EP1261711A2 - Zusammensetzungen und methoden zur diagnose und therapie von malignen mesotheliom - Google Patents

Zusammensetzungen und methoden zur diagnose und therapie von malignen mesotheliom

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Publication number
EP1261711A2
EP1261711A2 EP01920134A EP01920134A EP1261711A2 EP 1261711 A2 EP1261711 A2 EP 1261711A2 EP 01920134 A EP01920134 A EP 01920134A EP 01920134 A EP01920134 A EP 01920134A EP 1261711 A2 EP1261711 A2 EP 1261711A2
Authority
EP
European Patent Office
Prior art keywords
seq
peptide
wtl
use according
nucleic acid
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Withdrawn
Application number
EP01920134A
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English (en)
French (fr)
Inventor
Martin A. Cheever
Alexander Gaiger
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Corixa Corp
Original Assignee
Corixa Corp
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Filing date
Publication date
Application filed by Corixa Corp filed Critical Corixa Corp
Publication of EP1261711A2 publication Critical patent/EP1261711A2/de
Withdrawn legal-status Critical Current

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Classifications

    • 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
    • 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
    • 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

Definitions

  • the present invention relates generally to the fields of cancer diagnosis and therapy. More particularly, it concerns the surprising discovery of compositions and methods for the detection and immunotherapy of mesotheliomas, and particularly, malignant pleural mesothelioma.
  • the invention provides new, effective methods, compositions and kits for eliciting immune and T-cell response to Wilms' tumor antigen polypeptide-derived antigenic fragments, and methods for the use of such compositions for diagnosis, detection, treatment, monitoring, and/or prevention of human malignant pleural mesothelioma.
  • the Wilms 1 tumor gene encodes a nuclear-expressed polypeptide designated WTl, which is possesses the structural features of a DNA binding transcription factor.
  • WTl has alternatively spliced variants, including a 429-amino acid polypeptide comprising four contiguous zinc finger domains at its carboxy terminus, and a glutarnine/proline-rich region at its amino terminus, that mediates transcriptional suppression or activation in transient transfection assays.
  • WTl polyclonal antibodies exist, but they have particular disadvantages including cross-reactivity with closely related proteins, and inconsistent results in antigen specificity and binding affinity studies, because of their nature as polyclonal sera. Such sera are therefore not particularly desirable for diagnostic uses, and are not useful for developing therapeutic reagents for in vivo inhibition of WTl polypeptide.
  • mouse monoclonal antibody have also been reported, however most are unsuitable for most therapeutic and diagnostic applications because they either (a) recognize only particular unique splice variant sequences (which are expressed in only a subpopulation of the alternatively-spliced WTl mRNA); or (b) broadly cross-react with homologous, but functionally unrelated peptides, polypeptides, or proteins.
  • Malignant pleural mesothelioma is an increasingly common cancer, caused primarily by exposure to asbestos.
  • the millions of workers who were exposed to asbestos dust prior to the implementation of asbestos regulation and improved control measures are at risk for the disease.
  • workers continue to be exposed to significant amounts of asbestos, when asbestos materials are disturbed during renovation, repair or demolition.
  • Asbestos- containing materials continue to be found in industrial, commercial and residential settings throughout the U. S., resulting in a sizeable population that remains at risk for malignant mesothelioma.
  • the prognosis for malignant mesothelioma is influenced by the stage of the disease.
  • Surgery, as well as adjuvant immunological treatments e.g., interferon or interleukin
  • adjuvant immunological treatments can be effective treatment, but only in the rare event of an early stage diagnosis.
  • a major obstacle to contemporary cancer treatment is the problem of selectivity; that is, the ability to inhibit the multiplication of cancerous cells, while leaving unaffected the function of normal cells.
  • selectivity that is, the ability to inhibit the multiplication of cancerous cells, while leaving unaffected the function of normal cells.
  • most mesothelioma patients are diagnosed only in advanced stages, where neither radiation, nor chemotherapy, nor multimodality treatments can significantly alter the poor prognosis.
  • the absence of a standard effective therapy for these patients makes long-term survival unlikely (Von Bultzingslowen, 1999; Gennaro et al, 2000).
  • the poor survival rate for patients afflicted with malignant mesothelioma could be greatly improved by diagnostic methods that provide more accurate and earlier detection, as well as improved therapies that selectively inhibit the hyperproliferating meothelioma cells.
  • the present invention addresses the foregoing long-felt need and other deficiencies in the art by identifying new and effective strategies for the diagnosis, detection, prophylaxis, therapy, and immunomodulation of WTl -associated cancers, and in particular, malignant pleural mesothelioma.
  • the present invention is based, in part, upon the surprising and unexpected discovery that immune and T cell responses to particular antigenic peptide fragments of the Wilms' tumor (WT) gene product (e.g., WTl) can provide particularly advantageous compositions and methods for the diagnosis, prophylaxis and/or therapy for an animal having, suspected of having, or at risk for developing one or more malignant diseases characterized by increased WTl gene expression, and in particular, malignant pleural mesothelioma in a human.
  • WTl gene was originally identified and isolated on the basis of a cytogenetic deletion at chromosome 1 lpl3 in patients with Wilms' tumor (U. S. Patent No. 5,350,840).
  • the invention provides a method of generating an immune or a T-cell response in an animal, and in particular in a mammal such as a human.
  • the method concerns in a general sense the administration of at least a first composition to the animal that comprises at least a first isolated peptide of from 9 to about 60 amino acids in length, or at least a first nucleic acid segment that encodes such a peptide, wherein the peptide comprises a first contiguous amino acid sequence according to any one of SEQ ID NO:l to SEQ ID NO:4, SEQ ID NO:13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326, and more particularly, a contiguous amino acid sequence according to any one of SEQ ID NO:28 through SEQ ID NO:318, with peptides comprising one or more ofthe primary amino acid sequences disclosed in SEQ ID NO:2, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:49, SEQ ID NO:88, S
  • the invention encompasses peptides that may be of any intermediate length in the preferred ranges, such as for example, those peptides of about 55, about 50, about 45, about 40, about 35, about 30, about 25, about 20, or even about 15 amino acids or so in length, as well as those peptides having intermediate lengths including all integers within these ranges (e.g., the peptides may be about 54, about 53, about 52, about 51, about 49, about 48, about 47, about 46, about 44, about 43, about 42, about 41, about 39, about 38, about 27, or even about 36 or so amino acids in length, etc.).
  • the length ofthe peptide may be 9, or about 10, or about 11, or about 12, or about 13, or about 14 or even about 15 or so amino acids in length, so long as the peptide comprises at least a first contiguous amino acid sequence according to any one of SEQ ID NO:l, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, and SEQ ID NO:20, as well as any one of SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, SEQ ID NO.-321, SEQ ID NO:322, SEQ ID NO:323, SEQ ID NO:324, SEQ ID NO:325, and SEQ ID NO:326.
  • the length ofthe peptide may be about 16, or about 17, or about 18, or about 19, or about 20, or about 21, or about 22, or about 23, or about 24, or even about 25 or so amino acids in length, so long as the peptide comprises at least a first contiguous amino acid sequence according to any one of SEQ ID NO:l to SEQ ID NO:4, SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318 and SEQ ID NO:321 to SEQ ID NO:326.
  • the peptides may be on the order of about 26, or about 27, or about 28, or about 29, or about 30, or about 31, or about 32, or about 33, or about 34, or even about 35 or so amino acids in length, so long as they each comprise at least a first contiguous amino acid sequence according to any one of SEQ ID NO:l to SEQ ID NO:4, SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326.
  • These peptides comprise at least a first contiguous amino acid sequence according to any one of SEQ ID NO:l to SEQ ID NO:4, SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326, but may also, optionally comprise at least a second, at least a third, or even at least a fourth or greater contiguous amino acid sequence according to any one of SEQ ID NO:l to SEQ ID NO:4, SEQ ID NO.T3 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326.
  • a single peptide may contain only one of the contiguous amino acid sequences disclosed herein, or alternatively, a single peptide may comprise a plurality of contiguous amino acid sequences according to any one of SEQ ID NO:l to SEQ ID NO:4, SEQ ID NO:13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326.
  • the peptide may comprise a plurality of the same contiguous amino acid sequences, or they may comprise one or more different contiguous amino acid sequences disclosed in SEQ ID NO:l to SEQ ID NO:4, SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326.
  • a single peptide of from 9 to about 50 amino acids in length could comprise a single epitopic peptide disclosed herein, or could comprise 2, 3, 4, or even 5 distinct epitopic sequences as disclosed in any of SEQ ID NO:l to SEQ ID NO:4, SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326.
  • a single peptide of from 9 to about 50 amino acids in length could comprise 2, 3, 4, or even 5 identical epitopic sequences as disclosed in any one of SEQ ID NO:l to SEQ ID NO:4, SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326.
  • the peptide composition comprises at least a first isolated peptide of from 9 to about 40 amino acids in length, or at least a first nucleic acid segment that encodes such a peptide; wherein the peptide comprises at least a first contiguous amino acid sequence selected from the group consisting of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:49, SEQ ID NO:88, SEQ ID NO: 144, SEQ ID NO: 147, SEQ ID NO: 185, SEQ ID NO: 198, SEQ ID NO: 199, and SEQ ID NO:282.
  • Preferred peptides of the present invention likewise encompass those from 10 to about 60 amino acids in length, those from 11 to about 60 amino acids in length, those from 12 to about 60 amino acids in length, those from 13 to about 60 amino acids in length, as well as those from 14 to about 60 amino acids in length, and those from 15 to about 60 amino acids in length.
  • preferred peptides of the present invention encompass those from 16 to about 60 amino acids in length, and any and all lengths, and sub-ranges of lengths within the overall preferred range of peptides of from 9 to about 60 amino acids or so in length.
  • the invention also encompasses those peptides having a length of from 10 or 11 to about 55 or 60 amino acids in length, and those having a length of from 12 or 13 to about 45 or 50 amino acids in length, as well as those peptides having a length of from 14 or 15 to about 35 or 40 amino acids in length, those peptides having a length of from 16 or 17 to about 25 or 30 amino acids in length, and those peptides having a length of from 18 or 19 to about 20 or so amino acids in length, and so on, to include all sub-ranges within the overall range of from 9 to about 60 amino acids in length.
  • a phrase such as "a sequence as disclosed in SEQ ID NO.T to SEQ ID NO:4" is intended to encompass any and all contiguous amino acid sequences disclosed by any of these sequence identifiers, and particularly, the peptide sequences disclosed in Table 2 through Table 49 of the present specification. That is to say, "a sequence as disclosed in any of SEQ ID NO.T through SEQ ID NO:4" means a sequence that is disclosed in SEQ ID NO:l, SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4.
  • SEQ ID NOs:25 to 37 means any and all such sequences as disclosed in SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28, SEQ ID NO:29, SEQ ID NO:30, SEQ ID NO:31, SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:36, and SEQ ID NO:37, and so forth.
  • the invention encompasses peptides and polynucleotides encoding them that comprise at least a first contiguous amino acid sequence as disclosed in any one of the sequences identified as SEQ ID NOT to SEQ ID NO:4, SEQ ID NO:13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326.
  • the invention also encompasses polynucleotides that comprise at least a first sequence region that encodes one or more of the peptides or peptide variants as disclosed herein.
  • polynucleotides may comprise a sequence region of 27 to about 5000 nucleotides in length, or a sequence region of 27 to about 2000 nucleotides in length, or a sequence region of 27 to about 1000 nucleotides in length, or a sequence region of 27 to about 900, or about 800, or about 700, or about 600, or about 500, or about 400, or about 300, or about 200, or even about 100 or so nucleotides in length.
  • the length of the sequence region that encodes the peptide may be of any intermediate length in these ranges, such as those polynucleotides that comprise at least a first sequence region of from about 30 to about 750 nucleotides in length, those that comprise at least a first sequence region of from about 35 to about 650 nucleotides in length, and those that comprise at least a first sequence region of from about 40 to about 550, about 450, about 350, about 250, about 150, or even about 50 or so nucleotides in length.
  • sequence regions may be on the order of about 27, or about 28, or about 29, or about 30, or about 31, or about 32, or about 33, or about 34, or even about 35 or so nucleotides in length, so long as the sequence region encodes at least a first peptide that comprises at least a first contiguous amino acid sequence according to any one of SEQ ID NO.T to SEQ ID NO:4, SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326.
  • the nucleic acids that encode them may be on the order of about 40, about 45, or about 50, or about 55, or about 60, or about 65, or about 70, or about 75, or about 80, or even about 85 or 90 or so nucleotides in length, so long as they each encode at least a first peptide that comprises at least a first contiguous amino acid sequence according to any one of SEQ ID NOT to SEQ ID NO:4, SEQ ID NO:13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326.
  • nucleic acid sequence region encoding them will necessarily be longer in length.
  • a nucleic acid sequence region encoding a peptide or antigen binding fragment on the order of about 40 to 50 amino acids in length will necessarily be at least from about 120 to about 150 or so nucleotides in length, given the fact that a triplet codon is required to encode a single amino acid.
  • the polynucleotides comprising such sequence regions can be substantially larger than the coding region itself, particularly when the sequence region is operably linked to one or more promoters, or to one or more sequence regions that encode one or more signal sequences, and/or peptide fusion products.
  • the polynucleotide may be on the order of about 500, about 600, about 700, about 800, about 900, about 1000, about 1100, about 1200, about 1300, about 1400, or even about 1500, 1600, 1700, 1800, 1900, or even 2000 or so nucleotides in length, even up to and including those sequences that are on the order of about 10,000 or so nucleotides in length.
  • polynucleotides are particularly useful in the preparation of expression vectors, delivery vehicles, viral vectors, and transformed host cells that express the particular encoded peptide(s) and/or antigen-binding fragment(s) encoded by the sequence region comprised within the polynucleotide and/or genetic construct or expression element.
  • the peptide comprises at least a first isolated peptide of from 9 to about 11 amino acids in length, or at least a first nucleic acid segment that encodes the peptide; wherein the peptide consists essentially of the amino acid sequence of any one of SEQ ID NO:l to SEQ ID NO:4, SEQ ID NO:13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326.
  • the peptide comprises at least a first isolated peptide of from 9 to about 10 or 11 or so amino acids in length, or at least a first nucleic acid segment that encodes the peptide; wherein the peptide consists ofthe amino acid sequence of any one of SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, and SEQ ID NO:316 to SEQ ID NO:318, and particularly wherein the peptide consists of the amino acid sequence of any one of SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:49, SEQ ID NO:88, SEQ ID NO: 144, SEQ ID NO: 147, SEQ ID NO:185, SEQ ID NO:198, SEQ ID NO:199, and SEQ ID NO:282.
  • compositions that comprise 2, 3, 4, or more peptide species and/or the polynucleotides that encode such peptides.
  • Such pluralities of peptide and/or polynucleotide species are particularly desirable in the formulation of therapeutic agents that comprise pluralities of peptides having two or more different contiguous amino acid sequence as disclosed in the amino acid sequences of SEQ ID NOT to SEQ ID NO:4, SEQ ID NO:13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326, and/or a plurality of polynucleotides that encode such peptides.
  • the invention particularly contemplates the use of one, two, three or four distinct peptides, polynucleotides or derivatives thereof, up to and including a plurality of such compounds.
  • This exemplifies the use of singular terminology throughout the entire application, wherein the terms "a” and “an” are used in the sense that they mean "at least one”, “at least a first”, “one or more” or “a plurality” of the referenced components or steps, except in instances wherein an upper limit is thereafter specifically stated or would be understood by one of ordinary skill in the art.
  • compositions may further comprise one or more additional components, such as for example, a pharmaceutically acceptable excipient, buffer, or reagent as described in detail hereinbelow.
  • additional components such as for example, a pharmaceutically acceptable excipient, buffer, or reagent as described in detail hereinbelow.
  • Such compositions may also optionally further comprise at least a first immunostimulant or at least a first adjuvant as described herein.
  • Such immunostimulants and adjuvants preferentially enhance a T-cell response in a human, and may preferably be selected from the group consisting of Montanide ISA50, Seppic Montanide ISA720, a cytokine, a microsphere, a dimethyl dioctadecyl ammonium bromide adjuvant, AS-1, AS-2, Ribi Adjuvant, QS21, saponin, microfluidized Syntex adjuvant, MV, ddMV, an immune stimulating complex and an inactivated toxin.
  • compositions may be formulated for diagnostic or therapeutic uses, including their incorporation into one or more diagnostic or therapeutic kits for clinical packaging and/or commercial resale, with those formulations suitable for administration to a mammal, such as a human, with parenteral, intravenous, intraperitoneal, subcutaneous, intranasal, transdermal, and oral routes being particularly preferred.
  • compositions may further optionally comprise one or more detection reagents, one or more additional diagnostic reagents, one or more control reagents, and/or one or more therapeutic reagents.
  • diagnostic reagents the compositions may further optionally comprise one or more detectable labels that may be used in both in vitro and/or in vivo diagnostic and therapeutic methodologies.
  • the compositions of the invention may also further optionally comprise one or more additional anti-cancer, anti-mesothelioma or otherwise therapeutically-beneficial components as may be required in particular circumstances, and such like.
  • the invention also provides methods for inhibiting the development of malignant mesothelioma in a human patient, comprising administering to a human patient a pharmaceutical composition comprising: (a) a WTl peptide that comprises 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 ofthe variant to react with antigen-specific antibodies and/or T cell lines or clones is not substantially diminished; and (b) a physiologically acceptable carrier or excipient.
  • the patient is afflicted with malignant mesothelioma.
  • the composition is administered prophylactically to a patient considered at risk for the development of malignant mesothelioma.
  • the WTl peptide may, but need not, be present within a vaccine, which further comprises an immunostimulant, such as an adjuvant.
  • methods for inhibiting the development of malignant mesothelioma in a human patient, comprising administering to a human patient a pharmaceutical composition, comprising: (a) a polynucleotide encoding a WTl peptide, wherein the peptide comprises 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 antibodies and/or T cell lines or clones is not substantially diminished; and (b) a pharmaceutically acceptable carrier or excipient.
  • the patient is afflicted with malignant mesothelioma.
  • the composition is administered prophylactically to a patient considered at risk for the development of malignant mesothelioma.
  • the WTl polynucleotide may, but need not, be present within a vaccine, which further comprises an immunostimulant, such as an adjuvant.
  • Methods are further provided for inhibiting the development of malignant mesothelioma in a human patient, comprising administering to a human patient a pharmaceutical composition, comprising: (a) an antibody or antigen-binding fragment thereof that specifically binds to WTl; and (b) a pharmaceutically acceptable carrier or excipient.
  • a pharmaceutical composition comprising: (a) an antibody or antigen-binding fragment thereof that specifically binds to WTl; and (b) a pharmaceutically acceptable carrier or excipient.
  • the patient is afflicted with malignant mesothelioma.
  • the composition is administered prophylactically to a patient considered at risk for the development of malignant mesothelioma.
  • methods for inhibiting the development of malignant mesothelioma in a human patient, comprising administering to a human patient a pharmaceutical composition, comprising: (a) a T cell that specifically reacts with WTl; and (b) a pharmaceutically acceptable carrier or excipient.
  • a pharmaceutical composition comprising: (a) a T cell that specifically reacts with WTl; and (b) a pharmaceutically acceptable carrier or excipient.
  • the patient is afflicted with malignant mesothelioma.
  • the composition is administered prophylactically to a patient considered at risk for the development of malignant mesothelioma.
  • Further methods for inhibiting the development of malignant mesothelioma in a human patient comprise administering to a human patient a pharmaceutical composition, comprising: (a) an antigen-presenting cell that expresses (i) a WTl peptide that comprises 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 ofthe variant to react with antigen-specific antibodies and/or T cell lines or clones is not substantially diminished; and (b) a pharmaceutically acceptable carrier or excipient.
  • the patient is afflicted with malignant mesothelioma.
  • the composition is administered prophylactically to a patient considered at risk for the development of malignant mesothelioma.
  • the antigen presenting cell may, but need not, be present within a vaccine, which further comprises an immunostimulant, such as an adjuvant.
  • the present invention provides methods for inhibiting the development of malignant mesothelioma in a human patient, comprising administering to a human patient a preparation of stimulated and/or expanded T cells, wherein the T cells are stimulated and/or expanded by contact with a WTl peptide, a polynucleotide encoding a WTl peptide and/or an antigen-presenting cell that expresses a WTl peptide.
  • the T cells may be present, for example, within bone marrow, peripheral blood or a fraction of bone marrow or peripheral blood (e.g., obtained from a patient afflicted with malignant mesothelioma).
  • the T cells may, but need not, be cloned prior to expansion.
  • Methods are further provided for inhibiting the development of malignant mesothelioma 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 peptide; (ii) a polynucleotide encoding a WTl peptide; or (iii) an antigen-presenting cell that expresses a WTl peptide; such that the T cells proliferate; and (b) administering to the patient an effective amount ofthe proliferated T cells.
  • Further methods for inhibiting the development of malignant mesothelioma 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 peptide; (ii) a polynucleotide encoding a WTl peptide; or (iii) an antigen-presenting cell that expresses a WTl peptide; such that the T cells proliferate; (b) cloning one or more cells that proliferated in the presence of WTl peptide; and (c) administering to the patient an effective amount ofthe cloned T cells.
  • the present invention provides method for determining the presence or absence of malignant mesothelioma 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 peptide; (ii) a polynucleotide encoding a WTl peptide; or (iii) an antigen-presenting cell that expresses a WTl peptide; and (b) detecting the presence or absence of specific activation of the T cells.
  • the step of detecting may comprise, for example, detecting the presence or absence of proliferation ofthe T cells or the generation of cytolytic activity.
  • the present invention further provides methods for determining the presence or absence of malignant mesothelioma in a patient, comprising the steps of: (a) incubating a biological sample obtained from a patient with one or more of: (i) a WTl peptide; (ii) a polynucleotide encoding a WTl peptide; or (iii) an antigen-presenting cell that expresses a WTl peptide; 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 peptide and antibodies in the biological sample that specifically bind to the WTl peptide.
  • the step of detecting may comprise, for example, (a) incubating the immunocomplexes with a detection reagent that is capable of binding to the immuno- complexes, wherein the detection reagent comprises a reporter group, (b) removing unbound detection reagent, and (c) detecting the presence or absence ofthe reporter group.
  • Methods are further provided, within other aspects, for monitoring the effectiveness of an immunization or therapy for malignant mesothelioma in a patient, comprising the steps of: (a) incubating a first biological sample with one or more of: (i) a WTl peptide; (ii) a polynucleotide encoding a WTl peptide; or (iii) an antigen-presenting cell that expresses a WTl peptide, 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 peptide and antibodies in the biological sample that specifically bind to the WTl peptide; (c) repeating steps (a) and (b) using a second biological sample obtained from the patient following therapy or immunization; and (d) comparing the number of immunocomplex
  • the step of detecting may comprise, for example, (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 ofthe reporter group.
  • methods for monitoring the effectiveness of an immunization or therapy for malignant mesothelioma in a patient, comprising the steps of: (a) incubating a first biological sample with one or more of: (i) a WTl peptide; (ii) a WTl polynucleotide encoding a WTl peptide; or (iii) an antigen-presenting cell that expresses a WTl peptide; 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 in the biological sample; (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
  • an "effective inhibitory amount" is an amount of at least a first WTl compound effective to inhibit, and preferably to significantly inhibit, mesothelioma in an animal afflicted with such a disorder.
  • the effective inhibitory amounts are thus also amounts effective to inhibit, and preferably to significantly inhibit, a biological activity of native WTl polypeptide. More preferably, the effective inhibitory amounts are amounts of WTl compounds effective to inhibit, and preferably to significantly inhibit, the biological activity of native WTl polypeptide in a human having or suspected of having malignant pleural mesothelioma.
  • inhibiting requires a "reproducible,” /. e. , consistently observed, inhibition in one or more of he foregoing parameters.
  • a "significant inhibition” is a reproducible or consistently observed significant inhibition in one or more of the foregoing parameters, such as a reproducible inhibition of at least about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, or about 85% in comparison to control levels, i.e., in the absence of the WTl therapeutic composition.
  • inhibition levels of at least about 90%, about 92%, about 94%, about 96%, or even about 98% or higher are by no means excluded.
  • Execution of one or more of the therapeutic methods disclosed herein gives rise to effective therapies for preventing or treating malignant mesothelioma.
  • These methods which typically comprise providing to an animal or patient having, suspected of having, or at risk for developing malignant mesothelioma, an amount of at least a first WTl peptide, antibody, antigen presenting cell, T cell, antigen binding fragment, or polynucleotide effective to inhibit malignant mesothelioma within cells of the animal or patient, thereby preventing or treating malignant mesothelioma.
  • prophylactically and therapeutically effective amounts are thus encompassed within the terms “biologically effective amounts” and “effective inhibitory amounts” of WTl peptide, antibody, antigen presenting cell, T cell, antigen binding fragment, or polynucleotide compositions. All such “effective amounts” are amounts of the disclosed WTl compounds effective to produce some, and preferably some significant, benefit upon administration to an animal or patient.
  • the benefits include reducing symptoms, severity and/or duration, as well as lessening the chance of transmission and other veterinary and clinical benefits.
  • the routes of administration that may be used in the present invention are virtually limitless, so long as an effective amount of at least a first WTl peptide, antibody, antigen presenting cell, T cell, antigen binding fragment, or polynucleotide composition can be provided thereby.
  • Exemplary means for therapeutic delivery of the disclosed compositions including e.g., ingestion, inhalation, transdermal, parenteral administration, intranasal administration, subcutaneous injection, intravenous injection, continuous infusion, and the like are discussed in more detail hereinbelow.
  • compositions and methods of the invention may be combined for use with one or more other anti-cancer agents, such as at least a second, third, fourth or fifth, anti- mesothelioma agent or at least a first, second, third or fourth anti-cancer therapeutic agent.
  • a plurality of distinct anti-cancer or anti-mesothelioma therapeutic agents may be administered to an animal or patient, up to and including the dose limiting toxicity of the combination.
  • the invention can thus be used to form synergistic combinations with other therapies and/or known agents, particularly those methods and agents that previously failed to achieve maximal effectiveness in vivo, perhaps due to dose-limiting toxicity and/or resistance.
  • the at least a first WTl peptide, antibody, antigen presenting cell, T cell, antigen binding fragment, or polynucleotide, and at least a second anti-mesothelioma or anti-cancer therapeutic agent may be administered to the animal or patient substantially simultaneously, such as from a single pharmaceutical formulation or two distinct pharmaceutical formulations.
  • the at least a first WTl peptide, antibody, antigen presenting cell, T cell, antigen binding fragment, or polynucleotide, and at least a second anti-mesothelioma or anti-cancer therapeutic agent may be administered to the animal or patient sequentially, such as on alternate days.
  • kits comprise a therapeutically effective amount of at least a first WTl peptide, antibody, antigen presenting cell, T cell, antigen binding fragment, or polynucleotide composition and instructions for administering the composition to an animal or subject having or at risk for developing mesothelioma, and in particular, malignant pleural mesothelioma.
  • kits may be combined with effective amounts of at least one diagnostic agent that detects a WTl polypeptide or antibody, or at least one diagnostic agent that detects a mesothelioma cell; or with a therapeutically effective amount of at least one other anti-cancer, anti-mesothelioma or anti- WTl polypeptide therapeutic agent.
  • kits and uses of the compositions disclosed herein may comprise an effective amount of at least a first WTl peptide, antibody, antigen presenting cell, T cell, antigen binding fragment, or polynucleotide and an effective amount of at least one diagnostic agent that detects detects a mesothelioma cell; or an effective amount of at least one, two, three, four or any number of other anti-cancer, anti-mesothelioma or anti -WTl polypeptide therapeutic agents. Instructions may also be combined with these kits. Other biological agents or components may be included, such as those for making and using the drugs.
  • Exemplary diagnostic agents include molecular biological agents that detect at least a first WTl -encoding nucleic acid; at least a first WTl peptide or polypeptide, at least a first antibody that detects at least a first WTl protein or peptide; and at least a first WTl protein or peptide that detects at least a first antibody that binds to a WTl protein or peptide.
  • the range of additional therapeutic agents will be known those of ordinary skill in the art in light ofthe present disclosure, as exemplified by those described herein.
  • the diagnostic agents are preferably disposed within a distinct container of the kit.
  • the combined therapeutic agents may be combined within a single container of the kit, i.e., in the same composition as the WTl composition, such as in a "cocktail" or admixture. They may alternatively be maintained separately from the WTl compound, in a distinct container.
  • the invention thus provides combination therapeutics comprising, in any pharmaceutically acceptable form, a therapeutically effective amount of a WTl compound in combination with a therapeutically effective amount of at least a second anti-WTl, anti- mesothelioma or anti-cancer therapeutic agent.
  • compositions for use in the manufacture of a medicament or medicinal cocktail that comprise, in any pharmaceutically acceptable form, a therapeutically effective amount of at least a first WTl composition.
  • compositions for use in the manufacture of a medicament or medicinal cocktail that comprise, in any pharmaceutically acceptable form, a first WTl composition and a plurality of distinct anti-WTl, anti-mesothelioma or anti-cancer therapeutic agents.
  • Combined uses and medicaments in which a WTl compound is one component of a therapeutic approach are also encompassed within the present invention.
  • FIG. 1 depicts a comparison of the mouse (MO) (SEQ ID NO:320) and human (HU)
  • FIG. 2 depicts a histogram presenting the results of an ELISA assay to detect WT1- specific antibodies in malignant mesothelioma patients.
  • WTl 80 and WTC19, as indicated, represent positive controls.
  • D44 represents normal control serum, and the remaining samples were serum samples obtained from human patients afflicted with malignant mesothelioma;
  • FIG. 3A, FIG. 3B and FIG. 3C depict 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 (pl), pl 17-139 (p2) or p244-262 human (p3).
  • FIG. 4A and FIG. 4B show 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), pl 17-139 (pl l7), p244-262 ( ⁇ 244) (Vaccine A; FIG.
  • spleen cells pulsed with an irrelevant control peptide (irrelevant peptide) at 25 ⁇ g/ml and were assayed after 96 hr for proliferation by ( 3 H) thymidine incorporation.
  • Bars represent the stimulation index (SI), which is calculated as the mean ofthe experimental wells divided by the mean ofthe control (B6 spleen cells with no antigen);
  • FIG. 5A, FIG. 5B, FIG. 5C, and FIG. 5D are histograms illustrating the generation of proliferative T-cell lines and clones specific for pl 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 pl 17-139 and p6-22.
  • Clones were derived from both the p6-22 and pl 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), pl 17-139 (pl 17) or an irrelevant control peptide (irrelevant peptide) at 25 ⁇ g/ml and were assayed after 96 hr 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
  • FIG. 6A and FIG. 6B are graphs illustrating the elicitation of WTl peptide-specific CTL in mice immunized with WTl peptides.
  • FIG. 6A illustrates the lysis of target cells by allogeneic cell lines and
  • FIG. 6B 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 effector :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;
  • FIG. 7A, FIG. 7B, FIG. 7C, and FIG. 7D 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 Pl 17.
  • FIG. 7A illustrates that T-cells of non-immunized B6 mice do not kill WTl positive tumor cell lines.
  • FIG. 7B illustrates the lysis of the target cells by allogeneic cell lines.
  • FIG. 7C and FIG. 7D demonstrate the lysis of WTl positive tumor cell lines, as compared to WTl negative cell lines in two different studies.
  • FIG. 7D show the lysis of peptide- coated cell lines (WTl negative cell line E10 coated with the relevant WTl peptide P117).
  • WTl negative cell line E10 coated with the relevant WTl peptide P117 the % lysis (as determined by standard chromium release assays) is shown at three indicated effector: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 l7;
  • FIG. 8A and FIG. 8B are histograms illustrating the ability of representative peptide Pl 17-139 specific CTL to lyse WTl positive tumor cells.
  • spleen cells of mice that had been inoculated with the peptides p235-243 or p 117-139 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.
  • FIG. 8A 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 pl 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.
  • 8B shows cytotoxic activity of the pl 17-139 specific T cell line against EL-4; EL-4 pulsed with the relevant peptide Pl 17-139 (EL-4+pl l7) and EL-4 pulsed with the irrelevant peptides pl23-131 (EL-4+pl23), or pl28-136 (EL-4+pl28); BLK-SV40 and TRAMP-C, as indicated;
  • FIG. 9A and FIG. 9B 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.
  • FIG. 9A and FIG. 9B 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.
  • FIG. 9A shows the cytotoxic activity of the pl 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 pl 17-139 (TRAMP-C + pl l7 cold target) without 31 Cr labeling and TRAMP-C cells incubated with EL-4 pulsed with an irrelevant peptide without ⁇ 'Cr labeling (TRAMP-C + irrelevant cold target), as indicated.
  • FIG. 9B shows the cytotoxic activity of the pl 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 + pl l7 cold target) and BLK-SV40 cells incubated with the irrelevant cold target (BLK-SV40 + irrelevant cold target), as indicated;
  • FIG. 10A, FIG. 10B, and FIG. 10C are histograms depicting an evaluation of the nonapeptide CTL epitope within pl 17-139.
  • the pl 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 pl26-134 or pl30-138.
  • the bars represent the mean % specific lysis in chromium release assays performed in triplicate with an E:T ratio of 25:1.
  • FIG. 10A shows the cytotoxic activity of the pl 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 pl 17-139 (EL-4 + pl l7), pl 19-127 (EL-4 + pl l9), pl20-128 (EL-4 + pl20), pl23-131 (EL-4 + pl23), pl26-134 (EL-4 + pl26), pl28-136 (EL-4 + pl28), and pl30-138 (EL-4 + ⁇ l30).
  • FIG. 10B shows the cytotoxic activity of the CTL line after restimulation with p 126- 134 against the WTl negative cell line EL-4, EL-4 cells pulsed with pl 17-139 (EL-4 + pl l7), pl26-134 (EL-4 + pl26) and the WTl positive tumor cell line TRAMP-C; and
  • FIG. IOC shows the cytotoxic activity ofthe CTL line after restimulation with p 130- 138 against EL-4, EL-4 cells pulsed with pl 17-139 (EL-4 + pl l7), pl30-138 (EL-4 + pl30) and the WTl positive tumor cell line TRAMP-C.
  • the present invention is generally directed to compositions and methods for the immunotherapy and diagnosis of WTl -associated diseases, such as malignant mesothelioma.
  • WTl expression, and immune responses to WTl may be used as markers to identify patients with malignant mesothelioma and other WTl associated malignancies (such as leukemia (e.g., acute myeloid leukemia (AML), chronic myeloid leukemia (CML), acute lymphocytic leukemia (ALL) and childhood ALL), Myelodysplastic syndromes, myeloproliferative syndromes, prostate cancer, lung cancer, breast cancer, thyroid cancer, gastrointestinal cancer, kidney cancer, liver cancer, ovarian cancer, testicular cancer and melanoma).
  • WTl associated malignancies such as leukemia (e.g., acute myeloid leukemia (AML), chronic myeloid leukemia (CML), acute lymphocytic leukemia (ALL) and childhood ALL), Myelodysplastic syndromes, myeloproliferative syndromes, prostate cancer, lung cancer, breast cancer, thyroid cancer, gastrointestinal cancer, kidney cancer, liver cancer, ovarian cancer, testicular
  • Such diagnostic methods may be used for early diagnosis of cancer, and permit screening of healthy individuals who have or might have been exposed to asbestos. Patients found to be afflicted with such malignancies may benefit from the WT1- based vaccine or T-cell therapeutic methods provided herein.
  • compositions described herein generally comprise WTl peptides, WTl polynucleotides, antigen-presenting cells (APC; e.g., dendritic cells) that express a WTl peptide, agents such as antibodies that specifically bind to a WTl polypeptides and WT1- derived peptides; and/or immune system cells (e.g., T cells) specific for WTl.
  • WTl peptides ofthe 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, PNA, or RNA sequence that encodes all or a portion of such a peptide, 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 peptide.
  • T cells that may be employed within such compositions are generally cells (e.g., CD4 + and/or CD8 + ) that are specific for a WTl peptide. Certain methods described herein further employ one or more antigen-presenting cells that express at least a first WTl peptide or polypeptide as provided herein.
  • exemplary preferred WTl -derived antigenic peptides include those peptides of from 9 to about 100 amino acids in length, that comprises at least a first epitope, antigenic fragment, antibody binding site, or an immunogenic sequence that is selected from the group consisting of SEQ ID NOT to SEQ ID NO:4, SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326.
  • the WTl -derived peptides may be of any intermediate length provided that it comprises at least a first immunogenic portion or epitope, or antibody binding site, of a native WTl polypeptide or a variant thereof, and particularly those peptide sequences disclosed in any one of SEQ ID NOT to SEQ ID NO:4, SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326.
  • a WTl peptide may be an oligopeptide (/. e.
  • those consisting of a relatively small number of amino acid residues such as 9 to about 12 or 13 or so amino acid residues
  • larger oligopeptides i.e., those consisting of a relatively larger number of amino acid residues, such as for example, about 14 to about 20 or so amino acid residues
  • still larger peptides i.e., those consisting of a relatively larger number of amino acid residues, such as for example, about 21 to about 40 or so amino acid residues
  • so forth up to and including those peptides that consist of a J.5
  • WTl peptides that contain a small number of consecutive amino acid residues of a native WTl peptide is preferred. Such peptides are preferred for certain uses in which the generation of a T cell response is desired.
  • a WTl peptide preferably contain at least 9, or at least about 10, 11, 12, 13, 14, or 15 or more consecutive amino acid residues of the native WTl polypeptide.
  • Nonameric peptides (9-mers, or those comprising at least nine consecutive amino acid residues of a native WTl polypeptide) are particularly contemplated to be useful in the methods disclosed herein.
  • Additional sequences derived from the native Protein A and/or heterologous sequences may be present within any WTl peptide, and such sequences may (but need not) possess further immunogenic or antigenic properties.
  • Peptides as provided herein may further be associated (covalently or noncovalently) with other peptide or non- peptide compounds.
  • An "immunogenic portion,” as used herein is a portion of a peptide that is recognized
  • an immunogenic portion binds to an MHC class I or class II molecule.
  • 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.
  • the ability of a peptide 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 (Parker et al, 1994).
  • functional peptide competition assays that are known in the art may be employed.
  • immunogenic portions have one or more ofthe sequences recited within one or more of Tables 2-14.
  • Exemplary immunogenic peptides of the present invention include, but are not limited to, those disclosed in the Examples illustrated in Table 2 through Table 49, and particularly, peptides that comprise at least a first amino acid sequence as defined in any one of SEQ ID NO:l to SEQ ID NO:4, SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326.
  • WTl -derived peptide compositions include, but are not limited to, those that comprise at least a first amino acid sequence selected from the group consisting of SEQ ID NOT to SEQ ID NO:4, SEQ ID NO:13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, and SEQ ID NO:316 to SEQ ID NO:318, and particularly such sequences as disclosed in any one of the following: RDLNALLPAVPSLGGGG (human WTl residues 6-22; SEQ ID NOT), PSQASSGQARMFPNAPYLPSCLE (human and mouse WTl residues 117-139; SEQ ID NO:2 and SEQ ID NO: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
  • immunogenic fragments and peptides are provided herein, and others may generally be identified using well-known techniques (Paul, 1993).
  • Representative techniques for identifying immunogenic peptides, epitopes, and antibody binding motifs include, for example, screening peptides 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 (Harlow and Lane, 1988).
  • immunogenic portions may be identified using computer analysis, such as the Tsites program (Rofnbard and Taylor, 1988; Deavin et al., 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, 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.
  • the peptides of the present invention may comprise one or more variants ofthe amino acid sequences as disclosed herein.
  • a peptide "variant,” as used herein, is a peptide that differs from a particular primary amino acid sequence in one or more substitutions, deletions, additions and/or insertions, such that the immunogenicity of the peptide is substantially 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 peptide).
  • 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 peptide from which the variant was derived.
  • the biological activity of a peptide variant will not be diminished by more than 1%, and preferably still will not be diminished by more than 2%, relative to the biological activity of the unmodified peptide. More preferably, the biological activity of a peptide variant will not be diminished by more than 3%, and more preferably still will not be diminished by more than 4%, 5%, 6%, 7%, 8%, or 9%, relative to the biological activity of the unmodified peptide.
  • the biological activity of a peptide variant will not be diminished by more than 10%, and more preferably still, will not be diminished by more than 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, or 20% relative to the biological activity ofthe correseponding unmodified peptide.
  • preferred peptide variant of the present invention include those peptides that are from 9 to about 100 amino acids in length, and that comprise at least a first sequence region that is at least 75% identical to at least one of the amino acid sequences dislosed in any one of SEQ ID NO.T to SEQ ID NO:4, SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326, and more preferably those that comprise at least a first sequence region that is at least 80% identical to at least one of the amino acid sequences dislosed in any one of SEQ ID NOT to SEQ ID NO:4, SEQ ID NO:13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID
  • preferred peptide variants ofthe present invention are those peptides that comprise at least a first sequence region that is at least 85% identical to at least one ofthe amino acid sequences dislosed in any one of SEQ ID NO.T to SEQ ID NO:4, SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326, and more preferably those that comprise at least a first sequence region that is at least 90% identical to at least one of the amino acid sequences dislosed in any one of SEQ ID NOT to SEQ ID NO:4, SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:
  • Particularly preferred peptide variants of the present invention are those peptides that comprise at least a first sequence region that is at least 91%, 92%, 93%), 94%, or 95% identical to at least one ofthe amino acid sequences dislosed in any one of SEQ ID NOT to SEQ ID NO:4, SEQ ID NO:13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO:316 to SEQ ID NO:318, and SEQ ID NO:321 to SEQ ID NO:326, with those peptides that comprise at least a first sequence region that is at least 96%, 97%, 98%, or 99% identical to at least one ofthe amino acid sequences dislosed in any one of SEQ ID NOT to SEQ ID NO:4, SEQ ID NO: 13 to SEQ ID NO:20, SEQ ID NO:28 to SEQ ID NO:311, SEQ ID NO:313, SEQ ID NO:314, SEQ ID NO
  • Such peptide variants mav tvoicallv be nrenared hv modifying one of the nentidr:-
  • a relatively small number of conservative or neutral substitutions may be made within the sequence of the nonameric peptide epitopes disclosed herein, without substantially altering the biological activity of the peptide.
  • the substitution of one or more amino acids in a particular peptide may in fact serve to enhance or otherwise improve the ability of the peptide to elicit an immune or T-cell response in an animal that has been provided with a composition that comprises the modified peptide, or a polynucleotide that encodes the peptide.
  • Suitable substitutions may generally be identified by using computer programs, as described hereinbelow, and the effect of such substitutions may be confirmed based on the reactivity of the modified peptide with antisera and/or T-cells as described herein.
  • a WTl peptide for use in the disclosed diagnostic and therapeutic methods may comprise a primary amino acid sequence in which one or more amino acid residues are substituted by one or more replacement amino acids, such that the ability of the modified peptide to react with antigen-specific antisera and/or T- cell lines or clones is not significantly less than that for the unmodified peptide.
  • Exemplary such substitutions may preferably be located within one or more MHC binding sites on the peptide.
  • preferred peptide variants are those that contain one or more 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 peptide 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 ofthe 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 acid substitutions that represent a conservative change include: (1) replacement of one or more Ala, Pro, Gly, Glu, Asp, Gin, Asn, Ser, or Thr; residues with one or more residues from the same group; (2) replacement of one or more Cys, Ser, Tyr, or Thr residues with one or more residues from the same group; (3) replacement of one or more Val, He, Leu, Met, Ala, or Phe residues with one or more residues from the same group; (4) replacement of one or more Lys, Arg, or His residues with one or more residues from the same group; and (5) replacement of one or more Phe, Tyr, Trp, or His residues with one or more residues from the same group.
  • a variant may also, or alternatively, contain nonconservative changes, for example, by substituting one of the amino acid residues from group (1) with an amino acid residue from group (2), group (3), group (4), or group (5).
  • 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 ofthe peptide.
  • BIOLOGICAL FUNCTIONAL EQUIVALENTS Modification and changes may be made in the structure of the polynucleotides and peptides o the present invention and still obtain a functional molecule that encodes a peptide with desirable characteristics, or still obtain a genetic construct with the desirable expression specificity and/or properties.
  • various means of introducing mutations into a polynucleotide or peptide sequence known to those of skill in the art may be employed for the preparation of heterologous sequences that may be introduced into the selected cell or animal species.
  • the resulting encoded peptide sequence is altered by this mutation, or in other cases, the sequence ofthe peptide is unchanged by one or more mutations in the encoding polynucleotide.
  • one or more changes are introduced into the promoter and/or enhancer regions of the polynucleotide constructs to alter the activity, or specificity of the expression elements and thus alter the expression of the heterologous therapeutic nucleic acid segment operably positioned under the control ofthe elements.
  • the amino acid changes may be achieved by changing one or more ofthe codons ofthe encoding DNA sequence, according to Table 1.
  • amino acids may be substituted for other amino acids in a protein structure without appreciable loss of interactive binding capacity with structures such as, for example, antigen-binding regions of antibodies or binding sites on substrate molecules. Since it is the interactive capacity and nature of a protein that defines that protein's biological functional activity, certain amino acid sequence substitutions can be made in a protein sequence, and, of course, its underlying DNA coding sequence, and nevertheless obtain a protein with like properties. It is thus contemplated by the inventors that various changes may be made in the peptide sequences of the disclosed compositions, or corresponding DNA sequences which encode said peptides without appreciable loss of their biological utility or activity.
  • the hydropathic index of amino acids may be considered.
  • the importance of the hydropathic amino acid index in conferring interactive biologic function on a protein is generally understood in the art (Kyte and Doolittle, 1982, incorporate herein by reference). It is accepted that the relative hydropathic character ofthe amino acid contributes to the secondary structure of the resultant protein, which in turn defines the interaction of the protein with other molecules, for example, enzymes, substrates, receptors, DNA, antibodies, antigens, and the like.
  • Each amino acid has been assigned a hydropathic index on the basis of their hydrophobicity and charge characteristics (Kyte and Doolittle, 1982), these are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine(+2.5); methionine (+1.9); alanine (+1.8); glycine (-0.4); threonine (-0.7); serine (-0.8); tryptophan (-0.9); tyrosine (-1.3); proline (-1.6); histidine (-3.2); glutamate (-3.5); glutamine (-3.5); aspartate (-3.5); asparagine (-3.5); lysine (-3.9); and arginine (-4.5).
  • hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0 + 1); glutamate (+3.0 ⁇ 1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (-0.4); proline (-0.5 + 1); alanine (-0.5); histidine (-0.5); cysteine (-1.0); methionine (-1.3); valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (-2.3); phenylalanine (-2.5); tryptophan (-3.4).
  • an amino acid can be substituted for another having a similar hydrophilicity value and still obtain a biologically equivalent, and in particular, an immunologically equivalent protein.
  • substitution of amino acids whose hydrophilicity values are within ⁇ 2 is preferred, those that are within ⁇ 1 are particularly preferred, and those within +0.5 are even more particularly preferred.
  • amino acid substitutions are generally therefore based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like.
  • Exemplary substitutions which take several of the foregoing characteristics into consideration are well known to those of skill in the art and include: arginine and lysine; glutamate and aspartate; serine and threonine; glutamine and asparagine; and valine, leucine and isoleucine.
  • the peptides and peptide variants of the present invention may be conjugated to a signal (or leader) sequence at the N-terminal end of the peptide, which co-translationally or post-translationally directs transfer ofthe peptide.
  • the peptides may also, or alternatively, be conjugated to one or more linker sequences for ease of synthesis, purification or identification of the peptide (e.g., poly-His), or to enhance binding of the peptide to a solid support.
  • the peptides may be conjugated to an immunoglobulin Fc region.
  • the peptides and peptide variants of the present invention may be isolated and purified from native sources, such as for example, by isolating all or part of the primary amino acid sequence from a native WTl peptide, or alternatively, may be chemically synthesized in whole or in part using any of a variety of well-known peptide synthesis techniques.
  • peptides having less than about 100 amino acids, preferably less than about 90 or 80 amino acids, and more preferably less than about 70, less than about 60, or less than about 50, about 40, about 30, or about 20 amino acids 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 (Merrifield, 1963).
  • Equipment for automated synthesis of peptides is commercially available from suppliers such as Applied BioSystems, Inc. (Foster City, CA), and may be operated according to the manufacturer's instructions.
  • the peptides and peptide variants as described herein may also be readily prepared from recombinant WTl peptides, or may be prepared by translation of a polynucleotide sequence that encodes such a peptide.
  • any of a variety of expression vectors known to those of ordinary skill in the art may be employed to express recombinant peptides. Expression may be achieved in any appropriate host cell that has been transformed or transfected with an expression vector containing a nucleic acid molecule that encodes the peptide. 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.
  • peptides and polynucleotides as described herein are isolated.
  • An "isolated" peptide or polynucleotide is one that is removed from its original environment.
  • a naturally occurring peptide or polypeptide is isolated if it is separated from some or all ofthe coexisting materials in the natural system.
  • such peptides are at least about 80% or 85% pure, more preferably at least about 90% or 95% pure and most preferably at least about 96%, 97%, 98%, or 99% pure.
  • a polynucleotide is considered to be isolated if, for example, it is cloned into a vector that is not a part ofthe natural environment.
  • the present invention provides mimetics of WTl peptides.
  • 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 peptide 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 peptide 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 peptide.
  • 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 peptide 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 peptide.
  • 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 ofthe 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 art.
  • 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., 1985; Murphy et al.,- 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 10, about 20, about 30, about 40, or about 50 or so 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.
  • immunogenic proteins include tetanus, tuberculosis and hepatitis proteins (see, for example, Stoute et al, 1997).
  • the immunological fusion partner is derived from a Mycobacterium sp., such as a Mycobacterium tuberculosis-de ⁇ vQ ⁇ Ral2 fragment.
  • a Mycobacterium sp. such as a Mycobacterium tuberculosis-de ⁇ vQ ⁇ 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 kDa 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 (see for example, U. S. Patent Application 60/158,585; and Skeiky et al., 1999, each incorporated herein by reference).
  • C-terminal fragments ofthe MTB32A coding sequence express at high levels and remain as soluble polypeptides throughout the purification process.
  • Ral2 may enhance the immunogenicity of heterologous immunogenic polypeptides with which it is fused.
  • Ral2 fusion polypeptide comprises a 14-kDa 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 (Intl. Pat. Appl. Publ. No. 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).
  • LYTA is an autolysin that specifically degrades certain bonds in the peptidoglycan backbone.
  • the C-terminal domain ofthe 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.
  • 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.
  • 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 ofthe 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.
  • 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 peptide is not diminished, relative to a native WTl protein. The effect on the immunogenicity of the encoded peptide may generally be assessed as described herein.
  • Preferred peptide variants contain amino acid substitutions, deletions, insertions and/or additions at no more than about 20%), more preferably at no more than about 15%, and more preferably still, at no more than about 10% or 5% or less of the amino acid positions relative to the corresponding native unmodified WTl sequence.
  • polynucleotides encoding such peptide variants should preferably contain nucleotide substitutions, deletions, insertions and/or additions at no more than about 20%,- more preferably at no more than about 15%, and more preferably still, at no more than about 10%) or 5% or less of the nucleotide positions relative to the corresponding polynucleotide sequence that encodes the native unmodified WTl peptide sequence.
  • Certain polynucleotide variants may be substantially homologous to, or substantially identical to the corresponding region of the nucleotide sequence encoding an unmodified peptide.
  • Such polynucleotide variants are capable of hybridizing to a naturally occurring DNA sequence encoding a WTl peptide (or a complementary sequence) under moderately stringent, to highly stringent, to very highly stringent conditions.
  • Suitable moderately stringent conditions include prewashing in a solution containing about 5X SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at a temperature of from about 50°C to about 60°C in 5X SSC overnight; followed by washing twice at about 60 to 65°C for 20 min. with each of 2X, 0.5X and 0.2X SSC containing 0.1% SDS).
  • Suitable highly stringent conditions include prewashing in a solution containing about 5X SSC, 0.5% > SDS, 1.0 mM EDTA (pH 8.0); hybridizing at a temperature of from about 60°C to about 70°C in 5X SSC overnight; followed by washing twice at about 65 to 70°C for 20 min. with each of 2X, 0.5X and 0.2X SSC containing 0.1 % SDS).
  • Representative examples of very highly stringent hybridization conditions may include, for example, prewashing in a solution containing about 5X SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at a temperature of from about 70°C to about 75°C in 5X SSC overnight; followed by washing twice at about 70°C to about 75°C for 20 min. with each of 2X, 0.5X and 0.2X 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 poiymerase chain reaction (PCRTM). For this approach, sequence- specific primers may be designed based on the sequence of the immunogenic portion and may be purchased or synthesized.
  • PCRTM poiymerase chain reaction
  • suitable primers for PCRTM amplification of a human WTl gene include: first step - P118: 1434-1414: 5'-GAGAGTCAGACTTGAAAGCAGT-3' (SEQ ID NO:5) and P135: 5'-CTGAGCCTCAGCAAATGGGC-3' (SEQ ID NO:6); second step - P136: 5'-GAGCATGCATGGGCTCCGACGTGCGGG-3' (SEQ ID NO:7) and P137: 5'-GGGGTACCCACTGAACGGTCCCCGA-3' (SEQ ID NO:8).
  • Primers for PCRTM ampli- fication of a mouse WTl gene include: first step - P138: 5'-TCCGAGCCGCACCTCATG-3' (SEQ ID NO:9) and P139: 5'-GCCTGGGATGCTGGACTG-3' (SEQ ID NO: 10), second step - P140: 5 * -GAGCATGCGATGGGTTCCGACGTGCGG-3' (SEQ ID NO: 11) and P141 : 5'-GGGGTACCTCAAAGCGCCACGTGGAGTTT-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 well-known techniques.
  • 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 (Adelman et al, 1983). Alternatively, RNA molecules may be generated by in vitro or in vivo transcription of DNA sequences encoding a WTl peptide, provided that the DNA is incorporated into a vector with a suitable RNA poiymerase promoter (such as T7 or SP6). Certain portions may be used to prepare an encoded peptide, as described herein.
  • RNA poiymerase promoter such as T7 or SP6
  • a portion may be administered to a patient such that the encoded peptide is generated in vivo (e.g., by fransfecting antigen-presenting cells such as dendritic cells with a cDNA construct encoding a WTl peptide, and administering the transfected cells to the patient).
  • the encoded peptide is generated in vivo (e.g., by fransfecting antigen-presenting cells such as dendritic cells with a cDNA construct encoding a WTl peptide, and administering the transfected cells to the patient).
  • Polynucleotides that encode a WTl peptide may generally be used for production of the peptide, in vitro or in vivo.
  • WTl polynucleotides that are complementary to a coding sequence i.e., antisense polynucleotides
  • 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'- -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 polynucleo- tide 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 poxvirus (e.g., avian poxvirus). 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 Hposomes.
  • 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.
  • RNA or DNA and/or substituted polynucleotide compositions disclosed herein will be used to transfect an appropriate host cell.
  • Technology for introduction of RNAs and DNAs, and vectors comprising them into suitable host cells is well known to those of skill in the art.
  • polynucleotides may be used to genetically transform one or more host cells, when therapeutic administration of one or more active peptides, compounds or vaccines is achieved through the expression of one or more polynucleotide constructs that encode one or more therapeutic compounds of interest.
  • polynucleotides and/or polypeptides are known to those of skill in the art.
  • polynucleotides are contemplated for delivery to cells
  • non- viral methods for the transfer of expression constructs into cultured mammalian cells are available to the skilled artisan for his use.
  • a bacterial cell, a yeast cell, or an animal cell transformed with one or more of the disclosed expression vectors represent an important aspect of the present invention.
  • Such transformed host cells are often desirable for use in the expression of the various DNA gene constructs disclosed herein.
  • Such methods are routine to those of skill in the molecular genetic arts.
  • various manipulations may be employed for enhancing the expression ofthe messenger RNA, particularly by using an active promoter, and in particular, a tissue-specific promoter such as those disclosed herein, as well as by employing sequences, which enhance the stability of the messenger RNA in the particular transformed host cell.
  • the initiation and translational termination region will involve stop codon(s), a terminator region, and optionally, a polyadenylation signal.
  • the construct will involve the transcriptional regulatory region, if any, and the promoter, where the regulatory region may be either 5' or 3' of the promoter, the ribosomal binding site, the initiation codon, the structural gene having an open reading frame in phase with the initiation codon, the stop codon(s), the polyadenylation signal sequence, if any, and the terminator region.
  • This sequence as a double strand may be used by itself for transformation of a microorganism or eukaryotic host, but will usually be included with a DNA sequence involving a marker, where the second DNA sequence may be joined to the expression construct during introduction of the DNA into the host.
  • the construct will also preferably include a sequence of at least about 30 or about 40 or about 50 basepairs (bp) or so, preferably at least about 60, about 70, about 80, or about 90 to about 100 or so bp, and usually not more than about 500 to about 1000 or so bp of a sequence homologous with a sequence in the host.
  • the regulatory regions of the expression construct will be in close proximity to (and also operably positioned relative to) the selected therapeutic gene providing for complementation as well as the gene providing for the competitive advantage.
  • the selected therapeutic gene can be introduced between the transcriptional and translational initiation region and the transcriptional and translational termination region, so as to be under the regulatory control ofthe initiation region.
  • This construct may be included in a plasmid, which will include at least one replication system, but may include more than one, where one replication system is employed for cloning during the development of the plasmid and the second replication system is necessary for functioning in the ultimate host, in this case, a mammalian host cell.
  • one or more markers may be present, which have been described previously.
  • the plasmid will desirably include a sequence homologous with the host genome.
  • Genes or other nucleic acid segments, as disclosed herein, can be inserted into host cells using a variety of techniques that are well known in the art. Five general methods for delivering a nucleic segment into cells have been described: (1) chemical methods (Graham and VanDerEb, 1973); (2) physical methods such as microinjection (Capecchi, 1980), electroporation (U. S. Patent 5,472,869; Wong and Neumann, 1982; Fromm et al, 1985), microprojectile bombardment (U. S.
  • Patent 5,874,265 specifically incorporated herein by reference in its entirety
  • "gene gun” Yang et al, 1990
  • viral vectors Eglitis and Anderson, 1988
  • receptor-mediated mechanisms Curiel et al, 1991 ; Wagner et al, 1992
  • bacterial-mediated transformation (5) bacterial-mediated transformation.
  • the present invention further provides antibodies and antigen-binding fragments thereof, that specifically bind to (or are immunospecific for) at least a first peptide or peptide variant as disclosed herein.
  • an antibody or an antigen-binding fragment is said to "specifically bind" to a peptide if it reacts at a detectable level (within, for example, an ELISA) with the peptide, and does not react detectably with unrelated peptides or 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 formation 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" 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.
  • Such antibodies may be prepared by any of a variety of techniques known to those of ordinary skill in the art (Harlow and Lane, 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 peptide is initially injected into any of a wide variety of mammals (e.g., mice, rats, rabbits, sheep or goats).
  • the peptides of this invention may serve as the immunogen without modification.
  • a superior immune response may be elicited if the peptide 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 peptide may then be purified from such antisera by, for example, affinity chromatography using the peptide coupled to a suitable solid support.
  • Monoclonal antibodies specific for the antigenic peptide of interest may be prepared, for example, using the technique of Kohler and Milstein (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 peptide 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.
  • 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 supernatants tested for binding activity against the peptide. Hybridomas having high reactivity and specificity are preferred.
  • Monoclonal antibodies may be isolated from the supernatants 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 peptides of this invention may be used in the purification process in, for example, an affinity chromatography step.
  • 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, 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, I2 T, I3 T, 186 Re, 188 Re, 211 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 that is cleavable during or upon intemalization 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 (U. S. Patent No. 4,489,710), by irradiation of a photolabile bond (U. S. Patent No. 4,625,014), by hydrolysis of derivatized amino acid side chains (U. S. Patent No. 4,638,045), by serum complement-mediated hydrolysis (U. S. Patent No. 4,671,958), and acid-catalyzed hydrolysis (U. S. Patent No. 4,569,789).
  • 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 that 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 (U. S. Patent No. 4,507,234), peptides and polysaccharides such as aminodextran (U. S. Patent No.
  • a carrier may also bear an agent by noncovalent bonding or by encapsulation, such as within a liposome vesicle (U. S. Patent No. 4,429,008 and U. S. Patent No. 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. For example,
  • 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/ immuno- conjugate 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 an antigen-binding fragment thereof, that specifically binds to an immunogenic portion of WTl, using well- known techniques.
  • 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. Irrespective of the source of the original WTl peptide-specific antibody, the intact antibody, antibody multimers, or any one of a variety of functional, antigen-binding regions of the antibody may be used in the present invention.
  • Exemplary functional regions include scFv, Fv, Fab', Fab and F(ab') 2 fragments of the WTl peptide-specific antibodies. Techniques for preparing such constructs are well known to those in the art and are further exemplified herein.
  • the choice of antibody construct may be influenced by various factors. For example, prolonged half-life can result from the active readsorption of intact antibodies within the kidney, a property of the Fc piece of immunoglobulin. IgG based antibodies, therefore, are expected to exhibit slower blood clearance than their Fab' counterparts. However, Fab' fragment-based compositions will generally exhibit better tissue penetrating capability.
  • Antibody fragments can be obtained by proteolysis of the whole immunoglobulin by the non-specific thiol protease, papain. Papain digestion yields two identical antigen-binding fragments, termed "Fab fragments," each with a single antigen-binding site, and a residual "Fc fragment.” Papain should first be activated by reducing the sulphydryl group in the active site with cysteine, 2-mercaptoethanol or dithiothreitol. Heavy metals in the stock enzyme should be removed by chelation with EDTA (2 mM) to ensure maximum enzyme activity. Enzyme and substrate are normally mixed together in the ratio of 1 :100 by weight.
  • the reaction can be stopped by irreversible alkylation of the thiol group with iodoacetamide or simply by dialysis.
  • the completeness of the digestion should be monitored by SDS-PAGE and the various fractions separated by Protein A-Sepharose or ion exchange chromatography.
  • Pepsin treatment of intact antibodies yields an F(ab'), fragment that has two antigen- combining sites and is still capable of cross-linking antigen.
  • Digestion of rat IgG by pepsin requires conditions including dialysis in 0.1 M acetate buffer, pH 4.5, and then incubation for four hrs with 1% wt./wt. pepsin; IgG [ and IgG 2a digestion is improved if first dialyzed against 0.1 M formate buffer, pH 2.8, at 4°C, for 16 hrs followed by acetate buffer.
  • IgG 2b gives more consistent results with incubation in staphylococcalV8 protease (3% wt./wt.) in OT M sodium phosphate buffer, pH 7.8, for four hrs at 37°C.
  • a Fab fragment also contains the constant domain of the light chain and the first constant domain (CHI) of the heavy chain.
  • Fab' fragments differ from Fab fragments by the addition of a few residues at the carboxyl terminus of the heavy chain CHI domain including one or more cysteine(s) from the antibody hinge region.
  • F(ab') 2 antibody fragments were originally produced as pairs of Fab' fragments that have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
  • variable means that certain portions of the variable domains differ extensively in sequence among antibodies, and are used in the binding and specificity of each particular antibody to its particular antigen. However, the variability is not evenly distributed throughout the variable domains of antibodies. It is concentrated in three segments termed “hypervariable regions,” both in the light chain and the heavy chain variable domains. The more highly conserved portions of variable domains are called the framework region (FR).
  • the variable domains of native heavy and light chains each comprise four FRs (FR1 , FR2, FR3 and FR4, respectively), largely adopting a ⁇ -sheet configuration, connected by three hypervariable regions, which form loops connecting, and in some cases, forming part of, the ⁇ -sheet structure.
  • the hypervariable regions in each chain are held together in close proximity by the FRs and, with the hypervariable regions from the other chain, contribute to the formation of the antigen-binding site of antibodies (Kabat et al, 1991, specifically incorporated herein by reference).
  • the constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation ofthe antibody in antibody- dependent cellular toxicity.
  • hypervariable region refers to the amino acid residues of an antibody that are responsible for antigen-binding.
  • the hypervariable region comprises amino acid residues from a “complementarity determining region” or "CDR" (i.e.
  • "Framework" or "FR" residues are those variable domain residues other than the hypervariable region residues as herein defined.
  • an "Fv” fragment is the minimum antibody fragment that contains a complete antigen- recognition and binding site. This region consists of a dimer of one heavy chain and one light chain variable domain in tight, con-covalent association. It is in this configuration that three hypervariable regions of each variable domain interact to define an antigen-binding site on the surface of the V H -V L dimer. Collectively, six hypervariable regions confer antigen-binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three hypervariable regions specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site.
  • Single-chain Fv or “sFv” antibody fragments comprise the V H and V L domains of antibody, wherein these domains are present in a single polypeptide chain.
  • the Fv polypeptide further comprises a polypeptide linker between the V H and V L domains that enables the sFv to form the desired structure for antigen binding.
  • Diabodies are small antibody fragments with two antigen-binding sites, which fragments comprise a heavy chain variable domain (Vy) connected to a light chain variable domain (V L ) in the same polypeptide chain (V H - V L ). By using a linker that is too short to allow pairing between the two domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create two antigen-binding sites.
  • Diabodies are described in European Pat. Appl. No. EP 404,097 and Intl. Pat. Appl. Publ. No. WO 93/11161, each specifically incorporated herein by reference.
  • Linear antibodies which can be bispecific or monospecific, comprise a pair of tandem Fd segments (V H -C H 1-V H -C H 1) that form a pair of antigen binding regions, as described in Zapata et al. (1995), specifically incorporated herein by reference.
  • variants are antibodies with improved biological properties relative to the parent antibody from which they are generated.
  • Such variants, or second-generation compounds are typically substitutional variants involving one or more substituted hypervariable region residues of a parent antibody " .
  • a convenient way for generating such substitutional variants is affinity maturation using phage display.
  • hypervariable region sites e.g., 6 to 7 sites
  • the antibody variants thus generated are displayed in a monovalent fashion from filamentous phage particles as fusions to the gene III product of Ml 3 packaged within each particle.
  • the phage-displayed variants are then screened for their biological activity (e.g., binding affinity) as herein disclosed.
  • alanine-scanning mutagenesis can be performed on hypervariable region residues identified as contributing significantly to antigen binding.
  • the crystal structure of the antigen-antibody complex be delineated and analyzed to identify contact points between the antibody and target. Such contact residues and neighboring residues are candidates for substitution.
  • the panel of variants is subjected to screening, and antibodies with analogues but different or even superior properties in one or more relevant assays are selected for further development.
  • Fab' or antigen binding fragment of an antibody In using a Fab' or antigen binding fragment of an antibody, with the attendant benefits on tissue penetration, one may derive additional advantages from modifying the fragment to increase its half-life.
  • a variety of techniques may be employed, such as manipulation or modification of the antibody molecule itself, and also conjugation to inert carriers. Any conjugation for the sole purpose of increasing half-life, rather than to deliver an agent to a target, should be approached carefully in that Fab' and other fragments are chosen to penetrate tissues. Nonetheless, conjugation to non-protein polymers, such PEG and the like, is contemplated. Modifications other than conjugation are therefore based upon modifying the structure ofthe antibody fragment to render it more stable, and/or to reduce the rate of catabolism in the body.
  • Moderate conjugation-type modifications for use with the present invention include incorporating a salvage receptor binding epitope into the antibody fragment. Techniques for achieving this include mutation of the appropriate region of the antibody fragment or incorporating the epitope as a peptide tag that is attached to the antibody fragment. Intl. Pat. Appl. Publ. No. WO 96/32478 is specifically incorporated herein by reference for the purposes of further exemplifying such technology. Salvage receptor binding epitopes are typically regions of three or more amino acids from one or two lops ofthe Fc domain that are transferred to the analogous position on the antibody fragment. The salvage receptor-binding epitopes disclosed in Intl. Pat. Appl. Publ. No. WO 98/45331 are incorporated herein by reference for use with the present invention.
  • 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 IsolexTM System, available from Nexell Therapeutics, Inc. (Irvine, CA; see also U. S. Patent No. 5,240,856; U. S. Patent No. 5,215,926; Intl. Pat. Appl. Publ. No. WO 89/06280; Intl. Pat. Appl. Publ. No.
  • T cells may be derived from related or unrelated humans, non-human mammals, cell lines or cultures.
  • T cells may be stimulated with WTl peptide, polynucleotide encoding a WTl peptide and/or an antigen-presenting cell (APC) that expresses a WTl peptide.
  • WTl peptide 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 peptide.
  • WTl peptide e.g., 5 to 25 ⁇ g/ml
  • T cells are considered to be specific for a WTl peptide if the T cells kill target cells coated with a WTl peptide or expressing a gene encoding such a peptide.
  • T cell specificity may be evaluated using any of a variety of standard techniques. For example, within a cliromium 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. (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 2+ 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 peptide may be quantified.
  • WTl peptide 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 peptide, 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 ofthe generation of cytolytic activity.
  • CD4 + or CD8 + T cells that proliferate in response to the WTl peptide, 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 peptide, with or without the addition of T cell growth factors, such as interleukin-2, and/or stimulator cells that synthesize a WTl peptide.
  • T cell growth factors such as interleukin-2, and/or stimulator cells that synthesize a WTl peptide.
  • 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 peptide.
  • lymphocytes e.g., greater than 4 x 10 7
  • WTl peptide 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 10 7 irradiated peripheral blood mononuclear cells.
  • WTl peptide (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 peptide 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 rosetting and established in culture by stimulating with the nominal antigen in the presence of irradiated autologous filler cells.
  • WTl peptide 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 that produces WTl peptide 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 6 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.
  • Cloned and/or expanded cells may be administered back to the patient as described, for example, by Chang et al, (1996).
  • allogeneic T-cells may be primed (i.e., sensitized to
  • T cells are considered to be primed if, for example, contact with a WTl peptide 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 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.
  • peptides, polynucleotides, antibodies and/or T cells may be incorporated into pharmaceutical compositions or immunogenic compositions (i.e., 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 peptide.
  • Pharmaceutical compositions comprise one or more such compounds or cells and a physiologically acceptable carrier or excipient.
  • Vaccines may comprise one or more such compounds or cells and an immunostimulant, such as an adjuvant or a liposome (into which the compound is incorporated).
  • An immunostimu- lant may be any substance that enhances or potentiates an immune response (antibody- and/or cell-mediated) to an exogenous antigen.
  • immunostimulants include adjuvants, biodegradable microspheres (e.g., polylactic galactide) and Hposomes (into which the compound is incorporated) (U. S. Patent No. 4,235,877).
  • Vaccine preparation is generally described in, for example, Powell and Newman (1995).
  • Pharmaceutical compositions and vaccines within the scope of the present invention may also contain other compounds, which may be biologically active or inactive. For example, one or more immunogenic portions of other tumor antigens may be present, either incorporated into a fusion peptide or as a separate compound, within the composition or vaccine.
  • compositions and vaccines are designed to elicit T cell responses specific for a WTl peptide in a patient, such as a human.
  • T cell responses may be favored through the use of relatively short peptides (e.g., comprising less than 23 consecutive amino acid residues of a native WTl peptide, preferably 4-16 consecutive residues, more preferably 8-16 consecutive residues and still more preferably 8- 10 consecutive residues).
  • a vaccine may comprise an immunostimulant that preferentially enhances a T cell response.
  • the immunostimulant may enhance the level of a T cell response to a WTl peptide by an amount that is proportionally greater than the amount by which an antibody response is enhanced.
  • an immunostimulant 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 -negative control cell lines, while not detectably enhancing an antibody response.
  • the amount by which a T cell or antibody response to a WTl peptide is enhanced may generally be determined using any representative technique known in the art, such as the techniques provided herein.
  • a pharmaceutical composition or vaccine may contain DNA encoding one or more of the peptides as described above, such that the peptide is generated in situ.
  • the DNA may be present within any of a variety of delivery systems known to those of ordinary skill in the art, including nucleic acid expression systems, bacterial and viral expression systems and mammalian expression systems. Numerous gene delivery techniques are well known in the art (Rolland, 1998, and references cited therein). 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 peptide on its cell surface or secretes such an epitope.
  • 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 (Fisher-Hoch et al, 1989; Flexner et al, 1989; Flexner et al, 1990; U. S. Patent No. 4,603,112, U. S. Patent No. 4,769,330, U. S. Patent No.
  • the DNA may also be "naked,” as described, for example, in Ulmer et al. (1993) and reviewed by Cohen (1993).
  • the uptake of naked DNA may be increased by coating the DNA onto biodegradable beads, which are efficiently transported into the cells.
  • a vaccine may comprise both a polynucleotide and a peptide component. Such vaccines may provide for an enhanced immune response.
  • a pharmaceutical composition or vaccine may comprise an antigen- presenting cell that expresses a WTl peptide.
  • the antigen-presenting cell is preferably an autologous dendritic cell.
  • Such cells may be prepared and transfected using standard techniques (Reeves et al, 1996; Tuting et al, 1998; and Nair et al, 1998). Expression of a WTl peptide 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.
  • a vaccine may contain pharmaceutically acceptable salts of the polynucleotides and peptides provided herein.
  • Such salts may be prepared from pharmaceutically acceptable non-toxic bases, including organic bases (e.g., salts of primary, secondary and tertiary amines and basic amino acids) and inorganic bases (e.g., sodium, potassium, lithium, ammonium, calcium and magnesium salts).
  • organic bases e.g., salts of primary, secondary and tertiary amines and basic amino acids
  • inorganic bases e.g., sodium, potassium, lithium, ammonium, calcium and magnesium salts.
  • pharmaceutically or pharmacologically acceptable refer to molecular entities and compositions that do not produce an adverse, allergic or other significant untoward reaction when administered to an animal, or a human, as appropriate.
  • pharmaceutically acceptable carrier includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like.
  • the use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated.
  • preparations should meet sterility, pyrogenicity, and general safety and purity standards as required by the Food and Drug Administration Office of Biologies standards. Supplementary active ingredients can also be incorporated into the compositions.
  • 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 may also be employed as carriers for the pharmaceutical compositions of this invention.
  • Suitable biodegradable microspheres are disclosed, for example, in U. S. Patent Nos. 4,897,268; 5,075,109; 5,928,647; 5,811,128; 5,820,883; 5,853,763; 5,814,344 and 5,942,252.
  • 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, peptides or amino acids such as glycine, antioxidants, bacteriostats, chelating agents such as EDTA or glutathione, adjuvants (e.g., aluminum hydroxide), solutes that render the formulation isotonic, hypotonic or weakly hypertonic with the blood of a recipient, suspending agents, thickening agents and/or preservatives.
  • buffers e.g., neutral buffered saline or phosphate buffered saline
  • carbohydrates e.g., glucose, mannose, sucrose or dextrans
  • mannitol e.g., proteins, peptides or amino acids such as glycine, antioxidants, bacteriostats, chelating agents such as EDTA
  • compositions of the present invention may be formulated as a lyophilizate, or formulated with one or more hposomes, microspheres, nanoparticles, or micronized delivery systems using well-known technology.
  • immuno stimulants such as adjuvants
  • 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 adjuvants are commercially available as, for example, alum-based adjuvants (e.g., Alhydrogel, Rehydragel, aluminum phosphate, Algammulin, aluminum hydroxide); oil based adjuvants (Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, MI), Specol, RIBI, TiterMax, Montanide ISA50 or Seppic MONTANIDE ISA 720); nonionic block copolymer-based adjuvants, cytokines (e.g., GM-CSF or Flat3 -ligand); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, NJ); AS-2 (SmithKline Beecham, Philadelphia, PA); salts of calcium, iron or zinc; an insoluble suspension of acylated tyrosine; acylated sugars; cationically or anionically derivatized polysaccharides; polyphosphazenes; biodegradable microspheres
  • Cytokines such as GM-CSF or interleukin-2, -7, or - 12, may also be used as adjuvants. Hemocyanins and hemoerythrins may also be used in the invention. The use of hemocyanin from keyhole limpet (KLH) is particularly preferred, although other molluscan and arthropod hemocyanins and hemoerythrins may be employed.
  • KLH keyhole limpet
  • polysaccharide adjuvants may also be used. Polyamine varieties of polysaccharides are particularly preferred, such as chitin and chitosan, including deacetylated chitin.
  • a further preferred group of adjuvants are the muramyl dipeptide (MDP,
  • N-acetylmuramyl- -alanyl-D-isoglutamine group of bacterial peptidoglycans.
  • Derivatives of muramyl dipeptide such as the amino acid derivative threonyl-MDP, and the fatty acid derivative MTPPE, are also contemplated.
  • U. S. Patent No. 4,950,645 describes a lipophilic disaccharide-tripeptide derivative of muramyl dipeptide that is proposed for use in artificial Hposomes formed from phosphatidyl choline and phosphatidyl glycerol. It is said to be effective in activating human monocytes and destroying tumor cells, but is non-toxic in generally high doses.
  • the compounds of U. S. Patent No. 4,950,645, and Intl. Pat. Appl. Publ. No. WO 91/16347 are also proposed for use in achieving particular aspects ofthe present invention.
  • BCG and BCG-cell wall skeleton (CWS) may also be used as adjuvants in the invention, with or without trehalose dimycolate.
  • Trehalose dimycolate may be used itself. Azuma et al. (1988) show that trehalose dimycolate administration correlates with augmented resistance to influenza virus infection in mice. Trehalose dimycolate may be prepared as described in U. S. Patent No. 4,579,945. Amphipathic and surface-active agents, e.g., saponin and derivatives such as QS21
  • Nonionic block copolymer surfactants Roshanovich et al, 1994; Hunter et al, 1991
  • Oligonucleotides as described by Yamamoto et al. (1988) are another useful group of adjuvants.
  • Quil A and lentinen are also preferred adjuvants.
  • Superantigens are also contemplated for use as adjuvants in the present invention.
  • Superantigens are generally bacterial products that stimulate a greater proportion of T lymphocytes than peptide antigens without a requirement for antigen processing (Mooney et. al, 1994).
  • Superantigens include Staphylococcus exoproteins, such as the ⁇ , ⁇ , ⁇ and ⁇ enterotoxins from S. aureus and 5. epidermidis, and the ⁇ , ⁇ , ⁇ and ⁇ E. coli exotoxins.
  • Staphylococcus enterotoxins are known as staphylococcal enterotoxin A (SEA) and staphylococcal enterotoxin B (SEB), with enterotoxins through E (SEE) being described (Rott et. al, 1992).
  • Streptococcus pyogenes B (SEB) Clostridhim perfi-ingens enterotoxin (Bowness et. al, 1992), cytoplasmic membrane-associated protein (CAP) from S. pyogenes (Sato et. al, 1994) and toxic shock syndrome toxin-1 (TSST-1) from S. aureus (Schwab et. al, 1993) are further useful superantigens.
  • One group of adjuvants particularly preferred for use in the invention are the detoxified endotoxins, such as the refined detoxified endotoxin of U. S. Patent No. 4,866,034. These refined detoxified endotoxins are effective in producing adjuvant responses in mammals.
  • the detoxified endotoxins may be combined with other adjuvants.
  • Combination of detoxified endotoxins with trehalose dimycolate is contemplated, as described in U. S. Patent No. 4,435,386.
  • Combinations of detoxified endotoxins with trehalose dimycolate and endotoxic glycolipids is also contemplated (U. S. Patent No. 4,505,899), as is combination of detoxified endotoxins with cell wall skeleton (CWS) or CWS and trehalose dimycolate, as described in U. S. Patent Nos. 4,436,727, 4,436,728 and 4,505,900.
  • Combinations of just CWS and trehalose dimycolate, without detoxified endotoxins are also envisioned to be useful, as described in U. S. Patent No. 4,520,019.
  • MPL is currently one preferred immunopotentiating agent for use herein.
  • References that concern the uses of MPL include Tomai et al. (1987), Chen et al. (1991) and Garg and Subbarao (1992), that each concern certain roles of MPL in the reactions of aging mice;
  • Fitzgerald (1991) also reported on the use of MPL to up-regulate the immunogenicty of a syphilis vaccine and to confer significant protection against challenge infection in rabbits.
  • MPL is known to be safe for use, as shown in the above model systems.
  • Phase-I clinical trials have also shown MPL to be safe for use (Vosika et al, 1984). Indeed, 100 ⁇ g/m 2 is known to be safe for human use, even on an outpatient basis (Vosika et al, 1984).
  • MPL generally induces polyclonal B cell activation (Baker et al, 1994), and has been shown to augment antibody production in many systems, for example, in immunologically immature mice (Baker et al, 1988); in aging mice (Tomai and Johnson, 1989); and in nude and Xid mice (Madonna and Vogel, 1986; Myers et al, 1995).
  • Antibody production has been shown against erythrocytes (Hraba et al, 1993); T cell dependent and independent antigens; Pnu-immune vaccine (Garg and Subbarao, 1992); isolated tumor-associated antigens (U. S.
  • Patent 4,877,611 against syngeneic tumor cells (Livingston et al, 1985; Ravindranath et al, 1994a;b); and against tumor-associated gangliosides (Ravindranath et /., 1994a;b).
  • MPL Another useful attribute of MPL is that is augments IgM. responses, as shown by
  • MPL was conjugated to the hapten, TNP.
  • MPL was proposed for use as a carrier for other haptens, such as peptides.
  • MPL also activates and recruits macrophages (Verma et al, 1992). Tomai and Johnson (1989) showed that MPL-stimulated T cells enhance IL-1 secretion by macrophages. MPL is also known to activate superoxide production, lysozyme activity, phagocytosis, and killing of Candida in murine peritoneal macrophages (Chen et al, 1991).
  • MPL cytotoxic factor
  • TNF cytotoxic factor
  • Kovach et al. (1990) and Elliot et al. (1991) also show that MPL induces TNF activity.
  • MPL is known to act with TNF- ⁇ to induce release of IFN- ⁇ by NK cells.
  • IFN- ⁇ production by T cells in response to MPL was also documented by Tomai and Johnson (1989), and Odean et al. (1990).
  • MPL is also known to be a potent T cell adjuvant.
  • MPL stimulates proliferation of melanoma-antigen specific CTLs (Mitchell et al, 1988, 1993).
  • Baker et al. (1988b) showed that nontoxic MPL inactivated suppressor T cell activity.
  • the inactivation of T suppressor cells allows for increased benefit for the animal, as realized by, e.g., increased antibody production.
  • Johnson and Tomai (1988) have reported on the possible cellular and molecular mediators of the adjuvant action of MPL.
  • MPL is also known to induce aggregation of platelets and to phosphorylate a platelet protein prior to induction of serotonin secretion (Grabarek et al, 1990). This study shows that MPL is involved in protein kinase C activation and signal transduction.
  • MPL structure and function of MPL
  • Johnson et al. (1990) that describes the structural characterization of MPL homologs obtained from Salmonella minnesota Re595 lipopolysaccharide.
  • Johnson et al. (1990) found that three were particularly active, as assessed using human platelet responses.
  • the chemical components of the various MPL species were characterized by Johnson et al. (1990).
  • lipid A preparations with fatty acyl groups of relatively short chain length (C 10 to C 12 from Pseudomonas aeruginosa and Chromobacterium violaceum) or predominantly long chain length (C, 8 from Helicobacter pylori) are less prefened for use in this invention.
  • Baker et al. (1994) also showed that the lipid A proximal inner core region oligosaccharides of some bacterial lipopolysaccharides increase the expression of Ts activity; due mainly to the capacity of such oligosaccharides, which are relatively conserved in structure among gram-negative bacterial, to enlarge or expand upon the population of CD8 + Ts generated during the course of a normal antibody response to unrelated microbial antigens.
  • the minimal structure required for the expression ofthe added immunosuppression observed was reported to be a hexasaccharide containing one 2-keto-3-deoxyoctonate residue, two glucose residues, and three heptose residues to which are attached two pyrophosphorylethanolamine groups (Baker et al, 1994). This information may be considered in utilizing or even designing further adjuvants for use in the invention.
  • Tanamoto et al. (1994a;b; 1995) described the dissociation of endotoxic activities in a chemically synthesized Lipid A precursor after acetylation or succinylation.
  • compounds such as “acetyl 406" and “succinyl 516" are also contemplated for use in the invention.
  • Synthetic MPLs form a particularly prefened group of antigens.
  • Brade et al. (1993) described an artificial glycoconjugate containing the bisphosphorylated glucosamine disaccharide backbone of lipid A that binds to anti-Lipid A MAbs. This is one candidate for use in certain aspects ofthe invention.
  • the MPL derivatives described in U. S. Patent No. 4,987,237 are particularly contemplated for use in the present invention.
  • U. S. Patent No. 4,987,237 describes MPL derivatives that contain one or more free groups, such as amines, on a side chain attached to the primary hydroxyl groups of the monophosphoryl lipid A nucleus through an ester group.
  • the derivatives provide a convenient method for coupling the lipid A through coupling agents to various biologically active materials.
  • the immunostimulant properties of lipid A are maintained.
  • All MPL derivatives in accordance with U. S. Patent No. 4,987,237 are envisioned for use in the MPL adjuvant-incorporated cells of this invention.
  • adjuvants even those that are not commonly used in humans, may still be employed in animals, where, for example, one desires to raise antibodies or to subsequently obtain activated T cells.
  • the adjuvant composition is preferably designed to induce an immune response predominantly of the Thl type.
  • High levels of Thl -type cytokines e.g., IFN- ⁇ , TNF ⁇ , IL-2 and IL-12
  • high levels of Th2-type cytokines e.g., IL-4, IL-5, IL-6 and IL-10
  • a patient will support an immune response that includes Thl- and Th2-type responses.
  • Thl -type cytokines will increase to a greater extent than the level of Th2-type cytokines.
  • the levels of these cytokines may be readily assessed using standard assays. For a review of the families of cytokines see e.g., Mosmann and Coffman (1989).
  • Prefened adjuvants for use in eliciting a predominantly Thl -type response include, for example, a combination of monophosphoryl lipid A, preferably 3-de-O-acylated monophosphoryl lipid A (3D-MPL), together with an aluminum salt.
  • MPL adjuvants are available from Corixa Corporation (Seattle, WA; see e.g., U. S. Patent Nos. 4,436,727; 4,877,611; 4,866,034 and 4,912,094, each of which is specifically incorporated herein by reference in its entirety).
  • CpG-containing oligonucleotides in which the CpG dinucleotide is unmethylated also induce a predominantly Thl response.
  • Such oligonucleotides are well known and are described, for example, in Intl. Pat. Appl. Publ. No. WO 96/02555 and Intl. Pat. Appl. Publ. No. WO 99/33488.
  • Immunostimulatory DNA sequences are also described, for example, by Sato et al. (1996).
  • Another prefened adjuvant is a saponin, preferably QS21 (Aquila Biopharmaceuticals Inc., Framingham, MA), which may be used alone or in combination with other adjuvants.
  • QS21 Amla Biopharmaceuticals Inc., Framingham, MA
  • an enhanced system involves the combination of a monophosphoryl lipid A and saponin derivative, such as the combination of QS21 and 3D- MPL (see e.g., Intl. Pat. Appl. Publ. No. WO 94/00153), or a less reactogenic composition where the QS21 is quenched with cholesterol (see e.g., Intl. Pat. Appl. Publ. No.
  • prefened adjuvants include Montanide ISA 720 (Seppic), SAF (Chiron), ISCOMS (CSL), MF-59 (Chiron), the SBAS series of adjuvants (e.g., SBAS-2 or SBAS-4, available from SmithKline Beecham, Rixensart, Belgium), Detox (Corixa Corporation), RC- 529 (Corixa Corporation) and aminoalkyl glucosaminide 4-phosphates (AGPs).
  • SBAS-2 or SBAS-4 available from SmithKline Beecham, Rixensart, Belgium
  • Detox Corixa Corporation
  • RC- 529 Corixa Corporation
  • AGPs aminoalkyl glucosaminide 4-phosphates
  • Any vaccine provided herein may be prepared using well-known methods that result in a combination of one or more antigens, one or more immunostimulants or adjuvants and one or more suitable caniers, excipients, or pharmaceutically acceptable buffers.
  • the compositions described herein may be administered as part of a sustained release formulation (i.e., a formulation such as a capsule, sponge or gel [composed of polysaccharides, for example] that effects a slow release of compound following administration).
  • a sustained release formulation i.e., a formulation such as a capsule, sponge or gel [composed of polysaccharides, for example] that effects a slow release of compound following administration.
  • Such formulations may generally be prepared using well-known technology (Coombes et al, 1996) and administered by, for example, oral, rectal or subcutaneous implantation, or by implantation at the desired target site.
  • Sustained-release formulations may contain a peptide, polynucleotide or antibody dispersed in a
  • Caniers for use within such formulations are preferably biocompatible, and may also be biodegradable; preferably the formulation provides a relatively constant level of active component release.
  • Such caniers include microparticles of poly(lactide-co-glycolide), as well as polyacrylate, latex, starch, cellulose and dextran.
  • Other delayed-release caniers include supramolecular biovectors, which comprise a non-liquid hydrophilic core (e.g., a cross-linked polysaccharide or oligosaccharide) and, optionally, an external layer comprising an amphiphilic compound, such as a phospho lipid (U. S. Patent No. 5,151,254; Intl. Pat. Appl. Publ. No.
  • WO 94/20078 Intl. Pat. Appl. Publ. No. WO/94/23701; and Intl. Pat. Appl. Publ. No. WO 96/06638).
  • 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 ofthe condition to be treated or prevented.
  • Any of a variety of delivery vehicles may be employed within pharmaceutical compositions and vaccines to facilitate production of an antigen-specific immune response that targets tumor cells. Delivery vehicles include antigen-presenting cells (APCs), such as dendritic cells, macrophages, B cells, monocytes and other cells that may be engineered to be efficient APCs.
  • APCs antigen-presenting cells
  • Such cells may, but need not, be genetically modified to increase the capacity for presenting the antigen, to improve activation and/or maintenance of the T cell response, to have anti-tumor effects per se and/or to be immunologically compatible with the receiver (i.e., matched HLA haplotype).
  • APCs may generally be isolated from any of a variety of biological fluids and organs, including tumor and peritumoral tissues, and may be autologous, allogeneic, syngeneic or xenogeneic cells. Certain prefened embodiments of the present invention use dendritic cells or progenitors thereof as antigen-presenting cells.
  • Dendritic cells are highly potent APCs (Banchereau and Steinman, 1998) and have been shown to be effective as a physiological adjuvant for eliciting prophylactic or therapeutic antitumor immunity (Timmerman and Levy, 1999).
  • dendritic cells may be identified based on their typical shape (stellate in situ, with marked cytoplasmic processes (dendrites) visible in vitro), their ability to take up, process and present antigens with high efficiency and their ability to activate naive T cell responses.
  • Dendritic cells may, of course, be engineered to express specific cell-surface receptors or ligands that are not commonly found on dendritic cells in vivo or ex vivo, and such modified dendritic cells are contemplated by the present invention.
  • secreted vesicles antigen-loaded dendritic cells called exosomes
  • exosomes antigen-loaded dendritic cells
  • Dendritic cells and progenitors may be obtained from peripheral blood, bone manow, tumor-infiltrating cells, peritumoral tissues-infiltrating cells, lymph nodes, spleen, skin, umbilical cord blood or any other suitable tissue or fluid.
  • dendritic cells may be differentiated ex vivo by adding a combination of cytokines such as GM-CSF, IL-4, IL-13 and/or TNF ⁇ to cultures of monocytes harvested from peripheral blood.
  • CD34 positive cells harvested from peripheral blood, umbilical cord blood or bone manow may be differentiated into dendritic cells by adding to the culture medium combinations of GM-CSF, IL-3, TNF ⁇ , CD40 ligand, LPS, flt3 ligand and/or other compound(s) that induce differentiation, maturation and proliferation of dendritic cells.
  • Dendritic cells are conveniently categorized as “immature” and “mature” cells, which allows a simple way to discriminate between two well characterized phenotypes. However, this nomenclature should not be construed to exclude all possible intermediate stages of differentiation. Immature dendritic cells are characterized as APC with a high capacity for antigen uptake and processing, which conelates with the high expression of Fc ⁇ receptor and mannose receptor.
  • the mature phenotype is typically characterized by a lower expression of these markers, but a high expression of cell surface molecules responsible for T cell activation such as class I and class II MHC, adhesion molecules (e.g., CD54 and CD11) and costimulatory molecules (e.g., CD40, CD80, CD86 and 4-1BB).
  • cell surface molecules responsible for T cell activation such as class I and class II MHC, adhesion molecules (e.g., CD54 and CD11) and costimulatory molecules (e.g., CD40, CD80, CD86 and 4-1BB).
  • APCs may generally be transfected with a polynucleotide encoding a WTl peptide, such that the peptide, or an immunogenic portion thereof, is expressed on the cell surface. Such transfection may take place ex vivo, and a composition or vaccine comprising such transfected cells may then be used for therapeutic purposes, as described herein. Alter- natively, a gene delivery vehicle that targets a dendritic or other antigen-presenting cell may be administered to a patient, resulting in transfection that occurs in vivo. In vivo and ex vivo transfection of dendritic cells, for example, may generally be performed using any methods known in the art, such as those described in Intl. Pat. Appl. Publ. No.
  • Antigen loading of dendritic cells may be achieved by incubating dendritic cells or progenitor cells with the WTl peptide, DNA (naked or within a plasmid vector) or RNA; or with antigen-expressing recombinant bacterium or viruses (e.g., vaccinia, fowlpox, adenovirus or lentivirus vectors). Prior to loading, the peptide may be covalently conjugated to an immunological partner that provides T cell help (e.g., a canier molecule). Alternatively, a dendritic cell may be pulsed with a non-conjugated immunological partner, separately or in the presence ofthe peptide.
  • an immunological partner e.g., a canier molecule
  • Vaccines and pharmaceutical compositions may be presented in unit-dose or multi-dose containers, such as sealed ampoules or vials. Such containers are preferably hermetically sealed to preserve sterility of the formulation until use.
  • formulations may be stored as suspensions, solutions or emulsions in oily or aqueous vehicles.
  • a vaccine or pharmaceutical composition may be stored in a freeze-dried condition requiring only the addition of a sterile liquid canier immediately prior to use.
  • 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 ofthe disease generate detectably higher levels of a WTl peptide 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.
  • diseased cells e.g., tumor cells
  • 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.
  • a malignant disease that is not characterized by an increase in WTl expression may, at a
  • any malignant disease in which diseased cells formerly expressed, cunently express or are expected to subsequently express increased levels of WTl is considered to be "associated with WTl expression.”
  • the therapies provided herein are administered to a patient afflicted with, or considered at risk for, malignant mesothelioma.
  • 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 manow, peripheral blood or a fraction of bone marrow or peripheral blood). Fractions of bone manow or peripheral blood may be obtained using any standard technique in the art.
  • 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.
  • 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).
  • 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 malignant mesothelioma. Other .
  • WTl -associated conditions include leukemia (e.g., AML, CML, ALL or childhood ALL), a myelodysplastic syndrome (MDS) and 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-PCRTM, as described herein), as well as autoimmune diseases directed against WTl -expressing cells.
  • leukemia e.g., AML, CML, ALL or childhood ALL
  • MDS myelodysplastic syndrome
  • cancer e.g., gastrointestinal, lung, thyroid or breast cancer or a melanoma
  • 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
  • kidney cancer such as renal cell carcinoma, or Wilms tumor
  • Satoh et al (2000) and Campbell et al. (1998)
  • mesothelioma as described in Amin et al, (1995).
  • Harada et al. (1999) describe WTl gene expression in human testicular germ-cell tumors.
  • Nonomura et al. Hinyokika (1999) describe molecular staging of testicular cancer using poiymerase chain reaction of the testicular cancer-specific genes.
  • Shimizu et al (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, et al, (2000). WTl overexpression in ghoblastoma and other cancer was described by Menssen et al, (2000), "Wilms' tumor gene (WTl) expression in lung cancer, colon cancer and ghoblastoma 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 et al, 2000), "Wilms' tumor gene expression by normal and malignant human B lymphocytes.”
  • Pan et al. (2000) 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. (1999) reported WTl and GATA1 expression in myelodysplastic syndrome and acute leukemia. Tamaki et al (1999) reported that the Wilms tumor gene WTl is a good marker for diagnosis of disease progression of myelodysplastic syndromes.
  • 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. (1999).
  • compositions provided herein may be used alone or in combination with conven- tional therapeutic regimens such as surgery, inadiation, chemotherapy and/or bone manow 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 manow 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 WT1- 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., intracu- taneous, 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.
  • 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 peptide present in a dose ranges from about 100 ⁇ g to 5 mg. Suitable dose sizes will vary with the size ofthe patient, but will typically range from about 0.1 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.
  • 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 conelate 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 peptide or WTl -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.
  • T cells/M 2 are administered intravenously, intracavitary 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 ofthe patient.
  • T cells may be stimulated prior to autologous bone manow transplantation. Such stimulation may take place in vivo or in vitro.
  • bone manow and/or peripheral blood obtained from a patient may be contacted with a WTl peptide, a polynucleotide encoding a WTl peptide and/or an APC that expresses a WTl peptide under conditions and for a time sufficient to permit the stimulation of T cells as described above.
  • Bone manow, peripheral blood stem cells and/or WTl -specific T cells may then be administered to a patient using standard techniques.
  • T cells of a related or unrelated donor may be stimulated prior to syngeneic or allogeneic (related or unrelated) bone manow transplantation. Such stimulation may take place in vivo or in vitro.
  • bone manow and/or peripheral blood (or a fraction of bone manow or peripheral blood) obtained from a related or unrelated donor may be contacted with a WTl peptide, WTl polynucleotide and/or APC that expresses a WTl peptide under conditions and for a time sufficient to permit the stimulation of T cells as described above.
  • Bone manow, 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 manow, peripheral blood or a fraction of bone manow or peripheral blood (e.g., CD34 + enriched peripheral blood (PB) prior to administration to a patient).
  • Such methods may be performed by contacting bone manow 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 manow or peripheral blood.
  • Bone manow 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, including malignant mesothelioma, and that methods which enhance such immune responses may provide a preventive or therapeutic benefit. Diagnostic methods provided herein may provide early detection of these diseases, and permit the high throughput screening of patients considered at risk.
  • Such patients include, for example, individuals suspected of asbestos exposure, which may be at risk for the development of malignant mesothelioma.
  • 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 peptide, a polynucleotide encoding a WTl peptide and/or an APC that expresses a WTl peptide, 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 peptide (e.g., 5-25 ⁇ g/ml). It may be desirable to incubate another aliquot of a T cell sample in the absence of WTl peptide to serve as a control.
  • WTl peptide e.g., 5-25 ⁇ g/ml
  • activation is preferably detected by evaluating proliferation ofthe T cells.
  • 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 conelation 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.
  • 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 peptide, a polynucleotide encoding a WTl peptide and/or an APC that expresses a WTl peptide under conditions and for a time sufficient to allow immunocomplexes to form. Immunocomplexes formed between the WTl peptide and antibodies in the biological sample that specifically bind to the WTl peptide 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 manow, pleural effusion, and cerebrospinal fluid.
  • the biological sample is incubated with the WTl peptide in a reaction mixture under conditions and for a time sufficient to permit immunocomplexes to form between the peptide and antibodies specific for WTl.
  • a biological sample and WTl peptide may be incubated at 4°C for 24-48 hrs.
  • immunocomplexes formed between the WTl peptide and antibodies present in the biological sample may be accomplished by a variety of known tech- niques, 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 (Harlow and Lane, 1988). Assays that may be used include, but are not limited to, the double monoclonal antibody sandwich immunoassay technique (U. S. Patent No.
  • WTl peptide may either be labeled or unlabeled.
  • Unlabeled WTl peptide 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 peptide).
  • 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 peptide 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 peptide 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 poly- vinylchloride.
  • 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 peptide 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 prefened. In such cases, adsorption may be achieved by contacting the WTl peptide, 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.
  • contacting a well of a plastic microtiter plate (such as polystyrene or polyvinylchloride) with an amount of peptide ranging from about 10 ng to about 10 ⁇ g, and preferably about 100 ng to about 1 ⁇ g, is sufficient to immobilize an adequate amount of peptide.
  • any suitable blocking agent known to those of ordinary skill in the art such as bovine serum albumin, TweenTM 20TM (Sigma Chemical Co., St. Louis, MO), heat- inactivated nonnal goat serum (NGS), or BLOTTO (buffered solution of nonfat dry milk which also contains a preservative, salts, and an antifoaming agent) may be used.
  • 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 (0.1%- 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 appro- priate buffer, such as PBS containing 0.1 % TweenTM 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 ofthe 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 peptide, wherein the incubation is performed under conditions and for a time sufficient to allow immunocomplexes to form; (b) detecting immunocomplexes formed between the WTl peptide and antibodies in the biological sample that specifically bind to the WTl peptide; (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 peptide, or an APC expressing a WTl peptide may be employed in place of the WTl peptide.
  • immunocomplexes between the WTl peptide 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 manow, peripheral blood or a fraction thereof), obtained from a patient prior to a therapy or immunization, with a WTl peptide, 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 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 manow, 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 ofthe 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 present invention concerns formulation of one or more of the polynucleotide compositions disclosed herein in pharmaceutically acceptable solutions for administration to a cell or an animal, either alone, or in combination with one or more other modalities of anti-cancer therapy.
  • the nucleic acid segment, RNA, or DNA compositions disclosed herein may be administered in combination with other agents as well, such as, e.g., proteins or peptides or various pharmaceutically-active agents.
  • agents such as, e.g., proteins or peptides or various pharmaceutically-active agents.
  • the composition comprises at least one of the genetic expression constructs disclosed herein, there is virtually no limit to other components that may also be included, given that the additional agents do not cause a significant adverse effect upon contact with the target cells or host tissues.
  • the RNA- or DNA-derived compositions may thus be delivered along with various other agents as required in the particular instance.
  • Such RNA or DNA compositions may be purified from host cells or other biological sources, or alternatively may be chemically synthesized as described herein.
  • compositions may comprise substituted or derivatized RNA or DNA compositions.
  • Such compositions may include one or more therapeutic gene constructs, either alone, or in combination with one or more modified peptide or nucleic acid substituent derivatives, and/or other anticancer therapeutics.
  • compositions described herein are well-known to those of skill in the art, as is the development of suitable dosing and treatment regimens for using the particular compositions described herein in a variety of treatment regimens, including e.g., oral, intravenous, infranasal, transdermal, intraprostatic, intratumoral, and/or intramuscular administration and formulation.
  • compositions disclosed herein may be administered parenterally, intravenously, intramuscularly, or even intraperitoneally as described in U. S. Patent 5,543,158, U. S. Patent 5,641,515 and U. S. Patent 5,399,363 (each specifically incorporated herein by reference in its entirety).
  • Solutions ofthe active compounds as free-base or pharmacologically acceptable salts may be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose.
  • Dispersions may also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms.
  • the pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions (U. S. Patent 5,466,468, specifically incorporated herein by reference in its entirety).
  • the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
  • the canier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and/or vegetable oils.
  • Proper fluidity may be maintained, for example, by the use of a coating, such as lecithin, by the maintenance ofthe required particle size in the case of dispersion and by the use of surfactants .
  • the prevention of the action of microorganisms can be brought about by various antibacterial ad antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars or sodium chloride.
  • Prolonged absorption ofthe injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
  • aqueous solutions For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose.
  • aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration.
  • sterile aqueous media that can be employed will be known to those of skill in the art in light of the present disclosure.
  • one dosage may be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion, (see for example, Hoover, 1975). Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject.
  • preparations should meet sterility, pyrogenicity, and general safety and purity standards as required by FDA Office of Biologies standards.
  • Sterile injectable solutions may be prepared by incorporating the gene therapy constructs in the required amount in the appropriate solvent with several of the other ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those .enumerated above.
  • the prefened methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • compositions disclosed herein may be formulated in a neutral or salt form.
  • Pharmaceutically-acceptable salts include the acid addition salts and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or fenic hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like.
  • solutions Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective.
  • the formulations are easily administered in a variety of dosage forms such as injectable solutions, drug release capsules and the like.
  • canier includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, canier solutions, suspensions, colloids, and the like.
  • solvents dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, canier solutions, suspensions, colloids, and the like.
  • Nasal solutions are usually aqueous solutions designed for administration to the nasal passages in drops or sprays. Nasal solutions are prepared so that they are similar in many respects to nasal secretions, so that normal ciliary action is maintained. Thus, the aqueous nasal solutions usually are isotonic and slightly buffered to maintain a pH of from about 5.5 to about 6.5.
  • antimicrobial preservatives similar to those used in ophthalmic preparations, and appropriate drug stabilizers, if required, may be included in the formulation.
  • Various commercial nasal preparations are known.
  • Inhalations and inhalants are pharmaceutical preparations designed for delivering a drug or compound into the respiratory tree of a patient.
  • a vapor or mist is administered and reaches the affected area, often to give relief from symptoms of bronchial and nasal congestion.
  • this route can also be employed to deliver agents into the systemic circulation.
  • Inhalations may be administered by the nasal or oral respiratory routes. The administration of inhalation solutions is only effective if the droplets are sufficiently fine and uniform in size so that the mist reaches the bronchioles.
  • inhalations also known as inhalations, and sometimes called insufflations
  • insufflations consists of finely powdered or liquid drugs that are canied into the respiratory passages by the use of special delivery systems, such as pharmaceutical aerosols, that hold a solution or suspension of the drug in a liquefied gas propellant.
  • pharmaceutical aerosols When released through a suitable valve and oral adapter, a metered does ofthe inhalation is propelled into the respiratory tract ofthe patient.
  • Particle size is of importance in the administration of this type of preparation. It has been reported that the optimum particle size for penetration into the pulmonary cavity is of the order of about 0.5 to about 7 ⁇ m. Fine mists are produced by pressurized aerosols and hence their use in considered advantageous.
  • the inventors contemplate the use of Hposomes, nanocapsules, microparticles, microspheres, lipid particles, vesicles, and the like, for the introduction of the polynucleotide compositions ofthe present invention into suitable host cells.
  • the polynucleotide compositions of the present invention may be formulated for delivery either encapsulated in a lipid particle, a liposome, a vesicle, a nanosphere, or a nanoparticle or the like.
  • Such formulations may be prefened for the introduction of pharmaceutically acceptable formulations of the nucleic acids disclosed herein.
  • Hposomes are generally known to those of skill in the art (see for example, Couvreur et al, 1977; Couvreur, 1988; Lasic, 1998; which describes the use of Hposomes and nanocapsules in the targeted antibiotic therapy for intracellular bacterial infections and diseases).
  • Hposomes were developed with improved serum stability and circulation half-lives (Gabizon and Papahadjopoulos, 198S; Allen and Choun, 1987; U. S. Patent 5,741,516, specifically incorporated herein by reference in its entirety).
  • Liposomes have been used successfully with a number of cell types that are normally resistant to transfection by other procedures including T cell suspensions, primary hepatocyte cultures and PC 12 cells (Renneisenet ⁇ /., 1990; Mulleret al, 1990). In addition, liposomes are free ofthe DNA length constraints that are typical of viral-based delivery systems. Liposomes have been used effectively to introduce genes, drugs (Heath and Martin, 1986; Heath et al, 1986; Balazsovits et al, 1989; Fresta and Puglisi, 1996), radiotherapeutic agents (Pikul etal, 1987), enzymes (Imaizumi et al. , 1990a; Imaizumi et al.
  • Liposomes are formed from phospholipids that are dispersed in an aqueous medium and spontaneously form multilamellar concentric bilayer vesicles (also termed multilamellar vesicles (MLVs).
  • MLVs generally have ' diameters of from 25 nm to 4 ⁇ m. Sonication of MLVs results in the formation of small unilamellar vesicles (SUVs) with diameters in the range of 200 to 500 A, containing an aqueous solution in the core.
  • SUVs small unilamellar vesicles
  • Liposomes bear resemblance to cellular membranes and are contemplated for use in connection with the present invention as caniers for the peptide compositions. They are widely suitable as both water- and lipid-soluble substances can be entrapped, i.e. in the aqueous spaces and within the bilayer itself, respectively. It is possible that the drug-bearing liposomes may even be employed for site-specific delivery of active agents by selectively modifying the liposomal formulation.
  • Phospholipids can form a variety of structures other than liposomes when dispersed in water, depending on the molar ratio of lipid to water. At low ratios the liposome is the prefened structure. The physical characteristics of liposomes depend on pH, ionic strength and the presence of divalent cations. Liposomes can show low permeability to ionic and polar substances, but at elevated temperatures undergo a phase transition which markedly alters their permeability.
  • phase transition involves a change from a closely packed, ordered structure, known as the gel state, to a loosely packed, less-ordered structure, known as the fluid state. This occurs at a characteristic phase-transition temperature and results in an increase in permeability to ions, sugars, and drugs.
  • the invention provides for pharmaceutically acceptable nanocapsule formulations of the polynucleotide compositions ofthe present invention.
  • Nanocapsules can generally entrap compounds in a stable and reproducible way (Henry-Michelland et l, 1987; Quintanar-Guenero et al, 1998; Douglas et al, 1987).
  • ultraf ⁇ ne particles sized around 0.1 ⁇ m
  • Biodegradable polyalkyl-cyanoacrylate nanoparticles that meet these requirements are contemplated for use in the present invention, and such particles may be are easily made, as described (Couvreur et al, 1980; 1988; zur Muhlen et al, 1998; Zambaux et al. 1998; Pinto-Alphandry et al. 1995 and U. S. Patent 5,145,684, specifically incorporated herein by reference in its entirety).
  • methods of polynucleotide polynucleotide delivery to a target cell using either nanoparticles or nanospheres are also particularly contemplated to be useful in formulating the disclosed compositions for administration to an animal, and to a human in particular.
  • the invention also provides one or more of the WTl -specific antibodies or antigen binding fragments, or WTl -derived peptides or peptide variants formulated with one or more pharmaceutically acceptable excipients, caniers, diluents, adjuvants, and/or other components for administration to an animal in need thereof.
  • antibodies and antigen binding fragments, antibody- or antigen binding fragment-encoding polynucleotides or additional anticancer agents, polynucleotides, peptides, antigens, or other therapeutic compounds as may be employed in the formulation of particular compositions and formulations disclosed herein, and particularly in the preparation of anticancer agents or anti- mesothelioma therapies for administration to the affected mammal.
  • prefened animals for administration of the pharmaceutical compositions disclosed herein include mammals, and particularly humans.
  • Other prefened animals include primates, sheep, goats, bovines, equines, porcines, lupines, canines, and felines, as well as any other mammalian species commonly considered pets, livestock, or commercially relevant animal species.
  • compositions and formulations may include partially or significantly purified polypeptide, polynucleotide, or antibody or antigen binding fragment compositions, either alone, or in combination with one or more additional active ingredients, anticancer agents, vaccines, adjuvants, or other therapeutics which may be obtained from natural or recombinant sources, or which may be obtainable naturally or either chemically synthesized, or alternatively produced in vitro from recombinant host cells expressing one or more nucleic acid segments that encode one or more such additional active ingredients, caniers, adjuvants, cofactors, or other therapeutic compound.
  • kits comprising one or more such reagents for use in a variety of diagnostic assays, including for example, immunoassays such as ELISA and "sandwich"-type immunoassays.
  • diagnostic assays including for example, immunoassays such as ELISA and "sandwich"-type immunoassays.
  • kits may preferably include at least a first peptide, or a first antibody or antigen binding fragment of the invention, a functional fragment thereof, or a cocktail thereof, and means for signal generation.
  • the kit's components may be pre-attached to a solid support, or may be applied to the surface of a solid support when the kit is used.
  • the signal generating means may come pre-associated with an antibody ofthe invention or may require combination with one or more components, e.g., buffers, antibody- enzyme conjugates, enzyme substrates, or the like, prior to use.
  • Kits may also include additional reagents, e.g., blocking reagents for reducing nonspecific binding to the solid phase surface, washing reagents, enzyme substrates, and the like.
  • the solid phase surface may be in the form of microtiter plates, microspheres, or other materials suitable for immobilizing proteins, peptides, or polypeptides.
  • an enzyme that catalyzes the formation of a chemiluminescent or chromogenic product or the reduction of a chemiluminescent or chromogenic substrate is a component ofthe signal generating means.
  • Such enzymes are well known in the art.
  • kits are useful in the detection, monitoring and diagnosis of conditions characterized by over-expression or inappropriate expression of WTl, or WTl -derived peptides and/or polypeptides.
  • kits ofthe present invention may also be prepared that comprise at least one of the antibody, peptide, antigen binding fragment, hybridoma, vector, vaccine, polynucleotide, or cellular compositions disclosed herein and instructions for using the composition as a diagnostic reagent or therapeutic agent.
  • Containers for use in such kits may typically comprise at least one vial, test tube, flask, bottle, syringe or other suitable container, into which one or more ofthe diagnostic and/or therapeutic composition(s) may be placed, and preferably suitably aliquoted.
  • the kit may also contain a second distinct container into which this second diagnostic and/or therapeutic composition may be placed.
  • kits ofthe present invention will also typically include a means for containing the vial(s) in close confinement for commercial sale, such as, e.g., injection or blow-molded plastic containers into which the desired vial(s) are retained.
  • the labeling agent may be provided either in the same container as the diagnostic or therapeutic composition itself, or may alternatively be placed in a second distinct container means into which this second composition may be placed and suitably aliquoted.
  • the detection reagent and the label may be prepared in a single container means, and in most cases, the kit will also typically include a means for containing the vial(s) in close confinement for commercial sale and/or convenient packaging and delivery.
  • nucleic acid sequences include, but are not limited to, DNAs (including and not limited to genomic or extragenomic DNAs), genes, peptide nucleic acids (PNAs) RNAs (including, but not limited to, rRNAs, mRNAs and tRNAs), nucleosides, and suitable nucleic acid segments either obtained from native sources, chemically synthesized, modified, or otherwise prepared in whole or in part by the hand of man.
  • PNAs peptide nucleic acids
  • RNAs including, but not limited to, rRNAs, mRNAs and tRNAs
  • nucleosides include, but are not limited to, DNAs (including and not limited to, genomic or extragenomic DNAs), genes, peptide nucleic acids (PNAs) RNAs (including, but not limited to, rRNAs, mRNAs and tRNAs), nucleosides, and suitable nucleic acid segments either obtained from native sources, chemically synthesized, modified, or otherwise prepared in
  • Expression The combination of intracellular processes, including transcription and translation undergone by a polynucleotide such as a structural gene to synthesize the encoded peptide or polypeptide.
  • Promoter a term used to generally describe the region or regions of a nucleic acid sequence that regulates transcription.
  • Structural gene A gene or sequence region that is expressed to produce an encoded peptide or polypeptide.
  • Transformation A process of introducing an exogenous polynucleotide sequence (e.g., a vector, a recombinant DNA or RNA molecule) into a host cell or protoplast in which that exogenous nucleic acid segment is incorporated into at least a first chromosome or is capable of autonomous replication within the transformed host cell.
  • Transfection, electroporation, and naked nucleic acid uptake all represent examples of techniques used to transform a host cell with one or more polynucleotides.
  • Transformed cell A host cell whose nucleic acid complement has been altered by the introduction of one or more exogenous polynucleotides into that cell.
  • Transgenic cell Any cell derived or regenerated from a transformed cell or derived from a transgenic cell, or from the progeny or offspring of any generation of such a transformed host cell.
  • Transgenic animal An animal or a progeny or an offspring of any generation thereof that is derived from a transformed animal cell, wherein the animal's DNA contains an introduced exogenous nucleic acid molecule not originally present in a native, wild type, non- transgenic animal of the same species.
  • transgenic animal and transformed animal have sometimes been used in the art as synonymous terms to define an animal, the genetic contents of which has been modified to contain one or more exogenous nucleic acid segments.
  • a nucleic acid molecule typically comprised of DNA, capable of replication in a host cell and/or to which another nucleic acid segment can be operatively linked so as to bring about replication ofthe attached segment.
  • a plasmid, cosmid, or a virus is an exemplary vector.
  • the terms “substantially conesponds to”, “substantially homologous”, or “substantial identity” as used herein denotes a characteristic of a nucleic acid or an amino acid sequence, wherein a selected nucleic acid or amino acid sequence has at least about 70 or about 75 percent sequence identity as compared to a selected reference nucleic acid or amino acid sequence.
  • the selected sequence and the reference sequence will have at least about 76, 77, 78, 79, 80, 81, 82, 83, 84 or even 85 percent sequence identity, and more preferably at least about 86, 87, 88, 89, 90, 91, 92, 93, 94, or 95 percent sequence identity. More preferably still, highly homologous sequences often share greater than at least about 96, 97, 98, or 99 percent sequence identity between the selected sequence and the reference sequence to which it was compared. The percentage of sequence identity may be calculated over the entire length of the sequences to be compared, or may be calculated by excluding small deletions or additions which total less than about 25 percent or so of the chosen reference sequence.
  • the reference sequence may be a subset of a larger sequence, such as a portion of a gene or flanking sequence, or a repetitive portion of a chromosome. However, in the case of sequence homology of two or more polynucleotide sequences, the reference sequence will typically comprise at least about 18-25 nucleotides, more typically at least about 26 to 35 nucleotides, and even more typically at least about 40, 50, 60, 70, 80, 90, or even 100 or so nucleotides.
  • the extent of percent identity between the two sequences will be at least about 80%, preferably at least about 85%, and more preferably about 90%) or 95% or higher, as readily determined by one or more of the sequence comparison algorithms well-known to those of skill in the art, such as e.g., the FASTA program analysis described by Pearson and Lipman (1988).
  • naturally occuning refers to the fact that an object can be found in nature.
  • a polypeptide or polynucleotide sequence that is present in an organism (including viruses) that can be isolated from a source in nature and which has not been intentionally modified by the hand of man in a laboratory is naturally-occuning.
  • laboratory strains of rodents that may have been selectively bred according to classical genetics are considered naturally occuning animals.
  • heterologous is defined in relation to a predetermined referenced gene sequence.
  • a heterologous promoter is defined as a promoter which does not naturally occur adjacent to the referenced structural gene, but which is positioned by laboratory manipulation.
  • a heterologous gene or nucleic acid segment is defined as a gene or segment that does not naturally occur adjacent to the referenced promoter and/or enhancer elements.
  • Transcriptional regulatory element refers to a polynucleotide sequence that activates transcription alone or in combination with one or more other nucleic acid sequences.
  • a transcriptional regulatory element can, for example, comprise one or more promoters, one or more response elements, one or more negative regulatory elements, and/or one or more enhancers.
  • a "transcription factor recognition site” and a “transcription factor binding site” refer to a polynucleotide sequence(s) or sequence motif(s) which are identified as being sites for the sequence-specific interaction of one or more transcription factors, frequently taking the form of direct protein-DNA binding.
  • transcription factor binding sites can be identified by DNA footprinting, gel mobility shift assays, and the like, and/or can be predicted on the basis of known consensus sequence motifs, or by other methods known to those of skill in the art.
  • the term “operably linked” refers to a linkage of two or more polynucleotides or two or more nucleic acid sequences in a functional relationship.
  • a nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence.
  • a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the coding sequence.
  • Operably linked means that the DNA sequences being linked are typically contiguous and, where necessary to join two protein coding regions, contiguous and in reading frame.
  • enhancers generally function when separated from the promoter by several kilobases and intronic sequences may be of variable lengths, some polynucleotide elements may be operably linked but not contiguous.
  • Transcriptional unit refers to a polynucleotide sequence that comprises at least a first structural gene operably linked to at least a first cw-acting promoter sequence and optionally linked operably to one or more other cis-acting nucleic acid sequences necessary for efficient transcription ofthe structural gene sequences, and at least a first distal regulatory element as may be required for the appropriate tissue-specific and developmental transcription of the structural gene sequence operably positioned under the control of the promoter and/or enhancer elements, as well as any additional cis sequences that are necessary for efficient transcription and translation (e.g., polyadenylation site(s), mRNA stability controlling sequence(s), etc.
  • This example illustrates the use of WTl as a marker for malignant mesothelioma.
  • cDNA constructs representing the human WTl full length (amino acids 1-449), the N-terminus (amino acids 1-249) and C-terminus (amino acids 267- 449) regions were subcloned into a modified pET28 vector.
  • the resulting vector had a 5' His tag, followed by the thioredoxin (Trx) coding region, followed by a 3' Histidine tag, followed by a Thrombin and EK site.
  • Trx thioredoxin
  • a Source QTM anion exchange resin Amersham Pharmacia Biotech, Uppsala, Sweden
  • WTl polypeptide responses to WTl polypeptides were determined by Western blot analysis using both recombinant full-length and truncated WTl proteins and a WTl polypeptide designated WT N180 (Santa Cruz Biotechnology, Inc., Santa Cruz, CA).
  • WT N180 Santa Cruz Biotechnology, Inc., Santa Cruz, CA.
  • sera from immunized as well as non-immunized B6 mice or human AML patients was used in a 1:500 dilution with Tris-buffered saline/1% BSA and 0.1% NP-40TM.
  • a polygonal antimouse or antihuman-horseradish peroxidase-conjugated second antibody was used in a 1 :10,000 dilution.
  • the blots were then developed by using a chemiluminescent reaction (ECLTM Reagent, Amersham) after which they were exposed to Hyperfilm-ECLTM (Amersham). The film was developed and examined. All control blots were developed by using the commercially prepared WT1- specific antibodies, WT C-19 and WT 180 (Santa Cruz Biotechnology), and each demonstrated a strong band at the expected size ofthe TRX- WTl fusion proteins (TRX- WTl full-length (approximately 85 kDa); TRX- WTl N-terminus (approximately 60 kDa); TRX- WTl C-terminus (approximately 50 kDa).
  • TRX- WTl full-length approximately 85 kDa
  • TRX- WTl N-terminus approximately 60 kDa
  • TRX- WTl C-terminus approximately 50 kDa.
  • 96-well ELISA plates (Nunc) were coated with 50 ⁇ l/well of each of the WTl proteins.
  • WTl proteins were diluted to 5 ng/ ⁇ l in ELISA coating buffer (1 M Na 2 HCO 3 , pH 9.6). Plates were incubated over night at 4°C or 4 hrs at 37°C and then washed twice in PBS/0.1% TweenTM. Plates were blocked with 200 ⁇ l/well Blocking Buffer (10% normal goat sera/PBS/0.1%) TweenTM), incubated 2 hrs at room temperature and then washed twice. As a first step antibody, 50 ⁇ l of either patient samples, positive controls or negative control samples diluted in Blocking Buffer were added.
  • the first two columns show the positive controls (WTC19 and WTl 80).
  • the third column (designated D44) shows the results for normal control serum.
  • the remaining columns show the results for serum samples obtained from patients with malignant mesothelioma. Serum samples designated S337 and S339 had values that were greater than twice the mean of the normal control samples, and thus were considered positive for malignant mesothelioma.
  • This example illustrates the use of cells expressing WTl to induce a WTl specific antibody response in vivo.
  • mice were injected with TRAMP-C, a WTl positive tumor cell line of B6 origin. Briefly, male B6 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.
  • 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, 1988; Deavin et al, 1996), which searches for peptide motifs that have the potential to elicit Th responses. Peptides shown in Table 2 were synthesized and sequenced.
  • peptides were grouped as follows:
  • 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, 1994).
  • lymphocytes were cultured in 96-well plates at 2 x 10 5 cells per well with 4 x 10 5 inadiated (3000 rads) syngeneic spleen cells and the designated peptide.
  • FIG. 4A and FIG. 4B show the proliferative response observed for each of the three peptides within vaccine A (FIG. 4 A) and vaccine B (FIG. 4B).
  • Vaccine A elicited proliferative T cell responses to the immunizing peptides p6-22 and pl 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.
  • Nonameric peptides (9-mers) with motifs appropriate for binding to class I MHC were identified using a variety of analytical methods, including BIMAS HLA peptide binding prediction analysis (Parker et al, 1994). Peptides identified within such analyses are shown in Table 3 - Table 45. In each of these tables, the score reflects the theoretical binding affinity (half-time of dissociation) of the peptide to the MHC molecule indicated.
  • VLDFAPPGA SEQ ID NO:241
  • VPGVAPTLV (SEQ ID NO:242) 4.000
  • VPGVAPTLV SEQ ID NO:242

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US7655249B2 (en) 1998-09-30 2010-02-02 Corixa Corporation Compositions and methods for WT1 specific immunotherapy
US7115272B1 (en) 1998-09-30 2006-10-03 Corixa Corporation Compositions and methods for WT1 specific immunotherapy
US20030072767A1 (en) * 1998-09-30 2003-04-17 Alexander Gaiger Compositions and methods for WT1 specific immunotherapy
US7901693B2 (en) 1998-09-30 2011-03-08 Corixa Corporation Compositions and methods for WT1 specific immunotherapy
US7329410B1 (en) 1998-09-30 2008-02-12 Corixa Corporation Compositions and method for WT1 specific immunotherapy
US20030235557A1 (en) * 1998-09-30 2003-12-25 Corixa Corporation Compositions and methods for WT1 specific immunotherapy
KR100863853B1 (ko) 2001-03-22 2008-10-15 인터내셔널 인스티튜트 오브 캔서 이무놀로지 인코퍼레이티드 더블유티1 개변 펩티드
US7553494B2 (en) 2001-08-24 2009-06-30 Corixa Corporation WT1 fusion proteins
JP5230891B2 (ja) * 2001-09-28 2013-07-10 株式会社癌免疫研究所 抗原特異的ｔ細胞の新規な誘導方法
US20050002951A1 (en) * 2001-09-28 2005-01-06 Haruo Sugiyama Novel method of inducing antigen-specific t cells
DE10254601A1 (de) * 2002-11-22 2004-06-03 Ganymed Pharmaceuticals Ag Differentiell in Tumoren exprimierte Genprodukte und deren Verwendung
KR101213015B1 (ko) 2003-11-05 2012-12-26 인터내셔널 인스티튜트 오브 캔서 이무놀로지 인코퍼레이티드 Ｗｔ１ 로부터 유도된 ｈｌａ-ｄｒ 결합성 항원 펩티드
WO2005053618A2 (en) * 2003-12-01 2005-06-16 Sloan-Kettering Institute For Cancer Research Synthetic hla binding peptide analogues and uses thereof
DE102004024617A1 (de) 2004-05-18 2005-12-29 Ganymed Pharmaceuticals Ag Differentiell in Tumoren exprimierte Genprodukte und deren Verwendung
EP2565201B1 (de) 2005-10-17 2014-11-26 Sloan-Kettering Institute For Cancer Research WT1-HLA-Klasse II-bindende Peptide und Zusammensetzungen und Verfahren damit
EP1790664A1 (de) 2005-11-24 2007-05-30 Ganymed Pharmaceuticals AG Monoklonale Antikörper gegen Claudin-18 zur Behandlung von Krebs
CA2645766A1 (en) 2006-04-10 2007-10-25 Sloan Kettering Institute For Cancer Research Immunogenic wt-1 peptides and methods of use thereof
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CN104774910B (zh) 2007-02-27 2018-04-10 株式会社癌免疫研究所 活化辅助t细胞的方法以及用于该方法的组合物
MY170306A (en) 2010-10-05 2019-07-17 Int Inst Cancer Immunology Inc Method for activating helper t cell
CN104684577B (zh) * 2012-01-13 2018-05-08 纪念斯隆凯特林癌症中心 免疫原性wt-1肽及其使用方法
WO2013167153A1 (en) 2012-05-09 2013-11-14 Ganymed Pharmaceuticals Ag Antibodies useful in cancer diagnosis
JP6499079B2 (ja) 2012-11-13 2019-04-10 バイオエヌテック アーゲーＢｉｏＮＴｅｃｈ ＡＧ クローディンを発現するガン疾患を処置するための剤
MX2015007745A (es) 2012-12-17 2015-12-15 Otsuka Pharma Co Ltd Metodo para activar la celula t auxiliar.
PT2945647T (pt) 2013-01-15 2020-11-26 Memorial Sloan Kettering Cancer Center Péptidos imunogénicos wt-1 e métodos de uso dos mesmos
US10815273B2 (en) 2013-01-15 2020-10-27 Memorial Sloan Kettering Cancer Center Immunogenic WT-1 peptides and methods of use thereof
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