: Royal Women's Hospital of 132 Grattan Street, Carlton, Victoria 3053, Australia RICE, Gregory E; BAKER, Mark S and QUINN, Michael Actual Inventors: Address for Service: DAVIES COLLISON CAVE, Patent Trademark Attorneys, of 1 Nicholson Street, Melbourne, 3000, Victoria, Australia Ph: 03 9254 2777 Fax: 03 9254 2770 Attorney Code: DM Invention Title: Depletion of plasma proteins The following statement is a full description of this invention, including the best method of performing it known to us:- DEPLETION OF PLASMA PROTEINS u This application is a divisional of Australian Application No. 2003520621, the entire contents of which are incorporated herein by reference.

NO 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 In Cc fatty acids, are present together with more abundant O molecules of little or no interest. In particular, 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.

BACKGROUND OF THE INVENTION All references, including any patents or patent applications, cited in this specification are hereby incorporated by reference. No admission is made that any reference constitutes prior art. The discussion of the references states what their authors assert, and the applicants reserve the right to challenge the accuracy and pertinency of the cited documents. It will be clearly understood that, although a number of prior art publications are referred to herein, this reference does not constitute an admission that any of these documents forms part of the common general knowledge in the art, in Australia or in any other country.

Following the successful completion of the complete sequence of the human genome in the Human Genome Project, and corresponding successes with other genomes such as the mouse and the rat, there is an urgent-need in the art to determine the function of the proteins which WO 2004/019009 PCTA U 2003/001075 2 these genomes encode, and to determine how these proteins are expressed during various physiological states and in INC disease.

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 3 time in a given cellular location. Proteomics separates, O 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. 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. In routine diagnostic laboratories, identification of specific low abundant disease-associated proteins in serum relies heavily on time-consuming and expensive radiolabelled or enzymelinked 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 WO 2004/019009 PCT/AU2003/001075 3- 0C candidate biomarker to enhance already available Sdiagnostic or prognostic tests. It has been suggested N 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).

n One primary tool used in proteomic methods for O protein separation and analysis of proteins is twodimensional gel electrophoresis (2DE). Following Sseparation by 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.

Unfortunately, the analysis by 2DE gels of proteins in samples of biological fluids such as serum and plasma is very difficult. This is because of the limited amount of protein able to be resolved by a gel, and the great variation in the concentration of proteins in many samples. This variation in concentration is frequently referred to as "dynamic range". These factors result in data obtained by 2DE from complex samples, such as unfractionated serum and plasma, being dominated by the presence of proteins which are of high abundance in blood, for example human serum albumin, immunoglobulin G (IgG), haptoglobin, fibrinogen, transferrin, 1 ti-antiptrypsin, azmacroglobulin, IgA, and IgM. Of these, six (albumin, IgG, IgA, al-antitrypsin, transferrin and haptoglobin) constitute 85-90% of the protein mass in blood serum.

Proteins with a concentration higher than Img/mL are generally considered to be of high abundance, and such proteins may represent 2-60% of the total protein present.

Thus the application of current proteomic technologies is limited by the presence of high abundance WO 2004/019009 PCT/AU2003/001075 4 C "housekeeping" proteins like albumin and immunoglobulins, Swhich constitute approximately 60-97% of the total serum IND protein (Georgiou et al, 2001). Such proteins hinder the c 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 O obscure proteins with a similar pi and molecular weight.

F Theoretically, by removing albumin and immunoglobulin, Swhich 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.

In particular, the presence of these abundant proteins severely limits the utility of methods used in wide scale analysis of proteins present in complex mixtures of proteins, such as single dimension electrophoresis (IDE), 2DE, multi-dimensional liquid chromatography and MS. These methods are often used in the investigation of low-abundance proteins such as cytokines, signal transduction proteins, hormonal mediators, and cancer biomarkers. The dynamic range problem is illustrated in Figure 1, which 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 of the total protein present in plasma; see the circle in Figure 1. As the total amount of protein which can be loaded on to a gel is limited to less than approximately 120 mg, 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 WO 2004/019009 PCT/AU2003/001075 CI of other types of biological samples, such as urine, tissue extracts, and cell lysates.

ND 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 C plasma before analysis, thus increasing the sensitivity of n the analysis and hence the likelihood of identifying low abundance protein biological markers. In particular, 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.

SUMMARY OF THE INVENTION We have now surprisingly found that a simple immuno-affinity procedure, combined with the use of existing solid phase affinity capture supports, can be used to rapidly remove high abundance proteins from biological samples, giving a dramatic improvement in the separation of low-abundance proteins by 2DE.

It is to be clearly understood that while the invention is specifically illustrated with reference to proteins, a similar procedure may be used to separate any low-abundance molecule from a complex sample. In addition to low-abundance proteins, the procedure may also be used to separate low-abundance polysaccharides or fatty acids from a complex sample.

In a first aspect,. the invention provides a method of depleting a high-abundance protein molecule from a biological sample, comprising the steps of a) subjecting the sample to affinity depletion using an affinity support with high affinity for a high abundance molecule, and/or b) immunodepletion using an affinity support coupled to an antibody directed against whole or previously fractionated plasma or serum, in which the antibody binds to a high abundance WO 200}4/019009 PCT/AU2003/001075 -6 molecule.

Preferably the sample is subjected to both ND affinity depletion and immunodepletion. While it is possible to perform the steps in either order, we have found that by performing step before step much C less antibody is required for substantially complete removal of high abundance molecules. Therefore this order O is preferred.

Preferably the high abundance molecule is a protein. Even more preferably, the protein is albumin.

Preferably the antibody is an avian antibody.

Preferably the biological sample is a biological fluid, such as serum, plasma, lymph, cerebrospinal fluid, amniotic fluid, cervicovaginal fluid, uterine fluid, or seminal fluid. Alternatively 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.

Preferably 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.

In other words, 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 may be any such support which is known to have a high affinity for albumins, immunoglobulins or other highly abundant proteins. Typically the support will be a dye affinity WO 2004/019009 PCT/AU2003/001075 7-

O

O

c 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). Other dye-ligands which could also alternatively be employed to remove abundant blood proteins include Procion Red HE3B, Reactive Blue MRB, SReactive Green H4G, Reactive Green HE4BD, Reactive Green HE4BD, Reactive Yellow M8G, and Reactive Brown M4R, all of Swhich 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 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.

Similarly, any solid-phase support which can be coupled to an immunoglobulin to form an affinity support may be used in step 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 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.

WO 2004/019009 PCT/AU2003/001075 8- CI Most preferably the avian antibody is a chicken antibody.

In one embodiment the antibody is chicken IgY. The high- ,0 abundance molecule may be conjugated to a carrier protein c' if necessary in order to increase immunogenicity.

More preferably the antibody is a second generation polyclonal antibody raised against plasma or n serum which has already been subjected to at least one O 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 US patents No. 5367054, No. 5420253, No. 4550019 and No. 4056737.

It is also to be clearly understood that the procedure may be performed prior to any separation technology. Suitable separation technologies include, but are not limited to, one-dimensional gel electrophoresis (IDE), 2DE, capillary electrophoresis, mass spectrometry, high-pressure liquid chromatography (HPLC), gaschromatography, liquid chromatography multidimensional LC, or LC/MS.

Thus in a second aspect, 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. The separation methods described above are preferred.

In a third aspect, 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. Preferably the antibody is an avian polyclonal antibody, more preferably a second generation avian polyclonal antibody, and the high WO 2004/019009 PCT/AU2003/001075 9 abundance molecules are those present in serum or plasma.

Even more preferably the avian antibody is from chicken, IND and the serum or plasma molecules are serum or plasma *proteins. In one embodiment the antibody is chicken IgY.

As in step of the first aspect of the C3 invention, the support may be any solid-phase support Swhich may be coupled to immunoglobulin to form an affinity support. Many suitable supports are known in the art, such as Sepharose and the like, as described above.

In a fourth aspect, 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.

Preferably 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.

The term "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. In use, 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.

In one embodiment the receptacles are hypodermic syringes and the chamber is a Luer-type cartridge. More preferably both the chamber and the receptacles are made WO 2004/019009 PCT/AU2003/001075 Cl of plastics. In a second embodiment the chamber is Zadapted to be coupled directly to a separation or nO analytical apparatus such as an HPLC or LC column, or a I mass spectrometry. For example, a Sep-Pale type cartridge would be suitable.

In a fifth aspect, the invention provides a kit Itt 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; and b) a second affinity support coupled to an antibody directed against whole or previously fractionated serum or plasma, in which the antibody binds to a high abundance molecule.

Preferably the antibody is an avian antibody, and is directed against the whole serum or whole plasma, or against high abundance serum or plasma proteins.

Preferably 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.

In both the fourth and the fifth aspects of the invention the affinity supports are as described for the first aspect.

BRIEF DESCRIPTION OF THE FIGURES Figure 1 shows the results of 2DE of a sample of human plasma. The circle indicates spots representing albumin.

Figure 2A is a schematic illustration of the process for production of first and second generation polyclonal antibodies in chickens.

Figure 2B is a schematic illustration of the processes for affinity and immunodepletion of proteins from human plasma.

WO 2004/019009 PCT/AU2003/001075 t 11 c Figure 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.

c Figure 4 shows the results of 2DE of a sample of O human plasma subjected to 4-7 IPG isoelectric focusing and acrylamide SDS-PAGE (Criterion gel Bio-Rad), and Svisualized by SYPRO Ruby®. Figure 4A is a display of proteins present in unfractionated human plasma. Figure 4B is a display of proteins present after treatment of human plasma with Affi-gel Blue. Figure 4C is a display of proteins present after treatment of human plasma with Affi-gel blue and then anti-human plasma (AHP)-Sepharose 4B.

Figure 5 is a schematic representation of a cartridge device according to the invention for rapid processing of samples of biological fluids.

Figure 6 is a 2-DE profile of Untreated serum, Affi-Gel Blue and 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 Lg of protein was loaded on each gel. Results are representative of three independent experiments.

Figure 7 is a depiction of the reference profile of all protein spots identified by 2-DE. Protein spots enhanced by 5-fold after Affi-Gel Blue treatment (in green) and enhanced by 5-fold after Aurum kit treatment (in green).

Figure 8 is a depiction of the reference profile of all protein spots identified by 2-DE. Profile of proteins unique to Affi-Gel Blue treatment compared to untreated serum (in red), Profile of proteins unique to Aurum kit treatment compared to untreated serum (in red). Results are representative of three independent experiments.

WO 2004/019009 PCT/AU2003/001075 -12 I Figure 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. (b) Serum sample was treated with Affi-Gel Blue for 0 min 3 (untreated serum), 1 h and 16 h. 15 gg of protein was I loaded on each gel.

c, DETAILED DESCRIPTION OF THE INVENTION It is to be clearly understood that this invention is not limited to the particular materials and methods described herein, as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and it is not intended to limit the scope of the present invention, which will be limited only by the appended claims.

As used herein, the singular forms and "the" include the corresponding plural reference unless .the context clearly dictates otherwise. Thus, for example, a reference to "a protein" includes a plurality of such proteins, and a reference to "a molecule" is a reference to one or more molecules. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.

Although any materials and methods similar or equivalent to those described herein can be used to practice or test the present invention, the preferred materials and methods are now described.

In the claims which follow and in the preceding description of the invention, except where the context requires otherwise due to express language or necessary implication, the word "comprise" or variations such as "comprises" or "comprising" is used in an inclusive sense, i.e. to specify the presence of the stated features but not to preclude the presence or addition of further WO 2004/019009 PCT/AU2003/001075 13 features in various embodiments of the invention.

For the purposes of this specification, the term \O "Affinity depletion" means the removal of components from a complex mixture based upon chemical or immunological characteristics by specific agents.

The term "Affinity support" refers to a matrix or support to which specific agents are bound or coupled and Swhich is used to deplete components from a complex 1 mixture.

S"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. In general 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.

The terms "high abundance protein", "high abundance molecule", or "highly abundant protein" refer to a protein which is present at a concentration greater than Img/ml in a biological sample.

Abbreviations used herein are as follows AHP anti-human plasma antibody BPB bromophenol blue CHAPS 3-[(3-cholamidopropyl)-dimethylamino]-2hydroxyl-1-propane DTT dithiothreitol EDTA ethylene diamine tetraacetic acid IgY immunoglobulin Y WO 2004/019009 PCT/AU2003/001075 1" 14 C PEG polyethyleneglycol TBP tributylphosphine 0 2DE two-dimensional electrophoresis In a preferred embodiment of the invention, we have found that depletion of albumin using a Cibacron n Blue-based affinity support greatly reduces the number of Sprotein spots detectable by SYPRO Ruby® staining of 2DE gels. Using this step in conjunction with a second step Sof 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.

The avian equivalent of IgG, usually referred to as IgY, is significantly different in its chemical and physical properties from IgG. In particular, in addition to having different amino acid composition and sequence, 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.

Under certain conditions 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 NaC1 (low salt conditions), and is dimeric in 1.5 M NaC1 (high salt conditions), while IgG is monomeric at both low and high salt conditions. The properties of IgY are described in detail in US Patent No. 4550019. 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). Specific antibodies produced in chickens offer several important WO 2004/019009 PCT/AU2003/001075 15 C advantages over producing antibodies in other mammals, such as those mentioned above.

\NO Due to the phylogenetic distance between birds C and mammals, there is greater probability of producing a higher percentage of specific antibody against mammalian 1 antigens by immunizing chickens than by immunizing other r animals. Highly conserved mammalian proteins sometimes Sfail to elicit a humoral immune response in animals, such r- as rabbits, which are traditionally used for generating Spolyclonal antibody. Since chicken IgY does not crossreact with mammalian IgG, and does not bind bacterial or mammalian Fc receptors, non-specific binding is reduced, and the need for cross-species immunoabsorptions is also eliminated.

Two affinity supports were used in the prefractionation of serum or plasma prior to 2DE and the consequent display of the low abundance proteome. Affigel 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, az-macroglobulin, coagulation factors, and nucleic acidbinding proteins. Thus it depletes not only albumin but also a 2 -macroglobulin and coagulation factors from plasma.

A variety of ligands based on synthetic dyes, such as triazine or triphenylmethane compounds, are used in a technique known as "dye-ligand affinity chromatography".

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). Although these compounds are all synthetic rather than naturally-occurring, they are classified as affinity WO 2004/019009 PCT/AU2003/001075 1- 16 CI 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 C agents. For example, Cibacron Blue F3G-A consists of a chlorotriazine ring which has several substituents, one of which is an anthraquinone which interacts with enzymes Swhich have a binding site for NAD+, NADP+, or ATP.

0 These dye ligands can be produced in large quantities and demonstrate a high degree of selectivity Sand reproducibility. These properties have made them useful for the large-scale purification of dehydrogenases, kinases, albumin, a-fetoprotein, CoA-dependent enzymes, hydrolases, IgG, lipoproteins, nucleases, polymerases, synthetases, and transferases (Hage, 1998; Hermanson et al, 1992; Jones, 1991; Scawen, 1991).

The invention will now be described in detail by way of reference only to the following non-limiting examples and drawings.

Example 1 Production of Polyclonal Antibodies to Human Plasma First generation polyclonal antibodies to human plasma were produced in female chickens. The procedure is summarised in Figure 2. Chickens (14 week old White Leghorn Rhode Island Red cross) were immunised according to the recommendations of the 21 st European Centre for the Validation of Alternative Methods (ECVAM) workshop, using 1 mg plasma proteins/bird (12.5 gl of 80 mg/ml) suspended in saline (87.5 pl)/Freund's Incomplete Adjuvant (100 gi).

100 .1 of total plasma proteins were injected subcutaneously over the pectoralis major muscle, using a needle at four sites 50 p. per site).

Birds received three booster injections as described above, 4, 8 and 12 weeks later. Eggs were collected prior to immunization and the yolks stored at 0 C. Eggs were collected daily during the immunization schedule, up to 30 days after the last booster injection WO 2004/019009 PCT/AU2003/001075 17

O

C and the yolks extracted as described in Example 2.

Example 2 Extraction of IgY Egg yolks (10 per batch) were separated and then suspended in 2 volumes of 100 mM phosphate buffer (pH7.6) in a glass beaker. An equal volume of chloroform was n added and then stirred for 5 min at room temperature. The Sresultant emulsion was then transferred to 100 ml glass centrifuge tubes and centrifuged at 2000 g for 1 h at 4 0

C.

SThe supernatant was collected and its volume determined.

PEG 6000 (Sigma Chemical Company, St Louis, USA) was dissolved in the supernatant to final concentration of 12% w/v, incubated for 10min at room temperature and then centrifuged at 2000g for lh at 4 0 C. The supernatant was discarded and the pellet resuspended in 100 mM phosphate buffer pH7.6 (1/6 original yolk volume) and stored at -20 0

C

as 1 ml aliquots.

Egg yolks were collected for four weeks following the final immunization, pooled and extracted as described above.

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.

Example 3 Coupling of IgY to Sepharose 4B PEG 6000 was dissolved in 2ml IgY solution (17.3mg protein/ml), incubated for 10 min at room temperature and then centrifuged at 2000g for lh. The pellet was resuspended in coupling buffer (0.1M NaHCO 3 pH 8.3, containing 0.5M NaC1) to a final concentration of mg protein/ml.

CNBr-activated Sepharose 4B (Pharmacia; 1 g) was suspended in 20 ml of 1 mM HC1. The suspension was then washed with 200 ml ImM HC1 on a sintered glass filter.

The washed gel was resuspended in the IgY solution, and mixed on a rotary mixer for 18h at 4 0 C. The gel was then WO 2004/019009 PCT/AU2003/001075 18 C washed with 5 volumes of coupling buffer and incubated in 0.1M Tris-HCl buffer, pH8.0 for 2h at 4 0 C. The gel was IND washed 3 times alternately with 5 volumes 0.1M acetate buffer pH 4.0 containing 0.5M NaC1, and then 0.1M Tris HC1 pH 8.0 containing 0.5M NaCl. The anti-human plasma i antibody-Sepharose 4B (AHP-Sepharose) gel was then stored n at 4 0 C in 0.01 M phosphate-buffered saline, pH7.4, containing 0.05% sodium azide as a preservative.

Example 4 Preparation Of Affinity-depleted and Immunodepleted Plasma Plasma from normal human males was subjected to affinity depletion using Affi-gel Blue and immunodepletion using AHP-Sepharose. Affi-gel Blue (5ml gel suspension per ml of plasma) was suspended in sealed polypropylene columns -(Econo-Columns; Bio-Rad) and eluted with 2 volumes of 20mM phosphate buffer (pH7.1). Plasma (500 gl) was mixed with an equal volume of 20 mM phosphate buffer (pH7.1) and mixed on a rotary mixer for 4h 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 18h at 4 0 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 0 C for subsequent analysis.

The residual Affi-gel Blue-treated plasma was then subjected to AHP-Sepharose immunodepletion as follows. AHP-Sepharose (100 gl) was washed with 4 volumes of 100mM phosphate buffer (pH7.1) using a sintered glass filter. The washed gel was resuspended in Affi-gel Bluetreated plasma (100 il) in a 2ml microcentrifuge tube, and mixed on a rotary mixer for 18h at 4 0 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 0 C for subsequent analysis.

Affinity-depleted and immunodepleted plasma was WO 2004/019009 PCT/AU2003/001075 19 CI 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 CI individually and pooled for evaluation of their effects on the removal of proteins from untreated and Affi-gel Bluetreated plasma respectively. The process of antibody VB preparation is summarised in Figure 2.

Cq Example 5 Removal of High Abundance Proteins from Human Serum Samples Human serum samples were treated with Affi-gel Blue by the following process for the primary removal of albumin. For serum samples, whole blood (2ml) was collected by venepuncture into plain collection tubes, in which blood was allowed to clot at room temperature for min and then processed. Samples were then centrifuged at 2000g for 10 min, after which serum was collected. For plasma samples, whole blood was collected in the same way into EDTA anticoagulant tubes. An aliquot (100 jl) was removed for the determination of total protein. Serum and plasma samples were stored at -80 0 C until analysed.

Samples were thawed at room temperature and incubated with 5 volumes of Affi-gel Blue for 16h at 4 0

C

room on a rotary platform. Samples were then centrifuged at 2000g for 10 min. The supernatant was recovered, an aliquot (100 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 4h at 4 0 C. The samples were then centrifuged for min at 2000g at 4 0 C. The supernatant was recovered, an aliquot (50 was removed for determination of total protein, and the remainder stored at -80 0 C until subjected to 2DE analysis.

WO 2004/019009 PCT/AU2003/001075 17- 20 Example 6 Two-Dimensional Electrophoresis First Dimension Separation Cl 2 4. serum diluted in 48 4i of sample preparation buffer (62.5 mM Tris *HC1, 2% SDS, 25% glycerol, 0.01% bromophenol blue and 2.3 DTT, pH and incubated at

I

r 95 0 C for 5 min. 15 pg gl) of serum protein was mixed 0 with solubilization buffer for isoelectric focusing (7M O. urea, 2M thiourea, 100 mM DTT, 4% CHAPS, 0.5% carrier Sampholytes pH4-7, 0.01% BPB and 40mM Tris) to a final volume of 200 ll and incubated for lh at room temperature.

This mixture was then applied to a Ready Strip (11 cm, pH 4-7, Bio-Rad) and actively rehydrated at 50V and 20 0 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 35000Vh/gel, i.e. a total of 42000 Vh per gel. Ready Strips were then stored at -80 0 C until second dimension processing.

Second Dimension Separation Ready Strips from the first dimension separation were equilibrated in 6 ml of equilibration buffer (50 mM Tris-HC1 pH 8.8, 6M urea, 30% glycerol, 2% SDS, 0.01% BPB, 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 in running buffer containing BPB) was layered on top of the strip. Two wicks to which molecular weight markers were applied were inserted into the agarose. Gels were electrophoresed at 10mA/gel for lhr, for 2h and then at 30mA/gel for 30 min. Gels were fixed in methanol/acetic acid (40%/10% in deionised MilliQ water for lh at room temperature and then incubated in Sypro Ruby@ (Bio-Rad) for 16h at room temperature on a rocking platform. Gels were destained for 1 h in methanol/acetic acid in dH 2 The gels were WO 2004/019009 PCT/AU2003/001075 21 C< imaged using a Bio-Rad FX imager at 100 nM resolution.

SFigure 4 shows a comparison between the number of O protein species identifiable by 2DE which can be detected using pooled a) first and second round anti-human plasma chicken antiserum in control, untreated human v plasma, Sb) plasma subjected to plasma subjected to affinity depletion and immunodepletion using first generation polyclonal antibody, and c) plasma subjected to affinity depletion and immunodepletion using second generation polyclonal antibody.

The analysis of the protein spots in Figure 4 is summarised in Table 1. This shows that the method of this invention leads to the removal of the majority of the protein spots present in undiluted, untreated control plasma (neat plasma), while revealing a very high proportion of previously undetected proteins.

WO 2004/019009 PCT/AU2003/001075 22 TABLE 1 Comparison of protein spots identified by image analysis of 2DE display of untreated serum (neat), serum treated with Affi-gel blue (AGB) and serum treated with AHP- Sepharose.

neat AGB AHP PROTEIN SPOT OPRISION (untreated) Treated Sepharose COMPARISIONTreated Treated Total number of protein spots 248 152 157 displayed Number of spots common to both neat and post- NA 127 130 treatment protein displays Number of spots identified only after NA 25 27 treatment Number of protein spots increased by fold or greater NA 9 9 following treatment compared to neat Number of protein spots decreased by fold or greater NA 28 16 following treatment compared to neat Spot unique to specific treatment NA 14 (AGB vs AHP) Number of protein spots that were 2- NA 12 fold greater in AGB than AHP Sepharose Number of protein spots that were 2- NA fold less in AGB than AHP Sepharose NA not applicable WO 2004/019009 PCT/AU2003/001075 1^ 23- Example 7 Device for Rapid Sample Processing \D 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 C form of a sealed Luer-type cartridge suitable for use together with plastic syringes. Anti-human plasma Santibody resin (0.5ml) is sandwiched between two bands l (0.5ml each) of Affi-gel Blue resin, or other protein- Sbinding resin, in a 1.5 ml cartridge. A 2.5ml syringe containing lml 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 Figure 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.

Example 8 Comparison of Depletion with Affi-Gel Blue or Protein A Samples of normal human serum were subjected to affinity depletion with either Affi-Gel Blue or Affigel- Protein A plus Affi-Gel Blue prior to 2DE analysis.

Human blood was collected from healthy volunteers at the Royal Women's Hospital, Melbourne, after the provision of a participant information statement and with informed consent. Whole blood (10 ml) was collected by venepuncture into plain collection tubes for serum (blood was allowed to clot at room temperature for 30 min).

Samples were centrifuged at 2000g for 10 min after which serum was collected. An aliquot (100 pl) was removed for the determination of total protein. Serum was stored at 0 C until analyzed.

Total protein content was determined using a commercial protein assay kit with BSA standards according to the manufacturer's instruction (Pierce, Rockford, IL,

USA).

WO 2004/019009 PCT/AU2003/001075 24

O

C Serum samples were thawed at room temperature and Z incubated with 5 volumes of Affi-Gel Blue and incubated 0 for 1 h or 16 h at 4 0 C on a rotary platform. Samples were centrifuged at 2000 g for 10 min. The supernatants were recovered and aliquots (100 gl) were removed for the determination of total protein after correcting for dilution factors.

Affi-Gel Blue plus Affi-Gel Protein A SHuman serum samples were treated with the components of the 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) in 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 x g. Sixty i1 of serum was added to 180 R1 of binding buffer and mixed by vortexing. 200 4l was added to the Aurum matrix.

Following incubation at room temperature for 15 min, 1 h, h, or 16 h the column was centrifuged for 20 sec at 1000 x g to collect the eluate. The column was washed with 200 il 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.

2 Dimensional Electrophoresis First Dimension Separation: Fifty 1l of neat serum was diluted in sample preparation buffer and was incubated at 0 C for 5 min. Fifteen jig 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 0 C until second dimension processing.

WO 2004/019009 PCT/AU2003/001075 25

O

(N

SSecond Dimension Separation: Ready Strips from the first \NO dimension separation were subjected to second-dimension c separation as described for Example 7, except that Tris-HCl Precast Criterion Gels (Bio-Rad Laboratories, USA) were used. The gels were analyzed using PDQuest V' version 6. The computer program identified protein spots Sfrom the digitalized images of the gel. Each serum sample l was repeated three times, and variability between the Sexperiments 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 there was no significant change in the total number of detectable protein spots by 2-DE analysis.

WO 2004/019009 PCT/AU2003/001075 26 TABLE 2 Serum protein concentration and the number of protein spots obtained before and after treatment with Affi-Gel Blue or Aurum kit Treatment Total protein (mg/ml) Total Number of Spots Gel 1 Gel 2 Gel 3 Gel 1 Gel 2 Gel 3 Untreated 58.9 60.6 70.9 163 174 190 Mean 63.46±3.8 175±7 Affi-Gel 2.05 2.26 2.7 210 222 232 Blue Mean 2.34±0.33 220±5 Aurum kit 0.8 0.83 1.26 142 151 160 Mean 0.96±0.26 151±5 Values are mean different days.

SEM of three different gels run on three As shown in Figure 6, a SYPRO Ruby-stained 2-DE gel of serum samples revealed a typical 2-DE serum profile (Figure 6a). 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 (Figures 6a, b and c).

Removal of albumin resulted in a significant enhancement in the staining intensity of several protein spots, as summarized in Table 3 and illustrated in Figures 7a and 7b.

WO 2004/019009 PCT/AU2003/001075 27 TABLE 3 Increased protein spot counts in Affi-Gel Blue treated serum as compared to untreated serum.

Spots Increased Number of Spot Counts Two-fold 53 6 Five-fold 31 Ten-fold 12 3 Twenty-fold 6 1 Values are mean SEM of six different serum samples.

Affi-Gel Blue treatment resulted in the enhancement of 53 protein spots by 2-fold, 31 by 12 by 10-fold and 6 by 20-fold (Figure 7a). In parallel, 16 h Aurum kit treatment resulted in 2, 5, 10 and enhancement of 30, 13, 8 and 5 protein spots respectively, as shown in Table 4 and Figure 7b.

WO 2004/019009 PCT/AU2003/001075 28 TABLE 4 Increased protein spot counts in Aurum kit treated serum as compared to untreated serum Spots Increased Number of Spot Counts Two-fold 30 6 Five-fold 13 4 Ten-fold 8 4 Twenty-fold 5± 2 Values are mean SEM of six different serum samples.

The pattern of enhanced visualization of protein spots with both treatment methods was similar, but more protein spots were revealed following Affi-Gel Blue treatment.

Further analysis showed that 28 protein spots were found only after Affi-Gel Blue treatment, and were not visualized in untreated serum (Figure 8a). In contrast, only 2 protein spots were found after Aurum kit treatment, consistent with the loss of more protein with this treatment method (Figure 8b) These results suggest that Affi-Gel Blue or Aurum kit treatment of human serum results in the removal of high abundant proteins such as albumin, thereby not only increasing the detection of low abundance proteins, but also allowing the detection of some otherwise undetectable proteins, which in the presence of albumin would have remained obscured.

Individual variations in the protein profile of the same serum samples prepared on three different days WO 2004/019009 PCT/AU2003/001075 29 Cl and repeated three times were investigated to eliminate confounding factors which might arise from sample .O handling. No substantial variation in the profile of C l protein spots from the same sample repeated on different days was detected (Table 2).

I

n Example 9 Time Course of Albumin Removal STo determine if the removal of albumin by Affi- Gel Blue or the Aurum kit removes protein spots other than albumin with increasing time, a time course study was performed. Human serum samples were treated with Affi-Gel Blue for 1 and 16 h and with Aurum kit for 15 min, Ih, 5 h and 16 h respectively. 15 gg of these samples was analyzed after resolving by 2-DE. Within 15 min of Aurum kit treatment there was a 98% loss of total serum protein, with an accompanying decrease in albumin staining and a two-fold increase in the number of protein spots. Within 1 h of Affi-Gel Blue or Aurum kit treatment, significant depletion of albumin was achieved, with no significant loss of protein profile or number of protein spots.

However, treatment with Affi-Gel Blue or Aurum kit for 16 h resulted in the depletion of albumin, with an approximately 35% loss of total number of protein spots compared to 1 h treatment. These results are summarised in Tables 5 and 6, and illustrated in Figure 9.

WO 2004/019009 PCT/AU2003/001075 30 TABLE Time course of serum protein concentration and number of protein spots following Aurum kit treatment Treatment Protein Reduction in Number of Concentration Protein Spots (mg/ml) Concentration Untreated 62.3 0 174 min 1.45 98 365 1 h 1.02 99 337 h 1.02 99 287 16 h 0.92 99 221 TABLE 6 Time course of serum protein concentration and number of protein spots following Affi-Gel Blue treatment Treatment Protein Reduction Number of Concentrati in Protein Spots on (mg/ml) Concentrati on Untreated 62.3 0 174 1 h 2.65 96 330 16 h 2.20 96 220 These observations suggest that although 16 h exposure of human serum to Affi-Gel Blue or Aurum kit can result in significant depletion of albumin and consequent enhancement of several low-abundance proteins, it is also WO 2004/019009 PCT/AU2003/001075 31 CI associated with non-specific removal of serum protein other than albumin.

Our results demonstrate that Affi-Gel Blue and '1 Aurum kit treatment results in the removal of highly abundant albumin, and simultaneous enhancement in the detection of several other proteins. Within 16 h both Streatment methods removed 96-98% of total protein content of the serum, but there were no significant differences in the total number of protein spots analyzed after 2-DE analysis. We have also shown that Affi-Gel Blue and Aurum kit treatment removes high abundant albumin and enhances the staining intensity of different spots by several-fold.

In addition, with equal protein loading, 28 and 2 unique spots respectively were detected by Affi-Gel Blue and Aurum kit treatment compared to neat serum. These spots remained obscured in the neat untreated serum samples.

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. Hence nonspecific removal of protein other than albumin after 16 h of treatment with Affi-Gel Blue or the Aurum kit is not surprising. However, by using this protein depletion step for only 1 h, significant depletion of albumin can be achieved with minimal non-specific protein removal. While both Affi-Gel Blue and the Aurum kit are effective reagents for the depletion of highly abundant albumin, greater sensitivity in protein profiling without any WO 2004/019009) PCT/AU2003/001075 32 C significant loss of potential serum biomarker can be achieved only if the samples are exposed to the reagents \D for a period of I h. This approach can generate a pattern of protein profiles independent of the identity of individual proteins, and can be used as a discriminator of ,i a particular disease state.

It will be evident that a protein A absorption O step using the Aurum kit or another protein A affinity support can be combined with the immunodepletion step described herein, as an alternative to Affi-Gel blue.

Our data suggest that by using the method of the invention for sample processing before 2-DE or other methods of protein analysis, one can increase the likelihood of discovery of novel biomarkers of high sensitivity and specificity.

It will be apparent to the person skilled in the art that while the invention has been described in some detail for the purposes of clarity and understanding, various modifications and alterations to the embodiments and methods described herein may be made without departing from the scope of the inventive concept disclosed in this specification.

WO 2004/019009 PCT/AU2003/001075 33

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I REFERENCES O Daly M.B. and Ozols Cancer Cell, 2002, 1, 111-112.

Georgiou Rice and Baker Proteomics, 2001, 1, 1503-1506.

In 0 Hage (1998a) Affinity chromatography. In Katz E l Eksteen R Shoenmakers P Miller N eds. Handbook of HPLC S1998:483-498 (Marcel Dekker, New York.

Hage (1998b) A survey of recent advances in analytical applications of immunoaffinity chromatography.

J Chromatogr 1998;715:3-28.

Hage, D.S. Clinical Chemistry 1999;45:593-615 Hermanson G.T, Mallia A.K, Smith Immobilized affinity ligand techniques. New York: Academic Press, 1992:454 pp..

Jones A review of biotechnology and large scale affinity chromatography. Chromatographia 1991;32:469-480.

Larsson High-performance liquid affinity chromatography. Methods Enzymol 1987;104:212-223.

Scawen MD., Dye affinity chromatography. Anal Proc 1991;28:143-144.

Claims (42)

1. A method of depleting a high-abundance mlecule from a biological sample, comprising the steps of: CI a) subjecting the sample to affinity d pletion Susing an affinity support with high affinity for t e high abundance molecule; and b) immunodepletion using an affinity s pport coupled to an avian antibody directed against the igh- Cr abundance molecule.

2. A method according to claim 1, in which the antibody is a chicken antibody.

3. A method according to claim 1 or claim 21 in which the antibody is chicken IgY.

4. A method according to any one of claims to 3, in which the avian antibody used in step is a irst generation polyclonal antibody raised against whol4 serum or plasma, or against any fraction thereof.

5. A method according to any one of claims to 3, in which the avian antibody used in step is a second or higher generation polyclonal antibody raised ag inst plasma or serum which has already been subjected tc at least one round of affinity depletion and immunode etion with an affinity support coupled to IgY directed a-ainst homologous plasma or serum.

6. A method according to any one of claims 1 to in which step is performed before step

7. A method according to any one of claims 1 to 6, in which the high abundance molecule is a protein.

8. A method according to any one of claims 1 to 7, in which the protein is albumin or immunoglobulin.

9. A method according to any one of claims 1 to 8, in which the biological sample is a biological fluii.

10. A method according to any one of claims 1 to 8, in which the biological sample is conditioned medium from a cell or tissue culture, or is a tissue or cell extract. li\JMalck\Keep\peoi\P1391. AJinded Claimdo 323/11/04 AMENDED SHEET IPEA/AU PCT/AU2003/001075 ceived 23 November 2004

11. A method according to any one of claims 1 to i in which the affinity support used in step is a dye IN* affinity chromatography resin.

12. A method according to claim 11, in which the dye is a chlorotriazine compound.

13. A method according to claim 12, in which the Saffinity support is a Cibacron blue F3GA affinity support.

14. A method according to any one of claims 1 to C in which the affinity support used in step is a magnetic bead and the magnetic separation is effected by magnetic means.

A method of separation or analysis of a Low abundance molecule in a biological sample, comprising the step of depleting at least one high abundance mole ule from the sample by a method according to any one o claims 1 to 14, prior to subjecting the sample to one or ore separation or analytical steps for the separation or analysis of the low abundance molecule.

16. A method of identifying the expression of a low abundance molecule in a mammal, comprising the ste of depleting at least one high abundance molecule fro a biological sample from the mammal by a method acco ding to any one of claims 1 to 14, prior to subjecting the sample one or more analytical steps to detect the expression of the low abundance molecule.

17. A method according to claim 16, detects wiich a change in the expression of the low abundance molecule.

18. A composition for immunodepletion of a hi h abundance molecule from a biological sample, comprising an avian antibody preparation directed against the higi abundance molecule, coupled to an affinity support.

19. A composition according to claim 18, in which the avian antibody is a chicken antibody.

A composition according to claim 18 or 19 in which the avian antibody is chicken IgY.

21. A composition according to any one of cla ms 18 to 20, in which the avian antibody is a first generation H.\JMcIscl\Ke«p\Vpo.i\Pi h3. Amonded claime.doc 2/1/c4 AMENDED SHEET IPEA/AU PCT/AU2003/001075 Received 23 November 2004 -36 polyclonal antibody.

22. A composition according to claim 21, in which the IN antibody is a second or higher generation polyclo al Santibody.

23. A composition according to any one of claims 18 to 22, in which the high abundance molecule is one present I/ in serum or plasma.

24. A composition according to claim 23, in which the (C high abundance molecule is albumin or immunoglobulin.

25. A device for the rapid processing of biological Ssamples, comprising a chamber having two openings, in which a) each opening is adapted to fit seal ngly to a receptacle, b) the sample can be transferred from ne receptacle to the other via the chamber, and c) the chamber has transversely disposed within it an affinity support having high affinity for a high abundance molecule and an affinity support compled to one or more avian antibodies directed against the ligh abundance molecule.

26. A device according to claims 25, in which the antibody is a chicken antibody.

27. A device according to claim 26, in which the antibody is chicken IgY.

28. A device according to any one of claims 2 to 27, in which the antibody is a first generation avian polyclonal antibody.

29. A device according to any one of claims 25 to 27, in which the antibody is a second generation avian polyclonal antibody.

A device according to any one of claims 2 to 29, in which the high abundance molecule is one present in serum or plasma.

31. A device according to claim 30, in which he high abundance molecule is albumin or immunoglobulin.

32. A device according to any one of claims 2 to 31, a.\JMclc&b\terp\6peVl\FPP291 Aaendd olai=,sd 22/11/04 AMENDED SHEET IpEA/AU PCT/AU2003/001075 Recejved 23 November 2004 '4 1, 37 in which the receptacles are hypodermic syringes. r chamber is a Luer-type cartridge.

33. A device according to any one of claims 2 in which the chamber is adapted to couple directl separation or analytical apparatus.

34. -A kit for depletion of a high-abundance from a biological sample, comprising: a) a first affinity support with high for the high-abundance molecule; and b) a second affinity support coupled t avian antibody directed against the high-abundance molecule.

A kit according to claim 34, in which th antibody is a chicken antibody.

36. A kit according to claim 35, in which th antibody is chicken IgY.

37. A kit according to any one of claims 34 t which the antibody is a first generation avian poly antibody.

38. A kit according to any one of claims 34 which the antibody is a second generation avian po antibody.

39. A kit according to any one of claims 34 t which the high abundance molecule is one present ir or plasma.

A kit according to claim 39, in which the abundance molecule is albumin or immunoglobulin.

41. A kit according to any one of claims 34 t comprising a device according any one of claims 25

42. A kit according to any one of claims 34 t comprising a diluent suitable for use with biologic fluids. .\JNolach\Xeap\Bp Ci\P91 m21 Aended aLaiwm.d id the 5 to 32, to a olecule iffinity an o 36, in clonal o 36, in yclonal o 38, in serum high o to 33. 41, 22/11/04 ti AMENDED sHtu Irna U