WO2013116742A1

WO2013116742A1 - Predicting responses to androgen deprivation therapy and methods for treating prostate cancer

Info

Publication number: WO2013116742A1
Application number: PCT/US2013/024465
Authority: WO
Inventors: Manish Kohli; Ann L. Oberg; Douglas W. Mahoney; Roman M. ZENKA; Yuji ZHANG; Sheng Zhang
Original assignee: Mayo Foundation for Medical Education and Research; Cornell University; Mayo Clinic in Florida
Current assignee: Mayo Foundation for Medical Education and Research; Cornell University; Mayo Clinic in Florida
Priority date: 2012-02-01
Filing date: 2013-02-01
Publication date: 2013-08-08
Anticipated expiration: 2014-08-01

Abstract

This document provides methods and materials for predicting whether a prostate cancer patient is likely to respond to an androgen deprivation therapy for a prolonged period of time. For example, methods and materials for predicting whether or not a prostate cancer patient is likely to respond to an androgen deprivation therapy for a prolonged period of time based at least in part on the presence of an elevated level of 17-β-estradiol, an elevated level of estrone, an elevated level of a neuropilin-2 polypeptide, a reduced level of a zinc alpha-2 macroglobulin polypeptide, or a combination thereof are provided. This document also provides methods and materials for treating prostate cancer patients.

Description

PREDICTING RESPONSES TO ANDROGEN DEPRIVATION THERAPY AND METHODS FOR TREATING PROSTATE CANCER

CROSS-REFERENCE TO RELATED APPLICATIONS This application claims the benefit of priority to U.S. Provisional Application

Serial No. 61/593,702, filed February 1, 2012. The disclosure of the prior application is considered part of (and is incorporated by reference in) the disclosure of this application.

STATEMENT AS TO FEDERALLY SPONSORED RESEARCH

This invention was made with government support under CA133536 awarded by National Institutes of Health. The government has certain rights in the invention.

BACKGROUND

1. Technical Field

This document relates to methods and materials involved in predicting whether a prostate cancer patient is likely to respond to an androgen deprivation therapy for a prolonged time period. For example, this document provides methods and materials for predicting whether or not a prostate cancer patient is likely to respond to an androgen deprivation therapy for a prolonged time period (e.g., greater than three years) based at least in part on the presence of an elevated level of 17-P-estradiol, an elevated level of estrone, an elevated level of a neuropilin-2 polypeptide, a reduced level of a zinc alpha-2 macroglobulin polypeptide, or a combination thereof. 2. Background Information

Prostate cancer occurs when a malignant tumor forms in the tissue of the prostate. The prostate is a gland in the male reproductive system located below the bladder and in front of the rectum. The main function of the prostate gland, which is about the size of a walnut, is to make fluid for semen. Although there are several cell types in the prostate, nearly all prostate cancers start in the gland cells. This type of cancer is known as adenocarcinoma. Prostate cancer is the second leading cause of cancer-related death in American men. Most of the time, prostate cancer grows slowly. Autopsy studies show that many older men who died of other diseases also had prostate cancer that neither they nor their doctor were aware of. Sometimes, however, prostate cancer can grow and spread quickly. When localized to the prostate, treatments are delivered with curative intent, either with surgical prostatectomy or radiation. Clinical follow up post treatment is performed by monitoring serum prostate specific antigen (PSA), which can become immeasurable after successful localized therapy. However, in a large case series with adequate longitudinal follow-up, between 27% and 53% of men undergoing radical prostatectomy were detected to have a PSA elevation (also labeled-biochemical failure) within 10 years following primary prostate therapy (surgery) signaling the first evidence of progressive disease prior to the appearance of clinical metastasis. An initial treatment after biochemical failure and progression to advanced disease can be continuous androgen deprivation therapy (ADT), which is usually performed in the United States by using intra-muscular or subcutaneous depots of luteinizing hormone-releasing hormone (LHRH)-analogues, every three to four months.

SUMMARY

This document provides methods and materials for predicting whether a prostate cancer patient is likely to respond to an androgen deprivation therapy for a prolonged period of time. For example, this document provides methods and materials for predicting whether or not a prostate cancer patient is likely to respond to an androgen deprivation therapy for a prolonged period of time based at least in part on the presence of an elevated level of 17-P-estradiol, an elevated level of estrone, an elevated level of a neuropilin-2 polypeptide, a reduced level of a zinc alpha-2 macroglobulin polypeptide, or a combination thereof. As described herein, the presence of an elevated level of 17-β- estradiol, an elevated level of estrone, an elevated level of a neuropilin-2 polypeptide, or a reduced level of a zinc alpha-2 macroglobulin polypeptide within a serum sample obtained after androgen deprivation therapy (e.g., a serum sample obtained at least about three months after androgen deprivation therapy) can indicate that the cancer patient is likely to respond to the androgen deprivation therapy for a prolonged period of time (e.g., greater than about 15 months).

Having the ability to identify prostate cancer patients that are likely to respond to an androgen deprivation therapy can allow doctors and patients to proceed with appropriate treatment options. For example, a patient identified as having an elevated level of 17-P-estradiol, an elevated level of estrone, an elevated level of a neuropilin-2 polypeptide, a reduced level of a zinc alpha-2 macroglobulin polypeptide, or a combination thereof within a serum or blood sample obtained after androgen deprivation therapy can be instructed to rely on the androgen deprivation therapy. In some cases, a patient identified as not having an elevated level of 17-P-estradiol, as not having an elevated level of estrone, as not having an elevated level of a neuropilin-2 polypeptide, and as not having a reduced level of a zinc alpha-2 macroglobulin polypeptide within a serum sample obtained after androgen deprivation therapy can be instructed to consider additional therapies other than androgen deprivation alone such as therapies such as chemotherapy, abiraterone acetate, and TAK-700 (Orteronel).

In general, one aspect of this document features a method for identifying a prostate cancer patient likely to respond to androgen deprivation therapy. The method comprises (a) detecting, in a sample obtained from the patient after receiving the androgen deprivation therapy, the presence of an elevated level of 17-P-estradiol, an elevated level of estrone, an elevated level of a neuropilin-2 polypeptide, a reduced level of a zinc alpha-2 macroglobulin polypeptide, or a combination thereof, and (b) classifying the patient as being likely to respond to the androgen deprivation therapy without failure for a time greater than about 20 months based at least in part on the presence. The prostate cancer patient can be a human. The method can comprise detecting the presence of an elevated level of 17-P-estradiol. The method can comprise detecting the presence of an elevated level of estrone. The method can comprise detecting the presence of an elevated level of a neuropilin-2 polypeptide. The method can comprise detecting the presence of a reduced level of a zinc alpha-2 macroglobulin polypeptide.

In another embodiment, this document features a method for identifying a prostate cancer patient unlikely to respond to androgen deprivation therapy. The method comprises (a) detecting, in a sample obtained from the patient after receiving the androgen deprivation therapy, the absence of an elevated level of 17-P-estradiol, an elevated level of estrone, an elevated level of a neuropilin-2 polypeptide, and a reduced level of a zinc alpha-2 macroglobulin polypeptide, and (b) classifying the patient as being unlikely to respond to the androgen deprivation therapy without failure for a time greater than about 20 months based at least in part on the absence. The prostate cancer patient can be a human.

In another embodiment, this document features a method for treating a prostate cancer patient. The method comprises, or consists essentially of, (a) detecting, in a sample obtained from the patient after receiving an androgen deprivation therapy, the absence of (i) an elevated level of 17-P-estradiol, (ii) an elevated level of estrone, (iii) an elevated level of a neuropilin-2 polypeptide, (iv) a reduced level of a zinc alpha-2 macroglobulin polypeptide, or (v) a combination thereof, and (b) administering abiraterone acetate, enzalutamide, or orteronel to the patient, thereby treating prostate cancer. The prostate cancer patient can be a human. The method can comprise detecting the absence of an elevated level of 17-P-estradiol. The method can comprise detecting the absence of an elevated level of estrone. The method can comprise detecting the absence of an elevated level of a neuropilin-2 polypeptide. The method can comprise detecting the absence of a reduced level of a zinc alpha-2 macroglobulin polypeptide. The method can comprise detecting the absence of (i) an elevated level of 17-P-estradiol, (ii) an elevated level of estrone, (iii) an elevated level of a neuropilin-2 polypeptide, and (iv) a reduced level of a zinc alpha-2 macroglobulin polypeptide. The method can comprise administering abiraterone acetate to the patient. The method can comprise administering enzalutamide to the patient. The method can comprise administering orteronel to the patient.

Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains. Although methods and materials similar or equivalent to those described herein can be used to practice the invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.

DESCRIPTION OF THE DRAWINGS

Figure 1 is a diagram of the overall workflow for Example 1.

Figure 2 is a table of the cohort demographics.

Figure 3 is a Venn diagram of the differentially expressed polypeptides.

Figure 4 is a graph plotting the follow-up time (years) vs. the change in neuropilin-2 polypeptide expression for patients with or without recurrence.

Figure 5 is a graph plotting the follow-up time (years) vs. the change in zinc alpha-2 macroglobulin polypeptide expression for patients with or without recurrence.

Figure 6 is a graph plotting the change in PSA levels vs. the change in neuropilin- 2 polypeptide expression for patients with or without recurrence. Δ = post-AA vs. pre- AA levels. The median Δ change is represented by dashed vertical line.

Figure 7 is a graph plotting the change in PSA levels vs. the change in zinc alpha- 2 macroglobulin polypeptide expression for patients with or without recurrence. Δ = post-AA vs. pre-AA levels. The median Δ change is represented by dashed vertical line.

Figure 8 includes scatter plot graphs.

Figure 9 is a Venn diagram showing the number of polypeptides significant with FDR (False Discover Rate) < 0.2 and the number in common between each of the three comparisons performed.

Figure 10 is a plot of pathway enrichment network results of 47 polypeptides after comparing Post-ADT proteome with failure proteome (from the Venn diagram (areas G + C of Figure 9) showing beta estradiol (toward the left of center) as a gene implicated in the pathway network analysis (P value less than 10E-30 considered significant). The single starred items signify a decrease in polypeptide expression in the comparison, and the double starred items signify an increase in polypeptide expression.

DETAILED DESCRIPTION

This document provides methods and materials for predicting whether or not a prostate cancer patient is likely to respond to an androgen deprivation therapy based at least in part on the presence of an elevated level of 17-P-estradiol, an elevated level of estrone, an elevated level of a neuropilin-2 polypeptide, a reduced level of a zinc alpha-2 macroglobulin polypeptide, or a combination thereof. As described herein, a mammal (e.g., a human) that has an elevated serum level of 17-P-estradiol, an elevated serum level of estrone, an elevated serum level of a neuropilin-2 polypeptide, a reduced serum level of a zinc alpha-2 macroglobulin polypeptide, or a combination thereof following androgen deprivation therapy can be classified as being likely to respond to the androgen deprivation therapy for a prolonged period of time. The prolonged period of time can be greater than about 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, or 45 months. In some cases, the prolonged period of time can be between about 20 and 30 months. For example, a human prostate cancer patient having an elevated serum level of 17-P-estradiol, an elevated serum level of estrone, an elevated serum level of a neuropilin-2 polypeptide, a reduced serum level of a zinc alpha-2 macroglobulin polypeptide, or a combination thereof at least about three months after having received an androgen deprivation therapy can be classified as being likely to respond to the androgen deprivation therapy for a prolonged period of time. In some cases, a human prostate cancer patient lacking (a) an elevated serum level of 17-β- estradiol, (b) an elevated serum level of estrone, (c) an elevated serum level of a neuropilin-2 polypeptide, and (d) a reduced serum level of a zinc alpha-2 macroglobulin polypeptide at least about three months after having received an androgen deprivation therapy can be classified as being unlikely to respond to the androgen deprivation therapy for a prolonged period of time.

Examples of androgen deprivation therapy include, without limitation, chemical castrations (e.g., treatments with LHRH-analogues or gonadotrophin-releasing hormone (GnRH) antagonists) and physical castrations.

A neuropilin-2 polypeptide can be a human neuropilin-2 polypeptide and can have the amino acid sequence set forth in GenBank^® accession number NP 957718.1 (GenBank^® GI number 41872562). A zinc alpha-2 macroglobulin polypeptide can be a human zinc alpha-2 macroglobulin polypeptide and can have the amino acid sequence set forth in GenBank^® accession number NP 001176.1 (GenBank^® GI number 4502337).

Any appropriate method can be used to detect the level of 17-P-estradiol, estrone, a neuropilin-2 polypeptide, or a zinc alpha-2 macroglobulin polypeptide within a serum or blood sample. For example, gas chromatography or ELISA techniques can be used to determine the level of 17-P-estradiol or estrone within a sample (e.g., a serum or blood sample). In some cases, ELISAs, immunocytochemistry, flow cytometry, Western blotting, proteomic, and mass spectrometry techniques can be used to assess polypeptide levels (e.g., neuropilin-2 polypeptide or zinc alpha-2 macroglobulin polypeptide levels) within a sample (e.g., a serum or blood sample).

The term "elevated level" as used herein with respect to the level of 17-β- estradiol, estrone, or a neuropilin-2 polypeptide present in a sample obtained from a mammal (e.g., a human prostate cancer patient) after androgen deprivation therapy can be any level that is greater than the level for that molecule that is present in a comparable sample obtained from the same mammal prior to androgen deprivation therapy. In some cases, the term "elevated level" as used herein with respect to the level of 17-P-estradiol, estrone, or a neuropilin-2 polypeptide present in a sample obtained from a mammal (e.g., a human prostate cancer patient) after androgen deprivation therapy can be any level that is greater than a reference level for that molecule. The reference level can be the median level determined from a random sampling of 5, 10, 15, 20, 30, 40, 50, 100, 500, or more comparable samples obtained from comparable mammals either who do not have prostate cancer or who have prostate cancer but have not received androgen deprivation therapy.

The term "reduced level" as used herein with respect to the level of a zinc alpha-2 macroglobulin polypeptide present in a sample obtained from a mammal (e.g., a human prostate cancer patient) after androgen deprivation therapy can be any level that is less than the level of a zinc alpha-2 macroglobulin polypeptide that is present in a comparable sample obtained from the same mammal prior to androgen deprivation therapy. In some cases, the term "reduced level" as used herein with respect to the level of a zinc alpha-2 macroglobulin polypeptide present in a sample obtained from a mammal (e.g., a human prostate cancer patient) after androgen deprivation therapy can be any level that is less than a reference level for a zinc alpha-2 macroglobulin polypeptide. The reference level can be the median level determined from a random sampling of 5, 10, 15, 20, 30, 40, 50, 100, 500, or more comparable samples obtained from comparable mammals either who do not have prostate cancer or who have prostate cancer but have not received androgen deprivation therapy.

This document also provides methods and materials to assist medical or research professionals in determining whether or not a prostate cancer patient is likely to respond to an androgen deprivation therapy. Medical professionals can be, for example, doctors, nurses, medical laboratory technologists, and pharmacists. Research professionals can be, for example, principle investigators, research technicians, postdoctoral trainees, and graduate students. A professional can be assisted by (1) determining the presence of one or more of the elevated or reduced levels described herein, and (2) communicating information about those one or more levels to that professional.

Any method can be used to communicate information to another person (e.g., a professional). For example, information can be given directly or indirectly to a professional. In addition, any type of communication can be used to communicate the information. For example, mail, e-mail, telephone, and face-to-face interactions can be used. The information also can be communicated to a professional by making that information electronically available to the professional. For example, the information can be communicated to a professional by placing the information on a computer database such that the professional can access the information. In addition, the information can be communicated to a hospital, clinic, or research facility serving as an agent for the professional.

In some cases, a patient identified as being unlikely to respond to an androgen deprivation therapy based at least in part on the absence of an elevated level of 17-β- estradiol, an elevated level of estrone, an elevated level of a neuropilin-2 polypeptide, and/or a reduced level of a zinc alpha-2 macroglobulin polypeptide can be administered or instructed to receive an alternative or adjunct therapy to ADT. For example, a patient lacking an elevated level of 17-P-estradiol, an elevated level of estrone, an elevated level of a neuropilin-2 polypeptide, and a reduced level of a zinc alpha-2 macroglobulin polypeptide can be instructed to proceed with an abiraterone acetate, MDV3100

(Enzalutamide), or TAK-700 treatment sooner than he would have been had he had an elevated level of 17-P-estradiol, an elevated level of estrone, an elevated level of a neuropilin-2 polypeptide, or a reduced level of a zinc alpha-2 macroglobulin polypeptide.

The invention will be further described in the following examples, which do not limit the scope of the invention described in the claims. EXAMPLES

Example 1 - Serum proteomics guided discovery of predictive biomarkers of response to androgen ablation (AA) in prostate cancer

Serum from three non-localized prostate cancer cohorts was analyzed (Figures 1 and 2). The first cohort included 15 paired untreated hormone-sensitive "pre-AA" and 3- month "post-AA" specimens. The second included 10 "early AA failure" (median time to AA failure: 11 months), and the third included 10 "late AA failure" specimens (median time to AA failure: 95 months). Six additional patients on AA were added to cohorts 1 and 2 for patient analyses to verify proteomic results using ELISAs.

Processing and handling of serum specimens followed standardization methods.

For serum processing, blood was collected in BD SSTTM 6.0 mL vacutainers and processed within 30-45 minutes. Processing included an initial centrifugation at 3,000 rpm for 10 minutes to generate a serum preparation that was fractioned into multiple aliquots that were labeled with coded identifiers and stored at -80°C. After the initial centrifugation, a protease inhibitor cocktail was added; the ingredients of which included 10 mL PBS (Invitrogen No. 14190300), one tablet complete of mini, EDTA-free protease inhibitor (Roche No. 11 836 170 001), sodium vanadate Na₃V0₄, and PMSF (Sigma No. P7626-5G). One tablet of the protease inhibitor was completely dissolved in 10 mL PBS and 5 μΕ/mL Na₃V0₄ with 10 μΕ/mL PMSF added for stock solution preparation (with 100 mM of PMSF). 50 of the stock solution was added to each serum specimen. No serum specimen retrieved for research underwent any freeze-thaw cycles prior to performing affinity depletion and preparation for iTRAQ labeling.

Affinity depletion of high abundant proteins from human sera

Removal of high abundance proteins was performed using a Hu-14 Multiple

Affinity Removal Column, 4.6 x 100 mm (Product Number 5188-6558; Agilent

Technologies, Newcastle, DE USA), attached to an Agilent 1100 binary gradient HPLC system (Agilent Technologies, Inc. Santa Clara, CA) on all serum specimens. HPLC buffers were obtained from the column manufacturer, and the separation followed the manufacturer's recommended protocol with UV monitoring at 280 nm.

Protein concentrations obtained after depletion for each of the samples was determined by Bradford assay using BSA as the calibrant and further quantified by running SDS-mini gel followed by ImageQuant Software (GE Healthcare).

Protein digestion and iTRAQ labeling

50 μg protein of each sample was denatured for 10 minutes at room temperature.

Protein samples were digested with trypsin, and the tryptic peptides from four different samples were each labeled with iTRAQ reagents 114, 115, 116, and 117, respectively, according to the manufacturer's protocols in a randomized setting.

A total of 13 sets of iTRAQ 4-plex tagged samples was prepared and designed to cover all individually depleted samples with two samples in duplicates. After labeling, the four samples were pooled in each of the 13 sets and subjected to cation exchange chromatography using an Applied Biosystems cation-exchange cartridge system. This was followed by performing high pH reverse phase fractionation, which was completed using a Dionex UltiMate3000 HPLC system with built-in micro fraction collection option in its autosampler and UV detection (Sunnyvale, CA).

Nano-scale reverse phase chromatography and tandem mass spectrometry (nanoLC-MS/MS) was then carried out using a LTQ-Orbitrap Velos (Thermo-Fisher Scientific, San Jose, CA) mass spectrometer equipped with a "Plug and Play" nano ion source (CorSolutions, LLC, Ithaca, NY).

Data processing, protein identification, and data analysis

All MS and MS/MS raw spectra from iTRAQ experiments were processed using Proteome Discoverer 1.1 (PD1.1, Thermo), and the spectra from each DDA file were output as an MGF file for subsequent database search using Scaffold (version 3.0, Proteome software, Inc. Portland, OR).

Data Analyses and statistical methods

Global quality and bias were assessed via several plotting techniques. Box-and- whisker plots were used to assess global shifts in the distribution of abundance, and coverage plots were used to compare the number of identified features across

experiments. Based upon the plots described, all experiments were deemed of good quality.

The natural log abundance values of the samples were normalized using a linear model to remove global iTRAQ tag affinity, iTRAQ experiment run bias, and peptide effects. Linear mixed effects models with weighted variances were used to assess differential expression.

Differentially expressed candidate polypeptides were identified by comparisons of (i) paired pre/post- AA proteomes and (ii) post-AA proteome with the combined AA failure cohorts at a false discovery rate of 0.2. ELISA assays (NRP2 ELISA assays, LifeSciences Inc. UK; and ZAG ELISA assays, Bio Vendor Research and Diagnostics, USA) were used to verify candidate markers in a second stored aliquot of first cohort specimens. This cohort was followed for AA failure. Association of post-AA ELISA levels of candidate markers with time to AA failure was performed using Cox

proportional hazards regression, summarized as relative risk (RR) for AA failure.

Median PSA values in pre/post- AA first cohort were 3.15 ng/mL and 0.29 ng/mL. Median PSA values in the second and third cohorts were 27.3 and 4.3 ng/mL. Between post-AA and AA failure cohorts, 149 polypeptides were differentially expressed.

Between early and late AA failure, 98 polypeptides were differentially expressed. 47 polypeptides were common in both comparisons (Figure 3).

ELISA assays verified expression levels of 2/47 polypeptides in the first cohort, zinc alpha-2 macroglobulin (ZAG) and Neuropilin-2 (NPL2). Median change in ZAG decreased by 2073.5 ng/mL (post versus pre-AA), while median change in NPL2 levels increased by 2.9 ng/mL. After a median follow-up of 43 months from the post-AA time- point, 4/15 first cohort subjects had failed AA. The recovery rate of AA failure for ZAG levels below the median change was 3.8 (95% CI: 0.4-37), and 3.0 (95% CI: 0.3-29) for NPL2. See, Figures 4-7. 6/20 patients failed AA during median follow up of 43 months.

These results demonstrate that serum levels of ZAG and NPL2 polypeptides can be used to predict AA response.

Example 2 - 17-P-estradiol and estrone levels can predict response to androgen ablation in prostate cancer

Analytical procedures were used to determine the concentrations of testosterone, 17-P-estradiol, and estrone in human plasma samples from pateints pre- and post-AA. Briefly, the analytes and deuterated internal standards were extracted from 0.4 mL of human plasma using BondElut Certify^® solid-phase cartridges. The compounds were eluted from the cartridges with ethyl acetate and then underwent three separate derivatizations: (1) reaction with pentafluorobenzoyl chloride (PFB), (2) reaction with 0-(2,3,4,5,6-pentaflurorobenzyl)-hydroxylamine hydrochloride in pyridine, and (3) reaction with MSTFA. The derivatized analytes were separated by gas chromatography using a XTI-5MS GC column and detected by tandem mass spectrometry using negative ion chemical ionization. Calibration curves were obtained by performing a linear regression (weighted 1/x²) on the calibration standards. Concentration results were determined for testosterone, estradiol, and estrone.

The results are provided in Figure 8. These results demonstrate that serum levels of 17-P-estradiol and estrone can be used to predict AA response. Example 3 - Identification of serum polypeptides

A proteomic guided analytic approach was used to identify serum candidate polypeptides that predict response to ADT in hormone-sensitive, non-localized stage prostate cancer patients. The approach was performed using isobaric mass tags for relative and absolute quanititation (iTRAQ) analyzed by reverse-phase liquid

chromatography coupled to tandem mass spectrometry (LC/MS/MS).

The serum proteome of three non-localized prostate cancer cohorts was analyzed. The first cohort included fifteen untreated hormone-sensitive patients with paired "pre- ADT" serum specimen and a 4-month "post-ADT" serum specimen. The second included a cohort of ten patients failing ADT in a short period of time ("early ADT failure"), and the third included a separate cohort of ten patients failing ADT after a long response duration ("late ADT failure"). Differentially expressed polypeptides were identified at a False Discovery Rate of 0.2 by comparing proteomes of (i) the paired pre- versus post-ADT hormone sensitive patients; (ii) post-ADT hormone sensitive proteome with the combined ADT failure cohorts. To facilitate the biological interpretation of identified candidate markers, statistically significant interaction networks and pathways using the Ingenuity Pathway Analysis (IP A) software were generated. Candidate markers implicated in networks were pursued in an independent patient cohort for association with time to ADT failure using univariate Cox regression analysis.

Median PSAs of the pre/post- ADT first cohort were 3.15 ng/mL and 0.29 ng/mL. Median PSA values for the second and third cohorts were 27.3 and 4.3 ng/mL. Between post- ADT and ADT failure cohorts, 149 serum polypeptides were differentially expressed. Between early and late ADT failure, 98 serum polypeptides were

differentially expressed. 47 polypeptides were common in both comparisons. Network enrichment analysis by IPA identified four significant networks with p value less than 0.01. Network enrichment analysis of the 47 polypeptides by IPA identified four interaction networks (p<0.01), one of which highlighted a role for 17-P-estradiol (El). Gas chromatography used for measuring 3 -month post AA initiation serum El, estrone (E2), and testosterone levels in the independent cohort (N=38) detected an association of high El and E2 levels with longer time to AA failure (P=0.07 for El; P=0.08 for E2).

These results demonstrate that a global proteomic analysis identified serum estrone and 17 beta estradiol as candidate serum predictive markers of ADT response.

OTHER EMBODIMENTS

It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.

Claims

WHAT IS CLAIMED IS:

1. A method for identifying a prostate cancer patient likely to respond to androgen deprivation therapy, wherein said method comprises:

(a) detecting, in a sample obtained from said patient after receiving said androgen deprivation therapy, the presence of an elevated level of 17-P-estradiol, an elevated level of estrone, an elevated level of a neuropilin-2 polypeptide, a reduced level of a zinc alpha-2 macroglobulin polypeptide, or a combination thereof, and

(b) classifying said patient as being likely to respond to said androgen deprivation therapy without failure for a time greater than about 20 months based at least in part on said presence.

2. The method of claim 1, wherein said prostate cancer patient is a human.

3. The method of claim 1, wherein said method comprises detecting the presence of an elevated level of 17-P-estradiol.

4. The method of claim 1, wherein said method comprises detecting the presence of an elevated level of estrone.

5. The method of claim 1, wherein said method comprises detecting the presence of an elevated level of a neuropilin-2 polypeptide.

6. The method of claim 1, wherein said method comprises detecting the presence of a reduced level of a zinc alpha-2 macroglobulin polypeptide.

7. A method for identifying a prostate cancer patient unlikely to respond to androgen deprivation therapy, wherein said method comprises:

(a) detecting, in a sample obtained from said patient after receiving said androgen deprivation therapy, the absence of an elevated level of 17-P-estradiol, an elevated level of estrone, an elevated level of a neuropilin-2 polypeptide, and a reduced level of a zinc alpha-2 macroglobulin polypeptide, and

(b) classifying said patient as being unlikely to respond to said androgen deprivation therapy without failure for a time greater than about 20 months based at least in part on said absence.

8. The method of claim 7, wherein said prostate cancer patient is a human.

9. A method for treating a prostate cancer patient, wherein said method comprises:

(a) detecting, in a sample obtained from said patient after receiving an androgen deprivation therapy, the absence of (i) an elevated level of 17-P-estradiol, (ii) an elevated level of estrone, (iii) an elevated level of a neuropilin-2 polypeptide, (iv) a reduced level of a zinc alpha-2 macroglobulin polypeptide, or (v) a combination thereof, and

(b) administering abiraterone acetate, enzalutamide, or orteronel to said patient, thereby treating prostate cancer.

10. The method of claim 9, wherein said prostate cancer patient is a human.

11. The method of claim 9, wherein said method comprises detecting the absence of an elevated level of 17-P-estradiol.

12. The method of claim 9, wherein said method comprises detecting the absence of an elevated level of estrone.

13. The method of claim 9, wherein said method comprises detecting the absence of an elevated level of a neuropilin-2 polypeptide.

14. The method of claim 9, wherein said method comprises detecting the absence of a reduced level of a zinc alpha-2 macroglobulin polypeptide.

15. The method of claim 9, wherein said method comprises detecting the absence of (i) an elevated level of 17-P-estradiol, (ii) an elevated level of estrone, (iii) an elevated level of a neuropilin-2 polypeptide, and (iv) a reduced level of a zinc alpha-2

macroglobulin polypeptide.

16. The method of claim 9, wherein said method comprises administering abiraterone acetate to said patient.

17. The method of claim 9, wherein said method comprises administering

enzalutamide to said patient.

18. The method of claim 9, wherein said method comprises administering orteronel to said patient.