Compositions and methods for the therapy and diagnosis of kidney cancer

Abstract

Compositions and methods for the therapy and diagnosis of cancer, particularly kidney cancer, are disclosed. Illustrative compositions comprise one or more kidney tumor polypeptides, immunogenic portions thereof, polynucleotides that encode such polypeptides, antigen presenting cell that expresses such polypeptides, and T cells that are specific for cells expressing such polypeptides. The disclosed compositions are useful, for example, in the diagnosis, prevention and/or treatment of diseases, particularly kidney cancer.

Description

STATEMENT REGARDING SEQUENCE LISTING

[0001] The Sequence Listing associated with this application is provided on CD-ROM in lieu of a paper copy, and is hereby incorporated by reference into the specification. Three CD-ROMs are provided, containing identical copies of the sequence listing: CD-ROM No. 1 is labeled COPY 1, contains the file 572.app which is 1.4 MB and created on Mar. 19, 2002; CD-ROM No.2 is labeled COPY 2, contains the file 572.app which is 1.4 MB and created on Mar. 19, 2002; CD-ROM No. 3 is labeled CRF, contains the file 572.app which is 1.4 MB and created on Mar. 19, 2002.

BACKGROUND OF THE INVENTION

[0002] 1. Field of the Invention

[0003] The present invention relates generally to therapy and diagnosis of cancer, such as kidney cancer. The invention is more specifically related to polypeptides, comprising at least a portion of a kidney tumor protein, and to polynucleotides encoding such polypeptides. Such polypeptides and polynucleotides are useful in pharmaceutical compositions, e.g., vaccines, and other compositions for the diagnosis and treatment of kidney cancer.

[0004] 2. Description of the Related Art

[0005] Cancer is a significant health problem throughout the world. Although advances have been made in detection and therapy of cancer, no vaccine or other universally successful method for prevention and/or treatment is currently available. Current therapies, which are generally based on a combination of chemotherapy or surgery and radiation, continue to prove inadequate in many patients.

[0006] Cancer is a significant health problem throughout the world. Although advances have been made in detection and therapy of cancer, no vaccine or other universally successful method for prevention and/or treatment is currently available. Current therapies, which are generally based on a combination of chemotherapy or surgery and radiation, continue to prove inadequate in many patients.

[0007] The American Cancer Society predicted that there would be about 31,200 new cases of kidney cancer in the year 2000 in the United States alone. About 11,900 people, adults and children, will die from this disease each year. The cure rate of advanced stage kidney cancer is only fair and has improved little in the last two decades.

[0008] In spite of considerable research into therapies for these and other cancers, kidney cancer remains difficult to diagnose and treat effectively. Accordingly, there is a need in the art for improved methods for detecting and treating such cancers. The present invention fulfills these needs and further provides other related advantages.

BRIEF SUMMARY OF THE INVENTION

[0009] In one aspect, the present invention provides polynucleotide compositions comprising a sequence selected from the group consisting of:

[0010] (a) sequences provided in SEQ ID NOs:1-1847, 1852-1855, and 1859-1862;

[0011] (b) complements of the sequences provided in SEQ ID NOs:1-1847, 1852-1855, and 1859-1862;

[0012] (c) sequences consisting of at least 20, 25, 30, 35, 40, 45, 50, 75 and 100 contiguous residues of a sequence provided in SEQ ID NOs:1-1847, 1852-1855, and 1859-1862;

[0013] (d) sequences that hybridize to a sequence provided in SEQ ID NOs:1-1847, 1852-1855, and 1859-1862, under moderate or highly stringent conditions;

[0014] (e) sequences having at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to a sequence of SEQ ID NOs:1-1847, 1852-1855, and 1859-1862;

[0015] (f) degenerate variants of a sequence provided in SEQ ID NOs:1-1847, 1852-1855, and 1859-1862.

[0016] In one preferred embodiment, the polynucleotide compositions of the invention are expressed in at least about 20%, more preferably in at least about 30%, and most preferably in at least about 50% of kidney tumors samples tested, at a level that is at least about 2-fold, preferably at least about 5-fold, and most preferably at least about 10-fold higher than that for normal tissues.

[0017] The present invention, in another aspect, provides polypeptide compositions comprising an amino acid sequence that is encoded by a polynucleotide sequence described above.

[0018] The present invention further provides polypeptide compositions comprising an amino acid sequence selected from the group consisting of sequences recited in SEQ ID NOs:1848-1851, 1856-1858, and 1863.

[0019] In certain preferred embodiments, the polypeptides and/or polynucleotides of the present invention are immunogenic, i.e., they are capable of eliciting an immune response, particularly a humoral and/or cellular immune response, as further described herein.

[0020] The present invention further provides fragments, variants and/or derivatives of the disclosed polypeptide and/or polynucleotide sequences, wherein the fragments, variants and/or derivatives preferably have a level of immunogenic activity of at least about 50%, preferably at least about 70% and more preferably at least about 90% of the level of immunogenic activity of a polypeptide sequence set forth in SEQ ID NOs: 1848-1851, 1856-1858, and 1863, or a polypeptide sequence encoded by a polynucleotide sequence set forth in SEQ ID NOs:1-1847, 1852-1855, and 1859-1862.

[0021] The present invention further provides polynucleotides that encode a polypeptide described above, expression vectors comprising such polynucleotides and host cells transformed or transfected with such expression vectors.

[0022] Within other aspects, the present invention provides pharmaceutical compositions comprising a polypeptide or polynucleotide as described above and a physiologically acceptable carrier.

[0023] Within a related aspect of the present invention, the pharmaceutical compositions, e.g., vaccine compositions, are provided for prophylactic or therapeutic applications. Such compositions generally comprise an immunogenic polypeptide or polynucleotide of the invention and an immunostimulant, such as an adjuvant.

[0024] The present invention further provides pharmaceutical compositions that comprise: (a) an antibody or antigen-binding fragment thereof that specifically binds to a polypeptide of the present invention, or a fragment thereof; and (b) a physiologically acceptable carrier.

[0025] Within further aspects, the present invention provides pharmaceutical compositions comprising: (a) an antigen presenting cell that expresses a polypeptide as described above and (b) a pharmaceutically acceptable carrier or excipient. Illustrative antigen presenting cells include dendritic cells, macrophages, monocytes, fibroblasts and B cells.

[0026] Within related aspects, pharmaceutical compositions are provided that comprise: (a) an antigen presenting cell that expresses a polypeptide as described above and (b) an immunostimulant.

[0027] The present invention further provides, in other aspects, fusion proteins that comprise at least one polypeptide as described above, as well as polynucleotides encoding such fusion proteins, typically in the form of pharmaceutical compositions, e.g., vaccine compositions, comprising a physiologically acceptable carrier and/or an immunostimulant. The fusions proteins may comprise multiple immunogenic polypeptides or portions/variants thereof, as described herein, and may further comprise one or more polypeptide segments for facilitating the expression, purification and/or immunogenicity of the polypeptide(s).

[0028] Within further aspects, the present invention provides methods for stimulating an immune response in a patient, preferably a T cell response in a human patient, comprising administering a pharmaceutical composition described herein. The patient may be afflicted with kidney cancer, in which case the methods provide treatment for the disease, or patient considered at risk for such a disease may be treated prophylactically.

[0029] Within further aspects, the present invention provides methods for inhibiting the development of a cancer in a patient, comprising administering to a patient a pharmaceutical composition as recited above. The patient may be afflicted with kidney cancer, in which case the methods provide treatment for the disease, or patient considered at risk for such a disease may be treated prophylactically.

[0030] The present invention further provides, within other aspects, methods for removing tumor cells from a biological sample, comprising contacting a biological sample with T cells that specifically react with a polypeptide of the present invention, wherein the step of contacting is performed under conditions and for a time sufficient to permit the removal of cells expressing the protein from the sample.

[0031] Within related aspects, methods are provided for inhibiting the development of a cancer in a patient, comprising administering to a patient a biological sample treated as described above.

[0032] Methods are further provided, within other aspects, for stimulating and/or expanding T cells specific for a polypeptide of the present invention, comprising contacting T cells with one or more of: (i) a polypeptide as described above; (ii) a polynucleotide encoding such a polypeptide; and/or (iii) an antigen presenting cell that expresses such a polypeptide; under conditions and for a time sufficient to permit the stimulation and/or expansion of T cells. Isolated T cell populations comprising T cells prepared as described above are also provided.

[0033] Within further aspects, the present invention provides methods for inhibiting the development of a cancer in a patient, comprising administering to a patient an effective amount of a T cell population as described above.

[0034] The present invention further provides methods for inhibiting the development of a cancer in a patient, comprising the steps of: (a) incubating CD4+ and/or CD8+ T cells isolated from a patient with one or more of: (i) a polypeptide comprising at least an immunogenic portion of polypeptide disclosed herein; (ii) a polynucleotide encoding such a polypeptide; and (iii) an antigen-presenting cell that expressed such a polypeptide; and (b) administering to the patient an effective amount of the proliferated T cells, and thereby inhibiting the development of a cancer in the patient. Proliferated cells may, but need not, be cloned prior to administration to the patient.

[0035] Within further aspects, the present invention provides methods for determining the presence or absence of a cancer, preferably a kidney cancer, in a patient comprising: (a) contacting a biological sample obtained from a patient with a binding agent that binds to a polypeptide as recited above; (b) detecting in the sample an amount of polypeptide that binds to the binding agent; and (c) comparing the amount of polypeptide with a predetermined cut-off value, and therefrom determining the presence or absence of a cancer in the patient. Within preferred embodiments, the binding agent is an antibody, more preferably a monoclonal antibody.

[0036] The present invention also provides, within other aspects, methods for monitoring the progression of a cancer in a patient. Such methods comprise the steps of: (a) contacting a biological sample obtained from a patient at a first point in time with a binding agent that binds to a polypeptide as recited above; (b) detecting in the sample an amount of polypeptide that binds to the binding agent; (c) repeating steps (a) and (b) using a biological sample obtained from the patient at a subsequent point in time; and (d) comparing the amount of polypeptide detected in step (c) with the amount detected in step (b) and therefrom monitoring the progression of the cancer in the patient.

[0037] The present invention further provides, within other aspects, methods for determining the presence or absence of a cancer in a patient, comprising the steps of: (a) contacting a biological sample, e.g., tumor sample, serum sample, etc., obtained from a patient with an oligonucleotide that hybridizes to a polynucleotide that encodes a polypeptide of the present invention; (b) detecting in the sample a level of a polynucleotide, preferably mRNA, that hybridizes to the oligonucleotide; and (c) comparing the level of polynucleotide that hybridizes to the oligonucleotide with a predetermined cut-off value, and therefrom determining the presence or absence of a cancer in the patient. Within certain embodiments, the amount of mRNA is detected via polymerase chain reaction using, for example, at least one oligonucleotide primer that hybridizes to a polynucleotide encoding a polypeptide as recited above, or a complement of such a polynucleotide. Within other embodiments, the amount of mRNA is detected using a hybridization technique, employing an oligonucleotide probe that hybridizes to a polynucleotide that encodes a polypeptide as recited above, or a complement of such a polynucleotide.

[0038] In related aspects, methods are provided for monitoring the progression of a cancer in a patient, comprising the steps of: (a) contacting a biological sample obtained from a patient with an oligonucleotide that hybridizes to a polynucleotide that encodes a polypeptide of the present invention; (b) detecting in the sample an amount of a polynucleotide that hybridizes to the oligonucleotide; (c) repeating steps (a) and (b) using a biological sample obtained from the patient at a subsequent point in time; and (d) comparing the amount of polynucleotide detected in step (c) with the amount detected in step (b) and therefrom monitoring the progression of the cancer in the patient.

[0039] Within further aspects, the present invention provides antibodies, such as monoclonal antibodies, that bind to a polypeptide as described above, as well as diagnostic kits comprising such antibodies. Diagnostic kits comprising one or more oligonucleotide probes or primers as described above are also provided.

[0040] 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 each was incorporated individually.

BRIEF DESCRIPTION OF THE SEQUENCE IDENTIFIERS

[0041] SEQ ID NO:1-157 are the determined cDNA sequences for the clones described in Tables 2-3.

[0042] SEQ ID NO:158 is the determined cDNA sequence for clone 61931552.

[0043] SEQ ID NO:159 is the determined cDNA sequence for clone 61931599.

[0044] SEQ ID NO:160 is the determined cDNA sequence for clone 61931601.

[0045] SEQ ID NO:161 is the determined cDNA sequence for clone 61931551.

[0046] SEQ ID NO:162 is the determined cDNA sequence for clone 61931553.

[0047] SEQ ID NO:163 is the determined cDNA sequence for clone 61931555.

[0048] SEQ ID NO:164 is the determined cDNA sequence for clone 61931598.

[0049] SEQ ID NO:165 is the determined cDNA sequence for clone 61931600.

[0050] SEQ ID NO:166 is the determined cDNA sequence for clone 61931556.

[0051] SEQ ID NO:167 is the determined cDNA sequence for clone 61931558.

[0052] SEQ ID NO:168 is the determined cDNA sequence for clone 61931560.

[0053] SEQ ID NO:169 is the determined cDNA sequence for clone 61931603.

[0054] SEQ ID NO:170 is the determined cDNA sequence for clone 61931605.

[0055] SEQ ID NO:171 is the determined cDNA sequence for clone 61931607.

[0056] SEQ ID NO:172 is the determined cDNA sequence for clone 61931557.

[0057] SEQ ID NO:173 is the determined cDNA sequence for clone 61931559.

[0058] SEQ ID NO:174 is the determined cDNA sequence for clone 61931561.

[0059] SEQ ID NO:175 is the determined cDNA sequence for clone 61931604.

[0060] SEQ ID NO:176 is the determined cDNA sequence for clone 61931606.

[0061] SEQ ID NO:177 is the determined cDNA sequence for clone 61931608.

[0062] SEQ ID NO:178 is the determined cDNA sequence for clone 61931562.

[0063] SEQ ID NO:179 is the determined cDNA sequence for clone 61931564.

[0064] SEQ ID NO:180 is the determined cDNA sequence for clone 61931566.

[0065] SEQ ID NO:181 is the determined cDNA sequence for clone 61931609.

[0066] SEQ ID NO:182 is the determined cDNA sequence for clone 61931563.

[0067] SEQ ID NO:183 is the determined cDNA sequence for clone 61931565.

[0068] SEQ ID NO:184 is the determined cDNA sequence for clone 61931567.

[0069] SEQ ID NO:185 is the determined cDNA sequence for clone 61931610.

[0070] SEQ ID NO:186 is the determined cDNA sequence for clone 61931612.

[0071] SEQ ID NO:187 is the determined cDNA sequence for clone 61931568.

[0072] SEQ ID NO:188 is the determined cDNA sequence for clone 61931570.

[0073] SEQ ID NO:189 is the determined cDNA sequence for clone 61931572.

[0074] SEQ ID NO:190 is the determined cDNA sequence for clone 61931615.

[0075] SEQ ID NO:191 is the determined cDNA sequence for clone 61931617.

[0076] SEQ ID NO:192 is the determined cDNA sequence for clone 61931619.

[0077] SEQ ID NO:193 is the determined cDNA sequence for clone 61931569.

[0078] SEQ ID NO:194 is the determined cDNA sequence for clone 61931571.

[0079] SEQ ID NO:195 is the determined cDNA sequence for clone 61931573.

[0080] SEQ ID NO:196 is the determined cDNA sequence for clone 61931616.

[0081] SEQ ID NO:197 is the determined cDNA sequence for clone 61931618.

[0082] SEQ ID NO:198 is the determined cDNA sequence for clone 61931620.

[0083] SEQ ID NO:199 is the determined cDNA sequence for clone 61931574.

[0084] SEQ ID NO:200 is the determined cDNA sequence for clone 61931576.

[0085] SEQ ID NO:201 is the determined cDNA sequence for clone 61931578.

[0086] SEQ ID NO:202 is the determined cDNA sequence for clone 61931621.

[0087] SEQ ID NO:203 is the determined cDNA sequence for clone 61931623.

[0088] SEQ ID NO:204 is the determined cDNA sequence for clone 61931625.

[0089] SEQ ID NO:205 is the determined cDNA sequence for clone 61931575.

[0090] SEQ ID NO:206 is the determined cDNA sequence for clone 61931577.

[0091] SEQ ID NO:207 is the determined cDNA sequence for clone 61931579.

[0092] SEQ ID NO:208 is the determined cDNA sequence for clone 61931622.

[0093] SEQ ID NO:209 is the determined cDNA sequence for clone 61931624.

[0094] SEQ ID NO:210 is the determined cDNA sequence for clone 61931626.

[0095] SEQ ID NO:211 is the determined cDNA sequence for clone 61931580.

[0096] SEQ ID NO:212 is the determined cDNA sequence for clone 61931582.

[0097] SEQ ID NO:213 is the determined cDNA sequence for clone 61931584.

[0098] SEQ ID NO:214 is the determined cDNA sequence for clone 61931629.

[0099] SEQ ID NO:215 is the determined cDNA sequence for clone 61931631.

[0100] SEQ ID NO:216 is the determined cDNA sequence for clone 61931581.

[0101] SEQ ID NO:217 is the determined cDNA sequence for clone 61931583.

[0102] SEQ ID NO:218 is the determined cDNA sequence for clone 61931585.

[0103] SEQ ID NO:219 is the determined cDNA sequence for clone 61931628.

[0104] SEQ ID NO:220 is the determined cDNA sequence for clone 61931630.

[0105] SEQ ID NO:221 is the determined cDNA sequence for clone 61931632.

[0106] SEQ ID NO:222 is the determined cDNA sequence for clone 61931586.

[0107] SEQ ID NO:223 is the determined cDNA sequence for clone 61931588.

[0108] SEQ ID NO:224 is the determined cDNA sequence for clone 61931590.

[0109] SEQ ID NO:225 is the determined cDNA sequence for clone 61931633.

[0110] SEQ ID NO:226 is the determined cDNA sequence for clone 61931635.

[0111] SEQ ID NO:227 is the determined cDNA sequence for clone 61931637.

[0112] SEQ ID NO:228 is the determined cDNA sequence for clone 61931589.

[0113] SEQ ID NO:229 is the determined cDNA sequence for clone 61931591.

[0114] SEQ ID NO:230 is the determined cDNA sequence for clone 61931634.

[0115] SEQ ID NO:231 is the determined cDNA sequence for clone 61931636.

[0116] SEQ ID NO:232 is the determined cDNA sequence for clone 61931638.

[0117] SEQ ID NO:233 is the determined cDNA sequence for clone 61931592.

[0118] SEQ ID NO:234 is the determined cDNA sequence for clone 61931594.

[0119] SEQ ID NO:235 is the determined cDNA sequence for clone 61931596.

[0120] SEQ ID NO:236 is the determined cDNA sequence for clone 61931639.

[0121] SEQ ID NO:237 is the determined cDNA sequence for clone 61931641.

[0122] SEQ ID NO:238 is the determined cDNA sequence for clone 61931643.

[0123] SEQ ID NO:239 is the determined cDNA sequence for clone 61931593.

[0124] SEQ ID NO:240 is the determined cDNA sequence for clone 61931595.

[0125] SEQ ID NO:241 is the determined cDNA sequence for clone 61931597.

[0126] SEQ ID NO:242 is the determined cDNA sequence for clone 61931642.

[0127] SEQ ID NO:243 is the determined cDNA sequence for clone 61871832.

[0128] SEQ ID NO:244 is the determined cDNA sequence for clone 61871834.

[0129] SEQ ID NO:245 is the determined cDNA sequence for clone 61871879.

[0130] SEQ ID NO:246 is the determined cDNA sequence for clone 61871881.

[0131] SEQ ID NO:247 is the determined cDNA sequence for clone 61871831.

[0132] SEQ ID NO:248 is the determined cDNA sequence for clone 61871833.

[0133] SEQ ID NO:249 is the determined cDNA sequence for clone 61871835.

[0134] SEQ ID NO:250 is the determined cDNA sequence for clone 61871878.

[0135] SEQ ID NO:251 is the determined cDNA sequence for clone 61871880.

[0136] SEQ ID NO:252 is the determined cDNA sequence for clone 61871882.

[0137] SEQ ID NO:253 is the determined cDNA sequence for clone 61871836.

[0138] SEQ ID NO:254 is the determined cDNA sequence for clone 61871838.

[0139] SEQ ID NO:255 is the determined cDNA sequence for clone 61871840.

[0140] SEQ ID NO:256 is the determined cDNA sequence for clone 61871883.

[0141] SEQ ID NO:257 is the determined cDNA sequence for clone 61871885.

[0142] SEQ ID NO:258 is the determined cDNA sequence for clone 61871887.

[0143] SEQ ID NO:259 is the determined cDNA sequence for clone 61871837.

[0144] SEQ ID NO:260 is the determined cDNA sequence for clone 61871839.

[0145] SEQ ID NO:261 is the determined cDNA sequence for clone 61871841.

[0146] SEQ ID NO:262 is the determined cDNA sequence for clone 61871884.

[0147] SEQ ID NO:263 is the determined cDNA sequence for clone 61871886.

[0148] SEQ ID NO:264 is the determined cDNA sequence for clone 61871888.

[0149] SEQ ID NO:265 is the determined cDNA sequence for clone 61871846.

[0150] SEQ ID NO:266 is the determined cDNA sequence for clone 61871889.

[0151] SEQ ID NO:267 is the determined cDNA sequence for clone 61871891.

[0152] SEQ ID NO:268 is the determined cDNA sequence for clone 61871893.

[0153] SEQ ID NO:269 is the determined cDNA sequence for clone 61871843.

[0154] SEQ ID NO:270 is the determined cDNA sequence for clone 61871890.

[0155] SEQ ID NO:271 is the determined cDNA sequence for clone 61871892.

[0156] SEQ ID NO:272 is the determined cDNA sequence for clone 61871894.

[0157] SEQ ID NO:273 is the determined cDNA sequence for clone 61871848.

[0158] SEQ ID NO:274 is the determined cDNA sequence for clone 61871850.

[0159] SEQ ID NO:275 is the determined cDNA sequence for clone 61871852.

[0160] SEQ ID NO:276 is the determined cDNA sequence for clone 61871895.

[0161] SEQ ID NO:277 is the determined cDNA sequence for clone 61871897.

[0162] SEQ ID NO:278 is the determined cDNA sequence for clone 61871899.

[0163] SEQ ID NO:279 is the determined cDNA sequence for clone 61871849.

[0164] SEQ ID NO:280 is the determined cDNA sequence for clone 61871851.

[0165] SEQ ID NO:281 is the determined cDNA sequence for clone 61871853.

[0166] SEQ ID NO:282 is the determined cDNA sequence for clone 61871896.

[0167] SEQ ID NO:283 is the determined cDNA sequence for clone 61871898.

[0168] SEQ ID NO:284 is the determined cDNA sequence for clone 61871900.

[0169] SEQ ID NO:285 is the determined cDNA sequence for clone 61871854.

[0170] SEQ ID NO:286 is the determined cDNA sequence for clone 61871856.

[0171] SEQ ID NO:287 is the determined cDNA sequence for clone 61871858.

[0172] SEQ ID NO:288 is the determined cDNA sequence for clone 61871901.

[0173] SEQ ID NO:289 is the determined cDNA sequence for clone 61871903.

[0174] SEQ ID NO:290 is the determined cDNA sequence for clone 61871905.

[0175] SEQ ID NO:291 is the determined cDNA sequence for clone 61871855.

[0176] SEQ ID NO:292 is the determined cDNA sequence for clone 61871857.

[0177] SEQ ID NO:293 is the determined cDNA sequence for clone 61871859.

[0178] SEQ ID NO:294 is the determined cDNA sequence for clone 61871902.

[0179] SEQ ID NO:295 is the determined cDNA sequence for clone 61871904.

[0180] SEQ ID NO:296 is the determined cDNA sequence for clone 61871906.

[0181] SEQ ID NO:297 is the determined cDNA sequence for clone 61871860.

[0182] SEQ ID NO:298 is the determined cDNA sequence for clone 61871862.

[0183] SEQ ID NO:299 is the determined cDNA sequence for clone 61871864.

[0184] SEQ ID NO:300 is the determined cDNA sequence for clone 61871907.

[0185] SEQ ID NO:301 is the determined cDNA sequence for clone 61871909.

[0186] SEQ ID NO:302 is the determined cDNA sequence for clone 61871911.

[0187] SEQ ID NO:303 is the determined cDNA sequence for clone 61871861.

[0188] SEQ ID NO:304 is the determined cDNA sequence for clone 61871865.

[0189] SEQ ID NO:305 is the determined cDNA sequence for clone 61871908.

[0190] SEQ ID NO:306 is the determined cDNA sequence for clone 61871910.

[0191] SEQ ID NO:307 is the determined cDNA sequence for clone 61871866.

[0192] SEQ ID NO:308 is the determined cDNA sequence for clone 61871868.

[0193] SEQ ID NO:309 is the determined cDNA sequence for clone 61871870.

[0194] SEQ ID NO:310 is the determined cDNA sequence for clone 61871913.

[0195] SEQ ID NO:311 is the determined cDNA sequence for clone 61871915.

[0196] SEQ ID NO:312 is the determined cDNA sequence for clone 61871917.

[0197] SEQ ID NO:313 is the determined cDNA sequence for clone 61871867.

[0198] SEQ ID NO:314 is the determined cDNA sequence for clone 61871869.

[0199] SEQ ID NO:315 is the determined cDNA sequence for clone 61871871.

[0200] SEQ ID NO:316 is the determined cDNA sequence for clone 61871914.

[0201] SEQ ID NO:317 is the determined cDNA sequence for clone 61871916.

[0202] SEQ ID NO:318 is the determined cDNA sequence for clone 61871918.

[0203] SEQ ID NO:319 is the determined cDNA sequence for clone 61871872.

[0204] SEQ ID NO:320 is the determined cDNA sequence for clone 61871874.

[0205] SEQ ID NO:321 is the determined cDNA sequence for clone 61871876.

[0206] SEQ ID NO:322 is the determined cDNA sequence for clone 61871919.

[0207] SEQ ID NO:323 is the determined cDNA sequence for clone 61871923.

[0208] SEQ ID NO:324 is the determined cDNA sequence for clone 61871875

[0209] SEQ ID NO:325 is the determined cDNA sequence for clone 61871877.

[0210] SEQ ID NO:326 is the determined cDNA sequence for clone 61871920.

[0211] SEQ ID NO:327 is the determined cDNA sequence for clone 61871922.

[0212] SEQ ID NO:328 is the determined cDNA sequence for clone 61871181.

[0213] SEQ ID NO:329 is the determined cDNA sequence for clone 61871183.

[0214] SEQ ID NO:330 is the determined cDNA sequence for clone 61871230.

[0215] SEQ ID NO:331 is the determined cDNA sequence for clone 61871180.

[0216] SEQ ID NO:332 is the determined cDNA sequence for clone 61871182.

[0217] SEQ ID NO:333 is the determined cDNA sequence for clone 61871184.

[0218] SEQ ID NO:334 is the determined cDNA sequence for clone 61871227.

[0219] SEQ ID NO:335 is the determined cDNA sequence for clone 61871229.

[0220] SEQ ID NO:336 is the determined cDNA sequence for clone 61871231.

[0221] SEQ ID NO:337 is the determined cDNA sequence for clone 61871187.

[0222] SEQ ID NO:338 is the determined cDNA sequence for clone 61871189.

[0223] SEQ ID NO:339 is the determined cDNA sequence for clone 61871232.

[0224] SEQ ID NO:340 is the determined cDNA sequence for clone 61871234

[0225] SEQ ID NO:341 is the determined cDNA sequence for clone 61871236.

[0226] SEQ ID NO:342 is the determined cDNA sequence for clone 61871186.

[0227] SEQ ID NO:343 is the determined cDNA sequence for clone 61871188.

[0228] SEQ ID NO:344 is the determined cDNA sequence for clone 61871190.

[0229] SEQ ID NO:345 is the determined cDNA sequence for clone 61871233.

[0230] SEQ ID NO:346 is the determined cDNA sequence for clone 61871235.

[0231] SEQ ID NO:347 is the determined cDNA sequence for clone 61871237.

[0232] SEQ ID NO:348 is the determined cDNA sequence for clone 61871191.

[0233] SEQ ID NO:349 is the determined cDNA sequence for clone 61871193.

[0234] SEQ ID NO:350 is the determined cDNA sequence for clone 61871195.

[0235] SEQ ID NO:351 is the determined cDNA sequence for clone 61871238.

[0236] SEQ ID NO:352 is the determined cDNA sequence for clone 61871240.

[0237] SEQ ID NO:353 is the determined cDNA sequence for clone 61871242.

[0238] SEQ ID NO:354 is the determined cDNA sequence for clone 61871192.

[0239] SEQ ID NO:355 is the determined cDNA sequence for clone 61871194.

[0240] SEQ ID NO:356 is the determined cDNA sequence for clone 61871196.

[0241] SEQ ID NO:357 is the determined cDNA sequence for clone 61871239.

[0242] SEQ ID NO:358 is the determined cDNA sequence for clone 61871241.

[0243] SEQ ID NO:359 is the determined cDNA sequence for clone 61871243.

[0244] SEQ ID NO:360 is the determined cDNA sequence for clone 61871197.

[0245] SEQ ID NO:361 is the determined cDNA sequence for clone 61871199.

[0246] SEQ ID NO:362 is the determined cDNA sequence for clone 61871201.

[0247] SEQ ID NO:363 is the determined cDNA sequence for clone 61871244.

[0248] SEQ ID NO:364 is the determined cDNA sequence for clone 61871246.

[0249] SEQ ID NO:365 is the determined cDNA sequence for clone 61871248.

[0250] SEQ ID NO:366 is the determined cDNA sequence for clone 61871198.

[0251] SEQ ID NO:367 is the determined cDNA sequence for clone 61871200.

[0252] SEQ ID NO:368 is the determined cDNA sequence for clone 61871202.

[0253] SEQ ID NO:369 is the determined cDNA sequence for clone 61871245.

[0254] SEQ ID NO:370 is the determined cDNA sequence for clone 61871247.

[0255] SEQ ID NO:371 is the determined cDNA sequence for clone 61871249.

[0256] SEQ ID NO:372 is the determined cDNA sequence for clone 61871203.

[0257] SEQ ID NO:373 is the determined cDNA sequence for clone 61871205.

[0258] SEQ ID NO:374 is the determined cDNA sequence for clone 61871207.

[0259] SEQ ID NO:375 is the determined cDNA sequence for clone 61871250.

[0260] SEQ ID NO:376 is the determined cDNA sequence for clone 61871254.

[0261] SEQ ID NO:377 is the determined cDNA sequence for clone 61871204.

[0262] SEQ ID NO:378 is the determined cDNA sequence for clone 61871206.

[0263] SEQ ID NO:379 is the determined cDNA sequence for clone 61871208.

[0264] SEQ ID NO:380 is the determined cDNA sequence for clone 61871251.

[0265] SEQ ID NO:381 is the determined cDNA sequence for clone 61871253.

[0266] SEQ ID NO:382 is the determined cDNA sequence for clone 61871255.

[0267] SEQ ID NO:383 is the determined cDNA sequence for clone 61871209.

[0268] SEQ ID NO:384 is the determined cDNA sequence for clone 61871211.

[0269] SEQ ID NO:385 is the determined cDNA sequence for clone 61871213.

[0270] SEQ ID NO:386 is the determined cDNA sequence for clone 61871258.

[0271] SEQ ID NO:387 is the determined cDNA sequence for clone 61871260.

[0272] SEQ ID NO:388 is the determined cDNA sequence for clone 61871210.

[0273] SEQ ID NO:389 is the determined cDNA sequence for clone 61871212.

[0274] SEQ ID NO:390 is the determined cDNA sequence for clone 61871214.

[0275] SEQ ID NO:391 is the determined cDNA sequence for clone 61871257.

[0276] SEQ ID NO:392 is the determined cDNA sequence for clone 61871259.

[0277] SEQ ID NO:393 is the determined cDNA sequence for clone 61871261.

[0278] SEQ ID NO:394 is the determined cDNA sequence for clone 61871215.

[0279] SEQ ID NO:395 is the determined cDNA sequence for clone 61871217.

[0280] SEQ ID NO:396 is the determined cDNA sequence for clone 61871219.

[0281] SEQ ID NO:397 is the determined cDNA sequence for clone 61871264.

[0282] SEQ ID NO:398 is the determined cDNA sequence for clone 61871266.

[0283] SEQ ID NO:399 is the determined cDNA sequence for clone 61871218.

[0284] SEQ ID NO:400 is the determined cDNA sequence for clone 61871220.

[0285] SEQ ID NO:401 is the determined cDNA sequence for clone 61871263.

[0286] SEQ ID NO:402 is the determined cDNA sequence for clone 61871267.

[0287] SEQ ID NO:403 is the determined cDNA sequence for clone 61871221.

[0288] SEQ ID NO:404 is the determined cDNA sequence for clone 61871223.

[0289] SEQ ID NO:405 is the determined cDNA sequence for clone 61871225.

[0290] SEQ ID NO:406 is the determined cDNA sequence for clone 61871270.

[0291] SEQ ID NO:407 is the determined cDNA sequence for clone 61871272.

[0292] SEQ ID NO:408 is the determined cDNA sequence for clone 61871222.

[0293] SEQ ID NO:409 is the determined cDNA sequence for clone 61871226.

[0294] SEQ ID NO:410 is the determined cDNA sequence for clone 61871269.

[0295] SEQ ID NO:411 is the determined cDNA sequence for clone 61871271.

[0296] SEQ ID NO:412 is the determined cDNA sequence for clone 61590220.

[0297] SEQ ID NO:413 is the determined cDNA sequence for clone 61590265.

[0298] SEQ ID NO:414 is the determined cDNA sequence for clone 61590267.

[0299] SEQ ID NO:415 is the determined cDNA sequence for clone 61590217.

[0300] SEQ ID NO:416 is the determined cDNA sequence for clone 61590219.

[0301] SEQ ID NO:417 is the determined cDNA sequence for clone 61590264.

[0302] SEQ ID NO:418 is the determined cDNA sequence for clone 61590266.

[0303] SEQ ID NO:419 is the determined cDNA sequence for clone 61590268.

[0304] SEQ ID NO:420 is the determined cDNA sequence for clone 61590222.

[0305] SEQ ID NO:421 is the determined cDNA sequence for clone 61590224.

[0306] SEQ ID NO:422 is the determined cDNA sequence for clone 61590226.

[0307] SEQ ID NO:423 is the determined cDNA sequence for clone 61590269.

[0308] SEQ ID NO:424 is the determined cDNA sequence for clone 61590271.

[0309] SEQ ID NO:425 is the determined cDNA sequence for clone 61590273.

[0310] SEQ ID NO:426 is the determined cDNA sequence for clone 61590223.

[0311] SEQ ID NO:427 is the determined cDNA sequence for clone 61590225.

[0312] SEQ ID NO:428 is the determined cDNA sequence for clone 61590227.

[0313] SEQ ID NO:429 is the determined cDNA sequence for clone 61590270.

[0314] SEQ ID NO:430 is the determined cDNA sequence for clone 61590272.

[0315] SEQ ID NO:431 is the determined cDNA sequence for clone 61590274.

[0316] SEQ ID NO:432 is the determined cDNA sequence for clone 61590228.

[0317] SEQ ID NO:433 is the determined cDNA sequence for clone 61590232.

[0318] SEQ ID NO:434 is the determined cDNA sequence for clone 61590275.

[0319] SEQ ID NO:435 is the determined cDNA sequence for clone 61590277.

[0320] SEQ ID NO:436 is the determined cDNA sequence for clone 61590279.

[0321] SEQ ID NO:437 is the determined cDNA sequence for clone 61590229.

[0322] SEQ ID NO:438 is the determined cDNA sequence for clone 61590233.

[0323] SEQ ID NO:439 is the determined cDNA sequence for clone 61590280.

[0324] SEQ ID NO:440 is the determined cDNA sequence for clone 61590236.

[0325] SEQ ID NO:441 is the determined cDNA sequence for clone 61590238.

[0326] SEQ ID NO:442 is the determined cDNA sequence for clone 61590281.

[0327] SEQ ID NO:443 is the determined cDNA sequence for clone 61590283.

[0328] SEQ ID NO:444 is the determined cDNA sequence for clone 61590285.

[0329] SEQ ID NO:445 is the determined cDNA sequence for clone 61590237.

[0330] SEQ ID NO:446 is the determined cDNA sequence for clone 61590239.

[0331] SEQ ID NO:447 is the determined cDNA sequence for clone 61590284.

[0332] SEQ ID NO:448 is the determined cDNA sequence for clone 61590240.

[0333] SEQ ID NO:449 is the determined cDNA sequence for clone 61590242.

[0334] SEQ ID NO:450 is the determined cDNA sequence for clone 61590244.

[0335] SEQ ID NO:451 is the determined cDNA sequence for clone 61590287.

[0336] SEQ ID NO:452 is the determined cDNA sequence for clone 61590289.

[0337] SEQ ID NO:453 is the determined cDNA sequence for clone 61590291.

[0338] SEQ ID NO:454 is the determined cDNA sequence for clone 61590241.

[0339] SEQ ID NO:455 is the determined cDNA sequence for clone 61590243.

[0340] SEQ ID NO:456 is the determined cDNA sequence for clone 61590245.

[0341] SEQ ID NO:457 is the determined cDNA sequence for clone 61590288.

[0342] SEQ ID NO:458 is the determined cDNA sequence for clone 61590290.

[0343] SEQ ID NO:459 is the determined cDNA sequence for clone 61590292.

[0344] SEQ ID NO:460 is the determined cDNA sequence for clone 61590246.

[0345] SEQ ID NO:461 is the determined cDNA sequence for clone 61590248.

[0346] SEQ ID NO:462 is the determined cDNA sequence for clone 61590293.

[0347] SEQ ID NO:463 is the determined cDNA sequence for clone 61590295.

[0348] SEQ ID NO:464 is the determined cDNA sequence for clone 61590297.

[0349] SEQ ID NO:465 is the determined cDNA sequence for clone 61590247.

[0350] SEQ ID NO:466 is the determined cDNA sequence for clone 61590249.

[0351] SEQ ID NO:467 is the determined cDNA sequence for clone 61590251.

[0352] SEQ ID NO:468 is the determined cDNA sequence for clone 61590296.

[0353] SEQ ID NO:469 is the determined cDNA sequence for clone 61590298.

[0354] SEQ ID NO:470 is the determined cDNA sequence for clone 61590252.

[0355] SEQ ID NO:471 is the determined cDNA sequence for clone 61590254.

[0356] SEQ ID NO:472 is the determined cDNA sequence for clone 61590256.

[0357] SEQ ID NO:473 is the determined cDNA sequence for clone 61590299.

[0358] SEQ ID NO:474 is the determined cDNA sequence for clone 61590301.

[0359] SEQ ID NO:475 is the determined cDNA sequence for clone 61590303.

[0360] SEQ ID NO:476 is the determined cDNA sequence for clone 61590253.

[0361] SEQ ID NO:477 is the determined cDNA sequence for clone 61590255.

[0362] SEQ ID NO:478 is the determined cDNA sequence for clone 61590300.

[0363] SEQ ID NO:479 is the determined cDNA sequence for clone 61590302.

[0364] SEQ ID NO:480 is the determined cDNA sequence for clone 61590304.

[0365] SEQ ID NO:481 is the determined cDNA sequence for clone 61590260.

[0366] SEQ ID NO:482 is the determined cDNA sequence for clone 61590262.

[0367] SEQ ID NO:483 is the determined cDNA sequence for clone 61590305.

[0368] SEQ ID NO:484 is the determined cDNA sequence for clone 61590307.

[0369] SEQ ID NO:485 is the determined cDNA sequence for clone 61590259.

[0370] SEQ ID NO:486 is the determined cDNA sequence for clone 61590261.

[0371] SEQ ID NO:487 is the determined cDNA sequence for clone 61590263.

[0372] SEQ ID NO:488 is the determined cDNA sequence for clone 61590306.

[0373] SEQ ID NO:489 is the determined cDNA sequence for clone 61590308.

[0374] SEQ ID NO:490 is the determined cDNA sequence for clone 61871460.

[0375] SEQ ID NO:491 is the determined cDNA sequence for clone 61871507.

[0376] SEQ ID NO:492 is the determined cDNA sequence for clone 61871509.

[0377] SEQ ID NO:493 is the determined cDNA sequence for clone 61871459.

[0378] SEQ ID NO:494 is the determined cDNA sequence for clone 61871461.

[0379] SEQ ID NO:495 is the determined cDNA sequence for clone 61871463. SEQ ID NO:496 is the determined cDNA sequence for clone 61871506.

[0380] SEQ ID NO:497 is the determined cDNA sequence for clone 61871508.

[0381] SEQ ID NO:498 is the determined cDNA sequence for clone 61871464.

[0382] SEQ ID NO:499 is the determined cDNA sequence for clone 61871466.

[0383] SEQ ID NO:500 is the determined cDNA sequence for clone 61871468.

[0384] SEQ ID NO:501 is the determined cDNA sequence for clone 61871511.

[0385] SEQ ID NO:502 is the determined cDNA sequence for clone 61871513.

[0386] SEQ ID NO:503 is the determined cDNA sequence for clone 61871515.

[0387] SEQ ID NO:504 is the determined cDNA sequence for clone 61871465.

[0388] SEQ ID NO:505 is the determined cDNA sequence for clone 61871467.

[0389] SEQ ID NO:506 is the determined cDNA sequence for clone 61871469.

[0390] SEQ ID NO:507 is the determined cDNA sequence for clone 61871512.

[0391] SEQ ID NO:508 is the determined cDNA sequence for clone 61871514.

[0392] SEQ ID NO:509 is the determined cDNA sequence for clone 61871516.

[0393] SEQ ID NO:510 is the determined cDNA sequence for clone 61871470.

[0394] SEQ ID NO:511 is the determined cDNA sequence for clone 61871472.

[0395] SEQ ID NO:512 is the determined cDNA sequence for clone 61871517.

[0396] SEQ ID NO:513 is the determined cDNA sequence for clone 61871519.

[0397] SEQ ID NO:514 is the determined cDNA sequence for clone 61871521.

[0398] SEQ ID NO:515 is the determined cDNA sequence for clone 61871471.

[0399] SEQ ID NO:516 is the determined cDNA sequence for clone 61871475.

[0400] SEQ ID NO:517 is the determined cDNA sequence for clone 61871518.

[0401] SEQ ID NO:518 is the determined cDNA sequence for clone 61871520.

[0402] SEQ ID NO:519 is the determined cDNA sequence for clone 61871522.

[0403] SEQ ID NO:520 is the determined cDNA sequence for clone 61871476.

[0404] SEQ ID NO:521 is the determined cDNA sequence for clone 61871478.

[0405] SEQ ID NO:522 is the determined cDNA sequence for clone 61871480.

[0406] SEQ ID NO:523 is the determined cDNA sequence for clone 61871523.

[0407] SEQ ID NO:524 is the determined cDNA sequence for clone 61871525.

[0408] SEQ ID NO:525 is the determined cDNA sequence for clone 61871527.

[0409] SEQ ID NO:526 is the determined cDNA sequence for clone 61871477.

[0410] SEQ ID NO:527 is the determined cDNA sequence for clone 61871479.

[0411] SEQ ID NO:528 is the determined cDNA sequence for clone 61871481.

[0412] SEQ ID NO:529 is the determined cDNA sequence for clone 61871524.

[0413] SEQ ID NO:530 is the determined cDNA sequence for clone 61871526.

[0414] SEQ ID NO:531 is the determined cDNA sequence for clone 61871482.

[0415] SEQ ID NO:532 is the determined cDNA sequence for clone 61871484.

[0416] SEQ ID NO:533 is the determined cDNA sequence for clone 61871486.

[0417] SEQ ID NO:534 is the determined cDNA sequence for clone 61871529.

[0418] SEQ ID NO:535 is the determined cDNA sequence for clone 61871531.

[0419] SEQ ID NO:536 is the determined cDNA sequence for clone 61871483.

[0420] SEQ ID NO:537 is the determined cDNA sequence for clone 61871530.

[0421] SEQ ID NO:538 is the determined cDNA sequence for clone 61871532.

[0422] SEQ ID NO:539 is the determined cDNA sequence for clone 61871534.

[0423] SEQ ID NO:540 is the determined cDNA sequence for clone 61871488.

[0424] SEQ ID NO:541 is the determined cDNA sequence for clone 61871490.

[0425] SEQ ID NO:542 is the determined cDNA sequence for clone 61871492.

[0426] SEQ ID NO:543 is the determined cDNA sequence for clone 61871537.

[0427] SEQ ID NO:544 is the determined cDNA sequence for clone 61871539.

[0428] SEQ ID NO:545 is the determined cDNA sequence for clone 61871489.

[0429] SEQ ID NO:546 is the determined cDNA sequence for clone 61871493.

[0430] SEQ ID NO:547 is the determined cDNA sequence for clone 61871536.

[0431] SEQ ID NO:548 is the determined cDNA sequence for clone 61871538.

[0432] SEQ ID NO:549 is the determined cDNA sequence for clone 61871540.

[0433] SEQ ID NO:550 is the determined cDNA sequence for clone 61871494.

[0434] SEQ ID NO:551 is the determined cDNA sequence for clone 61871496.

[0435] SEQ ID NO:552 is the determined cDNA sequence for clone 61871498.

[0436] SEQ ID NO:553 is the determined cDNA sequence for clone 61871541.

[0437] SEQ ID NO:554 is the determined cDNA sequence for clone 61871543.

[0438] SEQ ID NO:555 is the determined cDNA sequence for clone 61871545.

[0439] SEQ ID NO:556 is the determined cDNA sequence for clone 61871495.

[0440] SEQ ID NO:557 is the determined cDNA sequence for clone 61871497.

[0441] SEQ ID NO:558 is the determined cDNA sequence for clone 61871499.

[0442] SEQ ID NO:559 is the determined cDNA sequence for clone 61871544.

[0443] SEQ ID NO:560 is the determined cDNA sequence for clone 61871546.

[0444] SEQ ID NO:561 is the determined cDNA sequence for clone 61871500.

[0445] SEQ ID NO:562 is the determined cDNA sequence for clone 61871502.

[0446] SEQ ID NO:563 is the determined cDNA sequence for clone 61871504.

[0447] SEQ ID NO:564 is the determined cDNA sequence for clone 61871547.

[0448] SEQ ID NO:565 is the determined cDNA sequence for clone 61871551.

[0449] SEQ ID NO:566 is the determined cDNA sequence for clone 61871501.

[0450] SEQ ID NO:567 is the determined cDNA sequence for clone 61871503.

[0451] SEQ ID NO:568 is the determined cDNA sequence for clone 61871505.

[0452] SEQ ID NO:569 is the determined cDNA sequence for clone 61871548.

[0453] SEQ ID NO:570 is the determined cDNA sequence for clone 61871550.

[0454] SEQ ID NO:571 is the determined cDNA sequence for clone 62416046.

[0455] SEQ ID NO:572 is the determined cDNA sequence for clone 62416047.

[0456] SEQ ID NO:573 is the determined cDNA sequence for clone 62416048.

[0457] SEQ ID NO:574 is the determined cDNA sequence for clone 62416049.

[0458] SEQ ID NO:575 is the determined cDNA sequence for clone 62416050.

[0459] SEQ ID NO:576 is the determined cDNA sequence for clone 62416051.

[0460] SEQ ID NO:577 is the determined cDNA sequence for clone 62416052.

[0461] SEQ ID NO:578 is the determined cDNA sequence for clone 62416053.

[0462] SEQ ID NO:579 is the determined cDNA sequence for clone 62416054.

[0463] SEQ ID NO:580 is the determined cDNA sequence for clone 62416055.

[0464] SEQ ID NO:581 is the determined cDNA sequence for clone 62416056.

[0465] SEQ ID NO:582 is the determined cDNA sequence for clone 62416057.

[0466] SEQ ID NO:583 is the determined cDNA sequence for clone 62416059.

[0467] SEQ ID NO:584 is the determined cDNA sequence for clone 62416060.

[0468] SEQ ID NO:585 is the determined cDNA sequence for clone 62416061.

[0469] SEQ ID NO:586 is the determined cDNA sequence for clone 62416062.

[0470] SEQ ID NO:587 is the determined cDNA sequence for clone 62416063.

[0471] SEQ ID NO:588 is the determined cDNA sequence for clone 62416064.

[0472] SEQ ID NO:589 is the determined cDNA sequence for clone 62416066.

[0473] SEQ ID NO:590 is the determined cDNA sequence for clone 62416067.

[0474] SEQ ID NO:591 is the determined cDNA sequence for clone 62416068.

[0475] SEQ ID NO:592 is the determined cDNA sequence for clone 62416069.

[0476] SEQ ID NO:593 is the determined cDNA sequence for clone 62416070.

[0477] SEQ ID NO:594 is the determined cDNA sequence for clone 62416071.

[0478] SEQ ID NO:595 is the determined cDNA sequence for clone 62416072.

[0479] SEQ ID NO:596 is the determined cDNA sequence for clone 62416073.

[0480] SEQ ID NO:597 is the determined cDNA sequence for clone 62416074.

[0481] SEQ ID NO:598 is the determined cDNA sequence for clone 62416075.

[0482] SEQ ID NO:599 is the determined cDNA sequence for clone 62416076.

[0483] SEQ ID NO:600 is the determined cDNA sequence for clone 62416078.

[0484] SEQ ID NO:601 is the determined cDNA sequence for clone 62416079.

[0485] SEQ ID NO:602 is the determined cDNA sequence for clone 62416080.

[0486] SEQ ID NO:603 is the determined cDNA sequence for clone 62416081.

[0487] SEQ ID NO:604 is the determined cDNA sequence for clone 62416082.

[0488] SEQ ID NO:605 is the determined cDNA sequence for clone 62416083.

[0489] SEQ ID NO:606 is the determined cDNA sequence for clone 62416084.

[0490] SEQ ID NO:607 is the determined cDNA sequence for clone 62416085.

[0491] SEQ ID NO:608 is the determined cDNA sequence for clone 62416086.

[0492] SEQ ID NO:609 is the determined cDNA sequence for clone 62416087.

[0493] SEQ ID NO:610 is the determined cDNA sequence for clone 62416088.

[0494] SEQ ID NO:611 is the determined cDNA sequence for clone 62416089.

[0495] SEQ ID NO:612 is the determined cDNA sequence for clone 62416090.

[0496] SEQ ID NO:613 is the determined cDNA sequence for clone 62416091.

[0497] SEQ ID NO:614 is the determined cDNA sequence for clone 62416092.

[0498] SEQ ID NO:615 is the determined cDNA sequence for clone 62416093.

[0499] SEQ ID NO:616 is the determined cDNA sequence for clone 62416094.

[0500] SEQ ID NO:617 is the determined cDNA sequence for clone 62416095.

[0501] SEQ ID NO:618 is the determined cDNA sequence for clone 62416096.

[0502] SEQ ID NO:619 is the determined cDNA sequence for clone 62416098.

[0503] SEQ ID NO:620 is the determined cDNA sequence for clone 62416099.

[0504] SEQ ID NO:621 is the determined cDNA sequence for clone 62416100.

[0505] SEQ ID NO:622 is the determined cDNA sequence for clone 62416101.

[0506] SEQ ID NO:623 is the determined cDNA sequence for clone 62416102.

[0507] SEQ ID NO:624 is the determined cDNA sequence for clone 62416103.

[0508] SEQ ID NO:625 is the determined cDNA sequence for clone 62416104.

[0509] SEQ ID NO:626 is the determined cDNA sequence for clone 62416105.

[0510] SEQ ID NO:627 is the determined cDNA sequence for clone 62416106.

[0511] SEQ ID NO:628 is the determined cDNA sequence for clone 62416107.

[0512] SEQ ID NO:629 is the determined cDNA sequence for clone 62416108.

[0513] SEQ ID NO:630 is the determined cDNA sequence for clone 62416109.

[0514] SEQ ID NO:631 is the determined cDNA sequence for clone 62416111.

[0515] SEQ ID NO:632 is the determined cDNA sequence for clone 62416112.

[0516] SEQ ID NO:633 is the determined cDNA sequence for clone 62416113.

[0517] SEQ ID NO:634 is the determined cDNA sequence for clone 62416115.

[0518] SEQ ID NO:635 is the determined cDNA sequence for clone 62416116.

[0519] SEQ ID NO:636 is the determined cDNA sequence for clone 62416118.

[0520] SEQ ID NO:637 is the determined cDNA sequence for clone 62416119.

[0521] SEQ ID NO:638 is the determined cDNA sequence for clone 62416121.

[0522] SEQ ID NO:639 is the determined cDNA sequence for clone 62416123.

[0523] SEQ ID NO:640 is the determined cDNA sequence for clone 62416124.

[0524] SEQ ID NO:641 is the determined cDNA sequence for clone 62416125.

[0525] SEQ ID NO:642 is the determined cDNA sequence for clone 62416126.

[0526] SEQ ID NO:643 is the determined cDNA sequence for clone 62416127.

[0527] SEQ ID NO:644 is the determined cDNA sequence for clone 62416129.

[0528] SEQ ID NO:645 is the determined cDNA sequence for clone 62416130.

[0529] SEQ ID NO:646 is the determined cDNA sequence for clone 62416131.

[0530] SEQ ID NO:647 is the determined cDNA sequence for clone 62416132.

[0531] SEQ ID NO:648 is the determined cDNA sequence for clone 62416133.

[0532] SEQ ID NO:649 is the determined cDNA sequence for clone 62416134.

[0533] SEQ ID NO:650 is the determined cDNA sequence for clone 62416135.

[0534] SEQ ID NO:651 is the determined cDNA sequence for clone 62416136.

[0535] SEQ ID NO:652 is the determined cDNA sequence for clone 62416137.

[0536] SEQ ID NO:653 is the determined cDNA sequence for clone 62416138.

[0537] SEQ ID NO:654 is the determined cDNA sequence for clone 61590032.

[0538] SEQ ID NO:655 is the determined cDNA sequence for clone 61590034.

[0539] SEQ ID NO:656 is the determined cDNA sequence for clone 61590079.

[0540] SEQ ID NO:657 is the determined cDNA sequence for clone 61590081.

[0541] SEQ ID NO:658 is the determined cDNA sequence for clone 61590031.

[0542] SEQ ID NO:659 is the determined cDNA sequence for clone 61590033.

[0543] SEQ ID NO:660 is the determined cDNA sequence for clone 61590035.

[0544] SEQ ID NO:661 is the determined cDNA sequence for clone 61590078.

[0545] SEQ ID NO:662 is the determined cDNA sequence for clone 61590080.

[0546] SEQ ID NO:663 is the determined cDNA sequence for clone 61590082.

[0547] SEQ ID NO:664 is the determined cDNA sequence for clone 61590036.

[0548] SEQ ID NO:665 is the determined cDNA sequence for clone 61590038.

[0549] SEQ ID NO:666 is the determined cDNA sequence for clone 61590040.

[0550] SEQ ID NO:667 is the determined cDNA sequence for clone 61590083.

[0551] SEQ ID NO:668 is the determined cDNA sequence for clone 61590085.

[0552] SEQ ID NO:669 is the determined cDNA sequence for clone 61590087.

[0553] SEQ ID NO:670 is the determined cDNA sequence for clone 61590037.

[0554] SEQ ID NO:671 is the determined cDNA sequence for clone 61590041.

[0555] SEQ ID NO:672 is the determined cDNA sequence for clone 61590084.

[0556] SEQ ID NO:673 is the determined cDNA sequence for clone 61590086.

[0557] SEQ ID NO:674 is the determined cDNA sequence for clone 61590088.

[0558] SEQ ID NO:675 is the determined cDNA sequence for clone 61590042.

[0559] SEQ ID NO:676 is the determined cDNA sequence for clone 61590044.

[0560] SEQ ID NO:677 is the determined cDNA sequence for clone 61590046.

[0561] SEQ ID NO:678 is the determined cDNA sequence for clone 61590089.

[0562] SEQ ID NO:679 is the determined cDNA sequence for clone 61590091.

[0563] SEQ ID NO:680 is the determined cDNA sequence for clone 61590093.

[0564] SEQ ID NO:681 is the determined cDNA sequence for clone 61590043.

[0565] SEQ ID NO:682 is the determined cDNA sequence for clone 61590045.

[0566] SEQ ID NO:683 is the determined cDNA sequence for clone 61590047.

[0567] SEQ ID NO:684 is the determined cDNA sequence for clone 61590090.

[0568] SEQ ID NO:685 is the determined cDNA sequence for clone 61590092.

[0569] SEQ ID NO:686 is the determined cDNA sequence for clone 61590094.

[0570] SEQ ID NO:687 is the determined cDNA sequence for clone 61590048.

[0571] SEQ ID NO:688 is the determined cDNA sequence for clone 61590050.

[0572] SEQ ID NO:689 is the determined cDNA sequence for clone 61590052.

[0573] SEQ ID NO:690 is the determined cDNA sequence for clone 61590095.

[0574] SEQ ID NO:691 is the determined cDNA sequence for clone 61590097.

[0575] SEQ ID NO:692 is the determined cDNA sequence for clone 61590099.

[0576] SEQ ID NO:693 is the determined cDNA sequence for clone 61590049.

[0577] SEQ ID NO:694 is the determined cDNA sequence for clone 61590053.

[0578] SEQ ID NO:695 is the determined cDNA sequence for clone 61590096.

[0579] SEQ ID NO:696 is the determined cDNA sequence for clone 61590098.

[0580] SEQ ID NO:697 is the determined cDNA sequence for clone 61590100.

[0581] SEQ ID NO:698 is the determined cDNA sequence for clone 61590054.

[0582] SEQ ID NO:699 is the determined cDNA sequence for clone 61590056.

[0583] SEQ ID NO:700 is the determined cDNA sequence for clone 61590058.

[0584] SEQ ID NO:701 is the determined cDNA sequence for clone 61590103.

[0585] SEQ ID NO:702 is the determined cDNA sequence for clone 61590105.

[0586] SEQ ID NO:703 is the determined cDNA sequence for clone 61590055.

[0587] SEQ ID NO:704 is the determined cDNA sequence for clone 61590057.

[0588] SEQ ID NO:705 is the determined cDNA sequence for clone 61590059.

[0589] SEQ ID NO:706 is the determined cDNA sequence for clone 61590104.

[0590] SEQ ID NO:707 is the determined cDNA sequence for clone 61590060.

[0591] SEQ ID NO:708 is the determined cDNA sequence for clone 61590064.

[0592] SEQ ID NO:709 is the determined cDNA sequence for clone 61590107.

[0593] SEQ ID NO:710 is the determined cDNA sequence for clone 61590109.

[0594] SEQ ID NO:711 is the determined cDNA sequence for clone 61590111.

[0595] SEQ ID NO:712 is the determined cDNA sequence for clone 61590061.

[0596] SEQ ID NO:713 is the determined cDNA sequence for clone 61590063.

[0597] SEQ ID NO:714 is the determined cDNA sequence for clone 61590065.

[0598] SEQ ID NO:715 is the determined cDNA sequence for clone 61590108.

[0599] SEQ ID NO:716 is the determined cDNA sequence for clone 61590112.

[0600] SEQ ID NO:717 is the determined cDNA sequence for clone 61590066.

[0601] SEQ ID NO:718 is the determined cDNA sequence for clone 61590068.

[0602] SEQ ID NO:719 is the determined cDNA sequence for clone 61590070.

[0603] SEQ ID NO:720 is the determined cDNA sequence for clone 61590113.

[0604] SEQ ID NO:721 is the determined cDNA sequence for clone 61590067.

[0605] SEQ ID NO:722 is the determined cDNA sequence for clone 61590069.

[0606] SEQ ID NO:723 is the determined cDNA sequence for clone 61590071.

[0607] SEQ ID NO:724 is the determined cDNA sequence for clone 61590114.

[0608] SEQ ID NO:725 is the determined cDNA sequence for clone 61590118.

[0609] SEQ ID NO:726 is the determined cDNA sequence for clone 61590072.

[0610] SEQ ID NO:727 is the determined cDNA sequence for clone 61590074.

[0611] SEQ ID NO:728 is the determined cDNA sequence for clone 61590076.

[0612] SEQ ID NO:729 is the determined cDNA sequence for clone 61590119.

[0613] SEQ ID NO:730 is the determined cDNA sequence for clone 61590121.

[0614] SEQ ID NO:731 is the determined cDNA sequence for clone 61590123.

[0615] SEQ ID NO:732 is the determined cDNA sequence for clone 61590073.

[0616] SEQ ID NO:733 is the determined cDNA sequence for clone 61590075.

[0617] SEQ ID NO:734 is the determined cDNA sequence for clone 61590120.

[0618] SEQ ID NO:735 is the determined cDNA sequence for clone 61590122.

[0619] SEQ ID NO:736 is the determined cDNA sequence for clone 61932203.

[0620] SEQ ID NO:737 is the determined cDNA sequence for clone 61932205.

[0621] SEQ ID NO:738 is the determined cDNA sequence for clone 61932252.

[0622] SEQ ID NO:739 is the determined cDNA sequence for clone 61932202.

[0623] SEQ ID NO:740 is the determined cDNA sequence for clone 61932204.

[0624] SEQ ID NO:741 is the determined cDNA sequence for clone 61932206.

[0625] SEQ ID NO:742 is the determined cDNA sequence for clone 61932251.

[0626] SEQ ID NO:743 is the determined cDNA sequence for clone 61932253.

[0627] SEQ ID NO:744 is the determined cDNA sequence for clone 61932207.

[0628] SEQ ID NO:745 is the determined cDNA sequence for clone 61932209.

[0629] SEQ ID NO:746 is the determined cDNA sequence for clone 61932211.

[0630] SEQ ID NO:747 is the determined cDNA sequence for clone 61932254.

[0631] SEQ ID NO:748 is the determined cDNA sequence for clone 61932256.

[0632] SEQ ID NO:749 is the determined cDNA sequence for clone 61932208.

[0633] SEQ ID NO:750 is the determined cDNA sequence for clone 61932210.

[0634] SEQ ID NO:751 is the determined cDNA sequence for clone 61932212.

[0635] SEQ ID NO:752 is the determined cDNA sequence for clone 61932257.

[0636] SEQ ID NO:753 is the determined cDNA sequence for clone 61932213.

[0637] SEQ ID NO:754 is the determined cDNA sequence for clone 61932215.

[0638] SEQ ID NO:755 is the determined cDNA sequence for clone 61932217.

[0639] SEQ ID NO:756 is the determined cDNA sequence for clone 61932260.

[0640] SEQ ID NO:757 is the determined cDNA sequence for clone 61932262.

[0641] SEQ ID NO:758 is the determined cDNA sequence for clone 61932264.

[0642] SEQ ID NO:759 is the determined cDNA sequence for clone 61932214.

[0643] SEQ ID NO:760 is the determined cDNA sequence for clone 61932216.

[0644] SEQ ID NO:761 is the determined cDNA sequence for clone 61932218.

[0645] SEQ ID NO:762 is the determined cDNA sequence for clone 61932261.

[0646] SEQ ID NO:763 is the determined cDNA sequence for clone 61932265.

[0647] SEQ ID NO:764 is the determined cDNA sequence for clone 61932219.

[0648] SEQ ID NO:765 is the determined cDNA sequence for clone 61932223.

[0649] SEQ ID NO:766 is the determined cDNA sequence for clone 61932268.

[0650] SEQ ID NO:767 is the determined cDNA sequence for clone 61932270.

[0651] SEQ ID NO:768 is the determined cDNA sequence for clone 61932220.

[0652] SEQ ID NO:769 is the determined cDNA sequence for clone 61932224.

[0653] SEQ ID NO:770 is the determined cDNA sequence for clone 61932267.

[0654] SEQ ID NO:771 is the determined cDNA sequence for clone 61932271.

[0655] SEQ ID NO:772 is the determined cDNA sequence for clone 61932225.

[0656] SEQ ID NO:773 is the determined cDNA sequence for clone 61932227.

[0657] SEQ ID NO:774 is the determined cDNA sequence for clone 61932229.

[0658] SEQ ID NO:775 is the determined cDNA sequence for clone 61932272.

[0659] SEQ ID NO:776 is the determined cDNA sequence for clone 61932228.

[0660] SEQ ID NO:777 is the determined cDNA sequence for clone 61932230.

[0661] SEQ ID NO:778 is the determined cDNA sequence for clone 61932273.

[0662] SEQ ID NO:779 is the determined cDNA sequence for clone 61932275.

[0663] SEQ ID NO:780 is the determined cDNA sequence for clone 61932277.

[0664] SEQ ID NO:781 is the determined cDNA sequence for clone 61932231.

[0665] SEQ ID NO:782 is the determined cDNA sequence for clone 61932233.

[0666] SEQ ID NO:783 is the determined cDNA sequence for clone 61932278.

[0667] SEQ ID NO:784 is the determined cDNA sequence for clone 61932280.

[0668] SEQ ID NO:785 is the determined cDNA sequence for clone 61932232.

[0669] SEQ ID NO:786 is the determined cDNA sequence for clone 61932234.

[0670] SEQ ID NO:787 is the determined cDNA sequence for clone 61932236.

[0671] SEQ ID NO:788 is the determined cDNA sequence for clone 61932279.

[0672] SEQ ID NO:789 is the determined cDNA sequence for clone 61932281.

[0673] SEQ ID NO:790 is the determined cDNA sequence for clone 61932237.

[0674] SEQ ID NO:791 is the determined cDNA sequence for clone 61932239.

[0675] SEQ ID NO:792 is the determined cDNA sequence for clone 61932284.

[0676] SEQ ID NO:793 is the determined cDNA sequence for clone 61932288.

[0677] SEQ ID NO:794 is the determined cDNA sequence for clone 61932238.

[0678] SEQ ID NO:795 is the determined cDNA sequence for clone 61932240.

[0679] SEQ ID NO:796 is the determined cDNA sequence for clone 61932242.

[0680] SEQ ID NO:797 is the determined cDNA sequence for clone 61932285.

[0681] SEQ ID NO:798 is the determined cDNA sequence for clone 61932287.

[0682] SEQ ID NO:799 is the determined cDNA sequence for clone 61932289.

[0683] SEQ ID NO:800 is the determined cDNA sequence for clone 61932243.

[0684] SEQ ID NO:801 is the determined cDNA sequence for clone 61932245.

[0685] SEQ ID NO:802 is the determined cDNA sequence for clone 61932247.

[0686] SEQ ID NO:803 is the determined cDNA sequence for clone 61932290.

[0687] SEQ ID NO:804 is the determined cDNA sequence for clone 61932292.

[0688] SEQ ID NO:805 is the determined cDNA sequence for clone 61932294.

[0689] SEQ ID NO:806 is the determined cDNA sequence for clone 61932244.

[0690] SEQ ID NO:807 is the determined cDNA sequence for clone 61932246.

[0691] SEQ ID NO:808 is the determined cDNA sequence for clone 61932248.

[0692] SEQ ID NO:809 is the determined cDNA sequence for clone 61932291.

[0693] SEQ ID NO:810 is the determined cDNA sequence for clone 61932293.

[0694] SEQ ID NO:811 is the determined cDNA sequence for clone 61814652.

[0695] SEQ ID NO:812 is the determined cDNA sequence for clone 61814654.

[0696] SEQ ID NO:813 is the determined cDNA sequence for clone 61814699.

[0697] SEQ ID NO:814 is the determined cDNA sequence for clone 61814651.

[0698] SEQ ID NO:815 is the determined cDNA sequence for clone 61814653.

[0699] SEQ ID NO:816 is the determined cDNA sequence for clone 61814655.

[0700] SEQ ID NO:817 is the determined cDNA sequence for clone 61814698.

[0701] SEQ ID NO:818 is the determined cDNA sequence for clone 61814700.

[0702] SEQ ID NO:819 is the determined cDNA sequence for clone 61814656.

[0703] SEQ ID NO:820 is the determined cDNA sequence for clone 61814658.

[0704] SEQ ID NO:821 is the determined cDNA sequence for clone 61814660.

[0705] SEQ ID NO:822 is the determined cDNA sequence for clone 61814703.

[0706] SEQ ID NO:823 is the determined cDNA sequence for clone 61814705.

[0707] SEQ ID NO:824 is the determined cDNA sequence for clone 61814707.

[0708] SEQ ID NO:825 is the determined cDNA sequence for clone 61814657.

[0709] SEQ ID NO:826 is the determined cDNA sequence for clone 61814659.

[0710] SEQ ID NO:827 is the determined cDNA sequence for clone 61814661.

[0711] SEQ ID NO:828 is the determined cDNA sequence for clone 61814704.

[0712] SEQ ID NO:829 is the determined cDNA sequence for clone 61814662.

[0713] SEQ ID NO:830 is the determined cDNA sequence for clone 61814664.

[0714] SEQ ID NO:831 is the determined cDNA sequence for clone 61814666.

[0715] SEQ ID NO:832 is the determined cDNA sequence for clone 61814709.

[0716] SEQ ID NO:833 is the determined cDNA sequence for clone 61814711.

[0717] SEQ ID NO:834 is the determined cDNA sequence for clone 61814663.

[0718] SEQ ID NO:835 is the determined cDNA sequence for clone 61814665.

[0719] SEQ ID NO:836 is the determined cDNA sequence for clone 61814667.

[0720] SEQ ID NO:837 is the determined cDNA sequence for clone 61814710.

[0721] SEQ ID NO:838 is the determined cDNA sequence for clone 61814712.

[0722] SEQ ID NO:839 is the determined cDNA sequence for clone 61814714.

[0723] SEQ ID NO:840 is the determined cDNA sequence for clone 61814668.

[0724] SEQ ID NO:841 is the determined cDNA sequence for clone 61814670.

[0725] SEQ ID NO:842 is the determined cDNA sequence for clone 61814672.

[0726] SEQ ID NO:843 is the determined cDNA sequence for clone 61814715.

[0727] SEQ ID NO:844 is the determined cDNA sequence for clone 61814717.

[0728] SEQ ID NO:845 is the determined cDNA sequence for clone 61814719.

[0729] SEQ ID NO:846 is the determined cDNA sequence for clone 61814669. SEQ ID NO:847 is the determined cDNA sequence for clone 61814671.

[0730] SEQ ID NO:848 is the determined cDNA sequence for clone 61814673.

[0731] SEQ ID NO:849 is the determined cDNA sequence for clone 61814716.

[0732] SEQ ID NO:850 is the determined cDNA sequence for clone 61814720.

[0733] SEQ ID NO:851 is the determined cDNA sequence for clone 61814674.

[0734] SEQ ID NO:852 is the determined cDNA sequence for clone 61814676.

[0735] SEQ ID NO:853 is the determined cDNA sequence for clone 61814678.

[0736] SEQ ID NO:854 is the determined cDNA sequence for clone 61814721.

[0737] SEQ ID NO:855 is the determined cDNA sequence for clone 61814723.

[0738] SEQ ID NO:856 is the determined cDNA sequence for clone 61814725.

[0739] SEQ ID NO:857 is the determined cDNA sequence for clone 61814675.

[0740] SEQ ID NO:858 is the determined cDNA sequence for clone 61814677.

[0741] SEQ ID NO:859 is the determined cDNA sequence for clone 61814679.

[0742] SEQ ID NO:860 is the determined cDNA sequence for clone 61814722.

[0743] SEQ ID NO:861 is the determined cDNA sequence for clone 61814724.

[0744] SEQ ID NO:862 is the determined cDNA sequence for clone 61814726.

[0745] SEQ ID NO:863 is the determined cDNA sequence for clone 61814682.

[0746] SEQ ID NO:864 is the determined cDNA sequence for clone 61814729.

[0747] SEQ ID NO:865 is the determined cDNA sequence for clone 61814731.

[0748] SEQ ID NO:866 is the determined cDNA sequence for clone 61814681.

[0749] SEQ ID NO:867 is the determined cDNA sequence for clone 61814683.

[0750] SEQ ID NO:868 is the determined cDNA sequence for clone 61814685.

[0751] SEQ ID NO:869 is the determined cDNA sequence for clone 61814728.

[0752] SEQ ID NO:870 is the determined cDNA sequence for clone 61814730.

[0753] SEQ ID NO:871 is the determined cDNA sequence for clone 61814732.

[0754] SEQ ID NO:872 is the determined cDNA sequence for clone 61814686.

[0755] SEQ ID NO:873 is the determined cDNA sequence for clone 61814688.

[0756] SEQ ID NO:874 is the determined cDNA sequence for clone 61814690.

[0757] SEQ ID NO:875 is the determined cDNA sequence for clone 61814733.

[0758] SEQ ID NO:876 is the determined cDNA sequence for clone 61814735.

[0759] SEQ ID NO:877 is the determined cDNA sequence for clone 61814737.

[0760] SEQ ID NO:878 is the determined cDNA sequence for clone 61814687.

[0761] SEQ ID NO:879 is the determined cDNA sequence for clone 61814689.

[0762] SEQ ID NO:880 is the determined cDNA sequence for clone 61814691.

[0763] SEQ ID NO:881 is the determined cDNA sequence for clone 61814734.

[0764] SEQ ID NO:882 is the determined cDNA sequence for clone 61814736.

[0765] SEQ ID NO:883 is the determined cDNA sequence for clone 61814738.

[0766] SEQ ID NO:884 is the determined cDNA sequence for clone 61814692.

[0767] SEQ ID NO:885 is the determined cDNA sequence for clone 61814696.

[0768] SEQ ID NO:886 is the determined cDNA sequence for clone 61814743.

[0769] SEQ ID NO:887 is the determined cDNA sequence for clone 61814693.

[0770] SEQ ID NO:888 is the determined cDNA sequence for clone 61814695.

[0771] SEQ ID NO:889 is the determined cDNA sequence for clone 61814697.

[0772] SEQ ID NO:890 is the determined cDNA sequence for clone 61814740.

[0773] SEQ ID NO:891 is the determined cDNA sequence for clone 61814742.

[0774] SEQ ID NO:892 is the determined cDNA sequence for clone 61570440.

[0775] SEQ ID NO:893 is the determined cDNA sequence for clone 61570487.

[0776] SEQ ID NO:894 is the determined cDNA sequence for clone 61570489.

[0777] SEQ ID NO:895 is the determined cDNA sequence for clone 61570439.

[0778] SEQ ID NO:896 is the determined cDNA sequence for clone 61570486.

[0779] SEQ ID NO:897 is the determined cDNA sequence for clone 61570488.

[0780] SEQ ID NO:898 is the determined cDNA sequence for clone 61570490.

[0781] SEQ ID NO:899 is the determined cDNA sequence for clone 61570444.

[0782] SEQ ID NO:900 is the determined cDNA sequence for clone 61570446.

[0783] SEQ ID NO:901 is the determined cDNA sequence for clone 61570448.

[0784] SEQ ID NO:902 is the determined cDNA sequence for clone 61570491.

[0785] SEQ ID NO:903 is the determined cDNA sequence for clone 61570493.

[0786] SEQ ID NO:904 is the determined cDNA sequence for clone 61570495.

[0787] SEQ ID NO:905 is the determined cDNA sequence for clone 61570445.

[0788] SEQ ID NO:906 is the determined cDNA sequence for clone 61570449.

[0789] SEQ ID NO:907 is the determined cDNA sequence for clone 61570492.

[0790] SEQ ID NO:908 is the determined cDNA sequence for clone 61570494.

[0791] SEQ ID NO:909 is the determined cDNA sequence for clone 61570496.

[0792] SEQ ID NO:910 is the determined cDNA sequence for clone 61570450.

[0793] SEQ ID NO:911 is the determined cDNA sequence for clone 61570452.

[0794] SEQ ID NO:912 is the determined cDNA sequence for clone 61570454.

[0795] SEQ ID NO:913 is the determined cDNA sequence for clone 61570497.

[0796] SEQ ID NO:914 is the determined cDNA sequence for clone 61570499.

[0797] SEQ ID NO:915 is the determined cDNA sequence for clone 61570501.

[0798] SEQ ID NO:916 is the determined cDNA sequence for clone 61570451.

[0799] SEQ ID NO:917 is the determined cDNA sequence for clone 61570455.

[0800] SEQ ID NO:918 is the determined cDNA sequence for clone 61570498.

[0801] SEQ ID NO:919 is the determined cDNA sequence for clone 61570500.

[0802] SEQ ID NO:920 is the determined cDNA sequence for clone 61570456.

[0803] SEQ ID NO:921 is the determined cDNA sequence for clone 61570460.

[0804] SEQ ID NO:922 is the determined cDNA sequence for clone 61570503.

[0805] SEQ ID NO:923 is the determined cDNA sequence for clone 61570505.

[0806] SEQ ID NO:924 is the determined cDNA sequence for clone 61570507.

[0807] SEQ ID NO:925 is the determined cDNA sequence for clone 61570457.

[0808] SEQ ID NO:926 is the determined cDNA sequence for clone 61570459.

[0809] SEQ ID NO:927 is the determined cDNA sequence for clone 61570461.

[0810] SEQ ID NO:928 is the determined cDNA sequence for clone 61570504.

[0811] SEQ ID NO:929 is the determined cDNA sequence for clone 61570506.

[0812] SEQ ID NO:930 is the determined cDNA sequence for clone 61570508.

[0813] SEQ ID NO:931 is the determined cDNA sequence for clone 61570462.

[0814] SEQ ID NO:932 is the determined cDNA sequence for clone 61570464.

[0815] SEQ ID NO:933 is the determined cDNA sequence for clone 61570466.

[0816] SEQ ID NO:934 is the determined cDNA sequence for clone 61570509.

[0817] SEQ ID NO:935 is the determined cDNA sequence for clone 61570511.

[0818] SEQ ID NO:936 is the determined cDNA sequence for clone 61570513.

[0819] SEQ ID NO:937 is the determined cDNA sequence for clone 61570463.

[0820] SEQ ID NO:938 is the determined cDNA sequence for clone 61570465.

[0821] SEQ ID NO:939 is the determined cDNA sequence for clone 61570467.

[0822] SEQ ID NO:940 is the determined cDNA sequence for clone 61570514.

[0823] SEQ ID NO:941 is the determined cDNA sequence for clone 61570468.

[0824] SEQ ID NO:942 is the determined cDNA sequence for clone 61570470.

[0825] SEQ ID NO:943 is the determined cDNA sequence for clone 61570472.

[0826] SEQ ID NO:944 is the determined cDNA sequence for clone 61570515.

[0827] SEQ ID NO:945 is the determined cDNA sequence for clone 61570519.

[0828] SEQ ID NO:946 is the determined cDNA sequence for clone 61570469.

[0829] SEQ ID NO:947 is the determined cDNA sequence for clone 61570471.

[0830] SEQ ID NO:948 is the determined cDNA sequence for clone 61570473.

[0831] SEQ ID NO:949 is the determined cDNA sequence for clone 61570516.

[0832] SEQ ID NO:950 is the determined cDNA sequence for clone 61570518.

[0833] SEQ ID NO:951 is the determined cDNA sequence for clone 61570520.

[0834] SEQ ID NO:952 is the determined cDNA sequence for clone 0.61570474.

[0835] SEQ ID NO:953 is the determined cDNA sequence for clone 61570478.

[0836] SEQ ID NO:954 is the determined cDNA sequence for clone 61570521.

[0837] SEQ ID NO:955 is the determined cDNA sequence for clone 61570523.

[0838] SEQ ID NO:956 is the determined cDNA sequence for clone 61570525.

[0839] SEQ ID NO:957 is the determined cDNA sequence for clone 61570475.

[0840] SEQ ID NO:958 is the determined cDNA sequence for clone 61570477.

[0841] SEQ ID NO:959 is the determined cDNA sequence for clone 61570479.

[0842] SEQ ID NO:960 is the determined cDNA sequence for clone 61570522.

[0843] SEQ ID NO:961 is the determined cDNA sequence for clone 61570524.

[0844] SEQ ID NO:962 is the determined cDNA sequence for clone 61570526.

[0845] SEQ ID NO:963 is the determined cDNA sequence for clone 61570482.

[0846] SEQ ID NO:964 is the determined cDNA sequence for clone 61570484.

[0847] SEQ ID NO:965 is the determined cDNA sequence for clone 61570529.

[0848] SEQ ID NO:966 is the determined cDNA sequence for clone 61570531.

[0849] SEQ ID NO:967 is the determined cDNA sequence for clone 61570481.

[0850] SEQ ID NO:968 is the determined cDNA sequence for clone 61570485.

[0851] SEQ ID NO:969 is the determined cDNA sequence for clone 61570528.

[0852] SEQ ID NO:970 is the determined cDNA sequence for clone 61570530.

[0853] SEQ ID NO:971 is the determined cDNA sequence for clone 61871274.

[0854] SEQ ID NO:972 is the determined cDNA sequence for clone 61871276.

[0855] SEQ ID NO:973 is the determined cDNA sequence for clone 61871321.

[0856] SEQ ID NO:974 is the determined cDNA sequence for clone 61871323.

[0857] SEQ ID NO:975 is the determined cDNA sequence for clone 61871275.

[0858] SEQ ID NO:976 is the determined cDNA sequence for clone 61871277.

[0859] SEQ ID NO:977 is the determined cDNA sequence for clone 61871320.

[0860] SEQ ID NO:978 is the determined cDNA sequence for clone 61871322.

[0861] SEQ ID NO:979 is the determined cDNA sequence for clone 61871280.

[0862] SEQ ID NO:980 is the determined cDNA sequence for clone 61871282.

[0863] SEQ ID NO:981 is the determined cDNA sequence for clone 61871329.

[0864] SEQ ID NO:982 is the determined cDNA sequence for clone 61871279.

[0865] SEQ ID NO:983 is the determined cDNA sequence for clone 61871281.

[0866] SEQ ID NO:984 is the determined cDNA sequence for clone 61871283.

[0867] SEQ ID NO:985 is the determined cDNA sequence for clone 61871326.

[0868] SEQ ID NO:986 is the determined cDNA sequence for clone 61871328.

[0869] SEQ ID NO:987 is the determined cDNA sequence for clone 61871330.

[0870] SEQ ID NO:988 is the determined cDNA sequence for clone 61871284.

[0871] SEQ ID NO:989 is the determined cDNA sequence for clone 61871286.

[0872] SEQ ID NO:990 is the determined cDNA sequence for clone 61871331.

[0873] SEQ ID NO:991 is the determined cDNA sequence for clone 61871333.

[0874] SEQ ID NO:992 is the determined cDNA sequence for clone 61871335.

[0875] SEQ ID NO:993 is the determined cDNA sequence for clone 61871285.

[0876] SEQ ID NO:994 is the determined cDNA sequence for clone 61871287.

[0877] SEQ ID NO:995 is the determined cDNA sequence for clone 61871332.

[0878] SEQ ID NO:996 is the determined cDNA sequence for clone 61871334.

[0879] SEQ ID NO:997 is the determined cDNA sequence for clone 61871336.

[0880] SEQ ID NO:998 is the determined cDNA sequence for clone 61871290.

[0881] SEQ ID NO:999 is the determined cDNA sequence for clone 61871292.

[0882] SEQ ID NO:1000 is the determined cDNA sequence for clone 61871294.

[0883] SEQ ID NO:1001 is the determined cDNA sequence for clone 61871337.

[0884] SEQ ID NO:1002 is the determined cDNA sequence for clone 61871341.

[0885] SEQ ID NO:1003 is the determined cDNA sequence for clone 61871291.

[0886] SEQ ID NO:1004 is the determined cDNA sequence for clone 61871293.

[0887] SEQ ID NO:1005 is the determined cDNA sequence for clone 61871295.

[0888] SEQ ID NO:1006 is the determined cDNA sequence for clone 61871338.

[0889] SEQ ID NO:1007 is the determined cDNA sequence for clone 61871340.

[0890] SEQ ID NO:1008 is the determined cDNA sequence for clone 61871342.

[0891] SEQ ID NO:1009 is the determined cDNA sequence for clone 61871296.

[0892] SEQ ID NO:1010 is the determined cDNA sequence for clone 61871298.

[0893] SEQ ID NO: 1011 is the determined cDNA sequence for clone 61871300.

[0894] SEQ ID NO:1012 is the determined cDNA sequence for clone 61871343.

[0895] SEQ ID NO:1013 is the determined cDNA sequence for clone 61871347.

[0896] SEQ ID NO:1014 is the determined cDNA sequence for clone 61871297.

[0897] SEQ ID NO:1015 is the determined cDNA sequence for clone 61871299.

[0898] SEQ ID NO:1016 is the determined cDNA sequence for clone 61871301.

[0899] SEQ ID NO:1017 is the determined cDNA sequence for clone 61871344.

[0900] SEQ ID NO:1018 is the determined cDNA sequence for clone 61871346.

[0901] SEQ ID NO:1019 is the determined cDNA sequence for clone 61871348.

[0902] SEQ ID NO:1020 is the determined cDNA sequence for clone 61871302.

[0903] SEQ ID NO:1021 is the determined cDNA sequence for clone 61871304.

[0904] SEQ ID NO:1022 is the determined cDNA sequence for clone 61871306.

[0905] SEQ ID NO:1023 is the determined cDNA sequence for clone 61871349.

[0906] SEQ ID NO:1024 is the determined cDNA sequence for clone 61871351.

[0907] SEQ ID NO:1025 is the determined cDNA sequence for clone 61871303.

[0908] SEQ ID NO:1026 is the determined cDNA sequence for clone 61871305.

[0909] SEQ ID NO:1027 is the determined cDNA sequence for clone 61871307.

[0910] SEQ ID NO:1028 is the determined cDNA sequence for clone 61871350.

[0911] SEQ ID NO:1029 is the determined cDNA sequence for clone 61871352.

[0912] SEQ ID NO:1030 is the determined cDNA sequence for clone 61871354.

[0913] SEQ ID NO:1031 is the determined cDNA sequence for clone 61871308.

[0914] SEQ ID NO:1032 is the determined cDNA sequence for clone 61871310.

[0915] SEQ ID NO:1033 is the determined cDNA sequence for clone 61871312.

[0916] SEQ ID NO:1034 is the determined cDNA sequence for clone 61871355.

[0917] SEQ ID NO:1035 is the determined cDNA sequence for clone 61871357.

[0918] SEQ ID NO:1036 is the determined cDNA sequence for clone 61871359.

[0919] SEQ ID NO: 1037 is the determined cDNA sequence for clone 61871309.

[0920] SEQ ID NO: 1038 is the determined cDNA sequence for clone 61871311.

[0921] SEQ ID NO:1039 is the determined cDNA sequence for clone 61871313.

[0922] SEQ ID NO:1040 is the determined cDNA sequence for clone 61871358.

[0923] SEQ ID NO:1041 is the determined cDNA sequence for clone 61871360.

[0924] SEQ ID NO:1042 is the determined cDNA sequence for clone 61871314.

[0925] SEQ ID NO:1043 is the determined cDNA sequence for clone 61871316.

[0926] SEQ ID NO:1044 is the determined cDNA sequence for clone 61871318.

[0927] SEQ ID NO:1045 is the determined cDNA sequence for clone 61871363.

[0928] SEQ ID NO:1046 is the determined cDNA sequence for clone 61871315.

[0929] SEQ ID NO:1047 is the determined cDNA sequence for clone 61871317.

[0930] SEQ ID NO:1048 is the determined cDNA sequence for clone 61871319.

[0931] SEQ ID NO:1049 is the determined cDNA sequence for clone 61871362.

[0932] SEQ ID NO:1050 is the determined cDNA sequence for clone 61871364.

[0933] SEQ ID NO:1051 is the determined cDNA sequence for clone 62004994.

[0934] SEQ ID NO:1052 is the determined cDNA sequence for clone 62004996.

[0935] SEQ ID NO:1053 is the determined cDNA sequence for clone 62005043.

[0936] SEQ ID NO:1054 is the determined cDNA sequence for clone 62004993.

[0937] SEQ ID NO:1055 is the determined cDNA sequence for clone 62004995.

[0938] SEQ ID NO:1056 is the determined cDNA sequence for clone 62004997.

[0939] SEQ ID NO:1057 is the determined cDNA sequence for clone 62005040.

[0940] SEQ ID NO:1058 is the determined cDNA sequence for clone 62005042.

[0941] SEQ ID NO:1059 is the determined cDNA sequence for clone 62005044.

[0942] SEQ ID NO:1060 is the determined cDNA sequence for clone 62004998.

[0943] SEQ ID NO:1061 is the determined cDNA sequence for clone 62005000.

[0944] SEQ ID NO:1062 is the determined cDNA sequence for clone 62005045.

[0945] SEQ ID NO:1063 is the determined cDNA sequence for clone 62005047.

[0946] SEQ ID NO:1064 is the determined cDNA sequence for clone 62005049.

[0947] SEQ ID NO:1065 is the determined cDNA sequence for clone 62004999.

[0948] SEQ ID NO:1066 is the determined cDNA sequence for clone 62005001.

[0949] SEQ ID NO:1067 is the determined cDNA sequence for clone 62005003.

[0950] SEQ ID NO:1068 is the determined cDNA sequence for clone 62005046.

[0951] SEQ ID NO:1069 is the determined cDNA sequence for clone 62005048.

[0952] SEQ ID NO:1070 is the determined cDNA sequence for clone 62005050.

[0953] SEQ ID NO: 1071 is the determined cDNA sequence for clone 62005004.

[0954] SEQ ID NO:1072 is the determined cDNA sequence for clone 62005006.

[0955] SEQ ID NO:1073 is the determined cDNA sequence for clone 62005008.

[0956] SEQ ID NO:1074 is the determined cDNA sequence for clone 62005051.

[0957] SEQ ID NO:1075 is the determined cDNA sequence for clone 62005053.

[0958] SEQ ID NO:1076 is the determined cDNA sequence for clone 62005055.

[0959] SEQ ID NO:1077 is the determined cDNA sequence for clone 62005005.

[0960] SEQ ID NO:1078 is the determined cDNA sequence for clone 62005007.

[0961] SEQ ID NO:1079 is the determined cDNA sequence for clone 62005009.

[0962] SEQ ID NO:1080 is the determined cDNA sequence for clone 62005052.

[0963] SEQ ID NO:1081 is the determined cDNA sequence for clone 62005054.

[0964] SEQ ID NO:1082 is the determined cDNA sequence for clone 62005056.

[0965] SEQ ID NO:1083 is the determined cDNA sequence for clone 62005012.

[0966] SEQ ID NO: 1084 is the determined cDNA sequence for clone 62005014.

[0967] SEQ ID NO:1085 is the determined cDNA sequence for clone 62005057.

[0968] SEQ ID NO:1086 is the determined cDNA sequence for clone 62005059.

[0969] SEQ ID NO:1087 is the determined cDNA sequence for clone 62005011.

[0970] SEQ ID NO:1088 is the determined cDNA sequence for clone 62005013.

[0971] SEQ ID NO:1089 is the determined cDNA sequence for clone 62005015.

[0972] SEQ ID NO:1090 is the determined cDNA sequence for clone 62005058.

[0973] SEQ ID NO:1091 is the determined cDNA sequence for clone 62005060.

[0974] SEQ ID NO:1092 is the determined cDNA sequence for clone 62005062.

[0975] SEQ ID NO:1093 is the determined cDNA sequence for clone 62005016.

[0976] SEQ ID NO: 1094 is the determined cDNA sequence for clone 62005018.

[0977] SEQ ID NO:1095 is the determined cDNA sequence for clone 62005020.

[0978] SEQ ID NO:1096 is the determined cDNA sequence for clone 62005063.

[0979] SEQ ID NO:1097 is the determined cDNA sequence for clone 62005065.

[0980] SEQ ID NO: 1098 is the determined cDNA sequence for clone 62005067.

[0981] SEQ ID NO:1099 is the determined cDNA sequence for clone 62005017.

[0982] SEQ ID NO:1100 is the determined cDNA sequence for clone 62005019.

[0983] SEQ ID NO:1101 is the determined cDNA sequence for clone 62005021.

[0984] SEQ ID NO:1102 is the determined cDNA sequence for clone 62005064.

[0985] SEQ ID NO:1103 is the determined cDNA sequence for clone 62005066.

[0986] SEQ ID NO:1104 is the determined cDNA sequence for clone 62005068.

[0987] SEQ ID NO:1105 is the determined cDNA sequence for clone 62005022.

[0988] SEQ ID NO:1106 is the determined cDNA sequence for clone 62005024.

[0989] SEQ ID NO:1107 is the determined cDNA sequence for clone 62005026.

[0990] SEQ ID NO:1108 is the determined cDNA sequence for clone 62005069.

[0991] SEQ ID NO:1109 is the determined cDNA sequence for clone 62005071. SEQ ID NO:1110 is the determined cDNA sequence for clone 62005073.

[0992] SEQ ID NO:1111 is the determined cDNA sequence for clone 62005023.

[0993] SEQ ID NO:1112 is the determined cDNA sequence for clone 62005025.

[0994] SEQ ID NO:1113 is the determined cDNA sequence for clone 62005027.

[0995] SEQ ID NO:1114 is the determined cDNA sequence for clone 62005070.

[0996] SEQ ID NO:1115 is the determined cDNA sequence for clone 62005072.

[0997] SEQ ID NO:1116 is the determined cDNA sequence for clone 62005074.

[0998] SEQ ID NO:1117 is the determined cDNA sequence for clone 62005030.

[0999] SEQ ID NO:1118 is the determined cDNA sequence for clone 62005032.

[1000] SEQ ID NO:1119 is the determined cDNA sequence for clone 62005075.

[1001] SEQ ID NO:1120 is the determined cDNA sequence for clone 62005077.

[1002] SEQ ID NO:1121 is the determined cDNA sequence for clone 62005079.

[1003] SEQ ID NO:1122 is the determined cDNA sequence for clone 62005029.

[1004] SEQ ID NO:1123 is the determined cDNA sequence for clone 62005031.

[1005] SEQ ID NO:1124 is the determined cDNA sequence for clone 62005033.

[1006] SEQ ID NO:1125 is the determined cDNA sequence for clone 62005076.

[1007] SEQ ID NO:1126 is the determined cDNA sequence for clone 62005078.

[1008] SEQ ID NO:1127 is the determined cDNA sequence for clone 62005080.

[1009] SEQ ID NO:1128 is the determined cDNA sequence for clone 62005034.

[1010] SEQ ID NO:1129 is the determined cDNA sequence for clone 62005036.

[1011] SEQ ID NO:1130 is the determined cDNA sequence for clone 62005038.

[1012] SEQ ID NO:1131 is the determined cDNA sequence for clone 62005081.

[1013] SEQ ID NO:1132 is the determined cDNA sequence for clone 62005083.

[1014] SEQ ID NO:1133 is the determined cDNA sequence for clone 62005035.

[1015] SEQ ID NO:1134 is the determined cDNA sequence for clone 62005082.

[1016] SEQ ID NO:1135 is the determined cDNA sequence for clone 62005084.

[1017] SEQ ID NO:1136 is the determined cDNA sequence for clone 62004808.

[1018] SEQ ID NO:1137 is the determined cDNA sequence for clone 62004855.

[1019] SEQ ID NO:1138 is the determined cDNA sequence for clone 62004857.

[1020] SEQ ID NO:1139 is the determined cDNA sequence for clone 62004807.

[1021] SEQ ID NO:1140 is the determined cDNA sequence for clone 62004809.

[1022] SEQ ID NO:1141 is the determined cDNA sequence for clone 62004811.

[1023] SEQ ID NO:1142 is the determined cDNA sequence for clone 62004856.

[1024] SEQ ID NO:1143 is the determined cDNA sequence for clone 62004858.

[1025] SEQ ID NO:1144 is the determined cDNA sequence for clone 62004812.

[1026] SEQ ID NO:1145 is the determined cDNA sequence for clone 62004814.

[1027] SEQ ID NO:1146 is the determined cDNA sequence for clone 62004816.

[1028] SEQ ID NO:1147 is the determined cDNA sequence for clone 62004859.

[1029] SEQ ID NO:1148 is the determined cDNA sequence for clone 62004861.

[1030] SEQ ID NO:1149 is the determined cDNA sequence for clone 62004863.

[1031] SEQ ID NO:1150 is the determined cDNA sequence for clone 62004813.

[1032] SEQ ID NO:1151 is the determined cDNA sequence for clone 62004817.

[1033] SEQ ID NO:1152 is the determined cDNA sequence for clone 62004860.

[1034] SEQ ID NO:1153 is the determined cDNA sequence for clone 62004862.

[1035] SEQ ID NO:1154 is the determined cDNA sequence for clone 62004864.

[1036] SEQ ID NO:1155 is the determined cDNA sequence for clone 62004818.

[1037] SEQ ID NO:1156 is the determined cDNA sequence for clone 62004820.

[1038] SEQ ID NO:1157 is the determined cDNA sequence for clone 62004822.

[1039] SEQ ID NO:1158 is the determined cDNA sequence for clone 62004865.

[1040] SEQ ID NO:1159 is the determined cDNA sequence for clone 62004867.

[1041] SEQ ID NO:1160 is the determined cDNA sequence for clone 62004869.

[1042] SEQ ID NO:1161 is the determined cDNA sequence for clone 62004819.

[1043] SEQ ID NO:1162 is the determined cDNA sequence for clone 62004821.

[1044] SEQ ID NO:1163 is the determined cDNA sequence for clone 62004823.

[1045] SEQ ID NO:1164 is the determined cDNA sequence for clone 62004866.

[1046] SEQ ID NO:1165 is the determined cDNA sequence for clone 62004868.

[1047] SEQ ID NO:1166 is the determined cDNA sequence for clone 62004826.

[1048] SEQ ID NO:1167 is the determined cDNA sequence for clone 62004828.

[1049] SEQ ID NO:1168 is the determined cDNA sequence for clone 62004871.

[1050] SEQ ID NO:1169 is the determined cDNA sequence for clone 62004873.

[1051] SEQ ID NO: 170 is the determined cDNA sequence for clone 62004875.

[1052] SEQ ID NO:1171 is the determined cDNA sequence for clone 62004825.

[1053] SEQ ID NO:1172 is the determined cDNA sequence for clone 62004827.

[1054] SEQ ID NO:1173 is the determined cDNA sequence for clone 62004829.

[1055] SEQ ID NO:1174 is the determined cDNA sequence for clone 62004872.

[1056] SEQ ID NO:1175 is the determined cDNA sequence for clone 62004874.

[1057] SEQ ID NO:1176 is the determined cDNA sequence for clone 62004876.

[1058] SEQ ID NO:1177 is the determined cDNA sequence for clone 62004832.

[1059] SEQ ID NO:1178 is the determined cDNA sequence for clone 62004834.

[1060] SEQ ID NO:1179 is the determined cDNA sequence for clone 62004877.

[1061] SEQ ID NO:1180 is the determined cDNA sequence for clone 62004879.

[1062] SEQ ID NO:1181 is the determined cDNA sequence for clone 62004881.

[1063] SEQ ID NO:1182 is the determined cDNA sequence for clone 62004831.

[1064] SEQ ID NO:1183 is the determined cDNA sequence for clone 62004833.

[1065] SEQ ID NO:1184 is the determined cDNA sequence for clone 62004835.

[1066] SEQ ID NO:1185 is the determined cDNA sequence for clone 62004878.

[1067] SEQ ID NO:1186 is the determined cDNA sequence for clone 62004880.

[1068] SEQ ID NO:1187 is the determined cDNA sequence for clone 62004882.

[1069] SEQ ID NO:1188 is the determined cDNA sequence for clone 62004836.

[1070] SEQ ID NO:1189 is the determined cDNA sequence for clone 62004838.

[1071] SEQ ID NO:1190 is the determined cDNA sequence for clone 62004840.

[1072] SEQ ID NO:1191 is the determined cDNA sequence for clone 62004883.

[1073] SEQ ID NO:1192 is the determined cDNA sequence for clone 62004885.

[1074] SEQ ID NO:1193 is the determined cDNA sequence for clone 62004887.

[1075] SEQ ID NO:1194 is the determined cDNA sequence for clone 62004837.

[1076] SEQ ID NO:1195 is the determined cDNA sequence for clone 62004839.

[1077] SEQ ID NO:1196 is the determined cDNA sequence for clone 62004841.

[1078] SEQ ID NO:1197 is the determined cDNA sequence for clone 62004884.

[1079] SEQ ID NO:1198 is the determined cDNA sequence for clone 62004886.

[1080] SEQ ID NO:1199 is the determined cDNA sequence for clone 62004888.

[1081] SEQ ID NO:1200 is the determined cDNA sequence for clone 62004842.

[1082] SEQ ID NO:1201 is the determined cDNA sequence for clone 62004844.

[1083] SEQ ID NO:1202 is the determined cDNA sequence for clone 62004889.

[1084] SEQ ID NO:1203 is the determined cDNA sequence for clone 62004893.

[1085] SEQ ID NO:1204 is the determined cDNA sequence for clone 62004843.

[1086] SEQ ID NO:1205 is the determined cDNA sequence for clone 62004847.

[1087] SEQ ID NO:1206 is the determined cDNA sequence for clone 62004890.

[1088] SEQ ID NO:1207 is the determined cDNA sequence for clone 62004892.

[1089] SEQ ID NO:1208 is the determined cDNA sequence for clone 62004894.

[1090] SEQ ID NO:1209 is the determined cDNA sequence for clone 62004848.

[1091] SEQ ID NO:1210 is the determined cDNA sequence for clone 62004850.

[1092] SEQ ID NO:1211 is the determined cDNA sequence for clone 62004895.

[1093] SEQ ID NO:1212 is the determined cDNA sequence for clone 62004897.

[1094] SEQ ID NO:1213 is the determined cDNA sequence for clone 62004899.

[1095] SEQ ID NO:1214 is the determined cDNA sequence for clone 62004849.

[1096] SEQ ID NO:1215 is the determined cDNA sequence for clone 62004851.

[1097] SEQ ID NO:1216 is the determined cDNA sequence for clone 62004896.

[1098] SEQ ID NO:1217 is the determined cDNA sequence for clone 62004898.

[1099] SEQ ID NO:1218 is the determined cDNA sequence for clone 62005926.

[1100] SEQ ID NO:1219 is the determined cDNA sequence for clone 62005971.

[1101] SEQ ID NO:1220 is the determined cDNA sequence for clone 62005973.

[1102] SEQ ID NO:1221 is the determined cDNA sequence for clone 62005923.

[1103] SEQ ID NO:1222 is the determined cDNA sequence for clone 62005925.

[1104] SEQ ID NO:1223 is the determined cDNA sequence for clone 62005927.

[1105] SEQ ID NO:1224 is the determined cDNA sequence for clone 62005970.

[1106] SEQ ID NO:1225 is the determined cDNA sequence for clone 62005972.

[1107] SEQ ID NO:1226 is the determined cDNA sequence for clone 62005974.

[1108] SEQ ID NO:1227 is the determined cDNA sequence for clone 62005928.

[1109] SEQ ID NO:1228 is the determined cDNA sequence for clone 62005930.

[1110] SEQ ID NO:1229 is the determined cDNA sequence for clone 62005932.

[1111] SEQ ID NO:1230 is the determined cDNA sequence for clone 62005975.

[1112] SEQ ID NO:1231 is the determined cDNA sequence for clone 62005977.

[1113] SEQ ID NO:1232 is the determined cDNA sequence for clone 62005979.

[1114] SEQ ID NO:1233 is the determined cDNA sequence for clone 62005929.

[1115] SEQ ID NO:1234 is the determined cDNA sequence for clone 62005931.

[1116] SEQ ID NO:1235 is the determined cDNA sequence for clone 62005933.

[1117] SEQ ID NO:1236 is the determined cDNA sequence for clone 62005978.

[1118] SEQ ID NO:1237 is the determined cDNA sequence for clone 62005980.

[1119] SEQ ID NO:1238 is the determined cDNA sequence for clone 62005936.

[1120] SEQ ID NO:1239 is the determined cDNA sequence for clone 62005938.

[1121] SEQ ID NO:1240 is the determined cDNA sequence for clone 62005983.

[1122] SEQ ID NO:1241 is the determined cDNA sequence for clone 62005985.

[1123] SEQ ID NO:1242 is the determined cDNA sequence for clone 62005935.

[1124] SEQ ID NO:1243 is the determined cDNA sequence for clone 62005937.

[1125] SEQ ID NO:1244 is the determined cDNA sequence for clone 62005939.

[1126] SEQ ID NO:1245 is the determined cDNA sequence for clone 62005982.

[1127] SEQ ID NO:1246 is the determined cDNA sequence for clone 62005984.

[1128] SEQ ID NO:1247 is the determined cDNA sequence for clone 62005940.

[1129] SEQ ID NO:1248 is the determined cDNA sequence for clone 62005944.

[1130] SEQ ID NO:1249 is the determined cDNA sequence for clone 62005987.

[1131] SEQ ID NO:1250 is the determined cDNA sequence for clone 62005989.

[1132] SEQ ID NO:1251 is the determined cDNA sequence for clone 62005991.

[1133] SEQ ID NO:1252 is the determined cDNA sequence for clone 62005941.

[1134] SEQ ID NO:1253 is the determined cDNA sequence for clone 62005943.

[1135] SEQ ID NO:1254 is the determined cDNA sequence for clone 62005945.

[1136] SEQ ID NO:1255 is the determined cDNA sequence for clone 62005988.

[1137] SEQ ID NO:1256 is the determined cDNA sequence for clone 62005990.

[1138] SEQ ID NO:1257 is the determined cDNA sequence for clone 62005946.

[1139] SEQ ID NO:1258 is the determined cDNA sequence for clone 62005948.

[1140] SEQ ID NO:1259 is the determined cDNA sequence for clone 62005950.

[1141] SEQ ID NO:1260 is the determined cDNA sequence for clone 62005995.

[1142] SEQ ID NO:1261 is the determined cDNA sequence for clone 62005997.

[1143] SEQ ID NO:1262 is the determined cDNA sequence for clone 62005947.

[1144] SEQ ID NO:1263 is the determined cDNA sequence for clone 62005949.

[1145] SEQ ID NO:1264 is the determined cDNA sequence for clone 62005951.

[1146] SEQ ID NO:1265 is the determined cDNA sequence for clone 62005994.

[1147] SEQ ID NO:1266 is the determined cDNA sequence for clone 62005996.

[1148] SEQ ID NO:1267 is the determined cDNA sequence for clone 62005952.

[1149] SEQ ID NO:1268 is the determined cDNA sequence for clone 62005954.

[1150] SEQ ID NO:1269 is the determined cDNA sequence for clone 62006001.

[1151] SEQ ID NO:1270 is the determined cDNA sequence for clone 62006003.

[1152] SEQ ID NO:1271 is the determined cDNA sequence for clone 62005953.

[1153] SEQ ID NO:1272 is the determined cDNA sequence for clone 62005955.

[1154] SEQ ID NO:1273 is the determined cDNA sequence for clone 62005957.

[1155] SEQ ID NO:1274 is the determined cDNA sequence for clone 62006000.

[1156] SEQ ID NO:1275 is the determined cDNA sequence for clone 62006002.

[1157] SEQ ID NO:1276 is the determined cDNA sequence for clone 62005960.

[1158] SEQ ID NO:1277 is the determined cDNA sequence for clone 62005962.

[1159] SEQ ID NO:1278 is the determined cDNA sequence for clone 62006005.

[1160] SEQ ID NO:1279 is the determined cDNA sequence for clone 62006007.

[1161] SEQ ID NO:1280 is the determined cDNA sequence for clone 62006009.

[1162] SEQ ID NO:1281 is the determined cDNA sequence for clone 62005959.

[1163] SEQ ID NO:1282 is the determined cDNA sequence for clone 62005961.

[1164] SEQ ID NO:1283 is the determined cDNA sequence for clone 62005963.

[1165] SEQ ID NO:1284 is the determined cDNA sequence for clone 62006006.

[1166] SEQ ID NO:1285 is the determined cDNA sequence for clone 62006010.

[1167] SEQ ID NO:1286 is the determined cDNA sequence for clone 62005968.

[1168] SEQ ID NO:1287 is the determined cDNA sequence for clone 62006011.

[1169] SEQ ID NO:1288 is the determined cDNA sequence for clone 62006013.

[1170] SEQ ID NO:1289 is the determined cDNA sequence for clone 62006015.

[1171] SEQ ID NO:1290 is the determined cDNA sequence for clone 62005967.

[1172] SEQ ID NO:1291 is the determined cDNA sequence for clone 62006014.

[1173] SEQ ID NO:1292 is the determined cDNA sequence for clone 62004436.

[1174] SEQ ID NO:1293 is the determined cDNA sequence for clone 62004438.

[1175] SEQ ID NO:1294 is the determined cDNA sequence for clone 62004483.

[1176] SEQ ID NO:1295 is the determined cDNA sequence for clone 62004485.

[1177] SEQ ID NO:1296 is the determined cDNA sequence for clone 62004435.

[1178] SEQ ID NO:1297 is the determined cDNA sequence for clone 62004439.

[1179] SEQ ID NO:1298 is the determined cDNA sequence for clone 62004482.

[1180] SEQ ID NO:1299 is the determined cDNA sequence for clone 62004484.

[1181] SEQ ID NO:1300 is the determined cDNA sequence for clone 62004486.

[1182] SEQ ID NO:1301 is the determined cDNA sequence for clone 62004440.

[1183] SEQ ID NO:1302 is the determined cDNA sequence for clone 62004442.

[1184] SEQ ID NO:1303 is the determined cDNA sequence for clone 62004444.

[1185] SEQ ID NO:1304 is the determined cDNA sequence for clone 62004487.

[1186] SEQ ID NO:1305 is the determined cDNA sequence for clone 62004489.

[1187] SEQ ID NO:1306 is the determined cDNA sequence for clone 62004491.

[1188] SEQ ID NO:1307 is the determined cDNA sequence for clone 62004441.

[1189] SEQ ID NO:1308 is the determined cDNA sequence for clone 62004443.

[1190] SEQ ID NO:1309 is the determined cDNA sequence for clone 62004445.

[1191] SEQ ID NO:1310 is the determined cDNA sequence for clone 62004488.

[1192] SEQ ID NO:1311 is the determined cDNA sequence for clone 62004490.

[1193] SEQ ID NO:1312 is the determined cDNA sequence for clone 62004492.

[1194] SEQ ID NO:1313 is the determined cDNA sequence for clone 62004446.

[1195] SEQ ID NO:1314 is the determined cDNA sequence for clone 62004448.

[1196] SEQ ID NO:1315 is the determined cDNA sequence for clone 62004493.

[1197] SEQ ID NO:1316 is the determined cDNA sequence for clone 62004495.

[1198] SEQ ID NO:1317 is the determined cDNA sequence for clone 62004497.

[1199] SEQ ID NO:1318 is the determined cDNA sequence for clone 62004447.

[1200] SEQ ID NO:1319 is the determined cDNA sequence for clone 62004451.

[1201] SEQ ID NO:1320 is the determined cDNA sequence for clone 62004494.

[1202] SEQ ID NO:1321 is the determined cDNA sequence for clone 62004498.

[1203] SEQ ID NO:1322 is the determined cDNA sequence for clone 62004452.

[1204] SEQ ID NO:1323 is the determined cDNA sequence for clone 62004454.

[1205] SEQ ID NO:1324 is the determined cDNA sequence for clone 62004456.

[1206] SEQ ID NO:1325 is the determined cDNA sequence for clone 62004499.

[1207] SEQ ID NO:1326 is the determined cDNA sequence for clone 62004501.

[1208] SEQ ID NO:1327 is the determined cDNA sequence for clone 62004503.

[1209] SEQ ID NO:1328 is the determined cDNA sequence for clone 62004453.

[1210] SEQ ID NO:1329 is the determined cDNA sequence for clone 62004455.

[1211] SEQ ID NO:1330 is the determined cDNA sequence for clone 62004500.

[1212] SEQ ID NO:1331 is the determined cDNA sequence for clone 62004502.

[1213] SEQ ID NO:1332 is the determined cDNA sequence for clone 62004504.

[1214] SEQ ID NO:1333 is the determined cDNA sequence for clone 62004458.

[1215] SEQ ID NO:1334 is the determined cDNA sequence for clone 62004460.

[1216] SEQ ID NO:1335 is the determined cDNA sequence for clone 62004462.

[1217] SEQ ID NO:1336 is the determined cDNA sequence for clone 62004505.

[1218] SEQ ID NO:1337 is the determined cDNA sequence for clone 62004507.

[1219] SEQ ID NO:1338 is the determined cDNA sequence for clone 62004509.

[1220] SEQ ID NO:1339 is the determined cDNA sequence for clone 62004459.

[1221] SEQ ID NO:1340 is the determined cDNA sequence for clone 62004461.

[1222] SEQ ID NO:1341 is the determined cDNA sequence for clone 62004463.

[1223] SEQ ID NO:1342 is the determined cDNA sequence for clone 62004506.

[1224] SEQ ID NO:1343 is the determined cDNA sequence for clone 62004510.

[1225] SEQ ID NO:1344 is the determined cDNA sequence for clone 62004464.

[1226] SEQ ID NO:1345 is the determined cDNA sequence for clone 62004466.

[1227] SEQ ID NO:1346 is the determined cDNA sequence for clone 62004468.

[1228] SEQ ID NO:1347 is the determined cDNA sequence for clone 62004511.

[1229] SEQ ID NO:1348 is the determined cDNA sequence for clone 62004513.

[1230] SEQ ID NO:1349 is the determined cDNA sequence for clone 62004515.

[1231] SEQ ID NO:1350 is the determined cDNA sequence for clone 62004467.

[1232] SEQ ID NO:1351 is the determined cDNA sequence for clone 62004469.

[1233] SEQ ID NO:1352 is the determined cDNA sequence for clone 62004512.

[1234] SEQ ID NO:1353 is the determined cDNA sequence for clone 62004514.

[1235] SEQ ID NO:1354 is the determined cDNA sequence for clone 62004516.

[1236] SEQ ID NO:1355 is the determined cDNA sequence for clone 62004470.

[1237] SEQ ID NO:1356 is the determined cDNA sequence for clone 62004472.

[1238] SEQ ID NO:1357 is the determined cDNA sequence for clone 62004474.

[1239] SEQ ID NO:1358 is the determined cDNA sequence for clone 62004517.

[1240] SEQ ID NO:1359 is the determined cDNA sequence for clone 62004519.

[1241] SEQ ID NO:1360 is the determined cDNA sequence for clone 62004521.

[1242] SEQ ID NO:1361 is the determined cDNA sequence for clone 62004471.

[1243] SEQ ID NO:1362 is the determined cDNA sequence for clone 62004473.

[1244] SEQ ID NO:1363 is the determined cDNA sequence for clone 62004475.

[1245] SEQ ID NO:1364 is the determined cDNA sequence for clone 62004518.

[1246] SEQ ID NO:1365 is the determined cDNA sequence for clone 62004520.

[1247] SEQ ID NO:1366 is the determined cDNA sequence for clone 62004478.

[1248] SEQ ID NO:1367 is the determined cDNA sequence for clone 62004523.

[1249] SEQ ID NO:1368 is the determined cDNA sequence for clone 62004525.

[1250] SEQ ID NO:1369 is the determined cDNA sequence for clone 62004477.

[1251] SEQ ID NO:1370 is the determined cDNA sequence for clone 62004479.

[1252] SEQ ID NO:1371 is the determined cDNA sequence for clone 62004481.

[1253] SEQ ID NO:1372 is the determined cDNA sequence for clone 62004524.

[1254] SEQ ID NO:1373 is the determined cDNA sequence for clone 62004526.

[1255] SEQ ID NO:1374 is the determined cDNA sequence for clone 61589753.

[1256] SEQ ID NO:1375 is the determined cDNA sequence for clone 61589755.

[1257] SEQ ID NO:1376 is the determined cDNA sequence for clone 61589800.

[1258] SEQ ID NO:1377 is the determined cDNA sequence for clone 61589802.

[1259] SEQ ID NO:1378 is the determined cDNA sequence for clone 61589754.

[1260] SEQ ID NO:1379 is the determined cDNA sequence for clone 61589756.

[1261] SEQ ID NO:1380 is the determined cDNA sequence for clone 61589799.

[1262] SEQ ID NO:1381 is the determined cDNA sequence for clone 61589801.

[1263] SEQ ID NO:1382 is the determined cDNA sequence for clone 61589803.

[1264] SEQ ID NO:1383 is the determined cDNA sequence for clone 61589759.

[1265] SEQ ID NO:1384 is the determined cDNA sequence for clone 61589761.

[1266] SEQ ID NO:1385 is the determined cDNA sequence for clone 61589804.

[1267] SEQ ID NO:1386 is the determined cDNA sequence for clone 61589806.

[1268] SEQ ID NO:1387 is the determined cDNA sequence for clone 61589808.

[1269] SEQ ID NO:1388 is the determined cDNA sequence for clone 61589758.

[1270] SEQ ID NO:1389 is the determined cDNA sequence for clone 61589760.

[1271] SEQ ID NO:1390 is the determined cDNA sequence for clone 61589762.

[1272] SEQ ID NO:1391 is the determined cDNA sequence for clone 61589805.

[1273] SEQ ID NO:1392 is the determined cDNA sequence for clone 61589807.

[1274] SEQ ID NO:1393 is the determined cDNA sequence for clone 61589809.

[1275] SEQ ID NO:1394 is the determined cDNA sequence for clone 61589763.

[1276] SEQ ID NO:1395 is the determined cDNA sequence for clone 61589765.

[1277] SEQ ID NO:1396 is the determined cDNA sequence for clone 61589767.

[1278] SEQ ID NO:1397 is the determined cDNA sequence for clone 61589814.

[1279] SEQ ID NO:1398 is the determined cDNA sequence for clone 61589764.

[1280] SEQ ID NO:1399 is the determined cDNA sequence for clone 61589766.

[1281] SEQ ID NO:1400 is the determined cDNA sequence for clone 61589768.

[1282] SEQ ID NO:1401 is the determined cDNA sequence for clone 61589811.

[1283] SEQ ID NO:1402 is the determined cDNA sequence for clone 61589813.

[1284] SEQ ID NO:1403 is the determined cDNA sequence for clone 61589815.

[1285] SEQ ID NO:1404 is the determined cDNA sequence for clone 61589769.

[1286] SEQ ID NO:1405 is the determined cDNA sequence for clone 61589771.

[1287] SEQ ID NO:1406 is the determined cDNA sequence for clone 61589773.

[1288] SEQ ID NO:1407 is the determined cDNA sequence for clone 61589816.

[1289] SEQ ID NO:1408 is the determined cDNA sequence for clone 61589818.

[1290] SEQ ID NO:1409 is the determined cDNA sequence for clone 61589820.

[1291] SEQ ID NO:1410 is the determined cDNA sequence for clone 61589772.

[1292] SEQ ID NO:1411 is the determined cDNA sequence for clone 61589774.

[1293] SEQ ID NO:1412 is the determined cDNA sequence for clone 61589817.

[1294] SEQ ID NO:1413 is the determined cDNA sequence for clone 61589819.

[1295] SEQ ID NO:1414 is the determined cDNA sequence for clone 61589821.

[1296] SEQ ID NO:1415 is the determined cDNA sequence for clone 61589777.

[1297] SEQ ID NO:1416 is the determined cDNA sequence for clone 61589779.

[1298] SEQ ID NO: 1417 is the determined cDNA sequence for clone 61589822.

[1299] SEQ ID NO:1418 is the determined cDNA sequence for clone 61589826.

[1300] SEQ ID NO:1419 is the determined cDNA sequence for clone 61589776.

[1301] SEQ ID NO:1420 is the determined cDNA sequence for clone 61589778.

[1302] SEQ ID NO:1421 is the determined cDNA sequence for clone 61589780.

[1303] SEQ ID NO:1422 is the determined cDNA sequence for clone 61589825.

[1304] SEQ ID NO:1423 is the determined cDNA sequence for clone 61589827.

[1305] SEQ ID NO: 1424 is the determined cDNA sequence for clone 61589781.

[1306] SEQ ID NO:1425 is the determined cDNA sequence for clone 61589783.

[1307] SEQ ID NO:1426 is the determined cDNA sequence for clone 61589785.

[1308] SEQ ID NO:1427 is the determined cDNA sequence for clone 61589830.

[1309] SEQ ID NO:1428 is the determined cDNA sequence for clone 61589832.

[1310] SEQ ID NO:1429 is the determined cDNA sequence for clone 61589782.

[1311] SEQ ID NO:1430 is the determined cDNA sequence for clone 61589786.

[1312] SEQ ID NO:1431 is the determined cDNA sequence for clone 61589829.

[1313] SEQ ID NO:1432 is the determined cDNA sequence for clone 61589833.

[1314] SEQ ID NO:1433 is the determined cDNA sequence for clone 61589787.

[1315] SEQ ID NO:1434 is the determined cDNA sequence for clone 61589789.

[1316] SEQ ID NO:1435 is the determined cDNA sequence for clone 61589791.

[1317] SEQ ID NO:1436 is the determined cDNA sequence for clone 61589834.

[1318] SEQ ID NO:1437 is the determined cDNA sequence for clone 61589836.

[1319] SEQ ID NO:1438 is the determined cDNA sequence for clone 61589788.

[1320] SEQ ID NO:1439 is the determined cDNA sequence for clone 61589790.

[1321] SEQ ID NO:1440 is the determined cDNA sequence for clone 61589835.

[1322] SEQ ID NO:1441 is the determined cDNA sequence for clone 61589837.

[1323] SEQ ID NO:1442 is the determined cDNA sequence for clone 61589839.

[1324] SEQ ID NO:1443 is the determined cDNA sequence for clone 61589793.

[1325] SEQ ID NO:1444 is the determined cDNA sequence for clone 61589795.

[1326] SEQ ID NO:1445 is the determined cDNA sequence for clone 61589797.

[1327] SEQ ID NO: 1446 is the determined cDNA sequence for clone 61589840.

[1328] SEQ ID NO:1447 is the determined cDNA sequence for clone 61589842.

[1329] SEQ ID NO:1448 is the determined cDNA sequence for clone 61589844.

[1330] SEQ ID NO:1449 is the determined cDNA sequence for clone 61589794.

[1331] SEQ ID NO:1450 is the determined cDNA sequence for clone 61589796.

[1332] SEQ ID NO:1451 is the determined cDNA sequence for clone 61589798.

[1333] SEQ ID NO:1452 is the determined cDNA sequence for clone 61589841.

[1334] SEQ ID NO:1453 is the determined cDNA sequence for clone 61589843.

[1335] SEQ ID NO:1454 is the determined cDNA sequence for clone 61589939.

[1336] SEQ ID NO:1455 is the determined cDNA sequence for clone 61589986.

[1337] SEQ ID NO:1456 is the determined cDNA sequence for clone 61589988.

[1338] SEQ ID NO:1457 is the determined cDNA sequence for clone 61589938.

[1339] SEQ ID NO:1458 is the determined cDNA sequence for clone 61589940.

[1340] SEQ ID NO:1459 is the determined cDNA sequence for clone 61589942.

[1341] SEQ ID NO:1460 is the determined cDNA sequence for clone 61589985.

[1342] SEQ ID NO:1461 is the determined cDNA sequence for clone 61589987.

[1343] SEQ ID NO:1462 is the determined cDNA sequence for clone 61589989.

[1344] SEQ ID N0:1463 is the determined cDNA sequence for clone 61589943.

[1345] SEQ ID NO:1464 is the determined cDNA sequence for clone 61589945.

[1346] SEQ ID NO:1465 is the determined cDNA sequence for clone 61589947.

[1347] SEQ ID NO:1466 is the determined cDNA sequence for clone 61589990.

[1348] SEQ ID NO:1467 is the determined cDNA sequence for clone 61589994.

[1349] SEQ ID NO:1468 is the determined cDNA sequence for clone 61589944.

[1350] SEQ ID NO:1469 is the determined cDNA sequence for clone 61589946.

[1351] SEQ ID NO:1470 is the determined cDNA sequence for clone 61589948.

[1352] SEQ ID NO:1471 is the determined cDNA sequence for clone 61589991.

[1353] SEQ ID NO:1472 is the determined cDNA sequence for clone 61589993.

[1354] SEQ ID NO:1473 is the determined cDNA sequence for clone 61589949.

[1355] SEQ ID NO:1474 is the determined cDNA sequence for clone 61589951.

[1356] SEQ ID NO: 1475 is the determined cDNA sequence for clone 61589953.

[1357] SEQ ID NO:1476 is the determined cDNA sequence for clone 61589996.

[1358] SEQ ID NO:1477 is the determined cDNA sequence for clone 61589998.

[1359] SEQ ID NO:1478 is the determined cDNA sequence for clone 61590000.

[1360] SEQ ID NO:1479 is the determined cDNA sequence for clone 61589950.

[1361] SEQ ID NO:1480 is the determined cDNA sequence for clone 61589952.

[1362] SEQ ID NO:1481 is the determined cDNA sequence for clone 61589954.

[1363] SEQ ID NO:1482 is the determined cDNA sequence for clone 61589997.

[1364] SEQ ID NO:1483 is the determined cDNA sequence for clone 61590001.

[1365] SEQ ID NO:1484 is the determined cDNA sequence for clone 61589955.

[1366] SEQ ID NO:1485 is the determined cDNA sequence for clone 61589957.

[1367] SEQ ID NO:1486 is the determined cDNA sequence for clone 61589959.

[1368] SEQ ID NO:1487 is the determined cDNA sequence for clone 61590002.

[1369] SEQ ID NO:1488 is the determined cDNA sequence for clone 61590004.

[1370] SEQ ID NO:1489 is the determined cDNA sequence for clone 61590006.

[1371] SEQ ID NO:1490 is the determined cDNA sequence for clone 61589956.

[1372] SEQ ID NO:1491 is the determined cDNA sequence for clone 61589958.

[1373] SEQ ID NO:1492 is the determined cDNA sequence for clone 61589960.

[1374] SEQ ID NO:1493 is the determined cDNA sequence for clone 61590003.

[1375] SEQ ID NO:1494 is the determined cDNA sequence for clone 61590007.

[1376] SEQ ID NO:1495 is the determined cDNA sequence for clone 61589961.

[1377] SEQ ID NO:1496 is the determined cDNA sequence for clone 61589963.

[1378] SEQ ID NO:1497 is the determined cDNA sequence for clone 61589965.

[1379] SEQ ID NO:1498 is the determined cDNA sequence for clone 61590008.

[1380] SEQ ID NO:1499 is the determined cDNA sequence for clone 61590010.

[1381] SEQ ID NO:1500 is the determined cDNA sequence for clone 61590012.

[1382] SEQ ID NO:1501 is the determined cDNA sequence for clone 61589962.

[1383] SEQ ID NO:1502 is the determined cDNA sequence for clone 61589964.

[1384] SEQ ID NO:1503 is the determined cDNA sequence for clone 61589966.

[1385] SEQ ID NO:1504 is the determined cDNA sequence for clone 61590009.

[1386] SEQ ID NO:1505 is the determined cDNA sequence for clone 61590011.

[1387] SEQ ID NO:1506 is the determined cDNA sequence for clone 61590013.

[1388] SEQ ID NO:1507 is the determined cDNA sequence for clone 61589967.

[1389] SEQ ID NO:1508 is the determined cDNA sequence for clone 61589969.

[1390] SEQ ID NO:1509 is the determined cDNA sequence for clone 61589971.

[1391] SEQ ID NO:1510 is the determined cDNA sequence for clone 61590014.

[1392] SEQ ID NO:1511 is the determined cDNA sequence for clone 61590018.

[1393] SEQ ID NO:1512 is the determined cDNA sequence for clone 61589968.

[1394] SEQ ID NO:1513 is the determined cDNA sequence for clone 61589970.

[1395] SEQ ID NO:1514 is the determined cDNA sequence for clone 61589972.

[1396] SEQ ID NO:1515 is the determined cDNA sequence for clone 61590015.

[1397] SEQ ID NO:1516 is the determined cDNA sequence for clone 61590017.

[1398] SEQ ID NO:1517 is the determined cDNA sequence for clone 61590019.

[1399] SEQ ID NO:1518 is the determined cDNA sequence for clone 61589973.

[1400] SEQ ID NO:1519 is the determined cDNA sequence for clone 61590020.

[1401] SEQ ID NO:1520 is the determined cDNA sequence for clone 61590022.

[1402] SEQ ID NO:1521 is the determined cDNA sequence for clone 61590024.

[1403] SEQ ID NO:1522 is the determined cDNA sequence for clone 61589974.

[1404] SEQ ID NO:1523 is the determined cDNA sequence for clone 61589976.

[1405] SEQ ID NO:1524 is the determined cDNA sequence for clone 61589978.

[1406] SEQ ID NO:1525 is the determined cDNA sequence for clone 61590021.

[1407] SEQ ID NO:1526 is the determined cDNA sequence for clone 61590023.

[1408] SEQ ID NO:1527 is the determined cDNA sequence for clone 61590025.

[1409] SEQ ID NO:1528 is the determined cDNA sequence for clone 61589979.

[1410] SEQ ID NO:1529 is the determined cDNA sequence for clone 61589981.

[1411] SEQ ID NO:1530 is the determined cDNA sequence for clone 61589983.

[1412] SEQ ID NO:1531 is the determined cDNA sequence for clone 61590026.

[1413] SEQ ID NO:1532 is the determined cDNA sequence for clone 61590028.

[1414] SEQ ID NO:1533 is the determined cDNA sequence for clone 61590030.

[1415] SEQ ID NO:1534 is the determined cDNA sequence for clone 61589980.

[1416] SEQ ID NO:1535 is the determined cDNA sequence for clone 61589982.

[1417] SEQ ID NO:1536 is the determined cDNA sequence for clone 61589984.

[1418] SEQ ID NO:1537 is the determined cDNA sequence for clone 61590027.

[1419] SEQ ID NO: 1538 is the determined cDNA sequence for clone 61590029.

[1420] SEQ ID NO:1539 is the determined cDNA sequence for clone 61931738.

[1421] SEQ ID NO:1540 is the determined cDNA sequence for clone 61931740.

[1422] SEQ ID NO:1541 is the determined cDNA sequence for clone 61931785.

[1423] SEQ ID NO:1542 is the determined cDNA sequence for clone 61931787.

[1424] SEQ ID NO:1543 is the determined cDNA sequence for clone 61931739.

[1425] SEQ ID NO:1544 is the determined cDNA sequence for clone 61931741.

[1426] SEQ ID NO:1545 is the determined cDNA sequence for clone 61931784.

[1427] SEQ ID NO:1546 is the determined cDNA sequence for clone 61931786.

[1428] SEQ ID NO:1547 is the determined cDNA sequence for clone 61931742.

[1429] SEQ ID NO:1548 is the determined cDNA sequence for clone 61931744.

[1430] SEQ ID NO:1549 is the determined cDNA sequence for clone 61931746.

[1431] SEQ ID NO:1550 is the determined cDNA sequence for clone 61931789.

[1432] SEQ ID NO:1551 is the determined cDNA sequence for clone 61931791.

[1433] SEQ ID NO:1552 is the determined cDNA sequence for clone 61931793.

[1434] SEQ ID NO:1553 is the determined cDNA sequence for clone 61931745.

[1435] SEQ ID NO:1554 is the determined cDNA sequence for clone 61931747.

[1436] SEQ ID NO:1555 is the determined cDNA sequence for clone 61931790.

[1437] SEQ ID NO:1556 is the determined cDNA sequence for clone 61931792.

[1438] SEQ ID NO:1557 is the determined cDNA sequence for clone 61931794.

[1439] SEQ ID NO:1558 is the determined cDNA sequence for clone 61931748.

[1440] SEQ ID NO:1559 is the determined cDNA sequence for clone 61931752.

[1441] SEQ ID NO:1560 is the determined cDNA sequence for clone 61931795.

[1442] SEQ ID NO:1561 is the determined cDNA sequence for clone 61931797.

[1443] SEQ ID NO:1562 is the determined cDNA sequence for clone 61931799.

[1444] SEQ ID NO:1563 is the determined cDNA sequence for clone 61931751.

[1445] SEQ ID NO:1564 is the determined cDNA sequence for clone 61931753.

[1446] SEQ ID NO:1565 is the determined cDNA sequence for clone 61931796.

[1447] SEQ ID NO:1566 is the determined cDNA sequence for clone 61931798.

[1448] SEQ ID NO:1567 is the determined cDNA sequence for clone 61931800.

[1449] SEQ ID NO:1568 is the determined cDNA sequence for clone 61931754.

[1450] SEQ ID NO:1569 is the determined cDNA sequence for clone 61931756.

[1451] SEQ ID NO:1570 is the determined cDNA sequence for clone 61931758.

[1452] SEQ ID NO:1571 is the determined cDNA sequence for clone 61931801.

[1453] SEQ ID NO:1572 is the determined cDNA sequence for clone 61931803.

[1454] SEQ ID NO:1573 is the-determined cDNA sequence for clone 61931805.

[1455] SEQ ID NO:1574 is the determined cDNA sequence for clone 61931755.

[1456] SEQ ID NO:1575 is the determined cDNA sequence for clone 61931757.

[1457] SEQ ID NO:1576 is the determined cDNA sequence for clone 61931759.

[1458] SEQ ID NO:1577 is the determined cDNA sequence for clone 61931802.

[1459] SEQ ID NO:1578 is the determined cDNA sequence for clone 61931804.

[1460] SEQ ID NO:1579 is the determined cDNA sequence for clone 61931806.

[1461] SEQ ID NO:1580 is the determined cDNA sequence for clone 61931760.

[1462] SEQ ID NO:1581 is the determined cDNA sequence for clone 61931762.

[1463] SEQ ID NO:1582 is the determined cDNA sequence for clone 61931764.

[1464] SEQ ID NO:1583 is the determined cDNA sequence for clone 61931809.

[1465] SEQ ID NO:1584 is the determined cDNA sequence for clone 61931811.

[1466] SEQ ID NO:1585 is the determined cDNA sequence for clone 61931761.

[1467] SEQ ID NO:1586 is the determined cDNA sequence for clone 61931763.

[1468] SEQ ID NO:1587 is the determined cDNA sequence for clone 61931765.

[1469] SEQ ID NO:1588 is the determined cDNA sequence for clone 61931808.

[1470] SEQ ID NO:1589 is the determined cDNA sequence for clone 61931810.

[1471] SEQ ID NO:1590 is the determined cDNA sequence for clone 61931812.

[1472] SEQ ID NO:1591 is the determined cDNA sequence for clone 61931768.

[1473] SEQ ID NO:1592 is the determined cDNA sequence for clone 61931770.

[1474] SEQ ID NO:1593 is the determined cDNA sequence for clone 61931813.

[1475] SEQ ID NO:1594 is the determined cDNA sequence for clone 61931815.

[1476] SEQ ID NO:1595 is the determined cDNA sequence for clone 61931817.

[1477] SEQ ID NO:1596 is the determined cDNA sequence for clone 61931767.

[1478] SEQ ID NO:1597 is the determined cDNA sequence for clone 61931769.

[1479] SEQ ID NO:1598 is the determined cDNA sequence for clone 61931771.

[1480] SEQ ID NO:1599 is the determined cDNA sequence for clone 61931814.

[1481] SEQ ID NO:1600 is the determined cDNA sequence for clone 61931816.

[1482] SEQ ID NO:1601 is the determined cDNA sequence for clone 61931818.

[1483] SEQ ID NO:1602 is the determined cDNA sequence for clone 61931772.

[1484] SEQ ID NO:1603 is the determined cDNA sequence for clone 61931774.

[1485] SEQ ID NO:1604 is the determined cDNA sequence for clone 61931776.

[1486] SEQ ID NO:1605 is the determined cDNA sequence for clone 61931821.

[1487] SEQ ID NO:1606 is the determined cDNA sequence for clone 61931823.

[1488] SEQ ID NO:1607 is the determined cDNA sequence for clone 61931773.

[1489] SEQ ID NO:1608 is the determined cDNA sequence for clone 61931775.

[1490] SEQ ID NO:1609 is the determined cDNA sequence for clone 61931777.

[1491] SEQ ID NO:1610 is the determined cDNA sequence for clone 61931820.

[1492] SEQ ID NO:1611 is the determined cDNA sequence for clone 61931822.

[1493] SEQ ID NO:1612 is the determined cDNA sequence for clone 61931824.

[1494] SEQ ID NO:1613 is the determined cDNA sequence for clone 61931778.

[1495] SEQ ID NO:1614 is the determined cDNA sequence for clone 61931780.

[1496] SEQ ID NO:1615 is the determined cDNA sequence for clone 61931782.

[1497] SEQ ID NO:1616 is the determined cDNA sequence for clone 61931825.

[1498] SEQ ID NO:1617 is the determined cDNA sequence for clone 61931827.

[1499] SEQ ID NO:1618 is the determined cDNA sequence for clone 61931829.

[1500] SEQ ID NO:1619 is the determined cDNA sequence for clone 61931779.

[1501] SEQ ID NO:1620 is the determined cDNA sequence for clone 61931781.

[1502] SEQ ID NO:1621 is the determined cDNA sequence for clone 61931783.

[1503] SEQ ID NO:1622 is the determined cDNA sequence for clone 61931826.

[1504] SEQ ID NO:1623 is the determined cDNA sequence for clone 61931828.

[1505] SEQ ID NO:1624 is the determined cDNA sequence for clone 61932017.

[1506] SEQ ID NO: 1625 is the determined cDNA sequence for clone 61932019.

[1507] SEQ ID NO:1626 is the determined cDNA sequence for clone 61932064.

[1508] SEQ ID NO:1627 is the determined cDNA sequence for clone 61932066.

[1509] SEQ ID NO:1628 is the determined cDNA sequence for clone 61932018.

[1510] SEQ ID NO:1629 is the determined cDNA sequence for clone 61932020.

[1511] SEQ ID NO:1630 is the determined cDNA sequence for clone 61932065.

[1512] SEQ ID NO:1631 is the determined cDNA sequence for clone 61932067.

[1513] SEQ ID NO:1632 is the determined cDNA sequence for clone 61932021.

[1514] SEQ ID NO: 1633 is the determined cDNA sequence for clone 61932023.

[1515] SEQ ID NO:1634 is the determined cDNA sequence for clone 61932025.

[1516] SEQ ID NO:1635 is the determined cDNA sequence for clone 61932068.

[1517] SEQ ID NO:1636 is the determined cDNA sequence for clone 61932070.

[1518] SEQ ID NO:1637 is the determined cDNA sequence for clone 61932072.

[1519] SEQ ID NO:1638 is the determined cDNA sequence for clone 61932024.

[1520] SEQ ID NO:1639 is the determined cDNA sequence for clone 61932026.

[1521] SEQ ID NO:1640 is the determined cDNA sequence for clone 61932073.

[1522] SEQ ID NO:1641 is the determined cDNA sequence for clone 61932027.

[1523] SEQ ID NO:1642 is the determined cDNA sequence for clone 61932031.

[1524] SEQ ID NO:1643 is the determined cDNA sequence for clone 61932074.

[1525] SEQ ID NO:1644 is the determined cDNA sequence for clone 61932076.

[1526] SEQ ID NO:1645 is the determined cDNA sequence for clone 61932078.

[1527] SEQ ID NO:1646 is the determined cDNA sequence for clone 61932028.

[1528] SEQ ID NO:1647 is the determined cDNA sequence for clone 61932030.

[1529] SEQ ID NO:1648 is the determined cDNA sequence for clone 61932075.

[1530] SEQ ID NO:1649 is the determined cDNA sequence for clone 61932077.

[1531] SEQ ID NO:1650 is the determined cDNA sequence for clone 61932079.

[1532] SEQ ID NO:1651 is the determined cDNA sequence for clone 61932035.

[1533] SEQ ID NO:1652 is the determined cDNA sequence for clone 61932037.

[1534] SEQ ID NO:1653 is the determined cDNA sequence for clone 61932080.

[1535] SEQ ID NO:1654 is the determined cDNA sequence for clone 61932082.

[1536] SEQ ID NO:1655 is the determined cDNA sequence for clone 61932084.

[1537] SEQ ID NO:1656 is the determined cDNA sequence for clone 61932038.

[1538] SEQ ID NO:1657 is the determined cDNA sequence for clone 61932083.

[1539] SEQ ID NO:1658 is the determined cDNA sequence for clone 61932085.

[1540] SEQ ID NO:1659 is the determined cDNA sequence for clone 61932039.

[1541] SEQ ID NO:1660 is the determined cDNA sequence for clone 61932043.

[1542] SEQ ID NO:1661 is the determined cDNA sequence for clone 61932086.

[1543] SEQ ID NO:1662 is the determined cDNA sequence for clone 61932088.

[1544] SEQ ID NO:1663 is the determined cDNA sequence for clone 61932090.

[1545] SEQ ID NO:1664 is the determined cDNA sequence for clone 61932040.

[1546] SEQ ID NO:1665 is the determined cDNA sequence for clone 61932042.

[1547] SEQ ID NO:1666 is the determined cDNA sequence for clone 61932044.

[1548] SEQ ID NO:1667 is the determined cDNA sequence for clone 61932089.

[1549] SEQ ID NO:1668 is the determined cDNA sequence for clone 61932045.

[1550] SEQ ID NO:1669 is the determined cDNA sequence for clone 61932047.

[1551] SEQ ID NO:1670 is the determined cDNA sequence for clone 61932049.

[1552] SEQ ID NO:1671 is the determined cDNA sequence for clone 61932092.

[1553] SEQ ID NO:1672 is the determined cDNA sequence for clone 61932096.

[1554] SEQ ID NO:1673 is the determined cDNA sequence for clone 61932046.

[1555] SEQ ID NO:1674 is the determined cDNA sequence for clone 61932050.

[1556] SEQ ID NO:1675 is the determined cDNA sequence for clone 61932093.

[1557] SEQ ID NO:1676 is the determined cDNA sequence for clone 61932095.

[1558] SEQ ID NO:1677 is the determined cDNA sequence for clone 61932051.

[1559] SEQ ID NO:1678 is the determined cDNA sequence for clone 61932053.

[1560] SEQ ID NO:1679 is the determined cDNA sequence for clone 61932055.

[1561] SEQ ID NO:1680 is the determined cDNA sequence for clone 61932098.

[1562] SEQ ID NO:1681 is the determined cDNA sequence for clone 61932100.

[1563] SEQ ID NO:1682 is the determined cDNA sequence for clone 61932102.

[1564] SEQ ID NO:1683 is the determined cDNA sequence for clone 61932052.

[1565] SEQ ID NO:1684 is the determined cDNA sequence for clone 61932054.

[1566] SEQ ID NO:1685 is the determined cDNA sequence for clone 61932056.

[1567] SEQ ID NO:1686 is the determined cDNA sequence for clone 61932101.

[1568] SEQ ID NO:1687 is the determined cDNA sequence for clone 61932103.

[1569] SEQ ID NO:1688 is the determined cDNA sequence for clone 61932059.

[1570] SEQ ID NO:1689 is the determined cDNA sequence for clone 61932061.

[1571] SEQ ID NO:1690 is the determined cDNA sequence for clone 61932106.

[1572] SEQ ID NO:1691 is the determined cDNA sequence for clone 61932062.

[1573] SEQ ID NO:1692 is the determined cDNA sequence for clone 61932105.

[1574] SEQ ID NO:1693 is the determined cDNA sequence for clone KAM202 G1, also referred to as K1549P.

[1575] SEQ ID NO:1694 is the determined cDNA sequence for clone SAM113 D8.

[1576] SEQ ID NO:1695 is the determined cDNA sequence for clone KAM207 D12.

[1577] SEQ ID NO:1696 is the determined cDNA sequence for clone KAM217 E6.

[1578] SEQ ID NO:1697 is the determined cDNA sequence for clone SAM121 C3.

[1579] SEQ ID NO:1698 is the determined cDNA sequence for clone LLAM27 D7.

[1580] SEQ ID NO:1699 is the determined cDNA sequence for clone SAM113 G7.

[1581] SEQ ID NO:1700 is the determined cDNA sequence for clone SAM115 F7.

[1582] SEQ ID NO:1701 is the determined cDNA sequence for clone DAM216 A10.

[1583] SEQ ID NO:1702 is the determined cDNA sequence for clone KAM202 C11, also referred to as K1548P.

[1584] SEQ ID NO:1703 is the determined cDNA sequence for clone SAM114 H4.

[1585] SEQ ID NO:1704 is the determined cDNA sequence for clone KAM210 C2.

[1586] SEQ ID NO:1705 is the determined cDNA sequence for clone SAM117 E10.

[1587] SEQ ID NO:1706 is the determined cDNA sequence for clone KAM218 D3.

[1588] SEQ ID NO:1707 is the determined cDNA sequence for clone KAM208 C12.

[1589] SEQ ID NO:1708 is the determined cDNA sequence for clone KAM202 B1.

[1590] SEQ ID NO:1709 is the determined cDNA sequence for clone KAM202 E8.

[1591] SEQ ID NO: 1710 is the determined cDNA sequence for clone KAM203 G5.

[1592] SEQ ID NO:1711 is the determined cDNA sequence for clone KAM206 D6.

[1593] SEQ ID NO:1712 is the determined cDNA sequence for clone KAM218 D7.

[1594] SEQ ID NO:1713 is the determined cDNA sequence for clone KAM209 H9.

[1595] SEQ ID NO:1714 is the determined cDNA sequence for clone KAM217 D2.

[1596] SEQ ID NO:1715 is the determined cDNA sequence for clone KAM208 F8.

[1597] SEQ ID NO:1716 is the determined cDNA sequence for clone KAM202 B7.

[1598] SEQ ID NO:1717 is the determined cDNA sequence for clone KAM212 A9.

[1599] SEQ ID NO:1718 is the determined cDNA sequence for clone KAM218 G1.

[1600] SEQ ID NO:1719 is the determined cDNA sequence for clone KAM217 D7.

[1601] SEQ ID NO:1720 is the determined cDNA sequence for clone KAM218 C10.

[1602] SEQ ID NO:1721 is the determined cDNA sequence for clone KAM201 C7.

[1603] SEQ ID NO:1722 is the determined cDNA sequence for clone SAM131 E12.

[1604] SEQ ID NO:1723 is the determined cDNA sequence for clone KAM214 B10.

[1605] SEQ ID NO:1724 is the determined cDNA sequence for clone LLAM25 B11.

[1606] SEQ ID NO:1725 is the determined cDNA sequence for clone LLAM29 E3.

[1607] SEQ ID NO:1726 is the determined cDNA sequence for clone SAMl16 B3.

[1608] SEQ ID NO:1727 is the determined cDNA sequence for clone KAM218 A9.

[1609] SEQ ID NO:1728 is the determined cDNA sequence for clone KAM208 B7.

[1610] SEQ ID NO:1729 is the determined cDNA sequence for clone LLAM28 B4.

[1611] SEQ ID NO:1730 is the determined cDNA sequence for clone KAM207 C12.

[1612] SEQ ID NO:1731 is the determined cDNA sequence for clone LLAM25 B6.

[1613] SEQ ID NO:1732 is the determined cDNA sequence for clone LLAM25 B1.

[1614] SEQ ID NO:1733 is the determined cDNA sequence for clone KAM211 H5.

[1615] SEQ ID NO:1734 is the determined cDNA sequence for clone LLAM29 H3.

[1616] SEQ ID NO:1735 is the determined cDNA sequence for clone LLAM25 A8.

[1617] SEQ ID NO:1736 is the determined cDNA sequence for clone KAM217 H11.

[1618] SEQ ID NO:1737 is the determined cDNA sequence for clone SAM114 A8.

[1619] SEQ ID NO:1738 is the determined cDNA sequence for clone SAM129 B11.

[1620] SEQ ID NO:1739 is the determined cDNA sequence for clone KAM215 H1.

[1621] SEQ ID NO:1740 is the determined cDNA sequence for clone KAM207 D7.

[1622] SEQ ID NO:1741 is the determined cDNA sequence for clone KAM217 D3.

[1623] SEQ ID NO:1742 is the determined cDNA sequence for clone KAM215 G3.

[1624] SEQ ID NO:1743 is the determined cDNA sequence for clone KAM202 H11.

[1625] SEQ ID NO:1744 is the determined cDNA sequence for clone KAM209 C5.

[1626] SEQ ID NO:1745 is the determined cDNA sequence for clone KAM205 D7.

[1627] SEQ ID NO:1746 is the determined cDNA sequence for clone KAM211 G11.

[1628] SEQ ID NO:1747 is the determined cDNA sequence for clone KAM200 D7.

[1629] SEQ ID NO:1748 is the determined cDNA sequence for clone KAM209 F3.

[1630] SEQ ID NO:1749 is the determined cDNA sequence for clone KAM212 B11.

[1631] SEQ ID NO:1750 is the determined cDNA sequence for clone KAM212 D10.

[1632] SEQ ID NO:1751 is the determined cDNA sequence for clone KAM200 F1.

[1633] SEQ ID NO:1752 is the determined cDNA sequence for clone KAM217 H7.

[1634] SEQ ID NO:1753 is the determined cDNA sequence for clone SAM120 G5.

[1635] SEQ ID NO:1754 is the determined cDNA sequence for clone SAM129 G1.

[1636] SEQ ID NO:1755 is the determined cDNA sequence for clone KAM205 A12.

[1637] SEQ ID NO:1756 is the determined cDNA sequence for clone KAM202 D8.

[1638] SEQ ID NO: 1757 is the determined cDNA sequence for clone KAM205 C7.

[1639] SEQ ID NO:1758 is the determined cDNA sequence for clone LLAM26 F3.

[1640] SEQ ID NO:1759 is the determined cDNA sequence for clone KAM218 G8.

[1641] SEQ ID NO:1760 is the determined cDNA sequence for clone KAM213 A4.

[1642] SEQ ID NO:1761 is the determined cDNA sequence for clone SAM116 E7.

[1643] SEQ ID NO:1762 is the determined cDNA sequence for clone SAM127 D8.

[1644] SEQ ID NO:1763 is the determined cDNA sequence for clone KAM211 H4.

[1645] SEQ ID NO:1764 is the determined cDNA sequence for clone KAM216 C3.

[1646] SEQ ID NO:1765 is the determined cDNA sequence for clone KAM213 F11.

[1647] SEQ ID NO:1766 is the determined cDNA sequence for clone KAM218 F4.

[1648] SEQ ID NO:1767 is the determined cDNA sequence for clone KAM202 A9.

[1649] SEQ ID NO: 1768 is the determined cDNA sequence for clone KAM217 E1.

[1650] SEQ ID NO:1769 is the determined cDNA sequence for clone KAM205 C6, also referred to as K1551 P.

[1651] SEQ ID NO:1770 is the determined cDNA sequence for clone KAM203 B8.

[1652] SEQ ID NO:1771 is the determined cDNA sequence for clone KAM210 C8.

[1653] SEQ ID NO:1772 is the determined cDNA sequence for clone LLAM25 D8.

[1654] SEQ ID NO:1773 is the determined cDNA sequence for clone KAM204 G2.

[1655] SEQ ID NO:1774 is the determined cDNA sequence for clone KAM218 C3.

[1656] SEQ ID NO:1775 is the determined cDNA sequence for clone KAM201 E10.

[1657] SEQ ID NO:1776 is the determined cDNA sequence for clone SAM113 C4.

[1658] SEQ ID NO:1777 is the determined cDNA sequence for clone KAM207 B8.

[1659] SEQ ID NO:1778 is the determined cDNA sequence for clone KAM207 C9.

[1660] SEQ ID NO:1779 is the determined cDNA sequence for clone KAM217 C3.

[1661] SEQ ID NO:1780 is the determined cDNA sequence for clone KAM204 A6.

[1662] SEQ ID NO:1781 is the determined cDNA sequence for clone SAM125 H7.

[1663] SEQ ID NO:1782 is the determined cDNA sequence for clone SAM129 G3.

[1664] SEQ ID NO:1783 is the determined cDNA sequence for clone LLAM27 F7.

[1665] SEQ ID NO:1784 is the determined cDNA sequence for clone LLAM26 F5.

[1666] SEQ ID NO:1785 is the determined cDNA sequence for clone KAM217 G11.

[1667] SEQ ID NO:1786 is the determined cDNA sequence for clone KAM217 G9.

[1668] SEQ ID NO:1787 is the determined cDNA sequence for clone SAM115 B3.

[1669] SEQ ID NO:1788 is the determined cDNA sequence for clone KAM211 B4.

[1670] SEQ ID NO:1789 is the determined cDNA sequence for clone KAM205 E9.

[1671] SEQ ID NO:1790 is the determined cDNA sequence for clone KAM210 B12.

[1672] SEQ ID NO:1791 is the determined cDNA sequence for clone KAM214 D1.

[1673] SEQ ID NO:1792 is the determined cDNA sequence for clone LLAM26 C2.

[1674] SEQ ID NO:1793 is the determined cDNA sequence for clone KAM209 B1.

[1675] SEQ ID NO:1794 is the determined cDNA sequence for clone KAM209 D9.

[1676] SEQ ID NO:1795 is the determined cDNA sequence for clone KAM213 D5.

[1677] SEQ ID NO:1796 is the determined cDNA sequence for clone KAM204 B7.

[1678] SEQ ID NO:1797 is the determined cDNA sequence for clone KAM203 A1.

[1679] SEQ ID NO:1798 is the determined cDNA sequence for clone KAM200 C7.

[1680] SEQ ID NO:1799 is the determined cDNA sequence for clone KAM216 G7.

[1681] SEQ ID NO: 1800 is the determined cDNA sequence for clone KAM212 H11.

[1682] SEQ ID NO:1801 is the determined cDNA sequence for clone KAM216 G8.

[1683] SEQ ID NO:1802 is the determined cDNA sequence for clone KAM213 F9.

[1684] SEQ ID NO:1803 is the determined cDNA sequence for clone KAM200 C11.

[1685] SEQ ID NO:1804 is the determined cDNA sequence for clone KAM217 D10.

[1686] SEQ ID NO:1805 is the determined cDNA sequence for clone KAM213 D11.

[1687] SEQ ID NO:1806 is the determined cDNA sequence for clone LLAM25 G9.

[1688] SEQ ID NO:1807 is the determined cDNA sequence for clone KAM212 B8.

[1689] SEQ ID NO:1808 is the determined cDNA sequence for clone KAM204 G8.

[1690] SEQ ID NO:1809 is the determined cDNA sequence for clone KAM216 G9.

[1691] SEQ ID NO:1810 is the determined cDNA sequence for clone DAM202 C5.

[1692] SEQ ID NO:1811 is the determined cDNA sequence for clone SAM105 D10.

[1693] SEQ ID NO:1812 is the determined cDNA sequence for clone KAM217 D6.

[1694] SEQ ID NO:1813 is the determined cDNA sequence for clone KAM217 B10.

[1695] SEQ ID NO:1814 is the determined cDNA sequence for clone KAM217 H1.

[1696] SEQ ID NO:1815 is the determined cDNA sequence for clone KAM208 B2.

[1697] SEQ ID NO:1816 is the determined cDNA sequence for clone LLAM26 A2.

[1698] SEQ ID NO:1817 is the determined cDNA sequence for clone KAM208 F10.

[1699] SEQ ID NO:1818 is the determined cDNA sequence for clone KAM204 F7.

[1700] SEQ ID NO:1819 is the determined cDNA sequence for clone SAM122 G5.

[1701] SEQ ID NO:1820 is the determined cDNA sequence for clone KAM201 A9.

[1702] SEQ ID NO:1821 is the determined cDNA sequence for clone KAM205 C3.

[1703] SEQ ID NO:1822 is the determined cDNA sequence for clone SAM124 G9.

[1704] SEQ ID NO:1823 is the determined cDNA sequence for clone KAM216 D9.

[1705] SEQ ID NO:1824 is the determined cDNA sequence for clone KAM216 B12.

[1706] SEQ ID NO:1825 is the determined cDNA sequence for clone KAM218 D8.

[1707] SEQ ID NO:1826 is the determined cDNA sequence for clone KAM215 B11.

[1708] SEQ ID NO:1827 is the determined cDNA sequence for clone SAM 130 A1.

[1709] SEQ ID NO:1828 is the determined cDNA sequence for clone KAM205 F5.

[1710] SEQ ID NO:1829 is the determined cDNA sequence for clone KAM205 C4.

[1711] SEQ ID NO:1830 is the determined cDNA sequence for clone SAM115 G12.

[1712] SEQ ID NO:1831 is the determined cDNA sequence for clone KAM207 D6.

[1713] SEQ ID NO:1832 is the determined cDNA sequence for clone LLAM28 C3.

[1714] SEQ ID NO:1833 is the determined cDNA sequence for clone KAM205 D5.

[1715] SEQ ID NO:1834 is the determined cDNA sequence for clone KAM205 G7.

[1716] SEQ ID NO:1835 is the determined cDNA sequence for clone SAM120 H3.

[1717] SEQ ID NO:1836 is the determined cDNA sequence for clone KAM201 A1.

[1718] SEQ ID NO:1837 is the determined cDNA sequence for clone KAM211 H3.

[1719] SEQ ID NO:1838 is the determined cDNA sequence for clone KAM216 B8.

[1720] SEQ ID NO:1839 is the determined cDNA sequence for clone KAM216 D4.

[1721] SEQ ID NO:1840 is the determined cDNA sequence for clone KAM201 E4.

[1722] SEQ ID NO:1841 is the determined cDNA sequence for clone KAM214 C7.

[1723] SEQ ID NO:1842 is the determined cDNA sequence for clone KAM206 C4.

[1724] SEQ ID NO:1843 is the determined cDNA sequence for clone KAM215 C1.

[1725] SEQ ID NO:1844 is the determined cDNA sequence for clone K1100C.

[1726] SEQ ID NO:1845 is the determined cDNA sequence for clone K1101 C.

[1727] SEQ ID NO:1846 is the determined cDNA sequence for clone K1102C.

[1728] SEQ ID NO:1847 is an extended cDNA sequence for K1551 P.

[1729] SEQ ID NO:1848 is the predicted amino acid sequence for K1548P.

[1730] SEQ ID NO:1849 is the predicted amino acid sequence for K1549P.

[1731] SEQ ID NO:1850 is the predicted amino acid sequence for K1551 P.

[1732] SEQ ID NO:1851 is an extended amino acid sequence for K1551 P.

[1733] SEQ ID NO:1852 is the determined full-length cDNA sequence for K1622P.

[1734] SEQ ID NO:1853 is the determined cDNA sequence for ORF #1 (no upstream stop codon) of K1622P.

[1735] SEQ ID NO:1854 is the determined cDNA sequence for ORF #2 (first Methionine) of K1622P.

[1736] SEQ ID NO:1855 is the determined cDNA sequence for ORF #3 (second methionine with Kozac) of K1622P.

[1737] SEQ ID NO:1856 is the predicted amino acid sequence for K1622P ORF #1, encoded by the cDNA set forth in SEQ ID NO:1853.

[1738] SEQ ID NO:1857 is the predicted amino acid sequence for K1622P ORF #2, encoded by the cDNA set forth in SEQ ID NO:1854.

[1739] SEQ ID NO:1858 is the predicted amino acid sequence for K1622P ORF #3, encoded by the cDNA set forth in SEQ ID NO:1855.

[1740] SEQ ID NO:1859 is the cDNA coding sequence K1548P.

[1741] SEQ ID NO:1860 is the cDNA coding sequence K1549P.

[1742] SEQ ID NO:1861 is the cDNA coding sequence K1550P.

[1743] SEQ ID NO:1862 is the cDNA coding sequence K1551 P.

[1744] SEQ ID NO:1863 is the amino acid sequence for K1550P, encoded by the polynucleotide set forth in SEQ ID NO:1861.

DETAILED DESCRIPTION OF THE INVENTION

[1745] U.S. patents, U.S. patent application publications, U.S. patent applications, foreign patents, foreign patent applications and non-patent publications referred to in this specification and/or listed in the Application Data Sheet, are incorporated herein by reference, in their entirety.

[1746] The present invention is directed generally to compositions and their use in the therapy and diagnosis of cancer, particularly kidney cancer. As described further below, illustrative compositions of the present invention include, but are not restricted to, polypeptides, particularly immunogenic polypeptides, polynucleotides encoding such polypeptides, antibodies and other binding agents, antigen presenting cells (APCs) and immune system cells (e.g., T cells).

[1747] The practice of the present invention will employ, unless indicated specifically to the contrary, conventional methods of virology, immunology, microbiology, molecular biology and recombinant DNA techniques within the skill of the art, many of which are described below for the purpose of illustration. Such techniques are explained fully in the literature. See, e.g., Sambrook, et al. Molecular Cloning: A Laboratory Manual (2nd Edition, 1989); Maniatis et al. Molecular Cloning: A Laboratory Manual (1982); DNA Cloning: A Practical Approach, vol. I & II (D. Glover, ed.); Oligonucleotide Synthesis (N. Gait, ed., 1984); Nucleic Acid Hybridization (B. Hames & S. Higgins, eds., 1985); Transcription and Translation (B. Hames & S. Higgins, eds., 1984); Animal Cell Culture (R. Freshney, ed., 1986); Perbal, A Practical Guide to Molecular Cloning (1984).

[1748] All publications, patents and patent applications cited herein, whether supra or infra, are hereby incorporated by reference in their entirety.

[1749] As used in this specification and the appended claims, the singular forms “a,” “an” and “the” include plural references unless the content clearly dictates otherwise.

[1750] Polypeptide Compositions

[1751] As used herein, the term “polypeptide” “is used in its conventional meaning, ie., as a sequence of amino acids. The polypeptides are not limited to a specific length of the product; thus, peptides, oligopeptides, and proteins are included within the definition of polypeptide, and such terms may be used interchangeably herein unless specifically indicated otherwise. This term also does not refer to or exclude post-expression modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations and the like, as well as other modifications known in the art, both naturally occurring and non-naturally occurring. A polypeptide may be an entire protein, or a subsequence thereof. Particular polypeptides of interest in the context of this invention are amino acid subsequences comprising epitopes, i.e., antigenic determinants substantially responsible for the immunogenic properties of a polypeptide and being capable of evoking an immune response.

[1752] Particularly illustrative polypeptides of the present invention comprise those encoded by a polynucleotide sequence set forth in any one of SEQ ID NOs:1-1847, 1852-1855, and 1859-1862, or a sequence that hybridizes under moderately stringent conditions, or, alternatively, under highly stringent conditions, to a polynucleotide sequence set forth in any one of SEQ ID NOs:1-1847, 1852-1855, and 1859-1862. Certain other illustrative polypeptides of the invention comprise amino acid sequences as set forth in any one of SEQ ID NOs:1848-1851, 1856-1858, and 1863.

[1753] The polypeptides of the present invention are sometimes herein referred to as kidney tumor proteins or kidney tumor polypeptides, as an indication that their identification has been based at least in part upon their increased levels of expression in kidney tumor samples. Thus, a “kidney tumor polypeptide” or “kidney tumor protein,” refers generally to a polypeptide sequence of the present invention, or a polynucleotide sequence encoding such a polypeptide, that is expressed in a substantial proportion of kidney tumor samples, for example preferably greater than about 20%, more preferably greater than about 30%, and most preferably greater than about 50% or more of kidney tumor samples tested, at a level that is at least two fold, and preferably at least five fold, greater than the level of expression in normal tissues, as determined using a representative assay provided herein. A kidney tumor polypeptide sequence of the invention, based upon its increased level of expression in tumor cells, has particular utility both as a diagnostic marker as well as a therapeutic target, as further described below.

[1754] In certain preferred embodiments, the polypeptides of the invention are immunogenic, i.e., they react detectably within an immunoassay (such as an ELISA or T-cell stimulation assay) with antisera and/or T-cells from a patient with kidney cancer. Screening for immunogenic activity can be performed using techniques well known to the skilled artisan. For example, such screens can be performed using methods such as those described in Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988. In one illustrative example, a polypeptide may be immobilized on a solid support and contacted with patient sera to allow binding of antibodies within the sera to the immobilized polypeptide. Unbound sera may then be removed and bound antibodies detected using, for example, 125I-labeled Protein A.

[1755] As would be recognized by the skilled artisan, immunogenic portions of the polypeptides disclosed herein are also encompassed by the present invention. An “immunogenic portion,” as used herein, is a fragment of an immunogenic polypeptide of the invention that itself is immunologically reactive (i.e., specifically binds) with the B-cells and/or T-cell surface antigen receptors that recognize the polypeptide. Immunogenic portions may generally be identified using well known techniques, such as those summarized in Paul, Fundamental Immunology, 3rd ed., 243-247 (Raven Press, 1993) and references cited therein. Such techniques include screening polypeptides for the ability to react with antigen-specific antibodies, antisera and/or T-cell lines or clones. As used herein, antisera and antibodies are “antigen-specific” if they specifically bind to an antigen (i.e., they react with the protein in an ELISA or other immunoassay, and do not react detectably with unrelated proteins). Such antisera and antibodies may be prepared as described herein, and using well-known techniques.

[1756] In one preferred embodiment, an immunogenic portion of a polypeptide of the present invention is a portion that reacts with antisera and/or T-cells at a level that is not substantially less than the reactivity of the full-length polypeptide (e.g., in an ELISA and/or T-cell reactivity assay). Preferably, the level of immunogenic activity of the immunogenic portion is at least about 50%, preferably at least about 70% and most preferably greater than about 90% of the immunogenicity for the full-length polypeptide. In some instances, preferred immunogenic portions will be identified that have a level of immunogenic activity greater than that of the corresponding full-length polypeptide, e.g., having greater than about 100% or 150% or more immunogenic activity.

[1757] In certain other embodiments, illustrative immunogenic portions may include peptides in which an N-terminal leader sequence and/or transmembrane domain have been deleted. Other illustrative immunogenic portions will contain a small N- and/or C-terminal deletion (e.g., 1-30 amino acids, preferably 5-15 amino acids), relative to the mature protein.

[1758] In another embodiment, a polypeptide composition of the invention may also comprise one or more polypeptides that are immunologically reactive with T cells and/or antibodies generated against a polypeptide of the invention, particularly a polypeptide having an amino acid sequence disclosed herein, or to an immunogenic fragment or variant thereof.

[1759] In another embodiment of the invention, polypeptides are provided that comprise one or more polypeptides that are capable of eliciting T cells and/or antibodies that are immunologically reactive with one or more polypeptides described herein, or one or more polypeptides encoded by contiguous nucleic acid sequences contained in the polynucleotide sequences disclosed herein, or immunogenic fragments or variants thereof, or to one or more nucleic acid sequences which hybridize to one or more of these sequences under conditions of moderate to high stringency.

[1760] The present invention, in another aspect, provides polypeptide fragments comprising at least about 5,10, 15, 20, 25, 50, or 100 contiguous amino acids, or more, including all intermediate lengths, of a polypeptide compositions set forth herein, such as those set forth in SEQ ID NOs: 1848-1851, 1856-1858, and 1863, or those encoded by a polynucleotide sequence set forth in a sequence of SEQ ID NOs:1-1847, 1852-1855, and 1859-1862.

[1761] In another aspect, the present invention provides variants of the polypeptide compositions described herein. Polypeptide variants generally encompassed by the present invention will typically exhibit at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identity (determined as described below), along its length, to a polypeptide sequences set forth herein.

[1762] In one preferred embodiment, the polypeptide fragments and variants provided by the present invention are immunologically reactive with an antibody and/or T-cell that reacts with a full-length polypeptide specifically set forth herein.

[1763] In another preferred embodiment, the polypeptide fragments and variants provided by the present invention exhibit a level of immunogenic activity of at least about 50%, preferably at least about 70%, and most preferably at least about 90% or more of that exhibited by a full-length polypeptide sequence specifically set forth herein.

[1764] A polypeptide “variant,” as the term is used herein, is a polypeptide that typically differs from a polypeptide specifically disclosed herein in one or more substitutions, deletions, additions and/or insertions. Such variants may be naturally occurring or may be synthetically generated, for example, by modifying one or more of the above polypeptide sequences of the invention and evaluating their immunogenic activity as described herein and/or using any of a number of techniques well known in the art.

[1765] For example, certain illustrative variants of the polypeptides of the invention include those in which one or more portions, such as an N-terminal leader sequence or transmembrane domain, have been removed. Other illustrative variants include variants in which a small portion (e.g., 1-30 amino acids, preferably 5-15 amino acids) has been removed from the N— and/or C-terminal of the mature protein.

[1766] In many instances, a variant will contain conservative substitutions. A “conservative substitution” is one in which an amino acid is substituted for another amino acid that has similar properties, such that one skilled in the art of peptide chemistry would expect the secondary structure and hydropathic nature of the polypeptide to be substantially unchanged. As described above, modifications may be made in the structure of the polynucleotides and polypeptides of the present invention and still obtain a functional molecule that encodes a variant or derivative polypeptide with desirable characteristics, e.g., with immunogenic characteristics. When it is desired to alter the amino acid sequence of a polypeptide to create an equivalent, or even an improved, immunogenic variant or portion of a polypeptide of the invention, one skilled in the art will typically change one or more of the codons of the encoding DNA sequence according to Table 1.

[1767] For example, certain amino acids may be substituted for other amino acids in a protein structure without appreciable loss of interactive binding capacity with structures such as, for example, antigen-binding regions of antibodies or binding sites on substrate molecules. Since it is the interactive capacity and nature of a protein that defines that protein's biological functional activity, certain amino acid sequence substitutions can be made in a protein sequence, and, of course, its underlying DNA coding sequence, and nevertheless obtain a protein with like properties. It is thus contemplated that various changes may be made in the peptide sequences of the disclosed compositions, or corresponding DNA sequences which encode said peptides without appreciable loss of their biological utility or activity.

TABLE 1
Amino Acids	Codons
Alanine	Ala	A	GGA GCC GCG GCU
Cysteine	Cys	C	UGC UGU
Aspartic acid	Asp	D	GAC GAU
Glutamic acid	Glu	E	GAA GAG
Phenylalanine	Phe	F	UUC UUU
Glycine	Gly	G	GGA GGC GGG GGU
Histidine	His	H	CAC CAU
Isoleucine	Ile	I	AUA AUC AUU
Lysine	Lys	K	AAA AAG
Leucine	Leu	L	UUA UUG CUA CUC CUG CUU
Methionine	Met	M	AUG
Asparagine	Asn	N	AAC AAU
Proline	Pro	P	CCA CCC CCG CCU
Glutamine	Gln	Q	CAA CAG
Arginine	Arg	R	AGA AGG CGA CGC CGG CGU
Serine	Ser	S	AGC AGU UCA UCC UCG UCU
Threonine	Thr	T	ACA ACC ACG ACU
Valine	Val	V	GUA GUC GUG GUU
Tryptophan	Trp	W	UGG
Tyrosine	Tyr	Y	UAC UAU

[1768] In making such changes, the hydropathic index of amino acids may be considered. The importance of the hydropathic amino acid index in conferring interactive biologic function on a protein is generally understood in the art (Kyte and Doolittle, 1982, incorporated herein by reference). It is accepted that the relative hydropathic character of the amino acid contributes to the secondary structure of the resultant protein, which in turn defines the interaction of the protein with other molecules, for example, enzymes, substrates, receptors, DNA, antibodies, antigens, and the like. Each amino acid has been assigned a hydropathic index on the basis of its hydrophobicity and charge characteristics (Kyte and Doolittle, 1982). These values are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cystine (+2.5); methionine (+1.9); alanine (+1.8); glycine (−0.4); threonine (−0.7); serine (−0.8); tryptophan (−0.9); tyrosine (−1.3); proline (−1.6); histidine (−3.2); glutamate (−3.5); glutamine (−3.5); aspartate (−3.5); asparagine (−3.5); lysine (−3.9); and arginine (−4.5).

[1769] It is known in the art that certain amino acids may be substituted by other amino acids having a similar hydropathic index or score and still result in a protein with similar biological activity, i.e. still obtain a biological functionally equivalent protein. In making such changes, the substitution of amino acids whose hydropathic indices are within +2 is preferred, those within +1 are particularly preferred, and those within +0.5 are even more particularly preferred. It is also understood in the art that the substitution of like amino acids can be made effectively on the basis of hydrophilicity. U.S. Pat. No. 4,554,101 (specifically incorporated herein by reference in its entirety), states that the greatest local average hydrophilicity of a protein, as governed by the hydrophilicity of its adjacent amino acids, correlates with a biological property of the protein.

[1770] As detailed in U.S. Pat. No. 4,554,101, the following hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0±1); glutamate (+3.0±1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (O); threonine (−0.4); proline (−0.5±1); alanine (−0.5); histidine (−0.5); cysteine (−1.0); methionine (−1.3); valine (−1.5); leucine (−1.8); isoleucine (−1.8); tyrosine (−2.3); phenylalanine (−2.5); tryptophan (−3.4). It is understood that an amino acid can be substituted for another having a similar hydrophilicity value and still obtain a biologically equivalent, and in particular, an immunologically equivalent protein. In such changes, the substitution of amino acids whose hydrophilicity values are within ±2 is preferred, those within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred.

[1771] As outlined above, amino acid substitutions are generally therefore based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like. Exemplary substitutions that take various of the foregoing characteristics into consideration are well known to those of skill in the art and include: arginine and lysine; glutamate and aspartate; serine and threonine; glutamine and asparagine; and valine, leucine and isoleucine.

[1772] In addition, any polynucleotide may be further modified to increase stability in vivo. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5′ and/or 3′ ends; the use of phosphorothioate or 2′ O-methyl rather than phosphodiesterase linkages in the backbone; and/or the inclusion of nontraditional bases such as inosine, queosine and wybutosine, as well as acetyl- methyl-, thio- and other modified forms of adenine, cytidine, guanine, thymine and uridine.

[1773] Amino acid substitutions may further be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity and/or the amphipathic nature of the residues. For example, negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine and valine; glycine and alanine; asparagine and glutamine; and serine, threonine, phenylalanine and tyrosine. Other groups of amino acids that may represent conservative changes include: (1) ala, pro, gly, glu, asp, gin, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala, phe; (4) lys, arg, his; and (5) phe, tyr, trp, his. A variant may also, or alternatively, contain nonconservative changes. In a preferred embodiment, variant polypeptides differ from a native sequence by substitution, deletion or addition of five amino acids or fewer. Variants may also (or alternatively) be modified by, for example, the deletion or addition of amino acids that have minimal influence on the immunogenicity, secondary structure and hydropathic nature of the polypeptide.

[1774] As noted above, polypeptides may comprise a signal (or leader) sequence at the N-terminal end of the protein, which co-translationally or post-translationally directs transfer of the protein. The polypeptide may also be conjugated to a linker or other sequence for ease of synthesis, purification or identification of the polypeptide (e.g., poly-His), or to enhance binding of the polypeptide to a solid support. For example, a polypeptide may be conjugated to an immunoglobulin Fc region.

[1775] When comparing polypeptide sequences, two sequences are said to be “identical” if the sequence of amino acids in the two sequences is the same when aligned for maximum correspondence, as described below. Comparisons between two sequences are typically performed by comparing the sequences over a comparison window to identify and compare local regions of sequence similarity. A “comparison window” as used herein, refers to a segment of at least about 20 contiguous positions, usually 30 to about 75, 40 to about 50, in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned.

[1776] Optimal alignment of sequences for comparison may be conducted using the Megalign program in the Lasergene suite of bioinformatics software (DNASTAR, Inc., Madison, Wis.), using default parameters. This program embodies several alignment schemes described in the following references: Dayhoff, M. O. (1978) A model of evolutionary change in proteins—Matrices for detecting distant relationships. In Dayhoff, M. O. (ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington D.C. Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990) Unified Approach to Alignment and Phylogenes pp. 626-645 Methods in Enzymology vol. 183, Academic Press, Inc., San Diego, Calif.; Higgins, D. G. and Sharp, P. M. (1989) CABIOS 5:151-153; Myers, E. W. and Muller W. (1988) CABIOS 4:11-17; Robinson, E. D. (1971) Comb. Theor 11:105; Saitou, N. Nei, M. (1987) Mol. Biol. Evol. 4:406-425; Sneath, P. H. A. and Sokal, R. R. (1973) Numerical Taxonomy—the Principles and Practice of Numerical Taxonomy, Freeman Press, San Francisco, Calif.; Wilbur, W. J. and Lipman, D. J. (1983) Proc. Natl. Acad., Sci. USA 80:726-730.

[1777] Alternatively, optimal alignment of sequences for comparison may be conducted by the local identity algorithm of Smith and Waterman (1981) Add. APL. Math 2:482, by the identity alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity methods of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. USA 85: 2444, by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection.

[1778] One preferred example of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1977) Nucl. Acids Res. 25:3389-3402 and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively. BLAST and BLAST 2.0 can be used, for example with the parameters described herein, to determine percent sequence identity for the polynucleotides and polypeptides of the invention. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. For amino acid sequences, a scoring matrix can be used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment.

[1779] In one preferred approach, the “percentage of sequence identity” is determined by comparing two optimally aligned sequences over a window of comparison of at least 20 positions, wherein the portion of the polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) of 20 percent or less, usually 5 to 15 percent, or 10 to 12 percent, as compared to the reference sequences (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the reference sequence (i.e., the window size) and multiplying the results by 100 to yield the percentage of sequence identity.

[1780] Within other illustrative embodiments, a polypeptide may be a xenogeneic polypeptide that comprises an polypeptide having substantial sequence identity, as described above, to the human polypeptide (also termed autologous antigen) which served as a reference polypeptide, but which xenogeneic polypeptide is derived from a different, non-human species. One skilled in the art will recognize that “self” antigens are often poor stimulators of CD8+ and CD4+ T-lymphocyte responses, and therefore efficient immunotherapeutic strategies directed against tumor polypeptides require the development of methods to overcome immune tolerance to particular self tumor polypeptides. For example, humans immunized with prostase protein from a xenogeneic (non human) origin are capable of mounting an immune response against the counterpart human protein, e.g. the human prostase tumor protein present on human tumor cells. Accordingly, the present invention provides methods for purifying the xenogeneic form of the tumor proteins set forth herein, such as the polypeptides set forth in SEQ ID NOs: 1848-1851, 1856-1858, and 1863 or the polypeptides encoded by polynucleotide sequences set forth in SEQ ID NOs:1-1847, 1852-1855, and 1859-1862.

[1781] Therefore, one aspect of the present invention provides xenogeneic variants of the polypeptide compositions described herein. Such xenogeneic variants generally encompassed by the present invention will typically exhibit at least about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more identity along their lengths, to a polypeptide sequences set forth herein.

[1782] More particularly, the invention is directed to mouse, rat, monkey, porcine and other non-human polypeptides which can be used as xenogeneic forms of human polypeptides set forth herein, to induce immune responses directed against tumor polypeptides of the invention.

[1783] Within other illustrative embodiments, a polypeptide may be a fusion polypeptide that comprises multiple polypeptides as described herein, or that comprises at least one polypeptide as described herein and an unrelated sequence, such as a known tumor protein. A fusion partner may, for example, assist in providing T helper epitopes (an immunological fusion partner), preferably T helper epitopes recognized by humans, or may assist in expressing the protein (an expression enhancer) at higher yields than the native recombinant protein. Certain preferred fusion partners are both immunological and expression enhancing fusion partners. Other fusion partners may be selected so as to increase the solubility of the polypeptide or to enable the polypeptide to be targeted to desired intracellular compartments. Still further fusion partners include affinity tags, which facilitate purification of the polypeptide.

[1784] Fusion polypeptides may generally be prepared using standard techniques, including chemical conjugation. Preferably, a fusion polypeptide is expressed as a recombinant polypeptide, allowing the production of increased levels, relative to a non-fused polypeptide, in an expression system. Briefly, DNA sequences encoding the polypeptide components may be assembled separately, and ligated into an appropriate expression vector. The 3′ end of the DNA sequence encoding one polypeptide component is ligated, with or without a peptide linker, to the 5′ end of a DNA sequence encoding the second polypeptide component so that the reading frames of the sequences are in phase. This permits translation into a single fusion polypeptide that retains the biological activity of both component polypeptides.

[1785] A peptide linker sequence may be employed to separate the first and second polypeptide components by a distance sufficient to ensure that each polypeptide folds into its secondary and tertiary structures. Such a peptide linker sequence is incorporated into the fusion polypeptide using standard techniques well known in the art. Suitable peptide linker sequences may be chosen based on the following factors: (1) their ability to adopt a flexible extended conformation; (2) their inability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides; and (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes. Preferred peptide linker sequences contain Gly, Asn and Ser residues. Other near neutral amino acids, such as Thr and Ala may also be used in the linker sequence. Amino acid sequences which may be usefully employed as linkers include those disclosed in Maratea et al., Gene 40:39-46,1985; Murphy et al., Proc. Natl. Acad. Sci. USA 83:8258-8262, 1986; U.S. Pat. No. 4,935,233 and U.S. Pat. No. 4,751,180. The linker sequence may generally be from 1 to about 50 amino acids in length. Linker sequences are not required when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference.

[1786] The ligated DNA sequences are operably linked to suitable transcriptional or translational regulatory elements. The regulatory elements responsible for expression of DNA are located only 5′ to the DNA sequence encoding the first polypeptides. Similarly, stop codons required to end translation and transcription termination signals are only present 3′ to the DNA sequence encoding the second polypeptide.

[1787] The fusion polypeptide can comprise a polypeptide as described herein together with an unrelated immunogenic protein, such as an immunogenic protein capable of eliciting a recall response. Examples of such proteins include tetanus, tuberculosis and hepatitis proteins (see, for example, Stoute et al. New Engl. J. Med., 336:86-91,1997).

[1788] In one preferred embodiment, the immunological fusion partner is derived from a Mycobacterium sp., such as a Mycobacterium tuberculosis-derived Ra12 fragment. Ra12 compositions and methods for their use in enhancing the expression and/or immunogenicity of heterologous polynucleotide/polypeptide sequences is described in U.S. Patent Application No. 60/158,585, the disclosure of which is incorporated herein by reference in its entirety. Briefly, Ra12 refers to a polynucleotide region that is a subsequence of a Mycobacterium tuberculosis MTB32A nucleic acid. MTB32A is a serine protease of 32 KD molecular weight encoded by a gene in virulent and avirulent strains of M. tuberculosis. The nucleotide sequence and amino acid sequence of MTB32A have been described (for example, U.S. Patent Application No. 60/158,585; see also, Skeiky et al., Infection and Immun. (1999) 67:3998-4007, incorporated herein by reference). C-terminal fragments of the MTB32A coding sequence express at high levels and remain as a soluble polypeptides throughout the purification process. Moreover, Ra12 may enhance the immunogenicity of heterologous immunogenic polypeptides with which it is fused. One preferred Ra12 fusion polypeptide comprises a 14 KD C-terminal fragment corresponding to amino acid residues 192 to 323 of MTB32A. Other preferred Ra12 polynucleotides generally comprise at least about 15 consecutive nucleotides, at least about 30 nucleotides, at least about 60 nucleotides, at least about 100 nucleotides, at least about 200 nucleotides, or at least about 300 nucleotides that encode a portion of a Ra12 polypeptide. Ra12 polynucleotides may comprise a native sequence (i.e., an endogenous sequence that encodes a Ra12 polypeptide or a portion thereof) or may comprise a variant of such a sequence. Ra12 polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions such that the biological activity of the encoded fusion polypeptide is not substantially diminished, relative to a fusion polypeptide comprising a native Ra12 polypeptide. Variants preferably exhibit at least about 70% identity, more preferably at least about 80% identity and most preferably at least about 90% identity to a polynucleotide sequence that encodes a native Ra12 polypeptide or a portion thereof.

[1789] Within other preferred embodiments, an immunological fusion partner is derived from protein D, a surface protein of the gram-negative bacterium Haemophilus influenza B (WO 91/18926). Preferably, a protein D derivative comprises approximately the first third of the protein (e.g., the first N-terminal 100-110 amino acids), and a protein D derivative may be lipidated. Within certain preferred embodiments, the first 109 residues of a Lipoprotein D fusion partner is included on the N-terminus to provide the polypeptide with additional exogenous T-cell epitopes and to increase the expression level in E. coli (thus functioning as an expression enhancer). The lipid tail ensures optimal presentation of the antigen to antigen presenting cells. Other fusion partners include the non-structural protein from influenzae virus, NS1 (hemaglutinin). Typically, the N-terminal 81 amino acids are used, although different fragments that include T-helper epitopes may be used.

[1790] In another embodiment, the immunological fusion partner is the protein known as LYTA, or a portion thereof (preferably a C-terminal portion). LYTA is derived from Streptococcus pneumoniae, which synthesizes an N-acetyl-L-alanine amidase known as amidase LYTA (encoded by the LytA gene; Gene 43:265-292, 1986). LYTA is an autolysin that specifically degrades certain bonds in the peptidoglycan backbone. The C-terminal domain of the LYTA protein is responsible for the affinity to the choline or to some choline analogues such as DEAE. This property has been exploited for the development of E. coli C-LYTA expressing plasmids useful for expression of fusion proteins. Purification of hybrid proteins containing the C-LYTA fragment at the amino terminus has been described (see Biotechnology 10:795-798,1992). Within a preferred embodiment, a repeat portion of LYTA may be incorporated into a fusion polypeptide. A repeat portion is found in the C-terminal region starting at residue 178. A particularly preferred repeat portion incorporates residues 188-305.

[1791] Yet another illustrative embodiment involves fusion polypeptides, and the polynucleotides encoding them, wherein the fusion partner comprises a targeting signal capable of directing a polypeptide to the endosomal/lysosomal compartment, as described in U.S. Pat. No. 5,633,234. An immunogenic polypeptide of the invention, when fused with this targeting signal, will associate more efficiently with MHC class II molecules and thereby provide enhanced in vivo stimulation of CD4+ T-cells specific for the polypeptide.

[1792] Polypeptides of the invention are prepared using any of a variety of well known synthetic and/or recombinant techniques, the latter of which are further described below. Polypeptides, portions and other variants generally less than about 150 amino acids can be generated by synthetic means, using techniques well known to those of ordinary skill in the art. In one illustrative example, such polypeptides are synthesized using any of the commercially available solid-phase techniques, such as the Merrifield solid-phase synthesis method, where amino acids are sequentially added to a growing amino acid chain. See Merrifield, J. Am. Chem. Soc. 85:2149-2146,1963. Equipment for automated synthesis of polypeptides is commercially available from suppliers such as Perkin Elmer/Applied BioSystems Division (Foster City, Calif.), and may be operated according to the manufacturer's instructions.

[1793] In general, polypeptide compositions (including fusion polypeptides) of the invention are isolated. An “isolated” polypeptide is one that is removed from its original environment. For example, a naturally-occurring protein or polypeptide is isolated if it is separated from some or all of the coexisting materials in the natural system. Preferably, such polypeptides are also purified, e.g., are at least about 90% pure, more preferably at least about 95% pure and most preferably at least about 99% pure.

[1794] Polynucleotide Compositions

[1795] The present invention, in other aspects, provides polynucleotide compositions. The terms “DNA” and “polynucleotide” are used essentially interchangeably herein to refer to a DNA molecule that has been isolated free of total genomic DNA of a particular species. “Isolated,” as used herein, means that a polynucleotide is substantially away from other coding sequences, and that the DNA molecule does not contain large portions of unrelated coding DNA, such as large chromosomal fragments or other functional genes or polypeptide coding regions. Of course, this refers to the DNA molecule as originally isolated, and does not exclude genes or coding regions later added to the segment by the hand of man.

[1796] As will be understood by those skilled in the art, the polynucleotide compositions of this invention can include genomic sequences, extra-genomic and plasmid-encoded sequences and smaller engineered gene segments that express, or may be adapted to express, proteins, polypeptides, peptides and the like. Such segments may be naturally isolated, or modified synthetically by the hand of man.

[1797] As will be also recognized by the skilled artisan, polynucleotides of the invention may be single-stranded (coding or antisense) or double-stranded, and may be DNA (genomic, cDNA or synthetic) or RNA molecules. RNA molecules may include HnRNA molecules, which contain introns and correspond to a DNA molecule in a one-to-one manner, and mRNA molecules, which do not contain introns. Additional coding or non-coding sequences may, but need not, be present within a polynucleotide of the present invention, and a polynucleotide may, but need not, be linked to other molecules and/or support materials.

[1798] Polynucleotides may comprise a native sequence (i.e., an endogenous sequence that encodes a polypeptide/protein of the invention or a portion thereof) or may comprise a sequence that encodes a variant or derivative, preferably and immunogenic variant or derivative, of such a sequence.

[1799] Therefore, according to another aspect of the present invention, polynucleotide compositions are provided that comprise some or all of a polynucleotide sequence set forth in any one of SEQ ID NOs:1-1847, 1852-1855, and 1859-1862, complements of a polynucleotide sequence set forth in any one of SEQ ID NOs:1-1847, 1852-1855, and 1859-1862, and degenerate variants of a polynucleotide sequence set forth in any one of SEQ ID NOs:1-1847, 1852-1855, and 1859-1862. In certain preferred embodiments, the polynucleotide sequences set forth herein encode immunogenic polypeptides, as described above.

[1800] In other related embodiments, the present invention provides polynucleotide variants having substantial identity to the sequences disclosed herein in SEQ ID NOs:1-1847, 1852-1855, and 1859-1862, for example those comprising at least 70% sequence identity, preferably at least 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% or higher, sequence identity compared to a polynucleotide sequence of this invention using the methods described herein, (e.g., BLAST analysis using standard parameters, as described below). One skilled in this art will recognize that these values can be appropriately adjusted to determine corresponding identity of proteins encoded by two nucleotide sequences by taking into account codon degeneracy, amino acid similarity, reading frame positioning and the like.

[1801] Typically, polynucleotide variants will contain one or more substitutions, additions, deletions and/or insertions, preferably such that the immunogenicity of the polypeptide encoded by the variant polynucleotide is not substantially diminished relative to a polypeptide encoded by a polynucleotide sequence specifically set forth herein). The term “variants” should also be understood to encompasses homologous genes of xenogenic origin.

[1802] In additional embodiments, the present invention provides polynucleotide fragments comprising or consisting of various lengths of contiguous stretches of sequence identical to or complementary to one or more of the sequences disclosed herein. For example, polynucleotides are provided by this invention that comprise or consist of at least about 10, 15, 20, 30, 40, 50, 75, 100, 150, 200, 300, 400, 500 or 1000 or more contiguous nucleotides of one or more of the sequences disclosed herein as well as all intermediate lengths there between. It will be readily understood that “intermediate lengths”, in this context, means any length between the quoted values, such as 16,17,18,19, etc.; 21,22, 23, etc.; 30,31, 32, etc.; 50, 51, 52, 53, etc.; 100, 101, 102, 103, etc.; 150, 151, 152, 153, etc.; including all integers through 200-500; 500-1,000, and the like. A polynucleotide sequence as described here may be extended at one or both ends by additional nucleotides not found in the native sequence. This additional sequence may consist of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides at either end of the disclosed sequence or at both ends of the disclosed sequence.

[1803] In another embodiment of the invention, polynucleotide compositions are provided that are capable of hybridizing under moderate to high stringency conditions to a polynucleotide sequence provided herein, or a fragment thereof, or a complementary sequence thereof. Hybridization techniques are well known in the art of molecular biology. For purposes of illustration, suitable moderately stringent conditions for testing the hybridization of a polynucleotide of this invention with other polynucleotides include prewashing in a solution of 5× SSC, 0.5% SDS, 1.0 mM EDTA (pH 8.0); hybridizing at 50° C.-60° C., 5× SSC, overnight; followed by washing twice at 65° C. for 20 minutes with each of 2×, 0.5× and 0.2× SSC containing 0.1% SDS. One skilled in the art will understand that the stringency of hybridization can be readily manipulated, such as by altering the salt content of the hybridization solution and/or the temperature at which the hybridization is performed. For example, in another embodiment, suitable highly stringent hybridization conditions include those described above, with the exception that the temperature of hybridization is increased, e.g., to 60-65° C. or 65-70° C.

[1804] In certain preferred embodiments, the polynucleotides described above, e.g., polynucleotide variants, fragments and hybridizing sequences, encode polypeptides that are immunologically cross-reactive with a polypeptide sequence specifically set forth herein. In other preferred embodiments, such polynucleotides encode polypeptides that have a level of immunogenic activity of at least about 50%, preferably at least about 70%, and more preferably at least about 90% of that for a polypeptide sequence specifically set forth herein.

[1805] The polynucleotides of the present invention, or fragments thereof, regardless of the length of the coding sequence itself, may be combined with other DNA sequences, such as promoters, polyadenylation signals, additional restriction enzyme sites, multiple cloning sites, other coding segments, and the like, such that their overall length may vary considerably. It is therefore contemplated that a nucleic acid fragment of almost any length may be employed, with the total length preferably being limited by the ease of preparation and use in the intended recombinant DNA protocol. For example, illustrative polynucleotide segments with total lengths of about 10,000, about 5000, about 3000, about 2,000, about 1,000, about 500, about 200, about 100, about 50 base pairs in length, and the like, (including all intermediate lengths) are contemplated to be useful in many implementations of this invention.

[1806] When comparing polynucleotide sequences, two sequences are said to be “identical” if the sequence of nucleotides in the two sequences is the same when aligned for maximum correspondence, as described below. Comparisons between two sequences are typically performed by comparing the sequences over a comparison window to identify and compare local regions of sequence similarity. A “comparison window” as used herein, refers to a segment of at least about 20 contiguous positions, usually 30 to about 75, 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.

[1807] Optimal alignment of sequences for comparison may be conducted using the Megalign program in the Lasergene suite of bioinformatics software (DNASTAR, Inc., Madison, Wis.), using default parameters. This program embodies several alignment schemes described in the following references: Dayhoff, M. O. (1978) A model of evolutionary change in proteins—Matrices for detecting distant relationships. In Dayhoff, M. O. (ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Washington D.C. Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990) Unified Approach to Alignment and Phylogenes pp. 626-645 Methods in Enzymology vol. 183, Academic Press, Inc., San Diego, Calif.; Higgins, D. G. and Sharp, P. M. (1989) CABIOS 5:151-153; Myers, E. W. and Muller W. (1988) CABIOS 4:11-17; Robinson, E. D. (1971) Comb. Theor 11:105; Santou, N. Nes, M. (1987) Mol. Biol. Evol. 4:406-425; Sneath, P. H. A. and Sokal, R. R. (1973) Numerical Taxonomy—the Principles and Practice of Numerical Taxonomy, Freeman Press, San Francisco, Calif.; Wilbur, W. J. and Lipman, D. J. (1983) Proc. Natl. Acad., Sci. USA 80:726-730.

[1808] Alternatively, optimal alignment of sequences for comparison may be conducted by the local identity algorithm of Smith and Waterman (1981) Add. APL. Math 2:482, by the identity alignment algorithm of Needleman and Wunsch (1970) J. Mol. Biol. 48:443, by the search for similarity methods of Pearson and Lipman (1988) Proc. Natl. Acad. Sci. USA 85: 2444, by computerized implementations of these algorithms (GAP, BESTFIT, BLAST, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group (GCG), 575 Science Dr., Madison, Wis.), or by inspection.

[1809] One preferred example of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al. (1977) Nucl. Acids Res. 25:3389-3402 and Altschul et al. (1990) J. Mol. Biol. 215:403-410, respectively. BLAST and BLAST 2.0 can be used, for example with the parameters described herein, to determine percent sequence identity for the polynucleotides of the invention. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. In one illustrative example, cumulative scores can be calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915) alignments, (B) of 50, expectation (E) of 10, M=5, N=-4 and a comparison of both strands.

[1810] 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 (ie., gaps) of 20 percent or less, usually 5 to 15 percent, or 10 to 12 percent, as compared to the reference sequences (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid bases occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the reference sequence (i.e., the window size) and multiplying the results by 100 to yield the percentage of sequence identity.

[1811] It will be appreciated by those of ordinary skill in the art that, as a result of the degeneracy of the genetic code, there are many nucleotide sequences that encode a polypeptide as described herein. Some of these polynucleotides bear minimal homology to the nucleotide sequence of any native gene. Nonetheless, polynucleotides that vary due to differences in codon usage are specifically contemplated by the present invention. Further, alleles of the genes comprising the polynucleotide sequences provided herein are within the scope of the present invention. Alleles are endogenous genes that are altered as a result of one or more mutations, such as deletions, additions and/or substitutions of nucleotides. The resulting mRNA and protein may, but need not, have an altered structure or function. Alleles may be identified using standard techniques (such as hybridization, amplification and/or database sequence comparison).

[1812] Therefore, in another embodiment of the invention, a mutagenesis approach, such as site-specific mutagenesis, is employed for the preparation of immunogenic variants and/or derivatives of the polypeptides described herein. By this approach, specific modifications in a polypeptide sequence can be made through mutagenesis of the underlying polynucleotides that encode them. These techniques provides a straightforward approach to prepare and test sequence variants, for example, incorporating one or more of the foregoing considerations, by introducing one or more nucleotide sequence changes into the polynucleotide.

[1813] Site-specific mutagenesis allows the production of mutants through the use of specific oligonucleotide sequences which encode the DNA sequence of the desired mutation, as well as a sufficient number of adjacent nucleotides, to provide a primer sequence of sufficient size and sequence complexity to form a stable duplex on both sides of the deletion junction being traversed. Mutations may be employed in a selected polynucleotide sequence to improve, alter, decrease, modify, or otherwise change the properties of the polynucleotide itself, and/or alter the properties, activity, composition, stability, or primary sequence of the encoded polypeptide.

[1814] In certain embodiments of the present invention, the inventors contemplate the mutagenesis of the disclosed polynucleotide sequences to alter one or more properties of the encoded polypeptide, such as the immunogenicity of a polypeptide vaccine. The techniques of site-specific mutagenesis are well-known in the art, and are widely used to create variants of both polypeptides and polynucleotides. For example, site-specific mutagenesis is often used to alter a specific portion of a DNA molecule. In such embodiments, a primer comprising typically about 14 to about 25 nucleotides or so in length is employed, with about 5 to about 10 residues on both sides of the junction of the sequence being altered.

[1815] As will be appreciated by those of skill in the art, site-specific mutagenesis techniques have often employed a phage vector that exists in both a single stranded and double stranded form. Typical vectors useful in site-directed mutagenesis include vectors such as the M13 phage. These phage are readily commercially-available and their use is generally well-known to those skilled in the art. Double-stranded plasmids are also routinely employed in site directed mutagenesis that eliminates the step of transferring the gene of interest from a plasmid to a phage.

[1816] In general, site-directed mutagenesis in accordance herewith is performed by first obtaining a single-stranded vector or melting apart of two strands of a double-stranded vector that includes within its sequence a DNA sequence that encodes the desired peptide. An oligonucleotide primer bearing the desired mutated sequence is prepared, generally synthetically. This primer is then annealed with the single-stranded vector, and subjected to DNA polymerizing enzymes such as E. coli polymerase I Klenow fragment, in order to complete the synthesis of the mutation-bearing strand. Thus, a heteroduplex is formed wherein one strand encodes the original non-mutated sequence and the second strand bears the desired mutation. This heteroduplex vector is then used to transform appropriate cells, such as E. coli cells, and clones are selected which include recombinant vectors bearing the mutated sequence arrangement.

[1817] The preparation of sequence variants of the selected peptide-encoding DNA segments using site-directed mutagenesis provides a means of producing potentially useful species and is not meant to be limiting as there are other ways in which sequence variants of peptides and the DNA sequences encoding them may be obtained. For example, recombinant vectors encoding the desired peptide sequence may be treated with mutagenic agents, such as hydroxylamine, to obtain sequence variants. Specific details regarding these methods and protocols are found in the teachings of Maloy et al., 1994; Segal, 1976; Prokop and Bajpai, 1991; Kuby, 1994; and Maniatis et al., 1982, each incorporated herein by reference, for that purpose.

[1818] As used herein, the term “oligonucleotide directed mutagenesis procedure” refers to template-dependent processes and vector-mediated propagation which result in an increase in the concentration of a specific nucleic acid molecule relative to its initial concentration, or in an increase in the concentration of a detectable signal, such as amplification. As used herein, the term “oligonucleotide directed mutagenesis procedure” is intended to refer to a process that involves the template-dependent extension of a primer molecule. The term template dependent process refers to nucleic acid synthesis of an RNA or a DNA molecule wherein the sequence of the newly synthesized strand of nucleic acid is dictated by the well-known rules of complementary base pairing (see, for example, Watson, 1987). Typically, vector mediated methodologies involve the introduction of the nucleic acid fragment into a DNA or RNA vector, the clonal amplification of the vector, and the recovery of the amplified nucleic acid fragment. Examples of such methodologies are provided by U.S. Pat. No. 4,237,224, specifically incorporated herein by reference in its entirety.

[1819] In another approach for the production of polypeptide variants of the present invention, recursive sequence recombination, as described in U.S. Pat. No. 5,837,458, may be employed. In this approach, iterative cycles of recombination and screening or selection are performed to “evolve” individual polynucleotide variants of the invention having, for example, enhanced immunogenic activity.

[1820] In other embodiments of the present invention, the polynucleotide sequences provided herein can be advantageously used as probes or primers for nucleic acid hybridization. As such, it is contemplated that nucleic acid segments that comprise or consist of a sequence region of at least about a 15 nucleotide long contiguous sequence that has the same sequence as, or is complementary to, a 15 nucleotide long contiguous sequence disclosed herein will find particular utility. Longer contiguous identical or complementary sequences, e.g., those of about 20, 30, 40, 50, 100, 200, 500, 1000 (including all intermediate lengths) and even up to full length sequences will also be of use in certain embodiments.

[1821] The ability of such nucleic acid probes to specifically hybridize to a sequence of interest will enable them to be of use in detecting the presence of complementary sequences in a given sample. However, other uses are also envisioned, such as the use of the sequence information for the preparation of mutant species primers, or primers for use in preparing other genetic constructions.

[1822] Polynucleotide molecules having sequence regions consisting of contiguous nucleotide stretches of 10-14, 15-20, 30, 50, or even of 100-200 nucleotides or so (including intermediate lengths as well), identical or complementary to a polynucleotide sequence disclosed herein, are particularly contemplated as hybridization probes for use in, e.g., Southern and Northern blotting. This would allow a gene product, or fragment thereof, to be analyzed, both in diverse cell types and also in various bacterial cells. The total size of fragment, as well as the size of the complementary stretch(es), will ultimately depend on the intended use or application of the particular nucleic acid segment. Smaller fragments will generally find use in hybridization embodiments, wherein the length of the contiguous complementary region may be varied, such as between about 15 and about 100 nucleotides, but larger contiguous complementarity stretches may be used, according to the length complementary sequences one wishes to detect.

[1823] The use of a hybridization probe of about 15-25 nucleotides in length allows the formation of a duplex molecule that is both stable and selective. Molecules having contiguous complementary sequences over stretches greater than 15 bases in length are generally preferred, though, in order to increase stability and selectivity of the hybrid, and thereby improve the quality and degree of specific hybrid molecules obtained. One will generally prefer to design nucleic acid molecules having gene-complementary stretches of 15 to 25 contiguous nucleotides, or even longer where desired.

[1824] Hybridization probes may be selected from any portion of any of the sequences disclosed herein. All that is required is to review the sequences set forth herein, or to any continuous portion of the sequences, from about 15-25 nucleotides in length up to and including the full length sequence, that one wishes to utilize as a probe or primer. The choice of probe and primer sequences may be governed by various factors. For example, one may wish to employ primers from towards the termini of the total sequence.

[1825] Small polynucleotide segments or fragments may be readily prepared by, for example, directly synthesizing the fragment by chemical means, as is commonly practiced using an automated oligonucleotide synthesizer. Also, fragments may be obtained by application of nucleic acid reproduction technology, such as the PCR™ technology of U.S. Pat. No. 4,683,202 (incorporated herein by reference), by introducing selected sequences into recombinant vectors for recombinant production, and by other recombinant DNA techniques generally known to those of skill in the art of molecular biology.

[1826] The nucleotide sequences of the invention may be used for their ability to selectively form duplex molecules with complementary stretches of the entire gene or gene fragments of interest. Depending on the application envisioned, one will typically desire to employ varying conditions of hybridization to achieve varying degrees of selectivity of probe towards target sequence. For applications requiring high selectivity, one will typically desire to employ relatively stringent conditions to form the hybrids, e.g., one will select relatively low salt and/or high temperature conditions, such as provided by a salt concentration of from about 0.02 M to about 0.15 M salt at temperatures of from about 50° C. to about 70° C. Such selective conditions tolerate little, if any, mismatch between the probe and the template or target strand, and would be particularly suitable for isolating related sequences.

[1827] Of course, for some applications, for example, where one desires to prepare mutants employing a mutant primer strand hybridized to an underlying template, less stringent (reduced stringency) hybridization conditions will typically be needed in order to allow formation of the heteroduplex. In these circumstances, one may desire to employ salt conditions such as those of from about 0.15 M to about 0.9 M salt, at temperatures ranging from about 20° C. to about 55° C. Cross-hybridizing species can thereby be readily identified as positively hybridizing signals with respect to control hybridizations. In any case, it is generally appreciated that conditions can be rendered more stringent by the addition of increasing amounts of formamide, which serves to destabilize the hybrid duplex in the same manner as increased temperature. Thus, hybridization conditions can be readily manipulated, and thus will generally be a method of choice depending on the desired results.

[1828] According to another embodiment of the present invention, polynucleotide compositions comprising antisense oligonucleotides are provided. Antisense oligonucleotides have been demonstrated to be effective and targeted inhibitors of protein synthesis, and, consequently, provide a therapeutic approach by which a disease can be treated by inhibiting the synthesis of proteins that contribute to the disease. The efficacy of antisense oligonucleotides for inhibiting protein synthesis is well established. For example, the synthesis of polygalactauronase and the muscarine type 2 acetylcholine receptor are inhibited by antisense oligonucleotides directed to their respective mRNA sequences (U.S. Pat. No. 5,739,119 and U.S. Pat. No. 5,759,829). Further, examples of antisense inhibition have been demonstrated with the nuclear protein cyclin, the multiple drug resistance gene (MDG1), ICAM-1, E-selectin, STK-1, striatal GABAA receptor and human EGF (Jaskulski et al., Science. 1988 Jun 10;240(4858):1544-6; Vasanthakumar and Ahmed, Cancer Commun. 1989;1 (4):225-32; Peris et al., Brain Res Mol Brain Res. 1998 Jun 15;57(2):310-20; U.S. Pat. No. 5,801,154; U.S. Pat. No. 5,789,573; U.S. Pat. No. 5,718,709 and U.S. Pat. No. 5,610,288). Antisense constructs have also been described that inhibit and can be used to treat a variety of abnormal cellular proliferations, e.g. cancer (U.S. Pat. No. 5,747,470; U.S. Pat. No. 5,591,317 and U.S. Pat. No. 5,783,683).

[1829] Therefore, in certain embodiments, the present invention provides oligonucleotide sequences that comprise all, or a portion of, any sequence that is capable of specifically binding to polynucleotide sequence described herein, or a complement thereof. In one embodiment, the antisense oligonucleotides comprise DNA or derivatives thereof. In another embodiment, the oligonucleotides comprise RNA or derivatives thereof. In a third embodiment, the oligonucleotides are modified DNAs comprising a phosphorothioated modified backbone. In a fourth embodiment, the oligonucleotide sequences comprise peptide nucleic acids or derivatives thereof. In each case, preferred compositions comprise a sequence region that is complementary, and more preferably substantially-complementary, and even more preferably, completely complementary to one or more portions of polynucleotides disclosed herein. Selection of antisense compositions specific for a given gene sequence is based upon analysis of the chosen target sequence and determination of secondary structure, Tm, binding energy, and relative stability. Antisense compositions may be selected based upon their relative inability to form dimers, hairpins, or other secondary structures that would reduce or prohibit specific binding to the target mRNA in a host cell. Highly preferred target regions of the mRNA, are those which are at or near the AUG translation initiation codon, and those sequences which are substantially complementary to 5′ regions of the mRNA. These secondary structure analyses and target site selection considerations can be performed, for example, using v.4 of the OLIGO primer analysis software and/or the BLASTN 2.0.5 algorithm software (Altschul et al., Nucleic Acids Res. 1997, 25(17):3389-402).

[1830] The use of an antisense delivery method employing a short peptide vector, termed MPG (27 residues), is also contemplated. The MPG peptide contains a hydrophobic domain derived from the fusion sequence of HIV gp41 and a hydrophilic domain from the nuclear localization sequence of SV40 T-antigen (Morris et al., Nucleic Acids Res. Jul. 15, 1997;25(14):2730-6). It has been demonstrated that several molecules of the MPG peptide coat the antisense oligonucleotides and can be delivered into cultured mammalian cells in less than 1 hour with relatively high efficiency (90%). Further, the interaction with MPG strongly increases both the stability of the oligonucleotide to nuclease and the ability to cross the plasma membrane.

[1831] According to another embodiment of the invention, the polynucleotide compositions described herein are used in the design and preparation of ribozyme molecules for inhibiting expression of the tumor polypeptides and proteins of the present invention in tumor cells. Ribozymes are RNA-protein complexes that cleave nucleic acids in a site-specific fashion. Ribozymes have specific catalytic domains that possess endonuclease activity (Kim and Cech, Proc Natl Acad Sci U S A. 1987 December;84(24):8788-92; Forster and Symons, Cell. Apr. 24, 1987;49(2):211-20). For example, a large number of ribozymes accelerate phosphoester transfer reactions with a high degree of specificity, often cleaving only one of several phosphoesters in an oligonucleotide substrate (Cech et al., Cell. 1981 December;27(3 Pt 2):487-96; Michel and Westhof, J. Mol. Biol. Dec. 5, 1990;216(3):585-610; Reinhold-Hurek and Shub, Nature. May 14, 1992;357(6374):173-6). This specificity has been attributed to the requirement that the substrate bind via specific base-pairing interactions to the internal guide sequence (“IGS”) of the ribozyme prior to chemical reaction.

[1832] Six basic varieties of naturally-occurring enzymatic RNAs are known presently. Each can catalyze the hydrolysis of RNA phosphodiester bonds in trans (and thus can cleave other RNA molecules) under physiological conditions. In general, enzymatic nucleic acids act by first binding to a target RNA. Such binding occurs through the target binding portion of a enzymatic nucleic acid which is held in close proximity to an enzymatic portion of the molecule that acts to cleave the target RNA. Thus, the enzymatic nucleic acid first recognizes and then binds a target RNA through complementary base-pairing, and once bound to the correct site, acts enzymatically to cut the target RNA. Strategic cleavage of such a target RNA will destroy its ability to direct synthesis of an encoded protein. After an enzymatic nucleic acid has bound and cleaved its RNA target, it is released from that RNA to search for another target and can repeatedly bind and cleave new targets.

[1833] The enzymatic nature of a ribozyme is advantageous over many technologies, such as antisense technology (where a nucleic acid molecule simply binds to a nucleic acid target to block its translation) since the concentration of ribozyme necessary to affect a therapeutic treatment is lower than that of an antisense oligonucleotide. This advantage reflects the ability of the ribozyme to act enzymatically. Thus, a single ribozyme molecule is able to cleave many molecules of target RNA. In addition, the ribozyme is a highly specific inhibitor, with the specificity of inhibition depending not only on the base pairing mechanism of binding to the target RNA, but also on the mechanism of target RNA cleavage. Single mismatches, or base-substitutions, near the site of cleavage can completely eliminate catalytic activity of a ribozyme. Similar mismatches in antisense molecules do not prevent their action (Woolf et al., Proc Natl Acad Sci U S A. Aug. 15, 1992;89(16):7305-9). Thus, the specificity of action of a ribozyme is greater than that of an antisense oligonucleotide binding the same RNA site.

[1834] The enzymatic nucleic acid molecule may be formed in a hammerhead, hairpin, a hepatitis δ virus, group I intron or RNaseP RNA (in association with an RNA guide sequence) or Neurospora VS RNA motif. Examples of hammerhead motifs are described by Rossi et al. Nucleic Acids Res. Sep. 11, 1992;20(17):4559-65. Examples of hairpin motifs are described by Hampel et al. (Eur. Pat. Appl. PubI. No. EP 0360257), Hampel and Tritz, Biochemistry Jun. 13, 1989;28(12):4929-33; Hampel et al., Nucleic Acids Res. Jan. 25, 1990;18(2):299-304 and U.S. Pat. No. 5,631,359. An example of the hepatitis δ virus motif is described by Perrotta and Been, Biochemistry. Dec. 1, 1992;31 (47):11843-52; an example of the RNaseP motif is described by Guerrier-Takada et al., Cell. 1983 December;35(3 Pt 2):849-57; Neurospora VS RNA ribozyme motif is described by Collins (Saville and Collins, Cell. May 18, 1990;61 (4):685-96; Saville and Collins, Proc Natl Acad Sci U S A. Oct. 1, 1991;88(19):8826-30; Collins and Olive, Biochemistry. Mar. 23, 1993;32(11):2795-9); and an example of the Group I intron is described in (U.S. Pat. No. 4,987,071). All that is important in an enzymatic nucleic acid molecule of this invention is that it has a specific substrate binding site which is complementary to one or more of the target gene RNA regions, and that it have nucleotide sequences within or surrounding that substrate binding site which impart an RNA cleaving activity to the molecule. Thus the ribozyme constructs need not be limited to specific motifs mentioned herein.

[1835] Ribozymes may be designed as described in Int. Pat. Appl. Publ. No. WO 93/23569 and Int. Pat. Appl. Publ. No. WO 94/02595, each specifically incorporated herein by reference) and synthesized to be tested in vitro and in vivo, as described. Such ribozymes can also be optimized for delivery. While specific examples are provided, those in the art will recognize that equivalent RNA targets in other species can be utilized when necessary.

[1836] Ribozyme activity can be optimized by altering the length of the ribozyme binding arms, or chemically synthesizing ribozymes with modifications that prevent their degradation by serum ribonucleases (see e.g., Int. Pat. Appl. Publ. No. WO 92/07065; Int. Pat. Appl. Publ. No. WO 93/15187; Int. Pat. Appl. Publ. No. WO 91/03162; Eur. Pat. Appi. Publ. No. 92110298.4; U.S. Pat. No. 5,334,711; and Int. Pat. Appl. Publ. No. WO 94/13688, which describe various chemical modifications that can be made to the sugar moieties of enzymatic RNA molecules), modifications which enhance their efficacy in cells, and removal of stem 11 bases to shorten RNA synthesis times and reduce chemical requirements.

[1837] Sullivan et al. (Int. Pat. Appi. Publ. No. WO 94/02595) describes the general methods for delivery of enzymatic RNA molecules. Ribozymes may be administered to cells by a variety of methods known to those familiar to the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesive microspheres. For some indications, ribozymes may be directly delivered ex vivo to cells or tissues with or without the aforementioned vehicles. Alternatively, the RNA/vehicle combination may be locally delivered by direct inhalation, by direct injection or by use of a catheter, infusion pump or stent. Other routes of delivery include, but are not limited to, intravascular, intramuscular, subcutaneous or joint injection, aerosol inhalation, oral (tablet or pill form), topical, systemic, ocular, intraperitoneal and/or intrathecal delivery. More detailed descriptions of ribozyme delivery and administration are provided in Int. Pat. Appl. Publ. No. WO 94/02595 and Int. Pat. Appl. Pubi. No. WO 93/23569, each specifically incorporated herein by reference.

[1838] Another means of accumulating high concentrations of a ribozyme(s) within cells is to incorporate the ribozyme-encoding sequences into a DNA expression vector. Transcription of the ribozyme sequences are driven from a promoter for eukaryotic RNA polymerase I (pol I), RNA polymerase II (pol II), or RNA polymerase III (pol III). Transcripts from pol II or pol III promoters will be expressed at high levels in all cells; the levels of a given pol II promoter in a given cell type will depend on the nature of the gene regulatory sequences (enhancers, silencers, etc.) present nearby. Prokaryotic RNA polymerase promoters may also be used, providing that the prokaryotic RNA polymerase enzyme is expressed in the appropriate cells Ribozymes expressed from such promoters have been shown to function in mammalian cells. Such transcription units can be incorporated into a variety of vectors for introduction into mammalian cells, including but not restricted to, plasmid DNA vectors, viral DNA vectors (such as adenovirus or adeno-associated vectors), or viral RNA vectors (such as retroviral, semliki forest virus, sindbis virus vectors).

[1839] In another embodiment of the invention, peptide nucleic acids (PNAs) compositions are provided. PNA is a DNA mimic in which the nucleobases are attached to a pseudopeptide backbone (Good and Nielsen, Antisense Nucleic Acid Drug Dev. 1997 7(4) 431-37). PNA is able to be utilized in a number methods that traditionally have used RNA or DNA. Often PNA sequences perform better in techniques than the corresponding RNA or DNA sequences and have utilities that are not inherent to RNA or DNA. A review of PNA including methods of making, characteristics of, and methods of using, is provided by Corey (Trends Biotechnol 1997 June;15(6):224-9). As such, in certain embodiments, one may prepare PNA sequences that are complementary to one or more portions of the ACE mRNA sequence, and such PNA compositions may be used to regulate, alter, decrease, or reduce the translation of ACE-specific mRNA, and thereby alter the level of ACE activity in a host cell to which such PNA compositions have been administered.

[1840] PNAs have 2-aminoethyl-glycine linkages replacing the normal phosphodiester backbone of DNA (Nielsen et al., Science Dec. 6, 1991;254(5037):1497-500; Hanvey et al., Science. Nov. 27, 1992;258(5087):1481-5; Hyrup and Nielsen, Bioorg Med Chem. 1996 January;4(1):5-23). This chemistry has three important consequences: firstly, in contrast to DNA or phosphorothioate oligonucleotides, PNAs are neutral molecules; secondly, PNAs are achiral, which avoids the need to develop a stereoselective synthesis; and thirdly, PNA synthesis uses standard Boc or Fmoc protocols for solid-phase peptide synthesis, although other methods, including a modified Merrifield method, have been used.

[1841] PNA monomers or ready-made oligomers are commercially available from PerSeptive Biosystems (Framingham, Mass.). PNA syntheses by either Boc or Fmoc protocols are straightforward using manual or automated protocols (Norton et al., Bioorg Med Chem. 1995 April;3(4):437-45). The manual protocol lends itself to the production of chemically modified PNAs or the simultaneous synthesis of families of closely related PNAs.

[1842] As with peptide synthesis, the success of a particular PNA synthesis will depend on the properties of the chosen sequence. For example, while in theory PNAs can incorporate any combination of nucleotide bases, the presence of adjacent purines can lead to deletions of one or more residues in the product. In expectation of this difficulty, it is suggested that, in producing PNAs with adjacent purines, one should repeat the coupling of residues likely to be added inefficiently. This should be followed by the purification of PNAs by reverse-phase high-pressure liquid chromatography, providing yields and purity of product similar to those observed during the synthesis of peptides.

[1843] Modifications of PNAs for a given application may be accomplished by coupling amino acids during solid-phase synthesis or by attaching compounds that contain a carboxylic acid group to the exposed N-terminal amine. Alternatively, PNAs can be modified after synthesis by coupling to an introduced lysine or cysteine. The ease with which PNAs can be modified facilitates optimization for better solubility or for specific functional requirements. Once synthesized, the identity of PNAs and their derivatives can be confirmed by mass spectrometry. Several studies have made and utilized modifications of PNAs (for example, Norton et al., Bioorg Med Chem. 1995 April;3(4):437-45; Petersen et al., J Pept Sci. 1995 May-June;1 (3):175-83; Orum et al., Biotechniques. 1995 September;19(3):472-80; Footer et al., Biochemistry. Aug. 20, 1996;35(33):10673-9; Griffith et al., Nucleic Acids Res. Aug. 11, 1995;23(15):3003-8; Pardridge et al., Proc Natl Acad Sci U S A. Jun. 6, 1995;92(12):5592-6; Boffa et al., Proc Natl Acad Sci U S A. Mar. 14, 1995;92(6):1901-5; Gambacorti-Passerini et al., Blood. Aug. 15, 1997;88(4):1411-7; Armitage et al., Proc Natl Acad Sci U S A. Nov. 11, 1997;94(23):12320-5; Seeger et al., Biotechniques. 1997 September;23(3):512-7). U.S. Pat. No. 5,700,922 discusses PNA-DNA—PNA chimeric molecules and their uses in diagnostics, modulating protein in organisms, and treatment of conditions susceptible to therapeutics.

[1844] Methods of characterizing the antisense binding properties of PNAs are discussed in Rose (Anal Chem. Dec. 15, 1993;65(24):3545-9) and Jensen et al. (Biochemistry. Apr. 22, 1997;36(16):5072-7). Rose uses capillary gel electrophoresis to determine binding of PNAs to their complementary oligonucleotide, measuring the relative binding kinetics and stoichiometry. Similar types of measurements were made by Jensen et al. using BIAcore™ technology.

[1845] Other applications of PNAs that have been described and will be apparent to the skilled artisan include use in DNA strand invasion, antisense inhibition, mutational analysis, enhancers of transcription, nucleic acid purification, isolation of transcriptionally active genes, blocking of transcription factor binding, genome cleavage, biosensors, in situ hybridization, and the like.

[1846] Polynucleotide Identification, Characterization and Expression

[1847] Polynucleotides compositions of the present invention may be identified, prepared and/or manipulated using any of a variety of well established techniques (see generally, Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, Cold Spring Harbor, N.Y., 1989, and other like references). For example, a polynucleotide may be identified, as described in more detail below, by screening a microarray of cDNAs for tumor-associated expression (i.e., expression that is at least two fold greater in a tumor than in normal tissue, as determined using a representative assay provided herein). Such screens may be performed, for example, using the microarray technology of Affymetrix, Inc. (Santa Clara, Calif.) according to the manufacturer's instructions (and essentially as described by Schena et al., Proc. Natl. Acad. Sci. USA 93:10614-10619, 1996 and Heller et al., Proc. Natl. Acad. Sci. USA 94:2150-2155, 1997). Alternatively, polynucleotides may be amplified from cDNA prepared from cells expressing the proteins described herein, such as tumor cells.

[1848] Many template dependent processes are available to amplify a target sequences of interest present in a sample. One of the best known amplification methods is the polymerase chain reaction (PCR™) which is described in detail in U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,800,159, each of which is incorporated herein by reference in its entirety. Briefly, in PCR™, two primer sequences are prepared which are complementary to regions on opposite complementary strands of the target sequence. An excess of deoxynucleoside triphosphates is added to a reaction mixture along with a DNA polymerase (e.g., Taq polymerase). If the target sequence is present in a sample, the primers will bind to the target and the polymerase will cause the primers to be extended along the target sequence by adding on nucleotides. By raising and lowering the temperature of the reaction mixture, the extended primers will dissociate from the target to form reaction products, excess primers will bind to the target and to the reaction product and the process is repeated. Preferably reverse transcription and PCR T amplification procedure may be performed in order to quantify the amount of mRNA amplified. Polymerase chain reaction methodologies are well known in the art.

[1849] Any of a number of other template dependent processes, many of which are variations of the PCR ™ amplification technique, are readily known and available in the art. Illustratively, some such methods include the ligase chain reaction (referred to as LCR), described, for example, in Eur. Pat. Appl. Publ. No. 320,308 and U.S. Pat. No. 4,883,750; Qbeta Replicase, described in PCT Intl. Pat. Appl. PubI. No. PCT/US87/00880; Strand Displacement Amplification (SDA) and Repair Chain Reaction (RCR). Still other amplification methods are described in Great Britain Pat. Appl. No. 2 202 328, and in PCT Intl. Pat. Appi. Publ. No. PCT/US89/01025. Other nucleic acid amplification procedures include transcription-based amplification systems (TAS) (PCT Intl. Pat. Appi. PubI. No. WO 88/10315), including nucleic acid sequence based amplification (NASBA) and 3SR. Eur. Pat. Appl. Publ. No. 329,822 describes a nucleic acid amplification process involving cyclically synthesizing single-stranded RNA (“ssRNA”), ssDNA, and double-stranded DNA (dsDNA). PCT Intl. Pat. Appl. PubI. No. WO 89/06700 describes a nucleic acid sequence amplification scheme based on the hybridization of a promoter/primer sequence to a target single-stranded DNA (“ssDNA”) followed by transcription of many RNA copies of the sequence. Other amplification methods such as “RACE” (Frohman, 1990), and “one-sided PCR” (Ohara, 1989) are also well-known to those of skill in the art.

[1850] An amplified portion of a polynucleotide of the present invention may be used to isolate a full length gene from a suitable library (e.g., a tumor cDNA library) using well known techniques. Within such techniques, a library (cDNA or genomic) is screened using one or more polynucleotide probes or primers suitable for amplification. Preferably, a library is size-selected to include larger molecules. Random primed libraries may also be preferred for identifying 5′ and upstream regions of genes. Genomic libraries are preferred for obtaining introns and extending 5′ sequences.

[1851] For hybridization techniques, a partial sequence may be labeled (e.g., by nick-translation or end-labeling with 32P) using well known techniques. A bacterial or bacteriophage library is then generally screened by hybridizing filters containing denatured bacterial colonies (or lawns containing phage plaques) with the labeled probe (see Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratories, Cold Spring Harbor, N.Y., 1989). Hybridizing colonies or plaques are selected and expanded, and the DNA is isolated for further analysis. cDNA clones may be analyzed to determine the amount of additional sequence by, for example, PCR using a primer from the partial sequence and a primer from the vector. Restriction maps and partial sequences may be generated to identify one or more overlapping clones. The complete sequence may then be determined using standard techniques, which may involve generating a series of deletion clones. The resulting overlapping sequences can then assembled into a single contiguous sequence. A full length cDNA molecule can be generated by ligating suitable fragments, using well known techniques.

[1852] Alternatively, amplification techniques, such as those described above, can be useful for obtaining a full length coding sequence from a partial cDNA sequence. One such amplification technique is inverse PCR (see Triglia et al., Nucl. Acids Res. 16:8186, 1988), which uses restriction enzymes to generate a fragment in the known region of the gene. The fragment is then circularized by intramolecular ligation and used as a template for PCR with divergent primers derived from the known region. Within an alternative approach, sequences adjacent to a partial sequence may be retrieved by amplification with a primer to a linker sequence and a primer specific to a known region. The amplified sequences are typically subjected to a second round of amplification with the same linker primer and a second primer specific to the known region. A variation on this procedure, which employs two primers that initiate extension in opposite directions from the known sequence, is described in WO 96/38591. Another such technique is known as “rapid amplification of cDNA ends” or RACE. This technique involves the use of an internal primer and an external primer, which hybridizes to a polyA region or vector sequence, to identify sequences that are 5′ and 3′ of a known sequence. Additional techniques include capture PCR (Lagerstrom et al., PCR Methods Applic. 1:111-19, 1991) and walking PCR (Parker et al., Nucl. Acids. Res. 19:3055-60, 1991). Other methods employing amplification may also be employed to obtain a full length cDNA sequence.

[1853] In certain instances, it is possible to obtain a full length cDNA sequence by analysis of sequences provided in an expressed sequence tag (EST) database, such as that available from GenBank. Searches for overlapping ESTs may generally be performed using well known programs (e.g., NCBI BLAST searches), and such ESTs may be used to generate a contiguous full length sequence. Full length DNA sequences may also be obtained by analysis of genomic fragments.

[1854] In other embodiments of the invention, polynucleotide sequences or fragments thereof which encode polypeptides of the invention, or fusion proteins or functional equivalents thereof, may be used in recombinant DNA molecules to direct expression of a polypeptide in appropriate host cells. Due to the inherent degeneracy of the genetic code, other DNA sequences that encode substantially the same or a functionally equivalent amino acid sequence may be produced and these sequences may be used to clone and express a given polypeptide.

[1855] As will be understood by those of skill in the art, it may be advantageous in some instances to produce polypeptide-encoding nucleotide sequences possessing non-naturally occurring codons. For example, codons preferred by a particular prokaryotic or eukaryotic host can be selected to increase the rate of protein expression or to produce a recombinant RNA transcript having desirable properties, such as a half-life which is longer than that of a transcript generated from the naturally occurring sequence.

[1856] Moreover, the polynucleotide sequences of the present invention can be engineered using methods generally known in the art in order to alter polypeptide encoding sequences for a variety of reasons, including but not limited to, alterations which modify the cloning, processing, and/or expression of the gene product. For example, DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences. In addition, site-directed mutagenesis may be used to insert new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, or introduce mutations, and so forth.

[1857] In another embodiment of the invention, natural, modified, or recombinant nucleic acid sequences may be ligated to a heterologous sequence to encode a fusion protein. For example, to screen peptide libraries for inhibitors of polypeptide activity, it may be useful to encode a chimeric protein that can be recognized by a commercially available antibody. A fusion protein may also be engineered to contain a cleavage site located between the polypeptide-encoding sequence and the heterologous protein sequence, so that the polypeptide may be cleaved and purified away from the heterologous moiety.

[1858] Sequences encoding a desired polypeptide may be synthesized, in whole or in part, using chemical methods well known in the art (see Caruthers, M. H. et al. (1980) Nucl. Acids Res. Symp. Ser. 215-223, Horn, T. et al. (1980) Nucl. Acids Res. Symp. Ser. 225-232). Alternatively, the protein itself may be produced using chemical methods to synthesize the amino acid sequence of a polypeptide, or a portion thereof. For example, peptide synthesis can be performed using various solid-phase techniques (Roberge, J. Y. et al. (1995) Science 269:202-204) and automated synthesis may be achieved, for example, using the ABI 431 A Peptide Synthesizer (Perkin Elmer, Palo Alto, Calif.).

[1859] A newly synthesized peptide may be substantially purified by preparative high performance liquid chromatography (e.g., Creighton, T. (1983) Proteins, Structures and Molecular Principles, WH Freeman and Co., New York, N.Y.) or other comparable techniques available in the art. The composition of the synthetic peptides may be confirmed by amino acid analysis or sequencing (e.g., the Edman degradation procedure). Additionally, the amino acid sequence of a polypeptide, or any part thereof, may be altered during direct synthesis and/or combined using chemical methods with sequences from other proteins, or any part thereof, to produce a variant polypeptide.

[1860] In order to express a desired polypeptide, the nucleotide sequences encoding the polypeptide, or functional equivalents, may be inserted into appropriate expression vector, i.e., a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence. Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding a polypeptide of interest and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Such techniques are described, for example, in Sambrook, J. et al. (1989) Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Press, Plainview, N.Y., and Ausubel, F. M. et al. (1989) Current Protocols in Molecular Biology, John Wiley & Sons, New York. N.Y.

[1861] A variety of expression vector/host systems may be utilized to contain and express polynucleotide sequences. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (e.g., baculovirus); plant cell systems transformed with virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems.

[1862] The “control elements” or “regulatory sequences” present in an expression vector are those non-translated regions of the vector—enhancers, promoters, 5′ and 3′ untranslated regions—which interact with host cellular proteins to carry out transcription and translation. Such elements may vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used. For example, when cloning in bacterial systems, inducible promoters such as the hybrid lacZ promoter of the pBLUESCRIPT phagemid (Stratagene, La Jolla, Calif.) or pSPORT1 plasmid (Gibco BRL, Gaithersburg, Md.) and the like may be used. In mammalian cell systems, promoters from mammalian genes or from mammalian viruses are generally preferred. If it is necessary to generate a cell line that contains multiple copies of the sequence encoding a polypeptide, vectors based on SV40 or EBV may be advantageously used with an appropriate selectable marker.

[1863] In bacterial systems, any of a number of expression vectors may be selected depending upon the use intended for the expressed polypeptide. For example, when large quantities are needed, for example for the induction of antibodies, vectors which direct high level expression of fusion proteins that are readily purified may be used. Such vectors include, but are not limited to, the multifunctional E. coli cloning and expression vectors such as pBLUESCRIPT (Stratagene), in which the sequence encoding the polypeptide of interest may be ligated into the vector in frame with sequences for the amino-terminal Met and the subsequent 7 residues of .beta.-galactosidase so that a hybrid protein is produced; pIN vectors (Van Heeke, G. and S. M. Schuster (1989) J. Biol. Chem. 264:5503-5509); and the like. pGEX Vectors (Promega, Madison, Wis.) may also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption to glutathione-agarose beads followed by elution in the presence of free glutathione. Proteins made in such systems may be designed to include heparin, thrombin, or factor XA protease cleavage sites so that the cloned polypeptide of interest can be released from the GST moiety at will.

[1864] In the yeast, Saccharomyces cerevisiae, a number of vectors containing constitutive or inducible promoters such as alpha factor, alcohol oxidase, and PGH may be used. For reviews, see Ausubel et al. (supra) and Grant et al. (1987) Methods Enzymol. 153:516-544.

[1865] In cases where plant expression vectors are used, the expression of sequences encoding polypeptides may be driven by any of a number of promoters. For example, viral promoters such as the 35S and 19S promoters of CaMV may be used alone or in combination with the omega leader sequence from TMV (Takamatsu, N. (1987) EMBO J. 6:307-311. Alternatively, plant promoters such as the small subunit of RUBISCO or heat shock promoters may be used (Coruzzi, G. et al. (1984) EMBO J. 3:1671-1680; Broglie, R. et al. (1984) Science 224:838-843; and Winter, J. et al. (1991) Results Probl. Cell Differ. 17:85-105). These constructs can be introduced into plant cells by direct DNA transformation or pathogen-mediated transfection. Such techniques are described in a number of generally available reviews (see, for example, Hobbs, S. or Murry, L. E. in McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York, N.Y.; pp. 191-196).

[1866] An insect system may also be used to express a polypeptide of interest. For example, in one such system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes in Spodoptera frugiperda cells or in Trichoplusia larvae. The sequences encoding the polypeptide may be cloned into a non-essential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter. Successful insertion of the polypeptide-encoding sequence will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein. The recombinant viruses may then be used to infect, for example, S. frugiperda cells or Trichoplusia larvae in which the polypeptide of interest may be expressed (Engelhard, E. K. et al. (1994) Proc. Natl. Acad. Sci. 91 :3224-3227).

[1867] In mammalian host cells, a number of viral-based expression systems are generally available. For example, in cases where an adenovirus is used as an expression vector, sequences encoding a polypeptide of interest may be ligated into an adenovirus transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a non-essential E1 or E3 region of the viral genome may be used to obtain a viable virus which is capable of expressing the polypeptide in infected host cells (Logan, J. and Shenk, T. (1984) Proc. Natl. Acad. Sci. 81:3655-3659). In addition, transcription enhancers, such as the Rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells.

[1868] Specific initiation signals may also be used to achieve more efficient translation of sequences encoding a polypeptide of interest. Such signals include the ATG initiation codon and adjacent sequences. In cases where sequences encoding the polypeptide, its initiation codon, and upstream sequences are inserted into the appropriate expression vector, no additional transcriptional or translational control signals may be needed. However, in cases where only coding sequence, or a portion thereof, is inserted, exogenous translational control signals including the ATG initiation codon should be provided. Furthermore, the initiation codon should be in the correct reading frame to ensure translation of the entire insert. Exogenous translational elements and initiation codons may be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers which are appropriate for the particular cell system which is used, such as those described in the literature (Scharf, D. et al. (1994) Results Probl. Cell Differ. 20:125-162).

[1869] In addition, a host cell strain may be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed protein in the desired fashion. Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation. glycosylation, phosphorylation, lipidation, and acylation. Post-translational processing which cleaves a “prepro” form of the protein may also be used to facilitate correct insertion, folding and/or function. Different host cells such as CHO, COS, HeLa, MDCK, HEK293, and W138, which have specific cellular machinery and characteristic mechanisms for such post-translational activities, may be chosen to ensure the correct modification and processing of the foreign protein.

[1870] For long-term, high-yield production of recombinant proteins, stable expression is generally preferred. For example, cell lines which stably express a polynucleotide of interest may be transformed using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells may be allowed to grow for 1-2 days in an enriched media before they are switched to selective media. The purpose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells which successfully express the introduced sequences. Resistant clones of stably transformed cells may be proliferated using tissue culture techniques appropriate to the cell type.

[1871] Any number of selection systems may be used to recover transformed cell lines. These include, but are not limited to, the herpes simplex virus thymidine kinase (Wigler, M. et al. (1977) Cell 11:223-32) and adenine phosphoribosyltransferase (Lowy, I. et al. (1990) Cell 22:817-23) genes which can be employed in tk.sup.- or aprt.sup.-cells, respectively. Also, antimetabolite, antibiotic or herbicide resistance can be used as the basis for selection; for example, dhfr which confers resistance to methotrexate (Wigler, M. et al. (1980) Proc. Natl. Acad. Sci. 77:3567-70); npt, which confers resistance to the aminoglycosides, neomycin and G-418 (Colbere-Garapin, F. et al (1981) J. Mol. Biol. 150:1-14); and als or pat, which confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively (Murry, supra). Additional selectable genes have been described, for example, trpB, which allows cells to utilize indole in place of tryptophan, or hisD, which allows cells to utilize histinol in place of histidine (Hartman, S. C. and R. C. Mulligan (1988) Proc. Natl. Acad. Sci. 85:8047-51). The use of visible markers has gained popularity with such markers as anthocyanins, beta-glucuronidase and its substrate GUS, and luciferase and its substrate luciferin, being widely used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system (Rhodes, C. A. et al. (1995) Methods Mol. Biol. 55:121-131).

[1872] Although the presence/absence of marker gene expression suggests that the gene of interest is also present, its presence and expression may need to be confirmed. For example, if the sequence encoding a polypeptide is inserted within a marker gene sequence, recombinant cells containing sequences can be identified by the absence of marker gene function. Alternatively, a marker gene can be placed in tandem with a polypeptide-encoding sequence under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem gene as well.

[1873] Alternatively, host cells that contain and express a desired polynucleotide sequence may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA—RNA hybridizations and protein bioassay or immunoassay techniques which include, for example, membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein.

[1874] A variety of protocols for detecting and measuring the expression of polynucleotide-encoded products, using either polyclonal or monoclonal antibodies specific for the product are known in the art. Examples include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), and fluorescence activated cell sorting (FACS). A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes on a given polypeptide may be preferred for some applications, but a competitive binding assay may also be employed. These and other assays are described, among other places, in Hampton, R. et al. (1990; Serological Methods, a Laboratory Manual, APS Press, St Paul. Minn.) and Maddox, D. E. et al. (1983; J. Exp. Med. 158:1211-1216).

[1875] A wide variety of labels and conjugation techniques are known by those skilled in the art and may be used in various nucleic acid and amino acid assays. Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides include oligolabeling, nick translation, end-labeling or PCR amplification using a labeled nucleotide. Alternatively, the sequences, or any portions thereof may be cloned into a vector for the production of an mRNA probe. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by addition of an appropriate RNA polymerase such as T7, T3, or SP6 and labeled nucleotides. These procedures may be conducted using a variety of commercially available kits.

[1876] Suitable reporter molecules or labels, which may be used include radionuclides, enzymes, fluorescent, chemiluminescent, or chromogenic agents as well as substrates, cofactors, inhibitors, magnetic particles, and the like.

[1877] Host cells transformed with a polynucleotide sequence of interest may be cultured under conditions suitable for the expression and recovery of the protein from cell culture. The protein produced by a recombinant cell may be secreted or contained intracellularly depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides of the invention may be designed to contain signal sequences which direct secretion of the encoded polypeptide through a prokaryotic or eukaryotic cell membrane. Other recombinant constructions may be used to join sequences encoding a polypeptide of interest to nucleotide sequence encoding a polypeptide domain which will facilitate purification of soluble proteins.

[1878] Such purification facilitating domains include, but are not limited to, metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilized metals, protein A domains that allow purification on immobilized immunoglobulin, and the domain utilized in the FLAGS extension/affinity purification system (Immunex Corp., Seattle, Wash.). The inclusion of cleavable linker sequences such as those specific for Factor XA or enterokinase (Invitrogen. San Diego, Calif.) between the purification domain and the encoded polypeptide may be used to facilitate purification. One such expression vector provides for expression of a fusion protein containing a polypeptide of interest and a nucleic acid encoding 6 histidine residues preceding a thioredoxin or an enterokinase cleavage site. The histidine residues facilitate purification on IMIAC (immobilized metal ion affinity chromatography) as described in Porath, J. et al. (1992, Prot. Exp. Purif. 3:263-281) while the enterokinase cleavage site provides a means for purifying the desired polypeptide from the fusion protein. A discussion of vectors which contain fusion proteins is provided in Kroll, D. J. et al. (1993; DNA Cell Biol. 12:441-453).

[1879] In addition to recombinant production methods, polypeptides of the invention, and fragments thereof, may be produced by direct peptide synthesis using solid-phase techniques (Merrifield J. (1963) J. Am. Chem. Soc. 85:2149-2154). Protein synthesis may be performed using manual techniques or by automation. Automated synthesis may be achieved, for example, using Applied Biosystems 431A Peptide Synthesizer (Perkin Elmer). Alternatively, various fragments may be chemically synthesized separately and combined using chemical methods to produce the full length molecule.

[1880] Antibody Compositions, Fragments Thereof and Other Binding Agents

[1881] According to another aspect, the present invention further provides binding agents, such as antibodies and antigen-binding fragments thereof, that exhibit immunological binding to a tumor polypeptide disclosed herein, or to a portion, variant or derivative thereof. An antibody, or antigen-binding fragment thereof, is said to “specifically bind,” “immunogically bind,” and/or is “immunologically reactive” to a polypeptide of the invention if it reacts at a detectable level (within, for example, an ELISA assay) with the polypeptide, and does not react detectably with unrelated polypeptides under similar conditions.

[1882] Immunological binding, as used in this context, generally refers to the non-covalent interactions of the type which occur between an immunoglobulin molecule and an antigen for which the immunoglobulin is specific. The strength, or affinity of immunological binding interactions can be expressed in terms of the dissociation constant (Kd) of the interaction, wherein a smaller Kd represents a greater affinity. Immunological binding properties of selected polypeptides can be quantified using methods well known in the art. One such method entails measuring the rates of antigen-binding site/antigen complex formation and dissociation, wherein those rates depend on the concentrations of the complex partners, the affinity of the interaction, and on geometric parameters that equally influence the rate in both directions. Thus, both the “on rate constant” (Kon) and the “off rate constant” (Koff) can be determined by calculation of the concentrations and the actual rates of association and dissociation. The ratio of Koff /Kon enables cancellation of all parameters not related to affinity, and is thus equal to the dissociation constant Kd. See, generally, Davies et al. (1990) Annual Rev. Biochem. 59:439-473.

[1883] An “antigen-binding site,” or “binding portion” of an antibody refers to the part of the immunoglobulin molecule that participates in antigen binding. The antigen binding site is formed by amino acid residues of the N-terminal variable (“V”) regions of the heavy (“H”) and light (“L”) chains. Three highly divergent stretches within the V regions of the heavy and light chains are referred to as “hypervariable regions” which are interposed between more conserved flanking stretches known as “framework regions,” or “FRs”. Thus the term “FR” refers to amino acid sequences which are naturally found between and adjacent to hypervariable regions in immunoglobulins. In an antibody molecule, the three hypervariable regions of a light chain and the three hypervariable regions of a heavy chain are disposed relative to each other in three dimensional space to form an antigen-binding surface. The antigen-binding surface is complementary to the three-dimensional surface of a bound antigen, and the three hypervariable regions of each of the heavy and light chains are referred to as “complementarity-determining regions,” or “CDRs.”

[1884] Binding agents may be further capable of differentiating between patients with and without a cancer, such as kidney cancer, using the representative assays provided herein. For example, antibodies or other binding agents that bind to a tumor protein will preferably generate a signal indicating the presence of a cancer in at least about 20% of patients with the disease, more preferably at least about 30% of patients. Alternatively, or in addition, the antibody will generate a negative signal indicating the absence of the disease in at least about 90% of individuals without the cancer. To determine whether a binding agent satisfies this requirement, biological samples (e.g., blood, sera, sputum, urine and/or tumor biopsies) from patients with and without a cancer (as determined using standard clinical tests) may be assayed as described herein for the presence of polypeptides that bind to the binding agent. Preferably, a statistically significant number of samples with and without the disease will be assayed. Each binding agent should satisfy the above criteria; however, those of ordinary skill in the art will recognize that binding agents may be used in combination to improve sensitivity.

[1885] Any agent that satisfies the above requirements may be a binding agent. For example, a binding agent may be a ribosome, with or without a peptide component, an RNA molecule or a polypeptide. In a preferred embodiment, a binding agent is an antibody or an antigen-binding fragment thereof. Antibodies may be prepared by any of a variety of techniques known to those of ordinary skill in the art. See, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988. In general, antibodies can be produced by cell culture techniques, including the generation of monoclonal antibodies as described herein, or via transfection of antibody genes into suitable bacterial or mammalian cell hosts, in order to allow for the production of recombinant antibodies. In one technique, an immunogen comprising the polypeptide is initially injected into any of a wide variety of mammals (e.g., mice, rats, rabbits, sheep or goats). In this step, the polypeptides of this invention may serve as the immunogen without modification. Alternatively, particularly for relatively short polypeptides, a superior immune response may be elicited if the polypeptide is joined to a carrier protein, such as bovine serum albumin or keyhole limpet hemocyanin. The immunogen is injected into the animal host, preferably according to a predetermined schedule incorporating one or more booster immunizations, and the animals are bled periodically. Polyclonal antibodies specific for the polypeptide may then be purified from such antisera by, for example, affinity chromatography using the polypeptide coupled to a suitable solid support.

[1886] Monoclonal antibodies specific for an antigenic polypeptide of interest may be prepared, for example, using the technique of Kohler and Milstein, Eur. J. Immunol 6:511-519, 1976, and improvements thereto. Briefly, these methods involve the preparation of immortal cell lines capable of producing antibodies having the desired specificity (i.e., reactivity with the polypeptide of interest). Such cell lines may be produced, for example, from spleen cells obtained from an animal immunized as described above. The spleen cells are then immortalized by, for example, fusion with a myeloma cell fusion partner, preferably one that is syngeneic with the immunized animal. A variety of fusion techniques may be employed. For example, the spleen cells and myeloma cells may be combined with a nonionic detergent for a few minutes and then plated at low density on a selective medium that supports the growth of hybrid cells, but not myeloma cells. A preferred selection technique uses HAT (hypoxanthine, aminopterin, thymidine) selection. After a sufficient time, usually about 1 to 2 weeks, colonies of hybrids are observed. Single colonies are selected and their culture supernatants tested for binding activity against the polypeptide. Hybridomas having high reactivity and specificity are preferred.

[1887] Monoclonal antibodies may be isolated from the supernatants of growing hybridoma colonies. In addition, various techniques may be employed to enhance the yield, such as injection of the hybridoma cell line into the peritoneal cavity of a suitable vertebrate host, such as a mouse. Monoclonal antibodies may then be harvested from the ascites fluid or the blood. Contaminants may be removed from the antibodies by conventional techniques, such as chromatography, gel filtration, precipitation, and extraction. The polypeptides of this invention may be used in the purification process in, for example, an affinity chromatography step.

[1888] A number of therapeutically useful molecules are known in the art which comprise antigen-binding sites that are capable of exhibiting immunological binding properties of an antibody molecule. The proteolytic enzyme papain preferentially cleaves IgG molecules to yield several fragments, two of which (the “F(ab)” fragments) each comprise a covalent heterodimer that includes an intact antigen-binding site. The enzyme pepsin is able to cleave IgG molecules to provide several fragments, including the “F(ab′)2 ” fragment which comprises both antigen-binding sites. An “Fv” fragment can be produced by preferential proteolytic cleavage of an IgM, and on rare occasions IgG or IgA immunoglobulin molecule. Fv fragments are, however, more commonly derived using recombinant techniques known in the art. The Fv fragment includes a non-covalent VH::VL heterodimer including an antigen-binding site which retains much of the antigen recognition and binding capabilities of the native antibody molecule. Inbar et al. (1972) Proc. Nat. Acad. Sci. USA 69:2659-2662; Hochman et al. (1976) Biochem 15:2706-2710; and Ehrlich et al. (1980) Biochem 19:4091-4096.

[1889] A single chain Fv (“sFv”) polypeptide is a covalently linked VH::VL heterodimer which is expressed from a gene fusion including VH- and VL-encoding genes linked by a peptide-encoding linker. Huston et al. (1988) Proc. Nat. Acad. Sci. USA 85(16):5879-5883. A number of methods have been described to discern chemical structures for converting the naturally aggregated—but chemically separated—light and heavy polypeptide chains from an antibody V region into an sFv molecule which will fold into a three dimensional structure substantially similar to the structure of an antigen-binding site. See, e.g., U.S. Pat. Nos. 5,091,513 and 5,132,405, to Huston et al.; and U.S. Pat. No. 4,946,778, to Ladner et al.

[1890] Each of the above-described molecules includes a heavy chain and a light chain CDR set, respectively interposed between a heavy chain and a light chain FR set which provide support to the CDRS and define the spatial relationship of the CDRs relative to each other. As used herein, the term “CDR set” refers to the three hypervariable regions of a heavy or light chain V region. Proceeding from the N-terminus of a heavy or light chain, these regions are denoted as “CDR1,” “CDR2,” and “CDR3” respectively. An antigen-binding site, therefore, includes six CDRs, comprising the CDR set from each of a heavy and a light chain V region. A polypeptide comprising a single CDR, (e.g., a CDR1, CDR2 or CDR3) is referred to herein as a “molecular recognition unit.” Crystallographic analysis of a number of antigen-antibody complexes has demonstrated that the amino acid residues of CDRs form extensive contact with bound antigen, wherein the most extensive antigen contact is with the heavy chain CDR3. Thus, the molecular recognition units are primarily responsible for the specificity of an antigen-binding site.

[1891] As used herein, the term “FR set” refers to the four flanking amino acid sequences which frame the CDRs of a CDR set of a heavy or light chain V region. Some FR residues may contact bound antigen; however, FRs are primarily responsible for folding the V region into the antigen-binding site, particularly the FR residues directly adjacent to the CDRS. Within FRs, certain amino residues and certain structural features are very highly conserved. In this regard, all V region sequences contain an internal disulfide loop of around 90 amino acid residues. When the V regions fold into a binding-site, the CDRs are displayed as projecting loop motifs which form an antigen-binding surface. It is generally recognized that there are conserved structural regions of FRs which influence the folded shape of the CDR loops into certain “canonical” structures—regardless of the precise CDR amino acid sequence. Further, certain FR residues are known to participate in non-covalent interdomain contacts which stabilize the interaction of the antibody heavy and light chains.

[1892] A number of “humanized” antibody molecules comprising an antigen-binding site derived from a non-human immunoglobulin have been described, including chimeric antibodies having rodent V regions and their associated CDRs fused to human constant domains (Winter et al. (1991) Nature 349:293-299;

[1893] Lobuglio et al. (1989) Proc. Nat. Acad. Sci. USA 86:4220-4224; Shaw et al. (1987) J. Immunol. 138:4534-4538; and Brown et al. (1987) Cancer Res. 47:3577-3583), rodent CDRs grafted into a human supporting FR prior to fusion with an appropriate human antibody constant domain (Riechmann et al. (1988) Nature 332:323-327; Verhoeyen et al. (1988) Science 239:1534-1536; and Jones et al. (1986) Nature 321:522-525), and rodent CDRs supported by recombinantly veneered rodent FRs (European Patent Publication No. 519,596, published Dec. 23, 1992). These “humanized” molecules are designed to minimize unwanted immunological response toward rodent antihuman antibody molecules which limits the duration and effectiveness of therapeutic applications of those moieties in human recipients.

[1894] As used herein, the terms “veneered FRs” and “recombinantly veneered FRs” refer to the selective replacement of FR residues from, e.g., a rodent heavy or light chain V region, with human FR residues in order to provide a xenogeneic molecule comprising an antigen-binding site which retains substantially all of the native FR polypeptide folding structure. Veneering techniques are based on the understanding that the ligand binding characteristics of an antigen-binding site are determined primarily by the structure and relative disposition of the heavy and light chain CDR sets within the antigen-binding surface. Davies et al. (1990) Ann. Rev. Biochem. 59:439-473. Thus, antigen binding specificity can be preserved in a humanized antibody only wherein the CDR structures, their interaction with each other, and their interaction with the rest of the V region domains are carefully maintained. By using veneering techniques, exterior (e.g., solvent-accessible) FR residues which are readily encountered by the immune system are selectively replaced with human residues to provide a hybrid molecule that comprises either a weakly immunogenic, or substantially non-immunogenic veneered surface.

[1895] The process of veneering makes use of the available sequence data for human antibody variable domains compiled by Kabat et al., in Sequences of Proteins of Immunological Interest, 4th ed., (U.S. Dept. of Health and Human Services, U.S. Government Printing Office, 1987), updates to the Kabat database, and other accessible U.S. and foreign databases (both nucleic acid and protein). Solvent accessibilities of V region amino acids can be deduced from the known three-dimensional structure for human and murine antibody fragments. There are two general steps in veneering a murine antigen-binding site. Initially, the FRs of the variable domains of an antibody molecule of interest are compared with corresponding FR sequences of human variable domains obtained from the above-identified sources. The most homologous human V regions are then compared residue by residue to corresponding murine amino acids. The residues in the murine FR which differ from the human counterpart are replaced by the residues present in the human moiety using recombinant techniques well known in the art. Residue switching is only carried out with moieties which are at least partially exposed (solvent accessible), and care is exercised in the replacement of amino acid residues which may have a significant effect on the tertiary structure of V region domains, such as proline, glycine and charged amino acids.

[1896] In this manner, the resultant “veneered” murine antigen-binding sites are thus designed to retain the murine CDR residues, the residues substantially adjacent to the CDRs, the residues identified as buried or mostly buried (solvent inaccessible), the residues believed to participate in non-covalent (e.g., electrostatic and hydrophobic) contacts between heavy and light chain domains, and the residues from conserved structural regions of the FRs which are believed to influence the “canonical” tertiary structures of the CDR loops. These design criteria are then used to prepare recombinant nucleotide sequences which combine the CDRs of both the heavy and light chain of a murine antigen-binding site into human-appearing FRs that can be used to transfect mammalian cells for the expression of recombinant human antibodies which exhibit the antigen specificity of the murine antibody molecule.

[1897] In another embodiment of the invention, monoclonal antibodies of the present invention may be coupled to one or more therapeutic agents. Suitable agents in this regard include radionuclides, differentiation inducers, drugs, toxins, and derivatives thereof. Preferred radionuclides include 90Y, 123I, 125I, 131I, 186Re, 188Re, 211At, and 212Bi. 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.

[1898] A therapeutic agent may be coupled (e.g., covalently bonded) to a suitable monoclonal antibody either directly or indirectly (e.g., via a linker group). A direct reaction between an agent and an antibody is possible when each possesses a substituent capable of reacting with the other. For example, a nucleophilic group, such as an amino or sulfhydryl group, on one may be capable of reacting with a carbonyl-containing group, such as an anhydride or an acid halide, or with an alkyl group containing a good leaving group (e.g., a halide) on the other.

[1899] Alternatively, it may be desirable to couple a therapeutic agent and an antibody via a linker group. A linker group can function as a spacer to distance an antibody from an agent in order to avoid interference with binding capabilities. A linker group can also serve to increase the chemical reactivity of a substituent on an agent or an antibody, and thus increase the coupling efficiency. An increase in chemical reactivity may also facilitate the use of agents, or functional groups on agents, which otherwise would not be possible.

[1900] 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, Ill.), may be employed as the linker group. Coupling may be effected, for example, through amino groups, carboxyl groups, sulfhydryl groups or oxidized carbohydrate residues. There are numerous references describing such methodology, e.g., U.S. Pat. No. 4,671,958, to Rodwell et al.

[1901] Where a therapeutic agent is more potent when free from the antibody portion of the immunoconjugates of the present invention, it may be desirable to use a linker group which is cleavable during or upon internalization into a cell. A number of different cleavable linker groups have been described. The mechanisms for the intracellular release of an agent from these linker groups include cleavage by reduction of a disulfide bond (e.g., U.S. Pat. No. 4,489,710, to Spitler), by irradiation of a photolabile bond (e.g., U.S. Pat. No. 4,625,014, to Senter et al.), by hydrolysis of derivatized amino acid side chains (e.g., U.S. Pat. No. 4,638,045, to Kohn et al.), by serum complement-mediated hydrolysis (e.g., U.S. Pat. No. 4,671,958, to Rodwell et al.), and acid-catalyzed hydrolysis (e.g., U.S. Pat. No. 4,569,789, to Blattler et al.).

[1902] It may be desirable to couple more than one agent to an antibody. In one embodiment, multiple molecules of an agent are coupled to one antibody molecule. In another embodiment, more than one type of agent may be coupled to one antibody. Regardless of the particular embodiment, immunoconjugates with more than one agent may be prepared in a variety of ways. For example, more than one agent may be coupled directly to an antibody molecule, or linkers that provide multiple sites for attachment can be used. Alternatively, a carrier can be used.

[1903] A carrier may bear the agents in a variety of ways, including covalent bonding either directly or via a linker group. Suitable carriers include proteins such as albumins (e.g., U.S. Pat. No. 4,507,234, to Kato et al.), peptides and polysaccharides such as aminodextran (e.g., U.S. Pat. No. 4,699,784, to Shih et al.). A carrier may also bear an agent by noncovalent bonding or by encapsulation, such as within a liposome vesicle (e.g., U.S. Pat. Nos. 4,429,008 and 4,873,088). Carriers specific for radionuclide agents include radiohalogenated small molecules and chelating compounds. For example, U.S. Pat. No. 4,735,792 discloses representative radiohalogenated small molecules and their synthesis. A radionuclide chelate may be formed from chelating compounds that include those containing nitrogen and sulfur atoms as the donor atoms for binding the metal, or metal oxide, radionuclide. For example, U.S. Pat. No. 4,673,562, to Davison et al. discloses representative chelating compounds and their synthesis.

[1904] T Cell Compositions

[1905] The present invention, in another aspect, provides T cells specific for a tumor polypeptide disclosed herein, or for a variant or derivative thereof. Such cells may generally be prepared in vitro or ex vivo, using standard procedures. For example, T cells may be isolated from bone marrow, peripheral blood, or a fraction of bone marrow or peripheral blood of a patient, using a commercially available cell separation system, such as the Isolex™ System, available from Nexell Therapeutics, Inc. (Irvine, Calif.; see also U.S. Pat. No. 5,240,856; U.S. Pat. No. 5,215,926; WO 89/06280; WO 91/16116 and WO 92/07243). Alternatively, T cells may be derived from related or unrelated humans, non-human mammals, cell lines or cultures.

[1906] T cells may be stimulated with a polypeptide, polynucleotide encoding a polypeptide and/or an antigen presenting cell (APC) that expresses such a polypeptide. Such stimulation is performed under conditions and for a time sufficient to permit the generation of T cells that are specific for the polypeptide of interest. Preferably, a tumor polypeptide or polynucleotide of the invention is present within a delivery vehicle, such as a microsphere, to facilitate the generation of specific T cells.

[1907] T cells are considered to be specific for a polypeptide of the present invention if the T cells specifically proliferate, secrete cytokines or kill target cells coated with the polypeptide or expressing a gene encoding the polypeptide. T cell specificity may be evaluated using any of a variety of standard techniques. For example, within a chromium release assay or proliferation assay, a stimulation index of more than two fold increase in lysis and/or proliferation, compared to negative controls, indicates T cell specificity. Such assays may be performed, for example, as described in Chen et al., Cancer Res. 54:1065-1070, 1994. Alternatively, detection of the proliferation of T cells may be accomplished by a variety of known techniques. For example, T cell proliferation can be detected by measuring an increased rate of DNA synthesis (e.g., by pulse-labeling cultures of T cells with tritiated thymidine and measuring the amount of tritiated thymidine incorporated into DNA). Contact with a tumor polypeptide (100 ng/ml-100 μg/ml, preferably 200 ng/ml-25 μg/ml) for 3-7 days will typically result in at least a two fold increase in proliferation of the T cells. Contact as described above for 2-3 hours should result in activation of the T cells, as measured using standard cytokine assays in which a two fold increase in the level of cytokine release (e.g., TNF or IFN-γ) is indicative of T cell activation (see Coligan et al., Current Protocols in Immunology, vol. 1, Wiley Interscience (Greene 1998)). T cells that have been activated in response to a tumor polypeptide, polynucleotide or polypeptide-expressing APC may be CD4+ and/or CD8+. Tumor polypeptide-specific T cells may be expanded using standard techniques. Within preferred embodiments, the T cells are derived from a patient, a related donor or an unrelated donor, and are administered to the patient following stimulation and expansion.

[1908] For therapeutic purposes, CD4+ or CD8+T cells that proliferate in response to a tumor polypeptide, polynucleotide or APC can be expanded in number either in vitro or in vivo. Proliferation of such T cells in vitro may be accomplished in a variety of ways. For example, the T cells can be re-exposed to a tumor polypeptide, or a short peptide corresponding to an immunogenic portion of such a polypeptide, with or without the addition of T cell growth factors, such as interleukin-2, and/or stimulator cells that synthesize a tumor polypeptide. Alternatively, one or more T cells that proliferate in the presence of the tumor polypeptide can be expanded in number by cloning. Methods for cloning cells are well known in the art, and include limiting dilution.

[1909] T Cell Receptor Compositions

[1910] The T cell receptor (TCR) consists of 2 different, highly variable polypeptide chains, termed the T-cell receptor α and β chains, that are linked by a disulfide bond (Janeway, Travers, Walport. Immunobiology. Fourth Ed., 148-159. Elsevier Science Ltd/Garland Publishing. 1999). The α/β heterodimer complexes with the invariant CD3 chains at the cell membrane. This complex recognizes specific antigenic peptides bound to MHC molecules. The enormous diversity of TCR specificities is generated much like immunoglobulin diversity, through somatic gene rearrangement. The β chain genes contain over 50 variable (V), 2 diversity (D), over 10 joining (J) segments, and 2 constant region segments (C). The α chain genes contain over 70 V segments, and over 60 J segments but no D segments, as well as one C segment. During T cell development in the thymus, the D to J gene rearrangement of the β chain occurs, followed by the V gene segment rearrangement to the DJ. This functional VDJβ exon is transcribed and spliced to join to a Cβ. For the α chain, a Vα gene segment rearranges to a Jα gene segment to create the functional exon that is then transcribed and spliced to the Cα. Diversity is further increased during the recombination process by the random addition of P and N-nucleotides between the V, D, and J segments of the β chain and between the V and J segments in the □ chain (Janeway, Travers, Walport. Immunobiology. Fourth Ed., 98 and 150. Elsevier Science Ltd/Garland Publishing. 1999).

[1911] The present invention, in another aspect, provides TCRs specific for a polypeptide disclosed herein, or for a variant or derivative thereof. In accordance with the present invention, polynucleotide and amino acid sequences are provided for the V-J or V-D-J junctional regions or parts thereof for the alpha and beta chains of the T-cell receptor which recognize tumor polypeptides described herein. In general, this aspect of the invention relates to T-cell receptors which recognize or bind tumor polypeptides presented in the context of MHC. In a preferred embodiment the tumor antigens recognized by the T-cell receptors comprise a polypeptide of the present invention. For example, cDNA encoding a TCR specific for a kidney tumor peptide can be isolated from T cells specific for a tumor polypeptide using standard molecular biological and recombinant DNA techniques.

[1912] This invention further includes the T-cell receptors or analogs thereof having substantially the same function or activity as the T-cell receptors of this invention which recognize or bind tumor polypeptides. Such receptors include, but are not limited to, a fragment of the receptor, or a substitution, addition or deletion mutant of a T-cell receptor provided herein. This invention also encompasses polypeptides or peptides that are substantially homologous to the T-cell receptors provided herein or that retain substantially the same activity. The term “analog” includes any protein or polypeptide having an amino acid residue sequence substantially identical to the T-cell receptors provided herein in which one or more residues, preferably no more than 5 residues, more preferably no more than 25 residues have been conservatively substituted with a functionally similar residue and which displays the functional aspects of the T-cell receptor as described herein.

[1913] The present invention further provides for suitable mammalian host cells, for example, non-specific T cells, that are transfected with a polynucleotide encoding TCRs specific for a polypeptide described herein, thereby rendering the host cell specific for the polypeptide. The α and β chains of the TCR may be contained on separate expression vectors or alternatively, on a single expression vector that also contains an internal ribosome entry site (IRES) for cap-independent translation of the gene downstream of the IRES. Said host cells expressing TCRs specific for the polypeptide may be used, for example, for adoptive immunotherapy of kidney cancer as discussed further below.

[1914] In further aspects of the present invention, cloned TCRs specific for a polypeptide recited herein may be used in a kit for the diagnosis of kidney cancer. For example, the nucleic acid sequence or portions thereof, of tumor-specific TCRs can be used as probes or primers for the detection of expression of the rearranged genes encoding the specific TCR in a biological sample. Therefore, the present invention further provides for an assay for detecting messenger RNA or DNA encoding the TCR specific for a polypeptide.

[1915] Pharmaceutical Compositions

[1916] In additional embodiments, the present invention concerns formulation of one or more of the polynucleotide, polypeptide, T-cell, TCR, and/or antibody compositions disclosed herein in pharmaceutically-acceptable carriers for administration to a cell or an animal, either alone, or in combination with one or more other modalities of therapy.

[1917] It will be understood that, if desired, a composition as disclosed herein may be administered in combination with other agents as well, such as, e.g., other proteins or polypeptides or various pharmaceutically-active agents. In fact, there is virtually no limit to other components that may also be included, given that the additional agents do not cause a significant adverse effect upon contact with the target cells or host tissues. The compositions may thus be delivered along with various other agents as required in the particular instance. Such compositions may be purified from host cells or other biological sources, or alternatively may be chemically synthesized as described herein. Likewise, such compositions may further comprise substituted or derivatized RNA or DNA compositions.

[1918] Therefore, in another aspect of the present invention, pharmaceutical compositions are provided comprising one or more of the polynucleotide, polypeptide, antibody, TCR, and/or T-cell compositions described herein in combination with a physiologically acceptable carrier. In certain preferred embodiments, the pharmaceutical compositions of the invention comprise immunogenic polynucleotide and/or polypeptide compositions of the invention for use in prophylactic and theraputic vaccine applications. Vaccine preparation is generally described in, for example, M. F. Powell and M. J. Newman, eds., “Vaccine Design (the subunit and adjuvant approach),” Plenum Press (NY, 1995). Generally, such compositions will comprise one or more polynucleotide and/or polypeptide compositions of the present invention in combination with one or more immunostimulants.

[1919] It will be apparent that any of the pharmaceutical compositions described herein can contain pharmaceutically acceptable salts of the polynucleotides and polypeptides of the invention. Such salts can be prepared, for example, from pharmaceutically acceptable non-toxic bases, including organic bases (e.g., salts of primary, secondary and tertiary amines and basic amino acids) and inorganic bases (e.g., sodium, potassium, lithium, ammonium, calcium and magnesium salts).

[1920] In another embodiment, illustrative immunogenic compositions, e.g., vaccine compositions, of the present invention comprise DNA encoding one or more of the polypeptides as described above, such that the polypeptide is generated in situ. As noted above, the polynucleotide may be administered within any of a variety of delivery systems known to those of ordinary skill in the art. Indeed, numerous gene delivery techniques are well known in the art, such as those described by Rolland, Crit. Rev. Therap. Drug Carrier Systems 15:143-198, 1998, and references cited therein. Appropriate polynucleotide expression systems will, of course, contain the necessary regulatory DNA regulatory sequences for expression in a patient (such as a suitable promoter and terminating signal). Alternatively, bacterial delivery systems may involve the administration of a bacterium (such as Bacillus-Calmette-Guerrin) that expresses an immunogenic portion of the polypeptide on its cell surface or secretes such an epitope.

[1921] Therefore, in certain embodiments, polynucleotides encoding immunogenic polypeptides described herein are introduced into suitable mammalian host cells for expression using any of a number of known viral-based systems. In one illustrative embodiment, retroviruses provide a convenient and effective platform for gene delivery systems. A selected nucleotide sequence encoding a polypeptide of the present invention can be inserted into a vector and packaged in retroviral particles using techniques known in the art. The recombinant virus can then be isolated and delivered to a subject. A number of illustrative retroviral systems have been described (e.g., U.S. Pat. No. 5,219,740; Miller and Rosman (1989) BioTechniques 7:980-990; Miller, A. D. (1990) Human Gene Therapy 1:5-14; Scarpa et al. (1991) Virology 180:849-852; Burns et al. (1993) Proc. Natl. Acad. Sci. USA 90:8033-8037; and Boris-Lawrie and Temin (1993) Cur. Opin. Genet. Develop. 3:102-109.

[1922] In addition, a number of illustrative adenovirus-based systems have also been described. Unlike retroviruses which integrate into the host genome, adenoviruses persist extrachromosomally thus minimizing the risks associated with insertional mutagenesis (Haj-Ahmad and Graham (1986) J. Virol. 57:267-274; Bett et al. (1993) J. Virol. 67:5911-5921; Mittereder et al. (1994) Human Gene Therapy 5:717-729; Seth et al. (1994) J. Virol. 68:933-940; Barr et al. (1994) Gene Therapy 1:51-58; Berkner, K. L. (1988) BioTechniques 6:616-629; and Rich et al. (1993) Human Gene Therapy 4:461-476).

[1923] Various adeno-associated virus (MV) vector systems have also been developed for polynucleotide delivery. MV vectors can be readily constructed using techniques well known in the art. See, e.g., U.S. Pat. Nos. 5,173,414 and 5,139,941; International Publication Nos. WO 92/01070 and WO 93/03769; Lebkowski et al. (1988) Molec. Cell. Biol. 8:3988-3996; Vincent et al. (1990) Vaccines 90 (Cold Spring Harbor Laboratory Press); Carter, B. J. (1992) Current Opinion in Biotechnology 3:533-539; Muzyczka, N. (1992) Current Topics in Microbiol. and Immunol. 158:97-129; Kotin, R. M. (1994) Human Gene Therapy 5:793-801; Shelling and Smith (1994) Gene Therapy 1 :165-169; and Zhou et al. (1994) J. Exp. Med. 179:1867-1875.

[1924] Additional viral vectors useful for delivering the polynucleotides encoding polypeptides of the present invention by gene transfer include those derived from the pox family of viruses, such as vaccinia virus and avian poxyirus. By way of example, vaccinia virus recombinants expressing the novel molecules can be constructed as follows. The DNA encoding a polypeptide is first inserted into an appropriate vector so that it is adjacent to a vaccinia promoter and flanking vaccinia DNA sequences, such as the sequence encoding thymidine kinase (TK). This vector is then used to transfect cells which are simultaneously infected with vaccinia. Homologous recombination serves to insert the vaccinia promoter plus the gene encoding the polypeptide of interest into the viral genome. The resulting TK.sup.(−) recombinant can be selected by culturing the cells in the presence of 5-bromodeoxyuridine and picking viral plaques resistant thereto.

[1925] A vaccinia-based infection/transfection system can be conveniently used to provide for inducible, transient expression or coexpression of one or more polypeptides described herein in host cells of an organism. In this particular system, cells are first infected in vitro with a vaccinia virus recombinant that encodes the bacteriophage T7 RNA polymerase. This polymerase displays exquisite specificity in that it only transcribes templates bearing T7 promoters. Following infection, cells are transfected with the polynucleotide or polynucleotides of interest, driven by a T7 promoter. The polymerase expressed in the cytoplasm from the vaccinia virus recombinant transcribes the transfected DNA into RNA which is then translated into polypeptide by the host translational machinery. The method provides for high level, transient, cytoplasmic production of large quantities of RNA and its translation products. See, e.g., Elroy-Stein and Moss, Proc. Natl. Acad. Sci. USA (1990) 87:6743-6747; Fuerst et al. Proc. Natl. Acad. Sci. USA (1986) 83:8122-8126.

[1926] Alternatively, avipoxyiruses, such as the fowipox and canarypox viruses, can also be used to deliver the coding sequences of interest. Recombinant avipox viruses, expressing immunogens from mammalian pathogens, are known to confer protective immunity when administered to non-avian species. The use of an Avipox vector is particularly desirable in human and other mammalian species since members of the Avipox genus can only productively replicate in susceptible avian species and therefore are not infective in mammalian cells. Methods for producing recombinant Avipoxyiruses are known in the art and employ genetic recombination, as described above with respect to the production of vaccinia viruses. See, e.g., WO 91/12882; WO 89/03429; and WO 92/03545.

[1927] Any of a number of alphavirus vectors can also be used for delivery of polynucleotide compositions of the present invention, such as those vectors described in U.S. Pat. Nos. 5,843,723; 6,015,686; 6,008,035 and 6,015,694. Certain vectors based on Venezuelan Equine Encephalitis (VEE) can also be used, illustrative examples of which can be found in U.S. Pat. Nos. 5,505,947 and 5,643,576.

[1928] Moreover, molecular conjugate vectors, such as the adenovirus chimeric vectors described in Michael et al. J. Biol. Chem. (1993) 268:6866-6869 and Wagner et al. Proc. Natl. Acad. Sci. USA (1992) 89:6099-6103, can also be used for gene delivery under the invention.

[1929] Additional illustrative information on these and other known viral-based delivery systems can be found, for example, in Fisher-Hoch et al., Proc. Natl. Acad. Sci. USA 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. Pat. Nos. 4,603,112, 4,769,330, and 5,017,487; WO 89/01973; U.S. Pat. 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., Proc. Natl. Acad. Sci. USA 91:215-219, 1994; Kass-Eisler et al., Proc. Natl. Acad. Sci. USA 90:11498-11502, 1993; Guzman et al., Circulation 88:2838-2848, 1993; and Guzman et al., Cir. Res. 73:1202-1207, 1993.

[1930] In certain embodiments, a polynucleotide may be integrated into the genome of a target cell. This integration may be in the specific location and orientation via homologous recombination (gene replacement) or it may be integrated in a random, non-specific location (gene augmentation). In yet further embodiments, the polynucleotide may be stably maintained in the cell as a separate, episomal segment of DNA. Such polynucleotide segments or “episomes” encode sequences sufficient to permit maintenance and replication independent of or in synchronization with the host cell cycle. The manner in which the expression construct is delivered to a cell and where in the cell the polynucleotide remains is dependent on the type of expression construct employed.

[1931] In another embodiment of the invention, a polynucleotide is administered/delivered as “naked” DNA, for example as described in Ulmer et al., Science 259:1745-1749, 1993 and reviewed by Cohen, Science 259:1691-1692, 1993. The uptake of naked DNA may be increased by coating the DNA onto biodegradable beads, which are efficiently transported into the cells.

[1932] In still another embodiment, a composition of the present invention can be delivered via a particle bombardment approach, many of which have been described. In one illustrative example, gas-driven particle acceleration can be achieved with devices such as those manufactured by Powderject Pharmaceuticals PLC (Oxford, UK) and Powderject Vaccines Inc. (Madison, Wis.), some examples of which are described in U.S. Pat. Nos. 5,846,796; 6,010,478; 5,865,796; 5,584,807; and EP Patent No. 0500 799. This approach offers a needle-free delivery approach wherein a dry powder formulation of microscopic particles, such as polynucleotide or polypeptide particles, are accelerated to high speed within a helium gas jet generated by a hand held device, propelling the particles into a target tissue of interest.

[1933] In a related embodiment, other devices and methods that may be useful for gas-driven needle-less injection of compositions of the present invention include those provided by Bioject, Inc. (Portland, OR), some examples of which are described in U.S. Pat. Nos. 4,790,824; 5,064,413; 5,312,335; 5,383,851; 5,399,163; 5,520,639 and 5,993,412.

[1934] According to another embodiment, the pharmaceutical compositions described herein will comprise one or more immunostimulants in addition to the immunogenic polynucleotide, polypeptide, antibody, T-cell, TCR, and/or APC compositions of this invention. An immunostimulant refers to essentially any substance that enhances or potentiates an immune response (antibody and/or cell-mediated) to an exogenous antigen. One preferred type of immunostimulant comprises an adjuvant. Many adjuvants contain a substance designed to protect the antigen from rapid catabolism, such as aluminum hydroxide or mineral oil, and a stimulator of immune responses, such as lipid A, Bortadella pertussis or Mycobacterium tuberculosis derived proteins. Certain adjuvants are commercially available as, for example, Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, Mich.); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.); AS-2 (SmithKline Beecham, Philadelphia, Pa.); aluminum salts such as aluminum hydroxide gel (alum) or aluminum phosphate; salts of calcium, iron or zinc; an insoluble suspension of acylated tyrosine; acylated sugars; cationically or an ion ically derivatized polysaccharides; polyphosphazenes; biodegradable microspheres; monophosphoryl lipid A and quil A. Cytokines, such as GM-CSF, interleukin-2, -7, -12, and other like growth factors, may also be used as adjuvants.

[1935] Within certain embodiments of the invention, the adjuvant composition is preferably one that induces an immune response predominantly of the Th1 type. High levels of Th1-type cytokines (e.g., IFN-γ, TNFα, IL-2 and IL-12) tend to favor the induction of cell mediated immune responses to an administered antigen. In contrast, high levels of Th2-type cytokines (e.g., IL-4, IL-5, IL-6 and IL-10) tend to favor the induction of humoral immune responses. Following application of a vaccine as provided herein, a patient will support an immune response that includes Th1- and Th2-type responses. Within a preferred embodiment, in which a response is predominantly Th1-type, the level of Th1-type cytokines will increase to a greater extent than the level of Th2-type cytokines. The levels of these cytokines may be readily assessed using standard assays. For a review of the families of cytokines, see Mosmann and Coffman, Ann. Rev. Immunol. 7:145-173,1989.

[1936] Certain preferred adjuvants for eliciting a predominantly Th1-type response include, for example, a combination of monophosphoryl lipid A, preferably 3-de-O-acylated monophosphoryl lipid A, together with an aluminum salt. MPL® adjuvants are available from Corixa Corporation (Seattle, Wash.; see, for example, U.S. Pat. Nos. 4,436,727; 4,877,611; 4,866,034 and 4,912,094). CpG-containing oligonucleotides (in which the CpG dinucleotide is unmethylated) also induce a predominantly Th1 response. Such oligonucleotides are well known and are described, for example, in WO 96/02555, WO 99/33488 and U.S. Pat. Nos. 6,008,200 and 5,856,462. Immunostimulatory DNA sequences are also described, for example, by Sato et al., Science 273:352, 1996. Another preferred adjuvant comprises a saponin, such as Quil A, or derivatives thereof, including QS21 and QS7 (Aquila Biopharmaceuticals Inc., Framingham, Mass.); Escin; Digitonin; or Gypsophila or Chenopodium quinoa saponins. Other preferred formulations include more than one saponin in the adjuvant combinations of the present invention, for example combinations of at least two of the following group comprising QS21, QS7, Quil A, β-escin, or digitonin.

[1937] Alternatively the saponin formulations may be combined with vaccine vehicles composed of chitosan or other polycationic polymers, polylactide and polylactide-co-glycolide particles, poly-N-acetyl glucosamine-based polymer matrix, particles composed of polysaccharides or chemically modified polysaccharides, liposomes and lipid-based particles, particles composed of glycerol monoesters, etc. The saponins may also be formulated in the presence of cholesterol to form particulate structures such as liposomes or ISCOMs. Furthermore, the saponins may be formulated together with a polyoxyethylene ether or ester, in either a non-particulate solution or suspension, or in a particulate structure such as a paucilamelar liposome or ISCOM. The saponins may also be formulated with excipients such as CarbopolR to increase viscosity, or may be formulated in a dry powder form with a powder excipient such as lactose.

[1938] In one preferred embodiment, the adjuvant system includes the combination of a monophosphoryl lipid A and a saponin derivative, such as the combination of QS21 and 3D-MPL® adjuvant, as described in WO 94/00153, or a less reactogenic composition where the QS21 is quenched with cholesterol, as described in WO 96/33739. Other preferred formulations comprise an oil-in-water emulsion and tocopherol. Another particularly preferred adjuvant formulation employing QS21, 3D-MPL! adjuvant and tocopherol in an oil-in-water emulsion is described in WO 95/17210.

[1939] Another enhanced adjuvant system involves the combination of a CpG-containing oligonucleotide and a saponin derivative particularly the combination of CpG and QS21 is disclosed in WO 00/09159. Preferably the formulation additionally comprises an oil in water emulsion and tocopherol.

[1940] Additional illustrative adjuvants for use in the pharmaceutical compositions of the invention include Montamide ISA 720 (Seppic, France), SAF (Chiron, California, United States), ISCOMS (CSL), MF-59 (Chiron), the SBAS series of adjuvants (e.g., SBAS-2 or SBAS-4, available from SmithKline Beecham, Rixensart, Belgium), Detox (Enhanzyn®) (Corixa, Hamilton, Mont.), RC-529 (Corixa, Hamilton, Mont.) and other aminoalkyl glucosaminide 4-phosphates (AGPs), such as those described in pending U.S. patent application Ser. Nos. 08/853,826 and 09/074,720, the disclosures of which are incorporated herein by reference in their entireties, and polyoxyethylene ether adjuvants such as those described in WO 99/52549A1.

[1941] Other preferred adjuvants include adjuvant molecules of the general formula

(I): HO(CH2CH2O)n—A—R,

[1942] wherein, n is 1-50, A is a bond or —C(O)—, R is C1-50 alkyl or Phenyl C1-50 alkyl.

[1943] One embodiment of the present invention consists of a vaccine formulation comprising a polyoxyethylene ether of general formula (I), wherein n is between 1 and 50, preferably 4-24, most preferably 9; the R component is C1-50, preferably C4-C20 alkyl and most preferably C12 alkyl, and A is a bond. The concentration of the polyoxyethylene ethers should be in the range 0.1-20%, preferably from 0.1-10%, and most preferably in the range 0.1-1%. Preferred polyoxyethylene ethers are selected from the following group: polyoxyethylene-9-lauryl ether, polyoxyethylene-9-steoryl ether, polyoxyethylene-8-steoryl ether, polyoxyethylene-4-lauryl ether, polyoxyethylene-35-lauryl ether, and polyoxyethylene-23-lauryl ether. Polyoxyethylene ethers such as polyoxyethylene lauryl ether are described in the Merck index (12th edition: entry 7717). These adjuvant molecules are described in WO 99/52549.

[1944] The polyoxyethylene ether according to the general formula (I) above may, if desired, be combined with another adjuvant. For example, a preferred adjuvant combination is preferably with CpG as described in the pending UK patent application GB 9820956.2.

[1945] According to another embodiment of this invention, an immunogenic composition described herein is delivered to a host via antigen presenting cells (APCs), such as dendritic cells, macrophages, B cells, monocytes and other cells that may be engineered to be efficient APCs. Such cells may, but need not, be genetically modified to increase the capacity for presenting the antigen, to improve activation and/or maintenance of the T cell response, to have anti-tumor effects per se and/or to be immunologically compatible with the receiver (i.e., matched HLA haplotype). APCs may generally be isolated from any of a variety of biological fluids and organs, including tumor and peritumoral tissues, and may be autologous, allogeneic, syngeneic or xenogeneic cells.

[1946] Certain preferred embodiments of the present invention use dendritic cells or progenitors thereof as antigen-presenting cells. Dendritic cells are highly potent APCs (Banchereau and Steinman, Nature 392:245-251,1998) and have been shown to be effective as a physiological adjuvant for eliciting prophylactic or therapeutic antitumor immunity (see Timmerman and Levy, Ann. Rev. Med. 50:507-529,1999). In general, dendritic cells may be identified based on their typical shape (stellate in situ, with marked cytoplasmic processes (dendrites) visible in vitro), their ability to take up, process and present antigens with high efficiency and their ability to activate naive T cell responses. Dendritic cells may, of course, be engineered to express specific cell-surface receptors or ligands that are not commonly found on dendritic cells in vivo or ex vivo, and such modified dendritic cells are contemplated by the present invention. As an alternative to dendritic cells, secreted vesicles antigen-loaded dendritic cells (called exosomes) may be used within a vaccine (see Zitvogel et al., Nature Med. 4:594-600,1998).

[1947] Dendritic cells and progenitors may be obtained from peripheral blood, bone marrow, tumor-infiltrating cells, peritumoral tissues-infiltrating cells, lymph nodes, spleen, skin, umbilical cord blood or any other suitable tissue or fluid. For example, dendritic cells may be differentiated ex vivo by adding a combination of cytokines such as GM-CSF, IL-4, IL-13 and/or TNFα to cultures of monocytes harvested from peripheral blood. Alternatively, CD34 positive cells harvested from peripheral blood, umbilical cord blood or bone marrow may be differentiated into dendritic cells by adding to the culture medium combinations of GM-CSF, IL-3, TNFα, CD40 ligand, LPS, flt3 ligand and/or other compound(s) that induce differentiation, maturation and proliferation of dendritic cells.

[1948] Dendritic cells are conveniently categorized as “immature” and “mature” cells, which allows a simple way to discriminate between two well characterized phenotypes. However, this nomenclature should not be construed to exclude all possible intermediate stages of differentiation. Immature dendritic cells are characterized as APC with a high capacity for antigen uptake and processing, which correlates with the high expression of Fcy receptor and mannose receptor. The mature phenotype is typically characterized by a lower expression of these markers, but a high expression of cell surface molecules responsible for T cell activation such as class I and class II MHC, adhesion molecules (e.g., CD54 and CD11) and costimulatory molecules (e.g., CD40, CD80, CD86 and 4-1BB).

[1949] APCs may generally be transfected with a polynucleotide of the invention (or portion or other variant thereof) such that the encoded polypeptide, or an immunogenic portion thereof, is expressed on the cell surface. Such transfection may take place ex vivo, and a pharmaceutical composition comprising such transfected cells may then be used for therapeutic purposes, as described herein. Alternatively, a gene delivery vehicle that targets a dendritic or other antigen presenting cell may be administered to a patient, resulting in transfection that occurs in vivo. In vivo and ex vivo transfection of dendritic cells, for example, may generally be performed using any methods known in the art, such as those described in WO 97/24447, or the gene gun approach described by Mahvi et al., Immunology and cell Biology 75:456-460,1997. Antigen loading of dendritic cells may be achieved by incubating dendritic cells or progenitor cells with the tumor polypeptide, DNA (naked or within a plasmid vector) or RNA; or with antigen-expressing recombinant bacterium or viruses (e.g., vaccinia, fowlpox, adenovirus or lentivirus vectors). Prior to loading, the polypeptide may be covalently conjugated to an immunological partner that provides T cell help (e.g., a carrier molecule). Alternatively, a dendritic cell may be pulsed with a non-conjugated immunological partner, separately or in the presence of the polypeptide. 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 typically vary depending on the mode of administration. Compositions of the present invention may be formulated for any appropriate manner of administration, including for example, topical, oral, nasal, mucosal, intravenous, intracranial, intraperitoneal, subcutaneous and intramuscular administration.

[1950] Carriers for use within such pharmaceutical compositions are biocompatible, and may also be biodegradable. In certain embodiments, the formulation preferably provides a relatively constant level of active component release. In other embodiments, however, a more rapid rate of release immediately upon administration may be desired. The formulation of such compositions is well within the level of ordinary skill in the art using known techniques. Illustrative carriers useful in this regard include microparticles of poly(lactide-co-glycolide), polyacrylate, latex, starch, cellulose, dextran and the like. Other illustrative delayed-release carriers include supramolecular biovectors, which comprise a non-liquid hydrophilic core (e.g., a cross-linked polysaccharide or oligosaccharide) and, optionally, an external layer comprising an amphiphilic compound, such as a phospholipid (see e.g., U.S. Pat. No. 5,151,254 and PCT applications WO 94/20078, WO/94/23701 and WO 96/06638). The amount of active compound contained within a sustained release formulation depends upon the site of implantation, the rate and expected duration of release and the nature of the condition to be treated or prevented.

[1951] In another illustrative embodiment, biodegradable microspheres (e.g., polylactate polyglycolate) are employed as carriers for the compositions of this invention. Suitable biodegradable microspheres are disclosed, for example, in U.S. Pat. Nos. 4,897,268; 5,075,109; 5,928,647; 5,811,128; 5,820,883; 5,853,763; 5,814,344, 5,407,609 and 5,942,252. Modified hepatitis B core protein carrier systems. such as described in WO/99 40934, and references cited therein, will also be useful for many applications. Another illustrative carrier/delivery system employs a carrier comprising particulate-protein complexes, such as those described in U.S. Pat. No. 5,928,647, which are capable of inducing a class I-restricted cytotoxic T lymphocyte responses in a host.

[1952] In another illustrative embodiment, calcium phosphate core particles are employed as carriers, vaccine adjuvants, or as controlled release matrices for the compositions of this invention. Exemplary calcium phosphate particles are disclosed, for example, in published patent application No. WO/0046147.

[1953] The pharmaceutical compositions of the invention will often further comprise one or more buffers (e.g., neutral buffered saline or phosphate buffered saline), carbohydrates (e.g., glucose, mannose, sucrose or dextrans), mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, bacteriostats, chelating agents such as EDTA or glutathione, adjuvants (e.g., aluminum hydroxide), solutes that render the formulation isotonic, hypotonic or weakly hypertonic with the blood of a recipient, suspending agents, thickening agents and/or preservatives. Alternatively, compositions of the present invention may be formulated as a lyophilizate.

[1954] The pharmaceutical compositions described herein may be presented in unit-dose or multi-dose containers, such as sealed ampoules or vials. Such containers are typically sealed in such a way to preserve the sterility and stability of the formulation until use. In general, formulations may be stored as suspensions, solutions or emulsions in oily or aqueous vehicles. Alternatively, a pharmaceutical composition may be stored in a freeze-dried condition requiring only the addition of a sterile liquid carrier immediately prior to use.

[1955] The development of suitable dosing and treatment regimens for using the particular compositions described herein in a variety of treatment regimens, including e.g., oral, parenteral, intravenous, intranasal, and intramuscular administration and formulation, is well known in the art, some of which are briefly discussed below for general purposes of illustration.

[1956] In certain applications, the pharmaceutical compositions disclosed herein may be delivered via oral administration to an animal. As such, these compositions may be formulated with an inert diluent or with an assimilable edible carrier, or they may be enclosed in hard- or soft-shell gelatin capsule, or they may be compressed into tablets, or they may be incorporated directly with the food of the diet.

[1957] The active compounds may even be incorporated with excipients and used in the form of ingestible tablets, buccal tables, troches, capsules, elixirs, suspensions, syrups, wafers, and the like (see, for example, Mathiowitz et al., Nature Mar. 27, 1997;386(6623):410-4; Hwang et al., Crit Rev Ther Drug Carrier Syst 1998;15(3):243-84; U.S. Pat. No. 5,641,515; U.S. Pat. No. 5,580,579 and U.S. Pat. No. 5,792,451). Tablets, troches, pills, capsules and the like may also contain any of a variety of additional components, for example, a binder, such as gum tragacanth, acacia, cornstarch, or gelatin; excipients, such as dicalcium phosphate; a disintegrating agent, such as corn starch, potato starch, alginic acid and the like; a lubricant, such as magnesium stearate; and a sweetening agent, such as sucrose, lactose or saccharin may be added or a flavoring agent, such as peppermint, oil of wintergreen, or cherry flavoring. When the dosage unit form is a capsule, it may contain, in addition to materials of the above type, a liquid carrier. Various other materials may be present as coatings or to otherwise modify the physical form of the dosage unit. For instance, tablets, pills, or capsules may be coated with shellac, sugar, or both. Of course, any material used in preparing any dosage unit form should be pharmaceutically pure and substantially non-toxic in the amounts employed. In addition, the active compounds may be incorporated into sustained-release preparation and formulations.

[1958] Typically, these formulations will contain at least about 0.1% of the active compound or more, although the percentage of the active ingredient(s) may, of course, be varied and may conveniently be between about 1 or 2% and about 60% or 70% or more of the weight or volume of the total formulation. Naturally, the amount of active compound(s) in each therapeutically useful composition may be prepared is such a way that a suitable dosage will be obtained in any given unit dose of the compound. Factors such as solubility, bioavailability, biological half-life, route of administration, product shelf life, as well as other pharmacological considerations will be contemplated by one skilled in the art of preparing such pharmaceutical formulations, and as such, a variety of dosages and treatment regimens may be desirable.

[1959] For oral administration the compositions of the present invention may alternatively be incorporated with one or more excipients in the form of a mouthwash, dentifrice, buccal tablet, oral spray, or sublingual orally-administered formulation. Alternatively, the active ingredient may be incorporated into an oral solution such as one containing sodium borate, glycerin and potassium bicarbonate, or dispersed in a dentifrice, or added in a therapeutically-effective amount to a composition that may include water, binders, abrasives, flavoring agents, foaming agents, and humectants. Alternatively the compositions may be fashioned into a tablet or solution form that may be placed under the tongue or otherwise dissolved in the mouth.

[1960] In certain circumstances it will be desirable to deliver the pharmaceutical compositions disclosed herein parenterally, intravenously, intramuscularly, or even intraperitoneally. Such approaches are well known to the skilled artisan, some of which are further described, for example, in U.S. Pat. Nos. 5,543,158; 5,641,515 and 5,399,363. In certain embodiments, solutions of the active compounds as free base or pharmacologically acceptable salts may be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions may also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations generally will contain a preservative to prevent the growth of microorganisms.

[1961] Illustrative pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions (for example, see U.S. Pat. No. 5,466,468). In all cases the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and/or vegetable oils. Proper fluidity may be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and/or by the use of surfactants. The prevention of the action of microorganisms can be facilitated by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.

[1962] In one embodiment, for parenteral administration in an aqueous solution, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this connection, a sterile aqueous medium that can be employed will be known to those of skill in the art in light of the present disclosure. For example, one dosage may be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion, (see for example, “Remington's Pharmaceutical Sciences” 15th Edition, pages 1035-1038 and 1570-1580). Some variation in dosage will necessarily occur depending on the condition of the subject being treated. Moreover, for human administration, preparations will of course preferably meet sterility, pyrogenicity, and the general safety and purity standards as required by FDA Office of Biologics standards.

[1963] In another embodiment of the invention, the compositions disclosed herein may be formulated in a neutral or salt form. Illustrative pharmaceutically-acceptable salts include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like. Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective.

[1964] The carriers can further comprise any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifungal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions. The phrase “pharmaceutically-acceptable” refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a human.

[1965] In certain embodiments, the pharmaceutical compositions may be delivered by intranasal sprays, inhalation, and/or other aerosol delivery vehicles. Methods for delivering genes, nucleic acids, and peptide compositions directly to the lungs via nasal aerosol sprays has been described, e.g., in U.S. Pat. No. 5,756,353 and U.S. Pat. No. 5,804,212. Likewise, the delivery of drugs using intranasal microparticle resins (Takenaga et al., J Controlled Release Mar. 2, 1998;52(1-2):81-7) and lysophosphatidyl-glycerol compounds (U.S. Pat. No. 5,725,871) are also well-known in the pharmaceutical arts. Likewise, illustrative transmucosal drug delivery in the form of a polytetrafluoroetheylene support matrix is described in U.S. Pat. No. 5,780,045.

[1966] In certain embodiments, liposomes, nanocapsules, microparticles, lipid particles, vesicles, and the like, are used for the introduction of the compositions of the present invention into suitable host cells/organisms. In particular, the compositions of the present invention may be formulated for delivery either encapsulated in a lipid particle, a liposome, a vesicle, a nanosphere, or a nanoparticle or the like. Alternatively, compositions of the present invention can be bound, either covalently or non-covalently, to the surface of such carrier vehicles.

[1967] The formation and use of liposome and liposome-like preparations as potential drug carriers is generally known to those of skill in the art (see for example, Lasic, Trends Biotechnol 1998 July;16(7):307-21; Takakura, Nippon Rinsho 1998 March;56(3):691-5; Chandran et al., Indian J Exp Biol. 1997 August;35(8):801-9; Margalit, Crit Rev Ther Drug Carrier Syst. 1995;12(2-3):233-61; U.S. Pat. Nos. 5,567,434; 5,552,157; 5,565,213; 5,738,868 and 5,795,587, each specifically incorporated herein by reference in its entirety).

[1968] Liposomes have been used successfully with a number of cell types that are normally difficult to transfect by other procedures, including T cell suspensions, primary hepatocyte cultures and PC 12 cells (Renneisen et al., J. Biol. Chem. Sep. 25, 1990;265(27):16337-42; Muller et al., DNA Cell Biol. 1990 April;9(3):221-9). In addition, liposomes are free of the DNA length constraints that are typical of viral-based delivery systems. Liposomes have been used effectively to introduce genes, various drugs, radiotherapeutic agents, enzymes, viruses, transcription factors, allosteric effectors and the like, into a variety of cultured cell lines and animals. Furthermore, he use of liposomes does not appear to be associated with autoimmune responses or unacceptable toxicity after systemic delivery.

[1969] In certain embodiments, liposomes are formed from phospholipids that are dispersed in an aqueous medium and spontaneously form multilamellar concentric bilayer vesicles (also termed multilamellar vesicles (MLVs).

[1970] Alternatively, in other embodiments, the invention provides for pharmaceutically-acceptable nanocapsule formulations of the compositions of the present invention. Nanocapsules can generally entrap compounds in a stable and reproducible way (see, for example, Quintanar-Guerrero et al., Drug Dev Ind Pharm. 1998 December;24(12):1113-28). To avoid side effects due to intracellular polymeric overloading, such ultrafine particles (sized around 0.1 μm) may be designed using polymers able to be degraded in vivo. Such particles can be made as described, for example, by Couvreur et al., Crit Rev Ther Drug Carrier Syst. 1988;5(1):1-20; zur Muhlen et al., Eur J Pharm Biopharm. 1998 March;45(2):149-55; Zambaux et al. J Controlled Release. Jan. 2, 1998;50(1-3):31-40; and U.S. Pat. No. 5,145,684.

[1971] Cancer Therapeutic Methods

[1972] Immunologic approaches to cancer therapy are based on the recognition that cancer cells can often evade the body's defenses against aberrant or foreign cells and molecules, and that these defenses might be therapeutically stimulated to regain the lost ground, e.g. pgs. 623-648 in Klein, Immunology (Wiley-Interscience, New York, 1982). Numerous recent observations that various immune effectors can directly or indirectly inhibit growth of tumors has led to renewed interest in this approach to cancer therapy, e.g. Jager, et al., Oncology 2001;60(1):1-7; Renner, et al., Ann Hematol 2000 December;79(12):651-9.

[1973] Four-basic cell types whose function has been associated with antitumor cell immunity and the elimination of tumor cells from the body are: i) B-lymphocytes which secrete immunoglobulins into the blood plasma for identifying and labeling the nonself invader cells; ii) monocytes which secrete the complement proteins that are responsible for lysing and processing the immunoglobulin-coated target invader cells; iii) natural killer lymphocytes having two mechanisms for the destruction of tumor cells, antibody-dependent cellular cytotoxicity and natural killing; and iv) T-lymphocytes possessing antigen-specific receptors and having the capacity to recognize a tumor cell carrying complementary marker molecules (Schreiber, H., 1989, in Fundamental Immunology (ed). W. E. Paul, pp. 923-955).

[1974] Cancer immunotherapy generally focuses on inducing humoral immune responses, cellular immune responses, or both. Moreover, it is well established that induction of CD4+ T helper cells is necessary in order to secondarily induce either antibodies or cytotoxic CD8+ T cells. Polypeptide antigens that are selective or ideally specific for cancer cells, particularly kidney cancer cells, offer a powerful approach for inducing immune responses against kidney cancer, and are an important aspect of the present invention.

[1975] Therefore, in further aspects of the present invention, the pharmaceutical compositions described herein may be used to stimulate an immune response against cancer, particularly for the immunotherapy of kidney cancer. Within such methods, the pharmaceutical compositions described herein are administered to a patient, typically a warm-blooded animal, preferably a human. A patient may or may not be afflicted with cancer. Pharmaceutical compositions and vaccines may be administered either prior to or following surgical removal of primary tumors and/or treatment such as administration of radiotherapy or conventional chemotherapeutic drugs. As discussed above, administration of the pharmaceutical compositions may be by any suitable method, including administration by intravenous, intraperitoneal, intramuscular, subcutaneous, intranasal, intradermal, anal, vaginal, topical and oral routes.

[1976] Within certain embodiments, immunotherapy may be active immunotherapy, in which treatment relies on the in vivo stimulation of the endogenous host immune system to react against tumors with the administration of immune response-modifying agents (such as polypeptides and polynucleotides as provided herein).

[1977] Within other embodiments, immunotherapy may be passive immunotherapy, in which treatment involves the delivery of agents with established tumor-immune reactivity (such as effector cells or antibodies) that can directly or indirectly mediate antitumor effects and does not necessarily depend on an intact host immune system. Examples of effector cells include T cells as discussed above, T lymphocytes (such as CD8+ cytotoxic T lymphocytes and CD4+ T-helper tumor-infiltrating lymphocytes), killer cells (such as Natural Killer cells and lymphokine-activated killer cells), B cells and antigen-presenting cells (such as dendritic cells and macrophages) expressing a polypeptide provided herein. T cell receptors and antibody receptors specific for the polypeptides recited herein may be cloned, expressed and transferred into other vectors or effector cells for adoptive immunotherapy. The polypeptides provided herein may also be used to generate antibodies or anti-idiotypic antibodies (as described above and in U.S. Pat. No. 4,918,164) for passive immunotherapy.

[1978] Monoclonal antibodies may be labeled with any of a variety of labels for desired selective usages in detection, diagnostic assays or therapeutic applications (as described in U.S. Pat. Nos. 6,090,365; 6,015,542; 5,843,398; 5,595,721; and 4,708,930, hereby incorporated by reference in their entirety as if each was incorporated individually). In each case, the binding of the labelled monoclonal antibody to the determinant site of the antigen will signal detection or delivery of a particular therapeutic agent to the antigenic determinant on the non-normal cell. A further object of this invention is to provide the specific monoclonal antibody suitably labelled for achieving such desired selective usages thereof.

[1979] Effector cells may generally be obtained in sufficient quantities for adoptive immunotherapy by growth in vitro, as described herein. Culture conditions for expanding single antigen-specific effector cells to several billion in number with retention of antigen recognition in vivo are well known in the art. Such in vitro culture conditions typically use intermittent stimulation with antigen, often in the presence of cytokines (such as IL-2) and non-dividing feeder cells. As noted above, immunoreactive polypeptides as provided herein may be used to rapidly expand antigen-specific T cell cultures in order to generate a sufficient number of cells for immunotherapy. In particular, antigen-presenting cells, such as dendritic, macrophage, monocyte, fibroblast and/or B cells, may be pulsed with immunoreactive polypeptides or transfected with one or more polynucleotides using standard techniques well known in the art. For example, antigen-presenting cells can be transfected with a polynucleotide having a promoter appropriate for increasing expression in a recombinant virus or other expression system. Cultured effector cells for use in therapy must be able to grow and distribute widely, and to survive long term in vivo. Studies have shown that cultured effector cells can be induced to grow in vivo and to survive long term in substantial numbers by repeated stimulation with antigen supplemented with IL-2 (see, for example, Cheever et al., Immunological Reviews 157:177, 1997). Alternatively, a vector expressing a polypeptide recited herein may be introduced into antigen presenting cells taken from a patient and clonally propagated ex vivo for transplant back into the same patient. Transfected cells may be reintroduced into the patient using any means known in the art, preferably in sterile form by intravenous, intracavitary, intraperitoneal or intratumor administration.

[1980] Routes and frequency of administration of the therapeutic compositions described herein, as well as dosage, will vary from individual to individual, and may be readily established using standard techniques. In general, the pharmaceutical compositions and vaccines may be administered by injection (e.g., intracutaneous, intramuscular, intravenous or subcutaneous), intranasally (e.g., by aspiration) or orally. Preferably, between 1 and 10 doses may be administered over a 52 week period. Preferably, 6 doses are administered, at intervals of 1 month, and booster vaccinations may be given periodically thereafter. Alternate protocols may be appropriate for individual patients. A suitable dose is an amount of a compound that, when administered as described above, is capable of promoting an anti-tumor immune response, and is at least 10-50% above the basal (i.e., untreated) level. Such response can be monitored by measuring the anti-tumor antibodies in a patient or by vaccine-dependent generation of cytolytic effector cells capable of killing the patient's tumor cells in vitro. Such vaccines should also be capable of causing an immune response that leads to an improved clinical outcome (e.g., more frequent remissions, complete or partial or longer disease-free survival) in vaccinated patients as compared to non-vaccinated patients. In general, for pharmaceutical compositions and vaccines comprising one or more polypeptides, the amount of each polypeptide present in a dose ranges from about 25 μg to 5 mg per kg of host. Suitable dose sizes will vary with the size of the patient, but will typically range from about 0.1 mL to about 5 mL.

[1981] In general, an appropriate dosage and treatment regimen provides the active compound(s) in an amount sufficient to provide therapeutic and/or prophylactic benefit. Such a response can be monitored by establishing an improved clinical outcome (e.g., more frequent remissions, complete or partial, or longer disease-free survival) in treated patients as compared to non-treated patients. Increases in preexisting immune responses to a tumor protein generally correlate with an improved clinical outcome. Such immune responses may generally be evaluated using standard proliferation, cytotoxicity or cytokine assays, which may be performed using samples obtained from a patient before and after treatment.

[1982] Cancer Detection and Diagnostic Compositions, Methods and Kits

[1983] In general, a cancer may be detected in a patient based on the presence of one or more kidney tumor proteins and/or polynucleotides encoding such proteins in a biological sample (for example, blood, sera, sputum urine and/or tumor biopsies) obtained from the patient. In other words, such proteins may be used as markers to indicate the presence or absence of a cancer such as kidney cancer. In addition, such proteins may be useful for the detection of other cancers. The binding agents provided herein generally permit detection of the level of antigen that binds to the agent in the biological sample.

[1984] Polynucleotide primers and probes may be used to detect the level of mRNA encoding a tumor protein, which is also indicative of the presence or absence of a cancer. In general, a tumor sequence should be present at a level that is at least two-fold, preferably three-fold, and more preferably five-fold or higher in tumor tissue than in normal tissue of the same type from which the tumor arose. Expression levels of a particular tumor sequence in tissue types different from that in which the tumor arose are irrelevant in certain diagnostic embodiments since the presence of tumor cells can be confirmed by observation of predetermined differential expression levels, e.g., 2-fold, 5-fold, etc, in tumor tissue to expression levels in normal tissue of the same type.

[1985] Other differential expression patterns can be utilized advantageously for diagnostic purposes. For example, in one aspect of the invention, overexpression of a tumor sequence in tumor tissue and normal tissue of the same type, but not in other normal tissue types, e.g. PBMCs, can be exploited diagnostically. In this case, the presence of metastatic tumor cells, for example in a sample taken from the circulation or some other tissue site different from that in which the tumor arose, can be identified and/or confirmed by detecting expression of the tumor sequence in the sample, for example using RT-PCR analysis. In many instances, it will be desired to enrich for tumor cells in the sample of interest, e.g., PBMCs, using cell capture or other like techniques.

[1986] There are a variety of assay formats known to those of ordinary skill in the art for using a binding agent to detect polypeptide markers in a sample. See, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988. In general, the presence or absence of a cancer in a patient may be determined by (a) contacting a biological sample obtained from a patient with a binding agent; (b) detecting in the sample a level of polypeptide that binds to the binding agent; and (c) comparing the level of polypeptide with a predetermined cut-off value.

[1987] In a preferred embodiment, the assay involves the use of binding agent immobilized on a solid support to bind to and remove the polypeptide from the remainder of the sample. The bound polypeptide may then be detected using a detection reagent that contains a reporter group and specifically binds to the binding agent/polypeptide complex. Such detection reagents may comprise, for example, a binding agent that specifically binds to the polypeptide or an antibody or other agent that specifically binds to the binding agent, such as an anti-immunoglobulin, protein G, protein A or a lectin. Alternatively, a competitive assay may be utilized, in which a polypeptide is labeled with a reporter group and allowed to bind to the immobilized binding agent after incubation of the binding agent with the sample. The extent to which components of the sample inhibit the binding of the labeled polypeptide to the binding agent is indicative of the reactivity of the sample with the immobilized binding agent. Suitable polypeptides for use within such assays include full length kidney tumor proteins and polypeptide portions thereof to which the binding agent binds, as described above.

[1988] The solid support may be any material known to those of ordinary skill in the art to which the tumor protein may be attached. For example, the solid support may be a test well in a microtiter plate or a nitrocellulose or other suitable membrane. Alternatively, the support may be a bead or disc, such as glass, fiberglass, latex or a plastic material such as polystyrene or polyvinylchloride. The support may also be a magnetic particle or a fiber optic sensor, such as those disclosed, for example, in U.S. Pat. No. 5,359,681. The binding agent may be immobilized on the solid support using a variety of techniques known to those of skill in the art, which are amply described in the patent and scientific literature. In the context of the present invention, the term “immobilization” refers to both noncovalent association, such as adsorption, and covalent attachment (which may be a direct linkage between the agent and functional groups on the support or may be a linkage by way of a cross-linking agent). Immobilization by adsorption to a well in a microtiter plate or to a membrane is preferred. In such cases, adsorption may be achieved by contacting the binding agent, in a suitable buffer, with the solid support for a suitable amount of time. The contact time varies with temperature, but is typically between about 1 hour and about 1 day. In general, contacting a well of a plastic microtiter plate (such as polystyrene or polyvinylchloride) with an amount of binding agent ranging from about 10 ng to about 10 μg, and preferably about 100 ng to about 1 μg, is sufficient to immobilize an adequate amount of binding agent.

[1989] Covalent attachment of binding agent to a solid support may generally be achieved by first reacting the support with a bifunctional reagent that will react with both the support and a functional group, such as a hydroxyl or amino group, on the binding agent. For example, the binding agent may be covalently attached to supports having an appropriate polymer coating using benzoquinone or by condensation of an aldehyde group on the support with an amine and an active hydrogen on the binding partner (see, e.g., Pierce Immunotechnology Catalog and Handbook, 1991, at A12-A13).

[1990] In certain embodiments, the assay is a two-antibody sandwich assay. This assay may be performed by first contacting an antibody that has been immobilized on a solid support, commonly the well of a microtiter plate, with the sample, such that polypeptides within the sample are allowed to bind to the immobilized antibody. Unbound sample is then removed from the immobilized polypeptide-antibody complexes and a detection reagent (preferably a second antibody capable of binding to a different site on the polypeptide) containing a reporter group is added. The amount of detection reagent that remains bound to the solid support is then determined using a method appropriate for the specific reporter group.

[1991] More specifically, once the antibody is immobilized on the support as described above, the remaining protein binding sites on the support are typically blocked. Any suitable blocking agent known to those of ordinary skill in the art, such as bovine serum albumin or Tween™ (Sigma Chemical Co., St. Louis, Mo.). The immobilized antibody is then incubated with the sample, and polypeptide is allowed to bind to the antibody. The sample may be diluted with a suitable diluent, such as phosphate-buffered saline (PBS) prior to incubation. In general, an appropriate contact time (i.e., incubation time) is a period of time that is sufficient to detect the presence of polypeptide within a sample obtained from an individual with kidney least about 95% of that achieved at equilibrium between bound and unbound polypeptide. Those of ordinary skill in the art will recognize that the time necessary to achieve equilibrium may be readily determined by assaying the level of binding that occurs over a period of time. At room temperature, an incubation time of about 30 minutes is generally sufficient.

[1992] Unbound sample may then be removed by washing the solid support with an appropriate buffer, such as PBS containing 0.1% Tween 20™. The second antibody, which contains a reporter group, may then be added to the solid support. Preferred reporter groups include those groups recited above.

[1993] The detection reagent is then incubated with the immobilized antibody-polypeptide complex for an amount of time sufficient to detect the bound polypeptide. An appropriate amount of time may generally be determined by assaying the level of binding that occurs over a period of time. Unbound detection reagent is then removed and bound detection reagent is detected using the reporter group. The method employed for detecting the reporter group depends upon the nature of the reporter group. For radioactive groups, scintillation counting or autoradiographic methods are generally appropriate. Spectroscopic methods may be used to detect dyes, luminescent groups and fluorescent groups. Biotin may be detected using avidin, coupled to a different reporter group (commonly a radioactive or fluorescent group or an enzyme). Enzyme reporter groups may generally be detected by the addition of substrate (generally for a specific period of time), followed by spectroscopic or other analysis of the reaction products.

[1994] To determine the presence or absence of a cancer, such as kidney cancer, the signal detected from the reporter group that remains bound to the solid support is generally compared to a signal that corresponds to a predetermined cut-off value. In one preferred embodiment, the cut-off value for the detection of a cancer is the average mean signal obtained when the immobilized antibody is incubated with samples from patients without the cancer. In general, a sample generating a signal that is three standard deviations above the predetermined cut-off value is considered positive for the cancer. In an alternate preferred embodiment, the cut-off value is determined using a Receiver Operator Curve, according to the method of Sackett et al., Clinical Epidemiology: A Basic Science for Clinical Medicine, Little Brown and Co., 1985, p. 106-7. Briefly, in this embodiment, the cut-off value may be determined from a plot of pairs of true positive rates (i.e., sensitivity) and false positive rates (100%-specificity) that correspond to each possible cut-off value for the diagnostic test result. The cut-off value on the plot that is the closest to the upper left-hand corner (i.e., the value that encloses the largest area) is the most accurate cut-off value, and a sample generating a signal that is higher than the cut-off value determined by this method may be considered positive. Alternatively, the cut-off value may be shifted to the left along the plot, to minimize the false positive rate, or to the right, to minimize the false negative rate. In general, a sample generating a signal that is higher than the cut-off value determined by this method is considered positive for a cancer.

[1995] In a related embodiment, the assay is performed in a flow-through or strip test format, wherein the binding agent is immobilized on a membrane, such as nitrocellulose. In the flow-through test, polypeptides within the sample bind to the immobilized binding agent as the sample passes through the membrane. A second, labeled binding agent then binds to the binding agent-polypeptide complex as a solution containing the second binding agent flows through the membrane. The detection of bound second binding agent may then be performed as described above. In the strip test format, one end of the membrane to which binding agent is bound is immersed in a solution containing the sample. The sample migrates along the membrane through a region containing second binding agent and to the area of immobilized binding agent. Concentration of second binding agent at the area of immobilized antibody indicates the presence of a cancer. Typically, the concentration of second binding agent at that site generates a pattern, such as a line, that can be read visually. The absence of such a pattern indicates a negative result. In general, the amount of binding agent immobilized on the membrane is selected to generate a visually discernible pattern when the biological sample contains a level of polypeptide that would be sufficient to generate a positive signal in the two-antibody sandwich assay, in the format discussed above. Preferred binding agents for use in such assays are antibodies and antigen-binding fragments thereof. Preferably, the amount of antibody immobilized on the membrane ranges from about 25 ng to about 1 μg, 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.

[1996] Of course, numerous other assay protocols exist that are suitable for use with the tumor proteins or binding agents of the present invention. The above descriptions are intended to be exemplary only. For example, it will be apparent to those of ordinary skill in the art that the above protocols may be readily modified to use tumor polypeptides to detect antibodies that bind to such polypeptides in a biological sample. The detection of such tumor protein specific antibodies may correlate with the presence of a cancer.

[1997] A cancer may also, or alternatively, be detected based on the presence of T cells that specifically react with a tumor protein in a biological sample. Within certain methods, a biological sample comprising CD4+ and/or CD8+ T cells isolated from a patient is incubated with a tumor polypeptide, a polynucleotide encoding such a polypeptide and/or an APC that expresses at least an immunogenic portion of such a polypeptide, and the presence or absence of specific activation of the T cells is detected. Suitable biological samples include, but are not limited to, isolated T cells. For example, T cells may be isolated from a patient by routine techniques (such as by Ficoll/Hypaque density gradient centrifugation of peripheral blood lymphocytes). T cells may be incubated in vitro for 2-9 days (typically 4 days) at 37° C. with polypeptide (e.g., 5-25 μg/ml). It may be desirable to incubate another aliquot of a T cell sample in the absence of tumor polypeptide to serve as a control. For CD4+ T cells, activation is preferably detected by evaluating proliferation of the T cells. For CD8+ T cells, activation is preferably detected by evaluating cytolytic activity. A level of proliferation that is at least two fold greater and/or a level of cytolytic activity that is at least 20% greater than in disease-free patients indicates the presence of a cancer in the patient.

[1998] As noted above, a cancer may also, or alternatively, be detected based on the level of mRNA encoding a tumor protein in a biological sample. For example, at least two oligonucleotide primers may be employed in a polymerase chain reaction (PCR) based assay to amplify a portion of a tumor cDNA derived from a biological sample, wherein at least one of the oligonucleotide primers is specific for (i.e., hybridizes to) a polynucleotide encoding the tumor protein. The amplified cDNA is then separated and detected using techniques well known in the art, such as gel electrophoresis.

[1999] Similarly, oligonucleotide probes that specifically hybridize to a polynucleotide encoding a tumor protein may be used in a hybridization assay to detect the presence of polynucleotide encoding the tumor protein in a biological sample.

[2000] To permit hybridization under assay conditions, oligonucleotide primers and probes should comprise an oligonucleotide sequence that has at least about 60%, preferably at least about 75% and more preferably at least about 90%, identity to a portion of a polynucleotide encoding a tumor protein of the invention that is at least 10 nucleotides, and preferably at least 20 nucleotides, in length. Preferably, oligonucleotide primers and/or probes hybridize to a polynucleotide encoding a polypeptide described herein under moderately stringent conditions, as defined above. Oligonucleotide primers and/or probes which may be usefully employed in the diagnostic methods described herein preferably are at least 10-40 nucleotides in length. In a preferred embodiment, the oligonucleotide primers comprise at least 10 contiguous nucleotides, more preferably at least 15 contiguous nucleotides, of a DNA molecule having a sequence as disclosed herein. Techniques for both PCR based assays and hybridization assays are well known in the art (see, for example, Mullis et al., Cold Spring Harbor Symp. Quant Biol., 51:263, 1987; Erlich ed., PCR Technology, Stockton Press, NY, 1989).

[2001] One preferred assay employs RT-PCR, in which PCR is applied in conjunction with reverse transcription. Typically, RNA is extracted from a biological sample, such as biopsy tissue, and is reverse transcribed to produce cDNA molecules. PCR amplification using at least one specific primer generates a cDNA molecule, which may be separated and visualized using, for example, gel electrophoresis. Amplification may be performed on biological samples taken from a test patient and from an individual who is not afflicted with a cancer. The amplification reaction may be performed on several dilutions of cDNA spanning two orders of magnitude. A two-fold or greater increase in expression in several dilutions of the test patient sample as compared to the same dilutions of the non-cancerous sample is typically considered positive.

[2002] In another aspect of the present invention, cell capture technologies may be used in conjunction, with, for example, real-time PCR to provide a more sensitive tool for detection of metastatic cells expressing kidney tumor antigens. Detection of kidney cancer cells in biological samples, e.g., bone marrow samples, peripheral blood, and small needle aspiration samples is desirable for diagnosis and prognosis in kidney cancer patients.

[2003] Immunomagnetic beads coated with specific monoclonal antibodies to surface cell markers, or tetrameric antibody complexes, may be used to first enrich or positively select cancer cells in a sample. Various commercially available kits may be used, including Dynabeads® Epithelial Enrich (Dynal Biotech, Oslo, Norway), StemSep™ (StemCell Technologies, Inc., Vancouver, BC), and RosetteSep (StemCell Technologies). A skilled artisan will recognize that other methodologies and kits may also be used to enrich or positively select desired cell populations. Dynabeads® Epithelial Enrich contains magnetic beads coated with mAbs specific for two glycoprotein membrane antigens expressed on normal and neoplastic epithelial tissues. The coated beads may be added to a sample and the sample then applied to a magnet, thereby capturing the cells bound to the beads. The unwanted cells are washed away and the magnetically isolated cells eluted from the beads and used in further analyses.

[2004] RosetteSep can be used to enrich cells directly from a blood sample and consists of a cocktail of tetrameric antibodies that targets a variety of unwanted cells and crosslinks them to glycophorin A on red blood cells (RBC) present in the sample, forming rosettes. When centrifuged over Ficoll, targeted cells pellet along with the free RBC. The combination of antibodies in the depletion cocktail determines which cells will be removed and consequently which cells will be recovered. Antibodies that are available include, but are not limited to: CD2, CD3, CD4, CD5, CD8, CD10, CD11b, CD14, CD15, CD16, CD19, CD20, CD24, CD25, CD29, CD33, CD34, CD36, CD38, CD41, CD45, CD45RA, CD45RO, CD56, CD66B, CD66e, HLA-DR, IgE, and TCRαβ.

[2005] Additionally, it is contemplated in the present invention that mAbs specific for kidney tumor antigens can be generated and used in a similar manner. For example, mAbs that bind to tumor-specific cell surface antigens may be conjugated to magnetic beads, or formulated in a tetrameric antibody complex, and used to enrich or positively select metastatic kidney tumor cells from a sample. Once a sample is enriched or positively selected, cells may be lysed and RNA isolated. RNA may then be subjected to RT-PCR analysis using kidney tumor-specific primers in a real-time PCR assay as described herein. One skilled in the art will recognize that enriched or selected populations of cells may be analyzed by other methods (e.g. in situ hybridization or flow cytometry).

[2006] In another embodiment, the compositions described herein may be used as markers for the progression of cancer. In this embodiment, assays as described above for the diagnosis of a cancer may be performed over time, and the change in the level of reactive polypeptide(s) or polynucleotide(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, a cancer is progressing in those patients in whom the level of polypeptide or polynucleotide detected increases over time. In contrast, the cancer is not progressing when the level of reactive polypeptide or polynucleotide either remains constant or decreases with time.

[2007] Certain in vivo diagnostic assays may be performed directly on a tumor. One such assay involves contacting tumor cells with a binding agent. The bound binding agent may then be detected directly or indirectly via a reporter group. Such binding agents may also be used in histological applications. Alternatively, polynucleotide probes may be used within such applications.

[2008] As noted above, to improve sensitivity, multiple tumor protein markers may be assayed within a given sample. It will be apparent that binding agents specific for different proteins provided herein may be combined within a single assay. Further, multiple primers or probes may be used concurrently. The selection of tumor protein markers may be based on routine experiments to determine combinations that results in optimal sensitivity. In addition, or alternatively, assays for tumor proteins provided herein may be combined with assays for other known tumor antigens.

[2009] The present invention further provides kits for use within any of the above diagnostic methods. Such kits typically comprise two or more components necessary for performing a diagnostic assay. Components may be compounds, reagents, containers and/or equipment. For example, one container within a kit may contain a monoclonal antibody or fragment thereof that specifically binds to a tumor protein. Such antibodies or fragments may be provided attached to a support material, as described above. One or more additional containers may enclose elements, such as reagents or buffers, to be used in the assay. Such kits may also, or alternatively, contain a detection reagent as described above that contains a reporter group suitable for direct or indirect detection of antibody binding.

[2010] Alternatively, a kit may be designed to detect the level of mRNA encoding a tumor protein in a biological sample. Such kits generally comprise at least one oligonucleotide probe or primer, as described above, that hybridizes to a polynucleotide encoding a tumor protein. Such an oligonucleotide may be used, for example, within a PCR or hybridization assay. Additional components that may be present within such kits include a second oligonucleotide and/or a diagnostic reagent or container to facilitate the detection of a polynucleotide encoding a tumor protein.

[2011] The following Examples are offered by way of illustration and not by way of limitation.

EXAMPLES

Example 1

Identification of Kidney Tumor Protein cDNAs

[2012] This Example illustrates the identification of cDNA molecules encoding kidney tumor proteins.

[2013] A PCR based subtraction method, as developed by Clontech (Palo Alto, Calif.), was utilized to create a cDNA library enriched for Kidney tumor-specific antigens. To construct this library (KAM1), transcripts from a pool of three primary kidney tumors (Tester) were subtracted with a set of transcripts from normal tissues (Driver) consisting of brain, pancreas, bone marrow, lung, skeletal muscle, heart, kidney, liver, and small intestine. The subtraction was executed according to Clontech recommendations with the following changes: 1) cDNA was restricted with a mixture of enzymes, including Mscl, PvuII, Stul, and Dral, instead of the Clontech recommended single enzyme, Rsal; 2) The ratio of driver to tester cDNA was increased to 76:1 in the hybridization steps to give a more stringent subtraction. To analyze the efficiency of the subtraction, the housekeeping gene actin was PCR amplified from dilutions of subtracted as well as unsubtracted PCR samples. Following PCR amplification, the cDNAs were cloned into the pCR2.1-TOPO plasmid (Invitrogen, Carlsbad, Calif.). The complexity and redundancy of the library was characterized by sequencing 192 clones. Of these, 157 had inserts that could be sequenced and analyzed by comparing to public databases (Genbank, GenSeq, huEST). These analyses suggest that the library is enriched for genes overexpressed in kidney tumor samples. Disclosed herein are 157 sequences derived from the KAM1 subtracted library. Those sequences showing some degree of similarity to known sequences in Genbank are shown in Table 2. Those cDNAs that showed no significant similiarity to any known sequences are listed in Table 3.

[2014] An additional 1,824 clones were screened, yielding 1,535 sequences, disclosed in SEQ ID NOs:158-1692, as set forth in the section entitled “Brief Description of the Sequence Identifiers”.

TABLE 2
GENBANK SEARCH RESULTS FOR cDNA MOLECULES
ENCODING KIDNEY TUMOR PROTEINS
SEQ.	Clone
ID. NO:	Identifier	Description
1	60668	camptothecin resistant clone CEM/C2 DNA
		topoisomerase I
3	60670	Nuclear prelamin A recognition factor (NARF)
4	60671	AML1 mRNA for AML1c protein (acute myeloid
		leukemia alternatively spliced product)
5	60672	Pendred syndrome (PDS)
7	60674	12p13.3 PAC RPCI1-96H9
8	60675	mRNA for RTP
9	60676	Clone HQ0518 PRO0518
10	60678	chr. 16 clone RP11-311O11
12	60680	integrin, alpha 6 (ITGA6)
13	60681	histone acetyltransferase (GCN5)
14	60682	Ku (p70/p80) subunit mRNA
16	60684	mRNA for KIAA0576 protein, partial cds
17	60685	ribosomal protein L9 (RPL9)
18	60686	fatty acid binding protein 7, brain (FABP7) mRNA
20	60688	clone 25077 mRNA seq
21	60689	cystatin B (stefin B) (CSTB)
22	60690	cytoplasmic antiproteinase = 38 kda intracellular
		serine proteinase inhibitor
23	60691	chr. 16 BAC clone CIT987SK-44M2
24	60692	heme oxygenase
25	60693	nickel-specific induction protein (Cap43)
26	60694	immunoglobulin lambda light chain gene
27	60695	chr. 22 Cosmid Clone 46a9 In DGCR Region
28	60697	H. sapiens ERF-1 mRNA 3′ end.
29	60698	cathepsin B mRNA
30	60699	guanylate binding protein isoform II (GBP-2)
		mRNA
33	60703	vacuolor sorting protein 29 (VPS29) mRNA,
		complete cds
34	60704	interferon-inducible mRNA (cDNA 6-26)
35	60705	BAC clone CTA-293F17 from 7p15-p21
36	60706	12p13.3 PAC RPCI1-96H9
37	60707	angiopoietin 1 (ANGPT1)
38	60708	H. sapiens (HepG2) LAL mRNA for lysosomal acid
		lipase
39	60709	CD9 antigen (p24) (CD9)
40	60711	protein tyrosine kinase 9 (PTK9) mRNA.
41	60712	calnexin
42	60715	DNA seq. from clone RP4-620E11 on chr. 20q11.2-
		12
43	60716	mRNA for lipocortin II
45	60718	proteasome subunit LMP7 (allele LMP7C) mRNA
46	60719	MHC class I region ORF
47	60720	aldehyde reductase mRNA
48	60721	DMRT2/terra-like protein (DMRT2) mRNA,
		alternatively spliced.
50	60723	insulin-like growth factor-binding protein-3 gene,
		clone HL1006d.
51	60725	DNA seq. from clone RP5-841K13 on chr. 20
52	60727	H. sapiens OZF
53	60729	a disintegrin and metalloproteinase domain 9
		(meltringamma) (ADAM9)
54	60730	vascular endothelial growth factor mRNA
55	60731	cDNA FLJ20343 fis, clone HEP13649.
56	60732	NADH dehydrogenase subunit 2 (ND2) gene
57	60733	HSPC147 mRNA
58	60734	complement C1q A chain precursor
59	60735	mRNA for sterol-C5-desaturase
60	60736	mRNA for docking protein BRDG1
61	60738	HFB30 mRNA
62	60739	sirtuin type 1 (SIRT1) mRNA
63	60742	serologically defined colon cancer antigen 1
		(SDCCAG1)
64	60743	chr. 17, clone HCIT48C15
65	60744	cDNA FLJ10684 fis, clone NT2RP3000220
66	60745	hnRNP H
67	60747	mammary tumor-associated protein INT6
68	60749	Rho GTPase activating protein 6 (ARHGAP6),
		transcript variant 1
69	60750	clone 24448 unknown mRNA
70	60751	calpastatin mRNA, partial cds, short 3′UTR
71	60752	endocytic receptor (macrophage mannose receptor
		fam.) (KIAA0709)
72	60753	mRNA; cDNA DKFZp761P019 (from clone
		DKFZp761P019).
74	60757	thymosin beta-4 mRNA
75	60758	mRNA for KIAA1252 protein
76	60759	H. sapiens SOD-2 gene for manganese superoxide
		dismutase
77	60760	HFB30 mRNA
78	60762	HTGN29
79	60763	R. norvegicus phosphatidylinositol 5-phosphate 4-
		kinase gamma
80	63967	uncharacterized bone marrow protein BM042
81	63968	nickel-specific induction protein (Cap43)
82	63969	Hu DNA seq. from clone RP11-481A22 on chr. 13
83	63970	mRNA for vimentin
84	63971	MEN1 (Multiple endocrine neoplasia type 1) region
		clone epsilon/beta
85	63972	Mus musculus putative transcription factor ALF-4
86	63973	H. sapiens clone RP11-2I8
87	63974	prostatic binding protein (PBP)
90	63978	calcium-binding transporter
91	63979	mRNA for high mobility group-1 protein (HMG-1)
92	63981	78 kdalton glucose-regulated protein (GRP78) gene
93	63982	brain my047 protein mRNA
94	63983	annexin A4 (ANXA4)
95	63984	vascular endothelial growth factor (VEGF) mRNA,
		3′UTR
96	63985	transaldolase-related protein gene, exons 3-8
98	63987	26-kDa cell surface protein TAPA-1 mRNA
100	63991	osteopontin mRNA
101	63994	beta-2 microglobulin gene
102	63995	PTD010 protein (PTD010) (from pituitary tumor)
103	63996	KIAA1007 protein (KIAA1007)
104	63997	mRNA for dTDP-4-keto-6-deoxy-D-glucose 4-
		reductase
105	63999	M. musculus Rel domain-containing transcription
		factor NFAT5
106	64000	HLA-B gene (HLA-B*0801 allele)
107	64001	UDP-glucose dehydrogenase (UGDH)
109	64005	major histocompatibility class I HLA-Cw2.2 heavy
		chain
110	64006	BAC clone CTA-293F17 from 7p15-p21
111	64007	mRNA for TM7XN1 protein.
113	64009	DNA for osteopontin
114	64010	mRNA for DEC1
115	64011	MEN1 region clone epsilon/beta mRNA, 3′
		fragment.
116	64012	KIAA0247 gene product (KIAA0247)
117	64013	splicing factor (CC1.3)
118	64016	lysosomal-associated protein transmembrane 4
		alpha(MBNT)
120	64019	cDNA: FLJ22952 fis, clone KAT09742
121	64020	cDNA DKFZp434M229 (from clone
		DKFZp434M229)
122	64022	parathyroid hormone-related protein
123	64023	cDNA: FLJ23027 fis, clone LNG01826
124	64025	KIT protein and alternatively spliced KIT protein
		(KIT) gene
125	64028	putative endothelin receptor type B-like protein
126	64029	SC35-interacting protein 1 (SRRP129)
127	64030	12 BAC RP11-427C3
128	64031	angiopoietin-related protein mRNA
129	64032	calcyclin binding protein (CACYBP)
130	64033	clone 24448 unknown mRNA
131	64034	11p14.3 PAC clone pDJ939m16
132	64035	PTB domain adaptor protein CED-6
133	64036	mRNA for KIAA1380 protein
135	64038	H. sapiens SPR-2 mRNA for GT box binding
		protein
136	64039	GL004 protein [novel gene fr. liver non-tumor-
		tissue; unpub.]
137	64040	KIAA0141 gene product (KIAA0141)
138	64041	CD9 antigen mRNA
139	64042	CGI-134 protein (LOC51023), mRNA.
140	64043	CGI-134 protein (LOC51023), mRNA.
141	64044	chr. 17, clone hRPK.209_D_14
142	64045	H. sapiens polyA site DNA.
143	64046	thymosin beta-4 mRNA
144	64047	nicotinamide N-methyltransferase (NNMT)
145	64048	M. musculus cytoplasmic dynein intermediate chain
		2 (Dncic2)
146	64049	mRNA for Sid1669p
147	64050	putative N-acetyltransferase CML1 (CML1)
148	64052	cDNA: FLJ21587 fis, clone COL06946.
149	64053	KIT protein and alternatively spliced KIT protein
		(KIT) gene
150	64054	H. sapiens interferon gamma receptor 1 gene,
		microsatelliteseq.
151	64055	H. sapiens alpha NAC
152	64056	mRNA for KIAA0662 protein
153	64058	mRNA for RTP
155	64060	fibrillin mRNA
156	64061	mRNA for LDL-receptor related protein
157	64062	BAC clone CTA-300C3 from 7q31.2

[2015]

TABLE 3
cDNA MOLECULES ENCODING KIDNEY TUMOR PROTEINS
SHOWING NO SIGNIFICANT SIMILARITY
TO KNOWN SEQUENCES
SEQ. ID. Clone
NO:      Identifier
2        60669
6        60673
11       60679
15       60683
19       60687
31       60700
32       60702
44       60717
49       60722
73       60756
88       63975
89       63976
97       63986
99       63990
108      64002
112      64008
119      64018
134      64037
154      64059

Example 2

Analysis of Expression of Kidney Tumor cDNAS Using Microarray Technology

[2016] In additional studies, kidney tumor- and tissue-specific cDNAs were identified and evaluated for overexpression in specific tumor tissues by microarray analysis. Using this approach, cDNA sequences were PCR amplified and their mRNA expression profiles in tumor and normal tissues were examined using cDNA microarray technology essentially as described (Shena, M. et al., 1995 Science 270:467-70). In brief, the clones were arrayed onto glass slides as multiple replicas, with each location corresponding to a unique cDNA clone (as many as 5500 clones can be arrayed on a single slide, or chip). Each chip was hybridized with a pair of cDNA probes that were fluorescence-labeled with Cy3 and Cy5, respectively. Typically, 1 μg of polyA+ RNA was used to generate each cDNA probe. After hybridization, the chips were scanned and the fluorescence intensity recorded for both Cy3 and Cy5 channels. There were multiple built-in quality control steps. First, the probe quality was monitored using a panel of ubiquitously expressed genes. Secondly, the control plate also included yeast DNA fragments of which complementary RNA may be spiked into the probe synthesis for measuring the quality of the probe and the sensitivity of the analysis. Currently, the technology offers a sensitivity of 1 in 100,000 copies of mRNA. Finally, the reproducibility of this technology was ensured by including duplicated control cDNA elements at different locations.

[2017] A total of 1824 clones from the KAM1 subtracted cDNA library described in Example 1, were arrayed. The arrays were probed with 32 probe pairs (normal tissues labeled with Cy5 and tumor-specific probes labeled with Cy3). Analysis consisted of determining the ratio of the mean hybridization signal for a particular element (cDNA) using the two sets of probes. The ratio represents a reflection of the over- or under-expression of the element (cDNA) within a probe population. Probe groups were set up to identify cDNAs with high differential expression in probe group#1 as compared to probe group#2. Probe group#1 consisted of 12 kidney tumors, whereas probe group#2 consisted of 31 normal tissues, including normal kidney tissue. A threshold (fold-overexpression in probe group#1) was set at 2.0.

[2018] cDNAs were grouped according to their value for mean signal 1 (probe group#1; kidney tumor) and mean signal 2 (probe group#2; normal tissues including kidney). cDNAs which had the potential for no normal tissue expression (mean 2<0.1) were grouped into “high” (mean 1>2.0), “medium” (mean 1=0.1-0.2) and “low” (mean 1<0.1) expression candidate groups. cDNAs that had a mean 2 of 0.1-0.2 were considered as having a potential for low normal tissue expression and elements that had a mean signal 2>0.2 were considered as candidates with a potential for higher normal tissue expression. Based on this initial analysis and visual analysis of the associated microArray data, elements with “high” (mean 1>2.0), “medium” (mean 10.1-0.2) and a “potential for low normal expression” (mean 2 of 0.1-0.2) were considered further as being candidates exhibiting overexpression in kidney tumor (and normal tissue).

[2019] The cDNAs identified as described above as being overexpressed in kidney tumors as compared to normal tissue were then sequenced, and used as a query in a BLAST search of public databases in order to identify extended sequence and to confirm their identity. The sequences are set forth in SEQ ID NOs:1693-1843. Table 4 summarizes the microarray and GenBank search results for those sequences that showed some degree of similarity to sequences in the public databases. Those sequences that showed no significant similarity to sequences in the GenBank database are listed in Table 5 (SEQ ID NOs:1836-1843 have hits in the huEST database). Full-length sequence from GenBank is presented for numerous cDNAs in SEQ ID NOs:1693-1793.

TABLE 4
cDNAs ENCODING KIDNEY TUMOR PROTEINS THAT SHOWED
SOME DEGREE OF SIMILARITY
TO SEQUENCES IN PUBLIC DATABASES
SEQ ID
NO.	Ratio	Clone	Candidate	GenBank ID	Description
1693	12.5	KKAM202 G1	K1549P	2645202	Fatty acid binding protein
					(FABP7)
11694	4.17	SSAM113 D8	K1554P	398163	Insulin-like growth factor
					binding protein-3
1695	4.17	KAM207 D12	K1553P	7327887	Renal cell carcinoma
					associated antigen G250
1696	3.32	KAM217 E6		533516	MAGE-4b antigen (MAGE4b)
1697	3.01	SAM121 C3		30125	Type I interstitial collagenase
1698	2.98	LLAM27 D7		181067	C-reactive protein gene
1699	2.59	SAM113 G7		182203	Estrogen receptor
1700	2.31	SAM115 F7		3860076	GW112 protein (GW112)
1701	2.3	KAM216 A10		12620131	Renal sodium/sulfate
					cotransporter
1702	15.58	KAM202 C11	K1548P	14721305	ESM-1, endothelial cell-
					specific molecule 1
1703	6.99	SAM114 H4		12653344	Junction plakoglobin
1704	5.44	KAM210 C2	K1619P	3719220	Vascular endothelial growth
					factor
1705	5.11	SAM117 E10		13027804	Matrix metalloproteinase 7
					(matrilysin, uterine), MMP7
1706	4.86	KAM218 D3	K1620P	1060889	Annexin IV (carbohydrate-
					binding protein p33/41)
1707	4.02	KAM208 C12	K1587P	187558	MET proto-oncogene
1708	3.76	KAM202 B11		4507466	Transforming growth factor,
					beta-induced, 68kD (TGFBI)
1709	3.35	KAM202 E8		2138313	Lysyl hydroxylase isoform 2
					(PLOD2)
1710	3.31	KAM203 G5		2463627	Monocarboxylate transporter
					(MCT) putative mRNA
1711	3.29	KAM206 D6		3600027	Dysferlin
1712	3.29	KAM218 D7		3426297	HIC protein isoform p40 and
					HIC protein isform p32
1713	3.19	KAM209 H9	K1588P	12583668	DEC2, bHLH protein
1714	2.93	KAM217 D2		1048988	CD9 antigen
1715	2.86	KAM208 F8		4689259	Sporting nexin 10 (SNX10)
1716	2.8	KAM202 B7		189852	Platelet-type
					Phosophofructokinase
1717	2.75	KAM212 A9		13325286	Enolase 1, (alpha)
1718	2.75	KAM218 G1		530822	Epidermal growth factor
					receptor kinase substrate
					(Eps8)
1719	2.73	KAM217 D7		188397	MHC class II HLA-DR2-Dw12
					mRNA DQw1-beta
1720	2.7	KAM218 C10		2338289	Proline-rich Gla protein 1
					(PRGP1)
1721	2.6	KAM201 C7		7705717	CGI-26 protein (LOC51071)
1722	2.58	SAM131 E12		187605	MHC class I HLA-A2 gene
1723	2.56	KAM214 B10		7019382	Fibronectin leucine rich
					transmembrane protein 3
					(FLRT3)
1724	2.52	LLAM25 B11		1907392	Proneurotensin/
					proneuromedin N
1725	2.52	LLAM29 E3		3550342	Cellular repressor of E1A-
					stimulated genes, CREG
1726	2.52	SAM116 B3		6563215	Ribosomal protein L13
1727	2.51	KAM218 A9		180676	C-type natiuretic peptide
1728	2.51	KAM208 B7		4588525	Nuclear chloride channel
					(NCC27)
1729	2.5	LLAM28 B4		2522321	PTPL1-associated RhoGAP
1730	2.49	KAM207 C12		4503916	Growth arrest specific 11
					(GAS11)
1731	2.48	LLAM25 B6		3493208	Aldo-keto reductase
1732	2.48	LLAM25 B1		14738930	Protease, serine, 11 (IGF
					binding) (PRSS11)
1733	2.47	KAM211 H5		1808577	Proteasome subunit p112
1734	2.46	LLAM29 H3		2181921	FUS gene, intron 7
1735	2.46	LLAM25 A8		6523802	Adrenal gland protein AD-005
					Mrna
1736	2.41	KAM217 H11		7542722	DHHC1 protein
1737	2.39	SAM114 A8		12737025	Transmembrane 4
					superfamily member 3
1738	2.34	SAM129 B11		12214174	ORF1-FL49, putative nuclear
					protein
1739	2.32	KAM215 H1		12653620	HIRA-interacting protein 3
1740	2.28	KAM207 D7		5731112	Translocon-associated
					protein alpha subunit
1741	2.27	KAM217 D3		12056961	Calpastatin
1742	2.27	KAM215 G3		4106060	CCR4-associated factor 1
					(POP2)
1743	2.24	KAM202 H11		31967	Histone H1, H1.2 gene
1744	2.23	KAM209 C5		12005668	HT028 Mrna
1745	2.22	KAM205 D7		3044063	PHD finger protein 2 (PHF2)
1746	2.21	KAM211 G11		7596916	Down syndrome candidate
					region protein (DSCR1)
1747	2.19	KAM200 D7		1654350	Hermansky-Pudlak syndrome
					protein (HPS)
1748	2.18	KAM209 F3		3513452	C2H2 zinc finger protein
					PLAGL1 (PLAGL1)
1749	2.18	KAM212 B11		13358172	Dectin-1, putative
					transmembrane protein
1750	2.18	KAM212 D10		4929634	CGI-83 protein
1751	2.15	KAM200 F11		13430284	C1orf13
1752	2.14	KAM217 H7		4826845	myosin VI (MYO6)
1753	2.12	SAM120 G5		179771	Carbonic anhydrase II
1754	2.09	SAM129 G1		12804950	Calcium-binding protein
					(intestinal-related)
1755	2.09	KAM205 A12		4557806	Ocular albinism I (Nettleship-
					Falls) (OA1)
1756	2.09	KAM202 D8		13112002	N-myc downstream regulated,
					clone MGC:4412
1757	2.08	KAM205 C7		12729191	Inositol 1,4,5-triphosphate
					receptor, type 1 (ITPR1)
1758	2.07	LLAM26 F3		190888	RASF-A PLA2
1759	2.04	KAM218 G8		190515	Phosphatase-1 catalytic
					subunit
1760	2.02	KAM213 A4		13649713	Dendritic cell-associated C-
					type lectin-1 beta
1761	2.01	SAM116 E7		7229100	CA11 mRNA
1762	2	SAM127 D8		12804646	Annexin A2
1763	7.83	KAM211 H4	K1621P	4499957	DKFZp564N1116
1764	4.35	KAM216 C3	K1550P	11431676	FLJ11342
1765	4.04	KAM213 F11		12729821	DKFZP434B103
1766	3.85	KAM218 F4	K1591P	10436988	FLJ21005
1767	3.55	KAM202 A9		7018479	DKFZp761D0223
1768	3.34	KAM217 E1	K1622P	12803864	KIAA1445
1769	3.02	KAM205 C6	K1551P	3882278	KIAA0779
1770	2.99	KAM203 B8		10437886	FLJ21730
1771	2.88	KAM210 C8		10432773	FLJ11506
1772	2.86	LLAM25 D8		14149943	KLJ23277
1773	2.64	KAM204 G2	K1555P	9506636	FLJ11116, similar to rab11-
					binding protein
1774	2.64	KAM218 C3	K1590P	10998290	QnpA-21739 cDNA from
					Macaca fascicularis brain
1775	2.61	KAM201 E10		9506622	hypothetical protein similar to
					ankyrin repeat-containing
					protein
1776	2.58	SAM113 C4		10241947	QnpA-10763 cDNAfrom
					Macaca fascicularis brain
1777	2.53	KAM207 B8		7018479	DKFZp761D00223
1778	2.48	KAM207 C9		559702	KIAA0068
1779	2.48	KAM217 C3		3243034	RuvB-like protein RUVBL1
1780	2.44	KAM204 A6		5262490	DKFZp564D0462
1781	2.39	SAM125 H7		6807811	DKFZp434P231
1782	2.24	SAM129 G3		13376194	FLJ23018
1783	2.18	LLAM27 F7		10435651	FLJ13598
1784	2.14	LLAM26 F5		13528719	MGC:10534 cDNA clone,
					similar to CG7083
1785	2.11	KAM217 G11		3327079	KIAA0633
1786	2.11	KAM217 G9		13376196	FLJ12529
1787	2.1	SAM115 B3		2280487	KIAA0392
1788	2.07	KAM211 B4		3043547	KIAA0512
1789	2.05	KAM205 E9		12052797	DKFZp564K142
1790	2.04	KAM210 B12		12224876	DKFZp667B0711
1791	2.02	KAM214 D1		10435597	FLJ13555
1792	2.02	LLAM26 C2		6841301	HSPC326
1793	2.01	KAM209 B11		5262707	DKFZp586K1123
1794	16.92	KAM209 D9	K1547P	8886966	chromosome 19 clone CTC-
					513N18
1795	3.12	KAM213 D5	c.f. 1547P	8886966	chromosome 19 clone CTC-
					513N18
1796	4.73	KAM204 B7	c.f. K1586P	11120989	chromosome 6 clone RP1-
					139G21
1797	4.68	KAM203 A1	K1586P	11120989	chromosome 6 clone RP1-
					139G21
1798	2.59	KAM200 C7		2842785	BAC clone CTA-293F17 from
					7p15-p21
1799	2.23	KAM216 G7		2842785	BAC clone CTA-293F17 from
					7p15-p21
1800	2.15	KAM212 H11		2842785	BAC clone CTA-293F17 from
					7p15-p21
1801	11.39	KAM216 G8	K1623P	8650282	gDNA from chromosome
					4q13
1802	8.55	KAM213 F9		8748931	BAC clone RP11-507K12
					from 7p11.2-p21
1803	6.86	KAM200 C11		13470139	chromosome 5 clone CTD-
					2062A1
1804	6.48	KAM217 D10		8886966	chromosome 19 clone
1805	5.36	KAM213 D11	K1589P	1809226	BAG clone RG104l04 from
					7q21-7q22
1806	4.28	LLAM25 G9	K1624P	14329875	chromosome Xq22 clone
					RP1-75H8
1807	4.01	KAM212 B8		9801555	chromosome 20 clone RP1-
					132F21
1808	3.78	KAM204 G8		4753230	BAC clone RP11-486P11
					from 7p21-p15.1
1809	3.65	KAM216 G9		13357387	chromosome 18, clone RP11-
					106E15
1810	3.36	KAM202 C5	K1592P	2887277	PAC 454G6 on chromosome
					1q24
1811	3.14	SAM105 D10	K1593P	11120958	BAG clone RP11-549B18
					from 18
1812	3.04	KAM217 D6		8844110	chromosome 19 clone
1813	3	KAM217 B10		10835353	chromosome 2, clone RP11-
					387A1
1814	2.93	KAM217 H1	K1552P	10185469	chromosome 13 clone RP11-
					251J8
1815	2.75	KAM208 B2		13560018	chromosome 6 clone RP11-
					294H11
1816	2.58	LLAM26 A2		13508860	chromosome 6 clone RP13-
					143G15
1817	2.55	KAM208 F10		7981300	chromosome 6 clone RP3-
					399E4
1818	2.35	KAM204 F7		4263638	chromosome 4 clone
1819	2.34	SAM122 G5		11038582	clone RP11-417F21
1820	2.33	KAM201 A9		2598081	Chromosome 11p15.5 pac
					pDJ608b4
1821	2.3	KAM205 G3		2337860	BAC clone CTA-364P16 from
					7q31
1822	2.25	SAM124 G9		13123898	chromosome 10
1823	2.22	KAM216 D9		11990063	chromosome 20 clone RP11-
					348I14
1824	2.21	KAM216 B12		5678818	chromosome 4 clone
1825	2.11	KAM218 D8		13173624	chromosome 5 clone CTD-
					2048J22
1826	2.1	KAM215 B11		3688105	chromosome 17, clone
					hRPC.1073_F_15, complete
					sequence
1827	2.08	SAM130 A1		1841541	chromosome 6
1828	2.05	KAM205 F5		13493060	12q BAC RP11-798P24
1829	2.04	KAM205 C4		3253131	chromosome 17
1830	2.01	SAM115 G12		13513077	chromosome 14

[2020]

TABLE 5
cDNAs ENCODING KIDNEY TUMOR PROTEINS THAT SHOWED
NO SIGNIFICANT SIMILARITY TO SEQUENCES IN GENBANK
	SEQ ID
	NO.	Ratio	Clone
	1831	3.7	KAM207 D6
	1832	2.73	LLAM28 C3
	1833	2.65	KAM205 D5
	1834	2.4	KAM205 G7
	1835	2.24	SAM120 H3
	1836	9.68	KAM201 A1
	1837	3.56	KAM211 H3
	1838	3.53	KAM216 B8
	1839	2.81	KAM216 D4
	1840	2.54	KAM201 E4
	1841	2.51	KAM214 C7
	1842	2.31	KAM206 C4
	1843	2.25	KAM215 C1

Example 3

Analysis of cDNA Expression Using Real-Time PCR

[2021] Several cDNAs identified by microarray analysis in Example 2 as being overexpressed in kidney tumors as compared to normal kidney and/or a variety of normal tissues were characterized further by Real-Time PCR analysis. These cDNAs were designated K1547P-K1555P, K1586P-K1593P, and K1619P-K1624P. The first-strand cDNA used in the quantitative real-time PCR was synthesized from 20 μg of total RNA that was treated with DNase I (Amplification Grade, Gibco BRL Life Technology, Gaithersburg, Md.), using Superscript Reverse Transcriptase (RT) (Gibco BRL Life Technology, Gaithersburg, Md.). Real-time PCR was performed with a GeneAmp™ 5700 sequence detection system (PE Biosystems, Foster City, Calif.). The 5700 system uses SYBRTM green, a fluorescent dye that only intercalates into double stranded DNA, and a set of gene-specific forward and reverse primers. The increase in fluorescence was monitored during the whole amplification process. The optimal concentration of primers was determined using a checkerboard approach and a pool of cDNAs from tumors was used in this process. The PCR reaction was performed in 25 μl volumes that included 2.5 μl of SYBR green buffer, 2 μl of cDNA template and 2.5 μl each of the forward and reverse primers for the gene of interest. The cDNAs used for RT reactions were diluted 1:10 for each gene of interest and 1:100 for the β-actin control. In order to quantitate the amount of specific cDNA (and hence initial mRNA) in the sample, a standard curve was generated for each run using the plasmid DNA containing the gene of interest. Standard curves were generated using the Ct values determined in the real-time PCR which were related to the initial cDNA concentration used in the assay. Standard dilution ranging from 20-2×106 copies of the gene of interest was used for this purpose. In addition, a standard curve was generated for β-actin ranging from 200 fg-2000 fg. This enabled standardization of the initial RNA content of a tissue sample to the amount of β-actin for comparison purposes. The mean copy number for each group of tissues tested was normalized to a constant amount of β-actin, allowing the evaluation of the over-expression levels seen with each of the genes.

[2022] MicroArray profiles, Real-Time data, and GenBank search results for the above listed clones are summarized in Table 6.

TABLE 6
				Description
SEQ ID	Candidate	Short		(Homo sapien unless
NO:	Number	Panel	Real Time Profile	otherwise specified
High Expression (mean 1 > .02, mean 2 < 1.0):
1794	K1547P	Y	7/9 T; low expn in normal	chromosome 19 clone
			thyroid and pancreas	CTC-513N18
1702	K1548P	Y	8/9 T; low/no expn in	ESM-1 protein, exon 3
			normal tissues
1693	K1549P	Y	5/9 T; low/no expn in	fatty acid binding protein
			normal tissues	(FABP7)
1805	K1589P	N		BAC clone RG104I04 from
				7q21-7q22
1797	K1586P	Y	7/9 low T; low expn in	choromosome 6 clone
			normal kidney, liver and	RP1-139G21
			bladder
1764	K1550P	Y	9/9 T; low expn in most	FLJ11342
			normal tissues
1695	c.f. K1553P	Y	8/9 T; expn in stomach,	renal cell carcinoma
			low expn in colon and	associated antigen G250
			pancreas
1694	K1554P	Y	8/9 T; low expn in normal	insulin-like growth factor
			heart and liver	binding protein-3
1707	K1587P	Y	9/9 low T: expn most	MET proto-oncogene
			normal tissues
1810	K1592P	Y	6/9 T: no normal	PAC 454G6 on
			expression	chromosome 1q24
1713	K1588P	Y	8/9 T: expn in several	bHLH protein DEC2
			normal tissues
1811	K1593P	Y	1/9 T; expn in most	BAC clone RP11-549B18
			normal tissues	from 18
1795	c.f. K1547P	Y	7/9 T; low expn in normal	chromosome 19 clone
			thyroid and pancreas	CTC-513N18
1769	K1551P	Y	8/9 T; low expn in most	KIAA0779
			normal tissues
1773	K1555P	Y	Not determined	FLJ11116, similar to rab11-
				binding protein
Medium Expression (mean 1 = 0.1-0.2, mean 2 < 0.1):
1766	K1591P	N		FLJ21005
1814	K1552P	Y	9/9 T; low expn in	chromosome 13 clone
			several normal tissues	RP11-251J8
1695	K1553P	Y	8/9 T; expn in stomach,	renal cell carcinoma
			low expn in colon and	associated antigen G250
			pancreas
1694	c.f. K1554P	N		insulin-like growth factor
				binding protein-3
1774	K1590P	Y	8/9 low T; expn in	QnpA-21739 cDNA clone
			several normal tissues	from Macaca fascicularis
				brain
Possible Low Normal Expression (mean 1 > 0.2, mean
2 = 0.1-0.2):
1801	K1623P	Y	6/9 T; low expn in normal	4q13 genomic sequence
			kidney and heart
1763	K1621P	Y	8/9 T; v. low expn in	cDNA DKFZp564N1116
			pancreas
1704	K1619P	Y	9/9 T; expn in heart, lung	vascular endothelial growth
			and pancreas	factor
1706	K1620P	Y	3/9 high expn in T; expn	annexin IV (carbohydrate-
			in pancreas	binding protein p33/41)
1806	K1624P	Y	4/9 KidT, low expn in livT	chromosome Xq22 clone
			and stomT; expn in	RP1-75H8
			pancreas
1768	K1622P	Y	7/9 T; low expn in brain	KIAA1445
			and heart
Abbreviations: Expn: expression; liv: liver; stom: stomach; T: tumor;

[2023] The summary shown in Table 6 of the Real Time expression profiles that most of the cDNAs showed overexpression in kidney tumor samples specific normal tissue expression in some candidates. However, 4 (K1548P, K1549P, K1592P, and K1621 P) showed exceptional n profiles with extensive overexpression in the majority of kidney tumor samples and little or no expression in the normal tissues. Nucleotide sequences for all the cDNAs with “high” (mean 1>2.0), “medium” (mean 1 0.1-0.2) and a “potential for low normal expression” (mean 2 of 0.1-0.2), are set forth in Table 6.

[2024] Thus, the cDNAs described herein are overexpressed in kidney (renal) tumors and provide candidates to which therapeutic monoclonal antibodies (naked or conjugated to toxins or radioisotopes) may be targeted. In addition these candidates may also be targets for therapeutic T-cell vaccines and can be used as diagnostic markers for the detection and monitoring of kidney (renal) malignancy.

Example 4

Analysis of cDNA Expression Using LifeSeq Gold Datamining and Real-Time PCR

[2025] The Incyte Genomics LifeSeq Gold database (June 2001 release) was searched to identify cDNA sequences that represent genes that are up-regulated in kidney tumor tissue as compared to normal essential tissues. First, all libraries were identified within the LifeSeq Gold database that were constructed from kidney tumor and fetal kidney tissues (a total of 19 libraries with 83,602 clones) (see Table 7). Fetal kidney libraries were used because it is believed that genes that are transcribed in early development but not in healthy adult tissues will sometimes be transcribed again upon tumorigenesis.

TABLE 7
LIFESEQ GOLD KIDNEY LIBRARIES FOR TRANSCRIPT IMAGING
Library Name	# clones	Library Description
KIDNTUP03	12,046	kidney tumor, clear cell type cancer, pool,
		NORM, 3′ CGAP
KIDNTUP06	7,669	kidney tumor, clear cell type cancer, pool,
		SUB, CGAP
KIDNTUP02	821	kidney tumor, renal cell CA, 3′ CGAP
KIDNTUTI4	3,861	kidney tumor, renal cell CA, 43 M,
		m/KIDNNOT20
KIDNTUE0	2,906	kidney tumor, renal cell CA, 46 M, 5 RP
KIDNTUT13	3,771	kidney tumor, renal cell CA, 51 F
KIDNTUT16	2,922	kidney tumor, renal cell CA, 53 F,
		m/KIDNNOT26
KIDNTUT15	3,941	kidney tumor, renal cell CA, 65 M
		m/KIDNNOT19
KIDNTUP01	5,141	kidney tumor, renal cell CA, pool, 3′/5′ CGAP
KIDNTUP05	2,690	kidney tumor, renal cell, 3′ CGAP
KIDNTUT01	3,724	kidney tumor, Wilms', 8 mF
KIDNTUM01	4,631	kidney tumor, Wilms', pool, WM/WN
KIDNFET01	7,834	kidney, aw/anencephaly, fetal, 17 wF
KIDNFET02	3,442	kidney, aw/hypoplastic left heart, fetal, 23 wM
KIDNFEE02	2,768	kidney, aw/hypoplastic left heart, fetal, 23 wM,
		5 RP
KIDNFEC01	5,501	kidney, fetal, 19-23 w, M/F, Ig cDNA
KIDNNOT09	3,749	kidney, fetal, 23 wM
KIDNFEP0I	1,105	kidney, fetal, TIGR
KIDNNOC0I	5,080	kidney, right/left, aw/Patau's, fetal, 20 wM,
		pool, Ig cDNA
	83,602	Total number of clones
	23,599	Number of LifeSeq Gene Bins with one or
		more clones from the above libraries

[2026] The “Transcript Imaging” software of the LifeSeq Gold database was then used to identify all LifeSeq Gold database gene bins that contain one or more clones from the selected kidney tumor and fetal kidney libraries. The output of the Transcript Imaging software includes a list of these gene bins as well as, for each gene bin, information regarding the total number of tumor kidney and fetal kidney clones within each gene bin (“absolute number”), the number of different libraries that gave rise to these kidney clones, and “percent specificity” which is the % of clones within the gene bin that came from the kidney tumor and fetal kidney libraries. Thus, a gene bin with 100% specificity contains only clones from the 19 kidney tumor and fetal kidney libraries, while a percentage less than 100 reflects the percentage of clones within that gene bin that were derived from the kidney tumor and fetal kidney libraries. In analysis of the gene bins identified by the Transcript Imaging software, the bins were sorted based on descending order of “percent specificity,” then sorted based on descending order of “absolute number.” By doing this, gene bins that had the greatest number of kidney tumor and fetal kidney clones as well as relatively high percent specificity were identified (Table 8).

TABLE 8
LIFESEQ PROFILES FOR KIDNEY ANTIGENS
Antigen		Gene		Abs.
Name	Gene Bin ID	Description	Found In	Abund	% Spec
K1102C	985271	Incyte Unique	1	5	81.62
K1101C	103552	Incyte Unique	3	4	78.04
K1100C	341942	Incyte Unique	2	4	78.04

[2027] The DNA sequences that made up the gene bins identified in this manner were then extracted from the LifeSeq Gold database and analyzed by BlastN sequence similarity searching as well as by quantitative real time PCR. Here we are disclosing the sequences for three sequences derived from gene bins that were identified by the Transcript Imaging software as described above. None of the three sequences showed significant similarity to known genes in GenBank or GeneSeq databases. However, the BlastN vs. GenBank nonredundant DNA database showed that K1100C (SEQ ID NO:1844) is located on Chromosome 7, K1101 C (SEQ ID NO:1845) is located on Chromosome 2, and K1102C (SEQ ID NO:1846) is located on Chromosome 13.

[2028] mRNA expression profiles for K1100C, K1101C, and K1102C were then determined using real-time PCR analysis on a panel of kidney tumor, normal kidney, and a variety of other normal tissues, as described in Example 3. K100C was shown to be highly over expressed (from 50-725 copies of K1100C/copy relative to bone marrow) in 66% of kidney tumor samples as compared to normal kidney and a panel of other normal tissues. Moderate over expression (about 25 copies of K1100C/copy relative to bone marrow) was observed in an additional kidney tumor sample, normal bladder, and normal lung. Lower levels of expression were also seen in normal breast, brain, and esophagus. K1101C was over expressed in 66% kidney tumor samples (2500-35000 copies K1101C/copy relative to activated PBMC) and in normal kidney. Over expression was also observed in stomach tumors and normal stomach. Lower levels of expression were seen in normal thyroid, colon, and heart. K1102C was over expressed in 77% kidney tumor samples as compared to normal kidney. Expression was also seen in normal esophagus. No expression was seen in any other normal tissue tested.

[2029] Thus, K1100C, K1101 C, and K1102C are over expressed in kidney (renal) tumors and provide candidates to which therapeutic monoclonal antibodies (naked or conjugated to toxins or radioisotopes) may be targeted. In addition these candidates may also be targets for therapeutic T-cell vaccines and can be used as diagnostic markers for the detection and monitoring of kidney (renal) malignancy.

Example 5

Extended cDNA Sequences and Open Reading Frames Identified for Kidney Tumor Antigens

[2030] Disclosed herein are the open reading frames for the previously disclosed kidney tumor antigens K1548P, K1549P, K1550P, and K1551 P (full-length cDNAs set forth in SEQ ID NOs:1702, 1693, 1764, and 1769, respectively). The protein coding sequences or open reading frames (ORFs) are set forth in SEQ ID NOs:1859-1862. The amino acid sequence of the ORFs are set forth in SEQ ID NOs:1848, 1849, 1863, and 1850, respectively. These kidney tumor antigens were shown by microarray and real time PCR analysis to be over expressed in kidney tumors as compared to normal kidney and a panel of other normal tissues. Searches against GenBank showed that K1548P has some similarity to ESM-1 and K1549P has some similarity to FABP7 (see Table 6). K1550P and K1551 P showed no significant similarity to known sequences in the database (see Table 6).

[2031] Additionally, the K1551 P cDNA sequence (SEQ ID NO:1769) was used as a query in a BlastN search of the GeneSeq DNA database and was found to share 100% identity to a longer cDNA sequence, GeneSeq Accession AAA16627. This DNA sequence encodes a 653 amino acid sequence (GeneSeq Accession AAY94907). The extended cDNA and protein sequences are disclosed herein in SEQ ID NOs:1847 and 1851, respectively. These may represent full-length sequences or alternative splice forms.

Example 6

Extended DNA and Protein Sequences Identified for Kidney Tumor Antigen, K1622P

[2032] This Example describes the identification of extended DNA and protein sequences for the kidney tumor antigen K1622P. This kidney tumor antigen was shown to be over expressed in kidney tumor as compared to normal kidney and a panel of other normal tissues.

[2033] SEQ ID NOs:1768 and 1580, encoding the K1622P kidney tumor antigen, were used as queries in Blast searches of public databases (including GenBank, GeneSeq DNA and protein databases, and High Throughput Gene Sequence database (HTGS)). This analysis identified an additional nucleotide sequence for K1622P (set forth in SEQ ID NO:1852) with a potential open reading frame that encodes a predicted transmembrane protein, semaphorin 5B (SEMA5b/SEMAG/SEMG), represented by accession # AB040878. This molecule contains a sema domain, seven thrombospondin repeats (type 1 and type 1-like), a transmembrane domain (TM) and a short cytoplasmic domain. An open reading frame (ORF) was identified (set forth in SEQ ID NO:1853) that encoded a protein (SEQ ID NO:1856). No in-frame “stop” codon was observed upstream of the most 5′-starting methionine, indicating that K1622P may contain additional 5′-nucleotide and corresponding amino-terminal protein sequence. Consequently, the protein sequence set forth in SEQ ID NO:1856 does not start with a methionine (met) and includes the largest predictable K1622P polypeptide encoded by this ORF. The first identified methionine encoding codon (gtctcftggATGC) was at nucleotide +154 of SEQ ID NO:1852, resulting in an ORF (set forth in SEQ ID NO:1854) that encodes a protein originating at this starting methionine (set forth in SEQ ID NO:1857). A second methionine encoding codon (gggcctatcATGG) was identified at nucleotide +328 of SEQ ID NO:1852, resulting in a shorter ORF (set forth in SEQ ID NO:1855) that encodes the protein set forth in SEQ ID NO:1858. This protein utilizes a starting methionine in a context that conforms better to the Kozak start of translation consensus sequence (gccgcca/gccATGG) and therefore may represent a polypeptide translated in vivo. Additional Blast analysis mapped K1622P to human chromosome 3 (accession #s AC078794, AC092975, AC084300, and AC083797) where it is encoded by at least 23 exons.

Example 7

Peptide Priming of T-Helper Lines

[2034] Generation of CD4+ T helper lines and identification of peptide epitopes derived from tumor-specific antigens that are capable of being recognized by CD4+ T cells in the context of HLA class II molecules, is carried out as follows:

[2035] Fifteen-mer peptides overlapping by 10 amino acids, derived from a tumor-specific antigen, are generated using standard procedures. Dendritic cells (DC) are derived from PBMC of a normal donor using GM-CSF and IL-4 by standard protocols. CD4+ T cells are generated from the same donor as the DC using MACS beads (Miltenyi Biotec, Auburn, Calif.) and negative selection. DC are pulsed overnight with pools of the 15-mer peptides, with each peptide at a final concentration of 0.25 μg/ml. Pulsed DC are washed and plated at 1×104 cells/well of 96-well V-bottom plates and purified CD4+ T cells are added at 1×105/well. Cultures are supplemented with 60 ng/ml IL-6 and 10 ng/ml IL-12 and incubated at 37° C. Cultures are restimulated as above on a weekly basis using DC generated and pulsed as above as antigen presenting cells, supplemented with 5 ng/ml IL-7 and 10 U/ml IL-2. Following 4 in vitro stimulation cycles, resulting CD4+ T cell lines (each line corresponding to one well) are tested for specific proliferation and cytokine production in response to the stimulating pools of peptide with an irrelevant pool of peptides used as a control.

Example 8

Generation of Tumor-Specific CTL Lines Using in vitro Whole-Gene Priming

[2036] Using in vitro whole-gene priming with tumor antigen-vaccinia infected DC (see, for example, Yee et al, The Journal of Immunology, 157(9):4079-86, 1996), human CTL lines are derived that specifically recognize autologous fibroblasts transduced with a specific tumor antigen, as determined by interferon-γ ELISPOT analysis. Specifically, dendritic cells (DC) are differentiated from monocyte cultures derived from PBMC of normal human donors by growing for five days in RPMI medium containing 10% human serum, 50 ng/ml human GM-CSF and 30 ng/ml human IL-4. Following culture, DC are infected overnight with tumor antigen-recombinant vaccinia virus at a multiplicity of infection (M.O.I) of five, and matured overnight by the addition of 3 μg/ml CD40 ligand. Virus is then inactivated by UV irradiation. CD8+ T cells are isolated using a magnetic bead system, and priming cultures are initiated using standard culture techniques. Cultures are restimulated every 7-10 days using autologous primary fibroblasts retrovirally transduced with previously identified tumor antigens. Following four stimulation cycles, CD8+ T cell lines are identified that specifically produce interferon-γ when stimulated with tumor antigen-transduced autologous fibroblasts. Using a panel of HLA-mismatched B-LCL lines transduced with a vector expressing a tumor antigen, and measuring interferon-γ production by the CTL lines in an ELISPOT assay, the HLA restriction of the CTL lines is determined.

Example 9

Generation and Characterization of Anti-Tumor Antigen Monoclonal Antibodies

[2037] Mouse monoclonal antibodies are raised against E. coli derived tumor antigen proteins as follows: Mice are immunized with Complete Freund's Adjuvant (CFA) containing 50 μg recombinant tumor protein, followed by a subsequent intraperitoneal boost with Incomplete Freund's Adjuvant (IFA) containing 10 μg recombinant protein. Three days prior to removal of the spleens, the mice are immunized intravenously with approximately 50%g of soluble recombinant protein. The spleen of a mouse with a positive titer to the tumor antigen is removed, and a single-cell suspension made and used for fusion to SP2/O myeloma cells to generate B cell hybridomas. The supernatants from the hybrid clones are tested by ELISA for specificity to recombinant tumor protein, and epitope mapped using peptides that spanned the entire tumor protein sequence. The mAbs are also tested by flow cytometry for their ability to detect tumor protein on the surface of cells stably transfected with the cDNA encoding the tumor protein.

Example 10

Synthesis of Polypeptides

[2038] Polypeptides are synthesized on a Perkin Elmer/Applied Biosystems Division 430A peptide synthesizer using FMOC chemistry with HPTU (O-Benzotriazole-N,N,N′,N′-tetramethyluronium hexafluorophosphate) activation. A Gly-Cys-Gly sequence is 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 is carried out using the following cleavage mixture: trifluoroacetic acid:ethanedithiol:thioanisole:water:phenol (40:1:2:2:3). After cleaving for 2 hours, the peptides are precipitated in cold methyl-t-butyl-ether. The peptide pellets are then 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) is used to elute the peptides. Following lyophilization of the pure fractions, the peptides are characterized using electrospray or other types of mass spectrometry and by amino acid analysis.

[2039] From the foregoing it will be appreciated that, although specific embodiments of the invention have been described herein for purposes of illustration, various modifications may be made without deviating from the spirit and scope of the invention. Accordingly, the invention is not limited except as by the appended claims.

Claims

1. An isolated polynucleotide comprising a sequence selected from the group consisting of: (a) sequences provided in SEQ ID NOs:1-1847, 1852-1855, and 1859-1862; (b) complements of the sequences provided in SEQ ID NOs:1-1847, 1852-1855, and 1859-1862; (c) sequences consisting of at least 20 contiguous residues of a sequence provided in SEQ ID NOs:1-1847, 1852-1855, and 1859-1862; (d) sequences that hybridize to a sequence provided in SEQ ID NOs:1-1847, 1852-1855, and 1859-1862, under highly stringent conditions; (e) sequences having at least 75% identity to a sequence of SEQ ID NOs:1-1847, 1852-1855, and 1859-1862; (f) sequences having at least 90% identity to a sequence of SEQ ID NOs:1-1847, 1852-1855, and 1859-1862; and (g) degenerate variants of a sequence provided in SEQ ID NOs:1-1847, 1852-1855, and 1859-1862.

2. An isolated polypeptide comprising an amino acid sequence selected from the group consisting of: (a) sequences encoded by a polynucleotide of claim 1;(b) sequences having at least 70% identity to a sequence encoded by a polynucleotide of claim 1;(c) sequences having at least 90% identity to a sequence encoded by a polynucleotide of claim 1;(d) sequences set forth in SEQ ID NOs:1848-1851, 1856-1858, and 1863; (e) sequences having at least 70% identity to a sequence set forth in 1848-1851, 1856-1858, and 1863; (f) sequences having at least 90% identity to a sequence set forth in 1848-1851, 1856-1858, and 1863.

3. An expression vector comprising a polynucleotide of claim 1 operably linked to an expression control sequence.

4. A host cell transformed or transfected with an expression vector according to claim 3.

5. An isolated antibody, or antigen-binding fragment thereof, that specifically binds to a polypeptide of claim 2.

6. A method for detecting the presence of a cancer in a patient, comprising the steps of: (a) obtaining a biological sample from the patient; (b) contacting the biological sample with a binding agent that binds to a polypeptide of claim 2;(c) detecting in the sample an amount of polypeptide that binds to the binding agent; and (d) comparing the amount of polypeptide to a predetermined cut-off value and therefrom determining the presence of a cancer in the patient.

7. A fusion protein comprising at least one polypeptide according to claim 2.

8. An oligonucleotide that hybridizes to a sequence recited in SEQ ID NOs:1-1847, 1852-1855, and 1859-1862 under highly stringent conditions.

9. A method for stimulating and/or expanding T cells specific for a tumor protein, comprising contacting T cells with at least one component selected from the group consisting of: (a) polypeptides according to claim 2;(b) polynucleotides according to claim 1; and (c) antigen-presenting cells that express a polynucleotide according to claim 1, under conditions and for a time sufficient to permit the stimulation and/or expansion of T cells.

10. An isolated T cell population, comprising T cells prepared according to the method of claim 9.

11. A composition comprising a first component selected from the group consisting of physiologically acceptable carriers and immunostimulants, and a second component selected from the group consisting of: (a) polypeptides according to claim 2;(b) polynucleotides according to claim 1;(c) antibodies according to claim 5;(d) fusion proteins according to claim 7;(e) T cell populations according to claim 10; and (f) antigen presenting cells that express a polypeptide according to claim 2.

12. A method for stimulating an immune response in a patient, comprising administering to the patient a composition of claim 11.

13. A method for the treatment of a kidney cancer in a patient, comprising administering to the patient a composition of claim 11.

14. A method for determining the presence of a cancer in a patient, comprising the steps of: (a) obtaining a biological sample from the patient; (b) contacting the biological sample with an oligonucleotide according to claim 8;(c) detecting in the sample an amount of a polynucleotide that hybridizes to the oligonucleotide; and (d) comparing the amount of polynucleotide that hybridizes to the oligonucleotide to a predetermined cut-off value, and therefrom determining the presence of the cancer in the patient.

15. A diagnostic kit comprising at least one oligonucleotide according to claim 8.

16. A diagnostic kit comprising at least one antibody according to claim 5 and a detection reagent, wherein the detection reagent comprises a reporter group.

17. A method for the treatment of kidney cancer in a patient, comprising the steps of: (a) incubating CD4+ and/or CD8+ T cells isolated from a patient with at least one component selected from the group consisting of: (i) polypeptides according to claim 2; (ii) polynucleotides according to claim 1; and (iii) antigen presenting cells that express a polypeptide of claim 2, such that T cell proliferate; (b) administering to the patient an effective amount of the proliferated T cells, and thereby inhibiting the development of a cancer in the patient.