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US-12618843-B2 - Biomarker combinations for determining aggressive prostate cancer

US12618843B2US 12618843 B2US12618843 B2US 12618843B2US-12618843-B2

Abstract

The present invention provides methods for the diagnosis of aggressive prostate cancer, including, but not limited to, methods for discerning between aggressive and non-aggressive forms of prostate cancer, and methods for detecting aggressive prostate cancer based on comparisons to a mixed control population of subjects with non-aggressive prostate cancer or not having prostate cancer.

Inventors

  • Douglas Campbell
  • Thao Ho-Le
  • Brad Walsh
  • Rachel Levin

Assignees

  • MINOMIC INTERNATIONAL LTD.

Dates

Publication Date
20260505
Application Date
20191004
Priority Date
20181005

Claims (20)

  1. 1 . A method for diagnosing aggressive prostate cancer (CaP) in a test subject, comprising: (a) detecting one or more analyte/s in a biological sample from the test subject to thereby obtain an analyte level for each said analyte in the test subject's biological sample, and obtaining a measurement of two or more clinical variables from the test subject; and (b) applying a suitable algorithm and/or transformation to a combination of the clinical variable measurements and analyte level/s of the test subject to thereby generate a test subject score value for comparison to a threshold value; (c) determining that the test subject has aggressive CaP when the subject test score value is above the threshold value; and (d) treating the subject diagnosed with aggressive CaP with one or more of surgery, radiation, or drugs, wherein: the one or more analyte/s comprise or consist of leptin, the two or more clinical variables comprise at least two of: total prostate-specific antigen (PSA), digital rectal examination (DRE), subject age, prostate volume, and the threshold value is determined by: detecting said one or more analyte/s in a series of biological samples obtained from a population of subjects having aggressive CaP and from a population of control subjects not having aggressive CaP, to thereby obtain an analyte level for each said analyte in each said biological sample of the series; combining each of said one or more analyte levels of the series with measurements of said two or more clinical variables obtained from each said subject from the population of subjects having aggressive CaP and from each subject from the population of control subjects, in a manner that allows discrimination between aggressive CaP and an absence of aggressive CaP, to thereby generate the threshold value; and wherein the two or more clinical variables and the one or more analyte/s comprise any one of the following: total PSA, prostate volume, leptin, subject age, IL-7 and VEGF; total PSA, prostate volume, leptin, subject age, IL-7, VEGF, osteopontin and CD40L; total PSA, % free PSA, prostate volume, leptin, osteopontin and HE4.WFDC2; total PSA, DRE, leptin, subject age, VEGF and IL-7; total PSA, DRE, leptin, subject age, VEGF, osteopontin; total PSA, DRE, leptin, subject age, VEGF, IL-7, GPC-1; total PSA, DRE, leptin, subject age, VEGF, osteopontin, GPC-1; total PSA, DRE, leptin, subject age, VEGF, IL-7, GPC-1, % free PSA; total PSA, DRE, leptin, subject age, VEGF, osteopontin, GPC-1, % free PSA; total PSA, DRE, leptin, subject age, prior negative biopsy, VEGF-C, osteopontin, GPC-1, CD40L, proPSA, % free PSA.
  2. 2 . The method of claim 1 , wherein the population of control subjects comprises subjects that do not have prostate cancer and subjects that have non-aggressive prostate cancer.
  3. 3 . A method for discerning whether a test subject has non-aggressive or aggressive prostate cancer (CaP), comprising: (a) detecting one or more analyte/s in a biological sample from the test subject to thereby obtain an analyte level for each said analyte in the test subject's biological sample, and obtaining a measurement of two or more clinical variable/s from the test subject; and (b) applying a suitable algorithm and/or transformation to a combination of the clinical variable measurements and analyte level/s to thereby generate a test subject score value for comparison to a threshold value; (c) determining that the test subject has aggressive CaP when the subject test score value is above the threshold value or determining that the test subject has non-aggressive CaP when the subject test score value is below the threshold value; and (d) treating the subject diagnosed with aggressive CaP with one or more of surgery, radiation, or drugs, wherein the test subject has previously been determined to have prostate cancer or a likelihood of having prostate cancer (e.g. by any one or more of a PSA-based test, digital rectal examination (DRE), family history, an ultrasound-based test, magnetic resonance imaging (MRI), a urine biomarker test, an exosome-based test), the one or more analyte/s comprise or consist of leptin, the two or more clinical variables comprise at least two of: total PSA, DRE, subject age, prostate volume, and the threshold value is determined by: detecting said one or more analyte/s in a series of biological samples obtained from a population of subjects having aggressive CaP and from a population of control subjects having non-aggressive CaP, to thereby obtain an analyte level for each said analyte in each said biological sample of the series; combining each of said one or more analyte levels of the series with measurements of said two or more clinical variables obtained from each subject from the population of subjects having aggressive CaP and from each subject from the population of control subjects, to thereby generate the threshold value; and wherein the two or more clinical variables and the one or more analyte/s comprise any one of the following: total PSA, prostate volume, leptin, subject age, IL-7 and VEGE; total PSA, prostate volume, leptin, subject age, IL-7, VEGF, osteopontin and CD40L; total PSA, % free PSA, prostate volume, leptin, osteopontin and HE4.WFDC2; total PSA, DRE, leptin, subject age, VEGF and IL-7; total PSA, DRE, leptin, subject age, VEGF, osteopontin; total PSA, DRE, leptin, subject age, VEGF, IL-7, GPC-1; total PSA, DRE, leptin, subject age, VEGF, osteopontin, GPC-1; total PSA, DRE, leptin, subject age, VEGF, IL-7, GPC-1, % free PSA; total PSA, DRE, leptin, subject age, VEGF, osteopontin, GPC-1, % free PSA; total PSA, DRE, leptin, subject age, prior negative biopsy, VEGF-C, osteopontin, GPC-1, CD40L, proPSA, % free PSA.
  4. 4 . The method of claim 1 or claim 3 , wherein the population of control subjects has non-aggressive CaP as defined by a Gleason score of 3+3.
  5. 5 . The method of claim 1 or 3 , comprising selecting a subset of the combined analyte/s and/or clinical variable measurements to generate the threshold value.
  6. 6 . The method of claim 1 or 3 , wherein said combining of each of said one or more analyte levels of the series with said measurements of the two or more clinical variables comprises combining a logistic regression score of the two or more clinical variable measurements and the one or more analyte level/s in a manner that maximizes said discrimination, in accordance with the formula: Logit ⁢ ( P ) = Log ⁡ ( P / 1 - P ) = intercept + ∑ i = 1 N ⁢ ( coefficient i × transformed ⁢ ( variable i ) ⁢ P = exp ⁢ ( Logit ( P ) ) 1 + exp ⁢ ( Logit ( P ) ) wherein: P is probability that the test subject has aggressive prostate cancer, the coefficient i is the natural log of the odds ratio of the variable, the transformed variable i is the natural log of the variable i value, excluding a variable age; or in accordance with the formula: Logit ⁢ ( P ) = Log ⁡ ( P / 1 - P ) = intercept + ∑ i = 1 N ⁢ ( coefficient i × transformed ⁢ ( variable i ) + coefficient Age × Age ⁢ P = exp ⁢ ( Logit ( P ) ) 1 + exp ⁢ ( Logit ( P ) ) wherein: P is probability that the test subject has aggressive prostate cancer, the coefficient i is the natural log of the odds ratio of the variable, the transformed variable i is the natural log of the variable i value, or in accordance with the formula: Logit ⁢ ( P ) = Log ⁢ ( P / 1 - P ) = intercept + ∑ i = 1 N ⁢ ( coefficient i × ( variable i ) + coefficient Age × Age ⁢ P = exp ⁢ ( Logit ( P ) ) 1 + exp ⁢ ( Logit ( P ) ) wherein: P is probability that the test subject has aggressive prostate cancer, and the coefficient i is the natural log of the odds ratio of the variable.
  7. 7 . The method of claim 1 or 3 , wherein said applying a suitable algorithm and/or transformation to the combination of the clinical variable measurements and analyte level/s comprises use of an exponential function, a logarithmic function, a power function and/or a root function.
  8. 8 . The method of claim 1 or 3 , wherein the suitable algorithm and/or transformation applied to the combination of the clinical variable measurements and analyte level/s of the test subject is in accordance with the formula: Logit ⁢ ( P ) = Log ⁡ ( P / 1 - P ) = intercept + ∑ i = 1 N ⁢ ( coefficient i × transformed ⁢ ( variable i ) ⁢ P = exp ⁢ ( Logit ( P ) ) 1 + exp ⁢ ( Logit ( P ) ) wherein: P is probability of that the test subject has aggressive prostate cancer, the coefficient i is the natural log of the odds ratio of the variable, the transformed variable i is the natural log of the variable i value, excluding a variable age; or in accordance with the formula: Logit ⁢ ( P ) = Log ⁡ ( P / 1 - P ) = intercept + ∑ i = 1 N ⁢ ( coefficient i × transformed ⁢ ( variable i ) + coefficient Age × Age ⁢ P = exp ⁢ ( Logit ( P ) ) 1 + exp ⁢ ( Logit ( P ) ) wherein: P is probability of that the test subject has aggressive prostate cancer, the coefficient i is the natural log of the odds ratio of the variable, the transformed variable i is the natural log of the variable i value; or in accordance with the formula: Logit ⁢ ( P ) = Log ⁡ ( P / 1 - P ) = intercept + ∑ i = 1 N ⁢ ( coefficient i × ( variable i ) + coefficient Age × Age ⁢ P = exp ⁢ ( Logit ( P ) ) 1 + exp ⁢ ( Logit ( P ) ) wherein: P is probability that the test subject has aggressive prostate cancer, the coefficient i is the natural log of the odds ratio of the variable; and said suitable algorithm and/or transformation is used to generate the subject test score that is compared to the threshold value to thereby determine whether or not the test subject has aggressive prostate cancer.
  9. 9 . The method of claim 1 or 3 , wherein said combining of each said analyte level of the series with measurements of said two or more clinical variables obtained from each said subject of the populations maximizes said discrimination.
  10. 10 . The method of claim 1 or 3 , wherein said combining of each said analyte level of the series with the measurements of two or more clinical variables obtained from each said subject of the populations is conducted in a manner that: (i) reduces the misclassification rate between the subjects having aggressive CaP and said control subjects; and/or (ii) increases sensitivity in discriminating between the subjects having aggressive CaP and said control subjects; and/or (iii) increases specificity in discriminating between the subjects having aggressive CaP and said control subjects.
  11. 11 . The method of claim 10 , wherein said combining in a manner that reduces the misclassification rate between the subjects having aggressive CaP and said control subjects comprises selecting a suitable true positive and/or true negative rate and/or minimizes the misclassification rate optionally by identifying a point where the true positive rate intersects the true negative rate.
  12. 12 . The method of claim 10 , wherein said selecting the threshold value from the combined clinical variable measurement/s and combined analyte level/s in a manner that increases specificity and/or sensitivity in discriminating between the subjects having aggressive CaP and said control subjects increases or maximizes said specificity.
  13. 13 . The method of claim 1 or 3 , wherein the two or more clinical variables and the one or more analytes consist of any one of the following: total PSA, prostate volume, leptin, subject age, IL-7 and VEGF; total PSA, prostate volume, leptin, subject age, IL-7, VEGF, osteopontin and CD40L; total PSA, % free PSA, prostate volume, leptin, osteopontin and HE4.WFDC2; total PSA, DRE, leptin, subject age, VEGF and IL-7; total PSA, DRE, leptin, subject age, VEGF, osteopontin; total PSA, DRE, leptin, subject age, VEGF, IL-7, GPC-1; total PSA, DRE, leptin, subject age, VEGF, osteopontin, GPC-1; total PSA, DRE, leptin, subject age, VEGF, IL-7, GPC-1, % free PSA; total PSA, DRE, leptin, subject age, VEGF, osteopontin, GPC-1, % free PSA; total PSA, DRE, leptin, subject age, prior negative biopsy, VEGF-C, osteopontin, GPC-1, CD40L, proPSA, % free PSA.
  14. 14 . The method of claim 1 or 3 , wherein the test subject has previously received a positive indication of aggressive prostate cancer, optionally by digital rectal exam (DRE) and/or by PSA testing.
  15. 15 . The method of claim 1 or 3 , wherein said detecting of one or more analyte/s in the biological sample from the test subject comprises: (i) measuring one or more fluorescent signals indicative of each said analyte level; (ii) obtaining a measurement of weight/volume of said analyte/s in the biological sample; (iii) measuring an absorbance signal indicative of each said analyte level; or (iv) using a technique selected from the group consisting of: mass spectrometry, a protein array technique, high performance liquid chromatography (HPLC), gel electrophoresis, radiolabeling, and any combination thereof.
  16. 16 . The method of claim 1 or 3 , wherein each said sample is contacted with first and second antibody populations for detection of each said analyte, wherein each said antibody population has binding specificity for one of said analytes, and the first and second antibody populations have different analyte binding specificities, optionally wherein the first and/or second antibody populations are labelled with a label selected from the group consisting of a radiolabel, a fluorescent label, a biotin-avidin amplification system, a chemiluminescence system, microspheres, and colloidal gold.
  17. 17 . The method of claim 16 , wherein binding of each said antibody population to the analyte is detected by a technique selected from the group consisting of: immunofluorescence, radiolabeling, immunoblotting, Western blotting, enzyme-linked immunosorbent assay (ELISA), flow cytometry, immunoprecipitation, immunohistochemistry, biofilm test, affinity ring test, antibody array optical density test, and chemiluminescence.
  18. 18 . The method of claim 1 or 3 , wherein the series of biological samples obtained from each said population and the test subject's biological sample are each whole blood, serum, plasma, saliva, tear/s, urine, or tissue.
  19. 19 . The method of claim 1 or 3 , wherein said test subject, said population of subjects having aggressive CaP, and said population of control subjects are human.
  20. 20 . The method of claim 1 or 3 , wherein the method further comprises a step of biopsy prior to treating the subject diagnosed with aggressive CaP, to confirm said diagnosis.

Description

INCORPORATION BY CROSS-REFERENCE This application is a national phase application based on PCT/AU2019/051080 filed on Oct. 4, 2019, which claims priority from Australian provisional patent application numbers 2018903763 filed on Oct. 5, 2018, and 2019900406 filed on Feb. 8, 2018, the entire contents of which are incorporated herein by cross-reference. TECHNICAL FIELD The present invention relates generally to the fields of immunology and medicine. More specifically, the present invention relates to the diagnosis of aggressive and non-aggressive forms of prostate cancer in subjects by assessing various combinations of biomarker/s and clinical variable/s. BACKGROUND Prostate cancer is the most frequently diagnosed visceral cancer and the second leading cause of cancer death in males. According to the National Cancer Institute's SEER program and the Centers for Disease Control's National Center for Health Statistics, 164,690 cases of prostate cancer are estimated to have arisen in 2018 (9.5% of all new cancer cases) with an estimated 29,430 deaths (4.8% of all cancer deaths) (see SEER Cancer Statistics Factsheets: Prostate Cancer. National Cancer Institute. Bethesda, MD, http://seer.cancer.gov/statfacts/html/prost.html). The relative proportion of aggressive prostate cancers (defined as Gleason 3+4 or higher) to non-aggressive prostate cancers (defined as Gleason 3+3 or lower) differs between studies. A recent study of 1012 US men proceeding to prostate biopsy with elevated PSA demonstrated 542 men were negative for prostate cancer on biopsy, 239 had Gleason 3+3 prostate cancer and 231 had Gleason 3+4 or higher prostate cancer (Parekh et al. Eur Urol. 2015 September; 68 (3): 464-70). Commonly used screening tests for prostate cancer include digital rectal exam (DRE) and detection of prostate specific antigen (PSA) in blood. DRE is invasive and imprecise, and the prevalence of false negative (i.e. cancer undetected) and false positive (i.e. indication of cancer where none exists) results from PSA assays is well documented. Upon a positive diagnosis with DRE or PSA screening, confirmatory diagnostic tests include transrectal ultrasound, biopsy, and transrectal magnetic resonance imaging (MRI) biopsy. These techniques are invasive and cause significant discomfort to the subject under examination. In 2012, the United States Preventative Services Taskforce (USPTF) issued a recommendation against routine prostate cancer screening using the PSA test. This led to a decrease in the number of men proceeding to biopsy following elevated PSA test results and an increase in the proportion of men presenting with aggressive prostate cancer (Fleshner & Carlsson, Nature Reviews Urology, volume 15, pages 532-534, 2018). A general need exists for more convenient, reliable and accurate diagnostic tests capable of discerning between aggressive and non-aggressive forms of prostate cancer and for detecting aggressive prostate cancer. SUMMARY OF THE INVENTION The present inventors have identified combinations of biomarker/s and clinical variable/s effective for detecting aggressive prostate cancer. Accordingly, the biomarker/clinical variable combinations disclosed herein can be used to detect the presence or absence of aggressive prostate cancer in a subject. The present invention relates at least to the following series of numbered embodiments below: Embodiment 1. A method for diagnosing aggressive prostate cancer (CaP) in a test subject, comprising: (a) detecting one or more analyte/s in a biological sample from the test subject to thereby obtain an analyte level for each said analyte in the test subject's biological sample, and obtaining a measurement of two or more clinical variables from the test subject; and(b) applying a suitable algorithm and/or transformation to a combination of the clinical variable measurements and analyte level/s of the test subject to thereby generate a test subject score value for comparison to a threshold value; and(c) determining whether the test subject has aggressive CaP by comparison of the subject test score value and the threshold value,wherein:the one or more analyte/s comprise or consist of leptin,the two or more clinical variables comprise at least two of: total PSA, DRE, subject age, prostate volume, andthe threshold value is determined by:detecting said one or more analyte/s in a series of biological samples obtained from a population of subjects having aggressive CaP and from a population of control subjects not having aggressive CaP, to thereby obtain an analyte level for each said analyte in each said biological sample of the series;combining each said analyte level of the series with measurements of said two or more clinical variables obtained from each said subject of the populations, in a manner that allows discrimination between aggressive CaP and an absence of aggressive CaP, to thereby generate the threshold value. Embodiment 2. The method of embodiment 1, wherein the population of