Methods and compositions for determining resistance to androgen receptor therapy

Abstract

Described herein are modified androgen receptor polypeptides that are resistant to inhibition by an androgen receptor inhibitor. Described herein are compositions, combinations, and kits containing the modified androgen receptor polypeptides and methods of using the modified androgen receptor polypeptides. Also described herein are methods of using the modified androgen receptor polypeptides as screening agents for the identification and design of third-generation androgen receptor modulators. Also described herein are third-generation androgen receptor modulators that inhibit the activity of the modified androgen receptor polypeptides. Also described are pharmaceutical compositions and medicaments that include the compounds described herein, as well as methods of using such androgen receptor modulators, alone and in combination with other compounds, for treating diseases or conditions, including cancers, such as castration resistant prostate cancers, that are mediated or dependent upon androgen receptors.

What is claimed is: 
     
         1 . A method for determining whether a subject is or will become less responsive to therapy with a first- or second-generation androgen receptor (AR) antagonist, comprising:
 (a) testing a sample containing a nucleic acid molecule encoding an AR polypeptide from the subject to determine whether the encoded AR polypeptide is modified at an amino acid position corresponding to amino acid position 876 of the amino acid sequence set forth in SEQ ID NO: 1; and   (b) characterizing the subject as resistant or will become resistant to therapy with a first- or second-generation AR antagonist if the subject has the modification.   
     
     
         2 . A method for optimizing the therapy of a subject receiving a first- or second-generation AR antagonist for treatment of a cancer, comprising:
 (a) testing a sample containing a nucleic acid molecule encoding an AR polypeptide from the subject to determine whether the encoded AR polypeptide is modified at an amino acid position corresponding to amino acid position 876 of the amino acid sequence set forth in SEQ ID NO: 1; and   (b) if the subject has the modification, discontinuing treatment with the first- or second-generation AR antagonist or; and   (c) if the subject does not have the modification, then
 (i) continuing treatment with a first- or second-generation AR antagonist; or 
 (ii) administering a third-generation AR antagonist that inhibits the modified receptor; or 
 (iii) both discontinuing treatment with a first- or second-generation AR antagonist and administering a third-generation AR antagonist that inhibits the modified receptor. 
   
     
     
         3 . A method for screening compounds that antagonize a modified AR, comprising:
 (a) expressing a modified AR in a cell, wherein the modified AR is modified at an amino acid position corresponding to amino acid position 876 of the amino acid sequence set forth in SEQ ID NO: 1;   (b) contacting the cell with a test compound being screened; and   (c) detecting the level of AR activity in the cell by analyzing the expression of the reporter gene, the cell comprising the reporter gene operably linked to an androgen responsive promoter.   
     
     
         4 . The method of  claim 3 , wherein the test compound (a) exhibits full antagonist activity toward the modified AR receptor; (b) does not exhibit agonist activity toward the modified AR receptor; or (c) both exhibits full antagonist activity toward the modified AR receptor and does not exhibit agonist activity toward the modified AR receptor. 
     
     
         5 . The method of  claim 3 , wherein the modification is a substitution or deletion of the amino acid at position 876 of the AR polypeptide. 
     
     
         6 . The method of  claim 5 , wherein the modification is a substitution of phenylalanine at position 876 of the AR polypeptide, the phenylalanine being replaced by leucine, isoleucine, valine, alanine, glycine, methionine, serine, threonine, cysteine, tryptophan, lysine, arginine, histidine, proline, tyrosine, asparagine, glutamine, aspartic acid, or glutamic acid. 
     
     
         7 . The method of  claim 6 , wherein the phenylalanine at position 876 of the AR polypeptide is replaced by glycine, alanine, valine, leucine, or isoleucine. 
     
     
         8 . The method of  claim 7 , wherein the phenylalanine at position 876 of the AR polypeptide is replaced by leucine. 
     
     
         9 . The method of  claim 3 , wherein the cell is deficient for the expression of wild-type AR, expresses a low level of wild-type AR, or expresses a modified AR receptor. 
     
     
         10 . The method of  claim 3 , wherein the cell is a HeLa, CV1, COS7, HepG2, HEK-293, DU145, PC3, TSY-PR1, LNCaP, CWR, VCaP or LAPC4 cell. 
     
     
         11 . The method of  claim 3 , wherein the promoter comprises an androgen response element. 
     
     
         12 . The method of  claim 11 , wherein the androgen response element is 4X ARE or a probasin element. 
     
     
         13 . The method of  claim 3 , wherein the promoter is a probasin, a prostate specific antigen, MMTV LTR, FASN, STEAP4, TMPRSS2, ORM1, or NKX3.1 promoter. 
     
     
         14 . The method of  claim 3 , wherein the reporter gene encodes a protein that is a luciferase, a fluorescent protein, a bioluminescent protein, or an enzyme. 
     
     
         15 . A method of treating cancer comprising administering to a subject in need of such treatment a therapeutically effective amount of a third-generation AR antagonist identified by the method of  claim 3 . 
     
     
         16 . The method of  claim 15 , wherein the cancer is a prostate cancer, a breast cancer, a bladder cancer or a hepatocellular cancer. 
     
     
         17 . The method of  claim 16 , wherein the cancer is a castration resistant prostate cancer. 
     
     
         18 . The method of  claim 15 , wherein the subject expresses a mutant AR, wherein the mutant AR comprises a substitution or a deletion of the amino acid at amino acid position 876 in the AR polypeptide. 
     
     
         19 . The method of  claim 18 , wherein the mutant AR comprises a substitution at amino acid position 876 in the AR polypeptide and the substitution is F876L. 
     
     
         20 . The method of  claim 15 , wherein the third-generation AR antagonist is administered with an additional therapeutic agent. 
     
     
         21 . The method of  claim 20 , wherein the third-generation AR antagonist and the additional therapeutic agent are administered sequentially, simultaneously or intermittently. 
     
     
         22 . The method of  claim 20 , wherein the additional therapeutic agent is a hormone, hormone receptor agonist or antagonist, corticosteroid, anti-emetic agent, analgesic, anti-cancer agent, anti-inflammatory agent, kinase inhibitor, HSP90 inhibitor, or histone deacetylase (HDAC) inhibitor. 
     
     
         23 . The method of  claim 20 , wherein the additional therapeutic agent is a gonadotropin-releasing hormone (GnRH) agonist or antagonist. 
     
     
         24 . The method of  claim 23 , wherein the GnRH agonist is leuprolide, bruserelin or goserelin. 
     
     
         25 . A method of maintenance therapy in a patient having a cancer, comprising:
 (a) administering to the patient a maintenance therapy regimen comprising administering a therapeutically effective dose of first- or second-generation AR antagonist; and   (b) monitoring the patient at predetermined intervals of time over the course of the maintenance therapy regimen to determine whether the subject has mutation in an endogenous gene encoding AR that results in a modification at an amino acid position corresponding to amino acid position 876 of the amino acid sequence set forth in SEQ ID NO: 1.   
     
     
         26 . The method of  claim 25 , wherein monitoring comprises:
 testing a sample containing a nucleic acid molecule encoding a AR polypeptide from the subject to determine whether the encoded AR polypeptide is modified at an amino acid position corresponding to amino acid position 876 of the amino acid sequence set forth in SEQ ID NO: 1.   
     
     
         27 . The method of  claim 25 , wherein the method further comprises discontinuing maintenance therapy regimen if the subject has the mutation or continuing maintenance therapy regimen if the subject does not have the modification. 
     
     
         28 . The method of  claim 25 , wherein the method further comprises administering third-generation AR antagonist that inhibits the modified AR if the subject has the modification. 
     
     
         29 . The method of  claim 25 , wherein the modification in the AR polypeptide is F876L. 
     
     
         30 . The method of  claim 25 , wherein the first- or second-generation AR antagonist inhibits a wild-type AR polypeptide by competitive antagonism. 
     
     
         31 . The method of  claim 25 , wherein the second-generation AR antagonist is selected from among ARN-509, enzalutamide (MDV3100), and RD162. 
     
     
         32 . The method of  claim 25 , wherein the cancer is a prostate cancer, a breast cancer, a bladder cancer, or a hepatocellular cancer. 
     
     
         33 . The method of  claim 32 , wherein the cancer is prostate cancer. 
     
     
         34 . The method any  claim 33 , wherein the cancer is a castration resistant prostate cancer. 
     
     
         35 . The method  claim 25 , wherein the predetermined interval of time is every week, every month, every 2 months, every 3 months, every 4 months, every 5 months, every 6 months, every 7 months, every 8 months, every 9 months, every 10 months, every 11 months, or every year.