U.S. patent application number 11/929396 was filed with the patent office on 2008-09-18 for compositions and methods for the therapy and diagnosis of prostate cancer.
This patent application is currently assigned to CORIXA CORPORATION. Invention is credited to Michael D. Kalos, John A. Stolk, Jiangchun Xu.
Application Number | 20080226620 11/929396 |
Document ID | / |
Family ID | 32505786 |
Filed Date | 2008-09-18 |
United States Patent
Application |
20080226620 |
Kind Code |
A1 |
Xu; Jiangchun ; et
al. |
September 18, 2008 |
COMPOSITIONS AND METHODS FOR THE THERAPY AND DIAGNOSIS OF PROSTATE
CANCER
Abstract
Compositions and methods for the therapy and diagnosis of
cancer, particularly prostate cancer, are disclosed. Illustrative
compositions comprise one or more prostate-specific polypeptides,
immunogenic portions thereof, polynucleotides that encode such
polypeptides, antigen presenting cell that expresses such
polypeptides, and T cells that are specific for cells expressing
such polypeptides. The disclosed compositions are useful, for
example, in the diagnosis, prevention and/or treatment of diseases,
particularly prostate cancer.
Inventors: |
Xu; Jiangchun; (Bellevue,
WA) ; Stolk; John A.; (Bothell, WA) ; Kalos;
Michael D.; (Pasadena, CA) |
Correspondence
Address: |
SEED INTELLECTUAL PROPERTY LAW GROUP PLLC
701 FIFTH AVE, SUITE 5400
SEATTLE
WA
98104
US
|
Assignee: |
CORIXA CORPORATION
Hamilton
MT
|
Family ID: |
32505786 |
Appl. No.: |
11/929396 |
Filed: |
October 30, 2007 |
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Current U.S.
Class: |
424/130.1 ;
424/93.71; 435/29; 435/366; 435/372.3; 435/6.14; 435/7.1; 514/1.1;
514/44R; 530/324; 530/325; 530/326; 530/327; 530/350; 530/387.1;
530/402; 536/23.1 |
Current CPC
Class: |
A61K 2035/124 20130101;
A61K 2039/505 20130101; C07K 16/3069 20130101; C12N 2760/16222
20130101; C07K 14/4748 20130101; C07K 2317/565 20130101; A61P 37/02
20180101; A61K 48/00 20130101; C12N 9/6424 20130101; A61K 2039/53
20130101; A61K 2039/55566 20130101; A01K 2227/105 20130101; C07K
14/705 20130101; G01N 33/57434 20130101; A61K 39/00 20130101; C07K
14/47 20130101; A01K 2267/0331 20130101; A61K 38/00 20130101; A61P
37/04 20180101; C07K 14/005 20130101; A61K 2039/5156 20130101; C07K
2317/73 20130101; C07K 2319/00 20130101; A61P 35/00 20180101 |
Class at
Publication: |
424/130.1 ;
530/327; 530/326; 530/325; 530/324; 530/350; 435/366; 530/387.1;
435/7.1; 530/402; 536/23.1; 435/6; 435/29; 435/372.3; 514/12;
514/13; 514/14; 514/15; 514/44; 424/93.71 |
International
Class: |
A61K 39/395 20060101
A61K039/395; C07K 7/00 20060101 C07K007/00; C07K 11/00 20060101
C07K011/00; C12N 15/64 20060101 C12N015/64; C12N 5/08 20060101
C12N005/08; C07K 16/00 20060101 C07K016/00; G01N 33/53 20060101
G01N033/53; C07K 19/00 20060101 C07K019/00; A61K 45/00 20060101
A61K045/00; C07H 21/04 20060101 C07H021/04; C12Q 1/68 20060101
C12Q001/68; C12Q 1/02 20060101 C12Q001/02; A61K 38/04 20060101
A61K038/04; A61K 38/16 20060101 A61K038/16; A61K 31/7088 20060101
A61K031/7088 |
Claims
1. An isolated polypeptide comprising no more than X amino acid
residues of SEQ ID NO: 113, wherein said polypeptide comprises SEQ
ID NO:1037, and wherein X is selected from the group consisting of
11-542.
2. The polypeptide of claim 1, wherein SEQ ID NO: 1037 comprises an
11 amino acid fragment of SEQ ID NO: 113 that contains naturally
processed T-cell epitopes for three Class I MHC alleles.
3. The polypeptide of claim 1, wherein X is selected from the group
consisting of 11-100.
4. The polypeptide of claim 1, wherein X is selected from the group
consisting of 11-50.
5. The polypeptide of claim 1, wherein X is selected from the group
consisting of 11-25.
6. An isolated polynucleotide comprising a sequence selected from
the group consisting of: (a) sequences provided in SEQ ID
NOs:1034-1036; (b) complements of the sequences provided in SEQ ID
NOs: 1034-1036; (c) sequences consisting of at least 20 contiguous
residues of a sequence provided in SEQ ID NOs: 1034-1036; (d)
sequences that hybridize to a sequence provided in SEQ ID NOs:
1034-1036, under highly stringent conditions; (e) sequences having
at least 75% identity to a sequence of SEQ ID NOs: 1034-1036; (f)
sequences having at least 90% identity to a sequence of SEQ ID NOs:
1034-1036; and (g) degenerate variants of a sequence provided in
SEQ ID NOs: 1034-1036; and (h) sequences encoding a polypeptide
according to claim 1.
7. An isolated polypeptide comprising an amino acid sequence
selected from the group consisting of: (a) sequences encoded by a
polynucleotide of claim 6; and (b) sequences having at least 70%
identity to a sequence encoded by a polynucleotide of claim 6; (c)
sequences having at least 90% identity to a sequence encoded by a
polynucleotide of claim 6; (d) sequences consisting of at least 5
contiguous amino acids of a sequence encoded by a polynucleotide of
claim 6; (e) sequences consisting of at least 10 contiguous amino
acids of a sequence encoded by a polynucleotide of claim 6; and (f)
sequences consisting of at least 20 contiguous amino acids of a
sequence encoded by a polynucleotide of claim 6.
8. An expression vector comprising a polynucleotide of claim 6
operably linked to an expression control sequence.
9. A host cell transformed or transfected with an expression vector
according to claim 8.
10. An isolated antibody, or antigen-binding fragment thereof, that
specifically binds to a polypeptide of claims 1 or 7.
11. A method for detecting the presence of a cancer in a patient,
comprising the steps of: (a) obtaining a biological sample from the
patient; (b) contacting the biological sample with a binding agent
that binds to a polypeptide of claims 1 or 7 or a polypeptide of
SEQ ID NO: 108; (c) detecting in the sample an amount of
polypeptide that binds to the binding agent; and (d) comparing the
amount of polypeptide to a predetermined cut-off value and
therefrom determining the presence of a cancer in the patient.
12. A fusion protein comprising at least one polypeptide according
to claims 1 or 7.
13. An oligonucleotide that hybridizes to a sequence recited in SEQ
ID NOs: 1034-1036 under highly stringent conditions.
14. A method for stimulating and/or expanding T cells specific for
a tumor protein, comprising contacting T cells with at least one
component selected from the group consisting of: (a) polypeptides
according to claims 1 or 7; (b) polynucleotides according to claim
6; and (c) antigen-presenting cells that express a polynucleotide
according to claim 6, under conditions and for a time sufficient to
permit the stimulation and/or expansion of T cells.
15. An isolated T cell population, comprising T cells prepared
according to the method of claim 14.
16. A composition comprising a first component selected from the
group consisting of physiologically acceptable carriers and
immunostimulants, and a second component selected from the group
consisting of: (a) polypeptides according to claims 1 or 7; (b)
polynucleotides according to claim 6; (c) antibodies according to
claim 10; (d) fusion proteins according to claim 12; (e) T cell
populations according to claim 15; and (f) antigen presenting cells
that express a polypeptide according to claims 1 or 7.
17. A method for stimulating an immune response in a patient,
comprising administering to the patient a composition of claim
16.
18. A method for the treatment of a prostate cancer in a patient,
comprising administering to the patient a composition of claim
16.
19. A method for determining the presence of a cancer in a patient,
comprising the steps of: (a) obtaining a biological sample from the
patient; (b) contacting the biological sample with an
oligonucleotide according to claim 13 or an oligonucleotide
specific for SEQ ID NO: 107; (c) detecting in the sample an amount
of a polynucleotide that hybridizes to the oligonucleotide; and (d)
comparing the amount of polynucleotide that hybridizes to the
oligonucleotide to a predetermined cut-off value, and therefrom
determining the presence of the cancer in the patient.
20. A diagnostic kit comprising at least one oligonucleotide
according to claim 13.
21. A diagnostic kit comprising at least one antibody according to
claim 10 and a detection reagent, wherein the detection reagent
comprises a reporter group.
22. A method for the treatment of prostate cancer in a patient,
comprising the steps of: (a) incubating CD4+ and/or CD8+ T cells
isolated from a patient with at least one component selected from
the group consisting of: (i) polypeptides according to claims 1 or
7; (ii) polynucleotides according to claim 6; and (iii) antigen
presenting cells that express a polypeptide of claims 1 or 7, such
that T cell proliferate; (b) administering to the patient an
effective amount of the proliferated T cells, and thereby
inhibiting the development of a cancer in the patient.
Description
STATEMENT REGARDING SEQUENCE LISTING
[0001] The Sequence Listing associated with this application is
provided in text format in lieu of a paper copy, and is hereby
incorporated by reference into the specification. The name of the
text file containing the Sequence Listing is
210121.sub.--427C36_SEQUENCE_LISTING.txt. The text file is 992 KB,
was created on Oct. 30, 2007, and is being submitted electronically
via EFS-Web, concurrent with the filing of the specification.
BACKGROUND OF THE INVENTION
[0002] 1. Field of the Invention
[0003] The present invention relates generally to therapy and
diagnosis of cancer, such as prostate cancer. The invention is more
specifically related to polypeptides, comprising at least a portion
of a prostate-specific protein, and to polynucleotides encoding
such polypeptides. Such polypeptides and polynucleotides are useful
in pharmaceutical compositions, e.g., vaccines, and other
compositions for the diagnosis and treatment of prostate
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 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] Prostate cancer is the most common form of cancer among
males, with an estimated incidence of 30% in men over the age of
50. Overwhelming clinical evidence shows that human prostate cancer
has the propensity to metastasize to bone, and the disease appears
to progress inevitably from androgen dependent to androgen
refractory status, leading to increased patient mortality. This
prevalent disease is currently the second leading cause of cancer
death among men in the U.S.
[0007] In spite of considerable research into therapies for the
disease, prostate cancer remains difficult to treat. Commonly,
treatment is based on surgery and/or radiation therapy, but these
methods are ineffective in a significant percentage of cases. Two
previously identified prostate specific proteins--prostate specific
antigen (PSA) and prostatic acid phosphatase (PAP)--have limited
therapeutic and diagnostic potential. For example, PSA levels do
not always correlate well with the presence of prostate cancer,
being positive in a percentage of non-prostate cancer cases,
including benign prostatic hyperplasia (BPH). Furthermore, PSA
measurements correlate with prostate volume, and do not indicate
the level of metastasis.
[0008] In spite of considerable research into therapies for these
and other cancers, prostate 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 NO: 1-111, 115-171,
173-175, 177, 179-305, 307-315, 326, 328, 330, 332-335, 340-375,
381, 382 and 384-476, 524, 526, 530, 531, 533, 535, 536, 552,
569-572, 587, 591, 593-606, 618-705, 709-774, 777, 789, 817, 823,
824, 878, 880-882, 894, 896, 907, 908, 916-919, 929-931, 938, 939,
942, 944, 945, 948, 967, 969-976, 991, 993-1002, 1004, 1006, 1007,
1010, 1013-1019, 1021, 1023-1027, and 1034-1036;
[0011] (b) complements of the sequences provided in SEQ ID NO:
1-111, 115-171, 173-175, 177,179-305, 307-315, 326, 328, 330,
332-335, 340-375, 381, 382 and 384-476, 524, 526, 530, 531, 533,
535, 536, 552, 569-572, 587, 591, 593-606, 618-705, 709-774, 777,
789, 817, 823, 824, 878, 880-882, 894, 896, 907, 908, 916-919,
929-931, 938, 939, 942, 944, 945, 948, 967, 969-976, 991, 993-1002,
1004, 1006, 1007, 1010, 1013-1019, 1021, 1023-1027, and
1034-1036;
[0012] (c) sequences consisting of at least 20 contiguous residues
of a sequence provided in SEQ ID NO: 1-111, 115-171, 173-175,
177,179-305, 307-315, 326, 328, 330, 332-335, 340-375, 381, 382 and
384-476, 524, 526, 530, 531, 533, 535, 536, 552, 569-572, 587, 591,
593-606, 618-705, 709-774, 777, 789, 817, 823, 824, 878, 880-882,
894, 896, 907, 908, 916-919, 929-931, 938, 939, 942, 944, 945, 948,
967, 969-976, 991, 993-1002, 1004, 1006, 1007, 1010, 1013-1019,
1021, 1023-1027, and 1034-1036;
[0013] (d) sequences that hybridize to a sequence provided in SEQ
ID NO: 1-111, 115-171, 173-175, 177,179-305, 307-315, 326, 328,
330, 332-335, 340-375, 381, 382 and 384-476, 524, 526, 530, 531,
533, 535, 536, 552, 569-572, 587, 591, 593-606, 618-705, 709-774,
777, 789, 817, 823, 824, 878, 880-882, 894, 896, 907, 908, 916-919,
929-931, 938, 939, 942, 944, 945, 948, 967, 969-976, 991, 993-1002,
1004, 1006, 1007, 1010, 1013-1019, 1021, 1023-1027, and 1034-1036,
under moderately stringent conditions;
[0014] (e) sequences having at least 75% identity to a sequence of
SEQ ID NO: 1-111, 115-171, 173-175, 177, 179-305, 307-315, 326,
328, 330, 332-335, 340-375, 381, 382 and 384-476, 524, 526, 530,
531, 533, 535, 536, 552, 569-572, 587, 591, 593-606, 618-705,
709-774, 777, 789, 817, 823, 824, 878, 880-882, 894, 896, 907, 908,
916-919, 929-931, 938, 939, 942, 944, 945, 948, 967, 969-976, 991,
993-1002, 1004, 1006, 1007, 1010, 1013-1019, 1021, 1023-1027, and
1034-1036;
[0015] (f) sequences having at least 90% identity to a sequence of
SEQ ID NO: 1-111, 115-171, 173-175, 177,179-305, 307-315, 326, 328,
330, 332-335, 340-375, 381, 382 and 384-476, 524, 526, 530, 531,
533, 535, 536, 552, 569-572, 587, 591, 593-606, 618-705, 709-774,
777, 789, 817, 823, 824, 878, 880-882, 894, 896, 907, 908, 916-919,
929-931, 938, 939, 942, 944, 945, 948, 967, 969-976, 991, 993-1002,
1004, 1006, 1007, 1010, 1013-1019, 1021, 1023-1027, and 1034-1036;
and
[0016] (g) degenerate variants of a sequence provided in SEQ ID NO:
1-111, 115-171, 173-175, 177, 179-305, 307-315, 326, 328, 330,
332-335, 340-375, 381, 382 and 384-476, 524, 526, 530, 531, 533,
535, 536, 552, 569-572, 587, 591, 593-606, 618-705, 709-774, 777,
789, 817, 823, 824, 878, 880-882, 894, 896, 907, 908, 916-919,
929-931, 938, 939, 942, 944, 945, 948, 967, 969-976, 991, 993-1002,
1004, 1006, 1007, 1010, 1013-1019, 1021, 1023-1027, and
1034-1036.
[0017] 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 prostate tissue samples tested, at a level that is at
least about 2-fold, preferably at least about 5-fold, and most
preferably at least about 10-fold higher than that for other normal
tissues.
[0018] The present invention, in another aspect, provides
polypeptide compositions comprising an amino acid sequence that is
encoded by a polynucleotide sequence described above.
[0019] The present invention further provides polypeptide
compositions comprising an amino acid sequence selected from the
group consisting of sequences recited in SEQ ID NO: 112-114, 172,
176, 178, 327, 329, 331, 336, 339, 376-380, 383, 477-483, 496, 504,
505, 519, 520, 522, 525, 527, 532, 534, 537-551, 553-568, 573-586,
588-590, 592, 706-708, 775, 776, 778, 780, 781, 811, 814, 818, 826,
827, 853, 855, 858, 860-862, 866-877, 879, 883-893, 895, 897, 898,
909-915, 920-928, 932-934, 940, 941, 943, 946, 947, 949-966, 968,
977-990, 992, 1003, 1005, 1008, 1009, 1011, 1012, 1020, 1022,
1028-1029, 1030-1033, and 1037.
[0020] 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.
[0021] In another illustrative embodiment, a P501S (SEQ ID NO: 113)
polypeptide of the present invention comprises a fragment of P501S
that will minimally comprise SEQ ID NO:1037, which represents an 11
amino acid fragment of P501S that was unexpectedly found to contain
naturally processed epitopes for at least three Class I MHC
alleles. In a related embodiment, the polypeptides of the present
invention comprise fragments of P501S that minimally contain SEQ ID
NO:1037, and that are at least 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54,
55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88,
89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103,
104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116,
117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129,
130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142,
143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155,
156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168,
169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181,
182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194,
195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207,
208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220,
221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233,
234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246,
247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259,
260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272,
273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285,
286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298,
299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311,
312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324,
325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337,
338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350,
351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363,
364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376,
377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389,
390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402,
403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415,
416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428,
429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441,
442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454,
455, 456, 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467,
468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480,
481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493,
494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506,
507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519,
520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532,
533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545,
546, 547, 548, 549, 550, 551, 552, or 553, amino acids in length
and contain SEQ ID NO:1037.
[0022] Certain other illustrative P501S polypeptides according to
this embodiment will consist of at least 11-542 amino acid
residues, 11-100 amino acid residues, 11-50 amino acid residues, or
11-25 amino acid residues of SEQ ID NO: 113 and will contain SEQ ID
NO: 1037.
[0023] The present invention further provides fragments, variants
and/or derivatives of the disclosed polypeptide and/or
polynucleotide sequences, wherein the fragments, variants and/or
derivatives preferably have a level of immunogenic activity of at
least about 50%, preferably at least about 70% and more preferably
at least about 90% of the level of immunogenic activity of a
polypeptide sequence set forth in SEQ ID NO: 112-114, 172, 176,
178, 327, 329, 331, 336, 339, 376-380, 383, 477-483, 496, 504, 505,
519, 520, 522, 525, 527, 532, 534, 537-551, 553-568, 573-586,
588-590, 592, 706-708, 775, 776, 778, 780, 781, 811, 814, 818, 826,
827, 853, 855, 858 or 860-862, 866-877, 879, 883-893, 895, 897,
898, 909-915, 920-928, 932-934, 940, 941, 943, 946, 947, 949-966,
968, 977-990, 992, 1003, 1005, 1008, 1009, 1011, 1012, 1020, 1022,
1028-1029, and 1030-1033 or a polypeptide sequence encoded by a
polynucleotide sequence set forth in SEQ ID NO: 1-111, 115-171,
173-175, 177, 179-305, 307-315, 326, 328, 330, 332-335, 340-375,
381, 382 and 384-476, 524, 526, 530, 531, 533, 535, 536, 552,
569-572, 587, 591, 593-606, 618-705, 709-774, 777, 789, 817, 823,
824, 878, 880-882, 894, 896, 907, 908, 916-919, 929-931, 938, 939,
942, 944, 945, 948, 967, 969-976, 991, 993-1002, 1004, 1006, 1007,
1010, 1013-1019, 1021, 1023-1027, and 1034-1037.
[0024] 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.
[0025] Within other aspects, the present invention provides
pharmaceutical compositions comprising a polypeptide or
polynucleotide as described above and a physiologically acceptable
carrier.
[0026] Within a related aspect of the present invention,
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, together with a physiologically acceptable carrier.
[0027] 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.
[0028] 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.
[0029] 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.
[0030] The present invention further provides, in other aspects,
fusion proteins that comprise at least one polypeptide as described
above, as well as polynucleotides encoding such fusion proteins,
typically in the form of pharmaceutical compositions, e.g., vaccine
compositions, comprising a physiologically acceptable carrier
and/or an immunostimulant. The fusions proteins may comprise
multiple immunogenic polypeptides or portions/variants thereof, as
described herein, and may further comprise one or more polypeptide
segments for facilitating and/or enhancing the expression,
purification and/or immunogenicity of the polypeptide(s).
[0031] 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 prostate cancer, in which case the methods provide
treatment for the disease, or a patient considered to be at risk
for such a disease may be treated prophylactically.
[0032] 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 prostate
cancer, in which case the methods provide treatment for the
disease, or a patient considered to be at risk for such a disease
may be treated prophylactically.
[0033] The present invention further provides, within other
aspects, methods for removing tumor cells from a biological sample,
comprising contacting a biological sample with T cells that
specifically react with a polypeptide of the present invention,
wherein the step of contacting is performed under conditions and
for a time sufficient to permit the removal of cells expressing the
polypeptide from the sample.
[0034] 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.
[0035] Methods are further provided, within other aspects, for
stimulating and/or expanding T cells specific for a polypeptide of
the present invention, comprising contacting T cells with one or
more of: (i) a polypeptide as described above; (ii) a
polynucleotide encoding such a polypeptide; and (iii) an antigen
presenting cell that expresses such a polypeptide; under conditions
and for a time sufficient to permit the stimulation and/or
expansion of T cells. Isolated T cell populations comprising T
cells prepared as described above are also provided.
[0036] 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.
[0037] The present invention further provides methods for
inhibiting the development of a cancer in a patient, comprising the
steps of: (a) incubating CD4.sup.+ and/or CD8.sup.+ T cells
isolated from a patient with one or more of: (i) a polypeptide
comprising at least an immunogenic portion of polypeptide disclosed
herein; (ii) a polynucleotide encoding such a polypeptide; and
(iii) an antigen-presenting cell that expressed such a polypeptide;
and (b) administering to the patient an effective amount of the
proliferated T cells, thereby inhibiting the development of a
cancer in the patient. Proliferated cells may, but need not, be
cloned prior to administration to the patient.
[0038] Within further aspects, the present invention provides
methods for determining the presence or absence of a cancer,
preferably a prostate cancer, in a patient comprising: (a)
contacting a biological sample obtained from a patient with a
binding agent that binds to a polypeptide as recited above; (b)
detecting in the sample an amount of polypeptide that binds to the
binding agent; and (c) comparing the amount of polypeptide with a
predetermined cut-off value, and therefrom determining the presence
or absence of a cancer in the patient. Within preferred
embodiments, the binding agent is an antibody, more preferably a
monoclonal antibody.
[0039] 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.
[0040] The present invention further provides, within other
aspects, methods for determining the presence or absence of a
cancer in a patient, comprising the steps of: (a) contacting a
biological sample obtained from a patient with an oligonucleotide
that hybridizes to a polynucleotide of the present invention; (b)
detecting in the sample a level of a polynucleotide, preferably
mRNA, that hybridizes to the oligonucleotide; and (c) comparing the
level of polynucleotide that hybridizes to the oligonucleotide with
a predetermined cut-off value, and therefrom determining the
presence or absence of a cancer in the patient. 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 of the present invention, 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 an inventive
polynucleotide, or a complement of such a polynucleotide.
[0041] 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 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.
[0042] 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.
[0043] These and other aspects of the present invention will become
apparent upon reference to the following detailed description and
attached drawings. All references disclosed herein are hereby
incorporated by reference in their entirety as if each was
incorporated individually.
BRIEF DESCRIPTION OF THE DRAWINGS AND SEQUENCE IDENTIFIERS
[0044] FIG. 1 illustrates the ability of T cells to kill
fibroblasts expressing the representative prostate-specific
polypeptide P502S, as compared to control fibroblasts. The
percentage lysis is shown as a series of effector:target ratios, as
indicated.
[0045] FIGS. 2A and 2B illustrate the ability of T cells to
recognize cells expressing the representative prostate-specific
polypeptide P502S. In each case, the number of .gamma.-interferon
spots is shown for different numbers of responders. In FIG. 2A,
data is presented for fibroblasts pulsed with the P2S-12 peptide,
as compared to fibroblasts pulsed with a control E75 peptide. In
FIG. 2B, data is presented for fibroblasts expressing P502S, as
compared to fibroblasts expressing H ER-2/neu.
[0046] FIG. 3 represents a peptide competition binding assay
showing that the P1S#10 peptide, derived from P501S, binds HLA-A2.
Peptide P1S#10 inhibits HLA-A2 restricted presentation of fluM58
peptide to CTL clone D150M58 in TNF release bioassay. D150M58 CTL
is specific for the HLA-A2 binding influenza matrix peptide
fluM58.
[0047] FIG. 4 illustrates the ability of T cell lines generated
from P1S#10 immunized mice to specifically lyse P1S#10-pulsed
Jurkat A2Kb targets and P501S-transduced Jurkat A2Kb targets, as
compared to EGFP-transduced Jurkat A2Kb. The percent lysis is shown
as a series of effector to target ratios, as indicated.
[0048] FIG. 5 illustrates the ability of a T cell clone to
recognize and specifically lyse Jurkat A2Kb cells expressing the
representative prostate-specific polypeptide P501S, thereby
demonstrating that the P1S#10 peptide may be a naturally processed
epitope of the P501S polypeptide.
[0049] FIGS. 6A and 6B are graphs illustrating the specificity of a
CD8.sup.+ cell line (3A-1) for a representative prostate-specific
antigen (P501S). FIG. 6A shows the results of a .sup.51Cr release
assay. The percent specific lysis is shown as a series of
effector:target ratios, as indicated. FIG. 6B shows the production
of interferon-gamma by 3A-1 cells stimulated with autologous B-LCL
transduced with P501S, at varying effector:target rations as
indicated.
[0050] FIG. 7 is a Western blot showing the expression of P501S in
baculovirus.
[0051] FIG. 8 illustrates the results of epitope mapping studies on
P501S.
[0052] FIG. 9 is a schematic representation of the P501S protein
showing the location of transmembrane domains and predicted
intracellular and extracellular domains.
[0053] FIG. 10 is a genomic map showing the location of the
prostate genes P775P, P704P, B305D, P712P and P774P within the Cat
Eye Syndrome region of chromosome 22q11.2
[0054] FIG. 11 shows the results of an ELISA assay to determine the
specificity of rabbit polyclonal antisera raised against P501S.
[0055] SEQ ID NO: 1 is the determined cDNA sequence for F1-13
[0056] SEQ ID NO: 2 is the determined 3' cDNA sequence for
F1-12
[0057] SEQ ID NO: 3 is the determined 5' cDNA sequence for
F1-12
[0058] SEQ ID NO: 4 is the determined 3' cDNA sequence for
F1-16
[0059] SEQ ID NO: 5 is the determined 3' cDNA sequence for H1-1
[0060] SEQ ID NO: 6 is the determined 3' cDNA sequence for H1-9
[0061] SEQ ID NO: 7 is the determined 3' cDNA sequence for H1-4
[0062] SEQ ID NO: 8 is the determined 3' cDNA sequence for
J1-17
[0063] SEQ ID NO: 9 is the determined 5' cDNA sequence for
J1-17
[0064] SEQ ID NO: 10 is the determined 3' cDNA sequence for
L1-12
[0065] SEQ ID NO: 11 is the determined 5' cDNA sequence for
L1-12
[0066] SEQ ID NO: 12 is the determined 3' cDNA sequence for
N1-1862
[0067] SEQ ID NO: 13 is the determined 5' cDNA sequence for
N1-1862
[0068] SEQ ID NO: 14 is the determined 3' cDNA sequence for
J1-13
[0069] SEQ ID NO: 15 is the determined 5' cDNA sequence for
J1-13
[0070] SEQ ID NO: 16 is the determined 3' cDNA sequence for
J1-19
[0071] SEQ ID NO: 17 is the determined 5' cDNA sequence for
J1-19
[0072] SEQ ID NO: 18 is the determined 3' cDNA sequence for
J1-25
[0073] SEQ ID NO: 19 is the determined 5' cDNA sequence for
J1-25
[0074] SEQ ID NO: 20 is the determined 5' cDNA sequence for
J1-24
[0075] SEQ ID NO: 21 is the determined 3' cDNA sequence for
J1-24
[0076] SEQ ID NO: 22 is the determined 5' cDNA sequence for
K1-58
[0077] SEQ ID NO: 23 is the determined 3' cDNA sequence for
K1-58
[0078] SEQ ID NO: 24 is the determined 5' cDNA sequence for
K1-63
[0079] SEQ ID NO: 25 is the determined 3' cDNA sequence for
K1-63
[0080] SEQ ID NO: 26 is the determined 5' cDNA sequence for
L1-4
[0081] SEQ ID NO: 27 is the determined 3' cDNA sequence for
L1-4
[0082] SEQ ID NO: 28 is the determined 5' cDNA sequence for
L1-14
[0083] SEQ ID NO: 29 is the determined 3' cDNA sequence for
L1-14
[0084] SEQ ID NO: 30 is the determined 3' cDNA sequence for
J1-12
[0085] SEQ ID NO: 31 is the determined 3' cDNA sequence for
J1-16
[0086] SEQ ID NO: 32 is the determined 3' cDNA sequence for
J1-21
[0087] SEQ ID NO: 33 is the determined 3' cDNA sequence for
K1-48
[0088] SEQ ID NO: 34 is the determined 3' cDNA sequence for
K1-55
[0089] SEQ ID NO: 35 is the determined 3' cDNA sequence for
L1-2
[0090] SEQ ID NO: 36 is the determined 3' cDNA sequence for
L1-6
[0091] SEQ ID NO: 37 is the determined 3' cDNA sequence for
N1-1858
[0092] SEQ ID NO: 38 is the determined 3' cDNA sequence for
N1-1860
[0093] SEQ ID NO: 39 is the determined 3' cDNA sequence for
N1-1861
[0094] SEQ ID NO: 40 is the determined 3' cDNA sequence for
N1-1864
[0095] SEQ ID NO: 41 is the determined cDNA sequence for P5
[0096] SEQ ID NO: 42 is the determined cDNA sequence for P8
[0097] SEQ ID NO: 43 is the determined cDNA sequence for P9
[0098] SEQ ID NO: 44 is the determined cDNA sequence for P18
[0099] SEQ ID NO: 45 is the determined cDNA sequence for P20
[0100] SEQ ID NO: 46 is the determined cDNA sequence for P29
[0101] SEQ ID NO: 47 is the determined cDNA sequence for P30
[0102] SEQ ID NO: 48 is the determined cDNA sequence for P34
[0103] SEQ ID NO: 49 is the determined cDNA sequence for P36
[0104] SEQ ID NO: 50 is the determined cDNA sequence for P38
[0105] SEQ ID NO: 51 is the determined cDNA sequence for P39
[0106] SEQ ID NO: 52 is the determined cDNA sequence for P42
[0107] SEQ ID NO: 53 is the determined cDNA sequence for P47
[0108] SEQ ID NO: 54 is the determined cDNA sequence for P49
[0109] SEQ ID NO: 55 is the determined cDNA sequence for P50
[0110] SEQ ID NO: 56 is the determined cDNA sequence for P53
[0111] SEQ ID NO: 57 is the determined cDNA sequence for P55
[0112] SEQ ID NO: 58 is the determined cDNA sequence for P60
[0113] SEQ ID NO: 59 is the determined cDNA sequence for P64
[0114] SEQ ID NO: 60 is the determined cDNA sequence for P65
[0115] SEQ ID NO: 61 is the determined cDNA sequence for P73
[0116] SEQ ID NO: 62 is the determined cDNA sequence for P75
[0117] SEQ ID NO: 63 is the determined cDNA sequence for P76
[0118] SEQ ID NO: 64 is the determined cDNA sequence for P79
[0119] SEQ ID NO: 65 is the determined cDNA sequence for P84
[0120] SEQ ID NO: 66 is the determined cDNA sequence for P68
[0121] SEQ ID NO: 67 is the determined cDNA sequence for P80 (also
referred to as P704P)
[0122] SEQ ID NO: 68 is the determined cDNA sequence for P82
[0123] SEQ ID NO: 69 is the determined cDNA sequence for
U1-3064
[0124] SEQ ID NO: 70 is the determined cDNA sequence for
U1-3065
[0125] SEQ ID NO: 71 is the determined cDNA sequence for
V1-3692
[0126] SEQ ID NO: 72 is the determined cDNA sequence for
1A-3905
[0127] SEQ ID NO: 73 is the determined cDNA sequence for
V1-3686
[0128] SEQ ID NO: 74 is the determined cDNA sequence for
R1-2330
[0129] SEQ ID NO: 75 is the determined cDNA sequence for
1B-3976
[0130] SEQ ID NO: 76 is the determined cDNA sequence for
V1-3679
[0131] SEQ ID NO: 77 is the determined cDNA sequence for
1G-4736
[0132] SEQ ID NO: 78 is the determined cDNA sequence for
1G-4738
[0133] SEQ ID NO: 79 is the determined cDNA sequence for
1G-4741
[0134] SEQ ID NO: 80 is the determined cDNA sequence for
1G-4744
[0135] SEQ ID NO: 81 is the determined cDNA sequence for
1G-4734
[0136] SEQ ID NO: 82 is the determined cDNA sequence for
1H-4774
[0137] SEQ ID NO: 83 is the determined cDNA sequence for
1H-4781
[0138] SEQ ID NO: 84 is the determined cDNA sequence for
1H-4785
[0139] SEQ ID NO: 85 is the determined cDNA sequence for
1H-4787
[0140] SEQ ID NO: 86 is the determined cDNA sequence for
1H-4796
[0141] SEQ ID NO: 87 is the determined cDNA sequence for
1I-4807
[0142] SEQ ID NO: 88 is the determined cDNA sequence for
1I-4810
[0143] SEQ ID NO: 89 is the determined cDNA sequence for
1I-4811
[0144] SEQ ID NO: 90 is the determined cDNA sequence for
1J-4876
[0145] SEQ ID NO: 91 is the determined cDNA sequence for
1K-4884
[0146] SEQ ID NO: 92 is the determined cDNA sequence for
1K-4896
[0147] SEQ ID NO: 93 is the determined cDNA sequence for
1G-4761
[0148] SEQ ID NO: 94 is the determined cDNA sequence for
1G-4762
[0149] SEQ ID NO: 95 is the determined cDNA sequence for
1H-4766
[0150] SEQ ID NO: 96 is the determined cDNA sequence for
1H-4770
[0151] SEQ ID NO: 97 is the determined cDNA sequence for
1H-4771
[0152] SEQ ID NO: 98 is the determined cDNA sequence for
1H-4772
[0153] SEQ ID NO: 99 is the determined cDNA sequence for
1D-4297
[0154] SEQ ID NO: 100 is the determined cDNA sequence for
1D-4309
[0155] SEQ ID NO: 101 is the determined cDNA sequence for
1D.1-4278
[0156] SEQ ID NO: 102 is the determined cDNA sequence for
1D-4288
[0157] SEQ ID NO: 103 is the determined cDNA sequence for
1D-4283
[0158] SEQ ID NO: 104 is the determined cDNA sequence for
1D-4304
[0159] SEQ ID NO: 105 is the determined cDNA sequence for
1D-4296
[0160] SEQ ID NO: 106 is the determined cDNA sequence for
1D-4280
[0161] SEQ ID NO: 107 is the determined full length cDNA sequence
for F1-12 (also referred to as P504S)
[0162] SEQ ID NO: 108 is the amino acid sequence for F1-12
[0163] SEQ ID NO: 109 is the determined full length cDNA sequence
for J1-17
[0164] SEQ ID NO: 110 is the determined full length cDNA sequence
for L1-12 (also referred to as P501S)
[0165] SEQ ID NO: 111 is the determined full length cDNA sequence
for N1-1862 (also referred to as P503S)
[0166] SEQ ID NO: 112 is the amino acid sequence for J1-17
[0167] SEQ ID NO: 113 is the amino acid sequence for L1-12 (also
referred to as P501S)
[0168] SEQ ID NO: 114 is the amino acid sequence for N1-1862 (also
referred to as P503S)
[0169] SEQ ID NO: 115 is the determined cDNA sequence for P89
[0170] SEQ ID NO: 116 is the determined cDNA sequence for P90
[0171] SEQ ID NO: 117 is the determined cDNA sequence for P92
[0172] SEQ ID NO: 118 is the determined cDNA sequence for P95
[0173] SEQ ID NO: 119 is the determined cDNA sequence for P98
[0174] SEQ ID NO: 120 is the determined cDNA sequence for P102
[0175] SEQ ID NO: 121 is the determined cDNA sequence for P110
[0176] SEQ ID NO: 122 is the determined cDNA sequence for P1
[0177] SEQ ID NO: 123 is the determined cDNA sequence for P114
[0178] SEQ ID NO: 124 is the determined cDNA sequence for P115
[0179] SEQ ID NO: 125 is the determined cDNA sequence for P116
[0180] SEQ ID NO: 126 is the determined cDNA sequence for P124
[0181] SEQ ID NO: 127 is the determined cDNA sequence for P126
[0182] SEQ ID NO: 128 is the determined cDNA sequence for P130
[0183] SEQ ID NO: 129 is the determined cDNA sequence for P133
[0184] SEQ ID NO: 130 is the determined cDNA sequence for P138
[0185] SEQ ID NO: 131 is the determined cDNA sequence for P143
[0186] SEQ ID NO: 132 is the determined cDNA sequence for P151
[0187] SEQ ID NO: 133 is the determined cDNA sequence for P156
[0188] SEQ ID NO: 134 is the determined cDNA sequence for P157
[0189] SEQ ID NO: 135 is the determined cDNA sequence for P166
[0190] SEQ ID NO: 136 is the determined cDNA sequence for P176
[0191] SEQ ID NO: 137 is the determined cDNA sequence for P178
[0192] SEQ ID NO: 138 is the determined cDNA sequence for P179
[0193] SEQ ID NO: 139 is the determined cDNA sequence for P185
[0194] SEQ ID NO: 140 is the determined cDNA sequence for P192
[0195] SEQ ID NO: 141 is the determined cDNA sequence for P201
[0196] SEQ ID NO: 142 is the determined cDNA sequence for P204
[0197] SEQ ID NO: 143 is the determined cDNA sequence for P208
[0198] SEQ ID NO: 144 is the determined cDNA sequence for P211
[0199] SEQ ID NO: 145 is the determined cDNA sequence for P213
[0200] SEQ ID NO: 146 is the determined cDNA sequence for P219
[0201] SEQ ID NO: 147 is the determined cDNA sequence for P237
[0202] SEQ ID NO: 148 is the determined cDNA sequence for P239
[0203] SEQ ID NO: 149 is the determined cDNA sequence for P248
[0204] SEQ ID NO: 150 is the determined cDNA sequence for P251
[0205] SEQ ID NO: 151 is the determined cDNA sequence for P255
[0206] SEQ ID NO: 152 is the determined cDNA sequence for P256
[0207] SEQ ID NO: 153 is the determined cDNA sequence for P259
[0208] SEQ ID NO: 154 is the determined cDNA sequence for P260
[0209] SEQ ID NO: 155 is the determined cDNA sequence for P263
[0210] SEQ ID NO: 156 is the determined cDNA sequence for P264
[0211] SEQ ID NO: 157 is the determined cDNA sequence for P266
[0212] SEQ ID NO: 158 is the determined cDNA sequence for P270
[0213] SEQ ID NO: 159 is the determined cDNA sequence for P272
[0214] SEQ ID NO: 160 is the determined cDNA sequence for P278
[0215] SEQ ID NO: 161 is the determined cDNA sequence for P105
[0216] SEQ ID NO: 162 is the determined cDNA sequence for P107
[0217] SEQ ID NO: 163 is the determined cDNA sequence for P137
[0218] SEQ ID NO: 164 is the determined cDNA sequence for P194
[0219] SEQ ID NO: 165 is the determined cDNA sequence for P195
[0220] SEQ ID NO: 166 is the determined cDNA sequence for P196
[0221] SEQ ID NO: 167 is the determined cDNA sequence for P220
[0222] SEQ ID NO: 168 is the determined cDNA sequence for P234
[0223] SEQ ID NO: 169 is the determined cDNA sequence for P235
[0224] SEQ ID NO: 170 is the determined cDNA sequence for P243
[0225] SEQ ID NO: 171 is the determined cDNA sequence for
P703P-DE1
[0226] SEQ ID NO: 172 is the amino acid sequence for P703P-DE1
[0227] SEQ ID NO: 173 is the determined cDNA sequence for
P703P-DE2
[0228] SEQ ID NO: 174 is the determined cDNA sequence for
P703P-DE6
[0229] SEQ ID NO: 175 is the determined cDNA sequence for
P703P-DE13
[0230] SEQ ID NO: 176 is the amino acid sequence for P703P-DE13
[0231] SEQ ID NO: 177 is the determined cDNA sequence for
P703P-DE14
[0232] SEQ ID NO: 178 is the amino acid sequence for P703P-DE14
[0233] SEQ ID NO: 179 is the determined extended cDNA sequence for
1G-4736
[0234] SEQ ID NO: 180 is the determined extended cDNA sequence for
1G-4738
[0235] SEQ ID NO: 181 is the determined extended cDNA sequence for
1G-4741
[0236] SEQ ID NO: 182 is the determined extended cDNA sequence for
1G-4744
[0237] SEQ ID NO: 183 is the determined extended cDNA sequence for
1H-4774
[0238] SEQ ID NO: 184 is the determined extended cDNA sequence for
1H-4781
[0239] SEQ ID NO: 185 is the determined extended cDNA sequence for
1H-4785
[0240] SEQ ID NO: 186 is the determined extended cDNA sequence for
1H-4787
[0241] SEQ ID NO: 187 is the determined extended cDNA sequence for
1H-4796
[0242] SEQ ID NO: 188 is the determined extended cDNA sequence for
1I-4807
[0243] SEQ ID NO: 189 is the determined 3' cDNA sequence for
1I-4810
[0244] SEQ ID NO: 190 is the determined 3' cDNA sequence for
1I-4811
[0245] SEQ ID NO: 191 is the determined extended cDNA sequence for
1I-4876
[0246] SEQ ID NO: 192 is the determined extended cDNA sequence for
1K-4884
[0247] SEQ ID NO: 193 is the determined extended cDNA sequence for
1K-4896
[0248] SEQ ID NO: 194 is the determined extended cDNA sequence for
1G-4761
[0249] SEQ ID NO: 195 is the determined extended cDNA sequence for
1G-4762
[0250] SEQ ID NO: 196 is the determined extended cDNA sequence for
1H-4766
[0251] SEQ ID NO: 197 is the determined 3' cDNA sequence for
1H-4770
[0252] SEQ ID NO: 198 is the determined 3' cDNA sequence for
1H-4771
[0253] SEQ ID NO: 199 is the determined extended cDNA sequence for
1H-4772
[0254] SEQ ID NO: 200 is the determined extended cDNA sequence for
1D-4309
[0255] SEQ ID NO: 201 is the determined extended cDNA sequence for
1D.1-4278
[0256] SEQ ID NO: 202 is the determined extended cDNA sequence for
1D-4288
[0257] SEQ ID NO: 203 is the determined extended cDNA sequence for
1D-4283
[0258] SEQ ID NO: 204 is the determined extended cDNA sequence for
1D-4304
[0259] SEQ ID NO: 205 is the determined extended cDNA sequence for
1D-4296
[0260] SEQ ID NO: 206 is the determined extended cDNA sequence for
1D-4280
[0261] SEQ ID NO: 207 is the determined cDNA sequence for
10-d8fwd
[0262] SEQ ID NO: 208 is the determined cDNA sequence for
10-H10con
[0263] SEQ ID NO: 209 is the determined cDNA sequence for
11-C8rev
[0264] SEQ ID NO: 210 is the determined cDNA sequence for
7.g6fwd
[0265] SEQ ID NO: 211 is the determined cDNA sequence for
7.g6rev
[0266] SEQ ID NO: 212 is the determined cDNA sequence for
8-b5fwd
[0267] SEQ ID NO: 213 is the determined cDNA sequence for
8-b5rev
[0268] SEQ ID NO: 214 is the determined cDNA sequence for
8-b6fwd
[0269] SEQ ID NO: 215 is the determined cDNA sequence for 8-b6
rev
[0270] SEQ ID NO: 216 is the determined cDNA sequence for
8-d4fwd
[0271] SEQ ID NO: 217 is the determined cDNA sequence for
8-d9rev
[0272] SEQ ID NO: 218 is the determined cDNA sequence for
8-g3fwd
[0273] SEQ ID NO: 219 is the determined cDNA sequence for
8-g3rev
[0274] SEQ ID NO: 220 is the determined cDNA sequence for
8-h11rev
[0275] SEQ ID NO: 221 is the determined cDNA sequence for
g-f12fwd
[0276] SEQ ID NO: 222 is the determined cDNA sequence for
g-f3rev
[0277] SEQ ID NO: 223 is the determined cDNA sequence for P509S
[0278] SEQ ID NO: 224 is the determined cDNA sequence for P510S
[0279] SEQ ID NO: 225 is the determined cDNA sequence for
P703DE5
[0280] SEQ ID NO: 226 is the determined cDNA sequence for 9-A11
[0281] SEQ ID NO: 227 is the determined cDNA sequence for 8-C6
[0282] SEQ ID NO: 228 is the determined cDNA sequence for 8-H7
[0283] SEQ ID NO: 229 is the determined cDNA sequence for
JPTPN13
[0284] SEQ ID NO: 230 is the determined cDNA sequence for
JPTPN14
[0285] SEQ ID NO: 231 is the determined cDNA sequence for
JPTPN23
[0286] SEQ ID NO: 232 is the determined cDNA sequence for
JPTPN24
[0287] SEQ ID NO: 233 is the determined cDNA sequence for
JPTPN25
[0288] SEQ ID NO: 234 is the determined cDNA sequence for
JPTPN30
[0289] SEQ ID NO: 235 is the determined cDNA sequence for
JPTPN34
[0290] SEQ ID NO: 236 is the determined cDNA sequence for
PTPN35
[0291] SEQ ID NO: 237 is the determined cDNA sequence for
JPTPN36
[0292] SEQ ID NO: 238 is the determined cDNA sequence for
JPTPN38
[0293] SEQ ID NO: 239 is the determined cDNA sequence for
JPTPN39
[0294] SEQ ID NO: 240 is the determined cDNA sequence for
JPTPN40
[0295] SEQ ID NO: 241 is the determined cDNA sequence for
JPTPN41
[0296] SEQ ID NO: 242 is the determined cDNA sequence for
JPTPN42
[0297] SEQ ID NO: 243 is the determined cDNA sequence for
JPTPN45
[0298] SEQ ID NO: 244 is the determined cDNA sequence for
JPTPN46
[0299] SEQ ID NO: 245 is the determined cDNA sequence for
JPTPN51
[0300] SEQ ID NO: 246 is the determined cDNA sequence for
JPTPN56
[0301] SEQ ID NO: 247 is the determined cDNA sequence for
PTPN64
[0302] SEQ ID NO: 248 is the determined cDNA sequence for
JPTPN65
[0303] SEQ ID NO: 249 is the determined cDNA sequence for
JPTPN67
[0304] SEQ ID NO: 250 is the determined cDNA sequence for
JPTPN76
[0305] SEQ ID NO: 251 is the determined cDNA sequence for
JPTPN84
[0306] SEQ ID NO: 252 is the determined cDNA sequence for
JPTPN85
[0307] SEQ ID NO: 253 is the determined cDNA sequence for
JPTPN86
[0308] SEQ ID NO: 254 is the determined cDNA sequence for
JPTPN87
[0309] SEQ ID NO: 255 is the determined cDNA sequence for
JPTPN88
[0310] SEQ ID NO: 256 is the determined cDNA sequence for JP1
F1
[0311] SEQ ID NO: 257 is the determined cDNA sequence for JP1F2
[0312] SEQ ID NO: 258 is the determined cDNA sequence for JP1C2
[0313] SEQ ID NO: 259 is the determined cDNA sequence for JP1B1
[0314] SEQ ID NO: 260 is the determined cDNA sequence for JP1B2
[0315] SEQ ID NO: 261 is the determined cDNA sequence for JP1D3
[0316] SEQ ID NO: 262 is the determined cDNA sequence for JP1A4
[0317] SEQ ID NO: 263 is the determined cDNA sequence for JP1F5
[0318] SEQ ID NO: 264 is the determined cDNA sequence for JP1E6
[0319] SEQ ID NO: 265 is the determined cDNA sequence for JP1D6
[0320] SEQ ID NO: 266 is the determined cDNA sequence for JP1B5
[0321] SEQ ID NO: 267 is the determined cDNA sequence for JP1A6
[0322] SEQ ID NO: 268 is the determined cDNA sequence for JP1E8
[0323] SEQ ID NO: 269 is the determined cDNA sequence for JP1D7
[0324] SEQ ID NO: 270 is the determined cDNA sequence for JP1D9
[0325] SEQ ID NO: 271 is the determined cDNA sequence for
JP1C10
[0326] SEQ ID NO: 272 is the determined cDNA sequence for JP1A9
[0327] SEQ ID NO: 273 is the determined cDNA sequence for
JP1F12
[0328] SEQ ID NO: 274 is the determined cDNA sequence for
JP1E12
[0329] SEQ ID NO: 275 is the determined cDNA sequence for
JP1D11
[0330] SEQ ID NO: 276 is the determined cDNA sequence for
JP1C11
[0331] SEQ ID NO: 277 is the determined cDNA sequence for
JP1C12
[0332] SEQ ID NO: 278 is the determined cDNA sequence for
JP1B12
[0333] SEQ ID NO: 279 is the determined cDNA sequence for
JP1A12
[0334] SEQ ID NO: 280 is the determined cDNA sequence for JP8G2
[0335] SEQ ID NO: 281 is the determined cDNA sequence for JP8H1
[0336] SEQ ID NO: 282 is the determined cDNA sequence for JP8H2
[0337] SEQ ID NO: 283 is the determined cDNA sequence for JP8A3
[0338] SEQ ID NO: 284 is the determined cDNA sequence for JP8A4
[0339] SEQ ID NO: 285 is the determined cDNA sequence for JP8C3
[0340] SEQ ID NO: 286 is the determined cDNA sequence for JP8G4
[0341] SEQ ID NO: 287 is the determined cDNA sequence for JP8B6
[0342] SEQ ID NO: 288 is the determined cDNA sequence for JP8D6
[0343] SEQ ID NO: 289 is the determined cDNA sequence for JP8F5
[0344] SEQ ID NO: 290 is the determined cDNA sequence for JP8A8
[0345] SEQ ID NO: 291 is the determined cDNA sequence for JP8C7
[0346] SEQ ID NO: 292 is the determined cDNA sequence for JP8D7
[0347] SEQ ID NO: 293 is the determined cDNA sequence for P8D8
[0348] SEQ ID NO: 294 is the determined cDNA sequence for JP8E7
[0349] SEQ ID NO: 295 is the determined cDNA sequence for JP8F8
[0350] SEQ ID NO: 296 is the determined cDNA sequence for JP8G8
[0351] SEQ ID NO: 297 is the determined cDNA sequence for
JP8B10
[0352] SEQ ID NO: 298 is the determined cDNA sequence for
JP8C10
[0353] SEQ ID NO: 299 is the determined cDNA sequence for JP8E9
[0354] SEQ ID NO: 300 is the determined cDNA sequence for
JP8E10
[0355] SEQ ID NO: 301 is the determined cDNA sequence for JP8F9
[0356] SEQ ID NO: 302 is the determined cDNA sequence for JP8H9
[0357] SEQ ID NO: 303 is the determined cDNA sequence for
JP8C12
[0358] SEQ ID NO: 304 is the determined cDNA sequence for
JP8E11
[0359] SEQ ID NO: 305 is the determined cDNA sequence for
JP8E12
[0360] SEQ ID NO: 306 is the amino acid sequence for the peptide
PS2#12
[0361] SEQ ID NO: 307 is the determined cDNA sequence for P711P
[0362] SEQ ID NO: 308 is the determined cDNA sequence for P712P
[0363] SEQ ID NO: 309 is the determined cDNA sequence for
CLONE23
[0364] SEQ ID NO: 310 is the determined cDNA sequence for P774P
[0365] SEQ ID NO: 311 is the determined cDNA sequence for P775P
[0366] SEQ ID NO: 312 is the determined cDNA sequence for P715P
[0367] SEQ ID NO: 313 is the determined cDNA sequence for P710P
[0368] SEQ ID NO: 314 is the determined cDNA sequence for P767P
[0369] SEQ ID NO: 315 is the determined cDNA sequence for P768P
[0370] SEQ ID NO: 316-325 are the determined cDNA sequences of
previously isolated genes
[0371] SEQ ID NO: 326 is the determined cDNA sequence for
P703PDE5
[0372] SEQ ID NO: 327 is the amino acid sequence for P703PDE5
[0373] SEQ ID NO: 328 is the determined cDNA sequence for
P703P6.26
[0374] SEQ ID NO: 329 is the amino acid sequence for P703P6.26
[0375] SEQ ID NO: 330 is the determined cDNA sequence for
P703PX-23
[0376] SEQ ID NO: 331 is the amino acid sequence for P703PX-23
[0377] SEQ ID NO: 332 is the determined full length cDNA sequence
for P509S
[0378] SEQ ID NO: 333 is the determined extended cDNA sequence for
P707P (also referred to as 11-C9)
[0379] SEQ ID NO: 334 is the determined cDNA sequence for P714P
[0380] SEQ ID NO: 335 is the determined cDNA sequence for P705P
(also referred to as 9-F3)
[0381] SEQ ID NO: 336 is the amino acid sequence for P705P
[0382] SEQ ID NO: 337 is the amino acid sequence of the peptide
P1S#10
[0383] SEQ ID NO: 338 is the amino acid sequence of the peptide
p5
[0384] SEQ ID NO: 339 is the amino acid sequence of P509S
[0385] SEQ ID NO: 340 is the determined cDNA sequence for P778P
[0386] SEQ ID NO: 341 is the determined cDNA sequence for P786P
[0387] SEQ ID NO: 342 is the determined cDNA sequence for P789P
[0388] SEQ ID NO: 343 is the determined cDNA sequence for a clone
showing homology to Homo sapiens MM46 mRNA
[0389] SEQ ID NO: 344 is the determined cDNA sequence for a clone
showing homology to Homo sapiens TNF-alpha stimulated ABC protein
(ABC50) mRNA
[0390] SEQ ID NO: 345 is the determined cDNA sequence for a clone
showing homology to Homo sapiens mRNA for E-cadherin
[0391] SEQ ID NO: 346 is the determined cDNA sequence for a clone
showing homology to Human nuclear-encoded mitochondrial serine
hydroxymethyltransferase (SHMT)
[0392] SEQ ID NO: 347 is the determined cDNA sequence for a clone
showing homology to Homo sapiens natural resistance-associated
macrophage protein2 (NRAMP2)
[0393] SEQ ID NO: 348 is the determined cDNA sequence for a clone
showing homology to Homo sapiens phosphoglucomutase-related protein
(PGMRP)
[0394] SEQ ID NO: 349 is the determined cDNA sequence for a clone
showing homology to Human mRNA for proteosome subunit p40
[0395] SEQ ID NO: 350 is the determined cDNA sequence for P777P
[0396] SEQ ID NO: 351 is the determined cDNA sequence for P779P
[0397] SEQ ID NO: 352 is the determined cDNA sequence for P790P
[0398] SEQ ID NO: 353 is the determined cDNA sequence for P784P
[0399] SEQ ID NO: 354 is the determined cDNA sequence for P776P
[0400] SEQ ID NO: 355 is the determined cDNA sequence for P780P
[0401] SEQ ID NO: 356 is the determined cDNA sequence for P544S
[0402] SEQ ID NO: 357 is the determined cDNA sequence for P745S
[0403] SEQ ID NO: 358 is the determined cDNA sequence for P782P
[0404] SEQ ID NO: 359 is the determined cDNA sequence for P783P
[0405] SEQ ID NO: 360 is the determined cDNA sequence for unknown
17984
[0406] SEQ ID NO: 361 is the determined cDNA sequence for P787P
[0407] SEQ ID NO: 362 is the determined cDNA sequence for P788P
[0408] SEQ ID NO: 363 is the determined cDNA sequence for unknown
17994
[0409] SEQ ID NO: 364 is the determined cDNA sequence for P781P
[0410] SEQ ID NO: 365 is the determined cDNA sequence for P785P
[0411] SEQ ID NO: 366-375 are the determined cDNA sequences for
splice variants of B305D.
[0412] SEQ ID NO: 376 is the amino acid sequence encoded by the
sequence of SEQ ID NO: 366.
[0413] SEQ ID NO: 377 is the amino acid sequence encoded by the
sequence of SEQ ID NO: 372.
[0414] SEQ ID NO: 378 is the amino acid sequence encoded by the
sequence of SEQ ID NO: 373.
[0415] SEQ ID NO: 379 is the amino acid sequence encoded by the
sequence of SEQ ID NO: 374.
[0416] SEQ ID NO: 380 is the amino acid sequence encoded by the
sequence of SEQ ID NO: 375.
[0417] SEQ ID NO: 381 is the determined cDNA sequence for
B716P.
[0418] SEQ ID NO: 382 is the determined full-length cDNA sequence
for P711P.
[0419] SEQ ID NO: 383 is the amino acid sequence for P711P.
[0420] SEQ ID NO: 384 is the cDNA sequence for P1000C.
[0421] SEQ ID NO: 385 is the cDNA sequence for CGI-82.
[0422] SEQ ID NO:386 is the cDNA sequence for 23320.
[0423] SEQ ID NO:387 is the cDNA sequence for CGI-69.
[0424] SEQ ID NO:388 is the cDNA sequence for
L-iditol-2-dehydrogenase.
[0425] SEQ ID NO:389 is the cDNA sequence for 23379.
[0426] SEQ ID NO:390 is the cDNA sequence for 23381.
[0427] SEQ ID NO:391 is the cDNA sequence for KIAA0122.
[0428] SEQ ID NO:392 is the cDNA sequence for clone 23399 (also
known as P554S).
[0429] SEQ ID NO:393 is the cDNA sequence for a previously
identified gene.
[0430] SEQ ID NO:394 is the cDNA sequence for HCLBP.
[0431] SEQ ID NO:395 is the cDNA sequence for transglutaminase.
[0432] SEQ ID NO:396 is the cDNA sequence for a previously
identified gene.
[0433] SEQ ID NO:397 is the cDNA sequence for PAP.
[0434] SEQ ID NO:398 is the cDNA sequence for Ets transcription
factor PDEF.
[0435] SEQ ID NO:399 is the cDNA sequence for hTGR.
[0436] SEQ ID NO:400 is the cDNA sequence for KIAA0295.
[0437] SEQ ID NO:401 is the cDNA sequence for 22545.
[0438] SEQ ID NO:402 is the cDNA sequence for 22547.
[0439] SEQ ID NO:403 is the cDNA sequence for 22548.
[0440] SEQ ID NO:404 is the cDNA sequence for 22550.
[0441] SEQ ID NO:405 is the cDNA sequence for 22551.
[0442] SEQ ID NO:406 is the cDNA sequence for 22552.
[0443] SEQ ID NO:407 is the cDNA sequence for 22553 (also known as
P1020C).
[0444] SEQ ID NO:408 is the cDNA sequence for 22558.
[0445] SEQ ID NO:409 is the cDNA sequence for 22562.
[0446] SEQ ID NO:410 is the cDNA sequence for 22565.
[0447] SEQ ID NO:411 is the cDNA sequence for 22567.
[0448] SEQ ID NO:412 is the cDNA sequence for 22568.
[0449] SEQ ID NO:413 is the cDNA sequence for 22570.
[0450] SEQ ID NO:414 is the cDNA sequence for 22571.
[0451] SEQ ID NO:415 is the cDNA sequence for 22572.
[0452] SEQ ID NO:416 is the cDNA sequence for 22573.
[0453] SEQ ID NO:417 is the cDNA sequence for 22573.
[0454] SEQ ID NO:418 is the cDNA sequence for 22575.
[0455] SEQ ID NO:419 is the cDNA sequence for 22580.
[0456] SEQ ID NO:420 is the cDNA sequence for 22581.
[0457] SEQ ID NO:421 is the cDNA sequence for 22582.
[0458] SEQ ID NO:422 is the cDNA sequence for 22583.
[0459] SEQ ID NO:423 is the cDNA sequence for 22584.
[0460] SEQ ID NO:424 is the cDNA sequence for 22585.
[0461] SEQ ID NO:425 is the cDNA sequence for 22586.
[0462] SEQ ID NO:426 is the cDNA sequence for 22587.
[0463] SEQ ID NO:427 is the cDNA sequence for 22588.
[0464] SEQ ID NO:428 is the cDNA sequence for 22589.
[0465] SEQ ID NO:429 is the cDNA sequence for 22590.
[0466] SEQ ID NO:430 is the cDNA sequence for 22591.
[0467] SEQ ID NO:431 is the cDNA sequence for 22592.
[0468] SEQ ID NO:432 is the cDNA sequence for 22593.
[0469] SEQ ID NO:433 is the cDNA sequence for 22594.
[0470] SEQ ID NO:434 is the cDNA sequence for 22595.
[0471] SEQ ID NO:435 is the cDNA sequence for 22596.
[0472] SEQ ID NO:436 is the cDNA sequence for 22847.
[0473] SEQ ID NO:437 is the cDNA sequence for 22848.
[0474] SEQ ID NO:438 is the cDNA sequence for 22849.
[0475] SEQ ID NO:439 is the cDNA sequence for 22851.
[0476] SEQ ID NO:440 is the cDNA sequence for 22852.
[0477] SEQ ID NO:441 is the cDNA sequence for 22853.
[0478] SEQ ID NO:442 is the cDNA sequence for 22854.
[0479] SEQ ID NO:443 is the cDNA sequence for 22855.
[0480] SEQ ID NO:444 is the cDNA sequence for 22856.
[0481] SEQ ID NO:445 is the cDNA sequence for 22857.
[0482] SEQ ID NO:446 is the cDNA sequence for 23601.
[0483] SEQ ID NO:447 is the cDNA sequence for 23602.
[0484] SEQ ID NO:448 is the cDNA sequence for 23605.
[0485] SEQ ID NO:449 is the cDNA sequence for 23606.
[0486] SEQ ID NO:450 is the cDNA sequence for 23612.
[0487] SEQ ID NO:451 is the cDNA sequence for 23614.
[0488] SEQ ID NO:452 is the cDNA sequence for 23618.
[0489] SEQ ID NO:453 is the cDNA sequence for 23622.
[0490] SEQ ID NO:454 is the cDNA sequence for folate hydrolase.
[0491] SEQ ID NO:455 is the cDNA sequence for LIM protein.
[0492] SEQ ID NO:456 is the cDNA sequence for a known gene.
[0493] SEQ ID NO:457 is the cDNA sequence for a known gene.
[0494] SEQ ID NO:458 is the cDNA sequence for a previously
identified gene.
[0495] SEQ ID NO:459 is the cDNA sequence for 23045.
[0496] SEQ ID NO:460 is the cDNA sequence for 23032.
[0497] SEQ ID NO:461 is the cDNA sequence for clone 23054.
[0498] SEQ ID NO:462-467 are cDNA sequences for known genes.
[0499] SEQ ID NO:468-471 are cDNA sequences for P710P.
[0500] SEQ ID NO:472 is a cDNA sequence for P1001C.
[0501] SEQ ID NO: 473 is the determined cDNA sequence for a first
splice variant of P775P (referred to as 27505).
[0502] SEQ ID NO: 474 is the determined cDNA sequence for a second
splice variant of P775P (referred to as 19947).
[0503] SEQ ID NO: 475 is the determined cDNA sequence for a third
splice variant of P775P (referred to as 19941).
[0504] SEQ ID NO: 476 is the determined cDNA sequence for a fourth
splice variant of P775P (referred to as 19937).
[0505] SEQ ID NO: 477 is a first amino acid sequence encoded by the
sequence of SEQ ID NO: 474.
[0506] SEQ ID NO: 478 is a second amino acid sequence encoded by
the sequence of SEQ ID NO: 474.
[0507] SEQ ID NO: 479 is the amino acid sequence encoded by the
sequence of SEQ ID NO: 475.
[0508] SEQ ID NO: 480 is a first amino acid sequence encoded by the
sequence of SEQ ID NO: 473.
[0509] SEQ ID NO: 481 is a second amino acid sequence encoded by
the sequence of SEQ ID NO: 473.
[0510] SEQ ID NO: 482 is a third amino acid sequence encoded by the
sequence of SEQ ID NO: 473.
[0511] SEQ ID NO: 483 is a fourth amino acid sequence encoded by
the sequence of SEQ ID NO: 473.
[0512] SEQ ID NO: 484 is the first 30 amino acids of the M.
tuberculosis antigen Ra12.
[0513] SEQ ID NO: 485 is the PCR primer AW025.
[0514] SEQ ID NO: 486 is the PCR primer AW003.
[0515] SEQ ID NO: 487 is the PCR primer AW027.
[0516] SEQ ID NO: 488 is the PCR primer AW026.
[0517] SEQ ID NO: 489-501 are peptides employed in epitope mapping
studies.
[0518] SEQ ID NO: 502 is the determined cDNA sequence of the
complementarity determining region for the anti-P503S monoclonal
antibody 20D4.
[0519] SEQ ID NO: 503 is the determined cDNA sequence of the
complementarity determining region for the anti-P503S monoclonal
antibody JA1.
[0520] SEQ ID NO: 504 & 505 are peptides employed in epitope
mapping studies.
[0521] SEQ ID NO: 506 is the determined cDNA sequence of the
complementarity determining region for the anti-P703P monoclonal
antibody 8H2.
[0522] SEQ ID NO: 507 is the determined cDNA sequence of the
complementarity determining region for the anti-P703P monoclonal
antibody 7H8.
[0523] SEQ ID NO: 508 is the determined cDNA sequence of the
complementarity determining region for the anti-P703P monoclonal
antibody 2D4.
[0524] SEQ ID NO: 509-522 are peptides employed in epitope mapping
studies.
[0525] SEQ ID NO: 523 is a mature form of P703P used to raise
antibodies against P703P.
[0526] SEQ ID NO: 524 is the putative full-length cDNA sequence of
P703P.
[0527] SEQ ID NO: 525 is the amino acid sequence encoded by SEQ ID
NO: 524.
[0528] SEQ ID NO: 526 is the full-length cDNA sequence for
P790P.
[0529] SEQ ID NO: 527 is the amino acid sequence for P790P.
[0530] SEQ ID NO: 528 & 529 are PCR primers.
[0531] SEQ ID NO: 530 is the cDNA sequence of a splice variant of
SEQ ID NO: 366.
[0532] SEQ ID NO: 531 is the cDNA sequence of the open reading
frame of SEQ ID NO: 530.
[0533] SEQ ID NO: 532 is the amino acid encoded by the sequence of
SEQ ID NO: 531.
[0534] SEQ ID NO: 533 is the DNA sequence of a putative ORF of
P775P.
[0535] SEQ ID NO: 534 is the amino acid sequence encoded by SEQ ID
NO: 533.
[0536] SEQ ID NO: 535 is a first full-length cDNA sequence for
P510S.
[0537] SEQ ID NO: 536 is a second full-length cDNA sequence for
P510S.
[0538] SEQ ID NO: 537 is the amino acid sequence encoded by SEQ ID
NO: 535.
[0539] SEQ ID NO: 538 is the amino acid sequence encoded by SEQ ID
NO: 536.
[0540] SEQ ID NO: 539 is the peptide P501S-370.
[0541] SEQ ID NO: 540 is the peptide P501S-376.
[0542] SEQ ID NO: 541-551 are epitopes of P501S.
[0543] SEQ ID NO: 552 is an extended cDNA sequence for P712P.
[0544] SEQ ID NO: 553-568 are the amino acid sequences encoded by
open reading frames within SEQ ID NO: 552.
[0545] SEQ ID NO: 569 is an extended cDNA sequence for P776P.
[0546] SEQ ID NO: 570 is the determined cDNA sequence for a splice
variant of P776P referred to as contig 6.
[0547] SEQ ID NO: 571 is the determined cDNA sequence for a splice
variant of P776P referred to as contig 7.
[0548] SEQ ID NO: 572 is the determined cDNA sequence for a splice
variant of P776P referred to as contig 14.
[0549] SEQ ID NO: 573 is the amino acid sequence encoded by a first
ORF of SEQ ID NO: 570.
[0550] SEQ ID NO: 574 is the amino acid sequence encoded by a
second ORF of SEQ ID NO: 570.
[0551] SEQ ID NO: 575 is the amino acid sequence encoded by a ORF
of SEQ ID NO: 571.
[0552] SEQ ID NO: 576-586 are amino acid sequences encoded by ORFs
of SEQ ID NO: 569.
[0553] SEQ ID NO: 587 is a DNA consensus sequence of the sequences
of P767P and P777P.
[0554] SEQ ID NO: 588-590 are amino acid sequences encoded by ORFs
of SEQ ID NO: 587.
[0555] SEQ ID NO: 591 is an extended cDNA sequence for P1020C.
[0556] SEQ ID NO: 592 is the amino acid sequence encoded by the
sequence of SEQ ID NO: P1020C.
[0557] SEQ ID NO: 593 is a splice variant of P775P referred to as
50748.
[0558] SEQ ID NO: 594 is a splice variant of P775P referred to as
50717. SEQ ID NO: 595 is a splice variant of P775P referred to as
45985.
[0559] SEQ ID NO: 596 is a splice variant of P775P referred to as
38769.
[0560] SEQ ID NO: 597 is a splice variant of P775P referred to as
37922.
[0561] SEQ ID NO: 598 is a splice variant of P510S referred to as
49274.
[0562] SEQ ID NO: 599 is a splice variant of P510S referred to as
39487.
[0563] SEQ ID NO: 600 is a splice variant of P504S referred to as
5167.16.
[0564] SEQ ID NO: 601 is a splice variant of P504S referred to as
5167.1.
[0565] SEQ ID NO: 602 is a splice variant of P504S referred to as
5163.46.
[0566] SEQ ID NO: 603 is a splice variant of P504S referred to as
5163.42.
[0567] SEQ ID NO: 604 is a splice variant of P504S referred to as
5163.34.
[0568] SEQ ID NO: 605 is a splice variant of P504S referred to as
5163.17.
[0569] SEQ ID NO: 606 is a splice variant of P501S referred to as
10640.
[0570] SEQ ID NO: 607-615 are the sequences of PCR primers.
[0571] SEQ ID NO: 616 is the determined cDNA sequence of a fusion
of P703P and PSA.
[0572] SEQ ID NO: 617 is the amino acid sequence of the fusion of
P703P and PSA.
[0573] SEQ ID NO: 618-689 are determined cDNA sequences of
prostate-specific clones.
[0574] SEQ ID NO: 690 is the cDNA sequence of the gene DD3.
[0575] SEQ ID NO: 691-697 are determined cDNA sequences of
prostate-specific clones.
[0576] SEQ ID NO: 698 is an extended cDNA sequence for P714P.
[0577] SEQ ID NO: 699-701 are the cDNA sequences for splice
variants of P704P.
[0578] SEQ ID NO: 702 is the cDNA sequence of a spliced variant of
P553S referred to as P553S-14.
[0579] SEQ ID NO: 703 is the cDNA sequence of a spliced variant of
P553S referred to as P553S-12.
[0580] SEQ ID NO: 704 is the cDNA sequence of a spliced variant of
P553S referred to as P553S-10.
[0581] SEQ ID NO: 705 is the cDNA sequence of a spliced variant of
P553S referred to as P553S-6.
[0582] SEQ ID NO: 706 is the amino acid sequence encoded by SEQ ID
NO: 705.
[0583] SEQ ID NO: 707 is the amino acid sequence encoded by SEQ ID
NO: 702 SEQ ID NO: 708 is a second amino acid sequence encoded by
SEQ ID NO: 702.
[0584] SEQ ID NO: 709-772 are determined cDNA sequences of
prostate-specific clones.
[0585] SEQ ID NO: 773 is a first full-length cDNA sequence for
prostate-specific transglutaminase gene (also referred to herein as
P558S).
[0586] SEQ ID NO: 774 is a second full-length cDNA sequence for
prostate-specific transglutaminase gene.
[0587] SEQ ID NO: 775 is the amino acid sequence encoded by the
sequence of SEQ ID NO: 773.
[0588] SEQ ID NO: 776 is the amino acid sequence encoded by the
sequence of SEQ ID NO: 774.
[0589] SEQ ID NO: 777 is the full-length cDNA sequence for
P788P.
[0590] SEQ ID NO: 778 is the amino acid sequence encoded by SEQ ID
NO: 777.
[0591] SEQ ID NO: 779 is the determined cDNA sequence for a
polymorphic variant of P788P.
[0592] SEQ ID NO: 780 is the amino acid sequence encoded by SEQ ID
NO: 779.
[0593] SEQ ID NO: 781 is the amino acid sequence of peptide 4 from
P703P.
[0594] SEQ ID NO: 782 is the cDNA sequence that encodes peptide 4
from P703P.
[0595] SEQ ID NO: 783-798 are the cDNA sequence encoding epitopes
of P703P.
[0596] SEQ ID NO: 799-814 are the amino acid sequences of epitopes
of P703P.
[0597] SEQ ID NO: 815 and 816 are PCR primers.
[0598] SEQ ID NO: 817 is the cDNA sequence encoding an N-terminal
portion of P788P expressed in E. coli.
[0599] SEQ ID NO: 818 is the amino acid sequence of the N-terminal
portion of P788P expressed in E. coli.
[0600] SEQ ID NO: 819 is the amino acid sequence of the M.
tuberculosis antigen Ra12.
[0601] SEQ ID NO: 820 and 821 are PCR primers.
[0602] SEQ ID NO: 822 is the cDNA sequence for the Ra12-P510S-C
construct.
[0603] SEQ ID NO: 823 is the cDNA sequence for the P510S-C
construct.
[0604] SEQ ID NO: 824 is the cDNA sequence for the P510S-E3
construct.
[0605] SEQ ID NO: 825 is the amino acid sequence for the
Ra12-P510S-C construct.
[0606] SEQ ID NO: 826 is the amino acid sequence for the P510S-C
construct.
[0607] SEQ ID NO: 827 is the amino acid sequence for the P510S-E3
construct.
[0608] SEQ ID NO: 828-833 are PCR primers.
[0609] SEQ ID NO: 834 is the cDNA sequence of the construct
Ra12-P775P-ORF3.
[0610] SEQ ID NO: 835 is the amino acid sequence of the construct
Ra12-P775P-ORF3.
[0611] SEQ ID NO: 836 and 837 are PCR primers.
[0612] SEQ ID NO: 838 is the determined amino acid sequence for a
P703P His tag fusion protein.
[0613] SEQ ID NO: 839 is the determined cDNA sequence for a P703P
His tag fusion protein.
[0614] SEQ ID NO: 840 and 841 are PCR primers.
[0615] SEQ ID NO: 842 is the determined amino acid sequence for a
P705P His tag fusion protein.
[0616] SEQ ID NO: 843 is the determined cDNA sequence for a P705P
His tag fusion protein.
[0617] SEQ ID NO: 844 and 845 are PCR primers.
[0618] SEQ ID NO: 846 is the determined amino acid sequence for a
P711P His tag fusion protein.
[0619] SEQ ID NO: 847 is the determined cDNA sequence for a P711P
His tag fusion protein.
[0620] SEQ ID NO: 848 is the amino acid sequence of the M.
tuberculosis antigen Ra12.
[0621] SEQ ID NO: 849 and 850 are PCR primers.
[0622] SEQ ID NO: 851 is the determined cDNA sequence for the
construct Ra12-P501S-E2.
[0623] SEQ ID NO: 852 is the determined amino acid sequence for the
construct Ra12-P501S-E2.
[0624] SEQ ID NO: 853 is the amino acid sequence for an epitope of
P501S.
[0625] SEQ ID NO: 854 is the DNA sequence encoding SEQ ID NO:
853.
[0626] SEQ ID NO: 855 is the amino acid sequence for an epitope of
P501S.
[0627] SEQ ID NO: 856 is the DNA sequence encoding SEQ ID NO:
855.
[0628] SEQ ID NO: 857 is a peptide employed in epitope mapping
studies.
[0629] SEQ ID NO: 858 is the amino acid sequence for an epitope of
P501S.
[0630] SEQ ID NO: 859 is the DNA sequence encoding SEQ ID NO:
858.
[0631] SEQ ID NO: 860-862 are the amino acid sequences for CD4
epitopes of P501S.
[0632] SEQ ID NO: 863-865 are the DNA sequences encoding the
sequences of SEQ ID NO: 860-862.
[0633] SEQ ID NO: 866-877 are the amino acid sequences for putative
CTL epitopes of P703P.
[0634] SEQ ID NO: 878 is the full-length cDNA sequence for
P789P.
[0635] SEQ ID NO: 879 is the amino acid sequence encoded by SEQ ID
NO: 878.
[0636] SEQ ID NO: 880 is the determined full-length cDNA sequence
for the splice variant of P776P referred to as contig 6.
[0637] SEQ ID NO: 881-882 are determined full-length cDNA sequences
for the splice variant of P776P referred to as contig 7.
[0638] SEQ ID NO: 883-887 are amino acid sequences encoded by SEQ
ID NO: 880.
[0639] SEQ ID NO: 888-893 are amino acid sequences encoded by the
splice variant of P776P referred to as contig 7.
[0640] SEQ ID NO: 894 is the full-length cDNA sequence for human
transmembrane protease serine 2.
[0641] SEQ ID NO: 895 is the amino acid sequence encoded by SEQ ID
NO: 894.
[0642] SEQ ID NO: 896 is the cDNA sequence encoding the first 209
amino acids of human transmembrane protease serine 2.
[0643] SEQ ID NO: 897 is the first 209 amino acids of human
transmembrane protease serine 2.
[0644] SEQ ID NO: 898 is the amino acid sequence of peptide 296-322
of P501S.
[0645] SEQ ID NO: 899-902 are PCR primers.
[0646] SEQ ID NO: 903 is the determined cDNA sequence of the Vb
chain of a T cell receptor for the P501S-specific T cell clone
4E5.
[0647] SEQ ID NO: 904 is the determined cDNA sequence of the Va
chain of a T cell receptor for the P501S-specific T cell clone
4E5.
[0648] SEQ ID NO: 905 is the amino acid sequence encoded by SEQ ID
NO 903.
[0649] SEQ ID NO: 906 is the amino acid sequence encoded by SEQ ID
NO 904.
[0650] SEQ ID NO: 907 is the full-length open reading frame for
P768P including stop codon.
[0651] SEQ ID NO: 908 is the full-length open reading frame for
P768P without stop codon.
[0652] SEQ ID NO: 909 is the amino acid sequence encoded by SEQ ID
NO: 908.
[0653] SEQ ID NO: 910-915 are the amino acid sequences for
predicted domains of P768P.
[0654] SEQ ID NO: 916 is the full-length cDNA sequence of
P835P.
[0655] SEQ ID NO: 917 is the cDNA sequence of the previously
identified clone FLJ13581.
[0656] SEQ ID NO: 918 is the cDNA sequence of the open reading
frame for P835P with stop codon.
[0657] SEQ ID NO: 919 is the cDNA sequence of the open reading
frame for P835P without stop codon.
[0658] SEQ ID NO: 920 is the full-length amino acid sequence for
P835P.
[0659] SEQ ID NO: 921-928 are the amino acid sequences of
extracellular and intracellular domains of P835P.
[0660] SEQ ID NO: 929 is the full-length cDNA sequence for
P1000C.
[0661] SEQ ID NO: 930 is the cDNA sequence of the open reading
frame for P1000C, including stop codon.
[0662] SEQ ID NO: 931 is the cDNA sequence of the open reading
frame for P1000C, without stop codon.
[0663] SEQ ID NO: 932 is the full-length amino acid sequence for
P1000C.
[0664] SEQ ID NO: 933 is amino acids 1-100 of SEQ ID NO: 932.
[0665] SEQ ID NO: 934 is amino acids 100-492 of SEQ ID NO: 932.
[0666] SEQ ID NO: 935-937 are PCR primers.
[0667] SEQ ID NO: 938 is the cDNA sequence of the expressed
full-length P767P coding region.
[0668] SEQ ID NO: 939 is the cDNA sequence of an expressed
truncated P767P coding region.
[0669] SEQ ID NO: 940 is the amino acid sequence encoded by SEQ ID
NO: 939.
[0670] SEQ ID NO: 941 is the amino acid sequence encoded by SEQ ID
NO: 938.
[0671] SEQ ID NO: 942 is the DNA sequence of a CD4 epitope of
P703P.
[0672] SEQ ID NO: 943 is the amino acid sequence of a CD4 epitope
of P703P.
[0673] SEQ ID NO: 944 and 945 are the cDNA sequences of two
alternative splice forms of P780P.
[0674] SEQ ID NO: 946 and 947 are the amino acid sequences encoded
by SEQ ID NO: 944 and 945, respectively.
[0675] SEQ ID NO: 948 is a corrected cDNA sequence for P705P.
[0676] SEQ ID NO: 949-956 are the amino acid sequences of P790P
peptides.
[0677] SEQ ID NO: 957-966 are the amino acid sequences of P775P
peptides.
[0678] SEQ ID NO: 967 is an extended cDNA sequence for P554S.
[0679] SEQ ID NO: 968 is the amino acid sequence for P554S.
[0680] SEQ ID NO: 969-976 are the cDNA sequences encoding epitopes
of P501S.
[0681] SEQ ID NO: 977-984 are the amino acid sequences of epitopes
of P501S.
[0682] SEQ ID NO: 985-987 are amino acid sequences of peptides of
P501S.
[0683] SEQ ID NO: 988-990 are amino acid sequences of peptides of
P703P.
[0684] SEQ ID NO:991 is the cDNA encoding a CD4+ T cell epitope of
P703P.
[0685] SEQ ID NO:992 is the amino acid sequence of a CD4+ T cell
epitope of P703P (encoded by SEQ ID NO:991).
[0686] SEQ ID NO: 993 represents the cDNA sequence for P706P clone
8-B6 that includes P3.
[0687] SEQ ID NO: 994 represents the cDNA sequence for P706P clone
8-B6 that includes P4.
[0688] SEQ ID NO: 995 represents the cDNA sequence for P706Pclone
8B6.P4 contig.
[0689] SEQ ID NO: 996 represents the cDNA sequence for P706P ESTs
1386-1902.
[0690] SEQ ID NO: 997 represents the cDNA sequence for P706P ESTs
4927-6088.
[0691] SEQ ID NO: 998 represents the cDNA sequence for P713P clone
PT4410A42.
[0692] SEQ ID NO: 999-1002 represent the four exons encoding the
prostatic secretory protein (PSP).
[0693] SEQ ID NO: 1003 represents the full length amino acid
sequence for PSP.
[0694] SEQ ID NO: 1004 represents an extended cDNA sequence for
clone P1E.
[0695] SEQ ID NO: 1005 represents the amino acid sequence of an
open reading frame encoded by SEQ ID NO: 1004.
[0696] SEQ ID NO: 1006 represents the DNA sequence of the coding
region of the expression construct P510.seq.
[0697] SEQ ID NO: 1007 represents the DNA sequence of coding region
of the expression construct MAPS-P510S.seq.
[0698] SEQ ID NO: 1008 represents the protein sequence encoded by
the DNA sequence of SEQ ID NO: 1007.
[0699] SEQ ID NO: 1009 represents the protein sequence encoded by
the DNA sequence of SEQ ID NO: 1006.
[0700] SEQ ID NO: 1010 represents the DNA sequence of the coding
region for a Trx-P501S fusion construct.
[0701] SEQ ID NO: 1011 represents the amino acid sequence for a
Trx-P501S fusion protein that is encoded by the DNA sequence of SEQ
ID NO: 1010.
[0702] SEQ ID NO:1012 represents the amino acid sequence for a
minimal P501S epitope recognized by clone 2H2-1A12.
[0703] SEQ ID NO:1013 represents the DNA sequence for a minimal
P501S epitope recognized by clone 2H2-1A12.
[0704] SEQ ID NO:1014 corresponds to the primer sequence for the
forward primer hPAPF1.
[0705] SEQ ID NO:1015 corresponds to the primer sequence for the
reverse primer hPAPRV1.
[0706] SEQ ID NO:1016 corresponds to the primer sequence for the
forward primer FOPP2F1.
[0707] SEQ ID NO:1017 corresponds to the primer sequence for the
reverse primer FOPPF1.
[0708] SEQ ID NO:1018 corresponds to the primer sequence for the
forward primer FOPP2RV1.
[0709] SEQ ID NO:1019 sets forth a DNA sequence for a fusion of
FOPP and hPAP, referred to as FOPP2.
[0710] SEQ ID NO:1020 sets forth an amino acid sequence for a
fusion of FOPP and hPAP, referred to as FOPP2.
[0711] SEQ ID NO:1021 sets forth a DNA sequence for a P501S minimal
CD8+ T cell epitope recognized by clone 1H1-1A6.
[0712] SEQ ID NO:1022 sets forth an amino acid sequence for a P501S
minimal CD8+ T cell epitope recognized by clone 1H1-1A6.
[0713] SEQ ID NO:1023 sets forth the sequence for the primer
PDM-930.
[0714] SEQ ID NO:1024 sets forth the sequence for the primer
PDM-165.
[0715] SEQ ID NO:1025 sets forth the sequence for the primer
PDM-929.
[0716] SEQ ID NO1026: sets forth a DNA sequence encoding the P501S
D protein (amino acids 316-553).
[0717] SEQ ID NO:1027 sets forth a DNA sequence encoding the P501S
C protein (amino acids 257-553).
[0718] SEQ ID NO:1028 sets forth an amino acid sequence
corresponding to the P501S D protein (amino acids 316-553).
[0719] SEQ ID NO:1029 sets forth an amino acid sequence
corresponding to the P501 S C protein (amino acids 257-553).
[0720] SEQ ID NO:1030 sets forth an amino acid for a P703P epitope
recognized by patient sera.
[0721] SEQ ID NO:1031 sets forth an amino acid for a P703P epitope
recognized by patient sera.
[0722] SEQ ID NO:1032 sets forth an amino acid for a P703P epitope
recognized by patient sera.
[0723] SEQ ID NO:1033 sets forth an amino acid for a P703P epitope
recognized by patient sera.
[0724] SEQ ID NO:1034 discloses an additional DNA sequence for the
prostate antigen P712P.
[0725] SEQ ID NO:1035 discloses an additional DNA sequence for the
prostate antigen P775P.
[0726] SEQ ID NO:1036 discloses an additional DNA sequence for the
prostate antigen P704P.
[0727] SEQ ID NO:1037 discloses an 11 amino acid fragment derived
from P501S that contains naturally processed epitopes for at least
three class I alleles.
[0728] SEQ ID NO:1038 discloses the polynucleotide sequence
encoding SEQ ID NO: 1037.
DETAILED DESCRIPTION OF THE INVENTION
[0729] U.S. patents, U.S. patent application publications, U.S.
patent applications, foreign patents, foreign patent applications
and non-patent publications referred to in this specification
and/or listed in the Application Data Sheet, are incorporated
herein by reference, in their entirety.
[0730] The present invention is directed generally to compositions
and their use in the therapy and diagnosis of cancer, particularly
prostate 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).
[0731] 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).
[0732] All publications, patents and patent applications cited
herein, whether supra or infra, are hereby incorporated by
reference in their entirety.
[0733] 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.
Polypeptide Compositions
[0734] 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.
[0735] Particularly illustrative polypeptides of the present
invention comprise those encoded by a polynucleotide sequence set
forth in any one of SEQ ID NO: 1-111, 115-171, 173-175,
177,179-305, 307-315, 326, 328, 330, 332-335, 340-375, 381, 382 and
384-476, 524, 526, 530, 531, 533, 535, 536, 552, 569-572, 587, 591,
593-606, 618-705, 709-774, 777, 789, 817, 823, 824, 878, 880-882,
894, 896, 907, 908, 916-919, 929-931, 938, 939, 942, 944, 945, 948,
967, 969-976, 991, 993-1002, 1004, 1006, 1007, 1010, 1013-1019,
1021, 1023-1027 and 1034-1036 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 NO: 1-111, 115-171, 173-175, 177, 179-305, 307-315,
326, 328, 330, 332-335, 340-375, 381, 382 and 384-476, 524, 526,
530, 531, 533, 535, 536, 552, 569-572, 587, 591, 593-606, 618-705,
709-774, 777, 789, 817, 823, 824, 878, 880-882, 894, 896, 907, 908,
916-919, 929-931, 938, 939, 942, 944, 945, 948, 967, 969-976, 991,
993-1002, 1004, 1006, 1007, 1010, 1013-1019, 1021, 1023-1027 and
1034-1036. In specific embodiments, the polypeptides of the
invention comprise amino acid sequences as set forth in any one of
SEQ ID NO: 112-114, 172, 176, 178, 327, 329, 331, 336, 339,
376-380, 383, 477-483, 496, 504, 505, 519, 520, 522, 525, 527, 532,
534, 537-551, 553-568, 573-586, 588-590, 592, 706-708, 775, 776,
778, 780, 781, 811, 814, 818, 826, 827, 853, 855, 858, 860-862,
866-877, 879, 883-893, 895, 897, 898, 909-915, 920-928, 932-934,
940, 941, 943, 946, 947, 949-966, 968, 977-990, 992, 1003, 1005,
1008, 1009, 1011, and 1012, 1020, 1022, 1028-1029, 1030-1033, and
1037.
[0736] The polypeptides of the present invention are sometimes
herein referred to as prostate-specific proteins or
prostate-specific polypeptides, as an indication that their
identification has been based at least in part upon their increased
levels of expression in prostate tissue samples. Thus, a
"prostate-specific polypeptide" or "prostate-specific protein,"
refers generally to a polypeptide sequence of the present
invention, or a polynucleotide sequence encoding such a
polypeptide, that is expressed in a substantial proportion of
prostate tissue samples, for example preferably greater than about
20%, more preferably greater than about 30%, and most preferably
greater than about 50% or more of prostate tissue samples tested,
at a level that is at least two fold, and preferably at least five
fold, greater than the level of expression in other normal tissues,
as determined using a representative assay provided herein. A
prostate-specific polypeptide sequence of the invention, based upon
its increased level of expression in tumor cells, has particular
utility both as a diagnostic marker as well as a therapeutic
target, as further described below.
[0737] 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 prostate 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, .sup.125I-labeled Protein
A.
[0738] 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.
[0739] 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.
[0740] In certain other embodiments, illustrative immunogenic
portions may include peptides in which an N-terminal leader
sequence and/or transmembrane domain has been deleted. Other
illustrative immunogenic portions will contain a small N- and/or
C-terminal deletion (e.g., 1-30 amino acids, preferably 5-15 amino
acids), relative to the mature protein.
[0741] 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.
[0742] 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.
[0743] The present invention, in another aspect, provides
polypeptide fragments comprising at least about 5, 10, 15, 20, 25,
50, or 100 contiguous amino acids, or more, including all
intermediate lengths, of a polypeptide composition set forth
herein, such as those set forth in SEQ ID NO: 112-114, 172, 176,
178, 327, 329, 331, 336, 339, 376-380, 383, 477-483, 496, 504, 505,
519, 520, 522, 525, 527, 532, 534, 537-551, 553-568, 573-586,
588-590, 592, 706-708, 775, 776, 778, 780, 781, 811, 814, 818, 826,
827, 853, 855, 858, 860-862, 866-877, 879, 883-893, 895, 897, 898,
909-915, 920-928, 932-934, 940, 941, 943, 946, 947, 949-966, 968,
977-990, 992, 1003, 1005, 1008, 1009, 1011, 1012, 1020, 1022,
1028-1029, 1030-1033, and 1033 or those encoded by a polynucleotide
sequence set forth in a sequence of SEQ ID NO: 1-111, 115-171,
173-175, 177, 179-305, 307-315, 326, 328, 330, 332-335, 340-375,
381, 382 and 384-476, 524, 526, 530, 531, 533, 535, 536, 552,
569-572, 587, 591, 593-606, 618-705, 709-774, 777, 789, 817, 823,
824, 878, 880-882, 894, 896, 907, 908, 916-919, 929-931, 938, 939,
942, 944, 945, 948, 967, 969-976, 991, 993-1002, 1004, 1006, 1007,
1010, 1013-1019, 1021, 1023-1027 and 1034-1036.
[0744] 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 sequence
set forth herein.
[0745] 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.
[0746] 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.
[0747] A polypeptide "variant," as the term is used herein, is a
polypeptide that typically differs from a polypeptide specifically
disclosed herein in one or more substitutions, deletions, additions
and/or insertions. Such variants may be naturally occurring or may
be synthetically generated, for example, by modifying one or more
of the above polypeptide sequences of the invention and evaluating
their immunogenic activity as described herein using any of a
number of techniques well known in the art.
[0748] 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.
[0749] 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.
[0750] For example, certain amino acids may be substituted for
other amino acids in a protein structure without appreciable loss
of interactive binding capacity with structures such as, for
example, antigen-binding regions of antibodies or binding sites on
substrate molecules. Since it is the interactive capacity and
nature of a protein that defines that protein's biological
functional activity, certain amino acid sequence substitutions can
be made in a protein sequence, and, of course, its underlying DNA
coding sequence, and nevertheless obtain a protein with like
properties. It is thus contemplated that various changes may be
made in the peptide sequences of the disclosed compositions, or
corresponding DNA sequences which encode said peptides without
appreciable loss of their biological utility or activity.
TABLE-US-00001 TABLE 1 Amino Acids Codons Alanine Ala A GCA GCC GCG
GCU Cysteine Cys C UGC UGU Aspartic acid Asp D GAC GAU Glutamic
acid Glu E GAA GAG Phenylalanine Phe F UUC UUU Glycine Gly G GGA
GGC GGG GGU Histidine His H CAC CAU Isoleucine Ile I AUA AUC AUU
Lysine Lys K AAA AAG Leucine Leu L UUA UUG CUA CUC CUG CUU
Methionine Met M AUG Asparagine Asn N AAC AAU Proline Pro P CCA CCC
CCG CCU Glutamine Gln Q CAA CAG Arginine Arg R AGA AGG CGA CGC CGG
CGU Serine Ser S AGC AGU UCA UCC UCG UCU Threonine Thr T ACA ACC
ACG ACU Valine Val V GUA GUC GUG GUU Tryptophan Trp W UGG Tyrosine
Tyr Y UAC UAU
[0751] 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).
[0752] 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.
[0753] 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.
[0754] 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.
[0755] 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.
[0756] Amino acid substitutions may further be made on the basis of
similarity in polarity, charge, solubility, hydrophobicity,
hydrophilicity and/or the amphipathic nature of the residues. For
example, negatively charged amino acids include aspartic acid and
glutamic acid; positively charged amino acids include lysine and
arginine; and amino acids with uncharged polar head groups having
similar hydrophilicity values include leucine, isoleucine and
valine; glycine and alanine; asparagine and glutamine; and serine,
threonine, phenylalanine and tyrosine. Other groups of amino acids
that may represent conservative changes include: (1) ala, pro, gly,
glu, asp, gin, asn, ser, thr; (2) cys, ser, tyr, thr; (3) val, ile,
leu, met, ala, phe; (4) lys, arg, his; and (5) phe, tyr, trp, his.
A variant may also, or alternatively, contain nonconservative
changes. In a preferred embodiment, variant polypeptides differ
from a native sequence by substitution, deletion or addition of
five amino acids or fewer. Variants may also (or alternatively) be
modified by, for example, the deletion or addition of amino acids
that have minimal influence on the immunogenicity, secondary
structure and hydropathic nature of the polypeptide.
[0757] 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.
[0758] 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.
[0759] Optimal alignment of sequences for comparison may be
conducted using the Megalign program in the Lasergene suite of
bioinformatics software (DNASTAR, Inc., Madison, Wis.), using
default parameters. This program embodies several alignment schemes
described in the following references: Dayhoff, M. O. (1978) A
model of evolutionary change in proteins--Matrices for detecting
distant relationships. In Dayhoff, M. O. (ed.) Atlas of Protein
Sequence and Structure, National Biomedical Research Foundation,
Washington D.C. Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990)
Unified Approach to Alignment and Phylogenes pp. 626-645 Methods in
Enzymology vol. 183, Academic Press, Inc., San Diego, Calif.;
Higgins, D. G. and Sharp, P. M. (1989) CABIOS 5:151-153; Myers, E.
W. and Muller W. (1988) CABIOS 4:11-17; Robinson, E. D. (1971)
Comb. Theor 11:105; Santou, N. Nes, M. (1987) Mol. Biol. Evol.
4:406-425; Sneath, P. H. A. and Sokal, R. R. (1973) Numerical
Taxonomy--the Principles and Practice of Numerical Taxonomy,
Freeman Press, San Francisco, Calif.; Wilbur, W. J. and Lipman, D.
J. (1983) Proc. Nat'l Acad., Sci. USA 80:726-730.
[0760] 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. Nat'l 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.
[0761] 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.
[0762] 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.
[0763] 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.
[0764] 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.
[0765] 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. Nat'l 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.
[0766] 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.
[0767] 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).
[0768] In one preferred embodiment, the immunological fusion
partner is derived from a Mycobacterium sp., such as a
Mycobacterium tuberculosis-derived Ra12 fragment. Ra12 compositions
and methods for their use in enhancing the expression and/or
immunogenicity of heterologous polynucleotide/polypeptide sequences
is described in U.S. Patent Application 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 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.
[0769] 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.
[0770] 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.
[0771] 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.sup.+ T-cells specific for the
polypeptide.
[0772] 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.
[0773] 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.
Polynucleotide Compositions
[0774] 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.
[0775] 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.
[0776] 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.
[0777] Polynucleotides may comprise a native sequence (i.e., an
endogenous sequence that encodes a polypeptide/protein of the
invention or a portion thereof) or may comprise a sequence that
encodes a variant or derivative, preferably an immunogenic variant
or derivative, of such a sequence.
[0778] 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 NO: 1-111, 115-171, 173-175, 177, 179-305, 307-315, 326,
328, 330, 332-335, 340-375, 381, 382 and 384-476, 524, 526, 530,
531, 533, 535, 536, 552, 569-572, 587, 591, 593-606, 618-705,
709-774, 777, 789, 817, 823, 824, 878, 880-882, 894, 896, 907, 908,
916-919, 929-931, 938, 939, 942, 944, 945, 948, 967, 969-976, 991,
993-1002, 1004, 1006, 1007, 1010, 1013-1019, 1021, 1023-1027 and
1034-1036, complements of a polynucleotide sequence set forth in
any one of SEQ ID NO: 1-111, 115-171, 173-175, 177, 179-305,
307-315, 326, 328, 330, 332-335, 340-375, 381, 382 and 384-476,
524, 526, 530, 531, 533, 535, 536, 552, 569-572, 587, 591, 593-606,
618-705, 709-774, 777, 789, 817, 823, 824, 878, 880-882, 894, 896,
907, 908, 916-919, 929-931, 938, 939, 942, 944, 945, 948, 967,
969-976, 991, 993-1002, 1004, 1006, 1007, 1010, 1013-1019, 1021,
1023-1027 and 1034-1036, and degenerate variants of a
polynucleotide sequence set forth in any one of SEQ ID NO: 1-111,
115-171, 173-175, 177, 179-305, 307-315, 326, 328, 330, 332-335,
340-375, 381, 382 and 384-476, 524, 526, 530, 531, 533, 535, 536,
552, 569-572, 587, 591, 593-606, 618-705, 709-774, 777, 789, 817,
823, 824, 878, 880-882, 894, 896, 907, 908, 916-919, 929-931, 938,
939, 942, 944, 945, 948, 967, 969-976, 991, 993-1002, 1004, 1006,
1007, 1010, 1013-1019, 1021, 1023-1027 and 1034-1036. In certain
preferred embodiments, the polynucleotide sequences set forth
herein encode immunogenic polypeptides, as described above.
[0779] In other related embodiments, the present invention provides
polynucleotide variants having substantial identity to the
sequences disclosed herein in SEQ ID NO: 1-111, 115-171, 173-175,
177, 179-305, 307-315, 326, 328, 330, 332-335, 340-375, 381, 382
and 384-476, 524, 526, 530, 531, 533, 535, 536, 552, 569-572, 587,
591, 593-606, 618-705, 709-774, 777, 789, 817, 823, 824, 878,
880-882, 894, 896, 907, 908, 916-919, 929-931, 938, 939, 942, 944,
945, 948, 967, 969-976, 991, 993-1002, 1004, 1006, 1007, 1010,
1013-1019, 1021, 1023-1027 and 1034-1036 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.
[0780] 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.
[0781] In additional embodiments, the present invention provides
polynucleotide fragments comprising various lengths of contiguous
stretches of sequence identical to, or complementary to, one or
more of the sequences disclosed herein. For example,
polynucleotides are provided by this invention that comprise at
least about 10, 15, 20, 30, 40, 50, 75, 100, 150, 200, 300, 400,
500 or 1000 or more contiguous nucleotides of one or more of the
sequences disclosed herein as well as all intermediate lengths
there between. 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.
[0782] 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.times.SSC, 0.5% SDS, 1.0 mM EDTA (pH
8.0); hybridizing at 50.degree. C.-60.degree. C., 5.times.SSC,
overnight; followed by washing twice at 65.degree. C. for 20
minutes with each of 2.times., 0.5.times. and 0.2.times.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.degree. C. or 65-70.degree. C.
[0783] 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.
[0784] 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.
[0785] 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, preferably
40 to about 50, in which a sequence may be compared to a reference
sequence of the same number of contiguous positions after the two
sequences are optimally aligned.
[0786] Optimal alignment of sequences for comparison may be
conducted using the Megalign program in the Lasergene suite of
bioinformatics software (DNASTAR, Inc., Madison, Wis.), using
default parameters. This program embodies several alignment schemes
described in the following references: Dayhoff, M. O. (1978) A
model of evolutionary change in proteins--Matrices for detecting
distant relationships. In Dayhoff, M. O. (ed.) Atlas of Protein
Sequence and Structure, National Biomedical Research Foundation,
Washington D.C. Vol. 5, Suppl. 3, pp. 345-358; Hein J. (1990)
Unified Approach to Alignment and Phylogenes pp. 626-645 Methods in
Enzymology vol. 183, Academic Press, Inc., San Diego, Calif.;
Higgins, D. G. and Sharp, P. M. (1989) CABIOS 5:151-153; Myers, E.
W. and Muller W. (1988) CABIOS 4:11-17; Robinson, E. D. (1971)
Comb. Theor 11:105; Santou, N. Nes, M. (1987) Mol. Biol. Evol.
4:406-425; Sneath, P. H. A. and Sokal, R. R. (1973) Numerical
Taxonomy--the Principles and Practice of Numerical Taxonomy,
Freeman Press, San Francisco, Calif.; Wilbur, W. J. and Lipman, D.
J. (1983) Proc. Nat'l Acad., Sci. USA 80:726-730.
[0787] 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. Nat'l 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.
[0788] 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. Nat'l Acad. Sci. USA 89:10915) alignments, (B) of 50,
expectation (E) of 10, M=5, N=-4 and a comparison of both
strands.
[0789] 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.
[0790] 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).
[0791] 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.
[0792] 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.
[0793] 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.
[0794] 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.
[0795] 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.
[0796] 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.
[0797] 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.
[0798] 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.
[0799] 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 a sequence
region of at least about 15 contiguous nucleotides that has the
same sequence as, or is complementary to, a 15 nucleotide long
contiguous sequence disclosed herein will find particular utility.
Longer contiguous identical or complementary sequences, e.g., those
of about 20, 30, 40, 50, 100, 200, 500, 1000 (including all
intermediate lengths) and even up to full length sequences will
also be of use in certain embodiments.
[0800] 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.
[0801] 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.
[0802] 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.
[0803] 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.
[0804] 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.TM. 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.
[0805] 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.degree. C. to about 70.degree. 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.
[0806] 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.degree. C. to about 55.degree. 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.
[0807] 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 GABA.sub.A receptor and human EGF
(Jaskulski et al., Science. 1988 Jun. 10; 240(4858):1544-6;
Vasanthakumar and Ahmed, Cancer Commun. 1989; 11(4):225-32; Peris
et al., Brain Res Mol Brain Res. 1998 Jun. 15; 57(2):310-20; U.S.
Pat. No. 5,801,154; U.S. Pat. No. 5,789,573; U.S. Pat. No.
5,718,709 and U.S. Pat. No. 5,610,288). Antisense constructs have
also been described that inhibit and can be used to treat a variety
of abnormal cellular proliferations, e.g. cancer (U.S. Pat. No.
5,747,470; U.S. Pat. No. 5,591,317 and U.S. Pat. No.
5,783,683).
[0808] 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, T.sub.m, binding energy, and relative
stability. Antisense compositions may be selected based upon their
relative inability to form dimers, hairpins, or other secondary
structures that would reduce or prohibit specific binding to the
target mRNA in a host cell. Highly preferred target regions of the
mRNA, are those which are at or near the AUG translation initiation
codon, and those sequences which are substantially complementary to
5' regions of the mRNA. 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
Sep. 1; 25(17):3389-402).
[0809] The use of an antisense delivery method employing a short
peptide vector, termed MPG (27 residues), is also contemplated. The
MPG peptide contains a hydrophobic domain derived from the fusion
sequence of HIV gp41 and a hydrophilic domain from the nuclear
localization sequence of SV40 T-antigen (Morris et al., Nucleic
Acids Res. 1997 Jul. 15; 25(14):2730-6). It has been demonstrated
that several molecules of the MPG peptide coat the antisense
oligonucleotides and can be delivered into cultured mammalian cells
in less than 1 hour with relatively high efficiency (90%). Further,
the interaction with MPG strongly increases both the stability of
the oligonucleotide to nuclease and the ability to cross the plasma
membrane.
[0810] 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 Nat'l Acad Sci U S A. 1987 December; 84(24):8788-92; Forster
and Symons, Cell. 1987 Apr. 24; 49(2):211-20). For example, a large
number of ribozymes accelerate phosphoester transfer reactions with
a high degree of specificity, often cleaving only one of several
phosphoesters in an oligonucleotide substrate (Cech et al., Cell.
1981 December; 27(3 Pt 2):487-96; Michel and Westhof, J Mol Biol.
1990 Dec. 5; 216(3):585-610; Reinhold-Hurek and Shub, Nature. 1992
May 14; 357(6374):173-6). This specificity has been attributed to
the requirement that the substrate bind via specific base-pairing
interactions to the internal guide sequence ("IGS") of the ribozyme
prior to chemical reaction.
[0811] 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.
[0812] 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 Nat'l Acad Sci USA. 1992 Aug. 15;
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.
[0813] The enzymatic nucleic acid molecule may be formed in a
hammerhead, hairpin, a hepatitis .delta. 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. 1992 Sep. 11;
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 1989 Jun. 13; 28(12):4929-33; Hampel et al., Nucleic
Acids Res. 1990 Jan. 25; 18(2):299-304 and U.S. Pat. No. 5,631,359.
An example of the hepatitis .delta. virus motif is described by
Perrotta and Been, Biochemistry. 1992 Dec. 1; 31(47):11843-52; an
example of the RNaseP motif is described by Guerrier-Takada et al.,
Cell. 1983 December; 35(3 Pt 2):849-57; Neurospora VS RNA ribozyme
motif is described by Collins (Saville and Collins, Cell. 1990 May
18; 61(4):685-96; Saville and Collins, Proc Nat'l Acad Sci USA.
1991 Oct. 1; 88(19):8826-30; Collins and Olive, Biochemistry. 1993
Mar. 23; 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.
[0814] 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.
[0815] 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.
[0816] 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.
[0817] Another means of accumulating high concentrations of a
ribozyme(s) within cells is to incorporate the ribozyme-encoding
sequences into a DNA expression vector. Transcription of the
ribozyme sequences are driven from a promoter for eukaryotic RNA
polymerase I (pol I), RNA polymerase II (pol II), or RNA polymerase
III (pol III). Transcripts from pol II or pol III promoters will be
expressed at high levels in all cells; the levels of a given pol II
promoter in a given cell type will depend on the nature of the gene
regulatory sequences (enhancers, silencers, etc.) present nearby.
Prokaryotic RNA polymerase promoters may also be used, providing
that the prokaryotic RNA polymerase enzyme is expressed in the
appropriate cells Ribozymes expressed from such promoters have been
shown to function in mammalian cells. Such transcription units can
be incorporated into a variety of vectors for introduction into
mammalian cells, including but not restricted to, plasmid DNA
vectors, viral DNA vectors (such as adenovirus or adeno-associated
vectors), or viral RNA vectors (such as retroviral, semliki forest
virus, sindbis virus vectors).
[0818] In another embodiment of the invention, peptide nucleic
acids (PNAs) compositions are provided. PNA is a DNA mimic in which
the nucleobases are attached to a pseudopeptide backbone (Good and
Nielsen, Antisense Nucleic Acid Drug Dev. 1997 7(4) 431-37). PNA is
able to be utilized in a number methods that traditionally have
used RNA or DNA. Often PNA sequences perform better in techniques
than the corresponding RNA or DNA sequences and have utilities that
are not inherent to RNA or DNA. A review of PNA including methods
of making, characteristics of, and methods of using, is provided by
Corey (Trends Biotechnol 1997 June; 15(6):224-9). As such, in
certain embodiments, one may prepare PNA sequences that are
complementary to one or more portions of the ACE mRNA sequence, and
such PNA compositions may be used to regulate, alter, decrease, or
reduce the translation of ACE-specific mRNA, and thereby alter the
level of ACE activity in a host cell to which such PNA compositions
have been administered.
[0819] PNAs have 2-aminoethyl-glycine linkages replacing the normal
phosphodiester backbone of DNA (Nielsen et al., Science 1991 Dec.
6; 254(5037):1497-500; Hanvey et al., Science. 1992 Nov. 27;
258(5087):1481-5; Hyrup and Nielsen, Bioorg Med. Chem. 1996
January; 4(1):5-23). This chemistry has three important
consequences: firstly, in contrast to DNA or phosphorothioate
oligonucleotides, PNAs are neutral molecules; secondly, PNAs are
achiral, which avoids the need to develop a stereoselective
synthesis; and thirdly, PNA synthesis uses standard Boc or Fmoc
protocols for solid-phase peptide synthesis, although other
methods, including a modified Merrifield method, have been
used.
[0820] PNA monomers or ready-made oligomers are commercially
available from PerSeptive Biosystems (Framingham, Mass.). PNA
syntheses by either Boc or Fmoc protocols are straightforward using
manual or automated protocols (Norton et al., Bioorg Med Chem. 1995
April; 3(4):437-45). The manual protocol lends itself to the
production of chemically modified PNAs or the simultaneous
synthesis of families of closely related PNAs.
[0821] 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.
[0822] Modifications of PNAs for a given application may be
accomplished by coupling amino acids during solid-phase synthesis
or by attaching compounds that contain a carboxylic acid group to
the exposed N-terminal amine. Alternatively, PNAs can be modified
after synthesis by coupling to an introduced lysine or cysteine.
The ease with which PNAs can be modified facilitates optimization
for better solubility or for specific functional requirements. Once
synthesized, the identity of PNAs and their derivatives can be
confirmed by mass spectrometry. Several studies have made and
utilized modifications of PNAs (for example, Norton et al., Bioorg
Med Chem. 1995 April; 3(4):437-45; Petersen et al., J Pept Sci.
1995 May-June; 1(3):175-83; Orum et al., Biotechniques. 1995
September; 19(3):472-80; Footer et al., Biochemistry. 1996 Aug. 20;
35(33):10673-9; Griffith et al., Nucleic Acids Res. 1995 Aug. 11;
23(15):3003-8; Pardridge et al., Proc Nat'l Acad Sci USA. 1995 Jun.
6; 92(12):5592-6; Boffa et al., Proc Nat'l Acad Sci USA. 1995 Mar.
14; 92(6):1901-5; Gambacorti-Passerini et al., Blood. 1996 Aug. 15;
88(4):1411-7; Armitage et al., Proc Nat'l Acad Sci USA. 1997 Nov.
11; 94(23):12320-5; Seeger et al., Biotechniques. 1997 September;
23(3):512-7). U.S. Pat. No. 5,700,922 discusses PNA-DNA-PNA
chimeric molecules and their uses in diagnostics, modulating
protein in organisms, and treatment of conditions susceptible to
therapeutics.
[0823] Methods of characterizing the antisense binding properties
of PNAs are discussed in Rose (Anal Chem. 1993 Dec. 15;
65(24):3545-9) and Jensen et al. (Biochemistry. 1997 Apr. 22;
36(16):5072-7). Rose uses capillary gel electrophoresis to
determine binding of PNAs to their complementary oligonucleotide,
measuring the relative binding kinetics and stoichiometry. Similar
types of measurements were made by Jensen et al. using BIAcore.TM.
technology.
[0824] 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.
Polynucleotide Identification, Characterization and Expression
[0825] Polynucleotide compositions of the present invention may be
identified, prepared and/or manipulated using any of a variety of
well established techniques (see generally, Sambrook et al.,
Molecular Cloning: A Laboratory Manual, Cold Spring Harbor
Laboratories, Cold Spring Harbor, 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. Nat'l Acad. Sci. USA 93:10614-10619, 1996 and Heller
et al., Proc. Nat'l 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.
[0826] 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.TM.) 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.TM., 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.TM. amplification procedure may be performed in order to
quantify the amount of mRNA amplified. Polymerase chain reaction
methodologies are well known in the art.
[0827] Any of a number of other template dependent processes, many
of which are variations of the PCR.TM. 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.
[0828] 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.
[0829] For hybridization techniques, a partial sequence may be
labeled (e.g., by nick-translation or end-labeling with .sup.32P)
using well known techniques. A bacterial or bacteriophage library
is then generally screened by hybridizing filters containing
denatured bacterial colonies (or lawns containing phage plaques)
with the labeled probe (see Sambrook et al., Molecular Cloning: A
Laboratory Manual, Cold Spring Harbor Laboratories, Cold Spring
Harbor, N.Y., 1989). Hybridizing colonies or plaques are selected
and expanded, and the DNA is isolated for further analysis. cDNA
clones may be analyzed to determine the amount of additional
sequence by, for example, PCR using a primer from the partial
sequence and a primer from the vector. Restriction maps and partial
sequences may be generated to identify one or more overlapping
clones. The complete sequence may then be determined using standard
techniques, which may involve generating a series of deletion
clones. The resulting overlapping sequences can then assembled into
a single contiguous sequence. A full length cDNA molecule can be
generated by ligating suitable fragments, using well known
techniques.
[0830] 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.
[0831] 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.
[0832] 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.
[0833] 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.
[0834] 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.
[0835] 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.
[0836] 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.).
[0837] 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.
[0838] 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.
[0839] 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.
[0840] 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.
[0841] 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
BLUESCRIPT (Stratagene), in which the sequence encoding the
polypeptide of interest may be ligated into the vector in frame
with sequences for the amino-terminal Met and the subsequent 7
residues of .beta.-galactosidase so that a hybrid protein is
produced; pIN vectors (Van Heeke, G. and S. M. 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.
[0842] 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.
[0843] In cases where plant expression vectors are used, the
expression of sequences encoding polypeptides may be driven by any
of a number of promoters. For example, viral promoters such as the
35S and 19S promoters of CaMV may be used alone or in combination
with the omega leader sequence from TMV (Takamatsu, N. (1987) EMBO
J. 6:307-311. Alternatively, plant promoters such as the small
subunit of RUBISCO or heat shock promoters may be used (Coruzzi, G.
et al. (1984) EMBO J. 3:1671-1680; Broglie, R. et al. (1984)
Science 224:838-843; and Winter, J. et al. (1991) Results Probl.
Cell Differ. 17:85-105). These constructs can be introduced into
plant cells by direct DNA transformation or pathogen-mediated
transfection. Such techniques are described in a number of
generally available reviews (see, for example, Hobbs, S. or Murry,
L. E. in McGraw Hill Yearbook of Science and Technology (1992)
McGraw Hill, New York, N.Y.; pp. 191-196).
[0844] 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. Nat'l Acad. Sci.
91:3224-3227).
[0845] 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. Nat'l 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.
[0846] 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).
[0847] In addition, a host cell strain may be chosen for its
ability to modulate the expression of the inserted sequences or to
process the expressed protein in the desired fashion. Such
modifications of the polypeptide include, but are not limited to,
acetylation, carboxylation. glycosylation, phosphorylation,
lipidation, and acylation. Post-translational processing which
cleaves a "prepro" form of the protein may also be used to
facilitate correct insertion, folding and/or function. Different
host cells such as CHO, COS, HeLa, MDCK, HEK293, and W138, which
have specific cellular machinery and characteristic mechanisms for
such post-translational activities, may be chosen to ensure the
correct modification and processing of the foreign protein.
[0848] 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.
[0849] 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. Nat'l 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. Nat'l 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).
[0850] 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.
[0851] 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.
[0852] 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).
[0853] 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.
[0854] 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).
[0855] 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.
Antibody Compositions, Fragments Thereof and Other Binding
Agents
[0856] 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.
[0857] 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 (K.sub.d) of the interaction, wherein a
smaller K.sub.d represents a greater affinity. Immunological
binding properties of selected polypeptides can be quantified using
methods well known in the art. One such method entails measuring
the rates of antigen-binding site/antigen complex formation and
dissociation, wherein those rates depend on the concentrations of
the complex partners, the affinity of the interaction, and on
geometric parameters that equally influence the rate in both
directions. Thus, both the "on rate constant" (K.sub.on) and the
"off rate constant" (K.sub.off) can be determined by calculation of
the concentrations and the actual rates of association and
dissociation. The ratio of K.sub.off/K.sub.on enables cancellation
of all parameters not related to affinity, and is thus equal to the
dissociation constant K.sub.d. See, generally, Davies et al. (1990)
Annual Rev. Biochem. 59:439-473.
[0858] 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."
[0859] Binding agents may be further capable of differentiating
between patients with and without a cancer, such as prostate
cancer, using the representative assays provided herein. 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.
[0860] 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.
[0861] 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.
[0862] 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.
[0863] 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').sub.2" fragment which comprises both antigen-binding sites.
An "Fv" fragment can be produced by preferential proteolytic
cleavage of an IgM, and on rare occasions IgG or IgA immunoglobulin
molecule. Fv fragments are, however, more commonly derived using
recombinant techniques known in the art. The Fv fragment includes a
non-covalent V.sub.H::V.sub.L 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.
[0864] A single chain Fv ("sFv") polypeptide is a covalently linked
V.sub.H::V.sub.L heterodimer which is expressed from a gene fusion
including V.sub.H- and V.sub.L-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.
[0865] 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.
[0866] 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.
[0867] 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.
[0868] 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.
[0869] 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.
[0870] 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.
[0871] 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 .sup.90Y,
.sup.123I, .sup.125I, .sup.131I, .sup.186Re, .sup.188Re,
.sup.211At, and .sup.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.
[0872] 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.
[0873] Alternatively, it may be desirable to couple a therapeutic
agent and an antibody via a linker group. A linker group can
function as a spacer to distance an antibody from an agent in order
to avoid interference with binding capabilities. A linker group can
also serve to increase the chemical reactivity of a substituent on
an agent or an antibody, and thus increase the coupling efficiency.
An increase in chemical reactivity may also facilitate the use of
agents, or functional groups on agents, which otherwise would not
be possible.
[0874] It will be evident to those skilled in the art that a
variety of bifunctional or polyfunctional reagents, both homo- and
hetero-functional (such as those described in the catalog of the
Pierce Chemical Co., Rockford, Ill.), may be employed as the linker
group. Coupling may be effected, for example, through amino groups,
carboxyl groups, sulfhydryl groups or oxidized carbohydrate
residues. There are numerous references describing such
methodology, e.g., U.S. Pat. No. 4,671,958, to Rodwell et al.
[0875] 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.).
[0876] 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.
[0877] 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.
T Cell Compositions
[0878] 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.TM. 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.
[0879] 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.
[0880] 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 .mu.g/ml, preferably 200 ng/ml-25 .mu.g/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-.gamma.) 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.sup.+
and/or CD8.sup.+. 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.
[0881] For therapeutic purposes, CD4.sup.+ or CD8.sup.+ 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.
Pharmaceutical Compositions
[0882] In additional embodiments, the present invention concerns
formulation of one or more of the polynucleotide, polypeptide,
T-cell and/or antibody compositions disclosed herein in
pharmaceutically-acceptable carriers for administration to a cell
or an animal, either alone, or in combination with one or more
other modalities of therapy.
[0883] 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.
[0884] Therefore, in another aspect of the present invention,
pharmaceutical compositions are provided comprising one or more of
the polynucleotide, polypeptide, antibody, 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 therapeutic 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.
[0885] It will be apparent that any of the pharmaceutical
compositions described herein can contain pharmaceutically
acceptable salts of the polynucleotides and polypeptides of the
invention. Such salts can be prepared, for example, from
pharmaceutically acceptable non-toxic bases, including organic
bases (e.g., salts of primary, secondary and tertiary amines and
basic amino acids) and inorganic bases (e.g., sodium, potassium,
lithium, ammonium, calcium and magnesium salts).
[0886] 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.
[0887] 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. Nat'l Acad. Sci. USA 90:8033-8037; and Boris-Lawrie
and Temin (1993) Cur. Opin. Genet. Develop. 3:102-109.
[0888] 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).
[0889] 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.
[0890] 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.
[0891] 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. Nat'l
Acad. Sci. USA (1990) 87:6743-6747; Fuerst et al. Proc. Nat'l Acad.
Sci. USA (1986) 83:8122-8126.
[0892] 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.
[0893] 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.
[0894] 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. Nat'l Acad. Sci.
USA (1992) 89:6099-6103, can also be used for gene delivery under
the invention.
[0895] Additional illustrative information on these and other known
viral-based delivery systems can be found, for example, in
Fisher-Hoch et al., Proc. Nat'l 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.
Nat'l Acad. Sci. USA 91:215-219, 1994; Kass-Eisler et al., Proc.
Nat'l 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.
[0896] In certain embodiments, a polynucleotide may be integrated
into the genome of a target cell. This integration may be in a
specific location and orientation via homologous recombination
(gene replacement) or it may be integrated in a random,
non-specific location (gene augmentation). 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.
[0897] 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.
[0898] 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.
[0899] 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.
[0900] 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 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.
[0901] 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-.gamma., TNF.beta., 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.
[0902] 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.RTM. 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,
.beta.-escin, or digitonin.
[0903] 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 Carbopol.sup.R to
increase viscosity, or may be formulated in a dry powder form with
a powder excipient such as lactose.
[0904] 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.RTM.
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.RTM. adjuvant
and tocopherol in an oil-in-water emulsion is described in WO
95/17210.
[0905] 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.
[0906] 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 (Enhanzyn.RTM.; 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.
[0907] Other preferred adjuvants include adjuvant molecules of the
general formula
HO(CH.sub.2CH.sub.2O).sub.n-A-R, (I)
wherein, n is 1-50, A is a bond or --C(O)--, R is C.sub.1-50 alkyl
or Phenyl C.sub.1-50 alkyl.
[0908] 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 C.sub.1-50, preferably
C.sub.4-C.sub.20 alkyl and most preferably C.sub.1-2 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 (12.sup.th edition: entry 7717). These adjuvant molecules are
described in WO 99/52549. The polyoxyethylene ether according to
the general formula (I) above may, if desired, be combined with
another adjuvant. For example, a preferred adjuvant combination is
preferably with CpG as described in the pending UK patent
application GB 9820956.2.
[0909] 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.
[0910] 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).
[0911] 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
TNF.beta. 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, TNF.alpha., CD40 ligand, LPS, flt3 ligand and/or
other compound(s) that induce differentiation, maturation and
proliferation of dendritic cells.
[0912] Dendritic cells are conveniently categorized as "immature"
and "mature" cells, which allows a simple way to discriminate
between two well characterized phenotypes. However, this
nomenclature should not be construed to exclude all possible
intermediate stages of differentiation. Immature dendritic cells
are characterized as APC with a high capacity for antigen uptake
and processing, which correlates with the high expression of
Fc.gamma. 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 4-1 BB).
[0913] 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.
[0914] 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.
[0915] 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.
[0916] 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.
[0917] 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.
[0918] 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.
[0919] 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.
[0920] 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.
[0921] The active compounds may even be incorporated with
excipients and used in the form of ingestible tablets, buccal
tables, troches, capsules, elixirs, suspensions, syrups, wafers,
and the like (see, for example, Mathiowitz et al., Nature 1997 Mar.
27; 386(6623):410-4; Hwang et al., Crit Rev Ther Drug Carrier Syst
1998; 15(3):243-84; U.S. 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.
[0922] 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.
[0923] 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.
[0924] 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.
[0925] 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.
[0926] 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.
[0927] 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.
[0928] 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.
[0929] 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 1998
Mar. 2; 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.
[0930] 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.
[0931] The formation and use of liposome and liposome-like
preparations as potential drug carriers is generally known to those
of skill in the art (see for example, Lasic, Trends Biotechnol 1998
July; 16(7):307-21; Takakura, Nippon Rinsho 1998 March;
56(3):691-5; Chandran et al., Indian J Exp Biol. 1997 August;
35(8):801-9; Margalit, Crit Rev Ther Drug Carrier Syst. 1995;
12(2-3):233-61; U.S. Pat. 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).
[0932] Liposomes have been used successfully with a number of cell
types that are normally difficult to transfect by other procedures,
including T cell suspensions, primary hepatocyte cultures and PC 12
cells (Renneisen et al., J Biol Chem. 1990 Sep. 25;
265(27):16337-42; Muller et al., DNA Cell Biol. 1990 April;
9(3):221-9). In addition, liposomes are free of the DNA length
constraints that are typical of viral-based delivery systems.
Liposomes have been used effectively to introduce genes, various
drugs, radiotherapeutic agents, enzymes, viruses, transcription
factors, allosteric effectors and the like, into a variety of
cultured cell lines and animals. Furthermore, the use of liposomes
does not appear to be associated with autoimmune responses or
unacceptable toxicity after systemic delivery.
[0933] 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).
[0934] Alternatively, in other embodiments, the invention provides
for pharmaceutically-acceptable nanocapsule formulations of the
compositions of the present invention. Nanocapsules can generally
entrap compounds in a stable and reproducible way (see, for
example, Quintanar-Guerrero et al., Drug Dev Ind Pharm. 1998
December; 24(12):1113-28). To avoid side effects due to
intracellular polymeric overloading, such ultrafine particles
(sized around 0.1 .mu.m) may be designed using polymers able to be
degraded in vivo. Such particles can be made as described, for
example, by Couvreur et al., Crit Rev Ther Drug Carrier Syst. 1988;
5(1):1-20; zur Muhlen et al., Eur J Pharm Biopharm. 1998 March;
45(2):149-55; Zambaux et al. J Controlled Release. 1998 Jan. 2;
50(1-3):31-40; and U.S. Pat. No. 5,145,684.
Cancer Therapeutic Methods
[0935] In further aspects of the present invention, the
pharmaceutical compositions described herein may be used for the
treatment of cancer, particularly for the immunotherapy of prostate
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. Accordingly, the above pharmaceutical
compositions may be used to prevent the development of a cancer or
to treat a patient afflicted with a cancer. Pharmaceutical
compositions and vaccines may be administered either prior to or
following surgical removal of primary tumors and/or treatment such
as administration of radiotherapy or conventional chemotherapeutic
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.
[0936] 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).
[0937] 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.sup.+ cytotoxic T lymphocytes and
CD4.sup.+ 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.
[0938] 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).
[0939] 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.
[0940] 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
.mu.g to 5 mg per kg of host. Suitable dose sizes will vary with
the size of the patient, but will typically range from about 0.1 mL
to about 5 mL.
[0941] 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.
Cancer Detection and Diagnostic Compositions, Methods and Kits
[0942] In general, a cancer may be detected in a patient based on
the presence of one or more prostate tumor proteins and/or
polynucleotides encoding such proteins in a biological sample (for
example, blood, sera, sputum urine and/or tumor biopsies) obtained
from the patient. In other words, such proteins may be used as
markers to indicate the presence or absence of a cancer such as
prostate cancer. In addition, such proteins may be useful for the
detection of other cancers. The binding agents provided herein
generally permit detection of the level of antigen that binds to
the agent in the biological sample. Polynucleotide primers and
probes may be used to detect the level of mRNA encoding a tumor
protein, which is also indicative of the presence or absence of a
cancer. In general, a prostate tumor sequence should be present at
a level that is at least three fold higher in tumor tissue than in
normal tissue
[0943] 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.
[0944] 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
prostate tumor proteins and polypeptide portions thereof to which
the binding agent binds, as described above.
[0945] 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 .mu.g, and preferably
about 100 ng to about 1 .mu.g, is sufficient to immobilize an
adequate amount of binding agent.
[0946] 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).
[0947] 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.
[0948] 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.TM. (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 prostate cancer. Preferably, the contact time is
sufficient to achieve a level of binding that is at least about 95%
of that achieved at equilibrium between bound and unbound
polypeptide. Those of ordinary skill in the art will recognize that
the time necessary to achieve equilibrium may be readily determined
by assaying the level of binding that occurs over a period of time.
At room temperature, an incubation time of about 30 minutes is
generally sufficient.
[0949] Unbound sample may then be removed by washing the solid
support with an appropriate buffer, such as PBS containing 0.1%
Tween 20.TM.. The second antibody, which contains a reporter group,
may then be added to the solid support. Preferred reporter groups
include those groups recited above.
[0950] 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.
[0951] To determine the presence or absence of a cancer, such as
prostate 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.
[0952] 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 .mu.g, and more preferably from
about 50 ng to about 500 ng. Such tests can typically be performed
with a very small amount of biological sample.
[0953] 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.
[0954] 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.sup.+ and/or CD8.sup.+ 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.degree. C. with polypeptide (e.g., 5-25 .mu.g/ml). It may be
desirable to incubate another aliquot of a T cell sample in the
absence of tumor polypeptide to serve as a control. For CD4.sup.+ T
cells, activation is preferably detected by evaluating
proliferation of the T cells. For CD8.sup.+ 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.
[0955] 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. 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.
[0956] 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).
[0957] 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.
[0958] 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.
[0959] 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.
[0960] 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.
[0961] In other aspects of the present invention, cell capture
technologies may be used prior to detection to improve the
sensitivity of the various detection methodologies disclosed
herein.
[0962] Exemplary cell enrichment methodologies employ
immunomagnetic beads that are 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.RTM. Epithelial Enrich (Dynal Biotech, Oslo,
Norway), StemSep.TM. (StemCell Technologies, Inc., Vancouver, BC),
and RosetteSep (StemCell Technologies). The skilled artisan will
recognize that other readily available methodologies and kits may
also be suitably employed to enrich or positively select desired
cell populations.
[0963] Dynabeads.RTM. 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.
[0964] RosetteSep can be used to enrich cells directly from a blood
sample and consists of a cocktail of tetrameric antibodies that
target 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.
[0965] 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
TCR.alpha..beta.. Additionally, it is contemplated in the present
invention that mAbs specific for prostate tumor antigens, can be
developed 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 prostate tumor cells
from a sample.
[0966] Once a sample is enriched or positively selected, cells may
be further analyzed. For example, the cells may be lysed and RNA
isolated. RNA may then be subjected to RT-PCR analysis using
prostate tumor-specific primers in a Real-time PCR assay as
described herein.
[0967] In another aspect of the present invention, cell capture
technologies may be used in conjunction with real-time PCR to
provide a more sensitive tool for detection of metastatic cells
expressing prostate tumor antigens. Detection of prostate cancer
cells in bone marrow samples, peripheral blood, biopsies, and other
samples is desirable for diagnosis and prognosis in prostate cancer
patients.
[0968] 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.
[0969] 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.
[0970] The following Examples are offered by way of illustration
and not by way of limitation.
EXAMPLES
Example 1
Isolation and Characterization of Prostate-Specific
Polypeptides
[0971] This Example describes the isolation of certain
prostate-specific polypeptides from a prostate tumor cDNA
library.
[0972] A human prostate tumor cDNA expression library was
constructed from prostate tumor poly A.sup.+ RNA using a
Superscript Plasmid System for cDNA Synthesis and Plasmid Cloning
kit (BRL Life Technologies, Gaithersburg, Md. 20897) following the
manufacturer's protocol. Specifically, prostate tumor tissues were
homogenized with polytron (Kinematica, Switzerland) and total RNA
was extracted using Trizol reagent (BRL Life Technologies) as
directed by the manufacturer. The poly A.sup.+ RNA was then
purified using a Qiagen oligotex spin column mRNA purification kit
(Qiagen, Santa Clarita, Calif. 91355) according to the
manufacturer's protocol. First-strand cDNA was synthesized using
the NotI/Oligo-dT18 primer. Double-stranded cDNA was synthesized,
ligated with EcoRI/BAXI adaptors (Invitrogen, San Diego, Calif.)
and digested with NotI. Following size fractionation with Chroma
Spin-1000 columns (Clontech, Palo Alto, Calif.), the cDNA was
ligated into the EcoRI/NotI site of pcDNA3.1 (Invitrogen) and
transformed into ElectroMax E. coli DH10B cells (BRL Life
Technologies) by electroporation.
[0973] Using the same procedure, a normal human pancreas cDNA
expression library was prepared from a pool of six tissue specimens
(Clontech). The cDNA libraries were characterized by determining
the number of independent colonies, the percentage of clones that
carried insert, the average insert size and by sequence analysis.
The prostate tumor library contained 1.64.times.10.sup.7
independent colonies, with 70% of clones having an insert and the
average insert size being 1745 base pairs. The normal pancreas cDNA
library contained 3.3.times.10.sup.6 independent colonies, with 69%
of clones having inserts and the average insert size being 1120
base pairs. For both libraries, sequence analysis showed that the
majority of clones had a full length cDNA sequence and were
synthesized from mRNA, with minimal rRNA and mitochondrial DNA
contamination.
[0974] cDNA library subtraction was performed using the above
prostate tumor and normal pancreas cDNA libraries, as described by
Hara et al. (Blood, 84:189-199, 1994) with some modifications.
Specifically, a prostate tumor-specific subtracted cDNA library was
generated as follows. Normal pancreas cDNA library (70 .mu.g) was
digested with EcoRI, NotI, and SfuI, followed by a filling-in
reaction with DNA polymerase Klenow fragment. After
phenol-chloroform extraction and ethanol precipitation, the DNA was
dissolved in 100 .mu.l of H.sub.2O, heat-denatured and mixed with
100 .mu.l (100 .mu.g) of Photoprobe biotin (Vector Laboratories,
Burlingame, Calif.). As recommended by the manufacturer, the
resulting mixture was irradiated with a 270 W sunlamp on ice for 20
minutes. Additional Photoprobe biotin (50 .mu.l) was added and the
biotinylation reaction was repeated. After extraction with butanol
five times, the DNA was ethanol-precipitated and dissolved in 23
.mu.l H.sub.2O to form the driver DNA.
[0975] To form the tracer DNA, 10 .mu.g prostate tumor cDNA library
was digested with BamHI and XhoI, phenol chloroform extracted and
passed through Chroma spin-400 columns (Clontech). Following
ethanol precipitation, the tracer DNA was dissolved in 5 .mu.l
H.sub.2O. Tracer DNA was mixed with 15 .mu.l driver DNA and 20
.mu.l of 2.times. hybridization buffer (1.5 M NaCl/10 mM EDTA/50 mM
HEPES pH 7.5/0.2% sodium dodecyl sulfate), overlaid with mineral
oil, and heat-denatured completely. The sample was immediately
transferred into a 68.degree. C. water bath and incubated for 20
hours (long hybridization [LH]). The reaction mixture was then
subjected to a streptavidin treatment followed by phenol/chloroform
extraction. This process was repeated three more times. Subtracted
DNA was precipitated, dissolved in 12 .mu.l H.sub.2O, mixed with 8
.mu.l driver DNA and 20 .mu.l of 2.times. hybridization buffer, and
subjected to a hybridization at 68.degree. C. for 2 hours (short
hybridization [SH]). After removal of biotinylated double-stranded
DNA, subtracted cDNA was ligated into BamHI/XhoI site of
chloramphenicol resistant pBCSK.sup.+ (Stratagene, La Jolla, Calif.
92037) and transformed into ElectroMax E. coli DH10B cells by
electroporation to generate a prostate tumor specific subtracted
cDNA library (referred to as "prostate subtraction 1").
[0976] To analyze the subtracted cDNA library, plasmid DNA was
prepared from 100 independent clones, randomly picked from the
subtracted prostate tumor specific library and grouped based on
insert size. Representative cDNA clones were further characterized
by DNA sequencing with a Perkin Elmer/Applied Biosystems Division
Automated Sequencer Model 373A (Foster City, Calif.). Six cDNA
clones, hereinafter referred to as F1-13, F1-12, F1-16, H1-1, H1-9
and H1-4, were shown to be abundant in the subtracted
prostate-specific cDNA library. The determined 3' and 5' cDNA
sequences for F1-12 are provided in SEQ ID NO: 2 and 3,
respectively, with determined 3' cDNA sequences for F1-13, F1-16,
H1-1, H1-9 and H1-4 being provided in SEQ ID NO: 1 and 4-7,
respectively.
[0977] The cDNA sequences for the isolated clones were compared to
known sequences in the gene bank using the EMBL and GenBank
databases (release 96). Four of the prostate tumor cDNA clones,
F1-13, F1-16, H1-1, and H1-4, were determined to encode the
following previously identified proteins: prostate specific antigen
(PSA), human glandular kallikrein, human tumor expression enhanced
gene, and mitochondria cytochrome C oxidase subunit II. H1-9 was
found to be identical to a previously identified human autonomously
replicating sequence. No significant homologies to the cDNA
sequence for F1-12 were found.
[0978] Subsequent studies led to the isolation of a full-length
cDNA sequence for F1-12 (also referred to as P504S). This sequence
is provided in SEQ ID NO: 107, with the corresponding amino acid
sequence being provided in SEQ ID NO: 108. cDNA splice variants of
P504S are provided in SEQ ID NO: 600-605.
[0979] To clone less abundant prostate tumor specific genes, cDNA
library subtraction was performed by subtracting the prostate tumor
cDNA library described above with the normal pancreas cDNA library
and with the three most abundant genes in the previously subtracted
prostate tumor specific cDNA library: human glandular kallikrein,
prostate specific antigen (PSA), and mitochondria cytochrome C
oxidase subunit II. Specifically, 1 .mu.g each of human glandular
kallikrein, PSA and mitochondria cytochrome C oxidase subunit II
cDNAs in pCDNA3.1 were added to the driver DNA and subtraction was
performed as described above to provide a second subtracted cDNA
library hereinafter referred to as the "subtracted prostate tumor
specific cDNA library with spike".
[0980] Twenty-two cDNA clones were isolated from the subtracted
prostate tumor specific cDNA library with spike. The determined 3'
and 5' cDNA sequences for the clones referred to as J1-17, L1-12,
N1-1862, J1-13, J1-19, J1-25, J1-24, K1-58, K1-63, L1-4 and L1-14
are provided in SEQ ID NO: 8-9, 10-11, 12-13, 14-15, 16-17, 18-19,
20-21, 22-23, 24-25, 26-27 and 28-29, respectively. The determined
3' cDNA sequences for the clones referred to as J1-12, J1-16,
J1-21, K1-48, K1-55, L1-2, L1-6, N1-1858, N1-1860, N1-1861, N1-1864
are provided in SEQ ID NO: 30-40, respectively. Comparison of these
sequences with those in the gene bank as described above, revealed
no significant homologies to three of the five most abundant DNA
species, (J1-17, L1-12 and N1-1862; SEQ ID NO: 8-9, 10-11 and
12-13, respectively). Of the remaining two most abundant species,
one (J1-12; SEQ ID NO:30) was found to be identical to the
previously identified human pulmonary surfactant-associated
protein, and the other (K1-48; SEQ ID NO:33) was determined to have
some homology to R. norvegicus mRNA for 2-arylpropionyl-CoA
epimerase. Of the 17 less abundant cDNA clones isolated from the
subtracted prostate tumor specific cDNA library with spike, four
(J1-16, K1-55, L1-6 and N1-1864; SEQ ID NO:31, 34, 36 and 40,
respectively) were found to be identical to previously identified
sequences, two (J1-21 and N1-1860; SEQ ID NO: 32 and 38,
respectively) were found to show some homology to non-human
sequences, and two (L1-2 and N1-1861; SEQ ID NO: 35 and 39,
respectively) were found to show some homology to known human
sequences. No significant homologies were found to the polypeptides
J1-13, J1-19, J1-24, J1-25, K1-58, K1-63, L1-4, L1-14 (SEQ ID NO:
14-15, 16-17, 20-21, 18-19, 22-23, 24-25, 26-27, 28-29,
respectively).
[0981] Subsequent studies led to the isolation of full length cDNA
sequences for J1-17, L1-12 and N1-1862 (SEQ ID NO: 109-111,
respectively). The corresponding amino acid sequences are provided
in SEQ ID NO: 112-114. L1-12 is also referred to as P501S. A cDNA
splice variant of P501S is provided in SEQ ID NO: 606.
[0982] As described below, N1-1862 (also referred to as P503S; SEQ
ID NO: 111) was found to show prostate-specific expression.
Immunohistochemistry and flow cytometry analysis indicated that
P503S is a plasma membrane-associated molecule. P503S contains four
transmembrane domains predicted to be encoded by amino acids 59-75,
90-106, 107-123 and 218-234. P503S contains a cleavable N-terminal
signal sequence at amino acids 1-29. The N-terminus of P503S
encoding amino acids 1-58 is internal, amino acids 76-89 are
extracellular, amino acids 124-217 are extracellular and amino
acids 235-241 are intracellular. Potential N-linked glycosylation
sites are at amino acids N-141, N154, N-178 and N-184.
Glycosylation of P503S has been confirmed experimentally using
enzymes that selectively strip sugar residues from protein and
Western blot analysis. P503S is a member of a family of molecules
collectively known as the tetraspanin family or TM4SF
(transmembrane 4 superfamily). This family of proteins has been
shown to interact, and homo and heterodimerize with, other family
members. Furthermore, the TM4SF family members associate with a
family of adhesion molecules known as integrins. TM4SF family
members have been shown to regulate cell adhesion as well as cell
proliferation by controlling signal transduction pathways
associated with these physiological responses.
[0983] In a further experiment, four additional clones were
identified by subtracting a prostate tumor cDNA library with normal
prostate cDNA prepared from a pool of three normal prostate poly A+
RNA (referred to as "prostate subtraction 2"). The determined cDNA
sequences for these clones, hereinafter referred to as U1-3064,
U1-3065, V1-3692 and 1A-3905, are provided in SEQ ID NO: 69-72,
respectively. Comparison of the determined sequences with those in
the gene bank revealed no significant homologies to U1-3065.
[0984] A second subtraction with spike (referred to as "prostate
subtraction spike 2") was performed by subtracting a prostate tumor
specific cDNA library with spike with normal pancreas cDNA library
and further spiked with PSA, J1-17, pulmonary surfactant-associated
protein, mitochondrial DNA, cytochrome c oxidase subunit II,
N1-1862, autonomously replicating sequence, L1-12 and tumor
expression enhanced gene. Four additional clones, hereinafter
referred to as V1-3686, R1-2330, 1B-3976 and V1-3679, were
isolated. The determined cDNA sequences for these clones are
provided in SEQ ID NO:73-76, respectively. Comparison of these
sequences with those in the gene bank revealed no significant
homologies to V1-3686 and R1-2330.
[0985] Further analysis of the three prostate subtractions
described above (prostate subtraction 2, subtracted prostate tumor
specific cDNA library with spike, and prostate subtraction spike 2)
resulted in the identification of sixteen additional clones,
referred to as 1G-4736, 1G-4738, 1G-4741, 1G-4744, 1G-4734,
1H-4774, 1H-4781, 1H-4785, 1H-4787, 1H-4796, 1I-4810, 1I-4811,
1I-4876, 1K-4884 and 1K-4896. The determined cDNA sequences for
these clones are provided in SEQ ID NO: 77-92, respectively.
Comparison of these sequences with those in the gene bank as
described above, revealed no significant homologies to 1G-4741,
1G-4734, 1I-4807, 1I-4876 and 1K-4896 (SEQ ID NO: 79, 81, 87, 90
and 92, respectively). Further analysis of the isolated clones led
to the determination of extended cDNA sequences for 1G-4736,
1G-4738, 1G-4741, 1G-4744, 1H-4774, 1H-4781, 1H-4785, 1H-4787,
1H-4796, 1I-4807, 1I-4876, 1K-4884 and 1K-4896, provided in SEQ ID
NO: 179-188 and 191-193, respectively, and to the determination of
additional partial cDNA sequences for 1I-4810 and 1I-4811, provided
in SEQ ID NO: 189 and 190, respectively.
[0986] Additional studies with prostate subtraction spike 2
resulted in the isolation of three more clones. Their sequences
were determined as described above and compared to the most recent
GenBank. All three clones were found to have homology to known
genes, which are Cysteine-rich protein, KIAA0242, and KIAA0280 (SEQ
ID NO: 317, 319, and 320, respectively). Further analysis of these
clones by Synteni microarray (Synteni, Palo Alto, Calif.)
demonstrated that all three clones were over-expressed in most
prostate tumors and prostate BPH, as well as in the majority of
normal prostate tissues tested, but low expression in all other
normal tissues.
[0987] An additional subtraction was performed by subtracting a
normal prostate cDNA library with normal pancreas cDNA (referred to
as "prostate subtraction 3"). This led to the identification of six
additional clones referred to as 1G-4761, 1G-4762, 1H-4766,
1H-4770, 1H-4771 and 1H-4772 (SEQ ID NO: 93-98). Comparison of
these sequences with those in the gene bank revealed no significant
homologies to 1G-4761 and 1H-4771 (SEQ ID NO: 93 and 97,
respectively). Further analysis of the isolated clones led to the
determination of extended cDNA sequences for 1G-4761, 1G-4762,
1H-4766 and 1H-4772 provided in SEQ ID NO: 194-196 and 199,
respectively, and to the determination of additional partial cDNA
sequences for 1H-4770 and 1H-4771, provided in SEQ ID NO: 197 and
198, respectively.
[0988] Subtraction of a prostate tumor cDNA library, prepared from
a pool of polyA+ RNA from three prostate cancer patients, with a
normal pancreas cDNA library (prostate subtraction 4) led to the
identification of eight clones, referred to as 1D-4297, 1D-4309,
1D.1-4278, 1D-4288, 1D-4283, 1D-4304, 1D-4296 and 1D-4280 (SEQ ID
NO: 99-107). These sequences were compared to those in the gene
bank as described above. No significant homologies were found to
1D-4283 and 1D-4304 (SEQ ID NO: 103 and 104, respectively). Further
analysis of the isolated clones led to the determination of
extended cDNA sequences for 1D-4309, 1D.1-4278, 1D-4288, 1D-4283,
1D-4304, 1D-4296 and 1D-4280, provided in SEQ ID NO: 200-206,
respectively.
[0989] cDNA clones isolated in prostate subtraction 1 and prostate
subtraction 2, described above, were colony PCR amplified and their
mRNA expression levels in prostate tumor, normal prostate and in
various other normal tissues were determined using microarray
technology (Synteni, Palo Alto, Calif.). Briefly, the PCR
amplification products were dotted onto slides in an array format,
with each product occupying a unique location in the array. mRNA
was extracted from the tissue sample to be tested, reverse
transcribed, and fluorescent-labeled cDNA probes were generated.
The microarrays were probed with the labeled cDNA probes, the
slides scanned and fluorescence intensity was measured. This
intensity correlates with the hybridization intensity. Two clones
(referred to as P509S and P510S) were found to be over-expressed in
prostate tumor and normal prostate and expressed at low levels in
all other normal tissues tested (liver, pancreas, skin, bone
marrow, brain, breast, adrenal gland, bladder, testes, salivary
gland, large intestine, kidney, ovary, lung, spinal cord, skeletal
muscle and colon). The determined cDNA sequences for P509S and
P510S are provided in SEQ ID NO: 223 and 224, respectively.
Comparison of these sequences with those in the gene bank as
described above, revealed some homology to previously identified
ESTs.
[0990] Additional, studies led to the isolation of the full-length
cDNA sequence for P509S. This sequence is provided in SEQ ID NO:
332, with the corresponding amino acid sequence being provided in
SEQ ID NO: 339. Two variant full-length cDNA sequences for P510S
are provided in SEQ ID NO: 535 and 536, with the corresponding
amino acid sequences being provided in SEQ ID NO: 537 and 538,
respectively. Additional splice variants of P510S are provided in
SEQ ID NO: 598 and 599.
[0991] P510S was found to be expressed in a prostate-specific
manner. Immunohistochemistry and flow cytometry analysis indicated
that P510S is a plasma membrane-associated molecule. Based on
sequence similarity to other multidrug resistance-associated
transporter proteins, P510S is predicted to be a cell surface
expressed drug transport protein that contains an ATP binding
cassette. P510S contains nine transmembrane domains predicted to be
encoded by amino acids 135-151, 233-249, 330-346, 351-367, 711-727,
775-791, 850-866, 867-883 and 954-970. The C-terminus of P510S is
predicted to be intracellular. Potential N-linked glycosylation
sites are at amino acids N-651, N-690, N-746 and N754, N792, N-1176
and N-1312.
[0992] The determined cDNA sequences for additional
prostate-specific clones isolated during characterization of
prostate specific cDNA libraries are provided in SEQ ID NO:
618-689, 691-697 and 709-772. Comparison of these sequences with
those in the public databases revealed no significant homologies to
any of these sequences.
Example 2
Determination of Tissue Specificity of Prostate-Specific
Polypeptides
[0993] Using gene specific primers, mRNA expression levels for the
representative prostate-specific polypeptides F1-16, H1-1, J1-17
(also referred to as P502S), L1-12 (also referred to as P501S),
F1-12 (also referred to as P504S) and N1-1862 (also referred to as
P503S) were examined in a variety of normal and tumor tissues using
RT-PCR.
[0994] Briefly, total RNA was extracted from a variety of normal
and tumor tissues using Trizol reagent as described above. First
strand synthesis was carried out using 1-2 .mu.g of total RNA with
SuperScript II reverse transcriptase (BRL Life Technologies) at
42.degree. C. for one hour. The cDNA was then amplified by PCR with
gene-specific primers. To ensure the semi-quantitative nature of
the RT-PCR, .beta.-actin was used as an internal control for each
of the tissues examined. First, serial dilutions of the first
strand cDNAs were prepared and RT-PCR assays were performed using
.beta.-actin specific primers. A dilution was then chosen that
enabled the linear range amplification of the .beta.-actin template
and which was sensitive enough to reflect the differences in the
initial copy numbers. Using these conditions, the .beta.-actin
levels were determined for each reverse transcription reaction from
each tissue. DNA contamination was minimized by DNase treatment and
by assuring a negative PCR result when using first strand cDNA that
was prepared without adding reverse transcriptase.
[0995] mRNA Expression levels were examined in four different types
of tumor tissue (prostate tumor from 2 patients, breast tumor from
3 patients, colon tumor, lung tumor), and sixteen different normal
tissues, including prostate, colon, kidney, liver, lung, ovary,
pancreas, skeletal muscle, skin, stomach, testes, bone marrow and
brain. F1-16 was found to be expressed at high levels in prostate
tumor tissue, colon tumor and normal prostate, and at lower levels
in normal liver, skin and testes, with expression being
undetectable in the other tissues examined. H1-1 was found to be
expressed at high levels in prostate tumor, lung tumor, breast
tumor, normal prostate, normal colon and normal brain, at much
lower levels in normal lung, pancreas, skeletal muscle, skin, small
intestine, bone marrow, and was not detected in the other tissues
tested. J1-17 (P502S) and L1-12 (P501S) appear to be specifically
over-expressed in prostate, with both genes being expressed at high
levels in prostate tumor and normal prostate but at low to
undetectable levels in all the other tissues examined. N1-1862
(P503S) was found to be over-expressed in 60% of prostate tumors
and detectable in normal colon and kidney. The RT-PCR results thus
indicate that F1-16, H1-1, J1-17 (P502S), N1-1862 (P503S) and L1-12
(P501S) are either prostate specific or are expressed at
significantly elevated levels in prostate.
[0996] Further RT-PCR studies showed that F1-12 (P504S) is
over-expressed in 60% of prostate tumors, detectable in normal
kidney but not detectable in all other tissues tested. Similarly,
R1-2330 was shown to be over-expressed in 40% of prostate tumors,
detectable in normal kidney and liver, but not detectable in all
other tissues tested. U1-3064 was found to be over-expressed in 60%
of prostate tumors, and also expressed in breast and colon tumors,
but was not detectable in normal tissues.
[0997] RT-PCR characterization of R1-2330, U1-3064 and 1D-4279
showed that these three antigens are over-expressed in prostate
and/or prostate tumors.
[0998] Northern analysis with four prostate tumors, two normal
prostate samples, two BPH prostates, and normal colon, kidney,
liver, lung, pancrease, skeletal muscle, brain, stomach, testes,
small intestine and bone marrow, showed that L1-12 (P501S) is
over-expressed in prostate tumors and normal prostate, while being
undetectable in other normal tissues tested. J1-17 (P502S) was
detected in two prostate tumors and not in the other tissues
tested. N1-1862 (P503S) was found to be over-expressed in three
prostate tumors and to be expressed in normal prostate, colon and
kidney, but not in other tissues tested. F1-12 (P504S) was found to
be highly expressed in two prostate tumors and to be undetectable
in all other tissues tested.
[0999] The microarray technology described above was used to
determine the expression levels of representative antigens
described herein in prostate tumor, breast tumor and the following
normal tissues: prostate, liver, pancreas, skin, bone marrow,
brain, breast, adrenal gland, bladder, testes, salivary gland,
large intestine, kidney, ovary, lung, spinal cord, skeletal muscle
and colon. L-1-2 (P501S) was found to be over-expressed in normal
prostate and prostate tumor, with some expression being detected in
normal skeletal muscle. Both J1-12 and F1-12 (P504S) were found to
be over-expressed in prostate tumor, with expression being lower or
undetectable in all other tissues tested. N1-1862 (P503S) was found
to be expressed at high levels in prostate tumor and normal
prostate, and at low levels in normal large intestine and normal
colon, with expression being undetectable in all other tissues
tested. R1-2330 was found to be over-expressed in prostate tumor
and normal prostate, and to be expressed at lower levels in all
other tissues tested. 1D-4279 was found to be over-expressed in
prostate tumor and normal prostate, expressed at lower levels in
normal spinal cord, and to be undetectable in all other tissues
tested.
[1000] Further microarray analysis to specifically address the
extent to which P501S (SEQ ID NO: 110) was expressed in breast
tumor revealed moderate over-expression not only in breast tumor,
but also in metastatic breast tumor (2/31), with negligible to low
expression in normal tissues. This data suggests that P501S may be
over-expressed in various breast tumors as well as in prostate
tumors.
[1001] The expression levels of 32 ESTs (expressed sequence tags)
described by Vasmatzis et al. (Proc. Nat'l Acad. Sci. USA
95:300-304, 1998) in a variety of tumor and normal tissues were
examined by microarray technology as described above. Two of these
clones (referred to as P1000C and P1001C) were found to be
over-expressed in prostate tumor and normal prostate, and expressed
at low to undetectable levels in all other tissues tested (normal
aorta, thymus, resting and activated PBMC, epithelial cells, spinal
cord, adrenal gland, fetal tissues, skin, salivary gland, large
intestine, bone marrow, liver, lung, dendritic cells, stomach,
lymph nodes, brain, heart, small intestine, skeletal muscle, colon
and kidney. The determined cDNA sequences for P1000C and P1001C are
provided in SEQ ID NO: 384 and 472, respectively. The sequence of
P1001C was found to show some homology to the previously isolated
Human mRNA for JM27 protein. Subsequent comparison of the sequence
of SEQ ID NO: 384 with sequences in the public databases, led to
the identification of a full-length cDNA sequence of P1000C (SEQ ID
NO: 929), which encodes a 492 amino acid sequence. Analysis of the
amino acid sequence using the PSORT II program led to the
identification of a putative transmembrane domain from amino acids
84-100. The cDNA sequence of the open reading frame of P1000C,
including the stop codon, is provided in SEQ ID NO: 930, with the
open reading frame without the stop codon being provided in SEQ ID
NO: 931. The full-length amino acid sequence of P1000C is provided
in SEQ ID NO: 932. SEQ ID NO: 933 and 934 represent amino acids
1-100 and 100-492 of P1000C, respectively.
[1002] The expression of the polypeptide encoded by the full length
cDNA sequence for F1-12 (also referred to as P504S; SEQ ID NO: 108)
was investigated by immunohistochemical analysis. Rabbit-anti-P504S
polyclonal antibodies were generated against the full length P504S
protein by standard techniques. Subsequent isolation and
characterization of the polyclonal antibodies were also performed
by techniques well known in the art. Immunohistochemical analysis
showed that the P504S polypeptide was expressed in 100% of prostate
carcinoma samples tested (n=5).
[1003] The rabbit-anti-P504S polyclonal antibody did not appear to
label benign prostate cells with the same cytoplasmic granular
staining, but rather with light nuclear staining. Analysis of
normal tissues revealed that the encoded polypeptide was found to
be expressed in some, but not all normal human tissues. Positive
cytoplasmic staining with rabbit-anti-P504S polyclonal antibody was
found in normal human kidney, liver, brain, colon and
lung-associated macrophages, whereas heart and bone marrow were
negative.
[1004] This data indicates that the P504S polypeptide is present in
prostate cancer tissues, and that there are qualitative and
quantitative differences in the staining between benign prostatic
hyperplasia tissues and prostate cancer tissues, suggesting that
this polypeptide may be detected selectively in prostate tumors and
therefore be useful in the diagnosis of prostate cancer.
Example 3
Isolation and Characterization of Prostate-Specific Polypeptides by
PCR-Based Subtraction
[1005] A cDNA subtraction library, containing cDNA from normal
prostate subtracted with ten other normal tissue cDNAs (brain,
heart, kidney, liver, lung, ovary, placenta, skeletal muscle,
spleen and thymus) and then submitted to a first round of PCR
amplification, was purchased from Clontech. This library was
subjected to a second round of PCR amplification, following the
manufacturer's protocol. The resulting cDNA fragments were
subcloned into the vector pT7 Blue T-vector (Novagen, Madison,
Wis.) and transformed into XL-1 Blue MRF' E. coli (Stratagene). DNA
was isolated from independent clones and sequenced using a Perkin
Elmer/Applied Biosystems Division Automated Sequencer Model
373A.
[1006] Fifty-nine positive clones were sequenced. Comparison of the
DNA sequences of these clones with those in the gene bank, as
described above, revealed no significant homologies to 25 of these
clones, hereinafter referred to as P5, P8, P9, P18, P20, P30, P34,
P36, P38, P39, P42, P49, P50, P53, P55, P60, P64, P65, P73, P75,
P76, P79 and P84. The determined cDNA sequences for these clones
are provided in SEQ ID NO: 41-45, 47-52 and 54-65, respectively.
P29, P47, P68, P80 and P82 (SEQ ID NO: 46, 53 and 66-68,
respectively) were found to show some degree of homology to
previously identified DNA sequences. To the best of the inventors'
knowledge, none of these sequences have been previously shown to be
present in prostate.
[1007] Further studies employing the sequence of SEQ ID NO: 67 as a
probe in standard full-length cloning methods, resulted in the
isolation of three cDNA sequences which appear to be splice
variants of P80 (also known as P704P). These sequences are provided
in SEQ ID NO: 699-701.
[1008] Further studies using the PCR-based methodology described
above resulted in the isolation of more than 180 additional clones,
of which 23 clones were found to show no significant homologies to
known sequences. The determined cDNA sequences for these clones are
provided in SEQ ID NO: 115-123, 127, 131, 137, 145, 147-151, 153,
156-158 and 160. Twenty-three clones (SEQ ID NO: 124-126, 128-130,
132-136, 138-144, 146, 152, 154, 155 and 159) were found to show
some homology to previously identified ESTs. An additional ten
clones (SEQ ID NO: 161-170) were found to have some degree of
homology to known genes. Larger cDNA clones containing the P20
sequence represent splice variants of a gene referred to as P703P.
The determined DNA sequence for the variants referred to as DE1,
DE13 and DE14 are provided in SEQ ID NO: 171, 175 and 177,
respectively, with the corresponding amino acid sequences being
provided in SEQ ID NO: 172, 176 and 178, respectively. The
determined cDNA sequence for an extended spliced form of P703 is
provided in SEQ ID NO: 225. The DNA sequences for the splice
variants referred to as DE2 and DE6 are provided in SEQ ID NO: 173
and 174, respectively.
[1009] mRNA Expression levels for representative clones in tumor
tissues (prostate (n=5), breast (n=2), colon and lung) normal
tissues (prostate (n=5), colon, kidney, liver, lung (n=2), ovary
(n=2), skeletal muscle, skin, stomach, small intestine and brain),
and activated and non-activated PBMC was determined by RT-PCR as
described above. Expression was examined in one sample of each
tissue type unless otherwise indicated.
[1010] P9 was found to be highly expressed in normal prostate and
prostate tumor compared to all normal tissues tested except for
normal colon which showed comparable expression. P20, a portion of
the P703P gene, was found to be highly expressed in normal prostate
and prostate tumor, compared to all twelve normal tissues tested. A
modest increase in expression of P20 in breast tumor (n=2), colon
tumor and lung tumor was seen compared to all normal tissues except
lung (1 of 2). Increased expression of P18 was found in normal
prostate, prostate tumor and breast tumor compared to other normal
tissues except lung and stomach. A modest increase in expression of
P5 was observed in normal prostate compared to most other normal
tissues. However, some elevated expression was seen in normal lung
and PBMC. Elevated expression of P5 was also observed in prostate
tumors (2 of 5), breast tumor and one lung tumor sample. For P30,
similar expression levels were seen in normal prostate and prostate
tumor, compared to six of twelve other normal tissues tested.
Increased expression was seen in breast tumors, one lung tumor
sample and one colon tumor sample, and also in normal PBMC. P29 was
found to be over-expressed in prostate tumor (5 of 5) and normal
prostate (5 of 5) compared to the majority of normal tissues.
However, substantial expression of P29 was observed in normal colon
and normal lung (2 of 2). P80 was found to be over-expressed in
prostate tumor (5 of 5) and normal prostate (5 of 5) compared to
all other normal tissues tested, with increased expression also
being seen in colon tumor.
[1011] Further studies resulted in the isolation of twelve
additional clones, hereinafter referred to as 10-d8, 10-h10, 11-c8,
7-g6, 8-b5, 8-b6, 8-d4, 8-d9, 8-g3, 8-h11, 9-f12 and 9-f3. The
determined DNA sequences for 10-d8, 10-h10, 11-c8, 8-d4, 8-d9,
8-h11, 9-f12 and 9-f3 are provided in SEQ ID NO: 207, 208, 209,
216, 217, 220, 221 and 222, respectively. The determined forward
and reverse DNA sequences for 7-g6, 8-b5, 8-b6 and 8-g3 are
provided in SEQ ID NO: 210 and 211; 212 and 213; 214 and 215; and
218 and 219, respectively. Comparison of these sequences with those
in the gene bank revealed no significant homologies to the sequence
of 9-f3. The clones 10-d8, 11-c8 and 8-h11 were found to show some
homology to previously isolated ESTs, while 10-h10, 8-b5, 8-b6,
8-d4, 8-d9, 8-g3 and 9-f12 were found to show some homology to
previously identified genes. Further characterization of 7-G6 and
8-G3 showed identity to the known genes PAP and PSA,
respectively.
[1012] mRNA expression levels for these clones were determined
using the micro-array technology described above. The clones 7-G6,
8-G3, 8-B5, 8-B6, 8-D4, 8-D9, 9-F3, 9-F12, 9-H3, 10-A2, 10-A4,
11-C9 and 11-F2 were found to be over-expressed in prostate tumor
and normal prostate, with expression in other tissues tested being
low or undetectable. Increased expression of 8-F11 was seen in
prostate tumor and normal prostate, bladder, skeletal muscle and
colon. Increased expression of 10-H10 was seen in prostate tumor
and normal prostate, bladder, lung, colon, brain and large
intestine. Increased expression of 9-B1 was seen in prostate tumor,
breast tumor, and normal prostate, salivary gland, large intestine
and skin, with increased expression of 11-C8 being seen in prostate
tumor, and normal prostate and large intestine.
[1013] An additional cDNA fragment derived from the PCR-based
normal prostate subtraction, described above, was found to be
prostate specific by both micro-array technology and RT-PCR. The
determined cDNA sequence of this clone (referred to as 9-A11) is
provided in SEQ ID NO: 226. Comparison of this sequence with those
in the public databases revealed 99% identity to the known gene
HOXB13.
[1014] Further studies led to the isolation of the clones 8-C6 and
8-H7. The determined cDNA sequences for these clones are provided
in SEQ ID NO: 227 and 228, respectively. These sequences were found
to show some homology to previously isolated ESTs.
[1015] PCR and hybridization-based methodologies were employed to
obtain longer cDNA sequences for clone P20 (also referred to as
P703P), yielding three additional cDNA fragments that progressively
extend the 5' end of the gene. These fragments, referred to as
P703PDE5, P703P6.26, and P703PX-23 (SEQ ID NO: 326, 328 and 330,
with the corresponding amino acid sequences being provided in SEQ
ID NO: 327, 329 and 331, respectively) contain additional 5'
sequence. P703PDE5 was recovered by screening of a cDNA library
(#141-26) with a portion of P703P as a probe. P703P6.26 was
recovered from a mixture of three prostate tumor cDNAs and
P703PX.sub.--23 was recovered from cDNA library (#438-48).
Together, the additional sequences include all of the putative
mature serine protease along with part of the putative signal
sequence. The full-length cDNA sequence for P703P is provided in
SEQ ID NO: 524, with the corresponding amino acid sequence being
provided in SEQ ID NO: 525.
[1016] Using computer algorithms, the following regions of P703P
were predicted to represent potential HLA A2-binding CTL epitopes:
amino acids 164-172 of SEQ ID NO: 525 (SEQ ID NO: 866); amino acids
160-168 of SEQ ID NO: 525 (SEQ ID NO: 867); amino acids 239-247 of
SEQ ID NO: 525 (SEQ ID NO: 868); amino acids 118-126 of SEQ ID NO:
525 (SEQ ID NO: 869); amino acids 112-120 of SEQ ID NO: 525 (SEQ ID
NO: 870); amino acids 155-164 of SEQ ID NO: 525 (SEQ ID NO: 871);
amino acids 117-126 of SEQ ID NO: 525 (SEQ ID NO: 872); amino acids
164-173 of SEQ ID NO: 525 (SEQ ID NO: 873); amino acids 154-163 of
SEQ ID NO: 525 (SEQ ID NO: 874); amino acids 163-172 of SEQ ID NO:
525 (SEQ ID NO: 875); amino acids 58-66 of SEQ ID NO: 525 (SEQ ID
NO: 876); and amino acids 59-67 of SEQ ID NO: 525 (SEQ ID NO:
877).
[1017] P703P was found to show some homology to previously
identified proteases, such as thrombin. The thrombin receptor has
been shown to be preferentially expressed in highly metastatic
breast carcinoma cells and breast carcinoma biopsy samples.
Introduction of thrombin receptor antisense cDNA has been shown to
inhibit the invasion of metastatic breast carcinoma cells in
culture. Antibodies against thrombin receptor inhibit thrombin
receptor activation and thrombin-induced platelet activation.
Furthermore, peptides that resemble the receptor's tethered ligand
domain inhibit platelet aggregation by thrombin. P703P may play a
role in prostate cancer through a protease-activated receptor on
the cancer cell or on stromal cells. The potential trypsin-like
protease activity of P703P may either activate a protease-activated
receptor on the cancer cell membrane to promote tumorgenesis or
activate a protease-activated receptor on the adjacent cells (such
as stromal cells) to secrete growth factors and/or proteases (such
as matrix metalloproteinases) that could promote tumor
angiogenesis, invasion and metastasis. P703P may thus promote tumor
progression and/or metastasis through the activation of
protease-activated receptor. Polypeptides and antibodies that block
the P703P-receptor interaction may therefore be usefully employed
in the treatment of prostate cancer.
[1018] To determine whether P703P expression increases with
increased severity of Gleason grade, an indicator of tumor stage,
quantitative PCR analysis was performed on prostate tumor samples
with a range of Gleason scores from 5 to >8. The mean level of
P703P expression increased with increasing Gleason score,
indicating that P703P expression may correlate with increased
disease severity.
[1019] Further studies using a PCR-based subtraction library of a
prostate tumor pool subtracted against a pool of normal tissues
(referred to as JP: PCR subtraction) resulted in the isolation of
thirteen additional clones, seven of which did not share any
significant homology to known GenBank sequences. The determined
cDNA sequences for these seven clones (P711P, P712P, novel 23,
P774P, P775P, P710P and P768P) are provided in SEQ ID NO: 307-311,
313 and 315, respectively. The remaining six clones (SEQ ID NO: 316
and 321-325) were shown to share some homology to known genes. By
microarray analysis, all thirteen clones showed three or more fold
over-expression in prostate tissues, including prostate tumors, BPH
and normal prostate as compared to normal non-prostate tissues.
Clones P711P, P712P, novel 23 and P768P showed over-expression in
most prostate tumors and BPH tissues tested (n=29), and in the
majority of normal prostate tissues (n=4), but background to low
expression levels in all normal tissues. Clones P774P, P775P and
P710P showed comparatively lower expression and expression in fewer
prostate tumors and BPH samples, with negative to low expression in
normal prostate.
[1020] Further studies led to the isolation of an extended cDNA
sequence for P712P (SEQ ID NO: 552). The amino acid sequences
encoded by 16 predicted open reading frames present within the
sequence of SEQ ID NO: 552 are provided in SEQ ID NO: 553-568.
[1021] The full-length cDNA for P711P was obtained by employing the
partial sequence of SEQ ID NO: 307 to screen a prostate cDNA
library. Specifically, a directionally cloned prostate cDNA library
was prepared using standard techniques. One million colonies of
this library were plated onto LB/Amp plates. Nylon membrane filters
were used to lift these colonies, and the cDNAs which were picked
up by these filters were denatured and cross-linked to the filters
by UV light. The P711P cDNA fragment of SEQ ID NO: 307 was
radio-labeled and used to hybridize with these filters. Positive
clones were selected, and cDNAs were prepared and sequenced using
an automatic Perkin Elmer/Applied Biosystems sequencer. The
determined full-length sequence of P711P is provided in SEQ ID NO:
382, with the corresponding amino acid sequence being provided in
SEQ ID NO: 383.
[1022] Using PCR and hybridization-based methodologies, additional
cDNA sequence information was derived for two clones described
above, 11-C9 and 9-F3, herein after referred to as P707P and P714P,
respectively (SEQ ID NO: 333 and 334). After comparison with the
most recent GenBank, P707P was found to be a splice variant of the
known gene HoxB13. In contrast, no significant homologies to P714P
were found. Further studies employing the sequence of SEQ ID NO:
334 as a probe in standard full-length cloning methods, resulted in
an extended cDNA sequence for P714P. This sequence is provided in
SEQ ID NO: 698. This sequence was found to show some homology to
the gene that encodes human ribosomal L23A protein.
[1023] Clones 8-B3, P89, P98, P130 and P201 (as disclosed in U.S.
patent application Ser. No. 09/020,956, filed Feb. 9, 1998) were
found to be contained within one contiguous sequence, referred to
as P705P (cDNA sequence provided in SEQ ID NO: 335, with the amino
acid sequence being provided in SEQ ID NO: 336), which was
determined to be a splice variant of the known gene NKX 3.1.
Subsequent studies led to the isolation of a corrected cDNA
sequence for P705P. The coding region of this sequence is provided
in SEQ ID NO: 948.
[1024] Further studies on P775P resulted in the isolation of four
additional sequences (SEQ ID NO: 473-476) which are all splice
variants of the P775P gene. The sequence of SEQ ID NO: 474 was
found to contain two open reading frames (ORFs). The amino acid
sequences encoded by these ORFs are provided in SEQ ID NO: 477 and
478. The cDNA sequence of SEQ ID NO: 475 was found to contain an
ORF which encodes the amino acid sequence of SEQ ID NO: 479. The
cDNA sequence of SEQ ID NO: 473 was found to contain four ORFs. The
amino acid sequences encoded by these ORFs are provided in SEQ ID
NO: 480-483. Additional splice variants of P775P are provided in
SEQ ID NO: 593-597.
[1025] Subsequent studies led to the identification of a genomic
region on chromosome 22q11.2, known as the Cat Eye Syndrome region,
that contains the five prostate genes P704P, P712P, P774P, P775P
and B305D. The relative location of each of these five genes within
the genomic region is shown in FIG. 10. This region may therefore
be associated with malignant tumors, and other potential tumor
genes may be contained within this region. These studies also led
to the identification of a potential open reading frame (ORF) for
P775P (provided in SEQ ID NO: 533), which encodes the amino acid
sequence of SEQ ID NO: 534.
[1026] Comparison of the clone of SEQ ID NO: 325 (referred to as
P558S) with sequences in the GenBank and GeneSeq DNA databases
showed that P558S is identical to the prostate-specific
transglutaminase gene, which is known to have two forms. The
full-length sequences for the two forms are provided in SEQ ID NO:
773 and 774, with the corresponding amino acid sequences being
provided in SEQ ID NO: 775 and 776, respectively. The cDNA sequence
of SEQ ID NO: 774 has a 15 pair base insert, resulting in a 5 amino
acid insert in the corresponding amino acid sequence (SEQ ID NO:
776). This insert is not present in the sequence of SEQ ID NO:
773.
[1027] Further studies on P768P (SEQ ID NO: 315) led to the
identification of the putative full-length open reading frame
(ORF). The cDNA sequence of the ORF with stop codon is provided in
SEQ ID NO: 907. The cDNA sequence of the ORF without stop codon is
provided in SEQ ID NO: 908, with the corresponding amino acid
sequence being provided in SEQ ID NO: 909. This sequence was found
to show 86% identity to a rat calcium transporter protein,
indicating that P768P may represent a human calcium transporter
protein. The locations of transmembrane domains within P768P were
predicted using the PSORT II computer algorithm. Six transmembrane
domains were predicted at amino acid positions 118-134, 172-188,
211-227, 230-246, 282-298 and 348-364. The amino acid sequences of
SEQ ID NO: 910-915 represent amino acids 1-134, 135-188, 189-227,
228-246, 247-298 and 299-511 of P768P, respectively.
Example 4
Synthesis of Polypeptides
[1028] Polypeptides may be synthesized on a Perkin Elmer/Applied
Biosystems 430A peptide synthesizer using FMOC chemistry with HPTU
(O-Benzotriazole-N,N,N',N'-tetramethyluronium hexafluorophosphate)
activation. A Gly-Cys-Gly sequence may be attached to the amino
terminus of the peptide to provide a method of conjugation, binding
to an immobilized surface, or labeling of the peptide. Cleavage of
the peptides from the solid support may be carried out using the
following cleavage mixture: trifluoroacetic
acid:ethanedithiol:thioanisole:water:phenol (40:1:2:2:3). After
cleaving for 2 hours, the peptides may be precipitated in cold
methyl-t-butyl-ether. The peptide pellets may then be dissolved in
water containing 0.1% trifluoroacetic acid (TFA) and lyophilized
prior to purification by C18 reverse phase HPLC. A gradient of
0%-60% acetonitrile (containing 0.1% TFA) in water (containing 0.1%
TFA) may be used to elute the peptides. Following lyophilization of
the pure fractions, the peptides may be characterized using
electrospray or other types of mass spectrometry and by amino acid
analysis.
Example 5
Further Isolation and Characterization of Prostate-Specific
Polypeptides by PCR-Based Subtraction
[1029] A cDNA library generated from prostate primary tumor mRNA as
described above was subtracted with cDNA from normal prostate. The
subtraction was performed using a PCR-based protocol (Clontech),
which was modified to generate larger fragments. 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 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. Two tester populations were
then created with different adapters, and the driver library
remained without adapters.
[1030] 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.
[1031] 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.
[1032] This PCR-based subtraction technique normalizes
differentially expressed cDNAs so that rare transcripts that are
overexpressed in prostate tumor tissue may be recoverable. Such
transcripts would be difficult to recover by traditional
subtraction methods.
[1033] In addition to genes known to be overexpressed in prostate
tumor, seventy-seven further clones were identified. Sequences of
these partial cDNAs are provided in SEQ ID NO: 29 to 305. Most of
these clones had no significant homology to database sequences.
Exceptions were JPTPN23 (SEQ ID NO: 231; similarity to pig
valosin-containing protein), JPTPN30 (SEQ ID NO: 234; similarity to
rat mRNA for proteasome subunit), JPTPN45 (SEQ ID NO: 243;
similarity to rat norvegicus cytosolic NADP-dependent isocitrate
dehydrogenase), JPTPN46 (SEQ ID NO: 244; similarity to human
subclone H8 4 d4 DNA sequence), JP1D6 (SEQ ID NO: 265; similarity
to G. gallus dynein light chain-A), JP8D6 (SEQ ID NO: 288;
similarity to human BAC clone RG016J04), JP8F5 (SEQ ID NO: 289;
similarity to human subclone H8 3 b5 DNA sequence), and JP8E9 (SEQ
ID NO: 299; similarity to human Alu sequence).
[1034] Additional studies using the PCR-based subtraction library
consisting of a prostate tumor pool subtracted against a normal
prostate pool (referred to as PT-PN PCR subtraction) yielded three
additional clones. Comparison of the cDNA sequences of these clones
with the most recent release of GenBank revealed no significant
homologies to the two clones referred to as P715P and P767P (SEQ ID
NO: 312 and 314). The remaining clone was found to show some
homology to the known gene KIAA0056 (SEQ ID NO: 318). Using
microarray analysis to measure mRNA expression levels in various
tissues, all three clones were found to be over-expressed in
prostate tumors and BPH tissues. Specifically, clone P715P was
over-expressed in most prostate tumors and BPH tissues by a factor
of three or greater, with elevated expression seen in the majority
of normal prostate samples and in fetal tissue, but negative to low
expression in all other normal tissues. Clone P767P was
over-expressed in several prostate tumors and BPH tissues, with
moderate expression levels in half of the normal prostate samples,
and background to low expression in all other normal tissues
tested.
[1035] Further analysis, by microarray as described above, of the
PT-PN PCR subtraction library and of a DNA subtraction library
containing cDNA from prostate tumor subtracted with a pool of
normal tissue cDNAs, led to the isolation of 27 additional clones
(SEQ ID NO: 340-365 and 381) which were determined to be
over-expressed in prostate tumor. The clones of SEQ ID NO: 341,
342, 345, 347, 348, 349, 351, 355-359, 361, 362 and 364 were also
found to be expressed in normal prostate. Expression of all 26
clones in a variety of normal tissues was found to be low or
undetectable, with the exception of P544S (SEQ ID NO: 356) which
was found to be expressed in small intestine. Of the 26 clones, 11
(SEQ ID NO: 340-349 and 362) were found to show some homology to
previously identified sequences. No significant homologies were
found to the clones of SEQ ID NO: 350, 351, 353-361, and
363-365.
[1036] Comparison of the sequence of SEQ ID NO: 362 with sequences
in the GenBank and GeneSeq DNA databases showed that this clone
(referred to as P788P) is identical to GeneSeq Accession No.
X27262, which encodes a protein found in the GeneSeq protein
Accession No. Y00931. The full length cDNA sequence of P788P is
shown in SEQ ID NO: 777, with the corresponding amino acid being
shown in SEQ ID NO: 778. Subsequently, a full-length cDNA sequence
for P788P that contains polymorphisms not found in the sequence of
SEQ ID NO: 779, was cloned multiple times by PCR amplification from
cDNA prepared from several RNA templates from three individuals.
This determined cDNA sequence of this polymorphic variant of P788P
is provided in SEQ ID NO: 779, with the corresponding amino acid
sequence being provided in SEQ ID NO: 780. The sequence of SEQ ID
NO: 780 differs from that of SEQ ID NO: 778 by six amino acid
residues. The P788P protein has 7 potential transmembrane domains
at the C-terminal portion and is predicted to be a plasma membrane
protein with an extracellular N-terminal region.
[1037] Further studies on the clone of SEQ ID NO: 352 (referred to
as P790P) led to the isolation of the full-length cDNA sequence of
SEQ ID NO: 526. The corresponding amino acid is provided in SEQ ID
NO: 527. Data from two quantitative PCR experiments indicated that
P790P is over-expressed in 11/15 tested prostate tumor samples and
is expressed at low levels in spinal cord, with no expression being
seen in all other normal samples tested. Data from further PCR
experiments and microarray experiments showed over-expression in
normal prostate and prostate tumor with little or no expression in
other tissues tested. P790P was subsequently found to show
significant homology to a previously identified G-protein coupled
prostate tissue receptor.
[1038] Additional studies on the clone of SEQ ID NO: 354 (referred
to as P776P) led to the isolation of an extended cDNA sequence,
provided in SEQ ID NO: 569. The determined cDNA sequences of three
additional splice variants of P776P are provided in SEQ ID NO:
570-572. The amino acid sequences encoded by two predicted open
reading frames (ORFs) contained within SEQ ID NO: 570, one
predicted ORF contained within SEQ ID NO: 571, and 11 predicted
ORFs contained within SEQ ID NO: 569, are provided in SEQ ID NO:
573-586, respectively. Further studies led to the isolation of the
full-length sequence for the clone of SEQ ID NO: 570 (provided in
SEQ ID NO: 880). Full-length cloning efforts on the clone of SEQ ID
NO: 571 led to the isolation of two sequences (provided in SEQ ID
NO: 881 and 882), representing a single clone, that are identical
with the exception of a polymorphic insertion/deletion at position
1293. Specifically, the clone of SEQ ID NO: 882 (referred to as
clone F1) has a C at position 1293. The clone of SEQ ID NO: 881
(referred to as clone F2) has a single base pair deletion at
position 1293. The predicted amino acid sequences encoded by 5 open
reading frames located within SEQ ID NO: 880 are provided in SEQ ID
NO: 883-887, with the predicted amino acid sequences encoded by the
clone of SEQ ID NO: 881 and 882 being provided in SEQ ID NO:
888-893.
[1039] Comparison of the cDNA sequences for the clones P767P (SEQ
ID NO: 314) and P777P (SEQ ID NO: 350) with sequences in the
GenBank human EST database showed that the two clones matched many
EST sequences in common, suggesting that P767P and P777P may
represent the same gene. A DNA consensus sequence derived from a
DNA sequence alignment of P767P, P777P and multiple EST clones is
provided in SEQ ID NO: 587. The amino acid sequences encoded by
three putative ORFs located within SEQ ID NO: 587 are provided in
SEQ ID NO: 588-590.
[1040] The clone of SEQ ID NO: 342 (referred to as P789P) was found
to show homology to a previously identified gene. The full length
cDNA sequence for P789P and the corresponding amino acid sequence
are provided in SEQ ID NO: 878 and 879, respectively.
[1041] Comparison of the sequence of SEQ ID NO: 355 (referred to as
P780P) with sequences in the Geneseq DNA database, revealed that
P780P shares 100% sequence identity with GeneSEQ accessions Z29049
and Z29050 (SEQ ID NO: 944 and 945, respectively). Z29049 and
Z29050 differ from each other in that Z29049 contains a 714 bp
deletion relative to Z29050. Thus, Z29049 and Z29050 appear to
represent 2 alternative splice forms of the gene P780P. Z29049
encodes a protein that is 379 amino acids in length (GeneSeq
Accession number Y15155; SEQ ID NO: 946). Z29050 encodes a protein
that is 617 amino acids in length (GeneSeq Accession number Y15156;
SEQ ID NO: 947). These two proteins are identical with the
exception that Y15155 contains a 238 amino acid deletion relative
to Y15156. This amino acid deletion corresponds to the 714 bp
deletion in Z29049.
Example 6
Peptide Priming of Mice and Propagation of CTL Lines
[1042] 6.1. This Example illustrates the preparation of a cytotoxic
T lymphocyte (CTL) cell line specific for cells expressing the
P502S gene.
[1043] Mice expressing the transgene for human HLA A2Kb (provided
by Dr L. Sherman, The Scripps Research Institute, La Jolla, Calif.)
were immunized with P2S#12 peptide (VLGWVAEL; SEQ ID NO: 306),
which is derived from the P502S gene (also referred to herein as
J1-17, SEQ ID NO: 8), as described by Theobald et al., Proc. Nat'l
Acad. Sci. USA 92:11993-11997, 1995 with the following
modifications. Mice were immunized with 100 .mu.g of P2S#12 and 120
.mu.g of an I-A.sup.b binding peptide derived from hepatitis B
Virus protein emulsified in incomplete Freund's adjuvant. Three
weeks later these mice were sacrificed and single cell suspensions
prepared. Cells were then resuspended at 6.times.10.sup.6 cells/ml
in complete media (RPMI-1640; Gibco BRL, Gaithersburg, Md.)
containing 10% FCS, 2 mM Glutamine (Gibco BRL), sodium pyruvate
(Gibco BRL), non-essential amino acids (Gibco BRL),
2.times.10.sup.-5 M 2-mercaptoethanol, 50 U/ml penicillin and
streptomycin, and cultured in the presence of irradiated (3000
rads) P2S#12-pulsed (5 mg/ml P2S#12 and 10 mg/ml
.beta.2-microglobulin) LPS blasts (A2 transgenic spleens cells
cultured in the presence of 7 .mu.g/ml dextran sulfate and 25
.mu.g/ml LPS for 3 days). Six days later, cells
(5.times.10.sup.5/ml) were restimulated with 2.5.times.10.sup.6/ml
peptide pulsed irradiated (20,000 rads) EL4A2Kb cells (Sherman et
al, Science 258:815-818, 1992) and 3.times.10.sup.6/ml A2
transgenic spleen feeder cells. Cells were cultured in the presence
of 20 U/ml IL-2. Cells continued to be restimulated on a weekly
basis as described, in preparation for cloning the line.
[1044] P2S#12 line was cloned by limiting dilution analysis with
peptide pulsed EL4 A2Kb tumor cells (1.times.10.sup.4 cells/well)
as stimulators and A2 transgenic spleen cells as feeders
(5.times.10.sup.5 cells/well) grown in the presence of 30 U/ml
IL-2. On day 14, cells were restimulated as before. On day 21,
clones that were growing were isolated and maintained in culture.
Several of these clones demonstrated significantly higher
reactivity (lysis) against human fibroblasts (HLA A2Kb expressing)
transduced with P502S than against control fibroblasts. An example
is presented in FIG. 1.
[1045] This data indicates that P2S #12 represents a naturally
processed epitope of the P502S protein that is expressed in the
context of the human HLA A2Kb molecule.
[1046] 6.2. This Example illustrates the preparation of murine CTL
lines and CTL clones specific for cells expressing the P501S
gene.
[1047] This series of experiments were performed similarly to that
described above. Mice were immunized with the P1S#10 peptide (SEQ
ID NO: 337), which is derived from the P501S gene (also referred to
herein as L1-12, SEQ ID NO: 110). The P1S#10 peptide was derived by
analysis of the predicted polypeptide sequence for P501S for
potential HLA-A2 binding sequences as defined by published HLA-A2
binding motifs (Parker, K C, et al, J. Immunol., 152:163, 1994).
P1S#10 peptide was synthesized as described in Example 4, and
empirically tested for HLA-A2 binding using a T cell based
competition assay. Predicted A2 binding peptides were tested for
their ability to compete HLA-A2 specific peptide presentation to an
HLA-A2 restricted CTL clone (D150M58), which is specific for the
HLA-A2 binding influenza matrix peptide fluM58. D150M58 CTL
secretes TNF in response to self-presentation of peptide fluM58. In
the competition assay, test peptides at 100-200 .mu.g/ml were added
to cultures of D150M58 CTL in order to bind HLA-A2 on the CTL.
After thirty minutes, CTL cultured with test peptides, or control
peptides, were tested for their antigen dose response to the fluM58
peptide in a standard TNF bioassay. As shown in FIG. 3, peptide
P1S#10 competes with HLA-A2 restricted presentation of fluM58,
demonstrating that peptide P1S#10 binds HLA-A2.
[1048] Mice expressing the transgene for human HLA A2Kb were
immunized as described by Theobald et al. (Proc. Nat'l Acad. Sci.
USA 92:11993-11997, 1995) with the following modifications. Mice
were immunized with 62.5 .mu.g of P1S #10 and 120 .mu.g of an
I-A.sup.b binding peptide derived from Hepatitis B Virus protein
emulsified in incomplete Freund's adjuvant. Three weeks later these
mice were sacrificed and single cell suspensions prepared using a
nylon mesh. Cells were then resuspended at 6.times.10.sup.6
cells/ml in complete media (as described above) and cultured in the
presence of irradiated (3000 rads) P1S#10-pulsed (2 .mu.g/ml P1S#10
and 10 mg/ml .beta.2-microglobulin) LPS blasts (A2 transgenic
spleens cells cultured in the presence of 7 .mu.g/ml dextran
sulfate and 25 .mu.g/ml LPS for 3 days). Six days later cells
(5.times.10.sup.5/ml) were restimulated with 2.5.times.10.sup.6/ml
peptide-pulsed irradiated (20,000 rads) EL4A2Kb cells, as described
above, and 3.times.10.sup.6/ml A2 transgenic spleen feeder cells.
Cells were cultured in the presence of 20 U/ml IL-2. Cells were
restimulated on a weekly basis in preparation for cloning. After
three rounds of in vitro stimulations, one line was generated that
recognized P1S#10-pulsed Jurkat A2Kb targets and P501S-transduced
Jurkat targets as shown in FIG. 4.
[1049] A P1S#1-specific CTL line was cloned by limiting dilution
analysis with peptide pulsed EL4 A2Kb tumor cells (1.times.10.sup.4
cells/well) as stimulators and A2 transgenic spleen cells as
feeders (5.times.10.sup.5 cells/well) grown in the presence of 30
U/ml IL-2. On day 14, cells were restimulated as before. On day 21,
viable clones were isolated and maintained in culture. As shown in
FIG. 5, five of these clones demonstrated specific cytolytic
reactivity against P501S-transduced Jurkat A2Kb targets. This data
indicates that P1S#10 represents a naturally processed epitope of
the P501S protein that is expressed in the context of the human
HLA-A2.1 molecule.
Example 7
Priming of CTL In Vivo Using Naked DNA Immunization with a Prostate
Antigen
[1050] The prostate-specific antigen L1-12, as described above, is
also referred to as P501S. HLA A2Kb Tg mice (provided by Dr L.
Sherman, The Scripps Research Institute, La Jolla, Calif.) were
immunized with 100 .mu.g P501S in the vector VR1012 either
intramuscularly or intradermally. The mice were immunized three
times, with a two week interval between immunizations. Two weeks
after the last immunization, immune spleen cells were cultured with
Jurkat A2Kb-P501S transduced stimulator cells. CTL lines were
stimulated weekly. After two weeks of in vitro stimulation, CTL
activity was assessed against P501S transduced targets. Two out of
8 mice developed strong anti-P501S CTL responses. These results
demonstrate that P501S contains at least one naturally processed
HLA-A2-restricted CTL epitope.
[1051] In subsequent experiments, mice were immunized with either
P501S in the vector VR1012 as described above or with a
P501S-adenovirus construct at 1.times.10.sup.8 pfu/animal. Three
weeks later, animals received a boost immunization, with animals
that were primed with P501S alone being boosted with either P501S
alone or P501S-adenovirus. Spleen cells were harvested at 3 and 6
weeks post-immunization and cultured with irradiated Jurkat A2Kb
cells (day 0). CTL activity was assayed on day 6, spleen cells
restimulated on day 7, and a secondary CTL assay was performed on
day 13. IgG1 and IgG2a responses against the N-terminal region of
P501S (amino acids 36-325 of SEQ ID NO: 113) and against a
truncated form of P501S (amino acids 342-538 of SEQ ID NO: 113)
were assayed using ELISA. The P501S-adenovirus construct
effectively elicited both T cell and antibody responses, with P501S
alone eliciting CTL responses but not antibody responses.
Immunization with P501S alone was found to be most effective in
combination with a P501S-adenovirus boost. Immunizations with P501S
alone generated T cells that respond to peptide 370 (CLSHSVAW). In
contrast, immunizations with P501S-adenovirus generated weak or no
reactivity to peptide 370. These studies indicate that a
combination of a DNA priming immunization followed by an adenovirus
boost is a potent approach for eliciting both CTL and antibody
response, and that distinct cytotoxic T cells, recognizing
different epitopes, may be elicited when immunizing with P501S or
P501S plus adenovirus versus immunizing with adenovirus alone.
Example 8
Ability of Human T Cells to Recognize Prostate-Specific
Polypeptides
[1052] This Example illustrates the ability of T cells specific for
a prostate tumor polypeptide to recognize human tumor.
[1053] Human CD8.sup.+ T cells were primed in vitro to the P2S-12
peptide (SEQ ID NO: 306) derived from P502S (also referred to as
J1-17) using dendritic cells according to the protocol of Van Tsai
et al. (Critical Reviews in Immunology 18:65-75, 1998). The
resulting CD8.sup.+ T cell microcultures were tested for their
ability to recognize the P2S-12 peptide presented by autologous
fibroblasts or fibroblasts which were transduced to express the
P502S gene in a .gamma.-interferon ELISPOT assay (see Lalvani et
al., J. Exp. Med. 186:859-865, 1997). Briefly, titrating numbers of
T cells were assayed in duplicate on 10.sup.4 fibroblasts in the
presence of 3 .mu.g/ml human .beta..sub.2-microglobulin and 1
.mu.g/ml P2S-12 peptide or control E75 peptide. In addition, T
cells were simultaneously assayed on autologous fibroblasts
transduced with the P502S gene or as a control, fibroblasts
transduced with HER-2/neu. Prior to the assay, the fibroblasts were
treated with 10 ng/ml .gamma.-interferon for 48 hours to upregulate
class I MHC expression. One of the microcultures (#5) demonstrated
strong recognition of both peptide pulsed fibroblasts as well as
transduced fibroblasts in a .gamma.-interferon ELISPOT assay. FIG.
2A demonstrates that there was a strong increase in the number of
.gamma.-interferon spots with increasing numbers of T cells on
fibroblasts pulsed with the P2S-12 peptide (solid bars) but not
with the control E75 peptide (open bars). This shows the ability of
these T cells to specifically recognize the P2S-12 peptide. As
shown in FIG. 2B, this microculture also demonstrated an increase
in the number of .gamma.-interferon spots with increasing numbers
of T cells on fibroblasts transduced to express the P502S gene but
not the HER-2/neu gene. These results provide additional
confirmatory evidence that the P2S-12 peptide is a naturally
processed epitope of the P502S protein. Furthermore, this also
demonstrates that there exists in the human T cell repertoire, high
affinity T cells which are capable of recognizing this epitope.
These T cells should also be capable of recognizing human tumors
which express the P502S gene.
Example 9
Elicitation of Prostate Antigen-Specific CTL Responses in Human
Blood and Identification of CTL Epitopes
[1054] This Example illustrates the ability of the
prostate-specific antigen P501S to elicit a cytotoxic T lymphocyte
(CTL) response in blood of normal humans and defines important
epitopes responsible for T-cell recognition. Such information
further confirms the immunogenicity of P501S and validates its use
in any of a number of illustrative immunodiagnostic and
immunotherapeutic embodiments described herein.
[1055] Autologous dendritic cells (DC) were differentiated from
monocyte cultures derived from PBMC of normal donors by growth for
five days in RPMI medium containing 10% human serum, 50 ng/ml GMCSF
and 30 ng/ml IL-4. Following culture, DC were infected overnight
with recombinant P501S-expressing vaccinia virus at an M.O.I. of 5
and matured for 8 hours by the addition of 2 micrograms/ml CD40
ligand. Virus was inactivated by UV irradiation, CD8.sup.+ cells
were isolated by positive selection using magnetic beads, and
priming cultures were initiated in 24-well plates. Following five
stimulation cycles using autologous fibroblasts retrovirally
transduced to express P501S and CD80, CD8+ lines were identified
that specifically produced interferon-gamma when stimulated with
autologous P501S-transduced fibroblasts. The P501S-specific
activity of cell line 3A-1 could be maintained following additional
stimulation cycles on autologous B-LCL transduced with P501S. Line
3A-1 was shown to specifically recognize autologous B-LCL
transduced to express P501S, but not EGFP-transduced autologous
B-LCL, as measured by cytotoxicity assays (.sup.51Cr release) and
interferon-gamma production (Interferon-gamma Elispot; see above
and Lalvani et al., J. Exp. Med. 186:859-865, 1997). The results of
these assays are presented in FIGS. 6A and 6B.
[1056] The ability of the prostate antigen P501S to elicit an
immune response in human males was examined as follows.
[1057] Dendritic Cells (DC) were isolated by Percol gradient
followed by differential adherence, and cultured for 5 days in the
presence of RPMI medium containing 1% human serum, 50 ng/ml GM-CSF
and 30 ng/ml IL-4. Following culture, DC were infected for 24 hours
with P501S-expressing Adenovirus at an MOI of 10 and matured for an
additional 24 hours by the addition of 2 ug/ml CD40 ligand. CD8
cells were enriched from PBMC of a normal male donor by the
subtraction of CD4+, CD14+ and CD16+ populations from PBMC with
magnetic beads. Priming cultures containing 10,000 P501S-expressing
DC and 100,000 CD8+ T cells per well were set up in 96-well
V-bottom plates in RPMI containing 10% human serum, 5 ng/ml IL-12
and 10 ng/ml IL-6. Cultures were stimulated every 7 days using
autologous fibroblasts retrovirally transduced to express P501S and
CD80, and were treated with IFN-gamma for 48-72 hours to upregulate
MHC Class I expression. Ten u/ml IL-2 was added at the time of
stimulation and on days 2 and 5 following stimulation. Following 4
stimulation cycles, multiple P501S-specific CD8+ T cell lines were
identified that produced IFN-gamma in response to IFN-gamma treated
P501S/CD80-expressing autologous fibroblasts, but not in response
to IFN-gamma treated P703P/CD80-expressing autologous fibroblasts
in a .gamma.-IFN Elispot assay. The three most promising lines,
referred to as 1H1, 2H2 and 6F1, were cloned in 96-well plates with
0.5 cell/well or 2 cells/well in the presence of 75,000 PBMC/well,
10,000 B-LCL/well, 30 ng/ml OKT3 and 50 u/ml IL-2 to isolate
P501S-specific clones.
[1058] To identify the class I restriction element for the
P501S-specific clones, HLA blocking and mismatch analyses were
performed as follows. In .gamma.-IFN Elispot assays, the specific
response of clones to P501S transduced autologous fibroblasts was
blocked by pre-incubation with 25 ug/ml W6/32 (pan-Class I blocking
antibody) and for 6F1 with BB7.2 (HLA-A2 blocking antibody), and
for 1H1 and 2H2 with B1.23.2 (HLA-B/C blocking antibody). The
results demonstrated that the P501S specific response of the clones
is restricted to an HLA-A2 and/or HLA-B or -C allele. For the HLA
mismatch analysis, autologous fibroblasts (D310, HLA-A2, A3, B44,
B51, Cw5, Cw14) and heterologous fibroblasts (D326, HLA-A1, A2, B8,
B51, Cw1, Cw7) that share the HLA-A-2 and HLAB51 allele were
transduced with P501S and used to stimulate the clones. In
.gamma.-IFN Elispot assays, 1H1 and 2H2 only recognized the
autologous fibroblasts, suggesting (together with the antibody
blocking assays above) that the relevant allele was B44, Cw5, or
Cw14, and 6F1 recognized both D310 and D326, suggesting the
response was restricted to HLA-A0201.
[1059] To confirm and extend the above restriction data, each of
the alleles from D310 was cloned into the pBIB expression vector
and cotransfected into Cos-7 cells together with full-length P501S.
1H1 and 2H2 clones specifically recognized Cos-7 cells
cotransfected with P501S and the Cw0501 alelle, while 6F1 clones
recognized Cos-7 cells cotransfected with P501S and the HLA-A0201
allele. These results demonstrate that the above alleles are
responsible for presenting P501S epitopes to the above CTL.
[1060] To identify a sub-fragment of P501S that contained the
epitope recognized by the CTL, 3' truncations of P501S were
cotransfected with the above alleles into Cos-7 cells. A 6F1 clone
was found to recognize an epitope derived from the initial 354
nucleotides of the P501S open reading frame (ORF), a 2H2 clone
(referred to as 2H2-1A12) recognized an epitope derived from the
sequence of P501S found between amino acids 471-553 of P501S (SEQ
ID NO: 113), and a 1H1 clone (referred to as 1H1-1A6) recognized an
epitope derived from the sequence of P501S found between amino
acids 278-353 of P501S (SEQ ID NO: 113).
[1061] To identify minimal epitopes recognized by these CTL, 15 or
19-mer peptides overlapping by 11 or 15 amino acids, respectively,
were synthesized, pulsed onto autologous B-LCL and used as antigen
presenting cells for the CTL in .gamma.-IFN ELISPOT assays. For
1H1-1A6, a pool of four 15-21 mers that spanned amino acids 246-325
of SEQ ID NO: 113 was specifically recognized by the CTL. In the
pool breakdown, peptide 291 (amino acids 291-310; SEQ ID NO: 983,
cDNA sequence provided in SEQ ID NO: 972) was specifically
recognized by the 1H1-1A6 CTL. Ten-mer peptides from amino acids
291-310 of P501S were then synthesized and tested as above.
Peptides 291, 292, and 293 (SEQ ID NO: 984, 982 and 980,
respectively; cDNA sequences provided in SEQ ID NO: 975, 976 and
973, respectively) were all specifically recognized by the CTL.
These results demonstrate that each of the three 10-mer peptides
contain the minimal epitope recognized by the CTL. The 8-mer
peptide common to the three 10-mers with the sequence TDFVGEGL (SEQ
ID NO: 981) was then synthesized and tested. In a peptide titration
assay, the CD8+ T cells specific for this epitope recognized APC
pulsed with 1-10 .mu.g/ml. The 8-mer was also recognized
efficiently by the CTL, demonstrating that a minimal naturally
processed peptide epitope recognized by the CTL spans SEQ ID NO:
981. Further analysis revealed that the minimal epitope for the
clone 1H1-1A6 was YTDFVGEGL (amino acids 292-300 of P501), the
amino acid and DNA sequences for which are disclosed in SEQ ID
NOs:1021 and 1022, respectively. Peptide titration assays revealed
that CD8+ T cells specific for this epitope recognized APC pulsed
with 0.0016 .mu.g/ml of the 9-mer. Therefore a minimal CD8+ T cell
epitope specific for P501 is YTDFVGEGL (SEQ ID NO:1022).
[1062] For 2H2-1A12, a pool of twenty 15-mers that spanned amino
acids 462-553 was pulsed onto autologous B-LCL and tested as above.
Peptides 462 and 465 (SEQ ID NO: 979 and 977, respectively; cDNA
sequences provided in SEQ ID NO: 971 and 969, respectively) were
both specifically recognized by the CTL. These results demonstrate
that each of the two 15-mer peptides contain the minimal epitope
recognized by the CTL. 10-mer peptides overlapping by a single
amino acid were then synthesized from the sequence in common to the
two above peptides and tested as above. Primarily peptide 464
(amino acids 464-474; SEQ ID NO: 978; cDNA sequence provided in SEQ
ID NO: 970) and also peptides 463 (amino acids 463-472) and 465
(amino acids 465-475) were specifically recognized by the CTL.
These results indicate that the sequence of SEQ ID NO: 978 (amino
acids 464-474 of P501S) contains the minimal epitope recognized by
2H2-1A12 CTL. Further analysis revealed that the minimal epitope
for the clone 2H2-1A12 was ACDVSVRVV (amino acids 465-473 of P501S)
the amino acid and DNA sequences of which are disclosed in SEQ ID
NOs:1012 and 1013, respectively. The recognition of peptides 463
and 465 either reflects contamination of these peptides with
peptide 464, or additional secondary and inefficient recognition of
these peptides by the CTL.
[1063] This example thus confirms that P501S is capable of
eliciting a human CTL response and identifies multiple CTL epitopes
responsible for T-cell recognition of this prostate-specific
antigen. Such information further validates P501S as an important
target for use in immunodiagnostic and immunotherapeutic
applications.
Example 10
Identification of a Naturally Processed CTL Epitope Contained
within the Prostate-Specific Antigen P703P
[1064] The 9-mer peptide p5 (SEQ ID NO: 338) was derived from the
P703P antigen (also referred to as P20). The p5 peptide is
immunogenic in human HLA-A2 donors and is a naturally processed
epitope. Antigen specific human CD8+ T cells can be primed
following repeated in vitro stimulations with monocytes pulsed with
p5 peptide. These CTL specifically recognize p5-pulsed and
P703P-transduced target cells in both ELISPOT (as described above)
and chromium release assays. Additionally, immunization of HLA-A2Kb
transgenic mice with p5 leads to the generation of CTL lines which
recognize a variety of HLA-A2Kb or HLA-A2 transduced target cells
expressing P703P.
[1065] Initial studies demonstrating that p5 is a naturally
processed epitope were done using HLA-A2Kb transgenic mice.
HLA-A2Kb transgenic mice were immunized subcutaneously in the
footpad with 100 .mu.g of p5 peptide together with 140 .mu.g of
hepatitis B virus core peptide (a Th peptide) in Freund's
incomplete adjuvant. Three weeks post immunization, spleen cells
from immunized mice were stimulated in vitro with peptide-pulsed
LPS blasts. CTL activity was assessed by chromium release assay
five days after primary in vitro stimulation. Retrovirally
transduced cells expressing the control antigen P703P and HLA-A2Kb
were used as targets. CTL lines that specifically recognized both
p5-pulsed targets as well as P703P-expressing targets were
identified.
[1066] Human in vitro priming experiments demonstrated that the p5
peptide is immunogenic in humans. Dendritic cells (DC) were
differentiated from monocyte cultures derived from PBMC of normal
human donors by culturing 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, the DC were pulsed with 1 ug/ml p5 peptide and
cultured with CD8+ T cell enriched PBMC. CTL lines were
restimulated on a weekly basis with p5-pulsed monocytes. Five to
six weeks after initiation of the CTL cultures, CTL recognition of
p5-pulsed target cells was demonstrated. CTL were additionally
shown to recognize human cells transduced to express P703P,
demonstrating that p5 is a naturally processed epitope.
[1067] Studies identifying a further peptide epitope (referred to
as peptide 4) derived from the prostate tumor-specific antigen
P703P that is capable of being recognized by CD4 T cells on the
surface of cells in the context of HLA class II molecules were
carried out as follows. The amino acid sequence for peptide 4 is
provided in SEQ ID NO: 781, with the corresponding cDNA sequence
being provided in SEQ ID NO: 782.
[1068] Twenty 15-mer peptides overlapping by 10 amino acids and
derived from the carboxy-terminal fragment of P703P were generated
using standard procedures. Dendritic cells (DC) were derived from
PBMC of a normal female donor using GM-CSF and IL-4 by standard
protocols. CD4 T cells were generated from the same donor as the DC
using MACS beads and negative selection. DC were pulsed overnight
with pools of the 15-mer peptides, with each peptide at a final
concentration of 0.25 microgram/ml. Pulsed DC were washed and
plated at 1.times.10.sup.4 cells/well of 96-well V-bottom plates
and purified CD4 T cells were added at 1.times.10.sup.5/well.
Cultures were supplemented with 60 ng/ml IL-6 and 10 ng/ml IL-12
and incubated at 37.degree. C. Cultures were restimulated as above
on a weekly basis using DC generated and pulsed as above as antigen
presenting cells, supplemented with 5 ng/ml IL-7 and 10 u/ml IL-2.
Following 4 in vitro stimulation cycles, 96 lines (each line
corresponding to one well) were tested for specific proliferation
and cytokine production in response to the stimulating pools with
an irrelevant pool of peptides derived from mammaglobin being used
as a control.
[1069] One line (referred to as 1-F9) was identified from pool #1
that demonstrated specific proliferation (measured by 3H
proliferation assays) and cytokine production (measured by
interferon-gamma ELISA assays) in response to pool #1 of P703P
peptides. This line was further tested for specific recognition of
the peptide pool, specific recognition of individual peptides in
the pool, and in HLA mismatch analyses to identify the relevant
restricting allele. Line 1-F9 was found to specifically proliferate
and produce interferon-gamma in response to peptide pool #1, and
also to peptide 4 (SEQ ID NO: 781). Peptide 4 corresponds to amino
acids 126-140 of SEQ ID NO: 327. Peptide titration experiments were
conducted to assess the sensitivity of line 1-F9 for the specific
peptide. The line was found to specifically respond to peptide 4 at
concentrations as low as 0.25 ng/ml, indicating that the T cells
are very sensitive and therefore likely to have high affinity for
the epitope.
[1070] To determine the HLA restriction of the P703P response, a
panel of antigen presenting cells (APC) was generated that was
partially matched with the donor used to generate the T cells. The
APC were pulsed with the peptide and used in proliferation and
cytokine assays together with line 1-F9. APC matched with the donor
at HLA-DRB0701 and HLA-DQB02 alleles were able to present the
peptide to the T cells, indicating that the P703P-specific response
is restricted to one of these alleles.
[1071] Antibody blocking assays were utilized to determine if the
restricting allele was HLA-DR0701 or HLA-DQ02. The anti-HLA-DR
blocking antibody L243 or an irrelevant isotype matched IgG2a were
added to T cells and APC cultures pulsed with the peptide
RMPTVLQCVNVSVVS (SEQ ID NO: 781) at 250 ng/ml. Standard
interferon-gamma and proliferation assays were performed. Whereas
the control antibody had no effect on the ability of the T cells to
recognize peptide-pulsed APC, in both assays the anti-HLA-DR
antibody completely blocked the ability of the T cells to
specifically recognize peptide-pulsed APC.
[1072] To determine if the peptide epitope RMPTVLQCVNVSVVS (SEQ ID
NO: 781) was naturally processed, the ability of line 1-F9 to
recognize APC pulsed with recombinant P703P protein was examined.
For these experiments a number of recombinant P703P sources were
utilized; E. coli-derived P703P, Pichia-derived P703P and
baculovirus-derived P703P. Irrelevant protein controls used were E.
coli-derived L3E a lung-specific antigen) and baculovirus-derived
mammaglobin. In interferon-gamma ELISA assays, line 1-F9 was able
to efficiently recognize both E. coli forms of P703P as well as
Pichia-derived recombinant P703P, while baculovirus-derived P703P
was recognized less efficiently. Subsequent Western blot analysis
revealed that the E coli and Pichia P703P protein preparations were
intact while the baculovirus P703P preparation was approximately
75% degraded. Thus, peptide RMPTVLQCVNVSVVS (SEQ ID NO: 781) from
P703P is a naturally processed peptide epitope derived from P703P
and presented to T cells in the context of HLA-DRB-0701
[1073] In further studies, twenty-four 15-mer peptides overlapping
by 10 amino acids and derived from the N-terminal fragment of P703P
(corresponding to amino acids 27-154 of SEQ ID NO: 525) were
generated by standard procedures and their ability to be recognized
by CD4 cells was determined essentially as described above. DC were
pulsed overnight with pools of the peptides with each peptide at a
final concentration of 10 microgram/ml. A large number of
individual CD4 T cell lines (65/480) demonstrated significant
proliferation and cytokine release (IFN-gamma) in response to the
P703P peptide pools but not to a control peptide pool. The CD4 T
cell lines which demonstrated specific activity were restimulated
on the appropriate pool of P703P peptides and reassayed on the
individual peptides of each pool as well as a peptide dose
titration of the pool of peptides in a IFN-gamma release assay and
in a proliferation assay.
[1074] Sixteen immunogenic peptides were recognized by the T cells
from the entire set of peptide antigens tested. The amino acid
sequences of these peptides are provided in SEQ ID NO: 799-814,
with the corresponding cDNA sequences being provided in SEQ ID NO:
783-798, respectively. In some cases the peptide reactivity of the
T cell line could be mapped to a single peptide, however some could
be mapped to more than one peptide in each pool. Those CD4 T cell
lines that displayed a representative pattern of recognition from
each peptide pool with a reasonable affinity for peptide were
chosen for further analysis (I-1A, -6A; II-4C, -5E; III-6E, IV-4B,
-3F, -9B, -10F, V-5B, -4D, and -10F). These CD4 T cells lines were
restimulated on the appropriate individual peptide and reassayed on
autologous DC pulsed with a truncated form of recombinant P703P
protein made in E. coli (a.a. 96-254 of SEQ ID NO: 525),
full-length P703P made in the baculovirus expression system, and a
fusion between influenza virus NS1 and P703P made in E. coli. Of
the T cell lines tested, line I-1A recognized specifically the
truncated form of P703P (E. coli) but no other recombinant form of
P703P. This line also recognized the peptide used to elicit the T
cells. Line 2-4C recognized the truncated form of P703P (E. coli)
and the full length form of P703P made in baculovirus, as well as
peptide. The remaining T cell lines tested were either
peptide-specific only (II-5E, II-6F, IV-4B, IV-3F, IV-9B, IV-10F,
V-5B and V-4D) or were non-responsive to any antigen tested
(V-10F). These results demonstrate that the peptide sequence
RPLLANDLMLIKLDE (SEQ ID NO: 814; corresponding to a.a. 110-124 of
SEQ ID NO: 525) recognized by the T cell line I-1A, and the peptide
sequences SVSESDTIRSISIAS (SEQ ID NO: 811; corresponding to a.a.
125-139 of SEQ ID NO: 525) and ISIASQCPTAGNSCL (SEQ ID NO: 810;
corresponding to a.a. 135-149 of SEQ ID NO: 525) recognized by the
T cell line II-4C may be naturally processed epitopes of the P703P
protein.
[1075] In further studies, forty 15-mer peptides overlapping by 10
amino acids and derived spanning amino acids 47 to 254 of P703P
(SEQ ID NO: 525) were generated by standard procedures and their
ability to be recognized by CD4 cells was determined essentially as
described above. DC were prepared from PBMC of a donor having
distinct HLA DR and DQ alleles from that used in previous
experiments. DC were pulsed overnight with pools of the peptides
with each peptide at a final concentration of 0.25 microgram/ml,
and each pool containing 10 peptides. Twelve lines were identified
that demonstrated specific proliferation and cytokine production
(measured in gamma-interferon ELISA assays) in response to the
stimulating peptide pool. These lines were further tested for
specific recognition of the peptide pool, specific recognition of
individual peptides in the pool, and specific recognition of
recombinant P703P protein. Lines 3A5H and 3A9H specifically
proliferated and produced gamma-interferon in response to
recombinant protein and one individual peptide as well as the
peptide pool. Following re-stimulation on targets loaded with the
specific peptide, only 3A9H responded specifically to targets
exposed to lysates of fibroblasts infected adenovirus expressing
full-length P703P. These results indicates that the line 3A9H can
respond to antigenic peptide derived from protein synthesized in
mammalian cells. The peptide to which the specific CD4 line
responded correspond to amino acids 155-170 of P703P (SEQ ID NO:
943). The DNA sequence for this peptide is provided in SEQ ID NO:
942.
Example 11
Expression of a Breast Tumor-Derived Antigen in Prostate
[1076] Isolation of the antigen B305D from breast tumor by
differential display is described in U.S. patent application Ser.
No. 08/700,014, filed Aug. 20, 1996. Several different splice forms
of this antigen were isolated. The determined cDNA sequences for
these splice forms are provided in SEQ ID NO: 366-375, with the
amino acid sequences corresponding to the sequences of SEQ ID NO:
292, 298 and 301-303 being provided in SEQ ID NO: 299-306,
respectively. In further studies, a splice variant of the cDNA
sequence of SEQ ID NO: 366 was isolated which was found to contain
an additional guanine residue at position 884 (SEQ ID NO: 530),
leading to a frameshift in the open reading frame. The determined
DNA sequence of this ORF is provided in SEQ ID NO: 531. This
frameshift generates a protein sequence (provided in SEQ ID NO:
532) of 293 amino acids that contains the C-terminal domain common
to the other isoforms of B305D but that differs in the N-terminal
region.
[1077] The expression levels of B305D in a variety of tumor and
normal tissues were examined by real time PCR and by Northern
analysis. The results indicated that B305D is highly expressed in
breast tumor, prostate tumor, normal prostate and normal testes,
with expression being low or undetectable in all other tissues
examined (colon tumor, lung tumor, ovary tumor, and normal bone
marrow, colon, kidney, liver, lung, ovary, skin, small intestine,
stomach). Using real-time PCR on a panel of prostate tumors,
expression of B305D in prostate tumors was shown to increase with
increasing Gleason grade, demonstrating that expression of B305D
increases as prostate cancer progresses.
Example 12
Generation of Human CTL In Vitro Using Whole Gene Priming and
Stimulation Techniques with the Prostate-Specific Antigen P501S
[1078] Using in vitro whole-gene priming with P501S-vaccinia
infected DC (see, for example, Yee et al, The Journal of
Immunology, 157(9):4079-86, 1996), human CTL lines were derived
that specifically recognize autologous fibroblasts transduced with
P501S (also known as L1-12), as determined by interferon-.gamma.
ELISPOT analysis as described above. Using a panel of
HLA-mismatched B-LCL lines transduced with P501S, these CTL lines
were shown to be likely restricted to HLAB class I allele.
Specifically, dendritic cells (DC) were 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
were infected overnight with recombinant P501S vaccinia virus at a
multiplicity of infection (M.O.I) of five, and matured overnight by
the addition of 3 .mu.g/ml CD40 ligand. Virus was inactivated by UV
irradiation. CD8+ T cells were isolated using a magnetic bead
system, and priming cultures were initiated using standard culture
techniques. Cultures were restimulated every 7-10 days using
autologous primary fibroblasts retrovirally transduced with P501S
and CD80. Following four stimulation cycles, CD8+ T cell lines were
identified that specifically produced interferon-.gamma. when
stimulated with P501S and CD80-transduced autologous fibroblasts. A
panel of HLA-mismatched B-LCL lines transduced with P501S were
generated to define the restriction allele of the response. By
measuring interferon-.gamma. in an ELISPOT assay, the P501S
specific response was shown to be likely restricted by HLA B
alleles. These results demonstrate that a CD8+ CTL response to
P501S can be elicited.
[1079] To identify the epitope(s) recognized, cDNA encoding P501S
was fragmented by various restriction digests, and sub-cloned into
the retroviral expression vector pBIB-KS. Retroviral supernatants
were generated by transfection of the helper packaging line
Phoenix-Ampho. Supernatants were then used to transduce Jurkat/A2Kb
cells for CTL screening. CTL were screened in IFN-gamma ELISPOT
assays against these A2Kb targets transduced with the "library" of
P501S fragments. Initial positive fragments P501S/H3 and P501S/F2
were sequenced and found to encode amino acids 106-553 and amino
acids 136-547, respectively, of SEQ ID NO: 113. A truncation of H3
was made to encode amino acid residues 106-351 of SEQ ID NO: 113,
which was unable to stimulate the CTL, thus localizing the epitope
to amino acid residues 351-547. Additional fragments encoding amino
acids 1-472 (Fragment A) and amino acids 1-351 (Fragment B) were
also constructed. Fragment A but not Fragment B stimulated the CTL
thus localizing the epitope to amino acid residues 351-472.
Overlapping 20-mer and 18-mer peptides representing this region
were tested by pulsing Jurkat/A2Kb cells versus CTL in an IFN-gamma
assay. Only peptides P501S-369(20) and P501S-369(18) stimulated the
CTL. Nine-mer and 10-mer peptides representing this region were
synthesized and similarly tested. Peptide P501S-370 (SEQ ID NO:
539) was the minimal 9-mer giving a strong response. Peptide
P501S-376 (SEQ ID NO: 540) also gave a weak response, suggesting
that it might represent a cross-reactive epitope.
[1080] In subsequent studies, the ability of primary human B cells
transduced with P501S to prime MHC class I-restricted,
P501S-specific, autologous CD8 T cells was examined. Primary B
cells were derived from PBMC of a homozygous HLA-A2 donor by
culture in CD40 ligand and IL-4, transduced at high frequency with
recombinant P501S in the vector pBIB, and selected with
blastocidin-S. For in vitro priming, purified CD8+ T cells were
cultured with autologous CD40 ligand+IL-4 derived, P501S-transduced
B cells in a 96-well microculture format. These CTL microcultures
were re-stimulated with P501S-transduced B cells and then assayed
for specificity. Following this initial screen, microcultures with
significant signal above background were cloned on autologous
EBV-transformed B cells (BLCL), also transduced with P501S. Using
IFN-gamma ELISPOT for detection, several of these CD8 T cell clones
were found to be specific for P501S, as demonstrated by reactivity
to BLCL/P501S but not BLCL transduced with control antigen. It was
further demonstrated that the anti-P501S CD8 T cell specificity is
HLA-A2-restricted. First, antibody blocking experiments with
anti-HLA-A,B,C monoclonal antibody (W6.32), anti-HLA-B,C monoclonal
antibody (B1.23.2) and a control monoclonal antibody showed that
only the anti-HLA-A,B,C antibody blocked recognition of
P501S-expressing autologous BLCL. Secondly, the anti-P501S CTL also
recognized an HLA-A2 matched, heterologous BLCL transduced with
P501S, but not the corresponding EGFP transduced control BLCL.
[1081] A naturally processed, CD8, class I-restricted peptide
epitope of P501S was identified as follows. Dendritic cells (DC)
were isolated by Percol gradient followed by differential
adherence, and cultured for 5 days in the presence of RPMI medium
containing 1% human serum, 50 ng/ml GM-CSF and 30 ng/ml IL-4.
Following culture, DC were infected for 24 hours with
P501S-expressing adenovirus at an MOI of 10 and matured for an
additional 24 hours by the addition of 2 ug/ml CD40 ligand. CD8
cells were enriched for by the subtraction of CD4+, CD14+ and CD16+
populations from PBMC with magnetic beads. Priming cultures
containing 10,000 P501S-expressing DC and 100,000 CD8+ T cells per
well were set up in 96-well V-bottom plates with RPMI containing
10% human serum, 5 ng/ml IL-12 and 10 ng/ml IL-6. Cultures were
stimulated every 7 days using autologous fibroblasts retrovirally
transduced to express P501S and CD80, and were treated with
IFN-gamma for 48-72 hours to upregulate MHC Class I expression. 10
u/ml IL-2 was added at the time of stimulation and on days 2 and 5
following stimulation. Following 4 stimulation cycles, one
P501S-specific CD8+ T cell line (referred to as 2A2) was identified
that produced IFN-gamma in response to IFN-gamma-treated P501S/CD80
expressing autologous fibroblasts, but not in response to
IFN-gamma-treated P703P/CD80 expressing autologous fibroblasts in a
.gamma.-IFN Elispot assay. Line 2A2 was cloned in 96-well plates
with 0.5 cell/well or 2 cells/well in the presence of 75,000
PBMC/well, 10,000 B-LCL/well, 30 ng/ml OKT3 and 50u/ml IL-2. Twelve
clones were isolated that showed strong P501S specificity in
response to transduced fibroblasts.
[1082] Fluorescence activated cell sorting (FACS) analysis was
performed on P501S-specific clones using CD3-, CD4- and
CD8-specific antibodies conjugated to PercP, FITC and PE
respectively. Consistent with the use of CD8 enriched T cells in
the priming cultures, P5401S-specific clones were determined to be
CD3+, CD8+ and CD4-.
[1083] To identify the relevant P501S epitope recognized by P501S
specific CTL, pools of 18-20 mer or 30-mer peptides that spanned
the majority of the amino acid sequence of P501S were loaded onto
autologous B-LCL and tested in .gamma.-IFN Elispot assays for the
ability to stimulate two P501S-specific CTL clones, referred to as
4E5 and 4E7. One pool, composed of five 18-20 mer peptides that
spanned amino acids 411-486 of P501S (SEQ ID NO: 113), was found to
be recognized by both P501S-specific clones. To identify the
specific 18-20 mer peptide recognized by the clones, each of the
18-20 mer peptides that comprised the positive pool were tested
individually in .gamma.-IFN Elispot assays for the ability to
stimulate the two P501S-specific CTL clones, 4E5 and 4E7. Both 4E5
and 4E7 specifically recognized one 20-mer peptide (SEQ ID NO: 853;
cDNA sequence provided in SEQ ID NO: 854) that spanned amino acids
453-472 of P501S. Since the minimal epitope recognized by CD8+ T
cells is almost always either a 9 or 10-mer peptide sequence,
10-mer peptides that spanned the entire sequence of SEQ ID NO: 853
were synthesized that differed by 1 amino acid. Each of these
10-mer peptides was tested for the ability to stimulate two
P501S-specific clones, (referred to as 1D5 and 1E12). One 10-mer
peptide (SEQ ID NO: 855; cDNA sequence provided in SEQ ID NO: 856)
was identified that specifically stimulated the P501S-specific
clones. This epitope spans amino acids 463-472 of P501S. This
sequence defines a minimal 10-mer epitope from P501S that can be
naturally processed and to which CTL responses can be identified in
normal PBMC. Thus, this epitope is a candidate for use as a vaccine
moiety, and as a therapeutic and/or diagnostic reagent for prostate
cancer.
[1084] To identify the class I restriction element for the
P501S-derived sequence of SEQ ID NO: 855, HLA blocking and mismatch
analyses were performed. In .gamma.-IFN Elispot assays, the
specific response of clones 4A7 and 4E5 to P501S-transduced
autologous fibroblasts was blocked by pre-incubation with 25 ug/ml
W6/32 (pan-Class I blocking antibody) and B1.23.2 (HLA-B/C blocking
antibody). These results demonstrate that the SEQ ID NO:
855-specific response is restricted to an HLA-B or HLA-C
allele.
[1085] For the HLA mismatch analysis, autologous B-LCL (HLA-A1, A2,
B8, B51, Cw1, Cw7) and heterologous B-LCL (HLA-A2, A3, B18, B51,
Cw5, Cw14) that share the HLAB51 allele were pulsed for one hour
with 20 ug/ml of peptide of SEQ ID NO: 855, washed, and tested in
.gamma.-IFN Elispot assays for the ability to stimulate clones 4A7
and 4E5. Antibody blocking assays with the B1.23.2 (HLA-B/C
blocking antibody) were also performed. SEQ ID NO: 855-specific
response was detected using both the autologous (D326) and
heterologous (D107) B-LCL, and furthermore the responses were
blocked by pre-incubation with 25 ug/ml of B1.23.2 HLA-B/C blocking
antibody. Together these results demonstrate that the
P501S-specific response to the peptide of SEQ ID NO: 855 is
restricted to the HLA-B51 class I allele. Molecular cloning and
sequence analysis of the HLA-B51 allele from D326 revealed that the
HLA-B51 subtype of D326 is HLA-B51011.
[1086] Based on the 10-mer P501S-derived epitope of SEQ ID NO: 855,
two 9-mers with the sequences of SEQ ID NO: 857 and 858 were
synthesized and tested in Elispot assays for the ability to
stimulate two P501S-specific CTL clones derived from line 2A2. The
10-mer peptide of SEQ ID NO: 855, as well as the 9-mer peptide of
SEQ ID NO: 858, but not the 9-mer peptide of SEQ ID NO: 857, were
capable of stimulating the P501S-specific CTL to produce IFN-gamma.
These results demonstrate that the peptide of SEQ ID NO: 858 is a
9-mer P501S-derived epitope recognized by P501S-specific CTL. The
DNA sequence encoding the epitope of SEQ ID NO: 858 is provided in
SEQ ID NO: 859.
[1087] To identify the class I restricting allele for the
P501S-derived peptide of SEQ ID NO: 855 and 858 specific response,
each of the HLA B and C alleles were cloned from the donor used in
the in vitro priming experiment. Sequence analysis indicated that
the relevant alleles were HLA-B8, HLA-B51, HLA-Cw01 and HLA-Cw07.
Each of these alleles were subcloned into an expression vector and
co-transfected together with the P501S gene into VA-13 cells.
Transfected VA-13 cells were then tested for the ability to
specifically stimulate the P501S-specific CTL in ELISPOT assays.
VA-13 cells transfected with P501S and HLA-B51 were capable of
stimulating the P501S-specific CTL to secrete gamma-IFN. VA-13
cells transfected with HLA-B51 alone or P501S+ the other
HLA-alleles were not capable of stimulating the P501S-specific CTL.
These results demonstrate that the restricting allele for the
P501S-specific response is the HLAB51 allele. Sequence analysis
revealed that the subtype of the relevant restricting allele is
HLA-B51011.
[1088] To determine if the P501S-specific CTL could recognize
prostate tumor cells that express P501S, the P501S-positive lines
LnCAP and CRL2422 (both expressing "moderate" amounts of P501S mRNA
and protein), and PC-3 (expressing low amounts of P501S mRNA and
protein), plus the P501S-negative cell line DU-145 were
retrovirally transduced with the HLA-B51011 allele that was cloned
from the donor used to generate the P501S-specific CTL. HLA-B51011-
or EGFP-transduced and selected tumor cells were treated with
gamma-interferon and androgen (to upregulate stimulatory functions
and P501S, respectively) and used in gamma-interferon Elispot
assays with the P501S-specific CTL clones 4E5 and 4E7. Untreated
cells were used as a control.
[1089] Both 4E5 and 4E7 efficiently and specifically recognized
LnCAP and CRL2422 cells that were transduced with the HLA-B51011
allele, but not the same cell lines transduced with EGFP.
Additionally, both CTL clones specifically recognized PC-3 cells
transduced with HLA-B51011, but not the P501S-negative tumor cell
line DU-145. Treatment with gamma-interferon or androgen did not
enhance the ability of CTL to recognize tumor cells. These results
demonstrate that P501S-specific CTL, generated by in vitro whole
gene priming, specifically and efficiently recognize prostate tumor
cell lines that express P501S.
[1090] A naturally processed CD4 epitope of P501S was identified as
follows.
[1091] CD4 cells specific for P501S were prepared as described
above. A series of 16 overlapping peptides were synthesized that
spanned approximately 50% of the amino terminal portion of the
P501S gene (amino acids 1-325 of SEQ ID NO: 113). For priming,
peptides were combined into pools of 4 peptides, pulsed at 4
.mu.g/ml onto dendritic cells (DC) for 24 hours, with TNF-alpha. DC
were then washed and mixed with negatively selected CD4+ T cells in
96 well U-bottom plates. Cultures were re-stimulated weekly on
fresh DC loaded with peptide pools. Following a total of 4
stimulation cycles, cells were rested for an additional week and
tested for specificity to APC pulsed with peptide pools using
.gamma.-IFN ELISA and proliferation assays. For these assays,
adherent monocytes loaded with either the relevant peptide pool at
4 ug/ml or an irrelevant peptide at .mu.g/ml were used as APC. T
cell lines that demonstrated either specific cytokine secretion or
proliferation were then tested for recognition of individual
peptides that were present in the pool. T cell lines could be
identified from pools A and B that recognized individual peptides
from these pools.
[1092] From pool A, lines AD9 and AE10 specifically recognized
peptide 1 (SEQ ID NO: 862), and line AF5 recognized peptide 39 (SEQ
ID NO: 861). From pool B, line BC6 could be identified that
recognized peptide 58 (SEQ ID NO: 860). Each of these lines were
stimulated on the specific peptide and tested for specific
recognition of the peptide in a titration assay as well as cell
lysates generated by infection of HEK 293 cells with adenovirus
expressing either P501S or an irrelevant antigen. For these assays,
APC-adherent monocytes were pulsed with either 10, 1, or 0.1
.mu.g/ml individual P501S peptides, and DC were pulsed overnight
with a 1:5 dilution of adenovirally infected cell lysates. Lines
AD9, AE10 and AF5 retained significant recognition of the relevant
P501S-derived peptides even at 0.1 mg/ml. Furthermore, line AD9
demonstrated significant (8.1 fold stimulation index) specific
activity for lysates from adenovirus-P501S infected cells. These
results demonstrate that high affinity CD4 T cell lines can be
generated toward P501S-derived epitopes, and that at least a subset
of these T cells specific for the P501S derived sequence of SEQ ID
NO: 862 are specific for an epitope that is naturally processed by
human cells. The DNA sequences encoding the amino acid sequences of
SEQ ID NO: 860-862 are provided in SEQ ID NO: 863-865,
respectively.
[1093] To further characterize the P501S-specific activity of AD9,
the line was cloned using anti-CD3. Three clones, referred to as
1A1, 1A9 and 1F5, were identified that were specific for the
P501S-1 peptide (SEQ ID NO: 862). To determine the HLA restriction
allele for the P501S-specific response, each of these clones was
tested in class II antibody blocking and HLA mismatch assays using
proliferation and gamma-interferon assays. In antibody blocking
assays and measuring gamma-interferon production using ELISA
assays, the ability of all three clones to recognize peptide pulsed
APC was specifically blocked by co-incubation with either a
pan-class II blocking antibody or a HLA-DR blocking antibody, but
not with a HLA-DQ or an irrelevant antibody. Proliferation assays
performed simultaneously with the same cells confirmed these
results. These data indicate that the P501S-specific response of
the clones is restricted by an HLA-DR allele. Further studies
demonstrated that the restricting allele for the P501S-specific
response is HLA-DRB1501.
Example 13
Identification of Prostate-Specific Antigens by Microarray
Analysis
[1094] This Example describes the isolation of certain
prostate-specific polypeptides from a prostate tumor cDNA
library.
[1095] A human prostate tumor cDNA expression library as described
above was screened using microarray analysis to identify clones
that display at least a three fold over-expression in prostate
tumor and/or normal prostate tissue, as compared to non-prostate
normal tissues (not including testis). 372 clones were identified,
and 319 were successfully sequenced. Table II presents a summary of
these clones, which are shown in SEQ ID NO:385-400. Of these
sequences SEQ ID NO:386, 389, 390 and 392 correspond to novel
genes, and SEQ ID NO: 393 and 396 correspond to previously
identified sequences. The others (SEQ ID NO:385, 387, 388, 391,
394, 395 and 397-400) correspond to known sequences, as shown in
Table II.
TABLE-US-00002 TABLE II SUMMARY OF PROSTATE TUMOR ANTIGENS
Previously Identified Known Genes Genes Novel Genes T-cell gamma
chain P504S 23379 (SEQ ID NO: 389) Kallikrein P1000C 23399 (SEQ ID
NO: 392) Vector P501S 23320 (SEQ ID NO: 386) CGI-82 protein mRNA
(23319; SEQ P503S 23381 (SEQ ID NO: 390) ID NO: 385) PSA P510S Ald.
6 Dehyd. P784P L-iditol-2 dehydrogenase (23376; SEQ P502S ID NO:
388) Ets transcription factor PDEF (22672; P706P SEQ ID NO: 398)
hTGR (22678; SEQ ID NO: 399) 19142.2, bangur.seq (22621; SEQ ID NO:
396) KIAA0295 (22685; SEQ ID NO: 400) 5566.1 Wang (23404; SEQ ID
NO: 393) Prostatic Acid Phosphatase (22655; P712P SEQ ID NO: 397)
transglutaminase (22611; SEQ ID P778P NO: 395) HDLBP (23508; SEQ ID
NO: 394) CGI-69 Protein (23367; SEQ ID NO: 387) KIAA0122 (23383;
SEQ ID NO: 391) TEEG
[1096] Subsequent studies led to the isolation of an extended cDNA
sequence for the clone of SEQ ID NO: 329 (also referred to as
P554S). This extended sequence is provided in SEQ ID NO: 967, with
the corresponding amino acid sequence being provided in SEQ ID NO:
968.
[1097] CGI-82 showed 4.06 fold over-expression in prostate tissues
as compared to other normal tissues tested. It was over-expressed
in 43% of prostate tumors, 25% normal prostate, not detected in
other normal tissues tested. L-iditol-2 dehydrogenase showed 4.94
fold over-expression in prostate tissues as compared to other
normal tissues tested. It was over-expressed in 90% of prostate
tumors, 100% of normal prostate, and not detected in other normal
tissues tested. Ets transcription factor PDEF showed 5.55 fold
over-expression in prostate tissues as compared to other normal
tissues tested. It was over-expressed in 47% prostate tumors, 25%
normal prostate and not detected in other normal tissues tested.
hTGR1 showed 9.11 fold over-expression in prostate tissues as
compared to other normal tissues tested. It was over-expressed in
63% of prostate tumors and is not detected in normal tissues tested
including normal prostate. KIAA0295 showed 5.59 fold
over-expression in prostate tissues as compared to other normal
tissues tested. It was over-expressed in 47% of prostate tumors,
low to undetectable in normal tissues tested including normal
prostate tissues. Prostatic acid phosphatase showed 9.14 fold
over-expression in prostate tissues as compared to other normal
tissues tested. It was over-expressed in 67% of prostate tumors,
50% of normal prostate, and not detected in other normal tissues
tested. Transglutaminase showed 14.84 fold over-expression in
prostate tissues as compared to other normal tissues tested. It was
over-expressed in 30% of prostate tumors, 50% of normal prostate,
and is not detected in other normal tissues tested. High density
lipoprotein binding protein (HDLBP) showed 28.06 fold
over-expression in prostate tissues as compared to other normal
tissues tested. It was over-expressed in 97% of prostate tumors,
75% of normal prostate, and is undetectable in all other normal
tissues tested. CGI-69 showed 3.56 fold over-expression in prostate
tissues as compared to other normal tissues tested. It is a low
abundant gene, detected in more than 90% of prostate tumors, and in
75% normal prostate tissues. The expression of this gene in normal
tissues was very low. KIAA0122 showed 4.24 fold over-expression in
prostate tissues as compared to other normal tissues tested. It was
over-expressed in 57% of prostate tumors, it was undetectable in
all normal tissues tested including normal prostate tissues.
19142.2 bangur showed 23.25 fold over-expression in prostate
tissues as compared to other normal tissues tested. It was
over-expressed in 97% of prostate tumors and 100% of normal
prostate. It was undetectable in other normal tissues tested.
5566.1 Wang showed 3.31 fold over-expression in prostate tissues as
compared to other normal tissues tested. It was over-expressed in
97% of prostate tumors, 75% normal prostate and was also
over-expressed in normal bone marrow, pancreas, and activated PBMC.
Novel clone 23379 (also referred to as P553S) showed 4.86 fold
over-expression in prostate tissues as compared to other normal
tissues tested. It was detectable in 97% of prostate tumors and 75%
normal prostate and is undetectable in all other normal tissues
tested. Novel clone 23399 showed 4.09 fold over-expression in
prostate tissues as compared to other normal tissues tested. It was
over-expressed in 27% of prostate tumors and was undetectable in
all normal tissues tested including normal prostate tissues. Novel
clone 23320 showed 3.15 fold over-expression in prostate tissues as
compared to other normal tissues tested. It was detectable in all
prostate tumors and 50% of normal prostate tissues. It was also
expressed in normal colon and trachea. Other normal tissues do not
express this gene at high level.
[1098] Subsequent full-length cloning studies on P553S, using
standard techniques, revealed that this clone is an incomplete
spliced form of P501S. The determined cDNA sequences for four
splice variants of P553S are provided in SEQ ID NO: 702-705. An
amino acid sequence encoded by SEQ ID NO: 705 is provided in SEQ ID
NO: 706. The cDNA sequence of SEQ ID NO: 702 was found to contain
two open reading frames (ORFs). The amino acid sequences encoded by
these two ORFs are provided in SEQ ID NO: 707 and 708.
Example 14
Identification of Prostate-Specific Antigens by Electronic
Subtraction
[1099] This Example describes the use of an electronic subtraction
technique to identify prostate-specific antigens.
[1100] Potential prostate-specific genes present in the GenBank
human EST database were identified by electronic subtraction
(similar to that described by Vasmatizis et al., Proc. Nat'l Acad.
Sci. USA 95:300-304, 1998). The sequences of EST clones (43,482)
derived from various prostate libraries were obtained from the
GenBank public human EST database. Each prostate EST sequence was
used as a query sequence in a BLASTN (National Center for
Biotechnology Information) search against the human EST database.
All matches considered identical (length of matching sequence
>100 base pairs, density of identical matches over this region
>70%) were grouped (aligned) together in a cluster. Clusters
containing more than 200 ESTs were discarded since they probably
represented repetitive elements or highly expressed genes such as
those for ribosomal proteins. If two or more clusters shared common
ESTs, those clusters were grouped together into a "supercluster,"
resulting in 4,345 prostate superclusters.
[1101] Records for the 479 human cDNA libraries represented in the
GenBank release were downloaded to create a database of these cDNA
library records. These 479 cDNA libraries were grouped into three
groups: Plus (normal prostate and prostate tumor libraries, and
breast cell line libraries, in which expression was desired), Minus
(libraries from other normal adult tissues, in which expression was
not desirable), and Other (libraries from fetal tissue, infant
tissue, tissues found only in women, non-prostate tumors and cell
lines other than prostate cell lines, in which expression was
considered to be irrelevant). A summary of these library groups is
presented in Table III.
TABLE-US-00003 TABLE III PROSTATE cDNA LIBRARIES AND ESTs Library #
of Libraries # of ESTs Plus 25 43,482 Normal 11 18,875 Tumor 11
21,769 Cell lines 3 2,838 Minus 166 Other 287
[1102] Each supercluster was analyzed in terms of the ESTs within
the supercluster. The tissue source of each EST clone was noted and
used to classify the superclusters into four groups: Type 1-EST
clones found in the Plus group libraries only; no expression
detected in Minus or Other group libraries; Type 2-EST clones
derived from the Plus and Other group libraries only; no expression
detected in the Minus group; Type 3-EST clones derived from the
Plus, Minus and Other group libraries, but the number of ESTs
derived from the Plus group is higher than in either the Minus or
Other groups; and Type 4-EST clones derived from Plus, Minus and
Other group libraries, but the number derived from the Plus group
is higher than the number derived from the Minus group. This
analysis identified 4,345 breast clusters (see Table IV). From
these clusters, 3,172 EST clones were ordered from Research
Genetics, Inc., and were received as frozen glycerol stocks in
96-well plates.
TABLE-US-00004 TABLE IV PROSTATE CLUSTER SUMMARY # of # of ESTs
Type Superclusters Ordered 1 688 677 2 2899 2484 3 85 11 4 673 0
Total 4345 3172
[1103] The EST clone inserts were PCR-amplified using amino-linked
PCR primers for Synteni microarray analysis. When more than one PCR
product was obtained for a particular clone, that PCR product was
not used for expression analysis. In total, 2,528 clones from the
electronic subtraction method were analyzed by microarray analysis
to identify electronic subtraction breast clones that had high
levels of tumor vs. normal tissue mRNA. Such screens were performed
using a Synteni (Palo Alto, Calif.) microarray, according to the
manufacturer's instructions (and essentially as described by Schena
et al., Proc. Nat'l Acad. Sci. USA 93:10614-10619, 1996 and Heller
et al., Proc. Nat'l Acad. Sci. USA 94:2150-2155, 1997). Within
these analyses, the clones were arrayed on the chip, which was then
probed with fluorescent probes generated from normal and tumor
prostate cDNA, as well as various other normal tissues. The slides
were scanned and the fluorescence intensity was measured.
[1104] Clones with an expression ratio greater than 3 (i.e., the
level in prostate tumor and normal prostate mRNA was at least three
times the level in other normal tissue mRNA) were identified as
prostate tumor-specific sequences (Table V). The sequences of these
clones are provided in SEQ ID NO: 401-453, with certain novel
sequences shown in SEQ ID NO: 407, 413, 416-419, 422, 426, 427 and
450.
TABLE-US-00005 TABLE V PROSTATE-TUMOR SPECIFIC CLONES Sequence SEQ
ID NO. Designation Comments 401 22545 previously identified P1000C
402 22547 previously identified P704P 403 22548 known 404 22550
known 405 22551 PSA 406 22552 prostate secretory protein 94 407
22553 novel 408 22558 previously identified P509S 409 22562
glandular kallikrein 410 22565 previously identified P1000C 411
22567 PAP 412 22568 B1006C (breast tumor antigen) 413 22570 novel
414 22571 PSA 415 22572 previously identified P706P 416 22573 novel
417 22574 novel 418 22575 novel 419 22580 novel 420 22581 PAP 421
22582 prostatic secretory protein 94 422 22583 novel 423 22584
prostatic secretory protein 94 424 22585 prostatic secretory
protein 94 425 22586 known 426 22587 novel 427 22588 novel 428
22589 PAP 429 22590 known 430 22591 PSA 431 22592 known 432 22593
Previously identified P777P 433 22594 T cell receptor gamma chain
434 22595 Previously identified P705P 435 22596 Previously
identified P707P 436 22847 PAP 437 22848 known 438 22849 prostatic
secretory protein 57 439 22851 PAP 440 22852 PAP 441 22853 PAP 442
22854 previously identified P509S 443 22855 previously identified
P705P 444 22856 previously identified P774P 445 22857 PSA 446 23601
previously identified P777P 447 23602 PSA 448 23605 PSA 449 23606
PSA 450 23612 novel 451 23614 PSA 452 23618 previously identified
P1000C 453 23622 previously identified P705P
[1105] Further studies on the clone of SEQ ID NO: 407 (also
referred to as P1020C) led to the isolation of an extended cDNA
sequence provided in SEQ ID NO: 591. This extended cDNA sequence
was found to contain an open reading frame that encodes the amino
acid sequence of SEQ ID NO: 592. The P1020C cDNA and amino acid
sequences were found to show some similarity to the human
endogenous retroviral HERV-K pol gene and protein.
Example 15
Further Identification of Prostate-Specific Antigens by Microarray
Analysis
[1106] This Example describes the isolation of additional
prostate-specific polypeptides from a prostate tumor cDNA
library.
[1107] A human prostate tumor cDNA expression library as described
above was screened using microarray analysis to identify clones
that display at least a three fold over-expression in prostate
tumor and/or normal prostate tissue, as compared to non-prostate
normal tissues (not including testis). 142 clones were identified
and sequenced. Certain of these clones are shown in SEQ ID NO:
454-467. Of these sequences, SEQ ID NO: 459-460 represent novel
genes. The others (SEQ ID NO: 454-458 and 461-467) correspond to
known sequences. Comparison of the determined cDNA sequence of SEQ
ID NO: 461 with sequences in the Genbank database using the BLAST
program revealed homology to the previously identified
transmembrane protease serine 2 (TMPRSS2). The full-length cDNA
sequence for this clone is provided in SEQ ID NO: 894, with the
corresponding amino acid sequence being provided in SEQ ID NO: 895.
The cDNA sequence encoding the first 209 amino acids of TMPRSS2 is
provided in SEQ ID NO: 896, with the first 209 amino acids being
provided in SEQ ID NO: 897.
[1108] The sequence of SEQ ID NO: 462 (referred to as P835P) was
found to correspond to the previously identified clone FLJ13518
(Accession AK023643; SEQ ID NO: 917), which had no associated open
reading frame (ORF). This clone was used to search the Geneseq DNA
database and matched a clone previously identified as a G
protein-coupled receptor protein (DNA Geneseq Accession A09351;
amino acid Geneseq Accession Y92365), that is characterized by the
presence of seven transmembrane domains. The sequences of fragments
between these domains are provided in SEQ ID NO: 921-928, with SEQ
ID NO: 921, 923, 925 and 927 representing extracellular domains and
SEQ ID NO: 922, 924, 926 and 928 representing intracellular
domains. SEQ ID NO: 921-928 represent amino acids 1-28, 53-61,
83-103, 124-143, 165-201, 226-238, 263-272 and 297-381,
respectively, of P835P. The full-length cDNA sequence for P835P is
provided in SEQ ID NO: 916. The cDNA sequence of the open reading
frame for P835P, including stop codon, is provided in SEQ ID NO:
918, with the open reading frame without stop codon being provided
in SEQ ID NO: 919 and the corresponding amino acid sequence being
provided in SEQ ID NO: 920.
Example 16
Further Characterization of Prostate-Specific Antigen P710P
[1109] This Example describes the full length cloning of P710P.
[1110] The prostate cDNA library described above was screened with
the P710P fragment described above. One million colonies were
plated on LB/Ampicillin plates. Nylon membrane filters were used to
lift these colonies, and the cDNAs picked up by these filters were
then denatured and cross-linked to the filters by UV light. The
P710P fragment was radiolabeled and used to hybridize with the
filters. Positive cDNA clones were selected and their cDNAs
recovered and sequenced by an automatic Perkin Elmer/Applied
Biosystems Division Sequencer. Four sequences were obtained, and
are presented in SEQ ID NO: 468-471. These sequences appear to
represent different splice variants of the P710P gene. Subsequent
comparison of the cDNA sequences of P710P with those in Genbank
releaved homology to the DD3 gene (Genbank accession numbers
AF103907 & AF103908). The cDNA sequence of DD3 is provided in
SEQ ID NO: 690.
Example 17
Protein Expression of Prostate-Specific Antigens
[1111] This example describes the expression and purification of
prostate-specific antigens in E. Coli baculovirus and mammalian
cells.
a) Expression of P501S in E. coli
[1112] Expression of the full-length form of P501S was attempted by
first cloning P501S without the leader sequence (amino acids 36-553
of SEQ ID NO: 113) downstream of the first 30 amino acids of the M.
tuberculosis antigen Ra12 (SEQ ID NO: 484) in pET17b. Specifically,
P501S DNA was used to perform PCR using the primers AW025 (SEQ ID
NO: 485) and AW003 (SEQ ID NO: 486). AW025 is a sense cloning
primer that contains a HindIII site. AW003 is an antisense cloning
primer that contains an EcoRI site. DNA amplification was performed
using 5 .mu.l 10.times.Pfu buffer, 1120 mM dNTPs, 1 .mu.l each of
the PCR primers at 10 .mu.M concentration, 40 .mu.l water, 1 .mu.l
Pfu DNA polymerase (Stratagene, La Jolla, Calif.) and 1 .mu.l DNA
at 100 ng/.mu.l. Denaturation at 95.degree. C. was performed for 30
sec, followed by 10 cycles of 95.degree. C. for 30 sec, 60.degree.
C. for 1 min and by 72.degree. C. for 3 min. 20 cycles of
95.degree. C. for 30 sec, 65.degree. C. for 1 min and by 72.degree.
C. for 3 min, and lastly by 1 cycle of 72.degree. C. for 10 min.
The PCR product was cloned to Ra12m/pET17b using HindIII and EcoRI.
The sequence of the resulting fusion construct (referred to as
Ra12-P501S-F) was confirmed by DNA sequencing.
[1113] The fusion construct was transformed into BL21 (DE3)pLysE,
pLysS and CodonPlus E. Coli (Stratagene) and grown overnight in LB
broth with kanamycin. The resulting culture was induced with IPTG.
Protein was transferred to PVDF membrane and blocked with 5%
non-fat milk (in PBS-Tween buffer), washed three times and
incubated with mouse anti-His tag antibody (Clontech) for 1 hour.
The membrane was washed 3 times and probed with HRP-Protein A
(Zymed) for 30 min. Finally, the membrane was washed 3 times and
developed with ECL (Amersham). No expression was detected by
Western blot. Similarly, no expression was detected by Western blot
when the Ra12-P501S-F fusion was used for expression in BL21
CodonPlus by CE6 phage (Invitrogen).
[1114] An N-terminal fragment of P501S (amino acids 36-325 of SEQ
ID NO: 113) was cloned down-stream of the first 30 amino acids of
the M. tuberculosis antigen Ra12 in pET17b as follows. P501S DNA
was used to perform PCR using the primers AW025 (SEQ ID NO: 485)
and AW027 (SEQ ID NO: 487). AW027 is an antisense cloning primer
that contains an EcoRI site and a stop codon. DNA amplification was
performed essentially as described above. The resulting PCR product
was cloned to Ra12 in pET17b at the HindIII and EcoRI sites. The
fusion construct (referred to as Ra12-P501S-N) was confirmed by DNA
sequencing.
[1115] The Ra12-P501S-N fusion construct was used for expression in
BL21 (DE3)pLysE, pLysS and CodonPlus, essentially as described
above. Using Western blot analysis, protein bands were observed at
the expected molecular weight of 36 kDa. Some high molecular weight
bands were also observed, probably due to aggregation of the
recombinant protein. No expression was detected by Western blot
when the Ra12-P501S-F fusion was used for expression in
BL21CodonPlus by CE6 phage.
[1116] A fusion construct comprising a C-terminal portion of P501S
(amino acids 257-553 of SEQ ID NO: 113) located down-stream of the
first 30 amino acids of the M. tuberculosis antigen Ra12 (SEQ ID
NO: 484) was prepared as follows. P501S DNA was used to perform PCR
using the primers AW026 (SEQ ID NO: 488) and AW003 (SEQ ID NO:
486). AW026 is a sense cloning primer that contains a HindIII site.
DNA amplification was performed essentially as described above. The
resulting PCR product was cloned to Ra12 in pET17b at the HindIII
and EcoRI sites. The sequence for the fusion construct (referred to
as Ra12-P501S-C) was confirmed.
[1117] The Ra12-P501S-C fusion construct was used for expression in
BL21 (DE3)pLysE, pLysS and CodonPlus, as described above. A small
amount of protein was detected by Western blot, with some molecular
weight aggregates also being observed. Expression was also detected
by Western blot when the Ra12-P501S-C fusion was used for
expression in BL21 CodonPlus induced by CE6 phage.
[1118] A fusion construct comprising a fragment of P501S (amino
acids 36-298 of SEQ ID NO: 113) located down-stream of the M.
tuberculosis antigen Ra12 (SEQ ID NO: 848) was prepared as follows.
P501S DNA was used to perform PCR using the primers AW042 (SEQ ID
NO: 849) and AW053 (SEQ ID NO: 850). AW042 is a sense cloning
primer that contains a EcoRI site. AW053 is an antisense primer
with stop and Xho I sites. DNA amplification was performed
essentially as described above. The resulting PCR product was
cloned to Ra12 in pET17b at the EcoRI and Xho I sites. The
resulting fusion construct (referred to as Ra12-P501S-E2) was
expressed in B834 (DE3) pLys S E. coli host cells in TB media for 2
h at room temperature. Expressed protein was purified by washing
the inclusion bodies and running on a Ni-NTA column. The purified
protein stayed soluble in buffer containing 20 mM Tris-HCl (pH 8),
100 mM NaCl, 10 mM .beta.-Me and 5% glycerol. The determined cDNA
and amino acid sequences for the expressed fusion protein are
provided in SEQ ID NO: 851 and 852, respectfully.
b) Expression of P501S in Baculovirus
[1119] The Bac-to-Bac baculovirus expression system (BRL Life
Technologies, Inc.) was used to express P501S protein in insect
cells. Full-length P501S (SEQ ID NO: 113) was amplified by PCR and
cloned into the XbaI site of the donor plasmid pFastBacl. The
recombinant bacmid and baculovirus were prepared according to the
manufacturer's instructions. The recombinant baculovirus was
amplified in Sf9 cells and the high titer viral stocks were
utilized to infect High Five cells (Invitrogen) to make the
recombinant protein. The identity of the full-length protein was
confirmed by N-terminal sequencing of the recombinant protein and
by Western blot analysis (FIG. 7). Specifically, 0.6 million High
Five cells in 6-well plates were infected with either the unrelated
control virus BV/ECD_PD (lane 2), with recombinant baculovirus for
P501S at different amounts or MOIs (lanes 4-8), or were uninfected
(lane 3). Cell lysates were run on SDS-PAGE under reducing
conditions and analyzed by Western blot with the anti-P501S
monoclonal antibody P501S-10E3-G4D3 (prepared as described below).
Lane 1 is the biotinylated protein molecular weight marker
(BioLabs).
[1120] The localization of recombinant P501S in the insect cells
was investigated as follows. The insect cells overexpressing P501S
were fractionated into fractions of nucleus, mitochondria, membrane
and cytosol. Equal amounts of protein from each fraction were
analyzed by Western blot with a monoclonal antibody against P501S.
Due to the scheme of fractionation, both nucleus and mitochondria
fractions contain some plasma membrane components. However, the
membrane fraction is basically free from mitochondria and nucleus.
P501S was found to be present in all fractions that contain the
membrane component, suggesting that P501S may be associated with
plasma membrane of the insect cells expressing the recombinant
protein.
c) Expression of P501S in Mammalian Cells
[1121] Full-length P501S (553 amino acids; SEQ ID NO: 113) was
cloned into various mammalian expression vectors, including pCEP4
(Invitrogen), pVR1012 (Vical, San Diego, Calif.) and a modified
form of the retroviral vector pBMN, referred to as pBIB.
Transfection of P501S/pCEP4 and P501S/pVR1012 into HEK293
fibroblasts was carried out using the Fugene transfection reagent
(Boehringer Mannheim). Briefly, 2 ul of Fugene reagent was diluted
into 100 ul of serum-free media and incubated at room temperature
for 5-10 min. This mixture was added to 1 ug of P501S plasmid DNA,
mixed briefly and incubated for 30 minutes at room temperature. The
Fugene/DNA mixture was added to cells and incubated for 24-48
hours. Expression of recombinant P501S in transfected HEK293
fibroblasts was detected by means of Western blot employing a
monoclonal antibody to P501S.
[1122] Transfection of p501S/pCEP4 into CHO-K cells (American Type
Culture Collection, Rockville, Md.) was carried out using
GenePorter transfection reagent (Gene Therapy Systems, San Diego,
Calif.). Briefly, 15 .mu.l of GenePorter was diluted in 500 .mu.l
of serum-free media and incubated at room temperature for 10 min.
The GenePorter/media mixture was added to 2 .mu.g of plasmid DNA
that was diluted in 500 .mu.l of serum-free media, mixed briefly
and incubated for 30 min at room temperature. CHO-K cells were
rinsed in PBS to remove serum proteins, and the GenePorter/DNA mix
was added and incubated for 5 hours. The transfected cells were
then fed an equal volume of 2.times. media and incubated for 24-48
hours.
[1123] FACS analysis of P501S transiently infected CHO-K cells,
demonstrated surface expression of P501S. Expression was detected
using rabbit polyclonal antisera raised against a P501S peptide, as
described below. Flow cytometric analysis was performed using a
FaCScan (Becton Dickinson), and the data were analyzed using the
Cell Quest program.
d) Expression of P703P in Baculovirus
[1124] The cDNA for full-length P703P-DE5 (SEQ ID NO: 326),
together with several flanking restriction sites, was obtained by
digesting the plasmid pCDNA703 with restriction endonucleases Xba I
and Hind III. The resulting restriction fragment (approx. 800 base
pairs) was ligated into the transfer plasmid pFastBacl which was
digested with the same restriction enzymes. The sequence of the
insert was confirmed by DNA sequencing. The recombinant transfer
plasmid pFBP703 was used to make recombinant bacmid DNA and
baculovirus using the Bac-To-Bac Baculovirus expression system (BRL
Life Technologies). High Five cells were infected with the
recombinant virus BVP703, as described above, to obtain recombinant
P703P protein.
e) Expression of P788P in E. Coli
[1125] A truncated, N-terminal portion, of P788P (residues 1-644 of
SEQ ID NO: 777; referred to as P788P-N) fused with a C-terminal
6.times.His Tag was expressed in E. coli as follows. P788P cDNA was
amplified using the primers AW080 and AW081 (SEQ ID NO: 815 and
816). AW080 is a sense cloning primer with an NdeI site. AW081 is
an antisense cloning primer with a XhoI site. The PCR-amplified
P788P, as well as the vector pCRX1, were digested with NdeI and
XhoI. Vector and insert were ligated and transformed into NovaBlue
cells. Colonies were randomly screened for insert and then
sequenced. P788P-N clone #6 was confirmed to be identical to the
designed construct. The expression construct P788P-N #6/pCRX1 was
transformed into E. coli BL21 CodonPlus-RIL competent cells. After
induction, most of the cells grew well, achieving OD600 of greater
than 2.0 after 3 hr. Coomassie stained SDS-PAGE showed an
over-expressed band at about 75 kD. Western blot analysis using a
6.times.HisTag antibody confirmed the band was P788P-N. The
determined cDNA sequence for P788P-N is provided in SEQ ID NO: 817,
with the corresponding amino acid sequence being provided in SEQ ID
NO: 818.
f) Expression of P510S in E. coli
[1126] The P510S protein has 9 potential transmembrane domains and
is predicted to be located at the plasma membrane. The C-terminal
protein of this protein, as well as the predicted third
extracellular domain of P510S were expressed in E. coli as
follows.
[1127] The expression construct referred to as Ra12-P501S-C was
designed to have a 6 HisTag at the N-terminal enc, followed by the
M. tuberculosis antigen Ra12 (SEQ ID NO: 819) and then the
C-terminal portion of P510S (amino residues 1176-1261 of SEQ ID NO:
538). Full-length P510S was used to amplify the P510S-C fragment by
PCR using the primers AW056 and AW057 (SEQ ID NO: 820 and 821,
respectively). AW056 is a sense cloning primer with an EcoRI site.
AW057 is an antisense primer with stop and XhoI sites. The
amplified P501S fragment and Ra12/pCRX1 were digested with EcoRI
and XhoI and then purified. The insert and vector were ligated
together and transformed into NovaBlue. Colonies were randomly
screened for insert and sequences. For protein expression, the
expression construct was transformed into E. coli BL21 (DE3)
CodonPlus-RIL competent cells. A mini-induction screen was
performed to optimize the expression conditions. After induction
the cells grew well, achieving OD 600 nm greater than 2.0 after 3
hours. Coomassie stain SDS-PAGE showed a highly over-expressed band
at approx. 30 kD. Though this is higher than the expected molecular
weight, western blot analysis was positive, showing this band to be
the His tag-containing protein. The optimized culture conditions
are as follows. Dilute overnight culture/daytime culture
(LB+kanamycin+chloramphenicol) into 2xYT (with kanamycin and
chloramphenicol) at a ratio of 25 ml culture to 1 liter 2xYT. Allow
to grow at 37.degree. C. until OD600=0.6. Take an aliquot out as TO
sample. Add 1 mM IPTG and allow to grow at 30.degree. C. for 3
hours. Take out a T3 sample, spin down cells and store at
-80.degree. C. The determined cDNA and amino acid sequences for the
Ra12-P510S-C construct are provided in SEQ ID NO: 822 and 825,
respectively.
[1128] The expression construct P510S-C was designed to have a 5'
added start codon and a glycine (GGA) codon and then the P510S C
terminal fragment followed by the in frame 6.times. histidine tag
and stop codon from the pET28b vector. The cloning strategy is
similar to that used for Ra12-P510S-C, except that the PCR primers
employed were those shown in SEQ ID NO: 828 and 829, respectively
and the NcoI/XhoI cut in pET28b was used. The primer of SEQ ID NO:
828 created a 5' NcoI site and added a start codon. The antisense
primer of SEQ ID NO: 829 creates a XhoI site on P510S C terminal
fragment. Clones were confirmed by sequencing. For protein
expression, the expression construct was transformed into E. coli
BL21 (DE3) CodonPlus-RIL competent cells. An OD600 of greater than
2.0 was obtained 30 hours after induction. Coomassie stained
SDS-PAGE showed an over-expressed band at about 11 kD. Western blot
analysis confirmed that the band was P510S-C, as did N-terminal
protein sequencing. The optimized culture conditions are as
follows: dilute overnight culture/daytime culture
(LB+kanamycin+chloramphenicol) into 2x YT (+kanamycin and
chloramphenicol) at a ratio of 25 mL culture to 1 liter 2x YT, and
allow to grow at 37.degree. C. until an OD 600 of about 0.5 is
reached. Take out an aliquot as TO sample. Add 1 mM IPTG and allow
to grow at 30.degree. C. for 3 hours. Spin down the cells and store
at -80.degree. C. until purification. The determined cDNA and amino
acid sequences for the P510S-C construct are shown in SEQ ID NO:
823 and 826, respectively.
[1129] The predicted third extracellular domain of P510S(P510S-E3;
residues 328-676 of SEQ ID NO: 538) was expressed in E. coli as
follows. The P510S fragment was amplified by PCR using the primers
shown in SEQ ID NO: 830 and 831. The primer of SEQ ID NO: 830 is a
sense primer with an NdeI site for use in ligating into pPDM. The
primer of SEQ ID NO: 831 is an antisense primer with an added XhoI
site for use in ligating into pPDM. The resulting fragment was
cloned to pPDM at the NdeI and XhoI sites. Clones were confirmed by
sequencing. For protein expression, the clone ws transformed into
E. coli BL21 (DE3) CodonPlus-RIL competent cells. After induction,
an OD600 of greater than 2.0 was achieved after 3 hours. Coomassie
stained SDS-PAGE showed an over-expressed band at about 39 kD, and
N-terminal sequencing confirmed the N-terminal to be that of
P510S-E3. Optimized culture conditions are as follows: dilute
overnight culture/daytime culture (LB+kanamycin+chloramphenicol)
into 2x YT (kanamycin and chloramphenicol) at a ratio of 25 ml
culture to 1 liter 2x YT. Allow to grow at 37.degree. C. until OD
600 equals 0.6. Take out an aliquot as TO sample. Add 1 mM IPTG and
allow to grow at 30.degree. C. for 3 hours. Take out a T3 sample,
spin down the cells and store at -80.degree. C. until purification.
The determined cDNA and amino acid sequences for the P501S-E3
construct are provided in SEQ ID NO: 824 and 827, respectively.
g) Expression of P775S in E. Coli
[1130] The antigen P775P contains multiple open reading frames
(ORF). The third ORF, encoding the protein of SEQ ID NO: 483, has
the best emotif score. An expression fusion construct containing
the M. tuberculosis antigen Ra12 (SEQ ID NO: 819) and P775P-ORF3
with an N-terminal 6.times.HisTag was prepared as follows.
P775P-ORF3 was amplified using the sense PCR primers of SEQ ID NO:
832 and the anti-sense PCR primer of SEQ ID NO: 833. The PCR
amplified fragment of P775P and Ra12/pCRX1 were digested with the
restriction enzymes EcoRI and XhoI. Vector and insert were ligated
and then transformed into NovaBlue cells. Colonies were randomly
screened for insert and then sequenced. A clone having the desired
sequence was transformed into E. coli BL21 (DE3) CodonPlus-RIL
competent cells. Two hours after induction, the cell density peaked
at OD600 of approximately 1.8. Coomassie stained SDS-PAGE showed an
over-expressed band at about 31 kD. Western blot using
6.times.HisTag antibody confirmed that the band was
Ra12-P775P-ORF3. The determined cDNA and amino acid sequences for
the fusion construct are provided in SEQ ID NO: 834 and 835,
respectively.
h) Expression of a P703P His Tag Fusion Protein in E. coli
[1131] The cDNA for the coding region of P703P was prepared by PCR
using the primers of SEQ ID NO: 836 and 837. The PCR product was
digested with EcoRI restriction enzyme, gel purified and cloned
into a modified pET28 vector with a His tag in frame, which had
been digested with Eco72I and EcoRI restriction enzymes. The
correct construct was confirmed by DNA sequence analysis and then
transformed into E. coli BL21 (DE3) pLys S expression host cells.
The determined amino acid and cDNA sequences for the expressed
recombinant P703P are provided in SEQ ID NO: 838 and 839,
respectively.
i) Expression of a P705P His Tag Fusion Protein in E. coli
[1132] The cDNA for the coding region of P705P was prepared by PCR
using the primers of SEQ ID NO: 840 and 841. The PCR product was
digested with EcoRI restriction enzyme, gel purified and cloned
into a modified pET28 vector with a His tag in frame, which had
been digested with Eco721I and EcoRI restriction enzymes. The
correct construct was confirmed by DNA sequence analysis and then
transformed into E. coli BL21 (DE3) pLys S and BL21 (DE3) CodonPlus
expression host cells. The determined amino acid and cDNA sequences
for the expressed recombinant P705P are provided in SEQ ID NO: 842
and 843, respectively.
i) Expression of a P711P His Tag Fusion Protein in E. coli
[1133] The cDNA for the coding region of P711P was prepared by PCR
using the primers of SEQ ID NO: 844 and 845. The PCR product was
digested with EcoRI restriction enzyme, gel purified and cloned
into a modified pET28 vector with a His tag in frame, which had
been digested with Eco721I and EcoRI restriction enzymes. The
correct construct was confirmed by DNA sequence analysis and then
transformed into E. coli BL21 (DE3) pLys S and BL21 (DE3) CodonPlus
expression host cells. The determined amino acid and cDNA sequences
for the expressed recombinant P711P are provided in SEQ ID NO: 846
and 847, respectively.
k) Expression of P767P in E. coli
[1134] The full-length coding region of P767P (amino acids 2-374 of
SEQ ID NO: 590) was amplified by PCR using the primers PDM-468 and
PDM-469 (SEQ ID NO: 935 and 936, respectively). DNA amplification
was performed using 10 .mu.l 10.times.Pfu buffer, 1 .mu.l 10 mM
dNTPs, 2 .mu.l each of the PCR primers at 10 .mu.M concentration,
83 .mu.l water, 1.5 .mu.l Pfu DNA polymerase (Stratagene, La Jolla,
Calif.) and 1 .mu.l DNA at 100 ng/.mu.l. Denaturation at 96.degree.
C. was performed for 2 min, followed by 40 cycles of 96.degree. C.
for 20 sec, 66.degree. C. for 15 sec and by 72.degree. C. for 2
min., and lastly by 1 cycle of 72.degree. C. for 4 min. The PCR
product was digested with XhoI and cloned into a modified pET28
vector with a histidine tag in frame on the 5' end that was
digested with Eco721I and XhoI. The construct was confirmed to be
correct through sequence analysis and transformed into E. coli BL21
pLysS and BL21 CodonPlus RP cells. The cDNA coding region for the
recombinant B767P protein is provided in SEQ ID NO: 938, with the
corresponding amino acid sequence being provided in SEQ ID NO: 941.
The full-length P767P did not express at high enough levels for
detection or purification.
[1135] A truncated coding region of P767P (referred to as B767P-B;
amino acids 47-374 of SEQ ID NO: 590) was amplified by PCR using
the primers PDM-573 and PDM-469 (SEQ ID NO: 937 and 936,
respectively) and the PCR conditions described above for
full-length P767P. The PCR product was digested with XhoI and
cloned into the modified pET28 vector that was digested with
Eco721I and XhoI. The construct was confirmed to be correct through
sequence analysis and transformed into E. coli BL21 pLysS and BL21
CodonPlus RP cells. The protein was found to be expressed in the
inclusion body pellet. The coding region for the expressed B767P-B
protein is provided in SEQ ID NO: 939, with the corresponding amino
acid sequence being provided in SEQ ID NO: 940.
l) Expression of P767P in Mammalian Cells
[1136] For recombinant expression in mammalian cells, the full
length P767P cDNA (SEQ ID NO: 587) was subcloned into the mammalian
expression vector pCEP4 (Invitrogen) that was modified to contain a
FLAG epitope tag. This construct was transfected into HEK293 cells
(American Type Culture Collection) using Fugene 6 reagent (Roche).
Briefly, the HEK cells were plated at a density of 100,000 cells/ml
in DMEM (Gibco) containing 10% FBS (Hyclone) and grown overnight.
The following day, 2 ul of Fugene 6 was added to 100 ul of DMEM
containing no FBS and incubated for 15 minutes at room temperature.
The Fugene 6/DMEM mixture was then added to 1 ug of P767P/pCEP4
plasmid DNA and incubated for 15 minutes at room temperature. The
Fugene/DNA mix was then added to the HEK293 cells and incubated for
48-72 hrs at 37.degree. C. with 7% CO.sub.2. Cells were rinsed with
PBS then collected and pelleted by centrifugation.
[1137] P767P expression was detect in transfected HEK293 whole cell
lysates by Western blot analysis using an anti-epitope tag
antibody. Specifically, whole cell lysates were generated by
incubating the cells in Triton-X100 containing lysis buffer for 30
minutes on ice. Lysates were then cleared by centrifugation at
5,000 rpm for 5 minutes at 4.degree. C. Samples were diluted with
SDS-PAGE loading buffer containing beta-mercaptoethanol, then
boiled for 10 minutes prior to loading the SDS-PAGE gel. Protein
was transferred to nitrocellulose and probed using an anti-FLAG
mouse monoclonal antibody (Sigma) at a dilution of 1 ug/ml. The
blot was revealed with a donkey anti-mouse Ig coupled to HRP
followed by incubation in ECL substrate.
[1138] P767P was found to be expressed on the surface of
transfected HEK293 cells by flow cytometry using rabbit anti-P767P
sera as follows. Cells were collected and washed with ice cold
staining buffer (PBS+1% BSA+Azide). Next, the cells were incubated
for 30 minutes on ice with undiluted anti-P767P rabbit polyclonal
sera. The cells were washed 3 times with staining buffer and then
incubated with a 1:100 dilution of a goat anti-rabbit Ig(H+L)-FITC
reagent (Southern Biotechnology) for 30 minutes on ice. Following 3
washes, the cells were resuspended in staining buffer containing
Propidium Iodide (PI), a vital stain that allows for identification
of permeable cells, and analyzed by FACS.
m) Expression of P788P in Mammalian Cells
[1139] For recombinant expression in mammalian cells, the full
length P788P cDNA was subcloned into the mammalian expression
vector pcDNA3.1 (Invitrogen). This construct was transfected into
HEK293 cells (American Type Culture Collection) using Fugene 6
reagent (Roche). Briefly, the HEK cells were plated at a density of
100,000 cells/ml in DMEM (Gibco) containing 10% FBS (Hyclone) and
grown overnight. The following day, 2 ul of Fugene6 was added to
100 ul of DMEM containing no FBS and incubated for 15 minutes at
room temperature. The Fugene6/DMEM mixture was then added to 1 ug
of P788P/pcDNA3.1 plasmid DNA and incubated for 15 minutes at room
temperature. The Fugene/DNA mix was then added to the HEK293 cells
and incubated for 48-72 hrs at 37.degree. C. with 7% CO.sub.2.
Cells were rinsed with PBS then collected and pelleted by
centrifugation.
[1140] P788P expression was detected in transfected HEK293 whole
cell lysates by Western blot analysis using rabbit anti-P788P sera
as probe. Specifically, whole cell lysates were generated by
incubating the cells in Triton-X100 containing lysis buffer for 30
minutes on ice. Lysates were then cleared by centrifugation at
5,000 rpm for 5 minutes at 4.degree. C. Samples were diluted with
SDS-PAGE loading buffer containing beta-mercaptoethanol, then
boiled for 10 minutes prior to loading the SDS-PAGE gel. Protein
was transferred to nitrocellulose and probed using purified
anti-P788P rabbit polyclonal sera at a concentration of 1 ug/ml.
The blot was revealed with a donkey anti-rabbit Ig coupled to HRP
(Jackson ImmunoResearch) followed by incubation in ECL
substrate.
[1141] P788P expression was detected on the surface of transfected
HEK293 cells by flow cytometry using rabbit anti-P788P sera. For
FACS analysis, cells were collected and washed with ice cold
staining buffer (PBS+1% BSA+Azide). Next, the cells were incubated
for 30 minutes on ice with anti-P788P polyclonal sera (10 ug/ml
final concentration). The cells were washed 3 times with staining
buffer and then incubated with a 1:100 dilution of a goat
anti-rabbit Ig(H+L)-FITC reagent (Southern Biotechnology) for 30
minutes on ice. Following 3 washes, the cells were resuspended in
staining buffer containing Propidium Iodide (PI), a vital stain
that allows for identification of permeable cells, and analyzed by
flow cytometry.
Example 18
Preparation and Characterization of Antibodies Against
Prostate-Specific Polypeptides
[1142] a) Preparation and Characterization of Polyclonal Antibodies
against P703P, P504S and P509S
[1143] Polyclonal antibodies against P703P, P504S, P509S, P501S,
P510S-E3, P510S-C, P705P, full-length P703P (referred to as P703
PFL), P711P, P767P, P788P-N, and peptides of P790P and P775P were
prepared as follows. The amino acid sequences of the P790P peptides
(referred to as P790P89, P790P120, P790P163, P790P180, P790P222,
P790P261, P790P287 and P790P307, respectively) are provided in SEQ
ID NO: 949-956, with the amino acid sequences of the P775P peptides
being provided in SEQ ID NO: 957-966.
[1144] Each prostate tumor antigen expressed in an E. coli
recombinant expression system was grown overnight in LB broth with
the appropriate antibiotics at 37.degree. C. in a shaking
incubator. The next morning, 10 ml of the overnight culture was
added to 500 ml to 2x YT plus appropriate antibiotics in a 2
L-baffled Erlenmeyer flask. When the Optical Density (at 560 nm) of
the culture reached 0.4-0.6, the cells were induced with IPTG (1
mM). Four hours after induction with IPTG, the cells were harvested
by centrifugation. The cells were then washed with phosphate
buffered saline and centrifuged again. The supernatant was
discarded and the cells were either frozen for future use or
immediately processed. Twenty ml of lysis buffer was added to the
cell pellets and vortexed. To break open the E. coli cells, this
mixture was then run through the French Press at a pressure of
16,000 psi. The cells were then centrifuged again and the
supernatant and pellet were checked by SDS-PAGE for the
partitioning of the recombinant protein. For proteins that
localized to the cell pellet, the pellet was resuspended in 10 mM
Tris pH 8.0, 1% CHAPS and the inclusion body pellet was washed and
centrifuged again. This procedure was repeated twice more. The
washed inclusion body pellet was solubilized with either 8 M urea
or 6 M guanidine HCl containing 10 mM Tris pH 8.0 plus 10 mM
imidazole. The solubilized protein was added to 5 ml of
nickel-chelate resin (Qiagen) and incubated for 45 min to 1 hour at
room temperature with continuous agitation. After incubation, the
resin and protein mixture were poured through a disposable column
and the flow through was collected. The column was then washed with
10-20 column volumes of the solubilization buffer. The antigen was
then eluted from the column using 8M urea, 10 mM Tris pH 8.0 and
300 mM imidazole and collected in 3 ml fractions. A SDS-PAGE gel
was run to determine which fractions to pool for further
purification.
[1145] As a final purification step, a strong anion exchange resin
such as HiPrepQ (Biorad) was equilibrated with the appropriate
buffer and the pooled fractions from above were loaded onto the
column. Each antigen was eluted off the column with a increasing
salt gradient. Fractions were collected as the column was run and
another SDS-PAGE gel was run to determine which fractions from the
column to pool. The pooled fractions were dialyzed against 10 mM
Tris pH 8.0. The proteins were then vialed after filtration through
a 0.22 micron filter and the antigens were frozen until needed for
immunization.
[1146] The P790P and P775P peptides were synthesized, conjugated to
KLH and frozen until needed for immunization.
[1147] Four hundred micrograms of each prostate antigen or peptide
was combined with 100 micrograms of muramyldipeptide (MDP) and
injected into a rabbit. Every four weeks rabbits were boosted with
100 micrograms of antigen/peptide mixed with an equal volume of
Incomplete Freund's Adjuvant (IFA). Seven days following each
boost, the animal was bled. Sera were generated by incubating the
blood at 4.degree. C. for 12-24 hours followed by
centrifugation.
[1148] Ninety-six well plates were coated with antigen by
incubating with 50 microliters (typically 1 microgram/microliter)
of recombinant protein at 4.degree. C. for 20 hours. 250
microliters of BSA blocking buffer was added to the wells and
incubated at room temperature for 2 hours. Plates were washed 6
times with PBS/0.1% Tween. Rabbit sera was diluted in PBS/0.1%
Tween/0.1% BSA. Fifty microliters of diluted sera was added to each
well and incubated at room temperature for 30 min. Plates were
washed as described above before 50 microliters of goat anti-rabbit
horse radish peroxidase (HRP) at a 1:10000 dilution was added and
incubated at room temperature for 30 min. Plates were again washed
as described above and 100 microliters of TMB microwell peroxidase
substrate was added to each well. Following a 15 min incubation in
the dark at room temperature, the colorimetric reaction was stopped
with 100 microliters of 1N H.sub.2SO.sub.4 and read immediately at
450 nm. All polyclonal antibodies showed immunoreactivity to the
appropriate antigen or peptide.
[1149] In order to determine which tissues express P509S,
immunohistochemistry (IHC) analysis was performed on a diverse
range of tissue sections. Tissue samples were fixed in formalin
solution for 12-24 hrs and embedded in paraffin before being sliced
into 8 micron sections. Steam heat induced epitope retrieval
(SHIER) in 0.1 M sodium citrate buffer (pH 6.0) was used for
optimal staining conditions. Sections were incubated with 10%
serum/PBS for 5 minutes. Primary antibody was added to each section
for 25 minutes at indicated concentrations followed by 25 minute
incubation with either anti-rabbit or anti-mouse biotinylated
antibody. Endogenous peroxidase activity was blocked by three 1.5
minute incubations with hydrogen peroxidase. The avidin biotin
complex/horse radish peroxidase (ABC/HRP) system was used along
with DAB chromogen to visualize antigen expression. Slides were
counterstained with hematoxylin to visualize cell nuclei. P509S
expression was detected in prostate cancer, BPH, colon, and kidney
but not in heart, lung and liver.
b) Preparation and Characterization of Antibodies Against P501S
[1150] A murine monoclonal antibody directed against the
carboxy-terminus of the prostate-specific antigen P501S was
prepared as follows.
[1151] A truncated fragment of P501S (amino acids 355-526 of SEQ ID
NO: 113) was generated and cloned into the pET28b vector (Novagen)
and expressed in E. coli as a thioredoxin fusion protein with a
histidine tag. The trx-P501S fusion protein was purified by nickel
chromatography, digested with thrombin to remove the trx fragment
and further purified by an acid precipitation procedure followed by
reverse phase HPLC.
[1152] Mice were immunized with truncated P501S protein. Serum
bleeds from mice that potentially contained anti-P501S polyclonal
sera were tested for P501S-specific reactivity using ELISA assays
with purified P501S and trx-P501S proteins. Serum bleeds that
appeared to react specifically with P501S were then screened for
P501S reactivity by Western analysis. Mice that contained a
P501S-specific antibody component were sacrificed and spleen cells
were used to generate anti-P501S antibody producing hybridomas
using standard techniques. Hybridoma supernatants were tested for
P501S-specific reactivity initially by ELISA, and subsequently by
FACS analysis of reactivity with P501S transduced cells. Based on
these results, a monoclonal hybridoma referred to as 10E3 was
chosen for further subcloning. A number of subclones were
generated, tested for specific reactivity to P501S using ELISA and
typed for IgG isotype. The results of this analysis are shown below
in Table V. Of the 16 subclones tested, the monoclonal antibody
10E3-G4-D3 was selected for further study.
TABLE-US-00006 TABLE VI ISOTYPE ANALYSIS OF MURINE ANTI-P501S
MONOCLONAL ANTIBODIES Estimated [Ig] in supernatant Hybridoma clone
Isotype (.mu.g/ml) 4D11 IgG1 14.6 1G1 IgG1 0.6 4F6 IgG1 72 4H5 IgG1
13.8 4H5-E12 IgG1 10.7 4H5-EH2 IgG1 9.2 4H5-H2-A10 IgG1 10
4H5-H2-A3 IgG1 12.8 4H5-H2-A10-G6 IgG1 13.6 4H5-H2-B11 IgG1 12.3
10E3 IgG2a 3.4 10E3-D4 IgG2a 3.8 10E3-D4-G3 IgG2a 9.5 10E3-D4-G6
IgG2a 10.4 10E3-E7 IgG2a 6.5 8H12 IgG2a 0.6
[1153] The specificity of 10E3-G4-D3 for P501S was examined by FACS
analysis. Specifically, cells were fixed (2% formaldehyde, 10
minutes), permeabilized (0.1% saponin, 10 minutes) and stained with
10E3-G4-D3 at 0.5-1 .mu.g/ml, followed by incubation with a
secondary, FITC-conjugated goat anti-mouse Ig antibody (Pharmingen,
San Diego, Calif.). Cells were then analyzed for FITC fluorescence
using an Excalibur fluorescence activated cell sorter. For FACS
analysis of transduced cells, B-LCL were retrovirally transduced
with P501S. For analysis of infected cells, B-LCL were infected
with a vaccinia vector that expresses P501S. To demonstrate
specificity in these assays, B-LCL transduced with a different
antigen (P703P) and uninfected B-LCL vectors were utilized.
10E3-G4-D3 was shown to bind with P501S-transduced B-LCL and also
with P501S-infected B-LCL, but not with either uninfected cells or
P703P-transduced cells.
[1154] To determine whether the epitope recognized by 10E3-G4-D3
was found on the surface or in an intracellular compartment of
cells, B-LCL were transduced with P501S or HLA-B8 as a control
antigen and either fixed and permeabilized as described above or
directly stained with 10E3-G4-D3 and analyzed as above. Specific
recognition of P501S by 10E3-G4-D3 was found to require
permeabilization, suggesting that the epitope recognized by this
antibody is intracellular.
[1155] The reactivity of 10E3-G4-D3 with the three prostate tumor
cell lines Lncap, PC-3 and DU-145, which are known to express high,
medium and very low levels of P501S, respectively, was examined by
permeabilizing the cells and treating them as described above.
Higher reactivity of 10E3-G4-D3 was seen with Lncap than with PC-3,
which in turn showed higher reactivity that DU-145. These results
are in agreement with the real time PCR and demonstrate that the
antibody specifically recognizes P501S in these tumor cell lines
and that the epitope recognized in prostate tumor cell lines is
also intracellular.
[1156] Specificity of 10E3-G4-D3 for P501S was also demonstrated by
Western blot analysis. Lysates from the prostate tumor cell lines
Lncap, DU-145 and PC-3, from P501S-transiently transfected HEK293
cells, and from non-transfected HEK293 cells were generated.
Western blot analysis of these lysates with 10E3-G4-D3 revealed a
46 kDa immunoreactive band in Lncap, PC-3 and P501S-transfected HEK
cells, but not in DU-145 cells or non-transfected HEK293 cells.
P501S mRNA expression is consistent with these results since
semi-quantitative PCR analysis revealed that P501S mRNA is
expressed in Lncap, to a lesser but detectable level in PC-3 and
not at all in DU-145 cells. Bacterially expressed and purified
recombinant P501S (referred to as P501SStr2) was recognized by
10E3-G4-D3 (24 kDa), as was full-length P501S that was transiently
expressed in HEK293 cells using either the expression vector VR1012
or pCEP4. Although the predicted molecular weight of P501S is 60.5
kDa, both transfected and "native" P501S run at a slightly lower
mobility due to its hydrophobic nature.
[1157] Immunohistochemical analysis was performed on prostate tumor
and a panel of normal tissue sections (prostate, adrenal, breast,
cervix, colon, duodenum, gall bladder, ileum, kidney, ovary,
pancreas, parotid gland, skeletal muscle, spleen and testis).
Tissue samples were fixed in formalin solution for 24 hours and
embedded in paraffin before being sliced into 10 micron sections.
Tissue sections were permeabilized and incubated with 10E3-G4-D3
antibody for 1 hr. HRP-labeled anti-mouse followed by incubation
with DAB chromogen was used to visualize P501S immunoreactivity.
P501S was found to be highly expressed in both normal prostate and
prostate tumor tissue but was not detected in any of the other
tissues tested.
[1158] To identify the epitope recognized by 10E3-G4-D3, an epitope
mapping approach was pursued. A series of 13 overlapping 20-21 mers
(5 amino acid overlap; SEQ ID NO: 489-501) was synthesized that
spanned the fragment of P501S used to generate 10E3-G4-D3. Flat
bottom 96 well microtiter plates were coated with either the
peptides or the P501S fragment used to immunize mice, at 1
microgram/ml for 2 hours at 37.degree. C. Wells were then aspirated
and blocked with phosphate buffered saline containing 1% (w/v) BSA
for 2 hours at room temperature, and subsequently washed in PBS
containing 0.1% Tween 20 (PBST). Purified antibody 10E3-G4-D3 was
added at 2 fold dilutions (1000 ng-16 ng) in PBST and incubated for
30 minutes at room temperature. This was followed by washing 6
times with PBST and subsequently incubating with HRP-conjugated
donkey anti-mouse IgG (H+L) Affinipure F(ab') fragment (Jackson
Immunoresearch, West Grove, Pa.) at 1:20000 for 30 minutes. Plates
were then washed and incubated for 15 minutes in tetramethyl
benzidine. Reactions were stopped by the addition of 1N sulfuric
acid and plates were read at 450 nm using an ELISA plate reader. As
shown in FIG. 8, reactivity was seen with the peptide of SEQ ID NO:
496 (corresponding to amino acids 439-459 of P501S) and with the
P501S fragment but not with the remaining peptides, demonstrating
that the epitope recognized by 10E3-G4-D3 is localized to amino
acids 439-459 of SEQ ID NO: 113.
[1159] In order to further evaluate the tissue specificity of
P501S, multi-array immunohistochemical analysis was performed on
approximately 4700 different human tissues encompassing all the
major normal organs as well as neoplasias derived from these
tissues. Sixty-five of these human tissue samples were of prostate
origin. Tissue sections 0.6 mm in diameter were formalin-fixed and
paraffin embedded. Samples were pretreated with HIER using 10 mM
citrate buffer pH 6.0 and boiling for 10 min. Sections were stained
with 10E3-G4-D3 and P501S immunoreactivity was visualized with HRP.
All the 65 prostate tissues samples (5 normal, 55 untreated
prostate tumors, 5 hormone refractory prostate tumors) were
positive, showing distinct perinuclear staining. All other tissues
examined were negative for P501S expression.
c) Preparation and Characterization of Antibodies against P503S
[1160] A fragment of P503S (amino acids 113-241 of SEQ ID NO: 114)
was expressed and purified from bacteria essentially as described
above for P501S and used to immunize both rabbits and mice. Mouse
monoclonal antibodies were isolated using standard hybridoma
technology as described above. Rabbit monoclonal antibodies were
isolated using Selected Lymphocyte Antibody Method (SLAM)
technology at Immgenics Pharmaceuticals (Vancouver, BC, Canada).
Table VI, below, lists the monoclonal antibodies that were
developed against P503S.
TABLE-US-00007 TABLE VII Antibody Species 20D4 Rabbit JA1 Rabbit
1A4 Mouse 1C3 Mouse 1C9 Mouse 1D12 Mouse 2A11 Mouse 2H9 Mouse 4H7
Mouse 8A8 Mouse 8D10 Mouse 9C12 Mouse 6D12 Mouse
[1161] The DNA sequences encoding the complementarity determining
regions (CDRs) for the rabbit monoclonal antibodies 20D4 and JA1
were determined and are provided in SEQ ID NO: 502 and 503,
respectively.
[1162] In order to better define the epitope binding region of each
of the antibodies, a series of overlapping peptides were generated
that span amino acids 109-213 of SEQ ID NO: 114. These peptides
were used to epitope map the anti-P503S monoclonal antibodies by
ELISA as follows. The recombinant fragment of P503S that was
employed as the immunogen was used as a positive control.
Ninety-six well microtiter plates were coated with either peptide
or recombinant antigen at 20 ng/well overnight at 4.degree. C.
Plates were aspirated and blocked with phosphate buffered saline
containing 1% (w/v) BSA for 2 hours at room temperature then washed
in PBS containing 0.1% Tween 20 (PBST). Purified rabbit monoclonal
antibodies diluted in PBST were added to the wells and incubated
for 30 min at room temperature. This was followed by washing 6
times with PBST and incubation with Protein-A HRP conjugate at a
1:2000 dilution for a further 30 min. Plates were washed six times
in PBST and incubated with tetramethylbenzidine (TMB) substrate for
a further 15 min. The reaction was stopped by the addition of 1N
sulfuric acid and plates were read at 450 nm using at ELISA plate
reader. ELISA with the mouse monoclonal antibodies was performed
with supernatants from tissue culture run neat in the assay.
[1163] All of the antibodies bound to the recombinant P503S
fragment, with the exception of the negative control SP2
supernatant. 20D4, JA1 and 1D12 bound strictly to peptide #2101
(SEQ ID NO: 504), which corresponds to amino acids 151-169 of SEQ
ID NO: 114. 1C3 bound to peptide #2102 (SEQ ID NO: 505), which
corresponds to amino acids 165-184 of SEQ ID NO: 114. 9C12 bound to
peptide #2099 (SEQ ID NO: 522), which corresponds to amino acids
120-139 of SEQ ID NO: 114. The other antibodies bind to regions
that were not examined in these studies.
[1164] Subsequent to epitope mapping, the antibodies were tested by
FACS analysis on a cell line that stably expressed P503S to confirm
that the antibodies bind to cell surface epitopes. Cells stably
transfected with a control plasmid were employed as a negative
control. Cells were stained live with no fixative. 0.5 ug of
anti-P503S monoclonal antibody was added and cells were incubated
on ice for 30 min before being washed twice and incubated with a
FITC-labelled goat anti-rabbit or mouse secondary antibody for 20
min. After being washed twice, cells were analyzed with an
Excalibur fluorescent activated cell sorter. The monoclonal
antibodies 1C3, 1D12, 9C12, 20D4 and JA1, but not 8D3, were found
to bind to a cell surface epitope of P503S.
[1165] In order to determine which tissues express P503S,
immunohistochemical analysis was performed, essentially as
described above, on a panel of normal tissues (prostate, adrenal,
breast, cervix, colon, duodenum, gall bladder, ileum, kidney,
ovary, pancreas, parotid gland, skeletal muscle, spleen and
testis). HRP-labeled anti-mouse or anti-rabbit antibody followed by
incubation with TMB was used to visualize P503S immunoreactivity.
P503S was found to be highly expressed in prostate tissue, with
lower levels of expression being observed in cervix, colon, ileum
and kidney, and no expression being observed in adrenal, breast,
duodenum, gall bladder, ovary, pancreas, parotid gland, skeletal
muscle, spleen and testis.
[1166] Western blot analysis was used to characterize anti-P503S
monoclonal antibody specificity. SDS-PAGE was performed on
recombinant (rec) P503S expressed in and purified from bacteria and
on lysates from HEK293 cells transfected with full length P503S.
Protein was transferred to nitrocellulose and then Western blotted
with each of the anti-P503S monoclonal antibodies (20D4, JA1, 1D12,
6D12 and 9C12) at an antibody concentration of 1 ug/ml. Protein was
detected using horse radish peroxidase (HRP) conjugated to either a
goat anti-mouse monoclonal antibody or to protein A-sepharose. The
monoclonal antibody 20D4 detected the appropriate molecular weight
14 kDa recombinant P503S (amino acids 113-241) and the 23.5 kDa
species in the HEK293 cell lysates transfected with full length
P503S. Other anti-P503S monoclonal antibodies displayed similar
specificity by Western blot.
d) Preparation and Characterization of Antibodies Against P703P
[1167] Rabbits were immunized with either a truncated (P703Ptr1;
SEQ ID NO: 172) or full-length mature form (P703Pfl; SEQ ID NO:
523) of recombinant P703P protein was expressed in and purified
from bacteria as described above. Affinity purified polyclonal
antibody was generated using immunogen P703Pfl or P703Ptr1 attached
to a solid support. Rabbit monoclonal antibodies were isolated
using SLAM technology at Immgenics Pharmaceuticals. Table VII below
lists both the polyclonal and monoclonal antibodies that were
generated against P703P.
TABLE-US-00008 TABLE VIII Antibody Immunogen Species/type Aff.
Purif. P703P (truncated); P703Ptrl Rabbit polyclonal #2594 Aff.
Purif. P703P (full length); P703Pfl Rabbit polyclonal #9245 2D4
P703Ptrl Rabbit monoclonal 8H2 P703Ptrl Rabbit monoclonal 7H8
P703Ptrl Rabbit monoclonal
[1168] The DNA sequences encoding the complementarity determining
regions (CDRs) for the rabbit monoclonal antibodies 8H2, 7H8 and
2D4 were determined and are provided in SEQ ID NO: 506-508,
respectively.
[1169] Epitope mapping studies were performed as described above.
Monoclonal antibodies 2D4 and 7H8 were found to specifically bind
to the peptides of SEQ ID NO: 509 (corresponding to amino acids
145-159 of SEQ ID NO: 172) and SEQ ID NO: 510 (corresponding to
amino acids 11-25 of SEQ ID NO: 172), respectively. The polyclonal
antibody 2594 was found to bind to the peptides of SEQ ID NO:
511-514, with the polyclonal antibody 9427 binding to the peptides
of SEQ ID NO: 515-517.
[1170] The specificity of the anti-P703P antibodies was determined
by Western blot analysis as follows. SDS-PAGE was performed on (1)
bacterially expressed recombinant antigen; (2) lysates of HEK293
cells and Ltk-/- cells either untransfected or transfected with a
plasmid expressing full length P703P; and (3) supernatant isolated
from these cell cultures. Protein was transferred to nitrocellulose
and then Western blotted using the anti-P703P polyclonal antibody
#2594 at an antibody concentration of 1 ug/ml. Protein was detected
using horse radish peroxidase (HRP) conjugated to an anti-rabbit
antibody. A 35 kDa immunoreactive band could be observed with
recombinant P703P. Recombinant P703P runs at a slightly higher
molecular weight since it is epitope tagged. In lysates and
supernatants from cells transfected with full length P703P, a 30
kDa band corresponding to P703P was observed. To assure
specificity, lysates from HEK293 cells stably transfected with a
control plasmid were also tested and were negative for P703P
expression. Other anti-P703P antibodies showed similar results.
[1171] Immunohistochemical studies were performed as described
above, using anti-P703P monoclonal antibody. P703P was found to be
expressed at high levels in normal prostate and prostate tumor
tissue but was not detectable in all other tissues tested (breast
tumor, lung tumor and normal kidney).
e) Preparation and Characterization of Antibodies Against P504S
[1172] Full-length P504S (SEQ ID NO: 108) was expressed and
purified from bacteria essentially as described above for P501S and
employed to raise rabbit monoclonal antibodies using Selected
Lymphocyte Antibody Method (SLAM) technology at Immgenics
Pharmaceuticals (Vancouver, BC, Canada). The anti-P504S monoclonal
antibody 13H4 was shown by Western blot to bind to both expressed
recombinant P504S and to native P504S in tumor cells.
[1173] Immunohistochemical studies using 13H4 to assess P504S
expression in various prostate tissues were performed as described
above. A total of 104 cases, including 65 cases of radical
prostatectomies with prostate cancer (PC), 26 cases of prostate
biopsies and 13 cases of benign prostate hyperplasia (BPH), were
stained with the anti-P504S monoclonal antibody 13H4. P504S showed
strongly cytoplasmic granular staining in 64/65 (98.5%) of PCs in
prostatectomies and 26/26 (100%) of PCs in prostatic biopsies.
P504S was stained strongly and diffusely in carcinomas (4+ in 91.2%
of cases of PC; 3+ in 5.5%; 2+ in 2.2% and 1+ in 1.1%) and high
grade prostatic intraepithelial neoplasia (4+ in all cases). The
expression of P504S did not vary with Gleason score. Only 17/91
(18.7%) of cases of NP/BPH around PC and 2/13 (15.4%) of BPH cases
were focally (1+, no 2+ to 4+ in all cases) and weakly positive for
P504S in large glands. Expression of P504S was not found in small
atrophic glands, postatrophic hyperplasia, basal cell hyperplasia
and transitional cell metaplasia in either biopsies or
prostatectomies. P504S was thus found to be over-expressed in all
Gleason scores of prostate cancer (98.5 to 100% of sensitivity) and
exhibited only focal positivities in large normal glands in 19/104
of cases (82.3% of specificity). These findings indicate that P504S
may be usefully employed for the diagnosis of prostate cancer.
Example 19
Characterization of Cell Surface Expression and Chromosome
Localization of the Prostate-Specific Antigen P501S
[1174] This example describes studies demonstrating that the
prostate-specific antigen P501S is expressed on the surface of
cells, together with studies to determine the probable chromosomal
location of P501S.
[1175] The protein P501S (SEQ ID NO: 113) is predicted to have 11
transmembrane domains. Based on the discovery that the epitope
recognized by the anti-P501S monoclonal antibody 10E3-G4-D3
(described above in Example 17) is intracellular, it was predicted
that following transmembrane determinants would allow the
prediction of extracellular domains of P501S. FIG. 9 is a schematic
representation of the P501S protein showing the predicted location
of the transmembrane domains and the intracellular epitope
described in Example 17. Underlined sequence represents the
predicted transmembrane domains, bold sequence represents the
predicted extracellular domains, and italicized sequence represents
the predicted intracellular domains. Sequence that is both bold and
underlined represents sequence employed to generate polyclonal
rabbit serum. The location of the transmembrane domains was
predicted using HHMTOP as described by Tusnady and Simon
(Principles Governing Amino Acid Composition of Integral Membrane
Proteins: Applications to Topology Prediction, J. Mol. Biol.
283:489-506, 1998).
[1176] Based on FIG. 9, the P501S domain flanked by the
transmembrane domains corresponding to amino acids 274-295 and
323-342 is predicted to be extracellular. The peptide of SEQ ID NO:
518 corresponds to amino acids 306-320 of P501S and lies in the
predicted extracellular domain. The peptide of SEQ ID NO: 519,
which is identical to the peptide of SEQ ID NO: 518 with the
exception of the substitution of the histidine with an asparginine,
was synthesized as described above. A Cys-Gly was added to the
C-terminus of the peptide to facilitate conjugation to the carrier
protein. Cleavage of the peptide from the solid support was carried
out using the following cleavage mixture: trifluoroacetic
acid:ethanediol:thioanisol:water:phenol (40:1:2:2:3). After
cleaving for two hours, the peptide was precipitated in cold ether.
The peptide pellet was then dissolved in 10% v/v acetic acid and
lyophilized prior to purification by C18 reverse phase hplc. A
gradient of 5-60% acetonitrile (containing 0.05% TFA) in water
(containing 0.05% TFA) was used to elute the peptide. The purity of
the peptide was verified by hplc and mass spectrometry, and was
determined to be >95%. The purified peptide was used to generate
rabbit polyclonal antisera as described above.
[1177] Surface expression of P501S was examined by FACS analysis.
Cells were stained with the polyclonal anti-P501S peptide serum at
10 .mu.g/ml, washed, incubated with a secondary FITC-conjugated
goat anti-rabbit Ig antibody (ICN), washed and analyzed for FITC
fluorescence using an Excalibur fluorescence activated cell sorter.
For FACS analysis of transduced cells, B-LCL were retrovirally
transduced with P501S. To demonstrate specificity in these assays,
B-LCL transduced with an irrelevant antigen (P703P) or
nontransduced were stained in parallel. For FACS analysis of
prostate tumor cell lines, Lncap, PC-3 and DU-145 were utilized.
Prostate tumor cell lines were dissociated from tissue culture
plates using cell dissociation medium and stained as above. All
samples were treated with propidium iodide (PI) prior to FACS
analysis, and data was obtained from PI-excluding (i.e., intact and
non-permeabilized) cells. The rabbit polyclonal serum generated
against the peptide of SEQ ID NO: 519 was shown to specifically
recognize the surface of cells transduced to express P501S,
demonstrating that the epitope recognized by the polyclonal serum
is extracellular.
[1178] To determine biochemically if P501S is expressed on the cell
surface, peripheral membranes from Lncap cells were isolated and
subjected to Western blot analysis. Specifically, Lncap cells were
lysed using a dounce homogenizer in 5 ml of homogenization buffer
(250 mM sucrose, 10 mM HEPES, 1 mM EDTA, pH 8.0, 1 complete
protease inhibitor tablet (Boehringer Mannheim)). Lysate samples
were spun at 1000 g for 5 min at 4.degree. C. The supernatant was
then spun at 8000 g for 10 min at 4.degree. C. Supernatant from the
8000 g spin was recovered and subjected to a 100,000 g spin for 30
min at 4.degree. C. to recover peripheral membrane. Samples were
then separated by SDS-PAGE and Western blotted with the mouse
monoclonal antibody 10E3-G4-D3 (described above in Example 17)
using conditions described above. Recombinant purified P501S, as
well as HEK293 cells transfected with and over-expressing P501S
were included as positive controls for P501S detection. LCL cell
lysate was included as a negative control. P501S could be detected
in Lncap total cell lysate, the 8000 g (internal membrane) fraction
and also in the 100,000 g (plasma membrane) fraction. These results
indicate that P501S is expressed at, and localizes to, the
peripheral membrane.
[1179] To demonstrate that the rabbit polyclonal antiserum
generated to the peptide of SEQ ID NO: 519 specifically recognizes
this peptide as well as the corresponding native peptide of SEQ ID
NO: 518, ELISA analyses were performed. For these analyses,
flat-bottomed 96 well microtiter plates were coated with either the
peptide of SEQ ID NO: 519, the longer peptide of SEQ ID NO: 520
that spans the entire predicted extracellular domain, the peptide
of SEQ ID NO: 521 which represents the epitope recognized by the
P501S-specific antibody 10E3-G4-D3, or a P501S fragment
(corresponding to amino acids 355-526 of SEQ ID NO: 113) that does
not include the immunizing peptide sequence, at 1 .mu.g/ml for 2
hours at 37.degree. C. Wells were aspirated, blocked with phosphate
buffered saline containing 1% (w/v) BSA for 2 hours at room
temperature and subsequently washed in PBS containing 0.1% Tween 20
(PBST). Purified anti-P501S polyclonal rabbit serum was added at 2
fold dilutions (1000 ng-125 ng) in PBST and incubated for 30 min at
room temperature. This was followed by washing 6 times with PBST
and incubating with HRP-conjugated goat anti-rabbit IgG (H+L)
Affinipure F(ab') fragment at 1:20000 for 30 min. Plates were then
washed and incubated for 15 min in tetramethyl benzidine. Reactions
were stopped by the addition of 1N sulfuric acid and plates were
read at 450 nm using an ELISA plate reader. As shown in FIG. 11,
the anti-P501S polyclonal rabbit serum specifically recognized the
peptide of SEQ ID NO: 519 used in the immunization as well as the
longer peptide of SEQ ID NO: 520, but did not recognize the
irrelevant P501S-derived peptides and fragments.
[1180] In further studies, rabbits were immunized with peptides
derived from the P501S sequence and predicted to be either
extracellular or intracellular, as shown in FIG. 9. Polyclonal
rabbit sera were isolated and polyclonal antibodies in the serum
were purified, as described above. To determine specific reactivity
with P501S, FACS analysis was employed, utilizing either B-LCL
transduced with P501S or the irrelevant antigen P703P, of B-LCL
infected with vaccinia virus-expressing P501S. For surface
expression, dead and non-intact cells were excluded from the
analysis as described above. For intracellular staining, cells were
fixed and permeabilized as described above. Rabbit polyclonal serum
generated against the peptide of SEQ ID NO: 548, which corresponds
to amino acids 181-198 of P501S, was found to recognize a surface
epitope of P501S. Rabbit polyclonal serum generated against the
peptide SEQ ID NO: 551, which corresponds to amino acids 543-553 of
P501S, was found to recognize an epitope that was either
potentially extracellular or intracellular since in different
experiments intact or permeabilized cells were recognized by the
polyclonal sera. Based on similar deductive reasoning, the
sequences of SEQ ID NO: 541-547, 549 and 550, which correspond to
amino acids 109-122, 539-553, 509-520, 37-54, 342-359, 295-323,
217-274, 143-160 and 75-88, respectively, of P501S, can be
considered to be potential surface epitopes of P501S recognized by
antibodies.
[1181] In further studies, mouse monoclonal antibodies were raised
against amino acids 296 to 322 to P501S, which are predicted to be
in an extracellular domain. A/J mice were immunized with
P501S/adenovirus, followed by subsequent boosts with an E. coli
recombinant protein, referred to as P501N, that contains amino
acids 296 to 322 of P501S, and with peptide 296-322 (SEQ ID NO:
898) coupled with KLH. The mice were subsequently used for splenic
B cell fusions to generate anti-peptide hybridomas. The resulting 3
clones, referred to as 4F4 (IgG1,kappa), 4G5 (IgG2a,kappa) and 9B9
(IgG1,kappa), were grown for antibody production. The 4G5 mAb was
purified by passing the supernatant over a Protein A-sepharose
column, followed by antibody elution using 0.2M glycine, pH 2.3.
Purified antibody was neutralized by the addition of 1M Tris, pH 8,
and buffer exchanged into PBS.
[1182] For ELISA analysis, 96 well plates were coated with P501S
peptide 296-322 (referred to as P501-long), an irrelevant P775
peptide, P501S-N, P501 TR2, P501S-long-KLH, P501S peptide 306-319
(referred to as P501-short)-KLH, or the irrelevant peptide
2073-KLH, all at a concentration of 2 ug/ml and allowed to incubate
for 60 minutes at 37.degree. C. After coating, plates were washed
5.times. with PBS+0.1% Tween and then blocked with PBS, 0.5% BSA,
0.4% Tween20 for 2 hours at room temperature. Following the
addition of supernatants or purified mAb, the plates were incubated
for 60 minutes at room temperature. Plates were washed as above and
donkey anti-mouse IgHRP-linked secondary antibody was added and
incubated for 30 minutes at room temperature, followed by a final
washing as above. TMB peroxidase substrate was added and incubated
15 minutes at room temperature in the dark. The reaction was
stopped by the addition of 1N H.sub.2SO.sub.4 and the OD was read
at 450 nM. All three hybrid clones secreted mAb that recognized
peptide 296-322 and the recombinant protein P501N.
[1183] For FACS analysis, HEK293 cells were transiently transfected
with a P501S/VR1012 expression constructs using Fugene 6 reagent.
After 2 days of culture, cells were harvested and washed, then
incubated with purified 4G5 mAb for 30 minutes on ice. After
several washes in PBS, 0.5% BSA, 0.01% azide, goat anti-mouse
Ig-FITC was added to the cells and incubated for 30 minutes on ice.
Cells were washed and resuspended in wash buffer including 1%
propidium iodide and subjected to FACS analysis. The FACS analysis
confirmed that amino acids 296-322 of P501S are in an extracellular
domain and are cell surface expressed.
[1184] The chromosomal location of P501S was determined using the
GeneBridge 4 Radiation Hybrid panel (Research Genetics). The PCR
primers of SEQ ID NO: 528 and 529 were employed in PCR with DNA
pools from the hybrid panel according to the manufacturer's
directions. After 38 cycles of amplification, the reaction products
were separated on a 1.2% agarose gel, and the results were analyzed
through the Whitehead Institute/MIT Center for Genome Research web
server (http://www-genome.wi.mit.edu/cgi-bin/contig/rhmapper.pl) to
determine the probable chromosomal location. Using this approach,
P501S was mapped to the long arm of chromosome 1 at WI-9641 between
q32 and q42. This region of chromosome 1 has been linked to
prostate cancer susceptibility in hereditary prostate cancer (Smith
et al. Science 274:1371-1374, 1996 and Berthon et al. Am. J. Hum.
Genet. 62:1416-1424, 1998). These results suggest that P501S may
play a role in prostate cancer malignancy.
Example 20
Regulation of Expression of the Prostate-Specific Antigen P501S
[1185] Steroid (androgen) hormone modulation is a common treatment
modality in prostate cancer. The expression of a number of prostate
tissue-specific antigens have previously been demonstrated to
respond to androgen. The responsiveness of the prostate-specific
antigen P501S to androgen treatment was examined in a tissue
culture system as follows.
[1186] Cells from the prostate tumor cell line LNCaP were plated at
1.5.times.10.sup.6 cells/T75 flask (for RNA isolation) or
3.times.10.sup.5 cells/well of a 6-well plate (for FACS analysis)
and grown overnight in RPMI 1640 media containing 10%
charcoal-stripped fetal calf serum (BRL Life Technologies,
Gaithersburg, Md.). Cell culture was continued for an additional 72
hours in RPMI 1640 media containing 10% charcoal-stripped fetal
calf serum, with 1 nM of the synthetic androgen Methyltrienolone
(R1881; New England Nuclear) added at various time points. Cells
were then harvested for RNA isolation and FACS analysis at 0, 1, 2,
4, 8, 16, 24, 28 and 72-hours post androgen addition. FACS analysis
was performed using the anti-P501S antibody 10E3-G4-D3 and
permeabilized cells.
[1187] For Northern analysis, 5-10 micrograms of total RNA was run
on a formaldehyde denaturing gel, transferred to Hybond-N nylon
membrane (Amersham Pharmacia Biotech, Piscataway, N.J.),
cross-linked and stained with methylene blue. The filter was then
prehybridized with Church's Buffer (250 mM Na.sub.2HPO.sub.4, 70 mM
H.sub.3PO.sub.4, 1 mM EDTA, 1% SDS, 1% BSA in pH 7.2) at 65.degree.
C. for 1 hour. P501S DNA was labeled with 32P using High Prime
random-primed DNA labeling kit (Boehringer Mannheim).
Unincorporated label was removed using MicroSpin S300-HR columns
(Amersham Pharmacia Biotech). The RNA filter was then hybridized
with fresh Church's Buffer containing labeled cDNA overnight,
washed with 1.times.SCP (0.1 M NaCl, 0.03 M
Na.sub.2HPO.sub.4.7H.sub.2O, 0.001 M Na.sub.2EDTA), 1% sarkosyl
(n-lauroylsarcosine) and exposed to X-ray film.
[1188] Using both FACS and Northern analysis, P501S message and
protein levels were found in increase in response to androgen
treatment.
Example 21
Preparation of Fusion Proteins of Prostate-Specific Antigens
[1189] The example describes the preparation of a fusion protein of
the prostate-specific antigen P703P and a truncated form of the
known prostate antigen PSA. The truncated form of PSA has a 21
amino acid deletion around the active serine site. The expression
construct for the fusion protein also has a restriction site at 3'
end, immediately prior to the termination codon, to aid in adding
cDNA for additional antigens.
[1190] The full-length cDNA for PSA was obtained by RT-PCR from a
pool of RNA from human prostate tumor tissues using the primers of
SEQ ID NO: 607 and 608, and cloned in the vector pCR-Blunt II-TOPO.
The resulting cDNA was employed as a template to make two different
fragments of PSA by PCR with two sets of primers (SEQ ID NO: 609
and 610; and SEQ ID NO: 611 and 612). The PCR products having the
expected size were used as templates to make truncated forms of PSA
by PCR with the primers of SEQ ID NO: 611 and 613, which generated
PSA (delta 208-218 in amino acids). The cDNA for the mature form of
P703P with a 6.times. histidine tag at the 5' end, was prepared by
PCR with P703P and the primers of SEQ ID NO: 614 and 615. The cDNA
for the fusion of P703P with the truncated form of PSA (referred to
as FOPP) was then obtained by PCR using the modified P703P cDNA and
the truncated form of PSA cDNA as templates and the primers of SEQ
ID NO: 614 and 615. The FOPP cDNA was cloned into the NdeI site and
XhoI site of the expression vector pCRX1, and confirmed by DNA
sequencing. The determined cDNA sequence for the fusion construct
FOPP is provided in SEQ ID NO: 616, with the amino acid sequence
being provided in SEQ ID NO: 617.
[1191] The fusion FOPP was expressed as a single recombinant
protein in E. coli as follows. The expression plasmid pCRX1 FOPP
was transformed into the E. coli strain BL21-CodonPlus RIL. The
transformant was shown to express FOPP protein upon induction with
1 mM IPTG. The culture of the corresponding expression clone was
inoculated into 25 ml LB broth containing 50 ug/ml kanamycin and 34
ug/ml chloramphenicol, grown at 37.degree. C. to OD600 of about 1,
and stored at 4.degree. C. overnight. The culture was diluted into
1 liter of TB LB containing 50 ug/ml kanamycin and 34 ug/ml
chloramphenicol, and grown at 37.degree. C. to OD600 of 0.4. IPTG
was added to a final concentration of 1 mM, and the culture was
incubated at 30.degree. C. for 3 hours. The cells were pelleted by
centrifugation at 5,000 RPM for 8 min. To purify the protein, the
cell pellet was suspended in 25 ml of 10 mM Tris-Cl pH 8.0, 2 mM
PMSF, complete protease inhibitor and 15 ug lysozyme. The cells
were lysed at 4.degree. C. for 30 minutes, sonicated several times
and the lysate centrifuged for 30 minutes at 10,000.times.g. The
precipitate, which contained the inclusion body, was washed twice
with 10 mM Tris-Cl pH 8.0 and 1% CHAPS. The inclusion body was
dissolved in 40 ml of 10 mM Tris-Cl pH 8.0, 100 mM sodium phosphate
and 8 M urea. The solution was bound to 8 ml Ni-NTA (Qiagen) for
one hour at room temperature. The mixture was poured into a 25 ml
column and washed with 50 ml of 10 mM Tris-Cl pH 6.3, 100 mM sodium
phosphate, 0.5% DOC and 8M urea. The bound protein was eluted with
350 mM imidazole, 10 mM Tris-Cl pH 8.0, 100 mM sodium phosphate and
8 M urea. The fractions containing FOPP proteins were combined and
dialyzed extensively against 10 mM Tris-Cl pH 4.6, aliquoted and
stored at -70.degree. C.
Example 22
Real-Time PCR Characterization of the Prostate-Specific Antigen
P501S in Peripheral Blood of Prostate Cancer Patients
[1192] Circulating epithelial cells were isolated from fresh blood
of normal individuals and metastatic prostate cancer patients, mRNA
isolated and cDNA prepared using real-time PCR procedures.
Real-time PCR was performed with the Taqman.TM. procedure using
both gene specific primers and probes to determine the levels of
gene expression.
[1193] Epithelial cells were enriched from blood samples using an
immunomagnetic bead separation method (Dynal A. S., Oslo, Norway).
Isolated cells were lysed and the magnetic beads removed. The
lysate was then processed for poly A+ mRNA isolation using magnetic
beads coated with Oligo(dT)25. After washing the beads in buffer,
bead/poly A+ RNA samples were suspended in 10 mM Tris HCl pH 8.0
and subjected to reversed transcription. The resulting cDNA was
subjected to real-time PCR using gene specific primers. Beta-actin
content was also determined and used for normalization. Samples
with P501S copies greater than the mean of the normal samples+3
standard deviations were considered positive. Real time PCR on
blood samples was performed using the Taqman.TM. procedure but
extending to 50 cycles using forward and reverse primers and probes
specific for P501S. Of the eight samples tested, 6 were positive
for P501S and .beta.-actin signal. The remaining 2 samples had no
detectable M-actin or P501S, No P501S signal was observed in the
four normal blood samples tested.
Example 23
Expression of the Prostate-Specific Antigens P703P and P501S in
SCID Mouse-Passaged Prostate Tumors
[1194] When considering the effectiveness of antigens in the
treatment of prostate cancer, the continued presence of the
antigens in tumors during androgen ablation therapy is important.
The presence of the prostate-specific antigens P703P and P501S in
prostate tumor samples grown in SCID mice in the presence of
testosterone was evaluated as follows.
[1195] Two prostate tumors that had metastasized to the bone were
removed from patients, implanted into SCID mice and grown in the
presence of testosterone. Tumors were evaluated for mRNA expression
of P703P, P501S and PSA using quantitative real time PCR with the
SYBR green assay method. Expression of P703P and P501S in a
prostate tumor was used as a positive control and the absence in
normal intestine and normal heart as negative controls. In both
cases, the specific mRNA was present in late passage tumors. Since
the bone metastases were grown in the presence of testosterone,
this implies that the presence of these genes would not be lost
during androgen ablation therapy.
Example 24
Identification of P501S and P703P-Specific Antibodies in Prostate
Cancer Patients
[1196] Antibody responses specific for the prostate antigens P501S
or P703P in sera of prostate cancer patients and normal healthy
donors were examined as follows.
[1197] Both Western blot analysis and ELISA analysis of sera were
performed using P501S peptides (SEQ ID NO: 985-987) and P703P
peptides (SEQ ID NO: 988-990). SEQ ID NO: 985, 986 and 987
represent amino acids 231-250, 246-266 and 492-521, respectively,
of P501S. SEQ ID NO: 988, 989, 990, 1030, 1031, 1032 1033, and 1037
represent amino acids 110-124, 140-154, 190-204, 62-76, 91-106,
200-214, and 229-245 respectively, of P703P. The results
demonstrated that some of the prostate cancer patients had
antibodies that recognize the same peptides (i.e. common epitopes)
of either P501S or P703P and that these common epitopes were either
not recognized or recognized at significantly lower levels by sera
from normal donors. The data showed that at least 14 out of 48
prostate cancer patients possessed P501S-specific antibodies, and
that 3 out of 48 prostate cancer patients possessed P703P-specific
antibodies with none of the patients having both antibodies
specific for P501S and antibodies specific for P703P.
Example 25
Anti-P503S Monoclonal Antibody Inhibits Tumor Growth In Vivo
[1198] The ability of the anti-P503S monoclonal antibody 20D4 to
suppress tumor formation in mice was examined as follows.
[1199] Ten SCID mice were injected subcutaneously with HEK293 cells
that expressed P503S. Five mice received 150 micrograms of 20D4
intravenously at day 0 (time of tumor cell injection), day 5 and
day 9. Tumor size was measured for 50 days. Of the five animals
that received no 20D4, three formed detectable tumors after about 2
weeks which continued to enlarge throughout the study. In contrast,
none of the five mice that received 20D4 formed tumors. These
results demonstrate that the anti-P503S Mab 20D4 displays potent
anti-tumor activity in vivo.
Example 26
Characterization of a T Cell Receptor Clone from a P501S-Specific T
Cell Clone
[1200] T cells have a limited lifespan. However, cloning of T cell
receptor (TCR) chains and subsequent transfer essentially enables
infinite propagation of the T cell specificity. Cloning of
tumor-antigen TCR chains allows the transfer of the specificity
into T cells isolated from patients that share the TCR
MHC-restricting allele. Such T cells could then be expanded and
used in adoptive transfer settings to introduce the tumor antigen
specificity into patients carrying tumors that express the antigen.
T cell receptor alpha and beta chains from a CD8 T cell clone
specific for the prostate-specific antigen P501S were isolated and
sequenced as follows.
[1201] Total mRNA from 2.times.10.sup.6 cells from CTL clone 4E5
(described above in Example 12) was isolated using Trizol reagent
and cDNA was synthesized. To determine Va and Vb sequences in this
clone, a panel of Va and Vb subtype-specific primers was
synthesized and used in RT-PCR reactions with cDNA generated from
each of the clones. The RT-PCR reactions demonstrated that each of
the clones expressed a common Vb sequence that corresponded to the
Vb7 subfamily. Furthermore, using cDNA generated from the clone,
the Va sequence expressed was determined to be Va6. To clone the
full TCR alpha and beta chains from clone 4E5, primers were
designed that spanned the initiator and terminator-coding TCR
nucleotides. The primers were as follows: TCR Valpha-6 5'(sense):
GGATCC-GCCGCCACC-ATGTCACTTTCTAGCCTGCT (SEQ ID NO: 899) BamHI site
Kozak TCR alpha sequence TCR alpha 3' (antisense):
GTCGAC-TCAGCTGGACCACAGCCGCAG (SEQ ID NO: 900) SalI site TCR alpha
constant sequence TCR Vbeta-7. 5'(sense):
GGATCC-GCCGCCACC-ATGGGCTGCAGGCTGCTCT (SEQ ID NO: 901) BamHI site
Kozak TCR alpha sequence TCR beta 3' (antisense):
GTCGAC-TCAGAAATCCTTTCTCTTGAC (SEQ ID NO: 902) SalI site TCR beta
constant sequence. Standard 35 cycle RT-PCR reactions were
established using cDNA synthesized from the CTL clone and the above
primers, employing the proofreading thermostable polymerase PWO
(Roche, Nutley, N.J.).
[1202] The resultant specific bands (approx. 850 bp for alpha and
approx. 950 for beta) were ligated into the PCR blunt vector
(Invitrogen) and transformed into E. coli. E. coli transformed with
plasmids containing full-length alpha and beta chains were
identified, and large scale preparations of the corresponding
plasmids were generated. Plasmids containing full-length TCR alpha
and beta chains were submitted for sequencing. The sequencing
reactions demonstrated the cloning of full-length TCR alpha and
beta chains with the determined cDNA sequences for the Vb and Va
chains being shown in SEQ ID NO: 903 and 904, respectively. The
corresponding amino acid sequences are shown in SEQ ID NO: 905 and
906, respectively. The Va sequence was shown by nucleotide sequence
alignment to be 99% identical (347/348) to Va6.2, and the Vb to be
99% identical to Vb7 (336/338).
Example 27
Capture of Prostate Specific Cells Using the Prostate Antigen
P503S
[1203] As described above, P503S is found on the surface of
prostate cells. Secondary coated microsphere beads specific for
mouse IgG were coupled with the purified P503S-specific monoclonal
antibody 1D12. The bound P503S antibody was then used to capture
HEK cells expressing recombinant P503S. This provides a model
system for prostate-specific cell capture which may be usefully
employed in the detection of prostate cells in blood, and therefore
in the detection of prostate cancer.
[1204] P503S-transfected HEK cells were harvested and redissolved
in wash buffer (PBS, 0.1% BSA, 0.6% sodium citrate) at an
appropriate volume to give at least 54 cells per sample. Round
bottom Eppendorf tubes were used for all procedures involving
beads. The stock concentrations were as shown below in Table
IX.
TABLE-US-00009 TABLE IX Stock concentrations Sample concentration
Amount needed Epithelial enrich beads 1.sup.7 beads/ml 125 ul stock
per 5 ml 4.sup.8 beads/ml (Dynal volume Biotech Inc. Lake Success,
NY) 1D12 ascites antibody 0.1 ug/ml (0.1X) to 5 0.05 ul to 2.5 ul
stock 2 mg/ml ug/ml (5X) titrations per sample .alpha.-Mamma Mu 1
ug/ml (1X) 1.1 ul stock per 0.9 mg/ml sample Pan-mouse IgG beads
1.sup.7 beads/ml 125 ul stock per 5 ml 4.sup.8 beads/ml (Dynal
volume Biotech)
[1205] Blocked immunomagnetic beads were pre-washed as follows: all
beads needed were pooled and washed once with 1 ml wash buffer. The
beads were resuspended in a 3.times. volume of 1% BSA (v/v) in wash
buffer and incubated for 15 min rotating at 4.degree. C. The beads
were then washed three times with 2.times. volume of wash buffer
and resuspended to original volume. Non-blocked beads were pooled,
washed three times with 2.times. volume of wash buffer and
resuspended to original volume.
[1206] Primary antibody was incubated with secondary beads in a
fresh Eppendorf for 30 minutes, rotating at 4.degree. C.
Approximately 200 ul wash buffer was added to increase the total
volume for even mixing of the sample. The antibody-bead solution
was transferred to a fresh Eppendorf, washed twice with an equal
volume of wash buffer and resuspended to original volume. Target
cells were added to each sample and incubated for 45 minutes,
rotating at 4.degree. C. The tubes were transferred to a magnet,
the supernatant removed, taking care not the agitate the beads, and
the samples were washed twice with 1 ml wash buffer. The samples
were then ready for RT-PCR using a Dynabeads mRNA direct microkit
(Dynal Biotech).
[1207] Epithelial cell enrichment was placed in a magnet and
supernant was removed. The epithelial enrichment beads were then
resuspended in 100 ul lysis/binding buffer fortified with Rnasin (2
U/ul per sample), and stored at -70.degree. C. until use. Oligo
(dT.sub.25) Dynabeads were pre-washed as follows: all beads needed
were pooled (23 ul/sample), washed three times with an excess
volume of lysis/binding buffer, and resuspended to original volume.
The lysis supernant was separated with a magnet and transferred to
a fresh Eppendorf. 20 ul oligo(dT25) Dynabeads were added per
sample and rolled for 5 min at room temperature. Supernant was
separated using a magnet and discarded, leaving the mRNA annealed
to the beads. The bead/mRNA complex was washed with buffer and
resuspended in cold Tris-HCl.
[1208] For RT-PCR, the Tris-HCl supernatant was separated and
discarded using MPS. For each sample containing 1.sup.5 cells or
less, the following was added to give a total volume of 30 ul:
14.25 ul H.sub.2O; 1.5 ul BSA; 6 ul first strand buffer; 0.75 mL 10
mM dNTP mix; 3 ul Rnasin; 3 ul 0.1M dTT; and 1.5 ul Superscript II.
The resulting solution was incubated for 1 hour at 42.degree. C.,
diluted 1:5 in H2O, heated at 80.degree. C. for 2 min to detach
cDNA from the beads, and immediately placed on MPS. The supernatant
containing cDNA was transferred to a new tube and stored at
-20.degree. C.
[1209] Table X shows the percentage of capture of P503S-transfected
HEK cells as determined by RT-PCR.
TABLE-US-00010 TABLE X % capture P503S- transfected HEK cells %
capture LnCAP cells 0.1 ug/ml P503S Mab 36.90 0.00 0.5 ug/ml P503S
Mab 67.40 2.93 1 ug/ml P503S Mab 40.22 0.00 5 ug/ml P503S Mab 13.11
0.00 Anti-Mu beads only, 1.42 0.00 non-blocked Anti-Mu beads only,
15.65 20.21 blocked Absolute control, non- 100.00 100.00 capture
cells
Example 28
Immunization of Mice with Recombinant P703P
[1210] In vivo immunogenicity studies were performed using a
variety of P703P recombinant protein formulations. Specifically,
groups of mice were immunized with the P703P formulations shown
below in Table XI, wherein "C'amidated P703P" represents P703P
amidated at the C terminal; "truncated-P703P" represents a
truncated form of P703P, and "FOPP" represents a fusion of P703P
and PSA.
TABLE-US-00011 TABLE XI GROUP ANTIGEN DOSE SOURCE ADJUVANT ROUTE 1
C'amidated 20 ug E. coli AS1 Im, sq (fp) P703P 2 Truncated 20 ug E.
coli AS1 Im, sq (fp) P703P 3 C'amidated 20 ug Pichia AS1 Im, sq
(fp) P703P 4 P703P 20 ug Pichia AS1 Im, sq (fp) 5 FOPP 20 ug E.
coli AS1 Im, sq (fp) 6 P703P 10.sup.7 pfu none Sq base of tail 7
C'amidated 20 ug E. coli MPL-SE Im, sq (fp) P703P 8 Truncated 20 ug
E. coli MPL-SE Im, sq (fp) P703P 9 C'amidated 20 ug Pichia MPL-SE
Im, sq (fp) P703P 10 P703P 20 ug Pichia MPL-SE Im, sq (fp) 11 FOPP
20 ug E. coli MPL-SE Im, sq (fp) 12 Naive (control)
[1211] Each protein immunization was done in four sites:
subcutaneously (sq) in both footpads and intramuscularly (im) in
the leg. Each immunization was done 3 weeks apart, with sera plus
spleen and lymph node (LN) cells being harvested 10 days following
the last immunization.
[1212] T cell proliferation and interferon-gamma assays were
performed as follows. 250,000 spleen or 100,000 LN cells were
plated in 96 well plates and stimulated with 1-10 ug/ml of antigen.
Antigens tested include the five proteins listed above, P703P
expressed in baculovirus, NS1 control protein, PSA (for FOPP groups
only), and P703P peptide pools. Peptide pools consisted of 20-mer
peptides overlapping by 15 amino acids with each pool containing
6-8 peptides. Con A was used as a positive control. Cultures were
pulsed with H3-thymidine on day 4 after initiation of culture for
assaying proliferation. For assaying IFN.gamma. levels by ELISA,
supernatants were also pulled on day 4. In addition, sera were
pooled and assayed by ELISA for IgG antibodies against the
recombinant proteins listed above.
[1213] All immunogens elicited strong antibody responses to the
immunogen. In all cases these responses reacted with other sources
of P703P protein, including strong reactivity with both Pichia
forms and baculovirus forms of P703P. AS1 adjuvant elicited
stronger antibody responses than MPL-SE. The best immunogen in
terms of eliciting a response against Pichia and baculovirus forms
of P703P was FOPP, but all of the immunogens elicited strong
reactive P703P antibody responses against the E. coli derived
P703P. In both the proliferation and interferon-gamma assays, all
immunogens elicited fairly good T cell response to the immunogen,
with most animals with detectable responses to their immunogen also
responding to other sources of P703P protein. Again, AS1 adjuvant
elicited better T cell responses than MPL-SE.
Example 29
Analysis of P703P Expression in Prostate Cancer and Normal Tissue
by Immunohistochemistry (IHC)
[1214] Protein expression of the prostate cancer antigen P703P was
analyzed in prostate cancer and normal tissue by IHC analysis using
an array of anti-P703P polyclonal and monoclonal antibodies (see
Table XII). P703P protein expression was also analyzed in
HEK293/P703P transfectants by flow cytometry and by Western blot
analysis using the same anti-P703P antibodies. The P703-R087 and
P703P-2059 antibodies stained HEK293/P703P transfectants by flow
cytometric analysis. P703P-2594 was used for Western blot
analysis.
TABLE-US-00012 TABLE XII ANTI-P703 ANTIBODIES Antibody Lot#
Species/type Immunogen Purification P703P-2594 370-84 Rabbit
bacteria derived Immunogen polyclonal truncated P703P (c- term 159
aa) P703P-9245 690.46 Rabbit bacteria derived full Immunogen
polyclonal length P703/NS1 fusion P703-2D4 Rabbit bacteria derived
Protein A polyclonal truncated P703P (c- term 159 aa) P703-8H2
Rabbit bacteria derived Protein A monoclonal truncated P703P (c-
term 159 aa) P703-7H8 Rabbit bacteria derived Protein A monoclonal
truncated P703P (c- term 159 aa) P703P-2059 690.88 Rabbit
Baulovirus derived Immunogen polyclonal full length form P703P-
Rabbit Baulovirus derived Protein A R087 monoclonal full length
form P703P- Rabbit Baulovirus derived Protein A R080 monoclonal
full length form PA-P703P- 858-130 Rabbit bacteria derived full
Protein A 9245 polyclonal length P703/NS1 fusion AP-P703P- 858-109
Rabbit bacteria derived full Baulovirus 9245 polyclonal length
P703/NS1 full length fusion
[1215] In order to further evaluate tissues expression of the
prostate cancer antigen P703P protein, immunohistochemistry (IHC)
analysis was performed on a diverse range of tissue sections.
Tissue samples were fixed in formalin solution for 12-24 hrs and
embedded in paraffin before being sliced into 8 micron sections.
Steam heat induced epitope retrieval (SHIER) in 0.1 M sodium
citrate buffer (pH 6.0) was used for optimal staining conditions.
Sections were incubated with 10% serum/PBS for 5 minutes. Primary
antibody was added to each section for 25 minutes at indicated
concentrations followed by 25 minute incubation with anti-rabbit
biotinylated antibody. Endogenous peroxidase activity was blocked
by three 1.5 minute incubations with hydrogen peroxidase. The
avidin biotin complex/horse radish peroxidase (ABC/HRP) system was
used along with DAB chromogen to visualize antigen expression.
Slides were counterstained with hematoxylin to visualize cell
nuclei. For Western blot analysis, whole cell lysates were
generated by incubating the cells in Triton-X 100 containing lysis
buffer for 30 minutes on ice. Lysates were then cleared by
centrifugation at 10,000 rpm for 5 minutes at 4.degree. C. Samples
were diluted with SDS-PAGE loading buffer containing
beta-mercaptoethanol, then boiled for 10 minutes prior to loading
the SDS-PAGE gel. Protein was transferred to nitrocellulose and
probed using 1 ug/ml purified anti-P703P rabbit polyclonal sera
2594 (lot #370-84) or rabbit monoclonal P703P-R087. Blots were
revealed using goat anti-rabbit Ig coupled to HRP followed by
incubation in ECL substrate. For FACS analysis, single cell
suspensions of P703P/HEK293 transfectants were generated and cells
were incubated in permeabilization buffer (PBS+saponin+BSA) at room
temp. The cells were then incubated for 30 minutes with 10 ug/ml of
purified anti-P703P polyclonal sera or monoclonal antibodies.
Following 3 washes in permeabilization buffer, cells were then
incubated with a 1:100 dilution of goat anti-rabbit
Ig(H+L)-FITC(Southern Biotechnology) for 30 minutes at RT. After 3
washes, the cells were resuspended in buffer and analyzed by
FACS.
[1216] Optimal IHC results were obtained using the heat retrieval
and affinity purified AP-P703P-9245 antibody against full-length
P703. IHC analysis using the above procedures with this antibody
showed weak staining in 6/23 metastatic prostate cancer sections.
24/33 primary prostate cancer sections stained positive with this
antibody. Additionally, staining was observed in malignant ducts,
benign (normal ducts) in various prostate tumors, basal,
myoepithelial cells in various prostate tumors, mast cells, and in
association with lipofuchsin granules.
[1217] A panel of normal tissue including brain, breast, uterus,
parotid, spleen, liver, ovary, adrenal, cervix, tonsil, esophagus,
bronchus, lung, kidney, testis, pancreas, skeletal muscle, colon,
small intestine, skin, and thyroid sections, were all negative.
Example 30
Detection of Circulating Prostate Tumor Cells in Peripheral Blood
Using Cell Capture Technology
[1218] The peripheral bloods of 55 urology patients, diagnosed with
prostate cancer, benign prostatic hyperplasia (BPH), bladder and
other prostate disorders, were collected and processed using the
Dynal Epithelial Enrich kit (Dynal, Lake Success, N.Y.), which uses
magnetic beads coated with the epithelial-specific antibody Ber-EP4
to specifically capture metastatic tumor cells. Total RNA was then
isolated using the QIAGEN RNeasy Mini Kit (QIAGEN, Valencia,
Calif.), DNase treated, and first strand cDNA was synthesized from
the cell capture fractions using Life Technologies Superscript II
Rnase H reverse transcriptase (Invitrogen Life Technologies,
Carlsbad, Calif.). Real-time PCR was performed to evaluate the
level of expression of prostate tumor genes P501S (also referred to
herein as L1-12, e.g., SEQ ID NO: 110), P703P (e.g., SEQ ID
NO:524), P503S (also referred to herein as N1-1862, e.g., SEQ ID
NO:11), P504S (also referred to herein as F1-12, e.g., SEQ ID
NO:107), P510S (e.g., SEQ ID NO:535 and 536), and P1020C (also
referred to as 22553, e.g., SEQ ID NO:591) using the housekeeping
genes, Actin, Beta-2-Microglobulin, and Cytokeratin 19, as
controls.
[1219] By combining the expression patterns of P501S and P504S, we
were able to detect at least two-fold overexpression of the two
genes combined for 10/24 prostate cancer patients and 4/25 BPH
patients as compared to the mean signal for the bladder and other
prostate disorders group. At least two-fold mean overexpression was
also detected in the cancer group as compared to the BPH and
Bladder cancer/other prostate disorders group for genes P501S,
P503S, P703P, P504S, and P510S. In addition, the same samples were
identified with P501S, P504S, and P510S. Thus, expression analysis
of prostate tumor sequences identified herein in blood samples
following cell capture can be utilized as a diagnostic tool, for
example in the detection of circulating tumor cells, e.g.,
metastatic tumor cells, in patients.
Example 31
Identification of a P703P-Derived CD4+ T Cell Epitope
[1220] A total of 40 15-mer peptides overlapping by 10 amino acids
spanning amino acids 47 to 254 of the P703P protein sequence were
generated by standard procedure. Dendritic cells (DC) were derived
from PBMC of a normal female donor using GMCSF and IL-4 by standard
procedures. CD4 T cells were generated from the same donor as the
DC using MACS beads and negative selection. DC were pulsed
overnight with pools containing 10 of the 15 mer peptides, with
each peptide at 0.25 microgram/ml final concentration. Pulsed DC
were washed and plated at 1.times.10e4 cells/well of 96-well round
bottom plates, and purified CD4 T cells were added at
1.times.10e5/well. Cultures were supplemented with 60 ng/ml IL-6
and 10 ng/ml IL-12 and incubated at 37.degree. C. Cultures were
re-stimulated as above on a weekly basis and were tested for
specific proliferation using as APC, DC generated and pulsed as
above, supplemented with 5 ng/ml IL-7 and 10 u/ml IL-2. Following 5
in-vitro stimulation cycles, lines (each line corresponds to one
well) were assayed for proliferation and cytokine production in
response to the stimulating pools vs an irrelevant pool of peptides
derived from the P703P sequence. 12 lines were identified that
demonstrated specific proliferation (measured in standard tritiated
thymidine proliferation assays) and cytokine production (measured
in .gamma.-interferon ELISA assays) in response to the stimulating
peptide pool. These lines were further tested for specific
recognition of the peptide pool, specific recognition of individual
peptides in the pool and specific recognition of recombinant P703P
protein. Using this approach, a peptide epitope derived from the
prostate tumor specific protein, P703P, recognized by CD4+ T cells
in the context of MHC class II, was identified. The peptide
corresponds to amino acids 145-159 of the P703P protein sequence of
SEQ ID NO: 525, and has the sequence GNSCLVSGWGLLANG (SEQ ID
NO:992). The cDNA sequence encoding this epitope is set forth in
SEQ ID NO:991.
Example 33
Identification of P706P Extended Sequences
[1221] Related clones were identified above in Example 1 (e.g., SEQ
ID NO: 46, 212, 213, 214, 215, 288 and 415) as having
prostate-specific expression patterns. Upon further analysis, an
extended sequence for these clones was identified as follows.
Sequence specific primers were used to amplify products from a
prostate tumor library, resulting in the identification of clones
8B6-P3 (SEQ ID NO: 993) and 8B6-P4 (SEQ ID NO: 994). Both clones
were transformed into appropriate cells, isolated, sequenced, and
the resulting sequences were used as queries to search against the
Genbank sequence database. This search revealed that 8B6-P3 and
8B6-P4 and other related EST sequences were components of the same
genomic 7q21 BAC clone. Based on the close proximity along the
genomic backbone and on the similar expression profiles, these
components were concluded to be part of the same gene, referred to
herein as P706P. Northern analysis demonstrated high
over-expression in prostate tumors and prostate tissues, and also
showed expression in brain and ovary. The four sequences disclosed
herein (SEQ ID NO: 993-997) are representatives of the 4 longest
contiguous pieces of cDNA-derived sequence along the genomic
backbone. Contigation of clones 8B6.P3 (SEQ ID NO: 993) and 8-B6.P4
(SEQ ID NO: 994), using also available EST sequences, allowed the
identification of the extended P706P sequence set forth in SEQ ID
NO: 995.
Example 34
Identification of P713P Extended Sequence
[1222] The identification of SEQ ID NO: 146, also referred to as
P219, was described above. This example describes the
identification of an extended sequence for this clone, as well as
the bioinformatic identification of the full length cDNA and
protein sequences containing the same. Full length laboratory
cloning efforts were initiated with an EST search and alignment.
The sequence identified by this approach was confirmed with a 5'
RACE assay (Clonetech; see also Chenchik et al., 1995, 1996) in
which a library of adaptor ligated prostate tumor cDNAs are used as
a template to amplify the desired 5' end of a gene using the 5'
adaptor primer and a gene specific 3' primer. Additional sequence
was identified using a nucleic acid-based screen in which a
phagemid prostate tumor library was screened by growing plaques,
transferring and immobilizing DNA onto nylon filters, and
hybridizing with a radioactive gene-specific probe. The filters
were then exposed to film and plaques corresponding to
radioactively exposed positive hits were picked and prepped for DNA
isolation. The DNA sequence identified using the above approach
both confirmed the original clone sequence and further yielded
additional 5' sequence. This extended cDNA sequence, also referred
to as P713P, is set forth in SEQ ID NO: 998. In a separate
analysis, it was determined that P713P corresponds to a protein
referred to as Prostatic Secretory Protein (PSP), the full length
cDNA sequence of which is set forth in SEQ ID NO: 999, encoding the
amino acid sequence set forth in SEQ ID NO: 1000.
Example 35
Identification of P1E Extended Sequence
[1223] The identification of the cDNA sequences set forth in SEQ ID
NO: 620, 621 and 622, also referred to as P1E, were described above
in Example 1. These sequences resulted from a serological
expression cloning effort and subsequent nucleic acid screening of
the same cDNA expression library. An expression cDNA library was
constructed from prostate tumor extracted mRNA using routine
methodologies. This library was screened with autologous patient
sera. (prostate tumor and patient sera were from the same
individual) 10,000 pfu were plated on 6 large LB agar plates,
allowed to grow up for 6 hrs, and IPTG-infused filters were applied
to induce expression and immobilize proteins as they were produced.
The filters were oriented to the plate and were removed 12 hours
later. The filters were blocked in PBS 1% tween, and then incubated
with the patient sera for 12 hours at 4 degrees Celsius. The washed
filters were incubated in I-125 conjugated protein A for 1 hour at
room temperature, washed again and exposed to film overnight.
Exposed spots on the film indicating expressed protein recognized
by the autologous sera were picked, purified, the plasmid excised,
and prepped for DNA isolation and subsequent sequencing. This
procedure resulted in the identification of clone PT44A22.
[1224] Primers were designed from the PT44A22 sequence in order to
further screen the same expression library. For probe labeling, PCR
amplification of the original PT4A22 DNA fragment was performed in
the presence of radioactive nucleotides. The probe was incubated
with nylon filters onto which the DNA of 10000-15000 clones of the
expression library were immobilized. After a few hours of
hybridization at 65 degrees in Church's hybridization buffer, the
filters were washed in a solution of 1.times.SCP, 1% sarkosyl. Film
was exposed to the washed filters overnight and positive signals
were used to pick the appropriate colonies. These picks, which
contained about 50 colonies each, were further purified by the
method described previously, resulting in a pure colony pick which
was then grown up and prepped for plasmid DNA. The plasmid
containing the clone of interest was digested for fragment size and
the insert was sequenced using flanking promoter primers. This
procedure resulted in the clone PT44.P2. Together, PT44A22 and
PT44.P2 make up the extended P1E sequence disclosed herein as SEQ
ID NO: 1004, encoding the amino acid sequence set forth in SEQ ID
NO: 1005.
Example 36
Immunohistochemical Analysis of P510S
[1225] Identification of the prostate specific gene P510S is
described above (e.g., Example 1). In order to evaluate P510S
protein expression, immunohistochemistry (IHC) analysis was
performed on a diverse range of tissue sections. Tissue samples
were fixed in formalin solution for 12-24 hours and embedded in
paraffin before being sliced into 8 micron sections. Steam heat
induced epitope retrieval (SHIER) in 0.1 M sodium citrate buffer
(pH 6.0) was used for optimal staining conditions. Sections were
incubated with 10% serum/PBS for 5 minutes. Primary antibody was
added to each section for 25 minutes at indicated concentrations
followed by a 25 minute incubation with anti-rabbit biotinylated
antibody. Endogenous peroxidase activity was blocked by three 1.5
minute incubations with hydrogen peroxidase. The avidin biotin
complex/horse radish peroxidase (ABC/HRP) system was used along
with DAB chromogen to visualize antigen expression. Slides were
counterstained with hematoxylin to visualize cell nuclei.
[1226] Using this approach, P510S protein expression was detected
in 31/32 primary prostate tumor samples and in 8/17 bone metastasis
samples. Some expression was also detected in 4/5 normal prostate
samples and 3/5 testis samples. No expression was detected in
thyroid, spleen, uterus, ovary, pancreas, lung, liver, kidney,
heart, stomach, large intestine, small intestine, brain and adrenal
gland.
Example 37
Diagnostic Evaluation of Prostate Antigen P504S
[1227] Identification of the prostate specific sequence P504S has
been described above (e.g., Example 1). In order to evaluate P504S
protein expression, immunohistochemistry (IHC) analysis was
performed on a diverse range of tissue sections. Tissue samples
were fixed in formalin solution for 12-24 hours and embedded in
paraffin before being sliced into 8 micron sections. Steam heat
induced epitope retrieval (SHIER) in 0.1 M sodium citrate buffer
(pH 6.0) was used for optimal staining conditions. Sections were
incubated with 10% serum/PBS for 5 minutes. Primary antibody was
added to each section for 25 minutes at indicated concentrations
followed by a 25 minute incubation with anti-rabbit biotinylated
antibody. Endogenous peroxidase activity was blocked by three 1.5
minute incubations with hydrogen peroxidase. The avidin biotin
complex/horse radish peroxidase (ABC/HRP) system was used along
with DAB chromogen to visualize antigen expression. Slides were
counterstained with hematoxylin to visualize cell nuclei.
A. P504S Expression in Colon Carcinomas: Correlation with Tumor
Grade and Patient Survival
[1228] This example evaluates the immunoreactivity of P504 is in
normal colon and invasive colon carcinomas, and also evaluates the
correlation between P504 expression and tumor grade, stage, and
patient survival. Routinely processed resected colon carcinomas
(n=44), villous adenomas (V, n=4) and tubular or tubulovillous
adenomas (TA/TVA, n=24) were cut at 5 .mu.m and immunostained with
P504 on a TechMate 1000 (Ventana Medical Systems, Tucson, Ariz.)
automated immunostainer using an avidin/biotin complex (ABC)
staining procedure. Positive immunostaining in cytoplasm was
graded: 0=negative staining; 1+=up to 33% cells positive;
2+=34-66%; 3+=>66%. Tumors were graded on review of H&E
stained slides, and stage, location, and follow up were obtained
from pathology reports and patient charts.
[1229] Invasive carcinomas were from 18 males and 26 females, ages
45-87, from right colon (23), transverse (6), left (14), and
unknown (1). Tumor stage was I (4), II (17), III (18), and IV (5).
Tumor grade was Grade 1 (23), 2 (9), and 3 (12). Remnant polyp was
present in 7 carcinomas. Immunostaining for p504S was weakly
positive in surface epithelium of normal colon. In carcinomas, P504
was graded 0 (16), 1+ (6), 2+ (8), and 3+ (14). There was no
difference between superficial and deep regions of the tumors.
Remnant polyp was 2+ or 3+ in 4 cases, 0 in 3 cases. The percentage
of carcinomas positive for each grade of P504S correlated inversely
with tumor grade and patient survival. There was no correlation
between P504S expression and TNM stage or overall stage. Most
adenomas (25/35) were 2+ or 3+, regardless of histologic type.
[1230] Thus, P504S was highly expressed in adenomas and
well-differentiated colon carcinomas, and weak or absent in normal
colon mucosa and poorly differentiated carcinomas. P504S expression
correlated inversely with patient survival. In view of these
results, immunostaining for P504S represents a useful adjunct with
prognostic significance in the diagnostic evaluation of colon
carcinomas.
B. Expression of P504S in Atypical Adenomatous Hyperplasia of the
Prostate
[1231] Atypical Adenomatous Hyperplasia (AAH), also known as
adenosis, is characterized by the abnormal architectural patterns
but without significant cytologic atypia in prostatic glandular
epithelium. AAH may represent a precursor lesion of prostatic
adenocarcinoma. P504S has been found to be highly expressed in
prostatic adenocarcinoma, but not in benign prostatic epithelium.
In this example, the expression of P504S was evaluated in AAH.
[1232] A total of 46 cases including 26 of AAH (prostatectomy:
N=18, biopsy: N=6, and transurethral resection: N=2), 10 cases of
adenocarcinomas with Gleason score 2+2=4 and 10 cases of benign
prostatic hyperplasia (BPH) were examined by immunohistochemistry
for P504S and high molecular weight cytokeratin 34.beta.E12.
34.beta.E12 staining confirmed the presence of patchy basal cells
in all 26 cases of AAH. P504S showed strong cytoplasmic granular
staining in all (10 of 10) low-grade carcinomas and in 4 of 26
cases of AAH (15%). No BPHs or benign glands adjacent to carcinomas
and AAH were positive for P504S. Diffuse P504S staining pattern was
found in low-grade carcinomas, while focal P504s positivity was
seen in AAH.
[1233] Thus, expression of P504S was found in all low-grade
carcinomas and a small percentage of AAH, but not in BPH or other
benign glands. These findings suggest that AAH is a lesion
different from low-grade cancer or BPH, at least with respect to
P504S expression. Moreover, AAH may be considered as a premalignant
or potentially premalignant lesion.
C. P504S as a Diagnostic Marker for Minimal Prostatic
Adenocarcinoma on Needle Biopsy
[1234] Establishing diagnosis of minimal prostatic cancer (PC) on
needle biopsy is a major diagnostic challenge. A marker specific
for prostate cancer will enhance our ability to detect minimal
disease. P504S, identified by cDNA subtraction and microarray
technology, has been demonstrated to be highly expressed in PC but
not in benign prostatic glands. The aim of this study was to
evaluate P504S expression as a means for detecting minimal PC.
[1235] A total of 111 prostate needle biopsies, including 52 of
minimal prostatic adenocarcinoma with Gleason Score 6 (N=51) or 8
(N=1) and 59 benign prostates, were examined by using
immunohistochemistry specific for P504S and high molecular weight
cytokeratin (34.beta.E12). Minimal PC, defined as a tumor focus
<1 mm in diameter on H&E staining, was present as only one
single focus in the entire biopsy (N=35), or as one small focus in
one needle core in addition to carcinoma present elsewhere
(N=18).
[1236] P504S immunopositivity was found in 51/52 cases (98%) of
minimal PC but not in any benign prostates (0/58) or benign glands
adjacent to malignant glands. Atrophy, basal cell hyperplasia and
transitional cell metaplasia were all negative for P504S. The only
case of PC with negative staining of P504S showed features of foamy
carcinoma in a biopsy obtained from the transition zone. High
molecular weight cytokeratin (34.beta.E12) immunostaining confirmed
the absence of basal cells in the focus of carcinoma in all 52
cases.
[1237] The high specificity and sensitivity of P504S for detecting
limited prostatic adenocarcinoma illustrates its diagnostic value
in a clinical setting. Using P504S as a immunohistochemical marker
can thus increase the accuracy in pathology diagnosis of minimal
prostatic adenocarcinoma on needle biopsy.
Example 38
Immunohistochemical Analysis of P767P
[1238] In order to evaluate protein expression of the prostate
antigen P767P, immunohistochemistry (IHC) analysis was performed on
a diverse range of tissue sections. Tissue samples were fixed in
formalin solution for 12-24 hours and embedded in paraffin before
being sliced into 8 micron sections. Steam heat induced epitope
retrieval (SHIER) in 0.1 M sodium citrate buffer (pH 6.0) was used
for optimal staining conditions. Sections were incubated with 10%
serum/PBS for 5 minutes. Primary antibody was added to each section
for 25 minutes at indicated concentrations followed by a 25 minute
incubation with anti-rabbit biotinylated antibody. Endogenous
peroxidase activity was blocked by three 1.5 minute incubations
with hydrogen peroxidase. The avidin biotin complex/horse radish
peroxidase (ABC/HRP) system was used along with DAB chromogen to
visualize antigen expression. Slides were counterstained with
hematoxylin to visualize cell nuclei. Using this approach, P767S
protein expression was detected in 7/7 prostate cancers, 5/5 normal
prostates, 1/1 normal kidney, 1/1 cerebellum, 0/1 normal liver, 0/1
normal heart, 1/1 normal lung, 1/1 normal colon, 1/1 normal tonsil,
and 1/1 normal cortex.
Example 39
P510S and MAPS-P510S Constructs for DNA Immunization and Antibody
Generation
[1239] The identification of prostate sequence P510S has been
identified above (e.g., Example 1). Plasmid DNA containing P510S
was used as template in a PCR reaction to amplify the open reading
frame of P510S using P510S-AW186 sense primers with Hind III sites
and a Kozak sequence, and P510S-AW187 antisense primers with Nhe I
sites and a stop codon. PCR product was purified from agarose gel,
digested with Hind III and Nhe I, and ligated to JA4304 vector that
had been linearized with the same two restriction enzymes. The
ligation mixture was transformed into E. coli and several clones
were randomly selected for restriction enzyme analysis and DNA
sequencing. P510S/JA4304#2 and #3 clones were confirmed to have the
desired P510S sequence. The determined DNA sequence for this
construct is set forth in SEQ ID NO: 1006, encoding the polypeptide
of SEQ ID NO: 1009.
[1240] For construction of MAPS-P510S, the pCRX4 vector was used.
pCRX4 is a MAPS fusion vector based on JA4304 that was made to
facilitate the cloning of MAPS fusion constructs. In pCRX4, MAPS
was cloned down stream of Kozak sequence and was followed by a
multiple cloning site. To generate the MAPS-P510S construct, a PCR
reaction was used to amplify the P510S coding region using
MAPS-P510S-AW184 sense primers with EcoR I sites, and P510S-AW185
antisense primers for MAPS-P510S with Kpn I sites and a stop codon.
PCR product was purified from agarose gel, digested with EcoR I and
Kpn I, and ligated to pCRX4 vector that had been linearized with
the same two restriction enzymes. The ligation mixture was
transformed into E. coli and several clones were randomly selected
for restriction enzyme analysis and DNA sequencing.
MAPS-P510S/pCRX4 #1 and #3 clones were confirmed. The determined
DNA sequence for this construct is set forth in SEQ ID NO: 1007,
encoding the polypeptide of SEQ ID NO: 1008.
Example 40
Detection of P501S and P703P-Specific Antibodies in Sera of
Prostate Cancer Patients and Normal Donors
[1241] The identification and characterization of prostate specific
antigens P501S and P703P are described above, illustrative forms of
which are set forth in SEQ ID NO: 113 (encoded by SEQ ID NO: 110)
and SEQ ID NO: 525 (encoded by SEQ ID NO: 524), respectively. This
example describes the detection of antibodies specific for these
proteins in the sera of prostate cancer patients. Effective
protein-based screening for prostate antigen-specific antibodies in
patient sera has been problematic due to protein instability and/or
contamination of small amounts of E. coli-derived proteins.
However, the carboxyamidation of recombinant P501S and P703P has
provided improved stability for these proteins, as confirmed by
SDS-PAGE. Thus, carboxyamidated P501S and P703P proteins were used
to screen for P501S- and P703P-specific antibodies in the sera of
55 prostate cancer patients and 13 normal male donors, as
follows.
[1242] Flat-bottomed immuno-plates were incubated and coated for at
least 3 hours at room temperature or overnight at 4 degrees C. with
50 ul coating buffer (0.1N carbonate buffer; pH 9.5) supplemented
with 600 ng of carboxyamidated P501S or 300 ng of carboxyamidated
P703P protein. The solution was removed and at least 150 ul of
blocking buffer (1:1 mixture of 10% NFDM (Non Fat Dry Milk)/PBS and
Superblock (Pierce) was added in each well and incubated for 3
hours at room temp or overnight at 4 degrees C. After washing at
least 3 times with 0.05% Tween 20-containing PBS and once with PBS,
50 ul of sera from prostate cancer patients or normal donors was
diluted with 10% NGS (normal goat sera; Gibco BRL, #16210-072)
containing PBS, added and incubated for 3 hours at room temperature
or for overnight at 4 degrees C. After washing at least 3 times
with 0.05% Tween-containing PBS and once with PBS, 100 ul of
HRP-conjugated anti-human IgG (Jackson ImmunoResearch Laboratories
Inc.; #709-036-149) (.times.8000 dilution by 1:1 mixture of 10%
NFDM/PBS+Superblock) were added and incubated for 30-60 minutes at
room temperature. After washing at least 6 times with 0.05%
Tween-containing PBS and once with PBS, 80-100 ul of the
TMB-substrate solution was added and incubated at room temperature.
After obtaining suitable colors on the standard of IgG between
10-30 min, 40-50 ul (a half volume of substrate) of 0.1N sulfuric
acid solution was added to stop the enzyme reaction. Absorbances
were then determined with a microplate reader (Biotec
Instruments).
[1243] Using this approach, P501S-specific antibodies were detected
in 32/55 prostate cancer patients and 5/13 normal donors.
P703-specific antibodies were detected in 24/55 prostate cancer
patients and 0/13 normal donors. These results confirm the in vivo
immunogenicity of P501S and P703P. Moreover, the results
demonstrate that the carboxyamidated forms of P501S and P703P
retain the epitopes that are recognized by rabbit/mouse antibodies,
as well as by antibodies from prostate cancer patients.
Example 41
Generation of Monoclonal Antibodies to P711P
[1244] The identification and characterization of P711P (SEQ ID NO:
382, encoding the protein of SEQ ID NO: 383) is described above
(e.g., Example 3). For production and purification of P711P protein
used for antibody generation, E. coli expressing recombinant P711P
protein were grown overnight in LB Broth with the appropriate
antibiotics at 37.degree. C. in a shaking incubator. The next
morning, 10 ml of the overnight culture was added to 500 ml of 2x
YT plus appropriate antibiotics in a 2 L-baffled Erlenmeyer flask.
When the optical density (at 560 nanometers) of the culture reached
0.4-0.6, the cells were induced with IPTG (1 mM). Four hours after
induction with IPTG the cells were harvested by centrifugation. The
cells were then washed with phosphate buffered saline and
centrifuged again. The supernatant was discarded and the cells were
either frozen for future use or immediately processed. Twenty
milliliters of lysis buffer was added to the cell pellets and the
suspension was vortexed. To break open the E. coli cells, this
mixture was then run through a French Press at a pressure of 16,000
psi. The cells were then centrifuged again and the supernatant and
pellet were checked by SDS-PAGE for the partitioning of the
recombinant protein. For proteins that localized to the cell
pellet, the pellet was resuspended in 10 mM Tris pH 8.0, 1% CHAPS
and the inclusion body pellet was washed and centrifuged again.
This procedure was repeated twice more. The washed inclusion body
pellet was solubilized with either 8 M urea or 6 M guanidine HCl
containing 10 mM Tris pH 8.0 plus 10 mM imidazole. The solubilized
protein was added to 5 ml of nickel-chelate resin (Qiagen) and
incubated for 45 minutes to 1 hour at room temperature with
continuous agitation. After incubation, the resin and protein
mixture were poured through a disposable column and the flow
through was collected. The column was then washed with 10-20 column
volumes of the solubilization buffer. The antigen was then eluted
from the column using 8M urea, 10 mM Tris pH 8.0 and 300 mM
imidazole and collected in 3 ml fractions. A SDS-PAGE gel was run
to determine which fractions to pool for further purification.
[1245] As a final purification step, a strong anion exchange resin,
e.g., Hi-Prep Q (Biorad) was equilibrated with the appropriate
buffer and the pooled fractions from above were loaded onto the
column. Each antigen was eluted off of the column with an
increasing salt gradient. Fractions were collected as the column
was run and another SDS-PAGE gel was run to determine which
fractions from the column to pool. The pooled fractions were
dialyzed against 10 mM Tris pH 8.0. This material was then
evaluated for purity as determined by SDS-PAGE or HPLC,
concentration as determined by Lowry assay or amino acid analysis,
identity as determined by amino terminal protein sequence, and
endotoxin level was determined by the Limulus (LAL) assay. The
proteins were then vialed after filtration through a 0.22-micron
filter and the antigens were frozen until needed for
immunization.
[1246] To generate anti-P711P mouse monoclonal antibodies, mice
were immunized intraperitoneally (IP) with 50 micrograms of
recombinant P711P protein that had been mixed to form an emulsion
with an equal volume of Complete Freund's Adjuvant (CFA). Every
three weeks animals were injected i.p. with 50 micrograms of
recombinant P711P protein that had been mixed with an equal volume
of IFA to form an emulsion. After the fourth injection, spleens
were isolated and standard hybridoma fusion procedures were used to
generate anti-P711P mouse monoclonal antibodies.
[1247] Anti-P711P monoclonal antibodies were screened by ELISA
analysis using the bacterially expressed recombinant P711P protein.
For characterization of anti-P711P monoclonal antibodies by ELISA,
96 well plates were coated with P711P antigen by incubating with 50
microliters (typically about 1 microgram) at 4 degrees C. for 20
hours. 250 microliters of BSA blocking buffer was added to the
wells and incubated at room temperature for 2 hours. Plates were
washed 6 times with PBS/0.01% TWEEN. Fifty microliters of each
undiluted monoclonal supernatant were added per well and incubated
at room temperature for 30 minutes. Plates were washed as described
above before 50 microliters of goat anti-mouse horseradish
peroxidase (HRP) at a 1:10000 dilution was added and incubated at
room temperature for 30 minutes. Plates were washed as described
above and 100 .mu.l of TMB Microwell Peroxidase Substrate was added
to each well. Following a 15 minute incubation in the dark at room
temperature the colorimetric reaction was stopped with 100 .mu.l 1N
H2SO4 and read immediately at 450 nm. For Western blot analysis,
recombinant P711P protein was diluted with SDS-PAGE loading buffer
containing beta-mercaptoethanol, then boiled for 10 minutes prior
to loading the SDS-PAGE gel. Protein was transferred to
nitrocellulose and probed with each of the anti-P711P hybridoma
supernatants. Anti-mouse-HRP was used to visualize the anti-P711P
reactive bands by incubation in ECL substrate. By this approach, at
least seven anti-P711P monoclonal antibodies were generated and
demonstrated to be reactive with recombinant P711 protein by ELISA
and/or Western analysis.
Example 42
Recognition of Carbamidomethylated CTL Epitope by P501S-Specific
T-Cells
[1248] The identification and characterization of prostate specific
antigen P501S has been described above, a representative full
length DNA sequence for which is set forth in SEQ ID NO: 110,
encoding the amino acid sequence set forth in SEQ ID NO: 113. CTL
specific for a peptide of P501S (peptide 370-378, amino acid
sequence CLSHSVAVV) were previously demonstrated to recognize
naturally processed P501S as demonstrated by recognition of P501S
transduced target cells. In this example, mice were immunized with
P501S DNA followed by a second immunization using a
P501S-containing adenovirus delivery vector 14 days later. On day
35, spleen cells were harvested and stimulated in vitro weekly
using irradiated Jurkat A2 kb-P501 cells. CTL lines were assayed
for lytic activity against parental Jurkat A2Kb cells, Jurkat A2Kb
cells transduced with P501S, Jurkat A2Kb cells pulsed with
p370-378, or Jurkat A2KbT cells pulsed with the carboxy amidated
p370-378 peptide. Using this approach, it was found that p370-378
specific T cells not only recognize the synthetic unmodified
370-378 peptide, but also recognize a carbamidomethylated form of
370-378. These results are important for demonstrating
cross-recognition of naturally processed P501, an ummodified
synthetic peptide corresponding to amino acids 370-378, P501S, and
the modified synthetic peptide 370-378. Thus, carbamidomethylation
of recombinant P501S does not impair T cell recognition of this CTL
epitope.
Example 43
Preparation of P501S Fusion Proteins
[1249] The identification and characterization of prostate specific
antigen P501S has been described above, a representative full
length DNA sequence for which is set forth in SEQ ID NO: 110,
encoding the amino acid sequence set forth in SEQ ID NO: 113. In
this example, illustrative P501S fusion constructs were made and
the encoded fusion proteins produced. Using sequence specific
primers, the C-terminal truncated region of P501S (amino acids
341-527) was PCR amplified using the following conditions:
[1250] 10 .mu.l 10.times.Pfu buffer
[1251] 1 .mu.l 10 mM dNTPs
[1252] 2 .mu.l 10 .mu.M each oligo
[1253] 83 .mu.l sterile water
[1254] 1.5 .mu.l Pfu DNA polymerase (Stratagene, La Jolla,
Calif.)
[1255] 50 .eta.g DNA
[1256] 96.degree. C. 2 minutes
[1257] 96.degree. C. 30 seconds 72.degree. C. 1 minute 30
seconds.times.40 cycles
[1258] 72.degree. C. 4 minutes
[1259] The resulting PCR product was digested with NcoI and NotI
and cloned into the commercially available vector pET32 (Novagen,
Madison Wis.) that was also digested with NcoI and NotI. The pET32
vector incorporates an N-terminal fusion with the Trx antigen,
which is Thioredoxin, an E. coli protein that can enhance
expression for difficult to express antigens, and can further
enhance solubility of the resulting fusion protein. The resulting
cDNA sequence for the coding region of this Trx-P501S fusion
construct is set forth in SEQ ID NO: 1010, encoding the fusion
amino acid sequence set forth in SEQ ID NO: 1011.
Example 44
Evaluation of P501S Immunogenicity
[1260] The identification and characterization of prostate specific
antigen P501S has been described above, a representative full
length DNA sequence for which is set forth in SEQ ID NO: 110,
encoding the amino acid sequence set forth in SEQ ID NO: 113. This
example describes the results of a preclinical in vivo
immunogenicity study evaluating vaccination with P501S protein
(either unmodified or carboxy amidated), in combination with
various adjuvants, compared with DNA/adenovirus P501S immunization.
The following experimental design was employed:
TABLE-US-00013 Adjuvant Group Antigen System 1 10 ug P501S AS1
unmodified 2 10 ug P501S AS2 unmodified 3 10 ug P501S AS7
unmodified 4 10 ug P501S AS1 carboxyamidated 5 10 ug P501S AS2
carboxyamidated 6 10 ug P501S AS7 carboxyamidated 7 100 ug P501S
None DNA/10.sup.8 pfu P501S adenovirus 8 Buffer AS2. 9 Naive -- 3
immunizations, 2 weeks apart; Harvest 8 days after last
immunization; Route = i.m. + f.p.; Mice = A2Tg females
(5/group);
[1261] Assays were subsequently performed for evaluating CTL
responses, antibody responses and CD4 responses (interferon-gamma
& proliferation). The results of this evaluation demonstrated
that both unmodified and carboxy amidated P501S protein delivered
in adjuvant are immunogenic, as assessed by antibody and CD4 T cell
responses. The CD4 and antibody responses observed with protein
administration were generally stronger than the response observed
with DNA/Adenovirus immunization. CTL responses were not detected
following protein immunization in the adjuvant systems tested.
However, CTL were consistently detectable following P501S
adenovirus immunization. The antibody and CD4 responses recognized
both unmodified P501S and P501S modified by carboxy amidation.
Comparative evaluation of responses obtained with various adjuvant
systems demonstrated little effect on immunogenicity, with the
exception that AS7 generated a stronger Th1 response.
Example 45
Identification of a Naturally Processed CTL Epitope for P501S
[1262] The identification and characterization of prostate specific
antigen P501S has been described above, a representative full
length DNA sequence for which is set forth in SEQ ID NO: 110,
encoding the amino acid sequence set forth in SEQ ID NO: 113. In
this example, a naturally processed, murine A2Kb CTL epitope has
been identified for P501S. This epitope was mapped using a series
of C-terminal deletion constructs, C-terminal subclones containing
the last 92 amino acids of P501S, and sets of peptides spanning
P501S regions of interest. The T cell clones used to map the
epitope were derived from limiting dilutions of splenocytes from
P501S DNA immunized and P501S-adenovirus immunized C57BL/6 A2Kb
transgenic mice. Thirty-seven T cell clones were identified as
reactive to P501S-transduced Jurkat A2Kb targets in CTL assays. The
lines, however, were not reactive to Jurkat A2Kb cells pulsed with
a previously identified naturally processed P501S epitope
corresponding to amino acid residues 370-378 of SEQ ID NO: 113.
This observation pointed to the existence of a second epitope other
than the 9-mer epitope of amino acid residues 370-378. The T cell
clones were thus tested with Jurkat A2Kb cells transduced with
C-terminal deletion constructs denoted FragA-FragE. None of the T
cell clones generated CTL responses to these deletion constructs,
indicating that the epitope likely mapped within the C-terminal 92
amino acids of P501S (461-553). Six T cell clones were demonstrated
to be responsive to Jurkat A2Kb clones expressing P501S amino acid
residues 462-553 or 462-517. Using a murine ELISPOT assay, these
transduced targets, and Jurkat A2Kb targets pulsed with various
20-mer, 15-mer, 10-mer and 9-mer peptides, allowed for the
identification of a naturally processed epitope for P501S, having
the sequence SACDVSVRV, and corresponding to amino acid residues
464-472 of SEQ ID NO: 113.
Example 46
Characterization of P790P Expression
[1263] The identification of prostate antigen P790P has been
described above, the full length cDNA sequence for which is set
forth in SEQ ID NO: 526, encoding the amino acid sequence set forth
in SEQ ID NO: 527. For recombinant expression in mammalian cells,
P790P was subcloned into pCEP4 and VR0113 (a polylinker modified
VR1012 vector) mammalian expression vectors. The constructs were
transfected into HEK293 cells (ATCC) using Lipofectamine 2000
(Gibco). The HEK293 cells were plated in a 6 well dish at a density
of 300,000 cells/ml in DMEM (Gibco) containing 10% FBS (Hyclone)
and allowed to incubate for 6-8 hours. One ug of DNA was then added
to 100 ul of DMEM containing no FBS and 3 ul of Lipofectamine 2000
was added to 100 ul of DMEM containing no FBS. Both were incubated
for 5 minutes at room temperature. The lipofectamine/DMEM mixture
was added to the DNA/DMEM mixture and incubated for 15 minutes at
room temperature. The lipofectamine 2000/DNA mix was then added to
the HEK293 cells and incubated for 48-72 hrs at 37 degrees C. with
7% CO2. Cells were collected and pelleted by centrifugation and
washed twice with PBS.
[1264] For Western blot analysis, whole cell lysates were generated
by diluting samples directly into SDS-PAGE loading buffer
containing beta-mercaptoethanol, then incubated for 10 minutes at
70 degrees C. prior to loading the SDS-PAGE gel. Protein was
transferred onto nitrocellulose and probed using the mouse
anti-FLAG antibody (Kodak Scientific Imaging, Cat#IB13026) at a
concentration of 10 ug/ml. The blot was detected with goat
anti-mouse-HRP followed by incubation in ECL substrate. An
identical blot was probed with anti-P790 peptide sera (3-13-2001,
3875 L) at 1/1000. This blot was detected with goat anti-rabbit-HRP
followed by incubation in ECL substrate. Using this approach,
expression of recombinant P790P protein was detected in transiently
transfected HEK293 cells using an anti-FLAG polyclonal
antibody.
Example 47
Expression of P504S in Adenomatous Hyperplasia of the Prostate
[1265] This example describes how the prostate antigen P504S, and
antibodies specific for P504S, represent important diagnostic
reagants useful in the detection of prostate carcinoma, and,
additionally, in the differentiation of atypical adenomatous
hyperplasia (AAH) from prostate carcinoma. AAH of the prostate,
also known as adenosis, is characterized by abnormal architectural
patterns, but without significant cytologic atypia, in prostatic
glandular epithelium. It is often difficult to distinguish AAH from
prostatic carcinoma. In addition, it has been suggested that AAH is
a precursor lesion of the protatic adenocarcinoma. P504S (the DNA
and amino acid sequences for which were disclosed in SEQ ID NOs:
107 and 108), is a protein that we have previously shown to be
highly over-expressed in prostatice adenocarcinoma, and therefore
represents an excellent marker for prostate cancer.
[1266] Here we use immunohistochemistry to determine the expression
profile of P504S in a number of different prostate samples. A total
of 80 samples were examined, including 40 of AAH (prostatectomy:
n=30, biopsy: n=6, and transurethral resection: n=4), 20 cases of
prostatic adenocarcinomas and 20 cases of benign prostatic
hyperplasia (BPH). Immunohistochemistry for P504S and a basal cell
specific marker, 34.beta.E12, was performed on all samples.
[1267] The 34.beta.E12 stain confirmed the presence of patchy basal
cells in all 40 cases of AAH. P504S staining showed strong
cytoplasmic granular staining in 20/20 prostatic carcinomas and in
6 of 40 cases of AAH (15%). No BPH or benign prostate glands
adjacent to carcinomas or adjacent to AAH were positive for P504S.
A diffuse staining pattern of P504S was found in prostate carcinoma
samples, while focal positivity was seen in the positive cases of
AAH.
[1268] These findings demonstrate that combination staining using
34.beta.E12 and P504S has a strong diagnostic value in
distinguishing AAH from prostatic adenocarcinoma, and thus further
validates the use of P504S in any of a variety of illustrative
diagnostic and therapeutic embodiments described herein, for
example.
Example 48
Generation of an Illustrative P703P Fusion Protein
[1269] The identification and characterization of related forms of
the prostate specific antigen P703P has been described above, one
representative DNA sequence for which is set forth in SEQ ID NO:
171, encoding an amino acid sequence set forth in SEQ ID NO: 172.
In this example, an illustrative P703P fusion construct was made
and the encoded fusion protein produced. This recombinant fusion
protein can be used, for example, in diagnostic methods for the
detection of prostate cancer and/or to elicit an immune response in
a subject for the prevention and/or treatment of prostate
cancer.
[1270] Full length human PAP DNA was obtained by PCR from a
prostate cancer tissue cDNA library (PT library) with primers
hPAPF1 and hPAPRV1. The sequences for these primers are:
TABLE-US-00014 hPAPF1 (SEQ ID NO: 1014)
5'CGGCGGATCCGCCGCCACCATGAGAGCTGCACCCCTCCTCCT-3' and hPAPRV1 (SEQ ID
NO: 1015) 5'CGGCCTCGAGCTAATCTGTACTGTCTTCAGTACCTTGATGGCTG-3'.
[1271] The PCR product was then cloned into the PCR BluntII TOPO
vector. To modify the hPAP a second PCR was performed with primers
FOPP2F1
TABLE-US-00015 5'GAGAAAACCGTCCAGGCCAGTAAGGAGTTGAAGTTTGTGACTTTG
GTG-3'
(SEQ ID NO: 1016) and HPAPRV1 (SEQ ID NO: 1015), using hPAP/TOPO
BluntII as a template.
[1272] FOPP/PCRX1 (P703P containing DNA) was also modified using
primers FOPPF1
TABLE-US-00016 FOPPF1 (SEQ ID NO: 1017)
5'CGGCGGGCATATGCATCACCATCACCATCACATCATAAACGGCGAGGA CTGCAG-3' and
FOPP2RV1 (SEQ ID NO: 1018)
5'CACCAAAGTCACAAACTTCAACTCCTTACTGGCCTGGACGGTTTT CTC-3'.
[1273] Finally, using primers FOPPF1 and hPAPRV1, and the modified
hPAP and P703P PCR products as templates, a PCR was performed to
generate FOPP2. This PCR product was then cloned in to the PCRX1
vector at the restriction enzyme cutting sites NdeI and XhoI. The
FOPP2/PCRX1 plasmid was then used to transform the E. coli strain
Tuner (DE3) pLys S and plated out on LB plates containing kanamycin
and chloamphenicol. Using SDS-PAGE analysis and Western blot
analysis with antibodies against His-Tag, the transformant was
shown to express the FOPP2 protein when expression was induced
using IPTG.
[1274] To generate large quantity of the FOPP2 protein, the
expression clone culture was inoculated into 20 ml of STB
containing 50 .mu.g/ml kanamycin and 34 .mu.g/ml chloamphenicol,
and grown at 37.degree. C. until the OD600 read approximately 1.
The culture was then diluted into 1 liter of STB containing 50
.mu.g/ml kanamycin and 34 .mu.g/ml chloamphenicol, and grown at
37.degree. C. until the OD600 read approximately 0.4. IPTG was then
added to a final concentration of 1 mM, and the culture was
incubated at 37.degree. C. for 2 hours. The cells were centrifuged
at 5000 RPM for 8 minutes, washed in PBS, re-centrifuged, and
stored at -70.degree. C.
[1275] To purify the protein, the cell pellet was re-suspended in
25 ml of 10 mM Tris-Cl (pH 8.0) containing 2 mM PMSF and protease
inhibitors. The cells were sonicated several times and the lysate
was centrifuged for 60 minutes at 4000 RPM. The precipitate,
containing the inclusion bodies, was washed twice with 10 mM
Tris-HCl (pH 8.0) containing 1% CHAPS. The inclusion body was
dissolved in 40 ml of binding buffer (10 mM Tris-HCl, pH 8.0, 100
mM sodium phosphate, and 8M urea). The solution was mixed with 10
ml of Ni-NTA resin (Qiagen) for 30 minutes at room temperature. The
mixture was then poured into a 25 ml column, and washed with 50 ml
of wash buffer (10 mM Tris-Cl pH 6.3, 100 mM sodium phosphate, 0.5%
DOC and 8M urea). The bound protein was then eluted using elution
buffer (10 mM Tris-Cl, pH 8.0, 350 mM Imidazole, 100 mM sodium
phosphate, and 8M urea). The fractions containing FOPP2 were
combined and dialyzed extensively using a large volume of Tris-Cl,
pH 8.0, aliquoted, and stored at -70.degree. C. The FOPP2 sequence
was confirmed, and the DNA and amino acid sequence disclosed in SEQ
ID NOs: 1019 and 1020, respectively.
Example 49
Expression of the Prostate Antigen P501S in E. Coli
[1276] This example describes the recombinant production of P501S
polypeptides that are useful, for example, in immunodiagnostic and
immunotherapeutic applications. The identification and
characterization of prostate specific antigen P501S has been
described above, a representative full length DNA sequence for
which is set forth in SEQ ID NO: 110, encoding the amino acid
sequence set forth in SEQ ID NO: 113. This example describes the
expression of recombinant P501S C (corresponding to amino acids
257-553) and P501S D (corresponding to amino acids 316-553)
antigens using an E. coli expression system combined with an
N-terminal histadine tag and a TAT (twin arginine translocator)
signal peptide fusion.
Expression of P501S C in E. coli:
[1277] The P501S C coding region was PCR amplified with the
following primers:
[1278] PDM-930 5'cttccacggctgcaccagctgtgc 3' (SEQ ID NO:1023)
[1279] PDM-165 5'cacggacgtgaattctacgctgagtatttggcc 3' (SEQ ID
NO:1024)
Expression of P501S D in E. coli:
[1280] The P501S D coding region was PCR amplified with the
following primers:
TABLE-US-00017 (SEQ ID NO: 1025) PDM-929
5'cactatgatgaaggcgttcggatgggcag3' (SEQ ID NO: 1024) PDM-165
5'cacggacgtgaattctacgctgagtatttggcc3'
The PCR was performed with the following reaction components:
[1281] 10 .mu.l 10.times.Pfu buffer
[1282] 1 .mu.l 10 mM dNTPs
[1283] 2 .mu.l 10 .mu.M of each primer
[1284] 83 .mu.l of sterile water
[1285] 1.5 .mu.l Pfu DNA polymerase (Stratagene, La Jolla,
Calif.)
[1286] 50 ng DNA
PCR amplification was performed using the following reaction
conditions:
[1287] 96.degree. C. for 2 minutes, followed by 40 cycles of:
[1288] 96.degree. C. for 20 seconds;
[1289] 67.degree. C. for 15 seconds; and
[1290] 72.degree. C. for 2 minutes, followed by a final extension
step of:
[1291] 72.degree. C. for 4 minutes.
[1292] The PCR products were digested with EcoRI and cloned into
pPDM and pTAT (pPDM using a TAT signal peptide leader) at the
Eco721I and EcoRI. Constructs were confirmed to be correct through
sequence analysis and transformed into BLR (DE3) pLys S, HMS 174
(DE3) pLys S, Rosetta (DE3), and Rosetta (DE3) pLys S cells to
confirm protein expression. The amino acid sequence for the P501S
C-His construct was confirmed, and is disclosed in SEQ ID NO:1029,
with the corresponding DNA sequence disclosed in SEQ ID NO:1027.
The amino acid sequence for the P501S D-His construct was
confirmed, and is disclosed in SEQ ID NO:1028, with the
corresponding DNA sequence disclosed in SEQ ID NO:1026. These
recombinant P501S polypeptides can be used, for example, in
immunodiagnostic and/or immunotherapeutic embodiments, such as
those described herein.
Example 50
Expression of the Prostate Antigen P504S in Malignant Neoplasms
[1293] This example describes how the prostate antigen P504S, and
antibodies specific for P504S, represent important therapeutic and
diagnostic reagants useful in the detection of various types of
carcinomas. P504S (the DNA and amino acid sequences for which were
disclosed in SEQ ID NOs: 107 and 108), is a protein that we have
previously shown to be highly over-expressed in prostatic
adenocarcinoma, and therefore represents an excellent diagnostic
marker for prostate cancer. Here, immunohistochemistry was used to
determine the expression profile of P504S in 515 cases of malignant
neoplasms with epithelioid components. The tissue sections were
stained with the anti-P504S antibody, 13H4, the generation of which
was described in Example 18. Staining positive for P504S were 81%
of hepatacellular carcinomas (17/21), 80% of colorectal carcinomas
(20/25), 75% of renal cell carcinomas (18/24), 31% of urothelial
carcinomas (9/29) and 27% of gastric carcinomas (4/15). Rarely
staining positive for P504S were, lung, breast, pancreas, bile
duct, adrenal gland, and salivary gland carcinomas. Consistently
negative for P504S staining were ovary, thyroid and endometrium
carcinomas, melanomas, squamous cell carcinomas, basal cell
carcinomas, soft tissue tumors including epitheloid sarcomas and
synovial sarcoma, thmomas and germ cell tumors.
[1294] These findings identify additional tumor types demonstrating
overexpression of P504S and further validate the use of P504S in
any of a variety of illustrative diagnostic and therapeutic
embodiments described herein.
Example 51
Extended cDNA Sequences for Prostate Antigens P704P, P712P and
P775P
[1295] This example describes additional cDNA sequences for the
prostate antigens P704P, P712P, and P775P. Screening the partial
sequences specific for the prostate antigens P704P, P712P, and
P775P, against a prostate tumor library using colony hybridization
and PCR, in addition to bioinformatics methods, led to the
identification of additional sequences for each of these
antigens.
[1296] Sequences for prostate antigen P704P were previously
provided in SEQ ID NOs:67, 402, and 699-701. Herein is provided an
additional extended cDNA sequence for P704S, which is disclosed in
SEQ ID NO:1036.
[1297] Sequences for prostate antigen P712P were previously
provided in SEQ ID NOs:308, 397, and 552, with corresponding amino
acid sequences disclosed in SEQ ID NOs:553-568. Herein is provided
an additional extended cDNA sequence for P712S, which is disclosed
in SEQ ID NO:1034.
[1298] Sequences for prostate antigen P775P were previously
provided in SEQ ID NOs:311, 473-476, 553, and 593-597, with
corresponding amino acid sequences disclosed in SEQ ID NOs:477-483
and 957-966. Herein is provided an additional extended cDNA
sequence for P712S, which is disclosed in SEQ ID NO:1035.
[1299] In view of the previously identified over-expression of
P704P, P712P, and P775P in prostate cancer, these additional
extended sequences also represent important reagants useful in the
detection and/or therapy of prostate cancer.
Example 52
The Identification of a P501S Minigene that Contains Three
Overlapping Class I Epitopes for Multi-Epitope Vaccine
Immunization
[1300] The identification and characterization of prostate specific
antigen P501S has been described above, a representative full
length DNA sequence for which is set forth in SEQ ID NO: 110,
encoding the amino acid sequence set forth in SEQ ID NO: 113.
Extensive analysis of P501S (described in the above examples)
including cDNA microarray, quantitative real-time PCR, and
immunohistochemical analyses, have shown it to be expressed almost
exclusively in normal prostate, benign prostate hyperplasia and
both primary and secondary prostate tumors.
[1301] This example describes the identification of a small 11
amino acid fragment derived from P501S that contains naturally
processed epitopes for at least three class I alleles. The peptide
corresponds to amino acids 463-473 of P501S (SEQ ID NO:113),
corresponding to the sequence ASACDVSVRVV (SEQ ID NO:1037, with the
corresponding polynucleotide sequence disclosed in SEQ ID N:1038).
This sequence was derived from the previous identification of 6
different CD8+ T cell epitopes. Example 9 described the
identification of two HLA-Cw*0501 restricted epitopes, SACDVSVRVV
(SEQ ID NO:978) and ACDVSVRVV (SEQ ID NO:1012). Example 12
described the identification of two HLA-B*51011 restricted
epitopes, ASACDVSVRV (SEQ ID NO:855) and SACDVSVRV (SEQ ID NO:858).
Example 48 described the identification of two HLA-A*0201
restricted epitopes, ASACDVSVRV and SACDVSVRV.
[1302] To examine the potential cross-reactivity of the HLA-B*51011
and HLA-Cw*0501 epitopes identified in the human in-vitro system,
d310 B-LCL, which endogenously express both the HLA-B*51011 and
HLA-Cw*0501 alleles, were pulsed with each of the purified peptides
SACDVSVRV, SACDVSVRVV, and ACDVSVRVV, and used as APC for the
HLA-B*51011 restricted clone 2A2-4E5 and the HLA-Cw*0501 restricted
clone 2H2-1A12. The 2A2-4E5 clone specifically recognized the
SACDVSVRV peptide, and failed to recognize either the SACDVSVRVV or
ACDVSVRVV peptides. Conversely, and in agreement with the
previously described fine specificity of this clone, the 2H2-1A12
clone specifically recognized both the SACDVSVRVV and ACDVSVRVV
peptides. However, 2H2-1A12 failed to recognize the SACDVSVRV
peptide. Thus the two clones show no cross-reactivity of peptide
recognition. Further evidence for the absence of cross-reactivity
between the two clones at the level of the MHC:peptide is the fact
that each of the two clones failed to recognize P501S expressing
cells that express the reciprocal restricting allele. Example 45
describes the identification of an HLA-A2 restricted epitope
derived from P501S using HLA-A2 kb transgenic mice. This epitope
comprises residues 464-475 of P501S.
[1303] Thus, 3 distinct class-I restricted epitopes are processed
from a 11 amino acid region of P501S. The phenomenon of a single T
cell epitope being presented to T cells by more than one HLA allele
has been previously described. Specifically, a single
MAGE-AL-derived epitope was shown to be presented to T cells by
both HLA-B*35 and HLA-A*1 alleles (Luiten et al, Tissue Antigens
56: 77-81, 2000). Although B and T cell epitope clustering has been
previously reported (Bellone et al, 1995), to our knowledge this is
the first demonstration of multiple T cell epitopes being
identified to be clustered to a minimal amino acid sequence. The
observation that at least one of the 3 epitopes appears to be
processed less efficiently suggests that the clustering of the
epitopes is not simply a function of preferential processing of
this region. The clustering of multiple T cell epitopes to this
small amino acid sequence indicates that this region of P501S will
be particularly useful in the development of P501S-specific T cell
vaccination strategies.
[1304] 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.
Sequence CWU 0 SQTB SEQUENCE LISTING The patent application
contains a lengthy "Sequence Listing" section. A copy of the
"Sequence Listing" is available in electronic form from the USPTO
web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20080226620A1).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
0 SQTB SEQUENCE LISTING The patent application contains a lengthy
"Sequence Listing" section. A copy of the "Sequence Listing" is
available in electronic form from the USPTO web site
(http://seqdata.uspto.gov/?pageRequest=docDetail&DocID=US20080226620A1).
An electronic copy of the "Sequence Listing" will also be available
from the USPTO upon request and payment of the fee set forth in 37
CFR 1.19(b)(3).
* * * * *
References