Expression vectors encoding epitopes of target-associated antigens and methods for their design

Abstract

The invention disclosed herein is directed to methods of identifying a polypeptide suitable for epitope liberation including, for example, the steps of identifying an epitope of interest; providing a substrate polypeptide sequence including the epitope, wherein the substrate polypeptide permits processing by a proteasome; contacting the substrate polypeptide with a composition including the proteasome, under conditions that support processing of the substrate polypeptide by the proteasome; and assaying for liberation of the epitope. The invention further relates to vectors including a housekeeping epitope expression cassette. The invention relates to epitope cluster regions and to vectors including epitope cluster regions. The invention also relates to a method of activating a T cell comprising contacting a substrate polypeptide with an APC and contacting the APC with a T cell.

Description

BACKGROUND OF THE INVENTION

[0002] 1. Field of the Invention

[0003] The invention disclosed herein is directed to methods for the design of epitope-encoding vectors, and epitope cluster regions, for use in compositions, including for example, pharmaceutical compositions capable of inducing an immune response in a subject to whom the compositions are administered. The invention is further directed to the vectors themselves. The epitope(s) expressed using such vectors can stimulate a cellular immune response against a target cell displaying the epitope(s).

[0004] 2. Description of the Related Art

[0005] The immune system can be categorized into two discrete effector arms. The first is innate immunity, which involves numerous cellular components and soluble factors that respond to all infectious challenges. The other is the adaptive immune response, which is customized to respond specifically to precise epitopes from infectious agents. The adaptive immune response is further broken down into two effector arms known as the humoral and cellular immune systems. The humoral arm is centered on the production of antibodies by B-lymphocytes while the cellular arm involves the killer cell activity of cytotoxic T Lymphocytes.

[0006] Cytotoxic T Lymphocytes (CTL) do not recognize epitopes on the infectious agents themselves. Rather, CTL detect fragments of antigens derived from infectious agents that are displayed on the surface of infected cells. As a result antigens are visible to CTL only after they have been processed by the infected cell and thus displayed on the surface of the cell.

[0007] The antigen processing and display system on the surface of cells has been well established. CTL recognize short peptide antigens, which are displayed on the surface in non-covalent association with class I major histocompatibility complex molecules (MHC). These class I peptides are in turn derived from the degradation of cytosolic proteins.

SUMMARY OF THE INVENTION

[0008] The invention disclosed herein relates to the identification of epitope cluster regions that are used to generate pharmaceutical compositions capable of inducing an immune response from a subject to whom the compositions have been administered. One embodiment of the disclosed invention relates to an epitope cluster, the cluster being derived from an antigen associated with a target, the cluster including or encoding at least two sequences having a known or predicted affinity for an MHC receptor peptide binding cleft, wherein the cluster is an incomplete fragment of the antigen.

[0009] In one aspect of the invention, the target is a neoplastic cell.

[0010] In another aspect of the invention, the MHC receptor may be a class I HLA receptor.

[0011] In yet another aspect of the invention, the cluster includes or encodes a polypeptide having a length, wherein the length is at least 10 amino acids. Advantageously, the length of the polypeptide may be less than about 75 amino acids.

[0012] In still another aspect of the invention, there is provided an antigen having a length, wherein the cluster consists of or encodes a polypeptide having a length, wherein the length of the polypeptide is less than about 80% of the length of the antigen. Preferably, the length of the polypeptide is less than about 50% of the length of the antigen. Most preferably, the length of the polypeptide is less than about 20% of the length of the antigen.

[0013] Embodiments of the invention particularly relate to epitope clusters identified in the tumor-associated antigen NY-ESO (SEQ ID NO: 11). One embodiment of the invention relates to an isolated nucleic acid containing a reading frame with a first sequence encoding one or more segments of NY-ESO, wherein the whole antigen is not encoded, wherein each segment contains an epitope cluster, and wherein each cluster contains at least two amino acid sequences with a known or predicted affinity for a same MHC receptor peptide binding cleft. In various aspects of the invention the epitope cluster can be amino acids 79-104, 86-171, 108-140, 108-174, 144-171, and 148-167 of NY-ESO. In other aspects the segments can consist of an epitope cluster; the first sequence can be a fragment of NY-ESO. The fragment can consist of a polypeptide having a length, wherein the length of the polypeptide is less than about 90, 80, 60, 50, 25, or 10% of the length of NY-ESO; and/or the fragment can consist essentially of an amino acid sequence beginning at amino acid 79, 86, 108, 144 and 148 and ending at amino acid 104, 140, 167, 171 and 174 of NY-ESO. Also, the NY-ESO fragment can consist essentially of, for example, amino acids 79-140, 79-167, 79-171, or 79-174; amino acids 86-140, 86-167, 86-171 or 86-174; also, amino acids 86-140, 86-167, 86-171 or 86-174; amino acids 108-167 or 108-171; amino acids 144-167 or 144-174; amino acids 148-171 or 148-174; amino acids 79-174; and/or amino acids. 77-180. Embodiments relate to a reading frame operably linked to a promoter. Further embodiments of the invention include a second sequence encoding essentially a housekeeping epitope. In one aspect of this embodiment the first and second sequences constitute a single reading frame. In aspects of the invention the reading frame is operably linked to a promoter. Other embodiments of the invention include the polypeptides encoded by the nucleic acid embodiments of the invention and immunogenic compositions containing the nucleic acids or polypeptides of the invention.

[0014] Embodiments of the invention provide expression cassettes, for example, for use in vaccine vectors, which encode one or more embedded housekeeping epitopes, and methods for designing and testing such expression cassettes. Housekeeping epitopes can be liberated from the translation product of such cassettes through proteolytic processing by the immunoproteasome of professional antigen presenting cells (pAPC). In one embodiment of the invention, sequences flanking the housekeeping epitope(s) can be altered to promote cleavage by the immunoproteasome at the desired location(s). Housekeeping epitopes, their uses, and identification are described in U.S. patent application Ser. Nos. 09/560,465 and 09/561,074 entitled EPITOPE SYNCHRONIZATION IN ANTIGEN PRESENTING CELLS, and METHOD OF EPITOPE DISCOVERY, respectively; both of which were filed on Apr. 28, 2000, and which are both incorporated herein by reference in their entireties.

[0015] Examples of housekeeping epitopes are disclosed in provisional U.S. patent applications entitled EPITOPE SEQUENCES, Nos. 60/282,211, filed on Apr. 6, 2001; 60/337,017, filed on Nov. 7, 2001; 60/363,210 filed Mar. 7, 2002; and 60/409,123, filed on Sep. 5, 2002; and U.S. application Ser. No. 10/117,937, filed on Apr. 4, 2002, which is also entitled EPITOPE SEQUENCES; which are all incorporated herein by reference in their entirety.

[0016] In other embodiments of the invention, the housekeeping epitope(s) can be flanked by arbitrary sequences or by sequences incorporating residues known to be favored in immunoproteasome cleavage sites. As used herein the term “arbitrary sequences” refers to sequences chosen without reference to the native sequence context of the epitope, their ability to promote processing or immunological function. In further embodiments of the invention multiple epitopes can be arrayed head-to-tail. These arrays can be made up entirely of housekeeping epitopes. Likewise, the arrays can include alternating housekeeping and immune epitopes. Alternatively, the arrays can include housekeeping epitopes flanked by immune epitopes, whether complete or distally truncated. Further, the arrays can be of any other similar arrangement. There is no restriction on placing a housekeeping epitope at the terminal positions of the array. The vectors can additionally contain authentic protein coding sequences or segments thereof containing epitope clusters as a source of immune epitopes. The term “authentic” refers to natural protein sequences.

[0017] Epitope clusters and their uses are described in U.S. patent application Ser. Nos. 09/561,571 entitled EPITOPE CLUSTERS, filed on Apr. 28, 2000; Ser. No. 10/005,905, entitled EPITOPE SYNCHRONIZATION IN ANTIGEN PRESENTING CELLS, filed on Nov. 7, 2001; and Ser. No. 10/026,066, filed on Dec. 7, 2001, also entitled EPITOPE SYNCHRONIZATION IN ANTIGEN PRESENTING CELLS; all of which are incorporated herein by reference in their entirety.

[0018] Embodiments of the invention can encompass screening the constructs to determine whether the housekeeping epitope is liberated. In constructs containing multiple housekeeping epitopes, embodiments can include screening to determine which epitopes are liberated. In a preferred embodiment, a vector containing an embedded epitope can be used to immunize HLA transgenic mice and the resultant CTL can be tested for their ability to recognize target cells presenting the mature epitope. In another embodiment, target cells expressing immunoproteasome can be transformed with the vector. The target cell may express immunoproteasome either constitutively, because of treatment with interferon (IFN), or through genetic manipulation, for example. CTL that recognize the mature epitope can be tested for their ability to recognize these target cells. In yet another embodiment, the embedded epitope can be prepared as a synthetic peptide. The synthetic peptide then can be subjected to digestion by an immunoproteasome preparation in vitro and the resultant fragments can be analyzed to determine the sites of cleavage. Such polypeptides, recombinant or synthetic, from which embedded epitopes can be successfully liberated, can also be incorporated into immunogenic compositions.

[0019] The invention disclosed herein relates to the identification of a polypeptide suitable for epitope liberation. One embodiment of the invention, relates to a method of identifying a polypeptide suitable for epitope liberation including, for example, the steps of identifying an epitope of interest; providing a substrate polypeptide sequence including the epitope, wherein the substrate polypeptide permits processing by a proteasome; contacting the substrate polypeptide with a composition including the proteasome, under conditions that support processing of the substrate polypeptide by the proteasome; and assaying for liberation of the epitope.

[0020] The epitope can be embedded in the substrate polypeptide, and in some aspects the substrate polypeptide can include more than one epitope, for example. Also, the epitope can be a housekeeping epitope.

[0021] In one aspect, the substrate polypeptide can be a synthetic peptide. Optionally, the substrate polypeptide can be included in a formulation promoting protein transfer. Alternatively, the substrate polypeptide can be a fusion protein. The fusion protein can further include a protein domain possessing protein transfer activity. Further, the contacting step can include immunization with the substrate polypeptide.

[0022] In another aspect, the substrate polypeptide can be encoded by a polynucleotide. The contacting step can include immunization with a vector including the polynucleotide, for example. The immunization can be carried out in an HLA-transgenic mouse or any other suitable animal, for example. Alternatively, the contacting step can include transforming a cell with a vector including the polynucleotide. In some embodiments the transformed cell can be a target cell that is targeted by CTL for purposes of assaying for proper liberation of epitope.

[0023] The proteasome processing can take place intracellularly, either in vitro or in vivo. Further, the proteasome processing can take place in a cell-free system.

[0024] The assaying step can include a technique selected from the group including, but not limited to, mass spectrometry, N-terminal pool sequencing, HPLC, and the like. Also, the assaying step can include a T cell target recognition assay. The T cell target recognition assay can be selected from the group including, but not limited to, a cytolytic activity assay, a chromium release assay, a cytokine assay, an ELISPOT assay, tetramer analysis, and the like.

[0025] In still another aspect, the amino acid sequence of the substrate polypeptide including the epitope can be arbitrary. Also, the substrate polypeptide in which the epitope is embedded can be derived from an authentic sequence of a target-associated antigen. Further, the substrate polypeptide in which the epitope is embedded can be conformed to a preferred immune proteasome cleavage site flanking sequence.

[0026] In another aspect, the substrate polypeptide can include an array of additional epitopes. Members of the array can be arranged head-to-tail, for example. The array can include more than one housekeeping epitope. The more than one housekeeping epitope can include copies of the same epitope. The array can include a housekeeping and an immune epitope, or alternating housekeeping and immune epitopes, for example. Also, the array can include a housekeeping epitope positioned between two immune epitopes in an epitope battery. The array can include multiple epitope batteries, so that there are two immune epitopes between each housekeeping epitope in the interior of the array. Optionally, at least one of the epitopes can be truncated distally to its junction with an adjacent epitope. The truncated epitopes can be immune epitopes, for example. The truncated epitopes can have lengths selected from the group including, but not limited to, 9, 8, 7, 6, 5, 4 amino acids, and the like.

[0027] In still another aspect, the substrate polypeptide can include an array of epitopes and epitope clusters. Members of the array can be arranged head-to-tail, for example.

[0028] In yet another aspect, the proteasome can be an immune proteasome.

[0029] Another embodiment of the disclosed invention relates to vectors including a housekeeping epitope expression cassette. The housekeeping epitope(s) can be derived from a target-associated antigen, and the housekeeping epitope can be liberatable, that is capable of liberation, from a translation product of the cassette by immunoproteasome processing.

[0030] In one aspect of the invention the expression cassette can encode an array of two or more epitopes or at least one epitope and at least one epitope cluster. The members of the array can be arranged head-to-tail, for example. Also, the members of the array can be arranged head-to-tail separated by spacing sequences, for example. Further, the array can include a plurality of housekeeping epitopes. The plurality of housekeeping epitopes can include more than one copy of the same epitope or single copies of distinct epitopes, for example. The array can include at least one housekeeping epitope and at least one immune epitope. Also, the array can include alternating housekeeping and immune epitopes. Further, the array includes a housekeeping epitope sandwiched between two immune epitopes so that there are two immune epitopes between each housekeeping epitope in the interior of the array. The immune epitopes can be truncated distally to their junction with the adjacent housekeeping epitope.

[0031] In another aspect, the expression cassette further encodes an authentic protein sequence, or segment thereof, including at least one immune epitope. Optionally, the segment can include at least one epitope cluster. The housekeeping epitope expression cassette and the authentic sequence including at least one immune epitope can be encoded in a single reading frame or transcribed as a single mRNA species, for example. Also, the housekeeping epitope expression cassette and the authentic sequence including at least one immune epitope may not be transcribed as a single mRNA species.

[0032] In yet another aspect, the vector can include a DNA molecule or an RNA molecule. The vector can encode, for example, SEQ ID NO. 4, SEQ ID NO. 17, SEQ ID NO. 20, SEQ ID NO. 26, SEQ ID NO. 27, SEQ ID NO. 29, SEQ ID NO. 33, and the like. Also, the vector can include SEQ ID NO. 9, SEQ ID NO. 19, SEQ ID NO. 21, SEQ ID NO. 30, SEQ ID NO. 34, and the like. Also, the vector can encode SEQ ID NO. 5 or SEQ ID NO. 18, for example.

[0033] In still another aspect, the target-associated antigen can be an antigen derived from or associated with a tumor or an intracellular parasite, and the intracellular parasite can be, for example, a virus, a bacterium, a protozoan, or the like.

[0034] Another embodiment of the invention relates to vectors including a housekeeping epitope identified according to any of the methods disclosed herein, claimed or otherwise. For example, embodiments can relate to vector encoding a substrate polypeptide that includes a housekeeping epitope by any of the methods described herein.

[0035] In one aspect, the housekeeping epitope can be liberated from the cassette translation product by immune proteasome processing

[0036] Another embodiment of the disclosed invention relates to methods of activating a T cell. The methods can include, for example, the steps of contacting a vector including a housekeeping epitope expression cassette with an APC. The housekeeping epitope can be derived from a target-associated antigen, for example, and the housekeeping epitope can be liberatable from a translation product of the cassette by immunoproteasome processing. The methods can further include contacting the APC with a T cell. The contacting of the vector with the APC can occur in vitro or in vivo.

[0037] Another embodiment of the disclosed invention relates to a substrate polypeptide including a housekeeping epitope wherein the housekeeping epitope can be liberated by immunoproteasome processing in a pAPC.

[0038] Another embodiment of the disclosed invention relates to a method of activating a T cell comprising contacting a substrate polypeptide including a housekeeping epitope with an APC wherein the housekeeping epitope can be liberated by immunoproteasome processing and contacting the APC with a T cell.

BRIEF DESCRIPTION OF THE DRAWINGS

[0039] FIG. 1 depicts the sequence of Melan-A (SEQ ID NO: 2), showing clustering of class I HLA epitopes.

[0040] FIG. 2 depicts the sequence of SSX-2 (SEQ ID NO: 40), showing clustering of class I HLA epitopes.

[0041] FIG. 3 depicts the sequence of NY-ESO (SEQ ID NO: 11), showing clustering of class I HLA epitopes.

[0042] FIG. 4. An illustrative drawing depicting pMA2M.

[0043] FIG. 5. Assay results showing the % of specific lysis of ELAGIGILTV pulsed and unpulsed T2 target cells by mock immunized CTL.

[0044] FIG. 6. Assay results showing the % of specific lysis of ELAGIGILTV pulsed and unpulsed T2 target cells by pVAXM3 immunized CTL.

[0045] FIG. 7. Assay results showing the % of specific lysis of ELAGIGILTV pulsed and unpulsed T2 target cells by pVAXM2 immunized CTL.

[0046] FIG. 8. Assay results showing the % of specific lysis of ELAGIGILTV pulsed and unpulsed T2 target cells by pVAXM1 immunized CTL.

[0047] FIG. 9. Illustrates a sequence of SEQ ID NO. 22 from which the NY-ESO-1157-165 epitope is liberated by immunoproteasomal processing.

[0048] FIG. 10. Shows the differential processing by immunoproteasome and housekeeping proteasome of the SLLMWITQC epitope (SEQ ID NO. 12) in its native context where the cleavage following the C is more efficiently produced by housekeeping than immunoproteasome.

[0049] FIG. 11. 11A: Shows the results of the human immunoproteasome digest of SEQ ID NO. 31. 11B: Shows the comparative results of mouse versus human immunoproteasome digestion of SEQ ID NO. 31.

[0050] FIG. 12. Shows the differential processing of SSX-231-68 by housekeeping and immunoproteasome.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

[0051] Definitions

[0052] Unless otherwise clear from the context of the use of a term herein, the following listed terms shall generally have the indicated meanings for purposes of this description.

[0053] PROFESSIONAL ANTIGEN-PRESENTING CELL (pAPC)—a cell that possesses T cell costimulatory molecules and is able to induce a T cell response. Well characterized pAPCs include dendritic cells, B cells, and macrophages.

[0054] PERIPHERAL CELL—a cell that is not a pAPC.

[0055] HOUSEKEEPING PROTEASOME—a proteasome normally active in peripheral cells, and generally not present or not strongly active in pAPCs.

[0056] IMMUNOPROTEASOME—a proteasome normally active in pAPCs; the immunoproteasome is also active in some peripheral cells in infected tissues or following exposure to interferon.

[0057] EPITOPE—a molecule or substance capable of stimulating an immune response. In preferred embodiments, epitopes according to this definition include but are not necessarily limited to a polypeptide and a nucleic acid encoding a polypeptide, wherein the polypeptide is capable of stimulating an immune response. In other preferred embodiments, epitopes according to this definition include but are not necessarily limited to peptides presented on the surface of cells, the peptides being non-covalently bound to the binding cleft of class I MHC, such that they can interact with T cell receptors (TCR). Epitopes presented by class I MHC may be in immature or mature form. “Mature” refers to an MHC epitope in distinction to any precursor (“immature”) that may include or consist essentially of a housekeeping epitope, but also includes other sequences in a primary translation product that are removed by processing, including without limitation, alone or in any combination, proteasomal digestion, N-terminal trimming, or the action of exogenous enzymatic activities. Thus, a mature epitope may be provided embedded in a somewhat longer polypeptide, the immunological potential of which is due, at least in part, to the embedded epitope; or in its ultimate form that can bind in the MHC binding cleft to be recognized by TCR, respectively.

[0058] MHC EPITOPE—a polypeptide having a known or predicted binding affinity for a mammalian class I or class II major histocompatibility complex (MHC) molecule.

[0059] HOUSEKEEPING EPITOPE—In a preferred embodiment, a housekeeping epitope is defined as a polypeptide fragment that is an MHC epitope, and that is displayed on a cell in which housekeeping proteasomes are predominantly active. In another preferred embodiment, a housekeeping epitope is defined as a polypeptide containing a housekeeping epitope according to the foregoing definition, that is flanked by one to several additional amino acids. In another preferred embodiment, a housekeeping epitope is defined as a nucleic acid that encodes a housekeeping epitope according to the foregoing definitions. Exemplary housekeeping epitopes are provide in U.S. application Ser. No. 10/117,937, filed on Apr. 4, 2002; and U.S. Provisional Application No. 60/282,211, filed on Apr. 6, 2001; 60/337,017, filed on November 7, 2001; 60/363,210 filed Mar. 7, 2002; and 60/409,123, filed on Sep. 5, 2002; all of which are entitled EPITOPE SEQUENCES, and all of which above were incorporated herein by reference in their entireties.

[0060] IMMUNE EPITOPE—In a preferred embodiment, an immune epitope is defined as a polypeptide fragment that is an MHC epitope, and that is displayed on a cell in which immunoproteasomes are predominantly active. In another preferred embodiment, an immune epitope is defined as a polypeptide containing an immune epitope according to the foregoing definition, that is flanked by one to several additional amino acids. In another preferred embodiment, an immune epitope is defined as a polypeptide including an epitope cluster sequence, having at least two polypeptide sequences having a known or predicted affinity for a class I MHC. In yet another preferred embodiment, an immune epitope is defined as a nucleic acid that encodes an immune epitope according to any of the foregoing definitions.

[0061] TARGET CELL—a cell to be targeted by the vaccines and methods of the invention. Examples of target cells according to this definition include but are not necessarily limited to: a neoplastic cell and a cell harboring an intracellular parasite, such as, for example, a virus, a bacterium, or a protozoan. Target cells can also include cells that are targeted by CTL as a part of assays to determine or confirm proper epitope liberation and processing by a cell expressing immunoproteasome, to determine T cell specificity or immunogenicity for a desired epitope. Such cells may be transferred to express the substrate or liberation sequence, or the cells can simply be pulsed with peptide/epitope.

[0062] TARGET-ASSOCIATED ANTIGEN (TAA)—a protein or polypeptide present in a target cell.

[0063] TUMOR-ASSOCIATED ANTIGENS (TuAA)—a TAA, wherein the target cell is a neoplastic cell.

[0064] HLA EPITOPE—a polypeptide having a known or predicted binding affinity for a human class I or class II HLA complex molecule.

[0065] ANTIBODY—a natural immunoglobulin (Ig), poly- or monoclonal, or any molecule composed in whole or in part of an Ig binding domain, whether derived biochemically or by use of recombinant DNA. Examples include inter alia, F(ab), single chain Fv, and Ig variable region-phage coat protein fusions.

[0066] ENCODE—an open-ended term such that a nucleic acid encoding a particular amino acid sequence can consist of codons specifying that (poly)peptide, but can also comprise additional sequences either translatable, or for the control of transcription, translation, or replication, or to facilitate manipulation of some host nucleic acid construct.

[0067] SUBSTANTIAL SIMILARITY—this term is used to refer to sequences that differ from a reference sequence in an inconsequential way as judged by examination of the sequence. Nucleic acid sequences encoding the same amino acid sequence are substantially similar despite differences in degenerate positions or modest differences in length or composition of any non-coding regions. Amino acid sequences differing only by conservative substitution or minor length variations are substantially similar. Additionally, amino acid sequences comprising housekeeping epitopes that differ in the number of N-terminal flanking residues, or immune epitopes and epitope clusters that differ in the number of flanking residues at either terminus, are substantially similar. Nucleic acids that encode substantially similar amino acid sequences are themselves also substantially similar.

[0068] FUNCTIONAL SIMILARITY—this term is used to refer to sequences that differ from a reference sequence in an inconsequential way as judged by examination of a biological or biochemical property, although the sequences may not be substantially similar. For example, two nucleic acids can be useful as hybridization probes for the same sequence but encode differing amino acid sequences. Two peptides that induce cross-reactive CTL responses are functionally similar even if they differ by non-conservative amino acid substitutions (and thus do not meet the substantial similarity definition). Pairs of antibodies, or TCRs, that recognize the same epitope can be functionally similar to each other despite whatever structural differences exist. In testing for functional similarity of immunogenicity one would generally immunize with the “altered” antigen and test the ability of the elicited response (Ab, CTL, cytokine production, etc.) to recognize the target antigen. Accordingly, two sequences may be designed to differ in certain respects while retaining the same function. Such designed sequence variants are among the embodiments of the present invention.

[0069] EXPRESSION CASSETTE—a polynucleotide sequence encoding a polypeptide, operably linked to a promoter and other transcription and translation control elements, including but not limited to enhancers, termination codons, internal ribosome entry sites, and polyadenylation sites. The cassette can also include sequences that facilitate moving it from one host molecule to another.

[0070] EMBEDDED EPITOPE—an epitope contained within a longer polypeptide, also can include an epitope in which either the N-terminus or the C-terminus is embedded such that the epitope is not in an interior position.

[0071] MATURE EPITOPE—a peptide with no additional sequence beyond that present when the epitope is bound in the MHC peptide-binding cleft.

[0072] EPITOPE CLUSTER—a polypeptide, or a nucleic acid sequence encoding it, that is a segment of a native protein sequence comprising two or more known or predicted epitopes with binding affinity for a shared MHC restriction element, wherein the density of epitopes within the cluster is greater than the density of all known or predicted epitopes with binding affinity for the shared MHC restriction element within the complete protein sequence, and as disclosed in U.S. patent application Ser. No. 09/561,571 entitled EPITOPE CLUSTERS.

[0073] SUBSTRATE OR LIBERATION SEQUENCE—a designed or engineered sequence comprising or encoding a housekeeping epitope (according to the first of the definitions offered above) embedded in a larger sequence that provides a context allowing the housekeeping epitope to be liberated by immunoproteasomal processing, directly or in combination with N-terminal trimming or other processes.

[0074] Epitope Clusters

[0075] Embodiments of the invention disclosed herein provide epitope cluster regions (ECRs) for use in vaccines and in vaccine design and epitope discovery. Specifically, embodiments of the invention relate to identifying epitope clusters for use in generating immunologically active compositions directed against target cell populations, and for use in the discovery of discrete housekeeping epitopes and immune epitopes. In many cases, numerous putative class I MHC epitopes may exist in a single target-associated antigen (TAA). Such putative epitopes are often found in clusters (ECRs), MHC epitopes distributed at a relatively high density within certain regions in the amino acid sequence of the parent TAA. Since these ECRs include multiple putative epitopes with potential useful biological activity in inducing an immune response, they represent an excellent material for in vitro or in vivo analysis to identify particularly useful epitopes for vaccine design. And, since the epitope clusters can themselves be processed inside a cell to produce active MHC epitopes, the clusters can be used directly in vaccines, with one or more putative epitopes in the cluster actually being processed into an active MHC epitope.

[0076] The use of ECRs in vaccines offers important technological advances in the manufacture of recombinant vaccines, and further offers crucial advantages in safety over existing nucleic acid vaccines that encode whole protein sequences. Recombinant vaccines generally rely on expensive and technically challenging production of whole proteins in microbial fermentors. ECRs offer the option of using chemically synthesized polypeptides, greatly simplifying development and manufacture, and obviating a variety of safety concerns. Similarly, the ability to use nucleic acid sequences encoding ECRs, which are typically relatively short regions of an entire sequence, allows the use of synthetic oligonucleotide chemistry processes in the development and manipulation of nucleic acid based vaccines, rather than the more expensive, time consuming, and potentially difficult molecular biology procedures involved with using whole gene sequences.

[0077] Since an ECR is encoded by a nucleic acid sequence that is relatively short compared to that which encodes the whole protein from which the ECR is found, this can greatly improve the safety of nucleic acid vaccines. An important issue in the field of nucleic acid vaccines is the fact that the extent of sequence homology of the vaccine with sequences in the animal to which it is administered determines the probability of integration of the vaccine sequence into the genome of the animal. A fundamental safety concern of nucleic acid vaccines is their potential to integrate into genomic sequences, which can cause deregulation of gene expression and tumor transformation. The Food and Drug Administration has advised that nucleic acid and recombinant vaccines should contain as little sequence homology with human sequences as possible. In the case of vaccines delivering tumor-associated antigens, it is inevitable that the vaccines contain nucleic acid sequences that are homologous to those which encode proteins that are expressed in the tumor cells of patients. It is, however, highly desirable to limit the extent of those sequences to that which is minimally essential to facilitate the expression of epitopes for inducing therapeutic immune responses. The use of ECRs thus offers the dual benefit of providing a minimal region of homology, while incorporating multiple epitopes that have potential therapeutic value.

[0078] Note that the following discussion sets forth the inventors' understanding of the operation of the invention. However, it is not intended that this discussion limit the patent to any particular theory of operation not set forth in the claims.

[0079] ECRs are Processed into MHC-Binding Epitopes in pAPCs

[0080] The immune system constantly surveys the body for the presence of foreign antigens, in part through the activity of pAPCs. The pAPCs endocytose matter found in the extracellular milieu, process that matter from a polypeptide form into shorter oligopeptides of about 3 to 23 amino acids in length, and display some of the resulting peptides to T cells via the MHC complex of the pAPCs. For example, a tumor cell upon lysis releases its cellular contents, including various proteins, into the extracellular milieu. Those released proteins can be endocytosed by pAPCs and processed into discrete peptides that are then displayed on the surface of the pAPCs via the MHC. By this mechanism, it is not the entire target protein that is presented on the surface of the pAPCs, but rather only one or more discrete fragments of that protein that are presented as MHC-binding epitopes. If a presented epitope is recognized by a T cell, that T cell is activated and an immune response results.

[0081] Similarly, the scavenger receptors on pAPC can take-up naked nucleic acid sequences or recombinant organisms containing target nucleic acid sequences. Uptake of the nucleic acid sequences into the pAPC subsequently results in the expression of the encoded products. As above, when an ECR can be processed into one or more useful epitopes, these products can be presented as MHC epitopes for recognition by T cells.

[0082] MHC-binding epitopes are often distributed unevenly throughout a protein sequence in clusters. Embodiments of the invention are directed to identifying epitope cluster regions (ECRs) in a particular region of a target protein. Candidate ECRs are likely to be natural substrates for various proteolytic enzymes and are likely to be processed into one or more epitopes for MHC display on the surface of an pAPC. In contrast to more traditional vaccines that deliver whole proteins or biological agents, ECRs can be administered as vaccines, resulting in a high probability that at least one epitope will be presented on MHC without requiring the use of a full length sequence.

[0083] The Use of ECRs in Identifying Discrete MHC-Binding Epitopes

[0084] Identifying putative MHC epitopes for use in vaccines often includes the use of available predictive algorithms that analyze the sequences of proteins or genes to predict binding affinity of peptide fragments for MHC. These algorithms rank putative epitopes according to predicted affinity or other characteristics associated with MHC binding. Exemplary algorithms for this kind of analysis include the Rammensee and NIH (Parker) algorithms. However, identifying epitopes that are naturally present on the surface of cells from among putative epitopes predicted using these algorithms has proven to be a difficult and laborious process. The use of ECRs in an epitope identification process can enormously simplify the task of identifying discrete MHC binding epitopes.

[0085] In a preferred embodiment, ECR polypeptides are synthesized on an automated peptide synthesizer and these ECRs are then subjected to in vitro digests using proteolytic enzymes involved in processing proteins for presentation of the epitopes. Mass spectrometry and/or analytical HPLC are then used to identify the digest products and in vitro MHC binding studies are used to assess the ability of these products to actually bind to MHC. Once epitopes contained in ECRs have been shown to bind MHC, they can be incorporated into vaccines or used as diagnostics, either as discrete epitopes or in the context of ECRs.

[0086] The use of an ECR (which because of its relatively short sequence can be produced through chemical synthesis) in this preferred embodiment is a significant improvement over what otherwise would require the use of whole protein. This is because whole proteins have to be produced using recombinant expression vector systems and/or complex purification procedures. The simplicity of using chemically synthesized ECRs enables the analysis and identification of large numbers of epitopes, while greatly reducing the time and expense of the process as compared to other currently used methods. The use of a defined ECR also greatly simplifies mass spectrum analysis of the digest, since the products of an ECR digest are a small fraction of the digest products of a whole protein.

[0087] In another embodiment, nucleic acid sequences encoding ECRs are used to express the polypeptides in cells or cell lines to assess which epitopes are presented on the surface. A variety of means can be used to detect the epitope on the surface. Preferred embodiments involve the lysis of the cells and affinity purification of the MHC, and subsequent elution and analysis of peptides from the MHC; or elution of epitopes from intact cells; (Falk, K. et al. Nature 351:290, 1991, and U.S. Pat. No. 5,989,565, respectively, both of which references are incorporated herein by reference in their entirety). A sensitive method for analyzing peptides eluted in this way from the MHC employs capillary or nanocapillary HPLC ESI mass spectrometry and on-line sequencing.

[0088] Target-Associated Antigens that Contain ECRs

[0089] TAAs from which ECRs may be defined include those from TuAAs, including oncofetal, cancer-testis, deregulated genes, fusion genes from errant translocations, differentiation antigens, embryonic antigens, cell cycle proteins, mutated tumor suppressor genes, and overexpressed gene products, including oncogenes. In addition, ECRs may be derived from virus gene products, particularly those associated with viruses that cause chronic diseases or are oncogenic, such as the herpes viruses, human papilloma viruses, human immunodeficiency virus, and human T cell leukemia virus. Also ECRs may be derived from gene products of parasitic organisms, such as Trypanosoma, Leishmania, and other intracellular or parasitic organisms.

[0090] Some of these TuAA include α-fetoprotein, carcinoembryonic antigen (CEA), esophageal cancer derived NY-ESO-1, and SSX genes, SCP-1, PRAME, MART-1/MelanA (MART-1), gp100 (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-2, MAGE-3, BAGE, GAGE-1, GAGE-2, p15; overexpressed oncogenes and mutated tumor-suppressor genes such as p53, Ras, HER-2/neu; unique tumor antigens resulting from chromosomal translocations such as BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR1 and viral antigens, EBNA1, EBNA2, HPV-E6, -E7; prostate specific antigen (PSA), prostate stem cell antigen (PSCA), MAAT-1, GP-100, TSP-180, MAGE-4, MAGE-5, MAGE-6, RAGE, p185erbB-2, p185erbB-3, c-met, nm-23H1, TAG-72, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras, β-Catenin, CDK4, Mum-1, p15, and p16.

[0091] Numerous other TAAs are also contemplated for both pathogens and tumors. In terms of TuAAs, a variety of methods are available and well known in the art to identify genes and gene products that are differentially expressed in neoplastic cells as compared to normal cells. Examples of these techniques include differential hybridization, including the use of microarrays; subtractive hybridization cloning; differential display, either at the level of mRNA or protein expression; EST sequencing; and SAGE (sequential analysis of gene expression). These nucleic acid techniques have been reviewed by Carulli, J. P. et al., J. Cellular Biochem Suppl. 30/31:286-296, 1998 (hereby incorporated by reference). Differential display of proteins involves, for example, comparison of two-dimensional poly-acrylamide gel electrophoresis of cell lysates from tumor and normal tissue, location of protein spots unique or overexpressed in the tumor, recovery of the protein from the gel, and identification of the protein using traditional biochemical- or mass spectrometry-based sequencing. An additional technique for identification of TAAs is the Serex technique, discussed in Türeci, Ö., Sahin, U., and Pfreundschuh, M., “Serological analysis of human tumor antigens: molecular definition and implications”, Molecular Medicine Today, 3:342, 1997, and hereby incorporated by reference.

[0092] Use of these and other methods provides one of skill in the art the techniques necessary to identify genes and gene products contained within a target cell that may be used as potential candidate proteins for generating the epitopes of the invention disclosed. However, it is not necessary, in practicing the invention, to identify a novel TuAA or TAA. Rather, embodiments of the invention make it possible to identify ECRs from any relevant protein sequence, whether the sequence is already known or is new.

[0093] Protein Sequence Analysis to Identify Epitope Clusters

[0094] In preferred embodiments of the invention, identification of ECRs involves two main steps: (1) identifying good putative epitopes; and (2) defining the limits of any clusters in which these putative epitopes are located. There are various preferred embodiments of each of these two steps, and a selected embodiment for the first step can be freely combined with a selected embodiment for the second step. The methods and embodiments that are disclosed herein for each of these steps are merely exemplary, and are not intended to limit the scope of the invention in any way. Persons of skill in the art will appreciate the specific tools that can be applied to the analysis of a specific TAA, and such analysis can be conducted in numerous ways in accordance with the invention.

[0095] Preferred embodiments for identifying good putative epitopes include the use of any available predictive algorithm that analyzes the sequences of proteins or genes to predict binding affinity of peptide fragments for MHC, or to rank putative epitopes according to predicted affinity or other characteristics associated with MHC binding. As described above, available exemplary algorithms for this kind of analysis include the Rammensee and NIH (Parker) algorithms. Likewise, good putative epitopes can be identified by direct or indirect assays of MHC binding. To choose “good” putative epitopes, it is necessary to set a cutoff point in terms of the score reported by the prediction software or in terms of the assayed binding affinity. In some embodiments, such a cutoff is absolute. For example, the cutoff can be based on the measured or predicted half time of dissociation between an epitope and a selected MHC allele. In such cases, embodiments of the cutoff can be any half time of dissociation longer than, for example, 0.5 minutes; in a preferred embodiment longer than 2.5 minutes; in a more preferred embodiment longer than 5 minutes; and in a highly stringent embodiment can be longer than 10, or 20, or 25 minutes. In these embodiments, the good putative epitopes are those that are predicted or identified to have good MHC binding characteristics, defined as being on the desirable side of the designated cutoff point. Likewise, the cutoff can be based on the measured or predicted binding affinity between an epitope and a selected MHC allele. Additionally, the absolute cutoff can be simply a selected number of putative epitopes.

[0096] In other embodiments, the cutoff is relative. For example, a selected percentage of the total number of putative epitopes can be used to establish the cutoff for defining a candidate sequence as a good putative epitope. Again the properties for ranking the epitopes are derived from measured or predicted MHC binding; the property used for such a determination can be any that is relevant to or indicative of binding. In preferred embodiments, identification of good putative epitopes can combine multiple methods of ranking candidate sequences. In such embodiments, the good epitopes are typically those that either represent a consensus of the good epitopes based on different methods and parameters, or that are particularly highly ranked by at least one of the methods.

[0097] When several good putative epitopes have been identified, their positions relative to each other can be analyzed to determine the optimal clusters for use in vaccines or in vaccine design. This analysis is based on the density of a selected epitope characteristic within the sequence of the TAA. The regions with the highest density of the characteristic, or with a density above a certain selected cutoff, are designated as ECRs. Various embodiments of the invention employ different characteristics for the density analysis. For example, one preferred characteristic is simply the presence of any good putative epitope (as defined by any appropriate method). In this embodiment, all putative epitopes above the cutoff are treated equally in the density analysis, and the best clusters are those with the highest density of good putative epitopes per amino acid residue. In another embodiment, the preferred characteristic is based on the parameter(s) previously used to score or rank the putative epitopes. In this embodiment, a putative epitope with a score that is twice as high as another putative epitope is doubly weighted in the density analysis, relative to the other putative epitope. Still other embodiments take the score or rank into account, but on a diminished scale, such as, for example, by using the log or the square root of the score to give more weight to some putative epitopes than to others in the density analysis.

[0098] Depending on the length of the TAA to be analyzed, the number of possible candidate epitopes, the number of good putative epitopes, the variability of the scoring of the good putative epitopes, and other factors that become evident in any given analysis, the various embodiments of the invention can be used alone or in combination to identify those ECRs that are most useful for a given application. Iterative or parallel analyses employing multiple approaches can be beneficial in many cases. ECRs are tools for increased efficiency of identifying true MHC epitopes, and for efficient “packaging” of MHC epitopes into vaccines. Accordingly, any of the embodiments described herein, or other embodiments that are evident to those of skill in the art based on this disclosure, are useful in enhancing the efficiency of these efforts by using ECRs instead of using complete TAAs in vaccines and vaccine design.

[0099] Since many or most TAAs have regions with low density of predicted MHC epitopes, using ECRs provides a valuable methodology that avoids the inefficiencies of including regions of low epitope density in vaccines and in epitope identification protocols. Thus, useful ECRs can also be defined as any portion of a TAA that is not the whole TAA, wherein the portion has a higher density of putative epitopes than the whole TAA, or than any regions of the TAA that have a particularly low density of putative epitopes. In this aspect of the invention, therefore, an ECR can be any fragment of a TAA with elevated epitope density. In some embodiments, an ECR can include a region up to about 80% of the length of the TAA. In a preferred embodiment, an ECR can include a region up to about 50% of the length of the TAA. In a more preferred embodiment, an ECR can include a region up to about 30% of the length of the TAA. And in a most preferred embodiment, an ECR can include a region of between 5 and 15% of the length of the TAA.

[0100] In another aspect of the invention, the ECR can be defined in terms of its absolute length. Accordingly, by this definition, the minimal cluster for 9-mer epitopes includes 10 amino acid residues and has two overlapping 9-mers with 8 amino acids in common. In a preferred embodiment, the cluster is between about 15 and 75 amino acids in length. In a more preferred embodiment, the cluster is between about 20 and 60 amino acids in length. In a most preferred embodiment, the cluster is between about 30 and 40 amino acids in length.

[0101] In practice, as described above, ECR identification can employ a simple density function such as the number of epitopes divided by the number of amino acids spanned by the those epitopes. It is not necessarily required that the epitopes overlap, but the value for a single epitope is not significant. If only a single value for a percentage cutoff is used and an absolute cutoff in the epitope prediction is not used, it is possible to set a single threshold at this step to define a cluster. However, using both an absolute cutoff and carrying out the first step using different percentage cutoffs, can produce variations in the global density of candidate epitopes. Such variations can require further accounting or manipulation. For example, an overlap of 2 epitopes is more significant if only 3 candidate epitopes were considered, than if 30 candidates were considered for any particular length protein. To take this feature into consideration, the weight given to a particular cluster can further be divided by the fraction of possible peptides actually being considered, in order to increase the significance of the calculation. This scales the result to the average density of predicted epitopes in the parent protein.

[0102] Similarly, some embodiments base the scoring of good putative epitopes on the average number of peptides considered per amino acid in the protein. The resulting ratio represents the factor by which the density of predicted epitopes in the putative cluster differs from the average density in the protein. Accordingly, an ECR is defined in one embodiment as any region containing two or more predicted epitopes for which this ratio exceeds 2, that is, any region with twice the average density of epitopes. In other embodiments, the region is defined as an ECR if the ratio exceeds 1.5, 3, 4, or 5, or more.

[0103] Considering the average number of peptides per amino acid in a target protein to calculate the presence of an ECR highlights densely populated ECRs without regard to the score/affinity of the individual constituents. This is most appropriate for use of score-based cutoffs. However, an ECR with only a small number of highly ranked candidates can be of more biological significance than a cluster with several densely packed but lower ranking candidates, particularly if only a small percentage of the total number of candidate peptides were designated as good putative epitopes. Thus in some embodiments it is appropriate to take into consideration the scores of the individual peptides. This is most readily accomplished by substituting the sum of the scores of the peptides in the putative cluster for the number of peptides in the putative cluster in the calculation described above.

[0104] This sum of scores method is more sensitive to sparsely populated clusters containing high scoring epitopes. Because the wide range of scores (i.e. half times of dissociation) produced by the BIMAS-NIH/Parker algorithm can lead to a single high scoring peptide dwarfing the contribution of other potential epitopes, the log of the score rather than the score itself is preferably used in this procedure.

[0105] Various other calculations can be devised under one or another condition. Generally speaking, the epitope density function is constructed so that it is proportional to the number of predicted epitopes, their scores, their ranks, and the like, within the putative cluster, and inversely proportional to the number of amino acids or fraction of protein contained within that putative cluster. Alternatively, the function can be evaluated for a window of a selected number of contiguous amino acids. In either case the function is also evaluated for all predicted epitopes in the whole protein. If the ratio of values for the putative cluster (or window) and the whole protein is greater than, for example, 1.5, 2, 3, 4, 5, or more, an ECR is defined.

[0106] Analysis of Target Gene Products For MHC Binding

[0107] Once a TAA has been identified, the protein sequence can be used to identify putative epitopes with known or predicted affinity to the MHC peptide binding cleft. Tests of peptide fragments can be conducted in vitro, or using the sequence can be computer analyzed to determine MHC receptor binding of the peptide fragments. In one embodiment of the invention, peptide fragments based on the amino acid sequence of the target protein are analyzed for their predicted ability to bind to the MHC peptide binding cleft. Examples of suitable computer algorithms for this purpose include that found at the world wide web page of Hans-Georg Rammensee, Jutta Bachmann, Niels Emmerich, Stefan Stevanovic: SYFPEITHI: An Internet Database for MHC Ligands and Peptide Motifs (access via hypertext transfer protocol: //134.2.96.221/scripts/hlaserver.dll/EpPredict.htm). Results obtained from this method are discussed in Rammensee, et al., “MHC Ligands and Peptide Motifs,” Landes Bioscience Austin, Tex., 224-227, 1997, which is hereby incorporated by reference in its entirety. Another site of interest is found at hypertext transfer protocol: //bimas.dcrt.nih.gov/molbio/hla_bind, which also contains a suitable algorithm. The methods of this web site are discussed in Parker, et al., “Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains,” J. Immunol. 152:163-175, which is hereby incorporated by reference in its entirety.

[0108] As an alternative to predictive algorithms, a number of standard in vitro receptor binding affinity assays are available to identify peptides having an affinity for a particular allele of MHC. Accordingly, by the method of this aspect of the invention, the initial population of peptide fragments can be narrowed to include only putative epitopes having an actual or predicted affinity for the selected allele of MHC. Selected common alleles of MHC I, and their approximate frequencies, are reported in the tables below.

TABLE 1
Estimated gene frequencies of HLA-A antigens
	CAU	AFR	ASI	LAT	NAT
Antigen	Gfa	SEb	Gf	SE	Gf	SE	Gf	SE	Gf	SE
A1	15.1843	0.0489	5.7256	0.0771	4.4818	0.0846	7.4007	0.0978	12.0316	0.2533
A2	28.6535	0.0619	18.8849	0.1317	24.6352	0.1794	28.1198	0.1700	29.3408	0.3585
A3	13.3890	0.0463	8.4406	0.0925	2.6454	0.0655	8.0789	0.1019	11.0293	0.2437
A28	4.4652	0.0280	9.9269	0.0997	1.7657	0.0537	8.9446	0.1067	5.3856	0.1750
A36	0.0221	0.0020	1.8836	0.0448	0.0148	0.0049	0.1584	0.0148	0.1545	0.0303
A23	1.8287	0.0181	10.2086	0.1010	0.3256	0.0231	2.9269	0.0628	1.9903	0.1080
A24	9.3251	0.0395	2.9668	0.0560	22.0391	0.1722	13.2610	0.1271	12.6613	0.2590
A9 unsplit	0.0809	0.0038	0.0367	0.0063	0.0858	0.0119	0.0537	0.0086	0.0356	0.0145
A9 total	11.2347	0.0429	13.2121	0.1128	22.4505	0.1733	16.2416	0.1382	14.6872	0.2756
A25	2.1157	0.0195	0.4329	0.0216	0.0990	0.0128	1.1937	0.0404	1.4520	0.0924
A26	3.8795	0.0262	2.8284	0.0547	4.6628	0.0862	3.2612	0.0662	2.4292	0.1191
A34	0.1508	0.0052	3.5228	0.0610	1.3529	0.0470	0.4928	0.0260	0.3150	0.0432
A43	0.0018	0.0006	0.0334	0.0060	0.0231	0.0062	0.0055	0.0028	0.0059	0.0059
A66	0.0173	0.0018	0.2233	0.0155	0.0478	0.0089	0.0399	0.0074	0.0534	0.0178
A10 unsplit	0.0790	0.0038	0.0939	0.0101	0.1255	0.0144	0.0647	0.0094	0.0298	0.0133
A10 total	6.2441	0.0328	7.1348	0.0850	6.3111	0.0993	5.0578	0.0816	4.2853	0.1565
A29	3.5796	0.0252	3.2071	0.0582	1.1233	0.0429	4.5156	0.0774	3.4345	0.1410
A30	2.5067	0.0212	13.0969	0.1129	2.2025	0.0598	4.4873	0.0772	2.5314	0.1215
A31	2.7386	0.0221	1.6556	0.0420	3.6005	0.0761	4.8328	0.0800	6.0881	0.1855
A32	3.6956	0.0256	1.5384	0.0405	1.0331	0.0411	2.7064	0.0604	2.5521	0.1220
A33	1.2080	0.0148	6.5607	0.0822	9.2701	0.1191	2.6593	0.0599	1.0754	0.0796
A74	0.0277	0.0022	1.9949	0.0461	0.0561	0.0096	0.2027	0.0167	0.1068	0.0252
A19 unsplit	0.0567	0.0032	0.2057	0.0149	0.0990	0.0128	0.1211	0.0129	0.0475	0.0168
A19 total	13.8129	0.0468	28.2593	0.1504	17.3846	0.1555	19.5252	0.1481	15.8358	0.2832
AX	0.8204	0.0297	4.9506	0.0963	2.9916	0.1177	1.6332	0.0878	1.8454	0.1925
aGene frequency.
bStandard error.

[0109]

TABLE 2
Estimated gene frequencies for HLA-B antigens
	CAU	AFR	ASI	LAT	NAT
Antigen	Gfa	SEb	Gf	SE	Gf	SE	Gf	SE	Gf	SE
B7	12.1782	0.0445	10.5960	0.1024	4.2691	0.0827	6.4477	0.0918	10.9845	0.2432
B8	9.4077	0.0397	3.8315	0.0634	1.3322	0.0467	3.8225	0.0715	8.5789	0.2176
B13	2.3061	0.0203	0.8103	0.0295	4.9222	0.0886	1.2699	0.0416	1.7495	0.1013
B14	4.3481	0.0277	3.0331	0.0566	0.5004	0.0287	5.4166	0.0846	2.9823	0.1316
B18	4.7980	0.0290	3.2057	0.0582	1.1246	0.0429	4.2349	0.0752	3.3422	0.1391
B27	4.3831	0.0278	1.2918	0.0372	2.2355	0.0603	2.3724	0.0567	5.1970	0.1721
B35	9.6614	0.0402	8.5172	0.0927	8.1203	0.1122	14.6516	0.1329	10.1198	0.2345
B37	1.4032	0.0159	0.5916	0.0252	1.2327	0.0449	0.7807	0.0327	0.9755	0.0759
B41	0.9211	0.0129	0.8183	0.0296	0.1303	0.0147	1.2818	0.0418	0.4766	0.0531
B42	0.0608	0.0033	5.6991	0.0768	0.0841	0.0118	0.5866	0.0284	0.2856	0.0411
B46	0.0099	0.0013	0.0151	0.0040	4.9292	0.0886	0.0234	0.0057	0.0238	0.0119
B47	0.2069	0.0061	0.1305	0.0119	0.0956	0.0126	0.1832	0.0159	0.2139	0.0356
B48	0.0865	0.0040	0.1316	0.0119	2.0276	0.0575	1.5915	0.0466	1.0267	0.0778
B53	0.4620	0.0092	10.9529	0.1039	0.4315	0.0266	1.6982	0.0481	1.0804	0.0798
B59	0.0020	0.0006	0.0032	0.0019	0.4277	0.0265	0.0055	0.0028	0c	—
B67	0.0040	0.0009	0.0086	0.0030	0.2276	0.0194	0.0055	0.0028	0.0059	0.0059
B70	0.3270	0.0077	7.3571	0.0866	0.8901	0.0382	1.9266	0.0512	0.6901	0.0639
B73	0.0108	0.0014	0.0032	0.0019	0.0132	0.0047	0.0261	0.0060	0c	—
B51	5.4215	0.0307	2.5980	0.0525	7.4751	0.1080	6.8147	0.0943	6.9077	0.1968
B52	0.9658	0.0132	1.3712	0.0383	3.5121	0.0752	2.2447	0.0552	0.6960	0.0641
B5 unsplit	0.1565	0.0053	0.1522	0.0128	0.1288	0.0146	0.1546	0.0146	0.1307	0.0278
B5 total	6.5438	0.0435	4.1214	0.0747	11.1160	0.1504	9.2141	0.1324	7.7344	0.2784
B44	13.4838	0.0465	7.0137	0.0847	5.6807	0.0948	9.9253	0.1121	11.8024	0.2511
B45	0.5771	0.0102	4.8069	0.0708	0.1816	0.0173	1.8812	0.0506	0.7603	0.0670
B12 unsplit	0.0788	0.0038	0.0280	0.0055	0.0049	0.0029	0.0193	0.0051	0.0654	0.0197
B12 total	14.1440	0.0474	11.8486	0.1072	5.8673	0.0963	11.8258	0.1210	12.6281	0.2584
B62	5.9117	0.0320	1.5267	0.0404	9.2249	0.1190	4.1825	0.0747	6.9421	0.1973
B63	0.4302	0.0088	1.8865	0.0448	0.4438	0.0270	0.8083	0.0333	0.3738	0.0471
B75	0.0104	0.0014	0.0226	0.0049	1.9673	0.0566	0.1101	0.0123	0.0356	0.0145
B76	0.0026	0.0007	0.0065	0.0026	0.0874	0.0120	0.0055	0.0028	0	—
B77	0.0057	0.0010	0.0119	0.0036	0.0577	0.0098	0.0083	0.0034	0c	0.0059
B15 unsplit	0.1305	0.0049	0.0691	0.0086	0.4301	0.0266	0.1820	0.0158	0.0059	0.0206
B15 total	6.4910	0.0334	3.5232	0.0608	12.2112	0.1344	5.2967	0.0835	0.0715	0.2035
									7.4290
B38	2.4413	0.0209	0.3323	0.0189	3.2818	0.0728	1.9652	0.0517	1.1017	0.0806
B39	1.9614	0.0188	1.2893	0.0371	2.0352	0.0576	6.3040	0.0909	4.5527	0.1615
B16 unsplit	0.0638	0.0034	0.0237	0.0051	0.0644	0.0103	0.1226	0.0130	0.0593	0.0188
B16 total	4.4667	0.0280	1.6453	0.0419	5.3814	0.0921	8.3917	0.1036	5.7137	0.1797
B57	3.5955	0.0252	5.6746	0.0766	2.5782	0.0647	2.1800	0.0544	2.7265	0.1260
B58	0.7152	0.0114	5.9546	0.0784	4.0189	0.0803	1.2481	0.0413	0.9398	0.0745
B17 unsplit	0.2845	0.0072	0.3248	0.0187	0.3751	0.0248	0.1446	0.0141	0.2674	0.0398
B17 total	4.5952	0.0284	11.9540	0.1076	6.9722	0.1041	3.5727	0.0691	3.9338	0.1503
B49	1.6452	0.0172	2.6286	0.0528	0.2440	0.0200	2.3353	0.0562	1.5462	0.0953
B50	1.0580	0.0138	0.8636	0.0304	0.4421	0.0270	1.8883	0.0507	0.7862	0.0681
B21 unsplit	0.0702	0.0036	0.0270	0.0054	0.0132	0.0047	0.0771	0.0103	0.0356	0.0145
B21 total	2.7733	0.0222	3.5192	0.0608	0.6993	0.0339	4.3007	0.0755	2.3680	0.1174
B54	0.0124	0.0015	0.0183	0.0044	2.6873	0.0660	0.0289	0.0063	0.0534	0.0178
B55	1.9046	0.0185	0.4895	0.0229	2.2444	0.0604	0.9515	0.0361	1.4054	0.0909
B56	0.5527	0.0100	0.2686	0.0170	0.8260	0.0368	0.3596	0.0222	0.3387	0.0448
B22 unsplit	0.1682	0.0055	0.0496	0.0073	0.2730	0.0212	0.0372	0.0071	0.1246	0.0272
B22 total	2.0852	0.0217	0.8261	0.0297	6.0307	0.0971	1.3771	0.0433	1.9221	0.1060
B60	5.2222	0.0302	1.5299	0.0404	8.3254	0.1135	2.2538	0.0553	5.7218	0.1801
B61	1.1916	0.0147	0.4709	0.0225	6.2072	0.0989	4.6691	0.0788	2.6023	0.1231
B40 unsplit	0.2696	0.0070	0.0388	0.0065	0.3205	0.0230	0.2473	0.0184	0.2271	0.0367
B40 total	6.6834	0.0338	2.0396	0.0465	14.8531	0.1462	7.1702	0.0963	8.5512	0.2168
BX	1.0922	0.0252	3.5258	0.0802	3.8749	0.0988	2.5266	0.0807	1.9867	0.1634
a Gene frequency.
b Standard error.
c The observed gene count was zero.

[0110]

TABLE 3
Estimated gene frequencies of HLA-DR antigens
	CAU	AFR	ASI	LAT	NAT
Antigen	Gfa	SEb	Gf	SE	Gf	SE	Gf	SE	Gf	SE
DR1	10.2279	0.0413	6.8200	0.0832	3.4628	0.0747	7.9859	0.1013	8.2512	0.2139
DR2	15.2408	0.0491	16.2373	0.1222	18.6162	0.1608	11.2389	0.1182	15.3932	0.2818
DR3	10.8708	0.0424	13.3080	0.1124	4.7223	0.0867	7.8998	0.1008	10.2549	0.2361
DR4	16.7589	0.0511	5.7084	0.0765	15.4623	0.1490	20.5373	0.1520	19.8264	0.3123
DR6	14.3937	0.0479	18.6117	0.1291	13.4471	0.1404	17.0265	0.1411	14.8021	0.2772
DR7	13.2807	0.0463	10.1317	0.0997	6.9270	0.1040	10.6726	0.1155	10.4219	0.2378
DR8	2.8820	0.0227	6.2673	0.0800	6.5413	0.1013	9.7731	0.1110	6.0059	0.1844
DR9	1.0616	0.0139	2.9646	0.0559	9.7527	0.1218	1.0712	0.0383	2.8662	0.1291
DR10	1.4790	0.0163	2.0397	0.0465	2.2304	0.0602	1.8044	0.0495	1.0896	0.0801
DR11	9.3180	0.0396	10.6151	0.1018	4.7375	0.0869	7.0411	0.0955	5.3152	0.1740
DR12	1.9070	0.0185	4.1152	0.0655	10.1365	0.1239	1.7244	0.0484	2.0132	0.1086
DR5 unsplit	1.2199	0.0149	2.2957	0.0493	1.4118	0.0480	1.8225	0.0498	1.6769	0.0992
DR5 total	12.4449	0.0045	17.0260	0.1243	16.2858	0.1516	10.5880	0.1148	9.0052	0.2218
DRX	1.3598	0.0342	0.8853	0.0760	2.5521	0.1089	1.4023	0.0930	2.0834	0.2037
a Gene frequency.
b Standard error.

[0111] It has been observed that predicted epitopes often cluster at one or more particular regions within the amino acid sequence of a TAA. The identification of such ECRs offers a simple and practicable solution to the problem of designing effective vaccines for stimulating cellular immunity. For vaccines in which immune epitopes are desired, an ECR is directly useful as a vaccine. This is because the immune proteasomes of the pAPCs can correctly process the cluster, liberating one or more of the contained MHC-binding peptides, in the same way a cell having immune proteasomes activity processes and presents peptides derived from the complete TAA. The cluster is also a useful a starting material for identification of housekeeping epitopes produced by the housekeeping proteasomes active in peripheral cells.

[0112] Identification of housekeeping epitopes using ECRs as a starting material is described in copending U.S. patent application Ser. No. 09/561,074 entitled “METHOD OF EPITOPE DISCOVERY,” filed Apr. 28, 2000, which is incorporated herein by reference in its entirety. Epitope synchronization technology and vaccines for use in connection with this invention are disclosed in copending U.S. patent application Ser. No. 09/560,465 entitled “EPITOPE SYNCHRONIZATION IN ANTIGEN PRESENTING CELLS,” filed Apr. 28, 2000, which is incorporated herein by reference in its entirety. Nucleic acid constructs useful as vaccines in accordance with the present invention are disclosed in copending U.S. patent application Ser. No. 09/561,572 entitled “EXPRESSION VECTORS ENCODING EPITOPES OF TARGET-ASSOCIATED ANTIGENS,” filed Apr. 28, 2000, which is incorporated herein by reference in its entirety.

[0113] Vector Design and Vectors

[0114] Degradation of cytosolic proteins takes place via the ubiquitin-dependent multi-catalytic multi-subunit protease system known as the proteasome. The proteasome degrades cytosolic proteins generating fragments that can then be translocated from the cytosol into the endoplasmic reticulum (ER) for loading onto class I MHC. Such protein fragments shall be referred to as class I peptides. The peptide loaded MHC are subsequently transported to the cell surface where they can be detected by CTL.

[0115] The multi-catalytic activity of the proteasome is the result of its multi-subunit structure. Subunits are expressed from different genes and assembled post-translationally into the proteasome complex. A key feature of the proteasome is its bimodal activity, which enables it to exert its protease, or cleavage function, with two discrete kinds of cleavage patterns. This bimodal action of the proteasome is extremely fundamental to understanding how CTL are targeted to recognize peripheral cells in the body and how this targeting requires synchronization between the immune system and the targeted cells.

[0116] The housekeeping proteasome is constitutively active in all peripheral cells and tissues of the body. The first mode of operation for the housekeeping proteasome is to degrade cellular protein, recycling it into amino acids. Proteasome function is therefore a necessary activity for cell life. As a corollary to its housekeeping protease activity, however, class I peptides generated by the housekeeping proteasome are presented on all of the peripheral cells of the body.

[0117] The proteasome's second mode of function is highly exclusive and occurs specifically in pAPCs or as a consequence of a cellular response to interferons (IFNs). In its second mode of activity the proteasome incorporates unique subunits, which replace the catalytic subunits of the constitutive housekeeping proteasome. This “modified” proteasome has been called the immunoproteasome, owing to its expression in pAPC and as a consequence of induction by IFN in body cells.

[0118] APC define the repertoire of CTL that recirculate through the body and are potentially active as killer cells. CTL are activated by interacting with class I peptide presented on the surface of a pAPC. Activated CTL are induced to proliferate and caused to recirculate through the body in search of diseased cells. This is why the CTL response in the body is defined specifically by the class I peptides produced by the pAPC. It is important to remember that pAPCs express the immunoproteasome, and that as a consequence of the bimodal activity of the proteasome, the cleavage pattern of proteins (and the resultant class I peptides produced) are different from those in peripheral body cells which express housekeeping proteasome. The differential proteasome activity in pAPC and peripheral body cells, therefore, is important to consider during natural infection and with therapeutic CTL vaccination strategies.

[0119] All cells of the body are capable of producing IFN in the event that they are infected by a pathogen such as a virus. IFN production in turn results in the expression of the immunoproteasome in the infected cell. Viral antigens are thereby processed by the immunoproteasome of the infected cell and the consequent peptides are displayed with class I MHC on the cell surface. At the same time, pAPC are sequestering virus antigens and are processing class I peptides with their immunoproteasome activity, which is normal for the pAPC cell type. The CTL response in the body is being stimulated specifically by the class I peptides produced by the pAPC. Fortunately, the infected cell is also producing class I peptides from the immunoproteasome, rather than the normal housekeeping proteasome. Thus, virus-related class I peptides are being produced that enable detection by the ensuing CTL response. The CTL immune response is induced by pAPC, which normally produce different class I peptides compared to peripheral body cells, owing to different proteasome activity. Therefore, during infection there is epitope synchronization between the infected cell and the immune system.

[0120] This is not the case with tumors and chronic viruses, which block the interferon system. For tumors there is no infection in the tumor cell to induce the immunoproteasome expression, and chronic virus infection either directly or indirectly blocks immunoproteasome expression. In both cases the diseased cell maintains its display of class I peptides derived from housekeeping proteasome activity and avoids effective surveillance by CTL.

[0121] In the case of therapeutic vaccination to eradicate tumors or chronic infections, the bimodal function of the proteasome and its differential activity in APC and peripheral cells of the body is significant. Upon vaccination with protein antigen, and before a CTL response can occur, the antigen must be acquired and processed into peptides that are subsequently presented on class I MHC on the pAPC surface. The activated CTL recirculate in search of cells with similar class I peptide on the surface. Cells with this peptide will be subjected to destruction by the cytolytic activity of the CTL. If the targeted diseased cell does not express the immunoproteasome, which is present in the pAPC, then the epitopes are not synchronized and CTL fail to find the desired peptide target on the surface of the diseased cell.

[0122] Preferably, therapeutic vaccine design takes into account the class I peptide that is actually present on the target tissue. That is, effective antigens used to stimulate CTL to attack diseased tissue are those that are naturally processed and presented on the surface of the diseased tissue. For tumors and chronic infection this generally means that the CTL epitopes are those that have been processed by the housekeeping proteasome. In order to generate an effective therapeutic vaccine, CTL epitopes are identified based on the knowledge that such epitopes are, in fact, produced by the housekeeping proteasome system. Once identified, these epitopes, embodied as peptides, can be used to successfully immunize or induce therapeutic CTL responses against housekeeping proteasome expressing target cells in the host.

[0123] However, in the case of DNA vaccines, there can be an additional consideration. The immunization with DNA requires that APCs take up the DNA and express the encoded proteins or peptides. It is possible to encode a discrete class I peptide on the DNA. By immunizing with this construct, APCs can be caused to express a housekeeping epitope, which is then displayed on class I MHC on the surface of the cell for stimulating an appropriate CTL response. Constructs for generation of proper termini of housekeeping epitopes have been described in U.S. patent application Ser. No. 09/561,572 entitled EXPRESSION VECTORS ENCODING EPITOPES OF TARGET-ASSOCIATED ANTIGENS, filed on Apr. 28, 2000, which is incorporated herein by reference in its entirety.

[0124] Embodiments of the invention provide expression cassettes that encode one or more embedded housekeeping epitopes, and methods for designing and testing such expression cassettes. The expression cassettes and constructs can encode epitopes, including housekeeping epitopes, derived from antigens that are associated with targets. Housekeeping epitopes can be liberated from the translation product(s) of the cassettes. For example, in some embodiments of the invention, the housekeeping epitope(s) can be flanked by arbitrary sequences or by sequences incorporating residues known to be favored in immunoproteasome cleavage sites. In further embodiments of the invention multiple epitopes can be arrayed head-to-tail. In some embodiments, these arrays can be made up entirely of housekeeping epitopes. Likewise, the arrays can include alternating housekeeping and immune epitopes. Alternatively, the arrays can include housekeeping epitopes flanked by immune epitopes, whether complete or distally truncated. In some preferred embodiments, each housekeeping epitope can be flanked on either side by an immune epitope, such that an array of such arrangements has two immune epitopes between each housekeeping epitope. Further, the arrays can be of any other similar arrangement. There is no restriction on placing a housekeeping epitope at the terminal positions of the array. The vectors can additionally contain authentic protein coding sequences or segments thereof containing epitope clusters as a source of immune epitopes.

[0125] Several disclosures make reference to polyepitopes or string-of-bead arrays. See, for example, WO0119408A1, Mar. 22, 2001; WO9955730A2, Nov. 4, 1999; WO0040261A2, Jul. 13, 2000; WO9603144A1, Feb. 8, 1996; EP1181314A1, Feb. 27, 2002; WO0123577A3, April 5; U.S. Pat. No. 6,074,817, Jun. 13, 2000; U.S. Pat. No. 5,965,381, Oct. 12, 1999; WO9741440A1, Nov. 6, 1997; U.S. Pat. No. 6,130,066, Oct. 10, 2000; U.S. Pat. No. 6,004,777, Dec. 21, 1999; U.S. Pat. No. 5,990,091, Nov. 23, 1999; WO9840501A1, Sep. 17, 1998; WO9840500A1, Sep. 17, 1998; WO0118035A2, Mar. 15, 2001; WO02068654A2, Sep. 6, 2002; WO0189281A2, Nov. 29, 2001; WO0158478A, Aug. 16, 2001; EP1118860A1, Jul. 25, 2001; WO0111040A1, Feb. 15, 2001; WO0073438A1, Dec. 7, 2000; WO0071158A1, Nov. 30, 2000; WO0066727A1, Nov. 9, 2000; WO0052451A1, Sep. 8, 2000; WO0052157A1, Sep. 8, 2000; WO0029008A2, May 25, 2000; WO0006723A1, Feb. 10, 2000; all of which are incorporated by reference in their entirety. Additional disclosures, all of which are hereby incorporated by reference in their entirety, include Palmowski M J, et al—J Immunol 2002;168(9):4391-8; Fang Z Y, et al—Virology 2001;291(2):272-84; Firat H, et al—J Gene Med 2002;4(1):38-45; Smith S G, et al—Clin Cancer Res 2001;7(12):4253-61; Vonderheide R H, et al—Clin Cancer Res 2001; 7(11):3343-8; Firat H, et al—Eur J Immunol 2001;31(10):3064-74; Le T T, et al—Vaccine 2001;19(32):4669-75; Fayolle C, et al—J Virol 2001;75(16):7330-8; Smith SG—Curr Opin Mol Ther 1999;1(1):10-5; Firat H, et al—Eur J Immunol 1999;29(10):3112-21; Mateo L, et al—J Immunol 1999;163(7):4058-63; Heemskerk M H, et al—Cell Immunol 1999;195(1):10-7; Woodberry T, et al—J Virol 1999;73(7):5320-5; Hanke T, et al—Vaccine 1998;16(4):426-35; Thomson S A, et al—J Immunol 1998;160(4):1717-23; Toes R E, et al—Proc Natl Acad Sci USA 1997;94(26):14660-5; Thomson S A, et al—J Immunol 1996;157(2):822-6; Thomson S A, et al—Proc Natl Acad Sci USA 1995;92(13):5845-9; Street M D, et al—Immunology 2002;106(4):526-36; Hirano K, et al—Histochem Cell Biol 2002;117(1):41-53; Ward S M, et al—Virus Genes 2001;23(1):97-104; Liu W J, et al—Virology 2000;273(2):374-82; Gariglio P, et al—Arch Med Res 1998;29(4):279-84; Suhrbier A—Immunol Cell Biol 1997;75(4):402-8; Fomsgaard A, et al—Vaccine 1999;18(7-8):681-91; An LL, et al—J Virol 1997;71(3):2292-302; Whitton J L, et al—J Virol 1993;67(1):348-52; Ripalti A, et al—J Clin Microbiol 1994;32(2):358-63; and Gilbert, S. C., et al., Nat. Biotech. 15:1280-1284, 1997.

[0126] One important feature that the disclosures in the preceding paragraph all share is their lack of appreciation for the desirability of regenerating housekeeping epitopes when the construct is expressed in a pAPC. This understanding was not apparent until the present invention. Embodiments of the invention include sequences, that when processed by an immune proteasome, liberate or generate a housekeeping epitope. Embodiments of the invention also can liberate or generate such epitopes in immunogenically effective amounts. Accordingly, while the preceding references contain disclosures relating to polyepitope arrays, none is enabling of the technology necessary to provide or select a polyepitope capable of liberating a housekeeping epitope by action of an immunoproteasome in a pAPC. In contrast, embodiments of the instant invention are based upon a recognition of the desirability of achieving this result. Accordingly, embodiments of the instant invention include any nucleic acid construct that encodes a polypeptide containing at least one housekeeping epitope provided in a context that promotes its generation via immunoproteasomal activity, whether the housekeeping epitope is embedded in a string-of-beads array or some other arrangement. Some embodiments of the invention include uses of one or more of the nucleic acid constructs or their products that are specifically disclosed in any one or more of the above-listed references. Such uses include, for example, screening a polyepitope for proper liberation context of a housekeeping epitope and/or an immune epitope, designing an effective immunogen capable of causing presentation of a housekeeping epitope and/or an immune epitope on a pAPC, immunizing a patient, and the like. Alternative embodiments include use of only a subset of such nucleic acid constructs or a single such construct, while specifically excluding one or more other such constructs, for any of the purposes disclosed herein. Some preferred embodiments employ these and/or other nucleic acid sequences encoding polyepitope arrays alone or in combination. For example, some embodiments exclude use of polyepitope arrays from one or more of the above-mentioned references. Other embodiments may exclude any combination or all of the polyepitope arrays from the above-mentioned references collectively. Some embodiments include viral and/or bacterial vectors encoding polyepitope arrays, while other embodiments specifically exclude such vectors. Such vectors can encode carrier proteins that may have some immunostimulatory effect. Some embodiments include such vectors with such immunostimulatory/immunopotentiating effects, as opposed to immunogenic effects, while in other embodiments such vectors may be included. Further, in some instances viral and bacterial vectors encode the desired epitope as a part of substantially complete proteins which are not associated with the target cell. Such vectors and products are included in some embodiments, while excluded from others. Some embodiments relate to repeated administration of vectors. In some of those embodiments, nonviral and nonbacterial vectors are included. Likewise, some embodiments include arrays that contain extra amino acids between epitopes, for example anywhere from 1-6 amino acids, or more, in some embodiments, while other embodiments specifically exclude such arrays.

[0127] Embodiments of the present invention also include methods, uses, therapies, and compositions directed to various types of targets. Such targets can include, for example, neoplastic cells such as those listed below, for example; and cells infected with any virus, bacterium, protozoan, fungus, or other agents, examples of which are listed below, in Tables 4-8, or which are disclosed in any of the references listed above. Alternative embodiments include the use of only a subset of such neoplastic cells and infected cells listed below, in Tables 4-8, or in any of the references disclosed herein, or a single one of the neoplastic cells or infected cells, while specifically excluding one or more other such neoplastic cells or infected cells, for any of the purposes disclosed herein. The following are examples of neoplastic cells that can be targeted: human sarcomas and carcinomas, e.g., fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilms' tumor, cervical cancer, testicular tumor, lung carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodendroglioma, meningioma, melanoma, neuroblastoma, retinoblastoma; leukemias, e.g., acute lymphocytic leukemia and acute myelocytic leukemia (myeloblastic, promyelocytic, myelomonocytic, monocytic and erythroleukemia); chronic leukemia (chronic myelocytic (granulocytic) leukemia and chronic lymphocytic leukemia); and polycythemia vera, lymphoma (Hodgkin's disease and non Hodgkin's disease), multiple myeloma, Waldenstrom's macroglobulinemia, heavy chain disease, hepatocellular cancer, brain cancer, stomach cancer, liver cancer, and the like. Examples of infectious agents that infect the target cells can include the following: adenovirus, cytomegalovirus, Epstein-Barr virus, herpes simplex virus 1, herpes simplex virus 2, human herpesvirus 6, varicella-zoster virus, hepatitis B virus, hepatitis D virus, papilloma virus, parvovirus B19, polyomavirus BK, polyomavirus JC, hepatitis C virus, measles virus, rubella virus, human immunodeficiency virus (HIV), human T cell leukemia virus I, human T cell leukemia virus II, Chlamydia, Listeria, Salmonella, Legionella, Brucella, Coxiella, Rickettsia, Mycobacterium, Leishmania, Trypanasoma, Toxoplasma, Plasmodium, and the like. Exemplary infectious agents and neoplastic cells are also included in Tables 4-8 below.

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[0129] Additional embodiments of the invention include methods, uses, therapies, and compositions relating to a particular antigen, whether the antigen is derived from, for example, a target cell or an infective agent, such as those mentioned above. Some preferred embodiments employ the antigens listed herein, in Tables 4-8, or in the list below, alone, as subsets, or in any combination. For example, some embodiments exclude use of one or more of those antigens. Other embodiments may exclude any combination or all of those antigens. Several examples of such antigens include MelanA (MART-I), gp100 (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, CEA, RAGE, NY-ESO, SCP-1, Hom/Mel-40, PRAME, p53, H-Ras, HER-2/neu, BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, Epstein Barr virus antigens, EBNA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE-5, MAGE-6, p185erbB2, p180erbB-3, c-met, nm-23H1, PSA, TAG-72-4, CAM 17.1, NuMa, K-ras, β-Catenin, CDK4, Mum-1, p16, as well as any of those set forth in the above mentioned references. Other antigens are included in Tables 4-7 below.

[0130] Further embodiments include methods, uses, compositions, and therapies relating to epitopes, including, for example those epitopes listed in Tables 4-8. These epitopes can be useful to flank housekeeping epitopes in screening vectors, for example. Some embodiments include one or more epitopes from Tables 4-8, while other embodiments specifically exclude one or more of such epitopes or combinations thereof.

TABLE 4
		AA	T cell epitope MHC
Virus	Protein	Position	ligand (Antigen)	MHC molecule
Adenovirus 3	E3 9Kd	30-38	LIVIGILIL	(SEQ. ID NO.:44)	HLA-A*0201
Adenovirus 5	EIA	234-243	SGPSNTPPEI	(SEQ. ID NO.:45)	H2-Db
Adenovirus 5	E1B	192-200	VNIRNCCYl	(SEQ. ID NO.:46)	H2-Db
Adenovirus 5	EIA	234-243	SGPSNIPPEI (T>I)	(SEQ. ID NO.:47)	H2-Db
CSFV	NS	2276-2284	ENALLVALF	(SEQ. ID NO.:48)	SLA, haplotype d/d
	polyprotein
Dengue virus 4	NS3	500-508	TPEGIIPTL	(SEQ. ID NO.:49)	HLA-B*3501
EBV	LMP-2	426-434	CLGGLLTMV	(SEQ. ID NO.:50)	HLA-A*0201
EBV	EBNA-1	480-484	NIAEGLRAL	(SEQ. ID NO.:51)	HLA-A*0201
EBV	EBNA-1	519-527	NLRRGTALA	(SEQ. ID NO.:52)	HLA-A*0201
EBV	EBNA-1	525-533	ALAIPQCRL	(SEQ. ID NO.:53)	HLA-A*0201
EBV	EBNA-1	575-582	VLKDAIKDL	(SEQ. ID NO.:54)	HLA-A*0201
EBV	EBNA-1	562-570	FMVFLQTHI	(SEQ. ID NO.:55)	HLA-A*0201
EBV	EBNA-2	15-23	HLIVDTDSL	(SEQ. ID NO.:56)	HLA-A*0201
EBV	EBNA-2	22-30	SLGNPSLSV	(SEQ. ID NO.:57)	HLA-A*0201
EBV	EBNA-2	126-134	PLASAMRML	(SEQ. ID NO.:58)	HLA-A*0201
EBV	EBNA-2	132-140	RMLWMANYl	(SEQ. ID NO.:59)	HLA-A*0201
EBV	EBNA-2	133-141	MLWMANYIV	(SEQ. ID NO.:60)	HLA-A*0201
EBV	EBNA-2	151-159	ILPQGPQTA	(SEQ. ID NO.:61)	HLA-A*0201
EBV	EBNA-2	171-179	PLRPTAPTI	(SEQ. ID NO.:62)	HLA-A*0201
EBV	EBNA-2	205-213	PLPPATLTV	(SEQ. ID NO.:63)	HLA-A*0201
EBV	EBNA-2	246-254	RMHLPVLHV	(SEQ. ID NO.:64)	HLA-A*0201
EBV	EBNA-2	287-295	PMPLPPSQL	(SEQ. ID NO.:65)	HLA-A*0201
EBV	EBNA-2	294-302	QLPPPAAPA	(SEQ. ID NO.:66)	HLA-A*0201
EBV	EBNA-2	381-389	SMPELSPVL	(SEQ. ID NO.:67)	HLA-A*0201
EBV	EBNA-2	453-461	DLDESWDYI	(SEQ. ID NO.:68)	HLA-A*0201
EBV	BZLF1	43-51	PLPCVLWPV	(SEQ. ID NO.:69)	HLA-A*0201
EBV	BZLF1	167-175	SLEECDSEL	(SEQ. ID NO.:70)	HLA-A*0201
EBV	BZLF1	176-184	EIKRYKNRV	(SEQ. ID NO.:71)	HLA-A*0201
EBV	BZLF1	195-203	QLLQHYREV	(SEQ. ID NO.:72)	HLA-A*0201
EBV	BZLF1	196-204	LLQHYREVA	(SEQ. ID NO.:73)	HLA-A*0201
EBV	BZLFI	217-225	LLKQMCPSL	(SEQ. ID NO.:74)	HLA-A*0201
EBV	BZLF1	229-237	SIIPRTPDV	(SEQ. ID NO.:75)	HLA-A*0201
EBV	EBNA-6	284-293	LLDFVRFMGV	(SEQ. ID NO.:76)	HLA-A*0201
EBV	EBNA-3	464-472	SVRDRLARL	(SEQ. ID NO.:77)	HLA-A*0203
EBV	EBNA-4	416-424	IVTDFSVIK	(SEQ. ID NO.:78)	HLA-A*1101
EBV	EBNA-4	399-408	AVFDRKSDAK	(SEQ. ID NO.:79)	HLA-A*0201
EBV	EBNA-3	246-253	RYSIFFDY	(SEQ. ID NO.:80)	HLA-A24
EBV	EBNA-6	881-889	QPRAPIRPI	(SEQ. ID NO.:81)	HLA-B7
EBV	EBNA-3	379-387	RPPIFIRRI.	(SEQ. ID NO.:82)	HLA-B7
EBV	EBNA-1	426-434	EPDVPPGAI	(SEQ. ID NO.:83)	HLA-B7
EBV	EBNA-1	228-236	IPQCRLTPL	(SEQ. ID NO.:84)	HLA-B7
EBV	EBNA-1	546-554	GPGPQPGPL	(SEQ. ID NO.:85)	HLA-B7
EBV	EBNA-1	550-558	QPGPLRESI	(SEQ. ID NO.:86)	HLA-B7
EBV	EBNA-1	72-80	R.PQKRPSCI	(SEQ. ID NO.:87)	HLA-B7
EBV	EBNA-2	224-232	PPTPLLTVL	(SEQ. ID NO.:88)	HLA-B7
EBV	EBNA-2	241-249	TPSPPRMHL	(SEQ. ID NO.:89)	HLA-B7
EBV	EBNA-2	244-252	PPRMHLPVL	(SEQ. ID NO.:90)	HLA-B7
EBV	EBNA-2	254-262	VPDQSMIHPL	(SEQ. ID NO.:91)	HLA-B7
EBV	EBNA-2	446-454	PPSIDPADL	(SEQ. ID NO.:92)	HLA-B7
EBV	BZLFI	44-52	LPCVLWPVL	(SEQ. ID NO.:93)	HLA-B7
EBV	BZLF1	222-231	CPSLDVDSII	(SEQ. ID NO.:94)	HLA-B7
EBV	BZLFI	234-242	TPDVLHEDL	(SEQ. ID NO.:95)	HLA-B7
EBV	EBNA-3	339-347	FLRGRAYGL	(SEQ. ID NO.:96)	HLA-B8
EBV	EBNA-3	26-34	QAKWRLQTL	(SEQ. ID NO.:97)	HLA-B8
EBV	EBNA-3	325-333	AYPLHEQHG	(SEQ. ID NO.:98)	HLA-B8
EBV	EBNA-3	158-166	YlKSFVSDA	(SEQ. ID NO.:99)	HLA-B8
EBV	LMP-2	236-244	RRRWRRLTV	(SEQ. ID NO.:100)	HLA-B*2704
EBV	EBNA-6	258-266	RRIYDLIEL	(SEQ. ID NO.:101)	HLA-B*2705
EBV	EBNA-3	458-466	YPLHEQHGM	(SEQ. ID NO.:102)	HLA-B*3501
EBV	EBNA-3	458-466	YPLHEQHGM	(SEQ. ID NO.:103)	HLA-B*3503
HCV	NS3	389-397	HSKKKCDEL	(SEQ. ID NO.:104)	HLA-B8
HCV	env E	44-51	ASRCWVAM	(SEQ. ID NO.:105)	HLA-B*3501
HCV	core	27-35	GQIVGGVYL	(SEQ. ID NO.:106)	HLA-B*40012
	protein
HCV	NSI	77-85	PPLTDFDQGW	(SEQ. ID NO.:107)	HLA-B*5301
HCV	core	18-27	LMGYIPLVGA	(SEQ. ID NO.:108)	H2-Dd
	protein
HCV	core	16-25	ADLMGYIPLV	(SEQ. ID NO.:109)	H2-Dd
	protein
HCV	NS5	409-424	MSYSWTGALVTPCAEE	(SEQ. ID NO.:110)	H2-Dd
HCV	NS1	205-213	KHPDATYSR	(SEQ. ID NO.:111)	Papa-A06
HCV-1	NS3	400-409	KLVALGINAV	(SEQ. ID NO.:112)	HLA-A*0201
HCV-1	NS3	440-448	GDFDSVIDC	(SEQ. ID NO.:113)	Patr-B16
HCV-1	env E	118-126	GNASRCWVA	(SEQ. ID NO.:114)	Patr-BI6
HCV-1	NSI	159-167	TRPPLGNWF	(SEQ. ID NO.:115)	Patr-B13
HCV-1	NS3	351-359	VPHPNIEEV	(SEQ. ID NO.:116)	Patr-B13
HCV-1	NS3	438-446	YTGDFDSVI	(SEQ. ID NO.:117)	Patr-B01
HCV-1	NS4	328-335	SWAIKWEY	(SEQ. ID NO.:118)	Patr-A1 1
HCV-1	NSI	205-213	KHPDATYSR	(SEQ. ID NO.:119)	Patr-A04
HCV-1	NS3	440-448	GDFDSVIDC	(SEQ. ID NO.:120)	Patr-A04
HIV	gp41	583-591	RYLKDQQLL	(SEQ. ID NO.:121)	HLA_A24
HIV	gagp24	267-275	IVGLNKLVR	(SEQ. ID NO.:122)	HLA-A*3302
HIV	gagp24	262-270	EIYKRWIIL	(SEQ. ID NO.:123)	HLA-B8
HIV	gagp24	261-269	GElYKRWIl	(SEQ. ID NO.:124)	HLA-B8
HIV	gagp17	93-101	EIKDTKEAL	(SEQ. ID NO.:125)	HLA-B8
HIV	gp41	586-593	YLKDQQLL	(SEQ. ID NO.:126)	HLA-B8
HIV	gagp24	267-277	ILGLNKIVRMY	(SEQ. ID NO.:127)	HLA-B*1501
HIV	gp41	584-592	ERYLKDQQL	(SEQ. ID NO.:128)	HLA-B14
HIV	nef	115-125	YHTQGYFPQWQ	(SEQ. ID NO.:129)	HLA-B17
HIV	nef	117-128	TQGYFPQWQNYT	(SEQ. ID NO.:130)	HLA-B17
HIV	gp120	314-322	GRAFVTlGK	(SEQ. ID NO.:131)	HLA-B*2705
HIV	gagp24	263-271	KRWIILGLN	(SEQ. ID NO.:132)	HLA-B*2702
HIV	nef	72-82	QVPLRPMTYK	(SEQ. ID NO.:133)	HLA-B*3501
HIV	nef	117-125	TQGYFPQWQ	(SEQ. ID NO.:134)	HLA-B*3701
HIV	gagp24	143-151	HQAISPRTI,	(SEQ. ID NO.:135)	HLA-Cw*0301
HIV	gagp24	140-151	QMVHQAISPRTL	(SEQ. ID NO.:136)	HLA-Cw*0301
HIV	gp120	431-440	MYAPPIGGQI	(SEQ. ID NO.:137)	H2-Kd
HIV	gp160	318-327	RGPGRAFVTI	(SEQ. ID NO.:138)	H2-Dd
HIV	gp120	17-29	MPGRAFVTI	(SEQ. ID NO.:139)	H2-Ld
HIV-1	RT	476-484	ILKEPVHGV	(SEQ. ID NO.:140)	HLA-A*0201
HIV-1	nef	190-198	AFHHVAREL	(SEQ. ID NO.:141)	HLA-A*0201
HIV-1	gpI60	120-128	KLTPLCVTL	(SEQ. ID NO.:142)	HLA-A*0201
HIV-1	gp]60	814-823	SLLNATDIAV	(SEQ. ID NO.:143)	HLA-A*0201
HIV-1	RT	179-187	VIYQYMDDL	(SEQ. ID NO.:144)	HLA-A*0201
HIV-1	gagp17	77-85	SLYNTVATL	(SEQ. ID NO.:145)	HLA-A*0201
HIV-1	gp160	315-329	RGPGRAFVTl	(SEQ. ID NO.:146)	HLA-A*0201
HIV-1	gp41	768-778	RLRDLLLIVTR	(SEQ. ID NO.:147)	HLA-A3
HIV-1	nef	73-82	QVPLRPMTYK	(SEQ. ID NO.:148)	HLA-A3
HIV-1	gp120	36-45	TVYYGVPVWK	(SEQ. ID NO.:149)	HLA-A3
HIV-1	gagp17	20-29	RLRPGGKKK	(SEQ. ID NO.:150)	HLA-A3
HIV-1	gp120	38-46	VYYGVPVWK	(SEQ. ID NO.:151)	HLA-A3
HIV-1	nef	74-82	VPLRPMTYK	(SEQ. ID NO.:152)	HLA-a*1101
HIV-1	gagp24	325-333	AIFQSSMTK	(SEQ. ID NO.:153)	HLA-A*1101
HIV-1	nef	73-82	QVPLRPMTYK	(SEQ. ID NO.:154)	HLA-A*1101
HIV-1	nef	83-94	AAVDLSHFLKEK	(SEQ. ID NO.:155)	HLA-A*1101
HIV-1	gagp24	349-359	ACQGVGGPGGHK	(SEQ. ID NO.:156)	HLA-A*1101
HIV-1	gagp24	203-212	ETINEEAAEW	(SEQ. ID NO.:157)	HLA-A25
HIV-1	nef	128-137	TPGPGVRYPL	(SEQ. ID NO.:158)	HLA-B7
HIV-1	gagp17	24-31	GGKKKYKL	(SEQ. ID NO.:159)	HLA-B8
HIV-1	gp120	2-10	RVKEKYQHL	(SEQ. ID NO.:160)	HLA-B8
HIV-1	gagp24	298-306	DRFYKTLRA	(SEQ. ID NO.:161)	HLA-B14
HIV-1	NEF	132-147	GVRYPLTFGWCYKLVP	(SEQ. ID NO.:162)	HLA-B18
HIV-1	gagp24	265-24	KRWIILGLNK	(SEQ. ID NO.:163)	HLA-B*2705
HIV-1	nef	190-198	AFHHVAREL	(SEQ. ID NO.:164)	HLA-B*5201
EBV	EBNA-6	335-343	KEHVIQNALF	(SEQ. ID NO.:165)	HLA-B44
EBV	EBNA-6	130-139	EENLLDFVRF	(SEQ. ID NO.:166)	HLA-B*4403
EBV	EBNA-2	42-51	DTPLIPLTIF	(SEQ. ID NO.:167)	HLA-B51
EBV	EBNA-6	213-222	QNGALAINTF	(SEQ. ID NO.:168)	HLA-1362
EBV	EBNA-3	603-611	RLRAEAGVK	(SEQ. ID NO.:169)	HLA-A3
HBV	sAg	348-357	GLSPTVWLSV	(SEQ. ID NO.:170)	HLA-A*0201
HBV	SAg	335-343	WLSLLVPFV	(SEQ. ID NO.:171)	HLA-A*0201
HBV	cAg	18-27	FLPSDFFPSV	(SEQ. ID NO.:172)	HLA-A*0201
HBV	cAg	18-27	FLPSDFFPSV	(SEQ. ID NO.:173)	HLA-A*0202
HBV	cAg	18-27	FLPSDFFPSV	(SEQ. ID NO.:174)	HLA-A*0205
HBV	cAg	18-27	FLPSDFFPSV	(SEQ. ID NO.:175)	HLA-A*0206
HBV	pol	575-583	FLLSLGIHL	(SEQ. ID NO.:176)	HLA-A*0201
HBV	pol	816-824	SLYADSPSV	(SEQ. ID NO.:177)	HLA-A*0201
HBV	pol	455-463	GLSRYVARL	(SEQ. ID NO.:178)	HLA-A*0201
HBV	env	338-347	LLVPFVQWFV	(SEQ. ID NO.:179)	HLA-A*0201
HBV	pol	642-650	ALMPLYACI	(SEQ. ID NO.:180)	HLA-A*0201
HBV	env	378-387	LLPIFFCLWV	(SEQ. ID NO.:181)	HLA-A*0201
HBV	pol	538-546	YMDDVVLGA	(SEQ. ID NO.:182)	HLA-A*0201
HBV	env	250-258	LLLCLIFLL	(SEQ. ID NO.:183)	HLA-A*0201
HBV	env	260-269	LLDYQGMLPV	(SEQ. ID NO.:184)	HLA-A*0201
HBV	env	370-379	SIVSPFIPLL	(SEQ. ID NO.:185)	HLA-A*0201
HBV	env	183-191	FLLTRILTI	(SEQ. ID NO.:186)	HLA-A*0201
HBV	cAg	88-96	YVNYNMGLK	(SEQ. ID NO.:187)	HLA-A*1101
HBV	cAg	141-151	STLPETTVVRR	(SEQ. ID NO.:188)	HLA-A*3101
HBV	cAg	141-151	STLPETTVVRR	(SEQ. ID NO.:189)	HLA-A*6801
HBV	cAg	18-27	FLPSDFFPSV	(SEQ. ID NO.:190)	HLA-A*6801
HBV	sAg	28-39	IPQSLDSWWTSL	(SEQ. ID NO.:191)	H2-Ld
HBV	cAg	93-100	MGLKFRQL	(SEQ. ID NO.:192)	H2-Kb
HBV	preS	141-149	STBXQSGXQ	(SEQ. ID NO.:193)	HLA-A*0201
HCMV	gp B	618-628	FIAGNSAYEYV	(SEQ. ID NO.:194)	HLA-A*0201
HCMV	E1	978-989	SDEEFAIVAYTL	(SEQ. ID NO.:195)	HLA-B18
HCMV	pp65	397-411	DDVWTSGSDSDEELV	(SEQ. ID NO.:196)	HLA-b35
HCMV	pp65	123-131	IPSINVKHY	(SEQ. ID NO.:197)	HLA-B*3501
HCMV	pp65	495-504	NLVPMVATVO	(SEQ. ID NO.:198)	HLA-A*0201
HCMV	pp65	415-429	RKTPRVTOGGAMAGA	(SEQ. ID NO.:199)	HLA-B7
HCV	MP	17-25	DLMGYIPLV	(SEQ. ID NO.:200)	HLA-A*0201
HCV	MP	63-72	LLALLSCLTV	(SEQ. ID NO.:201)	HLA-A*0201
HCV	MP	105-112	ILHTPGCV	(SEQ. ID NO.:202)	HLA-A*0201
HCV	env E	66-75	QLRRHIDLLV	(SEQ. ID NO.:203)	HLA-A*0201
HCV	env E	88-96	DLCGSVFLV	(SEQ. ID NO.:204)	HLA-A*0201
HCV	env E	172-180	SMVGNWAKV	(SEQ. ID NO.:205)	HLA-A*0201
HCV	NSI	308-316	HLIIQNIVDV	(SEQ. ID NO.:206)	HLA-A*0201
HCV	NSI	340-348	FLLLADARV	(SEQ. ID NO.:207)	HLA-A*0201
HCV	NS2	234-246	GLRDLAVAVEPVV	(SEQ. ID NO.:208)	HLA-A*0201
HCV	NSI	18-28	SLLAPGAKQNV	(SEQ. ID NO.:209)	HLA-A*0201
HCV	NSI	19-28	LLAPGAKQNV	(SEQ. ID NO.:210)	HLA-A*0201
HCV	NS4	192-201	LLFNILGGWV	(SEQ. ID NO.:211)	HLA-A*0201
HCV	NS3	579-587	YLVAYQATV	(SEQ. ID NO.:212)	HLA-A*0201
HCV	core	34-43	YLLPRRGPRL	(SEQ. ID NO.:213)	HLA-A*0201
	protein
HCV	MP	63-72	LLALLSCLTI	(SEQ. ID NO.:214)	HLA-A*0201
HCV	NS4	174-182	SLMAFTAAV	(SEQ. ID NO.:215)	HLA-A*0201
HCV	NS3	67-75	CINGVCWTV	(SEQ. ID NO.:216)	HLA-A*0201
HCV	NS3	163-171	LLCPAGHAV	(SEQ. ID NO.:217)	HLA-A*0201
HCV	NS5	239-247	ILDSFDPLV	(SEQ. ID NO.:218)	HLA-A*0201
HCV	NS4A	236-244	IAGYGAGV	(SEQ. ID NO.:219)	HLA-A*0201
HCV	NS5	714-722	GLQDCTMLV	(SEQ. ID NO.:220)	HLA-A*0201
HCV	NS3	281-290	TGAPVTYSTY	(SEQ. ID NO.:221)	HLA-A*0201
HCV	NS4A	149-157	HMWNFISGI	(SEQ. ID NO.:222)	HLA-A*0201
HCV	NS5	575-583	RVCEKMALY	(SEQ. ID NO.:223)	HLA-A*0201-A3
HCV	NS1	238-246	TINYTIFK	(SEQ. ID NO.:224)	HLA-A*1101
HCV	NS2	109-116	YISWCLWW	(SEQ. ID NO.:225)	HLA-A23
HCV	core	40-48	GPRLGVRAT	(SEQ. ID NO.:226)	HLA-B7
	protein
HIV-1	gp120	380-388	SFNCGGEFF	(SEQ. ID NO.:227)	HLA-Cw*0401
HIV-1	RT	206-214	TEMEKEGKI	(SEQ. ID NO.:228)	H2-Kk
HIV-1	p17	18-26	KIRLRPGGK	(SEQ. ID NO.:229)	HLA-A*031
HIV-1	P17	20-29	RLRPGGKKKY	(SEQ. ID NO.:230)	HLA-A*0301
HIV-1	RT	325-333	AIFQSSMTK	(SEQ. ID NO.:231)	HLA-A*0301
HIV-1	p17	84-92	TLYCVHQRI	(SEQ. ID NO.:232)	HLA-A11
HIV-1	RT	508-517	IYQEPFKNLK	(SEQ. ID NO.:233)	HLA-A11
HIV-1	p17	28-36	KYKLKHIVW	(SEQ. ID NO.:234)	HLA-A24
HIV-1	gp120	53-62	LFCASDAKAY	(SEQ. ID NO.:235)	HLA-A24
HIV-1	gagp24	145-155	QAISPRTLNAW	(SEQ. ID NO.:236)	HLA-A25
HIV-1	gagp24	167-175	EVIPMFSAL	(SEQ. ID NO.:237)	HLA-A26
HIV-1	RT	593-603	ETFYVDGAANR	(SEQ. ID NO.:238)	HLA-A26
HIV-1	gp41	775-785	RLRDLLLIVTR	(SEQ. ID NO.:239)	HLA-A31
HIV-1	RT	559-568	PIQKETWETW	(SEQ. ID NO.:240)	HLA-A32
HIV-1	gp120	419-427	RIKQIINMW	(SEQ. ID NO.:241)	HLA-A32
HIV-1	RT	71-79	ITLWQRPLV	(SEQ. ID NO.:242)	HLA-A*6802
HIV-1	RT	85-93	DTVLEEMNL	(SEQ. ID NO.:243)	HLA-A*6802
HIV-1	RT	71-79	ITLWQRPLV	(SEQ. ID NO.:244)	HLA-A*7401
HIV-1	gag p24	148-156	SPRTLNAWV	(SEQ. ID NO.:245)	HLA-B7
HIV-1	gagp24	179-187	ATPQDLNTM	(SEQ. ID NO.:246)	HLA-B7
HIV-1	gp120	303-312	RPNNNTRKSI	(SEQ. ID NO.:247)	HLA-B7
HIV-1	gp41	843-851	IPRRIRQGL	(SEQ. ID NO.:248)	HLA-B7
HIV-1	p17	74-82	ELRSLYNTV	(SEQ. ID NO.:249)	HLA-B8
HIV-1	nef	13-20	WPTVRERM	(SEQ. ID NO.:250)	HLA-B8
HIV-1	nef	90-97	FLKEKGGL	(SEQ. ID NO.:251)	HLA-B8
HIV-1	gag p24	183-191	DLNTMLNTV	(SEQ. ID NO.:252)	HLA-B14
HIV-1	P17	18-27	KIRLRPGGKK	(SEQ. ID NO.:253)	HLA-B27
HIV-1	p17	19-27	IRLRPGGKK	(SEQ. ID NO.:254)	HLA-B27
HIV-1	gp41	791-799	GRRGWEALKY	(SEQ. ID NO.:255)	HLA-B27
HIV-1	nef	73-82	QVPLRPMTYK	(SEQ. ID NO.:256)	HLA-B27
HIV-1	GP41	590-597	RYLKDQQL	(SEQ. ID NO.:257)	HLA-B27
HIV-1	nef	105-114	RRQDILDLWI	(SEQ. ID NO.:258)	HLA-B*2705
HIV-1	nef	134-141	RYPLTFGW	(SEQ. ID NO.:259)	HLA-B*2705
HIV-1	p17	36-44	WASRLELERF	(SEQ. ID NO.:260)	HLA-B35
HIV-1	GAG P24	262-270	TVLDVGDAY	(SEQ. ID NO.:261)	HLA-B35
HIV-1	gp120	42-52	VPVWKEATTTL	(SEQ. ID NO.:262)	HLA-B35
HIV-1	P17	36-44	NSSKVSQNY	(SEQ. ID NO.:263)	HLA-B35
HIV-1	gag p24	254-262	PPIPVGDIY	(SEQ. ID NO.:264)	HLA-B35
HIV-1	RT	342-350	HPDIVIYQY	(SEQ. ID NO.:265)	HLA-B35
HIV-1	gp41	611-619	TAVPWNASW	(SEQ. ID NO.:266)	HLA-B35
HIV-1	gag	245-253	NPVPVGNlY	(SEQ. ID NO.:267)	HLA-B35
HIV-1	nef	120-128	YFPDWQNYT	(SEQ. ID NO.:268)	HLA-B37
HIV-1	gag p24	193-201	GHQAAMQML	(SEQ. ID NO.:269)	HLA-B42
HIV-1	p17	20-29	RLRPGGKKKY	(SEQ. ID NO.:270)	HLA-B42
HIV-1	RT	438-446	YPGIKVRQL	(SEQ. ID NO.:271)	HLA-B42
HIV-1	RT	591-600	GAETFYVDGA	(SEQ. ID NO.:272)	HLA-B45
HIV-1	gag p24	325-333	NANPDCKTI	(SEQ. ID NO.:273)	HLA-B51
HIV-1	gag p24	275-282	RMYSPTSI	(SEQ. ID NO.:274)	HLA-B52
HIV-1	gp120	42-51	VPVWKEATTT	(SEQ. ID NO.:275)	HLA-B*5501
HIV-1	gag p24	147-155	ISPRTLNAW	(SEQ. ID NO.:276)	HLA-B57
HIV-1	gag p24	240-249	TSTLQEQIGW	(SEQ. ID NO.:277)	HLA-B57
HIV-1	gag p24	162-172	KAFSPEVIPMF	(SEQ. ID NO.:278)	HLA-B57
HIV-1	gagp24	311-319	QASQEVKNW	(SEQ. ID NO.:279)	HLA-B57
HIV-1	gagp24	311-319	QASQDVKNW	(SEQ. ID NO.:280)	HLA-B57
HIV-1	nef	116-125	HTQGYFPDWQ	(SEQ. ID NO.:281)	HLA-B57
HIV-1	nef	120-128	YFPDWQNYT	(SEQ. ID NO.:282)	HLA-B57
HIV-1	gag p24	240-249	TSTLQEQIGW	(SEQ. ID NO.:283)	HLA-B58
HIV-1	p17	20-29	RLRPGGKKKY	(SEQ. ID NO.:284)	HLA-B62
HIV-1	p24	268-277	LGLNKJVRMY	(SEQ. ID NO.:285)	HLA-B62
HIV-1	RT	415-426	LVGKLNWASQIY	(SEQ. ID NO.:286)	HLA-B62
HIV-1	RT	476-485	ILKEPVHGVY	(SEQ. ID NO.:287)	HLA-B62
HIV-1	nef	117-127	TQGYFPDWQNY	(SEQ. ID NO.:288)	HLA-B62
HIV-1	nef	84-91	AVDLSHFL	(SEQ. ID NO.:289)	HLA-B62
HIV-1	gag p24	168-175	VIPMIFSAL	(SEQ. ID NO.:290)	HLA-Cw*0102
HIV-1	gp120	376-384	FNCGGEFFY	(SEQ. ID NO.:291)	HLA-A29
HIV-1	gp120	375-383	SFNCGGEFF	(SEQ. ID NO.:292)	HLA-B15
HIV-1	nef	136-145	PLTFGWCYKL	(SEQ. ID NO.:293)	HLA-A*0201
HIV-1	nef	180-189	VLEWRFDSRL	(SEQ. ID NO.:294)	HLA-A*0201
HIV-1	nef	68-77	FPVTPQVPLR	(SEQ. ID NO.:295)	HLA-B7
HIV-1	nef	128-137	TPGPGVRYPL	(SEQ. ID NO.:296)	HLA-B7
HIV-1	gag p24	308-316	QASQEVKNW	(SEQ. ID NO.:297)	HLA-Cw*0401
HIV-1 IIIB	RT	273-282	VPLDEDFRKY	(SEQ. ID NO.:298)	HLA-B35
HIV-1 IIIB	RT	25-33	NPDIVIYQY	(SEQ. ID NO.:299)	HLA-B35
HIV-1 IIIB	gp41	557-565	RAIEAQAHL	(SEQ. ID NO.:300)	HLA-B51
HIV-1 IIIB	RT	231-238	TAFTIPSI	(SEQ. ID NO.:301)	HLA-B51
HIV-1 IIIB	p24	215-223	VHPVHAGPIA	(SEQ. ID NO.:302)	HLA-B*5501
HIV-1 IIIB	gp120	156-165	NCSFNISTSI	(SEQ. ID NO.:303)	HLA-Cw8
HIV-1 IIIB	gp120	241-249	CTNVSTVQC	(SEQ. ID NO.:304)	HLA-Cw8
HIV-1 5F2	gp120	312-320	IGPGRAFHT	(SEQ. ID NO.:305)	H2-Dd
HIV-1 5F2	pol	25-33	NPDIVIYQY	(SEQ. ID NO.:306)	HLA-B*3501
HIV-1 5F2	pol	432-441	EPIVGAETFY	(SEQ. ID NO.:307)	HLA-B*3501
HIV-1 5F2	pol	432-440	EPIVGAETF	(SEQ. ID NO.:308)	HLA-B*3501
HIV-1 5F2	pol	6-14	SPAIFQSSM	(SEQ. ID NO.:309)	HLA-B*3501
HIV-1 5F2	pol	59-68	VPLDKDFRKY	(SEQ. ID NO.:310)	HLA-B*3501
HIV-1 5F2	pol	6-14	IPLTEEAEL	(SEQ. ID NO.:311)	HLA-B*3501
HIV-1 5F2	nef	69-79	RPQVPLRPMTY	(SEQ. ID NO.:312)	HLA-B*3501
HIV-1 5F2	nef	66-74	FPVRPQVPL	(SEQ. ID NO.:313)	HLA-B*3501
HIV-1 5F2	env	10-18	DPNPQEVVL	(SEQ. ID NO.:314)	HLA-B*3501
HIV-1 5F2	env	7-15	RPIVSTQLL	(SEQ. ID NO.:315)	HLA-B*3501
HIV-1 5F2	pol	6-14	IPLTEEAEL	(SEQ. ID NO.:316)	HLA-B51
HIV-1 5F2	env	10-18	DPNPQEVVL	(SEQ. ID NO.:317)	HLA-B51
HIV-1 5F2	gagp24	199-207	AMQMLKETI	(SEQ. ID NO.:318)	H2-Kd
HIV-2	gagp24	182-190	TPYDrNQML	(SEQ. ID NO.:319)	HLA-B*5301
HIV-2	gag	260-269	RRWIQLGLQKV	(SEQ. ID NO.:320)	HLA-B*2703
HIV-1 5F2	gp41	593-607	GIWGCSGKLICTTAV	(SEQ. ID NO.:321)	HLA-B17
HIV-1 5F2	gp41	753-767	ALIWEDLRSLCLFSY	(SEQ. ID NO.:322)	HLA-B22
HPV 6b	E7	21-30	GLHCYEQLV	(SEQ. ID NO.:323)	HLA-A*0201
HPV 6b	E7	47-55	PLKQHFQIV	(SEQ. ID NO.:324)	HLA-A*0201
HPV11	E7	4-12	RLVTLKDIV	(SEQ. ID NO.:325)	HLA-A*0201
HPV16	E7	86-94	TLGIVCPIC	(SEQ. ID NO.:326)	HLA-A*0201
HPV16	E7	85-93	GTLGIVCPI	(SEQ. ID NO.:327)	HLA-A*0201
HPV16	E7	12-20	MLDLQPETT	(SEQ. ID NO.:328)	HLA-A*0201
HPV16	E7	11-20	YMLDLQPETT	(SEQ. ID NO.:329)	HLA-A*0201
HPV16	E6	15-22	RPRKLPQL	(SEQ. ID NO.:330)	HLA-B7
HPV16	E6	49-57	RAHYNIVTF	(SEQ. ID NO.:331)	HLA-Db
HSV	gp B	498-505	SSIEFARL	(SEQ. ID NO.:332)	H2-Kb
HSV-1	gp C	480-488	GIGIGVLAA	(SEQ. ID NO.:333)	HLA-A*0201
HSV-1	ICP27	448-456	DYATLGVGV	(SEQ. ID NO.:334)	H2-Kd
HSV-1	ICP27	322-332	LYRTFAGNPRA	(SEQ. ID NO.:335)	H2-Kd
HSV-1	UL39	822-829	QTFDFGRL	(SEQ. ID NO.:336)	H2-Kb
HSV-2	gpC	446-454	GAGIGVAVL	(SEQ. ID NO.:337)	HLA-A*0201
HLTV-1	TAX	11-19	LLFGYPVYV	(SEQ. ID NO.:338)	HLA-A*0201
Influenza	MP	58-66	GILGFVFTL	(SEQ. ID NO.:339)	HLA-A*0201
Influenza	MP	59-68	ILGFVFTLTV	(SEQ. ID NO.:340)	HLA-A*0201
Influenza	NP	265-273	ILRGSVAHK	(SEQ. ID NO.:341)	HLA-A3
Influenza	NP	91-99	KTGGPIYKR	(SEQ. ID NO.:342)	HLA-A*6801
Influenza	NP	380-388	ELRSRYWAI	(SEQ. ID NO.:343)	HLA-B8
Influenza	NP	381-388	LRSRYWAI	(SEQ. ID NO.:344)	HLA-B*2702
Influenza	NP	339-347	EDLRVLSFI	(SEQ. ID NO.:345)	HLA-B*3701
Influenza	NSI	158-166	GEISPLPSL	(SEQ. ID NO.:346)	HLA-B44
Influenza	NP	338-346	FEDLRVLSF	(SEQ. ID NO.:347)	HLA-B44
Influenza	NSI	158-166	GEISPLPSL	(SEQ. ID NO.:348)	HLA-B*4402
Influenza	NP	338-346	FEDLRVLSF	(SEQ. ID NO.:349)	HLA-B*4402
Influenza	PBI	591-599	VSDGGPKLY	(SEQ. ID NO.:350)	HLA-A1
Influenza A	NP	44-52	CTELKLSDY	(SEQ. ID NO.:351)	HLA-A1
Influenza	NSI	122-130	AIMDKNIIL	(SEQ. ID NO.:352)	HLA-A*0201
Influenza A	NSI	123-132	IMDKNIILKA	(SEQ. ID NO.:353)	HLA-A*0201
Influenza A	NP	383-391	SRYWAIRTR	(SEQ. ID NO.:354)	HLA-B*2705
Influenza A	NP	147-155	TYQRTRALV	(SEQ. ID NO.:355)	H2-Kd
Influenza A	HA	210-219	TYVSVSTSTL	(SEQ. ID NO.:356)	H2-Kd
Influenza A	HA	518-526	IYSTVASSL	(SEQ. ID NO.:357)	H2-Kd
Influenza A	HA	259-266	FEANGNLI	(SEQ. ID NO.:358)	H2-Kk
Influenza A	HA	10-18	IEGGWTGMl	(SEQ. ID NO.:359)	H2-Kk
Influenza A	NP	50-57	SDYEGRLI	(SEQ. ID NO.:360)	H2-Kk
Influenza a	NSI	152-160	EEGAIVGEI	(SEQ. ID NO.:361)	H2-Kk
Influenza A34	NP	336-374	ASNENMETM	(SEQ. ID NO.:362)	H2Db
Influenza A68	NP	366-374	ASNENMDAM	(SEQ. ID NO.:363)	H2Db
Influenza B	NP	85-94	KLGEFYNQMM	(SEQ. ID NO.:364)	HLA-A*0201
Influenza B	NP	85-94	KAGEFYNQMM	(SEQ. ID NO.:365)	HLA-A*0201
Influenza JAP	HA	204-212	LYQNVGTYV	(SEQ. ID NO.:366)	H2Kd
Influenza JAP	HA	210-219	TYVSVGTSTL	(SEQ. ID NO.:367)	H2-Kd
Influenza JAP	HA	523-531	VYQILATYA	(SEQ. ID NO.:368)	H2-Kd
Influenza JAP	HA	529-537	IYATVAGSL	(SEQ. ID NO.:369)	H2-Kd
Influenza JAP	HA	210-219	TYVSVGTSTI (L>I)	(SEQ. ID NO.:370)	H2-Kd
Influenza JAP	HA	255-262	FESTGNLI	(SEQ. ID NO.:371)	H2-Kk
JHMV	cAg	318-326	APTAGAFFF	(SEQ. ID NO.:372)	H2-Ld
LCMV	NP	118-126	RPQASGVYM	(SEQ. ID NO.:373)	H2-Ld
LCMV	NP	396-404	FQPQNGQFI	(SEQ. ID NO.:374)	H2-Db
LCMV	GP	276-286	SGVENPGGYCL	(SEQ. ID NO.:375)	H2-Db
LCMV	GP	33-42	KAVYNFATCG	(SEQ. ID NO.:376)	H2-Db
MCMV	pp89	168-176	YPHFMPTNL	(SEQ. ID NO.:377)	H2-Ld
MHV	spike	510-518	CLSWNGPHL	(SEQ. ID NO.:378)	H2-Db
	protein
MMTV	env gp 36	474-482	SFAVATTAL	(SEQ. ID NO.:379)	H2-Kd
MMTV	gag p27	425-433	SYETFISRL	(SEQ. ID NO.:380)	H2-Kd
MMTV	env gp73	544-551	ANYDFICV	(SEQ. ID NO.:381)	H2-Kb
MuLV	env p15E	574-581	KSPWFTTL	(SEQ. ID NO.:382)	H2-Kb
MuLV	env gp70	189-196	SSWDFITV	(SEQ. ID NO.:383)	H2-Kb
MuLV	gag 75K	75-83	CCLCLTVFL	(SEQ. ID NO.:384)	H2-Db
MuLV	env gp70	423-431	SPSYVYHQF	(SEQ. ID NO.:385)	H2Ld
MV	F protein	437-447	SRRYPDAVYLH	(SEQ. ID NO.:386)	HLA-B*2705
Mv	F protein	438-446	RRYPDAVYL	(SEQ. ID NO.:387)	HLA-B*2705
Mv	NP	281-289	YPALGLHEF	(SEQ. ID NO.:388)	H2-Ld
Mv	HA	343-351	DPVIDRLYL	(SEQ. ID NO.:389)	H2-Ld
MV	HA	544-552	SPGRSFSYF	(SEQ. ID NO.:390)	H2-Ld
Poliovirus	VP1	111-118	TYKDTVQL	(SEQ. ID NO.:391)	H2-kd
Poliovirus	VP1	208-217	FYDGFSKVPL	(SEQ. ID NO.:392)	H2-Kd
Pseudorabies	G111	455-463	IAGIGILAI	(SEQ. ID NO.:393)	HLA-A*0201
virus gp
Rabiesvirus	NS	197-205	VEAEIAHQI	(SEQ. ID NO.:394)	H2-Kk
Rotavirus	VP7	33-40	llYRFLLl	(SEQ. ID NO.:395)	H2-Kb
Rotavirus	VP6	376-384	VGPVFPPGM	(SEQ. ID NO.:396)	H2-Kb
Rotavirus	VP3	585-593	YSGYIFRDL	(SEQ. ID NO.:397)	H2-Kb
RSV	M2	82-90	SYIGSINNI	(SEQ. ID NO.:398)	H2-Kd
SIV	gagp11C	179-190	EGCTPYDTNQML	(SEQ. ID NO.:399)	Mamu-A*01
SV	NP	324-332	FAPGNYPAL	(SEQ. ID NO.:400)	H2-Db
SV	NP	324-332	FAPCTNYPAL	(SEQ. ID NO.:401)	H2-Kb
SV40	T	404-411	VVYDFLKC	(SEQ. ID NO.:402)	H2-Kb
SV40	T	206-215	SAINNYAQKL	(SEQ. ID NO.:403)	H2-Db
SV40	T	223-231	CKGVNKEYL	(SEQ. ID NO.:404)	H2-Db
SV40	T	489-497	QGINNLDNL	(SEQ. ID NO.:405)	H2-Db
SV40	T	492-500	NNLDNLRDY(L)	(SEQ. ID NO.:406)	H2-Db
		(501)
SV40	T	560-568	SEFLLEKRI	(SEQ. ID NO.:407)	H2-Kk
VSV	NP	52-59	RGYVYQGL	(SEQ. ID NO.:408)	H2-Kb

[0131]

TABLE 5
HLA-A1	Position (Antigen)	Source
T cell epitopes	EADPTGHSY	(SEQ. ID NO.:409)	MAGE-1 161-169
	VSDGGPNLY	(SEQ. ID NO.:410)	Influenza A PB 1591-599
	CTELKLSDY	(SEQ. ID NO.:411)	Influenza A NP 44-52
	EVDPIGHLY	(SEQ. ID NO.:412)	MAGE-3 168-176
HLA-A201	MLLSVPLLLG	(SEQ. ID NO.:413)	Calreticulin signal sequence 1-10
	STBXQSGXQ	(SEQ. ID NO.:414)	HBV PRE-S PROTEIN 141-149
	YMDGTMSQV	(SEQ. ID NO.:415)	Tyrosinase 369-377
	ILKEPVHGV	(SEQ. ID NO.:416)	HIV-I RT 476-484
	LLGFVFTLTV	(SEQ. ID NO.:417)	Influenza MP 59-68
	LLFGYPVYVV	(SEQ. ID NO.:418)	HTLV-1 tax 11-19
	GLSPTVWLSV	(SEQ. ID NO.:419)	HBV sAg 348-357
	WLSLLVPFV	(SEQ. ID NO.:420)	HBV sAg 335-343
	FLPSDFFPSV	(SEQ. ID NO.:421)	HBV cAg 18-27
	C L G 0 L L T M V	(SEQ. ID NO.:422)	EBV LMP-2 426-434
	FLAGNSAYEYV	(SEQ. ID NO.:423)	HCMV gp 618-628B
	KLGEFYNQMM	(SEQ. ID NO.:424)	Influenza BNP 85-94
	KLVALGINAV	(SEQ. ID NO.:425)	HCV-1 NS3 400-409
	DLMGYIPLV	(SEQ. ID NO.:426)	HCV MP 17-25
	RLVTLKDIV	(SEQ. ID NO.:427)	HPV 11 EZ 4-12
	MLLAVLYCL	(SEQ. ID NO.:428)	Tyrosinase 1-9
	AAGIGILTV	(SEQ. ID NO.:429)	Melan A\Mart-127-35
	YLEPGPVTA	(SEQ. ID NO.:430)	Pmel 17/gp 100 480-488
	ILDGTATLRL	(SEQ. ID NO.:431)	Pmel 17/gp 100 457-466
	LLDGTATLRL	(SEQ. ID NO.:432)	Pmel gp1OO 457-466
	ITDQVPFSV	(SEQ. ID NO.:433)	Pmel gp 100 209-217
	KTWGQYWQV	(SEQ. ID NO.:434)	Pmel gp 100 154-162
	TITDQVPFSV	(SEQ. ID NO.:435)	Pmel gp 100 208-217
	AFHIIVAREL	(SEQ. ID NO.:436)	HIV-I nef 190-198
	YLNKIQNSL	(SEQ. ID NO.:437)	P. falciparum CSP 334-342
	MMRKLAILSV	(SEQ. ID NO.:438)	P. falciparum CSP 1-10
	KAGEFYNQMM	(SEQ. ID NO.:439)	Influenza BNP 85-94
	NIAEGLRAL	(SEQ. ID NO.:440)	EBNA-1 480-488
	NLRRGTALA	(SEQ. ID NO.:441)	EBNA-1 519-527
	ALAIPQCRL	(SEQ. ID NO.:442)	EBNA-1 525-533
	VLKDAIKDL	(SEQ. ID NO.:443)	EBNA-1 575-582
	FMVFLQTHI	(SEQ. ID NO.:444)	EBNA-1 562-570
	HLIVDTDSL	(SEQ. ID NO.:445)	EBNA-2 15-23
	SLGNPSLSV	(SEQ. ID NO.:446)	EBNA-2 22-30
	PLASAMRML	(SEQ. ID NO.:447)	EBNA-2 126-134
	RMLWMANYI	(SEQ. ID NO.:448)	EBNA-2 132-140
	MLWMANYIV	(SEQ. ID NO.:449)	EBNA-2 133-141
	ILPQGPQTA	(SEQ. ID NO.:450)	EBNA-2 151-159
	PLRPTAPTTI	(SEQ. ID NO.:451)	EBNA-2 171-179
	PLPPATLTV	(SEQ. ID NO.:452)	EBNA-2 205-213
	R M H L P V L H V	(SEQ. ID NO.:453)	EBNA-2 246-254
	PMPLPPSQL	(SEQ. ID NO.:454)	EBNA-2 287-295
	QLPPPAAPA	(SEQ. ID NO.:455)	EBNA-2 294-302
	SMPELSPVL	(SEQ. ID NO.:456)	EBNA-2 381-389
	DLDESWDYl	(SEQ. ID NO.:457)	EBNA-2 453-461
	P L P C V L W P VV	(SEQ. ID NO.:458)	BZLF1 43-51
	SLEECDSEL	(SEQ. ID NO.:459)	BZLF1 167-175
	EIKRYKNRV	(SEQ. ID NO.:460)	BZLFI 176-184
	QLLQFIYREV	(SEQ. ID NO.:461)	BZLF1 195-203
	LLQHYREVA	(SEQ. ID NO.:462)	BZLFI 196-204
	LLKQMCPSL	(SEQ. ID NO.:463)	BZLFI 217-225
	SIIPRTPDV	(SEQ. ID NO.:464)	BZLFI 229-237
	AIMDKNIIL	(SEQ. ID NO.:465)	Influenza A NS1 122-130
	IMDKNIILKA	(SEQ. ID NO.:466)	Influenza A NS1 123-132
	LLALLSCLTV	(SEQ. ID NO.:467)	HCV MP 63-72
	ILHTPGCV	(SEQ. ID NO.:468)	HCV MP 105-112
	QLRRHIDLLV	(SEQ. ID NO.:469)	HCV env E 66-75
	DLCGSVFLV	(SEQ. ID NO.:470)	HCV env E 88-96
	SMVGNWAKV	(SEQ. ID NO.:471)	HCV env E 172-180
	HLHQNIVDV	(SEQ. ID NO.:472)	HCV NSI 308-316
	FLLLADARV	(SEQ. ID NO.:473)	HCV NSI 340-348
	GLRDLAVAVEPVV	(SEQ. ID NO.:474)	HCV NS2 234-246
	SLLAPGAKQNV	(SEQ. ID NO.:475)	HCV NS1 18-28
	LLAPGAKQNV	(SEQ. ID NO.:476)	HCV NS1 19-28
	FLLSLGIHL	(SEQ. ID NO.:477)	HBV pol 575-583
	SLYADSPSV	(SEQ. ID NO.:478)	HBV pol 816-824
	GLSRYVARL	(SEQ. ID NO.:479)	HBV POL 455-463
	KIFGSLAFL	(SEQ. ID NO.:480)	HER-2 369-377
	ELVSEFSRM	(SEQ. ID NO.:481)	HER-2 971-979
	KLTPLCVTL	(SEQ. ID NO.:482)	HIV-I gp 160 120-128
	SLLNATDIAV	(SEQ. ID NO.:483)	HIV-I GP 160 814-823
	VLYRYGSFSV	(SEQ. ID NO.:484)	Pmel gp100 476-485
	YIGEVLVSV	(SEQ. ID NO.:485)	Non-filament forming class I myosin
			family (HA-2)**
	LLFNILGGWV	(SEQ. ID NO.:486)	HCV NS4 192-201
	LLVPFVQWFW	(SEQ. ID NO.:487)	HBV env 338-347
	ALMPLYACI	(SEQ. ID NO.:488)	HBV pol 642-650
	YLVAYQATV	(SEQ. ID NO.:489)	HCV NS3 579-587
	TLGIVCPIC	(SEQ. ID NO.:490)	HIPV 16 E7 86-94
	YLLPRRGPRL	(SEQ. ID NO.:491)	HCV core protein 34-43
	LLPIFFCLWV	(SEQ. ID NO.:492)	HBV env 378-387
	YMDDVVLGA	(SEQ. ID NO.:493)	HBV Pol 538-546
	GTLGIVCPI	(SEQ. ID NO.:494)	HPV16 E7 85-93
	LLALLSCLTI	(SEQ. ID NO.:495)	HCV MP 63-72
	MLDLQPETT	(SEQ. ID NO.:496)	HPV 16 E7 12-20
	SLMAFTAAV	(SEQ. ID NO.:497)	HCV NS4 174-182
	CINGVCWTV	(SEQ. ID NO.:498)	HCV NS3 67-75
	VMNILLQYVV	(SEQ. ID NO.:499)	Glutarnic acid decarboxylase 114-123
	ILTVILGVL	(SEQ. ID NO.:500)	Melan A/Mart-32-40
	FLWGPRALV	(SEQ. ID NO.:501)	MAGE-3 271-279
	L L C P A G H A V	(SEQ. ID NO.:502)	HCV NS3 163-171
	ILDSFDPLV	(SEQ. ID NO.:503)	HCV NSS 239-247
	LLLCLIFLL	(SEQ. ID NO.:504)	HBV env 250-258
	LIDYQGMLPV	(SEQ. ID NO.:505)	HBV env 260-269
	SIVSPFIPLL	(SEQ. ID NO.:506)	HBV env 370-379
	FLLTRILTI	(SEQ. ID NO.:507)	HBV env 183-191
	HLGNVKYLV	(SEQ. ID NO.:508)	P. faciparum TRAP 3-11
	GIAGGLALL	(SEQ. ID NO.:509)	P. faciparum TRAP 500-508
	IILAGYGAGV	(SEQ. ID NO.:510)	HCV NS S4A 236-244
	GLQDCTMLV	(SEQ. ID NO.:511)	HCV NS5 714-722
	TGAPVTYSTY	(SEQ. ID NO.:512)	HCV NS3 281-290
	VIYQYMDDLV	(SEQ. ID NO.:513)	HIV-1RT 179-187
	VLPDVFIRCV	(SEQ. ID NO.:514)	N-acetylglucosaminyltransferase V Gnt-V
			intron
	VLPDVFIRC	(SEQ. ID NO.:515)	N-acetylglucosaminyltransferase V Gnt-V
			intron
	AVGIGIAVV	(SEQ. ID NO.:516)	Human CD9
	LVVLGLLAV	(SEQ. ID NO.:517)	Human glutamyltransferase
	ALGLGLLPV	(SEQ. ID NO.:518)	Human G protein coupled receptor
		164-172
	GIGIGVLAA	(SEQ. ID NO.:519)	HSV-I gp C 480-488
	GAGIGVAVL	(SEQ. ID NO.:520)	HSV-2 gp C 446-454
	IAGIGILAI	(SEQ. ID NO.:521)	Pseudorabies gpGIN 455-463
	LIVIGILIL	(SEQ. ID NO.:522)	Adenovirus 3 E3 9 kD 30-38
	LAGIGLLIAA	(SEQ. ID NO.:523)	S. Lincolnensis ImrA
	VDGIGTLTI	(SEQ. ID NO.:524)	Yeast ysa-1 77-85
	GAGIGVLTA	(SEQ. ID NO.:525)	B. polymyxa , βcndoxylanase 149-157
		157
	AAGIGIIQI	(SEQ. ID NO.:526)	E. coli methionine synthase 590-598
	QAGIGILLA	(SEQ. ID NO.:527)	E. coli hypothetical protein 4-12
	KARDPHSGHFV	(SEQ. ID NO.:528)	CDK4w1 22.32
	KACDPI-ISGIIFV	(SEQ. ID NO.:529)	CDK4-R24C 22-32
	ACDPFISGHFV	(SEQ. ID NO.:530)	CDK4-R24C 23-32
	SLYNTVATL	(SEQ. ID NO.:531)	HIV-I gag p 17 77-85
	ELVSEFSRV	(SEQ. ID NO.:532)	HER-2, m > V substituted 971-979
	RGPGRAFVTI	(SEQ. ID NO.:533)	HIV-I gp 160 315-329
	HMWNFISGI	(SEQ. ID NO.:534)	HCV NS4A 149-157
	NLVPMVATVQ	(SEQ. ID NO.:535)	HCMV pp65 495-504
	GLHCYEQLV	(SEQ. ID NO.:536)	HPV 6b E7 21-30
	PLKQHFQIV	(SEQ. ID NO.:537)	HPV 6b E7 47-55
	LLDFVRFMGV	(SEQ. ID NO.:538)	EBNA-6 284-293
	AIMEKNIML	(SEQ. ID NO.:539)	Influenza Alaska NS 1 122-130
	YLKTIQNSL	(SEQ. ID NO.:540)	P. falciparum cp36 CSP
	YLNKIQNSL	(SEQ. ID NO.:541)	P. falciparurn cp39 CSP
	YMLDLQPETT	(SEQ. ID NO.:542)	HPV 16 E7 11-20*
	LLMGTLGIV	(SEQ. ID NO.:543)	HPV16 E7 82-90**
	TLGIVCPI	(SEQ. ID NO.:544)	HPV 16 E7 86-93
	TLTSCNTSV	(SEQ. ID NO.:545)	HIV-1 gp120 197-205
	KLPQLCTEL	(SEQ. ID NO.:546)	HPV 16 E6 18-26
	TIHDIILEC	(SEQ. ID NO.:547)	HPV16 E6 29-37
	LGIVCPICS	(SEQ. ID NO.:548)	HPV16 E7 87-95
	VILGVLLLI	(SEQ. ID NO.:549)	Melan A/Mart-1 35-43
	ALMDKSLHV	(SEQ. ID NO.:550)	Melan A/Mart-1 56-64
	GILTVILGV	(SEQ. ID NO.:551)	Melan A/Mart-1 31-39
T cell epitopes	MINAYLDKL	(SEQ. ID NO.:552)	P. Falciparum STARP 523-531
	AAGIGILTV	(SEQ. ID NO.:553)	Melan A/Mart-127-35
	FLPSDFFPSV	(SEQ. ID NO.:554)	HBV cAg 18-27
Motif unknown	SVRDRLARL	(SEQ. ID NO.:555)	EBNA-3 464-472
T cell epitopes
T cell epitopes	AAGIGILTV	(SEQ. ID NO.:556)	Melan A/Mart-1 27-35
	FAYDGKDYI	(SEQ. ID NO.:557)	Human MHC I-ot 140-148
T cell epitopes	AAGIGILTV	(SEQ. ID NO.:558)	Melan A/Mart-1 27-35
	FLPSDFFPSV	(SEQ. ID NO.:559)	HBV cAg 18-27
Motif unknown	AAGIGILTV	(SEQ. ID NO.:560)	Meland A/Mart-1 27-35
T cell epitopes
	FLPSDFFPSV	(SEQ. ID NO.:561)	HBV cAg 18-27
	AAGIGILTV	(SEQ. ID NO.:562)	Melan A/Mart-1 27-35
	ALLAVGATK	(SEQ. ID NO.:563)	Pmel17 gp 100 17-25
T cell epitopes	R L R D L L L I V T R	(SEQ. ID NO.:564)	HIV-1 gp41 768-778
	QVPLRPMTYK	(SEQ. ID NO.:565)	HIV-1 nef 73-82
	TVYYGVPVWK	(SEQ. ID NO.:566)	HIV-1 gp120-36-45
	RLRPGGKKK	(SEQ. ID NO.:567)	HIV-1 gag p 17 20-29
	ILRGSVAHK	(SEQ. ID NO.:568)	Influenza NP 265-273
	RLRAEAGVK	(SEQ. ID NO.:569)	EBNA-3 603-611
	RLRDLLLIVTR	(SEQ. ID NO.:570)	HIV-1 gp41 770-780
	VYYGVPVWK	(SEQ. ID NO.:571)	HIV-I GP 120 38-46
	RVCEKMALY	(SEQ. ID NO.:572)	HCV NS5 575-583
Motif unknown	KIFSEVTLK	(SEQ. ID NO.:573)	Unknown; muta melanoma peptide ted (p
T cell epitope			I 83L) 175-183
	YVNVNMGLK*	(SEQ. ID NO.:574)	HBV cAg 88-96
T cell epitopes	IVTDFSVIIK	(SEQ. ID NO.:575)	EBNA-4 416-424
	ELNEALELK	(SEQ. ID NO.:576)	P53 343-351
	VPLRPMTYK	(SEQ. ID NO.:577)	HIV-1 NEF 74-82
	AIFQSSMTK	(SEQ. ID NO.:578)	HIV-I gag p24 325-333
	QVPLRPMTYK	(SEQ. ID NO.:579)	HIV-1 nef 73-82
	TINYTIFK HCV	(SEQ. ID NO.:580)	NSI 238-246
	AAVDLSHFLKEK	(SEQ. ID NO.:581)	HIV-1 nef 83-94
	ACQ G V G G P G G H K	(SEQ. ID NO.:582)	HIV-1 II 1B p24 349-359
HLA-A24	S Y L D S G I H F*	(SEQ. ID NO.:583)	β-catenin, mutated (proto-onocogen)
			29-37
T cell epitopes	RYLKDQQLL	(SEQ. ID NO.:584)	HIV GP 41 583-591
	AYGLDFYIL	(SEQ. ID NO.:585)	P15 melanoma Ag 10-18
	AFLPWHRLFL	(SEQ. ID NO.:586)	Tyrosinase 206-215
	AFLPWHRLF	(SEQ. ID NO.:587)	Tyrosinase 206-214
	RYSIFFDY	(SEQ. ID NO.:588)	Ebna-3 246-253
T cell epitope	ETINEEAAEW	(SEQ. ID NO.:589)	HIV-1 gag p24 203-212
T cell epitopes	STLPETTVVRR	(SEQ. ID NO.:590)	HBV cAg 141-151
	MSLQRQFLR	(SEQ. ID NO.:591)	ORF 3P-gp75 294-321 (bp)
	LLPGGRPYR	(SEQ. ID NO.:592)	TRP (tyrosinase rel.) 197-205
T cell epitope	IVGLNKIVR	(SEQ. ID NO.:593)	HIV gag p24 267-267-275
	AAGIGILTV	(SEQ. ID NO.:594)	Melan A/Mart-127 35

[0132] Table 6 sets forth additional antigens useful in the invention that are available from the Ludwig Cancer Institute. The Table refers to patents in which the identified antigens can be found and as such are incorporated herein by reference. TRA refers to the tumor-related antigen and the LUD No. refers to the Ludwig Institute number.

TABLE 6
	LUD		Date Patent
TRA	No.	Patent No.	Issued	Peptide (Antigen)	HLA
MAGE-4	5293	5,405,940	11 Apr. 1995	EVDPASNTY	(SEQ. ID NO.:979)	HLA-
						A1
MAGE-41	5293	5,405,940	11 Apr. 1995	EVDPTSNTY	(SEQ ID NO:595)	HLA-
						A I
MAGE-5	5293	5,405,940	11 Apr. 1995	EADPTSNTY	(SEQ ID NO:596)	HLA-
						A I
MAGE-51	5293	5,405,940	11 Apr. 1995	EADPTSNTY	(SEQ ID NO:597)	HLA-
						A I
MAGE-6	5294	5,405,940	11 Apr. 1995	EVDPIGHVY	(SEQ ID NO:598)	HLA-
						A1
	5299.2	5,487,974	30 Jan. 1996	MLLAVLYCLL	(SEQ ID NO:599)	HLA-
						A2
	5360	5,530,096	25 Jun. 1996	MLLAVLYGL	(SEQ ID NO:600)	HLA-
						B44
Tyrosinase	5360.1	5,519,117	21 May 1996	SEIWRDIDFA	(SEQ ID NO:601)	HLA-
						B44
				SEIWRDIDF	(SEQ ID NO:602)
Tyrosinase	5431	5,774,316	28 Apr. 1998	XEIWRDIDF	(SEQ ID NO:603)	HLA-
						B44
MAGE-2	5340	5,554,724	10 Sep. 1996	STLVEVTLGEV	(SEQ ID NO:604)	HLA-
						A2
				LVEVTLGEV	(SEQ ID NO:605)
				VIFSKASEYL	(SEQ ID NO:606)
				IIVLAIIAl	(SEQ ID NO:607)
				KIWEELSMLEV	(SEQ ID NO:608)
				LIETSYVKV	(SEQ ID NO:609)
	5327	5,585,461	17 Dec. 1996	FLWGPRALV	(SEQ ID NO:610)	HLA-
						A2
				TLVEVTLGEV	(SEQ ID NO:611)
				ALVETSYVKV	(SEQ ID NO:612)
MAGE-3	5344	5,554,506	10 Sep. 1996	KIWEELSVL	(SEQ ID NO:613)	HLA-
						A2
MAGE-3	5393	5,405,940	11 Apr. 1995	EVDPIGHLY	(SEQ ID NO:614)	HLA-
						A1
MAGE	5293	5,405,940	11 Apr. 1995	EXDX5Y	(SEQ. ID NO.:615)	HLA-
						A1
				(but not EADPTGHSY)	(SEQ. ID NO.:616)
				E (A/V) D X5 Y	(SEQ. ID NO.:617)
				E (A/V) D P X4 Y	(SEQ. ID NO.:618)
				E (A/V) D P (I/A/T) X3 Y	(SEQ. ID NO.:619)
				E (A/V) D P (I/A/T) (G/S) X2 Y	(SEQ. ID NO.:620)
				E (A/V) D P (I/A/T) (G/S) (H/N) X Y	(SEQ. ID NO.:621)
				E (A/V) DP (I/A/T) (G/S) (H/N)	(SEQ. 11) NO.:622)
				(L/T/V) Y
MAGE-1	5361	5,558.995	24 Sep. 1996	ELHSAYGEPRKLLTQD	(SEQ ID NO:623)	HLA-C
						Clone
						10
				EHSAYGEPRKLL	(SEQ ID NO:624)
				SAYGEPRKL	(SEQ ID NO:625)
MAGE-1	5253.4	TBA	TBA	EADPTGHSY	(SEQ ID NO:626)	HLA-
						A I
BAGE	5310.1	TBA	TBA	MAARAVFLALSAQLLQARLMKE	(SEQ ID NO:627)	HLA-C
						Clone
						10
				MAARAVFLALSAQLLQ	(SEQ ID NO:628)	HLA-C
						Clone
						10
				AARAVFLAL	(SEQ ID NO:629)	HLA-
						Clone
						10
GAGE	5323.2	5,648,226	15 Jul. 1997	YRPRPRRY	(SEQ. ID NO.:630)	HLA-
						CW6

[0133]

TABLE 7
				T cell epitope	SEQ.
		AA	MHC	MHC ligand	ID
Source	Protein	Position	molecules	(Antigen)	NO.:	Ref.
Synthetic	synthetic	synthetic	HLA-A2	ALFAAAAAV	631	Parker, et al., “Scheme
peptides	peptides	peptides				for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GIFGGVGGV	632	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLDKGGGV	633	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGFGGV	634	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGAGV	635	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGEGV	636	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGFGV	637	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGGGL	638	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGGGV	639	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGVGV	640	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGVGGV	641	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGVGKV	642	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFKGVGGV	643	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLGGGGFGV	644	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLLGGGVGV	645	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLYGGGGGV	646	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GMFGGGGGV	647	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GMFGGVGGV	648	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GQFGGVGGV	649	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GVFGGVGGV	650	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	KLFGGGGGV	651	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	KLFGGVGGV	652	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	AILGFVFTL	653	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GAIGFVFTL	654	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GALGFVFTL	655	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GELGFVFTL	656	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GIAGFVFTL	657	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GIEGFVFTL	658	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILAFVFTL	659	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILGAVFTL	660	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILGEVFTL	661	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILFGAFTL	662	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILGFEFTL	663	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILGFKFTL	664	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILGFVATL	665	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILGFVETL	666	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILGFVFAL	667	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILGFVFEL	668	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILGFVFKL	669	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILGFVFTA	670	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILGFVFTL	671	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILGFVFVL	672	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILGFVKTL	673	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILGKVFTL	674	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILKFVFTL	675	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GILPFVFTL	676	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GIVGFVFTL	677	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GKLGFVFTL	678	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLLGFVFTL	679	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GQLGFVFTL	680	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	KALGFVFTL	681	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	KILGFVFTL	682	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	KILGKVFTL	683	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	AILLGVFML	684	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	AIYKRWIIL	685	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	ALFFFDIDL	686	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	ATVELLSEL	687	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	CLFGYPVYV	688	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	FIFPNYTIV	689	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	IISLWDSQL	690	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	ILASLFAAV	691	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	ILESLFAAV	692	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	KLGEFFNQM	693	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	KLGEFYNQM	694	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	LLFGYPVYV	695	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	LLWKGEGAV	696	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	LMFGYPVYV	697	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	LNFGYPVYV	698	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	LQFGYPVYV	699	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	NIVAHTFKV	700	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	NLPMVATV	701	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	QMLLAIARL	702	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	QMWQARLTV	703	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	RLLQTGIHV	704	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	RLVNGSLAL	705	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	SLYNTVATL	706	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	TLNAWVKVV	707	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	WLYRETCNL	708	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	YLFKRMIDL	709	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GAFGGVGGV	710	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GAFGGVGGY	711	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GEFGGVGGV	712	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GGFGGVGGV	713	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GIFGGGGGV	714	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GIGGFGGGL	715	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GIGGGGGGL	716	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLDGGGGGV	717	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLDGKGGGV	718	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLDKKGGGV	719	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGFGF	720	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGFGG	721	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGFGN	722	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGFGS	723	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGGGI	724	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGGGM	725	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGGGT	726	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGGGY	727	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLGFGGGGV	728	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLGGFGGGV	729	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLGGGFGGV	730	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLGGGGGFV	731	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLGGGGGGY	732	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLGGGVGGV	733	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLLGGGGGV	734	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLPGGGGGV	735	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GNFGGVGGV	736	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GSFGGVGGV	737	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GTFGGVGGV	738	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	AGNSAYEYV	739	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFPGQFAY	740	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	HILLGVFML	741	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	ILESLFRAV	742	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	KLKKYKLKHI	743	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	MLASTDLKY	744	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	MLERELVRK	745	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	KLFGFVFTV	746	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	ILDKKVEKV	747	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	ILKEPVHGV	748	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	ALFAAAAAY	749	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GIGFGGGGL	750	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GKFGGVGGV	751	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GLFGGGGGK	752	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	EILGFVFTL	753	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GIKGFVFTL	754	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	GQLGFVFTK	755	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	ILGFVFTLT	756	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	KILGFVFTK	757	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	KKLGFVFTL	758	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	KLFEKVYNY	759	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
			HLA-A2	LRFGYPVYV	760	Parker, et al., “Scheme
						for ranking potential
						HLA-A2 binding
						peptides based on
						independent binding of
						individual peptide side-
						chains,” J. Immunol.
						152: 163-175
Human	HSP60	140-148	HLA-B27	IRRGVMLAV	761	Rammensee et al. 1997
						160
Human	HSP60	369-377	HLA-B27	KRIQEIIEQ	762	Rammensee et al. 1997
						160
Human	HSP60	469-477	HLA-B27	KRTLKIPAM	763	Rammensee et al. 1997
						160
Yersinia	HSP60	35-43	HLA-B27	GRNVVLDKS	764	Rammensee et al. 1997
						160
Yersinia	HSP60	117-125	HLA-B27	KRGIDKAVI	765	Rammensee et al. 1997
						160
Yersinia	HSP60	420-428	HLA-B27	IRAASAITA	766	Rammensee et al. 1997
						160
Yersinia	HSP 60	284-292	HLA-	RRKAMFEDI	767	169
			B*2705
P.	LSA-1	1850-1857	HLA-	KPKDELDY	768	170
falciparum			B3501
Influenza		379-387	HLA-	LELRSRYWA	769	183
NP			B*4402
	Tum-P35B	4-13	HLA-Dd	GPPHSNNFGY	770	230
Rotavirus	VP7	33-40		IIYRFLLI	771	262
	OGDH	104-112	H2-Ld	QLSPYPFDL	772	253
	(F108Y)
	TRP-2	181-188	p287	VYDFFVWL	773	284
	DEAD box	547-554	p287	SNIFVFAGI	774	283
	p 68
	Vector		p287	SVVEFSSL	775	260
	“artefact”
	Epitope		p287	AHYLFRNL	776	278
	mimic of
	tumor Ag
			p287	THYLFRNL	777	278
	Epitope		p287	LIVIYNTL	778	279
	mimic of
	H-3
	miHAg”
			p287	LIYEFNTL	779	279
			p287	IPYIYNTL	780	279
			p287	IIYIYHRL	781	279
			p287	LIYIFNTL	782	279
	HBV cAg	93-100	p287	MGLKLFRQL	783	280
Human	autoantigen	51-58	p287	IMIKFRNRL	784	281
	LA
Mouse	UTY		H2Db	WMHHNMDLI	785	303
	protein
Mouse	p53	232-240	H2Db	KYMCNSSCM	786	302
MURINE	MDM2	441-449	H2Db	GRPKNGCIV	787	277
	Epitope	AQHPNAELL	788	278
	mimic of
	natural
	MuLV	75-83	H2Db	CCLCLTVFL	789	301
	gag75K
P.	CSP	375-383	p290	YENDIEKK	790	315
Falciparum
P.	CSP	371-379	p290	DELDYENDI	791	315
Falciparum
HIV	−1RT	206-214	p290	TEMEKEGKI	792	316
Rabies	NS	197-205	p290	VEAEIAHQI	793	309, 310
Influenza A	NS	1152-160	p290	EEGAIVGEI	794	304
Murine	SMCY		p291	TENSGKDI	795	317
	MHC class	3-11	p293	AMAPRTLLL	796	318
	1 leader
	ND1alpha	1-12	p293	FFINILTLLVP	797	323
	ND Beta	1-12	p293	FFINILTLLVP	798	323
	ND alpha	1-17	p293	FFINILTLLVPI	799	324
				LIAM
	ND Beta	1-17	p293	FFINALTLLVPI	800	324
				LIAM
	COI	1-6	p293	FINRW	801	325
	mitochondrial
L.	LemA	1-6	p293	IGWII	802	326
monocyto -
genes
	SW gag	179-190	Mamu-	EGCTPYDINQ	803	334
	p11C		A*01	ML
	MAGE-3		HLA-A2	ALSRKVAEL	804	5,554,506
			HLA-A2	IMPKAGLLI	805	5,554,506
			HLA-A2	KIWEELSVL	806	5,554,506
			HLA-A2	ALVETSYVKV	807	5,554,506
			HLA-A2	ThrLeuValGluVal	808	5,554,506
				ThrLeuGlyGluVal
			HLA-A2	AlaLeuSerArgLys	809	5,554,506
				ValAlaGluLeu
			HLA-A2	IleMetProLysAla	810	5,554,506
				GlyLeuLeuIle
			HLA-A2	LysIleTrpGluGlu	811	5,554,506
				LeuSerValLeu
			HLA-A2	AlaLeuValGluThr	812	5,554,506
				SerTyrValLys
				Val
	peptides		HLA-A2	Lys Gly Ile Leu	813	5,989,565
	which bind			Gly Phe Val Phe
	to MHCs			Thr Leu Thr Val
			HLA-A2	Gly Ile Ile Gly	814	5,989,565
				Phe Val Phe Thr
				Ile
			HLA-A2	Gly Ile Ile Gly	815	5,989,565
				Phe Val Phe Thr
				Leu
			HLA-A2	Gly Ile Leu Gly	816	5,989,565
				Phe Val Phe Thr
				Leu
			HLA-A2	Gly Leu Leu Gly	817	5,989,565
				Phe Val Phe Thr
				Leu
			HLA-A2	XXTVXXGVX,	818	5,989,565
				X=Leu or Ile
				(6-37)
			HLA-A2	Ile Leu Thr Val	819	5,989,565
				Ile Leu Gly Val
				Leu
			HLA-A2	Tyr Leu Glu Pro	820	5,989,565
				Gly Ala
			HLA-A2	Gln Val Pro Leu	821	5,989,565
				Arg Tyr Lys
			HLA-A2	Asp Gly Leu Ala	822	5,989,565
				Pro Pro Gln His
				Leu Ile Arg
			HLA-A2	Leu Leu Gly Arg	823	5,989,565
				Asn Ser Phe Glu
				Val
	Peptides		HLA-C	GluHisSerAlaTyr	824	5,558,995
	from		clone 10	GlyGluProArgLys
	MAGE-1			LeuLeuThrGlnAsp
				Leu
			HLA-C	GluHisSerAlaTyr	825	5,558,995
			clone 10	GlyGluProArgLys
				LeuLeu
			HLA-C	SerAlaTyrGlyGly	826	5,558,995
			clone 10	ProArgLysLeu
	GAGE		HLA-Cw6	TyrArgProArgPro	827	5,648,226
				ArgArgTyr
			HLA-Cw6	ThrTyrArgProArg	828	5,648,226
				ProArgArgTyr
			HLA-Cw6	TyrArgProArgPro	829	5,648,226
				ArgArgTyrVal
			HLA-Cw6	ThrTyrArgProArg	830	5,648,226
				ProArgArgTyrVal
			HLA-Cw6	ArgProArgProArg	831	5,648,226
				ArgTyrValGlu
			HLA-Cw6	MetSerTrpArgGly	832	5,648,226
				ArgSerThrTyrArg
				ProArgProArgArg
			HLA-Cw6	ThrTyrArgProArg	833	5,648,226
				ProArgArgTyrVal
				GluProProGluMet
				Ile
	MAGE		HLA-A1,	Isolated	834	5,405,940
			primarily	nonapeptide
				having Glu at its
				N terminal, Tyr
				at its C-terminal,
				and Asp at the
				third residue
				from its N
				terminal, with
				the proviso that
				said isolated
				nonapeptide is
				not Glu Ala Asp
				Pro Thr Gly His
				Ser Tyr (SEQ ID
				NO: 1), and
				wherein said
				isolated
				nonapeptide
				binds to a human
				leukocyte
				antigen molecule
				on a cell to form
				a complex, said
				complex
				provoking lysis
				of said cell by a
				cytolytic T cell
				specific to said
				complex
			HLA-A1,	GluValValProIle	835	5,405,940
			primarily	SerHisLeuTyr
			HLA-A1,	GluValValArgIle	836	5,405,940
			primarily	GlyHisLeuTyr
			HLA-A1,	GluValAspProIle	837	5,405,940
			primarily	GlyHisLeuTyr
			HLA-A1,	GluValAspProAla	838	5,405,940
			primarily	SerAsnThrTyr
			HLA-A1,	GluValAspProThr	839	5,405,940
			primarily	SerAsnThrTyr
			HLA-A1,	GluAlaAspProThr	840	5,405,940
			primarily	SerAsnThrTyr
			HLA-A1,	GluValAspProIle	841	5,405,940
			primarily	GlyHisValTyr
			HLA-A1,	GAAGTGGTCC	842	5,405,940
			primarily	CCATCAGCCA
			HLA-A1,	CTTGTAC
			primarily	GAAGTGGTCC	843	5,405,940
			HLA-A1,	GCATCGGCCA
			primarily	CTTGTAC
			HLA-A1,	GAAGTGGAC	844	5,405,940
			primarily	CCCATCGGCC
			HLA-A1,	ACTTGTAC
			primarily	GAAGTGGAC	845	5,405,940
			HLA-A1,	CCCGCCAGCA
			primarily	ACACCTAC
			HLA-A1,	GAAGTGGAC	846	5,405,940
			primarily	CCCACCAGCA
			HLA-A1,	ACACCTAC
			primarily	GAAGCGGAC	847	5,405,940
			HLA-A1,	CCCACCAGCA
			primarily	ACACCTAC
			HLA-A1,	GAAGCGGAC	848	5,405,940
			primarily	CCCACCAGCA
			HLA-A1,	ACACCTAC
			primarily	GAAGTGGAC	849	5,405,940
			HLA-A1,	CCCATCGGCC
			primarily	ACGTGTAC
			HLA-A1,	GluAlaAspProThr	850	5,405,940
			primarily	GlyHisSer
			HLA-A1,	AlaAspProTrpGly	851	5,405,940
			primarily	HisSerTyr
	MAGE		HLA-A2	SerThrLeuValGlu	852	5,554,724
	peptides			ValThrLeuGlyGlu
				Val
	MAGE		HLA-A2	LeuValGluValThr	853	5,554,724
	peptides			LeuGlyGluVal
	MAGE		HLA-A2	LysMetValGluLeu	854	5,554,724
	peptides			ValHisPheLeu
	MAGE		HLA-A2	ValIlePheSerLys	855	5,554,724
	peptides			AlaSerGluTyrLeu
	MAGE		HLA-A2	TyrLeuGlnLeuVal	856	5,554,724
	peptides			PheGlyIleGluVal
	MAGE		HLA-A2	GlnLeuValPheGly	857	5,554,724
	peptides			IleGluValVal
	MAGE		HLA-A2	GlnLeuValPheGly	858	5,554,724
	peptides			IleGluValValGlu
				Val
	MAGE		HLA-A2	IleIleValLeuAla	859	5,554,724
	peptides			IleIleAlaIle
	MAGE		HLA-A2	LysIleTrpGluGlu	860	5,554,724
	peptides			LeuSerMetLeuGlu
				Val
	MAGE		HLA-A2	AlaLeuIleGluThr	861	5,554,724
	peptides			SerTyrValLysVal
	MAGE		HLA-A2	LeuIleGluThrSer	862	5,554,724
	peptides			TyrValLysVal
	MAGE		HLA-A2	GlyLeuGluAlaArg	863	5,554,724
	peptides			GlyGluAlaLeuGly
				Leu
	MAGE		HLA-A2	GlyLeuGluAlaArg	864	5,554,724
	peptides			GlyGluAlaLeu
	MAGE		HLA-A2	AlaLeuGlyLeuVal	865	5,554,724
	peptides			GlyAlaGlnAla
	MAGE		HLA-A2	GlyLeuValGlyAla	866	5,554,724
	peptides			GlnAlaProAla
	MAGE		HLA-A2	AspLeuGluSerGlu	867	5,554,724
	peptides			PheGlnAlaAla
	MAGE		HLA-A2	AspLeuGluSerGlu	868	5,554,724
	peptides			PheGlnAlaAlaIle
	MAGE		HLA-A2	AlaIleSerArgLys	869	5,554,724
	peptides			MetValGluLeuVal
	MAGE		HLA-A2	AlaIleSerArgLys	870	5,554,724
	peptides			MetValGluLeu
	MAGE		HLA-A2	LysMetValGluLeu	871	5,554,724
	peptides			ValHisPheLeuLeu
	MAGE		HLA-A2	LysMetValGluLeu	872	5,554,724
	peptides			ValHisPheLeuLeu
				Leu
	MAGE		HLA-A2	LeuLeuLeuLysTyr	873	5,554,724
	peptides			ArgAlaArgGluPro
				Val
	MAGE		HLA-A2	LeuLeuLysTyrArg	874	5,554,724
	peptides			AlaArgGluProVal
	MAGE		HLA-A2	ValLeuArgAsnCys	875	5,554,724
	peptides			GlnAspPhePhePro
				Val
	MAGE		HLA-A2	TyrLeuGlnLeuVal	876	5,554,724
	peptides			PheGlyIleGluVal
				Val
	MAGE		HLA-A2	GlyIleGluValVal	877	5,554,724
	peptides			GluValValProIle
	MAGE		HLA-A2	ProIleSerHisLeu	878	5,554,724
	peptides			TyrIleLeuVal
	MAGE		HLA-A2	HisLeuTyrIleLeu	879	5,554,724
	peptides			ValThrCysLeu
	MAGE		HLA-A2	HisLeuTyrIleLeu	880	5,554,724
	peptides			ValThrCysLeuGly
				Leu
	MAGE		HLA-A2	TyrIleLeuValThr	881	5,554,724
	peptides			CysLeuGlyLeu
	MAGE		HLA-A2	CysLeuGlyLeuSer	882	5,554,724
	peptides			TyrAspGlyLeu
	MAGE		HLA-A2	CysLeuGlyLeuSer	883	5,554,724
	peptides			TyrAspGlyLeu
				Leu
	MAGE		HLA-A2	ValMetProLysThr	884	5,554,724
	peptides			GlyLeuLeuIle
	MAGE		HLA-A2	ValMetProLysThr	885	5,554,724
	peptides			GlyLeuLeuIleIle
	MAGE		HLA-A2	ValMetProLysThr	886	5,554,724
	peptides			GlyLeuLeuIleIle
				Val
	MAGE		HLA-A2	GlyLeuLeuIleIle	887	5,554,724
	peptides			ValLeuAlaIleIle
	MAGE		HLA-A2	GlyLeuLeuIleIle	888	5,554,724
	peptides			ValLeuAlaIleIle
	MAGE		HLA-A2	GlyLeuLeuIleIle	889	5,554,724
	peptides			ValLeuAlaIleIle
				Ala
	MAGE		HLA-A2	LeuLeuIleIleVal	890	5,554,724
	peptides			LeuAlaIleIle
	MAGE		HLA-A2	LeuLeuIleIleVal	891	5,554,724
	peptides			LeuAlaIleIleAla
	MAGE		HLA-A2	LeuLeullelleVal	892	5,554,724
	peptides			LeuAlaIleIleAla
				Ile
	MAGE		HLA-A2	LeuIleIleValLeu	893	5,554,724
	peptides			AlaIleIleAla
	MAGE		HLA-A2	LeuIleIleValLeu	894	5,554,724
	peptides			AlaIleIleAlaIle
	MAGE		HLA-A2	IleIleAlaIleGlu	895	5,554,724
	peptides			GlyAspCysAla
	MAGE		HLA-A2	LysIleTrpGluGlu	896	5,554,724
	peptides			LeuSerMetLeu
	MAGE		HLA-A2	LeuMetGlnAspLeu	897	5,554,724
	peptides			ValGlnGluAsnTyr
				Leu
	MAGE		HLA-A2	PheLeuTrpGlyPro	898	5,554,724
	peptides			ArgAlaLeuIle
	MAGE		HLA-A2	LeuIleGluThrSer	899	5,554,724
	peptides			TyrValLysVal
	MAGE		HLA-A2	AlaLeuIleGluThr	900	5,554,724
	peptides			SerTyrValLysVal
				Leu
	MAGE		HLA-A2	ThrLeuLysIleGly	901	5,554,724
	peptides			GlyGluProHisIle
	MAGE		HLA-A2	HisIleSerTyrPro	902	5,554,724
	peptides			ProLeuHisGluArg
				Ala
	MAGE		HLA-A2	GlnThrAlaSerSer	903	5,554,724
	peptides			SerSerThrLeu
	MAGE		HLA-A2	GlnThrAlaSerSer	904	5,554,724
	peptides			SerSerThrLeuVal
	MAGE		HLA-A2	ValThrLeuGlyGlu	905	5,554,724
	peptides			ValProAlaAlaVal
	MAGE		HLA-A2	ValThrLysAlaGlu	906	5,554,724
	peptides			MetLeuGluSerVal
	MAGE		HLA-A2	ValThrLysAlaGlu	907	5,554,724
	peptides			MetLeuGluSerVal
				Leu
	MAGE		HLA-A2	ValThrCysLeuGly	908	5,554,724
	peptides			LeuSerTyrAspGly
				Leu
	MAGE		HLA-A2	LysThrGlyLeuLeu	909	5,554,724
	peptides			IleIleValLeu
	MAGE		HLA-A2	LysThrGlyLeuLeu	910	5,554,724
	peptides			IleIleValLeuAla
	MAGE		HLA-A2	LysThrGlyLeuLeu	911	5,554,724
	peptides			IleIleValLeuAla
				Ile
	MAGE		HLA-A2	HisThrLeuLysIle	912	5,554,724
	peptides			GlyGlyGluProHis
				Ile
	MAGE		HLA-A2	MetLeuAspLeuGln	913	5,554,724
	peptides			ProGluThrThr
	Mage-3		HLA-A2	GlyLeuGluAlaArg	914	5,585,461
	peptides			GlyGluAlaLeu
	Mage-3		HLA-A2	AlaLeuSerArgLys	915	5,585,461
	peptides			ValAlaGluLeu
	Mage-3		HLA-A2	PheLeuTrpGlyPro	916	5,585,461
	peptides			ArgAlaLeuVal
	Mage-3		HLA-A2	ThrLeuValGluVal	917	5,585,461
	peptides			ThrLeuGlyGluVal
	Mage-3		HLA-A2	AlaLeuSerArgLys	918	5,585,461
	peptides			ValAlaGluLeuVal
	Mage-3		HLA-A2	AlaLeuValGluThr	919	5,585,461
	peptides			SerTyrValLysVal
	Tyrosinase		HLA-A2	TyrMetAsnGlyThr	920	5,487,974
				MetSerGlnVal
	Tyrosinase		HLA-A2	MetLeuLeuAlaVal	921	5,487,974
				LeuTyrCysLeuLeu
	Tyrosinase		HLA-A2	MetLeuLeuAlaVal	922	5,530,096
				LeuTyrCysLeu
	Tyrosinase		HLA-A2	LeuLeuAlaValLeu	923	5,530,096
				TyrCysLeuLeu
	Tyrosinase		HLA-A2	SerGluIleTrpArg	924	5,519,117
			and HLA-	AspIleAspPheAla
			B44	HisGluAla
	Tyrosinase		HLA-A2	SerGlulleTrpArg	925	5,519,117
			and HLA-	AspIleAspPhe
			B44
	Tyrosinase		HLA-A2	GluGluAsnLeuLeu	926	5,519,117
			and HLA-	AspPheValArgPhe
			B44
	Melan			EAAGIGILTV	927	Jäger, E. et al.
	A/MART-1					Granulocyte-
						macrophage-colony-
						stimulating Factor
						Enhances Immune
						Responses To
						Melanoma-′associated
						Peptides in vivo Int. J
						Cancer 67, 54-62
						(1996)
	Tyrosinase			MLLAVLYCL	928	Jäger, E. et al.
						Granulocyte-
						macrophage-colony-
						stimulating Factor
						Enhances Immune
						Responses To
						Melanoma-′associated
						Peptides in vivo Int. J
						Cancer 67, 54-62
						(1996)
	Tyrosinase			YMDGTMSQV	929	Jäger, E. et al.
						Granulocyte-
						macrophage-colony-
						stimulating Factor
						Enhances Immune
						Responses To
						Melanoma-′associated
						Peptides in vivo Int. J
						Cancer 67, 54-62
						(1996)
	gp100/Pme117			YLEPGPVTA	930	Jäger, E. et al.
						Granulocyte-
						macrophage-colony-
						stimulating Factor
						Enhances Immune
						Responses To
						Melanoma-′associated
						Peptides in vivo Int. J
						Cancer 67, 54-62
						(1996)
	gp100/Pme117			LLDGTATLRL	931	Jäger, E. et al.
						Granulocyte-
						macrophage-colony-
						stimulating Factor
						Enhances Immune
						Responses To
						Melanoma-′associated
						Peptides in vivo Int. J
						Cancer 67, 54-62
						(1996)
	Influenza			GILGFVFTL	932	Jäger, E. et al.
	matrix					Granulocyte-
						macrophage-colony-
						stimulating Factor
						Enhances Immune
						Responses To
						Melanoma-′associated
						Peptides in vivo Int. J
						Cancer 67, 54-62
						(1996)
	MAGE-1			EADPTGHSY	933	Jäger, E. et al.
						Granulocyte-
						macrophage-colony-
						stimulating Factor
						Enhances Immune
						Responses To
						Melanoma-′associated
						Peptides in vivo Int. J
						Cancer 67, 54-62
						(1996)
	MAGE-1		HLA-A1	EADPTGHSY	934
	BAGE		HLA-C	MAARAVFLAL	935	Jäger, E. et al.
				SAQLLQARLM		Granulocyte-
				KE		macrophage-colony-
						stimulating Factor
						Enhances Immune
						Responses To
						Melanoma-′associated
						Peptides in vivo Int. J
						Cancer 67, 54-62
						(1996)
	BAGE		HLA-C	MAARAVFLAL	936	Jäger, E. et al.
				SAQLLQ		Granulocyte-
						macrophage-colony-
						stimulating Factor
						Enhances Immune
						Responses To
						Melanoma-′associated
						Peptides in vivo Int. J
						Cancer 67, 54-62
						(1996)
	BAGE		HLA-C	AARAVFLAL	937	Jäger, E. et al.
						Granulocyte-
						macrophage-colony-
						stimulating Factor
						Enhances Immune
						Responses To
						Melanoma-′associated
						Peptides in vivo Int. J
						Cancer 67, 54-62
						(1996)
Influenza	PR8 NP	147-154	Kd	IYQRIRALV	938	Falk et al., Allele-
						specific motifs revealed
						by sequencing of self-
						peptides eluted from
						MHC molecules
SELF	P815		Kd	SYFPEITHI	939	Falk et al., Allele-
PEPTIDE						specific motifs revealed
						by sequencing of self-
						peptides eluted from
						MHC molecules
Influenza	Jap HA		Kd	IYATVAGSL	940	Falk et al., Allele-
	523-549					specific motifs revealed
						by sequencing of self-
						peptides eluted from
						MHC molecules
Influenza	Jap HA		Kd	VYQILAIYA	941	Falk et al., Allele-
	523-549					specific motifs revealed
						by sequencing of self-
						peptides eluted from
						MHC molecules
Influenza	Jap HA		Kd	IYSTVASSL	942	Falk et al., Allele-
	523-549					specific motifs revealed
						by sequencing of self-
						peptides eluted from
						MHC molecules
Influenza	JAP HA		Kd	LYQNVGTYV	943	Falk et al., Allele-
	202-221					specific motifs revealed
						by sequencing of self-
						peptides eluted from
						MHC molecules
	HLA-A24		Kd	RYLENQKRT	944	Falk et al., Allele-
						specific motifs revealed
						by sequencing of self-
						peptides eluted from
						MHC molecules
	HLA-Cw3		Kd	RYLKNGKET	945	Falk et al., Allele-
						specific motifs revealed
						by sequencing of self-
						peptides eluted from
						MHC molecules
	P815		Kd	KYQAVTTTL	946	Falk et al., Allele-
						specific motifs revealed
						by sequencing of self-
						peptides eluted from
						MHC molecules
Plasmodium	CSP		Kd	SYIPSAEKI	947	Falk et al., Allele-
berghei						specific motifs revealed
						by sequencing of self-
						peptides eluted from
						MHC molecules
Plasmodium	CSP		Kd	SYVPSAFQI	948	Falk et al., Allele-
yoelii						specific motifs revealed
						by sequencing of self-
						peptides eluted from
						MHC molecules
Vesicular	NP 52-59		Kb	RGYVYQGL	949	Falk et al., Allele-
stomatitis						specific motifs revealed
virus						by sequencing of self-
						by sequencing of self-
						peptides eluted from
						MHC molecules
Ovalbumin			Kb	SIINFEKL	950	Falk et al., Allele-
						specific motifs revealed
						by sequencing of self-
						peptides eluted from
						MHC molecules
Sendai virus	NP 321-332		Kb	APGNYPAL	951	Falk et al., Allele-
						specific motifs revealed
						by sequencing of self-
						peptides eluted from
						MHC molecules
				VPYGSFKHV	952	Morel et al., Processing
						of some antigens by the
						standard proteasome
						but not by the
						immunoproteasome
						results in poor
						presentation by
						dendritic cells,
						Immunity, vol. 12: 107-
						117, 2000.
			MOTIFS
Influenza	PR8 NP		Kd	TYQRTRALV	953	5,747,269
			restricted
			peptide
			motif
Self peptide	P815		Kd	SYFPEITHI	954	5,747,269
			restricted
			peptide
			motif
Influenza	JAP HA		Kd	IYATVAGSL	955	5,747,269
			restricted
			peptide
			motif
Influenza	JAP HA		Kd	VYQILAIYA	956	5,747,269
			restricted
			peptide
			motif
Influenza	PR8 HA		Kd	IYSTVASSL	957	5,747,269
			restricted
			peptide
			motif
Influenza	JAP HA		Kd	LYQNVGTYV	958	5,747,269
			restricted
			peptide
			motif
			HLA-A24	RYLENGKETL	959	5,747,269
			HLA-Cw3	RYLKNGKETL	960	5,747,269
	P815		HLA-Cw3	KYQAVTTTL	961	5,747,269
	tumour
	antigen
Plasmodium	CSP		HLA-Cw3	SYIPSAEKI	962	5,747,269
berghei
Plasmodium	CSP		HLA-Cw3	SYVPSAEQI	963	5,747,269
yoelii
Influenza	NP		Db-	ASNENMETM	964	5,747,269
			restricted
			peptide
			motif
Adenovirus	E1A		Db-	SGPSNTPPEI	965	5,747,269
			restricted
			peptide
			motif
Lymphocytic			Db-	SGVENPGGYC	966	5,747,269
choriomen-			restricted	L
ingitis			peptide
			motif
Simian	40T		Db-	SAINNY . . .	967	5,747,269
virus			restricted
			peptide
			motif
HIV	reverse		HLA-	ILKEPVHGV	968	5,747,269
	transcriptase		A2.1-
			restricted
			peptide
			motif
	influenza		HLA-	GILGFVFTL	969	5,747,269
	matrix		A2.1-
	protein		restricted
			peptide
			motif
Influenza	influenza		HLA-	ILGFVFTLTV	970	5,747,269
	matrix		A2.1-
	protein		restricted
			peptide
			motif
HIV	Gag protein			FLQSRPEPT	971	5,747,269
HIV	Gag protein			AMQMLKE . . .	972	5,747,269
HIV	Gag protein			PIAPGQMRE	973	5,747,269
HIV	Gag protein			QMKDCTERQ	974	5,747,269
			HLA-	VYGVIQK	975	5,747,269
			A*0205-
			restricted
			peptide
			motif

[0134]

TABLE 8
VSV-NP peptide (49-62)
LCMV-NP peptide (118-132)
LCMV glycoprotein peptide. 33-41

[0135] Still further embodiments are directed to methods, uses, therapies and compositions related to epitopes with specificity for MHC, including, for example, those listed in Tables 9-13. Other embodiments include one or more of the MHCs listed in Tables 9-13, including combinations of the same, while other embodiments specifically exclude any one or more of the MHCs or combinations thereof. Tables 11-13 include frequencies for the listed HLA antigens.

TABLE 9
Class I MHC Molecules
Class I
Human
HLA-A1
HLA-A*0101
HLA-A*0201
HLA-A*0202
HLA-A*0203
HLA-A*0204
HLA-A*0205
HLA-A*0206
HLA-A*0207
HLA-A*0209
HLA-A*0214
HLA-A3
HLA-A*0301
HLA-A*1101
HLA-A23
HLA-A24
HLA-A25
HLA-A*2902
HLA-A*3101
HLA-A*3302
HLA-A*6801
HLA-A*6901
HLA-B7
HLA-B*0702
HLA-B*0703
HLA-B*0704
HLA-B*0705
HLA-B8
HLA-B13
HLA-B14
HLA-B*1501 (B62)
HLA-B17
HLA-B18
HLA-B22
HLA-B27
HLA-B*2702
HLA-B*2704
HLA-B*2705
HLA-B*2709
HLA-B35
HLA-B*3501
HLA-B*3502
HLA-B*3701
HLA-B*3801
HLA-B*39011
HLA-B*3902
HLA-B40
HLA-B*40012 (B60)
HLA-B*4006 (B61)
HLA-B44
HLA-B*4402
HLA-B*4403
HLA-B*4501
HLA-B*4601
HLA-B51
HLA-B*5101
HLA-B*5102
HLA-B*5103
HLA-B*5201
HLA-B*5301
HLA-B*5401
HLA-B*5501
HLA-B*5502
HLA-B*5601
HLA-B*5801
HLA-B*6701
HLA-B*7301
HLA-B*7801
HLA-Cw*0102
HLA-Cw*0301
HLA-Cw*0304
HLA-Cw*0401
HLA-Cw*0601
HLA-Cw*0602
HLA-Cw*0702
HLA-Cw8
HLA-Cw*1601 M
HLA-G
Murine
H2-Kd
H2-Dd
H2-Ld
H2-Kb
H2-Db
H2-Kk
H2-Kkml
Qa-1a
Qa-2
H2-M3
Rat
RT1.Aa
RT1.A1
Bovine
Bota-A11
Bota-A20
Chicken
B-F4
B-F12
B-F15
B-F19
Chimpanzee
Patr-A*04
Patr-A*11
Patr-B*01
Patr-B*13
Patr-B*16
Baboon
Papa-A*06
Macaque
Mamu-A*01
Swine
SLA (haplotype d/d)
Virus homolog
hCMV class I homolog UL18

[0136]

TABLE 10
Class I MHC Molecules
Class I
Human
HLA-A1
HLA-A*0101
HLA-A*0201
HLA-A*0202
HLA-A*0204
HLA-A*0205
HLA-A*0206
HLA-A*0207
HLA-A*0214
HLA-A3
HLA-A*1101
HLA-A24
HLA-A*2902
HLA-A*3101
HLA-A*3302
HLA-A*6801
HLA-A*6901
HLA-B7
HLA-B*0702
HLA-B*0703
HLA-B*0704
HLA-B*0705
HLA-B8
HLA-B14
HLA-B*1501 (B62)
HLA-B27
HLA-B*2702
HLA-B*2705
HLA-B35
HLA-B*3501
HLA-B*3502
HLA-B*3701
HLA-B*3801
HLA-B*39011
HLA-B*3902
HLA-B40
HLA-B*40012 (B60)
HLA-B*4006 (B61)
HLA-B44
HLA-B*4402
HLA-B*4403
HLA-B*4601
HLA-B51
HLA-B*5101
HLA-B*5102
HLA-B*5103
HLA-B*5201
HLA-B*5301
HLA-B*5401
HLA-B*5501
HLA-B*5502
HLA-B*5601
HLA-B*5801
HLA-B*6701
HLA-B*7301
HLA-B*7801
HLA-Cw*0102
HLA-Cw*0301
HLA-Cw*0304
HLA-Cw*0401
HLA-Cw*0601
HLA-Cw*0602
HLA-Cw*0702
HLA-G
Murine
H2-Kd
H2-Dd
H2-Ld
H2-Kb
H2-Db
H2-Kk
H2-Kkml
Qa-2
Rat
RT1.Aa
RT1.A1
Bovine
Bota-A11
Bota-A20
Chicken
B-F4
B-F12
B-F15
B-F19
Virus homolog
hCMV class I homolog UL18

[0137]

TABLE 11
Estimated gene frequencies of HLA-A antigens
	CAU	AFR	ASI	LAT	NAT
Antigen	Gfa	SEb	Gf	SE	Gf	SE	Gf	SE	Gf	SE
A1	15.1843	0.0489	5.7256	0.0771	4.4818	0.0846	7.4007	0.0978	12.0316	0.2533
A2	28.6535	0.0619	18.8849	0.1317	24.6352	0.1794	28.1198	0.1700	29.3408	0.3585
A3	13.3890	0.0463	8.4406	0.0925	2.6454	0.0655	8.0789	0.1019	11.0293	0.2437
A28	4.4652	0.0280	9.9269	0.0997	1.7657	0.0537	8.9446	0.1067	5.3856	0.1750
A36	0.0221	0.0020	1.8836	0.0448	0.0148	0.0049	0.1584	0.0148	0.1545	0.0303
A23	1.8287	0.0181	10.2086	0.1010	0.3256	0.0231	2.9269	0.0628	1.9903	0.1080
A24	9.3251	0.0395	2.9668	0.0560	22.0391	0.1722	13.2610	0.1271	12.6613	0.2590
A9 unsplit	0.0809	0.0038	0.0367	0.0063	0.0858	0.0119	0.0537	0.0086	0.0356	0.0145
A9 total	11.2347	0.0429	13.2121	0.1128	22.4505	0.1733	16.2416	0.1382	14.6872	0.2756
A25	2.1157	0.0195	0.4329	0.0216	0.0990	0.0128	1.1937	0.0404	1.4520	0.0924
A26	3.8795	0.0262	2.8284	0.0547	4.6628	0.0862	3.2612	0.0662	2.4292	0.1191
A34	0.1508	0.0052	3.5228	0.0610	1.3529	0.0470	0.4928	0.0260	0.3150	0.0432
A43	0.0018	0.0006	0.0334	0.0060	0.0231	0.0062	0.0055	0.0028	0.0059	0.0059
A66	0.0173	0.0018	0.2233	0.0155	0.0478	0.0089	0.0399	0.0074	0.0534	0.0178
A10 unsplit	0.0790	0.0038	0.0939	0.0101	0.1255	0.0144	0.0647	0.0094	0.0298	0.0133
A10 total	6.2441	0.0328	7.1348	0.0850	6.3111	0.0993	5.0578	0.0816	4.2853	0.1565
A29	3.5796	0.0252	3.2071	0.0582	1.1233	0.0429	4.5156	0.0774	3.4345	0.1410
A30	2.5067	0.0212	13.0969	0.1129	2.2025	0.0598	4.4873	0.0772	2.5314	0.1215
A31	2.7386	0.0221	1.6556	0.0420	3.6005	0.0761	4.8328	0.0800	6.0881	0.1855
A32	3.6956	0.0256	1.5384	0.0405	1.0331	0.0411	2.7064	0.0604	2.5521	0.1220
A33	1.2080	0.0148	6.5607	0.0822	9.2701	0.1191	2.6593	0.0599	1.0754	0.0796
A74	0.0277	0.0022	1.9949	0.0461	0.0561	0.0096	0.2027	0.0167	0.1068	0.0252
A19 unsplit	0.0567	0.0032	0.2057	0.0149	0.0990	0.0128	0.1211	0.0129	0.0475	0.0168
A19 total	13.8129	0.0468	28.2593	0.1504	17.3846	0.1555	19.5252	0.1481	15.8358	0.2832
AX	0.8204	0.0297	4.9506	0.0963	2.9916	0.1177	1.6332	0.0878	1.8454	0.1925
a Gene frequency.
b Standard error.

[0138]

TABLE 12
Estimated gene frequencies for HLA-B antigens
	CAU	AFR	ASI	LAT	NAT
Antigen	Gfa	SEb	Gf	SE	Gf	SE	Gf	SE	Gf	SE
B7	12.1782	0.0445	10.5960	0.1024	4.2691	0.0827	6.4477	0.0918	10.9845	0.2432
B8	9.4077	0.0397	3.8315	0.0634	1.3322	0.0467	3.8225	0.0715	8.5789	0.2176
B13	2.3061	0.0203	0.8103	0.0295	4.9222	0.0886	1.2699	0.0416	1.7495	0.1013
B14	4.3481	0.0277	3.0331	0.0566	0.5004	0.0287	5.4166	0.0846	2.9823	0.1316
B18	4.7980	0.0290	3.2057	0.0582	1.1246	0.0429	4.2349	0.0752	3.3422	0.1391
B27	4.3831	0.0278	1.2918	0.0372	2.2355	0.0603	2.3724	0.0567	5.1970	0.1721
B35	9.6614	0.0402	8.5172	0.0927	8.1203	0.1122	14.6516	0.1329	10.1198	0.2345
B37	1.4032	0.0159	0.5916	0.0252	1.2327	0.0449	0.7807	0.0327	0.9755	0.0759
B41	0.9211	0.0129	0.8183	0.0296	0.1303	0.0147	1.2818	0.0418	0.4766	0.0531
B42	0.0608	0.0033	5.6991	0.0768	0.0841	0.0118	0.5866	0.0284	0.2856	0.0411
B46	0.0099	0.0013	0.0151	0.0040	4.9292	0.0886	0.0234	0.0057	0.0238	0.0119
B47	0.2069	0.0061	0.1305	0.0119	0.0956	0.0126	0.1832	0.0159	0.2139	0.0356
B48	0.0865	0.0040	0.1316	0.0119	2.0276	0.0575	1.5915	0.0466	1.0267	0.0778
B53	0.4620	0.0092	10.9529	0.1039	0.4315	0.0266	1.6982	0.0481	1.0804	0.0798
B59	0.0020	0.0006	0.0032	0.0019	0.4277	0.0265	0.0055	0.0028	0c	—
B67	0.0040	0.0009	0.0086	0.0030	0.2276	0.0194	0.0055	0.0028	0.0059	0.0059
B70	0.3270	0.0077	7.3571	0.0866	0.8901	0.0382	1.9266	0.0512	0.6901	0.0639
B73	0.0108	0.0014	0.0032	0.0019	0.0132	0.0047	0.0261	0.0060	0c	—
B51	5.4215	0.0307	2.5980	0.0525	7.4751	0.1080	6.8147	0.0943	6.9077	0.1968
B52	0.9658	0.0132	1.3712	0.0383	3.5121	0.0752	2.2447	0.0552	0.6960	0.0641
B5 unsplit	0.1565	0.0053	0.1522	0.0128	0.1288	0.0146	0.1546	0.0146	0.1307	0.0278
B5 total	6.5438	0.0435	4.1214	0.0747	11.1160	0.1504	9.2141	0.1324	7.7344	0.2784
B44	13.4838	0.0465	7.0137	0.0847	5.6807	0.0948	9.9253	0.1121	11.8024	0.2511
B45	0.5771	0.0102	4.8069	0.0708	0.1816	0.0173	1.8812	0.0506	0.7603	0.0670
B12 unsplit	0.0788	0.0038	0.0280	0.0055	0.0049	0.0029	0.0193	0.0051	0.0654	0.0197
B12 total	14.1440	0.0474	11.8486	0.1072	5.8673	0.0963	11.8258	0.1210	12.6281	0.2584
B62	5.9117	0.0320	1.5267	0.0404	9.2249	0.1190	4.1825	0.0747	6.9421	0.1973
B63	0.4302	0.0088	1.8865	0.0448	0.4438	0.0270	0.8083	0.0333	0.3738	0.0471
B75	0.0104	0.0014	0.0226	0.0049	1.9673	0.0566	0.1101	0.0123	0.0356	0.0145
B76	0.0026	0.0007	0.0065	0.0026	0.0874	0.0120	0.0055	0.0028	0	—
B77	0.0057	0.0010	0.0119	0.0036	0.0577	0.0098	0.0083	0.0034	0c	0.0059
B15 unsplit	0.1305	0.0049	0.0691	0.0086	0.4301	0.0266	0.1820	0.0158	0.0059	0.0206
B15 total	6.4910	0.0334	3.5232	0.0608	12.2112	0.1344	5.2967	0.0835	0.0715	0.2035
									7.4290
B38	2.4413	0.0209	0.3323	0.0189	3.2818	0.0728	1.9652	0.0517	1.1017	0.0806
B39	1.9614	0.0188	1.2893	0.0371	2.0352	0.0576	6.3040	0.0909	4.5527	0.1615
B16 unsplit	0.0638	0.0034	0.0237	0.0051	0.0644	0.0103	0.1226	0.0130	0.0593	0.0188
B16 total	4.4667	0.0280	1.6453	0.0419	5.3814	0.0921	8.3917	0.1036	5.7137	0.1797
B57	3.5955	0.0252	5.6746	0.0766	2.5782	0.0647	2.1800	0.0544	2.7265	0.1260
B58	0.7152	0.0114	5.9546	0.0784	4.0189	0.0803	1.2481	0.0413	0.9398	0.0745
B17 unsplit	0.2845	0.0072	0.3248	0.0187	0.3751	0.0248	0.1446	0.0141	0.2674	0.0398
B17 total	4.5952	0.0284	11.9540	0.1076	6.9722	0.1041	3.5727	0.0691	3.9338	0.1503
B49	1.6452	0.0172	2.6286	0.0528	0.2440	0.0200	2.3353	0.0562	1.5462	0.0953
B50	1.0580	0.0138	0.8636	0.0304	0.4421	0.0270	1.8883	0.0507	0.7862	0.0681
B21 unsplit	0.0702	0.0036	0.0270	0.0054	0.0132	0.0047	0.0771	0.0103	0.0356	0.0145
B21 total	2.7733	0.0222	3.5192	0.0608	0.6993	0.0339	4.3007	0.0755	2.3680	0.1174
B54	0.0124	0.0015	0.0183	0.0044	2.6873	0.0660	0.0289	0.0063	0.0534	0.0178
B55	1.9046	0.0185	0.4895	0.0229	2.2444	0.0604	0.9515	0.0361	1.4054	0.0909
B56	0.5527	0.0100	0.2686	0.0170	0.8260	0.0368	0.3596	0.0222	0.3387	0.0448
B22 unsplit	0.1682	0.0055	0.0496	0.0073	0.2730	0.0212	0.0372	0.0071	0.1246	0.0272
B22 total	2.0852	0.0217	0.8261	0.0297	6.0307	0.0971	1.3771	0.0433	1.9221	0.1060
B60	5.2222	0.0302	1.5299	0.0404	8.3254	0.1135	2.2538	0.0553	5.7218	0.1801
B61	1.1916	0.0147	0.4709	0.0225	6.2072	0.0989	4.6691	0.0788	2.6023	0.1231
B40 unsplit	0.2696	0.0070	0.0388	0.0065	0.3205	0.0230	0.2473	0.0184	0.2271	0.0367
B40 total	6.6834	0.0338	2.0396	0.0465	14.8531	0.1462	7.1702	0.0963	8.5512	0.2168
BX	1.0922	0.0252	3.5258	0.0802	3.8749	0.0988	2.5266	0.0807	1.9867	0.1634
a Gene frequency.
b Standard error.
c The observed gene count was zero.

[0139]

TABLE 13
Estimated gene frequencies of HLA-DR antigens
	CAU	AFR	ASI	LAT	NAT
Antigen	Gfa	SEb	Gf	SE	Gf	SE	Gf	SE	Gf	SE
DR1	10.2279	0.0413	6.8200	0.0832	3.4628	0.0747	7.9859	0.1013	8.2512	0.2139
DR2	15.2408	0.0491	16.2373	0.1222	18.6162	0.1608	11.2389	0.1182	15.3932	0.2818
DR3	10.8708	0.0424	13.3080	0.1124	4.7223	0.0867	7.8998	0.1008	10.2549	0.2361
DR4	16.7589	0.0511	5.7084	0.0765	15.4623	0.1490	20.5373	0.1520	19.8264	0.3123
DR6	14.3937	0.0479	18.6117	0.1291	13.4471	0.1404	17.0265	0.1411	14.8021	0.2772
DR7	13.2807	0.0463	10.1317	0.0997	6.9270	0.1040	10.6726	0.1155	10.4219	0.2378
DR8	2.8820	0.0227	6.2673	0.0800	6.5413	0.1013	9.7731	0.1110	6.0059	0.1844
DR9	1.0616	0.0139	2.9646	0.0559	9.7527	0.1218	1.0712	0.0383	2.8662	0.1291
DR10	1.4790	0.0163	2.0397	0.0465	2.2304	0.0602	1.8044	0.0495	1.0896	0.0801
DR11	9.3180	0.0396	10.6151	0.1018	4.7375	0.0869	7.0411	0.0955	5.3152	0.1740
DR12	1.9070	0.0185	4.1152	0.0655	10.1365	0.1239	1.7244	0.0484	2.0132	0.1086
DR5 unsplit	1.2199	0.0149	2.2957	0.0493	1.4118	0.0480	1.8225	0.0498	1.6769	0.0992
DR5 total	12.4449	0.0045	17.0260	0.1243	16.2858	0.1516	10.5880	0.1148	9.0052	0.2218
DRX	1.3598	0.0342	0.8853	0.0760	2.5521	0.1089	1.4023	0.0930	2.0834	0.2037
a Gene frequency.
b Standard error.

[0140] It can be desirable to express housekeeping peptides in the context of a larger protein. Processing can be detected even when a small number of amino acids are present beyond the terminus of an epitope. Small peptide hormones are usually proteolytically processed from longer translation products, often in the size range of approximately 60-120 amino acids. This fact has led some to assume that this is the minimum size that can be efficiently translated. In some embodiments, the housekeeping peptide can be embedded in a translation product of at least about 60 amino acids, in others 70, 80, 90 amino acids, and in still others 100, 110 or 120 amino acids, for example. In other embodiments the housekeeping peptide can be embedded in a translation product of at least about 50, 30, or 15 amino acids.

[0141] Due to differential proteasomal processing, the immunoproteasome of the pAPC produces peptides that are different from those produced by the housekeeping proteasome in peripheral body cells. Thus, in expressing a housekeeping peptide in the context of a larger protein, it is preferably expressed in the pAPC in a context other than its full-length native sequence, because, as a housekeeping epitope, it is generally only efficiently processed from the native protein by the housekeeping proteasome, which is not active in the pAPC. In order to encode the housekeeping epitope in a DNA sequence encoding a larger polypeptide, it is useful to find flanking areas on either side of the sequence encoding the epitope that permit appropriate cleavage by the immunoproteasome in order to liberate that housekeeping epitope. Such a sequence promoting appropriate processing is referred to hereinafter as having substrate or liberation sequence function. Altering flanking amino acid residues at the N-terminus and C-terminus of the desired housekeeping epitope can facilitate appropriate cleavage and generation of the housekeeping epitope in the pAPC. Sequences embedding housekeeping epitopes can be designed de novo and screened to determine which can be successfully processed by immunoproteasomes to liberate housekeeping epitopes.

[0142] Alternatively, another strategy is very effective for identifying sequences allowing production of housekeeping epitopes in APC. A contiguous sequence of amino acids can be generated from head to tail arrangement of one or more housekeeping epitopes. A construct expressing this sequence is used to immunize an animal, and the resulting T cell response is evaluated to determine its specificity to one or more of the epitopes in the array. These immune responses indicate housekeeping epitopes that are processed in the pAPC effectively. The necessary flanking areas around this epitope are thereby defined. The use of flanking regions of about 4-6 amino acids on either side of the desired peptide can provide the necessary information to facilitate proteasome processing of the housekeeping epitope by the immunoproteasome. Therefore, a substrate or liberation sequence of approximately 16-22 amino acids can be inserted into, or fused to, any protein sequence effectively to result in that housekeeping epitope being produced in an APC. In some embodiments, a broader context of a substrate sequence can also influence processing. In such embodiments, comparisons of a liberaton sequence in a variety of contexts can be useful in further optimizing a particular substrate sequence. In alternate embodiments the whole head-to-tail array of epitopes, or just the epitopes immediately adjacent to the correctly processed housekeeping epitope can be similarly transferred from a test construct to a vaccine vector.

[0143] In a preferred embodiment, the housekeeping epitopes can be embedded between known immune epitopes, or segments of such, thereby providing an appropriate context for processing. The abutment of housekeeping and immune epitopes can generate the necessary context to enable the immunoproteasome to liberate the housekeeping epitope, or a larger fragment, preferably including a correct C-terminus. It can be useful to screen constructs to verify that the desired epitope is produced. The abutment of housekeeping epitopes can generate a site cleavable by the immunoproteasome. Some embodiments of the invention employ known epitopes to flank housekeeping epitopes in test substrates; in others, screening as described below is used, whether the flanking regions are arbitrary sequences or mutants of the natural flanking sequence, and whether or not knowledge of proteasomal cleavage preferences are used in designing the substrates.

[0144] Cleavage at the mature N-terminus of the epitope, while advantageous, is not required, since a variety of N-terminal trimming activities exist in the cell that can generate the mature N-terminus of the epitope subsequent to proteasomal processing. It is preferred that such N-terminal extension be less than about 25 amino acids in length and it is further preferred that the extension have few or no proline residues. Preferably, in screening, consideration is given not only to cleavage at the ends of the epitope (or at least at its C-terminus), but consideration also can be given to ensure limited cleavage within the epitope.

[0145] Shotgun approaches can be used in designing test substrates and can increase the efficiency of screening. In one embodiment multiple epitopes can be assembled one after the other, with individual epitopes possibly appearing more than once. The substrate can be screened to determine which epitopes can be produced. In the case where a particular epitope is of concern, a substrate can be designed in which it appears in multiple different contexts. When a single epitope appearing in more than one context is liberated from the substrate additional secondary test substrates, in which individual instances of the epitope are removed, disabled, or are unique, can be used to determine which are being liberated and truly confer substrate or liberation sequence function.

[0146] Several readily practicable screens exist. A preferred in vitro screen utilizes proteasomal digestion analysis, using purified immunoproteasomes, to determine if the desired housekeeping epitope can be liberated from a synthetic peptide embodying the sequence in question. The position of the cleavages obtained can be determined by techniques such as mass spectrometry, HPLC, and N-terminal pool sequencing; as described in greater detail in U.S. patent application Ser. Nos. 09/561,074, 09/560,465 and 10/117,937, and Provisional U.S. Patent Application Nos. 60/282,211, 60/337,017, and 60/363, 210, which were all cited and incorporated by reference above.

[0147] Alternatively, in vivo and cell-based screens such as immunization or target sensitization can be employed. For immunization a nucleic acid construct capable of expressing the sequence in question is used. Harvested CTL can be tested for their ability to recognize target cells presenting the housekeeping epitope in question. Such targets cells are most readily obtained by pulsing cells expressing the appropriate MHC molecule with synthetic peptide embodying the mature housekeeping epitope. Alternatively, immunization can be carried out using cells known to express housekeeping proteasome and the antigen from which the housekeeping epitope is derived, either endogenously or through genetic engineering. To use target sensitization as a screen, CTL, or preferably a CTL clone, that recognizes the housekeeping epitope can be used. In this case it is the target cell that expresses the embedded housekeeping epitope (instead of the pAPC during immunization) and it must express immunoproteasome. Generally, the cell or target cell can be transformed with an appropriate nucleic acid construct to confer expression of the embedded housekeeping epitope. Loading with a synthetic peptide embodying the embedded epitope using peptide loaded liposomes, or complexed with cationic lipid protein transfer reagents such as BIOPORTER™ (Gene Therapy Systems, San Diego, Calif.), represents an alternative.

[0148] Once sequences with substrate or liberation sequence function are identified they can be encoded in nucleic acid vectors, chemically synthesized, or produced recombinantly. In any of these forms they can be incorporated into immunogenic compositions. Such compositions can be used in vitro in vaccine development or in the generation or expansion of CTL to be used in adoptive immunotherapy. In vivo they can be used to induce, amplify or sustain and active immune response. The uptake of polypeptides for processing and presentation can be greatly enhanced by packaging with cationic lipid, the addition of a tract of cationic amino acids such as poly-L-lysine (Ryser, H. J. et al., J Cell Physiol. 113:167-178, 1982; Shen, W. C. & Ryser, H. J., Proc. Natl. Aced. Sci. USA 75:1872-1876, 1978), the incorporation into branched structures with importation signals (Sheldon, K. et al., Proc. Natl. Aced. Sci. USA 92:2056-2060, 1995), or mixture with or fusion to polypeptides with protein transfer function including peptide carriers such as pep-1 (Morris, M. C., et al., Nat. Biotech. 19:1173-1176, 2001), the PreS2 translocation motif of hepatitis B virus surface antigen, VP22 of herpes viruses, and HIV-TAT protein (Oess, S. & Hildt, E., Gene Ther. 7:750-758, 2000; Ford, K. G., et al., Gene Ther. 8:1-4, 2001; Hung, C. F. et al., J. Virol. 76:2676-2682, 2002; Oliveira, S. C., et a; Hum. Gene Ther. 12:1353-1359, 2001; Normand, N. et al., J. Biol. Chem. 276:15042-15050, 2001; Schwartz, J. J. & Zhang, S., Curr. Opin. Mol. Ther. 2:162-167, 2000; Elliot G., 7 Hare, P. Cell 88:223-233, 1997), among other methodologies. Particularly for fusion proteins the immunogen can be produced in culture and the purified protein administered or, in the alternative, the nucleic acid vector can be administered so that the immunogen is produced and secreted by cells transformed in vivo. In either scenario the transport function of the fusion protein facilitates uptake by pAPC.

[0149] The following examples are intended for illustration purposes only, and should not be construed as limiting the scope of the invention in any way.

EXAMPLES

Example 1

[0150] A recombinant DNA plasmid vaccine, pMA2M, which encodes one polypeptide with an HLA A2-specific CTL epitope ELAGIGILTV (SEQ ID NO. 1) from melan-A (26-35A27L), and a portion (amino acids 31-96) of melan-A (SEQ ID NO. 2) including the epitope clusters at amino acids 31-48 and 56-69, was constructed. These clusters were previously disclosed in U.S. patent application Ser. No. 09/561,571 entitled EPITOPE CLUSTERS incorporated by reference above. Flanking the defined melan-A CTL epitope are short amino acid sequences derived from human tyrosinase (SEQ ID NO. 3) to facilitate liberation of the melan-A housekeeping epitope by processing by the immunoproteasome. In addition, these amino acid sequences represent potential CTL epitopes themselves. The cDNA sequence for the polypeptide in the plasmid is under the control of promoter/enhancer sequence from cytomegalovirus (CMVp) (see FIG. 4), which allows efficient transcription of messenger for the polypeptide upon uptake by APCs. The bovine growth hormone polyadenylation signal (BGH polyA) at the 3′ end of the encoding sequence provides a signal for polyadenylation of the messenger to increase its stability as well as for translocation out of nucleus into the cytoplasm for translation. To facilitate plasmid transport into the nucleus after uptake, a nuclear import sequence (NIS) from simian virus 40 (SV40) has been inserted in the plasmid backbone. The plasmid carries two copies of a CpG immunostimulatory motif, one in the NIS sequence and one in the plasmid backbone. Lastly, two prokaryotic genetic elements in the plasmid are responsible for amplification in E. coli, the kanamycin resistance gene (Kan R) and the pMB1 bacterial origin of replication.

[0151] Substrate or Liberation Sequence

[0152] The amino acid sequence of the encoded polypeptide (94 amino acid residues in length) (SEQ ID NO. 4) containing a 28 amino acid substrate or liberation sequence at its N-terminus (SEQ ID NO. 5) is given below:

MLLAVLYCL-ELAGIGILTV-YMDGTMSQV-
GILTVILGVLLLIGCWYCRRRNGYRALMDKS
LHVGTQCALTRRCPQEGFDHRDSKVSLQEKN
CEPV

[0153] The first 9 amino acid residues are derived from tyrosinase1-9 (SEQ ID NO. 6), the next ten constitute melan-A (26-35A27L) (SEQ ID NO. 1), and amino acid residues 20 to 29 are derived from tyrosinase369-377 (SEQ ID NO. 7). These two tyrosinase nonamer sequences both represent potential HLA A2-specific CTL epitopes. Amino acid residues 10-19 constitute melan-A (26-35A27L) an analog of an HLA A2-specific CTL epitope from melan-A, EAAGIGILTV (SEQ ID NO. 8), with an elevated potency in inducing CTL responses during in vitro immunization of human PBMC and in vivo immunization in mice. The segment of melan-A constituting the rest of the polypeptide (amino acid residues 30 to 94) contain a number of predicted HLA A2-specific epitopes, including the epitope clusters cited above, and thus can be useful in generating a response to immune epitopes as described at length in the patent applications ‘Epitope Synchronization in Antigen Presenting Cells’ and ‘Epitope Clusters’ cited and incorporated by reference above. This region was also included to overcome any difficulties that can be associated with the expression of shorter sequences. A drawing of pMA2M is shown in FIG. 4.

[0154] Plasmid Construction

[0155] A pair of long complementary oligonucleotides was synthesized which encoded the first 30 amino acid residues. In addition, upon annealing, these oligonucleotides generated the cohesive ends of Afl II at the 5′ end and that of EcoR I at the 3′ end. The melan A31-96 region was amplified with PCR using oligonucleotides carrying restriction sites for EcoR I at the 5′ end and Not I at the 3′ end. The PCR product was digested with EcoR I and Not I and ligated into the vector backbone, described in Example 1, that had been digested with Afl II and Not I, along with the annealed oligonucleotides encoding the amino terminal region in a three-fragment ligation. The entire coding sequence was verified by DNA sequencing. The sequence of the entire insert, from the Afl II site at the 5′ end to the Not I site at the 3′ end is disclosed as SEQ ID NO. 9. Nucleotides 12-293 encode the polypeptide.

Example 2

[0156] Three vectors containing melan-A (26-35A27L) (SEQ ID NO. 1) as an embedded housekeeping epitope were tested for their ability to induce a CTL response to this epitope in HLA-A2 transgenic HHD mice (Pascolo et al. J. Exp. Med. 185:2043-2051, 1997). One of the vectors was pMA2M described above (called pVAXM3 in FIG. 6). In pVAXM2 the same basic group of 3 epitopes was repeated several times with the flanking epitopes truncated by differing degrees in the various repeats of the array. Specifically the cassette consisted of:

M-Tyr(5-9)-ELA-Tyr(369-373)-Tyr(4- (SEQ ID NO. 10)
9)-ELA-Tyr(369-374)-Tyr(3-9)-ELA-
Tyr(369-375)-Tyr(2-9)-ELA

[0157] where ELA represents melan-A (26-35A27L) (SEQ ID NO. 1). This cassette was inserted in the same plasmid backbone as used for pVAXM3. The third, pVAXM1 is identical to pVAXM2 except that the epitope array is followed by an IRES (internal ribosome entry site for encephalomyocarditis virus) linked to a reading frame encoding melan-A 31-70.

[0158] Four groups of three HHD A2.1 mice were injected intranodally in surgically exposed inguinal lymph nodes with 25 μl of 1 mg/ml plasmid DNA in PBS on days 0, 3, and 6, each group receiving one of the three vectors or PBS alone. On day 14 the spleens were harvested and restimulated in vitro one time with 3-day LPS blasts pulsed with peptide (melan-A (26-35A27L)(SEQ ID NO. 1)). The in vitro cultures were supplemented with Rat T-Stim (Collaborative Biomedical Products) on the 3rd day and assayed for cytolytic activity on the 7th day using a standard 51Cr-release assay. FIGS. 5 to 8 show % specific lysis obtained using the cells immunized with PBS, pVAXM1, pVAXM2, and pVAXM3, respectively on T2 target cells and T2 target cells pulsed with melan-A (26-35A27L) (ELA) (SEQ ID NO. 1). All three vectors generated strong CTL responses. These data indicated that the plasmids have been taken up by APCs, the encoded polypeptide has been synthesized and proteolytically processed to produce the decamer epitope in question (that is, it had substrate or liberation sequence function), and that the epitope became HLA-A2 bound for presentation. Also, an isolated variant of pVAXM2, that terminates after the 55th amino acid, worked similarly well as the full length version (data not shown). Whether other potential epitopes within the expression cassette can also be produced and be active in inducing CTL responses can be determined by testing for CTL activity against target cells pulsed with corresponding synthetic peptides.

Example 3

[0159] An NY-ESO-1 (SE ID NO. 11) Substrate/Liberation Sequence

[0160] Six other epitope arrays were tested leading to the identification of a substrate/liberation sequence for the housekeeping epitope NY-ESO-1157-165 (SEQ ID NO. 12). The component epitopes of the arrays were:

SSX-241-49:
KASEKIFYV	(SEQ ID NO. 13)	Array element A
NY-ESO-1157-165:
SLLMWITQC	(SEQ ID NO. 12)	Array element B
NY-ESO-1163-171:
TQCFLPVFL	(SEQ ID NO. 14)	Array element C
PSMA288-297:
GLPSIPVHPI	(SEQ ID NO. 15)	Array element D
TYR4-9:
AVLYCL	(SEQ ID NO. 16)	Array element E

[0161] The six arrays had the following arrangements of elements after starting with an initiator methionine:

pVAX-PC-A: B-A-D-D-A-B-A-A
pVAX-PC-B: D-A-B-A-A-D-B-A
pVAX-PC-C: E-A-D-B-A-B-E-A-A
pVAX-BC-A: B-A-C-B-A-A-C-A
pVAX-BC-B: C-A-B-C-A-A-B-A
pVAX-BC-C: E-A-A-B-C-B-A-A

[0162] These arrays were inserted into the same vector backbone described in the examples above. The plasmid vectors were used to immunize mice essentially as described in Example 2 and the resulting CTL were tested for their ability to specifically lyse target cells pulsed with the peptide NY-ESO-1157-165, corresponding to element B above. Both pVAX-PC-A and pVAX-BC-A were found to induce specific lytic activity. Comparing the contexts of the epitope (element B) in the various arrays, and particularly between pVAX-PC-A and pVAX-BC-A, between pVAX-PC-A and pVAX-PC-B, and between pVAX-BC-A and pVAX-BC-C, it was concluded that it was the first occurrence of the epitope in pVAX-PC-A and pVAX-BC-A that was being correctly processed and presented. In other words an initiator methionine followed by elements B-A constitute a substrate/liberation sequence for the presentation of element B. On this basis a new expression cassette for use as a vaccine was constructed encoding the following elements:

[0163] An initiator methionine,

[0164] NY-ESO-1157-165 (bold)—a housekeeping epitope,

[0165] SSX241-49 (italic)—providing appropriate context for processing, and

[0166] NY-ESO-177-180—to avoid “short sequence” problems and provide immune epitopes.

[0167] Thus the construct encodes the amino acid sequence:

M-SLLMWITQC-KASEKIFYV- (SEQ ID NO. 17)
RCGARGPESRLLEFYLAMPFATPMEAELARRSLA
QDAPPLPVPGVLLKEFTVSGNILTIRLTAADHRQ
LQLSISSCLQQLSLLMWITQCFLPVFLAQPPSGQ
RR

[0168] and MSLLMWITQCKASEKIFYV (SEQ ID NO. 18) constitutes the liberation or substrate sequence. A polynucleotide encoding SEQ ID NO. 17 (SEQ ID NO. 19: nucleotides 12-380) was inserted into the same plasmid backbone as used for pMA2M generating the plasmid pN157.

Example 4

[0169] A construct similar to pN157 containing the whole epitope array from pVAX-PC-A was also made and designated pBPL. Thus the encoded amino acid sequence in pBPL is:

M-SLLMWITQC-KASEKIFYV-GLPSIPVHPI- (SEQ ID NO. 20)
GLPSIPVHPI-KASEKIFYV-SLLMWITQC-KA
SEKIFYV-KASEKIFYV-RCGARGPESRLLEFY
LAMPFATPMEAELARRSLAQDAPPLPVPGVLLK
EFTVSGNILTIRLTAADHRQLQLSISSCLQQLS
LLMWITQCFLPVFLAQPPSGQRR.

[0170] SEQ ID NO. 21 is the polynucleotide encoding SEQ ID NO. 20 used in pBPL.

[0171] A portion of SEQ ID NO. 20, IKASEKIFYVSLLMWITQCKASEKIFYVK (SEQ ID NO. 22) was made as a synthetic peptide and subjected to in vitro proteasomal digestion analysis with human immunoproteasome, utilizing both mass spectrometry and N-terminal pool sequencing. The identification of a cleavage after the C residue indicates that this segment of the construct can function as a substrate or liberation sequence for NY-ESO-1157-165 (SEQ ID NO. 12) epitope (see FIG. 9). FIG. 10 shows the differential processing of the SLLMWITQC epitope (SEQ ID NO. 12) in its native context where the cleavage following the C is more efficiently produced by housekeeping than immunoproteasome. The immunoproteasome also produces a major cleavage internal to the epitope, between the T and the Q when the epitope is in its native context, but not in the context of SEQ ID NO. 22 (compare FIGS. 6 and 7).

Example 5

[0172] Screening of further epitope arrays led to the identification of constructs promoting the expression of the epitope SSX-241-49 (SEQ ID NO. 13). In addition to some of the array elements defined in Example 3, the following additional elements were also used:

SSX-457-65:
VMTKLGFKV	(SEQ ID NO. 23)	Array element F.
PSMA730-739:
RQIYVAAFTV	(SEQ ID NO. 24)	Array element G.

[0173] A construct, denoted CTLA02, encoding an initiator methionine and the array F-A-G-D-C-F-G-A, was found to successfully immunize HLA-A2 transgenic mice to generate a CTL response recognizing the peptide SSX-241-49 (SEQ ID NO. 13).

[0174] As described above, it can be desirable to combine a sequence with substrate or liberation sequence function with one that can be processed into immune epitopes. Thus SSX-215-183 (SEQ ID NO. 25) was combined with all or part of the array as follows:

CTLS1:	F-A-G-D-C-F-G-A-SSX-215-183	(SEQ ID NO. 26)
CTLS2:	SSX-215-183-F-A-G-D-C-F-G-A	(SEQ ID NO. 27)
CTLS3:	F-A-G-D-SSX-215-183	(SEQ ID NO. 28)
CTLS4:	SSX-215-183-C-F-G-A.	(SEQ ID NO. 29)

[0175] All of the constructs except CTLS3 were able to induce CTL recognizing the peptide SSX-241-49 (SEQ ID NO. 13). CTLS3 was the only one of these four constructs which did not include the second element A from CTLA02 suggesting that it was this second occurrence of the element that provided substrate or liberation sequence function. In CTLS2 and CTLS4 the A element is at the C-terminal end of the array, as in CTLA02. In CTLS1 the A element is immediately followed by the SSX-215-183 segment which begins with an alanine, a residue often found after proteasomal cleavage sites (Toes, R. E. M., et al., J. Exp. Med. 194:1-12, 2001). SEQ ID NO. 30 is the polynucleotide sequence encoding SEQ ID NO. 26 used in CTLS1, also called pCBP.

[0176] A portion of CTLS1 (SEQ ID NO. 26), encompassing array elements F-A-SSX-215-23 with the sequence RQIYVAAFTV-KASEKIFYV-AQIPEKIQK (SEQ ID NO. 31), was made as a synthetic peptide and subjected to in vitro proteasomal digestion analysis with human immunoproteasome, utilizing both mass spectrometry and N-terminal pool sequencing. The observation that the C-terminus of the SSX-241-49 epitope (SEQ ID NO. 13) was generated (see FIG. 11) provided further evidence in support of substrate or liberation sequence function. The data in FIG. 12 showed the differential processing of the SSX-241-49 epitope, KASEKIFYV (SEQ ID NO. 13), in its native context, where the cleavage following the V was the predominant cleavage produced by housekeeping proteasome, while the immunoproteasome had several major cleavage sites elsewhere in the sequence. By moving this epitope into the context provided by SEQ ID NO. 31 the desired cleavage became a major one and its relative frequency compared to other immunoproteasome cleavages was increased (compare FIGS. 11 and 12). The data in FIG. 11B also showed the similarity in specificity of mouse and human immunoproteasome lending support to the usefulness of the transgenic mouse model to predict human antigen processing.

Example 6

[0177] Screening also revealed substrate or liberation sequence function for a tyrosinase epitope, Tyr207-215 (SEQ ID NO. 32), as part of an array consisting of the sequence [Tyr1-17-Tyr207-215]4, [MLLAVLYCLLWSFQTSA-FLPWHRLFL]4, (SEQ ID NO. 33). The same vector backbone described above was used to express this array. This array differs from those of the other examples in that the Tyr1-17 segment, which was included as a source of immune epitopes, is used as a repeated element of the array. This is in contrast with the pattern shown in the other examples where sequence included as a source of immune epitopes and/or length occurred a single time at the beginning or end of the array, the remainder of which was made up of individual epitopes or shorter sequences.

[0178] Plasmid Construction

[0179] The polynucleotide encoding SEQ ID NO. 33 was generated by assembly of annealed synthetic oligonucleotides. Four pairs of complementary oligonucleotides were synthesized which span the entire coding sequence with cohesive ends of the restriction sites of Afl II and EcoR I at either terminus. Each complementary pair of oligonucleotides were first annealed, the resultant DNA fragments were ligated stepwise, and the assembled DNA fragment was inserted into the same vector backbone described above pre-digested with Afl II/EcoR I. The construct was called CTLT2/pMEL and SEQ ID NO. 34 is the polynucleotide sequence used to encode SEQ ID NO. 33.

Example 7

[0180] Administration of a DNA Plasmid Formulation of a Immunotherapeutic for Melanoma to Humans.

[0181] An MA2M melanoma vaccine with a sequence as described in Example 1 above, was formulated in 1% Benzyl alcohol, 1% ethyl alcohol, 0.5 mM EDTA, citrate-phosphate, pH 7.6. Aliquots of 200, 400, and 600 μg DNA/ml were prepared for loading into MINIMED 407C infusion pumps. The catheter of a SILHOUETTE infusion set was placed into an inguinal lymph node visualized by ultrasound imaging. The pump and infusion set assembly was originally designed for the delivery of insulin to diabetics. The usual 17 mm catheter was substituted with a 31 mm catheter for this application. The infusion set was kept patent for 4 days (approximately 96 hours) with an infusion rate of about 25 μl/hour resulting in a total infused volume of approximately 2.4 ml. Thus the total administered dose per infusion was approximately 500, and 1000 μg; and can be 1500 μg, respectively, for the three concentrations described above. Following an infusion, subjects were given a 10 day rest period before starting a subsequent infusion. Given the continued residency of plasmid DNA in the lymph node after administration and the usual kinetics of CTL response following disappearance of antigen, this schedule will be sufficient to maintain the immunologic CTL response.

Example 8

[0182] SEQ ID NO. 22 is made as a synthetic peptide and packaged with a cationic lipid protein transfer reagent. The composition is infused directly into the inguinal lymph node (see example 7) at a rate of 200 to 600 μg of peptide per day for seven days, followed by seven days rest. An initial treatment of 3-8 cycles are conducted.

Example 9

[0183] A fusion protein is made by adding SEQ ID NO. 34 to the 3′ end of a nucleotide sequence encoding herpes simplex virus 1 VP22 (SEQ ID NO. 42) in an appropriate mammalian expression vector; the vector used above is suitable. The vector is used to transform HEK 293 cells and 48 to 72 hours later the cells are pelleted, lysed and a soluble extract prepared. The fusion protein is purified by affinity chromatography using an anti-VP22 monoclonal antibody. The purified fusion protein is administered intranodally at a rate of 10 to 100 μg per day for seven days, followed by seven days rest. An initial treatment of 3-8 cycles are conducted.

Examples 10-13

[0184] The following examples, Examples 10-13, all concern the prediction of 9-mer epitopes presented by HLA-A2.1, although the procedure is equally applicable to any HLA type, or epitope length, for which a predictive algorithm or MHC binding assay is available.

Example 10

Melan-A/MART-1 (SEQ ID NO: 2)

[0185] This melanoma tumor-associated antigen (TuAA) is 118 amino acids in length. Of the 110 possible 9-mers, 16 are given a score ≧16 by the SYFPEITHI/Rammensee algorithm. (See Table 14). These represent 14.5% of the possible peptides and an average epitope density on the protein of 0.136 per amino acid. Twelve of these overlap, covering amino acids 22-49 of SEQ ID NO: 2 resulting in an epitope density for the cluster of 0.428, giving a ratio, as described above, of 3.15. Another two predicted epitopes overlap amino acids 56-69 of SEQ ID NO: 2, giving an epitope density for the cluster of 0.143, which is not appreciably different than the average, with a ratio of just 1.05. See FIG. 1.

TABLE 14
SYFPEITHI (Rammensee algorithm) Results for Melan-A/MART-1
(SEQ ID NO: 2)
Rank	Start	Score
1	31	27
2	56	26
3	35	26
4	32	25
5	27	25
6	29	24
7	34	23
8	61	20
9	33	19
10	22	19
11	99	18
12	36	18
13	28	18
14	87	17
15	41	17
16	40	16

[0186] Restricting the analysis to the 9-mers predicted to have a half time of dissociation of ≧5 minutes by the BIMAS-NIH/Parker algorithm leaves only 5. (See Table 15). The average density of epitopes in the protein is now only 0.042 per amino acid. Three overlapping peptides cover amino acids 31-48 of SEQ ID NO: 2 and the other two cover 56-69 of SEQ ID: 2, as before, giving ratios of 3.93 and 3.40, respectively. (See Table 16).

TABLE 15
BIMAS-NIH/Parker algorithm Results for Melan-A/MART-1
(SEQ ID NO: 2)
	Rank	Start	Score	Log(Score)
	1	40	1289.01	3.11
	2	56	1055.104	3.02
	3	31	81.385	1.91
	4	35	20.753	1.32
	5	61	4.968	0.70

[0187]

TABLE 16
Predicted Epitope Clusters for Melan-A/MART-1 (SEQ ID NO: 2)
	Calculations
	(Epitopes/AAs)
Cluster	AA	Peptides	Cluster	Whole protein	Ratio
1	31-48	3, 4, 1	0.17	0.042	3.93
2	56-69	2, 5	0.14	0.042	3.40

Example 11

SSX-2/HOM-MEL-40 (SEQ ID NO: 40)

[0188] This melanoma tumor-associated antigen (TuAA) is 188 amino acids in length. Of the 180 possible 9-mers, 11 are given a score ≧16 by the SYFPEITHI/Rammensee algorithm. These represent 6.1% of the possible peptides and an average epitope density on the protein of 0.059 amino acid. Three of these overlap, covering amino acids 99-114 of SEQ ID NO: 40 resulting in an epitope density for the cluster of 0.188, giving a ratio, as described above, of 3.18. There are also overlapping pairs of predicted epitopes at amino acids 16-28, 57-67, and 167-183 of SEQ ID NO: 40, giving ratios of 2.63, 3.11, and 2.01, respectively. There is an additional predicted epitope covering amino acids 5-28. Evaluating the region 5-28 SEQ ID NO: 40 containing three epitopes gives an epitope density of 0.125 and a ratio 2.14.

[0189] Restricting the analysis to the 9-mers predicted to have a half time of dissociation of ≧5 minutes by the BIMAS-NIH/Parker algorithm leaves only 6. The average density of epitopes in the protein is now only 0.032 per amino acid. Only a single pair overlap, at 167-180 of SEQ ID NO: 40, with a ratio of 4.48. However the top ranked peptide is close to another single predicted epitope if that region, amino acids 41-65 of SEQ ID NO: 40, is evaluated the ratio is 2.51, representing a substantial difference from the average. See FIG. 2.

TABLE 17
SYFPEITHI/Rammensee algorithm for SSX-2/HOM-MEL-40
(SEQ ID NO: 40)
Rank	Start	Score
1	103	23
2	167	22
3	41	22
4	16	21
5	99	20
6	59	19
7	20	17
8	5	17
9	175	16
10	106	16
11	57	16

[0190]

TABLE 18
Calculations(Epitopes/AAs) (SEQ ID NO: 40)
	Calculations
	(Epitopes/AAs)
Cluster	AA	Peptides	Cluster	Whole protein	Ratio
1	5 to 28	8, 4, 7	0.125	0.059	2.14
2	16-28	4, 7	0.15	0.059	2.63
3	57-67	11, 6	0.18	0.059	3.11
4	99-114	5, 1, 10	0.19	0.059	3.20
5	167-183	2, 9	0.12	0.059	2.01

[0191]

TABLE 19
BIMAS-NIH/Parker algorithm (SEQ ID NO: 40)
	Rank	Start	Score	Log(Score)
	1	41	1017.062	3.01
	2	167	21.672	1.34
	3	57	20.81	1.32
	4	103	10.433	1.02
	5	172	10.068	1.00
	6	16	6.442	0.81

[0192]

TABLE 20
Calculations(Epitopes/AAs) (SEQ ID NO: 40)
Cluster	AA	Peptides	Cluster	Whole protein	Ratio
1	41-65	1, 3	0.08	0.032	2.51
2	167-180	2, 5	0.14	0.032	4.48

Example 12

NY-ESO (SEQ ID NO: 11)

[0193] This tumor-associated antigen (TuAA) is 180 amino acids in length. Of the 172 possible 9-mers, 25 are given a score ≧16 by the SYFPEITHI/Rammensee algorithm. Like Melan-A above, these represent 14.5% of the possible peptides and an average epitope density on the protein of 0.136 per amino acid. However the distribution is quite different. Nearly half the protein is empty with just one predicted epitope in the first 78 amino acids. Unlike Melan-A where there was a very tight cluster of highly overlapping peptides, in NY-ESO the overlaps are smaller and extend over most of the rest of the protein. One set of 19 overlapping peptides covers amino acids 108-174 of SEQ ID NO: 11, resulting in a ratio of 2.04. Another 5 predicted epitopes cover 79-104 of SEQ ID NO: 11, for a ratio of just 1.38.

[0194] If instead one takes the approach of considering only the top 5% of predicted epitopes, in this case 9 peptides, one can examine whether good clusters are being obscured by peptides predicted to be less likely to bind to MHC. When just these predicted epitopes are considered we see that the region 108-140 of SEQ ID NO: 11 contains 6 overlapping peptides with a ratio of 3.64. There are also 2 nearby peptides in the region 148-167 of SEQ ID NO: 11 with a ratio of 2.00. Thus the large cluster 108-174 of SEQ ID NO: 11 can be broken into two smaller clusters covering much of the same sequence.

[0195] Restricting the analysis to the 9-mers predicted to have a half time of dissociation of ≧5 minutes by the BIMAS-NIH/Parker algorithm brings 14 peptides into consideration. The average density of epitopes in the protein is now 0.078 per amino acid. A single set of 10 overlapping peptides is observed, covering amino acids 144-171 of SEQ ID NO: 11, with a ratio of 4.59. All 14 peptides fall in the region 86-171 of SEQ ID NO: 11 which is still 2.09 times the average density of epitopes in the protein. While such a large cluster is larger than we consider ideal it still offers a significant advantage over working with the whole protein. See FIG. 3.

TABLE 21
SYFPEITHI (Rammensee algorithm) Results for NY-ESO
(SEQ ID NO: 11)
Rank	Start	Score
1	108	25
2	148	24
3	159	21
4	127	21
5	86	21
6	132	20
7	122	20
8	120	20
9	115	20
10	96	20
11	113	19
12	91	19
13	166	18
14	161	18
15	157	18
16	151	18
17	137	18
18	79	18
19	139	17
20	131	17
21	87	17
22	152	16
23	144	16
24	129	16
25	15	16

[0196]

TABLE 22
Calculations(Epitopes/AAs) (SEQ ID NO: 11)
Cluster	AA	Peptides	Cluster	Whole protein	Ratio
1	108-140	1, 9, 8, 7, 4, 6	0.18	0.05	3.64
2	148-167	2, 3	0.10	0.05	2.00
3	79-104	5 12, 10, 18, 21	0.19	0.14	1.38
4	108-174	1, 11, 9, 8, 7, 4,	0.28	0.14	2.04
		6, 17, 2, 16, 15,
		3, 14, 13, 24,
		20, 19, 23, 22

[0197]

TABLE 23
BIMAS-NIH/Parker algorithm Results for NY-ESO (SEQ ID NO: 11)
	Rank	Start	Score	Log(Score)
	1	159	1197.321	3.08
	2	86	429.578	2.63
	3	120	130.601	2.12
	4	161	83.584	1.92
	5	155	52.704	1.72
	6	154	49.509	1.69
	7	157	42.278	1.63
	8	108	21.362	1.33
	9	132	19.425	1.29
	10	145	13.624	1.13
	11	163	11.913	1.08
	12	144	11.426	1.06
	13	148	6.756	0.83
	14	152	4.968	0.70

[0198]

TABLE 24
Calculations(Epitopes/AAs) (SEQ ID NO: 11)
				Whole
Cluster	AA	Peptides	Cluster	protein	Ratio
1	86-171	2, 8, 3, 9, 10, 12, 13,	0.163	0.078	2.09
		14, 6, 5, 7, 1, 4, 11
2	144-171	10, 12, 13, 14, 6, 5,	0.36	0.078	4.59
		7, 1, 4, 11

Example 13

Tyrosinase (SEQ ID NO: 3)

[0199] This melanoma tumor-associated antigen (TuAA) is 529 amino acids in length. Of the 521 possible 9-mers, 52 are given a score ≧16 by the SYFPEITHI/Rammensee algorithm. These represent 10% of the possible peptides and an average epitope density on the protein of 0.098 per amino acid. There are 5 groups of overlapping peptides containing 2 to 13 predicted epitopes each, with ratios ranging from 2.03 to 4.41, respectively. There are an additional 7 groups of overlapping peptides, containing 2 to 4 predicted epitopes each, with ratios ranging from 1.20 to 1.85, respectively. The 17 peptides in the region 444-506 of SEQ ID NO: 3, including the 13 overlapping peptides above, constitutes a cluster with a ratio of 2.20.

[0200] Restricting the analysis to the 9-mers predicted to have a half time of dissociation of ≧5 minutes by the BIMAS-NIH/Parker algorithm brings 28 peptides into consideration. The average density of epitopes in the protein under this condition is 0.053 per amino acid. At this density any overlap represents more than twice the average density of epitopes. There are 5 groups of overlapping peptides containing 2 to 7 predicted epitopes each, with ratios ranging from 2.22 to 4.9, respectively. Only three of these clusters are common to the two algorithms. Several, but not all, of these clusters could be enlarged by evaluating a region containing them and nearby predicted epitopes.

TABLE 25
SYFPEITHI/Rammensee algorithm Results
for Tyrosinase (SEQ ID NO: 3)
Rank	Start	Score
1	490	34
2	491	31
3	487	28
4	1	27
5	2	25
6	482	23
7	380	23
8	369	23
9	214	23
10	506	22
11	343	22
12	207	22
13	137	22
14	57	22
15	169	20
16	118	20
17	9	20
18	488	19
19	483	19
20	480	19
21	479	19
22	478	19
23	473	19
24	365	19
25	287	19
26	200	19
27	5	19
28	484	18
29	476	18
30	463	18
31	444	18
32	425	18
33	316	18
34	187	18
35	402	17
36	388	17
37	346	17
38	336	17
39	225	17
40	224	17
41	208	17
42	186	17
43	171	17
44	514	16
45	494	16
46	406	16
47	385	16
48	349	16
49	184	16
50	167	16
51	145	16
52	139	16

[0201]

TABLE 26
Calculations(Epitopes/AAs) (SEQ ID NO: 3)
				Whole
Cluster	AA	Peptides	Cluster	protein	Ratio
1	1 to 17	4, 5, 27, 17	0.24	0.098	2.39
2	137-153	13, 52, 51	0.18	0.098	1.80
3	167-179	15, 43, 50	0.23	0.098	2.35
4	184-195	34, 42, 49	0.25	0.098	2.54
5	200-222	26, 41, 9, 12	0.17	0.098	1.77
6	224-233	39, 40	0.20	0.098	2.03
7	336-357	38, 11, 37, 48	0.18	0.098	1.85
8	365-377	24, 8	0.15	0.098	1.57
9	380-396	7, 47, 36	0.18	0.098	1.80
10	402-414	35, 46	0.15	0.098	1.57
11	473-502	29, 28, 23, 22, 21,	0.43	0.098	4.41
		20, 6, 19, 3, 18, 1, 2, 45
12	506-522	10, 44	0.12	0.098	1.20
	444-522	31, 30, 23, 29, 22,	0.22	0.098	2.20
		21, 20, 6, 19, 28, 3, 18,
		1, 2, 45, 10, 44

[0202]

TABLE 27
BIMAS-NIH/Parker algorithm Results (SEQ ID NO: 3)
	Rank	Start	Score	Log(Score)
	1	207	540.469	2.73
	2	369	531.455	2.73
	3	1	309.05	2.49
	4	9	266.374	2.43
	5	490	181.794	2.26
	6	214	177.566	2.25
	7	224	143.451	2.16
	8	171	93.656	1.97
	9	506	87.586	1.94
	10	487	83.527	1.92
	11	491	83.527	1.92
	12	2	54.474	1.74
	13	137	47.991	1.68
	14	200	30.777	1.49
	15	208	26.248	1.42
	16	460	21.919	1.34
	17	478	19.425	1.29
	18	365	17.14	1.23
	19	380	16.228	1.21
	20	444	13.218	1.12
	21	473	13.04	1.12
	22	57	10.868	1.04
	23	482	8.252	0.92
	24	483	7.309	0.86
	25	5	6.993	0.84
	26	225	5.858	0.77
	27	343	5.195	0.72
	28	514	5.179	0.71

[0203]

TABLE 28
Calculations(Epitopes/AAs) (SEQ ID NO: 3)
				Whole
Cluster	AA	Peptides	Cluster	protein	Ratio
1	1 to 17	3, 12, 25, 4	0.24	0.053	4.45
2	200-222	14, 1, 15, 6	0.17	0.053	3.29
3	224-233	7, 26	0.20	0.053	3.78
4	365-377	18, 2	0.15	0.053	2.91
5	473-499	21, 17, 23, 24, 10, 5,	0.26	0.053	4.90
		11
6	506-522	9, 28	0.12	0.053	2.22
7	365-388	18, 2, 19	0.13	0.053	2.36
8	444-499	20, 16, 21, 17, 23,	0.16	0.053	3.03
		24, 10, 5, 11
9	444-522	20, 16, 21, 17, 23, 24,	0.14	0.053	2.63
		10, 5, 11, 9, 28
10	200-233	14, 1, 15, 6, 7, 26	0.18	0.053	3.33

[0204] All references mentioned herein are hereby incorporated by reference in their entirety. Further, the present invention can utilize various aspects of the following, which are all incorporated by reference in their entirety: U.S. patent application Ser. No. 09/380,534, filed on Sep. 1, 1999, entitled A METHOD OF INDUCING A CTL RESPONSE; Ser. No. 09/776,232, filed on Feb. 2, 2001, entitled METHOD OF INDUCING A CTL RESPONSE; Ser. No. 09/715,835, filed on Nov. 16, 2000, entitled AVOIDANCE OF UNDESIRABLE REPLICATION INTERMEDIATES IN PLASMID PROPAGATION; Ser. No. 09/999,186, filed on Nov. 7, 2001, entitled METHODS OF COMMERCIALIZING AN ANTIGEN; and Provisional U.S. Patent Application No. 60/274,063, filed on Mar. 7, 2001, entitled ANTI-NEOVASCULAR VACClNES FOR CANCER.

TABLE 29
Partial listing of SEQ ID NOS.
1	ELAGIGILTV	melan-A 26-35 (A27L)
2	Melan-A protein	Accession number:
		NP_005502
3	Tyrosinase protein	Accession number:
		P14679
4	MLLAVLYCLELAGIGILTVYM	pMA2M expression
	DGTMSQVGILTVILGVLLLIGC	product
	WYCRRRNGYRALMDKSLHVG
	TQCALTRRCPQEGFDHRDSKV
	SLQEKNCEPV
5	MLLAVLYCLELAGIGILTVYM	Liberation or substrate
	DGTMSQV	sequence for SEQ ID
		NO. 1
		from pMA2M
6	MLLAVLYCL	tyrosinase 1-9
7	YMDGTMSQV	tyrosinase 369-377
8	EAAGIGILTV	melan-A 26-35
9	cttaagccaccatgttactagctgttttgtactgcctggaac	pMA2M insert
	tagcagggatcggcatattgacagtgtatatgga
	tggaacaatgtcccaggtaggaattctgacagtgatcctggg
	agtcttactgctcatcggctgttggtattgtaga
	agacgaaatggatacagagccttgatggataaaagtcttcat
	gttggcactcaatgtgccttaacaagaagatgcc
	cacaagaagggtttgatcatcgggacagcaaagtgtctcttc
	aagagaaaaactgtgaacctgtgtagtgagcggc
	cgc
10	MVLYCLELAGIGILTVYMDGT	Epitope array from
	AVLYCLELAGIGILTVYMDGT	pVAXM2 and
	MLAVLYCLELAGIGILTVYMD	pVAXM1
	GTMSLLAVLYCLELAGIGILTV
11	NY-ESO-1 protein	Accession number:
		P78358
12	SLLMWITQC	NY-ESO-1 157-165
13	KASEKIFYV	SSX-2 41-49
14	TQCFLPVFL	NY-ESO-1 163-171
15	GLPSIPVHPI	PSMA 288-297
16	AVLYCL	tyrosinase 4-9
17	MSLLMWITQCKASEKIFYVRCGARGPES	pN157 expression
	RLLEFYLAMPFATPMEAELARRSLAQDA	product
	PPLPVPGVLLKEFTVSGNILTIRLTAADHR
	QLQLSISSCLQQLSLLMWITQCFLPVFLAQ
	PPSGQRR
18	MSLLMWITQCKASEKIFYV	liberation or substrate
		sequence for SEQ ID
		NO. 12 from pN157
19	cttaagccaccatgtccctgttgatgtggatcacgcagtgca	Insert for pN157
	aagcttcggagaaaatcttctacgtacggtgcgg
	tgccagagggccggagagccgcctgcttgagttctacctcgc
	catgcctttcgcgacacccatggaagcagagctg
	gcccgcaggagcctggcccaggatgccccaccgcttcccgtg
	ccaggggtgcttctgaaggagttcactgtgtccg
	gcaacatactgactatccgactgactgctgcagaccaccgcc
	aactgcagctctccatcagctcctgtctccagca
	gctttccctgttgatgtggatcacgcagtgctttctgcccgt
	gtttttggctcagcctccctcagggcagaggcgc
	tagtgagaattc
20	MSLLMWITQCKASEKIFYVGLPSIPVHPIG	pBPL expression
	LPSIPVHPIKASEKIFYVSLLMWITQCKAS	product
	EKIFYVKASEKIFYVRCGARGPESRLLEFY
	LAMPFATPMEAELARRSLAQDAPPLPVP
	GVLLKEFTVSGNILTIRLTAADHRQLQLSI
	SSCLQQLSLLMWITQCFLPVFLAQPPSGQ
	RR
21	atgtccctgttgatgtggatcacgcagtgcaaagcttcggag	pBPL insert coding
	aaaatcttctatgtgggtcttccaagtattcctg	region
	ttcatccaattggtcttccaagtattcctgttcatccaatta
	aagcttcggagaaaatcttctatgtgtccctgtt
	gatgtggatcacgcagtgcaaagcttcggagaaaatcttcta
	tgtgaaagcttcggagaaaatcttctacgtacgg
	tgcggtgccagggggccggagagccgcctgcttgagttctac
	ctcgccatgcctttcgcgacacccatggaagcag
	agctggcccgcaggagcctggcccaggatgccccaccgcttc
	ccgtgccaggggtgcttctgaaggagttcactgt
	gtccggcaacatactgactatccgactgactgctgcagacca
	ccgccaactgcagctctccatcagctcctgtctc
	cagcagctttccctgttgatgtggatcacgcagtgctttctg
	cccgtgtttttggctcagcctccctcagggcaga
	ggcgctagtga
22	IKASEKIFYVSLLMWITQCKASEKIFYVK	Substrate in FIG. 9
23	VMTKLGFKV	SSX-457-65
24	RQIYVAAFTV	PSMA730-739
25	AQIPEKIQKAFDDIAKYFSKEEWEKMKAS	SSX-215-183
	EKIFYVYMKRKYEAMTKLGFKATLPPFM
	CNKRAEDFQGNDLDNDPNRGNQVERPQ
	MTFGRLQGISPKIMIPKKPAEEGNDSEEVP
	EASGPQNDGKELCPPGKPTTSEKIHERSG
	PKRGEHAWTHRLRERKQLVIYEEISDP
26	MVMTKLGFKVKASEKIFYVRQIYVAAFT	CTLS1/pCBP
	V	expression product
	GLPSIPVHIPITQCFLPVFLVMTKLGFKVRQ
	IYVAAFTVKASEKIFYVAQIPEKIQKAFDD
	IAKYFSKEEWEKMKASEKIFYVYMKRKY
	EAMTKLGFKATLPPFMCNKRAEDFQGND
	LDNDPNRGNQVERPQMTFGRLQGISPKI
	MPKKPAEEGNDSEEVPEASGPQNDGKEL
	CPPGKPTTSEKIHERSGPKRGEHAWTHRL
	RERKQLVIYEEISDP
27	MAQIPEKIQKAFDDIAKYFSKEEWEKMK	CTLS2 expression
	ASEKIFYVYMKRKYEAMTKLGFKATLPP	product
	FMCNKRAEDFQGNDLDNDPNRGNQVER
	PQMTFGRLQGISPKIMPKKPAEEGNDSEE
	VPEASGPQNDGKELCPPGKPTTSEKIHER
	SGPKRGEHAWTHRLRERKQLVIYEEISDP
	VMTKLGFKVKASEKIFYVRQIYVAAFTV
	GLPSIPVHPITQCFLPVFLVMTKLGFKVRQ
	IYVAAFTVKASEKIFYV
28	MVMTKLGFKVKASEKIFYVRQIYVAAFT	CTLS3 expression
	V	product
	GLPSIPVHIAQIPEKIQKAFDDIAKYFSKE
	EWEKMKASEKIFYVYMKRKYEAMTKLG
	FKATLPPFMCNKRAEDFQGNDLDNDPNR
	GNQVERPQMTFGRLQGISPKIMPKKPAEE
	GNDSEEVPEASGPQNDGKELCPPGKPTTS
	EKIHERSGPKRGEHAWTHRLRERKQLVIY
	EEISDP
29	MAQIPEKIQKAFDDIAKYFSKEEWEKMK	CTLS4 expression
	ASEKIFYVYMKRKYEAMTKLGFKATLPP	product
	FMCNKRAEDFQGNDLDNDPNRGNQVER
	PQMTFGRLQGISPKIMPKKPAEEGNDSEE
	VPEASGPQNDGKELCPPGKPTTSEKIHER
	SGPKRGEHAWTHRLRERKQLVIYEEISDP
	TQCFLPVFLVMTKLGFKVRQIYVAAFTV
	KASEKIFYV
30	atggtcatgactaaactaggtttcaaggtcaaagcttcggag	pCBP insert coding
	aaaatcttctatgtgagacagatttatgttgcag	region
	ccttcacagtgggtcttccaagtattcctgttcatccaatta
	cgcagtgctttctgcccgtgtttttggtcatgac
	taaactaggtttcaaggtcagacagatttatgttgcagcctt
	cacagtgaaagcttcggagaaaatcttctacgta
	gctcaaataccagagaagatccaaaaggccttcgatgatatt
	gccaaatacttctctaaggaagagtgggaaaaga
	tgaaagcctcggagaaaatcttctatgtgtatatgaagagaa
	agtatgaggctatgactaaactaggtttcaaggc
	caccctcccacctttcatgtgtaataaacgggccgaagactt
	ccaggggaatgatttggataatgaccctaaccgt
	gggaatcaggttgaacgtcctcagatgactttcggcaggctc
	cagggaatctccccgaagatcatgcccaagaagc
	cagcagaggaaggaaatgattcggaggaagtgccagaagcat
	ctggcccacaaaatgatgggaaagagctgtgccc
	cccgggaaaaccaactacctctgagaagattcacgagagatc
	tggacccaaaaggggggaacatgcctggacccac
	agactgcgtgagagaaaacagctggtgatttatgaagagatc
	agcgacccttagtga
31	RQIYVAAFTVKASEKIFYVAQIPEKIQK	FIG. 11 substrate/
		CTLS1-2
32	FLPWHRLFL	TYR207-215
33	MLLAVLYCLLWSFQTSAFLPWHRLFLML	CTLT2/pMEL
	LAVLYCLLWSFQTSAFLPWHRLFLMLLA	expression product
	VLYCLLWSFQTSAFLPWHRLFLMLLAVL
	YCLLWSFQTSAFLPWHRLFL
34	atgctcctggctgttttgtactgcctgctgtggagtttccag	CTLT2/pMEL insert
	acctccgcttttctgccttggcatagactcttct	coding region
	tgatgctcctggctgttttgtactgcctgctgtggagtttcc
	agacctccgcttttctgccttggcatagactctt
	cttgatgctcctggctgttttgtactgcctgctgtggagttt
	ccagacctccgcttttctgccttggcatagactc
	ttcttgatgctcctggctgttttgtactgcctgctgtggagt
	ttccagacctccgcttttctgccttggcatagac
	tcttcttgtagtga
35	MELAN-A cDNA	Accession number:
		NM_005511
36	Tyrosinase cDNA	Accession number:
		NM_000372
37	NY-ESO-1 cDNA	Accession number:
		U87459
38	PSMA protein	Accession number:
		NP_004467
39	PSMA cDNA	Accession number:
		NM_004476
40	SSX-2 protein	Accession number:
		NP_003138
41	SSX-2 cDNA	Accession number:
		NM_003147
42	atgacctctcgccgctccgtgaagtcgggtccgcgggaggttcc	From accession number:
	gcgcgatgagtacgaggatctgtactacaccccgtcttcaggtat	D10879
	ggcgagtcccgatagtccgcctgacacctcccgccgtggcgcc	Herpes Simplex virus 1
	ctacagacacgctcgcgccagaggggcgaggtccgtttcgtcca	UL49 coding sequence
	gtacgacgagtcggattatgccctctacgggggctcgtcatccga	(VP22)
	agacgacgaacacccggaggtcccccggacgcggcgtcccgt
	ttccggggcggttttgtccggcccggggcctgcgcgggcgcctc
	cgccacccgctgggtccggaggggccggacgcacacccacca
	ccgccccccgggccccccgaacccagcgggtggcgactaagg
	cccccgcggccccggcggcggagaccacccgcggcaggaaa
	tcggcccagccagaatccgccgcactcccagacgcccccgcgt
	cgacggcgccaacccgatccaagacacccgcgcaggggctgg
	ccagaaagctgcactttagcaccgcccccccaaaccccgacgc
	gccatggaccccccgggtggccggctttaacaagcgcgtcttct
	gcgccgcggtcgggcgcctggcggccatgcatgcccggatgg
	cggcggtccagctctgggacatgtcgcgtccgcgcacagacga
	agacctcaacgaactccttggcatcaccaccatccgcgtgacgg
	tctgcgagggcaaaaacctgcttcagcgcgccaacgagttggtg
	aatccagacgtggtgcaggacgtcgacgcggccacggcgactc
	gagggcgttctgcggcgtcgcgccccaccgagcgacctcgagc
	cccagcccgctccgcttctcgccccagacggcccgtcgag
43	MTSRRSVKSGPREVPRDEYEDLYYTPSSG	Accession number:
	MASPDSPPDTSRRGALFTQTRSRQRGEVR	P10233
	FVQYDESDYALYGGSSSEDDEHPEVPRT	Herpes Simplex virus 1
	RRPVSGAVLSGPGPARAPPPFTPAGSGGA	UL49/VP22 protein
	GRTPTTAPRAPRTQRVATKAPAAPAAET	sequence
	TRGRKSAQPESAALPDAPASTAPTFTRSK
	TPAQGLARKLHFSTAPPNPDAPWTPRVA
	GFNKRVFCAAVGRLAAMHARMAAVQL
	WDFTMSRPRTDEDLNELLGITTIRVTVCE
	GKNLLQRANELVNPDVVQDVDAATATR
	GRSAASRFTPTERPRAPARSASRPRRPVE

[0205] Melan-A mRNA Sequence

[0206] LOCUS NM—005511 1524 bp mRNA PRI 14-OCT-2001

[0207] DEFINITION Homo sapiens melan-A (MLANA), mRNA.

[0208] ACCESSION NM—005511

[0209] VERSION NM—005511.1 GI:5031912

	/translation = “MPREDAHFIYGYPKKGHGHSYTTAEEAAGIGILTVILGVLLLIGCWYCR	(SEQ ID NO. 2)
	RRNGYRALMDKSLHVGTQCALTRRCPQEGFDHRDSKVSLQEKNCEPVVPNAPPAYE
	KLSAEQSPPPYSP”
ORIGIN
1	agcagacaga ggactctcat taaggaaggt gtcctgtgcc ctgaccctac aagatgccaa	(SEQ ID NO. 35)
61	gagaagatgc tcacttcatc tatggttacc ccaagaaggg gcacggccac tcttacacca
121	cggctgaaga ggccgctggg atcggcatcc tgacagtgat cctgggagtc ttactgctca
181	tcggctgttg gtattgtaga agacgaaatg gatacagagc cttgatggat aaaagtcttc
241	atgttggcac tcaatgtgcc ttaacaagaa gatgcccaca agaagggttt gatcatcggg
301	acagcaaagt gtctcttcaa gagaaaaact gtgaacctgt ggttcccaat gctccacctg
361	cttatgagaa actctctgca gaacagtcac caccacctta ttcaccttaa gagccagcga
421	gacacctgag acatgctgaa attatttctc tcacactttt gcttgaattt aatacagaca
481	tctaatgttc tcctttggaa tggtgtagga aaaatgcaag ccatctctaa taataagtca
541	gtgttaaaat tttagtaggt ccgctagcag tactaatcat gtgaggaaat gatgagaaat
601	attaaattgg gaaaactcca tcaataaatg ttgcaatgca tgatactatc tgtgccagag
661	gtaatgttag taaatccatg gtgttatttt ctgagagaca gaattcaagt gggtattctg
721	gggccatcca atttctcttt acttgaaatt tggctaataa caaactagtc aggttttcga
781	accttgaccg acatgaactg tacacagaat tgttccagta ctatggagtg ctcacaaagg
841	atacttttac aggttaagac aaagggttga ctggcctatt tatctgatca agaacatgtc
901	agcaatgtct ctttgtgctc taaaattcta ttatactaca ataatatatt gtaaagatcc
961	tatagctctt tttttttgag atggagtttc gcttttgttg cccaggctgg agtgcaatgg
1021	cgcgatcttg gctcaccata acctccgcct cccaggttca agcaattctc ctgccttagc
1081	ctcctgagta gctgggatta caggcgtgcg ccactatgcc tgactaattt tgtagtttta
1141	gtagagacgg ggtttctcca tgttggtcag gctggtctca aactcctgac ctcaggtgat
1201	ctgcccgcct cagcctccca aagtgctgga attacaggcg tgagccacca cgcctggctg
1261	gatcctatat cttaggtaag acatataacg cagtctaatt acatttcact tcaaggctca
1321	atgctattct aactaatgac aagtattttc tactaaacca gaaattggta gaaggattta
1381	aataagtaaa agctactatg tactgcctta gtgctgatgc ctgtgtactg ccttaaatgt
1441	acctatggca atttagctct cttgggttcc caaatccctc tcacaagaat gtgcagaaga
1501	aatcataaag gatcagagat tctg

[0210] Tyrosinase mRNA Sequence

[0211] LOCUS NM—000372 1964 bp mRNA PR1 31-OCT-2000

[0212] DEFINITION Homo sapiens tyrosinase (oculocutaneous albinism IA) (TYR), mRNA.

[0213] ACCESSION NM—000372

[0214] VERSION NM—000372.1 GI:4507752

	/translation = “MLLAVLYCLLWSFQTSAGHFPRACVSSKNLMEKECCPPWSGDRS	(SEQ ID NO. 3)
	PCGQLSGRGSCQNILLSNAPLGPQFPFTGVDDRESWPSVFYNRTCQCSGNFMGFNCG
	NCKFGFWGPNCTERRLLVRRNIFDLSAPEKDKFFAYLTLAKHTISSDYVIPIGTYGQM
	KNGSTPMFNDINIYDLFVWMHYYVSMDALLGGSEIWRDIDFAHEAPAFLPWHRLFLL
	RWEQEIQKLTGDENFTIPYWDWRDAEKCDICTDEYMGGQHPTNPNLLSPASFFSSW
	QIVCSRLEEYNSHQSLCNGTPEGPLRRNPGNHDKSRTPRLPSSADVEFCLSLTQYESG
	SMDKAANFSFRNTLEGFASPLTGIADASQSSMHNALHIYMNGTMSQVQGSANDPIFL
	LHHAFVDSIFEQWLRRHRPLQEVYPEANAPIGHNRESYMVPFIPLYRNGDFFISSKDL
	GYDYSYLQDSDPDSFQDYIKSYLEQASRIWSWLLGAAMVGAVLTALLAGLVSLLCR
	HKRKQLP EEKQPLLMEKEDYHSLYQSHL”
ORIGIN
1	atcactgtag tagtagctgg aaagagaaat ctgtgactcc aattagccag ttcctgcaga	(SEQ ID NO. 36)
61	ccttgtgagg actagaggaa gaatgctcct ggctgttttg tactgcctgc tgtggagttt
121	ccagacctcc gctggccatt tccctagagc ctgtgtctcc tctaagaacc tgatggagaa
181	ggaatgctgt ccaccgtgga gcggggacag gagtccctgt ggccagcttt caggcagagg
241	ttcctgtcag aatatccttc tgtccaatgc accacttggg cctcaatttc ccttcacagg
301	ggtggatgac cgggagtcgt ggccttccgt cttttataat aggacctgcc agtgctctgg
361	caacttcatg ggattcaact gtggaaactg caagtttggc ttttggggac caaactgcac
421	agagagacga ctcttggtga gaagaaacat cttcgatttg agtgccccag agaaggacaa
481	attttttgcc tacctcactt tagcaaagca taccatcagc tcagactatg tcatccccat
541	agggacctat ggccaaatga aaaatggatc aacacccatg tttaacgaca tcaatattta
601	tgacctcttt gtctggatgc attattatgt gtcaatggat gcactgcttg ggggatctga
661	aatctggaga gacattgatt ttgcccatga agcaccagct tttctgcctt ggcatagact
721	cttcttgttg cggtgggaac aagaaatcca gaagctgaca ggagatgaaa acttcactat
781	tccatattgg gactggcggg atgcagaaaa gtgtgacatt tgcacagatg agtacatggg
841	aggtcagcac cccacaaatc ctaacttact cagcccagca tcattcttct cctcttggca
901	gattgtctgt agccgattgg aggagtacaa cagccatcag tctttatgca atggaacgcc
961	cgagggacct ttacggcgta atcctggaaa ccatgacaaa tccagaaccc caaggctccc
1021	ctcttcagct gatgtagaat tttgcctgag tttgacccaa tatgaatctg gttccatgga
1081	taaagctgcc aatttcagct ttagaaatac actggaagga tttgctagtc cacttactgg
1141	gatagcggat gcctctcaaa gcagcatgca caatgccttg cacatctata tgaatggaac
1201	aatgtcccag gtacagggat ctgccaacga tcctatcttc cttcttcacc atgcatttgt
1261	tgacagtatt tttgagcagt ggctccgaag gcaccgtcct cttcaagaag tttatccaga
1321	agccaatgca cccattggac ataaccggga atcctacatg gttcctttta taccactgta
1381	cagaaatggt gatttcttta tttcatccaa agatctgggc tatgactata gctatctaca
1441	agattcagac ccagactctt ttcaagacta cattaagtcc tatttggaac aagcgagtcg
1501	gatctggtca tggctccttg gggcggcgat ggtaggggcc gtcctcactg ccctgctggc
1561	agggcttgtg agcttgctgt gtcgtcacaa gagaaagcag cttcctgaag aaaagcagcc
1621	actcctcatg gagaaagagg attaccacag cttgtatcag agccatttat aaaaggctta
1681	ggcaatagag tagggccaaa aagcctgacc tcactctaac tcaaagtaat gtccaggttc
1741	ccagagaata tctgctggta tttttctgta aagaccattt gcaaaattgt aacctaatac
1801	aaagtgtagc cttcttccaa ctcaggtaga acacacctgt ctttgtcttg ctgttttcac
1861	tcagcccttt taacattttc ccctaagccc atatgtctaa ggaaaggatg ctatttggta
1921	atgaggaact gttatttgta tgtgaattaa agtgctctta tttt

[0215] NY-ESO-1 mRNA Sequence

[0216] LOCUS HSU87459 752 bp mRNA PR1 22-DEC-1999

[0217] DEFINITION Human autoimmunogenic cancer/testis antigen NY-ESO-1 mRNA, complete cds.

[0218] ACCESSION U87459

[0219] VERSION U87459.1 GI:1890098

	/translation = “MQAEGRGTGGSTGDADGPGGPGIPDGPGGNAGGPGEAGATGGRGPRG	(SEQ ID NO. 11)
	AGAARASGPGGGAPRGPHGGAASGLNGCCRCGARGPESRLLEFYLAMPFATPMEAE
	LARRSLAQDAPPLPVPGVLLKEFTVSGNILTIRLTAADHRQLQLSISSCLQQLSLLM
	WITQCFLPVFLAQPPSGQRR”
ORIGIN
1	atcctcgtgg gccctgacct tctctctgag agccgggcag aggctccgga gccatgcagg	(SEQ ID NO. 37)
61	ccgaaggccg gggcacaggg ggttcgacgg gcgatgctga tggcccagga ggccctggca
121	ttcctgatgg cccagggggc aatgctggcg gcccaggaga ggcgggtgcc acgggcggca
181	gaggtccccg gggcgcaggg gcagcaaggg cctcggggcc gggaggaggc gccccgcggg
241	gtccgcatgg cggcgcggct tcagggctga atggatgctg cagatgcggg gccagggggc
301	cggagagccg cctgcttgag ttctacctcg ccatgccttt cgcgacaccc atggaagcag
361	agctggcccg caggagcctg gcccaggatg ccccaccgct tcccgtgcca ggggtgcttc
421	tgaaggagtt cactgtgtcc ggcaacatac tgactatccg actgactgct gcagaccacc
481	gccaactgca gctctccatc agctcctgtc tccagcagct ttccctgttg atgtggatca
541	cgcagtgctt tctgcccgtg tttttggctc agcctccctc agggcagagg cgctaagccc
601	agcctggcgc cccttcctag gtcatgcctc ctcccctagg gaatggtccc agcacgagtg
661	gccagttcat tgtgggggcc tgattgtttg tcgctggagg aggacggctt acatgtttgt
721	ttctgtagaa aataaaactg agctacgaaa aa

[0220] PSMA cDNA Sequence

[0221] LOCUS NM—004476 2653 bp mRNA PRI 01-NOV-2000

[0222] DEFINITION Homo sapiens folate hydrolase (prostate-specific membrane antigen) 1 (FOLH1), mRNA.

[0223] ACCESSION NM—004476

[0224] VERSION NM—004476.1 GI:4758397

	/translation = “MWNLLHETDSAVATARRPRWLCAGALVLAGGFFLLGFLFGWFIKSSNE	(SEQ ID NO. 38)
	ATNITPKHNMKAFLDELKAENIKKFLYNFTQIPHLAGTEQNFQLAKQIQSQWKEFGL
	DSVELAHYDVLLSYPNKTHPNYISIINEDGNEIFNTSLFEPPPPGYENVSDIVPPFSAFSP
	QGMPEGDLVYVNYARTEDFFKLERDMKINCSGKIVIARYGKVFRGNKVKNAQLAG
	AKGVILYSDPADYFAPGVKSYPDGWNLPGGGVQRGNILNLNGAGDPLTPGYPANEY
	AYRRGIAEAVGLPSIPVHPIGYYDAQKLLEKMGGSAPPDSSWRGSLKVPYNVGPGFT
	GNFSTQKVKMHIHSTNEVTRIYNVIGTLRGAVEPDRYVILGGHRDSWVFGGIDPQSG
	AAVVHEIVRSFGTLKKEGWRPRRTILFASWDAEEFGLLGSTEWAEENSRLLQERGVA
	YINADSSIEGNYTLRVDCTPLMYSLVHNLTKELKSPDEGFEGKSLYESWTKKSPSPEF
	SGMPRISKLGSGNDFEVFFQRLGIASGRARYTKNWETNKFSGYPLYHSVYETYELVE
	KFYDPMFKYHLTVAQVRGGMVFELANSIVLPFDCRDYAVVLRKYADKIYSISMKHP
	QEMKTYSVSFDSLFSAVKNFTEIASKFSERLQDFDKSNPIVLRMMNDQLMFLERAFID
	PLGLPDRPFYRHVIYAPSSHNKYAGESFPGIYDALFDIESKVDPSKAWGEVKRQIYVA
	AFTVQAAAETLSEVA”
ORIGIN
1	ctcaaaaggg gccggatttc cttctcctgg aggcagatgt tgcctctctc tctcgctcgg	(SEQ ID NO. 39)
61	attggttcag tgcactctag aaacactgct gtggtggaga aactggaccc caggtctgga
121	gcgaattcca gcctgcaggg ctgataagcg aggcattagt gagattgaga gagactttac
181	cccgccgtgg tggttggagg gcgcgcagta gagcagcagc acaggcgcgg gtcccgggag
241	gccggctctg ctcgcgccga gatgtggaat ctccttcacg aaaccgactc ggctgtggcc
301	accgcgcgcc gcccgcgctg gctgtgcgct ggggcgctgg tgctggcggg tggcttcttt
361	ctcctcggct tcctcttcgg gtggtttata aaatcctcca atgaagctac taacattact
421	ccaaagcata atatgaaagc atttttggat gaattgaaag ctgagaacat caagaagttc
481	ttatataatt ttacacagat accacattta gcaggaacag aacaaaactt tcagcttgca
541	aagcaaattc aatcccagtg gaaagaattt ggcctggatt ctgttgagct agcacattat
601	gatgtcctgt tgtcctaccc aaataagact catcccaact acatctcaat aattaatgaa
661	gatggaaatg agattttcaa cacatcatta tttgaaccac ctcctccagg atatgaaaat
721	gtttcggata ttgtaccacc tttcagtgct ttctctcctc aaggaatgcc agagggcgat
781	ctagtgtatg ttaactatgc acgaactgaa gacttcttta aattggaacg ggacatgaaa
841	atcaattgct ctgggaaaat tgtaattgcc agatatggga aagttttcag aggaaataag
901	gttaaaaatg cccagctggc aggggccaaa ggagtcattc tctactccga ccctgctgac
961	tactttgctc ctggggtgaa gtcctatcca gatggttgga atcttcctgg aggtggtgtc
1021	cagcgtggaa atatcctaaa tctgaatggt gcaggagacc ctctcacacc aggttaccca
1081	gcaaatgaat atgcttatag gcgtggaatt gcagaggctg ttggtcttcc aagtattcct
1141	gttcatccaa ttggatacta tgatgcacag aagctcctag aaaaaatggg tggctcagca
1201	ccaccagata gcagctggag aggaagtctc aaagtgccct acaatgttgg acctggcttt
1261	actggaaact tttctacaca aaaagtcaag atgcacatcc actctaccaa tgaagtgaca
1321	agaatttaca atgtgatagg tactctcaga ggagcagtgg aaccagacag atatgtcatt
1381	ctgggaggtc accgggactc atgggtgttt ggtggtattg accctcagag tggagcagct
1441	gttgttcatg aaattgtgag gagctttgga acactgaaaa aggaagggtg gagacctaga
1501	agaacaattt tgtttgcaag ctgggatgca gaagaatttg gtcttcttgg ttctactgag
1561	tgggcagagg agaattcaag actccttcaa gagcgtggcg tggcttatat taatgctgac
1621	tcatetatag aaggaaacta cactctgaga gttgattgta caccgctgat gtacagcttg
1681	gtacacaacc taacaaaaga gctgaaaagc cctgatgaag gctttgaagg caaatctctt
1741	tatgaaagtt ggactaaaaa aagtccttcc ccagagttca gtggcatgcc caggataagc
1801	aaattgggat ctggaaatga ttttgaggtg ttcttccaac gacttggaat tgcttcaggc
1861	agagcacggt atactaaaaa ttgggaaaca aacaaattca gcggctatcc actgtatcac
1921	agtgtctatg aaacatatga gttggtggaa aagttttatg atccaatgtt taaatatcac
1981	ctcactgtgg cccaggttcg aggagggatg gtgtttgagc tagccaattc catagtgctc
2041	ccttttgatt gtcgagatta tgctgtagtt ttaagaaagt atgctgacaa aatctacagt
2101	atttctatga aacatccaca ggaaatgaag acatacagtg tatcatttga ttcacttttt
2161	tctgcagtaa agaattttac agaaattgct tccaagttca gtgagagact ccaggacttt
2221	gacaaaagca acccaatagt attaagaatg atgaatgatc aactcatgtt tctggaaaga
2281	gcatttattg atccattagg gttaccagac aggccttttt ataggcatgt catctatgct
2341	ccaagcagcc acaacaagta tgcaggggag tcattcccag gaatttatga tgctctgttt
2401	gatattgaaa gcaaagtgga cccttccaag gcctggggag aagtgaagag acagatttat
2461	gttgcagcct tcacagtgca ggcagctgca gagactttga gtgaagtagc ctaagaggat
2521	tctttagaga atccgtattg aatttgtgtg gtatgtcact cagaaagaat cgtaatgggt
2581	atattgataa attttaaaat tggtatattt gaaataaagt tgaatattat atataaaaaa
2641	aaaaaaaaaa aaa

[0225] NM 003147Homo sapiens synovial sarcoma, X breakpoint 2 (SSX2), mRNA

[0226] LOCUS NM—003147 766 bp mRNA PR1 14-MAR-2001

[0227] DEFINITION Homo sapiens synovial sarcoma, X breakpoint 2 (SSX2), mRNA.

[0228] ACCESSION NM—003147

[0229] VERSION NM—003147.1 GI:10337582

	/translation = “MNGDDAFARRPTVGAQIPEKIQKAFDDIAKYFSKEEWEKMKASE	SEQ ID NO. 40
	KIFYVYMKRKYEAMTKLGFKATLPPFMCNKRAEDFQGNDLDNDPNRGNQVERPQMTFG
	RLQGISPKIMPKKPAEEGNDSEEVPEASGPQNDGKELCPPGKPTTSEKIHERSGPKRG
	EHAWTHRLRERKQLVIYEEISDPEEDDE”
1	ctctctttcg attcttccat actcagagta cgcacggtct gattttctct ttggattctt	SEQ ID NO 41
61	ccaaaatcag agtcagactg ctcccggtgc catgaacgga gacgacgcct ttgcaaggag
121	acccacggtt ggtgctcaaa taccagagaa gatccaaaag gccttcgatg atattgccaa
181	atacttctct aaggaagagt gggaaaagat gaaagcctcg gagaaaatct tctatgtgta
241	tatgaagaga aagtatgagg ctatgactaa actaggtttc aaggccaccc tcccaccttt
301	catgtgtaat aaacgggccg aagacttcca ggggaatgat ttggataatg accctaaccg
361	tgggaatcag gttgaacgtc ctcagatgac tttcggcagg ctccagggaa tctccccgaa
421	gatcatgccc aagaagccag cagaggaagg aaatgattcg gaggaagtgc cagaagcatc
481	tggcccacaa aatgatggga aagagctgtg ccccccggga aaaccaacta cctctgagaa
541	gattcacgag agatctggac ccaaaagggg ggaacatgcc tggacccaca gactgcgtga
601	gagaaaacag ctggtgattt atgaagagat cagcgaccct gaggaagatg acgagtaact
661	cccctcaggg atacgacaca tgcccatgat gagaagcaga acgtggtgac ctttcacgaa
721	catgggcatg gctgcggacc cctcgtcatc aggtgcatag caagtg

[0230]

Claims

1. An isolated nucleic acid comprising a reading frame comprising a first sequence, wherein said first sequence encodes one or more segments of tumor-associated antigen NY-ESO (SEQ ID NO: 11), wherein the first sequence does not encode the complete NY-ESO antigen, and wherein each segment comprises an epitope cluster, said cluster comprising or encoding at least two amino acid sequences having a known or predicted affinity for a same MHC receptor peptide binding cleft.

2. The nucleic acid of claim 1, wherein said epitope cluster is chosen from the group consisting of amino acids 79-104, 86-171, 108-140, 108-174, 144-171, and 148-167 of NY-ESO.

3. The nucleic acid of claim 1, wherein said one or more segments consist of said epitope cluster.

4. The nucleic acid of claim 1, wherein said first sequence encodes a fragment of NY-ESO.

5. The nucleic acid of claim 4, wherein said encoded fragment consists of a polypeptide having a length, wherein the length of the polypeptide is less than about 90% of the length of NY-ESO.

6. The nucleic acid of claim 4, wherein said encoded fragment consists of a polypeptide having a length, wherein the length of the polypeptide is less than about 80% of the length of NY-ESO.

7. The nucleic acid of claim 4, wherein said encoded fragment consists of a polypeptide having a length, wherein the length of the polypeptide is less than about 60% of the length of NY-ESO.

8. The nucleic acid of claim 4, wherein said encoded fragment consists of a polypeptide having a length, wherein the length of the polypeptide is less than about 50% of the length of NY-ESO.

9. The nucleic acid of claim 4, wherein said encoded fragment consists of a polypeptide having a length, wherein the length of the polypeptide is less than about 25% of the length of NY-ESO.

10. The nucleic acid of claim 4, wherein said encoded fragment consists of a polypeptide having a length, wherein the length of the polypeptide is less than about 10% of the length of NY-ESO.

11. The nucleic acid of claim 4, wherein said encoded fragment consists essentially of amino acids 79-140, 79-167, 79-171, or 79-174.

12. The nucleic acid of claim 4, wherein said encoded fragment consists essentially of amino acids 86-140, 86-167, 86-171, or 86-174.

13. The nucleic acid of claim 4, wherein said encoded fragment consists essentially of amino acids 108-167 or 108-171.

14. The nucleic acid of claim 4, wherein said encoded fragment consists essentially of amino acids 144-167 or 144-174.

15. The nucleic acid of claim 4, wherein said encoded fragment consists essentially amino acids 148-171 or 148-174.

16. The nucleic acid of claim 4, wherein said encoded fragment consists essentially of amino acids 79-174 of NY-ESO.

17. The nucleic acid of claim 16, wherein said first sequence encodes exactly amino acids 77-180 of NY-ESO.

18. The nucleic acid of claim 4, wherein said encoded fragment consists essentially of an amino acid sequence beginning at one of amino acids selected from the group consisting of 79, 86, 108, 144, and 148 of NY-ESO, and ending at one of the amino acids selected from the group consisting of 104, 140, 167, 171, and 174 of NY-ESO.

19. The nucleic acid of claim 1, wherein said reading frame is operably linked to a promoter.

20. The nucleic acid of claim 1, further comprising a second sequence, wherein the second sequence encodes essentially a housekeeping epitope.

21. The nucleic acid of claim 20, wherein said first and second sequences constitute a single reading frame.

22. The nucleic acid of claim 21, wherein said reading frame is operably linked to a promoter.

23. An immunogenic composition comprising the nucleic acid of claim 22.

24. An isolated polypeptide comprising the amino acid sequence encoded in said reading frame of claim 22.

25. An immunogenic composition comprising the polypeptide of claim 24.

26. An isolated polypeptide comprising the amino acid sequence encoded in said reading frame of claim 1.

27. An immunogenic composition comprising the polypeptide of claim 26.

28. An immunogenic composition the nucleic acid of claim 1.