EP2630498A2 - Biomarqueurs pronostiques chez des patientes atteintes d'un cancer ovarien - Google Patents

Biomarqueurs pronostiques chez des patientes atteintes d'un cancer ovarien

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Publication number
EP2630498A2
EP2630498A2 EP11835211.1A EP11835211A EP2630498A2 EP 2630498 A2 EP2630498 A2 EP 2630498A2 EP 11835211 A EP11835211 A EP 11835211A EP 2630498 A2 EP2630498 A2 EP 2630498A2
Authority
EP
European Patent Office
Prior art keywords
biomarkers
ovarian cancer
subject
sample
prognosis
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Ceased
Application number
EP11835211.1A
Other languages
German (de)
English (en)
Other versions
EP2630498A4 (fr
Inventor
Estrid Hogdall
Eric T. Fung
Ib Jarle Christensen
Claus Hogdall
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Aspira Womens Health Inc
Original Assignee
Vermillion Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Vermillion Inc filed Critical Vermillion Inc
Publication of EP2630498A2 publication Critical patent/EP2630498A2/fr
Publication of EP2630498A4 publication Critical patent/EP2630498A4/fr
Ceased legal-status Critical Current

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Classifications

    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57449—Specifically defined cancers of ovaries
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N30/00—Investigating or analysing materials by separation into components using adsorption, absorption or similar phenomena or using ion-exchange, e.g. chromatography or field flow fractionation
    • G01N30/02—Column chromatography
    • G01N30/88—Integrated analysis systems specially adapted therefor, not covered by a single one of the groups G01N30/04 - G01N30/86
    • G01N2030/8809—Integrated analysis systems specially adapted therefor, not covered by a single one of the groups G01N30/04 - G01N30/86 analysis specially adapted for the sample
    • G01N2030/8813—Integrated analysis systems specially adapted therefor, not covered by a single one of the groups G01N30/04 - G01N30/86 analysis specially adapted for the sample biological materials
    • G01N2030/8831—Integrated analysis systems specially adapted therefor, not covered by a single one of the groups G01N30/04 - G01N30/86 analysis specially adapted for the sample biological materials involving peptides or proteins
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N27/00—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means
    • G01N27/26—Investigating or analysing materials by the use of electric, electrochemical, or magnetic means by investigating electrochemical variables; by using electrolysis or electrophoresis
    • G01N27/416—Systems
    • G01N27/447—Systems using electrophoresis
    • G01N27/44756—Apparatus specially adapted therefor
    • G01N27/44773—Multi-stage electrophoresis, e.g. two-dimensional electrophoresis
    • G01N27/44778—Multi-stage electrophoresis, e.g. two-dimensional electrophoresis on a common gel carrier, i.e. 2D gel electrophoresis
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/54—Determining the risk of relapse
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/56—Staging of a disease; Further complications associated with the disease

Definitions

  • Ovarian cancer is among the most lethal gynecologic malignancies in developed countries. Annually in the United States alone, approximately 23,000 women are diagnosed with the disease and almost 14,000 women die from it. (Jamal, A., et al., CA Cancer J. Clin, 2002; 52:23-47). Despite progress in cancer therapy, ovarian cancer mortality has remained virtually unchanged over the past two decades. Given the steep survival gradient relative to the stage at which the disease is diagnosed, early detection remains the most important factor in improving long-term survival of ovarian cancer patients.
  • tumor markers suitable for the early detection and diagnosis of cancer holds great promise to improve the clinical outcome of patients. It is especially important for patients presenting with vague or no symptoms or with tumors that are relatively inaccessible to physical examination. Despite considerable effort directed at early detection, women generally present with disseminated disease at diagnosis.
  • the present invention provides compositions and methods for determining ovarian cancer prognosis (e.g., predicting overall survival probability or predicting progression free survival probability). Such methods are useful in selecting an appropriate therapeutic regimen for the subject.
  • the invention provides compositions comprising one or more biomarkers and sensitive and rapid methods for using the kits to determine the survival status of patients with ovarian cancer by measuring the levels of particular biomarkers in a biological sample.
  • the detection and measurement of these biomarkers in patient samples provides information that diagnosticians can correlate with survival status of human ovarian cancer patients or a negative diagnosis (e.g. , normal or disease-free).
  • the markers are characterized by mass/charge ratio, molecular weight and/or by their known protein identities. The markers can be resolved from other proteins in a sample by using a variety of fractionation techniques, e.g.
  • the method of resolution involves Surface-Enhanced Laser Desorption/Ionization ("SELDI”) mass
  • the invention generally features a method of determining the prognosis of a subject having or suspected of having ovarian cancer, the method involving comparing the level of biomarkers inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein), transferrin (TFR), and beta-2 microglobin (B2M) or fragments thereof in a sample from the subject to the level present in a reference, wherein an increased level of said biomarkers relative to the reference is indicative of a poor prognosis.
  • biomarkers inter-alpha (globulin) inhibitor H4 plasma Kallikrein-sensitive glycoprotein), transferrin (TFR), and beta-2 microglobin (B2M) or fragments thereof in a sample from the subject to the level present in a reference, wherein an increased level of said biomarkers relative to the reference is indicative of a poor prognosis.
  • the invention generally features a method of determining the prognosis of a subject having or suspected of having ovarian cancer, the method involving comparing the level of biomarkers B2M, TrF and ITIH4 or fragments thereof, wherein an increased level of said biomarkers relative to the reference is indicative of a poor prognosis.
  • the invention generally features a method of determining the prognosis of a subject having or suspected of having ovarian cancer, the method involving comparing the level of biomarkers B2M and CTAP3 or fragments thereof, wherein an increased level of said biomarkers relative to the reference is indicative of a poor prognosis.
  • the invention generally features a method of determining the prognosis of a subject having or suspected of having ovarian cancer, the method involving comparing the level of biomarkers CA125, HEPC, B2M and CTAP3 or fragments thereof in a sample from the subject to the level present in a reference, wherein an increased level of said biomarkers relative to the reference is indicative of a poor prognosis.
  • the invention generally features a method of determining the prognosis of a subject having or suspected of having ovarian cancer, the method involving comparing the level of biomarkers APOA1, TT, HEPC, B2M, CTAP3, TrF and CA125 or fragments thereof in a sample from the subject to the level present in a reference, wherein an increased level of said biomarkers relative to the reference is indicative of a poor prognosis.
  • the invention generally features a method of qualifying ovarian cancer status in a human involving providing a subject sample of blood or a blood derivative; and fractionating proteins in the sample on an anion exchange resin and collecting fractions that contain inter-alpha (globulin) inhibitor H4 (plasma
  • IIH4 Kallikrein-sensitive glycoprotein
  • TFR transferrin
  • B2M beta-2 microglobin
  • the invention generally features a kit containing a capture reagent that binds a panel of biomarkers containing, inter-alpha (globulin) inhibitor H4 (plasma Kallikrein- sensitive glycoprotein) (ITIH4), transferrin (TFR), and ) beta-2 microglobin (B2M); and a container containingat the panel of biomarkers.
  • a capture reagent that binds a panel of biomarkers containing, inter-alpha (globulin) inhibitor H4 (plasma Kallikrein- sensitive glycoprotein) (ITIH4), transferrin (TFR), and ) beta-2 microglobin (B2M); and a container containingat the panel of biomarkers.
  • ITIH4 plasma Kallikrein- sensitive glycoprotein
  • TFR transferrin
  • B2M beta-2 microglobin
  • the invention generally features a kit containing capture reagents that binds the panel of biomarkers fragments containing inter-alpha
  • globulin inhibitor H4 plasma Kallikrein- sensitive glycoprotein (ITIH4), transferrin (TFR), and ) beta-2 microglobin (B2M); and instructions for using the capture reagents to detect the biomarkers.
  • the invention generally features a system containing a plurality of capture reagents each of which has bound to it a different biomarker
  • IIH4 insulin glycoprotein
  • TFR transferrin
  • B2M beta-2 microglobin
  • the invention generally features a method of determining an ovarian cancer patient's prognosis containingdetermining the concentration or expression levels or peak intensity values of inter-alpha (globulin) inhibitor H4 (plasma Kallikrein- sensitive glycoprotein) (ITIH4), transferrin (TFR), and beta-2 microglobin (B2M); and correlating the measurements with ovarian cancer patient survival status.
  • inter-alpha (globulin) inhibitor H4 plasma Kallikrein- sensitive glycoprotein) (ITIH4), transferrin (TFR), and beta-2 microglobin (B2M)
  • the invention generally features a method of determining an ovarian cancer patient's prognosis involving determining the concentration or expression levels or peak intensity values of a combination of two or more biomarkers in a sample from the subject, wherein the one or more biomarkers are selected from the group consisting of: inter-alpha (globulin) inhibitor H4 (plasma Kallikrein- sensitive glycoprotein) (ITIH4), transferrin (TFR), and beta-2 microglobin (B2M)and correlating the measurements with ovarian cancer patient survival status.
  • ITIH4 plasma Kallikrein- sensitive glycoprotein
  • TFR transferrin
  • B2M beta-2 microglobin
  • the invention generally features a method of determining an ovarian cancer patient's prognosis involving determining the concentration or expression levels or peak intensity values of inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein) (ITIH4), transferrin (TFR), and beta-2 microglobin (B2M); and correlating the measurements with ovarian cancer patient survival status.
  • inter-alpha (globulin) inhibitor H4 plasma Kallikrein-sensitive glycoprotein) (ITIH4), transferrin (TFR), and beta-2 microglobin (B2M)
  • the methods further involve comparing the level of one or more additional biomarkers to the level present in a reference, wherein the additional biomarkers are selected from the group consisting of apolipoprotein Al, transthyretin, inter-alpha trypsin inhibitor IV, transferrin, hepcidin, connective-tissue activating protein 3, and Serum Amyloid Al and beta-2 microglobin.
  • the methods further involve comparing the level of CA125 in the subject sample to the level present in a reference.
  • the method further comprises considering one or more of the following: radicality of primary surgery, age at diagnosis and treatment.
  • the method further comprises considering one or more of FIGO stage, histological type of tumor, and CA125.
  • the prognosis is predictive of overall survival or progression- free survival.
  • failure to detect an increased level in one or more of said biomarkers is indicative of a good prognosis.
  • a patient's prognosis is used in selecting a therapeutic regiment.
  • a poor prognosis indicates that the subject requires an aggressive therapeutic regimen and a good prognosis indicates that the subject requires a less aggressive therapeutic regimen.
  • an aggressive therapeutic regimen includes neoadjuvant chemotherapy.
  • the overall survival or progression free survival is selected from the group consisting of one to two years survival post diagnosis; two to five years post diagnosis; and beyond five years post diagnosis.
  • the panel of biomarkers is measured by immunoassay, mass spectrometry, or radioassay. In additional embodiments the panel of biomarkers is captured using immobilized antibodies. In yet other embodiments the panel of biomarkers is detected using immobilized antibodies. In certain embodiments the correlating is performed by a software classification algorithm. In yet other embodiments the sample is selected from ovarian tissue, lymph nodes, tissue biopsy (e.g., diaophram, intestine, lavage, omentum) ovarian cyst fluid, ascites, pleural effusion, urine, blood, serum, and plasma.
  • tissue biopsy e.g., diaophram, intestine, lavage, omentum
  • the capture reagent is an antibody. In other embodiments contain an MS probe to which the capture reagents are attached or is attachable. In other embodiments the capture reagents are immobilized metal chelates. In yet other embodiments the kits contain written instructions for use of the kit for detection of ovarian cancer status in a subject. In various embodiments of any of the above aspects or any other aspect of the invention delineated herein, an article of manufacture containing a panel of capture reagents that bind the panel of biomarkers or fragments of the respective biomarkers thereof.
  • biomarkers are inter-alpha (globulin) inhibitor H4 (plasma Kallikrein- sensitive glycoprotein) (ITIH4), transferrin (TFR), and beta-2 microglobin (B2M).
  • biomarkers are inter-alpha (globulin) inhibitor H4 (plasma Kallikrein- sensitive glycoprotein) (ITIH4), transferrin (TFR), and ) beta-2 microglobin (B2M).
  • biomarkers provides a surprisingly accurate prognosis for subjects having ovarian cancer.
  • the panel of biomarkers consists of inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein) (ITIH4), transferrin (TRF), and beta-2 microglobin (B2M). This panel of three biomarkers has been shown by the instant inventors to be highly indicative of the prognosis of subjects having ovarian cancer.
  • the panel of biomarkers is predictive of survival independent of the stage of cancer.
  • the present invention provides a method of assessing an ovarian cancer patient's survival status in a subject containing(a) measuring the panel of three biomarkers in a sample from the subject, and correlating the measurement with ovarian cancer patient survival status.
  • the measuring step comprises detecting the m/z (mass-to-charge ratio) values of markers in the sample using SELDI.
  • the instant invention provides methods for determining both progression free survival and overall survival in subjects diagnosed with ovarian cancer.
  • Preferred methods of the invention also include assessing ovarian cancer patient survival status comprising:
  • the methods further comprise managing subject treatment based on the status determined by the methods disclosed herein. For example, if the result of the methods of the present invention is inconclusive or there is reason that confirmation of status is necessary, the physician may order more tests. Alternatively, if the result of the methods of the present invention indicate a potentially poor prognosis, alternative or more aggressive therapies may be warranted. Furthermore, if the results show a potentially good prognosis, no or less aggressive therapies may be warranted.
  • Examples of more aggressive therapy include: a) The physician may after surgery treat the patient with more intensive and prolonged chemotherapy, b) Offer additional chemotherapy or biological treatments, c) The patient may be monitored more closely for relapse or progressive disease, d) Patients with both an indication of a poor prognosis and extensive disease, which on imaging indicate nonradical surgery, may be offered neoadjuvant chemotherapy and subsequent interval surgery.
  • the proteomic index may be part in the total clinical judgment of treatment versus palliative treatment in severe ill patients, f) Radical and correct staged patients with stage one and grade 1-2 may be offered adjuvant treatment, g) The patients must be selected for surgery by a gynecologic-oncologic surgeon experienced in performing extensive procedures Examples of less aggressive therapy include, a) The index may be part in the decision making for radical surgery, b) Radical and correct staged patients with stage one and grade 1-2 may avoid a potentially harmful chemotherapy, c) The patient may be operated by a less specialized gynecologist.
  • a prognostic index may in the future be used to select patients for
  • ovarian cancer patient survival status refers to the status of survival of the patient.
  • types of ovarian cancer survival statuses include, but are not limited to, disease free or overall survival one year after diagnosis, 2 years after diagnosis, 3 years after diagnosis, 4 years after diagnosis, and 5 or more years after diagnosis.
  • Another type of status is "treatment responsiveness” i.e. whether a patient has a high or low likelihood of responding to a given type of therapy.
  • a third type of status is "remission” i.e.
  • the mass accuracy of the spectral instrument is considered to be about within +/- 0.15 percent of the disclosed molecular weight value. Additionally, to such recognized accuracy variations of the instrument, the spectral mass determination can vary within resolution limits of from about 400 to 1000 m/dm, where m is mass and dm is the mass spectral peak width at 0.5 peak height.
  • a Cox proportional hazards model is a regression model for studying the association between time to event data and explanatory variables, e.g. tumor stage, age and gender.
  • the hazard rate (intensity of the event)on the log scale is the dependent variable which is a linear function of the explanatory
  • a HR above one indicates an increased intensity or risk for the event and a value below a decreased intensity or risk.
  • HR 1.62 for a patient with a stage III ovarian cancer compared to a patient with a stage I cancer. This means that the stage III patient has an increased intensity or risk of 62% for death compared to the stage I patient.
  • a HR above one a poor prognosis and a HR below one a more favorable prognosis.
  • a statistical test specifies a null hypothesis which is compared to the alternative hypothesis based on the probability of the observed outcome. If the probability of observing the outcome assuming the null hypothesis is below a prespecified threshold denoted the level of significance then the null hypothesis is rejected in favor of the alternative hypothesis. The probability of incorrectly rejecting the null hypothesis, i.e. the null hypothesis is true, is the chosen level of significance often denoted the Type I error. A good result is the rejection of the null hypothesis when the alternative is true, the probability of this is called the power of the test and is dependent on the difference compared to the null hypothesis and the chosen level of significance.
  • Biochip arrays useful in the invention include protein and nucleic acid arrays.
  • One or more markers are captured on the biochip array and subjected to laser ionization to detect the molecular weight of the markers.
  • Analysis of the markers is, for example, by molecular weight of the one or more markers against a threshold intensity that is normalized against total ion current.
  • logarithmic transformation is used for reducing peak intensity ranges to limit the number of markers detected.
  • Another method of measuring the biomarkers includes the use of a
  • the step of correlating the measurement of the biomarkers with ovarian cancer patient survival status is performed by a software classification algorithm.
  • data is generated on subject samples on a biochip array, by subjecting said biochip array to laser ionization and detecting intensity of signal for mass/charge ratio; and, transforming the data into computer readable form; and executing an algorithm that classifies the data according to user input parameters, for detecting signals that represent markers present in ovarian cancer patients and are lacking in non-cancer subject controls.
  • Biochip surfaces are, for example, ionic, anionic, comprised of immobilized nickel ions, comprised of a mixture of positive and negative ions, comprised of one or more antibodies, single or double stranded nucleic acids, proteins, peptides or fragments thereof, amino acid probes, or phage display libraries.
  • one or more of the markers are measured using laser desorption/ionization mass spectrometry, comprising providing a probe adapted for use with a mass spectrometer comprising an adsorbent attached thereto, and contacting the subject sample with the adsorbent, and; desorbing and ionizing the marker or markers from the probe and detecting the deionized/ionized markers with the mass spectrometer.
  • the laser desorption/ionization mass spectrometry comprises: providing a substrate comprising an adsorbent attached thereto; contacting the subject sample with the adsorbent; placing the substrate on a probe adapted for use with a mass spectrometer comprising an adsorbent attached thereto; and, desorbing and ionizing the marker or markers from the probe and detecting the desorbed/ionized marker or markers with the mass spectrometer.
  • the adsorbent can for example be hydrophobic, hydrophilic, ionic or metal chelate adsorbent, such as, nickel or an antibody, single- or double stranded oligonucleotide, amino acid, protein, peptide or fragments thereof.
  • the methods of the present invention can be performed on any type of patient sample that would be amenable to such methods, e.g., blood, serum and plasma.
  • kits comprising capture reagents that bind the biomarkers and a container comprising the panel of biomarkers.
  • capture reagent can be any type of reagent, preferably the reagent is a SELDI probe.
  • the capture reagent comprises an immobilized metal chelate ("IMAC").
  • IMAC immobilized metal chelate
  • kits of the present invention further comprise a wash solution that selectively allows retention of the bound biomarker to the capture reagent as compared with other biomarkers after washing.
  • the invention also provides kits comprising capture reagents that bind the three biomarkers and instructions for using the capture reagent to measure the biomarkers.
  • the capture reagent comprises an antibody.
  • kits further comprise an MS probe to which the capture reagent is attached or is attachable.
  • the capture reagent comprises an IMAC.
  • the kits may also contain a wash solution that selectively allows retention of the bound biomarker to the capture reagent as compared with other biomarkers after washing.
  • the kit comprises written instructions for use of the kit for determining ovarian cancer status and the instructions provide for contacting a test sample with the capture reagents and measuring one or more biomarkers retained by the capture reagents.
  • the kit also provides for capture reagents, which are antibodies, single or double stranded oligonucleotide, amino acid, protein, peptide or fragments thereof.
  • Measurement of one or more protein biomarkers using the kit is by mass spectrometry or immunoassays such as an ELISA.
  • Purified proteins for detection of ovarian cancer and/or generation of antibodies for further diagnostic assays are also provided for.
  • the invention also provides an article manufacture comprising capture reagents bound to the panel of biomarkers.
  • FIGS 1A-1D depicts representative spectra from non-progressing OC patients (top two spectra) and progressing OC patients (bottom two spectra).
  • A transthyretin (TRF);
  • B beta 2 microglobulin (B2M);
  • C ITIH4;
  • D CTAP3.
  • Figure 3 depicts a plot showing hazard ratios for different combinations of the 3 intensities, B2M on the abscissae and for 1 and third quartiles of TRF and ⁇ 4, all HR compared to a patient with a median level of each peak.
  • Adsorption refers to detectable non-covalent binding of an analyte to an adsorbent or capture reagent.
  • Antibody refers to a polypeptide ligand substantially encoded by an immunoglobulin gene or immunoglobulin genes, or fragments thereof, which specifically binds and recognizes an epitope (e.g. , an antigen).
  • the recognized immunoglobulin genes include the kappa and lambda light chain constant region genes, the alpha, gamma, delta, epsilon and mu heavy chain constant region genes, and the myriad immunoglobulin variable region genes. Antibodies exist, e.g.
  • antibody as used herein, also includes antibody fragments either produced by the modification of whole antibodies or those synthesized de novo using recombinant DNA methodologies. It also includes polyclonal antibodies, monoclonal antibodies, chimeric antibodies, humanized antibodies, or single chain antibodies. "Fc" portion of an antibody refers to that portion of an immunoglobulin heavy chain that comprises one or more heavy chain constant region domains, CHi, CH 2 and CH 3 , but does not include the heavy chain variable region.
  • Biochip refers to a solid substrate having a generally planar surface to which an adsorbent is attached. Frequently, the surface of the biochip comprises a plurality of addressable locations, each of which location has the adsorbent bound there.
  • Biochips can be adapted to engage a probe interface and, therefore, function as probes.
  • the "complexity" of a sample adsorbed to an adsorption surface of an affinity capture probe means the number of different protein species that are adsorbed.
  • a marker refers to differences in the quantity and/or the frequency of a marker present in a sample taken from a subject having or having a propensity to develop cancer as compared to a control subject.
  • the IAIH4 fragment is present at an elevated level in biological samples obtained from ovarian cancer patients as compared to samples from control subjects.
  • Apo Al and transthyretin described herein are present at a decreased level in samples obtained from ovarian cancer patients compared to samples from control subjects.
  • a marker can be a polypeptide, which is detected at a higher frequency or at a lower frequency in samples of human cancer patients compared to samples of control subjects.
  • a marker can be differentially present in terms of level, quantity, and/or frequency.
  • a polypeptide is differentially present between two samples if the
  • a polypeptide in one sample is different from the amount of the polypeptide in the other sample.
  • the difference is statistically significant.
  • a polypeptide is differentially present between the two samples if it is present at least about 120%, at least about 130%, at least about 150%, at least about 180%, at least about 200%, at least about 300%, at least about 500%, at least about 700%, at least about 900%, or at least about 1000% greater than it is present in the other sample, or if it is detectable in one sample and not detectable in the other.
  • a polypeptide is differentially present between two sets of samples if the frequency of detecting the polypeptide in the ovarian cancer patients' samples is statistically significantly higher or lower than in the control samples.
  • a polypeptide is differentially present between the two sets of samples if it is detected at least about 120%, at least about 130%, at least about 150%, at least about 180%, at least about 200%, at least about 300%, at least about 500%, at least about 700%, at least about 900%, or at least about 1000% more frequently or less frequently observed in one set of samples than the other set of samples.
  • Diagnostic means identifying the presence or nature of a pathologic condition, i.e., ovarian cancer. Diagnostic methods differ in their sensitivity and specificity.
  • the "sensitivity” of a diagnostic assay is the percentage of diseased individuals who test positive (percent of "true positives”). Diseased individuals not detected by the assay are “false negatives.” Subjects who are not diseased and who test negative in the assay, are termed “true negatives.”
  • the "specificity" of a diagnostic assay is 1 minus the false positive rate, where the "false positive” rate is defined as the proportion of those without the disease who test positive. While a particular diagnostic method may not provide a definitive diagnosis of a condition, it suffices if the method provides a positive indication that aids in diagnosis.
  • a "control amount" of a marker can be any amount or a range of amount, which is to be compared against a test amount of a marker.
  • a control amount of a marker can be the amount of a marker in a person without ovarian cancer.
  • a control amount is an absolute amount (e.g., ⁇ g/ml).
  • a control amount is the the relative level (e.g., relative intensity of signals).
  • a "diagnostic amount" of a marker refers to an amount of a marker in a subject's sample that is consistent with a diagnosis of ovarian cancer.
  • a diagnostic amount is the absolute amount (e.g. , g/ml) of analyte.
  • a diagnostic amount is the relative level (e.g., relative intensity of signals).
  • Eluant or “wash solution” refers to an agent, typically a solution, which is used to affect or modify adsorption of an analyte to an adsorbent surface and/or remove unbound materials from the surface.
  • the elution characteristics of an eluant can depend, for example, on pH, ionic strength, hydrophobicity, degree of
  • Gas phase ion spectrometer refers to an apparatus that detects gas phase ions.
  • Gas phase ion spectrometers include an ion source that supplies gas phase ions.
  • Gas phase ion spectrometers include, for example, mass spectrometers, ion mobility spectrometers, and total ion current measuring devices.
  • Gas phase ion spectrometry refers to the use of a gas phase ion spectrometer to detect gas phase ions.
  • Ion source refers to a sub-assembly of a gas phase ion spectrometer that provides gas phase ions.
  • the ion source provides ions through a desorption/ionization process.
  • Such embodiments generally comprise a probe interface that positionally engages a probe in an interrogatable relationship to a source of ionizing energy (e.g., a laser desorption/ionization source) and in concurrent communication at atmospheric or subatmospheric pressure with a detector of a gas phase ion spectrometer.
  • a source of ionizing energy e.g., a laser desorption/ionization source
  • Forms of ionizing energy for desorbing/ionizing an analyte from a solid phase include, for example: (1) laser energy; (2) fast atoms (used in fast atom
  • ionizing energy for solid phase analytes is a laser (used in laser desorption/ionization), in particular, nitrogen lasers, Nd-Yag lasers and other pulsed laser sources.
  • Fluence refers to the energy delivered per unit area of interrogated image.
  • a high fluence source, such as a laser, will deliver about 1 mJ / mm2 to 50 mJ / mm2.
  • a sample is placed on the surface of a probe, the probe is engaged with the probe interface and the probe surface is struck with the ionizing energy.
  • the energy desorbs analyte molecules from the surface into the gas phase and ionizes them.
  • ionizing energy for analytes include, for example: (1) electrons that ionize gas phase neutrals; (2) strong electric field to induce ionization from gas phase, solid phase, or liquid phase neutrals; and (3) a source that applies a combination of ionization particles or electric fields with neutral chemicals to induce chemical ionization of solid phase, gas phase, and liquid phase neutrals.
  • Laser desorption mass spectrometer refers to a mass spectrometer that uses laser energy as a means to desorb, volatilize, and ionize an analyte.
  • Managing subject treatment refers to the action of a clinician (e.g., physician( subsequent to a determination of ovarian cancer status in a subject. For example, if the result of the methods of the present invention is inconclusive or there is reason that confirmation of status is necessary, the physician may order more tests. Alternatively, if the result of the methods of the present invention indicates a potentially poor prognosis, alternative or more aggressive therapies may be warranted. Furthermore, if the results show a potentially good prognosis, no or less aggressive therapies may be warranted.
  • a clinician e.g., physician( subsequent to a determination of ovarian cancer status in a subject. For example, if the result of the methods of the present invention is inconclusive or there is reason that confirmation of status is necessary, the physician may order more tests. Alternatively, if the result of the methods of the present invention indicates a potentially poor prognosis, alternative or more aggressive therapies may be warranted. Furthermore, if the results show a potentially good prognosis
  • Examples of more aggressive therapy include: a) The physician may after surgery treat the patient with more intensive and prolonged chemotherapy, b) Offer additional chemotherapy or biological treatments, c) The patient may be monitored more closely for relapse or progressive disease, d) Patients with both an indication of a poor prognosis and extensive disease, which on imaging indicate nonradical surgery, may be offered neoadjuvant chemotherapy and subsequent interval surgery, e) The proteomic index may be part in the total clinical judgment of treatment versus palliative treatment in severe ill patients, f) Radical and correct staged patients with stage one and grade 1-2 may be offered adjuvant treatment, g) The patients may be selected for surgery by a gynecologic-oncologic surgeon experienced in performing extensive procedures.
  • Examples of less aggressive therapy include, a) The index may be part of the decision making for radical surgery, b) Radical and correct staged patients with stage one and grade 1-2 may avoid a potentially harmful chemotherapy, c) The patient may be operated on by a less specialized gynecologist.
  • a prognostic index may in the future be used to select patients for
  • a protein of the invention is the targets of the therapy.
  • Marker in the context of the present invention refers to a polypeptide that is differentially present in a sample taken from a patients having human cancer as compared to a reference.
  • the reference is a comparable sample taken from a control subject.
  • a control subject may be a person with a negative diagnosis or undetectable cancer, such as a normal or healthy subject.
  • biomarker is used interchangeably with the term “marker.”
  • measuring means methods which include detecting the presence or absence of marker(s) in the sample, quantifying the amount of marker(s) in the sample, and/or qualifying the type of biomarker. Measuring can be accomplished by methods known in the art and those further described herein, including but not limited to SELDI and immunoassay. Any suitable methods can be used to detect and measure one or more of the markers described herein. These methods include, without limitation, mass spectrometry (e.g., laser desorption/ionization mass spectrometry), fluorescence (e.g. sandwich immunoassay), surface plasmon resonance, ellipsometry and atomic force microscopy.
  • mass spectrometry e.g., laser desorption/ionization mass spectrometry
  • fluorescence e.g. sandwich immunoassay
  • surface plasmon resonance e.g., ellipsometry and atomic force microscopy.
  • Mass analyzer refers to a sub-assembly of a mass spectrometer that comprises a means for measuring a parameter that can be translated into mass-to- charge ratios of gas phase ions.
  • the mass analyzer comprises an ion optic assembly, a flight tube and an ion detector.
  • Mass spectrometer refers to a gas phase ion spectrometer that measures a parameter that can be translated into mass-to-charge ratios of gas phase ions. Mass spectrometers generally include an ion source and a mass analyzer. Examples of mass spectrometers are time-of-flight, magnetic sector, quadrupole filter, ion trap, ion cyclotron resonance, electrostatic sector analyzer and hybrids of these. “Mass spectrometry” refers to the use of a mass spectrometer to detect gas phase ions.
  • Tudem mass spectrometer refers to any mass spectrometer that is capable of performing two successive stages of m/z-based discrimination or measurement of ions, including ions in an ion mixture.
  • the phrase includes mass spectrometers having two mass analyzers that are capable of performing two successive stages of m/z-based discrimination or measurement of ions tandem-in-space.
  • the phrase further includes mass spectrometers having a single mass analyzer that is capable of performing two successive stages of m/z-based discrimination or measurement of ions tandem-in-time.
  • Probe in the context of this invention refers to a device adapted to engage a probe interface of a gas phase ion spectrometer (e.g., a mass spectrometer) and to present an analyte to ionizing energy for ionization and introduction into a gas phase ion spectrometer, such as a mass spectrometer.
  • a “probe” will generally comprise a solid substrate (either flexible or rigid) comprising a sample presenting surface on which an analyte is presented to the source of ionizing energy.
  • Solid support refers to a solid material which can be derivatized with, or otherwise attached to, a capture reagent.
  • exemplary solid supports include probes, microtiter plates and chromatographic resins.
  • Three biomarkers refers to a set of biomarkers identified herein.
  • the three biomarkers are inter-alpha (globulin) inhibitor H4 (plasma Kallikrein- sensitive glycoprotein) (ITIH4), transferrin (TFR), and beta-2 microglobin (B2M).
  • IMIH4 plasma Kallikrein-sensitive glycoprotein
  • TFR transferrin
  • B2M beta-2 microglobin
  • “Surface-enhanced laser desorption/ionization” or “SELDI” refers to a method of desorption/ionization gas phase ion spectrometry (e.g., mass spectrometry) in which the analyte is captured on the surface of a SELDI probe that engages the probe interface of the gas phase ion spectrometer.
  • SELDI MS the gas phase ion spectrometer is a mass spectrometer.
  • SELDI technology is described in, e.g., U.S. patent 5,719,060 (Hutchens and Yip) and U.S. patent 6,225,047 (Hutchens and Yip).
  • SEEC Surface-Enhanced Affinity Capture
  • Adsorbent surface refers to a surface to which is bound an adsorbent (also called a “capture reagent” or an “affinity reagent”).
  • An adsorbent is any material capable of binding an analyte (e.g., a target polypeptide or nucleic acid).
  • Chrographic adsorbent refers to a material typically used in chromatography.
  • Chromatographic adsorbents include, for example, ion exchange materials, metal chelators (e.g., nitriloacetic 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., nitriloacetic acid or iminodiacetic acid
  • immobilized metal chelates e.g., immobilized metal chelates
  • hydrophobic interaction adsorbents e.g., hydrophilic interaction adsorbents
  • dyes e.g., simple biomolecules (e.g., nucleotides, amino acids, simple sugars and
  • Biospecific adsorbent refers 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 analyte than chromatographic adsorbents. Further examples of adsorbents for use in SELDI can be found in U.S. Patent 6,225,047 (Hutchens and Yip, "Use of retentate chromatography to generate difference maps," May 1, 2001).
  • a SEAC probe is provided as a pre-activated surface which can be modified to provide an adsorbent of choice.
  • certain probes are provided with a reactive moiety that is capable of binding a biological molecule through a covalent bond.
  • Epoxide and carbodiimidizole are useful reactive moieties to covalently bind biospecific adsorbents such as antibodies or cellular receptors.
  • SEND Surface-Enhanced Neat Desorption
  • SEND probe. Energy absorbing molecules
  • EAM Electronic absorbing molecules
  • the phrase includes molecules used in MALDI , frequently referred to as “matrix”, and explicitly includes cinnamic acid derivatives, sinapinic acid (“SPA"), cyano-hydroxy-cinnamic acid (“CHCA”) and dihydroxybenzoic acid, ferulic acid, hydroxyacetophenone derivatives, as well as others. It also includes EAMs used in SELDI. SEND is further described in United States patent 5,719,060 and United States patent application 60/408,255, filed September 4, 2002 (Kitagawa, "Monomers And Polymers Having Energy Absorbing Moieties Of Use In
  • SEPAR Surface-Enhanced Photolabile Attachment and Release
  • SELDI Surface-Enhanced Photolabile Attachment and Release
  • Molecular binding partners and “specific binding partners” refer to pairs of molecules, typically pairs of biomolecules that exhibit specific binding. Molecular binding partners include, without limitation, receptor and ligand, antibody and antigen, biotin and avidin, and biotin and streptavidin.
  • Protein biochip refers to a biochip adapted for the capture of polypeptides.
  • Many protein biochips are described in the art. These include, for example, protein biochips produced by Ciphergen Biosystems (Fremont, CA), Packard Bioscience Company (Meriden CT), Zyomyx (Hayward, CA) and Phylos (Lexington, MA). Examples of such protein biochips are described in the following patents or patent applications: U.S. patent 6,225,047 (Hutchens and Yip, "Use of retentate
  • Ciphergen Biosystems comprise surfaces having chromatographic or biospecific adsorbents attached thereto at addressable locations.
  • Ciphergen ProteinChip® arrays include NP20, H4, H50, SAX-2, WCX-2, CM- 10, IMAC-3, IMAC-30, LSAX-30, LWCX-30, IMAC-40, PS-10, PS-20 and PG-20.
  • These protein biochips comprise an aluminum substrate in the form of a strip. The surface of the strip is coated with silicon dioxide.
  • silicon oxide functions as a hydrophilic adsorbent to capture hydrophilic proteins.
  • H4, H50, SAX-2, WCX-2, CM-10, IMAC-3, IMAC-30, PS-10 and PS-20 biochips further comprise a functionalized, cross-linked polymer in the form of a hydrogel physically attached to the surface of the biochip or covalently attached through a silane to the surface of the biochip.
  • the H4 biochip has isopropyl functionalities for hydrophobic binding.
  • the H50 biochip has nonylphenoxy- poly(ethylene glycol)methacrylate for hydrophobic binding.
  • the SAX-2 biochip has quaternary ammonium functionalities for anion exchange.
  • the WCX-2 and CM-10 biochips have carboxylate functionalities for cation exchange.
  • the IMAC-3 and IMAC-30 biochips have nitriloacetic acid functionalities that adsorb transition metal ions, such as Cu++ and Ni++, by chelation. These immobilized metal ions allow adsorption of peptide and proteins by coordinate bonding.
  • the PS-10 biochip has carboimidizole functional groups that can react with groups on proteins for covalent binding.
  • the PS-20 biochip has epoxide functional groups for covalent binding with proteins.
  • the PS-series biochips are useful for binding biospecific adsorbents, such as antibodies, receptors, lectins, heparin, Protein A, biotin/streptavidin and the like, to chip surfaces where they function to specifically capture analytes from a sample.
  • the PG-20 biochip is a PS-20 chip to which Protein G is attached.
  • the LSAX-30 (anion exchange), LWCX-30 (cation exchange) and EV1AC-40 (metal chelate) biochips have functionalized latex beads on their surfaces.
  • Such biochips are further described in: WO 00/66265 (Rich et al., "Probes for a Gas Phase Ion Spectrometer," November 9, 2000); WO 00/67293 (Beecher et al., "Sample Holder with Hydrophobic Coating for Gas Phase Mass Spectrometer,” November 9, 2000); U.S. patent application
  • analytes can be detected by a variety of detection methods selected from, for example, a gas phase ion spectrometry method, an optical method, an electrochemical method, atomic force microscopy and a radio frequency method.
  • Gas phase ion spectrometry methods are described herein. Of particular interest is the use of mass spectrometry and, in particular, SELDI.
  • Optical methods include, for example, detection of fluorescence, luminescence, chemiluminescence, absorbance, reflectance, transmittance, birefringence or refractive index (e.g., surface plasmon resonance, ellipsometry, a resonant mirror method, a grating coupler waveguide method or interferometry).
  • Optical methods include microscopy (both confocal and non-confocal), imaging methods and non-imaging methods.
  • Immunoassays in various formats are popular methods for detection of analytes captured on a solid phase.
  • Electrochemical methods include voltametry and amperometry methods.
  • Radio frequency methods include multipolar resonance spectroscopy.
  • test amount of a marker refers to an amount of a marker present in a sample being tested.
  • a test amount can be either in absolute amount (e.g., g/ml) or a relative amount (e.g., relative intensity of signals).
  • the present invention provides compositions and methods for determining the prognosis of subjects having or suspected of having ovarian cancer by detecting particular biomarkers.
  • the detection and measurement of these biomarkers in subject samples provides information that diagnosticians can correlate with overall survival and/or progression-free survival to select an appropriate therapeutic regimen for the subject.
  • the invention is based, at least in part, on the discovery that one or more of the following biomarkers are useful for detecting and/or characterizing ovarian cancer in a subject: apolipoprotein Al (APOA1), transthyretin (cysteinylated form) (TT), inter-alpha trypsin inhibitor IV (internal fragment) (ITIH4), transferrin (TrF), hepcidin (HEPC), connective-tissue activating protein 3 (CTAP3), Serum Amyloid Al (SAA), and beta-2 microglobin (B2M).
  • these biomarkers are used to determine a subject's prognosis (e.g., likely overall survival and/or progression free survival).
  • the biomarkers used are inter-alpha (globulin) inhibitor H4 (plasma Kallikrein- sensitive glycoprotein) (ITIH4), transferrin (TFR), and/or beta-2 microglobin (B2M).
  • biomarkers assess a patient's survival status after having developed ovarian cancer and could potentially provide additional information to physicians for clinical decision-making. This is supported by Cox multivariate analysis in an independent validation. For example, several large-scale studies have suggested that ovarian cancer patients with surgical procedures operated by gynecological oncologists tend to have a better long-term survival. However, other studies concluded that currently only about one third of ovarian cancer patients undergoing surgical procedures in the US are treated by gynecological oncologists. With the current total number of gynecological oncologists available, it is still not practical to have all patients undergoing surgery for suspected ovarian cancer be operated by gynecologic oncologists. The biomarkers have the potential to be used to identify patients with the lower probability of surviving ovarian cancer and recommend them for treatment by gynecologic oncologists.
  • bioinformatics tools provides a useful approach to screening for cancer markers.
  • the system used in the present invention utilizes chromatographic
  • ProteinChip ® Arrays to assay samples using SELDI Surface Enhanced Laser Desorption/Ionization
  • Proteins bound to the arrays are read in a ProteinChip ® Reader, a time-of-flight mass spectrometer.
  • the present invention is based upon the discovery of protein markers that are differentially present in samples of ovarian cancer patients and control subjects, and the application of this discovery in methods and kits for determining ovarian cancer status.
  • protein markers are found in samples from ovarian cancer patients at levels that are different than the levels in samples from women in whom human cancer is undetectable. Accordingly, the amount of one or more markers found in a test sample compared to a control, or the presence or absence of one or more markers in the test sample provides useful information regarding the ovarian cancer status of the patient.
  • CA125 The best-characterized tumor marker, CA125, is negative in approximately 30-40% of stage I ovarian carcinomas and its levels are elevated in a variety of benign diseases. Its use as a population-based screening tool for early detection and diagnosis of ovarian cancer is hindered by its low sensitivity and specificity.
  • ITIH4 fragments are described as biomarkers for ovarian cancer in US patent publication 2005-0059013 Al, International Patent Publication WO 2005/098447 and Fung et al., Int. J. Cancer 115:783-789 (2005).
  • ITIH4 fragments can be selected from the group consisting of ITIH4 fragment no. 1, ITIH4 fragment no. 2, and ITIH4 fragment no. 3.
  • ITIH4 fragment 1 SEQ ID NO: 5
  • MNFRPGVLSSRQLGLPGPPDVPDHAAYHPF ITIH4 fragment 2
  • PGVLSSRQLGLPGPPDVPDHAAYHPF ITIH4 fragment 3
  • G VLS SRQLGLPGPPD VPDH A A YHPF The present invention also includes all other known fragments of ITIHA4.
  • ITIH4 precursor is a 930 amino acid protein (SwissProt Q 14624).
  • ITIH4 fragment 1 spans amino acids 658-687 of human ITIH4 precursor.
  • ITIH4 fragment 2 spans amino acids 662-687 of ITIH4 precursor.
  • ITIH4 fragment 3 spans amino acids 663-687 of ITIH4 precursor.
  • preferred methods of the present invention include the use of modified forms of ITIH4 fragment.
  • Modification of ITIH4 fragment may include the post-translational addition of various chemical groups, for example, glycosylation, lipidation, cysteinylation, and glutathionylation.
  • TRANSFERRIN (TRF) may include the post-translational addition of various chemical groups, for example, glycosylation, lipidation, cysteinylation, and glutathionylation.
  • Transferrrin is described as a biomarker for ovarian cancer in US patent publication 2005-0214760 Al.
  • Transferrrin is a 679 amino acid protein derived from a 698 amino acid precursor (GenBank Accession No. NP_001054 GL4557871; SwissProt Accesion No. P02787) (SEQ ID NO: 10).
  • Transferrrin is recognized by antibodies available from, e.g., Dako (catalog A006) (www.dako.com, Glostrup, Denmark). Transferrin is glycosylated. Therefore, the measured molecular weight is higher than the theoretical weight, which does not take glycosylation into account.
  • ⁇ 2-microglobulin Another biomarker that is useful in the methods of the present invention is ⁇ 2- microglobulin.
  • p2-microglobulin is described as a biomarker for ovarian cancer in US provisional patent publication 60/693,679, filed June 24, 2005 (Fung et al.).
  • ⁇ 2- microglobulin is a 99 amino acid protein derived from an 119 amino acid precursor (GL179318; SwissProt Accession No. P61769) (SEQ ID NO: 11).
  • p2-microglobulin is recognized by antibodies available from, e.g., Abeam (catalog AB759)
  • biomarkers of this invention are identical to each other. Because, in one embodiment, the biomarkers of this invention are identical to each other.
  • biomarkers whose identity is not determined can be identified by, for example, determining the amino acid sequence of the polypeptides.
  • a biomarker can be peptide-mapped with a number of enzymes, such as trypsin or V8 protease, and the molecular weights of the digestion fragments can be used to search databases for sequences that match the molecular weights of the digestion fragments generated by the various enzymes.
  • protein biomarkers can be sequenced using tandem MS technology. In this method, the protein is isolated by, for example, gel electrophoresis.
  • a band containing the biomarker is cut out and the protein is subject to protease digestion. Individual protein fragments are separated by a first mass spectrometer. The fragment is then subjected to collision-induced cooling, which fragments the peptide and produces a polypeptide ladder. A polypeptide ladder is then analyzed by the second mass spectrometer of the tandem MS. The difference in masses of the members of the polypeptide ladder identifies the amino acids in the sequence. An entire protein can be sequenced this way, or a sequence fragment can be subjected to database mining to find identity candidates.
  • Pre-translational modified forms include allelic variants, slice variants and RNA editing forms.
  • Post- translationally modified forms include forms resulting from proteolytic cleavage (e.g., fragments of a parent protein), glycosylation, phosphorylation, lipidation, oxidation, methylation, cystinylation, sulphonation and acetylation.
  • proteins including a specific protein and all modified forms of it is referred to herein as a "protein cluster.”
  • the collection of all modified forms of a specific protein, excluding the specific protein, itself, is referred to herein as a "modified protein cluster.”
  • Modified forms of the biomarker of this invention also may be used, themselves, as biomarkers. In certain cases the modified forms may exhibit better discriminatory power in diagnosis than the specific forms set forth herein.
  • Modified forms of a biomarker can be initially detected by any methodology that can detect and distinguish the modified from the biomarker.
  • a preferred method for initial detection involves first capturing the biomarker and modified forms of it, e.g., with biospecific capture reagents, and then detecting the captured proteins by mass spectrometry. More specifically, the proteins are captured using biospecific capture reagents, such as antibodies, aptamers or Affibodies that recognize the biomarker and modified forms of it. This method also will also result in the capture of protein interactors that are bound to the proteins or that are otherwise recognized by antibodies and that, themselves, can be biomarkers. In certain embodiments, the biospecific capture reagents are bound to a solid phase.
  • the captured proteins can be detected by SELDI mass spectrometry or by eluting the proteins from the capture reagent and detecting the eluted proteins by traditional MALDI or by SELDI.
  • SELDI mass spectrometry is especially attractive because it can distinguish and quantify modified forms of a protein based on mass and without the need for labeling.
  • the biospecific capture reagent is bound to a solid phase, such as a bead, a plate, a membrane or a chip.
  • a solid phase such as a bead, a plate, a membrane or a chip.
  • Methods of coupling biomolecules, such as antibodies, to a solid phase are well known in the art. They can employ, for example, bifunctional linking agents, or the solid phase can be derivatized with a reactive group, such as an epoxide or an imidizole, that will bind the molecule on contact.
  • Biospecific capture reagents against different target proteins can be mixed in the same place, or they can be attached to solid phases in different physical or addressable locations. For example, one can load multiple columns with derivatized beads, each column able to capture a single protein cluster.
  • antibody-derivatized bead-based technologies such as xMAP technology of Luminex (Austin, TX) can be used to detect the protein clusters.
  • the biospecific capture reagents must be specifically directed toward the members of a cluster in order to differentiate them.
  • the surfaces of biochips can be derivatized with the capture reagents directed against protein clusters either in the same location or in physically different addressable locations.
  • One advantage of capturing different clusters in different addressable locations is that the analysis becomes simpler.
  • the modified form can be used as a biomarker in any of the methods of this invention.
  • detection of the modified form can be accomplished by any specific detection methodology including affinity capture followed by mass spectrometry, or traditional immunoassay directed specifically the modified form.
  • Immunoassay requires biospecific capture reagents, such as antibodies, to capture the analytes.
  • the assay must be designed to specifically distinguish protein and modified forms of protein. This can be done, for example, by employing a sandwich assay in which one antibody captures more than one form and second, distinctly labeled antibodies, specifically bind, and provide distinct detection of, the various forms.
  • Antibodies can be produced by immunizing animals with the biomolecules.
  • This invention contemplates traditional immunoassays including, for example, sandwich immunoassays including ELISA or fluorescence-based immunoassays, as well as other enzyme immunoassays.
  • Samples are collected from women who have been diagnosed with ovarian cancer in whom the test is being used to determine their prognosis. Samples may be collected from women who had been diagnosed with ovarian cancer and received treatment to eliminate the cancer, or perhaps are in remission. In a preferred embodiment, the subjects are women who have been previously diagnosed as having ovarian cancer.
  • the markers can be measured in different types of biological samples.
  • the sample is preferably a biological fluid sample.
  • a biological fluid sample useful in this invention include blood, blood serum, plasma, vaginal secretions, urine, ovarian cyst fluid, tears, saliva, etc. Because all of the markers are found in blood serum, blood serum is a preferred sample source for embodiments of the invention.
  • the sample can be prepared to enhance detectability of the markers.
  • a blood serum sample from the subject can be preferably fractionated by, e.g., Cibacron blue agarose chromatography and single stranded DNA affinity chromatography, anion exchange chromatography, affinity chromatography (e.g., with antibodies) and the like.
  • the method of fractionation depends on the type of detection method used. Any method that enriches for the protein of interest can be used.
  • Sample preparations, such as pre- fractionation protocols are optional and may not be necessary to enhance detectability of markers depending on the methods of detection used. For example, sample preparation may be unnecessary if antibodies that specifically bind markers are used to detect the presence of markers in a sample.
  • sample preparation involves fractionation of the sample and collection of fractions determined to contain the biomarkers.
  • Methods of pre- fractionation include, for example, size exclusion chromatography, ion exchange chromatography, heparin chromatography, affinity chromatography, sequential extraction, gel electrophoresis and liquid chromatography.
  • the analytes also may be modified prior to detection. These methods are useful to simplify the sample for further analysis. For example, it can be useful to remove high abundance proteins, such as albumin, from blood before analysis. Examples of methods of fractionation are described in PCT/US03/00531 (incorporated herein in its entirety).
  • the sample is pre-fractionated by anion exchange chromatography.
  • Anion exchange chromatography allows pre-fractionation of the proteins in a sample roughly according to their charge characteristics.
  • a Q anion-exchange resin can be used (e.g., Q HyperD F, Biosepra), and a sample can be sequentially eluted with eluants having different pH' s.
  • Anion exchange chromatography allows separation of biomolecules in a sample that are more negatively charged from other types of biomolecules. Proteins that are eluted with an eluant having a high pH is likely to be weakly negatively charged, and a fraction that is eluted with an eluant having a low pH is likely to be strongly negatively charged.
  • anion exchange chromatography separates proteins according to their binding characteristics.
  • the serum samples are fractionated via anion exchange chromatography.
  • Signal suppression of lower abundance proteins by high abundance proteins presents a significant challenge to SELDI mass spectrometry.
  • Fractionation of a sample reduces the complexity of the constituents of each fraction. This method can also be used to attempt to isolate high abundance proteins into a fraction, and thereby reduce its signal suppression effect on lower abundance proteins.
  • Anion exchange fractionation separates proteins by their isoelectric point (pi).
  • Proteins are comprised of amino acids, which are ambivalent-their charge changes based on the pH of the environment to which they are exposed.
  • a protein's pi is the pH at which the protein has no net charge.
  • a protein assumes a neutral charge when the pH of the environment is equivalent to pi of the protein. When the pH rises above the pi of the protein, the protein assumes a net negative charge. Similarly, when the pH of the environment falls below the pi of the protein, the protein has a net positive charge.
  • the serum samples were fractionated according to the protocol set forth in the Examples below to obtain the markers described herein.
  • Biomolecules in a sample can also be separated by high-resolution
  • electrophoresis e.g., one or two-dimensional gel electrophoresis.
  • a fraction containing a marker can be isolated and further analyzed by gas phase ion
  • two-dimensional gel electrophoresis is used to generate two-dimensional array of spots of biomolecules, including one or more markers. See, e.g., Jungblut and Thiede, Mass Spectr. Rev. 16:145-162 (1997).
  • the two-dimensional gel electrophoresis can be performed using methods known in the art. See, e.g., Deutscher ed., Methods In Enzymology vol. 182.
  • biomolecules in a sample are separated by, e.g., isoelectric focusing, during which biomolecules in a sample are separated in a pH gradient until they reach a spot where their net charge is zero (i.e., isoelectric point).
  • This first separation step results in one-dimensional array of biomolecules.
  • the biomolecules in one-dimensional array is further separated using a technique generally distinct from that used in the first separation step.
  • biomolecules separated by isoelectric focusing are further separated using a polyacrylamide gel, such as polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate (SDS- PAGE).
  • SDS-PAGE gel allows further separation based on molecular mass of biomolecules.
  • two-dimensional gel electrophoresis can separate chemically different biomolecules in the molecular mass range from 1000-200,000 Da within complex mixtures. The pi range of these gels is about 3-10 (wide range gels).
  • Biomolecules in the two-dimensional array can be detected using any suitable methods known in the art.
  • biomolecules in a gel can be labeled or stained (e.g., Coomassie Blue or silver staining). If gel electrophoresis generates spots that correspond to the molecular weight of one or more markers of the invention, the spot can be further analyzed by gas phase ion spectrometry. For example, spots can be excised from the gel and analyzed by gas phase ion
  • the gel containing biomolecules can be transferred to an inert membrane by applying an electric field. Then a spot on the membrane that approximately corresponds to the molecular weight of a marker can be analyzed by gas phase ion spectrometry.
  • gas phase ion spectrometry the spots can be analyzed using any suitable techniques, such as MALDI or SELDI (e.g., using ProteinChip array) as described herein.
  • cleaving reagents such as proteases (e.g., trypsin).
  • the digestion of biomolecules into small fragments provides a mass fingerprint of the biomolecules in the spot, which can be used to determine the identity of markers if desired.
  • HPLC High performance liquid chromatography
  • HPLC instruments typically consist of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. Biomolecules in a sample are separated by injecting an aliquot of the sample onto the column.
  • a fraction that corresponds to the molecular weight and/or physical properties of one or more markers can be collected.
  • the fraction can then be analyzed by gas phase ion spectrometry to detect markers.
  • the spots can be analyzed using either MALDI or SELDI (e.g., using ProteinChip array) as described herein.
  • a marker can be modified before analysis to improve its resolution or to determine its identity.
  • the markers may be subject to proteolytic digestion before analysis. Any protease can be used. Proteases, such as trypsin, that are likely to cleave the markers into a discrete number of fragments are particularly useful. The fragments that result from digestion function as a fingerprint for the markers, thereby enabling their detection indirectly. This is particularly useful where there are markers with similar molecular masses that might be confused for the marker in question. Also, proteolytic fragmentation is useful for high molecular weight markers because smaller markers are more easily resolved by mass
  • biomolecules can be modified to improve detection resolution.
  • neuraminidase can be used to remove terminal sialic acid residues from glycoproteins to improve binding to an anionic adsorbent (e.g., cationic exchange ProteinChip arrays) and to improve detection resolution.
  • the markers can be modified by the attachment of a tag of particular molecular weight that specifically bind to molecular markers, further distinguishing them.
  • the identity of the markers can be further determined by matching the physical and chemical characteristics of the modified markers in a protein database (e.g., SwissProt).
  • Biomarkers can be captured with capture reagents immobilized to a solid support, such as any biochip described herein, a multiwell microtiter plate or a resin.
  • the biomarkers of this invention are preferably captured on SELDI protein biochips. Capture can be on a chromatographic surface or a biospecific surface. Any of the SELDI protein biochips comprising reactive surfaces can be used to capture and detect the biomarkers of this invention. However, the biomarkers of this invention bind well to immobilized metal chelates.
  • the IMAC-3 and IMAC 30 biochips which nitriloacetic acid functionalities that adsorb transition metal ions, such as Cu ++ and Ni ++ , by chelation, are the preferred SELDI biochips for capturing the biomarkers of this invention.
  • Any of the SELDI protein biochips comprising reactive surfaces can be used to capture and detect the biomarkers of this invention.
  • These biochips can be derivatized with the antibodies that specifically capture the biomarkers, or they can be derivatized with capture reagents, such as protein A or protein G that bind immunoglobulins. Then the biomarkers can be captured in solution using specific antibodies and the captured markers isolated on chip through the capture reagent.
  • a sample containing the biomarkers such as serum
  • a suitable eluant such as phosphate buffered saline.
  • phosphate buffered saline a suitable eluant
  • markers can be detected and/or measured by a variety of detection methods including for example, gas phase ion spectrometry methods, optical methods, electrochemical methods, atomic force microscopy and radio frequency methods. Using these methods, one or more markers can be detected.
  • SELDI refers to a method of desorption/ionization gas phase ion spectrometry (e.g., mass spectrometry) in which the analyte is captured on the surface of a SELDI probe that engages the probe interface.
  • gas phase ion spectrometer is a mass spectrometer. SELDI technology is described in more detail above.
  • an immunoassay can be used to detect and analyze markers in a sample. This method comprises: (a) providing an antibody that specifically binds to a marker; (b) contacting a sample with the antibody; and (c) detecting the presence of a complex of the antibody bound to the marker in the sample.
  • An immunoassay is an assay that uses an antibody to specifically bind an antigen (e.g. , a marker).
  • the immunoassay is characterized by the use of specific binding properties of a particular antibody to isolate, target, and/or quantify the antigen.
  • the specified antibodies bind to a particular protein at least two times the background and do not substantially bind in a significant amount to other proteins present in the sample.
  • Specific binding to an antibody under such conditions may require an antibody that is selected for its specificity for a particular protein.
  • polyclonal antibodies raised to a marker from specific species such as rat, mouse, or human can be selected to obtain only those polyclonal antibodies that are specifically immunoreactive with that marker and not with other proteins, except for polymorphic variants and alleles of the marker. This selection may be achieved by subtracting out antibodies that cross-react with the marker molecules from other species.
  • antibodies that specifically bind to a marker can be prepared using any suitable methods known in the art. See, e.g., Coligan, Current Protocols in Immunology (1991); Harlow & Lane, Antibodies: A Laboratory Manual (1988); Goding, Monoclonal Antibodies:
  • Such techniques include, but are not limited to, antibody preparation by selection of antibodies from libraries of recombinant antibodies in phage or similar vectors, as well as preparation of polyclonal and monoclonal antibodies by immunizing rabbits or mice ⁇ see, e.g., Huse et ah, Science 246:1275-1281 (1989); Ward et ah, Nature 341:544-546 (1989)).
  • a specific or selective reaction will be at least twice background signal or noise and more typically more than 10 to 100 times background.
  • a sample obtained from a subject can be contacted with the antibody that specifically binds the marker.
  • the antibody can be fixed to a solid support to facilitate washing and subsequent isolation of the complex, prior to contacting the antibody with a sample.
  • solid supports include glass or plastic in the form of, e.g., a microtiter plate, a stick, a bead, or a microbead.
  • Antibodies can also be attached to a probe substrate or ProteinChip ® array described above.
  • the sample is preferably a biological fluid sample taken from a subject.
  • biological fluid samples include blood, serum, plasma, nipple aspirate, urine, tears, saliva etc.
  • the biological fluid comprises blood serum.
  • the sample can be diluted with a suitable eluant before contacting the sample to the antibody.
  • the mixture is washed and the antibody-marker complex formed can be detected.
  • This detection reagent may be, e.g., a second antibody which is labeled with a detectable label.
  • detectable labels include magnetic beads ⁇ e.g., DYNABEADSTM), fluorescent dyes, radiolabels, enzymes ⁇ e.g., horse radish peroxide, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic beads.
  • the marker in the sample can be detected using an indirect assay, wherein, for example, a second, labeled antibody is used to detect bound marker- specific antibody, and/or in a competition or inhibition assay wherein, for example, a monoclonal antibody which binds to a distinct epitope of the marker is incubated simultaneously with the mixture.
  • an indirect assay wherein, for example, a second, labeled antibody is used to detect bound marker- specific antibody, and/or in a competition or inhibition assay wherein, for example, a monoclonal antibody which binds to a distinct epitope of the marker is incubated simultaneously with the mixture.
  • Methods for measuring the amount of, or presence of, antibody-marker complex include, for example, detection of fluorescence, luminescence,
  • chemiluminescence absorbance, reflectance, transmittance, birefringence or refractive index (e.g., surface plasmon resonance, ellipsometry, a resonant mirror method, a grating coupler waveguide method or interferometry).
  • Optical methods include microscopy (both confocal and non-confocal), imaging methods and non- imaging methods.
  • Electrochemical methods include voltametry and amperometry methods.
  • Radio frequency methods include multipolar resonance spectroscopy. Methods for performing these assays are readily known in the art.
  • Useful assays include, for example, an enzyme immune assay (EIA) such as enzyme-linked immunosorbent assay (ELISA), a radioimmune assay (RIA), a Western blot assay, or a slot blot assay.
  • EIA enzyme immune assay
  • ELISA enzyme-linked immunosorbent assay
  • RIA radioimmune assay
  • Western blot assay or a slot blot assay.
  • incubation and/or washing steps may be required after each combination of reagents. Incubation steps can vary from about 5 seconds to several hours, preferably from about 5 minutes to about 24 hours. However, the incubation time will depend upon the assay format, marker, volume of solution, concentrations and the like. Usually the assays will be carried out at ambient temperature, although they can be conducted over a range of temperatures, such as 10°C to 40°C.
  • Immunoassays can be used to determine presence or absence of a marker in a sample as well as the quantity of a marker in a sample.
  • the amount of an antibody- marker complex can be determined by comparing to a standard.
  • a standard can be, e.g., a known compound or another protein known to be present in a sample.
  • the test amount of marker need not be measured in absolute units, as long as the unit of measurement can be compared to a control.
  • the methods for detecting these markers in a sample have many applications. For example, one or more markers can be measured to aid human cancer diagnosis or prognosis. In another example, the methods for detection of the markers can be used to monitor responses in a subject to cancer treatment. In another example, the methods for detecting markers can be used to assay for and to identify compounds that modulate expression of these markers in vivo or in vitro. In a preferred example, the biomarkers are used to differentiate between the different stages of tumor progression, thus aiding in determining appropriate treatment and extent of metastasis of the tumor.
  • the software can comprise code that converts signal from the mass spectrometer into computer readable form.
  • the software also can include code that applies an algorithm to the analysis of the signal to determine whether the signal represents a "peak" in the signal corresponding to a marker of this invention, or other useful markers.
  • the software also can include code that executes an algorithm that compares signal from a test sample to a typical signal characteristic of "normal” and human cancer and determines the closeness of fit between the two signals.
  • the software also can include code indicating which the test sample is closest to, thereby providing a probable diagnosis.
  • multiple biomarkers are measured.
  • the use of multiple biomarkers increases the predictive value of the test and provides greater utility in diagnosis, toxicology, patient stratification and patient monitoring.
  • the process called "Pattern recognition" detects the patterns formed by multiple biomarkers greatly improves the sensitivity and specificity of clinical proteomics for predictive medicine.
  • Subtle variations in data from clinical samples e.g., obtained using SELDI, indicate that certain patterns of protein expression can predict phenotypes such as the presence or absence of a certain disease, a particular stage of cancer progression, or a positive or adverse response to drug treatments.
  • Data generation in mass spectrometry begins with the detection of ions by an ion detector as described above. Ions that strike the detector generate an electric potential that is digitized by a high speed time-array recording device that digitally captures the analog signal.
  • Ciphergen's ProteinChip ® system employs an analog-to- digital converter (ADC) to accomplish this.
  • ADC analog-to- digital converter
  • the ADC integrates detector output at regularly spaced time intervals into time-dependent bins. The time intervals typically are one to four nanoseconds long. Furthermore, the time-of-flight spectrum
  • TOF-to-M/Z transformation involves the application of an algorithm that transforms times-of-flight into mass-to-charge ratio (M/Z).
  • M/Z mass-to-charge ratio
  • the signals are converted from the time domain to the mass domain. That is, each time-of-flight is converted into mass-to-charge ratio, or M/Z.
  • Calibration can be done internally or externally.
  • the sample analyzed contains one or more analytes of known M/Z. Signal peaks at times-of-flight representing these massed analytes are assigned the known M/Z. Based on these assigned M/Z ratios, parameters are calculated for a mathematical function that converts times-of-flight to M/Z.
  • a function that converts times-of-flight to M/Z such as one created by prior internal calibration, is applied to a time-of-flight spectrum without the use of internal calibrants.
  • Baseline subtraction improves data quantification by eliminating artificial, reproducible instrument offsets that perturb the spectrum. It involves calculating a spectrum baseline using an algorithm that incorporates parameters such as peak width, and then subtracting the baseline from the mass spectrum.
  • a typical smoothing function applies a moving average function to each time-dependent bin.
  • the moving average filter is a variable width digital filter in which the bandwidth of the filter varies as a function of, e.g., peak bandwidth, generally becoming broader with increased time-of-flight. See, e.g., WO 00/70648, November 23, 2000 (Gavin et al., "Variable Width Digital Filter for Time-of-flight Mass Spectrometry").
  • Peak selection can, of course, be done by eye.
  • Peak data from one or more spectra can be subject to further analysis by, for example, creating a spreadsheet in which each row represents a particular mass spectrum, each column represents a peak in the spectra defined by mass, and each cell includes the intensity of the peak in that particular spectrum.
  • Various statistical or pattern recognition approaches can applied to the data.
  • Ciphergen' s Biomarker PatternsTM Software is used to detect a pattern in the spectra that are generated.
  • the data is classified using a pattern recognition process that uses a classification model.
  • the spectra will represent samples from at least two different groups for which a classification algorithm is sought.
  • the groups can be pathological v. non-pathological (e.g., cancer v. non-cancer), drug responder v. drug non-responder, toxic response v. non-toxic response, progressor to disease state v. non-progressor to disease state, phenotypic condition present v. phenotypic condition absent.
  • the spectra that are generated in embodiments of the invention can be classified using a pattern recognition process that uses a classification model.
  • data derived from the spectra e.g. , mass spectra or time-of-flight spectra
  • samples such as "known samples”
  • a "known sample” is a sample that is pre-classified (e.g. , cancer or not cancer).
  • Data derived from the spectra e.g., mass spectra or time- of-flight spectra
  • a "known sample” is a sample that is pre- classified.
  • the data that are derived from the spectra and are used to form the classification model can be referred to as a "training data set”.
  • the classification model can recognize patterns in data derived from spectra generated using unknown samples.
  • the classification model can then be used to classify the unknown samples into classes. This can be useful, for example, in predicting whether or not a particular biological sample is associated with a certain biological condition (e.g., diseased vs. non diseased).
  • the training data set that is used to form the classification model may comprise raw data or pre-processed data.
  • raw data can be obtained directly from time-of-flight spectra or mass spectra, and then may be optionally "pre-processed” in any suitable manner.
  • signals above a predetermined signal-to-noise ratio can be selected so that a subset of peaks in a spectrum is selected, rather than selecting all peaks in a spectrum.
  • a predetermined number of peak "clusters" at a common value e.g., a particular time-of-flight value or mass-to-charge ratio value
  • a peak at a given mass-to-charge ratio is in less than 50% of the mass spectra in a group of mass spectra, then the peak at that mass-to-charge ratio can be omitted from the training data set.
  • Pre-processing steps such as these can be used to reduce the amount of data that is used to train the classification model.
  • Classification models can be formed using any suitable statistical
  • classification or "learning” method that attempts to segregate bodies of data into classes based on objective parameters present in the data.
  • Classification methods may be either supervised or unsupervised. Examples of supervised and unsupervised classification processes are described in Jain, "Statistical Pattern Recognition: A Review", IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 22, No. 1, January 2000, which is herein incorporated by reference in its entirety.
  • supervised classification training data containing examples of known categories are presented to a learning mechanism, which learns one more sets of relationships that define each of the known classes. New data may then be applied to the learning mechanism, which then classifies the new data using the learned relationships.
  • supervised classification processes include linear regression processes (e.g., multiple linear regression (MLR), partial least squares (PLS) regression and principal components regression (PCR)), binary decision trees (e.g., recursive partitioning processes such as CART - classification and regression trees), artificial neural networks such as backpropagation networks, discriminant analyses (e.g., Bayesian classifier or Fischer analysis), logistic classifiers, and support vector classifiers (support vector machines).
  • linear regression processes e.g., multiple linear regression (MLR), partial least squares (PLS) regression and principal components regression (PCR)
  • binary decision trees e.g., recursive partitioning processes such as CART - classification and regression trees
  • artificial neural networks such as backpropagation networks
  • discriminant analyses e.g.
  • a preferred supervised classification method is a recursive partitioning process.
  • Recursive partitioning processes use recursive partitioning trees to classify spectra derived from unknown samples. Further details about recursive partitioning processes are provided in U.S. 2002 0138208 Al (Paulse et al., "Method for analyzing mass spectra," September 26, 2002.
  • the classification models that are created can be formed using unsupervised learning methods.
  • Unsupervised classification attempts to learn classifications based on similarities in the training data set, without pre classifying the spectra from which the training data set was derived.
  • Unsupervised learning methods include cluster analyses. A cluster analysis attempts to divide the data into "clusters" or groups that ideally should have members that are very similar to each other, and very dissimilar to members of other clusters. Similarity is then measured using some distance metric, which measures the distance between data items, and clusters together data items that are closer to each other.
  • Clustering techniques include the MacQueen's K-means algorithm and the Kohonen's Self-Organizing Map algorithm.
  • the peak intensity data of samples from cancer patients and healthy controls were used as a "discovery set.” This data were combined and randomly divided into a training set and a test set to construct and test multivariate predictive models.
  • the data generated from Section IV above is inputted into a diagnostic algorithm (i.e., classification algorithm as described above).
  • classification algorithm is then generated based on the learning algorithm.
  • the process involves developing an algorithm that can generate the classification algorithm.
  • the methods of the present invention generate a more accurate
  • classification algorithm by accessing a number of ovarian cancer and normal samples of a sufficient number based on statistical sample calculations. The samples are used as a training set of data on learning algorithm.
  • the generation of the classification, i.e., diagnostic, algorithm is dependent upon the assay protocol used to analyze samples and generate the data obtained in Section IV above. It is imperative that the protocol for the detection and/or measurement of the markers (e.g., in step IV) must be the same as that used to obtain the data used for developing the classification algorithm.
  • the assay conditions which must be maintained throughout the training and classification systems include chip type and mass spectrometer parameters, as well as general protocols for sample preparation and testing. If the protocol for the detection and/or measurement of the markers (step IV) is changed, the learning algorithm and classification algorithm must also change. Similarly, if the learning algorithm and classification algorithm change, then the protocol for the detection and/or measurement of markers (step IV) must also change to be consistent with that used to generate classification algorithm.
  • the classification models can be formed on and used on any suitable digital computer.
  • Suitable digital computers include micro, mini, or large computers using any standard or specialized operating system such as a Unix, WindowsTM or LinuxTM based operating system.
  • the digital computer that is used may be physically separate from the mass spectrometer that is used to create the spectra of interest, or it may be coupled to the mass spectrometer. If it is separate from the mass spectrometer, the data must be inputted into the computer by some other means, whether manually or automated.
  • the training data set and the classification models according to embodiments of the invention can be embodied by computer code that is executed or used by a digital computer.
  • the computer code can be stored on any suitable computer readable media including optical or magnetic disks, sticks, tapes, etc., and can be written in any suitable computer programming language including C, C++, visual basic, etc. VI. VARIOUS EMBODIMENTS.
  • a serum sample is collected from a patient and then fractionated using an anion exchange resin as described above.
  • the biomarkers in the sample are captured using an IMAC copper ProteinChip array.
  • the markers can then be detected using SELDI.
  • IMIH4 plasma Kallikrein- sensitive glycoprotein
  • TFR transferrin
  • B2M beta-2 microglobin
  • the results are then entered into a computer system, which contains an algorithm that is designed using the same parameters that were used in the learning algorithm and classification algorithm to originally determine the biomarkers.
  • the algorithm produces a diagnosis based upon the data received relating to each biomarker. For example, the algorithm can determine the chances of progression free survival (PFS) or overall survival (OS).
  • PFS progression free survival
  • OS overall survival
  • the diagnosis is determined by examining the data produced from the SELDI tests with the classification algorithm that is developed using the biomarkers.
  • the classification algorithm depends on the particulars of the test protocol used to detect the biomarkers. These particulars include, for example, sample preparation, chip type, mass spectrometer parameters and/or immunoassay conditions. If the test parameters change, the algorithm must change. Similarly, if the algorithm changes, the test protocol must change.
  • the markers are captured and tested using non-
  • the sample is collected from the patient.
  • the biomarkers are captured on a substrate using other known means, e.g., antibodies to the markers.
  • the markers are detected using methods known in the art, e.g., optical methods and refractive index. Examples of optical methods include detection of fluorescence, e.g., ELISA. Examples of refractive index include surface plasmon resonance.
  • optical methods include detection of fluorescence, e.g., ELISA.
  • refractive index include surface plasmon resonance.
  • the results for the markers are then subjected to an algorithm, which may or may not require artificial intelligence. The algorithm produces a diagnosis based upon the data received relating to each biomarker.
  • the data from the sample may be fed directly from the detection means into a computer containing the diagnostic algorithm.
  • the data obtained can be fed manually, or via an automated means, into a separate computer that contains the diagnostic algorithm.
  • This panel of biomarkers comparing inter-alpha (globulin) inhibitor H4 plasma Kallikrein-sensitive glycoprotein) (ITIH4), transferrin (TFR), and beta-2 microglobin (B2M), is useful in aiding in the determination of ovarian cancer status.
  • ITIH4 plasma Kallikrein-sensitive glycoprotein
  • TFR transferrin
  • B2M beta-2 microglobin
  • the selected biomarkesr are measured in a subject sample using the methods described herein, e.g., capture on a SELDI biochip followed by detection by mass spectrometry. Then, the measurements is compared with a reference amount or control that allows for determination of the subject's prognosis. The test amounts as compared with the prognostic amount thus indicates ovarian cancer prognosis.
  • biomarkers are useful diagnostic markers, it has been found that the particular combination of biomarkers provides herein provides surprisingly greater predictive value than single markers alone or other combinations of markers previously disclosed in the art. Specifically, the detection of this panel of markers in a sample increases the percentage of true positive and true negative diagnoses and would decrease the percentage of false positive or false negative diagnoses. Thus, methods of the present invention comprise the measurement of more than one biomarker.
  • the correlation may take into account the amount of the marker or markers in the sample compared to a control amount of the marker or markers (up or down regulation of the marker or markers) (e.g., in normal subjects in whom human cancer is undetectable).
  • a control can be, e.g. , the average or median amount of marker present in comparable samples of subjects in which their prognosis is known.
  • the control amount is measured under the same or substantially similar experimental conditions as in measuring the test amount.
  • the methods further comprise managing subject treatment based on the status.
  • management describes the actions of the physician or clinician subsequent to determining ovarian cancer status.
  • the physician may order more tests.
  • the physician may schedule the patient for surgery.
  • the patient may receive chemotherapy either in lieu of, or in addition to, surgery.
  • the result is negative, e.g., the status indicates late stage ovarian cancer or if the status is otherwise acute, no further action may be warranted.
  • the results show that treatment has been successful, no further management may be necessary.
  • the invention also provides for such methods where the biomarkers (or specific combination of biomarkers) are measured again after subject management.
  • the methods are used to monitor the status of the cancer, e.g., response to cancer treatment, remission of the disease or progression of the disease. Because of the ease of use of the methods and the lack of invasiveness of the methods, the methods can be repeated after each treatment the patient receives. This allows the physician to follow the effectiveness of the course of treatment. If the results show that the treatment is not effective, the course of treatment can be altered accordingly. This enables the physician to be flexible in the treatment options.
  • the methods for detecting markers can be used to assay for and to identify compounds that modulate expression of these markers in vivo or in vitro.
  • kits for qualifying ovarian cancer status e.g., for determining the prognosis of a subject
  • the kits can be used to measure the markers of the present invention.
  • the kits can be used to measure the panel of markers described herein, which are useful in
  • kits can also be used to monitor the patient's response to a course of treatment, enabling the physician to modify the treatment based upon the results of the test.
  • the kits can be used to identify compounds that modulate expression of one or more of the markers in in vitro or in vivo animal models for ovarian cancer.
  • kits comprising (a) a capture reagent that binds the panel of three biomarkers; and (b) a container comprising at least one of the biomarkers.
  • the capture reagents may also bind at least one known bio marker, Marker 4, e.g., CA125.
  • the capture reagents can be any type of reagent, preferably the reagent is a SELDI probe.
  • the capture reagent comprises an IMAC.
  • the reagent is an antibody.
  • kits of the present invention further comprise a wash solution, or eluant, that selectively allows retention of the bound biomarkers to the capture reagents as compared with other biomarkers after washing.
  • the kit may contain instructions for making a wash solution, wherein the combination of the adsorbent and the wash solution allows detection of the markers using gas phase ion spectrometry.
  • the kit comprises written instructions for use of the kit for detection of the three biomarkers set forth herein and the instructions provide for contacting a test sample with the capture reagents and detecting the panel of biomarkers retained by the capture reagents.
  • the kit may have standard instructions informing a consumer how to wash the capture reagents (e.g., probes) after a sample of blood serum contacts the capture reagents.
  • the kit may have instructions for pre-fractionating a sample to reduce complexity of proteins in the sample.
  • the kit may have instructions for automating the fractionation or other processes.
  • kits can be prepared from the materials described above, and the previous discussion of these materials (e.g. , probe substrates, capture reagents, adsorbents, washing solutions, etc.) is fully applicable to this section and will not be repeated.
  • kits comprises (a) antibodies that specifically bind to the panel of biomarkers; and (b) a detection reagent.
  • a kit can be prepared from the materials described above, and the previous discussion regarding the materials (e.g., antibodies, detection reagents, immobilized supports, etc.) is fully applicable to this section and will not be repeated.
  • the kit may further comprise pre- fractionation spin columns.
  • the kit may further comprise instructions for suitable operation parameters in the form of a label or a separate insert.
  • the kit may further comprise a standard or control information so that the test sample can be compared with the control information standard to determine if the test amount of a marker detected in a sample is a diagnostic amount consistent with a good or bad prognosis for a subject having ovarian cancer.
  • the invention also provides an article manufacture comprising at least one capture reagent bound to the panel of biomarkers provided herein.
  • articles of manufacture of the present invention include, but are not limited to, ProteinChip Arrays, probes, microtitre plates, beads, test tubes, microtubes, and any other solid phase onto which a capture reagent can be incorporated.
  • OC Epithelial ovarian cancer
  • DGCD Danish Gynecologic Cancer Database
  • LMP lymphothelial growth factor
  • Proteomic approaches may provide new insights into biomarker discovery and application.
  • Techniques such as surface-enhanced laser desorption/ionization time of flight-mass spectrometry (SELDI-TOF-MS, SELDI) have the potential to measure large number of proteins in a single sample [12].
  • SELDI surface-enhanced laser desorption/ionization time of flight-mass spectrometry
  • Petricoin et al. [13] discovered patterns of proteins found in the blood of OC patients, and reported 100% sensitivity and 95% specificity for the investigated set of serum samples. Unfortunately, other OC data with the same level of sensitivity and specificity have not been reported [14].
  • [15] used a multivariable model to combine apolipoprotein Al (APOAl), transthyretin (cysteinylated form) (TT) and inter-alpha trypsin inhibitor IV (internal fragment) (ITIH4) values from 503 patients.
  • APOAl apolipoprotein Al
  • TT transthyretin
  • IIH4 inter-alpha trypsin inhibitor IV
  • IIH4 inter-alpha trypsin inhibitor IV
  • a large-scale multi-centre study evaluated a set of seven biomarkers (ITIH4, TT, APOAl, transferrin (TrF), hepcidin (HEPC), connective-tissue activating protein 3 (CTAP3) and Serum Amyloid Al (SAA), for the detection of OC.
  • proteomic techniques will likely provide insights into a patient's prognosis. Since patients with gross similarities in their disease burden do not share the same prognosis, differences in the tumor microenvironment likely contribute to their disparate outcomes. To clarify this, proteomics may provide additional information about potential confounding variables.
  • a Risk Malignancy Index was calculated based on the ultrasound score (U), the menopausal score (M), and value of serum CA125.
  • Multilocularity > 5 bilocular
  • solid areas solid areas
  • internal papilla internal papilla
  • bilaterality ascites
  • extraovarian tumors scored one point each.
  • Postmenopausal status was defined as more than 1 year of amenorrhea or a previous hysterectomy and age > 50.
  • Serum CA125 was entered directly into the equation:
  • RMI UxMxCA125. If RMI was >200, positron emission tomography/computed tomography (PET/CT) was performed and the patient operated by a specialist in gynaecologic oncology. If RMI was ⁇ 200 the patient could be operated by a general gynaecologist. In this study six patients had a RMI ⁇ 200 and 144 patients had a RMI >200. All 150 patients were operated by a specialist in gynaecologic oncology.
  • PET/CT positron emission tomography/computed tomography
  • FIGO stage distribution was 22 stage I patients, 14 stage II patients, 80 stage III patients and 34 stage IV patients.
  • progression-free survival was calculated from the date of surgery to the date of documented disease progression (clinical, ultrasound, CT or PET/CT) and/or biochemical) or end of study, which was January 2008. The collection of progression data is a more time consuming process than collection of survival information from registries. Progression data is up to one year older than survival data. At the end of follow-up, a total of 80 OC patients had no clinical symptoms of progression (median progression free survival: 15 months, range: 1-41) and 70 patients had progression (median progression free survival: 4 months, range: 0-31).
  • Serum CA125 was measured using a commercially available immuno assay, the CA125II assay (Kryptor reagents on the BRAHMS Kryptor, Immunodiagnostic systems, using the TRACE (Time Resolved Amplified Cryptate Emission) technology, based on non-radioactive transfer of energy.
  • the measurement of APOA1 , TT, HEPC, ITIH4, B2M, CTAP3 and TrF could be accomplished in four assays, depending on the optimal ProteinChip array chemistry each analyte bound to. All sample and reference dilutions, and array processing steps were automated using a combination of commercially available automated workstations, Tecan MCA- 150 Freedom EVO (Tecan, Durham, NC) and the BioMek 2000 (Beckman Coulter, Fullereton, CA) to prevent errors and maintain protocol consistency.
  • the proteomic index was then constructed as the linear combination of the selected variables using the estimated regression coefficients.
  • the chosen model was assessed using cross validation techniques [18].
  • the index values have been standardized by the mean value and standard deviation.
  • Kaplan-Meier estimates of survival probabilities were calculated by grouping patients using the index tertiles as cutpoints. The equality of strata were tested using the log rank test.
  • Multivariable Cox proportional hazard regression was done including the proteomic xb-pro index and adjusting for International Federation of Gynaecology and Obstetrics' (FIGO) stage (I, II, III and IV), residual tumor after primary surgery (yes/no), performance status (1, 2, 3, 4), age at diagnosis (linear), histological type of tumor (serous, mucinous, other types), serum CA125 levels and chemotherapy (yes/no).
  • the results for each variable are presented by the hazard ratio (HR) and their 95% confidence intervals (95% CI).
  • HR hazard ratio
  • 95% CI 95% confidence intervals
  • Example 2 Description of the seven markers: APOl, TT, HEPC, ITIH4, B2M, CTAP3 and TrF.
  • the patients included in the study were slightly older (65 years, range: 30-87) than the median age for Danish patients diagnosed with OC (60 year) [1]. Similarly with respect to stage and histology this study may reflect the group of women all treated at a University Hospital.
  • the median peak intensity was 6.97 for APOA1 (range: 4.65-8.20), 4.25 for TT (range: 1.66-5.69), 7.36 for HEPC (range: 6.64-10.28), 3.32 for ITIH4 (range: 3.32-8.32), 2.90 for B2M (range: 1.53- 5.56), 2.48 for CTAP3 (range: 0.97-4.10) and 1.15 for TrF (range: 0.32-2.21).
  • the median serum CA125 level was 558.5 U/ml (range: 6-17275). Representative spectra from non-progressing OC patients and from progressing OC patients are shown in Figures 1A-1D.
  • Serum proteomic xb-pro index and xb-pfs index for overall and progression-free survival.
  • the type III tests show that the largest chi-square was the xb-pro index (18.49), chemotherapy (13.66), radicality after primary surgery (12.02), age at diagnosis (6.39), FIGO stage (4.96), histological type of tumor (4.23), performance status (3.02) and CA125 (0.56).
  • the Cox survival analysis including the xb-pro index and the clinical covariates with independent prognostic value did not change the results.
  • the other 5 serum proteomic markers were found of no value to predict progression-free survival.
  • Cross validation suggested robust estimates of the linear predictor.
  • Protein expression profiling using proteomics techniques can be used to discover novel modified forms of proteins and to determine which combinations of proteins are most specifically associated with clinical conditions such as patient predictive value and prognosis. Because of its high mortality, OC has received much attention from proteomics analysis [13-16]. It is hoped that proteomics will allow the development of personalized patient therapy and monitoring of disease. Numerous markers have proven useful in individual studies. However, few have proven useful when applied to other different populations. This is one factor in determining the clinical relevance of candidate biomarkers. ApoAl, TT, and TrF are some of the biomarkers that have been successfully reproduced in other studies [15, 19-21].
  • the biomarker B2M has been found predictive in patients with OC [26] .
  • B2M is included in the proteomic xb-pro index and therefore the effect of this index on progression-free survival was analysed.
  • the optimal proteomic index (xb-pfs) was composed of two biomarkers, B2M and CTAP3, with the strongest effect from B2M. Therefore, these findings support the earlier observation of B2M as a predictive independent marker of OC.
  • proteomic index xb-pro
  • proteomic index xb-pfs
  • the proteomic index had a very strong independent prognostic value for overall survival - even stronger than FIGO stage and B2M as reported earlier.
  • the panel of three biomarkers provides surprisingly accurate predictive results of survival independent of the stage of the cancer.
  • Example 2 Prognostic panels of biomarkers were analyzed for efficacy.
  • APOAl_D and CTAP_D are 0.66, 0.56, 0.33 and 0.35 (for OS).
  • the following table presents univariable analyses of these peaks for Progression Free Survival (PFS) and overall survival (OS).
  • ITIH4_D 0.30 0.78 0.49-1.24 0.054 0.55 0.30-1.01
  • CTAP_D 0.006 2.63 1.32-5.24 0.044 1.76 1.02-3.05
  • Example 3 A panel including B2M_B, Trf_PR and ITH4_D had prognostic value
  • the 3 selected biomarkers are all statistically significant (p ⁇ 0.05).
  • the weakest covariate is ITIH4D.
  • the internal validation procedures suggested that B2M_B and TRF_PR are very robust estimates and that ⁇ 4 less so but still reasonably strong. See Figure 3.
  • CA125 has been included in the univariable and multivariable analyses, please see the tables. CA125 is not significant in the multivariable setting.
  • Petricoin EF Ardekani AM, Hitt BA et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 2002, 359, 572-577.
  • Multivariate prognostic models issues in developing models, evaluating assumptions and adequacy, and measuring and reducing errors. Stat Med 1996, 15, 361-387.

Abstract

La présente invention concerne des procédés pour donner un pronostic à une patiente atteinte d'un cancer ovarien. L'invention a également pour objet des procédés pour évaluer l'état d'un cancer ovarien chez une patiente. Ces procédés comprennent la détection, l'analyse et la classification de motifs biologiques dans des échantillons biologiques. Les motifs biologiques sont obtenus au moyen, par exemple, de systèmes de spectrométrie de masse et d'autres techniques.
EP11835211.1A 2010-10-22 2011-10-21 Biomarqueurs pronostiques chez des patientes atteintes d'un cancer ovarien Ceased EP2630498A4 (fr)

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US10324084B2 (en) 2014-04-23 2019-06-18 Nichirei Biosciences Inc. Combination product for detecting target marker
EP3435379A1 (fr) * 2017-07-27 2019-01-30 Roche Diagnostics GmbH Augmentation des valeurs de mesure d'échantillons biologiques
KR102082462B1 (ko) * 2017-10-31 2020-02-27 국립암센터 nc886 유전자를 이용한 난소암 예후 예측을 위한 정보제공방법
JP7272627B2 (ja) * 2019-01-24 2023-05-12 公立大学法人和歌山県立医科大学 卵巣腫瘍の評価用バイオマーカー

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WO2012054824A3 (fr) 2012-07-19
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