Ddx3 as a biomarker for cancer and methods related thereto

Abstract

The invention encompasses methods for treating or preventing diseases and disorders associated abnormal cell growth, for example, treating or preventing cancer or tumor growth, by administering to a subject in need thereof a composition comprising a therapeutically or prophylactically effective amount of a compound that downregulates DDX3, for example a fused diimidazodiazepine ring compound or a pharmaceutically acceptable salt thereof. The invention also encompasses the use of DDX3 as a biomarker for diagnostic and treatment purposes, for example, to identify a hyperproliferative disorder susceptible to treatment by down regulation of DDX3.

What is claimed is: 
     
         1 . A method of identifying a subject having a hyperproliferative disorder susceptible to treatment by down regulation of DDX3 comprising:
 a) obtaining a cell or tissue sample from tissue of the subject associated with or suspected to be associated with the disorder;   b) optionally isolating cells from the tissue;   c) measuring expression of DDX3 in the tissue or in the cells isolated from the tissue using qRT-PCR and the PCR primers and probes specific for DDX3, or using immunohistochemistry and antibodies specific for DDX3 or an antigen binding fragment thereof;   d) providing a reference non-neoplastic tissue sample;   e) comparing the level of expression of the DDX3 gene from the tissue sample of the subject, to the level of expression of the DDX3 gene of in a reference non-neoplastic tissue sample; and   f) identifying the subject as having the hyperproliferative disorder as susceptible to treatment by down regulation of DDX3 if DDX3 is expressed at an increased level in the tissue or cell sample of the subject when compared to the reference non-neoplastic tissue sample.   
     
     
         2 . The method of  claim 1 , further comprising administering to the subject an effective amount of a composition or formulation comprising a compound that downregulates DDX3. 
     
     
         3 . The method of  claim 2 , wherein the composition or formulation comprising a compound of Formula (I) that downregulates DDX3, wherein the compound of Formula (I) is: 
       
         
           
           
               
               
           
         
       
       or pharmaceutically acceptable salts and prodrugs thereof, 
       wherein:
 R, R′, and R″ are each independently a hydrogen, hydroxyl; substituted or unsubstituted: cyclic or acyclic alkyl group, cyclic or acyclic alkenyl group, cyclic or acyclic alkynyl group, aryl group, alkylaryl group, arylalkyl group, benzyl group, cyclic and acyclic heteroalkyl group, heteroaryl group; —C(O)R 3 ; —C(S)R 3 ; —S(O)R 3 ; —S(O) 2 R 3 ; —C(O)NR 3 R 4 ; —C(S)NR 3 R 4 ; C(S)YR 3 ; —C(O)YR 3 ; -β-D-ribosyl; -α-D-ribosyl; -β-L ribosyl; -α-L-ribosyl; 2′-deoxy-β-D-ribosyl; 2′-deoxy-β-L-ribosyl; 2′-deoxy-α-D ribosyl; 2′-deoxy-α-L-ribosyl; or ribose or deoxyribose sugars substituted with one or more halogens; 
 R, R′, and R″ can also form a ring with one or more C, S, O, N atoms such that, for example, R and R′ together include: 
 
       
         
           
           
               
               
           
         
         R 7  is a hydrogen; hydroxyl; substituted and unsubstituted: cyclic and acyclic alkyl group, group, alkenyl group, alkynyl group, aryl group, aryloxy group, alkylary group, aryalkyl group, heteroaryl group, heterocycloalkyl group; —C(O)alkyl; —C(O)alkenyl; —C(O)alkynyl; —C(O)aryl; —C(O)benzyl; —C(O)NR 3 R 4 ; —C(S)alkyl; —C(S)alkenyl; —C(S)alkynyl; —C(S)aryl; —C(S)benzyl; —C(S)NR 3 R 4 ; —C(O)NR 3 R 4 ; —C(S)YR 3 ; —C(O)YR 3 ; 
         wherein
 - - - - - Q is ═O, ═NH, or ═S; 
 Y is O or S; 
 Z is CH, N, P, or C; 
 — is a single bond or double bond; wherein if — is a double bond, R 2  or 
 
         R 7  is 
       
       independently O, S, or NH;
 n is 1, 2, 3, or 4; 
 R 3  and R 4  are independently a hydrogen; hydroxyl; substituted or unsubstituted: cyclic or acyclic alkyl group, cyclic or acyclic alkenyl group, cyclic or acyclic alkynyl group, aryl group, alkylary group, aryalkyl group, heteroaryl group, heterocycloalkyl group; and 
 
       r, r′, and r″ are each independently an integer from 1 to 3. 
     
     
         4 . The method of  claim 3 , wherein Formula (I) comprises a compound of Formula (IV): 
       
         
           
           
               
               
           
         
       
       or pharmaceutically acceptable salts and prodrugs thereof, 
       wherein:
 R 3  and R 4  are each independently a hydrogen; hydroxyl; substituted or unsubstituted: cyclic or acyclic alkyl group, cyclic or acyclic alkenyl group, cyclic or acyclic alkynyl group, aryl group, alkylary group, aryalkyl group, benzyl group, cyclic or acyclic heteroalkyl group, heteroaryl group; —C(O)R 5 ; —C(S)R 5 ; —S(O)R 5 ; —S(O) 2 R 5 ; —C(O)NR 5 R 6 ; —C(S)NR 5 R 6 ; —C(O)YR 5 ; —C(S)YR 5 ; -β-D-ribosyl; -α-D-ribosyl; -β-L-ribosyl; -α-L-ribosyl; 2′-deoxy-β-D-ribosyl; 2′-deoxy-β-L-ribosyl; 2′-deoxy-α-D-ribosyl; 2′-deoxy-α-L-ribosyl; or ribose or deoxyribose sugars substituted with one or more halogens; 
 R 5  and R 6  are independently a hydrogen; hydroxyl; substituted or unsubstituted: cyclic or acyclic alkyl group, cyclic or acyclic alkenyl group, cyclic or acyclic alkynyl group, aryl group, alkylary group, aryalkyl group, heteroaryl group, heterocycloalkyl group; and 
 Y is O or S. 
 
     
     
         5 . The method of  claim 4 , wherein the compound is 
       
         
           
           
               
               
           
         
       
     
     
         6 . The method of  claim 1 , wherein the hyperproliferative disorder is selected from the group consisting of group consisting of breast cancer, lung cancer, prostate cancer, glioblastoma, kidney cancer, leukemia, medulloblastoma, pontine tumors, or a sarcoma. 
     
     
         7 . The method of  claim 1 , wherein the hyperproliferative disorder is selected from the group consisting of breast cancer, lung cancer, prostate cancer or glioblastoma. 
     
     
         8 . The method of  claim 1 , wherein the hyperproliferative disorder is breast cancer. 
     
     
         9 . The method of  claim 1 , wherein the hyperproliferative disorder is lung cancer. 
     
     
         10 . The method of  claim 4 , wherein the sarcoma is selected from the group consisting of angiosacrcoma, chondrosarcoma, malignant fibrous histiocytoma (MFH), clear cell sarcoma, malignant peripheral nerve sheath tumor (MPNST), epithelioid sarcoma, myxoid sarcomas, Ewings Sarcoma (ESFT or PNET), Kaposi's sarcoma, leiomyosarcoma, pleomorphic sarcoma, fibrosarcoma, low-grade sarcoma, liposarcoma, and rhabdomyosarcoma (RMS). 
     
     
         11 . The method of  claim 1 , wherein measuring comprises immunohistochemistry analysis of the tissue sample. 
     
     
         12 . The method of  claim 1 , further comprising isolating cells from the tissue sample and measuring expression of DDX3 in the tissue comprises measuring expression of DDX3 in the cells. 
     
     
         13 . The method of  claim 12 , further comprising performing an assay by exposing the cells to a compound that downregulates DDX3, measuring cell viability as a function of concentration and identifying the hyperproliferative disorder as susceptible to treatment by down regulation of DDX3 if cell viability decreases as a function of concentration. 
     
     
         14 . The method of  claim 13 , wherein the assay comprises a MTS assay.