Compositions and methods for treating cancer and modulating stress granule formation

Abstract

The invention provides methods for treating or decreasing the likelihood of developing a stress-granule related disorder and/or cancer by administering one or more poly-ADP-ribose polymerase (PARP) inhibitors, one or more PARP activators, one or more poly-ADP-ribose glycosylase (PARG) activators, and/or one or more poly-ADP-ribose glycohydrolase ARH3 activators. The invention also provides corresponding methods of decreasing stress granule formation and/or proliferation in a cell or a population of cells. The invention further provides methods of increasing the number of stress granules and proliferation in a cell or a population of cells by administering one or more PARP activators, one or more PARP inhibitors, one or more PARG inhibitors, and/or one or more ARH3 inhibitors. The invention also provides methods for screening for agents for treating or decreasing the likelihood of developing a stress granule-related disorder or cancer, and methods for determining the propensity for developing a stress granule-related disorder or cancer, as well as compositions and kits containing one or more PARP inhibitors, one or more PARP activators, one or more PARG activators, and one or more ARH3 activators.

1 . A method of treating or decreasing the likelihood of developing a stress granule-related disorder in a subject comprising administering to said subject a therapeutically effective amount of one or more poly-ADP-ribose polymerase (PARP) inhibitor(s), one or more poly-ADP ribose glycolase (PARG) activators, and/or one or more PARP11 activators. 
     
     
         2 . The method of  claim 1 , wherein said one or more PARP inhibitor(s) selectively decrease the expression and/or one or more activities of one or more PARP(s) selected from the group consisting of PARP5a, PARP12, PARP13 isoform 1 (PARP13.1), PARP13 isoform 2 (PARP13.2), and PARP15. 
     
     
         3 . The method of  claim 1 , wherein said decrease in expression is a decrease in the level of one or more nucleic acid(s) comprising a nucleic acid sequence having at least 95% sequence identity to PARP5a (SEQ ID NO: 8 or 9), PARP5b (SEQ ID NO: 10), PARP13.1 (SEQ ID NO: 19), PARP13.2 (SEQ ID NO: 20), or PARP15 (SEQ ID NOS: 22 or 23), or a decrease in the level of one or more polypeptides encoded by said one or more nucleic acid(s); or said one or more activities of said one or more PARP(s) is poly-ADP-ribosylation of a target protein localized in a stress granule or a target protein involved in the formation or disassembly of a stress granule, or the formation or nucleation of a stress granule. 
     
     
         4 .- 6 . (canceled) 
     
     
         7 . The method of  claim 1 , wherein said one or more PARG activators selectively increase the expression and/or one or more activities of PARG protein or poly-ADP-ribose glycohydrolase ARH3. 
     
     
         8 . The method of  claim 7 , wherein said increase in expression is an increase in the level of one or more nucleic acid(s) comprising a nucleic acid sequence having at least 95% sequence identity to PARG (SEQ ID NO: 42) or ARH3 (SEQ ID NO: 41), or an increase in the level of one or more polypeptide(s) encoded by said one or more nucleic acid(s); or said one or more activities of PARG or ARH3 is hydrolysis of poly-ADP-ribose, the prevention of the assembly of a stress granule, or disassembly of a stress granule. 
     
     
         9 .- 12 . (canceled) 
     
     
         13 . The method of  claim 1 , wherein said one or more PARP11 activators selectively increase the expression and/or one or more activities of PARP11. 
     
     
         14 . The method of  claim 13 , wherein said increase in expression is an increase in the level of one or more nucleic acid(s) comprising a nucleic acid sequence having at least 95% sequence identity to PARP11 (SEQ ID NO: 17), or an increase in the level of one or more polypeptide(s) encoded by said one or more nucleic acid(s); or said one or more activities of PARP11 is poly-ADP-ribosylation of a target protein localized in a stress granule or a target protein involved in the formation or disassembly of a stress granule, the prevention of the assembly of a stress granule, or disassembly of a stress granule. 
     
     
         15 .- 17 . (canceled) 
     
     
         18 . The method of  claim 1 , wherein said one or more PARP inhibitors is an antibody or an antibody fragment that selectively binds one or more of PARP5a, PARP12, PARP13.1, PARP13.2, and PARP15 polypeptide, or an RNA aptamer, said one or more PARG activators is one or more nucleic acid(s) comprising a nucleic acid sequence having at least 95% sequence identity to PARG (SEQ ID NO: 42) or ARH3 (SEQ ID NO: 41); or said one or more PARP11 activators is one or more nucleic acid(s) comprising a nucleic acid sequence having at least 95% sequence identity to PARP11 (SEQ ID NO: 17). 
     
     
         19 .- 29 . (canceled) 
     
     
         30 . A method of decreasing the number of stress granules present in a cell or a population of cells comprising contacting said cell or population of cells with an effective amount of one or more poly-ADP-ribose polymerase (PARP) inhibitor(s), one or more poly-ADP ribose glycolase (PARG) activators, and/or one or more PARP11 activators. 
     
     
         31 .- 51 . (canceled) 
     
     
         52 . A method of treating or decreasing the likelihood of developing cancer in a subject comprising administering to said subject a therapeutically effective amount of one or more poly-ADP-ribose polymerase (PARP) inhibitor(s). 
     
     
         53 .- 64 . (canceled) 
     
     
         65 . A method of decreasing proliferation of a cell or a population of cells by contacting said cell or population of cells with an effective amount of one or more poly-ADP-ribose polymerase (PARP) inhibitor(s). 
     
     
         66 .- 74 . (canceled) 
     
     
         75 . A pharmaceutical composition comprising one or more PARP inhibitors, one or more PARG activators, and/or one or more PARP11 activators, wherein said one or more PARP inhibitor(s) selectively decrease the expression and/or one or more activities of one or more PARP(s) selected from the group consisting of PARP5a, PARP12, PARP13 isoform 1 (PARP13.1), PARP13 isoform 2 (PARP13.2), and PARP15. 
     
     
         76 .- 96 . (canceled) 
     
     
         97 . A kit comprising one or more pharmaceutical compositions of  claim 75  and instructions for administering the one or more compositions to a subject diagnosed with a stress granule-related disorder or diagnosed as having a propensity to develop a stress granule-related disorder. 
     
     
         98 . A pharmaceutical composition comprising one or more poly-ADP-ribose polymerase (PARP) inhibitor(s), wherein said one or more PARP inhibitor(s) selectively decrease the expression and/or one or more activities of one or more PARP(s) selected from the group consisting of PARP1, PARP2, PARP5A, PARP5B, PARP7, PARP8, PARP14, and PARP16. 
     
     
         99 .- 106 . (canceled) 
     
     
         107 . A kit comprising one or more pharmaceutical compositions of  claim 98  and instructions for administering the one or more compositions to a subject diagnosed with cancer or diagnosed as having a propensity to develop a cancer. 
     
     
         108 . A method for increasing the number of stress granules in a cell or a population of cells comprising contacting said cell or population of cells with one or more poly-ADP-ribose polymerase (PARP) activators(s), one or more poly-ADP ribose glycolase (PARG) inhibitors, and/or one or more PARP11 inhibitors. 
     
     
         109 .- 132 . (canceled) 
     
     
         133 . A method of increasing proliferation of a cell or a population of cells comprising contacting said cell or population of cells with an effective amount of one or more poly-ADP-ribose polymerase (PARP) activators(s). 
     
     
         134 .- 141 . (canceled) 
     
     
         142 . A method of identifying a candidate agent for treating or decreasing the likelihood of developing a stress granule-related disorder comprising the steps of:
 a) providing one or more PARP, PARG, and/or ARH3 proteins, and/or PARP, PARG, and/or ARH3 fusion proteins encoded by a nucleic acid comprising a nucleic acid sequence having at least 95% sequence identity to PARP5A (SEQ ID NO: 8 or 9), PARP12 (SEQ ID NO: 18), PARP13.1 (SEQ ID NO: 19), PARP13.2 (SEQ ID NO: 20) PARP15 (SEQ ID NO: 22 or 23), PARG (SEQ ID NO: 42), or ARH3 (SEQ ID NO: 41);   b) contacting said one or more PARP, PARG, and/or ARH3 proteins, and/or PARP, PARG, and/or ARH3 fusion proteins with said agent and a labeled nicotinamide adenine dinucleotide (NAD + ) substrate; and   c) measuring one or more activities of said one or more PARP, PARG, and/or ARH3 proteins, and/or PARP, PARG, and/or ARH3 fusion proteins, and/or the specific binding of said agent to said one or more PARP proteins or fusion proteins;   
       wherein an agent that decreases one or more activities and/or specifically binds to said one or more PARP proteins and/or PARP fusion proteins, and/or increases one or more activities of said one or more PARG and/or ARH3 proteins, and/or PARG and/or ARH3 fusion proteins is identified as a candidate agent for treating or decreasing the likelihood of developing a stress granule-related disorder. 
     
     
         143 .- 149 . (canceled) 
     
     
         150 . A method of identifying a candidate agent for treating or decreasing the likelihood of developing cancer comprising the steps of:
 a) providing one or more PARP proteins and/or PARP fusion proteins encoded by a nucleic acid comprising a nucleic acid sequence having at least 95% sequence identity to a PARP selected from PARP1 (SEQ ID NO: 1 or 2), PARP2 (SEQ ID NO: 3), PARP5A (SEQ ID NO: 8 or 9), PARP5B (SEQ ID NO: 10) PARP7 (SEQ ID NO: 12), PARP8 (SEQ ID NO: 13), PARP14 (SEQ ID NO: 21), or PARP16 (SEQ ID NO: 24);   b) contacting said one or more PARP proteins and/or PARP fusion proteins with said agent and a labeled nicotinamide adenine dinucleotide (NAD + ) substrate; and   c) measuring one or more activities of said one or more PARP proteins and/or   PARP fusion proteins or the specific binding of said agent to said one or more PARP proteins and/or PARP fusion proteins;   
       wherein an agent that decreases one or more activities and/or specifically binds to said one or more PARP proteins and/or fusion proteins is identified as a candidate agent for treating or decreasing the likelihood of developing cancer. 
     
     
         151 .- 157 . (canceled) 
     
     
         158 . A method for determining the propensity of a subject to develop a stress granule-related disorder comprising determining the expression and/or one or more activities of one or more of PARP5A, PARP11, PARP12, PARP13.1, PARP13.2, PARP15, PARG, and ARH3 in a subject, wherein an increase in the expression and/or one or more activities of one or more of PARP5A, PARP12, PARP13.1, PARP13.2, and PARP15, and/or a decrease in the expression or one or more activities of PARP11, PARG, or ARH3 indicates an increased propensity to develop a stress granule-related disorder. 
     
     
         159 .- 163 . (canceled) 
     
     
         164 . A method for determining the propensity of a subject to develop cancer comprising determining the expression and/or one or more activities of one or more of PARP1, PARP2, PARP5A, PARP5B, PARP7, PARP8, PARP14, and PARP16 in a subject, wherein an increase in the expression and/or one or more activities of one or more of PARP1, PARP2, PARP5A, PARP5B, PARP7, PARP8, PARP14, and PARP16 indicates an increased propensity to develop cancer. 
     
     
         165 . (canceled) 
     
     
         166 . (canceled)