Genomic screen for epigenetically silenced genes associated with cancer
AssigneeThe Johns Hopkins University School of Medicine
InventorsStephen B. Baylin, James Herman, Hiromu Suzuki
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Abstract
A method of identifying epigenetically silenced genes, e.g., methylation silenced genes, in cancer cells is provided. In addition, methods of identifying a cancer by detecting epigenetic silencing of gene expression are provided, as are methods of treating a subject having such a cancer, for example, a colorectal cancer and/or gastric cancer. Reagents for practicing such methods also are provided.
Claims127
A method of identifying at least one methylation silenced gene associated with at least one cancer, comprising:
- a) contacting an array of nucleotide sequences representative of a genome with nucleic acid subtraction products, which comprise nucleic acid molecules corresponding to RNA expressed in cancer cells contacted with a demethylating agent but not nucleic acid molecules corresponding to RNA expressed in normal cells corresponding to the cancer cells, under conditions suitable for selective hybridization of nucleic acid subtraction products to complementary nucleotide sequences of the array;
- and
- b) detecting selective hybridization of nucleic acid subtraction products to a subpopulation of nucleotide sequences of the array,
- wherein nucleic acid molecules corresponding to RNA expressed in the normal cells corresponding the cancer cells do not hybridize to the subpopulation of nucleotide sequences under said conditions suitable for selective hybridization, whereby the nucleic acid subtraction products that selectively hybridize to the subpopulation of nucleotide sequences of the array represent methylation silenced genes of the cancer cells, thereby identifying at least one methylation silenced genes associated with at least one cancer.
A method of identifying at least one epigenetically silenced gene associated with at least one cancer, comprising:
- a) contacting an array of nucleotide sequences representative of a genome with nucleic acid subtraction products, which comprise nucleic acid molecules corresponding to RNA expressed in cancer cells contacted with at least one agent that reactivates expression of epigenetically silenced genes but not RNA expressed in normal cells corresponding to the cancer cells, under conditions suitable for selective hybridization of nucleic acid subtraction products to complementary nucleotide sequences of the array;
- and
- b) detecting selective hybridization of nucleic acid subtraction products to a subpopulation of nucleotide sequences of the array,
- wherein nucleic acid molecules corresponding to RNA expressed in the normal cells corresponding the cancer cells do not hybridize to the subpopulation of nucleotide sequences under said conditions suitable for selective hybridization,
- whereby the nucleic acid subtraction products that selectively hybridize to the subpopulation of nucleotide sequences of the array represent epigenetically silenced genes of the cancer cells, thereby identifying at least one epigenetically silenced genes associated with at least one cancer.
A method for identifying a cell that exhibits or is predisposed to exhibiting unregulated growth, comprising detecting, in a test cell, epigenetic silencing of at least one gene comprising a nucleic acid molecule as set forth in Table 1, or a combination thereof, thereby identifying the test cell as a cell that exhibits or is predisposed to exhibiting unregulated growth.
A method of reducing or inhibiting unregulated growth of a cell exhibiting epigenetic silenced transcription of at least one gene associated with a cancer, the method comprising restoring expression of a polypeptide encoded by the epigenetic silenced gene in the cell, thereby reducing or inhibiting unregulated growth of the cell.
A method for treating a cancer patient, wherein cancer cells in the patient exhibit epigenetic silenced expression of at least one gene, the method comprising restoring expression of the at least one epigenetic silenced gene in cancer cells in the subject, thereby treating the cancer patient.
A method for selecting a therapeutic strategy for treating a cancer patient, comprising:
- a) identifying at least one methylation silenced gene associated with the cancer by
- contacting an array of nucleotide sequences representative of a genome with nucleic acid subtraction products, which comprise nucleic acid molecules corresponding to RNA expressed in cancer cells of the patient contacted with at least one agent that reactivates expression of methylation silenced genes but not RNA expressed in normal cells corresponding to the cancer cells, under conditions suitable for selective hybridization of nucleic acid subtraction products to complementary nucleotide sequences of the array;
- and
- detecting selective hybridization of nucleic acid subtraction products to a subpopulation of nucleotide sequences of the array, wherein nucleic acid molecules corresponding to RNA expressed in the normal cells corresponding the cancer cells of the patient do not hybridize to the subpopulation of nucleotide sequences under said conditions suitable for selective hybridization, whereby the nucleic acid subtraction products that selectively hybridize to the subpopulation of nucleotide sequences of the array represent methylation silenced genes in the cancer cells of the patient;
- and
- b) selecting an agent useful for restoring expression of the at least one methylation silenced gene in cancer cells of the patient, thereby selecting a therapeutic strategy for treating a cancer patient.
A method of treating a subject suffering from colorectal cancer (CRC), gastric cancer (GC), or CRC and GC, wherein cells associated with the CRC or GC contain at least one methylation silenced gene, comprising administering an amount of an agent that restores expression of the at least one methylation silenced gene to the subject sufficient to restore expression of the methylation silenced gene in cells associated with the CRC, RC or CRC and GC.
An isolated oligonucleotide, comprising any one of SEQ ID NOS:
- 1 to 296.
An amplification primer pair, comprising a forward primer and a reverse primer as set forth in SEQ ID NOS:
- 1 to 296, wherein the amplification primer pair can amplify a portion of a nucleic acid molecule of Table 1.
Dependencies are inferred from the claim text.