US20030185830A1 - Compositions and methods for the therapy and diagnosis of prostate cancer - Google Patents

Compositions and methods for the therapy and diagnosis of prostate cancer Download PDF

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Publication number
US20030185830A1
US20030185830A1 US10/294,025 US29402502A US2003185830A1 US 20030185830 A1 US20030185830 A1 US 20030185830A1 US 29402502 A US29402502 A US 29402502A US 2003185830 A1 US2003185830 A1 US 2003185830A1
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Prior art keywords
seq
sequence
cdna sequence
polypeptide
sequences
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Abandoned
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US10/294,025
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English (en)
Inventor
Jiangchun Xu
John Stolk
Michael Kalos
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Corixa Corp
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Corixa Corp
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Priority claimed from US09/020,956 external-priority patent/US6261562B1/en
Priority claimed from US09/030,607 external-priority patent/US6262245B1/en
Priority claimed from US09/115,453 external-priority patent/US6657056B2/en
Priority claimed from US09/159,812 external-priority patent/US6613872B1/en
Priority claimed from US09/232,149 external-priority patent/US6465611B1/en
Priority claimed from US09/352,616 external-priority patent/US6395278B1/en
Priority claimed from US09/439,313 external-priority patent/US6329505B1/en
Priority claimed from US09/570,737 external-priority patent/US7202342B1/en
Priority claimed from US09/593,793 external-priority patent/US7517952B1/en
Priority claimed from US09/636,215 external-priority patent/US6620922B1/en
Priority claimed from US09/651,236 external-priority patent/US6818751B1/en
Priority claimed from US09/657,279 external-priority patent/US6894146B1/en
Priority claimed from US09/679,426 external-priority patent/US6759515B1/en
Priority claimed from US09/685,166 external-priority patent/US6630305B1/en
Priority claimed from US09/759,143 external-priority patent/US6800746B2/en
Priority claimed from US09/780,669 external-priority patent/US20020051977A1/en
Priority claimed from US09/895,814 external-priority patent/US20020193296A1/en
Priority claimed from US10/012,896 external-priority patent/US6943236B2/en
Priority claimed from US10/144,678 external-priority patent/US7033827B2/en
Priority to US10/294,025 priority Critical patent/US20030185830A1/en
Application filed by Corixa Corp filed Critical Corixa Corp
Assigned to CORIXA CORPORATION reassignment CORIXA CORPORATION ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: XU, JIANGCHUN, KALOS, MICHAEL D., STOLK, JOHN A.
Publication of US20030185830A1 publication Critical patent/US20030185830A1/en
Priority to PCT/US2003/035961 priority patent/WO2004052276A2/fr
Priority to JP2004559110A priority patent/JP2006515749A/ja
Priority to AU2003302892A priority patent/AU2003302892A1/en
Priority to EP03812782A priority patent/EP1578380A4/fr
Priority to US11/928,375 priority patent/US20080233139A1/en
Priority to US11/928,383 priority patent/US20080219988A1/en
Priority to US11/928,369 priority patent/US7939646B2/en
Priority to US11/929,390 priority patent/US20080226607A1/en
Priority to US11/929,396 priority patent/US20080226620A1/en
Priority to US13/088,159 priority patent/US20120016340A1/en
Abandoned legal-status Critical Current

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
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    • 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]
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    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464493—Prostate associated antigens e.g. Prostate stem cell antigen [PSCA]; Prostate carcinoma tumor antigen [PCTA]; Prostatic acid phosphatase [PAP]; Prostate-specific G-protein-coupled receptor [PSGR]
    • A61K39/464494—Prostate specific antigen [PSA]
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    • 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
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    • 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
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    • C07—ORGANIC CHEMISTRY
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    • 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
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/30—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants from tumour cells
    • C07K16/3069—Reproductive system, e.g. ovaria, uterus, testes, prostate
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/48—Hydrolases (3) acting on peptide bonds (3.4)
    • C12N9/50—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25)
    • C12N9/64—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue
    • C12N9/6421—Proteinases, e.g. Endopeptidases (3.4.21-3.4.25) derived from animal tissue from mammals
    • C12N9/6424—Serine endopeptidases (3.4.21)
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G01N33/57434—Specifically defined cancers of prostate
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2227/00—Animals characterised by species
    • A01K2227/10—Mammal
    • A01K2227/105—Murine
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01K—ANIMAL HUSBANDRY; AVICULTURE; APICULTURE; PISCICULTURE; FISHING; REARING OR BREEDING ANIMALS, NOT OTHERWISE PROVIDED FOR; NEW BREEDS OF ANIMALS
    • A01K2267/00—Animals characterised by purpose
    • A01K2267/03—Animal model, e.g. for test or diseases
    • A01K2267/0331—Animal model for proliferative diseases
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    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/12—Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells
    • A61K2035/124—Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells the cells being hematopoietic, bone marrow derived or blood cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
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    • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
    • A—HUMAN NECESSITIES
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    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/515—Animal cells
    • A61K2039/5156—Animal cells expressing foreign proteins
    • A—HUMAN NECESSITIES
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    • A61K2039/55511—Organic adjuvants
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    • A61K2239/46—Indexing codes associated with cellular immunotherapy of group A61K39/46 characterised by the cancer treated
    • A61K2239/58—Prostate
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    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/50—Immunoglobulins specific features characterized by immunoglobulin fragments
    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
    • C07K2317/565—Complementarity determining region [CDR]
    • C—CHEMISTRY; METALLURGY
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    • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
    • C07K2317/73—Inducing cell death, e.g. apoptosis, necrosis or inhibition of cell proliferation
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
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    • C07K2319/00—Fusion polypeptide
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    • C12N2760/00011—Details
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    • C12N2760/16222—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes

Definitions

  • the present invention relates generally to therapy and diagnosis of cancer, such as prostate cancer.
  • the invention is more specifically related to polypeptides, comprising at least a portion of a prostate-specific protein, and to polynucleotides encoding such polypeptides.
  • polypeptides and polynucleotides are useful in pharmaceutical compositions, e.g., vaccines, and other compositions for the diagnosis and treatment of prostate cancer.
  • Cancer is a significant health problem throughout the world. Although advances have been made in detection and therapy of cancer, no vaccine or other universally successful method for prevention or treatment is currently available. Current therapies, which are generally based on a combination of chemotherapy or surgery and radiation, continue to prove inadequate in many patients.
  • Prostate cancer is the most common form of cancer among males, with an estimated incidence of 30% in men over the age of 50. Overwhelming clinical evidence shows that human prostate cancer has the propensity to metastasize to bone, and the disease appears to progress inevitably from androgen dependent to androgen refractory status, leading to increased patient mortality. This prevalent disease is currently the second leading cause of cancer death among men in the U.S.
  • PSA prostate specific antigen
  • PAP prostatic acid phosphatase
  • the present invention provides polynucleotide compositions comprising a sequence selected from the group consisting of:
  • sequences consisting of at least 20 contiguous residues of a sequence provided in SEQ ID NO: 1-111, 115-171, 173-175, 177, 179-305, 307-315, 326, 328, 330, 332-335, 340-375, 381, 382 and 384-476, 524, 526, 530, 531, 533, 535, 536, 552, 569-572, 587, 591, 593-606, 618-705, 709-774, 777, 789, 817, 823, 824, 878, 880-882, 894, 896, 907, 908, 916-919, 929-931, 938, 939, 942, 944, 945, 948, 967, 969-976, 991, 993-1002, 1004, 1006, 1007, 1010, 1013-1019, 1021, 1023-1027, and 1034-1036;
  • the polynucleotide compositions of the invention are expressed in at least about 20%, more preferably in at least about 30%, and most preferably in at least about 50% of prostate tissue samples tested, at a level that is at least about 2-fold, preferably at least about 5-fold, and most preferably at least about 10-fold higher than that for other normal tissues.
  • the present invention in another aspect, provides polypeptide compositions comprising an amino acid sequence that is encoded by a polynucleotide sequence described above.
  • the present invention further provides polypeptide compositions comprising an amino acid sequence selected from the group consisting of sequences recited in SEQ ID NO: 112-114, 172, 176, 178, 327, 329, 331, 336, 339, 376-380, 383, 477-483, 496, 504, 505, 519, 520, 522, 525, 527, 532, 534, 537-551, 553-568, 573-586, 588-590, 592, 706-708, 775, 776, 778, 780, 781, 811, 814, 818, 826, 827, 853, 855, 858, 860-862, 866-877, 879, 883-893, 895, 897, 898, 909-915, 920-928, 932-934, 940, 941, 943, 946, 947, 949-966, 968, 977-990, 992, 1003, 1005, 1008, 1009, 1011, 1012,
  • the polypeptides and/or polynucleotides of the present invention are immunogenic, i.e., they are capable of eliciting an immune response, particularly a humoral and/or cellular immune response, as further described herein.
  • a P501S (SEQ ID NO: 113) polypeptide of the present invention comprises a fragment of P501S that will minimally comprise SEQ ID NO: 1037, which represents an 11 amino acid fragment of P501S that was unexpectedly found to contain naturally processed epitopes for at least three Class I MHC alleles.
  • the polypeptides of the present invention comprise fragments of P501S that minimally contain SEQ ID NO: 1037, and that are at least 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109,
  • Certain other illustrative P501S polypeptides according to this embodiment will consist of at least 11-542 amino acid residues, 11-100 amino acid residues, 11-50 amino acid residues, or 11-25 amino acid residues of SEQ ID NO: 113 and will contain SEQ ID NO: 1037.
  • the present invention further provides fragments, variants and/or derivatives of the disclosed polypeptide and/or polynucleotide sequences, wherein the fragments, variants and/or derivatives preferably have a level of immunogenic activity of at least about 50%, preferably at least about 70% and more preferably at least about 90% of the level of immunogenic activity of a polypeptide sequence set forth in SEQ ID NO: 112-114, 172, 176, 178, 327, 329, 331, 336, 339, 376-380, 383, 477-483, 496, 504, 505, 519, 520, 522, 525, 527, 532, 534, 537-551, 553-568, 573-586, 588-590, 592, 706-708, 775, 776, 778, 780, 781, 811, 814, 818, 826, 827, 853, 855, 858 or 860-862, 866-877, 879, 883-893, 895, 8
  • the present invention further provides polynucleotides that encode a polypeptide described above, expression vectors comprising such polynucleotides and host cells transformed or transfected with such expression vectors.
  • compositions comprising a polypeptide or polynucleotide as described above and a physiologically acceptable carrier.
  • compositions for prophylactic or therapeutic applications.
  • Such compositions generally comprise an immunogenic polypeptide or polynucleotide of the invention and an immunostimulant, such as an adjuvant, together with a physiologically acceptable carrier.
  • the present invention further provides pharmaceutical compositions that comprise: (a) an antibody or antigen-binding fragment thereof that specifically binds to a polypeptide of the present invention, or a fragment thereof; and (b) a physiologically acceptable carrier.
  • compositions comprising: (a) an antigen presenting cell that expresses a polypeptide as described above and (b) a pharmaceutically acceptable carrier or excipient.
  • antigen presenting cells include dendritic cells, macrophages, monocytes, fibroblasts and B cells.
  • compositions comprise: (a) an antigen presenting cell that expresses a polypeptide as described above and (b) an immunostimulant.
  • the present invention further provides, in other aspects, fusion proteins that comprise at least one polypeptide as described above, as well as polynucleotides encoding such fusion proteins, typically in the form of pharmaceutical compositions, e.g., vaccine compositions, comprising a physiologically acceptable carrier and/or an immunostimulant.
  • the fusions proteins may comprise multiple immunogenic polypeptides or portions/variants thereof, as described herein, and may further comprise one or more polypeptide segments for facilitating and/or enhancing the expression, purification and/or immunogenicity of the polypeptide(s).
  • the present invention provides methods for stimulating an immune response in a patient, preferably a T cell response in a human patient, comprising administering a pharmaceutical composition described herein.
  • a patient may be afflicted with prostate cancer, in which case the methods provide treatment for the disease, or a patient considered to be at risk for such a disease may be treated prophylactically.
  • the present invention provides methods for inhibiting the development of a cancer in a patient, comprising administering to a patient a pharmaceutical composition as recited above.
  • the patient may be afflicted with prostate cancer, in which case the methods provide treatment for the disease, or a patient considered to be at risk for such a disease may be treated prophylactically.
  • the present invention further provides, within other aspects, methods for removing tumor cells from a biological sample, comprising contacting a biological sample with T cells that specifically react with a polypeptide of the present invention, wherein the step of contacting is performed under conditions and for a time sufficient to permit the removal of cells expressing the polypeptide from the sample.
  • methods for inhibiting the development of a cancer in a patient, comprising administering to a patient a biological sample treated as described above.
  • Methods are further provided, within other aspects, for stimulating and/or expanding T cells specific for a polypeptide of the present invention, comprising contacting T cells with one or more of: (i) a polypeptide as described above; (ii) a polynucleotide encoding such a polypeptide; and (iii) an antigen presenting cell that expresses such a polypeptide; under conditions and for a time sufficient to permit the stimulation and/or expansion of T cells.
  • Isolated T cell populations comprising T cells prepared as described above are also provided.
  • the present invention provides methods for inhibiting the development of a cancer in a patient, comprising administering to a patient an effective amount of a T cell population as described above.
  • the present invention further provides methods for inhibiting the development of a cancer 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 polypeptide comprising at least an immunogenic portion of polypeptide disclosed herein; (ii) a polynucleotide encoding such a polypeptide; and (iii) an antigen-presenting cell that expressed such a polypeptide; and (b) administering to the patient an effective amount of the proliferated T cells, thereby inhibiting the development of a cancer in the patient.
  • Proliferated cells may, but need not, be cloned prior to administration to the patient.
  • the present invention provides methods for determining the presence or absence of a cancer, preferably a prostate cancer, in a patient comprising: (a) contacting a biological sample obtained from a patient with a binding agent that binds to a polypeptide as recited above; (b) detecting in the sample an amount of polypeptide that binds to the binding agent; and (c) comparing the amount of polypeptide with a predetermined cut-off value, and therefrom determining the presence or absence of a cancer in the patient.
  • the binding agent is an antibody, more preferably a monoclonal antibody.
  • the present invention also provides, within other aspects, methods for monitoring the progression of a cancer in a patient.
  • Such methods comprise the steps of: (a) contacting a biological sample obtained from a patient at a first point in time with a binding agent that binds to a polypeptide as recited above; (b) detecting in the sample an amount of polypeptide that binds to the binding agent; (c) repeating steps (a) and (b) using a biological sample obtained from the patient at a subsequent point in time; and (d) comparing the amount of polypeptide detected in step (c) with the amount detected in step (b), and therefrom monitoring the progression of the cancer in the patient.
  • the present invention further provides, within other aspects, methods for determining the presence or absence of a cancer in a patient, comprising the steps of: (a) contacting a biological sample obtained from a patient with an oligonucleotide that hybridizes to a polynucleotide of the present invention; (b) detecting in the sample a level of a polynucleotide, preferably mRNA, that hybridizes to the oligonucleotide; and (c) comparing the level of polynucleotide that hybridizes to the oligonucleotide with a predetermined cut-off value, and therefrom determining the presence or absence of a cancer in the patient.
  • the amount of mRNA is detected via polymerase chain reaction using, for example, at least one oligonucleotide primer that hybridizes to a polynucleotide of the present invention, or a complement of such a polynucleotide.
  • the amount of mRNA is detected using a hybridization technique, employing an oligonucleotide probe that hybridizes to an inventive polynucleotide, or a complement of such a polynucleotide.
  • methods for monitoring the progression of a cancer in a patient comprising the steps of: (a) contacting a biological sample obtained from a patient with an oligonucleotide that hybridizes to a polynucleotide of the present invention; (b) detecting in the sample an amount of a polynucleotide that hybridizes to the oligonucleotide; (c) repeating steps (a) and (b) using a biological sample obtained from the patient at a subsequent point in time; and (d) comparing the amount of polynucleotide detected in step (c) with the amount detected in step (b), and therefrom monitoring the progression of the cancer in the patient.
  • the present invention provides antibodies, such as monoclonal antibodies, that bind to a polypeptide as described above, as well as diagnostic kits comprising such antibodies. Diagnostic kits comprising one or more oligonucleotide probes or primers as described above are also provided.
  • FIG. 1 illustrates the ability of T cells to kill fibroblasts expressing the representative prostate-specific polypeptide P502S, as compared to control fibroblasts. The percentage lysis is shown as a series of effector:target ratios, as indicated.
  • FIGS. 2A and 2B illustrate the ability of T cells to recognize cells expressing the representative prostate-specific polypeptide P502S. In each case, the number of ⁇ -interferon spots is shown for different numbers of responders.
  • FIG. 2A data is presented for fibroblasts pulsed with the P2S-12 peptide, as compared to fibroblasts pulsed with a control E75 peptide.
  • FIG. 2B data is presented for fibroblasts expressing P502S, as compared to fibroblasts expressing HER-2/neu.
  • FIG. 3 represents a peptide competition binding assay showing that the P1S#10 peptide, derived from P501S, binds HLA-A2.
  • Peptide P1S#10 inhibits HLA-A2 restricted presentation of fluM58 peptide to CTL clone D150M58 in TNF release bioassay.
  • D150M58 CTL is specific for the HLA-A2 binding influenza matrix peptide fluM58.
  • FIG. 4 illustrates the ability of T cell lines generated from P1S#10 immunized mice to specifically lyse P1S#10-pulsed Jurkat A2Kb targets and P501S-transduced Jurkat A2Kb targets, as compared to EGFP-transduced Jurkat A2Kb.
  • the percent lysis is shown as a series of effector to target ratios, as indicated.
  • FIG. 5 illustrates the ability of a T cell clone to recognize and specifically lyse Jurkat A2Kb cells expressing the representative prostate-specific polypeptide P501S, thereby demonstrating that the P1S#10 peptide may be a naturally processed epitope of the P501S polypeptide.
  • FIGS. 6A and 6B are graphs illustrating the specificity of a CD8 + cell line (3A-1) for a representative prostate-specific antigen (P501S).
  • FIG. 6A shows the results of a 51 Cr release assay. The percent specific lysis is shown as a series of effector:target ratios, as indicated.
  • FIG. 6B shows the production of interferon-gamma by 3A-1cells stimulated with autologous B-LCL transduced with P501S, at varying effector:target rations as indicated.
  • FIG. 7 is a Western blot showing the expression of P501S in baculovirus.
  • FIG. 8 illustrates the results of epitope mapping studies on P501S.
  • FIG. 9 is a schematic representation of the P501S protein showing the location of transmembrane domains and predicted intracellular and extracellular domains.
  • FIG. 10 is a genomic map showing the location of the prostate genes P775P, P704P, B305D, P712P and P774P within the Cat Eye Syndrome region of chromosome 22q11.2
  • FIG. 11 shows the results of an ELISA assay to determine the specificity of rabbit polyclonal antisera raised against P501S.
  • SEQ ID NO: 1 is the determined cDNA sequence for F1-13
  • SEQ ID NO: 2 is the determined 3′ cDNA sequence for F1-12
  • SEQ ID NO: 3 is the determined 5′ cDNA sequence for F1-12
  • SEQ ID NO: 4 is the determined 3′ cDNA sequence for F1-16
  • SEQ ID NO: 5 is the determined 3′ cDNA sequence for H1-1
  • SEQ ID NO: 6 is the determined 3′ cDNA sequence for H1-9
  • SEQ ID NO: 7 is the determined 3′ cDNA sequence for H1-4
  • SEQ ID NO: 8 is the determined 3′ cDNA sequence for J1-17
  • SEQ ID NO: 9 is the determined 5′ cDNA sequence for J1-17
  • SEQ ID NO: 10 is the determined 3′ cDNA sequence for L1-12
  • SEQ ID NO: 11 is the determined 5′ cDNA sequence for L1-12
  • SEQ ID NO: 12 is the determined 3′ cDNA sequence for N1-1862
  • SEQ ID NO: 13 is the determined 5′ cDNA sequence for N1-1862
  • SEQ ID NO: 14 is the determined 3′ cDNA sequence for J1-13
  • SEQ ID NO: 15 is the determined 5′ cDNA sequence for J1-13
  • SEQ ID NO: 16 is the determined 3′ cDNA sequence for J1-19
  • SEQ ID NO: 17 is the determined 5′ cDNA sequence for J1-19
  • SEQ ID NO: 18 is the determined 3′ cDNA sequence for J1-25
  • SEQ ID NO: 19 is the determined 5′ cDNA sequence for J1-25
  • SEQ ID NO: 20 is the determined 5′ cDNA sequence for J1-24
  • SEQ ID NO: 21 is the determined 3′ cDNA sequence for J1-24
  • SEQ ID NO: 22 is the determined 5′ cDNA sequence for K1-58
  • SEQ ID NO: 23 is the determined 3′ cDNA sequence for K1-58
  • SEQ ID NO: 24 is the determined 5′ cDNA sequence for K1-63
  • SEQ ID NO: 25 is the determined 3′ cDNA sequence for K1-63
  • SEQ ID NO: 26 is the determined 5′ cDNA sequence for L1-4
  • SEQ ID NO: 27 is the determined 3′ cDNA sequence for L1-4
  • SEQ ID NO: 28 is the determined 5′ cDNA sequence for L1-14
  • SEQ ID NO: 29 is the determined 3′ cDNA sequence for L1-14
  • SEQ ID NO: 30 is the determined 3′ cDNA sequence for J1-12
  • SEQ ID NO: 31 is the determined 3′ cDNA sequence for J1-16
  • SEQ ID NO: 32 is the determined 3′ cDNA sequence for J1-21
  • SEQ ID NO: 33 is the determined 3′ cDNA sequence for K1-48
  • SEQ ID NO: 34 is the determined 3′ cDNA sequence for K1-55
  • SEQ ID NO: 35 is the determined 3′ cDNA sequence for L1-2
  • SEQ ID NO: 36 is the determined 3′ cDNA sequence for L1-6
  • SEQ ID NO: 37 is the determined 3′ cDNA sequence for N1-1858
  • SEQ ID NO: 38 is the determined 3′ cDNA sequence for N1-1860
  • SEQ ID NO: 39 is the determined 3′ cDNA sequence for N1-1861
  • SEQ ID NO: 40 is the determined 3′ cDNA sequence for N1-1864
  • SEQ ID NO: 41 is the determined cDNA sequence for P5
  • SEQ ID NO: 42 is the determined cDNA sequence for P8
  • SEQ ID NO: 43 is the determined cDNA sequence for P9
  • SEQ ID NO: 44 is the determined cDNA sequence for P18
  • SEQ ID NO: 45 is the determined cDNA sequence for P20
  • SEQ ID NO: 46 is the determined cDNA sequence for P29
  • SEQ ID NO: 47 is the determined cDNA sequence for P30
  • SEQ ID NO: 48 is the determined cDNA sequence for P34
  • SEQ ID NO: 49 is the determined cDNA sequence for P36
  • SEQ ID NO: 50 is the determined cDNA sequence for P38
  • SEQ ID NO: 51 is the determined cDNA sequence for P39
  • SEQ ID NO: 52 is the determined cDNA sequence for P42
  • SEQ ID NO: 53 is the determined cDNA sequence for P47
  • SEQ ID NO: 54 is the determined cDNA sequence for P49
  • SEQ ID NO: 55 is the determined cDNA sequence for P50
  • SEQ ID NO: 56 is the determined cDNA sequence for P53
  • SEQ ID NO: 57 is the determined cDNA sequence for P55
  • SEQ ID NO: 58 is the determined cDNA sequence for P60
  • SEQ ID NO: 59 is the determined cDNA sequence for P64
  • SEQ ID NO: 60 is the determined cDNA sequence for P65
  • SEQ ID NO: 61 is the determined cDNA sequence for P73
  • SEQ ID NO: 62 is the determined cDNA sequence for P75
  • SEQ ID NO: 63 is the determined cDNA sequence for P76
  • SEQ ID NO: 64 is the determined cDNA sequence for P79
  • SEQ ID NO: 65 is the determined cDNA sequence for P84
  • SEQ ID NO: 66 is the determined cDNA sequence for P68
  • SEQ ID NO: 67 is the determined cDNA sequence for P80 (also referred to as P704P)
  • SEQ ID NO: 68 is the determined cDNA sequence for P82
  • SEQ ID NO: 69 is the determined cDNA sequence for U1-3064
  • SEQ ID NO: 70 is the determined cDNA sequence for U1-3065
  • SEQ ID NO: 71 is the determined cDNA sequence for V1-3692
  • SEQ ID NO: 72 is the determined cDNA sequence for 1A-3905
  • SEQ ID NO: 73 is the determined cDNA sequence for V1-3686
  • SEQ ID NO: 74 is the determined cDNA sequence for R1-2330
  • SEQ ID NO: 75 is the determined cDNA sequence for 1B-3976
  • SEQ ID NO: 76 is the determined cDNA sequence for V1-3679
  • SEQ ID NO: 77 is the determined cDNA sequence for 1G-4736
  • SEQ ID NO: 78 is the determined cDNA sequence for 1G-4738
  • SEQ ID NO: 79 is the determined cDNA sequence for 1G-4741
  • SEQ ID NO: 80 is the determined cDNA sequence for 1G-4744
  • SEQ ID NO: 81 is the determined cDNA sequence for 1G-4734
  • SEQ ID NO: 82 is the determined cDNA sequence for 1H-4774
  • SEQ ID NO: 83 is the determined cDNA sequence for 1H-4781
  • SEQ ID NO: 84 is the determined cDNA sequence for 1H-4785
  • SEQ ID NO: 85 is the determined cDNA sequence for 1H-4787
  • SEQ ID NO: 86 is the determined cDNA sequence for 1H-4796
  • SEQ ID NO: 87 is the determined cDNA sequence for 1I-4807
  • SEQ ID NO: 88 is the determined cDNA sequence for 1I-4810
  • SEQ ID NO: 89 is the determined cDNA sequence for 1I-4811
  • SEQ ID NO: 90 is the determined cDNA sequence for 1J-4876
  • SEQ ID NO: 91 is the determined cDNA sequence for 1K-4884
  • SEQ ID NO: 92 is the determined cDNA sequence for 1K-4896
  • SEQ ID NO: 93 is the determined cDNA sequence for 1G-4761
  • SEQ ID NO: 94 is the determined cDNA sequence for 1G-4762
  • SEQ ID NO: 95 is the determined cDNA sequence for 1H-4766
  • SEQ ID NO: 96 is the determined cDNA sequence for 1H-4770
  • SEQ ID NO: 97 is the determined cDNA sequence for 1H-4771
  • SEQ ID NO: 98 is the determined cDNA sequence for 1H-4772
  • SEQ ID NO: 99 is the determined cDNA sequence for 1D-4297
  • SEQ ID NO: 100 is the determined cDNA sequence for 1D-4309
  • SEQ ID NO: 101 is the determined cDNA sequence for 1D.1-4278
  • SEQ ID NO: 102 is the determined cDNA sequence for 1D-4288
  • SEQ ID NO: 103 is the determined cDNA sequence for 1D-4283
  • SEQ ID NO: 104 is the determined cDNA sequence for 1D-4304
  • SEQ ID NO: 105 is the determined cDNA sequence for 1D-4296
  • SEQ ID NO: 106 is the determined cDNA sequence for 1D-4280
  • SEQ ID NO: 107 is the determined full length cDNA sequence for F1-12 (also referred to as P504S)
  • SEQ ID NO: 108 is the amino acid sequence for F1-12
  • SEQ ID NO: 109 is the determined full length cDNA sequence for J1-17
  • SEQ ID NO: 110 is the determined full length cDNA sequence for L1-12 (also referred to as P501S)
  • SEQ ID NO: 111 is the determined full length cDNA sequence for N1-1862 (also referred to as P503S)
  • SEQ ID NO: 112 is the amino acid sequence for J1-17
  • SEQ ID NO: 113 is the amino acid sequence for L1-12 (also referred to as P501S)
  • SEQ ID NO: 114 is the amino acid sequence for N1-1862 (also referred to as P503S)
  • SEQ ID NO: 115 is the determined cDNA sequence for P89
  • SEQ ID NO: 116 is the determined cDNA sequence for P90
  • SEQ ID NO: 117 is the determined cDNA sequence for P92
  • SEQ ID NO: 118 is the determined cDNA sequence for P95
  • SEQ ID NO: 119 is the determined cDNA sequence for P98
  • SEQ ID NO: 120 is the determined cDNA sequence for P102
  • SEQ ID NO: 121 is the determined cDNA sequence for P110
  • SEQ ID NO: 122 is the determined cDNA sequence for P111
  • SEQ ID NO: 123 is the determined cDNA sequence for P114
  • SEQ ID NO: 124 is the determined cDNA sequence for P115
  • SEQ ID NO: 125 is the determined cDNA sequence for P116
  • SEQ ID NO: 126 is the determined cDNA sequence for P124
  • SEQ ID NO: 127 is the determined cDNA sequence for P126
  • SEQ ID NO: 128 is the determined cDNA sequence for P130
  • SEQ ID NO: 129 is the determined cDNA sequence for P133
  • SEQ ID NO: 130 is the determined cDNA sequence for P138
  • SEQ ID NO: 131 is the determined cDNA sequence for P143
  • SEQ ID NO: 132 is the determined cDNA sequence for P151
  • SEQ ID NO: 133 is the determined cDNA sequence for P156
  • SEQ ID NO: 134 is the determined cDNA sequence for P157
  • SEQ ID NO: 135 is the determined cDNA sequence for P166
  • SEQ ID NO: 136 is the determined cDNA sequence for P176
  • SEQ ID NO: 137 is the determined cDNA sequence for P178
  • SEQ ID NO: 138 is the determined cDNA sequence for P179
  • SEQ ID NO: 139 is the determined cDNA sequence for P185
  • SEQ ID NO: 140 is the determined cDNA sequence for P192
  • SEQ ID NO: 141 is the determined cDNA sequence for P201
  • SEQ ID NO: 142 is the determined cDNA sequence for P204
  • SEQ ID NO: 143 is the determined cDNA sequence for P208
  • SEQ ID NO: 144 is the determined cDNA sequence for P211
  • SEQ ID NO: 145 is the determined cDNA sequence for P213
  • SEQ ID NO: 146 is the determined cDNA sequence for P219
  • SEQ ID NO: 147 is the determined cDNA sequence for P237
  • SEQ ID NO: 148 is the determined cDNA sequence for P239
  • SEQ ID NO: 149 is the determined cDNA sequence for P248
  • SEQ ID NO: 150 is the determined cDNA sequence for P251
  • SEQ ID NO: 151 is the determined cDNA sequence for P255
  • SEQ ID NO: 152 is the determined cDNA sequence for P256
  • SEQ ID NO: 153 is the determined cDNA sequence for P259
  • SEQ ID NO: 154 is the determined cDNA sequence for P260
  • SEQ ID NO: 155 is the determined cDNA sequence for P263
  • SEQ ID NO: 156 is the determined cDNA sequence for P264
  • SEQ ID NO: 157 is the determined cDNA sequence for P266
  • SEQ ID NO: 158 is the determined cDNA sequence for P270
  • SEQ ID NO: 159 is the determined cDNA sequence for P272
  • SEQ ID NO: 160 is the determined cDNA sequence for P278
  • SEQ ID NO: 161 is the determined cDNA sequence for P105
  • SEQ ID NO: 162 is the determined cDNA sequence for P107
  • SEQ ID NO: 163 is the determined cDNA sequence for P137
  • SEQ ID NO: 164 is the determined cDNA sequence for P194
  • SEQ ID NO: 165 is the determined cDNA sequence for P195
  • SEQ ID NO: 166 is the determined cDNA sequence for P196
  • SEQ ID NO: 167 is the determined cDNA sequence for P220
  • SEQ ID NO: 168 is the determined cDNA sequence for P234
  • SEQ ID NO: 169 is the determined cDNA sequence for P235
  • SEQ ID NO: 170 is the determined cDNA sequence for P243
  • SEQ ID NO: 171 is the determined cDNA sequence for P703P-DE1
  • SEQ ID NO: 172 is the amino acid sequence for P703P-DE1
  • SEQ ID NO: 173 is the determined cDNA sequence for P703P-DE2
  • SEQ ID NO: 174 is the determined cDNA sequence for P703P-DE6
  • SEQ ID NO: 175 is the determined cDNA sequence for P703P-DE13
  • SEQ ID NO: 176 is the amino acid sequence for P703P-DE13
  • SEQ ID NO: 177 is the determined cDNA sequence for P703P-DE14
  • SEQ ID NO: 178 is the amino acid sequence for P703P-DE14
  • SEQ ID NO: 179 is the determined extended cDNA sequence for 1G-4736
  • SEQ ID NO: 180 is the determined extended cDNA sequence for 1G-4738
  • SEQ ID NO: 181 is the determined extended cDNA sequence for 1G-4741
  • SEQ ID NO: 182 is the determined extended cDNA sequence for 1G-4744
  • SEQ ID NO: 183 is the determined extended cDNA sequence for 1H-4774
  • SEQ ID NO: 184 is the determined extended cDNA sequence for 1H-4781
  • SEQ ID NO: 185 is the determined extended cDNA sequence for 1H-4785
  • SEQ ID NO: 186 is the determined extended cDNA sequence for 1H-4787
  • SEQ ID NO: 187 is the determined extended cDNA sequence for 1H-4796
  • SEQ ID NO: 188 is the determined extended cDNA sequence for 1I-4807
  • SEQ ID NO: 189 is the determined 3′ cDNA sequence for 1I-4810
  • SEQ ID NO: 190 is the determined 3′ cDNA sequence for 1I-4811
  • SEQ ID NO: 191 is the determined extended cDNA sequence for 1J-4876
  • SEQ ID NO: 192 is the determined extended cDNA sequence for 1K-4884
  • SEQ ID NO: 193 is the determined extended cDNA sequence for 1K-4896
  • SEQ ID NO: 194 is the determined extended cDNA sequence for 1G-4761
  • SEQ ID NO: 195 is the determined extended cDNA sequence for 1G-4762
  • SEQ ID NO: 196 is the determined extended cDNA sequence for 1H-4766
  • SEQ ID NO: 197 is the determined 3′ cDNA sequence for 1H-4770
  • SEQ ID NO: 198 is the determined 3′ cDNA sequence for 1H-4771
  • SEQ ID NO: 199 is the determined extended cDNA sequence for 1H-4772
  • SEQ ID NO: 200 is the determined extended cDNA sequence for 1D-4309
  • SEQ ID NO: 201 is the determined extended cDNA sequence for 1D.1-4278
  • SEQ ID NO: 202 is the determined extended cDNA sequence for 1D-4288
  • SEQ ID NO: 203 is the determined extended cDNA sequence for 1D-4283
  • SEQ ID NO: 204 is the determined extended cDNA sequence for 1D-4304
  • SEQ ID NO: 205 is the determined extended cDNA sequence for 1D-4296
  • SEQ ID NO: 206 is the determined extended cDNA sequence for 1D-4280
  • SEQ ID NO: 207 is the determined cDNA sequence for 10-d8fwd
  • SEQ ID NO: 208 is the determined cDNA sequence for 10-H10con
  • SEQ ID NO: 209 is the determined cDNA sequence for 11-C8rev
  • SEQ ID NO: 210 is the determined cDNA sequence for 7.6fwd
  • SEQ ID NO: 211 is the determined cDNA sequence for 7.g6rev
  • SEQ ID NO: 212 is the determined cDNA sequence for 8-b5fwd
  • SEQ ID NO: 213 is the determined cDNA sequence for 8-b5rev
  • SEQ ID NO: 214 is the determined cDNA sequence for 8-b6fwd
  • SEQ ID NO: 215 is the determined cDNA sequence for 8-b6 rev
  • SEQ ID NO: 216 is the determined cDNA sequence for 8-d4fwd
  • SEQ ID NO: 217 is the determined cDNA sequence for 8-d9rev
  • SEQ ID NO: 218 is the determined cDNA sequence for 8-g3fwd
  • SEQ ID NO: 219 is the determined cDNA sequence for 8-g3rev
  • SEQ ID NO: 220 is the determined cDNA sequence for 8-h 11rev
  • SEQ ID NO: 221 is the determined cDNA sequence for g-f12fwd
  • SEQ ID NO: 222 is the determined cDNA sequence for g-f3rev
  • SEQ ID NO: 223 is the determined cDNA sequence for P509S
  • SEQ ID NO: 224 is the determined cDNA sequence for P510S
  • SEQ ID NO: 225 is the determined cDNA sequence for P703DE5
  • SEQ ID NO: 226 is the determined cDNA sequence for 9-A11
  • SEQ ID NO: 227 is the determined cDNA sequence for 8-C6
  • SEQ ID NO: 228 is the determined cDNA sequence for 8-H7
  • SEQ ID NO: 229 is the determined cDNA sequence for JPTPN13
  • SEQ ID NO: 230 is the determined cDNA sequence for JPTPN14
  • SEQ ID NO: 231 is the determined cDNA sequence for JPTPN23
  • SEQ ID NO: 232 is the determined cDNA sequence for JPTPN24
  • SEQ ID NO: 233 is the determined cDNA sequence for JPTPN25
  • SEQ ID NO: 234 is the determined cDNA sequence for JPTPN30
  • SEQ ID NO: 235 is the determined cDNA sequence for JPTPN34
  • SEQ ID NO: 236 is the determined cDNA sequence for PTPN35
  • SEQ ID NO: 237 is the determined cDNA sequence for JPTPN36
  • SEQ ID NO: 238 is the determined cDNA sequence for JPTPN38
  • SEQ ID NO: 239 is the determined cDNA sequence for JPTPN39
  • SEQ ID NO: 240 is the determined cDNA sequence for JPTPN40
  • SEQ ID NO: 241 is the determined cDNA sequence for JPTPN41
  • SEQ ID NO: 242 is the determined cDNA sequence for JPTPN42
  • SEQ ID NO: 243 is the determined cDNA sequence for JPTPN45
  • SEQ ID NO: 244 is the determined cDNA sequence for JPTPN46
  • SEQ ID NO: 245 is the determined cDNA sequence for JPTPN51
  • SEQ ID NO: 246 is the determined cDNA sequence for JPTPN56
  • SEQ ID NO: 247 is the determined cDNA sequence for PTPN64
  • SEQ ID NO: 248 is the determined cDNA sequence for JPTPN65
  • SEQ ID NO: 249 is the determined cDNA sequence for JPTPN67
  • SEQ ID NO: 250 is the determined cDNA sequence for JPTPN76
  • SEQ ID NO: 251 is the determined cDNA sequence for JPTPN84
  • SEQ ID NO: 252 is the determined cDNA sequence for JPTPN85
  • SEQ ID NO: 253 is the determined cDNA sequence for JPTPN86
  • SEQ ID NO: 254 is the determined cDNA sequence for JPTPN87
  • SEQ ID NO: 255 is the determined cDNA sequence for JPTPN88
  • SEQ ID NO: 256 is the determined cDNA sequence for JP1F1
  • SEQ ID NO: 257 is the determined cDNA sequence for JP1F2
  • SEQ ID NO: 258 is the determined cDNA sequence for JP1C2
  • SEQ ID NO: 259 is the determined cDNA sequence for JP1B1
  • SEQ ID NO: 260 is the determined cDNA sequence for JP1B2
  • SEQ ID NO: 261 is the determined cDNA sequence for JP1D3
  • SEQ ID NO: 262 is the determined cDNA sequence for JP1A4
  • SEQ ID NO: 263 is the determined cDNA sequence for JP1F5
  • SEQ ID NO: 264 is the determined cDNA sequence for JP1E6
  • SEQ ID NO: 265 is the determined cDNA sequence for JP1D6
  • SEQ ID NO: 266 is the determined cDNA sequence for JP1B5
  • SEQ ID NO: 267 is the determined cDNA sequence for JP1A6
  • SEQ ID NO: 268 is the determined cDNA sequence for JP1E8
  • SEQ ID NO: 269 is the determined cDNA sequence for JP1D7
  • SEQ ID NO: 270 is the determined cDNA sequence for JP1D9
  • SEQ ID NO: 271 is the determined cDNA sequence for JP1C10
  • SEQ ID NO: 272 is the determined cDNA sequence for JP1A9
  • SEQ ID NO: 273 is the determined cDNA sequence for JP1F12
  • SEQ ID NO: 274 is the determined cDNA sequence for JP1E12
  • SEQ ID NO: 275 is the determined cDNA sequence for JP1D11
  • SEQ ID NO: 276 is the determined cDNA sequence for JP1C11
  • SEQ ID NO: 277 is the determined cDNA sequence for JP1C12
  • SEQ ID NO: 278 is the determined cDNA sequence for JP1B12
  • SEQ ID NO: 279 is the determined cDNA sequence for JP1A12
  • SEQ ID NO: 280 is the determined cDNA sequence for JP8G2
  • SEQ ID NO: 281 is the determined cDNA sequence for JP8H1
  • SEQ ID NO: 282 is the determined cDNA sequence for JP8H2
  • SEQ ID NO: 283 is the determined cDNA sequence for JP8A3
  • SEQ ID NO: 284 is the determined cDNA sequence for JP8A4
  • SEQ ID NO: 285 is the determined cDNA sequence for JP8C3
  • SEQ ID NO: 286 is the determined cDNA sequence for JP8G4
  • SEQ ID NO: 287 is the determined cDNA sequence for JP8B6
  • SEQ ID NO: 288 is the determined cDNA sequence for JP8D6
  • SEQ ID NO: 289 is the determined cDNA sequence for JP8F5
  • SEQ ID NO: 290 is the determined cDNA sequence for JP8A8
  • SEQ ID NO: 291 is the determined cDNA sequence for JP8C7
  • SEQ ID NO: 292 is the determined cDNA sequence for JP8D7
  • SEQ ID NO: 293 is the determined cDNA sequence for P8D8
  • SEQ ID NO: 294 is the determined cDNA sequence for JP8E7
  • SEQ ID NO: 295 is the determined cDNA sequence for JP8F8
  • SEQ ID NO: 296 is the determined cDNA sequence for JP8G8
  • SEQ ID NO: 297 is the determined cDNA sequence for JP8B10
  • SEQ ID NO: 298 is the determined cDNA sequence for JP8C10
  • SEQ ID NO: 299 is the determined cDNA sequence for JP8E9
  • SEQ ID NO: 300 is the determined cDNA sequence for JP8E10
  • SEQ ID NO: 301 is the determined cDNA sequence for JP8F9
  • SEQ ID NO: 302 is the determined cDNA sequence for JP8H9
  • SEQ ID NO: 303 is the determined cDNA sequence for JP8C12
  • SEQ ID NO: 304 is the determined cDNA sequence for JP8E 11
  • SEQ ID NO: 305 is the determined cDNA sequence for JP8E12
  • SEQ ID NO: 306 is the amino acid sequence for the peptide PS2#12
  • SEQ ID NO: 307 is the determined cDNA sequence for P711P
  • SEQ ID NO: 308 is the determined cDNA sequence for P712P
  • SEQ ID NO: 309 is the determined cDNA sequence for CLONE23
  • SEQ ID NO: 310 is the determined cDNA sequence for P774P
  • SEQ ID NO: 311 is the determined cDNA sequence for P775P
  • SEQ ID NO: 312 is the determined cDNA sequence for P715P
  • SEQ ID NO: 313 is the determined cDNA sequence for P710P
  • SEQ ID NO: 314 is the determined cDNA sequence for P767P
  • SEQ ID NO: 315 is the determined cDNA sequence for P768P
  • SEQ ID NO: 316-325 are the determined cDNA sequences of previously isolated genes
  • SEQ ID NO: 326 is the determined cDNA sequence for P703PDE5
  • SEQ ID NO: 327 is the amino acid sequence for P703PDE5
  • SEQ ID NO: 328 is the determined cDNA sequence for P703P6.26
  • SEQ ID NO: 329 is the amino acid sequence for P703P6.26
  • SEQ ID NO: 330 is the determined cDNA sequence for P703PX-23
  • SEQ ID NO: 331 is the amino acid sequence for P703PX-23
  • SEQ ID NO: 332 is the determined full length cDNA sequence for P509S
  • SEQ ID NO: 333 is the determined extended cDNA sequence for P707P (also referred to as 11-C9)
  • SEQ ID NO: 334 is the determined cDNA sequence for P714P
  • SEQ ID NO: 335 is the determined cDNA sequence for P705P (also referred to as 9-F3)
  • SEQ ID NO: 336 is the amino acid sequence for P705P
  • SEQ ID NO: 337 is the amino acid sequence of the peptide P1S#10
  • SEQ ID NO: 338 is the amino acid sequence of the peptide p5
  • SEQ ID NO: 339 is the amino acid sequence of P509S
  • SEQ ID NO: 340 is the determined cDNA sequence for P778P
  • SEQ ID NO: 341 is the determined cDNA sequence for P786P
  • SEQ ID NO: 342 is the determined cDNA sequence for P789P
  • SEQ ID NO: 343 is the determined cDNA sequence for a clone showing homology to Homo sapiens MM46 mRNA
  • SEQ ID NO: 344 is the determined cDNA sequence for a clone showing homology to Homo sapiens TNF-alpha stimulated ABC protein (ABC50) mRNA
  • SEQ ID NO: 345 is the determined cDNA sequence for a clone showing homology to Homo sapiens mRNA for E-cadherin
  • SEQ ID NO: 346 is the determined cDNA sequence for a clone showing homology to Human nuclear-encoded mitochondrial serine hydroxymethyltransferase (SHMT)
  • SEQ ID NO: 347 is the determined cDNA sequence for a clone showing homology to Homo sapiens natural resistance-associated macrophage protein2 (NRAMP2)
  • SEQ ID NO: 348 is the determined cDNA sequence for a clone showing homology to Homo sapiens phosphoglucomutase-related protein (PGMRP)
  • SEQ ID NO: 349 is the determined cDNA sequence for a clone showing homology to Human mRNA for proteosome subunit p40
  • SEQ ID NO: 350 is the determined cDNA sequence for P777P
  • SEQ ID NO: 351 is the determined cDNA sequence for P779P
  • SEQ ID NO: 352 is the determined cDNA sequence for P790P
  • SEQ ID NO: 353 is the determined cDNA sequence for P784P
  • SEQ ID NO: 354 is the determined cDNA sequence for P776P
  • SEQ ID NO: 355 is the determined cDNA sequence for P780P
  • SEQ ID NO: 356 is the determined cDNA sequence for P544S
  • SEQ ID NO: 357 is the determined cDNA sequence for P745S
  • SEQ ID NO: 358 is the determined cDNA sequence for P782P
  • SEQ ID NO: 359 is the determined cDNA sequence for P783P
  • SEQ ID NO: 360 is the determined cDNA sequence for unknown 17984
  • SEQ ID NO: 361 is the determined cDNA sequence for P787P
  • SEQ ID NO: 362 is the determined cDNA sequence for P788P
  • SEQ ID NO: 363 is the determined cDNA sequence for unknown 17994
  • SEQ ID NO: 364 is the determined cDNA sequence for P781P
  • SEQ ID NO: 365 is the determined cDNA sequence for P785P
  • SEQ ID NO: 366-375 are the determined cDNA sequences for splice variants of B305D.
  • SEQ ID NO: 376 is the amino acid sequence encoded by the sequence of SEQ ID NO: 366.
  • SEQ ID NO: 377 is the amino acid sequence encoded by the sequence of SEQ ID NO: 372.
  • SEQ ID NO: 378 is the amino acid sequence encoded by the sequence of SEQ ID NO: 373.
  • SEQ ID NO: 379 is the amino acid sequence encoded by the sequence of SEQ ID NO: 374.
  • SEQ ID NO: 380 is the amino acid sequence encoded by the sequence of SEQ ID NO: 375.
  • SEQ ID NO: 381 is the determined cDNA sequence for B716P.
  • SEQ ID NO: 382 is the determined full-length cDNA sequence for P711P.
  • SEQ ID NO: 383 is the amino acid sequence for P711P.
  • SEQ ID NO: 384 is the cDNA sequence for P1000C.
  • SEQ ID NO: 385 is the cDNA sequence for CGI-82.
  • SEQ ID NO: 386 is the cDNA sequence for 23320.
  • SEQ ID NO: 387 is the cDNA sequence for CGI-69.
  • SEQ ID NO: 388 is the cDNA sequence for L-iditol-2-dehydrogenase.
  • SEQ ID NO: 389 is the cDNA sequence for 23379.
  • SEQ ID NO: 390 is the cDNA sequence for 23381.
  • SEQ ID NO: 391 is the cDNA sequence for KIAA0122.
  • SEQ ID NO: 392 is the cDNA sequence for clone 23399 (also known as P554S).
  • SEQ ID NO: 393 is the cDNA sequence for a previously identified gene.
  • SEQ ID NO: 394 is the cDNA sequence for HCLBP.
  • SEQ ID NO: 395 is the cDNA sequence for transglutaminase.
  • SEQ ID NO: 396 is the cDNA sequence for a previously identified gene.
  • SEQ ID NO: 397 is the cDNA sequence for PAP.
  • SEQ ID NO: 398 is the cDNA sequence for Ets transcription factor PDEF.
  • SEQ ID NO: 399 is the cDNA sequence for hTGR.
  • SEQ ID NO: 400 is the cDNA sequence for KIAA0295.
  • SEQ ID NO: 401 is the cDNA sequence for 22545.
  • SEQ ID NO: 402 is the cDNA sequence for 22547.
  • SEQ ID NO: 403 is the cDNA sequence for 22548.
  • SEQ ID NO: 404 is the cDNA sequence for 22550.
  • SEQ ID NO: 405 is the cDNA sequence for 22551.
  • SEQ ID NO: 406 is the cDNA sequence for 22552.
  • SEQ ID NO: 407 is the cDNA sequence for 22553 (also known as P1020C).
  • SEQ ID NO: 408 is the cDNA sequence for 22558.
  • SEQ ID NO: 409 is the cDNA sequence for 22562.
  • SEQ ID NO: 410 is the cDNA sequence for 22565.
  • SEQ ID NO: 411 is the cDNA sequence for 22567.
  • SEQ ID NO: 412 is the cDNA sequence for 22568.
  • SEQ ID NO: 413 is the cDNA sequence for 22570.
  • SEQ ID NO: 414 is the cDNA sequence for 22571.
  • SEQ ID NO: 415 is the cDNA sequence for 22572.
  • SEQ ID NO: 416 is the cDNA sequence for 22573.
  • SEQ ID NO: 417 is the cDNA sequence for 22573.
  • SEQ ID NO: 418 is the cDNA sequence for 22575.
  • SEQ ID NO: 419 is the cDNA sequence for 22580.
  • SEQ ID NO: 420 is the cDNA sequence for 22581.
  • SEQ ID NO: 421 is the cDNA sequence for 22582.
  • SEQ ID NO: 422 is the cDNA sequence for 22583.
  • SEQ ID NO: 423 is the cDNA sequence for 22584.
  • SEQ ID NO: 424 is the cDNA sequence for 22585.
  • SEQ ID NO: 425 is the cDNA sequence for 22586.
  • SEQ ID NO: 426 is the cDNA sequence for 22587.
  • SEQ ID NO: 427 is the cDNA sequence for 22588.
  • SEQ ID NO: 428 is the cDNA sequence for 22589.
  • SEQ ID NO: 429 is the cDNA sequence for 22590.
  • SEQ ID NO: 430 is the cDNA sequence for 22591.
  • SEQ ID NO: 431 is the cDNA sequence for 22592.
  • SEQ ID NO: 432 is the cDNA sequence for 22593.
  • SEQ ID NO: 433 is the cDNA sequence for 22594.
  • SEQ ID NO: 434 is the cDNA sequence for 22595.
  • SEQ ID NO: 435 is the cDNA sequence for 22596.
  • SEQ ID NO: 436 is the cDNA sequence for 22847.
  • SEQ ID NO: 437 is the cDNA sequence for 22848.
  • SEQ ID NO: 438 is the cDNA sequence for 22849.
  • SEQ ID NO: 439 is the cDNA sequence for 22851.
  • SEQ ID NO: 440 is the cDNA sequence for 22852.
  • SEQ ID NO: 441 is the cDNA sequence for 22853.
  • SEQ ID NO: 442 is the cDNA sequence for 22854.
  • SEQ ID NO: 443 is the cDNA sequence for 22855.
  • SEQ ID NO: 444 is the cDNA sequence for 22856.
  • SEQ ID NO: 445 is the cDNA sequence for 22857.
  • SEQ ID NO: 446 is the cDNA sequence for 23601.
  • SEQ ID NO: 447 is the cDNA sequence for 23602.
  • SEQ ID NO: 448 is the cDNA sequence for 23605.
  • SEQ ID NO: 449 is the cDNA sequence for 23606.
  • SEQ ID NO: 450 is the cDNA sequence for 23612.
  • SEQ ID NO: 451 is the cDNA sequence for 23614.
  • SEQ ID NO: 452 is the cDNA sequence for 23618.
  • SEQ ID NO: 453 is the cDNA sequence for 23622.
  • SEQ ID NO: 454 is the cDNA sequence for folate hydrolase.
  • SEQ ID NO: 455 is the cDNA sequence for LIM protein.
  • SEQ ID NO: 456 is the cDNA sequence for a known gene.
  • SEQ ID NO: 457 is the cDNA sequence for a known gene.
  • SEQ ID NO: 458 is the cDNA sequence for a previously identified gene.
  • SEQ ID NO: 459 is the cDNA sequence for 23045.
  • SEQ ID NO: 460 is the cDNA sequence for 23032.
  • SEQ ID NO: 461 is the cDNA sequence for clone 23054.
  • SEQ ID NO: 462-467 are cDNA sequences for known genes.
  • SEQ ID NO: 468-471 are cDNA sequences for P710P.
  • SEQ ID NO: 472 is a cDNA sequence for P1001C.
  • SEQ ID NO: 473 is the determined cDNA sequence for a first splice variant of P775P (referred to as 27505).
  • SEQ ID NO: 474 is the determined cDNA sequence for a second splice variant of P775P (referred to as 19947).
  • SEQ ID NO: 475 is the determined cDNA sequence for a third splice variant of P775P (referred to as 19941).
  • SEQ ID NO: 476 is the determined cDNA sequence for a fourth splice variant of P775P (referred to as 19937).
  • SEQ ID NO: 477 is a first amino acid sequence encoded by the sequence of SEQ ID NO: 474.
  • SEQ ID NO: 478 is a second amino acid sequence encoded by the sequence of SEQ ID NO: 474.
  • SEQ ID NO: 479 is the amino acid sequence encoded by the sequence of SEQ ID NO: 475.
  • SEQ ID NO: 480 is a first amino acid sequence encoded by the sequence of SEQ ID NO: 473.
  • SEQ ID NO: 481 is a second amino acid sequence encoded by the sequence of SEQ ID NO: 473.
  • SEQ ID NO: 482 is a third amino acid sequence encoded by the sequence of SEQ ID NO: 473.
  • SEQ ID NO: 483 is a fourth amino acid sequence encoded by the sequence of SEQ ID NO: 473.
  • SEQ ID NO: 484 is the first 30 amino acids of the M. tuberculosis antigen Ra12.
  • SEQ ID NO: 485 is the PCR primer AW025.
  • SEQ ID NO: 486 is the PCR primer AW003.
  • SEQ ID NO: 487 is the PCR primer AW027.
  • SEQ ID NO: 488 is the PCR primer AW026.
  • SEQ ID NO: 489-501 are peptides employed in epitope mapping studies.
  • SEQ ID NO: 502 is the determined cDNA sequence of the complementarity determining region for the anti-P503S monoclonal antibody 20D4.
  • SEQ ID NO: 503 is the determined cDNA sequence of the complementarity determining region for the anti-P503S monoclonal antibody JA1.
  • SEQ ID NO: 504 & 505 are peptides employed in epitope mapping studies.
  • SEQ ID NO: 506 is the determined cDNA sequence of the complementarity determining region for the anti-P703P monoclonal antibody 8H2.
  • SEQ ID NO: 507 is the determined cDNA sequence of the complementarity determining region for the anti-P703P monoclonal antibody 7H8.
  • SEQ ID NO: 508 is the determined cDNA sequence of the complementarity determining region for the anti-P703P monoclonal antibody 2D4.
  • SEQ ID NO: 509-522 are peptides employed in epitope mapping studies.
  • SEQ ID NO: 523 is a mature form of P703P used to raise antibodies against P703P.
  • SEQ ID NO: 524 is the putative full-length cDNA sequence of P703P.
  • SEQ ID NO: 525 is the amino acid sequence encoded by SEQ ID NO: 524.
  • SEQ ID NO: 526 is the full-length cDNA sequence for P790P.
  • SEQ ID NO: 527 is the amino acid sequence for P790P.
  • SEQ ID NO: 528 & 529 are PCR primers.
  • SEQ ID NO: 530 is the cDNA sequence of a splice variant of SEQ ID NO: 366.
  • SEQ ID NO: 531 is the cDNA sequence of the open reading frame of SEQ ID NO: 530.
  • SEQ ID NO: 532 is the amino acid encoded by the sequence of SEQ ID NO: 531.
  • SEQ ID NO: 533 is the DNA sequence of a putative ORF of P775P.
  • SEQ ID NO: 534 is the amino acid sequence encoded by SEQ ID NO: 533.
  • SEQ ID NO: 535 is a first full-length cDNA sequence for P510S.
  • SEQ ID NO: 536 is a second full-length cDNA sequence for P510S.
  • SEQ ID NO: 537 is the amino acid sequence encoded by SEQ ID NO: 535.
  • SEQ ID NO: 538 is the amino acid sequence encoded by SEQ ID NO: 536.
  • SEQ ID NO: 539 is the peptide P501S-370.
  • SEQ ID NO: 540 is the peptide P501S-376.
  • SEQ ID NO: 541-551 are epitopes of P501S.
  • SEQ ID NO: 552 is an extended cDNA sequence for P712P.
  • SEQ ID NO: 553-568 are the amino acid sequences encoded by open reading frames within SEQ ID NO: 552.
  • SEQ ID NO: 569 is an extended cDNA sequence for P776P.
  • SEQ ID NO: 570 is the determined cDNA sequence for a splice variant of P776P referred to as contig 6.
  • SEQ ID NO: 571 is the determined cDNA sequence for a splice variant of P776P referred to as contig 7.
  • SEQ ID NO: 572 is the determined cDNA sequence for a splice variant of P776P referred to as contig 14.
  • SEQ ID NO: 573 is the amino acid sequence encoded by a first ORF of SEQ ID NO: 570.
  • SEQ ID NO: 574 is the amino acid sequence encoded by a second ORF of SEQ ID NO: 570.
  • SEQ ID NO: 575 is the amino acid sequence encoded by a ORF of SEQ ID NO: 571.
  • SEQ ID NO: 576-586 are amino acid sequences encoded by ORFs of SEQ ID NO: 569.
  • SEQ ID NO: 587 is a DNA consensus sequence of the sequences of P767P and P777P.
  • SEQ ID NO: 588-590 are amino acid sequences encoded by ORFs of SEQ ID NO: 587.
  • SEQ ID NO: 591 is an extended cDNA sequence for P1020C.
  • SEQ ID NO: 592 is the amino acid sequence encoded by the sequence of SEQ ID NO: P1020C.
  • SEQ ID NO: 593 is a splice variant of P775P referred to as 50748.
  • SEQ ID NO: 594 is a splice variant of P775P referred to as 50717.
  • SEQ ID NO: 595 is a splice variant of P775P referred to as 45985.
  • SEQ ID NO: 596 is a splice variant of P775P referred to as 38769.
  • SEQ ID NO: 597 is a splice variant of P775P referred to as 37922.
  • SEQ ID NO: 598 is a splice variant of P510S referred to as 49274.
  • SEQ ID NO: 599 is a splice variant of P510S referred to as 39487.
  • SEQ ID NO: 600 is a splice variant of P504S referred to as 5167.16.
  • SEQ ID NO: 601 is a splice variant of P504S referred to as 5167.1.
  • SEQ ID NO: 602 is a splice variant of P504S referred to as 5163.46.
  • SEQ ID NO: 603 is a splice variant of P504S referred to as 5163.42.
  • SEQ ID NO: 604 is a splice variant of P504S referred to as 5163.34.
  • SEQ ID NO: 605 is a splice variant of P504S referred to as 5163.17.
  • SEQ ID NO: 606 is a splice variant of P501S referred to as 10640.
  • SEQ ID NO: 607-615 are the sequences of PCR primers.
  • SEQ ID NO: 616 is the determined cDNA sequence of a fusion of P703P and PSA.
  • SEQ ID NO: 617 is the amino acid sequence of the fusion of P703P and PSA.
  • SEQ ID NO: 618-689 are determined cDNA sequences of prostate-specific clones.
  • SEQ ID NO: 690 is the cDNA sequence of the gene DD3.
  • SEQ ID NO: 691-697 are determined cDNA sequences of prostate-specific clones.
  • SEQ ID NO: 698 is an extended cDNA sequence for P714P.
  • SEQ ID NO: 699-701 are the cDNA sequences for splice variants of P704P.
  • SEQ ID NO: 702 is the cDNA sequence of a spliced variant of P553S referred to as P553S-14.
  • SEQ ID NO: 703 is the cDNA sequence of a spliced variant of P553S referred to as P553S-12.
  • SEQ ID NO: 704 is the cDNA sequence of a spliced variant of P553S referred to as P553S-10.
  • SEQ ID NO: 705 is the cDNA sequence of a spliced variant of P553S referred to as P553S-6.
  • SEQ ID NO: 706 is the amino acid sequence encoded by SEQ ID NO: 705.
  • SEQ ID NO: 707 is the amino acid sequence encoded by SEQ ID NO: 702
  • SEQ ID NO: 708 is a second amino acid sequence encoded by SEQ ID NO: 702.
  • SEQ ID NO: 709-772 are determined cDNA sequences of prostate-specific clones.
  • SEQ ID NO: 773 is a first full-length cDNA sequence for prostate-specific transglutaminase gene (also referred to herein as P558S).
  • SEQ ID NO: 774 is a second full-length cDNA sequence for prostate-specific transglutaminase gene.
  • SEQ ID NO: 775 is the amino acid sequence encoded by the sequence of SEQ ID NO: 773.
  • SEQ ID NO: 776 is the amino acid sequence encoded by the sequence of SEQ ID NO: 774.
  • SEQ ID NO: 777 is the full-length cDNA sequence for P788P.
  • SEQ ID NO: 778 is the amino acid sequence encoded by SEQ ID NO: 777.
  • SEQ ID NO: 779 is the determined cDNA sequence for a polymorphic variant of P788P.
  • SEQ ID NO: 780 is the amino acid sequence encoded by SEQ ID NO: 779.
  • SEQ ID NO: 781 is the amino acid sequence of peptide 4 from P703P.
  • SEQ ID NO: 782 is the cDNA sequence that encodes peptide 4 from P703P.
  • SEQ ID NO: 783-798 are the cDNA sequence encoding epitopes of P703P.
  • SEQ ID NO: 799-814 are the amino acid sequences of epitopes of P703P.
  • SEQ ID NO: 815 and 816 are PCR primers.
  • SEQ ID NO: 817 is the cDNA sequence encoding an N-terminal portion of P788P expressed in E. coli.
  • SEQ ID NO: 818 is the amino acid sequence of the N-terminal portion of P788P expressed in E. coli.
  • SEQ ID NO: 819 is the amino acid sequence of the M. tuberculosis antigen Ra12.
  • SEQ ID NO: 820 and 821 are PCR primers.
  • SEQ ID NO: 822 is the cDNA sequence for the Ra12-P510S-C construct.
  • SEQ ID NO: 823 is the cDNA sequence for the P510S-C construct.
  • SEQ ID NO: 824 is the cDNA sequence for the P510S-E3 construct.
  • SEQ ID NO: 825 is the amino acid sequence for the Ra12-P510S-C construct.
  • SEQ ID NO: 826 is the amino acid sequence for the P510S-C construct.
  • SEQ ID NO: 827 is the amino acid sequence for the P510S-E3 construct.
  • SEQ ID NO: 828-833 are PCR primers.
  • SEQ ID NO: 834 is the cDNA sequence of the construct Ra12-P775P-ORF3.
  • SEQ ID NO: 835 is the amino acid sequence of the construct Ra12-P775P-ORF3.
  • SEQ ID NO: 836 and 837 are PCR primers.
  • SEQ ID NO: 838 is the determined amino acid sequence for a P703P His tag fusion protein.
  • SEQ ID NO: 839 is the determined cDNA sequence for a P703P His tag fusion protein.
  • SEQ ID NO: 840 and 841 are PCR primers.
  • SEQ ID NO: 842 is the determined amino acid sequence for a P705P His tag fusion protein.
  • SEQ ID NO: 843 is the determined cDNA sequence for a P705P His tag fusion protein.
  • SEQ ID NO: 844 and 845 are PCR primers.
  • SEQ ID NO: 846 is the determined amino acid sequence for a P711P His tag fusion protein.
  • SEQ ID NO: 847 is the determined cDNA sequence for a P711P His tag fusion protein.
  • SEQ ID NO: 848 is the amino acid sequence of the M. tuberculosis antigen Ra12.
  • SEQ ID NO: 849 and 850 are PCR primers.
  • SEQ ID NO: 851 is the determined cDNA sequence for the construct Ra12-P501S-E2.
  • SEQ ID NO: 852 is the determined amino acid sequence for the construct Ra12-P501S-E2.
  • SEQ ID NO: 853 is the amino acid sequence for an epitope of P501S.
  • SEQ ID NO: 854 is the DNA sequence encoding SEQ ID NO: 853.
  • SEQ ID NO: 855 is the amino acid sequence for an epitope of P501S.
  • SEQ ID NO: 856 is the DNA sequence encoding SEQ ID NO: 855.
  • SEQ ID NO: 857 is a peptide employed in epitope mapping studies.
  • SEQ ID NO: 858 is the amino acid sequence for an epitope of P501S.
  • SEQ ID NO: 859 is the DNA sequence encoding SEQ ID NO: 858.
  • SEQ ID NO: 860-862 are the amino acid sequences for CD4 epitopes of P501S.
  • SEQ ID NO: 863-865 are the DNA sequences encoding the sequences of SEQ ID NO: 860-862.
  • SEQ ID NO: 866-877 are the amino acid sequences for putative CTL epitopes of P703P.
  • SEQ ID NO: 878 is the full-length cDNA sequence for P789P.
  • SEQ ID NO: 879 is the amino acid sequence encoded by SEQ ID NO: 878.
  • SEQ ID NO: 880 is the determined full-length cDNA sequence for the splice variant of P776P referred to as contig 6.
  • SEQ ID NO: 881-882 are determined full-length cDNA sequences for the splice variant of P776P referred to as contig 7.
  • SEQ ID NO: 883-887 are amino acid sequences encoded by SEQ ID NO: 880.
  • SEQ ID NO: 888-893 are amino acid sequences encoded by the splice variant of P776P referred to as contig 7.
  • SEQ ID NO: 894 is the full-length cDNA sequence for human transmembrane protease serine 2.
  • SEQ ID NO: 895 is the amino acid sequence encoded by SEQ ID NO: 894.
  • SEQ ID NO: 896 is the cDNA sequence encoding the first 209 amino acids of human transmembrane protease serine 2.
  • SEQ ID NO: 897 is the first 209 amino acids of human transmembrane protease serine 2.
  • SEQ ID NO: 898 is the amino acid sequence of peptide 296-322 of P501S.
  • SEQ ID NO: 899-902 are PCR primers.
  • SEQ ID NO: 903 is the determined cDNA sequence of the Vb chain of a T cell receptor for the P501S-specific T cell clone 4E5.
  • SEQ ID NO: 904 is the determined cDNA sequence of the Va chain of a T cell receptor for the P501S-specific T cell clone 4E5.
  • SEQ ID NO: 905 is the amino acid sequence encoded by SEQ ID NO 903.
  • SEQ ID NO: 906 is the amino acid sequence encoded by SEQ ID NO 904.
  • SEQ ID NO: 907 is the full-length open reading frame for P768P including stop codon.
  • SEQ ID NO: 908 is the full-length open reading frame for P768P without stop codon.
  • SEQ ID NO: 909 is the amino acid sequence encoded by SEQ ID NO: 908.
  • SEQ ID NO: 910-915 are the amino acid sequences for predicted domains of P768P.
  • SEQ ID NO: 916 is the full-length cDNA sequence of P835P.
  • SEQ ID NO: 917 is the cDNA sequence of the previously identified clone FLJ13581.
  • SEQ ID NO: 918 is the cDNA sequence of the open reading frame for P835P with stop codon.
  • SEQ ID NO: 919 is the cDNA sequence of the open reading frame for P835P without stop codon.
  • SEQ ID NO: 920 is the full-length amino acid sequence for P835P.
  • SEQ ID NO: 921-928 are the amino acid sequences of extracellular and intracellular domains of P835P.
  • SEQ ID NO: 929 is the full-length cDNA sequence for P1000C.
  • SEQ ID NO: 930 is the cDNA sequence of the open reading frame for P1000C, including stop codon.
  • SEQ ID NO: 931 is the cDNA sequence of the open reading frame for P1000C, without stop codon.
  • SEQ ID NO: 932 is the full-length amino acid sequence for P1000C.
  • SEQ ID NO: 933 is amino acids 1-100 of SEQ ID NO: 932.
  • SEQ ID NO: 934 is amino acids 100-492 of SEQ ID NO: 932.
  • SEQ ID NO: 935-937 are PCR primers.
  • SEQ ID NO: 938 is the cDNA sequence of the expressed full-length P767P coding region.
  • SEQ ID NO: 939 is the cDNA sequence of an expressed truncated P767P coding region.
  • SEQ ID NO: 940 is the amino acid sequence encoded by SEQ ID NO: 939.
  • SEQ ID NO: 941 is the amino acid sequence encoded by SEQ ID NO: 938.
  • SEQ ID NO: 942 is the DNA sequence of a CD4 epitope of P703P.
  • SEQ ID NO: 943 is the amino acid sequence of a CD4 epitope of P703P.
  • SEQ ID NO: 944 and 945 are the cDNA sequences of two alternative splice forms of P780P.
  • SEQ ID NO: 946 and 947 are the amino acid sequences encoded by
  • SEQ ID NO: 948 is a corrected cDNA sequence for P705P.
  • SEQ ID NO: 949-956 are the amino acid sequences of P790P peptides.
  • SEQ ID NO: 957-966 are the amino acid sequences of P775P peptides.
  • SEQ ID NO: 967 is an extended cDNA sequence for P554S.
  • SEQ ID NO: 968 is the amino acid sequence for P554S.
  • SEQ ID NO: 969-976 are the cDNA sequences encoding epitopes of P501S.
  • SEQ ID NO: 977-984 are the amino acid sequences of epitopes of P501S.
  • SEQ ID NO: 985-987 are amino acid sequences of peptides of P501S.
  • SEQ ID NO: 988-990 are amino acid sequences of peptides of P703P.
  • SEQ ID NO: 991 is the cDNA encoding a CD4+ T cell epitope of P703P.
  • SEQ ID NO: 992 is the amino acid sequence of a CD4+ T cell epitope of P703P (encoded by SEQ ID NO: 991).
  • SEQ ID NO: 993 represents the cDNA sequence for P706P clone 8-B6 that includes P3.
  • SEQ ID NO: 994 represents the cDNA sequence for P706P clone 8-B6 that includes P4.
  • SEQ ID NO: 995 represents the cDNA sequence for P706Pclone 8B6.P4 contig.
  • SEQ ID NO: 996 represents the cDNA sequence for P706P ESTs 1386-1902.
  • SEQ ID NO: 997 represents the cDNA sequence for P706P ESTs 4927-6088.
  • SEQ ID NO: 998 represents the cDNA sequence for P713P clone PT4410A4 2.
  • SEQ ID NO: 999-1002 represent the four exons encoding the prostatic secretory protein (PSP).
  • SEQ ID NO: 1003 represents the full length amino acid sequence for PSP.
  • SEQ ID NO: 1004 represents an extended cDNA sequence for clone P1E.
  • SEQ ID NO: 1005 represents the amino acid sequence of an open reading frame encoded by SEQ ID NO: 1004.
  • SEQ ID NO: 1006 represents the DNA sequence of the coding region of the expression construct P510.seq.
  • SEQ ID NO: 1007 represents the DNA sequence of coding region of the expression construct MAPS-P510 S.seq.
  • SEQ ID NO: 1008 represents the protein sequence encoded by the DNA sequence of SEQ ID NO: 1007.
  • SEQ ID NO: 1009 represents the protein sequence encoded by the DNA sequence of SEQ ID NO: 1006.
  • SEQ ID NO: 1010 represents the DNA sequence of the coding region for a Trx-P501S fusion construct.
  • SEQ ID NO: 1011 represents the amino acid sequence for a Trx-P501S fusion protein that is encoded by the DNA sequence of SEQ ID NO: 1010.
  • SEQ ID NO: 1012 represents the amino acid sequence for a minimal P501S epitope recognized by clone 2H2-1A12.
  • SEQ ID NO: 1013 represents the DNA sequence for a minimal P501S epitope recognized by clone 2H2-1A12.
  • SEQ ID NO: 1014 corresponds to the primer sequence for the forward primer hPAPF1.
  • SEQ ID NO: 1015 corresponds to the primer sequence for the reverse primer hPAPRV1.
  • SEQ ID NO: 1016 corresponds to the primer sequence for the forward primer FOPP2F1.
  • SEQ ID NO: 1017 corresponds to the primer sequence for the reverse primer FOPPF1.
  • SEQ ID NO: 1018 corresponds to the primer sequence for the forward primer FOPP2RV1.
  • SEQ ID NO: 1019 sets forth a DNA sequence for a fusion of FOPP and hPAP, referred to as FOPP2.
  • SEQ ID NO: 1020 sets forth an amino acid sequence for a fusion of FOPP and hPAP, referred to as FOPP2.
  • SEQ ID NO: 1021 sets forth a DNA sequence for a P501S minimal CD8+ T cell epitope recognized by clone 1H1-1A6.
  • SEQ ID NO: 1022 sets forth an amino acid sequence for a P501S minimal CD8+ T cell epitope recognized by clone 1H1-1A6.
  • SEQ ID NO: 1023 sets forth the sequence for the primer PDM-930.
  • SEQ ID NO: 1024 sets forth the sequence for the primer PDM-165.
  • SEQ ID NO: 1025 sets forth the sequence for the primer PDM-929.
  • SEQ ID NO: 1026 sets forth a DNA sequence encoding the P501S D protein (amino acids 316-553).
  • SEQ ID NO: 1027 sets forth a DNA sequence encoding the P501S C protein (amino acids 257-553).
  • SEQ ID NO: 1028 sets forth an amino acid sequence corresponding to the P501S D protein (amino acids 316-553).
  • SEQ ID NO: 1029 sets forth an amino acid sequence corresponding to the P501S C protein (amino acids 257-553).
  • SEQ ID NO: 1030 sets forth an amino acid for a P703P epitope recognized by patient sera.
  • SEQ ID NO: 1031 sets forth an amino acid for a P703P epitope recognized by patient sera.
  • SEQ ID NO: 1032 sets forth an amino acid for a P703P epitope recognized by patient sera.
  • SEQ ID NO: 1033 sets forth an amino acid for a P703P epitope recognized by patient sera.
  • SEQ ID NO: 1034 discloses an additional DNA sequence for the prostate antigen P712P.
  • SEQ ID NO: 1035 discloses an additional DNA sequence for the prostate antigen P775P.
  • SEQ ID NO: 1036 discloses an additional DNA sequece for the prostate antigen P704P.
  • SEQ ID NO: 1037 discloses an 11 amino acid fragment derived from P501S that contains naturally processed epitopes for at least three class I alleles.
  • SEQ ID NO: 1038 discloses the polynucleotide sequence encoding SEQ ID NO: 1037.
  • compositions of the present invention are directed generally to compositions and their use in the therapy and diagnosis of cancer, particularly prostate cancer.
  • illustrative compositions of the present invention include, but are not restricted to, polypeptides, particularly immunogenic polypeptides, polynucleotides encoding such polypeptides, antibodies and other binding agents, antigen presenting cells (APCs) and immune system cells (e.g., T cells).
  • APCs antigen presenting cells
  • T cells immune system cells
  • polypeptide As used herein, the term “polypeptide” “is used in its conventional meaning, i.e., as a sequence of amino acids.
  • the polypeptides are not limited to a specific length of the product; thus, peptides, oligopeptides, and proteins are included within the definition of polypeptide, and such terms may be used interchangeably herein unless specifically indicated otherwise.
  • This term also does not refer to or exclude post-expression modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations and the like, as well as other modifications known in the art, both naturally occurring and non-naturally occurring.
  • a polypeptide may be an entire protein, or a subsequence thereof.
  • polypeptides of interest in the context of this invention are amino acid subsequences comprising epitopes, i.e., antigenic determinants substantially responsible for the immunogenic properties of a polypeptide and being capable of evoking an immune response.
  • polypeptides of the present invention comprise those encoded by a polynucleotide sequence set forth in any one of SEQ ID NO: 1-111, 115-171, 173-175, 177, 179-305, 307-315, 326, 328, 330, 332-335, 340-375, 381, 382 and 384-476, 524, 526, 530, 531, 533, 535, 536, 552, 569-572, 587, 591, 593-606, 618-705, 709-774, 777, 789, 817, 823, 824, 878, 880-882, 894, 896, 907, 908, 916-919, 929-931, 938, 939, 942, 944, 945, 948, 967, 969-976, 991, 993-1002, 1004, 1006, 1007, 1010, 1013-1019, 1021, 1023-1027 and 1034-1036 or a sequence
  • polypeptides of the invention comprise amino acid sequences as set forth in any one of SEQ ID NO: 112-114, 172, 176, 178, 327, 329, 331, 336, 339, 376-380, 383, 477-483, 496, 504, 505, 519, 520, 522, 525, 527, 532, 534, 537-551, 553-568, 573-586, 588-590, 592, 706-708, 775, 776, 778, 780, 781, 811, 814, 818, 826, 827, 853, 855, 858, 860-862, 866-877, 879, 883-893, 895, 897, 898, 909-915, 920-928, 932-934, 940, 941, 943, 946, 947, 949-966, 968, 977-990, 992, 1003, 1005, 1008, 1009, 1011, and 1012, 1020, 1022, 10
  • polypeptides of the present invention are sometimes herein referred to as prostate-specific proteins or prostate-specific polypeptides, as an indication that their identification has been based at least in part upon their increased levels of expression in prostate tissue samples.
  • a “prostate-specific polypeptide” or “prostate-specific protein” refers generally to a polypeptide sequence of the present invention, or a polynucleotide sequence encoding such a polypeptide, that is expressed in a substantial proportion of prostate tissue samples, for example preferably greater than about 20%, more preferably greater than about 30%, and most preferably greater than about 50% or more of prostate tissue samples tested, at a level that is at least two fold, and preferably at least five fold, greater than the level of expression in other normal tissues, as determined using a representative assay provided herein.
  • a prostate-specific polypeptide sequence of the invention, based upon its increased level of expression in tumor cells, has particular utility both as a diagnostic marker as well as a therapeutic target, as further described below.
  • the polypeptides of the invention are immunogenic, i.e., they react detectably within an immunoassay (such as an ELISA or T-cell stimulation assay) with antisera and/or T-cells from a patient with prostate cancer. Screening for immunogenic activity can be performed using techniques well known to the skilled artisan. For example, such screens can be performed using methods such as those described in Harlow and Lane, Antibodies: A Laboratory Manual , Cold Spring Harbor Laboratory, 1988.
  • a polypeptide may be immobilized on a solid support and contacted with patient sera to allow binding of antibodies within the sera to the immobilized polypeptide. Unbound sera may then be removed and bound antibodies detected using, for example, 125 I-labeled Protein A.
  • immunogenic portions of the polypeptides disclosed herein are also encompassed by the present invention.
  • An “immunogenic portion,” as used herein, is a fragment of an immunogenic polypeptide of the invention that itself is immunologically reactive (i.e., specifically binds) with the B-cells and/or T-cell surface antigen receptors that recognize the polypeptide. Immunogenic portions may generally be identified using well known techniques, such as those summarized in Paul, Fundamental Immunology , 3rd ed., 243-247 (Raven Press, 1993) and references cited therein. Such techniques include screening polypeptides for the ability to react with antigen-specific antibodies, antisera and/or T-cell lines or clones.
  • antisera and antibodies are “antigen-specific” if they specifically bind to an antigen (i.e., they react with the protein in an ELISA or other immunoassay, and do not react detectably with unrelated proteins).
  • antisera and antibodies may be prepared as described herein, and using well-known techniques.
  • an immunogenic portion of a polypeptide of the present invention is a portion that reacts with antisera and/or T-cells at a level that is not substantially less than the reactivity of the full-length polypeptide (e.g., in an ELISA and/or T-cell reactivity assay).
  • the level of immunogenic activity of the immunogenic portion is at least about 50%, preferably at least about 70% and most preferably greater than about 90% of the immunogenicity for the full-length polypeptide.
  • preferred immunogenic portions will be identified that have a level of immunogenic activity greater than that of the corresponding full-length polypeptide, e.g., having greater than about 100% or 150% or more immunogenic activity.
  • illustrative immunogenic portions may include peptides in which an N-terminal leader sequence and/or transmembrane domain has been deleted.
  • Other illustrative immunogenic portions will contain a small N- and/or C-terminal deletion (e.g., 1-30 amino acids, preferably 5-15 amino acids), relative to the mature protein.
  • a polypeptide composition of the invention may also comprise one or more polypeptides that are immunologically reactive with T cells and/or antibodies generated against a polypeptide of the invention, particularly a polypeptide having an amino acid sequence disclosed herein, or to an immunogenic fragment or variant thereof.
  • polypeptides comprise one or more polypeptides that are capable of eliciting T cells and/or antibodies that are immunologically reactive with one or more polypeptides described herein, or one or more polypeptides encoded by contiguous nucleic acid sequences contained in the polynucleotide sequences disclosed herein, or immunogenic fragments or variants thereof, or to one or more nucleic acid sequences which hybridize to one or more of these sequences under conditions of moderate to high stringency.
  • the present invention in another aspect, provides polypeptide fragments comprising at least about 5, 10, 15, 20, 25, 50, or 100 contiguous amino acids, or more, including all intermediate lengths, of a polypeptide composition set forth herein, such as those set forth in SEQ ID NO: 112-114, 172, 176, 178, 327, 329, 331, 336, 339, 376-380, 383, 477-483, 496, 504, 505, 519, 520, 522, 525, 527, 532, 534, 537-551, 553-568, 573-586, 588-590, 592, 706-708, 775, 776, 778, 780, 781, 811, 814, 818, 826, 827, 853, 855, 858, 860-862, 866-877, 879, 883-893, 895, 897, 898, 909-915, 920-928, 932-934, 940, 941, 943, 946, 9
  • the present invention provides variants of the polypeptide compositions described herein.
  • Polypeptide variants generally encompassed by the present invention will typically exhibit at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identity (determined as described below), along its length, to a polypeptide sequence set forth herein.
  • polypeptide fragments and variants provided by the present invention are immunologically reactive with an antibody and/or T-cell that reacts with a full-length polypeptide specifically set forth herein.
  • polypeptide fragments and variants provided by the present invention exhibit a level of immunogenic activity of at least about 50%, preferably at least about 70%, and most preferably at least about 90% or more of that exhibited by a full-length polypeptide sequence specifically set forth herein.
  • a polypeptide “variant,” as the term is used herein, is a polypeptide that typically differs from a polypeptide specifically disclosed herein in one or more substitutions, deletions, additions and/or insertions. Such variants may be naturally occurring or may be synthetically generated, for example, by modifying one or more of the above polypeptide sequences of the invention and evaluating their immunogenic activity as described herein using any of a number of techniques well known in the art.
  • certain illustrative variants of the polypeptides of the invention include those in which one or more portions, such as an N-terminal leader sequence or transmembrane domain, have been removed.
  • Other illustrative variants include variants in which a small portion (e.g., 1-30 amino acids, preferably 5-15 amino acids) has been removed from the N- and/or C-terminal of the mature protein.
  • a variant will contain conservative substitutions.
  • a “conservative substitution” is one in which an amino acid is substituted for another amino acid that has similar properties, such that one skilled in the art of peptide chemistry would expect the secondary structure and hydropathic nature of the polypeptide to be substantially unchanged.
  • modifications may be made in the structure of the polynucleotides and polypeptides of the present invention and still obtain a functional molecule that encodes a variant or derivative polypeptide with desirable characteristics, e.g., with immunogenic characteristics.
  • 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 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, incorporated herein by reference). It is accepted that the relative hydropathic character of the 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 its hydrophobicity and charge characteristics (Kyte and Doolittle, 1982).
  • 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 within ⁇ 1are 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 that take various 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.
  • any polynucleotide may be further modified to increase stability in vivo. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5′ and/or 3′ ends; the use of phosphorothioate or 2′ O-methyl rather than phosphodiesterase linkages in the backbone; and/or the inclusion of nontraditional bases such as inosine, queosine and wybutosine, as well as acetyl- methyl-, thio- and other modified forms of adenine, cytidine, guanine, thymine and uridine.
  • Amino acid substitutions may further be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues.
  • negatively charged amino acids include aspartic acid and glutamic acid
  • positively charged amino acids include lysine and arginine
  • 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.
  • variant polypeptides differ from a native sequence by substitution, deletion or addition of five amino acids or fewer.
  • Variants may also (or alternatively) be modified by, for example, the deletion or addition of amino acids that have minimal influence on the immunogenicity, secondary structure and hydropathic nature of the polypeptide.
  • polypeptides may comprise a signal (or leader) sequence at the N-terminal end of the protein, which co-translationally or post-translationally directs transfer of the protein.
  • the polypeptide may also be conjugated to a linker or other sequence for ease of synthesis, purification or identification of the polypeptide (e.g., poly-His), or to enhance binding of the polypeptide to a solid support.
  • a polypeptide may be conjugated to an immunoglobulin Fc region.
  • two sequences are said to be “identical” if the sequence of amino acids in the two sequences is the same when aligned for maximum correspondence, as described below. Comparisons between two sequences are typically performed by comparing the sequences over a comparison window to identify and compare local regions of sequence similarity.
  • a “comparison window” as used herein refers to a segment of at least about 20 contiguous positions, usually 30 to about 75, 40 to about 50, in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.
  • Optimal alignment of sequences for comparison may be conducted using the Megalign program in the Lasergene suite of bioinformatics software (DNASTAR, Inc., Madison, Wis.), using default parameters.
  • This program embodies several alignment schemes described in the following references: Dayhoff, M. O. (1978) A model of evolutionary change in proteins—Matrices for detecting distant relationships. In Dayhoff, M. O. (ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington, D.C. Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990) Unified Approach to Alignment and Phylogenes pp. 626-645 Methods in Enzymology vol.
  • optimal alignment of sequences for comparison may be conducted by the local identity algorithm of Smith and Waterman (1981) Add. APL. Math 2:482, by the identity alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity methods of Pearson and Lipman (1988) Proc. Nat'l Acad. Sci. USA 85: 2444, by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection.
  • BLAST and BLAST 2.0 are described in Altschul et al. (1977) Nucl. Acids Res. 25:3389-3402 and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively.
  • BLAST and BLAST 2.0 can be used, for example with the parameters described herein, to determine percent sequence identity for the polynucleotides and polypeptides of the invention.
  • Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. For amino acid sequences, a scoring matrix can be used to calculate the cumulative score.
  • Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.
  • the BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment.
  • the “percentage of sequence identity” is determined by comparing two optimally aligned sequences over a window of comparison of at least 20 positions, wherein the portion of the polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) of 20 percent or less, usually 5 to 15 percent, or 10 to 12 percent, as compared to the reference sequences (which does not comprise additions or deletions) for optimal alignment of the two sequences.
  • the percentage is calculated by determining the number of positions at which the identical amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the reference sequence (i.e., the window size) and multiplying the results by 100 to yield the percentage of sequence identity.
  • a polypeptide may be a fusion polypeptide that comprises multiple polypeptides as described herein, or that comprises at least one polypeptide as described herein and an unrelated sequence, such as a known tumor protein.
  • a fusion partner may, for example, assist in providing T helper epitopes (an immunological fusion partner), preferably T helper epitopes recognized by humans, or may assist in expressing the protein (an expression enhancer) at higher yields than the native recombinant protein.
  • Certain preferred fusion partners are both immunological and expression enhancing fusion partners.
  • Other fusion partners may be selected so as to increase the solubility of the polypeptide or to enable the polypeptide to be targeted to desired intracellular compartments.
  • Still further fusion partners include affinity tags, which facilitate purification of the polypeptide.
  • Fusion polypeptides may generally be prepared using standard techniques, including chemical conjugation.
  • a fusion polypeptide is expressed as a recombinant polypeptide, allowing the production of increased levels, relative to a non-fused polypeptide, in an expression system.
  • DNA sequences encoding the polypeptide components may be assembled separately, and ligated into an appropriate expression vector.
  • the 3′ end of the DNA sequence encoding one polypeptide component is ligated, with or without a peptide linker, to the 5′ end of a DNA sequence encoding the second polypeptide component so that the reading frames of the sequences are in phase. This permits translation into a single fusion polypeptide that retains the biological activity of both component polypeptides.
  • a peptide linker sequence may be employed to separate the first and second polypeptide components by a distance sufficient to ensure that each polypeptide folds into its secondary and tertiary structures.
  • Such a peptide linker sequence is incorporated into the fusion polypeptide using standard techniques well known in the 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., Gene 40:39-46, 1985; Murphy et al., Proc. Nat'l Acad. Sci. USA 83:8258-8262,1986; U.S. Pat. No. 4,935,233 and U.S. Pat. No. 4,751,180.
  • the linker sequence may generally be from 1to about 50 amino acids in length. Linker sequences are not required when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference.
  • the ligated DNA sequences are operably linked to suitable transcriptional or translational regulatory elements.
  • the regulatory elements responsible for expression of DNA are located only 5′ to the DNA sequence encoding the first polypeptides.
  • stop codons required to end translation and transcription termination signals are only present 3′ to the DNA sequence encoding the second polypeptide.
  • the fusion polypeptide can comprise a polypeptide as described herein together with an unrelated immunogenic protein, such as an immunogenic protein capable of eliciting a recall response.
  • an immunogenic protein capable of eliciting a recall response.
  • immunogenic proteins include tetanus, tuberculosis and hepatitis proteins (see, for example, Stoute et al. New Engl. J. Med., 336:86-91,1997).
  • the immunological fusion partner is derived from a Mycobacterium sp., such as a Mycobacterium tuberculosis -derived Ra12 fragment.
  • a Mycobacterium sp. such as a Mycobacterium tuberculosis -derived Ra12 fragment.
  • Ra12 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 Ser. No. 60/158,585, the disclosure of which is incorporated herein by reference in its entirety.
  • Ra12 refers to a polynucleotide region that is a subsequence of a Mycobacterium tuberculosis MTB32A nucleic acid.
  • MTB32A is a serine protease of 32 KD molecular weight encoded by a gene in virulent and a virulent strains of M. tuberculosis .
  • the nucleotide sequence and amino acid sequence of MTB32A have been described (for example, U.S. patent application Ser. No. 60/158,585; see also, Skeiky et al., Infection and Immun . (1999) 67:3998-4007, incorporated herein by reference).
  • C-terminal fragments of the MTB32A coding sequence express at high levels and remain as a soluble polypeptides throughout the purification process.
  • Ra12 may enhance the immunogenicity of heterologous immunogenic polypeptides with which it is fused.
  • Ra12 fusion polypeptide comprises a 14 KD C-terminal fragment corresponding to amino acid residues 192 to 323 of MTB32A.
  • Other preferred Ra12 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 Ra12 polypeptide.
  • Ra12 polynucleotides may comprise a native sequence (i.e., an endogenous sequence that encodes a Ra12 polypeptide or a portion thereof) or may comprise a variant of such a sequence.
  • Ra12 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 Ra12 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 Ra12 polypeptide or a portion thereof.
  • an immunological fusion partner is derived from protein D, a surface protein of the gram-negative bacterium Haemophilus influenza B (WO 91/18926).
  • a protein D derivative comprises approximately the first third of the protein (e.g., the first N-terminal 100-110 amino acids), and a protein D derivative may be lipidated.
  • the first 109 residues of a Lipoprotein D fusion partner is included on the N-terminus to provide the polypeptide with additional exogenous T-cell epitopes and to increase the expression level in E. coli (thus functioning as an expression enhancer).
  • the lipid tail ensures optimal presentation of the antigen to antigen presenting cells.
  • Other fusion partners include the non-structural protein from influenzae virus, NS1(hemaglutinin). Typically, the N-terminal 81 amino acids are used, although different fragments that include T-helper epitopes may be used.
  • the immunological fusion partner is the protein known as LYTA, or a portion thereof (preferably a C-terminal portion).
  • LYTA is derived from Streptococcus pneumoniae , which synthesizes an N-acetyl-L-alanine amidase known as amidase LYTA (encoded by the LytA gene; Gene 43:265-292,1986).
  • LYTA is an autolysin that specifically degrades certain bonds in the peptidoglycan backbone.
  • the C-terminal domain of the LYTA protein is responsible for the affinity to the choline or to some choline analogues such as DEAE. This property has been exploited for the development of E.
  • coli C-LYTA expressing plasmids useful for expression of fusion proteins. Purification of hybrid proteins containing the C-LYTA fragment at the amino terminus has been described (see Biotechnology 10:795-798, 1992).
  • 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. Pat. No. 5,633,234.
  • a targeting signal capable of directing a polypeptide to the endosomal/lysosomal compartment, as described in U.S. Pat. No. 5,633,234.
  • An immunogenic polypeptide of the invention when fused with this targeting signal, will associate more efficiently with MHC class II molecules and thereby provide enhanced in vivo stimulation of CD4 + T-cells specific for the polypeptide.
  • Polypeptides of the invention are prepared using any of a variety of well known synthetic and/or recombinant techniques, the latter of which are further described below. Polypeptides, portions and other variants generally less than about 150 amino acids can be generated by synthetic means, using techniques well known to those of ordinary skill in the art. In one illustrative example, such polypeptides are synthesized using any of the commercially available solid-phase techniques, such as the Merrifield solid-phase synthesis method, where amino acids are sequentially added to a growing amino acid chain. See Merrifield, J. Am. Chem. Soc. 85:2149-2146, 1963. Equipment for automated synthesis of polypeptides is commercially available from suppliers such as Perkin Elmer/Applied BioSystems Division (Foster City, Calif.), and may be operated according to the manufacturer's instructions.
  • polypeptide compositions including fusion polypeptides of the invention are isolated.
  • An “isolated” polypeptide is one that is removed from its original environment.
  • a naturally-occurring protein or polypeptide is isolated if it is separated from some or all of the coexisting materials in the natural system.
  • polypeptides are also purified, e.g., are at least about 90% pure, more preferably at least about 95% pure and most preferably at least about 99% pure.
  • Polynucleotide Compositions The present invention, in other aspects, provides polynucleotide compositions.
  • DNA and “polynucleotide” are used essentially interchangeably herein to refer to a DNA molecule that has been isolated free of total genomic DNA of a particular species. “Isolated,” as used herein, means that a polynucleotide is substantially away from other coding sequences, and that the DNA molecule does not contain large portions of unrelated coding DNA, such as large chromosomal fragments or other functional genes or polypeptide coding regions. Of course, this refers to the DNA molecule as originally isolated, and does not exclude genes or coding regions later added to the segment by the hand of man.
  • polynucleotide compositions of this invention can include genomic sequences, extra-genomic and plasmid-encoded sequences and smaller engineered gene segments that express, or may be adapted to express, proteins, polypeptides, peptides and the like. Such segments may be naturally isolated, or modified synthetically by the hand of man.
  • polynucleotides of the invention may be single-stranded (coding or antisense) or double-stranded, and may be DNA (genomic, cDNA or synthetic) or RNA molecules.
  • RNA molecules may include HnRNA molecules, which contain introns and correspond to a DNA molecule in a one-to-one manner, and mRNA molecules, which do not contain introns. 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.
  • Polynucleotides may comprise a native sequence (i.e., an endogenous sequence that encodes a polypeptide/protein of the invention or a portion thereof) or may comprise a sequence that encodes a variant or derivative, preferably an immunogenic variant or derivative, of such a sequence.
  • polynucleotide compositions comprise some or all of a polynucleotide sequence set forth in any one of SEQ ID NO: 1-111, 115-171, 173-175, 177, 179-305, 307-315, 326, 328, 330, 332-335, 340-375, 381, 382 and 384-476, 524, 526, 530, 531, 533, 535, 536, 552, 569-572, 587, 591, 593-606, 618-705, 709-774, 777, 789, 817, 823, 824, 878, 880-882, 894, 896, 907, 908, 916-919, 929-931, 938, 939, 942, 944, 945, 948, 967, 969-976, 991, 993-1002, 1004, 1006, 1007, 1010, 1013-1019, 1021, 1023-1027 and
  • the present invention provides polynucleotide variants having substantial identity to the sequences disclosed herein in SEQ ID NO: 1-111, 115-171, 173-175, 177, 179-305, 307-315, 326, 328, 330, 332-335, 340-375, 381, 382 and 384-476, 524, 526, 530, 531, 533, 535, 536, 552, 569-572, 587, 591, 593-606, 618-705, 709-774, 777, 789, 817, 823, 824, 878, 880-882, 894, 896, 907, 908, 916-919, 929-931, 938, 939, 942, 944, 945, 948, 967, 969-976, 991, 993-1002, 1004, 1006, 1007, 1010, 1013-1019, 1021, 1023-1027 and 1034-1036 for example those comprising at least 70% sequence identity
  • polynucleotide variants will contain one or more substitutions, additions, deletions and/or insertions, preferably such that the immunogenicity of the polypeptide encoded by the variant polynucleotide is not substantially diminished relative to a polypeptide encoded by a polynucleotide sequence specifically set forth herein).
  • variants should also be understood to encompasses homologous genes of xenogenic origin.
  • the present invention provides polynucleotide fragments comprising various lengths of contiguous stretches of sequence identical to, or complementary to, one or more of the sequences disclosed herein.
  • polynucleotides are provided by this invention that comprise at least about 10, 15, 20, 30, 40, 50, 75, 100, 150, 200, 300, 400, 500 or 1000 or more contiguous nucleotides of one or more of the sequences disclosed herein as well as all intermediate lengths there between.
  • intermediate lengths means any length between the quoted values, such as 16, 17, 18, 19, etc.; 21, 22, 23, etc.; 30, 31, 32, etc.; 50, 51, 52, 53, etc.; 100, 101, 102, 103, etc.; 150, 151, 152, 153, etc.; including all integers through 200-500; 500-1,000, and the like.
  • polynucleotide compositions are provided that are capable of hybridizing under moderate to high stringency conditions to a polynucleotide sequence provided herein, or a fragment thereof, or a complementary sequence thereof.
  • Hybridization techniques are well known in the art of molecular biology.
  • suitable moderately stringent conditions for testing the hybridization of a polynucleotide of this invention with other polynucleotides include prewashing in a solution of 5 ⁇ SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at 50° C.-60° C., 5 ⁇ SSC, overnight; followed by washing twice at 65° C.
  • hybridization can be readily manipulated, such as by altering the salt content of the hybridization solution and/or the temperature at which the hybridization is performed.
  • suitable highly stringent hybridization conditions include those described above, with the exception that the temperature of hybridization is increased, e.g., to 60-65° C. or 65-70° C.
  • the polynucleotides described above e.g., polynucleotide variants, fragments and hybridizing sequences, encode polypeptides that are immunologically cross-reactive with a polypeptide sequence specifically set forth herein.
  • such polynucleotides encode polypeptides that have a level of immunogenic activity of at least about 50%, preferably at least about 70%, and more preferably at least about 90% of that for a polypeptide sequence specifically set forth herein.
  • polynucleotides of the present invention may be combined with other DNA sequences, such as promoters, polyadenylation signals, additional restriction enzyme sites, multiple cloning sites, other coding segments, and the like, such that their overall length may vary considerably. It is therefore contemplated that a nucleic acid fragment of almost any length may be employed, with the total length preferably being limited by the ease of preparation and use in the intended recombinant DNA protocol.
  • illustrative polynucleotide segments with total lengths of about 10,000, about 5000, about 3000, about 2,000, about 1,000, about 500, about 200, about 100, about 50 base pairs in length, and the like, (including all intermediate lengths) are contemplated to be useful in many implementations of this invention.
  • two sequences are said to be “identical” if the sequence of nucleotides in the two sequences is the same when aligned for maximum correspondence, as described below. Comparisons between two sequences are typically performed by comparing the sequences over a comparison window to identify and compare local regions of sequence similarity.
  • a “comparison window” as used herein refers to a segment of at least about 20 contiguous positions, usually 30 to about 75, preferably 40 to about 50, in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.
  • Optimal alignment of sequences for comparison may be conducted using the Megalign program in the Lasergene suite of bioinformatics software (DNASTAR, Inc., Madison, Wis.), using default parameters.
  • This program embodies several alignment schemes described in the following references: Dayhoff, M. O. (1978) A model of evolutionary change in proteins—Matrices for detecting distant relationships. In Dayhoff, M. O. (ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington, D.C. Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990) Unified Approach to Alignment and Phylogenes pp. 626-645 Methods in Enzymology vol.
  • optimal alignment of sequences for comparison may be conducted by the local identity algorithm of Smith and Waterman (1981) Add. APL. Math 2:482, by the identity alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity methods of Pearson and Lipman (1988) Proc. Nat'l Acad. Sci. USA 85: 2444, by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection.
  • BLAST and BLAST 2.0 are described in Altschul et al. (1977) Nucl. Acids Res. 25:3389-3402 and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively.
  • BLAST and BLAST 2.0 can be used, for example with the parameters described herein, to determine percent sequence identity for the polynucleotides of the invention.
  • Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information.
  • cumulative scores can be calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always ⁇ 0). Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached.
  • the BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment.
  • the “percentage of sequence identity” is determined by comparing two optimally aligned sequences over a window of comparison of at least 20 positions, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) of 20 percent or less, usually 5 to 15 percent, or 10 to 12 percent, as compared to the reference sequences (which does not comprise additions or deletions) for optimal alignment of the two sequences.
  • additions or deletions i.e., gaps
  • the percentage is calculated by determining the number of positions at which the identical nucleic acid bases occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the reference sequence (i.e., the window size) and multiplying the results by 100 to yield the percentage of sequence identity.
  • a mutagenesis approach such as site-specific mutagenesis, is employed for the preparation of immunogenic variants and/or derivatives of the polypeptides described herein.
  • site-specific mutagenesis By this approach, specific modifications in a polypeptide sequence can be made through mutagenesis of the underlying polynucleotides that encode them.
  • Site-specific mutagenesis allows the production of mutants through the use of specific oligonucleotide sequences which encode the DNA sequence of the desired mutation, as well as a sufficient number of adjacent nucleotides, to provide a primer sequence of sufficient size and sequence complexity to form a stable duplex on both sides of the deletion junction being traversed. Mutations may be employed in a selected polynucleotide sequence to improve, alter, decrease, modify, or otherwise change the properties of the polynucleotide itself, and/or alter the properties, activity, composition, stability, or primary sequence of the encoded polypeptide.
  • the inventors contemplate the mutagenesis of the disclosed polynucleotide sequences to alter one or more properties of the encoded polypeptide, such as the immunogenicity of a polypeptide vaccine.
  • the techniques of site-specific mutagenesis are well-known in the art, and are widely used to create variants of both polypeptides and polynucleotides.
  • site-specific mutagenesis is often used to alter a specific portion of a DNA molecule.
  • a primer comprising typically about 14 to about 25 nucleotides or so in length is employed, with about 5 to about 10 residues on both sides of the junction of the sequence being altered.
  • site-specific mutagenesis techniques have often employed a phage vector that exists in both a single stranded and double stranded form.
  • Typical vectors useful in site-directed mutagenesis include vectors such as the M13 phage. These phage are readily commercially-available and their use is generally well-known to those skilled in the art.
  • Double-stranded plasmids are also routinely employed in site directed mutagenesis that eliminates the step of transferring the gene of interest from a plasmid to a phage.
  • site-directed mutagenesis in accordance herewith is performed by first obtaining a single-stranded vector or melting apart of two strands of a double-stranded vector that includes within its sequence a DNA sequence that encodes the desired peptide.
  • An oligonucleotide primer bearing the desired mutated sequence is prepared, generally synthetically. This primer is then annealed with the single-stranded vector, and subjected to DNA polymerizing enzymes such as E. coli polymerase I Klenow fragment, in order to complete the synthesis of the mutation-bearing strand.
  • DNA polymerizing enzymes such as E. coli polymerase I Klenow fragment
  • sequence variants of the selected peptide-encoding DNA segments using site-directed mutagenesis provides a means of producing potentially useful species and is not meant to be limiting as there are other ways in which sequence variants of peptides and the DNA sequences encoding them may be obtained.
  • recombinant vectors encoding the desired peptide sequence may be treated with mutagenic agents, such as hydroxylamine, to obtain sequence variants.
  • mutagenic agents such as hydroxylamine
  • oligonucleotide directed mutagenesis procedure refers to template-dependent processes and vector-mediated propagation which result in an increase in the concentration of a specific nucleic acid molecule relative to its initial concentration, or in an increase in the concentration of a detectable signal, such as amplification.
  • oligonucleotide directed mutagenesis procedure is intended to refer to a process that involves the template-dependent extension of a primer molecule.
  • template dependent process refers to nucleic acid synthesis of an RNA or a DNA molecule wherein the sequence of the newly synthesized strand of nucleic acid is dictated by the well-known rules of complementary base pairing (see, for example, Watson, 1987).
  • vector mediated methodologies involve the introduction of the nucleic acid fragment into a DNA or RNA vector, the clonal amplification of the vector, and the recovery of the amplified nucleic acid fragment. Examples of such methodologies are provided by U.S. Pat. No. 4,237,224, specifically incorporated herein by reference in its entirety.
  • the polynucleotide sequences provided herein can be advantageously used as probes or primers for nucleic acid hybridization.
  • nucleic acid segments that comprise a sequence region of at least about 15 contiguous nucleotides that has the same sequence as, or is complementary to, a 15 nucleotide long contiguous sequence disclosed herein will find particular utility. Longer contiguous identical or complementary sequences, e.g., those of about 20, 30, 40, 50, 100, 200, 500, 1000 (including all intermediate lengths) and even up to full length sequences will also be of use in certain embodiments.
  • nucleic acid probes to specifically hybridize to a sequence of interest will enable them to be of use in detecting the presence of complementary sequences in a given sample.
  • sequence information for the preparation of mutant species primers, or primers for use in preparing other genetic constructions.
  • Polynucleotide molecules having sequence regions consisting of contiguous nucleotide stretches of 10-14, 15-20, 30, 50, or even of 100-200 nucleotides or so (including intermediate lengths as well), identical or complementary to a polynucleotide sequence disclosed herein, are particularly contemplated as hybridization probes for use in, e.g., Southern and Northern blotting. This would allow a gene product, or fragment thereof, to be analyzed, both in diverse cell types and also in various bacterial cells. The total size of fragment, as well as the size of the complementary stretch(es), will ultimately depend on the intended use or application of the particular nucleic acid segment.
  • hybridization probe of about 15-25 nucleotides in length allows the formation of a duplex molecule that is both stable and selective. Molecules having contiguous complementary sequences over stretches greater than 15 bases in length are generally preferred, though, in order to increase stability and selectivity of the hybrid, and thereby improve the quality and degree of specific hybrid molecules obtained.
  • Hybridization probes may be selected from any portion of any of the sequences disclosed herein. All that is required is to review the sequences set forth herein, or to any continuous portion of the sequences, from about 15-25 nucleotides in length up to and including the full length sequence, that one wishes to utilize as a probe or primer.
  • the choice of probe and primer sequences may be governed by various factors. For example, one may wish to employ primers from towards the termini of the total sequence.
  • Small polynucleotide segments or fragments may be readily prepared by, for example, directly synthesizing the fragment by chemical means, as is commonly practiced using an automated oligonucleotide synthesizer. Also, fragments may be obtained by application of nucleic acid reproduction technology, such as the PCRTM technology of U.S. Pat. No. 4,683,202 (incorporated herein by reference), by introducing selected sequences into recombinant vectors for recombinant production, and by other recombinant DNA techniques generally known to those of skill in the art of molecular biology.
  • the nucleotide sequences of the invention may be used for their ability to selectively form duplex molecules with complementary stretches of the entire gene or gene fragments of interest.
  • relatively stringent conditions e.g., one will select relatively low salt and/or high temperature conditions, such as provided by a salt concentration of from about 0.02 M to about 0.15 M salt at temperatures of from about 50° C. to about 70° C.
  • Such selective conditions tolerate little, if any, mismatch between the probe and the template or target strand, and would be particularly suitable for isolating related sequences.
  • polynucleotide compositions comprising antisense oligonucleotides are provided.
  • Antisense oligonucleotides have been demonstrated to be effective and targeted inhibitors of protein synthesis, and, consequently, provide a therapeutic approach by which a disease can be treated by inhibiting the synthesis of proteins that contribute to the disease.
  • the efficacy of antisense oligonucleotides for inhibiting protein synthesis is well established. For example, the synthesis of polygalactauronase and the muscarine type 2 acetylcholine receptor are inhibited by antisense oligonucleotides directed to their respective mRNA sequences (U.S. Pat. No.
  • Antisense constructs have also been described that inhibit and can be used to treat a variety of abnormal cellular proliferations, e.g. cancer (U.S. Pat. No. 5,747,470; U.S. Pat. No. 5,591,317 and U.S. Pat. No. 5,783,683).
  • the present invention provides oligonucleotide sequences that comprise all, or a portion of, any sequence that is capable of specifically binding to polynucleotide sequence described herein, or a complement thereof.
  • the antisense oligonucleotides comprise DNA or derivatives thereof.
  • the oligonucleotides comprise RNA or derivatives thereof.
  • the oligonucleotides are modified DNAs comprising a phosphorothioated modified backbone.
  • the oligonucleotide sequences comprise peptide nucleic acids or derivatives thereof.
  • compositions comprise a sequence region that is complementary, and more preferably substantially-complementary, and even more preferably, completely complementary to one or more portions of polynucleotides disclosed herein.
  • Selection of antisense compositions specific for a given gene sequence is based upon analysis of the chosen target sequence and determination of secondary structure, T m , binding energy, and relative stability.
  • Antisense compositions may be selected based upon their relative inability to form dimers, hairpins, or other secondary structures that would reduce or prohibit specific binding to the target mRNA in a host cell.
  • Highly preferred target regions of the mRNA are those which are at or near the AUG translation initiation codon, and those sequences which are substantially complementary to 5′ regions of the mRNA.
  • MPG short peptide vector
  • the MPG peptide contains a hydrophobic domain derived from the fusion sequence of HIV gp41 and a hydrophilic domain from the nuclear localization sequence of SV40 T-antigen (Morris et al., Nucleic Acids Res. Jul. 15, 1997;25(14):2730-6). It has been demonstrated that several molecules of the MPG peptide coat the antisense oligonucleotides and can be delivered into cultured mammalian cells in less than 1 hour with relatively high efficiency (90%). Further, the interaction with MPG strongly increases both the stability of the oligonucleotide to nuclease and the ability to cross the plasma membrane.
  • the polynucleotide compositions described herein are used in the design and preparation of ribozyme molecules for inhibiting expression of the tumor polypeptides and proteins of the present invention in tumor cells.
  • Ribozymes are RNA-protein complexes that cleave nucleic acids in a site-specific fashion. Ribozymes have specific catalytic domains that possess endonuclease activity (Kim and Cech, Proc Nat'l Acad Sci USA. 1987 Dec.;84(24):8788-92; Forster and Symons, Cell. Apr. 24, 1987;49(2):211-20).
  • ribozymes accelerate phosphoester transfer reactions with a high degree of specificity, often cleaving only one of several phosphoesters in an oligonucleotide substrate (Cech et al., Cell. 1981 December;27(3 Pt 2):487-96; Michel and Westhof, J Mol Biol. 1990 Dec 5;216(3):585-610; Reinhold-Hurek and Shub, Nature. 1992 May 14;357(6374):173-6).
  • This specificity has been attributed to the requirement that the substrate bind via specific base-pairing interactions to the internal guide sequence (“IGS”) of the ribozyme prior to chemical reaction.
  • IGS internal guide sequence
  • enzymatic nucleic acids act by first binding to a target RNA. Such binding occurs through the target binding portion of a enzymatic nucleic acid which is held in close proximity to an enzymatic portion of the molecule that acts to cleave the target RNA. Thus, the enzymatic nucleic acid first recognizes and then binds a target RNA through complementary base-pairing, and once bound to the correct site, acts enzymatically to cut the target RNA.
  • RNA Strategic cleavage of such a target RNA will destroy its ability to direct synthesis of an encoded protein. After an enzymatic nucleic acid has bound and cleaved its RNA target, it is released from that RNA to search for another target and can repeatedly bind and cleave new targets.
  • ribozyme The enzymatic nature of a ribozyme is advantageous over many technologies, such as antisense technology (where a nucleic acid molecule simply binds to a nucleic acid target to block its translation) since the concentration of ribozyme necessary to affect a therapeutic treatment is lower than that of an antisense oligonucleotide.
  • This advantage reflects the ability of the ribozyme to act enzymatically.
  • a single ribozyme molecule is able to cleave many molecules of target RNA.
  • the ribozyme is a highly specific inhibitor, with the specificity of inhibition depending not only on the base pairing mechanism of binding to the target RNA, but also on the mechanism of target RNA cleavage.
  • the enzymatic nucleic acid molecule may be formed in a hammerhead, hairpin, a hepatitis ⁇ virus, group I intron or RNaseP RNA (in association with an RNA guide sequence) or Neurospora VS RNA motif.
  • hammerhead motifs are described by Rossi et al. Nucleic Acids Res. Sep. 11, 1992;20(17):4559-65.
  • hairpin motifs are described by Hampel et al. (Eur. Pat. Appl. Publ. No. EP 0360257), Hampel and Tritz, Biochemistry Jun. 13, 1989;28(12):4929-33; Hampel et al., Nucleic Acids Res. Jan.
  • hepatitis ⁇ virus motif is described by Perrotta and Been, Biochemistry. Dec. 1, 1992;31(47):11843-52; an example of the RNaseP motif is described by Guerrier-Takada et al., Cell. 1983 December;35(3 Pt 2):849-57; Neurospora VS RNA ribozyme motif is described by Collins (Saville and Collins, Cell. May 18, 1990;61(4):685-96; Saville and Collins, Proc Nat'l Acad Sci U S A. Oct. 1, 1991;88(19):8826-30; Collins and Olive, Biochemistry. Mar.
  • Ribozymes may be designed as described in Int. Pat. Appl. Publ. No. WO 93/23569 and Int. Pat. Appl. Publ. No. WO 94/02595, each specifically incorporated herein by reference) and synthesized to be tested in vitro and in vivo, as described. Such ribozymes can also be optimized for delivery. While specific examples are provided, those in the art will recognize that equivalent RNA targets in other species can be utilized when necessary.
  • Ribozyme activity can be optimized by altering the length of the ribozyme binding arms, or chemically synthesizing ribozymes with modifications that prevent their degradation by serum ribonucleases (see e.g., Int. Pat. Appl. Publ. No. WO 92/07065; Int. Pat. Appl. Publ. No. WO 93/15187; Int. Pat. Appl. Publ. No. WO 91/03162; Eur. Pat. Appl. Publ. No. 92110298.4; U.S. Pat. No. 5,334,711; and Int. Pat. Appl. Publ. No. WO 94/13688, which describe various chemical modifications that can be made to the sugar moieties of enzymatic RNA molecules), modifications which enhance their efficacy in cells, and removal of stem II bases to shorten RNA synthesis times and reduce chemical requirements.
  • Ribozymes may be administered to cells by a variety of methods known to those familiar to the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesive microspheres.
  • ribozymes may be directly delivered ex vivo to cells or tissues with or without the aforementioned vehicles.
  • the RNA/vehicle combination may be locally delivered by direct inhalation, by direct injection or by use of a catheter, infusion pump or stent.
  • routes of delivery include, but are not limited to, intravascular, intramuscular, subcutaneous or joint injection, aerosol inhalation, oral (tablet or pill form), topical, systemic, ocular, intraperitoneal and/or intrathecal delivery. More detailed descriptions of ribozyme delivery and administration are provided in Int. Pat. Appl. Publ. No. WO 94/02595 and Int. Pat. Appl. Publ. No. WO 93/23569, each specifically incorporated herein by reference.
  • RNA polymerase I RNA polymerase I
  • RNA polymerase II RNA polymerase II
  • RNA polymerase III RNA polymerase III
  • Transcripts from pol II or pol III promoters will be expressed at high levels in all cells; the levels of a given pol II promoter in a given cell type will depend on the nature of the gene regulatory sequences (enhancers, silencers, etc.) present nearby.
  • Prokaryotic RNA polymerase promoters may also be used, providing that the prokaryotic RNA polymerase enzyme is expressed in the appropriate cells Ribozymes expressed from such promoters have been shown to function in mammalian cells.
  • Such transcription units can be incorporated into a variety of vectors for introduction into mammalian cells, including but not restricted to, plasmid DNA vectors, viral DNA vectors (such as adenovirus or adeno-associated vectors), or viral RNA vectors (such as retroviral, semliki forest virus, Sindbis virus vectors).
  • PNAs peptide nucleic acids
  • PNA is a DNA mimic in which the nucleobases are attached to a pseudopeptide backbone (Good and Nielsen, Antisense Nucleic Acid Drug Dev. 1997 7(4) 431-37).
  • PNA is able to be utilized in a number methods that traditionally have used RNA or DNA. Often PNA sequences perform better in techniques than the corresponding RNA or DNA sequences and have utilities that are not inherent to RNA or DNA.
  • a review of PNA including methods of making, characteristics of, and methods of using, is provided by Corey ( Trends Biotechnol 1997June;15(6):224-9).
  • PNAs have 2-aminoethyl-glycine linkages replacing the normal phosphodiester backbone of DNA (Nielsen et al., Science Dec. 6, 1991;254(5037):1497-500; Hanvey et al., Science. Nov. 27, 1992;258(5087):1481-5; Hyrup and Nielsen, Bioorg Med Chem. 1996 January;4(1):5-23).
  • PNAs are neutral molecules; secondly, PNAs are achiral, which avoids the need to develop a stereoselective synthesis; and thirdly, PNA synthesis uses standard Boc or Fmoc protocols for solid-phase peptide synthesis, although other methods, including a modified Merrifield method, have been used.
  • PNA monomers or ready-made oligomers are commercially available from PerSeptive Biosystems (Framingham, Mass.). PNA syntheses by either Boc or Fmoc protocols are straightforward using manual or automated protocols (Norton et al., Bioorg Med Chem. 1995 April;3(4):437-45). The manual protocol lends itself to the production of chemically modified PNAs or the simultaneous synthesis of families of closely related PNAs.
  • PNAs can incorporate any combination of nucleotide bases
  • the presence of adjacent purines can lead to deletions of one or more residues in the product.
  • Modifications of PNAs for a given application may be accomplished by coupling amino acids during solid-phase synthesis or by attaching compounds that contain a carboxylic acid group to the exposed N-terminal amine.
  • PNAs can be modified after synthesis by coupling to an introduced lysine or cysteine. The ease with which PNAs can be modified facilitates optimization for better solubility or for specific functional requirements.
  • the identity of PNAs and their derivatives can be confirmed by mass spectrometry.
  • Several studies have made and utilized modifications of PNAs (for example, Norton et al., Bioorg Med Chem. 1995 April;3(4):437-45; Petersen et al., J Pept Sci.
  • U.S. Pat. No. 5,700,922 discusses PNA-DNA-PNA chimeric molecules and their uses in diagnostics, modulating protein in organisms, and treatment of conditions susceptible to therapeutics.
  • PNAs include use in DNA strand invasion, antisense inhibition, mutational analysis, enhancers of transcription, nucleic acid purification, isolation of transcriptionally active genes, blocking of transcription factor binding, genome cleavage, biosensors, in situ hybridization, and the like.
  • Polynucleotide compositions of the present invention may be identified, prepared and/or manipulated using any of a variety of well established techniques (see generally, Sambrook et al., Molecular Cloning: A Laboratory Manual , Cold Spring Harbor Laboratories, Cold Spring Harbor, N.Y., 1989, and other like references).
  • a polynucleotide may be identified, as described in more detail below, by screening a microarray of cDNAs for tumor-associated expression (i.e., expression that is at least two fold greater in a tumor than in normal tissue, as determined using a representative assay provided herein). Such screens may be performed, for example, using the microarray technology of Affymetrix, Inc.
  • polynucleotides may be amplified from cDNA prepared from cells expressing the proteins described herein, such as tumor cells.
  • PCRTM polymerase chain reaction
  • the primers will bind to the target and the polymerase will cause the primers to be extended along the target sequence by adding on nucleotides.
  • the extended primers will dissociate from the target to form reaction products, excess primers will bind to the target and to the reaction product and the process is repeated.
  • reverse transcription and PCRTM amplification procedure may be performed in order to quantify the amount of mRNA amplified. Polymerase chain reaction methodologies are well known in the art.
  • LCR ligase chain reaction
  • SDA Strand Displacement Amplification
  • RCR Repair Chain Reaction
  • nucleic acid amplification procedures include transcription-based amplification systems (TAS) (PCT Intl. Pat. Appl. Publ. No. WO 88/10315), including nucleic acid sequence based amplification (NASBA) and 3SR.
  • TAS transcription-based amplification systems
  • NASBA nucleic acid sequence based amplification
  • 3SR nucleic acid sequence based amplification
  • ssRNA single-stranded RNA
  • dsDNA double-stranded DNA
  • WO 89/06700 describes a nucleic acid sequence amplification scheme based on the hybridization of a promoter/primer sequence to a target single-stranded DNA (“ssDNA”) followed by transcription of many RNA copies of the sequence.
  • Other amplification methods such as “RACE” (Frohman, 1990), and “one-sided PCR” (Ohara, 1989) are also well-known to those of skill in the art.
  • An amplified portion of a polynucleotide of the present invention may be used to isolate a full length gene from a suitable library (e.g., a tumor cDNA library) using well known techniques.
  • a library cDNA or genomic
  • a library is screened using one or more polynucleotide probes or primers suitable for amplification.
  • a library is size-selected to include larger molecules. Random primed libraries may also be preferred for identifying 5′ and upstream regions of genes. Genomic libraries are preferred for obtaining introns and extending 5′ sequences.
  • a partial sequence may be labeled (e.g., by nick-translation or end-labeling with 32 P) using well known techniques.
  • a bacterial or bacteriophage library is then generally screened by hybridizing filters containing denatured bacterial colonies (or lawns containing phage plaques) with the labeled probe (see Sambrook et al., Molecular Cloning: A Laboratory Manual , Cold Spring Harbor Laboratories, Cold Spring Harbor, N.Y., 1989). Hybridizing colonies or plaques are selected and expanded, and the DNA is isolated for further analysis.
  • cDNA clones may be analyzed to determine the amount of additional sequence by, for example, PCR using a primer from the partial sequence and a primer from the vector.
  • Restriction maps and partial sequences may be generated to identify one or more overlapping clones.
  • the complete sequence may then be determined using standard techniques, which may involve generating a series of deletion clones.
  • the resulting overlapping sequences can then assembled into a single contiguous sequence.
  • a full length cDNA molecule can be generated by ligating suitable fragments, using well known techniques.
  • amplification techniques can be useful for obtaining a full length coding sequence from a partial cDNA sequence.
  • One such amplification technique is inverse PCR (see Triglia et al., Nucl. Acids Res. 16:8186, 1988), which uses restriction enzymes to generate a fragment in the known region of the gene. The fragment is then circularized by intramolecular ligation and used as a template for PCR with divergent primers derived from the known region.
  • sequences adjacent to a partial sequence may be retrieved by amplification with a primer to a linker sequence and a primer specific to a known region.
  • the amplified sequences are typically subjected to a second round of amplification with the same linker primer and a second primer specific to the known region.
  • a variation on this procedure, which employs two primers that initiate extension in opposite directions from the known sequence, is described in WO 96/38591.
  • Another such technique is known as “rapid amplification of cDNA ends” or RACE.
  • This technique involves the use of an internal primer and an external primer, which hybridizes to a polyA region or vector sequence, to identify sequences that are 5′ and 3′ of a known sequence. Additional techniques include capture PCR (Lagerstrom et al., PCR Methods Applic. 1:111-19, 1991) and walking PCR (Parker et al., Nucl. Acids. Res. 19:3055-60, 1991). Other methods employing amplification may also be employed to obtain a full length cDNA sequence.
  • EST expressed sequence tag
  • Searches for overlapping ESTs may generally be performed using well known programs (e.g., NCBI BLAST searches), and such ESTs may be used to generate a contiguous full length sequence.
  • Full length DNA sequences may also be obtained by analysis of genomic fragments.
  • polynucleotide sequences or fragments thereof which encode polypeptides of the invention, or fusion proteins or functional equivalents thereof may be used in recombinant DNA molecules to direct expression of a polypeptide in appropriate host cells. Due to the inherent degeneracy of the genetic code, other DNA sequences that encode substantially the same or a functionally equivalent amino acid sequence may be produced and these sequences may be used to clone and express a given polypeptide.
  • codons preferred by a particular prokaryotic or eukaryotic host can be selected to increase the rate of protein expression or to produce a recombinant RNA transcript having desirable properties, such as a half-life which is longer than that of a transcript generated from the naturally occurring sequence.
  • polynucleotide sequences of the present invention can be engineered using methods generally known in the art in order to alter polypeptide encoding sequences for a variety of reasons, including but not limited to, alterations which modify the cloning, processing, and/or expression of the gene product.
  • DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences.
  • site-directed mutagenesis may be used to insert new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, or introduce mutations, and so forth.
  • natural, modified, or recombinant nucleic acid sequences may be ligated to a heterologous sequence to encode a fusion protein.
  • a heterologous sequence For example, to screen peptide libraries for inhibitors of polypeptide activity, it may be useful to encode a chimeric protein that can be recognized by a commercially available antibody.
  • a fusion protein may also be engineered to contain a cleavage site located between the polypeptide-encoding sequence and the heterologous protein sequence, so that the polypeptide may be cleaved and purified away from the heterologous moiety.
  • Sequences encoding a desired polypeptide may be synthesized, in whole or in part, using chemical methods well known in the art (see Caruthers, M. H. et al. (1980) Nucl. Acids Res. Symp. Ser. 215-223, Horn, T. et al. (1980) Nucl. Acids Res. Symp. Ser. 225-232).
  • the protein itself may be produced using chemical methods to synthesize the amino acid sequence of a polypeptide, or a portion thereof.
  • peptide synthesis can be performed using various solid-phase techniques (Roberge, J. Y. et al. (1995) Science 269:202-204) and automated synthesis may be achieved, for example, using the ABI 431A Peptide Synthesizer (Perkin Elmer, Palo Alto, Calif.).
  • a newly synthesized peptide may be substantially purified by preparative high performance liquid chromatography (e.g., Creighton, T. (1983) Proteins, Structures and Molecular Principles, W H Freeman and Co., New York, N.Y.) or other comparable techniques available in the art.
  • the composition of the synthetic peptides may be confirmed by amino acid analysis or sequencing (e.g., the Edman degradation procedure). Additionally, the amino acid sequence of a polypeptide, or any part thereof, may be altered during direct synthesis and/or combined using chemical methods with sequences from other proteins, or any part thereof, to produce a variant polypeptide.
  • the nucleotide sequences encoding the polypeptide, or functional equivalents may be inserted into appropriate expression vector, i.e., a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence.
  • appropriate expression vector i.e., a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence.
  • Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding a polypeptide of interest and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Such techniques are described, for example, in Sambrook, J. et al.
  • a variety of expression vector/host systems may be utilized to contain and express polynucleotide sequences. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (e.g., baculovirus); plant cell systems transformed with virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems.
  • microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors
  • yeast transformed with yeast expression vectors insect cell systems infected with virus expression vectors (e.g., baculovirus)
  • plant cell systems transformed with virus expression vectors e.g., cauliflower mosaic virus, CaMV; tobacco mosaic
  • control elements or “regulatory sequences” present in an expression vector are those non-translated regions of the vector—enhancers, promoters, 5′ and 3′ untranslated regions—which interact with host cellular proteins to carry out transcription and translation. Such elements may vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used.
  • inducible promoters such as the hybrid lacZ promoter of the PBLUESCRIPT phagemid (Stratagene, La Jolla, Calif.) or PSPORT1 plasmid (Gibco BRL, Gaithersburg, Md.) and the like may be used.
  • promoters from mammalian genes or from mammalian viruses are generally preferred. If it is necessary to generate a cell line that contains multiple copies of the sequence encoding a polypeptide, vectors based on SV40 or EBV may be advantageously used with an appropriate selectable marker.
  • any of a number of expression vectors may be selected depending upon the use intended for the expressed polypeptide.
  • vectors which direct high level expression of fusion proteins that are readily purified may be used.
  • Such vectors include, but are not limited to, the multifunctional E. coli cloning and expression vectors such as BLUESCRIPT (Stratagene), in which the sequence encoding the polypeptide of interest may be ligated into the vector in frame with sequences for the amino-terminal Met and the subsequent 7 residues of .beta.-galactosidase so that a hybrid protein is produced; pIN vectors (Van Heeke, G. and S. M.
  • pGEX Vectors may also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST).
  • GST glutathione S-transferase
  • fusion proteins are soluble and can easily be purified from lysed cells by adsorption to glutathione-agarose beads followed by elution in the presence of free glutathione.
  • Proteins made in such systems may be designed to include heparin, thrombin, or factor XA protease cleavage sites so that the cloned polypeptide of interest can be released from the GST moiety at will.
  • yeast Saccharomyces cerevisiae
  • a number of vectors containing constitutive or inducible promoters such as alpha factor, alcohol oxidase, and PGH may be used.
  • constitutive or inducible promoters such as alpha factor, alcohol oxidase, and PGH
  • sequences encoding polypeptides may be driven by any of a number of promoters.
  • viral promoters such as the 35S and 19S promoters of CaMV may be used alone or in combination with the omega leader sequence from TMV (Takamatsu, N. (1987) EMBO J. 3:17-311.
  • plant promoters such as the small subunit of RUBISCO or heat shock promoters may be used (Coruzzi, G. et al. (1984) EMBO J. 3:1671-1680; Broglie, R. et al. (1984) Science 224:838-843; and Winter, J. et al. (1991) Results Probl.
  • An insect system may also be used to express a polypeptide of interest.
  • Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes in Spodoptera frugiperda cells or in Trichoplusia larvae .
  • the sequences encoding the polypeptide may be cloned into a non-essential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter. Successful insertion of the polypeptide-encoding sequence will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein.
  • the recombinant viruses may then be used to infect, for example, S. frugiperda cells or Trichoplusia larvae in which the polypeptide of interest may be expressed (Engelhard, E. K. et al. (1994) Proc. Nat'l Acad. Sci. 91:3224-3227).
  • a number of viral-based expression systems are generally available.
  • sequences encoding a polypeptide of interest may be ligated into an adenovirus transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a non-essential E1 or E3 region of the viral genome may be used to obtain a viable virus which is capable of expressing the polypeptide in infected host cells (Logan, J. and Shenk, T. (1984) Proc. Nat'l Acad. Sci. 81:3655-3659).
  • transcription enhancers such as the Rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells.
  • RSV Rous sarcoma virus
  • Specific initiation signals may also be used to achieve more efficient translation of sequences encoding a polypeptide of interest. Such signals include the ATG initiation codon and adjacent sequences. In cases where sequences encoding the polypeptide, its initiation codon, and upstream sequences are inserted into the appropriate expression vector, no additional transcriptional or translational control signals may be needed. However, in cases where only coding sequence, or a portion thereof, is inserted, exogenous translational control signals including the ATG initiation codon should be provided. Furthermore, the initiation codon should be in the correct reading frame to ensure translation of the entire insert. Exogenous translational elements and initiation codons may be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers which are appropriate for the particular cell system which is used, such as those described in the literature (Scharf, D. et al. (1994) Results Probl. Cell Differ. 20:125-162).
  • a host cell strain may be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed protein in the desired fashion.
  • modifications of the polypeptide include, but are not limited to, acetylation, carboxylation. glycosylation, phosphorylation, lipidation, and acylation.
  • Post-translational processing which cleaves a “prepro” form of the protein may also be used to facilitate correct insertion, folding and/or function.
  • Different host cells such as CHO, COS, HeLa, MDCK, HEK293, and WI38, which have specific cellular machinery and characteristic mechanisms for such post-translational activities, may be chosen to ensure the correct modification and processing of the foreign protein.
  • cell lines which stably express a polynucleotide of interest may be transformed using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells may be allowed to grow for 1-2 days in an enriched media before they are switched to selective media.
  • the purpose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells which successfully express the introduced sequences.
  • Resistant clones of stably transformed cells may be proliferated using tissue culture techniques appropriate to the cell type.
  • any number of selection systems may be used to recover transformed cell lines. These include, but are not limited to, the herpes simplex virus thymidine kinase (Wigler, M. et al. (1977) Cell 11:223-32) and adenine phosphoribosyltransferase (Lowy, I. et al. (1990) Cell 22:817-23) genes which can be employed in tk.sup.- or aprt.sup.-cells, respectively. Also, antimetabolite, antibiotic or herbicide resistance can be used as the basis for selection; for example, dhfr which confers resistance to methotrexate (Wigler, M. et al. (1980) Proc.
  • npt which confers resistance to the aminoglycosides, neomycin and G-418 (Colbere-Garapin, F. et al (1981) J. Mol. Biol. 150:1-14); and als or pat, which confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively (Murry, supra). Additional selectable genes have been described, for example, trpB, which allows cells to utilize indole in place of tryptophan, or hisD, which allows cells to utilize histinol in place of histidine (Hartman, S. C. and R. C. Mulligan (1988) Proc.
  • marker gene expression suggests that the gene of interest is also present, its presence and expression may need to be confirmed.
  • sequence encoding a polypeptide is inserted within a marker gene sequence, recombinant cells containing sequences can be identified by the absence of marker gene function.
  • a marker gene can be placed in tandem with a polypeptide-encoding sequence under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem gene as well.
  • host cells that contain and express a desired polynucleotide sequence may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations and protein bioassay or immunoassay techniques which include, for example, membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein.
  • a variety of protocols for detecting and measuring the expression of polynucleotide-encoded products, using either polyclonal or monoclonal antibodies specific for the product are known in the art. Examples include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), and fluorescence activated cell sorting (FACS).
  • ELISA enzyme-linked immunosorbent assay
  • RIA radioimmunoassay
  • FACS fluorescence activated cell sorting
  • a two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes on a given polypeptide may be preferred for some applications, but a competitive binding assay may also be employed. These and other assays are described, among other places, in Hampton, R. et al. (1990; Serological Methods, a Laboratory Manual, APS Press, St Paul. Minn.) and Maddox, D. E. et al. (1983; J. Exp. Med.
  • a wide variety of labels and conjugation techniques are known by those skilled in the art and may be used in various nucleic acid and amino acid assays.
  • Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides include oligolabeling, nick translation, end-labeling or PCR amplification using a labeled nucleotide.
  • the sequences, or any portions thereof may be cloned into a vector for the production of an mRNA probe.
  • Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by addition of an appropriate RNA polymerase such as T7, T3, or SP6 and labeled nucleotides.
  • reporter molecules or labels include radionuclides, enzymes, fluorescent, chemiluminescent, or chromogenic agents as well as substrates, cofactors, inhibitors, magnetic particles, and the like.
  • Host cells transformed with a polynucleotide sequence of interest may be cultured under conditions suitable for the expression and recovery of the protein from cell culture.
  • the protein produced by a recombinant cell may be secreted or contained intracellularly depending on the sequence and/or the vector used.
  • expression vectors containing polynucleotides of the invention may be designed to contain signal sequences which direct secretion of the encoded polypeptide through a prokaryotic or eukaryotic cell membrane.
  • Other recombinant constructions may be used to join sequences encoding a polypeptide of interest to nucleotide sequence encoding a polypeptide domain which will facilitate purification of soluble proteins.
  • Such purification facilitating domains include, but are not limited to, metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilized metals, protein A domains that allow purification on immobilized immunoglobulin, and the domain utilized in the FLAGS extension/affinity purification system (Immunex Corp., Seattle, Wash.).
  • metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilized metals
  • protein A domains that allow purification on immobilized immunoglobulin
  • the domain utilized in the FLAGS extension/affinity purification system Immunex Corp., Seattle, Wash.
  • cleavable linker sequences such as those specific for Factor XA or enterokinase (Invitrogen. San Diego, Calif.) between the purification domain and the encoded polypeptide may be used to facilitate purification.
  • One such expression vector provides for expression of a fusion protein containing a polypeptide of interest and a nucleic acid encoding 6 histidine residues preceding a thioredoxin or an enterokinase cleavage site.
  • the histidine residues facilitate purification on IMIAC (immobilized metal ion affinity chromatography) as described in Porath, J. et al. (1992 , Prot. Exp. Purif. 3:263-281) while the enterokinase cleavage site provides a means for purifying the desired polypeptide from the fusion protein.
  • IMIAC immobilized metal ion affinity chromatography
  • polypeptides of the invention may be produced by direct peptide synthesis using solid-phase techniques (Merrifield J. (1963) J. Am. Chem. Soc. 85:2149-2154). Protein synthesis may be performed using manual techniques or by automation. Automated synthesis may be achieved, for example, using Applied Biosystems 431A Peptide Synthesizer (Perkin Elmer). Alternatively, various fragments may be chemically synthesized separately and combined using chemical methods to produce the full length molecule.
  • the present invention further provides binding agents, such as antibodies and antigen-binding fragments thereof, that exhibit immunological binding to a tumor polypeptide disclosed herein, or to a portion, variant or derivative thereof.
  • binding agents such as antibodies and antigen-binding fragments thereof, that exhibit immunological binding to a tumor polypeptide disclosed herein, or to a portion, variant or derivative thereof.
  • An antibody, or antigen-binding fragment thereof is said to “specifically bind,” “immunogically bind,” and/or is “immunologically reactive” to a polypeptide of the invention if it reacts at a detectable level (within, for example, an ELISA assay) with the polypeptide, and does not react detectably with unrelated polypeptides under similar conditions.
  • Immunological binding generally refers to the non-covalent interactions of the type which occur between an immunoglobulin molecule and an antigen for which the immunoglobulin is specific.
  • the strength, or affinity of immunological binding interactions can be expressed in terms of the dissociation constant (K d ) of the interaction, wherein a smaller K d represents a greater affinity.
  • Immunological binding properties of selected polypeptides can be quantified using methods well known in the art. One such method entails measuring the rates of antigen-binding site/antigen complex formation and dissociation, wherein those rates depend on the concentrations of the complex partners, the affinity of the interaction, and on geometric parameters that equally influence the rate in both directions.
  • both the “on rate constant” (K on ) and the “off rate constant” (K off ) can be determined by calculation of the concentrations and the actual rates of association and dissociation.
  • the ratio of K off /K on enables cancellation of all parameters not related to affinity, and is thus equal to the dissociation constant K d . See, generally, Davies et al. (1990) Annual Rev. Biochem. 59:439-473.
  • an “antigen-binding site,” or “binding portion” of an antibody refers to the part of the immunoglobulin molecule that participates in antigen binding.
  • the antigen binding site is formed by amino acid residues of the N-terminal variable (“V”) regions of the heavy (“H”) and light (“L”) chains.
  • V N-terminal variable
  • H heavy
  • L light
  • Three highly divergent stretches within the V regions of the heavy and light chains are referred to as “hypervariable regions” which are interposed between more conserved flanking stretches known as “framework regions,” or “FRs”.
  • FR refers to amino acid sequences which are naturally found between and adjacent to hypervariable regions in immunoglobulins.
  • the three hypervariable regions of a light chain and the three hypervariable regions of a heavy chain are disposed relative to each other in three dimensional space to form an antigen-binding surface.
  • the antigen-binding surface is complementary to the three-dimensional surface of a bound antigen, and the three hypervariable regions of each of the heavy and light chains are referred to as “complementarity-determining regions,” or “CDRs.”
  • Binding agents may be further capable of differentiating between patients with and without a cancer, such as prostate cancer, using the representative assays provided herein.
  • a cancer such as prostate cancer
  • binding agents may be further capable of differentiating between patients with and without a cancer, such as prostate cancer, using the representative assays provided herein.
  • antibodies or other binding agents that bind to a tumor protein will preferably generate a signal indicating the presence of a cancer in at least about 20% of patients with the disease, more preferably at least about 30% of patients.
  • the antibody will generate a negative signal indicating the absence of the disease in at least about 90% of individuals without the cancer.
  • biological samples e.g., blood, sera, sputum, urine and/or tumor biopsies
  • samples e.g., blood, sera, sputum, urine and/or tumor biopsies
  • a cancer as determined using standard clinical tests
  • a statistically significant number of samples with and without the disease will be assayed.
  • Each binding agent should satisfy the above criteria; however, those of ordinary skill in the art will recognize that binding agents may be used in combination to improve sensitivity.
  • a binding agent may be a ribosome, with or without a peptide component, an RNA molecule or a polypeptide.
  • a binding agent is an antibody or an antigen-binding fragment thereof.
  • Antibodies may be prepared by any of a variety of techniques known to those of ordinary skill in the art. See, e.g., Harlow and Lane, Antibodies: A Laboratory Manual , Cold Spring Harbor Laboratory, 1988.
  • antibodies can be produced by cell culture techniques, including the generation of monoclonal antibodies as described herein, or via transfection of antibody genes into suitable bacterial or mammalian cell hosts, in order to allow for the production of recombinant antibodies.
  • an immunogen comprising the polypeptide is initially injected into any of a wide variety of mammals (e.g., mice, rats, rabbits, sheep or goats).
  • the polypeptides of this invention may serve as the immunogen without modification.
  • a superior immune response may be elicited if the polypeptide is joined to a carrier protein, such as bovine serum albumin or keyhole limpet hemocyanin.
  • the immunogen is injected into the animal host, preferably according to a predetermined schedule incorporating one or more booster immunizations, and the animals are bled periodically.
  • Polyclonal antibodies specific for the polypeptide may then be purified from such antisera by, for example, affinity chromatography using the polypeptide coupled to a suitable solid support.
  • Monoclonal antibodies specific for an antigenic polypeptide of interest may be prepared, for example, using the technique of Kohler and Milstein, Eur. J. Immunol. 6:511-519, 1976, and improvements thereto. Briefly, these methods involve the preparation of immortal cell lines capable of producing antibodies having the desired specificity (i.e., reactivity with the polypeptide of interest). Such cell lines may be produced, for example, from spleen cells obtained from an animal immunized as described above. The spleen cells are then immortalized by, for example, fusion with a myeloma cell fusion partner, preferably one that is syngeneic with the immunized animal. A variety of fusion techniques may be employed.
  • 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 polypeptide. 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 polypeptides of this invention may be used in the purification process in, for example, an affinity chromatography step.
  • a number of therapeutically useful molecules are known in the art which comprise antigen-binding sites that are capable of exhibiting immunological binding properties of an antibody molecule.
  • the proteolytic enzyme papain preferentially cleaves IgG molecules to yield several fragments, two of which (the “F(ab)” fragments) each comprise a covalent heterodimer that includes an intact antigen-binding site.
  • the enzyme pepsin is able to cleave IgG molecules to provide several fragments, including the “F(ab′) 2 ”fragment which comprises both antigen-binding sites.
  • An “Fv” fragment can be produced by preferential proteolytic cleavage of an IgM, and on rare occasions IgG or IgA immunoglobulin molecule.
  • Fv fragments are, however, more commonly derived using recombinant techniques known in the art.
  • the Fv fragment includes a non-covalent V H ::V L heterodimer including an antigen-binding site which retains much of the antigen recognition and binding capabilities of the native antibody molecule.
  • V H ::V L heterodimer including an antigen-binding site which retains much of the antigen recognition and binding capabilities of the native antibody molecule.
  • a single chain Fv (“sFv”) polypeptide is a covalently linked V H ::V L heterodimer which is expressed from a gene fusion including V H - and V L -encoding genes linked by a peptide-encoding linker.
  • a number of methods have been described to discern chemical structures for converting the naturally aggregated—but chemically separated—light and heavy polypeptide chains from an antibody V region into an sFv molecule which will fold into a three dimensional structure substantially similar to the structure of an antigen-binding site. See, e.g., U.S. Pat. Nos. 5,091,513 and 5,132,405, to Huston et al.; and U.S. Pat. No. 4,946,778, to Ladner et al.
  • Each of the above-described molecules includes a heavy chain and a light chain CDR set, respectively interposed between a heavy chain and a light chain FR set which provide support to the CDRS and define the spatial relationship of the CDRs relative to each other.
  • CDR set refers to the three hypervariable regions of a heavy or light chain V region. Proceeding from the N-terminus of a heavy or light chain, these regions are denoted as “CDR1,” “CDR2,” and “CDR3” respectively.
  • An antigen-binding site therefore, includes six CDRs, comprising the CDR set from each of a heavy and a light chain V region.
  • a polypeptide comprising a single CDR (e.g., a CDR1, CDR2 or CDR3) is referred to herein as a “molecular recognition unit.” Crystallographic analysis of a number of antigen-antibody complexes has demonstrated that the amino acid residues of CDRs form extensive contact with bound antigen, wherein the most extensive antigen contact is with the heavy chain CDR3. Thus, the molecular recognition units are primarily responsible for the specificity of an antigen-binding site.
  • FR set refers to the four flanking amino acid sequences which frame the CDRs of a CDR set of a heavy or light chain V region. Some FR residues may contact bound antigen; however, FRs are primarily responsible for folding the V region into the antigen-binding site, particularly the FR residues directly adjacent to the CDRS. Within FRs, certain amino residues and certain structural features are very highly conserved. In this regard, all V region sequences contain an internal disulfide loop of around 90 amino acid residues. When the V regions fold into a binding-site, the CDRs are displayed as projecting loop motifs which form an antigen-binding surface.
  • a number of “humanized” antibody molecules comprising an antigen-binding site derived from a non-human immunoglobulin have been described, including chimeric antibodies having rodent V regions and their associated CDRs fused to human constant domains (Winter et al. (1991) Nature 349:293-299; Lobuglio et al. (1989) Proc. Nat. Acad. Sci. USA 86:4220-4224; Shaw et al. (1987) J Immunol. 138:4534-4538; and Brown et al. (1987) Cancer Res. 47:3577-3583), rodent CDRs grafted into a human supporting FR prior to fusion with an appropriate human antibody constant domain (Riechmann et al.
  • the terms “veneered FRs” and “recombinantly veneered FRs” refer to the selective replacement of FR residues from, e.g., a rodent heavy or light chain V region, with human FR residues in order to provide a xenogeneic molecule comprising an antigen-binding site which retains substantially all of the native FR polypeptide folding structure. Veneering techniques are based on the understanding that the ligand binding characteristics of an antigen-binding site are determined primarily by the structure and relative disposition of the heavy and light chain CDR sets within the antigen-binding surface. Davies et al. (1990) Ann. Rev. Biochem. 59:439-473.
  • antigen binding specificity can be preserved in a humanized antibody only wherein the CDR structures, their interaction with each other, and their interaction with the rest of the V region domains are carefully maintained.
  • exterior (e.g., solvent-accessible) FR residues which are readily encountered by the immune system are selectively replaced with human residues to provide a hybrid molecule that comprises either a weakly immunogenic, or substantially non-immunogenic veneered surface.
  • the process of veneering makes use of the available sequence data for human antibody variable domains compiled by Kabat et al., in Sequences of Proteins of Immunological Interest, 4th ed., (U.S. Dept. of Health and Human Services, U.S. Government Printing Office, 1987), updates to the Kabat database, and other accessible U.S. and foreign databases (both nucleic acid and protein). Solvent accessibilities of V region amino acids can be deduced from the known three-dimensional structure for human and murine antibody fragments. There are two general steps in veneering a murine antigen-binding site.
  • the FRs of the variable domains of an antibody molecule of interest are compared with corresponding FR sequences of human variable domains obtained from the above-identified sources.
  • the most homologous human V regions are then compared residue by residue to corresponding murine amino acids.
  • the residues in the murine FR which differ from the human counterpart are replaced by the residues present in the human moiety using recombinant techniques well known in the art. Residue switching is only carried out with moieties which are at least partially exposed (solvent accessible), and care is exercised in the replacement of amino acid residues which may have a significant effect on the tertiary structure of V region domains, such as proline, glycine and charged amino acids.
  • the resultant “veneered” murine antigen-binding sites are thus designed to retain the murine CDR residues, the residues substantially adjacent to the CDRs, the residues identified as buried or mostly buried (solvent inaccessible), the residues believed to participate in non-covalent (e.g., electrostatic and hydrophobic) contacts between heavy and light chain domains, and the residues from conserved structural regions of the FRs which are believed to influence the “canonical” tertiary structures of the CDR loops.
  • monoclonal antibodies of the present invention may be coupled to one or more therapeutic agents.
  • Suitable agents in this regard include radionuclides, differentiation inducers, drugs, toxins, and derivatives thereof.
  • Preferred radionuclides include 90 Y, 123I, 125 I, 131 I, 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.
  • a therapeutic agent may be coupled (e.g., covalently bonded) to a suitable monoclonal antibody either directly or indirectly (e.g., via a linker group).
  • a direct reaction between an agent and an antibody is possible when each possesses a substituent capable of reacting with the other.
  • a nucleophilic group such as an amino or sulfhydryl group
  • on one may be capable of reacting with a carbonyl-containing group, such as an anhydride or an acid halide, or with an alkyl group containing a good leaving group (e.g., a halide) on the other.
  • a linker group can function as a spacer to distance an antibody from an agent in order to avoid interference with binding capabilities.
  • a linker group can also serve to increase the chemical reactivity of a substituent on an agent or an antibody, and thus increase the coupling efficiency. An increase in chemical reactivity may also facilitate the use of agents, or functional groups on agents, which otherwise would not be possible.
  • a linker group which is cleavable during or upon internalization into a cell.
  • a number of different cleavable linker groups have been described. The mechanisms for the intracellular release of an agent from these linker groups include cleavage by reduction of a disulfide bond (e.g., U.S. Pat. No. 4,489,710, to Spitler), by irradiation of a photolabile bond (e.g., U.S. Pat. No.
  • immunoconjugates with more than one agent may be prepared in a variety of ways. For example, more than one agent may be coupled directly to an antibody molecule, or linkers that provide multiple sites for attachment can be used. Alternatively, a carrier can be used.
  • a carrier may bear the agents in a variety of ways, including covalent bonding either directly or via a linker group.
  • Suitable carriers include proteins such as albumins (e.g., U.S. Pat. No. 4,507,234, to Kato et al.), peptides and polysaccharides such as aminodextran (e.g., U.S. Pat. No. 4,699,784, to Shih et al.).
  • a carrier may also bear an agent by noncovalent bonding or by encapsulation, such as within a liposome vesicle (e.g., U.S. Pat. Nos. 4,429,008 and 4,873,088).
  • Carriers specific for radionuclide agents include radiohalogenated small molecules and chelating compounds.
  • U.S. Pat. No. 4,735,792 discloses representative radiohalogenated small molecules and their synthesis.
  • a radionuclide chelate may be formed from chelating compounds that include those containing nitrogen and sulfur atoms as the donor atoms for binding the metal, or metal oxide, radionuclide.
  • U.S. Pat. No. 4,673,562 to Davison et al. discloses representative chelating compounds and their synthesis.
  • the present invention in another aspect, provides T cells specific for a tumor polypeptide disclosed herein, or for a variant or derivative thereof.
  • Such cells may generally be prepared in vitro or ex vivo, using standard procedures.
  • T cells may be isolated from bone marrow, peripheral blood, or a fraction of bone marrow or peripheral blood of a patient, using a commercially available cell separation system, such as the IsolexTM System, available from Nexell Therapeutics, Inc. (Irvine, Calif.; see also U.S. Pat. No. 5,240,856; U.S. Pat. No. 5,215,926; WO 89/06280; WO 91/16116 and WO 92/07243).
  • T cells may be derived from related or unrelated humans, non-human mammals, cell lines or cultures.
  • T cells may be stimulated with a polypeptide, polynucleotide encoding a polypeptide and/or an antigen presenting cell (APC) that expresses such a polypeptide.
  • APC antigen presenting cell
  • Such stimulation is performed under conditions and for a time sufficient to permit the generation of T cells that are specific for the polypeptide of interest.
  • a tumor polypeptide or polynucleotide of the invention is present within a delivery vehicle, such as a microsphere, to facilitate the generation of specific T cells.
  • T cells are considered to be specific for a polypeptide of the present invention if the T cells specifically proliferate, secrete cytokines or kill target cells coated with the polypeptide or expressing a gene encoding the polypeptide.
  • T cell specificity may be evaluated using any of a variety of standard techniques. For example, within a chromium release assay or proliferation assay, a stimulation index of more than two fold increase in lysis and/or proliferation, compared to negative controls, indicates T cell specificity. Such assays may be performed, for example, as described in Chen et al., Cancer Res. 54:1065-1070, 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).
  • a tumor polypeptide 100 ng/ml-100 ⁇ g/ml, preferably 200 ng/ml-25 ⁇ g/ml
  • 3-7 days will typically result in at least a two fold increase in proliferation of the T cells.
  • T cells that have been activated in response to a tumor polypeptide, polynucleotide or polypeptide-expressing APC may be CD4 + and/or CD8 + .
  • Tumor polypeptide-specific T cells may be expanded using standard techniques.
  • the T cells are derived from a patient, a related donor or an unrelated donor, and are administered to the patient following stimulation and expansion.
  • CD4 + or CD8 + T cells that proliferate in response to a tumor polypeptide, polynucleotide or APC can be expanded in number either in vitro or in vivo. Proliferation of such T cells in vitro may be accomplished in a variety of ways. For example, the T cells can be re-exposed to a tumor polypeptide, or a short peptide corresponding to an immunogenic portion of such a polypeptide, with or without the addition of T cell growth factors, such as interleukin-2, and/or stimulator cells that synthesize a tumor polypeptide. Alternatively, one or more T cells that proliferate in the presence of the tumor polypeptide can be expanded in number by cloning. Methods for cloning cells are well known in the art, and include limiting dilution.
  • the present invention concerns formulation of one or more of the polynucleotide, polypeptide, T-cell and/or antibody compositions disclosed herein in pharmaceutically-acceptable carriers for administration to a cell or an animal, either alone, or in combination with one or more other modalities of therapy.
  • compositions as disclosed herein may be administered in combination with other agents as well, such as, e.g., other proteins or polypeptides or various pharmaceutically-active agents.
  • agents such as, e.g., other proteins or polypeptides or various pharmaceutically-active agents.
  • additional agents do not cause a significant adverse effect upon contact with the target cells or host tissues.
  • the compositions may thus be delivered along with various other agents as required in the particular instance.
  • Such compositions may be purified from host cells or other biological sources, or alternatively may be chemically synthesized as described herein.
  • such compositions may further comprise substituted or derivatized RNA or DNA compositions.
  • compositions comprising one or more of the polynucleotide, polypeptide, antibody, and/or T-cell compositions described herein in combination with a physiologically acceptable carrier.
  • the pharmaceutical compositions of the invention comprise immunogenic polynucleotide and/or polypeptide compositions of the invention for use in prophylactic and therapeutic vaccine applications.
  • Vaccine preparation is generally described in, for example, M. F. Powell and M. J. Newman, eds., “Vaccine Design (the subunit and adjuvant approach),” Plenum Press (NY, 1995).
  • such compositions will comprise one or more polynucleotide and/or polypeptide compositions of the present invention in combination with one or more immunostimulants.
  • any of the pharmaceutical compositions described herein can contain pharmaceutically acceptable salts of the polynucleotides and polypeptides of the invention.
  • Such salts can be prepared, for example, 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).
  • illustrative immunogenic compositions e.g., vaccine compositions, of the present invention comprise DNA encoding one or more of the polypeptides as described above, such that the polypeptide is generated in situ.
  • the polynucleotide may be administered within any of a variety of delivery systems known to those of ordinary skill in the art. Indeed, numerous gene delivery techniques are well known in the art, such as those described by Rolland, Crit. Rev. Therap. Drug Carrier Systems 15:143-198, 1998, and references cited therein. Appropriate polynucleotide expression systems will, of course, contain the necessary regulatory DNA regulatory sequences for expression in a patient (such as a suitable promoter and terminating signal).
  • bacterial delivery systems may involve the administration of a bacterium (such as Bacillus-Calmette-Guerrin) that expresses an immunogenic portion of the polypeptide on its cell surface or secretes such an epitope.
  • polynucleotides encoding immunogenic polypeptides described herein are introduced into suitable mammalian host cells for expression using any of a number of known viral-based systems.
  • retroviruses provide a convenient and effective platform for gene delivery systems.
  • a selected nucleotide sequence encoding a polypeptide of the present invention can be inserted into a vector and packaged in retroviral particles using techniques known in the art. The recombinant virus can then be isolated and delivered to a subject.
  • retroviral systems have been described (e.g., U.S. Pat. No.
  • adenovirus-based systems have also been described. Unlike retroviruses which integrate into the host genome, adenoviruses persist extrachromosomally thus minimizing the risks associated with insertional mutagenesis (Haj-Ahmad and Graham (1986) J. Virol. 57:267-274; Beft et al. (1993) J. Virol. 67:5911-5921; Mittereder et al. (1994) Human Gene Therapy 5:717-729; Seth et al. (1994) J. Virol. 68:933-940; Barr et al. (1994) Gene Therapy 1:51-58; Berkner, K. L. (1988) BioTechniques 6:616-629; and Rich et al. (1993) Human Gene Therapy 4:461-476).
  • MV vector systems have also been developed for polynucleotide delivery.
  • AAV vectors can be readily constructed using techniques well known in the art. See, e.g., U.S. Pat. Nos. 5,173,414 and 5,139,941; International Publication Nos. WO 92/01070 and WO 93/03769; Lebkowski et al. (1988) Molec. Cell. Biol. 8:3988-3996; Vincent et al. (1990) Vaccines 90 (Cold Spring Harbor Laboratory Press); Carter, B. J. (1992) Current Opinion in Biotechnology 3:533-539; Muzyczka, N. (1992) Current Topics in Microbiol.
  • Additional viral vectors useful for delivering the polynucleotides encoding polypeptides of the present invention by gene transfer include those derived from the pox family of viruses, such as vaccinia virus and avian poxvirus.
  • vaccinia virus recombinants expressing the novel molecules can be constructed as follows. The DNA encoding a polypeptide is first inserted into an appropriate vector so that it is adjacent to a vaccinia promoter and flanking vaccinia DNA sequences, such as the sequence encoding thymidine kinase (TK). This vector is then used to transfect cells which are simultaneously infected with vaccinia.
  • TK thymidine kinase
  • Homologous recombination serves to insert the vaccinia promoter plus the gene encoding the polypeptide of interest into the viral genome.
  • the resulting TK.sup.(-) recombinant can be selected by culturing the cells in the presence of 5-bromodeoxyuridine and picking viral plaques resistant thereto.
  • a vaccinia-based infection/transfection system can be conveniently used to provide for inducible, transient expression or coexpression of one or more polypeptides described herein in host cells of an organism.
  • cells are first infected in vitro with a vaccinia virus recombinant that encodes the bacteriophage T7 RNA polymerase.
  • This polymerase displays extraordinar specificity in that it only transcribes templates bearing T7 promoters.
  • cells are transfected with the polynucleotide or polynucleotides of interest, driven by a T7 promoter.
  • the polymerase expressed in the cytoplasm from the vaccinia virus recombinant transcribes the transfected DNA into RNA which is then translated into polypeptide by the host translational machinery.
  • the method provides for high level, transient, cytoplasmic production of large quantities of RNA and its translation products. See, e.g., Elroy-Stein and Moss, Proc. Nat'l Acad. Sci. USA (1990) 87:6743-6747; Fuerst et al. Proc. Nat'l Acad. Sci. USA (1986) 83:8122-8126.
  • avipoxviruses such as the fowlpox and canarypox viruses
  • canarypox viruses can also be used to deliver the coding sequences of interest.
  • Recombinant avipox viruses expressing immunogens from mammalian pathogens, are known to confer protective immunity when administered to non-avian species.
  • the use of an Avipox vector is particularly desirable in human and other mammalian species since members of the Avipox genus can only productively replicate in susceptible avian species and therefore are not infective in mammalian cells.
  • Methods for producing recombinant Avipoxviruses are known in the art and employ genetic recombination, as described above with respect to the production of vaccinia viruses. See, e.g., WO 91/12882; WO 89/03429; and WO 92/03545.
  • any of a number of alphavirus vectors can also be used for delivery of polynucleotide compositions of the present invention, such as those vectors described in U.S. Pat. Nos. 5,843,723; 6,015,686; 6,008,035 and 6,015,694.
  • Certain vectors based on Venezuelan Equine Encephalitis (VEE) can also be used, illustrative examples of which can be found in U.S. Pat. Nos. 5,505,947 and 5,643,576.
  • molecular conjugate vectors such as the adenovirus chimeric vectors described in Michael et al. J. Biol. Chem. (1993) 268:6866-6869 and Wagner et al. Proc. Nat'l Acad. Sci. USA (1992) 89:6099-6103, can also be used for gene delivery under the invention.
  • a polynucleotide may be integrated into the genome of a target cell. This integration may be in a specific location and orientation via homologous recombination (gene replacement) or it may be integrated in a random, non-specific location (gene augmentation).
  • the polynucleotide may be stably maintained in the cell as a separate, episomal segment of DNA. Such polynucleotide segments or “episomes” encode sequences sufficient to permit maintenance and replication independent of or in synchronization with the host cell cycle. The manner in which the expression construct is delivered to a cell and where in the cell the polynucleotide remains is dependent on the type of expression construct employed.
  • a polynucleotide is administered/delivered as “naked” DNA, for example as described in Ulmer et al., Science 259:1745-1749, 1993 and reviewed by Cohen, Science 259:1691-1692, 1993.
  • the uptake of naked DNA may be increased by coating the DNA onto biodegradable beads, which are efficiently transported into the cells.
  • a composition of the present invention can be delivered via a particle bombardment approach, many of which have been described.
  • gas-driven particle acceleration can be achieved with devices such as those manufactured by Powderject Pharmaceuticals PLC (Oxford, UK) and Powderject Vaccines Inc. (Madison, Wis.), some examples of which are described in U.S. Pat. Nos. 5,846,796; 6,010,478; 5,865,796; 5,584,807; and EP Patent No. 0500 799.
  • This approach offers a needle-free delivery approach wherein a dry powder formulation of microscopic particles, such as polynucleotide or polypeptide particles, are accelerated to high speed within a helium gas jet generated by a hand held device, propelling the particles into a target tissue of interest.
  • microscopic particles such as polynucleotide or polypeptide particles
  • compositions of the present invention include those provided by Bioject, Inc. (Portland, Oreg.), some examples of which are described in U.S. Pat. Nos. 4,790,824; 5,064,413; 5,312,335; 5,383,851; 5,399,163; 5,520,639 and 5,993,412.
  • the pharmaceutical compositions described herein will comprise one or more immunostimulants in addition to the immunogenic polynucleotide, polypeptide, antibody, T-cell and/or APC compositions of this invention.
  • An immunostimulant refers to essentially any substance that enhances or potentiates an immune response (antibody and/or cell-mediated) to an exogenous antigen.
  • One preferred type of immunostimulant comprises an adjuvant.
  • Many 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.
  • adjuvants are commercially available as, for example, Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, Mich.); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.); AS-2 (SmithKline Beecham, Philadelphia, Pa.); aluminum salts such as aluminum hydroxide gel (alum) or aluminum phosphate; salts of calcium, iron or zinc; an insoluble suspension of acylated tyrosine; acylated sugars; cationically or anionically derivatized polysaccharides; polyphosphazenes; biodegradable microspheres; monophosphoryl lipid A and quil A. Cytokines, such as GM-CSF, interleukin-2, -7, -12, and other like growth factors, may also be used as adjuvants.
  • GM-CSF interleukin-2, -7, -12, and other like growth factors
  • the adjuvant composition is preferably one that induces an immune response predominantly of the Th1 type.
  • High levels of Th1-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 Th1- and Th2-type responses.
  • Th1-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 Mosmann and Coffman, Ann. Rev. Immunol. 7:145-173, 1989.
  • Certain preferred adjuvants for eliciting a predominantly Th1-type response include, for example, a combination of monophosphoryl lipid A, preferably 3-de-O-acylated monophosphoryl lipid A, together with an aluminum salt.
  • MPL® adjuvants are available from Corixa Corporation (Seattle, Wash.; see, for example, U.S. Pat. Nos. 4,436,727; 4,877,611; 4,866,034 and 4,912,094).
  • CpG-containing oligonucleotides in which the CpG dinucleotide is unmethylated also induce a predominantly Th1 response.
  • oligonucleotides are well known and are described, for example, in WO 96/02555, WO 99/33488 and U.S. Pat. Nos. 6,008,200 and 5,856,462. Immunostimulatory DNA sequences are also described, for example, by Sato et al., Science 273:352, 1996.
  • Another preferred adjuvant comprises a saponin, such as Quil A, or derivatives thereof, including QS21 and QS7 (Aquila Biopharmaceuticals Inc., Framingham, Mass.); Escin; Digitonin; or Gypsophila or Chenopodium quinoa saponins .
  • Other preferred formulations include more than one saponin in the adjuvant combinations of the present invention, for example combinations of at least two of the following group comprising QS21, QS7, Quil A, ⁇ -escin, or digitonin.
  • the saponin formulations may be combined with vaccine vehicles composed of chitosan or other polycationic polymers, polylactide and polylactide-co-glycolide particles, poly-N-acetyl glucosamine-based polymer matrix, particles composed of polysaccharides or chemically modified polysaccharides, liposomes and lipid-based particles, particles composed of glycerol monoesters, etc.
  • vaccine vehicles composed of chitosan or other polycationic polymers, polylactide and polylactide-co-glycolide particles, poly-N-acetyl glucosamine-based polymer matrix, particles composed of polysaccharides or chemically modified polysaccharides, liposomes and lipid-based particles, particles composed of glycerol monoesters, etc.
  • the saponins may also be formulated in the presence of cholesterol to form particulate structures such as liposomes or ISCOMs.
  • the saponins may be formulated together with a polyoxyethylene ether or ester, in either a non-particulate solution or suspension, or in a particulate structure such as a paucilamelar liposome or ISCOM.
  • the saponins may also be formulated with excipients such as Carbopol R to increase viscosity, or may be formulated in a dry powder form with a powder excipient such as lactose.
  • the adjuvant system includes the combination of a monophosphoryl lipid A and a saponin derivative, such as the combination of QS21 and 3D-MPL® adjuvant, as described in WO 94/00153, or a less reactogenic composition where the QS21 is quenched with cholesterol, as described in WO 96/33739.
  • a monophosphoryl lipid A and a saponin derivative such as the combination of QS21 and 3D-MPL® adjuvant, as described in WO 94/00153
  • a less reactogenic composition where the QS21 is quenched with cholesterol
  • Other preferred formulations comprise an oil-in-water emulsion and tocopherol.
  • Another particularly preferred adjuvant formulation employing QS21, 3D-MPL® adjuvant and tocopherol in an oil-in-water emulsion is described in WO 95/17210.
  • Another enhanced adjuvant system involves the combination of a CpG-containing oligonucleotide and a saponin derivative particularly the combination of CpG and QS21 is disclosed in WO 00/09159.
  • the formulation additionally comprises an oil in water emulsion and tocopherol.
  • Additional illustrative adjuvants for use in the pharmaceutical compositions of the invention include Montanide ISA 720 (Seppic, France), SAF (Chiron, Calif., United States), ISCOMS (CSL), MF-59 (Chiron), the SBAS series of adjuvants (e.g., SBAS-2 or SBAS-4, available from SmithKline Beecham, Rixensart, Belgium), Detox (Enhanzyn®; Corixa, Hamilton, Mont.), RC-529 (Corixa, Hamilton, Mont.) and other aminoalkyl glucosaminide 4-phosphates (AGPs), such as those described in pending U.S. patent application Ser. Nos. 08/853,826 and 09/074,720, the disclosures of which are incorporated herein by reference in their entireties, and polyoxyethylene ether adjuvants such as those described in WO 99/52549A1.
  • n 1-50
  • A is a bond or —C(O)—
  • R is C 1-50 alkyl or Phenyl C 1-50 alkyl.
  • One embodiment of the present invention consists of a vaccine formulation comprising a polyoxyethylene ether of general formula (I), wherein n is between 1 and 50, preferably 4-24, most preferably 9; the R component is C 1-50 , preferably C 4 -C 20 alkyl and most preferably C 12 alkyl, and A is a bond.
  • the concentration of the polyoxyethylene ethers should be in the range 0.1-20%, preferably from 0.1-10%, and most preferably in the range 0.1-1%.
  • Preferred polyoxyethylene ethers are selected from the following group: polyoxyethylene-9-lauryl ether, polyoxyethylene-9-steoryl ether, polyoxyethylene-8-steoryl ether, polyoxyethylene-4-lauryl ether, polyoxyethylene-35-lauryl ether, and polyoxyethylene-23-lauryl ether.
  • Polyoxyethylene ethers such as polyoxyethylene lauryl ether are described in the Merck index (12 th edition: entry 7717). These adjuvant molecules are described in WO 99/52549.
  • the polyoxyethylene ether according to the general formula (I) above may, if desired, be combined with another adjuvant.
  • a preferred adjuvant combination is preferably with CpG as described in the pending UK patent application GB 9820956.2.
  • an immunogenic composition described herein is delivered to a host via 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.
  • Dendritic cells are highly potent APCs (Banchereau and Steinman, Nature 392:245-251, 1998) and have been shown to be effective as a physiological adjuvant for eliciting prophylactic or therapeutic antitumor immunity (see Timmerman and Levy, Ann. Rev. Med. 50:507-529,1999).
  • 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 marrow, 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 marrow 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 correlates 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 of the invention (or portion or other variant thereof) such that the encoded polypeptide, or an immunogenic portion thereof, is expressed on the cell surface. Such transfection may take place ex vivo, and a pharmaceutical composition comprising such transfected cells may then be used for therapeutic purposes, as described herein. Alternatively, 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 may generally be performed using any methods known in the art, such as those described in WO 97/24447, or the gene gun approach described by Mahvi et al., Immunology and cell Biology 75:456-460, 1997.
  • Antigen loading of dendritic cells may be achieved by incubating dendritic cells or progenitor cells with the tumor polypeptide, 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).
  • the polypeptide Prior to loading, the polypeptide may be covalently conjugated to an immunological partner that provides T cell help (e.g., a carrier molecule).
  • an immunological partner that provides T cell help e.g., a carrier molecule.
  • a dendritic cell may be pulsed with a non-conjugated immunological partner, separately or in the presence of the polypeptide.
  • compositions of this invention may be formulated for any appropriate manner of administration, including for example, topical, oral, nasal, mucosal, intravenous, intracranial, intraperitoneal, subcutaneous and intramuscular administration.
  • Carriers for use within such pharmaceutical compositions are biocompatible, and may also be biodegradable.
  • the formulation preferably provides a relatively constant level of active component release. In other embodiments, however, a more rapid rate of release immediately upon administration may be desired.
  • the formulation of such compositions is well within the level of ordinary skill in the art using known techniques.
  • Illustrative carriers useful in this regard include microparticles of poly(lactide-co-glycolide), polyacrylate, latex, starch, cellulose, dextran and the like.
  • illustrative delayed-release carriers 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 phospholipid (see e.g., U.S. Pat. No. 5,151,254 and PCT applications WO 94/20078, WO/94/23701 and 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 of the condition to be treated or prevented.
  • biodegradable microspheres e.g., polylactate polyglycolate
  • Suitable biodegradable microspheres are disclosed, for example, in U.S. Pat. Nos. 4,897,268; 5,075,109; 5,928,647; 5,811,128; 5,820,883; 5,853,763; 5,814,344, 5,407,609 and 5,942,252.
  • Modified hepatitis B core protein carrier systems such as described in WO/99 40934, and references cited therein, will also be useful for many applications.
  • Another illustrative carrier/delivery system employs a carrier comprising particulate-protein complexes, such as those described in U.S. Pat. No. 5,928,647, which are capable of inducing a class I-restricted cytotoxic T lymphocyte responses in a host.
  • compositions of the invention will often further comprise one or more buffers (e.g., neutral buffered saline or phosphate buffered saline), carbohydrates (e.g., glucose, mannose, sucrose or dextrans), mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, 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 proteins
  • proteins polypeptides or amino acids
  • proteins e.glycine
  • antioxidants e.g., gly
  • compositions described herein may be presented in unit-dose or multi-dose containers, such as sealed ampoules or vials. Such containers are typically sealed in such a way to preserve the sterility and stability of the formulation until use.
  • formulations may be stored as suspensions, solutions or emulsions in oily or aqueous vehicles.
  • a pharmaceutical composition may be stored in a freeze-dried condition requiring only the addition of a sterile liquid carrier immediately prior to use.
  • compositions disclosed herein may be delivered via oral administration to an animal.
  • these compositions may be formulated with an inert diluent or with an assimilable edible carrier, or they may be enclosed in hard- or soft-shell gelatin capsule, or they may be compressed into tablets, or they may be incorporated directly with the food of the diet.
  • the active compounds may even be incorporated with excipients and used in the form of ingestible tablets, buccal tables, troches, capsules, elixirs, suspensions, syrups, wafers, and the like (see, for example, Mathiowitz et al., Nature Mar. 27, 1997;386(6623):410-4; Hwang et al., Crit Rev Ther Drug Carrier Syst 1998;15(3):243-84; U.S. Pat. No. 5,641,515; U.S. Pat. No. 5,580,579 and U.S. Pat. No. 5,792,451).
  • Tablets, troches, pills, capsules and the like may also contain any of a variety of additional components, for example, a binder, such as gum tragacanth, acacia, cornstarch, or gelatin; excipients, such as dicalcium phosphate; a disintegrating agent, such as corn starch, potato starch, alginic acid and the like; a lubricant, such as magnesium stearate; and a sweetening agent, such as sucrose, lactose or saccharin may be added or a flavoring agent, such as peppermint, oil of wintergreen, or cherry flavoring.
  • a binder such as gum tragacanth, acacia, cornstarch, or gelatin
  • excipients such as dicalcium phosphate
  • a disintegrating agent such as corn starch, potato starch, alginic acid and the like
  • a lubricant such as magnesium stearate
  • a sweetening agent such as sucrose, lactose
  • any material used in preparing any dosage unit form should be pharmaceutically pure and substantially non-toxic in the amounts employed.
  • the active compounds may be incorporated into sustained-release preparation and formulations.
  • these formulations will contain at least about 0.1% of the active compound or more, although the percentage of the active ingredient(s) may, of course, be varied and may conveniently be between about 1 or 2% and about 60% or 70% or more of the weight or volume of the total formulation.
  • the amount of active compound(s) in each therapeutically useful composition may be prepared is such a way that a suitable dosage will be obtained in any given unit dose of the compound. Factors such as solubility, bioavailability, biological half-life, route of administration, product shelf life, as well as other pharmacological considerations will be contemplated by one skilled in the art of preparing such pharmaceutical formulations, and as such, a variety of dosages and treatment regimens may be desirable.

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US10/294,025 US20030185830A1 (en) 1997-02-25 2002-11-12 Compositions and methods for the therapy and diagnosis of prostate cancer
PCT/US2003/035961 WO2004052276A2 (fr) 2002-11-12 2003-11-12 Compositions et procedes pour la therapie et le diagnostic du cancer de la prostate
JP2004559110A JP2006515749A (ja) 2002-11-12 2003-11-12 前立腺癌の治療および診断のための組成物および方法
AU2003302892A AU2003302892A1 (en) 2002-11-12 2003-11-12 Compositions and methods for the therapy and diagnosis of prostate cancer
EP03812782A EP1578380A4 (fr) 2002-11-12 2003-11-12 Compositions et procedes pour la therapie et le diagnostic du cancer de la prostate
US11/928,375 US20080233139A1 (en) 1997-02-25 2007-10-30 Compositions and methods for the therapy and diagnosis of prostate cancer
US11/928,383 US20080219988A1 (en) 1997-02-25 2007-10-30 Compositions and methods for the therapy and diagnosis of prostate cancer
US11/928,369 US7939646B2 (en) 1997-02-25 2007-10-30 Compositions and methods for the therapy and diagnosis of prostate cancer
US11/929,390 US20080226607A1 (en) 1997-02-25 2007-10-30 Compositions and methods for the therapy and diagnosis of prostate cancer
US11/929,396 US20080226620A1 (en) 1997-02-25 2007-10-30 Compositions and methods for the therapy and diagnosis of prostate cancer
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US80609997A 1997-02-25 1997-02-25
US90480497A 1997-08-01 1997-08-01
US09/020,956 US6261562B1 (en) 1997-02-25 1998-02-09 Compounds for immunotherapy of prostate cancer and methods for their use
US09/030,607 US6262245B1 (en) 1997-02-25 1998-02-25 Compounds for immunotherapy of prostate cancer and methods for their use
US09/115,453 US6657056B2 (en) 1997-02-25 1998-07-14 Compounds for immunotherapy of prostate cancer and methods for their use
US09/159,812 US6613872B1 (en) 1997-02-25 1998-09-23 Compounds for immunotherapy of prostate cancer and methods for their use
US09/232,149 US6465611B1 (en) 1997-02-25 1999-01-15 Compounds for immunotherapy of prostate cancer and methods for their use
US28894699A 1999-04-09 1999-04-09
US09/352,616 US6395278B1 (en) 1997-02-25 1999-07-13 Prostate specific fusion protein compositions
US09/439,313 US6329505B1 (en) 1997-02-25 1999-11-12 Compositions and methods for therapy and diagnosis of prostate cancer
US44368699A 1999-11-18 1999-11-18
US48367200A 2000-01-14 2000-01-14
US53685700A 2000-03-27 2000-03-27
US56810000A 2000-05-09 2000-05-09
US09/570,737 US7202342B1 (en) 1999-11-12 2000-05-12 Compositions and methods for the therapy and diagnosis of prostate cancer
US09/593,793 US7517952B1 (en) 1997-02-25 2000-06-13 Compositions and methods for the therapy and diagnosis of prostate cancer
US60578300A 2000-06-27 2000-06-27
US09/636,215 US6620922B1 (en) 1997-02-25 2000-08-09 Compositions and methods for the therapy and diagnosis of prostate cancer
US09/651,236 US6818751B1 (en) 1997-08-01 2000-08-29 Compositions and methods for the therapy and diagnosis of prostate cancer
US09/657,279 US6894146B1 (en) 1997-02-25 2000-09-06 Compositions and methods for the therapy and diagnosis of prostate cancer
US09/679,426 US6759515B1 (en) 1997-02-25 2000-10-02 Compositions and methods for the therapy and diagnosis of prostate cancer
US09/685,166 US6630305B1 (en) 1999-11-12 2000-10-10 Compositions and methods for the therapy and diagnosis of prostate cancer
US70972900A 2000-11-09 2000-11-09
US09/759,143 US6800746B2 (en) 1997-02-25 2001-01-12 Compositions and methods for the therapy and diagnosis of prostate cancer
US09/780,669 US20020051977A1 (en) 1997-02-25 2001-02-09 Compositions and methods for the therapy and diagnosis of prostate cancer
US85291101A 2001-05-09 2001-05-09
US09/895,814 US20020193296A1 (en) 1997-02-25 2001-06-29 Compositions and methods for the therapy and diagnosis of prostate cancer
US10/012,896 US6943236B2 (en) 1997-02-25 2001-12-10 Compositions and methods for the therapy and diagnosis of prostate cancer
US10/144,678 US7033827B2 (en) 1997-02-25 2002-05-09 Prostate-specific polynucleotide compositions
US10/294,025 US20030185830A1 (en) 1997-02-25 2002-11-12 Compositions and methods for the therapy and diagnosis of prostate cancer

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US11/928,369 Continuation US7939646B2 (en) 1997-02-25 2007-10-30 Compositions and methods for the therapy and diagnosis of prostate cancer
US11/929,396 Continuation US20080226620A1 (en) 1997-02-25 2007-10-30 Compositions and methods for the therapy and diagnosis of prostate cancer
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US7939646B2 (en) 2011-05-10
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