Anti-jagged 1/jagged 2 cross-reactive antibodies, activatable anti-jagged antibodies and methods of use thereof

Abstract

This invention relates generally to the generation of antibodies, e.g., monoclonal antibodies including fully human monoclonal antibodies, that recognize Jagged 1 and/or Jagged 2, to antibodies, e.g., monoclonal antibodies including fully human antibodies that recognize Jagged 1 and/or Jagged 2, and nucleic acid molecules that encode antibodies, e.g., nucleic acid molecules that encode monoclonal antibodies including fully human cross-reactive antibodies that recognize both Jagged 1 and Jagged 2, and to methods of making the anti-Jagged antibodies and methods of using the anti-Jagged antibodies as therapeutics, prophylactics, and diagnostics. The invention also relates generally to activatable antibodies that include a masking moiety (MM), a cleavable moiety (CM), and an antibody (AB) that specifically bind to Jagged 1 and Jagged 2, and to methods of making and using these activatable anti-Jagged antibodies in a variety of therapeutic, diagnostic and prophylactic indications.

1 - 55 . (canceled) 
     
     
         56 . A method of detecting or measuring a level of a target in a subject or a sample, the method comprising:
 (a) contacting the subject or the sample with an isolated antibody that specifically binds Jagged 1 and/or Jagged 2; and   (b) detecting or measuring the level of the antibody bound to its target,   wherein the isolated antibody comprises a combination of amino acid sequences selected from the group consisting of:
 (a) VH CDR1 sequence comprising the amino acid sequence SYAMS (SEQ ID NO: 200); a VH CDR2 sequence comprising the amino acid sequence SIDPEGRQTYYADSVKG (SEQ ID NO: 208); a VH CDR3 sequence comprising the amino acid sequence DIGGRSAFDY (SEQ ID NO: 209); a VL CDR1 sequence comprising the amino acid sequence RASQSISSY (SEQ ID NO: 210); a VL CDR2 sequence comprising the amino acid sequence AASSLQS (SEQ ID NO: 211); and a VL CDR3 sequence comprising the amino acid sequence QQTVVAPPL (SEQ ID NO: 212), 
 (b) a combination of a VH CDR1 sequence, a VH CDR2 sequence, a VH CDR3 sequence, a VL CDR1 sequence, a VL CDR2 sequence, and a VL CDR3 sequence selected from the combinations shown in Table 2, and 
 (c) a combination of a variable heavy chain region and a variable light chain region from the combinations listed in Table 4. 
   
     
     
         57 . The method of  claim 56 , wherein the isolated antibody has one or more properties selected from the group consisting of:
 (i) the isolated antibody is a fully human monoclonal antibody,   (ii) the isolated antibody is an IgG isotype, and   (iii) the isolated antibody is an IgG 1  isotype.   
     
     
         58 . The method of  claim 56 , wherein the isolated antibody is labeled with a detectable moiety, and wherein the step of detecting or measuring the level of the antibody bound to its target comprises detecting or measuring the level of the detectable moiety associated with the antibody bound to its target. 
     
     
         59 . The method of  claim 58 , wherein the detectable moiety comprises a detectable agent selected from the group consisting of: an imaging agent, a contrasting agent, an enzyme, a fluorescent label, a chromophore, a dye, a metal ion, a ligand-based label, a radioisotope, and a labeled secondary antibody. 
     
     
         60 . A method of detecting the presence or absence of a cleaving agent and a target is a subject or a sample, the method comprising:
 (a) contacting the subject or the sample with an activatable antibody that in an activated state specifically binds Jagged 1 and/or Jagged 2; and   (b) detecting or measuring the level of activated activatable antibody in the subject or the sample,   wherein the activatable antibody comprises
 (1) an antibody or an antigen binding fragment thereof (AB) that specifically binds to Jagged 1 and/or Jagged 2; 
 (2) a masking moiety (MM) coupled to the AB, wherein the MM inhibits the binding of the AB to Jagged 1 and/or Jagged 2 when the activatable antibody is in an uncleaved state; and 
 (3) a cleavable moiety (CM) coupled to the AB, wherein the CM is a polypeptide that functions as a substrate for a protease, 
   wherein the antibody or the antigen binding fragment thereof (AB) comprises a combination of amino acid sequences selected from the group consisting of:
 (i) VH CDR1 sequence comprising the amino acid sequence SYAMS (SEQ ID NO: 200); a VH CDR2 sequence comprising the amino acid sequence SIDPEGRQTYYADSVKG (SEQ ID NO: 208); a VH CDR3 sequence comprising the amino acid sequence DIGGRSAFDY (SEQ ID NO: 209); a VL CDR1 sequence comprising the amino acid sequence RASQSISSY (SEQ ID NO: 210); a VL CDR2 sequence comprising the amino acid sequence AASSLQS (SEQ ID NO: 211); and a VL CDR3 sequence comprising the amino acid sequence QQTVVAPPL (SEQ ID NO: 212), 
 (ii) a combination of a VH CDR1 sequence, a VH CDR2 sequence, a VH CDR3 sequence, a VL CDR1 sequence, a VL CDR2 sequence, and a VL CDR3 sequence selected from the combinations shown in Table 2, 
 (iii) a combination of a variable heavy chain region and a variable light chain region from the combinations listed in Table 4, and 
 (iv) a light chain amino acid sequence of SEQ ID NOs: 74 and a heavy chain amino acid sequence selected from the group consisting of SEQ ID NOs: 76 and 148. 
   
     
     
         61 . The method of  claim 60 , wherein the activatable antibody in the uncleaved state has the structural arrangement from N-terminus to C-terminus as follows: MM-CM-AB or AB-CM-MM. 
     
     
         62 . The method of  claim 60 , wherein the MM of the activatable antibody has one or more properties selected from the group consisting of:
 (i) the MM has an equilibrium dissociation constant for binding to the AB which is greater than the equilibrium dissociation constant of the AB to Jagged 1 and/or Jagged 2,   (ii) the MM does not interfere or compete with the AB for binding to Jagged 1 and/or Jagged 2 when the activatable antibody is in a cleaved state,   (iii) the MM is a polypeptide of about 2 to 40 amino acids in length,   (iv) the MM polypeptide sequence is no more than 50% identical to any natural binding partner of the AB, and   (v) the MM comprises a sequence selected from the group consisting of the sequences shown in Table 9, Table 11, Table 12, Table 13, Table 14, Table 19, Table 20, Table 21, Table 22, or Table 23.   
     
     
         63 . The method of  claim 60 , wherein the protease is co-localized with Jagged 1 and/or Jagged 2 in the subject or the sample, and wherein the protease cleaves the CM in the activatable antibody when the activatable antibody is exposed to the protease. 
     
     
         64 . The method of  claim 60 , wherein the activatable antibody comprises a linking peptide between the MM and the CM. 
     
     
         65 . The method of  claim 60 , wherein the activatable antibody comprises a linking peptide between the CM and the AB. 
     
     
         66 . The method of  claim 60 , wherein the activatable antibody comprises a first linking peptide (LP1) and a second linking peptide (LP2), and wherein the activatable antibody follows in the uncleaved state has the structural arrangement from N-terminus to C-terminus as follows: MM-LP1-CM-LP2-AB or AB-LP2-CM-LP1-MM. 
     
     
         67 . The method of  claim 66 , wherein the two linking peptides are not identical to each other. 
     
     
         68 . The method of  claim 66 , wherein each of LP1 and LP2 is a peptide of about 1 to 20 amino acids in length. 
     
     
         69 . The method of  claim 60 , wherein the CM has one or more properties selected from the group consisting of:
 (i) the CM is a polypeptide of up to 15 amino acids in length, and   (ii) the CM is a substrate for an enzyme selected from the group consisting of uPA, legumain, matriptase, ADAM17, BMP-1, TMPRSS3, TMPRSS4, MMP-9, MMP-12, MMP-13, and MMP-14.   
     
     
         70 . The method of  claim 60 , wherein the antigen binding fragment thereof is selected from the group consisting of a Fab fragment, a F(ab′) 2  fragment, a scFv, a scAb, a dAb, a single domain heavy chain antibody, and a single domain light chain antibody. 
     
     
         71 . The method of  claim 60 , wherein the antibody or antigen-binding fragment thereof that binds Jagged 1 and/or Jagged 2 comprises a VH CDR1 sequence comprising the amino acid sequence SYAMS (SEQ ID NO: 200); a VH CDR2 sequence comprising the amino acid sequence SIDPEGRQTYYADSVKG (SEQ ID NO: 208); a VH CDR3 sequence comprising the amino acid sequence DIGGRSAFDY (SEQ ID NO: 209); a VL CDR1 sequence comprising the amino acid sequence RASQSISSY (SEQ ID NO: 210); a VL CDR2 sequence comprising the amino acid sequence AASSLQS (SEQ ID NO: 211); and a VL CDR3 sequence comprising the amino acid sequence QQTVVAPPL (SEQ ID NO: 212). 
     
     
         72 . The method of  claim 60 , wherein the activatable antibody comprises:
 a light chain amino acid sequence selected from the group consisting of SEQ ID NOs: 74, 132, 134, 136, 138, 140, 142, 144, 146, 180, 182, 184, 186, 188, 190, 192, 194, and 196; and   a heavy chain amino acid sequence selected from the group consisting of SEQ ID NOs: 76 and 148.   
     
     
         73 . The method of  claim 60 , wherein the AB comprises the heavy chain amino acid sequence of SEQ ID NO: 76 and the light chain sequence of SEQ ID NO: 134, wherein the X at residue 126 of SEQ ID NO: 134 is D. 
     
     
         74 . The method of  claim 60 ,
 wherein the AB comprises a heavy chain variable region comprising SEQ ID NO: 56 and the light chain variable region comprises SEQ ID NO: 54,   wherein the MM comprises the amino acid sequence CNIWLVGGDCRGWQG (SEQ ID NO: 102), and   wherein the CM comprises the amino acid sequence LSGRSDNH (SEQ ID NO: 213).   
     
     
         75 . The method of  claim 60 ,
 wherein the AB comprises a heavy chain comprising a VH CDR1 sequence comprising the amino acid sequence SYAMS (SEQ ID NO: 200), a VH CDR2 sequence comprising the amino acid sequence SIDPEGRQTYYADSVKG (SEQ ID NO: 208), and a VH CDR3 sequence comprising the amino acid sequence DIGGRSAFDY (SEQ ID NO: 209); wherein the AB comprises a light chain comprising a VL CDR1 sequence comprising the amino acid sequence RASQSISSY (SEQ ID NO: 210), a VL CDR2 sequence comprising the amino acid sequence AASSLQS (SEQ ID NO: 211), and a VL CDR3 sequence comprising the amino acid sequence QQTVVAPPL (SEQ ID NO: 212);   wherein the MM comprises the amino acid sequence CNIWLVGGDCRGWQG (SEQ ID NO: 102); and   wherein the CM comprises the amino acid sequence LSGRSDNH (SEQ ID NO: 213).   
     
     
         76 . The method of  claim 56 , wherein the isolated antibody comprises a VH CDR1 sequence comprising the amino acid sequence SYAMS (SEQ ID NO: 200); a VH CDR2 sequence comprising the amino acid sequence SIDPEGRQTYYADSVKG (SEQ ID NO: 208); a VH CDR3 sequence comprising the amino acid sequence DIGGRSAFDY (SEQ ID NO: 209); a VL CDR1 sequence comprising the amino acid sequence RASQSISSY (SEQ ID NO: 210); a VL CDR2 sequence comprising the amino acid sequence AASSLQS (SEQ ID NO: 211); and a VL CDR3 sequence comprising the amino acid sequence QQTVVAPPL (SEQ ID NO: 212). 
     
     
         77 . A kit for identifying or refining a patient population, the kit comprising:
 (a) an activatable antibody that in an activated state specifically binds Jagged 1 and/or Jagged 2, wherein the activatable antibody comprises
 (1) an antibody or an antigen binding fragment thereof (AB) that specifically binds to Jagged 1 and/or Jagged 2; 
 (2) a masking moiety (MM) coupled to the AB, wherein the MM inhibits the binding of the AB to Jagged 1 and/or Jagged 2 when the activatable antibody is in an uncleaved state; and 
 (3) a cleavable moiety (CM) coupled to the AB, wherein the CM is a polypeptide that functions as a substrate for a protease, 
   wherein the antibody or the antigen binding fragment thereof (AB) comprises a combination of amino acid sequences selected from the group consisting of:
 (i) VH CDR1 sequence comprising the amino acid sequence SYAMS (SEQ ID NO: 200); a VH CDR2 sequence comprising the amino acid sequence SIDPEGRQTYYADSVKG (SEQ ID NO: 208); a VH CDR3 sequence comprising the amino acid sequence DIGGRSAFDY (SEQ ID NO: 209); a VL CDR1 sequence comprising the amino acid sequence RASQSISSY (SEQ ID NO: 210); a VL CDR2 sequence comprising the amino acid sequence AASSLQS (SEQ ID NO: 211); and a VL CDR3 sequence comprising the amino acid sequence QQTVVAPPL (SEQ ID NO: 212), 
 (ii) a combination of a VH CDR1 sequence, a VH CDR2 sequence, a VH CDR3 sequence, a VL CDR1 sequence, a VL CDR2 sequence, and a VL CDR3 sequence selected from the combinations shown in Table 2, 
 (iii) a combination of a variable heavy chain region and a variable light chain region from the combinations listed in Table 4 and 
 (iv) a light chain amino acid sequence of SEQ ID NOs: 74 and a heavy chain amino acid sequence selected from the group consisting of SEQ ID NOs: 76 and 148; 
   (b) means for detecting or measuring a level of activated activatable antibody in a sample from a subject, wherein a detectable level of activated activatable antibody in the sample indicates that the sample is positive for the presence of Jagged 1 and/or Jagged 2 and a cleaving agent that cleaves the substrate in the cleavable moiety (CM) of the activatable antibody;   (c) means for identifying and selecting one or more subjects that test positive for the presence of Jagged 1 and/or Jagged 2 and the cleaving agent, thereby identifying or refining a patient population; and   (d) instructions for administering a therapeutically effective amount of an activatable antibody that in an activated stated specifically binds to Jagged 1 and/or Jagged 2 to the one or more subjects in the patient population that test positive for the presence of Jagged 1 and/or Jagged 2 and the cleaving agent.