Claims for Patent: 8,691,507

Summary for Patent: 8,691,507

Title:	Inhibitors of human EZH2 and methods of use thereof
Abstract:	The invention relates to determining the presence of an EZH2 gene mutation in a sample from a subject and inhibition of wild-type and certain mutant forms of human histone methyltransferase EZH2, the catalytic subunit of the PRC2 complex which catalyzes the mono-through tri-methylation of lysine 27 on histone H3 (H3-K27). In one embodiment the inhibition is selective for the mutant form of the EZH2, such that trimethylation of H3-K27, which is associated with certain cancers, is inhibited. The methods can be used to treat cancers including follicular lymphoma and diffuse large B-cell lymphoma (DLBCL). Also provided are methods for identifying small molecule selective inhibitors of the mutant forms of EZH2 and also methods for determining responsiveness to an EZH2 inhibitor in a subject.
Inventor(s):	Copeland; Robert A. (Lexington, MA), Richon; Victoria M. (Wellesley, MA), Scott; Margaret D. (Beverly, MA), Sneeringer; Christopher J. (San Francisco, CA), Kuntz; Kevin W. (Woburn, MA), Knutson; Sarah K. (Cambridge, MA), Pollock; Roy M. (Medford, MA)
Assignee:	Epizyme, Inc. (Cambridge, MA)
Application Number:	13/949,026
Patent Claims:	1. A method comprising: (i) providing a nucleic acid sample from a biological sample obtained from a subject; (ii) contacting the nucleic acid sample with at least one primer that specifically hybridizes to a portion of SEQ ID NO: 7 having a mutation at the nucleotides encoding position Tyr641 (Y641) of Enhancer of Zeste homolog 2 (EZH2) of SEQ ID NO: 1, wherein the mutation increases EZH2 trimethylation of Lys27 of histone H3 (H3-K27); (iii) detecting the presence of the mutation at the nucleotides encoding Y641 in the nucleic acid sample by detecting the presence of a nucleic acid encoding the mutation at Y641; (iv) identifying the subject as a candidate for treatment; and (v) administering a therapeutically effective amount of an EZH2 inhibitor to the subject identified in step (iv), wherein the EZH2 inhibitor inhibits the conversion of H3-K27 to trimethylated H3-K27. 2. The method of claim 1, wherein the subject has a cancer selected from leukemia, melanoma, and lymphoma, or is at risk of developing a cancer selected from leukemia, melanoma, and lymphoma. 3. The method of claim 2, wherein the lymphoma is selected from the group consisting of Non-Hodgkin's lymphoma, follicular lymphoma and diffuse large B-cell lymphoma (DLBCL) of germinal center B cell-like (GCB) subtype. 4. The method of claim 1, where in the EZH2 inhibitor is a small molecule. 5. A method comprising: (i) providing a nucleic acid sample from a biological sample obtained from a subject; (ii) contacting the nucleic acid sample with at least one primer that specifically hybridizes to a portion of SEQ ID NO: 7 having a mutation at the nucleotides encoding position Y641 of EZH2 of SEQ ID NO: 1, wherein the mutation increases EZH2 trimethylation of Lys27 of histone H3 (H3-K27); (iii) detecting the presence of the mutation at the nucleotides encoding Y641 in the nucleic acid sample by detecting the presence of a nucleic acid encoding the mutation at Y641; (iv) identifying the subject as a candidate for treatment; (v) selecting a therapy that includes the administration of a therapeutically effective amount of an EZH2 inhibitor to the subject identified in step (iv), wherein the EZH2 inhibitor inhibits the conversion of H3-K27 to trimethylated H3-K27; and (vi) administering the therapeutically effective amount of the EZH2 inhibitor that inhibits the conversion of H3-K27 to trimethylated H3-K27 to the subject. 6. The method of claim 5, wherein the subject has a cancer selected from leukemia, melanoma, and lymphoma, or is at risk of developing a cancer selected from leukemia, melanoma, and lymphoma. 7. The method of claim 6, wherein the lymphoma is selected from the group consisting of Non-Hodgkin's lymphoma, follicular lymphoma and diffuse large B-cell lymphoma (DLBCL) of germinal center B cell-like (GCB) subtype. 8. The method of claim 5, wherein the EZH2 inhibitor is a small molecule. 9. A method comprising, (i) providing a nucleic acid sample from a biological sample obtained from a subject; (ii) contacting the nucleic acid sample with at least one primer that specifically hybridizes to a portion of SEQ ID NO: 7 having a mutation at the nucleotides encoding position Y641 of EZH2 of SEQ ID NO: 1, wherein the mutation increases EZH2 trimethylation of Lys27 of histone H3 (H3-K27); (iii) amplifying the portion of SEQ ID NO:7 having a mutation at the nucleotides encoding position Y641; (iv) detecting the mutation at the nucleotides encoding position Y641 by detecting the presence of the amplified nucleic acid; (v) selecting a therapy that includes the administration of a therapeutically effective amount of an EZH2 inhibitor to the subject when the amplified nucleic acid is detected in step (iv), wherein the EZH2 inhibitor inhibits the conversion of H3-K27 to trimethylated H3-K27; and (vi) administering the therapeutically effective amount of the EZH2 inhibitor that inhibits the conversion of H3-K27 to trimethylated H3-K27 to the subject. 10. The method of claim 1 wherein the mutation at the nucleotides encoding position Y641 is selected from the group consisting of Y641F, Y641H, Y641N and Y641S. 11. The method of claim 5, wherein the mutation at the nucleotides encoding position Y641 is selected from the group consisting of Y641F, Y641H, Y641N and Y641S. 12. The method of claim 9, wherein the mutation at the nucleotides encoding position Y641 is selected from the group consisting of Y641F, Y641H, Y641N and Y641S.