AU2344399A - Compounds for therapy and diagnosis of lung cancer and methods for their use - Google Patents

Description

WO 99/38973 PCT/US99/01642 COMPOUNDS FOR THERAPY AND DIAGNOSIS OF LUNG CANCER AND METHODS FOR THEIR USE 5 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 10 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 15 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 20 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. 25 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 30 therapy of lung cancer. In a first aspect, isolated polynucleotides encoding lung tumor polypeptides are provided, such polynucleotides comprising a nucleotide sequence selected WO 99/38973 PCT/US99/01642 2 from the group consisting of: (a) sequences provided in SEQ ID NO: 1-11, 19, 22-25, 27-31, 51, 53, 55, 63, 70, 72, 79, 80, 86, 87, 89, 90, 102-107, 109, 139, 143-149, 151-154 and 156 158; (b) sequences complementary to a sequence provided in SEQ ID NO: 1-11. 19, 22-25, 27-31, 51, 53, 55, 63, 70, 72, 79, 80, 86, 87, 89, 90, 102-107, 109, 139, 143-149. 151-154 and 5 156-158; and (b) variants of the sequences of (a) or (b). In a second aspect, isolated polypeptides are provided that comprise at least an immunogenic portion of a lung tumor protein or a variant thereof. In specific embodiments, such polypeptides comprise an amino acid sequence encoded by a DNA sequence comprising a nucleotide sequence selected from the- group consisting of (a) sequences recited in SEQ ID 10 NO: 1-11, 19, 22-25, 27-31, 51, 53, 55, 63, 70, 72, 79, 80, 86, 87, 89, 90, 102-107, 109, 139, 143-149, 151-154 and 156-158; (b) sequences complementary to a sequence provided in SEQ ID NO: 1-11, 19, 22-25, 27-31, 51, 53, 55, 63, 70, 72, 79, 80, 86, 87, 89, 90, 102-107, 109, 139, 143-149, 151-154 and 156-158; and (c) variants of the sequences of (a) and (b). In related aspects, expression vectors comprising the inventive 15 polynucleotides., together with host cells transformed or transfected with such expression vectors are provided. In preferred embodiments, the host cells are selected from the group consisting of E. coli, yeast and mammalian cells. In another aspect, fusion proteins comprising a first and a second inventive polypeptide or. alternatively, an inventive polypeptide and a known lung tumor antigen, are 20 provided. The present invention further provides pharmaceutical compositions comprising one or more of the above polypeptides, fusion proteins or polynucleotides and a physiologically acceptable carrier, together with vaccines comprising one or more such polypeptides. fusion proteins or polynucleotides in combination with an immune response 25 enhancer. In related aspects. the present invention provides methods for inhibiting the development of lung cancer in a patient, comprising administering to a patient an effective amount of at least one of the above pharmaceutical compositions and/or vaccines. In yet a further aspect of the present invention, methods are provided for 30 detecting lung cancer in a patient, comprising: (a) contacting a biological sample obtained from a patient with a binding agent that is capable of binding to a polypeptide disclosed WO 99/38973 PCT/US99/01642 3 herein; and (b) detecting in the sample a protein or polypeptide that binds to the binding agent. In preferred embodiments, the binding agent is an antibody, most preferably a monoclonal antibody. In related aspects, methods are provided for monitoring the progression of 5 lung cancer in a patient, comprising: (a) contacting a biological sample obtained from a patient with a binding agent that is capable of binding to one of the polypeptides disclosed herein; (b) determining in the sample an amount of a protein or polypeptide that binds to the binding agent; (c) repeating steps (a) and (b); and comparing the amounts of polypeptide detected in steps (b) and (c). 10 Within related aspects, the present invention provides antibodies, preferably monoclonal antibodies, that bind to the inventive polypeptides, as well as diagnostic kits comprising such antibodies, and methods of using such antibodies to inhibit the development of lung cancer. The present invention further provides methods for detecting lung cancer 15 comprising: (a) obtaining a biological sample from a patient; (b) contacting the sample with a first and a second oligonucleotide primer in a polymerase chain reaction, at least one of the oligonucleotide primers being specific for a polynucleotide that encodes one of the polypeptides disclosed herein; and (c) detecting in the sample a DNA sequence that amplifies in the presence of the first and second oligonucleotide primers. In a preferred embodiment, at 20 least one of the oligonucleotide primers comprises at least about 10 contiguous nucleotides of a polynucleotide comprising a sequence selected from the group consisting of SEQ ID NO: 1 31, 49-55, 63, 64, 66, 68-72, 78-80, 84-92, 102-110, 116-120 and 126-181. In a further aspect, the present invention provides a method for detecting lung cancer in a patient comprising: (a) obtaining a biological sample from the patient; (b) 25 contacting the sample with an oligonucleotide probe specific for a polynucleotide that encodes one of the polypeptides disclosed herein; and (c) detecting in the sample a DNA sequence that hybridizes to the oligonucleotide probe. Preferably, the oligonucleotide probe comprises at least about 15 contiguous nucleotides of a polynucleotide comprising a sequence selected from the group consisting of SEQ ID NO: 1-31, 49-55, 63, 64, 66, 68-72, 78-80, 84 30 92, 102-110, 116-120 and 126-181.In related aspects, diagnostic kits comprising the above oligonucleotide probes or primers are provided.

WO 99/38973 PCT/US99/01642 4 In yet a further aspect, methods for the treatment of lung cancer in a patient are provided, the methods comprising obtaining PBMC from the patient, incubating the PBMC with a polypeptide of the present invention (or a polynucleotide that encodes such a polypeptide) to provide incubated T cells and administering the incubated T 5 cells to the patient. In present invention additionally provides methods for the treatment of lung cancer that comprise incubating antigen presenting cells with a polypeptide of the present invention (or a polynucleotide that encodes such a polypeptide) to provide incubated antigen presenting cells and administering the incubated antigen presenting cells to the patient. In certain embodiments, the-antigen presenting cells are selected from the group 10 consisting of dendritic cells and macrophages. Compositions for the treatment of lung cancer comprising T cells or antigen presenting cells that have been incubated with a polypeptide or polynucleotide of the present invention are also provided. These and other aspects of the present invention will become apparent upon reference to the following detailed description. All references disclosed herein are hereby incorporated by reference in their entirety as if 15 each was incorporated individually. SEQUENCE IDENTIFIERS SEQ ID NO: 1 is the determined cDNA sequence for L363C1.cons SEQ ID NO: 2 is the determined cDNA sequence for L263C2.cons 20 SEQ ID NO: 3 is the determined cDNA sequence for L263C2c SEQ ID NO: 4 is the determined cDNA sequence for L263C1.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 L164C1.cons 25 SEQ ID NO: 8 is the determined cDNA sequence for L366Cla SEQ ID NO: 9 is the determined cDNA sequence for L260C1.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 L255C1.cons 30 SEQ ID NO: 13 is the determined cDNA sequence for L255CIb WO 99/38973 PCT/US99/01642 5 SEQ ID NO: 14 is the determined cDNA sequence for L355C1 .cons SEQ ID NO: 15 is the determined cDNA sequence for L366C1.cons SEQ ID NO: 16 is the determined cDNA sequence for L163Cla SEQ ID NO: 17 is the determined cDNA sequence for LT86-1 5 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 10 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 LT86-1 0 SEQ ID NO: 27 is the determined cDNA sequence for LT86-11 15 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 20 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 25 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 LT86-1 1 30 SEQ ID NO: 43 is the predicted amino acid sequence for LT86-12 WO 99/38973 PCT/US99/01642 6 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) 12 AG primer 5 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 10 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 15 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 20 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 is the predicted amino acid sequence from the 5' end of LT86-9 SEQ ID NO: 66 is the determined extended cDNA sequence for LT86-4 SEQ ID NO: 67 is the predicted extended amino acid sequence for LT86-4 25 SEQ ID NO: 68 is the determined 5' cDNA sequence for LT86-20 SEQ ID NO: 69 is the determined 3' cDNA sequence for LT86-21 SEQ ID NO: 70 is the determined 5' cDNA sequence for LT86-22 SEQ ID NO: 71 is the determined 5' cDNA sequence for LT86-26 SEQ ID NO: 72 is the determined 5' cDNA sequence for LT86-27 30 SEQ ID NO: 73 is the predicted amino acid sequence for LT86-20 WO 99/38973 PCTIUS99/01642 7 SEQ ID NO: 74 is the predicted amino acid sequence for LT86-21 SEQ ID NO: 75 is the predicted amino acid sequence for LT86-22 SEQ ID NO: 76 is the predicted amino acid sequence for LT86-26 SEQ ID NO: 77 is the predicted amino acid sequence for LT86-27 5 SEQ ID NO: 78 is the determined extended cDNA sequence for L86S-12 SEQ ID NO: 79 is the determined extended cDNA sequence for L86S-36 SEQ ID NO: 80 is the determined extended cDNA sequence for L86S-46 SEQ ID NO: 81 is the predicted extended amino acid sequence for L86S-12 SEQ ID NO: 82 is the predicted extended amino acid sequence for L86S-36 10 SEQ ID NO: 83 is the predicted extended amino acid sequence for L86S-46 SEQ ID NO: 84 is the determined 5'cDNA sequence for L86S-6 SEQ ID NO: 85 is the determined 5'cDNA sequence for L86S-1 1 SEQ ID NO: 86 is the determined 5'cDNA sequence for L86S-14 SEQ ID NO: 87 is the determined 5'cDNA sequence for L86S-29 15 SEQ ID NO: 88 is the determined 5'cDNA sequence for L86S-34 SEQ ID NO: 89 is the determined 5'cDNA sequence for L86S-39 SEQ ID NO: 90 is the determined 5'cDNA sequence for L86S-47 SEQ ID NO: 91 is the determined 5'cDNA sequence for L86S-49 SEQ ID NO: 92 is the determined 5'cDNA sequence for L86S-51 20 SEQ ID NO: 93 is the predicted amino acid sequence for L86S-6 SEQ ID NO: 94 is the predicted amino acid sequence for L86S-1 1 SEQ ID NO: 95 is 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 25 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 30 SEQ ID NO: 103 is the determined 5' cDNA sequence for SLT-T2 WO 99/38973 PCT/US99/01642 8 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 5 SEQ ID NO: 108 is the determined 5' cDNA sequence for SLT-T10 SEQ ID NO: 109 is the determined 5' cDNA sequence for SLT-T1 1 SEQ ID NO: 110 is the determined 5' cDNA sequence for SLT-T12 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 10 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-T12 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 15 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 20 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 25 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 30 SEQ ID NO: 133 is the determined cDNA sequence for PSLT-40 WO 99/38973 PCTIUS99/01642 9 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 5 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-01 1 SEQ ID NO: 141 is the determined cDNA sequence for PSLT-041 SEQ ID NO: 142 is the determined cDNA sequence for PSLT-62 10 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 15 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 20 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 25 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 30 SEQ ID NO: 163 is the determined 5' cDNA sequence for SAL-14 WO 99/38973 PCTIUS99/01642 10 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 5 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 10 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 15 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 20 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 25 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 30 SEQ ID NO: 193 is the predicted amino acid sequence for SAL-104 WO 99/38973 PCT/US99/01642 11 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 5 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 10 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 15 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 20 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-10 SEQ ID NO: 216 is a second predicted amino acid sequence for SAL-50 25 DETAILED DESCRIPTION OF THE INVENTION As noted above, the present invention is generally directed to compositions and methods for the therapy of lung cancer. The compositions described herein include polypeptides, fusion proteins and polynucleotides. Also included within the present invention are molecules (such as an antibody or fragment thereof) that bind to the inventive 30 polypeptides. Such molecules are referred to herein as "binding agents." WO 99/38973 PCT/US99/01642 12 In one embodiment, the inventive polypeptides comprise at least a portion of a protein that is expressed at a greater level in human lung tumor tissue than in normal lung tissue. Preferably, the level of RNA encoding the polypeptide is at least 2-fold higher in tumor tissue. Such polypeptides include, but are not limited to, polypeptides (and 5 immunogenic portions thereof) encoded by the nucleotide sequences provided in SEQ ID NO: 1-16 and variants thereof. In a second embodiment, the inventive polypeptides comprise at least a portion of a immunogenic lung tumor protein, including but not limited to polypeptides wherein the lung tumor protein includes an amino acid sequence encoded by a polynucleotide 10 including a sequence selected from the group consisting of (a) nucleotide sequences recited in SEQ ID NO: 17-31, 49-55, 63,64, 66, 68-72, 78-80 and 84-92, (b) the complements of said nucleotide sequences, and (c) variants of such sequences. In a third embodiment, the inventive polypeptides comprise at least a portion of a lung tumor protein, including polypeptides wherein the lung tumor protein includes an 15 amino acid sequence encoded by a polynucleotide including a sequence selected from the group consisting of (a) nucleotide sequences recited in SEQ ID NO: 102-110, 116-120 and 126-181, (b) the complements of said nucleotide sequences, and (c) variants of such sequences. As used herein, the term "polypeptide" encompasses amino acid chains of any 20 length, including full length proteins, wherein the amino acid residues are linked by covalent peptide bonds. Thus, a polypeptide comprising a portion of one of the above lung tumor proteins may consist entirely of the portion, or the portion may be present within a larger polypeptide that contains additional sequences. The additional sequences may be derived from the native protein or may be heterologous, and such sequences may (but need not) be 25 immunoreactive and/or antigenic. As detailed below, such polypeptides may be isolated from lung tumor tissue or prepared by synthetic or recombinant means. As used herein, an "immunogenic portion" of a lung tumor protein is a portion that is capable of eliciting an immune response in a patient inflicted with lung cancer and as such binds to antibodies present within sera from a lung cancer patient. Such immunogenic 30 portions generally comprise at least about 5 amino acid residues, more preferably at least about 10, and most preferably at least about 20 amino acid residues. Immunogenic portions WO 99/38973 PCTIUS99/01642 13 of the proteins described herein may be identified in antibody binding assays. Such assays may generally be performed using any of a variety of means known to those of ordinary skill in the art, as described, for example, in Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1988. For example, a polypeptide 5 may be immobilized on a solid support (as described below) 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, 12 1-labeled Protein A. Alternatively, a polypeptide may be used to generate monoclonal and polyclonal antibodies for use in detection of the-polypeptide in blood or other fluids of lung cancer 10 patients. Methods for preparing and identifying immunogenic portions of antigens of known sequence are well known in the art and include those summarized in Paul, Fundamental Immunology, 3rd ed., Raven Press, 1993, pp. 243-247. The term "polynucleotide(s)," as used herein, means a single or double-stranded polymer of deoxyribonucleotide or ribonucleotide bases and includes DNA and 15 corresponding RNA molecules, including HnRNA and mRNA molecules, both sense and anti-sense strands, and comprehends cDNA, genomic DNA and recombinant DNA, as well as wholly or partially synthesized polynucleotides. An HnRNA molecule contains introns and corresponds to a DNA molecule in a generally one-to-one manner. An mRNA molecule corresponds to an HnRNA and DNA molecule from which the introns have been excised. A 20 polynucleotide may consist of an entire gene, or any portion thereof. Operable anti-sense polynucleotides may comprise a fragment of the corresponding polynucleotide, and the definition of "polynucleotide" therefore includes all such operable anti-sense fragments. The compositions and methods of the present invention also encompass variants of the above polypeptides and polynucleotides. 25 A polypeptide "variant," as used herein, is a polypeptide that differs from the recited polypeptide only in conservative substitutions and/or modifications, such that the antigenic properties of the polypeptide are retained. In a preferred embodiment, variant polypeptides differ from an identified sequence by substitution, deletion or addition of five amino acids or fewer. Such variants may generally be identified by modifying one of the 30 above polypeptide sequences, and evaluating the antigenic properties of the modified polypeptide using, for example, the representative procedures described herein. Polypeptide WO 99/38973 PCT/US99/01642 14 variants preferably exhibit at least about 70%, more preferably at least about 90% and most preferably at least about 95% identity (determined as described below) to the identified polypeptides. As used herein, a "conservative substitution" is one in which an amino acid is 5 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. In general, the following groups of amino acids represent conservative changes: (1) ala, pro, gly, glu, asp, gln, 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. 10 Variants may also, or alternatively, contain other modifications, including the deletion or addition of amino acids that have minimal influence on the antigenic properties, secondary structure and hydropathic nature of the polypeptide. For example, a polypeptide may be conjugated to a signal (or leader) sequence at the N-terminal end of the protein which co-translationally or post-translationally directs transfer of the protein. The polypeptide may 15 also be conjugated to a linker or other sequence for ease of synthesis, purification or identification of the polypeptide (e.g., poly-His), or to enhance binding of the polypeptide to a solid support. For example, a polypeptide may be conjugated to an immunoglobulin Fc region. A nucleotide "variant" is a sequence that differs from the recited nucleotide 20 sequence in having one or more nucleotide deletions, substitutions or additions. Such modifications may be readily introduced using standard mutagenesis techniques, such as oligonucleotide-directed site-specific mutagenesis as taught, for example, by Adelman et al. (DNA, 2:183, 1983). Nucleotide variants may be naturally occurring allelic variants, or non naturally occurring variants. Variant nucleotide sequences preferably exhibit at least about 25 70%, more preferably at least about 80% and most preferably at least about 90% identity (determined as described below) to the recited sequence. The lung tumor antigens provided by the present invention include variants that are encoded by DNA sequences which are substantially homologous to one or more of the DNA sequences specifically recited herein. "Substantial homology," as used herein, 30 refers to DNA sequences that are capable of hybridizing under moderately stringent conditions. Suitable moderately stringent conditions include prewashing in a solution of 5X WO 99/38973 PCT/US99/01642 15 SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at 50 0 C-65 0 C, 5X SSC, overnight or, in the event of cross-species homology, at 45'C with 0.5X SSC; followed by washing twice at 65*C for 20 minutes with each of 2X, 0.5X and 0.2X SSC containing 0.1% SDS. Such hybridizing DNA sequences are also within the scope of this invention, as are nucleotide 5 sequences that, due to code degeneracy, encode an immunogenic polypeptide that is encoded by a hybridizing DNA sequence. Two nucleotide or polypeptide sequences are said to be "identical" if the sequence of nucleotides or amino acid residues in the two sequences is the same when aligned for maximum correspondence as described below. Comparisons between two sequences are 10 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. 15 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 20 Protein Sequence and Structure. National Biomedical Resarch Foundaiton, Washington DC Vol. 5, Suppl. 3. pp. 345-358; Hein J. (1990) Unified Approach to Alignment and Phylogenes pp. 626-645 Methods in Enzymology vol. 183, Academic Press, Inc., San Diego, CA; Higgins, D.G. and Sharp, P.M. (1989) Fast and sensitive multiple sequence alignments on a microcomputer CABIOS 5:151-153; Myers, E.W. and Muller W. (1988) Optimal alignments 25 in linear space CABIOS 4:11-17; Robinson, E.D. (1971) Comb. Theor 11:105; Santou, N. Nes, M. (1987) The neighbor joining method. A new method for reconstructing phylogenetic trees 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) Rapid similarity searches of nucleic 30 acid and protein data banks Proc. Natl. Acad, Sci. USA 80:726-730.

WO 99/38973 PCT/US99/01642 16 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 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 5 percent, as compared to the reference sequences (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical 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. 10 the window size) and multiplying the results by 100 to yield the percentage of sequence identity. The lung tumor polypeptides of the present invention, and polynucleotides encoding such polypeptides, may be isolated from lung tumor tissue using any of a variety of methods well known in the art. For example, cDNA molecules encoding polypeptides 15 preferentially expressed in lung tumor tissue may be cloned on the basis of the lung tumor specific expression of the corresponding mRNAs, using differential display PCR. This technique compares the amplified products from RNA templates prepared from normal lung and lung tumor tissue. cDNA may be prepared by reverse transcription of RNA using a (dT) 2 AG primer. Following amplification of the cDNA using a random primer, a band 20 corresponding to an amplified product specific to the tumor RNA may be cut out from a silver stained gel and subcloned into a suitable vector. Examples of cDNA sequences that may be isolated using this procedure include those provided in SEQ ID NO: 1-16. cDNA molecules encoding immunogenic lung tumor polypeptides may be prepared by screening a cDNA expression library prepared from a lung tumor sample with 25 sera from the same patient as the tumor sample, as described in detail in Example 2 below. Examples of cDNA sequences that may be isolated using this procedure include those provided in SEQ ID NO: 17-3 1. Additional cDNA molecules encoding lung tumor polypeptides may be obtained by screening such a cDNA expression library with mouse anti lung tumor serum as described below in Example 3. Examples of cDNA sequences that may 30 thus be isolated are provided in SEQ ID NO: 49-55, 63, 64 and 126-148. cDNA sequences encoding lung tumor antigens may also be isolated by screening of lung tumor cDNA WO 99/38973 PCT/US99/01642 17 libraries prepared from SCID mice with mouse anti-tumor sera, as described below in Example 4. Examples of cDNA sequences that may be isolated using this technique are provided in SEQ ID NO: 149-18 1. A gene encoding a polypeptide described herein (or a portion thereof) may, 5 alternatively, be amplified from human genomic DNA, or from lung tumor cDNA, via polymerase chain reaction. For this approach, sequence-specific primers may be designed based on the nucleotide sequences provided herein and may be purchased or synthesized. An amplified portion of a specific nucleotide sequence may then be used to isolate the full length gene from a human genomic DNA library or from a lung tumor cDNA library, using well 10 known techniques, such as those described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, Cold Spring Harbor, NY (1989). Once a DNA sequence encoding a polypeptide is obtained, the polypeptide may be produced recombinantly by inserting the DNA sequence into an expression vector and expressing the polypeptide in an appropriate host. Any of a variety of expression vectors 15 known to those of ordinary skill in the art may be employed to express recombinant polypeptides of this invention. Expression may be achieved in any appropriate host cell that has been transformed or transfected with an expression vector containing a polynucleotide that encodes the recombinant polypeptide. Suitable host cells include prokaryotes, yeast and higher eukaryotic cells. Preferably, the host cells employed are E. coli, yeast or a mammalian 20 cell line, such as COS or CHO cells. The DNA sequences expressed in this manner may encode naturally occurring polypeptides, portions of naturally occurring polypeptides, or other variants thereof. Supernatants from suitable host/vector systems which secrete the recombinant polypeptide may be first concentrated using a commercially available filter. The concentrate may then be applied to a suitable purification matrix, such as an affinity matrix or 25 ion exchange resin. Finally, one or more reverse phase HPLC steps can be employed to further purify the recombinant polypeptide. Such techniques may also be used to prepare polypeptides comprising portions or variants of the native polypeptides. Portions and other variants having fewer than about 100 amino acids, and generally fewer than about 50 amino acids, may be generated using 30 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 WO 99/38973 PCTIUS99/01642 18 the Merrifield solid-phase synthesis method, where amino acids are sequentially added to a growing amino acid chain (see, for example, Merrifield, J. Am. Chem. Soc. 85:2149-2146, 1963). Equipment for automated synthesis of polypeptides is commercially available from suppliers such as Perkin Elmer/Applied BioSystems Division (Foster City, CA), and may be 5 operated according to the manufacturer's instructions. In general, regardless of the method of preparation, the polypeptides disclosed herein are prepared in an isolated, substantially pure form (i.e., the polypeptides are homogenous as determined by amino acid composition and primary sequence analysis). Preferably, the polypeptides are at least-about 90% pure, more preferably at least about 95% 10 pure and most preferably at least about 99% pure. In certain preferred embodiments, described in more detail below, the substantially pure polypeptides are incorporated into pharmaceutical compositions or vaccines for use in one or more of the methods disclosed herein. In a related aspect, the present invention provides fusion proteins comprising a 15 first and a second inventive polypeptide or, alternatively, a polypeptide of the present invention and a known lung tumor antigen, together with variants of such fusion proteins. The fusion proteins of the present invention may (but need not) include a linker peptide between the first and second polypeptides. A DNA sequence encoding a fusion protein of the present invention is 20 constructed using known recombinant DNA techniques to assemble separate DNA sequences encoding the first and second polypeptides into an appropriate expression vector. The 3' end of a DNA sequence encoding the first polypeptide is ligated, with or without a peptide linker, to the 5' end of a DNA sequence encoding the second polypeptide so that the reading frames of the sequences are in phase to permit mRNA translation of the two DNA sequences into a 25 single fusion protein that retains the biological activity of both the first and the second polypeptides. A peptide linker sequence may be employed to separate the first and the second polypeptides 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 30 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 WO 99/38973 PCT/US99/01642 19 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, 5 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 83:8258-8262, 1986; U.S. Patent No. 4,935,233 and U.S. Patent No. 4,751,180. The linker sequence may be from 1 to about 50 amino acids in length. Peptide sequences are not required when the first and second 10 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, 15 stop codons require 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, 20 tuberculosis and hepatitis proteins (see, for example, Stoute et al. New Engl. J. Med., 336:86 91 (1997)). Polypeptides that comprise an immunogenic portion of a lung tumor protein may generally be used for therapy of lung cancer, wherein the polypeptide stimulates the patient's own immune response to lung tumor cells. The present invention thus provides 25 methods for using one or more of the compounds described herein (which may be polypeptides, polynucleotides or fusion proteins) for immunotherapy of lung cancer in a patient. As used herein, a "patient" refers to any warm-blooded animal, preferably a human. A patient may be afflicted with disease, or may be free of detectable disease. Accordingly, the compounds disclosed herein may be used to treat lung cancer or to inhibit the 30 development of lung cancer. In a preferred embodiment, the compounds are administered WO 99/38973 PCT/US99/01642 20 either prior to or following surgical removal of primary tumors and/or treatment by administration of radiotherapy and conventional chemotherapeutic drugs. In these aspects, the inventive polypeptide is generally present within a pharmaceutical composition or a vaccine. Pharmaceutical compositions may comprise one or 5 more polypeptides, each of which may contain one or more of the above sequences (or variants thereof), and a physiologically acceptable carrier. The vaccines may comprise one or more such polypeptides and an immune response enhancer, such as an adjuvant, biodegradable microsphere (e.g., polylactic galactide) or a liposome (into which the polypeptide is incorporated). Pharmaceutical compositions and vaccines may also contain 10 other epitopes of lung tumor antigens, either incorporated into a fusion protein as described above (i.e., a single polypeptide that contains multiple epitopes) or present within a separate polypeptide. Alternatively, a pharmaceutical composition or vaccine may contain DNA encoding one or more of the above polypeptides and/or fusion proteins, such that the 15 polypeptide is generated in situ. In such pharmaceutical compositions and vaccines, 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. Appropriate nucleic acid expression systems contain the necessary DNA sequences for expression in the patient (such as a suitable promoter). Bacterial delivery systems involve the 20 administration of a bacterium (such as Bacillus-Calmette-Guerrin) that expresses an epitope of a lung cell antigen on its cell surface. In a preferred embodiment, the DNA may be introduced using a viral expression system (e.g., vaccinia or other pox virus, retrovirus, or adenovirus). which may involve the use of a non-pathogenic (defective), replication competent virus. Suitable systems are disclosed, for example, in Fisher-Hoch et al., PNAS 25 86:317-321, 1989; Flexner et al., Ann. N.Y Acad Sci. 569:86-103, 1989: Flexner et al., Vaccine 8:17-21, 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 6:616-627, 1988; Rosenfeld et al., Science 252:431-434, 1991; Kolls et al., PNAS 91:215-219, 1994; Kass-Eisler et al., PNAS 90:11498-11502, 1993; Guzman et 30 al., Circulation 88:2838-2848, 1993; and Guzman et al., Cir. Res. 73:1202-1207, 1993. Techniques for incorporating DNA into such expression systems are well known to those of WO 99/38973 PCTIUS99/01642 21 ordinary skill in the art. The DNA may also be "naked," as described, for example, in published PCT application WO 90/11092, and Ulmer et al., Science 259:1745-1749, 1993, 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 5 into the cells. Routes and frequency of administration, as well as dosage, will vary from individual to individual and may parallel those currently being used in immunotherapy of other diseases. In general, the pharmaceutical compositions and vaccines may be administered by injection (e.g., intracutaneous, intramuscular, intravenous or subcutaneous), 10 intranasally (e.g., by aspiration) or orally. Between 1 and 10 doses may be administered over a 3-24 week period. Preferably, 4 doses are administered, at an interval of 3 months, and booster administrations may be given periodically thereafter. Alternate protocols may be appropriate for individual patients. A suitable dose is an amount of polypeptide or DNA that is effective to raise an immune response (cellular and/or humoral) against lung tumor cells in 15 a treated patient. A suitable immune response is at least 10-50% above the basal (i.e., untreated) level. In general, the amount of polypeptide present in a dose (or produced in situ by the DNA in a dose) ranges from about I pg to about 100 mg per kg of host, typically from about 10 pg to about 1 mg, and preferably from about 100 pg to about 1 tg. Suitable dose sizes will vary with the size of the patient, but will typically range from about 0.01 mL to 20 about 5 mL. 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. For parenteral administration, such as subcutaneous injection, the carrier preferably comprises water, saline, alcohol, a lipid, a wax 25 and/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/or magnesium carbonate, may be employed. Biodegradable microspheres (e.g., polylactic glycolide) may also be employed as carriers for the pharmaceutical compositions of this invention. Suitable biodegradable microspheres are disclosed, for example, in U.S. 30 Patent Nos. 4,897,268 and 5,075,109.

WO 99/38973 PCT/US99/01642 22 Any of a variety of immune response enhancers 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 nonspecific stimulator of immune response, such as lipid A, 5 Bordella pertussis or Mycobacterium tuberculosis. Such adjuvants are commercially available as, for example, Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, MI), and Merck Adjuvant 65 (Merck and Company, Inc., Rahway, NJ). Within certain embodiments, polynucleotides of the present invention may be 10 formulated so as to permit entry into a cell of a mammal, preferably a human, and expression therein. Such formulations are particularly useful for therapeutic purposes. Those of skill in the art will appreciate that there are many ways to achieve expression of a polynucleotide in a target cells, 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 15 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 skill in the art. A retroviral vector may additionally transfer or incorporate a targeting moiety, such as a gene that encodes for 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 know to those of 20 ordinary skill in the art. Polypeptides disclosed herein may also be employed in adoptive immunotherapy for the treatment of cancer. Adoptive immunotherapy may be broadly classified into either active or passive immunotherapy. In active immunotherapy, treatment relies on the in vivo stimulation of the endogenous host immune system to react against 25 tumors with the administration of immune response-modifying agents (for example, tumor vaccines, bacterial adjuvants, and/or cytokines). In passive immunotherapy, treatment involves the delivery of biologic reagents 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 30 intact host immune system. Examples of effector cells include T lymphocytes (for example, CD8+ cytotoxic T-lymphocyte, CD4+ T-helper, tumor-infiltrating lymphocytes), killer cells WO 99/38973 PCT/US99/01642 23 (Natural Killer cells, lymphokine-activated killer cells), B cells, or antigen presenting cells (such as dendritic cells and macrophages) expressing the disclosed antigens. The polypeptides disclosed herein may also be used to generate antibodies or anti-idiotypic antibodies (as in U.S. Patent No. 4,918,164), for passive immunotherapy. 5 The predominant method of procuring adequate numbers of T-cells for adoptive immunotherapy is to grow immune T-cells in vitro. Culture conditions for expanding single antigen-specific T-cells to several billion in number with retention of antigen recognition in vivo are well known in the art. These in vitro culture conditions typically utilize intermittent stimulation with antigen, often in the presence of cytokines, such 10 as IL-2, and non-dividing feeder cells. As noted above, the immunoreactive polypeptides described herein may be used to rapidly expand antigen-specific T cell cultures in order to generate sufficient number of cells for immunotherapy. In particular, antigen-presenting cells, such as dendritic, macrophage or B-cells, may be pulsed with immunoreactive polypeptides or transfected with a polynucleotide sequence(s), using standard techniques well 15 known in the art. For cultured T-cells to be effective in therapy, the cultured T-cells must be able to grow and distribute widely and to survive long term in vivo. Studies have demonstrated that cultured T-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. Ibid). 20 The polypeptides disclosed herein may also be employed to generate and/or isolate tumor-reactive T-cells, which can then be administered to the patient. In one technique, antigen-specific T-cell lines may be generated by in vivo immunization with short peptides corresponding to immunogenic portions of the disclosed polypeptides. The resulting antigen specific CD8+ CTL clones may be isolated from the patient, expanded using standard 25 tissue culture techniques, and returned to the patient. Alternatively, peptides corresponding to immunogenic portions of the polypeptides may be employed to generate tumor reactive T cell subsets by selective in vitro stimulation and expansion of autologous T cells to provide antigen-specific T cells which may be subsequently transferred to the patient as described, for example, by Chang et al. 30 (Crit. Rev. Oncol. Hematol.. 22(3), 213, 1996).

WO 99/38973 PCT/US99/01642 24 In another embodiment, syngeneic or autologous dendritic cells may be pulsed with peptides corresponding to at least an immunogenic portion of a polypeptide disclosed herein. The resulting antigen-specific dendritic cells may either be transferred into a patient, or employed to stimulate T cells to provide antigen-specific T cells which may, in turn, be 5 administered to a patient. The use of peptide-pulsed dendritic cells to generate antigen specific T cells and the subsequent use of such antige-specific T cells to eradicate tumors in a murine model has been demonstrated by Cheever et al. ("Therapy With Cultured T Cells: Principles Revisited, " Immunological Reviews, 157:177, 1997 Additionally vectors expressing-the disclosed polynucleotides may be introduced into 10 stem cells taken from the patient and clonally propagated in vitro for autologous transplant back into the same patient. In one embodiment, cells of the immune system, such as T cells, may be isolated from the peripheral blood of a patient, using a commercially available cell separation system, such as CellPro Incorporated's (Bothell, WA) CEPRATET" system (see U.S. Patent 15 No. 5,240,856; U.S. Patent No. 5,215,926; WO 89/06280; WO 91/16116 and WO 92/07243). The separated cells are stimulated with one or more of the immunoreactive polypeptides contained within a delivery vehicle, such as a microsphere, to provide antigen-specific T cells. The population of tumor antigen-specific T cells is then expanded using standard techniques and the cells are administered back to the patient.Polypeptides and fusion proteins 20 of the present invention may also be used to generate binding agents, such as antibodies or fragments thereof, that are capable of detecting metastatic human lung tumors. Binding agents of the present invention may generally be prepared using methods known to those of ordinary skill in the art, including the representative procedures described herein. Binding agents are capable of differentiating between patients with and without lung cancer, using the 25 representative assays described herein. In other words, antibodies or other binding agents raised against a lung tumor protein, or a suitable portion thereof, will generate a signal indicating the presence of primary or metastatic lung cancer in at least about 20% of patients afflicted with the disease, and will generate a negative signal indicating the absence of the disease in at least about 90% of individuals without primary or metastatic lung cancer. 30 Suitable portions of such lung tumor proteins are portions that are able to generate a binding agent that indicates the presence of primary or metastatic lung cancer in substantially all (i.e., WO 99/38973 PCTIUS99/01642 25 at least about 80%, and preferably at least about 90%) of the patients for which lung cancer would be indicated using the full length protein, and that indicate the absence of lung cancer in substantially all of those samples that would be negative when tested with full length protein. The representative assays described below, such as the two-antibody sandwich 5 assay, may generally be employed for evaluating the ability of a binding agent to detect metastatic human lung tumors. The ability of a polypeptide prepared as described herein to generate antibodies capable of detecting primary or metastatic human lung tumors may generally be evaluated by raising one or more antibodies against the polypeptide (using, for example, a 10 representative method described herein) and determining the ability of such antibodies to detect such tumors in patients. This determination may be made by assaying biological samples from patients with and without primary or metastatic lung cancer for the presence of a polypeptide that binds to the generated antibodies. Such test assays may be performed, for example, using a representative procedure described below. Polypeptides that generate 15 antibodies capable of detecting at least 20% of primary or metastatic lung tumors by such procedures are considered to be useful in assays for detecting primary or metastatic human lung tumors. Polypeptide specific antibodies may be used alone or in combination to improve sensitivity. Polypeptides capable of detecting primary or metastatic human lung tumors 20 may be used as markers for diagnosing lung cancer or for monitoring disease progression in patients. In one embodiment, lung cancer in a patient may be diagnosed by evaluating a biological sample obtained from the patient for the level of one or more of the above polypeptides, relative to a predetermined cut-off value. As used herein, suitable "biological samples" include blood, sera, urine and/or lung secretions. 25 The level of one or more of the above polypeptides may be evaluated using any binding agent specific for the polypeptide(s). A "binding agent," in the context of this invention, is any agent (such as a compound or a cell) that binds to a polypeptide as described above. As used herein, "binding" refers to a noncovalent association between two separate molecules (each of which may be free (i.e., in solution) or present on the surface of a cell or a 30 solid support), such that a "complex" is formed. Such a complex may be free or immobilized (either covalently or noncovalently) on a support material. The ability to bind may generally WO 99/38973 PCT/US99/01642 26 be evaluated by 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 5 exceeds about 10' L/mol. The binding constant may be determined using methods well known to those of ordinary skill in the art. 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 peptide. In a preferred-embodiment, the binding partner is an antibody, or a 10 fragment thereof. Such antibodies may be polyclonal, or monoclonal. In addition, the antibodies may be single chain, chimeric, CDR-grafted or humanized. Antibodies may be prepared by the methods described herein and by other methods well known to those of skill in the art. There are a variety of assay formats known to those of ordinary skill in the art 15 for using a binding partner to detect polypeptide markers in a sample. See, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988. In a preferred embodiment, the assay involves the use of binding partner 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 second binding partner that contains a reporter 20 group. Suitable second binding partners include antibodies that bind to the binding partner/polypeptide complex. 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 partner after incubation of the binding partner with the sample. The extent to which components of the sample inhibit the binding of the labeled polypeptide to the binding 25 partner is indicative of the reactivity of the sample with the immobilized binding partner. The solid support may be any material known to those of ordinary skill in the art to which the antigen 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 30 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 WO 99/38973 PCT/US99/01642 27 be immobilized on the solid support using a variety of techniques known to those of skill in the art, which are amply described in the patent and scientific literature. In the context of the present invention, the term "immobilization" refers to both noncovalent association, such as adsorption, and covalent attachment (which may be a direct linkage between the antigen and 5 functional groups on the support or may be a linkage by way of a cross-linking agent). Immobilization by adsorption to a well in a microtiter plate or to a membrane is preferred. In such cases, adsorption may be achieved by contacting the binding agent, in a suitable buffer, with the solid support for a suitable amount of time. The contact time varies with temperature, but is typically between about I hour and about I day. In general, contacting a 10 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 Vtg, and preferably about 100 ng to about 1 pg, 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 15 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). 20 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 second antibody 25 (containing a reporter group) capable of binding to a different site on the polypeptide is added. The amount of second antibody 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. 30 Any suitable blocking agent known to those of ordinary skill in the art, such as bovine serum albumin or Tween 20TM (Sigma Chemical Co., St. Louis. MO). The immobilized antibody is WO 99/38973 PCT/US99/01642 28 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 that period of time that is sufficient to detect the presence of polypeptide within a sample obtained from an 5 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 10 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 enzymes (such as horseradish peroxidase), substrates, cofactors, inhibitors, dyes, 15 radionuclides, luminescent groups, fluorescent groups and biotin. The conjugation of antibody to reporter group may be achieved using standard methods known to those of ordinary skill in the art. The second antibody is then incubated with the immobilized antibody polypeptide complex for an amount of time sufficient to detect the bound polypeptide. An 20 appropriate amount of time may generally be determined by assaying the level of binding that occurs over a period of time. Unbound second antibody is then removed and bound second antibody 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 25 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. 30 To determine the presence or absence of lung cancer, the signal detected from the reporter group that remains bound to the solid support is generally compared to a signal WO 99/38973 PCT/US99/01642 29 that corresponds to a predetermined cut-off value. In one preferred embodiment, the cut-off value is the average mean signal obtained when the immobilized antibody is incubated with samples from patients without lung cancer. In general, a sample generating a signal that is three standard deviations above the predetermined cut-off value is considered positive for 5 lung 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 10 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 15 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 lung cancer. In a related embodiment, the assay is performed in a flow-through or strip test format, wherein the antibody is immobilized on a membrane, such as nitrocellulose. In the flow-through test, polypeptides within the sample bind to the immobilized antibody as the 20 sample passes through the membrane. A second, labeled antibody then binds to the antibody polypeptide complex as a solution containing the second antibody flows through the membrane. The detection of bound second antibody may then be performed as described above. In the strip test format, one end of the membrane to which antibody is bound is immersed in a solution containing the sample. The sample migrates along the membrane 25 through a region containing second antibody and to the area of immobilized antibody. Concentration of second antibody at the area of immobilized antibody indicates the presence of lung cancer. Typically, the concentration of second antibody 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 antibody immobilized on the membrane is selected 30 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 WO 99/38973 PCT/US99/01642 30 sandwich assay, in the format discussed above. Preferably, the amount of antibody immobilized on the membrane ranges from about 25 ng to about 1 pg, 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. 5 Of course, numerous other assay protocols exist that are suitable for use with the antigens or antibodies of the present invention. The above descriptions are intended to be exemplary only. In another embodiment, the above polypeptides may be used as markers for the progression of lung cancer. In this embodiment, assays as described above for the 10 diagnosis of lung cancer may be performed over time, and the change in the level of reactive polypeptide(s) 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, lung cancer is progressing in those patients in whom the level of polypeptide detected by the binding agent increases over time. In contrast, lung cancer is not progressing when the level of reactive 15 polypeptide either remains constant or decreases with time. Antibodies for use in the above methods 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 one such technique, an immunogen comprising the antigenic polypeptide is initially injected into any 20 of a wide variety of mammals (e.g., mice, rats, rabbits, sheep and 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 25 according to a predetermined schedule incorporating one or more booster immunizations, and the animals are bled periodically. Polyclonal antibodies specific for the polypeptide may then be purified from such antisera by, for example, affinity chromatography using the polypeptide coupled to a suitable solid support. Monoclonal antibodies specific for the antigenic polypeptide of interest may 30 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 WO 99/38973 PCT/US99/01642 31 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 5 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 10 time, usually about 1 to 2 weeks, colonies of hybrids are observed. Single colonies are selected and 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, 15 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 20 step. Monoclonal antibodies of the present invention may also be used as therapeutic reagents, to diminish or eliminate lung tumors. The antibodies may be used on their own (for instance, to inhibit metastases) or coupled to one or more therapeutic agents. Suitable agents in this regard include radionuclides, differentiation inducers, drugs, toxins, 25 and derivatives thereof. Preferred radionuclides include 90 Y, 123, 1251 1311 86 Re, 188 Re, 21 'At, and 212 Bi. Preferred drugs include methotrexate, and pyrimidine and purine analogs. Preferred differentiation inducers include phorbol esters and butyric acid. Preferred toxins include ricin, abrin, diptheria toxin, cholera toxin, gelonin, Pseudomonas exotoxin, Shigella toxin, and pokeweed antiviral protein. 30 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 WO 99/38973 PCTUS99/01642 32 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 5 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 10 thus increase the coupling efficiency. An increase in chemical reactivity may also facilitate the use of agents, or functional groups on agents, which otherwise would not be possible. It will be evident to those skilled in the art that a variety of bifunctional or polyfunctional reagents, both homo- and hetero-functional (such as those described in the catalog of the Pierce Chemical Co., Rockford, IL), may be employed as the linker group. 15 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 20 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. 25 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 30 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 WO 99/38973 PCT/US99/01642 33 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 5 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 10 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 15 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 20 on the tumor, and the rate of clearance of the antibody. Diagnostic reagents of the present invention may also comprise DNA sequences encoding one or more of the above polypeptides, or one or more portions thereof. For example, at least two oligonucleotide primers may be employed in a polymerase chain reaction (PCR) based assay to amplify lung tumor-specific cDNA derived from a biological 25 sample, wherein at least one of the oligonucleotide primers is specific for a polynucleotide encoding a lung tumor protein of the present invention. The presence of the amplified cDNA is then detected using techniques well known in the art, such as gel electrophoresis. Similarly, oligonucleotide probes specific for a polynucleotide encoding a lung tumor protein of the present invention may be used in a hybridization assay to detect the presence of an inventive 30 polypeptide in a biological sample.

WO 99/38973 PCT/US99/01642 34 As used herein, the term "oligonucleotide primer/probe specific for a polynucleotide" means an oligonucleotide sequence that has at least about 60%, preferably at least about 75% and more preferably at least about 90%, identity to the polynucleotide in question. Oligonucleotide primers and/or probes which may be usefully employed in the 5 inventive diagnostic methods preferably have at least about 10-40 nucleotides. In a preferred embodiment, the oligonucleotide primers comprise at least about 10 contiguous nucleotides of a polynucleotide having a partial sequence selected from SEQ ID NO: 1-31, 49-55, 63, 64, 66, 68-72, 78-80, 84-92, 102-110, 116-120 and 126-181. Preferably, oligonucleotide probes for use in the inventive diagnostic -methods comprise at least about 15 contiguous 10 oligonucleotides of a polynucleotide having a partial sequence provided in SEQ ID NO: 1-31, 49-55, 63, 64, 66, 68-72, 78-80, 84-92, 102-110, 116-120 and 126-181. Techniques for both PCR based assays and hybridization assays are well known in the art (see, for example, Mullis et al. Ibid; Ehrlich, Ibid). Primers or probes may thus be used to detect lung tumor specific sequences in biological samples, including blood, semen, lung tissue and/or lung 15 tumor tissue.

WO 99/38973 PCT/US99/01642 35 The following Examples are offered by way of illustration and not by way of limitation. EXAMPLES 5 Example 1 PREPARATION OF LUNG TUMOR-SPECIFIC cDNA SEQUENCES USING DIFFERENTIAL DISPLAY RT-PCR This example illustrates- the preparation of cDNA molecules encoding lung 10 tumor-specific polypeptides using a differential display screen. Tissue samples were prepared from breast 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 15 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 'C extension for 30 seconds. Bands that were repeatedly 20 observed to be specific to the RNA fingerprint pattern of the 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 25 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.

WO 99/38973 PCT/US99/01642 36 Example 2 USE OF PATIENT SERA TO IDENTIFY DNA SEQUENCES ENCODING LUNG TUMOR ANTIGENS 5 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 10 lung carcinoma and poly A+ RNA was isolated using the Message Maker kit (Gibco BRL, Gaithersburg, MD). The resulting library was screened using E. coli-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, 15 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 20 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. 25 Clones LT86-3, LT86-6 - LT86-9, LT86-1 1 - 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, LT86-1 1, 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 30 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 WO 99/38973 PCTIUS99/01642 37 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 5 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. 10 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 15 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. 20 WO 99/38973 PCT/US99/01642 38 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 5 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 10 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. 15 The determined cDNA sequences for 7 of the 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 20 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 25 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 30 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 WO 99/38973 PCT/US99/01642 39 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. 5 L86S-6, L86S-1l, 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 10 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 15 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 20 homology previously identified human polynucleotide sequences.

WO 99/38973 PCT/US99/01642 40 Example 4 USE OF MOUSE ANTISERA TO SCREEN LUNG TUMOR LIBRARIES PREPARED FROM SCID MICE 5 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 10 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. coli-absorbed mouse anti-SCID tumor serum. Positive plaques were identified 15 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 20 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 25 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, 30 157 and 158 were found to show some homology to previously isolated expressed sequence WO 99/38973 PCT/US99/01642 41 tags (ESTs). The sequences of SEQ ID NO: 150, 155 and 159-181 were found to show homology to sequences previously identified in humans.

WO 99/38973 PCT/US99/01642 42 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. 5 Briefly, total RNA was extracted from a variety of normal and tumor tissues using Trizol reagent. First strand synthesis was carried out using 2 pIg 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, 3-actin was used as an internal control for each of the 10 tissues examined. 1 Vtl of 1:30 dilution of cDNA was employed to enable the linear range amplification of the p-actin template and was sensitive enough to reflect the differences in the initial copy numbers. Using these conditions, the p-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 15 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 breast tumor), and different normal tissues, including lung from four patients, prostate, brain, kidney, liver, ovary, skeletal muscle, skin, small intestine, myocardium. retina and testes. 20 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 25 expressed in lung squamous tissue and normal tonsil, with expression being low or undetectable in all other tissues examined.

WO 99/38973 PCT/US99/01642 43 Example 6 ISOLATION OF DNA SEQUENCES ENCODING LUNG TUMOR ANTIGENS DNA sequences encoding antigens potentially involved in squamous cell lung 5 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 10 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-T1O, SLT-T1 1 and SLT-T12 being provided in SEQ ID NO: 103 110, respectively. The corresponding predicted amino acid sequence for SLT-T1, SLT-T2, 15 SLT-T3, SLT-TlO 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-Tll with those in the public databases as described above, revealed no significant homologies. The sequences for SLT-T10 and SLT-T12 were found to show some homology to sequences previously identified in humans. 20 The sequence of SLT-T1 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 25 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.

WO 99/38973 PCTIUS99/01642 44 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 5 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 10 120, 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 15 interferon-inducible protein 1-8U. SALT-T9 shows approximately 90% identity to human mucin MUC 5B.

WO 99/38973 PCT/US99/01642 45 Example 7 SYNTHESIS OF POLYPEPTIDES Polypeptides may be synthesized on a Perkin Elmer/Applied Biosystems 5 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 10 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 15 lyophilization of the pure fractions, the peptides may be characterized using electrospray or other types of mass spectrometry and by amino acid analysis. From the foregoing, it will be appreciated that, although specific embodiments of the invention have been described herein for the purposes of illustration, various 20 modifications may be made without deviating from the spirit and scope of the invention.

Claims (4)

1. An isolated polynucleotide comprising a nucleotide sequence selected from the group consisting of: 5 (a) sequences provided in SEQ ID NO: 1-11, 19, 22-25, 27-31, 51, 53, 55, 63, 70, 72, 79, 80, 86, 87, 89, 90, 102-107, 109, 139, 143-149, 151-154 and 156-158; (b) the complements of sequences provided in SEQ ID NO: 1-11, 19, 22 25, 27-31, 51, 53, 55, 63, 70, 72, 79, 80, 86, 87, 89, 90, 102-107, 109, 139, 143-149, 151-154 and 156-158; and 10 (c) variants of the sequences of (a) and (b).

2. An isolated polypeptide comprising an immunogenic portion of a lung tumor protein or a variant thereof, wherein said protein comprises an amino acid sequence encoded by a polynucleotide of claim 1. 15

3. The isolated polypeptide of claim 2 wherein the polypeptide comprises a sequence selected from the group of sequences recited in SEQ ID NO: 182, 184-193 and

216. 20 4. A polynucleotide comprising a nucleotide sequence encoding the polypeptide of claim 3. 5. An expression vector comprising the polynucleotide of claims 1 or 4. 25 6. A host cell transformed with the expression vector of claim 5. 7. The host cell of claim 6 wherein the host cell is selected from the group consisting of . coli, yeast and mammalian cell lines. 30 8. A pharmaceutical composition comprising the polypeptide of claim 2 and a physiologically acceptable carrier. WO 99/38973 PCT/US99/01642 47 9. A vaccine comprising the polypeptide of claim 2 and an immune response enhancer. 5 10. The vaccine of claim 9 wherein the immune response enhancer is an adjuvant. 11. A vaccine comprising the polynucleotide of claims I or 4 and an immune response enhancer. 10 12. The vaccine of claim 11 wherein the immune response enhancer is an adjuvant. 13. A pharmaceutical composition for the treatment of lung cancer 15 comprising a polypeptide and a physiologically acceptable carrier, the polypeptide comprising an immunogenic portion of a lung protein or of a variant thereof, wherein said protein comprises an amino acid sequence encoded by a polynucleotide comprising a sequence selected from the group consisting of: (a) sequences recited in SEQ ID NO: 12-18, 20, 21, 26, 49, 50, 52, 54, 64, 20 66, 68, 69, 71, 78, 84, 85, 88, 91, 92, 116-120, 126-138, 140-142, 150, 155 and 159-181; (b) sequences complementary to the sequences of SEQ ID NO: 12-18, 20, 21, 26, 49, 50, 52, 54, 64, 66, 68, 69, 71, 78, 84, 85, 88, 91, 92, 116-120, 126-138, 140-142, 150, 155 and 159-181; and (c) variants of the sequences of (a) and (b). 25 14. A vaccine for the treatment of lung cancer comprising a polypeptide and an immune response enhancer, said polypeptide comprising an immunogenic portion of a lung protein or of a variant thereof, wherein said protein comprises an amino acid sequence encoded by a polynucleotide comprising a sequence selected from the group consisting of: 30 (a) sequences recited in SEQ ID NO: 12-18, 20, 21, 26, 49, 50, 52, 54, 64, 66, 68, 69, 71. 78, 84, 85, 88, 91, 92, 116-120, 126-138, 140-142, 150, 155 and 159-181; WO 99/38973 PCT/US99/01642 48 (b) sequences complementary to the sequences of SEQ ID NO: 12-18, 20, 21, 26, 49, 50, 52, 54, 64, 66, 68, 69, 71, 78, 84, 85, 88, 91, 92, 116-120. 126-138. 140-142, 150, 155 and 159-181; and (c) variants of the sequences of (a) and (b). 5 15. A vaccine for the treatment of lung cancer comprising a polynucleotide and an immune response enhancer, the polynucleotide comprising a sequence selected from the group consisting of: (a) sequences recited-in SEQ ID NO: 12-18, 20, 21, 26. 49, 50, 52, 54, 64, 10 66, 68, 69, 71, 78, 84, 85, 88, 91, 92, 116-120, 126-138, 140-142, 150, 155 and 159-181; (b) sequences complementary to the sequences of SEQ ID NO: 12-18, 20, 21, 26, 49, 50, 52, 54, 64, 66, 68, 69, 71, 78, 84, 85, 88, 91, 92, 116-120. 126-138, 140-142, 150, 155 and 159-181; and (c) variants of the sequences of (a) and (b). 15 16. A method for inhibiting the development of lung cancer in a patient, comprising administering to the patient an effective amount of the pharmaceutical composition of claims 8 or 13. 20 17. A method for inhibiting the development of lung cancer in a patient, comprising administering to the patient an effective amount of the vaccine of any one of claims 9, 11, 14 or 15. 18. A fusion protein comprising at least one polypeptide according to 25 claim 2. 19. A fusion protein comprising at least two polypeptides according to claim 2. 30 20. A fusion protein comprising a polypeptide according to claim 2 and a known lung tumor antigen. WO 99/38973 PCT/US99/01642 49 21. A pharmaceutical composition comprising a fusion protein according to any one of claims 18-20 and a physiologically acceptable carrier. 5 22. A vaccine comprising a fusion protein according to any one of claims 18-20 and an immune response enhancer. 23. The vaccine of claim 22 wherein the immune response enhancer is an adjuvant. 10 24. A method for inhibiting the development of lung cancer in a patient, comprising administering to the patient an effective amount of the pharmaceutical composition of claim 21. 15 25. A method for inhibiting the development of lung cancer in a patient, comprising administering to the patient an effective amount of the vaccine of claim 22. 26. A method for inhibiting the development of lung cancer in a patient, comprising administering to the patient a polynucleotide under conditions such that the 20 polynucleotide enters a cell of the patient and is expressed therein, the polynucleotide having a sequence selected from the group consisting of: (a) a sequence provided in SEQ ID NO: 102; (b) sequences complementary to a sequence of SEQ ID NO: 102; and (c) variants of the sequence of SEQ ID NO: 102. 25 27. A method for detecting lung cancer in a patient, comprising: (a) contacting a biological sample obtained from the patient with a binding agent which is capable of binding to a polypeptide, the polypeptide comprising an immunogenic portion of a lung tumor protein or a variant thereof, wherein said protein comprises an amino acid sequence encoded by a polynucleotide comprising a nucleotide 30 sequence selected from the group consisting of sequences provided in SEQ ID NO: 1-31, 49- WO 99/38973 PCT/US99/01642 50 55, 63, 64, 66, 68-72, 78-80, 84-92, 102-110, 116-120 and 126-181, the complements of said sequences and variants thereof; and (b) detecting in the sample a polypeptide that binds to the binding agent, thereby detecting lung cancer in the patient. 5 28. The method of claim 27 wherein the binding agent is a monoclonal antibody. 29. The method of claim 28 wherein the binding agent is a polyclonal antibody. 30. A method for monitoring the progression of lung cancer in a patient, 10 comprising: (a) contacting a biological sample obtained from the patient with a binding agent that is capable of binding to a polypeptide, said polypeptide comprising an immunogenic portion of a lung tumor protein or a variant thereof, wherein said protein comprises an amino acid sequence encoded by a polynucleotide comprising a nucleotide 15 sequence selected from the group consisting of sequences recited in SEQ ID NO: 1-31, 49-5 5, 63, 64, 66, 68-72, 78-80, 84-92, 102-110, 116-120 and 126-181, the complements of said sequences and variants thereof; (b) determining in the sample an amount of a polypeptide that binds to the binding agent; 20 (c) repeating steps (a) and (b); and (d) comparing the amount of polypeptide detected in steps (b) and (c) to monitor the progression of lung cancer in the patient. 31. A monoclonal antibody that binds to a polypeptide comprising an 25 immunogenic portion of a lung tumor protein or a variant thereof, wherein said protein comprises an amino acid sequence encoded by a polynucleotide comprising a nucleotide sequence selected from the group consisting of: WO 99/38973 PCTIUS99/01642 51 (a) sequences recited in SEQ ID NO: 1-11, 19, 22-25, 27-31, 51, 53, 55, 63, 70, 72, 79, 80, 86, 87, 89, 90, 102-107, 109, 139, 143-149, 151-154 and 156-158; (b) the complements of nucleotide sequences recited in SEQ ID NO: 1-11, 5 19, 22-25, 27-31, 51, 53, 55, 63, 70, 72, 79, 80, 86, 87, 89, 90, 102 107, 109, 139, 143-149, 151-154 and 156-158; and (c) variants of the sequences of (a) and (b). 32. A method for inhibiting the development of lung cancer in a patient, comprising administering to the patient a therapeutically effective amount of a monoclonal 10 antibody according to claim 31. 33. The method of claim 32 wherein the monoclonal antibody is conjugated to a therapeutic agent. 34. A method for detecting lung cancer in a patient comprising: (a) obtaining a biological sample from the patient; 15 (b) contacting the sample with at least two oligonucleotide primers in a polymerase chain reaction, wherein at least one of the oligonucleotides is specific for a polynucleotide encoding a polypeptide comprising an immunogenic portion of a lung tumor protein or a variant thereof, said protein comprising an amino acid sequence encoded by a polynucleotide comprising a nucleotide sequence selected from the group consisting of 20 sequences recited in SEQ ID NO: 1-31, 49-55, 63, 64, 66, 68-72, 78-80, 84-92, 102-110, 116 120 and 126-181, the complements of said sequences and variants thereof; and (c) detecting in the sample a DNA sequence that amplifies in the presence of the oligonucleotide primers, thereby detecting lung cancer. 35. The method of claim 34, wherein at least one of the oligonucleotide 25 primers comprises at least about 10 contiguous nucleotides of a polynucleotide comprising a sequence selected from SEQ ID NO: 1-31, 49-55, 63, 64, 66, 68-72, 78-80, 84-92, 102-110, 116-120 and 126-181. WO 99/38973 PCT/US99/01642 52 36. A diagnostic kit comprising: (a) one or more monoclonal antibodies according to claim 31; and (b) a detection reagent. 37. The kit of claim 36 wherein the monoclonal antibody is immobilized 5 on a solid support. 38. The kit of claim 37 wherein the solid support comprises nitrocellulose, latex or a plastic material. 39. The kit of claim 36 wherein the detection reagent comprises a reporter group conjugated to a binding agent. 10 40. The kit of claim 39 wherein the binding agent is selected from the group consisting of anti-immunoglobulins, Protein G, Protein A and lectins. 41. The kit of claim 39 wherein the reporter group is selected from the group consisting of radioisotopes, fluorescent groups, luminescent groups, enzymes, biotin and dye particles. 15 42. A diagnostic kit comprising at least two oligonucleotide primers, at least one of the oligonucleotide primers being specific for a polynucleotide encoding a polypeptide comprising an immunogenic portion of a lung tumor protein or a variant thereof, said protein comprising an amino acid sequence encoded by a polynucleotide comprising a nucleotide sequence selected from the group consisting of sequences recited in SEQ ID NO: 20 1-31, 49-55, 63, 64, 66, 68-72, 78-80, 84-92, 102-110, 116-120 and 126-181, the complements of said sequences and variants thereof. 43. The diagnostic kit of claim 42 wherein at least one of the oligonucleotide primers comprises at least about 10 contiguous nucleotides of a polynucleotide having a nucleotide sequence selected from the group consisting of sequences WO 99/38973 PCT/US99/01642 53 provided in SEQ ID NO: 1-31, 49-55, 63, 64, 66, 68-72, 78-80, 84-92, 102-110, 116-120 and 126-181, the complements of said sequences and variants thereof. 44. A method for detecting lung cancer in a patient, comprising: (a) obtaining a biological sample from the patient; 5 (b) contacting the biological sample with an oligonucleotide probe specific for a polynucleotide encoding a polypeptide comprising an immunogenic portion of a lung tumor protein or a variant thereof, said protein comprising an amino acid sequence encoded by a polynucleotide comprising a nucleotide sequence selected from the group consisting of sequences recited in SEQ ID NO: 1-31, 49-55, 63, 64, 66, 68-72, 78-80, 84-92, 102-110, 116 10 120 and 126-181, the complements of said nucleotide sequences and variants thereof; and (c) detecting in the sample a DNA sequence that hybridizes to the oligonucleotide probe, thereby detecting lung cancer in the patient. 45. The method of claim 44 wherein the oligonucleotide probe comprises at least about 15 contiguous nucleotides of a polynucleotide having a nucleotide sequence 15 selected from the group consisting of sequences recited in SEQ ID NO: 1-31, 49-55, 63, 64, 66, 68-72, 78-80, 84-92, 102-110, 116-120 and 126-181, the complements of said nucleotide sequences and variants thereof. 46. A diagnostic kit comprising an oligonucleotide probe specific for a polynucleotide encoding a polypeptide comprising an immunogenic portion of a lung tumor 20 protein or a variant thereof, said protein comprising an amino acid sequence encoded by a polynucleotide comprising a nucleotide sequence selected from the group consisting of sequences recited in SEQ ID NO: 1-31, 49-55, 63, 64, 66, 68-72, 78-80, 84-92, 102-110, 116 120 and 126-181, the complements of said sequences and variants thereof. 47. The diagnostic kit of claim 46, wherein the oligonucleotide probe 25 comprises at least about 15 contiguous nucleotides of a polynucleotide having a nucleotide sequence selected from the group consisting of sequences recited in SEQ ID NO: 1-31, 49-55, WO 99/38973 PCT/US99/01642 54 63, 64, 66, 68-72, 78-80, 84-92 and 102-110, the complements of said sequences and variants thereof 48. A method for treating lung cancer in a patient, comprising the steps of: (a) obtaining peripheral blood cells from the patient; 5 (b) incubating the cells in the presence of at least one polypeptide of claim 2, such that T cells proliferate; and (c) administering the proliferated T cells to the patient. 49. A method for treating lung cancer in a patient, comprising the steps of: 10 (a) obtaining peripheral blood cells from the patient; (b) incubating the cells in the presence of at least one polynucleotide of claim 1, such that T cells proliferate; and (c) administering to the patient the proliferated T cells. 15 50. The method of any one of claims 48 and 49 wherein the step of incubating the T cells is repeated one or more times. 51. The method of any one of claims 48 and 49 wherein step (a) further comprises separating T cells from the peripheral blood cells, and the cells incubated in step 20 (b) are the T cells. 52. The method of any one of claims 48 and 49 wherein step (a) further comprises separating CD4+ cells or CD8+ cells from the peripheral blood cells, and the cells proliferated in step (b) are CD4+ or CD8+ T cells. 25 53. The method of any one of claims 48 and 49 wherein step (b) further comprises cloning one or more T cells that proliferated in the presence of the polypeptide. 54. A composition for the treatment of lung cancer in a patient, comprising 30 T cells proliferated in the presence of a polypeptide of claim 2, in combination with a WO 99/38973 PCT/US99/01642 55 pharmaceutically acceptable carrier. 55. A composition for the treatment of lung cancer in a patient, comprising T cells proliferated in the presence of a polynucleotide of claim 1, in combination with a 5 pharmaceutically acceptable carrier. 56. A method for treating lung cancer in a patient, comprising the steps of: (a) incubating antigen presenting cells in the presence of at least one polypeptide of claim 2; and 10 (b) administering to the patient the incubated antigen presenting cells. 57. A method for treating lung cancer in a patient, comprising the steps of: (a) incubating antigen presenting cells in the presence of at least one polynucleotide of claim 1; and 15 (b) administering to the patient the incubated antigen presenting cells. 58. The method of claims 54 or 55 wherein the antigen presenting cells are selected from the group consisting of dendritic cells and macrophage cells. 20 59. A composition for the treatment of lung cancer in a patient, comprising antigen presenting cells incubated in the presence of a polypeptide of claim 2, in combination with a pharmaceutically acceptable carrier. 60. A composition for the treatment of lung cancer in a patient, comprising 25 antigen presenting cells incubated in the presence of a polynucleotide of claim 1, in combination with a pharmaceutically acceptable carrier.