US20150010914A1 - Biomarkers for gastric cancer and uses thereof - Google Patents

Biomarkers for gastric cancer and uses thereof Download PDF

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US20150010914A1
US20150010914A1 US14/373,332 US201314373332A US2015010914A1 US 20150010914 A1 US20150010914 A1 US 20150010914A1 US 201314373332 A US201314373332 A US 201314373332A US 2015010914 A1 US2015010914 A1 US 2015010914A1
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expression level
biomarker
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Peter Hoffmann
Megan Penno
Matthias Robert Walter Ernst
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Adelaide Research and Innovation Pty Ltd
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    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
    • G01N33/57488—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites involving compounds identifable in body fluids
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    • G01N2333/575—Hormones
    • G01N2333/65—Insulin-like growth factors (Somatomedins), e.g. IGF-1, IGF-2
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    • G01N2800/60—Complex ways of combining multiple protein biomarkers for diagnosis

Definitions

  • the present invention relates to the identification of biological markers associated with gastric cancer. Specifically, an association between gastric cancer and the differential expression of a number of proteins has been identified.
  • the biological markers can be utilised for a range of purposes including methods for the diagnosis of gastric cancer, methods for identifying individuals susceptible to gastric cancer, and methods for assessing progression of gastric cancer.
  • GC Gastric cancer
  • Japan has one of the world's highest rates of GC.
  • the implementation of a mass screening program of asymptomatic individuals by gastric photofluorography in Japan has increased the number of GC cases detected at the early-stage, improving the overall 5-year survival rate to more than 50%.
  • the sensitivity and specificity of gastric photofluorography are good at 70-90% and 80-90%, respectively.
  • cost-effectiveness studies have indicated that a gastric photofluorography program is not viable in Western countries where the incidence of GC is lower.
  • a more suitable diagnostic approach would involve an accurate, non-invasive and cost-effective test for the detection of GC biomarkers involved in GC aetiology.
  • gp130 F/F a genetically engineered mouse model of inflammation-associated GC.
  • the gp130 F/F mice spontaneously and reproducibly develop adenomas in the glandular part of the stomach that show all the progressive histological hallmarks associated with intestinal-type GC in humans arising from chronic infection with H. pylori . This has led to the identification of new biomarker indicators of early-stage GC.
  • the present invention provides a method of diagnosing gastric cancer (GC) in a subject, the method including:
  • biomarkers are selected from the group consisting of vitamin D binding protein (VDBP), clusterin, insulin like growth factor binding protein complex acid labile subunit (IGFALS), and afamin;
  • VDBP vitamin D binding protein
  • IGFALS insulin like growth factor binding protein complex acid labile subunit
  • afamin afamin
  • the expression level of the one or more biomarkers is measured in a sample obtained from the subject.
  • the sample is a serum sample.
  • measuring the expression level of the one or more biomarkers includes measuring the level of biomarker protein in the sample.
  • the sample is a tissue sample.
  • measuring the expression level of the one or more biomarkers includes measuring the level of biomarker mRNA in the sample.
  • the biomarker is human VDBP.
  • an expression level of VDBP in the subject that is lower than the reference expression level for VDBP is indicative of GC in the subject.
  • the biomarker is human clusterin.
  • an expression level of clusterin in the subject that is lower than the reference expression level for clusterin is indicative of GC in the subject.
  • the biomarker is human IGFALS.
  • an expression level of IGFALS in the subject that is higher than the reference expression level for IGFALS is indicative of GC in the subject.
  • the biomarker is human afamin.
  • a level of afamin protein in the subject that is lower than the reference expression level for the afamin protein is indicative of GC in the subject.
  • the present invention provides a method of determining if a subject is susceptible to developing gastric cancer (GC), the method including:
  • biomarkers are selected from the group consisting of vitamin D binding protein (VDBP), clusterin, insulin like growth factor binding protein complex acid labile subunit (IGFALS), and afamin;
  • VDBP vitamin D binding protein
  • IGFALS insulin like growth factor binding protein complex acid labile subunit
  • afamin afamin
  • the expression level of the one or more biomarkers is measured in a sample obtained from the subject.
  • the sample is a serum sample.
  • measuring the expression level of the one or more biomarkers includes measuring the level of biomarker protein in the sample.
  • the sample is a tissue sample.
  • measuring the expression level of the one or more biomarkers includes measuring the level of biomarker mRNA in the sample.
  • the biomarker is human VDBP.
  • an expression level of VDBP in the subject that is lower than the reference expression level for VDBP is indicative of GC in the subject.
  • the biomarker is human clusterin.
  • an expression level of clusterin in the subject that is lower than the reference expression level for clusterin is indicative of GC in the subject.
  • the biomarker is human IGFALS.
  • an expression level of IGFALS in the subject that is higher than the reference expression level for IGFALS is indicative of GC in the subject.
  • the biomarker is human afamin.
  • a level of afamin protein in the subject that is lower than the reference expression level for the afamin protein is indicative of GC in the subject.
  • the present invention provides a method of assessing progression of gastric cancer (GC) in a subject, the method including:
  • biomarkers are selected from the group consisting of vitamin D binding protein (VDBP), clusterin, insulin like growth factor binding protein complex acid labile subunit (IGFALS), and afamin;
  • VDBP vitamin D binding protein
  • IGFALS insulin like growth factor binding protein complex acid labile subunit
  • afamin afamin
  • the subject is undergoing treatment for the GC.
  • the expression level of the one or more biomarkers is measured in a sample obtained from the subject.
  • the sample is a serum sample.
  • measuring the expression level of the one or more biomarkers includes measuring the level of biomarker protein in the sample.
  • the sample is a tissue sample.
  • measuring the expression level of the one or more biomarkers includes measuring the level of biomarker mRNA in the sample.
  • the biomarker is human VDBP.
  • an expression level of VDBP in the subject that is lower than the reference expression level for VDBP is indicative of GC in the subject.
  • the biomarker is human clusterin.
  • an expression level of clusterin in the subject that is lower than the reference expression level for clusterin is indicative of GC in the subject.
  • the biomarker is human IGFALS.
  • an expression level of IGFALS in the subject that is higher than the reference expression level for IGFALS is indicative of GC in the subject.
  • the biomarker is human afamin.
  • a level of afamin protein in the subject that is lower than the reference expression level for the afamin protein is indicative of GC in the subject.
  • the present invention provides a method for screening a candidate therapeutic agent useful for treating gastric cancer (GC) in a subject, the method including assaying the candidate therapeutic agent for activity in modulating the expression level of one or more biomarkers selected from the group consisting of vitamin D binding protein (VDBP), clusterin, insulin like growth factor binding protein complex acid labile subunit (IGFALS), and afamin.
  • VDBP vitamin D binding protein
  • IGFALS insulin like growth factor binding protein complex acid labile subunit
  • afamin selected from the group consisting of vitamin D binding protein (VDBP), clusterin, insulin like growth factor binding protein complex acid labile subunit (IGFALS), and afamin.
  • the method includes the steps of:
  • the candidate therapeutic agent is useful for treating GC in the subject.
  • the method includes the steps of:
  • the candidate therapeutic agent is useful for treating GC in a subject.
  • the candidate therapeutic agent increases the expression level of VDBP in the subject or cell to a level which approximates or is identical to the reference expression level for VDBP. In some embodiments, the candidate therapeutic agent increases the expression level of clusterin in the subject or cell to a level which approximates or is identical to the reference expression level for clusterin. In some embodiments, the candidate therapeutic agent decreases the expression level of IGFALS in the subject or cell to a level which approximates or is identical to the reference expression level for IGFALS. In some embodiments, the candidate therapeutic agent increases the expression level of afamin in the subject or cell to a level which approximates or is identical to the reference expression level for afamin.
  • the method further includes measuring an expression level of the biomarker apolipoprotein E (ApoE) and/or the biomarker haptoglobin in the subject or cell.
  • ApoE biomarker apolipoprotein E
  • the present invention provides a kit for diagnosing gastric cancer (GC) in a subject, determining if a subject is susceptible to developing GC, or assessing progression of GC in a subject, the kit including means for measuring an expression level of one or more biomarkers in the subject, wherein the one or more biomarkers are selected from the group consisting of vitamin D binding protein (VDBP), clusterin, insulin like growth factor binding protein complex acid labile subunit (IGFALS), and afamin.
  • VDBP vitamin D binding protein
  • IGFALS insulin like growth factor binding protein complex acid labile subunit
  • FIG. 1 Histological analysis pertaining to Example 1 was performed on week old mice of the indicated genotypes. Following excision of the stomach and opening along the outer curvature, stomachs were pinned out with the lumen facing the observer (insets). Longitudinal section along the dotted line were stained with H&E and oriented that the antrum faces to the left. Stomachs of all gp130 F/F and gp130 F/F ; Il6 ⁇ / ⁇ mice reveal 4-6 distinct adenomatous tumours (arrow) within the glandular part of the antrum (a) that are characterized by elongated and often branching glands in association with inflammatory infiltrates (asterisk).
  • FIG. 2 (A) Schematic of the strategy used in Example 1 for the discovery, verification and validation of candidate serum protein biomarkers of gastric cancer (GC). Steps outlined with rectangular boxes were experimental processes while those represented by diamonds were analytical processes. The dashed line indicates that three proteins identified at Stage 1 bypassed verification at Stage 2 and underwent direct validation by ELISA in human samples at Stage 3.
  • B Representative 2D gel spot map of a wild-type sample with non-GC phenotype.
  • C Representative 2D gel spot map of a gp130 F/F genotype mouse (FF) sample with GC phenotype.
  • D Hierarchical clustering dendogram generated from the 512 matched spots.
  • E Principal component analysis (PCA) scores plot generated from the 512 matched spots. The percentage of variance attributed to each principal component is shown.
  • PCA Principal component analysis
  • FIG. 3 A flow-chart depicting the experimental workflow of used in Example 1 for the identification of candidate GC biomarkers based on the 38 multiple affinity removal system (MARS) depleted mouse serum samples.
  • MARS multiple affinity removal system
  • ROC receiver operating characteristics
  • MS mass spectrometry
  • FIG. 4 Box-and-whisker plots of the standardized abundance values, also referred to as volumes, of two-dimensional difference in-gel electrophoresis (2D DIGE) spots identified in Example 1 and found to be associated with the gp130 F/F mutation rather than the GC phenotype.
  • 2D DIGE two-dimensional difference in-gel electrophoresis
  • FIG. 5 (A) A representative overlayed 2D DIGE image of a GC (green) and non-GC (red) sample showing the positions of the 38 spots-of-interest corresponding to eight candidate biomarker proteins identified in Example 1. Those spots outlined in green were up-regulated in GC and those in red were down-regulated. (B) Box-and-whisker plots of matched spot volumes associated with the eight proteins of interest on the 2D DIGE. For all 38 spots, the mean spot volumes obtained for the GC phenotype group (i.e. FF/FFIL6 genotypes) were significantly different to the mean of the non-GC phenotype group (i.e. WT/IL6/FFStat3 genotypes) with Student's T-test P values ⁇ 0.01.
  • FIG. 8 Shows depicting the ELISA results (standardized concentrations) for AACT and fibronectin in Example 1, which showed no apparent regulation between the GC patients and controls. P values were calculated using to the Mann-Whitney U test. Hollow data points are indicative of female subjects. Error bars represent the mean and standard error of the mean.
  • FIG. 10 ROC curves obtained for each of the five proteins analysed in Example 2 indicating sensitivity (true positive rate—TPR), specificity (false positive rate—FPR), and Area Under the Curve (AUC).
  • FIG. 11 ROC curves obtained for secondary combinations of the five proteins (Afamin—A; Clusterin—C; Haptoglobin—H; IGFALS—I; VDBP—V) analysed in Example 2.
  • FIG. 12 ROC curves obtained for tertiary combinations of the five proteins (Afamin—A; Clusterin—C; Haptoglobin—H; IGFALS—I; VDBP—V) analysed in Example 2.
  • the present invention is predicated in part on the identification of a number of biomarkers, the expression levels of which are altered in samples obtained from subjects with gastric cancer (GC).
  • GC gastric cancer
  • a biomarker is effectively an organic biomolecule which is differentially present in a sample taken from a subject of one phenotypic status (e.g. having a disease) as compared with another phenotypic status (e.g. not having the disease).
  • a biomarker is differentially present between different phenotypic status groups if the mean or median expression level of the biomarker is calculated to be different (i.e. higher or lower) between the groups. Therefore, biomarkers, alone or in combination, provide an indication that a subject belongs to one phenotypic status or another.
  • the present invention provides a method of diagnosing gastric cancer (GC) in a subject, the method including:
  • biomarkers are selected from the group consisting of vitamin D binding protein (VDBP), clusterin, insulin like growth factor binding protein complex acid labile subunit (IGFALS), and afamin;
  • VDBP vitamin D binding protein
  • IGFALS insulin like growth factor binding protein complex acid labile subunit
  • afamin afamin
  • the present invention provides a method of determining if a subject is susceptible to developing gastric cancer (GC), the method including:
  • biomarkers are selected from the group consisting of vitamin D binding protein (VDBP), clusterin, insulin like growth factor binding protein complex acid labile subunit (IGFALS), and afamin;
  • VDBP vitamin D binding protein
  • IGFALS insulin like growth factor binding protein complex acid labile subunit
  • afamin afamin
  • gastric cancer or “GC” as used thought the specification is taken to mean cancer of the stomach, including adenocarcinoma of the stomach.
  • the stomach includes the following four sections: cardia (including the cardial notch); fundus; body or corpus (including the angular incisure or notch); and pylorus (including the pyloric sphincter, pyloric antrum and pyloric canal).
  • cardia including the cardial notch
  • fundus including the angular incisure or notch
  • pylorus including the pyloric sphincter, pyloric antrum and pyloric canal.
  • pylorus including the pyloric sphincter, pyloric antrum and pyloric canal.
  • gastric cancer or “GC” also encompasses cancer of other regions of the gastrointestinal tract.
  • the methods of the aspects of the invention referred to above require measuring an expression level of one or more of the biomarkers VDBP, clusterin, IGFALS and afamin. These markers are discussed in detail below.
  • the term “measuring an expression level” of a biomarker includes: (1) measuring the level of transcription of the corresponding gene into a messenger RNA (mRNA) molecule; and/or (2) measuring the level of translation of the mRNA into protein (i.e. measuring the level of protein per se); and/or (3) measuring the level of activity of the translated protein.
  • mRNA messenger RNA
  • the expression level of a biomarker can be measured at the RNA and/or protein stages of expression.
  • biomarker includes, but is not limited to, proteins (polypeptides), polynucleotides (e.g. mRNA) and/or metabolites whose expression level (e.g. level of transcription, level of translation, and/or level of activity) in a subject with gastric cancer, or in a sample taken from a subject with gastric cancer, is increased or decreased when compared to the expression level of the same biomarker in a normal sample (i.e. a reference expression level).
  • Any biomarkers referred to herein also include their gene and protein synonyms as could be readily identified by a person skilled in the art.
  • gene is to be understood to mean a region of genomic nucleotide sequence (nuclear or mitochondrial) which includes a coding region that is transcribed and translated into protein.
  • a “gene” in the context of the present invention can therefore include regulatory regions (e.g. promoter regions), transcribed regions, exons, introns, untranslated regions and other functional and/or non-functional sequence regions associated with the gene.
  • the “expression level” of a biomarker in the subject or sample may be a reflection of the extent of transcription of the corresponding gene into mRNA in the subject or sample.
  • a protein is a functional biomolecule composed primarily of amino acids, with the amino acid sequence determined by a corresponding gene. Accordingly, in one embodiment the “expression level” of a biomarker in the subject or sample may be a reflection of the extent of translation of mRNA of the corresponding gene into protein in the subject or sample.
  • the level of a protein may be measured by techniques which include, but are not limited to, antibody-based testing (including Western blotting, immunoblotting, enzyme-linked immunosorbant assay (ELISA), radioimmunoassay (RIA), immunoprecipitation and dissociation-enhanced lanthanide fluoro immuno assay (DELFIA)), proteomics techniques, surface plasmon resonance (SPR), versatile fibre-based SPR, chemiluminescence, fluorescent polarization, phosphorescence, immunohistochemistry, immunofluorescence, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), as described in WO 2009/004576 (including surface enhanced laser desorption/ionization mass spectrometry (SELDI-MS), especially surface-enhanced affinity capture (SEAC), protein microarrays, surface-enhanced need desorption (SEND) or surface-enhanced
  • antibody-based testing including Western blotting, immunoblotting, enzyme-linked immunosorbant
  • antibodies or antisera preferably polyclonal antisera, and most preferably monoclonal antibodies specific for each protein under investigation, are used to detect the protein abundance.
  • the antibodies can be detected by direct labelling of the antibodies themselves, for example with radioactive labels, fluorescent labels, hapten labels such as, biotin, or an enzyme such as horseradish peroxidase or alkaline phosphatase.
  • unlabelled primary antibody may be used in conjunction with a labelled secondary antibody, comprising antisera, polyclonal antisera or a monoclonal antibody specific for the primary antibody.
  • Immunohistochemistry protocols and kits are well known in the art and are commercially available.
  • Antibodies can be produced by methods well known in the art, for example, by immunizing animals with the protein under investigation.
  • immunoassays including, for example, sandwich immunoassays including ELISA or fluorescence-based immunoassays, as well as other enzyme immunoassays.
  • Nephelometry is an assay performed in liquid phase, in which antibodies are in solution. Binding of the protein under investigation to the antibody results in a change in absorbance, which is measured.
  • SELDI-based immunoassay a biospecific capture reagent for the protein of interest is attached to the surface of an MS probe, such as a pre-activated ProteinChip array (see below). The protein is then specifically captured on the biochip through this reagent, and the captured protein is detected by mass spectrometry (see below).
  • VeSPR surface plasmon resonance
  • Traditional SPR is a well-established method for label-free bio-sensing that relies on the excitation of free electrons at the interface between a dielectric substrate and a thin metal coating.
  • the condition under which the incoming light couples into the plasmonic wave depends on the incidence angle and the wavelength of the incoming light as well as the physical properties (dielectric constant/refractive index) of the sensor itself and the surrounding environment. For this reason, SPR is sensitive to even small variations in the density (refractive index) in the close vicinity of the sensor, and does not require the use of fluorescent labels.
  • the small variation of refractive index induced by the binding biomolecules such as proteins onto the sensor surface can be measured by monitoring the coupling conditions via either the incidence angle or the wavelength of the incoming light.
  • Existing SPR systems use the bulky and expensive Krestchmann prism configuration where one side of the prism is coated with a metal such as gold or silver that can support a plasmonic wave.
  • Alternative SPR architectures have been developed based on optical fibres with the metallic coating deposited around a short section of the fibre. This approach reduces the complexity and cost of such sensors, opening a pathway to distinctive applications such as dip sensing. The material at the sensor surface is probed by monitoring the wavelength within a broad spectrum that is absorbed due to coupling to the surface plasmon.
  • VeSPR optical-fibre based SPR sensor
  • Proteomics can also be used to analyse the expression level of a protein of interest present in a sample at a certain point of time.
  • proteomic techniques can be used to assess the global changes of protein expression in a sample (also referred to as expression proteomics).
  • Proteomic analysis typically includes: (i) separation of individual proteins in a sample by 2-D gel electrophoresis (2-D PAGE); (ii) identification of the individual polypeptides recovered from the gel, for example by mass spectrometry or N-terminal sequencing; and (iii) analysis of the data using bioinformatics.
  • Protein microarrays may also be used to determine the level of expression of a protein of interest in a sample.
  • Many protein biochips are described in the art, including for example protein biochips produced by Ciphergen Biosystems, Inc. (Fremont, Calif.), Zyomyx (Hayward, Calif.), Invitrogen (Carlsbad, Calif.), Biacore (Uppsala, Sweden) and Procognia (Berkshire, UK). Examples of such protein biochips are described in the following patents or published patent applications: U.S. Pat. Nos. 6,225,047, 6,537,749, 6,329,209, and 5,242,828, and PCT International Publication Numbers WO 00/56934 and WO 03/048768.
  • the expression level of a protein of interest can also be measured by mass spectrometry, a method that employs a mass spectrometer to detect gas phase ions.
  • mass spectrometers are time-of-flight, magnetic sector, quadrupole filter, ion trap, ion cyclotron resonance, electrostatic sector analyzer and hybrids of these.
  • the mass spectrometer may be a laser desorption/ionization mass spectrometer.
  • the protein or proteins to be detected are placed on the surface of a mass spectrometry probe, a device adapted to engage a probe interface of the mass spectrometer and to present the protein or proteins to ionizing energy for ionization and introduction into a mass spectrometer.
  • a laser desorption mass spectrometer employs laser energy, typically from an ultraviolet laser, but also from an infrared laser, to desorb analytes from a surface, to volatilize and ionize them and make them available to the ion optics of the mass spectrometer.
  • the analysis of proteins by LDI can take the form of MALDI or of SELDI, as described below.
  • SELDI desorption/ionization gas phase ion spectrometry
  • an analyte in this instance one or more of the proteins to be detected
  • SELDI also encompasses affinity capture mass spectrometry, surface-enhanced affinity capture (SEAC) and immuno-capture mass spectrometry (icMS) as described by Penno M A et al., 2012 ( Res. Vet. Sci., 93: 611-617.
  • probes that have a material on the probe surface that captures proteins through a non-covalent affinity interaction (adsorption) between the material and the protein.
  • the material is variously called an “adsorbent,” a “capture reagent,” an “affinity reagent” or a “binding moiety.”
  • Such probes can be referred to as “affinity capture probes” and as having an “adsorbent surface.”
  • the capture reagent can be any material capable of binding a protein.
  • the capture reagent is attached to the probe surface by physisorption or chemisorption.
  • the probes may take the form of a functionalised biochip or magnetic bead, may have the capture reagent already attached to the surface, or the probes are pre-activated and include a reactive moiety that is capable of binding the capture reagent, e.g. through a reaction forming a covalent or coordinate covalent bond.
  • Epoxide and acyl-imidizole are useful reactive moieties to covalently bind protein capture reagents such as antibodies or cellular receptors.
  • Nitrilotriacetic acid and iminodiacetic acid are useful reactive moieties that function as chelating agents to bind metal ions that interact non-covalently with histidine containing proteins.
  • Adsorbents are generally classified as chromatographic adsorbents and biospecific adsorbents.
  • a chromatographic adsorbent refers to an adsorbent material typically used in chromatography.
  • Chromatographic adsorbents include, for example, ion exchange materials, metal chelators (e.g. nitrilotriacetic acid or iminodiacetic acid), immobilized metal chelates, hydrophobic interaction adsorbents, hydrophilic interaction adsorbents, dyes, simple biomolecules (e.g. nucleotides, amino acids, simple sugars and fatty acids) and mixed mode adsorbents (e.g. hydrophobic attraction/electrostatic repulsion adsorbents).
  • metal chelators e.g. nitrilotriacetic acid or iminodiacetic acid
  • immobilized metal chelates e.g. nitrilotriacetic acid or iminodiacetic acid
  • hydrophobic interaction adsorbents e.g. nucleotides, amino acids, simple
  • a biospecific adsorbent refers to an adsorbent comprising a biomolecule, e.g. a nucleic acid molecule (e.g. an aptamer), a polypeptide, a polysaccharide, a lipid, a steroid or a conjugate of these (e.g. a glycoprotein, a lipoprotein, a glycolipid, a nucleic acid (e.g. DNA-protein conjugate).
  • the biospecific adsorbent can be a macromolecular structure such as a multiprotein complex, a biological membrane or a virus. Examples of biospecific adsorbents are antibodies, receptor proteins and nucleic acids. Biospecific adsorbents typically have higher specificity for a target protein than chromatographic adsorbents.
  • a probe with an adsorbent surface is contacted with a sample being tested for a period of time sufficient to allow the protein under investigation to bind to the adsorbent. After an incubation period, the substrate is washed to remove unbound material. Any suitable washing solutions can be used; preferably, aqueous solutions are employed. The extent to which molecules remain bound can be manipulated by adjusting the stringency of the wash. The elution characteristics of a wash solution can depend, for example, on pH, ionic strength, hydrophobicity, degree of chaotropism, detergent strength, and temperature. Unless the probe has both SEAC and SEND properties (as described herein), an energy absorbing molecule then is applied to the substrate with the bound biomarkers.
  • the protein under investigation can be captured with a solid-phase bound immuno-adsorbent that has antibodies that specifically bind to the protein. After washing the adsorbent to remove unbound material, the protein is eluted from the solid phase and is detected by applying it to a biochip that binds the protein.
  • Proteins under investigation which are bound to the substrates are detected in a gas phase ion spectrometer such as a time-of-flight mass spectrometer.
  • the proteins are ionized by an ionization source such as a laser, the generated ions are collected by an ion optic assembly, and then a mass analyzer disperses and analyzes the passing ions.
  • the detector then translates information of the detected ions into mass-to-charge ratios. Detection of a protein typically will involve detection of signal intensity. Thus, both the quantity and mass of the protein can be determined.
  • SEND surface-enhanced neat desorption
  • SEND probe The phrase “energy absorbing molecules” (EAM) denotes molecules that are capable of absorbing energy from a laser desorption/ionization source and, thereafter, contribute to desorption and ionization of analyte molecules in contact therewith.
  • EAM energy absorbing molecules
  • the EAM category includes molecules used in MALDI, frequently referred to as “matrix,” and is exemplified by cinnamic acid derivatives, sinapinic acid (SPA), cyano-hydroxy-cinnamic acid (CHCA) and dihydroxybenzoic acid, ferulic acid, and hydroxyaceto-phenone derivatives.
  • the energy absorbing molecule may be incorporated into a linear or cross-linked polymer, e.g. a polymethacrylate.
  • the composition can be a co-polymer of ⁇ -cyano-4-methacryloyloxycinnamic acid and acrylate.
  • the composition may be a co-polymer of ⁇ -cyano-4-methacryloyloxycinnamic acid, acrylate and 3-(tri-ethoxy)silyl propyl methacrylate, or may be a co-polymer of ⁇ -cyano-4-methacryloyloxycinnamic acid and octadecylmethacrylate (“Cl 8 SEND”). SEND is further described in U.S. Pat. No. 6,124,137 and PCT International Publication Number WO 03/64594.
  • SEAC/SEND is a version of laser desorption mass spectrometry in which both a capture reagent and an energy absorbing molecule are attached to the sample presenting surface. SEAC/SEND probes therefore allow the capture of proteins under investigation through affinity capture and ionization/desorption without the need to apply external matrix.
  • the Cl 8 SEND biochip is a version of SEAC/SEND, comprising a Cl 8 moiety which functions as a capture reagent, and a CHCA moiety which functions as an energy absorbing moiety.
  • SEPAR surface-enhanced photolabile attachment and Release
  • SEPAR involves the use of probes having moieties attached to the surface that can covalently bind a protein, and then release the protein through breaking a photolabile bond in the moiety after exposure to light, e.g. to laser light.
  • SEPAR and other forms of SELDI are readily adapted to detecting a protein or protein profile, as required by the methods of the present invention.
  • MALDI is a traditional method of laser desorption/ionization.
  • the sample to be tested is mixed with matrix and deposited directly on a MALDI chip.
  • the protein being tested is preferably first captured with biospecific (e.g. an antibody) or chromatographic materials coupled to a solid support such as a resin (e.g. in a spin column). Specific affinity materials that may bind the protein being detected are described above. After purification on the affinity material, the protein under investigation is eluted and then detected by MALDI.
  • Time-of-flight mass spectrometry generates a time-of-flight spectrum.
  • the time-of-flight spectrum ultimately analyzed typically does not represent the signal from a single pulse of ionizing energy against a sample, but rather the sum of signals from a number of pulses. This reduces noise and increases dynamic range.
  • This time-of-flight data is then subject to data processing using specialized software. Data processing typically includes TOF-to-M/Z transformation to generate a mass spectrum, baseline subtraction to eliminate instrument offsets and high frequency noise filtering to reduce high frequency noise.
  • Data generated by desorption and detection of proteins can be analyzed with the use of a programmable digital computer.
  • the computer program analyzes the data to indicate the number of proteins detected, and optionally the strength of the signal and the determined molecular mass for each protein detected.
  • Data analysis can include steps of determining signal strength of a protein and removing data deviating from a predetermined statistical distribution. For example, the observed peaks can be normalized, by calculating the height of each peak relative to some reference.
  • the computer can transform the resulting data into various formats for display.
  • the standard spectrum can be displayed, but in one useful format only the peak height and mass information are retained from the spectrum view, yielding a cleaner image and enabling proteins with nearly identical molecular weights to be more easily seen.
  • two or more spectra are compared, conveniently highlighting proteins that have varying expression levels between samples. Using any of these formats, one can readily determine whether a particular protein is present in a sample and to what level.
  • Peak selection can be done visually, but commercial software can be used to automate the detection of peaks.
  • this software functions by identifying signals having a signal-to-noise ratio above a selected threshold and labelling the mass of the peak at the centroid of the peak signal.
  • many spectra are compared to identify identical peaks present in some selected percentage of the mass spectra.
  • One version of this software clusters all peaks appearing in the various spectra within a defined mass range, and assigns a mass (M/Z) to all the peaks that are near the mid-point of the mass (M/Z) cluster.
  • Software used to analyze the data can include code that applies an algorithm to the analysis of the signal to determine whether the signal represents a peak in a signal that corresponds to a protein under investigation.
  • the software also can subject the data regarding observed protein peaks to a classification tree or ANN analysis, to determine whether a protein peak or combination of protein peaks is present that indicates the status of the particular clinical parameter under examination. Analysis of the data may be “keyed” to a variety of parameters that are obtained, either directly or indirectly, from the mass spectrometric analysis of the sample.
  • These parameters include, but are not limited to, the presence or absence of one or more peaks, the shape of a peak or group of peaks, the height of one or more peaks, the log of the height of one or more peaks, and other arithmetic manipulations of peak height data.
  • VDBP is the major plasma carrier of vitamin D 3 and its metabolites and ensures that vitamin D is transported to the liver, 25(OH) 2 D 3 to the kidney, and 1,25(OH) 2 D 3 to target cells and organs.
  • VDBP also plays an important role in macrophage activation that is distinct from its vitamin D-binding ability.
  • VDBP has been shown to enhance the leukocyte chemotactic activity of activated complement peptides, which are the precursor of the macrophage-activator factor. Such activities can form the basis of assaying for activity of the VDBP protein.
  • clusterin this protein has been implicated in a variety of activities including programmed cell death, regulation of complement mediated cell lysis, membrane recycling, cell-cell adhesion and src induced transformation.
  • Clusterin also acts as a complement inhibitor as a part of the attack complex of complement.
  • clusterin binds to numerous partners such as immunoglobulins, lipids, heparin, bacteria, complement components, paraoxonase, beta amyloid, leptin and others.
  • activities and binding partners can form the basis of assaying for activity of the clusterin protein.
  • IGFALS this protein is known to bind insulin-like growth factors, increasing their half-life and their vascular localization.
  • IGFALS binds insulin-like growth factor binding protein-3 (IGFBP-3) and so assays could be utilised which measure the extent of binding between the two proteins.
  • IGFBP-3 insulin-like growth factor binding protein-3
  • afamin is known to possess vitamin E binding activity, and so assays which measure the amount or level of binding between the two will be a reflection of the level of afamin protein in a particular sample. This level can be compared to the level of binding in a normal control sample.
  • levels of mRNA may be measured by techniques which include, but are not limited to, Northern blotting, RNA in situ hybridisation, reverse-transcriptase PCR (RT-PCR), real-time (quantitative) RT-PCR, microarrays, or “tag based” technologies such as SAGE (serial analysis of gene expression).
  • RT-PCR reverse-transcriptase PCR
  • SAGE serial analysis of gene expression
  • Primers or probes may be designed based on nucleotide sequences of the genes or transcripts thereof.
  • the first step is typically the isolation of total RNA from a sample obtained from the subject under investigation.
  • a typical sample in this instance would be a tissue sample, such as a gastric tumour sample (and corresponding normal gastric tissue if possible), although other sample sources are contemplated as described below.
  • RNA can also be extracted, for example, from frozen or archived paraffin-embedded and fixed (e.g. formalin-fixed) tissue samples previously obtained from the subject.
  • Messenger RNA (mRNA) may be subsequently purified from the total RNA sample.
  • the total RNA sample (or purified mRNA) is then reverse transcribed into cDNA using a suitable reverse transcriptase.
  • the reverse transcription step is typically primed using oligo-dT primers, random hexamers, or primers specific for the relevant gene, depending on the RNA template.
  • the cDNA derived from the reverse transcription reaction then serves as a template for a typical PCR reaction.
  • two oligonucleotide PCR primers specific for the relevant gene are used to generate a PCR product.
  • a third oligonucleotide, or probe, designed to detect a nucleotide sequence located between the other two PCR primers is also used in the PCR reaction.
  • the probe is non-extendible by the Taq DNA polymerase enzyme used in the PCR reaction, and is labelled with a reporter fluorescent dye and a quencher fluorescent dye.
  • any laser-induced emission from the reporter dye is quenched by the quenching dye when the two dyes are located close together, as they are on the probe.
  • the Taq DNA polymerase enzyme cleaves the probe in a template-dependent manner.
  • the resultant probe fragments disassociate in solution, and signal from the released reporter dye is freed from the quenching effect of the second fluorophore.
  • One molecule of reporter dye is liberated for each new molecule synthesized, and detection of the unquenched reporter dye provides the basis for quantitative interpretation of the data.
  • RT-PCR In real-time RT-PCR the amount of product formed, and the timing at which the product is formed, in the PCR reaction correlates with the amount of starting template.
  • RT-PCR product will accumulate quicker in a sample having an increased level of mRNA compared to a standard or “normal” sample.
  • Real-time RT-PCR measures either the fluorescence of DNA intercalating dyes such as Sybr Green into the synthesized PCR product, or can measure PCR product accumulation through a dual-labelled fluorigenic probe (i.e., TaqMan probe).
  • the progression of the RT-PCR reaction can be monitored using PCR machines such as the Applied Biosystems' Prism 7000 or the Roche LightCycler which measure product accumulation in real-time.
  • Real-time RT-PCR is compatible both with quantitative competitive PCR and with quantitative comparative PCR. The former uses an internal competitor for each target sequence for normalization, while the latter uses a normalization gene contained within the sample, or a housekeeping gene for RT-PCR.
  • a nucleotide sequence for example an oligonucleotide, a cDNA, or genomic DNA
  • the substrate includes a multitude of nucleotide sequences such that one or more of the relevant genes can be assayed simultaneously.
  • a nucleic acid target sample for example total RNA or mRNA obtained from a subject of interest is then hybridized to the microarray and the amount of target nucleic acid hybridized to each probe on the array is quantified and compared to the hybridisation which occurs to a standard or “normal” sample.
  • One exemplary quantifying method is to use confocal microscope and fluorescent labels.
  • the Affymetrix GeneChipTM Array system (Affymetrix, Santa Clara, Calif.) and the AtlasTM Human cDNA Expression Array system are particularly suitable for quantifying the hybridization; however, it will be apparent to those of skill in the art that any similar systems or other effectively equivalent detection methods can also be used.
  • Fluorescently labelled cDNA probes may also represent the nucleic acid target sample.
  • Such probes can be generated through incorporation of fluorescent nucleotides during reverse transcription of total RNA or mRNA extracted from a sample of the subject to be tested.
  • Labelled cDNA probes applied to the microarray will hybridize with specificity to the equivalent spot of DNA on the array. Quantitation of hybridization of each arrayed element allows for assessment of corresponding mRNA abundance in the sample compared to the abundance observed in a standard or “normal” sample. With dual colour fluorescence, separately labelled cDNA probes generated from two sources of RNA are hybridized pairwise to the array. The relative abundance of the transcripts from the two sources corresponding to each specified gene is thus determined simultaneously.
  • the miniaturized scale of the hybridization using microarray analysis affords a convenient and rapid evaluation of the expression pattern for large numbers of genes.
  • Such methods have been shown to have the sensitivity required to detect rare transcripts, which are expressed at a few copies per cell, and to reproducibly detect at least approximately two-fold differences in the expression levels.
  • the expression level of one or more of the proteins may be measured directly, or in an alternative embodiment, the expression level of one or more of the proteins may be measured in a sample obtained from a subject. It is to be made clear that the sample obtained from the subject that is analysed by the methods of the present invention may have previously been obtained from the subject, and, for example, has been stored in an appropriate repository. In this instance, the sample would have been obtained from the subject in isolation of, and therefore separate to, the methods of the present invention.
  • the sample which is obtained from the subject may include, but is not limited to, a blood sample, or a sample derived from blood (for example a serum sample or a plasma sample or a fraction of a blood, serum or plasma sample, blood cells), saliva, buccal swab, gastric fluid, stool sample, bladder washing, semen, urine, and a gastrointestinal tissue sample (such as a stomach or esophageal tissue sample).
  • a sample may be manipulated in any way after procurement, such as by treatment with reagents, solubilization, or enrichment for certain components, such as the relevant protein or polynucleotide under investigation.
  • the sample is a serum sample obtained from the subject.
  • Serum is derived from blood plasma which is the yellow liquid component of blood, in which the blood cells in whole blood would normally be suspended. It makes up about 55% of the total blood volume. It is mostly water (90% by volume) and contains dissolved proteins, glucose, clotting factors, mineral ions, hormones and carbon dioxide.
  • Blood plasma is prepared by spinning a tube of fresh blood in a centrifuge until the blood cells fall to the bottom of the tube. The blood plasma is then poured or drawn off. Blood plasma, preferably supplemented with a clotting inhibitor, e.g. heparin or EDTA, has a density of approximately 1.025 kg/1. Blood serum is blood plasma without fibrinogen or the other clotting factors (i.e. whole blood minus both the cells and the clotting factors).
  • a clotting inhibitor e.g. heparin or EDTA
  • the sample is a tissue sample obtained from the subject.
  • the tissue sample may be a biopsy taken from the tumour.
  • the tissue sample may be fixed and stored indefinitely or until analysis is conducted. Tissue sections taken from the sample may be stained for histological analysis and for conducting the assays referred to above to determine the level of biomarker protein present in the sample.
  • RNA may be extracted from a tissue sample obtained from the subject and the RNA subject to the assays referred to above to determine the level of biomarker mRNA present in the sample. In instances where the sample is a tissue sample, ideally a sample of adjacent normal gastric tissue would be obtained for the purposes of comparison.
  • the reference expression level for a particular biomarker is a level of expression of the biomarker that is associated with a known gastric cancer (GC) status, i.e. a level of expression which is known to be found in a subject not suffering from GC (a “normal” subject in the context of the present invention).
  • GC gastric cancer
  • a reference expression level for each biomarker can also be obtained from one or more normal samples from a subject suspected to have GC.
  • the expression level of the one or more biomarkers may be increased in the sample being tested as compared to the reference expression level derived from one or more normal samples. In some embodiments, the expression level of the one or more biomarkers may be decreased in the sample being tested when compared to the reference expression level derived from one or more normal samples. This is described in further detail below.
  • the methods of the invention involve measuring an expression level of one or more biomarkers selected from the group consisting of vitamin D binding protein (VDBP), clusterin, insulin like growth factor binding protein complex acid labile subunit (IGFALS), and afamin.
  • VDBP vitamin D binding protein
  • IGFALS insulin like growth factor binding protein complex acid labile subunit
  • afamin afamin.
  • the human VDBP gene encodes three protein variants as represented by GenBank Accession Numbers NP — 000574.2 (variant 1), NP — 001191235.1 (variant 2) and NP — 001191236.1 (variant 3).
  • the human clusterin gene encodes the protein represented by GenBank Accession Number NP — 001822.3.
  • the human IGFALS gene encodes two protein variants as represented by GenBank Accession Numbers NP — 001139478.1 (variant 1) and NP — 004961.1 (variant 2). Finally, the human afamin gene encodes the protein represented by GenBank Accession Number NP — 001124.1.
  • the UniProt database www.uniprot.org
  • the UniProt ID for the human VDBP protein is P02774
  • human clusterin protein is P10909
  • human IGFALS is Q8TAY0 (variant 1 and 2) and P35858 (variant 2)
  • human afamin protein is P43652.
  • the human VDBP gene is transcribed into three variants as represented by GenBank Accession Numbers NM — 000583.3 (variant 1), NM — 001204306.1 (variant 2) and NM — 001204307.1 (variant 3).
  • the human clusterin gene is also transcribed into three variants as represented by GenBank Accession Numbers NM — 001831.3 (variant 1), NR — 038335.1 (variant 2) and NR — 045494.1 (variant 3). However, only transcript variant 1 encodes the functional protein.
  • the human IGFALS gene is also transcribed into three variants as represented by GenBank Accession Numbers NM — 001146006.1 (variant 1), NM — 004970.2 (variant 2) and NR — 027389.1 (variant 3). However, the third variant does not encode a functional protein.
  • the human afamin gene is transcribed into the nucleotide sequence as represented by GenBank Accession Number NM — 001133.2.
  • VDBP clusterin, IGFALS and afamin
  • a “variant” of a biomarker may exhibit an amino acid or nucleic acid sequence that is at least 80% identical, at least 90% identical, at least 95% identical, at least 98% identical, at least 99% identical, or at least 99.9% identical to the native biomarker.
  • a variant of a native biomarker may retain native biological activity or a substantial equivalent thereof.
  • a variant may have no substantial biological activity, such as those variants which are precursors for the biologically active biomarker. Examples of naturally occurring variants of VDBP, clusterin, IGFALS and afamin are described above.
  • the term “subject” refers to any animal (e.g. a mammal), including, but not limited to humans, non-human primates, dogs, cats, horses, cattle, sheep, deer, pigs, rodents, and any other animal known to get GC. Therefore, whilst human amino acid and mRNA sequences have been referred to above, it should be appreciated that the methods of the present invention are not limited to humans. Details of the specific proteins and their associated amino acid and mRNA sequences for different species may be readily accessed from the GenBank and UniProt databases (e.g.
  • the Gene ID for Mus musculus VDBP is 14473, for clusterin is 12759, for IGFALS is 16005, and for afamin is 280662) or sequences may be identified by BLAST searching.
  • primers, probes or antibodies that may be used to measure protein/gene expression in one species may also be used for unrelated species.
  • the biomarker may be VDBP, including for example human VDBP.
  • measuring the expression level of VDBP includes measuring the level of VDBP protein or mRNA in the subject, for example by using a method as described in detail above.
  • an expression level of VDBP in a subject which is lower than the reference expression level for VDBP is indicative of GC in the subject, or indicates that the subject is susceptible to developing GC.
  • Reference herein to “lower” with respect to the expression level of a biomarker as referred to herein, including VDBP, whether at the translational (protein) or transcriptional (mRNA) stage is intended to mean, for example, at least a 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 2.1-fold, 2.2-fold, 2.3-fold, 2.4-fold, 2.5-fold, 2.6-fold, 2.7-fold, 2.8-fold, 2.9-fold, 3-fold, 3.1-fold, 3.2-fold, 3.3-fold, 3.4-fold, 3.5-
  • the biomarker may be clusterin, including for example human clusterin.
  • measuring the expression level of clusterin includes measuring the level of clusterin protein or mRNA in the subject, for example by using a method as described in detail above.
  • an expression level of clusterin that is lower than the reference expression level for clusterin is indicative of GC in the subject, or indicates that the subject is susceptible to developing GC.
  • the biomarker may be IGFALS, including for example human IGFALS.
  • measuring the expression level of IGFALS includes measuring the level of IGFALS protein or mRNA in the subject, for example by using a method as described in detail above.
  • an expression level of IGFALS in a subject which is higher than the reference expression level for IGFALS is indicative of GC in the subject, or indicates that the subject is susceptible to developing GC.
  • Reference herein to “higher” with respect to the expression level of a biomarker referred to herein, including IGFALS, whether at the translational (protein) or transcriptional (mRNA) stage is intended to mean, for example, at least a 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 1.1-fold, 1.2-fold, 1.3-fold, 1.4-fold, 1.5-fold, 1.6-fold, 1.7-fold, 1.8-fold, 1.9-fold, 2-fold, 2.1-fold, 2.2-fold, 2.3-fold, 2.4-fold, 2.5-fold, 2.6-fold, 2.7-fold, 2.8-fold, 2.9-fold, 3-fold, 3.1-fold, 3.2-fold, 3.3-fold, 3.4-fold, 3.5-fold
  • the biomarker may be afamin, including for example human afamin.
  • measuring the expression level of afamin includes measuring the level of afamin protein or mRNA in the subject, for example by using a method as described in detail above.
  • an expression level of afamin that is lower than the reference expression level for afamin is indicative of GC in the subject, or indicates that the subject is susceptible to developing GC.
  • the identification of differential expression of the aforementioned biomarkers in GC also enables methods for assessing the therapeutic efficacy in a subject of a treatment for the GC.
  • the present invention provides a method of assessing progression of gastric cancer (GC) in a subject, the method including:
  • biomarkers are selected from the group consisting of vitamin D binding protein (VDBP), clusterin, insulin like growth factor binding protein complex acid labile subunit (IGFALS), and afamin;
  • VDBP vitamin D binding protein
  • IGFALS insulin like growth factor binding protein complex acid labile subunit
  • afamin afamin
  • an expression level of the one or more biomarkers is measured at more than one time points.
  • Such “serial” sampling is well suited, for example, to monitoring the progression of gastric cancer.
  • Serial sampling can be performed for any desired timeline, such as monthly, quarterly (i.e. every three months), semi-annually, annually, biennially, or less frequently.
  • the comparison between the measured expression level in the subject and the reference expression level may be carried out each time a new sample is measured, or the data relating to levels may be held for less frequent analysis.
  • the subject is undergoing treatment for the GC.
  • the treatment may be a conventional therapy such as chemotherapy or radiotherapy, or the treatment may be an alternative therapy.
  • the subject may not be undergoing treatment at all.
  • measuring the expression level of the VDBP, clusterin, IGFALS, and/or afamin biomarkers includes measuring the level of VDBP, clusterin, IGFALS, and/or afamin protein or mRNA in the subject, or in a sample taken from the subject.
  • an expression level of VDBP, clusterin, and/or afamin that is lower than a reference expression level for each biomarker is indicative of progression of GC in the subject.
  • an expression level of IGFALS which is higher than a reference expression level for IGFALS is indicative of progression of GC in the subject.
  • the method according to the third aspect of the invention may be used to perform clinical trials of a new drug, as well as to monitor the progress of a subject on the drug.
  • Therapy or clinical trials involve administering the drug being tested in a particular regimen.
  • the regimen may involve a single dose of the drug or multiple doses of the drug over time.
  • the doctor or clinical researcher monitors the effect of the drug on the subject over the course of administration. If the drug has a pharmacological impact on the GC, the expression level of the aforementioned biomarkers will approximate or be identical to the reference expression level for the proteins. Therefore, the trending of the expression levels of the biomarkers can be monitored in the subject during the course of treatment.
  • the expression level of the one or more biomarkers can be determined using the methods described in detail above.
  • One embodiment of this method involves determining the expression levels of the aforementioned biomarkers for at least two different time points during a course of drug therapy, e.g. a first time and a second time, and comparing the change in expression levels of the biomarkers, if any.
  • expression level of the biomarkers can be measured before and after drug administration or at two different time points during drug administration. The effect of therapy is determined based on these comparisons. If a treatment is effective, the expression level of the aforementioned biomarkers will approximate or be identical to the reference expression level for the biomarkers, while if treatment is ineffective, the expression level of the aforementioned biomarkers will remain higher or lower than the reference expression level for the biomarkers.
  • the present invention provides a method for screening a candidate therapeutic agent useful for treating gastric cancer, the method including assaying the candidate therapeutic agent for activity in modulating the expression level of one or more biomarkers selected from the group consisting of vitamin D binding protein (VDBP), clusterin, insulin like growth factor binding protein complex acid labile subunit (IGFALS), and afamin.
  • VDBP vitamin D binding protein
  • IGFALS insulin like growth factor binding protein complex acid labile subunit
  • afamin selected from the group consisting of vitamin D binding protein (VDBP), clusterin, insulin like growth factor binding protein complex acid labile subunit (IGFALS), and afamin.
  • Screening assays may be performed in vitro and/or in vivo.
  • prospective agents may be screened to identify candidate therapeutic agents for the treatment of gastric cancer in a cell-based assay.
  • each prospective agent is incubated with cultured cells (for example cells obtained from the GI tract of a normal subject or from a subject suffering from gastric cancer, or cell lines derived from a normal or affected subject), and modulation of the expression level of a biomarker is measured.
  • cultured cells for example cells obtained from the GI tract of a normal subject or from a subject suffering from gastric cancer, or cell lines derived from a normal or affected subject
  • modulation of the expression level of a biomarker is measured.
  • the method includes:
  • the candidate therapeutic agent is useful for treating GC in a subject.
  • candidate therapeutic agents may be screened in organ culture-based assays.
  • each prospective agent is incubated with either a whole organ or a portion of an organ (such as a portion of the GI tract of a normal of affected subject) derived from a non-human animal and modulation of the expression level of the target biomarker is measured.
  • the method includes measuring an expression level of the or each biomarker in the subject, wherein the expression level is measured after administration of the candidate therapeutic agent to the subject.
  • the expression level of the or each biomarker in the subject is then compared to a reference expression level for the or each biomarker. If the expression level of the or each biomarker in the subject approximates or is identical to the reference expression level for each biomarker, the candidate therapeutic agent can be said to be useful for the treatment of GC.
  • the expression level of the one or more biomarkers may be measured by the methods described in detail above.
  • the candidate therapeutic agent will increase the expression level of VDBP, clusterin or afamin, or will decrease the expression level of IGFALS, in the subject or cell to a level which approximates or is identical to the reference expression level for each biomarker.
  • the methods of the aforementioned aspects of the invention require the expression level of one or more of the VDBP, clusterin, IGFALS or afamin biomarkers to be measured.
  • the expression level of other biomarkers may be measured in addition or concurrently with VDBP, clusterin, IGFALS and/or afamin.
  • biomarkers which are known to be differentially expressed in GC can also be incorporated into the methods of the invention.
  • the inventors have also shown that apolipoprotein E (ApoE) and haptoglobin are differentially expressed in GC samples. Specifically, the expression levels of ApoE and haptoglobin are higher in GC samples than their expression level in “normal” samples. Therefore, the methods of the present invention may encompass measuring the expression level of one or more of VDBP, clusterin, IGFALS or afamin in combination with measuring the expression level of one or both of ApoE and haptoglobin. The expression level of ApoE and haptoglobin can be measured using the methods described in detail above.
  • the human ApoE gene encodes the protein represented by GenBank Accession Number is NP — 000032.1
  • the human haptoglobin gene encodes two protein variants represented by GenBank Accession Numbers NP — 005134.1 (variant 1) and NP — 0011195741.1 (variant 2).
  • the human ApoE gene is transcribed into the nucleotide sequence as represented by GenBank Accession Number NM — 000041.2.
  • the human haptoglobin gene is transcribed into two variants as represented by GenBank Accession Numbers NM — 005143.3 (variant 1) and NM — 001126102.1 (variant 2).
  • the present invention provides a kit for diagnosing gastric cancer (GC) in a subject, determining if a subject is susceptible to developing GC, or assessing progression of GC in a subject.
  • the kit includes means for measuring an expression level of one or more biomarkers in the subject, wherein the one or more biomarkers are selected from the group consisting of vitamin D binding protein (VDBP), clusterin, insulin like growth factor binding protein complex acid labile subunit (IGFALS), and afamin.
  • VDBP vitamin D binding protein
  • IGFALS insulin like growth factor binding protein complex acid labile subunit
  • the kit includes a solid support, such as a chip, sensor, a microtiter plate or a bead or resin having a capture reagent attached thereon, wherein the capture reagent binds protein corresponding to one or biomarkers of the invention.
  • the kit can comprise mass spectrometry probes for SELDI, such as ProteinChip® arrays, or a versatile fibre-based SPR sensing device.
  • the kit can comprise a solid support with a reactive surface, and a container comprising the biospecific capture reagent.
  • the kit can also include a washing solution or instructions for making a washing solution, in which the combination of the capture reagent and the washing solution allows capture of one or more of the biomarker proteins on the solid support for subsequent detection by, for example, mass spectrometry.
  • the kit may include more than one type of adsorbent, each present on a different solid support.
  • such a kit can include instructions for suitable operational parameters in the form of a label or separate insert.
  • the instructions may inform a consumer about how to collect the sample, how to wash the probe or the particular biomarker protein or proteins to be detected.
  • the kit can include one or more containers with samples that represent a reference expression level for each biomarker, and are therefore to be used as standards for calibration.
  • the inventors have utilised the gp130 F/F genetically engineered mouse (GEM) model of inflammation-associated gastric cancer (GC) for biomarker discovery followed by validation in human samples.
  • GEM genetically engineered mouse
  • GC inflammation-associated gastric cancer
  • gp130 F/F mice harbour a phenylalanine (F) substitution mutation of a regulatory tyrosine residue in the cytokine receptor gp130, they respond with excessive Stat3 signalling to the cognate gp130 receptor ligands, including interleukin 6 (IL-6) and interleukin 11 (IL-11). Accordingly, the onset and progression of gastric tumourigenesis in gp130 F/F mice is suppressed by genetically restricting the expression of Stat3 in compound gp130 F/F ; Stat3 +/ ⁇ (FFStat3) mice.
  • F phenylalanine
  • IL6 selectively normalizes the pan-inflammatory phenotype characteristic for gp130 F/F mice without affecting gastric tumourigenesis in the corresponding gp130 F/F ; Il6 ⁇ / ⁇ (FFIL6) mice.
  • FFIL6 ⁇ / ⁇ mice the different gp130 F/F compound mutants enable genetic dissection of inflammation-associated gastric tumourigenesis, and the systemic, inflammatory acute phase response that is elicited by IL6 coincides with a variety of pathologies.
  • Serum supernatants were aliquoted in 400 ⁇ L volumes (primary aliquots) and stored at ⁇ 80° C.
  • secondary and tertiary preparations of human sera were made for verification purposes by enzyme-linked immunosorbent assay (ELISA) and Western blotting.
  • ELISA enzyme-linked immunosorbent assay
  • Demographic information of the 24 human subjects is provided in Table 1.
  • the depleted serum samples were thawed and subjected to two rounds of buffer exchange in TUC4% using 10 kDa MWCO Vivaspin 500 centrifugal devices (GE Healthcare, Uppsala, Sweden).
  • the final samples were made up to ⁇ 200 ⁇ L with TUC4% and conductivities were assessed using a Horiba Twin Cond conductivity meter (model B-173, Horiba, Kyoto, Japan) to confirm levels were below 300 ⁇ S.
  • the protein concentrations of the samples were determined via an EZQ assay (Invitrogen, Carlsbad, Calif.) as per the manufacturer's recommendations.
  • Dye swaps of biological replicates were performed to control for potential dye-associated bias. Separate internal standards were prepared for each of the two experiment (refer to Results section) by pooling 35 ⁇ g of protein from samples included in the particular experiment (with minor exceptions). The internal standard was labelled with Cy2 at a ratio of 200 pmol dye/70 ⁇ g protein. Labelling reactions were performed on ice for 30 minutes in darkness and quenched with the addition of 1 ⁇ L of 10 mM lysine per 200 pmol of dye. The appropriate Cy3 and Cy5 samples were combined with 70 ⁇ g of the internal standard and sufficient amounts of TUC4% to bring the samples to equivalent volumes (refer to Supplementary Tables 1 and 2).
  • Dithiothreitol (DTT, Sigma-Aldrich) and pH 4-7 carrier ampholytes (IPG buffer; GE Healthcare) were also added such that the final samples contained 210 ⁇ g protein, 7 M urea, 2 M thiourea, 30 mM Tris, 4% w/v CHAPS, 10 mM DTT, 0.5% v/v ampholytes plus a trace amount of bromophenol blue for color.
  • sample volumes were reduced to ⁇ 150 ⁇ L using 10 kDa molecular weight cut-off Vivaspin 500 centrifugal devices (5-10 minutes at 8,200 ⁇ g; GE Healthcare) prior to cup-loading onto 24 cm 4-7 Immobiline DryStrips (GE Healthcare), which had been rehydrated overnight in 450 ⁇ L of rehydration buffer (TUC4% containing 0.5% v/v ampholytes, 1.2% v/v DeStreak reagent [GE Healthcare] and trace bromophenol blue). Requisite Cy3, Cy5 and Cy2 samples were combined for electrophoretic separation. IEF in the first dimension was carried out using an IPGphor II (GE Healthcare) for 70,000 total Vhours.
  • the strips were equilibrated for 15 minutes in reducing buffer (50 mM Tris-HCl pH 8.8, 6 M urea, 30% v/v glycerol, 2% w/v SDS, 1% w/v DTT) then alkylating buffer (as above with 2.5% w/v of iodoacetamide (IAA) in place of DTT).
  • reducing buffer 50 mM Tris-HCl pH 8.8, 6 M urea, 30% v/v glycerol, 2% w/v SDS, 1% w/v DTT
  • alkylating buffer as above with 2.5% w/v of iodoacetamide (IAA) in place of DTT.
  • IAA iodoacetamide
  • ECL Plex Rainbow markers were included on a selected few gels. Protein separation in the second dimension was carried out using an EttanDALT 12 unit (GE Healthcare) in the presence of the anode and cathode buffers (Serva Electrophoresis) at 25° C. using a three phase program: (1) 50 V; 5 mA/gel for 1 hour, (2) 100 V; 10 mA/gel for 1 hour, (3) 250 V; 30 mA/gel for 14 hours. Gels were scanned using an Ettan DIGE Imager (GE Healthcare) at 100 ⁇ m resolution using the following exposures: Cy2 channel, 0.4 seconds; Cy3 channel, 0.07 seconds; Cy5 channel 0.1 seconds. Once scanned the gels were stored without fixation at ⁇ 80° C. until required for spot picking.
  • DIA spot detection was performed based on an estimated 10,000 spots with an exclusion filter rejecting spots with volumes ⁇ 30,000. Background subtraction and in-gel normalization were carried out automatically by the software.
  • the DIA workspaces were imported into BVA for manual spot matching to the master gel. Manual spot matching was required due to the large number of spot trains that were not effectively matched when the task was performed by the software.
  • the same user-defined master gel was used for Experiments 1 and 2 to ensure consistency of spot identities.
  • the master gel also constituted an analytical gel.
  • the master gel was exported into BVA for this purpose only and was not included in the statistical analyses.
  • Multivariate statistical testing by hierarchical clustering and principal component analysis was performed using the Extended Data Analysis (EDA) module of DeCyder (Version 7.0) based on spots that were detected in >70% of the gels.
  • EDA Extended Data Analysis
  • normalized volumes of the matched spots were exported from DeCyder into Excel (Microsoft, Redmond, Wash.).
  • Standardized abundance values (herein referred to as “spot volumes”) were produced by dividing the spot volumes of the Cy3 and Cy5 channels by the Cy2 channel for each gel. The spot volumes were then log 10 transformed to normally distribute the data and, for each group within a given comparison, the standard deviation (SD) of each spot was calculated.
  • HCT Ultra 3D-Ion-Trap mass spectrometer (Bruker Daltonics, Billerica, Mass.) operating in positive ion mode.
  • the column was equilibrated with 0.1% FA, 3% ACN at 0.5 ⁇ L/min and the samples eluted with an ACN gradient (3%-31% over 32 minutes).
  • Ionizable species 300 ⁇ m/z ⁇ 1,200 were trapped and one or two of the most intense ions eluting at the time were fragmented by collision-induced dissociation. Active exclusion was used to exclude a precursor ion for 30 seconds following the acquisition of two spectra.
  • MS and MS/MS spectra were subjected to peak detection and de-convolution using DataAnalysis (Version 3.4, Bruker Daltonics).
  • the MS and MS/MS mass lists were exported into BioTools (Version 3.1, Bruker Daltonics) then submitted to Mascot (Version 2.2).
  • Protein identifications were made on the basis of having at least two matching peptides with ion scores above the specified threshold. Matches to trypsin and contaminating human keratins were ignored. When redundancy in protein identification was observed, for example, when different protein isoforms were matched to a list of identical masses, only the most suitable database entry corresponding to the full length sequence and/or the entry to which additional masses were matched to isoform-specific regions of the protein were considered. When multiple proteins were identified within a spot only the entry with the largest emPAI score was considered in as the major constituent of the spot and thus the likely contributor to its differential regulation (Ishihama Y et al., 2005 , Mol. Cell. Proteomics, 4: 1265-1272). Human homologues of mouse proteins were identified using the BLAST function of UniProt (http://www.uniprot.org/blast/)(UniProt Consortium, 2011 , Nucl. Acids Res. 39: D214-219).
  • Rabbit anti-human afamin (Abcam, Cambridge, England) 2. Rabbit anti-mouse apolipoprotein E (apoE) (Thermo, Rockford, Ill.) 3. Mouse anti-human apoE (Abcam) 4. Rabbit anti-human apolipoprotein J (clusterin) (Abcam) 5. Rabbit anti-human fibronectin (Abcam) 6. Rabbit anti-human haptoglobin (Sigma-Aldrich)
  • HRP horseradish peroxidise
  • Membranes were washed a further 3 ⁇ with TBS-T then detected with Sigma Enhanced Chemiluminescent Peroxidase Substrate (Sigma-Aldrich or Millipore) and autographic film (Agfa, Mortsel, Belgium).
  • Western Blot densitometry was performed using ImageJ (National Institutes of Health; http://rsb.info.nih.gov/ij/) or ImageQuant TL (Version 7.0, GE Healthcare).
  • the intensities of the bands of interest were normalized to the intensity of the immunoglobulin light-chain band evident on the AmidoBlack stained membrane at ⁇ 25 kDa to control for potential differences in gel loading.
  • Enzyme-linked immunosorbent assays were performed in accordance with the manufacturer's recommendations. The nine ELISA kits used in this investigation were:
  • Serum protein concentrations were interpolated from kit-specific standard curves generated in GraphPad Prism (GraphPad Software). Resulting serum protein concentrations were standardized against the mean concentration obtained for each measured protein in the control group. This facilitated the cross-candidate comparisons of the markers on an equivalent scale (Faca V M et al., 2008 , PLoS Med. 5: e123). Mann-Whitney U tests (two-tailed, significance threshold P ⁇ 0.05) and ROC were performed in GraphPad Prism.
  • mice spontaneously and reproducibly develop distinct adenomas in the glandular part of the stomach that become histologically visible as 3-5 individual lesions by approximately 4-6 weeks of age. They continuously grow over the following 2-3 months to yield a maximal tumour burden of approximately 250 mg, and thus contributing to 0.8-1% of the overall body weight of these mice. These tumours occur with 100% penetrance and irrespective of the genetic background of the mice. It has been shown previously that these lesions replicate many of the progressive histological hallmarks associated with intestinal-type GC in humans arising from chronic infection with H. pylori (Jenkins B J et al., 2005 , Nat. Med.
  • gp130 F/F GEM harbour a phenylalanine substitution mutation of a regulatory tyrosine residue in the cytokine receptor gp130
  • these mice respond with excessive Stat3 signalling to the cognate gp130 receptor ligands that include IL6 and IL11. Accordingly, the onset and progression of gastric tumourigenesis in FF mice is suppressed and delayed by genetically restricting the expression of the latent transcription factor Stat3 in compound FFStat3 mice (Jenkins B J et al., 2005 , Nat. Med. 11: 845-852) ( FIG. 1 ).
  • FFIL11R ⁇ mice which lack expression of the IL11-specific IL11R ⁇ receptor subunit and therefore are unable to respond to IL11, fail to develop gastric tumours and survival of FFIL11R ⁇ mice remained similar to that of their IL11R ⁇ proficient counterparts.
  • the biomarker identification workflow employed in this investigation can be broadly categorised into three stages.
  • the discovery stage examined sera collected from the genetic engineered mouse (GEM) model of gastric cancer (GC) to identify differentially expressed proteins as candidate serum biomarkers.
  • the second stage applied the semi-quantitative technique of Western blotting to verify the differential expression of a subset of candidate biomarkers in the GEM model.
  • the third stage tested biomarkers verified in the mouse against human sera of GC patients and healthy controls using Western blotting and also the clinically relevant diagnostic platform, the quantitative ELISA ( FIG. 2A ).
  • Unsupervised hierarchical clustering based on the 512 matched spot volumes revealed clusters based on mouse genotype at the lowest level of the hierarchy and on the GC versus non-GC phenotype at higher levels ( FIG. 2C ).
  • Principal component analysis also revealed distinct groupings based on genotype with a clear dichotomy between the GC and non-GC mice ( FIG. 2D ), suggesting that the expression of several matched spots was linked to the GC phenotype.
  • the predominant separation of the GC and non-GC groups based on the first principal component highlighted that the phenotype was the major source of variation within the experiment.
  • a filtering strategy was developed to distinguish between which of the 512 matched gel spots were regulated in association with the IL6-mediated acute phase response versus those that were associated with GC (i.e. the candidate biomarkers). This process is summarized graphically in FIG. 3 . Initially, three comparisons of the volumes of the 512 matched spots were made facilitated by the inclusion of multiple mutant genotypes in the study. In the first comparison, the spots of the seven WT mice were compared to the seven IL6 mice using T-tests (P ⁇ 0.01), calculations of the false discovery rate (q ⁇ 0.01) and a post-hoc power calculation (fold change>magnitude 2.1; refer to Supplementary Information Section 1.4).
  • the 512 spot volumes of the eight FF mice were compared to the eight FFIL6 mice using the same parameters described for comparison 1.
  • the 16 GC phenotype mice (FF/FFIL6 genotypes) were compared to the 22 non-GC phenotype (WT/IL6/FFStat3 genotypes) mice also using T-tests (P ⁇ 0.01), calculations of the false discovery rate (q ⁇ 0.01) and a post-hoc power calculation with a minimum fold-change of magnitude 1.8.
  • ROC 1 the GC phenotype (FF/FFIL6 genotypes) was considered positive and non-GC (WT/IL6/FFStat3 genotypes) negative.
  • AUC 1 area-under-the-curve 1
  • ROC 2 the FF mutation was considered positive (FF/FFIL6/FFStat3 genotypes) and wild-type gp130 was considered negative (WT/IL6 genotypes).
  • FIG. 5A The positions of the eight proteins on a representative 2D DIGE overlay gel is given in FIG. 5A .
  • Visual inspection of the box-and-whisker plots of the associated spot volumes demonstrated that each was specifically regulated in the GC versus non-GC phenotype (FF/FFIL6 versus WT/IL6/FFStat3) ( FIG. 5B ).
  • the serum levels of afamin, apoE, haptoglobin, fibronectin and clusterin together with VDBP, IGFALS and AACT were measured by ELISA.
  • an ELISA for serum CA72-4 was also performed. Higher CA 72-4 levels have been associated with an increased risk of death by GC with evidence suggesting it is more prognostic and specific for GC than CEA and CA19-9 (Ucar E et al., 2008 , Adv. Ther. 25: 1075-1084).
  • the concentrations of the nine proteins were standardized by dividing each individual's result by the mean concentration of the protein in the control group. Accordingly, the mean concentrations of all proteins in the control group were 1. This facilitated a cross-candidate comparison of the markers on an equivalent scale (Faca V M et al., 2008 , PLoS Med. 5:e123).
  • Serum concentrations of afamin, apoE, clusterin and haptoglobin were found to be significantly different between the GC patients and controls (P ⁇ 0.05) ( FIG. 7A ).
  • IGFALS and VDBP also showed differential expression between the groups based on the magnitude of fold change (P>0.05).
  • CA72-4 was slightly elevated in the GC group with a non-significant 1.3 fold increase in expression ( FIG. 7A ).
  • Scatter plots depicting the ELISA results for AACT and fibronectin, which showed no apparent regulation between the GC patients and controls (P>0.5), are provided in FIG. 8 .
  • ROC analysis The diagnostic capabilities of the regulated proteins, afamin, apoE, clusterin, and haptoglobin, as well as CA 72-4 were further explored by ROC analysis ( FIG. 7B ).
  • the sensitivities and specificities of afamin and clusterin were both 91% and 92%, respectively (both with 10/11 true positives, 12/13 true negatives).
  • the sensitivity and specificity of apoE was 91% and 85%, respectively (10/11 true positives, 11/13 true negative), while for haptoglobin the sensitivity was 64% with 100% specificity (7/11 true positives, 13/13 true negatives).
  • the sensitivity and specificity of CA72-4 was only 36% and 77%, respectively (4/11 true positive, 10/13 true negatives).
  • biomarker discovery strategy was developed based on (i) the employment of a highly predictable and clinically relevant mouse model of human disease; (ii) a state-of-the-art proteomics approach for candidate biomarker identification; and (iii) the translation of the identified candidate biomarkers in human samples using a well characterised diagnostic platform, the ELISA.
  • mice representing multiple mutant genotypes including FFIL6 mice that develop gastric tumours in the absences of systemic inflammation. Accordingly, these mice provide the genetic means to identify and verify proteomic changes associated with gastric tumourigenesis and the systemic acute phase response elicited by both IL-6 and IL-11.
  • this study provides further evidence for the on-going use of GEM models in cancer research whereby all proteins identified here in the mouse were validated in human sera with the expected direction of fold-change using two different platforms (Western blotting and ELISA).
  • Circulating serum glycoproteins are a promising source of cancer biomarkers. Changes in both protein expression and carbohydrate structure have been recognized as early hallmarks of cancer with glycoproteins playing an important role in tumour invasion and metastasis. Indeed, the current clinical marker CA 72-4 is a glycoprotein.
  • the sensitivity and specificity values obtained by ROC analysis here for CA 72-4 (36% sensitivity, 77% specificity) were slightly lower than those described in the literature (40% sensitivity, >95% specificity). This, however, may be a reflection of the small size of the dataset herein and/or the particular ELISA that was employed.
  • Example 1 The results referred to in Example 1 above were further validated in a second cohort of gastric cancer patients (25 in total).
  • blood was collected from both the male and female patients at the time of surgery and their sera stored at ⁇ 80° C. until required for enzyme-linked immunosorbent assays (ELISAs).
  • the cancers of the patients included a combination of five early (T1) and twenty late (T4) histological sub-types.
  • T1 and T4 five early histological sub-types.
  • a total of ten control samples were included for this experiment with blood being collected from the healthy volunteers by an experienced phlebotomist.
  • Sera from control blood were also stored at ⁇ 80° C. until required for ELISAs.
  • all experiments were approved by ethics committees of the Peter MacCallum Cancer Research Institute and the University of Sydney.
  • Sandwich ELISA kits for the afamin, clusterin, haptoglobin, IGFALS and VDBP proteins were obtained from a single commercial supplier (Uscn Life Science Inc., Wuhan, China) to ensure consistency and assays were performed according to the manufacturer's instructions.
  • collected serum was thawed and diluted with PBS, standards were prepared, and all samples were added in duplicate to 96-well microtitre plates coated with appropriate antibody for the specific proteins of interest.
  • avadin conjugated to Horseradish Peroxidase (HRP) was added to each well and incubated.
  • TMB substrate was added, resulting in only those wells containing the specific protein, bio-conjugated antibody, and enzyme conjugated avidin, exhibiting a change in colour. Subsequently, the reaction was terminated with the addition of sulphuric acid and the colour change measured spectrophotometrically at 450 nm.
  • the concentration of the specific protein was then determined by comparing the optical density of the samples to the standard curve. The optical density of standards was plotted against the known concentration of the standards on a log-log graph using Graphpad Prism and unknown concentrations interpolated from this. As described in Example 1, the concentrations of the five proteins were standardized/normalized by dividing the result for each test sample by the mean concentration of the protein in the control group. Accordingly, the mean concentrations of all proteins in the control group were 1. This facilitated a cross-candidate comparison of the markers on an equivalent scale.
  • Example 1 The aim of this study was to confirm the suitability of afamin, clusterin, haptoglobin, IGFALS and VDBP (as shown in Example 1) to represent a suite of biomarkers for detection of gastric cancer. Building on from the ELISA results of Example 1, analysis of a new cohort of patients was conducted using ELISA kits from one manufacturer, thereby providing consistency throughout analysis of the proteins.
  • the second aim of this study was also to determine whether these five biomarkers could be used to identify early stage GC.
  • Receiver Operating Condition (ROC) curves showing the sensitivity and specificity of each protein to distinguish true positive from false positive readings ( FIG. 10 ) show VDBP, clusterin and IGFALS to be of particular interest individually.
  • FIG. 11 shows secondary combinations of ROC curves for haptoglobin and VDBP, IGFALS and VDBP, IGFALS and afamin, clusterin and afamin, and VDBP and afamin. These pairings are of particular note for their potential for increasing the true positive rate and reducing the false positive rate for any diagnostic developed using this suite of proteins.
  • the tertiary combinations shown in the ROC curves of FIG. 12 also provide evidence of the ability of combinations of these proteins to increase the true positive rate and reduce the false positive rate for any diagnostic developed.

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