Inducing cellular immune responses to carcinoembryonic antigen using peptide and nucleic acid compositions

I. BACKGROUND OF THE INVENTION

[0001] A growing body of evidence suggests that cytotoxic T lymphocytes (CTL) are important in the immune response to tumor cells. CTL recognize peptide epitopes in the context of HLA class I molecules that are expressed on the surface of almost all nucleated cells. Following intracellular processing of endogenously synthesized tumor antigens, antigen-derived peptide epitopes bind to class I HLA molecules in the endoplasmic reticulum, and the resulting complex is then transported to the cell surface. CTL recognize the peptide-HLA class I complex, which then results in the destruction of the cell bearing the HLA-peptide complex directly by the CTL and/or via the activation of non-destructive mechanisms, e.g., activation of lymphokines such as tumor necrosis factor-α (TNF-α) or interferon-γ (IFNγ) which enhance the immune response and facilitate the destruction of the tumor cell.

[0002] Tumor-specific helper T lymphocytes (HTLs) are also known to be important for maintaining effective antitumor immunity. Their role in antitumor immunity has been demonstrated in animal models in which these cells not only serve to provide help for induction of CTL and antibody responses, but also provide effector functions, which are mediated by direct cell contact and also by secretion of lymphokines (e.g., IFNγ and TNF-α).

[0003] A fundamental challenge in the development of an efficacious tumor vaccine is immune suppression or tolerance that can occur. There is therefore a need to establish vaccine embodiments that elicit immune responses of sufficient breadth and vigor to prevent progression and/or clear the tumor.

[0004] The epitope approach employed in the present invention represents a solution to this challenge, in that it allows the incorporation of various antibody, CTL and HTL epitopes, from discrete regions of a target tumor-associated antigen (TAA), and/or regions of other TAAs, in a single vaccine composition. Such a composition can simultaneously target multiple dominant and subdominant epitopes and thereby be used to achieve effective immunization in a diverse population.

[0005] Carcinoembryonic antigen (CEA) is a 180 kD cell surface and secreted glycoprotein overexpressed on most human adenocarcinomas including colon, rectal, pancreatic and gastric (Muraro et al., Cancer Res. 45:5769-5780, 1985) as well as 50% of breast (Steward et al., Cancer (Phila) 33:1246-1252, 1974) and 70% of non-small cell lung carcinomas (Vincent et al., J. Thorac. Cardiovasc. Surg. 66:320-328, 1978).

[0006] CEA is also expressed, to some extent, on normal epithelium and in some fetal tissues (Thompson et al., J. Clin. Lab. Anal. 5:344-366, 1991). The abnormally high expression on cancer cells makes CEA an important target for immunotherapy.

[0007] The information provided in this section is intended to disclose the presently understood state of the art as of the filing date of the present application. Information is included in this section which was generated subsequent to the priority date of this application. Accordingly, information in this section is not intended, in any way, to delineate the priority date for the invention.

II. SUMMARY OF THE INVENTION

[0008] This invention applies our knowledge of the mechanisms by which antigen is recognized by T cells, for example, to develop epitope-based vaccines directed towards TAAs. More specifically, this application communicates our discovery of specific epitope pharmaceutical compositions and methods of use in the prevention and treatment of cancer.

[0009] Upon development of appropriate technology, the use of epitope-based vaccines has several advantages over current vaccines, particularly when compared to the use of whole antigens in vaccine compositions. For example, immunosuppressive epitopes that may be present in whole antigens can be avoided with the use of epitope-based vaccines. Such immunosuppressive epitopes may, e.g., correspond to immunodominant epitopes in whole antigens, which may be avoided by selecting peptide epitopes from non-dominant regions (see, e.g., Disis et al., J. Immunol. 156:3151-3158, 1996).

[0010] An additional advantage of an epitope-based vaccine approach is the ability to combine selected epitopes (CIL and HTL), and further, to modify the composition of the epitopes, achieving, for example, enhanced immunogenicity. Accordingly, the immune response can be modulated, as appropriate, for the target disease. Similar engineering of the response is not possible with traditional approaches.

[0011] Another major benefit of epitope-based immune-stimulating vaccines is their safety. The possible pathological side effects caused by infectious agents or whole protein antigens, which might have their own intrinsic biological activity, is eliminated.

[0012] An epitope-based vaccine also provides the ability to direct and focus an immune response to multiple selected antigens from the same pathogen (a “pathogen” may be an infectious agent or a tumor-associated molecule). Thus, patient-by-patient variability in the immune response to a particular pathogen may be alleviated by inclusion of epitopes from multiple antigens from the pathogen in a vaccine composition.

[0013] Furthermore, an epitope-based anti-tumor vaccine also provides the opportunity to combine epitopes derived from multiple tumor-associated molecules. This capability can therefore address the problem of tumor-to tumor variability that arises when developing a broadly targeted anti-tumor vaccine for a given tumor type and can also reduce the likelihood of tumor escape due to antigen loss. For example, a breast cancer tumor in one patient may express a target TAA that differs from a breast cancer tumor in another patient. Epitopes derived from multiple TAAs can be included in a polyepitopic vaccine that will target both breast cancer tumors.

[0014] One of the most formidable obstacles to the development of broadly efficacious epitope-based immunotherapeutics, however, has been the extreme polymorphism of HLA molecules. To date, effective non-genetically biased coverage of a population has been a task of considerable complexity; such coverage has required that epitopes be used that are specific for HLA molecules corresponding to each individual HLA allele. Impractically large numbers of epitopes would therefore have to be used in order to cover ethnically diverse populations. Thus, there has existed a need for peptide epitopes that are bound by multiple HLA antigen molecules for use in epitope-based vaccines. The greater the number of HLA antigen molecules bound, the greater the breadth of population coverage by the vaccine.

[0015] Furthermore, as described herein in greater detail, a need has existed to modulate peptide binding properties, e.g., so that peptides that are able to bind to multiple HLA molecules do so with an affinity that will stimulate an immune response. Identification of epitopes restricted by more than one HLA allele at an affinity that correlates with immunogenicity is important to provide thorough population coverage, and to allow the elicitation of responses of sufficient vigor to prevent or clear an infection in a diverse segment of the population. Such a response can also target a broad array of epitopes. The technology disclosed herein provides for such favored immune responses.

[0016] In a preferred embodiment, epitopes for inclusion in vaccine compositions of the invention are selected by a process whereby protein sequences of known antigens are evaluated for the presence of motif or supermotif-bearing epitopes. Peptides corresponding to a motif- or supermotif-bearing epitope are then synthesized and tested for the ability to bind to the HLA molecule that recognizes the selected motif. Those peptides that bind at an intermediate or high affinity ie., an IC50 (or a KD value) of 500 nM or less for HLA class I molecules or an IC50 of 1000 nM or less for HLA class II molecules, are further evaluated for their ability to induce a CTL or HTL response. Immunogenic peptide epitopes are selected for inclusion in vaccine compositions.

[0017] Supermotif-bearing peptides may additionally be tested for the ability to bind to multiple alleles within the HLA supertype family. Moreover, peptide epitopes may be analogued to modify binding affinity and/or the ability to bind to multiple alleles within an HLA supertype.

[0018] The invention also includes embodiments comprising methods for monitoring or evaluating an immune response to a TAA in a patient having a known HLA-type. Such methods comprise incubating a T lymphocyte sample from the patient with a peptide composition comprising a TAA epitope that has an amino acid sequence described in, for example, Tables XXII-VII and Table XI which binds the product of at least one HLA allele present in the patient, and detecting for the presence of a T lymphocyte that binds to the peptide. A CTL peptide epitope may, for example, be used as a component of a tetrameric complex for this type of analysis.

[0019] An alternative modality for defining the peptide epitopes in accordance with the invention is to recite the physical properties, such as length; primary structure; or charge, which are correlated with binding to a particular allele-specific HLA molecule or group of allele-specific HLA molecules. A further modality for defining peptide epitopes is to recite the physical properties of an HLA binding pocket, or properties shared by several allele-specific HLA binding pockets (e.g. pocket configuration and charge distribution) and reciting that the peptide epitope fits and binds to the pocket or pockets.

[0020] As will be apparent from the discussion below, other methods and embodiments are also contemplated. Further, novel synthetic peptides produced by any of the methods described herein are also part of the invention.

III. BRIEF DESCRIPTION OF THE FIGURES

[0021] not applicable

IV. DETAILED DESCRIPTION OF THE INVENTION

[0022] The peptide epitopes and corresponding nucleic acid compositions of the present invention are useful for stimulating an immune response to a TAA by stimulating the production of CTL or HTL responses. The peptide epitopes, which are derived directly or indirectly from native TAA protein amino acid sequences, are able to bind to HLA molecules and stimulate an immune response to the TAA. The complete sequence of the TAA proteins to be analyzed can be obtained from GenBank. Peptide epitopes and analogs thereof can also be readily determined from sequence information that may subsequently be discovered for heretofore unknown variants of particular TAAs, as will be clear from the disclosure provided below.

[0023] A list of target TAA includes, but is not limited to, the following antigens: MAGE 1, MAGE 2, MAGE 3, MAGE-11, MAGE-A10, BAGE, GAGE, RAGE, MAGE-C1, LAGE-1, CAG-3, DAM, MUC1, MUC2, MUC18, NY-ESO-1, MUM-1, CDK4, BRCA2, NY-LU-1, NY-LU-7, NY-LU-12, CASP8, RAS, KIAA-2-5, SCCs, p53, p73, CEA, Her 2/neu, Melan-A, gp100, tyrosinase, TRP2, gp75/TRP1, kallikrein, PSM, PAP, PSA, PT1-1, B-catenin, PRAME, Telomerase, FAK, cyclin D1 protein, NOEY2, EGF-R, SART-1, CAPB, HPVE7, p15, Folate receptor CDC27, PAGE-1, and PAGE4.

[0024] The peptide epitopes of the invention have been identified in a number of ways, as will be discussed below. Also discussed in greater detail is that analog peptides have been derived and the binding activity for HLA molecules modulated by modifying specific amino acid residues to create peptide analogs exhibiting altered immunogenicity. Further, the present invention provides compositions and combinations of compositions that enable epitope-based vaccines that are capable of interacting with HLA molecules encoded by various genetic alleles to provide broader population coverage than prior vaccines.

[0025] IV.A. Definitions

[0026] The invention can be better understood with reference to the following definitions, which are listed alphabetically:

[0027] A “computer” or “computer system” generally includes: a processor; at least one information storage/retrieval apparatus such as, for example, a hard drive, a disk drive or a tape drive; at least one input apparatus such as, for example, a keyboard, a mouse, a touch screen, or a microphone; and display structure. Additionally, the computer may include a communication channel in communication with a network. Such a computer may include more or less than what is listed above.

[0028] A “construct” as used herein generally denotes a composition that does not occur in nature. A construct can be produced by synthetic technologies, e.g., recombinant DNA preparation and expression or chemical synthetic techniques for nucleic or amino acids. A construct can also be produced by the addition or affiliation of one material with another such that the result is not found in nature in that form.

[0029] “Cross-reactive binding” indicates that a peptide is bound by more than one HLA molecule; a synonym is degenerate binding.

[0030] A “cryptic epitope” elicits a response by immunization with an isolated peptide, but the response is not cross-reactive in vitro when intact whole protein which comprises the epitope is used as an antigen.

[0031] A “dominant-epitope” is an epitope that induces an immune response upon immunization with a whole native antigen (see, e.g., Sercarz, et al., Annu. Rev. Immunol. 11:729-766, 1993). Such a response is cross-reactive in vitro with an isolated peptide epitope.

[0032] With regard to a particular amino acid sequence, an “epitope” is a set of amino acid residues which is involved in recognition by a particular immunoglobulin, or in the context of T cells, those residues necessary for recognition by T cell receptor proteins and/or Major Histocompatibility Complex (MHC) receptors. In an immune system setting, in vivo or in vitro, an epitope is the collective features of a molecule, such as primary, secondary and tertiary peptide structure, and charge, that together form a site recognized by an immunoglobulin, T cell receptor or HLA molecule. Throughout this disclosure epitope and peptide are often used interchangeably.

[0033] It is to be appreciated that protein or peptide molecules that comprise an epitope of the invention as well as additional amino acid(s) are within the bounds of the invention. In certain embodiments, there is a limitation on the length of a peptide of the invention which is not otherwise a construct as defined herein. An embodiment that is length-limited occurs when the protein/peptide comprising an epitope of the invention comprises a region (i.e., a contiguous series of amino acids) having 100% identity with a native sequence. In order to avoid a recited definition of epitope from reading, e.g., on whole natural molecules, the length of any region that has 100% identity with a native peptide sequence is limited. Thus, for a peptide comprising an epitope of the invention and a region with 100% identity with a native peptide sequence (and which is not otherwise a construct), the region with 100% identity to a native sequence generally has a length of: less than or equal to 600 amino acids, often less than or equal to 500 amino acids, often less than or equal to 400 amino acids, often less than or equal to 250 amino acids, often less than or equal to 100 amino acids, often less than or equal to 85 amino acids, often less than or equal to 75 amino acids, often less than or equal to 65 amino acids, and often less than or equal to 50 amino acids. In certain embodiments, an “epitope” of the invention which is not a construct is comprised by a peptide having a region with less than 51 amino acids that has 100% identity to a native peptide sequence, in any increment of (50, 49, 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5) down to 5 amino acids.

[0034] Certain peptide or protein sequences longer than 600 amino acids are within the scope of the invention. Such longer sequences are within the scope of the invention so long as they do not comprise any contiguous sequence of more than 600 amino acids that have 100% identity with a native peptide sequence, or if longer than 600 amino acids, they are a construct. For any peptide that has five contiguous residues or less that correspond to a native sequence, there is no limitation on the maximal length of that peptide in order to fall within the scope of the invention. It is presently preferred that a CTL epitope of the invention be less than 600 residues long in any increment down to eight amino acid residues.

[0035] “Human Leukocyte Antigen” or “HLA” is a human class I or class II Major Histocompatibility Complex (MHC) protein (see, e.g., Stites, et al., IMMUNOLOGY, 8TH ED., Lange Publishing, Los Altos, Calif., 1994).

[0036] An “HLA supertype or family”, as used herein, describes sets of HLA molecules grouped on the basis of shared peptide-binding specificities. HLA class I molecules that share somewhat similar binding affinity for peptides bearing certain amino acid motifs are grouped into HLA supertypes. The terms HLA superfamily, HLA supertype family, HLA family, and HLA xx-like molecules (where xx denotes a particular HLA type), are synonyms.

[0037] Throughout this disclosure, results are expressed in terms of “IC50's.” IC50 is the concentration of peptide in a binding assay at which 50% inhibition of binding of a reference peptide is observed. Given the conditions in which the assays are run (ie., limiting HLA proteins and labeled peptide concentrations), these values approximate KD values. Assays for determining binding are described in detail, e.g., in PCT publications WO 94/20127 and WO 94/03205. It should be noted that IC50 values can change, often dramatically, if the assay conditions are varied, and depending on the particular reagents used (e.g., HLA preparation, etc.). For example, excessive concentrations of HLA molecules will increase the apparent measured IC50 of a given ligand.

[0038] Alternatively, binding is expressed relative to a reference peptide. Although as a particular assay becomes more, or less, sensitive, the IC50's of the peptides tested may change somewhat, the binding relative to the reference peptide will not significantly change. For example, in an assay run under conditions such that the IC50 of the reference peptide increases 10-fold, the IC50 values of the test peptides will also shift approximately 10-fold. Therefore, to avoid ambiguities, the assessment of whether a peptide is a good, intermediate, weak, or negative binder is generally based on its IC, relative to the IC50 of a standard peptide.

[0039] Binding may also be determined using other assay systems including those using: live cells (e.g., Ceppellini et al., Nature 339:392, 1989; Christmick et al., Nature 352:67, 1991; Busch et al., Int. Immunol. 2:443, 19990; Hill et al., J. Immunol. 147:189, 1991; del Guercio et al., J. Immunol. 154:685, 1995), cell free systems using detergent lysates (e.g., Cerundolo et al., J. Immunol. 21:2069, 1991), immobilized purified MHC (e.g., Hill et al., J. Immunol. 152, 2890, 1994; Marshall et al., J. Immunol. 152:4946, 1994), ELISA systems (e.g., Reay et al, EMBO J. 11:2829, 1992), surface plasmon resonance (e.g., Khilko et al., J. Biol. Chem. 268:15425, 1993); high flux soluble phase assays (Hammer et al., J. Exp. Med. 180:2353, 1994), and measurement of class I MHC stabilization or assembly (e.g., Ljunggren et al., Nature 346:476, 1990; Schumacher et al., Cell 62:563, 1990; Townsend et al., Cell 62:285, 1990; Parker et al., J. Immunol. 149:1896, 1992).

[0040] As used herein, “high affinity” with respect to HLA class I molecules is defined as binding with an IC50, or KD value, of 50 nM or less; “intermediate affinity” is binding with an IC50 or KD value of between about 50 and about 500 nM. “High affinity” with respect to binding to HLA class II molecules is defined as binding with an IC50 or KD value of 100 nM or less; “intermediate affinity” is binding with an IC50 or KD value of between about 100 and about 1000 nM.

[0041] The terms “identical” or percent “identity,” in the context of two or more peptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues that are the same, when compared and aligned for maximum correspondence over a comparison window, as measured using a sequence comparison algorithm or by manual alignment and visual inspection.

[0042] An “immunogenic peptide” or “peptide epitope” is a peptide that comprises an allele-specific motif or supermotif such that the peptide will bind an HLA molecule and induce a CTL and/or HTL response. Thus, immunogenic peptides of the invention are capable of binding to an appropriate HLA molecule and thereafter inducing a cytotoxic T cell response, or a helper T cell response, to the antigen from which the inmnunogenic peptide is derived.

[0043] The phrases “isolated” or “biologically pure” refer to material which is substantially or essentially free from components which normally accompany the material as it is found in its native state. Thus, isolated peptides in accordance with the invention preferably do not contain materials normally associated with the peptides in their in situ environment.

[0044] “Link” or “join” refers to any method known in the art for functionally connecting peptides, including, without limitation, recombinant fusion, covalent bonding, disulfide bonding, ionic bonding, hydrogen bonding, and electrostatic bonding.

[0045] “Major Histocompatibility Complex” or “MHC” is a cluster of genes that plays a role in control of the cellular interactions responsible for physiologic immune responses. In humans, the MHC complex is also known as the HLA complex. For a detailed description of the MHC and HLA complexes, see, Paul, FUNDAMENTAL IMMUNOLOGY, 3RD ED., Raven Press, New York, 1993.

[0046] The term “motif” refers to the pattern of residues in a peptide of defined length, usually a peptide of from about 8 to about 13 amino acids for a class I HLA motif and from about 6 to about 25 amino acids for a class II HLA motif, which is recognized by a particular HLA molecule. Peptide motifs are typically different for each protein encoded by each human HLA allele and differ in the pattern of the primary and secondary anchor residues.

[0047] A “negative binding residue” or “deleterious residue” is an amino acid which, if present at certain positions (typically not primary anchor positions) in a peptide epitope, results in decreased binding affinity of the peptide for the peptide's corresponding HLA molecule.

[0048] A “non-native” sequence or “construct” refers to a sequence that is not found in nature, i.e., is “non-naturally occurring”. Such sequences include, e.g., peptides that are lipidated or otherwise modified, and polyepitopic compositions that contain epitopes that are not contiguous in a native protein sequence.

[0049] The term “peptide” is used interchangeably with “oligopeptide” in the present specification to designate a series of residues, typically L-amino acids, connected one to the other, typically by peptide bonds between the α-amino and carboxyl groups of adjacent amino acids. The preferred CTL-inducing peptides of the invention are 13 residues or less in length and usually consist of between about 8 and about 11 residues, preferably 9 or 10 residues. The preferred HTL-inducing oligopeptides are less than about 50 residues in length and usually consist of between about 6 and about 30 residues, more usually between themselves. In one embodiment, for example, the primary anchor residues are located at position 2 (from the amino terminal position) and at the carboxyl terminal position of a 9-residue peptide epitope in accordance with the invention. The primary anchor positions for each motif and supermotif are set forth in Table 1. For example, analog peptides can be created by altering the presence or absence of particular residues in these primary anchor positions. Such analogs are used to modulate the binding affinity of a peptide comprising a particular motif or supermotif.

[0050] “Promiscuous recognition” is where a distinct peptide is recognized by the same T cell clone in the context of various HLA molecules. Promiscuous recognition or binding is synonymous with cross-reactive binding.

[0051] A “protective immune response” or “therapeutic immune response” refers to a CTL and/or an HTL response to an antigen derived from an infectious agent or a tumor antigen, which prevents or at least partially arrests disease symptoms or progression. The immune response may also include an antibody response which has been facilitated by the stimulation of helper T cells.

[0052] The term “residue” refers to an amino acid or amino acid mimetic incorporated into an oligopeptide by an amide bond or amide bond mimetic.

[0053] A “secondary anchor residue” is an amino acid at a position other than a primary anchor position in a peptide which may influence peptide binding. A secondary anchor residue occurs at a significantly higher frequency amongst bound peptides than would be expected by random distribution of amino acids at one position. The secondary anchor residues are said to occur at “secondary anchor positions.” A secondary anchor residue can be identified as a residue which is present at a higher frequency among high or intermediate affinity binding peptides, or a residue otherwise associated with high or intermediate affinity binding. For example, analog peptides can be created by altering the presence or absence of particular residues in these secondary anchor positions. Such analogs are used to finely modulate the binding affinity of a peptide comprising a particular motif or supermotif.

[0054] A “subdominant epitope” is an epitope which evokes little or no response upon immunization with whole antigens which comprise the epitope, but for which a response can be obtained by immunization with an isolated peptide, and this response (unlike the case of cryptic epitopes) is detected when whole protein is used to recall the response in vitro or in vivo.

[0055] A “supermotifs is a peptide binding specificity shared by HLA molecules encoded by two or more HLA alleles. Preferably, a supermotif-bearing peptide is recognized with high or intermediate affinity (as defined herein) by two or more HLA molecules.

[0056] “Synthetic peptide” refers to a peptide that is man-made using such methods as chemical synthesis or recombinant DNA technology.

[0057] As used herein, a “vaccine” is a composition that contains one or more peptides of the invention. There are numerous embodiments of vaccines in accordance with the invention, such as by a cocktail of one or more peptides; one or more epitopes of the invention comprised by a polyepitopic peptide; or nucleic acids that encode such peptides or polypeptides, e.g., a minigene that encodes a polyepitopic peptide. The “one or more peptides” can include any whole unit integer from 1-1 50, e.g., at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, or 150 or more peptides of the invention. The peptides or polypeptides can optionally be modified, such as by lipidation, addition of targeting or other sequences. HLA class I-binding peptides of the invention can be admixed with, or linked to, HLA class II-binding peptides, to facilitate activation of both cytotoxic T lymphocytes and helper T lymphocytes. Vaccines can also comprise peptide-pulsed antigen presenting cells, e.g., dendritic cells.

[0058] The nomenclature used to describe peptide compounds follows the conventional practice wherein the amino group is presented to the left (the N-terminus) and the carboxyl group to the right (the C-terminus) of each amino acid residue. When amino acid residue positions are referred to in a peptide epitope they are numbered in an amino to carboxyl direction with position one being the position closest to the amino terminal end of the epitope, or the peptide or protein of which it may be a part. In the formulae representing selected specific embodiments of the present invention, the amino- and carboxyl-terminal groups, although not specifically shown, are in the form they would assume at physiologic pH values, unless otherwise specified. In the amino acid structure formulae, each residue is generally represented by standard three letter or single letter designations. The L-form of an amino acid residue is represented by a capital single letter or a capital first letter of a three-letter symbol, and the D-form for those amino acids having D-forms is represented by a lower case single letter or a lower case three letter symbol. Glycine has no asymmetric carbon atom and is simply referred to as “Gly” or G. The amino acid sequences of peptides set forth herein are generally designated using the standard single letter symbol. (A, Alanine; C, Cysteine; D, Aspartic Acid; E, Glutamic Acid; F, Phenylalanine; G, Glycine; H, Histidine; I, Isoleucine; K, Lysine; L, Leucine; M, Methionine; N, Asparagine; P, Proline; Q, Glutamine; R, Arginine; S, Serine; T, Threonine; V, Valine; W, Tryptophan; and Y, Tyrosine.) In addition to these symbols, “B” in the single letter abbreviations used herein designates α-amino butyric acid.

[0059] IV.B. Stimulation of CTL and HTL Responses

[0060] The mechanism by which T cells recognize antigens has been delineated during the past ten years. Based on our understanding of the immune system we have developed efficacious peptide epitope vaccine compositions that can induce a therapeutic or prophylactic immune response to a TAA in a broad population. For an understanding of the value and efficacy of the claimed compositions, a brief review of immunology-related technology is provided. The review is intended to disclose the presently understood state of the art as of the filing date of the present application. Information is included in this section which was generated subsequent to the priority date of this application. Accordingly, information in this section is not intended, in any way, to delineate the priority date for the invention.

[0061] A complex of an HLA molecule and a peptidic antigen acts as the ligand recognized by HLA-restricted T cells (Buus, S. et al., Cell 47:1071, 1986; Babbitt, B. P. et al., Nature 317:359, 1985; Townsend, A. and Bodmer, H., Annu. Rev. Immunol. 7:601, 1989; Germain, R. N., Annu. Rev. Immunol. 11:403, 1993). Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues that correspond to motifs required for specific binding to HLA antigen molecules have been identified and are described herein and are set forth in Tables I, II, and m (see also, e.g., Southwood, et al., J. Immunol. 160:3363, 1998; Raminensee, et al., Immunogenetics 41:178, 1995; Rammensee et al., SYFPEITHI, access via web at: http://134.2.96.221/scripts.hlaserver.dll/home.htm; Sette, A. and Sidney, J. Curr. Opin. Immunol. 10:478, 1998; Engeihard, V. H., Curr. Opin. Immunol. 6:13, 1994; Sette, A. and Grey, H. M., Curr. Opin. Immunol. 4:79, 1992; Sinigaglia, F. and Hammer, J. Curr. Biol. 6:52, 1994; Ruppert et al., Cell 74:929-937, 1993; Kondo et al., J. Immunol. 155:4307-4312, 1995; Sidney et al., J. Immunol. 157:3480-3490, 1996; Sidney et al., Human Immunol. 45:79-93, 1996; Sette, A. and Sidney, J. Immunogenetics 1999 November;50(3-4):201-12, Review).

[0062] Furthermore, x-ray crystallographic analysis of HLA-peptide complexes has revealed pockets within the peptide binding cleft of HLA molecules which accommodate, in an allele-specific mode, residues borne by peptide ligands; these residues in turn determine the HLA binding capacity of the peptides in which they are present. (See, e.g., Madden, D. R. Annu. Rev. Immunol. 13:587, 1995; Smith, et al, Immunity 4:203, 1996; Fremont et al., Immunity 8:305, 1998; Stem et al., Structure 2:245, 1994; Jones, E. Y. Curr. Opin. Immunol. 9:75, 1997; Brown, J. H. et al., Nature 364:33, 1993; Guo, H. C. et al., Proc. Natl. Acad Sci USA 90:8053, 1993; Guo, H. C. et al., Nature 360:364, 1992; Silver, M. L. et al., Nature 360:367, 1992; Matsumura, M. et al., Science 257:927, 1992; Madden et al., Cell 70:1035, 1992; Fremont, D. H. et al., Science 257:919, 1992; Saper, M. A., Bjorkman, P. J. and Wiley, D. C., J. Mol. Biol. 219:277, 1991.)

[0063] Accordingly, the definition of class I and class II allele-specific HLA binding motifs, or class I or class II supermotifs allows identification of regions within a protein that have the potential of binding particular HLA molecules.

[0064] The present inventors have found that the correlation of binding affinity with immunogenicity, which is disclosed herein, is an important factor to be considered when evaluating candidate peptides. Thus, by a combination of motif searches and HLA-peptide binding assays, candidates for epitope-based vaccines have been identified. After determining their binding affinity, additional confirmatory work can be performed to select, amongst these vaccine candidates, epitopes with preferred characteristics in terms of population coverage, antigenicity, and immunogenicity.

[0065] Various strategies can be utilized to evaluate immunogenicity, including:

[0066] 1) Evaluation of primary T cell cultures from normal individuals (see, e.g., Wentworth, P. A. et al., Mol. Immunol. 32:603, 1995; Celis, E. et al., Proc. Natl. Acad. Sci. USA 91:2105, 1994; Tsai, V. et al., J. Immunol. 158:1796, 1997; Kawashima, I. et al., Human Immunol. 59:1, 1998); This procedure involves the stimulation of peripheral blood lymphocytes (PBL) from normal subjects with a test peptide in the presence of antigen presenting cells in vitro over a period of several weeks. T cells specific for the peptide become activated during this time and are detected using, e.g., a 51Cr-release assay involving peptide sensitized target cells.

[0067] 2) Immunization of HLA transgenic mice (see, e.g., Wentworth, P. A. et al., J. Immunol. 26:97, 1996; Wentworth, P. A. et al., Int. Immunol. 8:651, 1996; Alexander, J. et al., J. Immunol. 159:4753, 1997); In this method, peptides in incomplete Freund's adjuvant are administered subcutaneously to HLA transgenic mice. Several weeks following immunization, splenocytes are removed and cultured in vitro in the presence of test peptide for approximately one week. Peptide-specific T cells are detected using, e.g., a 51Cr-release assay involving peptide sensitized target cells and target cells expressing endogenously generated antigen.

[0068] 3) Demonstration of recall T cell responses from patients who have been effectively vaccinated or who have a tumor; (see, e.g., Rehermann, B. et al., J. Exp. Med. 181:1047, 1995; Doolan, D. L. et al., Immunity 7:97, 1997; Bertoni, R. et al., J. Clin. Invest. 100:503, 1997; Threlkeld, S. C. et al., J. Immunol. 159:1648, 1997; Diepolder, H. M. et al., J. Virol. 71:6011, 1997; Tsang et al., J. Natl. Cancer Inst. 87:982-990, 1995; Disis et al., J. Immunol. 156:3151-3158, 1996). In applying this strategy, recall responses are detected by culturing PBL from patients with cancer who have generated an immune response “naturally”, or from patients who were vaccinated with tumor antigen vaccines. PBL from subjects are cultured in vitro for 1-2 weeks in the presence of test peptide plus antigen presenting cells (APC) to allow activation of “memory” T cells, as compared to “naive” T cells. At the end of the culture period, T cell activity is detected using assays for T cell activity including 51Cr release involving peptide-sensitized targets, T cell proliferation, or lymphokine release.

[0069] The following describes peptides epitopes and corresponding nucleic acids of the invention.

[0070] IV.C. Binding Affinity of Peptide Epitopes for HLA Molecules

[0071] As indicated herein, the large degree of HLA polymorphism is an important factor to be taken into account with the epitope-based approach to vaccine development. To address this factor, epitope selection encompassing identification of peptides capable of binding at high or intermediate affinity to multiple HLA molecules is preferably utilized, most preferably these epitopes bind at high or intermediate affinity to two or more allele-specific HLA molecules.

[0072] CTL-inducing peptides of interest for vaccine compositions preferably include those that have an IC50 or binding affinity value for class I HLA molecules of 500 nM or better (ie., the value is ≦500 nM). HTL-inducing peptides preferably include those that have an IC50 or binding affinity value for class II HLA molecules of 1000 nM or better, (i.e., the value is ≦1,000 nM). For example, peptide binding is assessed by testing the capacity of a candidate peptide to bind to a purified HLA molecule in vitro. Peptides exhibiting high or intermediate affinity are then considered for further analysis. Selected peptides are tested on other members of the supertype family. In preferred embodiments, peptides that exhibit cross-reactive binding are then used in cellular screening analyses or vaccines.

[0073] As disclosed herein, higher HLA binding affinity is correlated with greater immunogenicity. Greater immunogenicity can be manifested in several different ways. Immunogenicity corresponds to whether an immune response is elicited at all, and to the vigor of any particular response, as well as to the extent of a population in which a response is elicited. For example, a peptide might elicit an immune response in a diverse array of the population, yet in no instance produce a vigorous response. Moreover, higher binding affinity peptides lead to more vigorous immunogenic responses. As a result, less peptide is required to elicit a similar biological effect if a high or intermediate affinity binding peptide is used. Thus, in preferred embodiments of the invention, high or intermediate affinity binding epitopes are particularly useful.

[0074] The relationship between binding affinity for HLA class I molecules and immunogenicity of discrete peptide epitopes on bound antigens has been determined for the first time in the art by the present inventors. The correlation between binding affinity and immunogenicity was analyzed in two different experimental approaches (see, e.g., Sette, et al., J. Immunol. 153:5586-5592, 1994). In the first approach, the immunogenicity of potential epitopes ranging in HLA binding affinity over a 10,000-fold range was analyzed in HLA-A*0201 trnnsgenic mice. In the second approach, the antigenicity of approximately 100 different hepatitis B virus (HBV)-derived potential epitopes, all carrying A*0201 binding motifs, was assessed by using PBL from acute hepatitis patients. Pursuant to these approaches, it was determined that an affinity threshold value of approximately 500 nM (preferably 50 nM or less) determines the capacity of a peptide epitope to elicit a CTL response. These data are true for class I binding affinity measurements for naturally processed peptides and for synthesized T cell epitopes. These data also indicate the important role of determinant selection in the shaping of T cell responses (see, e.g., Schaeffer et al., Proc. Natl. Acad. Sci. USA 86:4649-4653, 1989).

[0075] An affinity threshold associated with immunogenicity in the context of HLA class II DR molecules has also been delineated (see, e.g., Southwood et al. J. Immunology 160:3363-3373,1998, and co-pending U.S. Ser. No. 09/009,953 filed Jan. 21, 1998). In order to define a biologically significant threshold of DR binding affinity, a database of the binding affinities of 32 DR-restricted epitopes for their restricting element (ie., the HLA molecule that binds the motif) was compiled In approximately half of the cases (15 of 32 epitopes), DR restriction was associated with high binding affinities, i.e. binding affinity values of 100 nM or less. In the other half of the cases (16 of 32), DR restriction was associated with intermediate affinity (binding affinity values in the 100-1000 nM range). In only one of 32 cases was DR restriction associated with an IC50 of 1000 nM or greater. Thus, 1000 nM can be defined as an affinity threshold associated with immunogenicity in the context of DR molecules.

[0076] In the case of tumor-associated antigens, many CTL peptide epitopes that have been shown to induce CTL that lyse peptide-pulsed target cells and tumor cell targets endogenously expressing the epitope exhibit binding affinity or IC50 values of 200 nM or less. In a study that evaluated the association of binding affinity and immunogenicity of such TAA epitopes, 100% (10/10) of the high binders, Le., peptide epitopes binding at an affinity of 50 nM or less, were immunogenic and 80% ({fraction (8/10)}) of them elicited CTLs that specifically recognized tumor cells. In the 51 to 200 nM range, very similar figures were obtained. CTL inductions positive for peptide and tumor cells were noted for 86% ({fraction (6/7)}) and 71% ({fraction (5/7)}) of the peptides, respectively. In the 201-500 nM range, most peptides (⅘ wildtype) were positive for induction of CTL recognizing wildtype peptide, but tumor recognition was not detected.

[0077] The binding affinity of peptides for HLA molecules can be determined as described in Example 1, below.

[0078] IV.D. Peptide Epitope Binding Motifs and Supermotifs

[0079] Through the study of single amino acid substituted antigen analogs and the sequencing of endogenously bound, naturally processed peptides, critical residues required for allele-specific binding to HLA molecules have been identified. The presence of these residues correlates with binding affinity for HLA molecules. The identification of motifs and/or supermotifs that correlate with high and intermediate affinity binding is an important issue with respect to the identification of immunogenic peptide epitopes for the inclusion in a vaccine. Kast et al. (J. Immunol. 152:3904-3912, 1994) have shown that motif-bearing peptides account for 90% of the epitopes that bind to allele-specific HLA class I molecules. In this study all possible peptides of 9 amino acids in length and overlapping by eight amino acids (240 peptides), which cover the entire sequence of the E6 and E7 proteins of human papillomavirus type 16, were evaluated for binding to five allele-specific HLA molecules that are expressed at high frequency among different ethnic groups. This unbiased set of peptides allowed an evaluation of the predictive value of HLA class I motifs. From the set of 240 peptides, 22 peptides were identified that bound to an allele-specific HLA molecule with high or intermediate affinity. Of these 22 peptides, 20 (i.e. 91%) were motif-bearing. Thus, this study demonstrates the value of motifs for the identification of peptide epitopes for inclusion in a vaccine: application of motif-based identification techniques will identify about 90% of the potential epitopes in a target antigen protein sequence.

[0080] Such peptide epitopes are identified in the Tables described below.

[0081] Peptides of the present invention also comprise epitopes that bind to MHC class II DR molecules. A greater degree of heterogeneity in both size and binding frame position of the motif, relative to the N and C termini of the peptide, exists for class II peptide ligands. This increased heterogeneity of HLA class II peptide ligands is due to the structure of the binding groove of the HLA class II molecule which, unlike its class I counterpart, is open at both ends. Crystallographic analysis of HLA class II DRB*0101-peptide complexes showed that the major energy of binding is contributed by peptide residues complexed with complementary pockets on the DRB*0101 molecules. An important anchor residue engages the deepest hydrophobic pocket (see, e.g., Madden, D. R. Ann. Rev. Immunol. 13:587, 1995) and is referred to as position I (P1). P1 may represent the N-terminal residue of a class II binding peptide epitope, but more typically is flanked towards the N-terminus by one or more residues. Other studies have also pointed to an important role for the peptide residue in the 6′ position towards the C-terminus, relative to P1, for binding to various DR molecules.

[0082] In the past few years evidence has accumulated to demonstrate that a large fraction of HLA class I and class II molecules can be classified into a relatively few supertypes, each characterized by largely overlapping peptide binding repertoires, and consensus structures of the main peptide binding pockets. Thus, peptides of the present invention are identified by any one of several HLA-specific amino acid motifs (see, e.g., Tables I-III), or if the presence of the motif corresponds to the ability to bind several allele-specific HLA molecules, a supermotif. The HLA molecules that bind to peptides that possess a particular amino acid supermotif are collectively referred to as an HLA “supertype.”

[0083] The peptide motifs and supermotifs described below, and summarized in Tables I-III, provide guidance for the identification and use of peptide epitopes in accordance with the invention.

[0084] Examples of peptide epitopes bearing a respective supermotif or motif are included in Tables as designated in the description of each motif or supermotif below. The Tables include a binding affinity ratio listing for some of the peptide epitopes. The ratio may be converted to IC50 by using the following formula: IC50 of the standard peptide/ratio=IC50 of the test peptide (i.e., the peptide epitope). The IC50 values of standard peptides used to determine binding affinities for Class I peptides are shown in Table IV. The IC50 values of standard peptides used to determine binding affinities for Class II peptides are shown in Table V. The peptides used as standards for the binding assays described herein are examples of standards; alternative standard peptides can also be used when performing binding studies.

[0085] To obtain the peptide epitope sequences listed in each of Tables VII-XX, the amino acid sequence of CEA was evaluated for the presence of the designated supermotif or motif, i.e., the amino acid sequence was searched for the presence of the primary anchor residues as set out in Table I (for Class I motifs) or Table III (for Class II motifs) for each respective motif or supermotif.

[0086] In the Tables, motif- and/or supermotif-bearing epitopes in the CEA sequence are indicated by position number and length of the epitope with reference to the CEA sequence and numbering provided below. The “pos” (position) column designates the amino acid position in the CEA protein sequence that corresponds to the first amino acid residue of the epitope. The “number of amino acids” indicates the number of residues in the epitope sequence and hence the length of the epitope. For example, the first peptide epitope listed in Table VII is a sequence of 8 residues in length starting at position 440. Accordingly, the amino acid sequence of the epitope is ASNPPAQY.

[0087] Binding data presented in Tables VII-XX is expressed as a relative binding ratio, supra.

[0088] CEA Amino Acid Sequence

11MESPSAPPHR WCIPWQRLLL TASLLTFWNP PTTAKLTIES TPFNVAEGKE VLLLVHNLPQ 60HLFGYSWYKG ERVDGNRQII GYVIGTQQAT PGPAYSGREI IYPNASLLIQ NIIQNDTGFY120TLHVIKSDLV NEEATGQFRV YPELPKPSIS SNNSKPVEDK DAVAFTCEPE TQDATYLWWV180NNQSLPVSPR LQLSNGNRTL TLFNVTRNDT ASYKCETQNP VSARRSDSVI LNVLYGPDAP240TISPLNTSYR SGENLNLSCH AASNPPAQYS WFVNGTFQQS TQELFIPNIT VNNSGSYTCQ300AHNSDTGLNR TTVTTITVYA EPPKPFITSN NSNPVEDEDA VALTCEPEIQ NTTYLWWVNN360QSLPVSPRLQ LSNDNRTLTL LSVTRNDVGP YECGIQNELS VDHSDPVILN VLYGPDDPTI420SPSYTYYRPG VNLSLSCHAA SNPPAQYSWL IDGNIQQHTQ ELFISNITEK NSGLYTCQAN480NSASGHSRTT VKTITVSAEL PKPSISSNNS KPVEDKDAVA FTCEPEAQNT TYLWWVNGQS540LPVSPRLQLS NGNRTLTLFN VTRNDARAYV CGIQNSVSAN RSDPVTLDVL YGPDTPIISP600PDSSYLSGAN LNLSCHSASN PSPQYSWRIN GIPQQHTQVL FIAKITPNNN GTYACFVSNL660ATGRNNSIVK SITVSASGTS PGLSAGATVG IMIGVLVGVA LI702

[0089] HLA Class I Motifs Indicative of CTL Inducing Peptide Epitopes:

[0090] The primary anchor residues of the HLA class I peptide epitope supermotifs and motifs delineated below are summarized in Table I. The HLA class I motifs set out in Table I(a) are those most particularly relevant to the invention claimed here. Primary and secondary anchor positions are summarized in Table II. Allele-specific HLA molecules that comprise HLA class I supertype families are listed in Table VI. In some cases, peptide epitopes are listed in both a motif and a supermotif Table because of the overlapping primary anchor specificity. The relationship of a particular motif and respective supermotif is indicated in the description of the individual motifs.

[0091] IV.D.1. HLA-A1 Supermotif

[0092] The HLA-A1 supernotif is characterized by the presence in peptide ligands of a small (T or S) or hydrophobic (L, I, V, or M) primary anchor residue in position 2, and an aromatic (Y, F, or W) primary anchor residue at the C-terminal position of the epitope. The corresponding family of HLA molecules that bind to the A1 supermotif (i.e., the HLA-A1 supertype) is comprised of at least: A*0101, A*2601, A*2602, A*2501, and A*3201 (see, e.g., DiBrino, M. et al., J. Immunol. 151:5930, 1993; DiBrino, M. et al., J. Immunol. 152:620, 1994; Kondo, A. et al., Immunogenetics 45:249, 1997). Other allele-specific HLA molecules predicted to be members of the A1 superfamily are shown in Table VI. Peptides binding to each of the individual HLA proteins can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

[0093] Representative peptide epitopes that comprise the A1 supermotif are set forth in Table VII.

[0094] IV.D.2. HLA-A2 Supermotif

[0095] Primary anchor specificities for allele-specific HLA-A2.1 molecules (see, e.g., Falk et al., Nature 351:290-296, 1991; Hunt et al., Science 255:1261-1263, 1992; Parker et al, J. Immunol. 149:3580-3587, 1992; Ruppert et al., Cell 74:929-937, 1993) and cross-reactive binding among HLA-A2 and -A28 molecules have been described. (See, e.g., Fruci et al, Human Immunol. 38:187-192, 1993; Tanigaki et al., Human Immunol. 39:155-162, 1994; Del Guercio et al., J. Immunol. 154:685-693, 1995; Kast et al., J. Immunol. 152:3904-3912, 1994 for reviews of relevant data.) These primary anchor residues define the HLA-A2 supermotif; which presence in peptide ligands corresponds to the ability to bind several different HLA-A2 and -A28 molecules. The HLA-A2 supermotif comprises peptide ligands with L, I, V, M, A, T, or Q as a primary anchor residue at position 2 and L, I, V, M, A, or T as a primary anchor residue at the C-terminal position of the epitope.

[0096] The corresponding family of HLA molecules (ie., the HLA-A2 supertype that binds these peptides) is comprised of at least: A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*0209, A*0214, A*6802, and A*6901. Other allele-specific HLA molecules predicted to be members of the A2 superfamily are shown in Table VI. As explained in detail below, binding to each of the individual allele-specific HLA molecules can be modulated by substitutions at the primary anchor and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

[0097] Representative peptide epitopes that comprise an A2 supermotif are set forth in Table VIII. The motifs comprising the primary anchor residues V, A, T, or Q at position 2 and L, I, V, A, or T at the C-terminal position are those most particularly relevant to the invention claimed herein.

[0098] IV.D.3. HLA-A3 Supermotif

[0099] The HLA-A3 supermotif is characterized by the presence in peptide ligands of A, L, I, V, M, S, or, T as a primary anchor at position 2, and a positively charged residue, R or K, at the C-terminal position of the epitope, e.g., in position 9 of 9-mers (see, e.g., Sidney et al, Hum. Immunol 45:79, 1996). Exemplary members of the corresponding family of HLA molecules (the HLA-A3 supertype) that bind the A3 supermotif include at least: A*0301, A*1101, A*3101, A*3301, and A*6801. Other allele-specific HLA molecules predicted to be members of the A3 supertype are shown in Table VI. As explained in detail below, peptide binding to each of the individual allele-specific HLA proteins can be modulated by substitutions of amino acids at the primary and/or secondary anchor positions of the peptide, preferably choosing respective residues specified for the supermotif.

[0100] Representative peptide epitopes that comprise the A3 supermotif are set forth in Table IX.

[0101] IV.D.4. EHLA-A24 Supermotif

[0102] The HLA-A24 supermotif is characterized by the presence in peptide ligands of an aromatic (F, W, or Y) or hydrophobic aliphatic (L, I, V, M, or T) residue as a primary anchor in position 2, and Y, F, W, L, I, or M as primary anchor at the C-terminal position of the epitope (see, e.g., Sette and Sidney, Immunogenetics 1999 November;50(3-4):201-12, Review). The corresponding family of HLA molecules that bind to the A24 supermotif (ie., the A24 supertype) includes at least: A*2402, A*3001, and A*2301. Other allele-specific HLA molecules predicted to be members of the A24 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

[0103] Representative peptide epitopes that comprise the A24 supermotif are set forth in Table X.

[0104] V.D.5. HLA-B7 Supermotif

[0105] The HLA-B7 supermotif is characterized by peptides bearing proline in position 2 as a primary anchor, and a hydrophobic or aliphatic amino acid (L, I, V, M, A, F, W, or Y) as the primary anchor at the C-terminal position of the epitope. The corresponding family of HLA molecules that bind the B7 supermotif (i.e., the HLA-B7 supertype) is comprised of at least twenty six HLA-B proteins comprising at least: B*0702, B*0703, B*0704, B*0705, B*1508, B*3501, B*3502, B*3503, B*3504, B*3505, B*3506, B*3507, B*3508, B*5101, B*5102, B*5103, B*5104, B*5105, B*5301, B*5401, B*5501, B*5502, B*5601, B*5602, B*6701, and B*7801 (see, e.g., Sidney, et al., J. Immunol. 154:247, 1995; Barber, et al., Curr. Biol. 5:179, 1995; Hill, et al, Nature 360:434, 1992; Rammensee, et al., Immunogenetics 41:178, 1995 for reviews of relevant data). Other allele-specific HLA molecules predicted to be members of the B7 supertype are shown in Table VI. As explained in detail below, peptide binding to each of the individual allele-specific HLA proteins can be modulated by substitutions at the primary and/or secondary anchor positions of the peptide, preferably choosing respective residues specified for the supermotif.

[0106] Representative peptide epitopes that comprise the B7 supermotif are set forth in Table XI.

[0107] IV.D.6. HLA-B27 Supermotif

[0108] The HLA-B27 supermotif is characterized by the presence in peptide ligands of a positively charged (R, H, or K) residue as a primary anchor at position 2, and a hydrophobic (F, Y, L, W, M, I, A, or 35 V) residue as a primary anchor at the C-termiinal position of the epitope (see, e.g., Sidney and Sette, Immunogenetics 1999 November;50(3-4):201-12, Review). Exemplary members of the corresponding family of HLA molecules that bind to the B27 supermotif (i.e., the B27 supertype) include at least B*1401, B*1402, B*1509, B*2702, B*2703, B*2704, B*2705, B*2706, B*3801, B*3901, B*3902, and B*7301. Other allele-specific HLA molecules predicted to be members of the B27 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

[0109] Representative peptide epitopes that comprise the B27 supermotif are set forth in Table XII.

[0110] IV.D.7. HLA-B44 Supermotif

[0111] The HLA-B44 supermotif is characterized by the presence in peptide ligands of negatively charged (D or E) residues as a primary anchor in position 2, and hydrophobic residues (F, W, Y, L, 1, M, V, or A) as a primary anchor at the C-terminal position of the epitope (see, e.g., Sidney et al., Immunol. Today 17:261, 1996). Exemplary members of the corresponding family of HLA molecules that bind to the B44 supermotif (i.e., the B44 supertype) include at least: B*1801, B*1802, B*3701, B*4001, B*4002, B*4006, B*4402, B*4403, and B*4404. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions; preferably choosing respective residues specified for the supermotif.

[0112] IV.D.8. HLA-B58 Supermotif

[0113] The HLA-B58 supermotif is characterized by the presence in peptide ligands of a small aliphatic residue (A, S, or T) as a primary anchor residue at position 2, and an aromatic or hydrophobic residue (F, W, Y, L, I, V, M, or A) as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Sidney and Sette, Immunogenetics 1999 November;50(34):201-12, Review). Exemplary members of the corresponding family of HLA molecules that bind to the B58 supermotif (ie., the B58 supertype) include at least: B*1516,B*1517,B*5701,B*5702, and B*5801. Other allele-specific HLA molecules predicted to be members of the B58 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

[0114] Representative peptide epitopes that comprise the B58 supermotif are set forth in Table XIII.

[0115] IV.D.9. HLA-B62 Supermotif

[0116] The HLA-B62 supermotif is characterized by the presence in peptide ligands of the polar aliphatic residue Q or a hydrophobic aliphatic residue (L, V, M, I, or P) as a primary anchor in position 2, and a hydrophobic residue (F, W, Y, M, I, V, L, or A) as a primary anchor at the C-terminal position of the epitope (see, e.g., Sidney and Sette, Immunogenetics 1999 November;50(3-4):201-12, Review). Exemplary members of the corresponding family of HLA molecules that bind to the B62 supermotif (i.e., the B62 supertype) include at least: B*1501,B*1502,B*1513, and B5201. Other allele-specific HLA molecules predicted to be members of the B62 supertype are shown in Table VI. Peptide binding to each of the allele-specific HLA molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

[0117] Representative peptide epitopes that comprise the B62 supermotif are set forth in Table XIV.

[0118] IV.D.10. HLA-A1 Motif

[0119] The HLA-A1 motif is characterized by the presence in peptide ligands of T, S, or M as a primary anchor residue at position 2 and the presence of Y as a primary anchor residue at the C-terminal position of the epitope. An alternative allele-specific A1 motif is characterized by a primary anchor residue at position 3 rather than position 2. This motif is characterized by the presence of D, E, A, or S as a primary anchor residue in position 3, and a Y as a primary anchor residue at the C-terminal position of the epitope (see, e.g., DiBrino et al., J. Immunol., 152:620, 1994; Kondo et al., Immunogenetics 45:249, 1997; and Kubo et al, J. Immunol. 152:3913, 1994 for reviews of relevant data). Peptide binding to HLA-A1 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

[0120] Representative peptide epitopes that comprise either A1 motif are set forth in Table XV. Those epitopes comprising T, S, or M at position 2 and Y at the C-terminal position are also included in the listing of HLA-A1 supermotif-bearing peptide epitopes listed in Table VII, as these residues are a subset of the A1 supermotif primary anchors.

[0121] IV.D.11. HLA-A*0201 Motif

[0122] An HLA-A2*0201 motif was determined to be characterized by the presence in peptide ligands of L or M as a primary anchor residue in position 2, and L or V as a primary anchor residue at the C-terminal position of a 9-residue peptide (see, e.g., Falk et al., Nature 351:290-296, 1991) and was further found to comprise an I at position 2 and I or A at the C-terminal position of a nine amino acid peptide (see, e.g., Hunt et al., Science 255:1261-1263, Mar. 6, 1992; Parker et al., J. Immunol. 149:3580-3587, 1992). The A*0201 allele-specific motif has also been defined by the present inventors to additionally comprise V, A, T, or Q as a primary anchor residue at position 2, and M or T as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Kast et al., J. Immunol. 152:3904-3912, 1994). Thus, the HLA-A*0201 motif comprises peptide ligands with L, I, V, M, A, T, or Q as primary anchor residues at position 2 and L, I, V, M, A, or T as a primary anchor residue at the C-terminal position of the epitope. The preferred and tolerated residues that characterize the primary anchor positions of the HLA-A*0201 motif are identical to the residues describing the A2 supermotif. (For reviews of relevant data, see, e.g., del Guercio et al., J. Immunol. 154:685-693, 1995; Ruppert et al., Cell 74:929-937, 1993; Sidney et al., Immunol. Today 17:261-266, 1996; Sette and Sidney, Curr. Opin. in Immunol. 10:478-482, 1998). Secondary anchor residues that characterize the A*0201 motif have additionally been defined (see, e.g., Ruppert et al., Cell 74:929-937, 1993). These are shown in Table II. Peptide binding to HLA-A*0201 molecules can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

[0123] Representative peptide epitopes that comprise an A*0201 motif are set forth in Table VIII. The A*0201 motifs comprising the primary anchor residues V, A, T, or Q at position 2 and L, I, V, A, or T at the C-terminal position are those most particularly relevant to the invention claimed herein.

[0124] IV.D.1 2. fL-A-A3 Motif

[0125] The HLA-A3 motif is characterized by the presence in peptide ligands of L, M, V, I, S, A, T, F, C, G, or D as a primary anchor residue at position 2, and the presence of K, sY, R, H, F, or A as a primary anchor residue at the C-terminal position of the epitope (see, e.g., DiBrino et al., Proc. Natl. Acad. Sci USA 90:1508, 1993; and Kubo et al., J. Immunol. 152:3913-3924, 1994). Peptide binding to HLA-A3 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

[0126] Representative peptide epitopes that comprise the A3 motif are set forth in Table XVI. Those peptide epitopes that also comprise the A3 supermotif are also listed in Table LX. The A3 supermotif primary anchor residues comprise a subset of the A3- and A11-allele specific motif primary anchor residues.

[0127] IV.D.13. HLA-A11 Motif

[0128] The HLA-A11 motif is characterized by the presence in peptide ligands of V, T, M, L, I, S, A, G, N, C, D, or F as a primary anchor residue in position 2, and K, R, Y, or H as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Zhang et al., Proc. Natl. Acad. Sci USA 90:2217-2221, 1993; and Kubo et al., J. Immunol. 152:3913-3924, 1994). Peptide binding to HLA-A11 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

[0129] Representative peptide epitopes that comprise the A11 motif are set forth in Table XVII; peptide epitopes comprising the A3 allele-specific motif are also present in this Table because of the extensive overlap between the A3 and A11 motif primary anchor specificities. Further, those peptide epitopes that comprise the A3 supermotif are also listed in Table IX.

[0130] IV.D.14. HLA-A24 Motif

[0131] The HLA-A24 motif is characterized by the presence in peptide ligands of Y, F, W, or M as a primary anchor residue in position 2, and F, L, I, or W as a primary anchor residue at the C-terminal position of the epitope (see, e.g., Kondo et al, J. Immunol. 155:43074312, 1995; and Kubo et al., J. Immunol. 152:3913-3924, 1994). Peptide binding to HLA-A24 molecules can be modulated by substitutions at primary and/or secondary anchor positions; preferably choosing respective residues specified for the motif.

[0132] Representative peptide epitopes that comprise the A24 motif are set out in Table XVIII. These epitopes are also listed in Table X, which sets forth HLA-A24-supermotif-bearing peptide epitopes, as the primary anchor residues characterizing the A24 allele-specific motif comprise a subset of the A24 supermotif primary anchor residues.

[0133] Motifs Indicative of Class H HTL Inducing Peptide Epitones

[0134] The primary and secondary anchor residues of the HLA class II peptide epitope supermotifs and motifs delineated below are summarized in Table III.

[0135] IV.D.15. HLA DR-14-7 Supermotif

[0136] Motifs have also been identified for peptides that bind to three common HLA class II allele-specific HLA molecules; HLA DRB1*0401, DRBI*0101, and DRB1*0701 (see, e.g., the review by Southwood et al. J. Immunology 160:3363-3373,1998). Collectively, the common residues from these motifs delineate the HLA DR-1-4-7 supermotif. Peptides that bind to these DR molecules carry a supermotif characterized by a large aromatic or hydrophobic residue (Y, F, W, L, I, V, or M) as a primary anchor residue in position 1, and a small, non-charged residue (S, T, C, A, P, V, I, L, or M) as a primary anchor residue in position 6 of a 9-mer core region. Allele-specific secondary effects and secondary anchors for each of these HLA types have also been identified (Southwood et al., supra). These are set forth in Table II. Peptide binding to HILA-DRB1*0401, DRBI*0101, and/or DRB1*0701 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the supermotif.

[0137] Potential epitope 9-mer core regions comprising the DR-1-4-7 supermotif, wherein position 1 of the supermotif is at position 1 of the nine-residue core, are set forth in Table XIX. Respective exemplary peptide epitopes of 15 amino acid residues in length, each of which comprise the nine residue core, are also shown in the Table along with cross-reactive binding data for the exemplary 15-residue supermotif-bearing peptides.

[0138] IV.D.16. HLA DR3 Motifs

[0139] Two alternative motifs (i.e., submotifs) characterize peptide epitopes that bind to HLA-DR3 molecules (see, e.g., Geluk et al., J. Immunol. 152:5742, 1994). In the first motif (submotif DR3a) a large, hydrophobic residue (L, I, V, M, F, or Y) is present in anchor position 1 of a 9-mer core, and D is present as an anchor at position 4, towards the carboxyl terminus of the epitope. As in other class II motifs, core position I may or may not occupy the peptide N-terminal position.

[0140] The alternative DR3 submotif provides for lack of the large, hydrophobic residue at anchor position 1, and/or lack of the negatively charged or amide-like anchor residue at position 4, by the presence of a positive charge at position 6 towards the carboxyl terminus of the epitope. Thus, for the alternative allele-specific DR3 motif (submotif DR3b): L, I, V, M, F, Y, A, or Y is present at anchor position 1; D, N, Q, E, S, or T is present at anchor position 4; and K, R) or H is present at anchor position 6. Peptide binding to HLA-DR3 can be modulated by substitutions at primary and/or secondary anchor positions, preferably choosing respective residues specified for the motif.

[0141] Potential peptide epitope 9-mer core regions corresponding to a nine residue sequence comprising the DR3a submotif (wherein position 1 of the motif is at position 1 of the nine residue core) are set forth in Table XXa. Respective exemplary peptide epitopes of 15 amino acid residues in length, each of which comprise the nine residue core, are also shown in Table XXa along with binding data for exemplary DR3 submotif a-bearing peptides.

[0142] Potential peptide epitope 9-mer core regions comprising the DR3b submotif and respective exemplary 15-mer peptides comprising the DR3 submotif-b epitope are set forth in Table XXb along with binding data of exemplary DR3 submotif b-bearing peptides.

[0143] Each of the HLA class I or class II peptide epitopes set out in the Tables herein are deemed singly to be an inventive aspect of this application. Further, it is also an inventive aspect of this application that each peptide epitope may be used in combination with any other peptide epitope.

[0144] IV.E. Enhancing Population Coverage of the Vaccine

[0145] Vaccines that have broad population coverage are preferred because they are more commercially viable and generally applicable to the most people. Broad population coverage can be obtained using the peptides of the invention (and nucleic acid compositions that encode such peptides) through selecting peptide epitopes that bind to HLA alleles which, when considered in total, are present in most of the population. Table XXI lists the overall frequencies of the HLA class I supertypes in various ethnicities (Table XXIa) and the combined population coverage achieved by the A2-, A3-, and B7-supertypes (Table XXIb). The A2-, A3-, and B7 supertypes are each present on the average of over 40% in each of these five major ethnic groups. Coverage in excess of 80% is achieved with a combination of these supermotifs.

[0146] These results suggest that effective and non-ethnically biased population coverage is achieved upon use of a limited number of cross-reactive peptides. Although the population coverage reached with these three main peptide specificities is high, coverage can be expanded to reach 95% population coverage and above, and more easily achieve truly multispecific responses upon use of additional supermotif or allele-specific motif bearing peptides.

[0147] The B44-, A1-, and A24-supertypes are each present, on average, in a range from 25% to 40% in these major ethnic populations (Table XXIa). While less prevalent overall, the B27-, B58-, and B62 supertypes are each present with a frequency >25% in at least one major ethnic group (Table XXIa). Table XXIb summarizes the estimated prevalence of combinations of HLA supertypes that have been identified in five major ethnic groups. The incremental coverage obtained by the inclusion of A1,- A24-, and B44-supertypes to the A2, A3, and B7 coverage and coverage obtained with all of the supertypes described herein, is shown.

[0148] The data presented herein, together with the previous definition of the A2-, A3-, and B7-supertypes, indicates that all antigens, with the possible exception of A29, B8, and B46, can be classified into a total of nine HLA supertypes. By including epitopes from the six most frequent supertypes, an average population coverage of 99% is obtained for five major ethnic groups.

[0149] IV.F. Immune Response-Stimulating Peptide Analogs

[0150] In general, CTL and HTL responses are not directed against all possible epitopes. Rather, they are restricted to a few “immunodominant” determinants (Zinkernagel, et al., Adv. Immunol. 27:5159, 1979; Bennink, et al., J. Exp. Med. 168:1935-1939, 1988; Rawle, et al., J. Immunol. 146:3977-3984, 1991). It has been recognized that immunodominance (Benacerraf, et al., Science 175:273-279, 1972) could be explained by either the ability of a given epitope to selectively bind a particular HLA protein (determinant selection theory) (Vitiello, et al., J. Immunol. 131:1635, 1983); Rosenthal, et al., Nature 267:156-158, 1977), or to be selectively recognized by the existing TCR (T cell receptor) specificities (repertoire theory) (Klein, J., IMMUNOLOGY, THE SCIENCE OF SELF/NONSELF DISCRIMINATION, John Wiley & Sons, New York, pp. 270-310, 1982). It has been demonstrated that additional factors, mostly linked to processing events, can also play a key role in dictating, beyond strict immunogenicity, which of the many potential determinants will be presented as immunodominant (Sercarz, et al., Annu. Rev. Immunol. 11:729-766, 1993).

[0151] Because tissue specific and developmental TAAs are expressed on normal tissue at least at some point in time or location within the body, it may be expected that T cells to them, particularly dominant epitopes, are eliminated during immunological surveillance and that tolerance is induced. However, CTL responses to tumor epitopes in both normal donors and cancer patient has been detected, which may indicate that tolerance is incomplete (see, e.g., Kawashima et al., Hum. Immunol. 59:1, 1998; Tsang, J. Natl. Cancer Inst. 87:82-90, 1995; Rongcun et al., J. Immunol. 163:1037, 1999). Thus, immune tolerance does not completely eliminate or inactivate CTL precursors capable of recognizing high affinity HLA class I binding peptides.

[0152] An additional strategy to overcome tolerance is to use analog peptides. Without intending to be bound by theory, it is believed that because T cells to dominant epitopes may have been clonally deleted, selecting subdominant epitopes may allow existing T cells to be recruited, which will then lead to a therapeutic or prophylactic response. However, the binding of HLA molecules to subdominant epitopes is often less vigorous than to dominant ones. Accordingly, there is a need to be able to modulate the binding affinity of particular immunogenic epitopes for one or more HLA molecules, and thereby to modulate the immune response elicited by the peptide, for example to prepare analog peptides which elicit a more vigorous response.

[0153] Although peptides with suitable cross-reactivity among all alleles of a superfamily are identified by the screening procedures described above, cross-reactivity is not always as complete as possible, and in certain cases procedures to increase cross-reactivity of peptides can be useful; moreover, such procedures can also be used to modify other properties of the peptides such as binding affinity or peptide stability.

[0154] Having established the general rules that govern cross-reactivity of peptides for HLA alleles within a given motif or supermotif, modification (i.e., analoging) of the structure of peptides of particular interest in order to achieve broader (or otherwise modified) HLA binding capacity can be performed. More specifically, peptides which exhibit the broadest cross-reactivity patterns, can be produced in accordance with the teachings herein. The present concepts related to analog generation are set forth in greater detail in co-pending U.S. Ser. No. 09/226,775 filed Jan. 6, 1999.

[0155] In brief, the strategy employed utilizes the motifs or supermotifs which correlate with binding to certain HLA molecules. The motifs or supermotifs are defined by having primary anchors, and in many cases secondary anchors. Analog peptides can be created by substituting amino acid residues at primary anchor, secondary anchor, or at primary and secondary anchor positions. Generally, analogs are made for peptides that already bear a motif or supermotif. Preferred secondary anchor residues of supermotifs and motifs that have been defined for HLA class I and class II binding peptides are shown in Tables II and III, respectively.

[0156] For a number of the motifs or supermotifs in accordance with the invention, residues are defined which are deleterious to binding to allele-specific HLA molecules or members of HLA supertypes that bind the respective motif or supermotif (Tables II and II). Accordingly, removal of such residues that are detrimental to binding can be performed in accordance with the present invention. For example, in the case of the A3 supertype, when all peptides that have such deleterious residues are removed from the population of peptides used in the analysis, the incidence of cross-reactivity increased from 22% to 37% (see, e.g., Sidney, J. et al., Hu. Immunol. 45:79, 1996). Thus, one strategy to improve the cross-reactivity of peptides within a given supermotif is simply to delete one or more of the deleterious residues present within a peptide and substitute a small “neutral” residue such as Ala (that may not influence T cell recognition of the peptide). An enhanced likelihood of cross-reactivity is expected if, together with elimination of detrimental residues within a peptide, “preferred” residues associated with high affinity binding to an allele-specific HLA molecule or to multiple HLA molecules within a superfamily are inserted.

[0157] To ensure that an analog peptide, when used as a vaccine, actually elicits a CTL response to the native epitope in vivo (or, in the case of class II epitopes, elicits helper T cells that cross-react with the wild type peptides), the analog peptide may be used to immunize T cells in vitro from individuals of the appropriate HLA allele. Thereafter, the immunized cells' capacity to induce lysis of wild type peptide sensitized target cells is evaluated. It will be desirable to use as antigen presenting cells, cells that have been either infected, or transfected with the appropriate genes, or, in the case of class II epitopes only, cells that have been pulsed with whole protein antigens, to establish whether endogenously produced antigen is also recognized by the relevant T cells.

[0158] Another embodiment of the invention is to create analogs of weak binding peptides, to thereby ensure adequate numbers of cross-reactive cellular binders. Class I binding peptides exhibiting binding affinities of 500-5000 nM, and carrying an acceptable but suboptimal primary anchor residue at one or both positions can be “fixed” by substituting preferred anchor residues in accordance with the respective supertype. The analog peptides can then be tested for crossbinding activity.

[0159] Another embodiment for generating effective peptide analogs involves the substitution of residues that have an adverse impact on peptide stability or solubility in, e.g., a liquid environment. This substitution may occur at any position of the peptide epitope. For example, a cysteine can be substituted out in favor of α-amino butyric acid (“B” in the single letter abbreviations for peptide sequences listed herein). Due to its chemical nature, cysteine has the propensity to form disulfide bridges and sufficiently alter the peptide structurally so as to reduce binding capacity. Substituting α-amino butyric acid for cysteine not only alleviates this problemn, but actually improves binding and crossbinding capability in certain instances (see, e.g., the review by Sette et al., In: Persistent Viral Infections, Eds. R. Ahmed and I. Chen, John Wiley & Sons, England, 1999).

[0160] Representative analog peptides are set forth in Tables XXI-XXVII. The Table indicates the length and sequence of the analog peptide as well as the motif or supermotif, if appropriate. The “source” column indicates the residues substituted at the indicated position numbers for the respective analog.

[0161] IV.G. Computer Screening of Protein Sequences from Disease-Related Antigens for Supermotif- or Motif-Bearing Peptides

[0162] In order to identify supermotif- or motif-bearing epitopes in a target antigen, a native protein sequence, e.g., a tumor-associated antigen, or sequences from an infectious organism, or a donor tissue for transplantation, is screened using a means for computing, such as an intellectual calculation or a computer, to determine the presence of a supermotif or motif within the sequence. The information obtained from the analysis of native peptide can be used directly to evaluate the status of the native peptide or may be utilized subsequently to generate the peptide epitope.

[0163] Computer programs that allow the rapid screening of protein sequences for the occurrence of the subject supermotifs or motifs are encompassed by the present invention; as are programs that permit the generation of analog peptides. These programs are implemented to analyze any identified amino acid sequence or operate on an unknown sequence and simultaneously determine the sequence and identify motif-bearing epitopes thereof; analogs can be simultaneously determined as well. Generally, the identified sequences will be from a pathogenic organism or a tumor-associated peptide. For example, the target TAA molecules include, without limitation, CEA, MAGE, p53 and her2/neu.

[0164] It is important that the selection criteria utilized for prediction of peptide binding are as accurate as possible, to correlate most efficiently with actual binding. Prediction of peptides that bind, for example, to HLA-A*0201, on the basis of the presence of the appropriate primary anchors, is positive at about a 30% rate (see, e.g., Ruppert, J. et al. Cell 74:929, 1993). However, by extensively analyzing peptide-HLA binding data disclosed herein, data in related patent applications, and data in the art, the present inventors have developed a number of allele-specific polynomial algorithms that dramatically increase the predictive value over identification on the basis of the presence of primary anchor residues alone. These algorithms take into account not only the presence or absence of primary anchors, but also consider the positive or deleterious presence of secondary anchor residues (to account for the impact of different amino acids at different positions). The algorithms are essentially based on the premise that the overall affinity (or ΔG) of peptide-HLA interactions can be approximated as a linear polynomial function of the type:

ΔG=a1i×a2i×a3i . . . ×ani

[0165] where ani is a coefficient that represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. An important assumption of this method is that the effects at each position are essentially independent of each other. This assumption is justified by studies that demonstrated that peptides are bound to HLA molecules and recognized by T cells in essentially an extended conformation. Derivation of specific algorithm coefficients has been described, for example, in Gulukota, K. et al., J. Mol. Biol. 267:1258, 1997.

[0166] Additional methods to identify preferred peptide sequences, which also make use of specific motifs, include the use of neural networks and molecular modeling programs (see, e.g., Milik et al., Nature Biotechnology 16:753, 1998; Altuvia et al., Hum. Immunol. 58:1, 1997; Altuvia et al, J. Mol. Biol. 249:244, 1995; Buus, S. Curr. Opin. Immunol. 11:209-213, 1999; Brusic, V. et al., Bioinformatics 14:121-130, 1998; Parker et al., J. Immunol. 152:163, 1993; Meister et al., Vaccine 13:581, 1995; Hanmner et al., J. Exp. Med. 180:2353, 1994; Sturniolo et al., Nature Biotechnol. 17:555 1999).

[0167] For example, it has been shown that in sets of A*0201 motif-bearing peptides containing at least one preferred secondary anchor residue while avoiding the presence of any deleterious secondary anchor residues, 69% of the peptides will bind A*0201 with an IC50 less than 500 nM (Ruppert, J. et al. Cell 74:929, 1993). These algorithms are also flexible in that cut-off scores may be adjusted to select sets of peptides with greater or lower predicted binding properties, as desired.

[0168] In utilizing computer screening to identify peptide epitopes, a protein sequence or translated sequence may be analyzed using software developed to search for motifs, for example the “FINDPATTERNS’ program (Devereux, et al. Nucl. Acids Res. 12:387-395, 1984) or MotifSearch 1.4 software program (D. Brown, San Diego, Calif.) to identify potential peptide sequences containing appropriate HLA binding motifs. The identified peptides can be scored using customized polynomial algorithms to predict their capacity to bind specific HLA class I or class II alleles. As appreciated by one of ordinary skill in the art, a large array of computer programming software and hardware options are available in the relevant art which can be employed to implement the motifs of the invention in order to evaluate (e.g., without limitation, to identify epitopes, identify epitope concentration per peptide length, or to generate analogs) known or unknown peptide sequences.

[0169] In accordance with the procedures described above, CEA peptide epitopes and analogs thereof that are able to bind HLA supertype groups or allele-specific HLA molecules have been identified (Tables VII-XX; Table XXII-XXXI).

[0170] IV.H. Preparation of Peptide Epitopes

[0171] Peptides in accordance with the invention can be prepared synthetically, by recombinant DNA technology or chemical synthesis, or from natural sources such as native tumors or pathogenic organisms. Peptide epitopes may be synthesized individually or as polyepitopic peptides. Although the peptide will preferably be substantially free of other naturally occurring host cell proteins and fragments thereof, in some embodiments the peptides may be synthetically conjugated to native fragments or particles.

[0172] The peptides in accordance with the invention can be a variety of lengths, and either in their neutral (uncharged) forms or in forms which are salts. The peptides in accordance with the invention are either free of modifications such as glycosylation, side chain oxidation, or phosphorylation; or they contain these modifications, subject to the condition that modifications do not destroy the biological activity of the peptides as described herein.

[0173] When possible, it may be desirable to optimize HLA class I binding epitopes of the invention, such as can be used in a polyepitopic construct, to a length of about 8 to about 13 amino acid residues, often 8 to 11, preferably 9 to 10. HLA class II binding peptide epitopes of the invention may be optimized to a length of about 6 to about 30 amino acids in length, preferably to between about 13 and about 20 residues. Preferably, the peptide epitopes are commensurate in size with endogenously processed pathogen-derived peptides or tumor cell peptides that are bound to the relevant HLA molecules, however, the identification and preparation of peptides that comprise epitopes of the invention can also be carried out using the techniques described herein.

[0174] In alternative embodiments, epitopes of the invention can be linked as a polyepitopic peptide, or as a minigene that encodes a polyepitopic peptide.

[0175] In another embodiment, it is preferred to identify native peptide regions that contain a high concentration of class I and/or class II epitopes. Such a sequence is generally selected on the basis that it contains the greatest number of epitopes per amino acid length. It is to be appreciated that epitopes can be present in a nested or overlapping manner, e.g. a 10 amino acid long peptide could contain two 9 amino acid long epitopes and one 10 amino acid long epitope; upon intracellular processing, each epitope can be exposed and bound by an HLA molecule upon administration of such a peptide. This larger, preferably multi-epitopic, peptide can be generated synthetically, recombinantly, or via cleavage from the native source.

[0176] The peptides of the invention can be prepared in a wide variety of ways. For the preferred relatively short size, the peptides can be synthesized in solution or on a solid support in accordance with conventional techniques. Various automatic synthesizers are commercially available and can be used in accordance with known protocols. (See, for example, Stewart & Young, SOLID PHASE PEPTIDE SYNTHESIS, 2D. ED., Pierce Chemical Co., 1984). Further, individual peptide epitopes can be joined using chemical ligation to produce larger peptides that are still within the bounds of the invention.

[0177] Alternatively, recombinant DNA technology can be employed wherein a nucleotide sequence which encodes an immunogenic peptide of interest is inserted into an expression vector, transformed or transfected into an appropriate host cell and cultivated under conditions suitable for expression. These procedures are generally known in the art, as described generally in Sambrook et at, MOLECULAR CLONING, A LABORATORY MANUAL, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989). Thus, recombinant polypeptides which comprise one or more peptide sequences of the invention can be used to present the appropriate T cell epitope.

[0178] The nucleotide coding sequence for peptide epitopes of the preferred lengths contemplated herein can be synthesized by chemical techniques, for example, the phosphotriester method of Matteucci, et al, J. Am. Chem. Soc. 103:3185 (1981). Peptide analogs can be made simply by substituting the appropriate and desired nucleic acid base(s) for those that encode the native peptide sequence; exemplary nucleic acid substitutions are those that encode an amino acid defined by the motifs/supermotifs herein. The coding sequence can then be provided with appropriate linkers and ligated into expression vectors commonly available in the art, and the vectors used to transform suitable hosts to produce the desired fusion protein. A number of such vectors and suitable host systems are now available. For expression of the fusion proteins, the coding sequence will be provided with operably linked start and stop codons, promoter and terminator regions and usually a replication system to provide an expression vector for expression in the desired cellular host. For example, promoter sequences compatible with bacterial hosts are provided in plasmids containing convenient restriction sites for insertion of the desired coding sequence. The resulting expression vectors are transformed into suitable bacterial hosts. Of course, yeast, insect or maramalian cell hosts may also be used, employing suitable vectors and control sequences.

[0179] IV.I. Assays to Detect T-Cell Responses

[0180] Once HLA binding peptides are identified, they can be tested for the ability to elicit a T-cell response. The preparation and evaluation of motif-bearing peptides are described in PCT publications WO 94/20127 and WO 94/03205. Briefly, peptides comprising epitopes from a particular antigen are synthesized and tested for their ability to bind to the appropriate HLA proteins. These assays may involve evaluating the binding of a peptide of the invention to purified HLA class I molecules in relation to the binding of a radioiodinated reference peptide. Alternatively, cells expressing empty class I molecules (Le. lacking peptide therein) may be evaluated for peptide binding by immunofluorescent staining and flow microfluorimetry. Other assays that may be used to evaluate peptide binding include peptide-dependent class I assembly assays and/or the inhibition of CTL recognition by peptide competition. Those peptides that bind to the class I molecule, typically with an affinity of 500 nM or less, are further evaluated for their ability to serve as targets for CTLs derived from infected or immunized individuals, as well as for their capacity to induce primary in vitro or in vivo CTL responses that can give rise to CTL populations capable of reacting with selected target cells associated with a disease. Corresponding assays are used for evaluation of HLA class II binding peptides. HLA class II motif-bearing peptides that are shown to bind, typically at an affinity of 1000 nM or less, are further evaluated for the ability to stimulate HTL responses.

[0181] Conventional assays utilized to detect T cell responses include proliferation assays, lymphokine secretion assays, direct cytotoxicity assays, and limiting dilution assays. For example, antigen-presenting cells that have been incubated with a peptide can be assayed for the ability to induce CTL responses in responder cell populations. Antigen-presenting cells can be normal cells such as peripheral blood mononuclear cells or dendritic cells. Alternatively, mutant non-human mammalian cell lines that are deficient in their ability to load class I molecules with internally processed peptides and that have been transfected with the appropriate human class I gene, may be used to test for the capacity of the peptide to induce in vitro primary CTL responses.

[0182] Peripheral blood mononuclear cells (PBMCs) may be used as the responder cell source of CTL precursors. The appropriate antigen-presenting cells are incubated with peptide, after which the peptide-loaded antigen-presenting cells are then incubated with the responder cell population under optimized culture conditions. Positive CTL activation can be determined by assaying the culture for the presence of CTLs that kill radio-labeled target cells, both specific peptide-pulsed targets as well as target cells expressing endogenously processed forms of the antigen from which the peptide sequence was derived.

[0183] More recently, a method has been devised which allows direct quantification of antigen-specific T cells by staining with Fluorescein-labelled HLA tetrameric complexes (Altman, J. D. et at, Proc. Natl. Acad. Sci. USA 90:10330, 1993; Altman, J. D. et al., Science 274:94, 1996). Other relatively recent technical developments include staining for intracellular lymphokines, and interferon-release assays or ELISPOT assays. Tetramer staining, intracellular lymphokine staining and ELISPOT assays all appear to be at least 10-fold more sensitive than more conventional assays (Lalvani, A. et al, J. Exp. Med. 186:859, 1997; Dunbar, P. R. et al., Curr. Biol. 8:413, 1998; Murali-Krishna, K. et at, Immunity 8:177, 1998).

[0184] HTL activation may also be assessed using such techniques known to those in the art such as T cell proliferation and secretion of lymphokines, e.g. IL-2 (see, e.g. Alexander et al, Immunity 1:751-761, 1994).

[0185] Alternatively, immunization of HLA transgenic mice can be used to determine immunogenicity of peptide epitopes. Several transgenic mouse models including mice with human A2.1, A11 (which can additionally be used to analyze HLA-A3 epitopes), and B7 alleles have been characterized and others (e.g., transgenic mice for HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed. Additional transgenic mouse models with other HLA alleles may be generated as necessary. Mice may be immunized with peptides emulsified in Incomplete Freund's Adjuvant and the resulting T cells tested for their capacity to recognize peptide-pulsed target cells and target cells transfected with appropriate genes. CTL responses may be analyzed using cytotoxicity assays described above. Similarly, HTL responses may be analyzed using such assays as T cell proliferation or secretion of lymphokines.

[0186] IV.J. Use of Peptide Epitopes as Diagnostic Agents and for Evaluating Immune Responses

[0187] In one embodiment of the invention, HLA class I and class II binding peptides as described herein are used as reagents to evaluate an immune response. The immune response to be evaluated is induced by using as an immunogen any agent that may result in the production of antigen-specific CTLs or HTLs that recognize and bind to the peptide epitope(s) to be employed as the reagent. The peptide reagent need not be used as the immunogen. Assay systems that are used for such an analysis include relatively recent technical developments such as tetramers, staining for intracellular lymphokines and interferon release assays, or ELISPOT assays.

[0188] For example, peptides of the invention are used in tetramer staining assays to assess peripheral blood mononuclear cells for the presence of antigen-specific CTLs following exposure to a tumor cell antigen or an immunogen. The HLA-tetrameric complex is used to directly visualize antigen-specific CTLs (see, e.g., Ogg et al., Science 279:2103-2106, 1998; and Altman et al., Science 174:94-96, 1996) and determine the frequency of the antigen-specific CTL population in a sample of peripheral blood mononuclear cells. A tetramer reagent using a peptide of the invention is generated as follows: A peptide that binds to an HLA molecule is refolded in the presence of the corresponding HLA heavy chain and β2-microglobulin to generate a trimolecular complex. The complex is biotinylated at the carboxyl terminal end of the heavy chain at a site that was previously engineered into the protein. Tetramer formation is then induced by the addition of streptavidin. By means of fluorescently labeled streptavidin, the tetramer can be used to stain antigen-specific cells. The cells can then be identified, for example, by flow cytometry. Such an analysis may be used for diagnostic or prognostic purposes. Cells identified by the procedure can also be used for therapeutic purposes.

[0189] Peptides of the invention are also used as reagents to evaluate immune recall responses (see, e.g., Bertoni et al., J. Clin. Invest. 100:503-513, 1997 and Penna et al., J. Exp. Med. 174:1565-1570, 1991). For example, patient PBMC samples from individuals with cancer are analyzed for the presence of antigen-specific CTLs or HTLs using specific peptides. A blood sample containing mononuclear cells can be evaluated by cultivating the PBMCs and stimulating the cells with a peptide of the invention. After an appropriate cultivation period, the expanded cell population can be analyzed, for example, for CTL or for HTL activity.

[0190] The peptides are also used as reagents to evaluate the efficacy of a vaccine. PBMCs obtained from a patient vaccinated with an immunogen are analyzed using, for example, either of the methods described above. The patient is HLA typed, and peptide epitope reagents that recognize the allele-specific molecules present in that patient are selected for the analysis. The immunogenicity of the vaccine is indicated by the presence of epitope-specific CTLs and/or HTLs in the PBMC sample.

[0191] The peptides of the invention are also used to make antibodies, using techniques well known in the art (see, e.g. CURRENT PROTOCOLS IN IMMUNOLOGY, Wiley/Greene, NY; and Antibodies A Laboratory Manual, Harlow and Lane, Cold Spring Harbor Laboratory Press, 1989), which may be useful as reagents to diagnose or monitor cancer. Such antibodies include those that recognize a peptide in the context of an HLA molecule, i.e., antibodies that bind to a peptide-MHC complex.

[0192] IV.K. Vaccine Compositions

[0193] Vaccines and methods of preparing vaccines that contain an immunogenically effective amount of one or more peptides as described herein are further embodiments of the invention. Once appropriately immunogenic epitopes have been defined, they can be sorted and delivered by various means, herein referred to as “vaccine” compositions. Such vaccine compositions can include, for example, lipopeptides (e.g., Vitiello, A. et al., J. Clin. Invest. 95:341, 1995), peptide compositions encapsulated in poly(DL-lactide-co-glycolide) (“PLG”) microspheres (see, e.g., Eldridge, et al., Molec. Immunol. 28:287-294, 1991: Alonso et al., Vaccine 12:299-306, 1994; Jones et al., Vaccine 13:675-681, 1995), peptide compositions contained in immune stimulating complexes (ISCOMS) (see, e.g., Takahashi et al., Nature 344:873-875, 1990; Hu et al., Clin Exp Immunol. 113:235-243, 1998), multiple antigen peptide systems (MAPs) (see e.g., Tam, J. P., Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413, 1988; Tam, J.P., J. Immunol. Methods 196:17-32, 1996), peptides formulated as multivalent peptides; peptides for use in ballistic delivery systems, typically crystallized peptides, viral delivery vectors (Perkus, M. E. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 379, 1996; Chakrabarti, S. et al., Nature 320:535, 1986; Hu, S. L. et al., Nature 320:537, 1986; Kieny, M.-P. et al., AIDS Bio/Technology 4:790, 1986; Top, F. H. et al., J. Infect. Dis. 124:148, 1971; Chanda, P. K. et al., Virology 175:535, 1990), particles of viral or synthetic origin (e.g., Kofler, N. et al., J. Immunol. Methods. 192:25, 1996; Eldridge, J. H. et al., Sem. Hematol. 30:16, 1993; Falo, L. D., Jr. et al., Nature Med. 7:649, 1995), adjuvants (Warren, H. S., Vogel, F. R., and Chedid, L. A. Annu. Rev. Immunol. 4:369, 1986; Gupta, R. K et al., Vaccine 11:293, 1993), liposomes (Reddy, R. et al., J. Immunol. 148:1585, 1992; Rock, K L., Immunol. Today 17:131, 1996), or, naked or particle absorbed cDNA (Ulmer, J. B. et al., Science 259:1745, 1993; Robinson, H. L., Hunt, L. A., and Webster, R G., Vaccine 11:957, 1993; Shiver, J. W. et al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed., p. 423, 1996; Cease, K. B., and Berzofsky, J. A., Annu. Rev. Immunol. 12:923, 1994 and Eldridge, J. H. et al, Sem. Hematol. 30:16, 1993). Toxin-targeted delivery technologies, also known as receptor mediated targeting, such as those of Avant Immunotherapeutics, Inc. (Needham, Mass.) can also be used.

[0194] Vaccines of the invention include nucleic acid-mediated modalities. DNA or RNA encoding one or more of the peptides of the invention can also be administered to a patient. This approach is described, for instance, in Wolff et. al., Science 247:1465 (1990) as well as U.S. Pat. Nos. 5,580,859; 5,589,466; 5,804,566; 5,739,118; 5,736,524; 5,679,647; WO 98/04720; and in more detail below. Examples of DNA-based delivery technologies include “naked DNA”, facilitated (bupivicaine, polymers, peptide-mediated) delivery, cationic lipid complexes, and particle-mediated (“gene gun”) or pressure-mediated delivery (see, e.g., U.S. Pat. No. 5,922,687).

[0195] For therapeutic or prophylactic immunization purposes, the peptides of the invention can also be expressed by viral or bacterial vectors. Examples of expression vectors include attenuated viral hosts, such as vaccinia or fowlpox. As an example of this approach, vaccinia virus is used as a vector to express nucleotide sequences that encode the peptides of the invention. Upon introduction into a host bearing a tumor, the recombinant vaccinia virus expresses the immunogenic peptide, and thereby elicits a host CTL and/or HTL response. Vaccinia vectors and methods useful in immunization protocols are described in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG vectors are described in Stover et al., Nature 351:456-460(1991). A wide variety of other vectors useful for therapeutic administration or immunization of the peptides of the invention, e.g. adeno and adeno-associated virus vectors, retroviral vectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, and the like, will be apparent to those skilled in the art from the description herein.

[0196] Furthermore, vaccines in accordance with the invention encompass compositions of one or more of the claimed peptides. A peptide can be present in a vaccine individually. Alternatively, the peptide can exist as a homopolymer comprising multiple copies of the same peptide, or as a heteropolymer of various peptides. Polymers have the advantage of increased immunological reaction and, where different peptide epitopes are used to make up the polymer, the additional ability to induce antibodies and/or CTLs that react with different antigenic determinants of the pathogenic organism or tumor-related peptide targeted for an immune response. The composition can be a naturally occurring region of an antigen or can be prepared, e.g., recombinantly or by chemical synthesis.

[0197] Carriers that can be used with vaccines of the invention are well known in the art, and include, e.g., thyroglobulin, albumins such as human serum albumin, tetanus toxoid, polyamino acids such as poly L-lysine, poly L-glutamic acid, influenza, hepatitis B virus core protein, and the like. The vaccines can contain a physiologically tolerable (i.e., acceptable) diluent such as water, or saline, preferably phosphate buffered saline. The vaccines also typically include an adjuvant. Adjuvants such as incomplete Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum are examples of materials well known in the art. Additionally, as disclosed herein, CTL responses can be primed by conjugating peptides of the invention to lipids, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P3CSS).

[0198] Upon immunization with a peptide composition in accordance with the invention, via injection, aerosol, oral, transdermal, transmucosal, intrapleural, intrathecal, or other suitable routes, the immune system of the host responds to the vaccine by producing large amounts of CTLs and/or HTLs specific for the desired antigen. Consequently, the host becomes at least partially immune to later infection, or at least partially resistant to developing an ongoing chronic infection, or derives at least some therapeutic benefit when the antigen was tumor-associated.

[0199] In some embodiments, it may be desirable to combine the class I peptide components with components that induce or facilitate neutralizing antibody and or helper T cell responses to the target antigen of interest. A preferred embodiment of such a composition comprises class I and class II epitopes in accordance with the invention. An alternative embodiment of such a composition comprises a class I and/or class II epitope in accordance with the invention, along with an HLA class II cross-reactive binding molecue such as a PADRE™ (Epimmune, San Diego, Calif.) molecule (described, for example, in U.S. Pat. No. 5,736,142).

[0200] A vaccine of the invention can also include antigen-presenting cells (APC), such as dendritic cells (DC), as a vehicle to present peptides of the invention. Vaccine compositions can be created in vitro, following dendritic cell mobilization and harvesting, whereby loading of dendritic cells occurs in vitro. For example, dendritic cells are transfected, e.g., with a minigene in accordance with the invention, or are pulsed with peptides. The dendritic cell can then be administered to a patient to elicit immune responses in vivo.

[0201] Vaccine compositions, either DNA- or peptide-based, can also be administered in vivo in combination with dendritic cell mobilization whereby loading of dendritic cells occurs in vivo.

[0202] Antigenic peptides are used to elicit a CTL and/or HTL response ex vivo, as well. The resulting CTL or HTL cells, can be used to treat tumors in patients that do not respond to other conventional forms of therapy, or will not respond to a therapeutic vaccine peptide or nucleic acid in accordance with the invention. Ex vivo CTL or HTL responses to a particular tumor-associated antigen are induced by incubating in tissue culture the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of antigen-presenting cells, such as dendritic cells, and the appropriate immunogenic peptide. After an appropriate incubation time (typically about 7-28 days), in which the precursor cells are activated and expanded into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cell (an infected cell or a tumor cell). Transfected dendritic cells may also be used as antigen presenting cells.

[0203] The vaccine compositions of the invention can also be used in combination with other treatments used for cancer, including use in combination with immune adjuvants such as IL-2, IL-12, GM-CSF, and the like.

[0204] Preferably, the following principles are utilized when selecting an array of epitopes for inclusion in a polyepitopic composition for use in a vaccine, or for selecting discrete epitopes to be included in a vaccine and/or to be encoded by nucleic acids such as a minigene. Exemplary epitopes that may be utilized in a vaccine to treat or prevent cancer are set out in Tables XXIII-XXVII and XXX. It is preferred that each of the following principles are balanced in order to make the selection. The multiple epitopes to be incorporated in a given vaccine composition can be, but need not be, contiguous in sequence in the native antigen from which the epitopes are derived.

[0205] 1.) Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with tumor clearance. For HLA Class I this includes 34 epitopes that come from at least one TAA. For HLA Class II a similar rationale is employed; again 3-4 epitopes are selected from at least one TAA (see e.g., Rosenberg et al., Science 278:1447-1450). Epitopes from one TAA may be used in combination with epitopes from one or more additional TAAs to produce a vaccine that targets tumors with varying expression patterns of frequently-expressed TAAs as described, e.g., in Example 15.

[0206] 2.) Epitopes are selected that have the requisite binding affinity established to be correlated with immunogenicity: for HLA Class I an IC50 of 500 nM or less, or for Class II an IC50 of 1000 DM or less.

[0207] 3.) Sufficient supermotif bearing-peptides, or a sufficient array of allele-specific motif-bearing peptides, are selected to give broad population coverage. For example, it is preferable to have at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess the breadth, or redundancy of, population coverage.

[0208] 4.) When selecting epitopes from cancer-related antigens it is often useful to select analogs because the patient may have developed tolerance to the native epitope. When selecting epitopes for infectious disease-related antigens it is preferable to select either native or analoged epitopes.

[0209] 5.) Of particular relevance are epitopes referred to as “nested epitopes.” Nested epitopes occur where at least two epitopes overlap in a given peptide sequence. A nested peptide sequence can comprise both HLA class I and HLA class II epitopes. When providing nested epitopes, a general objective is to provide the greatest number of epitopes per sequence. Thus, an aspect is to avoid providing a peptide that is any longer than the amino terminus of the amino terminal epitope and the carboxyl terminus of the carboxyl terminal epitope in the peptide. When providing a multi-epitopic sequence, such as a sequence comprising nested epitopes, it is generally important to screen the sequence in order to insure that it does not have pathological or other deleterious biological properties.

[0210] 6.) If a polyepitopic protein is created, or when creating a minigene, an objective is to generate the smallest peptide that encompasses the epitopes of interest. This principle is similar, if not the same as that employed when selecting a peptide comprising nested epitopes. However, with an artificial polyepitopic peptide, the size minimization objective is balanced against the need to integrate any spacer sequences between epitopes in the polyepitopic protein. Spacer amino acid residues can, for example, be introduced to avoid junctional epitopes (an epitope recognized by the immune system not present in the target antigen, and only created by the man-made juxtaposition of epitopes), or to facilitate cleavage between epitopes and thereby enhance epitope presentation. Junctional epitopes are generally to be avoided because the recipient may generate an immune response to that non-native epitope. Of particular concern is a junctional epitope that is a “dominant epitope.” A dominant epitope may lead to such a zealous response that immune responses to other epitopes are diminished or suppressed.

[0211] IV.K1. Minigene Vaccines

[0212] A number of different approaches are available which allow simultaneous delivery of multiple epitopes. Nucleic acids encoding the peptides of the invention are a particularly useful embodiment of the invention. Epitopes for inclusion in a minigene are preferably selected according to the guidelines set forth in the previous section. A preferred means of administering nucleic acids encoding the peptides of the invention uses minigene constructs encoding a peptide comprising one or multiple epitopes of the invention.

[0213] The use of multi-epitope minigenes is described below and in, e.g., co-pending application U.S. Ser. No. 09/311,784; Ishioka et al., J. Immunol. 162:3915-3925, 1999; An, L. and Whitton, J. L., J. Virol. 71:2292, 1997; Thomson, S. A. et al., J. Immunol. 157:822, 1996; Whitton, J. L. et al., J. Virol. 67:348, 1993; Hanke, R. et al, Vaccine 16:426, 1998. For example, a multi-epitope DNA plasmid encoding supermotif- and/or motif-bearing CEA epitopes derived from multiple regions of CEA, a universal helper T cell epitope e.g., the PADRE™ (or multiple HTL epitopes from CEA), and an endoplasmic reticulum-translocating signal sequence can be engineered. A vaccine may also comprise epitopes, in addition to CEA epitopes, that are derived from other TAAs.

[0214] The inmmunogenicity of a multi-epitopic minigene can be tested in transgenic mice to evaluate the magnitude of CTL induction responses against the epitopes tested. Further, the immunogenicity of DNA-encoded epitopes in vivo can be correlated with the in vitro responses of specific CTL lines against target cells transfected with the DNA plasmid. Thus, these experiments can show that the minigene serves to both: 1.) generate a CTL response and 2.) that the induced CTLs recognized cells expressing the encoded epitopes.

[0215] For example, to create a DNA sequence encoding the selected epitopes (minigene) for expression in human cells, the amino acid sequences of the epitopes may be reverse translated. A human codon usage table can be used to guide the codon choice for each amino acid. These epitope-encoding DNA sequences may be directly adjoined, so that when translated, a continuous polypeptide sequence is created. To optimize expression and/or immunogenicity, additional elements can be incorporated into the minigene design. Examples of amino acid sequences that can be reverse translated and included in the minigene sequence include: HLA class I epitopes, HLA class II epitopes, a ubiquitination signal sequence, and/or an endoplasmic reticulum targeting signal. In addition, HLA presentation of CTL and HTL epitopes may be improved by including synthetic (e.g. poly-alanine) or naturally-occurring flanking sequences adjacent to the CTL or HTL epitopes; these larger peptides comprising the epitope(s) are within the scope of the invention.

[0216] The minigene sequence may be converted to DNA by assembling oligonucleotides that encode the plus and minus strands of the minigene. Overlapping oligonucleotides (30-100 bases long) may be synthesized, phosphorylated, purified and annealed under appropriate conditions using well known techniques. The ends of the oligonucleotides can be joined, for example, using T4 DNA ligase. This synthetic minigene, encoding the epitope polypeptide, can then be cloned into a desired expression vector.

[0217] Standard regulatory sequences well known to those of skill in the art are preferably included in the vector to ensure expression in the target cells. Several vector elements are desirable: a promoter with a down-stream cloning site for minigene insertion; a polyadenylation signal for efficient transcription termination; an E. coli origin of replication; and an E. coli selectable marker (e.g. ampicillin or kanamycin resistance). Numerous promoters can be used for this purpose, e.g., the human cytomegalovirus (hCMV) promoter. See, e.g., U.S. Pat. Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.

[0218] Additional vector modifications may be desired to optimize minigene expression and immunogenicity. In some cases, introns are required for efficient gene expression, and one or more synthetic or naturally-occurring introns could be incorporated into the transcribed region of the minigene. The inclusion of mRNA stabilization sequences and sequences for replication in mammalian cells may also be considered for increasing minigene expression.

[0219] Once an expression vector is selected, the minigene is cloned into the polylinker region downstream of the promoter. This plasmid is transformed into an appropriate E. coli strain, and DNA is prepared using standard techniques. The orientation and DNA sequence of the minigene, as well as all other elements included in the vector, are confirmed using restriction mapping and DNA sequence analysis. Bacterial cells harboring the correct plasmid can be stored as a master cell bank and a working cell bank.

[0220] In addition, immunostimulatory sequences (ISSs or CpGs) appear to play a role in the immunogenicity of DNA vaccines. These sequences may be included in the vector, outside the minigene coding sequence, if desired to enhance immunogenicity.

[0221] In some embodiments, a bi-cistronic expression vector which allows production of both the minigene-encoded epitopes and a second protein (included to enhance or decrease immunogenicity) can be used. Examples of proteins or polypeptides that could beneficially enhance the immune response if co-expressed include cytokines (e.g., IL-2, IL-12, GM-CSF), cytokine-inducing molecules (e.g., LeIF), costimulatory molecules, or for HTL responses, pan-DR binding proteins (PADRE™, Epimmune, San Diego, Calif.). Helper (HTL) epitopes can be joined to intracellular targeting signals and expressed separately from expressed CTL epitopes; this allows direction of the HTL epitopes to a cell compartment different than that of the CTL epitopes. If required, this could facilitate more efficient entry of HTL epitopes into the HLA class II pathway, thereby improving HTL induction. In contrast to HTL or CTL induction, specifically decreasing the immune response by co-expression of immunosuppressive molecules (e.g. TGF-β) may be beneficial in certain diseases.

[0222] Therapeutic quantities of plasmid DNA can be produced for example, by fermentation in E. coli, followed by purification. Aliquots from the working cell bank are used to inoculate growth medium, and grown to saturation in shaker flasks or a bioreactor according to well known techniques. Plasmid DNA can be purified using standard bioseparation technologies such as solid phase anion-exchange resins supplied by QIAGEN, Inc. (Valencia, Calif.). If required, supercoiled DNA can be isolated from the open circular and linear forms using gel electrophoresis or other methods.

[0223] Purified plasmid DNA can be prepared for injection using a variety of formulations. The simplest of these is reconstitution of lyophilized DNA in sterile phosphate-buffered saline (PBS). This approach, known as “naked DNA,” is currently being used for intramuscular (IM) administration in clinical trials. To maximize the immunotherapeutic effects of minigene DNA vaccines, an alternative method for formulating purified plasmid DNA may be desirable. A variety of methods have been described, and new techniques may become available. Cationic lipids, glycolipids, and fusogenic liposomes can also be used in the formulation (see, e.g., as described by WO 93/24640; Mannino & Gould-Fogerite, BioTechniques 6(7): 682 (1988); U.S. Pat. No. 5,279,833; WO 91/06309; and Felgner, et al., Proc. Nat'l Acad. Sci. USA 84:7413 (1987). In addition, peptides and compounds referred to collectively as protective, interactive, non-condensing compounds (PINC) could also be complexed to purified plasmid DNA to influence variables such as stability, intramuscular dispersion, or trafficking to specific organs or cell types.

[0224] Target cell sensitization can be used as a functional assay for expression and HLA class I presentation of minigene-encoded CTL epitopes. For example, the plasmid DNA is introduced into a marnnalian cell line that is suitable as a target for standard CTL chromium release assays. The transfection method used will be dependent on the final formulation. Electroporation can be used for “naked” DNA, whereas cationic lipids allow direct in vitro transfection. A plasmid expressing green fluorescent protein (GFP) can be co-transfected to allow enrichment of transfected cells using fluorescence activated cell sorting (FACS). These cells are then chromium-51 (51Cr) labeled and used as target cells for epitope-specific CTL lines; cytolysis, detected by 51Cr release, indicates both production of, and HLA presentation of, minigene-encoded CTL epitopes. Expression of HTL epitopes may be evaluated in an analogous manner using assays to assess HTL activity.

[0225] In vivo immunogenicity is a second approach for functional testing of minigene DNA formulations. Transgenic mice expressing appropriate human HLA proteins are immunized with the DNA product. The dose and route of administration are formulation dependent (e.g., IM for DNA in PBS, intraperitoneal (IP) for lipid-complexed DNA). Twenty-one days after immunization, splenocytes are harvested and restimulated for one week in the presence of peptides encoding each epitope being tested. Thereafter, for CTL effector cells, assays are conducted for cytolysis of peptide-loaded, 51Cr-labeled target cells using standard techniques. Lysis of target cells that were sensitized by HLA loaded with peptide epitopes, corresponding to minigene-encoded epitopes, demonstrates DNA vaccine function for in vivo induction of CTLs. Immunogenicity of HTL epitopes is evaluated in transgenic mice in an analogous manner.

[0226] Alternatively, the nucleic acids can be administered using ballistic delivery as described, for instance, in U.S. Pat. No. 5,204,253. Using this technique, particles comprised solely of DNA are administered. In a further alternative embodiment, DNA can be adhered to particles, such as gold particles.

[0227] Minigenes can also be delivered using other bacterial or viral delivery systems well known in the art, e.g., an expression construct encoding epitopes of the invention can be incorporated into a viral vector such as vaccinia.

[0228] IV.K.2. Combinations of CTL Peptides with Helper Peptides

[0229] Vaccine compositions comprising the peptides of the present invention, or analogs thereof, which have immunostimulatory activity may be modified to provide desired attributes, such as improved serum half-life, or to enhance immunogenicity.

[0230] For instance, the ability of a peptide to induce CTL activity can be enhanced by linking the peptide to a sequence which contains at least one epitope that is capable of inducing a T helper cell response. The use of T helper epitopes in conjunction with CTL epitopes to enhance immunogenicity is illustrated, for example, in the co-pending applications U.S. Ser. No. 08/820,360, U.S. Ser. No. 08/197,484, and U.S. Ser. No. 08/464,234.

[0231] Although a CTL peptide can be directly linked to a T helper peptide, often CTL epitope/HTL epitope conjugates are linked by a spacer molecule. The spacer is typically comprised of relatively small, neutral molecules, such as amino acids or amino acid mimetics, which are substantially uncharged under physiological conditions. The spacers are typically selected from, e.g., Ala, Gly, or other neutral spacers of nonpolar amino acids or neutral polar amino acids. It will be understood that the optionally present spacer need not be comprised of the same residues and thus may be a hetero- or homo-oligomer. When present, the spacer will usually be at least one or two residues, more usually three to six residues and sometimes 10 or more residues. The CTL peptide epitope can be linked to the T helper peptide epitope either directly or via a spacer either at the amino or carboxy terminus of the CTL peptide. The amino terminus of either the immunogenic peptide or the T helper peptide may be acylated.

[0232] In certain embodiments, the T helper peptide is one that is recognized by T helper cells present in the majority of the population. This can be accomplished by selecting amino acid sequences that bind to many, most, or all of the HLA class II molecules. These are known as “loosely HLA-restricted” or “promiscuous” T helper sequences. Examples of peptides that are promiscuous include sequences from antigens such as tetanus toxoid at positions 830-843 (QYIKANSKFIGITE), Plasmodium falciparum circumsporozoite (CS) protein at positions 378-398 (DIEKK AK KASSVFNVVNS), and Streptococcus 18 kD protein at positions 116 (GAVDSILGGVATYGAA). Other examples include peptides bearing a DR 1-4-7 supermotif, or either of the DR3 motifs.

[0233] Alternatively, it is possible to prepare synthetic peptides capable of stimulating T helper lymphocytes, in a loosely HLA-restricted fashion, using amino acid sequences not found in nature (see, e.g., PCT publication WO 95/07707). These synthetic compounds called Pan-DR-binding epitopes (e.g., PADRE™, Epimnmune, Inc., San Diego, Calif.) are designed to most preferrably bind most HLA-DR (human HLA class II) molecules. For instance, a pan-DR-binding epitope peptide having the formula: aKXVAAWTLKAAa, where “X” is either cyclohexylalanine, phenylalanine, or tyrosine, and “a” is either D-alanine or L-alanine, has been found to bind to most HLA-DR alleles, and to stimulate the response of T helper lymphocytes from most individuals, regardless of their HLA type. An alternative of a pan-DR binding epitope comprises all “L” natural amino acids and can be provided in the form of nucleic acids that encode the epitope.

[0234] HTL peptide epitopes can also be modified to alter their biological properties. For example, they can be modified to include D-amino acids to increase their resistance to proteases and thus extend their serum half life, or they can be conjugated to other molecules such as lipids, proteins, carbohydrates, and the like to increase their biological activity. For example, a T helper peptide can be conjugated to one or more palmitic acid chains at either the amino or carboxyl termini.

[0235] IV.K3. Combinations of CTL Peptides with T Cell Priming Agents

[0236] In some embodiments it may be desirable to include in the pharmaceutical compositions of the invention at least one component which primes cytotoxic T lymphocytes. Lipids have been identified as agents capable of priming CTL in vivo against viral antigens. For example, palmitic acid residues can be attached to the ε- and α-amino groups of a lysine residue and then linked, e.g. via one or more linking residues such as Gly, Gly-Gly-, Ser, Ser-Ser, or the like, to an immunogenic peptide. The lipidated peptide can then be administered either directly in a micelle or particle, incorporated into a liposome, or emulsified in an adjuvant, e.g., incomplete Freund's adjuvant. A preferred immunogenic composition comprises palmitic acid attached to ε- and α-amino groups of Lys, which is attached via linkage, e.g., Ser-Ser, to the amino terminus of the immunogenic peptide.

[0237] As another example of lipid priming of CTL responses, E. coli lipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P3CSS) can be used to prime virus specific CTL when covalently attached to an appropriate peptide (see, e.g., Deres, et al., Nature 342:561, 1989). Peptides of the invention can be coupled to P3CSS, for example, and the lipopeptide administered to an individual to specifically prime a CTL response to the target antigen. Moreover, because the induction of neutralizing antibodies can also be primed with P3CSS-conjugated epitopes, two such compositions can be combined to more effectively elicit both humoral and cell-mediated responses.

[0238] CTL and/or HTL peptides can also be modified by the addition of amino acids to the termini of a peptide to provide for ease of linking peptides one to another, for coupling to a carrier support or larger peptide, for modifying the physical or chemical properties of the peptide or oligopeptide, or the like. Amino acids such as tyrosine, cysteine, lysine, glutamic or aspartic acid, or the like, can be introduced at the C- or N-terminus of the peptide or oligopeptide, particularly class I peptides. However, it is to be noted that modification at the carboxyl terminus of a CTL epitope may, in some cases, alter binding characteristics of the peptide. In addition, the peptide or oligopeptide sequences can differ from the natural sequence by being modified by terminal-NH2 acylation, e.g., by alkanoyl (C1-C20) or thioglycolyl acetylation, terminal-carboxyl amidation, e.g., ammonia, methylamine, etc. In some instances these modifications may provide sites for linking to a support or other molecule.

[0239] IV.K.4. Vaccine Compositions Comprising DC Pulsed with CTL and/or HTL Peptides

[0240] An embodiment of a vaccine composition in accordance with the invention comprises ex vivo administration of a cocktail of epitope-bearing peptides to PBMC, or isolated DC therefrom, from the patient's blood. A pharmaceutical to facilitate harvesting of DC can be used, such as Progenipoietin™ (Monsanto, St. Louis, Mo.) or GM-CSF/IL4. After pulsing the DC with peptides and prior to reinfusion into patients, the DC are washed to remove unbound peptides. In this embodiment, a vaccine comprises peptide-pulsed DCs which present the pulsed peptide epitopes complexed with HLA molecules on their surfaces.

[0241] The DC can be pulsed ex vivo with a cocktail of peptides, some of which stimulate CTL response to one or more antigens of interest, e.g., tumor-associated antigens such as CEA, p53, Her2/neu, MAGE, prostate cancer-associated antigens and the like. Optionally, a helper T cell peptide such as a PADRE™ family molecule, can be included to facilitate the CTL response.

[0242] IV.L. Administration of Vaccines for Therapeutic or Prophylactic Purposes

[0243] The peptides of the present invention and pharmaceutical and vaccine compositions of the invention are typically used therapeutically to treat cancer. Vaccine compositions containing the peptides of the invention are typically administered to a cancer patient who has a malignancy associated with expression of one or more tumor-associated antigens. Alternatively, vaccine compositions can be administered to an individual susceptible to, or otherwise at risk for developing a particular type of cancer, e.g., breast cancer.

[0244] In therapeutic applications, peptide and/or nucleic acid compositions are administered to a patient in an amount sufficient to elicit an effective CTL and/or HTL response to the tumor antigen and to cure or at least partially arrest or slow symptoms and/or complications. An amount adequate to accomplish this is defined as “therapeutically effective dose.” Amounts effective for this use will depend on, e.g., the particular composition administered, the manner of administration, the stage and severity of the disease being treated, the weight and general state of health of the patient, and the judgment of the prescribing physician.

[0245] As noted above, peptides comprising CTL and/or HTL epitopes of the invention induce immune responses when presented by HLA molecules and contacted with a CTL or HTL specific for an epitope comprised by the peptide. The manner in which the peptide is contacted with the CTL or HTL is not critical to the invention. For instance, the peptide can be contacted with the CTL or HTL either in vivo or in vitro. If the contacting occurs in vivo, the peptide itself can be administered to the patient, or other vehicles, e.g., DNA vectors encoding one or more peptides, viral vectors encoding the peptide(s), liposomes and the like, can be used, as described herein.

[0246] When the peptide is contacted in vitro, the vaccinating agent can comprise a population of cells, e.g., peptide-pulsed dendritic cells, or TAA-specific CTLs, which have been induced by pulsing antigen-presenting cells in vitro with the peptide. Such a cell population is subsequently administered to a patient in a therapeutically effective dose.

[0247] For pharmaceutical compositions, the immunogenic peptides of the invention, or DNA encoding them, are generally administered to an individual already diagnosed with cancer. The peptides or DNA encoding them can be administered individually or as fusions of one or more peptide sequences.

[0248] For therapeutic use, administration should generally begin at the first diagnosis of cancer. This is followed by boosting doses until at least symptoms are substantially abated and for a period thereafter. The embodiment of the vaccine composition (i.e., including, but not limited to embodiments such as peptide cocktails, polyepitopic polypeptides, minigenes, or TAA-specific CTLs) delivered to the patient may vary according to the stage of the disease. For example, a vaccine comprising TAA-specific CTLs may be more efficacious in killing tumor cells in patients with advanced disease than alternative embodiments.

[0249] The vaccine compositions of the invention may also be used therapeutically in combination with treatments such as surgery. An example is a situation in which a patient has undergone surgery to remove a primary tumor and the vaccine is then used to slow or prevent recurrence and/or metastasis.

[0250] Where susceptible individuals, e.g., individuals who may be diagnosed as being genetically pre-disposed to developing a particular type of tumor, are identified prior to diagnosis of cancer, the composition can be targeted to them, thus minimizing the need for administration to a larger population.

[0251] The dosage for an initial therapeutic immunization generally occurs in a unit dosage range where the lower value is about 1, 5, 50, 500, or 1,000 μg and the higher value is about 10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a human typically range from about 500 μg to about 50,000;g per 70 kilogram patient. Boosting dosages of between about 1.0 μg to about 50,000 μg of peptide pursuant to a boosting regimen over weeks to months may be administered depending upon the patient's response and condition as determined by measuring the specific activity of CIL and HTE obtained from the patient's blood.

[0252] Administration should continue until at least clinical symptoms or laboratory tests indicate that the tumor has been eliminated or that the tumor cell burden has been substantially reduced and for a period thereafter. The dosages, routes of administration, and dose schedules are adjusted in accordance with methodologies known in the art.

[0253] In certain embodiments, peptides and compositions of the present invention are employed in serious disease states, that is, life-threatening or potentially life threatening situations. In such cases, as a result of the minimal amounts of extraneous substances and the relative nontoxic nature of the peptides in preferred compositions of the invention, it is possible and may be felt desirable by the treating physician to administer substantial excesses of these peptide compositions relative to these stated dosage amounts.

[0254] The pharmaceutical compositions for therapeutic treatment are intended for parenteral topical, oral, intrathecal, or local administration. Preferably, the pharmaceutical compositions are administered parentally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly. Thus, the invention provides compositions for parenteral administration which comprise a solution of the immunogenic peptides dissolved or suspended in an acceptable carrier, preferably an aqueous carrier. A variety of aqueous carriers may be used, e.g., water, buffered water, 0.8% saline, 0.3% glycine, hyaluronic acid and the like. These compositions may be sterilized by conventional, well known sterilization techniques, or may be sterile filtered. The resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH-adjusting and buffering agents, tonicity adjusting agents, wetting agents, preservatives, and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.

[0255] The concentration of peptides of the invention in the pharmaceutical formulations can vary widely, ie., from less than about 0.1%, usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected primarily by fluid volumes, viscosities, etc., in accordance with the particular mode of administration selected.

[0256] A human unit dose form of the peptide composition is typically included in a pharmaceutical composition that comprises a human unit dose of an acceptable carrier, preferably an aqueous carrier, and is administered in a volume of fluid that is known by those of skill in the art to be used for administration of such compositions to humans (see, e.g., Remington's Pharmaceutical Sciences, 17th Edition, A. Gennaro, Editor, Mack Publishing Co., Easton, Pa., 1985).

[0257] The peptides of the invention may also be administered via liposomes, which serve to target the peptides to a particular tissue, such as lymphoid tissue, or to target selectively to infected cells, as well as to increase the half-life of the peptide composition. Liposomes include emulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations, the peptide to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to a receptor prevalent among lymphoid cells, such as monoclonal antibodies which bind to the CD45 antigen, or with other therapeutic or immunogenic compositions. Thus, liposomes either filled or decorated with a desired peptide of the invention can be directed to the site of lymphoid cells, where the liposomes then deliver the peptide compositions. Liposomes for use in accordance with the invention are formed from standard vesicle-forming lipids, which generally include neutral and negatively charged phospholipids and a sterol, such as cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka, et al., Ann. Rev. Biophys. Bioeng. 9:467 (1980), and U.S. Pat. Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.

[0258] For targeting cells of the immune system, a ligand to be incorporated into the liposome can include, e.g., antibodies or fragments thereof specific for cell surface determinants of the desired immune system cells. A liposome suspension containing a peptide may be administered intravenously, locally, topically, etc. in a dose which varies according to, inter alia, the manner of administration, the peptide being delivered, and the stage of the disease being treated.

[0259] For solid compositions, conventional nontoxic solid carriers may be used which include, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any of the normally employed excipients, such as those carriers previously listed, and generally 10-95% of active ingredient, that is, one or more peptides of the invention, and more preferably at a concentration of 250/-75%.

[0260] For aerosol administration, the immunogenic peptides are preferably supplied in finely divided form along with a surfactant and propellant. Typical percentages of peptides are 0.01%-20% by weight, preferably 1%-10%. The surfactant must, of course, be nontoxic, and preferably soluble in the propellant. Representative of such agents are the esters or partial esters of fatty acids containing from 6 to 22 carbon atoms, such as caproic, octanoic, lauric, paimitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides may be employed. The surfactant may constitute 0.1%-20% by weight of the composition, preferably 0.25-5%. The balance of the composition is ordinarily propellant. A carrier can also be included, as desired, as with, e.g., lecithin for intranasal delivery.

[0261] IV.M. HLA Expression: Impications for T Cell-Based Immununotherapy

[0262] Disease Progression in Cancer and Infectious Disease

[0263] It is well recognized that a dynamic interaction between exists between host and disease, both in the cancer and infectious disease settings. In the infectious disease setting, it is well established that pathogens evolve during disease. The strains that predominate early in HIV infection are different from the ones that are associated with AIDS and later disease stages (NS versus S strains). It has long been hypothesized that pathogen forms that are effective in establishing infection may differ from the ones most effective in terms of replication and chronicity.

[0264] Similarly, it is widely recognized that the pathological process by which an individual succumbs to a neoplastic disease is complex. During the course of disease, many changes occur in cancer cells. The tumor accumulates alterations which are in part related to dysfunctional regulation of growth and differentiation, but also related to maximizing its growth potential, escape from drug treatment and/or the body's immunosurveillance. Neoplastic disease results in the accumulation of several different biochemical alterations of cancer cells, as a function of disease progression. It also results in significant levels of intra- and inter-cancer heterogeneity, particularly in the late, metastatic stage.

[0265] Familiar examples of cellular alterations affecting treatment outcomes include the outgrowth of radiation or chemotherapy resistant tumors during the course of therapy. These examples parallel the emergence of drug resistant viral strains as a result of aggressive chemotherapy, e.g., of chronic HBV and HIV infection, and the current resurgence of drug resistant organisms that cause Tuberculosis and Malaria. It appears that significant heterogeneity of responses is also associated with other approaches to cancer therapy, including anti-angiogenesis drugs, passive antibody immunotherapy, and active T ceU-based immunotherapy. Thus, in view of such phenomena, epitopes from multiple disease-related antigens can be used in vaccines and therapeutics thereby counteracting the ability of diseased cells to mutate and escape treatment.

[0266] The Interplay Between Disease and the Immune System

[0267] One of the main factors contributing to the dynamic interplay between host and disease is the immune response mounted against the pathogen, infected cell, or malignant cell. In many conditions such immune responses control the disease. Several animal model systems and prospective studies of natural infection in humans suggest that immune responses against a pathogen can control the pathogen, prevent progression to severe disease and/or eliminate the pathogen. A common theme is the requirement for a multispecific T cell response, and that narrowly focused responses appear to be less effective. These observations guide skilled artisan as to embodiments of methods and compositions of the present invention that provide for a broad immune response.

[0268] In the cancer setting there are several findings that indicate that immune responses can impact neoplastic growth:

[0269] First, the demonstration in many different animal models, that anti-tumor T cells, restricted by MHC class I, can prevent or treat tumors.

[0270] Second, encouraging results have come from immunotherapy trials.

[0271] Third, observations made in the course of natural disease correlated the type and composition of T cell infiltrate within tumors with positive clinical outcomes (Coulie PG, et al. Antitumor immunity at work in a melanoma patient In Advances in Cancer Research, 213-242, 1999).

[0272] Finally, tumors commonly have the ability to mutate, thereby changing their immunological recognition. For example, the presence of monospecific CTL was also correlated with control of tumor growth, until antigen loss emerged (Riker A, et al., Immune selection after antigen-specific immunotherapy of melanoma Surgery, Aug: 126(2):112-20, 1999; Marchand M, et al, Tumor regressions observed in patients with metastatic melanoma treated with an antigenic peptide encoded by gene MAGE-3 and presented by HLA-A1 Int. J. Cancer 80(2):219-30, Jan. 18, 1999). Similarly, loss of beta 2 microglobulin was detected in 5/13 lines established from melanoma patients after receiving immunotherapy at the NCI (Restifo N P, et at, Loss of functional Beta2-microglobulin in metastatic melanomas from five patients receiving immunotherapy Journal of the National Cancer Institute, Vol. 88 (2), 100-108, January 1996). It has long been recognized that HLA class I is frequently altered in various tumor types. This has led to a hypothesis that this phenomenon might reflect immune pressure exerted on the tumor by means of class I restricted CTL. The extent and degree of alteration in HLA class I expression appears to be reflective of past immune pressures, and may also have prognostic value (van Duinen S G, et at, Level of HLA antigens in locoregional metastases and clinical course of the disease in patients with melanoma Cancer Research 48, 1019-1025, February 1988; Moller P, et al., Influence of major histocompatibility complex class I and II antigens on survival in colorectal carcinoma Cancer Research 51, 729-736, January 1991). Taken together, these observations provide a rationale for immunotherapy of cancer and infectious disease, and suggest that effective strategies need to account for the complex series of pathological changes associated with disease.

[0273] The Three Main Types of Alterations in HLA Expression in Tumors and Their Functional Significance

[0274] The level and pattern of expression of HLA class I antigens in tumors has been studied in many different tumor types and alterations have been reported in all types of tumors studied. The molecular mechanisms underlining HLA class I alterations have been demonstrated to be quite heterogeneous. They include alterations in the TAP/processing pathways, mutations of p2-microglobulin and specific HLA heavy chains, alterations in the regulatory elements controlling over class I expression and loss of entire chromosome sections. There are several reviews on this topic, see, e.g.,: Garrido F, et at, Natural history of HLA expression during tumour development Immunol Today 14(10):491-499, 1993; Kaklamanis L, et al., Loss of HLA class-I alleles, heavy chains and O2-microglobulin in colorectal cancer Int. J. Cancer, 51 (3):379-85, May 28, 1992. There are three main types of HLA Class I alteration (complete loss, allele-specific loss and decreased expression). The functional significance of each alteration is discussed separately:

[0275] Complete Loss of HLA Expression

[0276] Complete loss of HLA expression can result from a variety of different molecular mechanisms, reviewed in (Algarra I, et al., The HLA crossroad in tumor immunology Human Immunology 61, 65-73, 2000; Browning M, et a!, Mechanisms of loss of HLA class I expression on colorectal tumor cells Tissue Antigens 47:364-371, 1996; Ferrone S, et al., Loss of HLA class I antigens by melanoma cells: molecular mechanisms, functional significance and clinical relevance Immunology Today, 16(10): 487494, 1995; Garrido F, et al., Natural history of HLA expression during tumour development Immunology Today 14(10):491499, 1993; Tait, BD, HLA Class I expression on human cancer cells: Implications for effective immunotherapy Hum Immunol 61, 158-165, 2000). In functional terms, this type of alteration has several important implications.

[0277] While the complete absence of class I expression will eliminate CTL recognition of those tumor cells, the loss of HLA class I will also render the tumor cells extraordinary sensitive to lysis from NK cells (Ohnmacht, Ga., et al., Heterogeneity in expression of human leukocyte antigens and melanoma-associated antigens in advanced melanoma J Cellular Phys 182:332-338, 2000; Liunggren H G, et al., Host resistance directed selectively against H-2 deficient lymphoma variants: Analysis of the mechanism J. Exp. Med., Dec 1;162(6):1745-59, 1985; Maio M, et al., Reduction in susceptibility to natural killer cell-mediated lysis of human FO-1 melanoma cells after induction of HLA class I antigen expression by transfection with B2m gene J. Clin. Invest. 88(1):282-9, July 1991; Schrier P I, et al., Relationship between myc oncogene activation and MHC class I expression Adv. Cancer Res., 60:181-246, 1993).

[0278] The complementary interplay between loss of HLA expression and gain in NK sensitivity is exemplified by the classic studies of Coulie and coworkers (Coulie, P G, et al., Antitumor immunity at work in a melanoma patient. In Advances in Cancer Research 213-242, 1999) which described the evolution of a patient's immune response over the course of several years. Because of increased sensitivity to NK lysis, it is predicted that approaches leading to stimulation of innate immunity in general and NK activity in particular would be of special significance. An example of such approach is the induction of large amounts of dendritic cells (DC) by various hematopoietic growth factors, such as Flt3 ligand or ProGP. The rationale for this approach resides in the well known fact that dendritic cells produce large amounts of IL-12, one of the most potent stimulators for innate immunity and NK activity in particular. Alternatively, IL-12 is administered directly, or as nucleic acids that encode it. In this light, it is interesting to note that Flt3 ligand treatment results in transient tumor regression of a class I negative prostate murine cancer model (Ciavarra R P, et al., Flt3-Ligand induces transient tumor regression in an ectopic treatment model of major histocompatibility complex-negative prostate cancer Cancer Res 60:2081-84, 2000). In this context, specific anti-tumor vaccines in accordance with the invention synergize with these types of hematopoietic growth factors to facilitate both CTL and NK cell responses, thereby appreciably impairing a cell's ability to mutate and thereby escape efficacious treatment. Thus, an embodiment of the present invention comprises a composition of the invention together with a method or composition that augments functional activity or numbers of NK cells. Such an embodiment can comprise a protocol that provides a composition of the invention sequentially with an NK-inducing modality, or contemporaneous with an NK-inducing modality.

[0279] Secondly, complete loss of HLA frequently occurs only in a fraction of the tumor cells, while the remainder of tumor cells continue to exhibit normal expression. In functional terms, the tumor would still be subject, in part, to direct attack from a CTL response; the portion of cells lacking HLA subject to an NK response. Even if only a CTL response were used, destruction of the HLA expressing fraction of the tumor has dramatic effects on survival times and quality of life.

[0280] It should also be noted that in the case of heterogeneous HLA expression, both normal HLA-expressing as well as defective cells are predicted to be susceptible to immune destruction based on “bystander effects.” Such effects were demonstrated, e.g., in the studies of Rosendahl and colleagues that investigated in vivo mechanisms of action of antibody targeted superantigens (Rosendahl A, et al., Perforin and IFN-gamma are involved in the antitumor effects of antibody-targeted superantigens J. Immunol. 160(11):5309-13, Jun. 1, 1998). The bystander effect is understood to be mediated by cytokines elicited from, e.g., CTLs acting on an HLA-bearing target cell, whereby the cytokines are in the environment of other diseased cells that are concomitantly killed.

[0281] Allele-Specific Loss

[0282] One of the most common types of alterations in class I molecules is the selective loss of certain alleles in individuals heterozygous for HLA. Allele-specific alterations might reflect the tumor adaptation to immune pressure, exerted by an immmunodominant response restricted by a single HLA restriction element. This type of alteration allows the tumor to retain class I expression and thus escape NK cell recognition, yet still be susceptible to a CTL-based vaccine in accordance with the invention which comprises epitopes corresponding to the remaining HLA type. Thus, a practical solution to overcome the potential hurdle of allele-specific loss relies on the induction of multispecific responses. Just as the inclusion of multiple disease-associated antigens in a vaccine of the invention guards against mutations that yield loss of a specific disease antigens, simultaneously targeting multiple HLA specificities and multiple disease-related antigens prevents disease escape by allele-specific losses.

[0283] Decrease in Expression (Allele-Specific or Not)

[0284] The sensitivity of effector CTL has long been demonstrated (Brower, R C, et al., Mimal requirements for peptide mediated activation of CD8+CTL Mol. Immunol., 31; 1285-93, 1994; Chriustnick, ET, et al. Low numbers of MHC class I-peptide complexes required to trigger a T cell response Nature 352:67-70, 1991; Sykulev, Y, et al., Evidence that a single peptide-MHC complex on a target cell can elicit a cytolytic T cell response Immunity, 4(6):565-71, June 1996). Even a single peptide/MHC complex can result in tumor cells lysis and release of anti-tumor lymphokines. The biological significance of decreased HLA expression and possible tumor escape from immune recognition is not fully known. Nevertheless, it has been demonstrated that CTL recognition of as few as one MHC/peptide complex is sufficient to lead to tumor cell lysis.

[0285] Further, it is commonly observed that expression of HLA can be upregulated by gamma IFN, commonly secreted by effector CTL. Additionally, HLA class I expression can be induced in vivo by both alpha and beta IFN (Halloran, et al Local T cell responses induce widespread MHC expression. J Immunol 148:3837, 1992; Pestka, S, et al., Interferons and their actions Annu. Rev. Biochem. 56:727-77, 1987). Conversely, decreased levels of HLA class I expression also render cells more susceptible to NK lysis.

[0286] With regard to gamma IFN, Torres et al (Torres, M J, et al., Loss of an HLA haplotype in pancreas cancer tissue and its corresponding tumor derived cell line. Tissue Antigens 47:372-81, 1996) note that HLA expression is upregulated by gamma IFN in pancreatic cancer, unless a total loss of haplotype has occurred. Simflarly, Rees and Mian note that allelic deletion and loss can be restored, at least partially, by cytokines such as IFN-gamma (Rees, R, et al Selective MHC expression in tumours modulates adaptive and innate antitumour responses Cancer Immunol Immunother 48:374-81, 1999). It has also been noted that IFN-gamma treatment results in upregulation of class I molecules in the majority of the cases studied (Browning M, et at, Mechanisms of loss of HLA class I expression on colorectal tumor cells. Tissue Antigens 47:364-71, 1996). Kaklamakis, et al. also suggested that adjuvant immunotherapy with IFN-gamma may be beneficial in the case of HLA class I negative tumors (Kaklamanis L, Loss of transporter in antigen processing 1 transport protein and major histocompatibility complex class I molecules in metastatic versus primary breast cancer. Cancer Research 55:5191-94, November 1995). It is important to underline that IFN-gamma production is induced and self-amplified by local inflammation/immunization (Halloran, et al. Local T cell responses induce widespread MHC expression J. Immunol 148:3837, 1992), resulting in large increases in MHC expressions even in sites distant from the inflammatory site.

[0287] Finally, studies have demonstrated that decreased HLA expression can render tumor cells more susceptible to NK lysis (Ohnmacht, Ga., et al, Heterogeneity in expression of human leukocyte antigens and melanoma-associated antigens in advanced melanoma J Cellular Phys 182:332-38, 2000; Liunggren HG, et al, Host resistance directed selectively against H-2 deficient lymphoma variants: Analysis of the mechanism J. Exp. Med., 162(6):1745-59, Dec. 1, 1985; Maio M, et al., Reduction in susceptibility to natural killer cell-mediated lysis of human FO-1 melanoma cells after induction of HLA class I antigen expression by transfection with β2 m gene J. Clin. Invest. 88(1):282-9, July 1991; Schrier P I, et al., Relationship between myc oncogene activation and MHC class I expression Adv. Cancer Res., 60:181-246, 1993). If decreases in HLA expression benefit a tumor because it facilitates CTL escape, but render the tumor susceptible to NK lysis, then a minimal level of HLA expression that allows for resistance to NK activity would be selected for (Garrido F, et al., Implications for immunosurveillance of altered HLA class I phenotypes in human tumours Immunol Today 18(2):89-96, February 1997). Therefore, a therapeutic compositions or methods in accordance with the invention together with a treatment to upregulate HLA expression and/or treatment with high affinity T-cells renders the tumor sensitive to CTL destruction.

[0288] Frequency of Alterations in HLA Expression

[0289] The frequency of alterations in class I expression is the subject of numerous studies (Algarra I, et al., The HLA crossroad in tumor immunology Human Immunology 61, 65-73, 2000). Rees and Mian estimate allelic loss to occur overall in 3-20% of tumors, and allelic deletion to occur in 15-50% of tumors. It should be noted that each cell carries two separate sets of class I genes, each gene carrying one HLA-A and one HLA-B locus. Thus, fully heterozygous individuals carry two different HLA-A molecules and two different HLA-B molecules. Accordingly, the actual frequency of losses for any specific allele could be as little as one quarter of the overall frequency. They also note that, in general, a gradient of expression exists between normal cells, primary tumors and tumor metastasis. In a study from Natali and coworkers (Natali PG, et al., Selective changes in expression of HLA class I polymorphic determinants in human solid tumors PNAS USA 86:6719-6723, September 1989), solid tumors were investigated for total HLA expression, using W6/32 antibody, and for allele-specific expression of the A2 antigen, as evaluated by use of the BB7.2 antibody. Tumor samples were derived from primary cancers or metastasis, for 13 different tumor types, and scored as negative if less than 20%, reduced if in the 30-80% range, and normal above 80%. All tumors, both primary and metastatic, were HLA positive with W6/32. In terms of A2 expression, a reduction was noted in 16.1% of the cases, and A2 was scored as undetectable in 39.4% of the cases. Garrido and coworkers (Garrido F, et al., Natural history of HLA expression during tumour development Immunol Today 14(10):491-99, 1993) emphasize that HLA changes appear to occur at a particular step in the progression from benign to most aggressive. Jiminez et al (Jiminez P, et al., Microsatellite instability analysis in tumors with different mechanisms for total loss of HLA expression. Cancer Immunol Immunother 48:684-90, 2000) have analyzed 118 different tumors (68 colorectal 34 laryngeal and 16 melanomas). The frequencies reported for total loss of HLA expression were 11% for colon, 18% for melanoma and 13% for larynx. Thus, HLA class I expression is altered in a significant fraction of the tumor types, possibly as a reflection of immune pressure, or simply a reflection of the accumulation of pathological changes and alterations in diseased cells.

[0290] Immunotherapy in the Context of HLA Loss

[0291] A majority of the tumors express HLA class I, with a general tendency for the more severe alterations to be found in later stage and less differentiated tumors. This pattern is encouraging in the context of immunotherapy, especially considering that: 1) the relatively low sensitivity of immunohistochemical techniques might underestimate HLA expression in tumors; 2) class I expression can be induced in tumor cells as a result of local inflammation and lymphokine release; and, 3) class I negative cells are sensitive to lysis by NK cells.

[0292] Accordingly, various embodiments of the present invention can be selected in view of the fact that there can be a degree of loss of HLA molecules, particularly in the context of neoplastic disease. For example, the treating physician can assay a patient's tumor to ascertain whether HLA is being expressed. If a percentage of tumor cells express no class I HLA, then embodiments of the present invention that comprise methods or compositions that elicit NK cell responses can be employed. As noted herein, such NK-inducing methods or composition can comprise a Flt3 ligand or ProGP which facilitate mobilization of dendritic cells, the rationale being that dendritic cells produce large amounts of IL-12. IL-12 can also be administered directly in either amino acid or nucleic acid form. It should be noted that compositions in accordance with the invention can be administered concurrently with NK cell-inducing compositions, or these compositions can be administered sequentially.

[0293] In the context of allele-specific HLA loss, a tumor retains class I expression and may thus escape NK cell recognition, yet still be susceptible to a CTL-based vaccine in accordance with the invention which comprises epitopes corresponding to the remaining HLA type. The concept here is analogous to embodiments of the invention that include multiple disease antigens to guard against mutations that yield loss of a specific antigen. Thus, one can simultaneously target multiple HLA specificities and epitopes from multiple disease-related antigens to prevent tumor escape by allele-specific loss as well as disease-related antigen loss. In addition, embodiments of the present invention can be combined with alternative therapeutic compositions and methods. Such alternative compositions and methods comprise, without limitation, radiation, cytotoxic pharmaceuticals, and/or compositions/methods that induce humoral antibody responses.

[0294] Moreover, it has been observed that expression of HLA can be upregulated by gamma IFN, which is commonly secreted by effector CTL, and that HLA class I expression can be induced in vivo by both alpha and beta IFN. Thus, embodiments of the invention can also comprise alpha, beta and/or gamma IFN to facilitate upregualtion of HLA.

[0295] IV.N. Reprieve Periods From Therapies That Induce Side Effects: “Scheduled Treatment Interruptions or Drug Holidays”

[0296] Recent evidence has shown that certain patients infected with a pathogen, whom are initially treated with a therapeutic regimen to reduce pathogen load, have been able to maintain decreased pathogen load when removed from the therapeutic regimen, i.e., during a “drug holiday” (Rosenberg, E., et al., Immune control of HIV-1 after early treatment of acute infection Nature 407:523-26, Sep. 28, 2000) As appreciated by those skilled in the art, many therapeutic regimens for both pathogens and cancer have numerous, often severe, side effects. During the drug holiday, the patient's immune system is keeping the disease in check. Methods for using compositions of the invention are used in the context of drug holidays for cancer and pathogenic infection.

[0297] For treatment of an infection, where therapies are not particularly imnmunosuppressive, compositions of the invention are administered concurrently with the standard therapy. During this period, the patient's immune system is directed to induce responses against the epitopes comprised by the present inventive compositions. Upon removal from the treatment having side effects, the patient is primed to respond to the infectious pathogen should the pathogen load begin to increase. Composition of the invention can be provided during the drug holiday as well.

[0298] For patients with cancer, many therapies are immunosuppressive. Thus, upon achievement of a remission or identification that the patient is refractory to standard treatment, then upon removal from the immunosuppressive therapy, a composition in accordance with the invention is administered. Accordingly, as the patient's immune system reconstitutes, precious immune resources are simultaneously directed against the cancer. Composition of the invention can also be administered concurrently with an immunosuppressive regimen if desired.

[0299] Iv.O. Kits

[0300] The peptide and nucleic acid compositions of this invention can be provided in kit form together with instructions for vaccine administration. Typically the kit would include desired peptide compositions in a container, preferably in unit dosage form and instructions for administration. An alternative kit would include a minigene construct with desired nucleic acids of the invention in a container, preferably in unit dosage form together with instructions for administration. Lymphokines such as IL-2 or IL-12 may also be included in the kit. Other kit components that may also be desirable include, for example, a sterile syringe, booster dosages, and other desired excipients.

[0301] IV.P. Overview

[0302] Epitopes in accordance with the present invention were successfully used to induce an immune response. Immune responses with these epitopes have been induced by administering the epitopes in various forms. The epitopes have been administered as peptides, as nucleic acids, and as viral vectors comprising nucleic acids that encode the epitope(s) of the invention. Upon administration of peptide-based epitope forms, immune responses have been induced by direct loading of an epitope onto an empty HLA molecule that is expressed on a cell and via internalization of the epitope and processing via the HLA class I pathway; in either event, the HLA molecule expressing the epitope was then able to interact with and induce a CTL response. Peptides can be delivered directly or using such agents as liposomes. They can additionally be delivered using ballistic delivery, in which the peptides are typically in a crystalline form. When DNA is used to induce an immune response, it is administered either as naked DNA, generally in a dose range of approximately 1-5 mg, or via the ballistic “gene gun” delivery, typically in a dose range of approximately 10-100 g. The DNA can be delivered in a variety of conformations, e.g., linear, circular etc. Various viral vectors have also successfully been used that comprise nucleic acids which encode epitopes in accordance with the invention.

[0303] Accordingly compositions in accordance with the invention exist in several forms. Embodiments of each of these composition forms in accordance with the invention have been successfiully used to induce an immune response.

[0304] One composition in accordance with the invention comprises a plurality of peptides. This plurality or cocktail of peptides is generally admixed with one or more pharmaceutically acceptable excipients. The peptide cocktail can comprise multiple copies of the same peptide or can comprise a mixture of peptides. The peptides can be analogs of naturally occurring epitopes. The peptides can comprise artificial amino acids and/or chemical modifications such as addition of a surface active molecule, e.g., lipidation; acetylation, glycosylation, biotinylation, phosphorylation etc. The peptides can be CTh or HTL epitopes. In a preferred embodiment the peptide cocktail comprises a plurality of different CTL epitopes and at least one HTL epitope. The HTL epitope can be naturally or non-naturally (e.g., PADRE®, Epimmune Inc., San Diego, Calif.). The number of distinct epitopes in an embodiment of the invention is generally a whole unit integer from one through two hundred (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 105, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200).

[0305] An additional embodiment of a composition in accordance with the invention comprises a polypeptide multi-epitope construct, i.e., a polyepitopic peptide. Polyepitopic peptides in accordance with the invention are prepared by use of technologies well-known in the art. By use of these known technologies, epitopes in accordance with the invention are connected one to another. The polyepitopic peptides can be linear or non-linear, e.g., multivalent. These polyepitopic constructs can comprise artificial amino acids, spacing or spacer amino acids, flanking amino acids, or chemical modifications between adjacent epitope units. The polyepitopic construct can be a heteropolymer or a homopolymer. The polyepitopic constructs generally comprise epitopes in a quantity of any whole unit integer between 2-200 (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, etc.). The polyepitopic construct can comprise CTL and/or HTL epitopes. One or more of the epitopes in the construct can be modified, e.g., by addition of a surface active material, e.g. a lipid, or chemically modified, e.g., acetylation, etc. Moreover, bonds in the multiepitopic construct can be other than peptide bonds, e.g., covalent bonds, ester or ether bonds, disulfide bonds, hydrogen bonds, ionic bonds etc.

[0306] Alternatively, a composition in accordance with the invention comprises construct which comprises a series, sequence, stretch, etc., of amino acids that have homology to (i.e., corresponds to or is contiguous with) to a native sequence. This stretch of amino acids comprises at least one subsequence of amino acids that, if cleaved or isolated from the longer series of amino acids, functions as an HLA class I or HLA class II epitope in accordance with the invention. In this embodiment, the peptide sequence is modified, so as to become a construct as defined herein, by use of any number of techniques known or to be provided in the art. The polyepitopic constructs can contain homology to a native sequence in any whole unit integer increment from 70-100%, e.g., 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or, 100 percent.

[0307] A further embodiment of a composition in accordance with the invention is an antigen presenting cell that comprises one or more epitopes in accordance with the invention. The antigen presenting cell can be a “professional” antigen presenting cell, such as a dendritic cell. The antigen presenting cell can comprise the epitope of the invention by any means known or to be determined in the art. Such means include pulsing of dendritic cells with one or more individual epitopes or with one or more peptides that comprise multiple epitopes, by nucleic acid administration such as ballistic nucleic acid delivery or by other techniques in the art for administration of nucleic acids, including vector-based, e.g. viral vector, delivery of nucleic acids.

[0308] Further embodiments of compositions in accordance with the invention comprise nucleic acids that encode one or more peptides of the invention, or nucleic acids which encode a polyepitopic peptide in accordance with the invention. As appreciated by one of ordinary skill in the art, various nucleic acids compositions will encode the same peptide due to the redundancy of the genetic code. Each of these nucleic acid compositions falls within the scope of the present invention. This embodiment of the invention comprises DNA or RNA, and in certain embodiments a combination of DNA and RNA. It is to be appreciated that any composition comprising nucleic acids that will encode a peptide in accordance with the invention or any other peptide based composition in accordance with the invention, falls within the scope of this invention.

[0309] It is to be appreciated that peptide-based forms of the invention (as well as the nucleic acids that encode them) can comprise analogs of epitopes of the invention generated using principles already known, or to be known, in the art. Principles related to analoging are now known in the art, and are disclosed herein; moreover, analoging principles (heteroclitic analoging) are disclosed in co-pending application serial number U.S. Ser. No. 09/226,775 filed 6 Jan. 1999. Generally the compositions of the invention are isolated or purified.

[0310] The invention will be described in greater detail by way of specific examples. The following examples are offered for illustrative purposes, and are not intended to limit the invention in any manner.

[0311] Those of skill in the art will readily recognize a variety of non-critical parameters that can be changed or modified to yield alternative embodiments in accordance with the invention.

V. EXAMPLES

[0312] The following examples illustrate identification, selection, and use of inmnunogenic Class I and Class II peptide epitopes for inclusion in vaccine compositions.

Example 1

HLA Class I and Class H Binding Assays

[0313] The following example of peptide binding to HLA molecules demonstrates quantification of binding affinities of HLA class I and class II peptides. Binding assays can be performed with peptides that are either motif-bearing or not motif-bearing.

[0314] HLA class I and class II binding assays using purified HLA molecules were performed in accordance with disclosed protocols (e.g., PCT publications WO 94/20127 and WO 94/03205; Sidney et al., Current Protocols in Immunology 18.3.1 (1998); Sidney, et al., J. Immunol. 154:247 (1995); Sette, et al., Mol. Immunol. 31:813 (1994)). Briefly, purified MHC molecules (5 to 500 nM) were incubated with various unlabeled peptide inhibitors and 1-10 nM 125I-radiolabeled probe peptides as described. Following incubation, MHC-peptide complexes were separated from free peptide by gel filtration and the fraction of peptide bound was determined. Typically, in preliminary experiments, each MHC preparation was titered in the presence of fixed amounts of radiolabeled peptides to determine the concentration of HLA molecules necessary to bind 10-20% of the total radioactivity. All subsequent inhibition and direct binding assays were performed using these HLA concentrations.

[0315] Since under these conditions [label]<[HLA] and IC50≧[HLA], the measured IC50 values are reasonable approximations of the true KD values. Peptide inhibitors are typically tested at concentrations ranging from 120 μg/ml to 1.2 ng/ml, and are tested in two to four completely independent experiments. To allow comparison of the data obtained in different experiments, a relative binding figure is calculated for each peptide by dividing the IC50 of a positive control for inhibition by the IC50 for each tested peptide (typically unlabeled versions of the radiolabeled probe peptide). For database purposes, and inter-experiment comparisons, relative binding values are compiled. These values can subsequently be converted back into IC50 nM values by dividing the IC50 nM of the positive controls for inhibition by the relative binding of the peptide of interest. This method of data compilation has proven to be the most accurate and consistent for comparing peptides that have been tested on different days, or with different lots of purified MHC.

[0316] Binding assays as outlined above can be used to analyze supermotif and/or motif-bearing epitopes as, for example, described in Example 2.

Example 2

Identification of HLA Sunertnotif- and Motif-Bearing CTL Candidate Epitopes

[0317] Vaccine compositions of the invention may include multiple epitopes that comprise multiple HLA supermotifs or motifs to achieve broad population coverage. This example illustrates the identification of supermotif- and motif-bearing epitopes for the inclusion in such a vaccine composition. Calculation of population coverage is performed using the strategy described below.

[0318] Computer Searches and Algorthims for Identification of Supermotif and/or Motif-Bearing Epitopes

[0319] The searches performed to identify the motif-bearing peptide sequences in Examples 2 and 5 employed protein sequence data for the tumor-associated antigen CEA (GenBank access number M59255).

[0320] Computer searches for epitopes bearing HLA Class I or Class II supermotifs or motifs were performed as follows. All translated protein sequences were analyzed using a text string search software program, e.g., MotifSearch 1.4 (D. Brown, San Diego) to identify potential peptide sequences containing appropriate HLA binding motifs; alternative programs are readily produced in accordance with information in the art in-view of the motif/supermotif disclosure herein. Furthermore, such calculations can be made mentally. Identified A2-, A3-, and DR-supermotif sequences were scored using polynomial algorithms to predict their capacity to bind to specific HLA-Class I or Class II molecules. These polynomial algorithms take into account both extended and refined motifs (that is, to account for the impact of different amino acids at different positions), and are essentially based on the premise that the overall affinity (or G) of peptide-HLA molecule interactions can be approximated as a linear polynomial function of the type:

“G”=a1i×a2i×a3i . . . ×ani

[0321] where aji is a coefficient which represents the effect of the presence of a given amino acid (j) at a given position (i) along the sequence of a peptide of n amino acids. The crucial assumption of this method is that the effects at each position are essentially independent of each other (i.e., independent binding of individual side-chains). When residue j occurs at position i in the peptide, it is assumed to contribute a constant amount ji to the free energy of binding of the peptide irrespective of the sequence of the rest of the peptide. This assumption is justified by studies from our laboratories that demonstrated that peptides are bound to MHC and recognized by T cells in essentially an extended conformation (data omitted herein).

[0322] The method of derivation of specific algorithm coefficients has been described in Gulukota et al., J. Mol. Biol. 267:1258-126, 1997; (see also Sidney et al., Human Immunol. 45:79-93, 1996; and Southwood et al, J. Immunol. 160:3363-3373, 1998). Briefly, for all i positions, anchor and non-anchor alike, the geometric mean of the average relative binding (ARB) of all peptides carryingj is calculated relative to the remainder of the group, and used as the estimate of ji. For Class II peptides, if multiple alignments are possible, only the highest scoring alignment is utilized, following an iterative procedure. To calculate an algorithm score of a given peptide in a test set, the ARB values corresponding to the sequence of the peptide are multiplied. If this product exceeds a chosen threshold, the peptide is predicted to bind. Appropriate thresholds are chosen as a function of the degree of stringency of prediction desired.

[0323] Selection of HLA-A2 Supertype Cross-Reactive Peptides

[0324] The complete protein sequence from CEA was scanned, utilizing motif identification software, to identify 8-, 9-, 10-, and 11-mer sequences containing the HLA-A2-supermotif main anchor specificity.

[0325] A total of 336 HLA-A2 supermotif-positive sequences were identified. Of these, 266 peptides corresponding to the sequences were then synthesized and tested for their capacity to bind purified HLA-A*0201 molecules in vitro (HLA-A*0201 is considered a prototype A2 supertype molecule). Fourteen of the 266 peptides bound A*0201 with IC50 values ≦500 nM.

[0326] The fourteen A*0201-binding peptides were subsequently tested for the capacity to bind to additional A2-supertype molecules (A*0202, A*0203, A*0206, and A*6802). As shown in Table XXII, 10 of the 14 peptides were found to be A2-supertype cross-reactive binders, binding at least three of the five A2-supertype alleles tested.

[0327] Selection of HLA-A3 Supermotif-Bearing Epitopes

[0328] The protein sequences scanned above are also examined for the presence of peptides with the HLA-A3-supermotif primary anchors using methodology similar to that performed to identify HLA-A2 supermotif-bearing epitopes.

[0329] Peptides corresponding to the supermotif-bearing sequences are then synthesized and tested for binding to HLA-A*0301 and HLA-A*1101 molecules, the two most prevalent A3-supertype alleles. The peptides that are found to bind one of the two alleles with binding affinities of <500 nM are then tested for binding cross-reactivity to the other common A3-supertype alleles (A*3101, A*3301, and A*6801) to identify those that can bind at least three of the five HLA-A3-supertype molecules tested. Examples of HLA-A3 cross-binding supermotif-bearing peptides identified in accordance with this procedure are provided in Table XXIII.

[0330] Selection of HLA-B7 Supermotif Bearing Epitopes

[0331] The same target antigen protein sequences are also analyzed to identify HLA-B7-supermotif-bearing sequences. The corresponding peptides are then synthesized and tested for binding to HLA-B*0702, the most common B7-supertype allele (i.e., the prototype B7 supertype allele). Those peptides that bind B*0702 with IC50 of <500 nM are then tested for binding to other common B7-supertype molecules (B*3501, B*5101, B*5301, and B*5401) to identify those peptides that are capable of binding to three or more of the five B7-supertype alleles tested. Examples of HLA-B7 cross-binding supermotif-bearing peptides identified in accordance with this procedure are provided in Table XXIV.

[0332] Selection of A1 and A24 Motif-Bearing Epitopes

[0333] To further increase population coverage, HLA-A1 and -A24 motif-bearing epitopes can also be incorporated into potential vaccine constructs. An analysis of the protein sequence data from the target antigen utilized above is also performed to identify HLA-A1- and A24-motif-containing conserved sequences. The corresponding peptide sequence are then synthesized and tested for binding to the appropriate allele-specific HLA molecule, HLA-A1 or HLA-24. Peptides are identified that bind to the allele-specific HLA molecules at an IC50 of <500 nM. Examples of peptides identified in accordance with this procedure are provided in Tables XXV and XXVI.

Example 3

Confirmation of Immunogenicity

[0334] Nine of the ten cross-reactive candidate CTL A2-supermotif-bearing peptides were selected for in vitro inmmunogenicity testing. Testing was performed using the following methodology:

[0335] Target Cell Lines for Cellular Screening:

[0336] The 0.221A2.1 cell line, produced by transferring the HLA-A2.1 gene into the HLA-A, -B, -C null mutant human B-lymphoblastoid cell line 721.221, was used as the peptide-loaded target to measure activity of HLA-A2.1-restricted CTL. The HLA-typed melanoma cell lines (624mel and 888mel) were obtained from Y. Kawakami and S. Rosenberg, National Cancer Institute, Bethesda, Md. The colon adenocarcinoma cell lines SW403 and HT-20, the osteosarcoma line Saos-2 and the breast tumor line BT540 were obtained from the American Type Culture Collection (ATCC) (Rockville, Md.). The gastric cancer line, KATO III was obtained from the Japanese Cancer Research Resources Bank. The Saos-2/175 (Saos-2 transfected with the p53 gene containing a mutation at position 175) was obtained from Dr. Levine, Princeton University, Princeton, N.J. The cell lines that were obtained from ATCC were maintained under the culture conditions recommended by the supplier. All other cell lines were grown in RPMI-1640 medium supplemented with antibiotics, sodium pyruvate, nonessential amino acids and 10% (v/v) heat inactivated FCS. The melanoma, colon and gastric cancer cells were treated with 100 U/ml IFN (Genzyme) for 48 hours at 37° C. before use as targets in the 51Cr release and in situ IFN assays. The p53 tumor targets were treated with 20 ng/nml IFN and 3 ng/ml TNF for 24 hours prior to assay (see, e.g., Theobald et al., Proc. Natl. Acad. Sc. USA 92:11993, 1995).

[0337] Primary CTL Induction Cultures:

[0338] Generation of Dendritic Cells (DC): PBMCs were thawed in RPMI with 30 g/ml DNAse, washed twice and resuspended in complete medium (RPMI-1640 plus 5% AB human serum, non-essential amino acids, sodium pyruvate, L-glutamine and penicillin/strpetomycin). The monocytes were purified by plating 10×106 PBMC/well in a 6-well plate. After 2 hours at 37° C., the non-adherent cells were removed by gently shaking the plates and aspirating the supernatants. The wells were washed a total of three times with 3 ml RPMI to remove most of the non-adherent and loosely adherent cells. Three ml of complete medium containing 50 ng/ml of GM-CSF and 1,000 U/ml of IL-4 were then added to each well. DC were used for CTL induction cultures following 7 days of culture.

[0339] Induction of CTL with DC and Peptide: CD8+ T-cells were isolated by positive selection with Dynal immunomagnetic beads (Dynabeads® M-450) and the detacha-bead® reagent. Typically about 200-250×106 PBMC were processed to obtain 24×106 CD8+ T-cells (enough for a 48-well plate culture). Briefly, the PBMCs were thawed in RPMI with 30 μg/ml DNAse, washed once with PBS containing 1% human AB serum and resuspended in PBS/1% AB serum at a concentration of 20×106cel/ml. The magnetic beads were washed 3 times with PBS/AB serum, added to the cells (140 μl beads/20×106 cells) and incubated for 1 hour at 4° C. with continuous mixing. The beads and cells were washed 4× with PBS/AB serum to remove the nonadherent cells and resuspended at 100×106 cells/ml (based on the original cell number) in PBS/AB serum containing 100 μl/ml detacha-bead® reagent and 30 μg/ml DNAse. The mixture is incubated for 1 hour at room temperature with continuous mixing. The beads were washed again with PBS/AB/DNAse to collect the CD8+ T-cells. The DC were collected and centrifuged at 1300 rpm for 5-7 minutes, washed once with PBS with 1% BSA, counted and pulsed with 40 μg/ml of peptide at a cell concentration of 1-2×106/ml in the presence of 3 μg/ml β2-microglobulin for 4 hours at 20° C. The DC were then irradiated (4,200 rads), washed 1 time with medium and counted again.

[0340] Setting up induction cultures: 0.25 ml cytokine-generated DC (@1×105 cells/ml) were co-cultured with 0.25 ml of CD8+ T-cells (82×106 cell/ml) in each well of a 48-well plate in the presence of 10 ng/ml of IL-7. rHuman IL10 was added the next day at a final concentration of 10 ng/ml and rhuman IL2 was added 48 hours later at 10 IU/ml.

[0341] Restimulation of the induction cultures with peptide-pulsed adherent cells: Seven and fourteen days after the primary induction the cells were restimulated with peptide-pulsed adherent cells. The PBMCS were thawed and washed twice with RPMI and DNAse. The cells were resuspended at 5×106 cells/ml and irradiated at ˜4200 rads. The PBMCs were plated at 2×106 in 0.5 ml complete medium per well and incubated for 2 hours at 37° C. The plates were washed twice with RPMI by tapping the plate gently to remove the nonadherent cells and the adherent cells pulsed with 10 μg/ml of peptide in the presence of 3 μg/ml β2 microglobulin in 0.25 ml RPMI/5% AB per well for 2 hours at 37° C. Peptide solution from each well was aspirated and the wells were washed once with RPMI. Most of the media was aspirated from the induction cultures (CD8+ cells) and brought to 0.5 ml with fresh media. The cells were then transferred to the wells containing the peptide-pulsed adherent cells. Twenty four hours later rhuman IL10 was added at a final concentration of 10 ng/ml and rhuman IL2 was added the next day and again 2-3 days later at 50 IU/ml (Tsai et al., Critical Reviews in Immunolog 18(1-2):65-75, 1998). Seven days later the cultures were assayed for CTL activity in a 51Cr release assay. In some experiments the cultures were assayed for peptide-specific recognition in the in situ IFNγ ELISA at the time of the second restimulation followed by assay of endogenous recognition 7 days later. After expansion, activity was measured in both assays for a side by side comparison.

[0342] Measurement of CTL Lytic Activity by 51Cr Release.

[0343] Seven days after the second restimulation, cytotoxicity was determined in a standard (5 hr) 51Cr release assay by assaying individual wells at a single E:T. Peptide-pulsed targets were prepared by incubating the cells with 10 μg/ml peptide overnight at 37° C.

[0344] Adherent target cells were removed from culture flasks with trypsin-EDTA. Target cells were labelled with 200 μCi of 51Cr sodium chromate (Dupont, Wilmington, Del.) for 1 hour at 37° C. Labelled target cells are resuspended at 106 per ml and diluted 1:10 with K562 cells at a concentration of 3.3×106/ml (an NK-sensitive erythroblastoma cell line used to reduce non-specific lysis). Target cells (100 l) and 100 μl of effectors were plated in 96 well round-bottom plates and incubated for 5 hours at 37° C. At that time, 100 μl of supernatant were collected from each well and percent lysis was determined according to the formula: [(cpm of the test sample−cpm of the spontaneous 51Cr release sample)/(cpm of the maximal 51Cr release sample-cpm of the spontaneous 51Cr release sample)]×100. Maximum and spontaneous release were determined by incubating the labelled targets with 1% Trition X-100 and media alone, respectively. A positive culture was defined as one in which the specific lysis (sample-background) was 10% or higher in the case of individual wells and was 15% or more at the 2 highest E:T ratios when expanded cultures were assayed.

[0345] In Situ Measurement of Human γIFN Production as an Indicator of Peptide-Specific and Endogenous Recognition

[0346] Immulon 2 plates were coated with mouse anti-human IFN monoclonal antibody (4 g/ml 0.1 M NaHCO3, pH8.2) overnight at 4° C. The plates were washed with Ca2+, Mg2+-free PBS/0.05% Tween 20 and blocked with PBS/10% FCS for 2 hours, after which the CTLs (100 l/well) and targets (100 l/well) were added to each well, leaving empty wells for the standards and blanks (which received media only). The target cells, either peptide-pulsed or endogenous targets, were used at a concentration of 1×106 cells/ml. The plates were incubated for 48 hours at 37° C. with 5% CO2.

[0347] Recombinant human IFN was added to the standard wells starting at 400 pg or 1200 pg/100 l/well and the plate incubated for 2 hours at 37° C. The plates were washed and 100 l of biotinylated mouse anti-human IFN monoclonal antibody (4 g/ml in PBS/3% FCS/0.05% Tween 20) were added and incubated for 2 hours at room temperature. After washing again, 100 l HRP-streptavidin were added and incubated for 1 hour at room temperature. The plates were then washed 6× with wash buffer, 100 l/well developing solution (TMB 1:1) were added, and the plates allowed to develop for 5-15 minutes. The reaction was stopped with 50 l/well 1M H3PO4 and read at OD450. A culture was considered positive if it measured at least 50 pg of IFN/well above background and was twice the background level of expression.

[0348] CTL Expansion. Those cultures that demonstrated specific lytic activity against peptide-pulsed targets and/or tumor targets were expanded over a two week period with anti-CD3. Briefly, 5×104 CD8+ cells were added to a T25 flask containing the following: 1×106 irradiated (4,200 rad) PBMC (autologous or allogeneic) per ml, 2×105 irradiated (8,000 rad) EBV-transformed cells per ml, and OKT3 (anti-CD3) at 30 ng per ml in RPMI-1640 containing 10% (v/v) human AB serum non-essential amino acids, sodium pyruvate, 25 μM 2-mercaptoethanol, L-glutamine and penicillin/streptomycin. rHuman IL2 was added 24 hours later at a final concentration of 200 IU/ml and every 3 days thereafter with fresh media at 50 IU/ml. The cells were split if the cell concentration exceeded 1×106/ml and the cultures were assayed between days 13 and 15 at E:T ratios of 30, 10, 3 and 1:1 in the 51Cr release assay or at 1×106/ml in the in situ IFN assay using the same targets as before the expansion.

[0349] Immunogenicity of A2.Supermotif-Bearing Peptides

[0350] A2-supermotif cross-reactive binding peptides were tested in the cellular assay for the ability to induce peptide-specific CTL in normal individuals. In this analysis, a peptide was considered to be an epitope if it induced peptide-specific CTLs in at least 2 donors (unless otherwise noted) and if those CTLs also recognized the endogenously expressed peptide. Table XXVII identifies examples of peptides that were able to induce a peptide-specific CTL response in at least 2 normal donors. Further analysis demonstrated those that also recognized target cells pulsed with the wild-type peptide and tumor targets that endogenously express CEA (Table XXVII).

[0351] The CEA epitopes 691 and 605 were previously identifed (see Kawashima et al., Hum. Immunol. 59:1-14, 1998). Four immunogenic epitopes were further evaluated. Peptide specific CTLs to CEA.233, CEA.569, and CEA.687 were observed in one to two donors but endogenous recognition was observed only with CEA.687.

[0352] The CTL that demonstrated a positive response to CEA.687 in a 51Cr release assay were expanded and re-assayed against peptide-pulsed and endogenous target. Of the four individual cultures, three also recognized the endogenous target. One culture demonstrated significant lysis of peptide-pulsed target, but not tumor target. Two of the individual positive cultures were also tested against 221A2.1 target cells pulsed with different concentrations of peptide to measure CTL avidity. One line demonstrated high specific lysis at concentrations down to 1 ng/ml while both cultures exhibited a titration of activity further validating CEA.687 as an epitope. In a cold target inhibition assay in which peptide-pulsed targets were incubated with 51Cr-labelled targets to compete for lysis by the CTL, lysis of radiolabelled target cells by two different CTL lines was blocked by increasing the number of target cells pulsed with CEA.687. The non-specific peptide HBVc.18 did not inhibit lysis, thus further demonstrating the epitope specificity of the CTLs.

[0353] Evaluation of A*03/A11 Immunogenicity

[0354] HLA-A3 supermotif-bearing cross-reactive binding peptides are also evaluated for inmmunogenicity using methodology analogous for that used to evaluate the immunogenicity of the HLA-A2 supermotif peptides. Using this procedure, peptides that induce an immune response are identified. Examples of such peptides are shown in Table XXIII.

[0355] Evaluation of Immunogenicity of Motif/Supermotif-Bearing Peptides:

[0356] Analogous methodology, as appreciated by one of ordinary skill in the art, is employed to determine immunogenicity of peptides bearing HLA class I motifs and/or supermotifs set out herein. Using such a procedure peptides that induce an immune response are identified (see, e.g., Table XXVI).

Example 4

Implementation of the Extended Supermotif to Improve the Binding Capacity of Native Epitopes by Creating Analogs

[0357] HLA motifs and supermotifs (comprising primary and/or secondary residues) are useful in the identification and preparation of highly cross-reactive native peptides, as demonstrated herein. Moreover, the definition of HLA motifs and supermotifs also allows one to engineer highly cross-reactive epitopes by identifying residues within a native peptide sequence which can be analogued, or “fixed” to confer upon the peptide certain characteristics, e.g. greater cross-reactivity within the group of HLA molecules that comprise a supertype, and/or greater binding affinity for some or all of those HLA molecules. Examples of analog peptides that exhibit modulated binding affinity are set forth in this example and provided in Tables XXII through XXVII.

[0358] Analoguing at Primary Anchor Residues

[0359] Peptide engineering strategies were implemented to further increase the cross-reactivity of the epitopes identified above. On the basis of the data disclosed, e.g., in related and co-pending U.S.S.N 09/226,775, the main anchors of A2-supernotif-bearing peptides are altered, for example, to introduce a preferred L, I, V, or M at position 2, and I or V at the C-terminus.

[0360] Peptides that exhibit at least weak A*0201 binding (IC50 of 5000 nM or less), and carrying suboptimal anchor residues at either position 2, the C-terminal position, or both, can be fixed by introducing canonical substitutions (L at position 2 and V at the C-terminus). Those analogued peptides that show at least a three-fold increase in A*0201 binding and bind with an IC50 of 500 nM, or less were then tested for A2 cross-reactive binding along with their wild-type (WT) counterparts. Analogued peptides that bind at least three of the five A2 supertype alleles were then selected for cellular screening analysis.

[0361] Additionally, the selection of analogs for cellular screening analysis was further restricted by the capacity of the WT parent peptide to bind at least weakly, i.e., bind at an IC50 of 500 nM or less, to three of more A2 supertype alleles. The rationale for this requirement is that the WT peptides must be present endogenously in sufficient quantity to be biologically relevant. Analogued peptides have been shown to have increased inmmunogenicity and cross-reactivity by T cells specific for the WT epitope (see, e.g., Parkhurst et al., J. Immunol. 157:2539, 1996; and Pogue et al., Proc. Natl. Acad. Sci. USA 92:8166, 1995).

[0362] In the cellular screening of these peptide analogs, it is important to demonstrate that analog-specific CTLs are also able to recognize the wild-type peptide and, when possible, tumor targets that endogenously express the epitope.

[0363] Sixty-five CEA peptides met the criteria for analoguing at primary anchor residues by introducing a canonical substitution: these peptides showed at least weak A*0201 binding (IC50 of 5000 nM or less) and carried suboptimal anchor residues.

[0364] Analogs of nine of these peptides were generated and evaluated for cross-reactive binding to other A2 supertype molecules (Table XXII). Eight of these bound minimally to 3 of the 5 A2 supertype alleles, and their WT parents also bound at least weakly to 3 of 5 alleles. In the case of peptide CEA.605, the analog did not exhibit a three-fold increase in A*0201 binding affinity. This peptide did, however, show increased cross-reactivity and therefore was included in the selection of peptides to be analyzed for immunogenicity.

[0365] Eight analogs were selected for cellular screening studies. One of these CEA.24V9, was previously identified as an epitope (Kawashima et al., Hum. Immunol. 59:1-14, 1998). Three additional peptides were screened and, as shown in Table XXVII, CEA.233V10, CEA.605V9, and CEA.589V9 all induced CIL that were able to recognize peptide-pulsed and/or tumor targets. After expansion of the positive cultures, the CTLs were again tested against the analog and the parental WT peptide and tumor targets. CTLs to both analogs demonstrated recognition of the WT peptide and the tumor cell line, KATO m. In addition to being immunogenic, CEA.233V10 and CEA.605V9 showed improved overall binding when compared to the corresponding WT peptide as well as cross-reactive binding to 4 alleles. An additional epitope, CEA.589V9, was immunogenic and CEA.589V9-specific CTLs recognized the wildtype peptide, but endogenous recognition was not observed.

[0366] Using methodology similar to that used to develop HLA-A2 analogs, analogs of HLA-A3 and HLA-B7 supermotif-bearing epitopes are also generated. For example, peptides binding at least weakly to 3/5 of the A3-supertype molecules can be engineered at primary anchor residues to possess a preferred residue (V, S, M, or A) at position 2. The analog peptides are then tested for the ability to bind A*03 and A*11 (prototype A3 supertype alleles). Those peptides that demonstrate <500 nM binding capacity are then tested for A3-supertype cross-reactivity. Examples of HLA-A3 supermotif analog peptides are provided in Table XXIII.

[0367] B7 supermotif-bearing peptides can, for example, be engineered to possess a preferred residue (V, I, L, or F) at the C-terminal primary anchor position (see, e.g. Sidney et al. (J. Immunol. 157:3480-3490, 1996). Analoged peptides are then tested for cross-reactive binding to B7 supertype alleles. Examples of B7-supermotif-bearing analog peptides are provided in Table XXV.

[0368] Similarly, HLA-A1 and HLA-A24 motif-bearing peptides can be engineered at primary anchor residues to improve binding to the allele-specific HLA molecule or to improve cross-reactive binding. Examples of analoged HLA-A1 and HLA-A24 motif-bearing peptides are provided in Tables XXV and XXVI.

[0369] Analoged peptides that exhibit improved binding and/or or cross-reactivity are evaluated for immunogenicity using methodology similar to that described for the analysis of HLA-A2 supermotif-bearing peptides. Using such a procedure, peptides that induce an immune response are identified, e.g., XXII and XXVI.

[0370] Analoguing at Secondary Anchor Residues

[0371] Moreover, HLA supermotifs are of value in engineering highly cross-reactive peptides and/or peptides that bind HLA molecules with increased affinity by identifying particular residues at secondary anchor positions that are associated with such properties. Examples of such analoged peptides are provided in Table XXIV.

[0372] For example, the binding capacity of a B7 supermotif-bearing peptide representing a discreet single amino acid substitution at position 1 can be analyzed. A peptide can, for example, be analogued to substitute L with F at position I and subsequently be evaluated for increased binding affinity/and or increased cross-reactivity. This procedure will identify analogued peptides with modulated binding affinity.

[0373] Analoged peptides that exhibit improved binding and/or or cross-reactivity are evaluated for immunogenicity using methodology similar to that described for the analysis of HLA-A2 supermotif-bearing peptides. Using such a procedure, peptides that induce an immune response are identified.

[0374] Other Analoguing Strategies

[0375] Another form of peptide analoguing, unrelated to the anchor positions, involves the substitution of a cysteine with α-amino butyric acid. Due to its chemical nature, cysteine has the propensity to form disulfide bridges and sufficiently alter the peptide structurally so as to reduce binding capacity. Subtitution of α-amino butyric acid for cysteine not only alleviates this problem, but has been shown to improve binding and crossbinding capabilities in some instances (see, e.g., the review by Sette et al., In: Persistent Viral Infections, Eds. R. Ahmed and I. Chen, John Wiley & Sons, England, 1999).

[0376] Analoged peptides that exhibit improved binding and/or or cross-reactivity are evaluated for inmmunogenicity using methodology similar to that described for the analysis of HLA-A2 supermotif-bearing peptides. Using such a procedure, peptides that induce an immune response are identified.

[0377] This Example therefore demonstrates that by the use of even single amino acid substitutions, the binding affinity and/or cross-reactivity of peptide ligands for HLA supertype molecules is modulated.

Example 5

Identification of Peptide Epitope Sequences with HLA-DR Binding Motifs

[0378] Peptide epitopes bearing an HLA class II supermotif or motif may also be identified as outlined below using methodology similar to that described in Examples 1-3.

[0379] Selection of HLA-DR-Supermotif-Bearing Epitopes

[0380] To identify HLA class II HTL epitopes, the CEA protein sequence was analyzed for the presence of sequences bearing an HLA-DR-motif or supermotif. Specifically, 15-mer sequences were selected comprising a DR-supermotif, further comprising a 9-mer core, and three-residue N- and C-terminal flanking regions (15 amino acids total).

[0381] Protocols for predicting peptide binding to DR molecules have been developed (Southwood et al., J. Immunol. 160:3363-3373, 1998). These protocols, specific for individual DR molecules, allow the scoring, and ranking, of 9-mer core regions. Each protocol not only scores peptide sequences for the presence of DR-supermotif primary anchors (i.e., at position 1 and position 6) within a 9-mer core, but additionally evaluates sequences for the presence of secondary anchors. Using allele specific selection tables (see, e.g., Southwood et al., ibid.), it has been found that these protocols efficiently select peptide sequences with a high probability of binding a particular DR molecule. Additionally, it has been found that performing these protocols in tandem, specifically those for DR1, DR4w4, and DR7, can efficiently select DR cross-reactive peptides.

[0382] The CEA-derived peptides identified above were tested for their binding capacity for various common HLA-DR molecules. All peptides were initially tested for binding to the DR molecules in the primary panel: DR1, DR4w4, and DR7. Peptides binding at least 2 of these 3 DR molecules with an IC50 value of 1000 nM or less, were then tested for binding to DR5*0101, DRBl*1501, DRB1*1101, DRB1*0802, and DRB1*1302. Peptides were considered to be cross-reactive DR supertype binders if they bound at an IC50 value of 1000 nM or less to at least 5 of the 8 alleles tested.

[0383] Following the strategy outlined above, 100 DR supermotif-bearing sequences were identified within the CEA protein sequence. Of those, 24 scored positive in 2 of the 3 combined DR 147 algorithms. These peptides were synthesized and tested for binding to HLA-DRB1*0101, DRB1*0401, DRB1*0701. Of the 24 peptides tested, 10 bound at least 2 of the 3 alleles (Table XXI)

[0384] These 10 peptides were then tested for binding to secondary DR supertype alleles: DRB5*0101, DRB1*1501, DRB1*1101, DRB1*0802, and DRB1*1302. Five peptides were identified that bound at least 5 of the 8 alleles tested and which occurred in distinct, non-overlapping regions (Table XXIX).

[0385] Selection of DR3-Motif Peptides

[0386] Because HLA-DR3 is an allele that is prevalent in Caucasian, Black, and Hispanic populations, DR3 binding capacity is an important criterion in the selection of HTL epitopes. However, data generated previously indicated that DR3 only rarely cross-reacts with other DR alleles (Sidney et al., J. Immunol. 149:2634-2640, 1992; Geluk et al, J. Immunol. 152:5742-5748, 1994; Southwood et al., J. Immunol. 160:3363-3373, 1998). This is not entirely surprising in that the DR3 peptide-binding motif appears to be distinct from the specificity of most other DR alleles. For maximum efficiency in developing vaccine candidates it would be desirable for DR3 motifs to be clustered in proximity with DR supermotif regions.

[0387] Thus, peptides shown to be candidates may also be assayed for their DR3 binding capacity. However, in view of the distinct binding specificity of the DR3 motif, peptides binding only to DR3 can also be considered as candidates for inclusion in a vaccine formulation.

[0388] To efficiently identify peptides that bind DR3, the CEA protein sequence was analyzed for conserved sequences carrying one of the two DR3 specific binding motifs (Table III) reported by Geluk et al. (J. Immunol. 152:5742-5748, 1994). Thirty motif-positive peptides were identified. The corresponding peptides were then synthesized and tested for the ability to bind DR3 with an affinity of 1000 nM or better, i.e., less than 1000 nM. Two peptides were found that met this binding criterion (Table XXX), and thereby qualify as HLA class II high affinity binders. Additionally, the 2 DR3 binders were tested for binding to the DR supertype alleles (Table XXXI). For both peptides, binding to other DR supertype molecules was observed, but neither peptide could be categorized as a DR supertype cross-reactive binding peptide. Conversely, The DR supertype cross-reactive binding peptides were also tested for DR3 binding capacity. One peptide, CEA.50, exhibited DR3 binding (Table X).

[0389] DR3 binding epitopes identified in this manner may then be included in vaccine compositions with DR supermotif-bearing peptide epitopes.

[0390] In summary, 5 DR supertype cross-reactive binding peptides and 3 DR3 binding peptides were identified from the CEA protein sequence, with one peptide shared between the two motifs.

Example 6

Immunogenicity of HTL Epitopes

[0391] This example determines immunogenic DR supermotif- and DR3 motif-bearing epitopes among those identified using the methodology in Example 5. Immunogenicity of HTL epitopes are evaluated in a manner analogous to the determination of immunogenicity of CTL epitopes by assessing the ability to stimulate HTL responses and/or by using appropriate transgenic mouse models. Immunogenicity is determined by screening for: 1.) in vitro primary induction using normal PBMC or 2.) recall responses from cancer patient PBMCs. Such a procedure identifies epitopes that induce an HTL response.

Example 7

Calculation of phenotypic Frequencies of HLA-Supertypes in Various Ethnic Backgrounds to Determine Breadth of Population Coverage

[0392] This example illustrates the assessment of the breadth of population coverage of a vaccine composition comprised of multiple epitopes comprising multiple supermotifs and/or motifs.

[0393] In order to analyze population coverage, gene frequencies of HLA alleles were determined. Gene frequencies for each HLA allele were calculated from antigen or allele frequencies utilizing the binomial distributionformulae gf=1−(SQRT(1−af)) (see, e.g., Sidney et al., Human Immunol. 45:79-93, 1996). To obtain overall phenotypic frequencies, cumulative gene frequencies were calculated, and the cumulative antigen frequencies derived by the use of the inverse formula [af=1−(1−Cgf)2].

[0394] Where frequency data was not available at the level of DNA typing, correspondence to the serologically defined antigen frequencies was assumed. To obtain total potential supertype population coverage no linkage disequilibrium was assumed, and only alleles confirmed to belong to each of the supertypes were included (minimal estimates). Estimates of total potential coverage achieved by inter-loci combinations were made by adding to the A coverage the proportion of the non-A covered population that could be expected to be covered by the B alleles considered (e.g., total=A+B*(1−A)). Confirmed members of the A3-like supertype are A3, A11, A31, A*3301, and A*6801. Although the A3-like supertype may also include A34, A66, and A*7401, these alleles were not included in overall frequency calculations. Likewise, confirmed members of the A2-like supertype family are A*0201, A*0202, A*0203, A*0204, A*0205, A*0206, A*0207, A*6802, and A*6901. Finally, the B7-like supertype-confirmed alleles are: B7, B*3501-03, B51, B*5301, B*5401, B*5501-2, B*5601, B*6701, and B*7801 (potentially also B*1401, B*3504-06,B*4201, and B*5602).

[0395] Population coverage achieved by combining the A2-, A3- and B7-supertypes is approximately 86% in five major ethnic groups (see Table XXI). Coverage may be extended by including peptides bearing the A1 and A24 motifs. On average, A1 is present in 12% and A24 in 29% of the population across five different major ethnic groups (Caucasian, North American Black, Chinese, Japanese, and Hispanic). Together, these alleles are represented with an average frequency of 39% in these same ethnic populations. The total coverage across the major ethnicities when A1 and A24 are combined with the coverage of the A2-, A3- and B7-supertype alleles is >95%. An analogous approach can be used to estimate population coverage achieved with combinations of class II motif-bearing epitopes.

Example 8

Recognition of Endogenous Processed Antigens After Priming

[0396] This example determines that CTL induced by native or analogued peptide epitopes identified and selected as described in Examples 1-6 recognize endogenously synthesized, i.e., native antigens, using a transgenic mouse model.

[0397] Effector cells isolated from transgenic mice that are immunized with peptide epitopes (as described, e.g., in Wentworth et al., Mol. Immunol. 32:603, 1995), for example HLA-A2 supermotif-bearing epitopes, are re-stimulated in vitro using peptide-coated stimulator cells. Six days later, effector cells are assayed for cytotoxicity and the cell lines that contain peptide-specific cytotoxic activity are further re-stimulated. An additional six days later, these cell lines are tested for cytotoxic activity on 51Cr labeled Jurkat-A2.1/Kb target cells in the absence or presence of peptide, and also tested on 51Cr labeled target cells bearing the endogenously synthesized antigen, i.e. cells that are stably transfected with TAA expression vectors.

[0398] The result will demonstrate that CTL lines obtained from animals primed with peptide epitope recognize endogenously synthesized antigen. The choice of transgenic mouse model to be used for such an analysis depends upon the epitope(s) that is being evaluated. In addition to HLA-A*0201/Kb transgenic mice, several other transgenic mouse models including mice with human A11, which may also be used to evaluate A3 epitopes, and B7 alleles have been characterized and others (e.g., transgenic mice for HLA-A 1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse models have also been developed, which may be used to evaluate HTL epitopes.

Example 9

Activity Of CTL-HTL Conjugated Epitopes in Transgenic Mice

[0399] This example illustrates the induction of CTLs and HTLs in transgenic mice by use of a tumor associated antigen CTL/HTL peptide conjugate whereby the vaccine composition comprises peptides to be administered to a cancer patient. The peptide composition can comprise multiple CTL and/or HTL epitopes and further, can comprise epitopes selected from multiple-tumor associated antigens. The epitopes are identified using methodology as described in Examples 1-6 This analysis demonstrates the enhanced immunogenicity that can be achieved by inclusion of one or more HTL epitopes in a vaccine composition. Such a peptide composition can comprise an HTL epitope conjugated to a preferred CTL epitope containing, for example, at least one CTL epitope selected from Tables XXIII-XXVII, or other analogs of that epitope. The HTL epitope is, for example, selected from Table XXI. The peptides may be lipidated, if desired.

[0400] Immunization procedures: Immunization of transgenic mice is performed as described (Alexander et al., J. Immunol. 159:4753-4761, 1997). For example, A2/Kb mice, which are transgenic for the human HLA A2.1 allele and are useful for the assessment of the immunogenicity of HLA-A*0201 motif- or HLA-A2 supermotif-bearing epitopes, are primed subcutaneously (base of the tail) with 0.1 ml of peptide conjugate formulated in saline, or DMSO/saline. Seven days after priming, splenocytes obtained from these animals are restimulated with syngenic irradiated LPS-activated lymphoblasts coated with peptide.

[0401] The target cells for peptide-specific cytotoxicity assays are Jurkat cells transfected with the HLA-A2.1/Kb chimeric gene (e.g., Vitiello et al., J. Exp. Med. 173:1007, 1991).

[0402] In vitro CTL activation: One week after priming, spleen cells (30×106 cells/flask) are co-cultured at 37° C. with syngeneic, irradiated (3000 rads), peptide coated lymphoblasts (10×106 cells/flask) in 10 ml of culture medium/T25 flask. After six days, effector cells are harvested and assayed for cytotoxic activity.

[0403] Assay for cytotoxic activity: Target cells (1.0 to 1.5×106) are incubated at 37° C. in the presence of 200 μl of 51Cr. After 60 minutes, cells are washed three times and resuspended in medium. Peptide is added where required at a concentration of 1 μg/ml. For the assay, 104 51Cr-labeled target cells are added to different concentrations of effector cells (final volume of 200 μl) in U-bottom 96-well plates. After a 6 hour incubation period at 37° C., a 0.1 ml aliquot of supernatant is removed from each well and radioactivity is determined in a Micromedic automatic gamma counter. The percent specific lysis is determined by the formula: percent specific release=100×(experimental release−spontaneous release)/(maximum release−spontaneous release). To facilitate comparison between separate CTL assays run under the same conditions, % 51Cr release data is expressed as lytic units/105 cells. One lytic unit is arbitrarily defined as the number of effector cells required to achieve 30% lysis of 10,000 target cells in a 6 hour 51Cr release assay. To obtain specific lytic units/106, the lytic units/106 obtained in the absence of peptide is subtracted from the lytic units/106 obtained in the presence of peptide. For example, if 30% 51Cr release is obtained at the effector (E): target (T) ratio of 50:1 (i.e., 5×105 effector cells for 10,000 targets) in the absence of peptide and 5:1 (i.e.; 5×104 effector cells for 10,000 targets) in the presence of peptide, the specific lytic units would be: [({fraction (1/50,000)})−({fraction (1/500,000)})]×106=18 LU.

[0404] The results are analyzed to assess the magnitude of the CTL responses of animals injected with the inmnunogenic CTL/HTL conjugate vaccine preparation. The frequency and degree of CTL response can also be compared to the CTL response achieved using the CTL epitopes by themselves. Analyses similar to this may be performed to evaluate the immunogenicity of peptide conjugates containing multiple CTL epitopes and/or multiple HTL epitopes. In accordance with these procedures it is found that a CTL response is induced, and concomitantly that an HTL response is induced upon administration of such compositions.

Example 10

Selection of CTL and HTL Epitopes for Inclusion in a Cancer Vaccine

[0405] This example illustrates the procedure for the selection of peptide epitopes for vaccine compositions of the invention. The peptides in the composition can be in the form of a nucleic acid sequence, either single or one or more sequences (i.e., minigene) that encodes peptide(s), or may be single and/or polyepitopic peptides.

[0406] The following principles are utilized when selecting an array of epitopes for inclusion in a vaccine composition. Each of the following principles is balanced in order to make the selection.

[0407] Epitopes are selected which, upon administration, mimic immune responses that have been observed to be correlated with tumor clearance. For example, a vaccine can include 3-4 epitopes that come from at least one TAA. Epitopes from one TAA can be used in combination with epitopes from one or more additional TAAs to produce a vaccine that targets tumors with varying expression patterns of frequently-expressed TAAs as described, e.g., in Example 15.

[0408] Epitopes are preferably selected that have a binding affinity (IC50) of 500 nM or less, often 200 nM or less, for an HLA class I molecule, or for a class II molecule, 1000 nM or less.

[0409] Sufficient supermotif bearing peptides, or a sufficient array of allele-specific motif bearing peptides, are selected to give broad population coverage. For example, epitopes are selected to provide at least 80% population coverage. A Monte Carlo analysis, a statistical evaluation known in the art, can be employed to assess breadth, or redundancy, of population coverage.

[0410] When selecting epitopes from cancer-related antigens it is often preferred to select analogs because the patient may have developed tolerance to the native epitope.

[0411] When creating a polyepitopic composition, e.g. a minigene, it is typically desirable to generate the smallest peptide possible that encompasses the epitopes of interest, although spacers or other flanking sequences can also be incorporated. The principles employed are often similar as those employed when selecting a peptide comprising nested epitopes. Additionally, however, upon determination of the nucleic acid sequence to be provided as a minigene, the peptide sequence encoded thereby is analyzed to determine whether any “junctional epitopes” have been created. A junctional epitope is a potential HLA binding epitope, as predicted, e.g., by motif analysis. Junctional epitopes are generally to be avoided because the recipient may bind to an HLA molecule and generate an immune response to that epitope, which is not present in a native protein sequence.

[0412] Epitopes for inclusion in vaccine compositions are, for example, selected from those listed in Tables XXII-XXVII and XXX. A vaccine composition comprised of selected peptides, when administered, is safe, efficacious, and elicits an immune response that results in tumor cell killing and reduction of tumor size or mass.

Example 11

Construction of Minigene Multi-Epitope DNA Plasmids

[0413] This example provides general guidance for the construction of a minigene expression plasmid. Minigene plasmids may, of course, contain various configurations of CTL and/or HTL epitopes or epitope analogs as described herein. Expression plasmids have been constructed and evaluated as described, for example, in co-pending U.S. Ser. No. 09/311,784 filed May 13, 1999.

[0414] A minigene expression plasmid may include multiple CTL and HTL peptide epitopes. In the present example, HLA-A2, -A3, -B7 supermotif-bearing peptide epitopes and HLA-A1 and -A24 motif-bearing peptide epitopes are used in conjunction with DR supermotif-bearing epitopes and/or DR3 epitopes. Preferred epitopes are identified, for example, in Tables XXIII-XXVII and XXXI. HLA class I supermotif or motif-bearing peptide epitopes derived from multiple TAAs are selected such that multiple supermotifs/motifs are represented to ensure broad population coverage. Similarly, HLA class II epitopes are selected from multiple tumor antigens to provide broad population coverage, ie. both HLA DR-1-4-7 supermotif-bearing epitopes and HLA DR-3 motif-bearing epitopes are selected for inclusion in the minigene construct. The selected CTL and HTL epitopes are then incorporated into a minigene for expression in an expression vector.

[0415] This example illustrates the methods to be used for construction of such a minigene-bearing expression plasmid. Other expression vectors that may be used for minigene compositions are available and known to those of skill in the art.

[0416] The minigene DNA plasmid contains a consensus Kozak sequence and a consensus murine kappa Ig-light chain signal sequence followed by CTL and/or HTL epitopes selected in accordance with principles disclosed herein. The sequence encodes an open reading frame fused to the Myc and His antibody epitope tag coded for by the pcDNA 3.1 Myc-His vector.

[0417] Overlapping oligonucleotides, for example eight oligonucleotides, averaging approximately 70 nucleotides in length with 15 nucleotide overlaps, are synthesized and HPLC-purified. The oligonucleotides encode the selected peptide epitopes as well as appropriate linker nucleotides, Kozak sequence, and signal sequence. The final multiepitope minigene is assembled by extending the overlapping oligonucleotides in three sets of reactions using PCR. A Perkin/Elmer 9600 PCR machine is used and a total of 30 cycles are performed using the following conditions: 95° C. for 15 sec, annealing temperature (5° below the lowest calculated Tm of each primer pair) for 30 sec, and 72° C. for 1 min.

[0418] For the first PCR reaction, 5 μg of each of two oligonucleotides are annealed and extended: Oligonucleotides 1+2, 3+4, 5+6, and 7+8 are combined in 100 μl reactions containing Pfu polymerase buffer (1×=10 mM KCL, 10 mM (NH4)2SO4, 20 mM Tris-chloride, pH 8.75, 2 mM MgSO4, 0.1% Triton X-100, 100 μg/ml BSA), 0.25 mM each dNTP, and 2.5 U of polymerase. The fu-length dimer products are gel-purified, and two reactions containing the product of 1+2 and 3+4, and the product of 5+6 and 7+8 are mixed, annealed, and extended for 10 cycles. Half of the two reactions are then mixed, and 5 cycles of annealing and extension carried out before flanking primers are added to amplify the full length product for 25 additional cycles. The full-length product is gel-purified and cloned into pCR-blunt (Invitrogen) and individual clones are screened by sequencing.

Example 12

The Plasmid Construct and the Degree to Which it Induces Immunogenicity

[0419] The degree to which the plasmid construct prepared using the methodology outlined in Example 11 is able to induce immunogenicity is evaluated through in vivo injections into mice and subsequent in vitro assessment of CTL and HTL activity, which are analysed using cytotoxicity and proliferation assays, respectively, as detailed e.g., in U.S. Ser. No. 09/311,784 filed May 13, 1999 and Alexander et al., Immunity 1:751-761, 1994.

[0420] Alternatively, plasmid constructs can be evaluated in vitro by testing for epitope presentation by APC following transduction or transfection of the APC with an epitope-expressing nucleic acid construct. Such a study determines “antigenicity” and allows the use of human APC. The assay determines the ability of the epitope to be presented by the APC in a context that is recognized by a T cell by quantifying the density of epitope-HLA class I complexes on the cell surface. Quantitation can be performed by directly measuring the amount of peptide eluted from the APC (see, e.g., Sijts et al., J. Immunol. 156:683-692, 1996; Demotz et al., Nature 342:682-684, 1989); or the number of peptide-HLA class I complexes can be estimated by measuring the amount of lysis or lymphokine release induced by infected or transfected target cells, and then determining the concentration of peptide necessary to obtained equivalent levels of lysis or lymphokine release (see, e.g., Kageyama et al., J. Immunol. 154:567-576, 1995).

[0421] To assess the capacity of the pMin minigene construct (e.g., a pMin minigene construct generated as decribed in U.S. Ser. No. 09/311,784) to induce CTLs in vivo, HLA-A11/Kb transgenic mice, for example, are immunized intramuscularly with 100 μg of naked cDNA. As a means of comparing the level of CTLs induced by cDNA immunization, a control group of animals is also immunized with an actual peptide composition that comprises multiple epitopes synthesized as a single polypeptide as they would be encoded by the minigene.

[0422] Splenocytes from immunized animals are stimulated twice with each of the respective compositions (eptide epitopes encoded in the minigene or the polyepitopic peptide), then assayed for peptide-specific cytotoxic activity in a 51Cr release assay. The results indicate the magnitude of the CTL response directed against the A3-restricted epitope, thus indicating the in vivo immunogenicity of the minigene vaccine and polyepitopic vaccine. It is, therefore, found that the minigene elicits immune responses directed toward the HLA-A3 supermotif peptide epitopes as does the polyepitopic peptide vaccine. A similar analysis is also performed using other HLA-A2 and HLA-B7 transgenic mouse models V to assess CTL induction by HLA-A2 and HLA-B7 motif or supermotif epitopes.

[0423] To assess the capacity of a class II epitope encoding minigene to induce HTLs in vivo, I-Ab restricted mice, for example, are immunized intramuscularly with 100 μg of plasmid DNA. As a means of comparing the level of HTLs induced by DNA immunization, a group of control animals is also immunized with an actual peptide composition emulsified in complete Freund's adjuvant. CD4+ T cells, ie. HTLs, are purified from splenocytes of immunized animals and stimulated with each of the respective compositions (peptides encoded in the minigene). The HTL response is measured using a 3H-thymidine incorporation proliferation assay, (see, e.g., Alexander et al. Immunity 1:751-761, 1994). The results indicate the magnitude of the HTL response, thus demonstrating the in vivo immunogenicity of the minigene.

[0424] DNA minigenes, constructed as described in Example 11, may also be evaluated as a vaccine in combination with a boosting agent using a prime boost protocol. The boosting agent may consist of recombinant protein (e.g., Barnett et al., Aids Res. and Human Retroviruses 14, Supplement 3:S299-S309, 1998) or recombinant vaccinia, for example, expressing a minigene or DNA encoding the complete protein of interest (see, e.g., Hanke et al., Vaccine 16:439-445, 1998; Sedegah et al., Proc. Natl. Acad. Sci USA 95:7648-53, 1998; Hanke and McMichael, Immunol. Letters 66:177-181, 1999; and Robinsonet al., Nature Med 5:526-34, 1999).

[0425] For example, the efficacy of the DNA minigene may be evaluated in transgenic mice. In this example, A2.1/Kb transgenic mice are immunized IM with 100 g of the DNA minigene encoding the immunogenic peptides. After an incubation period (ranging from 3-9 weeks), the mice are boosted IP with 107 pfu/mouse of a recombinant vaccinia virus expressing the same sequence encoded by the DNA minigene. Control mice are immunized with 100 g of DNA or recombinant vaccinia without the minigene sequence, or with DNA encoding the minigene, but without the vaccinia boost. After an additional incubation period of two weeks, splenocytes from the mice are immediately assayed for peptide-specific activity in an ELISPOT assay. Additionally, splenocytes are stimulated in vitro with the A2-restricted peptide epitopes encoded in the minigene and recombinant vaccinia, then assayed for peptide-specific activity in an IFN-ELISA. It is found that the minigene utilized in a prime-boost mode elicits greater immune responses toward the HLA-A2 supermotif peptides than with DNA alone. Such an analysis is also performed using other HLA-A11 and HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3 and HLA-B7 motif or supermotif epitopes.

Example 13

Peptide Composition for Prophylactic Uses

[0426] Vaccine compositions of the present invention are used to prevent cancer in persons who are at risk for developing a tumor. For example, a polyepitopic peptide epitope composition (or a nucleic acid comprising the same) containing multiple CTL and HTL epitopes such as those selected in Examples 9 and/or 10, which are also selected to target greater than 80% of the population, is administered to an individual at risk for a cancer, e.g., breast cancer. The composition is provided as a single polypeptide that encompasses multiple epitopes. The vaccine is administered in an aqueous carrier comprised of Freunds Incomplete Adjuvant. The dose of peptide for the initial immunization is from about 1 to about 50,000 μg, generally 100-5,000 μg, for a 70 kg patient The initial administration of vaccine is followed by booster dosages at 4 weeks followed by evaluation of the magnitude of the immune response in the patient, by techniques that determine the presence of epitope-specific CTL populations in a PBMC sample. Additional booster doses are administered as required. The composition is found to be both safe and efficacious as a prophylaxis against cancer.

[0427] Alternatively, the polyepitopic peptide composition can be administered as a nucleic acid in accordance with methodologies known in the art and disclosed herein.

Example 14

Polyepitopic Vaccine Compositions Derived from Native TAA Sequences

[0428] A native TAA polyprotein sequence is screened, preferably using computer algorithms defined for each class I and/or class II supermotif or motif, to identify “relatively short” regions of the polyprotein that comprise multiple epitopes and is preferably less in length than an entire native antigen. This relatively short sequence that contains multiple distinct even overlapping, epitopes is selected and used to generate a minigene construct. The construct is engineered to express the peptide, which corresponds to the native protein sequence. The “relatively short” peptide is generally less than 1000, 500, or 250 amino acids in length, often less than 100 amino acids in length, preferably less than 75 amino acids in length, and more preferably less than 50 amino acids in length. The protein sequence of the vaccine composition is selected because it has maximal number of epitopes contained within the sequence, i.e., it has a high concentration of epitopes. As noted herein, epitope motifs may be nested or overlapping (i.e., frame shifted relative to one another). For example, with frame shifted overlapping epitopes, two 9-mer epitopes and one 10-mer epitope can be present in a 10 amino acid peptide. Such a vaccine composition is administered for therapeutic or prophylactic purposes.

[0429] The vaccine composition will preferably include, for example, three CTL epitopes and at least one HTL epitope from TAAs. This polyepitopic native sequence is administered either as a peptide or as a nucleic acid sequence which encodes the peptide. Alternatively, an analog can be made of this native sequence, whereby one or more of the epitopes comprise substitutions that alter the cross-reactivity and/or binding affinity properties of the polyepitopic peptide.

[0430] The embodiment of this example provides for the possibility that an as yet undiscovered aspect of immune system processing will apply to the native nested sequence and thereby facilitate the production of therapeutic or prophylactic immune response-inducing vaccine compositions. Additionally such an embodiment provides for the possibility of motif-bearing epitopes for an HLA makeup that is presently unknown. Furthermore, this embodiment (absent analogs) directs the immune response to multiple peptide sequences that are actually present in native TAAs thus avoiding the need to evaluate any junctional epitopes. Lastly, the embodiment provides an economy of scale when producing nucleic acid vaccine compositions.

[0431] Related to this embodiment, computer programs can be derived in accordance with principles in the art, which identify in a target sequence, the greatest number of epitopes per sequence length.

Example 15

Polyepitopic Vaccine Compositions Directed to Multiple Tumors

[0432] The CEA peptide epitopes of the present invention are used in conjunction with peptide epitopes from other target tumor antigens to create a vaccine composition that is useful for the treatment of various types of tumors. For example, a set of TAA epitopes can be selected that allows the targeting of most common epithelial tumors (see, e.g., Kawashima et al., Hum. Immunol. 59:1-14, 1998). Such a composition includes epitopes from CEA, HER-2/neu, and MAGE2/3, all of which are expressed to appreciable degrees (20-60%) in frequently found tumors such as lung, breast, and gastrointestinal tumors.

[0433] The composition can be provided as a single polypeptide that incorporates the multiple epitopes from the various TAAs, or can be administered as a composition comprising one or more discrete epitopes. Alternatively, the vaccine can be administered as a minigene construct or as dendritic cells which have been loaded with the peptide epitopes in vitro.

[0434] Targeting multiple tumor antigens is also important to provide coverage of a large fraction of tumors of any particular type. A single TAA is rarely expressed in the majority of tumors of a given type. For example, approximately 50% of breast tumors express CEA, 20% express MAGE3, and 30% express HER-2/neu. Thus, the use of a single antigen for immunotherapy would offer only limited patient coverage. The combination of the three TAAs, however, would address approximately 70% of breast tumors. Furthermore, with the inclusion of CTL epitopes derived from p53, which is overexpressed in approximately 50% of breast tumors, coverage of approximately 85% of all breast tumors could be achieved. A vaccine composition comprising epitopes from multiple tumor antigens also reduces the potential for escape mutants due to loss of expression of an individual tumor antigen.

Example 16

Use of Peptides to Evaluate an Immune Response

[0435] Peptides of the invention may be used to analyze an immune response for the presence of specific CTL or HTL populations directed to a TAA. Such an analysis may be performed using multimeric complexes as described, e.g., by Ogg et al., Science 279:2103-2106, 1998 and Greten et al., Proc. Natl. Acad. Sci. USA 95:7568-7573, 1998. In the following example, peptides in accordance with the invention are used as a reagent for diagnostic or prognostic purposes, not as an immunogen.

[0436] In this example, highly sensitive human leukocyte antigen tetrameric complexes (“tetramers”) are used for a cross-sectional analysis of, for example, tumor-associated antigen HLA-A*020]-specific CTL frequencies from HLA A*0201-positive individuals at different stages of disease or following immunization using a TAA peptide containing an A*0201 motif. Tetrameric complexes are synthesized as described (Musey et al., N. Engl. J. Med. 337:1267, 1997). Briefly, purified HLA heavy chain (A*0201 in this example) and β2-microglobulin are synthesized by means of a prokaryotic expression system. The heavy chain is modified by deletion of the transmembrane-cytosolic tail and COOH-terminal addition of a sequence containing a BirA enzymatic biotinylation site. The heavy chain, O2-microglobulin, and peptide are refolded by dilution. The 45-kD refolded product is isolated by fast protein liquid chromatography and then biotinylated by BirA in the presence of biotin (Sigma, St. Louis, Mo.), adenosine 5′triphosphate and magnesium. Streptavidin-phycoerythrin conjugate is added in a 1:4 molar ratio, and the tetrameric product is concentrated to 1 mg/ml. The resulting product is referred to as tetramer-phycoerythrin.

[0437] For the analysis of patient blood samples, approximately one million PBMCs are centrifuged at 300 g for 5 minutes and resuspended in 50 μl of cold phosphate-buffered saline. Tri-color analysis is performed with the tetramer-phycoerythrin, along with anti-CD8-Tricolor, and anti-CD38. The PBMCs are incubated with tetramer and antibodies on ice for 30 to 60 min and then washed twice before formaldehyde fixation. Gates are applied to contain >99.98% of control samples. Controls for the tetramers include both IA*0201-negative individuals and A*0201-positive uninfected donors. The percentage of cells stained with the tetramer is then determined by flow cytometry. The results indicate the number of cells in the PBMC sample that contain epitope-restricted CTLs, thereby readily indicating the extent of immune response to the TAA epitope, and thus the stage of tumor progression or exposure to a vaccine that elicits a protective or therapeutic response.

Example 17

Use of Peptide Epitopes to Evaluate Recall Responses

[0438] The peptide epitopes of the invention are used as reagents to evaluate T cell responses, such as acute or recall responses, in patients. Such an analysis may be performed on patients who are in remission, have a tumor, or who have been vaccinated with a TAA vaccine.

[0439] For example, the class I restricted CTL response of persons who have been vaccinated may be analyzed. The vaccine may be any TAA vaccine. PBMC are collected from vaccinated individuals and HLA typed. Appropriate peptide epitopes of the invention that, optimally, bear supermotifs to provide cross-reactivity with multiple HLA supertype family members, are then used for analysis of samples derived from individuals who bear that HLA type.

[0440] PBMC from vaccinated individuals are separated on Ficoll-Histopaque density gradients (Sigma Chemical Co., St. Louis, Mo.), washed three times in HBSS (GIBCO Laboratories), resuspended in RPMI-1640 (GIBCO Laboratories) supplemented with L-glutamine (2 mM), penicillin (50 U/ml), streptomycin (50 g/ml), and Hepes (10 mM) containing 10% heat-inactivated human AB serum (complete RPMI) and plated using microculture formats. A synthetic peptide comprising an epitope of the invention is added at 10 μg/ml to each well and HBV core 128-140 epitope is added at 1 μg/ml to each well as a source of T cell help during the first week of stimulation.

[0441] In the microculture format, 4×105 PBMC are stimulated with peptide in 8 replicate cultures in 96-well round bottom plate in 100 μl/well of complete RPMI. On days 3 and 10, 100 l of complete RPMI and 20 U/ml final concentration of rIL-2 are added to each well. On day 7 the cultures are transferred into a 96-well flat-bottom plate and restimulated with peptide, rIL-2 and 105 irradiated (3,000 rad) autologous feeder cells. The cultures are tested for cytotoxic activity on day 14. A positive CTL response requires two or more of the eight replicate cultures to display greater than 10% specific 51Cr release, based on comparison with uninfected control subjects as previously described (Rehermann, et al., Nature Med. 2:1104,1108, 1996; Rehermann et al., J. Clin. Invest. 97:1655-1665, 1996; and Rehermann et al. J. Clin. Invest. 98:1432-1440, 1996).

[0442] Target cell lines are autologous and allogeneic EBV-transformed B-LCL that are either purchased from the American Society for Histocompatibility and Immunogenetics (ASHI, Boston, Mass.) or established from the pool of patients as described (Guilhot, et al. J. Virol. 66:2670-2678, 1992). Cytotoxicity assays are performed in the following manner. Target cells consist of either allogeneic HIA-matched or autologous EBV-transformed B lymphoblastoid cell line that are incubated overnight with the synthetic peptide epitope of the invention at 10 μM, and labeled with 100 μCi of 51Cr (Amersham Corp., Arlington Heights, Ill.) for 1 hour after which they are washed four times with HBSS.

[0443] Cytolytic activity is determined in a standard 4 hour, split-well 51Cr release assay using U-bottomed 96 well plates containing 3,000 targets/well. Stimulated PBMC are tested at effector/target (E/T) ratios of 20-50:1 on day 14. Percent cytotoxicity is determined from the formula: 100×[(experimental release-spontaneous release)/maximum release-spontaneous release)]. Maximum release is determined by lysis of targets by detergent (2% Triton X-100; Sigma Chemical Co., St. Louis, Mo.). Spontaneous release is <25% of maximum release for all experiments.

[0444] The results of such an analysis indicate the extent to which HLA-restricted CTL populations have been stimulated by previous exposure to the TAA or TAA vaccine.

[0445] The class H restricted HTL responses may also be analyzed. Purified PBMC are cultured in a 96-well flat bottom plate at a density of 1.5×105 cells/well and are stimulated with 10 μg/ml synthetic peptide, whole antigen, or PHA. Cells are routinely plated in replicates of 4-6 wells for each condition. After seven days of culture, the medium is removed and replaced with fresh medium containing 10 U/ml IL-2. Two days later, 1 μCi 3H-thyrmidine is added to each well and incubation is continued for an additional 18 hours. Cellular DNA is then harvested on glass fiber mats and analyzed for 3H-thymidine incorporation. Antigen-specific T cell proliferation is calculated as the ratio of 3H-thymidine incorporation in the presence of antigen divided by the 3H-thynidine incorporation in the absence of antigen.

Example 18

Induction Of Specific CTL Response in Humans

[0446] A human clinical trial for an immunogenic composition comprising CTL and HTL epitopes of the invention is set up as an IND Phase I, dose escalation study. Such a trial is designed, for example, as follows:

[0447] A total of about 27 subjects are enrolled and divided into 3 groups:

[0448] Group I: 3 subjects are injected with placebo and 6 subjects are injected with 5 μg of peptide composition;

[0449] Group II: 3 subjects are injected with placebo and 6 subjects are injected with 50 μg peptide composition;

[0450] Group m: 3 subjects are injected with placebo and 6 subjects are injected with 500 μg of peptide composition.

[0451] After 4 weeks following the fist injection, all subjects receive a booster inoculation at the same dosage. Additional booster inoculations can be administered on the same schedule.

[0452] The endpoints measured in this study relate to the safety and tolerability of the peptide composition as well as its immunogenicity. Cellular immune responses to the peptide composition are an index of the intrinsic activity of the peptide composition, and can therefore be viewed as a measure of biological efficacy. The following summarize the clinical and laboratory data that relate to safety and efficacy endpoints.

[0453] Safety: The incidence of adverse events is monitored in the placebo and drug treatment group and assessed in terms of degree and reversibility.

[0454] Evaluation of Vaccine Efficacy: For evaluation of vaccine efficacy, subjects are bled before and after injection. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.

[0455] The vaccine is found to be both safe and efficacious.

Example 19

Therapeutic Use in Cancer Patients

[0456] Evaluation of vaccine compositions are performed to validate the efficacy of the CTL-HTL peptide compositions in cancer patients. The main objectives of the trials are to determine an effective dose and regimen for inducing CTLs in cancer patients, to establish the safety of inducing a CTL and HTL response in these patients, and to see to what extent activation of CTLs improves the clinical picture of cancer patients, as manifested by a reduction in tumor cell numbers. Such a study is designed, for example, as follows:

[0457] The studies are performed in multiple centers. The trial design is an open-label, uncontrolled, dose escalation protocol wherein the peptide composition is administered as a single dose followed six weeks later by a single booster shot of the same dose. The dosages are 50, 500 and 5,000 micrograms per injection. Drug-associated adverse effects (severity and reversibility) are recorded.

[0458] There are three patient groupings. The first group is injected with 50 micrograms of the peptide composition and the second and third groups with 500 and 5,000 micrograms of peptide composition, respectively. The patients within each group range in age from 21-65, include both males and females (unless the tumor is sex-specific, e.g., breast or prostate cancer), and represent diverse ethnic backgrounds.

Example 20

Induction of CTL Responses Using a Prime Boost Protocol

[0459] A prime boost protocol similar in its underlying principle to that used to evaluate the efficacy of a DNA vaccine in trasgenic mice, which was described in Example 12, may also be used for the administration of the vaccine to humans. Such a vaccine regimen may include an initial administration of, for example, naked DNA followed by a boost using recombinant virus encoding the vaccine, or recombinant protein/polypeptide or a peptide mixture administered in an adjuvant.

[0460] For example, the initial immunization may be performed using an expression vector, such as that constructed in Example 11, in the form of naked nucleic acid administered IM (or SC or ID) in the amounts of 0.5-5 mg at multiple sites. The nucleic acid (0.1 to 1000 μg) can also be administered using a gene gun. Following an incubation period of 34 weeks, a booster dose is then administered. The booster can be recombinant fowlpox virus administered at a dose of 5-107 to 5×109 pfu. An alternative recombinant virus, such as an MVA, canarypox, adenovirus, or adeno-associated virus, can also be used for the booster, or the polyepitopic protein or a mixture of the peptides can be administered. For evaluation of vaccine efficacy, patient blood samples will be obtained before immunization as well as at intervals following administration of the initial vaccine and booster doses of the vaccine. Peripheral blood mononuclear cells are isolated from fresh heparinized blood by Ficoll-Hypaque density gradient centrifugation, aliquoted in freezing media and stored frozen. Samples are assayed for CTL and HTL activity.

[0461] Analysis of the results will indicate that a magnitude of response sufficient to achieve protective immunity against cancer is generated.

Example 21

Administration of Vaccine Compositions Using Dendritic Cells

[0462] Vaccines comprising peptide epitopes of the invention may be administered using antigen-presenting cells (APCs), or “professional” APCs such as dendritic cells (DC). In this example, the peptide-pulsed DC are administered to a patient to stimulate a CTL response in vivo. In this method, dendritic cells are isolated, expanded, and pulsed with a vaccine comprising peptide CTL and HTL epitopes of the invention. The dendritic cells are infused back into the patient to elicit CTL and HTL responses in vivo. The induced CTL and HTL then destroy (CTL) or facilitate destruction (HTL) of the specific target tumor cells that bear the proteins from which the epitopes in the vaccine are derived.

[0463] For example, a cocktail of epitope-bearing peptides is administered ex vivo to PBMC, or isolated DC therefrom, from the patient's blood. A pharmaceutical to facilitate harvesting of DC can be used, such as Progenipoietin™ (Monsanto, St. Louis, Mo.) or GM-CSF/IL4. After pulsing the DC with peptides and prior to reinfusion into patients, the DC are washed to remove unbound peptides. As appreciated clinically, and readily determined by one of skill based on clinical outcomes, the number of dendritic cells reinfused into the patient can vary (see, e.g., Nature Med. 4:328, 1998; Nature Med. 2:52, 1996 and Prostate 32:272, 1997). Although 2-50×106 dendritic cells per patient are typically administered, larger number of dendritic cells, such as 107 or 108 can also be provided. Such cell populations typically contain between 50-90% dendritic cells.

[0464] In some embodiments, peptide-loaded PBMC are injected into patients without purification of the DC. For example, PBMC containing DC generated after treatment with an agent such as Progenipoietin™ are injected into patients without purification of the DC. The total number of PBMC that are administered often ranges from 108 to 1010. Generally, the cell doses injected into patients is based on the percentage of DC in the blood of each patient, as determined, for example, by immunofluorescence analysis with specific anti-DC antibodies. Thus, for example, if Progenipoietin™ mobilizes 2% DC in the peripheral blood of a given patient, and that patient is to receive 5×106 DC, then the patient will be injected with a total of 2.5×108 peptide-loaded PBMC. The percent DC mobilized by an agent such as Progenipoietin™ is typically estimated to be between 2-10%, but can vary as appreciated by one of skill in the art.

[0465] Ex Vivo Activation of CTL/HTL Responses

[0466] Alternatively, ex vivo CTL or HTL responses to a particular tumor-associated antigen can be induced by incubating in tissue culture the patient's, or genetically compatible, CTL or HTL precursor cells together with a source of antigen-presenting cells (APC), such as dendritic cells, and the appropriate immunogenic peptides. After an appropriate incubation time (typically about 7-28 days), in which the precursor cells are activated and expanded into effector cells, the cells are infused back into the patient, where they will destroy (CTL) or facilitate destruction (HTL) of their specific target cells, ie., tumor cells.

Example 22

Alternative Method of Identifying Motif-Bearing Peptides

[0467] Another way of identifying motif-bearing peptides is to elute them from cells bearing defined MHC molecules. For example, EBV transformed B cell lines used for tissue typing, have been extensively characterized to determine which HLA molecules they express. In certain cases these cells express only a single type of HLA molecule. These cells can then be infected with a pathogenic organism or transfected with nucleic acids that express the tumor antigen of interest. Thereafter, peptides produced by endogenous antigen processing of peptides produced consequent to infection (or as a result of transfection) will bind to HLA molecules within the cell and be transported and displayed on the cell surface.

[0468] The peptides are then eluted from the HLA molecules by exposure to mild acid conditions and their amino acid sequence determined, e.g., by mass spectral analysis (e.g., Kubo et al., J. Immunol. 152:3913, 1994). Because, as disclosed herein, the majority of peptides that bind a particular HLA molecule are motif-bearing, this is an alternative modality for obtaining the motif-bearing peptides correlated with the particular HLA molecule expressed on the cell.

[0469] Alternatively, cell lines that do not express any endogenous HLA molecules can be transfected with an expression construct encoding a single HLA allele. These cells may then be used as described, ie., they may be infected with a pathogenic organism or transfected with nucleic acid encoding an antigen of interest to isolate peptides corresponding to the pathogen or antigen of interest that have been presented on the cell surface. Peptides obtained from such an analysis will bear motif(s) that correspond to binding to the single HLA allele that is expressed in the cell.

[0470] As appreciated by one in the art, one can perform a similar analysis on a cell bearing more than one HLA allele and subsequently determine peptides specific for each HLA allele expressed. Moreover, one of skill would also recognize that means other than infection or transfection, such as loading with a protein antigen, can be used to provide a source of antigen to the cell.

[0471] The above examples are provided to illustrate the invention but not to limit its scope. For example, the human terminology for the Major Histocompatibility Complex, namely HLA, is used throughout this document. It is to be appreciated that these principles can be extended to other species as well. Thus, other variants of the invention will be readily apparent to one of ordinary skill in the art and are encompassed by the appended claims. All publications, patents, and patent application cited herein are hereby incorporated by reference for all purposes.

2TABLE IPOSITIONPOSITIONPOSITIONC Terminus (Primary2 (Primary Anchor)3 (Primary Anchor)Anchor)SUPERMOTIFSA1T, I, L, V, M, SF, W, YA2L, I, V, M, A, T, QI, V, M, A, T, LA3V, S, M, A, T, L, IR, KA24Y, F, W, I, V, L, M, TF, I, Y, W, L, MB7PV, I, L, F, M, W, Y, AB27R, H, KF, Y, L, W, M, I, V, AB44E, DF, W, L, I, M, V, AB58A, T, SF, W, Y, L, I, V, M, AB62Q, L, I, V, M, PF, W, Y, M, I, V, L, AMOTIFSA1T, S, MYA1D, E, A, SYA2.1L, M, V, Q, I, A, TV, L, I, M, A, TA3L, M, V, I, S, A, T, F,K, Y, R, H, F, AC, G, DA11V, T, M, L, I, S, A,K, R, Y, HG, N, C, D, FA24Y, F, W, MF, L, I, WA*3101M, V, T, A, L, I, SR, KA*3301M, V, A, L, F, I, S, TR, KA*6801A, V, T, M, S, L, IR, KB*0702PL, M, F, W, Y, A, I, VB*3501PL, M, F, W, Y, I, V, AB51PL, I, V, F, W, Y, A, MB*5301PI, M, F, W, Y, A, L, VB*5401PA, T, I, V, L, M, F, W, YBolded residues are preferred, italicized residues are less preferred: A peptide is considered motif-bearing if it has primary anchors at each primary anchor position for a motif or supermotif as specified in the above table.

[0472]

3

TABLE Ia

POSITION

POSITION
POSITION
C Terminus (Primary

2 (Primary Anchor)
3 (Primary Anchor)
Anchor)

SUPERMOTIFS

A1

T
, I, L, V, M, S

F
, W, Y

A2

V
, Q, A, T

I
, V, L, M, A, T

A3

V
, S, M, A, T, L, I

R
, K

A24

Y
, F, W, I, V, L, M, T

F
, I, Y, W, L, M

B7

P

V
, I, L, F, M, W, Y, A

B27

R
, H, K

F
, Y, L, W, M, I, V, A

B58

A
, T, S

F
, W, Y, L, I, V, M, A

B62

Q
, L, I, V, M, P

F
, W, Y, M, I, V, L, A

MOTIFS

A1

T
, S, M

Y

A1

D
, E, A, S

Y

A2.1

V
, Q, A, T*

V
, L, I, M, A, T

A3.2

L
, M, V, I, S, A, T, F,

K
, Y, R, H, F, A

C
, G, D

A11

V
, T, M, L, I, S, A,

K
, R, H, Y

G
, N, C, D, F

A24

Y
, F, W

F
, L, I, W

*If 2 is V, or Q, the C-term is not L

Bolded residues are preferred, italicized residues are less preferred: A peptide is considered motif-bearing if it has primary anchors at each primary anchor position for a motif or supermotif as specified in the above table.

[0473]

4

TABLE II

POSITION

SUPER-

MOTIFS

A1

1° Anchor

T,I,L,V,M,S

A2

1° Anchor

L,I,V,M,A,

T
,Q

A3
preferred

1° Anchor

Y,F,W,(4/5)

V,S,M,A,T,

L
,I

deleterious
D,E (3/5); P,(5/5)

D,E,(4/5)

A24

1° Anchor

Y,F,W,I,V,

L
,M,T

B7
preferred
F,W,Y (5/5)

1° Anchor

F,W,Y (4/5)

L,I,V,M,(3/5)
P

deleterious
D,E (3/5); P(5/5);

G(4/5); A(3/5);

Q,N,(3/5)

B27

1° Anchor

R,H,K

B44

1° Anchor

E,D

B58

1° Anchor

A,T,S

B62

1° Anchor

Q,L,I,V,M,

P

MOTIFS

A1
preferred
G,F,Y,W,

1° Anchor

D,E,A,
Y,F,W,

9-mer

S,T,M,

deleterious
D,E,

R,H,K,L,I,V
A,

M,P,

A1
preferred
G,R,H,K
A,S,T,C,L,I

1° Anchor

G,S,T,C,

9-mer

V,M,
D,E,A,S

deleterious
A
R,H,K,D,E,

D,E,

P,Y,F,W,

POSITION

C-terminus

SUPER-

MOTIFS

A1

1° Anchor

F,W,Y

A2

1° Anchor

L,I,V,M,A,T

A3
preferred

Y,F,W,
Y,F,W,(4/5)
P,(4/5)

1° Anchor

(3/5)

R,K

deleterious

A24

1° Anchor

F,I,Y,W,L,M

B7
preferred

F,W,Y,

1° Anchor

(3/5)
V,I,L,F,M,W,Y,A

deleterious
D,E,(3/5)
G,(4/5)
Q,N,(4/5)
D,E,(4/5)

B27

1° Anchor

F,Y,L,W,M,V,A

B44

1° Anchor

F,W,Y,L,I,M,V,A

B58

1° Anchor

F,W,Y,L,I,V,M,A

B62

1° Anchor

F,W,Y,M,I,V,L,A

MOTIFS

A1
preferred

P,
D,E,Q,N,
Y,F,W,

1° Anchor

9-mer

Y

deleterious
G,
A,

A1
preferred

A,S,T,C,
L,I,V,M,
D,E,

1° Anchor

9-mer

Y

deleterious
P,Q,N,
R,H,K,
P,G,
G,P,

POSITION

A1
preferred
Y,F,W,

1° Anchor

D,E,A,Q,N,
A,
Y,F,W,Q,N,

10-mer

S,T,M

deleterious
G,P,

R,H,K,G,L,I
D,E,
R,H,K,

V,M,

A1
preferred
Y,F,W,
S,T,C,L,I,V

1° Anchor

A,
Y,F,W,

10-mer

M,
D,E,A,S

deleterious
R,H,K,
R,H,K,D,E,

P,

P,Y,F,W,

A2.1
preferred
Y,F,W,

1° Anchor

Y,F,W,
S,T,C,
Y,F,W,

9-mer

L,M,I,V,Q,

A
,T

deleterious
D,E,P,

D,E,R,K,H

A2.1
preferred
A,Y,F,W,

1° Anchor

L,V,I,M,
G,

10-mer

L,M,I,V,Q,

A
,T

deleterious
D,E,P,

D,E,
R,K,H,A,
P,

A3
preferred
R,H,K,

1° Anchor

Y,F,W,
P,R,H,K,Y,
A,

L,M,V,I,S,

F,W,

A,T,F,C,G,

D

deleterious
D,E,P,

D,E

A11
preferred
A,

1° Anchor

Y,F,W,
Y,F,W,
A,

V,T,L,M,I,

S,A,G,N,C,

D
,F

deleterious
D,E,P,

A24
preferred
Y,F,W,R,H,K,

1° Anchor

S,T,C

9-mer

Y,F,W,M

deleterious
D,E,G,

D,E,
G,
Q,N,P,

A24
preferred

1° Anchor

P,
Y,F,W,P,

10-mer

Y,F,W,M

deleterious

G,D,E
Q,N
R,H,K

A3101
preferred
R,H,K,

1° Anchor

Y,F,W,
P,

M,V,T,A,L,

I
,S

deleterious
D,E,P,

D,E,

A,D,E,

A3301
preferred

1° Anchor

Y,F,W

M,V,A,L,F,

I
,S,T

deleterious
G,P

D,E

A6801
preferred
Y,F,W,S,T,C,

1° Anchor

Y,F,W,L,I,

A,V,T,M,S,

V,M

L
,I

deleterious
G,P,

D,E,G,

R,H,K,

B0702
preferred
R,H,K,F,W,Y,

1° Anchor

R,H,K,

R,H,K,

P

deleterious
D,E,Q,N,P,

D,E,P,
D,E,
D,E,

B3501
preferred
F,W,Y,L,I,V,M,

1° Anchor

F,W,Y,

P

deleterious
A,G,P,

G,

B51
preferred
L,I,V,M,F,W,Y,

1° Anchor

F,W,Y,
S,T,C,
F,W,Y,

P

deleterious
A,G,P,D,E,R,H,K,

DE,

S,T,C,

B5301
preferred
L,I,V,M,F,W,Y,

1° Anchor

F,W,Y,
S,T,C,
F,W,Y,

P

deleterious
A,G,P,Q,N,

B5401
preferred
F,W,Y,

1° Anchor

F,W,Y,L,I,V,

L,I,V,M,

P
M,

deleterious
G,P,Q,N,D,E,

G,D,E,S,T,C,

R,H,K,D,E,

POSITION

C-terminus
C-terminus

A1
preferred

P,A,S,T,C,
G,D,E,
P,

1° Anchor

10-mer

Y

deleterious
Q,N,A
R,H,K,Y,F,
R,H,K,
A

W,

A1
preferred

P,G,
G,
Y,F,W,

1° Anchor

10-mer

Y

deleterious
G,

P,R,H,K,
Q,N,

A2.1
preferred

A,
P

1° Anchor

9-mer

V,L,I,M,A,T

deleterious
R,K,H
D,E,R,K,H

A2.1
preferred
G,

F,Y,W,L,

1° Anchor

10-mer

V,I,M,

V,L,I,M,A,T

deleterious

R,K,H,
D,E,R,K,
R,K,H,

H,

A3
preferred
Y,F,W,

P,

1° Anchor

K,Y,R,H,F,A

deleterious

A11
preferred
Y,F,W,
Y,F,W,
P,

1° Anchor

K,,RY,H

deleterious

A
G

A24
preferred

Y,F,W,
Y,F,W,

1° Anchor

9-mer

F,L,I,W

deleterious
D,E,R,H,K,
G,
A,Q,N,

A24
preferred

P,

1° Anchor

10-mer

F,L,I,W

deleterious
D,E
A
Q,N,
D,E,A,

A3101
preferred
Y,F,W,
Y,F,W,
A,P,

1° Anchor

R,K

deleterious
D,E,
D,E,
D,E,

A3301
preferred

A,Y,F,W

1° Anchor

R,K

deleterious

A6801
preferred

Y,F,W,
P,

1° Anchor

R,K

deleterious

A,

B0702
preferred
R,H,K,
R,H,K,
P,A,

1° Anchor

L,M,F,W,Y,A,

I
,V

deleterious
G,D,E,
Q,N,
D,E,

B3501
preferred

F,W,Y,

1° Anchor

L,M,F,W,Y,I,

V
,A

deleterious
G,

B51
preferred

G,
F,W,Y,

1° Anchor

L,I,V,F,W,

Y
,A,M

deleterious
G,
D,E,Q,N,
G,D,E,

B5301
preferred

L,I,V,M,F,
F,W,Y,

1° Anchor

W,Y,

I,M,F,W,Y,

A
,L,V

deleterious
G,
R,H,K,Q,N,
D,E,

B5401
preferred

A,L,I,V,M,
F,W,Y,A,P,

1° Anchor

A,T,I,V,L,

M
,F,W,Y

deleterious
D,E,
Q,N,D,G,E,
D,E,

Italicized residues indicate less preferred or “tolerated” residues.

The information in Table II is specific for 9-mers unless otherwise specified.

Secondary anchor specificities are designated for each position independently.

[0474]

5

TABLE III

POSITION

MOTIFS

DR4
preferred
F,M,Y,L,I,
M,
T,

I,
V,S,T,C,P,A,
M,H,

M,H

V
,W,

L
,I,M,

deleterious

W,

R,

W,D,E

DR1
preferred
M,F,L,I,V,

P,A,M,Q,

V,M,A,T,S,P,
M,

A,V,M

W
,Y,

L
,I,C,

deleterious

C,
C,H
F,D,
C,W,D,

G,D,E,
D

DR7
preferred
M,F,L,I,V,
M,
W,
A,

I,V,M,S,A,C,
M,

I,V

W
,Y,

T
,P,L,

deleterious

C,

G,

G,R,D,
N,
G

DR Supermotif

M,F,L,I,V,

V,M,S,T,A,C,

W
,Y

P
,L,I

DR3 MOTIFS

motif a

L,I,V,M,F,

preferred

Y

D

motif b

L,I,V,M,F,

D,N,Q,E,

preferred

A,Y

S,T

K,R,H

Italicized residues indicate less preferred or “tolerated” residues.

Secondary anchor specificities are designated for each position independently.

[0475]

6

TABLE IV

HLA Class I Standard

Peptide Binding Affinity.

STANDARD

STANDARD
SEQUENCE
BINDING

ALLELE
PEPTIDE
(SEQ ID NO:)
AFFINITY (nM)

A*0101
944.02
YLEPAIAKY
25

A*0201
941.01
FLPSDYFPSV
5.0

A*0202
941.01
FLPSDYFPSV
4.3

A*0203
941.01
FLPSDYFPSV
10

A*0205
941.01
FLPSDYFPSV
4.3

A*0206
941.01
FLPSDYFPSV
3.7

A*0207
941.01
FLPSDYFPSV
23

A*6802
1072.34
YVIKVSARV
8.0

A*0301
941.12
KVFPYALINK
11

A*1101
940.06
AVDLYHFLK
6.0

A*3101
941.12
KVFPYALINK
18

A*3301
1083.02
STLPETYVVRR
29

A*6801
941.12
KVFPYALINK
8.0

A*2402
979.02
AYIDNYNKF
12

B*0702
1075.23
APRTLVYLL
5.5

B*3501
1021.05
FPFKYAAAF
7.2

B51
1021.05
FPFKYAAAF
5.5

B*5301
1021.05
FPFKYAAAF
9.3

B*5401
1021.05
FPFKYAAAF
10

[0476]

7

TABLE V

HLA Class II Standard

Peptide Binding Affinity.

Binding

Nomen-
Standard
Sequence
Affinity

Allele
clature
Peptide
(SEQ ID NO:)
(nM)

DRB1*0101
DR1
515.01
PKYVKQNTLKLAT
5.0

DRB1*0301
DR3
829.02
YKTIAFDEEARR
300

DRB1*0401
DR4w4
515.01
PKYVKQNTLKLAT
45

DRB1*0404
DR4w14
717.01
YARFQSQTTLKQKT
50

DRB1*0405
DR4w15
717.01
YARFQSQTTLKQKT
38

DRB1*0701
DR7
553.01
QYIKANSKFIGITE
25

DRB1*0802
DR8w2
553.01
QYIKANSKFIGITE
49

DRB1*0803
DR8w3
553.01
QYIKANSKFIGITE
1600

DRB1*0901
DR9
553.01
QYIKANSKFIGITE
75

DRB1*1101
DR5w11
553.01
QYIKANSKFIGITE
20

DRB1*1201
DRSw12
1200.05
EALIHQLKINPYVLS
298

DRB1*1302
DR6w19
650.22
QYIKANAKFIGITE
3.5

DRB1*1501
DR2w2β1
507.02
GRTQDENPVVHFFKN
9.1

IVTPRTPPP

DRB3*0101
DR52a
511
NGQIGNDPNRDIL
470

DRB4*0101
DRw53
717.01
YARFQSQTTLKQKT
58

DRB5*0101
DR2w2β2
553.01
QYIKANSKFIGITE
20

[0477]

8

TABLE VI

HLA-
Allelle-specific HLA-supertype members

supertype
Verifieda
Predictedb

A1
A*0101, A*2501, A*2601, A*2602, A*3201
A*0102, A*2604, A*3601, A*4301, A*8001

A2
A*0201, A*0202, A*0203, A*0204, A*0205, A*0206,
A*0208, A*0210, A*0211, A*0212, A*0213

A*0207, A*0209, A*0214, A*6802, A*6901

A3
A*0301, A*1101, A*3101, A*3301, A*6801
A*0302, A*1102, A*2603, A*3302, A*3303,

A*3401, A*3402, A*6601, A*6602, A*7401

A24
A*2301, A*2402, A*3001
A*2403, A*2404, A*3002, A*3003

B7
B*0702, B*0703, B*0704, B*0705, B*1508, B*3501, B*3502, B*3503,
B*1511, B*4201, B*5901

B*3503, B*3504, B*3505, B*3506, B*3507, B*3508, B*5101, B*5102,

B*5103, B*5104, B*5105, B*5301, B*5401, B*5501, B*5502, B*5601,

B*5602, B*6701, B*7801

B27
B*1401, B*1402, B*1509, B*2702, B*2703, B*2704, B*2705, B*2706,
B*2701, B*2707, B*2708, B*3802, B*3903,

B*3801, B*3901, B*3902, B*7301
B*3904, B*3905, B*4801, B*4802, B*1510,

B*1518, B*1503

B44
B*1801, B*1802, B*3701, B*4402, B*4403, B*4404, B*4001, B*4002,
B*4101, B*4501, B*4701, B*4901, B*5001

B*4006

B58
B*5701, B*5702, B*5801, B*5802, B*1516, B*1517

B62
B*1501, B*1502, B*1513, B*5201
B*1301, B*1302, B*1504, B*1505, B*1506,

B*1507, B*1515, B*1520, B*1521, B*1512,

B*1514, B*1510

a
Verified alleles include alleles whose specificity has been determined by pool sequencing analysis, peptide binding assays, or by analysis of the sequences of CTL epitopes.

b
Predicted alleles are alleles whose specificity is predicted on the basis of B and F pocket structure to overlap with the supertype specificity.

[0478]

9

TABLE VII

CEA A01 Supermotif Peptides with Binding Data

No. of

Position
Amino Acids
A*0101

440
8
0.0120

440
10

262
11

618
8
0.0085

618
10

134
8
−0.0021

128
11

227
9
−0.0021

348
9

348
10

2
10

170
9

170
10

631
11

275
11

85
11
0.0069

61
8

616
10
0.3400

403
11
0.9700

112
8

112
9

597
9
0.0021

242
8
−0.0021

598
8
−0.0021

420
8
0.0030

467
9
0.0390

645
9
0.0049

289
9
0.0100

316
11

644
10

35
9

18
10

18
11

19
9

19
10

53
11

549
11

381
11
0.0100

20
8

20
9

36
8

54
10

129
10

111
9

111
10

454
10

466
10

288
10

57
9

57
11

560
10

204
10

596
10

4
8

240
10
0.0250

418
9
0.0035

418
10
0.0770

512
10

406
8

584
8

17
11

581
11
3.2000

225
11
0.5300

310
10
0.0041

72
11
0.0850

228
8

382
10

241
9
0.0024

419
8
0.0038

419
9
0.0240

311
9
0.0011

290
8

312
8

317
10

561
9
0.0011

205
9
0.0011

383
9
−0.0021

95
8
0.0150

269
9

[0479]

10

TABLE VIII

CEA A02 Supermotif with Binding Data

No. of

Position
Amino Acids
A*0201
A*0202
A*0203
A*0206
A*6802

342
8
0.0002

342
11
−0.0001

527
10

267
10

445
11

134
11
−0.0001

661
8
−0.0002

661
9
−0.0002

687
9
0.0280
0.1100
0.1300
0.1500
1.6000

687
10
0.0007

687
11
0.0160

518
10
0.0003

162
10

340
10
0.0002

12
8
−0.0002

12
9
0.0002

12
10
0.0031

12
11
0.0003

299
8

299
10

238
8
−0.0002

238
10
−0.0002

565
9
−0.0002

173
8
0.0001

517
11
−0.0001

161
11

339
11
−0.0001

128
8

209
9
−0.0002

116
9
0.0009

116
10
−0.0002

305
8
−0.0002

305
9
−0.0002

305
10
−0.0002

305
11
0.0001

387
9
−0.0002

588
8
−0.0002

588
10
0.0003

588
11
0.0001

526
8
−0.0002

526
11
0.0011

133
8
0.0001

99
9
−0.0002

99
10
−0.0002

99
11
0.0004

348
8
−0.0002

348
11
0.0004

283
8

283
9

461
8
−0.0002

398
10
0.0001

398
11
−0.0001

170
8
−0.0002

170
11
0.0002

216
8
−0.0002

50
9

326
10
0.0001

277
8

277
10

521
10
0.0003

521
11
0.0059

165
10
−0.0002

165
11
0.0005

272
10
0.0003

608
11
−0.0001

686
8
−0.0002

686
10
0.0006

686
11
0.0051

690
8
0.0089

690
10
0.0880
0.0110
0.1500
0.0250
0.0260

690
11
0.0015

631
9
0.0002

631
10
−0.0002

394
8
0.0001

572
8
−0.0002

307
8

307
9
0.0011

307
10
0.0004

307
11
0.0001

682
8
0.0008

682
10
0.0037

682
11
0.0001

473
11
0.0290

136
9

538
10

275
10

85
10

678
8

678
10
−0.0002

678
11
−0.0001

651
10
0.0002

651
11
0.0004

694
8
−0.0002

694
9
0.0030

430
10
−0.0001

430
11
0.0022

438
8

458
10
−0.0001

458
11
0.0013

636
8
0.0036

636
10
0.0012

636
11
0.0059

123
8
−0.0002

642
11
−0.0001

79
8
0.0005

79
11
−0.0001

112
10
0.0011

112
11
0.0130

597
10
0.0003

100
8
−0.0002

100
9
0.0034

100
10
0.0058

230
10
0.0007

691
9
0.1500

691
10
0.0160

691
11
0.0029

113
9

113
10

109
9

349
10

455
8

455
10

467
8
−0.0002

467
10
−0.0002

645
8
−0.0002

645
10
0.0002

327
9
0.0006

289
10

672
8
−0.0002

668
9
−0.0002

644
9
−0.0002

644
11
0.0002

35
11

492
9
0.0020

660
9
−0.0002

660
10
−0.0002

450
10
−0.0002

108
10
0.0003

107
11
0.0140

18
8

18
9

52
11
0.0011

380
9
0.0003

19
8

24
9
0.0260

24
10

24
11

53
10
0.0008

369
9

369
10

369
11

547
9

547
10

547
11

343
10
−0.0002

343
11
−0.0001

25
8

25
9

25
10

36
10

36
11

556
11
0.0004

200
11
−0.0001

378
11
0.0150

54
9
−0.0002

692
8
0.0120

692
9
0.0009

692
10
0.0004

692
11
0.0025

104
9
−0.0002

104
10
−0.0002

111
11
0.0006

454
9
0.0002

454
11
0.0001

466
9
−0.0002

466
11
−0.0001

288
11

659
10
−0.0002

659
11
0.0001

254
8

254
9

610
9
0.0003

432
8
−0.0002

432
9
0.0110
0.0015
0.0069
0.0002
0.0003

360
10

246
10
−0.0002

529
8

44
8

44
9

44
10

44
11

232
8
0.0001

232
10
−0.0002

232
11
0.0001

410
10
−0.0002

410
11
0.0013

560
9
−0.0002

560
11
−0.0001

204
8
−0.0002

266
8
−0.0002

266
11
0.0007

444
8

93
8
−0.0002

93
9
−0.0002

596
11
−0.0001

633
8

633
10

633
11

623
10

240
8
−0.0002

418
8
−0.0002

31
8

31
11

334
8
0.0002

334
9
−0.0002

334
10
−0.0002

334
11
−0.0001

512
8

512
9

512
11

220
10
−0.0002

220
11
−0.0001

542
8

300
9
−0.0002

78
9
0.0270
0.0780
0.0730
0.1200
0.2600

370
8
−0.0002

370
9
0.0001

370
10
−0.0002

370
11
0.0001

548
8

548
9

548
10

548
11

87
8

456
9

634
9

634
10

278
9

638
8
0.0007

638
9
0.0008

567
11
0.0099

628
10
−0.0002

17
8
0.0023

17
9
0.0068

17
10
0.0036

368
10
−0.0002

368
11
0.0001

546
10

546
11

77
8

77
10

554
8
0.0078

554
9
−0.0002

376
8

376
9

488
8
−0.0002

488
9
−0.0002

488
11
0.0064

310
8
−0.0002

310
9
0.0012

310
11
0.0020

72
8

72
9
−0.0002

139
11
−0.0001

497
9
−0.0002

684
8
−0.0002

684
9
−0.0002

684
10
−0.0002

578
8

578
9

578
10

5
9
−0.0002

222
8
−0.0002

222
9
−0.0002

222
10
−0.0002

482
8
−0.0002

482
9
−0.0002

482
10
−0.0002

675
9
−0.0002

675
11
0.0001

504
10
−0.0002

671
9
−0.0002

667
8
−0.0002

667
10
0.0004

106
8
0.0008

23
10
0.0022

23
11

540
8

540
10

280
10

280
11

400
8
0.0001

400
9
−0.0002

400
10
−0.0002

576
10
−0.0002

576
11
−0.0001

33
9

210
8
0.0001

37
9

37
10

493
8
−0.0002

586
10
0.0002

557
10
0.0011

201
10
0.0003

201
11
0.0110

121
9
0.0002

121
10
0.0017

379
10
0.0018

555
8
0.0001

377
8

171
10

281
9

281
10

281
11

459
9

459
10

86
9

637
9

637
10

32
10

489
8
−0.0002

489
10
−0.0002

311
8
0.0006

311
10
0.0025

688
8
0.0004

688
9
0.0014

688
10
0.0015

490
9
−0.0002

490
11
0.0004

290
9

495
11
−0.0001

673
11
−0.0001

312
9
0.0047

317
11
−0.0001

45
8

45
9

45
10

45
11

519
9
0.0011

163
9

341
9
0.0009

83
8

124
11

229
11
0.0001

639
8
0.0005

51
8

695
8
0.0073

233
9
0.0030

233
10
0.0110
0.0130
1.0000
0.0033
0.0016

411
9
0.0005

411
10
0.0200
0.0130
0.0720
0.0007
0.0003

589
9
0.0160

589
10
0.0057

585
11
−0.0001

561
8
−0.0002

561
10
0.0002

313
8
0.0009

449
11
0.0005

15
8

15
10

15
11

535
9
0.0020

357
9
0.0012

653
8
0.0002

653
9
0.0002

653
10
0.0046

319
9
−0.0002

319
10
−0.0002

605
9
0.3600

532
10
0.1400

354
10
0.4200

297
10
−0.0002

475
9
−0.0002

120
10
0.0023

120
11
0.0083

424
8
0.0003

424
10
0.0018

569
9
0.0260
0.0097
0.0210
0.0300
0.0200

569
11
0.0018

82
8

82
9

[0480]

11

TABLE VIX

CEA A03 Supermotif with Binding Data

No. of

Position
Amino Acids
A*0301
A*1101
A*3101
A*3301
A*6801

483
10
0.0008
0.0140
0.0002
0.0005
0.0002

618
11
0.0016
0.0056

661
10
0.0017
0.0045

89
10
0.0004
0.0190
0.0490
0.0180
0.0075

116
11
−0.0009
0.0031

461
10
0.0028
0.0030

2
9
−0.0002
−0.0001

39
11

216
9
0.0011
0.0012

216
10
−0.0002
0.0002

463
8
0.0038
0.0019

656
9
0.0019
0.0490
0.0540
0.2800
0.9800

572
10
0.0018
0.0052

61
9
4.9000
2.5000
0.8800
1.6000
2.3000

636
9
0.0093
0.1700
0.1700
0.2200
0.0500

242
9
0.0004
0.0008

420
9
0.0082
0.0420
0.8500
0.0560
0.7100

494
9
0.0080
0.1900
0.0002
0.0005
0.0510

316
9
0.0006
0.0170
0.0002
0.0005
0.0610

492
11
0.3600
0.1600
−0.0006
−0.0013
0.0130

660
11
0.0008
−0.0002

25
11

556
8
−0.0007
0.0006

378
8

129
11
−0.0009
0.0013

481
8
0.0040
−0.0004

303
8
−0.0004
−0.0004

509
8
−0.0007
−0.0001

560
8
−0.0004
−0.0004

204
11
−0.0002
−0.0002

503
9
−0.0008
−0.0001

621
8
0.0070
0.0009

240
11
0.0025
0.0041

418
11
−0.0002
0.1300
0.4100
0.0370
0.1400

300
11
−0.0009
−0.0002

478
11
−0.0009
−0.0002

88
11

539
8

368
9
−0.0010
0.0002

546
9
0.0270
0.0013

554
10
0.1600
1.1000

376
10
0.0210
0.1100
2.9000
0.0280
0.0500

139
8
0.0130
0.0440
0.0010
0.0012
0.0004

482
11
0.0013
0.0006

504
8
−0.0007
0.0006

506
11
−0.0003
0.0004

40
10

241
10
0.0069
0.0380
0.0870
0.0510
1.8000

419
10
0.0032
0.2800
0.2500
0.1700
2.6000

493
10
0.0023
0.0490
0.0002
0.0005
0.0250

315
10
0.0005
0.0035

557
11
0.0075
0.0003

555
9
0.0021
0.0006

377
9

314
11
0.0200
0.0280
0.0008
−0.0013
0.3900

495
8
0.0037
0.0320
−0.0004
0.0012
0.0053

317
8
0.0160
0.0220
−0.0004
0.0014
0.0140

657
8
−0.0009
0.0021

205
10
−0.0009
0.0014

65
8

[0481]

12

TABLE X

CEA A24 Supermotif Peptides with Binding Data

No. of

Position
Amino Acids
A*2401

342
8

134
8

134
11

661
8

687
10

340
10

94
8
0.0003

94
9

12
8

12
9

128
11

116
10

387
9

588
10

588
11

99
9

99
10

99
11

348
8

348
9

348
10

398
11

170
8

170
9

170
10

50
9

27
10
0.0300

119
11
0.0250

118
8
0.0010

631
10

631
11

307
10

682
10

682
11

275
10

275
11

85
11

651
10

694
8

694
9

61
8

458
10

636
10

112
8

112
9

112
11

597
9

597
10

100
8

100
9

100
10

691
11

467
8

467
9

645
9

289
9

316
11

101
8
0.0680

101
9
6.9000

644
10

35
9

492
9

18
8

18
10

18
11

52
11

19
9

19
10

53
10

53
11

20
8

20
9

36
8

54
9

54
10

129
10

533
9
0.0082

355
9
0.0220

234
9
0.2100

412
9
0.0340

590
8
0.0011

590
9
0.2600

692
10

692
11

111
9

111
10

454
9

454
10

454
11

466
9

466
10

288
10

659
10

57
9

57
11

246
10

44
9

44
10

44
11

232
11

410
11

560
10

204
10

42
11
−0.0005

596
10

596
11

240
10

418
9

418
10

31
8

334
10

512
10

406
8

220
11

542
8

584
8

14
11
0.0370

390
10
0.0002

137
8
0.0006

370
9

370
11

548
9

548
11

638
8

268
10
3.4000

446
10
0.0150

624
9
0.0270

17
8

17
9

17
11

368
11

546
11

310
10

72
8

72
9

72
11

139
11

10
9
0.0130

10
10
0.0390

10
11
0.0790

106
8

540
8

540
10

280
10

400
9

400
10

228
8

382
10

270
8
0.0250

448
8
0.0005

604
8
0.0051

604
10
0.0580

248
8
−0.0003

248
10
0.0002

423
11
0.0550

276
9
0.0012

276
10
0.0160

276
11
0.0011

26
11
0.0026

241
9

419
8

419
9

493
8

121
9

311
9

688
9

490
11

290
8

495
11

673
11

312
8

317
10

317
11

652
9
1.2000

531
11
0.1300

353
11
0.1400

425
9
0.0650

425
11
0.0910

51
8

695
8

233
10

411
10

589
9

589
10

561
9

205
9

383
9

318
9
0.2900

318
10
0.0180

140
10
0.0079

534
8
0.0012

356
8
0.0009

605
9

532
10

354
10

120
10

424
10

426
8
0.0220

426
10
0.1400

[0482]

13

TABLE XI

CEA B07 Supermotif Peptides with Binding Data

No. of

Position
Amino Acids
B*0702

6
8
0.0006

6
10
0.0290

239
11
−0.0002

417
8
−0.0006

417
10
−0.0002

417
11
−0.0002

405
8
−0.0006

405
9
−0.0002

583
8
−0.0006

583
9
−0.0002

524
9
−0.0002

524
10
0.0001

524
11
−0.0003

346
9
−0.0002

346
10
0.0001

346
11
−0.0003

168
9
−0.0002

168
10
0.0001

168
11
−0.0003

92
9
0.2000

92
10
0.0076

92
11
0.0013

236
10
0.0048

414
11
−0.0002

389
11
0.0006

632
8
0.0017

632
9
0.1600

632
10
1.0180

632
11
0.0016

13
8
0.1100

13
10
0.0440

511
8
−0.0002

511
9
0.0081

511
10
0.0010

511
11
0.0012

58
8
−0.0006

58
10
−0.0002

58
11
−0.0002

541
9
0.9100

442
8
0.0002

264
9
0.0001

264
10
0.0013

442
9
0.0051

442
10
0.0004

29
8
0.0005

29
10
0.0190

620
8
−0.0002

620
10
−0.0002

333
8
−0.0002

333
9
0.0001

333
10
−0.0002

333
11
−0.0002

219
11
−0.0002

265
8
0.0011

265
9
0.0001

443
8
0.0002

443
9
0.0002

600
10
−0.0002

7
9
−0.0002

30
9
0.0003

428
8
0.0720

680
8
0.0008

680
10
0.0027

599
8
−0.0006

599
11
−0.0003

622
8
0.0004

622
11
0.0043

3
9
0.0013

3
11
0.0022

421
11
0.0026

41
11
0.0007

90
11
0.0014

595
11
−0.0002

646
8
−0.0006

646
9
0.0011

646
11
0.0008

141
9
0.0120

102
8
0.0280

102
11
0.0007

[0483]

14

TABLE XII

B27 Supermotif Peptides

No. of

Position
Amino Acids

301
8

643
11

34
10

566
8

223
8

223
9

437
11

615
11

402
8

402
11

71
9

71
10

485
10

48
11

97
11

663
10

9
10

9
11

122
8

76
9

580
8

580
11

309
8

309
11

8
8

8
11

60
8

60
9

457
8

457
11

635
8

635
11

16
9

16
10

224
8

224
11

487
8

562
8

206
8

384
8

55
8

55
9

55
11

491
10

427
9

[0484]

15

TABLE XIII

B58 Supermotif Peptides

No. of

Position
Amino Acids
SEQ ID NO.

439
9

439
11

483
9

676
8

105
8

105
9

440
8

440
10

262
11

440
11

618
8

618
10

211
11

134
8

134
11

661
8

661
9

687
9

687
10

687
11

238
8

565
9

173
8

339
11

602
10

227
8

227
9

116
9

116
10

305
9

526
8

526
9

526
10

526
11

133
8

133
9

2
10

170
8

170
9

170
10

170
11

686
8

686
10

686
11

275
10

275
11

85
11

651
10

438
10

616
10

403
9

403
10

403
11

486
9

486
11

458
10

636
10

464
11

242
8

598
8

598
9

420
8

505
9

467
8

467
9

645
9

327
9

289
9

316
11

492
9

660
9

660
10

683
9

683
10

683
11

606
8

371
8

371
10

371
11

549
8

549
10

549
11

399
9

399
10

399
11

381
8

381
11

20
8

20
9

36
8

36
10

378
11

104
9

104
10

481
11

303
11

666
9

509
11

331
11

575
11

246
10

529
8

266
8

444
8

93
8

93
9

93
10

4
8

4
10

503
11

621
9

422
10

240
10

418
9

418
10

31
8

300
9

88
8

539
9

539
11

279
8

279
11

567
11

581
9

581
10

581
11

225
9

225
10

225
11

250
8

554
8

376
8

488
9

310
9

310
10

497
9

684
8

684
9

684
10

578
8

578
10

5
9

5
11

222
8

222
9

222
10

482
10

675
9

617
9

617
11

506
8

603
9

603
11

280
10

33
11

21
8

328
8

679
11

247
9

247
11

489
8

311
8

311
9

45
8

45
9

45
10

45
11

341
9

496
10

577
9

577
11

221
9

221
10

221
11

674
10

561
9

561
10

205
9

383
9

653
8

319
8

319
9

95
8

269
9

447
9

625
8

65
9

120
10

120
11

424
8

424
10

[0485]

16

TABLE XIV

B62 Supermotif Peptides

No. of

Position
Amino Acids

342
8

6
8

6
10

239
11

527
8

527
9

527
10

267
11

445
11

340
10

128
11

417
8

417
10

417
11

405
9

583
9

387
9

588
10

588
11

99
11

348
9

348
10

348
11

283
9

398
10

398
11

524
9

524
11

346
9

346
11

168
9

168
11

326
10

277
9

277
10

690
8

690
10

631
9

631
11

394
8

307
10

682
8

682
10

682
11

92
9

92
10

92
11

414
11

694
9

61
8

123
8

112
8

112
9

597
9

100
10

691
9

632
8

632
10

632
11

113
8

109
11

349
8

349
9

349
10

455
9

455
10

644
10

35
9

35
11

511
9

511
11

18
10

18
11

380
9

19
9

19
10

53
11

58
8

58
10

58
11

54
10

129
10

692
8

692
11

111
9

111
10

454
10

454
11

466
10

288
10

659
10

659
11

57
9

57
11

442
8

264
9

264
10

442
10

29
10

620
8

620
10

333
9

219
11

44
8

232
11

410
11

560
10

560
11

204
10

596
10

265
8

265
9

443
9

7
9

30
9

59
9

59
10

633
9

633
10

623
10

334
8

512
8

512
10

406
8

220
10

220
11

584
8

87
9

456
8

456
9

634
8

634
9

278
8

278
9

638
8

17
11

77
8

72
8

72
9

72
11

139
11

504
10

667
8

106
8

680
10

622
8

622
11

3
9

3
11

421
11

400
8

400
9

228
8

576
10

382
10

37
9

241
9

419
8

419
9

121
10

379
10

41
11

90
11

595
11

646
8

646
11

171
8

171
9

171
10

281
9

281
11

459
9

86
10

637
9

688
8

688
10

290
8

495
11

312
8

317
10

317
11

695
8

233
10

411
10

589
9

589
10

535
9

357
9

141
9

102
8

102
11

569
9

[0486]

17

TABLE XV

CEA A01 Motif Peptides with Binding Data

No. of

Position
Amino Acids
A*0101

134
8
−0.0021

95
8
0.0150

242
8
−0.0021

262
8
0.0120

420
8
0.0030

440
8
0.0120

598
8
−0.0021

618
8
0.0085

205
9
0.0011

289
9
0.0100

311
9
0.0011

383
9
−0.0021

418
9
0.0035

467
9
0.0390

561
9
0.0011

645
9
0.0049

227
9
−0.0021

240
10
0.0250

310
10
0.0041

418
10
0.0770

616
10
0.3400

85
11
0.0069

225
11
0.5300

381
11
0.0100

403
11
0.9700

581
11
3.2000

525
8
−0.0021

419
8
0.0038

168
9

346
9

524
9

87
9
−0.0021

94
9
0.0011

241
9
0.0024

261
9
−0.0021

419
9
0.0240

439
9
−0.0021

597
9
0.0021

617
9
0.0031

415
10
0.0012

132
10
−0.0017

260
10
0.0012

438
10
0.0012

226
10
0.0041

72
11
0.0850

414
11

131
11
−0.0017

166
11
−0.0017

344
11
−0.0017

522
11
0.0017

92
11

259
11
0.0019

437
11
0.0019

615
11
0.0026

[0487]

18

TABLE XVI

CEA A03 Motif Peptides with Binding Data

No. of

Position
Amino Acids
A*0301

439
9

654
8

654
11

520
8

164
11

483
10
0.0008

676
10

440
8

262
11

618
8

618
11
0.0016

134
8

661
10
0.0017

89
10
0.0004

518
10

655
10

393
11

571
9

571
11

12
11

517
11

416
9

416
11

74
9

128
11

602
8

227
9

116
8

116
11
−0.0009

133
9

514
8

47
10

461
10
0.0028

2
8

2
9
−0.0002

39
8

39
11

216
8

216
9
0.0011

216
10
−0.0002

63
10

463
8
0.0038

165
10

656
9
0.0019

608
9

608
11

118
9

690
11

631
11

394
10

572
8

572
10
0.0018

473
11

295
8

275
11

85
10

85
11

678
8

678
10

651
11

430
9

430
10

430
11

438
8

438
10

61
8

61
9
4.9000

616
10
0.0006

403
11

636
8

636
9
0.0093

451
8

84
11

693
8

80
10

79
11

112
8

112
9

597
9

230
10

691
10
0.0035

242
8

242
9
0.0004

598
8

420
8

420
9
0.0082

467
9

645
9
0.0008

645
10

289
9
0.0008

494
9
0.0080

316
9
0.0006

316
11

668
9

214
10

214
11

69
9

644
10

644
11

35
9

126
9

492
11
0.3600

660
11
0.0008

62
8

62
11

462
9

558
9

558
10

558
11

202
10

450
9

18
10

52
10

19
9
0.0011

24
11

53
9

53
11

435
11

606
11

433
8

549
11

381
11

20
8

25
10

25
11

36
8

36
11

556
8
−0.0007

556
11

378
8

54
8

54
10

129
10

129
11
−0.0009

692
9

115
9

551
9

537
10

111
9

111
10

454
10

466
10

288
10

254
8

254
9

610
9

57
9

432
8

432
9

481
8
0.0040

303
8
−0.0004

471
9

293
9

293
10

666
11

509
8
−0.0007

509
10

331
10

232
8

560
8
−0.0004

560
9

560
10

204
8

204
10

204
11
−0.0002

93
10

415
10

601
9

42
8

91
8

429
10

429
11

596
10

503
9
−0.0008

621
8
0.0070

240
10
0.0006

240
11
0.0025

418
9

418
10
0.0006

418
11
−0.0002

334
9

512
9

512
10

406
8

584
8

300
11
−0.0009

478
9

478
11
−0.0009

88
8

88
11

137
10

539
8

628
9
0.1000

17
11

368
9
−0.0010

546
9
0.0270

581
11

225
11

250
11

554
10
0.1600

376
10
0.0210

488
11

310
10
0.0007

310
11

72
11

139
8
0.0130

482
11
0.0013

675
11

617
9

436
10

127
8

404
10

582
10

226
10

607
10

251
10

251
11

484
9
0.0006

472
8

96
10

294
8

294
9
0.0006

677
9

677
11

504
8
−0.0007

667
10

506
11
−0.0003

40
10

228
8

382
10

33
11

522
11

344
11

166
9

166
11

476
8

476
11

276
10

26
9

26
10
0.0070

117
10
0.0005

662
9

37
10

241
9

241
10
0.0069

419
8

419
9

419
10
0.0032

493
10
0.0023

315
10
0.0005

557
10

557
11
0.0075

201
11

555
9
0.0021

377
9

679
9

314
11
0.0200

489
10

311
9
0.0008

311
10

490
9

290
8

495
8
0.0037

312
8

312
9

317
8
0.0160

317
10
0.0005

519
9

570
10

73
10

124
11

229
11

51
11

657
8
−0.0009

561
8

561
9
0.0014

205
9
0.0024

205
10
−0.0009

383
9

313
8

449
10

653
9

319
8

95
8

95
11

269
9
0.0011

65
8

475
9

569
11

82
8

[0488]

19

TABLE XVII

CEA A11 Motif Peptides with Binding Data

No. of

Position
Amino Acids
A*1101

439
9

654
11

609
8

479
8

479
10

483
10
0.0140

440
8

618
8

618
11
0.0056

134
8

661
10
0.0045

89
10
0.0190

655
10

393
11

571
11

416
9

416
11

74
9

227
9

116
8

116
11
0.0031

133
9

47
10

461
10
0.0030

253
8

2
8

2
9
−0.0001

39
11

216
9
0.0012

216
10
0.0002

63
10

463
8
0.0019

559
9

559
11

203
11

656
9
0.0490

608
9

118
9

394
10

572
10
0.0052

75
8

295
8

85
11

430
9

438
10

61
8

61
9
2.5000

56
10

302
9

616
10
0.0001

403
11

636
9
0.1700

451
8

112
9

597
9

629
8

242
8

242
9
0.0008

598
8

420
8

420
9
0.0420

467
9

645
9
0.0001

289
9
0.0002

494
9
0.1900

316
9
0.0170

214
11

69
9

644
10

492
11
0.1600

660
11
−0.0002

62
8

62
11

462
9

558
10

450
9

52
10

53
9

606
11

381
11

25
11

556
8
0.0006

378
8

54
8

129
11
0.0013

115
9

537
10

111
10

466
10

288
10

57
9

359
10

480
9

292
11

508
9

481
8
−0.0004

303
8
−0.0004

293
10

509
8
−0.0001

560
8
−0.0004

560
10

204
10

204
11
−0.0002

93
10

415
10

42
8

91
8

429
10

596
10

287
11

503
9
−0.0001

621
8
0.0009

240
10
0.0002

240
11
0.0041

418
9

418
10
0.0018

418
11
0.1300

406
8

584
8

300
11
−0.0002

478
9

478
11
−0.0002

88
8

88
11

137
10

114
10

396
8

110
11

218
8

574
8

539
8

628
9
0.0094

368
9
0.0002

546
9
0.0013

207
8

581
11

225
11

250
11

554
10
1.1000

376
10
0.1100

310
10
0.0013

72
11

139
8
0.0440

482
11
0.0006

617
9

404
10

582
10

226
10

607
10

251
10

484
9
0.0011

294
9
0.0001

504
8
0.0006

465
11

507
10

619
10

506
11
0.0004

40
10

228
8

382
10

522
11

344
11

166
11

476
11

26
10
0.0110

117
10
0.0085

662
9

241
9

241
10
0.0380

419
8

419
9

419
10
0.2800

493
10
0.0490

315
10
0.0035

557
11
0.0003

555
9
0.0006

377
9

314
11
0.0280

311
9
0.0003

290
8

495
8
0.0320

312
8

317
8
0.0220

73
10

51
11

130
10

536
11

431
8

358
11

657
8
0.0021

561
9
0.0002

205
9
0.0002

205
10
0.0014

383
9

449
10

28
8

95
8

65
8

[0489]

20

TABLE XVIII

CEA A24 Motif Peptides with Binding Data

No. of

Position
Amino Acids
A*2401

94
8
0.0003

27
10
0.0300

119
11
0.0250

118
8
0.0010

691
11

101
8
0.0680

101
9
6.9000

533
9
0.0082

355
9
0.0220

234
9
0.2100

412
9
0.0340

590
8
0.0011

590
9
0.2600

42
11
−0.0005

14
11
0.0370

390
10
0.0002

137
8
0.0006

268
10
3.4000

446
10
0.0150

624
9
0.0270

10
9
0.0130

10
10
0.0390

10
11
0.0790

270
8
0.0250

448
8
0.0005

604
8
0.0051

604
10
0.0580

248
8
−0.0003

248
10
0.0002

423
11
0.0550

276
9
0.0012

276
10
0.0160

276
11
0.0011

26
11
0.0026

652
9
1.2000

531
11
0.1300

353
11
0.1400

425
9
0.0650

425
11
0.0910

318
9
0.2900

318
10
0.0180

140
10
0.0079

534
8
0.0012

356
8
0.0009

426
8
0.0220

426
10
0.1400

[0490]

21

TABLE XIX

CEA DR Super Motif Peptides with Binding Data

Core
Exemplary
Posi-

SEQ

Sequence
Sequence
tion
DR1
DR2wB1
DR2w2B2
DR3
DR4w4
DR4w15
DR5w11
DR5w12
ID NO.

IPWQRLLLT
RWCIPWQRLLLTASL
10
0.6100
0.0110
−0.0007
0.0150
0.0830

−0.0005

1815

WQRLLLTAS
CIPWQRLLLTASLLT
12

1816

LLLTASLLT
WQRLLLTASLLTFWN
15

1817

LLTASLLTF
QRLLLTASLLTFWNP
16
−0.0004

−0.0022

1818

LTASLLTFW
RLLTASLLTFWNPP
17

1819

LTFWNPPIT
ASLLTFWNPPTTAKL
22

1820

FWNPPTTAK
LLTFWNPPTTAKLTI
24

1821

WNPPTTAKL
LTFWNPPTTAKLTIE
25

1822

LTIESTPFN
TAKLTIESTPFNVAE
33

1823

LLVHNLPQH
EVLLLVHNLPQHLFG
50
2.5000
0.2300
0.0013
0.8900
0.8600

0.0340

1824

LVHNLPQHL
VLLLVHNLPQHLFGY
51

1825

YKGERVDGN
YSWYKGERVDGNRQI
65

1826

HGYVIGTQ
NRQHGYVIGTQQAT
76

1827

IGTQQATPG
GYVIGTQQATPGPAY
81

1828

YSGREHYP
GPAYSGREHYPNAS
92

1829

HYPNASLL
GREHYPNASLLIQN
97
0.6200
0.3800
0.0024
0.2700
0.0930

0.0029

1830

IYPNASLLI
REHYPNASLLIQNI
98

1831

YPNASLLIQ
EHYPNASLLIQNH
99
0.3500
0.1600
−0.0007
0.1400
0.0390

−0.0005

1832

LLIQNHQN
NASLLIQNHQNDTG
104
0.0011

−0.0022

1833

LIQNHQND
ASLLIQNHQNDTGF
105

1834

HQNDTGFY
IQNHQNDTGFYTLH
109

1835

FYTLHVIKS
DTGFYTLHVIKSDLV
116
0.0720
0.0180
0.0250
0.0013
0.0260

0.0080

1836

YTLHVIKSD
TGFYTLHVIKSDLVN
117

1837

LHVIKSDLV
FYTLHVIKSDLVNEE
119

1838

VIKSDLVNE
TLHVIKSDLVNEEAT
121

1839

IKSDLVNEE
LHVIKSDLVNEEATG
122

0.1300

1840

LVNEEATGQ
KSDLVNEEATGQFRV
126

0.0058

1841

VNEEATGQF
SDLVNEEATGQFRVY
127

−0.0027

1842

VYPELPKPS
QFRVYPELPKPSISS
137

−0.0027

1843

LPKPSISSN
YPELPKPSISSNNSK
141
0.0009

−0.0022

1844

ISSNNSKPV
KPSISSNNSKPVEDK
146
0.0021

−0.0022

1845

VEDKDAVAF
SKPVEDKDAVAFTCE
154

1846

WVNNQSLPV
YLWWVNNQSLPVSPR
176
8.4000
0.0830
0.0095
0.1300
5.6000

0.7000

1847

VNNQSLPVS
LWWVNNQSLPVSPRL
177
0.02300

0.0290

1848

LTLFNVTRN
NRTLTLFNVTRNDTA
197

1849

VTRNDTASY
LFNVTRNDTASYKCE
202

1850

VSARRSDSV
QNPVSARRSDSVILN
218

1851

VILNVLYGP
SDSVILNVLYGPDAP
226

1852

LYGPDAPTI
LNVLYGPDAPTISPL
231

1853

YGPDAPTIS
NVLYGPDAPTISPLN
232

−0.0027

1854

ISPLNTSYR
APTISPLNTSYRSGE
239

1855

LSCHAASNP
NLNLSCHAASNPPAQ
254

1856

WFVNGTFQQ
QYSWFVNGTFQQSTQ
268
0.0260
−0.0007
0.0033
0.0280
0.5600

0.0540

1857

LFHPNITVN
TQELFIPNITVNNSG
281

1858

FIPNHVNN
QELFIPNITVNNSGS
282

1859

IPNITVNNS
ELFIPNITVNNSGSY
283

1860

ITVNNSGSY
IPNITVNNSGSYTCQ
286

1861

VNNSGSYTC
NITVNNSGSYTCQAH
288

1862

LNRTTVTTI
DTGLNRTTVTTTVY
305
−0.0004

−0.0022

1863

VTTTTVYAE
RTTVTTTTVYAEPPK
310

1864

VYAEPPKPF
TITVYAEPPKPFITS
315

0.0042

1865

ITSNNSNPV
KPFITSNNSNPVEDE
324
−0.0004

−0.0022

1866

VEDEDAVAL
SNPVEDEDAVALTCE
332

0.0054

1867

LTLLSVTRN
NRTLTLLSVTRNNDVG
375
0.0210

−0.0022

1868

VTRNDVGPY
LLSVTRNDVGPYECG
380

1869

VGPYECGIQ
RNDVGPYECGIONEL
385

1870

IQNELSVDH
ECGIQNELSVDISDP
392

−0.0027

1871

LSVDHSDPV
QNELSVDHSDPVILN
396

0.0820

1872

VDHSDPVIL
ELSVDHSDPVILNVL
398

1873

VILNVLYGP
SDPVILNVLYGPDDP
404

1874

YGPDDPTIS
NVLYGPDDPTISPSY
410

−0.0027

1875

ISPSYTYYR
DPTISPSYTYYRPGV
417

1876

YTYYRPGVN
SPSYTYYRPGVNLSL
421

1877

YYRPGVNLS
SYTYYRPGVNLSLSC
423

1878

VNLSLSCHA
RPGVNLSLSCHAASN
428

1879

LSCHAASNP
NLSLSCHAASNPPAQ
432

1880

LIDGNIQQH
YSWLIDGNIQQHTQE
447

1881

LFISNITEK
TQELFISNITEKNSG
459

1882

FISNITEKN
QELFSNITEKNSGL
460
0.0005

0.0180

1883

ITEKNSGLY
ISNITEKNSGLYTCQ
464

1884

LYTCQANNS
NSGLYTCQANNSASG
471

1885

VKTITVSAE
RTTVKTITVSAELPK
488
0.0110
0.0250
0.0009
0.0010
0.0064

−0.0005

1886

VSAELPKPS
TTTVSAELPKPSISS
493

−0.0027

1887

LPKPSISSN
SAELPKPSISSNNSK
497
−0.0004

−0.0022

1888

WVNGQSLPV
YLWWVNGQSLPVSPR
532

1889

VNGQSLPVS
LWWVNGQSLPVSPRL
533

1890

LTLFNVTRN
NRTLTLFNVTRNDAR
553

1891

VTRNDARAY
LFNVTRNDARAYVCG
558

1892

IQNSVSANR
VCGIQNSVSANRSDP
570

1893

VSANRDPV
QNSYSANRSDPVTLD
574

1894

VTLDVLYGP
SDPVTLDVLYGPDTP
582

−0.0027

1895

LYGPDTPH
LDVLYGPDTPHSPP
587
−0.0004

−0.0022

1896

YGPDTPHS
DVLYGPDTPHSPPD
588

0.0037

1897

ISPPDSSYL
TPHSPPDSSYLSGA
595

1898

LSGANLNLS
SSYLSGANLNLSCHS
603

1899

LSCHSASNP
NLNLSCHSASNPSPQ
610

1900

WRINGIPQQ
QYSWRINGIPQQHTQ
624

1901

IPQQHTQVL
INGIPQQHTQVLFIA
629

1902

LFIAKTTPN
TQVLFIAKITPNNNG
637
0.0820

0.0037

1903

FIAKITPNN
QVLFIAKITPNNNGT
638
0.1200

0.0240

1904

IAKITPNNN
VLFIAKITPNNNGTY
639

1905

YACFVSNLA
NGTYACFVSNLATGR
650

1906

FVSNLATGR
YACFVSNLATGRNNS
653
0.0240

0.0270

1907

VSNLATGRN
ACFVSNLATGRNNSI
654

1908

IVKSITVSA
NNSIVKSITVSASGT
665
0.0550
0.0029
−0.0007
0.1100
1.8000

0.0016

1909

VKSITVSAS
NSIVKSITVSASGTS
666
0.0640
0.0023
−0.0007
0.0750
1.8000

0.0012

1910

ITVSASGTS
VKSITVSASGTSPGL
669

1911

VSASGTSPG
SITVSASGTSPGLSA
671

1912

LSAGATVGI
SPGLSAGATVGIMIG
680

1913

IMIGVLVGV
TVGIMIGVLVGVALI
688

1914

LTIESTPFN
TAKLTIESTPFNVAE
33

1915

YKGERVDGN
YSWYKGERVDGNRQI
65

1916

LPVSPRLQL
NQSLPVSPRLQLSNG
182

1917

LNLSCHAAS
GENLNLSCHAASNPP
252

1918

LPVSPRLQL
GQSLPVSPRLQLSNG
538

1919

Core
Exemplary

Sequence
Sequence
DR6w19
DR7
DR8w2
DR9
DRw53
SEQ ID NO.

IPWQRLLLT
RWCIPWQRLLLTASL
0.0110
0.0700
−0.0004

1815

WQRLLLTAS
CIPWQRLLLTASLLT

1816

LLLTASLLT
WQRLLLTASLLTFWN

1817

LLTASLLTF
QRLLLTASLLTFWNP

−0.0013

1818

LTASLLTFW
RLLLTASLLTFWNPP

1819

LTFWNPPTT
ASLLTFWNPPTTAKL

1820

FWNPPTTAK
LLTFWNPPTTAKLTI

1821

WNPPTTAKL
LTFWNPPTAKLTIE

1822

LTIESTPFN
TAKLTIESTPFNVAE

1823

LLVINLPQH
EVLLLVINLPQHLFG
3.4000
0.4700
0.1200

1824

LVHNLPQHL
VLLLVHNLPQHLFGY

1825

YKGERVDGN
YSWYKGERVDGNRQI

1826

HGYVIGTO
NRQHGYVIGTQQAT

1827

IGTQQATPG
GYVIGTQQATPGPAY

1828

YSGREHYP
GPAYSGREHYPNAS

1829

HYPNASLL
GREHYPNASLLIQN
1.2000
0.5600
0.0083

1830

IYPNASLLI
REHYPNASLLIQNI

1831

YPNASLLIQ
EHYPNASLLIQNH
0.3100
0.1600
0.0029

1832

LLIQNHQN
NASLLIQNHQNDTG

−0.0013

1833

LIQNHQND
ASLLIQNHQNDTGF

1834

HQNDTGFY
IQNHQNDTGFYTLH

1835

FYTLHVIKS
DTGFYTLHVIKSDLV
0.0009
0.1100
0.0620

1836

YTLHVIKSD
TGFYTLHVIKSDLVN

1837

LHVIKSDLV
FYTLHVIKSDLVNEE

1838

VIKSDLVNE
TLHVIKSDLVNEEAT

1839

IKSDLVNEE
LHVIKSDLVNEEATG

1840

LVNEEATGQ
KSDLVNEEATGQFRV

1841

VNEEATGQF
SDLVNEEATGQFRVY

1842

VYPELPKPS
QFRVYPELPKPSISS

1843

LPKPSISSN
YPELPKPSISSNNSK

−0.0013

1844

ISSNNSKPV
KPSISSNNSKPVEDK

0.0033

1845

VEDKDAVAF
SKPVEDKDAVAFTCE

1846

WVNNQSLPV
YLWWVNNQSLPVSPR
1.5000
0.6000
0.0460

1847

VNNQSLPVS
LWWVNNQSLPVSPRL

0.0082

1848

LTLFNVTRN
NRTLTLFNVTRNDTA

1849

VTRNDTASY
LFNVTRNDTASYKCE

1850

VSARRSDSV
QNPVSARRSDSVILN

1851

VILNVLYGP
SDSVILNVLYGPDAP

1852

LYGPDAPTI
LNVLYGPDAPTISPL

1853

YGPDAPTIS
NVLYGPDAPTISPLN

1854

ISPLNTSYR
APTISPLNTSYRSGE

1855

LSCHAASNP
NLNLSCHAASNPPAQ

1856

WFVNGTFQQ
QYSWFVNGTFQQSTQ
0.0006
0.0270
0.0039

1857

LFIPNITVN
TQELFIPNITVNNSG

1858

FIPNITVNN
QELFIPNITVNNSGS

1859

IPNITVNNS
ELFIPNITVNNSGSY

1860

ITVNNSGSY
IPNITVNNSGSYTCQ

1861

VNNSGSYTC
NITVNNSGSYTCQAH

1862

LNRTTVTTI
DTGLNRTTVTTTTVY

0.0088

1863

VTTITVYAE
RTTVTTTTVYAEPPK

1864

VYAEPPKPF
TITVYAEPPKPFITS

1865

ITSNNSNPV
KPFITSNNSNPVEDE

−0.0013

1866

VEDEDAVAL
SNPVEDEDAVALTCE

1867

LTLLSVTRN
NRTLTLLSVTRNDVG

0.0021

1868

VTRNDVGPY
LLSVTRNDVGPYECG

1869

VGPYECGIQ
RNDVGPYECGIQNEL

1870

IQNELSVDH
ECGIQNELSVDHSDP

1871

LSVDHSDPV
QNELSVDHSDPVILN

1872

VDHSDPVIL
ELSVDHSDPVILNVL

1873

VILNVLYGP
SDPVILNVLYGPDDP

1874

YGPDDPTIS
NVLYGPDDPTISPSY

1875

ISPSYTYYR
DPTISPSYTYYRPGV

1876

YTYYRPGVN
SPSYTYYRPGVNLSL

1877

YYRPGVNLS
SYTYYRPGVNLSLSC

1878

VNLSLSCHA
RPGVNLSLSCIIAASN

1879

LSCHAASNP
NLSLSCHAASNPPAQ

1880

LIDGNIQQH
YSWLIDGNIQQHTQE

1881

LFISNITEK
TQELFISNITEKNSG

1882

FISNITEKN
QELFISNITEKNSGL

−0.0013

1883

ITEKNSGLY
ISNITEKNSGLYTCQ

1884

LYTCQANNS
NSGLYTCQANNSASG

1885

VKTITVSAE
RTTVKTITVSAELPK
0.0050
0.0790
−0.0004

1886

VSAELPKPS
TITVSAELPKPSISS

1887

LPKPSISSN
SAELPKPSISSNNSK

−0.0013

1888

WVNGQSLPV
YLWWVNGQSLPVSPR

1889

VNGQSLPVS
LWWVNGQSLPVSPRL

1890

LTLFNVTRN
NRTLTLFNVTRNDAR

1891

VTRNDARAY
LFNVTRNDARAYVCG

1892

IQNSVSANR
VCGIQNSVSANRSDP

1893

VSANRSDPV
QNSVSANRSDPVTLD

1894

VTLDVLYGP
SDPVTLDVLYGPDTP

1895

LYGPDTPII
LDVLYGPDTPIISPP

−0.0013

1896

YGPDTPIIS
DVLYGPDTPIISPPD

1897

ISPPDSSYL
TPIISPPDSSYLSGA

1898

LSGANLNLS
SSYLSGANLNLSCHS

1899

LSCHSASNP
NLNLSCHSASNPSPQ

1900

WRINGIPQQ
QYSWRINGIPQQHTQ

1901

IPQQHTQVL
INGIPQQHTQVLFIA

1902

LFIAKITPN
TQVLFIAKITPNNNG

0.0038

1903

FIAKITPNN
QVLFIAKITPNNNGT

0.0024

1904

IAKITPNNN
VLFIAKITPNNNGTY

1905

YACFVSNLA
NGTYACFVSNLATGR

1906

FVSNLATGR
YACFVSNLATGRNNS

0.0070

1907

VSNLATGRN
ACFVSNLATGRNNSI

1908

IVKSITVSA
NNSIVKSITVSASGT
0.0690
0.0370
0.0120

1909

VKSITVSAS
NSIVKSITVSASGTS
0.0460
0.0760
0.0170

1910

ITVSASGTS
VKSITVSASGTSPGL

1911

VSASGTSPG
SITVSASGTSPGLSA

1912

LSAGATVGI
SPGLSAGATVGIMIG

1913

IMIGVLVGV
TVGIMIGVLVGVALI

1914

LTIESTPFN
TAKLTIESTPFNVAE

1915

YKGERVDGN
YSWYKGERVDGNRQI

1916

LPVSPRLQL
NQSLPVSPRLQLSNG

1917

LNLSCHAAS
GENLNLSCHAASNPP

1918

LPVSPRLQL
GQSLPVSPRLQLSNG

1919

[0491]

22

TABLE XXa

CEA DR 3a Motif Peptides with Binding Data

Core
Exemplary

SEQ

Sequence
Sequence
Position
DR1
DR2w2B1
DR2w2B2
DR3
DR4w4
DR4w15
DR5w11
DR5w12
ID NO.

IQNDTGFYT
QNIIQNDTGFYTLHV
110
0.0044
0.0105
0.0007
0.3200
−0.0055

−0.0008

1920

IKSDLVNEE
LHVIKSDLVNEEATG
122

0.1300

1921

LVNEEATGQ
KSDLVNEEATGQFRV
126

0.0058

1922

VNEEATGQF
SDLVNEEATGQFRVY
127

−0.0027

1923

VYPELPKPS
QFRVYPELPKPSISS
137

−0.0027

1924

FTCEPETQD
AVAFTCEPETQDATY
162

−0.0027

1925

YKCETQNPV
TASYKCETQNPVSAR
210

−0.0027

1926

YGPDAPTIS
NVLYGPDAPTISPLN
232

−0.0027

1927

VYAEPPKPF
TITVYAEPPKPFITS
315

0.0042

1928

VEDEDAVAL
SNPVEDEDAVALTCE
332

0.0054

1929

LTCEPEIQN
AVALTCEPEIQNTTY
340

0.0039

1930

IQNELSVDH
ECGIQNELSVDHSDP
392

−0.0027

1931

LSVDHSDPV
QNELSVDHSDPVILN
396

0.0820

1932

YGPDDPTIS
NVLYGPDDPTISPSY.
410

−0.0027

1933

VSAELPKPS
TITVSAELPKPSISS
493

−0.0027

1934

FTCEPEAQN
AVAFTCEPEAQNTTY
518

−0.0027

1935

VTLDVLYGP
SDPVTLDVLYGPDTP
582

−0.0027

1936

YGPDTPIIS
DVLYGPDTPIISPPD
588

0.0037

1937

Core
Exemplary

Sequence
Sequence
DR6w19
DR7
DR8w2
DR9
DRw53
SEQ ID NO.

IQNDTGFYT
QNIIQNDTGFYTLHV
0.3600
−0.0017
−0.0009

1920

IKSDLVNEE
LHVIKSDLVNEEATG

1921

LVNEEATGQ
KSDLVNEEATGQFRV

1922

VNEEATGQF
SDLVNEEATGQFRVY

1923

VYPELPKPS
QFRVYPELPKPSISS

1924

FTCEPETQD
AVAFTCEPETQDATY

1925

YKCETQNPV
TASYKCETQNPVSAR

1926

YGPDAPTIS
NVLYGPDAPTISPLN

1927

VYAEPPKPF
TITVYAEPPKPFITS

1928

VEDEDAVAL
SNPVEDEDAVALTCE

1929

LTCEPEIQN
AVALTCEPEIQNTTY

1930

IQNELSVDH
ECGIQNELSVDHSDP

1931

LSVDHSDPV
QNELSVDHSDPVILN

1932

YGPDDPTIS
NVLYGPDDPTISPSY

1933

VSAELPKPS
TITVSAELPKPSISS

1934

FTCEPEAQN
AVAFTCEPEAQNTTY

1935

VTLDVLYGP
SDPVTLDVLYGPDTP

1936

YGPDTPIIS
DVLYGPDTPIISPPD

1937

[0492]

23

TABLE XXb

CEA DR 3b Motif Peptides with Binding Data

SEQ

Core
Exemplary

ID

Sequence
Sequence
Position
DR1
DR2w281
DR2w282
DR3
DR4w4
DR4w15
DR5w11
DR5w12
NO.

ATGQFRVYP
NEEATGQFRVYPELP
131

−0.0027

1938

LNTSYRSGE
ISPLNTSYRSGENLN
242

−0.0027

1939

YTCQAHNSD
SGSYTCQAJINSDTGL
294

−0.0027

1940

LPVSPRLQL
NQSLPVSPRLQLSND
360

0.0071

1941

LSNDNRTLT
RLQLSNDNRTLTLLS
368
0.0001
−0.0006
−0.0007
0.3200
−0.0055

−0.0008

1942

LSLSCHAAS
GVNLSLSCHAASNPP
430

0.0075

1943

LNLSCHSAS
GANLNLSCHSASNPS
608

−0.0027

1944

ASPETHLDM
RLPASPETHLDMLRH
34

−0.0027

1945

AHNQVRQVP
VLIAHNQVRQVPLQR
84

0.0290

1946

LIDTNRSRA
ALTLIDTNRSRACHP
180

0.0350

1947

IHHNTHLCF
LALIHHNTHLCFVHT
465
0.0140
0.0990
0.0009
0.3100
−0.0055

0.0025

1948

LFRNPHQAL
WDQLFRNPHQALLHT
482
−0.0001
0.0015
−0.0007
0.9000
−0.0055

−0.0008

1949

VDLDDKGCP
HSCVDLDDKGCPAEQ
632

−0.0027

1950

YLEDVRLVH
GMSYLEDVRLVHRDL
832

0.1800

1951

IDSECRPRF
CWMIDSECRPRFREL
958
0.0036
−0.0006
0.0150
0.4500
−0.0055

−0.0008

1952

AAPQPHPPP
QGGAAPQPHPPPAFS
1200

−0.0025

1953

AAISRKMVE
EFQAAISRKMVELVH
104

0.0039

1954

LHHTLKIGG
VKVLHHTLKIGGEPH
284

−0.0025

1955

IGGEPHISY
TLKIGGEPHISYPPL
290

−0.0025

1956

AALSRKVAE
EFQAALSRKVAELVH
104

0.0027

1957

ILGDPKKLL
EDSILGDPKKLLTQH
235
0.0003
−0.0006
−0.0010
0.6700
−0.0055

−0.0008

1958

YKQSQHMTE
MAIYKQSQHMTEVVR
160

−0.0025

1959

VEGNLRVEY
LIRVEGNLRVEYLDD
194

0.0930

1960

FTLQIRGRE
GEYFTLQIRGRERFE
325

0.0290

1961

Core
Exemplary

Sequence
Sequence
DR6w19
DR7
DR8w2
DR9
DRw53
SEQ ID NO.

ATGQFRVYP
NEEATGQFRVYPELP

1938

LNTSYRSGE
ISPLNTSYRSGENLN

1939

YTCQAHNSD
SGSYTCQAHNSDTGL

1940

LPVSPRLQL
NQSLPVSPRLQLSND

1941

LSNDNRTLT
RLQLSNDNRTLTLLS
0.0048
−0.0017
−0.0009

1942

LSLSCHAAS
GVNLSLSCHAASNPP

1943

LNLSCHSAS
GANLNLSCHSASNPS

1944

ASPETHLDM
RLPASPETHLDMLRH

1945

AHNQVRQVP
VLIAHNQVRQVPLQR

1946

LIDTNRSRA
ALTLIDTNRSRACHP

1947

IHHNTHLCF
LALIHHNTHLCFVHT
0.7500
0.0200
0.0330

1948

LFRNPHQAL
WDQLFRNPHQALLHT
0.0410
−0.0017
−0.0009

1949

VDLDDKGCP
HSCVDLDDKGCPAEQ

1950

YLEDVRLVH
GMSYLEDVRLVHRDL

1951

IDSECRPRF
CWMIDSECRPRFREL
(0.0001)
−0.0014
0.0028

1952

AAPQPHPPP
QGGAAPQPHPPPAFS

1953

AAISRKMVE
EFQAAISRKMVELVH

1954

LHHTLKIGG
VKVLHHTLKIGGEPH

1955

IGGEPHISY
TLKIGGEPHISYPPL

1956

AALSRKVAE
EFQAALSRKVAELVH

1957

ILGDPKKLL
EDSILGDPKKLLTQH
0.0130
−0.0014
0.0029

1958

YKQSQHMTE
MAIYKQSQHMTEVVR

1959

VEGNLRVEY
LIRVEGNLRVEYLDD

1960

FTLQIRGRE
GEYFTLQIRGRERFE

1961

[0493]

24

TABLE XXI

Population coverage with combined HLA Supertypes

PHENOTYPIC FREQUENCY

North

American

HLA-SUPERTYPES
Caucasian
Black
Japanese
Chinese
Hispanic
Average

a. Individual Supertypes

A2
45.8
39.0
42.4
45.9
43.0
43.2

A3
37.5
42.1
45.8
52.7
43.1
44.2

B7
43.2
55.1
57.1
43.0
49.3
49.5

A1
47.1
16.1
21.8
14.7
26.3
25.2

A24
23.9
38.9
58.6
40.1
38.3
40.0

B44
43.0
21.2
42.9
39.1
39.0
37.0

B27
28.4
26.1
13.3
13.9
35.3
23.4

B62
12.6
4.8
36.5
25.4
11.1
18.1

B58
10.0
25.1
1.6
9.0
5.9
10.3

b. Combined Supertypes

A2, A3, B7
84.3
86.8
89.5
89.8
86.8
87.4

A2, A3, B7, A24, B44, A1
99.5
98.1
100.0
99.5
99.4
99.3

A2, A3, B7, A24, B44, A1,
99.9
99.6
100.0
99.8
99.9
99.8

B27, B62, B58

[0494]

25

TABLE XXII

Crossbinding data A2 supermotif peptides

No. A2

A*0201
A*0202
A*0203
A*0206
A*6802
Alleles

Source
AA
Sequence
nM
nM
nM
nM
nM
Crossbound

CEA.24
9
LLTFWNPPT
179
1720
67
755
—2
2

CEA.24M2V9
9
LMTFWNPPV
4.5
782
7.7
34
3333
3

CEA.24V9
9
LLTFWNPPV
16
307
26
56
952
4

CEA.78
9
QIIGYVIGT
313
148
106
100
150
5

CEA.78L2V9
9
QLIGYVIGV
9.4
5.9
2.3
21
2.3
5

CEA.233
10
VLYGPDAPTI
128
606
270
804
—
2

CEA.233V10
10
VLYGPDAPTV
26
430
16
206
952
4

CEA.354
10
YLWWVNNQSL
26
108
26
487
67
5

CEA.411
10
VLYGPDDPTI
294
358
476
7400
—
3

CEA.411V10
10
VLYGPDDPTV
161
105
91
2467
—
3

CEA.432
9
NLSLSCHAA
455
2867
1449
18500
—
1

CEA.532
10
YLWWVNGQSL
33
331
21
2056
286
4

CEA.569
9
YVCGIQNSV
98
358
159
80
181
5

CEA.569L2
9
YLCGIQNSV
50
24
12
31
3478
4

CEA.589
9
VLYGPDTPI
200
878
53
638
—
2

CEA.589V9
9
VLYGPDTPV
20
165
91
154
9756
4

CEA.605
9
YLSGANLNL
28
165
2.4
804
—
3

CEA.605V9
9
YLSGANLNV
73
13
13
80
1600
4

CEA.687
9
ATVGIMIGV
36
8.8
20
11
0.80
5

CEA.687L2
9
ALVGIMIGV
10
63
31
100
102
5

CEA.690
10
GIMIGVLVGV
64
205
31
142
500
5

CEA.691
9
IMIGVLVGV
69
62
13
106
89
5

CEA.691L2
9
ILIGVLVGV
22
8.0
3.2
16
160
5

CEA.691
10
IMIGVLVGVA
227
68.0
44.0
726
1509
3

1
Wild-type peptides presented for reference purposes.

2
— indicates binding affinity = 10,000 nM.

[0495]

26

TABLE XXIII

HLA-A3 Supermotif-bearing Peptides

No. of A3
CTL

Published
Published

A*0301
A*1101
A*3101
A*3301
A*6801
Alleles
Wild-
CTL
CTL
CTL

AA
Sequence
Source
nM
nM
nM
nM
nM
Crossbound
type
Tumor
Wildtype
Tumor

9
HLFGYSWYK
CEA.61
2.2
2.4
21
18
3.5
5
3/4
2/4
+1)
+

10
TVSPLNTSYR
CEA.241.V2
458
55
188
558
8.7
4

10
TVSPLNTSYK
CEA.241.V2K10
17
6
—
—
7.3
3

10
TISPLNTSYR
CEA.241
1594
158
207
569
4.4
3

10
TISPLNTSYK
CEA.241.K10
61
182
—
—
116
3
1/1
0/1

10
RVLTLLSVTR
CEA.376.V2
344
222
11
6042
667
3

10
RVLTLLSVTK
CEA.376.V2K10
38
50
164
—
5714
3

10
RTLTLLSVTR
CEA.376
524
55
6.2
1036
160
3

11
PTISPSYTYYR
CEA.418
—
46
44
784
57
3

10
TVSPSYTYYR
CEA.419.V2
2340
3000
29
264
8.6
3

10
TVSPSYTYYK
CEA.419.V2K10
69
43
3674
—
6.7
3

10
TISPSYTYYR
CEA.419
3438
21
72
171
3.1
4

9
IVPSYTYYR
CEA.420.V2
92
13
26
58
2.6
5

9
IVPSYTYYK
CEA.420.V2K9
17
55
720
4328
22
3

9
ISPSYTYYR
CEA.420
1342
143
21
518
11
3

10
RVLTLFNVTR
CEA.554.V2
297
94
9.0
7632
42
4

10
RVLTLFNVTK
CEA.554.V42K10
21
32
234
—
2353
3

10
RTLTLFNVTR
CEA.554
111
13
5
1611
99
4
1/1
nt

9
HTQVLFIAK
CEA.636
1183
35
106
132
160
4

9
FVSNLATGR
CEA.656
5790
122
333
104
8.2
4

9
FVSNLATGK
CEA.656.K9
1467
207
—
—
5.3
3

1)
Kawashima et al., Cancer Research 59: 431, 1999

[0496] indicates binding affinity >10,000 nM.

27TABLE XXIVB7 Supermotif PeptidesNo. of B7B*0702B*3501B*5101B*5301B*5401AllelesAASequenceSourcenMnMnMnMnMCrossbound9FPSAPPHRICEA.3.F1I95036001525814410FPPHRWCIPICEA.6.F1I1098—423845522239FPHRWCIPICEA.7.F1I92.5257671351.9510IPWQRLLLTACEA.13125—211526573.2210IPWQRLLLTICEA.13.I1039—1929127048FPWQRLLLCEA.13.F120175622944371410FPWQRLLLTICEA.13.F1I10290211813784.2410LPQHLFGYSICEA.58.I10212—26293017238FPQHLFGICEA.58.F1393—21210690.40310FPQHLFGYSICEA.58.F1I102299002041431649FPAYSGREICEA.92.F12.172001836642938YPNASLLICEA.1021965148.140137410FPDAPTISPICEA.236.F1I101831333371022278310FPDAPTISPLCEA.236.F137327290193871439FPVSPRLQICEA.363.F1I9135539112163349FPVSPRLQLCEA.363.F10.70600823104448FPGVNLSLCEA.428.F1192775509511548FPQQHTQICEA.632.F1220—46775018539FPQQHTQVICEA.632.F1I93.413911291.759FPQQHTQVLCEA.632.F10.90341839337510FPQQHTQVLFCEA.632.F1465155047556310FPQQHTQVLICEA.632.F1I10134809504927848FPNNNGTICEA.646.F1275—19930031338FPGLSAGICEA.680.F1I8167589.033220410FPGLSAGATICEA.680.F1212—2914761053

[0497]

28

TABLE XXVa

HLA-A1 Motif-Bearing Peptides

A*0101

AA
Sequence
Source
nM

11
RVDGNRQIIGY
CEA.72
294

11
RSDSVILNVLY
CEA.225
47

10
PTDSPLNTSY
CEA.240.D3
266

9
ITDNNSGSY
CEA.289.D3
96

11
HSDPVILNVLY
CEA.403
26

10
PTISPSYTYY
CEA.418
325

10
PTDSPSYTYY
CEA.418.D3
1.1

9
TIDPSYTYY
CEA.419.D3
3.1

9
ITDKNSGLY
CEA.467.D3
12

11
RSDPVTLDVLY
CEA.581
7.8

10
HSASNPSPQY
CEA.616
74

10
HTASNPSPQY
CEA.616.T2
132

10
HSDSNPSPQY
CEA.616.D3
45

[0498]

29

TABLE XXVb

A A01 Analog Peptides

Peptide
AA
Sequence
Source
A*0101 nM

52.0105
11
RVDGNRQIIGY
CEA.72
294.1

52.0109
11
RSDSVILNVLY
CEA.225
47.2

52.0113
11
HSDPVILNVLY
CEA.403
25.8

52.0116
11
RSDPVTLDVLY
CEA.581
7.8

57.0004
9
QQDTPGPAY
CEA.87.D3
56.8

57.0007
9
AADNPPAQY
CEA.261.D3
45.5

57.0008
9
ITDNNSGSY
CEA.289.D3
96.2

57.001
9
VTDNDVGPY
CEA.383.D3
4.1

57.0011
9
PTDSPSYTY
CEA.418.D3
37.9

57.0012
9
TIDPSYTYY
CEA.419.D3
3.1

57.0013
9
AADNPPAQY
CEA.439.D3
44.6

57.0014
9
ITDKNSGLY
CEA.467.D3
11.9

57.0103
10
PTDSPLNTSY
CEA.240.D3
266

57.0104
10
PTDSPSYTYY
CEA.418.D3
1.1

57.0105
10
HTASNPSPQY
CEA.616.T2
131.6

57.0106
10
HSDSNPSPQY
CEA.616.D3
44.6

[0499]

30

TABLE XXVI

HLA-A24 Motif-Bearing Peptides

Pub-

lished

Published
CTL

A*2402
CTL
Tu-

AA
Sequence
Source
nM
Wildtype
mor

10
RWCIPWQRLL
CEA.10
308

11
RWCIPWQRLLL
CEA.10
152

9
RYCIPWQRF
CEA.10.Y2F9
191

10
RYCIPWQRLF
CEA.10.Y2F10
26

11
PWQRLLLTASL
CEA.14
324

10
FWNPPTTAKL
CEA.27
400

8
IYPNASLL
CEA.101
177

9
IYPNASLLI
CEA.101
1.7

9
IYPNASLLF
CEA.101.F9
2.2

11
FYTLHVIKSDL
CEA.119
480

10
VYPELPKPSF
CEA.140.F10
106

11
TYLWWVNNQSL
CEA.175
46

9
LYWVNNQSF
CEA.177Y2F9
63

9
LYGPDAPTI
CEA.234
57

9
LYGPDAPTF
CEA.234.F9
63

10
QYSWFVNGTF
CEA.268
3.5
+1)
+

8
SWFVNGTF
CEA.270
480

10
TYQQSTQELF
CEA.276.Y2
308

9
VYAEPPKPF
CEA.318
41

10
VYAEPPKPFF
CEA.318.F10
27

9
LYGPDDPTI
CEA.412
353

11
SYTYYRPGVNL
CEA.423
218

9
TYYRPGVNL
CEA.425
185

11
TYYRPGVNLSL
CEA.425
132

9
TYYRPGVNF
CEA.425.F9
52

10
YYRPGVNLSL
CEA.426
86

10
YYRPGVNLSF
CEA.426.F10
10

10
QYSWLIDGNF
CEA.446.F10
60

11
TYLWWVNGQSL
CEA.531
92

9
LYWVNGQSF
CEA.533.Y2F9
16

9
LYGPDTPII
CEA.590
46

10
SYLSGANLNL
CEA.604
207

10
SYLSGANLNF
CEA.604.F10
10

9
QYSWRINGI
CEA.624
444

9
QYSWRINGF
CEA.624.F9
109

9
TYACFVSNL
CEA.652
10
+2)
+

9
TYACFVSNF
CEA.652.F9
8.6

1)
Nukaya et al., International Journal of Cancer 80(1): 92, 1997

2)
Kim et al., Cancer Immunotherapy 47: 90, 1998

[0500]

31

TABLE XXVIIa

HLA-A2 Supermotif-bearing Peptides

No. of A2

A*0201
A*0202
A*0203
A*0206
A*6802
Alleles
CTL
CTL
CTL
CTL

AA
Sequence
Source
nM
nM
nM
nM
nM
Crossbound
Wildtype1
Tumor1
Wildtype2
Tumor2

9
LLTFWNPPV
CEA.24.V9
16
307
26
56
952
4
1/1
1/1

9
QIIGYVIGT
CEA.78
313
148
106
100
150
5

9
QLIGYVIGV
CEA.78.L2V9
9.4
5.9
2.3
21
2.3
5

10
VLYGPDAPTV
CEA.233.V10
26
430
16
206
952
4
2/2
1/4

10
YLWWVNNQSL
CEA 354
26
108
26
487
333
5
1/2

10
VLYGPDDPTI
CEA.411
294
358
476
7400
—
3

10
VLYGPDDPTV
CEA.411.V10
161
105
91
2467
—
3

9
YVCGIQNSV
CEA.569
98
358
159
80
181
5
1/2

9
VLYGPDTPV
CEA.589.V9
20
165
91
154
9756
4

9
YLSGANLNL
CEA.605
28
165
2.4
804
—
3
2/2
1/2

9
YLSGANLNV
CEA.605.V9
73
13
13
80
1600
4
3/4
1/4

9
ATVGIMIGV
CEA.687
36
8.8
20
11
0.80
5
1/1
1/1

9
IMIGVLVGV
CEA.691
69
62
13
106
89
5
8/8
4/7

9
ILIGVLVGV
CEA.691.L2
22
8.0
3.2
16
160
5

1
Number of donors yielding a positive response/total tested

2
Data from ovarian cancer patients

[0501]

32

TABLE XXVIIb

Immunogenicity A2 supermotif analog peptides

No. A2

A*0201
A*0202
A*0203
A*0206
A*6802
Alleles
CTL
CTL
CTL

Source
AA
Sequence
nM
nM
nM
nM
nM
Crossbound
Peptide1
Wild-type
Tumor

CEA.24
9
LLTFWNPPT
179
1720
67
755
—2
2

0/1
0/1

CEA.24V9
9
LLTFWNPPV
16
307
26
56
952
4
1/1

1/1

CEA.233
10
VLYGPDAPTI
128
606
270
804
—
2

2/4
0/3

CEA.233V10
10
VLYGPDAPTV
26
430
16
206
952
4
3/4
2/2
1/4

CEA.589
9
VLYGPDTPI
200
878
53
638
—
2

1/1
0/1

CEA.589V9
9
VLYGPDTPV
20
165
91
154
9756
4
2/2
2/2
0/2

CEA.605
9
YLSGANLNL
28
165
2.4
804
—
3

2/2
1/2

CEA.605V9
9
YLSGANLNV
73
13
13
80
1600
4
4/4
3/4
1/4

1
Number of donors yielding a positive response/total tested.

2
— indicates binding affinity = 10,000 nM.

[0502]

33

TABLE XXVIII

DR supertype primary binding

DR147

DR147

Algo

DR1
DR4w4
DR7
Cross-

Sum
Sequence
Source
nM
nM
nM
reactivity

2
RWCIPWQRLLLTASL
CEA.10
8.2
542
357
3

3
QRLLLTASLLTFWNP
CEA.16
—
—
—
0

2
EVLLLVHNLPQHLFG
CEA.50
2.0
52
53
3

3
GREIIYPNASLLIQN
CEA.97
8.1
484
45
3

2
EIIYPNASLLIQNII
CEA.99
14
1154
156
2

2
NASLLIQNIIQNDTG
CEA.104
4546
—
—
0

3
DTGFYTLHVIKSDLV
CEA.116
69
1731
227
2

2
YPELPKPSISSNNSK
CEA.141
5556
—
—
0

2
KPSISSNNSKPVEDK
CEA.146
2381
—
7576
0

3
YLWWVNNQSLPVSPR
CEA.176
0.59
8.0
42
3

3
LWWVNNQSLPVSPRL
CEA.177
217
1552
3049
1

2
QYSWFVNGTFQQSTQ
CEA.268
192
80
926
3

2
DTGLNRTTVTTITVY
CEA.305
—
—
2841
0

2
KPFITSNNSNPVEDE
CEA.324
—
—
—
0

2
NRTLTLLSVTRNDVG
CEA.375
238
—
—
1

2
QELFISNITEKNSGL
CEA.460
—
2500
—
0

3
RTTVKTITVSAELPK
CEA.488
455
7031
317
2

2
SAELPKPSISSNNSK
CEA.497
—
—
—
0

2
LDVLYGPDTPIISPP
CEA.587
—
—
—
0

2
TQVLFIAKITPNNNG
CEA.637
61
—
6579
1

2
QVLFIAKITPNNNGT
CEA.638
42
1875
—
1

3
YACFVSNLATGRNNS
CEA.653
208
1667
3571
1

2
NNSIVKSITVSASGT
CEA.665
91
25
676
3

3
NSIVKSITVSASGTS
CEA.666
78
25
329
3

— indicates binding affinity = 10,000 nM

[0503]

34

TABLE XXIX

DR supertype crossbinding

Broad Cross-

DR1
DR4w4
DR7
DR2w2β1
DR2w2β2
DR6w19
DR5w11
DR8w2
DR147
reactivity

Sequence
Source
nM
nM
nM
nM
nM
nM
nM
nM
Degen
(5/8)

RWCIPWQRLLLTASL
CEA.10
8.2
542
357
827
—
318
—
—
3
5

EVLLLVHNLPQHLFG
CEA.50
2.0
52
53
40
—
1.0
588
408
3
7

GREIIYPNASLLIQN
CEA.97
8.1
484
45
24
8333
2.9
6897
5904
3
5

EIIYPNASLLIQNII
CEA.99
14
1154
156
57
—
11
—
—
2
4

DTGFYTLHVIKSDLV
CEA.116
69
1731
227
506
800
3889
2500
790
2
5

YLWWVNNQSLPVSPR
CEA.176
0.60
8.0
42
110
2105
2.3
29
1065
3
6

QYSWFVNGTFQQSTQ
CEA.268
192
80
926
—
6061
5833
370
—
3
4

RTTVKTITVSAELPK
CEA.488
455
7031
317
364
—
700
—
—
2
4

NNSIVKSITVSASGT
CEA.665
91
25
676
3138
—
51
—
4083
3
4

NSIVKSITVSASGTS
CEA.666
78
25
329
3957
—
76
—
2882
3
4

— indicates binding affinity = 10,000 nM

[0504]

35

TABLE XXX

DR3 binding

DR3

Sequence
Source
nM

QNIIQNDTGFYTLHV
CEA.110
938

LHVIKSDLVNEEATG
CEA.122
2308

KSDLVNEEATGQFRV
CEA.126
—

SDLVNEEATGQFRVY
CEA.127
—

NEEATGQFRVYPELP
CEA.131
—

QFRVYPELPKPSISS
CEA.137
—

AVAFTCEPETQDATY
CEA.162
—

TASYKCETQNPVSAR
CEA.210
—

NVLYGPDAPTISPLN
CEA.232
—

ISPLNTSYRSGENLN
CEA.242
—

SGSYTCQAHNSDTGL
CEA.294
—

TITVYAEPPKPFITS
CEA.315
—

SNPVEDEDAVALTCE
CEA.332
—

AVALTCEPEIQNTTY
CEA.340
—

NQSLPVSPRLQLSND
CEA.360
—

RLQLSNDNRTLTLLS
CEA.368
938

ECGIQNELSVDHSDP
CEA.392
—

QNELSVDHSDPVILN
CEA.396
3659

NVLYGPDDPTISPSY
CEA.410
—

GVNLSLSCHAASNPP
CEA.430
—

TTTVSAELPKPSISS
CEA.493
—

AVAFTCEPEAQNTTY
CEA.518
—

SDPVTLDVLYGPDTP
CEA.582
—

DVLYGPDTPIISPPD
CEA.588
—

GANLNLSCHSASNPS
CEA.608
—

— indicates binding affinity = 10,000 nM

[0505]

36

TABLE XXXI

HLA Class II Binding Motif and Supermotif-Bearing Epitopes

DRB1*
DRB1*
DRB1*
DRB1*
DRB1*
DRB1*
DRB1*
DRB1*
DRB5*
No. of DR

0101
0301
0401
0701
0802
1101
1302
1501
0101
Alleles

Sequence
Source
nM
nM
nM
nM
nM
nM
nM
nM
nM
Crossbound

RWCIPWQRLLLTASL
CEA.10
8.2
—
542
357
—
—
318
827
—
5

EVLLLVHNLPQHLFG
CEA.50
2.0
336
52
53
408
588
1.0
40
—
7

GREIIYPNASLLIQN
CEA.97
8.1
1123
484
45
5904
6897
2.9
24
8333
5

QNIIQNDTGFYTLHV
CEA.110
1136
938
>8182
—
—
—
9.7
867
—
2

DTGFYTLHVIKSDLV
CEA.116
69
—
1731
227
790
2500
3889
506
800
5

YLWWVNNQSLPVSPR
CEA.176
0.60
2310
8.0
42
1065
29
2.3
110
2105
6

RLQLSNDNRTLTLLS
CEA.368
—
938
>8182
—
—
—
729
—
—
1

— indicates binding affinity = less than 10,000 nM

[0506]

Inducing cellular immune responses to carcinoembryonic antigen using peptide and nucleic acid compositions

Information

Publication Number

Date Filed

Date Published

Inventors

CPC

US Classifications

International Classifications

Abstract

Description

Claims

PCT Information