PCA3, PCA3 GENES, AND METHODS OF USE

• US 20100047809A1
• Filed: 10/30/2009
• Published: 02/25/2010
• Est. Priority Date: 04/10/1997
• Status: Active Grant

• Current Assignee: Johns Hopkins University
• Original Assignee: Johns Hopkins University
• Inventors: BUSSEMAKERS, Marion J.G., Isaacs, William B.
• Granted Patent: US 8,551,699 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: A01K 2217/05 Animals comprising random inserted nucleic acids (transgenic)
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: A61P 13/08 of the prostate
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C07K 14/47 from mammals
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/158 Expression markers

Abstract

The present invention relates, in general, to a prostate-specific antigen, PCA3. In particular, the present invention relates to nucleic acid molecules coding for the PCA3 protein; purified PCA3 proteins and polypeptides; recombinant nucleic acid molecules; cells containing the recombinant nucleic acid molecules; antibodies having binding affinity specifically to PCA3 proteins and polypeptides; hybridomas containing the antibodies; nucleic acid probes for the detection of nucleic acids encoding PCA3 proteins; a method of detecting nucleic acids encoding PCA3 proteins or polypeptides in a sample; kits containing nucleic acid probes or antibodies; bioassays using the nucleic acid sequence, protein or antibodies of this invention to diagnose, assess, or prognose a mammal afflicted with prostate cancer; therapeutic uses; and methods of preventing prostate cancer in an animal.

Claims

1. A method of determining whether a sample contains a PCA3 nucleic acid, comprising:

a) contacting said sample with a nucleic acid molecule 10 to 100 nucleotides in length comprising a sequence of at least 10 consecutive nucleotides contained within SEQ ID NO;

1, SEQ ID NO;

3, SEQ ID NO;

4, SEQ ID NO;

6 or a sequence fully complementary thereto; and

b) detecting binding of said nucleic acid molecule to the PCA3 nucleic acid, whereby it is determined that said sample contains the PCA3 nucleic acid.

2. The method of claim 1, wherein said sequence of at least 10 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4, SEQ ID NO;

6 or a sequence fully complementary thereto is a sequence of at least 15 consecutive nucleotides contained within SEQ ID NO;

1, SEQ ID NO;

3, SEQ ID NO;

4, SEQ ID NO;

6 or a sequence fully complementary thereto.

3. The method of claim 2, wherein said oligonucleotide of 10 to 100 nucleotides in length is an oligonucleotide 10 to 50 nucleotides in length.

4. The method of claim 2, wherein said oligonucleotide of 10 to 100 nucleotides in length is an oligonucleotide 10 to 35 nucleotides in length.

5. The method of claim 2, wherein said oligonucleotide of 10 to 100 nucleotides in length is an oligonucleotide of 20 to 100 nucleotides in length.

6. The method of claim 2, wherein said sequence of at least 15 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4 or SEQ ID NO;

6 encodes a plurality of consecutive amino acids of the predicted PCA3 polypeptide of SEQ ID NO;

2.

7. The method of claim 6, wherein said nucleic acid molecule of 10 to 100 nucleotides in length is a nucleic acid molecule of 20 to 100 nucleotides in length.

8. The method of claim 2, wherein the detecting comprises detecting in a nucleic acid hybridization procedure, and wherein said nucleic acid molecule comprises a detectable label.

9. The method of claim 6, wherein the detecting comprises detecting in a nucleic acid hybridization procedure, and wherein said nucleic acid molecule comprises a detectable label.

10. The method of claim 6, wherein said sequence of at least 15 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4 or SEQ ID NO;

6 that encodes said plurality of consecutive amino acids of the predicted PCA3 polypeptide of SEQ ID NO;

2 comprises nucleotides 381-400 of SEQ ID NO;

1.

11. The method of claim 6, wherein said sequence of at least 15 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4 or SEQ ID NO;

6 that encodes said plurality of consecutive amino acids of the predicted PCA3 polypeptide of SEQ ID NO;

2 comprises nucleotides 381-410 of SEQ ID NO;

1.

12. The method of claim 6, wherein said sequence of at least 15 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4 or SEQ ID NO;

6 that encodes said plurality of consecutive amino acids of the predicted PCA3 polypeptide of SEQ ID NO;

2 comprises nucleotides 401-420 of SEQ ID NO;

1.

13. The method of claim 6, wherein said sequence of at least 15 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4 or SEQ ID NO;

6 that encodes said plurality of consecutive amino acids of the predicted PCA3 polypeptide of SEQ ID NO;

2 comprises nucleotides 401-430 of SEQ ID NO;

1.

14. The method of claim 6, wherein said sequence of at least 15 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4 or SEQ ID NO;

6 that encodes said plurality of consecutive amino acids of the PCA3 predicted polypeptide of SEQ ID NO;

2 comprises nucleotides 427-446 of SEQ ID NO;

1.

15. The method of claim 6, wherein said sequence of at least 15 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4 or SEQ ID NO;

6 that encodes said plurality of consecutive amino acids of the predicted PCA3 polypeptide of SEQ ID NO;

2 comprises nucleotides 447-466 of SEQ ID NO;

1.

31. The method of claim 1, wherein said sequence of at least 10 consecutive nucleotides is contained within a PCA3 exon sequence selected from the group consisting of:

a) PCA3 exon 1, as set forth between nucleotides 1-98 of SEQ ID NO;

1 or 1-120 of SEQ ID NO;

6;

b) PCA3 exon 2, as set forth between nucleotides 99-263 of SEQ ID NO;

1 or 121-285 of SEQ ID NO;

6;

c) PCA3 exon 3, as set forth between nucleotides 264-446 of SEQ ID NO;

1 or 286-468 of SEQ ID NO;

6;

d) PCA3 exon 4a, as set forth between nucleotides 447-985 of SEQ ID NO;

1 or 469-1007 of SEQ ID NO;

6;

e) PCA3 exon 4b, as set forth between nucleotides 986-2037 of SEQ ID NO;

1 or 1008-2066 of SEQ ID NO;

6;

f) PCA3 exon 4c, as set forth between nucleotides 2067-2622 of SEQ ID NO;

6;

g) PCA3 exon 4d, as set forth between nucleotides 2623-3582 of SEQ ID NO;

6; and

h) a combination of said PCA3 exon sequences of a) to g).

32. The method of claim 1, wherein said nucleic acid molecule is or is complementary to the polynucleotide sequence encoding the predicted PCA3 open reading frame (ORF) set forth from nucleotides 379 to 531 of SEQ ID NO:

1 or from nucleotides 401 to 553 of SEQ ID NO;

6.

16. A method of determining whether a sample contains a PCA3 nucleic acid, comprising:

a) contacting said sample with a nucleic acid molecule 10 to 100 nucleotides in length comprising a sequence of at least 10 consecutive nucleotides contained within SEQ ID NO;

1, SEQ ID NO;

3, SEQ ID NO;

4, SEQ ID NO;

6 or a sequence fully complementary thereto,

b) detecting binding of said nucleic acid molecule to the PCA3 nucleic acid, whereby it is determined that said sample contains the PCA3 nucleic acid,

wherein said nucleic acid molecule does not specifically hybridize to nucleotides 511-985 of SEQ ID NO;

1, nucleotides 346-820 of SEQ ID NO;

3, nucleotides 346-820 of SEQ ID NO;

4 or nucleotides 533-1007 of SEQ ID NO;

6 under stringent conditions of 0.2×

SSC and 0.1% SDS at 68 degrees C.

17. The method of claim 16, wherein said sequence of at least 10 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4, SEQ ID NO;

6 or a sequence fully complementary thereto is a sequence of at least 15 consecutive nucleotides contained within SEQ ID NO;

1, SEQ ID NO;

3, SEQ ID NO;

4, SEQ ID NO;

6 or a sequence fully complementary thereto.

18. The method of claim 17, wherein said oligonucleotide of 10 to 100 nucleotides in length is an oligonucleotide 10 to 50 nucleotides in length.

19. The method of claim 17, wherein said oligonucleotide of 10 to 100 nucleotides in length is an oligonucleotide of 10 to 35 nucleotides in length.

20. The method of claim 17, wherein said oligonucleotide of 10 to 100 nucleotides in length is an oligonucleotide of 20 to 100 nucleotides in length.

21. The method of claim 17, wherein said sequence of at least 15 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4 or SEQ ID NO;

6 encodes a plurality of consecutive amino acids of the predicted PCA3 polypeptide of SEQ ID NO;

2.

22. The method of claim 21, wherein said nucleic acid molecule of 10 to 100 nucleotides in length is a nucleic acid molecule of 20 to 100 nucleotides in length.

23. The method of claim 17, wherein the detecting comprises detecting in a nucleic acid hybridization procedure, and wherein said nucleic acid molecule comprises a detectable label.

24. The method of claim 21, wherein the detecting comprises detecting in a nucleic acid hybridization procedure, and wherein said nucleic acid molecule comprises a detectable label.

25. The method of claim 21, wherein said sequence of at least 15 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4 or SEQ ID NO;

6 that encodes said plurality of consecutive amino acids of the predicted PCA3 polypeptide of SEQ ID NO;

2 comprises nucleotides 381-400 of SEQ ID NO;

1.

26. The method of claim 21, wherein said sequence of at least 15 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4 or SEQ ID NO;

6 that encodes said plurality of consecutive amino acids of the predicted PCA3 polypeptide of SEQ ID NO;

2 comprises nucleotides 381-410 of SEQ ID NO;

1.

27. The method of claim 21, wherein said sequence of at least 15 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4 or SEQ ID NO;

6 that encodes said plurality of consecutive amino acids of the predicted PCA3 polypeptide of SEQ ID NO;

2 comprises nucleotides 401-420 of SEQ ID NO;

1.

28. The method of claim 21, wherein said sequence of at least 15 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4 or SEQ ID NO;

6 that encodes said plurality of consecutive amino acids of the predicted PCA3 polypeptide of SEQ ID NO;

2 comprises nucleotides 401-430 of SEQ ID NO;

1.

29. The method of claim 21, wherein said sequence of at least 15 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4 or SEQ ID NO;

6 that encodes said plurality of consecutive amino acids of the PCA3 polypeptide of SEQ ID NO;

2 comprises nucleotides 427-446 of SEQ ID NO;

1.

30. The method of claim 21, wherein said sequence of at least 15 consecutive nucleotides contained within SEQ ID NO:

1, SEQ ID NO;

3, SEQ ID NO;

4 or SEQ ID NO;

6 that encodes said plurality of consecutive amino acids of the predicted PCA3 polypeptide of SEQ ID NO;

2 comprises nucleotides 447-466 of SEQ ID NO;

1.