WO2001051633A2 - 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
WO2001051633A2
WO2001051633A2 PCT/US2001/001574 US0101574W WO0151633A2 WO 2001051633 A2 WO2001051633 A2 WO 2001051633A2 US 0101574 W US0101574 W US 0101574W WO 0151633 A2 WO0151633 A2 WO 0151633A2
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Prior art keywords
seq
sequence
cdna sequence
polypeptide
sequences
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PCT/US2001/001574
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English (en)
French (fr)
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WO2001051633A3 (en
WO2001051633A9 (en
Inventor
Jiangchun Xu
Davin C. Dillon
Jennifer L. Mitcham
Susan L. Harlocker
Yuqiu Jiang
Steven G. Reed
Michael D. Kalos
Gary Richard Fanger
Craig H. Day
Marc W. Retter
John A. Stolk
Yasir A.W. Skeiky
Aijun Wang
Madeleine Joy Meagher
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Corixa Corporation
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Priority to HU0203968A priority Critical patent/HUP0203968A3/hu
Priority to BR0107643-4A priority patent/BR0107643A/pt
Priority to CA002397741A priority patent/CA2397741A1/en
Priority to MXPA02006934A priority patent/MXPA02006934A/es
Priority to AU34474/01A priority patent/AU3447401A/en
Priority to EP01906582A priority patent/EP1261708A2/en
Application filed by Corixa Corporation filed Critical Corixa Corporation
Priority to JP2001551207A priority patent/JP2003528591A/ja
Priority to IL15073201A priority patent/IL150732A0/xx
Publication of WO2001051633A2 publication Critical patent/WO2001051633A2/en
Publication of WO2001051633A3 publication Critical patent/WO2001051633A3/en
Priority to NO20023402A priority patent/NO20023402L/no
Publication of WO2001051633A9 publication Critical patent/WO2001051633A9/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/461—Cellular immunotherapy characterised by the cell type used
    • A61K39/4611—T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/463—Cellular immunotherapy characterised by recombinant expression
    • A61K39/4632—T-cell receptors [TCR]; antibody T-cell receptor constructs
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464493—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]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • A61P37/02—Immunomodulators
    • A61P37/04—Immunostimulants
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • 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)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/53—DNA (RNA) vaccination
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2760/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses negative-sense
    • C12N2760/00011—Details
    • C12N2760/16011—Orthomyxoviridae
    • C12N2760/16022—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 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. In spite of considerable research into therapies for the disease, prostate cancer remains difficult to treat. Commonly, treatment is based on surgery and/or radiation therapy, but these methods are ineffective in a significant percentage of cases. Two previously identified prostate specific proteins - prostate specific antigen (PSA) and prostatic acid phosphatase (PAP) - have limited therapeutic and diagnostic potential.
  • PSA prostate specific antigen
  • PAP prostatic acid phosphatase
  • PSA levels do not always correlate well with the presence of prostate cancer, being positive in a percentage of non-prostate cancer cases, including benign prostatic hyperplasia (BPH). Furthermore, PSA measurements correlate with prostate volume, and do not indicate the level of metastasis.
  • BPH benign prostatic hyperplasia
  • 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, 618-626, 630, 631, 634, 636, 639-655, 674, 680, 681, 711, 713, 716, 720-722, 735, 737-739, 751, 753, 764, 765, 773-776 and 786-788;
  • 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, 627-629, 632, 633, 635, 637, 638, 656-671, 675, 683, 684, 710, 712, 714, 715, 717-719, 723-734, 736, 740-750, 752, 754, 755, 766-772, 777-785 and 789-791.
  • 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.
  • 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, 627- 629, 632, 633, 635, 637, 638, 656-671, 675, 683, 684, 710, 712, 714, 715, 717-719, 723-734, 736, 740-750, 752,
  • 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.
  • the present invention provides pharmaceutical 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 that 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 inimunogenicity 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.
  • Figure 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 effecto ⁇ target ratios, as indicated.
  • Figures 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.
  • Figure 2A data is presented for fibroblasts pulsed with the P2S-12 peptide, as compared to fibroblasts pulsed with a control E75 peptide.
  • Figure 2B data is presented for fibroblasts expressing P502S, as compared to fibroblasts expressing HER.-2/neu.
  • Figure 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.
  • Figure 4 illustrates the ability of T cell lines generated from P1S#10 immunized mice to specifically lyse PlS#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.
  • Figure 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.
  • Figures 6A and 6B are graphs illustrating the specificity of a CD8 + cell line (3A-1) for a representative prostate-specific antigen (P501S).
  • Figure 6A shows the results of a 51 Cr release assay. The percent specific lysis is shown as a series of effecto ⁇ target ratios, as indicated.
  • Figure 6B shows the production of interferon- gamma by 3A-1 cells stimulated with autologous B-LCL transduced with P501S, at varying effector:target rations as indicated.
  • Figure 7 is a Western blot showing the expression of P501S in baculovirus.
  • Figure 8 illustrates the results of epitope mapping studies on P501S.
  • Figure 9 is a schematic representation of the P501S protein showing the location of transmembrane domains and predicted intracellular and extracellular domains.
  • Figure 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 22q 11.2
  • Figure 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 F 1-13
  • SEQ ID NO 53 s the determined cDNA sequence for P47 SEQ ID NO 54 s the determined cDNA sequence for P49 SEQ ID NO 55 s the determined cDNA sequence for P50 SEQ ID NO 56 s the determined cDNA sequence for P53 SEQ ID NO 57 s the determined cDNA sequence for P55 SEQ ID NO 58 s the determined cDNA sequence for P60 SEQ ID NO 59 s the determined cDNA sequence for P64 SEQ ID NO 60 s the dete ⁇ nined cDNA sequence for P65 SEQ ID NO 61 s the determined cDNA sequence for P73 SEQ ID NO 62 s the determined cDNA sequence for P75 SEQ ID NO 63 s 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
  • SEQ ID NO: 68 is the determined cDNA sequence for P82 SEQ ID NO: 69 is the determined cDNA sequence for Ul-3064 SEQ ID NO: 70 is the determined cDNA sequence for Ul-3065 SEQ ID NO: 71 is the determined cDNA sequence for Vl-3692 SEQ ID NO: 72 is the determined cDNA sequence for 1 A-3905 SEQ ID NO: 73 is the determined cDNA sequence for VI -3686 SEQ ID NO: 74 is the determined cDNA sequence for Rl-2330 SEQ ID NO: 75 is the determined cDNA sequence for 1B-3976 SEQ ID NO: 76 is the determined cDNA sequence for Vl-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:
  • 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 Fl-12
  • SEQ ID NO: 108 is the predicted amino acid sequence for Fl-12
  • SEQ ID NO: 109 is the determined full length cDNA sequence for Jl-17
  • SEQ ID NO: 110 is the determined full length cDNA sequence for Ll-12 (also referred to as P501 S)
  • SEQ ID NO: 111 is the determined full length cDNA sequence for Nl- 1862 (also referred to as P503S)
  • SEQ ID NO: 112 is the predicted amino acid sequence for Jl-17
  • SEQ ID NO: 113 is the predicted amino acid sequence for Ll-12 (also referred to as P501S)
  • SEQ ID NO: 114 is the predicted amino acid sequence for Nl-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 PI 02 SEQ ID NO: 121 is the determined cDNA sequence for PI 10 SEQ ID NO: 122 is the determined cDNA sequence for PI 11 SEQ ID NO: 123 is the determined cDNA sequence for PI 14 SEQ ID NO: 124 is the determined cDNA sequence for PI 15 SEQ ID NO: 125 is the determined cDNA sequence for PI 16 SEQ ID NO: 126 is the determined cDNA sequence for PI 24 SEQ ID NO: 127 is the determined cDNA sequence for PI 26 SEQ ID NO: 128 is the determined cDNA sequence for P130 SEQ ID NO: 129 is the
  • 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 PI 37
  • SEQ ID NO: 164 is the deteimined cDNA sequence for P194
  • SEQ ID NO: 165 is the determined cDNA sequence for PI 95
  • SEQ ID NO: 166 is the determined cDNA sequence for PI 96
  • 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 predicted 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 predicted amino acid sequence for P703P-DE13
  • SEQ ID NO: 177 is the determined cDNA sequence for P703P-DE14
  • SEQ ID NO: 178 is the predicted amino acid sequence for P703P-DE14
  • SEQ ID NO: 179 is the determined extended cDNA sequence for 1G-
  • 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-
  • SEQ ID NO: 182 is the determined extended cDNA sequence for 1G-
  • SEQ ID NO: 183 is the determined extended cDNA sequence for 1H-
  • SEQ ID NO: 184 is the determined extended cDNA sequence for 1H-
  • 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-
  • SEQ ID NO: 187 is the determined extended cDNA sequence for 1H-
  • SEQ ID NO: 188 is the determined extended cDNA sequence for II-
  • SEQ ID NO: 189 is the determined 3' cDNA sequence for 11-4810
  • SEQ ID NO: 190 is the determined 3' cDNA sequence for 11-4811
  • 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-
  • SEQ ID NO: 193 is the determined extended cDNA sequence for 1K-
  • 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-
  • 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-
  • SEQ ID NO: 201 is the determined extended cDNA sequence for 1D.1-
  • SEQ ID NO: 202 is the determined extended cDNA sequence for 1D-
  • SEQ ID NO: 203 is the determined extended cDNA sequence for 1D-
  • 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-
  • SEQ ID NO: 206 is the determined extended cDNA sequence for 1D-
  • SEQ ID NO: 207 is the determined cDNA sequence for 10-d8fwd
  • SEQ ID NO: 208 is the determined cDNA sequence for 10-HlOcon
  • SEQ ID NO: 209 is the determined cDNA sequence for 11-C8rev
  • SEQ ID NO: 210 is the determined cDNA sequence for 7.g6fwd
  • 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
  • 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: 308 is the detennined 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 predicted amino acid sequence for P703PDE5 SEQ ID NO: 328 is the determined cDNA sequence for P703P6.26 SEQ ID NO: 329 is the predicted amino acid sequence for P703P6.26 SEQ ID NO: 330 is the determined cDNA sequence for P703PX-23
  • SEQ ID NO: 331 is the predicted 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 predicted 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 predicted 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
  • SEQ ID NO: 347 is the determined cDNA sequence for a clone showing homology to Homo sapiens natural resistance-associated macrophage protein2
  • 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 deteimined 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 predicted amino acid sequence encoded by the sequence of SEQ ID NO: 366.
  • SEQ ID NO: 377 is the predicted amino acid sequence encoded by the sequence of SEQ ID NO: 372.
  • SEQ ID NO: 378 is the predicted amino acid sequence encoded by the sequence of SEQ ID NO: 373.
  • SEQ ID NO: 379 is the predicted amino acid sequence encoded by the sequence of SEQ ID NO: 374.
  • SEQ ID NO: 380 is the predicted 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 predicted amino acid sequence for P71 IP.
  • SEQ ID NO: 384 is the cDNA sequence for PIOOOC.
  • 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 23399.
  • 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
  • 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
  • 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 P71 OP.
  • SEQ ID NO:472 is a cDNA sequence for PIOOIC.
  • 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 predicted amino acid sequence encoded by the sequence of SEQ ID NO: 474.
  • SEQ ID NO: 478 is a second predicted amino acid sequence encoded by the sequence of SEQ ID NO: 474.
  • SEQ ID NO: 479 is the predicted amino acid sequence encoded by the sequence of SEQ ID NO: 475.
  • SEQ ID NO: 480 is a first predicted amino acid sequence encoded by the sequence of SEQ ID NO: 473.
  • SEQ ID NO: 481 is a second predicted amino acid sequence encoded by the sequence of SEQ ID NO: 473.
  • SEQ ID NO: 482 is a third predicted amino acid sequence encoded by the sequence of SEQ ID NO: 473.
  • SEQ ID NO: 483 is a fourth predicted 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 Ral 2.
  • 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 predicted amino acid sequence encoded by SEQ
  • SEQ ID NO: 526 is the full-length cDNA sequence for P790P.
  • SEQ ID NO: 527 is the predicted 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: 530
  • SEQ ID NO: 531 is the cDNA sequence of the open reading frame of SEQ ID NO: 530.
  • SEQ ID NO: 532 is the predicted 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 predicted 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 predicted amino acid sequence encoded by SEQ ID NO: 535.
  • SEQ ID NO: 538 is the predicted amino acid sequence encoded by SEQ
  • SEQ ID NO: 539 is the peptide P501S-370.
  • SEQ ID NO: 540 is the peptide P501 S-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 predicted 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 predicted
  • SEQ ID NO: 574 is the amino acid sequence encoded by a second predicted ORF of SEQ ID NO: 570.
  • SEQ ID NO: 575 is the amino acid sequence encoded by a predicted ORF of SEQ ID NO: 571.
  • SEQ ID NO: 576-586 are amino acid sequences encoded by predicted 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 predicted
  • SEQ ID NO: 591 is an extended cDNA sequence for P1020C.
  • SEQ ID NO: 592 is the predicted 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 P51 OS 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
  • SEQ ID NO: 618 is the cDNA sequence of the gene DD3.
  • SEQ ID NO: 619 is an extended cDNA sequence for P714P.
  • SEQ ID NO: 620-622 are the cDNA sequences for splice variants of P704P.
  • SEQ ID NO: 623 is the cDNA sequence of a splice variant of P553S referred to as P553S- 14.
  • SEQ ID NO: 624 is the cDNA sequence of a splice variant of P553S referred to as P553S-12.
  • SEQ ID NO: 625 is the cDNA sequence of a splice variant of P553S referred to as P553S-10.
  • SEQ ID NO: 626 is the cDNA sequence of a splice variant of P553S referred to as P553S-6.
  • SEQ ID NO: 627 is the amino acid sequence encoded by SEQ ID NO: 626.
  • SEQ ID NO: 628 is a first amino acid sequence encoded by SEQ ID NO: 623.
  • SEQ ID NO: 629 is a second amino acid sequence encoded by SEQ ID NO: 628.
  • SEQ ID NO: 630 is a first full-length cDNA sequence for prostate-specific transglutaminase gene (also referred to herein as P558S).
  • SEQ ID NO: 631 is a second full-length cDNA sequence for prostate-specific transglutaminase gene.
  • SEQ ID NO: 632 is the amino acid sequence encoded by the sequence of SEQ ID NO: 630.
  • SEQ ID NO: 633 is the amino acid sequence encoded by the sequence of SEQ ID NO: 631.
  • SEQ ID NO: 634 is the full-length cDNA sequence for P788P.
  • SEQ ID NO: 635 is the amino acid sequence encoded by SEQ ID NO: 634.
  • SEQ ID NO: 636 is the determined cDNA sequence for a polymorphic variant of P788P.
  • SEQ ID NO: 637 is the amino acid sequence encoded by SEQ ID NO:
  • SEQ ID NO: 638 is the amino acid sequence of peptide 4 from P703P.
  • SEQ ID NO: 639 is the cDNA sequence that encodes peptide 4 from P703P.
  • SEQ ID NO: 640-655 are cDNA sequences encoding epitopes of P703P.
  • SEQ ID NO: 656-671 are the amino acid sequences of epitopes of P703P.
  • SEQ ID NO: 672 and 673 are PCR primers.
  • SEQ ID NO: 674 is the cDNA sequence encoding an N-terminal portion of P788P expressed in E. coli.
  • SEQ ID NO: 675 is the amino acid sequence of the N-terminal portion of P788P expressed in E. coli.
  • SEQ ID NO: 676 is the amino acid sequence of the M. tuberculosis antigen Ral 2.
  • SEQ ID NO: 677 and 678 are PCR primers.
  • SEQ ID NO: 679 is the cDNA sequence for the Ral2-P510S-C construct.
  • SEQ ID NO: 680 is the cDNA sequence for the P510S-C construct.
  • SEQ ID NO: 681 is the cDNA sequence for the P510S-E3 construct.
  • SEQ ID NO: 682 is the amino acid sequence for the Ral2-P510S-C construct.
  • SEQ ID NO: 683 is the amino acid sequence for the P510S-C construct.
  • SEQ ID NO: 684 is the amino acid sequence for the P510S-E3 construct.
  • SEQ ID NO: 685-690 are PCR primers.
  • SEQ ID NO: 691 is the cDNA sequence of the constract Ral2-P775P- ORF3.
  • SEQ ID NO: 692 is the amino acid sequence of the construct Ral 2- P775P-ORF3.
  • SEQ ID NO: 693 and 694 are PCR primers.
  • SEQ ID NO: 695 is the determined amino acid sequence for a P703P His tag fusion protein.
  • SEQ ID NO: 696 is the determined cDNA sequence for a P703P His tag fusion protein.
  • SEQ ID NO: 697 and 698 are PCR primers.
  • SEQ ID NO: 699 is the determined amino acid sequence for a P705P His tag fusion protein.
  • SEQ ID NO: 700 is the determined cDNA sequence for a P705P His tag fusion protein.
  • SEQ ID NO: 701 and 702 are PCR primers.
  • SEQ ID NO: 703 is the determined amino acid sequence for a P71 IP His tag fusion protein.
  • SEQ ID NO: 704 is the determined cDNA sequence for a P71 IP His tag fusion protein.
  • SEQ ID NO: 705 is the amino acid sequence of the M. tuberculosis antigen Ral 2.
  • SEQ ID NO: 706 and 707 are PCR primers.
  • SEQ ID NO: 708 is the determined cDNA sequence for the construct Ral2-P501S-E2.
  • SEQ ID NO: 709 is the determined amino acid sequence for the construct Ral2-P501S-E2.
  • SEQ ID NO: 710 is the amino acid sequence for an epitope of P501S.
  • SEQ ID NO: 711 is the DNA sequence encoding SEQ ID NO: 710.
  • SEQ ID NO: 712 is the amino acid sequence for an epitope of P501S.
  • SEQ ID NO: 713 is the DNA sequence encoding SEQ ID NO: 712.
  • SEQ ID NO: 714 is a peptide employed in epitope mapping studies.
  • SEQ ID NO: 715 is the amino acid sequence for an epitope of P501S.
  • SEQ ID NO: 716 is the DNA sequence encoding SEQ ID NO: 715.
  • SEQ ID NO: 717-719 are the amino acid sequences for CD4 epitopes of
  • SEQ ID NO: 720-722 are the DNA sequences encoding the sequences of SEQ ID NO: 717-719.
  • SEQ ID NO: 723-734 are the amino acid sequences for putative CTL epitopes of P703P.
  • SEQ ID NO: 735 is the full-length cDNA sequence for P789P.
  • SEQ ID NO: 736 is the amino acid sequence encoded by SEQ ID NO: 735.
  • SEQ ID NO: 737 is the determined full-length cDNA sequence for the splice variant of P776P referred to as contig 6.
  • SEQ ID NO: 738-739 are determined full-length cDNA sequences for the splice variant of P776P referred to as contig 7.
  • SEQ ID NO: 740-744 are amino acid sequences encoded by SEQ ID NO: 737.
  • SEQ ID NO: 745-750 are amino acid sequences encoded by the splice variant of P776P referred to as contig 7.
  • SEQ ID NO: 751 is the full-length cDNA sequence for human transmembrane protease serine 2.
  • SEQ ID NO: 752 is the amino acid sequence encoded by SEQ ID NO: 751.
  • SEQ ID NO: 753 is the cDNA sequence encoding the first 209 amino acids of human transmembrane protease serine 2.
  • SEQ ID NO: 754 is the first 209 amino acids of human transmembrane protease serine 2.
  • SEQ ID NO: 755 is the amino acid sequence of peptide 296-322 of
  • SEQ ID NO: 756-759 are PCR primers.
  • SEQ ID NO: 760 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: 761 is the determined cDNA sequence of the Va chain of a
  • SEQ ID NO: 762 is the amino acid sequence encoded by SEQ ID NO 760.
  • SEQ ID NO: 763 is the amino acid sequence encoded by SEQ ID NO 761.
  • SEQ ID NO: 764 is the full-length open reading frame for P768P including stop codon.
  • SEQ ID NO: 765 is the full-length open reading frame for P768P without stop codon.
  • SEQ ID NO: 766 is the amino acid sequence encoded by SEQ ID NO:
  • SEQ ID NO: 767-772 are the amino acid sequences for predicted domains of P768P.
  • SEQ ID NO: 773 is the full-length cDNA sequence of P835P.
  • SEQ ID NO: 774 is the cDNA sequence of the previously identified clone FLJ13581.
  • SEQ ID NO: 775 is the cDNA sequence of the open reading frame for P835P with stop codon.
  • SEQ ID NO: 776 is the cDNA sequence of the open reading frame for P835P without stop codon.
  • SEQ ID NO: 777 is the full-length amino acid sequence for P835P.
  • SEQ ID NO: 778-785 are the amino acid sequences of extracellular and intracellular domains of P835P.
  • SEQ ID NO: 786 is the full-length cDNA sequence for PIOOOC.
  • SEQ ID NO: 787 is the cDNA sequence of the open reading frame for
  • SEQ ID NO: 788 is the cDNA sequence of the open reading frame for PIOOOC, without stop codon.
  • SEQ ID NO: 789 is the full-length amino acid sequence for PIOOOC.
  • SEQ ID NO: 790 is amino acids 1-100 of SEQ ID NO: 789.
  • SEQ ID NO: 791 is amino acids 100-492 of SEQ ID NO: 789.
  • SEQ ID NO: 792 is the amino acid sequence of an ⁇ prepro-P501S recombinant protein.
  • 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 NOs: 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- 626, 630, 631, 634, 636, 639-655, 674, 680, 681, 711, 713, 716, 720-722, 735, 737-739, 751, 753, 764, 765, 773-776 and 786-788, or a sequence that hybridizes under moderately stringent conditions, or, alternatively, under highly stringent conditions, to a polynucleotide sequence set forth in any one of SEQ ID NOs: 1-111,
  • 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, 627-629, 632, 633, 635, 637, 638, 656-671, 675, 683, 684, 710, 712, 714, 715, 717-719, 723-734, 736, 740- 750, 752, 754, 755, 766-772, 777-785 and 789-791.
  • 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.
  • an immunoassay such as an ELISA or T-cell stimulation assay
  • 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.
  • 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.
  • 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, 627-629, 632, 633, 635, 637, 638, 656-671, 675, 683, 684, 710, 712, 714, 715, 717-719, 723-734, 736, 740-750, 752, 754, 755, 766-772, 777-785 and 789-791, or those encoded by a polynucleotide
  • 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 stracture 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 stracture 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 stracture of the resultant protein, which in turn defines the interaction of the protein with other molecules, for example, enzymes, substrates, receptors, D ⁇ A, 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).
  • hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0 + 1); glutamate (+3.0 ⁇ 1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); threonine (-0.4); proline (-0.5 ⁇ 1); alanine (-0.5); histidine (-0.5); cysteine (-1-0); methionine (-1.3); valine (-1.5); leucine (-1.8); isoleucine (-1.8); tyrosine (- 2.3); phenylalanine (-2.5); tryptophan (-3.4).
  • an amino acid can be substituted for another having a similar hydrophilicity value and still obtain a biologically equivalent, and in particular, an immunologically equivalent protein.
  • substitution of amino acids whose hydrophilicity values are within +2 is prefened, those within ⁇ 1 are particularly preferred, and those within ⁇ 0.5 are even more particularly preferred.
  • amino acid substitutions are generally therefore based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like.
  • Exemplary substitutions 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, WI), 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 DC 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. Natl. 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, WI), 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.
  • 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 stracture that could interact with functional epitopes on the first and second polypeptides; and (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes.
  • Preferred peptide linker sequences contain Gly, Asn and Ser residues.
  • linker sequences which may be usefully employed as linkers include those disclosed in Maratea et al., Gene 40:39-46, 1985; Murphy et al., Proc. Natl. Acad. Sci. USA ⁇ 3:8258-8262, 1986; U.S. Patent No. 4,935,233 and U.S. Patent No. 4,751,180.
  • the linker sequence may generally be from 1 to about 50 amino acids in length. Linker sequences are not required when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference.
  • the ligated DNA sequences are operably linked to suitable transcriptional or translational regulatory elements.
  • the regulatory elements responsible for expression of DNA are located only 5' to the DNA sequence encoding the first polypeptides.
  • stop codons required to end translation and transcription termination signals are only present 3' to the DNA sequence encoding the second polypeptide.
  • the fusion polypeptide can comprise a polypeptide as described herein together with an unrelated immunogenic protein, such as an immunogenic protein capable of eliciting a recall response.
  • an immunogenic protein capable of eliciting a recall response.
  • 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 Ral 2 fragment.
  • a Mycobacterium sp. such as a Mycobacterium tuberculosis-derived Ral 2 fragment.
  • Ral 2 compositions and methods for their use in enhancing the expression and/or immunogenicity of heterologous polynucleotide/polypeptide sequences is described in U.S. Patent Application 60/158,585, the disclosure of which is incorporated herein by reference in its entirety. Briefly, Ral 2 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 aviralent strains of M. tuberculosis.
  • the nucleotide sequence and amino acid sequence of MTB32A have been described (for example, U.S. Patent Application 60/158,585; see also, Skeiky et al, Infection and Immun. (1999) 67:3998-4007, incorporated herein by reference).
  • C-terminal fragments of the MTB32A coding sequence express at high levels and remain as a soluble polypeptides throughout the purification process.
  • Ral 2 may enhance the immunogenicity of heterologous immunogenic polypeptides with which it is fused.
  • Ral 2 fusion polypeptide comprises a 14 KD C-terminal fragment corresponding to amino acid residues 192 to 323 of MTB32A.
  • Other preferred Ral 2 polynucleotides generally comprise at least about 15 consecutive nucleotides, at least about 30 nucleotides, at least about 60 nucleotides, at least about 100 nucleotides, at least about 200 nucleotides, or at least about 300 nucleotides that encode a portion of a Ral2 polypeptide.
  • Ral2 polynucleotides may comprise a native sequence (i.e., an endogenous sequence that encodes a Ral 2 polypeptide or a portion thereof) or may comprise a variant of such a sequence.
  • Ral 2 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 Ral 2 polypeptide.
  • Variants preferably exhibit at least about 10% identity, more preferably at least about 80% identity and most preferably at least about 90% identity to a polynucleotide sequence that encodes a native Ral 2 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-termihal 81 amino acids are used, although different fragments that include T-helper epitopes may be used.
  • the immunological fusion partner is the protein known as LYTA, or a portion thereof (preferably a C-terminal portion).
  • LYTA is derived from Streptococcus pneumoniae, which synthesizes an N-acetyl-L-alanine amidase known as amidase LYTA (encoded by the LytA gene; Gene 43:265-292, 1986).
  • LYTA is an autolysin that specifically degrades certain bonds in the peptidoglycan backbone.
  • the C-terminal domain of the LYTA protein is responsible for the affinity to the choline or to some choline analogues such as DEAE. This property has been exploited for the development of E.
  • coli C-LYTA expressing plasmids useful for expression of fusion proteins. Purification of hybrid proteins containing the C-LYTA fragment at the amino terminus has been described (see Biotechnology 10:195-198, 1992). Within a preferred embodiment, a repeat portion of LYTA may be incorporated into a fusion polypeptide. A repeat portion is found in the C-terminal region starting at residue 178. A particularly preferred repeat portion incorporates residues 188-305.
  • Yet another illustrative embodiment involves fusion polypeptides, and the polynucleotides encoding them, wherein the fusion partner comprises a targeting signal capable of directing a polypeptide to the endosomal/lysosomal compartment, as described in U.S. Patent No. 5,633,234.
  • a targeting signal capable of directing a polypeptide to the endosomal/lysosomal compartment, as described in U.S. Patent No. 5,633,234.
  • An immunogenic polypeptide of the invention when fused with this targeting signal, will associate more efficiently with MHC class II molecules and thereby provide enhanced in vivo stimulation of CD4 + T-cells specific for the polypeptide.
  • 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. 55:2149-2146, 1963. Equipment for automated synthesis of polypeptides is commercially available from suppliers such as Perkin Elmer/Applied BioSystems Division (Foster City, CA), and may be operated according to the manufacturer's instractions.
  • 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.
  • the present invention 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 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 NOs: 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, 618-626, 630, 631, 634, 636, 639-655, 674, 680, 681, 711, 713, 716, 720-722, 735, 737-739, 751, 753, 764, 765, 773-776 and 786-788, complements of a polynucleotide sequence set forth in any one of SEQ ID NOs: 1-111, 115-171, 173-175, 177,
  • the present invention provides polynucleotide variants having substantial identity to the sequences disclosed herein in SEQ ID NOs: 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, 618-626, 630, 631, 634, 636, 639-655, 674, 680, 681, 711, 713, 716, 720-722, 735, 737-739, 751, 753, 764, 765, 773-776 and 786-788, for example those comprising at least 70% sequence identity, preferably at least 75%, 80%, 85%, 90%, 95%), 96%, 97%, 98%, or 99% or higher, sequence identity compared to a polynu
  • 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 X SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at 50°C-60°C, 5 X SSC, overnight; followed by washing twice at 65°C for 20 minutes with each of 2X, 0.5X and 0.2X SSC containing 0.1% SDS.
  • 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.
  • 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 perfomied 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, WI), using default parameters.
  • This program embodies several aligmnent 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 Stracture, National Biomedical Research Foundation, Washington DC 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. Natl. 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, WI), 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.
  • nucleotide sequences that encode a polypeptide as described herein. Some of these polynucleotides bear minimal homology to the nucleotide sequence of any native gene. Nonetheless, polynucleotides that vary due to differences in codon usage are specifically contemplated by the present invention. Further, alleles of the genes comprising the polynucleotide sequences provided herein are within the scope of the present invention. Alleles are endogenous genes that are altered as a result of one or more mutations, such as deletions, additions and/or substitutions of nucleotides.
  • mRNA and protein may, but need not, have an altered structure or function. Alleles may be identified using standard techniques (such as hybridization, amplification and/or database sequence comparison). Therefore, in another embodiment of the invention, a mutagenesis approach, such as site-specific mutagenesis, is employed for the preparation of immunogenic variants and/or derivatives of the polypeptides described herein. By this approach, specific modifications in a polypeptide sequence can be made through mutagenesis of the underlying polynucleotides that encode them. These techniques provides a straightforward approach to prepare and test sequence variants, for example, incorporating one or more of the foregoing considerations, by introducing one or more nucleotide sequence changes into the polynucleotide.
  • 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 Ml 3 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.
  • the tenn "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 rales 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. Patent No. 4,237,224, specifically incorporated herein by reference in its entirety.
  • recursive sequence recombination as described in U.S. Patent No. 5,837,458, may be employed. In this approach, iterative cycles of recombination and screening or selection are performed to "evolve" individual polynucleotide variants of the invention having, for example, enhanced immunogenic activity.
  • 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. One will generally prefer to design nucleic acid molecules having gene- complementary stretches of 15 to 25 contiguous nucleotides, or even longer where desired. Hybridization probes may be selected from any portion of any of the sequences disclosed herein.
  • probe and primer sequences are 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. Patent 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. Patent 5,739,119 and U. S.
  • Patent 5,759,829) examples of antisense inhibition have been demonstrated with the nuclear protein cyclin, the multiple drag resistance gene (MDG1), ICAM-1, E-selectin, STK-1, striatal GABA A receptor and human EGF (Jaskulski et al, Science. 1988 Jun 10;240(4858): 1544-6; Vasanrhakumar and Ahmed, Cancer Commun. 1989;1(4):225- 32; Peris et al, Brain Res Mol Brain Res. 1998 Jun 15;57(2):310-20; U. S. Patent 5,801,154; U.S. Patent 5,789,573; U. S. Patent 5,718,709 and U.S. Patent 5,610,288).
  • MDG1 multiple drag resistance gene
  • 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. Patent 5,747,470; U. S. Patent 5,591,317 and U. S. Patent 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 use of an antisense delivery method employing a short peptide vector, termed MPG (27 residues), is also contemplated.
  • 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. 1997 Jul 15;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 Natl Acad Sci U S A. 1987 Dec;84(24):8788-92; Forster and Symons, Cell. 1987 Apr 24;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 Dec;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. 1992 Sep 11 ;20(17):4559-65.
  • hairpin motifs are described by Hampel et al. (Eur. Pat. Appl. Publ. No. EP 0360257), Hampel and Tritz, Biochemistry 1989 Jun 13;28(12):4929-33; Hampel et al, Nucleic Acids Res. 1990 Jan 25;18(2):299-304 and U.
  • 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. Patent 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 adenoviras or adeno-associated vectors), or viral RNA vectors (such as retroviral, semliki forest viras, Sindbis viras vectors).
  • PNAs peptide nucleic acids compositions.
  • PNA is a DNA mimic in which the nucleobases are attached to a pseudopeptide backbone (Good and Nielsen, Antisense Nucleic Acid Drag 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 1997 Jun;15(6):224-9).
  • PNAs have 2-aminoethyl-glycine linkages replacing the normal phosphodiester backbone of DNA (Nielsen et al, Science 1991 Dec 6;254(5037):1497- 500; Hanvey et al, Science. 1992 Nov 27;258(5087):1481-5; Hyrap and Nielsen, Bioorg Med Chem. 1996 Jan;4(l):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, MA). PNA syntheses by either Boc or Fmoc protocols are straightforward using manual or automated protocols (Norton et al, Bioorg Med Chem. 1995 Apr;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 Apr;3(4):437-45; Petersen et al, J Pept Sci.
  • U.S. Patent 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. Methods of characterizing the antisense binding properties of PNAs are discussed in Rose (Anal Chem. 1993 Dec 15;65(24):3545-9) and Jensen et al (Biochemistry. 1997 Apr 22;36(16):5072-7).
  • Rose uses capillary gel electrophoresis to determine binding of PNAs to their complementary oligonucleotide, measuring the relative binding kinetics and stoichiometry. Similar types of measurements were made by Jensen et al. using BIAcoreTM technology.
  • 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, NY, 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) 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, NY, 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. 76:8186, 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 poly A 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: 11-19, 1991) and walking PCR (Parker et al., Nucl Acids. Res. 79:3055-60, 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.
  • polypeptide-encoding nucleotide sequences possessing non-naturally occurring codons For example, 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.
  • the 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 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 Carathers, 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 431 A Peptide Synthesizer (Perkin Elmer, Palo Alto, CA).
  • a newly synthesized peptide may be substantially purified by preparative high performance liquid chromatography (e.g., Creighton, T. (1983) Proteins, Structures and Molecular Principles, WH Freeman and Co., New York, NN.) 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 constract 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 D ⁇ A expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with viras expression vectors (e.g., baculoviras); plant cell systems transformed with viras expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic viras, 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 D ⁇ A expression vectors
  • yeast transformed with yeast expression vectors insect cell systems infected with viras expression vectors (e.g., baculoviras)
  • 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. For example, when cloning in bacterial systems, 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.
  • 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
  • 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 S V40 or EB V 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. ⁇ 5:307-311.
  • 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.
  • An insect system may also be used to express a polypeptide of interest.
  • Autographa califomica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes in Spodoptera fragiperda cells or in Trichoplusia larvae.
  • the sequences encoding the polypeptide may be cloned into a non-essential region of the viras, 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.
  • a number of viral-based expression systems are generally available.
  • sequences encoding a polypeptide of interest may be ligated into an adenoviras transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a non-essential El 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. Natl Acad. Sci. 81:3655-3659).
  • transcription enhancers such as the Rous sarcoma virus (RSV) enhancer
  • 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.
  • RSV Rous sarcoma virus
  • 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 22:811-23) 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. Natl Acad.
  • npt which confers resistance to the aminoglycosides, neomycin and G-418 (Colbere-Garapin, F. et al (1981) J. Mol Biol 750:1-14); 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. Natl. Acad. Sci.
  • 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.
  • a competitive binding assay may also be employed.
  • 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. 158: 1211-1216).
  • 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. These procedures may be conducted using a variety of commercially available kits.
  • Suitable reporter molecules or labels which may be used include radionuchdes, 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 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.
  • the inclusion of 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 (Menifield J. (1963) J. Am. Chem. Soc. 55:2149-2154). Protein synthesis may be performed using manual techniques or by automation. Automated synthesis may be achieved, for example, using Applied Biosy stems 431 A Peptide Synthesizer (Perkin Elmer). Alternatively, various fragments may be chemically synthesized separately and combined using chemical methods to produce the full length molecule. Antibody Compositions. Fragments Thereof and Other Binding Agents
  • 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 o g) can be detennined by calculation of the concentrations and the actual rates of association and dissociation.
  • the ratio of K 0ff /K on enables cancellation of all parameters not related to affinity, and is thus equal to the dissociation constant K .
  • 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.
  • 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. In general, antibodies can be produced by cell culture techniques, including the generation of monoclonal antibodies as described herein, or via transfection of antibody genes into suitable bacterial or mammalian cell hosts, in order to allow for the production of recombinant antibodies.
  • 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 cliromatography 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. (5:511-519, 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 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 heterodimer which is expressed from a gene fusion including V H - and Viz-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 stracture substantially similar to the stracture 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 stractural 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.
  • 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.
  • veneering techniques 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.
  • V region amino acids can be deduced from the known three-dimensional stracture for human and murine antibody fragments.
  • 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 stracture 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 stractural 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 radionuchdes, differentiation inducers, drags, toxins, and derivatives thereof.
  • Preferred radionuchdes include 90 Y, m ⁇ , 125 I, 131 I, 186 Re, 188 Re, 211 At, and 2I2 Bi.
  • Preferred drags 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. Patent No. 4,489,710, to Spitler), by irradiation of a photolabile bond (e.g., U.S. Patent No. 4,625,014, to Senter et al.), by hydrolysis of derivatized amino acid side chains (e.g., U.S. Patent No.
  • 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. Patent No. 4,507,234, to Kato et al.), peptides and polysaccharides such as aminodextran (e.g., U.S. Patent 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. Patent Nos. 4,429,008 and 4,873,088).
  • Carriers specific for radionuchde agents include radiohalogenated small molecules and chelating compounds.
  • U.S. Patent No. 4,735,792 discloses representative radiohalogenated small molecules and their synthesis.
  • a radionuchde 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, radionuchde.
  • U.S. Patent No. 4,673,562 to Davison et al. discloses representative chelating compounds and their synthesis.
  • T cells specific for a tumor polypeptide disclosed herein, or for a variant or derivative thereof 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, CA; see also U.S. Patent No. 5,240,856; U.S. Patent No. 5,215,926; WO 89/06280; WO 91/16116 and WO 92/07243).
  • T cells may be derived from related or unrelated humans, non-human 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. 54:1065-1010, 1994. Alternatively, detection of the proliferation of T cells may be accomplished by a variety of known techniques.
  • T cell proliferation can be detected by measuring an increased rate of DNA synthesis (e.g., by pulse-labeling cultures of T cells with tritiated thymidine and measuring the amount of tritiated thymidine incorporated into DNA).
  • 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 theraputic 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.
  • 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 75:143-198, 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). Alternatively, 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.
  • bacterium such as Bacillus-Calmette-Guerrin
  • 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.
  • retrovirases 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.
  • adenoviruses persist extrachromosomally thus minimizing the risks associated with insertional mutagenesis (Haj-Ahmad and Graham (1986) J. Virol. 57:267-274; Bert 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).
  • AAV 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.
  • 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 virases, such as vaccinia virus and avian poxvirus.
  • vaccinia viras 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. In this particular system, cells are first infected in vitro with a vaccinia viras recombinant that encodes the bacteriophage T7 RNA polymerase.
  • This polymerase displays unparalleled 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. Natl. Acad. Sci. USA (1990) 87:6743- 6747; Fuerst et al. Proc. Natl. Acad. Sci. USA (1986) 83:8122-8126.
  • avipoxviruses such as the fowlpox and canarypox virases
  • Recombinant avipox virases 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 Avipoxvirases are known in the art and employ genetic recombination, as described above with respect to the production of vaccinia virases. See, e.g., WO 91/12882; WO 89/03429; and WO 92/03545.
  • alphaviras vectors can also be used for delivery of polynucleotide compositions of the present invention, such as those vectors described in U.S. Patent 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. Patent Nos. 5,505,947 and 5,643,576.
  • molecular conjugate vectors such as the adenoviras chimeric vectors described in Michael et al. J. Biol. Chem. (1993) 268:6866-6869 and Wagner et al. Proc. Natl. 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 259:1145-1149, 1993 and reviewed by Cohen, Science 259:1691-1692, 1993.
  • the uptake of naked DNA may be increased by coating the DNA onto biodegradable beads, which are efficiently transported into the cells.
  • 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, WI), some examples of which are described in U.S. Patent 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, OR), some examples of which are described in U.S. Patent 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, MI); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, NJ); 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.
  • the adjuvant composition is preferably one that induces an immune response predominantly of the Thl type.
  • High levels of Thl -type cytokines e.g., IFN- ⁇ , TNF ⁇ , IL-2 and IL-12
  • Th2-type cytokines e.g., IL-4, IL-5, IL-6 and IL-10
  • a patient will support an immune response that includes Thl- and Th2- type responses.
  • Thl -type cytokines will increase to a greater extent than the level of Th2-type cytokines.
  • the levels of these cytokines may be readily assessed using standard assays. For a review of the families of cytokines, see Mosmann and Coffman, Ann. Rev. Immunol. 7:145-173, 1989.
  • Certain preferred adjuvants for eliciting a predominantly Thl -type response include, for example, a combination of monophosphoryl lipid A, preferably 3- de-O-acylated monophosphoryl lipid A, together with an aluminum salt.
  • MPL ® adjuvants are available from Corixa Corporation (Seattle, WA; see, for example, US Patent Nos. 4,436,727; 4,877,611; 4,866,034 and 4,912,094).
  • CpG-containing oligonucleotides in which the CpG dinucleotide is linmethylated also induce a predominantly Thl response.
  • oligonucleotides are well known and are described, for example, in WO 96/02555, WO 99/33488 and U.S. Patent Nos. 6,008,200 and 5,856,462. Immunostimulatory DNA sequences are also described, for example, by Sato et al., Science 273:352, 1996.
  • Another preferred adjuvant comprises a saponin, such as Quil A, or derivatives thereof, including QS21 and QS7 (Aquila Biopharmaceuticals Inc., Framingham, MA); Escin; Digitonin; or Gypsophila or Chenopodium quinoa saponins .
  • Other preferred formulations include more than one saponin in the adjuvant combinations of the present invention, for example combinations of at least two of the following group comprising QS21, QS7, Quil A, ⁇ - escin, or digitonin.
  • 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 as described in WO 96/33739.
  • 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, California, United States), ISCOMS (CSL), MF-59 (Chiron), the SBAS series of adjuvants (e.g., SBAS-2 or SBAS-4, available from SmithKline Beecham, Rixensart, Belgium), Detox (Enhanzyn ® ; Corixa, Hamilton, MT), RC-529 (Corixa, Hamilton, MT) and other aminoalkyl glucosaminide 4-phosphates (AGPs), such as those described in pending U.S. Patent Application Serial Nos. 08/853,826 and 09/074,720, the disclosures of which are incorporated herein by reference in their entireties, and polyoxyethylene ether adjuvants such as those described in WO 99/52549A1.
  • n 1-50, A is a bond or -C(O)-, R is C1. 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 .so, preferably C -C 0 alkyl and most preferably C 12 alkyl, and A is a bond.
  • 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: poly oxy ethylene-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.
  • 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. Certain preferred embodiments of the present invention use dendritic cells or progenitors thereof as antigen-presenting 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. 50:501-529, 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) may be used within a vaccine (see Zitvogel et al., Nature Med. 4:594-600, 1998).
  • 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, fit3 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 GDI 1) 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 GDI 1) 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, adenoviras or lentiviras 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 the present 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 earners 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. Patent No. 5,151,254 and PCT applications WO 94/20078, WO/94/23701 and WO 96/06638).
  • 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. Patent 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. Patent 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 1997 Mar 27;386(6623):410-4; Hwang et al, Crit Rev Ther Drug Carrier Syst 1998;15(3):243-84; U. S. Patent 5,641,515; U. S. Patent 5,580,579 and U. S. Patent 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, comstarch, 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, comstarch, 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, lacto
  • 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.
  • compositions of the present invention may alternatively be incorporated with one or more excipients in the form of a mouthwash, dentifrice, buccal tablet, oral spray, or sublingual orally-administered formulation.
  • the active ingredient may be incorporated into an oral solution such as one containing sodium borate, glycerin and potassium bicarbonate, or dispersed in a dentifrice, or added in a therapeutically-effective amount to a composition that may include water, binders, abrasives, flavoring agents, foaming agents, and humectants.
  • the compositions may be fashioned into a tablet or solution form that may be placed under the tongue or otherwise dissolved in the mouth.
  • solutions of the active compounds as free base or pharmacologically acceptable salts may be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose.
  • Dispersions may also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils.
  • compositions suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions (for example, see U. S. Patent 5,466,468).
  • sterile aqueous solutions or dispersions for example, see U. S. Patent 5,466,468,.
  • the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and/or vegetable oils.
  • polyol e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like
  • suitable mixtures thereof e.g., vegetable oils
  • vegetable oils e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like
  • suitable mixtures thereof e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like
  • vegetable oils e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like
  • Proper fluidity may be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion
  • isotonic agents for example, sugars or sodium chloride.
  • Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
  • the solution for parenteral administration in an aqueous solution, should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose.
  • aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration.
  • a sterile aqueous medium that can be employed will be known to those of skill in the art in light of the present disclosure.
  • one dosage may be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion, (see for example, "Remington's Pharmaceutical Sciences” 15th Edition, pages 1035-1038 and 1570- 1580). Some variation in dosage will necessarily occur depending on the condition of the subject being treated. Moreover, for human administration, preparations will of course preferably meet sterility, pyrogenicity, and the general safety and purity standards as required by FDA Office of Biologies standards.
  • compositions disclosed herein may be formulated in a neutral or salt form.
  • Illustrative pharmaceutically-acceptable salts include the acid addition salts (formed with the free amino groups of the protein) and which are fomied with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like. Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective.
  • the carriers can further comprise any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like.
  • solvents dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like.
  • the use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.
  • pharmaceutically-acceptable refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a human.
  • the pharmaceutical compositions may be delivered by intranasal sprays, inhalation, and/or other aerosol delivery vehicles.
  • Methods for delivering genes, nucleic acids, and peptide compositions directly to the lungs via nasal aerosol sprays has been described, e.g., in U. S. Patent 5,756,353 and U. S. Patent 5,804,212.
  • the delivery of drags using intranasal microparticle resins (Takenaga et al, J Controlled Release 1998 Mar 2;52(l-2):81-7) and lysophosphatidyl-glycerol compounds (U. S. Patent 5,725,871) are also well-known in the pharmaceutical arts.
  • illustrative transmucosal drag delivery in the form of a polytetrafluoroetheylene support matrix is described in U. S. Patent 5,780,045.
  • compositions of the present invention are used for the introduction of the compositions of the present invention into suitable host cells/organisms.
  • the compositions of the present invention may be formulated for delivery either encapsulated in a lipid particle, a liposome, a vesicle, a nanosphere, or a nanoparticle or the like.
  • compositions of the present invention can be bound, either covalently or non-covalenfiy, to the surface of such carrier vehicles.
  • liposome and liposome-like preparations as potential drug carriers is generally known to those of skill in the art (see for example, Lasic, Trends Biotechnol 1998 Jul;16(7):307-21; Takakura, Nippon Rinsho 1998 Mar;56(3):691-5; Chandran et al, Indian J Exp Biol. 1997 Aug;35(8):801-9; Margalit, Crit Rev Ther Drag Carrier Syst. 1995;12(2-3):233-61; U.S. Patent 5,567,434; U.S. Patent 5,552,157; U.S. Patent 5,565,213; U.S. Patent 5,738,868 and U.S.
  • Liposomes have been used successfully with a number of cell types that are normally difficult to transfect by other procedures, including T cell suspensions, primary hepatocyte cultures and PC 12 cells (Renneisen et al, J Biol Chem. 1990 Sep 25;265(27): 16337-42; Muller et al, DNA Cell Biol. 1990 Apr;9(3):221-9).
  • liposomes are free of the DNA length constraints that are typical of viral-based delivery systems. Liposomes have been used effectively to introduce genes, various drugs, radiotherapeutic agents, enzymes, virases, transcription factors, allosteric effectors and the like, into a variety of cultured cell lines and animals.
  • liposomes are formed from phospholipids that are dispersed in an aqueous medium and spontaneously form multilamellar concentric bilayer vesicles (also termed multilamellar vesicles (MLVs).
  • MLVs multilamellar vesicles
  • the invention provides for pharmaceutically-acceptable nanocapsule formulations of the compositions of the present invention.
  • Nanocapsules can generally entrap compounds in a stable and reproducible way (see, for example, Quintanar-Guerrero et al, Drag Dev Ind Pharm. 1998 Dec;24(12):l 113-28).
  • ultrafine particles sized around 0.1 ⁇ m
  • Such particles can be made as described, for example, by Couvreur et al, Crit Rev Ther Drug Carrier Syst.
  • the pharmaceutical compositions described herein may be used for the treatment of cancer, particularly for the immunotherapy of prostate cancer.
  • the pharmaceutical compositions described herein are administered to a patient, typically a warm-blooded animal, preferably a human.
  • a patient may or may not be afflicted with cancer.
  • the above pharmaceutical compositions may be used to prevent the development of a cancer or to treat a patient afflicted with a cancer.
  • Pharmaceutical compositions and vaccines may be administered either prior to or following surgical removal of primary tumors and/or treatment such as administration of radiotherapy or conventional chemotherapeutic drags.
  • administration of the pharmaceutical compositions may be by any suitable method, including administration by intravenous, intraperitoneal, intramuscular, subcutaneous, intranasal, intradermal, anal, vaginal, topical and oral routes.
  • immunotherapy may be active immunotherapy, in which treatment relies on the in vivo stimulation of the endogenous host immune system to react against tumors with the administration of immune response-modifying agents (such as polypeptides and polynucleotides as provided herein).
  • immunotherapy may be passive immunotherapy, in which treatment involves the delivery of agents with established tumor-immune reactivity (such as effector cells or antibodies) that can directly or indirectly mediate antitumor effects and does not necessarily depend on an intact host immune system.
  • effector cells include T cells as discussed above, T lymphocytes (such as CD8 cytotoxic T lymphocytes and CD4 T-helper tumor- infiltrating lymphocytes), killer cells (such as Natural Killer cells and lymphokine- activated killer cells), B cells and antigen-presenting cells (such as dendritic cells and macrophages) expressing a polypeptide provided herein.
  • T cell receptors and antibody receptors specific for the polypeptides recited herein may be cloned, expressed and transferred into other vectors or effector cells for adoptive immunotherapy.
  • the polypeptides provided herein may also be used to generate antibodies or anti-idiotypic antibodies (as described above and in U.S. Patent No. 4,918,164) for passive immunotherapy .
  • Effector cells may generally be obtained in sufficient quantities for adoptive immunotherapy by growth in vitro, as described herein.
  • Culture conditions for expanding single antigen-specific effector cells to several billion in number with retention of antigen recognition in vivo are well known in the art.
  • Such in vitro culture conditions typically use intermittent stimulation with antigen, often in the presence of cytokines (such as IL-2) and non-dividing feeder cells.
  • cytokines such as IL-2
  • immunoreactive polypeptides as provided herein may be used to rapidly expand antigen-specific T cell cultures in order to generate a sufficient number of cells for immunotherapy.
  • antigen-presenting cells such as dendritic, macrophage, monocyte, fibroblast and/or B cells
  • antigen-presenting cells may be pulsed with immunoreactive polypeptides or transfected with one or more polynucleotides using standard techniques well known in the art.
  • antigen-presenting cells can be transfected with a polynucleotide having a promoter appropriate for increasing expression in a recombinant virus or other expression system.
  • Cultured effector cells for use in therapy must be able to grow and distribute widely, and to survive long term in vivo.
  • a vector expressing a polypeptide recited herein may be introduced into antigen presenting cells taken from a patient and clonally propagated ex vivo for transplant back into the same patient.
  • Transfected cells may be reintroduced into the patient using any means known in the art, preferably in sterile form by intravenous, intracavitary, intraperitoneal or intratumor administration.
  • the pharmaceutical compositions and vaccines may be administered by injection (e.g., intracutaneous, intramuscular, intravenous or subcutaneous), intranasally (e.g., by aspiration) or orally.
  • injection e.g., intracutaneous, intramuscular, intravenous or subcutaneous
  • intranasally e.g., by aspiration
  • between 1 and 10 doses may be administered over a 52 week period.
  • 6 doses are administered, at intervals of 1 month, and booster vaccinations may be given periodically thereafter.
  • Alternate protocols may be appropriate for individual patients.
  • a suitable dose is an amount of a compound that, when administered as described above, is capable of promoting an anti-tumor immune response, and is at least 10-50% above the basal (i.e., untreated) level.
  • Such response can be monitored by measuring the anti-tumor antibodies in a patient or by vaccine- dependent generation of cytolytic effector cells capable of killing the patient's tumor cells in vitro.
  • Such vaccines should also be capable of causing an immune response that leads to an improved clinical outcome (e.g., more frequent remissions, complete or partial or longer disease-free survival) in vaccinated patients as compared to non- vaccinated patients.
  • the amount of each polypeptide present in a dose ranges from about 25 ⁇ g to 5 mg per kg of host. Suitable dose sizes will vary with the size of the patient, but will typically range from about 0.1 mL to about 5 mL.
  • an appropriate dosage and treatment regimen provides the active compound(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit.
  • a response can be monitored by establishing an improved clinical outcome (e.g., more frequent remissions, complete or partial, or longer disease-free survival) in treated patients as compared to non-treated patients.
  • Increases in preexisting immune responses to a tumor protein generally correlate with an improved clinical outcome.
  • Such immune responses may generally be evaluated using standard proliferation, cytotoxicity or cytokine assays, which may be performed using samples obtained from a patient before and after treatment.
  • a cancer may be detected in a patient based on the presence of one or more prostate tumor proteins and/or polynucleotides encoding such proteins in a biological sample (for example, blood, sera, sputum urine and/or tumor biopsies) obtained from the patient.
  • a biological sample for example, blood, sera, sputum urine and/or tumor biopsies
  • proteins may be used as markers to indicate the presence or absence of a cancer such as prostate cancer.
  • proteins may be useful for the detection of other cancers.
  • the binding agents provided herein generally permit detection of the level of antigen that binds to the agent in the biological sample.
  • Polynucleotide primers and probes may be used to detect the level of mRNA encoding a tumor protein, which is also indicative of the presence or absence of a cancer.
  • a prostate tumor sequence should be present at a level that is at least three fold higher in tumor tissue than in normal tissue
  • the presence or absence of a cancer in a patient may be determined by (a) contacting a biological sample obtained from a patient with a binding agent; (b) detecting in the sample a level of polypeptide that binds to the binding agent; and (c) comparing the level of polypeptide with a predetermined cut-off value.
  • the assay involves the use of binding agent immobilized on a solid support to bind to and remove the polypeptide from the remainder of the sample.
  • the bound polypeptide may then be detected using a detection reagent that contains a reporter group and specifically binds to the binding agent/polypeptide complex.
  • detection reagents may comprise, for example, a binding agent that specifically binds to the polypeptide or an antibody or other agent that specifically binds to the binding agent, such as an anti-immunoglobulin, protein G, protein A or a lectin.
  • a competitive assay may be utilized, in which a polypeptide is labeled with a reporter group and allowed to bind to the immobilized binding agent after incubation of the binding agent with the sample.
  • the extent to which components of the sample inhibit the binding of the labeled polypeptide to the binding agent is indicative of the reactivity of the sample with the immobilized binding agent.
  • Suitable polypeptides for use within such assays include full length prostate tumor proteins and polypeptide portions thereof to which the binding agent binds, as described above.
  • the solid support may be any material known to those of ordinary skill in the art to which the tumor protein may be attached.
  • the solid support may be a test well in a microtiter plate or a nitrocellulose or other suitable membrane.
  • the support may be a bead or disc, such as glass, fiberglass, latex or a plastic material such as polystyrene or polyvinylchloride.
  • the support may also be a magnetic particle or a fiber optic sensor, such as those disclosed, for example, in U.S. Patent No. 5,359,681.
  • the binding agent may be immobilized on the solid support using a variety of techniques known to those of skill in the art, which are amply described in the patent and scientific literature.
  • immobilization refers to both noncovalent association, such as adsorption, and covalent attachment (which may be a direct linkage between the agent and functional groups on the support or may be a linkage by way of a cross-linking agent). Immobilization by adsorption to a well in a microtiter plate or to a membrane is preferred. In such cases, adsorption may be achieved by contacting the binding agent, in a suitable buffer, with the solid support for a suitable amount of time. The contact time varies with temperature, but is typically between about 1 hour and about 1 day.
  • contacting a well of a plastic microtiter plate (such as polystyrene or polyvinylchloride) with an amount of binding agent ranging from about lOng to about 10 ⁇ g, and preferably about 100 ng to about 1 ⁇ g, is sufficient to immobilize an adequate amount of binding agent.
  • a plastic microtiter plate such as polystyrene or polyvinylchloride
  • Covalent attachment of binding agent to a solid support may generally be achieved by first reacting the support with a bifunctional reagent that will react with both the support and a functional group, such as a hydroxyl or amino group, on the binding agent.
  • a bifunctional reagent that will react with both the support and a functional group, such as a hydroxyl or amino group, on the binding agent.
  • the binding agent may be covalently attached to supports having an appropriate polymer coating using benzoquinone or by condensation of an aldehyde group on the support with an amine and an active hydrogen on the binding partner (see, e.g., Pierce Immunotechnology Catalog and Handbook, 1991, at A12-A13).
  • the assay is a two-antibody sandwich assay. This assay may be performed by first contacting an antibody that has been immobilized on a solid support, commonly the well of a microtiter plate, with the sample, such that polypeptides within the sample are allowed to bind to the immobilized antibody.
  • Unbound sample is then removed from the immobilized polypeptide-antibody complexes and a detection reagent (preferably a second antibody capable of binding to a different site on the polypeptide) containing a reporter group is added.
  • a detection reagent preferably a second antibody capable of binding to a different site on the polypeptide
  • the amount of detection reagent that remains bound to the solid support is then determined using a method appropriate for the specific reporter group.
  • the immobilized antibody is then incubated with the sample, and polypeptide is allowed to bind to the antibody.
  • the sample may be diluted with a suitable diluent, such as phosphate-buffered saline (PBS) prior to incubation.
  • PBS phosphate-buffered saline
  • an appropriate contact time is a period of time that is sufficient to detect the presence of polypeptide within a sample obtained from an individual with prostate cancer.
  • the contact time is sufficient to achieve a level of binding that is at least about 95% of that achieved at equilibrium between bound and unbound polypeptide.
  • time necessary to achieve equilibrium may be readily determined by assaying the level of binding that occurs over a period of time. At room temperature, an incubation time of about 30 minutes is generally sufficient.
  • Unbound sample may then be removed by washing the solid support with an appropriate buffer, such as PBS containing 0.1% Tween 20TM.
  • the second antibody which contains a reporter group, may then be added to the solid support.
  • Preferred reporter groups include those groups recited above.
  • the detection reagent is then incubated with the immobilized antibody- polypeptide complex for an amount of time sufficient to detect the bound polypeptide.
  • An appropriate amount of time may generally be determined by assaying the level of binding that occurs over a period of time. Unbound detection reagent is then removed and bound detection reagent is detected using the reporter group.
  • the method employed for detecting the reporter group depends upon the nature of the reporter group. For radioactive groups, scintillation counting or autoradiographic methods are generally appropriate. Spectroscopic methods may be used to detect dyes, luminescent groups and fluorescent groups. Biotin may be detected using avidin, coupled to a different reporter group (commonly a radioactive or fluorescent group or an enzyme). Enzyme reporter groups may generally be detected by the addition of substrate (generally for a specific period of time), followed by spectroscopic or other analysis of the reaction products.
  • the signal detected from the reporter group that remains bound to the solid support is generally compared to a signal that corresponds to a predetermined cut-off value.
  • the cut-off value for the detection of a cancer is the average mean signal obtained when the immobilized antibody is incubated with samples from patients without the cancer.
  • a sample generating a signal that is three standard deviations above the predetermined cut-off value is considered positive for the cancer.
  • the cut-off value is determined using a Receiver Operator Curve, according to the method of Sackett et al., Clinical Epidemiology: A Basic Science for Clinical Medicine, Little Brown and Co., 1985, p. 106-7.
  • the cut-off value may be determined from a plot of pairs of true positive rates (i.e., sensitivity) and false positive rates (100%-specificity) that correspond to each possible cut-off value for the diagnostic test result.
  • the cut-off value on the plot that is the closest to the upper left-hand comer i.e., the value that encloses the largest area
  • a sample generating a signal that is higher than the cut-off value determined by this method may be considered positive.
  • the cut-off value may be shifted to the left along the plot, to minimize the false positive rate, or to the right, to minimize the false negative rate.
  • a sample generating a signal that is higher than the cut-off value determined by this method is considered positive for a cancer.
  • the assay is performed in a flow-through or strip test format, wherein the binding agent is immobilized on a membrane, such as nitrocellulose.
  • a membrane such as nitrocellulose.
  • polypeptides within the sample bind to the immobilized binding agent as the sample passes through the membrane.
  • a second, labeled binding agent then binds to the binding agent-polypeptide complex as a solution containing the second binding agent flows through the membrane.
  • the detection of bound second binding agent may then be performed as described above.
  • the strip test format one end of the membrane to which binding agent is bound is immersed in a solution containing the sample.
  • the sample migrates along the membrane through a region containing second binding agent and to the area of immobilized binding agent.
  • Concentration of second binding agent at the area of immobilized antibody indicates the presence of a cancer.
  • concentration of second binding agent at that site generates a pattern, such as a line, that can be read visually. The absence of such a pattern indicates a negative result.
  • the amount of binding agent immobilized on the membrane is selected to generate a visually discernible pattern when the biological sample contains a level of polypeptide that would be sufficient to generate a positive signal in the two-antibody sandwich assay, in the format discussed above.
  • Preferred binding agents for use in such assays are antibodies and antigen-binding fragments thereof.
  • the amount of antibody immobilized on the membrane ranges from about 25 ng to about l ⁇ g, and more preferably from about 50 ng to about 500 ng. Such tests can typically be performed with a very small amount of biological sample.
  • tumor proteins or binding agents of the present invention are suitable for use with the tumor proteins or binding agents of the present invention.
  • the above descriptions are intended to be exemplary only.
  • the above protocols may be readily modified to use tumor polypeptides to detect antibodies that bind to such polypeptides in a biological sample.
  • the detection of such tumor protein specific antibodies may correlate with the presence of a cancer.
  • a cancer may also, or alternatively, be detected based on the presence of T cells that specifically react with a tumor protein in a biological sample.
  • a biological sample comprising CD4 + and/or CD8 + T cells isolated from a patient is incubated with a rumor polypeptide, a polynucleotide encoding such a polypeptide and/or an APC that expresses at least an immunogenic portion of such a polypeptide, and the presence or absence of specific activation of the T cells is detected.
  • Suitable biological samples include, but are not limited to, isolated T cells.
  • T cells may be isolated from a patient by routine techniques (such as by Ficoll/Hypaque density gradient centrifugation of peripheral blood lymphocytes).
  • T cells may be incubated in vitro for 2-9 days (typically 4 days) at 37°C with polypeptide (e.g., 5 - 25 ⁇ g/ml). It may be desirable to incubate another aliquot of a T cell sample in the absence of tumor polypeptide to serve as a control.
  • activation is preferably detected by evaluating proliferation of the T cells.
  • activation is preferably detected by evaluating cytolytic activity.
  • a level of proliferation that is at least two fold greater and/or a level of cytolytic activity that is at least 20% greater than in disease-free patients indicates the presence of a cancer in the patient.
  • a cancer may also, or alternatively, be detected based on the level of mRNA encoding a tumor protein in a biological sample.
  • at least two oligonucleotide primers may be employed in a polymerase chain reaction (PCR) based assay to amplify a portion of a tumor cDNA derived from a biological sample, wherein at least one of the oligonucleotide primers is specific for (i.e., hybridizes to) a polynucleotide encoding the tumor protein.
  • PCR polymerase chain reaction
  • the amplified cDNA is then separated and detected using techniques well known in the art, such as gel electrophoresis.
  • oligonucleotide probes that specifically hybridize to a polynucleotide encoding a tumor protein may be used in a hybridization assay to detect the presence of polynucleotide encoding the tumor protein in a biological sample.
  • oligonucleotide primers and probes should comprise an oligonucleotide sequence that has at least about 60%, preferably at least about 75% and more preferably at least about 90%, identity to a portion of a polynucleotide encoding a tumor protein of the invention that is at least 10 nucleotides, and preferably at least 20 nucleotides, in length.
  • oligonucleotide primers and/or probes hybridize to a polynucleotide encoding a polypeptide described herein under moderately stringent conditions, as defined above.
  • Oligonucleotide primers and/or probes which may be usefully employed in the diagnostic methods described herein preferably are at least 10-40 nucleotides in length.
  • the oligonucleotide primers comprise at least 10 contiguous nucleotides, more preferably at least 15 contiguous nucleotides, of a DNA molecule having a sequence as disclosed herein.
  • Techniques for both PCR based assays and hybridization assays are well known in the art (.see, for example, Mullis et al., Cold Spring Harbor Symp. Quant. Biol, 51:263, 1987; Erlich ed., PCR Technology, Stockton Press, NY, 1989).
  • RNA is extracted from a biological sample, such as biopsy tissue, and is reverse transcribed to produce cDNA molecules.
  • PCR amplification using at least one specific primer generates a cDNA molecule, which may be separated and visualized using, for example, gel electrophoresis.
  • Amplification may be performed on biological samples taken from a test patient and from an individual who is not afflicted with a cancer. The amplification reaction may be performed on several dilutions of cDNA spanning two orders of magnitude. A two-fold or greater increase in expression in several dilutions of the test patient sample as compared to the same dilutions of the non-cancerous sample is typically considered positive.
  • compositions described herein may be used as markers for the progression of cancer.
  • assays as described above for the diagnosis of a cancer may be performed over time, and the change in the level of reactive polypeptide(s) or polynucleotide(s) evaluated.
  • the assays may be performed every 24-72 hours for a period of 6 months to 1 year, and thereafter performed as needed.
  • a cancer is progressing in those patients in whom the level of polypeptide or polynucleotide detected increases over time.
  • the cancer is not progressing when the level of reactive polypeptide or polynucleotide either remains constant or decreases with time.
  • Certain in vivo diagnostic assays may be performed directly on a tumor.
  • One such assay involves contacting tumor cells with a binding agent.
  • the bound binding agent may then be detected directly or indirectly via a reporter group.
  • binding agents may also be used in histological applications.
  • polynucleotide probes may be used within such applications.
  • kits for use within any of the above diagnostic methods typically comprise two or more components necessary for performing a diagnostic assay. Components may be compounds, reagents, containers and/or equipment.
  • one container within a kit may contain a monoclonal antibody or fragment thereof that specifically binds to a tumor protein.
  • Such antibodies or fragments may be provided attached to a support material, as described above.
  • One or more additional containers may enclose elements, such as reagents or buffers, to be used in the assay.
  • Such kits may also, or alternatively, contain a detection reagent as described above that contains a reporter group suitable for direct or indirect detection of antibody binding.
  • a kit may be designed to detect the level of mRNA encoding a tumor protein in a biological sample.
  • Such kits generally comprise at least one oligonucleotide probe or primer, as described above, that hybridizes to a polynucleotide encoding a tumor protein.
  • Such an oligonucleotide may be used, for example, within a PCR or hybridization assay. Additional components that may be present within such kits include a second oligonucleotide and/or a diagnostic reagent or container to facilitate the detection of a polynucleotide encoding a tumor protein.
  • This Example describes the isolation of certain prostate-specific polypeptides from a prostate tumor cDNA library.
  • a human prostate tumor cDNA expression library was constructed from prostate tumor poly A + RNA using a Superscript Plasmid System for cDNA Synthesis and Plasmid Cloning kit (BRL Life Technologies, Gaithersburg, MD 20897) following the manufacturer's protocol. Specifically, prostate tumor tissues were homogenized with polytron (Kinematica, Switzerland) and total RNA was extracted using Trizol reagent (BRL Life Technologies) as directed by the manufacturer. The poly A + RNA was then purified using a Qiagen oligotex spin column mRNA purification kit (Qiagen, Santa Clarita, CA 91355) according to the manufacturer's protocol. First-strand cDNA was synthesized using the NotI/Oligo-dT18 primer. Double-stranded cDNA was synthesized, ligated with EcoRI BAXI adaptors (Invitrogen, San Diego, CA) and digested with Notl. Following size fractionation with Chroma Spin- 1000 columns
  • a normal human pancreas cDNA expression library was prepared from a pool of six tissue specimens (Clontech).
  • the cDNA libraries were characterized by determining the number of independent colonies, the percentage of clones that carried insert, the average insert size and by sequence analysis.
  • the prostate tumor library contained 1.64 x 10 7 independent colonies, with 70% of clones having an insert and the average insert size being 1745 base pairs.
  • the normal pancreas cDNA library contained 3.3 x 10 6 independent colonies, with 69% of clones having inserts and the average insert size being 1120 base pairs.
  • sequence analysis showed that the majority of clones had a full length cDNA sequence and were synthesized from mRNA, with minimal rRNA and mitochondrial DNA contamination.
  • cDNA library subtraction was performed using the above prostate tumor and normal pancreas cDNA libraries, as described by Hara et al. (Blood, 54:189-199, 1994) with some modifications. Specifically, a prostate tumor-specific subtracted cDNA library was generated as follows. Normal pancreas cDNA library (70 ⁇ g) was digested with EcoRI, Notl, and Sful, followed by a filling-in reaction with DNA polymerase Klenow fragment. After phenol-chloroform extraction and ethanol precipitation, the DNA was dissolved in 100 ⁇ l of H O, heat-denatured and mixed with 100 ⁇ l (100 ⁇ g) of Photoprobe biotin (Vector Laboratories, Burlingame, CA).
  • the resulting mixture was irradiated with a 270 W sunlamp on ice for 20 minutes. Additional Photoprobe biotin (50 ⁇ l) was added and the biotinylation reaction was repeated. After extraction with butanol five times, the DNA was ethanol-precipitated and dissolved in 23 ⁇ l H O to form the driver DNA.
  • 10 ⁇ g prostate tumor cDNA library was digested with BamHI and Xhol, phenol chloroform extracted and passed through Chroma spin-400 columns (Clontech). Following ethanol precipitation, the tracer DNA was dissolved in 5 ⁇ l H O.
  • Tracer DNA was mixed with 15 ⁇ l driver DNA and 20 ⁇ l of 2 x hybridization buffer (1.5 M NaCl/10 mM EDTA/50 mM HEPES pH 7.5/0.2% sodium dodecyl sulfate), overlaid with mineral oil, and heat-denatured completely.
  • 2 x hybridization buffer 1.5 M NaCl/10 mM EDTA/50 mM HEPES pH 7.5/0.2% sodium dodecyl sulfate
  • the sample was immediately transferred into a 68 °C water bath and incubated for 20 hours (long hybridization [LH]).
  • the reaction mixture was then subjected to a streptavidin treatment followed by phenol/chloroform extraction. This process was repeated three more times.
  • Subtracted DNA was precipitated, dissolved in 12 ⁇ l H 2 O, mixed with 8 ⁇ l driver DNA and 20 ⁇ l of 2 x hybridization buffer, and subjected to a hybridization at 68 °C for 2 hours (short hybridization [SH]).
  • subtracted cDNA was ligated into BamHI/XhoI site of chloramphenicol resistant pBCSK + (Stratagene, La Jolla, CA 92037) and transformed into ElectroMax E. coli DH10B cells by electroporation to generate a prostate tumor specific subtracted cDNA library (referred to as "prostate subtraction 1").
  • plasmid DNA was prepared from 100 independent clones, randomly picked from the subtracted prostate tumor specific library and grouped based on insert size. Representative cDNA clones were further characterized by DNA sequencing with a Perkin Elmer/Applied Biosystems Division Automated Sequencer Model 373 A (Foster City, CA). Six cDNA clones, hereinafter referred to as Fl-13, Fl-12, Fl-16, Hl-1, Hl-9 and Hl-4, were shown to be abundant in the subtracted prostate-specific cDNA library.
  • the determined 3' and 5' cDNA sequences for Fl-12 are provided in SEQ ID NO: 2 and 3, respectively, with determined 3' cDNA sequences for Fl-13, Fl-16, Hl-1, Hl-9 and Hl-4 being provided in SEQ ID NO: 1 and 4-7, respectively.
  • the cDNA sequences for the isolated clones were compared to known sequences in the gene bank using the EMBL and GenBank databases (release 96).
  • PSA prostate specific antigen
  • Hl-9 was found to be identical to a previously identified human autonomously replicating sequence. No significant homologies to the cDNA sequence for Fl-12 were found.
  • cDNA library subtraction was performed by subtracting the prostate tumor cDNA library described above with the normal pancreas cDNA library and with the three most abundant genes in the previously subtracted prostate tumor specific cDNA library: human glandular kallikrein, prostate specific antigen (PSA), and mitochondria cytochrome C oxidase subunit II. Specifically, 1 ⁇ g each of human glandular kallikrein, PSA and mitochondria cytochrome C oxidase subunit II cDNAs in pCDNA3.1 were added to the driver DNA and subtraction was performed as described above to provide a second subtracted cDNA library hereinafter referred to as the "subtracted prostate tumor specific cDNA library with spike".
  • cDNA clones were isolated from the subtracted prostate tumor specific cDNA library with spike.
  • the determined 3' and 5' cDNA sequences for the clones referred to as Jl-17, Ll-12, Nl-1862, Jl-13, Jl-19, Jl-25, Jl-24, Kl-58, Kl- 63, Ll-4 and Ll-14 are provided in SEQ ID NOS: 8-9, 10-11, 12-13, 14-15, 16-17, 18- 19, 20-21, 22-23, 24-25, 26-27 and 28-29, respectively.
  • the determined 3' cDNA sequences for the clones referred to as Jl-12, Jl-16, Jl-21, Kl-48, Kl-55, Ll-2, Ll-6, Nl-1858, Nl-1860, Nl-1861, Nl-1864 are provided in SEQ ID NOS: 30-40, respectively. Comparison of these sequences with those in the gene bank as described above, revealed no significant homologies to three of the five most abundant DNA species, (Jl-17, Ll-12 and Nl-1862; SEQ ID NOS: 8-9, 10-11 and 12-13, respectively).
  • Jl-12 SEQ ID NO:30
  • Kl-48 SEQ ID NO:33
  • a second subtraction with spike (referred to as "prostate subtraction spike 2") was performed by subtracting a prostate tumor specific cDNA library with spike with normal pancreas cDNA library and further spiked with PSA, Jl-17, pulmonary surfactant-associated protein, mitochondrial DNA, cytochrome c oxidase subunit II, Nl-1862, autonomously replicating sequence, Ll-12 and tumor expression enhanced gene.
  • Four additional clones hereinafter referred to as VI -3686, Rl-2330, 1B-3976 and Vl-3679, were isolated.
  • the determined cDNA sequences for these clones are provided in SEQ ID NO:73-76, respectively. Comparison of these sequences with those in the gene bank revealed no significant homologies to Vl-3686 and Rl- 2330.
  • prostate subtraction 3 An additional subtraction was performed by subtracting a normal prostate cDNA library with normal pancreas cDNA (referred to as "prostate subtraction 3"). This led to the identification of six additional clones referred to as 1G-4761, 1G- 4762, 1H-4766, 1H-4770, 1H-4771 and 1H-4772 (SEQ ID NOS: 93-98). Comparison of these sequences with those in the gene bank revealed no significant homologies to 1G-4761 and 1H-4771 (SEQ ID NOS: 93 and 97, respectively).
  • cDNA clones isolated in prostate subtraction 1 and prostate subtraction 2 were colony PCR amplified and their mRNA expression levels in prostate tumor, normal prostate and in various other normal tissues were determined using microarray technology (Synteni, Palo Alto, CA). Briefly, the PCR amplification products were dotted onto slides in an array fonnat, with each product occupying a unique location in the array.
  • mRNA was extracted from the tissue sample to be tested, reverse transcribed, and fluorescent-labeled cDNA probes were generated.
  • the microarrays were probed with the labeled cDNA probes, the slides scanned and fluorescence intensity was measured. This intensity correlates with the hybridization intensity.
  • Two clones (referred to as P509S and P510S) were found to be over- expressed in prostate tumor and normal prostate and expressed at low levels in all other normal tissues tested (liver, pancreas, skin, bone marrow, brain, breast, adrenal gland, bladder, testes, salivary gland, large intestine, kidney, ovary, lung, spinal cord, skeletal muscle and colon).
  • the determined cDNA sequences for P509S and P510S are provided in SEQ ID NO: 223 and 224, respectively. Comparison of these sequences with those in the gene bank as described above, revealed some homology to previously identified ESTs.
  • mRNA expression levels for the representative prostate-specific polypeptides Fl-16, Hl-1, Jl-17 (also referred to as P502S), Ll-12 (also referred to as P501S), Fl-12 (also referred to as P504S) and Nl- 1862 (also referred to as P503S) were examined in a variety of normal and tumor tissues using RT-PCR.
  • ⁇ -actin was used as an internal control for each of the tissues examined.
  • serial dilutions of the first strand cDNAs were prepared and RT-PCR assays were performed using ⁇ -actin specific primers.
  • ⁇ -actin levels were determined for each reverse transcription reaction from each tissue. DNA contamination was minimized by DNase treatment and by assuring a negative PCR result when using first strand cDNA that was prepared without adding reverse transcriptase.
  • mRNA Expression levels were examined in four different types of tumor tissue (prostate tumor from 2 patients, breast tumor from 3 patients, colon tumor, lung tumor), and sixteen different normal tissues, including prostate, colon, kidney, liver, lung, ovary, pancreas, skeletal muscle, skin, stomach, testes, bone manow and brain.
  • Fl-16 was found to be expressed at high levels in prostate tumor tissue, colon tumor and normal prostate, and at lower levels in normal liver, skin and testes, with expression being undetectable in the other tissues examined.
  • Hl-1 was found to be expressed at high levels in prostate tumor, lung tumor, breast tumor, normal prostate, normal colon and normal brain, at much lower levels in normal lung, pancreas, skeletal muscle, skin, small intestine, bone marrow, and was not detected in the other tissues tested.
  • Jl-17 (P502S) and Ll-12 (P501S) appear to be specifically over-expressed in prostate, with both genes being expressed at high levels in prostate tumor and normal prostate but at low to undetectable levels in all the other tissues examined.
  • Nl-1862 (P503S) was found to be over-expressed in 60% of prostate tumors and detectable in normal colon and kidney.
  • the RT-PCR results thus indicate that Fl-16, Hl-1, Jl-17 (P502S), Nl- 1862 (P503S) and Ll-12 (P501S) are either prostate specific or are expressed at significantly elevated levels in prostate.
  • Ll-12 (P501S) is over-expressed in prostate tumors and normal prostate, while being undetectable in other normal tissues tested.
  • Jl-17 (P502S) was detected in two prostate tumors and not in the other tissues tested.
  • Nl-1862 (P503S) was found to be over- expressed in three prostate tumors and to be expressed in normal prostate, colon and kidney, but not in other tissues tested.
  • Fl-12 (P504S) was found to be highly expressed in two prostate tumors and to be undetectable in all other tissues tested.
  • Ll-12 (P501S) was found to be over-expressed in normal prostate and prostate tumor, with some expression being detected in normal skeletal muscle.
  • Jl-12 and Fl-12 (P504S) were found to be over-expressed in prostate tumor, with expression being lower or undetectable in all other tissues tested.
  • Nl-1862 (P503S) was found to be expressed at high levels in prostate tumor and normal prostate, and at low levels in normal large intestine and normal colon, with expression being undetectable in all other tissues tested.
  • Rl-2330 was found to be over-expressed in prostate tumor and normal prostate, and to be expressed at lower levels in all other tissues tested.
  • 1D-4279 was found to be over- expressed in prostate tumor and normal prostate, expressed at lower levels in normal spinal cord, and to be undetectable in all other tissues tested.
  • PIOOOC and PI 001 C Two of these clones (referred to as PIOOOC and PI 001 C) were found to be over-expressed in prostate tumor and normal prostate, and expressed at low to undetectable levels in all other tissues tested (normal aorta, thymus, resting and activated PBMC, epithelial cells, spinal cord, adrenal gland, fetal tissues, skin, salivary gland, large intestine, bone marrow, liver, lung, dendritic cells, stomach, lymph nodes, brain, heart, small intestine, skeletal muscle, colon and kidney.
  • the determined cDNA sequences for PIOOOC and PIOOIC are provided in SEQ ID NO: 384 and 472, respectively.
  • the sequence of PIOOIC was found to show some homology to the previously isolated Human mRNA for JM27 protein. Subsequent comparison of the sequence of SEQ ID NO: 384 with sequences in the public databases, led to the identification of a full-length cDNA sequence of PIOOOC (SEQ ID NO: 786), which encodes a 492 amino acid sequence. Analysis of the amino acid sequence using the PSORT II program led to the identification of a putative transmembrane domain from amino acids 84-100.
  • the cDNA sequence of the open reading frame of PIOOOC, including the stop codon, is provided in SEQ ID NO: 787, with the open reading frame without the stop codon being provided in SEQ ID NO: 788.
  • the full-length amino acid sequence of PIOOOC is provided in SEQ ID NO: 789.
  • SEQ ID NO: 790 and 791 represent amino acids 1-100 and 100-492 of PIOOOC, respectively.
  • the expression of the polypeptide encoded by the full length cDNA sequence for Fl-12 was investigated by immunohistochemical analysis.
  • Rabbit-anti-P504S polyclonal antibodies were generated against the full length P504S protein by standard techniques. Subsequent isolation and characterization of the polyclonal antibodies were also performed by techniques well known in the art. Immunohistochemical analysis showed that the
  • the rabbit-anti-P504S polyclonal antibody did not appear to label benign prostate cells with the same cytoplasmic granular staining, but rather with light nuclear staining. Analysis of normal tissues revealed that the encoded polypeptide was found to be expressed in some, but not all normal human tissues. Positive cytoplasmic staining with rabbit-anti-P504S polyclonal antibody was found in normal human kidney, liver, brain, colon and lung-associated macrophages, whereas heart and bone marrow were negative.
  • a cDNA subtraction library containing cDNA from normal prostate subtracted with ten other normal tissue cDNAs (brain, heart, kidney, liver, lung, ovary, placenta, skeletal muscle, spleen and thymus) and then submitted to a first round of PCR amplification, was purchased from Clontech. This library was subjected to a second round of PCR amplification, following the manufacturer's protocol. The resulting cDNA fragments were subcloned into the vector pT7 Blue T-vector (Novagen, Madison, WI) and transformed into XL-1 Blue MRF' E. coli (Stratagene). DNA was isolated from independent clones and sequenced using a Perkin Elmer/Applied Biosystems Division Automated Sequencer Model 373A.
  • Fifty-nine positive clones were sequenced. Comparison of the DNA sequences of these clones with those in the gene bank, as described above, revealed no significant homologies to 25 of these clones, hereinafter referred to as P5, P8, P9, PI 8, P20, P30, P34, P36, P38, P39, P42, P49, P50, P53, P55, P60, P64, P65, P73, P75, P76, P79 and P84.
  • the determined cDNA sequences for these clones are provided in SEQ ID NO: 41-45, 47-52 and 54-65, respectively.
  • P29, P47, P68, P80 and P82 (SEQ ID NO: 46, 53 and 66-68, respectively) were found to show some degree of homology to previously identified DNA sequences. To the best of the inventors' knowledge, none of these sequences have been previously shown to be present in prostate.
  • cDNA clones containing the P20 sequence represent splice variants of a gene referred to as P703P.
  • the determined DNA sequence for the variants refened to as DEI, DEI 3 and DEI 4 are provided in SEQ ID NOS: 171, 175 and 177, respectively, with the corresponding predicted amino acid sequences being provided in SEQ ID NO: 172, 176 and 178, respectively.
  • the determined cDNA sequence for an extended spliced form of P703 is provided in SEQ ID NO: 225.
  • the DNA sequences for the splice variants referred to as DE2 and DE6 are provided in SEQ ID NOS: 173 and 174, respectively.
  • P9 was found to be highly expressed in normal prostate and prostate tumor compared to all normal tissues tested except for normal colon which showed comparable expression.
  • P30 similar expression levels were seen in normal prostate and prostate tumor, compared to six of twelve other normal tissues tested. Increased expression was seen in breast tumors, one lung tumor sample and one colon tumor sample, and also in normal PBMC. P29 was found to be over-expressed in prostate tumor (5 of 5) and normal prostate (5 of 5) compared to the majority of normal tissues. However, substantial expression of P29 was observed in normal colon and normal lung (2 of 2). P80 was found to be over-expressed in prostate tumor (5 of 5) and normal prostate (5 of 5) compared to all other normal tissues tested, with increased expression also being seen in colon tumor.
  • the detennined DNA sequences for 10-d8, 10-hlO, 1 l-c8, 8-d4, 8- d9, 8-hl l, 9-fl2 and 9-f3 are provided in SEQ ID NO: 207, 208, 209, 216, 217, 220, 221 and 222, respectively.
  • the determined forward and reverse DNA sequences for 7- g6, 8-b5, 8-b6 and 8-g3 are provided in SEQ ID NO: 210 and 211; 212 and 213; 214 and 215; and 218 and 219, respectively. Comparison of these sequences with those in the gene bank revealed no significant homologies to the sequence of 9-f3.
  • the clones 10-d8, 11 -c8 and 8-hll were found to show some homology to previously isolated ESTs, while 10-hlO, 8-b5, 8-b6, 8-d4, 8-d9, 8-g3 and 9-fl2 were found to show some homology to previously identified genes. Further characterization of 7-G6 and 8-G3 showed identity to the known genes PAP and PSA, respectively.
  • mRNA expression levels for these clones were determined using the micro-array technology described above.
  • the clones 7-G6, 8-G3, 8-B5, 8-B6, 8-D4, 8- D9, 9-F3, 9-F12, 9-H3, 10-A2, 10-A4, 11-C9 and 11-F2 were found to be over- expressed in prostate tumor and normal prostate, with expression in other tissues tested being low or undetectable.
  • Increased expression of 8-F11 was seen in prostate tumor and normal prostate, bladder, skeletal muscle and colon.
  • Increased expression of 10- H10 was seen in prostate tumor and normal prostate, bladder, lung, colon, brain and large intestine.
  • 9-B1 Increased expression of 9-B1 was seen in prostate tumor, breast tumor, and normal prostate, salivary gland, large intestine and skin, with increased expression of 11-C8 being seen in prostate tumor, and normal prostate and large intestine.
  • the determined cDNA sequence of this clone (referred to as 9-A11) is provided in SEQ ID NO: 226. Comparison of this sequence with those in the public databases revealed 99% identity to the known gene HOXB13.
  • P703PDE5 P703P6.26, and P703PX-23 (SEQ ID NO: 326, 328 and 330, with the predicted corresponding amino acid sequences being provided in SEQ ID NO: 327, 329 and 331, respectively) contain additional 5' sequence.
  • P703PDE5 was recovered by screening of a cDNA library (#141-26) with a portion of P703P as a probe.
  • P703P6.26 was recovered from a mixture of three prostate tumor cDNAs and P703PX_23 was recovered from cDNA library (#438-48).
  • the additional sequences include all of the putative mature serine protease along with part of the putative signal sequence.
  • the full-length cDNA sequence for P703P is provided in SEQ ID NO: 524, with the corresponding amino acid sequence being provided in SEQ ID NO: 525.
  • amino acids 164-172 of SEQ ID NO: 525 (SEQ ID NO: 723); amino acids 160-168 of SEQ ID NO: 525 (SEQ ID NO: 724); amino acids 239-247 of SEQ ID NO: 525 (SEQ ID NO: 725); amino acids 118-126 of SEQ ID NO: 525 (SEQ ID NO: 726); amino acids 112-120 of SEQ ID NO: 525 (SEQ ID NO: 727); amino acids 155-164 of SEQ ID NO: 525 (SEQ ID NO: 728); amino acids 117-126 of SEQ ID NO: 525 (SEQ ID NO: 729); amino acids 164-173 of SEQ ID NO: 525 (SEQ ID NO: 730); amino acids 154-163 of SEQ ID NO: 525 (SEQ ID NO: 731); amino acids 163-172 of SEQ ID NO: 525 (SEQ ID NO: 723); amino acids 160-168 of SEQ ID NO: 525 (SEQ ID NO: 724); amino acids 239
  • P703P was found to show some homology to previously identified proteases, such as thrombin.
  • the thrombin receptor has been shown to be preferentially expressed in highly metastatic breast carcinoma cells and breast carcinoma biopsy samples.
  • Introduction of thrombin receptor antisense cDNA has been shown to inhibit the invasion of metastatic breast carcinoma cells in culture.
  • Antibodies against thrombin receptor inhibit thrombin receptor activation and thrombin-induced platelet activation.
  • peptides that resemble the receptor's tethered ligand domain inhibit platelet aggregation by thrombin.
  • P703P may play a role in prostate cancer through a protease-activated receptor on the cancer cell or on stromal cells.
  • the potential trypsin-like protease activity of P703P may either activate a protease-activated receptor on the cancer cell membrane to promote tumorgenesis or activate a protease- activated receptor on the adjacent cells (such as stromal cells) to secrete growth factors and/or proteases (such as matrix metalloproteinases) that could promote tumor angiogenesis, invasion and metastasis. P703P may thus promote tumor progression and/or metastasis through the activation of protease-activated receptor. Polypeptides and antibodies that block the P703P-receptor interaction may therefore be usefully employed in the treatment of prostate cancer.
  • JP PCR subtraction
  • Clones P774P, P775P and P710P showed comparatively lower expression and expression in fewer prostate tumors and BPH samples, with negative to low expression in normal prostate.
  • SEQ ID NO: 552 The amino acid sequences encoded by 16 predicted open reading frames present within the sequence of SEQ ID NO: 552 are provided in SEQ ID NO: 553-568.
  • the full-length cDNA for P711P was obtained by employing the partial sequence of SEQ ID NO: 307 to screen a prostate cDNA library. Specifically, a directionally cloned prostate cDNA library was prepared using standard techniques. One million colonies of this library were plated onto LB/Amp plates. Nylon membrane filters were used to lift these colonies, and the cDNAs which were picked up by these filters were denatured and cross-linked to the filters by UV light.
  • the P711P cDNA fragment of SEQ ID NO: 307 was radio-labeled and used to hybridize with these filters. Positive clones were selected, and cDNAs were prepared and sequenced using an automatic Perkin Elmer/Applied Biosystems sequencer. The determined full-length sequence of P7 I IP is provided in SEQ ID NO: 382, with the corresponding predicted amino acid sequence being provided in SEQ ID NO: 383.
  • P707P and P714P were derived for two clones described above, 11 -C9 and 9-F3, herein after referred to as P707P and P714P, respectively (SEQ ID NO: 333 and 334).
  • P707P was found to be a splice variant of the known gene HoxB13. In contrast, no significant homologies to P714P were found.
  • the cDNA sequence of SEQ ID NO: 475 was found to contain an ORF which encodes the amino acid sequence of SEQ ID NO: 479.
  • the cDNA sequence of SEQ ID NO: 473 was found to contain four ORFs.
  • the predicted amino acid sequences encoded by these ORFs are provided in SEQ ID NO: 480-483. Additional splice variants of P775P are provided in SEQ ID NO: 593-597.
  • P558S is identical to the prostate-specific transglutaminase gene, which is known to have two forms.
  • the full-length sequences for the two forms are provided in SEQ ID NO: 630 and 631, with the corresponding amino acid sequences being provided in SEQ ID NO: 632 and 633, respectively.
  • the cDNA sequence of SEQ ID NO: 631 has a 15 pair base insert, resulting in a 5 amino acid insert in the corresponding amino acid sequence (SEQ ID NO: 633). This insert is not present in the sequence of SEQ ID NO: 630.
  • amino acid positions 118-134, 172-188, 211-227, 230-246, 282-298 and 348-364 Six transmembrane domains were predicted at amino acid positions 118-134, 172-188, 211-227, 230-246, 282-298 and 348-364.
  • the amino acid sequences of SEQ ID NO: 767-772 represent amino acids 1-134, 135-188, 189-227, 228-246, 247-298 and 299-511 of P768P, respectively.
  • Polypeptides may be synthesized on a Perkin Elmer/ Applied Biosystems 430A peptide synthesizer using FMOC chemistry with HPTU (O-Benzotriazole- N,N,N',N'-tetramethyluronium hexafluorophosphate) activation.
  • HPTU O-Benzotriazole- N,N,N',N'-tetramethyluronium hexafluorophosphate
  • a Gly-Cys-Gly sequence may be attached to the amino terminus of the peptide to provide a method of conjugation, binding to an immobilized surface, or labeling of the peptide.
  • Cleavage of the peptides from the solid support may be carried out using the following cleavage mixture: trifluoroacetic acid:ethanedithiol:thioanisole:water:phenol (40:1:2:2:3).
  • the peptides may be precipitated in cold methyl-t-butyl-ether.
  • the peptide pellets may then be dissolved in water containing 0.1% trifluoroacetic acid (TFA) and lyophilized prior to purification by C18 reverse phase HPLC.
  • TFA trifluoroacetic acid
  • a gradient of 0%-60% acetonitrile (containing 0.1% TFA) in water (containing 0.1% TFA) may be used to elute the peptides.
  • the peptides may be characterized using electrospray or other types of mass spectrometry and by amino acid analysis.
  • PROSTATE-SPECIFIC POLYPEPTIDES BY PCR-BASED SUBTRACTION
  • a cDNA library generated from prostate primary tumor mRNA as described above was subtracted with cDNA from normal prostate.
  • the subtraction was performed using a PCR-based protocol (Clontech), which was modified to generate larger fragments.
  • tester and driver double stranded cDNA were separately digested with five restriction enzymes that recognize six-nucleotide restriction sites (M , Mscl, PvuII, Sail and Stul). This digestion resulted in an average cDNA size of 600 bp, rather than the average size of 300 bp that results from digestion with Rsal according to the Clontech protocol. This modification did not affect the subtraction efficiency.
  • Two tester populations were then created with different adapters, and the driver library remained without adapters.
  • driver was separately hybridized with each of the two tester cDNA populations. This resulted in populations of (a) unhybridized tester cDNAs, (b) tester cDNAs hybridized to other tester cDNAs, (c) tester cDNAs hybridized to driver cDNAs and (d) unhybridized driver cDNAs. The two separate hybridization reactions were then combined, and rehybridized in the presence of additional denatured driver cDNA. Following this second hybridization, in addition to populations (a) through (d), a fifth population (e) was generated in which tester cDNA with one adapter hybridized to tester cDNA with the second adapter.
  • the second hybridization step resulted in enrichment of differentially expressed sequences which could be used as templates for PCR amplification with adaptor-specific primers.
  • the ends were then filled in, and PCR amplification was performed using adaptor-specific primers. Only population (e), which contained tester cDNA that did not hybridize to driver cDNA, was amplified exponentially.
  • a second PCR amplification step was then performed, to reduce background and further enrich differentially expressed sequences.
  • This PCR-based subtraction technique normalizes differentially expressed cDNAs so that rare transcripts that are overexpressed in prostate tumor tissue may be recoverable. Such transcripts would be difficult to recover by traditional subtraction methods.
  • seventy-seven further clones were identified. Sequences of these partial cDNAs are provided in SEQ ID NO: 29 to 305. Most of these clones had no significant homology to database sequences.
  • JPTPN23 (SEQ ID NO: 231; similarity to pig valosin-containing protein), JPTPN30 (SEQ ID NO: 234; similarity to rat mRNA for proteasome subunit), JPTPN45 (SEQ ID NO: 243; similarity to rat norvegicus cytosolic NADP-dependent isocitrate dehydrogenase), JPTPN46 (SEQ ID NO: 244; similarity to human subclone H8 4 d4 DNA sequence), JP1D6 (SEQ ID NO: 265; similarity to G.
  • JP8D6 SEQ ID NO: 288; similarity to human BAC clone RG016J04
  • JP8F5 SEQ ID NO: 289; similarity to human subclone H8 3 b5 DNA sequence
  • JP8E9 SEQ ID NO: 299; similarity to human Alu sequence
  • PT-PN PCR subtraction consisting of a prostate tumor pool subtracted against a normal prostate pool. Comparison of the cDNA sequences of these clones with the most recent release of GenBank revealed no significant homologies to the two clones referred to as P715P and P767P (SEQ ID NO: 312 and 314). The remaining clone was found to show some homology to the known gene KIAA0056 (SEQ ID NO: 318). Using microarray analysis to measure mRNA expression levels in various tissues, all three clones were found to be over-expressed in prostate tumors and BPH tissues.
  • clone P715P was over-expressed in most prostate tumors and BPH tissues by a factor of three or greater, with elevated expression seen in the majority of normal prostate samples and in fetal tissue, but negative to low expression in all other normal tissues.
  • Clone P767P was over-expressed in several prostate tumors and BPH tissues, with moderate expression levels in half of the normal prostate samples, and background to low expression in all other normal tissues tested.
  • the Ml length cDNA sequence of P788P is provided in SEQ ID NO: 634, with the corresponding predicted amino acid being provided in SEQ ID NO: 635.
  • a Ml-length cDNA sequence for P788P that contains polymorphisms not found in the sequence of SEQ ID NO: 634 was cloned multiple times by PCR amplification from cDNA prepared from several RNA templates from three individuals.
  • This determined cDNA sequence of this polymorphic variant of P788P is provided in SEQ ID NO: 636, with the corresponding amino acid sequence being provided in SEQ ID NO: 637.
  • SEQ ID NO: 637 differs from that of SEQ ID NO: 635 by six amino acid residues.
  • the P788P protein has 7 potential transmembrane domains at the C-terminal portion and is predicted to be a plasma membrane protein with an extracellular N-terminal region. Further studies on the clone of SEQ ID NO: 352 (referred to as P790P) led to the isolation of the full-length cDNA sequence of SEQ ID NO: 526. The corresponding predicted amino acid is provided in SEQ ID NO: 527.
  • Data from two quantitative PCR experiments indicated that P790P is over-expressed in 11/15 tested prostate tumor samples and is expressed at low levels in spinal cord, with no expression being seen in all other normal samples tested. Data from further PCR experiments and microarray experiments showed over-expression in normal prostate and prostate tumor with little or no expression in other tissues tested.
  • P790P was subsequently found to show significant homology to a previously identified G-protein coupled prostate tissue receptor.
  • SEQ ID NO: 569 Additional studies on the clone of SEQ ID NO: 354 (referred to as P776P) led to the isolation of an extended cDNA sequence, provided in SEQ ID NO: 569.
  • the determined cDNA sequences of three additional splice variants of P776P are provided in SEQ ID NO: 570-572.
  • the amino acid sequences encoded by two predicted open reading frames (ORFs) contained within SEQ ID NO: 570, one predicted ORF contained within SEQ ID NO: 571, and 11 predicted ORFs contained within SEQ ID NO: 569, are provided in SEQ ID NO: 573-586, respectively.
  • the predicted amino acid sequences encoded by 5 open reading frames located within SEQ ID NO: 737 are provided in SEQ ID NO: 740-744, with the predicted amino acid sequences encoded by the clone of SEQ ID NO: 738 and 739 being provided in SEQ ID NO: 745-750.
  • This Example illustrates the preparation of a CTL cell line specific for cells expressing the P502S gene.
  • mice Three weeks later these mice were sacrificed and using a nylon mesh single cell suspensions prepared. Cells were then resuspended at 6 x 10 6 cells/ml in complete media (RPMI- 1640; Gibco BRL, Gaithersburg, MD) containing 10% FCS, 2mM Glutamine (Gibco BRL), sodium pyravate (Gibco BRL), non-essential amino acids (Gibco BRL), 2 x 10 "5 M 2- mercaptoethanol, 50U/ml penicillin and streptomycin, and cultured in the presence of irradiated (3000 rads) P2S#12-pulsed (5mg/ml P2S#12 and lOmg/ml ⁇ 2-microglobulin) LPS blasts (A2 transgenic spleens cells cultured in the presence of 7 ⁇ g/ml dextran sulfate and 25 ⁇ g/ml LPS for 3 days).
  • complete media RPMI- 1640; Gibco
  • cells (5 x lOVml) were restimulated with 2.5 x 10 6 /ml peptide pulsed irradiated (20,000 rads) EL4A2Kb cells (Sherman et al, Science 255:815-818, 1992) and 3 x 10 6 /ml A2 transgenic spleen feeder cells.
  • Cells were cultured in the presence of 20U/ml IL-2. Cells continued to be restimulated on a weekly basis as described, in preparation for cloning the line.
  • P2S#12 line was cloned by limiting dilution analysis with peptide pulsed EL4 A2Kb tumor cells (1 x 10 4 cells/ well) as stimulators and A2 transgenic spleen cells as feeders ( 5 x 10 5 cells/ well) grown in the presence of 30U/ml IL-2. On day 14, cells were restimulated as before. On day 21, clones that were growing were isolated and maintained in culture. Several of these clones demonstrated significantly higher reactivity (lysis) against human fibroblasts (HLA A2Kb expressing) transduced with P502S than against control fibroblasts. An example is presented in Figure 1.
  • P2S #12 represents a naturally processed epitope of the P502S protein that is expressed in the context of the human HLA A2Kb molecule.
  • mice were immunized with the P1S#10 peptide (SEQ ID NO: 337), which is derived from the P501S gene (also referred to herein as Ll-12, SEQ ID NO: 110).
  • the P1S#10 peptide was derived by analysis of the predicted polypeptide sequence for P501S for potential HLA-A2 binding sequences as defined by published HLA-A2 binding motifs (Parker, KC, et al, J. Immunol, 152:163, 1994). P1S#10 peptide was synthesized as described in Example 4, and empirically tested for HLA-A2 binding using a T cell based competition assay.
  • Predicted A2 binding peptides were tested for their ability to compete HLA-A2 specific peptide presentation to an HLA-A2 restricted CTL clone (D150M58), which is specific for the HLA-A2 binding influenza matrix peptide fluM58.
  • D150M58 CTL secretes TNF in response to self-presentation of peptide fluM58.
  • test peptides at 100-200 ⁇ g/ml were added to cultures of D 150M58 CTL in order to bind HLA-A2 on the CTL. After thirty minutes, CTL cultured with test peptides, or control peptides, were tested for their antigen dose response to the fluM58 peptide in a standard TNF bioassay.
  • peptide P1S#10 competes HLA-A2 restricted presentation of fluM58, demonstrating that peptide PI S#l 0 binds HLA-A2.
  • Mice expressing the transgene for human HLA A2Kb were immunized as described by Theobald et al. (Proc. Natl Acad. Sci. USA 92:11993-11997, 1995) with the following modifications. Mice were immunized with 62.5 ⁇ g of PIS #10 and 120 ⁇ g of an I-A b binding peptide derived from Hepatitis B Virus protein emulsified in incomplete Freund's adjuvant. Three weeks later these mice were sacrificed and single cell suspensions prepared using a nylon mesh.
  • a PlS#10-specific CTL line was cloned by limiting dilution analysis with peptide pulsed EL4 A2Kb tumor cells (1 x 10 4 cells/ well) as stimulators and A2 transgenic spleen cells as feeders (5 x 10 5 cells/ well) grown in the presence of 30U/ml IL-2. On day 14, cells were restimulated as before. On day 21, viable clones were isolated and maintained in culture. As shown in Figure 5, five of these clones demonstrated specific cytolytic reactivity against P501S-transduced Jurkat A2Kb targets. This data indicates that P1S#10 represents a naturally processed epitope of the P501S protein that is expressed in the context of the human HLA-A2.1 molecule.
  • EXAMPLE 7 PRIMING OF CTLIN VIVO USING NAKED DNA IMMUNIZATION
  • the prostate-specific antigen Ll-12 as described above, is also referred to as P501S.
  • HLA A2Kb Tg mice provided by Dr L. Sherman, The Scripps Research
  • mice were immunized with 100 ⁇ g P501S in the vector VR1012 either intramuscularly or intradermally.
  • the mice were immunized three times, with a two week interval between immunizations.
  • immune spleen cells were cultured with Jurkat A2Kb-P501S transduced stimulator cells.
  • CTL lines were stimulated weekly. After two weeks of in vitro stimulation, CTL activity was assessed against P501S transduced targets.
  • Two out of 8 mice developed strong anti-P501S CTL responses.
  • CD8 + T cell microcultures were tested for their ability to recognize the P2S-12 peptide presented by autologous fibroblasts or fibroblasts which were transduced to express the P502S gene in a ⁇ -interferon ELISPOT assay (see Lalvani et al., J. Exp. Med. 186:859-865, 1997).
  • T cells were assayed in duplicate on 10 fibroblasts in the presence of 3 ⁇ g/ml human ⁇ - microglobulin and 1 ⁇ g/ml P2S-12 peptide or control E75 peptide:
  • T cells were simultaneously assayed on autologous fibroblasts transduced with the P502S gene or as a control, fibroblasts transduced with ⁇ ER-2/neu.
  • the fibroblasts were treated with 10 ng/ml ⁇ -interferon for 48 hours to upregulate class I MHC expression.
  • FIG. 2A demonstrates that there was a strong increase in the number of ⁇ -interferon spots with increasing numbers of T cells on fibroblasts pulsed with the P2S-12 peptide (solid bars) but not with the control E75 peptide (open bars). This shows the ability of these T cells to specifically recognize the P2S-12 peptide.
  • FIG. 2B this microculture also demonstrated an increase in the number of ⁇ - interferon spots with increasing numbers of T cells on fibroblasts transduced to express the P502S gene but not the ⁇ R-2/neu gene.
  • This Example illustrates the ability of a prostate-specific antigen to elicit a CTL response in blood of normal humans.
  • DC dendritic cells
  • monocyte cultures derived from PBMC of normal donors by growth for five days in RPMI medium containing 10% human seram, 50 ng/ml GMCSF and 30 ng/ml IL-4.
  • DC were infected overnight with recombinant P501S-expressing vaccinia virus at an M.O.I, of 5 and matured for 8 hours by the addition of 2 micrograms/ml CD40 ligand.
  • Virus was inactivated by UV irradiation, CD8 + cells were isolated by positive selection using magnetic beads, and priming cultures were initiated in 24-well plates.
  • CD8+ lines were identified that specifically produced interferon-gamma when stimulated with autologous P501S- transduced fibroblasts.
  • the P501S-specific activity of cell line 3A-1 could be maintained following additional stimulation cycles on autologous B-LCL transduced with P501S.
  • Line 3A-1 was shown to specifically recognize autologous B-LCL transduced to express P501S, but not EGFP-transduced autologous B-LCL, as measured by cytotoxicity assays ( 51 Cr release) and interferon-gamma production (Interferon- gamma Elispot; see above and Lalvani et al., J Exp. Med. 186:859-865, 1997). The results of these assays are presented in Figures 6 A and 6B.
  • the 9-mer peptide p5 (SEQ ID NO: 338) was derived from the P703P antigen (also referred to as P20).
  • the p5 peptide is immunogenic in human HLA-A2 donors and is a naturally processed epitope.
  • Antigen specific human CD8+ T cells can be primed following repeated in vitro stimulations with monocytes pulsed with p5 peptide.
  • These CTL specifically recognize p5-pulsed and P703P-transduced target cells in both ELISPOT (as described above) and chromium release assays.
  • immunization of HLA-A2Kb transgenic mice with p5 leads to the generation of CTL lines which recognize a variety of HLA-A2Kb or HLA-A2 transduced target cells expressing P703P.
  • HLA-A2Kb transgenic mice were immunized subcutaneously in the footpad with 100 ⁇ g of p5 peptide together with 140 ⁇ g of hepatitis B viras core peptide (a Th peptide) in Freund's incomplete adjuvant.
  • spleen cells from immunized mice were stimulated in vitro with peptide-pulsed LPS blasts.
  • CTL activity was assessed by chromium release assay five days after primary in vitro stimulation.
  • Retrovirally transduced cells expressing the control antigen P703P and HLA-A2Kb were used as targets. CTL lines that specifically recognized both p5-pulsed targets as well as P703P-expressing targets were identified.
  • DC Dendritic cells
  • RPMI medium containing 10% human serum, 50 ng/ml human GM-CSF and 30 ng/ml human IL-4.
  • the DC were pulsed with 1 ug/ml p5 peptide and cultured with CD8+ T cell enriched PBMC.
  • CTL lines were restimulated on a weekly basis with p5-pulsed monocytes. Five to six weeks after initiation of the CTL cultures, CTL recognition of p5-pulsed target cells was demonstrated. CTL were additionally shown to recognize human cells transduced to express P703P, demonstrating that p5 is a naturally processed epitope.
  • peptide 4 a further peptide epitope derived from the prostate tumor-specific antigen P703P that is capable of being recognized by CD4 T cells on the surface of cells in the context of HLA class II molecules was carried out as follows.
  • the amino acid sequence for peptide 4 is provided in SEQ ID NO: 638, with the corresponding cDNA sequence being provided in SEQ ID NO: 639.
  • DC Dendritic cells
  • CD4 T cells were generated from the same donor as the DC using MACS beads and negative selection.
  • Pulsed DC were washed and plated at 1 x 10 4 cells/well of 96- well V-bottom plates and purified CD4 T cells were added at 1 x 10 5 /well.
  • Cultures were supplemented with 60 ng/ml IL-6 and 10 ng/ml IL-12 and incubated at 37 °C. Cultures were restimulated as above on a weekly basis using DC generated and pulsed as above as antigen presenting cells, supplemented with 5 ng/ml IL-7 and 10 u/ml IL-2. Following 4 in vitro stimulation cycles, 96 lines (each line corresponding to one well) were tested for specific proliferation and cytokine production in response to the stimulating pools with an irrelevant pool of peptides derived from mammaglobin being used as a control.
  • One line (referred to as 1-F9) was identified from pool #1 that demonstrated specific proliferation (measured by 3H proliferation assays) and cytokine production (measured by interferon-gamma ELISA assays) in response to pool #1 of
  • P703P peptides This line was further tested for specific recognition of the peptide pool, specific recognition of individual peptides in the pool, and in HLA mismatch analyses to identify the relevant restricting allele.
  • Line 1-F9 was found to specifically proliferate and produce interferon-gamma in response to peptide pool #1, and also to peptide 4 (SEQ ID NO: 638).
  • Peptide 4 corresponds to amino acids 126-140 of SEQ ID NO:
  • Antibody blocking assays were utilized to determine if the restricting allele was HLA-DR0701 or HLA-DQ02.
  • the anti-HLA-DR blocking antibody L243 or an irrelevant isotype matched IgG2a were added to T cells and APC cultures pulsed with the peptide RMPTVLQCVNVSVVS (SEQ ID NO: 638) at 250 ng/ml. Standard interferon-gamma and proliferation assays were performed. Whereas the control antibody had no effect on the ability of the T cells to recognize peptide-pulsed APC, in both assays the anti-HLA-DR antibody completely blocked the ability of the T cells to specifically recognize peptide-pulsed APC.
  • CD4 T cell lines which demonstrated specific activity were restimulated on the appropriate pool of P703P peptides and reassayed on the individual peptides of each pool as well as a peptide dose titration of the pool of peptides in a IFN-gamma release assay and in a proliferation assay.
  • immunogenic peptides were recognized by the T cells from the entire set of peptide antigens tested.
  • the amino acid sequences of these peptides are provided in S ⁇ Q ID NO: 656-671, with the corresponding cDNA sequences being provided in S ⁇ Q ID NO: 640-655, respectively.
  • the peptide reactivity of the T cell line could be mapped to a single peptide, however some could be mapped to more than one peptide in each pool.
  • CD4 T cell lines that displayed a representative pattern of recognition from each peptide pool with a reasonable affinity for peptide were chosen for further analysis (I-l A, -6A; II-4C, -5 ⁇ ; III-6E, IV-4B, -3F, - 9B, -10F, V-5B, -4D, and -10F). These CD4 T cells lines were restimulated on the appropriate individual peptide and reassayed on autologous DC pulsed with a truncated form of recombinant P703P protein made in E. coli (a.a.
  • line I-l A recognized specifically the truncated form of P703P (E. coli) but no other recombinant form of P703P. This line also recognized the peptide used to elicit the T cells.
  • Line 2- 4C recognized the truncated form of P703P (E. coli) and the Ml length form of P703P made in baculoviras, as well as peptide.
  • T cell lines tested were either peptide-specific only (II-5 ⁇ , II-6F, IV-4B, IV-3F, IV-9B, IV-10F, V-5B and V-4D) or were non-responsive to any antigen tested (V-10F).
  • RPLLANDLMLIKLDE SEQ ID NO: 671; corresponding to a.a. 110- 124 of SEQ ID NO: 525) recognized by the T cell line I-l A
  • the determined DNA sequence of this ORF is provided in SEQ ID NO: 531.
  • This frameshift generates a protein sequence (provided in SEQ ID NO: 532) of 293 amino acids that contains the C-terminal domain common to the other isoforms of B305D but that differs in the N-terminal region.
  • B305D The expression levels of B305D in a variety of tumor and normal tissues were examined by real time PCR and by Northern analysis. The results indicated that B305D is highly expressed in breast tumor, prostate tumor, normal prostate and normal testes, with expression being low or undetectable in all other tissues examined (colon tumor, lung tumor, ovary tumor, and normal bone marrow, colon, kidney, liver, lung, ovary, skin, small intestine, stomach).
  • colon tumor, lung tumor, ovary tumor, and normal bone marrow, colon, kidney, liver, lung, ovary, skin, small intestine, stomach Using real-time PCR on a panel of prostate tumors, expression of B305D in prostate tumors was shown to increase with increasing Gleason grade, demonstrating that expression of B305D increases as prostate cancer progresses.
  • DC dendritic cells
  • monocyte cultures derived from PBMC of normal human donors by growing for five days in RPMI medium containing 10% human serum, 50 ng/ml human GM-CSF and 30 ng/ml human IL-4.
  • DC were infected overnight with recombinant P501S vaccinia virus at a multiplicity of infection (M.O.I) of five, and matured overnight by the addition of 3 ⁇ g/ml CD40 ligand.
  • Virus was inactivated by UV inadiation.
  • CD 8+ T cells were isolated using a magnetic bead system, and priming cultures were initiated using standard culture techniques.
  • cDNA encoding P501S was fragmented by various restriction digests, and sub-cloned into the retroviral expression vector pBIB-KS. Retroviral supernatants were generated by transfection of the helper packaging line Phoenix-Ampho. Supernatants were then used to transduce Jurkat/A2Kb cells for CTL screening. CTL were screened in IFN-gamma ELISPOT assays against these A2Kb targets transduced with the "library" of P501S fragments.
  • Initial positive fragments P501S/H3 and P501S/F2 were sequenced and found to encode amino acids 106-553 and amino acids 136-547, respectively, of SEQ ID NO: 113.
  • CD8+ T cells were cultured with autologous CD40 ligand + IL-4 derived, P501S-transduced B cells in a 96- well microculture format. These CTL microcultures were re-stimulated with P501S-transduced B cells and then assayed for specificity. Following this initial screen, microcultures with significant signal above background were cloned on autologous EBV-transformed B cells (BLCL), also transduced with P501S. Using IFN-gamma ELISPOT for detection, several of these CD8 T cell clones were found to be specific for P501S, as demonstrated by reactivity to BLCL/P501S but not BLCL transduced with control antigen.
  • BLCL autologous EBV-transformed B cells
  • anti-P501S CD8 T cell specificity is HLA-A2-restricted.
  • antibody blocking experiments with anti-HLA-A,B,C monoclonal antibody (W6.32), anti-HLA-B,C monoclonal antibody (B 1.23.2) and a control monoclonal antibody showed that only the anti-HLA-A,B,C antibody blocked recognition of P501S- expressing autologous BLCL.
  • the anti-P501S CTL also recognized an HLA-
  • CD8 class I-restricted peptide epitope of P501S was identified as follows.
  • Dendritic Cells DC were isolated by Percol gradient followed by differential adherence, and cultured for 5 days in the presence of RPMI medium containing 1% human serum, 50ng/ml GM-CSF and 30ng/ml IL-4. Following culture, DC were infected for 24 hours with P501S-expressing adenoviras at an MOI of 10 and matured for an additional 24 hours by the addition of 2ug/ml CD40 ligand.
  • CD8 cells were enriched for by the subtraction of CD4+, CD 14+ and CD 16+ populations from PBMC with magnetic beads.
  • one P501 S-specific CD8+ T cell line (refen-ed to as 2A2) was identified that produced IFN-gamma in response to IFN-gamma-treated P501S/CD80 expressing autologous fibroblasts, but not in response to IFN-gamma-treated P703P/CD80 expressing autologous fibroblasts in a ⁇ -IFN Elispot assay.
  • Line 2A2 was cloned in 96-we ⁇ l plates with 0.5 cell/well or 2 cells/well in the presence of 75,000 PBMC/well, 10,000 B- LCL/well, 30ng/ml OKT3 and 50u/ml IL-2. Twelve clones were isolated that showed strong P501 S specificity in response to transduced fibroblasts.
  • Fluorescence activated cell sorting analysis was performed on P501 S-specific clones using CD3-, CD4- and CD8-specific antibodies conjugated to PercP, FITC and PE respectively. Consistent with the use of CD8 enriched T cells in the priming cultures, P5401 S-specific clones were determined to be CD3+, CD8+ and CD4-.
  • pools of 18-20 mer or 30-mer peptides that spanned the majority of the amino acid sequence of P501S were loaded onto autologous B-LCL and tested in ⁇ -IFN Elispot assays for the ability to stimulate two P501 S-specific CTL clones, referred to as 4E5 and 4E7.
  • each of the 18-20 mer peptides that comprised the positive pool were tested individually in ⁇ -IFN Elispot assays for the ability to stimulate the two P501 S-specific CTL clones, 4E5 and 4E7. Both 4E5 and 4E7 specifically recognized one 20-mer peptide (SEQ ID NO: 710; cDNA sequence provided in SEQ ID NO: 711) that spanned amino acids 453-472 of P501S.
  • This sequence defines a minimal 10- mer epitope from P501S that can be naturally processed and to which CTL responses can be identified in normal PBMC.
  • this epitope is a candidate for use as a vaccine moiety, and as a therapeutic and/or diagnostic reagent for prostate cancer.
  • SEQ ID NO: 712-specific response was detected using both the autologous (D326) and heterologous (D107) B- LCL, and furthermore the responses were blocked by pre-incubation with 25ug/ml of B 1.23.2 HLA-B/C blocking antibody. Together these results demonstrate that the P501 S-specific response to the peptide of SEQ ID NO: 712 is restricted to the HLA- B51 class I allele. Molecular cloning and sequence analysis of the HLA-B51 allele from D3326 revealed that the HLA-B51 subtype of D326 is HLA-B51011.
  • each of the HLA B and C alleles were cloned from the donor used in the in vitro priming experiment. Sequence analysis indicated that the relevant alleles were HLA-B8, HLA-B51, HLA-CwOl and HLA- Cw07. Each of these alleles were subcloned into an expression vector and co- transfected together with the P501S gene into VA-13 cells. Transfected VA-13 cells were then tested for the ability to specifically stimulate the P501 S-specific CTL in ELISPOT assays.
  • VA-13 cells transfected with P501S and HLA-B51 were capable of stimulating the P501 S-specific CTL to secrete gamma-IFN.
  • VA-13 cells transfected with HLA-B51 alone or P501S + the other HLA-alleles were not capable of stimulating the P501 S-specific CTL.
  • the P501S-positive lines LnCAP and CRL2422 both expressing "moderate” amounts of P501S mRNA and protein
  • PC-3 expressing low amounts of P501S mRNA and protein
  • the P501S-negative cell line DU-145 were retrovirally transduced with the HLA-B51011 allele that was cloned from the donor used to generate the P501 S-specific CTL.
  • HLA-B51011- or EGFP-transduced and selected tumor cells were treated with gamma-interferon and androgen (to upregulate stimulatory functions and P501S, respectively) and used in gamma- interferon Elispot assays with the P501 S-specific CTL clones 4E5 and 4E7. Untreated cells were used as a control.
  • CD4 cells specific for P501S were prepared as described above. A series of 16 overlapping peptides were synthesized that spanned approximately 50% of the amino terminal portion of the P501S gene (amino acids 1- 325 of SEQ ID NO: 113).
  • peptides were combined into pools of 4 peptides, pulsed at 4 ⁇ g/ml onto dendritic cells (DC) for 24 hours, with TNF-alpha. DC were then washed and mixed with negatively selected CD4+ T cells in 96 well U-bottom plates. Cultures were re- stimulated weekly on fresh DC loaded with peptide pools. Following a total of 4 stimulation cycles, cells were rested for an additional week and tested for specificity to
  • APC pulsed with peptide pools using ⁇ -IFN ELISA and proliferation assays were used as APC.
  • adherent monocytes loaded with either the relevant peptide pool at 4ug/ml or an irrelevant peptide at ⁇ g/ml were used as APC.
  • T cell lines that demonstrated either specific cytokine secretion or proliferation were then tested for recognition of individual peptides that were present in the pool. T cell lines could be identified from pools A and
  • lines AD9 and AE10 specifically recognized peptide 1 (SEQ ID NO: 719), and line AF5 recognized peptide 39 (SEQ ID NO: 718).
  • line BC6 could be identified that recognized peptide 58 (SEQ ID NO: 717). Each of these lines were stimulated on the specific peptide and tested for specific recognition of the peptide in a titration assay as well as cell lysates generated by infection of HEK 293 cells with adenoviras expressing either P501S or an irrelevant antigen.
  • APC-adherent monocytes were pulsed with either 10, 1, or 0.1 ⁇ g/ml individual P501S peptides, and DC were pulsed overnight with a 1 :5 dilution of adenovirally infected cell lysates.
  • Lines AD9, AE10 and AF5 retained significant recognition of the relevant P501S-derived peptides even at 0.1 mg/ml.
  • line AD9 demonstrated significant (8.1 fold stimulation index) specific activity for lysates from adenovirus- P501S infected cells.
  • This Example describes the isolation of certain prostate-specific polypeptides from a prostate tumor cDNA library.
  • a human prostate tumor cDNA expression library as described above was screened using microarray analysis to identify clones that display at least a three fold over-expression in prostate tumor and/or normal prostate tissue, as compared to non-prostate normal tissues (not including testis). 372 clones were identified, and 319 were successfully sequenced. Table I presents a summary of these clones, which are shown in SEQ ID NOs:385-400. Of these sequences SEQ ID NOs:386, 389, 390 and 392 conespond to novel genes, and SEQ ID NOs: 393 and 396 correspond to previously identified sequences. The others (SEQ ID NOs:385, 387, 388, 391, 394, 395 and 397- 400) conespond to known sequences, as shown in Table I.
  • CGI-82 showed 4.06 fold over-expression in prostate tissues as compared to other normal tissues tested. It was over-expressed in 43% of prostate tumors, 25% normal prostate, not detected in other normal tissues tested.
  • L-iditol-2 dehydrogenase showed 4.94 fold over-expression in prostate tissues as compared to other normal tissues tested. It was over-expressed in 90%> of prostate tumors, 100% of normal prostate, and not detected in other normal tissues tested.
  • Ets transcription factor PDEF showed 5.55 fold over-expression in prostate tissues as compared to other normal tissues tested. It was over-expressed in 47% prostate tumors, 25% normal prostate and not detected in other normal tissues tested.
  • hTGRl showed 9.11 fold over-expression in prostate tissues as compared to other normal tissues tested.
  • KIAN0295 showed 5.59 fold over-expression in prostate tissues as compared to other normal tissues tested. It was over-expressed in 47% of prostate tumors, low to undetectable in normal tissues tested including normal prostate tissues.
  • Prostatic acid phosphatase showed 9.14 fold over-expression in prostate tissues as compared to other normal tissues tested. It was over-expressed in 67% of prostate tumors, 50% of normal prostate, and not detected in other normal tissues tested.
  • Transglutaminase showed 14.84 fold over-expression in prostate tissues as compared to other normal tissues tested. It was over-expressed in 30% of prostate tumors, 50% of normal prostate, and is not detected in other noimal tissues tested.
  • High density lipoprotein binding protein showed 28.06 fold over-expression in prostate tissues as compared to other normal tissues tested. It was over-expressed in 97% of prostate tumors, 75% of normal prostate, and is undetectable in all other normal tissues tested.
  • CGI-69 showed 3.56 fold over-expression in prostate tissues as compared to other normal tissues tested. It is a low abundant gene, detected in more than 90% of prostate tumors, and in 75% normal prostate tissues. The expression of this gene in normal tissues was very low.
  • KIAA0122 showed 4.24 fold over-expression in prostate tissues as compared to other normal tissues tested. It was over-expressed in 57% of prostate tumors, it was undetectable in all normal tissues tested including normal prostate tissues.
  • Novel clone 23399 showed 4.09 fold over-expression in prostate tissues as compared to other normal tissues tested. It was over-expressed in 27% of prostate tumors and was undetectable in all normal tissues tested including normal prostate tissues. Novel clone 23320 showed 3.15 fold over-expression in prostate tissues as compared to other noimal tissues tested. It was detectable in all prostate tumors and 50% of normal prostate tissues. It was also expressed in normal colon and trachea. Other normal tissues do not express this gene at high level.
  • This Example describes the use of an electronic subtraction technique to identify prostate-specific antigens.
  • Potential prostate-specific genes present in the GenBank human EST database were identified by electronic subtraction (similar to that described by Vasmatizis et al, Proc. Natl. Acad. Sci. USA 95:300-304, 1998).
  • the sequences of EST clones (43,482) derived from various prostate libraries were obtained from the GenBank public human EST database. Each prostate EST sequence was used as a query sequence in a BLASTN (National Center for Biotechnology Information) search against the human EST database. All matches considered identical (length of matching sequence >100 base pairs, density of identical matches over this region > 70%) were grouped (aligned) together in a cluster.
  • BLASTN National Center for Biotechnology Information
  • Clusters containing more than 200 ESTs were discarded since they probably represented repetitive elements or highly expressed genes such as those for ribosomal proteins. If two or more clusters shared common ESTs, those clusters were grouped together into a "supercluster,” resulting in 4,345 prostate superclusters.
  • Each supercluster was analyzed in terms of the ESTs within the supercluster.
  • the tissue source of each EST clone was noted and used to classify the superclusters into four groups: Type 1- EST clones found in the Plus group libraries only; no expression detected in Minus or Other group libraries; Type 2- EST clones derived from the Plus and Other group libraries only; no expression detected in the Minus group; Type 3- EST clones derived from the Plus, Minus and Other group libraries, but the number of ESTs derived from the Plus group is higher than in either the Minus or Other groups; and Type 4- EST clones derived from Plus, Minus and Other group libraries, but the number derived from the Plus group is higher than the number derived from the Minus group.
  • This analysis identified 4,345 breast clusters (see Table III). From these clusters, 3,172 EST clones were ordered from Research Genetics, Inc., and were received as frozen glycerol stocks in 96-well plates.
  • the EST clone inserts were PCR-amplified using amino-linked PCR primers for Synteni microarray analysis. When more than one PCR product was obtained for a particular clone, that PCR product was not used for expression analysis.
  • 2,528 clones from the electronic subtraction method were analyzed by microarray analysis to identify electronic subtraction breast clones that had high levels of tumor vs. normal tissue mRNA. Such screens were performed using a Synteni (Palo Alto, CA) microarray, according to the manufacturer's instructions (and essentially as described by Schena et al., Proc. Natl. Acad. Sci. USA 95:10614-10619, 1996 and Heller et al., Proc.
  • Clones with an expression ratio greater than 3 i.e., the level in prostate tumor and normal prostate mRNA was at least three times the level in other normal tissue mRNA
  • the sequences of these clones are provided in SEQ ID NO: 401-453, with certain novel sequences shown in SEQ ID NO: 407, 413, 416-419, 422, 426, 427 and 450.
  • Table IV Prostate-tumor Specific Clones
  • SEQ ID NO: 407 also referred to as P1020C
  • P1020C extended cDNA sequence
  • SEQ ID NO: 591 This extended cDNA sequence was found to contain an open reading frame that encodes the predicted amino acid sequence of SEQ ID NO: 592.
  • the P1020C cDNA and amino acid sequences were found to show some similarity to the human endogenous retroviral HERV-K pol gene and protein.
  • This Example describes the isolation of additional prostate-specific polypeptides from a prostate tumor cDNA library.
  • a human prostate tumor cDNA expression library as described above was screened using microarray analysis to identify clones that display at least a three fold over-expression in prostate tumor and/or normal prostate tissue, as compared to non-prostate normal tissues (not including testis).
  • 142 clones were identified and sequenced. Certain of these clones are shown in SEQ ID NO: 454-467. Of these sequences, SEQ ID NO: 459-460 represent novel genes. The others (SEQ ID NO: 454- 458 and 461-467) correspond to known sequences.
  • Comparison of the determined cDNA sequence of SEQ ID NO: 461 with sequences in the Genbank database using the BLAST program revealed homology to the previously identified transmembrane protease serine 2 (TMPRSS2).
  • the Ml-length cDNA sequence for this clone is provided in SEQ ID NO: 751, with the corresponding amino acid sequence being provided in SEQ ID NO: 752.
  • the cDNA sequence encoding the first 209 amino acids of TMPRSS2 is provided in SEQ ID NO: 753, with the first 209 amino acids being provided in SEQ ID NO: 754.
  • SEQ ID NO: 462 The sequence of SEQ ID NO: 462 (referred to as P835P) was found to correspond to the previously identified clone FLJ13518 (Accession AK023643; SEQ ID NO: 774), which had no associated open reading frame (ORF). This clone was used to search the Geneseq DNA database and matched a clone previously identified as a G protein-coupled receptor protein (DNA Geneseq Accession A09351; amino acid Geneseq Accession Y92365), that is characterized by the presence of seven transmembrane domains.
  • SEQ ID NO: 778-785 The sequences of fragments between these domains are provided in SEQ ID NO: 778-785, with SEQ ID NO: 778, 780, 782 and 784 representing extracellular domains and SEQ ID NO: 779, 781, 783 and 785 representing intracellular domains.
  • SEQ ID NO: 778-785 represent amino acids 1-28, 53-61, 83- 103, 124-143, 165-201, 226-238, 263-272 and 297-381, respectively, of P835P.
  • the Ml-length cDNA sequence for P835P is provided in SEQ ID NO: 773.
  • the cDNA sequence of the open reading frame for P835P, including stop codon, is provided in SEQ ID NO: 775, with the open reading frame without stop codon being provided in SEQ ID NO: 776 and the corresponding amino acid sequence being provided in SEQ ID NO: 777.
  • This Example describes the Ml length cloning of P710P.
  • the prostate cDNA library described above was screened with the P710P fragment described above.
  • One million colonies were plated on LB/Ampicillin plates.
  • Nylon membrane filters were used to lift these colonies, and the cDNAs picked up by these filters were then denatured and cross-linked to the filters by UV light.
  • the P710P fragment was radiolabeled and used to hybridize with the filters.
  • Positive cDNA clones were selected and their cDNAs recovered and sequenced by an automatic Perkin Elmer/ Applied Biosystems Division Sequencer. Four sequences were obtained, and are presented in SEQ ID NO: 468-471. These sequences appear to represent different splice variants of the P710P gene.
  • This example describes the expression and purification of prostate-specific antigens in E. coli, baculoviras, mammalian and yeast cells.
  • P501S DNA was used to perform PCR using the primers AW025 (SEQ ID NO: 485) and AW003 (SEQ ID NO: 486).
  • AW025 is a sense cloning primer that contains a Hindlll site.
  • AW003 is an antisense cloning primer that contains an EcoRI site.
  • DNA amplification was performed using 5 ⁇ l 10X Pfu buffer, 1 ⁇ l 20 mM dNTPs, 1 ⁇ l each of the PCR primers at 10 ⁇ M concentration, 40 ⁇ l water, 1 ⁇ l Pfu DNA polymerase (Stratagene, La Jolla, CA) and 1 ⁇ l DNA at 100 ng/ ⁇ l. Denaturation at 95°C was performed for 30 sec, followed by 10 cycles of 95°C for 30 sec, 60°C for 1 min and by 72°C for 3 min. 20 cycles of 95°C for 30 sec, 65°C for 1 min and by 72°C for 3 min, and lastly by 1 cycle of 72°C for 10 min.
  • the PCR product was cloned to Ral2m/pET17b using Hindlll and EcoRI. The sequence of the resulting fusion construct (referred to as Ral2-P501S-F) was confirmed by DNA sequencing.
  • the fusion constract was transformed into BL21(DE3)pLysE, pLysS and CodonPlus E. coli (Stratagene) and grown overnight in LB broth with kanamycin. The resulting culture was induced with IPTG. Protein was transferred to PVDF membrane and blocked with 5% non-fat milk (in PBS-Tween buffer), washed three times and incubated with mouse anti-His tag antibody (Clontech) for 1 hour. The membrane was washed 3 times and probed with HRP-Protein A (Zymed) for 30 min. Finally, the membrane was washed 3 times and developed with ECL (Amersham). No expression was detected by Western blot. Similarly, no expression was detected by Western blot when the Ral2-P501S-F fusion was used for expression in BL21 CodonPlus by CE6 phage (Invitrogen).
  • P501S amino acids 36-325 of SEQ ID NO: 113 was cloned down-stream of the first 30 amino acids of the M. tuberculosis antigen Ral2 in pET17b as follows.
  • P501S DNA was used to perform PCR using the primers AW025 (SEQ ID NO: 485) and AW027 (SEQ ID NO: 487).
  • AW027 is an antisense cloning primer that contains an EcoRI site and a stop codon. DNA amplification was perfonned essentially as described above.
  • the resulting PCR product was cloned to Ral 2 in pET17b at the Hindlll and EcoRI sites.
  • the fusion constract (referred to as Ral2-P501 S-N) was confirmed by DNA sequencing.
  • the Ral2-P501S-N fusion constract was used for expression in BL21(DE3)pLysE, pLysS and CodonPlus, essentially as described above.
  • BL21(DE3)pLysE, pLysS and CodonPlus essentially as described above.
  • protein bands were observed at the expected molecular weight of 36 kDa. Some high molecular weight bands were also observed, probably due to aggregation of the recombinant protein. No expression was detected by Western blot when the Ral2-P501S-F fusion was used for expression in BL21CodonPlus by CE6 phage.
  • a fusion constract comprising a C-terminal portion of P501S (amino acids 257-553 of SEQ ID NO: 113) located down-stream of the first 30 amino acids of the M. tuberculosis antigen Ral2 (SEQ ID NO: 484) was prepared as follows.
  • P501S DNA was used to perform PCR using the primers AW026 (SEQ ID NO: 488) and AW003 (SEQ ID NO: 486).
  • AW026 is a sense cloning primer that contains a Hindlll site. DNA amplification was performed essentially as described above. The resulting PCR product was cloned to Ral 2 in pET17b at the Hindlll and EcoRI sites.
  • the sequence for the fusion constract (referred to as Ral2-P501 S-C) was confirmed.
  • the Ral2-P501S-C fusion constract was used for expression in BL21(DE3)pLysE, pLysS and CodonPlus, as described above. A small amount of protein was detected by Western blot, with some molecular weight aggregates also being observed. Expression was also detected by Western blot when the Ral2-P501S-C fusion was used for expression in BL21 CodonPlus induced by CE6 phage.
  • a fusion constract comprising a fragment of P501S (amino acids 36-298 of SEQ ID NO: 113) located down-stream of the M. tuberculosis antigen Ral 2 (SEQ ID NO: 705) was prepared as follows.
  • P501S DNA was used to perform PCR using the primers AW042 (SEQ ID NO: 706) and AW053 (SEQ ID NO: 707).
  • AW042 is a sense cloning primer that contains a EcoRI site.
  • AW053 is an antisense primer with stop and Xho I sites. DNA amplification was performed essentially as described above. The resulting PCR product was cloned to Ral2 in pET17b at the EcoRI and Xho I sites.
  • the resulting fusion constract (referred to as Ral2-P501S-E2) was expressed in B834 (DE3) pLys S E. coli host cells in TB media for 2 h at room temperature.
  • Expressed protein was purified by washing the inclusion bodies and running on a Ni-NTA column. The purified protein stayed soluble in buffer containing 20 mM Tris-HCl (pH 8), 100 mM NaCl, 10 mM ⁇ -Me and 5% glycerol.
  • the determined cDNA and amino acid sequences for the expressed fusion protein are provided in SEQ ID NO: 708 and 709, respectfully.
  • the Bac-to-Bac baculoviras expression system (BRL Life Technologies, Inc.) was used to express P501S protein in insect cells.
  • Full-length P501S (SEQ ID NO: 113) was amplified by PCR and cloned into the Xbal site of the donor plasmid pFastBacI.
  • the recombinant bacmid and baculoviras were prepared according to the manufacturer's instractions.
  • the recombinant baculoviras was amplified in Sf9 cells and the high titer viral stocks were utilized to infect High Five cells (Invitrogen) to make the recombinant protein.
  • the localization of recombinant P501S in the insect cells was investigated as follows.
  • the insect cells overexpressing P501S were fractionated into fractions of nucleus, mitochondria, membrane and cytosol. Equal amounts of protein from each fraction were analyzed by Western blot with a monoclonal antibody against P501S. Due to the scheme of fractionation, both nucleus and mitochondria fractions contain some plasma membrane components. However, the membrane fraction is basically free from mitochondria and nucleus. P501S was found to be present in all fractions that contain the membrane component, suggesting that P501S may be associated with plasma membrane of the insect cells expressing the recombinant protein.
  • P501S 553 amino acids; SEQ ID NO: 113 was cloned into various mammalian expression vectors, including pCEP4 (Invitrogen), pVR1012 (Vical, San Diego, CA) and a modified form of the retroviral vector pBMN, referred to as pBIB.
  • Transfection of P501S/pCEP4 and P501S/pVR1012 into HEK293 fibroblasts was carried out using the Fugene transfection reagent (Boehringer Mannheim). Briefly, 2 ul of Fugene reagent was diluted into 100 ul of serum-free media and incubated at room temperature for 5-10 min.
  • Transfection of p501S/pCEP4 into CHO-K cells was carried out using GenePorter transfection reagent (Gene Therapy Systems, San Diego, CA). Briefly, 15 ⁇ l of GenePorter was diluted in 500 ⁇ l of serum-free media and incubated at room temperature for 10 min. The GenePorter/media mixture was added to 2 ⁇ g of plasmid DNA that was diluted in 500 ⁇ l of serum-free media, mixed briefly and incubated for 30 min at room temperature. CHO-K cells were rinsed in PBS to remove seram proteins, and the GenePorter/DNA mix was added and incubated for 5 hours. The transfected cells were then fed an equal volume of 2x media and incubated for 24-48 hours.
  • FACS analysis of P501S transiently infected CHO-K cells demonstrated surface expression of P501S. Expression was detected using rabbit polyclonal antisera raised against a P501S peptide, as described below. Flow cytometric analysis was performed using a FaCScan (Becton Dickinson), and the data were analyzed using the Cell Quest program.
  • the ⁇ prepro signal sequence of S. cerevisiae linked to amino acids 55-553 of SEQ ID NO: 113 with a His tag tail was cloned into the plasmid pRIT15068 with the CUP1 promoter and transfected into S. cerevisiae strain Y1790.
  • the Y1790 strain is Leu+ and His-.
  • Expression of protein was induced by addition of either 500 ⁇ M or 250 ⁇ M of CuSO 4 at 30 °C in minimal medium supplemented with histidine. Cells were harvested 24 hours after induction.
  • Extracts were prepared by growing cells to a concentration of OD600 5.0 in 50 mM citrate phosphate buffer (pH 4.0) plus 130 mM NaCl supplemented with protease inhibitors. Cells were disrapted using glass beads and centrifuged for 20 min at 15,000 g. The recombinant protein was found to be 100% pellet associated.
  • Fermentation processes for the production of the ⁇ prepro-P501S-His tag recombinant protein in S. cerevisiae were evaluated as follows. One hundred ⁇ l of a master seed containing 2.5 x 10 8 cells/ml of transformed S. cerevisiae Y1790 were spread on FSC004AA solid medium.
  • the composition of the FSC004AA medium is as follows: glucose 10 g/1; Na 2 MoO .2H 2 O 0.0002 g/1; folic acid 0.000064 g/1; KH 2 PO 4 1 g/1; MnSO 4 .H 2 O 0.0004 g/1; Inositol 0.064 g/1; MgSO 4 .7H 2 O 0.5 g/1; H 3 BO 3 0.0005 g/1; Pyridoxine 0.008 g/1; CaCl 2 .2H 2 O 0.1 g/1; KI 0.0001 g/1; Thia ine 0.008 g/1; NaCl 0.1 g/1; CoCl 2 .6H 2 O 0.00009 g/1; Niacin 0.000032 g/1; FeCl 3 .6H 2 O 0.0002 g/1; Riboflavin 0.000016 g/1; Panthotenate Ca 0.008 g/1; CuSO 4 .5H 2 O 0.00004
  • the composition of the FSC007AA medium is as follows: Glucose 10 g/1; Na 2 MoO 4 .2H 2 O 0.0002 g/1; folic acid 0.000064 g/1; KH 2 PO 4 1 g/1; MnSO 4 .H 2 O 0.0004 g/1; Inositol 0.064 g/1; MgSO 4 .7H 2 O 0.5 g/1; H 3 BO 3 0.0005 g/1; Pyridoxine 0.008 g/1; CaCl 2 .2H 2 O 0.1 g/1; KI 0.0001 g/1; Thiamine 0.008 g/1; NaCl 0.1 g/1; CoCl 2 .6H 2 O 0.00009 g/1; Niacine 0.000032 g/1; FeCl 3 .6H 2 O 0.0002 g/1; Riboflavin 0.000016 g/1; Panthotenate Ca 0.008 g/1; CuSO 4 .5H 2 O
  • the composition of the FSC002AA medium is as follows: (NH 4 ) 2 SO 4 6.4 g/1; Na 2 MoO .2H 2 O 2.05 mg/1; folic acid 0.54 mg/1; KH 2 PO 4 8.25 g/1; MnSO 4 .H 2 O 4.1 mg/1; inositol 540 mg/; MgSO 4 .7H 2 O 4.69 g/1; H 3 BO 3 5.17 m/1; pyridoxine 68 mg/1; CaCl 2 .2H 2 O 0.92 g/1; KI 1.03 mg/1; thiamine 68 mg/1; NaCl 0.06g/l; CoCl 2 .6H 2 O 0.92 mg/1; Niacine 0.27 mg/1; HC1 1 ml/1
  • the carbon source was supplemented by a continuous feeding of FFB004AA medium.
  • the composition of the FFB004AA medium is as follows: glucose 350 g/1; Na 2 MoO 4 .2H 2 O 5.15 mg/1; folic acid 1.36 mg/1; KH 2 PO 4 20.6 g/1; MnSO 4 .H 2 O 10.3 mg/1; inositol 1350 mg/1; MgSO 4 .7H 2 O 11.7 g/1; H 3 BO 3 12.9 m/1; pyridoxine 170 mg/1; CaCl 2 .2H 2 O 2.35 g/1; KI 2.6 mg/1; thiamine 170 g/1; NaCl 0.15 g/1; CoCl 2 .6H 2 O 2.3 mg/1; niacine 0.67 mg/1; HC1 2.5 ml/1; FeCl 3 .6H 2 O 24.8 mg/1; riboflavin; 0.33 mg/1; CuSO 4 .5H 2 O 1.03
  • the residual glucose concentration was maintained very low (D50 mg/L) in order to minimize ethanol production by fermentation. This was achieved by limiting the development of the microorganism using a limited glucose feed rate.
  • the Standard biomass content (OD 80-90) was reached in fermentation after 44 hour growth phase.
  • CUP1 promoter was then induced by adding 500 ⁇ M CuSO 4 in order to produce P501 S antigen.
  • CuSO 4 addition was followed by ethanol accumulation (up to 6 g/L), and the glucose feeding rate was then reduced in order to consume the ethanol.
  • the copper available for the microorganism was monitored by testing Cu ion concentration in the broth supernatant using a spectrophotometric copper assay (DETC method).
  • the fermentation was then supplemented by CuSO 4 tiiroughout the induction phase in order to maintain its concentration between 150 and 250 ⁇ M in the supernatant.
  • the biomass reached an OD of 100 at the end of induction. Cells were harvested after 8 hours of induction.
  • Cell homogenate was prepared and analysed by SDS-PAGE and Western Blot using standard protocols.
  • a major protein band with the expected molecular weight of 62KD was detected by Western blot using anti-P501S monoclonal antibodies.
  • Western blot analysis also showed that the major 62KD band was progressively produced from 30 minutes of induction on, and reached a maximum after 3 hours. No more antigen seemed to be produced between 3 and 12 hours of induction.
  • the number of passages through a French Press necessary to extract all the antigen from the cells was evaluated. One, three and five passages were tested and total cell lysates, supernatants and pellets of cell lysates were analysed by Western blot. Three passages through a French Press were sufficient to completely extract the antigen. The antigen was present in the insoluble fraction.
  • the cDNA for Ml-length P703P-DE5 (SEQ ID NO: 326), together with several flanking restriction sites, was obtained by digesting the plasmid pCDNA703 with restriction endonucleases Xba I and Hind III. The resulting restriction fragment (approx. 800 base pairs) was ligated into the transfer plasmid pFastBacl which was digested with the same restriction enzymes. The sequence of the insert was confirmed by DNA sequencing.
  • the recombinant transfer plasmid pFBP703 was used to make recombinant bacmid DNA and baculoviras using the Bac-To-Bac Baculoviras expression system (BRL Life Technologies). High Five cells were infected with the recombinant viras BVP703, as described above, to obtain recombinant P703P protein.
  • P788P-N A truncated, N-terminal portion, of P788P (residues 1-644 of SEQ ID NO: 777; referred to as P788P-N) fused with a C-terminal 6xHis Tag was expressed in E. coli as follows.
  • P788P cDNA was amplified using the primers AW080 and AW081 (SEQ ID NO: 672 and 673).
  • AW080 is a sense cloning primer with an Ndel site.
  • AW081 is an antisense cloning primer with a Xhol site.
  • the PCR-amplified P788P, as well as the vector pCRXl, were digested with Ndel and Xhol.
  • the P510S protein has 9 potential transmembrane domains and is predicted to be located at the plasma membrane.
  • the C-terminal protein of this protein, as well as the predicted third extracellular domain of P510S were expressed in E. coli as follows.
  • Ral2-P501S-C The expression construct referred to as Ral2-P501S-C was designed to have a 6 HisTag at the N-terminal enc, followed by the M. tuberculosis antigen Ral 2 (SEQ ID NO: 676) and then the C-terminal portion of P510S (amino residues 1176- 1261 of SEQ ID NO: 538).
  • Full-length P510S was used to amplify the P510S-C fragment by PCR using the primers AW056 and AW057 (SEQ ID NO: 677 and 678, respectively).
  • AW056 is a sense cloning primer with an EcoRI site.
  • AW057 is an antisense primer with stop and Xhol sites.
  • the amplified P501S fragment and Ral2/pCRXl were digested with EcoRI and Xhol and then purified.
  • the insert and vector were ligated together and transformed into NovaBlue. Colonies were randomly screened for insert and sequences.
  • the expression constract was transformed into E. coli BL21 (D ⁇ 3) CodonPlus-RIL competent cells.
  • a mini- induction screen was performed to optimize the expression conditions. After induction the cells grew well, achieving OD 600 nm greater than 2.0 after 3 hours.
  • Coomassie stain SDS-PAGE showed a highly over-expressed band at approx. 30 kD. Though this is higher than the expected molecular weight, western blot analysis was positive, showing this band to be the His tag-containing protein.
  • the expression construct P510S-C was designed to have a 5' added start codon and a glycine (GGA) codon and then the P510S C terminal fragment followed by the in frame 6x histidine tag and stop codon from the pET28b vector.
  • the cloning strategy is similar to that used for Ral2-P510S-C, except that the PCR primers employed were those shown in SEQ ID NO: 685 and 686, respectively and the Ncol/Xhol cut in pET28b was used.
  • the primer of SEQ ID NO: 685 created a 5' Ncol site and added a start codon.
  • the antisense primer of SEQ ID NO: 686 creates a Xhol site on P510S C terminal fragment. Clones were confirmed by sequencing.
  • the expression constract was transformed into E. coli BL21 (DE3) CodonPlus-RIL competent cells. An OD600 of greater than 2.0 was obtained 30 hours after induction. Coomassie stained SDS-PAGE showed an over-expressed band at about 11 kD. Western blot analysis confirmed that the band was P510S-C, as did N-terminal protein sequencing.
  • the optimized culture conditions are as follows: dilute overnight culture/daytime culture (LB + kanamycin + chloramphenicol) into 2x YT (+ kanamycin and chloramphenicol) at a ratio of 25 mL culture to 1 liter 2x YT, and allow to grow at 37 °C until an OD 600 of about 0.5 is reached.
  • the 328-676 of SEQ ID NO: 538) was expressed in E. coli as follows.
  • the P510S fragment was amplified by PCR using the primers shown in SEQ ID NO: 687 and 688.
  • the primer of SEQ ID NO: 687 is a sense primer with an Ndel site for use in ligating into pPDM.
  • the primer of SEQ ID NO: 688 is an antisense primer with an added Xhol site for use in ligating into pPDM.
  • the resulting fragment was cloned to pPDM at the Ndel and Xhol sites. Clones were confirmed by sequencing.
  • the clone ws transformed into E. coli BL21 (DE3) CodonPlus-RIL competent cells.
  • Optimized culture conditions are as follows: dilute overnight culture/daytime culture (LB + kanamycin + chloramphenicol) into 2x YT (kanamycin and chloramphenicol) at a ratio of 25 ml culture to 1 liter 2x YT. Allow to grow at 37 °C until OD 600 equals 0.6. Take out an aliquot as TO sample. Add 1 mM IPTG and allow to grow at 30 °C for 3 hours. Take out a T3 sample, spin down the cells and store at -80 °C until purification.
  • the determined cDNA and amino acid sequences for the P501S-E3 construct are provided in SEQ ID NO: 681 and 684, respectively.
  • the antigen P775P contains multiple open reading frames (ORF).
  • ORF open reading frames
  • the third ORF, encoding the protein of SEQ ID NO: 483, has the best emotif score.
  • An expression fusion constract containing the M. tuberculosis antigen Ral 2 (SEQ ID NO: 676) and P775P-ORF3 with an N-terminal 6x HisTag was prepared as follows.
  • P775P- ORF3 was amplified using the sense PCR primers of SEQ ID NO: 689 and the anti- sense PCR primer of SEQ ID NO: 690.
  • the PCR amplified fragment of P775P and Ral2/pCRXl were digested with the restriction enzymes EcoRI and Xhol. Vector and insert were ligated and then transformed into NovaBlue cells.
  • Colonies were randomly screened for insert and then sequenced. A clone having the desired sequence was transformed into E. coli BL21 (DE3) CodonPlus-RIL competent cells. Two hours after induction, the cell density peaked at OD600 of approximately 1.8. Coomassie stained SDS-PAGE showed an over-expressed band at about 31 kD. Western blot using 6x HisTag antibody confirmed that the band was Ral2-P775P-ORF3. The determined cDNA and amino acid sequences for the fusion constract are provided in SEQ ID NO: 691 and 692, respectively.
  • the cDNA for the coding region of P711P was prepared by PCR using the primers of SEQ ID NO: 701 and 702.
  • the PCR product was digested with EcoRI restriction enzyme, gel purified and cloned into a modified pET28 vector with a His tag in frame, which had been digested with Eco72I and EcoRI restriction enzymes.
  • the correct constract was confirmed by DNA sequence analysis and then transformed into E. coli BL21 (DE3) pLys S and BL21 (DE3) CodonPlus expression host cells.
  • the determined amino acid and cDNA sequences for the expressed recombinant P71 IP are provided in SEQ ID NO: 703 and 704, respectively.
  • Polyclonal antibodies against P703P, P504S and P509S were prepared as follows. Each prostate tumor antigen expressed in an E. coli recombinant expression system was grown overnight in LB broth with the appropriate antibiotics at
  • the cells were induced with IPTG (1 mM).
  • IPTG 1 mM
  • the cells were harvested by centrifugation. The cells were then washed with phosphate buffered saline and centrifuged again. The supernatant was discarded and the cells were either frozen for Mure use or immediately processed. Twenty ml of lysis buffer was added to the cell pellets and vortexed. To break open the E. coli cells, this mixture was then run through the French Press at a pressure of 16,000 psi.
  • the cells were then centrifuged again and the supernatant and pellet were checked by SDS-PAGE for the partitioning of the recombinant protein.
  • the pellet was resuspended in 10 mM Tris pH 8.0, 1% CHAPS and the inclusion body pellet was washed and centrifuged again. This procedure was repeated twice more.
  • the washed inclusion body pellet was solubilized with either 8 M urea or 6 M guanidine HC1 containing 10 mM Tris pH 8.0 plus 10 mM imidazole.
  • the solubilized protein was added to 5 ml of nickel-chelate resin (Qiagen) and incubated for 45 min to 1 hour at room temperature with continuous agitation.
  • HiPrepQ Biorad
  • HiPrepQ Biorad
  • the appropriate buffer was equilibrated with the appropriate buffer and the pooled fractions from above were loaded onto the column. Each antigen was eluted off the column with a increasing salt gradient. Fractions were collected as the column was run and another SDS-PAGE gel was run to determine which fractions from the column to pool. The pooled fractions were dialyzed against 10 mM Tris pH 8.0. The proteins were then vialed after filtration through a 0.22 micron filter and the antigens were frozen until needed for immunization.
  • a murine monoclonal antibody directed against the carboxy-terminus of the prostate-specific antigen P501S was prepared as follows.
  • a truncated fragment of P501S (amino acids 355-526 of SEQ ID NO: 113) was generated and cloned into the pET28b vector (Novagen) and expressed in E. coli as a thioredoxin fusion protein with a histidine tag.
  • the trx-P501S fusion protein was purified by nickel chromatography, digested with thrombin to remove the trx fragment and further purified by an acid precipitation procedure followed by reverse phase HPLC. Mice were immunized with truncated P501 S protein.
  • Serum bleeds from mice that potentially contained anti-P501S polyclonal sera were tested for P501S- specific reactivity using ELISA assays with purified P501S and trx-P501S proteins. Serum bleeds that appeared to react specifically with P501S were then screened for P501S reactivity by Western analysis. Mice that contained a P501 S-specific antibody component were sacrificed and spleen cells were used to generate anti-P501S antibody producing hybridomas using standard techniques. Hybridoma supernatants were tested for P501 S-specific reactivity initially by ELISA, and subsequently by FACS analysis of reactivity with P501S transduced cells.
  • a monoclonal hybridoma referred to as 10E3 was chosen for further subcloning.
  • a number of subclones were generated, tested for specific reactivity to P501S using ELISA and typed for IgG isotype. The results of this analysis are shown below in Table V.
  • the monoclonal antibody 10E3-G4-D3 was selected for further study.
  • 10E3-G4-D3 for P501S was examined by FACS analysis. Specifically, cells were fixed (2% formaldehyde, 10 minutes), permeabihzed (0.1% saponin, 10 minutes) and stained with 10E3-G4-D3 at 0.5 - 1 ⁇ g/ml, followed by incubation with a secondary, FITC-conjugated goat anti-mouse lg antibody (Pharmingen, San Diego, CA). Cells were then analyzed for FITC fluorescence using an Excalibur fluorescence activated cell sorter. For FACS analysis of transduced cells, B-LCL were retrovirally transduced with P501S.
  • B-LCL were infected with a vaccinia vector that expresses P501S.
  • B-LCL transduced with a different antigen (P703P) and uninfected B- LCL vectors were utilized.
  • 10E3-G4-D3 was shown to bind with P501S-transduced B- LCL and also with P501S-infected B-LCL, but not with either uninfected cells or P703P-transduced cells.
  • B-LCL were transduced with P501S or HLA-B8'as a control antigen and either fixed and permeabihzed as described above or directly stained with 10E3-G4-D3 and analyzed as above.
  • P501S P501S
  • HLA-B8'as a control antigen P501S or HLA-B8'as a control antigen
  • 10E3-G4-D3 Specific recognition of P501S by 10E3-G4-D3 was found to require permeabilization, suggesting that the epitope recognized by this antibody is intracellular.
  • 10E3-G4-D3 for P501S was also demonstrated by Western blot analysis. Lysates from the prostate tumor cell lines Lncap, DU-145 and PC-3, from P501S-transiently transfected HEK293 cells, and from non-transfected HEK293 cells were generated. Western blot analysis of these lysates with 10E3-G4-D3 revealed a 46 kDa immunoreactive band in Lncap, PC-3 and P501S-transfected HEK cells, but not in DU-145 cells or non-transfected HEK293 cells.
  • P501S mRNA expression is consistent with these results since semi-quantitative PCR analysis revealed that P501S mRNA is expressed in Lncap, to a lesser but detectable level in PC-3 and not at all in DU-145 cells.
  • Bacterially expressed and purified recombinant P501S (referred to as P501SStr2) was recognized by 10E3-G4-D3 (24 kDa), as was Ml-length P501S that was transiently expressed in HEK293 cells using either the expression vector VR1012 or pCEP4. Although the predicted molecular weight of P501S is 60.5 kDa, both transfected and "native" P501S ran at a slightly lower mobility due to its hydrophobic nature.
  • Immunohistochemical analysis was performed on prostate tumor and a panel of normal tissue sections (prostate, adrenal, breast, cervix, colon, duodenum, gall bladder, ileum, kidney, ovary, pancreas, parotid gland, skeletal muscle, spleen and testis). Tissue samples were fixed in formalin solution for 24 hours and embedded in paraffin before being sliced into 10 micron sections. Tissue sections were permeabihzed and incubated with 10E3-G4-D3 antibody for 1 hr. HRP-labeled anti- mouse followed by incubation with DAB chromogen was used to visualize P501S immunoreactivity.
  • P501S was found to be highly expressed in both normal prostate and prostate tumor tissue but was not detected in any of the other tissues tested.
  • an epitope mapping approach was pursued.
  • a series of 13 overlapping 20-21 mers (5 amino acid overlap; SEQ ID NO: 489-501) was synthesized that spanned the fragment of P501S used to generate 10E3-G4-D3.
  • Flat bottom 96 well microtiter plates were coated with either the peptides or the P501S fragment used to immunize mice, at 1 microgram/ml for 2 hours at 37 °C.

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