Method for isolating hepatitis c virus peptides

Abstract

Described are methods for isolating Hepatitis C Virus peptides (HPs) that have a binding capacity to a MHC/HLA molecule or a complex comprising the HCV-peptide and the MHC/HLA molecule. In one aspect, these methods include providing a pool of HCV-peptide, said pool containing HCV-peptides which bind to said MHC/HLA molecule and HCV-peptides which do not bind to said MHC/HLA molecule, contacting said MHC/HLA molecule with said pool of HCV-peptides whereby a HCV-peptide which has a binding capacity to said MHC/HLA molecule binds to said MHC/HLA molecule and a complex comprising said HCV-peptide and said MHC/HLA molecule is formed, detecting and optionally separating said complex from the HCV-peptide which do not bind to said MHC/HLA molecule and optionally isolating and characterizing the HCV-peptide from said complex. Also described are immunogenic compositions that stimulate a specific T cell response to hepatitis C virus when administered to a subject in an effective amount.

1 . An immunogenic composition comprising a pharmaceutically acceptable carrier and one or more epitopes from polypeptides A120-A124, B25-B30, B46-B48, B84-B92, C106, C113-C114, 1627, 1628, 1629, 1604, 1630, C97, 1547, B94-B98, A272-A276, B120, B122, C108, C134, C152, 1606, 1607, 1577, 1578, B50-52, 1623, C130, 1603, C96, C191, A216-A224, A242-A244, C92-C93, A174, B32-B38, B100-B102, C135, C162, 1618, 1622, 1624, 1546, 1556, A114, B58, B112-B118, B18-B22, C112, C116, C122, C127, C144, C159-C160, C174, 1558, 1581, C95, C129, C157-C158, A254-A258, 1605, C109, C161, 1547, 1555, 1558, 1559, 1560, 1563, 1592, 1605, 1616, 1621, 1623, 1625, 1649, 1650, 1651, 1652, 1654, 1655, 1656, 1545, 1552, 1557, 1615, 1617, 1631, 1632, 1641, 1647, 1653, A141, C114, C134, C135, 1426, 1506, 1526, 1553, 1562, 1565, 1580, 1587, 1624, 1627, 1843, or 1838, wherein the immunogenic composition stimulates a specific T cell response to hepatitis C virus when administered to a subject in an effective amount. 
     
     
         2 . The immunogenic composition of  claim 1 , wherein the epitope further comprises 1 to 30 naturally occurring amino acid residues at its N-terminus, its C-terminus or at its N- and C-terminus. 
     
     
         3 . The immunogenic composition of  claim 1 , wherein the epitope further comprises 2 to 10 naturally occurring amino acid residues at its N-terminus, its C-terminus or at its N- and C-terminus. 
     
     
         4 . The immunogenic composition of  claim 1 , wherein the epitope further comprises 2 to 6 naturally occurring amino acid residues at its N-terminus, its C-terminus or at its N- and C-terminus. 
     
     
         5 . The immunogenic composition of  claim 1 , wherein the epitope further comprises 2 to 100 non-naturally occurring amino acid residues at its N-terminus, its C-terminus or at its N- and C-terminus. 
     
     
         6 . The immunogenic composition of  claim 1 , wherein the epitope further comprises 2 to 20 non-naturally occurring amino acid residues at its N-terminus, its C-terminus or at its N- and C-terminus. 
     
     
         7 . The immunogenic composition of  claim 1 , wherein the epitope further comprises 1 to 1000 non-naturally occurring amino acid residues at its N-terminus, its C-terminus or at its N- and C-terminus. 
     
     
         8 . The immunogenic composition of  claim 1 , wherein at least one of the epitopes is an HLA A0201 binding epitope from polypeptide 1545, 1552, 1555, 1558, 1559, 1560, 1577, 1592, 1604, 1605, 1615, 1617, 1621, 1627, 1631, 1632, 1641, 1647, 1650, 1651, 1652, 1653, 1654, or 1655. 
     
     
         9 . The immunogenic composition of  claim 1 , wherein at least one of the epitopes is an HLA-B*0702 binding epitope from polypeptide 1506, 1526, 1547, 1552, 1553, 1555, 1558, 1562, 1563, 1565, 1577, 1578, 1580, 1587, 1592, 1604, 1605, 1621, 1623, 1624, 1627, 1628, 1647, 1650, 1651, 1843 or 1838. 
     
     
         10 . The immunogenic composition of  claim 1 , further comprising an immunomodulating substance. 
     
     
         11 . The immunogenic composition of  claim 1 , wherein the immuno-modulating substance is a polycationic polypeptide, an immunomodulating nucleic acid, or mixtures thereof. 
     
     
         12 . The immunogenic composition of  claim 1 , wherein immunomodulating nucleic acid is a deoxyinosine and/or deoxyuracil containing oligodeoxynucleotide. 
     
     
         13 . The immunogenic composition of  claim 1 , wherein the epitope is provided in a dendritic cell pulsed with a protein, peptide, or RNA or transfected with a DNA comprising the epitope. 
     
     
         14 . A method for stimulating a specific immune response against hepatitis C virus (HCV) in a subject comprising administering to the subject an effective amount of an immunogenic composition comprising one or more epitopes from polypeptides A120-A124, B25-B30, B46-B48, B84-B92, C106, C113-C114, 1627, 1628, 1629, 1604, 1630, C97, 1547, B94-B98, A272-A276, B120, B122, C108, C134, C152, 1606, 1607, 1577, 1578, B50-52, 1623, C130, 1603, C96, C191, A216-A224, A242-A244, C92-C93, A174, B32-B38, B100-B102, C135, C162, 1618, 1622, 1624, 1546, 1556, A114, B58, B112-B118, B18-B22, C112, C116, C122, C127, C144, C159-C160, C174, 1558, 1581, C95, C129, C157-C158, A254-A258, 1605, C109, C161, 1547, 1555, 1558, 1559, 1560, 1563, 1592, 1605, 1616, 1621, 1623, 1625, 1649, 1650, 1651, 1652, 1654, 1655, 1656, 1545, 1552, 1557, 1615, 1617, 1631, 1632, 1641, 1647, 1653, A141, C114, C134, C135, 1426, 1506, 1526, 1553, 1562, 1565, 1580, 1587, 1624, 1627, 1843, or 1838, wherein the specific immune response to hepatitis C virus is stimulated in the subject. 
     
     
         15 . The method of  claim 14 , wherein the immunogenic composition further comprising an immunomodulating substance. 
     
     
         16 . The method of  claim 15 , wherein the immunomodulating substance is a polycationic polypeptide, an immunomodulating nucleic acid, or mixtures thereof. 
     
     
         17 . The method of  claim 16 , wherein immunomodulating nucleic acid is a deoxyinosine and/or deoxyuracile containing oligodeoxynucleotide. 
     
     
         18 . The method of  claim 14 , wherein the epitope is provided in a dendritic cell pulsed with a protein, peptide, or RNA or transfected with a DNA comprising the epitope. 
     
     
         19 . The method of  claim 14 , wherein at least one of the epitopes is an HLA A0201 binding epitope from polypeptide 1545, 1552, 1555, 1558, 1559, 1560, 1577, 1592, 1604, 1605, 1615, 1617, 1621, 1627, 1631, 1632, 1641, 1647, 1650, 1651, 1652, 1653, 1654, or 1655. 
     
     
         20 . The method of  claim 14 , wherein at least one of the epitopes is an HLA-B*0702 binding epitope from polypeptide 1506, 1526, 1547, 1552, 1553, 1555, 1558, 1562, 1563, 1565, 1577, 1578, 1580, 1587, 1592, 1604, 1605, 1621, 1623, 1624, 1627, 1628, 1647, 1650, 1651, 1843 or 1838. 
     
     
         21 . An isolated T cell that specifically recognizes an epitope of polypeptide A120-A124, B25-B30, B46-B48, B84-B92, C106, C113-C114, 1627, 1628, 1629, 1604, 1630, C97, 1547, B94-B98, A272-A276, B120, B122, C108, C134, C152, 1606, 1607, 1577, 1578, B50-52, 1623, C130, 1603, C96, C191, A216-A224, A242-A244, C92-C93, A174, B32-B38, B100-B102, C135, C162, 1618, 1622, 1624, 1546, 1556, A114, B58, B112-B118, B18-B22, C112, C116, C122, C127, C144, C159-C160, C174, 1558, 1581, C95, C129, C157-C158, A254-A258, 1605, C109, C161, 1547, 1555, 1558, 1559, 1560, 1563, 1592, 1605, 1616, 1621, 1623, 1625, 1649, 1650, 1651, 1652, 1654, 1655, 1656, 1545, 1552, 1557, 1615, 1617, 1631, 1632, 1641, 1647, 1653, A141, C114, C134, C135, 1426, 1506, 1526, 1553, 1562, 1565, 1580, 1587, 1624, 1627, 1843, or 1838. 
     
     
         22 . A method of treating a hepatitis C virus infection in a subject comprising administering to the subject an effective amount of a composition comprising a T cell that specifically recognizes an epitope of polypeptide A120-A124, B25-B30, B46-B48, B84-B92, C106, C113-C114, 1627, 1628, 1629, 1604, 1630, C97, 1547, B94-B98, A272-A276, B120, B122, C108, C134, C152, 1606, 1607, 1577, 1578, B50-52, 1623, C130, 1603, C96, C191, A216-A224, A242-A244, C92-C93, A174, B32-B38, B100-B102, C135, C162, 1618, 1622, 1624, 1546, 1556, A114, B58, B112-B118, B18-B22, C112, C116, C122, C127, C144, C159-C160, C174, 1558, 1581, C95, C129, C157-C158, A254-A258, 1605, C109, C161, 1547, 1555, 1558, 1559, 1560, 1563, 1592, 1605, 1616, 1621, 1623, 1625, 1649, 1650, 1651, 1652, 1654, 1655, 1656, 1545, 1552, 1557, 1615, 1617, 1631, 1632, 1641, 1647, 1653, A141, C114, C134, C135, 1426, 1545, 1552, 1555, 1558, 1559, 1560, 1577, 1592, 1604, 1605, 1615, 1617, 1621, 1627, 1631, 1632, 1641, 1647, 1650, 1651, 1652, 1653, 1654, 1655, 1506, 1526, 1552, 1553, 1562, 1565, 1577, 1578, 1580, 1587, 1623, 1624, 1628, 1843, or 1838, wherein the hepatitis C virus infection is treated in the subject. 
     
     
         23 . A method of stimulating an HLA-B*08 specific immune response against a hepatitis C virus in a subject comprising administering to the subject an effective amount of a composition comprising one or more epitopes of peptide sequences QRKTKRNTN (SEQ ID NO: 167), QRKTKRNT (SEQ ID NO: 166), SAKSKFGYG (SEQ ID NO: 193), SAKSKYGYG (SEQ ID NO: 194), or SARSKYGYG (SEQ ID NO: 195), wherein the HLA-B*08 specific immune response against the hepatitis C virus is stimulated in the subject. 
     
     
         24 . A method of stimulating an HLA-B*2705 specific immune response against a hepatitis C virus in a subject comprising administering to the subject an effective amount of a composition comprising a peptide having sequence RKTKRNTNR (SEQ ID NO: 170), wherein the HLA-B*2705 specific immune response against the hepatitis C virus in the subject. 
     
     
         25 . A method of stimulating an HLA-B*2705 and HLA-B*2709 specific immune responses against a hepatitis C virus in a subject comprising administering to the subject an effective amount of a composition comprising a peptide having sequence ARLIVFPDL (SEQ ID NO: 1053), wherein the HLA-B*2705 and HLA-B*2709 specific immune responses against the hepatitis C virus in the subject. 
     
     
         26 . A method for stimulating a specific immune response against hepatitis C virus (HCV) in a subject comprising administering to the subject an effective amount of an immunogenic composition comprising one or more epitopes from polypeptides 1835, 84EX, 87EX, 89EX, 1426, 1650, 1836, 1846, 1651, 1800, 1799, C114, 1827, C112, C114EX, 1827EX, 1798, 1604, 1829, 1579, 1624, 1848, 1547, A1A7, A122EX, A122, 1825, A241, B8B38, C70EX, C92, C97, C106, or C134, wherein the specific immune response against the hepatitis C virus (HCV) is stimulated in the subject.