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US20100278772A1 - Dna methylation markers and methods of use - Google Patents

Dna methylation markers and methods of use Download PDF

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US20100278772A1
US20100278772A1 US12/515,735 US51573507A US2010278772A1 US 20100278772 A1 US20100278772 A1 US 20100278772A1 US 51573507 A US51573507 A US 51573507A US 2010278772 A1 US2010278772 A1 US 2010278772A1
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nucleic acid
genes
hypermethylation
proliferative disease
tumor
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Malcolm V. Brock
Stephen Baylin
James Gordon Herman
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Johns Hopkins University
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    • 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
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
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    • 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
    • C12Q2600/112—Disease subtyping, staging or classification
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/118—Prognosis of disease development
    • 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
    • C12Q2600/154—Methylation markers
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays

Definitions

  • the present invention relates to the use of nucleic acid methylation and methylation profiles to detect metastatic disease.
  • the invention relates to methods for identifying metastases by detecting nucleic acid hypermethylation of one or more genes in one or more samples and, in particular, in tumor tissue and lymph nodes.
  • the invention further relates to DNA hypermethylation as a predictor of disease recurrence and patient prognosis, specifically in patients suffering from cancer.
  • Cancer remains one of the leading causes of death in the United States.
  • Clinically a broad variety of medical approaches, including surgery, radiation therapy and chemotherapeutic drug therapy are currently being used in the treatment of human cancer (see the textbook CANCER: Principles & Practice of Oncology, 2d Edition, De Vita et al., eds., J. B. Lippincott Company, Philadelphia, Pa., 1985).
  • CANCER Principles & Practice of Oncology, 2d Edition, De Vita et al., eds., J. B. Lippincott Company, Philadelphia, Pa., 1985.
  • it is recognized that such approaches continue to be limited by an inability to predict the likelihood of metastasis and tumor recurrence or the most efficacious treatment regime for minimizing the occurrence of these negative outcomes.
  • Human cancer cells typically contain somatically altered nucleic acids, characterized by mutation, amplification, or deletion of critical genes.
  • nucleic acids from human cancer cells often display somatic changes in DNA methylation (36, 37, 38).
  • DNA methylation 36, 37, 38.
  • a precise role for, and the significance of, abnormal DNA methylation in human tumorigenesis has not been well established.
  • Loss of gene function is cancer can occur by both genetic and epigenetic mechanisms.
  • the best-defined epigenetic alteration of cancer genes involves DNA methylation of clustered CpG dinucleotides, or CpG islands, in promoter regions associated with the transcriptional inactivation of the affected genes.
  • CpG islands are short sequences rich in the CpG dinucleotide, and can be found in the 5′ region of about half of all human genes.
  • Methylation of cytosine within 5′ CGIs is associated with loss of gene expression and has been seen in a number of physiological conditions, including X chromosome inactivation and genomic imprinting.
  • CpG island methylation Aberrant methylation of CpG islands has been detected in genetic diseases such as the fragile-X syndrome, in aging cells and in neoplasia. About half of the tumor suppressor genes which have been shown to be mutated in the germline of patients with familial cancer syndromes have also been shown to be aberrantly methylated in some proportion of sporadic cancers, including Rb, VHL, p16, hMLH1, and BRCA1 (reviewed in Baylin, et al, Adv. Cancer Res. 72:141-196 1998). Methylation of tumor suppressor genes in cancer is usually associated with (1) lack of gene transcription and (2) absence of coding region mutation. Thus CpG island methylation can serve as an alternative mechanism of gene inactivation in cancer.
  • Cancer treatments in general, have a higher rate of success if the cancer is diagnosed early, and treatment is started earlier in the disease process. A relationship between improved prognosis and stage of disease at diagnosis can be seen across a majority of cancers. Identification of the earliest changes in cells associated with cancer is thus a major focus in molecular cancer research. Diagnostic approaches based on identification of these changes in specific genes may allow implementation of early detection strategies and novel therapeutic approaches. Targeting these early changes will lead to more effective cancer treatment.
  • the invention features methods for identifying metastases by detecting nucleic acid hypermethylation of one or more genes in one or more samples, and in particular in tumor tissue and lymph nodes.
  • the invention features methods for identifying metastases in a subject comprising detecting nucleic acid hypermethylation of one or more genes in one or more samples, wherein detecting nucleic acid hypermethylation identifies metastases.
  • the sample comprises cells or tissues selected from the group consisting of tumor, lymph nodes, bone marrow and blood.
  • the sample is from a tumor.
  • the sample is from a lymph node.
  • the lymph node is a N1 lymph node or a mediastinal lymph node.
  • the invention features methods for identifying metastases in a subject comprising detecting nucleic acid hypermethylation of one or more genes in tumor tissue or lymph node, wherein the genes are selected from the group consisting of genes involved in tumor suppression, DNA repair, apoptosis, anti-proliferation, ras signaling, adhesion, differentiation, development, and cell cycle regulation, wherein detecting nucleic acid hypermethylation identifies metastases.
  • the metastases are micrometastases.
  • the one or more genes comprise one or more CpG islands.
  • the one or more genes is selected from the group consisting of H-cadherin, p16, APC, RASSF1A, MGMT, DAPK, and ASC.
  • H-cadherin in certain exemplary embodiments is encoded by NCBI accession No. AAB18912 and is shown in (SEQ ID NO:1) below:
  • p-16 in certain exemplary embodiments is encoded by NCBI accession No. CAB58124 and is shown in (SEQ ID NO:2) below:
  • APC in certain exemplary embodiments is encoded by NCBI accession No. NP — 000029 and is shown in (SEQ ID NO:3) below:
  • RASSF1A in certain exemplary embodiments is encoded by NCBI accession No. NP — 009113 and is shown in (SEQ ID NO:4) below:
  • MGMT in certain exemplary embodiments is encoded by NCBI accession No. AAH00824 and is shown in (SEQ ID NO:5) below:
  • DAPK in certain exemplary embodiments is encoded by NCBI accession No. NP — 004929 and is shown in (SEQ ID NO:6) below:
  • ASC in certain exemplary embodiments is encoded by NCBI accession No. NP — 037390 and is shown in (SEQ ID NO:7) below:
  • hypermethylation of at least one of the genes is detected. In still other embodiments of the above aspects, hypermethylation of at least two of the genes is detected.
  • the invention features methods for identifying micrometastases in a subject comprising detecting nucleic acid hypermethylation of at least one or more genes in a sample comprising tumor and lymph nodes, wherein the sample genes are selected from the group consisting of H-cadherin, p16, APC, RASSF1A, MGMT, DAPK, and ASC, and wherein detecting nucleic acid methylation identifies micrometastases.
  • hypermethylation of at least two of the genes is detected.
  • at least two of the genes are selected from p-16 and H-cadherin, H-cadherin and APC, APC and p16, or RASSf1A and p16.
  • the detection of metastases is used to detect or diagnose a proliferative disease.
  • the detection or diagnosis is performed after surgery or therapy to treat a proliferative disease. In other certain embodiments, the detection is used to predict the recurrence of a proliferative disease. In other certain embodiments, the detection is used to stage a proliferative disease. In still other certain embodiments, the detection is further used to determine a course of treatment for a subject.
  • the invention features a method for detecting or diagnosing a proliferative disease in a subject comprising detecting nucleic acid hypermethylation of one or more genes in one or more samples, wherein detecting nucleic acid hypermethylation is used to detect or diagnose a proliferative disease.
  • the invention features a method for predicting the recurrence of a proliferative disease in a subject comprising detecting nucleic acid hypermethylation of one or more genes wherein detecting nucleic acid hypermethylation of one or more genes is a predictor of the recurrence of a proliferative disease.
  • hypermethylation of one or more genes is detected in tumor or lymph nodes.
  • detection of hypermethylation of one or more genes in lymph nodes is predictive of aggressive disease recurrence.
  • the invention features a method for staging or re-staging a proliferative disease in a subject comprising detecting nucleic acid hypermethylation of one or more genes wherein detecting nucleic acid hypermethylation is used for staging or re-staging a proliferative disease.
  • the stage of proliferative disease is predictive of disease recurrence. In a further embodiment, the stage of proliferative disease determines course of treatment.
  • the invention features a method for determining the prognosis of a subject suffering from a proliferative disease comprising detecting nucleic acid hypermethylation of one or more genes wherein the detection of nucleic acid hypermethylation is used for determining the prognosis of a subject suffering from a proliferative disease.
  • the prognosis determines course of treatment.
  • the subject is a human.
  • the method is performed prior to therapeutic intervention for the disease.
  • the method is performed after therapeutic intervention for the disease.
  • the therapeutic intervention is selected from treatment with an agent or surgery.
  • hypermethylation is detected in CpG islands of the one or more genes.
  • hypermethylation is detected in CpG islands.
  • the invention features methods for detecting or diagnosing a proliferative disease in a subject comprising extracting nucleic acid from one or more cell or tissue samples, detecting nucleic acid hypermethylation of one or more genes in the sample; and identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes indicates a proliferative disease.
  • the invention features methods for predicting the recurrence of a proliferative disease in a subject comprising extracting nucleic acid from one or more cell or tissue samples, detecting nucleic acid hypermethylation of one or more genes in the sample; and identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes is indicative of the recurrence of a proliferative disease.
  • the invention features methods for staging or re-staging a proliferative disease in a subject comprising extracting nucleic acid from one or more cell or tissue samples, detecting nucleic acid hypermethylation of one or more genes in the sample; and identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes is used for staging or re-staging of a proliferative disease.
  • the tissue samples are selected from tumor, lymph node, bone marrow or blood or a combination thereof.
  • the method determines the course of disease treatment.
  • the method is performed prior to therapeutic intervention for the disease.
  • the method is performed after therapeutic intervention for the disease.
  • the therapeutic intervention is selected from treatment with an agent or surgery.
  • the invention features methods of treating a subject having or at risk for having a proliferative disease comprising identifying nucleic acid hypermethylation of one or more genes, where nucleic acid hypermethylation indicates having or a risk for having a proliferative disease, and administering to the subject a therapeutically effective amount of a demethylating agent, thereby treating a subject having or at risk for having a proliferative disease.
  • the method is used in combination with one or more chemotherapeutic agents.
  • the method further comprises comparing the nucleic acid hypermethylation of one or more genes in the sample with comparable samples obtained from a normal subject.
  • detecting nucleic acid hypermethylation of one or more genes indicates the presence of metastases.
  • the metastases are micrometastases.
  • the proliferative disease is a neoplasia.
  • the neoplasia is cancer.
  • the cancer is a solid tumor.
  • the cancer is selected from the group consisting of lung cancer, pancreatic cancer, esophageal cancer, head and neck cancer, stomach cancer, liver cancer, prostate cancer, gastrointestinal cancer, ovarian cancer, and uterine cancer.
  • the cells or tissues are selected from the group consisting of tumor, lymph nodes, bone marrow or blood.
  • the cells or tissues are from a tumor or the lymph nodes.
  • the lymph node is a N1 lymph node or a mediastinal lymph node.
  • the invention features a method of identifying an agent that de-methylates hypermethylated nucleic acid comprising identifying one or more cell or tissue samples with hypermethylated nucleic acid, extracting the hypermethylated nucleic acid, contacting the nucleic acid with one or more nucleic acid de-methylating candidate agents and a control agent, identifying the nucleic acid hypermethylation state, wherein nucleic acid de-methylation of genes in the sample by the candidate agent compared to the control indicates a demethylating agent, and thereby identifying an agent that de-methylates hypermethylated nucleic acid.
  • the one or more genes are selected from the group consisting of genes involved in tumor suppression, DNA repair, anti-proliferation, apoptosis, ras signaling, adhesion, differentiation, development, and cell cycle regulation.
  • the one or more genes are selected from a panel consisting of (1) genes involved in tumor suppression and cell adhesion, (2) genes involved in cell cycle regulation and adhesion, (3) genes involved in tumor suppression and cell cycle regulation, and (4) genes involved in ras signaling and cell cycle control.
  • the one or more genes comprise one or more CpG islands.
  • the genes are selected from the group consisting of p-16, H-cadherin, APC, RASSF1A, MGMT, DAPK, and ASC.
  • the hypermethylation of at least one of the genes is detected. In a further related embodiment, the hypermethylation of at least two of the genes is detected. In still another related embodiment, the two genes are selected from p-16 and H-cadherin, H-cadherin and APC, APC and p16, or RASSf1A and p16.
  • the detection of nucleic acid methylation is by a quantitative method.
  • the detection of nucleic acid methylation is carried out by polymerase chain reaction (PCR) analysis.
  • PCR polymerase chain reaction
  • MSP methylation specific PCR
  • the method of detecting nucleic acid methylation is performed as a high-throughput method.
  • the method is used in combination with the detection of other epigenetic markers.
  • the other epigenetic markers are plasma or tumor epigenetic markers.
  • hypermethylation is detected in CpG islands of the one or more genes. In a further embodiment of the above-described aspects, hypermethylation is detected in CpG islands of the promoter region.
  • kits for identifying the nucleic acid hypermethylation state of one or more genes comprising gene specific primers for use in polymerase chain reaction (PCR), and instructions for use.
  • PCR polymerase chain reaction
  • kits for detecting metastases by detecting nucleic acid hypermethylation of one or more genes comprising gene specific primers for use in polymerase chain reaction (PCR), and instructions for use.
  • PCR polymerase chain reaction
  • the metastases are micrometastases.
  • the PCR is methylation specific PCR (MSP).
  • the one or more genes are selected from the group consisting of genes involved in tumor suppression, DNA repair, anti-proliferation, apotosis, ras signaling, adhesion, differentiation, development, and cell cycle regulation.
  • the one or more genes are selected from a panel consisting of (1) genes involved in tumor suppression and cell adhesion, (2) genes involved in cell cycle regulation and adhesion, (3) genes involved in tumor suppression and cell cycle regulation, and (4) genes involved in ras signaling and cell cycle control.
  • the one or more genes comprise one or more CpG islands.
  • the CpG islands are in the promoter region.
  • the genes are selected from the group consisting of p-16, H-cadherin, APC, RASSF1A, MGMT, DAPK, and ASC
  • the hypermethylation of at least one of the genes is detected. In still another embodiment, the hypermethylation of at least two of the genes is detected. In still another further embodiment, the two genes are selected from p-16 and H-cadherin, H-cadherin and APC, APC and p16, or RASSf1A and p16.
  • FIG. 1 shows the results of multivariate logistic regression analysis performed using the four genes that exhibited the largest univariate distribution differences in methylation: p16, H-cadherin, APC, and RASSF1A.
  • FIG. 2 (A-L) are graphs showing Kaplan-Meier estimates of recurrence-free survival of pathologic Stage 1 lung cancer patients at the Johns Hopkins Hospital, according to number of methylated genes in a 4-gene panel at time of surgical resection.
  • FIG. 3 shows Methylation Specific PCR for the H-cadherin gene.
  • the presence of a visible PCR product in Lanes marked U indicates the presence of an unmethylated promoter region amplified and serves as a control for sample preparation; the presence of product in Lanes M indicates a methylated gene promoter and was scored as positive for methylation.
  • * represents the molecular weight marker.
  • control is meant a standard or reference condition.
  • phrases “in combination with” is intended to refer to all forms of administration that provide a de-methylating agent, or the methods of the instant invention (e.g. methods of detection of hypermethylation) together with a second agent, such as a chemotherapeutic agent, or a de-methylating agent, where the two are administered concurrently or sequentially in any order.
  • agent as used herein is meant to refer to a polypeptide, polynucleotide, or fragment, or analog thereof, small molecule, or other biologically active molecule.
  • CpG island refers to a sequence of nucleic acid with an increased density relative to other nucleic acid regions of the dinucleotide CpG.
  • epigenetic marker or “epigenetic change” as used herein is meant to refer to a change in the DNA sequences or gene expression by a process or processes that do not change the DNA coding sequence itself.
  • methylation is an epigenetic marker.
  • hypermethylation refers to the presence of methylated alleles in one or more nucleic acids.
  • hypermethylation is detected using methylation specific polymerase chain reaction (MSP).
  • MSP methylation specific polymerase chain reaction
  • metastatic tumor is meant to refer to the spread of a malignant tumor from its sight of origin. Cancer cells may metastasize through the bloodstream, through the lymphatic system, across body cavities, or any combination thereof.
  • a metastatic tumor can arise from a multitude of primary tumor types, including but not limited to lung, breast, thyroid, head and neck, brain, lymphoid, gastrointestinal (mouth, esophagus, stomach, small intestine, colon, rectum), genito-urinary tract (uterus, ovary, cervix, bladder, testicle, penis, prostate), kidney, pancreas, liver, bone, muscle or skin.
  • micrometastases is meant to refer to a metastasis that cannot be detected by routine histological evaluation, for example by Hematoxylin and Eosin (H & E) staining and microscopic assessment.
  • H & E Hematoxylin and Eosin
  • neoplasm or “neoplasia” as used herein refers to inappropriately high levels of cell division, inappropriately low levels of apoptosis, or both.
  • a neoplasm creates an unstructured mass (a tumor), which can be either benign or malignant.
  • cancer is a neoplasia.
  • cancers include, without limitation, leukemias (e.g., acute leukemia, acute lymphocytic leukemia, acute myelocytic leukemia, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monocytic leukemia, acute erythroleukemia, chronic leukemia, chronic myelocytic leukemia, chronic lymphocytic leukemia), polycythemia vera, lymphoma (Hodgkin's disease, non-Hodgkin's disease), Waldenstrom's macroglobulinemia, heavy chain disease, and solid tumors such as sarcomas and carcinomas (e.g., fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma
  • nucleic acid refers to an oligonucleotide, nucleotide, polynucleotide, or to a fragment of any of these, to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent a sense or antisense strand, peptide nucleic acid (PNA), or to any DNA-like or RNA-like material, natural or synthetic in origin.
  • PNA peptide nucleic acid
  • the nucleic acid is RNA
  • the deoxynucleotides A, G, C, and T are replaced by ribonucleotides A, G, C, and U, respectively.
  • proliferative disorder refers to an abnormal growth of cells.
  • a cell proliferative disorder as described herein may be a neoplasm.
  • gene refers to a segment of deoxyribonucleic acid that encodes a polypeptide including the upstream and downstream regulatory sequences. Specifically, the term gene includes the promoter region upstream of the gene.
  • promoter or “promoter region” refers to a minimal sequence sufficient to direct transcription or to render promoter-dependent gene expression that is controllable for cell-type specific, tissue-specific, or is inducible by external signals or agents. Promoters may be located in the 5′ or 3′ regions of the gene. Promoter regions, in whole or in part, of a number of nucleic acids can be examined for sites of CpG-island methylation.
  • sample refers to any biological or chemical mixture for use in the method of the invention.
  • the sample can be a biological sample.
  • the biological samples are generally derived from a patient, preferably as a bodily fluid (such as tumor tissue, lymph node, sputum, blood, bone marrow, cerebrospinal fluid, phlegm, saliva, or urine) or cell lysate.
  • the cell lysate can be prepared from a tissue sample (e.g. a tissue sample obtained by biopsy), for example, a tissue sample (e.g. a tissue sample obtained by biopsy), blood, cerebrospinal fluid, phlegm, saliva, urine, or the sample can be cell lysate.
  • stage or “staging” as used herein is meant to refer to the extent or progression of proliferative disease, e.g. cancer, in a subject.
  • Staging can be “clinical” and is according to the “stage classification” corresponding to the TNM classification (“Rinsho, Byori, Genpatsusei Kangan Toriatsukaikiyaku (Clinical and Pathological Codes for Handling Primary Liver Cancer)”: 22p. Nihon Kangangaku Kenkyukai (Liver Cancer Study Group of Japan) edition (3rd revised edition), Kanehara Shuppan, 1992).
  • Staging in certain embodiments can refer to “molecular staging” as defined by nucleic acid hypermethylation of one or more genes in one or more samples.
  • the “molecular stage” stage of a cancer is determined by detection of nucleic acid hypermethylation of one or more genes in a sample from the lymph nodes.
  • subject as used herein is meant to include vertebrates, preferably a mammal. Mammals include, but are not limited to, humans.
  • tumor as used herein is intended to include an abnormal mass or growth of cells or tissue.
  • a tumor can be benign or malignant.
  • the invention is based upon the discovery that the hypermethylation of certain genes, including promoter regions, can serve as prognostic and diagnostic markers for cellular proliferative disorders. This is the first time that promoter hypermethylation of certain genes, such as p16, H-cadherin, RASSf1A and APC, in the lymph nodes has been associated with the ability to predict recurrence and aggressiveness of certain cancers, such as lung cancer.
  • DNA methylases transfer methyl groups from the universal methyl donor S-adenosyl methionine to specific sites on the DNA.
  • Several biological functions have been attributed to the methylated bases in DNA.
  • the most established biological function for methylated DNA is the protection of DNA from digestion by cognate restriction enzymes.
  • the restriction modification phenomenon has, so far, been observed only in bacteria.
  • Mammalian cells possess a different methylase that exclusively methylates cytosine residues that are 5′ neighbors of guanine (CpG). This modification of cytosine residues has important regulatory effects on gene expression, especially when involving CpG rich areas, known as CpG islands, located in the promoter regions of many genes.
  • Methylation has been shown by several lines of evidence to play a role in gene activity, cell differentiation, tumorigenesis, X-chromosome inactivation, genomic imprinting and other major biological processes (Razin, A., H., and Riggs, R. D. eds. in DNA Methylation Biochemistry and Biological Significance, Springer-Verlag, New York, 1984).
  • methylation of cytosine residues that are immediately 5′ to a guanosine occurs predominantly in CG poor regions (Bird, A., Nature, 321:209, 1986).
  • CpG islands remain unmethylated in normal cells, except during X-chromosome inactivation and parental specific imprinting (Li, et al., Nature, 366:362, 1993) where methylation of 5′ regulatory regions can lead to transcriptional repression.
  • De novo methylation of the Rb gene has been demonstrated in a small fraction of retinoblastomas (Sakai, et al., Am. J. Hum. Genet., 48:880, 1991), and recently, a more detailed analysis of the VHL gene showed aberrant methylation in a subset of sporadic renal cell carcinomas (Herman, et al., Proc. Natl. Acad.
  • DNA is methylated only at cytosines located 5′ to guanosine in the CpG dinucleotide. This modification has important regulatory effects on gene expression, especially when involving CpG rich areas, known as CpG islands, located in the promoter regions of many genes. While almost all gene-associated islands are protected from methylation on autosomal chromosomes, extensive methylation of CpG islands has been associated with transcriptional inactivation of selected imprinted genes and genes on the inactive X-chromosome of females. Aberrant methylation of normally unmethylated CpG islands has been described as a frequent event in immortalized and transformed cells, and has been associated with transcriptional inactivation of defined tumor suppressor genes in human cancers.
  • Any method that is sufficient to detect hypermethylation e.g. a method that can detect methylation of nucleotides at levels as low as 0.1%, is a suitable for use in the methods of the invention.
  • a number of different methods can be used to detect hypermethylation.
  • the ability to monitor the real-time progress of the PCR changes the way one approaches PCR-based quantification of DNA and RNA. Reactions are characterized by the point in time during cycling when amplification of a PCR product is first detected rather than the amount of PCR product accumulated after a fixed number of cycles. The higher the starting copy number of the nucleic acid target, the sooner a significant increase in fluorescence is observed.
  • An amplification plot is the plot of fluorescence signal versus cycle number. In the initial cycles of PCR, there is little change in fluorescence signal. This defines the baseline for the amplification plot. An increase in fluorescence above the baseline indicates the detection of accumulated PCR product. A fixed fluorescence threshold can be set above the baseline.
  • the parameter C T is defined as the fractional cycle number at which the fluorescence passes the fixed threshold.
  • the PCR cycle number at which fluorescence reaches a threshold value of 10 times the standard deviation of baseline emission may be used as C T and it is inversely proportional to the starting amount of target cDNA.
  • a plot of the log of initial target copy number for a set of standards versus C T is a straight line. Quantification of the amount of target in unknown samples is accomplished by measuring C T and using the standard curve to determine starting copy number.
  • Real-time PCR requires an instrumentation platform that consists of a thermal cycler, computer, optics for fluorescence excitation and emission collection, and data acquisition and analysis software. These machines, available from several manufacturers, differ in sample capacity (some are 96-well standard format, others process fewer samples or require specialized glass capillary tubes), method of excitation (some use lasers, others broad spectrum light sources with tunable filters), and overall sensitivity. There are also platform-specific differences in how the software processes data. Real-time PCR machines are available at core facilities or labs that have the need for high throughput quantitative analysis.
  • the number of target gene copies can be extrapolated from a standard curve equation using the absolute quantitation method.
  • cDNA from a positive control is first generated from RNA by the reverse transcription reaction.
  • the gene under investigation is amplified using the primers by means of a standard PCR reaction.
  • the amount of amplicon obtained is then quantified by spectrophotometry and the number of copies calculated on the basis of the molecular weight of each individual gene amplicon. Serial dilutions of this amplicon are tested with the Q-PCR assay to generate the gene specific standard curve.
  • Optimal standard curves are based on PCR amplification efficiency from 90 to 100% (100% meaning that the amount of template is doubled after each cycle), as demonstrated by the slope of the standard curve equation. Linear regression analysis of all standard curves should show a high correlation (R 2 coefficient .gtoreq.0.98). Genomic DNA can be similarly quantified.
  • transcripts of a target gene When measuring transcripts of a target gene, the starting material, transcripts of a housekeeping gene are quantified as an endogenous control. Beta-actin is one of the most used nonspecific housekeeping genes. For each experimental sample, the value of both the target and the housekeeping gene are extrapolated from the respective standard curve. The target value is then divided by the endogenous reference value to obtain a normalized target value independent of the amount of starting material.
  • the above-described quantitative real-time PCR methodology has been adapted to perform quantitative methylation-specific PCR (QM-MSP) by utilizing the external primers pairs in round one (multiplex) PCR and internal primer pairs in round two (real time MSP) PCR.
  • QM-MSP quantitative methylation-specific PCR
  • each set of genes has one pair of external primers and two sets of three internal primers/probe (internal sets are specific for unmethylated or methylated DNA).
  • the external primer pairs can co-amplify a cocktail of genes, each pair selectively hybridizing to a member of the panel of genes being investigated using the invention method.
  • the method of methylation-specific PCR (QM-MSP) has been described in US Patent Application 20050239101, incorporated by reference in its entirety herein.
  • Hypermethylation can be detected using two-stage, or “nested” PCR, for example as described in U.S. Pat. No. 7,214,485, incorporated by reference in its entirety herein.
  • two-stage, or “nested” polymerase chain reaction method is disclosed for detecting methylated DNA sequences at sufficiently high levels of sensitivity to permit cancer screening in biological fluid samples, such as sputum, obtained non-invasively.
  • MSP primers themselves are specifically designed to recognize CpG sites to take advantage of the differences in methylation to amplify specific products to be identified by the invention assay.
  • the methods of MSP include modification of DNA by sodium bisulfite or a comparable agent that converts all unmethylated but not methylated cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA.
  • MSP methylation specific PCR
  • MSP provides significant advantages over previous PCR and other methods used for assaying methylation. MSP is markedly more sensitive than Southern analyses, facilitating detection of low numbers of methylated alleles and the study of DNA from small samples. MSP allows the study of paraffin-embedded materials, which could not previously be analyzed by Southern analysis. MSP also allows examination of all CpG sites, not just those within sequences recognized by methylation-sensitive restriction enzymes. This markedly increases the number of such sites which can be assessed and will allow rapid, fine mapping of methylation patterns throughout CpG rich regions. MSP also eliminates the frequent false positive results due to partial digestion of methylation-sensitive enzymes inherent in previous PCR methods for detecting methylation.
  • MSP can provide similar information as genomic sequencing, but can be performed with some advantages as follows. MSP is simpler and requires less time than genomic sequencing, with a typical PCR and gel analysis taking 4-6 hours. In contrast, genomic sequencing, amplification, cloning, and subsequent sequencing may take days. MSP also avoids the use of expensive sequencing reagents and the use of radioactivity. Both of these factors make MSP better suited for the analysis of large numbers of samples.
  • the use of PCR as the step to distinguish methylated from unmethylated DNA in MSP allows for significant increase in the sensitivity of methylation detection.
  • Multiplex methylation-specific PCR is a unique version of methylation-specific PCR. Methylation-specific PCR is described in U.S. Pat. Nos. 5,786,146; 6,200,756; 6,017,704 and 6,265,171, each of which is incorporated herein by reference in its entirety. Multiplex methylation-specific PCR utilizes MSP primers for a multiplicity of markers, for example three or more different markers, in a two-stage nested PCR amplification reaction. The primers used in the first PCR reaction are selected to amplify a larger portion of the target sequence than the primers of the second PCR reaction.
  • the primers used in the first PCR reaction are referred to herein as “external primers” or DNA primers” and the primers used in the second PCR reaction are referred to herein as “MSP primers.”
  • MSP primers Two sets of primers (i.e., methylated and unmethylated for each of the markers targeted in the reaction) are used as the MSP primers.
  • a small amount (i.e., 1 ⁇ l) of a 1:10 to about 10 6 dilution of the reaction product of the first “external” PCR reaction is used in the second “internal” MSP PCR reaction.
  • primer refers to a sequence comprising two or more deoxyribonucleotides or ribonucleotides, preferably more than three, and most preferably more than 8, which sequence is capable of initiating synthesis of a primer extension product, which is substantially complementary to a polymorphic locus strand.
  • Environmental conditions conducive to synthesis include the presence of nucleoside triphosphates and an agent for polymerization, such as DNA polymerase, and a suitable temperature and pH.
  • the primer is preferably single stranded for maximum efficiency in amplification, but may be double stranded. If double stranded, the primer is first treated to separate its strands before being used to prepare extension products.
  • the primer is an oligodeoxy ribonucleotide.
  • the primer must be sufficiently long to prime the synthesis of extension products in the presence of the inducing agent for polymerization.
  • the exact length of primer will depend on many factors, including temperature, buffer, and nucleotide composition.
  • the oligonucleotide primer typically contains 12-20 or more nucleotides, although it may contain fewer nucleotides.
  • Primers of the invention are designed to be “substantially” complementary to each strand of the oligonucleotide to be amplified and include the appropriate G or C nucleotides as discussed above. This means that the primers must be sufficiently complementary to hybridize with their respective strands under conditions that allow the agent for polymerization to perform. In other words, the primers should have sufficient complementarity with a 5′ and 3′ oligonucleotide to hybridize therewith and permit amplification of CpG containing nucleic acid sequence.
  • Primers of the invention are employed in the amplification process, which is an enzymatic chain reaction that produces exponentially increasing quantities of target locus relative to the number of reaction steps involved (e.g., polymerase chain reaction or PCR).
  • one primer is complementary to the negative ( ⁇ ) strand of the locus (antisense primer) and the other is complementary to the positive (+) strand (sense primer).
  • the product of the chain reaction is a discrete nucleic acid duplex with termini corresponding to the ends of the specific primers employed.
  • oligonucleotide primers used in invention methods may be prepared using any suitable method, such as conventional phosphotriester and phosphodiester methods or automated embodiments thereof.
  • diethylphos-phoramidites are used as starting materials and may be synthesized as described by Beaucage, et al. (Tetrahedron Letters, 22:1859-1862, 1981).
  • Beaucage, et al. Tetrahedron Letters, 22:1859-1862, 1981.
  • One method for synthesizing oligonucleotides on a modified solid support is described in U.S. Pat. No. 4,458,066.
  • MSP primers for the non-methylated DNA preferably have a T in the 3′ CG pair to distinguish, it from the C retained in methylated DNA, and the complement is designed for the antisense primer.
  • MSP primers usually contain relatively few Cs or Gs in the sequence since the Cs will be absent in the sense primer and the Gs absent in the antisense primer (C becomes modified to U (uracil) which is amplified as T (thymidine) in the amplification product).
  • the primers of the invention embrace oligonucleotides of sufficient length and appropriate sequence so as to provide specific initiation of polymerization on a significant number of nucleic acids in the polymorphic locus.
  • the nucleic acid sequence of interest contains two strands, it is necessary to separate the strands of the nucleic acid before it can be used as a template for the amplification process.
  • Strand separation can be effected either as a separate step or simultaneously with the synthesis of the primer extension products. This strand separation can be accomplished using various suitable denaturing conditions, including physical, chemical, or enzymatic means, the word “denaturing” includes all such means.
  • One physical method of separating nucleic acid strands involves heating the nucleic acid until it is denatured.
  • Typical heat denaturation may involve temperatures ranging from about 80.degree. to 105.degree C. for times ranging from about 1 to 10 minutes.
  • Strand separation may also be induced by an enzyme from the class of enzymes known as helicases or by the enzyme RecA, which has helicase activity, and in the presence of riboATP, is known to denature DNA.
  • the reaction conditions suitable for strand separation of nucleic acids with helicases are described by Kuhn Hoffmann-Berling (CSH-Quantitative Biology, 43:63, 1978) and techniques for using RecA are reviewed in C. Radding (Ann. Rev. Genetics, 16:405-437, 1982).
  • any nucleic acid specimen in purified or nonpurified form, can be utilized as the starting nucleic acid or acids, provided it contains, or is suspected of containing, the specific nucleic acid sequence containing the target locus (e.g., CpG).
  • the target locus e.g., CpG
  • the separated strands are ready to be used as a template for the synthesis of additional nucleic acid strands.
  • This synthesis is performed under conditions allowing hybridization of primers to templates to occur. Generally synthesis occurs in a buffered aqueous solution, preferably at a pH of 7-9, most preferably about 8.
  • a molar excess for genomic nucleic acid, usually about 10 8 :1 primer:template
  • a molar excess for genomic nucleic acid, usually about 10 8 :1 primer:template
  • the amount of complementary strand may not be known if the process of the invention is used for diagnostic applications, so that the amount of primer relative to the amount of complementary strand cannot be determined with certainty.
  • the amount of primer added will generally be in molar excess over the amount of complementary strand (template) when the sequence to be amplified is contained in a mixture of complicated lona-chain nucleic acid strands. A large molar excess is preferred to improve the efficiency of the process.
  • the deoxyribonucleoside triphosphates dATP, dCTP, dGTP, and dTTP are added to the synthesis mixture, either separately or together with the primers, in adequate amounts and the resulting solution is heated to about 90 C -100 C. from about 1 to 10 minutes, preferably from 1 to 4 minutes. After this heating period, the solution is allowed to cool to room temperature, which is preferable for the primer hybridization. To the cooled mixture is added an appropriate agent for effecting the primer extension reaction (called herein “agent for polymerization”), and the reaction is allowed to occur under conditions known in the art.
  • agent for polymerization may also be added together with the other reagents if it is heat stable.
  • This synthesis (or amplification) reaction may occur at room temperature up to a temperature above which the agent for polymerization no longer functions.
  • the temperature is generally no greater than about 40 C. Most conveniently the reaction occurs at room temperature.
  • the agent for polymerization may be any compound or system which will function to accomplish the synthesis of primer extension products, including enzymes.
  • Suitable enzymes for this purpose include, for example, E. coli DNA polymerase I, Klenow fragment of E. coli DNA polymerase I, T4 DNA polymerase, other available DNA polymerases, polymerase muteins, reverse transcriptase, and other enzymes, including heat-stable enzymes (i.e., those enzymes which perform primer extension after being subjected to temperatures sufficiently elevated to cause denaturation).
  • Suitable enzymes will facilitate combination of the nucleotides in the proper manner to form the primer extension products which are complementary to each locus nucleic acid strand.
  • the synthesis will be initiated at the 3′ end of each primer and proceed in the 5′ direction along the template strand, until synthesis terminates, producing molecules of different lengths.
  • nucleic acid hybridization reactions the conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (e.g., GC v. AT content), and nucleic acid type (e.g., RNA v. DNA) of the hybridizing regions of the nucleic acids can be considered in selecting hybridization conditions. An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter.
  • the method of amplifying is by PCR, as described herein and as is commonly used by those of ordinary skill in the art.
  • Alternative methods of amplification have been described and can also be employed as long as the methylated and non-methylated loci amplified by PCR using the primers of the invention is similarly amplified by the alternative means.
  • the amplified products are preferably identified as methylated or non-methylated by sequencing. Sequences amplified by the methods of the invention can be further evaluated, detected, cloned, sequenced, and the like, either in solution or after binding to a solid support, by any method usually applied to the detection of a specific DNA sequence such as PCR, oligomer restriction (39), allele-specific oligonucleotide (ASO) probe analysis (40), oligonucleotide ligation assays (OLAs) (41), and the like. Molecular techniques for DNA analysis have been reviewed (42).
  • the methylation pattern of the nucleic acid can be confirmed by restriction enzyme digestion and Southern blot analysis.
  • methylation sensitive restriction endonucleases which can be used to detect 5′CpG methylation include Smal, SacII, EagI, MspI, HpaII, BstUI and BssHII, for example.
  • the invention provides a method for detecting a cell having a hypermethylated CpG island or a cell proliferative disorder associated with hypermethylated CpG in a tissue or biological fluid of a subject, comprising contacting a target cellular component suspected of expressing a gene having a methylated CpG or having a CpG-associated disorder, with an agent which binds to the component.
  • the target cell component can be nucleic acid, such as DNA or RNA, or protein.
  • the reagent is a nucleic acid probe or PCR primer.
  • the reagent is an antibody probe.
  • the probes can be detectably labeled, for example, with a radioisotope, a fluorescent compound, a bioluminescent compound, a chemiluminescent compound, a metal chelator, or an enzyme.
  • a radioisotope for example, with a fluorescent compound, a bioluminescent compound, a chemiluminescent compound, a metal chelator, or an enzyme.
  • Those of ordinary skill in the art will know of other suitable labels for binding to the antibody, or will be able to ascertain such, using routine experimentation.
  • Actively transcribed genes generally contain fewer methylated CGs than the average number in DNA. Hypermethylation can also be detected by restriction endonuclease treatment and Southern blot analysis. Therefore, in certain preferred embodiments, when the cellular component detected is DNA, restriction endonuclease analysis is preferable to detect hypermethylation of the promoter for example. Any restriction endonuclease that includes CG as part of its recognition site and that is inhibited when the C is methylated can be utilized. In certain preferred examples, the methylation sensitive restriction endonuclease is BssHII, MspI, or HpaII, used alone or in combination. Other methylation sensitive restriction endonucleases will be known to those of skill in the art.
  • an antibody or nucleic acid probe specific for a gene or gene product may be used to detect the presence of methylation either by detecting the level of polypeptide (using antibody) or methylation of the polynucleotide (using nucleic acid probe) in biological fluids or tissues. For antibody-based detection, the level of the polypeptide is compared with the level of polypeptide found in a corresponding “normal” tissue.
  • Oligonucleotide primers based on any coding sequence region of the promoter in gene selected from genes involved in tumor suppression, nucleic acid repair, apoptosis, anti-proliferation, ras signaling, adhesion, differentiation, development, and cell cycle regulation. In particular, oligonucleotide primers are based on coding sequence region of the promoter in the gene selected from the following are useful for amplifying DNA, for example by PCR:
  • H-cadherin in certain exemplary embodiments is encoded by NCBI accession No. AAB18912, comprising (SEQ ID NO:1) below:
  • p-16 in certain exemplary embodiments is encoded by NCBI accession No. CAB58124 comprising (SEQ ID NO:2) below:
  • APC in certain exemplary embodiments is encoded by NCBI accession No. NP — 000029 comprising (SEQ ID NO:3) below:
  • RASSF1A in certain exemplary embodiments is encoded by NCBI accession No. NP — 009113 comprising (SEQ ID NO:4) below:
  • MGMT in certain exemplary embodiments is encoded by NCBI accession
  • AAH00824 comprising (SEQ ID NO:5) below:
  • DAPK in certain exemplary embodiments is encoded by NCBI accession No. NP — 004929 comprising (SEQ ID NO:6) below:
  • ASC in certain exemplary embodiments is encoded by NCBI accession No. NP — 037390 comprising (SEQ ID NO:7) below:
  • Any specimen containing a detectable amount of polynucleotide or antigen can be used.
  • the subject is human.
  • the present invention provides the finding that gene hypermethylation of not only the primary malignancy, but also lymph nodes, may be used to restage and assess prognosis of patients with stage I tumors, in particular examples patients with stage I non small cell lung carcinoma (NSCLC). These markers are shown to also be potential targets for reversal of gene silencing and may be important in adjuvant approaches to reduce disease recurrence.
  • NSCLC non small cell lung carcinoma
  • any gene such as genes involved in tumor suppression, nucleic acid repair, apoptosis, anti-proliferation, ras signaling, adhesion, differentiation, development, and cell cycle regulation
  • the appropriate course of treatment can be employed (e.g., sense gene therapy or drug therapy).
  • the expression pattern of the gene may vary with the stage of malignancy of a cell, therefore, a sample such as NSCLC or breast tissue can be screened with a panel of gene or gene product specific reagents (i.e., nucleic acid probes or antibodies) to detect gene expression and then diagnose the stage of malignancy of the cell.
  • the methods of the invention as described herein are used in certain exemplary embodiments to identify metastases by detecting hypermethylation of one or more genes in one or more samples. In this way, the detection of nucleic acid hypermethylation identifies metastases.
  • conditions associated with aberrant methylation of genes that can be detected or monitored include, but are not limited to, metastases associated with carcinomas and sarcomas of all kinds, including one or more specific types of cancer, e.g., a lung cancer, breast cancer, an alimentary or gastrointestinal tract cancer such as colon, esophageal and pancreatic cancer, a liver cancer, a skin cancer, an ovarian cancer, an endometrial cancer, a prostate cancer, a lymphoma, hematopoietic tumors, such as a leukemia, a kidney cancer, a bronchial cancer, a muscle cancer, a bone cancer, a bladder cancer or a brain cancer, such as astrocytoma, anaplastic astrocytoma, glioblastoma, medulloblastoma, and neuroblastoma and their metastases.
  • Suitable pre-malignant lesions to be detected or monitored using the invention include, but are not limited to, lobular carcinoma in
  • the invention methods can be used to assay the DNA of any mammalian subject, including, but not limited to, humans, pet (e.g., dogs, cats, ferrets) and farm animals (meat and dairy).
  • the invention features in certain aspects a method for identifying metastases in a subject comprising detecting nucleic acid hypermethylation of one or more genes in one or more samples, wherein detecting nucleic acid hypermethylation identifies metastases.
  • hypermethylation refers to the presence of methylated alleles in one or more nucleic acids.
  • hypermethylation is detected using methylation specific polymerase chain reaction (MSP).
  • the samples can be from tumor tissue, lymph nodes, bone marrow or blood.
  • the invention can be used to identify metastases in a subject comprising detecting nucleic acid hypermethylation of one or more genes in tumor tissues or in lymph nodes, wherein detecting nucleic acid hypermethylation identifies metastases.
  • Hypermethylation can be detected in tumor tissue alone, e.g. primary tumor tissue, or tumor tissue and lymph nodes.
  • detection of hypermethylation in the lymph nodes indicates an early recurring disease.
  • detection of hypermethylation in the lymph nodes indicates a more aggressive disease. Often, an early recurring disease is a more aggressive disease although the two are not mutually exclusive.
  • the invention features a method for identifying micrometastases in a subject comprising detecting nucleic acid hypermethylation of one or more genes in tumor tissue or lymph node, wherein the genes are selected from the group consisting of: genes involved in tumor suppression, DNA repair, apoptosis, anti-proliferation, ras signaling, adhesion, differentiation, development, and cell cycle regulation, in one or more cells or tissues, wherein detecting nucleic acid hypermethylation identifies micrometastases.
  • the invention as described herein features a method for identifying micrometastases in a subject comprising detecting nucleic acid hypermethylation of at least one or more genes in a sample comprising tumor and lymph nodes, where the sample genes are selected from genes involved in tumor suppression, nucleic acid repair, apoptosis, anti-proliferation, ras signaling, adhesion, differentiation, development, and cell cycle regulation, in one or more cells or tissues, and where detecting nucleic acid methylation identifies micrometastases.
  • the method for detecting or diagnosing a proliferative disease in a subject comprises, in certain embodiments, extracting nucleic acid from one or more cell or tissue samples, detecting nucleic acid hypermethylation of one or more genes in the sample; and identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes indicates a proliferative disease.
  • the proliferative disease is cancer.
  • the one or more genes comprise one or more CpG islands in the promoter regions. Accordingly, any gene that contains one or more CpG island in the promoter region is suitable for use in the methods of the invention; however in certain preferred examples, the one or more genes may be selected from any of p-16, H-cadherin, APC, RASSF1A, MGMT, DAPK, or ASC, and as described in SEQ ID NOs 1-7.
  • hypermethylation of at least one of the genes is detected. In other certain embodiments, hypermethylation of at least two of the genes is detected. In other certain embodiments, hypermethylation of at least three of the genes is detected.
  • the detection of metastases as described in these methods can be used to detect or diagnose a proliferative disease.
  • the detection of metastases as described in these methods can be used after surgery or therapy to treat a proliferative disease.
  • the detection of metastases as described in these methods can be used to predict the recurrence of a proliferative disease.
  • the detection of metastases as described in these methods can be used to stage a proliferative disease.
  • the detection of metastases as described in these methods can be used to determine a course of treatment for a subject.
  • the invention as described herein can be used to treat a subject having or at risk for having a proliferative disease, such as cancer. Accordingly, the method comprises identifying nucleic acid hypermethylation of one or more genes, where nucleic acid hypermethylation indicates having or a risk for having a proliferative disease, and administering to the subject a therapeutically effective amount of a demethylating agent, thereby treating a subject having or at risk for having a proliferative disease.
  • Anti-cancer drugs that may be used in the various embodiments of the invention, including pharmaceutical compositions and dosage forms and kits of the invention, include, but are not limited to: acivicin; aclarubicin; acodazole hydrochloride; acronine; adozelesin; aldesleukin; altretamine; ambomycin; ametantrone acetate; aminoglutethimide; amsacrine; anastrozole; anthramycin; asparaginase; asperlin; azacitidine; azetepa; azotomycin; batimastat; benzodepa; bicalutamide; bisantrene hydrochloride; bisnafide dimesylate; bizelesin; bleomycin sulfate; brequinar sodium; bropirimine; busulfan; cactinomycin; calusterone; caracemid
  • the invention features methods of identifying an agent that de-methylates hypermethylated nucleic acids comprising identifying one or more cell or tissue samples with hypermethylated nucleic acid, extracting the hypermethylated nucleic acid, contacting the nucleic acid with one or more nucleic acid de-methylating candidate agents and a control agent, and identifying the nucleic acid hypermethylation state, wherein nucleic acid de-methylation of genes in the sample by the candidate agent compared to the control indicates a demethylating agent, thereby identifying an agent that de-methylates hypermethylated nucleic acid.
  • the invention features methods for predicting the recurrence of proliferative diseases, e.g. cancer.
  • the invention features methods for predicting the recurrence of a proliferative disease in a subject comprising detecting nucleic acid hypermethylation of one or more genes wherein detecting nucleic acid hypermethylation of one or more genes is a predictor of the recurrence of a proliferative disease.
  • the method comprises extracting nucleic acid from one or more cell or tissue samples, detecting nucleic acid hypermethylation of one or more genes in the sample, and identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes is indicative of the recurrence of a proliferative disease.
  • the rate of recurrence of a proliferative disease can be correlated with the detection of hypermethylation in a cell or tissue sample.
  • the cell or tissue sample is tumor tissue or lymph node.
  • the rate of recurrence of a proliferative disease is more rapid when gene hypermethylation is detected in lymph node.
  • gene hypermethylation e.g. p16 or H-cadherin
  • the odds of recurrence may be less than when the same genes are hypermethylated in N1 lymph nodes.
  • the odds of recurrence may be the greatest compared to the former tissues (primary tumor and N1 lymph nodes).
  • Adjuvant and neoadjuvant therapy are promising treatment modalities, however although adjuvant chemotherapy has been demonstrated to improve survival, for example in node negative breast cancer patients (43), problems remain, for example in the uncertainty as to how to best identify patients whose risk of disease recurrence exceeds their risk of significant therapeutic toxicity.
  • adjuvant chemotherapy has been demonstrated to improve survival, for example in node negative breast cancer patients (43)
  • problems remain, for example in the uncertainty as to how to best identify patients whose risk of disease recurrence exceeds their risk of significant therapeutic toxicity.
  • a need remains for that enable clinical decisions on adjuvant and neoadjuvant therapy, tumor surveillance and the likelihood of disease progression based on validated tumor markers correlated with metastasis and recurrence.
  • the invention features a method for determining the prognosis of a subject suffering from a proliferative disease comprising: detecting nucleic acid hypermethylation of one or more genes wherein the detection of nucleic acid hypermethylation is used for determining the prognosis of a subject suffering from a proliferative disease.
  • prognosis can be used by the clinician to determine the course of treatment, and to monitor the course of treatment. As is understood by the skilled practicioner, prognosis is a prediction and can change during the course of treatment.
  • a proliferative disease e.g. a neoplasia or cancer.
  • Staging can refer to “clinical” staging or “molecular” staging.
  • Clinical staging describes the extent or severity of an individual's cancer based on the extent of the original (primary) tumor and the extent of spread in the body.
  • clinical staging is used in determining a subject's course of treatment and to estimate the subject's prognosis.
  • the TNM system is one of the most commonly used staging systems.
  • the formal TNM staging system promulgated by the American Joint Committee on Cancer (AJCC), is based almost exclusively on the anatomical extent of disease, which is assessed using a combination of tumor size or depth (T), lymph node spread (N), and presence or absence of metastases (M). Since its inception in 1958, the TNM system has provided a standardized, anatomical basis for staging with several important functions. It provides a basis for prediction of survival, choice of initial treatment, stratification of patients in clinical trials, accurate communication among healthcare providers, and uniform reporting of outcomes. For most tumor types, disease burden and spread have been considered the most reliable predictors of survival and determinants of the type and intensity of therapy to be used.
  • TMJ staging Less often, tumor grade, histological subtype or patient age has been added to TNM staging when the AJCC became convinced that such information would significantly improve the prediction of survival or response to therapy.
  • TMJ system a number is added to each letter to indicate the size or extent of the tumor and the extent of spread.
  • TX indicates that the primary tumor cannot be evaluated
  • TO indicates no evidence of primary tumor
  • Tis indicates carcinoma in situ (early cancer that has not spread to neighboring tissue)
  • T1, T2, T3, T4 indicates size and/or extent of the primary tumor.
  • NX indicates the regional lymph nodes cannot be evaluated
  • NO indicates there is no regional lymph node involvement (no cancer found in the lymph nodes)
  • N1, N2, N3 indicates the involvement of regional lymph nodes (number and/or extent of spread).
  • MX indicates that distant metastasis cannot be evaluated
  • MO indicates no distant metastasis (cancer has not spread to other parts of the body)
  • M1 indicates distant metastasis (cancer has spread to distant parts of the body).
  • Criteria for stages differ for different types of cancer. More information on clinical staging can be found on the world wide web, for example at http://www.cancer.gov/cancertopics/factsheet/Detection/staging.
  • the instant invention provides the incorporation of biomarkers into TNM staging.
  • the instant invention provides a method of molecular staging and re-staging by determining the nucleic acid hypermethylation of one or more certain genes.
  • the invention provides methods of molecular restaging that can be used to re-stage any cancer with metastatic capability.
  • hypermethylated nucleic acids are detected in the lymph nodes.
  • the invention provides methods of detection of early recurrence of proliferative disease, e.g. cancer, that are unable to be detected by methods of clinical staging.
  • molecular re-staging as described herein can predict early recurrence of cancer, and thereby detect aggressive cancers at an earlier stage in their progression.
  • the invention features a method for staging or re-staging a proliferative disease in a subject comprising detecting nucleic acid hypermethylation of one or more genes wherein detecting nucleic acid hypermethylation is used for staging a proliferative disease.
  • the stage of proliferative disease is predictive of disease recurrence.
  • Determining the stage of a proliferative disease can be used by the clinician to determine the course of treatment.
  • the terms “treat,” treating,” “treatment,” and the like are meant to refer to reducing or ameliorating a disorder and/or symptoms associated therewith. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated. In certain cases, an early recurring cancer may be treated with more aggressive therapy.
  • the term “aggressive treatment regimen” is intended to mean reducing or ameliorating a disorder and/or symptoms associated therewith with a method of treatment (e.g. combination of chemotherapeutic agents) more intensive or comprehensive than usual, for instance in dosage or extent. It will be appreciated that, although not precluded, aggressively treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated.
  • the invention also features a method for staging or re-staging a proliferative disease in a subject comprising extracting nucleic acid from one or more cell or tissue samples, detecting nucleic acid hypermethylation of one or more genes in the sample; and identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes is used for staging or re-staging of a proliferative disease.
  • tissue sample is suitable for use in the methods of staging or re-staging.
  • the tissue samples are selected from tumor, lymph node, bone marrow or blood or a combination thereof.
  • the samples are from the lymph nodes.
  • the molecular grading methods as described herein cab be performed prior to or after therapeutic intervention for the proliferative disease, e.g. cancer.
  • the therapeutic intervention can be selected from treatment with an agent or can be a surgical procedure.
  • the methods for staging or re-staging a proliferative disease in a subject comprising detecting nucleic acid hypermethylation of one or more genes as described herein can be used as adjuvant or neoadjuvant therapy.
  • Samples for use in the methods of the invention include cells or tissues obtained from any solid tumor, samples taken from lymph nodes, from bone marrow or from blood. Additionally, the sample may be a sample that is taken from plasma, serum, sputum, or other fluid. Tumor DNA can be found in various body fluids and these fluids can potentially serve as diagnostic material.
  • nucleic acid specimen in purified or nonpurified form, can be utilized as the starting nucleic acid or acids, provided it contains, or is suspected of containing, the specific nucleic acid sequence containing the target locus (e.g., CpG).
  • the process may employ, for example, DNA or RNA, including messenger RNA, wherein DNA or RNA may be single stranded or double stranded.
  • RNA is to be used as a template
  • enzymes, and/or conditions optimal for reverse transcribing the template to DNA would be utilized.
  • a DNA-RNA hybrid which contains one strand of each may be utilized.
  • a mixture of nucleic acids may also be employed, or the nucleic acids produced in a previous amplification reaction herein, using the same or different primers may be so utilized.
  • the specific nucleic acid sequence to be amplified i.e., the target locus, may be a fraction of a larger molecule or can be present initially as a discrete molecule, so that the specific sequence constitutes the entire nucleic acid. It is not necessary that the sequence to be amplified be present initially in a pure form; it may be a minor fraction of a complex mixture, such as contained in whole human DNA.
  • the nucleic acid-containing sample or specimen used for detection of methylated CpG may be from any solid tumor or any source including brain, colon, urogenital, hematopoietic, thymus, testis, ovarian, uterine, prostate, breast, colon, lung and renal tissue and may be extracted by a variety of techniques such as that described by Maniatis, et al. (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y., pp 280, 281, 1982).
  • the extracted sample is impure (e.g., plasma, serum, stool, ejaculate, sputum, saliva, ductal cells, nipple aspiration fluid, ductal lavage fluid, cerebrospinal fluid or blood or a sample embedded in parrafin), it may be treated before amplification with an amount of a reagent effective to open the cells, fluids, tissues, or animal cell membranes of the sample, and to expose and/or separate the strand(s) of the nucleic acid(s). This lysing and nucleic acid denaturing step to expose and separate the strands will allow amplification to occur much more readily
  • the method of amplifying is by PCR, as described herein and as is commonly used by those of ordinary skill in the art.
  • alternative methods of amplification have been described and can also be employed.
  • PCR techniques and many variations of PCR are known. Basic PCR techniques are described by Saiki et al. (1988 Science 239:487-491) and by U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,800,159, each of which is incorporated herein by reference.
  • the conditions generally required for PCR include temperature, salt, cation, pH and related conditions needed for efficient copying of the master-cut fragment.
  • PCR conditions include repeated cycles of heat denaturation (i.e. heating to at least about 95° C.) and incubation at a temperature permitting primer: adaptor hybridization and copying of the master-cut DNA fragment by the amplification enzyme.
  • Heat stable amplification enzymes like the pwo, Thermus aquaticus or Thermococcus litoralis DNA polymerases which eliminate the need to add enzyme after each denaturation cycle, are commercially available.
  • the salt, cation, pH and related factors needed for enzymatic amplification activity are available from commercial manufacturers of amplification enzymes.
  • an amplification enzyme is any enzyme which can be used for in vitro nucleic acid amplification, e.g. by the above-described procedures.
  • amplification enzymes include pwo, Escherichia coli DNA polymerase I, Klenow fragment of E.
  • coli polymerase I T4 DNA polymerase, T7 DNA polymerase, Thermus aquaticus (Taq) DNA polymerase, Thermococcus litoralis DNA polymerase, SP6 RNA polymerase, T7 RNA polymerase, T3 RNA polymerase, T4 polynucleotide kinase, Avian Myeloblastosis Virus reverse transcriptase, Moloney Murine Leukemia Virus reverse transcriptase, T4 DNA ligase, E. coli DNA ligase or Q.beta. replicase.
  • Preferred amplification enzymes are the pwo and Taq polymerases. The pwo enzyme is especially preferred because of its fidelity in replicating DNA.
  • the nucleic acid can be attached to a solid support, such as a membrane, and can be hybridized with any probe of interest, to detect any nucleic acid sequence.
  • a solid support such as a membrane
  • membranes are known to one of skill in the art for the adhesion of nucleic acid sequences. Specific non-limiting examples of these membranes include nitrocellulose (NITROPURE®) or other membranes used in for detection of gene expression such as polyvinylchloride, diazotized paper and other commercially available membranes such as GENESCREEN®, ZETAPROBE.RTM. (Biorad), and NYTRAN®. Methods for attaching nucleic acids to these membranes are well known to one of skill in the art. Alternatively, screening can be done in a liquid phase.
  • nucleic acid hybridization reactions the conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (e.g., GC v. AT content), and nucleic acid type (e.g., RNA v. DNA) of the hybridizing regions of the nucleic acids can be considered in selecting hybridization conditions. An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter.
  • the probe of interest can be detectably labeled, for example, with a radioisotope, a fluorescent compound, a bioluminescent compound, a chemiluminescent compound, a metal chelator, or an enzyme.
  • a radioisotope for example, with a fluorescent compound, a bioluminescent compound, a chemiluminescent compound, a metal chelator, or an enzyme.
  • Those of ordinary skill in the art will know of other suitable labels for binding to the probe, or will be able to ascertain such, using routine experimentation.
  • kits The methods of the invention are ideally suited for the preparation of kits.
  • kits for identifying the nucleic acid hypermethylation state of one or more genes comprising gene specific primers for use in polymerase chain reaction (PCR), and instructions for use.
  • PCR polymerase chain reaction
  • kits for detecting metastases by detecting nucleic acid hypermethylation of one or more genes comprising gene specific primers for use in polymerase chain reaction (PCR), and instructions for use.
  • the metastases are micrometastases.
  • the PCR in particularly preferred examples, is methylation specific PCR (MSP).
  • MSP methylation specific PCR
  • any gene comprising one or more CpG islands in the promoter region can be detected using the kits of the invention.
  • the one or more genes are selected from the group consisting of genes involved in tumor suppression, nucleic acid repair, anti-proliferation, apoptosis, ras signaling, adhesion, differentiation, development, and cell cycle regulation.
  • the genes are selected from the group consisting of: p-16, H-cadherin, APC, RASSF1A, MGMT, DAPK, and ASC
  • kits can be used to detect hypermethylation of at least one of the genes as described herein. In some examples, can be used to detect hypermethylation of at least two of the genes as described herein. In other examples, the kits can be used to detect hypermethylation of at least three of the genes as described herein.
  • the two genes can be selected from the following: p-16 and H-cadherin, H-cadherin and APC, APC and p16, or RASSf1A and p16.
  • Carrier means are suited for containing one or more container means such as vials, tubes, and the like, each of the container means comprising one of the separate elements to be used in the method.
  • container means such as vials, tubes, and the like
  • each of the container means comprising one of the separate elements to be used in the method.
  • the container means can comprise a container containing gene specific primers for use in polymerase chain reaction methods of the invention.
  • container means can also be included which comprise a methylation sensitive restriction endonuclease.
  • gene hypermethylation versus traditional histopathology was tested to predict disease recurrence in solid tumors.
  • the examples presented herein show that gene hypermethylation of not only the primary malignancy, but also lymph nodes, may be used to restage and assess prognosis of patients with stage I tumors, in particular examples patients with stage I NSCLC. These markers are shown to also be potential targets for reversal of gene silencing and may be important in adjuvant approaches to reduce disease recurrence.
  • Pathologic tumor stage showed the strongest risk for predicting disease recurrence independent of other covariates, with patients with stage 1B disease (T2 malignancies ⁇ 3 cm and/or visceral pleural invasion) having a 1.71 (95%CI, 0.86-3.41) fold risk for disease recurrence compared to patients with smaller sized tumors and no pleural invasion (stage 1A).
  • Methylation profiles using 7 genes were obtained on 727 of 731 paraffin blocks corresponding to 167 patients.
  • FIG. 1 shows multivariate logistic regression analysis that was performed using the four genes that exhibited the largest univariate distribution differences in methylation: p16, H-cadherin, APC, and RASSF1A.
  • the prognostic value of each molecular variable was assessed in a model that adjusted for stage (1A/1B), age (continuous), sex, race (Caucasian/African American), histology (adenocarcinoma, squamous cell, other), smoking status (ever/never) and then graphed as a Forest Plot. On the whole, regardless of the genes considered, hypermethylation of the mediastinal lymph node tissue had the highest prognostic value for estimating lung cancer recurrence versus no methylation.
  • methylation of both p16 and H-cadherin had robust odds ratios for recurrence for primary tumor, regional, and mediastinal lymph nodes. Methylation of either RASSF1A or APC in primary tumor or N2 nodes was also associated with a modest elevation in odds of recurrence but this was not statistically significant. If a patient with pathologic stage 1 disease (T1-2N0) had concomitant methylation of p16 as well as H-cadherin in both tumor and mediastinal lymph nodes, the estimated odds of lung cancer recurrence was over 15 as compared to those patients without concomitant methylation in these tissues.
  • pathologic stage 1 disease T1-2N0
  • the Kaplan-Meier estimates for time to recurrence indicate that for both tumor as well as for regional (N1) and mediastinal (N2) lymph nodes, as the number of methylated genes in the panel increases, there is a significant reduction in the recurrence-free survival (Panels A-C, E-G).
  • the Kaplan-Meier estimates reflect the recurrence-free survivals of patients with a clinically useful risk classification system as determined by our epigenetic marker panel.
  • Patients without methylation of the gene combination p16 and H-cadherin in both primary tumor and mediastinal lymph nodes have a significantly improved 5 year recurrence-free period than those with these genes methylated (64% vs. 14%, p ⁇ 0.001, respectively, Panel H).
  • the results presented herein demonstrate two related features for the detection of promoter region methylation in cancer.
  • the detection of promoter methylation within the resected primary tumor for key genes can be associated with a more aggressive, recurrent phenotype as has been shown in other settings (28,29).
  • the loss of function in key regulatory genes for cell cycle control (p16), invasion and metastasis (H-Cadherin, APC), as well as Ras signaling (RASSF1a) might be expected to result in a more aggressive primary tumor.
  • the ability to detect methylation within local or regional nodes provides a second layer of information to this subset identification, and demonstrates an additional approach for detecting micrometastatic disease.
  • stage 1 lung cancer patients who were not staged optimally by routine pathological analysis.
  • the current staging system for NSCLC is imprecise, and in stage 1 (T1-2N0) disease, in particular, the clinicopathologic criteria understages patients.
  • the results presented herein show that gene promoter methylation detection within NSCLC primary tumors can be used to identify cells with high potential for metastatic spread, and also to detect histologically occult micrometastases in lymph nodes used to stage NSCLC.
  • the methylation detected could represent free tumor DNA that has drained from the primary tumor via lymphatics, this is unlikely, particularly for N2 nodes, since these are located distant from the lung in a separate body compartment, the mediastinum. While the detection of methylation of these genes in tumor or N1 nodes was often associated with increased risk of recurrence, in the N2 lymph nodes, especially, the markers were very strongly prognostic, strengthening the contention that the DNA methylation is detecting micrometastatic disease.
  • This molecular distribution of markers in patients with rapid recurrence mirrors the biological basis of current histological staging systems that identify intact tumor cells that have traversed the mediastinal pleura to the N2 nodes and are associated with increased risk of recurrence.
  • the methods described herein present a molecular tool that parallels the use of histologic examination in accepted clinical pathology practice, but is more sensitive. This differs from previous studies that have relied solely on molecular characteristics of the primary malignancy (30-33). This ability to utilize the predictive power inherent in identifying micrometastases to lymph nodes may allow a more robust and reliable molecular staging built upon tumor characteristics and the detection of micrometastatic disease. Furthermore, recent promising results from examining methylation changes in sputum for predicting risk of lung cancer (34), or its recurrence (18), means the detection of these changes could provide valuable pre-surgical information as to disease stage and the metastatic potential of a patient's tumor.
  • the invention was carried out using methods that include the following.
  • stage 1 pathologically proven stage 1 (T1-2N0) patients diagnosed with non-small cell lung carcinoma (NSCLC) (International Classification of Diseases-ninth revision-Clinical Modification [ICD-9-CM] code 162.3-162.9) who underwent lobectomy or greater resections at the Johns Hopkins Hospital between Jan. 1, 1986 and Jul. 31, 2002. Only patients followed for recurrent disease at the institution were eligible for the analysis.
  • the study cohort consisted of 71 patients (cases) who despite receiving surgery with curative intent for pathological stage 1 (T1-2N0) primary NSCLC, recurred at the institution within 40 months of surgery and died of their cancer.
  • stage 1 lung cancer It was estimated that by 40 months approximately 80% of patients with resected stage 1 lung cancer would recur. Using patient age, stage, date of surgery (within 5 years), and sex, the cases were matched to 158 stage 1 patients (controls) from the remainder of the study population. These 71 cases and 158 controls formed the basic case-control population. From the above patients, samples were gathered for methylation analysis for 51 cases and 116 matched controls. Neither cases nor controls received adjuvant chemotherapy since surgery was performed between 1986-2002 when guidelines did not recommend adjuvant therapy for stage 1B patients (20, 21).
  • TNM classification criteria (5) which include histological status of mediastinal lymph nodes sampled from levels 2, 4, 7, 8, 9, and 10 on the right, and 5, 6, 7, 8, 9 on the left side.
  • Regional lymph nodes confined to the pleural space, were resected en bloc with the tumor. Patients were excluded as cases if they had surgery involving less than a lobectomy because there is strong evidence that patients with such resections are at significantly increased risk of local recurrence (22). Patients were also excluded as cases if they had any macroscopic or microscopically positive surgical margins, or underwent incomplete resection. In accord with this nested design, seven individuals with recurrences after 40 months postoperatively were considered as controls.
  • the 20 patients in the validation set consisting of 11 cases and 9 matched controls, had 162 paraffin blocks evaluated. All cases in the independent validation cohort, except for two, underwent resection at our institution after August 2002. The study was approved by the Institutional Review Board of the Johns Hopkins Medical Institutions.
  • Wizard DNA purification resin Promega, Madison, Wis.
  • MSP Methylation Specific PCR
  • DNA methylation for all lung cancer and lymph node DNA, was determined by MSP performed by 3 individuals blinded to the results of other investigators. Each individual extracted DNA and performed all steps of the MSP reaction separately. There were 889 total samples of tumor and lymph nodes examined. A multiplex-nested MSP assay as previously described was used for all samples24. The nested approach amplifies bisulfite-modified DNA initially with flanking PCR primers without preferentially amplifying methylated or unmethylated DNA. The resulting fragment is then used as the template for MSP.
  • Primer sequences and conditions of p16, MGMT, DAPK, RASSF1A, H-cadherin, ASC and APC have all been previously describedl6, 18, 24-26 including conditions optimized to achieve specific detection of methylation in tumor but not in normal lymphocytes, and are shown in Table 5, below (16, 18, 24-26).
  • FIG. 3 shows methylation specific PCR for the H-cadherin gene in 36 samples of tumors and lymph nodes, numbered at top of each panel. * represents the molecular weight marker.
  • the presence of a visible PCR product in Lanes U indicates the presence of an unmethylated promoter region amplified and serves as a control for sample preparation; the presence of product in Lanes M indicates a methylated gene promoter and was scored as positive for methylation.
  • Samples 7 and 16 did not amplify for this gene. Samples 1, 2, 3, 4, 8, 9, 11, 13, 14, 20, 21, 22, 23, 26, 30, 32, 33, 36 are scored as unmethylated.
  • Samples 5, 10, 12, 15, 17, 18, 19, 25, 27, 28, 31, 34, and 35 are methylated and samples 24 and 29 had very minimal M amplification that was scored as negative.
  • Placental DNA treated in vitro with SssI methyltransferase (New England Biolabs, Beverly, Mass.) was used as a positive control.
  • DNA from normal lymphocytes and water (bisulfite-modified and unmodified water) were used as negative controls.
  • PCR products were visualized using 2% agarose or 6% nondenaturing polyacrylamide gels, and visually scored as methylated or unmethylated according to the presence or absence of a PCR product ( FIG. 3 ), blinded to both the clinical outcomes and sources of DNA. (9, 25, 27).

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Abstract

The present invention provides methods for identifying metastases by detecting nucleic acid hypermethylation of one or more genes in one or more samples, and in particular in the lymph nodes. The invention further relates to DNA methylation as a predictor of disease recurrence and patient prognosis, specifically in the field of cancer biology.

Description

    RELATED APPLICATIONS
  • This application claims the benefit of US Provisional Application No. 60/860,196, filed Nov. 20, 2006. The entire contents of the aforementioned application are hereby incorporated herein by reference.
    • FIELD OF THE INVENTION
  • The present invention relates to the use of nucleic acid methylation and methylation profiles to detect metastatic disease. In particular, the invention relates to methods for identifying metastases by detecting nucleic acid hypermethylation of one or more genes in one or more samples and, in particular, in tumor tissue and lymph nodes. The invention further relates to DNA hypermethylation as a predictor of disease recurrence and patient prognosis, specifically in patients suffering from cancer.
    • BACKGROUND OF THE INVENTION
  • Cancer remains one of the leading causes of death in the United States. Clinically, a broad variety of medical approaches, including surgery, radiation therapy and chemotherapeutic drug therapy are currently being used in the treatment of human cancer (see the textbook CANCER: Principles & Practice of Oncology, 2d Edition, De Vita et al., eds., J. B. Lippincott Company, Philadelphia, Pa., 1985). However, it is recognized that such approaches continue to be limited by an inability to predict the likelihood of metastasis and tumor recurrence or the most efficacious treatment regime for minimizing the occurrence of these negative outcomes.
  • Human cancer cells typically contain somatically altered nucleic acids, characterized by mutation, amplification, or deletion of critical genes. In addition, the nucleic acids from human cancer cells often display somatic changes in DNA methylation (36, 37, 38). However, a precise role for, and the significance of, abnormal DNA methylation in human tumorigenesis has not been well established.
  • Loss of gene function is cancer can occur by both genetic and epigenetic mechanisms. The best-defined epigenetic alteration of cancer genes involves DNA methylation of clustered CpG dinucleotides, or CpG islands, in promoter regions associated with the transcriptional inactivation of the affected genes. CpG islands are short sequences rich in the CpG dinucleotide, and can be found in the 5′ region of about half of all human genes. Methylation of cytosine within 5′ CGIs is associated with loss of gene expression and has been seen in a number of physiological conditions, including X chromosome inactivation and genomic imprinting. Aberrant methylation of CpG islands has been detected in genetic diseases such as the fragile-X syndrome, in aging cells and in neoplasia. About half of the tumor suppressor genes which have been shown to be mutated in the germline of patients with familial cancer syndromes have also been shown to be aberrantly methylated in some proportion of sporadic cancers, including Rb, VHL, p16, hMLH1, and BRCA1 (reviewed in Baylin, et al, Adv. Cancer Res. 72:141-196 1998). Methylation of tumor suppressor genes in cancer is usually associated with (1) lack of gene transcription and (2) absence of coding region mutation. Thus CpG island methylation can serve as an alternative mechanism of gene inactivation in cancer.
  • Cancer treatments, in general, have a higher rate of success if the cancer is diagnosed early, and treatment is started earlier in the disease process. A relationship between improved prognosis and stage of disease at diagnosis can be seen across a majority of cancers. Identification of the earliest changes in cells associated with cancer is thus a major focus in molecular cancer research. Diagnostic approaches based on identification of these changes in specific genes may allow implementation of early detection strategies and novel therapeutic approaches. Targeting these early changes will lead to more effective cancer treatment.
  • Despite advances in targeted therapy, surgery with curative intent remains the best therapeutic option for lung cancer patients with the earliest stages of disease. Ensuring in these patients that no occult metastatic cells have disseminated outside the area of curative resection is critical, because early spread of tumor cells is a leading cause of relapse (1-3). Despite the curative aim of early surgery, approximately 30%-40% of lung cancer patients with discrete lesions and histologically proven cancer negative lymph nodes (stage 1:T1-2N0) still die of recurrent disease (4-6). Further, many of these recurrences are systemic, underscoring the probability that these patients had metastatic disease that was undetectable, and beyond the margins of surgical resection.
  • Accordingly, there is a need in the art for improved methods of detection of proliferative disease, and in particular, for improved methods of detection of metastatic cancer that is undetectable by current methodologies.
    • SUMMARY
  • The invention features methods for identifying metastases by detecting nucleic acid hypermethylation of one or more genes in one or more samples, and in particular in tumor tissue and lymph nodes.
  • In one aspect, the invention features methods for identifying metastases in a subject comprising detecting nucleic acid hypermethylation of one or more genes in one or more samples, wherein detecting nucleic acid hypermethylation identifies metastases.
  • In one embodiment, the sample comprises cells or tissues selected from the group consisting of tumor, lymph nodes, bone marrow and blood. In a particular embodiment, the sample is from a tumor. In another particular embodiment, the sample is from a lymph node. In a more particular embodiment, the lymph node is a N1 lymph node or a mediastinal lymph node.
  • In another aspect the invention features methods for identifying metastases in a subject comprising detecting nucleic acid hypermethylation of one or more genes in tumor tissue or lymph node, wherein the genes are selected from the group consisting of genes involved in tumor suppression, DNA repair, apoptosis, anti-proliferation, ras signaling, adhesion, differentiation, development, and cell cycle regulation, wherein detecting nucleic acid hypermethylation identifies metastases.
  • In certain preferred embodiments of the above aspects, the metastases are micrometastases. In other preferred embodiments of the above aspects, the one or more genes comprise one or more CpG islands. In a further embodiment, the one or more genes is selected from the group consisting of H-cadherin, p16, APC, RASSF1A, MGMT, DAPK, and ASC.
  • H-cadherin, in certain exemplary embodiments is encoded by NCBI accession No. AAB18912 and is shown in (SEQ ID NO:1) below:
  • 1 mqprtplvlc vllsqvlllt saedldctpg fqqkvfhinq paefiedqsi lnltfsdckg
    61 ndklryevss pyfkvnsdgg lvalrnitav gktlfvhart phaedmaelv ivggkdiqgs
    121 lqdifkfart spvprqkrsi vvspilipen qrqpfprdvg kvvdsdrper skfrltgkgv
    181 dqepkgifri nentgsvsvt rtldreviav yqlfvettdv ngktlegpvp levividqnd
    241 nrpifregpy ighvmegspt gttvmrmtaf daddpatdna llrynirqqt pdkpspnmfy
    301 idpekgdivt vvspalldre tlenpkyeli ieaqdmagld vgltgtatat imiddkndhs
    361 pkftkkefqa tveegavgvi vnltvedkdd pttgawraay tiingnpgqs feihtnpqtn
    421 egmlsvvkpl dyeisafhtl likvenedpl vpdvsygpss tatvhitvld vnegpvfypd
    481 pmmvtrqedl svgsvlltvn atdpdslqhq tirysvykdp agwlninpin gtvdttavld
    541 respfvdnsv ytalflaids gnppatgtgt llitledvnd napfiyptva evcddaknls
    601 vvilgasdkd lhpntdpfkf eihkqavpdk vwkiskinnt halvsllqnl nkanynlpim
    661 vtdsgkppmt nitdlrvqvc scrnskvdcn aagalrfslp svlllslfsl acl
  • p-16, in certain exemplary embodiments is encoded by NCBI accession No. CAB58124 and is shown in (SEQ ID NO:2) below:
  • 1 gshsmryfft svsrpgrgep rfiavgyvdd tqfvrfdsda asqrmeprap wieqegpeyw
    61 dgetrkvkah sqtdrvdlgt lrgyynqsea gshtiqmmyg cdvgpdgrll rgyqqdaydg
    121 kdyialnedl rswtaadmaa qitqrkweaa rvaeqlrayl egtcvewlrr ylengketlq
    181 rt
  • APC, in certain exemplary embodiments is encoded by NCBI accession No. NP—000029 and is shown in (SEQ ID NO:3) below:
  • 1 maaasydqll kqvealkmen snlrqeledn snhltklete asnmkevlkq lqgsiedeam
    61 assgqidlle rlkelnldss nfpgvklrsk mslrsygsre gsvssrsgec spvpmgsfpr
    121 rgfvngsres tgyleeleke rsllladldk eekekdwyya qlqnltkrid slpltenfsl
    181 qtdmtrrqle yearqirvam eeqlgtcqdm ekraqrriar iqqiekdilr irqllqsqat
    241 eaerssqnkh etgshdaerq negqgvgein matsgngqgs ttrmdhetas vlssssthsa
    301 prrltshlgt kvemvyslls mlgthdkddm srtllamsss qdscismrqs gclplliqll
    361 hgndkdsvll gnsrgskear arasaalhni ihsqpddkrg rreirvlhll eqiraycetc
    421 wewqeahepg mdqdknpmpa pvehqicpav cvlmklsfde ehrhamnelg glqaiaellq
    481 vdcemygltn dhysitlrry agmaltnltf gdvankatlc smkgcmralv aqlksesedl
    541 qqviasvlrn lswradvnsk ktlrevgsvk almecalevk kestlksvls alwnlsahct
    601 enkadicavd galaflvgtl tyrsqtntla iiesgggilr nvssliatne dhrqilrenn
    661 clqtllqhlk shsltivsna cgtlwnlsar npkdqealwd mgaysmlknl ihskhkmiam
    721 gsaaalrnlm anrpakykda nimspgsslp slhvrkqkal eaeldaqhls etfdnidnls
    781 pkashrskqr hkqslygdyv fdtnrhddnr sdnfntgnmt vlspylnttv lpsssssrgs
    841 ldssrsekdr slerergigl gnyhpatenp gtsskrglqi sttaaqiakv meevsaihts
    901 qedrssgstt elhcvtdern alrrssaaht hsntynftks ensnrtcsmp yakleykrss
    961 ndslnsysss dgygkrgqmk psiesysedd eskfcsygqy padlahkihs anhmddndge
    1021 ldtpinyslk ysdeqlnsgr qspsqnerwa rpkhiiedei kqseqrqsrn qsttypvyte
    1081 stddkhlkfq phfgqqecvs pyrsrgangs etnrvgsnhg inqnvsqslcqeddyeddkp
    1141 tnyserysee eqheeeerpt nysikyneek rhvdqpidys lkyatdipss qkqsfsfsks
    1201 ssgqsskteh mssssentst pssnakrqnq lhpssaqsrs gqpqkaatck vssinqetiq
    1261 tycvedtpic fsresslssl ssaedeigcn qttqeadsan tlqiaeikek igtrsaedpv
    1321 sevpavsqhp rtkssrlqgs slssesarhk avefssgaks psksgaqtpk sppehyvqet
    1381 plmfsrctsv ssldsfesrs iassvqsepc sgmvsgiisp sdlpdspgqt mppsrsktpp
    1441 pppqtaqtkr evpknkapta ekresgpkqa avnaavqrvq vlpdadtllh fatestpdgf
    1501 scssslsals ldepfiqkdv elrimppvqe ndngnetese qpkesnenqe keaektidse
    1561 kdllddsddd dieileecii samptkssrk akkpaqtask lpppvarkps qlpvykllps
    1621 qnrlqpqkhv sftpgddmpr vycvegtpin fstatslsdl tiesppnela agegvrggaq
    1681 sgefekrdti ptegrstdea qggktssvti pelddnkaee gdilaecins ampkgkshkp
    1741 frvkkimdqv qqasasssap nknqldgkkk kptspvkpip qnteyrtrvrknadsknnln
    1801 aervfsdnkd skkqnlknns kvfndklpnn edrvrgsfaf dsphhytpie gtpycfsrnd
    1861 slssldfddd dvdlsrekae lrkakenkes eakvtshtel tsnqqsankt qaiakqpinr
    1921 gqpkpilqkq stfpqsskdi pdrgaatdek lqnfaientp vcfshnssls slsdidqenn
    1981 nkenepiket eppdsqgeps kpqasgyapk sfhvedtpvc fsrnsslssl sidseddllq
    2041 ecissampkk kkpsrlkgdn ekhsprnmgg ilgedltldl kdiqrpdseh glspdsenfd
    2101 wkaiqegans ivsslhqaaa aaclsrqass dsdsilslks gislgspfhl tpdqeekpft
    2161 snkgprilkp gekstletkk ieseskgikg gkkvykslit gkvrsnseis gqmkqplqan
    2221 mpsisrgrtm ihipgvrnss sstspvskkg pplktpasks psegqtatts prgakpsvks
    2281 elspvarqts qiggsskaps rsgsrdstps rpaqqplsrp iqspgrnsis pgrngisppn
    2341 klsqlprtss pstastkssg sgkmsytspg rqmsqqnltk qtglsknass iprsesaskg
    2401 lnqmnngnga nkkvelsrms stkssgsesd rserpvlvrq stfikeapsp tlrrkleesa
    2461 sfeslspssr pasptrsqaq tpvlspslpd mslsthssvq aggwrklppn lsptieyndg
    2521 rpakrhdiar shsespsrlp inrsgtwkre hskhssslpr vstwrrtgss ssilsasses
    2581 sekaksedek hvnsisgtkq skenqvsakg twrkikenef sptnstsqtv ssgatngaes
    2641 ktliyqmapa vsktedvwvr iedcpinnpr sgrsptgntp pvidsvseka npnikdskdn
    2701 qakqnvgngs vpmrtvglen rlnsfiqvda pdqkgteikp gqnnpvpvse tnessivert
    2761 pfsssssskh sspsgtvaar vtpfnynpsp rkssadstsa rpsqiptpvn nntkkrdskt
    2821 dstessgtqs pkrhsgsylv tsv
  • RASSF1A, in certain exemplary embodiments is encoded by NCBI accession No. NP—009113 and is shown in (SEQ ID NO:4) below:
  • 1 msgepeliel relapagrag kgrtrleran alriargtac nptrqlvpgr ghrfqpagpa
    61 thtwcdlcgd fiwgvvrkgl qcahckftch yrcralvcld ccgprdlgwe paverdtnvd
    121 epvewetpdl sqaeieqkik eynaqinsnl fmslnkdgsy tgfikvqlkl vrpvsvpssk
    181 kppslqdarr gpgrgtsvrr rtsfylpkda vkhlhvlsrt rarevieall rkflvvddpr
    241 kfalferaer hgqvylrkll ddeqplrlrl lagpsdkals fvlkendsge vnwdafsmpe
    301 lhnflrilqr eeeehlrqil qkysycrqki qealhacplg
  • MGMT, in certain exemplary embodiments is encoded by NCBI accession No. AAH00824 and is shown in (SEQ ID NO:5) below:
  • 1 mdkdcemkrt tldsplgkle lsgceqglhe ikllgkgtsa adavevpapa avlggpeplm
    61 qctawlnayf hqpeaieefp vpalhhpvfq qesftrqvlw kllkvvkfge visyqqlaal
    121 agnpkaarav ggamrgnpvp ilipchrvvc ssgavgnysg glavkewllaheghrlgkpg
    181 lggssglaga wlkgagatsg sppagrn
  • DAPK, in certain exemplary embodiments is encoded by NCBI accession No. NP—004929 and is shown in (SEQ ID NO:6) below:
  • 1 mtvfrqenvd dyydtgeelg sgqfavvkkc rekstglqya akfikkrrtk ssrrgvsred
    61 ierevsilke iqhpnvitlh evyenktdvi lilelvagge lfdflaekes lteeeatefl
    121 kqilngvyyl hslqiahfdl kpenimlldr nvpkprikii dfglahkidf gnefknifgt
    181 pefvapeivn yeplgleadm wsigvityil lsgaspflgd tkqetlanvs avnyefedey
    241 fsntsalakd firrllvkdp kkrmtiqdsl qhpwikpkdt qqalsrkasa vnmekfkkfa
    301 arkkwkqsvr lislcqrlsr sflsrsnmsv arsddtldee dsfvmkaiih ainddnvpgl
    361 qhllgslsny dvnqpnkhgt pplliaagcg niqilqllik rgsridvqdk ggsnavywaa
    421 rhghvdtlkf lsenkcpldv kdksgemalh vaaryghadv aqllcsfgsn pniqdkeeet
    481 plhcaawhgy ysvakalcea gcnvniknre getplltasa rgyhdivecl aehgadlnac
    541 dkdghialhl avrrcqmevi ktllsqgcfv dyqdrhgntp lhvackdgnm pivvalcean
    601 cnldisnkyg rtplhlaann gildvvrylc lmgasvealt tdgktaedla rseqhehvag
    661 llarlrkdth rglfiqqlrp tqnlqprikl klfghsgsgk ttlveslkcg llrsffrrrr
    721 prlsstnssr fppsplaskp tvsvsinnly pgcenvsvrs rsmmfepglt kgmlevfvap
    781 thhphcsadd qstkaidiqn aylngvgdfs vwefsgnpvy fccydyfaan dptsihvvvf
    841 sleepyeiql nqvifwlsfl kslvpveepi afggklknpl qvvlvathad imnvprpagg
    901 efgydkdtsl lkeirnrfgn dlhisnklfv ldagasgskd mkvlrnhlqe irsqivsvcp
    961 pmthlcekii stlpswrkln gpnqlmslqq fvydvqdqln plaseedlrr iaqqlhstge
    1021 inimqsetvq dvllldprwl ctnvlgklls vetpralhhy rgrytvediq rlvpdsdvee
    1081 llqildamdi cardlssgtm vdvpaliktd nlhrswadee devmvyggvr ivpvehltpf
    1141 pcgifhkvqv nlcrwihqqs tegdadirlw vngcklanrg aellvllvnh gqgievqvrg
    1201 letekikccl lldsvcstie nvmattlpgl ltvkhylspq qlrehhepvm iyqprdffra
    1261 qtlketsltn tmggykesfs simcfgchdv ysqaslgmdi hasdlnlltr rklsrlldpp
    1321 dplgkdwcll amnlglpdlv akyntsngap kdflpsplha llrewttype stvgtlmskl
    1381 relgrrdaad fllkassvfk inldgngqea yasscnsgts ynsissvvsr
  • ASC, in certain exemplary embodiments is encoded by NCBI accession No. NP—037390 and is shown in (SEQ ID NO:7) below:
  • 1 mgrardaild alenltaeel kkfklkllsv plregygrip rgallsmdal dltdklvsfy
    61 letygaelta nvlrdmglqe magqlqaath qgsgaapagi qappqsaakp glhfidqhra
    121 aliarvtnve wlldalygkv ltdeqyqavr aeptnpskmr klfsftpawn wtckdlllqa
    181 lresqsylve dlers
  • In other embodiments of the above aspects, hypermethylation of at least one of the genes is detected. In still other embodiments of the above aspects, hypermethylation of at least two of the genes is detected.
  • In other aspects, the invention features methods for identifying micrometastases in a subject comprising detecting nucleic acid hypermethylation of at least one or more genes in a sample comprising tumor and lymph nodes, wherein the sample genes are selected from the group consisting of H-cadherin, p16, APC, RASSF1A, MGMT, DAPK, and ASC, and wherein detecting nucleic acid methylation identifies micrometastases.
  • In a preferred embodiment, hypermethylation of at least two of the genes is detected. In another embodiment, at least two of the genes are selected from p-16 and H-cadherin, H-cadherin and APC, APC and p16, or RASSf1A and p16.
  • In another further embodiment, the detection of metastases is used to detect or diagnose a proliferative disease.
  • In certain embodiments, the detection or diagnosis is performed after surgery or therapy to treat a proliferative disease. In other certain embodiments, the detection is used to predict the recurrence of a proliferative disease. In other certain embodiments, the detection is used to stage a proliferative disease. In still other certain embodiments, the detection is further used to determine a course of treatment for a subject.
  • In other aspects, the invention features a method for detecting or diagnosing a proliferative disease in a subject comprising detecting nucleic acid hypermethylation of one or more genes in one or more samples, wherein detecting nucleic acid hypermethylation is used to detect or diagnose a proliferative disease.
  • In still other aspects, the invention features a method for predicting the recurrence of a proliferative disease in a subject comprising detecting nucleic acid hypermethylation of one or more genes wherein detecting nucleic acid hypermethylation of one or more genes is a predictor of the recurrence of a proliferative disease.
  • In one embodiment, hypermethylation of one or more genes is detected in tumor or lymph nodes.
  • In a related embodiment, detection of hypermethylation of one or more genes in lymph nodes is predictive of aggressive disease recurrence.
  • In another aspect, the invention features a method for staging or re-staging a proliferative disease in a subject comprising detecting nucleic acid hypermethylation of one or more genes wherein detecting nucleic acid hypermethylation is used for staging or re-staging a proliferative disease.
  • In a related embodiment, the stage of proliferative disease is predictive of disease recurrence. In a further embodiment, the stage of proliferative disease determines course of treatment.
  • In another aspect, the invention features a method for determining the prognosis of a subject suffering from a proliferative disease comprising detecting nucleic acid hypermethylation of one or more genes wherein the detection of nucleic acid hypermethylation is used for determining the prognosis of a subject suffering from a proliferative disease.
  • In a related embodiment, the prognosis determines course of treatment.
  • In an embodiment of any of the above-mentioned aspects, the subject is a human.
  • In another embodiment of any of the above-mentioned aspects, the method is performed prior to therapeutic intervention for the disease.
  • In another embodiment of any of the above-mentioned aspects, the method is performed after therapeutic intervention for the disease. In a related embodiment, the therapeutic intervention is selected from treatment with an agent or surgery. In another related embodiment, hypermethylation is detected in CpG islands of the one or more genes. In a further related embodiment, hypermethylation is detected in CpG islands.
  • In another aspect, the invention features methods for detecting or diagnosing a proliferative disease in a subject comprising extracting nucleic acid from one or more cell or tissue samples, detecting nucleic acid hypermethylation of one or more genes in the sample; and identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes indicates a proliferative disease.
  • In a further aspect, the invention features methods for predicting the recurrence of a proliferative disease in a subject comprising extracting nucleic acid from one or more cell or tissue samples, detecting nucleic acid hypermethylation of one or more genes in the sample; and identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes is indicative of the recurrence of a proliferative disease.
  • In a further aspect, the invention features methods for staging or re-staging a proliferative disease in a subject comprising extracting nucleic acid from one or more cell or tissue samples, detecting nucleic acid hypermethylation of one or more genes in the sample; and identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes is used for staging or re-staging of a proliferative disease.
  • In one embodiment of the above-metioned aspects, the tissue samples are selected from tumor, lymph node, bone marrow or blood or a combination thereof.
  • In another embodiment of the above-metioned aspects, the method determines the course of disease treatment.
  • In still another embodiment of the above-metioned aspects, the method is performed prior to therapeutic intervention for the disease.
  • In still another embodiment of the above-metioned aspects, the method is performed after therapeutic intervention for the disease.
  • In a further embodiment, the therapeutic intervention is selected from treatment with an agent or surgery.
  • In another aspect, the invention features methods of treating a subject having or at risk for having a proliferative disease comprising identifying nucleic acid hypermethylation of one or more genes, where nucleic acid hypermethylation indicates having or a risk for having a proliferative disease, and administering to the subject a therapeutically effective amount of a demethylating agent, thereby treating a subject having or at risk for having a proliferative disease.
  • In one particular embodiment, the method is used in combination with one or more chemotherapeutic agents.
  • In another particular embodiment of the above-mentioned aspects, the method further comprises comparing the nucleic acid hypermethylation of one or more genes in the sample with comparable samples obtained from a normal subject.
  • In a further embodiment of the above-mentioned aspects, detecting nucleic acid hypermethylation of one or more genes indicates the presence of metastases.
  • In a particular embodiment, the metastases are micrometastases.
  • In another particular embodiment of any one of the above-mentioned aspects, the proliferative disease is a neoplasia. In a preferred embodiment, the neoplasia is cancer. In another preferred embodiment, the cancer is a solid tumor. In a further embodiment, the cancer is selected from the group consisting of lung cancer, pancreatic cancer, esophageal cancer, head and neck cancer, stomach cancer, liver cancer, prostate cancer, gastrointestinal cancer, ovarian cancer, and uterine cancer.
  • In another particular embodiment of the above-mentioned aspects, the cells or tissues are selected from the group consisting of tumor, lymph nodes, bone marrow or blood. In a related embodiment, the cells or tissues are from a tumor or the lymph nodes. In a further embodiment, the lymph node is a N1 lymph node or a mediastinal lymph node.
  • In another aspect, the invention features a method of identifying an agent that de-methylates hypermethylated nucleic acid comprising identifying one or more cell or tissue samples with hypermethylated nucleic acid, extracting the hypermethylated nucleic acid, contacting the nucleic acid with one or more nucleic acid de-methylating candidate agents and a control agent, identifying the nucleic acid hypermethylation state, wherein nucleic acid de-methylation of genes in the sample by the candidate agent compared to the control indicates a demethylating agent, and thereby identifying an agent that de-methylates hypermethylated nucleic acid.
  • In one embodiment of any of the above-mentioned aspects, the one or more genes are selected from the group consisting of genes involved in tumor suppression, DNA repair, anti-proliferation, apoptosis, ras signaling, adhesion, differentiation, development, and cell cycle regulation.
  • In another embodiment of any of the above-mentioned aspects, the one or more genes are selected from a panel consisting of (1) genes involved in tumor suppression and cell adhesion, (2) genes involved in cell cycle regulation and adhesion, (3) genes involved in tumor suppression and cell cycle regulation, and (4) genes involved in ras signaling and cell cycle control.
  • In still another embodiment of any of the above-mentioned aspects, the one or more genes comprise one or more CpG islands.
  • In a related embodiment, the genes are selected from the group consisting of p-16, H-cadherin, APC, RASSF1A, MGMT, DAPK, and ASC.
  • In another related embodiment, the hypermethylation of at least one of the genes is detected. In a further related embodiment, the hypermethylation of at least two of the genes is detected. In still another related embodiment, the two genes are selected from p-16 and H-cadherin, H-cadherin and APC, APC and p16, or RASSf1A and p16.
  • In another embodiment of any of the above-mentioned aspects, the detection of nucleic acid methylation is by a quantitative method.
  • In another embodiment of any of the above-mentioned aspects, the detection of nucleic acid methylation is carried out by polymerase chain reaction (PCR) analysis. In a related embodiment, the PCR is methylation specific PCR (MSP).
  • In a particular embodiment, the method of detecting nucleic acid methylation is performed as a high-throughput method.
  • In another particular embodiment, the method is used in combination with the detection of other epigenetic markers. In a particular related embodiment, the other epigenetic markers are plasma or tumor epigenetic markers.
  • In an embodiment of the above-described aspects, hypermethylation is detected in CpG islands of the one or more genes. In a further embodiment of the above-described aspects, hypermethylation is detected in CpG islands of the promoter region.
  • In other aspects, the invention features kits for identifying the nucleic acid hypermethylation state of one or more genes comprising gene specific primers for use in polymerase chain reaction (PCR), and instructions for use.
  • In still other aspects, the invention features kits for detecting metastases by detecting nucleic acid hypermethylation of one or more genes, the kit comprising gene specific primers for use in polymerase chain reaction (PCR), and instructions for use.
  • In one embodiment, the metastases are micrometastases.
  • In another embodiment, the PCR is methylation specific PCR (MSP).
  • In still another embodiment, the one or more genes are selected from the group consisting of genes involved in tumor suppression, DNA repair, anti-proliferation, apotosis, ras signaling, adhesion, differentiation, development, and cell cycle regulation.
  • In another embodiment, the one or more genes are selected from a panel consisting of (1) genes involved in tumor suppression and cell adhesion, (2) genes involved in cell cycle regulation and adhesion, (3) genes involved in tumor suppression and cell cycle regulation, and (4) genes involved in ras signaling and cell cycle control.
  • In a related embodiment, the one or more genes comprise one or more CpG islands. In a further related embodiment, the CpG islands are in the promoter region. In another related embodiment, the genes are selected from the group consisting of p-16, H-cadherin, APC, RASSF1A, MGMT, DAPK, and ASC
  • In another embodiment, the hypermethylation of at least one of the genes is detected. In still another embodiment, the hypermethylation of at least two of the genes is detected. In still another further embodiment, the two genes are selected from p-16 and H-cadherin, H-cadherin and APC, APC and p16, or RASSf1A and p16.
  • Other aspects of the invention are described infra.
    • BRIEF DESCRIPTION OF THE FIGURES
  • FIG. 1 shows the results of multivariate logistic regression analysis performed using the four genes that exhibited the largest univariate distribution differences in methylation: p16, H-cadherin, APC, and RASSF1A.
  • FIG. 2 (A-L) are graphs showing Kaplan-Meier estimates of recurrence-free survival of pathologic Stage 1 lung cancer patients at the Johns Hopkins Hospital, according to number of methylated genes in a 4-gene panel at time of surgical resection.
  • FIG. 3 shows Methylation Specific PCR for the H-cadherin gene. For each sample, the presence of a visible PCR product in Lanes marked U indicates the presence of an unmethylated promoter region amplified and serves as a control for sample preparation; the presence of product in Lanes M indicates a methylated gene promoter and was scored as positive for methylation. * represents the molecular weight marker.
    •  DEFINITIONS
  • Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person skilled in the art to which this invention belongs. The following references provide one of skill with a general definition of many of the terms used in this invention: Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge Dictionary of Science and Technology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer Verlag (1991); and Hale & Marham, The Harper Collins Dictionary of Biology (1991). As used herein, the following terms have the meanings ascribed to them unless specified otherwise.
  • In this disclosure, “comprises,” “comprising,” “containing” and “having” and the like can have the meaning ascribed to them in U.S. Patent law and can mean “includes,” “including,” and the like; “consisting essentially of” or “consists essentially” likewise has the meaning ascribed in U.S. Patent law and the term is open-ended, allowing for the presence of more than that which is recited so long as basic or novel characteristics of that which is recited is not changed by the presence of more than that which is recited, but excludes prior art embodiments.
  • By “control” is meant a standard or reference condition.
  • The phrase “in combination with” is intended to refer to all forms of administration that provide a de-methylating agent, or the methods of the instant invention (e.g. methods of detection of hypermethylation) together with a second agent, such as a chemotherapeutic agent, or a de-methylating agent, where the two are administered concurrently or sequentially in any order.
  • The term “agent” as used herein is meant to refer to a polypeptide, polynucleotide, or fragment, or analog thereof, small molecule, or other biologically active molecule.
  • The term “CpG island” refers to a sequence of nucleic acid with an increased density relative to other nucleic acid regions of the dinucleotide CpG.
  • The term “epigenetic marker” or “epigenetic change” as used herein is meant to refer to a change in the DNA sequences or gene expression by a process or processes that do not change the DNA coding sequence itself. In an exemplary embodiment, methylation is an epigenetic marker.
  • The term “hypermethylation” as used herein refers to the presence of methylated alleles in one or more nucleic acids. In preferred embodiments, hypermethylation is detected using methylation specific polymerase chain reaction (MSP).
  • The term “metastases” is meant to refer to the spread of a malignant tumor from its sight of origin. Cancer cells may metastasize through the bloodstream, through the lymphatic system, across body cavities, or any combination thereof. A metastatic tumor can arise from a multitude of primary tumor types, including but not limited to lung, breast, thyroid, head and neck, brain, lymphoid, gastrointestinal (mouth, esophagus, stomach, small intestine, colon, rectum), genito-urinary tract (uterus, ovary, cervix, bladder, testicle, penis, prostate), kidney, pancreas, liver, bone, muscle or skin.
  • The term “micrometastases” is meant to refer to a metastasis that cannot be detected by routine histological evaluation, for example by Hematoxylin and Eosin (H & E) staining and microscopic assessment.
  • The term “neoplasm” or “neoplasia” as used herein refers to inappropriately high levels of cell division, inappropriately low levels of apoptosis, or both. A neoplasm creates an unstructured mass (a tumor), which can be either benign or malignant. For example, cancer is a neoplasia. Examples of cancers include, without limitation, leukemias (e.g., acute leukemia, acute lymphocytic leukemia, acute myelocytic leukemia, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monocytic leukemia, acute erythroleukemia, chronic leukemia, chronic myelocytic leukemia, chronic lymphocytic leukemia), polycythemia vera, lymphoma (Hodgkin's disease, non-Hodgkin's disease), Waldenstrom's macroglobulinemia, heavy chain disease, and solid tumors such as sarcomas and carcinomas (e.g., fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, nile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilm's tumor, cervical cancer, uterine cancer, testicular cancer, lung carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodenroglioma, schwannoma, meningioma, melanoma, neuroblastoma, and retinoblastoma). Lymphoproliferative disorders are also considered to be proliferative diseases.
  • The phrase “nucleic acid” as used herein refers to an oligonucleotide, nucleotide, polynucleotide, or to a fragment of any of these, to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent a sense or antisense strand, peptide nucleic acid (PNA), or to any DNA-like or RNA-like material, natural or synthetic in origin. As will be understood by those of skill in the art, when the nucleic acid is RNA, the deoxynucleotides A, G, C, and T are replaced by ribonucleotides A, G, C, and U, respectively.
  • The term “proliferative disorder” as used herein refers to an abnormal growth of cells. A cell proliferative disorder as described herein may be a neoplasm.
  • The term “gene” refers to a segment of deoxyribonucleic acid that encodes a polypeptide including the upstream and downstream regulatory sequences. Specifically, the term gene includes the promoter region upstream of the gene.
  • The term “promoter” or “promoter region” refers to a minimal sequence sufficient to direct transcription or to render promoter-dependent gene expression that is controllable for cell-type specific, tissue-specific, or is inducible by external signals or agents. Promoters may be located in the 5′ or 3′ regions of the gene. Promoter regions, in whole or in part, of a number of nucleic acids can be examined for sites of CpG-island methylation.
  • The term “sample” as used herein refers to any biological or chemical mixture for use in the method of the invention. The sample can be a biological sample. The biological samples are generally derived from a patient, preferably as a bodily fluid (such as tumor tissue, lymph node, sputum, blood, bone marrow, cerebrospinal fluid, phlegm, saliva, or urine) or cell lysate. The cell lysate can be prepared from a tissue sample (e.g. a tissue sample obtained by biopsy), for example, a tissue sample (e.g. a tissue sample obtained by biopsy), blood, cerebrospinal fluid, phlegm, saliva, urine, or the sample can be cell lysate.
  • The term “stage” or “staging” as used herein is meant to refer to the extent or progression of proliferative disease, e.g. cancer, in a subject. Staging can be “clinical” and is according to the “stage classification” corresponding to the TNM classification (“Rinsho, Byori, Genpatsusei Kangan Toriatsukaikiyaku (Clinical and Pathological Codes for Handling Primary Liver Cancer)”: 22p. Nihon Kangangaku Kenkyukai (Liver Cancer Study Group of Japan) edition (3rd revised edition), Kanehara Shuppan, 1992). Staging in certain embodiments can refer to “molecular staging” as defined by nucleic acid hypermethylation of one or more genes in one or more samples. In preferred embodiments of the invention, the “molecular stage” stage of a cancer is determined by detection of nucleic acid hypermethylation of one or more genes in a sample from the lymph nodes. The term “subject” as used herein is meant to include vertebrates, preferably a mammal. Mammals include, but are not limited to, humans.
  • The term “tumor” as used herein is intended to include an abnormal mass or growth of cells or tissue. A tumor can be benign or malignant.
    • DETAILED DESCRIPTION OF THE INVENTION
  • The invention is based upon the discovery that the hypermethylation of certain genes, including promoter regions, can serve as prognostic and diagnostic markers for cellular proliferative disorders. This is the first time that promoter hypermethylation of certain genes, such as p16, H-cadherin, RASSf1A and APC, in the lymph nodes has been associated with the ability to predict recurrence and aggressiveness of certain cancers, such as lung cancer.
    • I. Detection of Methylation
  • DNA methylases transfer methyl groups from the universal methyl donor S-adenosyl methionine to specific sites on the DNA. Several biological functions have been attributed to the methylated bases in DNA. The most established biological function for methylated DNA is the protection of DNA from digestion by cognate restriction enzymes. The restriction modification phenomenon has, so far, been observed only in bacteria. Mammalian cells, however, possess a different methylase that exclusively methylates cytosine residues that are 5′ neighbors of guanine (CpG). This modification of cytosine residues has important regulatory effects on gene expression, especially when involving CpG rich areas, known as CpG islands, located in the promoter regions of many genes.
  • Methylation has been shown by several lines of evidence to play a role in gene activity, cell differentiation, tumorigenesis, X-chromosome inactivation, genomic imprinting and other major biological processes (Razin, A., H., and Riggs, R. D. eds. in DNA Methylation Biochemistry and Biological Significance, Springer-Verlag, New York, 1984). In eukaryotic cells, methylation of cytosine residues that are immediately 5′ to a guanosine, occurs predominantly in CG poor regions (Bird, A., Nature, 321:209, 1986). In contrast, CpG islands remain unmethylated in normal cells, except during X-chromosome inactivation and parental specific imprinting (Li, et al., Nature, 366:362, 1993) where methylation of 5′ regulatory regions can lead to transcriptional repression. De novo methylation of the Rb gene has been demonstrated in a small fraction of retinoblastomas (Sakai, et al., Am. J. Hum. Genet., 48:880, 1991), and recently, a more detailed analysis of the VHL gene showed aberrant methylation in a subset of sporadic renal cell carcinomas (Herman, et al., Proc. Natl. Acad. Sci., U.S.A., 91:9700, 1994). Expression of a tumor suppressor gene can also be abolished by de novo DNA methylation of a normally unmethylated CpG island (Issa, et al., Nature Genet., 7:536, 1994; Herman, et al., supra; Merlo, et al., Nature Med., 1:686, 1995; Herman, et al., Cancer Res., 56:722, 1996; Graff, et al., Cancer Res., 55:5195, 1995; Herman, et al., Cancer Res., 55:4525, 1995).
  • In higher order eukaryotes DNA is methylated only at cytosines located 5′ to guanosine in the CpG dinucleotide. This modification has important regulatory effects on gene expression, especially when involving CpG rich areas, known as CpG islands, located in the promoter regions of many genes. While almost all gene-associated islands are protected from methylation on autosomal chromosomes, extensive methylation of CpG islands has been associated with transcriptional inactivation of selected imprinted genes and genes on the inactive X-chromosome of females. Aberrant methylation of normally unmethylated CpG islands has been described as a frequent event in immortalized and transformed cells, and has been associated with transcriptional inactivation of defined tumor suppressor genes in human cancers.
  • Any method that is sufficient to detect hypermethylation, e.g. a method that can detect methylation of nucleotides at levels as low as 0.1%, is a suitable for use in the methods of the invention. A number of different methods can be used to detect hypermethylation.
  • The ability to monitor the real-time progress of the PCR changes the way one approaches PCR-based quantification of DNA and RNA. Reactions are characterized by the point in time during cycling when amplification of a PCR product is first detected rather than the amount of PCR product accumulated after a fixed number of cycles. The higher the starting copy number of the nucleic acid target, the sooner a significant increase in fluorescence is observed. An amplification plot is the plot of fluorescence signal versus cycle number. In the initial cycles of PCR, there is little change in fluorescence signal. This defines the baseline for the amplification plot. An increase in fluorescence above the baseline indicates the detection of accumulated PCR product. A fixed fluorescence threshold can be set above the baseline. The parameter CT (threshold cycle) is defined as the fractional cycle number at which the fluorescence passes the fixed threshold. For example, the PCR cycle number at which fluorescence reaches a threshold value of 10 times the standard deviation of baseline emission may be used as CT and it is inversely proportional to the starting amount of target cDNA. A plot of the log of initial target copy number for a set of standards versus CT is a straight line. Quantification of the amount of target in unknown samples is accomplished by measuring CT and using the standard curve to determine starting copy number.
  • The entire process of calculating CTS, preparing a standard curve, and determining starting copy number for unknowns can be performed by software, for example that of the 7700 system or 7900 system of Applied Biosystems. Real-time PCR requires an instrumentation platform that consists of a thermal cycler, computer, optics for fluorescence excitation and emission collection, and data acquisition and analysis software. These machines, available from several manufacturers, differ in sample capacity (some are 96-well standard format, others process fewer samples or require specialized glass capillary tubes), method of excitation (some use lasers, others broad spectrum light sources with tunable filters), and overall sensitivity. There are also platform-specific differences in how the software processes data. Real-time PCR machines are available at core facilities or labs that have the need for high throughput quantitative analysis.
  • Briefly, in the Q-PCR method the number of target gene copies can be extrapolated from a standard curve equation using the absolute quantitation method. For each gene, cDNA from a positive control is first generated from RNA by the reverse transcription reaction. Using about 1 μl of this cDNA, the gene under investigation is amplified using the primers by means of a standard PCR reaction. The amount of amplicon obtained is then quantified by spectrophotometry and the number of copies calculated on the basis of the molecular weight of each individual gene amplicon. Serial dilutions of this amplicon are tested with the Q-PCR assay to generate the gene specific standard curve. Optimal standard curves are based on PCR amplification efficiency from 90 to 100% (100% meaning that the amount of template is doubled after each cycle), as demonstrated by the slope of the standard curve equation. Linear regression analysis of all standard curves should show a high correlation (R2 coefficient .gtoreq.0.98). Genomic DNA can be similarly quantified.
  • When measuring transcripts of a target gene, the starting material, transcripts of a housekeeping gene are quantified as an endogenous control. Beta-actin is one of the most used nonspecific housekeeping genes. For each experimental sample, the value of both the target and the housekeeping gene are extrapolated from the respective standard curve. The target value is then divided by the endogenous reference value to obtain a normalized target value independent of the amount of starting material.
  • The above-described quantitative real-time PCR methodology has been adapted to perform quantitative methylation-specific PCR (QM-MSP) by utilizing the external primers pairs in round one (multiplex) PCR and internal primer pairs in round two (real time MSP) PCR. Thus each set of genes has one pair of external primers and two sets of three internal primers/probe (internal sets are specific for unmethylated or methylated DNA). The external primer pairs can co-amplify a cocktail of genes, each pair selectively hybridizing to a member of the panel of genes being investigated using the invention method. The method of methylation-specific PCR (QM-MSP) has been described in US Patent Application 20050239101, incorporated by reference in its entirety herein.
  • Hypermethylation can be detected using two-stage, or “nested” PCR, for example as described in U.S. Pat. No. 7,214,485, incorporated by reference in its entirety herein. For example, two-stage, or “nested” polymerase chain reaction method is disclosed for detecting methylated DNA sequences at sufficiently high levels of sensitivity to permit cancer screening in biological fluid samples, such as sputum, obtained non-invasively.
  • A method for assessment of the methylation status of any group of CpG sites within a CpG island, independent of the use of methylation-sensitive restriction enzymes, is described in U.S. Pat. No. 6,017,704 incorporated by reference in its entirety herein and described briefly as follows. This method employs primers that specific for the bisulfite reaction such that the PCR reaction itself is used to distinguish between the chemically modified methylated and unmethylated DNA, which adds an improved sensitivity of methylation detection. Unlike previous genomic sequencing methods for methylation identification which utilizes amplification primers which are specifically designed to avoid the CpG sequences, MSP primers themselves are specifically designed to recognize CpG sites to take advantage of the differences in methylation to amplify specific products to be identified by the invention assay. The methods of MSP include modification of DNA by sodium bisulfite or a comparable agent that converts all unmethylated but not methylated cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. This method of “methylation specific PCR” or MSP, requires only small amounts of DNA, is sensitive to 0.1% of methylated alleles of a given CpG island locus, and can be performed on DNA extracted from paraffin-embedded samples, for example. In addition, MSP eliminates the false positive results inherent to previous PCR-based approaches which relied on differential restriction enzyme cleavage to distinguish methylated from unmethylated DNA.
  • MSP provides significant advantages over previous PCR and other methods used for assaying methylation. MSP is markedly more sensitive than Southern analyses, facilitating detection of low numbers of methylated alleles and the study of DNA from small samples. MSP allows the study of paraffin-embedded materials, which could not previously be analyzed by Southern analysis. MSP also allows examination of all CpG sites, not just those within sequences recognized by methylation-sensitive restriction enzymes. This markedly increases the number of such sites which can be assessed and will allow rapid, fine mapping of methylation patterns throughout CpG rich regions. MSP also eliminates the frequent false positive results due to partial digestion of methylation-sensitive enzymes inherent in previous PCR methods for detecting methylation. Furthermore, with MSP, simultaneous detection of unmethylated and methylated products in a single sample confirms the integrity of DNA as a template for PCR and allows a semi-quantitative assessment of allele types which correlates with results of Southern analysis. Finally, the ability to validate the amplified product by differential restriction patterns is an additional advantage.
  • MSP can provide similar information as genomic sequencing, but can be performed with some advantages as follows. MSP is simpler and requires less time than genomic sequencing, with a typical PCR and gel analysis taking 4-6 hours. In contrast, genomic sequencing, amplification, cloning, and subsequent sequencing may take days. MSP also avoids the use of expensive sequencing reagents and the use of radioactivity. Both of these factors make MSP better suited for the analysis of large numbers of samples. The use of PCR as the step to distinguish methylated from unmethylated DNA in MSP allows for significant increase in the sensitivity of methylation detection. For example, if cloning is not used prior to genomic sequencing of the DNA, less than 10% methylated DNA in a background of unmethylated DNA cannot be seen (Myohanen, et al., supra). The use of PCR and cloning does allow sensitive detection of methylation patterns in very small amounts of DNA by genomic sequencing (Frommer, et al., Proc. Natl. Acad. Sci. USA, 89:1827, 1992; Clark, et al., Nucleic Acids Research, 22:2990, 1994). However, this means in practice that it would require sequencing analysis of 10 clones to detect 10% methylation, 100 clones to detect 1% methylation, and to reach the level of sensitivity we have demonstrated with MSP (1:1000), one would have to sequence 1000 individual clones.
  • “Multiplex methylation-specific PCR” is a unique version of methylation-specific PCR. Methylation-specific PCR is described in U.S. Pat. Nos. 5,786,146; 6,200,756; 6,017,704 and 6,265,171, each of which is incorporated herein by reference in its entirety. Multiplex methylation-specific PCR utilizes MSP primers for a multiplicity of markers, for example three or more different markers, in a two-stage nested PCR amplification reaction. The primers used in the first PCR reaction are selected to amplify a larger portion of the target sequence than the primers of the second PCR reaction. The primers used in the first PCR reaction are referred to herein as “external primers” or DNA primers” and the primers used in the second PCR reaction are referred to herein as “MSP primers.” Two sets of primers (i.e., methylated and unmethylated for each of the markers targeted in the reaction) are used as the MSP primers. In addition in multiplex methylation-specific PCR, as described herein, a small amount (i.e., 1 μl) of a 1:10 to about 106 dilution of the reaction product of the first “external” PCR reaction is used in the second “internal” MSP PCR reaction.
  • The term “primer” as used herein refers to a sequence comprising two or more deoxyribonucleotides or ribonucleotides, preferably more than three, and most preferably more than 8, which sequence is capable of initiating synthesis of a primer extension product, which is substantially complementary to a polymorphic locus strand. Environmental conditions conducive to synthesis include the presence of nucleoside triphosphates and an agent for polymerization, such as DNA polymerase, and a suitable temperature and pH. The primer is preferably single stranded for maximum efficiency in amplification, but may be double stranded. If double stranded, the primer is first treated to separate its strands before being used to prepare extension products. Preferably, the primer is an oligodeoxy ribonucleotide. The primer must be sufficiently long to prime the synthesis of extension products in the presence of the inducing agent for polymerization. The exact length of primer will depend on many factors, including temperature, buffer, and nucleotide composition. The oligonucleotide primer typically contains 12-20 or more nucleotides, although it may contain fewer nucleotides.
  • Primers of the invention are designed to be “substantially” complementary to each strand of the oligonucleotide to be amplified and include the appropriate G or C nucleotides as discussed above. This means that the primers must be sufficiently complementary to hybridize with their respective strands under conditions that allow the agent for polymerization to perform. In other words, the primers should have sufficient complementarity with a 5′ and 3′ oligonucleotide to hybridize therewith and permit amplification of CpG containing nucleic acid sequence.
  • Primers of the invention are employed in the amplification process, which is an enzymatic chain reaction that produces exponentially increasing quantities of target locus relative to the number of reaction steps involved (e.g., polymerase chain reaction or PCR). Typically, one primer is complementary to the negative (−) strand of the locus (antisense primer) and the other is complementary to the positive (+) strand (sense primer). Annealing the primers to denatured nucleic acid followed by extension with an enzyme, such as the large fragment of DNA Polymerase I (Klenow) and nucleotides, results in newly synthesized + and − strands containing the target locus sequence. Because these newly synthesized sequences are also templates, repeated cycles of denaturing, primer annealing, and extension results in exponential production of the region (i.e., the target locus sequence) defined by the primer. The product of the chain reaction is a discrete nucleic acid duplex with termini corresponding to the ends of the specific primers employed.
  • The oligonucleotide primers used in invention methods may be prepared using any suitable method, such as conventional phosphotriester and phosphodiester methods or automated embodiments thereof. In one such automated embodiment, diethylphos-phoramidites are used as starting materials and may be synthesized as described by Beaucage, et al. (Tetrahedron Letters, 22:1859-1862, 1981). One method for synthesizing oligonucleotides on a modified solid support is described in U.S. Pat. No. 4,458,066.
  • The primers used in the invention for amplification of the CpG-containing nucleic acid in the specimen, after bisulfite modification, specifically distinguish between untreated or unmodified DNA, methylated, and non-methylated DNA. MSP primers for the non-methylated DNA preferably have a T in the 3′ CG pair to distinguish, it from the C retained in methylated DNA, and the complement is designed for the antisense primer. MSP primers usually contain relatively few Cs or Gs in the sequence since the Cs will be absent in the sense primer and the Gs absent in the antisense primer (C becomes modified to U (uracil) which is amplified as T (thymidine) in the amplification product).
  • The primers of the invention embrace oligonucleotides of sufficient length and appropriate sequence so as to provide specific initiation of polymerization on a significant number of nucleic acids in the polymorphic locus. Where the nucleic acid sequence of interest contains two strands, it is necessary to separate the strands of the nucleic acid before it can be used as a template for the amplification process. Strand separation can be effected either as a separate step or simultaneously with the synthesis of the primer extension products. This strand separation can be accomplished using various suitable denaturing conditions, including physical, chemical, or enzymatic means, the word “denaturing” includes all such means. One physical method of separating nucleic acid strands involves heating the nucleic acid until it is denatured. Typical heat denaturation may involve temperatures ranging from about 80.degree. to 105.degree C. for times ranging from about 1 to 10 minutes. Strand separation may also be induced by an enzyme from the class of enzymes known as helicases or by the enzyme RecA, which has helicase activity, and in the presence of riboATP, is known to denature DNA. The reaction conditions suitable for strand separation of nucleic acids with helicases are described by Kuhn Hoffmann-Berling (CSH-Quantitative Biology, 43:63, 1978) and techniques for using RecA are reviewed in C. Radding (Ann. Rev. Genetics, 16:405-437, 1982).
  • As described herein, any nucleic acid specimen, in purified or nonpurified form, can be utilized as the starting nucleic acid or acids, provided it contains, or is suspected of containing, the specific nucleic acid sequence containing the target locus (e.g., CpG).
  • When complementary strands of nucleic acid or acids are separated, regardless of whether the nucleic acid was originally double or single stranded, the separated strands are ready to be used as a template for the synthesis of additional nucleic acid strands. This synthesis is performed under conditions allowing hybridization of primers to templates to occur. Generally synthesis occurs in a buffered aqueous solution, preferably at a pH of 7-9, most preferably about 8. Preferably, a molar excess (for genomic nucleic acid, usually about 108:1 primer:template) of the two oligonucleotide primers is added to the buffer containing the separated template strands. It is understood, however, that the amount of complementary strand may not be known if the process of the invention is used for diagnostic applications, so that the amount of primer relative to the amount of complementary strand cannot be determined with certainty. As a practical matter, however, the amount of primer added will generally be in molar excess over the amount of complementary strand (template) when the sequence to be amplified is contained in a mixture of complicated lona-chain nucleic acid strands. A large molar excess is preferred to improve the efficiency of the process.
  • The deoxyribonucleoside triphosphates dATP, dCTP, dGTP, and dTTP are added to the synthesis mixture, either separately or together with the primers, in adequate amounts and the resulting solution is heated to about 90 C -100 C. from about 1 to 10 minutes, preferably from 1 to 4 minutes. After this heating period, the solution is allowed to cool to room temperature, which is preferable for the primer hybridization. To the cooled mixture is added an appropriate agent for effecting the primer extension reaction (called herein “agent for polymerization”), and the reaction is allowed to occur under conditions known in the art. The agent for polymerization may also be added together with the other reagents if it is heat stable. This synthesis (or amplification) reaction may occur at room temperature up to a temperature above which the agent for polymerization no longer functions. Thus, for example, if DNA polymerase is used as the agent, the temperature is generally no greater than about 40 C. Most conveniently the reaction occurs at room temperature.
  • In certain preferred embodiments, the agent for polymerization may be any compound or system which will function to accomplish the synthesis of primer extension products, including enzymes. Suitable enzymes for this purpose include, for example, E. coli DNA polymerase I, Klenow fragment of E. coli DNA polymerase I, T4 DNA polymerase, other available DNA polymerases, polymerase muteins, reverse transcriptase, and other enzymes, including heat-stable enzymes (i.e., those enzymes which perform primer extension after being subjected to temperatures sufficiently elevated to cause denaturation). Suitable enzymes will facilitate combination of the nucleotides in the proper manner to form the primer extension products which are complementary to each locus nucleic acid strand. Generally, the synthesis will be initiated at the 3′ end of each primer and proceed in the 5′ direction along the template strand, until synthesis terminates, producing molecules of different lengths. There may be agents for polymerization, however, which initiate synthesis at the 5′ end and proceed in the other direction, using the same process as described above.
  • In nucleic acid hybridization reactions, the conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (e.g., GC v. AT content), and nucleic acid type (e.g., RNA v. DNA) of the hybridizing regions of the nucleic acids can be considered in selecting hybridization conditions. An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter.
  • An example of progressively higher stringency conditions is as follows:
    • 2.times.SSC/0.1% SDS at about room temperature (hybridization conditions);
    • 0.2.times.SSC/0.1% SDS at about room temperature (low stringency conditions);
    • 0.2.times.SSC/0.1% SDS at about 42.degree. C. (moderate stringency conditions); and
    • 0.1.times.SSC at about 68.degree. C. (high stringency conditions). Washing can be carried out using only one of these conditions, e.g., high stringency conditions, or each of the conditions can be used, e.g., for 10-15 minutes each, in the order listed above, repeating any or all of the steps listed. However, as mentioned above, optimal conditions will vary, depending on the particular hybridization reaction involved, and can be determined empirically.
  • Preferably, the method of amplifying is by PCR, as described herein and as is commonly used by those of ordinary skill in the art. Alternative methods of amplification have been described and can also be employed as long as the methylated and non-methylated loci amplified by PCR using the primers of the invention is similarly amplified by the alternative means.
  • The amplified products are preferably identified as methylated or non-methylated by sequencing. Sequences amplified by the methods of the invention can be further evaluated, detected, cloned, sequenced, and the like, either in solution or after binding to a solid support, by any method usually applied to the detection of a specific DNA sequence such as PCR, oligomer restriction (39), allele-specific oligonucleotide (ASO) probe analysis (40), oligonucleotide ligation assays (OLAs) (41), and the like. Molecular techniques for DNA analysis have been reviewed (42).
  • Optionally, the methylation pattern of the nucleic acid can be confirmed by restriction enzyme digestion and Southern blot analysis. Examples of methylation sensitive restriction endonucleases which can be used to detect 5′CpG methylation include Smal, SacII, EagI, MspI, HpaII, BstUI and BssHII, for example.
  • The invention provides a method for detecting a cell having a hypermethylated CpG island or a cell proliferative disorder associated with hypermethylated CpG in a tissue or biological fluid of a subject, comprising contacting a target cellular component suspected of expressing a gene having a methylated CpG or having a CpG-associated disorder, with an agent which binds to the component. The target cell component can be nucleic acid, such as DNA or RNA, or protein. When the component is nucleic acid, the reagent is a nucleic acid probe or PCR primer. When the cell component is protein, the reagent is an antibody probe. The probes can be detectably labeled, for example, with a radioisotope, a fluorescent compound, a bioluminescent compound, a chemiluminescent compound, a metal chelator, or an enzyme. Those of ordinary skill in the art will know of other suitable labels for binding to the antibody, or will be able to ascertain such, using routine experimentation.
  • Actively transcribed genes generally contain fewer methylated CGs than the average number in DNA. Hypermethylation can also be detected by restriction endonuclease treatment and Southern blot analysis. Therefore, in certain preferred embodiments, when the cellular component detected is DNA, restriction endonuclease analysis is preferable to detect hypermethylation of the promoter for example. Any restriction endonuclease that includes CG as part of its recognition site and that is inhibited when the C is methylated can be utilized. In certain preferred examples, the methylation sensitive restriction endonuclease is BssHII, MspI, or HpaII, used alone or in combination. Other methylation sensitive restriction endonucleases will be known to those of skill in the art.
  • For purposes of the invention, an antibody or nucleic acid probe specific for a gene or gene product may be used to detect the presence of methylation either by detecting the level of polypeptide (using antibody) or methylation of the polynucleotide (using nucleic acid probe) in biological fluids or tissues. For antibody-based detection, the level of the polypeptide is compared with the level of polypeptide found in a corresponding “normal” tissue. Oligonucleotide primers based on any coding sequence region of the promoter in gene selected from genes involved in tumor suppression, nucleic acid repair, apoptosis, anti-proliferation, ras signaling, adhesion, differentiation, development, and cell cycle regulation. In particular, oligonucleotide primers are based on coding sequence region of the promoter in the gene selected from the following are useful for amplifying DNA, for example by PCR:
  • H-cadherin, in certain exemplary embodiments is encoded by NCBI accession No. AAB18912, comprising (SEQ ID NO:1) below:
  • 1 mqprtplvlc vllsqvlllt saedldctpg fqqkvthinq paefiedqsi lnltfsdckg
    61 ndklryevss pyfkvnsdgg lvalrnitav gktlfvhart phaedmaelv ivggkdiqgs
    121 lqdifkfart spvprqkrsi vvspilipen qrqpfprdvg kvvdsdrper skfrltgkgv
    181 dqepkgifri nentgsvsvt rtldreviav yqlfvettdv ngktlegpvp levividqnd
    241 nrpifregpy ighvmegspt gttvmrmtaf daddpatdna llrynirqqt pdkpspnmfy
    301 idpekgdivt vvspalldre tlenpkyeli ieaqdmagld vgltgtatat imiddkndhs
    361 pkftkkefqa tveegavgvi vnltvedkdd pttgawraay tiingnpgqs feihtnpqtn
    421 egmlsvvkpl dyeisafhtl likvenedpl vpdvsygpss tatvhitvld vnegpvfypd
    481 pmmvtrqedl svgsvlltvn atdpdslqhq tirysvykdp agwlninpin gtvdttavld
    541 respfvdnsv ytalflaids gnppatgtgt llitledvnd napfiyptva evcddaknls
    601 vvilgasdkd lhpntdpfkf eihkqavpdk vwkiskinnt halvsllqnl nkanynlpim
    661 vtdsgkppmt nitdlrvqvc scrnskvdcn aagalrfslp svlllslfsl acl
  • p-16, in certain exemplary embodiments is encoded by NCBI accession No. CAB58124 comprising (SEQ ID NO:2) below:
  • 1 gshsmryfft svsrpgrgep rfiavgyvdd tqfvrfdsda asqrmeprap wieqegpeyw
    61 dgetrkvkah sqtdrvdlgt lrgyynqsea gshtiqmmyg cdvgpdgrll rgyqqdaydg
    121 kdyialnedl rswtaadmaa qitqrkweaa rvaeqlrayl egtcvewlrr ylengketlq
    181 rt
  • APC, in certain exemplary embodiments is encoded by NCBI accession No. NP—000029 comprising (SEQ ID NO:3) below:
  • 1 maaasydqll kqvealkmen snlrqeledn snhltklete asnmkevlkq lqgsiedeam
    61 assgqidlle rlkelnldss nfpgvklrsk mslrsygsre gsvssrsgec spvpmgsfpr
    121 rgfvngsres tgyleeleke rsllladldk eekekdwyya qlqnltkrid slpltenfsl
    181 qtdmtrrqle yearqirvam eeqlgtcqdm ekraqrriar iqqiekdilr irqllqsqat
    241 eaerssqnkh etgshdaerq negqgvgein matsgngqgs ttrmdhetas vlssssthsa
    301 prrltshlgt kvemvyslls mlgthdkddm srtllamsss qdscismrqs gclplliqll
    361 hgndkdsvll gnsrgskear arasaalhni ihsqpddkrg rreirvlhll eqiraycetc
    421 wewqeahepg mdqdknpmpa pvehqicpav cvlmklsfde ehrhamnelg glqaiaellq
    481 vdcemygltn dhysitlrry agmaltnltf gdvankatlc smkgcmralv aqlksesedl
    541 qqviasvlrn lswradvnsk ktlrevgsvk almecalevk kestlksvls alwnlsahct
    601 enkadicavd galaflvgtl tyrsqtntla iiesgggilr nvssliatne dhrqilrenn
    661 clqtllqhlk shsltivsna cgtlwnlsar npkdqealwd mgavsmlknl ihskhkmiam
    721 gsaaalrnlm anrpakykda nimspgsslp slhvrkqkal eaeldaqhls etfdnidnls
    781 pkashrskqr hkqslygdyv fdtnrhddnr sdnfntgnmt vlspylnttv lpsssssrgs
    841 ldssrsekdr slerergigl gnyhpatenp gtsskrglqi sttaaqiakv meevsaihts
    901 qedrssgstt elhcvtdern alrrssaaht hsntynftks ensnrtcsmp yakleykrss
    961 ndslnsvsss dgygkrgqmk psiesysedd eskfcsygqy padlahkihs anhmddndge
    1021 ldtpinyslk ysdeqlnsgr qspsqnerwa rpkhiiedei kqseqrqsrn qsttypvyte
    1081 stddkhlkfq phfgqqecvs pyrsrgangs etnrvgsnhg inqnvsqslcqeddyeddkp
    1141 tnyserysee eqheeeerpt nysikyneek rhvdqpidys lkyatdipss qkqsfsfsks
    1201 ssgqsskteh mssssentst pssnakrqnq lhpssaqsrs gqpqkaatck vssinqetiq
    1261 tycvedtpic fsrcsslssl ssaedeigcn qttqeadsan tlqiaeikek igtrsaedpv
    1321 sevpavsqhp rtkssrlqgs slssesarhk avefssgaks psksgaqtpk sppehyvqet
    1381 plmfsrctsv ssldsfesrs iassvqsepc sgmvsgiisp sdlpdspgqt mppsrsktpp
    1441 pppqtaqtkr evpknkapta ekresgpkqa avnaavqrvq vlpdadtllh fatestpdgf
    1501 scssslsals ldepfiqkdv elrimppvqe ndngnetese qpkesnenqe keaektidse
    1561 kdllddsddd dieileecii samptkssrk akkpaqtask lpppvarkps qlpvykllps
    1621 qnrlqpqkhv sftpgddmpr vycvegtpin fstatslsdl tiesppnela agegvrggaq
    1681 sgefekrdti ptegrstdea qggktssvti pelddnkaee gdilaecins ampkgkshkp
    1741 frvkkimdqv qqasasssap nknqldgkkk kptspvkpip qnteyrtrvrknadsknnln
    1801 aervfsdnkd skkqnlknns kvfndklpnn edrvrgsfaf dsphhytpie gtpycfsrnd
    1861 slssldfddd dvdlsrekae lrkakenkes eakvtshtel tsnqqsankt qaiakqpinr
    1921 gqpkpilqkq stfpqsskdi pdrgaatdek lqnfaientp vcfshnssls slsdidqenn
    1981 nkenepiket eppdsqgeps kpqasgyapk sfhvedtpvc fsrnsslssl sidseddllq
    2041 ecissampkk kkpsrlkgdn ekhsprnmgg ilgedltldl kdiqrpdseh glspdsenfd
    2101 wkaiqegans ivsslhqaaa aaclsrqass dsdsilslks gislgspfhl tpdqeekpft
    2161 snkgprilkp gekstletkk ieseskgikg gkkvykslit gkvrsnseis gqmkqplqan
    2221 mpsisrgrtm ihipgvrnss sstspvskkg pplktpasks psegqtatts prgakpsvks
    2281 elspvarqts qiggsskaps rsgsrdstps rpaqqplsrp iqspgrnsis pgrngisppn
    2341 klsqlprtss pstastkssg sgkmsytspg rqmsqqnltk qtglsknass iprsesaskg
    2401 lnqmnngnga nkkvelsrms stkssgsesd rserpvlvrq stfikeapsp tlrrkleesa
    2461 sfeslspssr pasptrsqaq tpvlspslpd mslsthssvq aggwrklppn lsptieyndg
    2521 rpakrhdiar shsespsrlp inrsgtwkre hskhssslpr vstwrrtgss ssilsasses
    2581 sekaksedek hvnsisgtkq skenqvsakg twrkikenef sptnstsqtv ssgatngaes
    2641 ktliyqmapa vsktedvwvr iedcpinnpr sgrsptgntp pvidsvseka npnikdskdn
    2701 qakqnvgngs vpmrtvglen rlnsfiqvda pdqkgteikp gqnnpvpvse tnessivert
    2761 pfsssssskh sspsgtvaar vtpfnynpsp rkssadstsa rpsqiptpvn nntkkrdskt
    2821 dstessgtqs pkrhsgsylv tsv
  • RASSF1A, in certain exemplary embodiments is encoded by NCBI accession No. NP—009113 comprising (SEQ ID NO:4) below:
  • 1 msgepeliel relapagrag kgrtrleran alriargtac nptrqlvpgr ghrfqpagpa
    61 thtwcdlcgd fiwgvvrkgl qcahckftch yrcralvcld ccgprdlgwe paverdtnvd
    121 epvewetpdl sqaeieqkik eynaqinsnl fmslnkdgsy tgfikvqlkl vrpvsvpssk
    181 kppslqdarr gpgrgtsvrr rtsfylpkda vkhlhvlsrt rarevieall rkflvvddpr
    241 kfalferaer hgqvylrkll ddeqplrlrl lagpsdkals fvlkendsge vnwdafsmpe
    301 lhnflrilqr eeeehlrqil qkysycrqki qealhacplg
  • MGMT, in certain exemplary embodiments is encoded by NCBI accession
  • No. AAH00824 comprising (SEQ ID NO:5) below:
  • 1 mdkdcemkrt tldsplgkle lsgceqglhe ikllgkgtsa adavevpapa avlggpeplm
    61 qctawlnayf hqpeaieefp vpalhhpvfq qesftrqvlw kllkvvkfge visyqqlaal
    121 agnpkaarav ggamrgnpvp ilipchrvvc ssgavgnysg glavkewllaheghrlgkpg
    181 lggssglaga wlkgagatsg sppagrn
  • DAPK, in certain exemplary embodiments is encoded by NCBI accession No. NP—004929 comprising (SEQ ID NO:6) below:
  • 1 mtvfrqenvd dyydtgeelg sgqfavvkkc rekstglqya akfikkrrtk ssrrgvsred
    61 ierevsilke iqhpnvitlh evyenktdvi lilelvagge lfdflaekes lteeeatefl
    121 kqilngvyyl hslqiahfdl kpenimlldr nvpkprikii dfglahkidf gnefknifgt
    181 pefvapeivn yeplgleadm wsigvityil lsgaspflgd tkqetlanvs avnyefedey
    241 fsntsalakd firrllvkdp kkrmtiqdsl qhpwikpkdt qqalsrkasa vnmekfkkfa
    301 arkkwkqsvr lislcqrlsr sflsrsnmsv arsddtldee dsfvmkaiih ainddnvpgl
    361 qhllgslsny dvnqpnkhgt pplliaagcg niqilqllik rgsridvqdk ggsnavywaa
    421 rhghvdtlkf lsenkcpldv kdksgemalh vaaryghadv aqllcsfgsn pniqdkeeet
    481 plhcaawhgy ysvakalcea gcnvniknre getplltasa rgyhdivecl aehgadlnac
    541 dkdghialhl avrrcqmevi ktllsqgcfv dyqdrhgntp lhvackdgnm pivvalcean
    601 cnldisnkyg rtplhlaann gildvvrylc lmgasvealt tdgktaedla rseqhehvag
    661 llarlrkdth rglfiqqlrp tqnlqprikl klfghsgsgk ttlveslkcg llrsffrrrr
    721 prlsstnssr fppsplaskp tvsvsinnly pgcenvsvrs rsmmfepglt kgmlevfvap
    781 thhphcsadd qstkaidiqn aylngvgdfs vwefsgnpvy fccydyfaan dptsihvvvf
    841 sleepyeiql nqvifwlsfl kslvpveepi afggklknpl qvvlvathad imnvprpagg
    901 efgydkdtsl lkeirnrfgn dlhisnklfv ldagasgskd mkvlrnhlqe irsqivsvcp
    961 pmthlcekii stlpswrkln gpnqlmslqq fvydvqdqln plaseedlrr iaqqlhstge
    1021 inimqsetvq dvllldprwl ctnvlgklls vetpralhhy rgrytvediq rlvpdsdvee
    1081 llqildamdi cardlssgtm vdvpaliktd nlhrswadee devmvyggvr ivpvehltpf
    1141 pcgifhkvqv nlcrwihqqs tegdadirlw vngcklanrg aellvllvnh gqgievqvrg
    1201 letekikccl lldsvcstie nvmattlpgl ltvkhylspq qlrehhepvm iyqprdffra
    1261 qtlketsltn tmggykesfs simcfgchdv ysqaslgmdi hasdlnlltr rklsrlldpp
    1321 dplgkdwcll amnlglpdlv akyntsngap kdflpsplha llrewttype stvgtlmskl
    1381 relgrrdaad fllkassvfk inldgngqea yasscnsgts ynsissvvsr
  • ASC, in certain exemplary embodiments is encoded by NCBI accession No. NP—037390 comprising (SEQ ID NO:7) below:
  • 1 mgrardaild alenltaeel kkfklkllsv plregygrip rgallsmdal dltdklvsfy
    61 letygaelta nvlrdmglqe magqlqaath qgsgaapagi qappqsaakp glhfidqhra
    121 aliarvtnve wlldalygkv ltdeqyqavr aeptnpskmr klfsftpawn wtckdlllqa
    181 lresqsylve dlers
  • These genes are merely listed as examples and are not meant to be limiting.
  • In certain preferred embodiments of the invention the genes can be detected in panels consisting of the following:
  • (1) genes involved in tumor suppression and cell adhesion
  • (2) genes involved in cell cycle regulation and adhesion
  • (3) genes involved in tumor suppression and cell cycle regulation
  • (4) genes involved in ras signaling and cell cycle control.
  • Any specimen containing a detectable amount of polynucleotide or antigen can be used. Preferably the subject is human.
  • The present invention provides the finding that gene hypermethylation of not only the primary malignancy, but also lymph nodes, may be used to restage and assess prognosis of patients with stage I tumors, in particular examples patients with stage I non small cell lung carcinoma (NSCLC). These markers are shown to also be potential targets for reversal of gene silencing and may be important in adjuvant approaches to reduce disease recurrence.
  • Using the methods of the invention, expression of any gene, such as genes involved in tumor suppression, nucleic acid repair, apoptosis, anti-proliferation, ras signaling, adhesion, differentiation, development, and cell cycle regulation, can be identified in a cell and the appropriate course of treatment can be employed (e.g., sense gene therapy or drug therapy). The expression pattern of the gene may vary with the stage of malignancy of a cell, therefore, a sample such as NSCLC or breast tissue can be screened with a panel of gene or gene product specific reagents (i.e., nucleic acid probes or antibodies) to detect gene expression and then diagnose the stage of malignancy of the cell.
  • Any of the methods as described herein can be used in high throughput analysis of DNA methylation. For example, U.S. Pat. No. 7,144,701, incorporated by reference in its entirety herein, describes differential methylation hybridization (DMH) for a high-throughput analysis of DNA methylation.
    • II. Methods of Detection and Diagnosis
  • The methods of the invention as described herein are used in certain exemplary embodiments to identify metastases by detecting hypermethylation of one or more genes in one or more samples. In this way, the detection of nucleic acid hypermethylation identifies metastases.
  • In mammals, conditions associated with aberrant methylation of genes that can be detected or monitored include, but are not limited to, metastases associated with carcinomas and sarcomas of all kinds, including one or more specific types of cancer, e.g., a lung cancer, breast cancer, an alimentary or gastrointestinal tract cancer such as colon, esophageal and pancreatic cancer, a liver cancer, a skin cancer, an ovarian cancer, an endometrial cancer, a prostate cancer, a lymphoma, hematopoietic tumors, such as a leukemia, a kidney cancer, a bronchial cancer, a muscle cancer, a bone cancer, a bladder cancer or a brain cancer, such as astrocytoma, anaplastic astrocytoma, glioblastoma, medulloblastoma, and neuroblastoma and their metastases. Suitable pre-malignant lesions to be detected or monitored using the invention include, but are not limited to, lobular carcinoma in situ and ductal carcinoma in situ.
  • The invention methods can be used to assay the DNA of any mammalian subject, including, but not limited to, humans, pet (e.g., dogs, cats, ferrets) and farm animals (meat and dairy).
  • The invention features in certain aspects a method for identifying metastases in a subject comprising detecting nucleic acid hypermethylation of one or more genes in one or more samples, wherein detecting nucleic acid hypermethylation identifies metastases. The term “hypermethylation” as used herein refers to the presence of methylated alleles in one or more nucleic acids. In preferred embodiments, hypermethylation is detected using methylation specific polymerase chain reaction (MSP).
  • The samples, in certain embodiments, can be from tumor tissue, lymph nodes, bone marrow or blood. Thus, the invention can be used to identify metastases in a subject comprising detecting nucleic acid hypermethylation of one or more genes in tumor tissues or in lymph nodes, wherein detecting nucleic acid hypermethylation identifies metastases. Hypermethylation can be detected in tumor tissue alone, e.g. primary tumor tissue, or tumor tissue and lymph nodes. In certain preferred embodiments, detection of hypermethylation in the lymph nodes indicates an early recurring disease. In other certain preferred embodiments, detection of hypermethylation in the lymph nodes indicates a more aggressive disease. Often, an early recurring disease is a more aggressive disease although the two are not mutually exclusive.
  • In other aspects, the invention features a method for identifying micrometastases in a subject comprising detecting nucleic acid hypermethylation of one or more genes in tumor tissue or lymph node, wherein the genes are selected from the group consisting of: genes involved in tumor suppression, DNA repair, apoptosis, anti-proliferation, ras signaling, adhesion, differentiation, development, and cell cycle regulation, in one or more cells or tissues, wherein detecting nucleic acid hypermethylation identifies micrometastases.
  • In other examples, the invention as described herein features a method for identifying micrometastases in a subject comprising detecting nucleic acid hypermethylation of at least one or more genes in a sample comprising tumor and lymph nodes, where the sample genes are selected from genes involved in tumor suppression, nucleic acid repair, apoptosis, anti-proliferation, ras signaling, adhesion, differentiation, development, and cell cycle regulation, in one or more cells or tissues, and where detecting nucleic acid methylation identifies micrometastases.
  • In practice, the method for detecting or diagnosing a proliferative disease in a subject comprises, in certain embodiments, extracting nucleic acid from one or more cell or tissue samples, detecting nucleic acid hypermethylation of one or more genes in the sample; and identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes indicates a proliferative disease. In preferred examples, the proliferative disease is cancer.
  • As described herein, in certain preferred examples, the one or more genes comprise one or more CpG islands in the promoter regions. Accordingly, any gene that contains one or more CpG island in the promoter region is suitable for use in the methods of the invention; however in certain preferred examples, the one or more genes may be selected from any of p-16, H-cadherin, APC, RASSF1A, MGMT, DAPK, or ASC, and as described in SEQ ID NOs 1-7.
  • In certain embodiments, hypermethylation of at least one of the genes is detected. In other certain embodiments, hypermethylation of at least two of the genes is detected. In other certain embodiments, hypermethylation of at least three of the genes is detected.
  • The detection of metastases as described in these methods can be used to detect or diagnose a proliferative disease.
  • The detection of metastases as described in these methods can be used after surgery or therapy to treat a proliferative disease.
  • The detection of metastases as described in these methods can be used to predict the recurrence of a proliferative disease.
  • The detection of metastases as described in these methods can be used to stage a proliferative disease.
  • The detection of metastases as described in these methods can be used to determine a course of treatment for a subject.
  • These embodiments are discussed in further detail herein.
  • Methods of Treatment
  • The invention as described herein can be used to treat a subject having or at risk for having a proliferative disease, such as cancer. Accordingly, the method comprises identifying nucleic acid hypermethylation of one or more genes, where nucleic acid hypermethylation indicates having or a risk for having a proliferative disease, and administering to the subject a therapeutically effective amount of a demethylating agent, thereby treating a subject having or at risk for having a proliferative disease.
  • The method can be used in combination with one or more chemotherapeutic agents. Anti-cancer drugs that may be used in the various embodiments of the invention, including pharmaceutical compositions and dosage forms and kits of the invention, include, but are not limited to: acivicin; aclarubicin; acodazole hydrochloride; acronine; adozelesin; aldesleukin; altretamine; ambomycin; ametantrone acetate; aminoglutethimide; amsacrine; anastrozole; anthramycin; asparaginase; asperlin; azacitidine; azetepa; azotomycin; batimastat; benzodepa; bicalutamide; bisantrene hydrochloride; bisnafide dimesylate; bizelesin; bleomycin sulfate; brequinar sodium; bropirimine; busulfan; cactinomycin; calusterone; caracemide; carbetimer; carboplatin; carmustine; carubicin hydrochloride; carzelesin; cedefingol; chlorambucil; cirolemycin; cisplatin; cladribine; crisnatol mesylate; cyclophosphamide; cytarabine; dacarbazine; dactinomycin; daunorubicin hydrochloride; decitabine; dexormaplatin; dezaguanine; dezaguanine mesylate; diaziquone; docetaxel; doxorubicin; doxorubicin hydrochloride; droloxifene; droloxifene citrate; dromostanolone propionate; duazomycin; edatrexate; eflornithine hydrochloride; elsamitrucin; enloplatin; enpromate; epipropidine; epirubicin hydrochloride; erbulozole; esorubicin hydrochloride; estramustine; estramustine phosphate sodium; etanidazole; etoposide; etoposide phosphate; etoprine; fadrozole hydrochloride; fazarabine; fenretinide; floxuridine; fludarabine phosphate; fluorouracil; flurocitabine; fosquidone; fostriecin sodium; gemcitabine; gemcitabine hydrochloride; hydroxyurea; idarubicin hydrochloride; ifosfamide; ilmofosine; interleukin II (including recombinant interleukin II, or rIL2), interferon alfa-2a; interferon alfa-2b; interferon alfa-n1; interferon alfa-n3; interferon beta-I a; interferon gamma-I b; iproplatin; irinotecan hydrochloride; lanreotide acetate; letrozole; leuprolide acetate; liarozole hydrochloride; lometrexol sodium; lomustine; losoxantrone hydrochloride; masoprocol; maytansine; mechlorethamine, mechlorethamine oxide hydrochloride rethamine hydrochloride; megestrol acetate; melengestrol acetate; melphalan; menogaril; mercaptopurine; methotrexate; methotrexate sodium; metoprine; meturedepa; mitindomide; mitocarcin; mitocromin; mitogillin; mitomalcin; mitomycin; mitosper; mitotane; mitoxantrone hydrochloride; mycophenolic acid; nocodazole; nogalamycin; ormaplatin; oxisuran; paclitaxel; pegaspargase; peliomycin; pentamustine; peplomycin sulfate; perfosfamide; pipobroman; piposulfan; piroxantrone hydrochloride; plicamycin; plomestane; porfimer sodium; porfiromycin; prednimustine; procarbazine hydrochloride; puromycin; puromycin hydrochloride; pyrazofurin; riboprine; rogletimide; safingol; safingol hydrochloride; semustine; simtrazene; sparfosate sodium; sparsomycin; spirogermanium hydrochloride; spiromustine; spiroplatin; streptonigrin; streptozocin; sulofenur; talisomycin; tecogalan sodium; tegafur; teloxantrone hydrochloride; temoporfin; teniposide; teroxirone; testolactone; thiamiprine; thioguanine; thiotepa; tiazofurin; tirapazamine; toremifene citrate; trestolone acetate; triciribine phosphate; trimetrexate; trimetrexate glucuronate; triptorelin; tubulozole hydrochloride; uracil mustard; uredepa; vapreotide; verteporfin; vinblastine sulfate; vincristine sulfate; vindesine; vindesine sulfate; vinepidine sulfate; vinglycinate sulfate; vinleurosine sulfate; vinorelbine tartrate; vinrosidine sulfate; vinzolidine sulfate; vorozole; zeniplatin; zinostatin; zorubicin hydrochloride, improsulfan, benzodepa, carboquone, triethylenemelamine, triethylenephosphoramide, triethylenethiophosphoramide, trimethylolomelamine, chlornaphazine, novembichin, phenesterine, trofosfamide, estermustine, chlorozotocin, gemzar, nimustine, ranimustine, dacarbazine, mannomustine, mitobronitol,aclacinomycins, actinomycin F(1), azaserine, bleomycin, carubicin, carzinophilin, chromomycin, daunorubicin, daunomycin, 6-diazo-5-oxo-1-norleucine, doxorubicin, olivomycin, plicamycin, porfiromycin, puromycin, tubercidin, zorubicin, denopterin, pteropterin, 6-mercaptopurine, ancitabine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, enocitabine, pulmozyme, aceglatone, aldophosphamide glycoside, bestrabucil, defofamide, demecolcine, elfornithine, elliptinium acetate, etoglucid, flutamide, hydroxyurea, lentinan, phenamet, podophyllinic acid, 2-ethylhydrazide, razoxane, spirogermanium, tamoxifen, taxotere, tenuazonic acid, triaziquone, 2,2′,2″-trichlorotriethylamine, urethan, vinblastine, vincristine, vindesine and related agents. 20-epi-1,25 dihydroxyvitamin D3; 5-ethynyluracil; abiraterone; aclarubicin; acylfulvene; adecypenol; adozelesin; aldesleukin; ALL-TK antagonists; altretamine; ambamustine; amidox; amifostine; aminolevulinic acid; amrubicin; amsacrine; anagrelide; anastrozole; andrographolide; angiogenesis inhibitors; antagonist D; antagonist G; antarelix; anti-dorsalizing morphogenetic protein-1; antiandrogen, prostatic carcinoma; antiestrogen; antineoplaston; antisense oligonucleotides; aphidicolin glycinate; apoptosis gene modulators; apoptosis regulators; apurinic acid; ara-CDP-DL-PTBA; arginine deaminase; asulacrine; atamestane; atrimustine; axinastatin 1; axinastatin 2; axinastatin 3; azasetron; azatoxin; azatyrosine; baccatin III derivatives; balanol; batimastat; BCR/ABL antagonists; benzochlorins; benzoylstaurosporine; beta lactam derivatives; beta-alethine; betaclamycin B; betulinic acid; bFGF inhibitor; bicalutamide; bisantrene; bisaziridinylspermine; bisnafide; bistratene A; bizelesin; breflate; bropirimine; budotitane; buthionine sulfoximine; calcipotriol; calphostin C; camptothecin derivatives; canarypox IL-2; capecitabine; carboxamide-amino-triazole; carboxyamidotriazole; CaRest M3; CARN 700; cartilage derived inhibitor; carzelesin; casein kinase inhibitors (ICOS); castanospermine; cecropin B; cetrorelix; chlorins; chloroquinoxaline sulfonamide; cicaprost; cisporphyrin; cladribine; clomifene analogues; clotrimazole; collismycin A; collismycin B; combretastatin A4; combretastatin analogue; conagenin; crambescidin 816; crisnatol; cryptophycin 8; cryptophycin A derivatives; curacin A; cyclopentanthraquinones; cycloplatam; cypemycin; cytarabine ocfosfate; cytolytic factor; cytostatin; dacliximab; decitabine; dehydrodidemnin B; deslorelin; dexamethasone; dexifosfamide; dexrazoxane; dexverapamil; diaziquone; didemnin B; didox; diethylnorspermine; dihydro-5-azacytidine; dihydrotaxol, 9-; dioxamycin; diphenyl spiromustine; docetaxel; docosanol; dolasetron; doxifluridine; droloxifene; dronabinol; duocarmycin SA; ebselen; ecomustine; edelfosine; edrecolomab; eflornithine; elemene; emitefur; epirubicin; epristeride; estramustine analogue; estrogen agonists; estrogen antagonists; etanidazole; etoposide phosphate; exemestane; fadrozole; fazarabine; fenretinide; filgrastim; finasteride; flavopiridol; flezelastine; fluasterone; fludarabine; fluorodaunorunicin hydrochloride; forfenimex; formestane; fostriecin; fotemustine; gadolinium texaphyrin; gallium nitrate; galocitabine; ganirelix; gelatinase inhibitors; gemcitabine; glutathione inhibitors; hepsulfam; heregulin; hexamethylene bisacetamide; hypericin; ibandronic acid; idarubicin; idoxifene; idramantone; ilmofosine; ilomastat; imidazoacridones; imiquimod; immunostimulant peptides; insulin-like growth factor-1 receptor inhibitor; interferon agonists; interferons; interleukins; iobenguane; iododoxorubicin; ipomeanol, 4-; iroplact; irsogladine; isobengazole; isohomohalicondrin B; itasetron; jasplakinolide; kahalalide F; lamellarin-N triacetate; lanreotide; leinamycin; lenograstim; lentinan sulfate; leptolstatin; letrozole; leukemia inhibiting factor; leukocyte alpha interferon; leuprolide+estrogen+progesterone;leuprorelin; levamisole; liarozole; linear polyamine analogue; lipophilic disaccharide peptide; lipophilic platinum compounds; lissoclinamide 7; lobaplatin; lombricine; lometrexol; lonidamine; losoxantrone; lovastatin; loxoribine; lurtotecan; lutetium texaphyrin; lysofylline; lytic peptides; maitansine; mannostatin A; marimastat; masoprocol; maspin; matrilysin inhibitors; matrix metalloproteinase inhibitors; menogaril; merbarone; meterelin; methioninase; metoclopramide; MIF inhibitor; mifepristone; miltefosine; mirimostim; mismatched double stranded RNA; mitoguazone; mitolactol; mitomycin analogues; mitonafide; mitotoxin fibroblast growth factor-saporin; mitoxantrone; mofarotene; molgramostim; monoclonal antibody, human chorionic gonadotrophin; monophosphoryl lipid A+myobacterium cell wall sk; mopidamol; multiple drug resistance gene inhibitor; multiple tumor suppressor 1-based therapy; mustard anticancer agent; mycaperoxide B; mycobacterial cell wall extract; myriaporone; N-acetyldinaline; N-substituted benzamides; nafarelin; nagrestip; naloxone+pentazocine; napavin; naphterpin; nartograstim; nedaplatin; nemorubicin; nemoronic acid; neutral endopeptidase; nilutamide; nisamycin; nitric oxide modulators; nitroxide antioxidant; nitrullyn; O6-benzylguanine; octreotide; okicenone; oligonucleotides; onapristone; ondansetron; ondansetron; oracin; oral cytokine inducer; ormaplatin; osaterone; oxaliplatin; oxaunomycin; taxel; taxel analogues; taxel derivatives; palauamine; palmitoylrhizoxin; pamidronic acid; panaxytriol; panomifene; parabactin; pazelliptine; pegaspargase; peldesine; pentosan polysulfate sodium; pentostatin; pentrozole; perflubron; perfosfamide; perillyl alcohol; phenazinomycin; phenylacetate; phosphatase inhibitors; picibanil; pilocarpine hydrochloride; pirarubicin; piritrexim; placetin A; placetin B; plasminogen activator inhibitor; platinum complex; platinum compounds; platinum-triamine complex; porfimer sodium; porfiromycin; prednisone; propyl bis-acridone; prostaglandin J2; proteasome inhibitors; protein A-based immune modulator; protein kinase C inhibitor; protein kinase C inhibitors, microalgal; protein tyrosine phosphatase inhibitors; purine nucleoside phosphorylase inhibitors; purpurins; pyrazoloacridine; pyridoxylated hemoglobin polyoxyethylene conjugate; raf antagonists; raltitrexed; ramosetron; ras farnesyl protein transferase inhibitors; ras inhibitors; ras-GAP inhibitor; retelliptine demethylated; rhenium Re 186 etidronate; rhizoxin; ribozymes; RII retinamide; rogletimide; rohitukine; romurtide; roquinimex; rubiginone B1; ruboxyl; safingol; saintopin; SarCNU; sarcophytol A; sargramostim; Sdi 1 mimetics; semustine; senescence derived inhibitor 1; sense oligonucleotides; signal transduction inhibitors; signal transduction modulators; single chain antigen binding protein; sizofiran; sobuzoxane; sodium borocaptate; sodium phenylacetate; solverol; somatomedin binding protein; sonermin; sparfosic acid; spicamycin D; spiromustine; splenopentin; spongistatin 1; squalamine; stem cell inhibitor; stem-cell division inhibitors; stipiamide; stromelysin inhibitors; sulfinosine; superactive vasoactive intestinal peptide antagonist; suradista; suramin; swainsonine; synthetic glycosaminoglycans; tallimustine; tamoxifen methiodide; tauromustine; tazarotene; tecogalan sodium; tegafur; tellurapyrylium; telomerase inhibitors; temoporfin; temozolomide; teniposide; tetrachlorodecaoxide; tetrazomine; thaliblastine; thiocoraline; thrombopoietin; thrombopoietin mimetic; thymalfasin; thymopoietin receptor agonist; thymotrinan; thyroid stimulating hormone; tin ethyl etiopurpurin; tirapazamine; titanocene bichloride; topsentin; toremifene; totipotent stem cell factor; translation inhibitors; tretinoin; triacetyluridine; triciribine; trimetrexate; triptorelin; tropisetron; turosteride; tyrosine kinase inhibitors; tyrphostins; UBC inhibitors; ubenimex; urogenital sinus-derived growth inhibitory factor; urokinase receptor antagonists; vapreotide; variolin B; vector system, erythrocyte gene therapy; velaresol; veramine; verdins; verteporfin; vinorelbine; vinxaltine; vitaxin; vorozole; zanoterone; zeniplatin; zilascorb; and zinostatin stimalamer. Preferred additional anti-cancer drugs are 5-fluorouracil and leucovorin. Additional cancer therapeutics include monoclonal antibodies such as rituximab, trastuzumab and cetuximab.
  • Demethylating Agents
  • In certain embodiments, the invention features methods of identifying an agent that de-methylates hypermethylated nucleic acids comprising identifying one or more cell or tissue samples with hypermethylated nucleic acid, extracting the hypermethylated nucleic acid, contacting the nucleic acid with one or more nucleic acid de-methylating candidate agents and a control agent, and identifying the nucleic acid hypermethylation state, wherein nucleic acid de-methylation of genes in the sample by the candidate agent compared to the control indicates a demethylating agent, thereby identifying an agent that de-methylates hypermethylated nucleic acid.
    • III. Methods of Predicting DIsease Recurrence
  • In other certain aspects, the invention features methods for predicting the recurrence of proliferative diseases, e.g. cancer.
  • Accordingly, the invention features methods for predicting the recurrence of a proliferative disease in a subject comprising detecting nucleic acid hypermethylation of one or more genes wherein detecting nucleic acid hypermethylation of one or more genes is a predictor of the recurrence of a proliferative disease.
  • In certain preferred embodiments, the method comprises extracting nucleic acid from one or more cell or tissue samples, detecting nucleic acid hypermethylation of one or more genes in the sample, and identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes is indicative of the recurrence of a proliferative disease.
  • In certain cases, the rate of recurrence of a proliferative disease can be correlated with the detection of hypermethylation in a cell or tissue sample. In certain embodiments, the cell or tissue sample is tumor tissue or lymph node. In exemplary embodiments, the rate of recurrence of a proliferative disease is more rapid when gene hypermethylation is detected in lymph node. For example, when gene hypermethylation (e.g. p16 or H-cadherin) is detected the primary tumor, the odds of recurrence may be less than when the same genes are hypermethylated in N1 lymph nodes. Moreover, if the same genes (e.g. p16 or H-cadherin) were examined for hypermethylation in the mediastinal lymph nodes, the odds of recurrence may be the greatest compared to the former tissues (primary tumor and N1 lymph nodes).
  • The discovery and clinical validation of markers for cancer of all types which can predict prognosis, likelihood of invasive or metastatic spread is one of the major challenges facing in the field of oncology today. Adjuvant and neoadjuvant therapy (e.g. chemotherapy) are promising treatment modalities, however although adjuvant chemotherapy has been demonstrated to improve survival, for example in node negative breast cancer patients (43), problems remain, for example in the uncertainty as to how to best identify patients whose risk of disease recurrence exceeds their risk of significant therapeutic toxicity. Thus, a need remains for methods for that enable clinical decisions on adjuvant and neoadjuvant therapy, tumor surveillance and the likelihood of disease progression based on validated tumor markers correlated with metastasis and recurrence.
  • In other certain aspects, the invention features a method for determining the prognosis of a subject suffering from a proliferative disease comprising: detecting nucleic acid hypermethylation of one or more genes wherein the detection of nucleic acid hypermethylation is used for determining the prognosis of a subject suffering from a proliferative disease.
  • The prognosis can be used by the clinician to determine the course of treatment, and to monitor the course of treatment. As is understood by the skilled practicioner, prognosis is a prediction and can change during the course of treatment.
    • IV. Methods of Staging
  • The methods of the invention as described herein are used in exemplary embodiments to stage or re-stage a proliferative disease, e.g. a neoplasia or cancer.
  • Staging can refer to “clinical” staging or “molecular” staging. Clinical staging describes the extent or severity of an individual's cancer based on the extent of the original (primary) tumor and the extent of spread in the body. Typically, clinical staging is used in determining a subject's course of treatment and to estimate the subject's prognosis.
  • The TNM system is one of the most commonly used staging systems. The formal TNM staging system, promulgated by the American Joint Committee on Cancer (AJCC), is based almost exclusively on the anatomical extent of disease, which is assessed using a combination of tumor size or depth (T), lymph node spread (N), and presence or absence of metastases (M). Since its inception in 1958, the TNM system has provided a standardized, anatomical basis for staging with several important functions. It provides a basis for prediction of survival, choice of initial treatment, stratification of patients in clinical trials, accurate communication among healthcare providers, and uniform reporting of outcomes. For most tumor types, disease burden and spread have been considered the most reliable predictors of survival and determinants of the type and intensity of therapy to be used. Less often, tumor grade, histological subtype or patient age has been added to TNM staging when the AJCC became convinced that such information would significantly improve the prediction of survival or response to therapy. In the TMJ system, a number is added to each letter to indicate the size or extent of the tumor and the extent of spread. In a Primary Tumor (T), the designation TX indicates that the primary tumor cannot be evaluated, TO indicates no evidence of primary tumor, Tis indicates carcinoma in situ (early cancer that has not spread to neighboring tissue) and T1, T2, T3, T4 indicates size and/or extent of the primary tumor. In the regional lymph nodes (N), NX indicates the regional lymph nodes cannot be evaluated, NO indicates there is no regional lymph node involvement (no cancer found in the lymph nodes) and N1, N2, N3 indicates the involvement of regional lymph nodes (number and/or extent of spread). For distant metastasis (M), the designation MX indicates that distant metastasis cannot be evaluated, MO indicates no distant metastasis (cancer has not spread to other parts of the body), M1 indicates distant metastasis (cancer has spread to distant parts of the body). Criteria for stages differ for different types of cancer. More information on clinical staging can be found on the world wide web, for example at http://www.cancer.gov/cancertopics/factsheet/Detection/staging.
  • The instant invention provides the incorporation of biomarkers into TNM staging. The instant invention provides a method of molecular staging and re-staging by determining the nucleic acid hypermethylation of one or more certain genes. The invention provides methods of molecular restaging that can be used to re-stage any cancer with metastatic capability. In preferred embodiments, hypermethylated nucleic acids are detected in the lymph nodes. By molecular staging and re-staging through the detection of hypermethylated nucleic acids in the lymph nodes, the invention provides methods of detection of early recurrence of proliferative disease, e.g. cancer, that are unable to be detected by methods of clinical staging.
  • For example, in certain embodiments, molecular re-staging can detect hypermethylation in lymph nodes that are have a clinical designation of N=x, meaning that there is no clinical detection of cancer in the lymph nodes.
  • Accordingly, molecular re-staging as described herein can predict early recurrence of cancer, and thereby detect aggressive cancers at an earlier stage in their progression.
  • In preferred aspects, the invention features a method for staging or re-staging a proliferative disease in a subject comprising detecting nucleic acid hypermethylation of one or more genes wherein detecting nucleic acid hypermethylation is used for staging a proliferative disease. In certain examples, the stage of proliferative disease is predictive of disease recurrence.
  • Determining the stage of a proliferative disease can be used by the clinician to determine the course of treatment. The terms “treat,” treating,” “treatment,” and the like are meant to refer to reducing or ameliorating a disorder and/or symptoms associated therewith. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated. In certain cases, an early recurring cancer may be treated with more aggressive therapy. The term “aggressive treatment regimen” is intended to mean reducing or ameliorating a disorder and/or symptoms associated therewith with a method of treatment (e.g. combination of chemotherapeutic agents) more intensive or comprehensive than usual, for instance in dosage or extent. It will be appreciated that, although not precluded, aggressively treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated.
  • The invention also features a method for staging or re-staging a proliferative disease in a subject comprising extracting nucleic acid from one or more cell or tissue samples, detecting nucleic acid hypermethylation of one or more genes in the sample; and identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes is used for staging or re-staging of a proliferative disease.
  • Any tissue sample is suitable for use in the methods of staging or re-staging. In preferred examples, the tissue samples are selected from tumor, lymph node, bone marrow or blood or a combination thereof. In certain preferred examples, the samples are from the lymph nodes.
  • The molecular grading methods as described herein cab be performed prior to or after therapeutic intervention for the proliferative disease, e.g. cancer. The therapeutic intervention can be selected from treatment with an agent or can be a surgical procedure. In this way, the methods for staging or re-staging a proliferative disease in a subject comprising detecting nucleic acid hypermethylation of one or more genes as described herein can be used as adjuvant or neoadjuvant therapy.
    • V. Samples
  • Samples for use in the methods of the invention include cells or tissues obtained from any solid tumor, samples taken from lymph nodes, from bone marrow or from blood. Additionally, the sample may be a sample that is taken from plasma, serum, sputum, or other fluid. Tumor DNA can be found in various body fluids and these fluids can potentially serve as diagnostic material.
  • Any nucleic acid specimen, in purified or nonpurified form, can be utilized as the starting nucleic acid or acids, provided it contains, or is suspected of containing, the specific nucleic acid sequence containing the target locus (e.g., CpG). Thus, the process may employ, for example, DNA or RNA, including messenger RNA, wherein DNA or RNA may be single stranded or double stranded. In the event that RNA is to be used as a template, enzymes, and/or conditions optimal for reverse transcribing the template to DNA would be utilized. In addition, a DNA-RNA hybrid which contains one strand of each may be utilized. A mixture of nucleic acids may also be employed, or the nucleic acids produced in a previous amplification reaction herein, using the same or different primers may be so utilized. The specific nucleic acid sequence to be amplified, i.e., the target locus, may be a fraction of a larger molecule or can be present initially as a discrete molecule, so that the specific sequence constitutes the entire nucleic acid. It is not necessary that the sequence to be amplified be present initially in a pure form; it may be a minor fraction of a complex mixture, such as contained in whole human DNA.
  • The nucleic acid-containing sample or specimen used for detection of methylated CpG may be from any solid tumor or any source including brain, colon, urogenital, hematopoietic, thymus, testis, ovarian, uterine, prostate, breast, colon, lung and renal tissue and may be extracted by a variety of techniques such as that described by Maniatis, et al. (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y., pp 280, 281, 1982).
  • If the extracted sample is impure (e.g., plasma, serum, stool, ejaculate, sputum, saliva, ductal cells, nipple aspiration fluid, ductal lavage fluid, cerebrospinal fluid or blood or a sample embedded in parrafin), it may be treated before amplification with an amount of a reagent effective to open the cells, fluids, tissues, or animal cell membranes of the sample, and to expose and/or separate the strand(s) of the nucleic acid(s). This lysing and nucleic acid denaturing step to expose and separate the strands will allow amplification to occur much more readily
  • Preferably, the method of amplifying is by PCR, as described herein and as is commonly used by those of ordinary skill in the art. However, alternative methods of amplification have been described and can also be employed. PCR techniques and many variations of PCR are known. Basic PCR techniques are described by Saiki et al. (1988 Science 239:487-491) and by U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,800,159, each of which is incorporated herein by reference.
  • The conditions generally required for PCR include temperature, salt, cation, pH and related conditions needed for efficient copying of the master-cut fragment. PCR conditions include repeated cycles of heat denaturation (i.e. heating to at least about 95° C.) and incubation at a temperature permitting primer: adaptor hybridization and copying of the master-cut DNA fragment by the amplification enzyme. Heat stable amplification enzymes like the pwo, Thermus aquaticus or Thermococcus litoralis DNA polymerases which eliminate the need to add enzyme after each denaturation cycle, are commercially available. The salt, cation, pH and related factors needed for enzymatic amplification activity are available from commercial manufacturers of amplification enzymes.
  • As provided herein an amplification enzyme is any enzyme which can be used for in vitro nucleic acid amplification, e.g. by the above-described procedures. Such amplification enzymes include pwo, Escherichia coli DNA polymerase I, Klenow fragment of E. coli polymerase I, T4 DNA polymerase, T7 DNA polymerase, Thermus aquaticus (Taq) DNA polymerase, Thermococcus litoralis DNA polymerase, SP6 RNA polymerase, T7 RNA polymerase, T3 RNA polymerase, T4 polynucleotide kinase, Avian Myeloblastosis Virus reverse transcriptase, Moloney Murine Leukemia Virus reverse transcriptase, T4 DNA ligase, E. coli DNA ligase or Q.beta. replicase. Preferred amplification enzymes are the pwo and Taq polymerases. The pwo enzyme is especially preferred because of its fidelity in replicating DNA.
  • Once amplified, the nucleic acid can be attached to a solid support, such as a membrane, and can be hybridized with any probe of interest, to detect any nucleic acid sequence. Several membranes are known to one of skill in the art for the adhesion of nucleic acid sequences. Specific non-limiting examples of these membranes include nitrocellulose (NITROPURE®) or other membranes used in for detection of gene expression such as polyvinylchloride, diazotized paper and other commercially available membranes such as GENESCREEN®, ZETAPROBE.RTM. (Biorad), and NYTRAN®. Methods for attaching nucleic acids to these membranes are well known to one of skill in the art. Alternatively, screening can be done in a liquid phase.
  • In nucleic acid hybridization reactions, the conditions used to achieve a particular level of stringency will vary, depending on the nature of the nucleic acids being hybridized. For example, the length, degree of complementarity, nucleotide sequence composition (e.g., GC v. AT content), and nucleic acid type (e.g., RNA v. DNA) of the hybridizing regions of the nucleic acids can be considered in selecting hybridization conditions. An additional consideration is whether one of the nucleic acids is immobilized, for example, on a filter.
  • An example of progressively higher stringency conditions is as follows:
    • 2×SSC/0.1% SDS at about room temperature (hybridization conditions);
    • 0.2×SSC/0.1% SDS at about room temperature (low stringency conditions);
    • 0.2×SSC/0.1% SDS at about 42° C. (moderate stringency conditions); and 0.1×SSC at about 68° C. (high stringency conditions). Washing can be carried out using only one of these conditions, e.g., high stringency conditions, or each of the conditions can be used, e.g., for 10-15 minutes each, in the order listed above, repeating any or all of the steps listed. However, as mentioned above, optimal conditions will vary, depending on the particular hybridization reaction involved, and can be determined empirically. In general, conditions of high stringency are used for the hybridization of the probe of interest.
  • The probe of interest can be detectably labeled, for example, with a radioisotope, a fluorescent compound, a bioluminescent compound, a chemiluminescent compound, a metal chelator, or an enzyme. Those of ordinary skill in the art will know of other suitable labels for binding to the probe, or will be able to ascertain such, using routine experimentation.
    • VI. Kits
  • The methods of the invention are ideally suited for the preparation of kits.
  • The invention features kits for identifying the nucleic acid hypermethylation state of one or more genes comprising gene specific primers for use in polymerase chain reaction (PCR), and instructions for use.
  • The invention also features kits for detecting metastases by detecting nucleic acid hypermethylation of one or more genes, the kit comprising gene specific primers for use in polymerase chain reaction (PCR), and instructions for use. In preferred embodiments, the metastases are micrometastases.
  • As described above, the PCR, in particularly preferred examples, is methylation specific PCR (MSP).
  • In certain embodiments, any gene comprising one or more CpG islands in the promoter region can be detected using the kits of the invention. In certain preferred examples, the one or more genes are selected from the group consisting of genes involved in tumor suppression, nucleic acid repair, anti-proliferation, apoptosis, ras signaling, adhesion, differentiation, development, and cell cycle regulation.
  • In certain preferred embodiments of the invention the genes can be detected in a panel consisting of the following:
  • (1) genes involved in tumor suppression and cell adhesion
  • (2) genes involved in cell cycle regulation and adhesion
  • (3) genes involved in tumor suppression and cell cycle regulation
  • (4) genes involved in ras signaling and cell cycle control
  • In certain examples, the genes are selected from the group consisting of: p-16, H-cadherin, APC, RASSF1A, MGMT, DAPK, and ASC
  • The kits can be used to detect hypermethylation of at least one of the genes as described herein. In some examples, can be used to detect hypermethylation of at least two of the genes as described herein. In other examples, the kits can be used to detect hypermethylation of at least three of the genes as described herein.
  • The two genes can be selected from the following: p-16 and H-cadherin, H-cadherin and APC, APC and p16, or RASSf1A and p16.
  • Carrier means are suited for containing one or more container means such as vials, tubes, and the like, each of the container means comprising one of the separate elements to be used in the method. In view of the description provided herein of invention methods, those of skill in the art can readily determine the apportionment of the necessary reagents among the container means. For example, one of the container means can comprise a container containing gene specific primers for use in polymerase chain reaction methods of the invention. In addition, one or more container means can also be included which comprise a methylation sensitive restriction endonuclease.
  • The following examples are offered by way of illustration, not by way of limitation. While specific examples have been provided, the above description is illustrative and not restrictive. Any one or more of the features of the previously described embodiments can be combined in any manner with one or more features of any other embodiments in the present invention. Furthermore, many variations of the invention will become apparent to those skilled in the art upon review of the specification. The scope of the invention should, therefore, be determined not with reference to the above description, but instead should be determined with reference to the appended claims along with their full scope of equivalents.
    • Examples
  • In the examples provided herein, gene hypermethylation versus traditional histopathology was tested to predict disease recurrence in solid tumors. The examples presented herein show that gene hypermethylation of not only the primary malignancy, but also lymph nodes, may be used to restage and assess prognosis of patients with stage I tumors, in particular examples patients with stage I NSCLC. These markers are shown to also be potential targets for reversal of gene silencing and may be important in adjuvant approaches to reduce disease recurrence.
    • Example 1 Patient Characteristics
  • Cases and controls were similar with respect to clinical and demographic variables, as shown in Table 1, below. By the American Society of Anesthesia Physical Status Classification, both cases and controls were equally fit for surgery. The most frequent site of recurrence was the ipsilateral chest (45%) followed by metastases to bone (14%), brain (12%) and mediastinum (12%). Although 15% of controls underwent sublobar resections, all pulmonary resections in controls were curative of cancer for the study period.
  • TABLE 1
    Table 1. Characteristics of the patients (N = 187).
    Recurrent Control Validation
    Group Group Group
    Characteristic (N = 51) (N = 116) (N = 20)
    Age - yr
    Median
    64 67 66
    Interquartile range 58-71 60-72 57-72
    Sex - no. (%)
    Male 24 (47.1) 54 (46.6) 8 (40.0)
    Female 27 (52.9) 62 (53.4) 12 (60.0)
    Race - no. (%)
    Caucasian 43 (64.3) 96 (62.7) 15 (75.0)
    African-American 6 (11.8) 19 (16.4) 5 (25.0)
    Other 2 (3.9) 1 (0.9) 0 (0.0)
    Stage - no. (%)
    IA (T1N0) 26 (51.0) 75 (64.7) 9 (45.0)
    IB (T2N0) 25 (49.0) 41 (35.3) 11 (55.0)
    Tumor Size - no. (%)
    <3 cm 25 (49.0) 72 (62.1) 13 (65.0)
    >3 cm 26 (51.0) 44 (37.9) 7 (35.0)
    Surgical Procedure -
    no. (%)
    Lobectomy 46 (90.2) 95 (81.9) 20 (100)
    Pnuemonectomy/ 4 (7.8) 4 (3.4) 0 0.0
    Bilobectomy
    Sublobar Resections 1 (2.0) 17 (14.7) 0 0.0
    Histology - no. (%)
    Adenocarcinoma* 30 (56.8) 62 (53.5) 15 (75.0)
    Squamous cell 15 (29.4) 42 (36.2) 4 (20.0)
    Other† 6 (11.8) 12 (10.3) 1 (5.0)
    Grade - no. (%)
    Well Differentiated 5 (9.6) 10 (8.6) 2 (10.0)
    Moderately 22 (43.1) 30 (25.9) 11 (55.0)
    Differentiated
    Poorly Differentiated 20 (39.3) 45 (36.8) 7 (35.0)
    Unknown 4 (7.8) 31 (26.7) 0 (0.0)
    ASA Physical Status  3  3  3
    Smoking - no. (%)
    Ever 43 (64.3) 102 (67.9) 20 (100)
    Never 8 (15.7) 12 (10.4) 0 (0.0)
    Unknown 0 (0.0) 2 (1.7) 0 (0.0)
    *Includes bronchioloalveolar carcinoma and adeno-squamous histologies
    †Other includes large cell, basaloid, and mucoepidermoid.
    ASA—American Society Anesthesia Physical States Classification
    Cases were matched with controls on age, sex, stage, and date of surgery.
    • Example 2 Risk of Recurrence-Gene Methylation
  • Risk of Recurrence Using Clinical Predictors
  • The clinicopathologic covariates of pathologic stage, age, sex, tumor histology, smoking, and race did not predict risk of disease recurrence in NSCLC patients with histological negative lymph nodes, as shown in Table 2, below. Pathologic tumor stage showed the strongest risk for predicting disease recurrence independent of other covariates, with patients with stage 1B disease (T2 malignancies ≧3 cm and/or visceral pleural invasion) having a 1.71 (95%CI, 0.86-3.41) fold risk for disease recurrence compared to patients with smaller sized tumors and no pleural invasion (stage 1A).
  • TABLE 2
    Supplemental Table 2. Crude and Adjusted Odds Ratios
    (ORs) and 95% Confidence Limits for Risk of Recurrence
    for Selected Demographic Characteristics.
    Characteristic Crude OR 95% CL Adjusted OR* 95% CL
    Stage
    1A 1.00 — 1.00 —
    1B 1.76 0.90-3.43 1.71 0.88-3.41
    Age, continuous 0.98 0.94-1.01 0.97 0.94-1.01
    Sex
    Female 1.00 — 1.00 —
    Male 1.02 0.53-1.97 0.98 0.49-1.96
    Race
    Caucasian 1.00 — 1.00 —
    African American 0.89 0.36-2.19 0.84 0.33-2.12
    Histology
    Adenocarcinoma 1.00 — 1.00 —
    Squamous Cell 0.79 0.37-1.66 0.81 0.37-1.79
    Other** 1.07 0.36-3.18 0.89 0.28-2.76
    Smoking status
    Never 1.00 — 1.00 —
    Ever 0.63 0.24-1.66 0.72 0.26-1.99
    *Multivariable logistic regression model adjusted for stage (1A/1B), age (continuous), sex, race (C/AA), histology (adenocarcinona, squamous celll, other), smoking status (ever/never).
  • Gene Methylation Predicts Risk of Recurrence in Tumor and Lymph Nodes
  • Methylation profiles using 7 genes were obtained on 727 of 731 paraffin blocks corresponding to 167 patients. The prevalence for methylation of four genes, p16, H-cadherin, RASSF1A and APC, especially in tumors and/or N2 lymph nodes, differed between cases and controls, as shown in Table 3.
  • TABLE 3
    Table 2. Prevalence of Individual Gene Hypermethylation in Tumor,
    N1, and N2 Lymph Nodes in Recurrent Cases and Controls. (N = 167)
    Tumor Samples N1 Lymph Node Samples N2 Lymph Node Samples
    Control Case Control Case Control Case
    (n = 104) (n = 50) p- (n = 82) (n = 41) p- (n = 56) (n = 34) p-
    Characteristics % % value* % % value* % % value*
    MGMT 0.87 0.36 0.44
    Methylated 36.1 34.7 29.5 37.5 35.8 44.1
    ASC 0.65 0.81 0.91
    Methylated 34.9 38.8 27.2 29.3 42.9 44.1
    DAPK 0.93 0.91 0.41
    Methylated 35.3 36.0 41.5 42.5 30.8 39.4
    APC 0.81 0.46 0.06
    Methylated 34.0 36.0 18.7 13.5 13.0 29.4
    RASSF1A 0.10 0.61 0.15
    Methylated 35.9 50.0 16.5 12.8 9.6 20.6
    P16 <0.01 <0.01 <0.01
    Methylated 26.0 52.0 13.7 35.0 16.7 48.5
    H-Cadherin 0.04 0.12 0.04
    Methylated 22.8 38.8 19.5 32.5 25.0 46.9
    *Chi-squared test for homogeneity.
  • FIG. 1 shows multivariate logistic regression analysis that was performed using the four genes that exhibited the largest univariate distribution differences in methylation: p16, H-cadherin, APC, and RASSF1A. The prognostic value of each molecular variable was assessed in a model that adjusted for stage (1A/1B), age (continuous), sex, race (Caucasian/African American), histology (adenocarcinoma, squamous cell, other), smoking status (ever/never) and then graphed as a Forest Plot. On the whole, regardless of the genes considered, hypermethylation of the mediastinal lymph node tissue had the highest prognostic value for estimating lung cancer recurrence versus no methylation. As single gene epigenetic markers, methylation of both p16 and H-cadherin had robust odds ratios for recurrence for primary tumor, regional, and mediastinal lymph nodes. Methylation of either RASSF1A or APC in primary tumor or N2 nodes was also associated with a modest elevation in odds of recurrence but this was not statistically significant. If a patient with pathologic stage 1 disease (T1-2N0) had concomitant methylation of p16 as well as H-cadherin in both tumor and mediastinal lymph nodes, the estimated odds of lung cancer recurrence was over 15 as compared to those patients without concomitant methylation in these tissues. In particular, when either p16 or H-cadherin was methylated in the primary tumor, the adjusted odds of recurrence was 3.50 (95%CI, 1.65-7.41) and 2.12 (95%CI,0.98-4.59), respectively (FIG. 1). When these same genes were methylated in N1 lymph nodes, the odds of recurrence was 3.62 (95%CI, 1.41-9.32) and 1.99 (95%CI,0.81-4.88), respectively. If methylation of p16 or H-cadherin was observed in mediastinal lymph nodes, the odds of recurrence was increased to 4.67 (95%CI,1.52-14.4) and 3.98 (95%CI,1.22-13.0) fold, respectively, as shown in FIG. 1. Methylation of either RASSF1A or APC in primary NSCLC or N2 nodes was also associated with a modest elevation in risk for recurrence but this was not statistically significant (FIG. 1).
  • Two gene combinations of methylation, for p16 and H-cadherin, H-cadherin and APC, APC and p16, as well as RASSF1A and p16, all were associated with increased risks of recurrence, especially in either primary tumors or N2 nodes (FIG. 1). Concomitant methylation of the best gene combination, p16 and H-cadherin, was significantly associated with recurrent cancer in all three tissue types—primary tumor, N1, as well as N2 lymph nodes. If a patient exhibited methylation of p16 and H-cadherin in the primary tumor, the odds of recurrence was eight times higher than if there was no methylation. Even more striking, positive p16 and H-cadherin methylation in both paired primary tumors and mediastinal lymph nodes denotes an estimated odds of recurrent cancer of 15.5 (95%CI, 1.61-185) (FIG. 1), with a positive predictive value of 86%.
  • The above findings were re-tested for methylation of the 4-gene panel by assaying the methylation status of these genes in a validation set. 162 separate samples were obtained, representing an independent set of 20 stage 1 patients (11 cases and 9 controls) resected at a later date at the Johns Hopkins Hospital (“the institution”), as shown in Table 1, above.
  • FIG. 2 shows Kaplan-Meier Estimates of Recurrence-Free Survival of Pathologic Stage 1 Lung Cancer Patients (n=167) at the Johns Hopkins Hospital, according to the number of methylated genes in a 4-gene panel at the time of surgical resection. The Kaplan-Meier estimates for time to recurrence indicate that for both tumor as well as for regional (N1) and mediastinal (N2) lymph nodes, as the number of methylated genes in the panel increases, there is a significant reduction in the recurrence-free survival (Panels A-C, E-G). Furthermore, if concomitant methylation of both tumor and mediastinal lymph nodes versus little or no methylation is considered (Panels D and H), the Kaplan-Meier estimates reflect the recurrence-free survivals of patients with a clinically useful risk classification system as determined by our epigenetic marker panel. Patients without methylation of the gene combination p16 and H-cadherin in both primary tumor and mediastinal lymph nodes have a significantly improved 5 year recurrence-free period than those with these genes methylated (64% vs. 14%, p<0.001, respectively, Panel H). An independent cohort of 20 patients validated the above findings as those with concomitant methylation of both tumor and mediastinal lymph nodes in two or more genes had a shorter time to recurrence than those with two or more genes unmethylated in these tissues (Panel I). Similarly, concomitant methylation of p16 and H-cadherin in tumors and N2 nodes resulted in a worse 5 year disease-free recurrence than if no methylation of this gene combination occurred (Panel J). In the combined original and validation datasets (n=187), patients with 2 or more genes in tumor and N2 nodes methylated also have a worse 5 year recurrence rate than those with these genes unmethylated in both tissues (Panel K). For both the original and validation patients with p16 and H-cadherin measured, both genes methylated in the tumor and N2 nodes resulted in a significantly shorter time to recurrence than if p16 and H-cadherin were unmethylated (Panel L). As was the case with the original cohort, univariate and multivariate analysis showed that methylation of the panel of genes in both tumor and lymph nodes was more predictive of disease recurrence than any clinical or pathological variable (FIG. 2: Panels I and J). In particular, positive p16 and H-cadherin methylation in both paired primary tumors and mediastinal lymph nodes occurred in 4 cases and no controls yielding an infinite odds of recurrent disease reflected in FIG. 2, Panel J. This finding strongly supports the original finding of an elevated odds ratio for recurrence when p16 and H-cadherin methylation is found in these tissues (FIG. 1). Moreover, the estimated odds of recurrent cancer for the original and validation datasets combined, for this gene combination when found in both tumor and N2 nodes, increased to 25.25 (95%CI, 2.53-252.35). This is shown in Table 4, below.
  • TABLE 4
    Table 3. Multivariate Odds Ratios (OR) and 95% Confidence
    Limits (95% CL) for Estimation of Risk of Recurrence
    by Methylation Status for Selected Gene Markers.
    Original Original and Validation
    (n = 167) (n = 187)
    Gene Marker OR* 95% CL OR* 95% CL
    Single Genes Unmethylated 1.00 referent 1.00 referent
    APC
    Tumor 0.95 0.45-2.04 1.31 0.67-2.58
    N1 0.69 0.22-2.10 0.78 0.32-1.91
    N2 2.26 0.66-7.71 1.67 0.65-5.56
    Tumor and N2 2.37  0.52-10.83 2.00 0.55-7.33
    RASSF1A
    Tumor 1.79 0.85-3.75 1.65 0.94-3.63
    N1 0.71 0.23-2.20 0.82 0.31-2.15
    N2 1.66 0.43-6.43 2.13 0.65-6.96
    Tumor and N2 0.66 0.11-3.68 0.97 0.23-3.98
    P16
    Tumor 3.50 1.55-7.41 3.55 1.77-7.13
    N1 3.52 1.41-9.32 4.14 1.81-9.49
    N2 4.67  1.53-14.42 5.09  1.96-13.18
    Tumor and N2 5.23  1.33-20.46 8.41  2.42-29.20
    HCAD
    Tumor 2.12 0.98-4.59 2.33 1.16-4.69
    N1 1.99 0.81-4.88 2.67 1.20-5.93
    N2 3.98  1.22-13.01 4.04  1.53-13.63
    Tumor and N2 6.89  1.36-34.87 7.55  1.98-25.60
    Gene APC & RASSF1A
    Combinations Tumor 1.88 0.74-4.78 2.25 1.02-5.00
    N1 1.22  0.15-14.53 2.34  0.46-11.75
    N2** — — 3.49  0.30-40.75
    Tumor and N2** — — 2.37  0.17-33.12
    APC & P16
    Tumor 4.16  1.60-10.81 4.48  1.91-10.51
    N1 2.59  0.34-19.74 2.43 0.59-9.94
    N2 13.10  1.20-142.73 7.45  1.35-41.20
    Tumor and N2 5.27  0.38-73.57 7.70  0.70-84.879
    APC & HCAD
    Tumor 1.54 0.55-4.31 2.14 0.94-4.91
    N1 2.24  0.41-12.22 3.30  0.88-12.40
    N2 4.58  1.50-20.01 3.13  0.89-11.01
    Tumor and N2 11.79  0.65-163.34 9.48  0.87-103.16
    RASSF1A & P16
    Tumor 5.95  2.15-16.56 5.25  2.13-13.00
    N1 1.07 0.15-7.55 1.92 0.39-9.45
    N2 3.01  0.49-18.64 4.60  0.85-25.03
    Tumor and N2 2.91  0.24-35.36 3.67  0.32-41.69
    RASSF1A & HCAD
    Tumor 1.51 0.69-3.89 1.71 0.78-3.74
    N1 0.49 0.09-2.63 0.68 0.25-3.04
    N2 1.36 0.22-8.48 1.91 0.40-9.21
    Tumor and N2 2.49  0.16-34.29 3.51  0.32-39.57
    P16 & HCAD
    Tumor 8.00  2.50-25.51 6.71  2.50-18.00
    N1 4.08  1.05-15.70 6.13  1.99-18.69
    N2 4.32  1.06-17.65 4.66  1.53-14.16
    Tumor and N2 15.50  1.61-185.02 25.25  2.53-252.35
    *Multivariate logistic regression model adjusted for stage (1A/1B), age (continuous), sex, race (C/AA), histology (adenocarcinoma, squamous cell, other), smoking status (ever/never).
    **No Methylation in controls.
    • Example 3 Tumor Biology and Translational Implications
  • An observation is that, among those 51 patients in the cohort who recurred, the presence of methylation in more than two genes in paired primary tumors and mediastinal lymph nodes identifies those who recur early versus those cases without markers that recur late (9 months (range 5-30) vs. 25 months (range 6-40);p0.04). Thus, those who lack these epigenetic marks recur late and appear to behave similarly to control patients who do not have recurrences within the 40 month time frame studied, as is reflected in the various risk for recurrence curves shown in FIG. 2.
  • Second, estimates of time to recurrence indicate that for both cases and controls, as the number of methylated genes in the 4-gene panel increases in primary tumor, regional and mediastinal lymph nodes, there is a significant reduction in recurrence-free survival (FIG. 2: Panels A-C, E-G). Moreover, if concomitant methylation of both tumor and mediastinal lymph nodes is considered (Panels D and H), the prognostic value of the epigenetic markers is further increased. In Panels D and H, the recurrence estimates of the stage 1 subjects with ≧2 genes methylated reflect the historic cancer-specific survivals of patients who would be pathologically staged as stage 3 or higher (5). In the original cohort, those patients with the combination of p16 and H-cadherin methylation in tumor and mediastinal lymph nodes have a significantly reduced 5-year recurrence-free survival compared to those without methylation (64% vs. 14%, p<0.001, respectively). This finding also emerged in the small validation study of 20 patients as shown in FIG. 2, panel J. Moreover, patients in the validation set with ≧2 genes methylated in tumor and mediastinal lymph nodes have significantly reduced 5-year recurrence-free survivals compared to those without methylation (FIG. 2, panel I). Thus, when the original and validation datasets are combined, the methylation status for these parameters is now even more strongly prognostic of disease-free survival (FIG. 2, panels K and L).
  • In the entire study population including the original and validation patients, 91 individuals, 50 controls and 41 cases, had p16 and H-cadherin methylation measured in both primary tumor and N2 lymph nodes. Of those patients who were positive for both markers in both sites, 10 of 11 were cases. All 10 had disease recurrence within 30 months, 9 within 17 months, and 8 within a year. Thus, the methylation status of p16 and H-cadherin in tumor and N2 nodal DNA, appears to identify a subset, 25%, of stage 1 patients with a likelihood of rapid disease recurrence with a positive predictive value of 91% and a specificity of 98%.
  • The results presented herein demonstrate two related features for the detection of promoter region methylation in cancer. First, the detection of promoter methylation within the resected primary tumor for key genes can be associated with a more aggressive, recurrent phenotype as has been shown in other settings (28,29). The loss of function in key regulatory genes for cell cycle control (p16), invasion and metastasis (H-Cadherin, APC), as well as Ras signaling (RASSF1a) might be expected to result in a more aggressive primary tumor. In addition, the ability to detect methylation within local or regional nodes provides a second layer of information to this subset identification, and demonstrates an additional approach for detecting micrometastatic disease.
  • The data presented herein demonstrate that this approach may be used to identify aggressive stage 1 lung cancer patients who were not staged optimally by routine pathological analysis. The current staging system for NSCLC is imprecise, and in stage 1 (T1-2N0) disease, in particular, the clinicopathologic criteria understages patients. The results presented herein show that gene promoter methylation detection within NSCLC primary tumors can be used to identify cells with high potential for metastatic spread, and also to detect histologically occult micrometastases in lymph nodes used to stage NSCLC. Although it is possible that the methylation detected could represent free tumor DNA that has drained from the primary tumor via lymphatics, this is unlikely, particularly for N2 nodes, since these are located distant from the lung in a separate body compartment, the mediastinum. While the detection of methylation of these genes in tumor or N1 nodes was often associated with increased risk of recurrence, in the N2 lymph nodes, especially, the markers were very strongly prognostic, strengthening the contention that the DNA methylation is detecting micrometastatic disease. This molecular distribution of markers in patients with rapid recurrence mirrors the biological basis of current histological staging systems that identify intact tumor cells that have traversed the mediastinal pleura to the N2 nodes and are associated with increased risk of recurrence.
  • The methods described herein present a molecular tool that parallels the use of histologic examination in accepted clinical pathology practice, but is more sensitive. This differs from previous studies that have relied solely on molecular characteristics of the primary malignancy (30-33). This ability to utilize the predictive power inherent in identifying micrometastases to lymph nodes may allow a more robust and reliable molecular staging built upon tumor characteristics and the detection of micrometastatic disease. Furthermore, recent promising results from examining methylation changes in sputum for predicting risk of lung cancer (34), or its recurrence (18), means the detection of these changes could provide valuable pre-surgical information as to disease stage and the metastatic potential of a patient's tumor.
    • Methods
  • The invention was carried out using methods that include the following.
    • Patients
  • Evidence for recurrent disease was evaluated on 715 pathologically proven stage 1 (T1-2N0) patients diagnosed with non-small cell lung carcinoma (NSCLC) (International Classification of Diseases-ninth revision-Clinical Modification [ICD-9-CM] code 162.3-162.9) who underwent lobectomy or greater resections at the Johns Hopkins Hospital between Jan. 1, 1986 and Jul. 31, 2002. Only patients followed for recurrent disease at the institution were eligible for the analysis. The study cohort consisted of 71 patients (cases) who despite receiving surgery with curative intent for pathological stage 1 (T1-2N0) primary NSCLC, recurred at the institution within 40 months of surgery and died of their cancer. It was estimated that by 40 months approximately 80% of patients with resected stage 1 lung cancer would recur. Using patient age, stage, date of surgery (within 5 years), and sex, the cases were matched to 158 stage 1 patients (controls) from the remainder of the study population. These 71 cases and 158 controls formed the basic case-control population. From the above patients, samples were gathered for methylation analysis for 51 cases and 116 matched controls. Neither cases nor controls received adjuvant chemotherapy since surgery was performed between 1986-2002 when guidelines did not recommend adjuvant therapy for stage 1B patients (20, 21). All patients were staged according to the new TNM classification criteria (5), which include histological status of mediastinal lymph nodes sampled from levels 2, 4, 7, 8, 9, and 10 on the right, and 5, 6, 7, 8, 9 on the left side. Regional lymph nodes, confined to the pleural space, were resected en bloc with the tumor. Patients were excluded as cases if they had surgery involving less than a lobectomy because there is strong evidence that patients with such resections are at significantly increased risk of local recurrence (22). Patients were also excluded as cases if they had any macroscopic or microscopically positive surgical margins, or underwent incomplete resection. In accord with this nested design, seven individuals with recurrences after 40 months postoperatively were considered as controls. The 20 patients in the validation set, consisting of 11 cases and 9 matched controls, had 162 paraffin blocks evaluated. All cases in the independent validation cohort, except for two, underwent resection at our institution after August 2002. The study was approved by the Institutional Review Board of the Johns Hopkins Medical Institutions.
    • Preparation of Tumor and Lymph Nodes
  • All specimens were labeled only with study-specific coded identifiers to blind laboratory investigators as to case or control status as well as to whether DNA samples came from tumor or lymph nodes. DNA was extracted from three sequential 10 μm sections from unstained, paraffin embedded slides of resected tumors and lymph nodes (both N1 and N2). For each sample, adjacent sections were H&E stained for histological confirmation of either the presence of malignancy for tumor samples, or the lack of neoplastic cells for all lymph nodes. Tumor grading was at the time of surgery. Unstained tissue sections were deparaffinized and DNA was extracted as described previously23. DNA was quantified spectrophotometrically, and 1 μg was denatured with sodium hydroxide and modified with sodium bisulfite. Samples were then purified with the Wizard DNA purification resin (Promega, Madison, Wis.), treated again with sodium hydroxide, precipitated with ethanol, and resuspended in water.
    • Methylation Specific PCR (MSP)
  • DNA methylation, for all lung cancer and lymph node DNA, was determined by MSP performed by 3 individuals blinded to the results of other investigators. Each individual extracted DNA and performed all steps of the MSP reaction separately. There were 889 total samples of tumor and lymph nodes examined. A multiplex-nested MSP assay as previously described was used for all samples24. The nested approach amplifies bisulfite-modified DNA initially with flanking PCR primers without preferentially amplifying methylated or unmethylated DNA. The resulting fragment is then used as the template for MSP. Primer sequences and conditions of p16, MGMT, DAPK, RASSF1A, H-cadherin, ASC and APC have all been previously describedl6, 18, 24-26 including conditions optimized to achieve specific detection of methylation in tumor but not in normal lymphocytes, and are shown in Table 5, below (16, 18, 24-26).
  • TABLE 5
    Supplemental Table 1: METHYLATED SPECIFIC
    PCR CONDITIONS USED
    FLANK PCR for APC, MGMT, ASC, P16, DAPK, H-CADHERIN,
    RASSF1A: Using 1:500 diluted Flank PCR product as the
    PCR templates:
    95° C. 5 Min  1 cycle
    95° C. 30 Sec
    55° C. 30 Sec
    72° C. 40 Sec 36 cycles
    72° C. 5 Min  1 cycle
    INSIDE PCR for APC, MGMT, DAPK, RASSF1A:
    95° C. 5 Min  1 cycle
    95° C. 30 Sec
    60° C. 30 Sec
    72° C. 30 Sec 25 cycles
    72° C. 5 Min  1 cycle
    INSIDE for P16:
    95° C. 5 Min  1 cycle
    95° C. 30 Sec
    64° C. 30 Sec
    72° C. 30 Sec 20 cycles
    72° C. 5 Min  1 cycle
    INSIDE for ASC:
    95° C. 5 Min  1 cycle
    95° C. 30 Sec
    66° C. 30 Sec
    72° C. 30 Sec 20 cycles
    72° C. 5 Min  1 cycle
    INSIDE for H-CADHERIN:
    95° C. 5 Min  1 cycle
    95° C. 30 Sec
    64° C. 30 Sec
    72° C. 30 Sec 30 cycles
    72° C. 5 Min  1 cycle
  • FIG. 3 shows methylation specific PCR for the H-cadherin gene in 36 samples of tumors and lymph nodes, numbered at top of each panel. * represents the molecular weight marker. For each sample, the presence of a visible PCR product in Lanes U indicates the presence of an unmethylated promoter region amplified and serves as a control for sample preparation; the presence of product in Lanes M indicates a methylated gene promoter and was scored as positive for methylation. Samples 7 and 16 did not amplify for this gene. Samples 1, 2, 3, 4, 8, 9, 11, 13, 14, 20, 21, 22, 23, 26, 30, 32, 33, 36 are scored as unmethylated. Samples 5, 10, 12, 15, 17, 18, 19, 25, 27, 28, 31, 34, and 35 are methylated and samples 24 and 29 had very minimal M amplification that was scored as negative. Placental DNA treated in vitro with SssI methyltransferase (New England Biolabs, Beverly, Mass.) was used as a positive control. DNA from normal lymphocytes and water (bisulfite-modified and unmodified water) were used as negative controls. PCR products were visualized using 2% agarose or 6% nondenaturing polyacrylamide gels, and visually scored as methylated or unmethylated according to the presence or absence of a PCR product (FIG. 3), blinded to both the clinical outcomes and sources of DNA. (9, 25, 27).
    • Statistical Methods
  • Histopathological results and reports of events (death, or recurrent disease) were verified during follow-up by reexamining original hospital paper and electronic records. The primary endpoint was recurrent disease (including local, regional, and distant recurrences), measured from the date of surgery to cancer-related death or censor. Control subjects who were alive and had no evidence of disease at the end of study were censored for recurrence and death. All deaths were cancer-related and no subjects were lost to follow-up. The association between prognostic factors and recurrence (case vs. control) was assessed using univariable and multivariable logistic regression. Results of all models are reported as relative risks with 95% confidence intervals (Stata Statistical Software, College Station, Tex.). Associations were considered to be significant when P was <0.05 (two-sided).
  • It was hypothesized that 40 percent or more of the cases would have positive microscopic disease in their lymph nodes. For controls, this number was expected to be less than or equal to 20 percent, yielding a risk ratio of 2. Under these assumptions, the study would have 80 percent power to detect the effect as statistically significant (two-sided 0.05 alpha level test) with 167 subjects and 2:1 matching.
  • The present invention has been described in detail, including the preferred embodiments thereof. However, it will be appreciated that those skilled in the art, upon consideration of the present disclosure, may make modifications and/or improvements of this invention and still be within the scope and spirit of this invention as set forth in the following claims.
  • All publications and patent documents cited in this application are incorporated by reference in their entirety for all purposes to the same extent as if each individual publication or patent document were so individually denoted. By their citation of various references in this document, Applicants do not admit any particular reference is “prior art” to their invention.
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Claims (30)

1. A method for identifying metastases in a subject comprising detecting nucleic acid hypermethylation of one or more genes in one or more samples, wherein detecting nucleic acid hypermethylation identifies metastases.
2. The method of claim 1, wherein the sample comprises cells or tissues selected from the group consisting of: tumor, lymph nodes, bone marrow and blood.
3-5. (canceled)
6. A method for identifying metastases in a subject comprising detecting nucleic acid hypermethylation of one or more genes in tumor tissue or lymph node, wherein the genes are selected from the group consisting of: genes involved in tumor suppression, DNA repair, apoptosis, anti-proliferation, ras signaling, adhesion, differentiation, development, and cell cycle regulation, wherein detecting nucleic acid hypermethylation identifies metastases.
7-11. (canceled)
12. A method for identifying micrometastases in a subject comprising detecting nucleic acid hypermethylation of at least one or more genes in a sample comprising tumor and lymph nodes, wherein the sample genes are selected from the group consisting of: H-cadherin, p16, APC, RASSF1A, MGMT, DAPK, and ASC, and wherein detecting nucleic acid methylation identifies micrometastases.
13. The method of claim 12, wherein hypermethylation of at least two of the genes is detected.
14. The method of claim 11, wherein at least two of the genes are selected from p-16 and H-cadherin, H-cadherin and APC, APC and p16, or RASSf1A and p16.
15. The method of claim 1 claim 1, wherein the detection of metastases is used to detect or diagnose a proliferative disease.
16-19. (canceled)
20. A method for detecting or diagnosing a proliferative disease in a subject comprising detecting nucleic acid hypermethylation of one or more genes in one or more samples, wherein detecting nucleic acid hypermethylation is used to detect or diagnose a proliferative disease.
21. A method for predicting the recurrence of a proliferative disease in a subject comprising: detecting nucleic acid hypermethylation of one or more genes wherein detecting nucleic acid hypermethylation of one or more genes is a predictor of the recurrence of a proliferative disease.
22. The method of claim 21, wherein hypermethylation of one or more genes is detected in tumor or lymph nodes.
23. (canceled)
24. A method for staging or re-staging a proliferative disease in a subject comprising: detecting nucleic acid hypermethylation of one or more genes wherein detecting nucleic acid hypermethylation is used for staging or re-staging a proliferative disease.
25-26. (canceled)
27. A method for determining the prognosis of a subject suffering from a proliferative disease comprising: detecting nucleic acid hypermethylation of one or more genes wherein the detection of nucleic acid hypermethylation is used for determining the prognosis of a subject suffering from a proliferative disease.
28-34. (canceled)
35. A method for detecting or diagnosing a proliferative disease in a subject comprising:
extracting nucleic acid from one or more cell or tissue samples;
detecting nucleic acid hypermethylation of one or more genes in the sample; and
identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes indicates a proliferative disease.
36. A method for predicting the recurrence of a proliferative disease in a subject comprising:
extracting nucleic acid from one or more cell or tissue samples;
detecting nucleic acid hypermethylation of one or more genes in the sample; and
identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes is indicative of the recurrence of a proliferative disease.
37. A method for staging or re-staging a proliferative disease in a subject comprising:
extracting nucleic acid from one or more cell or tissue samples;
detecting nucleic acid hypermethylation of one or more genes in the sample; and
identifying the nucleic acid hypermethylation state of one or more genes, wherein nucleic acid hypermethylation of genes is used for staging or re-staging of a proliferative disease.
38-42. (canceled)
43. A method of treating a subject having or at risk for having a proliferative disease comprising:
identifying nucleic acid hypermethylation of one or more genes, where nucleic acid hypermethylation indicates having or a risk for having a proliferative disease; and
administering to the subject a therapeutically effective amount of a demethylating agent,
thereby treating a subject having or at risk for having a proliferative disease.
44-54. (canceled)
55. A method of identifying an agent that de-methylates hypermethylated nucleic acid comprising:
identifying one or more cell or tissue samples with hypermethylated nucleic acid;
extracting the hypermethylated nucleic acid;
contacting the nucleic acid with one or more nucleic acid de-methylating candidate agents and a control agent;
identifying the nucleic acid hypermethylation state, wherein nucleic acid de-methylation of genes in the sample by the candidate agent compared to the control indicates a demethylating agent,
thereby identifying an agent that de-methylates hypermethylated nucleic acid.
56-70. (canceled)
71. A kit for identifying the nucleic acid hypermethylation state of one or more genes comprising gene specific primers for use in polymerase chain reaction (PCR), and instructions for use.
72. A kit for detecting metastases by detecting nucleic acid hypermethylation of one or more genes, the kit comprising gene specific primers for use in polymerase chain reaction (PCR), and instructions for use.
73. hThe kit of claim 72, wherein the metastases are micrometastases.
74-82. (canceled)
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