Epigeneiic silencing of NMT2
The finding that multiple cancers lack one of two NMTs, while stromal and normal tissues do not, enables the treatment of NMT2-deficient cancer cells with an NMT inhibitor. It is shown herein that NMT2 expression is reduced or eliminated in certain cancers, and in one example lymphomas, via an epigenetic mechanism(s). Reduction or elimination of NMT2 expression renders the cancer sensitive inhibitors of NMT.
1. A method comprising determining hypermethylation of a promoter region of an NMT2 gene in a tumor sample from a human subject with lymphoma, optionally compared to a control, and administering an NMT inhibitor to said subject, wherein said NMT inhibitor is DDD85646 or DDD86481, wherein determining hypermethylation of the promoter region of the NMT2 gene comprises:
i) performing bisulfite modification to a nucleic acid obtained from the sample of the subject,
ii) determining methylation of the promoter region of the NMT2 gene in the bisulfite-modified nucleic acid of the sample using PCR primers and/or probes specific for the promoter region of the NMT2 gene, optionally wherein the methylation of the promoter region is compared to a control.
2. A method comprising:
a) obtaining nucleic acid from a tumor sample from a human subject with lymphoma;
b) determining hypermethylation of a promoter region of an NMT2 gene in the sample, optionally compared to a control, and
c) administering an NMT inhibitor to said subject, wherein said NMT inhibitor is DDD85646 or DDD86481,
wherein determining hypermethylation of the promoter region of the NMT2 gene comprises:
i) performing bisulfite modification to the nucleic acid in said sample, and
ii) determining methylation of the promoter region of the NMT2 gene in the bisulfite-modified nucleic acid of the sample using PCR primers and/or probes specific for the promoter region of the NMT2 gene from step i), wherein step ii) is performed on the bisulfite modified nucleic acid from step i) by a method selected from the group consisting of PCR, methylation-specific PCR, quantitative methylation specific PCR (QMSP), realtime methylation-specific PCR, a PCR assay using a methylation DNA-specific binding protein, quantitative PCR, DNA chip-based assay, pyrosequencing, and bisulfite sequencing.
3. The method of claim 2 , wherein said PCR primers comprise SEQ ID NO:1 and/or SEQ ID NO: 2.
4. The method of claim 2 , wherein said method further comprises administering a histone acetyl transferase inhibitor, a DNA demethylase Inhibitor, and/or a histone demethylase inhibitor to said subject.
5. The method of claim 4 , wherein said histone acetyl transferase inhibitor is anacardic acid, CPTH2, MB-3, and/or Curcumin.
6. The method of claim 4 , wherein said histone demethylase inhibitor is Daminozide, GSK J1, GSK J2, GSK J4, GSK J5, GSK LSD 1 dihydrochloride, IOX 1, JIB 04, RN 1 dihydrochloride, TC-E 5002, and/or Tranylcypromine hydrochloride.
7. The method of claim 2 , wherein said method further comprises administering CHOP (cyclophosphamide, doxorubicin, vincristine, and prednisone), GAP-BOP (cyclophosphamide, doxorubicin, procarbazine, bleomycin, vincristine, and prednisone), m-BACOD (methotrexate, bleomycin, doxorubicin, cyclophosphamide, vincristine, dexamethasone, and leucovorin), ProMACE-MOPP (prednisone, methotrexate, doxorubicin, cyclophosphamide, etoposide, leucovorin with standard MOPP), ProMACE-CytaBOM (prednisone, doxorubicin, cyclophosphamide, etoposide, cytarabine, bleomycin, vincristine, methotrexate, and leucovorin), or MACOP-B (methotrexate, doxorubicin, cyclophosphamide, vincristine, prednisone, bleomycin, and leucovorin) to said subject.
8. The method of claim 1 , wherein the determination of hypermethylation in the promoter region of the NMT2 gene is performed by a method selected from the group consisting of PCR, methylation-specific PCR, realtime methylation-specific PCR, a PCR assay using a methylation DNA-specific binding protein, quantitative PCR, DNA chip-based assay, pyrosequencing, and bisulfite sequencing.