WO2011146725A1 - Biomarqueurs pour un inhibiteur à multiples kinases - Google Patents

Biomarqueurs pour un inhibiteur à multiples kinases Download PDF

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Publication number
WO2011146725A1
WO2011146725A1 PCT/US2011/037166 US2011037166W WO2011146725A1 WO 2011146725 A1 WO2011146725 A1 WO 2011146725A1 US 2011037166 W US2011037166 W US 2011037166W WO 2011146725 A1 WO2011146725 A1 WO 2011146725A1
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cancer
level
cell
ck18m30
regorafenib
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PCT/US2011/037166
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English (en)
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Michael Jeffers
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Bayer Healthcare Llc
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    • 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
    • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/136—Screening for pharmacological compounds
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • 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

Definitions

  • the invention relates generally to cancer and biomarkers, and more particularly to identification of clinically useful serum (plasma treatment) and/or tumor biomarkers and expression signatures that can be used for prognostication and guidance for the treatment of cancer patients, such as patients with renal cell carcinoma (RCC), with a multikinase inhibitor, such as, for example, Regorafenib (solely or in combination with other agents).
  • plasma treatment clinically useful serum
  • tumor biomarkers and expression signatures that can be used for prognostication and guidance for the treatment of cancer patients, such as patients with renal cell carcinoma (RCC), with a multikinase inhibitor, such as, for example, Regorafenib (solely or in combination with other agents).
  • Renal cell carcinoma is the most common type of kidney cancer in adults and is one of the most lethal tumors. Where the tumor is confined to the renal parenchyma, the 5- year survival rate is 60-70%, but this is lowered considerably where metastases have spread. As such, there is a strong need for advancement in prognosis, early detection, and treatment of RCC.
  • Diaryl urea compounds such as Regorafenib, 4 ⁇ 4-[3-(4-chloro-3- trifluoromethylphenyl)-ureido] -3 -fluorophenoxy ⁇ -pyridine-2-carboxylic acid methylamide, and its derivatives as described for example in US 20050038080, are potent anti-cancer and anti-angiogenic agents that possess various activities, including inhibitory activity on the VEGFR, PDGFR, raf, p38, and/or flt-3 kinase signaling molecules.
  • diaryl urea compounds have been previously characterized as having various activities, including for inhibiting the Raf/MEK ERK pathway, raf kinase, p38 kinase, VEGFR kinase, PDGFR kinase. These activities and their use in treating various diseases and conditions are disclosed in, e.g., WO 2005/009961.
  • Regorafenib is an investigational anti-cancer drug with a distinct profile targeting angiogenic (VEGFR, TIE-2), stromal (PDGFR) and oncogenic (RAF, RET and c-KIT) receptor tyrosine kinases.
  • US Patent 7,833736 discloses ten protein biomarkers: Heat Shock Protein-27 (HSP- 27), Cortactin, Cdc25C (or phospho-Cdc25C (Ser216 or Thr48)), phospho-MAPKAPK-2 (Thr334), phospho-Cyclin E (Thr62), Stathmin, phospho-ATF2 (Thr69 or Thr71), phospho- Histone H3 (Thr3), phospho-EIF-4B (Ser422), and phospho-Rpbl (Ser2 or Ser5), that are said to predictive of cancer resistance or responsiveness to targeted inhibitors of certain Receptor Tyrosine Kinases (RTKs).
  • HSP- 27 Heat Shock Protein-27
  • Cortactin Cdc25C
  • Cdc25C or phospho-Cdc25C (Ser216 or Thr48)
  • phospho-MAPKAPK-2 Thr334)
  • phospho-Cyclin E Thr62
  • Stathmin phospho-ATF2 (
  • kits for identifying the resistance or responsiveness of certain cancers, tumors, and patients to these inhibitors which comprise detectable reagents for three or more of the 10 biomarker proteins. It is said the kits can be employed on biopsy samples, fine needle aspirates, or biological fluids such as serum, blood plasma, or bone marrow, and may comprise whole cells or a cell lysate, whether or not isolated.
  • the present invention relates to biomarkers and the use of biomarkers for the prediction and prognosis of cancer as well as the use of biomarkers to monitor the efficacy of cancer treatment.
  • this invention relates to the use of PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF as biomarkers for efficacy of treatment with diaryl urea multikinase inhibitors such as Regorafenib.
  • sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF decreased in subjects treated with Regorafenib, while PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, or ANG2 levels increased.
  • these markers can be used to determine the efficacy of Regorafenib treatment.
  • Another embodiment of the present invention is a method for screening the effects of a drug on a tissue or cell sample comprising the step of analyzing the level of expression of one or more genes and/or gene products, wherein the gene expression and/or gene product levels in the tissue or cell sample are analyzed before and after exposure to the drug, and a variation in the expression level of the gene and/or gene product is indicative of a drug effect or provides a patient diagnosis or predicts a patient's response to the treatment.
  • the drug is a Regorafenib.
  • the gene or gene product is PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF, and soluble forms thereof.
  • the invention further provides a method for identifying a compound useful for the treatment of cancer comprising administering to a subject with cancer a test compound, and measuring the activity of the polypeptide, wherein a change in the activity of the polypeptide is indicative of the test compound being useful for the treatment of cancer.
  • the polypeptide is PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, SVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF and soluble forms thereof (e.g., detection of shed VEGFR2), and in another embodiment, the compound is a Regorafenib.
  • the invention provides methods which may be used to identify compounds which may act, for example, as regulators or modulators such as agonists and antagonists, partial agonists, inverse agonists, activators, co-activators, and inhibitors. Accordingly, the invention provides reagents and methods for regulating the expression of a polynucleotide or a polypeptide associated with cancer.
  • Reagents that modulate the expression, stability, or amount of a polynucleotide or the activity of the polypeptide may be a protein, a peptide, a peptidomimetic, a nucleic acid, a nucleic acid analogue (e.g., peptide nucleic acid, locked nucleic acid), or a small molecule.
  • the present invention also provides a method for providing a patient diagnosis comprising the step of analyzing the level of expression of one or more genes and/or gene products, wherein the gene expression and/or gene product levels of normal and patient samples are analyzed, and a variation in the expression level of the gene and/or gene product in the patient sample is diagnostic of a disease.
  • the patient samples include, but are not limited to, blood, amniotic fluid, plasma, semen, bone marrow, and tissue biopsy.
  • the gene or gene product is PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF and soluble forms thereof.
  • the present invention still further provides a method of diagnosing cancer in a subject comprising measuring the activity of the polypeptide in a subject suspected of having cancer, wherein if there is a difference in the activity of the polypeptide, relative to the activity of the polypeptide in a subject not suspected of having cancer, then the subject is diagnosed has having cancer.
  • the polypeptide is PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF and soluble forms thereof.
  • the invention provides a method for detecting cancer in a patient sample in which an antibody to a protein is used to react with proteins in the patient sample.
  • the antibody is specific for PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF and soluble forms thereof.
  • Antibodies can be generated routinely, e.g., to exposed regions of the polypeptides. For example, antibodies can be routinely generated to the extracellular domain of sVEGFR-2.
  • Another aspect of the present invention is a method for distinguishing between normal and disease states comprising the step of analyzing the level of expression of one or more genes and/or gene products, wherein the gene expression and/or gene product levels of normal and disease tissues are analyzed, and a variation in the expression level of the gene and/or gene product is indicative of a disease state.
  • the gene or gene product is PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF.
  • the invention pertains to a method of determining the phenotype of cells comprising detecting the differential expression, relative to normal cells, of at least one gene, wherein the gene is differentially expressed by at least a factor of two, at least a factor of five, at least a factor of twenty, or at least a factor of fifty.
  • the gene encodes PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, SVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF.
  • the invention pertains to a method of determining the phenotype of cells, comprising detecting the differential expression, relative to normal cells, of at least one polypeptide, wherein the protein is differentially expressed by at least a factor of two, at least a factor of five, at least a factor of twenty, an up to at least a factor of fifty.
  • the polypeptide is PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF and soluble forms thereof.
  • modulation of sKIT, CYTC or CK18M30 by Regorafenib exhibits a correlation between degree of change and clinical response.
  • baseline levels of IL16, SCF, HGF or TIMP2 are associated with clinical response to Regorafenib. Assays testing for these biomarkers may be advantageously employed to identify patients that would be likely to respond to Regorafenib. Such a selection of patients would be useful in the prescription of Regorafenib to patients.
  • the invention provides a test kit for identifying the presence of cancerous cells or tissues, comprising a probe/primer, for measuring a level of a nucleic acid in a sample of cells isolated from a patient.
  • the kit may further include instructions for using the kit, solutions for suspending or fixing the cells, detectable tags or labels, solutions for rendering a nucleic acid susceptible to hybridization, solutions for lysing cells, or solutions for the purification of nucleic acids.
  • the probe/primer comprises a nucleotide sequence encoding a fragment of PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF.
  • the invention provides a test kit for identifying the presence of cancer cells or tissues, comprising an antibody specific for a protein.
  • the kit further includes instructions for using the kit.
  • the kit may further include solutions for suspending or fixing the cells, detectable tags or labels, solutions for rendering a polypeptide susceptible to the binding of an antibody, solutions for lysing cells, or solutions for the purification of polypeptides.
  • the antibody is specific for PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF.
  • the invention provides a test kit for monitoring the efficacy of a compound or therapeutic, such as Regorafenib, in cancerous cells or tissues, comprising a probe/primer, for measuring a level of a nucleic acid in a sample of cells isolated from a patient.
  • the kit may further include instructions for using the kit, solutions for suspending or fixing the cells, detectable tags or labels, solutions for rendering a nucleic acid susceptible to hybridization, solutions for lysing cells, or solutions for the purification of nucleic acids.
  • the probe/primer comprises the nucleotide sequence encoding PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, SVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF.
  • the invention provides a test kit for monitoring the efficacy of a compound or therapeutic in cancer cells or tissues, comprising an antibody specific for a protein.
  • the kit further includes instructions for using the kit.
  • the kit may further include solutions for suspending or fixing the cells, detectable tags or labels, solutions for rendering a polypeptide susceptible to the binding of an antibody, solutions for lysing cells, or solutions for the purification of polypeptides.
  • the antibody is specific for PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF.
  • Kits of this invention may advantageously comprise one or more (and often three or more) detectable reagents suitable for assaying the biomarkers discussed above.
  • detectable reagents may preferably be antibodies, as described above, either alone or in combination with reagents for the detection of proteins other than the biomarkers discussed above.
  • the kits may also include ancillary agents such as buffering agents and protein stabilizing agents, e.g., polysaccharides and the like.
  • Reference to diaryl urea multikinase inhibitors herein is intended to include the Regorafenib.
  • Reference to Regorafenib is intended to include a compound of formula I or a pharmaceutically acceptable salt, polymorph, solvate, hydrate, metabolite, prodrug or diastereoisomeric form thereof.
  • An "address" on an array refers to a location at which an element, for example, an oligonucleotide, is attached to the solid surface of the array.
  • agonist is meant to refer to an agent that mimics or up- regulates (e.g., potentiates or supplements) the bioactivity of a protein.
  • An agonist may be a wild-type protein or derivative thereof having at least one bioactivity of the wild-type protein.
  • An agonist may also be a compound that up-regulates expression of a gene or which increases at least one bioactivity of a protein.
  • An agonist can also be a compound which increases the interaction of a polypeptide with another molecule, for example, a target peptide or nucleic acid.
  • amplification relates to the production of additional copies of a nucleic acid sequence.
  • amplification may be carried out using polymerase chain reaction (PCR) technologies which are well known in the art. (see, e.g., Dieffenbach and Dveksler (1995) PCR Primer, A Laboratory Manual, Cold Spring Harbor Press, Plainview, N.Y.)
  • Antagonist is meant to refer to an agent that down-regulates (e.g., suppresses or inhibits) at least one bioactivity of a protein.
  • a Regorafenib is an example of such an antagonist.
  • An antagonist may be a compound which inhibits or decreases the interaction between a protein and another molecule, for example, a target peptide or enzyme substrate.
  • An antagonist may also be a compound that down-regulates expression of a gene or which reduces the amount of expressed protein present.
  • antibody is intended to include whole antibodies, for example, of any isotype (IgG, IgA, IgM, IgE, etc.), and includes fragments thereof which are also specifically reactive with a vertebrate (e.g., mammalian) protein.
  • Antibodies may be fragmented using conventional techniques and the fragments screened for utility in the same manner as described above for whole antibodies.
  • the term includes segments of proteolytically-cleaved or recombinantly-prepared portions of an antibody molecule that are capable of selectively reacting with a certain protein.
  • Non-limiting examples of such proteolytic and/or recombinant fragments include Fab, F(ab')2, Fab', Fv, and single chain antibodies (scFv) containing a V[L] and/or V[H] domain joined by a peptide linker.
  • the scFv's may be covalently or non-covalently linked to form antibodies having two or more binding sites.
  • the subject invention includes polyclonal, monoclonal, or other purified preparations of antibodies and recombinant antibodies.
  • array or “matrix” refer to an arrangement of addressable locations or “addresses” on a device.
  • the locations can be arranged in two-dimensional arrays, three- dimensional arrays, or other matrix formats.
  • the number of locations may range from several to at least hundreds of thousands. Most importantly, each location represents a totally independent reaction site.
  • a "nucleic acid array” refers to an array containing nucleic acid probes, such as oligonucleotides or larger portions of genes.
  • the nucleic acid on the array is preferably single-stranded.
  • oligonucleotide arrays Arrays wherein the probes are oligonucleotides are referred to as “oligonucleotide arrays” or “oligonucleotide chips.”
  • a “microarray,” also referred to herein as a “biochip” or “biological chip,” is an array of regions having a density of discrete regions of at least about 100/cm 2 , and preferably at least about 1000/cm 2 .
  • the regions in a microarray have typical dimensions, for example, diameters, in the range of between about 10-250 ⁇ , and are separated from other regions in the array by about the same distance.
  • Bioactivity or “bioactivity” or “activity” or “biological function,” which are used interchangeably, herein mean an effector or antigenic function that is directly or indirectly performed by a polypeptide (whether in its native or denatured conformation), or by any subsequence thereof.
  • Biological activities include binding to polypeptides, binding to other proteins or molecules, activity as a DNA binding protein, as a transcription regulator, ability to bind damaged DNA, etc.
  • a bioactivity can be modulated by directly affecting the subject polypeptide.
  • a bioactivity can be altered by modulating the level of the polypeptide, such as by modulating expression of the corresponding gene.
  • biological sample refers to a sample obtained from an organism or from components (e.g., cells) of an organism.
  • the sample may be of any biological tissue or fluid.
  • the sample may be a sample which is derived from a patient.
  • samples include, but are not limited to, sputum, blood, blood cells (e.g., white cells), tissue or biopsy samples (e.g., tumor biopsy), urine, peritoneal fluid, and pleural fluid, or cells therefrom.
  • Biological samples may also include sections of tissues such as frozen sections taken for histological purposes.
  • Biomarker encompasses a broad range of intra- and extracellular events as well as whole-organism physiological changes.
  • Biomarkers may be represent essentially any aspect of cell function, for example, but not limited to, levels or rate of production of signaling molecules, transcription factors, metabolites, gene transcripts as well as post-translational modifications of proteins.
  • Biomarkers may include whole genome analysis of transcript levels or whole proteome analysis of protein levels and/or modifications.
  • a biomarker may also refer to a gene or gene product which is up- or down-regulated in a compound-treated, diseased cell of a subject having the disease compared to an untreated diseased cell. That is, the gene or gene product is sufficiently specific to the treated cell that it may be used, optionally with other genes or gene products, to identify, predict, or detect efficacy of a small molecule.
  • a biomarker is a gene or gene product that is characteristic of efficacy of a compound in a diseased cell or the response of that diseased cell to treatment by the compound.
  • a nucleotide sequence is "complementary" to another nucleotide sequence if each of the bases of the two sequences match, that is, are capable of forming Watson-Crick base pairs.
  • the term "complementary strand” is used herein interchangeably with the term “complement.”
  • the complement of a nucleic acid strand may be the complement of a coding strand or the complement of a non-coding strand.
  • Detection agents of genes refers to agents that can be used to specifically detect the gene or other biological molecules relating to it, for example, RNA transcribed from the gene or polypeptides encoded by the gene.
  • exemplary detection agents are nucleic acid probes, which hybridize to nucleic acids corresponding to the gene, and antibodies.
  • cancer includes, but is not limited to, solid tumors, such as cancers of the breast, respiratory tract, brain, reproductive organs, digestive tract, urinary tract, eye, liver, skin, head and neck, thyroid, parathyroid, and their distant metastases.
  • solid tumors such as cancers of the breast, respiratory tract, brain, reproductive organs, digestive tract, urinary tract, eye, liver, skin, head and neck, thyroid, parathyroid, and their distant metastases.
  • lymphomas, sarcomas, and leukemia include lymphomas, sarcomas, and leukemia.
  • breast cancer examples include, but are not limited to, invasive ductal carcinoma, invasive lobular carcinoma, ductal carcinoma in situ, and lobular carcinoma in situ.
  • cancers of the respiratory tract include, but are not limited to, small-cell and non-small-cell lung carcinoma, as well as bronchial adenoma and pleuropulmonary blastoma.
  • brain cancers include, but are not limited to, brain stem and hypophtalmic glioma, cerebellar and cerebral astrocytoma, medulloblastoma, ependymoma, as well as neuroectodermal and pineal tumor.
  • Tumors of the male reproductive organs include, but are not limited to, prostate and testicular cancer.
  • Tumors of the female reproductive organs include, but are not limited to, endometrial, cervical, ovarian, vaginal, and vulvar cancer, as well as sarcoma of the uterus.
  • Tumors of the digestive tract include, but are not limited to, anal, colon, colorectal, esophageal, gallbladder, gastric, pancreatic, rectal, small-intestine, and salivary gland cancers.
  • Tumors of the urinary tract include, but are not limited to, bladder, penile, kidney, renal (e.g., renal cell carcinoma) pelvis, ureter, and urethral cancers.
  • Eye cancers include, but are not limited to, intraocular melanoma and retinoblastoma.
  • liver cancers include, but are not limited to, hepatocellular carcinoma (liver cell carcinomas with or without fibrolamellar variant), cholangiocarcinoma (intrahepatic bile duct carcinoma), and mixed hepatocellular cholangiocarcinoma.
  • Skin cancers include, but are not limited to, squamous cell carcinoma, Kaposi's sarcoma, malignant melanoma, Merkel cell skin cancer, and non-melanoma skin cancer.
  • Head-and-neck cancers include, but are not limited to, laryngeal / hypopharyngeal / nasopharyngeal / oropharyngeal cancer, and lip and oral cavity cancer.
  • Lymphomas include, but are not limited to, AIDS-related lymphoma, non-Hodgkin's lymphoma, cutaneous T-cell lymphoma, Hodgkin's disease, and lymphoma of the central nervous system.
  • Sarcomas include, but are not limited to, sarcoma of the soft tissue, osteosarcoma, malignant fibrous histiocytoma, lymphosarcoma, and rhabdomyosarcoma.
  • Leukemias include, but are not limited to, acute myeloid leukemia, acute lymphoblastic leukemia, chronic lymphocytic leukemia, chronic myelogenous leukemia, and hairy cell leukemia.
  • a diseased cell of cancer refers to a cell present in subjects having cancer. That is, a cell which is a modified form of a normal cell and is not present in a subject not having cancer, or a cell which is present in significantly higher or lower numbers in subjects having cancer relative to subjects not having cancer.
  • Equivalent is understood to include nucleotide sequences encoding functionally equivalent polypeptides.
  • Equivalent nucleotide sequences may include sequences that differ by one or more nucleotide substitutions, additions, or deletions, such as allelic variants.
  • expression profile which is used interchangeably herein with “gene expression profile” and “fingerprint” of a cell refers to a set of values representing mRNA levels of one or more genes in a cell.
  • An expression profile preferably comprises values representing expression levels of at least about 10 genes, preferably at least about 50, 100, 200 or more genes.
  • Expression profiles may also comprise an mRNA level of a gene which is expressed at similar levels in multiple cells and conditions (e.g., a housekeeping gene such as GAPDH).
  • an expression profile of a diseased cell of cancer refers to a set of values representing mRNA levels of 10 or more genes in a diseased cell.
  • the term "gene” refers to a nucleic acid sequence that comprises control and coding sequences necessary for the production of a polypeptide or precursor.
  • the polypeptide can be encoded by a full length coding sequence or by any portion of the coding sequence.
  • the gene may be derived in whole or in part from any source known to the art, including a plant, a fungus, an animal, a bacterial genome or episome, eukaryotic, nuclear or plasmid DNA, cDNA, viral DNA, or chemically synthesized DNA.
  • a gene may contain one or more modifications in either the coding or the untranslated regions which could affect the biological activity or the chemical structure of the expression product, the rate of expression, or the manner of expression control.
  • Such modifications include, but are not limited to, mutations, insertions, deletions, and substitutions of one or more nucleotides.
  • the gene may constitute an uninterrupted coding sequence or it may include one or more introns, bound by the appropriate splice junctions.
  • Hybridization refers to any process by which a strand of nucleic acid binds with a complementary strand through base pairing.
  • two single- stranded nucleic acids "hybridize” when they form a double- stranded duplex.
  • the region of double-strandedness may include the full-length of one or both of the single- stranded nucleic acids, or all of one single- stranded nucleic acid and a subsequence of the other single- stranded nucleic acid, or the region of double-strandedness may include a subsequence of each nucleic acid.
  • Hybridization also includes the formation of duplexes which contain certain mismatches, provided that the two strands are still forming a double-stranded helix.
  • “Stringent hybridization conditions” refers to hybridization conditions resulting in essentially specific hybridization.
  • isolated refers to molecules separated from other DNAs or RNAs, respectively, that are present in the natural source of the macromolecule.
  • isolated as used herein also refers to a nucleic acid or peptide that is substantially free of cellular material, viral material, culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized.
  • an "isolated nucleic acid” may include nucleic acid fragments which are not naturally occurring as fragments and would not be found in the natural state.
  • isolated is also used herein to refer to polypeptides which are isolated from other cellular proteins and is meant to encompass both purified and recombinant polypeptides.
  • label and “detectable label” refer to a molecule capable of detection, including, but not limited to, radioactive isotopes, fluorophores, chemiluminescent moieties, enzymes, enzyme substrates, enzyme cofactors, enzyme inhibitors, dyes, metal ions, ligands (e.g., biotin or haptens), and the like.
  • fluorescer refers to a substance or a portion thereof which is capable of exhibiting fluorescence in the detectable range.
  • the term “level of expression” refers to the measurable expression level of a given nucleic acid.
  • the level of expression of a nucleic acid is determined by methods well known in the art.
  • the term “differentially expressed” or “differential expression” refers to an increase or decrease in the measurable expression level of a given nucleic acid.
  • “differentially expressed” or “differential expression” means the difference in the level of expression of a nucleic acid is at least 1.4-fold or more in two samples used for comparison, both of which are compared to the same normal standard sample.
  • “Differentially expressed” or “differential expression” also means a 1.4-fold, or more, up to and including 2-fold, 5 -fold, 10-fold, 20-fold, 50-fold or more difference in the level of expression of a nucleic acid in two samples used for comparison.
  • a nucleic acid is also said to be “differentially expressed” in two samples if one of the two samples contains no detectable expression of a given nucleic acid, provided that the detectably expressed nucleic acid is expressed at +/- at least 1.4 fold.
  • Differential expression of a nucleic acid sequence is "inhibited" the difference in the level of expression of the nucleic acid in two or more samples used for comparison is altered such that it is no longer at least a 1.4 fold difference.
  • Absolute quantification of the level of expression of a nucleic acid may be accomplished by including a known concentration(s) of one or more control nucleic acid species, generating a standard curve based on the amount of the control nucleic acid and extrapolating the expression level of the "unknown" nucleic acid species from the hybridization intensities of the unknown with respect to the standard curve.
  • nucleic acid refers to polynucleotides such as deoxyribonucleic acid (DNA) and, where appropriate, ribonucleic acid (RNA).
  • DNA deoxyribonucleic acid
  • RNA ribonucleic acid
  • Chromosomes, cDNAs, mRNAs, rRNAs, and ESTs are representative examples of molecules that may be referred to as nucleic acids.
  • oligonucleotide refers to a nucleic acid molecule comprising, for example, from about 10 to about 1000 nucleotides. Oligonucleotides for use in the present invention are preferably from about 15 to about 150 nucleotides, more preferably from about 150 to about 1000 in length.
  • the oligonucleotide may be a naturally occurring oligonucleotide or a synthetic oligonucleotide. Oligonucleotides may be prepared by the phosphoramidite method (Beaucage and Carruthers, Tetrahedron Lett. 22: 1859-62, 1981), or by the triester method (Matteucci, et al., J. Am. Chem. Soc. 103:3185, 1981), or by other chemical methods known in the art.
  • patient or "subject” as used herein includes mammals (e.g., humans and animals).
  • a nucleic acid or other molecule attached to an array is referred to as a "probe” or “capture probe.”
  • probe or capture probe
  • a gene-probe set may consist of, for example, about 2 to about 20 probes, preferably from about 2 to about 10 probes, and most preferably about 5 probes.
  • the "profile" of a cell's biological state refers to the levels of various constituents of a cell that are known to change in response to drug treatments and other perturbations of the biological state of the cell.
  • Constituents of a cell include, for example, levels of RNA, levels of protein abundances, or protein activity levels.
  • protein is used interchangeably herein with the terms “peptide” and “polypeptide.”
  • An expression profile in one cell is "similar" to an expression profile in another cell when the level of expression of the genes in the two profiles are sufficiently similar that the similarity is indicative of a common characteristic, for example, the same type of cell. Accordingly, the expression profiles of a first cell and a second cell are similar when at least 75% of the genes that are expressed in the first cell are expressed in the second cell at a level that is within a factor of two relative to the first cell.
  • Small molecule refers to a composition with a molecular weight of less than about 5 kD and most preferably less than about 4 kD. Small molecules can be nucleic acids, peptides, polypeptides, peptidomimetics, carbohydrates, lipids, or other organic or inorganic molecules. Many pharmaceutical companies have extensive libraries of chemical and/or biological mixtures, often fungal, bacterial, or algal extracts, which can be screened with any of the assays of the invention to identify compounds that modulate a bioactivity.
  • hybridization of a probe to a target site of a template nucleic acid refers to hybridization of the probe predominantly to the target, such that the hybridization signal can be clearly interpreted.
  • such conditions resulting in specific hybridization vary depending on the length of the region of homology, the GC content of the region, and the melting temperature ("Tm") of the hybrid.
  • Tm melting temperature
  • hybridization conditions may vary in salt content, acidity, and temperature of the hybridization solution and the washes.
  • a "variant" of polypeptide refers to a polypeptide having an amino acid sequence in which one or more amino acid residues is altered.
  • the variant may have "conservative” changes, wherein a substituted amino acid has similar structural or chemical properties (e.g., replacement of leucine with isoleucine).
  • a variant may also have "nonconservative” changes (e.g., replacement of glycine with tryptophan).
  • Analogous minor variations may include amino acid deletions or insertions, or both.
  • Guidance in determining which amino acid residues may be substituted, inserted, or deleted without abolishing biological or immunological activity may be identified using computer programs well known in the art, for example, LASERGENE software (DNASTAR).
  • variants when used in the context of a polynucleotide sequence, may encompass a polynucleotide sequence related to that of a particular gene or the coding sequence thereof. This definition may also include, for example, "allelic,” “splice,” “species,” or “polymorphic” variants.
  • a splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate splicing of exons during mRNA processing.
  • the corresponding polypeptide may possess additional functional domains or an absence of domains.
  • Species variants are polynucleotide sequences that vary from one species to another.
  • polymorphic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species.
  • Polymorphic variants also may encompass "single nucleotide polymorphisms" (SNPs) in which the polynucleotide sequence varies by one base. The presence of SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.
  • SNPs single nucleotide polymorphisms
  • An aspect of the invention is directed to the identification of agents, such as Regorafenib, as to their capability of modulating the differentiation and proliferation of cells characterized by aberrant proliferation. More specifically, the invention relates to methods of screening candidate compounds, such as Regorafenib, for their ability to regulate the differential expression of nucleic acid sequences. That is, if a nucleic acid sequence is overexpressed in cancer cells, then the candidate compounds (e.g., Regorafenib) are tested/screened for their ability to decrease expression, and if a nucleic acid sequence is underexpressed in cancer cells, then a test compound (e.g., Regorafenib) is tested/screened for its ability to increase expression.
  • candidate compounds e.g., Regorafenib
  • a test compound e.g., Regorafenib
  • the invention relates to screening assays to identify whether test compounds, such as Regorafenib, can modulate the activity of one or more polypeptides which are encoded by the differentially expressed sequences described herein.
  • test compounds such as Regorafenib
  • the invention provides assays for determining whether compounds, such as Regorafenib, modulate the expression of marker nucleic acids and/or alter the bioactivity of the encoded polypeptide. Screening for modulation of differential expression
  • Drug screening is performed by adding a test compound (e.g., Regorafenib and derivatives thereof) to a sample of cells, and monitoring the effect. A parallel sample which does not receive the test compound is also monitored as a control.
  • the treated and untreated cells are then compared by any suitable phenotypic criteria, including but not limited to microscopic analysis, viability testing, ability to replicate, histological examination, the level of a particular RNA or polypeptide associated with the cells, the level of enzymatic activity expressed by the cells or cell lysates, and the ability of the cells to interact with other cells or compounds. Differences between treated and untreated cells indicates effects attributable to the test compound.
  • Desirable effects of a test compound include an effect on any phenotype that was conferred by the cancer-associated marker nucleic acid sequence. Examples include a test compound that limits the overabundance of mRNA, limits production of the encoded protein, or limits the functional effect of the protein. The effect of the test compound would be apparent when comparing results between treated and untreated cells.
  • the invention thus, also encompasses methods of screening for agents (e.g., Regorafenib and derivatives thereof) which inhibit or enhance the expression of the nucleic acid markers in vitro, comprising exposing a cell or tissue in which the marker nucleic acid mRNA (e.g., PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF ) is detectable in cultured cells to an agent in order to determine whether the agent is capable of inhibiting or enhancing production of the mRNA; and determining the level of mRNA in the exposed cells or tissue, wherein a decrease in the level of the mRNA after exposure of the cell line to the agent is indicative of inhibition of the marker nucleic acid mRNA production and an increase in mRNA levels is indicative of enhancement of maker mRNA production.
  • agents e.g., Regora
  • the screening method may include in vitro screening of a cell or tissue in which marker protein is detectable in cultured cells to an agent suspected of inhibiting or enhancing production of the marker protein; and determining the level of the marker protein in the cells or tissue, wherein a decrease in the level of marker protein after exposure of the cells or tissue to the agent is indicative of inhibition of marker protein production and an increase on the level of marker protein is indicative of enhancement of marker protein production.
  • the invention also encompasses in vivo methods of screening for agents which inhibit or enhance expression of the marker nucleic acids, comprising exposing a subject having tumor cells in which marker mRNA or protein is detectable to an agent suspected of inhibiting or enhancing production of marker mRNA or protein; and determining the level of marker mRNA or protein in tumor cells of the exposed mammal.
  • a decrease in the level of marker mRNA or protein after exposure of the subject to the agent is indicative of inhibition of marker nucleic acid expression and an increase in the level of marker mRNA or protein is indicative of enhancement of marker nucleic acid expression.
  • the invention provides a method comprising incubating a cell expressing the marker nucleic acids with a test compound and measuring the mRNA or protein level.
  • the invention further provides a method for quantitatively determining the level of expression of the marker nucleic acids in a cell population, and a method for determining whether an agent is capable of increasing or decreasing the level of expression of the marker nucleic acids in a cell population.
  • the method for determining whether an agent is capable of increasing or decreasing the level of expression of the marker nucleic acids in a cell population comprises the steps of (a) preparing cell extracts from control and agent-treated cell populations, (b) isolating the marker polypeptides from the cell extracts, and (c) quantifying (e.g., in parallel) the amount of an immunocomplex formed between the marker polypeptide and an antibody specific to said polypeptide.
  • the marker polypeptides of this invention may also be quantified by assaying for its bioactivity.
  • Agents that induce an increase in the marker nucleic acid expression may be identified by their ability to increase the amount of immunocomplex formed in the treated cell as compared with the amount of the immunocomplex formed in the control cell.
  • agents that decrease expression of the marker nucleic acid may be identified by their ability to decrease the amount of the immunocomplex formed in the treated cell extract as compared to the control cell.
  • the present invention provides a method for identifying a nucleotide sequence which is differentially regulated in a subject with cancer, comprising: hybridizing a nucleic acid sample corresponding to RNA obtained from the subject to a nucleic acid sample comprising one or more nucleic acid molecules of known identity; and measuring the hybridization of the nucleic acid sample to the one or more nucleic acid molecules of known identity, wherein a two-fold difference in the hybridization of the nucleic acid sample to the one or more nucleic acid molecules of known identity relative to a nucleic acid sample obtained from a subject without cancer is indicative of the differential expression of the nucleotide sequence in a subject with cancer.
  • the present invention provides a method for identifying nucleic acid sequences which are differentially regulated in a subject with cancer comprising isolating messenger RNA from a subject, generating cRNA from the mRNA sample, hybridizing the cRNA to a microarray comprising a plurality of nucleic acid molecules stably associated with discrete locations on the array, and identifying patterns of hybridization of the cRNA to the array.
  • a nucleic acid molecule which hybridizes to a given location on the array is said to be differentially regulated if the hybridization signal is at least two-fold higher or lower than the hybridization signal at the same location on an identical array hybridized with a nucleic acid sample obtained from a subject that does not have cancer.
  • Determining gene expression levels may be accomplished utilizing microarrays. Generally, the following steps may be involved: (a) obtaining an mRNA sample from a subject and preparing labeled nucleic acids therefrom (the "target nucleic acids” or “targets”); (b) contacting the target nucleic acids with an array under conditions sufficient for the target nucleic acids to bind to the corresponding probes on the array, for example, by hybridization or specific binding; (c) optional removal of unbound targets from the array; (d) detecting the bound targets, and (e) analyzing the results, for example, using computer based analysis methods.
  • “nucleic acid probes” or “probes” are nucleic acids attached to the array
  • target nucleic acids are nucleic acids that are hybridized to the array.
  • Nucleic acid specimens may be obtained from a subject to be tested using either “invasive” or “non-invasive” sampling means.
  • a sampling means is said to be “invasive” if it involves the collection of nucleic acids from within the skin or organs of an animal (including murine, human, ovine, equine, bovine, porcine, canine, or feline animal).
  • invasive methods include, for example, blood collection, semen collection, needle biopsy, pleural aspiration, umbilical cord biopsy. Examples of such methods are discussed by Kim, et al., (J. Virol. 66:3879-3882, 1992); Biswas, et al., (Ann. NY Acad. Sci. 590:582-583, 1990); and Biswas, et al., (J. Clin. Microbiol. 29:2228-2233, 1991).
  • a “non-invasive” sampling means is one in which the nucleic acid molecules are recovered from an internal or external surface of the animal.
  • Examples of such "non-invasive” sampling means include, for example, “swabbing,” collection of tears, saliva, urine, fecal material, sweat or perspiration, hair.
  • RNA is isolated from the cells.
  • a sample of peripheral blood leukocytes (PBLs) cells is obtained from the subject. It is also possible to obtain a cell sample from a subject, and then to enrich the sample for a desired cell type. For example, cells may be isolated from other cells using a variety of techniques, such as isolation with an antibody binding to an epitope on the cell surface of the desired cell type.
  • the desired cells are in a solid tissue
  • particular cells may be dissected, for example, by microdissection or by laser capture microdissection (LCM) (see, e.g., Bonner, et al., Science 278: 1481, 1997; Emmert-Buck, et al., Science 274:998, 1996; Fend, et al., Am. J. Path. 154:61, 1999; and Murakami, et al., Kidney Int. 58: 1346, 2000).
  • LCM laser capture microdissection
  • RNA may be extracted from tissue or cell samples by a variety of methods, for example, guanidium thiocyanate lysis followed by CsCl centrifugation (Chirgwin, et al., Biochemistry 18:5294-5299, 1979).
  • RNA from single cells may be obtained as described in methods for preparing cDNA libraries from single cells (see, e.g., Dulac, Curr. Top. Dev. Biol. 36:245, 1998; Jena, et al., J. Immunol. Methods 190: 199, 1996).
  • RNA sample can be further enriched for a particular species.
  • poly(A)+ RNA may be isolated from an RNA sample.
  • the RNA population may be enriched for sequences of interest by primer-specific cDNA synthesis, or multiple rounds of linear amplification based on cDNA synthesis and template- directed in vitro transcription (see, e.g., Wang, et al., Proc. Natl. Acad. Sci. USA 86:9717, 1989; Dulac, et al., supra; Jena, et al., supra).
  • RNA may be further amplified by a variety of amplification methods including, for example, PCR; ligase chain reaction (LCR) (see, e.g., Wu and Wallace, Genomics 4:560, 1989; Landegren, et al., Science 241 : 1077, 1988); self-sustained sequence replication (SSR) (see, e.g., Guatelli, et al., Proc. Natl. Acad. Sci. USA 87: 1874, 1990); nucleic acid based sequence amplification (NASBA) and transcription amplification (see, e.g., Kwoh, et al., Proc. Natl.
  • LCR ligase chain reaction
  • SSR self-sustained sequence replication
  • NASBA nucleic acid based sequence amplification
  • transcription amplification see, e.g., Kwoh, et al., Proc. Natl.
  • PCR technology Principles and Applications for DNA Amplification (ed. H. A. Erlich, Freeman Press, N.Y., N.Y., 1992); PCR Protocols: A Guide to Methods and Applications (eds. Innis, et al., Academic Press, San Diego, Calif., 1990); Mattila, et al., Nucleic Acids Res. 19:4967, 1991; Eckert, et al., PCR Methods and Applications 1: 17, 1991 ; PCR (eds. McPherson et al., IRL Press, Oxford); and U.S. Pat. No.
  • RNA amplification and cDNA synthesis may also be conducted in cells in situ (see, e.g., Eberwine, et al. Proc. Natl. Acad. Sci. USA 89:3010, 1992).
  • the nucleic acid molecules may be labeled to permit detection of hybridization of the nucleic acid molecules to a microarray. That is, the probe may comprise a member of a signal producing system and thus, is detectable, either directly or through combined action with one or more additional members of a signal producing system.
  • the nucleic acids may be labeled with a fluorescently labeled dNTP (see, e.g., Kricka, 1992, Nonisotopic DNA Probe Techniques, Academic Press San Diego, Calif.), biotinylated dNTPs or rNTP followed by addition of labeled streptavidin, chemiluminescent labels, or isotopes.
  • Hybridization may be also be determined, for example, by plasmon resonance (see, e.g., Thiel, et al. Anal. Chem. 69:4948, 1997).
  • a plurality (e.g., 2, 3, 4, 5, or more) of sets of target nucleic acids are labeled and used in one hybridization reaction ("multiplex" analysis).
  • one set of nucleic acids may correspond to RNA from one cell and another set of nucleic acids may correspond to RNA from another cell.
  • the plurality of sets of nucleic acids may be labeled with different labels, for example, different fluorescent labels (e.g., fluorescein and rhodamine) which have distinct emission spectra so that they can be distinguished.
  • the sets may then be mixed and hybridized simultaneously to one microarray (see, e.g., Shena, et al., Science 270:467-470, 1995).
  • Microarrays for use according to the invention include one or more probes of genes characteristic of small molecule efficacy.
  • the microarray comprises probes corresponding to one or more of genes selected from the group consisting of genes which are up-regulated in cancer and genes which are down-regulated in cancer.
  • the microarray may comprise probes corresponding to at least 10, preferably at least 20, at least 50, at least 100 or at least 1000 genes characteristic of small molecule efficacy.
  • a microarray may contain from 2 to 20 probes corresponding to one gene and preferably about 5 to 10.
  • the probes may correspond to the full-length RNA sequence or complement thereof of genes characteristic of small molecule efficacy, or the probe may correspond to a portion thereof, which portion is of sufficient length to permit specific hybridization.
  • Such probes may comprise from about 50 nucleotides to about 100, 200, 500, or 1000 nucleotides or more than 1000 nucleotides.
  • microarrays may contain oligonucleotide probes, consisting of about 10 to 50 nucleotides, preferably about 15 to 30 nucleotides and more preferably about 20-25 nucleotides.
  • the probes are preferably single-stranded and will have sufficient complementarity to its target to provide for the desired level of sequence specific hybridization.
  • the arrays used in the present invention will have a site density of greater than 100 different probes per cm 2 .
  • the arrays will have a site density of greater than 500/cm 2 , more preferably greater than about 1000/cm 2 , and most preferably, greater than about 10,000/cm 2 .
  • the arrays will have more than 100 different probes on a single substrate, more preferably greater than about 1000 different probes, still more preferably, greater than about 10,000 different probes and most preferably, greater than 100,000 different probes on a single substrate.
  • Arrays preferably include control and reference nucleic acids.
  • Control nucleic acids include, for example, prokaryotic genes such as bioB, bioC and bioD, ere from PI bacteriophage or polyA controls, such as dap, lys, phe, thr, and trp.
  • Reference nucleic acids allow the normalization of results from one experiment to another and the comparison of multiple experiments on a quantitative level.
  • exemplary reference nucleic acids include housekeeping genes of known expression levels, for example, GAPDH, hexokinase, and actin.
  • an array of oligonucleotides may be synthesized on a solid support.
  • Exemplary solid supports include glass, plastics, polymers, metals, metalloids, ceramics, organics, etc.
  • chip masking technologies and photoprotective chemistry it is possible to generate ordered arrays of nucleic acid probes.
  • These arrays which are known, for example, as "DNA chips” or very large scale immobilized polymer arrays (“VLSIPSTM" arrays), may include millions of defined probe regions on a substrate having an area of about 1 cm 2 to several cm 2 , thereby incorporating from a few to millions of probes (see, e.g., U.S. Patent No. 5,631,734).
  • labeled nucleic acids may be contacted with the array under conditions sufficient for binding between the target nucleic acid and the probe on the array.
  • the hybridization conditions may be selected to provide for the desired level of hybridization specificity; that is, conditions sufficient for hybridization to occur between the labeled nucleic acids and probes on the microarray.
  • Hybridization may be carried out in conditions permitting essentially specific hybridization.
  • the length and GC content of the nucleic acid will determine the thermal melting point and thus, the hybridization conditions necessary for obtaining specific hybridization of the probe to the target nucleic acid. These factors are well known to a person of skill in the art, and may also be tested in assays.
  • An extensive guide to nucleic acid hybridization may be found in Tijssen, et al. (Laboratory Techniques in Biochemistry and Molecular Biology, Vol. 24: Hybridization With Nucleic Acid Probes, P. Tijssen, ed. Elsevier, N.Y., (1993)).
  • the methods described above result in the production of hybridization patterns of labeled target nucleic acids on the array surface.
  • the resultant hybridization patterns of labeled nucleic acids may be visualized or detected in a variety of ways, with the particular manner of detection selected based on the particular label of the target nucleic acid.
  • Representative detection means include scintillation counting, autoradiography, fluorescence measurement, colorimetric measurement, light emission measurement, light scattering, and the like.
  • One such method of detection utilizes an array scanner that is commercially available (Affymetrix, Santa Clara, CA), for example, the 417TM Arrayer, the 418TM Array Scanner, or the Agilent GeneArrayTM Scanner.
  • This scanner is controlled from a system computer with an interface and easy-to-use software tools. The output may be directly imported into or directly read by a variety of software applications.
  • Preferred scanning devices are described in, for example, U.S. Patent Nos. 5,143,854 and 5,424,186.
  • the fluorescence emissions at each site of a transcript array may be, preferably, detected by scanning confocal laser microscopy.
  • a laser may be used that allows simultaneous specimen illumination at wavelengths specific to the two fluorophores and emissions from the two fluorophores may be analyzed simultaneously (see, e.g., Shalon, et al., Genome Res. 6:639-645, 1996).
  • the arrays may be scanned with a laser fluorescent scanner with a computer controlled X-Y stage and a microscope objective. Fluorescence laser scanning devices are described in Shalon, et al., supra.
  • Various algorithms are available for analyzing gene expression data, for example, the type of comparisons to perform.
  • a preferred embodiment for identifying such groups of genes involves clustering algorithms (for reviews of clustering algorithms, see, e.g., Fukunaga, 1990, Statistical Pattern Recognition, 2nd Ed., Academic Press, San Diego; Everitt, 1974, Cluster Analysis, London: Heinemann Educ. Books; Hartigan, 1975, Clustering Algorithms, New York: Wiley; Sneath and Sokal, 1973, Numerical Taxonomy, Freeman; Anderberg, 1973, Cluster Analysis for Applications, Academic Press: New York).
  • Expression patterns may be used to derive a panel of biomarkers that can be used to predict the efficacy of drug treatment in the patients.
  • the biomarkers may consist of gene expression levels from microarray experiments on RNA isolated from biological samples, RNA isolated from frozen samples of tumor biopsies, or mass spectrometry-derived protein masses in the serum.
  • a typical procedure for developing a panel of biomarkers is as follows. The data (gene expression levels or mass spectra) are collected for each patient prior to treatment. As the study progresses, the patients are classified according to their response to the drug treatment; either as efficacious or non-efficacious.
  • the protein and/or gene expression data may be analyzed by a number of techniques known in the art. Many of the techniques are derived from traditional statistics as well from the field of machine learning. These techniques serve two purposes:
  • plasma (1 ⁇ ) may be applied to a hydrophobic SELDI-target, washed extensively in water, and analyzed by the SELDI-Tof mass spectrometer. This may be repeated on 100 or more patient samples.
  • the protein profiles resulting from the intensities of some 16,000 m/z values in each sample would be statistically analyzed in order to identify sets of specific m/z values that are predictive of drug efficacy.
  • Identical experiments using other SELDI-targets, such as ion-exchange or IMAC surfaces could also be conducted. These will capture different subsets of the proteins present in plasma.
  • the plasma may be denatured and prefractionated prior to application onto the SELDI target.
  • the present invention provides methods for determining whether a subject is at risk for developing a disease or condition characterized by unwanted cell proliferation by detecting biomarkers (e.g., PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, SVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF), that is, nucleic acids and/or polypeptide markers for cancer.
  • biomarkers e.g., PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, SVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF
  • human tissue samples may be screened for the presence and/or absence of biomarkers identified herein.
  • samples could consist of needle biopsy cores, surgical resection samples, lymph node tissue, or serum.
  • these methods include obtaining a biopsy, which is optionally fractionated by cryostat sectioning to enrich tumor cells to about 80% of the total cell population.
  • nucleic acids extracted from these samples may be amplified using techniques well known in the art. The levels of selected markers detected would be compared with statistically valid groups of metastatic, non-metastatic malignant, benign, or normal tissue samples.
  • the diagnostic method comprises determining whether a subject has an abnormal mRNA and/or protein level of the biomarkers (e.g., PLGF, CALX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF), such as by Northern blot analysis, reverse transcription-polymerase chain reaction (RT-PCR), in situ hybridization, immunoprecipitation, Western blot hybridization, or immunohistochemistry.
  • the biomarkers e.g., PLGF, CALX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF
  • cells may be obtained from a subject and the levels of the biomarkers, protein, or mRNA level, are determined and compared to the level of these markers in a healthy subject.
  • An abnormal level of the biomarker polypeptide or mRNA levels is likely to be indicative of cancer.
  • the method comprises using a nucleic acid probe to determine the presence of cancerous cells in a tissue from a patient. Specifically, the method comprises:
  • nucleic acid probe comprising a nucleotide sequence at least 10 nucleotides in length, preferably at least 15 nucleotides, more preferably, 25 nucleotides, and most preferably at least 40 nucleotides, and up to all or nearly all of the coding sequence which is complementary to a portion of the coding sequence of a nucleic acid sequence and is differentially expressed in tumors cells;
  • RNA of each of said first and second tissue samples e.g., in a Northern blot or in situ hybridization assay
  • the method comprises in situ hybridization with a probe derived from a given marker nucleic acid sequence (e.g., PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF).
  • a given marker nucleic acid sequence e.g., PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF.
  • the method comprises contacting the labeled hybridization probe with a sample of a given type of tissue potentially containing cancerous or pre-cancerous cells as well as normal cells, and determining whether the probe labels some cells of the given tissue type to a degree significantly different (e.g., by at least a factor of two, or at least a factor of five, or at least a factor of twenty, or at least a factor of fifty) than the degree to which it labels other cells of the same tissue type.
  • a degree significantly different e.g., by at least a factor of two, or at least a factor of five, or at least a factor of twenty, or at least a factor of fifty
  • Also within the invention is a method of determining the phenotype of a test cell from a given human tissue, for example, whether the cell is (a) normal, or (b) cancerous or precancerous, by contacting the mRNA of a test cell with a nucleic acid probe at least 12 nucleotides in length, preferably at least 15 nucleotides, more preferably at least 25 nucleotides, and most preferably at least 40 nucleotides, and up to all or nearly all of a sequence which is complementary to a portion of the coding sequence of a nucleic acid sequence, and which is differentially expressed in tumor cells as compared to normal cells of the given tissue type; and determining the approximate amount of hybridization of the probe to the mRNA, an amount of hybridization either more or less than that seen with the mRNA of a normal cell of that tissue type being indicative that the test cell is cancerous or precancerous.
  • the above diagnostic assays may be carried out using antibodies to detect the protein product encoded by the marker nucleic acid sequence (e.g., PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF).
  • the marker nucleic acid sequence e.g., PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF.
  • the assay would include contacting the proteins of the test cell with an antibody specific for the gene product of a nucleic acid, the marker nucleic acid being one which is expressed at a given control level in normal cells of the same tissue type as the test cell, and determining the approximate amount of immunocomplex formation by the antibody and the proteins of the test cell, wherein a statistically significant difference in the amount of the immunocomplex formed with the proteins of a test cell as compared to a normal cell of the same tissue type is an indication that the test cell is cancerous or pre-cancerous.
  • the antibody is specific for PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF, especially its extracellular domain.
  • Another such method includes the steps of: providing an antibody specific for the gene product of a marker nucleic acid sequence, the gene product being present in cancerous tissue of a given tissue type at a level more or less than the level of the gene product in noncancerous tissue of the same tissue type; obtaining from a patient a first sample of tissue of the given tissue type, which sample potentially includes cancerous cells; providing a second sample of tissue of the same tissue type (which may be from the same patient or from a normal control, e.g.
  • this second sample containing normal cells and essentially no cancerous cells; contacting the antibody with protein (which may be partially purified, in lysed but unfractionated cells, or in situ) of the first and second samples under conditions permitting immunocomplex formation between the antibody and the marker nucleic acid sequence product present in the samples; and comparing (a) the amount of immunocomplex formation in the first sample, with (b) the amount of immunocomplex formation in the second sample, wherein a statistically significant difference in the amount of immunocomplex formation in the first sample less as compared to the amount of immunocomplex formation in the second sample is indicative of the presence of cancerous cells in the first sample of tissue.
  • protein which may be partially purified, in lysed but unfractionated cells, or in situ
  • the subject invention further provides a method of determining whether a cell sample obtained from a subject possesses an abnormal amount of marker polypeptide which comprises (a) obtaining a cell sample from the subject, (b) quantitatively determining the amount of the marker polypeptide in the sample so obtained, and (c) comparing the amount of the marker polypeptide so determined with a known standard, so as to thereby determine whether the cell sample obtained from the subject possesses an abnormal amount of the marker polypeptide.
  • marker polypeptides may be detected by immunohistochemical assays, dot-blot assays, ELISA, and the like.
  • Immunoassays are commonly used to quantitate the levels of proteins in cell samples, and many other immunoassay techniques are known in the art.
  • the invention is not limited to a particular assay procedure, and therefore, is intended to include both homogeneous and heterogeneous procedures.
  • Exemplary immunoassays which may be conducted according to the invention include fluorescence polarization immunoassay (FPIA), fluorescence immunoassay (FIA), enzyme immunoassay (EIA), nephelometric inhibition immunoassay (NIA), enzyme-linked immunosorbent assay (ELISA), and radioimmunoassay (RIA).
  • An indicator moiety, or label group may be attached to the subject antibodies and is selected so as to meet the needs of various uses of the method which are often dictated by the availability of assay equipment and compatible immunoassay procedures. Conditions suitable for the formation of antibody- antigen complexes are well known in the art. General techniques to be used in performing the various immunoassays noted above are known to those of ordinary skill in the art. See generally E. Maggio, Enzyme-Immunoassay, (1980) (CRC Press, Inc., Boca Raton, Fla.); see also, e.g., U.S. Pat. No.
  • Monoclonal antibodies of the invention may be used in a "two-site” or “sandwich” assay, with a single cell line serving as a source for both the labeled monoclonal antibody and the bound monoclonal antibody.
  • assays are described in U.S. Pat. No. 4,376,110.
  • concentration of detectable reagent should be sufficient such that the binding of mutant BCR-ABL is detectable compared to background. It will be understood that more than one antibody may be used in the practice of the above-described methods.
  • the level of the encoded product, or alternatively the level of the polypeptide, in a biological fluid (e.g., blood or urine) of a patient may be determined as a way of monitoring the level of expression of the marker nucleic acid sequence in cells of that patient.
  • a biological fluid e.g., blood or urine
  • Such a method would include the steps of obtaining a sample of a biological fluid from the patient, contacting the sample (or proteins from the sample) with an antibody specific for an encoded marker polypeptide, and determining the amount of immune complex formation by the antibody, with the amount of immune complex formation being indicative of the level of the marker encoded product in the sample. This determination is particularly instructive when compared to the amount of immune complex formation by the same antibody in a control sample taken from a normal individual or in one or more samples previously or subsequently obtained from the same person.
  • the method may be used to determine the amount of marker polypeptide present in a cell, which in turn may be correlated with progression of a hyperproliferative disorder.
  • the level of the marker polypeptide may be used predictively to evaluate whether a sample of cells contains cells which are, or are predisposed towards becoming, transformed cells.
  • the subject method may be used to assess the phenotype of cells which are known to be transformed, the phenotyping results being useful in planning a particular therapeutic regimen. For example, very high levels of the marker polypeptide in sample cells is a powerful diagnostic and prognostic marker for a cancer. The observation of marker polypeptide levels may be utilized in decisions regarding, for example, the use of more aggressive therapies.
  • one aspect of the present invention relates to diagnostic assays for determining, in the context of cells isolated from a patient, if the level of a marker polypeptide is significantly reduced in the sample cells.
  • the term "significantly reduced” refers to a cell phenotype wherein the cell possesses a reduced cellular amount of the marker polypeptide relative to a normal cell of similar tissue origin.
  • a cell may have less than about 50%, 25%, 10%, or 5% of the marker polypeptide compared to that of a normal control cell.
  • the assay evaluates the level of marker polypeptide in the test cells, and, preferably, compares the measured level with marker polypeptide detected in at least one control cell, for example, a normal cell and/or a transformed cell of known phenotype.
  • the number of cells with a particular marker polypeptide phenotype may then be correlated with patient prognosis.
  • the marker polypeptide phenotype of a lesion is determined as a percentage of cells in a biopsy which are found to have abnormally high/low levels of the marker polypeptide. Such expression may be detected by immunohistochemical assays, dot-blot assays, ELISA, and the like.
  • immunohistochemical staining may be used to determine the number of cells having the marker polypeptide phenotype.
  • a multiblock of tissue may be taken from the biopsy or other tissue sample and subjected to proteolytic hydrolysis, employing such agents as protease K or pepsin.
  • proteolytic hydrolysis employing such agents as protease K or pepsin.
  • tissue samples are fixed by treatment with a reagent such as formalin, glutaraldehyde, methanol, or the like.
  • a reagent such as formalin, glutaraldehyde, methanol, or the like.
  • the samples are then incubated with an antibody, preferably a monoclonal antibody, with binding specificity for the marker polypeptides.
  • This antibody may be conjugated to a label for subsequent detection of binding.
  • Samples are incubated for a time sufficient for formation of the immunocomplexes. Binding of the antibody is then detected by virtue of a label conjugated to this antibody.
  • a second labeled antibody may be employed, for example, which is specific for the isotype of the anti-marker polypeptide antibody.
  • labels which may be employed include radionuclides, fluorescers, chemiluminescers, enzymes, and the like.
  • the substrate for the enzyme may be added to the samples to provide a colored or fluorescent product.
  • suitable enzymes for use in conjugates include horseradish peroxidase, alkaline phosphatase, malate dehydrogenase, and the like. Where not commercially available, such antibody-enzyme conjugates are readily produced by techniques known to those skilled in the art.
  • the assay is performed as a dot blot assay.
  • the dot blot assay finds particular application where tissue samples are employed as it allows determination of the average amount of the marker polypeptide associated with a single cell by correlating the amount of marker polypeptide in a cell-free extract produced from a predetermined number of cells.
  • the invention provides for a battery of tests utilizing a number of probes of the invention, in order to improve the reliability and/or accuracy of the diagnostic test.
  • the present invention also provides a method wherein nucleic acid probes are immobilized on a DNA chip in an organized array.
  • Oligonucleotides may be bound to a solid support by a variety of processes, including lithography.
  • a chip may hold up to 250,000 oligonucleotides.
  • nucleic acid probes comprise a nucleotide sequence at least about 12 nucleotides in length, preferably at least about 15 nucleotides, more preferably at least about 25 nucleotides, and most preferably at least about 40 nucleotides, and up to all or nearly all of a sequence which is complementary to a portion of the coding sequence of a marker nucleic acid sequence and is differentially expressed in tumor cells.
  • the present invention provides significant advantages over the available tests for various cancers, because it increases the reliability of the test by providing an array of nucleic acid markers on a single chip.
  • the method includes obtaining a biopsy, which is optionally fractionated by cryostat sectioning to enrich tumor cells to about 80% of the total cell population.
  • the DNA or RNA is then extracted, amplified, and analyzed with a DNA chip to determine the presence of absence of the marker nucleic acid sequences.
  • the nucleic acid probes are spotted onto a substrate in a two- dimensional matrix or array.
  • Samples of nucleic acids may be labeled and then hybridized to the probes.
  • Double-stranded nucleic acids, comprising the labeled sample nucleic acids bound to probe nucleic acids, may be detected once the unbound portion of the sample is washed away.
  • the probe nucleic acids may be spotted on substrates including glass, nitrocellulose, etc.
  • the probes can be bound to the substrate by either covalent bonds or by non-specific interactions, such as hydrophobic interactions.
  • the sample nucleic acids can be labeled using radioactive labels, fluorophores, chromophores, etc.
  • arrays may be used to examine differential expression of genes and may be used to determine gene function.
  • arrays of nucleic acid sequences may be used to determine if any of the nucleic acid sequences are differentially expressed between normal cells and cancer cells. Increased expression of a particular message in a cancer cell, which is not observed in a corresponding normal cell, may indicate a cancer-specific protein.
  • nucleic acid molecules may be used to generate microarrays on a solid surface (e.g., a membrane) such that the arrayed nucleic acid molecules may be used to determine if any of the nucleic acids are differentially expressed between normal cells or tissue and cancerous cells or tissue.
  • the nucleic acid molecules of the invention may be cDNA or may be used to generate cDNA molecules to be subsequently amplified by PCR and spotted on nylon membranes. The membranes may then be reacted with radiolabeled target nucleic acid molecules obtained from equivalent samples of cancerous and normal tissue or cells.
  • the invention contemplates using a panel of antibodies which are generated against the marker polypeptides of this invention.
  • the antibodies are generated against PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, SVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF.
  • a panel of antibodies may be used as a reliable diagnostic probe for cancer.
  • the assay of the present invention comprises contacting a biopsy sample containing cells, for example, lung cells, with a panel of antibodies to one or more of the encoded products to determine the presence or absence of the marker polypeptides.
  • the diagnostic methods of the subject invention may also be employed as follow-up to treatment, for example, quantitation of the level of marker polypeptides may be indicative of the effectiveness of current or previously employed cancer therapies as well as the effect of these therapies upon patient prognosis.
  • marker nucleic acids or marker polypeptides may be utilized as part of a diagnostic panel for initial detection, follow-up screening, detection of reoccurrence, and post-treatment monitoring for chemotherapy or surgical treatment.
  • the present invention makes available diagnostic assays and reagents for detecting gain and/or loss of marker polypeptides from a cell in order to aid in the diagnosis and phenotyping of proliferative disorders arising from, for example, tumorigenic transformation of cells.
  • the diagnostic assays described above may be adapted to be used as prognostic assays, as well. Such an application takes advantage of the sensitivity of the assays of the invention to events which take place at characteristic stages in the progression of a tumor. For example, a given marker gene may be up- or down-regulated at a very early stage, perhaps before the cell is irreversibly committed to developing into a malignancy, while another marker gene may be characteristically up- or down-regulated only at a much later stage.
  • Such a method could involve the steps of contacting the mRNA of a test cell with a nucleic acid probe derived from a given marker nucleic acid which is expressed at different characteristic levels in cancerous or precancerous cells at different stages of tumor progression, and determining the approximate amount of hybridization of the probe to the mRNA of the cell, such amount being an indication of the level of expression of the gene in the cell, and thus an indication of the stage of tumor progression of the cell; alternatively, the assay may be carried out with an antibody specific for the gene product of the given marker nucleic acid, contacted with the proteins of the test cell.
  • a battery of such tests will disclose not only the existence and location of a tumor, but also will allow the clinician to select the mode of treatment most appropriate for the tumor, and to predict the likelihood of success of that treatment.
  • the methods of the invention may also be used to follow the clinical course of a tumor.
  • the assay of the invention may be applied to a tissue sample from a patient; following treatment of the patient for the cancer, another tissue sample is taken and the test repeated. Successful treatment will result in either removal of all cells which demonstrate differential expression characteristic of the cancerous or precancerous cells, or a substantial increase in expression of the gene in those cells, perhaps approaching or even surpassing normal levels.
  • a biomarker associated with the anti-cancer agent may be analyzed in a biological sample (e.g., tumor sample, plasma) before, during, and following treatment.
  • a biological sample e.g., tumor sample, plasma
  • the expression of PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF, polypeptide may be detected in plasma.
  • changes in the baseline plasma concentration of these polypeptides may be monitored in patients with cancer.
  • increased levels of PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD or ANG2 and decreased levels of SVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF can be associated with Regorafenib efficacy.
  • VEGF-A VEGF-D PLGF, ANG2
  • HGF pro-angiogenic factors
  • bFGF pro-angiogenic factors
  • Soluble forms of receptors that may be targeted by Regorafenib generally decreased in response to Regorafenib (sVEGFR2, sTIE- l,s-c-Kit).
  • Metalloproteinase inhibitors TIMP2 and TIMP4 decreased in response to Regorafenib.
  • Regorafenib increased the levels of P1GF in 96% of the patients and decreased the levels of sVEGFR2 and TIMP2 in 100% of patients.
  • polypeptide levels may also be monitored by quantitative immunohistochemistry using paraffin-embedded tumor biopsies.
  • Another approach to monitor treatment is an evaluation of serum proteomic spectra.
  • plasma samples may be subjected to mass spectroscopy (e.g., surface-enhanced laser desorption and ionization) and a proteomic spectra may be generated for each patient.
  • mass spectroscopy e.g., surface-enhanced laser desorption and ionization
  • a set of spectra, derived from analysis of plasma from patients before and during treatment may be analyzed by an iterative searching algorithm, which can identify a proteomic pattern that completely discriminates the treated samples from the untreated samples. The resulting pattern may then be used to predict the clinical benefit following treatment.
  • RNA isolated from cells derived from whole blood from patients before and during treatment may be used to generate blood cell gene expression profiles utilizing Affymetrix GeneChip technology and algorithms. These gene expression profiles may then predict the clinical benefit from treatment with a particular anti-cancer agent.
  • Figure 1 is six graphs showing the Regorafenib-mediated changes in PLGF
  • Figure 2 is three graphs showing the predictive value of raf mediated changes in plasma protein levels.
  • Figure 3 is five graphs showing the predicative value of base line plasma protein levels
  • Patients and methods Patients selected for treatment with Regorafenib and analysis for biomarkers had previously untreated metastatic or unresectable clear cell RCC. These patients received oral Regorafenib (160 mg/day) in repeating cycles of 3 weeks on / 1 week off until disease progression or until patients met the criteria for removal from study. Primary efficacy endpoint was overall objective response rate. Secondary efficacy endpoints included overall survival, progression-free survival (PFS), time to progression, duration of response, duration of stable disease, disease control rate and clinical benefit rate. Safety was assessed by analysis of adverse events (AEs) and changes in laboratory, vital signs, and electrocardiogram measurements.
  • AEs adverse events
  • Plasma protein biomarkers were quantified using multiplex bead immunoassays. Plasma was obtained at baseline and after 15 days of daily Regorafenib treatment from 29 patients (pts) with previously untreated unresectable or metastatic RCC enrolled in a Phase II trial that demonstrated Regorafenib clinical activity. Biomarkers examined included soluble forms of receptors inhibited by Regorafenib, for example, soluble VEGF receptor-2 (sVEGFR2), soluble KIT (sKIT) and their ligands, for example, VEGF, SCF.
  • sVEGF receptor-2 soluble VEGF receptor-2
  • KIT soluble KIT
  • HGF hypoxia
  • CAFX hypoxia
  • apoptosis for example, CK18M30, CYTC
  • tumor invasion for example, TIMP2
  • Results indicate that a subset of biomarkers was altered by exposure to Regorafenib.
  • PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2 levels were increased.
  • the levels of sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, SCF were decreased.
  • the most consistent, robust changes were in PLGF (increase in 27/28 pts (96%); median fold change of +3.3; p ⁇ 0.0001) and sVEGFR2 (decrease in 28/28 pts(100%); median fold change of -1.6; p ⁇ 0.0001) and TIMP2 (decrease in 28/28 pts(100%)).
  • circulating levels of several receptors that may be targeted by Regorafenib were decreased.
  • sVEGFR2, sKIT, sTIEl Several members of the VEGF family of ligands (PLGF, VEGFA, VEGFD) were increased.
  • Potential biomarkers that did not change included ANG1, GCSF, HGF, IL16, MCSF, sMCSFR, OPN, PDGFAA, AB and BB, SDFloc, sTIE2, TIMP1 and 3, VEGFC, sVEGFRl and sVEGFR3.
  • Figure 2 shows the changes in Regorafenib-mediated plasma levels of CK18M30 in patients grouped based on maximum tumor shrinkage and best response, and changes in s-c- kit based on maximum tumor shrinkage.
  • the degree change(s) in sKIT, CYTC or CK18M30 levels is/are correlated with clinical response to Regorafenib.
  • baseline levels of IL16, SCF, HGF or TIMP2 are associated with clinical response to Regorafenib. Assays testing for these biomarkers may be advantageously employed to identify patients that would be likely to respond to Regorafenib.
  • Tissue specimens can optionally be analyzed for VHL gene mutation status (only for patients consenting to genetic analysis) by DNA sequencing, and phospho-ERK (pERK) levels by immunohistochemistry (IHC).
  • mRNA can be isolated from blood and analyzed by microarrays for gene expression profiles that correlate with patient outcome. Additionally or alternatively, a mass spectrometry-based approach can be used to assess plasma for a protein signature, and urine can optionally be analyzed by ⁇ -NMR for patterns of small molecules that correlate with patient outcome.
  • Pre- and post-treatment plasma samples are analyzed by ELISA for PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF, and changes in these molecules related to Regorafenib treatment are investigated.
  • the PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF levels in patients can be examined to identify correlations with clinical outcome (time to death (TTD) and progression-free survival (PFS) using a Cox regression analysis.
  • TTD time to death
  • PFS progression-free survival
  • Baseline levels of PLGF, CAIX, FASL, CYTC, CK18M30, VEGFA, VEGFD, ANG2, sVEGFR2, sKIT, sTIEl, bFGF, TIMP2, TIMP4, or SCF are first determined and changes in the baseline levels are determined after treatment, preferably at about week 18 of treatment. The effects observed were adjusted for age, gender, ECOG status or Motzer score. These adjustments were minimal.

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Abstract

La présente invention concerne des biomarqueurs et l'utilisation de biomarqueurs pour la prédiction et le pronostic du cancer, ainsi que l'utilisation de biomarqueurs pour surveiller la réponse à un traitement par un agent anticancéreux.
PCT/US2011/037166 2010-05-19 2011-05-19 Biomarqueurs pour un inhibiteur à multiples kinases WO2011146725A1 (fr)

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CN102854322A (zh) * 2012-07-31 2013-01-02 吴克 一种vefg受体酶联诊断试剂盒及其制备方法
CN105136956A (zh) * 2015-09-11 2015-12-09 江苏嘉逸医药有限公司 一种快速测定瑞戈非尼含量的方法
WO2017110764A1 (fr) * 2015-12-24 2017-06-29 公益財団法人がん研究会 Procédé de test permettant de prédire l'efficacité et la sécurité d'un inhibiteur multikinase, kit de test et biomarqueur
WO2017182985A1 (fr) * 2016-04-20 2017-10-26 Morphotek, Inc. Pronostic d'un cancer de l'ovaire séreux à l'aide de marqueurs biologiques
US9957232B2 (en) 2006-10-11 2018-05-01 Bayer Healthcare Llc 4-[4-({[4-chloro-3-(trifluoromethyl)phenyl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide monohydrate
CN113533728A (zh) * 2021-06-03 2021-10-22 中国科学院生物物理研究所 一种脑胶质瘤的生物标志物及其应用

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