WO2000060077A2 - Compounds for therapy and diagnosis of lung cancer and methods for their use - Google Patents

Compounds for therapy and diagnosis of lung cancer and methods for their use Download PDF

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Publication number
WO2000060077A2
WO2000060077A2 PCT/US2000/008560 US0008560W WO0060077A2 WO 2000060077 A2 WO2000060077 A2 WO 2000060077A2 US 0008560 W US0008560 W US 0008560W WO 0060077 A2 WO0060077 A2 WO 0060077A2
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Prior art keywords
seq
polynucleotide
patient
sequences
polypeptide
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PCT/US2000/008560
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French (fr)
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WO2000060077A3 (en
Inventor
Steven G. Reed
Michael J. Lodes
Raodoh Mohamath
Heather Secrist
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Corixa Corporation
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Priority claimed from US09/370,838 external-priority patent/US6444425B1/en
Application filed by Corixa Corporation filed Critical Corixa Corporation
Priority to AU41851/00A priority Critical patent/AU4185100A/en
Priority to EP00921551A priority patent/EP1187915A2/en
Priority to JP2000609568A priority patent/JP2002540790A/en
Publication of WO2000060077A2 publication Critical patent/WO2000060077A2/en
Publication of WO2000060077A3 publication Critical patent/WO2000060077A3/en
Priority to HK02106838.1A priority patent/HK1045332A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/461—Cellular immunotherapy characterised by the cell type used
    • A61K39/4611—T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464499—Undefined tumor antigens, e.g. tumor lysate or antigens targeted by cells isolated from tumor
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K39/46
    • A61K2239/46—Indexing codes associated with cellular immunotherapy of group A61K39/46 characterised by the cancer treated
    • A61K2239/55—Lung
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies

Definitions

  • the present invention relates generally to compositions and methods for the treatment of lung cancer.
  • the invention is more specifically related to nucleotide sequences that are preferentially expressed in lung tumor tissue, together with polypeptides encoded by such nucleotide sequences.
  • the inventive nucleotide sequences and polypeptides may be used in vaccines and pharmaceutical compositions for the treatment of lung cancer.
  • Lung cancer is the primary cause of cancer death among both men and women in the U.S., with an estimated 172,000 new cases being reported in 1994.
  • the five-year survival rate among all lung cancer patients, regardless of the stage of disease at diagnosis, is only 13%. This contrasts with a five-year survival rate of 46% among cases detected while the disease is still localized.
  • only 16% of lung cancers are discovered before the disease has spread.
  • Early detection is difficult since clinical symptoms are often not seen until the disease has reached an advanced stage.
  • diagnosis is aided by the use of chest x-rays, analysis of the type of cells contained in sputum and fiberoptic examination of the bronchial passages.
  • Treatment regimens are determined by the type and stage of the cancer, and include surgery, radiation therapy and/or chemotherapy. In spite of considerable research into therapies for the disease, lung cancer remains difficult to treat.
  • the present invention provides compounds and methods for the therapy and diagnosis of cancer, such as lung cancer.
  • the present invention provides polypeptides comprising at least a portion of a lung tumor protein, or a variant thereof. Certain portions and other variants are immunogenic. such that the ability of the variant to react with antigen-specific antisera is not substantially diminished.
  • the polypeptide comprises a sequence that is encoded by a polynucleotide sequence selected from the group consisting of: (a) sequences recited in SEQ ID NOS: 218-222, 224-226, 249, 250, 253, 256, 266, 276, 277, 282, 285, 293, 295, 298, 299, 301, 304, 306, 316, 321, 326, 333, 336, 337, 342, 353, 359, 361, 364, 369, 372, 373, 377, 379 and 386; (b) variants of a sequence recited in SEQ ID NOS: 218-222, 224-226, 249, 250, 253, 256, 266, 276, 277, 282.
  • the present invention further provides polynucleotides that encode a polypeptide as described above, or a portion thereof (such as a portion encoding at least 15 contiguous amino acid residues of a lung tumor protein), expression vectors comprising such polynucleotides and host cells transformed or transfected with such expression vectors.
  • compositions comprising a polypeptide or polynucleotide as described above and a physiologically acceptable carrier.
  • vaccines are provided.
  • Such vaccines comprise a polypeptide or polynucleotide as described above and an immunostimulant.
  • the present invention further provides pharmaceutical compositions that comprise: (a) an antibody or antigen-binding fragment thereof that specifically binds to a lung tumor protein; 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.
  • vaccines are provided 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.
  • compositions comprising a fusion protein, or a polynucleotide encoding a fusion protein, in combination with a physiologically acceptable carrier are provided.
  • Vaccines are further provided, within other aspects, that comprise a fusion protein, or a polynucleotide encoding a fusion protein, in combination with an immunostimulant.
  • the present invention provides methods for inhibiting the development of a cancer in a patient, comprising administering to a patient a pharmaceutical composition or vaccine as recited above.
  • 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 lung tumor protein, wherein the step of contacting is performed under conditions and for a time sufficient to permit the removal of cells expressing the protein 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 lung tumor protein, comprising contacting T cells with one or more of: (i) a polypeptide as described above; (ii) a polynucleotide encoding such a polypeptide: and/or (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 a lung tumor protein; (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, and 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 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 cancer may be lung cancer.
  • 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 that encodes a lung tumor protein; (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 encoding a polypeptide as recited above, or a complement of such a polynucleotide.
  • the amount of mRNA is detected using a hybridization technique, employing an oligonucleotide probe that hybridizes to a polynucleotide that encodes a polypeptide as recited above, 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 that encodes a lung tumor protein; (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 ofthe 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.
  • SEQ ID NO: 1 is the determined cDNA sequence for L363Cl.
  • SEQ ID NO: 2 is the determined cDNA sequence for L263C2.
  • Cons SEQ ID NO: 3 is the determined cDNA sequence for L263C2c
  • SEQ ID NO: 4 is the determined cDNA sequence for L263Cl.
  • Cons SEQ ID NO: 5 is the determined cDNA sequence for L263Clb
  • SEQ ID NO: 6 is the determined cDNA sequence for L164C2.
  • Cons SEQ ID NO: 7 is the determined cDNA sequence for L164Cl.
  • SEQ ID NO: 8 is the determined cDNA sequence for L366Cla
  • SEQ ID NO: 9 is the determined cDNA sequence for L260Cl.
  • cons SEQ ID NO: 10 is the determined cDNA sequence for L163Clc
  • SEQ ID NO: 11 is the determined cDNA sequence for L163Clb
  • SEQ ID NO: 12 is the determined cDNA sequence for
  • SEQ ID NO 283 s the determined cDNA sequence for 2LT-129
  • SEQ ID NO. 284 s the determined cDNA sequence for 2LT-133
  • SEQ ID NO: 285 s the determined cDNA sequence for 2LT-137
  • SEQ ID NO: 286 s the determined cDNA sequence for LT4690-71
  • SEQ ID NO: 287 s the determined cDNA sequence for LT4690-82
  • SEQ ID NO: 288 s the determined full-length cDNA sequence for SSLT-74
  • SEQ ID NO: 289 s the determined cDNA sequence for SSLT-78
  • SEQ ID NO: 290 s the determined cDNA sequence for SCC1-8.
  • SEQ ID NO: 291 s the determined cDNA sequence for SCC1-12.
  • SEQ ID NO: 292 s the determined cDNA sequence for SCC 1-336
  • SEQ ID NO: 293 s the determined cDNA sequence for SCC 1-344
  • SEQ ID NO: 294 s the determined cDNA sequence for SCC 1-345
  • SEQ ID NO: 295 s the determined cDNA sequence for SCC 1-346
  • SEQ ID NO: 296 s the determined cDNA sequence for SCC 1-348
  • SEQ ID NO: 297 s the determined cDNA sequence for SCC 1-350
  • SEQ ID NO: 298 s the determined cDNA sequence for SCC 1-352
  • SEQ ID NO: 299 s the determined cDNA sequence for SCC 1-354
  • SEQ ID NO: 300 s the determined cDNA sequence for SCC 1-355
  • SEQ ID NO: 301 s the determined cDNA sequence for SCCl-356
  • SEQ ID NO: 302 s the determined cDNA sequence for SCC1-357
  • SEQ ID NO: 303 s the determined cDNA sequence for SCC1-501
  • SEQ ID NO: 304 s the determined cDNA sequence for SCC 1-503
  • SEQ ID NO: 305 s the determined cDNA sequence for SCC 1-513
  • SEQ ID NO: 306 s the determined cDNA sequence for SCC 1-516
  • SEQ ID NO: 307 s the determined cDNA sequence for SCC 1-518
  • SEQ ID NO: 308 s the determined cDNA sequence for SCC 1-519
  • SEQ ID NO: 309 s the determined cDNA sequence for SCC 1-522
  • SEQ ID NO: 310 s the determined cDNA sequence for SCC 1-523
  • SEQ ID NO: 311 s the determined cDNA sequence for SCC 1-525
  • SEQ ID NO: 312 s the determined cDNA sequence for SCC 1-527
  • SEQ ID NO: 313 iis the determined cDNA sequence for SCC 1-529
  • SEQ ID NO: 314 iis the determined cDNA sequence for SCC 1-530
  • SEQ ID NO: 315 iis the determined cDNA sequence for SCC 1-531
  • SEQ ID NO: 316 i is the determined cDNA sequence for SCC 1-532
  • SEQ ID NO: 317 i is the determined cDNA sequence for SCC 1-533
  • SEQ ID NO: 318 iis the determined cDNA sequence for SCC1-536
  • SEQ ID NO: 319 iis the determined cDNA sequence for SCC 1-538
  • SEQ ID NO: 320 i is the determined cDNA sequence for SCC1-539
  • SEQ ID NO: 321 i is the determined cDNA sequence for SCC 1-541
  • SEQ ID NO: 322 i is the determined cDNA sequence for SCC 1-542
  • SEQ ID NO: 323 i is the determined cDNA sequence for SCC 1-546
  • SEQ ID NO: 324 iis the determined cDNA sequence for SCC 1-549
  • SEQ ID NO: 325 iis the determined cDNA sequence for SCC1-551
  • SEQ ID NO: 326 i is the determined cDNA sequence for SCC1-552
  • SEQ ID NO: 327 iis the determined cDNA sequence for SCCl-554
  • SEQ ID NO: 328 i is the determined cDNA sequence for SCC1-558
  • SEQ ID NO: 329 i is the determined cDNA sequence for SCC 1-559
  • SEQ ID NO: 330 iis the determined cDNA sequence for SCC 1-561
  • SEQ ID NO: 331 i is the determined cDNA sequence for SCC 1-562
  • SEQ ID NO: 332 i is the determined cDNA sequence for SCC 1-564
  • SEQ ID NO: 333 i is the determined cDNA sequence for SCC 1-565
  • SEQ ID NO: 334 iis the determined cDNA sequence for SCC 1-566
  • SEQ ID NO: 335 iis the determined cDNA sequence for SCC 1-567
  • SEQ ID NO: 336 iis the determined cDNA sequence for SCC 1-568
  • SEQ ID NO: 337 i is the determined cDNA sequence for SCC 1-570
  • SEQ ID NO: 338 iis the determined cDNA sequence for SCC 1-572
  • SEQ ID NO: 339 i is the determined cDNA sequence for SCC 1-575
  • SEQ ID NO: 340 i is the determined cDNA sequence for SCC 1-576
  • SEQ ID NO: 341 i is the determined cDNA sequence for SCC 1-577
  • SEQ ID NO: 342 i is the determined cDNA sequence for SCC 1-578
  • SEQ ID NO 344 is the determined cDNA sequence for SCC1-583
  • SEQ ID NO 345 s the determined cDNA sequence for SCC 1-586
  • SEQ ID NO 346 s the determined cDNA sequence for SCC 1-588
  • SEQ ID NO 347 s the determined cDNA sequence for SCC 1-590
  • SEQ ID NO 348 s the determined cDNA sequence for SCC 1-591
  • 350 s the determined cDNA sequence for SCC 1-593
  • SEQ ID NO 351 s the determined cDNA sequence for SCC 1-594
  • SEQ ID NO 352 s the determined cDNA sequence for SCC 1-595
  • SEQ ID NO 353 s the determined cDNA sequence for SCC 1-596
  • SEQ ID NO 354 s the determined cDNA sequence for SCC 1
  • the present invention is generally directed to compositions and methods for the therapy and diagnosis of cancer, such as lung cancer.
  • the compositions described herein may include lung tumor polypeptides, polynucleotides encoding such polypeptides, binding agents such as antibodies, antigen presenting cells (APCs) and/or immune system cells (e.g., T cells).
  • Polypeptides of the present invention generally comprise at least a portion (such as an immunogenic portion) of a lung tumor protein or a variant thereof.
  • a "lung tumor protein” is a protein that is expressed in lung tumor cells at a level that is at least two fold, and preferably at least five fold, greater than the level of expression in a normal tissue, as determined using a representative assay provided herein.
  • Certain lung tumor proteins are tumor proteins that react detectably (within an immunoassay, such as an ELISA or Western blot) with antisera of a patient afflicted with lung cancer.
  • Polynucleotides of the subject invention generally comprise a DNA or RNA sequence that encodes all or a portion of such a polypeptide, or that is complementary to such a sequence.
  • Antibodies are generally immune system proteins, or antigen-binding fragments thereof, that are capable of binding to a polypeptide as described above.
  • Antigen presenting cells include dendritic cells, macrophages, monocytes, fibroblasts and B-cells that express a polypeptide as described above.
  • T cells that may be employed within such compositions are generally T cells that are specific for a polypeptide as described above.
  • the present invention is based on the discovery of human lung tumor proteins. Sequences of polynucleotides encoding specific tumor proteins are provided in SEQ ID NOS: 1-31, 49-55, 63,64, 66, 68-72, 78-80, 84-92 and 217-389.
  • any polynucleotide that encodes a lung tumor protein or a portion or other variant thereof as described herein is encompassed by the present invention.
  • Preferred polynucleotides comprise at least 15 consecutive nucleotides, preferably at least 30 consecutive nucleotides and more preferably at least 45 consecutive nucleotides, that encode a portion of a lung tumor protein. More preferably, a polynucleotide encodes an immunogenic portion of a lung tumor protein.
  • Polynucleotides complementary to any such sequences are also encompassed by the present invention. Polynucleotides may be single-stranded (coding or antisense) or double-stranded, and may be DNA (genomic, cDNA or synthetic) or RNA molecules.
  • RNA molecules 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 lung tumor protein or a portion thereof) or may comprise a variant of such a sequence.
  • Polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions such that the immunogenicity of the encoded polypeptide is not diminished, relative to a native tumor protein. The effect on the immunogenicity of the encoded polypeptide may generally be assessed as described herein.
  • Variants preferably exhibit at least about 70% identity, more preferably at least about 80%) identity and most preferably at least about 90% identity to a polynucleotide sequence that encodes a native lung tumor protein or a portion thereof.
  • Two polynucleotide or polypeptide sequences are said to be “identical” if the sequence of nucleotides or 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 En ⁇ ymology vol.
  • 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 or 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 ofthe two sequences.
  • the percentage is calculated by determining the number of positions at which the identical nucleic acid bases or 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.
  • Variants may also, or alternatively, be substantially homologous to a native gene, or a portion or complement thereof.
  • Such polynucleotide variants are capable of hybridizing under moderately stringent conditions to a naturally occurring DNA sequence encoding a native lung tumor protein (or a complementary sequence). Suitable moderately stringent conditions include prewashing in a solution of 5 X SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at 50°C-65°C, 5 X SSC, overnight; followed by washing twice at 65°C for 20 minutes with each of 2X, 0.5X and 0.2X SSC containing 0.1% SDS.
  • 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. The resulting 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).
  • Polynucleotides may be prepared using any of a variety of techniques.
  • 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 five fold greater in a lung tumor than in normal tissue, as determined using a representative assay provided herein). Such screens may be performed using a Synteni microarray (Palo Alto, CA) according to the manufacturer's instructions (and essentially 9
  • polypeptides may be amplified from cDNA prepared from cells expressing the proteins described herein, such as lung tumor cells.
  • Such polynucleotides may be amplified via polymerase chain reaction (PCR).
  • sequence-specific primers may be designed based on the sequences provided herein, and may be purchased or synthesized.
  • An amplified portion may be used to isolate a full length gene from a suitable library (e.g., a lung 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 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 are 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 for obtaining a full length coding sequence from a partial cDNA sequence.
  • amplification is generally performed via PCR. Any of a variety of commercially available kits may be used to perform the amplification step.
  • Primers may be designed using, for example, software well known in the art. Primers are preferably 22-30 nucleotides in length, have a GC content of at least 50%> and anneal to the target sequence at temperatures of about 68°C to 72°C.
  • the amplified region may be sequenced as described above, and overlapping sequences assembled into a contiguous sequence.
  • amplification technique is inverse PCR (see Triglia et al., Nucl. Acids Res. 7(5:8186, 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.
  • RACE Rapid amplification of cDNA ends
  • This technique involves the use of an internal primer and an external primer, which hybridizes to a polyA region or vector sequence, to identify sequences that are 5' and 3' of a known sequence. Additional techniques include capture PCR (Lagerstrom et al., PCR Methods Applic. 7 : 111 - 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
  • nucleic acid sequences of cDNA molecules encoding portions of lung tumor proteins are provided in SEQ ID NO: 1-31, 49-55, 63,64, 66, 68-72, 78-80, 84-92 and 217-389. The isolation of these sequences is described in detail below.
  • Polynucleotide variants may generally be prepared by any method known in the art, including chemical synthesis by, for example, solid phase phosphoramidite chemical synthesis. Modifications in a polynucleotide sequence may also be introduced using standard mutagenesis techniques, such as oligonucleotide- directed site-specific mutagenesis (see Adelman et al., DNA 2:183, 1983). Alternatively, RNA molecules may be generated by in vitro or in vivo transcription of DNA sequences encoding a lung tumor protein, or portion thereof, provided that the DNA is incorporated into a vector with a suitable RNA polymerase promoter (such as T7 or SP6). Certain portions may be used to prepare an encoded polypeptide, as described herein.
  • a suitable RNA polymerase promoter such as T7 or SP6
  • a portion may be admimstered to a patient such that the encoded polypeptide is generated in vivo (e.g., by transfecting antigen-presenting cells, such as dendritic cells, with a cDNA construct encoding a lung tumor polypeptide. and administering the transfected cells to the patient).
  • antigen-presenting cells such as dendritic cells
  • a portion of a sequence complementary to a coding sequence may also be used as a probe or to modulate gene expression.
  • cDNA constructs that can be transcribed into antisense RNA may also be introduced into cells of tissues to facilitate the production of antisense RNA.
  • An antisense polynucleotide may be used, as described herein, to inhibit expression of a tumor protein.
  • Antisense technology can be used to control gene expression through triple- helix formation, which compromises the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors or regulatory molecules (see Gee et al., In Huber and Carr, Molecular and Immunologic Approaches, Futura Publishing Co. (Mt.
  • an antisense molecule may be designed to hybridize with a control region of a gene (e.g., promoter, enhancer or transcription initiation site), and block transcription of the gene; or to block translation by inhibiting binding of a transcript to ribosomes.
  • a control region of a gene e.g., promoter, enhancer or transcription initiation site
  • a portion of a coding sequence, or of a complementary sequence, may also be designed as a probe or primer to detect gene expression.
  • Probes may be labeled with a variety of reporter groups, such as radionuclides and enzymes, and are preferably at least 10 nucleotides in length, more preferably at least 20 nucleotides in length and still more preferably at least 30 nucleotides in length.
  • Primers as noted above, are preferably 22-30 nucleotides in length. Any polynucleotide may be further modified to increase stability in vivo.
  • flanking sequences at the 5' and/or 3' ends Possible modifications include, but are not limited to, the addition of flanking sequences at the 5' and/or 3' ends; the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages in the backbone; and/or the inclusion of nontraditional bases such as inosine, queosine and wybutosine, as well as acetyl-, methyl-, thio- and other modified forms of adenine, cytidine, guanine, thymine and uridine.
  • flanking sequences at the 5' and/or 3' ends Possible modifications include, but are not limited to, the addition of flanking sequences at the 5' and/or 3' ends; the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages in the backbone; and/or the inclusion of nontraditional bases such as inosine, queosine and wybutosine, as well
  • Nucleotide sequences as described herein may be joined to a variety of other nucleotide sequences using established recombinant DNA techniques.
  • a polynucleotide may be cloned into any of a variety of cloning vectors, including plasmids. phagemids, lambda plfage derivatives and cosmids.
  • Vectors of particular interest include expression vectors, replication vectors, probe generation vectors and sequencing vectors.
  • a vector will contain an origin of replication functional in at least one organism, convenient restriction endonuclease sites and one or more selectable markers. Other elements will depend upon the desired use. and will be apparent to those of ordinary skill in the art.
  • polynucleotides may be formulated so as to permit entry into a cell of a mammal, and expression therein. Such formulations are particularly useful for therapeutic purposes, as described below.
  • a polynucleotide may be incorporated into a viral vector such as, but not limited to, adenovirus, adeno-associated virus, retrovirus, or vaccinia or other pox virus (e.g., avian pox virus). Techniques for incorporating DNA into such vectors are well known to those of ordinary skill in the art.
  • a retroviral vector may additionally transfer or incorporate a gene for a selectable marker (to aid in the identification or selection of transduced cells) and/or a targeting moiety, such as a gene that encodes a ligand for a receptor on a specific target cell, to render the vector target specific. Targeting may also be accomplished using an antibody, by methods known to those of ordinary skill in the art.
  • Other formulations for therapeutic purposes include colloidal dispersion systems, such as macromolecule complexes, nanocapsules. microspheres. beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes.
  • a preferred colloidal system for use as a delivery vehicle in vitro and in vivo is a liposome (i.e., an artificial membrane vesicle). The preparation and use of such systems is well known in the art.
  • polypeptides may comprise at least an immunogenic portion of a lung tumor protein or a variant thereof, as described herein.
  • a "lung tumor protein” is a protein that is expressed by lung tumor cells. Proteins that are lung tumor proteins also react detectably within an immunoassay (such as an ELISA) with antisera from a patient with lung cancer.
  • Polypeptides as described herein may be of any length. Additional sequences derived from the native protein and/or heterologous sequences may be present, and such sequences may (but need not) possess further immunogenic or antigenic properties.
  • immunogenic portion is a portion of a protein that is recognized (i.e., specifically bound) by a B-cell and/or T-cell surface antigen receptor.
  • immunogenic portions generally comprise at least 5 amino acid residues, more preferably at least 10, and still more preferably at least 20 amino acid residues of a lung tumor protein or a variant thereof.
  • Certain preferred immunogenic portions include peptides in which an N-terminal leader sequence and/or transmembrane domain have been deleted.
  • Other preferred immunogenic portions may 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.
  • Immunogenic portions may generally be identified using well known techniques, such as those summarized in Paul, Fundamental Immunology, 3rd ed., 243- 247 (Raven Press, 1993) and references cited therein. Such techniques include screening polypeptides for the ability to react with antigen-specific antibodies, antisera and/or T-cell lines or clones.
  • antisera and antibodies are "antigen- specific" if they specifically bind to an antigen (i.e.. they react with the protein in an ELISA or other immunoassay, and do not react detectably with unrelated proteins).
  • antisera and antibodies may be prepared as described herein, and using well known techniques.
  • An immunogenic portion of a native lung tumor protein is a portion that reacts with such antisera and/or T-cells at a level that is not substantially less than the reactivity of the full length polypeptide (e.g., in an ELISA and/or T-cell reactivity assay). Such immunogenic portions may react within such assays at a level that is similar to or greater than the reactivity ofthe full length polypeptide.
  • Such screens may generally be performed using methods well known to those of ordinary skill in the art. such as those described in Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988.
  • a polypeptide may be immobilized on a solid support and contacted with patient sera to allow binding of antibodies within the sera to the immobilized polypeptide. Unbound sera may then be removed and bound antibodies detected using, for example, 125 I-labeled Protein A.
  • a composition may comprise a variant of a native lung tumor protein.
  • a polypeptide "variant,” as used herein, is a polypeptide that differs from a native lung tumor protein in one or more substitutions, deletions, additions and/or insertions, such that the immunogenicity of the polypeptide is not substantially diminished.
  • the ability of a variant to react with antigen-specific antisera may be enhanced or unchanged, relative to the native protein, or may be diminished by less than 50%, and preferably less than 20%, relative to the native protein.
  • Such variants may generally be identified by modifying one of the above polypeptide sequences and evaluating the reactivity of the modified polypeptide with antigen-specific antibodies or antisera as described herein.
  • Preferred variants include those in which one or more portions, such as an N-terminal leader sequence or transmembrane domain, have been removed.
  • Other preferred 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 ofthe mature protein.
  • Polypeptide variants preferably exhibit at least about 70%, more preferably at least about 90% and most preferably at least about 95% identity (determined as described above) to the identified polypeptides.
  • a variant contains conservative substitutions.
  • a "conservative substitution” is one in which an amino acid is substituted for another amino acid that has similar properties, such that one skilled in the art of peptide chemistry would expect the secondary structure and hydropathic nature of the polypeptide to be substantially unchanged.
  • Amino acid substitutions may generally be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues.
  • negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine and valine; glycine and alanine; asparagine and glutamine; and serine, threonine, phenylalanine and tyrosine.
  • 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 ofthe 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 ofthe polypeptide to a solid support.
  • a polypeptide may be conjugated to an immunoglobulin Fc region.
  • Polypeptides may be prepared using any of a variety of well known techniques. Recombinant polypeptides encoded by DNA sequences as described above may be readily prepared from the DNA sequences using any of a variety of expression vectors known to those of ordinary skill in the art. Expression may be achieved in any appropriate host cell that has been transformed or transfected with an expression vector containing a DNA molecule that encodes a recombinant polypeptide. Suitable host cells include prokaryotes, yeast and higher eukaryotic cells. Preferably, the host cells employed are E. coli, yeast or a mammalian cell line such as COS or CHO.
  • Supernatants from suitable host/vector systems which secrete recombinant protein or polypeptide into culture media may be first concentrated using a commercially available filter. Following concentration, the concentrate may be applied to a suitable purification matrix such as an affinity matrix or an ion exchange resin. Finally, one or more reverse phase HPLC steps can be employed to further purify a recombinant polypeptide.
  • a suitable purification matrix such as an affinity matrix or an ion exchange resin.
  • Portions and other variants having fewer than about 100 amino acids, and generally fewer than about 50 amino acids, may also be generated by synthetic means, using techniques well known to those of ordinary skill in the art.
  • such polypeptides may be synthesized using any of the commercially available solid- phase techniques, such as the Merrifield solid-phase synthesis method, where amino acids are sequentially added to a growing amino acid chain. See Merrifield, J. Am. Chem. Soc. 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 instructions.
  • a polypeptide may be a fusion protein 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 protein or to enable the protein to be targeted to desired intracellular compartments.
  • Still further fusion partners include affinity tags, which facilitate purification ofthe protein.
  • Fusion proteins may generally be prepared using standard techniques, including chemical conjugation.
  • a fusion protein is expressed as a recombinant protein, allowing the production of increased levels, relative to a non-fused protein, 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 protein that retains the biological activity of both component polypeptides.
  • a peptide linker sequence may be employed to separate the first and the 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 protein using standard techniques well known in the art.
  • Suitable peptide linker sequences may be chosen based on the following factors: (1) their ability to adopt a flexible extended conformation; (2) their inability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides; and (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes.
  • Preferred peptide linker sequences contain Gly, Asn and Ser residues.
  • linker sequences which may be usefully employed as linkers include those disclosed in Maratea et al, Gene 40:39-46, 1985; Murphy et al., Proc. Natl. Acad. Sci. USA 53:8258-8262, 1986; U.S. Patent No. 4,935,233 and U.S. Patent No. 4,751,180.
  • the linker sequence may generally be from 1 to about 50 amino acids in length. Linker sequences are not required when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference.
  • the ligated DNA sequences are operably linked to suitable transcriptional or translational regulatory elements.
  • the regulatory elements responsible for expression of DNA are located only 5' to the DNA sequence encoding the first polypeptides.
  • stop codons required to end translation and transcription termination signals are only present 3' to the DNA sequence encoding the second polypeptide.
  • Fusion proteins are also provided that comprise a polypeptide of the present invention together with an unrelated immunogenic protein.
  • the immunogenic protein is capable of eliciting a recall response.
  • examples of such proteins include tetanus, tuberculosis and hepatitis proteins (see, for example, Stoute et al. New Engl. J. Med., 336:86-91, 1997).
  • 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 ⁇ -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 ⁇ -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.
  • fusion partners include the non-structural protein from influenzae virus, ⁇ S1 (hemaglutinin). Typically, the ⁇ -terminal 81 amino acids are used, although different fragments that include T-helper epitopes may be used.
  • the immunological fusion partner is the protein known as LYTA, or a portion thereof (preferably a C-terminal portion).
  • LYTA is derived from Streptococcus pneumoniae, which synthesizes an ⁇ -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 D ⁇ A ⁇ . 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).
  • a repeat portion of LYTA may be incorporated into a fusion protein. A repeat portion is found in the C- terminal region starting at residue 178. A particularly preferred repeat portion incorporates residues 188-305.
  • polypeptides including fusion proteins and polynucleotides as described herein are isolated.
  • An "isolated" polypeptide or polynucleotide is one that is removed from its original environment.
  • a naturally-occurring protein is isolated if it is separated from some or all of the coexisting materials in the natural system.
  • polypeptides are at least about 90% pure, more preferably at least about 95% pure and most preferably at least about 99% pure.
  • a polynucleotide is considered to be isolated if, for example, it is cloned into a vector that is not a part of the natural environment.
  • the present invention further provides agents, such as antibodies and antigen-binding fragments thereof, that specifically bind to a lung tumor protein.
  • an antibody, or antigen-binding fragment thereof is said to "specifically bind" to a lung tumor protein if it reacts at a detectable level (within, for example, an ELISA) with a lung tumor protein, and does not react detectably with unrelated proteins under similar conditions.
  • binding refers to a noncovalent association between two separate molecules such that a complex is formed. The ability to bind may be evaluated by, for example, determining a binding constant for the formation of the complex. The binding constant is the value obtained when the concentration of the complex is divided by the product of the component concentrations. In general, two compounds are said to "bind,” in the context of the present invention, when the binding constant for complex formation exceeds about 10 3 L/mol. The binding constant may be determined using methods well known in the art.
  • Binding agents may be further capable of differentiating between patients with and without a cancer, such as lung cancer, using the representative assays provided herein.
  • a cancer such as lung cancer
  • antibodies or other binding agents that bind to a lung tumor protein will generate a signal indicating the presence of a cancer in at least about 20%) of patients with the disease, and 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, urine and/or tumor biopsies
  • a cancer as determined using standard clinical tests
  • 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 chromatography using the polypeptide coupled to a suitable solid support.
  • Monoclonal antibodies specific for an antigenic polypeptide of interest may be prepared, for example, using the technique of Kohler and Milstein, Eur. J. Immunol. 6:511-519, 1976, and improvements thereto. Briefly, these methods involve the preparation of immortal cell lines capable of producing antibodies having the desired specificity (i.e., reactivity with the polypeptide of interest). Such cell lines may be produced, for example, from spleen cells obtained from an animal immunized as described above. The spleen cells are then immortalized by, for example, fusion with a myeloma cell fusion partner, preferably one that is syngeneic with the immunized animal. A variety of fusion techniques may be employed.
  • the spleen cells and myeloma cells may be combined with a nonionic detergent for a few minutes and then plated at low density on a selective medium that supports the growth of hybrid cells, but not myeloma cells.
  • a preferred selection technique uses HAT (hypoxanthine, aminopterin, thymidine) selection. After a sufficient time, usually about 1 to 2 weeks, colonies of hybrids are observed. Single colonies are selected and their culture supernatants tested for binding activity against the polypeptide. Hybridomas having high reactivity and specificity are preferred.
  • Monoclonal antibodies may be isolated from the supernatants of growing hybridoma colonies.
  • various techniques may be employed to enhance the yield, such as injection of the hybridoma cell line into the peritoneal cavity of a suitable vertebrate host, such as a mouse.
  • Monoclonal antibodies may then be harvested from the ascites fluid or the blood.
  • Contaminants may be removed from the antibodies by conventional techniques, such as chromatography, gel filtration, precipitation, and extraction.
  • the polypeptides of this invention may be used in the purification process in, for example, an affinity chromatography step.
  • antigen-binding fragments of antibodies may be preferred.
  • Such fragments include Fab fragments, which may be prepared using standard techniques. Briefly, immunoglobulins may be purified from rabbit serum by affinity chromatography on Protein A bead columns (Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988) and digested by papain to yield Fab and Fc fragments. The Fab and Fc fragments may be separated by affinity chromatography on protein A bead columns.
  • Monoclonal antibodies ofthe present invention may be coupled to one or more therapeutic agents.
  • Suitable agents in this regard include radionuclides, differentiation inducers, drugs, toxins, and derivatives thereof.
  • Preferred radionuclides include 90 Y, I23 I, 125 I, 131 I, 186 Re, 1S8 Re, 21 , At, and 21 Bi.
  • Preferred drugs include methotrexate, and pyrimidine and purine analogs.
  • Preferred differentiation inducers include phorbol esters and butyric acid.
  • Preferred toxins include ricin, abrin, diptheria toxin, cholera toxin, gelonin, Pseudomonas exotoxin. Shigella toxin, and pokeweed antiviral protein.
  • a therapeutic agent may be coupled (e.g., covalently bonded) to a suitable monoclonal antibody either directly or indirectly (e.g., via a linker group).
  • a direct reaction between an agent and an antibody is possible when each possesses a substituent capable of reacting with the other.
  • a nucleophilic group such as an amino or sulfhydryl group
  • on one may be capable of reacting with a carbonyl- containing group, such as an anhydride or an acid halide, or with an alkyl group containing a good leaving group (e.g., a halide) on the other.
  • a linker group can function as a spacer to distance an antibody from an agent in order to avoid interference with binding capabilities.
  • a linker group can also serve to increase the chemical reactivity of a substituent on an agent or an antibody, and thus increase the coupling efficiency. An increase in chemical reactivity may also facilitate the use of agents, or functional groups on agents, which otherwise would not be possible. It will be evident to those skilled in the art that a variety of bifunctional or polyfunctional reagents, both homo- and hetero-functional (such as those described in the catalog ofthe Pierce Chemical Co., Rockford, IL), may be employed as the linker group.
  • Coupling may be effected, for example, through amino groups, carboxyl groups, sulfhydryl groups or oxidized carbohydrate residues.
  • 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 which provide multiple sites for attachment can be used. Alternatively, a carrier can be used.
  • a carrier may bear the agents in a variety of ways, including covalent bonding either directly or via a linker group.
  • Suitable carriers include proteins such as albumins (e.g., U.S. Patent No. 4,507,234. to Kato et al.), peptides and polysaccharides such as aminodextran (e.g., U.S. Patent No. 4,699,784, 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 radionuclide agents include radiohalogenated small molecules and chelating compounds.
  • U.S. Patent No. 4,735,792 discloses representative radiohalogenated small molecules and their synthesis.
  • a radionuclide chelate may be formed from chelating compounds that include those containing nitrogen and sulfur atoms as the donor atoms for binding the metal, or metal oxide, radionuclide.
  • U.S. Patent No. 4,673,562 to Davison et al. discloses representative chelating compounds and their synthesis.
  • routes of administration for the antibodies and immunoconjugates may be used. Typically, administration will be intravenous, intramuscular, subcutaneous or in the bed of a resected tumor. It will be evident that the precise dose of the antibody/immunoconjugate will vary depending upon the antibody used, the antigen density on the tumor, and the rate of clearance ofthe antibody.
  • Immunotherapeutic compositions may also, or alternatively, comprise T cells specific for a lung tumor protein.
  • T cells may generally be prepared in vitro or ex vivo, using standard procedures.
  • T cells may be isolated from bone marrow, peripheral blood, or a fraction of bone marrow or peripheral blood of a patient, using a commercially available cell separation system, such as the ISOLEXTM system. available from Nexell Therapeutics Inc., Irvine. 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 lung tumor polypeptide, polynucleotide encoding a lung tumor 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.
  • a lung tumor polypeptide or polynucleotide 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 lung tumor polypeptide if the T cells kill target cells coated with the polypeptide or expressing a gene encoding the polypeptide.
  • T cell specificity may be evaluated using any of a variety of standard techniques. For example, within a chromium release assay or proliferation assay, a stimulation index of more than two fold increase in lysis and/or proliferation, compared to negative controls, indicates T cell specificity. Such assays may be performed, for example, as described in Chen et al., Cancer Res. 54:1065-1070, 1994. Alternatively, detection of the proliferation of T cells may be accomplished by a variety of known techniques.
  • T cell proliferation can be detected by measuring an increased rate of DNA synthesis (e.g., by pulse-labeling cultures of T cells with tritiated thymidine and measuring the amount of tritiated thymidine incorporated into DNA).
  • a lung tumor polypeptide 100 ng/ml - 100 ⁇ g/ml, preferably 200 ng/ml - 25 ⁇ g/ml
  • contact with a lung tumor polypeptide 100 ng/ml - 100 ⁇ g/ml, preferably 200 ng/ml - 25 ⁇ g/ml
  • T cells that have been activated in response to a lung tumor polypeptide, polynucleotide or polypeptide-expressing APC may be CD4" and/or CD8 + .
  • Lung tumor protein-specific T cells may be expanded using standard techniques.
  • the T cells are derived from either a patient or a related, or unrelated, donor and are administered to the patient following stimulation and expansion.
  • CD4 + or CD8 + T cells that proliferate in response to a lung 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.
  • the T cells can be re-exposed to a lung 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 lung tumor polypeptide.
  • T cell growth factors such as interleukin- 2
  • one or more T cells that proliferate in the presence of a lung tumor protein can be expanded in number by cloning. Methods for cloning cells are well known in the art, and include limiting dilution.
  • polypeptides, polynucleotides, T cells and/or binding agents disclosed herein may be inco ⁇ orated into pharmaceutical compositions or immunogenic compositions (i.e., vaccines).
  • Pharmaceutical compositions comprise one or more such compounds and a physiologically acceptable carrier.
  • Vaccines may comprise one or more such compounds and an immunostimulant.
  • An immunostimulant may be any substance that enhances or potentiates an immune response to an exogenous antigen. Examples of immunostimulants include adjuvants, biodegradable microspheres (e.g., polylactic galactide) and liposomes (into which the compound is inco ⁇ orated; see e.g., Fullerton, U.S. Patent No. 4,235,877).
  • compositions and vaccines within the scope of the present invention may also contain other compounds, which may be biologically active or inactive.
  • one or more immunogenic portions of other tumor antigens may be present, either inco ⁇ orated into a fusion polypeptide or as a separate compound, within the composition or vaccine.
  • a pharmaceutical composition or vaccine may contain DNA encoding one or more of the polypeptides as described above, such that the polypeptide is generated in situ.
  • the DNA may be present within any of a variety of delivery systems known to those of ordinary skill in the art, including nucleic acid expression systems, bacteria and viral expression systems. 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 nucleic acid expression systems contain the necessary DNA sequences for expression in the patient (such as a suitable promoter and terminating signal).
  • Bacterial delivery systems involve the administration of a bacterium (such as Bacillus-Calmette- Guerrin) that expresses an immunogenic portion ofthe polypeptide on its cell surface or secretes such an epitope.
  • the DNA may be introduced using a viral expression system (e.g., vaccinia or other pox virus, retrovirus. or adenovirus), which may involve the use of a non-pathogenic (defective), replication competent virus.
  • a viral expression system e.g., vaccinia or other pox virus, retrovirus. or adenovirus
  • vaccinia or other pox virus, retrovirus. or adenovirus may involve the use of a non-pathogenic (defective), replication competent virus.
  • Suitable systems are disclosed, for example, in Fisher-Hoch et al., Proc. Natl. Acad. Sci. USA 56:317-321, 1989; Flexner et al, Ann. N. Y. Ac ⁇ d. Sci. 569:86-103, 1989; Flexner et al., Vaccine 5:17-21, 1990; U.S. Patent Nos.
  • compositions of the present invention may be formulated for any appropriate manner of administration, including for example, topical, oral, nasal, intravenous, intracranial. intraperitoneal, subcutaneous or intramuscular administration.
  • the carrier preferably comprises water, saline, alcohol, a fat. a wax or a buffer.
  • any of the above carriers or a solid carrier such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, glucose, sucrose, and magnesium carbonate, may be employed.
  • Biodegradable microspheres may also be employed as carriers for the pharmaceutical compositions of this invention.
  • Suitable biodegradable microspheres are disclosed, for example, in U.S. Patent Nos. 4,897,268 and 5,075,109.
  • compositions may also comprise buffers (e.g., neutral buffered saline or phosphate buffered saline), carbohydrates (e.g., glucose, mannose, sucrose or dextrans), mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, chelating agents such as EDTA or glutathione, adjuvants (e.g., aluminum hydroxide) and or preservatives.
  • buffers e.g., neutral buffered saline or phosphate buffered saline
  • carbohydrates e.g., glucose, mannose, sucrose or dextrans
  • mannitol proteins
  • proteins polypeptides or amino acids
  • proteins e.g., polypeptides or amino acids
  • chelating agents such as EDTA or glutathione
  • adjuvants e.g., aluminum hydroxide
  • compositions of the present invention may be formulated as a lyophilizate.
  • Compounds
  • adjuvants contain a substance designed to protect the antigen from rapid catabolism. such as aluminum hydroxide or mineral oil, and a stimulator of immune responses, such as lipid A, Bortadella pertussis or Mycobacterium tuberculosis derived proteins.
  • Suitable adjuvants are commercially available as, for example, Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, MI); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, NJ); 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 or interleukin-2. -7, or -12, may also be used as adjuvants.
  • the adjuvant composition is preferably designed to induce an immune response predominantly of the Thl type.
  • High levels of Thl -type cytokines e.g., IFN- ⁇ , TNF ⁇ , IL-2 and IL-12
  • 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.
  • Preferred adjuvants for use in eliciting a predominantly Thl -type response include, for example, a combination of monophosphoryl lipid A, preferably 3- de-O-acylated monophosphoryl lipid A (3D-MPL), together with an aluminum salt.
  • MPL adjuvants are available from Ribi ImmunoChem Research Inc. (Hamilton, MT) (see 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 unmethylated also induce a predominantly Thl response. Such oligonucleotides are well known and are described, for example, in WO 96/02555.
  • Another preferred adjuvant is a saponin, preferably QS21, which may be used alone or in combination with other adjuvants.
  • an enhanced system involves the combination of a monophosphoryl lipid A and saponin derivative, such as the combination of QS21 and 3D-MPL as described in WO 94/00153, or a less reactogenic composition where the QS21 is quenched with cholesterol, as described in WO 96/33739.
  • Other preferred formulations comprises an oil-in- water emulsion and tocopherol.
  • a particularly potent adjuvant formulation involving QS21, 3D-MPL and tocopherol in an oil-in- water emulsion is described in WO 95/17210.
  • Any vaccine provided herein may be prepared using well known methods that result in a combination of antigen, immune response enhancer and a suitable carrier or excipient.
  • compositions described herein may be administered as part of a sustained release formulation (i.e., a formulation such as a capsule, sponge or gel (composed of polysaccharides, for example) that effects a slow release of compound following administration).
  • sustained release formulations may generally be prepared using well known technology and administered by, for example, oral, rectal or subcutaneous implantation, or by implantation at the desired target site.
  • Sustained-release formulations may contain a polypeptide. polynucleotide or antibody dispersed in a carrier matrix and or contained within a reservoir surrounded by a rate controlling membrane.
  • Carriers for use within such formulations are biocompatible, and may also be biodegradable; preferably the formulation provides a relatively constant level of active component release. The amount of active compound contained within a sustained release formulation depends upon the site of implantation, the rate and expected duration of release and the nature ofthe condition to be treated or prevented.
  • Delivery vehicles include antigen presenting cells (APCs), such as dendritic cells, macrophages, B cells, monocytes and other cells that may be engineered to be efficient APCs.
  • APCs antigen presenting cells
  • Such cells may, but need not, be genetically modified to increase the capacity for presenting the antigen, to improve activation and or maintenance of the T cell response, to have anti-tumor effects ?er 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. 50:507-529, 1999).
  • dendritic cells may be identified based on their typical shape (stellate in situ, with marked cytoplasmic processes (dendrites) visible in vitro), their ability to take up, process and present antigens with high efficiency, and their ability to activate naive T cell responses.
  • Dendritic cells may, of course, be engineered to express specific cell- surface receptors or ligands that are not commonly found on dendritic cells in vivo or ex vivo, and such modified dendritic cells are contemplated by the present invention.
  • secreted vesicles antigen-loaded dendritic cells (called exosomes) may be used within a vaccine (see Zitvogel et al.. Nature Med. - :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, flt3 ligand and/or other compound(s) that induce 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 pheno types. 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, mannose receptor and DEC-205 marker.
  • the mature phenotype is typically characterized by a lower expression of these markers, but a high expression of cell surface molecules responsible for T cell activation such as class I and class II MHC, adhesion molecules (e.g., CD54 and CD11) and costimulatory molecules (e.g., CD40, CD80, CD86 and 4-1BB).
  • cell surface molecules responsible for T cell activation such as class I and class II MHC, adhesion molecules (e.g., CD54 and CD11) and costimulatory molecules (e.g., CD40, CD80, CD86 and 4-1BB).
  • APCs may generally be transfected with a polynucleotide encoding a lung tumor protein (or portion or other variant thereof) such that the lung tumor polypeptide, or an immunogenic portion thereof, is expressed on the cell surface. Such transfection may take place ex vivo, and a composition or vaccine comprising such transfected cells may then be used for therapeutic pu ⁇ oses, 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, for example, may generally be performed using any methods known in the art.
  • Antigen loading of dendritic cells may be achieved by incubating dendritic cells or progenitor cells with the lung tumor polypeptide, DNA (naked or within a plasmid vector) or RNA; or with antigen-expressing recombinant bacterium or viruses (e.g., vaccinia, fowlpox, adenovirus or lentivirus vectors).
  • the polypeptide may be covalently conjugated to 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 described herein may be used for immunotherapy of cancer, such as lung cancer.
  • pharmaceutical compositions and vaccines are typically administered to a patient.
  • a patient refers to any warm-blooded animal, preferably a human.
  • a patient may or may not be afflicted with cancer.
  • the above pharmaceutical compositions and vaccines may be used to prevent the development of a cancer or to treat a patient afflicted with a cancer.
  • a cancer may be diagnosed using criteria generally accepted in the art, including the presence of a malignant tumor.
  • 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 drugs.
  • 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 admimstration of immune response-modifying agents (such as polypeptides and polynucleotides disclosed herein).
  • immune response-modifying agents such as polypeptides and polynucleotides disclosed 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.
  • agents with established tumor-immune reactivity such as effector cells or antibodies
  • 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 or B cells
  • 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 ofthe patient, but will typically range from about 0.1 mL to about 5 mL.
  • an appropriate dosage and treatment regimen provides the active compound(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit.
  • a response can be monitored by establishing an improved clinical outcome (e.g., more frequent 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 lung 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 lung tumor proteins and/or polynucleotides encoding such proteins in a biological sample (for example, blood, sera, urine and/or tumor biopsies) obtained from the patient.
  • a biological sample for example, blood, sera, urine and/or tumor biopsies
  • such proteins may be used as markers to indicate the presence or absence of a cancer such as lung 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 lung 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.
  • Suitable polypeptides for use within such assays include full length lung tumor proteins and 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 adso ⁇ tion, 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 adso ⁇ tion to a well in a microtiter plate or to a membrane is preferred. In such cases, adso ⁇ tion 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 10 ng 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. The amount of detection reagent that remains bound to the solid support is then determined using a method appropriate for the specific reporter group.
  • a detection reagent preferably a second antibody capable of binding to a different site on the polypeptide
  • 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 lung 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.
  • the time necessary to achieve equilibrium may be readily determined by assaying the level of binding that occurs over a period of time. At room temperature, an incubation time of about 30 minutes is generally sufficient.
  • Unbound sample may then be removed by washing the solid support with an appropriate buffer, such as PBS containing 0.1% Tween 20TM.
  • 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.
  • substrate generally for a specific period of time
  • 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. Briefly, in this embodiment, 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 corner is the most accurate cut-off value, and 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.
  • 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.
  • 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 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.
  • a cancer may also, or alternatively, be detected based on the presence of T cells that specifically react with a lung tumor protein in a biological sample.
  • a biological sample comprising CD4 + and/or CD8 ⁇ T cells isolated from a patient is incubated with a lung tumor 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 lung 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 lung 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 lung 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 lung 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 lung 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%o, preferably at least about 75% and more preferably at least about 90%, identity to a portion of a polynucleotide encoding a lung tumor protein that is at least 10 nucleotides, and preferably at least 20 nucleotides, in length.
  • oligonucleotide primers and/or probes will hybridize to a polynucleotide encoding a polypeptide disclosed 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 recited in SEQ ID NOS: 1-31, 49-55. 63.64, 66, 68-72, 78-80, 84-92 and 217- 389.
  • 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, 57:263, 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.
  • the disclosed compositions 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 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.
  • multiple lung tumor protein markers may be assayed within a given sample. It will be apparent that binding agents specific for different proteins provided herein may be combined within a single assay. Further, multiple primers or probes may be used concurrently. The selection of tumor protein markers may be based on routine experiments to determine combinations that results in optimal sensitivity. In addition, or alternatively, assays for tumor proteins provided herein may be combined with assays for other known tumor antigens.
  • kits for use within any of the above diagnostic methods.
  • Such kits 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 lung 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.
  • kits may be designed to detect the level of mRNA encoding a lung tumor protein in a biological sample.
  • kits generally comprise at least one oligonucleotide probe or primer, as described above, that hybridizes to a polynucleotide encoding a lung 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 lung tumor protein.
  • This example illustrates the preparation of cDNA molecules encoding lung tumor-specific polypeptides using a differential display screen.
  • Tissue samples were prepared from lung tumor and normal tissue of a patient with lung cancer that was confirmed by pathology after removal of samples from the patient.
  • Normal RNA and tumor RNA was extracted from the samples and mRNA was isolated and converted into cDNA using a (dT) 12 AG (SEQ ID NO: 47) anchored 3' primer.
  • Differential display PCR was then executed using a randomly chosen primer (SEQ ID NO: 48).
  • Amplification conditions were standard buffer containing 1.5 mM MgCl 2 , 20 pmol of primer, 500 pmol dNTP and 1 unit of Taq DNA polymerase (Perkin-Elmer, Branchburg, NJ). Forty cycles of amplification were performed using 94 °C denaturation for 30 seconds, 42 °C annealing for 1 minute and 72
  • RNA finge ⁇ rint pattern ofthe tumor were cut out of a silver stained gel, subcloned into the pGEM-T vector (Promega, Madison, WI) and sequenced.
  • the isolated 3' sequences are provided in SEQ ID NO: 1-16.
  • This example illustrates the isolation of cDNA sequences encoding lung tumor antigens by expression screening of lung tumor samples with autologous patient sera.
  • a human lung tumor directional cDNA expression library was constructed employing the Lambda ZAP Express expression system (Stratagene, La Jolla. CA). Total RNA for the library was taken from a late SCID mouse passaged human squamous epithelial lung carcinoma and poly A+ RNA was isolated using the Message Maker kit (Gibco BRL, Gaithersburg, MD). The resulting library was screened using E.
  • LT86-1 - LT86- 15 Fifteen clones were isolated, referred to hereinafter as LT86-1 - LT86- 15.
  • the isolated cDNA sequences for LT86-1 - LT86-8 and LT86-10 - LT86-15 are provided in SEQ ID NO: 17-24 and 26-31, respectively, with the corresponding predicted amino acid sequences being provided in SEQ ID NO: 32-39 and 41-46, respectively.
  • the determined cDNA sequence for LT86-9 is provided in SEQ ID NO: 25, with the corresponding predicted amino acid sequences from the 3' and 5' ends being provided in SEQ ID NO: 40 and 65, respectively. These sequences were compared to those in the gene bank as described above. Clones LT86-3, LT86-6 - LT86-9.
  • LT86-11 - LT86-13 and LT86-15 were found to show some homology to previously identified expressed sequence tags (ESTs), with clones LT86-6, LT86-8, LT86-11, LT86-12 and LT86-15 appearing to be similar or identical to each other.
  • Clone LT86-3 was found to show some homology with a human transcription repressor.
  • Clones LT86-6, 8, 9, 11, 12 and 15 were found to show some homology to a yeast RNA Pol II transcription regulation mediator.
  • Clone LT86-13 was found to show some homology with a C. elegans leucine aminopeptidase.
  • Clone LT86-9 appears to contain two inserts, with the 5' sequence showing homology to the previously identified antisense sequence of interferon alpha- induced P27, and the 3' sequence being similar to LT86-6.
  • Clone LT86-14 (SEQ ID NO: 30) was found to show some homology to the trithorax gene and has an "RGD" cell attachment sequence and a beta-Lactamase A site which functions in hydrolysis of penicillin.
  • LT86-5 and LT86-10 were found to show homology to previously identified genes.
  • a subsequently determined extended cDNA sequence for LT86-4 is provided in SEQ ID NO: 66.
  • LT86-20, LT86-21, LT86-22, LT86-26 and LT86-27 The determined 5' cDNA sequences for LT86-20, LT86-22, LT86-26 and LT86-27 are provided in SEQ ID NO: 68 and 70-72, respectively, with the determined 3' cDNA sequences for LT86-21 being provided in SEQ ID NO: 69.
  • the corresponding predicted amino acid sequences for LT86-20, LT86-21. LT86-22, LT86-26 and LT86-27 are provided in SEQ ID NO: 73- 77, respectively.
  • LT86-22 and LT86-27 were found to be highly similar to each other. Comparison of these sequences to those in the gene bank as described above, revealed no significant homologies to LT86-22 and LT86-27. LT86-20, LT86-21 and LT86-26 were found to show homology to previously identified genes.
  • a cDNA expression library was prepared using mRNA from a lung small cell carcinoma cell line in the lambda ZAP Express expression vector (Stratagene), and screened as described above, with a pool of two lung small cell carcinoma patient sera. The sera pool was adsorbed with E. coli lysate and human PBMC lysate was added to the serum to block antibody to proteins found in normal tissue. Seventy-three clones were isolated.
  • the determined cDNA sequences of these clones are provided in SEQ ID NO: 290-362.
  • the sequences of SEQ ID NO: 289-292. 294. 296-297, 300, 302, 303. 305. 307-315, 317-320, 322-325. 327-332, 334, 335, 338- 341, 343-352, 354-358, 360 and 362 were found to show some homology to previously isolated genes.
  • the sequences of SEQ ID NO: 293, 295, 298. 299, 301, 304. 306, 316, 321, 326, 333. 336. 337, 342, 353, 359 and 361 were found to show some homology to previously identified ESTs.
  • This example illustrates the isolation of cDNA sequences encoding lung tumor antigens by screening of lung tumor cDNA libraries with mouse anti-tumor sera.
  • a directional cDNA lung tumor expression library was prepared as described above in Example 2.
  • Sera was obtained from SCID mice containing late passaged human squamous cell and adenocarcinoma tumors. These sera were pooled and injected into normal mice to produce anti-lung tumor serum. Approximately 200,000 PFUs were screened from the unamplified library using this antiserum. Using a goat anti-mouse IgG-A-M (H+L) alkaline phosphatase second antibody developed with NBT/BCIP (BRL Labs.), approximately 40 positive plaques were identified.
  • Phage was purified and phagemid excised for 9 clones with inserts in a pBK-CMV vector for expression in prokaryotic or eukaryotic cells.
  • the determined cDNA sequences for 7 ofthe isolated clones (hereinafter referred to as L86S-3, L86S-12, L86S-16, L86S-25, L86S-36, L86S-40 and L86S-46) are provided in SEQ ID NO: 49-55, with the corresponding predicted amino acid sequences being provided in SEQ ID NO: 56-62, respectively.
  • the 5' cDNA sequences for the remaining 2 clones (hereinafter referred to as L86S-30 and L86S-41) are provided in SEQ ID NO: 63 and 64.
  • L86S-36 and L86S-46 were subsequently determined to represent the same gene. Comparison of these sequences with those in the public database as described above, revealed no significant homologies to clones L86S-30, L86S-36 and L86S-46 (SEQ ID NO: 63, 53 and 55, respectively). L86S-16 (SEQ ID NO: 51) was found to show some homology to an EST previously identified in fetal lung and germ cell tumor. The remaining clones were found to show at least some degree of homology to previously identified human genes.
  • L86S-30, L86S-39 and L86S-47 were found to be similar to each other. Comparison of these sequences with those in the gene bank as described above, revealed no significant homologies to L86S-14. L86S-29 was found to show some homology to a previously identified EST. L86S-6. L86S-11, L86S-34, L86S-39, L86S- 47, L86S-49 and L86S-51 were found to show some homology to previously identified genes.
  • RNA for the library was isolated from two primary squamous lung tumors and poly A+ RNA was isolated using an oligo dT column.
  • Antiserum was developed in normal mice using a pool of sera from three SCID mice implanted with human squamous lung carcinomas. Approximately 700,000 PFUs were screened from the unamplified library with E. coli absorbed mouse anti-SCID tumor serum. Positive plaques were identified as described above. Phage was purified and phagemid excised for 180 clones with inserts in a pBK- CMV vector for expression in prokaryotic or eukaryotic cells.
  • the determined cDNA sequences for 23 of the isolated clones are provided in SEQ ID NO: 126-148. Comparison of these sequences with those in the public database as described above revealed no significant homologies to the sequences of SEQ ID NO: 139 and 143-148. The sequences of SEQ ID NO: 126-138 and 140-142 were found to show homology to previously identified human polynucleotide sequences.
  • This example illustrates the isolation of cDNA sequences encoding lung tumor antigens by screening of lung tumor cDNA libraries prepared from SCID mice with mouse anti-tumor sera.
  • a directional cDNA lung tumor expression library was prepared using a Stratagene kit with a Lambda Zap Express vector.
  • Total RNA for the library was taken from a late passaged lung adenocarcinoma grown in SCID mice.
  • Poly A+ RNA was isolated using a Message Maker Kit (Gibco BRL).
  • Sera was obtained from two SCID mice implanted with lung adenocarcinomas. These sera were pooled and injected into normal mice to produce anti-lung tumor serum. Approximately 700,000 PFUs were screened from the unamplified library with E. c ⁇ //-absorbed mouse anti-SCID tumor serum.
  • SEQ ID NO: 149-181 The determined 5' cDNA sequences for 33 of the isolated clones are provided in SEQ ID NO: 149-181.
  • the corresponding predicted amino acid sequences for SEQ ID NO: 149, 150, 152-154, 156-158 and 160-181 are provided in SEQ ID NO: 182, 183, 186, 188-193 and 194-215, respectively.
  • SAL-25 The clone of SEQ ID NO: 151 (referred to as SAL-25) was found to contain two open reading frames (ORFs).
  • ORFs open reading frames
  • the predicted amino acid sequences encoded by these ORFs are provided in SEQ ID NO: 184 and 185.
  • SAL-50 The clone of SEQ ID NO: 153 (referred to as SAL-50) was found to contain two open reading frames encoding the predicted amino acid sequences of SEQ ID NO: 187 and 216.
  • SAL-66 the clone of SEQ ID NO: 155 (referred to as SAL-66) was found to contain two open reading frames encoding the predicted amino acid sequences of SEQ ID NO: 189 and 190.
  • Comparison of the isolated sequences with those in the public database revealed no significant homologies to the sequences of SEQ ID NO: 151, 153 and 154.
  • the sequences of SEQ ID NO: 149, 152, 156, 157 and 158 were found to show some homology to previously isolated expressed sequence tags (ESTs).
  • ESTs previously isolated expressed sequence tags
  • two directional cDNA libraries (referred to as LT46-90 and LT86-21) were prepared from two late passaged lung squamous carcinomas grown in SCID mice and screened with sera obtained from SCID mice implanted with human squamous lung carcinomas.
  • the determined cDNA sequences for the isolated clones are provided in SEQ ID NO: 217-237 and 286-289.
  • SEQ ID NO: 286 was found to be a longer sequence of LT4690-71 (SEQ ID NO: 237). Comparison of these sequences with those in the public databases revealed no known homologies to the sequences of SEQ ID NO: 219, 220. 225, 226, 287 and 288. The sequences of SEQ ID NO: 218.
  • SEQ ID NO: 221, 222 and 224 were found to show some homology to previously identified sequences of unknown function.
  • the sequence of SEQ ID NO: 236 was found to show homology to a known mouse mRNA sequence.
  • the sequences of SEQ ID NO: 217, 223, 227-237, 286 and 289 showed some homology to known human DNA and/or RNA sequences.
  • one ofthe cDNA libraries described above was screened with E. c ⁇ /z-absorbed mouse anti- SCID tumor serum. This serum was obtained from normal mice immunized with a pool of 3 sera taken from SCID mice implanted with human squamous lung carcinomas.
  • the determined cDNA sequences for the isolated clones are provided in SEQ ID NO: 238-285. Comparison of these sequences with those in the public databases revealed no significant homologies to the sequences of SEQ ID NO: 253, 260, 277 and 285.
  • the sequences of SEQ ID NO: 249, 250, 256, 266, 276 and 282 were found to show some homology to previously isolated expressed sequence tags (ESTs).
  • SEQ ID NO: 238-248, 251, 252, 254, 255. 257-259, 261-263, 265, 267-275, 278-281, 283 and 284 were found to show some homology to previously identified DNA or RNA sequences.
  • Example 5 DETERMINATION OF TISSUE SPECIFICITY OF LUNG TUMOR
  • mRNA expression levels for representative lung tumor polypeptides were examined in a variety of normal and tumor tissues using RT-PCR.
  • First strand synthesis was carried out using 2 ⁇ g of total RNA with Superscript II reverse transcriptase (BRL Life Technologies) at 42 °C for one hour.
  • the cDNA was then amplified by PCR with gene-specific primers.
  • ⁇ -actin was used as an internal control for each of the tissues examined. 1 ⁇ l of 1 :30 dilution of cDNA was employed to enable the linear range amplification of the ⁇ -actin template and was sensitive enough to reflect the differences in the initial copy numbers. Using these conditions, the ⁇ -actin levels were determined for each reverse transcription reaction from each tissue.
  • mRNA Expression levels were examined in five different types of tumor tissue (lung squamous tumor from 3 patients, lung adenocarcinoma, prostate tumor, colon tumor and lung tumor), and different normal tissues, including lung from four patients, prostate, brain, kidney, liver, ovary, skeletal muscle, skin, small intestine, myocardium, retina and testes. L86S-46 was found to be expressed at high levels in lung squamous tumor, colon tumor and prostate tumor, and was undetectable in the other tissues examined.
  • L86S-5 was found to be expressed in the lung tumor samples and in 2 out of 4 normal lung samples, but not in the other normal or tumor tissues tested.
  • L86S-16 was found to be expressed in all tissues except normal liver and normal stomach.
  • L86S-46 was found to be over-expressed in lung squamous tissue and normal tonsil, with expression being low or undetectable in all other tissues examined.
  • Example 6 ISOLATION OF DNA SEQUENCES ENCODING LUNG TUMOR ANTIGENS
  • DNA sequences encoding antigens potentially involved in squamous cell lung tumor formation were isolated as follows.
  • a lung tumor directional cDNA expression library was constructed employing the Lambda ZAP Express expression system (Stratagene, La Jolla, CA). Total RNA for the library was taken from a pool of two human squamous epithelial lung carcinomas and poly A+ RNA was isolated using oligo-dT cellulose (Gibco BRL, Gaithersburg, MD). Phagemid were rescued at random and the cDNA sequences of isolated clones were determined.
  • the determined cDNA sequence for the clone SLT-Tl is provided in SEQ ID NO: 102, with the determined 5' cDNA sequences for the clones SLT-T2, SLT-T3, SLT-T5, SLT-T7, SLT-T9, SLT-T10, SLT-Tl 1 and SLT-T12 being provided in SEQ ID NO: 103-1 10, respectively.
  • the corresponding predicted amino acid sequence for SLT-Tl, SLT-T2, SLT-T3, SLT-T10 and SLT-T12 are provided in SEQ ID NO: 111-115, respectively.
  • SLT-Tl was determined to show some homology to a PAC clone of unknown protein function.
  • the cDNA sequence of SLT-Tl (SEQ ID NO: 102) was found to contain a mutator (MUTT) domain.
  • MUTT mutator domains
  • Such domains are known to function in removal of damaged guanine from DNA that can cause A to G transversions (see, for example, el-Deiry, W.S., 1997 Curr. Opin. Oncol. 9:79-87; Okamoto, K. et al. 1996 Int. J. Cancer 65:437-41; Wu, C. et al. 1995 Biochem. Biophys. Res. Commun. 214:1239-45; Porter, D.W. et al.
  • SLT-Tl may thus be of use in the treatment, by gene therapy, of lung cancers caused by, or associated with, a disruption in DNA repair.
  • DNA sequences encoding antigens potentially involved in adenocarcinoma lung tumor formation were isolated as follows.
  • a human lung tumor directional cDNA expression library was constructed employing the Lambda ZAP Express expression system (Stratagene. La Jolla. CA).
  • Total RNA for the library was taken from a late SCID mouse passaged human adenocarcinoma and poly A+ RNA was isolated using the Message Maker kit (Gibco BRL, Gaithersburg, MD). Phagemid were rescued at random and the cDNA sequences of isolated clones were determined.
  • SALT-T3, SALT-T4, SALT-T7, SALT-T8, and SALT-T9 are provided in SEQ ID NO: 116-120, with the corresponding predicted amino acid sequences being provided in SEQ ID NO: 121-125.
  • SALT-T3 was found to show 98% identity to the previously identified human transducin-like enhancer protein TLE2.
  • SALT-T4 appears to be the human homologue of the mouse H beta 58 gene.
  • SALT-T7 was found to have 97% identity to human 3-mercaptopyruvate sulfurtransferase and SALT-T8 was found to show homology to human interferon-inducible protein 1-8U.
  • SALT-T9 shows approximately 90%) identity to human mucin MUC 5B.
  • cDNA sequences encoding antigens potentially involved in small cell lung carcinoma development were isolated as follows. cDNA expression libraries were constructed with mRNA from the small cell lung carcinoma cell lines NCIH69, NCIH128 and DMS79 (all available from the American Type Culture Collection, Manassas, VA) employing the Lambda ZAP Express expression system (Stratagene. La Jolla, CA). Phagemid were rescued at random and the cDNA sequences of 27 isolated clones were determined. Comparison of the determined cDNA sequences revealed no significant homologies to the sequences of SEQ ID NO: 372 and 373.
  • SEQ ID NO: 364, 369, 377, 379 and 386 showed some homology to previously isolated ESTs.
  • the sequences ofthe remaining 20 clones showed some homology to previously identified genes.
  • the cDNA sequences of these clones are provided in SEQ ID NO: 363, 365-368, 370, 371, 374-376, 378. 380-385 and 387-389, wherein SEQ ID NO: 363, 366-368, 370, 375. 376, 378, 380-382, 384 and 385 are full-length sequences.
  • SEQ ID NO: 363, 366-368, 370, 375. 376, 378, 380-382, 384 and 385 are full-length sequences.
  • Polypeptides may be synthesized on a Perkin Elmer/Applied Biosystems Division 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
  • 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.
  • Lung tumor antigens may also be identified by T cell expression cloning.
  • One source of tumor specific T cells is from surgically excised tumors from human patients.
  • a non-small cell lung carcinoma was minced and enzymatically digested for several hours to release tumor cells and infiltrating lymphocytes (tumor infiltrating T cells, or TILs).
  • TILs tumor infiltrating T cells
  • the cells were washed in HBSS buffer and passed over a Ficoll (100%/75%)/HBSS) discontinuous gradient to separate tumor cells and lymphocytes from non-viable cells.
  • Two bands were harvested from the interfaces; the upper band at the 75%/HBSS interface contained predominantly tumor cells, while the lower band at the 100%o/75%)/HBSS interface contained a majority of lymphocytes.
  • the TILs were expanded in culture, either in 24-well plates with culture media supplemented with 10 ng/ml IL-7 and 100 U/ml IL-2, or alternatively, 24-well plates that have been pre-coated with the anti-CD3 monoclonal antibody OKT3.
  • the resulting TIL cultures were analyzed by FACS to confirm that a high percentage were CD8+ T cells (>90%> of gated population) with only a small percentage of CD4+ cells.
  • non-small cell lung carcinoma cells were expanded in culture using standard techniques to establish a tumor cell line, which was later confirmed to be a lung carcinoma cell line by immunohistochemical analysis.
  • This tumor cell line was transduced with a retroviral vector to express human CD80, and characterized by FACS analysis to confirm high expression levels of CD80, and class I and II MHC molecules.
  • TIL lines The specificity of the TIL lines to lung tumor was confirmed by INF- ⁇ and/or TNF- ⁇ cytokine release assays.
  • TIL cells from day 21 cultures were co-cultured with either autologous or allogeneic tumor cells, EBV-immortalized LCL, or control cell lines Daudi and K562, and the culture supernatant monitored by ELISA for the presence of cytokines.
  • the TIL specifically recognized autologous tumor but not allogeneic tumor.
  • EBV-immortalized LCL or the control cell lines there was no recognition of EBV-immortalized LCL or the control cell lines, indicating that the TIL lines are tumor specific and are potentially recognizing a tumor antigen presented by autologous MHC molecules.
  • the characterized tumor-specific TIL lines were expanded to suitable numbers for T cell expression cloning using soluble anti-CD3 antibody in culture with irradiated EBV transformed LCLs and PBL feeder cells in the presence of 20 U/ml IL- 2.
  • Clones from the expanded TIL lines were generated by standard limiting dilution techniques. Specifically, TIL cells were seeded at 0.5 cells/well in a 96-well U bottom plate and stimulated with CD-80-transduced autologous tumor cells, EBV transformed LCL. and PBL feeder cells in the presence of 50 U/ml IL-2. These clones were further analyzed for tumor specificity by 51 Cr microcytotoxicity and IFN- ⁇ bioassays. The MHC restriction element recognized by the TIL clones may be determined by antibody blocking studies.
  • CTL lines or clones prepared as described above may be employed to identify tumor specific antigens.
  • autologous fibroblasts or LCL from a patient may be transfected or transduced with polynucleotide fragments derived from a lung tumor cDNA library to generate target cells expressing tumor polypeptides.
  • the target cells expressing tumor polypeptides in the context of MHC will be recognized by the CTL line or clone, resulting in T-cell activation which can be monitored by cytokine detection assays.
  • the tumor gene being expressed by the target cell and recognized by the tumor-specific CTL may then be isolated.

Abstract

Compositions and methods for the therapy and diagnosis of cancer, such as lung cancer, are disclosed. Compositions may comprise one or more lung tumor proteins, immunogenic portions thereof, or polynucleotides that encode such portions. Alternatively, a therapeutic composition may comprise an antigen presenting cell that expresses a lung tumor protein, or a T cell that is specific for cells expressing such a protein. Such compositions may be used, for example, for the prevention and treatment of diseases such as lung cancer. Diagnostic methods based on detecting a lung tumor protein, or mRNA encoding such a protein, in a sample are also provided.

Description

COMPOUNDS FOR THERAPY AND DIAGNOSIS OF LUNG CANCER AND METHODS FOR THEIR USE
TECHNICAL FIELD
The present invention relates generally to compositions and methods for the treatment of lung cancer. The invention is more specifically related to nucleotide sequences that are preferentially expressed in lung tumor tissue, together with polypeptides encoded by such nucleotide sequences. The inventive nucleotide sequences and polypeptides may be used in vaccines and pharmaceutical compositions for the treatment of lung cancer.
BACKGROUND OF THE INVENTION
Lung cancer is the primary cause of cancer death among both men and women in the U.S., with an estimated 172,000 new cases being reported in 1994. The five-year survival rate among all lung cancer patients, regardless of the stage of disease at diagnosis, is only 13%. This contrasts with a five-year survival rate of 46% among cases detected while the disease is still localized. However, only 16% of lung cancers are discovered before the disease has spread. Early detection is difficult since clinical symptoms are often not seen until the disease has reached an advanced stage. Currently, diagnosis is aided by the use of chest x-rays, analysis of the type of cells contained in sputum and fiberoptic examination of the bronchial passages. Treatment regimens are determined by the type and stage of the cancer, and include surgery, radiation therapy and/or chemotherapy. In spite of considerable research into therapies for the disease, lung cancer remains difficult to treat.
Accordingly, there remains a need in the art for improved vaccines, treatment methods and diagnostic techniques for lung cancer.
SUMMARY OF THE INVENTION
Briefly stated, the present invention provides compounds and methods for the therapy and diagnosis of cancer, such as lung cancer. In one aspect, the present invention provides polypeptides comprising at least a portion of a lung tumor protein, or a variant thereof. Certain portions and other variants are immunogenic. such that the ability of the variant to react with antigen-specific antisera is not substantially diminished. Within certain embodiments, the polypeptide comprises a sequence that is encoded by a polynucleotide sequence selected from the group consisting of: (a) sequences recited in SEQ ID NOS: 218-222, 224-226, 249, 250, 253, 256, 266, 276, 277, 282, 285, 293, 295, 298, 299, 301, 304, 306, 316, 321, 326, 333, 336, 337, 342, 353, 359, 361, 364, 369, 372, 373, 377, 379 and 386; (b) variants of a sequence recited in SEQ ID NOS: 218-222, 224-226, 249, 250, 253, 256, 266, 276, 277, 282. 285, 293, 295, 298, 299, 301, 304, 306, 316, 321, 326. 333, 336, 337, 342. 353, 359, 361, 364, 369, 372, 373, 377, 379 and 386; and (c) complements of a sequence of (a) or (b).
The present invention further provides polynucleotides that encode a polypeptide as described above, or a portion thereof (such as a portion encoding at least 15 contiguous amino acid residues of a lung tumor protein), expression vectors comprising such polynucleotides and host cells transformed or transfected with such expression vectors.
Within other aspects, the present invention provides pharmaceutical compositions comprising a polypeptide or polynucleotide as described above and a physiologically acceptable carrier.
Within a related aspect of the present invention, vaccines are provided. Such vaccines comprise a polypeptide or polynucleotide as described above and an immunostimulant.
The present invention further provides pharmaceutical compositions that comprise: (a) an antibody or antigen-binding fragment thereof that specifically binds to a lung tumor protein; and (b) a physiologically acceptable carrier.
Within further aspects, the present invention provides pharmaceutical 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. Within related aspects, vaccines are provided 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.
Within related aspects, pharmaceutical compositions comprising a fusion protein, or a polynucleotide encoding a fusion protein, in combination with a physiologically acceptable carrier are provided. Vaccines are further provided, within other aspects, that comprise a fusion protein, or a polynucleotide encoding a fusion protein, in combination with an immunostimulant.
Within further aspects, the present invention provides methods for inhibiting the development of a cancer in a patient, comprising administering to a patient a pharmaceutical composition or vaccine as recited above.
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 lung tumor protein, wherein the step of contacting is performed under conditions and for a time sufficient to permit the removal of cells expressing the protein from the sample.
Within related aspects, methods are provided 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 lung tumor protein, comprising contacting T cells with one or more of: (i) a polypeptide as described above; (ii) a polynucleotide encoding such a polypeptide: and/or (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.
Within further aspects, 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 a lung tumor protein; (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, and thereby inhibiting the development of a cancer in the patient. Proliferated cells may, but need not. be cloned prior to administration to the patient.
Within further aspects, the present invention provides methods for determining the presence or absence of a 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. Within preferred embodiments, the binding agent is an antibody, more preferably a monoclonal antibody. The cancer may be lung cancer. 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 that encodes a lung tumor protein; (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. Within certain embodiments, the amount of mRNA is detected via polymerase chain reaction using, for example, at least one oligonucleotide primer that hybridizes to a polynucleotide encoding a polypeptide as recited above, or a complement of such a polynucleotide. Within other embodiments, the amount of mRNA is detected using a hybridization technique, employing an oligonucleotide probe that hybridizes to a polynucleotide that encodes a polypeptide as recited above, or a complement of such a polynucleotide.
In related aspects, methods are provided 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 that encodes a lung tumor protein; (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 ofthe cancer in the patient. Within further aspects, 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.
These and other aspects of the present invention will become apparent upon reference to the following detailed description and attached drawings. All references disclosed herein are hereby incorporated by reference in their entirety as if each was incorporated individually.
SEQUENCE IDENTIFIERS SEQ ID NO: 1 is the determined cDNA sequence for L363Cl.cons SEQ ID NO: 2 is the determined cDNA sequence for L263C2.cons SEQ ID NO: 3 is the determined cDNA sequence for L263C2c SEQ ID NO: 4 is the determined cDNA sequence for L263Cl.cons SEQ ID NO: 5 is the determined cDNA sequence for L263Clb SEQ ID NO: 6 is the determined cDNA sequence for L164C2.cons SEQ ID NO: 7 is the determined cDNA sequence for L164Cl.cons SEQ ID NO: 8 is the determined cDNA sequence for L366Cla SEQ ID NO: 9 is the determined cDNA sequence for L260Cl.cons SEQ ID NO: 10 is the determined cDNA sequence for L163Clc SEQ ID NO: 11 is the determined cDNA sequence for L163Clb SEQ ID NO: 12 is the determined cDNA sequence for L255Cl.cons SEQ ID NO: 13 is the determined cDNA sequence for L255Clb SEQ ID NO: 14 is the determined cDNA sequence for L355Cl.cons SEQ ID NO: 15 is the determined cDNA sequence for L366Cl.cons SEQ ID NO: 16 is the determined cDNA sequence for L163Cla SEQ ID NO: 17 is the determined cDNA sequence for LT86- 1 SEQ ID NO: 18 is the determined cDNA sequence for LT86-2 SEQ ID NO: 19 is the determined cDNA sequence for LT86-3 SEQ ID NO: 20 is the determined cDNA sequence for LT86-4 SEQ ID NO: 21 is the determined cDNA sequence for LT86-5 SEQ ID NO: 22 is the determined cDNA sequence for LT86-6 SEQ ID NO: 23 is the determined cDNA sequence for LT86-7 SEQ ID NO: 24 is the determined cDNA sequence for LT86-8 SEQ ID NO: 25 is the determined cDNA sequence for LT86-9 SEQ ID NO: 26 is the determined cDNA sequence for LT86-10 SEQ ID NO: 27 is the determined cDNA sequence for LT86-11 SEQ ID NO: 28 is the determined cDNA sequence for LT86-12 SEQ ID NO: 29 is the determined cDNA sequence for LT86-13 SEQ ID NO: 30 is the determined cDNA sequence for LT86-14 SEQ ID NO: 31 is the determined cDNA sequence for LT86-15 SEQ ID NO: 32 is the predicted amino acid sequence for LT86-1 SEQ ID NO: 33 is the predicted amino acid sequence for LT86-2 SEQ ID NO: 34 is the predicted amino acid sequence for LT86-3 SEQ ID NO: 35 is the predicted amino acid sequence for LT86-4 SEQ ID NO: 36 is the predicted amino acid sequence for LT86-5 SEQ ID NO: 37 is the predicted amino acid sequence for LT86-6 SEQ ID NO: 38 is the predicted amino acid sequence for LT86-7 SEQ ID NO: 39 is the predicted amino acid sequence for LT86-8 SEQ ID NO: 40 is the predicted amino acid sequence for LT86-9 SEQ ID NO: 41 is the predicted amino acid sequence for LT86-10 SEQ ID NO: 42 is the predicted amino acid sequence for LT86-11 SEQ ID NO: 43 is the predicted amino acid sequence for LT86-12 SEQ ID NO: 44 is the predicted amino acid sequence for LT86-13 SEQ ID NO: 45 is the predicted amino acid sequence for LT86-14 SEQ ID NO: 46 is the predicted amino acid sequence for LT86-15 SEQ ID NO: 47 is a (dT)12AG primer SEQ ID NO: 48 is a primer
SEQ ID NO: 49 is the determined 5' cDNA sequence for L86S-3 SEQ ID NO: 50 is the determined 5' cDNA sequence for L86S-12 SEQ ID NO: 51 is the determined 5' cDNA sequence for L86S-16 SEQ ID NO: 52 is the determined 5' cDNA sequence for L86S-25 SEQ ID NO: 53 is the determined 5' cDNA sequence for L86S-36 SEQ ID NO: 54 is the determined 5' cDNA sequence for L86S-40 SEQ ID NO: 55 is the determined 5' cDNA sequence for L86S-46 SEQ ID NO: 56 is the predicted amino acid sequence for L86S-3 SEQ ID NO: 57 is the predicted amino acid sequence for L86S-12 SEQ ID NO: 58 is the predicted amino acid sequence for L86S-16 SEQ ID NO: 59 is the predicted amino acid sequence for L86S-25 SEQ ID NO: 60 is the predicted amino acid sequence for L86S-36 SEQ ID NO: 61 is the predicted amino acid sequence for L86S-40 SEQ ID NO: 62 is the predicted amino acid sequence for L86S-46 SEQ ID NO: 63 is the determined 5' cDNA sequence for L86S-30 SEQ ID NO: 64 is the determined 5' cDNA sequence for L86S-41 SEQ ID NO 65 s the predicted amino acid sequence from the 5' end of LT86-9 SEQ ID NO 66 s the determined extended cDNA sequence for LT86-4 SEQ ID NO 67 s the predicted extended amino acid sequence for LT86-4 SEQ ID NO 68 s the determined 5' cDNA sequence for LT86-20 SEQ ID NO 69 s the determined 3' cDNA sequence for LT86-21 SEQ ID NO 70 s the determined 5' cDNA sequence for LT86-22 SEQ ID NO 71 s the determined 5' cDNA sequence for LT86-26 SEQ ID NO 72 s the determined 5' cDNA sequence for LT86-27 SEQ ID NO 73 s the predicted amino acid sequence for LT86-20 SEQ ID NO 74 s the predicted amino acid sequence for LT86-21 SEQ ID NO 75 s the predicted amino acid sequence for LT86-22 SEQ ID NO 76 s the predicted amino acid sequence for LT86-26 SEQ ID NO 77 s the predicted amino acid sequence for LT86-27 SEQ ID NO 78 s the determined extended cDNA sequence for L86S-12 SEQ ID NO 79 s the determined extended cDNA sequence for L86S-36 SEQ ID NO 80 s the determined extended cDNA sequence for L86S-46 SEQ ID NO 81 s the predicted extended amino acid sequence for L86S-12 SEQ ID NO 82 s the predicted extended amino acid sequence for L86S-36 SEQ ID NO 83 s the predicted extended amino acid sequence for L86S-46 SEQ ID NO 84 s the determined 5'cDNA sequence for L86S-6 SEQ ID NO 85 s the determined 5'cDNA sequence for L86S-11 SEQ ID NO 86 s the determined 5'cDNA sequence for L86S-14 SEQ ID NO 87 s the determined 5'cDNA sequence for L86S-29 SEQ ID NO 88 s the determined 5'cDNA sequence for L86S-34 SEQ ID NO 89 s the determined 5'cDNA sequence for L86S-39 SEQ ID NO 90 s the determined 5'cDNA sequence for L86S-47 SEQ ID NO 91 s the determined 5'cDNA sequence for L86S-49 SEQ ID NO 92 s the determined 5'cDNA sequence for L86S-51 SEQ ID NO 93 s the predicted amino acid sequence for L86S-6 SEQ ID NO 94 s the predicted amino acid sequence for L86S-1 1 SEQ ID NO 95 s the predicted amino acid sequence for L86S-14 SEQ ID NO: 96 is the predicted amino acid sequence for L86S-29 SEQ ID NO: 97 is the predicted amino acid sequence for L86S-34 SEQ ID NO: 98 is the predicted amino acid sequence for L86S-39 SEQ ID NO: 99 is the predicted amino acid sequence for L86S-47 SEQ ID NO: 100 is the predicted amino acid sequence for L86S-49 SEQ ID NO: 101 is the predicted amino acid sequence for L86S-51 SEQ ID NO: 102 is the determined DNA sequence for SLT-Tl SEQ ID NO: 103 is the determined 5' cDNA sequence for SLT-T2 SEQ ID NO: 104 is the determined 5' cDNA sequence for SLT-T3 SEQ ID NO: 105 is the determined 5' cDNA sequence for SLT-T5 SEQ ID NO: 106 is the determined 5' cDNA sequence for SLT-T7 SEQ ID NO: 107 is the determined 5' cDNA sequence for SLT-T9 SEQ ID NO: 108 is the determined 5' cDNA sequence for SLT-Tl 0 SEQ ID NO: 109 is the determined 5' cDNA sequence for SLT-Tl 1 SEQ ID NO: 110 is the determined 5 ' cDNA sequence for SLT-Tl 2 SEQ ID NO: 111 is the predicted amino acid sequence for SLT-Tl SEQ ID NO: 112 is the predicted amino acid sequence for SLT-T2 SEQ ID NO: 113 is the predicted amino acid sequence for SLT-T3 SEQ ID NO: 114 is the predicted amino acid sequence for SLT-T10 SEQ ID NO: 115 is the predicted amino acid sequence for SLT-Tl 2 SEQ ID NO: 116 is the determined 5' cDNA sequence for SALT-T3 SEQ ID NO: 117 is the determined 5' cDNA sequence for SALT-T4 SEQ ID NO: 118 is the determined 5' cDNA sequence for SALT-T7 SEQ ID NO: 119 is the determined 5' cDNA sequence for SALT-T8 SEQ ID NO: 120 is the determined 5' cDNA sequence for SALT-T9 SEQ ID NO: 121 is the predicted amino acid sequence for SALT-T3 SEQ ID NO: 122 is the predicted amino acid sequence for SALT-T4 SEQ ID NO: 123 is the predicted amino acid sequence for SALT-T7 SEQ ID NO: 124 is the predicted amino acid sequence for SALT-T8 SEQ ID NO: 125 is the predicted amino acid sequence for SALT-T9 SEQ ID NO: 126 is the determined cDNA sequence for PSLT-1 SEQ ID NO 127 is the determined cDNA sequence for PSLT-2 SEQ ID NO 128 is the determined cDNA sequence for PSLT-7 SEQ ID NO 129 is the determined cDNA sequence for PSLT-13 SEQ ID NO 130 is the determined cDNA sequence for PSLT-27 SEQ ID NO 131 is the determined cDNA sequence for PSLT-28 SEQ ID NO 132 is the determined cDNA sequence for PSLT-30 SEQ ID NO 133 is the determined cDNA sequence for PSLT-40 SEQ ID NO 134 is the determined cDNA sequence for PSLT-69 SEQ ID NO 135 is the determined cDNA sequence for PSLT-71 SEQ ID NO 136 is the determined cDNA sequence for PSLT-73 SEQ ID NO 137 is the determined cDNA sequence for PSLT-79 SEQ ID NO 138 is the determined cDNA sequence for PSLT-03 SEQ ID NO 139 is the determined cDNA sequence for PSLT-09 SEQ ID NO 140 is the determined cDNA sequence for PSLT-011 SEQ ID NO 141 is the determined cDNA sequence for PSLT-041 SEQ ID NO 142 is the determined cDNA sequence for PSLT-62 SEQ ID NO 143 is the determined cDNA sequence for PSLT-6 SEQ ID NO 144 is the determined cDNA sequence for PSLT-37 SEQ ID NO 145 is the determined cDNA sequence for PSLT-74 SEQ ID NO 146 is the determined cDNA sequence for PSLT-010 SEQ ID NO 147 is the determined cDNA sequence for PSLT-012 SEQ ID NO 148 is the determined cDNA sequence for PSLT-037 SEQ ID NO 149 is the determined 5' cDNA sequence for SAL-3 SEQ ID NO 150 is the determined 5' cDNA sequence for SAL-24 SEQ ID NO 151 is the determined 5' cDNA sequence for SAL-25 SEQ ID NO 152 is the determined 5' cDNA sequence for SAL-33 SEQ ID NO 153 is the determined 5' cDNA sequence for SAL-50 SEQ ID NO 154 is the determined 5' cDNA sequence for SAL-57 SEQ ID NO 155 is the determined 5' cDNA sequence for SAL-66 SEQ ID NO 156 is the determined 5' cDNA sequence for SAL-82 SEQ ID NO 157 is the determined 5' cDNA sequence for SAL-99 SEQ ID NO 158 is the determined 5 cDNA sequence for SAL- 104 SEQ ID NO 159 is the determined 5 cDNA sequence for SAL- 109 SEQ ID NO 160 is the determined 5 cDNA sequence for SAL-5 SEQ ID NO 161 is the determined 5 cDNA sequence for SAL-8 SEQ ID NO 162 is the determined 5 cDNA sequence for SAL- 12 SEQ ID NO 163 is the determined 5 cDNA sequence for SAL- 14 SEQ ID NO 164 is the determined 5 cDNA sequence for SAL- 16 SEQ ID NO 165 is the determined 5 cDNA sequence for SAL-23 SEQ ID NO 166 is the determined 5 cDNA sequence for SAL-26 SEQ ID NO 167 is the determined 5 cDNA sequence for SAL-29 SEQ ID NO 168 is the determined 5 cDNA sequence for SAL-32 SEQ ID NO 169 is the determined 5 cDNA sequence for SAL-39 SEQ ID NO 170 is the determined 5 cDNA sequence for SAL-42 SEQ ID NO 171 is the determined 5 cDNA sequence for SAL-43 SEQ ID NO 172 is the determined 5 cDNA sequence for SAL-44 SEQ ID NO 173 is the determined 5 cDNA sequence for SAL-48 SEQ ID NO 174 is the determined 5 cDNA sequence for SAL-68 SEQ ID NO 175 is the determined 5 cDNA sequence for SAL-72 SEQ ID NO 176 is the determined 5 cDNA sequence for SAL-77 SEQ ID NO 177 is the determined 5 cDNA sequence for SAL-86 SEQ ID NO 178 is the determined 5 cDNA sequence for SAL-88 SEQ ID NO 179 is the determined 5 cDNA sequence for SAL-93 SEQ ID NO 180 is the determined 5 cDNA sequence for SAL- 100 SEQ ID NO 181 is the determined 5 cDNA sequence for SAL- 105 SEQ ID NO 182 is the predicted amino acid sequence for SAL-3 SEQ ID NO 183 is the predicted amino acid sequence for SAL-24 SEQ ID NO 184 is a first predicted amino acid sequence for SAL-25 SEQ ID NO 185 is a second predicted amino acid sequence for SAL-25 SEQ ID NO 186 is the predicted amino acid sequence for SAL-33 SEQ ID NO 187 is a first predicted amino acid sequence for SAL-50 SEQ ID NO 188 is the predicted amino acid sequence for SAL-57 SEQ ID NO: 189 is a first predicted amino acid sequence for SAL-66 SEQ ID NO: 190 is a second predicted amino acid sequence for SAL-66 SEQ ID NO: 191 is the predicted amino acid sequence for SAL-82 SEQ ID NO: 192 is the predicted amino acid sequence for SAL-99 SEQ ID NO: 193 is the predicted amino acid sequence for SAL- 104 SEQ ID NO: 194 is the predicted amino acid sequence for SAL-5 SEQ ID NO: 195 is the predicted amino acid sequence for SAL-8 SEQ ID NO: 196 is the predicted amino acid sequence for SAL- 12 SEQ ID NO: 197 is the predicted amino acid sequence for SAL- 14 SEQ ID NO: 198 is the predicted amino acid sequence for SAL-16 SEQ ID NO: 199 is the predicted amino acid sequence for SAL-23 SEQ ID NO: 200 is the predicted amino acid sequence for SAL-26 SEQ ID NO: 201 is the predicted amino acid sequence for SAL-29 SEQ ID NO: 202 is the predicted amino acid sequence for SAL-32 SEQ ID NO: 203 is the predicted amino acid sequence for SAL-39 SEQ ID NO: 204 is the predicted amino acid sequence for SAL-42 SEQ ID NO: 205 is the predicted amino acid sequence for SAL-43 SEQ ID NO: 206 is the predicted amino acid sequence for SAL-44 SEQ ID NO: 207 is the predicted amino acid sequence for SAL-48 SEQ ID NO: 208 is the predicted amino acid sequence for SAL-68 SEQ ID NO: 209 is the predicted amino acid sequence for SAL-72 SEQ ID NO: 210 is the predicted amino acid sequence for SAL-77 SEQ ID NO: 211 is the predicted amino acid sequence for SAL-86 SEQ ID NO: 212 is the predicted amino acid sequence for SAL-88 SEQ ID NO: 213 is the predicted amino acid sequence for SAL-93 SEQ ID NO: 214 is the predicted amino acid sequence for SAL- 100 SEQ ID NO: 215 is the predicted amino acid sequence for SAL-105 SEQ ID NO: 216 is a second predicted amino acid sequence for SAL-50 SEQ ID NO: 217 is the determined cDNA sequence for SSLT-4 SEQ ID NO: 218 is the determined cDNA sequence for SSLT-9 SEQ ID NO: 219 is the determined cDNA sequence for SSLT-10 SEQ ID NO 220 s the determined cDNA sequence for SSLT-12 SEQ ID NO 221 s the determined cDNA sequence for SSLT-19 SEQ ID NO 222 s the determined cDNA sequence for SSLT-31 SEQ ID NO 223 s the determined cDNA sequence for SSLT-38 SEQ ID NO 224 s the determined cDNA sequence for LT4690-2 SEQ ID NO 225 s the determined cDNA sequence for LT4690-3 SEQ ID NO 226 s the determined cDNA sequence for LT4690-22 SEQ ID NO 227 s the determined cDNA sequence for LT4690-24 SEQ ID NO 228 s the determined cDNA sequence for LT4690-37 SEQ ID NO 229 s the determined cDNA sequence for LT4690-39 SEQ ID NO 230 s the determined cDNA sequence for LT4690-40 SEQ ID NO 231 s the determined cDNA sequence for LT4690-41 SEQ ID NO 232 s the determined cDNA sequence for LT4690-49 SEQ ID NO 233 s the determined 3' cDNA sequence for LT4690-55 SEQ ID NO 234 s the determined 5' cDNA sequence for LT4690-55 SEQ ID NO 235 s the determined cDNA sequence for LT4690-59 SEQ ID NO 236 s the determined cDNA sequence for LT4690-63 SEQ ID NO 237 s the determined cDNA sequence for LT4690-71 SEQ ID NO 238 s the determined cDNA sequence for 2LT-3 SEQ ID NO 239 s the determined cDNA sequence for 2LT-6 SEQ ID NO 240 s the determined cDNA sequence for 2LT-22 SEQ ID NO 241 s the determined cDNA sequence for 2LT-25 SEQ ID NO 242 s the determined cDNA sequence for 2LT-26 SEQ ID NO 243 s the determined cDNA sequence for 2LT-31 SEQ ID NO 244 s the determined cDNA sequence for 2LT-36 SEQ ID NO 245 s the determined cDNA sequence for 2LT-42 SEQ ID NO 246 s the determined cDNA sequence for 2LT-44 SEQ ID NO 247 s the determined cDNA sequence for 2LT-54 SEQ ID NO 248 s the determined cDNA sequence for 2LT-55 SEQ ID NO 249 s the determined cDNA sequence for 2LT-57 SEQ ID NO 250 s the determined cDNA sequence for 2LT-58 SEQ ID NO: 251 is the determined cDNA sequence for 2LT-59 SEQ ID NO: 252 is the determined cDNA sequence for 2LT-62 SEQ ID NO: 253 is the determined cDNA sequence for 2LT-63 SEQ ID NO: 254 is the determined cDNA sequence for 2LT-65 SEQ ID NO: 255 is the determined cDNA sequence for 2LT-66 SEQ ID NO: 256 is the determined cDNA sequence for 2LT-70 SEQ ID NO: 257 is the determined cDNA sequence for 2LT-73 SEQ ID NO: 258 is the determined cDNA sequence for 2LT-74 SEQ ID NO: 259 is the determined cDNA sequence for 2LT-76 SEQ ID NO: 260 is the determined cDNA sequence for 2LT-77 SEQ ID NO: 261 is the determined cDNA sequence for 2LT-78 SEQ ID NO: 262 is the determined cDNA sequence for 2LT-80 SEQ ID NO: 263 is the determined cDNA sequence for 2LT-85 SEQ ID NO: 264 is the determined cDNA sequence for 2LT-87 SEQ ID NO: 265 is the determined cDNA sequence for 2LT-89 SEQ ID NO: 266 is the determined cDNA sequence for 2LT-94 SEQ ID NO: 267 is the determined cDNA sequence for 2LT-95 SEQ ID NO: 268 is the determined cDNA sequence for 2LT-98 SEQ ID NO: 269 is the determined cDNA sequence for 2LT-100 SEQ ID NO: 270 is the determined cDNA sequence for 2LT- 103 SEQ ID NO: 271 is the determined cDNA sequence for 2LT-105 SEQ ID NO: 272 is the determined cDNA sequence for 2LT-107 SEQ ID NO: 273 is the determined cDNA sequence for 2LT-108 SEQ ID NO: 274 is the determined cDNA sequence for 2LT-109 SEQ ID NO: 275 is the determined cDNA sequence for 2LT-118 SEQ ID NO: 276 is the determined cDNA sequence for 2LT-120 SEQ ID NO: 277 is the determined cDNA sequence for 2LT-121 SEQ ID NO: 278 is the determined cDNA sequence for 2LT-122 SEQ ID NO: 279 is the determined cDNA sequence for 2LT-124 SEQ ID NO: 280 is the determined cDNA sequence for 2LT-126 SEQ ID NO: 281 is the determined cDNA sequence for 2LT-127 SEQ ID NO 282 is the determined cDNA sequence for 2LT-128
SEQ ID NO 283 s the determined cDNA sequence for 2LT-129
SEQ ID NO. 284 s the determined cDNA sequence for 2LT-133
SEQ ID NO: 285 s the determined cDNA sequence for 2LT-137
SEQ ID NO: 286 s the determined cDNA sequence for LT4690-71
SEQ ID NO: 287 s the determined cDNA sequence for LT4690-82
SEQ ID NO: 288 s the determined full-length cDNA sequence for SSLT-74
SEQ ID NO: 289 s the determined cDNA sequence for SSLT-78
SEQ ID NO: 290 s the determined cDNA sequence for SCC1-8.
SEQ ID NO: 291 s the determined cDNA sequence for SCC1-12.
SEQ ID NO: 292 s the determined cDNA sequence for SCC 1-336
SEQ ID NO: 293 s the determined cDNA sequence for SCC 1-344
SEQ ID NO: 294 s the determined cDNA sequence for SCC 1-345
SEQ ID NO: 295 s the determined cDNA sequence for SCC 1-346
SEQ ID NO: 296 s the determined cDNA sequence for SCC 1-348
SEQ ID NO: 297 s the determined cDNA sequence for SCC 1-350
SEQ ID NO: 298 s the determined cDNA sequence for SCC 1-352
SEQ ID NO: 299 s the determined cDNA sequence for SCC 1-354
SEQ ID NO: 300 s the determined cDNA sequence for SCC 1-355
SEQ ID NO: 301 s the determined cDNA sequence for SCCl-356
SEQ ID NO: 302 s the determined cDNA sequence for SCC1-357
SEQ ID NO: 303 s the determined cDNA sequence for SCC1-501
SEQ ID NO: 304 s the determined cDNA sequence for SCC 1-503
SEQ ID NO: 305 s the determined cDNA sequence for SCC 1-513
SEQ ID NO: 306 s the determined cDNA sequence for SCC 1-516
SEQ ID NO: 307 s the determined cDNA sequence for SCC 1-518
SEQ ID NO: 308 s the determined cDNA sequence for SCC 1-519
SEQ ID NO: 309 s the determined cDNA sequence for SCC 1-522
SEQ ID NO: 310 s the determined cDNA sequence for SCC 1-523
SEQ ID NO: 311 s the determined cDNA sequence for SCC 1-525
SEQ ID NO: 312 s the determined cDNA sequence for SCC 1-527 SEQ ID NO: 313 iis the determined cDNA sequence for SCC 1-529
SEQ ID NO: 314 iis the determined cDNA sequence for SCC 1-530
SEQ ID NO: 315 iis the determined cDNA sequence for SCC 1-531
SEQ ID NO: 316 iis the determined cDNA sequence for SCC 1-532
SEQ ID NO: 317 iis the determined cDNA sequence for SCC 1-533
SEQ ID NO: 318 iis the determined cDNA sequence for SCC1-536
SEQ ID NO: 319 iis the determined cDNA sequence for SCC 1-538
SEQ ID NO: 320 iis the determined cDNA sequence for SCC1-539
SEQ ID NO: 321 iis the determined cDNA sequence for SCC 1-541
SEQ ID NO: 322 iis the determined cDNA sequence for SCC 1-542
SEQ ID NO: 323 iis the determined cDNA sequence for SCC 1-546
SEQ ID NO: 324 iis the determined cDNA sequence for SCC 1-549
SEQ ID NO: 325 iis the determined cDNA sequence for SCC1-551
SEQ ID NO: 326 iis the determined cDNA sequence for SCC1-552
SEQ ID NO: 327 iis the determined cDNA sequence for SCCl-554
SEQ ID NO: 328 iis the determined cDNA sequence for SCC1-558
SEQ ID NO: 329 iis the determined cDNA sequence for SCC 1-559
SEQ ID NO: 330 iis the determined cDNA sequence for SCC 1-561
SEQ ID NO: 331 iis the determined cDNA sequence for SCC 1-562
SEQ ID NO: 332 iis the determined cDNA sequence for SCC 1-564
SEQ ID NO: 333 iis the determined cDNA sequence for SCC 1-565
SEQ ID NO: 334 iis the determined cDNA sequence for SCC 1-566
SEQ ID NO: 335 iis the determined cDNA sequence for SCC 1-567
SEQ ID NO: 336 iis the determined cDNA sequence for SCC 1-568
SEQ ID NO: 337 iis the determined cDNA sequence for SCC 1-570
SEQ ID NO: 338 iis the determined cDNA sequence for SCC 1-572
SEQ ID NO: 339 iis the determined cDNA sequence for SCC 1-575
SEQ ID NO: 340 iis the determined cDNA sequence for SCC 1-576
SEQ ID NO: 341 iis the determined cDNA sequence for SCC 1-577
SEQ ID NO: 342 iis the determined cDNA sequence for SCC 1-578
SEQ ID NO: 343 iis the determined cDNA sequence for SCC1-582 SEQ ID NO 344 is the determined cDNA sequence for SCC1-583 SEQ ID NO 345 s the determined cDNA sequence for SCC 1-586 SEQ ID NO 346 s the determined cDNA sequence for SCC 1-588 SEQ ID NO 347 s the determined cDNA sequence for SCC 1-590 SEQ ID NO 348 s the determined cDNA sequence for SCC 1-591 SEQ ID NO 349 s the determined cDNA sequence for SCC 1-592 SEQ ID NO 350 s the determined cDNA sequence for SCC 1-593 SEQ ID NO 351 s the determined cDNA sequence for SCC 1-594 SEQ ID NO 352 s the determined cDNA sequence for SCC 1-595 SEQ ID NO 353 s the determined cDNA sequence for SCC 1-596 SEQ ID NO 354 s the determined cDNA sequence for SCC 1-598 SEQ ID NO 355 s the determined cDNA sequence for SCC 1-599 SEQ ID NO 356 s the determined cDNA sequence for SCC 1-602 SEQ ID NO 357 s the determined cDNA sequence for SCC 1-604 SEQ ID NO 358 s the determined cDNA sequence for SCC 1-605 SEQ ID NO 359 s the determined cDNA sequence for SCC 1-606 SEQ ID NO 360 s the determined cDNA sequence for SCC 1-607 SEQ ID NO 361 s the determined cDNA sequence for SCC 1-608 SEQ ID NO 362 s the determined cDNA sequence for SCC 1-610 SEQ ID NO 363 s the determined cDNA sequence for clone DMS79T1 SEQ ID NO 364 s the determined cDNA sequence for clone DMS79T2 SEQ ID NO 365 s the determined cDNA sequence for clone DMS79T3 SEQ ID NO 366 s the determined cDNA sequence for clone DMS79T5 SEQ ID NO 367 s the determined cDNA sequence for clone DMS79T6 SEQ ID NO 368 s the determined cDNA sequence for clone DMS79T7 SEQ ID NO 369 s the determined cDNA sequence for clone DMS79T9 SEQ ID NO 370 s the determined cDNA sequence for clone DMS79T10 SEQ ID NO 371 s the determined cDNA sequence for clone DMS79T11 SEQ ID NO 372 s the determined cDNA sequence for clone 128T1 SEQ ID NO 373 s the determined cDNA sequence for clone 128T2 SEQ ID NO 374 s the determined cDNA sequence for clone 128T3 SEQ ID NO 375 s the determined cDNA sequence for clone 128T4 SEQ ID NO 376 s the determined cDNA sequence for clone 128T5 SEQ ID NO 377 s the determined cDNA sequence for clone 128T7 SEQ ID NO 378 s the determined cDNA sequence for clone 128T9 SEQ ID NO 379 s the determined cDNA sequence for clone 128T10 SEQ ID NO 380 s the determined cDNA sequence for clone 128T11 SEQ ID NO 381 s the determined cDNA sequence for clone 128T12 SEQ ID NO 382 s the determined cDNA sequence for clone NCIH69T3 SEQ ID NO 383 s the determined cDNA sequence for clone NCIH69T5 SEQ ID NO 384 s the determined cDNA sequence for clone NCIH69T6 SEQ ID NO 385 s the determined cDNA sequence for clone NCIH69T7 SEQ ID NO 386 s the determined cDNA sequence for clone NCIH69T9 SEQ ID NO 387 s the determined cDNA sequence for clone NCIH69T10 SEQ ID NO 388 s the determined cDNA sequence for clone NCIH69T11 SEQ ID NO 389 s the determined cDNA sequence for clone NCIH69T12
DETAILED DESCRIPTION OF THE INVENTION
As noted above, the present invention is generally directed to compositions and methods for the therapy and diagnosis of cancer, such as lung cancer. The compositions described herein may include lung tumor polypeptides, polynucleotides encoding such polypeptides, binding agents such as antibodies, antigen presenting cells (APCs) and/or immune system cells (e.g., T cells). Polypeptides of the present invention generally comprise at least a portion (such as an immunogenic portion) of a lung tumor protein or a variant thereof. A "lung tumor protein" is a protein that is expressed in lung tumor cells at a level that is at least two fold, and preferably at least five fold, greater than the level of expression in a normal tissue, as determined using a representative assay provided herein. Certain lung tumor proteins are tumor proteins that react detectably (within an immunoassay, such as an ELISA or Western blot) with antisera of a patient afflicted with lung cancer. Polynucleotides of the subject invention generally comprise a DNA or RNA sequence that encodes all or a portion of such a polypeptide, or that is complementary to such a sequence. Antibodies are generally immune system proteins, or antigen-binding fragments thereof, that are capable of binding to a polypeptide as described above. Antigen presenting cells include dendritic cells, macrophages, monocytes, fibroblasts and B-cells that express a polypeptide as described above. T cells that may be employed within such compositions are generally T cells that are specific for a polypeptide as described above.
The present invention is based on the discovery of human lung tumor proteins. Sequences of polynucleotides encoding specific tumor proteins are provided in SEQ ID NOS: 1-31, 49-55, 63,64, 66, 68-72, 78-80, 84-92 and 217-389.
LUNG TUMOR PROTEIN POLYNUCLEOTIDES
Any polynucleotide that encodes a lung tumor protein or a portion or other variant thereof as described herein is encompassed by the present invention. Preferred polynucleotides comprise at least 15 consecutive nucleotides, preferably at least 30 consecutive nucleotides and more preferably at least 45 consecutive nucleotides, that encode a portion of a lung tumor protein. More preferably, a polynucleotide encodes an immunogenic portion of a lung tumor protein. Polynucleotides complementary to any such sequences are also encompassed by the present invention. Polynucleotides may be single-stranded (coding or antisense) or double-stranded, and may be DNA (genomic, cDNA or synthetic) or RNA molecules. RNA molecules 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 lung tumor protein or a portion thereof) or may comprise a variant of such a sequence. Polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions such that the immunogenicity of the encoded polypeptide is not diminished, relative to a native tumor protein. The effect on the immunogenicity of the encoded polypeptide may generally be assessed as described herein. Variants preferably exhibit at least about 70% identity, more preferably at least about 80%) identity and most preferably at least about 90% identity to a polynucleotide sequence that encodes a native lung tumor protein or a portion thereof.
Two polynucleotide or polypeptide sequences are said to be "identical" if the sequence of nucleotides or 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 En∑ymology vol. 183, Academic Press, Inc., San Diego, CA; Higgins, D.G. and Sharp, P.M. (1989) CABIOS 5:151-153; Myers, E.W. and Muller W. (1988) CABIOS 4:11-11; Robinson, E.D. (1971) Comb. Theor 77:105; Santou, N. Nes, M. (1987) Mol. Biol. Evol. 4:406- 425; Sneath, P.H. A. and Sokal, R.R. (1973) Numerical Taxonomy - the Principles and Practice of Numerical Taxonomy, Freeman Press, San Francisco, CA; Wilbur, W.J. and Lipman, D.J. (1983) Proc. Natl. Acad, Sci. USA 80:126-130.
Preferably, 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 or 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 ofthe two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid bases or 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.
Variants may also, or alternatively, be substantially homologous to a native gene, or a portion or complement thereof. Such polynucleotide variants are capable of hybridizing under moderately stringent conditions to a naturally occurring DNA sequence encoding a native lung tumor protein (or a complementary sequence). Suitable moderately stringent conditions include prewashing in a solution of 5 X SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at 50°C-65°C, 5 X SSC, overnight; followed by washing twice at 65°C for 20 minutes with each of 2X, 0.5X and 0.2X SSC containing 0.1% SDS. It will be appreciated by those of ordinary skill in the art that, as a result of the degeneracy of the genetic code, there are many nucleotide sequences that encode a 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. The resulting 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).
Polynucleotides may be prepared using any of a variety of techniques.
For example, 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 five fold greater in a lung tumor than in normal tissue, as determined using a representative assay provided herein). Such screens may be performed using a Synteni microarray (Palo Alto, CA) according to the manufacturer's instructions (and essentially 9
as described by Schena et al., Proc. Natl. Acad. Sci. USA 95:10614-10619. 1996 and Heller et al., Proc. Natl. Acad. Sci. USA 9^:2150-2155, 1997). Alternatively, polypeptides may be amplified from cDNA prepared from cells expressing the proteins described herein, such as lung tumor cells. Such polynucleotides may be amplified via polymerase chain reaction (PCR). For this approach, sequence-specific primers may be designed based on the sequences provided herein, and may be purchased or synthesized. An amplified portion may be used to isolate a full length gene from a suitable library (e.g., a lung tumor cDNA library) using well known techniques. Within such techniques, a library (cDNA or genomic) is screened using one or more polynucleotide probes or primers suitable for amplification. Preferably, 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.
For hybridization techniques, a partial sequence may be labeled (e.g., by nick-translation or end-labeling with 32P) using well known techniques. A bacterial or bacteriophage library is then 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 are then assembled into a single contiguous sequence. A full length cDNA molecule can be generated by ligating suitable fragments, using well known techniques.
Alternatively, there are numerous amplification techniques for obtaining a full length coding sequence from a partial cDNA sequence. Within such techniques, amplification is generally performed via PCR. Any of a variety of commercially available kits may be used to perform the amplification step. Primers may be designed using, for example, software well known in the art. Primers are preferably 22-30 nucleotides in length, have a GC content of at least 50%> and anneal to the target sequence at temperatures of about 68°C to 72°C. The amplified region may be sequenced as described above, and overlapping sequences assembled into a contiguous sequence.
One such amplification technique is inverse PCR (see Triglia et al., Nucl. Acids Res. 7(5:8186, 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. Within an alternative approach, sequences adjacent to a partial sequence may be retrieved by amplification with a primer to a linker sequence and a primer specific to a known region. The amplified sequences are typically subjected to a second round of amplification with the same linker primer and a second primer specific to the known region. A variation on this procedure, which employs two primers that initiate extension in opposite directions from the known sequence, is described in WO 96/38591. Another such technique is known as "rapid amplification of cDNA ends" or RACE. This technique involves the use of an internal primer and an external primer, which hybridizes to a polyA region or vector sequence, to identify sequences that are 5' and 3' of a known sequence. Additional techniques include capture PCR (Lagerstrom et al., PCR Methods Applic. 7 : 111 - 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.
In certain instances, it is possible to obtain a full length cDNA sequence by analysis of sequences provided in an expressed sequence tag (EST) database, such as that available from GenBank. 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.
Certain nucleic acid sequences of cDNA molecules encoding portions of lung tumor proteins are provided in SEQ ID NO: 1-31, 49-55, 63,64, 66, 68-72, 78-80, 84-92 and 217-389. The isolation of these sequences is described in detail below.
Polynucleotide variants may generally be prepared by any method known in the art, including chemical synthesis by, for example, solid phase phosphoramidite chemical synthesis. Modifications in a polynucleotide sequence may also be introduced using standard mutagenesis techniques, such as oligonucleotide- directed site-specific mutagenesis (see Adelman et al., DNA 2:183, 1983). Alternatively, RNA molecules may be generated by in vitro or in vivo transcription of DNA sequences encoding a lung tumor protein, or portion thereof, provided that the DNA is incorporated into a vector with a suitable RNA polymerase promoter (such as T7 or SP6). Certain portions may be used to prepare an encoded polypeptide, as described herein. In addition, or alternatively, a portion may be admimstered to a patient such that the encoded polypeptide is generated in vivo (e.g., by transfecting antigen-presenting cells, such as dendritic cells, with a cDNA construct encoding a lung tumor polypeptide. and administering the transfected cells to the patient).
A portion of a sequence complementary to a coding sequence (i.e., an antisense polynucleotide) may also be used as a probe or to modulate gene expression. cDNA constructs that can be transcribed into antisense RNA may also be introduced into cells of tissues to facilitate the production of antisense RNA. An antisense polynucleotide may be used, as described herein, to inhibit expression of a tumor protein. Antisense technology can be used to control gene expression through triple- helix formation, which compromises the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors or regulatory molecules (see Gee et al., In Huber and Carr, Molecular and Immunologic Approaches, Futura Publishing Co. (Mt. Kisco, NY; 1994)). Alternatively, an antisense molecule may be designed to hybridize with a control region of a gene (e.g., promoter, enhancer or transcription initiation site), and block transcription of the gene; or to block translation by inhibiting binding of a transcript to ribosomes.
A portion of a coding sequence, or of a complementary sequence, may also be designed as a probe or primer to detect gene expression. Probes may be labeled with a variety of reporter groups, such as radionuclides and enzymes, and are preferably at least 10 nucleotides in length, more preferably at least 20 nucleotides in length and still more preferably at least 30 nucleotides in length. Primers, as noted above, are preferably 22-30 nucleotides in length. Any polynucleotide may be further modified to increase stability in vivo. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5' and/or 3' ends; the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages in the backbone; and/or the inclusion of nontraditional bases such as inosine, queosine and wybutosine, as well as acetyl-, methyl-, thio- and other modified forms of adenine, cytidine, guanine, thymine and uridine.
Nucleotide sequences as described herein may be joined to a variety of other nucleotide sequences using established recombinant DNA techniques. For example, a polynucleotide may be cloned into any of a variety of cloning vectors, including plasmids. phagemids, lambda plfage derivatives and cosmids. Vectors of particular interest include expression vectors, replication vectors, probe generation vectors and sequencing vectors. In general, a vector will contain an origin of replication functional in at least one organism, convenient restriction endonuclease sites and one or more selectable markers. Other elements will depend upon the desired use. and will be apparent to those of ordinary skill in the art.
Within certain embodiments, polynucleotides may be formulated so as to permit entry into a cell of a mammal, and expression therein. Such formulations are particularly useful for therapeutic purposes, as described below. Those of ordinary skill in the art will appreciate that there are many ways to achieve expression of a polynucleotide in a target cell, and any suitable method may be employed. For example, a polynucleotide may be incorporated into a viral vector such as, but not limited to, adenovirus, adeno-associated virus, retrovirus, or vaccinia or other pox virus (e.g., avian pox virus). Techniques for incorporating DNA into such vectors are well known to those of ordinary skill in the art. A retroviral vector may additionally transfer or incorporate a gene for a selectable marker (to aid in the identification or selection of transduced cells) and/or a targeting moiety, such as a gene that encodes a ligand for a receptor on a specific target cell, to render the vector target specific. Targeting may also be accomplished using an antibody, by methods known to those of ordinary skill in the art. Other formulations for therapeutic purposes include colloidal dispersion systems, such as macromolecule complexes, nanocapsules. microspheres. beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. A preferred colloidal system for use as a delivery vehicle in vitro and in vivo is a liposome (i.e., an artificial membrane vesicle). The preparation and use of such systems is well known in the art.
LUNG TUMOR POLYPEPTIDES
Within the context of the present invention, polypeptides may comprise at least an immunogenic portion of a lung tumor protein or a variant thereof, as described herein. As noted above, a "lung tumor protein" is a protein that is expressed by lung tumor cells. Proteins that are lung tumor proteins also react detectably within an immunoassay (such as an ELISA) with antisera from a patient with lung cancer. Polypeptides as described herein may be of any length. Additional sequences derived from the native protein and/or heterologous sequences may be present, and such sequences may (but need not) possess further immunogenic or antigenic properties. An "immunogenic portion," as used herein is a portion of a protein that is recognized (i.e., specifically bound) by a B-cell and/or T-cell surface antigen receptor. Such immunogenic portions generally comprise at least 5 amino acid residues, more preferably at least 10, and still more preferably at least 20 amino acid residues of a lung tumor protein or a variant thereof. Certain preferred immunogenic portions include peptides in which an N-terminal leader sequence and/or transmembrane domain have been deleted. Other preferred immunogenic portions may 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.
Immunogenic portions may generally be identified using well known techniques, such as those summarized in Paul, Fundamental Immunology, 3rd ed., 243- 247 (Raven Press, 1993) and references cited therein. Such techniques include screening polypeptides for the ability to react with antigen-specific antibodies, antisera and/or T-cell lines or clones. As used herein, 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). Such antisera and antibodies may be prepared as described herein, and using well known techniques. An immunogenic portion of a native lung tumor protein is a portion that reacts with such antisera and/or T-cells at a level that is not substantially less than the reactivity of the full length polypeptide (e.g., in an ELISA and/or T-cell reactivity assay). Such immunogenic portions may react within such assays at a level that is similar to or greater than the reactivity ofthe full length polypeptide. Such screens may generally be performed using methods well known to those of ordinary skill in the art. such as those described in Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988. For example, a polypeptide may be immobilized on a solid support and contacted with patient sera to allow binding of antibodies within the sera to the immobilized polypeptide. Unbound sera may then be removed and bound antibodies detected using, for example, 125I-labeled Protein A.
As noted above, a composition may comprise a variant of a native lung tumor protein. A polypeptide "variant," as used herein, is a polypeptide that differs from a native lung tumor protein in one or more substitutions, deletions, additions and/or insertions, such that the immunogenicity of the polypeptide is not substantially diminished. In other words, the ability of a variant to react with antigen-specific antisera may be enhanced or unchanged, relative to the native protein, or may be diminished by less than 50%, and preferably less than 20%, relative to the native protein. Such variants may generally be identified by modifying one of the above polypeptide sequences and evaluating the reactivity of the modified polypeptide with antigen-specific antibodies or antisera as described herein. Preferred variants include those in which one or more portions, such as an N-terminal leader sequence or transmembrane domain, have been removed. Other preferred 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 ofthe mature protein.
Polypeptide variants preferably exhibit at least about 70%, more preferably at least about 90% and most preferably at least about 95% identity (determined as described above) to the identified polypeptides.
Preferably, a variant contains conservative substitutions. A "conservative substitution" is one in which an amino acid is substituted for another amino acid that has similar properties, such that one skilled in the art of peptide chemistry would expect the secondary structure and hydropathic nature of the polypeptide to be substantially unchanged. Amino acid substitutions may generally be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues. For example, negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine and valine; glycine and alanine; asparagine and glutamine; and serine, threonine, phenylalanine and tyrosine. Other groups of amino acids that may represent conservative changes include: (1) ala, pro, gly, glu, asp, gin, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala, phe; (4) lys, arg, his; and (5) phe, tyr, trp, his. A variant may also, or alternatively, contain nonconservative changes. In a preferred embodiment, 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 ofthe polypeptide.
As noted above, 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 ofthe polypeptide to a solid support. For example, a polypeptide may be conjugated to an immunoglobulin Fc region.
Polypeptides may be prepared using any of a variety of well known techniques. Recombinant polypeptides encoded by DNA sequences as described above may be readily prepared from the DNA sequences using any of a variety of expression vectors known to those of ordinary skill in the art. Expression may be achieved in any appropriate host cell that has been transformed or transfected with an expression vector containing a DNA molecule that encodes a recombinant polypeptide. Suitable host cells include prokaryotes, yeast and higher eukaryotic cells. Preferably, the host cells employed are E. coli, yeast or a mammalian cell line such as COS or CHO. Supernatants from suitable host/vector systems which secrete recombinant protein or polypeptide into culture media may be first concentrated using a commercially available filter. Following concentration, the concentrate may be applied to a suitable purification matrix such as an affinity matrix or an ion exchange resin. Finally, one or more reverse phase HPLC steps can be employed to further purify a recombinant polypeptide.
Portions and other variants having fewer than about 100 amino acids, and generally fewer than about 50 amino acids, may also be generated by synthetic means, using techniques well known to those of ordinary skill in the art. For example, such polypeptides may be synthesized using any of the commercially available solid- phase techniques, such as the Merrifield solid-phase synthesis method, where amino acids are sequentially added to a growing amino acid chain. See Merrifield, J. Am. Chem. Soc. 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 instructions.
Within certain specific embodiments, a polypeptide may be a fusion protein 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 protein or to enable the protein to be targeted to desired intracellular compartments. Still further fusion partners include affinity tags, which facilitate purification ofthe protein.
Fusion proteins may generally be prepared using standard techniques, including chemical conjugation. Preferably, a fusion protein is expressed as a recombinant protein, allowing the production of increased levels, relative to a non-fused protein, in an expression system. Briefly, DNA sequences encoding the polypeptide components may be assembled separately, and ligated into an appropriate expression vector. The 3' end of the DNA sequence encoding one polypeptide component is ligated, with or without a peptide linker, to the 5' end of a DNA sequence encoding the second polypeptide component so that the reading frames of the sequences are in phase. This permits translation into a single fusion protein that retains the biological activity of both component polypeptides.
A peptide linker sequence may be employed to separate the first and the 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 protein using standard techniques well known in the art. Suitable peptide linker sequences may be chosen based on the following factors: (1) their ability to adopt a flexible extended conformation; (2) their inability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides; and (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes. Preferred peptide linker sequences contain Gly, Asn and Ser residues. Other near neutral amino acids, such as Thr and Ala may also be used in the linker sequence. Amino acid sequences which may be usefully employed as linkers include those disclosed in Maratea et al, Gene 40:39-46, 1985; Murphy et al., Proc. Natl. Acad. Sci. USA 53:8258-8262, 1986; U.S. Patent No. 4,935,233 and U.S. Patent No. 4,751,180. The linker sequence may generally be from 1 to about 50 amino acids in length. Linker sequences are not required when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference.
The ligated DNA sequences are operably linked to suitable transcriptional or translational regulatory elements. The regulatory elements responsible for expression of DNA are located only 5' to the DNA sequence encoding the first polypeptides. Similarly, stop codons required to end translation and transcription termination signals are only present 3' to the DNA sequence encoding the second polypeptide.
Fusion proteins are also provided that comprise a polypeptide of the present invention together with an unrelated immunogenic protein. Preferably the immunogenic protein is capable of eliciting a recall response. Examples of such proteins include tetanus, tuberculosis and hepatitis proteins (see, for example, Stoute et al. New Engl. J. Med., 336:86-91, 1997).
Within preferred embodiments, an immunological fusion partner is derived from protein D, a surface protein of the gram-negative bacterium Haemophilus influenza B (WO 91/18926). Preferably, a protein D derivative comprises approximately the first third of the protein (e.g., the first Ν-terminal 100-110 amino acids), and a protein D derivative may be lipidated. Within certain preferred embodiments, the first 109 residues of a Lipoprotein D fusion partner is included on the Ν-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, ΝS1 (hemaglutinin). Typically, the Ν-terminal 81 amino acids are used, although different fragments that include T-helper epitopes may be used. In another embodiment, the immunological fusion partner is the protein known as LYTA, or a portion thereof (preferably a C-terminal portion). LYTA is derived from Streptococcus pneumoniae, which synthesizes an Ν-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 DΕAΕ. 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 protein. A repeat portion is found in the C- terminal region starting at residue 178. A particularly preferred repeat portion incorporates residues 188-305.
In general, polypeptides (including fusion proteins) and polynucleotides as described herein are isolated. An "isolated" polypeptide or polynucleotide is one that is removed from its original environment. For example, a naturally-occurring protein is isolated if it is separated from some or all of the coexisting materials in the natural system. Preferably, such polypeptides are at least about 90% pure, more preferably at least about 95% pure and most preferably at least about 99% pure. A polynucleotide is considered to be isolated if, for example, it is cloned into a vector that is not a part of the natural environment.
BINDING AGENTS
The present invention further provides agents, such as antibodies and antigen-binding fragments thereof, that specifically bind to a lung tumor protein. As used herein, an antibody, or antigen-binding fragment thereof, is said to "specifically bind" to a lung tumor protein if it reacts at a detectable level (within, for example, an ELISA) with a lung tumor protein, and does not react detectably with unrelated proteins under similar conditions. As used herein, "binding" refers to a noncovalent association between two separate molecules such that a complex is formed. The ability to bind may be evaluated by, for example, determining a binding constant for the formation of the complex. The binding constant is the value obtained when the concentration of the complex is divided by the product of the component concentrations. In general, two compounds are said to "bind," in the context of the present invention, when the binding constant for complex formation exceeds about 103 L/mol. The binding constant may be determined using methods well known in the art.
Binding agents may be further capable of differentiating between patients with and without a cancer, such as lung cancer, using the representative assays provided herein. In other words, antibodies or other binding agents that bind to a lung tumor protein will generate a signal indicating the presence of a cancer in at least about 20%) of patients with the disease, and will generate a negative signal indicating the absence of the disease in at least about 90% of individuals without the cancer. To determine whether a binding agent satisfies this requirement, biological samples (e.g., blood, sera, urine and/or tumor biopsies) from patients with and without a cancer (as determined using standard clinical tests) may be assayed as described herein for the presence of polypeptides that bind to the binding agent. It will be apparent that a statistically significant number of samples with and without the disease should 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.
Any agent that satisfies the above requirements may be a binding agent. For example, a binding agent may be a ribosome, with or without a peptide component, an RNA molecule or a polypeptide. In a preferred embodiment, 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. In one technique, an immunogen comprising the polypeptide is initially injected into any of a wide variety of mammals (e.g., mice, rats, rabbits, sheep or goats). In this step, the polypeptides of this invention may serve as the immunogen without modification. Alternatively, particularly for relatively short polypeptides, a superior immune response may be elicited if the polypeptide is joined to a carrier protein, such as bovine serum albumin or keyhole limpet hemocyanin. The immunogen is injected into the animal host, preferably according to a predetermined schedule incorporating one or more booster immunizations, and the animals are bled periodically. Polyclonal antibodies specific for the polypeptide may then be purified from such antisera by, for example, affinity chromatography using the polypeptide coupled to a suitable solid support.
Monoclonal antibodies specific for an antigenic polypeptide of interest may be prepared, for example, using the technique of Kohler and Milstein, Eur. J. Immunol. 6:511-519, 1976, and improvements thereto. Briefly, these methods involve the preparation of immortal cell lines capable of producing antibodies having the desired specificity (i.e., reactivity with the polypeptide of interest). Such cell lines may be produced, for example, from spleen cells obtained from an animal immunized as described above. The spleen cells are then immortalized by, for example, fusion with a myeloma cell fusion partner, preferably one that is syngeneic with the immunized animal. A variety of fusion techniques may be employed. For example, the spleen cells and myeloma cells may be combined with a nonionic detergent for a few minutes and then plated at low density on a selective medium that supports the growth of hybrid cells, but not myeloma cells. A preferred selection technique uses HAT (hypoxanthine, aminopterin, thymidine) selection. After a sufficient time, usually about 1 to 2 weeks, colonies of hybrids are observed. Single colonies are selected and their culture 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. In addition, various techniques may be employed to enhance the yield, such as injection of the hybridoma cell line into the peritoneal cavity of a suitable vertebrate host, such as a mouse. Monoclonal antibodies may then be harvested from the ascites fluid or the blood. Contaminants may be removed from the antibodies by conventional techniques, such as chromatography, gel filtration, precipitation, and extraction. The polypeptides of this invention may be used in the purification process in, for example, an affinity chromatography step.
Within certain embodiments, the use of antigen-binding fragments of antibodies may be preferred. Such fragments include Fab fragments, which may be prepared using standard techniques. Briefly, immunoglobulins may be purified from rabbit serum by affinity chromatography on Protein A bead columns (Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988) and digested by papain to yield Fab and Fc fragments. The Fab and Fc fragments may be separated by affinity chromatography on protein A bead columns.
Monoclonal antibodies ofthe present invention may be coupled to one or more therapeutic agents. Suitable agents in this regard include radionuclides, differentiation inducers, drugs, toxins, and derivatives thereof. Preferred radionuclides include 90Y, I23I, 125I, 131I, 186Re, 1S8Re, 21 ,At, and 21 Bi. Preferred drugs include methotrexate, and pyrimidine and purine analogs. Preferred differentiation inducers include phorbol esters and butyric acid. Preferred toxins include ricin, abrin, diptheria toxin, cholera toxin, gelonin, Pseudomonas exotoxin. Shigella toxin, and pokeweed antiviral protein. A therapeutic agent may be coupled (e.g., covalently bonded) to a suitable monoclonal antibody either directly or indirectly (e.g., via a linker group). A direct reaction between an agent and an antibody is possible when each possesses a substituent capable of reacting with the other. For example, a nucleophilic group, such as an amino or sulfhydryl group, on one may be capable of reacting with a carbonyl- containing group, such as an anhydride or an acid halide, or with an alkyl group containing a good leaving group (e.g., a halide) on the other.
Alternatively, it may be desirable to couple a therapeutic agent and an antibody via a linker group. A linker group can function as a spacer to distance an antibody from an agent in order to avoid interference with binding capabilities. A linker group can also serve to increase the chemical reactivity of a substituent on an agent or an antibody, and thus increase the coupling efficiency. An increase in chemical reactivity may also facilitate the use of agents, or functional groups on agents, which otherwise would not be possible. It will be evident to those skilled in the art that a variety of bifunctional or polyfunctional reagents, both homo- and hetero-functional (such as those described in the catalog ofthe Pierce Chemical Co., Rockford, IL), may be employed as the linker group. Coupling may be effected, for example, through amino groups, carboxyl groups, sulfhydryl groups or oxidized carbohydrate residues. There are numerous references describing such methodology, e.g., U.S. Patent No. 4,671,958, to Rodwell et al.
Where a therapeutic agent is more potent when free from the antibody portion of the immunoconjugates of the present invention, it may be desirable to use a linker group which is cleavable during or upon internalization into a cell. A number of different cleavable linker groups have been described. The mechanisms for the intracellular release of an agent from these linker groups include cleavage by reduction of a disulfide bond (e.g., U.S. Patent No. 4,489,710, to Spitler), by irradiation of a photolabile bond (e.g., U.S. Patent No. 4,625,014, to Senter et al.), by hydrolysis of derivatized amino acid side chains (e.g., U.S. Patent No. 4.638,045, to Kohn et al.), by serum complement-mediated hydrolysis (e.g., U.S. Patent No. 4,671,958, to Rodwell et al.), and acid-catalyzed hydrolysis (e.g.. U.S. Patent No. 4.569.789. to Blattler et al.). It may be desirable to couple more than one agent to an antibody. In one embodiment, multiple molecules of an agent are coupled to one antibody molecule. In another embodiment, more than one type of agent may be coupled to one antibody. Regardless of the particular embodiment, immunoconjugates with more than one agent may be prepared in a variety of ways. For example, more than one agent may be coupled directly to an antibody molecule, or linkers which provide multiple sites for attachment can be used. Alternatively, a carrier can be used.
A carrier may bear the agents in a variety of ways, including covalent bonding either directly or via a linker group. Suitable carriers include proteins such as albumins (e.g., U.S. Patent No. 4,507,234. to Kato et al.), peptides and polysaccharides such as aminodextran (e.g., U.S. Patent No. 4,699,784, 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 radionuclide agents include radiohalogenated small molecules and chelating compounds. For example, U.S. Patent No. 4,735,792 discloses representative radiohalogenated small molecules and their synthesis. A radionuclide chelate may be formed from chelating compounds that include those containing nitrogen and sulfur atoms as the donor atoms for binding the metal, or metal oxide, radionuclide. For example, U.S. Patent No. 4,673,562, to Davison et al. discloses representative chelating compounds and their synthesis. A variety of routes of administration for the antibodies and immunoconjugates may be used. Typically, administration will be intravenous, intramuscular, subcutaneous or in the bed of a resected tumor. It will be evident that the precise dose of the antibody/immunoconjugate will vary depending upon the antibody used, the antigen density on the tumor, and the rate of clearance ofthe antibody.
T CELLS
Immunotherapeutic compositions may also, or alternatively, comprise T cells specific for a lung tumor protein. Such cells may generally be prepared in vitro or ex vivo, using standard procedures. For example, 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 ISOLEX™ 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). Alternatively, T cells may be derived from related or unrelated humans, non-human mammals, cell lines or cultures. T cells may be stimulated with a lung tumor polypeptide, polynucleotide encoding a lung tumor polypeptide and/or an antigen presenting cell (APC) that expresses such a polypeptide. Such stimulation is performed under conditions and for a time sufficient to permit the generation of T cells that are specific for the polypeptide. Preferably, a lung tumor polypeptide or polynucleotide 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 lung tumor polypeptide if the T cells kill target cells coated with the polypeptide or expressing a gene encoding the polypeptide. T cell specificity may be evaluated using any of a variety of standard techniques. For example, within a chromium release assay or proliferation assay, a stimulation index of more than two fold increase in lysis and/or proliferation, compared to negative controls, indicates T cell specificity. Such assays may be performed, for example, as described in Chen et al., Cancer Res. 54:1065-1070, 1994. Alternatively, detection of the proliferation of T cells may be accomplished by a variety of known techniques. For example, T cell proliferation can be detected by measuring an increased rate of DNA synthesis (e.g., by pulse-labeling cultures of T cells with tritiated thymidine and measuring the amount of tritiated thymidine incorporated into DNA). Contact with a lung tumor polypeptide (100 ng/ml - 100 μg/ml, preferably 200 ng/ml - 25 μg/ml) for 3 - 7 days should result in at least a two fold increase in proliferation of the T cells. Contact as described above for 2-3 hours should result in activation ofthe T cells, as measured using standard cytokine assays in which a two fold increase in the level of cytokine release (e.g., TNF or IFN-γ) is indicative of T cell activation (see Coligan et al.. Current Protocols in Immunology, vol. 1, Wiley Interscience (Greene 1998)). T cells that have been activated in response to a lung tumor polypeptide, polynucleotide or polypeptide-expressing APC may be CD4" and/or CD8+. Lung tumor protein-specific T cells may be expanded using standard techniques. Within preferred embodiments, the T cells are derived from either a patient or a related, or unrelated, donor and are administered to the patient following stimulation and expansion.
For therapeutic purposes, CD4+ or CD8+ T cells that proliferate in response to a lung 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 lung 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 lung tumor polypeptide. Alternatively, one or more T cells that proliferate in the presence of a lung tumor protein can be expanded in number by cloning. Methods for cloning cells are well known in the art, and include limiting dilution.
PHARMACEUTICAL COMPOSITIONS AND VACCINES
Within certain aspects, polypeptides, polynucleotides, T cells and/or binding agents disclosed herein may be incoφorated into pharmaceutical compositions or immunogenic compositions (i.e., vaccines). Pharmaceutical compositions comprise one or more such compounds and a physiologically acceptable carrier. Vaccines may comprise one or more such compounds and an immunostimulant. An immunostimulant may be any substance that enhances or potentiates an immune response to an exogenous antigen. Examples of immunostimulants include adjuvants, biodegradable microspheres (e.g., polylactic galactide) and liposomes (into which the compound is incoφorated; see e.g., Fullerton, U.S. Patent No. 4,235,877). 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). Pharmaceutical compositions and vaccines within the scope of the present invention may also contain other compounds, which may be biologically active or inactive. For example, one or more immunogenic portions of other tumor antigens may be present, either incoφorated into a fusion polypeptide or as a separate compound, within the composition or vaccine. A pharmaceutical composition or vaccine may contain DNA encoding one or more of the polypeptides as described above, such that the polypeptide is generated in situ. As noted above, the DNA may be present within any of a variety of delivery systems known to those of ordinary skill in the art, including nucleic acid expression systems, bacteria and viral expression systems. 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 nucleic acid expression systems contain the necessary DNA sequences for expression in the patient (such as a suitable promoter and terminating signal). Bacterial delivery systems involve the administration of a bacterium (such as Bacillus-Calmette- Guerrin) that expresses an immunogenic portion ofthe polypeptide on its cell surface or secretes such an epitope. In a preferred embodiment, the DNA may be introduced using a viral expression system (e.g., vaccinia or other pox virus, retrovirus. or adenovirus), which may involve the use of a non-pathogenic (defective), replication competent virus. Suitable systems are disclosed, for example, in Fisher-Hoch et al., Proc. Natl. Acad. Sci. USA 56:317-321, 1989; Flexner et al, Ann. N. Y. Acαd. Sci. 569:86-103, 1989; Flexner et al., Vaccine 5:17-21, 1990; U.S. Patent Nos. 4,603,112, 4,769,330, and 5,017,487; WO 89/01973; U.S. Patent No. 4,777,127; GB 2,200,651; EP 0,345,242; WO 91/02805; Berkner, Biotechniques 6:616-621, 1988; Rosenfeld et al., Science 252:431-434, 1991; Kolls et al., Proc. Natl. Acad. Sci. USA 97:215-219, 1994; Kass-Eisler et al., Proc. Natl. Acad. Sci. USA 90:11498-11502, 1993; Guzman et al., Circulation 55:2838-2848, 1993; and Guzman et al., Cir. Res. 73:1202-1207, 1993. Techniques for incoφorating DNA into such expression systems are well known to those of ordinary skill in the art. The DNA may also be "naked," as described, for example, in Ulmer et al., Science 259:1745-1749, 1993 and reviewed by Cohen, Science 259:1691-1692, 1993. The uptake of naked DNA may be increased by coating the DNA onto biodegradable beads, which are efficiently transported into the cells.
While any suitable carrier known to those of ordinary skill in the art may be employed in the pharmaceutical compositions of this invention, the type of carrier will vary depending on the mode of administration. Compositions of the present invention may be formulated for any appropriate manner of administration, including for example, topical, oral, nasal, intravenous, intracranial. intraperitoneal, subcutaneous or intramuscular administration. For parenteral administration, such as subcutaneous injection, the carrier preferably comprises water, saline, alcohol, a fat. a wax or a buffer. For oral administration, any of the above carriers or a solid carrier, such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, glucose, sucrose, and magnesium carbonate, may be employed. Biodegradable microspheres (e.g., polylactate polyglycolate) may also be employed as carriers for the pharmaceutical compositions of this invention. Suitable biodegradable microspheres are disclosed, for example, in U.S. Patent Nos. 4,897,268 and 5,075,109.
Such compositions may also comprise buffers (e.g., neutral buffered saline or phosphate buffered saline), carbohydrates (e.g., glucose, mannose, sucrose or dextrans), mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, chelating agents such as EDTA or glutathione, adjuvants (e.g., aluminum hydroxide) and or preservatives. Alternatively, compositions of the present invention may be formulated as a lyophilizate. Compounds may also be encapsulated within liposomes using well known technology. Any of a variety of immunostimulants may be employed in the vaccines of this invention. For example, an adjuvant may be included. Most adjuvants contain a substance designed to protect the antigen from rapid catabolism. such as aluminum hydroxide or mineral oil, and a stimulator of immune responses, such as lipid A, Bortadella pertussis or Mycobacterium tuberculosis derived proteins. Suitable adjuvants are commercially available as, for example, Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, MI); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, NJ); 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 or interleukin-2. -7, or -12, may also be used as adjuvants.
Within the vaccines provided herein, the adjuvant composition is preferably designed to induce an immune response predominantly of the Thl type. High levels of Thl -type cytokines (e.g., IFN-γ, TNFα, IL-2 and IL-12) tend to favor the induction of cell mediated immune responses to an administered antigen. In contrast, high levels of Th2-type cytokines (e.g., IL-4, IL-5, IL-6 and IL-10) tend to favor the induction of humoral immune responses. Following application of a vaccine as provided herein, a patient will support an immune response that includes Thl- and Th2- type responses. Within a preferred embodiment, in which a response is predominantly Thl -type, the level of 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.
Preferred adjuvants for use in eliciting a predominantly Thl -type response include, for example, a combination of monophosphoryl lipid A, preferably 3- de-O-acylated monophosphoryl lipid A (3D-MPL), together with an aluminum salt. MPL adjuvants are available from Ribi ImmunoChem Research Inc. (Hamilton, MT) (see 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 unmethylated) also induce a predominantly Thl response. Such oligonucleotides are well known and are described, for example, in WO 96/02555. Another preferred adjuvant is a saponin, preferably QS21, which may be used alone or in combination with other adjuvants. For example, an enhanced system involves the combination of a monophosphoryl lipid A and saponin derivative, such as the combination of QS21 and 3D-MPL as described in WO 94/00153, or a less reactogenic composition where the QS21 is quenched with cholesterol, as described in WO 96/33739. Other preferred formulations comprises an oil-in- water emulsion and tocopherol. A particularly potent adjuvant formulation involving QS21, 3D-MPL and tocopherol in an oil-in- water emulsion is described in WO 95/17210. Any vaccine provided herein may be prepared using well known methods that result in a combination of antigen, immune response enhancer and a suitable carrier or excipient.
The compositions described herein may be administered as part of a sustained release formulation (i.e., a formulation such as a capsule, sponge or gel (composed of polysaccharides, for example) that effects a slow release of compound following administration). Such formulations may generally be prepared using well known technology and administered by, for example, oral, rectal or subcutaneous implantation, or by implantation at the desired target site. Sustained-release formulations may contain a polypeptide. polynucleotide or antibody dispersed in a carrier matrix and or contained within a reservoir surrounded by a rate controlling membrane. Carriers for use within such formulations are biocompatible, and may also be biodegradable; preferably the formulation provides a relatively constant level of active component release. The amount of active compound contained within a sustained release formulation depends upon the site of implantation, the rate and expected duration of release and the nature ofthe condition to be treated or prevented.
Any of a variety of delivery vehicles may be employed within pharmaceutical compositions and vaccines to facilitate production of an antigen-specific immune response that targets tumor cells. Delivery vehicles include antigen presenting cells (APCs), such as dendritic cells, macrophages, B cells, monocytes and other cells that may be engineered to be efficient APCs. 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 ?er 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. 50:507-529, 1999). In general, 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. As an alternative to dendritic cells, secreted vesicles antigen-loaded dendritic cells (called exosomes) may be used within a vaccine (see Zitvogel et al.. Nature Med. - :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. For example, dendritic cells may be differentiated ex vivo by adding a combination of cytokines such as GM-CSF, IL-4, IL-13 and/or TNFα to cultures of monocytes harvested from peripheral blood. Alternatively, 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, TNFα, CD40 ligand, LPS, flt3 ligand and/or other compound(s) that induce 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 pheno types. 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 Fcγ receptor, mannose receptor and DEC-205 marker. The mature phenotype is typically characterized by a lower expression of these markers, but a high expression of cell surface molecules responsible for T cell activation such as class I and class II MHC, adhesion molecules (e.g., CD54 and CD11) and costimulatory molecules (e.g., CD40, CD80, CD86 and 4-1BB).
APCs may generally be transfected with a polynucleotide encoding a lung tumor protein (or portion or other variant thereof) such that the lung tumor polypeptide, or an immunogenic portion thereof, is expressed on the cell surface. Such transfection may take place ex vivo, and a composition or vaccine comprising such transfected cells may then be used for therapeutic puφoses, 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, for example, 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 lung tumor polypeptide, DNA (naked or within a plasmid vector) or RNA; or with antigen-expressing recombinant bacterium or viruses (e.g., vaccinia, fowlpox, adenovirus or lentivirus vectors). Prior to loading, the polypeptide may be covalently conjugated to an immunological partner that provides T cell help (e.g., a carrier molecule). Alternatively, a dendritic cell may be pulsed with a non-conjugated immunological partner, separately or in the presence of the polypeptide.
CANCER THERAPY
In further aspects of the present invention, the compositions described herein may be used for immunotherapy of cancer, such as lung cancer. Within such methods, pharmaceutical compositions and vaccines are typically administered to a patient. As used herein, a "patient" refers to any warm-blooded animal, preferably a human. A patient may or may not be afflicted with cancer. Accordingly, the above pharmaceutical compositions and vaccines may be used to prevent the development of a cancer or to treat a patient afflicted with a cancer. A cancer may be diagnosed using criteria generally accepted in the art, including the presence of a malignant tumor. 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 drugs.
Within certain embodiments, 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 admimstration of immune response-modifying agents (such as polypeptides and polynucleotides disclosed herein).
Within other embodiments, 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. Examples of 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. As noted above, 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. In particular, antigen-presenting cells, such as dendritic, macrophage, monocyte, fibroblast or B cells, may be pulsed with immunoreactive polypeptides or transfected with one or more polynucleotides using standard techniques well known in the art. For example, 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. Studies have shown that cultured effector cells can be induced to grow in vivo and to survive long term in substantial numbers by repeated stimulation with antigen supplemented with IL-2 (see, for example. Cheever et al.. Immunological Reviews 157:111, 1997).
Alternatively, 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.
Routes and frequency of administration of the therapeutic compositions disclosed herein, as well as dosage, will vary from individual to individual, and may be readily established using standard techniques. In general, the pharmaceutical compositions and vaccines may be administered by injection (e.g., intracutaneous, intramuscular, intravenous or subcutaneous), intranasally (e.g., by aspiration) or orally. Preferably, between 1 and 10 doses may be administered over a 52 week period. Preferably, 6 doses are administered, at intervals of 1 month, and booster vaccinations may be given periodically thereafter. Alternate protocols may be appropriate for individual patients. A suitable dose is an amount of a compound that, when administered as described above, is capable of promoting an anti-tumor immune response, 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. In general, for pharmaceutical compositions and vaccines comprising one or more polypeptides, the amount of each polypeptide present in a dose ranges from about 25 μg to 5 mg per kg of host. Suitable dose sizes will vary with the size ofthe patient, but will typically range from about 0.1 mL to about 5 mL.
In general, an appropriate dosage and treatment regimen provides the active compound(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit. Such a response can be monitored by establishing an improved clinical outcome (e.g., more frequent 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 lung 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. METHODS FOR DETECTING CANCER
In general, a cancer may be detected in a patient based on the presence of one or more lung tumor proteins and/or polynucleotides encoding such proteins in a biological sample (for example, blood, sera, urine and/or tumor biopsies) obtained from the patient. In other words, such proteins may be used as markers to indicate the presence or absence of a cancer such as lung cancer. In addition, such 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. In general, a lung tumor sequence should be present at a level that is at least three fold higher in tumor tissue than in normal tissue
There are a variety of assay formats known to those of ordinary skill in the art for using a binding agent to detect polypeptide markers in a sample. See, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988. In general, 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. In a preferred embodiment, 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. Such 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. Alternatively, 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 lung tumor proteins and 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. For example, the solid support may be a test well in a microtiter plate or a nitrocellulose or other suitable membrane. Alternatively, the support may be a bead or disc, such as glass, fiberglass, latex or a plastic material such as polystyrene or polyvinylchloride. The support may also be a magnetic particle or a fiber optic sensor, such as those disclosed, for example, in U.S. Patent No. 5,359,681. The 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. In the context of the present invention, the term "immobilization" refers to both noncovalent association, such as adsoφtion, 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 adsoφtion to a well in a microtiter plate or to a membrane is preferred. In such cases, adsoφtion 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. In general, contacting a well of a plastic microtiter plate (such as polystyrene or polyvinylchloride) with an amount of binding agent ranging from about 10 ng to about 10 μg, and preferably about 100 ng to about 1 μg, is sufficient to immobilize an adequate amount of binding agent.
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. For example, 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).
In certain embodiments, 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. The amount of detection reagent that remains bound to the solid support is then determined using a method appropriate for the specific reporter group.
More specifically, once the antibody is immobilized on the support as described above, the remaining protein binding sites on the support are typically blocked. Any suitable blocking agent known to those of ordinary skill in the art, such as bovine serum albumin or Tween 20™ (Sigma Chemical Co., St. Louis, MO). 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. In general, an appropriate contact time (i.e., incubation time) is a period of time that is sufficient to detect the presence of polypeptide within a sample obtained from an individual with lung cancer. Preferably, the contact time is sufficient to achieve a level of binding that is at least about 95%) of that achieved at equilibrium between bound and unbound polypeptide. Those of ordinary skill in the art will recognize that the time necessary to achieve equilibrium may be readily determined by assaying the level of binding that occurs over a period of time. At room temperature, an incubation time of about 30 minutes is generally sufficient.
Unbound sample may then be removed by washing the solid support with an appropriate buffer, such as PBS containing 0.1% Tween 20™. 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. To determine the presence or absence of a cancer, such as lung cancer, 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. In one preferred embodiment, 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. In general, a sample generating a signal that is three standard deviations above the predetermined cut-off value is considered positive for the cancer. In an alternate preferred embodiment, 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. Briefly, in this embodiment, 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 corner (i.e., the value that encloses the largest area) is the most accurate cut-off value, and a sample generating a signal that is higher than the cut-off value determined by this method may be considered positive. Alternatively, 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. In general, a sample generating a signal that is higher than the cut-off value determined by this method is considered positive for a cancer. In a related embodiment, the assay is performed in a flow-through or strip test format, wherein the binding agent is immobilized on a membrane, such as nitrocellulose. In the flow-through test, 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. In 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. Typically, the 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. In general, 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. Preferably, the amount of antibody immobilized on the membrane ranges from about 25 ng to about lμg, 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.
Of course, numerous other assay protocols exist that are suitable for use with the tumor proteins or binding agents of the present invention. The above descriptions are intended to be exemplary only. For example, it will be apparent to those of ordinary skill in the art that the above protocols may be readily modified to use lung tumor polypeptides to detect antibodies that bind to such polypeptides in a biological sample. The detection of such lung 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 lung tumor protein in a biological sample. Within certain methods, a biological sample comprising CD4+ and/or CD8~ T cells isolated from a patient is incubated with a lung tumor 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. For example, T cells may be isolated from a patient by routine techniques (such as by Ficoll/Hypaque density gradient centrifugation of peripheral blood lymphocytes). T cells may be incubated in vitro for 2-9 days (typically 4 days) at 37°C with polypeptide (e.g., 5 - 25 μg/ml). It may be desirable to incubate another aliquot of a T cell sample in the absence of lung tumor polypeptide to serve as a control. For CD4+ T cells, activation is preferably detected by evaluating proliferation of the T cells. For CD8+ T cells, activation is preferably detected by evaluating cytolytic activity. A level of proliferation that is at least two fold greater and/or a level of cytolytic activity that is at least 20%) greater than in disease-free patients indicates the presence of a cancer in the patient.
As noted above, a cancer may also, or alternatively, be detected based on the level of mRNA encoding a lung tumor protein in a biological sample. For example, at least two oligonucleotide primers may be employed in a polymerase chain reaction (PCR) based assay to amplify a portion of a lung 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 lung tumor protein. The amplified cDNA is then separated and detected using techniques well known in the art, such as gel electrophoresis. Similarly, oligonucleotide probes that specifically hybridize to a polynucleotide encoding a lung tumor protein may be used in a hybridization assay to detect the presence of polynucleotide encoding the tumor protein in a biological sample.
To permit hybridization under assay conditions, oligonucleotide primers and probes should comprise an oligonucleotide sequence that has at least about 60%o, preferably at least about 75% and more preferably at least about 90%, identity to a portion of a polynucleotide encoding a lung tumor protein that is at least 10 nucleotides, and preferably at least 20 nucleotides, in length. Preferably, oligonucleotide primers and/or probes will hybridize to a polynucleotide encoding a polypeptide disclosed 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. In a preferred embodiment, the oligonucleotide primers comprise at least 10 contiguous nucleotides, more preferably at least 15 contiguous nucleotides. of a DNA molecule having a sequence recited in SEQ ID NOS: 1-31, 49-55. 63.64, 66, 68-72, 78-80, 84-92 and 217- 389. 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, 57:263, 1987; Erlich ed.. PCR Technology, Stockton Press, NY, 1989).
One preferred assay employs RT-PCR, in which PCR is applied in conjunction with reverse transcription. Typically, 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.
In another embodiment, the disclosed compositions may be used as markers for the progression of cancer. In this embodiment, 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 evaluated. For example, the assays may be performed every 24-72 hours for a period of 6 months to 1 year, and thereafter performed as needed. In general, a cancer is progressing in those patients in whom the level of polypeptide or polynucleotide detected increases over time. In contrast, 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. Such binding agents may also be used in histological applications. Alternatively, polynucleotide probes may be used within such applications.
As noted above, to improve sensitivity, multiple lung tumor protein markers may be assayed within a given sample. It will be apparent that binding agents specific for different proteins provided herein may be combined within a single assay. Further, multiple primers or probes may be used concurrently. The selection of tumor protein markers may be based on routine experiments to determine combinations that results in optimal sensitivity. In addition, or alternatively, assays for tumor proteins provided herein may be combined with assays for other known tumor antigens.
DIAGNOSTIC KITS
The present invention further provides kits for use within any of the above diagnostic methods. Such kits typically comprise two or more components necessary for performing a diagnostic assay. Components may be compounds, reagents, containers and/or equipment. For example, one container within a kit may contain a monoclonal antibody or fragment thereof that specifically binds to a lung 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.
Alternatively, a kit may be designed to detect the level of mRNA encoding a lung 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 lung 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 lung tumor protein.
The following Examples are offered by way of illustration and not by way of limitation. EXAMPLES
Example 1 PREPARATION OF LUNG TUMOR-SPECIFIC cDNA SEQUENCES USING DIFFERENTIAL DISPLAY RT-PCR
This example illustrates the preparation of cDNA molecules encoding lung tumor-specific polypeptides using a differential display screen.
Tissue samples were prepared from lung tumor and normal tissue of a patient with lung cancer that was confirmed by pathology after removal of samples from the patient. Normal RNA and tumor RNA was extracted from the samples and mRNA was isolated and converted into cDNA using a (dT)12AG (SEQ ID NO: 47) anchored 3' primer. Differential display PCR was then executed using a randomly chosen primer (SEQ ID NO: 48). Amplification conditions were standard buffer containing 1.5 mM MgCl2, 20 pmol of primer, 500 pmol dNTP and 1 unit of Taq DNA polymerase (Perkin-Elmer, Branchburg, NJ). Forty cycles of amplification were performed using 94 °C denaturation for 30 seconds, 42 °C annealing for 1 minute and 72
°C extension for 30 seconds. Bands that were repeatedly observed to be specific to the
RNA fingeφrint pattern ofthe tumor were cut out of a silver stained gel, subcloned into the pGEM-T vector (Promega, Madison, WI) and sequenced. The isolated 3' sequences are provided in SEQ ID NO: 1-16.
Comparison of these sequences to those in the public databases using the
BLASTN program, revealed no significant homologies to the sequences provided in
SEQ ID NO: 1-11. To the best of the inventors' knowledge, none of the isolated DNA sequences have previously been shown to be expressed at a greater level in human lung tumor tissue than in normal lung tissue. Example 2 USE OF PATIENT SERA TO IDENTIFY DNA SEQUENCES ENCODING LUNG
TUMOR ANTIGENS
This example illustrates the isolation of cDNA sequences encoding lung tumor antigens by expression screening of lung tumor samples with autologous patient sera.
A human lung tumor directional cDNA expression library was constructed employing the Lambda ZAP Express expression system (Stratagene, La Jolla. CA). Total RNA for the library was taken from a late SCID mouse passaged human squamous epithelial lung carcinoma and poly A+ RNA was isolated using the Message Maker kit (Gibco BRL, Gaithersburg, MD). The resulting library was screened using E. cø/z-absorbed autologous patient serum, as described in Sambrook et al., (Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, Cold Spring Harbor, NY, 1989), with the secondary antibody being goat anti-human IgG-A- M (H + L) conjugated with alkaline phosphatase, developed with NBT/BCIP (Gibco BRL). Positive plaques expressing immunoreactive antigens were purified. Phagemid from the plaques was rescued and the nucleotide sequences of the clones was determined.
Fifteen clones were isolated, referred to hereinafter as LT86-1 - LT86- 15. The isolated cDNA sequences for LT86-1 - LT86-8 and LT86-10 - LT86-15 are provided in SEQ ID NO: 17-24 and 26-31, respectively, with the corresponding predicted amino acid sequences being provided in SEQ ID NO: 32-39 and 41-46, respectively. The determined cDNA sequence for LT86-9 is provided in SEQ ID NO: 25, with the corresponding predicted amino acid sequences from the 3' and 5' ends being provided in SEQ ID NO: 40 and 65, respectively. These sequences were compared to those in the gene bank as described above. Clones LT86-3, LT86-6 - LT86-9. LT86-11 - LT86-13 and LT86-15 (SEQ ID NO: 19, 22-25, 27-29 and 31, respectively) were found to show some homology to previously identified expressed sequence tags (ESTs), with clones LT86-6, LT86-8, LT86-11, LT86-12 and LT86-15 appearing to be similar or identical to each other. Clone LT86-3 was found to show some homology with a human transcription repressor. Clones LT86-6, 8, 9, 11, 12 and 15 were found to show some homology to a yeast RNA Pol II transcription regulation mediator. Clone LT86-13 was found to show some homology with a C. elegans leucine aminopeptidase. Clone LT86-9 appears to contain two inserts, with the 5' sequence showing homology to the previously identified antisense sequence of interferon alpha- induced P27, and the 3' sequence being similar to LT86-6. Clone LT86-14 (SEQ ID NO: 30) was found to show some homology to the trithorax gene and has an "RGD" cell attachment sequence and a beta-Lactamase A site which functions in hydrolysis of penicillin. Clones LT86-1 , LT86-2, LT86-4. LT86-5 and LT86-10 (SEQ ID NOS: 17, 18, 20, 21 and 26. respectively) were found to show homology to previously identified genes. A subsequently determined extended cDNA sequence for LT86-4 is provided in SEQ ID NO: 66. with the corresponding predicted amino acid sequence being provided in SEQ ID NO: 67. Subsequent studies led to the isolation of five additional clones, referred to as LT86-20, LT86-21, LT86-22, LT86-26 and LT86-27. The determined 5' cDNA sequences for LT86-20, LT86-22, LT86-26 and LT86-27 are provided in SEQ ID NO: 68 and 70-72, respectively, with the determined 3' cDNA sequences for LT86-21 being provided in SEQ ID NO: 69. The corresponding predicted amino acid sequences for LT86-20, LT86-21. LT86-22, LT86-26 and LT86-27 are provided in SEQ ID NO: 73- 77, respectively. LT86-22 and LT86-27 were found to be highly similar to each other. Comparison of these sequences to those in the gene bank as described above, revealed no significant homologies to LT86-22 and LT86-27. LT86-20, LT86-21 and LT86-26 were found to show homology to previously identified genes. In further studies, a cDNA expression library was prepared using mRNA from a lung small cell carcinoma cell line in the lambda ZAP Express expression vector (Stratagene), and screened as described above, with a pool of two lung small cell carcinoma patient sera. The sera pool was adsorbed with E. coli lysate and human PBMC lysate was added to the serum to block antibody to proteins found in normal tissue. Seventy-three clones were isolated. The determined cDNA sequences of these clones are provided in SEQ ID NO: 290-362. The sequences of SEQ ID NO: 289-292. 294. 296-297, 300, 302, 303. 305. 307-315, 317-320, 322-325. 327-332, 334, 335, 338- 341, 343-352, 354-358, 360 and 362 were found to show some homology to previously isolated genes. The sequences of SEQ ID NO: 293, 295, 298. 299, 301, 304. 306, 316, 321, 326, 333. 336. 337, 342, 353, 359 and 361 were found to show some homology to previously identified ESTs.
Example 3 USE OF MOUSE ANTISERA TO IDENTIFY DNA SEQUENCES ENCODING
LUNG TUMOR ANTIGENS
This example illustrates the isolation of cDNA sequences encoding lung tumor antigens by screening of lung tumor cDNA libraries with mouse anti-tumor sera.
A directional cDNA lung tumor expression library was prepared as described above in Example 2. Sera was obtained from SCID mice containing late passaged human squamous cell and adenocarcinoma tumors. These sera were pooled and injected into normal mice to produce anti-lung tumor serum. Approximately 200,000 PFUs were screened from the unamplified library using this antiserum. Using a goat anti-mouse IgG-A-M (H+L) alkaline phosphatase second antibody developed with NBT/BCIP (BRL Labs.), approximately 40 positive plaques were identified. Phage was purified and phagemid excised for 9 clones with inserts in a pBK-CMV vector for expression in prokaryotic or eukaryotic cells. The determined cDNA sequences for 7 ofthe isolated clones (hereinafter referred to as L86S-3, L86S-12, L86S-16, L86S-25, L86S-36, L86S-40 and L86S-46) are provided in SEQ ID NO: 49-55, with the corresponding predicted amino acid sequences being provided in SEQ ID NO: 56-62, respectively. The 5' cDNA sequences for the remaining 2 clones (hereinafter referred to as L86S-30 and L86S-41) are provided in SEQ ID NO: 63 and 64. L86S-36 and L86S-46 were subsequently determined to represent the same gene. Comparison of these sequences with those in the public database as described above, revealed no significant homologies to clones L86S-30, L86S-36 and L86S-46 (SEQ ID NO: 63, 53 and 55, respectively). L86S-16 (SEQ ID NO: 51) was found to show some homology to an EST previously identified in fetal lung and germ cell tumor. The remaining clones were found to show at least some degree of homology to previously identified human genes. Subsequently determined extended cDNA sequences for L86S-12, L86S-36 and L86S-46 are provided in SEQ ID NO: 78-80, respectively, with the corresponding predicted amino acid sequences being provided in SEQ ID NO: 81-83. Subsequent studies led to the determination of 5" cDNA sequences for an additional nine clones, referred to as L86S-6. L86S-11, L86S-14, L86S-29. L86S-34, L86S-39. L86S-47, L86S-49 and L86S-51 (SEQ ID NO: 84-92, respectively). The corresponding predicted amino acid sequences are provided in SEQ ID NO: 93-101, respectively. L86S-30, L86S-39 and L86S-47 were found to be similar to each other. Comparison of these sequences with those in the gene bank as described above, revealed no significant homologies to L86S-14. L86S-29 was found to show some homology to a previously identified EST. L86S-6. L86S-11, L86S-34, L86S-39, L86S- 47, L86S-49 and L86S-51 were found to show some homology to previously identified genes.
In further studies, a directional cDNA library was constructed using a Stratagene kit with a Lambda Zap Express vector. Total RNA for the library was isolated from two primary squamous lung tumors and poly A+ RNA was isolated using an oligo dT column. Antiserum was developed in normal mice using a pool of sera from three SCID mice implanted with human squamous lung carcinomas. Approximately 700,000 PFUs were screened from the unamplified library with E. coli absorbed mouse anti-SCID tumor serum. Positive plaques were identified as described above. Phage was purified and phagemid excised for 180 clones with inserts in a pBK- CMV vector for expression in prokaryotic or eukaryotic cells.
The determined cDNA sequences for 23 of the isolated clones are provided in SEQ ID NO: 126-148. Comparison of these sequences with those in the public database as described above revealed no significant homologies to the sequences of SEQ ID NO: 139 and 143-148. The sequences of SEQ ID NO: 126-138 and 140-142 were found to show homology to previously identified human polynucleotide sequences.
Example 4
USE OF MOUSE ANTISERA TO SCREEN LUNG TUMOR LIBRARIES
PREPARED FROM SCID MICE
This example illustrates the isolation of cDNA sequences encoding lung tumor antigens by screening of lung tumor cDNA libraries prepared from SCID mice with mouse anti-tumor sera.
A directional cDNA lung tumor expression library was prepared using a Stratagene kit with a Lambda Zap Express vector. Total RNA for the library was taken from a late passaged lung adenocarcinoma grown in SCID mice. Poly A+ RNA was isolated using a Message Maker Kit (Gibco BRL). Sera was obtained from two SCID mice implanted with lung adenocarcinomas. These sera were pooled and injected into normal mice to produce anti-lung tumor serum. Approximately 700,000 PFUs were screened from the unamplified library with E. cø//-absorbed mouse anti-SCID tumor serum. Positive plaques were identified with a goat anti-mouse IgG-A-M (H+L) alkaline phosphatase second antibody developed with NBT/BCIP (Gibco BRL). Phage was purified and phagemid excised for 100 clones with insert in a pBK-CMV vector for expression in prokaryotic or eukaryotic cells.
The determined 5' cDNA sequences for 33 of the isolated clones are provided in SEQ ID NO: 149-181. The corresponding predicted amino acid sequences for SEQ ID NO: 149, 150, 152-154, 156-158 and 160-181 are provided in SEQ ID NO: 182, 183, 186, 188-193 and 194-215, respectively. The clone of SEQ ID NO: 151 (referred to as SAL-25) was found to contain two open reading frames (ORFs). The predicted amino acid sequences encoded by these ORFs are provided in SEQ ID NO: 184 and 185. The clone of SEQ ID NO: 153 (referred to as SAL-50) was found to contain two open reading frames encoding the predicted amino acid sequences of SEQ ID NO: 187 and 216. Similarly, the clone of SEQ ID NO: 155 (referred to as SAL-66) was found to contain two open reading frames encoding the predicted amino acid sequences of SEQ ID NO: 189 and 190. Comparison of the isolated sequences with those in the public database revealed no significant homologies to the sequences of SEQ ID NO: 151, 153 and 154. The sequences of SEQ ID NO: 149, 152, 156, 157 and 158 were found to show some homology to previously isolated expressed sequence tags (ESTs). The sequences of SEQ ID NO: 150, 155 and 159-181 were found to show homology to sequences previously identified in humans.
Using the procedures described above, two directional cDNA libraries (referred to as LT46-90 and LT86-21) were prepared from two late passaged lung squamous carcinomas grown in SCID mice and screened with sera obtained from SCID mice implanted with human squamous lung carcinomas. The determined cDNA sequences for the isolated clones are provided in SEQ ID NO: 217-237 and 286-289. SEQ ID NO: 286 was found to be a longer sequence of LT4690-71 (SEQ ID NO: 237). Comparison of these sequences with those in the public databases revealed no known homologies to the sequences of SEQ ID NO: 219, 220. 225, 226, 287 and 288. The sequences of SEQ ID NO: 218. 221, 222 and 224 were found to show some homology to previously identified sequences of unknown function. The sequence of SEQ ID NO: 236 was found to show homology to a known mouse mRNA sequence. The sequences of SEQ ID NO: 217, 223, 227-237, 286 and 289 showed some homology to known human DNA and/or RNA sequences.
In further studies using the techniques described above, one ofthe cDNA libraries described above (LT86-21) was screened with E. cø/z-absorbed mouse anti- SCID tumor serum. This serum was obtained from normal mice immunized with a pool of 3 sera taken from SCID mice implanted with human squamous lung carcinomas. The determined cDNA sequences for the isolated clones are provided in SEQ ID NO: 238-285. Comparison of these sequences with those in the public databases revealed no significant homologies to the sequences of SEQ ID NO: 253, 260, 277 and 285. The sequences of SEQ ID NO: 249, 250, 256, 266, 276 and 282 were found to show some homology to previously isolated expressed sequence tags (ESTs). The sequences of SEQ ID NO: 238-248, 251, 252, 254, 255. 257-259, 261-263, 265, 267-275, 278-281, 283 and 284 were found to show some homology to previously identified DNA or RNA sequences. Example 5 DETERMINATION OF TISSUE SPECIFICITY OF LUNG TUMOR
POLYPEPTIDES
Using gene specific primers, mRNA expression levels for representative lung tumor polypeptides were examined in a variety of normal and tumor tissues using RT-PCR.
Briefly, total RNA was extracted from a variety of normal and tumor tissues using Trizol reagent. First strand synthesis was carried out using 2 μg of total RNA with Superscript II reverse transcriptase (BRL Life Technologies) at 42 °C for one hour. The cDNA was then amplified by PCR with gene-specific primers. To ensure the semi-quantitative nature of the RT-PCR, β-actin was used as an internal control for each of the tissues examined. 1 μl of 1 :30 dilution of cDNA was employed to enable the linear range amplification of the β-actin template and was sensitive enough to reflect the differences in the initial copy numbers. Using these conditions, the β-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 five different types of tumor tissue (lung squamous tumor from 3 patients, lung adenocarcinoma, prostate tumor, colon tumor and lung tumor), and different normal tissues, including lung from four patients, prostate, brain, kidney, liver, ovary, skeletal muscle, skin, small intestine, myocardium, retina and testes. L86S-46 was found to be expressed at high levels in lung squamous tumor, colon tumor and prostate tumor, and was undetectable in the other tissues examined. L86S-5 was found to be expressed in the lung tumor samples and in 2 out of 4 normal lung samples, but not in the other normal or tumor tissues tested. L86S-16 was found to be expressed in all tissues except normal liver and normal stomach. Using real-time PCR, L86S-46 was found to be over-expressed in lung squamous tissue and normal tonsil, with expression being low or undetectable in all other tissues examined. Example 6 ISOLATION OF DNA SEQUENCES ENCODING LUNG TUMOR ANTIGENS
DNA sequences encoding antigens potentially involved in squamous cell lung tumor formation were isolated as follows.
A lung tumor directional cDNA expression library was constructed employing the Lambda ZAP Express expression system (Stratagene, La Jolla, CA). Total RNA for the library was taken from a pool of two human squamous epithelial lung carcinomas and poly A+ RNA was isolated using oligo-dT cellulose (Gibco BRL, Gaithersburg, MD). Phagemid were rescued at random and the cDNA sequences of isolated clones were determined.
The determined cDNA sequence for the clone SLT-Tl is provided in SEQ ID NO: 102, with the determined 5' cDNA sequences for the clones SLT-T2, SLT-T3, SLT-T5, SLT-T7, SLT-T9, SLT-T10, SLT-Tl 1 and SLT-T12 being provided in SEQ ID NO: 103-1 10, respectively. The corresponding predicted amino acid sequence for SLT-Tl, SLT-T2, SLT-T3, SLT-T10 and SLT-T12 are provided in SEQ ID NO: 111-115, respectively. Comparison of the sequences for SLT-T2, SLT-T3, SLT-T5, SLT-T7, SLT-T9 and SLT-Tl 1 with those in the public databases as described above, revealed no significant homologies. The sequences for SLT-Tl 0 and SLT-T12 were found to show some homology to sequences previously identified in humans.
The sequence of SLT-Tl was determined to show some homology to a PAC clone of unknown protein function. The cDNA sequence of SLT-Tl (SEQ ID NO: 102) was found to contain a mutator (MUTT) domain. Such domains are known to function in removal of damaged guanine from DNA that can cause A to G transversions (see, for example, el-Deiry, W.S., 1997 Curr. Opin. Oncol. 9:79-87; Okamoto, K. et al. 1996 Int. J. Cancer 65:437-41; Wu, C. et al. 1995 Biochem. Biophys. Res. Commun. 214:1239-45; Porter, D.W. et al. 1996 Chem. Res. Toxicol 9:1375-81). SLT-Tl may thus be of use in the treatment, by gene therapy, of lung cancers caused by, or associated with, a disruption in DNA repair. In further studies, DNA sequences encoding antigens potentially involved in adenocarcinoma lung tumor formation were isolated as follows. A human lung tumor directional cDNA expression library was constructed employing the Lambda ZAP Express expression system (Stratagene. La Jolla. CA). Total RNA for the library was taken from a late SCID mouse passaged human adenocarcinoma and poly A+ RNA was isolated using the Message Maker kit (Gibco BRL, Gaithersburg, MD). Phagemid were rescued at random and the cDNA sequences of isolated clones were determined.
The determined 5' cDNA sequences for five isolated clones (referred to as SALT-T3, SALT-T4, SALT-T7, SALT-T8, and SALT-T9) are provided in SEQ ID NO: 116-120, with the corresponding predicted amino acid sequences being provided in SEQ ID NO: 121-125. SALT-T3 was found to show 98% identity to the previously identified human transducin-like enhancer protein TLE2. SALT-T4 appears to be the human homologue of the mouse H beta 58 gene. SALT-T7 was found to have 97% identity to human 3-mercaptopyruvate sulfurtransferase and SALT-T8 was found to show homology to human interferon-inducible protein 1-8U. SALT-T9 shows approximately 90%) identity to human mucin MUC 5B. cDNA sequences encoding antigens potentially involved in small cell lung carcinoma development were isolated as follows. cDNA expression libraries were constructed with mRNA from the small cell lung carcinoma cell lines NCIH69, NCIH128 and DMS79 (all available from the American Type Culture Collection, Manassas, VA) employing the Lambda ZAP Express expression system (Stratagene. La Jolla, CA). Phagemid were rescued at random and the cDNA sequences of 27 isolated clones were determined. Comparison of the determined cDNA sequences revealed no significant homologies to the sequences of SEQ ID NO: 372 and 373. The sequences of SEQ ID NO: 364, 369, 377, 379 and 386 showed some homology to previously isolated ESTs. The sequences ofthe remaining 20 clones showed some homology to previously identified genes. The cDNA sequences of these clones are provided in SEQ ID NO: 363, 365-368, 370, 371, 374-376, 378. 380-385 and 387-389, wherein SEQ ID NO: 363, 366-368, 370, 375. 376, 378, 380-382, 384 and 385 are full-length sequences. Example 7 SYNTHESIS OF POLYPEPTIDES
Polypeptides may be synthesized on a Perkin Elmer/Applied Biosystems Division 430A peptide synthesizer using FMOC chemistry with HPTU (O- Benzotriazole-N,N,N',N' -tetramethyluronium hexafluorophosphate) activation. 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). After cleaving for 2 hours, 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. A gradient of 0%>-60%> acetonitrile (containing 0.1% TFA) in water (containing 0.1% TFA) may be used to elute the peptides. Following lyophilization of the pure fractions, the peptides may be characterized using electrospray or other types of mass spectrometry and by amino acid analysis.
Example 8 ISOLATION AND CHARACTERIZATION OF DNA SEQUENCES ENCODING
LUNG TUMOR ANTIGENS BY T-CELL EXPRESSION CLONING
Lung tumor antigens may also be identified by T cell expression cloning. One source of tumor specific T cells is from surgically excised tumors from human patients.
A non-small cell lung carcinoma was minced and enzymatically digested for several hours to release tumor cells and infiltrating lymphocytes (tumor infiltrating T cells, or TILs). The cells were washed in HBSS buffer and passed over a Ficoll (100%/75%)/HBSS) discontinuous gradient to separate tumor cells and lymphocytes from non-viable cells. Two bands were harvested from the interfaces; the upper band at the 75%/HBSS interface contained predominantly tumor cells, while the lower band at the 100%o/75%)/HBSS interface contained a majority of lymphocytes. The TILs were expanded in culture, either in 24-well plates with culture media supplemented with 10 ng/ml IL-7 and 100 U/ml IL-2, or alternatively, 24-well plates that have been pre-coated with the anti-CD3 monoclonal antibody OKT3. The resulting TIL cultures were analyzed by FACS to confirm that a high percentage were CD8+ T cells (>90%> of gated population) with only a small percentage of CD4+ cells.
In addition, non-small cell lung carcinoma cells were expanded in culture using standard techniques to establish a tumor cell line, which was later confirmed to be a lung carcinoma cell line by immunohistochemical analysis. This tumor cell line was transduced with a retroviral vector to express human CD80, and characterized by FACS analysis to confirm high expression levels of CD80, and class I and II MHC molecules.
The specificity of the TIL lines to lung tumor was confirmed by INF-γ and/or TNF-α cytokine release assays. TIL cells from day 21 cultures were co-cultured with either autologous or allogeneic tumor cells, EBV-immortalized LCL, or control cell lines Daudi and K562, and the culture supernatant monitored by ELISA for the presence of cytokines. The TIL specifically recognized autologous tumor but not allogeneic tumor. In addition, there was no recognition of EBV-immortalized LCL or the control cell lines, indicating that the TIL lines are tumor specific and are potentially recognizing a tumor antigen presented by autologous MHC molecules.
The characterized tumor-specific TIL lines were expanded to suitable numbers for T cell expression cloning using soluble anti-CD3 antibody in culture with irradiated EBV transformed LCLs and PBL feeder cells in the presence of 20 U/ml IL- 2. Clones from the expanded TIL lines were generated by standard limiting dilution techniques. Specifically, TIL cells were seeded at 0.5 cells/well in a 96-well U bottom plate and stimulated with CD-80-transduced autologous tumor cells, EBV transformed LCL. and PBL feeder cells in the presence of 50 U/ml IL-2. These clones were further analyzed for tumor specificity by 51Cr microcytotoxicity and IFN-γ bioassays. The MHC restriction element recognized by the TIL clones may be determined by antibody blocking studies.
CTL lines or clones prepared as described above may be employed to identify tumor specific antigens. For example, autologous fibroblasts or LCL from a patient may be transfected or transduced with polynucleotide fragments derived from a lung tumor cDNA library to generate target cells expressing tumor polypeptides. The target cells expressing tumor polypeptides in the context of MHC will be recognized by the CTL line or clone, resulting in T-cell activation which can be monitored by cytokine detection assays. The tumor gene being expressed by the target cell and recognized by the tumor-specific CTL may then be isolated.
From the foregoing, it will be appreciated that, although specific embodiments of the invention have been described herein for the puφoses of illustration, various modifications may be made without deviating from the spirit and scope ofthe invention.

Claims

Claims 1. An isolated polypeptide, comprising at least an immunogenic portion of a lung tumor protein, or a variant thereof, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence selected from the group consisting of:
(a) sequences recited in SEQ ID NOs: 2, 8, 15, 16, 22, 24, 30. 32-34, 36, 38, 40, 41. 46-49, 52, 54, 59, 60, 65-69. 79, 89, 90, 93, 99-101, 109- 111, 116-119, 123-132, 138-142, 143, 148, 149, 156, 168, 170-182, 184, 189, 191-193, 196, 205, 207, 210-212, 214, 215, 218. 224-226, 228, 233, 234, 236, 238, 241, 242, 245, 246, 248, 250, 253. 254, 256,
259, 260, 262. 263. 266, 267, 270-273, 279, 282. 291, 293. 294, 298, 300, 302, 303, 310-313, 315, 317, 320, 322, 324. 332-335, 345, 347, 356, 358, 361, 362. 366, 369, 371-378, 380-404, 406, 409-417, 419- 423, 425, 427-429, 433-436, 438-441, 443, 446-451, 454. 455, 457- 461, 476. 477, 479, 483, 488, 491, 492, 497, 498, 500, 510, 519, 527,
528, 543, 545, 547, 553, 556, 559, 561, 564, 565, 568, 569, 574-577, 579, 580, 584, 585, 587, 592, 595, 598, 603, 608, 610, 613, 621-623, 626, 642, 648 and 668;
(b) sequences that hybridize to a sequence recited in any one of SEQ ID NOs:_ 2. 8, 15, 16. 22, 24, 30, 32-34, 36, 38, 40, 41, 46-49, 52, 54,
59, 60, 65-69, 79, 89, 90, 93, 99-101, 109-111, 116-119, 123-132, 138-142, 143, 148, 149, 156, 168, 170-182, 184, 189, 191-193, 196, 205, 207, 210-212, 214, 215, 218, 224-226, 228, 233, 234. 236, 238, 241, 242, 245, 246, 248, 250, 253, 254, 256, 259, 260. 262. 263, 266, 267, 270-273, 279, 282, 291, 293, 294, 298, 300, 302, 303, 310-313,
315, 317, 320, 322. 324, 332-335, 345, 347, 356, 358, 361, 362, 366, 369, 371-378, 380-404. 406, 409-417, 419-423, 425, 427-429, 433- 436, 438-441. 443, 446-451, 454, 455. 457-461, 476, 477. 479, 483, 488, 491. 492. 497, 498, 500, 510, 519. 527, 528. 543, 545. 547, 553, 556, 559, 561, 564, 565. 568, 569, 574-577, 579. 580, 584. 585, 587,
592, 595. 598. 603. 608, 610, 613, 621-623. 626. 642. 648 and 668 under moderately stringent conditions; and (c) complements of sequences of (a) or (b).
2. An isolated polypeptide according to claim 1. wherein the polypeptide comprises an amino acid sequence that is encoded by a polynucleotide sequence recited in any one of SEQ ID NOs: 218-222, 224-226. 249, 250, 253, 256, 266, 276, 277, 282, 285. 293, 295, 298, 299, 301, 304, 306, 316, 321, 326, 333, 336, 337, 342, 353, 359, 361, 364, 369, 372, 373, 377, 379 and 386. or a complement of any ofthe foregoing polynucleotide sequences.
3. An isolated polynucleotide encoding at least 15 amino acid residues of a lung tumor protein, or a variant thereof that differs in one or more substitutions, deletions, additions and/or insertions such that the ability of the variant to react with antigen-specific antisera is not substantially diminished, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide comprising a sequence recited in any one of SEQ ID Nos: 218-222, 224-226, 249, 250, 253, 256, 266, 276, 277, 282, 285, 293, 295, 298, 299, 301, 304, 306, 316, 321, 326, 333, 336, 337, 342, 353, 359, 361, 364, 369, 372, 373, 377, 379 and 386, or a complement of any ofthe foregoing sequences.
4. An isolated polynucleotide encoding a lung tumor protein, or a variant thereof, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide comprising a sequence recited in any one of SEQ ID NOs:_ 218-222, 224-226, 249, 250, 253, 256, 266, 276, 277, 282, 285, 293, 295, 298, 299, 301, 304, 306, 316, 321, 326, 333, 336, 337, 342, 353, 359, 361, 364, 369, 372, 373, 377, 379 and 386, or a complement of any ofthe foregoing sequences.
5. An isolated polynucleotide, comprising a sequence recited in any one of SEQ ID NOs:_ 218-222, 224-226, 249, 250, 253, 256, 266, 276, 277. 282, 285, 293. 295. 298, 299, 301, 304, 306, 316, 321, 326, 333, 336. 337, 342, 353, 359, 361, 364, 369, 372, 373, 377, 379 and 386.
6. An isolated polynucleotide. comprising a sequence that hybridizes to a sequence recited in any one of SEQ ID NOs:_ 218-222. 224-226. 249, 250, 253. 256, 266, 276, 277, 282, 285, 293, 295, 298, 299, 301, 304. 306, 316, 321, 326, 333. 336, 337. 342, 353, 359, 361, 364, 369, 372, 373, 377, 379 and 386 under moderately stringent conditions.
7. An isolated polynucleotide complementary to a polynucleotide according to any one ofclaims 3-6.
8. An expression vector, comprising a polynucleotide according to any one of claims 3-8.
9. A host cell transformed or transfected with an expression vector according to claim 8.
10. An isolated antibody, or antigen-binding fragment thereof, that specifically binds to a lung tumor protein that comprises an amino acid sequence that is encoded by a polynucleotide sequence recited in any one of SEQ ID NOs:_ 218-222, 224-226. 249, 250, 253, 256, 266, 276, 277, 282, 285, 293, 295, 298, 299, 301, 304, 306, 316, 321, 326, 333, 336, 337, 342, 353, 359, 361, 364, 369, 372, 373, 377, 379 and 386, or a complement of any ofthe foregoing polynucleotide sequences.
11. A fusion protein, comprising at least one polypeptide according to claim 1.
12. A fusion protein according to claim 11, wherein the fusion protein comprises an expression enhancer that increases expression ofthe fusion protein in a host cell transfected with a polynucleotide encoding the fusion protein.
13. A fusion protein according to claim 11, wherein the fusion protein comprises a T helper epitope that is not present within the polypeptide of claim 1.
14. A fusion protein according to claim 1 1. wherein the fusion protein comprises an affinity tag.
15. An isolated polynucleotide encoding a fusion protein according to claim 11.
16. A pharmaceutical composition, comprising a physiologically acceptable carrier and at least one component selected from the group consisting of:
(a) a polypeptide according to claim 1 ;
(b) a polynucleotide according to claim 3;
(c) an antibody according to claim 10; (d) a fusion protein according to claim 11 ; and
(e) a polynucleotide according to claim 15.
17. A vaccine comprising an immunostimulant and at least one component selected from the group consisting of: (a) a polypeptide according to claim 1 ;
(b) a polynucleotide according to claim 3;
(c) an antibody according to claim 10;
(d) a fusion protein according to claim 11 ; and
(e) a polynucleotide according to claim 15.
18. A vaccine according to claim 17, wherein the immunostimulant is an adjuvant.
19. A vaccine according to any claim 17, wherein the immunostimulant induces a predominantly Type I response.
20. A method for inhibiting the development of a cancer in a patient, comprising administering to a patient an effective amount of a pharmaceutical composition according to claim 16.
21. A method for inhibiting the development of a cancer in a patient, comprising administering to a patient an effective amount of a vaccine according to claim 17.
22. A pharmaceutical composition comprising an antigen-presenting cell that expresses a polypeptide according to claim 1, in combination with a pharmaceutically acceptable carrier or excipient.
23. A pharmaceutical composition according to claim 22, wherein the antigen presenting cell is a dendritic cell or a macrophage.
24. A vaccine comprising an antigen-presenting cell that expresses a polypeptide comprising at least an immunogenic portion of a lung tumor protein, or a variant thereof, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence selected from the group consisting of: (a) sequences recited in SEQ ID NOs: 217-389;
(b) sequences that hybridize to a sequence recited in any one of SEQ ID NOs: 217-389 under moderately stringent conditions; and
(c) complements of sequences of (i) or (ii); in combination with an immunostimulant.
25. A vaccine according to claim 24, wherein the immunostimulant is an adjuvant.
26. A vaccine according to claim 24, wherein the immunostimulant induces a predominantly Type I response.
27. A vaccine according to claim 24, wherein the antigen-presenting cell is a dendritic cell.
28. A method for inhibiting the development of a cancer in a patient, comprising administering to a patient an effective amount of an antigen-presenting cell that expresses a polypeptide comprising at least an immunogenic portion of a lung tumor protein, or a variant thereof, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence selected from the group consisting of: (a) sequences recited in SEQ ID NOs: 217-389;
(b) sequences that hybridize to a sequence recited in any one of SEQ ID NOs: 217-389 under moderately stringent conditions; and
(c) complements of sequences of (i) or (ii)encoded by a polynucleotide recited in any one of SEQ ID NOs: 217-389; and thereby inhibiting the development of a cancer in the patient.
29. A method according to claim 28, wherein the antigen-presenting cell is a dendritic cell.
30. A method according to any one of claims 20, 21 and 28. wherein the cancer is lung cancer.
31. A method for removing tumor cells from a biological sample, comprising contacting a biological sample with T cells that specifically react with a lung tumor protein, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence selected from the group consisting of:
(i) polynucleotides recited in any one of SEQ ID NOs: 217- 389; and
(ii) complements ofthe foregoing polynucleotides; wherein the step of contacting is performed under conditions and for a time sufficient to permit the removal of cells expressing the antigen from the sample.
32. A method according to claim 31 , wherein the biological sample is blood or a fraction thereof.
33. A method for inhibiting the development of a cancer in a patient, comprising administering to a patient a biological sample treated according to the method of claim 31.
34. A method for stimulating and/or expanding T cells specific for a lung tumor protein, comprising contacting T cells with at least one component selected from the group consisting of:
(a) polypeptides comprising at least an immunogenic portion of a lung tumor protein, or a variant thereof, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence selected from the group consisting of:
(i) sequences recited in SEQ ID NOs: 217-389; (ii) sequences that hybridize to a sequence recited in any one of SEQ ID NOs: 217-389 under moderately stringent conditions; and (iii) complements of sequences of (i) or (ii); (b) polynucleotides encoding a polypeptide of (a); and
(c) antigen presenting cells that express a polypeptide of (a); under conditions and for a time sufficient to permit the stimulation and/or expansion of T cells.
35. An isolated T cell population, comprising T cells prepared according to the method of claim 34.
36. A method for inhibiting the development of a cancer in a patient, comprising administering to a patient an effective amount of a T cell population according to claim 35.
37. A method 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 at least one component selected from the group consisting of: (i) polypeptides comprising at least an immunogenic portion of a lung tumor protein, or a variant thereof, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence selected from the group consisting of:
(1) sequences recited in SEQ ID NOs: 217-389; (2) sequences that hybridize to a sequence recited in any one of SEQ ID NOs: 217-389 under moderately stringent conditions; and
(3) complements of sequences of (1) or (2); (ii) polynucleotides encoding a polypeptide of (i); and (iii) antigen presenting cells that expresses a polypeptide of (i); such that T cells proliferate; and
(b) administering to the patient an effective amount of the proliferated T cells, and thereby inhibiting the development of a cancer in the patient.
38. A method 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 at least one component selected from the group consisting of: (i) polypeptides comprising at least an immunogenic portion of a lung tumor protein, or a variant thereof, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence selected from the group consisting of:
(1) sequences recited in SEQ ID NOs: 217-389; (2) sequences that hybridize to a sequence recited in any one of SEQ ID NOs: 217-389 under moderately stringent conditions; and
(3) complements of sequences of (1) or (2); (ii) polynucleotides encoding a polypeptide of (i); and
(iii) antigen presenting cells that express a polypeptide of (i); such that T cells proliferate;
(b) cloning at least one proliferated cell to provide cloned T cells; and
(c) administering to the patient an effective amount of the cloned T cells, and thereby inhibiting the development of a cancer in the patient.
39. A method 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 a binding agent that binds to a lung tumor protein, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence recited in any one of SEQ ID NOs: 217-389 or a complement of any of the foregoing polynucleotide sequences;
(b) detecting in the sample an amount of polypeptide that binds to the binding agent; and
(c) comparing the amount of polypeptide to a predetermined cut-off value, and therefrom determining the presence or absence of a cancer in the patient.
40. A method according to claim 39, wherein the binding agent is an antibody.
41. A method according to claim 42, wherein the antibody is a monoclonal antibody.
42. A method according to claim 39, wherein the cancer is lung cancer.
43. A method for monitoring the progression of a cancer in a patient, comprising 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 lung tumor protein, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence recited in any one of SEQ ID NOs: 217-389 or a complement of any of the foregoing polynucleotide sequences;
(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) to the amount detected in step (b) and therefrom monitoring the progression of the cancer in the patient.
44. A method according to claim 43, wherein the binding agent is an antibody.
45. A method according to claim 44, wherein the antibody is a monoclonal antibody.
46. A method according to claim 43, wherein the cancer is a lung cancer.
47. A method 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 that encodes a lung tumor protein, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence recited in any one of SEQ ID NOs: 217-389 or a complement of any of the foregoing polynucleotide sequences;
(b) detecting in the sample an amount of a polynucleotide that hybridizes to the oligonucleotide; and
(c) comparing the amount of polynucleotide that hybridizes to the oligonucleotide to a predetermined cut-off value, and therefrom determining the presence or absence of a cancer in the patient.
48. A method according to claim 47, wherein the amount of polynucleotide that hybridizes to the oligonucleotide is determined using a polymerase chain reaction.
49. A method according to claim 47, wherein the amount of polynucleotide that hybridizes to the oligonucleotide is determined using a hybridization assay.
50. A method 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 that encodes a lung tumor protein, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence recited in any one of SEQ ID NOs: 217-389 or a complement of any ofthe foregoing polynucleotide sequences;
(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) to the amount detected in step (b) and therefrom monitoring the progression of the cancer in the patient.
51. A method according to claim 50, wherein the amount of polynucleotide that hybridizes to the oligonucleotide is determined using a polymerase chain reaction.
52. A method according to claim 50. wherein the amount of polynucleotide that hybridizes to the oligonucleotide is determined using a hybridization assay.
53. A diagnostic kit, comprising:
(a) one or more antibodies according to claim 10; and (b) a detection reagent comprising a reporter group.
54. A kit according to claim 53, wherein the antibodies are immobilized on a solid support.
55. A kit according to claim 53, wherein the detection reagent comprises an anti-immunoglobulin, protein G, protein A or lectin.
56. A kit according to claim 53, wherein the reporter group is selected from the group consisting of radioisotopes, fluorescent groups, luminescent groups, enzymes, biotin and dye particles.
57. An oligonucleotide comprising 10 to 40 contiguous nucleotides that hybridize under moderately stringent conditions to a polynucleotide that encodes a lung tumor protein, wherein the tumor protein comprises an amino acid sequence that is encoded by a polynucleotide sequence recited in any one of SEQ ID NOs:_ 218-222, 224-226, 249, 250, 253, 256, 266, 276, 277, 282, 285, 293, 295, 298, 299, 301, 304, 306, 316, 321, 326, 333, 336, 337, 342, 353, 359, 361, 364, 369, 372, 373, 377, 379 and 386, or a complement of any ofthe foregoing polynucleotides.
58. A oligonucleotide according to claim 57, wherein the oligonucleotide comprises 10-40 contiguous nucleotides recited in any one of SEQ ID NOs:_ 218-222. 224-226. 249, 250, 253. 256. 266, 276, 277. 282, 285, 293. 295, 298, 299, 301. 304, 306, 316, 321, 326, 333. 336, 337. 342, 353. 359, 361, 364, 369, 372, 373, 377. 379 and 386.
59. A diagnostic kit. comprising:
(a) an oligonucleotide according to claim 58; and
(b) a diagnostic reagent for use in a polymerase chain reaction or hybridization assay.
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Cited By (32)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001027269A2 (en) * 1999-10-11 2001-04-19 Chiron Spa Vip54 protein and related materials
WO2001072295A2 (en) * 2000-03-29 2001-10-04 Corixa Corporation Compositions and methods for the therapy and diagnosis of lung cancer
EP1314779A1 (en) * 2000-08-28 2003-05-28 Teijin Limited Airway-specific trypsin-like enzymes and method of using the same
US6759508B2 (en) 2000-09-01 2004-07-06 Corixa Corporation Compositions and methods for the therapy and diagnosis of lung cancer
EP1576132A2 (en) * 2002-08-16 2005-09-21 Agensys, Inc. Nucleic acids and corresponding proteins entitled 273p4b7 useful in treatment and detection of cancer
US7364864B2 (en) 2001-06-21 2008-04-29 Isis Innovation Limited ANGE gene in atopy
EP2181595A1 (en) * 2002-08-16 2010-05-05 Yeda Research And Development Company Ltd. Tumor associated antigen, peptides thereof, and use of same as anti-tumor vaccines
AU2007216892B2 (en) * 2002-08-16 2011-02-10 Agensys, Inc. Nucleic acids and corresponding proteins entitled 273P4B7 useful in treatment and detection of cancer
CN102171570A (en) * 2008-08-05 2011-08-31 东丽株式会社 Cancer detection method
US8709418B2 (en) 2010-02-04 2014-04-29 Toray Industries, Inc. Pharmaceutical composition for treating CAPRIN-1 expressing cancer
US8828398B2 (en) 2010-02-04 2014-09-09 Toray Industries, Inc. Pharmaceutical composition for treating and/or preventing cancer
US8911740B2 (en) 2010-02-04 2014-12-16 Toray Industries, Inc. Pharmaceutical composition for treating and/or preventing cancer
US8937160B2 (en) 2010-02-04 2015-01-20 Toray Industries, Inc. Pharmaceutical composition for treating and/or preventing cancer
US9115200B2 (en) 2010-02-04 2015-08-25 Toray Industries, Inc. Pharmaceutical composition for treating cancer using a monoclonal antibody having immunological reactivity with CAPRIN-1
US9175074B2 (en) 2011-08-04 2015-11-03 Toray Industries, Inc. Pharmaceutical composition for treatment and/or prophylaxis of cancer
US9181334B2 (en) 2011-08-04 2015-11-10 Toray Industries, Inc. Pharmaceutical composition for treatment and/or prophylaxis of cancer
US9181348B2 (en) 2011-08-04 2015-11-10 Toray Industries, Inc. Pharmaceutical composition for treatment and/or prophylaxis of cancer
US9180187B2 (en) 2010-02-04 2015-11-10 Toray Industries, Inc. Medicament for treating and/or preventing cancer
US9180188B2 (en) 2011-08-04 2015-11-10 Toray Industries, Inc. Pharmaceutical composition for treatment and/or prophylaxis of cancer
US9260513B2 (en) 2012-02-21 2016-02-16 Toray Industries, Inc. Pharmaceutical composition for treatment and/or prevention of cancer
US9266958B2 (en) 2012-02-21 2016-02-23 Toray Industries, Inc. Pharmaceutical composition for treatment and/or prevention of cancer
US9273128B2 (en) 2011-08-04 2016-03-01 Toray Industries, Inc Pharmaceutical composition for treatment and/or prophylaxis of cancer
US9273130B2 (en) 2012-02-21 2016-03-01 Toray Industries, Inc. Pharmaceutical composition for treatment and/or prevention of cancer
US9409993B2 (en) 2011-08-04 2016-08-09 Toray Industries, Inc. Pharmaceutical composition for treatment and/or prevention of pancreatic cancer
US9416193B2 (en) 2012-03-30 2016-08-16 Toray Industries, Inc. Pharmaceutical composition for treatment and/or prevention of liver cancer
US9428581B2 (en) 2012-03-30 2016-08-30 Toray Industries, Inc. Pharmaceutical composition for treatment and/or prevention of gallbladder cancer
US9573993B2 (en) 2012-02-21 2017-02-21 Toray Industries, Inc. Pharmaceutical composition for treatment of cancer comprising an anti-CAPRIN-1 peptide antibody
US9753038B2 (en) 2012-07-19 2017-09-05 Toray Industries, Inc. Method for detecting cancer via measurement of caprin-1 expression level
US9772332B2 (en) 2012-07-19 2017-09-26 Toray Industries, Inc. Method for detecting CAPRIN-1 in a biological sample
US9796775B2 (en) 2011-08-04 2017-10-24 Toray Industries, Inc. Method for detecting pancreatic cancer
US9862774B2 (en) 2013-08-09 2018-01-09 Toray Industries, Inc. Pharmaceutical composition for treatment and/or prevention of cancer
US9982059B2 (en) 2008-08-05 2018-05-29 Toray Industries, Inc. Pharmaceutical composition for treatment and prevention of cancers

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP5648261B2 (en) * 2006-12-20 2015-01-07 東レ株式会社 Cancer detection method

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1996002552A1 (en) * 1994-07-19 1996-02-01 Cytoclonal Pharmaceutics, Inc. Lung cancer marker
WO1999038973A2 (en) * 1998-01-28 1999-08-05 Corixa Corporation Compounds for therapy and diagnosis of lung cancer and methods for their use

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1996002552A1 (en) * 1994-07-19 1996-02-01 Cytoclonal Pharmaceutics, Inc. Lung cancer marker
WO1999038973A2 (en) * 1998-01-28 1999-08-05 Corixa Corporation Compounds for therapy and diagnosis of lung cancer and methods for their use

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
CHEN S-L ET AL: "Isolation and characterizaton of a novel gene expressed in multiple cancers" ONCOGENE,GB,BASINGSTOKE, HANTS, vol. 12, no. 4, 15 February 1996 (1996-02-15), pages 741-751-751, XP002106655 ISSN: 0950-9232 *
G]RE ET AL: "Human lung cancer antigens recognized by autologous antibodies: definition of a novel cDNA derived from the tumor suppressor gene locus on chromosome 3p21.3" CANCER RESEARCH,US,AMERICAN ASSOCIATION FOR CANCER RESEARCH, BALTIMORE, MD, vol. 58, no. 58, 1 March 1998 (1998-03-01), pages 1034-1041-41, XP002103188 ISSN: 0008-5472 *

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