Compositions and methods for the therapy and diagnosis of colon cancer

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 563.app which is 2.2 MB and created on Feb. 1, 2002; CD-ROM No.2 is labeled COPY 2, contains the file 563.app which is 2.2 MB and created on Feb. 1, 2002; CD-ROM No. 3 is labeled CRF, contains the file 563.app which is 2.2 MB and created on Feb. 1, 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 colon cancer. The invention is more specifically related to polypeptides, comprising at least a portion of a colon 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 colon 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] Colon cancer is the second most frequently diagnosed malignancy in the United States as well as the second most common cause of cancer death. The five-year survival rate for patients with colorectal cancer detected in an early localized stage is 92%; unfortunately, only 37% of colorectal cancer is diagnosed at this stage. The survival rate drops to 64% if the cancer is allowed to spread to adjacent organs or lymph nodes, and to 7% in patients with distant metastases.

[0007] The prognosis of colon cancer is directly related to the degree of penetration of the tumor through the bowel wall and the presence or absence of nodal involvement, consequently, early detection and treatment are especially important. Currently, diagnosis is aided by the use of screening assays for fecal occult blood, sigmoidoscopy, colonoscopy and double contrast barium enemas. Treatment regimens are determined by the type and stage of the cancer, and include surgery, radiation therapy and/or chemotherapy. Recurrence following surgery (the most common form of therapy) is a major problem and is often the ultimate cause of death. In spite of considerable research into therapies for the disease, colon cancer remains difficult to diagnose and treat. In spite of considerable research into therapies for these and other cancers, colon 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.

[0008] In spite of considerable research into therapies for these and other cancers, colon 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: 1-1421, 1425, 1427, and 1430-3417;

[0011] (b) complements of the sequences provided in SEQ ID NOs: 1-1421, 1425, 1427, and 1430-3417;

[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: 1-1421, 1425, 1427, and 1430-3417;

[0013] (d) sequences that hybridize to a sequence provided in SEQ ID NOs: 1-1421, 1425, 1427, and 1430-3417, 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: 1-1421, 1425, 1427, and 1430-3417;

[0015] (f) degenerate variants of a sequence provided in SEQ ID NOs: 1-1421, 1425, 1427, and 1430-3417.

[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 colon tumor 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: 1422-1424, 1426, 1428, and 1429.

[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: 1422-1424, 1426, 1428, and 1429 or a polypeptide sequence encoded by a polynucleotide sequence set forth in SEQ ID NOs: 1-1421, 1425, 1427, and 1430-3417.

[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 colon 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 colon 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 colon 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: 1-254 are the determined cDNA sequences described in Tables 2-10.

[0042] SEQ ID NO: 255 is the determined cDNA sequence for clone 63716879.

[0043] SEQ ID NO: 256 is the determined cDNA sequence for clone 63716880.

[0044] SEQ ID NO: 257 is the determined cDNA sequence for clone 63716882.

[0045] SEQ ID NO: 258 is the determined cDNA sequence for clone 63716883.

[0046] SEQ ID NO: 259 is the determined cDNA sequence for clone 63716884.

[0047] SEQ ID NO: 260 is the determined cDNA sequence for clone 63716885.

[0048] SEQ ID NO: 261 is the determined cDNA sequence for clone 63716886.

[0049] SEQ ID NO: 262 is the determined cDNA sequence for clone 63716887.

[0050] SEQ ID NO: 263 is the determined cDNA sequence for clone 63716888.

[0051] SEQ ID NO: 264 is the determined cDNA sequence for clone 63716889.

[0052] SEQ ID NO: 265 is the determined cDNA sequence for clone 63716890.

[0053] SEQ ID NO: 266 is the determined cDNA sequence for clone 63716891.

[0054] SEQ ID NO: 267 is the determined cDNA sequence for clone 63716892.

[0055] SEQ ID NO: 268 is the determined cDNA sequence for clone 63716894.

[0056] SEQ ID NO: 269 is the determined cDNA sequence for clone 63716895.

[0057] SEQ ID NO: 270 is the determined cDNA sequence for clone 63716896.

[0058] SEQ ID NO: 271 is the determined cDNA sequence for clone 63716897.

[0059] SEQ ID NO: 272 is the determined cDNA sequence for clone 63716898.

[0060] SEQ ID NO: 273 is the determined cDNA sequence for clone 63716899.

[0061] SEQ ID NO: 274 is the determined cDNA sequence for clone 63716901.

[0062] SEQ ID NO: 275 is the determined cDNA sequence for clone 63716902.

[0063] SEQ ID NO: 276 is the determined cDNA sequence for clone 63716903.

[0064] SEQ ID NO: 277 is the determined cDNA sequence for clone 63716904.

[0065] SEQ ID NO: 278 is the determined cDNA sequence for clone 63716905.

[0066] SEQ ID NO: 279 is the determined cDNA sequence for clone 63716906.

[0067] SEQ ID NO: 280 is the determined cDNA sequence for clone 63716907.

[0068] SEQ ID NO: 281 is the determined cDNA sequence for clone 63716908.

[0069] SEQ ID NO: 282 is the determined cDNA sequence for clone 63716909.

[0070] SEQ ID NO: 283 is the determined cDNA sequence for clone 63716910.

[0071] SEQ ID NO: 284 is the determined cDNA sequence for clone 63716911.

[0072] SEQ ID NO: 285 is the determined cDNA sequence for clone 63716912.

[0073] SEQ ID NO: 286 is the determined cDNA sequence for clone 63716914.

[0074] SEQ ID NO: 287 is the determined cDNA sequence for clone 63716915.

[0075] SEQ ID NO: 288 is the determined cDNA sequence for clone 63716916.

[0076] SEQ ID NO: 289 is the determined cDNA sequence for clone 63716918.

[0077] SEQ ID NO: 290 is the determined cDNA sequence for clone 63716919.

[0078] SEQ ID NO: 291 is the determined cDNA sequence for clone 63716920.

[0079] SEQ ID NO: 292 is the determined cDNA sequence for clone 63716922.

[0080] SEQ ID NO: 293 is the determined cDNA sequence for clone 63716923.

[0081] SEQ ID NO: 294 is the determined cDNA sequence for clone 63716924.

[0082] SEQ ID NO: 295 is the determined cDNA sequence for clone 63716925.

[0083] SEQ ID NO: 296 is the determined cDNA sequence for clone 63716926.

[0084] SEQ ID NO: 297 is the determined cDNA sequence for clone 63716927.

[0085] SEQ ID NO: 298 is the determined cDNA sequence for clone 63716928.

[0086] SEQ ID NO: 299 is the determined cDNA sequence for clone 63716929.

[0087] SEQ ID NO: 300 is the determined cDNA sequence for clone 63716930.

[0088] SEQ ID NO: 301 is the determined cDNA sequence for clone 63716931.

[0089] SEQ ID NO: 302 is the determined cDNA sequence for clone 63716932.

[0090] SEQ ID NO: 303 is the determined cDNA sequence for clone 63716933.

[0091] SEQ ID NO: 304 is the determined cDNA sequence for clone 63716934.

[0092] SEQ ID NO: 305 is the determined cDNA sequence for clone 63716935.

[0093] SEQ ID NO: 306 is the determined cDNA sequence for clone 63716936.

[0094] SEQ ID NO: 307 is the determined cDNA sequence for clone 63716937.

[0095] SEQ ID NO: 308 is the determined cDNA sequence for clone 63716938.

[0096] SEQ ID NO: 309 is the determined cDNA sequence for clone 63716939.

[0097] SEQ ID NO: 310 is the determined cDNA sequence for clone 63716940.

[0098] SEQ ID NO: 311 is the determined cDNA sequence for clone 63716941.

[0099] SEQ ID NO: 312 is the determined cDNA sequence for clone 63716942.

[0100] SEQ ID NO: 313 is the determined cDNA sequence for clone 63716943.

[0101] SEQ ID NO: 314 is the determined cDNA sequence for clone 63716944.

[0102] SEQ ID NO: 315 is the determined cDNA sequence for clone 63716945.

[0103] SEQ ID NO: 316 is the determined cDNA sequence for clone 63716946.

[0104] SEQ ID NO: 317 is the determined cDNA sequence for clone 63716948.

[0105] SEQ ID NO: 318 is the determined cDNA sequence for clone 63716949.

[0106] SEQ ID NO: 319 is the determined cDNA sequence for clone 63716950.

[0107] SEQ ID NO: 320 is the determined cDNA sequence for clone 63716951.

[0108] SEQ ID NO: 321 is the determined cDNA sequence for clone 63716953.

[0109] SEQ ID NO: 322 is the determined cDNA sequence for clone 63716954.

[0110] SEQ ID NO: 323 is the determined cDNA sequence for clone 63716955.

[0111] SEQ ID NO: 324 is the determined cDNA sequence for clone 63716956.

[0112] SEQ ID NO: 325 is the determined cDNA sequence for clone 63716957.

[0113] SEQ ID NO: 326 is the determined cDNA sequence for clone 63716958.

[0114] SEQ ID NO: 327 is the determined cDNA sequence for clone 63716959.

[0115] SEQ ID NO: 328 is the determined cDNA sequence for clone 63716960.

[0116] SEQ ID NO: 329 is the determined cDNA sequence for clone 63716961.

[0117] SEQ ID NO: 330 is the determined cDNA sequence for clone 63716962.

[0118] SEQ ID NO: 331 is the determined cDNA sequence for clone 63716963.

[0119] SEQ ID NO: 332 is the determined cDNA sequence for clone 63716964.

[0120] SEQ ID NO: 333 is the determined cDNA sequence for clone 63716965.

[0121] SEQ ID NO: 334 is the determined cDNA sequence for clone 63716966.

[0122] SEQ ID NO: 335 is the determined cDNA sequence for clone 63716967.

[0123] SEQ ID NO: 336 is the determined cDNA sequence for clone 63716968.

[0124] SEQ ID NO: 337 is the determined cDNA sequence for clone 63716970.

[0125] SEQ ID NO: 338 is the determined cDNA sequence for clone 63716971.

[0126] SEQ ID NO: 339 is the determined cDNA sequence for clone 63716786.

[0127] SEQ ID NO: 340 is the determined cDNA sequence for clone 63716787.

[0128] SEQ ID NO: 341 is the determined cDNA sequence for clone 63716788.

[0129] SEQ ID NO: 342 is the determined cDNA sequence for clone 63716789.

[0130] SEQ ID NO: 343 is the determined cDNA sequence for clone 63716790.

[0131] SEQ ID NO: 344 is the determined cDNA sequence for clone 63716792.

[0132] SEQ ID NO: 345 is the determined cDNA sequence for clone 63716793.

[0133] SEQ ID NO: 346 is the determined cDNA sequence for clone 63716794.

[0134] SEQ ID NO: 347 is the determined cDNA sequence for clone 63716798.

[0135] SEQ ID NO: 348 is the determined cDNA sequence for clone 63716799.

[0136] SEQ ID NO: 349 is the determined cDNA sequence for clone 63716802.

[0137] SEQ ID NO: 350 is the determined cDNA sequence for clone 63716803.

[0138] SEQ ID NO: 351 is the determined cDNA sequence for clone 63716806.

[0139] SEQ ID NO: 352 is the determined cDNA sequence for clone 63716807.

[0140] SEQ ID NO: 353 is the determined cDNA sequence for clone 63716810.

[0141] SEQ ID NO: 354 is the determined cDNA sequence for clone 63716811.

[0142] SEQ ID NO: 355 is the determined cDNA sequence for clone 63716812.

[0143] SEQ ID NO: 356 is the determined cDNA sequence for clone 63716813.

[0144] SEQ ID NO: 357 is the determined cDNA sequence for clone 63716814.

[0145] SEQ ID NO: 358 is the determined cDNA sequence for clone 63716815.

[0146] SEQ ID NO: 359 is the determined cDNA sequence for clone 63716816.

[0147] SEQ ID NO: 360 is the determined cDNA sequence for clone 63716817.

[0148] SEQ ID NO: 361 is the determined cDNA sequence for clone 63716818.

[0149] SEQ ID NO: 362 is the determined cDNA sequence for clone 63716819.

[0150] SEQ ID NO: 363 is the determined cDNA sequence for clone 63716820.

[0151] SEQ ID NO: 364 is the determined cDNA sequence for clone 63716822.

[0152] SEQ ID NO: 365 is the determined cDNA sequence for clone 63716824.

[0153] SEQ ID NO: 366 is the determined cDNA sequence for clone 63716825.

[0154] SEQ ID NO: 367 is the determined cDNA sequence for clone 63716826.

[0155] SEQ ID NO: 368 is the determined cDNA sequence for clone 63716828.

[0156] SEQ ID NO: 369 is the determined cDNA sequence for clone 63716829.

[0157] SEQ ID NO: 370 is the determined cDNA sequence for clone 63716830.

[0158] SEQ ID NO: 371 is the determined cDNA sequence for clone 63716831.

[0159] SEQ ID NO: 372 is the determined cDNA sequence for clone 63716834.

[0160] SEQ ID NO: 373 is the determined cDNA sequence for clone 63716835.

[0161] SEQ ID NO: 374 is the determined cDNA sequence for clone 63716836.

[0162] SEQ ID NO: 375 is the determined cDNA sequence for clone 63716837.

[0163] SEQ ID NO: 376 is the determined cDNA sequence for clone 63716838.

[0164] SEQ ID NO: 377 is the determined cDNA sequence for clone 63716839.

[0165] SEQ ID NO: 378 is the determined cDNA sequence for clone 63716842.

[0166] SEQ ID NO: 379 is the determined cDNA sequence for clone 63716843.

[0167] SEQ ID NO: 380 is the determined cDNA sequence for clone 63716844.

[0168] SEQ ID NO: 381 is the determined cDNA sequence for clone 63716846.

[0169] SEQ ID NO: 382 is the determined cDNA sequence for clone 63716847.

[0170] SEQ ID NO: 383 is the determined cDNA sequence for clone 63716848.

[0171] SEQ ID NO: 384 is the determined cDNA sequence for clone 63716851.

[0172] SEQ ID NO: 385 is the determined cDNA sequence for clone 63716852.

[0173] SEQ ID NO: 386 is the determined cDNA sequence for clone 63716853.

[0174] SEQ ID NO: 387 is the determined cDNA sequence for clone 63716855.

[0175] SEQ ID NO: 388 is the determined cDNA sequence for clone 63716858.

[0176] SEQ ID NO: 389 is the determined cDNA sequence for clone 63716860.

[0177] SEQ ID NO: 390 is the determined cDNA sequence for clone 63716861.

[0178] SEQ ID NO: 391 is the determined cDNA sequence for clone 63716862.

[0179] SEQ ID NO: 392 is the determined cDNA sequence for clone 63716863.

[0180] SEQ ID NO: 393 is the determined cDNA sequence for clone 63716865.

[0181] SEQ ID NO: 394 is the determined cDNA sequence for clone 63716866.

[0182] SEQ ID NO: 395 is the determined cDNA sequence for clone 63716868.

[0183] SEQ ID NO: 396 is the determined cDNA sequence for clone 63716869.

[0184] SEQ ID NO: 397 is the determined cDNA sequence for clone 63716870.

[0185] SEQ ID NO: 398 is the determined cDNA sequence for clone 63716871.

[0186] SEQ ID NO: 399 is the determined cDNA sequence for clone 63716873.

[0187] SEQ ID NO: 400 is the determined cDNA sequence for clone 63716875.

[0188] SEQ ID NO: 401 is the determined cDNA sequence for clone 63716876.

[0189] SEQ ID NO: 402 is the determined cDNA sequence for clone 63716877.

[0190] SEQ ID NO: 403 is the determined cDNA sequence for clone 63716878.

[0191] SEQ ID NO: 404 is the determined cDNA sequence for clone 63717158.

[0192] SEQ ID NO: 405 is the determined cDNA sequence for clone 63717160.

[0193] SEQ ID NO: 406 is the determined cDNA sequence for clone 63717161.

[0194] SEQ ID NO: 407 is the determined cDNA sequence for clone 63717163.

[0195] SEQ ID NO: 408 is the determined cDNA sequence for clone 63717164.

[0196] SEQ ID NO: 409 is the determined cDNA sequence for clone 63717165.

[0197] SEQ ID NO: 410 is the determined cDNA sequence for clone 63717166.

[0198] SEQ ID NO: 411 is the determined cDNA sequence for clone 63717167.

[0199] SEQ ID NO: 412 is the determined cDNA sequence for clone 63717169.

[0200] SEQ ID NO: 413 is the determined cDNA sequence for clone 63717171.

[0201] SEQ ID NO: 414 is the determined cDNA sequence for clone 63717172.

[0202] SEQ ID NO: 415 is the determined cDNA sequence for clone 63717173.

[0203] SEQ ID NO: 416 is the determined cDNA sequence for clone 63717174.

[0204] SEQ ID NO: 417 is the determined cDNA sequence for clone 63717175.

[0205] SEQ ID NO: 418 is the determined cDNA sequence for clone 63717176.

[0206] SEQ ID NO: 419 is the determined cDNA sequence for clone 63717177.

[0207] SEQ ID NO: 420 is the determined cDNA sequence for clone 63717178.

[0208] SEQ ID NO: 421 is the determined cDNA sequence for clone 63717179.

[0209] SEQ ID NO: 422 is the determined cDNA sequence for clone 63717180.

[0210] SEQ ID NO: 423 is the determined cDNA sequence for clone 63717181.

[0211] SEQ ID NO: 424 is the determined cDNA sequence for clone 63717182.

[0212] SEQ ID NO: 425 is the determined cDNA sequence for clone 63717183.

[0213] SEQ ID NO: 426 is the determined cDNA sequence for clone 63717184.

[0214] SEQ ID NO: 427 is the determined cDNA sequence for clone 63717186.

[0215] SEQ ID NO: 428 is the determined cDNA sequence for clone 63717187.

[0216] SEQ ID NO: 429 is the determined cDNA sequence for clone 63717189.

[0217] SEQ ID NO: 430 is the determined cDNA sequence for clone 63717190.

[0218] SEQ ID NO: 431 is the determined cDNA sequence for clone 63717191.

[0219] SEQ ID NO: 432 is the determined cDNA sequence for clone 63717192.

[0220] SEQ ID NO: 433 is the determined cDNA sequence for clone 63717193.

[0221] SEQ ID NO: 434 is the determined cDNA sequence for clone 63717194.

[0222] SEQ ID NO: 435 is the determined cDNA sequence for clone 63717197.

[0223] SEQ ID NO: 436 is the determined cDNA sequence for clone 63717199.

[0224] SEQ ID NO: 437 is the determined cDNA sequence for clone 63717200.

[0225] SEQ ID NO: 438 is the determined cDNA sequence for clone 63717201.

[0226] SEQ ID NO: 439 is the determined cDNA sequence for clone 63717202.

[0227] SEQ ID NO: 440 is the determined cDNA sequence for clone 63717203.

[0228] SEQ ID NO: 441 is the determined cDNA sequence for clone 63717204.

[0229] SEQ ID NO: 442 is the determined cDNA sequence for clone 63717205.

[0230] SEQ ID NO: 443 is the determined cDNA sequence for clone 63717206.

[0231] SEQ ID NO: 444 is the determined cDNA sequence for clone 63717207.

[0232] SEQ ID NO: 445 is the determined cDNA sequence for clone 63717208.

[0233] SEQ ID NO: 446 is the determined cDNA sequence for clone 63717209.

[0234] SEQ ID NO: 447 is the determined cDNA sequence for clone 63717211.

[0235] SEQ ID NO: 448 is the determined cDNA sequence for clone 63717212.

[0236] SEQ ID NO: 449 is the determined cDNA sequence for clone 63717213.

[0237] SEQ ID NO: 450 is the determined cDNA sequence for clone 63717214.

[0238] SEQ ID NO: 451 is the determined cDNA sequence for clone 63717215.

[0239] SEQ ID NO: 452 is the determined cDNA sequence for clone 63717216.

[0240] SEQ ID NO: 453 is the determined cDNA sequence for clone 63717217.

[0241] SEQ ID NO: 454 is the determined cDNA sequence for clone 63717218.

[0242] SEQ ID NO: 455 is the determined cDNA sequence for clone 63717219.

[0243] SEQ ID NO: 456 is the determined cDNA sequence for clone 63717221.

[0244] SEQ ID NO: 457 is the determined cDNA sequence for clone 63717222.

[0245] SEQ ID NO: 458 is the determined cDNA sequence for clone 63717223.

[0246] SEQ ID NO: 459 is the determined cDNA sequence for clone 63717224.

[0247] SEQ ID NO: 460 is the determined cDNA sequence for clone 63717227.

[0248] SEQ ID NO: 461 is the determined cDNA sequence for clone 63717228.

[0249] SEQ ID NO: 462 is the determined cDNA sequence for clone 63717229.

[0250] SEQ ID NO: 463 is the determined cDNA sequence for clone 63717231.

[0251] SEQ ID NO: 464 is the determined cDNA sequence for clone 63717233.

[0252] SEQ ID NO: 465 is the determined cDNA sequence for clone 63717234.

[0253] SEQ ID NO: 466 is the determined cDNA sequence for clone 63717235.

[0254] SEQ ID NO: 467 is the determined cDNA sequence for clone 63717236.

[0255] SEQ ID NO: 468 is the determined cDNA sequence for clone 63717237.

[0256] SEQ ID NO: 469 is the determined cDNA sequence for clone 63717238.

[0257] SEQ ID NO: 470 is the determined cDNA sequence for clone 63717239.

[0258] SEQ ID NO: 471 is the determined cDNA sequence for clone 63717240.

[0259] SEQ ID NO: 472 is the determined cDNA sequence for clone 63717241.

[0260] SEQ ID NO: 473 is the determined cDNA sequence for clone 63717242.

[0261] SEQ ID NO: 474 is the determined cDNA sequence for clone 63717243.

[0262] SEQ ID NO: 475 is the determined cDNA sequence for clone 63717244.

[0263] SEQ ID NO: 476 is the determined cDNA sequence for clone 63717246.

[0264] SEQ ID NO: 477 is the determined cDNA sequence for clone 63717248.

[0265] SEQ ID NO: 478 is the determined cDNA sequence for clone 63717250.

[0266] SEQ ID NO: 479 is the determined cDNA sequence for clone 63716972.

[0267] SEQ ID NO: 480 is the determined cDNA sequence for clone 63716973.

[0268] SEQ ID NO: 481 is the determined cDNA sequence for clone 63716975.

[0269] SEQ ID NO: 482 is the determined cDNA sequence for clone 63716976.

[0270] SEQ ID NO: 483 is the determined cDNA sequence for clone 63716977.

[0271] SEQ ID NO: 484 is the determined cDNA sequence for clone 63716978.

[0272] SEQ ID NO: 485 is the determined cDNA sequence for clone 63716979.

[0273] SEQ ID NO: 486 is the determined cDNA sequence for clone 63716980.

[0274] SEQ ID NO: 487 is the determined cDNA sequence for clone 63716981.

[0275] SEQ ID NO: 488 is the determined cDNA sequence for clone 63716982.

[0276] SEQ ID NO: 489 is the determined cDNA sequence for clone 63716984.

[0277] SEQ ID NO: 490 is the determined cDNA sequence for clone 63716985.

[0278] SEQ ID NO: 491 is the determined cDNA sequence for clone 63716986.

[0279] SEQ ID NO: 492 is the determined cDNA sequence for clone 63716987.

[0280] SEQ ID NO: 493 is the determined cDNA sequence for clone 63716988.

[0281] SEQ ID NO: 494 is the determined cDNA sequence for clone 63716989.

[0282] SEQ ID NO: 495 is the determined cDNA sequence for clone 63716991.

[0283] SEQ ID NO: 496 is the determined cDNA sequence for clone 63716992.

[0284] SEQ ID NO: 497 is the determined cDNA sequence for clone 63716993.

[0285] SEQ ID NO: 498 is the determined cDNA sequence for clone 63716994.

[0286] SEQ ID NO: 499 is the determined cDNA sequence for clone 63716995.

[0287] SEQ ID NO: 500 is the determined cDNA sequence for clone 63716996.

[0288] SEQ ID NO: 501 is the determined cDNA sequence for clone 63716997.

[0289] SEQ ID NO: 502 is the determined cDNA sequence for clone 63716998.

[0290] SEQ ID NO: 503 is the determined cDNA sequence for clone 63716999.

[0291] SEQ ID NO: 504 is the determined cDNA sequence for clone 63717000.

[0292] SEQ ID NO: 505 is the determined cDNA sequence for clone 63717001.

[0293] SEQ ID NO: 506 is the determined cDNA sequence for clone 63717002.

[0294] SEQ ID NO: 507 is the determined cDNA sequence for clone 63717003.

[0295] SEQ ID NO: 508 is the determined cDNA sequence for clone 63717004.

[0296] SEQ ID NO: 509 is the determined cDNA sequence for clone 63717005.

[0297] SEQ ID NO: 510 is the determined cDNA sequence for clone 63717006.

[0298] SEQ ID NO: 511 is the determined cDNA sequence for clone 63717007.

[0299] SEQ ID NO: 512 is the determined cDNA sequence for clone 63717008.

[0300] SEQ ID NO: 513 is the determined cDNA sequence for clone 63717012.

[0301] SEQ ID NO: 514 is the determined cDNA sequence for clone 63717014.

[0302] SEQ ID NO: 515 is the determined cDNA sequence for clone 63717015.

[0303] SEQ ID NO: 516 is the determined cDNA sequence for clone 63717016.

[0304] SEQ ID NO: 517 is the determined cDNA sequence for clone 63717017.

[0305] SEQ ID NO: 518 is the determined cDNA sequence for clone 63717020.

[0306] SEQ ID NO: 519 is the determined cDNA sequence for clone 63717021.

[0307] SEQ ID NO: 520 is the determined cDNA sequence for clone 63717022.

[0308] SEQ ID NO: 521 is the determined cDNA sequence for clone 63717024.

[0309] SEQ ID NO: 522 is the determined cDNA sequence for clone 63717025.

[0310] SEQ ID NO: 523 is the determined cDNA sequence for clone 63717026.

[0311] SEQ ID NO: 524 is the determined cDNA sequence for clone 63717027.

[0312] SEQ ID NO: 525 is the determined cDNA sequence for clone 63717028.

[0313] SEQ ID NO: 526 is the determined cDNA sequence for clone 63717029.

[0314] SEQ ID NO: 527 is the determined cDNA sequence for clone 63717033.

[0315] SEQ ID NO: 528 is the determined cDNA sequence for clone 63717034.

[0316] SEQ ID NO: 529 is the determined cDNA sequence for clone 63717035.

[0317] SEQ ID NO: 530 is the determined cDNA sequence for clone 63717036.

[0318] SEQ ID NO: 531 is the determined cDNA sequence for clone 63717037.

[0319] SEQ ID NO: 532 is the determined cDNA sequence for clone 63717038.

[0320] SEQ ID NO: 533 is the determined cDNA sequence for clone 63717039.

[0321] SEQ ID NO: 534 is the determined cDNA sequence for clone 63717040.

[0322] SEQ ID NO: 535 is the determined cDNA sequence for clone 63717041.

[0323] SEQ ID NO: 536 is the determined cDNA sequence for clone 63717044.

[0324] SEQ ID NO: 537 is the determined cDNA sequence for clone 63717046.

[0325] SEQ ID NO: 538 is the determined cDNA sequence for clone 63717050.

[0326] SEQ ID NO: 539 is the determined cDNA sequence for clone 63717051.

[0327] SEQ ID NO: 540 is the determined cDNA sequence for clone 63717052.

[0328] SEQ ID NO: 541 is the determined cDNA sequence for clone 63717054.

[0329] SEQ ID NO: 542 is the determined cDNA sequence for clone 63717055.

[0330] SEQ ID NO: 543 is the determined cDNA sequence for clone 63717056.

[0331] SEQ ID NO: 544 is the determined cDNA sequence for clone 63717057.

[0332] SEQ ID NO: 545 is the determined cDNA sequence for clone 63717058.

[0333] SEQ ID NO: 546 is the determined cDNA sequence for clone 63717059.

[0334] SEQ ID NO: 547 is the determined cDNA sequence for clone 63717062.

[0335] SEQ ID NO: 548 is the determined cDNA sequence for clone 63717064.

[0336] SEQ ID NO: 549 is the determined cDNA sequence for clone 63716600.

[0337] SEQ ID NO: 550 is the determined cDNA sequence for clone 63716601.

[0338] SEQ ID NO: 551 is the determined cDNA sequence for clone 63716602.

[0339] SEQ ID NO: 552 is the determined cDNA sequence for clone 63716603.

[0340] SEQ ID NO: 553 is the determined cDNA sequence for clone 63716604.

[0341] SEQ ID NO: 554 is the determined cDNA sequence for clone 63716605.

[0342] SEQ ID NO: 555 is the determined cDNA sequence for clone 63716608.

[0343] SEQ ID NO: 556 is the determined cDNA sequence for clone 63716609.

[0344] SEQ ID NO: 557 is the determined cDNA sequence for clone 63716610.

[0345] SEQ ID NO: 558 is the determined cDNA sequence for clone 63716611.

[0346] SEQ ID NO: 559 is the determined cDNA sequence for clone 63716612.

[0347] SEQ ID NO: 560 is the determined cDNA sequence for clone 63716613.

[0348] SEQ ID NO: 561 is the determined cDNA sequence for clone 63716614.

[0349] SEQ ID NO: 562 is the determined cDNA sequence for clone 63716616.

[0350] SEQ ID NO: 563 is the determined cDNA sequence for clone 63716618.

[0351] SEQ ID NO: 564 is the determined cDNA sequence for clone 63716619.

[0352] SEQ ID NO: 565 is the determined cDNA sequence for clone 63716620.

[0353] SEQ ID NO: 566 is the determined cDNA sequence for clone 63716621.

[0354] SEQ ID NO: 567 is the determined cDNA sequence for clone 63716622.

[0355] SEQ ID NO: 568 is the determined cDNA sequence for clone 63716623.

[0356] SEQ ID NO: 569 is the determined cDNA sequence for clone 63716626.

[0357] SEQ ID NO: 570 is the determined cDNA sequence for clone 63716627.

[0358] SEQ ID NO: 571 is the determined cDNA sequence for clone 63716628.

[0359] SEQ ID NO: 572 is the determined cDNA sequence for clone 63716629.

[0360] SEQ ID NO: 573 is the determined cDNA sequence for clone 63716630.

[0361] SEQ ID NO: 574 is the determined cDNA sequence for clone 63716631.

[0362] SEQ ID NO: 575 is the determined cDNA sequence for clone 63716632.

[0363] SEQ ID NO: 576 is the determined cDNA sequence for clone 63716633.

[0364] SEQ ID NO: 577 is the determined cDNA sequence for clone 63716634.

[0365] SEQ ID NO: 578 is the determined cDNA sequence for clone 63716635.

[0366] SEQ ID NO: 579 is the determined cDNA sequence for clone 63716636.

[0367] SEQ ID NO: 580 is the determined cDNA sequence for clone 63716638.

[0368] SEQ ID NO: 581 is the determined cDNA sequence for clone 63716639.

[0369] SEQ ID NO: 582 is the determined cDNA sequence for clone 63716640.

[0370] SEQ ID NO: 583 is the determined cDNA sequence for clone 63716641.

[0371] SEQ ID NO: 584 is the determined cDNA sequence for clone 63716642.

[0372] SEQ ID NO: 585 is the determined cDNA sequence for clone 63716643.

[0373] SEQ ID NO: 586 is the determined cDNA sequence for clone 63716645.

[0374] SEQ ID NO: 587 is the determined cDNA sequence for clone 63716647.

[0375] SEQ ID NO: 588 is the determined cDNA sequence for clone 63716648.

[0376] SEQ ID NO: 589 is the determined cDNA sequence for clone 63716649.

[0377] SEQ ID NO: 590 is the determined cDNA sequence for clone 63716650.

[0378] SEQ ID NO: 591 is the determined cDNA sequence for clone 63716651.

[0379] SEQ ID NO: 592 is the determined cDNA sequence for clone 63716652.

[0380] SEQ ID NO: 593 is the determined cDNA sequence for clone 63716654.

[0381] SEQ ID NO: 594 is the determined cDNA sequence for clone 63716656.

[0382] SEQ ID NO: 595 is the determined cDNA sequence for clone 63716657.

[0383] SEQ ID NO: 596 is the determined cDNA sequence for clone 63716658.

[0384] SEQ ID NO: 597 is the determined cDNA sequence for clone 63716659.

[0385] SEQ ID NO: 598 is the determined cDNA sequence for clone 63716660.

[0386] SEQ ID NO: 599 is the determined cDNA sequence for clone 63716661.

[0387] SEQ ID NO: 600 is the determined cDNA sequence for clone 63716662.

[0388] SEQ ID NO: 601 is the determined cDNA sequence for clone 63716663.

[0389] SEQ ID NO: 602 is the determined cDNA sequence for clone 63716665.

[0390] SEQ ID NO: 603 is the determined cDNA sequence for clone 63716666.

[0391] SEQ ID NO: 604 is the determined cDNA sequence for clone 63716667.

[0392] SEQ ID NO: 605 is the determined cDNA sequence for clone 63716669.

[0393] SEQ ID NO: 606 is the determined cDNA sequence for clone 63716671.

[0394] SEQ ID NO: 607 is the determined cDNA sequence for clone 63716672.

[0395] SEQ ID NO: 608 is the determined cDNA sequence for clone 63716674.

[0396] SEQ ID NO: 609 is the determined cDNA sequence for clone 63716675.

[0397] SEQ ID NO: 610 is the determined cDNA sequence for clone 63716677.

[0398] SEQ ID NO: 611 is the determined cDNA sequence for clone 63716678.

[0399] SEQ ID NO: 612 is the determined cDNA sequence for clone 63716679.

[0400] SEQ ID NO: 613 is the determined cDNA sequence for clone 63716680.

[0401] SEQ ID NO: 614 is the determined cDNA sequence for clone 63716681.

[0402] SEQ ID NO: 615 is the determined cDNA sequence for clone 63716682.

[0403] SEQ ID NO: 616 is the determined cDNA sequence for clone 63716684.

[0404] SEQ ID NO: 617 is the determined cDNA sequence for clone 63716685.

[0405] SEQ ID NO: 618 is the determined cDNA sequence for clone 63716686.

[0406] SEQ ID NO: 619 is the determined cDNA sequence for clone 63716687.

[0407] SEQ ID NO: 620 is the determined cDNA sequence for clone 63716688.

[0408] SEQ ID NO: 621 is the determined cDNA sequence for clone 63716691.

[0409] SEQ ID NO: 622 is the determined cDNA sequence for clone 63716692.

[0410] SEQ ID NO: 623 is the determined cDNA sequence for clone 63716693.

[0411] SEQ ID NO: 624 is the determined cDNA sequence for clone 63716695.

[0412] SEQ ID NO: 625 is the determined cDNA sequence for clone 63716696.

[0413] SEQ ID NO: 626 is the determined cDNA sequence for clone 63716697.

[0414] SEQ ID NO: 627 is the determined cDNA sequence for clone 63716698.

[0415] SEQ ID NO: 628 is the determined cDNA sequence for clone 63716701.

[0416] SEQ ID NO: 629 is the determined cDNA sequence for clone 63716702.

[0417] SEQ ID NO: 630 is the determined cDNA sequence for clone 63716703.

[0418] SEQ ID NO: 631 is the determined cDNA sequence for clone 63716704.

[0419] SEQ ID NO: 632 is the determined cDNA sequence for clone 63716705.

[0420] SEQ ID NO: 633 is the determined cDNA sequence for clone 63716707.

[0421] SEQ ID NO: 634 is the determined cDNA sequence for clone 63716708.

[0422] SEQ ID NO: 635 is the determined cDNA sequence for clone 63716710.

[0423] SEQ ID NO: 636 is the determined cDNA sequence for clone 63716711.

[0424] SEQ ID NO: 637 is the determined cDNA sequence for clone 63716712.

[0425] SEQ ID NO: 638 is the determined cDNA sequence for clone 63716713.

[0426] SEQ ID NO: 639 is the determined cDNA sequence for clone 63716715.

[0427] SEQ ID NO: 640 is the determined cDNA sequence for clone 63716716.

[0428] SEQ ID NO: 641 is the determined cDNA sequence for clone 63716717.

[0429] SEQ ID NO: 642 is the determined cDNA sequence for clone 63716718.

[0430] SEQ ID NO: 643 is the determined cDNA sequence for clone 63716720.

[0431] SEQ ID NO: 644 is the determined cDNA sequence for clone 63716721.

[0432] SEQ ID NO: 645 is the determined cDNA sequence for clone 63716722.

[0433] SEQ ID NO: 646 is the determined cDNA sequence for clone 63716723.

[0434] SEQ ID NO: 647 is the determined cDNA sequence for clone 63716724.

[0435] SEQ ID NO: 648 is the determined cDNA sequence for clone 63716725.

[0436] SEQ ID NO: 649 is the determined cDNA sequence for clone 63716726.

[0437] SEQ ID NO: 650 is the determined cDNA sequence for clone 63716727.

[0438] SEQ ID NO: 651 is the determined cDNA sequence for clone 63716728.

[0439] SEQ ID NO: 652 is the determined cDNA sequence for clone 63716729.

[0440] SEQ ID NO: 653 is the determined cDNA sequence for clone 63716730.

[0441] SEQ ID NO: 654 is the determined cDNA sequence for clone 63716732.

[0442] SEQ ID NO: 655 is the determined cDNA sequence for clone 63716733.

[0443] SEQ ID NO: 656 is the determined cDNA sequence for clone 63716734.

[0444] SEQ ID NO: 657 is the determined cDNA sequence for clone 63716735.

[0445] SEQ ID NO: 658 is the determined cDNA sequence for clone 63716736.

[0446] SEQ ID NO: 659 is the determined cDNA sequence for clone 63716737.

[0447] SEQ ID NO: 660 is the determined cDNA sequence for clone 63716738.

[0448] SEQ ID NO: 661 is the determined cDNA sequence for clone 63716739.

[0449] SEQ ID NO: 662 is the determined cDNA sequence for clone 63716742.

[0450] SEQ ID NO: 663 is the determined cDNA sequence for clone 63716743.

[0451] SEQ ID NO: 664 is the determined cDNA sequence for clone 63716744.

[0452] SEQ ID NO: 665 is the determined cDNA sequence for clone 63716745.

[0453] SEQ ID NO: 666 is the determined cDNA sequence for clone 63716746.

[0454] SEQ ID NO: 667 is the determined cDNA sequence for clone 63716747.

[0455] SEQ ID NO: 668 is the determined cDNA sequence for clone 63716748.

[0456] SEQ ID NO: 669 is the determined cDNA sequence for clone 63716749.

[0457] SEQ ID NO: 670 is the determined cDNA sequence for clone 63716750.

[0458] SEQ ID NO: 671 is the determined cDNA sequence for clone 63716754.

[0459] SEQ ID NO: 672 is the determined cDNA sequence for clone 63716757.

[0460] SEQ ID NO: 673 is the determined cDNA sequence for clone 63716758.

[0461] SEQ ID NO: 674 is the determined cDNA sequence for clone 63716759.

[0462] SEQ ID NO: 675 is the determined cDNA sequence for clone 63716760.

[0463] SEQ ID NO: 676 is the determined cDNA sequence for clone 63716761.

[0464] SEQ ID NO: 677 is the determined cDNA sequence for clone 63716762.

[0465] SEQ ID NO: 678 is the determined cDNA sequence for clone 63716763.

[0466] SEQ ID NO: 679 is the determined cDNA sequence for clone 63716764.

[0467] SEQ ID NO: 680 is the determined cDNA sequence for clone 63716765.

[0468] SEQ ID NO: 681 is the determined cDNA sequence for clone 63716766.

[0469] SEQ ID NO: 682 is the determined cDNA sequence for clone 63716768.

[0470] SEQ ID NO: 683 is the determined cDNA sequence for clone 63716769.

[0471] SEQ ID NO: 684 is the determined cDNA sequence for clone 63716770.

[0472] SEQ ID NO: 685 is the determined cDNA sequence for clone 63716771.

[0473] SEQ ID NO: 686 is the determined cDNA sequence for clone 63716773.

[0474] SEQ ID NO: 687 is the determined cDNA sequence for clone 63716774.

[0475] SEQ ID NO: 688 is the determined cDNA sequence for clone 63716775.

[0476] SEQ ID NO: 689 is the determined cDNA sequence for clone 63716776.

[0477] SEQ ID NO: 690 is the determined cDNA sequence for clone 63716777.

[0478] SEQ ID NO: 691 is the determined cDNA sequence for clone 63716778.

[0479] SEQ ID NO: 692 is the determined cDNA sequence for clone 63716779.

[0480] SEQ ID NO: 693 is the determined cDNA sequence for clone 63716780.

[0481] SEQ ID NO: 694 is the determined cDNA sequence for clone 63716781.

[0482] SEQ ID NO: 695 is the determined cDNA sequence for clone 63716782.

[0483] SEQ ID NO: 696 is the determined cDNA sequence for clone 63716783.

[0484] SEQ ID NO: 697 is the determined cDNA sequence for clone 63716784.

[0485] SEQ ID NO: 698 is the determined cDNA sequence for clone 63716785.

[0486] SEQ ID NO: 699 is the determined cDNA sequence for clone 63716509.

[0487] SEQ ID NO: 700 is the determined cDNA sequence for clone 63716510.

[0488] SEQ ID NO: 701 is the determined cDNA sequence for clone 63716511.

[0489] SEQ ID NO: 702 is the determined cDNA sequence for clone 63716512.

[0490] SEQ ID NO: 703 is the determined cDNA sequence for clone 63716516.

[0491] SEQ ID NO: 704 is the determined cDNA sequence for clone 63716517.

[0492] SEQ ID NO: 705 is the determined cDNA sequence for clone 63716518.

[0493] SEQ ID NO: 706 is the determined cDNA sequence for clone 63716520.

[0494] SEQ ID NO: 707 is the determined cDNA sequence for clone 63716521.

[0495] SEQ ID NO: 708 is the determined cDNA sequence for clone 63716522.

[0496] SEQ ID NO: 709 is the determined cDNA sequence for clone 63716527.

[0497] SEQ ID NO: 710 is the determined cDNA sequence for clone 63716528.

[0498] SEQ ID NO: 711 is the determined cDNA sequence for clone 63716531.

[0499] SEQ ID NO: 712 is the determined cDNA sequence for clone 63716532.

[0500] SEQ ID NO: 713 is the determined cDNA sequence for clone 63716533.

[0501] SEQ ID NO: 714 is the determined cDNA sequence for clone 63716534.

[0502] SEQ ID NO: 715 is the determined cDNA sequence for clone 63716535.

[0503] SEQ ID NO: 716 is the determined cDNA sequence for clone 63716536.

[0504] SEQ ID NO: 717 is the determined cDNA sequence for clone 63716537.

[0505] SEQ ID NO: 718 is the determined cDNA sequence for clone 63716538.

[0506] SEQ ID NO: 719 is the determined cDNA sequence for clone 63716540.

[0507] SEQ ID NO: 720 is the determined cDNA sequence for clone 63716541.

[0508] SEQ ID NO: 721 is the determined cDNA sequence for clone 63716543.

[0509] SEQ ID NO: 722 is the determined cDNA sequence for clone 63716544.

[0510] SEQ ID NO: 723 is the determined cDNA sequence for clone 63716545.

[0511] SEQ ID NO: 724 is the determined cDNA sequence for clone 63716547.

[0512] SEQ ID NO: 725 is the determined cDNA sequence for clone 63716548.

[0513] SEQ ID NO: 726 is the determined cDNA sequence for clone 63716549.

[0514] SEQ ID NO: 727 is the determined cDNA sequence for clone 63716550.

[0515] SEQ ID NO: 728 is the determined cDNA sequence for clone 63716551.

[0516] SEQ ID NO: 729 is the determined cDNA sequence for clone 63716552.

[0517] SEQ ID NO: 730 is the determined cDNA sequence for clone 63716553.

[0518] SEQ ID NO: 731 is the determined cDNA sequence for clone 63716555.

[0519] SEQ ID NO: 732 is the determined cDNA sequence for clone 63716557.

[0520] SEQ ID NO: 733 is the determined cDNA sequence for clone 63716558.

[0521] SEQ ID NO: 734 is the determined cDNA sequence for clone 63716559.

[0522] SEQ ID NO: 735 is the determined cDNA sequence for clone 63716560.

[0523] SEQ ID NO: 736 is the determined cDNA sequence for clone 63716561.

[0524] SEQ ID NO: 737 is the determined cDNA sequence for clone 63716562.

[0525] SEQ ID NO: 738 is the determined cDNA sequence for clone 63716563.

[0526] SEQ ID NO: 739 is the determined cDNA sequence for clone 63716564.

[0527] SEQ ID NO: 740 is the determined cDNA sequence for clone 63716566.

[0528] SEQ ID NO: 741 is the determined cDNA sequence for clone 63716568.

[0529] SEQ ID NO: 742 is the determined cDNA sequence for clone 63716569.

[0530] SEQ ID NO: 743 is the determined cDNA sequence for clone 63716570.

[0531] SEQ ID NO: 744 is the determined cDNA sequence for clone 63716571.

[0532] SEQ ID NO: 745 is the determined cDNA sequence for clone 63716572.

[0533] SEQ ID NO: 746 is the determined cDNA sequence for clone 63716573.

[0534] SEQ ID NO: 747 is the determined cDNA sequence for clone 63716574.

[0535] SEQ ID NO: 748 is the determined cDNA sequence for clone 63716575.

[0536] SEQ ID NO: 749 is the determined cDNA sequence for clone 63716577.

[0537] SEQ ID NO: 750 is the determined cDNA sequence for clone 63716578.

[0538] SEQ ID NO: 751 is the determined cDNA sequence for clone 63716579.

[0539] SEQ ID NO: 752 is the determined cDNA sequence for clone 63716580.

[0540] SEQ ID NO: 753 is the determined cDNA sequence for clone 63716581.

[0541] SEQ ID NO: 754 is the determined cDNA sequence for clone 63716582.

[0542] SEQ ID NO: 755 is the determined cDNA sequence for clone 63716583.

[0543] SEQ ID NO: 756 is the determined cDNA sequence for clone 63716584.

[0544] SEQ ID NO: 757 is the determined cDNA sequence for clone 63716585.

[0545] SEQ ID NO: 758 is the determined cDNA sequence for clone 63716586.

[0546] SEQ ID NO: 759 is the determined cDNA sequence for clone 63716587.

[0547] SEQ ID NO: 760 is the determined cDNA sequence for clone 63716588.

[0548] SEQ ID NO: 761 is the determined cDNA sequence for clone 63716589.

[0549] SEQ ID NO: 762 is the determined cDNA sequence for clone 63716590.

[0550] SEQ ID NO: 763 is the determined cDNA sequence for clone 63716591.

[0551] SEQ ID NO: 764 is the determined cDNA sequence for clone 63716593.

[0552] SEQ ID NO: 765 is the determined cDNA sequence for clone 63716594.

[0553] SEQ ID NO: 766 is the determined cDNA sequence for clone 63716596.

[0554] SEQ ID NO: 767 is the determined cDNA sequence for clone 63716597.

[0555] SEQ ID NO: 768 is the determined cDNA sequence for clone 63716598.

[0556] SEQ ID NO: 769 is the determined cDNA sequence for clone 63716599.

[0557] SEQ ID NO: 770 is the determined cDNA sequence for clone 63716321.

[0558] SEQ ID NO: 771 is the determined cDNA sequence for clone 63716322.

[0559] SEQ ID NO: 772 is the determined cDNA sequence for clone 63716323.

[0560] SEQ ID NO: 773 is the determined cDNA sequence for clone 63716324.

[0561] SEQ ID NO: 774 is the determined cDNA sequence for clone 63716325.

[0562] SEQ ID NO: 775 is the determined cDNA sequence for clone 63716326.

[0563] SEQ ID NO: 776 is the determined cDNA sequence for clone 63716327.

[0564] SEQ ID NO: 777 is the determined cDNA sequence for clone 63716328.

[0565] SEQ ID NO: 778 is the determined cDNA sequence for clone 63716329.

[0566] SEQ ID NO: 779 is the determined cDNA sequence for clone 63716330.

[0567] SEQ ID NO: 780 is the determined cDNA sequence for clone 63716331.

[0568] SEQ ID NO: 781 is the determined cDNA sequence for clone 63716333.

[0569] SEQ ID NO: 782 is the determined cDNA sequence for clone 63716335.

[0570] SEQ ID NO: 783 is the determined cDNA sequence for clone 63716336.

[0571] SEQ ID NO: 784 is the determined cDNA sequence for clone 63716337.

[0572] SEQ ID NO: 785 is the determined cDNA sequence for clone 63716338.

[0573] SEQ ID NO: 786 is the determined cDNA sequence for clone 63716339.

[0574] SEQ ID NO: 787 is the determined cDNA sequence for clone 63716341.

[0575] SEQ ID NO: 788 is the determined cDNA sequence for clone 63716342.

[0576] SEQ ID NO: 789 is the determined cDNA sequence for clone 63716343.

[0577] SEQ ID NO: 790 is the determined cDNA sequence for clone 63716344.

[0578] SEQ ID NO: 791 is the determined cDNA sequence for clone 63716345.

[0579] SEQ ID NO: 792 is the determined cDNA sequence for clone 63716346.

[0580] SEQ ID NO: 793 is the determined cDNA sequence for clone 63716347.

[0581] SEQ ID NO: 794 is the determined cDNA sequence for clone 63716350.

[0582] SEQ ID NO: 795 is the determined cDNA sequence for clone 63716353.

[0583] SEQ ID NO: 796 is the determined cDNA sequence for clone 63716354.

[0584] SEQ ID NO: 797 is the determined cDNA sequence for clone 63716355.

[0585] SEQ ID NO: 798 is the determined cDNA sequence for clone 63716356.

[0586] SEQ ID NO: 799 is the determined cDNA sequence for clone 63716357.

[0587] SEQ ID NO: 800 is the determined cDNA sequence for clone 63716359.

[0588] SEQ ID NO: 801 is the determined cDNA sequence for clone 63716360.

[0589] SEQ ID NO: 802 is the determined cDNA sequence for clone 63716361.

[0590] SEQ ID NO: 803 is the determined cDNA sequence for clone 63716362.

[0591] SEQ ID NO: 804 is the determined cDNA sequence for clone 63716363.

[0592] SEQ ID NO: 805 is the determined cDNA sequence for clone 63716364.

[0593] SEQ ID NO: 806 is the determined cDNA sequence for clone 63716365.

[0594] SEQ ID NO: 807 is the determined cDNA sequence for clone 63716366.

[0595] SEQ ID NO: 808 is the determined cDNA sequence for clone 63716368.

[0596] SEQ ID NO: 809 is the determined cDNA sequence for clone 63716370.

[0597] SEQ ID NO: 810 is the determined cDNA sequence for clone 63716371.

[0598] SEQ ID NO: 811 is the determined cDNA sequence for clone 63716372.

[0599] SEQ ID NO: 812 is the determined cDNA sequence for clone 63716373.

[0600] SEQ ID NO: 813 is the determined cDNA sequence for clone 63716374.

[0601] SEQ ID NO: 814 is the determined cDNA sequence for clone 63716375.

[0602] SEQ ID NO: 815 is the determined cDNA sequence for clone 63716376.

[0603] SEQ ID NO: 816 is the determined cDNA sequence for clone 63716377.

[0604] SEQ ID NO: 817 is the determined cDNA sequence for clone 63716378.

[0605] SEQ ID NO: 818 is the determined cDNA sequence for clone 63716379.

[0606] SEQ ID NO: 819 is the determined cDNA sequence for clone 63716380.

[0607] SEQ ID NO: 820 is the determined cDNA sequence for clone 63716381.

[0608] SEQ ID NO: 821 is the determined cDNA sequence for clone 63716382.

[0609] SEQ ID NO: 822 is the determined cDNA sequence for clone 63716383.

[0610] SEQ ID NO: 823 is the determined cDNA sequence for clone 63716384.

[0611] SEQ ID NO: 824 is the determined cDNA sequence for clone 63716385.

[0612] SEQ ID NO: 825 is the determined cDNA sequence for clone 63716386.

[0613] SEQ ID NO: 826 is the determined cDNA sequence for clone 63716387.

[0614] SEQ ID NO: 827 is the determined cDNA sequence for clone 63716388.

[0615] SEQ ID NO: 828 is the determined cDNA sequence for clone 63716390.

[0616] SEQ ID NO: 829 is the determined cDNA sequence for clone 63716391.

[0617] SEQ ID NO: 830 is the determined cDNA sequence for clone 63716392.

[0618] SEQ ID NO: 831 is the determined cDNA sequence for clone 63716393.

[0619] SEQ ID NO: 832 is the determined cDNA sequence for clone 63716394.

[0620] SEQ ID NO: 833 is the determined cDNA sequence for clone 63716396.

[0621] SEQ ID NO: 834 is the determined cDNA sequence for clone 63716398.

[0622] SEQ ID NO: 835 is the determined cDNA sequence for clone 63716399.

[0623] SEQ ID NO: 836 is the determined cDNA sequence for clone 63716400.

[0624] SEQ ID NO: 837 is the determined cDNA sequence for clone 63716401.

[0625] SEQ ID NO: 838 is the determined cDNA sequence for clone 63716402.

[0626] SEQ ID NO: 839 is the determined cDNA sequence for clone 63716403.

[0627] SEQ ID NO: 840 is the determined cDNA sequence for clone 63716404.

[0628] SEQ ID NO: 841 is the determined cDNA sequence for clone 63716405.

[0629] SEQ ID NO: 842 is the determined cDNA sequence for clone 63716406.

[0630] SEQ ID NO: 843 is the determined cDNA sequence for clone 63716407.

[0631] SEQ ID NO: 844 is the determined cDNA sequence for clone 63716408.

[0632] SEQ ID NO: 845 is the determined cDNA sequence for clone 63716409.

[0633] SEQ ID NO: 846 is the determined cDNA sequence for clone 63716411.

[0634] SEQ ID NO: 847 is the determined cDNA sequence for clone 63716412.

[0635] SEQ ID NO: 848 is the determined cDNA sequence for clone 63716413.

[0636] SEQ ID NO: 849 is the determined cDNA sequence for clone 63298609.

[0637] SEQ ID NO: 850 is the determined cDNA sequence for clone 63298610.

[0638] SEQ ID NO: 851 is the determined cDNA sequence for clone 63298612.

[0639] SEQ ID NO: 852 is the determined cDNA sequence for clone 63298613.

[0640] SEQ ID NO: 853 is the determined cDNA sequence for clone 63298614.

[0641] SEQ ID NO: 854 is the determined cDNA sequence for clone 63298615.

[0642] SEQ ID NO: 855 is the determined cDNA sequence for clone 63298617.

[0643] SEQ ID NO: 856 is the determined cDNA sequence for clone 63298618.

[0644] SEQ ID NO: 857 is the determined cDNA sequence for clone 63298619.

[0645] SEQ ID NO: 858 is the determined cDNA sequence for clone 63298620.

[0646] SEQ ID NO: 859 is the determined cDNA sequence for clone 63298621.

[0647] SEQ ID NO: 860 is the determined cDNA sequence for clone 63298622.

[0648] SEQ ID NO: 861 is the determined cDNA sequence for clone 63298623.

[0649] SEQ ID NO: 862 is the determined cDNA sequence for clone 63298624.

[0650] SEQ ID NO: 863 is the determined cDNA sequence for clone 63298625.

[0651] SEQ ID NO: 864 is the determined cDNA sequence for clone 63298626.

[0652] SEQ ID NO: 865 is the determined cDNA sequence for clone 63298627.

[0653] SEQ ID NO: 866 is the determined cDNA sequence for clone 63298628.

[0654] SEQ ID NO: 867 is the determined cDNA sequence for clone 63298629.

[0655] SEQ ID NO: 868 is the determined cDNA sequence for clone 63298630.

[0656] SEQ ID NO: 869 is the determined cDNA sequence for clone 63298632.

[0657] SEQ ID NO: 870 is the determined cDNA sequence for clone 63298633.

[0658] SEQ ID NO: 871 is the determined cDNA sequence for clone 63298634.

[0659] SEQ ID NO: 872 is the determined cDNA sequence for clone 63298635.

[0660] SEQ ID NO: 873 is the determined cDNA sequence for clone 63298636.

[0661] SEQ ID NO: 874 is the determined cDNA sequence for clone 63298637.

[0662] SEQ ID NO: 875 is the determined cDNA sequence for clone 63298638.

[0663] SEQ ID NO: 876 is the determined cDNA sequence for clone 63298639.

[0664] SEQ ID NO: 877 is the determined cDNA sequence for clone 63298640.

[0665] SEQ ID NO: 878 is the determined cDNA sequence for clone 63298641.

[0666] SEQ ID NO: 879 is the determined cDNA sequence for clone 63298642.

[0667] SEQ ID NO: 880 is the determined cDNA sequence for clone 63298643.

[0668] SEQ ID NO: 881 is the determined cDNA sequence for clone 63298644.

[0669] SEQ ID NO: 882 is the determined cDNA sequence for clone 63298645.

[0670] SEQ ID NO: 883 is the determined cDNA sequence for clone 63298646.

[0671] SEQ ID NO: 884 is the determined cDNA sequence for clone 63298647.

[0672] SEQ ID NO: 885 is the determined cDNA sequence for clone 63298649.

[0673] SEQ ID NO: 886 is the determined cDNA sequence for clone 63298650.

[0674] SEQ ID NO: 887 is the determined cDNA sequence for clone 63298651.

[0675] SEQ ID NO: 888 is the determined cDNA sequence for clone 63298652.

[0676] SEQ ID NO: 889 is the determined cDNA sequence for clone 63298653.

[0677] SEQ ID NO: 890 is the determined cDNA sequence for clone 63298654.

[0678] SEQ ID NO: 891 is the determined cDNA sequence for clone 63298655.

[0679] SEQ ID NO: 892 is the determined cDNA sequence for clone 63298656.

[0680] SEQ ID NO: 893 is the determined cDNA sequence for clone 63298657.

[0681] SEQ ID NO: 894 is the determined cDNA sequence for clone 63298658.

[0682] SEQ ID NO: 895 is the determined cDNA sequence for clone 63298659.

[0683] SEQ ID NO: 896 is the determined cDNA sequence for clone 63298660.

[0684] SEQ ID NO: 897 is the determined cDNA sequence for clone 63298662.

[0685] SEQ ID NO: 898 is the determined cDNA sequence for clone 63298663.

[0686] SEQ ID NO: 899 is the determined cDNA sequence for clone 63298665.

[0687] SEQ ID NO: 900 is the determined cDNA sequence for clone 63298666.

[0688] SEQ ID NO: 901 is the determined cDNA sequence for clone 63298667.

[0689] SEQ ID NO: 902 is the determined cDNA sequence for clone 63298668.

[0690] SEQ ID NO: 903 is the determined cDNA sequence for clone 63298669.

[0691] SEQ ID NO: 905 is the determined :DNA sequence for clone 63298671.

[0692] SEQ ID NO: 906 is the determined cDNA sequence for clone 63298672.

[0693] SEQ ID NO: 907 is the determined cDNA sequence for clone 63298673.

[0694] SEQ ID NO: 908 is the determined cDNA sequence for clone 63298675.

[0695] SEQ ID NO: 909 is the determined cDNA sequence for clone 63298677.

[0696] SEQ ID NO: 909 is the determined cDNA sequence for clone 63298678.

[0697] SEQ ID NO: 910 is the determined cDNA sequence for clone 63298679.

[0698] SEQ ID NO: 912 is the determined cDNA sequence for clone 63298678.

[0699] SEQ ID NO: 913 is the determined cDNA sequence for clone 63298682.

[0700] SEQ ID NO: 914 is the determined cDNA sequence for clone 63298683.

[0701] SEQ ID NO: 915 is the determined cDNA sequence for clone 63298685.

[0702] SEQ ID NO: 915 is the determined cDNA sequence for clone 63298685.

[0703] SEQ ID NO: 916 is the determined cDNA sequence for clone 63298686.

[0704] SEQ ID NO: 917 is the determined cDNA sequence for clone 63298687.

[0705] SEQ ID NO: 918 is the determined cDNA sequence for clone 63298688.

[0706] SEQ ID NO: 919 is the determined cDNA sequence for clone 63298689.

[0707] SEQ ID NO: 920 is the determined cDNA sequence for clone 63298690.

[0708] SEQ ID NO: 921 is the determined cDNA sequence for clone 63298691.

[0709] SEQ ID NO: 922 is the determined cDNA sequence for clone 63298692.

[0710] SEQ ID NO: 923 is the determined cDNA sequence for clone 63298693.

[0711] SEQ ID NO: 924 is the determined cDNA sequence for clone 63298694.

[0712] SEQ ID NO: 925 is the determined cDNA sequence for clone 63298695.

[0713] SEQ ID NO: 926 is the determined cDNA sequence for clone 63298697.

[0714] SEQ ID NO: 927 is the determined cDNA sequence for clone 63298698.

[0715] SEQ ID NO: 928 is the determined cDNA sequence for clone 63298700.

[0716] SEQ ID NO: 929 is the determined cDNA sequence for clone 63298701.

[0717] SEQ ID NO: 930 is the determined cDNA sequence for clone 63716228.

[0718] SEQ ID NO: 931 is the determined cDNA sequence for clone 63716229.

[0719] SEQ ID NO: 932 is the determined cDNA sequence for clone 63716231.

[0720] SEQ ID NO: 933 is the determined cDNA sequence for clone 63716232.

[0721] SEQ ID NO: 934 is the determined cDNA sequence for clone 63716233.

[0722] SEQ ID NO: 935 is the determined cDNA sequence for clone 63716234.

[0723] SEQ ID NO: 936 is the determined cDNA sequence for clone 63716235.

[0724] SEQ ID NO: 937 is the determined cDNA sequence for clone 63716236.

[0725] SEQ ID NO: 938 is the determined cDNA sequence for clone 63716237.

[0726] SEQ ID NO: 939 is the determined cDNA sequence for clone 63716238.

[0727] SEQ ID NO: 940 is the determined cDNA sequence for clone 63716241.

[0728] SEQ ID NO: 941 is the determined cDNA sequence for clone 63716242.

[0729] SEQ ID NO: 942 is the determined cDNA sequence for clone 63716243.

[0730] SEQ ID NO: 943 is the determined cDNA sequence for clone 63716244.

[0731] SEQ ID NO: 944 is the determined cDNA sequence for clone 63716245.

[0732] SEQ ID NO: 945 is the determined cDNA sequence for clone 63716246.

[0733] SEQ ID NO: 946 is the determined cDNA sequence for clone 63716247.

[0734] SEQ ID NO: 947 is the determined cDNA sequence for clone 63716248.

[0735] SEQ ID NO: 948 is the determined cDNA sequence for clone 63716250.

[0736] SEQ ID NO: 949 is the determined cDNA sequence for clone 63716251.

[0737] SEQ ID NO: 950 is the determined cDNA sequence for clone 63716252.

[0738] SEQ ID NO: 951 is the determined cDNA sequence for clone 63716253.

[0739] SEQ ID NO: 952 is the determined cDNA sequence for clone 63716254.

[0740] SEQ ID NO: 953 is the determined cDNA sequence for clone 63716255.

[0741] SEQ ID NO: 954 is the determined cDNA sequence for clone 63716256.

[0742] SEQ ID NO: 955 is the determined cDNA sequence for clone 63716257.

[0743] SEQ ID NO: 956 is the determined cDNA sequence for clone 63716260.

[0744] SEQ ID NO: 957 is the determined cDNA sequence for clone 63716261.

[0745] SEQ ID NO: 958 is the determined cDNA sequence for clone 63716262.

[0746] SEQ ID NO: 959 is the determined cDNA sequence for clone 63716263.

[0747] SEQ ID NO: 960 is the determined cDNA sequence for clone 63716264.

[0748] SEQ ID NO: 961 is the determined cDNA sequence for clone 63716265.

[0749] SEQ ID NO: 962 is the determined cDNA sequence for clone 63716266.

[0750] SEQ ID NO: 963 is the determined cDNA sequence for clone 63716267.

[0751] SEQ ID NO: 964 is the determined cDNA sequence for clone 63716268.

[0752] SEQ ID NO: 965 is the determined cDNA sequence for clone 63716269.

[0753] SEQ ID NO: 966 is the determined cDNA sequence for clone 63716270.

[0754] SEQ ID NO: 967 is the determined cDNA sequence for clone 63716272.

[0755] SEQ ID NO: 968 is the determined cDNA sequence for clone 63716273.

[0756] SEQ ID NO: 969 is the determined cDNA sequence for clone 63716275.

[0757] SEQ ID NO: 970 is the determined cDNA sequence for clone 63716277.

[0758] SEQ ID NO: 971 is the determined cDNA sequence for clone 63716278.

[0759] SEQ ID NO: 972 is the determined cDNA sequence for clone 63716279.

[0760] SEQ ID NO: 973 is the determined cDNA sequence for clone 63716281.

[0761] SEQ ID NO: 974 is the determined cDNA sequence for clone 63716282.

[0762] SEQ ID NO: 975 is the determined cDNA sequence for clone 63716283.

[0763] SEQ ID NO: 976 is the determined cDNA sequence for clone 63716284.

[0764] SEQ ID NO: 977 is the determined cDNA sequence for clone 63716285.

[0765] SEQ ID NO: 978 is the determined cDNA sequence for clone 63716286.

[0766] SEQ ID NO: 979 is the determined cDNA sequence for clone 63716287.

[0767] SEQ ID NO: 980 is the determined cDNA sequence for clone 63716289.

[0768] SEQ ID NO: 981 is the determined cDNA sequence for clone 63716290.

[0769] SEQ ID NO: 982 is the determined cDNA sequence for clone 63716291.

[0770] SEQ ID NO: 983 is the determined cDNA sequence for clone 63716292.

[0771] SEQ ID NO: 984 is the determined cDNA sequence for clone 63716293.

[0772] SEQ ID NO: 985 is the determined cDNA sequence for clone 63716294.

[0773] SEQ ID NO: 986 is the determined cDNA sequence for clone 63716295.

[0774] SEQ ID NO: 987 is the determined cDNA sequence for clone 63716296.

[0775] SEQ ID NO: 988 is the determined cDNA sequence for clone 63716297.

[0776] SEQ ID NO: 989 is the determined cDNA sequence for clone 63716298.

[0777] SEQ ID NO: 990 is the determined cDNA sequence for clone 63716299.

[0778] SEQ ID NO: 991 is the determined cDNA sequence for clone 63716300.

[0779] SEQ ID NO: 992 is the determined cDNA sequence for clone 63716301.

[0780] SEQ ID NO: 993 is the determined cDNA sequence for clone 63716303.

[0781] SEQ ID NO: 994 is the determined cDNA sequence for clone 63716304.

[0782] SEQ ID NO: 995 is the determined cDNA sequence for clone 63716306.

[0783] SEQ ID NO: 996 is the determined cDNA sequence for clone 63716307.

[0784] SEQ ID NO: 997 is the determined cDNA sequence for clone 63716308.

[0785] SEQ ID NO: 998 is the determined cDNA sequence for clone 63716309.

[0786] SEQ ID NO: 999 is the determined cDNA sequence for clone 63716310.

[0787] SEQ ID NO: 1000 is the determined cDNA sequence for clone 63716311.

[0788] SEQ ID NO: 1001 is the determined cDNA sequence for clone 63716312.

[0789] SEQ ID NO: 1002 is the determined cDNA sequence for clone 63716313.

[0790] SEQ ID NO: 1003 is the determined cDNA sequence for clone 63716314.

[0791] SEQ ID NO: 1004 is the determined cDNA sequence for clone 63716315.

[0792] SEQ ID NO: 1005 is the determined cDNA sequence for clone 63716316.

[0793] SEQ ID NO: 1006 is the determined cDNA sequence for clone 63716317.

[0794] SEQ ID NO: 1007 is the determined cDNA sequence for clone 63716318.

[0795] SEQ ID NO: 1008 is the determined cDNA sequence for clone 63716319.

[0796] SEQ ID NO: 1009 is the determined cDNA sequence for clone 63716320.

[0797] SEQ ID NO: 1010 is the determined cDNA sequence for clone 63751255.

[0798] SEQ ID NO: 1011 is the determined cDNA sequence for clone 63751256.

[0799] SEQ ID NO: 1012 is the determined cDNA sequence for clone 63751259.

[0800] SEQ ID NO: 1013 is the determined cDNA sequence for clone 63751261.

[0801] SEQ ID NO: 1014 is the determined cDNA sequence for clone 63751265.

[0802] SEQ ID NO: 1015 is the determined cDNA sequence for clone 63751266.

[0803] SEQ ID NO: 1016 is the determined cDNA sequence for clone 63751267.

[0804] SEQ ID NO: 1017 is the determined cDNA sequence for clone 63751268.

[0805] SEQ ID NO: 1018 is the determined cDNA sequence for clone 63751269.

[0806] SEQ ID NO: 1019 is the determined cDNA sequence for clone 63751270.

[0807] SEQ ID NO: 1020 is the determined cDNA sequence for clone 63751271.

[0808] SEQ ID NO: 1021 is the determined cDNA sequence for clone 63751272.

[0809] SEQ ID NO: 1022 is the determined cDNA sequence for clone 63751277.

[0810] SEQ ID NO: 1023 is the determined cDNA sequence for clone 63751278.

[0811] SEQ ID NO: 1024 is the determined cDNA sequence for clone 63751279.

[0812] SEQ ID NO: 1025 is the determined cDNA sequence for clone 63751280.

[0813] SEQ ID NO: 1026 is the determined cDNA sequence for clone 63751281.

[0814] SEQ ID NO: 1027 is the determined cDNA sequence for clone 63751283.

[0815] SEQ ID NO: 1028 is the determined cDNA sequence for clone 63751288.

[0816] SEQ ID NO: 1029 is the determined cDNA sequence for clone 63751289.

[0817] SEQ ID NO: 1030 is the determined cDNA sequence for clone 63751290.

[0818] SEQ ID NO: 1031 is the determined cDNA sequence for clone 63751291.

[0819] SEQ ID NO: 1032 is the determined cDNA sequence for clone 63751294.

[0820] SEQ ID NO: 1033 is the determined cDNA sequence for clone 63751295.

[0821] SEQ ID NO: 1034 is the determined cDNA sequence for clone 63751296.

[0822] SEQ ID NO: 1035 is the determined cDNA sequence for clone 63751300.

[0823] SEQ ID NO: 1036 is the determined cDNA sequence for clone 63751301.

[0824] SEQ ID NO: 1037 is the determined cDNA sequence for clone 63751302.

[0825] SEQ ID NO: 1038 is the determined cDNA sequence for clone 63751303.

[0826] SEQ ID NO: 1039 is the determined cDNA sequence for clone 63751304.

[0827] SEQ ID NO: 1040 is the determined cDNA sequence for clone 63751305.

[0828] SEQ ID NO: 1041 is the determined cDNA sequence for clone 63751306.

[0829] SEQ ID NO: 1042 is the determined cDNA sequence for clone 63751307.

[0830] SEQ ID NO: 1043 is the determined cDNA sequence for clone 63751308.

[0831] SEQ ID NO: 1044 is the determined cDNA sequence for clone 63751309.

[0832] SEQ ID NO: 1045 is the determined cDNA sequence for clone 63751312.

[0833] SEQ ID NO: 1046 is the determined cDNA sequence for clone 63751313.

[0834] SEQ ID NO: 1047 is the determined cDNA sequence for clone 63751314.

[0835] SEQ ID NO: 1048 is the determined cDNA sequence for clone 63751315.

[0836] SEQ ID NO: 1049 is the determined cDNA sequence for clone 63751316.

[0837] SEQ ID NO: 1050 is the determined cDNA sequence for clone 63751317.

[0838] SEQ ID NO: 1051 is the determined cDNA sequence for clone 63751318.

[0839] SEQ ID NO: 1052 is the determined cDNA sequence for clone 63751319.

[0840] SEQ ID NO: 1053 is the determined cDNA sequence for clone 63751320.

[0841] SEQ ID NO: 1054 is the determined cDNA sequence for clone 63751321.

[0842] SEQ ID NO: 1055 is the determined cDNA sequence for clone 63751322.

[0843] SEQ ID NO: 1056 is the determined cDNA sequence for clone 63751324.

[0844] SEQ ID NO: 1057 is the determined cDNA sequence for clone 63751325.

[0845] SEQ ID NO: 1058 is the determined cDNA sequence for clone 63751326.

[0846] SEQ ID NO: 1059 is the determined cDNA sequence for clone 63751327.

[0847] SEQ ID NO: 1060 is the determined cDNA sequence for clone 63751328.

[0848] SEQ ID NO: 1061 is the determined cDNA sequence for clone 63751329.

[0849] SEQ ID NO: 1062 is the determined cDNA sequence for clone 63751330.

[0850] SEQ ID NO: 1063 is the determined cDNA sequence for clone 63751331.

[0851] SEQ ID NO: 1064 is the determined cDNA sequence for clone 63751332.

[0852] SEQ ID NO: 1065 is the determined cDNA sequence for clone 63751333.

[0853] SEQ ID NO: 1066 is the determined cDNA sequence for clone 63751334.

[0854] SEQ ID NO: 1067 is the determined cDNA sequence for clone 63751335.

[0855] SEQ ID NO: 1068 is the determined cDNA sequence for clone 63751336.

[0856] SEQ ID NO: 1069 is the determined cDNA sequence for clone 63751337.

[0857] SEQ ID NO: 1070 is the determined cDNA sequence for clone 63751339.

[0858] SEQ ID NO: 1071 is the determined cDNA sequence for clone 63751340.

[0859] SEQ ID NO: 1072 is the determined cDNA sequence for clone 63751341.

[0860] SEQ ID NO: 1073 is the determined cDNA sequence for clone 63751342.

[0861] SEQ ID NO: 1074 is the determined cDNA sequence for clone 63751343.

[0862] SEQ ID NO: 1075 is the determined cDNA sequence for clone 63751344.

[0863] SEQ ID NO: 1076 is the determined cDNA sequence for clone 63751345.

[0864] SEQ ID NO: 1077 is the determined cDNA sequence for clone 63751346.

[0865] SEQ ID NO: 1078 is the determined cDNA sequence for clone 63298704.

[0866] SEQ ID NO: 1079 is the determined cDNA sequence for clone 63298705.

[0867] SEQ ID NO: 1080 is the determined cDNA sequence for clone 63298706.

[0868] SEQ ID NO: 1081 is the determined cDNA sequence for clone 63298707.

[0869] SEQ ID NO: 1082 is the determined cDNA sequence for clone 63298708.

[0870] SEQ ID NO: 1083 is the determined cDNA sequence for clone 63298709.

[0871] SEQ ID NO: 1084 is the determined cDNA sequence for clone 63298710.

[0872] SEQ ID NO: 1085 is the determined cDNA sequence for clone 63298711.

[0873] SEQ ID NO: 1086 is the determined cDNA sequence for clone 63298712.

[0874] SEQ ID NO: 1087 is the determined cDNA sequence for clone 63298714.

[0875] SEQ ID NO: 1088 is the determined cDNA sequence for clone 63298715.

[0876] SEQ ID NO: 1089 is the determined cDNA sequence for clone 63298716.

[0877] SEQ ID NO: 1090 is the determined cDNA sequence for clone 63298717.

[0878] SEQ ID NO: 1091 is the determined cDNA sequence for clone 63298718.

[0879] SEQ ID NO: 1092 is the determined cDNA sequence for clone 63298719.

[0880] SEQ ID NO: 1093 is the determined cDNA sequence for clone 63298720.

[0881] SEQ ID NO: 1094 is the determined cDNA sequence for clone 63298721.

[0882] SEQ ID NO: 1095 is the determined cDNA sequence for clone 63298722.

[0883] SEQ ID NO: 1096 is the determined cDNA sequence for clone 63298723.

[0884] SEQ ID NO: 1097 is the determined cDNA sequence for clone 63298724.

[0885] SEQ ID NO: 1098 is the determined cDNA sequence for clone 63298725.

[0886] SEQ ID NO: 1099 is the determined cDNA sequence for clone 63298726.

[0887] SEQ ID NO: 1100 is the determined cDNA sequence for clone 63298727.

[0888] SEQ ID NO: 1101 is the determined cDNA sequence for clone 63298728.

[0889] SEQ ID NO: 1102 is the determined cDNA sequence for clone 63298729.

[0890] SEQ ID NO: 1103 is the determined cDNA sequence for clone 63298730.

[0891] SEQ ID NO: 1104 is the determined cDNA sequence for clone 63298731.

[0892] SEQ ID NO: 1105 is the determined cDNA sequence for clone 63298732.

[0893] SEQ ID NO: 1106 is the determined cDNA sequence for clone 63298733.

[0894] SEQ ID NO: 1107 is the determined cDNA sequence for clone 63298734.

[0895] SEQ ID NO: 1108 is the determined cDNA sequence for clone 63298735.

[0896] SEQ ID NO: 1109 is the determined cDNA sequence for clone 63298736.

[0897] SEQ ID NO: 1110 is the determined cDNA sequence for clone 63298738.

[0898] SEQ ID NO: 1111 is the determined cDNA sequence for clone 63298739.

[0899] SEQ ID NO: 1112 is the determined cDNA sequence for clone 63298740.

[0900] SEQ ID NO: 1113 is the determined cDNA sequence for clone 63298741.

[0901] SEQ ID NO: 1114 is the determined cDNA sequence for clone 63298742.

[0902] SEQ ID NO: 1115 is the determined cDNA sequence for clone 63298743.

[0903] SEQ ID NO: 1116 is the determined cDNA sequence for clone 63298744.

[0904] SEQ ID NO: 1117 is the determined cDNA sequence for clone 63298745.

[0905] SEQ ID NO: 1118 is the determined cDNA sequence for clone 63298746.

[0906] SEQ ID NO: 1119 is the determined cDNA sequence for clone 63298747.

[0907] SEQ ID NO: 1120 is the determined cDNA sequence for clone 63298748.

[0908] SEQ ID NO: 1121 is the determined cDNA sequence for clone 63298749.

[0909] SEQ ID NO: 1122 is the determined cDNA sequence for clone 63298750.

[0910] SEQ ID NO: 1123 is the determined cDNA sequence for clone 63298751.

[0911] SEQ ID NO: 1124 is the determined cDNA sequence for clone 63298753.

[0912] SEQ ID NO: 1125 is the determined cDNA sequence for clone 63298754.

[0913] SEQ ID NO: 1126 is the determined cDNA sequence for clone 63298755.

[0914] SEQ ID NO: 1127 is the determined cDNA sequence for clone 63298756.

[0915] SEQ ID NO: 1128 is the determined cDNA sequence for clone 63298759.

[0916] SEQ ID NO: 1129 is the determined cDNA sequence for clone 63298761.

[0917] SEQ ID NO: 1130 is the determined cDNA sequence for clone 63298762.

[0918] SEQ ID NO: 1131 is the determined cDNA sequence for clone 63298763.

[0919] SEQ ID NO: 1132 is the determined cDNA sequence for clone 63298764.

[0920] SEQ ID NO: 1133 is the determined cDNA sequence for clone 63298765.

[0921] SEQ ID NO: 1134 is the determined cDNA sequence for clone 63298766.

[0922] SEQ ID NO: 1135 is the determined cDNA sequence for clone 63298767.

[0923] SEQ ID NO: 1136 is the determined cDNA sequence for clone 63298768.

[0924] SEQ ID NO: 1137 is the determined cDNA sequence for clone 63298769.

[0925] SEQ ID NO: 1138 is the determined cDNA sequence for clone 63298770.

[0926] SEQ ID NO: 1139 is the determined cDNA sequence for clone 63298771.

[0927] SEQ ID NO: 1140 is the determined cDNA sequence for clone 63298772.

[0928] SEQ ID NO: 1141 is the determined cDNA sequence for clone 63298774.

[0929] SEQ ID NO: 1142 is the determined cDNA sequence for clone 63298776.

[0930] SEQ ID NO: 1143 is the determined cDNA sequence for clone 63298777.

[0931] SEQ ID NO: 1144 is the determined cDNA sequence for clone 63298778.

[0932] SEQ ID NO: 1145 is the determined cDNA sequence for clone 63298779.

[0933] SEQ ID NO: 1146 is the determined cDNA sequence for clone 63298780.

[0934] SEQ ID NO: 1147 is the determined cDNA sequence for clone 63298781.

[0935] SEQ ID NO: 1148 is the determined cDNA sequence for clone 63298782.

[0936] SEQ ID NO: 1149 is the determined cDNA sequence for clone 63298783.

[0937] SEQ ID NO: 1150 is the determined cDNA sequence for clone 63298786.

[0938] SEQ ID NO: 1151 is the determined cDNA sequence for clone 63298787.

[0939] SEQ ID NO: 1152 is the determined cDNA sequence for clone 63298788.

[0940] SEQ ID NO: 1153 is the determined cDNA sequence for clone 63298789.

[0941] SEQ ID NO: 1154 is the determined cDNA sequence for clone 63298790.

[0942] SEQ ID NO: 1155 is the determined cDNA sequence for clone 63298791.

[0943] SEQ ID NO: 1156 is the determined cDNA sequence for clone 63298792.

[0944] SEQ ID NO: 1157 is the determined cDNA sequence for clone 63298793.

[0945] SEQ ID NO: 1158 is the determined cDNA sequence for clone 63298794.

[0946] SEQ ID NO: 1159 is the determined cDNA sequence for clone 63298981.

[0947] SEQ ID NO: 1160 is the determined cDNA sequence for clone 63298983.

[0948] SEQ ID NO: 1161 is the determined cDNA sequence for clone 63298984.

[0949] SEQ ID NO: 1162 is the determined cDNA sequence for clone 63298985.

[0950] SEQ ID NO: 1163 is the determined cDNA sequence for clone 63298986.

[0951] SEQ ID NO: 1164 is the determined cDNA sequence for clone 63298987.

[0952] SEQ ID NO: 1165 is the determined cDNA sequence for clone 63298988.

[0953] SEQ ID NO: 1166 is the determined cDNA sequence for clone 63298989.

[0954] SEQ ID NO: 1167 is the determined cDNA sequence for clone 63298990.

[0955] SEQ ID NO: 1168 is the determined cDNA sequence for clone 63298991.

[0956] SEQ ID NO: 1169 is the determined cDNA sequence for clone 63298994.

[0957] SEQ ID NO: 1170 is the determined cDNA sequence for clone 63298995.

[0958] SEQ ID NO: 1171 is the determined cDNA sequence for clone 63298997.

[0959] SEQ ID NO: 1172 is the determined cDNA sequence for clone 63298999.

[0960] SEQ ID NO: 1173 is the determined cDNA sequence for clone 63299000.

[0961] SEQ ID NO: 1174 is the determined cDNA sequence for clone 63299001.

[0962] SEQ ID NO: 1175 is the determined cDNA sequence for clone 63299002.

[0963] SEQ ID NO: 1176 is the determined cDNA sequence for clone 63299003.

[0964] SEQ ID NO: 1177 is the determined cDNA sequence for clone 63299004.

[0965] SEQ ID NO: 1178 is the determined cDNA sequence for clone 63299005.

[0966] SEQ ID NO: 1179 is the determined cDNA sequence for clone 63299006.

[0967] SEQ ID NO: 1180 is the determined cDNA sequence for clone 63299008.

[0968] SEQ ID NO: 1181 is the determined cDNA sequence for clone 63299009.

[0969] SEQ ID NO: 1182 is the determined cDNA sequence for clone 63299010.

[0970] SEQ ID NO: 1183 is the determined cDNA sequence for clone 63299011.

[0971] SEQ ID NO: 1184 is the determined cDNA sequence for clone 63299012.

[0972] SEQ ID NO: 1185 is the determined cDNA sequence for clone 63299013.

[0973] SEQ ID NO: 1186 is the determined cDNA sequence for clone 63299014.

[0974] SEQ ID NO: 1187 is the determined cDNA sequence for clone 63299027.

[0975] SEQ ID NO: 1188 is the determined cDNA sequence for clone 63299028.

[0976] SEQ ID NO: 1189 is the determined cDNA sequence for clone 63299029.

[0977] SEQ ID NO: 1190 is the determined cDNA sequence for clone 63299030.

[0978] SEQ ID NO: 1191 is the determined cDNA sequence for clone 63299031.

[0979] SEQ ID NO: 1192 is the determined cDNA sequence for clone 63299032.

[0980] SEQ ID NO: 1193 is the determined cDNA sequence for clone 63299033.

[0981] SEQ ID NO: 1194 is the determined cDNA sequence for clone 63299034.

[0982] SEQ ID NO: 1195 is the determined cDNA sequence for clone 63299035.

[0983] SEQ ID NO: 1196 is the determined cDNA sequence for clone 63299036.

[0984] SEQ ID NO: 1197 is the determined cDNA sequence for clone 63299037.

[0985] SEQ ID NO: 1198 is the determined cDNA sequence for clone 63299038.

[0986] SEQ ID NO: 1199 is the determined cDNA sequence for clone 63299039.

[0987] SEQ ID NO: 1200 is the determined cDNA sequence for clone 63299040.

[0988] SEQ ID NO: 1201 is the determined cDNA sequence for clone 63299042.

[0989] SEQ ID NO: 1202 is the determined cDNA sequence for clone 63299043.

[0990] SEQ ID NO: 1203 is the determined cDNA sequence for clone 63299044.

[0991] SEQ ID NO: 1204 is the determined cDNA sequence for clone 63299045.

[0992] SEQ ID NO: 1205 is the determined cDNA sequence for clone 63299047.

[0993] SEQ ID NO: 1206 is the determined cDNA sequence for clone 63299048.

[0994] SEQ ID NO: 1207 is the determined cDNA sequence for clone 63299051.

[0995] SEQ ID NO: 1208 is the determined cDNA sequence for clone 63299052.

[0996] SEQ ID NO: 1209 is the determined cDNA sequence for clone 63299053.

[0997] SEQ ID NO: 1210 is the determined cDNA sequence for clone 63299055.

[0998] SEQ ID NO: 1211 is the determined cDNA sequence for clone 63299057.

[0999] SEQ ID NO: 1212 is the determined cDNA sequence for clone 63299058.

[1000] SEQ ID NO: 1213 is the determined cDNA sequence for clone 63299059.

[1001] SEQ ID NO: 1214 is the determined cDNA sequence for clone 63299060.

[1002] SEQ ID NO: 1215 is the determined cDNA sequence for clone 63299061.

[1003] SEQ ID NO: 1216 is the determined cDNA sequence for clone 63299062.

[1004] SEQ ID NO: 1217 is the determined cDNA sequence for clone 63299063.

[1005] SEQ ID NO: 1218 is the determined cDNA sequence for clone 63299064.

[1006] SEQ ID NO: 1219 is the determined cDNA sequence for clone 63299065.

[1007] SEQ ID NO: 1220 is the determined cDNA sequence for clone 63299066.

[1008] SEQ ID NO: 1221 is the determined cDNA sequence for clone 63299067.

[1009] SEQ ID NO: 1222 is the determined cDNA sequence for clone 63299070.

[1010] SEQ ID NO: 1223 is the determined cDNA sequence for clone 63299071.

[1011] SEQ ID NO: 1224 is the determined cDNA sequence for clone 63299072.

[1012] SEQ ID NO: 1225 is the determined cDNA sequence for clone 63299073.

[1013] SEQ ID NO: 1226 is the determined cDNA sequence for clone 63717532.

[1014] SEQ ID NO: 1227 is the determined cDNA sequence for clone 63717533.

[1015] SEQ ID NO: 1228 is the determined cDNA sequence for clone 63717535.

[1016] SEQ ID NO: 1229 is the determined cDNA sequence for clone 63717537.

[1017] SEQ ID NO: 1230 is the determined cDNA sequence for clone 63717538.

[1018] SEQ ID NO: 1231 is the determined cDNA sequence for clone 63717539.

[1019] SEQ ID NO: 1232 is the determined cDNA sequence for clone 63717540.

[1020] SEQ ID NO: 1233 is the determined cDNA sequence for clone 63717542.

[1021] SEQ ID NO: 1234 is the determined cDNA sequence for clone 63717543.

[1022] SEQ ID NO: 1235 is the determined cDNA sequence for clone 63717544.

[1023] SEQ ID NO: 1236 is the determined cDNA sequence for clone 63717545.

[1024] SEQ ID NO: 1237 is the determined cDNA sequence for clone 63717546.

[1025] SEQ ID NO: 1238 is the determined cDNA sequence for clone 63717547.

[1026] SEQ ID NO: 1239 is the determined cDNA sequence for clone 63717548.

[1027] SEQ ID NO: 1240 is the determined cDNA sequence for clone 63717549.

[1028] SEQ ID NO: 1241 is the determined cDNA sequence for clone 63717550.

[1029] SEQ ID NO: 1242 is the determined cDNA sequence for clone 63717551.

[1030] SEQ ID NO: 1243 is the determined cDNA sequence for clone 63717552.

[1031] SEQ ID NO: 1244 is the determined cDNA sequence for clone 63717553.

[1032] SEQ ID NO: 1245 is the determined cDNA sequence for clone 63717554.

[1033] SEQ ID NO: 1246 is the determined cDNA sequence for clone 63717555.

[1034] SEQ ID NO: 1247 is the determined cDNA sequence for clone 63717557.

[1035] SEQ ID NO: 1248 is the determined cDNA sequence for clone 63717558.

[1036] SEQ ID NO: 1249 is the determined cDNA sequence for clone 63717559.

[1037] SEQ ID NO: 1250 is the determined cDNA sequence for clone 63717560.

[1038] SEQ ID NO: 1251 is the determined cDNA sequence for clone 63717561.

[1039] SEQ ID NO: 1252 is the determined cDNA sequence for clone 63717562.

[1040] SEQ ID NO: 1253 is the determined cDNA sequence for clone 63717563.

[1041] SEQ ID NO: 1254 is the determined cDNA sequence for clone 63717564.

[1042] SEQ ID NO: 1255 is the determined cDNA sequence for clone 63717565.

[1043] SEQ ID NO: 1256 is the determined cDNA sequence for clone 63717566.

[1044] SEQ ID NO: 1257 is the determined cDNA sequence for clone 63717567.

[1045] SEQ ID NO: 1258 is the determined cDNA sequence for clone 63717568.

[1046] SEQ ID NO: 1259 is the determined cDNA sequence for clone 63717569.

[1047] SEQ ID NO: 1260 is the determined cDNA sequence for clone 63717571.

[1048] SEQ ID NO: 1261 is the determined cDNA sequence for clone 63717572.

[1049] SEQ ID NO: 1262 is the determined cDNA sequence for clone 63717573.

[1050] SEQ ID NO: 1263 is the determined cDNA sequence for clone 63717574.

[1051] SEQ ID NO: 1264 is the determined cDNA sequence for clone 63717575.

[1052] SEQ ID NO: 1265 is the determined cDNA sequence for clone 63717576.

[1053] SEQ ID NO: 1266 is the determined cDNA sequence for clone 63717578.

[1054] SEQ ID NO: 1267 is the determined cDNA sequence for clone 63717579.

[1055] SEQ ID NO: 1268 is the determined cDNA sequence for clone 63717580.

[1056] SEQ ID NO: 1269 is the determined cDNA sequence for clone 63717581.

[1057] SEQ ID NO: 1270 is the determined cDNA sequence for clone 63717582.

[1058] SEQ ID NO: 1271 is the determined cDNA sequence for clone 63717583.

[1059] SEQ ID NO: 1272 is the determined cDNA sequence for clone 63717584.

[1060] SEQ ID NO: 1273 is the determined cDNA sequence for clone 63717586.

[1061] SEQ ID NO: 1274 is the determined cDNA sequence for clone 63717587.

[1062] SEQ ID NO: 1275 is the determined cDNA sequence for clone 63717588.

[1063] SEQ ID NO: 1276 is the determined cDNA sequence for clone 63717589.

[1064] SEQ ID NOs: 1277-1323 are the determined cDNA sequences described in Tables 11 and 12.

[1065] SEQ ID NO: 1324 is the determined cDNA sequence for clone R0639: B04_C882P.

[1066] SEQ ID NO: 1325 is the determined cDNA sequence for clone RO647: A08_Homo.

[1067] SEQ ID NO: 1326 is the determined cDNA sequence for clone RO638: G01_Homo.

[1068] SEQ ID NO: 1327 is the determined cDNA sequence for clone RO637: E03_Homo.

[1069] SEQ ID NO: 1328 is the determined cDNA sequence for clone RO637: E04_C919P.

[1070] SEQ ID NO: 1329 is the determined cDNA sequence for clone RO647: D08_Homo.

[1071] SEQ ID NO: 1330 is the determined cDNA sequence for clone RO639: D12_C968P.

[1072] SEQ ID NO: 1331 is the determined cDNA sequence for clone RO644: C03_C915P.

[1073] SEQ ID NO: 1332 is the determined cDNA sequence for clone RO643: B12_C919P.

[1074] SEQ ID NO: 1333 is the determined cDNA sequence for clone R0641: C09_Homo.

[1075] SEQ ID NO: 1334 is the determined cDNA sequence for clone RO637: H11_Novel.

[1076] SEQ ID NO: 1335 is the determined cDNA sequence for clone R0636: D12_Homo.

[1077] SEQ ID NO: 1336 is the determined cDNA sequence for clone RO638: G10-Homo.

[1078] SEQ ID NO: 1337 is the determined cDNA sequence for clone RO642: G06_Homo.

[1079] SEQ ID NO: 1338 is the determined cDNA sequence for clone R0637: B08_Homo.

[1080] SEQ ID NO: 1339 is the determined cDNA sequence for clone R0636: E09_Homo.

[1081] SEQ ID NO: 1340 is the determined cDNA sequence for clone R0637: B03_Human.

[1082] SEQ ID NO: 1341 is the determined cDNA sequence for clone 637D12_Homo.

[1083] SEQ ID NO: 1342 is the determined cDNA sequence for clone RO642: G04_Homo.

[1084] SEQ ID NO: 1343 is the determined cDNA sequence for clone R0641: G08_Homo.

[1085] SEQ ID NO: 1344 is the determined cDNA sequence for clone R0642: F08_Human.

[1086] SEQ ID NO: 1345 is the determined cDNA sequence for clone RO644: F01—H.sapiens.

[1087] SEQ ID NO: 1346 is the determined cDNA sequence for clone RO637: E06_Homo.

[1088] SEQ ID NO: 1347 is the determined cDNA sequence for clone R0642: G07_Human.

[1089] SEQ ID NO: 1348 is the determined cDNA sequence for clone R0641: C04_Homo.

[1090] SEQ ID NO: 1349 is the determined cDNA sequence for clone R0639: E11_Homo.

[1091] SEQ ID NO: 1350 is the determined cDNA sequence for clone RO641: A06_Homo.

[1092] SEQ ID NO: 1351 is the determined cDNA sequence for clone R0636: F05_Homo.

[1093] SEQ ID NO: 1352 is the determined cDNA sequence for clone R0640: F09_Homo.

[1094] SEQ ID NO: 1353 is the determined cDNA sequence for clone R0643: E06_C882P.

[1095] SEQ ID NO: 1354 is the determined cDNA sequence for clone RO639: H11_Homo.

[1096] SEQ ID NO: 1355 is the determined cDNA sequence for clone R0642: F02_B723P.

[1097] SEQ ID NO: 1356 is the determined cDNA sequence for clone R0644: B_C27E.

[1098] SEQ ID NO: 1357 is the determined cDNA sequence for clone R0644: A12_C882P.

[1099] SEQ ID NO: 1358 is the determined cDNA sequence for clone RO636: D06_Homo.

[1100] SEQ ID NO: 1359 is the determined cDNA sequence for clone R0636: B04_Homo.

[1101] SEQ ID NO: 1360 is the determined cDNA sequence for clone R0641: C07_Novel.

[1102] SEQ ID NO: 1361 is the determined cDNA sequence for clone RO646: H07_H.

[1103] SEQ ID NO: 1362 is the determined cDNA sequence for clone R0641: D01_Novel.

[1104] SEQ ID NO: 1363 is the determined cDNA sequence for clone 70848_B512S.

[1105] SEQ ID NO: 1364 is the determined cDNA sequence for clone 70855_C798P.

[1106] SEQ ID NO: 1365 is the determined cDNA sequence for clone 70875_Homo.

[1107] SEQ ID NO: 1366 is the determined cDNA sequence for clone 70919_Homo.

[1108] SEQ ID NO: 1367 is the determined cDNA sequence for clone 70830_Homo.

[1109] SEQ ID NO: 1368 is the determined cDNA sequence for clone 70847_Homo.

[1110] SEQ ID NO: 1369 is the determined cDNA sequence for clone 70869_Homo.

[1111] SEQ ID NO: 1370 is the determined cDNA sequence for clone 70836_C968P.

[1112] SEQ ID NO: 1371 is the determined cDNA sequence for clone 70849_Novel.

[1113] SEQ ID NO: 1372 is the determined cDNA sequence for clone 70878_Human.

[1114] SEQ ID NO: 1373 is the determined cDNA sequence for clone 70844_Homo.

[1115] SEQ ID NO: 1374 is the determined cDNA sequence for clone 67024.2.

[1116] SEQ ID NO: 1375 is the determined cDNA sequence for clone 65134.2.

[1117] SEQ ID NO: 1376 is the determined cDNA sequence for clone 65328.2.

[1118] SEQ ID NO: 1377 is the determined cDNA sequence for clone 71341.2.

[1119] SEQ ID NO: 1378 is the determined cDNA sequence for clone 70249.2.

[1120] SEQ ID NO: 1379 is the determined cDNA sequence for clone 70254.2.

[1121] SEQ ID NO: 1380 is the determined cDNA sequence for clone 71347.2.

[1122] SEQ ID NO: 1381 is the determined cDNA sequence for clone 71352.2.

[1123] SEQ ID NO: 1382 is the determined cDNA sequence for clone 71353.2.

[1124] SEQ ID NO: 1383 is the determined cDNA sequence for clone 71353.1.

[1125] SEQ ID NO: 1384 is the determined cDNA sequence for clone 71354.2.

[1126] SEQ ID NO: 1385 is the determined cDNA sequence for clone 71355.1.

[1127] SEQ ID NO: 1386 is the determined cDNA sequence for clone 71356.2.

[1128] SEQ ID NO: 1387 is the determined cDNA sequence for clone 71358.2.

[1129] SEQ ID NO: 1388 is the determined cDNA sequence for clone 71362.2.

[1130] SEQ ID NO: 1389 is the determined cDNA sequence for clone 70261.2.

[1131] SEQ ID NO: 1390 is the determined cDNA sequence for clone 71366.2.

[1132] SEQ ID NO: 1391 is the determined cDNA sequence for clone 70263.2.

[1133] SEQ ID NO: 1392 is the determined cDNA sequence for clone 71367.1.

[1134] SEQ ID NO: 1393 is the determined cDNA sequence for clone 71368.1.

[1135] SEQ ID NO: 1394 is the determined cDNA sequence for clone 70265.2.

[1136] SEQ ID NO: 1395 is the determined cDNA sequence for clone 71372.2.

[1137] SEQ ID NO: 1396 is the determined cDNA sequence for clone 71385.2.

[1138] SEQ ID NO: 1397 is the determined cDNA sequence for clone 71388.2.

[1139] SEQ ID NO: 1398 is the determined cDNA sequence for clone 73031.2.

[1140] SEQ ID NO: 1399 is the determined cDNA sequence for clone 73038.2.

[1141] SEQ ID NO: 1400 is the determined cDNA sequence for clone 73044.2.

[1142] SEQ ID NO: 1401 is the determined cDNA sequence for clone 73049.2.

[1143] SEQ ID NO: 1402 is the determined cDNA sequence for clone 73052.2.

[1144] SEQ ID NO: 1403 is the determined cDNA sequence for clone 73058.1.

[1145] SEQ ID NO: 1404 is the determined cDNA sequence for clone 73061.2.

[1146] SEQ ID NO: 1405 is the determined cDNA sequence for clone 73062.2.

[1147] SEQ ID NO: 1406 is the determined cDNA sequence for clone 73068.2.

[1148] SEQ ID NO: 1407 is the determined cDNA sequence for clone 73072.1.

[1149] SEQ ID NO: 1408 is the determined cDNA sequence for clone 73076.2.

[1150] SEQ ID NO: 1409 is the determined cDNA sequence for clone 75425.2.

[1151] SEQ ID NO: 1410 is the determined cDNA sequence for clone 75444.2.

[1152] SEQ ID NO: 1411 is the determined cDNA sequence for clone 75451.2.

[1153] SEQ ID NO: 1412 is the determined cDNA sequence for clone 75456.2.

[1154] SEQ ID NO: 1413 is the determined cDNA sequence for clone 75461.2.

[1155] SEQ ID NO: 1414 is the determined cDNA sequence for clone 75462.2.

[1156] SEQ ID NO: 1415 is the determined cDNA sequence for clone 75465.2.

[1157] SEQ ID NO: 1416 is the determined cDNA sequence for clone 75483.2.

[1158] SEQ ID NO: 1417 is the determined cDNA sequence for clone 75486.2.

[1159] SEQ ID NO: 1418 is the determined cDNA sequence for C634S.

[1160] SEQ ID NO: 1419 is the determined cDNA sequence for C635S.

[1161] SEQ ID NO: 1420 is the determined cDNA sequence for C636S.

[1162] SEQ ID NO: 1421 is the determined cDNA sequence for C637S.

[1163] SEQ ID NO: 1422 is the predicted amino acid sequence of C634S, encoded by the nucleotide sequence set forth in SEQ ID NO: 1418.

[1164] SEQ ID NO: 1423 is the predicted amino acid sequence of C635S, encoded 25 by the nucleotide sequence set forth in SEQ ID NO: 1419.

[1165] SEQ ID NO: 1424 is the predicted amino acid sequence of C637S, encoded by the nucleotide sequence set forth in SEQ ID NO: 1421.

[1166] SEQ ID NO: 1425 is the determined cDNA sequence for C640S.

[1167] SEQ ID NO: 1426 is the predicted amino acid sequence of C640S, encoded by the nucleotide sequence set forth in SEQ ID NO: 1421.

[1168] SEQ ID NO: 1427 is the extended determined cDNA sequence for C636S.

[1169] SEQ ID NO: 1428 is the amino acid sequence of one of the potential ORFs of C636S.

[1170] SEQ ID NO: 1429 is the amino acid sequence of a second potential ORF of C636S.

[1171] SEQ ID NOs: 1430-3417 are the determined cDNA sequences from subtracted colon tumor libraries as described in Examples 12 and 13 and set forth in the table below.

1Sequence IdentifiercDNA Clone No:SEQ ID NO: 143062116379SEQ ID NO: 143162116380SEQ ID NO: 143262116381SEQ ID NO: 143362116382SEQ ID NO: 143462116384SEQ ID NO: 143562116385SEQ ID NO: 143662116386SEQ ID NO: 143762116387SEQ ID NO: 143862116388SEQ ID NO: 143962116389SEQ ID NO: 144062116390SEQ ID NO: 144162116391SEQ ID NO: 144262116392SEQ ID NO: 144362116393SEQ ID NO: 144462116395SEQ ID NO: 144562116397SEQ ID NO: 144662116398SEQ ID NO: 144762116399SEQ ID NO: 144862116400SEQ ID NO: 144962116401SEQ ID NO: 145062116403SEQ ID NO: 145162116404SEQ ID NO: 145262116405SEQ ID NO: 145362116406SEQ ID NO: 145462116407SEQ ID NO: 145562116408SEQ ID NO: 145662116409SEQ ID NO: 145762116410SEQ ID NO: 145862116411SEQ ID NO: 145962116412SEQ ID NO: 146062116413SEQ ID NO: 146162116414SEQ ID NO: 146262116415SEQ ID NO: 146362116416SEQ ID NO: 146462116417SEQ ID NO: 146562116418SEQ ID NO: 146662116419SEQ ID NO: 146762116420SEQ ID NO: 146862116422SEQ ID NO: 146962116423SEQ ID NO: 147062116424SEQ ID NO: 147162116425SEQ ID NO: 147262116427SEQ ID NO: 147362116428SEQ ID NO: 147462116429SEQ ID NO: 147562116430SEQ ID NO: 147662116431SEQ ID NO: 147762116432SEQ ID NO: 147862116433SEQ ID NO: 147962116434SEQ ID NO: 148062116435SEQ ID NO: 148162116436SEQ ID NO: 148262116437SEQ ID NO: 148362116438SEQ ID NO: 148462116439SEQ ID NO: 148562116440SEQ ID NO: 148662116441SEQ ID NO: 148762116442SEQ ID NO: 148862116443SEQ ID NO: 148962116444SEQ ID NO: 149062116446SEQ ID NO: 149162116447SEQ ID NO: 149262116448SEQ ID NO: 149362116449SEQ ID NO: 149462116452SEQ ID NO: 149562116453SEQ ID NO: 149662116454SEQ ID NO: 149762116455SEQ ID NO: 149862116456SEQ ID NO: 149962116457SEQ ID NO: 150062116458SEQ ID NO: 150162116460SEQ ID NO: 150262116461SEQ ID NO: 150362116464SEQ ID NO: 150462116465SEQ ID NO: 150562116466SEQ ID NO: 150662116467SEQ ID NO: 150762116468SEQ ID NO: 150862116469SEQ ID NO: 150962116470SEQ ID NO: 151062116471SEQ ID NO: 151162108766SEQ ID NO: 151262108767SEQ ID NO: 151362108769SEQ ID NO: 151462108770SEQ ID NO: 151562108771SEQ ID NO: 151662108772SEQ ID NO: 151762108773SEQ ID NO: 151862108774SEQ ID NO: 151962108775SEQ ID NO: 152062108776SEQ ID NO: 152162108777SEQ ID NO: 152262108778SEQ ID NO: 152362108779SEQ ID NO: 152462108780SEQ ID NO: 152562108781SEQ ID NO: 152662108782SEQ ID NO: 152762108783SEQ ID NO: 152862108784SEQ ID NO: 152962108785SEQ ID NO: 153062108786SEQ ID NO: 153162108787SEQ ID NO: 153262108788SEQ ID NO: 153362108789SEQ ID NO: 153462108790SEQ ID NO: 153562108793SEQ ID NO: 153662108795SEQ ID NO: 153762108796SEQ ID NO: 153862108797SEQ ID NO: 153962108798SEQ ID NO: 154062108799SEQ ID NO: 154162108800SEQ ID NO: 154262108801SEQ ID NO: 154362108802SEQ ID NO: 154462108803SEQ ID NO: 154562108807SEQ ID NO: 154662108809SEQ ID NO: 154762108810SEQ ID NO: 154862108811SEQ ID NO: 154962108812SEQ ID NO: 155062108813SEQ ID NO: 155162108815SEQ ID NO: 155262108817SEQ ID NO: 155362108818SEQ ID NO: 155462108819SEQ ID NO: 155562108820SEQ ID NO: 155662108823SEQ ID NO: 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DETAILED DESCRIPTION OF THE INVENTION

[1172] The present invention is directed generally to compositions and their use in the therapy and diagnosis of cancer, particularly colon 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).

[1173] 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).

[1174] All publications, patents and patent applications cited herein, whether supra or infra, are hereby incorporated by reference in their entirety.

[1175] 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.

[1176] Polypeptide Compositions

[1177] As used herein, the term “polypeptide” is used in its conventional meaning, i.e., as a sequence of amino acids. The polypeptides are not limited to a specific length of the product; thus, peptides, oligopeptides, and proteins are included within the definition of polypeptide, and such terms may be used interchangeably herein unless specifically indicated otherwise. This term also does not refer to or exclude post-expression modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations and the like, as well as other modifications known in the art, both naturally occurring and non-naturally occurring. A polypeptide may be an entire protein, or a subsequence thereof. 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.

[1178] Particularly illustrative polypeptides of the present invention comprise those encoded by a polynucleotide sequence set forth in any one of SEQ ID NOs: 1-1421, 1425, 1427, and 1430-3417, 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: 1-1421, 1425, 1427, and 1430-3417. Certain other illustrative polypeptides of the invention comprise amino acid sequences as set forth in any one of SEQ ID NOs: 1422-1424, 1426, 1428, and 1429.

[1179] The polypeptides of the present invention are sometimes herein referred to as colon tumor proteins or colon tumor polypeptides, as an indication that their identification has been based at least in part upon their increased levels of expression in colon tumor samples. Thus, a “colon tumor polypeptide” or “colon 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 colon 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 colon 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 colon 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.

[1180] 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 colon 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.

[1181] 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.

[1182] 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.

[1183] 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.

[1184] 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.

[1185] 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.

[1186] 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: 1422-1424, 1426, 1428, and 1429, or those encoded by a polynucleotide sequence set forth in a sequence of SEQ ID NOs: 1-1421, 1425, 1427, and 1430-3417.

[1187] 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.

[1188] 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.

[1189] 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.

[1190] 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.

[1191] 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.

[1192] 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.

[1193] 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.

2TABLE 1Amino AcidsCodonsAlanineAlaAGCAGCCGCGGCUCysteineCysCUGCUGUAspartic acidAspDGACGAUGlutamic acidGluEGAAGAGPhenylalaninePheFUUCUUUGlycineGlyGGGAGGCGGGGGUHistidineHisHCACCAUIsoleucineIleIAUAAUCAUULysineLysKAAAAAGLeucineLeuLUUAUUGCUACUCCUGCUUMethionineMetMAUGAsparagineAsnNAACAAUProlineProPCCACCCCCGCCUGlutamineGlnQCAACAGArginineArgRAGAAGGCGACGCCGGCGUSerineSerSAGCAGUUCAUCCUCGUCUThreonineThrTACAACCACGACUValineValVGUAGUCGUGGUUTryptophanTrpWUGGTyrosineTyrYUACUAU

[1194] 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).

[1195] 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.

[1196] 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 (0); threonine (−0.4); proline (−0.5±1); alanine (−0.5); histidine (−0.5); cysteine (−1.0); methionine (−1.3); valine (−1.5); leucine (−1.8); isoleucine (−1.8); tyrosine (−2.3); phenylalanine (−2.5); tryptophan (−3.4). 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.

[1197] 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.

[1198] 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.

[1199] 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, gln, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile, leu, met, ala, phe; (4) lys, arg, his; and (5) phe, tyr, trp, his. 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.

[1200] 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.

[1201] 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.

[1202] 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 DC Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990) Unified Approach to Alignment and Phylogenes pp. 626-645 Methods in Enzymology vol. 183, Academic Press, Inc., San Diego, 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.

[1203] 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.

[1204] 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.

[1205] 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.

[1206] 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: 1422-1424, 1426, 1428, and 1429, or those encoded by polynucleotide sequences set forth in SEQ ID NOs: 1-1421, 1425, 1427, and 1430-3417.

[1207] 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.

[1208] 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.

[1209] 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.

[1210] 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.

[1211] 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.

[1212] 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.

[1213] 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).

[1214] In one preferred embodiment, the immunological fusion partner is derived from a Mycobacterium sp., such as a Mycobacterium tuberculosis-derived Ral2 fragment. Ral2 compositions and methods for their use in enhancing the expression and/or immunogenicity of heterologous polynucleotide/polypeptide sequences is described in U.S. patent application Ser. No. 60/158,585, the disclosure of which is incorporated herein by reference in its entirety. 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 Ser. No. 60/158,585; see also, Skeiky et al., Infection and Immun. (1999) 67:3998-4007, incorporated herein by reference). C-terminal fragments of the MTB32A coding sequence express at high levels and remain as a soluble polypeptides throughout the purification process. 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.

[1215] 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.

[1216] 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.

[1217] 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.

[1218] 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.

[1219] 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.

[1220] Polynucleotide Compositions

[1221] 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.

[1222] 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.

[1223] 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.

[1224] 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.

[1225] 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: 1-1421, 1425, 1427, and 1430-3417, complements of a polynucleotide sequence set forth in any one of SEQ ID NOs: 1-1421, 1425, 1427, and 1430-3417, and degenerate variants of a polynucleotide sequence set forth in any one of SEQ ID NOs: 1-1421, 1425, 1427, and 1430 2417. In certain preferred embodiments, the polynucleotide sequences set forth herein encode immunogenic polypeptides, as described above.

[1226] In other related embodiments, the present invention provides polynucleotide variants having substantial identity to the sequences disclosed herein in SEQ ID NOs: 1-1421, 1425, 1427, and 1430-3417, 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.

[1227] 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.

[1228] 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.

[1229] 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.

[1230] 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.

[1231] 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.

[1232] 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.

[1233] 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 DC Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990) Unified Approach to Alignment and Phylogenes pp. 626-645 Methods in Enzymology vol. 183, Academic Press, Inc., San Diego, 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.

[1234] 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.

[1235] 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.

[1236] Preferably, the “percentage of sequence identity” is determined by comparing two optimally aligned sequences over a window of comparison of at least 20 positions, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) of 20 percent or less, usually 5 to 15 percent, or 10 to 12 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.

[1237] 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).

[1238] 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.

[1239] 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.

[1240] 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.

[1241] 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.

[1242] 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.

[1243] 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.

[1244] 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.

[1245] 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.

[1246] 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.

[1247] 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.

[1248] 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.

[1249] 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.

[1250] 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.

[1251] 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.

[1252] 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.

[1253] 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.

[1254] 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. June 1988, 10;240(4858):1544-6; Vasanthakumar and Ahmed, Cancer Commun. 1989;1(4):225-32; Peris et al., Brain Res Mol Brain Res. June 1998, 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).

[1255] 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).

[1256] 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.

[1257] 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. December 1987;84(24):8788-92; Forster and Symons, Cell. Apr. 24, 1997;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. December 1981;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.

[1258] 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.

[1259] 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.

[1260] 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. Publ. 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. December 1983;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.

[1261] 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.

[1262] Ribozyme activity can be optimized by altering the length of the ribozyme binding arms, or chemically synthesizing ribozymes with modifications that prevent their degradation by serum ribonucleases (see e.g, Int. Pat. Appl. Publ. No. WO 92/07065; Int. Pat. Appl. Publ. No. WO 93/15187; Int. Pat. Appl. Publ. No. WO 91/03162; Eur. Pat. Appl. Publ. No. 92110298.4; U.S. Pat. No. 5,334,711; and Int. Pat. Appl. Publ. No. WO 94/13688, which describe various chemical modifications that can be made to the sugar moieties of enzymatic RNA molecules), modifications which enhance their efficacy in cells, and removal of stem II bases to shorten RNA synthesis times and reduce chemical requirements.

[1263] Sullivan et al. (Int. Pat. Appl. 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. Publ. No. WO 93/23569, each specifically incorporated herein by reference.

[1264] 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 (poi 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).

[1265] 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 June 1997;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.

[1266] 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. January 1996;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.

[1267] 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. April 1995;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.

[1268] 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.

[1269] 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. April 1995;3(4):437-45; Petersen et al., J Pept Sci. May-June 1995;1(3):175-83; Orum et al., Biotechniques. September 1995;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 USA. Jun. 6, 1995;92(12):5592-6; Boffa et al., Proc Natl Acad Sci USA. Mar. 14, 1995;92(6):1901-5; Gambacorti-Passerini et al., Blood. Aug. 15, 1996;88(4):1411-7; Armitage et al., Proc Natl Acad Sci USA. Nov. 11, 1997;94(23):12320-5; Seeger et al., Biotechniques. September 1997;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.

[1270] 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.

[1271] 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.

[1272] Polynucleotide Identification, Characterization and Expression

[1273] 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.

[1274] 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™ amplification procedure may be performed in order to quantify the amount of mRNA amplified. Polymerase chain reaction methodologies are well known in the art.

[1275] 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. Publ. 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. Appl. Publ. No. PCT/US89/01025. Other nucleic acid amplification procedures include transcription-based amplification systems (TAS) (PCT Intl. Pat. Appl. Publ. No. WO 88/10315), including nucleic acid sequence based amplification (NASBA) and 3SR. 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. Publ. 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.

[1276] 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.

[1277] 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, NY, 1989). Hybridizing colonies or plaques are selected and expanded, and the DNA is isolated for further analysis. cDNA clones may be analyzed to determine the amount of additional sequence by, for example, PCR using a primer from the partial sequence and a primer from the vector. Restriction maps and partial sequences may be generated to identify one or more overlapping clones. The complete sequence may then be determined using standard techniques, which may involve generating a series of deletion clones. The resulting overlapping sequences can then assembled into a single contiguous sequence. A full length cDNA molecule can be generated by ligating suitable fragments, using well known techniques.

[1278] 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.

[1279] 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.

[1280] 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.

[1281] 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.

[1282] 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.

[1283] 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.

[1284] 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 431A Peptide Synthesizer (Perkin Elmer, Palo Alto, Calif.).

[1285] 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.

[1286] 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.

[1287] 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.

[1288] 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.

[1289] 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.

[1290] 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.

[1291] 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. 6:307-31 1. 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).

[1292] 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).

[1293] 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.

[1294] 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).

[1295] 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 WI38, which have specific cellular machinery and characteristic mechanisms for such post-translational activities, may be chosen to ensure the correct modification and processing of the foreign protein.

[1296] 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.

[1297] 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).

[1298] 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.

[1299] 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.

[1300] 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).

[1301] 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. 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.

[1302] 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. 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).

[1303] 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.

[1304] Antibody Compositions, Fragments Thereof and Other Binding Agents

[1305] 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.

[1306] 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 “loff 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.

[1307] 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.”

[1308] Binding agents may be further capable of differentiating between patients with and without a cancer, such as colon 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.

[1309] Any agent that satisfies the above requirements may be a binding agent. For example, a binding agent may be a ribosome, with or without a peptide component, an RNA molecule or a polypeptide. In a preferred embodiment, a binding agent is an antibody or an antigen-binding fragment thereof. Antibodies may be prepared by any of a variety of techniques known to those of ordinary skill in the art. See, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, 1988. In general, antibodies can be produced by cell culture techniques, including the generation of monoclonal antibodies as described herein, or via transfection of antibody genes into suitable bacterial or mammalian cell hosts, in order to allow for the production of recombinant antibodies. In one technique, an immunogen comprising the polypeptide is initially injected into any of a wide variety of mammals (e.g., mice, rats, rabbits, sheep or goats). In this step, the polypeptides of this invention may serve as the immunogen without modification. Alternatively, particularly for relatively short polypeptides, a superior immune response may be elicited if the polypeptide is joined to a carrier protein, such as bovine serum albumin or keyhole limpet hemocyanin. The immunogen is injected into the animal host, preferably according to a predetermined schedule incorporating one or more booster immunizations, and the animals are bled periodically. Polyclonal antibodies specific for the polypeptide may then be purified from such antisera by, for example, affinity chromatography using the polypeptide coupled to a suitable solid support. Monoclonal antibodies specific for an antigenic polypeptide of interest may be prepared, for example, using the technique of Kohler and Milstein, Eur. J. Immunol. 6:511-519, 1976, and improvements thereto. Briefly, these methods involve the preparation of immortal cell lines capable of producing antibodies having the desired specificity (i.e., reactivity with the polypeptide of interest). Such cell lines may be produced, for example, from spleen cells obtained from an animal immunized as described above. The spleen cells are then immortalized by, for example, fusion with a myeloma cell fusion partner, preferably one that is syngeneic with the immunized animal. A variety of fusion techniques may be employed. For example, the spleen cells and myeloma cells may be combined with a nonionic detergent for a few minutes and then plated at low density on a selective medium that supports the growth of hybrid cells, but not myeloma cells. A preferred selection technique uses HAT (hypoxanthine, aminopterin, thymidine) selection. After a sufficient time, usually about 1 to 2 weeks, colonies of hybrids are observed. Single colonies are selected and their culture supernatants tested for binding activity against the polypeptide. Hybridomas having high reactivity and specificity are preferred.

[1310] 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.

[1311] 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.

[1312] 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.

[1313] 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.

[1314] 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.

[1315] A number of “humanized” antibody molecules comprising an antigen-binding site derived from a non-human immunoglobulin have been described, including chimeric antibodies having rodent V regions and their associated CDRs fused to human constant domains (Winter et al. (1991) Nature 349:293-299; Lobuglio et al. (1989) Proc. Nat. Acad. Sci. USA 86:4220-4224; Shaw et al. (1987) J Immunol. 138:4534-4538; and Brown et al. (1987) Cancer Res. 47:3577-3583), rodent CDRs grafted into a human supporting FR prior to fusion with an appropriate human antibody constant domain (Riechmann et al. (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.

[1316] 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.

[1317] 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.

[1318] 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.

[1319] 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.

[1320] 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.

[1321] 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 subtituent 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.

[1322] 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 affected, 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.

[1323] 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.).

[1324] 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.

[1325] 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.

[1326] T Cell Compositions

[1327] 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.

[1328] 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.

[1329] 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.

[1330] 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.

[1331] T Cell Receptor Compositions

[1332] 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 a chain (Janeway, Travers, Walport. Immunobiology. Fourth Ed., 98 and 150. Elsevier Science Ltd/Garland Publishing. 1999).

[1333] 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 colon tumor peptide can be isolated from T cells specific for a tumor polypeptide using standard molecular biological and recombinant DNA techniques.

[1334] 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.

[1335] 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 colon cancer as discussed further below.

[1336] 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 colon 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 enconding 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.

[1337] Pharmaceutical Compositions

[1338] 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.

[1339] 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.

[1340] 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.

[1341] It will be apparent that any of the pharmaceutical compositions described herein can contain pharmaceutically acceptable salts off 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).

[1342] 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.

[1343] 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.

[1344] 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).

[1345] Various adeno-associated virus (AAV) vector systems have also been developed for polynucleotide delivery. AAV vectors can be readily constructed using techniques well known in the art. See, e.g., U.S. Pat. Nos. 5,173,414 and 5,139,941; International Publication Nos. WO 92/01070 and WO 93/03769; Lebkowski et al. (1988) Molec. Cell. Biol. 8:3988-3996; Vincent et al. (1990) Vaccines 90 (Cold Spring Harbor Laboratory Press); Carter, B. J. (1992) Current Opinion in Biotechnology 3:533-539; Muzyczka, N. (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.

[1346] Additional viral vectors useful for delivering the polynucleotides encoding polypeptides of the present invention by gene transfer include those derived from the pox family of viruses, such as vaccinia virus and avian poxvirus. 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.

[1347] 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.

[1348] Alternatively, avipoxviruses, such as the fowlpox 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 Avipoxviruses are known in the art and employ genetic recombination, as described above with respect to the production of vaccinia viruses. See, e.g., WO 91/12882; WO 89/03429; and WO 92/03545.

[1349] 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.

[1350] 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.

[1351] 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.

[1352] 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.

[1353] 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.

[1354] 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.

[1355] 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, Oreg.), some examples of which are described in U.S. Pat. Nos. 4,790,824; 5,064,413; 5,312,335; 5,383,851; 5,399,163; 5,520,639 and 5,993,412.

[1356] 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 anionically derivatized polysaccharides; polyphosphazenes; biodegradable microspheres; monophosphoryl lipid A and quil A. Cytokines, such as GM-CSF, interleukin-2, -7, -12, and other like growth factors, may also be used as adjuvants.

[1357] 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.

[1358] 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.

[1359] 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.

[1360] 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.

[1361] 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.

[1362] Additional illustrative adjuvants for use in the pharmaceutical compositions of the invention include Montanide ISA 720 (Seppic, France), SAF (Chiron, Calif., United States), ISCOMS (CSL), MF-59 (Chiron), the SBAS series of adjuvants (e.g., SBAS-2 or SBAS-4, available from SmithKline Beecham, Rixensart, Belgium), Detox (Enhanzyno) (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.

[1363] Other preferred adjuvants include adjuvant molecules of the general formula

HO(CH2CH2O)n—A—R, (I)

[1364] wherein, n is 1-50, A is a bond or —C(O)—, R is C1-50 alkyl or Phenyl C1-50 alkyl.

[1365] 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.

[1366] 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.

[1367] 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.

[1368] 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).

[1369] 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.

[1370] 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 Fcγ 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).

[1371] 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.

[1372] 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.

[1373] 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.

[1374] 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.

[1375] 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.

[1376] 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.

[1377] 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.

[1378] 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.

[1379] 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.

[1380] 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.

[1381] 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.

[1382] 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.

[1383] 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. No. 5,543,158; U.S. Pat. No. 5,641,515 and U.S. Pat. No. 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.

[1384] 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.

[1385] 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.

[1386] 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.

[1387] 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.

[1388] 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.

[1389] 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.

[1390] 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 July 1998;16(7):307-21; Takakura, Nippon Rinsho March 1998;56(3):691-5; Chandran et al., Indian J Exp Biol. August 1997;35(8):801-9; Margalit, Crit Rev Ther Drug Carrier Syst. 1995;12(2-3):233-61; U.S. Pat. No. 5,567,434; U.S. Pat. No. 5,552,157; U.S. Pat. No. 5,565,213; U.S. Pat. No. 5,738,868 and U.S. Pat. No. 5,795,587, each specifically incorporated herein by reference in its entirety).

[1391] 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. April 1990;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.

[1392] 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).

[1393] 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. December 1998;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. March 1998;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.

[1394] Cancer Therapeutic Methods

[1395] 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 December 2000;79(12):651-9.

[1396] 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).

[1397] 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 colon cancer cells, offer a powerful approach for inducing immune responses against colon cancer, and are an important aspect of the present invention.

[1398] 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 colon 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.

[1399] 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).

[1400] 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.

[1401] 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.

[1402] 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).

[1403] 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.

[1404] 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.

[1405] 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.

[1406] Cancer Detection and Diagnostic Compositions, Methods and Kits

[1407] In general, a cancer may be detected in a patient based on the presence of one or more colon 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 colon 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.

[1408] 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.

[1409] 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.

[1410] 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.

[1411] 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 colon tumor proteins and polypeptide portions thereof to which the binding agent binds, as described above.

[1412] 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.

[1413] 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).

[1414] 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.

[1415] More specifically, once the antibody is immobilized on the support as described above, the remaining protein binding sites on the support are typically blocked. Any suitable blocking agent known to those of ordinary skill in the art, such as bovine serum albumin or Tween 20™ (Sigma Chemical Co., St. Louis, Mo.). The immobilized antibody is then incubated with the sample, and polypeptide is allowed to bind to the antibody. The sample may be diluted with a suitable diluent, such as phosphate-buffered saline (PBS) prior to incubation. In general, an appropriate contact time (i.e., incubation time) is a period of time that is sufficient to detect the presence of polypeptide within a sample obtained from an individual with colon cancer at least about 95% of that achieved at equilibrium between bound and unbound polypeptide. Those of ordinary skill in the art will recognize that the time necessary to achieve equilibrium may be readily determined by assaying the level of binding that occurs over a period of time. At room temperature, an incubation time of about 30 minutes is generally sufficient.

[1416] 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.

[1417] 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.

[1418] To determine the presence or absence of a cancer, such as colon 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.

[1419] 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.

[1420] 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.

[1421] 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.

[1422] 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.

[1423] 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.

[1424] 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).

[1425] 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.

[1426] 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 colon tumor antigens. Detection of colon cancer cells in biological samples, e.g., bone marrow samples, peripheral blood, and small needle aspiration samples is desirable for diagnosis and prognosis in colon cancer patients.

[1427] 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.

[1428] 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:.

[1429] Additionally, it is contemplated in the present invention that mAbs specific for colon 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 colon 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 colon 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).

[1430] 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.

[1431] 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.

[1432] 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.

[1433] 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.

[1434] 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.

[1435] The following Examples are offered by way of illustration and not limitation.

EXAMPLES

Example 1

[1436] Identification of Duke's Stage D, Grade II Primary Colon Tumor Protein cDNAs from a PCR-based Subtraction Library

[1437] This Example illustrates the identification of cDNA molecules encoding colon tumor proteins from a PCR-based subtraction library.

[1438] Fifty six individual clones were characterized by DNA sequencing, all representing cDNA fragments from Duke's Stage D, Grade II primary colon tumors subtracted with normal tissues including lymph node, PBMC, small intestine, stomach, pancreas, lung, brain, heart, and normal colon. This subtraction, based on a PCR-based subtraction protocol developed by Clontech (Palo Alto, Calif.), generated a library representing genes that are over-expressed or exclusively expressed in Duke's Stage D and Grade II colon tumor tissue.

[1439] Briefly, the cDNA library was constructed and cloned into the PCR2.1 vector (Invitrogen, Carlsbad, Calif.) by subtracting a pool of one or more tumors with a pool of normal tissues, for example, colon, spleen, brain, liver, kidney, lung, stomach and small intestine, using PCR subtraction methodologies (Clontech, Palo Alto, Calif.). The subtraction was performed using a PCR-based protocol, which was modified to generate larger fragments. Within this protocol, tester and driver double stranded cDNA were separately digested with five restriction enzymes that recognize six-nucleotide restriction sites (MluI, MscI, PvuII, SalI and StuI). This digestion results in an average cDNA size of 600 bp, rather than the average size of 300 bp that results from digestion with RsaI according to the Clontech protocol. This modification does not affect the subtraction efficiency. Two tester populations were then created with different adapters, such that the driver library remained without adapters.

[1440] The tester and driver libraries were then hybridized using excess driver cDNA. In the first hybridization step, driver was separately hybridized with each of the two tester cDNA populations. This resulted in populations of (a) unhybridized tester cDNAs, (b) tester cDNAs hybridized to other tester cDNAs, (c) tester cDNAs hybridized to driver cDNAs, and (d) unhybridized driver cDNAs. The two separate hybridization reactions were then combined, and rehybridized in the presence of additional denatured driver cDNA. Following this second hybridization, in addition to populations (a) through (d), a fifth population (e) was generated in which tester cDNA with one adapter hybridized to tester cDNA with the second adapter. Accordingly, the second hybridization step results in enrichment of differentially expressed sequences which can be used as templates for PCR amplification with adaptor-specific primers.

[1441] The ends were then filled in, and PCR amplification was performed using adaptor-specific primers. Only population (e), which contained tester cDNA that did not hybridize to driver cDNA, was amplified exponentially. A second PCR amplification step was then performed, to reduce background and further enrich differentially expressed sequences.

[1442] This PCR-based subtraction technique normalizes differentially expressed cDNA so that rare transcripts that were over-expressed in colon tumor tissue may be recoverable. Such transcripts would be difficult to recover by traditional subtraction methods.

[1443] The cDNAs isolated were searched against public databases including Genbank and those showing some degree of similarity with known sequences in the database shown in Table 2. Several cDNAs were isolated from this subtracted library that showed no significant similarity to known sequences. These are listed in Table 3.

3TABLE 2GENBANK SEARCH RESULTS FOR cDNA MOLECULESENCODING DUKE'S D, GRADE II COLON TUMOR PROTEINSSEQ IDCloneNO:IdentifierGenbank Search Results166211Eukaryotic translation initiation factor 3266179Neural polypyrimidine tract binding protein366191Runt-related transcription factor 3466192CEA566143Human ribophorin II666214Mitochondria genome766203Histamine N-methyltransferase866174Human cyclin G1966170Nuclear cap binding protein subunit 11066160Suppressor of G2 allele of SKP11166190pre-mRNA splicing factor1266171Human cadherin1366209Human rac1 gene1466137Human phosphoserine phosphatase-like1566187CD164 antigen, sialomucin1666208Histone acetyltransferase 11766181Death effector domain-containing proteinDEDPRO11866145CEA1966197Human pro-alpha 2(I) collagen (COL1A2) gene2066204Human lipocalin 22166184Human transmembrane trafficking protein (TMP21)2266133Chloride channel, calcium activated 12366182Human gastrointestinal peptide (PEC-60)2466141Human mitochondrion2566220Human proteasome subunit p1122666161Human tumor-associated calcium signal transducer 12766223Human COP9 complex subunit 42866205Keratin 192966225Human SUI1 isolog3066177Human gene for ATP synthase gamma-subunit3166152Human mitochondrial genome3266176Human ribosomal protein L413366154Human nonspecific crossreacting antigen3466219Human hepatocellular carcinoma associated-geneTB63566224Human actin binding protein anillin3666222Human nonspecific crossreacting antigen3766169cDNA FLJ21386fis, clone COL034143866172Sequence from clone RP1-12G143966149Chromosome 17, clone hRPK.63_A_14066164KIAA04514166213Chromosome 11p14.3 PAC clone pDJ239b224266188Patent WO99544614366158cDNAFLJ13772 fis, clone PLACE40003004466195Human clone HQ02294566155Clone 2067c2t7 map 13qtel sequence4666138Patent WO99544614766201BAC clone CTA-356E1 from 7q11.23-q21.14866221Human chromosome 5 clone CTB-94B104966196KIAA1038

[1444]

4

TABLE 3

cDNA MOLECULES ENCODING DUKE'S D, GRADE II

COLON TUMOR PROTEINS SHOWING NO SIGNIFICANT

SIMILARITY TO KNOWN SEQUENCES

SEQ ID
Clone

NO:
Identifier

50
66140

51
66199

52
66157

53
66132

54
66159

55
66150

56
66217

Example 2

[1445] Identification of Duke's B Colon Tumor Protein cDNAs from A Biotin-streptavidin-based Subtraction Library

[1446] This Example illustrates the identification of cDNA molecules encoding colon tumor proteins from a biotin-streptavidin-based subtraction library.

[1447] The colon tumor Duke's B subtraction 9 (CTBS9) library was generated using a traditional biotin-streptavidin subtraction protocol as follows:

[1448] Tester: 12 μg Colon Tumor Duke's B Library in pZErO™-2 (754-17)

[1449] Driver: 25 μg Normal Colon in pZErO™-2.

[1450] 25 μg Liver and Salivary Gland in pZErO™-2

[1451] 50 μg Pooled Driver in pZErO™-2 (liver, pancreas, skin, bone marrow, resting PBMC, stomach, whole brain)

[1452] Briefly, the tester was cut with BamH I and Xho I while all drivers were cut with EcoR I, Not I, and Nco I. One overnight hybridization of tester and driver was performed at 68° C. and followed by the first biotin-streptavidin subtraction. Another 2-hour hybridization at 68° C. was followed by a second subtraction. cDNA remaining after the two subtractions was ligated into pCR2.1-TOPO, electroporated into ElectroMAX DH10B cells, and grown on agar plates containing ampicillin. This library represents genes that are over-expressed or exclusively expressed in Duke's B colon tumor tissue. The 89 individual sequences and 11 contig consensus sequences disclosed here represent clones that were randomly selected for amplification by polymerase chain reaction (PCR). Clones amplified by PCR were characterized by sequencing and the resulting sequence searched against public databases. Those cDNAs showing some degree of similarity with known sequences in the database are described in Table 4. Several cDNAs isolated from this subtracted library showed no significant similarity with any known sequences in the database. These are listed in Table 5. Multiple sequences from Tables 4 and 5 align to form 11 different consensus (contig) sequences, described in Table 6.

5TABLE 4GENBANK SEARCH RESULTS FOR cDNA MOLECULESENCODING DUKE'S B COLON TUMOR PROTEINSSEQ IDClonePresent inNO:IdentifierContig #Genbank Search Results5765685Homo sapiens myosin, heavy polypeptide-like(110kD) (MYHL) mRNA58656867Human mitochondrion, complete genome5965687Human DNA sequence from clone RP5-881L22on chromosome 20 (bp 51-186) & Homo sapiens hepatocyte nuclear factor 4, alpha (HNF4A)mRNA (bp 186-292)626569244Homo sapiens PEG1/MEST mRNA, completecds636569518Homo sapiens cDNA: FLJ23156 fis, cloneLNG096096465696Homo sapiens cDNA: FLJ21933 fis, cloneHEP043376565698H. sapiens mRNA for ATL-derivedfactor/thiredoxin666570043Homo sapiens guanine nucleotide binding protein(G protein), betapolypeptide 2-like 1 (GNB2L1),mRNA686570333Homo sapiens putative G protein-coupledreceptor (GPCR150), mRNA696570543Homo sapiens guanine nucleotide binding protein(G protein), betapolypeptide 2-like 1 (GNB2L1),mRNA70657138Homo sapiens ribosomal protein L10 (RPL10),mRNA7165714Homo sapiens solute carrier family 1 (neutralamino acidtransporter), member 5 (SLC1A5)mRNA7265715Human mRNA for glutathione-insulintranshydrogenase (EC 5.3.4.1/1.8.4.2)736571843Homo sapiens guanine nucleotide binding protein(G protein), betapolypeptide 2-like 1 (GNB2L1),mRNA746572019Human mRNA for pro-alpha-1 type 3 collagen7565722Homo sapiens mRNA for KIAA0356 protein,partial cds766572622Human nonspecific crossreacting antigen mRNA,complete cds7765727Homo sapiens full length insert cDNA cloneYI64E107865728Homo sapiens targeting protein for Xklp2(TPX2) mRNA, partial cds7965729Human mitochondrion, complete genome8165731Homo sapiens mRNA for KIAA1101 protein,complete cds82657337Human mitochondrion, complete genome83657345Human mitochondrion, complete genome8465736Homo sapiens acetyl-Coenzyme A transporter(ACATN), mRNA8565739Homo sapiens hydroxyacyl-Coenzyme Adehydrogenase/3-ketoacyl-CoenzymeAthiolase/enoyl-Coenzyme A hydratase(trifunctionalprotein), beta subunit (HADHB)mRNA866574143Homo sapiens guanine nucleotide binding protein(G protein), betapolypeptide 2-like 1 (GNB2L1),mRNA876574219Human mRNA for pro-alpha-1 type 3 collagen8865745Homo sapiens alanyl-tRNA synthetase (AARS)mRNA89657479Human mitochondrion, complete genome9065749Homo sapiens mRNA for FLJ00085 protein,partial cds916575143Homo sapiens guanine nucleotide binding protein(G protein), betapolypeptide 2-like 1 (GNB2L1),mRNA9265752Homo sapiens guanine nucleotide binding protein(G protein), betapolypeptide 2-like 1 (GNB2L1),mRNA9365753Homo sapiens cDNA: FLJ22454 fis, cloneHRC097039465757Homo sapiens Chromosome 11q13 BAC Clone18h3, complete sequence9565760Human carcinoembryonic antigen mRNA (CEA),complete cds9765762Homo sapiens ribosomal protein S2 (RPS2)mRNA986576443Homo sapiens guanine nucleotide binding protein(G protein), betapolypeptide 2-like 1 (GNB2L1),mRNA9965767Homo sapiens hypothetical protein FLJ20315(FLJ20315), mRNA1006630322Human nonspecific crossreacting antigen mRNA,complete cds101663065Human mitochondrion, complete genome102663088Homo sapiens ribosomal protein L10 (RPL10),mRNA10466310Homo sapiens chondroitin sulfate proteoglycan 2(versican) (CSPG2), mRNA1056631522Human nonspecific crossreacting antigen mRNA,complete cds1066631644Homo sapiens PEG1/MEST mRNA, completecds10766317Homo sapiens claudin 4 (CLDN4), mRNA10866319Human ADP/ATP translocase mRNA, 3′ end,clone pHAT310966320integrin alpha 6B [human, mRNA Partial, 528 nt]110663245Human mitochondrion, complete genome11166327Human mRNA for KIAA0182 gene, partial cds1126632822Human nonspecific crossreacting antigen mRNA,complete cds11366331Human lumican mRNA, complete cds11466332Human beta-thromboglobulin-like proteinmRNA, complete cds11666337Homo sapiens vascular endothelial growth factor(VEGF) mRNA, 3′UTR1176633819Human mRNA for pro-alpha-1 type 3 collagen11866339Homo sapiens mRNA; cDNA DKFZp434P155(from clone DKFZp434P155)11966340Homo sapiens HRS gene, partial cds12066341Homo sapiens chromosome 16 clone RPCI-11_67I13, complete sequence12166343Human DNA sequence from clone RP5-862P8 onchromosome 1q42.2-43, complete sequence12266345Homo sapiens mRNA; cDNA DKFZp564L176(from clone DKFZp564L176)1236634643Homo sapiens guanine nucleotide binding protein(G protein), betapolypeptide 2-like 1 (GNB2L1),mRNA1246634718Homo sapiens cDNA: FLJ23156 fis, cloneLNG0960912566348Homo sapiens cDNA: FLJ21569 fis, cloneCOL0650812666354Homo sapiens cDNA: FLJ21427 fis, cloneCOL041771276635643Homo sapiens guanine nucleotide binding protein(G protein), betapolypeptide 2-like 1 (GNB2L1),mRNA1286635721Homo sapiens SFRS protein kinase 1 (SRPK1),mRNA12966358Homo sapiens mRNA for KIAA1430 protein,partial cds130663599Human mitochondrion, complete genome13166360Homo sapiens clone PP1446 unknown mRNA13266362Homo sapiens API5-like 1 (API5L1), mRNA13366368Homo sapiens hypothetical protein FLJ20274(FLJ20274), mRNA13566370Homo sapiens carcinoembryonic antigen-relatedcell adhesion molecule7 (CEACAM7), mRNA13666373Homo sapiens serine/threonine proteinphosphatase catalytic subunit (LOC51723),mRNA1376637643Homo sapiens guanine nucleotide binding protein(G protein), betapolypeptide 2-like 1 (GNB2L1),mRNA13866377Human DNA sequence from clone RP11-131A5on chromosome 9q22.1-22.33, completesequence13966378Homo sapiens mRNA for KIAA0746 protein,partial cds14066380H. sapiens mRNA for fibrillin14166384Human ribosomal protein L23a mRNA, completecds14266386Homo sapiens cDNA FLJ13630 fis, clonePLACE10110571436639233Homo sapiens putative G protein-coupledreceptor (GPCR150), mRNA1446639321Homo sapiens SFRS protein kinase 1 (SRPK1),mRNA1456639519Human mRNA for pro-alpha-1 type 3 collagen

[1453]

6

TABLE 5

cDNA MOLECULES ENCODING DUKE'S B COLON TUMOR

PROTEINS SHOWING NO SIGNIFICANT SIMILARITY WITH

ANY KNOWN SEQUENCES

SEQ ID
Clone
Present in

NO:
Identifier
Contig #
Genbank Search Results

60
65688

may be related to Mus musculus

complement component 1, q subcompo-

nent, c polypeptide (C1qc), mRNA

61
65690

67
65701

80
65730

96
65761

103
66309

115
66335

134
66369

[1454]

7

TABLE 6

MULTIPLE SEQUENCES FROM CTBS9 ALIGN TO FORM 11 CONTIGS

SEQ

ID NO:
Clone Identifier
Genbank Search Results

146
CTBS9contig.5
Human mitochondrion, complete genome

147
CTBS9contig.7
Human mitochondrion, complete genome

148
CTBS9contig.8

Homo sapiens
ribosomal protein L10 (RPL10), mRNA

149
CTBS9contig.9
Human mitochondrion, complete genome

150
CTBS9contig.18

Homo sapiens
cDNA: FLJ23156 fis, clone LNG09609

151
CTBS9contig.19
Human mRNA for pro-alpha-1 type 3 collagen

152
CTBS9contig.21

Homo sapiens
SFRS protein kinase 1 (SRPK1), mRNA

153
CTBS9contig.22
Human nonspecific crossreacting antigen mRNA,

complete cds

154
CTBS9contig.33

Homo sapiens
putative G protein-coupled receptor

(GPCR150), mRNA

155
CTBS9contig.43

Homo sapiens
guanine nucleotide binding protein (G

protein), betapolypeptide 2-like 1 (GNB2L1), mRNA

156
CTBS9contig.44

Homo sapiens
PEG1/MEST mRNA, complete cds

[1455] An additional 1022 clones from this library were randomly amplified and sequenced. These are disclosed in SEQ ID NOS:255-1276.

Example 3

[1456] Identification of cDNAs Encoding Duke's Stage C and D, Grade II-III Colon Tumor Proteins

[1457] This Example illustrates the identification of cDNA molecules encoding Duke's Stage C and D, grade II-III colon tumor proteins.

[1458] Fifteen hundred clones from a subtraction library were characterized by microarray analysis, all representing cDNA fragments from Duke's Stage C and D, grade II-III primary colon tumors subtracted with normal tissues including lymph node, PBMC, small intestine, stomach, pancreas, lung, brain, heart, and normal colon. This subtraction, based on a PCR-based subtraction protocol developed by Clontech (Palo Alto, Calif.), generated a library representing genes that are over-expressed or exclusively expressed in Duke's Stage C and D colon tumor tissue.

[1459] Random clones from this library were PCR amplified and found to be overexpressed in specific tumor tissues as determined by microarray analysis. Using this approach, cDNA sequences were PCR amplified and their mRNA expression profiles in tumor and normal tissues are examined using cDNA microarray technology essentially as described (Schena, 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 are fluorescence-labeled with Cy3 and Cy5, respectively. Typically, 1 μg of polyA+ RNA is 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 generally monitored using a panel of ubiquitously expressed genes. Secondly, the control plate included yeast DNA fragments of which complementary RNA was 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 about 1 in 100,000 copies of mRNA. Finally, the reproducibility of this technology was ensured by including duplicated control cDNA elements at different locations.

[1460] The microarray data were analyzed. Twenty-two clones with two-fold overexpression in colon tumors as compared to normal colon tissue, were selected and their sequences were determined by DNA sequencing. Seventeen of the 22 represented unique clones and these were then searched against public databases including Genbank and EST. Those showing some degree of similarity with known sequences in the databases are described in Table 7. Two cDNAs were identified that showed no significant similarity to any known sequences. These are listed in Table 8.

8TABLE 7GENBANK SEARCH RESULTS FOR cDNA MOLECULESENCODING DUKE'S C AND D COLON TUMOR PROTEINSSEQ IDCloneNO:IdentifierGenbank Search Results15768066DNA-dependent protein kinase catalytic subunit15868065Bumetanide-sensitive Na-K-Cl cotransporter15968076Histone deacetylase 116068067CD9 antigen16168061Coatomer protein complex, subunit beta16268071Bumetanide-sensitive Na-K-Cl cotransporter16368069Lysyl-tRNA synthetase16468064U4/U6 snRNP 60 kDa protein gene16568059Myosin regulatory light chain16668073Fibronectin16768057cDNA FLJ21409 fis, clone COL0392416868062Chromosome 8p11.2, clone:91h23 to 9-411696806312p13.3 PAC RPCI1-96H917068070KIAA1077 protein17168075cDNA DKFZp564M0264

[1461]

9

TABLE 8

cDNA MOLECULES ENCODING DUKE'S C AND D COLON TUMOR

PROTEINS THAT SHOWED NO SIGNIFICANT SIMILARITY TO

KNOWN SEQUENCES

SEQ ID
Clone

NO:
Identifier

172
68060

173
68058

Example 4

[1462] Identification of Additional cDNAs Encoding Duke's Stage C and D, Grade II-III Colon Tumor Proteins

[1463] This Example illustrates the identification of additional cDNA molecules encoding Duke's Stage C and D, grade II-III colon tumor proteins.

[1464] Fifteen hundred clones from a subtraction library were characterized by microarray analysis, all representing cDNA fragments from Duke's Stage C and D, grade II-III primary colon tumors subtracted with normal tissues including lymph node, PBMC, small intestine, stomach, pancreas, lung, brain, heart, and normal colon. This subtraction, based on a PCR-based subtraction protocol developed by Clontech (Palo Alto, Calif.) and described in Example 1, generated a library representing genes that are over-expressed or exclusively expressed in Dukes Stage C and D colon tumor tissue.

[1465] Random clones from this library were PCR amplified and found to be overexpressed in specific tumor tissues as determined by microarray analysis as described in Example 3. One hundred and eight clones with two-fold overexpression in colon tumors as compared to normal colon tissue were selected and their sequences were determined by DNA sequencing. Eighty-one of these 108 represented unique clones and were searched against public databases including Genbank and EST. Those showing some degree of similarity with sequences in the databases are described in Table 9. Five cDNAs were identified that showed no significant similarity to known sequences in the database. These are listed in Table 10.

10TABLE 9GENBANK SEARCH RESULTS FOR cDNA MOLECULESENCODING DUKE'S STAGE C AND D COLON TUMOR PROTEINSCloneSEQ IDIdenti-NO:fierGenbank Search Results17468384Hepatocellular carcinoma associated-gene TB617568421DNA of undertermined origin found 5′ to NCA17668459Tumor-associated calcium signal transducer 117768461Keratin 1817868435Serine protease inhibitor, Kunitz type 217968405Human ADP/ATP carrier protein18068460Human Ig J chain gene18168448Chloride channel, calcium activated, familymember 118268493Human hephaestin18368477Tumor-associated calcium signal transducer 118468431Ribosomal protein, large, P018568476Human Tis 11d gene18668466Human cell-type T-cell immunoglobulin gamma-chain, V region18768446Protein tyrosine phosphatase, non-receptor type 1218868444Proteasome subunit, beta type, 118968388Human epithelial membrane protein 119068470Human Tis 11d gene19168465Human junction plakoglobin19268463Human collagen, type I, alpha 219368468Human pyruvate dehydrogenase alpha 119468439Human ubiquitin-conjugating enzyme E2 variant 119568438Human neutrophil-activating ENA-78 prepeptidegene19668436Human nonspecific crossreacting antigen19768484Human GTT1 protein19868478Human proteolipid protein 2 (colonic epithelium-enriched)19968490Human ribosomal protein L320068488Human fibronectin20168485Human antigen CD9 gene20268491Human pro alpha 1 (I) collagen gene20368483Human myosin regulatory light chain20468382Human CD24 antigen20568494Human nonspecific crossreacting antigen20668391Human mucin 2, intestinal/tracheal20768481Human glutathione peroxidase 2 (gastrointestinal)20868386Human mucin 2, intestinal/tracheal20968467Human non-histone chromosomal protein HMG-14gene21068394Human lysosomal-associated protein transmembrane4 alpha21168407Human tight junction protein 121268427Human epidermal growth factor receptor21368496Human collagen, type III, alpha 121468430CEA21568447Human epithelial V-like antigen 121668417Human glycoprotein A33 (transmembrane)21768401Human mitogen-activated protein kinase kinasekinase kinase 321868389Human Na, K-ATPase alpha aubunit21968455Human histone deacetylase 122068393Human transmembrane 4 superfamily member 322168404Human glutathione S-transferae pi22268457Human epithelial sodium channel alpha-subunit gene22368458Human Ran_GTP binding protein 522468450Human integrin, beta 122568418Human bumetanide-sensitive Na-K-Cl cotransporter22668422Human cathepsin C22768409Human UDP-N-acetylglucosamine 2-epimerase gene2286842542 kda myristoylated alanine-rich C kinase substrate22968415Human HALPHA44 gene for alpha-tubulin23068414Human nonspecific crossreacting antigen23168437cDNA FLJ22131 fis, clone HEP2024523268392Human BAC clone RP11-467H10 from 723368406KIAA121723468400Chromosome 17, clone hRPK.318_A_1523568442cDNA FLJ23142 fis, clone LNG0911523668443cDNA FLJ21353 fis, clone COL0277123768381KIAA020623868441KIAA119123968440cDNA FLJ12933 fis, clone NT2Rp200496224068479Human chromosome 17, clone hRPC.1073_F_1524168390cDNA FLJ22182 fis, clone HRC0095324268380KIAA018424368403KIAA003824468416KIAA019624568424cDNA DKFZp564O012224668413Human clone 25076 mRNA sequence24768419BAC clone RP11-697M17 from 824868420Human clone 24659 mRNA sequence24968411cDNA FLJ21339 fis, clone COL02601

[1466]

11

TABLE 10

cDNA MOLECULES ENCODING DUKE'S STAGE C AND D COLON

TUMOR PROTEINS THAT SHOWED NO SIGNIFICANT

SIMILARITY TO KNOWN SEQUENCES

SEQ ID
Clone

NO:
Identifier

250
68471

251
68492

252
68399

253
68412

254
68451

Example 5

[1467] Identification of Colon Tumor Antigens from an Expression Library

[1468] This example describes the isolation of cDNAs encoding colon tumor antigens by screening an expression library.

[1469] Total membrane preparations were made using the CT391-12 colon tumor cell line as described below and used to generate rabbit anti serum. Colon tumor antigens were then cloned by serological screening of a colon expression library with the rabbit plasma membrane anti serum. The library was constructed with mRNA extracted from the CT391-12 cell line in the Lambda Zap Express vector (Stratagene, La Jolla, Calif.).

[1470] For the membrane preparation, CT391-12 cells were pelleted and homogenized with a Dounce Homogenizer in 250 mM sucrose, 10 mM HEPES, 1 mM EDTA, and one complete protease inhibitor tablet (Roche), at pH 7.4. The homogenized cells were pelleted at 800×g to remove cell debris and then at 8000×g to remove organelles. The remaining supernatant was ultracentrifuged at 100,000×g to pellet the membranes. Protein concentration was determined by the method of Lowry and the membranes injected into rabbits at 0.5 mg/ml for the generation of antiserum.

[1471] Immuno-reactive proteins were screened from approximately 4×105 PFU from the unamplified cDNA expression library. Fifteen 150 mm LB agar petri dishes were plated with approximately 3×104 PFU and incubated at 42° C. until plaques formed. Nitrocellulose filters (Schleicher and Schuell), pre-wet with 10 mM IPTG, were placed on the plates and then incubated at 37° C. over night. Filters were then removed and washed 3× with PBS, 0.1% Tween 20, blocked with 1.0% BSA (Sigma) in PBS, 0.1% Tween 20, and finally washed 3× with PBS, 0.1% Tween 20. Blocked filters were then incubated overnight at 4° C. with rabbit antiserum that was developed against a total membrane preparation of the cell line, diluted 1:200 in PBS, 0.1% Tween-20 and preadsorbed with E. coli lysates and other proteins such as galactin 4, murin type C retrovirus envelope protein, and GAPDH to remove superfluous and irrelevant antibodies. Normal tissue lysates, PBMC, trachea, and prostate epithelial cell line, were also added to the antiserum. The filters were then washed 3× with PBS-Tween 20 and incubated with a goat-anti-rabbit IgG (H and L) secondary antibody (diluted 1:1000 with PBS-Tween 20) conjugated with alkaline phosphatase (Rockland Laboratories) for 1 hr. These filters were then washed 3× with PBS, Tween 20 and 2× with alkaline phosphatase buffer (pH 9.5) and finally developed with NBT/BCIP (Gibco BRL). Reactive plaques were excised from the LB agarose plates and a second or third plaque purification was performed following the same protocol. Excision of phagemid followed the Stratagene Lambda ZAP Express protocol, and resulting plasmid DNA was sequenced with an automated sequencer (ABI) using M13 forward, reverse and internal DNA sequencing primers. Nucleic acid homology searches were performed against the GenBank nucleic acid database. Those sequences showing some degree of similarity to known sequences in the database are described in Table 11. Those sequences that showed no significant similarity to known sequences in the database are listed in Table 12.

12TABLE 11GENBANK SEARCH RESULTS FOR cDNA MOLECULES ENCODING CT391-12COLON TUMOR ANTIGENSSEQ IDCloneGenBankNO:IdentifierGenbank Search ResultsAccession #127759978Human major Yo paraneoplastic antigen (CDR2)M63256mRNA127859979Mink cell focus forming virus long terminal repeatM26170(LTR) RNA127959980Unknown Hu. chromosome 16 clone RPCI-AC02066311_127I20128059984Hu. secreted cement gland protein XAG-2 homologAF038451128159987Human growth factor-inducible 2A9 geneM14300128259990Ribosomal protein L19 [human, breast cancer cellS56985line128360003Human mRNA for ezrin.X51521128460005Unknown Hu. BAC clone GS1-286B23 fromAC0061517q21.1-q21.3128567009Vaculor sorting protein 29; Homo sapiens x 007AF168716protein mRNA128660007Hu. mRNA translocon-associated protein deltaZ69043subunit128760009Mink cell focus-forming 247 MuLV env geneJ02249128860012Human MRL3 mRNA for ribosomal protein L3X06323homologue128960018Human ribosomal protein S13 (RPS13) mRNAL01124129163822Unknown Hu. mRNA for KIAA0242 protein;D87684FLJ23318129263823Hu. X-ray repair complementing defective repairNM02114180kD CC5)129363824Hu. cadherin 17, LI cadherin (liver-intestine)NM004063(CDH17) mRNA129467014Hu. lectin, galactoside-binding, soluble, 4 (galectinNM0061494)129563847Hu. Wiskott-Aldrich syndrome-like (WASL),NM003941mRNA129667023Homo sapiens mRNA for galectin-3AB006780129763859Murine type C retrovirus, complete genomeNC001702129864405Ribosome binding protein 1AB037819129965037Hu. aspartate beta-hydroxylase (ASPH) mRNANM004318130065047Hu. adaptor-related protein complex 3, mu 2NM006803subunit(AP3M2)130165058Murine leukemia virus mRNA for env proteinD00620130365085Hu. methionine adenosyltransferase II, alphaNM005911(MAT2A) Mrna130465087Homo sapiens peptidase D (PEPD) mRNANM000285130565089Unknown Hu. mRNA; cDNA DKFZp434E0727AL133017130665101Unknown Hu. DNA from chromosome 19, cosmidAC004030F21856130765112Homo sapiens ribosomal protein L34 (RPL34)NM000995mRNA130865118Hu. eukaryotic translation elongation factor 1 deltaNM001960130965124Hu. DEAD/H (Asp-Glu-Ala-Asp/His) boxNM004396polypeptide 5 DX5)131065125Hu. calcyclin binding protein (CACYBP), MrnaNM014412131165142Human cytovillin 2 (VIL2) mRNAJ05021131265143Hu. itochondrial matrix protein P1 (nuclearM22382encoded)131365146Hu. transmembrane protein (63 kD)NM006825131465227Homo sapiens scaffold attachment factor B (SAFB)NM002967131565229Homo sapiens putative secreted protein XAGAF088867mRNA131665230Homo sapiens ribosomal protein s21 (RPS21)NM001024mRNA131765231Hu. farnesyltransferase, CAAX box, alpha (FNTA)NM002027131865233Hu. sapiens mRNA for TGN46 proteinX94333131965235Human mitochondrion, complete genomeNC001807132065237Hu. synaptogyrin 2 (SYNGR2) mRNANM004710132167041Unknown Homo sapiens HSPC250 mRNAAF151084132265291Hu. ribosomal protein L26 (RPL26)NM000987132365330Hu. acetyl-Coenzyme A acyltransferase 1NM001607mitochondrial protein

[1472]

13

TABLE 12

cDNA MOLECULES ENCODING CT391-12 COLON TUMOR

ANTIGENS THAT SHOWED NO SIGNIFICANT SIMILARITY

TO KNOWN SEQUENCES

Seq ID
Clone

GenBank

NO:
Identifier
Genbank Search Results
Accession #

1290
60024
Novel
L02953

1302
65075

Example 6

[1473] Microarray Analysis of Additional cDNAS Obtained from the CTBS9 Subtraction Library

[1474] To further identify genes overexpressed in colon tumors, an additional 1404 clones originating from the CTBS9 subtraction library described in Example 2 were placed on Colon Chip 5 and analyzed using microarray technologies as described in Example 3. A list of probes used to interrogate these clones is shown in Table 13. Clones that showed greater than two-fold overexpression in colon tumors versus a set of normal tissues were selected for further analysis. Of the 1404 clones placed on Colon Chip 5 from the CTBS9 library, 414 clones were selected based on this criteria and sequenced. Four hundred of the clones yielded sequence which could be analyzed. Fifty unique sequences identified from this analysis were searched against public databases and are disclosed herein (see SEQ ID NOs: 1324-1373 and Table 14 and Table 15). Those sequences showing some degree of similarity to known sequences in the database are described in Table 14. Those sequences that showed no significant similarity to known sequences in the database are listed in Table 15.

14TABLE 13PROBES USED IN MICROARRAY ANALYSIS OF cDNA CLONESFROM CTBS9 SUBTRACTION LIBRARYInternalExternalTissueStateID No:ID No:Colon TumorDukes A650A864cy3Thymus NormalClontechSPAAm5864cy5Colon TumorDukes A1000A865cy3Colon NormalND285865cy5Colon TumorDukes A1001A866cy3Colon NormalND670A866cy5Colon TumorDukes A1002A867cy3Colon NormalND286867cy5Colon TumorDukes A647A868cy3Colon NormalND287868cy5Colon TumorDukes A648A869cy3Colon NormalND1003A869cy5Colon TumorDukes A645A873cy3Kidney NormalND069CD873cy5Colon TumorDukes A646A874cy3Lung NormalPool 2000LN2000874cy5Colon TumorDukes B685875cy3Liver NormalclontechSPACT91875cy5Colon TumorDukes BS17876cy3Heart NormalClontechSPACT87876cy5Colon TumorDukes B239A877cy3Esophagus NormalPool243/502877cy5Colon TumorDukes B1026A8879cy3Small Intestine NormalClontechSPACT65879cy5Colon TumorDukes B259A880cy3Stomach NormalND073A880cy5Colon TumorDukes B574881cy3Pancreas NormalND282A881cy5Colon TumorDukes B235A882cy3Adrenal Gland NormalClontechSPACT76882cy5Colon TumorDukes B218A883cy3Spleen NormalClontechSPACT44883cy5Colon TumorDukes B575A884cy3Bronchus NormalND600CD884cy5Colon TumorDukes B633A886cy3Brain NormalClontechSPACT85886cy5Colon TumorDukes C1018A887cy3PBMC RestingND1194A887cy5Colon TumorDukes C657A2888cy3Bone Marrow NormalND410B888cy5Colon TumorDukes C653A889cy3Aorta NormalND415ABD889cy5Colon TumorDukes C1022A890cy3Spinal Cord NormalPool881/882890cy5Colon TumorDukes C1021A891cy3Skeletal Muscle NormalClontechSPACT40891cy5Colon TumorDukes C863A2892cy3Skin NormalPool490/601892cy5Colon TumorDukes C240A893cy3Fetal tissue NormalNDS91893cy5Colon TumorDukes D PrimaryS19894cy3Breast NormalNDS82894cy5Colon TumorDukes D primary663A895cy3Salivary Gland NormalND323B895cy5Colon TumorDukes D primary659A896cy3Dendritic cells NormalND272A896cy5Colon TumorDukes D mets to liver635A897cy3Lymph Nodes NormalNDSPACT6897cy5Colon TumorDukes D mets1014A2901cy3Trachea NormalND779B901cy5Colon TumorDukes D mets660A902cy3Pituitary Gland NormalClontechSPACT67902cy5Colon TumorDukes D707A903cy3Bladder NormalND1062A903cy5Colon TumorDukes D mets1015B904cy3Thyroid NormalND367A904cy5Colon TumorDukes D636A905cy3PBMC activated NormalND1155A905cy5ND: not determined

[1475]

15

TABLE 14

GENBANK SEARCH RESULTS FOR cDNA MOLECULES ISOLATED

FROM THE CTBS9 SUBTRACTION LIBRARY

SEQ ID

# clones

NO:
Clone Identifier
isolated
Genbank Search Results

1345
RO644:F01
1

H.sapiens
nek3 mRNA for protein kinase

1354
RO639:H11
1

Homo sapiens
BAC clone RP11-255L13 from

8, complete sequence

1366
70919
1

Homo sapiens
cathepsin C (CTSC), mRNA

1368
70847/RO639:B12
1

Homo sapiens
cDNA FLJ11493 fis, clone

HEMBA1001940

1350
RO641:A06
2

Homo sapiens
cDNA: FLJ21386 fis, clone

COL03414

1329
RO647:D08
5

Homo sapiens
cDNA: FLJ21569 fis, clone

COL06508

1348
R0641:C04
1

Homo sapiens
cDNA: FLJ21908 fis, clone

HEP03830

1337
RO642:G06
4

Homo sapiens
cDNA: FLJ23156 fis, clone

LNG09609

1361
RO646:H07
1

Homo sapiens
cDNA: FLJ23270 fis, clone

COL10309, highly similar to HSU33271 Human

normal keratinocyte

1339
R0636:E09
1

Homo sapiens
chromosome 16, P1 clone 94-

10H (LANL), complete sequence

1326
RO638:G1
31

Homo sapiens
chromosome 19 clone LLNLF-

112E5, (CEA)

1346
RO637:E06
1

Homo sapiens
chromosome 5 clone CTD-

2048F20, complete sequence

1335
RO636:D12
1

Homo sapiens
cytochrome P450, subfamily

XXVIIB (25-hydroxyvitaminD-1-alpha-

hydroxylase), polypeptide 1 (CYP27B1)

1367
70830
1

Homo sapiens
ectodermal dysplasia 1,

anhidrotic (ED1), mRNA

1365
70875/RO641:E01
1

Homo sapiens
genomic DNA, chromosome

22q11.2, Cat Eye Syndrome

region, clone:c60D12 (95% Identity)

1349
R0639:E11
1

Homo sapiens
hypothetical protein FLJ10040

(FLJ10040), mRNA

1364
70855/C798P
2

Homo sapiens
hypothetical protein FLJ20315

(FLJ20315), mRNA

1336
RO638:G10
4

Homo sapiens
hypothetical protein SP192

(SP192), mRNA

1338
R0637:B08
10

Homo sapiens
integrin, alpha 6 (ITGA6),

mRNA (Contigs 15 and 29)

1352
R0640:F09
10

Homo sapiens
integrin, alpha 6 (ITGA6),

mRNA (Contigs 15 and 29)

1324
R0639:B04
73

Homo sapiens
interleukin 8 (IL8), mRNA

(Contigs 1 and 34)

1357
R0644:A12
73

Homo sapiens
interleukin 8 (IL8), mRNA

(Contigs 1 and 34)

1358
RO636:D06
1

Homo sapiens
karyopherin (importin) beta 3

(KPNB3), mRNA

1341
RO637:D12
1

Homo sapiens
mRNA for KIAA0746 protein,

partial cds

1342
RO642:G04
1

Homo sapiens
mRNA for KIAA1157 protein,

partial cds

1363
70848/B512S
1

Homo sapiens
mRNA for TRAF and TNF

receptor associated protein (ttrap gene)

1331
RO644:C03/C915P
19

Homo sapiens
NADPH oxidase 1 (NOX1),

transcript variant NOH-1L, mRNA

1333
RO641:C09
1

Homo sapiens
PAC clone RP1-170O19 from

7p15-p21, complete sequence

1351
R0636:F05
1

Homo sapiens
phosphatidylinositol transfer

protein, membrane-associated (PITPNM)

1327
RO637:E03
7

Homo sapiens
putative G protein-coupled

receptor (GPCR150), mRNA

1343
R0641:G08
1

Homo sapiens
SDHD gene for small subunit of

cytochrome b of succinatedehydrogenase

1356
R0644:B10/C27E
175

Homo sapiens
secreted cement gland protein

XAG-2 homolog (hAG-2/R) mRNA, complete

1369
70869
1

Homo sapiens
serine protease-like protein

isoform (NSP) mRNA, alternatively spliced,

complete cds (MAD homologue)

1359
R0636:B04
1

Homo sapiens
serine/threonine kinase 24

(Ste20, yeast homolog) (STK24), mRNA

1328
RO637:E04/C919P
12

Homo sapiens
SFRS protein kinase 1 (SRPK1),

mRNA (Contigs 5 and 9)

1332
RO64:B12/C919P
12

Homo sapiens
SFRS protein kinase 1 (SRPK1),

mRNA (Contigs 5 and 9)

1373
70844/RO639:B05
1

Homo sapiens
targeting protein for Xklp2

(TPX2) mRNA, partial cds

1325
RO647:A08
7

Homo sapiens
tumor-associated calcium signal

transducer 1 (TACSTD1), mRNA

1347
R0642:G07
1
Human BAC clone CTB-66D11 from 7q22,

complete sequence [Homo sapiens]

1344
R0642:F08
11
Human carcinoembryonic antigen (CEA) gene,

exon 10

1340
R0637:B03
1
Human DNA sequence from clone RP11-46B11

on chromosome 6, completesequence

1353
R0643:E06/C882P
3
Human DNA sequence from clone RP5-1056H1

on chromosome 20, complete sequence

1372
70878
1
Human microsomal stress 70 protein ATPase

core (stch) mRNA, complete cds

[1476]

16

TABLE 15

cDNA MOLECULES FROM THE CTBS9 SUBTRACTION

LIBRARY THAT SHOWED NO SIGNIFICANT

SIMILARITY TO KNOWN SEQUENCES

SEQ ID

# clones

NO:
Clone Identifiers
isolated

1330
RO639:D12/C968P/70836
1

1371
70849
1

1334
RO637:H11/Contig 11
1

1355
R0642:F02/B723P/Contig 33
1

1360
R0641:C07/Contig 38
1

1362
R0641:D01/Contig 41
1

1370
70836/C968P/Contig 7
4

Example 7

[1477] Microarray Analysis of cDNAs Obtained from the CT391-12 Expression Library

[1478] The clones originating from the CT391-12 Expression library described in Example 5 were placed on Colon Chip 5 and further analyzed using microarray technologies as described in Example 3. Microarray data, confirmed by visual analysis, showed cDNAs that appear to be overexpressed by at least two fold over normal tissues. The sequences of the overexpressed cDNAs were then searched against public databases. Those sequences showing some degree of similarity with known sequences in the database are shown in Table 16. Included in this table are three additional cDNA sequences designated CTM-94,-226 and -303. Those sequences showing no significant similarity to sequences in the database are described in Table 17.

17TABLE 16GENBANK SEARCH RESULTS FOR cDNA MOLECULES ENCODING CT391-12COLON TUMOR ANTIGENS OVEREXPRESSED IN COLON TUMORSSEQ IDCloneNO:CloneIdentifierInsertGenseqDescriptionExpression*1318CTM-270652331.6A08035Hu.sapiens mRNA forVisualTGN46 protein1376CTM-303653283A08035H.sapiens mRNA for3.23/-TGN46 protein1321CTM-278670410.9A12405Unknown Homo sapiensVisualHSPC250 mRNA1305CTM-170650891.6A26961Unknown Hu. mRNA;2.47/-cDNA DKFZp434E07271303CTM-166650853.5A43214Hu.methionineVisualadenosyltransferase II,alpha (MAT2A) Mrna1374CTM-94670243.2C01319Human cytovillin 2 (VIL2)VisualmRNA1304CTM-168650870.5Q04531Homo sapiens peptidase DVisual(PEPD) mRNA1300CTM-128650472T29388Hu.adaptor-related proteinVisualcomplex 3, mu 2subunit(AP3M2),1279CTM-7599801.5T47520Bone marrow protVisualBM045/chrom. 16 cloneRPCI-11 127I201294CTM-81670141.6T59539Hu.lectin, galactoside-3.33/-binding, soluble, 4(galectin 4)1315CTM-265652291.9T84476Home sapiens putative3.37/2.97secreted protein XAGmRNA1298CTM-116644053V41922Ribosome-binding proteinVisual1/mRNA for KIAA13981306CTM-182651011.5V62310Unknown Hu.DNA from2.30/-chromosome 19, cosmidF218561284CTM-29600051Z09252LINE1 (L1.3)/BAC cloneVisualGS1-286B23 from7q21.1-q21.31310CTM-215651253.6Z33476Hu.calcyclin binding2.03/-protein (CACYBP), Mrna1375CTM-226651343Z57868Scaffold attachment factorVisualB/cDNA KIAA01381296CTM-93670231Z77549Homo sapiens mRNA for2.23/-galectin-31288CTM-36600121.2Z80559Human MRL3 mRNA forVisualribosomal protein L3homologue* Mean expression value: (Tumor/Normal minus colon)/(Tumor/Normal). Visual: visual analysis only

[1479]

18

TABLE 17

cDNA MOLECULES ENCODING CT391-12 COLON TUMOR ANTIGENS

OVEREXPRESSED IN COLON TUMORS THAT SHOWED NO SIGNIFICANT

SIMILARITY TO KNOWN SEQUENCES

SEQ ID

Clone

NO:
Clone
Identifier
Insert
Description
Expression*

1291
CTM-64
63822
4
Unknown Hu.mRNA for KIAA0242
Visual

protein/FLJ23318fis

1302
CTM-156
65075
3

Visual

1313
CTM-239
65146
2.08
Hu.transmembrane protein (63kD)
2.12/-

*Mean expression value: (Tumor/Normal minus colon)/(Tumor/Normal). Visual: visual analysis only.

Example 8

[1480] Identification of Additional Colon Tumor Antigens from an Expression Library

[1481] Additional clones originating from the CT391-12 expression library described in Example 5 were sequenced using standard methods and then searched against public databases. These sequences are disclosed in SEQ ID NOs: 1377-1417. Those sequences showing some degree of similarity with known sequences in the database are shown in Table 18. Those sequences showing no significant similarity to sequences in the e are described in Table 19.

19TABLE 18GENBANK SEARCH RESULTS FOR cDNA MOLECULES ENCODING CT391-12COLON TUMOR ANTIGENSSEQCloneID NO.CloneIDInsertDescription1377CTM2-4713413.8Hu. villin 2 (ezrin) (VIL2), mRNA1378CTM2-10702491.4Hu. anterior gradient 2 (Xenepus laevis)homolog1380CTM2-18713472.7Hu. ribosomal protein L18a (RPL18A), mRNA1381CTM2-30713520.8Hu. calcyclin binding protein (CACYBP),mRNA1384CTM2-34713541.4Hu. hypoxia-inducible gene 1 (HIG1) mRNA1385CTM2-35713552Hu. heat shock 60 kD protein 1 (chaperonin)(HSPD11386CTM2-41713560.6Hu. heat shock 10 kD protein 1 (chaperonin 10)(HSPE1) mRNA1388CTM2-48713622.5Hu. ninein (LOC51199), mRNA1389CTM2-52702610.9Hu. anterior gradient 2 (Xenepus laevis)homolog (AGR2), mRNA1390CTM2-54713662Hu. SCO (cytochrome oxidase deficient, yeast)homolog 11391CTM2-59702630.6Hu. ribosomal protein L24 (RPL24)1393CTM2-62713683Hu. IgG Fc binding protein (FC(GAMMA)BP)mRNA1394CTM2-66702650.6Hu. endoplasmic reticulum lumenal protein(ERP28), mRNA1395CTM2-69713721.2Human prothymosin alpha mRNA1398CTM2-104730314Hu. ataxin-1 ubiquitin-like interacting protein(A1U), mRNA1399CTM2-111730381.6Human liver mRNA for 3-oxoacyl-CoAthiolase1400CTM2-119730440.4Hu. actin related protein 2/3 complex1401CTM2-124730491Hu. transmembrane trafficking protein(TMP21)1402CTM2-127730520.5Hu. hypothetical protein Nop10p (Nop10p),mRNA1403CTM2-142730583Hu. villin 2 (ezrin) (VIL2), mrNA1404CTM2-146730610.9Hu. ribosomal protein L5 (RPL5)1405CTM2-147730620.8Hu. sperm antigen-36 mRNA1406CTM2-154730680.9Hu. mRNA for galectin-31407CTM2-158730722Hu. acetyl-Coenzyme A acyltransferase 11408CTM2-162730760.4Hu. IgG Fc binding protein (FC(GAMMA)BP)mRNA1409CTM2-180754250.5Hu. acetyl-Coenzyme A acyltransferase 11410CTM2-235754440.8Hu. eukaryotic translation initiation factor 4A1411CTM2-244754513.4Hu. sapiens mRNA for TGN46 protein1412CTM2-248754563Hu. cadherin 17, LI cadherin (liver-intestine)1413CTM2-253754612.8Hu. cadherin 17, LI cadherin (liver-intestine)1415CTM2-259754650.7Hu. lectin, galactoside-binding, soluble, 31416CTM2-278754833Hu. uveal autoantigen mRNA1417CTM2-281754861Hu. thimet oligopeptidase 1, clone MGC:8357,mRNA1382,CTM2-33713532.8Hu. small intestinal mucin (MUC3) mRNA1383

[1482]

20

TABLE 19

cDNA MOLECULES ENCODING CT391-12 COLON TUMOR

ANTIGENS THAT SHOWED NO SIGNIFICANT SIMILARITY

TO KNOWN SEQUENCES

SEQ

Clone

ID NO.
Clone
ID
Insert
Description

1379
CTM2-17
70254
2.1
KIAA0105, mRNA

1387
CTM2-43
71358
1.4
Hu. sapiens cDNA; FLJ22523

fis, clone HRC12507

1392
CTM2-60
71367
2
DKFZP564B167 protein

(DKFZP564B167)

1396
CTM2-92
71385
1.2
Hu. cDNA FLJ10051 fis,

clone HEMBA1001281

1397
CTM2-95
71388
2.6
Hu. chromosome 5 clone

CTC-534A2

1414
CTM2-254
75462
1.6
Hu. chromosome 19, cosmid

F24200

Example 9

[1483] Analysis of cDNA Expression using Real-time PCR

[1484] As described in Example 6, 50 cDNA sequences were identified by microarray and sequence analysis. Subsequent visual inspection of the microarray results yielded 15 clones that were selected for further analysis by quantitative (real time) PCR. 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 SYBR™ 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 breast tumor 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.

[1485] Of the fifteen clones analyzed by real time PCR, four showed overexpression in colon tumor and were assigned the following tumor antigen identities: C634S, C635S, C636S and C637S. The nucleotide sequences for these candidates are set forth in SEQ ID NOs: 1418-1421, respectively. Bioinformatic analyses were also performed using the fully elucidated insert sequences. Based on these sequences, potential open reading frames have been identified for C634S (SEQ ID NO: 1422), C635S (SEQ ID NO: 1423) and C637S (SEQ ID NO: 1424). A summary of the real-time and bioinformatics results is shown in Table 20. This summary contains the microarray, real-time PCR, and Genbank identity of each clone (if known).

21TABLE 20REAL-TIME PCR AND GENBANK ANALYSIS OF COLON TUMOR ANTIGENSElevatedNormalGenbankSEQ IDCandidateTissueSearchNO:NameElementRatioCTCNExpressionResult1334,C634SRO637:H113.66 95%LowThymus,H. sapiens1418,bonecMyc target1422marrow,JP01 mRNA,esophagus,complete cdslymph node,1350,C6355RO641:A062.26100%Mediumheart,H. sapiens1419,pancreas, sal.cDNA:FLJ211423gland,386 fis, clonetrachea,COL03414esophagus1365,C636SRO641:E012.28 95%LowTracheaChrom.142022q11.2, cateye syndromeregion,clone:c60D121361,C637SRO646:H072.48100%LowEsophagus,CDNA:FLJ21421,pancreas3270 fis,1424cloneCOL10309,similar tokeratinocytemRNA

Example 10

[1486] Bioinformatic and Real-time PCR Analysis of Colon Tumor Antigen C640S

[1487] The colon tumor antigen, C640S (SEQ ID NO: 1373), was further analyzed by real-time PCR as described in Example 9, and using bioinformatics. Real-time PCR expression profiling showed that this gene is overexpressed in 100% of colon tumor samples tested as compared to normal colon samples. Overexpression was also seen in bone marrow. Very low levels of expression were observed in skeletal muscle, esophagus, liver, brain, pancreas, and skin. A search of the sequence against Genbank showed that C640S is identified as the TPX2 gene (SEQ ID NO: 1425). The predicted ORF (SEQ ID NO: 1426) and potential protein functional information was further analyzed by PSORT II. This analysis indicates a protein of 747 amino acids that is likely targeted to the nucleus.

Example 11

[1488] Additional Bioinformatic Analysis of Colon Tumor Antigen C636S

[1489] A Lifeseq Gold database search and analysis was performed to obtain additional sequence information for the colon tumor antigen, C636S, (set forth in SEQ ID NOs: 1365 and 1420). An additional 494 base pairs were obtained, extending beyond the 5′ end of the sequence. The extended cDNA sequence of C636S is set forth in SEQ ID NO: 1427). Two potential open reading frames of 89 and 62 amino acids were identified (SEQ ID NOs: 1428 and 1429, respectively).

Example 12

[1490] Identification of Additional Colon Tumor Protein cDNAs

[1491] This Example illustrates the identification of additional cDNA molecules differentially expressed in colon tumors versus normal tissues.

[1492] A cDNA subtraction library containing cDNA from primary colon tumors subtracted with cDNA from normal tissues (liver, salivary gland, small intestine, stomach, heart, brain, bone marrow and normal lung) was constructed as follows. Total RNA was extracted from primary tissues using Trizol reagent (Gibco BRL Life Technologies, Gaithersburg, Md.) as described by the manufacturer. The polyA+ RNA was purified using an oligo(dT) cellulose column according to standard protocols. First strand cDNA was synthesized using the primer supplied in a Clontech PCR-Select cDNA Subtraction Kit (Clontech, Palo Alto, Calif.). The driver DNA consisted of cDNAs from normal tissues with the tester cDNA being from two primary colon tumors. Double-stranded cDNA was synthesized for both tester and driver, and digested with a combination of endonucleases (MluI, MscI, PvuII, SalI and StuI) which recognize six-nucleotide restriction sites. This modification of the digestion procedure resulted in an average cDNA size of 600 bp, rather than the average size of 300 bp that results from digestion with RsaI according to the Clontech protocol. This modification did not affect the subtraction efficiency. The digested tester cDNAs were ligated to two different adaptors and the subtraction was performed according to Clontech's protocol.

[1493] The tester and driver libraries were then hybridized using excess driver cDNA. In the first hybridization step, driver was separately hybridized with each of the two tester cDNA populations. This resulted in populations of (a) unhybridized tester cDNAs, (b) tester cDNAs hybridized to other tester cDNAs, (c) tester cDNAs hybridized to driver cDNAs and (d) unhybridized driver cDNAs. The two separate hybridization reactions were then combined, and rehybridized in the presence of additional denatured driver cDNA. Following this second hybridization, in addition to populations (a) through (d), a fifth population (e) was generated in which tester cDNA with one adapter hybridized to tester cDNA with the second adapter. Accordingly, the second hybridization step resulted in enrichment of differentially expressed sequences which could be used as templates for PCR amplification with adaptor-specific primers.

[1494] The ends were then filled in, and PCR amplification was performed using adaptor-specific primers. Only population (e), which contained tester cDNA that did not hybridize to driver cDNA, was amplified exponentially. A second PCR amplification step was then performed, to reduce background and further enrich differentially expressed sequences.

[1495] This PCR-based subtraction technique normalizes differentially expressed cDNAs so that transcripts that are overexpressed in colon tumor tissue may be recoverable. Such transcripts would be difficult to recover by traditional subtraction methods.

[1496] The resulting PCR products were subcloned into the TA cloning vector, pCRII (Invitrogen, San Diego, Calif.) and transformed into ElectroMax E. coli DH10B cells (Gibco BRL Life, Technologies) by electroporation. DNA was isolated from independent clones and sequenced using a Perkin Elmer/Applied Biosystems Division (Foster City, Calif.) Automated Sequencer Model 373A.

[1497] One thousand seven hundred ninety six randomly selected cDNA clones in the subtracted colon tumor-specific eDNA library were characterized by DNA sequencing and by subsequent Genbank and EST Blast database searches. Sequences of these partial cDNAs are provided in SEQ ID NO: 1430-3225.

Example 13

[1498] Identification of Additional Colon Tumor Protein cDNAs

[1499] This Example illustrates the identification of additional cDNA molecules differentially expressed in colon tumors versus normal tissues.

[1500] One hundred and ninety-two individual clones were characterized by DNA sequencing as described above, all representing cDNA fragments from the PCR-based subtracted cDNA library enriched for clones that are overexpressed in colon tumors described in Example 12. These sequences are disclosed herein as SEQ ID NO: 3226-3417.

Example 14

[1501] Peptide Priming of T-helper Lines

[1502] 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:

[1503] 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 15

[1504] Generation of Tumor-specific CTL Lines using in Vitro Whole-gene Priming

[1505] 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-y 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 16

[1506] Generation and Characterization of Anti-tumor Antigen Monoclonal Antibodies

[1507] 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 μg 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 17

[1508] Synthesis of Polypeptides

[1509] 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.

[1510] 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.

Number	Date	Country
60313077	Aug 2001	US
60290322	May 2001	US
60267400	Feb 2001	US
60305265	Jul 2001	US
60267382	Feb 2001	US

Compositions and methods for the therapy and diagnosis of colon cancer

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