Methods, compositions and screens for therapeutics for the treatment of synovial sarcoma

Abstract

Methods and compositions are provided for treating human synovial sarcoma (SS). Also provided are screens to identify therapeutics for the treatment of synovial sarcoma. These methods, compositions, and screens are based on the discovery that promoting the assembly of wild type BAF (also called mSWI/SNF) complexes in SS cells by increasing levels of wild type SS18 and/or decreasing levels of SS18-SSX fusion protein leads to the cessation of proliferation of malignant cells in synovial sarcoma.

1 - 6 . (canceled) 
     
     
         7 . A method for screening a candidate agent for the ability to treat an individual having a synovial sarcoma, the method comprising:
 contacting a cell comprising an SS18-SSX fusion protein with a candidate agent, and   detecting a cellular parameter,   wherein a change in the parameter in the cell as compared to in a cell not contacted with candidate agent indicates that the candidate agent will promote the assembly of wildtype BAF complexes, and will treat the individual having the synovial sarcoma.   
     
     
         8 . The method according to  claim 7 , wherein the candidate agent is selected from the group consisting of a small molecule, a nucleic acid, and a polypeptide. 
     
     
         9 . (canceled) 
     
     
         10 . The method according to  claim 7 , wherein the cellular parameter is the amount of BAF47 polypeptide in the cell,
 wherein an increase in the amount of BAF47 polypeptide in the cell as compared to in a cell not contacted with candidate agent indicates that the candidate agent promotes the assembly of wild-type BAF complexes, and wherein the detecting comprises detecting the amount of BAF47 protein in the cell with an agent that is specific for BAF47.   
     
     
         11 . (canceled) 
     
     
         12 . The method according to  claim 10 , wherein the cell comprises a detectably labeled BAF47 polypeptide, wherein the detecting comprises detecting the detectable label of the BAF47 polypeptide. 
     
     
         13 - 15 . (canceled) 
     
     
         16 . The method according to  claim 10 , further comprising the step of comparing the amount of BAF47 polypeptide detected in the cell contacted by candidate agent to the amount of BAF47 polypeptide in a cell contacted with a control. 
     
     
         17 . The method according to  claim 16 , wherein the control is a positive control selected from the group consisting of a wild type SS18 polypeptide or active fragment thereof, a nucleic acid that encodes a wild type SS18 polypeptide or active fragment thereof, and a nucleic acid inhibitor that is specific for an SS18-SSX fusion transcript selected from the group consisting of antisense RNA, antigomer RNA, siRNA, and shRNA. 
     
     
         18 . The method according to claim  1 , wherein the cellular parameter is the activity of the Ink4a promoter or Sox2 promoter,
 wherein an increase in the amount of Ink4a promoter activity or a decrease in the amount of Sox2 promoter activity in the cell as compared to in a cell not contacted with candidate agent indicates that the candidate agent promotes the assembly of wild-type BAF complexes, and wherein the detecting comprises detecting the amount of Ink4a RNA, Ink4a polypeptide, Sox2 RNA, and/or Sox2 polypeptide in the cell with an agent that is specific for Ink4a or Sox2.   
     
     
         19 . (canceled) 
     
     
         20 . The method according to  claim 18 , wherein the cell comprises a coding sequence that encodes an Ink4a polypeptide or fragment thereof fused to a detectable label, and/or a coding sequence that encodes a Sox2 polypeptide or fragment thereof fused to a detectable label,
 wherein the detecting step comprises detecting the detectable label(s).   
     
     
         21 . The method according to  claim 18 , wherein the cell comprises a coding sequence that encodes an Ink4a polypeptide or fragment thereof that is fused to a selectable marker, and/or a coding sequence that encodes a Sox2 polypeptide or fragment thereof that is fused to a selectable marker,
 wherein the detecting step comprises selecting for the selectable marker(s).   
     
     
         22 . The method according to  claim 18 , wherein the cell comprises an Ink4a promoter operably linked to a reporter, and/or a Sox2 promoter operably linked to a reporter,
 wherein the detecting step comprises detecting the reporter(s).   
     
     
         23 . The method according to  claim 18 , further comprising the step of comparing the amount of Ink4a promoter activity detected in the cell contacted by candidate agent to the amount of Ink4a promoter activity in a cell contacted with a control, and/or comparing the amount of Sox2 promoter activity detected in the cell contacted by candidate agent to the amount of Sox2 promoter activity in a cell contacted with a control. 
     
     
         24 . The method according to  claim 23 , wherein the control is a positive control selected from the group consisting of a wild type SS18 polypeptide or active fragment thereof, a nucleic acid that encodes a wild type SS18 polypeptide or active fragment thereof, and a nucleic acid inhibitor that is specific for an SS18-SSX fusion transcript selected from the group consisting of an antisense RNA, antigomer RNA, siRNA, shRNA, and a CRISPRi. 
     
     
         25 . The method according to  claim 7 , wherein the cell endogenously expresses SS18-SSX. 
     
     
         26 . The method according to  claim 7 , wherein the cell ectopically expresses SS18-SSX. 
     
     
         27 . (canceled) 
     
     
         28 . The method according to  claim 7 , wherein the identifying comprises:
 contacting a BAF complex comprising SS18-SSX fusion protein with a candidate agent in the presence of BAF47, and   detecting the incorporation of BAF47 into the complex.   
     
     
         29 . The method according to  claim 28 , wherein the BAF complex is bound to a detection bead and the BAF47 is detectably labeled, wherein the detecting comprises detecting the proximity of the BAF47 to the detection bead. 
     
     
         30 . (canceled) 
     
     
         31 . The method according to  claim 28 , wherein the BAF complex is tagged with a first moiety and the BAF47 is tagged with a second moiety, wherein the detecting comprises detecting a signal produced by the proximity of the first moiety with the second moiety. 
     
     
         32 . The method according to  claim 28 , wherein the BAF complex is tagged with a first moiety and the SS18-SSX fusion protein is tagged with a second moiety, wherein the detecting comprises detecting the loss of a signal produced by the proximity of the first moiety with the second moiety. 
     
     
         33 - 34 . (canceled) 
     
     
         35 . The method according to  claim 7 , wherein the identifying comprises:
 contacting SS18-SSX fusion protein with a candidate agent, and   detecting the binding of candidate agent to SS18-SSX fusion protein,   wherein an agent that binds SS18-SSX and not wild type SS18 will promote the assembly of wild-type BAF complexes in the presence of SS18-SSX fusion protein.   
     
     
         36 . (canceled) 
     
     
         37 . The method according to  claim 35 , wherein the method further comprises:
 contacting wild type SS18 protein with the candidate agent, and   detecting the binding of candidate agent to wild type SS18 protein.