WO2002028414A1 - Compositions and methods for wt1 specific immunotherapy - Google Patents

Compositions and methods for wt1 specific immunotherapy Download PDF

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Publication number
WO2002028414A1
WO2002028414A1 PCT/US2001/031139 US0131139W WO0228414A1 WO 2002028414 A1 WO2002028414 A1 WO 2002028414A1 US 0131139 W US0131139 W US 0131139W WO 0228414 A1 WO0228414 A1 WO 0228414A1
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Prior art keywords
wtl
polypeptide
cells
seq
patient
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PCT/US2001/031139
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French (fr)
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WO2002028414B1 (en
Inventor
Alexander Gaiger
Patricia D. Mcneill
Molly Smithgall
Gus Moulton
Thomas S. Vedvick
Paul R. Sleath
Sally Mossman
Lawrence Evans
A. Gregory Spies
Jeremy Boydston
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Corixa Corporation
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Priority claimed from US09/684,361 external-priority patent/US7115272B1/en
Priority claimed from US09/685,830 external-priority patent/US7329410B1/en
Priority claimed from US09/785,019 external-priority patent/US7144581B2/en
Priority to AU9660801A priority Critical patent/AU9660801A/en
Priority to JP2002532238A priority patent/JP4130359B2/en
Priority to CA2425072A priority patent/CA2425072C/en
Application filed by Corixa Corporation filed Critical Corixa Corporation
Priority to MXPA03002983A priority patent/MXPA03002983A/en
Priority to EP01977493A priority patent/EP1328287B1/en
Priority to KR1020037004933A priority patent/KR100858231B1/en
Priority to DE60135005T priority patent/DE60135005D1/en
Priority to AU2001296608A priority patent/AU2001296608B2/en
Publication of WO2002028414A1 publication Critical patent/WO2002028414A1/en
Publication of WO2002028414B1 publication Critical patent/WO2002028414B1/en
Priority to HK04109753.4A priority patent/HK1067538A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4748—Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07H—SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS
    • C07H21/00—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
    • C07H21/04—Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/461—Cellular immunotherapy characterised by the cell type used
    • A61K39/4611—T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464452—Transcription factors, e.g. SOX or c-MYC
    • A61K39/464453—Wilms tumor 1 [WT1]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/02—Antineoplastic agents specific for leukemia
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/04—Immunostimulants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/515—Animal cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide

Definitions

  • the present invention relates generally to the immunotherapy of malignant diseases such as leukemia and cancers.
  • the invention is more specifically related to compositions for generating or enhancing an immune response to WTl, and to the use of such compositions for preventing and/or treating malignant diseases.
  • Cancer and leukemia are significant health problems in the United States and throughout the world. Although advances have been made in detection and treatment of such diseases, no vaccine or other universally successful method for prevention or treatment of cancer and leukemia is currently available. Management of the diseases currently relies on a combination of early diagnosis and aggressive treatment, which may include one or more of a variety of treatments such as surgery, radiotherapy, chemotherapy and hormone therapy. The course of treatment for a particular cancer is often selected based on a variety of prognostic parameters, including an analysis of specific tumor markers. However, the use of established markers often leads to a result that is difficult to interpret, and the high mortality continues to be observed in many cancer patients.
  • Immunotherapies have the potential to substantially improve cancer and leukemia treatment and survival. Recent data demonstrate that leukemia can be cured by immunotherapy in the context of bone marrow transplantation (e.g., donor lymphocyte infusions). Such therapies may involve the generation or enhancement of an immune response to a tumor-associated antigen (TAA).
  • TAA tumor-associated antigen
  • relatively few TAAs are known and the generation of an immune response against such antigens has, with rare exception, not been shown to be therapeutically beneficial.
  • this invention provides compositions and methods for the diagnosis and therapy of diseases such as leukemia and cancer.
  • the present invention provides polypeptides comprising an immunogenic portion of a native WTl, or a variant thereof that differs in one or more substitutions, deletions, additions and/or insertions such that the ability of the variant to react with antigen-specific antisera and/or T-cell lines or clones is not substantially diminished.
  • the polypeptide comprises no more than 16 consecutive amino acid residues of a native WTl polypeptide.
  • the polypeptide comprises an immunogenic portion of amino acid residues 1 - 174 of a native WTl polypeptide or a variant thereof, wherein the polypeptide comprises no more than 16 consecutive amino acid residues present within amino acids 175 to 449 of the native WTl polypeptide.
  • the immunogenic portion preferably binds to an MHC class I and/or class II molecule.
  • the polypeptide comprises a sequence selected from the group consisting of (a) sequences recited in any one or more of Tables II - XL VI, (b) variants of the foregoing sequences that differ in one or more substitutions, deletions, additions and/or insertions such that the ability of the variant to react with antigen-specific antisera and/or T-cell lines or clones is not substantially diminished and (c) mimetics of the polypeptides recited above, such that the ability of the mimetic to react with antigen-specific antisera and/or T cell lines or clones is not substantially diminished.
  • the polypeptide comprises a sequence selected from the group consisting of (a) ALLPAVPSL (SEQ ID NO:34), GATLKGVAA (SEQ ID NO:88), CMTWNQMNL (SEQ ID NOs: 49 and 258), SCLESQPTI (SEQ ID NOs: 199 and 296), SCLESQPAI (SEQ ID NO: 198), NLYQMTSQL (SEQ ID NOs: 147 and 284), ALLPAVSSL (SEQ ID NOs: 35 and 255), RMFPNAPYL (SEQ ID NOs: 185 and 293), VLDFAPPGA (SEQ ID NO:241), VLDFAPPGAS (SEQ ID NO:411), (b) variants of the foregoing sequences that differ in one or more substitutions, deletions, additions and/or insertions such that the ability of the variant to react with antigen-specific antisera and/or T-cell lines or clones is not substantially diminished and (c) mimetics of the group consisting of
  • the present invention provides polypeptides comprising a variant of an immunogenic portion of a WTl- protein, wherein the variant differs from the immunogenic portion due to substitutions at between 1 and 3 amino acid positions within the immunogenic portion such that the ability of the variant to react with antigen-specific antisera and/or T-cell lines or clones is enhanced relative to a native WTl protein.
  • the present invention further provides WTl polynucleotides that encode a WTl polypeptide as described above.
  • the present invention provides pharmaceutical compositions and vaccines.
  • Pharmaceutical compositions may comprise a polypeptide or mimetic as described above and/or one or more of (i) a WTl polynucleotide; (ii) an antibody or antigen-binding fragment thereof that specifically binds to a WTl polypeptide; (iii) a T cell that specifically reacts with a WTl polypeptide or (iv) an antigen-presenting cell that expresses a WTl polypeptide, in combination with a pharmaceutically acceptable carrier or excipient.
  • Vaccines comprise a polypeptide as described above and/or one or more of (i) a WTl polynucleotide, (ii) an antigen- presenting cell that expresses a WTl polypeptide or (iii) an anti-idiotypic antibody, and a non-specific immune response enhancer.
  • a WTl polynucleotide e.g., an antigen-presenting cell that expresses a WTl polypeptide or (iii) an anti-idiotypic antibody, and a non-specific immune response enhancer.
  • the immune response enhancer may be an adjuvant.
  • an immune response enhancer enhances a T cell response.
  • the present invention further provides methods for enhancing or inducing an immune response in a patient, comprising administering to a patient a pharmaceutical composition or vaccine as described above.
  • the patient is a human.
  • the present invention further provides methods for inhibiting the development of a malignant disease in a patient, comprising administering to a patient a pharmaceutical composition or vaccine as described above.
  • Malignant diseases include, but are not limited to leukemias (e.g., acute myeloid, acute lymphocytic and chronic myeloid) and cancers (e.g., breast, lung, thyroid or gastrointestinal cancer or a melanoma).
  • leukemias e.g., acute myeloid, acute lymphocytic and chronic myeloid
  • cancers e.g., breast, lung, thyroid or gastrointestinal cancer or a melanoma
  • the patient may, but need not, be afflicted with the malignant disease, and the administration of the pharmaceutical composition or vaccine may inhibit the onset of such a disease, or may inhibit progression and/or metastasis of an existing disease.
  • the present invention further provides, within other aspects, methods for removing cells expressing WTl from bone marrow and/or peripheral blood or fractions thereof, comprising contacting bone marrow, peripheral blood or a fraction of bone marrow or peripheral blood with T cells that specifically react with a WTl polypeptide, wherein the step of contacting is performed under conditions and for a time sufficient to permit the removal of WTl positive cells to less than 10%, preferably less than 5% and more preferably less than 1%, of the number of myeloid or lymphatic cells in the bone marrow, peripheral blood or fraction.
  • Bone marrow, peripheral blood and fractions may be obtained from a patient afflicted with a disease associated with WTl expression, or may be obtained from a human or non-human mammal not afflicted with such a disease.
  • the present invention provides methods for inhibiting the development of a malignant disease in a patient, comprising administering to a patient bone marrow, peripheral blood or a fraction of bone marrow or peripheral blood prepared as described above.
  • Such bone marrow, peripheral blood or fractions may be autologous, or may be derived from a related or unrelated human or non-human animal (e.g., syngeneic or allogeneic).
  • the present invention provides methods for stimulating (or priming) and/or expanding T cells, comprising contacting T cells with a WTl polypeptide under conditions and for a time sufficient to permit the stimulation and/or expansion of T cells.
  • T cells may be autologous, allogeneic, syngeneic or unrelated WTl -specific T cells, and may be stimulated in vitro or in vivo.
  • Expanded T cells may, within certain embodiments, be present within bone marrow, peripheral blood or a fraction of bone marrow or peripheral blood, and may (but need not) be clonal.
  • T cells may be present in a mammal during stimulation and/or expansion.
  • WTl -specific T cells may be used, for example, within donor lymphocyte infusions.
  • T cells prepared as described above.
  • T cells may, within certain embodiments, be autologous, syngeneic or allogeneic.
  • the present invention further provides, within other aspects, methods for monitoring the effectiveness of an immunization or therapy for a malignant disease associated with WTl expression in a patient. Such methods are based on monitoring antibody, CD4+ T cell and/or CD8+ T cell responses in the patient.
  • a method may comprise the steps of: (a) incubating a first biological sample with one or more of: (i) a WTl polypeptide; (ii) a polynucleotide encoding a WTl polypeptide; or (iii) an antigen presenting cell that expresses a WTl polypeptide, wherein the first biological sample is obtained from a patient prior to a therapy or immunization, and wherein the incubation is performed under conditions and for a time sufficient to allow immunocomplexes to form; (b) detecting immunocomplexes formed between the WTl polypeptide and antibodies in the biological sample that specifically bind to the WTl polypeptide; (c) repeating steps (a) and (b) using a second biological sample obtained from the same patient following therapy or immunization; and (d) comparing the number of immunocomplexes detected in the first and second biological samples, and therefrom monitoring the effectiveness of the therapy or immunization in the patient.
  • the step of detecting comprises (a) incubating the immunocomplexes with a detection reagent that is capable of binding to the immunocomplexes, wherein the detection reagent comprises a reporter group, (b) removing unbound detection reagent, and (c) detecting the presence or absence of the reporter group.
  • the detection reagent may comprise, for example, a second antibody, or antigen-binding fragment thereof, capable of binding to the antibodies that specifically bind to the WTl polypeptide or a molecule such as Protein A.
  • a reporter group is bound to the WTl polypeptide, and the step of detecting comprises removing unbound WTl polypeptide and subsequently detecting the presence or absence of the reporter group.
  • methods for monitoring the effectiveness of an immunization or therapy for a malignant disease associated with WTl expression in a patient may comprise the steps of: (a) incubating a first biological sample with one or more of: (i) a WTl polypeptide; (ii) a polynucleotide encoding a WTl polypeptide; or (iii) an antigen presenting cell that expresses a WTl polypeptide, wherein the biological sample comprises CD4+ and/or CD8+ T cells and is obtained from a patient prior to a therapy or immunization, and wherein the incubation is performed under conditions and for a time sufficient to allow specific activation, proliferation and/or lysis of T cells; (b) detecting an amount of activation, proliferation and/or lysis of the T cells; (c) repeating steps (a) and (b) using a second biological sample comprising CD4+ and or CD8+ T cells, wherein the second biological sample is obtained from the same patient following therapy or
  • the present invention further provides methods for inhibiting the development of a malignant disease associated with WTl expression in a patient, comprising the steps of: (a) incubating CD4 + and/or CD8+ T cells isolated from a patient with one or more of: (i) a WTl polypeptide; (ii) a polynucleotide encoding a WTl polypeptide; or (iii) an antigen presenting cell that expresses a WTl polypeptide, such that the T cells proliferate; and (b) administering to the patient an effective amount of the proliferated T cells, and therefrom inhibiting the development of a malignant disease in the patient.
  • the step of incubating the T cells may be repeated one or more times.
  • the present invention provides methods for inhibiting the development of a malignant disease associated with WTl expression in a patient, comprising the steps of: (a) incubating CD4 + and/or CD 8+ T cells isolated from a patient with one or more of: (i) a WTl polypeptide; (ii) a polynucleotide encoding a WTl polypeptide; or (iii) an antigen presenting cell that expresses a WTl polypeptide, such that the T cells proliferate; (b) cloning one or more cells that proliferated; and (c) administering to the patient an effective amount of the cloned T cells.
  • methods for determining the presence or absence of a malignant disease associated with WTl expression in a patient, comprising the steps of: (a) incubating CD4 + and/or CD8+ T cells isolated from a patient with one or more of: (i) a WTl polypeptide; (ii) a polynucleotide encoding a WTl polypeptide; or (iii) an antigen presenting cell that expresses a WTl polypeptide; and (b) detecting the presence or absence of specific activation of the T cells, therefrom determining the presence or absence of a malignant disease associated with WTl expression.
  • the step of detecting comprises detecting the presence or absence of proliferation of the T cells.
  • the present invention provides methods for determining the presence or absence of a malignant disease associated with WTl expression in a patient, comprising the steps of: (a) incubating a biological sample obtained from a patient with one or more of: (i) a WTl polypeptide; (ii) a polynucleotide encoding a WTl polypeptide; or (iii) an antigen presenting cell that expresses a WTl polypeptide, wherein the incubation is performed under conditions and for a time sufficient to allow immunocomplexes to form; and (b) detecting immunocomplexes formed between the WTl polypeptide and antibodies in the biological sample that specifically bind to the WTl polypeptide; and therefrom determining the presence or absence of a malignant disease associated with WTl expression.
  • Figure 1 depicts a comparison of the mouse (MO) and human (HU) WTl protein sequences (SEQ ID NOS: 320 and 319 respectively).
  • Figure 2 is a Western blot illustrating the detection of WTl specific antibodies in patients with hematological malignancy (AML).
  • Lane 1 shows molecular weight markers;
  • lane 2 shows a positive control (WTl positive human leukemia cell line immunoprecipitated with a WTl specific antibody);
  • lane 3 shows a negative control (WTl positive cell line immunoprecipitated with mouse sera);
  • lane 4 shows a WTl positive cell line immunoprecipitated with sera of a patient with AML.
  • the immunoprecipitate was separated by gel electrophoresis and probed with a WTl specific antibody.
  • Figure 3 is a Western blot illustrating the detection of a WTl specific antibody response in B6 mice immunized with TRAMP-C, a WTl positive tumor cell line.
  • Lanes 1, 3 and 5 show molecular weight markers, and lanes 2, 4 and 6 show a WTl specific positive control (N180, Santa Cruz Biotechnology, polypeptide spanning 180 amino acids of the N-terminal region of the WTl protein, migrating on the Western blot at 52 kD).
  • the primary antibody used was WTl 80 in lane 2, sera of non- immunized B6 mice in lane 4 and sera of the immunized B6 mice in lane 6.
  • FIG 4 is a Western blot illustrating the detection of WTl specific antibodies in mice immunized with representative WTl peptides.
  • Lanes 1, 3 and 5 show molecular weight markers and lanes 2, 4 and 6 show a WTl specific positive control (N180, Santa Cruz Biotechnology, polypeptide spanning 180 amino acids of the N-terminal region of the WTl protein, migrating on the Western blot at 52 kD).
  • the primary antibody used was WTl 80 in lane 2, sera of non-immunized B6 mice in lane 4 and sera of the immunized B6 mice in lane 6.
  • Figures 5 A to 5 C are graphs illustrating the stimulation of proliferative T cell responses in mice immunized with representative WTl peptides.
  • Thymidine incorporation assays were performed using one T cell line and two different clones, as indicated, and results were expressed as cpm. Controls indicated on the x axis were no antigen (No Ag) and B6/media; antigens used were p6-22 human (pi), pi 17-139 (p2) or p244-262 human (p3).
  • FIGS. 6A and 6B are histograms illustrating the stimulation of proliferative T cell responses in mice immunized with representative WTl peptides.
  • spleen cells of mice that had been inoculated with Vaccine A or Vaccine B were cultured with medium alone (medium) or spleen cells and medium (B6/no antigen), B6 spleen cells pulsed with the peptides p6-22 (p6), pi 17-139 (pi 17), p244-262 (p244) (Vaccine A; Figure 6A) or p287-301 (p287), p299- 313 (p299), p421-435 (p421) (Vaccine B; Figure 6B) and spleen cells pulsed with an irrelevant control peptide (irrelevant peptide) at 25ug/ml and were assayed after 96hr for proliferation by ( 3 H) thymidine incorporation. Bars represent the stimulation index
  • Figures 7A-7D are histograms illustrating the generation of proliferative T-cell lines and clones specific for pi 17-139 and p6-22.
  • IVS in vitro stimulations
  • the initial three in vitro stimulations (IVS) were carried out using all three peptides of Vaccine A or B, respectively.
  • Subsequent IVS were carried out as single peptide stimulations using only the two relevant peptides pi 17-139 and p6-22.
  • Clones were derived from both the p6-22 and pi 17-139 specific T cell lines, as indicated.
  • T cells were cultured with medium alone (medium) or spleen cells and medium (B6/no antigen), B6 spleen cells pulsed with the peptides p6-22 (p6), pi 17-139 (pi 17) or an irrelevant control peptide (irrelevant peptide) at 25ug/ml and were assayed after 96hr for proliferation by ( 3 H) thymidine incorporation. Bars represent the stimulation index (SI), which is calculated as the mean of the experimental wells divided by the mean of the control (B6 spleen cells with no antigen).
  • SI stimulation index
  • WTl (SEQ ID NO:319) for peptides that have the potential to elicit Th responses.
  • Regions indicated by “A” are AMPHI midpoints of blocks, "R” indicates residues matching the Rothbard/'Taylor motif, “D” indicates residues matching the IAd motif, and 'd' indicates residues matching the IEd motif.
  • Figures 9A and 9B are graphs illustrating the elicitation of WTl peptide- specific CTL in mice immunized with WTl peptides.
  • Figure 9A illustrates the lysis of target cells by allogeneic cell lines and
  • Figure 9B shows the lysis of peptide coated cell lines. In each case, the % lysis (as determined by standard chromium release assays) is shown at three indicated effecto ⁇ target ratios. Results are provided for lymphoma cells (LSTRA and E10), as well as E10 + p235-243 (E10+P235). E10 cells are also referred to herein as EL-4 cells.
  • Figures 10A-10D are graphs illustrating the elicitation of WTl specific CTL, which kill WTl positive tumor cell lines but do not kill WTl negative cell lines, following vaccination of B6 mice with WTl peptide PI 17.
  • Figure 10A illustrates that T-cells of non-immunized B6 mice do not kill WTl positive tumor cell lines.
  • Figure 10B illustrates the lysis of the target cells by allogeneic cell lines.
  • Figures IOC and 10D demonstrate the lysis of WTl positive tumor cell lines, as compared to WTl negative cell lines in two different experiments.
  • Figures IOC and 10D show the lysis of peptide-coated cell lines (WTl negative cell line E10 coated with the relevant WTl peptide PI 17) In each case, the % lysis (as determined by standard chromium release assays) is shown at tliree indicated effecto ⁇ target ratios. Results are provided for lymphoma cells (E10), prostate cancer cells (TRAMP-C), a transformed fibroblast cell line (BLK-SV40), as well as E10+pl 17.
  • E10 lymphoma cells
  • TRAMP-C prostate cancer cells
  • BLK-SV40 transformed fibroblast cell line
  • Figures 1 1A and 11B are histograms illustrating the ability of representative peptide PI 17-139 specific CTL to lyse WTl positive tumor cells.
  • Three weeks after the third immunization spleen cells of mice that had been inoculated with the peptides p235-243 or pi 17-139 were stimulated in vitro with the relevant peptide and tested for ability to lyse targets incubated with WTl peptides as well as WTl positive and negative tumor cells.
  • the bars represent the mean % specific lysis in chromium release assays performed in triplicate with an E:T ratio of 25:1.
  • Figure 11A shows the cytotoxic activity of the p235-243 specific T cell line against the WTl negative cell line EL-4 (EL-4, WTl negative); EL-4 pulsed with the relevant (used for immunization as well as for restimulation) peptide p235-243 (EL-4+p235); EL-4 pulsed with the irrelevant peptides pi 17-139 (EL-4+pl l7), pl26-134 (EL-4+pl26) or pl30- 138 (EL-4+pl30) and the WTl positive tumor cells BLK-SV40 (BLK-SV40, WTl positive) and TRAMP-C (TRAMP-C, WTl positive), as indicated.
  • EL-4 EL-4, WTl negative
  • EL-4 pulsed with the relevant (used for immunization as well as for restimulation) peptide p235-243 EL-4+p235
  • EL-4 pulsed with the irrelevant peptides pi 17-139 EL-4+pl l7
  • Figure 11B shows cytotoxic activity of the pi 17-139 specific T cell line against EL-4; EL-4 pulsed with the relevant peptide PI 17-139 (EL-4+ l l7) and EL-4 pulsed with the irrelevant peptides pl23-131 (EL-4+pl23), or p!28-136 (EL-4+pl28); BLK-SV40 and TRAMP- C, as indicated.
  • Figures 12A and 12B are histograms illustrating the specificity of lysis of WTl positive tumor cells, as demonstrated by cold target inhibition. The bars represent the mean % specific lysis in chromium release assays performed in triplicate with an E:T ratio of 25:1.
  • Figure 12A shows the cytotoxic activity of the pi 17-139 specific T cell line against the WTl negative cell line EL-4 (EL-4, WTl negative); the WTl positive tumor cell line TRAMP-C (TRAMP-C, WTl positive); TRAMP-C cells incubated with a ten-fold excess (compared to the hot target) of EL-4 cells pulsed with the relevant peptide pi 17-139 (TRAMP-C + pi 17 cold target) without 51 Cr labeling and TRAMP-C cells incubated with EL-4 pulsed with an irrelevant peptide without 51 Cr labeling (TRAMP-C + irrelevant cold target), as indicated.
  • Figure 12B shows the cytotoxic activity of the pi 17-139 specific T cell line against the WTl negative cell line EL-4 (EL-4, WTl negative); the WTl positive tumor cell line BLK-SV40 (BLK-SV40, WTl positive); BLK-SV40 cells incubated with the relevant cold target (BLK-SV40 + pi 17 cold target) and BLK-SV40 cells incubated with the irrelevant cold target (BLK- SV40 + irrelevant cold target), as indicated.
  • Figures 13A-13C are histograms depicting an evaluation of the 9mer CTL epitope within pi 17-139.
  • the pi 17-139 tumor specific CTL line was tested against peptides within aal 17-139 containing or lacking an appropriate H-2 b class I binding motif and following restimulation with pi 26- 134 or pi 30-138.
  • the bars represent the mean % specific lysis in chromium release assays performed in triplicate with an E:T ratio of 25:1.
  • Figure 13A shows the cytotoxic activity of the pi 17- 139 specific T cell line against the WTl negative cell line EL-4 (EL-4, WTl negative) and EL-4 cells pulsed with the peptides pi 17-139 (EL-4 + pi 17), pi 19-127 (EL-4 + pi 19), pl20-128 (EL-4 + pl20), pl23-131 (EL-4 + p!23), pl26-134 (EL-4 + p!26), p!28-136 (EL-4 + pl28), and pl30-138 (EL-4 + pl30).
  • Figure 13B shows the cytotoxic activity of the CTL line after restimulation with pl26-134 against the WTl negative cell line EL-4, EL-4 cells pulsed with pi 17-139 (EL-4 + pi 17), pl26-134 (EL-4 + pl26) and the WTl positive tumor cell line TRAMP-C.
  • Figure 13C shows the cytotoxic activity of the CTL line after restimulation with pi 30- 138 against EL-4, EL-4 cells pulsed with pi 17-139 (EL-4 + pi 17), pl30-138 (EL-4 + pl30) and the WTl positive tumor cell line TRAMP-C.
  • Figure 14 depicts serum antibody reactivity to WTl in 63 patients with AML. Reactivity of serum antibody to WTl /N-terminus protein was evaluated by ELISA in patients with AML.
  • the first and second lanes represent the positive and negative controls, respectively.
  • the first and second lanes represent the ositive and negative controls, respectively.
  • Commercially obtained WTl specific antibody WTl 80 was used for the positive control.
  • the next 63 lanes represent results using sera from each individual patient.
  • the OD values depicted were from ELISA using a 1 :500 serum dilution. The figure includes cumulative data from 3 separate experiments.
  • Figure 15 depicts serum antibody reactivity to WTl proteins and control proteins in 2 patients with AML. Reactivity of serum antibody to WTl /full-length, WTlN-terminus, TRX and Ral2 proteins was evaluated by ELISA in 2 patients with AML. The OD values depicted were from ELISA using a 1:500 serum dilution. AML- 1 and AML-2 denote serum from 2 of the individual patients in Figure 1 with demonstrated antibody reactivity to WTl /full-length. The WTl full-length protein was expressed as a fusion protein with Ral2. The WTl /N-terminus protein was expressed as a fusion protein with TRX. The control Ral2 and TRX proteins were purified in a similar manner. The results confirm that the serum antibody reactivity against the WTl fusion proteins is directed against the WTl portions of the protein.
  • Figure 16 depicts serum antibody reactivity to WTl in 81 patients with CML. Reactivity of serum antibody to WTl/full-length protein was evaluated by ELISA in patients with AML. The first and second lanes represent the positive and negative controls, respectively. Commercially obtained WTl specific antibody WTl 80 was used for the positive control. The next 81 lanes represent results using sera from each individual patient. The OD values depicted were from ELISA using a 1:500 serum dilution. The figure includes cumulative data from 3 separate experiments.
  • Figure 17 depicts serum antibody reactivity to WTl proteins and control proteins in 2 patients with CML. Reactivity of serum antibody to WTl /full-length, WTl N-terminus, TRX and Ral2 proteins was evaluated by ELISA in 2 patients with CML. The OD values depicted were from ELISA using a 1 :500 serum dilution. CML- 1 and CML-2 denote serum from 2 of the individual patients in Figure 3 with demonstrated antibody reactivity to WTl /full-length. The WTl /full-length protein was expressed as a fusion protein with Ral2. The WTl/N-terminus protein was expressed
  • Figure 18 provides the characteristics of the recombinant WTl proteins used for serological analysis.
  • Figure 19A-19E is a bar graph depicting the antibody responses in mice elicited by vaccination with different doses of WTl protein.
  • Figure 20 A and 20B is a bar graph of the proliferative T-cell responses in mice immunized with WTl protein.
  • Figure 21 is a photograph of human DC, examined by fluorescent microscopy, expressing WTl following adeno WTl and Vaccinia WTl infection.
  • Figure 22 is a photograph that demonstrates that WTl expression in human DC is reproducible following adeno WTl infection and is not induced by a control Adeno infection.
  • Figure 23 is a graph of an IFN-gamma ELISPOT assay showing that WTl whole gene in vitro priming elicits WTl specific T-cell responses.
  • the present invention is generally directed to compositions and methods for the immunotherapy and diagnosis of malignant diseases.
  • compositions described herein may include WTl polypeptides, WTl polynucleotides, antigen-presenting cells (APC, e.g., dendritic cells) that express a WTl polypeptide, agents such as antibodies that bind to a WTl polypeptide and/or immune system cells (e.g., T cells) specific for WTl.
  • WTl Polypeptides of the present invention generally comprise at least a portion of a Wilms Tumor gene product (WTl) or a variant thereof.
  • Nucleic acid sequences of the subject invention generally comprise a DNA or RNA sequence that encodes all or a portion of such a polypeptide, or that is complementary to such a sequence.
  • Antibodies are generally immune system proteins, or antigen-binding fragments thereof, that are capable of binding to a portion of a WTl polypeptide.
  • T cells that may be employed within such compositions are generally T cells (e.g., CD4 + and/or CD8 + ) that are specific for a WTl polypeptide. Certain methods described herein further employ antigen-presenting cells that express a WTl polypeptide as provided herein.
  • the present invention is based on the discovery that an immune response raised against a Wilms Tumor (WT) gene product (e.g., WTl) can provide prophylactic and/or therapeutic benefit for patients afflicted with malignant diseases characterized by increased WTl gene expression.
  • WT Wilms Tumor
  • diseases include, but are not limited to, leukemias (e.g., acute myeloid leukemia (AML), chronic myeloid leukemia (CML), acute lymphocytic leukemia (ALL) and childhood ALL), as well as many cancers such as lung, breast, thyroid and gastrointestinal cancers and melanomas.
  • the WTl gene was originally identified and isolated on the basis of a cytogenetic deletion at chromosome l lpl3 in patients with Wilms 1 tumor (see Call et al., U.S. Patent No. 5,350,840).
  • the gene consists of 10 exons and encodes a zinc finger transcription factor, and sequences of mouse and human WTl proteins are provided in Figure 1 and SEQ ID NOs: 319 and 320.
  • a WTl polypeptide is a polypeptide that comprises at least an immunogenic portion of a native WTl (i.e., a WTl protein expressed by an organism that is not genetically modified), or a variant thereof, as described herein.
  • a WTl polypeptide may be of any length, provided that it comprises at least an immunogenic portion of a native protein or a variant thereof.
  • a WTl polypeptide may be an oligopeptide (i.e., consisting of a relatively small number of amino acid residues, such as 8-10 residues, joined by peptide bonds), a full length WTl protein (e.g., present within a human or non-human animal, such as a mouse) or a polypeptide of intermediate size.
  • WTl polypeptides that contain a small number of consecutive amino acid residues of a native WTl polypeptide is preferred. Such polypeptides are preferred for certain uses in which the generation of a T cell response is desired.
  • such a WTl polypeptide may contain less than 23, preferably no more than 18, and more preferably no more than 15 consecutive amino acid residues, of a native WTl polypeptide.
  • Polypeptides comprising nine consecutive amino acid residues of a native WTl polypeptide are generally suitable for such purposes. Additional sequences derived from the native protein and/or heterologous sequences may be present within any WTl polypeptide, and such sequences may (but need not) possess further immunogenic or antigenic properties.
  • Polypeptides as provided herein may further be associated (covalently or noncovalently) with other polypeptide or non-polypeptide compounds.
  • an immunogenic portion is a portion of a polypeptide that is recognized (i.e., specifically bound) by a B-cell and/or T-cell surface antigen receptor. Certain preferred immunogenic portions bind to an MHC class I or class II molecule. As used herein, an immunogenic portion is said to "bind to" an MHC class I or class II molecule if such binding is detectable using any assay known in the art. For example, the ability of a polypeptide to bind to MHC class I may be evaluated indirectly by monitoring the ability to promote incorporation of 125 I labeled ⁇ 2-microglobulin ( ⁇ 2m) into MHC class I/ ⁇ 2m/peptide heterotrimeric complexes (see Parker et al., J.
  • immunogenic portions have one or more of the sequences recited within one or more of Tables II - XTV.
  • Representative immunogenic portions include, but are not limited to, RDLNALLPAVPSLGGGG (human WTl residues 6-22; SEQ ID NO:l), PSQASSGQARMFPNAPYLPSCLE (human and mouse WTl residues 117-139; SEQ ID NOs: 2 and 3 respectively), GATLKGVAAGSSSSVKWTE (human WTl residues 244-262; SEQ ID NO:4), GATLKGVAA (human WTl residues 244-252; SEQ ID NO:88), CMTWNQMNL (human and mouse WTl residues 235-243; SEQ ID NOs: 49 and 258 respectively), SCLESQPTI (mouse WTl residues 136-144; SEQ ID NO:296), SCLESQPAI (mouse WTl residues 136-144; SEQ ID NO:296), SCLESQPAI (mouse
  • immunogenic portions are provided herein, and others may generally be identified using well known techniques, such as those summarized in Paul, Fundamental Immunology, 3rd ed., 243-247 (Raven Press, 1993) and references cited therein. Representative techniques for identifying immunogenic portions include screening polypeptides for the ability to react with antigen-specific antisera and/or T- cell lines or clones.
  • An immunogenic portion of a native WTl polypeptide is a portion that reacts with such antisera and/or T-cells at a level that is not substantially less than the reactivity of the full length WTl (e.g., in an ELISA and/or T-cell reactivity assay).
  • an immunogenic portion may react within such assays at a level that is similar to or greater than the reactivity of the full length polypeptide.
  • Such screens may generally be performed using methods well known to those of ordinary skill in the art, such as those described in Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988.
  • immunogenic portions may be identified using computer analysis, such as the Tsites program (see Rothbard and Taylor, EMBO J. 7:93-100, 1988; Deavin et al., Mol. Immunol. 33:145-155, 1996), which searches for peptide motifs that have the potential to elicit Th responses.
  • CTL peptides with motifs appropriate for binding to murine and human class I or class II MHC may be identified according to BIMAS (Parker et al., J. Immunol. 152:163, 1994) and other HLA peptide binding prediction analyses.
  • a peptide may be tested using an HLA A2 transgenic mouse model and/or an in vitro stimulation assay using dendritic cells, fibroblasts or peripheral blood cells.
  • composition may comprise a variant of a native WTl protein.
  • a polypeptide "variant,” as used herein, is a polypeptide that differs from a native polypeptide in one or more substitutions, deletions, additions and/or insertions, such that the immunogenicity of the polypeptide is retained (i.e., the ability of the variant to react with antigen-specific antisera and/or T-cell lines or clones is not substantially diminished relative to the native polypeptide).
  • the ability of a variant to react with antigen-specific antisera and/or T-cell lines or clones may be enhanced or unchanged, relative to the native polypeptide, or may be diminished by less than 50%, and preferably less than 20%, relative to the native polypeptide.
  • Such variants may generally be identified by modifying one of the above polypeptide sequences and evaluating the reactivity of the modified polypeptide with antisera and/or T-cells as described herein. It has been found, within the context of the present invention, that a relatively small number of substitutions (e.g., 1 to 3) within an immunogenic portion of a WTl polypeptide may serve to enhance the ability of the polypeptide to elicit an immune response.
  • Suitable substitutions may generally be identified by using computer programs, as described above, and the effect confirmed based on the reactivity of the modified polypeptide with antisera and/or T-cells as described herein. Accordingly, within certain preferred embodiments, a WTl polypeptide comprises a variant in which 1 to 3 amino acid resides within an immunogenic portion are substituted such that the ability to react with antigen-specific antisera and/or T-cell lines or clones is statistically greater than that for the unmodified polypeptide. Such substitutions are preferably located within an MHC binding site of the polypeptide, which may be identified as described above. Preferred substitutions allow increased binding to MHC class I or class II molecules.
  • a "conservative substitution” is one in which an amino acid is substituted for another amino acid that has similar properties, such that one skilled in the art of peptide chemistry would expect the secondary structure and hydropathic nature of the polypeptide to be substantially unchanged.
  • Amino acid substitutions may generally be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues.
  • negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine and valine; glycine and alanine; asparagine and glutamine; and serine, threonine, phenylalanine and tyrosine.
  • amino acids that may represent conservative changes include: (1) ala, pro, gly, glu, asp, gin, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala, phe; (4) lys, arg, his; and (5) phe, tyr, tip, his.
  • a variant may also, or alternatively, contain nonconservative changes.
  • Variants may also (or alternatively) be modified by, for example, the deletion or addition of amino acids that have minimal influence on the immunogenicity, secondary structure and hydropathic nature of the polypeptide.
  • a variant polypeptide of the WTl N-terminus (amino acids 1-249) is constructed, wherein the variant polypeptide is capable of binding to an antibody that recognizes full-length WTl and or WTl N-terminus polypeptide.
  • an antibody is anti WTl antibody WTl 80 (Santa Cruz Biotechnology, Inc., Santa Cruz, CA).
  • WTl polypeptides may be conjugated to a signal (or leader) sequence at the N-terminal end of the protein which co-translationally or post- translationally directs transfer of the protein.
  • a polypeptide may also, or alternatively, be conjugated to a linker or other sequence for ease of synthesis, purification or identification of the polypeptide (e.g., poly-His), or to enhance binding of the polypeptide to a solid support.
  • a polypeptide may be conjugated to an immunoglobulin Fc region.
  • WTl polypeptides may be prepared using any of a variety of well known techniques.
  • Recombinant polypeptides encoded by a WTl polynucleotide as described herein may be readily prepared from the polynucleotide.
  • any of a variety of expression vectors known to those of ordinary skill in the art may be employed to express recombinant WTl polypeptides.
  • Expression may be achieved in any appropriate host cell that has been transformed or transfected with an expression vector containing a DNA molecule that encodes a recombinant polypeptide.
  • Suitable host cells include prokaryotes, yeast and higher eukaryotic cells.
  • the host cells employed are E. coli, yeast or a mammalian cell line such as COS or CHO.
  • Supernatants from suitable host/vector systems which secrete recombinant protein or polypeptide into culture media may be first concentrated using a commercially available filter. The concentrate may then be applied to a suitable purification matrix such as an affinity matrix or an ion exchange resin. Finally, one or more reverse phase HPLC steps can be employed to further purify a recombinant polypeptide.
  • a suitable purification matrix such as an affinity matrix or an ion exchange resin.
  • one or more reverse phase HPLC steps can be employed to further purify a recombinant polypeptide.
  • Such techniques may be used to prepare native polypeptides or variants thereof. For example, polynucleotides that encode a variant of a native polypeptide may generally be prepared using standard mutagenesis techniques, such as oligonucleotide-directed site-specific mutagenesis, and sections of the DNA sequence may be removed to permit preparation of truncated polypeptides.
  • polypeptides having fewer than about 500 amino acids, preferably fewer than about 100 amino acids, and more preferably fewer than about 50 amino acids may be synthesized.
  • Polypeptides may be synthesized using any of the commercially available solid-phase techniques, such as the Merrifield solid-phase synthesis method, where amino acids are sequentially added to a growing amino acid chain. See Merrifield, J. Am. Chem. Soc. ⁇ 5:2149-2146, 1963.
  • Equipment for automated synthesis of polypeptides is commercially available from suppliers such as Applied BioSystems, Inc. (Foster City, CA), and may be operated according to the manufacturer's instructions.
  • polypeptides and polynucleotides as described herein are isolated.
  • An "isolated" polypeptide or polynucleotide is one that is removed from its original environment.
  • a naturally-occurring protein is isolated if it is separated from some or all of the coexisting materials in the natural system.
  • polypeptides are at least about 90% pure, more preferably at least about 95% pure and most preferably at least about 99% pure.
  • a polynucleotide is considered to be isolated if, for example, it is cloned into a vector that is not a part of the natural environment.
  • the present invention provides mimetics of WTl polypeptides.
  • Such mimetics may comprise amino acids linked to one or more amino acid mimetics (i.e., one or more amino acids within the WTl protein may be replaced by an amino acid mimetic) or may be entirely nonpeptide mimetics.
  • An amino acid mimetic is a compound that is conformationally similar to an amino acid such that it can be substituted for an amino acid within a WTl polypeptide without substantially diminishing the ability to react with antigen-specific antisera and/or T cell lines or clones.
  • a nonpeptide mimetic is a compound that does not contain amino acids, and that has an overall conformation that is similar to a WTl polypeptide such that the ability of the mimetic to react with WTl-specific antisera and/or T cell lines or clones is not substantially diminished relative to the ability of a WTl polypeptide.
  • Such mimetics may be designed based on standard techniques (e.g., nuclear magnetic resonance and computational techniques) that evaluate the three dimensional structure of a peptide sequence. Mimetics may be designed where one or more of the side chain functionalities of the WTl polypeptide are replaced by groups that do not necessarily have the same size or volume, but have similar chemical and/or physical properties which produce similar biological responses. It should be understood that, within embodiments described herein, a mimetic may be substituted for a WTl polypeptide.
  • a polypeptide may be a fusion polypeptide that comprises multiple polypeptides as described herein, or that comprises at least one polypeptide as described herein and an unrelated sequence, such as a known tumor protein.
  • a fusion partner may, for example, assist in providing T helper epitopes (an immunological fusion partner), preferably T helper epitopes recognized by humans, or may assist in expressing the protein (an expression enhancer) at higher yields than the native recombinant protein.
  • Certain preferred fusion partners are both immunological and expression enhancing fusion partners.
  • Other fusion partners may be selected so as to increase the solubility of the polypeptide or to enable the polypeptide to be targeted to desired intracellular compartments.
  • Still further fusion partners include affinity tags, which facilitate purification of the polypeptide.
  • Fusion polypeptides may generally be prepared using standard techniques, including chemical conjugation.
  • a fusion polypeptide is expressed as a recombinant polypeptide, allowing the production of increased levels, relative to a non-fused polypeptide, in an expression system.
  • DNA sequences encoding the polypeptide components may be assembled separately, and ligated into an appropriate expression vector.
  • the 3' end of the DNA sequence encoding one polypeptide component is ligated, with or without a peptide linker, to the 5' end of a DNA sequence encoding the second polypeptide component so that the reading frames of the sequences are in phase. This permits translation into a single fusion polypeptide that retains the biological activity of both component polypeptides.
  • a peptide linker sequence may be employed to separate the first and second polypeptide components by a distance sufficient to ensure that each polypeptide folds into its secondary and tertiary structures.
  • Such a peptide linker sequence is incorporated into the fusion polypeptide using standard techniques well known in the ait.
  • Suitable peptide linker sequences may be chosen based on the following factors: (1) their ability to adopt a flexible extended conformation; (2) their inability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides; and (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes.
  • Preferred peptide linker sequences contain Gly, Asn and Ser residues.
  • linker sequences which may be usefully employed as linkers include those disclosed in Maratea et al., Gene 40:39-46, 1985; Murphy et al., Proc. Natl. Acad. Sci. USA 53:8258-8262, 1986; U.S. Patent No. 4,935,233 and U.S. Patent No. 4,751,180.
  • the linker sequence may generally be from 1 to about 50 amino acids in length. Linker sequences are not required when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference.
  • the ligated DNA sequences are operably linked to suitable transcriptional or translational regulatory elements.
  • the regulatory elements responsible for expression of DNA are located only 5' to the DNA sequence encoding the first polypeptides.
  • stop codons required to end translation and transcription termination signals are only present 3' to the DNA sequence encoding the second polypeptide.
  • the fusion polypeptide can comprise a polypeptide as described herein together with an unrelated immunogenic protein, such as an immunogenic protein capable of eliciting a recall response.
  • an immunogenic protein capable of eliciting a recall response.
  • examples of such proteins include tetanus, tuberculosis and hepatitis proteins (see, for example, Stoute et al. New Engl. J. Med., 336:86-91, 1997).
  • the immunological fusion partner is derived from a Mycobacterium sp., such as a Mycobacterium tuberculosis-derived Ral2 fragment.
  • Ral2 compositions and methods for their use in enhancing the expression and/or immunogenicity of heterologous polynucleotide/polypeptide sequences is described in U.S.
  • Ral2 refers to a polynucleotide region that is a subsequence of a Mycobacterium tuberculosis MTB32A nucleic acid.
  • MTB32A is a serine protease of 32 KD molecular weight encoded by a gene in virulent and avirulent strains of M. tuberculosis.
  • the nucleotide sequence and amino acid sequence of MTB32A have been described (for example, U.S. Patent Application 60/158,585; see also, Skeiky et al, Infection and Immun. (1999) 67:3998-4007, incorporated herein by reference).
  • Ral2 may enhance the immunogenicity of heterologous immunogenic polypeptides with which it is fused.
  • One preferred Ral2 fusion polypeptide comprises a 14 KD C-terminal fragment corresponding to amino acid residues 192 to 323 of MTB32A.
  • Other preferred Ral2 polynucleotides generally comprise at least about 15 consecutive nucleotides, at least about 30 nucleotides, at least about 60 nucleotides, at least about 100 nucleotides, at least about 200 nucleotides, or at least about 300 nucleotides that encode a portion of a Ral2 polypeptide.
  • Ral2 polynucleotides may comprise a native sequence (i.e., an endogenous sequence that encodes a Ral2 polypeptide or a portion thereof) or may comprise a variant of such a sequence.
  • Ral2 polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions such that the biological activity of the encoded fusion polypeptide is not substantially diminished, relative to a fusion polypeptide comprising a native Ral2 polypeptide.
  • Variants preferably exhibit at least about 70% identity, more preferably at least about 80% identity and most preferably at least about 90%) identity to a polynucleotide sequence that encodes a native Ral2 polypeptide or a portion thereof.
  • an immunological fusion partner is derived from protein D, a surface protein of the gram-negative bacterium Haemophilus influenza B (WO 91/18926).
  • a protein D derivative comprises approximately the first third of the protein (e.g., the first N-terminal 100-110 amino acids), and a protein D derivative may be lipidated.
  • the first 109 residues of a Lipoprotein D fusion partner is included on the N-terminus to provide the polypeptide with additional exogenous T-cell epitopes and to increase the expression level in E. coli (thus functioning as an expression enhancer).
  • the lipid tail ensures optimal presentation of the antigen to antigen presenting cells.
  • Other fusion partners include the non-structural protein from influenzae virus, NS1 (hemaglutinin). Typically, the N-terminal 81 amino acids are used, although different fragments that include T-helper epitopes may be used.
  • the immunological fusion partner is the protein known as LYTA, or a portion thereof (preferably a C-terminal portion).
  • LYTA is derived from Streptococcus pneumoniae, which synthesizes an N-acetyl-L-alanine amidase known as amidase LYTA (encoded by the LytA gene; Gene 43:265-292, 1986).
  • LYTA is an autolysin that specifically degrades certain bonds in the peptidoglycan backbone.
  • the C-terminal domain of the LYTA protein is responsible for the affinity to the choline or to some choline analogues such as DEAE. This property has been exploited for the development of E.
  • coli C-LYTA expressing plasmids useful for expression of fusion proteins. Purification of hybrid proteins containing the C-LYTA fragment at the amino terminus has been described (see Biotechnology 10:195-198, 1992). Within a preferred embodiment, a repeat portion of LYTA may be incorporated into a fusion polypeptide. A repeat portion is found in the C-terminal region starting at residue 178. A particularly preferred repeat portion incorporates residues 188-305.
  • Yet another illustrative embodiment involves fusion polypeptides, and the polynucleotides encoding them, wherein the fusion partner comprises a targeting signal capable of directing a polypeptide to the endosomal/lysosomal compartment, as described in U.S. Patent No. 5,633,234.
  • An immunogenic polypeptide of the invention when fused with this targeting signal, will associate more efficiently with MHC class II molecules and thereby provide enhanced in vivo stimulation of CD4 T-cells specific for the polypeptide.
  • the invention provides truncated forms of WTl polypeptides that can be recombinantly expressed in E. coli without the addition of a fusion partner.
  • Examples of these truncated forms are shown in SEQ ID NOs:342-346, and are encoded by polynucleotides shown in SEQ ID NOs:337-341.
  • the first 76 amino acids of WTl can be fused to the C-terminus of the protein, creating a recombinant protein that is easier to express in E. coli.
  • Other hosts in addition to E. coli can also be used, such as, for example, B. megaterium.
  • the protein can further be prepared without a histidine tag.
  • different subunits can be made and fused together in an order which differs from that of native WTl.
  • fusions can be made with, for example, Ral2.
  • Exemplary fusion proteins are shown in SEQ ID NOs: 332- 336 and can be encoded by polynucleotides shown in SEQ ID NOs: 327-331.
  • any polynucleotide that encodes a WTl polypeptide as described herein is a WTl polynucleotide encompassed by the present invention.
  • Such polynucleotides may be single-stranded (coding or antisense) or double-stranded, and may be DNA (genomic, cDNA or synthetic) or RNA molecules. Additional coding or non-coding sequences may, but need not, be present within a polynucleotide of the present invention, and a polynucleotide may, but need not, be linked to other molecules and/or support materials.
  • WTl polynucleotides may encode a native WTl protein, or may encode a variant of WTl as described herein.
  • Polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions such that the immunogenicity of the encoded polypeptide is not diminished, relative to a native WTl protein. The effect on the immunogenicity of the encoded polypeptide may generally be assessed as described herein.
  • Preferred variants contain nucleotide substitutions, deletions, insertions and/or additions at no more than 20%, preferably at no more than 10%, of the nucleotide positions that encode an immunogenic portion of a native WTl sequence.
  • Certain variants are substantially homologous to a native gene, or a portion thereof.
  • Such polynucleotide variants are capable of hybridizing under moderately stringent conditions to a naturally occurring DNA sequence encoding a WTl polypeptide (or a complementary sequence).
  • Suitable moderately stringent conditions include prewashing in a solution of 5 X SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at 50°C- 65°C, 5 X SSC, overnight; followed by washing twice at 65°C for 20 minutes with each of 2X, 0.5X and 0JX SSC containing 0.1% SDS).
  • Such hybridizing DNA sequences are also within the scope of this invention.
  • a WTl polynucleotide may be prepared using any of a variety of techniques. For example, a WTl polynucleotide may be amplified from cDNA prepared from cells that express WTl . Such polynucleotides may be amplified via polymerase chain reaction (PCR). For this approach, sequence-specific primers may be designed based on the sequence of the immunogenic portion and may be purchased or synthesized.
  • PCR polymerase chain reaction
  • suitable primers for PCR amplification of a human WTl gene include: first step - PI 18: 1434-1414: 5' GAG AGT CAG ACT TGA AAG CAGT 3' (SEQ ID NO:5) and P135: 5' CTG AGC CTC AGC AAA TGG GC 3' (SEQ ID NO:6); second step - P136: 5' GAG CAT GCA TGG GCT CCG ACG TGC GGG 3' (SEQ ID NO:7) and P137: 5' GGG GTA CCC ACT GAA CGG TCC CCG A 3' (SEQ ID NO:8).
  • Primers for PCR amplification of a mouse WTl gene include: first step - P138: 5' TCC GAG CCG CAC CTC ATG 3' (SEQ ID NO:9) and P139: 5' GCC TGG GAT GCT GGA CTG 3' (SEQ ID NO.J0), second step - P140: 5' GAG CAT GCG ATG GGT TCC GAC GTG CGG 3' (SEQ ID NO:l 1) and P141: 5' GGG GTA CCT CAA AGC GCC ACG TGG AGT TT 3' (SEQ ID NO: 12).
  • WTl polynucleotides may also be prepared by synthesizing oligonucleotide components, and ligating components together to generate the complete polynucleotide. WTl polynucleotides may also be synthesized by any method known in the art, including chemical synthesis (e.g., solid phase phosphoramidite chemical synthesis).
  • RNA molecules may be generated by in vitro or in vivo transcription of DNA sequences encoding a WTl polypeptide, provided that the DNA is incorporated into a vector with a suitable RNA polymerase promoter (such as T7 or SP6). Certain portions may be used to prepare an encoded polypeptide, as described herein.
  • a portion may be administered to a patient such that the encoded polypeptide is generated in vivo (e.g., by transfecting antigen-presenting cells such as dendritic cells with a cDNA construct encoding a WTl polypeptide, and administering the transfected cells to the patient).
  • antigen-presenting cells such as dendritic cells
  • a cDNA construct encoding a WTl polypeptide
  • Polynucleotides that encode a WTl polypeptide may generally be used for production of the polypeptide, in vitro or in vivo.
  • WTl polynucleotides that are complementary to a coding sequence i.e., antisense polynucleotides
  • cDNA constructs that can be transcribed into antisense RNA may also be introduced into cells of tissues to facilitate the production of antisense RNA. Any polynucleotide may be further modified to increase stability in vivo.
  • flanking sequences at the 5' and/or 3' ends Possible modifications include, but are not limited to, the addition of flanking sequences at the 5' and/or 3' ends; the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages in the backbone; and/or the inclusion of nontraditional bases such as inosine, queosine and wybutosine, as well as acetyl- methyl-, thio- and other modified forms of adenine, cytidine, guanine, thymine and uridine.
  • Nucleotide sequences as described herein may be joined to a variety of other nucleotide sequences using established recombinant DNA techniques.
  • a polynucleotide may be cloned into any of a variety of cloning vectors, including plasmids, phagemids, lambda phage derivatives and cosmids.
  • Vectors of particular interest include expression vectors, replication vectors, probe generation vectors and sequencing vectors.
  • a vector will contain an origin of replication functional in at least one organism, convenient restriction endonuclease sites and one or more selectable markers. Other elements will depend upon the desired use, and will be apparent to those of ordinary skill in the art.
  • polynucleotides may be formulated so as to permit entry into a cell of a mammal, and expression therein. Such formulations are particularly useful for therapeutic purposes, as described below.
  • a polynucleotide may be incorporated into a viral vector such as, but not limited to, adenovirus, adeno-associated virus, retrovirus, or vaccinia or other pox virus (e.g., avian pox virus). Techniques for incorporating DNA into such vectors are well known to those of ordinary skill in the art.
  • a retroviral vector may additionally transfer or incorporate a gene for a selectable marker (to aid in the identification or selection of transduced cells) and/or a targeting moiety, such as a gene that encodes a ligand for a receptor on a specific target cell, to render the vector target specific. Targeting may also be accomplished using an antibody, by methods known to those of ordinary skill in the art.
  • cDNA constructs within such a vector may be used, for example, to transfect human or animal cell lines for use in establishing WTl positive tumor models which may be used to perform tumor protection and adoptive immunotherapy experiments to demonstrate tumor or leukemia-growth inhibition or lysis of such cells.
  • colloidal dispersion systems such as macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes.
  • a preferred colloidal system for use as a delivery vehicle in vitro and in vivo is a liposome (i.e., an artificial membrane vesicle). The preparation and use of such systems is well known in the art.
  • the present invention further provides binding agents, such as antibodies and antigen-binding fragments thereof, that specifically bind to a WTl polypeptide.
  • an agent is said to "specifically bind" to a WTl polypeptide if it reacts at a detectable level (within, for example, an ELISA) with a WTl polypeptide, and does not react detectably with unrelated proteins under similar conditions.
  • binding refers to a noncovalent association between two separate molecules such that a "complex" is formed. The ability to bind may be evaluated by, for example, determining a binding constant for the fo ⁇ nation of the complex.
  • the binding constant is the value obtained when the concentration of the complex is divided by the product of the component concentrations.
  • two compounds are said to "bind,” in the context of the present invention, when the binding constant for complex formation exceeds about 10 3 L/mol.
  • the binding constant maybe determined using methods well known in the art.
  • a binding agent is an antibody or an antigen-binding fragment thereof.
  • Certain antibodies are commercially available from, for example, Santa Cruz Biotechnology (Santa Cruz, CA).
  • antibodies may be prepared by any of a variety of techniques known to those of ordinary skill in the art. See, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988.
  • antibodies can be produced by cell culture techniques, including the generation of monoclonal antibodies as described herein, or via transfection of antibody genes into suitable bacterial or mammalian cell hosts, in order to allow for the production of recombinant antibodies.
  • an immunogen comprising the polypeptide is initially injected into any of a wide variety of mammals (e.g., mice, rats, rabbits, sheep or goats).
  • the polypeptides of this invention may serve as the immunogen without modification.
  • a superior immune response may be elicited if the polypeptide is joined to a carrier protein, such as bovine serum albumin or keyhole limpet hemocyanin.
  • the immunogen is injected into the animal host, preferably according to a predetermined schedule incorporating one or more booster immunizations, and the animals are bled periodically.
  • Monoclonal antibodies specific for the antigenic polypeptide of interest may be prepared, for example, using the technique of Kohler and Milstein, Eur. J. Immunol. 6:511-519, 1976, and improvements thereto. Briefly, these methods involve the preparation of immortal cell lines capable of producing antibodies having the desired specificity (i.e., reactivity with the polypeptide of interest). Such cell lines may be produced, for example, from spleen cells obtained from an animal immunized as described above.
  • the spleen cells are then immortalized by, for example, fusion with a myeloma cell fusion partner, preferably one that is syngeneic with the immunized animal.
  • a myeloma cell fusion partner preferably one that is syngeneic with the immunized animal.
  • a variety of fusion techniques may be employed.
  • the spleen cells and myeloma cells may be combined with a nonionic detergent for a few minutes and then plated at low density on a selective medium that supports the growth of hybrid cells, but not myeloma cells.
  • a preferred selection technique uses HAT (hypoxanthine, aminopterin, thymidine) selection. After a sufficient time, usually about 1 to 2 weeks, colonies of hybrids are observed. Single colonies are selected and their culture supematants tested for binding activity against the polypeptide. Hybridomas having high reactivity and specificity are preferred.
  • Monoclonal antibodies may be isolated from the supematants of growing hybridoma colonies.
  • various techniques may be employed to enhance the yield, such as injection of the hybridoma cell line into the peritoneal cavity of a suitable vertebrate host, such as a mouse.
  • Monoclonal antibodies may then be harvested from the ascites fluid or the blood. Contaminants may be removed from the antibodies by conventional techniques, such as chromatography, gel filtration, precipitation, and extraction.
  • the polypeptides of this invention may be used in the purification process in, for example, an affinity chromatography step.
  • the use of antigen-binding fragments of antibodies may be preferred. Such fragments include Fab fragments, which may be prepared using standard techniques.
  • immunoglobulins may be purified from rabbit serum by affinity chromatography on Protein A bead columns (Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988) and digested by papain to yield Fab and Fc fragments.
  • the Fab and Fc fragments may be separated by affinity chromatography on protein A bead columns.
  • Monoclonal antibodies and fragments thereof may be coupled to one or more therapeutic agents. Suitable agents in this regard include radioactive tracers and chemotherapeutic agents, which may be used, for example, to purge autologous bone marrow in vitro).
  • Representative therapeutic agents include radionuclides, differentiation inducers, drugs, toxins, and derivatives thereof.
  • Preferred radionuclides include 90 Y, 123 I, 1 5 I, 131 I, 186 Re, 188 Re, 11 At, and 212 Bi.
  • Preferred drugs include methotrexate, and pyrimidine and purine analogs.
  • Preferred differentiation inducers include phorbol esters and butyric acid.
  • Preferred toxins include ricin, abrin, diptheria toxin, cholera toxin, gelonin, Pseudomonas exotoxin, Shigella toxin, and pokeweed antiviral protein.
  • coupling of radioactive agents may be used to facilitate tracing of metastases or to determine the location of WTl -positive tumors.
  • a therapeutic agent may be coupled (e.g., covalently bonded) to a suitable monoclonal antibody either directly or indirectly (e.g., via a linker group).
  • a direct reaction between an agent and an antibody is possible when each possesses a substituent capable of reacting with the other.
  • a nucleophilic group such as an amino or sulfhydryl group
  • on one may be capable of reacting with a carbonyl- containing group, such as an anhydride or an acid halide, or with an alkyl group containing a good leaving group (e.g., a halide) on the other.
  • a linker group can function as a spacer to distance an antibody from an agent in order to avoid interference with binding capabilities.
  • a linker group can also serve to increase the chemical reactivity of a substituent on an agent or an antibody, and thus increase the coupling efficiency. An increase in chemical reactivity may also facilitate the use of agents, or functional groups on agents, which otherwise would not be possible.
  • a linker group which is cleavable during or upon internalization into a cell.
  • a number of different cleavable linker groups have been described.
  • the mechanisms for the intracellular release of an agent from these linker groups include cleavage by reduction of a disulfide bond (e.g., U.S. Patent No. 4,489,710, to Spitler), by irradiation of a photolabile bond (e.g., U.S. Patent No. 4,625,014, to Senter et al.), by hydrolysis of derivatized amino acid side chains (e.g., U.S. Patent No.
  • multiple molecules of an agent are coupled to one antibody molecule.
  • more than one type of agent may be coupled to one antibody.
  • immunoconjugates with more than one agent may be prepared in a variety of ways.
  • more than one agent may be coupled directly to an antibody molecule, or linkers which provide multiple sites for attachment can be used.
  • a carrier can be used.
  • a carrier may bear the agents in a variety of ways, including covalent bonding either directly or via a linker group.
  • Suitable carriers include proteins such as albumins (e.g., U.S. Patent No. 4,507,234, to Kato et al.), peptides and polysaccharides such as aminodextran (e.g., U.S. Patent No. 4,699,184, to Shih et al).
  • a carrier may also bear an agent by noncovalent bonding or by encapsulation, such as within a liposome vesicle (e.g., U.S. Patent Nos. 4,429,008 and 4,873,088).
  • Carriers specific for radionuclide agents include radiohalogenated small molecules and chelating compounds.
  • U.S. Patent No. 4,735,792 discloses representative radiohalogenated small molecules and their synthesis.
  • a radionuclide chelate may be formed from chelating compounds that include those containing nitrogen and sulfur atoms as the donor atoms for binding the metal, or metal oxide, radionuclide.
  • U.S. Patent No. 4,673,562 to Davison et al.
  • a variety of routes of administration for the antibodies and immunoconjugates may be used. Typically, administration will be intravenous, intramuscular, subcutaneous or in the bed of a resected tumor. It will be evident that the precise dose of the antibody/immunoconjugate will vary depending upon the antibody used, the antigen density on the tumor, and the rate of clearance of the antibody.
  • anti-idiotypic antibodies that mimic an immunogenic portion of WTl. Such antibodies may be raised against an antibody, or antigen-binding fragment thereof, that specifically binds to an immunogenic portion of WTl, using well known teclmiques.
  • Anti-idiotypic antibodies that mimic an immunogenic portion of WTl are those antibodies that bind to an antibody, or antigen- binding fragment thereof, that specifically binds to an immunogenic portion of WTl, as described herein.
  • Immunotherapeutic compositions may also, or alternatively, comprise T cells specific for WTl.
  • T cells may generally be prepared in vitro or ex vivo, using standard procedures.
  • T cells may be present within (or isolated from) bone marrow, peripheral blood or a fraction of bone marrow or peripheral blood of a mammal, such as a patient, using a commercially available cell separation system, such as the CEPRATETM system, available from CellPro Inc., Bothell WA (see also U.S. Patent No. 5,240,856; U.S. Patent No. 5,215,926; WO 89/06280; WO 91/16116 and WO 92/07243).
  • T cells may be derived from related or unrelated humans, non-human animals, cell lines or cultures.
  • T cells may be stimulated with WTl polypeptide, polynucleotide encoding a WTl polypeptide and/or an antigen presenting cell (APC) that expresses a WTl polypeptide.
  • WTl polypeptide or polynucleotide is present within a delivery vehicle, such as a microsphere, to facilitate the generation of antigen-specific T cells.
  • T cells which may be isolated from a patient or a related or unrelated donor by routine techniques (such as by Ficoll/Hypaque density gradient centrifugation of peripheral blood lymphocytes), are incubated with WTl polypeptide.
  • T cells may be incubated in vitro for 2-9 days (typically 4 days) at 37°C with WTl polypeptide (e.g., 5 to 25 ⁇ g/ml) or cells synthesizing a comparable amount of WTl polypeptide. It may be desirable to incubate a separate aliquot of a T cell sample in the absence of WTl polypeptide to serve as a control.
  • T cells are considered to be specific for a WTl polypeptide if the T cells kill target cells coated with a WTl polypeptide or expressing a gene encoding such a polypeptide.
  • T cell specificity may be evaluated using any of a variety of standard techniques. For example, within a chromium release assay or proliferation assay, a stimulation index of more than two fold increase in lysis and/or proliferation, compared to negative controls, indicates T cell specificity. Such assays may be performed, for example, as described in Chen et al., Cancer Res. 54:1065-1010, 1994. Alternatively, detection of the proliferation of T cells may be accomplished by a variety of known techniques.
  • T cell proliferation can be detected by measuring an increased rate of DNA synthesis (e.g., by pulse-labeling cultures of T cells with tritiated thymidine and measuring the amount of tritiated thymidine incorporated into DNA).
  • Other ways to detect T cell proliferation include measuring increases in interleukin-2 (IL-2) production, Ca ⁇ + flux, or dye uptake, such as 3-(4,5-dimethylthiazol-2-yl)-2,5- diphenyl-tetrazolium.
  • synthesis of lymphokines (such as interferon- gamma) can be measured or the relative number of T cells that can respond to a WTl polypeptide may be quantified.
  • WTl polypeptide 200 ng/ml - 100 ⁇ g/ml, preferably 100 ng/ml - 25 ⁇ g/ml
  • WTl specific T cells may be expanded using standard techniques.
  • the T cells are derived from a patient or a related or unrelated donor and are administered to the patient following stimulation and expansion.
  • T cells that have been activated in response to a WTl polypeptide, polynucleotide or WTl -expressing APC may be CD4 + and/or CD8 + .
  • Specific activation of CD4 + or CD8 + T cells may be detected in a variety of ways. Methods for detecting specific T cell activation include detecting the proliferation of T cells, the production of cytokines (e.g., lymphokines), or the generation of cytolytic activity (i.e., generation of cytotoxic T cells specific for WTl).
  • cytokines e.g., lymphokines
  • cytolytic activity i.e., generation of cytotoxic T cells specific for WTl.
  • CD4 + T cells a preferred method for detecting specific T cell activation is the detection of the proliferation of T cells.
  • CD8 + T cells a preferred method for detecting specific T cell activation is the detection of the generation of cytolytic activity.
  • CD4 + or CD8 + T cells that proliferate in response to the WTl polypeptide, polynucleotide or APC can be expanded in number either in vitro or in vivo. Proliferation of such T cells in vitro may be accomplished in a variety of ways.
  • the T cells can be re-exposed to WTl polypeptide, with or without the addition of T cell growth factors, such as interleukin-2, and/or stimulator cells that synthesize a WTl polypeptide.
  • T cell growth factors such as interleukin-2, and/or stimulator cells that synthesize a WTl polypeptide.
  • the addition of stimulator cells is preferred where generating CD8 + T cell responses.
  • T cells can be grown to large numbers in vitro with retention of specificity in response to intermittent restimulation with WTl polypeptide.
  • lymphocytes e.g., greater than 4 x 10 ⁇
  • WTl polypeptide e.g., peptide at 10 ⁇ g/ml
  • tetanus toxoid e.g., 5 ⁇ g/ml
  • the flasks may then be incubated (e.g., 37°C for 7 days).
  • T cells are then harvested and placed in new flasks with 2-3 x l ⁇ 7 irradiated peripheral blood mononuclear cells.
  • WTl polypeptide (e.g., 10 ⁇ g/ml) is added directly.
  • the flasks are incubated at 37°C for 7 days.
  • 2-5 units of interleukin-2 (IL-2) may be added.
  • the T cells may be placed in wells and stimulated with the individual's own EBV transformed B cells coated with the peptide.
  • IL-2 may be added on days 2 and 4 of each cycle. As soon as the cells are shown to be specific cytotoxic T cells, they may be expanded using a 10 day stimulation cycle with higher IL-2 (20 units) on days 2, 4 and 6.
  • one or more T cells that proliferate in the presence of WTl polypeptide can be expanded in number by cloning.
  • Methods for cloning cells are well known in the art, and include limiting dilution.
  • Responder T cells may be purified from the peripheral blood of sensitized patients by density gradient centrifugation and sheep red cell resetting and established in culture by stimulating with the nominal antigen in the presence of irradiated autologous filler cells.
  • WTl polypeptide is used as the antigenic stimulus and autologous peripheral blood lymphocytes (PBL) or lymphoblastoid cell lines (LCL) immortalized by infection with Epstein Barr virus are used as antigen presenting cells.
  • PBL peripheral blood lymphocytes
  • LCL lymphoblastoid cell lines
  • autologous antigen-presenting cells transfected with an expression vector which produces WTl polypeptide may be used as stimulator cells.
  • Established T cell lines may be cloned 2-4 days following antigen stimulation by plating stimulated T cells at a frequency of 0.5 cells per well in 96-well flat-bottom plates with 1 x 10° irradiated PBL or LCL cells and recombinant interleukin-2 (rIL2) (50 U/ml).
  • Wells with established clonal growth may be identified at approximately 2-3 weeks after initial plating and restimulated with appropriate antigen in the presence of autologous antigen-presenting cells, then subsequently expanded by the addition of low doses of rIL2 (10 U/ml) 2-3 days following antigen stimulation.
  • T cell clones may be maintained in 24-well plates by periodic restimulation with antigen and rIL2 approximately every two weeks.
  • allogeneic T-cells may be primed (i.e., sensitized to WTl) in vivo and/or in vitro.
  • Such priming may be achieved by contacting T cells with a WTl polypeptide, a polynucleotide encoding such a polypeptide or a cell producing such a polypeptide under conditions and for a time sufficient to permit the priming of T cells.
  • T cells are considered to be primed if, for example, contact with a WTl polypeptide results in proliferation and/or activation of the T cells, as measured by standard proliferation, chromium release and/or cytokine release assays as described herein.
  • Cells primed in vitro may be employed, for example, within a bone marrow transplantation or as donor lymphocyte infusion.
  • T cells specific for WTl can kill cells that express WTl protein.
  • Introduction of genes encoding T-cell receptor (TCR) chains for WTl are used as a means to quantitatively and qualitatively improve responses to WTl bearing leukemia and cancer cells.
  • Vaccines to increase the number of T cells that can react to WTl positive cells are one method of targeting WTl bearing cells.
  • T cell therapy with T cells specific for WTl is another method.
  • An alternative method is to introduce the TCR chains specific for WTl into T cells or other cells with lytic potential.
  • the TCR alpha and beta chains are cloned out from a WTl specific T cell line and used for adoptive T cell therapy, such as described in WO96/30516, incorporated herein by reference.
  • polypeptides, polynucleotides, antibodies and/or T cells may be incorporated into pharmaceutical compositions or vaccines.
  • a pharmaceutical composition may comprise an antigen-presenting cell (e.g., a dendritic cell) transfected with a WTl polynucleotide such that the antigen presenting cell expresses a WTl polypeptide.
  • Pharmaceutical compositions comprise one or more such compounds or cells and a physiologically acceptable carrier or excipient.
  • Certain vaccines may comprise one or more such compounds or cells and a non-specific immune response enhancer, such as an adjuvant or a liposome (into which the compound is incorporated).
  • compositions and vaccines may additionally contain a delivery system, such as biodegradable microspheres which are disclosed, for example, in U.S. Patent Nos. 4,897,268 and 5,075,109.
  • Pharmaceutical compositions and vaccines within the scope of the present invention may also contain other compounds, which may be biologically active or inactive.
  • pharmaceutical compositions and vaccines are designed to elicit T cell responses specific for a WTl polypeptide in a patient, such as a human.
  • T cell responses may be favored through the use of relatively short polypeptides (e.g., comprising less than 23 consecutive amino acid residues of a native WTl polypeptide, preferably 4-16 consecutive residues, more preferably 8-16 consecutive residues and still more preferably 8-10 consecutive residues.
  • a vaccine may comprise a non-specific immune response enhancer that preferentially enhances a T cell response.
  • the immune response enhancer may enhance the level of a T cell response to a WTl polypeptide by an amount that is proportionally greater than the amount by which an antibody response is enhanced.
  • an immune response enhancer that preferentially enhances a T cell response may enhance a proliferative T cell response by at least two fold, a lytic response by at least 10%, and/or T cell activation by at least two fold compared to WTl-megative control cell lines, while not detectably enhancing an antibody response.
  • the amount by which a T cell or antibody response to a WTl polypeptide is enhanced may generally be determined using any representative technique known in the art, such as the teclmiques provided herein.
  • a pharmaceutical composition or vaccine may contain DNA encoding one or more of the polypeptides as described above, such that the polypeptide is generated in situ.
  • the DNA may be present within any of a variety of delivery systems known to those of ordinaiy skill in the art, including nucleic acid expression systems, bacterial and viral expression systems and mammalian expression systems. Appropriate nucleic acid expression systems contain the necessary DNA, cDNA or RNA sequences for expression in the patient (such as a suitable promoter and terminating signal).
  • Bacterial delivery systems involve the administration of a bacterium (such as Bacillus-Calmette-Guerrin) that expresses an immunogenic portion of the polypeptide on its cell surface.
  • the DNA may be introduced using a viral expression system (e.g., vaccinia or other pox virus, retrovirus, or adenovirus), which may involve the use of a non-pathogenic (defective), replication competent virus.
  • a viral expression system e.g., vaccinia or other pox virus, retrovirus, or adenovirus
  • a non-pathogenic (defective), replication competent virus e.g., vaccinia or other pox virus, retrovirus, or adenovirus
  • a non-pathogenic (defective), replication competent virus e.g., vaccinia or other pox virus, retrovirus, or adenovirus
  • Techniques for incorporating DNA into such expression systems are well known to those of ordinary skill in the art.
  • the DNA may also be "naked,” as described, for example, in Ulmer et al., Science 259:1145-1149, 1993 and reviewed by Cohen, Science 259:1691-1692, 1993.
  • a pharmaceutical composition or vaccine may comprise an antigen-presenting cell that expresses a WTl polypeptide.
  • the antigen presenting cell is preferably an autologous dendritic cell.
  • Such cells may be prepared and transfected using standard techniques, such as those described by Reeves et al., Cancer Res. 56:5612-5611, 1996; Tuting et al., J. Immunol. 750:1139-1147, 1998; and Nair et al., Nature Biotechnol i 6:364-369, 1998).
  • Expression of a WTl polypeptide on the surface of an antigen-presenting cell may be confirmed by in vitro stimulation and standard proliferation as well as chromium release assays, as described herein.
  • compositions of the present invention may be formulated for any appropriate manner of administration, including for example, topical, oral, nasal, intravenous, intracranial, intraperitoneal, subcutaneous or intramuscular administration.
  • parenteral administration such as subcutaneous injection
  • the carrier preferably comprises water, saline, alcohol, a fat, a wax or a buffer.
  • any of the above carriers or a solid carrier such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, glucose, sucrose, and magnesium carbonate, may be employed.
  • Biodegradable microspheres e.g., polylactate polyglycolate
  • formulation as a cream or lotion, using well known components is preferred.
  • compositions may also comprise buffers (e.g., neutral buffered saline or phosphate buffered saline), carbohydrates (e.g., glucose, mannose, sucrose or dextrans), mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, chelating agents such as EDTA or glutathione, adjuvants (e.g., aluminum hydroxide) and/or preservatives.
  • buffers e.g., neutral buffered saline or phosphate buffered saline
  • carbohydrates e.g., glucose, mannose, sucrose or dextrans
  • mannitol proteins
  • proteins polypeptides or amino acids
  • proteins e.glycine
  • antioxidants e.g., antioxidants, chelating agents such as EDTA or glutathione
  • adjuvants e.g., aluminum hydroxide
  • preservatives e.g., aluminum hydroxide
  • compositions comprise a buffer comprising one or more sugars including, but not limited to, trehalose, maltose, sucrose, fructose, and glucose, each at a concentration generally between about 1 and 25%, typically between about 7 and 13 %. In a further embodiment, the concentration is between about 8 and about 12%. In yet a further embodiment the concentration is about 10%.
  • the compositions may comprise ethanolamine; cysteine; or Polysorbate-80, generally at concentrations effective for enhancing the efficacy, stability and/or solubility of the formulation. Any of a variety of non-specific immune response enhancers, such as adjuvants, may be employed in the vaccines of this invention.
  • adjuvants contain a substance designed to protect the antigen from rapid catabolism, such as aluminum hydroxide or mineral oil, and a stimulator of immune responses, such as lipid A, Bortadella pertussis or Mycobacterium tuberculosis derived proteins.
  • Suitable nonspecific immune response enhancers include alum-based adjuvants (e.g., Alhydrogel, Rehydragel, aluminum phosphate, Algammulin, aluminum hydroxide); oil based adjuvants (Freund's adjuvant (FA), Specol, RIBI, TiterMax, Montanide ISA50 or Montanide ISA 720 (Seppic, France); cytokines (e.g., GM-CSF or Flat3 -ligand); microspheres; nonionic block copolymer-based adjuvants; dimethyl dioctadecyl ammoniumbromide (DDA) based adjuvants AS-1, AS-2 (Smith Kline Beecham); Ribi Adjuvant system based adjuvants; QS21 (Aquila); saponin based adjuvants (crude saponin, the saponin Quil A ); muramyl dipeptide (MDP) based adjuvants such as SAF (Syntex
  • Additional illustrative adjuvants for use in the pharmaceutical compositions of the invention include, SAF (Chiron, California, United States), ISCOMS (CSL), MF-59 (Chiron), the SBAS series of adjuvants (e.g., SBAS-2 or SBAS-4, available from SmithKline Beecham, Rixensart, Belgium), Detox (Enhanzyn ® ) (Corixa, Hamilton, MT), RC-529 (Corixa, Hamilton, MT) and other aminoalkyl glucosaminide 4-phosphates (AGPs), such as those described in pending U.S. Patent Application Serial Nos. 08/853,826 and 09/074,720, the disclosures of which are incorporated herein by reference in their entireties, and polyoxyethylene ether adjuvants such as those described in WO 99/52549A1.
  • n 1-50, A is a bond or -C(O)-, R is C]- 5 o alkyl or Phenyl C ⁇ -5 o alkyl.
  • One embodiment of the present invention consists of a vaccine formulation comprising a polyoxyethylene ether of general formula (I), wherein n is between 1 and 50, preferably 4-24, most preferably 9; the R component is C 1 -. 50 , preferably C -C 20 alkyl and most preferably C 12 alkyl, and A is a bond.
  • the concentration of the polyoxyethylene ethers should be in the range 0.1-20%, preferably from OJ-10%, and most preferably in the range OJ-1%.
  • Preferred polyoxyethylene ethers are selected from the following group: polyoxyethylene-9-lauryl ether, polyoxyethylene-9-steoryl ether, polyoxyethylene- 8-steoryl ether, polyoxyethylene-4- lauryl ether, polyoxyethylene-35-lauryl ether, and polyoxyethylene-23-lauryl ether.
  • Polyoxyethylene ethers such as polyoxyethylene lauryl ether are described in the Merck index (12 th edition: entry 7717). These adjuvant molecules are described in WO 99/52549.
  • polyoxyethylene ether according to the general formula (I) above may, if desired, be combined with another adjuvant.
  • a preferred adjuvant combination is preferably with CpG as described in the pending UK patent application GB 9820956.2.
  • immune response enhancers are chosen for their ability to preferentially elicit or enhance a T cell response (e.g., CD4 + and/or CD8 + ) to a WTl polypeptide.
  • Such immune response enhancers are well known in the art, and include (but are not limited to) Montanide ISA50, Seppic MONTANIDE ISA 720, cytokines (e.g., GM-CSF, Flat3 -ligand), microspheres, dimethyl dioctadecyl ammoniumbromide (DDA) based adjuvants, AS-1 (Smith Kline Beecham), AS-2 (Smith Kline Beecham), Ribi Adjuvant system based adjuvants, QS21 (Aquila), saponin based adjuvants (crude saponin, the saponin Quil A), Syntex adjuvant in its microfluidized form (SAF-m), MV, ddMV (Genesis), immune stimulating complex (iscom
  • compositions may comprise adjuvants for eliciting a predominantly Thl -type response.
  • Certain preferred adjuvants for eliciting a predominantly Thl -type response include, for example, a combination of monophosphoryl lipid A, preferably 3-de-O-acylated monophosphoryl lipid A, together with an aluminum salt.
  • MPL adjuvants, such as MPL-SE are available from Corixa Corporation (Seattle, WA; see, for example, US Patent Nos. 4,436,727; 4,877,611 ; 4,866,034 and 4,912,094, incorporated herein in their entirety).
  • CpG-containing oligonucleotides in which the CpG dinucleotide is unmefhylated also induce a predominantly Thl response.
  • Such oligonucleotides are well known and are described, for example, in WO 96/02555, WO 99/33488 and U.S. Patent Nos. 6,008,200 and 5,856,462. Immunostimulatory DNA sequences are also described, for example, by Sato et al., Science 273:352, 1996.
  • Another preferred adjuvant comprises a saponin, such as Quil A, or derivatives thereof, including QS21 and QS7 (Aquila Biopharmaceuticals Inc., Framingham, MA); Escin; Digitonin; or Gypsophila or Chenopodium quinoa saponins .
  • Other preferred formulations include more than one saponin in the adjuvant combinations of the present invention, for example combinations of at least two of the following group comprising QS21, QS7, Quil A, ⁇ - escin, or digitonin.
  • compositions and vaccines described herein may be administered as part of a sustained release formulation (i.e., a formulation such as a capsule or sponge that effects a slow release of compound following administration).
  • a sustained release formulation i.e., a formulation such as a capsule or sponge that effects a slow release of compound following administration.
  • Such formulations may generally be prepared using well known technology and administered by, for example, oral, rectal or subcutaneous implantation, or by implantation at the desired target site.
  • Sustained-release formulations may contain a polypeptide, polynucleotide, antibody or cell dispersed in a carrier matrix and/or contained within a reservoir surrounded by a rate controlling membrane.
  • Carriers for use within such formulations are biocompatible, and may also be biodegradable; preferably the formulation provides a relatively constant level of active component release. The amount of active compound contained within a sustained release formulation depends upon the site of implantation, the rate and expected duration of release and the nature of the condition to be treated or prevented.
  • compositions and vaccines described herein may be used to inhibit the development of malignant diseases (e.g., progressive or metastatic diseases or diseases characterized by small tumor burden such as minimal residual disease).
  • malignant diseases e.g., progressive or metastatic diseases or diseases characterized by small tumor burden such as minimal residual disease.
  • such methods may be used to prevent, delay or treat a disease associated with WTl expression.
  • therapeutic methods provided herein may be used to treat an existing WTl -associated disease, or may be used to prevent or delay the onset of such a disease in a patient who is free of disease or who is afflicted with a disease that is not yet associated with WTl expression.
  • a disease is "associated with WTl expression” if diseased cells (e.g., tumor cells) at some time during the course of the disease generate detectably higher levels of a WTl polypeptide than normal cells of the same tissue. Association of WTl expression with a malignant disease does not require that WTl be present on a tumor. For example, overexpression of WTl may be involved with initiation of a tumor, but the protein expression may subsequently be lost. Alternatively, a malignant disease that is not characterized by an increase in WTl expression may, at a later time, progress to a disease that is characterized by increased WTl expression. Accordingly, any malignant disease in which diseased cells formerly expressed, currently express or are expected to subsequently express increased levels of WTl is considered to be "associated with WTl expression.”
  • Immunotherapy may be performed using any of a variety of techniques, in which compounds or cells provided herein function to remove WTl -expressing cells from a patient. Such removal may take place as a result of enhancing or inducing an immune response in a patient specific for WTl or a cell expressing WTl.
  • WTl -expressing cells may be removed ex vivo (e.g., by treatment of autologous bone marrow, peripheral blood or a fraction of bone marrow or peripheral blood). Fractions of bone marrow or peripheral blood may be obtained using any standard technique in the art.
  • pharmaceutical compositions and vaccines may be administered to a patient.
  • a "patient” refers to any warm-blooded animal, preferably a human.
  • a patient may or may not be afflicted with a malignant disease. Accordingly, the above pharmaceutical compositions and vaccines may be used to prevent the onset of a disease (i.e., prophylactically) or to treat a patient afflicted with a disease (e.g., to prevent or delay progression and/or metastasis of an existing disease).
  • a patient afflicted with a disease may have a minimal residual disease (e.g., a low tumor burden in a leukemia patient in complete or partial remission or a cancer patient following reduction of the tumor burden after surgery radiotherapy and/or chemotherapy).
  • Such a patient may be immunized to inhibit a relapse (i.e., prevent or delay the relapse, or decrease the severity of a relapse).
  • the patient is afflicted with a leukemia (e.g., AML, CML, ALL or childhood ALL), a myelodysplastic syndrome (MDS) or a cancer (e.g., gastrointestinal, lung, thyroid or breast cancer or a melanoma), where the cancer or leukemia is WTl positive (i.e., reacts detectably with an anti-WTl antibody, as provided herein or expresses WTl mRNA at a level detectable by RT-PCR, as described herein) or suffers from an autoimmune disease directed against WTl -expressing cells.
  • a leukemia e.g., AML, CML, ALL or childhood ALL
  • MDS myelodysplastic syndrome
  • a cancer e.g., gastrointestinal, lung, thyroid or breast cancer or a mel
  • kidney cancer such as renal cell carcinoma, or Wilms tumor
  • kidney cancer such as renal cell carcinoma, or Wilms tumor
  • mesothelioma as described in Amin, K.M. et al., Am. J. Pathol. 146(2):344-56 (1995).
  • Harada et al. Mol. Urol 3(4):357-364 (1999) describe WTl gene expression in human testicular germ-cell tumors. Nonomura et al.
  • Hinyokika Kiyo 45(8):593-7 (1999) describe molecular staging of testicular cancer using polymerase chain reaction of the testicular cancer-specific genes.
  • Shimizu et al., Int. J. Gynecol. Pathol. 19(2): 158-63 (2000) describe the immunohistochemical detection of the Wilms' tumor gene (WTl) in epithelial ovarian tumors.
  • WTl Wilms' tumor gene
  • WTl overexpression was also described in desmoplastic small round cell tumors, by Barnoud, R. et al., Am. J. Surg. Pathol. 24(6):830-6 (2000); and Pathol. Res. Pract. 194(10):693-700 (1998). WTl overexpression in glioblastoma and other cancer was described by Menssen, H.D. et al., J. Cancer Res. Clin. Oncol.
  • WTl tumor gene
  • Other diseases showing WTl overexpression include EBV associated diseases, such as Burkitt's lymphoma and nasopharyngeal cancer (Spinsanti P. et al., Leuk.
  • Pan et al. describe in vitro IL-12 treatment of peripheral blood mononuclear cells from patients with leukemia or myelodysplastic syndromes, and reported an increase in cytotoxicity and reduction in WTl gene expression.
  • Patmasiriwat et al. reported WTl and GATA1 expression in myelodysplastic syndrome and acute leukemia.
  • Leukemia 13(3):393-9 (1999) Tamaki et al.
  • the Wilms' tumor gene WTl is a good marker for diagnosis of disease progression of myelodysplastic syndromes. Expression of the Wilms' tumor gene WTl in solid tumors, and its involvement in tumor cell growth, was discussed in relation to gastric cancer, colon cancer, lung cancer, breast cancer cell lines, germ cell tumor cell line, ovarian cancer, the uterine cancer, thyroid cancer cell line, hepatocellular carcinoma, in Oji et al., Jpn. J. Cancer Res. 90(2):194-204 (1999).
  • compositions provided herein may be used alone or in combination with conventional therapeutic regimens such as surgery, irradiation, chemotherapy and/or bone marrow transplantation (autologous, syngeneic, allogeneic or unrelated).
  • binding agents and T cells as provided herein may be used for purging of autologous stem cells. Such purging may be beneficial prior to, for example, bone marrow transplantation or transfusion of blood or components thereof.
  • Binding agents, T cells, antigen presenting cells (APC) and compositions provided herein may further be used for expanding and stimulating (or priming) autologous, allogeneic, syngeneic or unrelated WTl -specific T-cells in vitro and/or in vivo.
  • WTl -specific T cells may be used, for example, within donor lymphocyte infusions.
  • compositions and vaccines may be administered by injection (e.g., intracutaneous, intramuscular, intravenous or subcutaneous), intranasally (e.g., by aspiration) or orally.
  • pharmaceutical compositions or vaccines may be administered locally (by, for example, rectocoloscopy, gastroscopy, videoendoscopy, angiography or other methods known in the art).
  • between 1 and 10 doses may be administered over a 52 week period.
  • 6 doses are administered, at intervals of 1 month, and booster vaccinations may be given periodically thereafter. Alternate protocols may be appropriate for individual patients.
  • a suitable dose is an amount of a compound that, when administered as described above, is capable of promoting an anti-tumor immune response that is at least 10-50% above the basal (i.e., untreated) level.
  • Such response can be monitored by measuring the anti-tumor antibodies in a patient or by vaccine-dependent generation of cytolytic effector cells capable of killing the patient's tumor cells in vitro.
  • Such vaccines should also be capable of causing an immune response that leads to an improved clinical outcome (e.g., more frequent complete or partial remissions, or longer disease-free and/or overall survival) in vaccinated patients as compared to non- vaccinated patients.
  • the amount of each polypeptide present in a dose ranges from about 100 ⁇ g to 5 mg. Suitable dose sizes will vary with the size of the patient, but will typically range from about 0J mL to about 5 mL.
  • an appropriate dosage and treatment regimen provides the active compound(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit.
  • Such a response can be monitored by establishing an improved clinical outcome (e.g., more frequent complete or partial remissions, or longer disease-free and/or overall survival) in treated patients as compared to non-treated patients.
  • Increases in preexisting immune responses to WTl generally correlate with an improved clinical outcome.
  • Such immune responses may generally be evaluated using standard proliferation, cytotoxicity or cytokine assays, which may be performed using samples obtained from a patient before and after treatment.
  • methods for inhibiting the development of a malignant disease associated with WTl expression involve the administration of autologous T cells that have been activated in response to a WTl polypeptide or WT1- expressing APC, as described above.
  • T cells may be CD4 + and/or CD8 + , and may be proliferated as described above.
  • the T cells may be administered to the individual in an amount effective to inhibit the development of a malignant disease. Typically, about
  • T cells/M are administered intravenously, intracavitaiy or in the bed of a resected tumor. It will be evident to those skilled in the art that the number of cells and the frequency of administration will be dependent upon the response of the patient.
  • T cells may be stimulated prior to an autologous bone marrow transplantation. Such stimulation may take place in vivo or in vitro.
  • bone marrow and/or peripheral blood obtained from a patient may be contacted with a WTl polypeptide, a polynucleotide encoding a WTl polypeptide and/or an APC that expresses a WTl polypeptide under conditions and for a time sufficient to permit the stimulation of T cells as described above.
  • Bone marrow, peripheral blood stem cells and/or WTl -specific T cells may then be administered to a patient using standard teclmiques.
  • T cells of a related or unrelated donor may be stimulated prior to a syngeneic or allogeneic (related or unrelated) bone marrow transplantation. Such stimulation may take place in vivo or in vitro.
  • bone marrow and/or peripheral blood (or a fraction of bone marrow or peripheral blood) obtained from a related or unrelated donor may be contacted with a WTl polypeptide, WTl polynucleotide and/or APC that expresses a WTl polypeptide under conditions and for a time sufficient to permit the stimulation of T cells as described above.
  • Bone marrow, peripheral blood stem cells and/or WTl -specific T cells may then be administered to a patient using standard techniques.
  • WTl -specific T cells as described herein may be used to remove cells expressing WTl from autologous bone marrow, peripheral blood or a fraction of bone marrow or peripheral blood (e.g., CD34 + enriched peripheral blood (PB) prior to administration to a patient).
  • Such methods may be performed by contacting bone marrow or PB with such T cells under conditions and for a time sufficient to permit the reduction of WTl expressing cells to less than 10%, preferably less than 5% and more preferably less than 1%, of the total number of myeloid or lymphatic cells in the bone marrow or peripheral blood.
  • Bone marrow or PB may then be administered to a patient using standard techniques.
  • the present invention further provides methods for detecting a malignant disease associated with WTl expression, and for monitoring the effectiveness of an immunization or therapy for such a disease.
  • Such methods are based on the discovery, within the present invention, that an immune response specific for WTl protein can be detected in patients afflicted with such diseases, and that methods which enhance such immune responses may provide a preventive or therapeutic benefit.
  • a patient may be tested for the level of T cells specific for WTl.
  • a biological sample comprising CD4 + and/or CD8 + T cells isolated from a patient is incubated with a WTl polypeptide, a polynucleotide encoding a WTl polypeptide and/or an APC that expresses a WTl polypeptide, and the presence or absence of specific activation of the T cells is detected, as described herein.
  • Suitable biological samples include, but are not limited to, isolated T cells.
  • T cells may be isolated from a patient by routine techniques (such as by Ficoll/Hypaque density gradient centrifugation of peripheral blood lymphocytes).
  • T cells may be incubated in vitro for 2-9 days (typically 4 days) at 37°C with WTl polypeptide (e.g., 5 - 25 ⁇ g/ml). It may be desirable to incubate another aliquot of a T cell sample in the absence of WTl polypeptide to serve as a control.
  • WTl polypeptide e.g., 5 - 25 ⁇ g/ml
  • activation is preferably detected by evaluating proliferation of the T cells.
  • CD8 + T cells activation is preferably detected by cytolytic activity.
  • a level of proliferation that is at least two fold greater and/or a level of cytolytic activity that is at least 20% greater than in disease- free patients indicates the presence of a malignant disease associated with WTl expression.
  • a biological sample obtained from a patient is tested for the level of antibody specific for WTl.
  • the biological sample is incubated with a WTl polypeptide, a polynucleotide encoding a WTl polypeptide and/or an APC that expresses a WTl polypeptide under conditions and for a time sufficient to allow immunocomplexes to form.
  • Immunocomplexes formed between the WTl polypeptide and antibodies in the biological sample that specifically bind to the WTl polypeptide are then detected.
  • a biological sample for use within such methods may be any sample obtained from a patient that would be expected to contain antibodies. Suitable biological samples include blood, sera, ascites, bone marrow, pleural effusion, and cerebrospinal fluid.
  • the biological sample is incubated with the WTl polypeptide in a reaction mixture under conditions and for a time sufficient to permit immunocomplexes to form between the polypeptide and antibodies specific for WTl.
  • a biological sample and WTl polypeptide may be incubated at 4°C for 24-48 hours.
  • the reaction mixture is tested for the presence of immunocomplexes. Detection of immunocomplexes formed between the WTl polypeptide and antibodies present in the biological sample may be accomplished by a variety of known techniques, such as radioimmunoassays (RIA) and enzyme linked immunosorbent assays (ELISA).
  • RIA radioimmunoassays
  • ELISA enzyme linked immunosorbent assays
  • Suitable assays are well known in the art and are amply described in the scientific and patent literature (e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988). Assays that may be used include, but are not limited to, the double monoclonal antibody sandwich immunoassay technique of David et al. (U.S. Patent 4,376,H0); monoclonal-polyclonal antibody sandwich assays (Wide et al., in Kirkham and Hunter, eds., Radioimmunoassay Methods, E. and S. Livingstone, Edinburgh, 1970); the "western blot" method of Gordon et al. (U.S.
  • Patent 4,452,901 immunoprecipitation of labeled ligand (Brown et al., J. Biol. Chem. 255:4980-4983, 1980); enzyme-linked immunosorbent assays as described by, for example, Raines and Ross (J. Biol. Chem. 257:5154-5160, 1982); immunocytochemical techniques, including the use of fluorochromes (Brooks et al, Clin. Exp. Immunol. 39: 477, 1980); and neutralization of activity (Bowen-Pope et al., Proc. Natl. Acad. Sci. USA 5.7:2396-2400, 1984).
  • Other immunoassays include, but are not limited to, those described in U.S. Patent Nos.: 3,817,827; 3,850,752; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; and 4,098,876.
  • WTl polypeptide may either be labeled or unlabeled.
  • Unlabeled WTl polypeptide may be used in agglutination assays or in combination with labeled detection reagents that bind to the immunocomplexes (e.g., anti-immunoglobulin, protein G, protein A or a lectin and secondary antibodies, or antigen-binding fragments thereof, capable of binding to the antibodies that specifically bind to the WTl polypeptide).
  • the reporter group may be any suitable reporter group known in the art, including radioisotopes, fluorescent groups, luminescent groups, enzymes, biotin and dye particles.
  • unlabeled WTl polypeptide is immobilized on a solid support.
  • the solid support may be any material known to those of ordinary skill in the art to which the polypeptide may be attached.
  • the solid support may be a test well in a microtiter plate or a nitrocellulose or other suitable membrane.
  • the support may be a bead or disc, such as glass, fiberglass, latex or a plastic material such as polystyrene or polyvinylchloride.
  • the support may also be a magnetic particle or a fiber optic sensor, such as those disclosed, for example, in U.S. Patent No. 5,359,681.
  • the polypeptide may be immobilized on the solid support using a variety of techniques known to those of skill in the art, which are amply described in the patent and scientific literature.
  • immobilization refers to both noncovalent association, such as adsorption, and covalent attachment (which may be a direct linkage between the antigen and functional groups on the support or may be a linkage by way of a cross-linking agent). Immobilization by adsorption to a well in a microtiter plate or to a membrane is preferred. In such cases, adsorption may be achieved by contacting the WTl polypeptide, in a suitable buffer, with the solid support for a suitable amount of time.
  • the contact time varies with temperature, but is typically between about 1 hour and about 1 day.
  • the remaining protein binding sites on the support are typically blocked. Any suitable blocking agent known to those of ordinary skill in the art, such as bovine serum albumin, Tween 20TM (Sigma Chemical Co., St. Louis, MO), heat-inactivated normal goat serum (NGS), or BLOTTO (buffered solution of nonfat dry milk which also contains a preservative, salts, and an antifoaming agent).
  • the support is then incubated with a biological sample suspected of containing specific antibody.
  • the sample can be applied neat, or, more often, it can be diluted, usually in a buffered solution which contains a small amount (0J%-5.0% by weight) of protein, such as BSA, NGS, or BLOTTO.
  • an appropriate contact time is a period of time that is sufficient to detect the presence of antibody that specifically binds WTl within a sample containing such an antibody.
  • the contact time is sufficient to achieve a level of binding that is at least about 95% of that achieved at equilibrium between bound and unbound antibody.
  • the time necessary to achieve equilibrium may be readily determined by assaying the level of binding that occurs over a period of time. At room temperature, an incubation time of about 30 minutes is generally sufficient.
  • Unbound sample may then be removed by washing the solid support with an appropriate buffer, such as PBS containing 0.1% Tween 20TM.
  • a detection reagent that binds to the immunocomplexes and that comprises a reporter group may then be added.
  • the detection reagent is incubated with the immunocomplex for an amount of time sufficient to detect the bound antibody.
  • An appropriate amount of time may generally be determined by assaying the level of binding that occurs over a period of time.
  • Unbound detection reagent is then removed and bound detection reagent is detected using the reporter group.
  • the method employed for detecting the reporter group depends upon the nature of the reporter group. For radioactive groups, scintillation counting or autoradiographic methods are generally appropriate.
  • Spectroscopic methods may be used to detect dyes, luminescent groups and fluorescent groups.
  • Biotin may be detected using avidin, coupled to a different reporter group (commonly a radioactive or fluorescent group or an enzyme).
  • Enzyme reporter groups e.g., horseradish peroxidase, beta-galactosidase, alkaline phosphatase and glucose oxidase
  • substrate generally for a specific period of time
  • a level of bound detection reagent that is at least two fold greater than background indicates the presence of a malignant disease associated with WTl expression.
  • methods for monitoring the effectiveness of an immunization or therapy involve monitoring changes in the level of antibodies or T cells specific for WTl in the patient.
  • Methods in which antibody levels are monitored may comprise the steps of: (a) incubating a first biological sample, obtained from a patient prior to a therapy or immunization, with a WTl polypeptide, wherein the incubation is performed under conditions and for a time sufficient to allow immunocomplexes to form; (b) detecting immunocomplexes formed between the WTl polypeptide and antibodies in the biological sample that specifically bind to the WTl polypeptide; (c) repeating steps (a) and (b) using a second biological sample taken from the patient following therapy or immunization; and (d) comparing the number of immunocomplexes detected in the first and second biological samples.
  • a polynucleotide encoding a WTl polypeptide, or an APC expressing a WTl polypeptide may be employed in place of the WTl polypeptide.
  • immunocomplexes between the WTl polypeptide encoded by the polynucleotide, or expressed by the APC, and antibodies in the biological sample are detected.
  • Methods in which T cell activation and/or the number of WTl specific precursors are monitored may comprise the steps of: (a) incubating a first biological sample comprising CD4+ and/or CD8+ cells (e.g., bone marrow, peripheral blood or a fraction thereof), obtained from a patient prior to a therapy or immunization, with a WTl polypeptide, wherein the incubation is performed under conditions and for a time sufficient to allow specific activation, proliferation and/or lysis of T cells; (b) detecting an amount of activation, proliferation and/or lysis of the T cells; (c) repeating steps (a) and (b) using a second biological sample comprising CD4+ and/or CD8+ T cells, and taken from the same patient following therapy or immunization; and (d) comparing the amount of activation, proliferation and/or lysis of T cells in the first and second biological samples.
  • a first biological sample comprising CD4+ and/or CD8+ cells (e.g., bone m
  • a biological sample for use within such methods may be any sample obtained from a patient that would be expected to contain antibodies, CD4+ T cells and/or CD8+ T cells. Suitable biological samples include blood, sera, ascites, bone marrow, pleural effusion and cerebrospinal fluid.
  • a first biological sample may be obtained prior to initiation of therapy or immunization or part way through a therapy or vaccination regime.
  • the second biological sample should be obtained in a similar manner, but at a time following additional therapy or immunization.
  • the second biological sample may be obtained at the completion of, or part way through, therapy or immunization, provided that at least a portion of therapy or immunization takes place between the isolation of the first and second biological samples.
  • Incubation and detection steps for both samples may generally be performed as described above.
  • a statistically significant increase in the number of immunocomplexes in the second sample relative to the first sample reflects successful therapy or immunization.
  • EXAMPLE 1 IDENTIFICATION OF AN IMMUNE RESPONSE TO WTl IN PATIENTS WITH HEMATOLOGICAL MALIGNANCIES This Example illustrates the identification of an existent immune response in patients with a hematological malignancy.
  • This Western blot analysis identified potential WTl specific antibodies in patients with hematological malignancy.
  • a representative Western blot showing the results for a patient with AML is shown in Figure 2.
  • a 52 kD protein in the immunoprecipitate generated using the patient sera was recognized by the WTl specific antibody.
  • the 52 kD protein migrated at the same size as the positive control.
  • the Ral2-WTl/full-length fusion region was cloned 3' to a histidine-tag in a histidine-tag modified pET28 vector.
  • the WTl N-terminus region was subcloned into a modified pET28 vector that has a 5' histidine-tag followed by the thioredoxin (TRX)- WTl /N-terminus fusion region followed by a 3' histidine-tag.
  • TRX thioredoxin
  • the WTl/C-terminus coding region was subcloned into a modified pET28 vector without a fusion partner containing only the 5' and 3' histidine-tag, followed by a Thrombin and EK site.
  • BL21 pLysS E. coli (Stratagene, La Jolla, CA) were transformed with the three WTl expression constructs, grown overnight and induced with isopropyl- ⁇ -D- thiogalactoside (IPTG).
  • WTl proteins were purified as follows: Cells were harvested and lysed by incubation in lOmM Tris, pH 8.0 with Complete Protease Inhibitor Tablets (Boehringer Mannheim Biochemicals, Indianapolis, IN) at 37°C followed by repeated rounds of sonication. Inclusion bodies were washed twice with lOmM Tris, pH 8.0.
  • Proteins were then purified by metal chelate affinity chromatography over nickel- nitrilotriacetic acid resin (QIAGEN Inc., Valencia, CA; Hochuli et al, Biologically Active Molecules :217, 1989) followed by chromatography on a Source Q anion exchange resin (Amersham Pharmacia Biotech, Upsala, Sweden). The identity of the WTl proteins was confirmed by N-terminal sequencing.
  • WTl is an internal protein.
  • CTL responses are likely to be the most effective in terms of leukemia therapy and the most toxic arm of immunity. Thus, these data provide evidence that therapeutic vaccines directed against WTl will be able to elicit an immune response to WTl.
  • EXAMPLE 2 INDUCTION OF ANTIBODIES TO WTl IN MICE IMMUNIZED WITH CELL LINES EXPRESSING WTl
  • This Example illustrates the use of cells expressing WTl to induce a WTl specific antibody response in vivo. Detection of existent antibodies to WTl in patients with leukemia strongly implied that it is possible to immunize to WTl protein to elicit immunity to WTl. To test whether immunity to WTl can be generated by vaccination, mice were injected with TRAMP-C, a WTl positive tumor cell line of B6 origin.
  • mice were immunized with 5 x 10 6 TRAMP-C cells subcutaneously and boosted twice with 5 x 10 6 cells at three week intervals.
  • sera were obtained and single cell suspensions of spleens were prepared in RPMI 1640 medium (GIBCO) with 25 ⁇ M ⁇ -2-mercaptoethanol, 200 units of penicillin per ml, lOmM L-glutamine, and 10% fetal bovine serum.
  • peptides were grouped as follows:
  • Group A contained peptides present within the amino terminus portion of WTl (exon 1) and Group B contained peptides present within the carboxy terminus, which contains a four zinc finger region with sequence homology to other DNA-binding proteins.
  • group B p287-301 and p299-313 were derived from exon 7, zinc finger 1, and p421-435 was derived from exon 10, zinc finger IV.
  • B6 mice were immunized with a group of WTl peptides or with a control peptide. Peptides were dissolved in 1ml sterile water for injection, and B6 mice were immunized 3 times at time intervals of three weeks. Adjuvants used were CFA/IFA, GM-CSF, and Montinide. The presence of antibodies specific for WTl was then determined as described in Examples 1 and 2, and proliferative T cell responses were evaluated using a standard thymidine incorporation assay, in which cells were cultured in the presence of antigen and proliferation was evaluated by measuring incorporated radioactivity (Chen et al., Cancer Res. 54: 1065- 1070, 1994). In particular, lymphocytes were cultured in 96-well plates at 2x10 cells per well with 4x10 irradiated (3000 rads) syngeneic spleen cells and the designated peptide.
  • Figures 6A and 6B show the proliferative response observed for each of the three peptides within vaccine A ( Figure 6 A) and vaccine B ( Figure 6B).
  • Vaccine A elicited proliferative T cell responses to the immunizing peptides p6-22 and pi 17-139, with stimulation indices (SI) varying between 3 and 8 (bulk lines).
  • SI stimulation indices
  • This Example illustrates the ability of WTl peptides to elicit CTL immunity.
  • Peptides (9-mers) with motifs appropriate for binding to class I MHC were identified using a BIMAS HLA peptide binding prediction analysis (Parker et al., J. Immunol. 152:163, 1994). Peptides identified within such analyses are shown in Tables II - XLIV. In each of these tables, the score reflects the theoretical binding affinity (half-time of dissociation) of the peptide to the MHC molecule indicated.
  • RMA-S leukemia cell line
  • FCS 1% FCS
  • a total of 10 6 RMA-S cells were added into each well of a 24-well plate and incubated either alone or with the designated peptide (25ug/ml) for 16 hours at 26°C and additional 3 hours at 37°C in complete medium. Cells were then washed three times and stained with fluorescein isothiocyanate-conjugated anti D b or anti-K antibody (PharMingen, San Diego, CA).
  • Labeled cells were washed twice, resuspended and fixed in 500ul of PBS with 1% paraformaldehyde and analyzed for fluorescence intensity in a flow cytometer (Becton-Dickinson FACSCalibur®). The percentage of increase of D b or K b molecules on the surface of the RMA-S cells was measured by increased mean fluorescent intensity of cells incubated with peptide compared with that of cells incubated in medium alone.
  • mice were immunized with the peptides capable of binding to murine class I MHC. Following immunization, spleen cells were stimulated in vitro and tested for the ability to lyse targets incubated with WTl peptides. CTL were evaluated with a standard chromium release assay (Chen et al., Cancer Res. 54:1065-1070, 1994). 10 6 target cells were incubated at 37°C with 150 ⁇ Ci of sodium 51 Cr for 90 minutes, in the presence or absence of specific peptides. Cells were washed three times and resuspended in RPMI with 5% fetal bovine serum.
  • This Example illustrates the ability of a representative WTl polypeptide to elicit CTL immunity capable of killing WTl positive tumor cell lines.
  • PI 17-139 a peptide with motifs appropriate for binding to class I and class II MHC, was identified as described above using TSITES and BIMAS HLA peptide binding prediction analyses.
  • Mice were immunized as described in Example 3. Following immunization, spleen cells were stimulated in vitro and tested for the ability to lyse targets incubated with WTl peptides, as well as WTl positive and negative tumor cells. CTL were evaluated with a standard chromium release assay. The results, presented in Figures 10A-10D, show that PI 17 can elicit WTl specific CTL capable of killing WTl positive tumor cells, whereas no killing of WTl negative cells was observed.
  • CTL lysis demands that the target WTl peptides are endogenously processed and presented in association with tumor cell class I MHC molecules.
  • the above WTl peptide specific CTL were tested for ability to lyse WTl positive versus negative tumor cell lines.
  • CTL specific for p235-243 lysed targets incubated with the p235-243 peptides, but failed to lyse cell lines that expressed WTl proteins ( Figure 11 A).
  • CTL specific for pi 17-139 lysed targets incubated with pi 17-139 peptides and also lysed malignant cells expressing WTl ( Figure 1 IB).
  • E10 lyse WTl negative EL-4
  • Lysis of TRAMP-C by pi 17-139 specific CTL was blocked from 58% to 36%> by EL-4 incubated with the relevant peptide pi 17-139, but not with EL-4 incubated with an irrelevant peptide ( Figure 12A).
  • lysis of BLK-SV40 was blocked from 18% to 0% by EL-4 incubated with the relevant peptide pi 17-139 ( Figure 12B).
  • Results validate that WTl peptide specific CTL specifically kill malignant cells by recognition of processed WTl .
  • the pi 17-139 specific CTL line was restimulated with either pl26-134 or pl30-138. Following restimulation with pl26-134 or pl30-138, both T cell lines demonstrated peptide specific lysis, but only pi 30-138 specific CTL showed lysis of a
  • pl30-138 appears to be the naturally processed epitope.
  • EXAMPLE 6 IDENTIFICATION OF WTl SPECIFIC MRNA IN MOUSE TUMOR CELL LINES This Example illustrates the use of RT-PCR to detect WTl specific mRNA in cells and cell lines.
  • Primers for amplification of WTl in mouse cell lines were: PI 15: 1458- 1478: 5' CCC AGG CTG CAA TAA GAG ATA 3' (forward primer; SEQ ID NO:21); and PI 16: 1767-1787: 5' ATG TTG TGA TGG CGG ACC AAT 3' (reverse primer; SEQ ID NO:22) (see Inoue et al, Blood 88:2261-2218, 1996; Fraizer et al., Blood ⁇ (5:4704-4706, 1995).
  • Beta Actin primers used in the control reactions were: 5' GTG GGG CGC CCC AGG CAC CA 3' (sense primer; SEQ ID NO:23); and 5' GTC CTT AAT GTC ACG CAC GAT TTC 3' (antisense primer; SEQ ID NO:24)
  • Primers for use in amplifying human WTl include: PI 17: 954-974: 5'
  • primers may be: PI 19: 1023-1043: 5' GCT GTC CCA CTT ACA GAT GCA 3' (SEQ ID NO:26); and P120: 1345-1365: 5' TCA AAG CGC CAG CTG GAG TTT 3' (SEQ ID NO:27).
  • Table XLVIII shows the results of WTl PCR analysis of mouse tumor cell lines.
  • (+++) indicates a strong WTl PCR amplification product in the first step RT PCR
  • (+) indicates a WTl amplification product that is detectable by first step WTl RT PCR
  • (+) indicates a product that is detectable only in the second step of WTl RT PCR
  • (-) indicates WTl PCR negative.
  • PCR product was digested with EcoRI restriction enzyme, gel purified and then cloned into pTrx 2H vector (a modified pET28 vector with a Trx fusion on the N-terminal and two His tags surrounding the Trx fusion. After the Trx fusion there exists protease cleavage sites for thrombin and enterokinase).
  • the pTrx2H construct was digested with Stul and EcoRI restriction enzymes. The correct constructs were confirmed by DNA sequence analysis and then transformed into BL21 (DE3) pLys S and BL21 (DE3) CodonPlus expression host cells.
  • EXAMPLE 8 EXPRESSION IN E. COLI OF WTl A His TAG FUSION CONSTRUCTS
  • WTl A The N-terminal open reading frame of WTl (WTl A) was PCR amplified with the following primers: Forward Primer starting at amino acid 2
  • PDM-335 (SEQ ID NO. 345) 5'gaattctcaaagcgccagctggagtttggt 3' Tm 64°C
  • the PCR was performed under the following conditions: lO ⁇ l l OX Pfu buffer l ⁇ l lOmM dNTPs
  • the PCR product was digested with EcoRI restriction enzyme, gel purified and then cloned into pPDM, a modified pET28 vector with a His tag in frame, which had been digested with Eco72I and EcoRI restriction enzymes.
  • the PCR product was also transformed into pTrx 2H vector.
  • the pTrx2H construct was digested with Stul and EcoRI restriction enzymes. The correct constructs were confirmed by DNA sequence analysis and then transformed into BL21 (DE3) pLys S and BL21 (DE3) CodonPlus expression host cells.
  • EXAMPLE 9 EXPRESSION IN E. COLI OF WTl B His TAG FUSION CONSTRUCTS
  • WTl A The truncated open reading frame of WTl (WTl A) was PCR amplified with the following primers: Forward Primer starting at amino acid 250
  • PDM-346 (SEQ ID NO. 346) 5' cacagcacagggtacgagagc 3' Tm 58°C
  • the PCR product was digested with EcoRI restriction enzyme, gel purified and then cloned into pPDM, a modified pET28 vector with a His tag in frame, which had been digested with Eco72I and EcoRI restriction enzymes.
  • the PCR product was also transformed into pTrx 2H vector.
  • the pTrx 2H construct was digested with Stul and EcoRI restriction enzymes. The correct constructs were confirmed by DNA sequence analysis and then transformed into BL21 (DE3) pLys S and BL21 (DE3) CodonPlus expression host cells.
  • SEQ ID NO. 327 is the determined cDNA sequence for Trx_WTl_B
  • SEQ ID NO. 328 is the determined cDNA sequence for Trx_WTl_A
  • SEQ ID NO. 329 is the determined cDNA sequence for Trx WTl
  • SEQ ID NO. 330 is the determined cDNA sequence for WT1_A
  • SEQ ID NO. 331 is the determined cDNA sequence for WT 1_B
  • SEQ ID NO. 332 is the predicted amino acid sequence encoded by SEQ ID No. 327
  • SEQ ID NO. 333 is the predicted amino acid sequence encoded by SEQ ID No. 328
  • SEQ ID NO. 334 is the predicted amino acid sequence encoded by SEQ ID No. 329
  • SEQ ID NO. 335 is the predicted amino acid sequence encoded by SEQ ID No. 330
  • SEQ ID NO. 336 is the predicted amino acid sequence encoded by SEQ ID No. 331
  • PDM-441 (SEQ ID NO. 348) 5' cacgaagaacagtgcctgagcgcattcac 3' Tm 63°C
  • PDM-442 (SEQ ID NO. 349) 5' ccggcgaattcatcagtataaattgtcactgc 3' TM 62°C
  • PDM-443 (SEQ ID NO. 350) 5' caggctttgctgctgaggacgccc 3' Tm 64°C
  • PDM-444 (SEQ ID NO. 351) 5' cacggagaattcatcactggtatggtttctcacc Tm 64°C
  • PDM-445 (SEQ ID NO. 352) 5' cacagcaggaagcacactggtgagaaac 3' Tm 63°C
  • PDM-446 (SEQ ID NO. 353) 5' ggatatctgcagaattctcaaagcgccagc 3' TM 63°C The PCR was performed under the following conditions:
  • the PCR products were digested with EcoRI and cloned into pPDM His
  • PDM-504 (SEQ ID NO. 354) 5' cactccttcatcaaacaggaac 3' Tm 61°C
  • PDM-446 (SEQ ID NO. 355) 5' ggatatctgcagaattctcaaagcgccagc 3' Tm 63 °C
  • the PCR was performed under the following conditions:
  • the PCR product was digested with EcoRI and cloned into pPDM His which had been digested with Eco72I and EcoRI. The sequence was confirmed through sequence analysis and then transformed into BLR pLys S and BLR which is co- transformed with CodonPlus RP.
  • This example was performed to determine the effect of changing proline codon usage on expression.
  • PDM-505 (SEQ ID NO. 356) 5' ggttccgacgtgcgggacctgaacgcactgctg 3 '
  • PDM-506 (SEQ ID NO. 357) 5' ctgccggcagcagtgcgttcaggtcccgcacgtcggaacc 3'
  • PDM-507 (SEQ ID NO. 358) 5' ccggcagttccatccctgggtggcggtggaggctg 3'
  • PDM-508 (SEQ ID NO. 359) 5' cggcagtgcgcagcctccaccgccacccagggatggaa 3 '
  • PDM-509 5' cgcactgccggttagcggtgcagcacagtgggctc 3' PDM-510 (SEQ ID NO. 361) 5' cagaactggagcccactgtgctgcaccgctaac 3 ' 4.
  • PDM-511 SEQ ID NO. 362
  • PDM-512 SEQ ID NO. 363
  • PDM-513 (SEQ ID NO. 364) 5' ggttccctgggtggtccagcacctccgcccgcaacgcc 3 '
  • PDM-514 (SEQ ID NO. 365) 5' ggcggtgggggggcgttgcgggcggaggtgctggaccacc 3 '
  • PDM-515 (SEQ ID NO. 366) 5' cccaccgcctccaccgcccccgcactccttcatcaaacag 3 '
  • PDM-516 (SEQ ID NO. 367) 5' ctaggttcctgtttgatgaaggagtgcgggggcggtgga 3 '
  • PDM-517 (SEQ ID NO. 368) 5' gaacctagctggggtggtgcagaaccgcacgaagaaca 3 '
  • PDM-518 (SEQ ID NO. 369) 5' ctcaggcactgttcttcgtgcggttctgcaccaccccag 3 '
  • PDM-520 (SEQ ID NO. 371) 5' gtgtgatggatatctgcagaattctcagaatgcg 3'
  • oligo pair was separately combined then annealed. The pairs were then ligated together and one ⁇ l of ligation mix was used for PCR conditions below: lO ⁇ l l OX Pfu buffer l ⁇ l lOmM dNTPs 2 ⁇ l lO ⁇ M each oligo
  • SEQ ID NO:337 is the determined cDNA sequence for WTl_Trl
  • SEQ ID NO:338 is the determined cDNA sequence for WTl_Tr2
  • SEQ ID NO:339 is the determined cDNA sequence for WTl_Tr3
  • SEQ ID NO:340 is the determined cDNA sequence for WTl_Tr4
  • SEQ ID NO:341 is the determined cDNA sequence for WT1_C
  • SEQ ID NO:342 is the predicted amino acid sequence encoded by SEQ ID NO:337
  • SEQ ID NO:343 is the predicted amino acid sequence encoded by SEQ ID NO:338
  • SEQ ID NO:344 is the predicted amino acid sequence encoded by SEQ ID NO:339
  • SEQ ID NO:345 is the predicted amino acid sequence encoded by SEQ ID NO:340
  • SEQ ID NO:346 is the predicted amino acid sequence encoded by SEQ ID NO:341
  • the WTl C sequence represents a polynucleotide having the coding regions of TR2, TR3 and TR4.
  • the WTl TR-1 synthetic sequence represents a polynucleotide in which alternative codons for proline were substituted for the native codons, producing a polynucleotide capable of expressing WTl TR-1 in E. coli.
  • the purpose of this example is to analyze the immunogenicity and potential systemic histopathological and toxicological effects of WTl protein immunization in a multiple dose titration in mice.
  • mice with WTl protein The experimental design for immunization of mice with WTl protein is outlined in Table L.
  • Vaccination to WTl protein using MPL-SE as adjuvant in a multiple dose titration study (doses ranging from 25 ⁇ g, lOO ⁇ g to lOOO ⁇ g WTl protein) in female C57/B6 mice elicited a strong WTl -specific antibody response (Figure 19) and cellular T-cell responses (Figure 20).
  • WBC white blood cells
  • RBC red blood cells
  • Hg. hemoglobin
  • HCT hematocrit
  • MCV Mean corpuscular volume
  • MCH mean corpuscular hemoglobin
  • MCHC mean corpuscular hemoglobin concentration
  • Pit. platelets
  • Abs. Absolute
  • Baso basophils
  • Eos eosinophils
  • Abs. Bands: immature neutrophils
  • Polys polymorphonuclear cells
  • Lymph lymphocytes
  • Mono monocytes
  • BUN blood urea nitrogen
  • EXAMPLE 14 ELICITATION OF HUMAN WTl -SPECIFIC T-CELL RESPONSES BY WHOLE GENE IN VITRO
  • DC Dendritic cells
  • monocyte cultures derived from PBMC of normal donors by growth for 4-10 days in RPMI medium containing 10% human serum, 50 ng/ml GMCSF and 30 ng/ml IL-4.
  • DC were infected 16 hours with recombinant WTl -expressing vaccinia virus at an M.O.I, of 5, or for 3 days with recombinant WTl -expressing adenovirus at an M.O.I, of 10 ( Figures 21 and 22).
  • Vaccinia virus was inactivated by UN. irradiation.
  • CD8+ T-cells were isolated by positive selection using magnetic beads, and priming cultures were initiated in 96-well plates.
  • EXAMPLE 15 FORMULATION OF RA12-W ⁇ l FOR INJECTION: USE OF EXCIPIENTS TO STABILIZE
  • LYOPHILIZED PRODUCT This example describes the formulation that allows the complete solubilization of lyophilized Ral2-WT1.
  • Recombinant Ral2-WT1 concentration 0.5 - 1.0 mg/ml; Buffer: 10-20 mM Ethanolamine, pH 10.0; 1.0 - 5.0 mM Cysteine; 0.05 % Tween-80 (Polysorbate-
  • the lyophilized protein with the sugar excipient was found to dissolve significantly more than without the sugar excipient. Analysis by coomassie stained SDS-PAGE showed no signs of remaining solids in the dissolved material.
  • EXAMPLE 16 FORMULATION OF A WTl PROTEIN VACCINE This example describes the induction of WTl -specific immune responses following immunization with WTl protein and 2 different adjuvant formulations.
  • WTl protein in combination with MPL-SE induces a strong Ab and Interferon- ⁇ (IFN- ⁇ ) response to WTl.
  • IFN- ⁇ Interferon- ⁇
  • mice C57BL/6 mice were immunized with 20 ⁇ g rRal2-WTl combined with either MPL-SE or Enhanzyn adjuvants.
  • One group of control mice was immunized with rRal2-WTl without adjuvant and one group was immunized with saline alone.
  • Three intramuscular (IM) immunizations were given, three weeks apart. Spleens and sera were harvested 2 weeks post-final immunization.
  • Sera were analyzed for antibody responses by ELISA on plates coated with Ral2-WT1 fusion, Ral2 or WTl TRX.
  • mice immunized with Ral2-WT1+MPL-SE and Ral2-WT1+Enhanzyn Similar levels of IgG2a and IgGl antibody titers were observed in mice immunized with Ral2-WT1+MPL-SE and Ral2-WT1+Enhanzyn. Mice immunized with rRal2-WTl without adjuvant showed lower levels of IgG2a antibodies.
  • CD4 responses were assessed by measuring Interferon- ⁇ production following stimulation of splenocytes in vitro with rRal2-WTl, rRal2 or with WTl peptides p6, pi 17 and p287. Both adjuvants improved the CD4 responses over mice immunized with rRA12-WTl alone.
  • results indicate that rRA12- WT1+MPL-SE induced a stronger CD4 response than did rRA12-WTl+Enhanzyn.
  • IFN- ⁇ OD readings ranged from 1.4-1.6 in the mice immunized with rRA12- WT1+MPL-SE as compared to 1-1.2 in the mice immunized with rRA12- WTl+Enhanzyn.
  • Peptide responses were only observed against pi 17, and then only in mice immunized with rRal2-WTl+MPL-SE. Strong IFN- ⁇ responses to the positive control, ConA, were observed in all mice. Only responses to ConA were observed in the negative control mice immunized with saline indicating that the responses were specific to rRA12-WTl .
  • the nucleic acid sequence of human WTl was randomly mutated using a polymerase chain reaction method in the presence of 8-oxo dGTP and dPTP Gournal of Molecular Biology 1996; 255:589-603).
  • the complete unspliced human WTl gene is disclosed in SEQ ID NO:380 and the corresponding protein sequence is set forth in SEQ ID NO:404.
  • a splice variant of WTl was used as a template for the PCR reactions and is disclosed in SEQ ID NOs:381 (DNA) and 408 (protein). Conditions were selected so that the frequency of nucleic acid alterations led to a targeted change in the amino acid sequence, usually 5-30% of the PCR product.
  • the mutated PCR product was then amplified in the absence of the nucleotide analogues using the four normal dNTPs.
  • This PCR product was subcloned into mammalian expression vectors and viral vectors for immunization.
  • This library therefore, contains a mixed population of randomly mutated WTl clones. Several clones were selected and sequenced.
  • the mutated WTl variant DNA sequences are disclosed in SEQ ID NOs:377-379 and the predicted amino acid sequences of the variants are set forth in SEQ ID NOs:405-407. These altered sequences, and others from the library, can be used as immunogens to induce stronger T cell responses against WTl protein in cancer cells.
  • a tripartite fusion was constructed using the polymerase chain reaction and synthetic oligonucleotides containing the desired junctions of human lysosomal associated membrane protein- 1 (LAMP-1) and a splice variant of the human WTl sequence.
  • LAMP-1 human lysosomal associated membrane protein- 1
  • the signal peptide of LAMP-1 (base pairs 1-87 of LAMP) was fused to the 5 -prime end of the human WTl open reading frame (1,290 base pairs in length), then the transmembrane and cytoplasmic domain of LAMP-1 (base pairs 1161 to 1281 of LAMP) was fused to the 3-prime end of the WTl sequence.
  • the sequence of the resulting WT1-LAMP construct is set forth in SEQ ID NO:382 (DNA) and SEQ ID NO:409 (protein).
  • the construct was designed so that when it is expressed in eukaryotic cells, the signal peptide directs the protein to the endoplasmic reticulum (ER) where the localization signals in the transmembrane and cytoplasmic domain of LAMP-1 direct transport of the fusion protein to the lysosomal location where peptides are loaded on to Class II MHC molecules.
  • ER endoplasmic reticulum
  • the human ubiquitin open reading frame (SEQ ID NO: 384) was mutated such that the nucleotides encoding the last amino acid encode an alanine instead of a glycine.
  • This mutated open reading frame was cloned in frame just upstream of the first codon of a splice variant of human WTl (SEQ ID NOs:381 and 408, DNA and protein, respectively).
  • the G->A mutation prevents co-translational cleavage of the nacent protein by the proteases that normally process poly-ubiquitin during translation.
  • the DNA and predicted amino acid sequence for the resulting contract are set forth in SEQ ID NOs:385 and 410, respectively.
  • the resulting protein demonstrated decreased cellular cytotoxicity when it was expressed in human cells.
  • a splice variant of human WTl (SEQ ID NO:381) was cloned into an El and E3 deleted adenovirus serotype 5 vector.
  • the expression of the WTl gene is controlled by the CMV promoter mediating high levels of WTl protein expression.
  • Infection of human cells with this reagent leads to a high level of expression of the WTl protein.
  • the antigenic nature of the adenoviral proteins introduced into the host cell during and produced at low levels subsequent to infection can act to increase immune surveillance and immune recognition of WTl as an immunological target.
  • This vector can be also used to generate immune responses against the WTl protein when innoculated into human subjects. If these subjects are positive for WTl expressing tumor cells the immune response could have a theraputic or curative effect on the course of the disease.
  • a splice variant of the full length human WTl gene (SEQ ID NO:381) was cloned into the thymidine kinase locus of the Western Reserve strain of the vaccinia virus using the pSCl 1 shuttle vector.
  • the WTl gene is under the control of a hybrid vaccinia virus promoter that mediates gene expression throughout the course of vaccinia virus infection.
  • This reagent can be used to express the WTl protein in human cells in vivo or in vitro.
  • WTl is a self protein that is overexpressed on some human tumor cells.
  • WTl WTl.
  • expression of the protein in the intracellular compartment by the vaccinia virus vector will allow high level MHC class I presentation and recognition of the WTl protein by CD8+ T cells.
  • Expression of the WTl protein by the vaccinia virus vector will also lead to presentation of WTl peptides in the context of MHC class II and thus to recognition by CD4+ T cells.
  • the uses of this invention include its use as a cancer vaccine. Immunization of human subjects bearing WTl positive tumors could lead to a theraputic or curative response. The expression of WTl within the cell will lead to recognition of the protein by both CD4 and CD8 positive T cells.
  • DC Dendritic cells
  • monocyte cultures derived from PBMC of normal donors by growth for 4-6 days in RPMI medium containing 10% human serum, 50 ng/ml GM-CSF and 30 ng/ml IL-4.
  • DC were infected 16 hours with recombinant WTl -expressing vaccinia virus (described in Example 21) at a multiplicity of infection (MOI) of 5 or for 3 days with recombinat WTl -expressing adenovirus at an MOI of 10.
  • MOI multiplicity of infection
  • Vaccinia virus was inactivated by UN. irradiation.
  • CD8+ T-cells were isolated by negative depletion using magnetic beads, and priming cultures were initiated in 96-well plates.
  • CD8+ T-cell lines could be identified that specifically produced interferon-gamma when stimulated with autologous- WTl expressing dendritic cells or fibroblasts. These lines were cloned and demonstrated to specifically recognize WTl transduced autologous fibroblasts but not EGFP transduced fibroblasts by Elispot assays.
  • WTl Wilms' tumor
  • the advantages of whole gene immunization are that several helper and CTL epitopes can be included in a single vaccine, thus not restricting the vaccine to specific HLA types.
  • the data disclosed herein demonstrate the induction of WTl specific immune responses using whole gene in vitro priming, and that WTl specific CD8+ T-cell clones can be generated. Given that existent immunity to WTl is present in some patients with leukemia and that murine and human WTl are 96% identical at the amino acid level and vaccination to WTl protein, DNA or peptides can elicit WTl specific Ab, and cellular T-cell responses in mice without toxicity to normal tissues in mice, these human in vitro priming experiments provide further validation of WTl as a tumor/leukemia vaccine. Furthermore, the ability to generate WTl specific CD 8+ T-cell clones may lead to the treatment of malignancies associated with WTl overexpression using genetically engineered T-cells.
  • PDM-780 (SEQ ID NO:396) 5' gacgaaagcatatgcactccttcatcaaac 3' Tm
  • PDM-779 (SEQ ID NO:397) 5' cgcgtgaattcatcactgaatgcctctgaag 3' Tm 63°C
  • PCR cycling conditions were used: lO ⁇ l 10X Pfu buffer, l ⁇ l lOmM dNTPs, 2 ⁇ l lO ⁇ M each oligo, 83 ⁇ l sterile water 1.5 ⁇ l Pfu DNA polymerase (Stratagene, La Jolla, CA), 50 ⁇ g DNA (pPDMRal2 WT-1 No His).
  • the reaction was denatured initially at 96°C for 2 minutes, followed by 40 cylces of 96°C for 20 seconds, 62°C for 15 seconds, and 72°C for 1 minute and 40 seconds. This was followed by a final extension of 72°C for 4 minutes.
  • the PCR product was digested with Ndel and EcoRI and cloned into pPDM His (a modified pET28 vector) that had been digested with Ndel and EcoRI.
  • the construct was confirmed through sequence analysis and then transformed into BLR (DE3) pLys S and HMS 174 (DE3) pLys S cells.
  • This construct - pPDM WT-1 E was then digested with Ncol and Xbal and used as the vector backbone for the Ncol and Xbal insert from pPDM Ral2 WT-1 F (see below).
  • the construct was confirmed through sequence analysis and then tranformed into BLR (DE3) pLys S and HMS 174 (DE3) pLys S cells. Protein expression was confirmed by Coomassie stained SDS-PAGE and N-terminal protein sequence analysis.
  • the Ral2 WT-1 reading frame was PCR amplified with the following primers:
  • PDM-777 (SEQ ID NO:398) 5' cgataagcatatgacggccgcgtccgataac 3' Tm 66°C PDM-779 (SEQ ID NO:399) 5' cgcgtgaattcatcactgaatgcctctgaag 3' Tm
  • PCR cycling conditions were used: lO ⁇ l 10X Pfu buffer, l ⁇ l lOmM dNTPs, 2 ⁇ l lO ⁇ M each oligo, 83 ⁇ l sterile water 1.5 ⁇ l Pfu DNA polymerase (Stratagene, La Jolla, CA), 50 ⁇ g DNA (pPDMRal2 WT-1 No His).
  • the reaction was denatured initially at 96°C for 2 minutes, followed by 40 cylces of 96°C for 20 seconds, 58°C for 15 seconds, and 72°C for 3 minutes. This was followed by a final extension of 72°C for 4 minutes.
  • the PCR product was digested with Ndel and cloned into pPDM His that had been digested with Ndel and Eco72I. The sequence was confirmed through sequence analysis and then transformed into BLR (DE3) pLys S and HMS 174 (DE3) pLysS cells. Protein expression was confirmed by Coomassie stained SDS-PAGE and N-terminal protein sequence analysis.
  • the Ral2 WT-1 reading frame was PCR amplified with the following primers: PDM-777 (SEQ ID NO:400) 5' cgataagcatatgacggccgcgtccgataac 3' Tm
  • the WT-1 C reading frame was PCR amplified with the following p ⁇ mers:
  • PDM-780 (SEQ ID NO:402) 5' gacgaaagcatatgcactccttcatcaaac 3' Tm 60°C
  • PDM-778 (SEQ ID NO:403) 5' gtctgcagcggccgctcaaagcgccagc 3' Tm 70°C
  • PCR cycling conditions we ' re used: lO ⁇ l 10X Pfu buffer, l ⁇ l lOmM dNTPs, 2 ⁇ l lO ⁇ M each oligo, 83 ⁇ l sterile water 1.5 ⁇ l Pfu DNA polymerase (Stratagene, La Jolla, CA), 50 ⁇ g DNA (pPDMRal2 WT-1 No His).
  • the reaction was denatured initially at 96°C for 2 minutes, followed by 40 cylces of 96°C for 20 seconds, 62°C for 15 seconds, and 72°C for 2 minutes. This was followed by a final extension of 72°C for 4 minutes.
  • the PCR product was digested with Ndel and cloned into pPDM His that had been digested with Ndel and Eco72I. The sequence was confirmed through sequence analysis and then transformed into BLR (DE3) pLys S and HMS 174 (DE3) pLys S cells. Protein expression was confirmed by Coomassie stained SDS-PAGE and N-terminal protein sequence analysis.
  • Adeno and Vaccinia virus delivery vehicles were used to generate WTl -specific T cell lines.
  • a T cell clone from the line was shown to be specific for WTl and further, the epitope recognized by this clone was identified.
  • DC Dendritic cells
  • monocyte cultures derived from PBMC of normal donors by growth for 4-6 days in RPMI medium containing 10% human serum, 50 ng/ml GM-CSF and 30 ng/ml IL-4.
  • DC were infected 16 hours with recombinant WTl -expressing vaccinia virus at a multiplicity of infection (MOI) of 5 or for 2-3 days with recombinant WTl -expressing adeno viras at an MOI of 3-10.
  • MOI multiplicity of infection
  • Vaccinia virus was inactivated by UN. irradiation.
  • CD 8+ T-cells were isolated by negative depletion using antibodies to CD4, CD14, CD16, CD19 and CD56+ cells, followed by magnetic beads specific for the Fc portion of these Abs.
  • fibroblasts derived from an additional donor (D475), sharing only the HLA-A2 allele with the donor (D349) from which the T-cell clone was established were transduced with WTl .
  • ELISPOT analysis demonstrated recognition of these D475 target cells by the T-cell clone.
  • HLA-A2 negative K562 cells were used as controls for nonspecific IFN- ⁇ release.
  • ELISPOT analysis demonstrated that the T cells recognized the A2 positive K562 cell line, but not the A2 negative K562 cells. Further proof of specificity and HLA-A2 restriction of the recognition was documented by HLA-A2 antibody blocking experiments.
  • WTl epitope 4 truncated WTl retro viral constructs were generated. Donor 475 fibroblasts were then transduced with these constructs. ELISPOT assays demonstrated recognition of D475 fibroblasts transduced with the WTl Trl construct (aa2-aa92), thus demonstrating that the WTl epitope is localized within the first 91 N-terminal amino acids of the WTl protein. To fine map the epitope, 15mer peptides of the WTl protein, overlapping by 11 amino acids, were synthesized.
  • the WTl specific T-cell clone recognized two overlapping 15mer peptides, peptide 9 (QWAPVLDFAPPGASA) (SEQ ID NO: 412) and peptide 10 (VLDFAPPGASAYGSL) (SEQ ID NO: 413).
  • QWAPVLDFAPPGASA QWAPVLDFAPPGASA
  • VLDFAPPGASAYGSL peptide 10
  • shared 9mer and lOmer peptides of the 15mers (5 total) were used to analyse the specificity of the clone.
  • the clone specifically recognized the 9mer, VLDFAPPGA (SEQ ID NO:241), and the lOmer, VLDFAPPGAS (SEQ ID NO:411).
  • T cell receptor (TCR) alpha and beta chains from CD 8+ T cell clones specific for WTl are cloned. Sequence analysis is carried to demonstrate the family origin of the the alpha and beta chains of the TCR. Additionally, unique diversity and joining segments (contributing to the specificity of the response) are identified.
  • Total mRNA from 2 x IO 6 cells from a WTl specific CD8+ T cell clone is isolated using Trizol reagent and cDNA is synthesized using Ready-to-go kits (Pharmacia).
  • a panel of V ⁇ and V ⁇ subtype specific primers are synthesized (based on primer sequences generated by Clontech, Palo Alto, CA) and used in RT-PCR reactions with cDNA generated from each clone. The RT-PCR reactions demonstrate which V ⁇ and V ⁇ sequence is expressed by each clone.

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Abstract

Compositions and methods for the therapy of malignant diseases, such as leukemia and cancer, are disclosed. The compositions comprise one or more of a WT1 polynucleotide, a WT1 polypeptide, an antigen-presenting cell presenting a WT1 polypeptide, an antibody that specifically binds to a WT1 polypeptide; or a T cell that specifically reacts with a WT1 polypeptide. Such compositions may be used, for example, for the prevention and treatment of metastatic diseases.

Description

COMPOSITIONS AND METHODS FOR WTl SPECIFIC IMMUNOTHERAPY
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT This invention was made in part with government support under NIH
SBIR Phase I grant number IR43 CA81752-01A1. The Government may have certain rights in this invention.
BACKGROUND OF THE INVENTION Field of the Invention The present invention relates generally to the immunotherapy of malignant diseases such as leukemia and cancers. The invention is more specifically related to compositions for generating or enhancing an immune response to WTl, and to the use of such compositions for preventing and/or treating malignant diseases.
Description of the Related Art Cancer and leukemia are significant health problems in the United States and throughout the world. Although advances have been made in detection and treatment of such diseases, no vaccine or other universally successful method for prevention or treatment of cancer and leukemia is currently available. Management of the diseases currently relies on a combination of early diagnosis and aggressive treatment, which may include one or more of a variety of treatments such as surgery, radiotherapy, chemotherapy and hormone therapy. The course of treatment for a particular cancer is often selected based on a variety of prognostic parameters, including an analysis of specific tumor markers. However, the use of established markers often leads to a result that is difficult to interpret, and the high mortality continues to be observed in many cancer patients.
Immunotherapies have the potential to substantially improve cancer and leukemia treatment and survival. Recent data demonstrate that leukemia can be cured by immunotherapy in the context of bone marrow transplantation (e.g., donor lymphocyte infusions). Such therapies may involve the generation or enhancement of an immune response to a tumor-associated antigen (TAA). However, to date relatively few TAAs are known and the generation of an immune response against such antigens has, with rare exception, not been shown to be therapeutically beneficial.
Accordingly, there is a need in the art for improved methods for leukemia and cancer prevention and therapy. The present invention fulfills these needs and further provides other related advantages.
BRIEF SUMMARY OF THE INVENTION
Briefly stated, this invention provides compositions and methods for the diagnosis and therapy of diseases such as leukemia and cancer. In one aspect, the present invention provides polypeptides comprising an immunogenic portion of a native WTl, or a variant thereof that differs in one or more substitutions, deletions, additions and/or insertions such that the ability of the variant to react with antigen-specific antisera and/or T-cell lines or clones is not substantially diminished. Within certain embodiments, the polypeptide comprises no more than 16 consecutive amino acid residues of a native WTl polypeptide. Within other embodiments, the polypeptide comprises an immunogenic portion of amino acid residues 1 - 174 of a native WTl polypeptide or a variant thereof, wherein the polypeptide comprises no more than 16 consecutive amino acid residues present within amino acids 175 to 449 of the native WTl polypeptide. The immunogenic portion preferably binds to an MHC class I and/or class II molecule. Within certain embodiments, the polypeptide comprises a sequence selected from the group consisting of (a) sequences recited in any one or more of Tables II - XL VI, (b) variants of the foregoing sequences that differ in one or more substitutions, deletions, additions and/or insertions such that the ability of the variant to react with antigen-specific antisera and/or T-cell lines or clones is not substantially diminished and (c) mimetics of the polypeptides recited above, such that the ability of the mimetic to react with antigen-specific antisera and/or T cell lines or clones is not substantially diminished.
Within other embodiments, the polypeptide comprises a sequence selected from the group consisting of (a) ALLPAVPSL (SEQ ID NO:34), GATLKGVAA (SEQ ID NO:88), CMTWNQMNL (SEQ ID NOs: 49 and 258), SCLESQPTI (SEQ ID NOs: 199 and 296), SCLESQPAI (SEQ ID NO: 198), NLYQMTSQL (SEQ ID NOs: 147 and 284), ALLPAVSSL (SEQ ID NOs: 35 and 255), RMFPNAPYL (SEQ ID NOs: 185 and 293), VLDFAPPGA (SEQ ID NO:241), VLDFAPPGAS (SEQ ID NO:411), (b) variants of the foregoing sequences that differ in one or more substitutions, deletions, additions and/or insertions such that the ability of the variant to react with antigen-specific antisera and/or T-cell lines or clones is not substantially diminished and (c) mimetics of the polypeptides recited above, such that the ability of the mimetic to react with antigen-specific antisera and/or T cell lines or clones is not substantially diminished. Mimetics may comprises amino acids in combination with one or more amino acid mimetics or may be entirely nonpeptide mimetics.
Within further aspects, the present invention provides polypeptides comprising a variant of an immunogenic portion of a WTl- protein, wherein the variant differs from the immunogenic portion due to substitutions at between 1 and 3 amino acid positions within the immunogenic portion such that the ability of the variant to react with antigen-specific antisera and/or T-cell lines or clones is enhanced relative to a native WTl protein.
The present invention further provides WTl polynucleotides that encode a WTl polypeptide as described above. Within other aspects, the present invention provides pharmaceutical compositions and vaccines. Pharmaceutical compositions may comprise a polypeptide or mimetic as described above and/or one or more of (i) a WTl polynucleotide; (ii) an antibody or antigen-binding fragment thereof that specifically binds to a WTl polypeptide; (iii) a T cell that specifically reacts with a WTl polypeptide or (iv) an antigen-presenting cell that expresses a WTl polypeptide, in combination with a pharmaceutically acceptable carrier or excipient. Vaccines comprise a polypeptide as described above and/or one or more of (i) a WTl polynucleotide, (ii) an antigen- presenting cell that expresses a WTl polypeptide or (iii) an anti-idiotypic antibody, and a non-specific immune response enhancer. Within certain embodiments, less than 23 consecutive amino acid residues, preferably less than 17 amino acid residues, of a native WTl polypeptide are present within a WTl polypeptide employed within such pharmaceutical compositions and vaccines. The immune response enhancer may be an adjuvant. Preferably, an immune response enhancer enhances a T cell response.
The present invention further provides methods for enhancing or inducing an immune response in a patient, comprising administering to a patient a pharmaceutical composition or vaccine as described above. In certain embodiments, the patient is a human.
The present invention further provides methods for inhibiting the development of a malignant disease in a patient, comprising administering to a patient a pharmaceutical composition or vaccine as described above. Malignant diseases include, but are not limited to leukemias (e.g., acute myeloid, acute lymphocytic and chronic myeloid) and cancers (e.g., breast, lung, thyroid or gastrointestinal cancer or a melanoma). The patient may, but need not, be afflicted with the malignant disease, and the administration of the pharmaceutical composition or vaccine may inhibit the onset of such a disease, or may inhibit progression and/or metastasis of an existing disease. The present invention further provides, within other aspects, methods for removing cells expressing WTl from bone marrow and/or peripheral blood or fractions thereof, comprising contacting bone marrow, peripheral blood or a fraction of bone marrow or peripheral blood with T cells that specifically react with a WTl polypeptide, wherein the step of contacting is performed under conditions and for a time sufficient to permit the removal of WTl positive cells to less than 10%, preferably less than 5% and more preferably less than 1%, of the number of myeloid or lymphatic cells in the bone marrow, peripheral blood or fraction. Bone marrow, peripheral blood and fractions may be obtained from a patient afflicted with a disease associated with WTl expression, or may be obtained from a human or non-human mammal not afflicted with such a disease. Within related aspects, the present invention provides methods for inhibiting the development of a malignant disease in a patient, comprising administering to a patient bone marrow, peripheral blood or a fraction of bone marrow or peripheral blood prepared as described above. Such bone marrow, peripheral blood or fractions may be autologous, or may be derived from a related or unrelated human or non-human animal (e.g., syngeneic or allogeneic). In other aspects, the present invention provides methods for stimulating (or priming) and/or expanding T cells, comprising contacting T cells with a WTl polypeptide under conditions and for a time sufficient to permit the stimulation and/or expansion of T cells. Such T cells may be autologous, allogeneic, syngeneic or unrelated WTl -specific T cells, and may be stimulated in vitro or in vivo. Expanded T cells may, within certain embodiments, be present within bone marrow, peripheral blood or a fraction of bone marrow or peripheral blood, and may (but need not) be clonal. Within certain embodiments, T cells may be present in a mammal during stimulation and/or expansion. WTl -specific T cells may be used, for example, within donor lymphocyte infusions.
Within related aspects, methods are provided for inhibiting the development of a malignant disease in a patient, comprising administering to a patient T cells prepared as described above. Such T cells may, within certain embodiments, be autologous, syngeneic or allogeneic. The present invention further provides, within other aspects, methods for monitoring the effectiveness of an immunization or therapy for a malignant disease associated with WTl expression in a patient. Such methods are based on monitoring antibody, CD4+ T cell and/or CD8+ T cell responses in the patient. Within certain such aspects, a method may comprise the steps of: (a) incubating a first biological sample with one or more of: (i) a WTl polypeptide; (ii) a polynucleotide encoding a WTl polypeptide; or (iii) an antigen presenting cell that expresses a WTl polypeptide, wherein the first biological sample is obtained from a patient prior to a therapy or immunization, and wherein the incubation is performed under conditions and for a time sufficient to allow immunocomplexes to form; (b) detecting immunocomplexes formed between the WTl polypeptide and antibodies in the biological sample that specifically bind to the WTl polypeptide; (c) repeating steps (a) and (b) using a second biological sample obtained from the same patient following therapy or immunization; and (d) comparing the number of immunocomplexes detected in the first and second biological samples, and therefrom monitoring the effectiveness of the therapy or immunization in the patient. Within certain embodiments of the above methods, the step of detecting comprises (a) incubating the immunocomplexes with a detection reagent that is capable of binding to the immunocomplexes, wherein the detection reagent comprises a reporter group, (b) removing unbound detection reagent, and (c) detecting the presence or absence of the reporter group. The detection reagent may comprise, for example, a second antibody, or antigen-binding fragment thereof, capable of binding to the antibodies that specifically bind to the WTl polypeptide or a molecule such as Protein A. Within other embodiments, a reporter group is bound to the WTl polypeptide, and the step of detecting comprises removing unbound WTl polypeptide and subsequently detecting the presence or absence of the reporter group.
Within further aspects, methods for monitoring the effectiveness of an immunization or therapy for a malignant disease associated with WTl expression in a patient may comprise the steps of: (a) incubating a first biological sample with one or more of: (i) a WTl polypeptide; (ii) a polynucleotide encoding a WTl polypeptide; or (iii) an antigen presenting cell that expresses a WTl polypeptide, wherein the biological sample comprises CD4+ and/or CD8+ T cells and is obtained from a patient prior to a therapy or immunization, and wherein the incubation is performed under conditions and for a time sufficient to allow specific activation, proliferation and/or lysis of T cells; (b) detecting an amount of activation, proliferation and/or lysis of the T cells; (c) repeating steps (a) and (b) using a second biological sample comprising CD4+ and or CD8+ T cells, wherein the second biological sample is obtained from the same patient following therapy or immunization; and (d) comparing the amount of activation, proliferation and/or lysis of T cells in the first and second biological samples, and therefrom monitoring the effectiveness of the therapy or immunization in the patient. The present invention further provides methods for inhibiting the development of a malignant disease associated with WTl expression in a patient, comprising the steps of: (a) incubating CD4+ and/or CD8+ T cells isolated from a patient with one or more of: (i) a WTl polypeptide; (ii) a polynucleotide encoding a WTl polypeptide; or (iii) an antigen presenting cell that expresses a WTl polypeptide, such that the T cells proliferate; and (b) administering to the patient an effective amount of the proliferated T cells, and therefrom inhibiting the development of a malignant disease in the patient. Within certain embodiments, the step of incubating the T cells may be repeated one or more times.
Within other aspects, the present invention provides methods for inhibiting the development of a malignant disease associated with WTl expression in a patient, comprising the steps of: (a) incubating CD4+ and/or CD 8+ T cells isolated from a patient with one or more of: (i) a WTl polypeptide; (ii) a polynucleotide encoding a WTl polypeptide; or (iii) an antigen presenting cell that expresses a WTl polypeptide, such that the T cells proliferate; (b) cloning one or more cells that proliferated; and (c) administering to the patient an effective amount of the cloned T cells.
Within other aspects, methods are provided for determining the presence or absence of a malignant disease associated with WTl expression in a patient, comprising the steps of: (a) incubating CD4+ and/or CD8+ T cells isolated from a patient with one or more of: (i) a WTl polypeptide; (ii) a polynucleotide encoding a WTl polypeptide; or (iii) an antigen presenting cell that expresses a WTl polypeptide; and (b) detecting the presence or absence of specific activation of the T cells, therefrom determining the presence or absence of a malignant disease associated with WTl expression. Within certain embodiments, the step of detecting comprises detecting the presence or absence of proliferation of the T cells. Within further aspects, the present invention provides methods for determining the presence or absence of a malignant disease associated with WTl expression in a patient, comprising the steps of: (a) incubating a biological sample obtained from a patient with one or more of: (i) a WTl polypeptide; (ii) a polynucleotide encoding a WTl polypeptide; or (iii) an antigen presenting cell that expresses a WTl polypeptide, wherein the incubation is performed under conditions and for a time sufficient to allow immunocomplexes to form; and (b) detecting immunocomplexes formed between the WTl polypeptide and antibodies in the biological sample that specifically bind to the WTl polypeptide; and therefrom determining the presence or absence of a malignant disease associated with WTl expression. These and other aspects of the present invention will become apparent upon reference to the following detailed description and attached drawings. All references disclosed herein are hereby incorporated by reference in their entirety as if each was incorporated individually.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 depicts a comparison of the mouse (MO) and human (HU) WTl protein sequences (SEQ ID NOS: 320 and 319 respectively).
Figure 2 is a Western blot illustrating the detection of WTl specific antibodies in patients with hematological malignancy (AML). Lane 1 shows molecular weight markers; lane 2 shows a positive control (WTl positive human leukemia cell line immunoprecipitated with a WTl specific antibody); lane 3 shows a negative control (WTl positive cell line immunoprecipitated with mouse sera); and lane 4 shows a WTl positive cell line immunoprecipitated with sera of a patient with AML. For lanes 2-4, the immunoprecipitate was separated by gel electrophoresis and probed with a WTl specific antibody.
Figure 3 is a Western blot illustrating the detection of a WTl specific antibody response in B6 mice immunized with TRAMP-C, a WTl positive tumor cell line. Lanes 1, 3 and 5 show molecular weight markers, and lanes 2, 4 and 6 show a WTl specific positive control (N180, Santa Cruz Biotechnology, polypeptide spanning 180 amino acids of the N-terminal region of the WTl protein, migrating on the Western blot at 52 kD). The primary antibody used was WTl 80 in lane 2, sera of non- immunized B6 mice in lane 4 and sera of the immunized B6 mice in lane 6.
Figure 4 is a Western blot illustrating the detection of WTl specific antibodies in mice immunized with representative WTl peptides. Lanes 1, 3 and 5 show molecular weight markers and lanes 2, 4 and 6 show a WTl specific positive control (N180, Santa Cruz Biotechnology, polypeptide spanning 180 amino acids of the N-terminal region of the WTl protein, migrating on the Western blot at 52 kD). The primary antibody used was WTl 80 in lane 2, sera of non-immunized B6 mice in lane 4 and sera of the immunized B6 mice in lane 6. Figures 5 A to 5 C are graphs illustrating the stimulation of proliferative T cell responses in mice immunized with representative WTl peptides. Thymidine incorporation assays were performed using one T cell line and two different clones, as indicated, and results were expressed as cpm. Controls indicated on the x axis were no antigen (No Ag) and B6/media; antigens used were p6-22 human (pi), pi 17-139 (p2) or p244-262 human (p3).
Figure 6A and 6B are histograms illustrating the stimulation of proliferative T cell responses in mice immunized with representative WTl peptides. Three weeks after the third immunization, spleen cells of mice that had been inoculated with Vaccine A or Vaccine B were cultured with medium alone (medium) or spleen cells and medium (B6/no antigen), B6 spleen cells pulsed with the peptides p6-22 (p6), pi 17-139 (pi 17), p244-262 (p244) (Vaccine A; Figure 6A) or p287-301 (p287), p299- 313 (p299), p421-435 (p421) (Vaccine B; Figure 6B) and spleen cells pulsed with an irrelevant control peptide (irrelevant peptide) at 25ug/ml and were assayed after 96hr for proliferation by (3H) thymidine incorporation. Bars represent the stimulation index (SI), which is calculated as the mean of the experimental wells divided by the mean of the control (B6 spleen cells with no antigen).
Figures 7A-7D are histograms illustrating the generation of proliferative T-cell lines and clones specific for pi 17-139 and p6-22. Following in vivo immunization, the initial three in vitro stimulations (IVS) were carried out using all three peptides of Vaccine A or B, respectively. Subsequent IVS were carried out as single peptide stimulations using only the two relevant peptides pi 17-139 and p6-22. Clones were derived from both the p6-22 and pi 17-139 specific T cell lines, as indicated. T cells were cultured with medium alone (medium) or spleen cells and medium (B6/no antigen), B6 spleen cells pulsed with the peptides p6-22 (p6), pi 17-139 (pi 17) or an irrelevant control peptide (irrelevant peptide) at 25ug/ml and were assayed after 96hr for proliferation by (3H) thymidine incorporation. Bars represent the stimulation index (SI), which is calculated as the mean of the experimental wells divided by the mean of the control (B6 spleen cells with no antigen). Figures 8 A and 8B present the results of TSITES Analysis of human
WTl (SEQ ID NO:319) for peptides that have the potential to elicit Th responses. Regions indicated by "A" are AMPHI midpoints of blocks, "R" indicates residues matching the Rothbard/'Taylor motif, "D" indicates residues matching the IAd motif, and 'd' indicates residues matching the IEd motif.
Figures 9A and 9B are graphs illustrating the elicitation of WTl peptide- specific CTL in mice immunized with WTl peptides. Figure 9A illustrates the lysis of target cells by allogeneic cell lines and Figure 9B shows the lysis of peptide coated cell lines. In each case, the % lysis (as determined by standard chromium release assays) is shown at three indicated effectoπtarget ratios. Results are provided for lymphoma cells (LSTRA and E10), as well as E10 + p235-243 (E10+P235). E10 cells are also referred to herein as EL-4 cells.
Figures 10A-10D are graphs illustrating the elicitation of WTl specific CTL, which kill WTl positive tumor cell lines but do not kill WTl negative cell lines, following vaccination of B6 mice with WTl peptide PI 17. Figure 10A illustrates that T-cells of non-immunized B6 mice do not kill WTl positive tumor cell lines. Figure 10B illustrates the lysis of the target cells by allogeneic cell lines. Figures IOC and 10D demonstrate the lysis of WTl positive tumor cell lines, as compared to WTl negative cell lines in two different experiments. In addition, Figures IOC and 10D show the lysis of peptide-coated cell lines (WTl negative cell line E10 coated with the relevant WTl peptide PI 17) In each case, the % lysis (as determined by standard chromium release assays) is shown at tliree indicated effectoπtarget ratios. Results are provided for lymphoma cells (E10), prostate cancer cells (TRAMP-C), a transformed fibroblast cell line (BLK-SV40), as well as E10+pl 17.
Figures 1 1A and 11B are histograms illustrating the ability of representative peptide PI 17-139 specific CTL to lyse WTl positive tumor cells. Three weeks after the third immunization, spleen cells of mice that had been inoculated with the peptides p235-243 or pi 17-139 were stimulated in vitro with the relevant peptide and tested for ability to lyse targets incubated with WTl peptides as well as WTl positive and negative tumor cells. The bars represent the mean % specific lysis in chromium release assays performed in triplicate with an E:T ratio of 25:1. Figure 11A shows the cytotoxic activity of the p235-243 specific T cell line against the WTl negative cell line EL-4 (EL-4, WTl negative); EL-4 pulsed with the relevant (used for immunization as well as for restimulation) peptide p235-243 (EL-4+p235); EL-4 pulsed with the irrelevant peptides pi 17-139 (EL-4+pl l7), pl26-134 (EL-4+pl26) or pl30- 138 (EL-4+pl30) and the WTl positive tumor cells BLK-SV40 (BLK-SV40, WTl positive) and TRAMP-C (TRAMP-C, WTl positive), as indicated. Figure 11B shows cytotoxic activity of the pi 17-139 specific T cell line against EL-4; EL-4 pulsed with the relevant peptide PI 17-139 (EL-4+ l l7) and EL-4 pulsed with the irrelevant peptides pl23-131 (EL-4+pl23), or p!28-136 (EL-4+pl28); BLK-SV40 and TRAMP- C, as indicated.
Figures 12A and 12B are histograms illustrating the specificity of lysis of WTl positive tumor cells, as demonstrated by cold target inhibition. The bars represent the mean % specific lysis in chromium release assays performed in triplicate with an E:T ratio of 25:1. Figure 12A shows the cytotoxic activity of the pi 17-139 specific T cell line against the WTl negative cell line EL-4 (EL-4, WTl negative); the WTl positive tumor cell line TRAMP-C (TRAMP-C, WTl positive); TRAMP-C cells incubated with a ten-fold excess (compared to the hot target) of EL-4 cells pulsed with the relevant peptide pi 17-139 (TRAMP-C + pi 17 cold target) without 51Cr labeling and TRAMP-C cells incubated with EL-4 pulsed with an irrelevant peptide without 51Cr labeling (TRAMP-C + irrelevant cold target), as indicated. Figure 12B shows the cytotoxic activity of the pi 17-139 specific T cell line against the WTl negative cell line EL-4 (EL-4, WTl negative); the WTl positive tumor cell line BLK-SV40 (BLK-SV40, WTl positive); BLK-SV40 cells incubated with the relevant cold target (BLK-SV40 + pi 17 cold target) and BLK-SV40 cells incubated with the irrelevant cold target (BLK- SV40 + irrelevant cold target), as indicated.
Figures 13A-13C are histograms depicting an evaluation of the 9mer CTL epitope within pi 17-139. The pi 17-139 tumor specific CTL line was tested against peptides within aal 17-139 containing or lacking an appropriate H-2b class I binding motif and following restimulation with pi 26- 134 or pi 30-138. The bars represent the mean % specific lysis in chromium release assays performed in triplicate with an E:T ratio of 25:1. Figure 13A shows the cytotoxic activity of the pi 17- 139 specific T cell line against the WTl negative cell line EL-4 (EL-4, WTl negative) and EL-4 cells pulsed with the peptides pi 17-139 (EL-4 + pi 17), pi 19-127 (EL-4 + pi 19), pl20-128 (EL-4 + pl20), pl23-131 (EL-4 + p!23), pl26-134 (EL-4 + p!26), p!28-136 (EL-4 + pl28), and pl30-138 (EL-4 + pl30). Figure 13B shows the cytotoxic activity of the CTL line after restimulation with pl26-134 against the WTl negative cell line EL-4, EL-4 cells pulsed with pi 17-139 (EL-4 + pi 17), pl26-134 (EL-4 + pl26) and the WTl positive tumor cell line TRAMP-C. Figure 13C shows the cytotoxic activity of the CTL line after restimulation with pi 30- 138 against EL-4, EL-4 cells pulsed with pi 17-139 (EL-4 + pi 17), pl30-138 (EL-4 + pl30) and the WTl positive tumor cell line TRAMP-C.
Figure 14 depicts serum antibody reactivity to WTl in 63 patients with AML. Reactivity of serum antibody to WTl /N-terminus protein was evaluated by ELISA in patients with AML. The first and second lanes represent the positive and negative controls, respectively. The first and second lanes represent the ositive and negative controls, respectively. Commercially obtained WTl specific antibody WTl 80 was used for the positive control. The next 63 lanes represent results using sera from each individual patient. The OD values depicted were from ELISA using a 1 :500 serum dilution. The figure includes cumulative data from 3 separate experiments.
Figure 15 depicts serum antibody reactivity to WTl proteins and control proteins in 2 patients with AML. Reactivity of serum antibody to WTl /full-length, WTlN-terminus, TRX and Ral2 proteins was evaluated by ELISA in 2 patients with AML. The OD values depicted were from ELISA using a 1:500 serum dilution. AML- 1 and AML-2 denote serum from 2 of the individual patients in Figure 1 with demonstrated antibody reactivity to WTl /full-length. The WTl full-length protein was expressed as a fusion protein with Ral2. The WTl /N-terminus protein was expressed as a fusion protein with TRX. The control Ral2 and TRX proteins were purified in a similar manner. The results confirm that the serum antibody reactivity against the WTl fusion proteins is directed against the WTl portions of the protein.
Figure 16 depicts serum antibody reactivity to WTl in 81 patients with CML. Reactivity of serum antibody to WTl/full-length protein was evaluated by ELISA in patients with AML. The first and second lanes represent the positive and negative controls, respectively. Commercially obtained WTl specific antibody WTl 80 was used for the positive control. The next 81 lanes represent results using sera from each individual patient. The OD values depicted were from ELISA using a 1:500 serum dilution. The figure includes cumulative data from 3 separate experiments.
Figure 17 depicts serum antibody reactivity to WTl proteins and control proteins in 2 patients with CML. Reactivity of serum antibody to WTl /full-length, WTl N-terminus, TRX and Ral2 proteins was evaluated by ELISA in 2 patients with CML. The OD values depicted were from ELISA using a 1 :500 serum dilution. CML- 1 and CML-2 denote serum from 2 of the individual patients in Figure 3 with demonstrated antibody reactivity to WTl /full-length. The WTl /full-length protein was expressed as a fusion protein with Ral2. The WTl/N-terminus protein was expressed
> as a fusion protein with TRX. The control Ral2 and TRX proteins were purified in a similar manner. The results confirm that the serum antibody reactivity against the WTl fusion proteins is directed against the WTl portions of the protein.
Figure 18 provides the characteristics of the recombinant WTl proteins used for serological analysis. Figure 19A-19E is a bar graph depicting the antibody responses in mice elicited by vaccination with different doses of WTl protein.
Figure 20 A and 20B is a bar graph of the proliferative T-cell responses in mice immunized with WTl protein.
Figure 21 is a photograph of human DC, examined by fluorescent microscopy, expressing WTl following adeno WTl and Vaccinia WTl infection.
Figure 22 is a photograph that demonstrates that WTl expression in human DC is reproducible following adeno WTl infection and is not induced by a control Adeno infection.
Figure 23 is a graph of an IFN-gamma ELISPOT assay showing that WTl whole gene in vitro priming elicits WTl specific T-cell responses.
DETAILED DESCRIPTION OF THE INVENTION
As noted above, the present invention is generally directed to compositions and methods for the immunotherapy and diagnosis of malignant diseases.
The compositions described herein may include WTl polypeptides, WTl polynucleotides, antigen-presenting cells (APC, e.g., dendritic cells) that express a WTl polypeptide, agents such as antibodies that bind to a WTl polypeptide and/or immune system cells (e.g., T cells) specific for WTl. WTl Polypeptides of the present invention generally comprise at least a portion of a Wilms Tumor gene product (WTl) or a variant thereof. Nucleic acid sequences of the subject invention generally comprise a DNA or RNA sequence that encodes all or a portion of such a polypeptide, or that is complementary to such a sequence. Antibodies are generally immune system proteins, or antigen-binding fragments thereof, that are capable of binding to a portion of a WTl polypeptide. T cells that may be employed within such compositions are generally T cells (e.g., CD4+ and/or CD8+) that are specific for a WTl polypeptide. Certain methods described herein further employ antigen-presenting cells that express a WTl polypeptide as provided herein.
The present invention is based on the discovery that an immune response raised against a Wilms Tumor (WT) gene product (e.g., WTl) can provide prophylactic and/or therapeutic benefit for patients afflicted with malignant diseases characterized by increased WTl gene expression. Such diseases include, but are not limited to, leukemias (e.g., acute myeloid leukemia (AML), chronic myeloid leukemia (CML), acute lymphocytic leukemia (ALL) and childhood ALL), as well as many cancers such as lung, breast, thyroid and gastrointestinal cancers and melanomas. The WTl gene was originally identified and isolated on the basis of a cytogenetic deletion at chromosome l lpl3 in patients with Wilms1 tumor (see Call et al., U.S. Patent No. 5,350,840). The gene consists of 10 exons and encodes a zinc finger transcription factor, and sequences of mouse and human WTl proteins are provided in Figure 1 and SEQ ID NOs: 319 and 320.
WTl Polypeptides Within the context of the present invention, a WTl polypeptide is a polypeptide that comprises at least an immunogenic portion of a native WTl (i.e., a WTl protein expressed by an organism that is not genetically modified), or a variant thereof, as described herein. A WTl polypeptide may be of any length, provided that it comprises at least an immunogenic portion of a native protein or a variant thereof. In other words, a WTl polypeptide may be an oligopeptide (i.e., consisting of a relatively small number of amino acid residues, such as 8-10 residues, joined by peptide bonds), a full length WTl protein (e.g., present within a human or non-human animal, such as a mouse) or a polypeptide of intermediate size. Within certain embodiments, the use of WTl polypeptides that contain a small number of consecutive amino acid residues of a native WTl polypeptide is preferred. Such polypeptides are preferred for certain uses in which the generation of a T cell response is desired. For example, such a WTl polypeptide may contain less than 23, preferably no more than 18, and more preferably no more than 15 consecutive amino acid residues, of a native WTl polypeptide. Polypeptides comprising nine consecutive amino acid residues of a native WTl polypeptide are generally suitable for such purposes. Additional sequences derived from the native protein and/or heterologous sequences may be present within any WTl polypeptide, and such sequences may (but need not) possess further immunogenic or antigenic properties. Polypeptides as provided herein may further be associated (covalently or noncovalently) with other polypeptide or non-polypeptide compounds. An "immunogenic portion," as used herein is a portion of a polypeptide that is recognized (i.e., specifically bound) by a B-cell and/or T-cell surface antigen receptor. Certain preferred immunogenic portions bind to an MHC class I or class II molecule. As used herein, an immunogenic portion is said to "bind to" an MHC class I or class II molecule if such binding is detectable using any assay known in the art. For example, the ability of a polypeptide to bind to MHC class I may be evaluated indirectly by monitoring the ability to promote incorporation of 125I labeled β2-microglobulin (β2m) into MHC class I/β2m/peptide heterotrimeric complexes (see Parker et al., J. Immunol. 152:163, 1994). Alternatively, functional peptide competition assays that are known in the art may be employed. Certain immunogenic portions have one or more of the sequences recited within one or more of Tables II - XTV. Representative immunogenic portions include, but are not limited to, RDLNALLPAVPSLGGGG (human WTl residues 6-22; SEQ ID NO:l), PSQASSGQARMFPNAPYLPSCLE (human and mouse WTl residues 117-139; SEQ ID NOs: 2 and 3 respectively), GATLKGVAAGSSSSVKWTE (human WTl residues 244-262; SEQ ID NO:4), GATLKGVAA (human WTl residues 244-252; SEQ ID NO:88), CMTWNQMNL (human and mouse WTl residues 235-243; SEQ ID NOs: 49 and 258 respectively), SCLESQPTI (mouse WTl residues 136-144; SEQ ID NO:296), SCLESQPAI (human WTl residues 136-144; SEQ ID NO: 198), NLYQMTSQL (human and mouse WTl residues 225-233; SEQ ID NOs: 147 and 284 respectively); ALLPAVSSL (mouse WTl residues 10-18; SEQ ID NO.J55); RMFPNAPYL (human and mouse WTl residues 126-134; SEQ ID NOs: 185 and 293 respectively), VLDFAPPGA (human WTl residues 37-45; SEQ ID NO:241), or VLDFAPPGAS (human WTl residues 37-46; SEQ ID NO:411). Further immunogenic portions are provided herein, and others may generally be identified using well known techniques, such as those summarized in Paul, Fundamental Immunology, 3rd ed., 243-247 (Raven Press, 1993) and references cited therein. Representative techniques for identifying immunogenic portions include screening polypeptides for the ability to react with antigen-specific antisera and/or T- cell lines or clones. An immunogenic portion of a native WTl polypeptide is a portion that reacts with such antisera and/or T-cells at a level that is not substantially less than the reactivity of the full length WTl (e.g., in an ELISA and/or T-cell reactivity assay). In other words, an immunogenic portion may react within such assays at a level that is similar to or greater than the reactivity of the full length polypeptide. Such screens may generally be performed using methods well known to those of ordinary skill in the art, such as those described in Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988. Alternatively, immunogenic portions may be identified using computer analysis, such as the Tsites program (see Rothbard and Taylor, EMBO J. 7:93-100, 1988; Deavin et al., Mol. Immunol. 33:145-155, 1996), which searches for peptide motifs that have the potential to elicit Th responses. CTL peptides with motifs appropriate for binding to murine and human class I or class II MHC may be identified according to BIMAS (Parker et al., J. Immunol. 152:163, 1994) and other HLA peptide binding prediction analyses. To confirm immunogenicity, a peptide may be tested using an HLA A2 transgenic mouse model and/or an in vitro stimulation assay using dendritic cells, fibroblasts or peripheral blood cells.
As noted above, a composition may comprise a variant of a native WTl protein. A polypeptide "variant," as used herein, is a polypeptide that differs from a native polypeptide in one or more substitutions, deletions, additions and/or insertions, such that the immunogenicity of the polypeptide is retained (i.e., the ability of the variant to react with antigen-specific antisera and/or T-cell lines or clones is not substantially diminished relative to the native polypeptide). In other words, the ability of a variant to react with antigen-specific antisera and/or T-cell lines or clones may be enhanced or unchanged, relative to the native polypeptide, or may be diminished by less than 50%, and preferably less than 20%, relative to the native polypeptide. Such variants may generally be identified by modifying one of the above polypeptide sequences and evaluating the reactivity of the modified polypeptide with antisera and/or T-cells as described herein. It has been found, within the context of the present invention, that a relatively small number of substitutions (e.g., 1 to 3) within an immunogenic portion of a WTl polypeptide may serve to enhance the ability of the polypeptide to elicit an immune response. Suitable substitutions may generally be identified by using computer programs, as described above, and the effect confirmed based on the reactivity of the modified polypeptide with antisera and/or T-cells as described herein. Accordingly, within certain preferred embodiments, a WTl polypeptide comprises a variant in which 1 to 3 amino acid resides within an immunogenic portion are substituted such that the ability to react with antigen-specific antisera and/or T-cell lines or clones is statistically greater than that for the unmodified polypeptide. Such substitutions are preferably located within an MHC binding site of the polypeptide, which may be identified as described above. Preferred substitutions allow increased binding to MHC class I or class II molecules.
Certain variants contain conservative substitutions. A "conservative substitution" is one in which an amino acid is substituted for another amino acid that has similar properties, such that one skilled in the art of peptide chemistry would expect the secondary structure and hydropathic nature of the polypeptide to be substantially unchanged. Amino acid substitutions may generally be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues. For example, negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine and valine; glycine and alanine; asparagine and glutamine; and serine, threonine, phenylalanine and tyrosine. Other groups of amino acids that may represent conservative changes include: (1) ala, pro, gly, glu, asp, gin, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala, phe; (4) lys, arg, his; and (5) phe, tyr, tip, his. A variant may also, or alternatively, contain nonconservative changes. Variants may also (or alternatively) be modified by, for example, the deletion or addition of amino acids that have minimal influence on the immunogenicity, secondary structure and hydropathic nature of the polypeptide.
In a preferred embodiment, a variant polypeptide of the WTl N-terminus (amino acids 1-249) is constructed, wherein the variant polypeptide is capable of binding to an antibody that recognizes full-length WTl and or WTl N-terminus polypeptide. A non-limiting example of an antibody is anti WTl antibody WTl 80 (Santa Cruz Biotechnology, Inc., Santa Cruz, CA).
As noted above, WTl polypeptides may be conjugated to a signal (or leader) sequence at the N-terminal end of the protein which co-translationally or post- translationally directs transfer of the protein. A polypeptide may also, or alternatively, be conjugated to a linker or other sequence for ease of synthesis, purification or identification of the polypeptide (e.g., poly-His), or to enhance binding of the polypeptide to a solid support. For example, a polypeptide may be conjugated to an immunoglobulin Fc region. WTl polypeptides may be prepared using any of a variety of well known techniques. Recombinant polypeptides encoded by a WTl polynucleotide as described herein may be readily prepared from the polynucleotide. In general, any of a variety of expression vectors known to those of ordinary skill in the art may be employed to express recombinant WTl polypeptides. Expression may be achieved in any appropriate host cell that has been transformed or transfected with an expression vector containing a DNA molecule that encodes a recombinant polypeptide. Suitable host cells include prokaryotes, yeast and higher eukaryotic cells. Preferably, the host cells employed are E. coli, yeast or a mammalian cell line such as COS or CHO. Supernatants from suitable host/vector systems which secrete recombinant protein or polypeptide into culture media may be first concentrated using a commercially available filter. The concentrate may then be applied to a suitable purification matrix such as an affinity matrix or an ion exchange resin. Finally, one or more reverse phase HPLC steps can be employed to further purify a recombinant polypeptide. Such techniques may be used to prepare native polypeptides or variants thereof. For example, polynucleotides that encode a variant of a native polypeptide may generally be prepared using standard mutagenesis techniques, such as oligonucleotide-directed site-specific mutagenesis, and sections of the DNA sequence may be removed to permit preparation of truncated polypeptides.
Certain portions and other variants may also be generated by synthetic means, using techniques well known to those of ordinary skill in the art. For example, polypeptides having fewer than about 500 amino acids, preferably fewer than about 100 amino acids, and more preferably fewer than about 50 amino acids, may be synthesized. Polypeptides may be synthesized using any of the commercially available solid-phase techniques, such as the Merrifield solid-phase synthesis method, where amino acids are sequentially added to a growing amino acid chain. See Merrifield, J. Am. Chem. Soc. §5:2149-2146, 1963. Equipment for automated synthesis of polypeptides is commercially available from suppliers such as Applied BioSystems, Inc. (Foster City, CA), and may be operated according to the manufacturer's instructions.
In general, polypeptides and polynucleotides as described herein are isolated. An "isolated" polypeptide or polynucleotide is one that is removed from its original environment. For example, a naturally-occurring protein is isolated if it is separated from some or all of the coexisting materials in the natural system. Preferably, such polypeptides are at least about 90% pure, more preferably at least about 95% pure and most preferably at least about 99% pure. A polynucleotide is considered to be isolated if, for example, it is cloned into a vector that is not a part of the natural environment.
Within further aspects, the present invention provides mimetics of WTl polypeptides. Such mimetics may comprise amino acids linked to one or more amino acid mimetics (i.e., one or more amino acids within the WTl protein may be replaced by an amino acid mimetic) or may be entirely nonpeptide mimetics. An amino acid mimetic is a compound that is conformationally similar to an amino acid such that it can be substituted for an amino acid within a WTl polypeptide without substantially diminishing the ability to react with antigen-specific antisera and/or T cell lines or clones. A nonpeptide mimetic is a compound that does not contain amino acids, and that has an overall conformation that is similar to a WTl polypeptide such that the ability of the mimetic to react with WTl-specific antisera and/or T cell lines or clones is not substantially diminished relative to the ability of a WTl polypeptide. Such mimetics may be designed based on standard techniques (e.g., nuclear magnetic resonance and computational techniques) that evaluate the three dimensional structure of a peptide sequence. Mimetics may be designed where one or more of the side chain functionalities of the WTl polypeptide are replaced by groups that do not necessarily have the same size or volume, but have similar chemical and/or physical properties which produce similar biological responses. It should be understood that, within embodiments described herein, a mimetic may be substituted for a WTl polypeptide.
Within other illustrative embodiments, a polypeptide may be a fusion polypeptide that comprises multiple polypeptides as described herein, or that comprises at least one polypeptide as described herein and an unrelated sequence, such as a known tumor protein. A fusion partner may, for example, assist in providing T helper epitopes (an immunological fusion partner), preferably T helper epitopes recognized by humans, or may assist in expressing the protein (an expression enhancer) at higher yields than the native recombinant protein. Certain preferred fusion partners are both immunological and expression enhancing fusion partners. Other fusion partners may be selected so as to increase the solubility of the polypeptide or to enable the polypeptide to be targeted to desired intracellular compartments. Still further fusion partners include affinity tags, which facilitate purification of the polypeptide.
Fusion polypeptides may generally be prepared using standard techniques, including chemical conjugation. Preferably, a fusion polypeptide is expressed as a recombinant polypeptide, allowing the production of increased levels, relative to a non-fused polypeptide, in an expression system. Briefly, DNA sequences encoding the polypeptide components may be assembled separately, and ligated into an appropriate expression vector. The 3' end of the DNA sequence encoding one polypeptide component is ligated, with or without a peptide linker, to the 5' end of a DNA sequence encoding the second polypeptide component so that the reading frames of the sequences are in phase. This permits translation into a single fusion polypeptide that retains the biological activity of both component polypeptides.
A peptide linker sequence may be employed to separate the first and second polypeptide components by a distance sufficient to ensure that each polypeptide folds into its secondary and tertiary structures. Such a peptide linker sequence is incorporated into the fusion polypeptide using standard techniques well known in the ait. Suitable peptide linker sequences may be chosen based on the following factors: (1) their ability to adopt a flexible extended conformation; (2) their inability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides; and (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes. Preferred peptide linker sequences contain Gly, Asn and Ser residues. Other near neutral amino acids, such as Thr and Ala may also be used in the linker sequence. Amino acid sequences which may be usefully employed as linkers include those disclosed in Maratea et al., Gene 40:39-46, 1985; Murphy et al., Proc. Natl. Acad. Sci. USA 53:8258-8262, 1986; U.S. Patent No. 4,935,233 and U.S. Patent No. 4,751,180. The linker sequence may generally be from 1 to about 50 amino acids in length. Linker sequences are not required when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference. The ligated DNA sequences are operably linked to suitable transcriptional or translational regulatory elements. The regulatory elements responsible for expression of DNA are located only 5' to the DNA sequence encoding the first polypeptides. Similarly, stop codons required to end translation and transcription termination signals are only present 3' to the DNA sequence encoding the second polypeptide.
The fusion polypeptide can comprise a polypeptide as described herein together with an unrelated immunogenic protein, such as an immunogenic protein capable of eliciting a recall response. Examples of such proteins include tetanus, tuberculosis and hepatitis proteins (see, for example, Stoute et al. New Engl. J. Med., 336:86-91, 1997). In one preferred embodiment, the immunological fusion partner is derived from a Mycobacterium sp., such as a Mycobacterium tuberculosis-derived Ral2 fragment. Ral2 compositions and methods for their use in enhancing the expression and/or immunogenicity of heterologous polynucleotide/polypeptide sequences is described in U.S. Patent Application 60/158,585, the disclosure of which is incorporated herein by reference in its entirety. Briefly, Ral2 refers to a polynucleotide region that is a subsequence of a Mycobacterium tuberculosis MTB32A nucleic acid. MTB32A is a serine protease of 32 KD molecular weight encoded by a gene in virulent and avirulent strains of M. tuberculosis. The nucleotide sequence and amino acid sequence of MTB32A have been described (for example, U.S. Patent Application 60/158,585; see also, Skeiky et al, Infection and Immun. (1999) 67:3998-4007, incorporated herein by reference). C-terminal fragments of the MTB32A coding sequence express at high levels and remain as soluble polypeptides throughout the purification process. Moreover, Ral2 may enhance the immunogenicity of heterologous immunogenic polypeptides with which it is fused. One preferred Ral2 fusion polypeptide comprises a 14 KD C-terminal fragment corresponding to amino acid residues 192 to 323 of MTB32A. Other preferred Ral2 polynucleotides generally comprise at least about 15 consecutive nucleotides, at least about 30 nucleotides, at least about 60 nucleotides, at least about 100 nucleotides, at least about 200 nucleotides, or at least about 300 nucleotides that encode a portion of a Ral2 polypeptide. Ral2 polynucleotides may comprise a native sequence (i.e., an endogenous sequence that encodes a Ral2 polypeptide or a portion thereof) or may comprise a variant of such a sequence. Ral2 polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions such that the biological activity of the encoded fusion polypeptide is not substantially diminished, relative to a fusion polypeptide comprising a native Ral2 polypeptide. Variants preferably exhibit at least about 70% identity, more preferably at least about 80% identity and most preferably at least about 90%) identity to a polynucleotide sequence that encodes a native Ral2 polypeptide or a portion thereof. Within other preferred embodiments, an immunological fusion partner is derived from protein D, a surface protein of the gram-negative bacterium Haemophilus influenza B (WO 91/18926). Preferably, a protein D derivative comprises approximately the first third of the protein (e.g., the first N-terminal 100-110 amino acids), and a protein D derivative may be lipidated. Within certain preferred embodiments, the first 109 residues of a Lipoprotein D fusion partner is included on the N-terminus to provide the polypeptide with additional exogenous T-cell epitopes and to increase the expression level in E. coli (thus functioning as an expression enhancer). The lipid tail ensures optimal presentation of the antigen to antigen presenting cells. Other fusion partners include the non-structural protein from influenzae virus, NS1 (hemaglutinin). Typically, the N-terminal 81 amino acids are used, although different fragments that include T-helper epitopes may be used.
In another embodiment, the immunological fusion partner is the protein known as LYTA, or a portion thereof (preferably a C-terminal portion). LYTA is derived from Streptococcus pneumoniae, which synthesizes an N-acetyl-L-alanine amidase known as amidase LYTA (encoded by the LytA gene; Gene 43:265-292, 1986). LYTA is an autolysin that specifically degrades certain bonds in the peptidoglycan backbone. The C-terminal domain of the LYTA protein is responsible for the affinity to the choline or to some choline analogues such as DEAE. This property has been exploited for the development of E. coli C-LYTA expressing plasmids useful for expression of fusion proteins. Purification of hybrid proteins containing the C-LYTA fragment at the amino terminus has been described (see Biotechnology 10:195-198, 1992). Within a preferred embodiment, a repeat portion of LYTA may be incorporated into a fusion polypeptide. A repeat portion is found in the C-terminal region starting at residue 178. A particularly preferred repeat portion incorporates residues 188-305.
Yet another illustrative embodiment involves fusion polypeptides, and the polynucleotides encoding them, wherein the fusion partner comprises a targeting signal capable of directing a polypeptide to the endosomal/lysosomal compartment, as described in U.S. Patent No. 5,633,234. An immunogenic polypeptide of the invention, when fused with this targeting signal, will associate more efficiently with MHC class II molecules and thereby provide enhanced in vivo stimulation of CD4 T-cells specific for the polypeptide. The invention provides truncated forms of WTl polypeptides that can be recombinantly expressed in E. coli without the addition of a fusion partner. Examples of these truncated forms are shown in SEQ ID NOs:342-346, and are encoded by polynucleotides shown in SEQ ID NOs:337-341. In variations of these truncations, the first 76 amino acids of WTl can be fused to the C-terminus of the protein, creating a recombinant protein that is easier to express in E. coli. Other hosts in addition to E. coli can also be used, such as, for example, B. megaterium. The protein can further be prepared without a histidine tag.
In other embodiments, different subunits can be made and fused together in an order which differs from that of native WTl. In addition, fusions can be made with, for example, Ral2. Exemplary fusion proteins are shown in SEQ ID NOs: 332- 336 and can be encoded by polynucleotides shown in SEQ ID NOs: 327-331.
WTl Polynucleotides
Any polynucleotide that encodes a WTl polypeptide as described herein is a WTl polynucleotide encompassed by the present invention. Such polynucleotides may be single-stranded (coding or antisense) or double-stranded, and may be DNA (genomic, cDNA or synthetic) or RNA molecules. Additional coding or non-coding sequences may, but need not, be present within a polynucleotide of the present invention, and a polynucleotide may, but need not, be linked to other molecules and/or support materials.
WTl polynucleotides may encode a native WTl protein, or may encode a variant of WTl as described herein. Polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions such that the immunogenicity of the encoded polypeptide is not diminished, relative to a native WTl protein. The effect on the immunogenicity of the encoded polypeptide may generally be assessed as described herein. Preferred variants contain nucleotide substitutions, deletions, insertions and/or additions at no more than 20%, preferably at no more than 10%, of the nucleotide positions that encode an immunogenic portion of a native WTl sequence. Certain variants are substantially homologous to a native gene, or a portion thereof. Such polynucleotide variants are capable of hybridizing under moderately stringent conditions to a naturally occurring DNA sequence encoding a WTl polypeptide (or a complementary sequence). Suitable moderately stringent conditions include prewashing in a solution of 5 X SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at 50°C- 65°C, 5 X SSC, overnight; followed by washing twice at 65°C for 20 minutes with each of 2X, 0.5X and 0JX SSC containing 0.1% SDS). Such hybridizing DNA sequences are also within the scope of this invention.
It will be appreciated by those of ordinary skill in the art that, as a result of the degeneracy of the genetic code, there are many nucleotide sequences that encode a WTl polypeptide. Some of these polynucleotides bear minimal homology to the nucleotide sequence of any native gene. Nonetheless, polynucleotides that vary due to differences in codon usage are specifically contemplated by the present invention.
Once an immunogenic portion of WTl is identified, as described above, a WTl polynucleotide may be prepared using any of a variety of techniques. For example, a WTl polynucleotide may be amplified from cDNA prepared from cells that express WTl . Such polynucleotides may be amplified via polymerase chain reaction (PCR). For this approach, sequence-specific primers may be designed based on the sequence of the immunogenic portion and may be purchased or synthesized. For example, suitable primers for PCR amplification of a human WTl gene include: first step - PI 18: 1434-1414: 5' GAG AGT CAG ACT TGA AAG CAGT 3' (SEQ ID NO:5) and P135: 5' CTG AGC CTC AGC AAA TGG GC 3' (SEQ ID NO:6); second step - P136: 5' GAG CAT GCA TGG GCT CCG ACG TGC GGG 3' (SEQ ID NO:7) and P137: 5' GGG GTA CCC ACT GAA CGG TCC CCG A 3' (SEQ ID NO:8). Primers for PCR amplification of a mouse WTl gene include: first step - P138: 5' TCC GAG CCG CAC CTC ATG 3' (SEQ ID NO:9) and P139: 5' GCC TGG GAT GCT GGA CTG 3' (SEQ ID NO.J0), second step - P140: 5' GAG CAT GCG ATG GGT TCC GAC GTG CGG 3' (SEQ ID NO:l 1) and P141: 5' GGG GTA CCT CAA AGC GCC ACG TGG AGT TT 3' (SEQ ID NO: 12).
An amplified portion may then be used to isolate a full length gene from a human genomic DNA library or from a suitable cDNA library, using vell known techniques. Alternatively, a full length gene can be constructed from multiple PCR fragments. WTl polynucleotides may also be prepared by synthesizing oligonucleotide components, and ligating components together to generate the complete polynucleotide. WTl polynucleotides may also be synthesized by any method known in the art, including chemical synthesis (e.g., solid phase phosphoramidite chemical synthesis). Modifications in a polynucleotide sequence may also be introduced using standard mutagenesis techniques, such as oligonucleotide-directed site-specific mutagenesis (see Adelman et al., DNA 2:183, 1983). Alternatively, RNA molecules may be generated by in vitro or in vivo transcription of DNA sequences encoding a WTl polypeptide, provided that the DNA is incorporated into a vector with a suitable RNA polymerase promoter (such as T7 or SP6). Certain portions may be used to prepare an encoded polypeptide, as described herein. In addition, or alternatively, a portion may be administered to a patient such that the encoded polypeptide is generated in vivo (e.g., by transfecting antigen-presenting cells such as dendritic cells with a cDNA construct encoding a WTl polypeptide, and administering the transfected cells to the patient).
Polynucleotides that encode a WTl polypeptide may generally be used for production of the polypeptide, in vitro or in vivo. WTl polynucleotides that are complementary to a coding sequence (i.e., antisense polynucleotides) may also be used as a probe or to inhibit WTl expression. cDNA constructs that can be transcribed into antisense RNA may also be introduced into cells of tissues to facilitate the production of antisense RNA. Any polynucleotide may be further modified to increase stability in vivo.
Possible modifications include, but are not limited to, the addition of flanking sequences at the 5' and/or 3' ends; the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages in the backbone; and/or the inclusion of nontraditional bases such as inosine, queosine and wybutosine, as well as acetyl- methyl-, thio- and other modified forms of adenine, cytidine, guanine, thymine and uridine.
Nucleotide sequences as described herein may be joined to a variety of other nucleotide sequences using established recombinant DNA techniques. For example, a polynucleotide may be cloned into any of a variety of cloning vectors, including plasmids, phagemids, lambda phage derivatives and cosmids. Vectors of particular interest include expression vectors, replication vectors, probe generation vectors and sequencing vectors. In general, a vector will contain an origin of replication functional in at least one organism, convenient restriction endonuclease sites and one or more selectable markers. Other elements will depend upon the desired use, and will be apparent to those of ordinary skill in the art.
Within certain embodiments, polynucleotides may be formulated so as to permit entry into a cell of a mammal, and expression therein. Such formulations are particularly useful for therapeutic purposes, as described below. Those of ordinary skill in the art will appreciate that there are many ways to achieve expression of a polynucleotide in a target cell, and any suitable method may be employed. For example, a polynucleotide may be incorporated into a viral vector such as, but not limited to, adenovirus, adeno-associated virus, retrovirus, or vaccinia or other pox virus (e.g., avian pox virus). Techniques for incorporating DNA into such vectors are well known to those of ordinary skill in the art. A retroviral vector may additionally transfer or incorporate a gene for a selectable marker (to aid in the identification or selection of transduced cells) and/or a targeting moiety, such as a gene that encodes a ligand for a receptor on a specific target cell, to render the vector target specific. Targeting may also be accomplished using an antibody, by methods known to those of ordinary skill in the art. cDNA constructs within such a vector may be used, for example, to transfect human or animal cell lines for use in establishing WTl positive tumor models which may be used to perform tumor protection and adoptive immunotherapy experiments to demonstrate tumor or leukemia-growth inhibition or lysis of such cells.
Other therapeutic formulations for polynucleotides include colloidal dispersion systems, such as macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. A preferred colloidal system for use as a delivery vehicle in vitro and in vivo is a liposome (i.e., an artificial membrane vesicle). The preparation and use of such systems is well known in the art.
Antibodies and Fragments Thereof
The present invention further provides binding agents, such as antibodies and antigen-binding fragments thereof, that specifically bind to a WTl polypeptide. As used herein, an agent is said to "specifically bind" to a WTl polypeptide if it reacts at a detectable level (within, for example, an ELISA) with a WTl polypeptide, and does not react detectably with unrelated proteins under similar conditions. As used herein, "binding" refers to a noncovalent association between two separate molecules such that a "complex" is formed. The ability to bind may be evaluated by, for example, determining a binding constant for the foπnation of the complex. The binding constant is the value obtained when the concentration of the complex is divided by the product of the component concentrations. In general, two compounds are said to "bind," in the context of the present invention, when the binding constant for complex formation exceeds about 103 L/mol. The binding constant maybe determined using methods well known in the art.
Any agent that satisfies the above requirements may be a binding agent. In a preferred embodiment, a binding agent is an antibody or an antigen-binding fragment thereof. Certain antibodies are commercially available from, for example, Santa Cruz Biotechnology (Santa Cruz, CA). Alternatively, antibodies may be prepared by any of a variety of techniques known to those of ordinary skill in the art. See, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988. In general, antibodies can be produced by cell culture techniques, including the generation of monoclonal antibodies as described herein, or via transfection of antibody genes into suitable bacterial or mammalian cell hosts, in order to allow for the production of recombinant antibodies. In one technique, an immunogen comprising the polypeptide is initially injected into any of a wide variety of mammals (e.g., mice, rats, rabbits, sheep or goats). In this step, the polypeptides of this invention may serve as the immunogen without modification. Alternatively, particularly for relatively short polypeptides, a superior immune response may be elicited if the polypeptide is joined to a carrier protein, such as bovine serum albumin or keyhole limpet hemocyanin. The immunogen is injected into the animal host, preferably according to a predetermined schedule incorporating one or more booster immunizations, and the animals are bled periodically. Polyclonal antibodies specific for the polypeptide may then be purified from such antisera by, for example, affinity chromatography using the polypeptide coupled to a suitable solid support. Monoclonal antibodies specific for the antigenic polypeptide of interest may be prepared, for example, using the technique of Kohler and Milstein, Eur. J. Immunol. 6:511-519, 1976, and improvements thereto. Briefly, these methods involve the preparation of immortal cell lines capable of producing antibodies having the desired specificity (i.e., reactivity with the polypeptide of interest). Such cell lines may be produced, for example, from spleen cells obtained from an animal immunized as described above. The spleen cells are then immortalized by, for example, fusion with a myeloma cell fusion partner, preferably one that is syngeneic with the immunized animal. A variety of fusion techniques may be employed. For example, the spleen cells and myeloma cells may be combined with a nonionic detergent for a few minutes and then plated at low density on a selective medium that supports the growth of hybrid cells, but not myeloma cells. A preferred selection technique uses HAT (hypoxanthine, aminopterin, thymidine) selection. After a sufficient time, usually about 1 to 2 weeks, colonies of hybrids are observed. Single colonies are selected and their culture supematants tested for binding activity against the polypeptide. Hybridomas having high reactivity and specificity are preferred.
Monoclonal antibodies may be isolated from the supematants of growing hybridoma colonies. In addition, various techniques may be employed to enhance the yield, such as injection of the hybridoma cell line into the peritoneal cavity of a suitable vertebrate host, such as a mouse. Monoclonal antibodies may then be harvested from the ascites fluid or the blood. Contaminants may be removed from the antibodies by conventional techniques, such as chromatography, gel filtration, precipitation, and extraction. The polypeptides of this invention may be used in the purification process in, for example, an affinity chromatography step. Within certain embodiments, the use of antigen-binding fragments of antibodies may be preferred. Such fragments include Fab fragments, which may be prepared using standard techniques. Briefly, immunoglobulins may be purified from rabbit serum by affinity chromatography on Protein A bead columns (Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988) and digested by papain to yield Fab and Fc fragments. The Fab and Fc fragments may be separated by affinity chromatography on protein A bead columns. Monoclonal antibodies and fragments thereof may be coupled to one or more therapeutic agents. Suitable agents in this regard include radioactive tracers and chemotherapeutic agents, which may be used, for example, to purge autologous bone marrow in vitro). Representative therapeutic agents include radionuclides, differentiation inducers, drugs, toxins, and derivatives thereof. Preferred radionuclides include 90Y, 123I, 1 5I, 131I, 186Re, 188Re, 11At, and 212Bi. Preferred drugs include methotrexate, and pyrimidine and purine analogs. Preferred differentiation inducers include phorbol esters and butyric acid. Preferred toxins include ricin, abrin, diptheria toxin, cholera toxin, gelonin, Pseudomonas exotoxin, Shigella toxin, and pokeweed antiviral protein. For diagnostic purposes, coupling of radioactive agents may be used to facilitate tracing of metastases or to determine the location of WTl -positive tumors.
A therapeutic agent may be coupled (e.g., covalently bonded) to a suitable monoclonal antibody either directly or indirectly (e.g., via a linker group). A direct reaction between an agent and an antibody is possible when each possesses a substituent capable of reacting with the other. For example, a nucleophilic group, such as an amino or sulfhydryl group, on one may be capable of reacting with a carbonyl- containing group, such as an anhydride or an acid halide, or with an alkyl group containing a good leaving group (e.g., a halide) on the other.
Alternatively, it may be desirable to couple a therapeutic agent and an antibody via a linker group. A linker group can function as a spacer to distance an antibody from an agent in order to avoid interference with binding capabilities. A linker group can also serve to increase the chemical reactivity of a substituent on an agent or an antibody, and thus increase the coupling efficiency. An increase in chemical reactivity may also facilitate the use of agents, or functional groups on agents, which otherwise would not be possible.
It will be evident to those skilled in the art that a variety of bifunctional or polyfunctional reagents, both homo- and hetero-functional (such as those described in the catalog of the Pierce Chemical Co., Rockford, IL), may be employed as the linker group. Coupling may be effected, for example, through amino groups, carboxyl groups, sulfhydryl groups or oxidized caibohydrate residues. There are numerous references describing such methodology, e.g., U.S. Patent No. 4,671,958, to Rodwell et al. Where a therapeutic agent is more potent when free from the antibody portion of the immunoconjugates of the present invention, it may be desirable to use a linker group which is cleavable during or upon internalization into a cell. A number of different cleavable linker groups have been described. The mechanisms for the intracellular release of an agent from these linker groups include cleavage by reduction of a disulfide bond (e.g., U.S. Patent No. 4,489,710, to Spitler), by irradiation of a photolabile bond (e.g., U.S. Patent No. 4,625,014, to Senter et al.), by hydrolysis of derivatized amino acid side chains (e.g., U.S. Patent No. 4,638,045, to Kohn et al.), by serum complement-mediated hydrolysis (e.g., U.S. Patent No. 4,671,958, to Rodwell et al.), and acid-catalyzed hydrolysis (e.g. , U.S. Patent No. 4,569,789, to Blattler et al.).
It may be desirable to couple more than one agent to an antibody. In one embodiment, multiple molecules of an agent are coupled to one antibody molecule. In another embodiment, more than one type of agent may be coupled to one antibody.
Regardless of the particular embodiment, immunoconjugates with more than one agent may be prepared in a variety of ways. For example, more than one agent may be coupled directly to an antibody molecule, or linkers which provide multiple sites for attachment can be used. Alternatively, a carrier can be used. A carrier may bear the agents in a variety of ways, including covalent bonding either directly or via a linker group. Suitable carriers include proteins such as albumins (e.g., U.S. Patent No. 4,507,234, to Kato et al.), peptides and polysaccharides such as aminodextran (e.g., U.S. Patent No. 4,699,184, to Shih et al). A carrier may also bear an agent by noncovalent bonding or by encapsulation, such as within a liposome vesicle (e.g., U.S. Patent Nos. 4,429,008 and 4,873,088). Carriers specific for radionuclide agents include radiohalogenated small molecules and chelating compounds. For example, U.S. Patent No. 4,735,792 discloses representative radiohalogenated small molecules and their synthesis. A radionuclide chelate may be formed from chelating compounds that include those containing nitrogen and sulfur atoms as the donor atoms for binding the metal, or metal oxide, radionuclide. For example, U.S. Patent No. 4,673,562, to Davison et al. discloses representative chelating compounds and their synthesis. A variety of routes of administration for the antibodies and immunoconjugates may be used. Typically, administration will be intravenous, intramuscular, subcutaneous or in the bed of a resected tumor. It will be evident that the precise dose of the antibody/immunoconjugate will vary depending upon the antibody used, the antigen density on the tumor, and the rate of clearance of the antibody.
Also provided herein are anti-idiotypic antibodies that mimic an immunogenic portion of WTl. Such antibodies may be raised against an antibody, or antigen-binding fragment thereof, that specifically binds to an immunogenic portion of WTl, using well known teclmiques. Anti-idiotypic antibodies that mimic an immunogenic portion of WTl are those antibodies that bind to an antibody, or antigen- binding fragment thereof, that specifically binds to an immunogenic portion of WTl, as described herein.
T Cells
Immunotherapeutic compositions may also, or alternatively, comprise T cells specific for WTl. Such cells may generally be prepared in vitro or ex vivo, using standard procedures. For example, T cells may be present within (or isolated from) bone marrow, peripheral blood or a fraction of bone marrow or peripheral blood of a mammal, such as a patient, using a commercially available cell separation system, such as the CEPRATE™ system, available from CellPro Inc., Bothell WA (see also U.S. Patent No. 5,240,856; U.S. Patent No. 5,215,926; WO 89/06280; WO 91/16116 and WO 92/07243). Alternatively, T cells may be derived from related or unrelated humans, non-human animals, cell lines or cultures.
T cells may be stimulated with WTl polypeptide, polynucleotide encoding a WTl polypeptide and/or an antigen presenting cell (APC) that expresses a WTl polypeptide. Such stimulation is performed under conditions and for a time sufficient to permit the generation of T cells that are specific for the WTl polypeptide. Preferably, a WTl polypeptide or polynucleotide is present within a delivery vehicle, such as a microsphere, to facilitate the generation of antigen-specific T cells. Briefly, T cells, which may be isolated from a patient or a related or unrelated donor by routine techniques (such as by Ficoll/Hypaque density gradient centrifugation of peripheral blood lymphocytes), are incubated with WTl polypeptide. For example, T cells may be incubated in vitro for 2-9 days (typically 4 days) at 37°C with WTl polypeptide (e.g., 5 to 25 μg/ml) or cells synthesizing a comparable amount of WTl polypeptide. It may be desirable to incubate a separate aliquot of a T cell sample in the absence of WTl polypeptide to serve as a control.
T cells are considered to be specific for a WTl polypeptide if the T cells kill target cells coated with a WTl polypeptide or expressing a gene encoding such a polypeptide. T cell specificity may be evaluated using any of a variety of standard techniques. For example, within a chromium release assay or proliferation assay, a stimulation index of more than two fold increase in lysis and/or proliferation, compared to negative controls, indicates T cell specificity. Such assays may be performed, for example, as described in Chen et al., Cancer Res. 54:1065-1010, 1994. Alternatively, detection of the proliferation of T cells may be accomplished by a variety of known techniques. For example, T cell proliferation can be detected by measuring an increased rate of DNA synthesis (e.g., by pulse-labeling cultures of T cells with tritiated thymidine and measuring the amount of tritiated thymidine incorporated into DNA). Other ways to detect T cell proliferation include measuring increases in interleukin-2 (IL-2) production, Ca^+ flux, or dye uptake, such as 3-(4,5-dimethylthiazol-2-yl)-2,5- diphenyl-tetrazolium. Alternatively, synthesis of lymphokines (such as interferon- gamma) can be measured or the relative number of T cells that can respond to a WTl polypeptide may be quantified. Contact with a WTl polypeptide (200 ng/ml - 100 μg/ml, preferably 100 ng/ml - 25 μg/ml) for 3 - 7 days should result in at least a two fold increase in proliferation of the T cells and/or contact as described above for 2-3 hours should result in activation of the T cells, as measured using standard cytokine assays in which a two fold increase in the level of cytokine release (e.g., TNF or IFN-γ) is indicative of T cell activation (see Coligan et al., Current Protocols in Immunology, vol. 1, Wiley Interscience (Greene 1998). WTl specific T cells may be expanded using standard techniques. Within preferred embodiments, the T cells are derived from a patient or a related or unrelated donor and are administered to the patient following stimulation and expansion.
T cells that have been activated in response to a WTl polypeptide, polynucleotide or WTl -expressing APC may be CD4+ and/or CD8+. Specific activation of CD4+ or CD8+ T cells may be detected in a variety of ways. Methods for detecting specific T cell activation include detecting the proliferation of T cells, the production of cytokines (e.g., lymphokines), or the generation of cytolytic activity (i.e., generation of cytotoxic T cells specific for WTl). For CD4+ T cells, a preferred method for detecting specific T cell activation is the detection of the proliferation of T cells. For CD8+ T cells, a preferred method for detecting specific T cell activation is the detection of the generation of cytolytic activity.
For therapeutic purposes, CD4+ or CD8+ T cells that proliferate in response to the WTl polypeptide, polynucleotide or APC can be expanded in number either in vitro or in vivo. Proliferation of such T cells in vitro may be accomplished in a variety of ways. For example, the T cells can be re-exposed to WTl polypeptide, with or without the addition of T cell growth factors, such as interleukin-2, and/or stimulator cells that synthesize a WTl polypeptide. The addition of stimulator cells is preferred where generating CD8+ T cell responses. T cells can be grown to large numbers in vitro with retention of specificity in response to intermittent restimulation with WTl polypeptide. Briefly, for the primary in vitro stimulation (IVS), large numbers of lymphocytes (e.g., greater than 4 x 10^) may be placed in flasks with media containing human serum. WTl polypeptide (e.g., peptide at 10 μg/ml) may be added directly, along with tetanus toxoid (e.g., 5 μg/ml). The flasks may then be incubated (e.g., 37°C for 7 days). For a second IVS, T cells are then harvested and placed in new flasks with 2-3 x lθ7 irradiated peripheral blood mononuclear cells. WTl polypeptide (e.g., 10 μg/ml) is added directly. The flasks are incubated at 37°C for 7 days. On day 2 and day 4 after the second IVS, 2-5 units of interleukin-2 (IL-2) may be added. For a third IVS, the T cells may be placed in wells and stimulated with the individual's own EBV transformed B cells coated with the peptide. IL-2 may be added on days 2 and 4 of each cycle. As soon as the cells are shown to be specific cytotoxic T cells, they may be expanded using a 10 day stimulation cycle with higher IL-2 (20 units) on days 2, 4 and 6.
Alternatively, one or more T cells that proliferate in the presence of WTl polypeptide can be expanded in number by cloning. Methods for cloning cells are well known in the art, and include limiting dilution. Responder T cells may be purified from the peripheral blood of sensitized patients by density gradient centrifugation and sheep red cell resetting and established in culture by stimulating with the nominal antigen in the presence of irradiated autologous filler cells. In order to generate CD4+ T cell lines, WTl polypeptide is used as the antigenic stimulus and autologous peripheral blood lymphocytes (PBL) or lymphoblastoid cell lines (LCL) immortalized by infection with Epstein Barr virus are used as antigen presenting cells. In order to generate CD8+ T cell lines, autologous antigen-presenting cells transfected with an expression vector which produces WTl polypeptide may be used as stimulator cells. Established T cell lines may be cloned 2-4 days following antigen stimulation by plating stimulated T cells at a frequency of 0.5 cells per well in 96-well flat-bottom plates with 1 x 10° irradiated PBL or LCL cells and recombinant interleukin-2 (rIL2) (50 U/ml). Wells with established clonal growth may be identified at approximately 2-3 weeks after initial plating and restimulated with appropriate antigen in the presence of autologous antigen-presenting cells, then subsequently expanded by the addition of low doses of rIL2 (10 U/ml) 2-3 days following antigen stimulation. T cell clones may be maintained in 24-well plates by periodic restimulation with antigen and rIL2 approximately every two weeks.
Within certain embodiments, allogeneic T-cells may be primed (i.e., sensitized to WTl) in vivo and/or in vitro. Such priming may be achieved by contacting T cells with a WTl polypeptide, a polynucleotide encoding such a polypeptide or a cell producing such a polypeptide under conditions and for a time sufficient to permit the priming of T cells. In general, T cells are considered to be primed if, for example, contact with a WTl polypeptide results in proliferation and/or activation of the T cells, as measured by standard proliferation, chromium release and/or cytokine release assays as described herein. A stimulation index of more than two fold increase in proliferation or lysis, and more than three fold increase in the level of cytokine, compared to negative controls, indicates T-cell specificity. Cells primed in vitro may be employed, for example, within a bone marrow transplantation or as donor lymphocyte infusion.
T cells specific for WTl can kill cells that express WTl protein. Introduction of genes encoding T-cell receptor (TCR) chains for WTl are used as a means to quantitatively and qualitatively improve responses to WTl bearing leukemia and cancer cells. Vaccines to increase the number of T cells that can react to WTl positive cells are one method of targeting WTl bearing cells. T cell therapy with T cells specific for WTl is another method. An alternative method is to introduce the TCR chains specific for WTl into T cells or other cells with lytic potential. In a suitable embodiment, the TCR alpha and beta chains are cloned out from a WTl specific T cell line and used for adoptive T cell therapy, such as described in WO96/30516, incorporated herein by reference.
Pharmaceutical Compositions and Vaccines
Within certain aspects, polypeptides, polynucleotides, antibodies and/or T cells may be incorporated into pharmaceutical compositions or vaccines. Alternatively, a pharmaceutical composition may comprise an antigen-presenting cell (e.g., a dendritic cell) transfected with a WTl polynucleotide such that the antigen presenting cell expresses a WTl polypeptide. Pharmaceutical compositions comprise one or more such compounds or cells and a physiologically acceptable carrier or excipient. Certain vaccines may comprise one or more such compounds or cells and a non-specific immune response enhancer, such as an adjuvant or a liposome (into which the compound is incorporated). Pharmaceutical compositions and vaccines may additionally contain a delivery system, such as biodegradable microspheres which are disclosed, for example, in U.S. Patent Nos. 4,897,268 and 5,075,109. Pharmaceutical compositions and vaccines within the scope of the present invention may also contain other compounds, which may be biologically active or inactive. Within certain embodiments, pharmaceutical compositions and vaccines are designed to elicit T cell responses specific for a WTl polypeptide in a patient, such as a human. In general, T cell responses may be favored through the use of relatively short polypeptides (e.g., comprising less than 23 consecutive amino acid residues of a native WTl polypeptide, preferably 4-16 consecutive residues, more preferably 8-16 consecutive residues and still more preferably 8-10 consecutive residues. Alternatively, or in addition, a vaccine may comprise a non-specific immune response enhancer that preferentially enhances a T cell response. In other words, the immune response enhancer may enhance the level of a T cell response to a WTl polypeptide by an amount that is proportionally greater than the amount by which an antibody response is enhanced. For example, when compared to a standard oil based adjuvant, such as CFA, an immune response enhancer that preferentially enhances a T cell response may enhance a proliferative T cell response by at least two fold, a lytic response by at least 10%, and/or T cell activation by at least two fold compared to WTl-megative control cell lines, while not detectably enhancing an antibody response. The amount by which a T cell or antibody response to a WTl polypeptide is enhanced may generally be determined using any representative technique known in the art, such as the teclmiques provided herein.
A pharmaceutical composition or vaccine may contain DNA encoding one or more of the polypeptides as described above, such that the polypeptide is generated in situ. As noted above, the DNA may be present within any of a variety of delivery systems known to those of ordinaiy skill in the art, including nucleic acid expression systems, bacterial and viral expression systems and mammalian expression systems. Appropriate nucleic acid expression systems contain the necessary DNA, cDNA or RNA sequences for expression in the patient (such as a suitable promoter and terminating signal). Bacterial delivery systems involve the administration of a bacterium (such as Bacillus-Calmette-Guerrin) that expresses an immunogenic portion of the polypeptide on its cell surface. In a preferred embodiment, the DNA may be introduced using a viral expression system (e.g., vaccinia or other pox virus, retrovirus, or adenovirus), which may involve the use of a non-pathogenic (defective), replication competent virus. Techniques for incorporating DNA into such expression systems are well known to those of ordinary skill in the art. The DNA may also be "naked," as described, for example, in Ulmer et al., Science 259:1145-1149, 1993 and reviewed by Cohen, Science 259:1691-1692, 1993. The uptake of naked DNA may be increased by coating the DNA onto biodegradable beads, which are efficiently transported into the cells.
As noted above, a pharmaceutical composition or vaccine may comprise an antigen-presenting cell that expresses a WTl polypeptide. For therapeutic purposes, as described herein, the antigen presenting cell is preferably an autologous dendritic cell. Such cells may be prepared and transfected using standard techniques, such as those described by Reeves et al., Cancer Res. 56:5612-5611, 1996; Tuting et al., J. Immunol. 750:1139-1147, 1998; and Nair et al., Nature Biotechnol i 6:364-369, 1998). Expression of a WTl polypeptide on the surface of an antigen-presenting cell may be confirmed by in vitro stimulation and standard proliferation as well as chromium release assays, as described herein.
While any suitable carrier known to those of ordinary skill in the art may be employed in the pharmaceutical compositions of this invention, the type of carrier will vary depending on the mode of administration. Compositions of the present invention may be formulated for any appropriate manner of administration, including for example, topical, oral, nasal, intravenous, intracranial, intraperitoneal, subcutaneous or intramuscular administration. For parenteral administration, such as subcutaneous injection, the carrier preferably comprises water, saline, alcohol, a fat, a wax or a buffer. For oral administration, any of the above carriers or a solid carrier, such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, glucose, sucrose, and magnesium carbonate, may be employed. Biodegradable microspheres (e.g., polylactate polyglycolate) may also be employed as earners for the pharmaceutical compositions of this invention. For certain topical applications, formulation as a cream or lotion, using well known components, is preferred.
Such compositions may also comprise buffers (e.g., neutral buffered saline or phosphate buffered saline), carbohydrates (e.g., glucose, mannose, sucrose or dextrans), mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, chelating agents such as EDTA or glutathione, adjuvants (e.g., aluminum hydroxide) and/or preservatives. Alternatively, compositions of the present invention may be formulated as a lyophilizate. Compounds may also be encapsulated within liposomes using well known technology. In one embodiment of the present invention, compositions comprise a buffer comprising one or more sugars including, but not limited to, trehalose, maltose, sucrose, fructose, and glucose, each at a concentration generally between about 1 and 25%, typically between about 7 and 13 %. In a further embodiment, the concentration is between about 8 and about 12%. In yet a further embodiment the concentration is about 10%. In an additional aspect of the present invention, the compositions may comprise ethanolamine; cysteine; or Polysorbate-80, generally at concentrations effective for enhancing the efficacy, stability and/or solubility of the formulation. Any of a variety of non-specific immune response enhancers, such as adjuvants, may be employed in the vaccines of this invention. Most adjuvants contain a substance designed to protect the antigen from rapid catabolism, such as aluminum hydroxide or mineral oil, and a stimulator of immune responses, such as lipid A, Bortadella pertussis or Mycobacterium tuberculosis derived proteins. Suitable nonspecific immune response enhancers include alum-based adjuvants (e.g., Alhydrogel, Rehydragel, aluminum phosphate, Algammulin, aluminum hydroxide); oil based adjuvants (Freund's adjuvant (FA), Specol, RIBI, TiterMax, Montanide ISA50 or Montanide ISA 720 (Seppic, France); cytokines (e.g., GM-CSF or Flat3 -ligand); microspheres; nonionic block copolymer-based adjuvants; dimethyl dioctadecyl ammoniumbromide (DDA) based adjuvants AS-1, AS-2 (Smith Kline Beecham); Ribi Adjuvant system based adjuvants; QS21 (Aquila); saponin based adjuvants (crude saponin, the saponin Quil A ); muramyl dipeptide (MDP) based adjuvants such as SAF (Syntex adjuvant in its microfluidized form (SAF-m)); dimethyl-dioctadecyl ammonium bromide (DDA); human complement based adjuvants m. vaccae and derivatives; immune stimulating complex (iscom) based adjuvants; inactivated toxins; and attenuated infectious agents (such as M. tuberculosis).
Additional illustrative adjuvants for use in the pharmaceutical compositions of the invention include, SAF (Chiron, California, United States), ISCOMS (CSL), MF-59 (Chiron), the SBAS series of adjuvants (e.g., SBAS-2 or SBAS-4, available from SmithKline Beecham, Rixensart, Belgium), Detox (Enhanzyn®) (Corixa, Hamilton, MT), RC-529 (Corixa, Hamilton, MT) and other aminoalkyl glucosaminide 4-phosphates (AGPs), such as those described in pending U.S. Patent Application Serial Nos. 08/853,826 and 09/074,720, the disclosures of which are incorporated herein by reference in their entireties, and polyoxyethylene ether adjuvants such as those described in WO 99/52549A1.
Other preferred adjuvants include adjuvant molecules of the general formula
(I): HO(CH2CH20)n-A-R, wherein, n is 1-50, A is a bond or -C(O)-, R is C]-5o alkyl or Phenyl Cι-5o alkyl. One embodiment of the present invention consists of a vaccine formulation comprising a polyoxyethylene ether of general formula (I), wherein n is between 1 and 50, preferably 4-24, most preferably 9; the R component is C1-.50, preferably C -C20 alkyl and most preferably C12 alkyl, and A is a bond. The concentration of the polyoxyethylene ethers should be in the range 0.1-20%, preferably from OJ-10%, and most preferably in the range OJ-1%. Preferred polyoxyethylene ethers are selected from the following group: polyoxyethylene-9-lauryl ether, polyoxyethylene-9-steoryl ether, polyoxyethylene- 8-steoryl ether, polyoxyethylene-4- lauryl ether, polyoxyethylene-35-lauryl ether, and polyoxyethylene-23-lauryl ether. Polyoxyethylene ethers such as polyoxyethylene lauryl ether are described in the Merck index (12th edition: entry 7717). These adjuvant molecules are described in WO 99/52549.
The polyoxyethylene ether according to the general formula (I) above may, if desired, be combined with another adjuvant. For example, a preferred adjuvant combination is preferably with CpG as described in the pending UK patent application GB 9820956.2.
As noted above, within certain embodiments, immune response enhancers are chosen for their ability to preferentially elicit or enhance a T cell response (e.g., CD4+ and/or CD8+) to a WTl polypeptide. Such immune response enhancers are well known in the art, and include (but are not limited to) Montanide ISA50, Seppic MONTANIDE ISA 720, cytokines (e.g., GM-CSF, Flat3 -ligand), microspheres, dimethyl dioctadecyl ammoniumbromide (DDA) based adjuvants, AS-1 (Smith Kline Beecham), AS-2 (Smith Kline Beecham), Ribi Adjuvant system based adjuvants, QS21 (Aquila), saponin based adjuvants (crude saponin, the saponin Quil A), Syntex adjuvant in its microfluidized form (SAF-m), MV, ddMV (Genesis), immune stimulating complex (iscom) based adjuvants and inactivated toxins.
In another aspect of the present invention, compositions may comprise adjuvants for eliciting a predominantly Thl -type response. Certain preferred adjuvants for eliciting a predominantly Thl -type response include, for example, a combination of monophosphoryl lipid A, preferably 3-de-O-acylated monophosphoryl lipid A, together with an aluminum salt. MPL adjuvants, such as MPL-SE, are available from Corixa Corporation (Seattle, WA; see, for example, US Patent Nos. 4,436,727; 4,877,611 ; 4,866,034 and 4,912,094, incorporated herein in their entirety). CpG-containing oligonucleotides (in which the CpG dinucleotide is unmefhylated) also induce a predominantly Thl response. Such oligonucleotides are well known and are described, for example, in WO 96/02555, WO 99/33488 and U.S. Patent Nos. 6,008,200 and 5,856,462. Immunostimulatory DNA sequences are also described, for example, by Sato et al., Science 273:352, 1996. Another preferred adjuvant comprises a saponin, such as Quil A, or derivatives thereof, including QS21 and QS7 (Aquila Biopharmaceuticals Inc., Framingham, MA); Escin; Digitonin; or Gypsophila or Chenopodium quinoa saponins . Other preferred formulations include more than one saponin in the adjuvant combinations of the present invention, for example combinations of at least two of the following group comprising QS21, QS7, Quil A, β- escin, or digitonin.
The compositions and vaccines described herein may be administered as part of a sustained release formulation (i.e., a formulation such as a capsule or sponge that effects a slow release of compound following administration). Such formulations may generally be prepared using well known technology and administered by, for example, oral, rectal or subcutaneous implantation, or by implantation at the desired target site. Sustained-release formulations may contain a polypeptide, polynucleotide, antibody or cell dispersed in a carrier matrix and/or contained within a reservoir surrounded by a rate controlling membrane. Carriers for use within such formulations are biocompatible, and may also be biodegradable; preferably the formulation provides a relatively constant level of active component release. The amount of active compound contained within a sustained release formulation depends upon the site of implantation, the rate and expected duration of release and the nature of the condition to be treated or prevented.
Therapy of Malignant Diseases
In further aspects of the present invention, the compositions and vaccines described herein may be used to inhibit the development of malignant diseases (e.g., progressive or metastatic diseases or diseases characterized by small tumor burden such as minimal residual disease). In general, such methods may be used to prevent, delay or treat a disease associated with WTl expression. In other words, therapeutic methods provided herein may be used to treat an existing WTl -associated disease, or may be used to prevent or delay the onset of such a disease in a patient who is free of disease or who is afflicted with a disease that is not yet associated with WTl expression.
As used herein, a disease is "associated with WTl expression" if diseased cells (e.g., tumor cells) at some time during the course of the disease generate detectably higher levels of a WTl polypeptide than normal cells of the same tissue. Association of WTl expression with a malignant disease does not require that WTl be present on a tumor. For example, overexpression of WTl may be involved with initiation of a tumor, but the protein expression may subsequently be lost. Alternatively, a malignant disease that is not characterized by an increase in WTl expression may, at a later time, progress to a disease that is characterized by increased WTl expression. Accordingly, any malignant disease in which diseased cells formerly expressed, currently express or are expected to subsequently express increased levels of WTl is considered to be "associated with WTl expression."
Immunotherapy may be performed using any of a variety of techniques, in which compounds or cells provided herein function to remove WTl -expressing cells from a patient. Such removal may take place as a result of enhancing or inducing an immune response in a patient specific for WTl or a cell expressing WTl. Alternatively, WTl -expressing cells may be removed ex vivo (e.g., by treatment of autologous bone marrow, peripheral blood or a fraction of bone marrow or peripheral blood). Fractions of bone marrow or peripheral blood may be obtained using any standard technique in the art. Within such methods, pharmaceutical compositions and vaccines may be administered to a patient. As used herein, a "patient" refers to any warm-blooded animal, preferably a human. A patient may or may not be afflicted with a malignant disease. Accordingly, the above pharmaceutical compositions and vaccines may be used to prevent the onset of a disease (i.e., prophylactically) or to treat a patient afflicted with a disease (e.g., to prevent or delay progression and/or metastasis of an existing disease). A patient afflicted with a disease may have a minimal residual disease (e.g., a low tumor burden in a leukemia patient in complete or partial remission or a cancer patient following reduction of the tumor burden after surgery radiotherapy and/or chemotherapy). Such a patient may be immunized to inhibit a relapse (i.e., prevent or delay the relapse, or decrease the severity of a relapse). Within certain preferred embodiments, the patient is afflicted with a leukemia (e.g., AML, CML, ALL or childhood ALL), a myelodysplastic syndrome (MDS) or a cancer (e.g., gastrointestinal, lung, thyroid or breast cancer or a melanoma), where the cancer or leukemia is WTl positive (i.e., reacts detectably with an anti-WTl antibody, as provided herein or expresses WTl mRNA at a level detectable by RT-PCR, as described herein) or suffers from an autoimmune disease directed against WTl -expressing cells.
Other diseases associated with WTl overexpression include kidney cancer (such as renal cell carcinoma, or Wilms tumor), as described in Satoh F., et al., Pathol Int. 50(6):458-71(2000), and Campbell C. E. et al., Int. J. Cancer 78(2):182-8 (1998); and mesothelioma, as described in Amin, K.M. et al., Am. J. Pathol. 146(2):344-56 (1995). Harada et al. (Mol. Urol 3(4):357-364 (1999) describe WTl gene expression in human testicular germ-cell tumors. Nonomura et al. Hinyokika Kiyo 45(8):593-7 (1999) describe molecular staging of testicular cancer using polymerase chain reaction of the testicular cancer-specific genes. Shimizu et al., Int. J. Gynecol. Pathol. 19(2): 158-63 (2000) describe the immunohistochemical detection of the Wilms' tumor gene (WTl) in epithelial ovarian tumors.
WTl overexpression was also described in desmoplastic small round cell tumors, by Barnoud, R. et al., Am. J. Surg. Pathol. 24(6):830-6 (2000); and Pathol. Res. Pract. 194(10):693-700 (1998). WTl overexpression in glioblastoma and other cancer was described by Menssen, H.D. et al., J. Cancer Res. Clin. Oncol. 126(4):226-32 (2000), "Wilms* tumor gene (WTl) expression in lung cancer, colon cancer and glioblastoma cell lines compared to freshly isolated tumor specimens." Other diseases showing WTl overexpression include EBV associated diseases, such as Burkitt's lymphoma and nasopharyngeal cancer (Spinsanti P. et al., Leuk. Lymphoma 38(5- 6):611-9 (2000), "Wilms' tumor gene expression by normal and malignant human B lymphocytes." In Leukemia 14(9):1634-4 (2000), Pan et al., describe in vitro IL-12 treatment of peripheral blood mononuclear cells from patients with leukemia or myelodysplastic syndromes, and reported an increase in cytotoxicity and reduction in WTl gene expression. In Leukemia 13(6):891-900 (1999), Patmasiriwat et al. reported WTl and GATA1 expression in myelodysplastic syndrome and acute leukemia. In Leukemia 13(3):393-9 (1999), Tamaki et al. reported that the Wilms' tumor gene WTl is a good marker for diagnosis of disease progression of myelodysplastic syndromes. Expression of the Wilms' tumor gene WTl in solid tumors, and its involvement in tumor cell growth, was discussed in relation to gastric cancer, colon cancer, lung cancer, breast cancer cell lines, germ cell tumor cell line, ovarian cancer, the uterine cancer, thyroid cancer cell line, hepatocellular carcinoma, in Oji et al., Jpn. J. Cancer Res. 90(2):194-204 (1999).
The compositions provided herein may be used alone or in combination with conventional therapeutic regimens such as surgery, irradiation, chemotherapy and/or bone marrow transplantation (autologous, syngeneic, allogeneic or unrelated). As discussed in greater detail below, binding agents and T cells as provided herein may be used for purging of autologous stem cells. Such purging may be beneficial prior to, for example, bone marrow transplantation or transfusion of blood or components thereof. Binding agents, T cells, antigen presenting cells (APC) and compositions provided herein may further be used for expanding and stimulating (or priming) autologous, allogeneic, syngeneic or unrelated WTl -specific T-cells in vitro and/or in vivo. Such WTl -specific T cells may be used, for example, within donor lymphocyte infusions.
Routes and frequency of administration, as well as dosage, will vary from individual to individual, and may be readily established using standard techniques. In general, the pharmaceutical compositions and vaccines may be administered by injection (e.g., intracutaneous, intramuscular, intravenous or subcutaneous), intranasally (e.g., by aspiration) or orally. In some tumors, pharmaceutical compositions or vaccines may be administered locally (by, for example, rectocoloscopy, gastroscopy, videoendoscopy, angiography or other methods known in the art). Preferably, between 1 and 10 doses may be administered over a 52 week period. Preferably, 6 doses are administered, at intervals of 1 month, and booster vaccinations may be given periodically thereafter. Alternate protocols may be appropriate for individual patients. A suitable dose is an amount of a compound that, when administered as described above, is capable of promoting an anti-tumor immune response that is at least 10-50% above the basal (i.e., untreated) level. Such response can be monitored by measuring the anti-tumor antibodies in a patient or by vaccine-dependent generation of cytolytic effector cells capable of killing the patient's tumor cells in vitro. Such vaccines should also be capable of causing an immune response that leads to an improved clinical outcome (e.g., more frequent complete or partial remissions, or longer disease-free and/or overall survival) in vaccinated patients as compared to non- vaccinated patients. In general, for pharmaceutical compositions and vaccines comprising one or more polypeptides, the amount of each polypeptide present in a dose ranges from about 100 μg to 5 mg. Suitable dose sizes will vary with the size of the patient, but will typically range from about 0J mL to about 5 mL. In general, an appropriate dosage and treatment regimen provides the active compound(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit. Such a response can be monitored by establishing an improved clinical outcome (e.g., more frequent complete or partial remissions, or longer disease-free and/or overall survival) in treated patients as compared to non-treated patients. Increases in preexisting immune responses to WTl generally correlate with an improved clinical outcome. Such immune responses may generally be evaluated using standard proliferation, cytotoxicity or cytokine assays, which may be performed using samples obtained from a patient before and after treatment.
Within further aspects, methods for inhibiting the development of a malignant disease associated with WTl expression involve the administration of autologous T cells that have been activated in response to a WTl polypeptide or WT1- expressing APC, as described above. Such T cells may be CD4+ and/or CD8+, and may be proliferated as described above. The T cells may be administered to the individual in an amount effective to inhibit the development of a malignant disease. Typically, about
9 11 2 1 x 10 to 1 x 10 T cells/M are administered intravenously, intracavitaiy or in the bed of a resected tumor. It will be evident to those skilled in the art that the number of cells and the frequency of administration will be dependent upon the response of the patient.
Within certain embodiments, T cells may be stimulated prior to an autologous bone marrow transplantation. Such stimulation may take place in vivo or in vitro. For in vitro stimulation, bone marrow and/or peripheral blood (or a fraction of bone marrow or peripheral blood) obtained from a patient may be contacted with a WTl polypeptide, a polynucleotide encoding a WTl polypeptide and/or an APC that expresses a WTl polypeptide under conditions and for a time sufficient to permit the stimulation of T cells as described above. Bone marrow, peripheral blood stem cells and/or WTl -specific T cells may then be administered to a patient using standard teclmiques.
Within related embodiments, T cells of a related or unrelated donor may be stimulated prior to a syngeneic or allogeneic (related or unrelated) bone marrow transplantation. Such stimulation may take place in vivo or in vitro. For in vitro stimulation, bone marrow and/or peripheral blood (or a fraction of bone marrow or peripheral blood) obtained from a related or unrelated donor may be contacted with a WTl polypeptide, WTl polynucleotide and/or APC that expresses a WTl polypeptide under conditions and for a time sufficient to permit the stimulation of T cells as described above. Bone marrow, peripheral blood stem cells and/or WTl -specific T cells may then be administered to a patient using standard techniques.
Within other embodiments, WTl -specific T cells as described herein may be used to remove cells expressing WTl from autologous bone marrow, peripheral blood or a fraction of bone marrow or peripheral blood (e.g., CD34+ enriched peripheral blood (PB) prior to administration to a patient). Such methods may be performed by contacting bone marrow or PB with such T cells under conditions and for a time sufficient to permit the reduction of WTl expressing cells to less than 10%, preferably less than 5% and more preferably less than 1%, of the total number of myeloid or lymphatic cells in the bone marrow or peripheral blood. The extent to which such cells have been removed may be readily determined by standard methods such as, for example, qualitative and quantitative PCR analysis, morphology, immunohistochemistry and FACS analysis. Bone marrow or PB (or a fraction thereof) may then be administered to a patient using standard techniques.
Diagnostic Methods
The present invention further provides methods for detecting a malignant disease associated with WTl expression, and for monitoring the effectiveness of an immunization or therapy for such a disease. Such methods are based on the discovery, within the present invention, that an immune response specific for WTl protein can be detected in patients afflicted with such diseases, and that methods which enhance such immune responses may provide a preventive or therapeutic benefit. To determine the presence or absence of a malignant disease associated with WTl expression, a patient may be tested for the level of T cells specific for WTl. Within certain methods, a biological sample comprising CD4+ and/or CD8+ T cells isolated from a patient is incubated with a WTl polypeptide, a polynucleotide encoding a WTl polypeptide and/or an APC that expresses a WTl polypeptide, and the presence or absence of specific activation of the T cells is detected, as described herein. Suitable biological samples include, but are not limited to, isolated T cells. For example, T cells may be isolated from a patient by routine techniques (such as by Ficoll/Hypaque density gradient centrifugation of peripheral blood lymphocytes). T cells may be incubated in vitro for 2-9 days (typically 4 days) at 37°C with WTl polypeptide (e.g., 5 - 25 μg/ml). It may be desirable to incubate another aliquot of a T cell sample in the absence of WTl polypeptide to serve as a control. For CD4+ T cells, activation is preferably detected by evaluating proliferation of the T cells. For CD8+ T cells, activation is preferably detected by evaluating cytolytic activity. A level of proliferation that is at least two fold greater and/or a level of cytolytic activity that is at least 20% greater than in disease- free patients indicates the presence of a malignant disease associated with WTl expression. Further correlation may be made, using methods well known in the art, between the level of proliferation and/or cytolytic activity and the predicted response to therapy. In particular, patients that display a higher antibody, proliferative and/or lytic response may be expected to show a greater response to therapy. Within other methods, a biological sample obtained from a patient is tested for the level of antibody specific for WTl. The biological sample is incubated with a WTl polypeptide, a polynucleotide encoding a WTl polypeptide and/or an APC that expresses a WTl polypeptide under conditions and for a time sufficient to allow immunocomplexes to form. Immunocomplexes formed between the WTl polypeptide and antibodies in the biological sample that specifically bind to the WTl polypeptide are then detected. A biological sample for use within such methods may be any sample obtained from a patient that would be expected to contain antibodies. Suitable biological samples include blood, sera, ascites, bone marrow, pleural effusion, and cerebrospinal fluid.
The biological sample is incubated with the WTl polypeptide in a reaction mixture under conditions and for a time sufficient to permit immunocomplexes to form between the polypeptide and antibodies specific for WTl. For example, a biological sample and WTl polypeptide may be incubated at 4°C for 24-48 hours. Following the incubation, the reaction mixture is tested for the presence of immunocomplexes. Detection of immunocomplexes formed between the WTl polypeptide and antibodies present in the biological sample may be accomplished by a variety of known techniques, such as radioimmunoassays (RIA) and enzyme linked immunosorbent assays (ELISA). Suitable assays are well known in the art and are amply described in the scientific and patent literature (e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988). Assays that may be used include, but are not limited to, the double monoclonal antibody sandwich immunoassay technique of David et al. (U.S. Patent 4,376,H0); monoclonal-polyclonal antibody sandwich assays (Wide et al., in Kirkham and Hunter, eds., Radioimmunoassay Methods, E. and S. Livingstone, Edinburgh, 1970); the "western blot" method of Gordon et al. (U.S. Patent 4,452,901); immunoprecipitation of labeled ligand (Brown et al., J. Biol. Chem. 255:4980-4983, 1980); enzyme-linked immunosorbent assays as described by, for example, Raines and Ross (J. Biol. Chem. 257:5154-5160, 1982); immunocytochemical techniques, including the use of fluorochromes (Brooks et al, Clin. Exp. Immunol. 39: 477, 1980); and neutralization of activity (Bowen-Pope et al., Proc. Natl. Acad. Sci. USA 5.7:2396-2400, 1984). Other immunoassays include, but are not limited to, those described in U.S. Patent Nos.: 3,817,827; 3,850,752; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; and 4,098,876.
For detection purposes, WTl polypeptide may either be labeled or unlabeled. Unlabeled WTl polypeptide may be used in agglutination assays or in combination with labeled detection reagents that bind to the immunocomplexes (e.g., anti-immunoglobulin, protein G, protein A or a lectin and secondary antibodies, or antigen-binding fragments thereof, capable of binding to the antibodies that specifically bind to the WTl polypeptide). If the WTl polypeptide is labeled, the reporter group may be any suitable reporter group known in the art, including radioisotopes, fluorescent groups, luminescent groups, enzymes, biotin and dye particles.
Within certain assays, unlabeled WTl polypeptide is immobilized on a solid support. The solid support may be any material known to those of ordinary skill in the art to which the polypeptide may be attached. For example, the solid support may be a test well in a microtiter plate or a nitrocellulose or other suitable membrane. Alternatively, the support may be a bead or disc, such as glass, fiberglass, latex or a plastic material such as polystyrene or polyvinylchloride. The support may also be a magnetic particle or a fiber optic sensor, such as those disclosed, for example, in U.S. Patent No. 5,359,681. The polypeptide may be immobilized on the solid support using a variety of techniques known to those of skill in the art, which are amply described in the patent and scientific literature. In the context of the present invention, the term "immobilization" refers to both noncovalent association, such as adsorption, and covalent attachment (which may be a direct linkage between the antigen and functional groups on the support or may be a linkage by way of a cross-linking agent). Immobilization by adsorption to a well in a microtiter plate or to a membrane is preferred. In such cases, adsorption may be achieved by contacting the WTl polypeptide, in a suitable buffer, with the solid support for a suitable amount of time. The contact time varies with temperature, but is typically between about 1 hour and about 1 day. In general, contacting a well of a plastic microtiter plate (such as polystyrene or polyvinylchloride) with an amount of polypeptide ranging from about 10 ng to about 10 μg, and preferably about 100 ng to about 1 μg, is sufficient to immobilize an adequate amount of polypeptide.
Following immobilization, the remaining protein binding sites on the support are typically blocked. Any suitable blocking agent known to those of ordinary skill in the art, such as bovine serum albumin, Tween 20™ (Sigma Chemical Co., St. Louis, MO), heat-inactivated normal goat serum (NGS), or BLOTTO (buffered solution of nonfat dry milk which also contains a preservative, salts, and an antifoaming agent). The support is then incubated with a biological sample suspected of containing specific antibody. The sample can be applied neat, or, more often, it can be diluted, usually in a buffered solution which contains a small amount (0J%-5.0% by weight) of protein, such as BSA, NGS, or BLOTTO. In general, an appropriate contact time (i.e., incubation time) is a period of time that is sufficient to detect the presence of antibody that specifically binds WTl within a sample containing such an antibody. Preferably, the contact time is sufficient to achieve a level of binding that is at least about 95% of that achieved at equilibrium between bound and unbound antibody. Those of ordinary skill in the art will recognize that the time necessary to achieve equilibrium may be readily determined by assaying the level of binding that occurs over a period of time. At room temperature, an incubation time of about 30 minutes is generally sufficient.
Unbound sample may then be removed by washing the solid support with an appropriate buffer, such as PBS containing 0.1% Tween 20™. A detection reagent that binds to the immunocomplexes and that comprises a reporter group may then be added. The detection reagent is incubated with the immunocomplex for an amount of time sufficient to detect the bound antibody. An appropriate amount of time may generally be determined by assaying the level of binding that occurs over a period of time. Unbound detection reagent is then removed and bound detection reagent is detected using the reporter group. The method employed for detecting the reporter group depends upon the nature of the reporter group. For radioactive groups, scintillation counting or autoradiographic methods are generally appropriate. Spectroscopic methods may be used to detect dyes, luminescent groups and fluorescent groups. Biotin may be detected using avidin, coupled to a different reporter group (commonly a radioactive or fluorescent group or an enzyme). Enzyme reporter groups (e.g., horseradish peroxidase, beta-galactosidase, alkaline phosphatase and glucose oxidase) may generally be detected by the addition of substrate (generally for a specific period of time), followed by spectroscopic or other analysis of the reaction products. Regardless of the specific method employed, a level of bound detection reagent that is at least two fold greater than background (i.e., the level observed for a biological sample obtained from a disease-free individual) indicates the presence of a malignant disease associated with WTl expression.
In general, methods for monitoring the effectiveness of an immunization or therapy involve monitoring changes in the level of antibodies or T cells specific for WTl in the patient. Methods in which antibody levels are monitored may comprise the steps of: (a) incubating a first biological sample, obtained from a patient prior to a therapy or immunization, with a WTl polypeptide, wherein the incubation is performed under conditions and for a time sufficient to allow immunocomplexes to form; (b) detecting immunocomplexes formed between the WTl polypeptide and antibodies in the biological sample that specifically bind to the WTl polypeptide; (c) repeating steps (a) and (b) using a second biological sample taken from the patient following therapy or immunization; and (d) comparing the number of immunocomplexes detected in the first and second biological samples. Alternatively, a polynucleotide encoding a WTl polypeptide, or an APC expressing a WTl polypeptide may be employed in place of the WTl polypeptide. Within such methods, immunocomplexes between the WTl polypeptide encoded by the polynucleotide, or expressed by the APC, and antibodies in the biological sample are detected.
Methods in which T cell activation and/or the number of WTl specific precursors are monitored may comprise the steps of: (a) incubating a first biological sample comprising CD4+ and/or CD8+ cells (e.g., bone marrow, peripheral blood or a fraction thereof), obtained from a patient prior to a therapy or immunization, with a WTl polypeptide, wherein the incubation is performed under conditions and for a time sufficient to allow specific activation, proliferation and/or lysis of T cells; (b) detecting an amount of activation, proliferation and/or lysis of the T cells; (c) repeating steps (a) and (b) using a second biological sample comprising CD4+ and/or CD8+ T cells, and taken from the same patient following therapy or immunization; and (d) comparing the amount of activation, proliferation and/or lysis of T cells in the first and second biological samples. Alternatively, a polynucleotide encoding a WTl polypeptide, or an APC expressing a WTl polypeptide may be employed in place of the WTl polypeptide. A biological sample for use within such methods may be any sample obtained from a patient that would be expected to contain antibodies, CD4+ T cells and/or CD8+ T cells. Suitable biological samples include blood, sera, ascites, bone marrow, pleural effusion and cerebrospinal fluid. A first biological sample may be obtained prior to initiation of therapy or immunization or part way through a therapy or vaccination regime. The second biological sample should be obtained in a similar manner, but at a time following additional therapy or immunization. The second biological sample may be obtained at the completion of, or part way through, therapy or immunization, provided that at least a portion of therapy or immunization takes place between the isolation of the first and second biological samples.
Incubation and detection steps for both samples may generally be performed as described above. A statistically significant increase in the number of immunocomplexes in the second sample relative to the first sample reflects successful therapy or immunization.
The following Examples are offered by way of illustration and not by way of limitation. EXAMPLES
EXAMPLE 1 IDENTIFICATION OF AN IMMUNE RESPONSE TO WTl IN PATIENTS WITH HEMATOLOGICAL MALIGNANCIES This Example illustrates the identification of an existent immune response in patients with a hematological malignancy.
To evaluate the presence of preexisting WTl specific antibody responses in patients, sera of patients with acute myelogenous leukemia (AML), acute lymphocytic leukemia (ALL), chronic myelogenous leukemia (CML) and severe aplastic anemia were analyzed using Western blot analysis. Sera were tested for the ability to immunoprecipitate WTl from the human leukemic cell line K562 (American Type Culture Collection, Manassas, VA). In each case, immunoprecipitates were separated by gel electrophoresis, transferred to membrane and probed with the anti WTl antibody WTl 80 (Santa Cruz Biotechnology, Inc., Santa Cruz, CA). This Western blot analysis identified potential WTl specific antibodies in patients with hematological malignancy. A representative Western blot showing the results for a patient with AML is shown in Figure 2. A 52 kD protein in the immunoprecipitate generated using the patient sera was recognized by the WTl specific antibody. The 52 kD protein migrated at the same size as the positive control.
Additional studies analyzed the sera of patients with AML and CML for the presence of antibodies to full-length and truncated WTl proteins. CDNA constructs representing the human WTl /full-length (aa 1-449), the N-terminus (aa 1-249) (WTl /N-terminus) and C-terminus (aa 267-449) (WTl /C-terminus) region were subcloned into modified pET28 vectors. The WTl/full-length and WTl /N-terminus proteins were expressed as Ral2 fusion proteins. Ral2 is the C-terminal fragment of a secreted Mycobacterium tuberculosis protein, denoted as MTB32B. (Skeiky et al., Infect Immun. 67;3998, 1999). The Ral2-WTl/full-length fusion region was cloned 3' to a histidine-tag in a histidine-tag modified pET28 vector. The WTl N-terminus region was subcloned into a modified pET28 vector that has a 5' histidine-tag followed by the thioredoxin (TRX)- WTl /N-terminus fusion region followed by a 3' histidine-tag. The WTl/C-terminus coding region was subcloned into a modified pET28 vector without a fusion partner containing only the 5' and 3' histidine-tag, followed by a Thrombin and EK site.
BL21 pLysS E. coli (Stratagene, La Jolla, CA) were transformed with the three WTl expression constructs, grown overnight and induced with isopropyl-β-D- thiogalactoside (IPTG). WTl proteins were purified as follows: Cells were harvested and lysed by incubation in lOmM Tris, pH 8.0 with Complete Protease Inhibitor Tablets (Boehringer Mannheim Biochemicals, Indianapolis, IN) at 37°C followed by repeated rounds of sonication. Inclusion bodies were washed twice with lOmM Tris, pH 8.0. Proteins were then purified by metal chelate affinity chromatography over nickel- nitrilotriacetic acid resin (QIAGEN Inc., Valencia, CA; Hochuli et al, Biologically Active Molecules :217, 1989) followed by chromatography on a Source Q anion exchange resin (Amersham Pharmacia Biotech, Upsala, Sweden). The identity of the WTl proteins was confirmed by N-terminal sequencing.
Sera from adult patients with de nova AML or CML were studied for the presence of WTl specific Ab. Recombinant proteins were adsorbed to TC microwell plates (Nunc, Roskilde, Denmark). Plates were washed with PBS/0.5%Tween 20 and blocked with 1% BSA/PBS/OJ%Tween 20. After washing, serum dilutions were added and incubated overnight at 4°C. Plates were washed and Donkey anti-human IgG-HRP secondary antibody was added (Jackson-Immunochem, West Grove, PA) and incubated for 2h at room temperature. Plates were washed, incubated with TMB Peroxidase substrate solution (Kirkegaard and Perry Laboratories, MA), quenched with IN H2S04, and immediately read (Cyto-Fluor 2350; Millipore, Bedford, MA).
For the serological survey, human sera were tested by ELISA over a range of serial dilutions from 1:50 to 1:20,000. A positive reaction was defined as an OD value of a 1:500 diluted serum that exceeded the mean OD value of sera from normal donors (n=96) by three (WTl /full-length, WTl C-terminus) standard deviations. Due to a higher background in normal donors to the WTl /N-terminus protein a positive reaction to WTl/N-terminus was defined as an OD value of 1 :500 diluted serum that exceeded the mean OD value of sera from normal donors by four standard deviations. To verify that the patient Ab response was directed against WTl and not to the Ral2 or TRX fusion part of the protein or possible E. coli contaminant proteins, controls included the Ral2 and TRX protein alone purified in a similar manner. Samples that showed reactivity against the Ral2 and/or TRX proteins were excluded from the analysis.
To evaluate for the presence of immunity to WTl, Ab to recombinant full-length and truncated WTl proteins in the sera of normal individuals and patients with leukemia were determined. Antibody reactivity was analyzed by ELISA reactivity to WTl /full-length protein, WTl /N-terminus protein and WTl/C-terminus protein.
Only 2 of 96 normal donors had serum antibodies reactive with WTl/full-length protein (Figure 18). One of those individuals had antibody to WT1/N- terminus protein and one had antibody to WTl/C-terminus protein. In contrast, 16 of 63 patients (25%) with AML had serum antibodies reactive with WTl/full-length protein. By marked contrast, only 2 of 63 patients (3%) had reactivity to WTl/C- terminus protein. Fifteen of 81 patients (19%) with CML had serum antibodies reactive with WTl/full-length protein and 12 of 81 patients (15%) had serum antibodies reactive with WTl/N-terminus. Only 3 of 81 patients (3%) had reactivity to WTl/C-terminus protein. (Figures 16 and 17.)
These data demonstrate that Ab responses to WTl are detectable in some patients with AML and CML. The greater incidence of antibody in leukemia patients provides strong evidence that immunization to the WTl protein occurred as a result of patients bearing malignancy that expresses or at some time expressed WTl. Without being limited to a specific theory, it is believed that the observed antibody responses to WTl most probably result from patients becoming immune to WTl on their own leukemia cells and provide direct evidence that WTl can be immunogenic despite being a "self protein.
The presence of antibody to WTl strongly implies that concurrent helper T cell responses are also present in the same patients. WTl is an internal protein. Thus,
CTL responses are likely to be the most effective in terms of leukemia therapy and the most toxic arm of immunity. Thus, these data provide evidence that therapeutic vaccines directed against WTl will be able to elicit an immune response to WTl.
The majority of the antibodies detected were reactive with epitopes within the N-terminus while only a small subgroup of patients showed a weak antibody response to the C-terminus. This is consistent with observations in the animal model, where immunization with peptides derived from the N-terminus elicited antibody, helper T cell and CTL responses, whereas none of the peptides tested from the C- terminus elicited antibody or T cell responses (Gaiger et al., Blood 96: 1334, 2000).
EXAMPLE 2 INDUCTION OF ANTIBODIES TO WTl IN MICE IMMUNIZED WITH CELL LINES EXPRESSING WTl This Example illustrates the use of cells expressing WTl to induce a WTl specific antibody response in vivo. Detection of existent antibodies to WTl in patients with leukemia strongly implied that it is possible to immunize to WTl protein to elicit immunity to WTl. To test whether immunity to WTl can be generated by vaccination, mice were injected with TRAMP-C, a WTl positive tumor cell line of B6 origin. Briefly, male B6 mice were immunized with 5 x 106 TRAMP-C cells subcutaneously and boosted twice with 5 x 106 cells at three week intervals. Three weeks after the final immunization, sera were obtained and single cell suspensions of spleens were prepared in RPMI 1640 medium (GIBCO) with 25μM β-2-mercaptoethanol, 200 units of penicillin per ml, lOmM L-glutamine, and 10% fetal bovine serum.
Following immunization to TRAMP-C, a WTl specific antibody response in the immunized animals was detectable. A representative Western blot is shown in Figure 3. These results show that immunization to WTl protein can elicit an immune response to WTl protein.
EXAMPLE 3
INDUCTION OF TH AND ANTIBODY RESPONSES IN MICE IMMUNIZED WITH WTl PEPTIDES This Example illustrates the ability of immunization with WTl peptides to elicit an immune response specific for WTl.
Peptides suitable for eliciting Ab and proliferative T cell responses were identified according to the Tsites program (Rothbard and Taylor, EMBO J. 7:93-100,
1988; Deavin et al., Mol. Immunol. 33:145-155, 1996), which searches for peptide motifs that have the potential to elicit Th responses. Peptides shown in Table I were synthesized and sequenced.
Table I WTl Peptides
Figure imgf000057_0001
Figure imgf000058_0001
For immunization, peptides were grouped as follows:
Group A: p6-22 human: 10.9mg in 1ml (lOμl = lOOμg) pi 17-139 human/mouse: 7.6mg in 1ml (14μl = lOOμg) p244-262 human: 4.6.mg in 1ml (22μl = 1 OOμg)
Group B: p287-301 human/mouse: 7.2mg in 1ml (14μl = lOOμg) mouse p299-313: 6.6.mg in 1ml (15μl = lOOμg) p421-435 human/mouse: 3.3mg in 1ml (30μl = lOOμg)
Control: (FBL peptide 1 OOμg) + CFA/IFA
Control: (CD45 peptide 1 OOμg) + CFA/IFA
Group A contained peptides present within the amino terminus portion of WTl (exon 1) and Group B contained peptides present within the carboxy terminus, which contains a four zinc finger region with sequence homology to other DNA-binding proteins. Within group B, p287-301 and p299-313 were derived from exon 7, zinc finger 1, and p421-435 was derived from exon 10, zinc finger IV.
B6 mice were immunized with a group of WTl peptides or with a control peptide. Peptides were dissolved in 1ml sterile water for injection, and B6 mice were immunized 3 times at time intervals of three weeks. Adjuvants used were CFA/IFA, GM-CSF, and Montinide. The presence of antibodies specific for WTl was then determined as described in Examples 1 and 2, and proliferative T cell responses were evaluated using a standard thymidine incorporation assay, in which cells were cultured in the presence of antigen and proliferation was evaluated by measuring incorporated radioactivity (Chen et al., Cancer Res. 54: 1065- 1070, 1994). In particular, lymphocytes were cultured in 96-well plates at 2x10 cells per well with 4x10 irradiated (3000 rads) syngeneic spleen cells and the designated peptide.
Immunization of mice with the group of peptides designated as Group A elicited an antibody response to WTl (Figure 4). No antibodies were detected following immunization to Vaccine B, which is consistent with a lack of helper T cell response from immunization with Vaccine B. PI 17-139 elicited proliferative T cell responses (Figures 5A-5C). The stimulation indices (SI) varied between 8 and 72. Other peptides (P6-22 and P299-313) also were shown to elicit proliferative T cell responses. Immunization with P6-22 resulted in a stimulation index (SI) of 2.3 and immunization with P299-313 resulted in a SI of 3.3. Positive controls included ConA stimulated T cells, as well as T cells stimulated with known antigens, such as CD45 and FBL, and allogeneic T cell lines (DeBruijn et al., Eur. J. Immunol. 21:2963-2910, 1991).
Figures 6A and 6B show the proliferative response observed for each of the three peptides within vaccine A (Figure 6 A) and vaccine B (Figure 6B). Vaccine A elicited proliferative T cell responses to the immunizing peptides p6-22 and pi 17-139, with stimulation indices (SI) varying between 3 and 8 (bulk lines). No proliferative response to p244-262 was detected (Figure 6A).
Subsequent in vitro stimulations were carried out as single peptide stimulations using only p6-22 and pi 17-139. Stimulation of the Vaccine A specific T cell line with pi 17-139 resulted in proliferation to pi 17-139 with no response to p6-22 (Figure7A). Clones derived from the line were specific for pi 17-139 (Figure 7B). By contrast, stimulation of the Vaccine A specific T cell line with p6-22 resulted in proliferation to p6-22 with no response to pi 17-139 (Figure 7C). Clones derived from the line were specific for p6-22 (Figure 7D).
These results show that vaccination with WTl peptides can elicit antibody responses to WTl protein and proliferative T cell responses to the immunizing peptides. EXAMPLE 4 INDUCTION OF CTL RESPONSES IN MICE IMMUNIZED WITH WTl PEPTIDES
This Example illustrates the ability of WTl peptides to elicit CTL immunity.
Peptides (9-mers) with motifs appropriate for binding to class I MHC were identified using a BIMAS HLA peptide binding prediction analysis (Parker et al., J. Immunol. 152:163, 1994). Peptides identified within such analyses are shown in Tables II - XLIV. In each of these tables, the score reflects the theoretical binding affinity (half-time of dissociation) of the peptide to the MHC molecule indicated.
Peptides identified using the Tsites program (Rothbard and Taylor, EMBO J. 7:93-100, 1988; Deavin et al., Mol. Immunol. 33:145-155, 1996), which searches for peptide motifs that have the potential to elicit Th responses are further shown in Figures 8A and 8B, and Table XLV.
Table II
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA Al
Figure imgf000060_0001
Figure imgf000061_0001
Table III
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA A 0201
Figure imgf000061_0002
Table IV
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA A 0205
Figure imgf000062_0001
Table V
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA A24
Figure imgf000062_0002
Figure imgf000063_0001
Table VI
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA A3
Figure imgf000063_0002
Figure imgf000064_0001
Table VII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA A68.1
Figure imgf000064_0002
Table VIII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA A 1101
Figure imgf000065_0001
Table IX
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA A 3101
Figure imgf000065_0002
Figure imgf000066_0001
Table X
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA A 3302
Figure imgf000066_0002
Figure imgf000067_0001
Table XI
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B14
Figure imgf000067_0002
Table XII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B40
Figure imgf000068_0001
Table XIII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B60
Figure imgf000068_0002
Figure imgf000069_0001
Table XIV
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B61
Figure imgf000069_0002
Figure imgf000070_0001
Table XV
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B62
Figure imgf000070_0002
Table XVI
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B7
Figure imgf000071_0001
Table XVII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B8
Figure imgf000071_0002
Figure imgf000072_0001
Table XVIII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B 2702
Figure imgf000072_0002
Figure imgf000073_0001
Table XIX
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B 2705
Figure imgf000073_0002
Table XX
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B 3501
Figure imgf000074_0001
Table XXI
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B 3701
Figure imgf000074_0002
Figure imgf000075_0001
Table XXII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B 3801
Figure imgf000075_0002
Figure imgf000076_0001
Table XXIII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B 3901
Figure imgf000076_0002
Table XXIV
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B 3902
Figure imgf000077_0001
Table XXV
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B 4403
Figure imgf000077_0002
Figure imgf000078_0001
Table XXVI
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B 5101
Figure imgf000078_0002
Figure imgf000079_0001
Table XXVII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B 5102
Figure imgf000079_0002
Table XXVIII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B 5201
Figure imgf000080_0001
Table XXfX
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA B 5801
Figure imgf000080_0002
Figure imgf000081_0001
Table XXX
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA CW0301
Figure imgf000081_0002
Figure imgf000082_0001
Table XXXI
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA CW0401
Figure imgf000082_0002
Table XXXII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA CW0602
Figure imgf000083_0001
Table XXXIII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Human HLA CW0702
Figure imgf000083_0002
Figure imgf000084_0001
Table XXXIV
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Mouse MHC Class I Db
Figure imgf000084_0002
Figure imgf000085_0001
Table XXXV
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Mouse MHC Class I Dd
Figure imgf000085_0002
Table XXXVI
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Mouse MHC Class I Kb
Figure imgf000086_0001
Table XXXVII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Mouse MHC Class I Kd
Figure imgf000086_0002
Figure imgf000087_0001
Table XXXVIII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Mouse MHC Class I Kk
Figure imgf000087_0002
Figure imgf000088_0001
Table XXXIX
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Mouse MHC Class I Ld
Figure imgf000088_0002
Table XL
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Human WTl Peptides to Cattle HLA A20
Figure imgf000089_0001
Table XLI Results of BIMAS HLA Peptide Binding Prediction Analysis for Binding of Mouse WTl Peptides to Mouse MHC Class I A 0201
Figure imgf000089_0002
Figure imgf000090_0001
Table XLII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Mouse WTl Peptides to Mouse MHC Class I Db
Figure imgf000090_0002
Figure imgf000091_0001
Table XLIII
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Mouse WTl Peptides to Mouse MHC Class I Kb
Figure imgf000091_0002
Table XLIV
Results of BIMAS HLA Peptide Binding Prediction Analysis for
Binding of Mouse WTl Peptides to Mouse MHC Class I Kd
Figure imgf000092_0001
Table XLV
Results of TSites Peptide Binding Prediction Analysis for
Human WTl Peptides Capable of Eliciting a Helper T cell Response
Peptide Sequence p6-23 RDLNALLPAVPSLGGGG (SEQ ID NO:!) p30-35 GAAQWA (SEQ ID NO:309) p45-56 ASAYGSLGGPAP (SEQ ID NO:310) p91-105 AFTVHFSGQFTGTAG (SEQ ID NO:311) pll7-139 PSQASSGQARMFPNAPYLPSCLE (SEQ ID NO:2) p!67-171 HAAQF (SEQ ID NO:312) p202-233 CHTPTDSCTGSQALLLRTPYSSDNLYQMTSQL (SEQ ID NO:313) p244-262 GATLKGVAAGSSSSVKWTE (SEQ ID NO:4) Peptide Sequence p287-318 RIHTHGVFRGIQDVRRVPGVAPTLVRSASETS (SEQ ID N0:314) p333-336 RYFK (SEQ ID NO:315) p361-374 ERRFSRSDQLKRHQ (SEQ ID NO:316) p389-410 QRKFSRSDHLKTHTRTHTGKTS (SEQ ID NO:317) p421-441 CQKKFARSDELVRHHNMHQRN (SEQ ID NO:318)
Certain CTL peptides (shown in Table XLVI) were selected for further study. For each peptide in Table XLVI, scores obtained using BIMAS HLA peptide binding prediction analysis are provided. Table XLVI
WTl Peptide Sequences and HLA Peptide Binding Predictions
Figure imgf000093_0001
Peptide binding to C57B1/6 murine MHC was confirmed using the leukemia cell line RMA-S, as described by Ljunggren et al., Nature 346:416-480, 1990. In brief, RMA-S cells were cultured for 7 hours at 26°C in complete medium supplemented with 1% FCS. A total of 106 RMA-S cells were added into each well of a 24-well plate and incubated either alone or with the designated peptide (25ug/ml) for 16 hours at 26°C and additional 3 hours at 37°C in complete medium. Cells were then washed three times and stained with fluorescein isothiocyanate-conjugated anti Db or anti-K antibody (PharMingen, San Diego, CA). Labeled cells were washed twice, resuspended and fixed in 500ul of PBS with 1% paraformaldehyde and analyzed for fluorescence intensity in a flow cytometer (Becton-Dickinson FACSCalibur®). The percentage of increase of Db or Kb molecules on the surface of the RMA-S cells was measured by increased mean fluorescent intensity of cells incubated with peptide compared with that of cells incubated in medium alone.
Mice were immunized with the peptides capable of binding to murine class I MHC. Following immunization, spleen cells were stimulated in vitro and tested for the ability to lyse targets incubated with WTl peptides. CTL were evaluated with a standard chromium release assay (Chen et al., Cancer Res. 54:1065-1070, 1994). 106 target cells were incubated at 37°C with 150μCi of sodium 51Cr for 90 minutes, in the presence or absence of specific peptides. Cells were washed three times and resuspended in RPMI with 5% fetal bovine serum. For the assay, 10 51 Cr-labeled target cells were incubated with different concentrations of effector cells in a final volume of 200μl in U-bottomed 96-well plates. Supematants were removed after 4 to 7 hours at 37°C, and the percentage specific lysis was determined by the formula: . % specific lysis = 100 x (experimental release - spontaneous release)/(maximum release-spontaneous release).
The results, presented in Table XLVII, show that some WTl peptides can bind to class I MHC molecules, which is essential for generating CTL. Moreover, several of the peptides were able to elicit peptide specific CTL (Figures 9A and 9B), as determined using chromium release assays. Following immunization to CTL peptides pl0-18 human, pl36-144 human, pl36-144 mouse and p235-243, peptide specific CTL lines were generated and clones were established. These results indicate that peptide specific CTL can kill malignant cells expressing WTl .
Table XLVII Binding of WTl CTL Peptides to mouse B6 class I antigens
Figure imgf000095_0001
EXAMPLE 5 USE OF A WTl POLYPEPTIDE TO ELICIT WTl SPECIFIC CTL IN MICE
This Example illustrates the ability of a representative WTl polypeptide to elicit CTL immunity capable of killing WTl positive tumor cell lines.
PI 17-139, a peptide with motifs appropriate for binding to class I and class II MHC, was identified as described above using TSITES and BIMAS HLA peptide binding prediction analyses. Mice were immunized as described in Example 3. Following immunization, spleen cells were stimulated in vitro and tested for the ability to lyse targets incubated with WTl peptides, as well as WTl positive and negative tumor cells. CTL were evaluated with a standard chromium release assay. The results, presented in Figures 10A-10D, show that PI 17 can elicit WTl specific CTL capable of killing WTl positive tumor cells, whereas no killing of WTl negative cells was observed. These results demonstrate that peptide specific CTL in fact kill malignant cells expressing WTl and that vaccine and T cell therapy are effective against malignancies that express WTl. Similar immunizations were performed using the 9-mer class I MHC binding peptides pl36-144, p225-233, p235-243 as well as the 23-mer peptide pi 17- 139. Following immunization, spleen cells were stimulated in vitro with each of the 4 peptides and tested for ability to lyse targets incubated with WTl peptides. CTL were generated specific for pi 36-144, p235-243 and pi 17-139, but not for p225-233. CTL data for p235-243 and pi 17-139 are presented in Figures 11A and 11B. Data for peptides pl36-144 and p225-233 are not depicted.
CTL lysis demands that the target WTl peptides are endogenously processed and presented in association with tumor cell class I MHC molecules. The above WTl peptide specific CTL were tested for ability to lyse WTl positive versus negative tumor cell lines. CTL specific for p235-243 lysed targets incubated with the p235-243 peptides, but failed to lyse cell lines that expressed WTl proteins (Figure 11 A). By marked contrast, CTL specific for pi 17-139 lysed targets incubated with pi 17-139 peptides and also lysed malignant cells expressing WTl (Figure 1 IB). As a negative control, CTL specific for pi 17-139 did not lyse WTl negative EL-4 (also referred to herein as E10).
Specificity of WTl specific lysis was confirmed by cold target inhibition (Figures 12A-12B). Effector cells were plated for various effector: target ratios in 96- well U-bottom plates. A ten-fold excess (compared to hot target) of the indicated peptide-coated target without 51Cr labeling was added. Finally, 104 slCr-labeled target cells per well were added and the plates incubated at 37°C for 4 hours. The total volume per well was 200μl.
Lysis of TRAMP-C by pi 17-139 specific CTL was blocked from 58% to 36%> by EL-4 incubated with the relevant peptide pi 17-139, but not with EL-4 incubated with an irrelevant peptide (Figure 12A). Similarly, lysis of BLK-SV40 was blocked from 18% to 0% by EL-4 incubated with the relevant peptide pi 17-139 (Figure 12B). Results validate that WTl peptide specific CTL specifically kill malignant cells by recognition of processed WTl .
Several segments with putative CTL motifs are contained within pi 17- 139. To determine the precise sequence of the CTL epitope all potential 9-mer peptides within pi 17-139 were synthesized (Table XLVIIJ). Two of these peptides (pi 26- 134 and pi 30- 138) were shown to bind to H-2b class I molecules (Table XLVIII). CTL generated by immunization with pi 17-139 lysed targets incubated with pl26-134 and pl30-138, but not the other 9-mer peptides within pi 17-139 (Figure 13A).
The pi 17-139 specific CTL line was restimulated with either pl26-134 or pl30-138. Following restimulation with pl26-134 or pl30-138, both T cell lines demonstrated peptide specific lysis, but only pi 30-138 specific CTL showed lysis of a
WTl positive tumor cell line (Figures 13B and 13C). Thus, pl30-138 appears to be the naturally processed epitope.
Table XLVIII Binding of WTl CTL 9mer Peptides within pi 17-139 to mouse B6 class I antigens
Figure imgf000097_0001
EXAMPLE 6 IDENTIFICATION OF WTl SPECIFIC MRNA IN MOUSE TUMOR CELL LINES This Example illustrates the use of RT-PCR to detect WTl specific mRNA in cells and cell lines.
Mononuclear cells were isolated by density gradient centrifugation, and were immediately frozen and stored at -80°C until analyzed by RT-PCR for the presence of WTl specific mRNA. RT-PCR was generally performed as described by Fraizer et al., Blood 86:4104-4106, 1995. Total RNA was extracted from 107 cells according to standard procedures. RNA pellets were resuspended in 25 μL diethylpyrocarbonate treated water and used directly for reverse transcription. The zinc- finger region (exons 7 to 10) was amplified by PCR as a 330 bp mouse cDNA. Amplification was performed in a thermocycler during one or, when necessary, two sequential rounds of PCR. AmpliTaq DNA Polymerase (Perkin Elmer Cetus, Norwalk, CT), 2.5 mM MgCl2 and 20 pmol of each primer in a total reaction volume of 50μl were used. Twenty μL aliquots of the PCR products were electrophoresed on 2% agarose gels stained with ethidium bromide. The gels were photographed with Polaroid film (Polaroid 667, Polaroid Ltd., Hertfordshire, England). Precautions against cross contamination were taken following the recommendations of Kwok and Higuchi, Nature 339:231-238, 1989. Negative controls included the cDNA- and PCR-reagent mixes with water instead of cDNA in each experiment. To avoid false negatives, the presence of intact RNA and adequate cDNA generation was evaluated for each sample by a control PCR using β-actin primers. Samples that did not amplify with these primers were excluded from analysis.
Primers for amplification of WTl in mouse cell lines were: PI 15: 1458- 1478: 5' CCC AGG CTG CAA TAA GAG ATA 3' (forward primer; SEQ ID NO:21); and PI 16: 1767-1787: 5' ATG TTG TGA TGG CGG ACC AAT 3' (reverse primer; SEQ ID NO:22) (see Inoue et al, Blood 88:2261-2218, 1996; Fraizer et al., Blood §(5:4704-4706, 1995).
Beta Actin primers used in the control reactions were: 5' GTG GGG CGC CCC AGG CAC CA 3' (sense primer; SEQ ID NO:23); and 5' GTC CTT AAT GTC ACG CAC GAT TTC 3' (antisense primer; SEQ ID NO:24) Primers for use in amplifying human WTl include: PI 17: 954-974: 5'
GGC ATC TGA GAC CAG TGA GAA 3' (SEQ ID NO:25); and PI 18: 1434-1414: 5' GAG AGT CAG ACT TGA AAG CAGT 3' (SEQ ID NO:5). For nested RT-PCR, primers may be: PI 19: 1023-1043: 5' GCT GTC CCA CTT ACA GAT GCA 3' (SEQ ID NO:26); and P120: 1345-1365: 5' TCA AAG CGC CAG CTG GAG TTT 3' (SEQ ID NO:27). Table XLVIII shows the results of WTl PCR analysis of mouse tumor cell lines. Within Table IV, (+++) indicates a strong WTl PCR amplification product in the first step RT PCR, (++) indicates a WTl amplification product that is detectable by first step WTl RT PCR, (+) indicates a product that is detectable only in the second step of WTl RT PCR, and (-) indicates WTl PCR negative.
Table XLIX Detection of WTl mRNA in Mouse Tumor Cell Lines
Figure imgf000099_0001
EXAMPLE 7 EXPRESSION IN E. COLI OF WTl TRX FUSION CONSTRUCT The truncated open reading frame of WTl (WT1B) was PCR amplified with the following primers: Forward Primer starting at amino acid 2
P-37 (SEQ ID NO. 342) 5' ggctccgacgtgcgggacctg 3' Tm 64°C
Reverse Primer creating EcoRI site after stop codon P-23 (SEQ ID NO. 343) 5' gaattctcaaagcgccagctggagtttggt 3' Tm
63 °C The PCR was performed under the following conditions:
lOμl 1 OX Pfu buffer lμl lOmM dNTPs 2μl lOμM each oligo 83 μL sterile water 1.5μl Pfu DNA polymerase (Stratagene, La Jolla, CA)
50 ng DNA (pPDM FL WTl)
96°C 2 minutes
96°C 20 seconds 63 °C 15 seconds 72°C 3 minutes x 40 cycles
72°C 4 minutes The PCR product was digested with EcoRI restriction enzyme, gel purified and then cloned into pTrx 2H vector (a modified pET28 vector with a Trx fusion on the N-terminal and two His tags surrounding the Trx fusion. After the Trx fusion there exists protease cleavage sites for thrombin and enterokinase). The pTrx2H construct was digested with Stul and EcoRI restriction enzymes. The correct constructs were confirmed by DNA sequence analysis and then transformed into BL21 (DE3) pLys S and BL21 (DE3) CodonPlus expression host cells. EXAMPLE 8 EXPRESSION IN E. COLI OF WTl A His TAG FUSION CONSTRUCTS
The N-terminal open reading frame of WTl (WTl A) was PCR amplified with the following primers: Forward Primer starting at amino acid 2
P-37 (SEQ ID NO. 344) 5'ggctccgacgtgcgggacctg 3' Tm 64°C
Reverse Primer creating EcoRI site after an artificial stop codon put after amino acid 249.
PDM-335 (SEQ ID NO. 345) 5'gaattctcaaagcgccagctggagtttggt 3' Tm 64°C
The PCR was performed under the following conditions: lOμl l OX Pfu buffer lμl lOmM dNTPs
2μl lOμM each oligo 83 μL sterile water
1.5μl Pfu DNA polymerase (Stratagene, La Jolla, CA)
50 ng DNA (pPDM FL WTl)
96°C 2 minutes
96°C 20 seconds 63°C 15 seconds 72°C 1 minute 20 seconds x 40 cycles
72°C 4 minutes
The PCR product was digested with EcoRI restriction enzyme, gel purified and then cloned into pPDM, a modified pET28 vector with a His tag in frame, which had been digested with Eco72I and EcoRI restriction enzymes. The PCR product was also transformed into pTrx 2H vector. The pTrx2H construct was digested with Stul and EcoRI restriction enzymes. The correct constructs were confirmed by DNA sequence analysis and then transformed into BL21 (DE3) pLys S and BL21 (DE3) CodonPlus expression host cells. EXAMPLE 9 EXPRESSION IN E. COLI OF WTl B His TAG FUSION CONSTRUCTS
The truncated open reading frame of WTl (WTl A) was PCR amplified with the following primers: Forward Primer starting at amino acid 250
PDM-346 (SEQ ID NO. 346) 5' cacagcacagggtacgagagc 3' Tm 58°C
Reverse Primer creating EcoRI site after stop codon P-23 (SEQ ID NO. 347) 5'gaattctcaaagcgccagctggagtttggt 3' Tm
63°C The PCR was performed under the following conditions:
lOμl l OX Pfu buffer lμl lOmM dNTPs 2μl 1 OμM each oligo 83μL sterile water 1.5μl Pfu DNA polymerase (Stratagene, La olla, CA)
50 ng DNA (pPDM FL WTl)
96°C 2 minutes
96°C 20 seconds 63 °C 15 seconds 72°C 1 minute 30 seconds x
40 cycles 72°C 4 minutes
The PCR product was digested with EcoRI restriction enzyme, gel purified and then cloned into pPDM, a modified pET28 vector with a His tag in frame, which had been digested with Eco72I and EcoRI restriction enzymes. The PCR product was also transformed into pTrx 2H vector. The pTrx 2H construct was digested with Stul and EcoRI restriction enzymes. The correct constructs were confirmed by DNA sequence analysis and then transformed into BL21 (DE3) pLys S and BL21 (DE3) CodonPlus expression host cells.
For Examples 7-9, the following SEQ ID NOs. are disclosed: SEQ ID NO. 327 is the determined cDNA sequence for Trx_WTl_B SEQ ID NO. 328 is the determined cDNA sequence for Trx_WTl_A SEQ ID NO. 329 is the determined cDNA sequence for Trx WTl SEQ ID NO. 330 is the determined cDNA sequence for WT1_A SEQ ID NO. 331 is the determined cDNA sequence for WT 1_B
SEQ ID NO. 332 is the predicted amino acid sequence encoded by SEQ ID No. 327 SEQ ID NO. 333 is the predicted amino acid sequence encoded by SEQ ID No. 328 SEQ ID NO. 334 is the predicted amino acid sequence encoded by SEQ ID No. 329 SEQ ID NO. 335 is the predicted amino acid sequence encoded by SEQ ID No. 330 SEQ ID NO. 336 is the predicted amino acid sequence encoded by SEQ ID No. 331
EXAMPLE 10
TRUNCATED FORMS OF WTl EXPRESSED IN E. COLI
Three reading frames of WTl were amplified by PCR using the following primers:
For WTl Tr2:
PDM-441 (SEQ ID NO. 348) 5' cacgaagaacagtgcctgagcgcattcac 3' Tm 63°C
PDM-442 (SEQ ID NO. 349) 5' ccggcgaattcatcagtataaattgtcactgc 3' TM 62°C
For WTl Tr3:
PDM-443 (SEQ ID NO. 350) 5' caggctttgctgctgaggacgccc 3' Tm 64°C
PDM-444 (SEQ ID NO. 351) 5' cacggagaattcatcactggtatggtttctcacc Tm 64°C
For WTl Tr4:
PDM-445 (SEQ ID NO. 352) 5' cacagcaggaagcacactggtgagaaac 3' Tm 63°C
PDM-446 (SEQ ID NO. 353) 5' ggatatctgcagaattctcaaagcgccagc 3' TM 63°C The PCR was performed under the following conditions:
lOμl l OX Pfu buffer lμl lOmM dNTPs 2μl lOμM each oligo 83 μL sterile water
1.5μl Pfu DNA polymerase (Stratagene, La Jolla, CA) 50 ng DNA (pPDM FL WTl)
96°C 2 minutes
96°C 20 seconds 63°C 15 seconds 72°C 30 seconds x 40 cycles
72°C 4 minutes
The PCR products were digested with EcoRI and cloned into pPDM His
(a modified pET28 vector with a His tag in frame on the 5' end) which has been digested with Eco72I and EcoRI. The constructs were confirmed to be correct through sequence analysis and transformed into BL21 pLys S and BL21 CodonPlus cells or BLR pLys S and BLR CodonPlus cells.
EXAMPLE 11 WTl C (amino acids 76-437) AND WTl D (amino acids 91-437) EXPRESSION IN E. COLI The WTl C reading frame was amplified by PCR using the following primers:
PDM-504 (SEQ ID NO. 354) 5' cactccttcatcaaacaggaac 3' Tm 61°C PDM-446 (SEQ ID NO. 355) 5' ggatatctgcagaattctcaaagcgccagc 3' Tm 63 °C The PCR was performed under the following conditions:
lOμl l OX Pfu buffer lμl lOmM dNTPs 2μl lOμM each oligo 83 μL sterile water 1.5μl Pfu DNA polymerase (Stratagene, La Jolla, CA) 50 ng DNA (pPDM FL WTl)
96°C 2 minutes
96°C 20 seconds 63°C 15 seconds 72°C 2 minutes x 40 cycles
72°C 4 minutes
The PCR product was digested with EcoRI and cloned into pPDM His which had been digested with Eco72I and EcoRI. The sequence was confirmed through sequence analysis and then transformed into BLR pLys S and BLR which is co- transformed with CodonPlus RP.
EXAMPLE 12 SYNTHETIC PRODUCTION OF WTl TR-1 BY ANNEALING OVERLAPPING OLIGOS
This example was performed to determine the effect of changing proline codon usage on expression.
The following pairs of oligos were annealed:
1. PDM-505 (SEQ ID NO. 356) 5' ggttccgacgtgcgggacctgaacgcactgctg 3 ' PDM-506 (SEQ ID NO. 357) 5' ctgccggcagcagtgcgttcaggtcccgcacgtcggaacc 3'
2. PDM-507 (SEQ ID NO. 358) 5' ccggcagttccatccctgggtggcggtggaggctg 3' , PDM-508 (SEQ ID NO. 359) 5' cggcagtgcgcagcctccaccgccacccagggatggaa 3 '
3. PDM-509 (SEQ ID NO. 360) 5' cgcactgccggttagcggtgcagcacagtgggctc 3' PDM-510 (SEQ ID NO. 361) 5' cagaactggagcccactgtgctgcaccgctaac 3 ' 4. PDM-511 (SEQ ID NO. 362) 5' cagttctggacttcgcaccgcctggtgcatccgcatac 3 ' PDM-512 (SEQ ID NO. 363) 5' cagggaaccgtatgcggatgcaccaggcggtgcgaagtc 3'
5. PDM-513 (SEQ ID NO. 364) 5' ggttccctgggtggtccagcacctccgcccgcaacgcc 3 ' PDM-514 (SEQ ID NO. 365) 5' ggcggtgggggcgttgcgggcggaggtgctggaccacc 3 '
6. PDM-515 (SEQ ID NO. 366) 5' cccaccgcctccaccgcccccgcactccttcatcaaacag 3 '
PDM-516 (SEQ ID NO. 367) 5' ctaggttcctgtttgatgaaggagtgcgggggcggtgga 3 '
7. PDM-517 (SEQ ID NO. 368) 5' gaacctagctggggtggtgcagaaccgcacgaagaaca 3 ' PDM-518 (SEQ ID NO. 369) 5' ctcaggcactgttcttcgtgcggttctgcaccaccccag 3 '
8. PDM-519 (SEQ ID NO. 370) 5' gtgcctgagcgcattctgagaattctgcagat 3'
PDM-520 (SEQ ID NO. 371) 5' gtgtgatggatatctgcagaattctcagaatgcg 3'
Each oligo pair was separately combined then annealed. The pairs were then ligated together and one μl of ligation mix was used for PCR conditions below: lOμl l OX Pfu buffer lμl lOmM dNTPs 2μl lOμM each oligo
83 μL sterile water 1.5μl Pfu DNA polymerase (Stratagene, La Jolla, CA) 96°C 2 minutes
96°C 20 seconds 63°C 15 seconds 72°C 30 seconds x 40 cycles
72°C 4 minutes The PCR product was digested with EcoRI and cloned into pPDM His which had been digested with Eco72I and EcoRI. The sequence was confirmed and then transformed into BLR pLys S and BLR which is co-transformed with CodonPlus RP.
For examples 10-12, the following SEQ ID NOs. are disclosed: SEQ ID NO:337 is the determined cDNA sequence for WTl_Trl SEQ ID NO:338 is the determined cDNA sequence for WTl_Tr2 SEQ ID NO:339 is the determined cDNA sequence for WTl_Tr3 SEQ ID NO:340 is the determined cDNA sequence for WTl_Tr4 SEQ ID NO:341 is the determined cDNA sequence for WT1_C SEQ ID NO:342 is the predicted amino acid sequence encoded by SEQ ID NO:337 SEQ ID NO:343 is the predicted amino acid sequence encoded by SEQ ID NO:338 SEQ ID NO:344 is the predicted amino acid sequence encoded by SEQ ID NO:339 SEQ ID NO:345 is the predicted amino acid sequence encoded by SEQ ID NO:340 SEQ ID NO:346 is the predicted amino acid sequence encoded by SEQ ID NO:341
The WTl C sequence represents a polynucleotide having the coding regions of TR2, TR3 and TR4.
The WTl TR-1 synthetic sequence represents a polynucleotide in which alternative codons for proline were substituted for the native codons, producing a polynucleotide capable of expressing WTl TR-1 in E. coli. EXAMPLE 13
EVALUATION OF THE SYSTEMIC HISTOPATHOLOGICAL AND TOXICOLOGICAL EFFECTS OF
WTl IMMUNIZATION IN MICE
The purpose of this example is to analyze the immunogenicity and potential systemic histopathological and toxicological effects of WTl protein immunization in a multiple dose titration in mice.
The experimental design for immunization of mice with WTl protein is outlined in Table L.
Table L Experimental Design of WTl Immunization in Mice
Figure imgf000108_0001
Vaccination to WTl protein using MPL-SE as adjuvant, in a multiple dose titration study (doses ranging from 25μg, lOOμg to lOOOμg WTl protein) in female C57/B6 mice elicited a strong WTl -specific antibody response (Figure 19) and cellular T-cell responses (Figure 20).
No systemic histopathological or toxicological effects of immunization with WTl protein was observed. No histological evidence for toxicity was seen in the following tissues: adrenal gland, brain, cecum, colon, duodenum, eye, femur and marrow, gall bladder, heart, ileum, jejunum, kidney, larynx, lacrimal gland, liver, lung, lymph node, muscle, esophagus, ovary, pancreas, parathyroid, salivary gland, sternum and marrow, spleen, stomach, thymus, trachea, thyroid, urinary bladder and uterus.
Special emphasis was put on evaluation of potential hematopoietic toxicity. The myeloid/erythroid ratio in sternum and femur marrow was normal. All evaluable blood cell counts and blood chemistry (BUN, creatinine, bilirubin, albumin, globulin) were within the normal range (Table LI).
Given that existent immunity to WTl is present in some patients with leukemia and that vaccination to WTl protein can elicit WTl specific Ab and cellular T-cell responses in mice without toxicity to normal tissues, these experiments validate WTl as a tumor/leukemia vaccine.
Table LI Clinical Chemistry and Hematology Analysis
Table Ll: WT1 Dose Titration Study Clinical Chemistry and Hematology Analysis
K/uL M/uL g/di % fL pg %
Animal # WBC RBC Hg. HCT WICV CH MCHC
Normal 5.4-16.0 6.7-12.5 10.2-16.6 32-54 31-62 9.2-20.8 : 22.0-35.5
Group 1
1 (0) 5.6 8.41 12.8 43.5 53 15.2 29.4
2 (0) 5.5 9.12 13.4 47.5 53 14.7 28.2
3 (0) 7.5 9.22 13.5 48 54 14.7 28.1
4 (0) 3.9 9.27 13.6 46 52 14.7 29.6
Mean 5.6 9.0 13.3 46.3 53.0 14.8 28.8
STD 1.5 0.4 0.4 JO 0.8 0.3 0.8
Group 2
5 (1.5) 6.6 9 13.1 46 54 14.5 28.5
6 (1.6) 5.2 8.58 12.6 44 53 14.7 28.6
7 (1J) 7.8 9.21 13.6 46 53 14.7 29.6
8 (1.8) 6.3 NA NA 41 NA NA NA
Mean 6.5 8.9 13.1 44.3 53.3 14.6 28.9
STD 1.1 0.3 0.5 2.4 0.6 0.1 0.6
Group 3
9 (2.5) 8.3 9.16 13.6 50.3 55 14.9 27.1
10 (2.6) 5 8.78 13 44.2 50 14.8 29.3 Table Ll: WT1 Dose Titration Study
Clinical Chemistry and Hematology Analysis
K/uL M/uL g/di % fL pg %
Animal # WBC RBC Hg. HCT MCV MCH MCHC
Normal 5.4-16.0 I 3.7-12.5 10.2-16.6 32-54 31-62 9.2-20.8 22.0-35.5
11 (2.7) 4 8.94 13.2 48.3 54 14.7 27.3
12 (2.8) 8.2 NA NA 41 NA NA NA
Mean 6.4 9.0 13.3 46.0 53.0 14.8 27.9
STD 2.2 0.2 0.3 4.2 2.6 0.1 1.2
Group 4
13 (3.5) 6.1 8.82 13.1 46 54 14.9 28.5
14 (3.6) 6.1 8.64 12.9 46 54 15 28
15 (3.7) 9.3 8.93 13.2 48 55 14.8 27.5
16 (3.8) 4.8 8.19 12.6 44 55 15.3 28.6
Mean 6.6 8.6 13.0 46.0 54.5 15.0 28.2
STD 1.9 0.3 0.3 1.6 0.6 0.2 0.5
Group 5
17 (4.5) 3.1 8.48 12.6 46 54 14.9 27.5
18 (4.6) 5.7 9.12 13.7 48 54 15 28.5
19 (4.7) 5.3 8.58 13 44.5 55 15.2 29.2
20 (4.8) 5.3 NA NA 40 NA NA NA
Mean 4.9 8.7 13.1 44.6 54.3 15.0 28.4
STD 1.2 0.3 0.6 3.4 0.6 0.2 0.9
Group 6
21 (1.1) 3.5 9.36 13.5 37.6 40 14.4 35.9
22 (1.2) 6.9 8.93 13.6 37.3 42 15.3 36.6
23 (1.3) 3.6 8.3 12.5 35.3 43 15.1 35.5
24 (1.4) NA NA NA NA NA NA NA
Mean 4J 8.9 13.2 36.7 41.7 14.9 36.0
STD 1.9 0.5 0.6 1.3 1.5 0.5 0.6
Group 7
25 (2.1) 4 NA NA 40 NA NA NA
26 (2.2) 7.4 9.12 13.2 38.5 42 14.5 34.3
27 (2.3) 4.5 8.19 12.1 34.5 42 14.8 35.1
28 (2.4) 5.8 8.25 12.3 34.1 41 14.9 36.1
Mean 5.4 8.5 12.5 36.8 41 J 14.7 35.2
STD 1.5 0.5 0.6 2.9 0.6 0.2 0.9
Group 8
29 (3.1) 5.1 8.53 12.6 34.9 41 14.7 36
30 (3.2) 7.6 8.42 13 36.1 43 15.4 35.9
31 (3.3) 3.4 8.45 12.6 34.9 41 14.9 36.1
32 (3.4) 6.1 8.11 12.3 34.8 43 15.2 35.5
Mean 5.6 8.4 12.6 35.2 42.0 15.1 35.9
STD 1.8 0.2 0.3 0.6 1.2 0.3 0.3 Table Ll: WT1 Dose Titration Study
Clinical Chemistry and Hematology Analysis
KtuL M/uL g/di % fL pg %
Animal # WBC RBC Hg. HCT MCV MCH MCHC
Normal 5.4-16.0 6.7-12.5 10.2-16.6 32-54 31-62 9.2-20.8 22.0-35.5
Group 9
33 (4.1) NA NA NA NA NA NA NA
34 (4.2) 4.5 8.63 12.8 36.2 42 14.8 35.2
35 (4.3) 3.9 8.85 13 36.6 41 14J 35.6
36 (4.4) 4.7 8.14 12.3 33.8 42 15.1 36.3
Mean 4.4 8.5 12.7 35.5 41.7 14.9 35.7
STD 0.4 0.4 0.4 1.5 0.6 0.2 0.6
Table Ll (cont'd): WT1 Dose Titration Study Clinical Chemistry and Hematology Analysis yestno K/uL Abs. Abs. Abs. Abs. Abs. Abs.
Animal # Pit. clump Platelets Baso Eos Bands Polys Lymph Mono
Normal no 150-1500 0.0-0.15 0.0-0.51 0.0-0.32 8.0-42.9 8.0-18.0 0.0-1.5
Group 1 KtuL KtuL K/uL K/uL KtuL KtuL
1 (0) yes 726 0 56 0 336 5208 0
2 (0) no 860 0 0 0 55 5445 0
3 (0) no 875 0 375 0 525 6525 75
4 (0) yes 902 0 0 0 156 3744 0
Mean 840.8 0.0 107.8 0.0 268.0 5230.5 18.8
STD 78.4 0.0 180.1 0.0 207.0 1144.8 37.5
Group 2
5 (1.5) no 1193 0 132 0 792 5214 462
6 (1.6) no 1166 0 52 0 624 4472 52
7 (1.7) no 1087 0 234 0 1170 6396 0
8 (1.8) yes NA 0 126 0 126 5922 126
Mean 1148.7 0.0 136.0 0.0 678.0 5501.0 160.0
STD 55.1 0.0 74.8 0.0 433.1 840.5 207.9
Group 3
9 (2.5) no 705 0 166 0 664 7387 83
10 (2.6) no 1140 0 150 0 500 4350 0
11 (2.7) no 952 0 120 0 680 3200 0
12 (2.8) yes NA 0 164 0 656 7216 164
Mean 932.3 0.0 150.0 0.0 625.0 5538.3 61.8
STD 218.2 0.0 21.2 0.0 83.9 2090.6 78.6
Group 4
13 (3.5) no 785 0 488 0 732 4636 244
14 (3.6) yes 973 0 0 0 488 5307 305 15 (3.7) yes 939 0 465 0 558 7812 465
16 (3.8) yes 1622 0 192 0 480 4080 48
Mean 1079.8 0.0 286.3 0.0 564.5 5458.8 265.5
STD 370.6 0.0 233.4 0.0 117.0 1647.1 172.4
Group 5
17 (4.5) no 892 0 31 0 620 2449 0
18 (4.6) yes 966 57 114 0 855 4674 0
19 (47) yes 883 0 53 0 742 4452 53
20 (4.8) yes NA 0 106 0 53 5141 0
Mean 913.7 14.3 76.0 0.0 567.5 4179.0 13.3
STD 45.5 28.5 40.4 0.0 356.2 1188.5 26.5
Table Ll (cont'd): WT1 Dose Titration Study Clinical Chemistry and Hematology Analysis yes/no K/uL Abs. Abs. Abs. Abs. Abs. Abs.
Animal # Pit. clump Platelets Baso Eos Bands Polys Lymph Mono
Normal no 150-1500 0.0-0.15 0.0-0.51 0.0-0.32 8.0-42.9 8.0-18.0 0.0-1.5
Group 6
21 (1.1) yes 784 0 35 0 385 2870 210
22 (1.2) yes 806 0 69 0 207 6486 138
23 (1.3) yes 790 0 180 0 396 2988 36
24 (1.4) NA NA NA NA NA NA NA NA
Mean 793.3 0.0 94.7 0.0 329.3 4114.7 128.0
STD 11.4 0.0 75.8 0.0 106.1 2054.5 87.4
Group 7
25 (2.1) yes NA 0 80 0 200 3720 0
26 (2.2) yes 753 0 0 0 518 6734 148
27 (2.3) yes 725 0 90 0 225 4140 45
28 (2.4) ' yes 792 0 232 0 754 4814 0
Mean 756.7 0.0 100.5 0.0 424.3 4852.0 48.3
STD 33.7 0.0 96.5 0.0 263.0 1333.1 69.8
Group 8
29 (3.1) yes 784 0 153 0 561 4233 153
30 (3.2) yes 512 0 152 0 304 6992 152
31 (3.3) yes 701 0 0 0 238 3094 68
32 (3.4) yes 631 0 305 0 305 5368 122
Mean 657.0 0.0 152.5 0.0 352.0 4921.8 123.8
STD 115.1 0.0 124.5 0.0 142.8 1663.3 39.9
Group 9
33 (4.1) NA NA NA NA NA NA NA NA
34 (4.2) yes 724 0 125 0 540 3780 45
35 (4.3) yes 758 0 117 0 429 3315 39
36 (4.4) yes 808 0 47 0 329 4089 235
Mean 763.3 0.0 96.3 0.0 432.7 3728.0 106.3
STD 42.3 0.0 42.9 0.0 105.5 389.6 111.5
Figure imgf000113_0001
Table Ll (cont'd): WT1 Dose Titration Study Clinical Chemistry and Hematology Analysis mg/dl mg/dl g/dl g/dl < g/dl mg/dl
Animal # BUN Creatinine T. protein Albumin Globulin T. Bilirubin
Normal 13.9-28.3 0.3-1.0 4.0-8.6 2.5-4.8 1.5-3.8 0.10-0.90
Group 6
21 (1.1) 28 0.3 5.1 3.4 1.7 0.2
22 (1.2) 36 0.3 5.1 3.8 1.3 0.2
23 (1.3) 32 0.4 4.9 3.5 1.4 0.1
24 (1.4) NA NA NA NA NA NA
Mean 32.0 0.3 5.0 3.6 1.5 0.2
STD 4.0 0.1 0.1 0.2 0.2 0.1
Group 7
25 (2.1) 32 0.2 5 3.4 1.6 0.2
26 (2.2) 24 0.3 4.2 2.8 1.4 0.1
27 (2.3) 28 0.3 4.8 3.2 1.6 0.2
28 (2.4) 27 0.3 5 3.4 1.6 0.1
Mean 27.8 0.3 4.8 3.2 1.6 0.2
STD 3.3 0.0 0.4 0.3 0.1 0.1
Group 8
29 (3.1) 32 0.3 4.9 3.3 1.6 0.2
30 (3.2) NA NA NA NA NA NA
31 (3.3) 18 0.3 4.8 3.1 1.7 0.2
32 (3.4) 26 0.2 4.2 2.9 1.3 0
Mean 25.3 0.3 4.6 3.1 1.5 0.1
STD 7.0 0.1 0.4 0.2 0.2 0.1
Group 9
33 (4.1) 25 0.2 4.1 2.7 1.4 0.3
34 (4.2) NA NA NA NA NA NA
35 (4.3) 23 0.2 4.7 3.1 1.6 0.2
36 (4.4) 29 0.3 4.7 3.2 1.5 0.3
Mean 25.7 0.2 4.5 3.0 1.5 0.3
STD 3.1 0.1 0.3 0.3 0.1 0.1
Abbreviations: WBC: white blood cells; RBC: red blood cells; Hg.: hemoglobin; HCT: hematocrit ; MCV: Mean corpuscular volume; MCH: mean corpuscular hemoglobin; MCHC: mean corpuscular hemoglobin concentration; Pit.: platelets; Abs.: Absolute; Baso: basophils; Eos: eosinophils; Abs. Bands: immature neutrophils ; Polys: polymorphonuclear cells; Lymph: lymphocytes; Mono: monocytes; BUN: blood urea nitrogen EXAMPLE 14 ELICITATION OF HUMAN WTl -SPECIFIC T-CELL RESPONSES BY WHOLE GENE IN VITRO
PRIMING
This example demonstrates that WTl specific T-cell responses can be generated from the blood of normal individuals.
Dendritic cells (DC) were differentiated from monocyte cultures derived from PBMC of normal donors by growth for 4-10 days in RPMI medium containing 10% human serum, 50 ng/ml GMCSF and 30 ng/ml IL-4. Following culture, DC were infected 16 hours with recombinant WTl -expressing vaccinia virus at an M.O.I, of 5, or for 3 days with recombinant WTl -expressing adenovirus at an M.O.I, of 10 (Figures 21 and 22). Vaccinia virus was inactivated by UN. irradiation. CD8+ T-cells were isolated by positive selection using magnetic beads, and priming cultures were initiated in 96-well plates. Cultures were restimulated every 7-10 days using autologous dendritic cells adeno or vaccinia infected to express WTl . Following 3-6 stimulation cycles, CD 8+ lines could be identified that specifically produced interferon-gamma when stimulated with autologous- WTl -expressing dendritic cells or fibroblasts. The WTl -specific activity of these lines could be maintained following additional stimulation cycles. These lines were demonstrated to specifically recognize adeno or vaccinia WTl infected autologous dendritic cells but not adeno or vaccinia EGFP- infected autologous dendritic cells by Elispot assays (Figure 23).
EXAMPLE 15 FORMULATION OF RA12-Wτl FOR INJECTION: USE OF EXCIPIENTS TO STABILIZE
LYOPHILIZED PRODUCT This example describes the formulation that allows the complete solubilization of lyophilized Ral2-WT1.
The following formulation allowed for the recombinant protein Ral2- WT1 to be dissolved into an aqueous medium after being lyophylized to dryness:
Recombinant Ral2-WT1 concentration: 0.5 - 1.0 mg/ml; Buffer: 10-20 mM Ethanolamine, pH 10.0; 1.0 - 5.0 mM Cysteine; 0.05 % Tween-80 (Polysorbate-
80); Sugar: 10% Trehalose (T5251, Sigma, MO) 10% Maltose (M9171, Sigma, MO) 10% Sucrose (S7903, Sigma, MO) 10% Fructose (F2543, Sigma, MO) 10% Glucose (G7528, Sigma, MO).
The lyophilized protein with the sugar excipient was found to dissolve significantly more than without the sugar excipient. Analysis by coomassie stained SDS-PAGE showed no signs of remaining solids in the dissolved material.
EXAMPLE 16 FORMULATION OF A WTl PROTEIN VACCINE This example describes the induction of WTl -specific immune responses following immunization with WTl protein and 2 different adjuvant formulations.
According to this example, WTl protein in combination with MPL-SE induces a strong Ab and Interferon-γ (IFN-γ) response to WTl. Described in detail below are the methods used to induce WTl specific immune responses following WTl protein immunization using MPL-SE or Enhanzyn as adjuvant in C57/B6 mice.
C57BL/6 mice were immunized with 20 μg rRal2-WTl combined with either MPL-SE or Enhanzyn adjuvants. One group of control mice was immunized with rRal2-WTl without adjuvant and one group was immunized with saline alone. Three intramuscular (IM) immunizations were given, three weeks apart. Spleens and sera were harvested 2 weeks post-final immunization. Sera were analyzed for antibody responses by ELISA on plates coated with Ral2-WT1 fusion, Ral2 or WTl TRX. Similar levels of IgG2a and IgGl antibody titers were observed in mice immunized with Ral2-WT1+MPL-SE and Ral2-WT1+Enhanzyn. Mice immunized with rRal2-WTl without adjuvant showed lower levels of IgG2a antibodies. CD4 responses were assessed by measuring Interferon-γ production following stimulation of splenocytes in vitro with rRal2-WTl, rRal2 or with WTl peptides p6, pi 17 and p287. Both adjuvants improved the CD4 responses over mice immunized with rRA12-WTl alone. Additionally, the results indicate that rRA12- WT1+MPL-SE induced a stronger CD4 response than did rRA12-WTl+Enhanzyn. IFN-γ OD readings ranged from 1.4-1.6 in the mice immunized with rRA12- WT1+MPL-SE as compared to 1-1.2 in the mice immunized with rRA12- WTl+Enhanzyn. Peptide responses were only observed against pi 17, and then only in mice immunized with rRal2-WTl+MPL-SE. Strong IFN-γ responses to the positive control, ConA, were observed in all mice. Only responses to ConA were observed in the negative control mice immunized with saline indicating that the responses were specific to rRA12-WTl .
EXAMPLE 17 CONSTRUCTION OF A RANDOMLY MUTATED WTl LIBRARY
The nucleic acid sequence of human WTl was randomly mutated using a polymerase chain reaction method in the presence of 8-oxo dGTP and dPTP Gournal of Molecular Biology 1996; 255:589-603). The complete unspliced human WTl gene is disclosed in SEQ ID NO:380 and the corresponding protein sequence is set forth in SEQ ID NO:404. A splice variant of WTl was used as a template for the PCR reactions and is disclosed in SEQ ID NOs:381 (DNA) and 408 (protein). Conditions were selected so that the frequency of nucleic acid alterations led to a targeted change in the amino acid sequence, usually 5-30% of the PCR product. The mutated PCR product was then amplified in the absence of the nucleotide analogues using the four normal dNTPs. This PCR product was subcloned into mammalian expression vectors and viral vectors for immunization. This library, therefore, contains a mixed population of randomly mutated WTl clones. Several clones were selected and sequenced. The mutated WTl variant DNA sequences are disclosed in SEQ ID NOs:377-379 and the predicted amino acid sequences of the variants are set forth in SEQ ID NOs:405-407. These altered sequences, and others from the library, can be used as immunogens to induce stronger T cell responses against WTl protein in cancer cells.
EXAMPLE 18 CONSTRUCTION OF WTl -LAMP FUSIONS
A tripartite fusion was constructed using the polymerase chain reaction and synthetic oligonucleotides containing the desired junctions of human lysosomal associated membrane protein- 1 (LAMP-1) and a splice variant of the human WTl sequence. The splice variant of WTl and the LAMP-1 sequence used for these fusions are disclosed in SEQ ID NOs:381 and 383. Specifically, the signal peptide of LAMP-1 (base pairs 1-87 of LAMP) was fused to the 5 -prime end of the human WTl open reading frame (1,290 base pairs in length), then the transmembrane and cytoplasmic domain of LAMP-1 (base pairs 1161 to 1281 of LAMP) was fused to the 3-prime end of the WTl sequence. The sequence of the resulting WT1-LAMP construct is set forth in SEQ ID NO:382 (DNA) and SEQ ID NO:409 (protein). The construct was designed so that when it is expressed in eukaryotic cells, the signal peptide directs the protein to the endoplasmic reticulum (ER) where the localization signals in the transmembrane and cytoplasmic domain of LAMP-1 direct transport of the fusion protein to the lysosomal location where peptides are loaded on to Class II MHC molecules.
EXAMPLE 19 CONSTRUCTION OF WT 1 -UBIQUITIN FUSIONS FOR ENHANCED MHC CLASS I PRESENTATION
The human ubiquitin open reading frame (SEQ ID NO: 384) was mutated such that the nucleotides encoding the last amino acid encode an alanine instead of a glycine. This mutated open reading frame was cloned in frame just upstream of the first codon of a splice variant of human WTl (SEQ ID NOs:381 and 408, DNA and protein, respectively). The G->A mutation prevents co-translational cleavage of the nacent protein by the proteases that normally process poly-ubiquitin during translation. The DNA and predicted amino acid sequence for the resulting contract are set forth in SEQ ID NOs:385 and 410, respectively. The resulting protein demonstrated decreased cellular cytotoxicity when it was expressed in human cells. Whereas it was not possible to generate stable lines expressing native WTl, cell lines expressing the fusion protein were readily obtained. The resulting protein is predicted to be targeted to the proteosome by virtue of the added ubiquitin molecule. This should result in more efficient recognition of the protein by WTl specific CD8+ T cells. EXAMPLE 20 CONSTRUCTION OF AN ADENOVIRUS VECTOR EXPRESSING HUMAN WTl
A splice variant of human WTl (SEQ ID NO:381) was cloned into an El and E3 deleted adenovirus serotype 5 vector. The expression of the WTl gene is controlled by the CMV promoter mediating high levels of WTl protein expression.
Infection of human cells with this reagent leads to a high level of expression of the WTl protein. The antigenic nature of the adenoviral proteins introduced into the host cell during and produced at low levels subsequent to infection can act to increase immune surveillance and immune recognition of WTl as an immunological target. This vector can be also used to generate immune responses against the WTl protein when innoculated into human subjects. If these subjects are positive for WTl expressing tumor cells the immune response could have a theraputic or curative effect on the course of the disease.
EXAMPLE 21 CONSTRUCTION OF A VACCINIA VIRUS VECTOR EXPRESSING HUMAN WTl
A splice variant of the full length human WTl gene (SEQ ID NO:381) was cloned into the thymidine kinase locus of the Western Reserve strain of the vaccinia virus using the pSCl 1 shuttle vector. The WTl gene is under the control of a hybrid vaccinia virus promoter that mediates gene expression throughout the course of vaccinia virus infection. This reagent can be used to express the WTl protein in human cells in vivo or in vitro. WTl is a self protein that is overexpressed on some human tumor cells. Thus, immunological responses to WTl delivered as a protein are unlikely to lead to Major Histocompatibility Class I (MHC class I)-mediated recognition of
WTl. However, expression of the protein in the intracellular compartment by the vaccinia virus vector will allow high level MHC class I presentation and recognition of the WTl protein by CD8+ T cells. Expression of the WTl protein by the vaccinia virus vector will also lead to presentation of WTl peptides in the context of MHC class II and thus to recognition by CD4+ T cells. The uses of this invention include its use as a cancer vaccine. Immunization of human subjects bearing WTl positive tumors could lead to a theraputic or curative response. The expression of WTl within the cell will lead to recognition of the protein by both CD4 and CD8 positive T cells.
EXAMPLE 22 GENERATION OF WTI -SPECIFIC CD8+ T-CELL CLONES USING WHOLE GENE PRIMING
Dendritic cells (DC) were differentiated from monocyte cultures derived from PBMC of normal donors by growth for 4-6 days in RPMI medium containing 10% human serum, 50 ng/ml GM-CSF and 30 ng/ml IL-4. Following culture, DC were infected 16 hours with recombinant WTl -expressing vaccinia virus (described in Example 21) at a multiplicity of infection (MOI) of 5 or for 3 days with recombinat WTl -expressing adenovirus at an MOI of 10. Vaccinia virus was inactivated by UN. irradiation. CD8+ T-cells were isolated by negative depletion using magnetic beads, and priming cultures were initiated in 96-well plates. Cultures were restimulated every 7-10 days using autologous dendritic cells infected with adeno or vaccinia virus engineered to express WTl . Following 4-5 stimulation cycles, CD8+ T-cell lines could be identified that specifically produced interferon-gamma when stimulated with autologous- WTl expressing dendritic cells or fibroblasts. These lines were cloned and demonstrated to specifically recognize WTl transduced autologous fibroblasts but not EGFP transduced fibroblasts by Elispot assays.
The Wilms' tumor (WTl) gene participates in leukemogenesis and is overexpressed in most human leukemias as well as in several solid tumors. Previous studies in humans have demonstrated the presence of WTl specific antibody (Ab) responses in 16/63 (25%) of AML and in 15/81 (19%) of CML patients studied. Previous studies in mice have shown that WTl peptide based vaccines elicit WTl specific Ab, Th and CTL responses. The use of peptides as vaccines in humans is limited by their HLA restriction and the tendency to elicit peptide specific responses and only in a minority of patients tumor specific CTL. The advantages of whole gene immunization are that several helper and CTL epitopes can be included in a single vaccine, thus not restricting the vaccine to specific HLA types. The data disclosed herein demonstrate the induction of WTl specific immune responses using whole gene in vitro priming, and that WTl specific CD8+ T-cell clones can be generated. Given that existent immunity to WTl is present in some patients with leukemia and that murine and human WTl are 96% identical at the amino acid level and vaccination to WTl protein, DNA or peptides can elicit WTl specific Ab, and cellular T-cell responses in mice without toxicity to normal tissues in mice, these human in vitro priming experiments provide further validation of WTl as a tumor/leukemia vaccine. Furthermore, the ability to generate WTl specific CD 8+ T-cell clones may lead to the treatment of malignancies associated with WTl overexpression using genetically engineered T-cells.
EXAMPLE 23 RECOMBINANT CONSTRUCTS FOR CLINICAL MANUFACTURING OF WTl
Five constructs were made as described in detail below, for the production of clinical grade WTl.
Design of Ral2/WT-E (SEQ ID NOs:388 (cDNA) and 391 (protein)) and WT-1 E (SEQ ID NOs:386 (cDNA) and 395 (protein)) with No His tag: The WT-1 E reading frame was PCR amplified with the following primers for the non-His non fusion construct:
PDM-780 (SEQ ID NO:396) 5' gacgaaagcatatgcactccttcatcaaac 3' Tm
60°C
PDM-779 (SEQ ID NO:397) 5' cgcgtgaattcatcactgaatgcctctgaag 3' Tm 63°C
The following PCR cycling conditions were used: lOμl 10X Pfu buffer, lμl lOmM dNTPs, 2μl lOμM each oligo, 83μl sterile water 1.5μl Pfu DNA polymerase (Stratagene, La Jolla, CA), 50 ηg DNA (pPDMRal2 WT-1 No His). The reaction was denatured initially at 96°C for 2 minutes, followed by 40 cylces of 96°C for 20 seconds, 62°C for 15 seconds, and 72°C for 1 minute and 40 seconds. This was followed by a final extension of 72°C for 4 minutes. The PCR product was digested with Ndel and EcoRI and cloned into pPDM His (a modified pET28 vector) that had been digested with Ndel and EcoRI. The construct was confirmed through sequence analysis and then transformed into BLR (DE3) pLys S and HMS 174 (DE3) pLys S cells. This construct - pPDM WT-1 E was then digested with Ncol and Xbal and used as the vector backbone for the Ncol and Xbal insert from pPDM Ral2 WT-1 F (see below). The construct was confirmed through sequence analysis and then tranformed into BLR (DE3) pLys S and HMS 174 (DE3) pLys S cells. Protein expression was confirmed by Coomassie stained SDS-PAGE and N-terminal protein sequence analysis.
Design of Ral2-WT-1-F (a.a. 1-281) with No His tag (SEQ ID NOs:389 (cDNA) and 393 (protein)):
The Ral2 WT-1 reading frame was PCR amplified with the following primers:
PDM-777 (SEQ ID NO:398) 5' cgataagcatatgacggccgcgtccgataac 3' Tm 66°C PDM-779 (SEQ ID NO:399) 5' cgcgtgaattcatcactgaatgcctctgaag 3' Tm
63°C
, The following PCR cycling conditions were used: lOμl 10X Pfu buffer, lμl lOmM dNTPs, 2μl lOμM each oligo, 83μl sterile water 1.5μl Pfu DNA polymerase (Stratagene, La Jolla, CA), 50 ηg DNA (pPDMRal2 WT-1 No His). The reaction was denatured initially at 96°C for 2 minutes, followed by 40 cylces of 96°C for 20 seconds, 58°C for 15 seconds, and 72°C for 3 minutes. This was followed by a final extension of 72°C for 4 minutes. The PCR product was digested with Ndel and cloned into pPDM His that had been digested with Ndel and Eco72I. The sequence was confirmed through sequence analysis and then transformed into BLR (DE3) pLys S and HMS 174 (DE3) pLysS cells. Protein expression was confirmed by Coomassie stained SDS-PAGE and N-terminal protein sequence analysis.
Design of Ral2-WT-1 with No His tag (SEQ ID NOs:390 (cDNA) and 392 (protein)):
The Ral2 WT-1 reading frame was PCR amplified with the following primers: PDM-777 (SEQ ID NO:400) 5' cgataagcatatgacggccgcgtccgataac 3' Tm
66°C PDM-778 (SEQ ID NO:401) 5' gtctgcagcggccgctcaaagcgccagc 3' Tm
70°C The following PCR cycling conditions were used: lOμl 10X Pfu buffer, lμl lOmM dNTPs, 2μl lOμM each oligo, 83μl sterile water 1.5μl Pfu DNA polymerase (Stratagene, La Jolla, CA), 50 ηg DNA (pPDMRal2 WT-1 No His). The reaction was denatured initially at 96°C for 2 minutes, followed by 40 cylces of 96°C for 20 seconds, 68°C for 15 seconds, and 72°C for 2 minutes and 30 seconds. This was followed by a final extension of 72°C for 4 minutes. The PCR product was digested with Notl and Ndel and cloned into pPDM His that had been digested with Ndel and Notl. The sequence was confirmed through sequence anaysis and then transformed into BLR (DE3) pLys S and HMS 174 (DE3) pLysS cells. Protein expression was confirmed by Coomassie stained SDS-PAGE and N-terminal protein sequence analysis. Design of WT-1 C (a.a. 69-430) in E. coli without His tag (SEQ ID
NOs:387 (cDNA) and 394 (protein)):
The WT-1 C reading frame was PCR amplified with the following pπmers:
PDM-780 (SEQ ID NO:402) 5' gacgaaagcatatgcactccttcatcaaac 3' Tm 60°C PDM-778 (SEQ ID NO:403) 5' gtctgcagcggccgctcaaagcgccagc 3' Tm 70°C
The following PCR cycling conditions we're used: lOμl 10X Pfu buffer, lμl lOmM dNTPs, 2μl lOμM each oligo, 83μl sterile water 1.5μl Pfu DNA polymerase (Stratagene, La Jolla, CA), 50 ηg DNA (pPDMRal2 WT-1 No His). The reaction was denatured initially at 96°C for 2 minutes, followed by 40 cylces of 96°C for 20 seconds, 62°C for 15 seconds, and 72°C for 2 minutes. This was followed by a final extension of 72°C for 4 minutes. The PCR product was digested with Ndel and cloned into pPDM His that had been digested with Ndel and Eco72I. The sequence was confirmed through sequence analysis and then transformed into BLR (DE3) pLys S and HMS 174 (DE3) pLys S cells. Protein expression was confirmed by Coomassie stained SDS-PAGE and N-terminal protein sequence analysis.
EXAMPLE 24 GENERATION OF WTI-SPECIFIC CD8+ T CELL CLONES USING WHOLE GENE PRIMING AND
IDENTIFICATION OF AN HLA-A2-RESTRICTED WTl EPITOPE
In this example, Adeno and Vaccinia virus delivery vehicles were used to generate WTl -specific T cell lines. A T cell clone from the line was shown to be specific for WTl and further, the epitope recognized by this clone was identified.
Dendritic cells (DC) were differentiated from monocyte cultures derived from PBMC of normal donors by growth for 4-6 days in RPMI medium containing 10% human serum, 50 ng/ml GM-CSF and 30 ng/ml IL-4. Following culture, DC were infected 16 hours with recombinant WTl -expressing vaccinia virus at a multiplicity of infection (MOI) of 5 or for 2-3 days with recombinant WTl -expressing adeno viras at an MOI of 3-10. Vaccinia virus was inactivated by UN. irradiation. CD 8+ T-cells were isolated by negative depletion using antibodies to CD4, CD14, CD16, CD19 and CD56+ cells, followed by magnetic beads specific for the Fc portion of these Abs.
Priming cultures were initiated in 96-well plates. Cultures were restimulated every 7-14 days using autologous dendritic cells infected with adeno or vaccinia virus engineered to express WTl. Following 4-5 stimulation cycles, CD 8+ T cell lines could be identified that specifically produced interferon-γ (IFΝ-γ) when stimulated with autologous- WTl expressing dendritic cells or fibroblasts. These lines were cloned and demonstrated to specifically recognize WTl transduced autologous fibroblasts but not control transduced fibroblasts by Elispot assays.
To further analyze HLA restriction of these WTl specific CD 8+ T-cell clones, fibroblasts derived from an additional donor (D475), sharing only the HLA-A2 allele with the donor (D349) from which the T-cell clone was established, were transduced with WTl . ELISPOT analysis demonstrated recognition of these D475 target cells by the T-cell clone. To further demonstrate HLA A2 restriction and demonstrate that this epitope is expressed by tumor cells "naturally" overxpressing WTl (as part of their malignant transformation), the leukemia cell line K562 was tested. K562 was transduced with the HLA A2 molecule, and HLA-A2 negative K562 cells were used as controls for nonspecific IFN-γ release. ELISPOT analysis demonstrated that the T cells recognized the A2 positive K562 cell line, but not the A2 negative K562 cells. Further proof of specificity and HLA-A2 restriction of the recognition was documented by HLA-A2 antibody blocking experiments.
To further define the WTl epitope, 4 truncated WTl retro viral constructs were generated. Donor 475 fibroblasts were then transduced with these constructs. ELISPOT assays demonstrated recognition of D475 fibroblasts transduced with the WTl Trl construct (aa2-aa92), thus demonstrating that the WTl epitope is localized within the first 91 N-terminal amino acids of the WTl protein. To fine map the epitope, 15mer peptides of the WTl protein, overlapping by 11 amino acids, were synthesized. The WTl specific T-cell clone recognized two overlapping 15mer peptides, peptide 9 (QWAPVLDFAPPGASA) (SEQ ID NO: 412) and peptide 10 (VLDFAPPGASAYGSL) (SEQ ID NO: 413). To further characterize the minimal epitope recognized, shared 9mer and lOmer peptides of the 15mers (5 total) were used to analyse the specificity of the clone. The clone specifically recognized the 9mer, VLDFAPPGA (SEQ ID NO:241), and the lOmer, VLDFAPPGAS (SEQ ID NO:411).
EXAMPLE 25
CLONING AND SEQUENCING OF TCR ALPHA AND BETA CHAINS DERIVED FROM A CD8 T
CELL SPECIFIC FOR WTl
T cell receptor (TCR) alpha and beta chains from CD 8+ T cell clones specific for WTl are cloned. Sequence analysis is carried to demonstrate the family origin of the the alpha and beta chains of the TCR. Additionally, unique diversity and joining segments (contributing to the specificity of the response) are identified.
Total mRNA from 2 x IO6 cells from a WTl specific CD8+ T cell clone is isolated using Trizol reagent and cDNA is synthesized using Ready-to-go kits (Pharmacia). To determine Vα and Vβ sequences in a clone, a panel of Vα and Vβ subtype specific primers are synthesized (based on primer sequences generated by Clontech, Palo Alto, CA) and used in RT-PCR reactions with cDNA generated from each clone. The RT-PCR reactions demonstrate which Vβ and Vα sequence is expressed by each clone.
To clone the full-length TCR alpha and beta chains from a clone, primers are designed that span the initiator and terminator-coding TCR nucleotides. Standard 35 cycle RT-PCR reactions are established using cDNA synthesized from the CTL clone and the above primers using the proofreading thermostable polymerase PWO (Roche, Basel, Switzerland). The resultant specific bands (~850 bp for alpha and -950 for beta) are ligated into the PCR blunt vector (Invitrogen, Carlsbad, CA) and transformed into E.coli. E.coli transformed with plasmids containing full-length alpha and beta chains are identified, and large scale preparations of the corresponding plasmids are generated. Plasmids containing full-length TCR alpha and beta chains are then sequenced using standard methods. The diversity-joining (DJ) region that contributes to the specificity of the TCR is thus determined.
From the foregoing it will be appreciated that, although specific embodiments of the invention have been described herein for purposes of illustration, various modifications may be made without deviating from the spirit and scope of the invention. Accordingly, the invention is not limited except as by the appended claims.

Claims

CLAIMSWhat is Claimed:
1. An isolated polynucleotide comprising a sequence selected from the group consisting of:
(a) sequences provided in SEQ ID NOs:327-331, 337-341, and 377- 390;
(b) complements of the sequences provided in SEQ ID NOs:327- 331, 337-341, and 377-390;
(c) sequences consisting of at least 20 contiguous residues of a sequence provided in SEQ ID NOs:327-331, 337-341, and 377-390;
(d) sequences that hybridize to a sequence provided in SEQ ID NOs:327-331, 337-341, and 377-390, under moderately stringent conditions;
(e) sequences having at least 75% identity to a sequence of SEQ ID NOs:327-331, 337-341, and 377-390;
(f) sequences having at least 90% identity to a sequence of SEQ ID NOs:327-331, 337-341, and 377-390; and
(g) degenerate variants of a sequence provided in SEQ ID NOs:327- 331, 337-341, and 377-390.
2. An isolated polypeptide comprising an amino acid sequence selected from the group consisting of:
(a) sequences encoded by a polynucleotide of claim 1 ; and
(b) sequences having at least 70% identity to a sequence encoded by a polynucleotide of claim 1; and
(c) sequences having at least 90% identity to a sequence encoded by a polynucleotide of claim 1 ;
(d) sequences set forth in SEQ ID NOs:241, 332-336, 342-346, 391- 395, and 404-413; (e) sequences having at least 7u% identity to a sequence set forth in SEQ ID NOs:241, 332-33,6, 342-346, 391-395, and 404-413; and
(f) sequences having at least 90% identity to a sequence set forth in SEQ ID NOs:241, 332-336, 342-346, 391-395, and 404-413;
3. An expression vector comprising a polynucleotide of claim 1 operably linked to an expression control sequence.
4. A host cell transformed or transfected with an expression vector according to claim 3.
5. An isolated antibody, or antigen-binding fragment thereof, that specifically binds to a polypeptide of claim 2.
6. A method for detecting the presence of a cancer in a patient, comprising the steps of:
(a) obtaining a biological sample from the patient;
(b) contacting the biological sample with a binding agent that binds to a polypeptide of claim 2;
(c) detecting in the sample an amount of polypeptide that binds to the binding agent; and
(d) comparing the amount of polypeptide to a predetermined cut-off value and therefrom determining the presence of a cancer in the patient.
7. A fusion protein comprising at least one polypeptide according to claim 2.
8. An oligonucleotide that hybridizes to a sequence recited in SEQ ID NOs:327-331, 337-341, and 377-390 under moderately stringent conditions.
9. A method for stimulating and/or expanding T cells specific for a tumor protein, comprising contacting T cells with at least one component selected from the group consisting of:
(a) polypeptides according to claim 2;
(b) polynucleotides according to claim 1 ; and
(c) antigen-presenting cells that express a polynucleotide according to claim 1, under conditions and for a time sufficient to permit the stimulation and/or expansion of T cells.
10. An isolated T cell population, comprising T cells prepared according to the method of claim 9.
11. A composition comprising a first component selected from the group consisting of physiologically acceptable carriers and immunostimulants, and a second component selected from the group consisting of:
(a) polypeptides according to claim 2;
(b) polynucleotides according to claim 1 ;
(c) antibodies according to claim 5;
(d) fusion proteins according to claim 7;
(e) T cell populations according to claim 10; and
(f) antigen presenting cells that express a polypeptide according to claim 2.
12. A method for stimulating an immune response in a patient, comprising administering to the patient a composition of claim 11.
13. A method for the treatment of a cancer in a patient, comprising administering to the patient a composition of claim 11.
14. A method for determining the presence of a cancer in a patient, comprising the steps of:
(a) obtaining a biological sample from the patient;
(b) contacting the biological sample with an oligonucleotide according to claim 8;
(c) detecting in the sample an amount of a polynucleotide that hybridizes to the oligonucleotide; and
(d) compare the amount of polynucleotide that hybridizes to the oligonucleotide to a predetermined cut-off value, and therefrom determining the presence of the cancer in the patient.
15. A diagnostic kit comprising at least one oligonucleotide according to claim 8.
16. A diagnostic kit comprising at least one antibody according to claim 5 and a detection reagent, wherein the detection reagent comprises a reporter group.
17. A method for inhibiting the development of a cancer in a patient, comprising the steps of:
(a) incubating CD4+ and/or CD 8+ T cells isolated from a patient with at least one component selected from the group consisting of: (i) polypeptides according to claim 2; (ii) polynucleotides according to claim 1; and (iii) antigen presenting cells that express a polypeptide of claim 2, such that T cell proliferate;
(b) administering to the patient an effective amount of the proliferated T cells, and thereby inhibiting the development of a cancer in the patient.
18. A composition comprising a WTl polypeptide resuspended in a buffer comprising at least one sugar selected from the group consisting of trehalose, maltose, sucrose, fructose, and glucose, at a concentration of between about 7 and about 13 %.
19. The composition of claim 18 wherein said concentration is between about 8 and about 12%.
20. The composition of claim 18 wherein said concentration is about 10%.
21. A composition comprising a WTl polypeptide resuspended in a buffer comprising at least 2 sugars selected from the group consisting of trehalose, maltose, sucrose, fructose, and glucose, at a concentration of between about 7 and about 13 %.
22. The composition of claim 21 wherein said concentration is between about 8 and about 12%.
23. The composition of claim 21 wherein said concentration is about 10%.
24. A composition comprising a WTl polypeptide resuspended in a buffer comprising at least 3 sugars selected from the group consisting of trehalose, maltose, sucrose, fructose, and glucose, at a concentration of between about 7 and about 13 %.
25. The composition of claim 24 wherein said concentration is between about 8 and about 12%.
26. The composition of claim 24 wherein said concentration is about 10%.
27. A composition comprising a WTl polypeptide resuspended in a buffer comprising:
(a) at least one sugar selected from the group consisting of trehalose, maltose, sucrose, fructose, and glucose, at a concentration of between about 7 and about 13 %;
(b) ethanolamine;
(c) cysteine; and
(d) Polysorbate-80.
28. The composition of claim 27 wherein said concentration is between about 8 and about 12%.
29. The composition of claim 27 wherein said concentration is about 10%.
30. A composition according to any one of claims 18-29 wherein the WTl polypeptide comprises an Ral2-WT1 fusion polypeptide.
31. A composition comprising a WTl polypeptide and MPL-SE.
32. The composition of claim 31 wherein the WTl polypeptide comprises an Ral2-WT1 fusion polypeptide.
33. A composition comprising a WTl polypeptide and Enhanzyn.
34. The composition of claim 33 wherein the WTl polypeptide comprises an Ral2-WT1 fusion polypeptide.
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DE60135005T DE60135005D1 (en) 2000-10-06 2001-10-03 COMPOUNDS AND METHODS FOR WT1-SPECIFIC IMMUNOTHERAPY
KR1020037004933A KR100858231B1 (en) 2000-10-06 2001-10-03 Compositions for WT1 specific immunotherapy
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CA2425072A CA2425072C (en) 2000-10-06 2001-10-03 Wt1 fusion polypeptides and methods for wt1 immunotherapy
AU9660801A AU9660801A (en) 2000-10-06 2001-10-03 Compositions and methods for wt1 specific immunotherapy
MXPA03002983A MXPA03002983A (en) 2000-10-06 2001-10-03 Compositions and methods for wt1 specific immunotherapy.
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US09/685,830 US7329410B1 (en) 1998-09-30 2000-10-09 Compositions and method for WT1 specific immunotherapy
US09/685,830 2000-10-09
US09/785,019 US7144581B2 (en) 2000-10-09 2001-02-15 Compositions and methods for WT1 specific immunotherapy
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