mRNA Ratios in Urinary Sediments and/or Urine as a Prognostic and/or Theranostic Marker for Prostate Cancer

• US 20100021884A1
• Filed: 12/23/2005
• Published: 01/28/2010
• Est. Priority Date: 12/24/2004
• Status: Active Grant

• Current Assignee: Stichting Katholieke Universiteit
• Original Assignee: Stichting Katholieke Universiteit
• Inventors: Witjes, Alfred J., Schalken, Jack A., Hessels, Daphne, Verhaegh, Gerald
• Granted Patent: US 7,960,109 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G01N 2333/96455 Kallikrein (3.4.21.34; 3.4.21.35)
• CPC Class Codes: G01N 33/57434 of prostate

Abstract

Described herein are methods and kits for prognosis of prostate cancer in a subject. The methods comprises: (a) determining the ratio of PCA3 and PSA expression in a urine sample and (b) correlating the value of the PCA3/PSA ratio with the aggressiveness and mortality risk of prostate cancer in the subject. Kits for prognosing prostate cancer are also described. More particularly, the present invention features a method for prognosing prostate cancer in a biological sample of a patient comprising: assessing the amount of a prostate cancer specific PCA3 mRNA and the amount of PSA in the biological sample; determining a ratio value of this amount of prostate cancer specific PCA3 mRNA over the amount of PSA; comparing the ratio value to at least one predetermined cut-off value, wherein a ratio value above the predetermined cut-off value is indicative of a higher risk of mortality of prostate cancer as compared to a ratio value below the predetermined cut-off value.

Claims

1. A method for prognosing prostate cancer in a biological sample of a patient comprising:

a) assessing the amount of a prostate cancer specific PCA3 mRNA and the amount of PSA in said biological sample;

b) determining a ratio value of said amount of said prostate cancer specific PCA3 mRNA over said amount of PSA; and

c) comparing said ratio value to at least one predetermined cut-off value,

wherein a ratio value above said predetermined cut-off value is indicative of a higher risk of mortality of prostate cancer as compared to a ratio value below said predetermined cut-off value.

2. The method of claim 1, wherein said biological sample is selected from the group consisting of:

urine, prostate tissue resection, prostate tissue biopsy, ejaculate and bladder washing.

3. The method of claim 2, wherein said biological sample is a urine sample obtained after a digital rectal examination.

4. The method of claim 1, wherein said amount of PSA is the amount of PSA mRNA.

9. The method of claim 1, wherein an amplification reaction is used for determining the amount of said prostate cancer specific PCA3 nucleic acid.

10. The method of claim 9, wherein said amplification reaction is selected from the group consisting of:

a) polymerase chain reaction (PCR);

b) nucleic acid sequence-based amplification assay (NASBA);

c) transcription mediated amplification (TMA);

d) ligase chain reaction (LCR); and

e) strand displacement amplification (SDA).

12. The method of claim 1, wherein the amount of said prostate cancer specific PCA3 nucleic acid is assessed by using at least one oligonucleotide that hybridizes to a PCA3 nucleic acid sequence selected from the group consisting of:

a) a nucleic acid sequence set forth in SEQ ID NO;

1;

b) a nucleic acid sequence set forth in SEQ ID NO;

2; and

c) a nucleic acid sequence that hybridizes under high stringency conditions to a nucleic acid sequence in a) or b).

13. The method of claim 12, wherein the amount of said PSA is assessed by using at least one oligonucleotide that hybridizes under high stringency conditions to a PSA nucleic acid sequence selected from the group consisting of:

a) a nucleic acid sequence set forth in SEQ ID NO;

38; and

b) a nucleic acid sequence that hybridizes under high stringency conditions to a nucleic acid sequence in a);

14. The method of claim 1, wherein the amount of PSA protein contained in said biological sample is assessed.

15. The method of claim 14, wherein an antibody is used to assess said amount of PSA protein.

18. The method of claim 1, further comprising determining the gleason score of a prostate sample from said patient and correlating said PCA3/PSA ratio value and said gleason score with a mortality risk associated with said disease.

19. The method of claim 18, wherein said PCA3/PSA ratio value and said Gleason score is correlated with a prediction of drug efficacy, patient outcome and/or a forecast of disease risk.

25. The method of claim 1, wherein said cut-off value is selected from 132×

10<sup>−

3</sup> and 200×

10<sup>−

3</sup>.

26. The method of claim 1 further comprising the use of a cut-off value of 3 ng/ml of serum PSA protein.

5. A method for prognosing prostate cancer in a biological sample comprising:

a) contacting a biological sample with at least one oligonucleotide that hybridizes to a prostate cancer specific PCA3 mRNA;

b) contacting said biological sample with at least one oligonucleotide that hybridizes to a PSA mRNA;

c) determining the amount of PCA3 mRNA and the amount of PSA mRNA present in said biological sample;

d) determining a ratio value of said amount of PCA3 mRNA over said amount of PSA mRNA;

e) comparing said ratio value of said amount of PCA3 mRNA over said amount of PSA mRNA to at least one predetermined cut-off value,

wherein a ratio value above said predetermined cut-off value is indicative of the presence of a more aggressive cancer as compared to a ratio value below said predetermined cut-off value which is indicative of the presence of a less aggressive cancer.

11. The method of claim 5, wherein the amount of said prostate cancer specific PCA3 nucleic acid and of said PSA nucleic acid is determined using a hybridization assay.

6. A method for assessing prostate cancer tumor volume in a biological sample comprising:

a) assessing the amount of a prostate cancer specific PCA3 nucleic acid and the amount of PSA in a sample;

b) determining a ratio value of said amount of said prostate cancer specific PCA3 nucleic acid over said amount of PSA;

c) comparing said ratio value to at least one predetermined cut-off value,

wherein a ratio value above said predetermined cut-off value is indicative of a greater prostate cancer tumor volume as compared to a ratio value below said predetermined cut-off value.

7. A method of monitoring prostate cancer tumor growth in a biological sample of a patient comprising:

a) assessing the amount of a prostate cancer specific PCA3 nucleic acid and the amount of PSA in said biological sample at a first point in time;

b) determining a ratio value of said amount of said prostate cancer specific PCA3 nucleic acid over said amount of PSA;

c) repeating steps a) and b) using a biological sample from said patient at a subsequent point in time; and

d) comparing the ratio value obtained in step b) with the ratio value obtained in step c)

wherein a higher ratio value in step b) compared to the ratio value obtained in step c) is indicative of the progression of prostate cancer and of a greater tumor volume.

21. The method of claim 7, wherein said biological sample is obtained from a patient undergoing a prostate cancer treatment between said first and said subsequent point in time thereby monitoring an effect of said treatment on cancer tumor growth or cancer progression.

23. The method of one of claim 21, wherein said ratio is superior to about 200×

10<sup>−

3</sup>, between about 75×

10<sup>−

3</sup> and about 200×

10<sup>−

3</sup> or between about 0 and about 75×

10<sup>−

3</sup>.

8. A method of monitoring the progression of prostate cancer in a biological sample comprising:

a) contacting a biological sample with at least one oligonucleotide that hybridizes to a prostate cancer specific PCA3 nucleic acid;

b) contacting said biological sample with at least one oligonucleotide that hybridizes to a PSA nucleic acid;

c) determining the amount of PCA3 nucleic acid and the amount of PSA nucleic acid present in said biological sample;

d) determining a ratio value of said amount of PCA3 nucleic acid over said amount of PSA nucleic acid; and

e) repeating steps a) to d) in a subsequent point in time; and

f) comparing the ratio value obtained in step d) with the ratio value obtained in step e)

wherein a higher ratio value in step e) compared to the ratio value obtained in step d) is indicative of the progression of prostate cancer.

16. A diagnostic and prognostic kit for prostate cancer comprising at least one container means having disposed therein

a) at least one oligonucleotide that hybridizes to a prostate cancer specific PCA3 nucleic acid selected from the group consisting of:

i. a nucleic acid sequence set forth in SEQ ID NO;

1;

ii. a nucleic acid sequence set forth in SEQ ID NO;

2;

iii. a nucleic acid sequence fully complementary to i or ii; and

iv. a nucleic acid sequence that hybridizes under high stringency condition to the nucleic acid sequence in i, ii or iii;

b) at least one oligonucleotide that hybridizes to a PSA nucleic acid selected from the group consisting of;

i. a nucleic acid sequence set forth in SEQ ID NO;

1;

ii. a nucleic acid sequence fully complementary to i;

iii. a nucleic acid sequence that hybridizes under high stringency condition to the nucleic acid sequence in i or ii; and

c) instructions for determining prostate cancer diagnosis and prognosis based on the detection of a particular ratio of prostate cancer specific PCA3 nucleic acid level over PSA nucleic acid level.

17. A method of determining the risk of progression of prostate cancer after therapy comprising:

a) assessing the amount of a prostate cancer specific PCA3 nucleic acid and the amount of PSA in a sample before therapy;

b) determining a ratio value of said amount of said prostate cancer specific PCA3 nucleic acid over said amount of PSA;

c) repeating steps a) and b) using a biological sample from the said patient after said therapy; and

d) comparing the ratio value obtained after therapy with the ratio value obtained before therapy,

wherein a higher ratio value in said sample after therapy compared to the ratio value obtained before said therapy is indicative of the progression of prostate cancer.

20. A method of staging prostate cancer in a biological sample of a patient comprising:

a) assessing the amount of a prostate cancer specific PCA3 nucleic acid and the amount of PSA in said biological sample;

b) determining a ratio value of said amount of said prostate cancer specific PCA3 nucleic acid over said amount of PSA;

c) comparing said ratio value with at least one predetermined cut-off value; and

d) correlating a ratio value with a particular stage of prostate cancer,

wherein a ratio value above a predetermined cut-off value indicates a more advanced stage of prostate cancer as compared to a ratio value below said predetermined cut-off value, thereby staging prostate cancer.

22. A method for prognosing prostate cancer in a human patient, comprising:

a) performing an in vitro nucleic acid amplification assay on a biological sample of said patient or extract thereof using a first primer pair which is specific to a prostate cancer specific PCA3 nucleic acid sequence and a second primer pair which is specific to a PSA nucleic acid sequence;

b) quantifying said PCA3 nucleic acid sequence and said PSA nucleic acid sequence; and

c) calculating a normalized ratio of PCA3 over PSA, wherein said ratio can be correlated to a PCA3 mRNA level and a PSA mRNA level in said patient,

wherein said normalized ratio of PCA3 over PSA positively correlates with a grade or stage of prostate cancer.

24. A kit for prognosing prostate cancer in a patient comprising:

a) a first primer pair specific for amplifying a PCA3 nucleic acid associated with prostate cancer present in a patient sample;

b) a second primer pair specific for amplifying a PSA nucleic acid;

c) reagents enabling a quantitative detection of PCA3 and of PSA nucleic acid amplification products when said PCA3 and second prostate-specific nucleic acid sequence are present; and

d) instructions for determining prostate cancer diagnosis and prognosis based on the detection of a particular ratio of prostate cancer specific PCA3 nucleic acid level over PSA nucleic acid level.