Compositions and methods for the modulation of dna damage responses using bal1 and bbap

Abstract

The invention provides methods and compositions for enhancing the efficacy of cancer therapies through modulation of BAL1 and/or BBAP. Also provided are methods for predicting the efficacy of cancer therapies or treating cancer in a subject through modulation of BAL1 and/or BBAP. Further provided are methods for identifying compounds that are capable of modulating BAL1-BBAP complexes.

1 - 51 . (canceled) 
     
     
         52 . An isolated nucleic acid molecule selected from the group consisting of:
 a) an isolated nucleic acid molecule which encodes at least one BBAP binding domain of a BAL1 protein and which does not encode full-length BAL1;   b) an isolated nucleic acid molecule which encodes at least one BBAP binding domain of a BAL1 protein and which does not encode one or more functional domain(s) of a BAL1 protein selected from the group consisting of Macro1, Macro 2, and PARP domains;   c) an isolated nucleic acid molecule which encodes a polypeptide comprising an amino acid sequence having at least 70% identity to the amino acid sequence of 453-702 of SEQ ID NO:2 and which does not encode full-length BAL1 and/or which does not encode one or more functional domain(s) of a BAL1 protein selected from the group consisting of Macro1, Macro 2, and PARP domains;   d) an isolated nucleic acid molecule which encodes a polypeptide consisting essentially of an amino acid sequence having at least 70% identity to the amino acid sequence of 453-702 of SEQ ID NO:2 and which does not encode full-length BAL1 and/or which does not encode one or more functional domain(s) of a BAL1 protein selected from the group consisting of Macro1, Macro 2, and PARP domains;   e) an isolated nucleic acid molecule which encodes at least one BAL1 binding domain of a BBAP protein and which does not encode full-length BBAP;   f) an isolated nucleic acid molecule which encodes at least one BAL1 binding domain of a BBAP protein and which does not encode one or more functional domain(s) of a BBAP protein selected from the group consisting of BBAP dimerization and RING domains;   g) an isolated nucleic acid molecule which encodes a polypeptide comprising an amino acid sequence having at least 70% identity to the amino acid sequence of 423-617 of SEQ ID NO:10 and which does not encode full-length BBAP and/or which does not encode one or more functional domain(s) of a BBAP protein selected from the group consisting of BBAP dimerization and RING domains; and   h) an isolated nucleic acid molecule which encodes a polypeptide consisting essentially of an amino acid sequence having at least 70% identity to the amino acid sequence of 423-617 of SEQ ID NO:10 and which does not encode full-length BBAP and/or which does not encode one or more functional domain(s) of a BBAP protein selected from the group consisting of BBAP dimerization and RING domains.   
     
     
         53 . An isolated nucleic acid molecule comprising a nucleotide sequence which is complementary to the nucleic acid sequence of  claim 52 . 
     
     
         54 . The isolated nucleic acid molecule of  claim 52 , further comprising a nucleic acid sequence encoding a heterologous polypeptide. 
     
     
         55 . The isolated nucleic acid molecule of  claim 54 , wherein the heterologous polypeptide is selected from the group consisting of a signal peptide, a peptide tag, a dimerization domain, an oligomerization domain, an antibody, or an antibody fragment. 
     
     
         56 . A vector comprising the nucleic acid molecule of  claim 52 . 
     
     
         57 . The vector of  claim 56 , which is an expression vector. 
     
     
         58 . A host cell transfected with the expression vector of  claim 56 . 
     
     
         59 . A method of producing a polypeptide comprising culturing the host cell of  claim 58  in an appropriate culture medium to thereby produce the polypeptide. 
     
     
         60 . The method of  claim 59 , wherein the host cell is selected from the group consisting of a bacterial cell, a eukaryotic cell, and a cell genetically engineered to express a selectable marker. 
     
     
         61 . The method of  claim 59 , further comprising the step of isolating the polypeptide from the medium or host cell. 
     
     
         62 . An isolated polypeptide selected from the group consisting of:
 a) an isolated polypeptide fragment of a BAL1 protein comprising at least one BBAP binding domain and is not full-length BAL1;   b) an isolated polypeptide fragment of a BAL1 protein comprising at least one BBAP binding domain and which lacks one or more functional domain(s) selected from the group consisting of Macro1, Macro 2, and PARP domains;   c) an isolated polypeptide comprising an amino acid sequence that is at least 70% identical to the amino acid sequence of residues 453-702 of SEQ ID NO:2 and is not full-length BAL1 and/or which lacks one or more functional domain(s) of a BAL1 protein selected from the group consisting of Macro1, Macro 2, and PARP domains;   d) an isolated polypeptide consisting essentially of an amino acid sequence that is at least 70% identical to the amino acid sequence comprising residues 453-702 of SEQ ID NO:2 and is not full-length BAL1 and/or which lacks one or more functional domain(s) of a BAL1 protein selected from the group consisting of Macro1, Macro 2, and PARP domains;   e) an isolated polypeptide fragment of a BBAP protein which is encoded by a nucleic acid molecule comprising a nucleotide sequence encoding at least one BBAP binding domain and does not encode full-length BAL1;   f) an isolated polypeptide fragment of a BAL1 protein which is encoded by a nucleic acid molecule comprising a nucleotide sequence encoding at least one BBAP binding domain and which does not encode one or more functional domain(s) selected from the group consisting of Macro1, Macro 2, and PARP domains;   g) an isolated polypeptide which is encoded by a nucleic acid molecule comprising a nucleotide sequence encoding an amino acid sequence that is at least 70% identical to the amino acid sequence of residues 453-702 of SEQ ID NO:2 and which does not encode full-length BAL1 and/or which does not encode one or more functional domain(s) of a BAL1 protein selected from the group consisting of Macro1, Macro 2, and PARP domains;   h) an isolated polypeptide which is encoded by a nucleic acid molecule consisting essentially of a nucleotide sequence encoding an amino acid sequence that is at least 70% identical to the amino acid sequence of residues 453-702 of SEQ ID NO:2 and does not encode full-length BAL1 and/or does not encode one or more functional domain(s) of a BAL1 protein selected from the group consisting of Macro1, Macro 2, and PARP domains;   i) an isolated polypeptide fragment of a BBAP protein comprising at least one BAL1 binding domain and is not full-length BBAP;   j) an isolated polypeptide fragment of a BBAP protein comprising at least one BAL1 binding domain and which lacks one or more functional domain(s) selected from the group consisting of BBAP dimerization and RING domains;   k) an isolated polypeptide comprising an amino acid sequence that is at least 70% identical to the amino acid sequence of residues 423-617 of SEQ ID NO:10 and is not full-length BBAP and/or which lacks one or more functional domain(s) of a BBAP protein selected from the group consisting of BBAP dimerization and RING domains;   l) an isolated polypeptide consisting essentially of an amino acid sequence that is at least 70% identical to the amino acid sequence comprising residues 423-617 of SEQ ID NO:10 and is not full-length BBAP and/or which lacks one or more functional domain(s) of a BBAP protein selected from the group consisting of BBAP dimerization and RING domains;   m) an isolated polypeptide fragment of a BBAP protein which is encoded by a nucleic acid molecule comprising a nucleotide sequence encoding at least one BAL1 binding domain and does not encode full-length BBAP;   n) an isolated polypeptide fragment of a BBAP protein which is encoded by a nucleic acid molecule comprising a nucleotide sequence encoding at least one BAL1 binding domain and which does not encode one or more functional domain(s) selected from the group consisting of BBAP dimerization and RING domains;   o) an isolated polypeptide which is encoded by a nucleic acid molecule comprising a nucleotide sequence encoding an amino acid sequence that is at least 70% identical to the amino acid sequence of residues 423-617 of SEQ ID NO:10 and which does not encode full-length BBAP and/or which does not encode one or more functional domain(s) of a BBAP protein selected from the group consisting of BBAP dimerization and RING domains; and   p) an isolated polypeptide which is encoded by a nucleic acid molecule consisting essentially of a nucleotide sequence encoding an amino acid sequence that is at least 70% identical to the amino acid sequence of residues 423-617 of SEQ ID NO:10 and does not encode full-length BBAP and/or does not encode one or more functional domain(s) of a BBAP protein selected from the group consisting of BBAP dimerization and RING domains.   
     
     
         63 . The isolated polypeptide of  claim 62 , wherein the isolated polypeptide maintains the ability to promote one or more biological activities selected from the group consisting of:
 a) binding to a BAL1 polypeptide or fragment thereof;   b) binding to a BBAP polypeptide or fragment thereof;   c) forming a BAL1-BBAP complex;   d) inhibiting localization and/or binding of BAL1 and/or BBAP to DNA damage sites;   e) inhibiting binding of BAL1 to poly(ADP-ribose) (PAR) chains;   f) inhibiting BBAP monoubiquitylation of histones;   g) inhibiting BBAP-mediated methylation of histones;   h) inhibiting localization and/or binding to DNA damage sites of at least one polypeptide selected from the group consisting of 53 BP1, RAP80, BRCA1, ATM, γH2AX, and MDC1; and   i) inhibiting DNA damage responses (DDR).   
     
     
         64 . The isolated polypeptide of  claim 62 , wherein the isolated polypeptide contains one or more conservative amino acid substitutions. 
     
     
         65 . The isolated polypeptide of  claim 62 , further comprising a heterologous polypeptide. 
     
     
         66 . A composition comprising the isolated polypeptide of  claim 62  and a pharmaceutically acceptable agent selected from the group consisting of excipients, diluents, and carriers. 
     
     
         67 . The isolated polypeptide of  claim 62 , wherein the polypeptide is immobilized on an object selected from the group consisting of a cell, a metal, a resin, a polymer, a ceramic, a glass, a microelectrode, a graphitic particle, a bead, a gel, a plate, an array, and a capillary tube. 
     
     
         68 - 92 . (canceled)