# Patent

## Title
Multi-epitope peptide-loaded dendritic cell immunotherapy for cancer

## Abstract

The invention involves peptides of from about 7 to about 50 amino acid residues in length that have epitopes that bind to more than one HLA class II protein and stimulate CD4+ T cells for treatment of cancer from one of three serine proteases overexpressed in ovarian cancer and other cancers—stratum corneum chymotryptic enzyme, matriptase, and hepsin. Since the peptides bind to more than one HLA class II protein variant, they can be used to treat cancer in most patients of a population having a variety of HLA class II alleles. The peptides can be loaded onto autologous dendritic cells of a cancer patient and infused into the patient to activate a CD4+ and CD8+ T cell response that recognizes tumor cells expressing the peptide antigen.

## Background
This patent application claims the benefit of priority under 35 U.S.C. 119(e) from U.S. provisional patent application Ser. No. 60/860,714, filed Nov. 22, 2006.


GOVERNMENT SUPPORT
This invention was made with government support under grants ROI CA 098927 and R41 CA 108257 awarded by the United States National Institutes of Health. The government has certain rights in the invention.


BACKGROUND OF THE INVENTION
Ovarian cancer ranks fifth among malignancies affecting women in the United States. The onset of ovarian cancer is insidious and the symptoms are nonspecific, such that two-thirds of women present with advanced disease at diagnosis. Although the initial response rate of patients with advanced disease after treatment with platinum and taxol is 73% to 77%, a large majority develop recurrent disease. These factors contribute to ovarian cancer having the highest mortality rate of all gynecologic tumors. Thus, alternative methods for treatment are a priority for ovarian cancer.
The identification of ovarian tumor-specific antigens that can serve as targets for CD8+ cytotoxic T lymphocytes (CTLs) (9) and the harnessing of dendritic cells that possess the ability to induce CTL responses to those targets (11, 12) suggests that dendritic cell immunotherapy may be of potential therapeutic benefit. Monocyte-derived dendritic cells loaded with tumor lysate antigen can induce tumor-specific CTL lysis of autologous tumor cells from patients with ovarian cancer or uterine serous papillary carcinoma (13, 14), and dendritic cells pulsed with peptides acid-eluted from HLA class I on the surface of ovarian tumor cells can stimulate CTL killing of autologous tumor (16).
The identification of appropriate tumor-specific antigens is a critical component for the development of successful ovarian tumor-specific immunotherapy.
Tumor-associated serine proteases are involved in many biological functions of cancer cells, including activation of growth and angiogenic factors and promotion of invasion and metastasis. Among the serine proteases overexpressed in some cancers is stratum corneum chymotryptic enzyme. Stratum corneum chymotryptic enzyme (SCCE), also known as kallikrein 7, is a serine protease that is overexpressed by ovarian cancer cells but not expressed by normal ovaries or other normal adult tissues, except the outermost cornified layer of the skin (15). Immunohistochemical analysis of 14 ovarian tumors showed positive staining localized to the cytoplasm and cell membrane, suggesting that SCCE may be expressed as both secreted and membrane forms (15). Quantitative RT-PCR revealed SCCE expression in >88% of serous ovarian tumors, 100% of endometrioid and clear cell tumors, but only 29% (two of seven) of mucinous tumors (15). SCCE is also overexpressed in cervical cancer (10).
Hepsin is a transmembrane serine protease that is overexpressed in prostate cancer and ovarian cancer, as well as renal cell carcinoma (19-26). In at least one report its overexpression was linked to metastasis and tumor progression (21).
Matriptase (also known as TADG-15) is a transmembrane serine protease that was discovered in 1993 and cloned in 1999 (3, 7). It is overexpressed in many tumors of epithelial origin, including carcinomas of the head and neck, mesothelium, breast, ovary, cervix, prostate, lung, and gastrointestinal tract, as well as in cell lines derived from these tumors (8).
Its expression has been linked to increased tumor invasiveness (5-6). It is expressed in a high percentage of ovarian carcinomas but not in normal ovary tissue (4). New treatments for ovarian and other cancers are needed. New targets for cancer immunotherapy are needed.
SUMMARY OF THE INVENTION
The invention involves peptides of from about 7 to about 50 amino acid residues in length that have epitopes that bind to more than one HLA class II protein and stimulate CD4+ T cells for treatment of cancer. CD4+ T cells have the CD4 antigen on their surface and are also known as helper T cells. CD4+ T cells activate the response of other cells in the immune system, including antibody-producing B cells and cytotoxic CD8+ T cells. CD8+ T cells, also known as cytotoxic T lymphocyctes (CTL), are the cells primarily responsible for directly killing cancer cells when an immune response is raised to cancer cells. But CD4+ T cells are crucial to activate the CD8+ T cell response and crucial for maintaining long-term immune memory that will recognize cancer cells in the future to prevent disease recurrence. CD4+ T cells may also have the ability to kill tumor cells directly without CD8+ T cells.
Antigens are presented as short peptides bound to HLA class I or class II proteins on the surface of target cells for recognition by T cells. CD8+ T cells recognize antigenic peptides bound to HLA class I proteins. CD4+ T cells recognize antigenic peptides bound to HLA class II proteins. There are several variants of HLA class I and class II proteins (expressed from different alleles), and peptides that bind to one HLA class I or class II protein may not bind to other variants. This makes it difficult to select universal peptides that will activate an immune response in all or most individuals in a population.
The inventors have utilized an algorithm to predict peptides that will bind to three common HLA class II variant proteins (1). Peptides that bind to these variants are also likely to bind to other HLA class II variants (1). The invention involves the selection of peptides from serine proteases overexpressed in tumor cells—namely SCCE, hepsin, and matriptase—that have at least one epitope predicted to bind to HLA class II alleles and the identification of peptides that activate CD4+ T cells, preferably CD4+ T cells from a plurality of persons having different HLA class II alleles.
Preferably the peptides have a cluster of more than one epitope predicted to bind to HLA class II allelic variants. The inventors have tested peptides containing at least one epitope predicted to bind to HLA class II allelic variants and identified peptides that activate CD4+ T cells from all the volunteers tested. Although the epitopes that bind to HLA class I proteins to activate CD8+ T cells can be different from those that bind to HLA class II proteins, the peptides tested also activated CD8+ T cells.
Thus, one embodiment of the invention comprises a purified peptide of 7-50 amino acid residues comprising an antigenic matriptase sequence (or hepsin sequence) of 7-50 amino acid residues; wherein when the purified peptide is contacted with dendritic cells to generate peptide-loaded dendritic cells and the peptide-loaded dendritic cells are contacted with T cells, the peptide-loaded dendritic cells activate CD4+ T cells (helper T cells) that recognize the matriptase (or hepsin) sequence.
Another embodiment of the invention provides a method of treating cancer that involves: (a) contacting dendritic cells with a purified peptide of 7-50 amino acid residues comprising an antigenic matriptase sequence (or hepsin sequence) of 7-50 amino acid residues; (b) contacting the peptide-loaded dendritic cells with T cells to amplify CD8+ T cells and CD4+ T cells that recognize the antigenic matriptase (or hepsin) sequence; and (c) contacting the amplified CD8+ T cells with cancer cells expressing matriptase (or hepsin) to kill the cancer cells.
Another embodiment of the invention provides a composition comprising: purified dendritic cells loaded ex vivo with a purified peptide of 7-50 amino acid residues comprising an antigenic matriptase sequence (or hepsin sequence) of 7-50 amino acid residues; wherein when the purified peptide is contacted with dendritic cells to generate peptide-loaded dendritic cells and the peptide-loaded dendritic cells are contacted with T cells, the peptide-loaded dendritic cells amplify CD4+ T cells (helper T cells) that recognize the matriptase (or hepsin) sequence.
Another embodiment of the invention provides a method of treating cancer that involves: (a) contacting dendritic cells with a peptide comprising an antigenic matriptase sequence (or hepsin sequence) of at least 7 amino acid residues; (b) contacting the peptide-loaded dendritic cells with T cells to amplify CD8+ T cells and CD4+ T cells that recognize the antigenic matriptase (or hepsin) sequence; and (c) contacting the amplified CD8+ T cells with cancer cells expressing matriptase (or hepsin) to kill the cancer cells.
Another embodiment of the invention provides a composition comprising: purified dendritic cells loaded ex vivo with a peptide comprising an antigenic matriptase sequence (or hepsin sequence) of at least 7 amino acid residues; wherein when the purified peptide is contacted with dendritic cells to generate peptide-loaded dendritic cells and the peptide-loaded dendritic cells are contacted with T cells, the peptide-loaded dendritic cells amplify CD4+ T cells (helper T cells) that recognize the matriptase sequence.
The invention also involves peptides, methods, and dendritic cell compositions involving SCCE peptides.
One embodiment of the invention provides a purified peptide of 7-50 amino acid residues comprising an antigenic stratum corneum chymotryptic enzyme (SCCE) sequence of 7-50 amino acid residues; wherein when the purified peptide is contacted with dendritic cells to generate peptide-loaded dendritic cells and the peptide-loaded dendritic cells are contacted with T cells, the peptide-loaded dendritic cells amplify CD4+ T cells (helper T cells) that recognize the SCCE sequence. The antigenic SCCE sequence is SEQ ID NO: 15 (residues 1-23 of SCCE), SEQ ID NO:16 (residues 61-84), SEQ ID NO:17 (residues 143-160), or a fragment thereof.
Another embodiment provides a method of treating cancer comprising: (a) contacting dendritic cells with a purified peptide of 7-50 amino acid residues comprising an antigenic SCCE sequence of 7-50 amino acid residues; (b) contacting the peptide-loaded dendritic cells with T cells to amplify CD8+ T cells and CD4+ T cells that recognize the antigenic SCCE sequence; and (c) contacting the amplified CD8+ T cells with cancer cells expressing SCCE to kill the cancer cells. The antigenic SCCE sequence is SEQ ID NO: 15 (residues 1-23 of SCCE), SEQ ID NO:16 (residues 61-84), SEQ ID NO:17 (residues 143-160), or a fragment thereof.
Another embodiment of the invention provides a composition comprising: purified dendritic cells loaded ex vivo with a purified peptide of 7-50 amino acid residues comprising an antigenic SCCE sequence of 7-50 amino acid residues; wherein when the purified peptide is contacted with dendritic cells to generate peptide-loaded dendritic cells and the peptide-loaded dendritic cells are contacted with T cells, the peptide-loaded dendritic cells amplify CD4+ T cells (helper T cells) that recognize the SCCE sequence. The antigenic SCCE sequence is SEQ ID NO:15 (residues 1-23 of SCCE), SEQ ID NO:16 (residues 61-84), SEQ ID NO:17 (residues 143-160), or a fragment thereof.
Another embodiment of the invention provides a method of treating cancer comprising: (a) contacting dendritic cells with a peptide comprising an antigenic SCCE sequence of at least 7 amino acid residues; (b) contacting the peptide-loaded dendritic cells with T cells to amplify CD8+ T cells and CD4+ T cells that recognize the antigenic SCCE sequence; and (c) contacting the amplified CD8+ T cells with cancer cells expressing SCCE to kill the cancer cells. The antigenic SCCE sequence is SEQ ID NO: 15 (residues 1-23 of SCCE), SEQ ID NO:16 (residues 61-84), SEQ ID NO:17 (residues 143-160), or a fragment thereof.
Another embodiment of the invention provides a composition comprising: purified dendritic cells loaded ex vivo with a peptide comprising an antigenic SCCE sequence of at least 7 amino acid residues; wherein when the purified peptide is contacted with dendritic cells to generate peptide-loaded dendritic cells and the peptide-loaded dendritic cells are contacted with T cells, the peptide-loaded dendritic cells amplify CD4+ T cells (helper T cells) that recognize the SCCE sequence. The antigenic SCCE sequence is SEQ ID NO: 15 (residues 1-23 of SCCE), SEQ ID NO:16 (residues 61-84), SEQ ID NO:17 (residues 143-160), or a fragment thereof.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1. Intracellular TNF∀ and IL-4 expression by CD4+ T cells specific for SCCE 1-23 (panel A), 61-84 (panel B), and 143-160 (panel C). Peptide-specific CD4+ T cells were stimulated overnight with peptide-loaded autologous LCL and analyzed by flow cytometry.
FIG. 2. SCCE peptide-specific CD8+ CTL responses. Peripheral blood T cells from a volunteer donor were stimulated with dendritic cells loaded with SCCE peptides 1-23 (panel A), 61-84 (panel B), or 143-160 (panel C), and tested for lysis against LCL loaded with the respective peptide. Targets were peptide-loaded autologous lymphoblastoid cell line cells (LCL) (▪), peptide-pulsed HLA A2.1-matched allogeneic LCL (●), and peptide-pulsed HLA B27-matched allogeneic LCL (◯), peptide-loaded B40-matched allogeneic LCL (▴), and peptide-loaded HLA class 1-mismatched LCL (♦). Control unpulsed LCL were not lysed (data not shown).



DETAILED DESCRIPTION
Definitions
The term “peptide” as used herein can refer to peptides of any suitable length, up to full-length proteins, unless a length limitation is specified.
CD4+ or CD8+ T cells are considered to “recognize” a particular sequence if the CD4+ or CD8+ T cells show a response when contacted with antigen-presenting cells or target cells pulsed with a peptide consisting of the sequence. The response may be cytolysis of target cells pulsed with the peptide consisting of the sequence, or cytokine release or amplification in response to contacting antigen-presenting cells pulsed with the peptide consisting of the sequence.
Description
The invention involves peptides, preferably of from about 7 to about 50 amino acid residues in length, that have epitopes that collectively or individually bind to more than one HLA class II protein for stimulation of CD4+ T cells, and the use of the peptides for treatment of cancer. The peptides are derived from one of three serine proteases overexpressed on ovarian cancer cells and other cancer cells—SCCE, hepsin, and matriptase. Preferably the peptides have more than one epitope that binds to HLA class II protein variants. The presence of multiple epitopes allows greater confidence that the peptide will activate a CD4+ T cell response in a broad cross section of the population and not be limited to persons with particular HLA class II alleles. Preferably the peptide contains sequence segments that collectively or individually are predicted by the algorithms disclosed herein to bind to at least two, more preferably all three, of the HLA class II allelic gene products DRB*0401, DRB*0101, and DRB1*0701.
To select the peptides it is not necessary to use algorithms to predict whether any sequence in the peptide binds to HLA class I alleles. The inventors have found that the majority of the peptides are able to activate a peptide-specific CD8+ T cell response, indicating the peptides contain antigenic sequences that bind to HLA class I proteins, and probably to multiple HLA class I proteins.
The HLA class II peptide-binding site holds peptides of 12-15 amino acid residues in length. The algorithm used to predict the peptides binding to the HLA class II proteins calculates binding for a 9-amino-acid motif. 9-mer peptides or even shorter peptides can bind to class II alleles in some cases. But preferably, the peptides contain an extension of at least 3 amino acid residues on each end of a predicted 9-mer HLA class II binding sequence and are at least 15 amino acid residues in length.
Peptides to screen for use in the invention were selected by processing the sequences of SCCE, hepsin, and matriptase with an algorithm that predicts 9-mer sequences that bind to three HLA class II proteins. Extended peptides containing multiple 9-mer epitope sequences predicted to bind to the HLA class II proteins were preferentially selected for testing. The multiple 9-mer predicted epitope sequences may be overlapping or non-overlapping in the peptides. The peptides were limited in length to about 40 amino acid residues to avoid including sequences that may be present in other proteins and lead to an immune response targeted to other proteins in the body.
The peptides of the invention are preferably portions of the complete proteins. Preferably the peptides are 7-60 amino acid residues, more preferably 7-50, more preferably 9-50, more preferably 9-40 amino acid residues in length. In specific embodiments, the peptides are 7-40, 9-40, 12-40, 15-40, or 20-40 amino acid residues in length. In other specific embodiments, the peptides are 7-50, 9-50, 12-50, 15-50, or 20-50 amino acid residues in length.
The invention includes peptides comprising an antigenic matriptase, hepsin, or SCCE sequence of at least 7 amino acid residues, wherein the peptide can be used to amplify CD4+ T cells that recognize the antigenic matriptase, hepsin, or SCCE sequence. Preferably, when the peptide is contacted with dendritic cells to generate peptide-loaded dendritic cells and the peptide-loaded dendritic cells are contacted with T cells, the peptide-loaded dendritic cells also amplify CD8+ T cells that recognize the matriptase, hepsin, or SCCE sequence.
Preferably, the amplified CD8+ T cells kill autologous cancer cells expressing matriptase, hepsin, or SCCE. Preferably the killing is dependent on the cell's expressing matriptase, hepsin, or SCCE, which can be assayed by comparing killing of control autologous cells that do not express the protein.
Preferably, the peptide is able to activate CD4+ T cells in most persons of a population, i.e., has an epitope or epitopes able to bind to more than one HLA class II protein. This can be shown by showing a peptide-specific CD4+ T cell response in two different donors having no HLA class II alleles in common. The CD4+ T cell response can be proliferation, cytokine release, or cytolysis. HLA typing is routinely carried out by clinical laboratories and blood banks.
In particular embodiments, the peptides can be used with dendritic cells to activate CD4+ T cells from at least two donors with no HLA class II alleles in common.
In a particular embodiment, the purified matriptase (or hepsin or SCCE) peptide contains two antigenic matriptase (or hepsin or SCCE) sequences wherein CD4+ T cells from one of the donors recognizes one antigenic sequence and CD4+ T cells from the other donor recognizes the other antigenic matriptase sequence.
In a particular embodiment the purified peptide comprises two antigenic matriptase (or hepsin or SCCE) sequences wherein one of the two different lines of CD4+ T cells recognizes one antigenic sequence and the other CD4+ T cell line recognizes the other antigenic sequence.
In a particular embodiment, CD8+ T cells amplified with the peptide perform peptide-dependent lysis of at least two lines of target allogeneic cells pulsed with the peptide, wherein the two lines of target allogeneic cells are matched to the CD8+ T cells in different and non-overlapping HLA class I alleles.
In a more specific embodiment, the purified peptide comprises two matriptase (or SCCE or hepsin) epitopes, wherein the CD8+ T cells recognize one matriptase (or SCCE or hepsin) epitope on one target allogeneic cell line and the other matriptase (or SCCE or hepsin) epitope on the other target allogeneic cell line.
The matriptase peptides that have been tested (Example 3 below) are SEQ ID NO:4 (residues 170-204 of matriptase, SEQ ID NO:3), SEQ ID NO:5 (residues 273-296 of matriptase), SEQ ID NO:6 (residues 308-343 of matriptase) and SEQ ID NO:7 (residue 379-399 of matriptase). All of these peptides amplify CD4+ T cells that recognize the peptide. Thus, in particular embodiments, the peptide comprises one of these sequences or an antigenic fragment of one of these sequences.
The hepsin peptides that have been tested are SEQ ID NO:8 (residues 48-84 of hepsin, SEQ ID NO:2), SEQ ID NO:9 (residues 90-117 of hepsin), SEQ ID NO: 10 (residues 396-412 of hepsin), SEQ ID NO: 11 (residues 214-236 of hepsin), SEQ ID NO: 12 (residues 177-210 of hepsin), SEQ ID NO: 13 (residues 255-287 of hepsin), and SEQ ID NO: 14 (residues 226-250 of hepsin). All of these peptides amplify CD4+ T cells that recognize the peptide. Thus, in particular embodiments, the peptide comprises one of these sequences or an antigenic fragment of one of these sequences.
The SCCE peptides that have been tested are SEQ ID NO: 15 (residues 1-23 of SCCE, SEQ ID NO:1), SEQ ID NO:16 (residues 61-84 of SCCE), and SEQ ID NO:17 (residues 143-160 of SCCE). All of these peptides amplify CD4+ T cells that recognize the peptide. Thus, in particular embodiments, the peptide comprises one of these sequences or an antigenic fragment of one of these sequences.
Another embodiment of the invention provides a method of treating cancer that involves: (a) contacting dendritic cells with a peptide comprising an antigenic matriptase sequence (or hepsin or SCCE sequence) of at least 7 amino acid residues; (b) contacting the peptide-loaded dendritic cells with T cells to amplify CD8+ T cells and CD4+ T cells that recognize the antigenic matriptase (or hepsin or SCCE) sequence; and (c) contacting the amplified CD8+ T cells with cancer cells expressing matriptase (or hepsin or SCCE) to kill the cancer cells.
This can be performed as described in Example 4 below. If a patient's tumor is positive for any one of matriptase, SCCE, or hepsin, she can be treated with dendritic cells loaded with one peptide from the appropriate protein or with a mixture of peptides from the protein. A patient whose tumor is positive for at least two of matriptase, hepsin, and SCCE can also be treated with dendritic cells contacted with a mixture of peptides including peptides from the appropriate two or all three of matriptase, hepsin, and SCCE.
Typically to treat patients, dendritic cells would be matured ex vivo in contact with the peptides, and then the dendritic cells would be infused into the patient. In vivo the dendritic cells would amplify CD8+ T cells that would recognize and kill the tumor cells and/or CD4+ T cells that would support this response and/or kill the tumor cells directly. However, the dendritic cells could also be used to amplify CD4+ and/or CD8+ T cells specific for the peptides ex vivo, and the amplified T cells could be infused into the patient.
The dendritic cells are typically autologous.
Ex vivo amplified CD4+ and CD8+ T cells if used to treat a cancer patient typically would be autologous.
Another embodiment of the invention provides a composition comprising: purified dendritic cells loaded ex vivo with a peptide comprising an antigenic matriptase (or SCCE or hepsin) sequence of at least 7 amino acid residues; wherein when the peptide is contacted with dendritic cells to generate peptide-loaded dendritic cells and the peptide-loaded dendritic cells are contacted with T cells, the peptide-loaded dendritic cells amplify CD4+ T cells (helper T cells) that recognize the matriptase (or SCCE or hepsin) sequence. The dendritic cells can be prepared, for example, as described in Example 4 below.
The following examples are intended to illustrate the invention but not limit its scope.
EXAMPLES
Example 1
Stratum Corneum Chymotryptic Enzyme (SCCE)
SCCE, also known as kallikrein 7, is a serine protease that is overexpressed by ovarian cancer cells but not by normal ovaries or other normal adult tissues, except the outermost cornified layer of the skin (15). Immunohistochemical analysis of 14 ovarian tumors showed positive staining localized to the cytoplasm and cell membrane, suggesting that SCCE may be expressed as both secreted and membrane forms (15). Quantitative RT-PCR revealed SCCE expression in >88% of serous ovarian tumors, 100% of endometrioid and clear cell tumors, but only 29% (two of seven) mucinous tumors (15). SCCE is also overexpressed in cervical cancer (10).
The tightly limited tissue distribution of SCCE and overexpression in ovarian tumors suggests that it would be a favorable target antigen for immunotherapy. In this Example, we used computer algorithms to select several extended SCCE peptides predicted to have epitopes that bind to multiple HLA class II allelic proteins. The extended peptides were tested when loaded onto dendritic cells for amplification of CD4+ T cells and CD8+ T cells.
1. Calculation of Peptide Binding Affinity to HLA Class II and Class I Proteins.
The sequence of SCCE was scanned to calculate the predicted binding affinity of 9-mer peptides within SCCE for three common HLA class II allelic proteins—DRB*0401, DRB*0101, and DRB1*0701, using algorithms reported in reference (1). To develop the algorithms, a adjusted relative binding (ARB) value was assigned to each amino acid in each of the 9 positions of a 9-mer based on the experimentally determined binding affinity of 384 test peptides to each of the three HLA class II allelic proteins tested. All the test peptides contained a hydrophobic residue at position p1 and an small uncharged side chain residue at position p6. To develop the algorithms, it was assumed that each individual side chains bind independently. When residue R occurs at position i in the peptide, it is assumed to contribute a constant amount Ri to the free energy of binding irrespective of the sequence of the rest of the peptide. For all i positions, the geometric mean of the average relative binding (ARB) of all peptides carrying R is calculated relative to the remainder of the group and used as an estimate of Ri. The algorithms calculate a binding affinity value of a hypothetical 9-mer peptide by multiplying the ARB values of each residue of the peptides. The ARB values of each amino acid residue at each position in a peptide for the DRB1*0401, DRB1*0101, and DRB1*0701 are shown in reference 1, which is hereby incorporated by reference.
It has been experimentally determined that peptides that bind to at least two of the class II alleles DRB1*0401, DRB1*0101, and DRB1*0701, are also more likely to bind to several other class II alleles, including DRB5*0101, DRB1*1501, BRB1*0901, and DRB1*1302 than peptides that bind to one or fewer of DRB1*0401, DRB1*0101, and DRB1*0701. Thus, these algorithms predict peptides that will activate CD4+ cells in most individuals of the population.
SCCE was scanned to identify extended peptide sequences of up to 40 residues in SCCE that have clusters of predicted HLA class II binding epitopes.
Optionally, the sequences can be further processed to determine whether the peptides also have sequences predicted to bind to HLA class I molecules. HLA-A2.1 is the most common HLA class I allele. Peptides with the potential to bind to HLA-A2.1 can be predicted by two computer programs. The first is at bimas.dcrt.nih.gov/molbio/hla_bind (2) and the second at the website 134.2.96.221/scripts/hlaserver.dll/EpPredict.htm (3).
2. CD4+ T Cell and CD8+ T Cell Responses to the SCCE Peptides.
SCCE peptides 1-23, 61-84, and 143-160 were synthesized. The peptides were loaded onto dendritic cells or other antigen presenting cells and used to amplify CD4+ T cells and CD8+ T cells. The amplified T cells were then tested for peptide-specific cytokine release, cellular proliferation, or cytolysis of target cells carrying the peptide.
2A. Materials and Methods:
Cell Lines, Antibodies, and Cytokines.
K562, lymphoblastoid cell lines, and HLA class I-negative C1R cells were grown in RPMI supplemented with 10% FCS, 50:M 2-βmercaptoethanol, 3 mmol/L L-glutamine, 100 IU/mL penicillin, and 100 μg/mL streptomycin (RPMI/10). Macrophages and dendritic cells were grown in AIM-V (Invitrogen). T cells were grown in RPMI supplemented with 10% human AB serum (Valley Biomedical, Winchester, Va.), 50:M 2-β-mercaptoethanol, 3 mmol/L L-glutamine, 100 IU/mL penicillin, and 100 μg/mL streptomycin (RPMI/10 Hu).
Fluorochrome-conjugated anti-CD4 monoclonal antibody (MAb), anti-CD8 and anti-IL-10 were purchased from Caltag (Burlingame, Calif.). Fluorochrome-conjugated MAb specific for interleukin (IL)-4, IFN-(, IL-13, tumor necrosis factor-∀, and IL-2 were purchased from BD Immunocytometry (San Jose, Calif.). W6/32 (anti-HLA class I), L243 (anti-HLA class II), and BB7.2 (anti-HLA-A2.1) MAb were prepared from hybridomas purchased from the American Type Culture Collection.
Cytokines for the establishment of dendritic cells and T cell cultures included granulocyte macrophage colony-stimulating factor (Immunex, Seattle, Wash.), IL-4, tumor necrosis factor-∀ (both from R&D Systems, Minneapolis, Minn.), prostaglandin E2 (Sigma, St. Louis, Mo.), IL-1β, and IL-2 (both from the Biological Response Modifiers Program, National Cancer Institute).
Dendritic Cells and Stratum Corneum Chymotryptic Enzyme-Specific T Cells.
Peripheral blood was drawn from healthy adult volunteer donors, following an Institutional Review Board-approved protocol. Peripheral blood mononuclear cells were recovered by gradient centrifugation (Lymphoprep; Greiner Bio-One, Longwood, Fla.).
For preparation of dendritic cells, peripheral blood mononuclear cells were placed in six-well plates (Costar, Cambridge, Mass.) at a concentration of 5×106 per well in AIM-V medium. After incubation for 2 to 3 hours at 37° C., nonadherent cells were removed from the culture and the medium was replaced with AIM-V plus 800 units/mL granulocyte macrophage colony-stimulating factor and 500 units/mL IL-4. On days 3 and 5, half the medium was removed and replaced with AIM-V plus 800 units/mL granulocyte macrophage colony-stimulating factor and 500 units/mL IL-4. A mix of maturation cytokines (1 μmol/L/mL prostaglandin E2, 1,000 units/mL tumor necrosis factor-∀, and 500 units/mL IL-1β) was added on day 5 or 6. For stimulation of CD8+ T cells specific for HLA-A2.1-binding SCCE peptide epitopes, mature dendritic cells were collected after maturation for 48 hours, and pulsed with 50 μg/mL of peptide for 2 hours in AIM-V at 37° C. The dendritic cells were then washed once with AIM-V medium and used for T cell stimulation at a peripheral blood mononuclear cell/dendritic cell ratio of 30:1. After 7 days, T cells were collected and restimulated with peptide-pulsed dendritic cells. After the second stimulation, CD8+ T cells were recovered by positive selection with anti-CD8 magnetic beads (Dynal Biotech, Brown Deer, Wis.). During the second and third T cell stimulation and passage, 50 to 100 units/mL IL-2 was added to the medium, and T cells were periodically fed (every 2-3 days) by changing 50% to 70% of the medium and addition of fresh IL-2. Further passaging of CD8+ T cell lines used peptide-loaded autologous peripheral blood lymphocytes as antigen-presenting cells.
For stimulation of SCCE peptide-specific CD4+ helper T cell and CD8+ CTL responses, 50 μg/mL of the appropriate SCCE peptide was added to dendritic cells on days 5 or 6 (at the time of addition of maturation mix) and the dendritic cells were harvested 48 hours later. Initial T cell stimulation was the same as described above. After the second stimulation, CD4+ and CD8+ T cells were recovered by positive selection with anti-CD4 or anti-CD8 magnetic beads (Dynal). During the second and subsequent T cell passages, 20 to 50 units/mL IL-2 was added to the medium, and the cultures were periodically fed (every 2-3 days) by changing 50% to 70% of the medium and addition of fresh IL-2. Dendritic cells were used as antigen-presenting cells for the first three to five antigen stimulations. Later antigen stimulations were done with autologous lymphoblastoid cell lines pulsed overnight with 50 μg/mL SCCE peptide.
Cytotoxicity Assays.
Standard 51Cr-release assays were done as described previously (17). Autologous lymphoblastoid cell lines were pulsed with 50 μg/mL of appropriate CTL peptide, or left unpulsed. Lymphoblastoid cell lines were pulsed overnight with 50 μg/mL of extended SCCE peptide at 37° C. in AIM-V medium, whereas dendritic cells were pulsed with 50 μg/mL peptide for 48 hours during final maturation. Peptide-pulsed targets were then labeled with 50 μCi Na2[51Cr]O4 for an additional hour and washed three times before use. K562 cells, which are sensitive to natural killer cell lysis, were labeled similarly with 51Cr. Blocking antibodies were added to target cells at concentrations indicated for each assay immediately prior to plating. Target cells were plated at 1×104 per well in 96-well round-bottomed plates with effector T cells at the ratios indicated for each assay. Assays were done in triplicate wells. The percentage of target cell lysis was calculated as described (17).
Cytokine Assays.
Intracellular cytokine expression was measured by flow cytometry after overnight coculture of T cells with peptide-pulsed or unpulsed lymphoblastoid cell lines, dendritic cells, or tumor cell lines. T cells (1.5×106) were plated in 12-well Costar plates in 2 mL RPMI/10 Hu. T cells were stimulated with phorbol 12-myristate 13-acetate (50 ng/mL) and ionomycin (500 ng/mL) as a positive control. Negative controls included T cells cultured alone, or with unpulsed lymphoblastoid cell lines or dendritic cells. At the onset of coculture, 10 μg/mL of Brefeldin A was added to block cytokine release. Cells were collected after the overnight stimulation and fixed in 2% paraformaldehyde in PBS for 10 minutes at room temperature. The cells were washed once in PBS and again in 0.5% saponin and 1% bovine serum albumin in PBS. T cells were labeled with cytokine-specific MAb conjugated to PE or FITC for 30 minutes at room temperature. After staining, the cells were washed twice in 0.5% saponin and 1% bovine serum albumin in PBS, once with 0.5% bovine serum albumin in PBS, and fixed in 2% paraformaldehyde in PBS. Fluorescence was measured with a FACSCalibur (Becton Dickinson, San Jose, Calif.) and data were analyzed with WinMDI software.
2B. Results
Three peptides were selected from the sequence of SCCE as having clusters of possible HLA class II protein binding segments. The peptides were residues 1-23, 61-84, and 143-160 of SCCE.
The peptides were prepared by chemical synthesis and loaded onto dendritic cells as described above in Materials and Methods.
CD4+ T cells were amplified as described above in Materials and Methods with the peptide-loaded dendritic cells. The amplified CD4+ T cells were tested for secretion of the cytokines TNF-alpha and IL-4 when stimulated with autologous LCL loaded with the peptide used to amplify the CD4+ T cells. Secretion of the cytokines was monitored by flow cytometry, and the results are shown in FIG. 1. All three of the peptides stimulated cytokine expression. The CD4+ cells were stimulated to release TNF-∀ but not IL-4.
CD8+ T cells amplified with the three tested SCCE peptides were tested for ability to lyse target LCL pulsed with the corresponding peptide. Lysis was tested against autologous LCL as well as allogeneic LCL matched in specific HLA class I alleles. The results are shown in FIG. 1. All three of the peptides stimulated lysis of autologous LCL pulsed with the peptide. Peptide 1-23 also stimulated lysis of HLA B27-matched allogeneic LCL. Peptide 61-84 stimulated lysis of HLA A2.1-matched LCL. Peptide 143-160 stimulated lysis of HLA-A2.1-matched LCL.
Results of further cytokine secretion assays are shown in Table 1.







TABLE 1







CD4+ T cell cytokine secretion in response to SCCE peptides.

















Percent




HLA-DR
Cyto-
Stimulator
secreting


Peptide
Donor
type
kine
cells
cells
















 1-23
MDC
DR15, DR17,
TNF-∀
Control LCL
3%





DR51, DR52






LCL + peptide
21%



MJC
DR3, DR52
TNF-∀
Control LCL
3%






LCL + peptide
6%


61-84
MJC
DR3, DR52

Control LCL
<1%





TNF-∀
LCL + peptide
75%





Inter-
LCL + peptide
30%





feron-





gamma





IL-2
LCL + peptide
30%


143-160
MJC
DR3, DR52
IL-2
LCL control
1%






LCL + peptide
6-11%









2C. Conclusions

All three extended SCCE peptides tested stimulated CD4+ T cell proliferation and cytokine secretion from each of the donors tested. Peptide 1-23 was tested with one donor and peptides 61-84 and 143-160 were tested with two donors. CD8+ T cells amplified with each of the three extended SCCE peptides also lysed autologous target cells pulsed with the peptide in a peptide-specific manner.
Example 2
Hepsin Peptides
Hepsin is a transmembrane serine protease that is overexpressed in prostate cancer and ovarian cancer, as well as renal cell carcinoma (19-26). In at least one report its overexpression was linked to metastasis and tumor progression (21). In this Example the hepsin sequence (SEQ ID NO:2) was scanned to identify regions predicted to have multiple epitopes that bind to a variety of HLA class II allelic proteins. Peptides containing the predicted epitopes were synthesized and used to amplify CD4+ and CD8+ T cells and the response of the amplified T cells to the peptides was tested.
Results:
The sequence of hepsin was processed using the algorithms described in Example 1 to identify epitopes predicted to bind to HLA class II alleles DRB1*0401, DRB1*0101, and DRB1*0701. Peptides were synthesized corresponding to sequences in hepsin predicted to have multiple epitopes that bind to at least two of those three HLA class II allelic proteins. The selected peptides were residues 48-84, 90-117, 177-210, 214-236, 226-250, and 255-287 of hepsin.
The peptides were loaded onto dendritic cells, and the peptide-loaded dendritic cells were used to amplify CD4+ T cells and CD8+ T cells as described in Example 1. The amplified CD4+ T cells were tested for cytokine secretion in response to stimulation by peptide-loaded LCL. The results are shown in Table 2. All of the hepsin peptides stimulated cytokine secretion from CD4+ T cells stimulated with autologous peptide-loaded cells. Tumor necrosis factor alpha (TNF-∀) was the cytokine whose secretion was stimulated the most. Interferon, interleukin-2, and interleukin-4 secretion were also stimulated.







TABLE 2







CD4+ T cell cytotokine secretion in response to hepsin peptides.

















Percent




HLA DR
Cyto-
Stimulator
secreting


Peptide
Donor
type
kine
cells
cells
















48-84
MDC
DR15, DR17,
TNF-∀
Control LCL
3%





DR52, DR53






LCL + peptide
34%



MJC
DR3, DR52
various
Control LCL
1-3%





TNF-∀
LCL + peptide
32%





Inter-
LCL + peptide
9%





feron-





gamma





IL-2
LCL + peptide
6%





IL-4
LCL + peptide
4%


 90-117
MDC
DR15, DR17,
TNF-∀
Control LCL
2%




DR51, DR52






LCL + peptide
16%



MJC
DR3, DR52
various
Control LCL
1-6%





TNF-∀
LCL + peptide
38%





Inter-
LCL + peptide
30%





feron





IL-2
LCL + peptide
13%





IL-4
LCL + peptide
7%


177-210
976
DR1, DR7
various
Control LCL
1%





TNF-∀
LCL + peptide
54%





Inter-
LCL + peptide
4%





feron





IL-2
LCL + peptide
9%





IL-4
LCL + peptide
7-9%



819
DR4, DR13
various
Control LCL
0%





TNF-∀
LCL + peptide
13%





Inter-
LCL + peptide
27%





feron





IL-2
LCL + peptide
1%


255-287
976
DR1, DR7
various
Control LCL
0-1%





TNF-∀
LCL + peptide
37%





Inter-
LCL + peptide
16%





feron





IL-2
LCL + peptide
5%





IL-4
LCL + peptide
10-11%



MJC
DR3, DR52
TNF-∀
Control LCL
0%






LCL + peptide
10%


214-236
666
DR1, DR8
TNF-∀
Control LCL
2%






LCL + peptide
21%



679
DR4, DR7
various
Control LCL
0%





TNF-∀
LCL + peptide
49%





Inter-
LCL + peptide
10%





feron





IL-2
LCL + peptide
27%





IL-4
LCL + peptide
10%









The CD4+ T cells were also tested for cytotoxicity against peptide-loaded target cells. The results are shown in Table 3. Each of the peptides tested amplified CD4+ T cells from every donor tested, and the amplified CD4+ T cells showed peptide-specific cytolysis of autologous cells loaded with the peptide.







TABLE 3







CD4+ T cell cytotoxicity against


hepsin peptide-loaded target cells.















Percent cell


Peptide
Donor
HLA-DR type
Target cells
killing.















48-84
MJC
DR3, DR52
LCL control
4%






LCL + peptide
42%


 90-117
MJC
DR3, DR52
LCL
6%





LCL + peptide
65%


396-412
MJC
DR3, DR52
LCL
12%





LCL + peptide
22%


214-236
666
DR1, DR8
LCL
3.5%





LCL + peptide
13%


226-250
679
DR4, DR7
LCL
17%





LCL + peptide
35%









CD4+ T cells are the helper T cells that function primarily to activate and control the immune response of other immune cells including antibody-producing cells and CD8+ cytotoxic T cells. CD8+ T cells are the cells primarily responsible for cytolysis of target tumor cells. The ability of peptide-amplified CD8+ T cells to lyse target cells was also assayed, and the results are shown in Table 4. Each of the six tested peptides amplified CD8+ T cells that were cytotoxic against autologous cells loaded with the peptide.







TABLE 4







CD8+ T cell cytotoxicity against hepsin peptide-loaded target cells.













HLA Class I

Percent cell


Peptide
Donor
type
Target cells
killing.















48-84
MDC
A2, B8, B27
autologous LCL control
3%






autologous LCL + peptide
21%





A2-matched allogeneic
42%





LCL + peptide





B27-matched allogeneic
31.3%





LCL + peptide





B61/B51-matched allogeneic
27.1%





LCL + peptide





complete mismatched
1.8%





LCL + peptide


 90-117
MDC
A2, B8, B27
autologous LCL
2.5%





autologous LCL + peptide
11.6%



MJC
A1, A2, B8, B27
autologous LCL
3%





autologous LCL + peptide
9%


396-412
MJC
A1, A2, B8, B27
autologous LCL
45%





autologous LCL + peptide
65%


177-210
976
A2, A3, B13, B65
autologous LCL
7.3%





autologous LCL + peptide
21.3%


214-236
666
A2, A3, B35, B51
autologous LCL
6%





autologous LCL + peptide
30%


226-250
679
A2, A23, B27, B60
autologous LCL
2.2%





autologous LCL + peptide
20%









Conclusions:

Every hepsin extended peptide tested amplified CD4+ cells that were stimulated by autologous cells loaded with the peptide. The stimulated CD4+ cells released TNF-∀ and interferon, and lesser amounts of IL-2 and IL-4. Each of the peptides also amplified CD4+ that showed peptide-specific cytotoxicity against autologous cells from various donors loaded with the peptide. Six of the peptides were tested for their ability to stimulate CD8+ cells that were cytotoxic to autologous cells loaded with the peptide. Each of the six tested peptides generated CD8+ T cells that showed peptide-specific killing of autologous cells.
Example 3
Matriptase Peptides
Matriptase (also known as TADG-15) is a transmembrane serine protease that was discovered in 1993 and cloned in 1999 (3, 7). It is overexpressed in many tumors of epithelial origin, including carcinomas of the head and neck, mesothelium, breast, ovary, cervix, prostate, lung, and gastrointestinal tract, as well as in cell lines derived from these tumors (8). Its expression has been linked to increased tumor invasiveness (5-6). It is expressed in a high percentage of ovarian carcinomas but not in normal ovary tissue (4). Matriptase's pattern of overexpression in many tumors makes it an attractive target for immunotherapy in ovarian and other cancers. The importance of matriptase expression in prostate cancer progression has been emphasized by studies showing that a selective matriptase inhibitor inhibits growth of androgen-independent human prostate tumor xenografts in nude mice (6). Furthermore, overexpression of matriptase in the skin of transgenic mice resulted in spontaneous squamous cell carcinoma, suggesting a causal role for matriptase in epithelial cancers (27).
The sequence of matriptase was processed using the algorithms described in Example 1 to identify epitopes predicted to bind to HLA class II alleles DRB1*0401, DRB1*0101, and DRB1*0701. Peptides were synthesized corresponding to sequences in matriptase predicted to have multiple epitopes that bind to at least two of those three HLA class II allelic proteins. The selected peptides were residues 170-204, 273-296, 308-343, and 379-399.
The peptides were loaded onto dendritic cells, and the peptide-loaded dendritic cells were used to amplify CD4+ T cells and CD8+ T cells as described in Example 1. The amplified CD4+ T cells were tested for cytokine secretion in response to stimulation by peptide-loaded LCL. The results are shown in Table 5. All of the peptides stimulated release of at least TNF-∀ in each donor tested, which in some cases was one donor and in other cases two donors.







TABLE 5







CD4+ T cell cytotokine secretion


in response to matriptase peptides.

















Percent




HLA-DR
Cyto-
Stimulator
secreting


Peptide
Donor
type
kine
cells
cells
















170-204
976
DR1, DR7
various
Control LCL
1-2%






TNF-∀
LCL + peptide
23%





Interferon-
LCL + peptide
6%





gamma





IL-2
LCL + peptide
15%





IL-4
LCL + peptide
7-8%



MJC
DR3, DR52
various
Control LCL
1-2%





TNF-∀
LCL + peptide
16%





Interferon
LCL + peptide
6%


273-296
976
DR1, DR7
TNF-∀
Control LCL
5%%






LCL + peptide
9%


308-343
976
DR1, DR7
various
Control LCL
0.5-1%





TNF-∀
LCL + peptide
23%





Interferon
LCL + peptide
7%





IL-2
LCL + peptide
10%





IL-4
LCL + peptide
5-6%



MJC
Dr3, DR52
TNF-∀
Control LCL
3%





TNF-∀
LCL + peptide
19%





Interferon
Control LCL
1%





Interferon
LCL + peptide
3%


379-399
976
DR1, DR7
various
Control LCL
2-10%





TNF-∀
LCL + peptide
60%





Interferon
LCL + peptide
7%





IL-2
LCL + peptide
4%





IL-4
LCL + peptide
1-2%









The ability of the peptides to amplify CD8+ T cells that lysed target cells loaded with the peptide was also assayed. The results are shown in Table 6. Only the peptide 170-204 was assayed. It generated CD8+ T cells that displayed peptide-specific cytolysis against LCL loaded with the peptide.







TABLE 6







CD8+ T cell cytotoxicity against matriptase


peptide-loaded target cells.













HLA Class I

Percent cell


Peptide
Donor
type
Target cells
killing















170-204
976
A2, A3,
autologous LCL control
13%





B13, B65





autologous LCL +
59%





peptide





A3-matched allogeneic
29%





LCL + peptide





B13-matched allogeneic
0%





LCL + peptide





A2-matched allogeneic
0%





LCL + peptide





complete mismatched
0%





LCL + peptide



MJC
A1, A2,
autologous LCL control
0%




B8, B27





autologous LCL +
6%





peptide









Conclusion:

All of the matriptase peptides tested stimulated CD4+ T cell cytokine secretion. The one peptide tested for CD8+ cytotoxic response, 170-204, amplified CD8+ T cells that showed peptide-specific cytolysis against cells loaded with the peptide.
Example 4
Infusing Dendritic Cells Loaded with a Matriptase, Hepsin, or SCCE Peptide to Treat Ovarian Cancer
Ovarian cancer patients having tumors positive for expression of matriptase, hepsin, or SCCE are treated in this Example. Patients undergo leukopheresis using a COBE separator. Peripheral blood leukocytes (PBL) from the patients are used for generation of dendritic cells (DC). Monocyte-derived DC are cultured in AIM-V (Gibco-BRL) supplemented with GM-CSF and IL-4 as described in Example 1. After 5 days' culture, DC maturation is induced by addition of TNF∀, IL-1∃, and GPE2, as described in Example 1. At the time of induction of maturation, one or more matriptase, hepsin, and/or SCCE peptides is also added, at a concentration of 50:g/ml of each peptide. The cells are incubated for 48 hours to mature and process the peptides. The DC are then washed twice to remove unbound peptides. The DC are then suspended in PBS supplemented with 10% autologous serum, and infused intravenously into the patient over a period of one hour. Typically, all of the DC that could be obtained are infused into the patient.
Patients receive a total of five treatments at three-week intervals.
The treated patients are observed to have less tumor growth, more tumor shrinkage, or longer remissions than comparable patients who do not receive the treatment.
The sequences of SCCE, hepsin, and matriptase that were used to select peptides are as shown below.








Stratum Corneum Chymotryptic Enzyme, SEQ ID NO: 1,



accession no. AAC37551.









  1
marslllplq illlslalet ageeaqgdki idgapcargs




hpwqvallsg nqlhcggvlv


 


 61
nerwvltaah ckmneytvhl gsdtlgdrra qrikasksfr



hpgystqthv ndlmlvklns


 


121
qarlssmvkk vrlpsrcepp gttctvsgwg tttspdvtfp



sdlmcvdvkl ispqdctkvy


 


181
kdllensmlc agipdskkna cngdsggplv crgtlqglvs



wgtfpcgqpn dpgvytqvck


 


241
ftkwindtmk khr














Hepsin, SEQ ID NO: 2, accession no. AAC37551.










  1
maqkeggrtv pccsrpkvaa ltagtllllt aigaaswaiv




avllrsdqep lypvqvssad


 


 61
arlmvfdkte gtwrllcssr snarvaglsc eemgflralt



hseldvrtag angtsgffcv


 


121
degrlphtqr llevisvcdc prgrflaaic qdcgrrklpv



drivggrdts lgrwpwqvsl


 


181
rydgahlcgg sllsgdwvlt aahcfpernr vlsrwrvfag



avaqasphgl qlgvqavvyh


 


241
ggylpfrdpn seensndial vhlssplplt eyiqpvclpa



agqalvdgki ctvtgwgntq


 


301
yygqqagvlq earvpiisnd vcngadfygn qikpkmfcag



ypeggidacq gdsggpfvce


 


361
dsisrtprwr lcgivswgtg calaqkpgvy tkvsdfrewi



fqaikthsea sgmvtql














Matriptase, SEQ ID NO: 3, accession no. AAG15395.










  1
mgsdrarkgg ggpkdfgagl kynsrhekvn gleegveflp




vnnvkkvekh gpgrwvvlaa


 


 61
vliglllvll gigflvwhlq yrdvrvqkvf ngymritnen



fvdayensns tefvslaskv


 


121
kdalkllysg vpflgpyhke savtafsegs viayywsefs



ipqhlveeae rvmaeervvm


 


181
lpprarslks fvvtsvvafp tdsktvqrtq dnscsfglha



rgvelmrftt pgfpdspypa


 


241
harcqwalrg dadsvlsltf rsfdlascde rgsdlvtvyn



tlspmephal vqlcgtypps


 


301
ynltfhssqn vllitlitnt errhpgfeat ffqlprmssc



ggrlrkaqgt fnspyypghy


 


361
ppnidctwni evpnnqhvkv sfkffyllep gvpagtcpkd



yveingekyc gersqfvvts


 


421
nsnkitvrfh sdqsytdtgf laeylsydss dpcpgqftcr



tgrcirkelr cdgwadctdh


 


481
sdelncscda ghqftcknkf ckplfwvcds vndcgdnsde



qgcscpaqtf rcsngkclsk


 


541
sqqcngkddc gdgsdeascp kvnvvtctkh tyrclnglcl



skgnpecdgk edcsdgsdek


 


601
dcdcglrsft rqarvvggtd adegewpwqv slhalgqghi



cgaslispnw lvsaahcyid


 


661
drgfrysdpt qwtaflglhd qsqrsapgvq errlkriish



pffndftfdy diallelekp


 


721
aeyssmvrpi clpdashvfp agkaiwvtgw ghtqyggtga



lilqkgeirv inqttcenll


 


781
pqqitprmmc vgflsggvds cqgdsggpls sveadgrifq



agvvswgdgc aqrnkpgvyt


 


841
rlplfrdwik entgv






REFERENCES


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All patents, patent documents, and other references cited herein are incorporated by reference.

## Claims

1. A purified peptide of 12-50 amino acid residues comprising an antigenic stratum corneum chymotryptic enzyme (SCCE) sequence of 12-50 amino acid residues;
wherein when the purified peptide is contacted with dendritic cells to generate peptide-loaded dendritic cells and the peptide-loaded dendritic cells are contacted with T cells, the peptide-loaded dendritic cells amplify CD4+ T cells (helper T cells) that recognize the SCCE sequence;
wherein the antigenic SCCE sequence is SEQ ID NO:15 (residues 1-23 of SCCE), SEQ ID NO:16 (residues 61-84), SEQ ID NO:17 (residues 143-160), or a fragment thereof that comprises at least 12 consecutive amino acid residues of SEQ ID NO:15, at least 12 consecutive amino acid residues of SEQ ID NO:16, or at least 12 consecutive amino acid residues of SEQ ID NO:17.

2. The purified peptide of claim 1 wherein when the purified peptide is contacted with dendritic cells to generate peptide-loaded dendritic cells and the peptide-loaded dendritic cells are contacted with T cells, the peptide-loaded dendritic cells amplify CD8+ T cells (cytotoxic T lymphocytes, CTL) that recognize the antigenic SCCE sequence.

3. The purified peptide of claim 1 wherein the peptide can be used with dendritic cells to activate CD4+ T cells from at least two donors with no HLA class II alleles in common.

4. The purified peptide of claim 2 wherein CD8+ T cells amplified with the peptide perform peptide-dependent lysis of at least two lines of target allogeneic cells pulsed with the peptide, wherein the two lines of target allogeneic cells are matched to the CD8+ T cells in different and non-overlapping HLA class I alleles.

5. The purified peptide of claim 1 wherein the peptide is 12-40 amino acid residues.

6. The purified peptide of claim 1 wherein the purified peptide comprises SEQ ID NO:15 (residues 1-23 of SEQ ID NO:1), SEQ ID NO:16 (residues 61-84 of SEQ ID NO:1), or SEQ ID NO:17 (residues 143-160 of SEQ ID NO:1).

7. The purified peptide of claim 1 wherein the peptide comprises an antigenic fragment of any one of SEQ ID NOS:15, 16, and 17.

8. A composition of matter comprising:
purified dendritic cells loaded ex vivo with a purified peptide of 12-50 amino acid residues comprising an antigenic SCCE sequence of 12-50 amino acid residues;
wherein when the purified peptide is contacted with dendritic cells to generate peptide-loaded dendritic cells and the peptide-loaded dendritic cells are contacted with T cells, the peptide-loaded dendritic cells amplify CD4+ T cells (helper T cells) that recognize the SCCE sequence;
wherein the antigenic SCCE sequence is SEQ ID NO:15 (residues 1-23 of SCCE), SEQ ID NO:16 (residues 61-84), SEQ ID NO:17 (residues 143-160), or a fragment thereof that comprises at least 12 consecutive amino acid residues of SEQ ID NO:15, at least 12 consecutive amino acid residues of SEQ ID NO:16, or at least 12 consecutive amino acid residues of SEQ ID NO:17.

9. The composition of claim 8 wherein when the purified peptide is contacted with dendritic cells to generate peptide-loaded dendritic cells and the peptide-loaded dendritic cells are contacted with T cells, the peptide-loaded dendritic cells amplify CD8+ T cells (cytotoxic T lymphocytes, CTL) that recognize the SCCE sequence.

10. The composition of claim 9 wherein the amplified CD8+ T cells kill autologous cancer cells expressing SCCE.

11. A composition of matter comprising:
purified dendritic cells loaded ex vivo with a purified peptide comprising an antigenic SCCE sequence of at least 12 amino acid residues;
wherein when the purified peptide is contacted with dendritic cells to generate peptide-loaded dendritic cells and the peptide-loaded dendritic cells are contacted with T cells, the peptide-loaded dendritic cells amplify CD4+ T cells (helper T cells) that recognize the SCCE sequence;
wherein the antigenic SCCE sequence is SEQ ID NO:15 (residues 1-23 of SCCE), SEQ ID NO:16 (residues 61-84), SEQ ID NO:17 (residues 143-160), or a fragment thereof that comprises at least 12 consecutive amino acid residues of SEQ ID NO:15, at least 12 consecutive amino acid residues of SEQ ID NO:16, or at least 12 consecutive amino acid residues of SEQ ID NO:17.

12. The composition of matter of claim 11 wherein the peptide can be used with dendritic cells to activate CD4+ T cells from at least two donors with no HLA class II alleles in common.

13. The composition of matter of claim 8 wherein the peptide can be used with dendritic cells to activate CD4+ T cells from at least two donors with no HLA class II alleles in common.

14. The purified peptide of claim 1 wherein the antigenic SCCE sequence is SEQ ID NO:15 or a fragment thereof.

15. The purified peptide of claim 1 wherein the antigenic SCCE sequence is SEQ ID NO:16 or a fragment thereof.

16. The purified peptide of claim 1 wherein the antigenic SCCE sequence is SEQ ID NO:17 or a fragment thereof.