Methods of downregulating translocated oncogene expression using bromodomain inhibitors

Abstract

Disclosed herein are novel methods and compositions useful for inhibiting interaction between a bromodomain protein and an immunoglobulin (Ig) regulatory element. The methods and compositions are particularly useful for downregulating expression of an oncogene translocated with an Ig locus, as well as for treating a cancer (e.g., hematological malignancy) characterized by increased expression of an oncogene which is translocated with an Ig locus. Also disclosed herein are methods and assays for identifying agents that interfere with binding of bromodomain proteins to Ig regulatory elements, as well as methods and assays for identifying inhibitors of bromodomain

1 . (canceled) 
     
     
         2 . A method for downregulating expression of an oncogene translocated with an Ig locus comprising contacting said locus with an effective amount of an inhibitor of a bromodomain protein. 
     
     
         3 .- 4 . (canceled) 
     
     
         5 . The method of  claim 2  wherein downregulating expression of said oncogene comprises decreasing the level or activity of an expression product of said oncogene. 
     
     
         6 . (canceled) 
     
     
         7 . The method of  claim 2  wherein said oncogene is not c-Myc. 
     
     
         8 . The method of  claim 2  wherein said oncogene is selected from the group consisting of Bcl2, Ccnd1, c-Maf, Pax5, Pim1, Bc16, Irf4, Il3, Lyt10, Bc13, and Malt1. 
     
     
         9 . The method of  claim 2  wherein said oncogene is c-Myc. 
     
     
         10 .- 11 . (canceled) 
     
     
         12 . The method of  claim 2  wherein said inhibitor interferes with binding of said bromodomain protein to a transcriptional start site of said oncogene. 
     
     
         13 .- 19 . (canceled) 
     
     
         20 . The method of  claim 2  wherein said inhibitor is selected from the group consisting of an anti sense oligonucleotide, an aptamer, an intrabody, an oligopeptide, a ribozyme, an siRNA, a shRNA, and a small molecule. 
     
     
         21 . The method of  claim 2  wherein said bromodomain protein is a BET bromodomain protein. 
     
     
         22 . The method of  claim 2  wherein said bromodomain protein is selected from the group consisting of Brd2, Brd3, Brd4, and BrdT. 
     
     
         23 . (canceled) 
     
     
         24 . A method for treating a cancer comprising:
 (a) determining the level of expression of an oncogene translocated with an Ig locus in a sample obtained from an individual having or suspected of having said cancer, wherein overexpression of said translocated oncogene in said sample in comparison with a control is indicative that said individual is an individual who would potentially benefit from treatment with an inhibitor of a bromodomain protein; and   (b) administering an effective amount of said inhibitor to said individual if said translocated oncogene is overexpressed in said sample.   
     
     
         25 . A method for treating a cancer comprising administering an effective amount of an inhibitor of a bromodomain protein to an individual exhibiting overexpression of an oncogene translocated with an Ig locus. 
     
     
         26 . (canceled) 
     
     
         27 . The method of  claim 24  wherein said cancer is a hematological malignancy. 
     
     
         28 . The method of  claim 27  wherein said hematological malignancy is a leukemia, lymphoma or myeloma selected from the group consisting of acute lymphoblastic lymphoma (ALL), Burkitt's lymphoma, chronic lymphoid leukemia (CLL), diffuse large cell lymphoma, extranodal lymphoma, follicular lymphoma, lymphoplasmacytoid lymphoma, mantle zone lymphoma, monoclonal gammopathy of undetermined significance (MGUS), multiple myeloma, and mucosa-associated lymphatic tissue (MALT)-type lymphoma. 
     
     
         29 .- 46 . (canceled) 
     
     
         47 . The method of  claim 24  wherein said inhibitor is selected from the group consisting of an antisense oligonucleotide, an aptamer, an intrabody, an oligopeptide, a ribozyme, an siRNA, a shRNA, and a small molecule. 
     
     
         48 . The method of  claim 24  wherein said inhibitor is small molecule JQ1. 
     
     
         49 . The method of  claim 24  wherein said inhibitor is administered with a pharmaceutically acceptable carrier. 
     
     
         50 . The method of  claim 24  wherein said inhibitor is co-administered with at least one chemotherapeutic agent. 
     
     
         51 .- 53 . (canceled) 
     
     
         54 . A method for identifying an agent that interferes with binding of a bromodomain protein to an Ig regulatory element comprising:
 (a) contacting a suitably conditioned cell containing a target gene under control of one or more Ig regulatory elements and a bromodomain protein which binds to said one or more Ig regulatory elements and activates expression of said target gene with a candidate agent; and   (b) detecting expression of said target gene, wherein decreased expression of said target gene in the presence of said candidate agent as compared with expression of said target gene in the absence of said candidate agent is indicative of said agent's ability to interfere with binding of said bromodomain protein to said Ig regulatory element.   
     
     
         55 . The method of  claim 54  further comprising contacting said bromodomain protein immobilized onto a solid support with said candidate agent and a known inhibitor of said bromodomain protein, wherein said candidate agent's ability to outcompete said known inhibitor for binding to said bromodomain protein is indicative of said candidate agent's ability to interfere with binding of said bromodomain protein to said Ig regulatory element. 
     
     
         56 .- 66 . (canceled) 
     
     
         67 . A method for identifying an inhibitor of a bromodomain protein comprising:
 (a) contacting a cell line expressing an oncogene translocated with an Ig locus with a candidate agent;   (b) measuring the level of bromodomain protein occupancy at a regulatory element of said Ig locus; and   (c) comparing said level of bromodomain occupancy at said regulatory element of said Ig locus to a control, wherein decreased bromodomain protein occupancy at said regulatory element of said Ig locus in the presence of the candidate agent as compared to in the absence of said candidate agent is indicative of bromodomain inhibitory activity of said candidate agent.   
     
     
         68 .- 75 . (canceled) 
     
     
         76 . The method of  claim 25  wherein said cancer is a hematological malignancy. 
     
     
         77 . The method of  claim 76  wherein said hematological malignancy is a leukemia, lymphoma or myeloma selected from the group consisting of acute lymphoblastic lymphoma (ALL), Burkitt's lymphoma, chronic lymphoid leukemia (CLL), diffuse large cell lymphoma, extranodal lymphoma, follicular lymphoma, lymphoplasmacytoid lymphoma, mantle zone lymphoma, monoclonal gammopathy of undetermined significance (MGUS), multiple myeloma, and mucosa-associated lymphatic tissue (MALT)-type lymphoma. 
     
     
         78 . The method of  claim 25  wherein said inhibitor is selected from the group consisting of an antisense oligonucleotide, an aptamer, an intrabody, an oligopeptide, a ribozyme, an siRNA, a shRNA, and a small molecule. 
     
     
         79 . The method of  claim 25  wherein said inhibitor is small molecule JQ1. 
     
     
         80 . The method of  claim 25  wherein said inhibitor is administered with a pharmaceutically acceptable carrier. 
     
     
         81 . The method of  claim 25  wherein said inhibitor is co-administered with at least one chemotherapeutic agent.