Hpv-specific binding molecules

Abstract

Provided are binding molecules, such as TCRs or antigen binding fragments thereof and antibodies and antigen-binding fragments thereof, such as those that recognize or bind human papilloma virus (HPV) 16, including HPV16 E6 and HPV16 E7. Also provided are engineered cells containing such binding molecules, compositions containing the binding molecules or engineered cells, and methods of treatment, such as administration of the binding molecules, engineered cells, or compositions.

What is claimed: 
     
         1 . An engineered T cell containing a heterologous TCR or antigen binding fragment thereof that binds to or recognizes a peptide epitope of human papillomavirus (HPV) 16 E7 or E6 in the context of a major histocompatibility complex (MHC) molecule, wherein the cell contains a genetic disruption of a T cell receptor alpha constant (TRAC) gene and/or T cell receptor beta constant (TRBC) gene. 
     
     
         2 . The engineered T cell of  claim 1 , wherein the genetic disruption of the TRAC gene reduces or prevents expression of the endogenous TCR constant alpha (Cα) chain in the cell. 
     
     
         3 . The engineered T cell of  claim 1 , wherein the TRBC gene is one or both of a T cell receptor beta constant 1 (TRBC1) or T cell receptor beta constant 2 (TRBC2) gene. 
     
     
         4 . The engineered T cell of  claim 1 , wherein the genetic disruption of the TRBC gene reduces or prevents expression of an endogenous TCR constant beta (Cβ) chain in the cell. 
     
     
         5 . An engineered T cell containing a heterologous TCR or antigen binding fragment thereof that binds to or recognizes a peptide epitope of human papillomavirus (HPV) 16 E7 or E6 in the context of a major histocompatibility complex (MHC) molecule, wherein the cell contains a genetic disruption of a T cell receptor alpha constant (TRAC) gene. 
     
     
         6 . An engineered T cell containing a heterologous TCR or antigen binding fragment thereof that binds to or recognizes a peptide epitope of human papillomavirus (HPV) 16 E7 or E6 in the context of a major histocompatibility complex (MHC) molecule, wherein the cell contains a genetic disruption of a T cell receptor alpha constant (TRAC) gene and a T cell receptor beta constant (TRBC) gene. 
     
     
         7 . The engineered T cell of  claim 1 , wherein the genetic disruption reduces or prevents expression of the endogenous TCR in the cell and/or increases expression of the heterologous TCR or antigen binding fragment thereof by 1.5 fold, 2-fold, 3-fold, 4-fold, 5-fold or more. 
     
     
         8 . The engineered T cell of  claim 1 , wherein the heterologous TCR or antigen-binding fragment thereof binds to or recognizes a peptide epitope of human papillomavirus (HPV) 16 E7 in the context of an MHC molecule that is or contains the sequence set forth in any of SEQ ID NOs: 236, 235, or 237-239. 
     
     
         9 . The engineered T cell of  claim 1 , wherein the heterologous TCR or antigen-binding fragment thereof binds to or recognizes a peptide epitope of HPV 16 E7 in the context of an MHC molecule, comprising an alpha chain comprising a variable alpha (Vα) region and a beta chain comprising a variable beta (Vβ) region, wherein:
 the Vα region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 151, 152, and 153, respectively, and the Vβ region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 154, 155, and 156, respectively; 
 the Vα region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 157, 158, and 159, respectively, and the Vβ region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 154, 155, and 160, respectively; or 
 the Vα region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 151, 152, and 301, respectively, and the Vβ region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 154, 155, and 156, respectively. 
 
     
     
         10 . The engineered T cell of  claim 1 , wherein:
 the Vα region comprises the amino acid sequence set forth in SEQ ID NO: 117 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ region comprises the amino acid sequence set forth in SEQ ID NO: 118, or an amino acid sequence that has at least 90% sequence identity thereto;   the Vα region comprises the amino acid sequence set forth in SEQ ID NO: 117 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ region comprises the amino acid sequence set forth in SEQ ID NO: 296, or an amino acid sequence that has at least 90% sequence identity thereto;   the Vα region comprises the amino acid sequence set forth in SEQ ID NO: 119 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ region comprises the amino acid sequence set forth in SEQ ID NO: 120, or an amino acid sequence that has at least 90% sequence identity thereto;   the Vα region comprises the amino acid sequence set forth in SEQ ID NO: 295 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ region comprises the amino acid sequence set forth in SEQ ID NO: 118, or an amino acid sequence that has at least 90% sequence identity thereto; or   the Vα region comprises the amino acid sequence set forth in SEQ ID NO: 295 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ region comprises the amino acid sequence set forth in SEQ ID NO: 296, or an amino acid sequence that has at least 90% sequence identity thereto.   
     
     
         11 . The engineered T cell of  claim 1 , wherein the heterologous TCR or antigen-binding fragment thereof binds to or recognizes a peptide epitope of human papillomavirus (HPV) 16 E6 in the context of an MHC molecule that is or contains the sequence set forth in any of SEQ ID NOs: 233, 232 or 234. 
     
     
         12 . The engineered T cell of  claim 1 , wherein the heterologous TCR or antigen-binding fragment thereof binds to or recognizes a peptide epitope of HPV 16 E6 in the context of an MHC molecule, comprising an alpha chain comprising a variable alpha (Vα) region and a beta chain comprising a variable beta (Vβ) region, wherein:
 the Vα region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 136, 137, and 138, respectively, and the Vβ region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 139, 140, and 141, respectively; 
 the Vα region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 142, 143, and 144, respectively, and the Vβ region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 145, 140, and 146, respectively; 
 the Vα region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 136, 137, and 147, respectively, and the Vβ region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 148, 149, and 150, respectively; 
 the Vα region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 161, 162, and 163, respectively, and the Vβ region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 148, 149, and 164, respectively; 
 the Vα region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 165, 166, and 167, respectively, and the Vβ region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 168, 169, and 170, respectively; 
 the Vα region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 171, 172, and 173, respectively, and the Vβ region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 148, 149, and 174, respectively; 
 the Vα region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 302, 303, and 304, respectively, and the Vβ region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 139, 140, and 305, respectively; or 
 the Vα region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 306, 307, and 308, respectively, and the Vβ region comprises a CDR-1, CDR-2, and CDR-3, comprising the amino acid sequences of SEQ ID NOs: 148, 149, and 309, respectively. 
 
     
     
         13 . The engineered T cell of  claim 12 , wherein:
 the Vα region comprises the amino acid sequence of SEQ ID NO: 111, or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ region comprises the amino acid sequence of SEQ ID NO: 112, or an amino acid sequence that has at least 90% sequence identity thereto;   the Vα region comprises the amino acid sequence of SEQ ID NO: 113, or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ region comprises the amino acid sequence of SEQ ID NO: 114, or an amino acid sequence that has at least 90% sequence identity thereto;   the Vα region comprises the amino acid sequence of SEQ ID NO: 115, or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ region comprises the amino acid sequence of SEQ ID NO: 116, or an amino acid sequence that has at least 90% sequence identity thereto;   the Vα region comprises the amino acid sequence of SEQ ID NO: 121, or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ region comprises the amino acid sequence of SEQ ID NO: 122, or an amino acid sequence that has at least 90% sequence identity thereto;   the Vα region comprises the amino acid sequence of SEQ ID NO: 123, or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ region comprises the amino acid sequence of SEQ ID NO: 124, or an amino acid sequence that has at least 90% sequence identity thereto;   the Vα region comprises the amino acid sequence of SEQ ID NO: 125, or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ region comprises the amino acid sequence of SEQ ID NO: 126, or an amino acid sequence that has at least 90% sequence identity thereto;   the Vα region comprises the amino acid sequence of SEQ ID NO: 297, or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ region comprises the amino acid sequence of SEQ ID NO: 298, or an amino acid sequence that has at least 90% sequence identity thereto; or   the Vα region comprises the amino acid sequence of SEQ ID NO: 299, or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ region comprises the amino acid sequence of SEQ ID NO: 300, or an amino acid sequence that has at least 90% sequence identity thereto.   
     
     
         14 . The engineered T cell of  claim 1 , wherein the heterologous TCR comprises an alpha chain and a beta chain with an alpha constant (Cα) region and beta constant (Cβ) region, respectively, that are human or are a cysteine-modified region thereof comprising amino acid replacement to introduce one or more cysteine residues that are capable of forming one or more non-native disulfide bridges between the alpha chain and beta chain. 
     
     
         15 . A method for producing the engineered T cell of  claim 1 , the method comprising:
 i) introducing a vector comprising a nucleic acid encoding the TCR or antigen binding fragment thereof into a cell in vitro or ex vivo; and   ii) introducing into the cell one or more agents, wherein each of the one or more agents is independently capable of inducing a genetic disruption of the TRAC gene and/or the TRBC gene.   
     
     
         16 . The method of  claim 15 , wherein the one or more agents comprise a clustered regularly interspaced short palindromic nucleic acid (CRISPR)-associated nuclease (Cas) complexed with a guide RNA (gRNA) having a targeting domain that is complementary for a target site within the TRAC and/or TRBC gene. 
     
     
         17 . The method of  claim 16 , wherein the one or more agent is introduced as a ribonucleoprotein (RNP) complex containing the gRNA and a Cas9 protein. 
     
     
         18 . The method of  claim 17 , wherein the RNP is introduced via electroporation, particle gun, calcium phosphate transfection, cell compression or squeezing. 
     
     
         19 . A composition containing an engineered cell of  claim 1  and a pharmaceutically acceptable excipient. 
     
     
         20 . A method of treatment, comprising administering the composition of  claim 1  to a subject having a disease or disorder associated with HPV.