Histone anti-cancer vaccines

Abstract

The present invention pertains to novel immunogenic peptide sequences that can be used as vaccines in the treatment of cancer diseases such as brain cancers and specifically glioma. The cancer vaccines of the invention are designed based on the K27M mutated variant of the human Histone 3. Provided are further fusion proteins comprising the sequences of the cancer vaccines, nucleic acids encoding such vaccines, such as RNA vaccines, and vectors and host cells comprising these sequences. Furthermore the invention pertains to T cells and T cell receptors binding the cancer vaccines of the invention, preferably when presented by the human Major Histocompatibility Complex (MHC). The peptide immunogens of the invention elicit a HLA restricted immune response and therefore are of use in the treatment of cancer diseases, in particular glioma. Further aspects of the invention pertain to pharmaceutical compositions as well as diagnostic methods based on the immunogenic capacity of the disclosed peptides.

1 . A peptide comprising an amino acid sequence of K27M variant of human Histone H3.3, wherein the peptide comprises the K27M mutated amino acid position and is not the full length K27M variant of human Histone H3.3. 
     
     
         2 . The peptide according to  claim 1 , which is capable of eliciting a T cell-mediated immune response in a mammal that is specific for the K27M variant of human Histone H3.3. 
     
     
         3 . The peptide according to  claim 1  wherein the sequence of the peptide comprises the K27M mutation of human Histone H3.3. 
     
     
         4 . The peptide according to  claim 1 , consisting of (i) the amino acid sequence of SEQ ID NO: 11, or (ii) an amino acid sequence having a sequence identity of at least 95% to the sequence of SEQ ID NO: 11. 
     
     
         5 . A fusion protein comprising an amino acid sequence having:
 i) the amino acid sequences of at least two different peptides according to  claim 1 ,   ii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a heat shock protein (HSP) binding domain, or   iii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a I ISP or a functional variant thereof.   
     
     
         6 . A nucleic acid comprising a nucleotide sequence encoding:
 a) a peptide according to  claim 1 , or   b) a fusion protein comprising an amino acid sequence having:
 i) the amino acid sequences of at least two different peptides according to  claim 1 , 
 ii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a heat shock protein (HSP) binding domain, or 
 iii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a HSP or a functional variant thereof; 
   wherein the nucleic acid does not encode the full length K27M variant of human Histone H3.3.   
     
     
         7 . An expression vector comprising a nucleic acid according to  claim 6 . 
     
     
         8 . An in-vitro method for producing an activated T-lymphocyte, comprising the step of contacting a T-cell in-vitro with an MHC class I or II molecule binding to a peptide according to  claim 1 , wherein the MHC class I or II molecule binding to, and presenting, the peptide, is expressed on an antigen presenting cell, or is in the form of an antigen presenting construct. 
     
     
         9 . An in-vitro method for producing a T-cell receptor, the method comprising isolating a T-cell receptor from an activated T-lymphocyte produced with a method according to  claim 8 . 
     
     
         10 . An in-vitro method for producing a T-cell receptor, the method comprising,
 A) immunizing a non-human animal with:
 a) a peptide according to  claim 1 , 
 b) a fusion protein comprising an amino acid sequence having:
 i) the amino acid sequences of at least two different peptides according to  claim 1 , 
 ii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a heat shock protein (HSP) binding domain, or 
 iii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a HSP or a functional variant thereof, and/or 
 
 c) a nucleic acid comprising a nucleotide sequence encoding a peptide according to  claim 1 , or encoding a fusion protein comprising an acid sequence having:
 i) the amino acid sequences of at least two different peptides according to  claim 1 , 
 ii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a heat shock protein (HSP) binding domain, or 
 
 iii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a HSP or a functional variant thereof; 
 wherein the nucleic acid does not encode the full length K27M variant of human Histone H3.3; and or 
   B) isolating, from the immunized non-human animal, T-cells that are reactive to the peptide according to  claim 1 , and isolating from said T-cells the T-cell receptor.   
     
     
         11 . An isolated T-cell receptor, characterized in that the T-Cell receptor comprises a variable domain mediating a specific binding of the T-cell receptor to a peptide according to  claim 1 . 
     
     
         12 . A recombinant host cell comprising at least one of:
 a) a peptide according to  claim 1 ;   b) a fusion protein comprising an amino acid sequence having:
 i) the amino acid sequences of at least two different peptides according to  claim 1 , 
 ii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a heat shock protein (HSP) binding domain, or 
 iii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a HSP or a functional variant thereof; and 
   c) a nucleic acid comprising a nucleotide sequence encoding a peptide according to  claim 1 , or encoding a fusion protein comprising an amino acid sequence having:
 i) the amino acid sequences of at least two different peptides according to  claim 1 , 
 ii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a heat shock protein (HSP) binding domain, or 
 iii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a HSP or a functional variant thereof wherein the nucleic acid does not encode the full length K27M variant of human Histone H3.3. 
   
     
     
         13 . A pharmaceutical composition comprising at least one of:
 a) a peptide according to  claim 1 ,   b) fusion protein comprising an amino acid sequence having:
 i) the amino acid sequences of at least two different peptides according to  claim 1 , 
 ii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a heat shock protein (HSP) binding domain, or 
 iii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a HSP or a functional variant thereof or 
   c) a nucleic acid comprising a nucleotide sequence encoding a peptide according to  claim 1 , or encoding a fusion protein comprising an amino acid sequence having:
 i) the amino acid sequences of at least two different peptides according to  claim 1 , 
 ii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a heat shock protein (HSP) binding domain, or 
 iii) the amino acid sequence of a peptide according to  claim 1 , and the amino acid sequence of a HSP or a functional variant thereof wherein the nucleic acid does not encode the full length K27M variant of human Histone H3.3, 
   d) an isolated T-cell receptor, characterized in that the T-Cell receptor comprises a variable domain mediating a specific binding of the T-cell receptor to a peptide according to  claim 1 , and   e) a recombinant host cell comprising a peptide of part a), a fusion protein of part b), a nucleic acid of part c), and/or an isolated T-cell receptor of part d);   optionally together with pharmaceutically acceptable excipients and/or carriers.   
     
     
         14 . An in-vitro method for diagnosing cancer in a subject, the method comprising:
 i) providing a biological sample of the subject,   ii) in-vitro detecting the presence or absence of an antibody specific for K27M variant and not the wild-type variant of human Histone H3.3 in the biological sample, wherein the antibody is detected using a peptide library composed of at least one K27M-peptide, wherein the at least one K27M peptide comprises a sequence of at least 8 contiguous amino acids of the amino acid sequence of the K27M variant of human Histone 113.3, said at least 8 adjacent amino acids comprising the K27M mutation of human Histone 113.3,   
       wherein the presence of an antibody that is specific for the Histone H3.3 K27M variant in the biological sample is indicative for the presence of a cancer expressing the K27M variant of human Histone H3.3 in the subject. 
     
     
         15 . The in-vitro method according to  claim 14 , wherein the cancer is a glioma. 
     
     
         16 . An in-vitro method for monitoring a cancer disease in a subject, the method comprising performing the method according to  claim 14 , wherein an increase of detected antibody over time indicates a worsening of the cancer disease in the subject, whereas a decrease of the amount of detected antibody over time indicates an alleviation of the disease. 
     
     
         17 . A method for the prevention or treatment of cancer in a subject wherein said method comprises administering, to a subject in need of such prevention or treatment, a pharmaceutical composition of  claim 13 . 
     
     
         18 . The method, according to  claim 17 , wherein the cancer is a glioma.