Anti-lamp1 antibodies and antibody drug conjugates, and uses thereof

Abstract

Antibodies are provided which specifically bind human and Macaca fascicularis lysosomal-associated membrane protein 1 (LAMP1) proteins and immunoconjugates comprising said antibodies conjugated or linked to a growth inhibitory agent. Pharmaceutical compositions comprising antibodies or immunoconjugates of the invention and use of the antibodies or immunoconjugates for the treatment of cancer are also provided, as well as LAMP1 antibodies, isolated nucleic acids, vectors and host cells comprising a sequence encoding said antibodies and the use of said antibody as a diagnostic tool. The application further provides for the detection of LAMP1 gene amplification or gain in cancer cells leading to the determination if patients with cancer are likely to respond to anti-LAMP1 therapy. Therefore, it is proposed an in vitro method of selecting patients with cancer which comprises determining, in a biological sample of a patient with cancer which includes cancer cells, if said patient harbors a LAMP1 gene copy number gain; and selecting the patient based on the presence of LAMP1 gene copy number gain. Anti-LAMP1 therapeutic agent for use for treating cancer in a patient harboring LAMP1 gene copy number gain in cancer cells is further provided.

1 . An immunoconjugate comprising a) an antibody or antigen binding fragment thereof wherein said antibody or antigen binding fragment thereof
 i) binds to a first lumenal domain of human LAMP1 protein, or   ii) binds to a domain consisting of loops one to three of human LAMP1 protein, or   iii) binds to a fourth loop of human LAMP1 protein; and   b) at least one growth inhibitory agent, wherein the at least one growth inhibitory agent is linked to the antibody or antigen binding fragment thereof.   
     
     
         2 - 5 . (canceled) 
     
     
         6 . The immunoconjugate according to  claim 1 , wherein the antibody or antigen binding fragment thereof competes for binding to the first lumenal domain of human LAMP1 protein with an antibody selected from the group consisting of
 (i) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 1 and a light chain variable domain having an amino acid sequence SEQ ID NO: 5; or   (ii) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 8 and a light chain variable domain having an amino acid sequence SEQ ID NO: 12; or   (iii) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 15 and a light chain variable domain having an amino acid sequence of SEQ ID NO: 16; or   (i) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 42 and a light chain variable domain having an amino acid sequence of SEQ ID NO: 46; or   (iv) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 42 and a light chain variable domain having an amino acid sequence of SEQ ID NO: 51; or   (v) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 53 and a light chain variable domain having an amino acid sequence of SEQ ID NO: 56; or   (vi) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 54 and a light chain variable domain having an amino acid sequence of SEQ ID NO: 57; or   (vii) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 55 and a light chain variable domain having an amino acid sequence of SEQ ID NO: 58.   
     
     
         7 - 8 . (canceled) 
     
     
         9 . The immunoconjugate according to  claim 1 ,
 wherein the antibody or antigen binding fragment thereof comprises:   (i) a CDR1-H having an amino acid sequence of SEQ ID NO: 2, a CDR2-H having an amino acid sequence of SEQ ID NO: 3, a CDR3-H having an amino acid sequence of SEQ ID NO: 4, a CDR1-L having an amino acid sequence of SEQ ID NO: 6, a CDR2-L having an amino acid sequence of DTS, and   a CDR3-L having an amino acid sequence of SEQ ID NO: 7; or   (ii) a CDR1-H having an amino acid sequence of SEQ ID NO: 9, a CDR2-H having an amino acid sequence of SEQ ID NO: 10, a CDR3-H having an amino acid sequence of SEQ ID NO: 11, a CDR1-L having an amino acid sequence of SEQ ID NO: 13, a CDR2-L having an amino acid sequence of AAS, and a CDR3-L having an amino acid sequence of SEQ ID NO: 14; or   (iii) a CDR1-H having an amino acid sequence of SEQ ID NO: 43, a CDR2-H having an amino acid sequence of SEQ ID NO: 44, a CDR3-H having an amino acid sequence of SEQ ID NO: 45, a CDR1-L having an amino acid sequence of SEQ ID NO: 47, a CDR2-L having an amino acid sequence of YTS, and a CDR3-L having an amino acid sequence of SEQ ID NO: 48 or SEQ ID NO: 52.   
     
     
         10 - 12 . (canceled) 
     
     
         13 . The immunoconjugate according to  claim 1  wherein the antibody is a chimeric or a humanised antibody. 
     
     
         14 . The immunoconjugate according to  claim 1 , wherein the antibody comprises:
 i) a heavy chain having an amino acid sequence of SEQ ID NO: 17 and a light chain having an amino acid sequence of SEQ ID NO: 18; or   ii) a heavy chain having an amino acid sequence of SEQ ID NO: 19 and a light chain having an amino acid sequence of SEQ ID NO: 20; or   iii) a heavy chain having an amino acid sequence of SEQ ID NO: 21 and a light chain having an amino acid sequence of SEQ ID NO: 22; or   iv) a heavy chain having an amino acid sequence of SEQ ID NO: 49 and a light chain having an amino acid sequence of SEQ ID NO: 50, or   v) a heavy chain having an amino acid sequence of SEQ ID NO: 49 and a light chain having an amino acid sequence of SEQ ID NO: 81, or   vi) a heavy chain having an amino acid sequence of SEQ ID NO: 60 and a light chain having an amino acid sequence of SEQ ID NO: 59; or   vii) a heavy chain having an amino acid sequence of SEQ ID NO: 62 and a light chain having an amino acid sequence of SEQ ID NO: 61; or   Viii) a heavy chain having an amino acid sequence of SEQ ID NO: 64 and a light chain having an amino acid sequence of SEQ ID NO: 63.   
     
     
         15 . (canceled) 
     
     
         16 . The immunoconjugate according to  claim 1 , wherein the antibody or antigen binding fragment thereof binds to a region of Loop 4 comprising the amino acids 360 to 375 of human LAMP1 (SEQ ID NO: 82). 
     
     
         17 . The immunoconjugate according to  claim 16 , wherein the antibody or antigen binding fragment thereof comprises a CDR1-H having an amino acid sequence of SEQ ID NO: 83, a CDR2-H having an amino acid sequence of SEQ ID NO: 84, a CDR3-H having an amino acid sequence of SEQ ID NO: 85, a CDR1-L having an amino acid sequence of SEQ ID NO: 86, a CDR2-L having an amino acid sequence of NAK, and a CDR3-L having an amino acid sequence of SEQ ID NO: 87. 
     
     
         18 - 22 . (canceled) 
     
     
         23 . The immunoconjugate according to  claim 1 , wherein said at least one growth inhibitory agent is a cytotoxic agent or a radioactive isotope. 
     
     
         24 - 26 . (canceled) 
     
     
         27 . The immunoconjugate conjugate according to  claim 23 , wherein said growth inhibitory agent is (N 2′ -deacetyl-N 2′ -(3-mercapto-1-oxopropyl)-maytansine) DM1 or N 2′ -deacetyl-N 2′ (4-methyl-4-mercapto-1-oxopentyl)-maytansine (DM4). 
     
     
         28 . (canceled) 
     
     
         29 . The immunoconjugate according to  claim 1 , wherein said growth inhibitory agent is covalently attached to the antibody or antigen binding fragment thereof via a linker is selected from the group consisting of N-succinimidyl pyridyldithiobutyrate (SPDB), 4-(Pyridin-2-yldisulfanyl)-2-sulfo-butyric acid (sulfo-SPDB), and succinimidyl (N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC). 
     
     
         30 . The immunoconjugate according to  claim 29 , wherein said linker is N-succinimidyl pyridyldithiobutyrate (SPDB) and the growth inhibitory agent is N 2′ -deacetyl-N 2′ -(4-methyl-4-mercapto-1-oxopentyl)-maytansine (DM4). 
     
     
         31 . The immunoconjugate according to  claim 29 , wherein said linker is 4-(Pyridin-2-yldisulfanyl)-2-sulfo-butyric acid (sulfo-SPDB) and the growth inhibitory agent is N 2′ -deacetyl-N 2′ -(4-methyl-4-mercapto-1-oxopentyl)-maytansine (DM4). 
     
     
         32 . The immunoconjugate according to  claim 29 , wherein said linker is succinimidyl (N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC) and the growth inhibitory agent is N 2′ -deacetyl-N 2′ -(3-mercapto-1-oxopropyl)-maytansine (DM1). 
     
     
         33 . The immunoconjugate according to  claim 27 , wherein the immunoconjugate is characterised by a drug-to-antibody ratio (DAR) ranging from 1 to 10, the DAR being calculated from the ratio of the drug concentration to that of the antibody:
     DAR=C   D   /C   A        wherein       C   D =[(ε A280   ×A   252 )−(ε A252   ×A   280 )]/[(ε D252 ×ε A280 )−(ε A252 ×ε D280 )]
       C   A   =[A   280 −( C   D ×ε D280 )]/ε A280  
   
       and
 ε D252  and ε D280  are respectively the molar extinction coefficients of the drug at 252 nm and 280 nm; 
 ε A252  and ε A280  are respectively the molar extinction coefficients of the antibody at 252 nm and 280 nm; 
 (A 252 ) and A 280  are respectively the absorbances for the conjugate at 252 nm (A 252 ) and at 280 nm (A 280 ), measured using a classic spectrophotometer apparatus. 
 
     
     
         34 . An isolated antibody or antigen binding fragment thereof, wherein said antibody or antigen binding fragment thereof binds to i) a first lumenal domain of human LAMP1 protein, or ii) binds to a domain consisting of loops one to three of human LAMP1 protein, or iii) binds to a fourth loop of human LAMP1 protein. 
     
     
         35 . The isolated antibody or antigen binding fragment thereof according to  claim 34 , wherein the antibody or antigen binding fragment thereof competes for binding to the first lumenal domain of human LAMP1 protein with an antibody selected from the group consisting of
 (i) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 1 and a light chain variable domain having an amino acid sequence of SEQ ID NO: 5; or   (ii) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 8 and a light chain variable domain having an amino acid sequence of SEQ ID NO: 12; or   (iii) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 15 and a light chain variable domain having an amino acid sequence of SEQ ID NO: 16; or   (ii) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 42 and a light chain variable domain having an amino acid sequence of SEQ ID NO: 46; or   (iv) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 42 and a light chain variable domain having an amino acid sequence of SEQ ID NO: 51; or   (v) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 53 and a light chain variable domain having an amino acid sequence of SEQ ID NO: 56, or   (vi) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 54 and a light chain variable domain having an amino acid sequence of SEQ ID NO: 57, or   (vii) an antibody comprising a heavy chain variable domain having an amino acid sequence of SEQ ID NO: 55 and a light chain variable domain having an amino acid sequence of SEQ ID NO: 58.   
     
     
         36 - 41 . (canceled) 
     
     
         42 . An isolated anti-LAMP-1 antibody or antigen binding fragment thereof according to  claim 34 , wherein said antibody or antigen binding fragment thereof comprises:
 (i) a CDR1-H having an amino acid sequence of SEQ ID NO: 2, a CDR2-H having an amino acid sequence of SEQ ID NO: 3, and a CDR3-H having an amino acid sequence of SEQ ID NO: 4; and
 a CDR1-L having an amino acid sequence of SEQ ID NO: 6, a CDR2-L having an amino acid sequence of DTS, and a CDR3-L having an amino acid sequence of SEQ ID NO: 7; or 
   (ii) a CDR1-H having an amino acid sequence of SEQ ID NO: 9, a CDR2-H having an amino acid sequence of SEQ ID NO: 10, a CDR3-H having an amino acid sequence of SEQ ID NO: 11; and
 a CDR1-L having an amino acid sequence of SEQ ID NO: 13, a CDR2-L having an amino acid sequence of AAS, and a CDR3-L having an amino acid sequence of SEQ ID NO: 14; or 
   (iii) a CDR1-H having an amino acid sequence of SEQ ID NO: 43, a CDR2-H having an amino acid sequence of SEQ ID NO: 44, and a CDR3-H having an amino acid sequence of SEQ ID NO: 45, and
 a CDR1-L having an amino acid sequence of SEQ ID NO: 47, a CDR2-L having an amino acid sequence of YTS, and a CDR3-L having an amino acid sequence of SEQ ID NO: 48 or SEQ ID NO: 52; or 
   (iv) CDR1-H having an amino acid sequence of SEQ ID NO: 83, a CDR2-H having an amino acid sequence of SEQ ID NO: 84, a CDR3-H having an amino acid sequence of SEQ ID NO: 85, and a CDR1-L having an amino acid sequence of SEQ ID NO: 86, a CDR2-L having an amino acid sequence of NAK, and a CDR3-L having an amino acid sequence of SEQ ID NO: 87.   
     
     
         43 . (canceled) 
     
     
         44 . A pharmaceutical composition comprising an immunoconjugate according to  claim 1  and a pharmaceutically acceptable carrier. 
     
     
         45 - 50 . (canceled) 
     
     
         51 . An isolated nucleic acid comprising a sequence encoding an antibody or antigen binding fragment thereof wherein said antibody or antigen binding fragment thereof comprises
 (i) a CDR1-H having an amino acid sequence of SEQ ID NO: 2, a CDR2-H having an amino acid sequence of SEQ ID NO: 3, and a CDR3-H having an amino acid sequence of SEQ ID NO: 4; and a CDR1-L having an amino acid sequence of SEQ ID NO: 6, a CDR2-L having an amino acid sequence of DTS, and a CDR3-L having an amino acid sequence of SEQ ID NO: 7; or   (ii) a CDR1-H having an amino acid sequence of SEQ ID NO: 9, a CDR2-H having an amino acid sequence of SEQ ID NO: 10, a CDR3-H having an amino acid sequence of SEQ ID NO: 11; and a CDR1-L having an amino acid sequence of SEQ ID NO: 13, a CDR2-L having an amino acid sequence of AAS, and a CDR3-L having an amino acid sequence of SEQ ID NO: 14; or   (iii) a CDR1-H having an amino acid sequence of SEQ ID NO: 43, a CDR2-H having an amino acid sequence of SEQ ID NO: 44, and a CDR3-H having an amino acid sequence of SEQ ID NO: 45, and a CDR1-L having an amino acid sequence of SEQ ID NO: 47, a CDR2-L having an amino acid sequence of YTS, and a CDR3-L having an amino acid sequence of SEQ ID NO: 48 or SEQ ID NO: 52; or   (iv) CDR1-H having an amino acid sequence of SEQ ID NO: 83, a CDR2-H having an amino acid sequence of SEQ ID NO: 84, a CDR3-H having an amino acid sequence of SEQ ID NO: 85, and a CDR1-L having an amino acid sequence of SEQ ID NO: 86, a CDR2-L having an amino acid sequence of NAK, and a CDR3-L having an amino acid sequence of SEQ ID NO: 87.   
     
     
         52 . A host cell which has been transformed by a nucleic acid according to  claim 51 . 
     
     
         53 . An in vitro method of selecting patients with cancer who are likely to respond to anti-LAMP1 therapy, wherein said method comprises:
 a) determining, in a biological sample of a patient with cancer which includes cancer cells, if said patient harbors a LAMP1 gene copy number gain; and   b) selecting the patient based on the presence of LAMP1 gene copy number gain, and wherein said patient is selected as likely to respond to anti-LAMP1 therapy if said patient harbors a LAMP1 gene copy number gain.   
     
     
         54 - 68 . (canceled) 
     
     
         69 . A method a patient in need thereof comprising administering to the patient an antibody or antigen binding fragment thereof wherein said antibody or antigen binding fragment thereof i) binds to the first lumenal domain of human LAMP1 protein, or binds to a domain consisting of loops one to three of human LAMP1 protein, or HD binds to a fourth loop of human LAMP1 protein; wherein the patient has a LAMP1 expressing cancer. 
     
     
         70 . The method according to  claim 69 , wherein the antibody or antigen binding fragment thereof is linked to at least one growth inhibitory agent, wherein the at least one growth inhibitory.