BIOMARKER FOR PROSTATE CANCER

Information

  • Patent Application
  • 20250076301
  • Publication Number
    20250076301
  • Date Filed
    September 05, 2024
    a year ago
  • Date Published
    March 06, 2025
    9 months ago
Abstract
Provided is a method of accurate and sensitive characterization and prognosis of prostate cancer in a subject. The method includes obtaining a biological sample from the subject and determining the level of identified biomarkers.
Description
BACKGROUND
1. Technical Field

This disclosure relates to methods for monitoring prostate cancer in a subject in need thereof. This disclosure also relates to methods and kits for detecting, diagnosing, prognosing, and characterizing prostate cancer in a subject in need thereof.


2. Description of Associated Art

Prostate cancer is the commonest non-epithelial cancer in men in the developed countries. Approximately 9 million new cases are diagnosed worldwide annually, and approximately 260,000 deaths occur due to prostate cancer. If prostate cancer is discovered early, 90% of the cases may be cured with surgery with the five-year survival rate for localized cancer at 100%. However, upon progression, the survival rate drops to less than 50%. It is, therefore, important to diagnose the cancer as early as possible and to monitor closely and effectively.


As of present, prostate cancer is screened using digital rectal examination (DRE), an imaging test such as transrectal ultrasound (TRUS), MRI, or a “fusion” of the two, and/or the measurement of the serum levels of prostate specific antigen (PSA). However, these approaches have low sensitivity and specificity due to high false-positives. For example, more than half of people screened with an elevated PSA level actually do not have prostate cancer as determined by subsequent confirmatory prostate biopsies. This implies that invasive biopsies are done more than needed. Indeed, many complications such as infection, internal bleeding, allergic reactions, impotence, and urinary incontinence can be resulted from invasive needle biopsies. These unnecessary biopsies and the accompanying complications lead to increased cost to the already burdened healthcare system. Obviously, there is an unmet need for safe and efficient prostate cancer screening and tumor grading system to improve the accuracy of prostate cancer detection and further risk stratification.


In addition to an accurate diagnosis, an effective cancer treatment regimen involves many different considerations and strategies. Following the diagnosis of cancer, an informative and accurate characterization of a cancer stage is of crucial importance in determining the proper treatment regimen, along with consideration of different aspects of patient, such as age and other disease history. It is valuable to determine an appropriate treatment for patient along the progression of the disease, and to ensure that precious clinical resources are targeted as effectively as possible on those that will benefit most from primary treatment (surgery, radiotherapy or active surveillance) and may also benefit from the most intensive post-treatment follow-up, and additional treatment upon recurrence where necessary (e.g., anti-androgens, androgen synthesis inhibitors, chemotherapy, beamline radiotherapy). As such, the current tests are not specific and robust enough to screen for prostate cancer. More reliable biological markers for providing prostate cancer diagnosis, risk stratification and prognoses and for monitoring disease progression are in need.


SUMMARY

Herein, the present disclosure is therefore provided with groups of biomarkers and a method to characterize, diagnose, prognosticate, stratify and monitor the progression or recurrence of prostate cancer in a subject in need thereof. By the method of the present disclosure, the subject for characterization, diagnosis, monitoring and determining prognosis of cancer is able to receive a personalized treatment plan and/or customized healthcare, and accordingly an improved life quality is ensured when compared to ordinary methods prior to this disclosure.


The present disclosure provides a method to characterize prostate cancer in a subject in need thereof, comprising detecting a level of a prostate cancer marker in a biological sample from the subject, wherein the prostate cancer marker comprises one or more of the metabolite markers in Tables 1, 2, 5 and 6.


In one embodiment of the present disclosure, the prostate cancer marker comprises at least one metabolite marker selected from the group consisting of Ethanimidic acid, N-(trimethylsilyl)-, trimethylsilyl ester; ethanolamine; Glycine, di-TMS; pyruvic acid; Beta-alanine 1; L-(+) lactic acid; 2-hydroxypyridine; Diethanolamine, 3TMS derivative; glyceric acid; Pentenoic acid, 4-[(trimethylsilyl)oxy]-, trimethylsilyl ester; guanidinoacetic acid 2; tartronic acid; Butanoic acid, 2,4-bis[(trimethylsilyl) oxy]-, trimethylsilyl ester; L-pyroglutamic acid; DL-isoleucine 2; 1H-Indole, 1-(trimethylsilyl)-5-[(trimethylsilyl)oxy]; 2,3,4-Trihydroxybutyric acid tetrakis(trimethylsilyl) deriv., (, (R*,R*)—); 1-Deoxypentitol, 4TMS derivative; 4-hydroxybenzoic acid; 4-acetamidobutyric acid 1; L-glutamine 2; D-lyxose 2; Arabinofuranose, 1,2,3,5-tetrakis-O-(trimethylsilyl); xanthine; Ribitol TMS; xylitol; L-(−)-Arabitol, 5TMS derivative; Furan, tetrahydro-2,5-dipropyl-; 1,5-anhydro-D-sorbitol; L-Phenylalanine, 2TMS derivative; 3,4-Dihydroxyphenylacetic Acid, 3TMS derivative; DL-4-hydroxymandelic acid; 3-methyl-L-histidine; trans-aconitic acid; Ethyl (E)-1-penten-3-ynesulfonate; D-allose 2; D-allose 1; L-tyrosine 2; quinic acid; galacturonic acid 2; Ononitol TMS; D-Gluconic acid, 6TMS derivative; pantothenic acid 2; N-acetyl-D-mannosamine 1; D-Allose, pentakis(trimethylsilyl) ether, ethyloxime (isomer 2); Pseudo uridine penta-tms; palmitic acid; 2-phenyl-3,5,7-tris(trimethylsilyloxy)-1-benzopyran-4-one; stearic acid; Guanosine, N,N-dimethyl-1-(trimethylsilyl)-2′,3′,5′-tris-O-(trimethylsilyl)-; 1-Monopalmitin, 2TMS derivative; lactose 1; 2-Monostearin, 2TMS derivative; 1-stearoyl-rac-glycerol; 3-Phenyl-5,10-secocholesta-1(10),2-dien-5-one.


In one embodiment of the present disclosure, the biological sample is peripheral blood, sera, plasma, urine, semen, prostatic fluid, Cowper's fluid, or pre-ejaculatory fluid and any combination thereof.


In one embodiment of the present disclosure, the method further comprising detecting a level of prostate specific antigen in the biological sample from the subject.


In one embodiment of the present disclosure, the method further comprising grouping the subject by NCCN risk classification into six groups of different severities of prostate cancer, wherein the six groups are benign group, very low-risk/low-risk prostate cancer, favorable-intermediate-risk prostate cancer, unfavorable-intermediate-risk prostate cancer, high-risk/very high-risk prostate cancer, and metastasis prostate cancer group.


In one embodiment of the present disclosure, the method further comprising distinguishing the severity of prostate cancer in the subject in one group from the other groups.


The present disclosure further provides a method for determining a need of biopsy for prostate cancer diagnosis in a subject in need thereof, comprising detecting a level of a prostate cancer marker in a biological sample from the subject, wherein the prostate cancer marker is selected from the group consisting of panels in Tables 3, 4, 7 and 8.


In one embodiment of the present disclosure, the prostate cancer marker is selected from the group consisting of panel 1, panel 2, panel 3, panel 4, and any combination thereof, and wherein:

    • panel 1 is selected from the group consisting of C10 H21 N4O2, C12H17NO, C12H2NOPS, C12H9O9P, C13H19N5O5, C17H32N3O7, C18H16N6O3, C18H33NO4, C18H43N4O3, C19H35NO5, C19H38N2O3, C24H42N7O3, C27H12N9, C34H23N7O5, C5H11NO, C51H29N5O4, C6H15N, C8H9N, C9H4N5O9, C9H8O2, and any combination thereof;
    • panel 2 is selected from the group consisting of C11H5NOPS, C12H16NO7, C12H2 NOPS, C12H9O9P, C13H25NO2, C13H25NO3, C14H30N4O2, C16H13N3O3P, C17H41N4O3, C19H19N8, C22H45NO4, C26H51N4O5, C26H58N13P, C27H12N9, C27H55N8O3, C30H57NO7, C30H64N15O2P, C41H23N11O2, C5, C5H7NO3, C6HCl5, C6H16N3O5, C8H16NO5, and any combination thereof;
    • panel 3 is selected from the group consisting of C10H18N2O5, C12H21NO4, C13H23NO6, C13H25NO3, C14H30N4O2, C15H30N10OP, C16H13N3O3P, C19H31N6O2, C22H45NO4, C27H12N9, C28H57N8O4, C30H61N8O5, C30H64N15O2P, C35H71N8O7, C40H38N22O4, C41H23N11O2, C43H40N20O3, C5H11NO, C5H1NO2S, C5H2O2P, C8H16NO5, and any combination thereof; and
    • panel 4 is selected from the group consisting of C11H20O2, C11H5NOPS, C12H2NOPS, C12H25NO4P, C12H9O9P, C13H25NO2, C13H25NO3, C14H30N4O2, C16H30N3O2, C17H41N4O3, C18H34O5, C19H31N6O2, C21H36N4O3, C22H45NO4, C23H47N8O2, C24H41N14O8, C27H12N9, C30H57NO7, C30H64N15O2P, C35H71N8O7, C43H40N20O3, C5H11NO, C5H1NO2S, C6H14N2O5P, and any combination thereof.


In one embodiment of the present disclosure, the prostate cancer marker is selected from the group consisting of panel 5, panel 6, panel 7, panel 8, and any combination thereof, and wherein:

    • panel 5 is selected from the group consisting of C10H16O4, C10H18N2O4, C11H20NO3P3, C12H7N4O2, C15H28N6OP2, C16H39N8OP, C19H14O3, C21H33N3O3, C23H27O11S, C23H42N7O, C25H46N7O3, C27H48P2, C27H54O6, C33H22O7, C34H73N8O2P, C38H48O12, C40H85NOP3, C5H4O3, C5H8N2O2, C6H13N4O3P, C6H13N4OP2, C7H10O4, C7H17O7P2, C7H6O6S, C8H14O4, and any combination thereof;
    • panel 6 is selected from the group consisting of C10H16O4, C11H16N4O4, C12H7N4O2, C14H20N2O5, C16H32O2, C17H34N9O2, C21H33N3O3, C23H27O11S, C26H43NO6, C27H48P2, C28H52N7O, C34H73N8O2P, C38H48O12, C39H26O7, C4H6O4, C40H85NOP3, C5H4N4O2, C5H8N2O2, C6H11N4O2P, C6H13N4OP2, C6H6N4O2, C6H8N2O4, C7H10O4, C7H17O7P2, C7H6O6S, C9H16O4, C9H9NO3, and any combination thereof;
    • panel 7 is selected from the group consisting of C10H18N2O4, C10H19N5P3, C12H7N4O2, C15H28N6OP2, C16H32O2, C17H34N9O2, C19H14O3, C21H33N3O3, C21H39N4OP, C27H48P2, C38H48O12, C39H26O7, C40H85NOP3, C5H10N2O3, C5H4N4O2, C6H10O4S, C6H11N4O2P, C6H13N4OP2, C6H15O8P, C7H10O4, C7H17O7P2, C7H21N3OP3, C7H22N4O9PS, C7H8O6S, C8H9O6, C9H16O4, C9H17N O4S, C9H9NO3, and any combination thereof; and
    • panel 8 is selected from the group consisting of C10H19N5P3, C12H7N4O2, C15H28N6OP2, C17H34N9O2, C17H42N3OP2, C21H33N3O3, C22H38N7O, C24H40N4O3, C25H46N7O3, C25 H50O6, C27H54O6, C39H26O7, C39H78O6, C40H85NOP3, C6H11N4O2P, C6H15O8P, C6H5N2OP, C6H8O6S, C7H10O4, C7H17O7P2, C7H21N3OP3, C8H16N2O5P, C8H18NO6P, C8H4N4O3, C9H16O4, C9H9NO3, and any combination thereof.


In one embodiment of the present disclosure, the prostate cancer marker is selected from the group consisting of panel 9, panel 10, panel 11, panel 12, and any combination thereof, and wherein:

    • panel 9 is selected from the group consisting of Pyruvic acid, 4-Acetamidobutyric acid, 1,5-Anhydro-D-glucitol, Beta-Alanine, Glyceric acid, D-Lyxose, Galacturonic acid, D-Allose, L-Tyrosine, 3-Methyl-L-histidine, L-Glutamine, L-Pyroglutamic acid, Guanidinoacetic acid, Lactose, 2-Hydroxypyridine, N-acetyl-D-mannosamine, Palmitic acid, 1-Deoxy-d-ribitol, Monopalmitin, 2-Stearoylglycerol, Galangin, 6-ethoxyiminohexane-1,2,3,4,5-pentol, D-Gluconic acid, N,N-Dimethylguanosine, Pseudouridine, Ribitol, and any combination thereof;
    • panel 10 is selected from the group consisting of Pyruvic acid, Xanthine, 4-Acetamidobutyric acid, 1,5-Anhydro-D-glucitol, Beta-Alanine, 1-Stearoyl-rac-glycerol, Glyceric acid, Galacturonic acid, Quinic acid, Xylitol, L-Pyroglutamic acid, Guanidinoacetic acid, Lactose, Ononitol, 5-Hydroxyindole, Monopalmitin, Galangin, 3,4-Dihydroxyphenylacetic acid, 3-Phenyl-5,10-secocholesta-1 (10),2-dien-5-one, Acetamide, Ethyl 1-penten-3-ynesulfonate, 2,5-Dipropyltetrahydrofuran, L-Phenylalanine, Pseudouridine, and any combination thereof;
    • panel 11 is selected from the group consisting of L-Lactic acid, Xanthine, 4-Acetamidobutyric acid, Beta-Alanine, 1-Stearoyl-rac-glycerol, 4-hydroxymandelic acid, trans-Aconitic acid, D-Allose, Tartronic acid, Stearic acid, L-Tyrosine, Quinic acid, Ethanolamine, Guanidinoacetic acid, DL-isoleucine, Palmitic acid, Monopalmitin, Arabinofuranose, 2,4-Dihydroxybutanoic acid, Diethanolamine, Acetamide, 2,5-Dipropyltetrahydrofuran, Glycine, L-Arabinitol, Levulinic acid, Pseudouridine, and any combination thereof; and
    • panel 12 is selected from the group consisting of Pyruvic acid, Xanthine, 4-Hydroxybenzoic acid, Beta-Alanine, 1-Stearoyl-rac-glycerol, Galacturonic acid, D-Allose, Tartronic acid, Quinic acid, Pantothenic acid, Xylitol, Guanidinoacetic acid, 1-Deoxy-d-ribitol, Monopalmitin, Threonic acid, Galangin, Arabinofuranose, 2,4-Dihydroxybutanoic acid, D-Gluconic acid, 2,5-Dipropyltetrahydrofuran, Levulinic acid, Pseudouridine, and any combination thereof.


In one embodiment of the present disclosure, the prostate cancer marker is selected from the group consisting of panel 13, panel 14, panel 15, panel 16, and any combination thereof, and wherein:

    • panel 13 is selected from the group consisting of 1-Methoxymethyl-2-phenylthioindole-3-carbaldehyde, 2,3-Dihydroxybutanoic acid, 2-Hydroxypyridine, 2-Stearoylglycerol, 3-Hydroxyphenylacetic acid, 3-Indoleacetic acid, 3-Methyl-L-histidine, 4-Acetamidobutyric acid, 4-hydroxymandelic acid, 6-ethoxyiminohexane-1,2,3,4,5-pentol, alpha-Hydroxyisobutyric acid, D-Altrose, D-Gluconic acid, D-Lyxose, Galacturonic acid, Galangin, Glyceric acid, Lactose, L-Fucose, L-Pyroglutamic acid, Monopalmitin, Ononitol, Oxamide, Palmitic acid, Pseudouridine, Pyruvic acid, Ribitol, trans-Aconitic acid and any combination thereof;
    • panel 14 is selected from the group consisting of 1-Stearoyl-rac-glycerol, 2,5-Dipropyltetrahydrofuran, 3,4-Dihydroxyphenylacetic acid, Acetamide, Beta-Alanine, Cyclohexylamine, Ethyl 1-penten-3-ynesulfonate, Galacturonic acid
    • Galangin, Glyceric acid, Guanidinoacetic acid, Levulinic acid, Monopalmitin, Ononitol, Palmitic acid, p-Tolyl-beta-D-glucopyranosid-uronsaeure, Quinic acid, Stearic acid, Sucrose, Uric acid, Xanthine, Xylitol, and any combination thereof;
    • panel 15 is selected from the group consisting of (22S,23S,25R)-3β-methoxy-16β,23:22,26-diepoxy-5α-cholestane, 1-Methoxymethyl-2-phenylthioindole-3-carbaldehyde, 1-Stearoyl-rac-glycerol, 2,4-Dihydroxybutanoic acid, 2,5-Dipropyltetrahydrofuran, 4-hydroxymandelic acid, Acetamide, Arabinofuranose, Beta-Alanine, Daidzein, D-Allose, DL-isoleucine, D-tagatofuranose, Ethanolamine, Galangin, Guanidinoacetic acid, L-Arabinitol, Levulinic acid, L-Lactic acid, Monopalmitin, Palmitic acid, Pseudouridine, Quinic acid, Stearic acid, Sucrose, Tartronic acid, Xanthine, and any combination thereof; and
    • panel 16 is selected from the group consisting of (4RS,5SR)-5-hydroperoxy-4-decanol, 2,5-Dipropyltetrahydrofuran, 3,4,5-Trihydroxypentanoic acid, 4-Hydroxybenzoic acid, 6-ethoxyiminohexane-1,2,3,4,5-pentol, Acetamide, Arabinofuranose, Beta-Alanine, D-Allose, DL-4-Hydroxy-3-methoxymandelic acid, Ethyl 1-penten-3-ynesulfonate, Galacturonic acid, Galangin, Glyceric acid, Guanidinoacetic acid, Hippuric Acid, Levulinic acid, L-Pyroglutamic acid, Pantothenic acid, Pseudouridine, Pyruvic acid, Quinic acid, Tartronic acid, Uric acid, Xanthine, and any combination thereof.


The present disclosure further provides a method for monitoring a prostate cancer subject on active surveillance (AS), comprising detecting a level of a prostate cancer marker in a biological sample from the subject, wherein the prostate cancer marker is selected from the group consisting of markers in Tables 1, 2, 5 and 6.







DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

The present disclosure provides a method and biomarkers to diagnose, stratify, prognosticate and monitor prostate cancer in a subject in need thereof by analyzing the levels of one or more biomarker in a sample obtained from the subject. All terms including descriptive or technical terms which are used herein should be construed as having meanings that are obvious to one of ordinary skill in the art. However, the terms may have different meanings according to an intention of one of ordinary skill in the art, case precedents, or appearance of new technologies. Also, some terms may be arbitrarily selected by the applicant, and in this case, the meaning of the selected terms will be described in detail in the comprehensive descriptions of the present disclosure. Thus, the terms used herein have to be defined based on meaning of the terms together with descriptions throughout the specification.


Also, when a part “includes” or “comprises” a component or a step, unless there is a particular description contrary thereto, the part can further include other components or other steps, not excluding the others.


It is further noted that, as used in this disclosure, the singular forms “a,” “an,” and “the” include plural referents unless expressly and unequivocally limited to one referent. The term “or” is used interchangeably with the term “and/or” unless the context clearly indicates otherwise.


The term “to characterize” in a subject or individual may include, but is not limited to, to provide the diagnosis of a disease or a condition, to determine the stratification of a disease risk, to assess the risk of a disease, to provide the prognosis of a disease or a condition, to determine a disease stage or a condition stage, to determine the severity of a disease, to evaluate the malignancy potential of a disease, to monitor a recurrence of cancer, to evaluate a drug efficacy, to describe a physiological condition, to evaluate an organ distress or organ rejection, to monitor disease or condition progression, to determine therapy-related association to a disease or a condition, or to describe a specific physiological or biological state.


As used herein, prognosis of cancer may include predicting the clinical outcome of the patient, assessing the risk of cancer recurrence, determining treatment modality, or determining treatment efficacy.


As used herein, the term “metastasis” describes the spread of a cancer from one part of the body to another. A tumor formed by cells that have spread can be called a “metastatic tumor” or a “metastasis.” The metastatic tumor often contains cells that are similar to those in the original (primary) tumor, and have, but not limited to, genomic, epigenetic, transcriptomic, and metabolic alterations.


As used herein, the term “progression” describes the course of a disease, such as a cancer, as it becomes worse or spreads in the body.


The terms “subject,” “patient” and “individual” are used interchangeably herein and refer to a warm-blooded animal, such as a mammal that is afflicted with, or suspected of having, at risk for or being pre-disposed to, or being screened for cancer, e.g., actual or suspected cancer. These terms include, but are not limited to, domestic animals, sports animals, primates and humans. For example, the terms refer to a human.


The term “detect,” “detecting” or “detection” includes assaying, or otherwise establishing the presence or absence of the target biomarker(s), subunits, or combinations of reagent-bound targets, and the like, or assaying for ascertaining, establishing, characterizing, predicting or otherwise determining one or more factual characteristics of a cancer such as stage, aggressiveness, metastatic potential or patient survival, or assisting with the same. A cut-off value or a standard may correspond to levels quantitated for samples from control healthy subjects with no disease or low-grade cancer or from other samples of the subject.


As used herein, the term “marker” or “biomarker” is a biological molecule, or a panel of biological molecules, whose altered level in a tissue, cell or sample as compared to its level in normal or healthy tissue, cell or sample is associated with a disease state, such as an abnormal prostate state, including disease in an early stage, e.g., prior to the detection of one or more symptoms associated with the disease. In an aspect of the disclosure, prostate cancer may be characterized by identifying and measuring the level of one or more biomarkers listed in Tables 1 to 8 in a biological sample.


The biological sample obtained from the subject may be any bodily fluid. For example, the biological sample can be peripheral blood, sera, plasma, ascites, urine, cerebrospinal fluid (CSF), sputum, saliva, bone marrow, synovial fluid, aqueous humor, cerumen, bronchoalveolar lavage fluid, semen, prostatic fluid, Cowper's fluid or pre-ejaculatory fluid, sweat, fecal matter, hair, tears, cyst fluid, pleural and peritoneal fluid, pericardial fluid, lymph, chyme, chyle, bile, interstitial fluid, pus, sebum, vomit, mucosal secretion, stool water, pancreatic juice, lavage fluids from sinus cavities, bronchopulmonary aspirates or other lavage fluids.


In one embodiment, the marker is detected in a urine sample. In another embodiment, the marker is detected in a blood sample, e.g., serum or plasma. In one embodiment, the marker is detected in serum. In one embodiment, the marker is detected in plasma. In some embodiments, the serum or plasma can be further processed to remove abundant blood proteins (e.g., albumin) or irrelevant proteins that are not marker proteins prior to analysis.


Examples of biomarkers include, but are not limited to, polypeptides, peptides, polypeptide fragments, antibodies, hormones, polynucleotides, RNA or RNA fragments, microRNAs (miRNAs), lipids, metabolites, or polysaccharides. In some embodiments, biomarker may be a metabolite marker. In one embodiment, the severity of prostate cancer in a subject can be determined or predicted by a panel of biomarkers or by a combination of two panels that are established by metabolites markers, respectively, through the processes including, but not limited to, K-fold cross validation, forward selection, reverse selection, logistic regression, and/or decision tree analysis. As such, the disclosure can effectively improve the predication index such as, but not limited to, area under the curve (AUC), sensitivity, specificity, positive predictive value (PPV), or negative predictive value (NPV). In some embodiment, the efficacy of combination of two panels of metabolite markers may be better than that of individual panel thereof. As used herein, “panel” refers to a particular combination of biomarkers that is used to determine or predict severity of prostate cancer in a subject, and assign subjects into different groups according to the severity of prostate cancer. As used herein, “group” refers to a selection of subjects being determined to have similar condition or severity of prostate cancer. As used herein, a “model” refers to use of different panels of biomarkers in determining and assigning potential prostate cancer patients in different groups of severity.


In some embodiments, the biomarker involves in the pathway such as, but not limited to, fatty acid biosynthesis, purine metabolism, tryptophan metabolism, pyrimidine metabolism, arginine proline metabolism, pentose and glucuronate interconversion, valine degradation/pyrimidine metabolism, glyoxylate metabolism, ubiquinone biosynthesis, or any combination thereof. In one embodiment, the biomarker is a metabolite marker.


EXAMPLE

Exemplary embodiments of the present disclosure are further described in the following examples, which do not limit the scope of the present disclosure.


Example 1: Grouping of Prostate Cancer Patients

For efficient identification of prostate cancer patients with different severities, Gleason's pattern scale (from grade 1 to 5) is assigned to each prostate tissue biopsy core by experienced pathologist. Grade 1 is given to cells that look like normal prostate tissue while the grade 5 is assigned to cancer cells with very abnormal growth patterns. Most prostate cancers score a grade of 3 or higher. Grade 1 and 2 are not used in the biopsy reports. Prostate tumors are often made up of multiple foci with different grades. Two grades are usually assigned for each patient to give rise to a Gleason sum or Gleason scores. A primary grade is given to describe the cells that make up the largest area of the tumor, and a second grade is given to describe cells of the next largest area. Based on patient's disease risk and severities, six different groups were used to stratify patients in a more precise manner.


The first group is a benign group where no cancer was found; the second group is the metastatic prostate cancer group (mPC) with cancer cells breaking the prostate capsule barrier and invading into other organs (e.g., lymph nodes or bones); the third group is very-low-risk/low-risk prostate cancer group (VLR/LR PC) with all below criteria: Gleason score less than or equal to 6 (e.g., 3+3, the first 3 is the primary grade and the second 3 is the secondary grade), clinical T1 to T2a stage, and PSA of 10 ng/mL or less; the fourth group is high-risk/very-high-risk prostate cancer group (HR/VHR PC) with one of the below criteria: clinical T3a or more, Gleason sum of 8 or more, and PSA of more than 20 ng/mL; the fifth and sixth groups are intermediate-risk prostate cancer group with at least one intermediate-risk criteria below: clinical T2b-2c, Gleason score of 4+3 or 3+4, and PSA of 10 to 20 ng/mL. Among them, the fifth group is favorable-intermediate-risk prostate cancer group (FIR PC) with the below three criteria: only one intermediate-risk factor, Gleason score of 3+4 or less, and less than 50% biopsy cores positive for prostate cancer. The sixth group is the unfavorable-intermediate-risk prostate cancer group (UIR PC) with one of the below three criteria: 2 or 3 intermediate-risk factors, Gleason score of 4+3, and 50% or more of biopsy cores positive for prostate cancer.


Currently, assessing and dividing potential prostate cancer patients into these six groups as mentioned above rely on invasive needle biopsy. With the present disclosure herewith, efficient assessment of patients can be made with the use of corresponding panel of biomarkers with a proper method of analysis. Different models, through the use of different panels of biomarkers, to determine and distinguish potential prostate cancer patients in different groups of severity is adopted and useful under various clinical scenarios. These models identify and distinguish a potential prostate cancer patient in one or more severity groups from the rest of the groups. For example, patients can be distinguished between the benign group versus the rest groups, VLR/LR PC, FIR PC, UIR PC, HR/VHR PC and mPC, for population screening or general health checkup. In another population screening or health check-up, VLR/LR PC can be regarded as benign and divided the subjects under test into a group of benign and VLR/LR PC versus another group consisting of FIR PC, UIR PC, HR/VHR PC and mPC. In another clinical scenario with elder prostate cancer patients, such as those older than 75 years old, an analysis to distinguish between the group of benign, VLR/LR PC or FIR PC versus the group of UIR PC, HR/VHR PC and mPC would be meaningful, considering the risk derived from VLR/LR PC or FIR PC may unlikely blunt a life-span expectation of a man older than 75 years old.


While in a clinical scenario involving a new positive biopsy that the patient is in need of risk stratification and prognosis, an analysis dividing the subject between the group of VLR/LR PC or FIR PC versus the group of UIR PC, HR/VHR PC and mPC is required. Another clinical scenario that could find this analysis useful is for monitoring prostate cancer among patients with VLR/LR PC or FIR PC under active surveillance (AS).


Furthermore, when there is a young prostate cancer patient with a new positive biopsy, then an analysis on whether he belongs to VLR/LR PC versus FIR/UIR/HR/VHR PC or mPC group is useful, considering that the risk of FIR/UIR/HR/VHR PC or mPC may significantly blunt his life-span expectation and impair his social-economical contribution, if not diagnosed in time and properly treated. This analysis that distinguishes an VLR/LR PC group from FIR/UIR/HR/VHR PC or mPC groups is also meaningful for a young prostate cancer patient seeking for AS options.


Therefore, for monitoring patients under AS, different models of comparison and/or panels of markers can be used based on the age of the patient, other physiological condition or clinical manifestations, e.g., PSA level. Doctors can decide which model of comparison and/or panels of markers to be used to allow the best AS option for each patient. For example, for elder patients such as those aged greater than 75-year-old, the AS will adopt the model of comparison that distinguishes benign, VLR/LR PC or FIR PC from those of UIR/HR/VHR PC or mPC, and for younger patients such as those aged less than 60-year-old, the AS will adopt the model of comparison that distinguishes benign, VLR/LR PC from those of FIR/UIR/HR/VHR PC or mPC.


Example 2: Identification of Metabolite Markers for assessing prostate cancer Risk and Assigning Patients in Different Group of Severity Using Liquid Chromatography-Mass Spectrometry (LC/MS) Analysis

Two modes of metabolite analysis were carried out with different columns using liquid chromatography-mass spectrometry (LC/MS) analysis, which are the positive mode with BEH C18 column and negative mode with HILIC column. For positive mode, the urine samples were diluted with water (1:10 vol/vol), and then centrifuged at 4° C. and 13200 rpm for 10 minutes. The supernatants were then transferred to the new sample vial for LC/MS analysis with respective columns.


The LC/MS system used is Agilent 1290 Infinity II ultra-performance liquid chromatography (UPLC) system (Agilent Technologies, Palo Alto, CA, USA) coupled online to the Dual AJS electrospray ionization (ESI) source of an Agilent 6545 quadrupole time-of-flight (Q-TOF) mass spectrometer (Agilent Technologies, Palo Alto, CA, USA). The sample was separated by using ACQUITY UPLC BEH C18 column (1.7 μm, 2.1×100 mm, Waters Corp., Milford, MA, USA) and ACQUITY UPLC BEH amide column (1.7 μm, 2.1×100 mm, Waters Corp., Milford, MA, USA). The column temperature was 40° C. The mobile phase for BEH C18 column was H2O (eluent A) and acetonitrile (eluent B), both eluents with 0.1% formic acid. The gradient condition was: 0 to 1 min, 2% B; 1 to 4 min, 2 to 40% B; 4 to 8 min, 40 to 70% B; 8 to 10 min, 70 to 95% B; 10 to 12 min, 95% B; 12 to 13 min, 95 to 2% B; 13 to 16 min, 2% B. The flow rate was 400 μL/min, and the injection volume of sample was 1 μL. The mobile phase for BEH amide column was H2O (eluent A) and 90% acetonitrile (eluent B), both eluents with 15 mM ammonium acetate and 0.3% NH4OH. The gradient condition was: 0 to 7 min, 90% B; 7 to 8 min, 70 to 50% B; 8 to 10 min, 50% B; 10 to 11 min, 50 to 90% B; 11 to 16 min, 90% B. The post time of elution was 4 min. The flow rate was 300 μL/min, and the injection volume of sample was 2 μL. The instrument was operated in positive full-scan mode with BEH C18 column and negative full-scan mode with BEH amide column, both methods collected from an m/z of 60 to 1700. The MS operating conditions were optimized as follows: Vcap voltage, 3.5 kV; nozzle voltage, 0.5 kV; nebulizer, 45 psi; gas temperature, 300° C.; sheath gas temperature, 325° C.; sheath gas flow (nitrogen), 8 L/min; drying gas (nitrogen), 8 L/min.


For negative mode with HILIC column, the urine samples were diluted with acetonitrile (1:10 vol/vol), then centrifuged at 4° C. and 13200 rpm for 10 min. The supernatants were transferred to the new sample vial for LC/MS analysis. The LC/MS method is same with BEH C18 column as described above.


The chromatogram acquisition, detection of mass spectral peaks, and their waveform processing were performed using Agilent Qualitative Analysis 10.0 and Agilent Profinder 10.0 software (Agilent, USA).


To identify and select the specific metabolites as markers for distinguishing different groups, a univariate logistic regression to select differentially accumulated metabolites with P values less than 0.1. The identified differential compounds were further analyzed by Receiver operating characteristic (ROC), using Medcalc software version 11.2 (Medcalc Software, Belgium). Furthermore, a K-fold cross validation and a followed reverse selection-based logistic regression were applied to select discriminator sets with improved AUC performance.


To find urine biomarkers that distinguish prostate tumors with different malignancy potential, four different models of comparison were performed by analyzing metabolites from LC/MS with BEH C18 column. The union of all these four sets of markers from LC/MS with BEH C18 column is listed in Table 1 below.









TABLE 1







Mass to charge ratio (m/z) of the union of all sets of potential


metabolite markers from LC/MS with BEH C18 column for distinguishing


patients of prostate tumor-with different malignancy potential











Marker

Retention

CAS


metabolites
m/z
time (min)
Annotation by SIRIUS
Number














C5
59.9999
0.6




C5H11NO
101.0842
13.2
N-Butylformamide
871-71-6


C6H15N
101.1201
13.2




C8H9N
119.0732
1.9
Isoindoline
496-12-8


C5H2O2P
124.9791
0.6




C5H7NO3
129.0427
3.2
5-Oxo-D-proline
4042-36-8


C9H8O2
148.052
7.4
Pyruvophenone
579-07-07


C5H11NO2S
149.0505
0.9
Methionine
59-51-8


C11H20O2
184.1458
5.4
Undecylenic acid
112-38-9


C12H17NO
191.1302
5.6
Hexanilide
621-15-8


C8H16NO5
206.1025
2.5




C6H16N3O5
210.1089
0.7




C6H14N2O5P
225.0635
2.7
Vanilloylglycine
1212-04-0


C13H25NO2
227.1883
5.7
Undecylenamide MEA
20545-92-0


C10H21N4O2
229.1673
5
N-decanoylglycine
14305-32-9


C11H5NOPS
229.9828
0.9




C12H2NOPS
238.9582
0.6




C12H21NO4
243.1467
3
3-(Cyclobutanecarbonyloxy)-4-






(trimethylazaniumyl)butanoate


C13H25NO3
243.1826
5.1
N-Undecanoylglycine
83871-09-4


C10H18N2O5
246.1209
2.7




C6HCl5
247.8566
13.4




C12H25NO4P
278.1509
9
Dibutyl phthalate
84-74-2


C12 H16NO7
286.0931
3.2




C14H30N4O2
286.2362
0.7




C13H23NO6
289.1519
2.4
O-adipoyl-L-carnitine
102636-83-9


C16H30N3O2
296.2339
8.1
10-Hydroxyoctadeca-12,15-
34932-14-4





dienoic acid


C13H19N5O5
325.1379
2
N(2),N(2),7-trimethylguanosine



C9H4N5O9
325.9998
6.6




C16H13N3O3P
326.0699
8.1




C18H33NO4
327.2396
7




C12H9O9P
327.9969
6.6




C18H34O5
330.2395
5.7




C19H38N2O3
342.2868
6.3
Cocamidopropyl betaine
4292/10/8


C17H41N4O3
349.3176
10.3




C19H35NO5
357.2518
6.3
[3-carboxy-2-[(Z)-3-






hydroxydodec-9-





enoyl]oxypropyl]-





trimethylazanium


C19H19N8
359.1742
8.5
N-(1,4-Dihydroxy-4-
2058332-33-3





methylpentan-2-YL)-3-hydroxy-





5-oxo-6-phenylhexanamide


C18H43N4O3
363.3334
10.8
1,2-Propanediol, 3-((2-
34719-62-5





hydroxyheptadecyl)oxy)-


C18H16N6O3
364.1293
8.6




C19H31N6O2
375.2519
6.6
1,3,5-Tris(2,2-
745070-61-5





dimethylpropionylamino)benzene


C22H45NO4
387.3335
11.6




C17H32N3O7
390.2231
2.5




C21H36N4O3
392.2789
6.6
(2R)-N-[(2S)-1-amino-3-
1212507-31-7





cyclohexyl-1-oxopropan-2-yl]-1-





(cyclohexanecarbonyl)piperazine-





2-carboxamide


C15H30N10OP
397.2335
6.6
Lysylthreonyllysine
106326-71-0


C27H12N9
462.1229
10




C23H47N8O2
467.3828
9.8




C24H42N7O3
476.3347
6.6




C26H51N4O5
499.388
10.2




C27H55N8O3
539.4401
10.7




C30H57NO7
543.4126
10.2




C28H57N8O4
569.4509
10.2




C26H58N13P
583.4642
10.7




C34H23N7O5
609.1765
12.1




C30H61N8O5
613.477
10.2




C24H41N14O8
653.3222
10.4




C30H64N15O2P
697.5124
10.7




C41H23N11O2
701.2021
12




C35H71N8O7
715.5414
10.6




C51H29N5O4
775.2244
12.9




C43H40N20O3
884.3598
11.2




C40H38N22O4
890.3456
12.4











To find urine biomarkers that distinguish prostate tumors with different malignancy potential, metabolites from LC/MS with HILIC column in four different models of comparison were analyzed. The union of all these four sets of markers from LC/MS with HILIC column for distinguishing different malignancy potential of prostate tumors is listed in Table 2 below.









TABLE 2







Mass to charge ratio (m/z) of the union of all sets of potential


metabolite markers from LC/MS with HILIC column for distinguishing


prostate tumors with different malignancy potential













Retention




Marker

time
Annotation by
CAS


metabolites
m/z
(min)
SIRIUS
Number














C5H4O3
112.016
5.1
2-Furoate
88-14-2


C4H6O4
118.0263
4
Succinate
110-15-6


C5H8N2O2
128.0578
1.6
1,3-Diazepane-
75548-99-1





2,4-dione


C5H10N2O3
146.0691
1.6
Alanylglycine
1188-01-8


C6H5N2OP
152.0134
1.8




C5H4N4O2
152.0328
2.4
Xanthine
69-89-6


C7H10O4
158.0575
3.7
Hept-2-
1085697-





enedioic acid
38-6


C6H6N4O2
166.0491
1.6
1-Methylxanthine
6136-37-4


C6H8N2O4
172.0481
2.6
Hydantoin-
5624-26-0





propionate


C8H14O4
174.089
3.4
Suberic acid
505-48-6


C6H10O4S
178.03
1.5
3,3′-






Thiodipropanoate


C9H9NO3
179.0584
1.4
Hippurate
495-69-2


C9H16O4
188.1045
3.2
Azelaic acid
123-99-9


C10H16O4
200.1049
1
Radioplex
10018-78-7


C8H9O6
201.0396
1.4




C6H11N4O2P
202.0602
2.3




C8H4N4O3
204.0299
1.6




C6H8O6S
208.0033
1




C7H6O6S
217.9884
1.6
Salicylsulfuric
89-45-2





acid


C6H11N4O3P
218.055
3.4




C6H13N4OP2
219.0564
1.9
S-(3-Oxopropyl)-
140226-30-8





N-acetylcysteine


C7H8O6S
220.0041
0.9
1-Methyl-






pyrogallol-3-O-





sulphate


C10H18N2O4
230.1258
2
DI-Acetyl-lysine
499-86-5


C9H17NO4S
235.0868
1.6
S-(D-
1632078-





Carboxybutyl)-L-
43-3





homocysteine


C12H7N4O2
239.0556
1.9




C6H15O8P
246.0504
3.4




C8H16N2O5P
251.0787
1.5
N-
1220-05-9





Feruloylglycine


C8H18NO6P
255.0875
2.1
Pantothenate
79-83-4


C7H21N3OP3
256.0895
4.5




C16H32O2
256.2403
0.9
Hexadecanoic
1957/10/3





acid


C11H16N4O4
268.1169
3.1
Acetylcarnosine



C7H17O7P2
275.0449
1
L-Tyrosine
81660-41-5





methyl ester 4-





sulfate


C19H14O3
290.0942
0.8




C14H20N2O5
296.1362
1.5




C10H19N5P3
302.0856
1.6




C11H20NO3P3
307.0652
2.7




C7H22N4O9PS
369.084
2.8




C15H28N6OP2
370.18
0.9
DHT-sulfate
2641-48-7


C21H33N3O3
375.2509
0.9




C16H39N8OP
390.2988
0.9




C21H39N4OP
394.2848
1.7




C17H42N5OP2
394.2849
0.9




C17H34N9O2
396.2825
1.7




C22H38N7O
416.3138
1




C24H40N4O3
432.3084
0.9




C23H42N7O
432.3413
0.9




C27H48P2
434.3237
0.9




C25H50O6
446.3605
0.9




C26H43NO6
465.3085
1.7




C27H54O6
474.3916
0.9




C25H46N7O3
492.3639
0.9




C28H52N7O
502.4229
0.9




C23H27O11S
511.1262
1.4




C33H22O7
530.1361
0.8




C39H26O7
606.1673
0.8




C39H78O6
642.5768
0.9




C34H73N8O2P
656.5583
0.9




C40H85NOP3
688.5843
1




C38H48O12
696.3159
0.9











In each of different models of comparison designed for diverse clinical scenarios, a representative panel of metabolite markers was identified from LC/MS with BEH C18 column, as shown in Table 3 below, with their prediction ability evaluated by AUC analysis. Sensitivity and specificity of the prediction are also shown in bracket following AUC.









TABLE 3







Representative panels of metabolite markers from LC/MS with BEH C18 column for


distinguishing patients of prostate tumors with different malignancy potential














AUC
AUC





(sensitivity/
(sensitivity/



Models of
Metabolite markers
specificity)
specificity)


No
comparison
(N = Number of markers)
without PSA
with PSA





1
Benign
N = 20
0.89 (90%/55%)
0.91 (90%/64%)



vs.
C10H21N4O2



VLR PC/LR
C12H17NO



PC/FIR PC/UIR
C12H2NOPS



PC/HR PC/VHR
C12H9O9P



PC/mPC
C13H19N5O5




C17H32N3O7




C18H16N6O3




C18H33NO4




C18H43N4O3




C19H35NO5




C19H38N2O3




C24H42N7O3




C27H12N9




C34H23N7O5




C5H11NO




C51H29N5O4




C6H15N




C8H9N




C9H4N5O9




C9H8O2


2
Benign/VLR
N = 23
0.84 (90%/49%)
0.89 (90%/62%)



PC/LR PC
C11H5NOPS



vs.
C12H16NO7



FIR PC/UIR
C12H2NOPS



PC/HR PC/VHR
C12H9O9P



PC/mPC
C13H25NO2




C13H25NO3




C14H30N4O2




C16H13N3O3P




C17H41N4O3




C19H19N8




C22H45NO4




C26H51N4O5




C26H58N13P




C27H12N9




C27H55N8O3




C30H57NO7




C30H64N15O2P




C41H23N11O2




C5




C5H7NO3




C6HCl5




C6H16N3O5




C8H16NO5


3
Benign/VLR
N = 21
0.78 (90%/47%)
0.86 (90%/61%)



PC/LR PC/FIR PC
C10H18N2O5



vs.
C12H21NO4



UIR PC/HR
C13H23NO6



PC/VHR PC/mPC
C13H25NO3




C14H30N4O2




C15H30N10OP




C16H13N3O3P




C19H31N6O2




C22H45NO4




C27H12N9




C28H57N8O4




C30H61N8O5




C30H64N15O2P




C35H71N8O7




C40H38N22O4




C41H23N11O2




C43H40N20O3




C5H11NO




C5H11NO2S




C5H2O2P




C8H16NO5


4
Benign/PC with
N = 24
0.82 (90%/48%)
0.86 (90%/57%)



GS < 7
C11H20O2



vs.
C11H5NOPS



PG with GS >= 7
C12H2NOPS




C12H25NO4P




C12H9O9P




C13H25NO2




C13H25NO3




C14H30N4O2




C16H30N3O2




C17H41N4O3




C18H34O5




C19H31N6O2




C21H36N4O3




C22H45NO4




C23H47N8O2




C24H41N14O8




C27H12N9




C30H57NO7




C30H64N15O2P




C35H71N8O7




C43H40N20O3




C5H11NO




C5H11NO2S




C6H14N2O5P









In each of different models of comparison designed for diverse clinical scenarios, a representative panel of metabolite markers from LC/MS with HILIC column was also identified, as shown in Table 4 below. The prediction ability was evaluated by AUC analysis, with or without inclusion of PSA level in calculation. Sensitivity and specificity of the prediction is shown in bracket following AUC.









TABLE 4







Representative panels of metabolite markers from LC/MS with HILIC column


for distinguishing prostate tumors with different malignancy potential














AUC
AUC





(sensitivity/
(sensitivity/



Models of
Metabolite markers
specificity)
specificity)


No
comparison
(N = Number of markers)
without PSA
with PSA





1
Benign
N = 25
0.86 (90%/51%)
0.88 (90%/65%)



vs.
C10H16O4



VLR PC/LR
C10H18N2O4



PC/FIR PC/UIR
C11H20NO3P3



PC/HR PC/VHR
C12H7N4O2



PC/mPC
C15H28N6OP2




C16H39N8OP




C19H14O3




C21H33N3O3




C23H27O11S




C23H42N7O




C25H46N7O3




C27H48P2




C27H54O6




C33H22O7




C34H73N8O2P




C38H48O12




C40H85NOP3




C5H4O3




C5H8N2O2




C6H11N4O3P




C6H13N4OP2




C7H10O4




C7H17O7P2




C7H6O6S




C8H14O4


2
Benign/VLR
N = 27
0.80 (90%/46%)
0.86 (90%/53%)



PC/LR PC
C10H16O4



vs.
C11H16N4O4



FIR PC/UIR
C12H7N4O2



PC/HR PC/VHR
C14H20N2O5



PC/mPC
C16H32O2




C17H34N9O2




C21H33N3O3




C23H27O11S




C26H43NO6




C27H48P2




C28H52N7O




C34H73N8O2P




C38H48O12




C39H26O7




C4H6O4




C40H85NOP3




C5H4N4O2




C5H8N2O2




C6H11N4O2P




C6H13N4OP2




C6H6N4O2




C6H8N2O4




C7H10O4




C7H17O7P2




C7H6O6S




C9H16O4




C9H9NO3


3
Benign/VLR
N = 28
0.77 (90%/42%)
0.86 (90%/56%)



PC/LR PC/FIR PC
C10H18N2O4



vs.
C10H19N5P3



UIR PC/HR
C12H7N4O2



PC/VHR PC/mPC
C15H28N6OP2




C16H32O2




C17H34N9O2




C19H14O3




C21H33N3O3




C21H39N4OP




C27H48P2




C38H48O12




C39H26O7




C40H85NOP3




C5H10N2O3




C5H4N4O2




C6H10O4S




C6H11N4O2P




C6H13N4OP2




C6H15O8P




C7H10O4




C7H17O7P2




C7H21N3OP3




C7H22N4O9PS




C7H8O6S




C8H9O6




C9H16O4




C9H17NO4S




C9H9NO3


4
Benign/PC with
N = 26
0.81 (90%/53%)
0.87 (90%/57%)



GS < 7
C10H19N5P3



vs.
C12H7N4O2



PG with GS >= 7
C15H28N6OP2




C17H34N9O2




C17H42N5OP2




C21H33N3O3




C22H38N7O




C24H40N4O3




C25H46N7O3




C25H50O6




C27H54O6




C39H26O7




C39H78O6




C40H85NOP3




C6H11N4O2P




C6H15O8P




C6H5N2OP




C6H8O6S




C7H10O4




C7H17O7P2




C7H21N3OP3




C8H16N2O5P




C8H18NO6P




C8H4N4O3




C9H16O4




C9H9NO3









Example 3: Identification of Metabolite Markers for Assessing Prostate Cancer Risk and Grouping of Patients Using Gas Chromatography-Mass Spectrometry (GC/MS) Analysis

First, urine sample preparation started with incubating an individual urine sample with urease enzyme to deplete excess urea, as a high abundance of urea is a major chromatographic interference. 100 U of urease was added to 100 μL of each human urine sample, followed by incubation at 37° C. with mild shaking at 650 rpm for 1 hour to decompose and remove excess urea. Subsequently, termination of urease activity and extraction of metabolites were carried out by admixing 1 mL of methanol with vortex for 30 seconds, and precipitated proteins were removed by centrifugation at 13,200 rpm for 15 min at 4° C. The supernatants were transferred to a 2-mL microcentrifugation tube and then dried in SpeedVac vacuum concentrators. The dried metabolic extract was derivatized by bis(trimethylsilyl)-trifluoroacetamide (BSTFA) containing 1% trimethylchlorosilane (TMCS) and analyzed using GC/MS as explained below.


The derivatized samples were analyzed using Agilent 7890B gas chromatography coupled with 7250 quadrupole time-of-flight mass spectrometer (GC-Q-TOF/MS) equipped with electron ionization (EI). The separation was performed on Zorbax DB5-MS+10 m Duragard Capillary Column (30 m×0.25 mm×0.25 mm, Agilent). The GC temperature profile was held at 60° C. for 1 minute and then raised at 10° C./min to 325° C. and held at 325° C. for 10 minutes. The transfer line and the ion source temperature were set at 300° C. and 280° C., respectively. The mass range monitored was from 50 to 600 Daltons. Mass spectra were compared against the NIST 2017, Fiehn, and Wiley Registry 11th Edition mass spectral library.


A univariate logistic regression to select differentially accumulated metabolites with P values less than 0.1. The identified differential compounds were further analyzed by Receiver operating characteristic (ROC), using Medcalc software version 11.2 (Medcalc Software, Belgium). Furthermore, a K-fold cross validation and a followed reverse selection-based logistic regression were applied to select discriminator sets with improved AUC performance.


To identify urine biomarkers that distinguish prostate tumors with different malignancy potential, five different models of comparison analyzing metabolites from GC/MS were performed. The union of all these five sets of markers is listed in Table 5. For the patients with PSA less than 20 ng/ml, the union of these five sets of markers is shown in Table 6.









TABLE 5







The union of all sets of potential metabolite markers from GC/MS for


distinguishing prostate tumors with different malignancy potential









Metabolite markers
CAS number
MW g/mol












Ethanimidic acid, N-(trimethylsilyl)-, trimethylsilyl ester
60-35-5
59.07


[700] ethanolamine [9.879]
141-43-5
61.08


Glycine, di-TMS
56-40-6
75.07


[1060] pyruvic acid [6.714]
127-17-3
88.06


[239] Beta-alanine 1 [12.044]
107-95-9
89.09


[107689] L-(+) lactic acid [6.851]
79-33-4
90.08


[8871] 2-hydroxypyridine [6.519]
142-08-05
95.1


Diethanolamine, 3TMS derivative
111-42-2
105.14


[439194] glyceric acid [10.735]
473-81-4
106.08


Pentenoic acid, 4-[(trimethylsilyl)oxy]-, trimethylsilyl ester
123-76-2
116.12


[763] guanidinoacetic acid 2 [14.751]
352-97-6
117.108


[45] tartronic acid [11.523]
80-69-3
120.06


Butanoic acid, 2,4-bis[(trimethylsilyl)oxy]-, trimethylsilyl ester
1518-62-3
120.1


[7405] L-pyroglutamic acid [13.218]
98-79-3
129.11


[791] DL-isoleucine 2 [10.225]
443-79-8
131.17


1H-Indole, 1-(trimethylsilyl)-5-[(trimethylsilyl)oxy]-
1953-54-4
133.15


2,3,4-Trihydroxybutyric acid tetrakis(trimethylsilyl) deriv., (, (R*,R*)-)
3909/12/4
136.1


1-Deoxypentitol, 4TMS derivative
13046-76-9
136.15


[135] 4-hydroxybenzoic acid [14.505]
99-96-7
138.12


[18189] 4-acetamidobutyric acid 1 [12.863]
3025-96-5
145.16


[738] L-glutamine 2 [14.083]
56-85-9
146.14


[439240] D-lyxose 2 [14.889]
1114-34-7
150.13


Arabinofuranose, 1,2,3,5-tetrakis-O-(trimethylsilyl)-
13221-22-2
150.13


[1188] xanthine [18.574]
69-89-6
152.11


Ribitol TMS
488-81-3
152.15


[6912] xylitol [15.376]
87-99-0
152.15


L-(−)-Arabitol, 5TMS derivative
7643-75-6
152.15


Furan, tetrahydro-2,5-dipropyl-
4457-62-9
156.26


[219984] 1,5-anhydro-D-sorbitol [16.967]
154-58-5
164.16


L-Phenylalanine, 2TMS derivative
63-91-2
165.19


3,4-Dihydroxyphenylacetic Acid, 3TMS derivative
102-32-9
168.15


[328] DL-4-hydroxymandelic acid [16.126]
1198-84-1
168.15


[64969] 3-methyl-L-histidine [16.423]
368-16-1
169.18


[444212] trans-aconitic acid [15.842]
4023-65-8
174.11


Ethyl (E)-1-penten-3-ynesulfonate
171816-65-2
174.22


[448388] D-allose 2 [17.521]
2595-97-3
180.156


[448388] D-allose 1 [17.278]
2595-97-3
180.16


[6057] L-tyrosine 2 [17.856]
60-18-4
181.19


[6508] quinic acid [17.076]
77-95-2
192.17


[445929] galacturonic acid 2 [18.105]
685-73-4
194.14


Ononitol TMS
6090-97-7
194.18


D-Gluconic acid, 6TMS derivative
526-95-4
196.16


[6613] pantothenic acid 2 [18.371]
79-83-4
219.23


[899] N-acetyl-D-mannosamine 1 [19.177]
7772-94-3
221.21


D-Allose, pentakis(trimethylsilyl) ether, ethyloxime (isomer 2)
2058302-87-5
223.22


Pseudo uridine penta-tms
1445-07-04
244.2


[985] palmitic acid [18.846]
1957/10/3
256.4


2-phenyl-3,5,7-tris(trimethylsilyloxy)-1-benzopyran-4-one
548-83-4
270.24


[5281] stearic acid [20.675]
1957/11/4
284.48


Guanosine, N,N-dimethyl-1-(trimethylsilyl)-2′,3′,5′-tris-O-(trimethylsilyl)-
2140-67-2
311.29


1-Monopalmitin, 2TMS derivative
542-44-9
330.5


[84571] lactose 1 [24.386]
63-42-3
342.3


2-Monostearin, 2TMS derivative
621-61-4
358.56


[24699] 1-stearoyl-rac-glycerol [24.913]
123-94-4
358.6


3-Phenyl-5,10-secocholesta-1(10),2-dien-5-one
—*
460.74
















TABLE 6







The union of all sets of potential metabolite markers from


GC/MS for distinguishing prostate tumors (with PSA level


less than 20 ng/mL) with different malignancy potential








No.
Name of metabolites











1
(4RS,5SR)-5-hydroperoxy-4-decanol


2
(22S,23S,25R)-3β-methoxy-16β,23:22,26-diepoxy-5α-cholestane


3
1-Methoxymethyl-2-phenylthioindole-3-carbaldehyde


4
1-Stearoyl-rac-glycerol


5
2,3-Dihydroxybutanoic acid


6
2,4-Dihydroxybutanoic acid


7
2,5-Dipropyltetrahydrofuran


8
2-Hydroxypyridine


9
2-Stearoylglycerol


10
3,4,5-Trihydroxypentanoic acid


11
3,4-Dihydroxyphenylacetic acid


12
3-Hydroxyphenylacetic acid


13
3-Indoleacetic acid


14
3-Methyl-L-histidine


15
4-Acetamidobutyric acid


16
4-Hydroxybenzoic acid


17
4-hydroxymandelic acid


18
6-ethoxyiminohexane-1,2,3,4,5-pentol


19
Acetamide


20
alpha-Hydroxyisobutyric acid


21
Arabinofuranose


22
Beta-Alanine


23
Cyclohexylamine


24
Daidzein


25
D-Allose


26
D-Altrose


27
D-Gluconic acid


28
DL-4-Hydroxy-3-methoxymandelic acid


29
DL-isoleucine


30
D-Lyxose


31
D-tagatofuranose


32
Ethanolamine


33
Ethyl 1-penten-3-ynesulfonate


34
Galacturonic acid


35
Galangin


36
Glyceric acid


37
Guanidinoacetic acid


38
Hippuric Acid


39
Lactose


40
L-Arabinitol


41
Levulinic acid


42
L-Fucose


43
L-Lactic acid


44
L-Pyroglutamic acid


45
Monopalmitin


46
Ononitol


47
Oxamide


48
Palmitic acid


49
Pantothenic acid


50
Pseudouridine


51
p-Tolyl-beta-D-glucopyranosid-uronsaeure


52
Pyruvic acid


53
Quinic acid


54
Ribitol


55
Stearic acid


56
Sucrose


57
Tartronic acid


58
trans-Aconitic acid


59
Uric acid


60
Xanthine


61
Xylitol









Example 4: Metabolite Markers From GC/MS Analysis for Assessing Prostate Cancer Risk and Grouping of Patients

In each of different models of comparison designed for different patients, a representative panel of metabolite markers from GC/MS was identified, as shown in Table 7 below. The prediction ability was evaluated by AUC analysis, with or without inclusion of PSA level in calculation. Sensitivity and specificity of the prediction are also shown in bracket following AUC. For the patients with PSA less than 20 ng/ml, the representative panel of metabolite markers is listed in Table 8.









TABLE 7







Representative panels of GC/MS-derived metabolite markers for distinguishing


the malignancy potential of patients with prostate tumors














AUC
AUC





(sensitivity/
(sensitivity/



Models of
Metabolite markers
specificity)
specificity)


No
comparison
(N = Number of markers)
without PSA
with PSA





1
Benign
N = 26
0.94
0.94



vs.
Pyruvic acid
(90%/79%)
(90%/82%)



VLR/LR/FIR/
4-Acetamidobutyric acid



UIR/HR/VHR
1,5-Anhydro-D-glucitol



PC and mPC
Beta-Alanine




Glyceric acid




D-Lyxose




Galacturonic acid




D-Allose




L-Tyrosine




3-Methyl-L-histidine




L-Glutamine




L-Pyroglutamic acid




Guanidinoacetic acid




Lactose




2-Hydroxypyridine




N-acetyl-D-mannosamine




Palmitic acid




1-Deoxy-d-ribitol




Monopalmitin




2-Stearoylglycerol




Galangin




6-ethoxyiminohexane-




1,2,3,4,5-pentol




D-Gluconic acid




N,N-Dimethylguanosine




Pseudouridine




Ribitol


2
Benign and
N = 24
0.85
0.90



VLR/LR PC
Pyruvic acid
(90%/63%)
(90%/73%)



vs.
Xanthine



FIR/UIR/HR/
4-Acetamidobutyric acid



VHR PC and
1,5-Anhydro-D-glucitol



mPC
Beta-Alanine




1-Stearoyl-rac-glycerol




Glyceric acid




Galacturonic acid




Quinic acid




Xylitol




L-Pyroglutamic acid




Guanidinoacetic acid




Lactose




Ononitol




5-Hydroxyindole




Monopalmitin




Galangin




3,4-Dihydroxyphenylacetic




acid




3-Phenyl-5,10-secocholesta-




1(10),2-dien-5-one




Acetamide




Ethyl 1-penten-3-ynesulfonate




2,5-Dipropyltetrahydrofuran




L-Phenylalanine




Pseudouridine


3
Benign and
N = 26
0.82
0.90



VLR/LR/FIR
L-Lactic acid
(90%/50%)
(90%/67%)



PC
Xanthine



vs.
4-Acetamidobutyric acid



UIR/HR/VHR
Beta-Alanine



PC and mPC
1-Stearoyl-rac-glycerol




4-hydroxymandelic acid




trans-Aconitic acid




D-Allose




Tartronic acid




Stearic acid




L-Tyrosine




Quinic acid




Ethanolamine




Guanidinoacetic acid




DL-isoleucine




Palmitic acid




Monopalmitin




Arabinofuranose




2,4-Dihydroxybutanoic acid




Diethanolamine




Acetamide




2,5-Dipropyltetrahydrofuran




Glycine




L-Arabinitol




Levulinic acid




Pseudouridine


4
Benign +
N = 22
0.80
0.85



GS < 7 PC
Pyruvic acid
(90%/46%)
(90%/55%)



vs.
Xanthine



GS ≥ 7 PC
4-Hydroxybenzoic acid




Beta-Alanine




1-Stearoyl-rac-glycerol




Galacturonic acid




D-Allose




Tartronic acid




Quinic acid




Pantothenic acid




Xylitol




Guanidinoacetic acid




1-Deoxy-d-ribitol




Monopalmitin




Threonic acid




Galangin




Arabinofuranose




2,4-Dihydroxybutanoic acid




D-Gluconic acid




2,5-Dipropyltetrahydrofuran




Levulinic acid




Pseudouridine
















TABLE 8







Representative panels of GC/MS metabolite markers for distinguishing the malignancy


potential of patients with prostate tumors (PSA level less than 20 ng/mL)














AUC
AUC





(sensitivity/
(sensitivity/



Models of
Metabolite markers
specificity)
specificity)


No
comparison
(N = Number of markers)
without PSA
with PSA





1
Benign
N = 28
0.93
0.95



vs.
1-Methoxymethyl-2-
(90%/73%)
(90%/82%)



VLR/LR/FIR/
phenylthioindole-3-



UIR/HR/VHR
carbaldehyde



PC and mPC
2,3-Dihydroxybutanoic acid




2-Hydroxypyridine




2-Stearoylglycerol




3-Hydroxyphenylacetic acid




3-Indoleacetic acid




3-Methyl-L-histidine




4-Acetamidobutyric acid




4-hydroxymandelic acid




6-ethoxyiminohexane-




1,2,3,4,5-pentol




alpha-Hydroxyisobutyric acid




D-Altrose




D-Gluconic acid




D-Lyxose




Galacturonic acid




Galangin




Glyceric acid




Lactose




L-Fucose




L-Pyroglutamic acid




Monopalmitin




Ononitol




Oxamide




Palmitic acid




Pseudouridine




Pyruvic acid




Ribitol




trans-Aconitic acid


2
Benign and
N = 22
0.87
0.90



VLR/LR PC
1-Stearoyl-rac-glycerol
(90%/62%)
(90%/72%)



vs.
2,5-Dipropyltetrahydrofuran



FIR/UIR/HR/
3,4-Dihydroxyphenylacetic



VHR PC and
acid



mPC
Acetamide




Beta-Alanine




Cyclohexylamine




Ethyl 1-penten-3-ynesulfonate




Galacturonic acid




Galangin




Glyceric acid




Guanidinoacetic acid




Levulinic acid




Monopalmitin




Ononitol




Palmitic acid




p-Tolyl-beta-D-




glucopyranosid-uronsaeure




Quinic acid




Stearic acid




Sucrose




Uric acid




Xanthine




Xylitol


3
Benign and
N = 27
0.83
0.90



VLR/LR/FIR
(22S,23S,25R)-3β-methoxy-
(90%/55%)
(90%/70%)



PC
16β,23:22,26-diepoxy-5α-



vs.
cholestane



UIR/HR/VHR
1-Methoxymethyl-2-



PC and mPC
phenylthioindole-3-




carbaldehyde




1-Stearoyl-rac-glycerol




2,4-Dihydroxybutanoic acid




2,5-Dipropyltetrahydrofuran




4-hydroxymandelic acid




Acetamide




Arabinofuranose




Beta-Alanine




Daidzein




D-Allose




DL-isoleucine




D-tagatofuranose




Ethanolamine




Galangin




Guanidinoacetic acid




L-Arabinitol




Levulinic acid




L-Lactic acid




Monopalmitin




Palmitic acid




Pseudouridine




Quinic acid




Stearic acid




Sucrose




Tartronic acid




Xanthine


4
Benign +
N = 25
0.78
0.82



GS < 7 PC
(4RS,5SR)-5-hydroperoxy-4-
(90%/38%)
(90%/45%)



vs.
decanol



GS ≥ 7 PC
2,5-Dipropyltetrahydrofuran




3,4,5-Trihydroxypentanoic




acid




4-Hydroxybenzoic acid




6-ethoxyiminohexane-




1,2,3,4,5-pentol




Acetamide




Arabinofuranose




Beta-Alanine




D-Allose




DL-4-Hydroxy-3-




methoxymandelic acid




Ethyl 1-penten-3-ynesulfonate




Galacturonic acid




Galangin




Glyceric acid




Guanidinoacetic acid




Hippuric Acid




Levulinic acid




L-Pyroglutamic acid




Pantothenic acid




Pseudouridine




Pyruvic acid




Quinic acid




Tartronic acid




Uric acid




Xanthine








Claims
  • 1. A method to characterize prostate cancer in a subject in need thereof, comprising detecting a level of a prostate cancer marker in a biological sample from the subject, wherein the prostate cancer marker comprises one or more of metabolite markers in Tables 1, 2, 5 and 6.
  • 2. The method of claim 1, wherein the prostate cancer marker comprises at least one metabolite marker selected from the group consisting of Ethanimidic acid, N-(trimethylsilyl)-, trimethylsilyl ester; ethanolamine; Glycine, di-TMS; pyruvic acid; Beta-alanine 1; L-(+) lactic acid; 2-hydroxypyridine; Diethanolamine, 3TMS derivative; glyceric acid; Pentenoic acid, 4-[(trimethylsilyl)oxy]-, trimethylsilyl ester; guanidinoacetic acid 2; tartronic acid; Butanoic acid, 2,4-bis[(trimethylsilyl)oxy]-, trimethylsilyl ester; L-pyroglutamic acid; DL-isoleucine 2; 1H-Indole, 1-(trimethylsilyl)-5-[(trimethylsilyl)oxy]; 2,3,4-Trihydroxybutyric acid tetrakis(trimethylsilyl) deriv., (, (R*,R*)—); 1-Deoxypentitol, 4TMS derivative; 4-hydroxybenzoic acid; 4-acetamidobutyric acid 1; L-glutamine 2; D-lyxose 2; Arabinofuranose, 1,2,3,5-tetrakis-O-(trimethylsilyl); xanthine; Ribitol TMS; xylitol; L-(−)-Arabitol, 5TMS derivative; Furan, tetrahydro-2,5-dipropyl-; 1,5-anhydro-D-sorbitol; L-Phenylalanine, 2TMS derivative; 3,4-Dihydroxyphenylacetic Acid, 3TMS derivative; DL-4-hydroxymandelic acid; 3-methyl-L-histidine; trans-aconitic acid; Ethyl (E)-1-penten-3-ynesulfonate; D-allose 2; D-allose 1; L-tyrosine 2; quinic acid; galacturonic acid 2; Ononitol TMS; D-Gluconic acid, 6TMS derivative; pantothenic acid 2; N-acetyl-D-mannosamine 1; D-Allose, pentakis(trimethylsilyl) ether, ethyloxime (isomer 2); Pseudo uridine penta-tms; palmitic acid; 2-phenyl-3,5,7-tris(trimethylsilyloxy)-1-benzopyran-4-one; stearic acid; Guanosine, N,N-dimethyl-1-(trimethylsilyl)-2′,3′,5′-tris-O-(trimethylsilyl)-; 1-Monopalmitin, 2TMS derivative; lactose 1; 2-Monostearin, 2TMS derivative; 1-stearoyl-rac-glycerol; and 3-Phenyl-5,10-secocholesta-1(10),2-dien-5-one.
  • 3. The method of claim 2, wherein the biological sample is peripheral blood, sera, plasma, urine, semen, prostatic fluid, Cowper's fluid, pre-ejaculatory fluid, or any combination thereof.
  • 4. The method of claim 3, further comprising detecting a level of prostate specific antigen in the biological sample from the subject.
  • 5. The method of claim 4, further comprising grouping the subject by NCCN risk classification into six groups of different severities of prostate cancer, wherein the six groups are benign group, very low-risk/low-risk prostate cancer, favorable-intermediate-risk prostate cancer, unfavorable-intermediate-risk prostate cancer, high-risk/very high-risk prostate cancer, and metastasis prostate cancer group.
  • 6. The method of claim 5, further comprising distinguishing the severity of prostate cancer in the subject in one group from the other groups.
  • 7. The method of claim 6, further comprising distinguishing the severity of prostate cancer in the subject in more than one group from the other groups.
  • 8. A method for determining a need of biopsy for prostate cancer diagnosis in a subject in need thereof, comprising detecting a level of a prostate cancer marker in a biological sample from the subject, wherein the prostate cancer marker is selected from the group consisting of panels in Tables 3, 4, 7 and 8.
  • 9. The method of claim 8, wherein the prostate cancer marker is selected from the group consisting of panel 1, panel 2, panel 3, panel 4, and any combination thereof, and wherein: panel 1 is selected from the group consisting of C10H21N4O2, C12H17NO, C12H2NOPS, C12H9O9P, C13H19N5O5, C17H32N3O7, C18H16N6O3, C18H33NO4, C18H43N4O3, C19H35NO5, C19H38N2O3, C24H42N7O3, C27H12N9, C34H23N7O5, C5H1 NO, C51H29N5O4, C6H15N, C8H9N, C9H4N5O9, C9H8O2, and any combination thereof;panel 2 is selected from the group consisting of C11H5NOPS, C12H16NO7, C12H2NOPS, C12H9O9P, C13H25NO2, C13H25NO3, C14H30N4O2, C16H13N3O3P, C17H41N4O3, C19H19N8, C22H45NO4, C26H51N4O5, C26H58N13P, C27H12N9, C27H55N8O3, C30H57NO7, C30H64N15O2P, C41H23N11O2, C5, C5H7NO3, C6HCl5, C6H16N3O5, C8H16NO5, and any combination thereof;panel 3 is selected from the group consisting of C10H18N2O5, C12H21NO4, C13H23NO6, C13H25NO3, C14H30N4O2, C15H30N10OP, C16H13N3O3P, C19H31N6O2, C22H45NO4, C27H12N9, C28H57N8O4, C30H61N8O5, C30H64N15O2P, C35H71N8O7, C40H38N22O4, C41H23N11O2, C43H40N20O3, C5H11NO, C5H11NO2S, C5H2O2P, C8H16NO5, and any combination thereof; andpanel 4 is selected from the group consisting of C11H20O2, C11H5NOPS, C12H2NOPS, C12H25NO4P, C12H9O9P, C13H25NO2, C13H25NO3, C14H30N4O2, C16H30N3O2, C17H41N4O3, C18H34O5, C19H31N6O2, C21H36N4O3, C22H45NO4, C23H47N8O2, C24H41N14O8, C27H12N9, C30H57NO7, C30H64N15O2P, C35H71N8O7, C43H40N20O3, C5H11NO, C5H11NO2S, C6H14N2O5P, and any combination thereof.
  • 10. The method of claim 8, wherein the prostate cancer marker is selected from the group consisting of panel 5, panel 6, panel 7, panel 8, and any combination thereof, and wherein: panel 5 is selected from the group consisting of C10H16O4, C10H18N2O4, C11H20NO3P3, C12H7N4O2, C15H28N6OP2, C16H39N8OP, C19H14O3, C21H33N3O3, C23H27O11S, C23H42N7O, C25H46N7O3, C27H48P2, C27H54O6, C33H22O7, C34H73N8O2P, C38H48O12, C40H85NOP3, C5H4O3, C5H3N2O2, C6H11N4O3P, C6H13N4OP2, C7H10O4, C7H17O7P2, C7H6O6S, C8H14O4, and any combination thereof;panel 6 is selected from the group consisting of C10H16O4, C11H16N4O4, C12H7N4O2, C14H20N2O5, C16H32O2, C17H34N9O2, C21H33N3O3, C23H27O11S, C26H43NO6, C27H48P2, C28H52N7O, C34H73N8O2P, C38H48O12, C39H26O7, C4H6O4, C40H85NOP3, C5H4N4O2, C5H3N2O2, C6H11N4O2P, C6H13N4OP2, C6H6N4O2, C6H8N2O4, C7H10O4, C7H17O7P2, C7H6O6S, C9H16O4, C9H9NO3, and any combination thereof;panel 7 is selected from the group consisting of C10H18N2O4, C10H19N5P3, C12H7N4O2, C15H28N6O P2, C16H32O2, C17H34N9O2, C19H14O3, C21H33N3O3, C21H39N4OP, C27H48P2, C38H48O12, C39H26O7, C40H85NOP3, C5H10N2O3, C5H4N4O2, C6H10O4S, C6H1N4O2P, C6H13N4OP2, C6H15O8P, C7H10O4, C7H17O7P2, C7H21N3OP3, C7H22N4O9PS, C7H8O6S, C8H9O6, C9H16O4, C9H17NO4S, C9H9NO3, and any combination thereof; andpanel 8 is selected from the group consisting of C10H19N5P3, C12H7N4O2, C15H28N6OP2, C17H34N9O2, C17H42N5OP2, C21H33N3O3, C22H38N7O, C24H40N4O3, C25H46N7O3, C25H50O6, C27H54O6, C39H26O7, C39H78O6, C40H85NOP3, C6H11N4O2P, C6H15O8P, C6H5N2OP, C6H8O6S, C7H10O4, C7H17O7P2, C7H21N3OP3, C8H16N2O5P, C8H18NO6P, C8H4N4O3, C9H16O4, C9H9NO3, and any combination thereof.
  • 11. The method of claim 8, wherein the prostate cancer marker is selected from the group consisting of panel 9, panel 10, panel 11, panel 12, and any combination thereof, and wherein: panel 9 is selected from the group consisting of Pyruvic acid, 4-Acetamidobutyric acid, 1,5-Anhydro-D-glucitol, Beta-Alanine, Glyceric acid, D-Lyxose, Galacturonic acid, D-Allose, L-Tyrosine, 3-Methyl-L-histidine, L-Glutamine, L-Pyroglutamic acid, Guanidinoacetic acid, Lactose, 2-Hydroxypyridine, N-acetyl-D-mannosamine, Palmitic acid, 1-Deoxy-d-ribitol, Monopalmitin, 2-Stearoylglycerol, Galangin, 6-ethoxyiminohexane-1,2,3,4,5-pentol, D-Gluconic acid, N,N-Dimethylguanosine, Pseudouridine, Ribitol, and any combination thereof;panel 10 is selected from the group consisting of Pyruvic acid, Xanthine, 4-Acetamidobutyric acid, 1,5-Anhydro-D-glucitol, Beta-Alanine, 1-Stearoyl-rac-glycerol, Glyceric acid, Galacturonic acid, Quinic acid, Xylitol, L-Pyroglutamic acid, Guanidinoacetic acid, Lactose, Ononitol, 5-Hydroxyindole, Monopalmitin, Galangin, 3,4-Dihydroxyphenylacetic acid, 3-Phenyl-5,10-secocholesta-1 (10),2-dien-5-one, Acetamide, Ethyl 1-penten-3-ynesulfonate, 2,5-Dipropyltetrahydrofuran, L-Phenylalanine, Pseudouridine, and any combination thereof;panel 11 is selected from the group consisting of L-Lactic acid, Xanthine, 4-Acetamidobutyric acid, Beta-Alanine, 1-Stearoyl-rac-glycerol, 4-hydroxymandelic acid, trans-Aconitic acid, D-Allose, Tartronic acid, Stearic acid, L-Tyrosine, Quinic acid, Ethanolamine, Guanidinoacetic acid, DL-isoleucine, Palmitic acid, Monopalmitin, Arabinofuranose, 2,4-Dihydroxybutanoic acid, Diethanolamine, Acetamide, 2,5-Dipropyltetrahydrofuran, Glycine, L-Arabinitol, Levulinic acid, Pseudouridine, and any combination thereof; andpanel 12 is selected from the group consisting of Pyruvic acid, Xanthine, 4-Hydroxybenzoic acid, Beta-Alanine, 1-Stearoyl-rac-glycerol, Galacturonic acid, D-Allose, Tartronic acid, Quinic acid, Pantothenic acid, Xylitol, Guanidinoacetic acid, 1-Deoxy-d-ribitol, Monopalmitin, Threonic acid, Galangin, Arabinofuranose, 2,4-Dihydroxybutanoic acid, D-Gluconic acid, 2,5-Dipropyltetrahydrofuran, Levulinic acid, Pseudouridine, and any combination thereof.
  • 12. The method of claim 8, wherein the prostate cancer marker is selected from the group consisting of panel 13, panel 14, panel 15, panel 16, and any combination thereof, and wherein: panel 13 is selected from the group consisting of 1-Methoxymethyl-2-phenylthioindole-3-carbaldehyde, 2,3-Dihydroxybutanoic acid, 2-Hydroxypyridine, 2-Stearoylglycerol, 3-Hydroxyphenylacetic acid, 3-Indoleacetic acid, 3-Methyl-L-histidine, 4-Acetamidobutyric acid, 4-hydroxymandelic acid, 6-ethoxyiminohexane-1,2,3,4,5-pentol, alpha-Hydroxyisobutyric acid, D-Altrose, D-Gluconic acid, D-Lyxose, Galacturonic acid, Galangin, Glyceric acid, Lactose, L-Fucose, L-Pyroglutamic acid, Monopalmitin, Ononitol, Oxamide, Palmitic acid, Pseudouridine, Pyruvic acid, Ribitol, trans-Aconitic acid and any combination thereof;panel 14 is selected from the group consisting of 1-Stearoyl-rac-glycerol, 2,5-Dipropyltetrahydrofuran, 3,4-Dihydroxyphenylacetic acid, Acetamide, Beta-Alanine, Cyclohexylamine, Ethyl 1-penten-3-ynesulfonate, Galacturonic acidGalangin, Glyceric acid, Guanidinoacetic acid, Levulinic acid, Monopalmitin, Ononitol, Palmitic acid, p-Tolyl-beta-D-glucopyranosid-uronsaeure, Quinic acid, Stearic acid, Sucrose, Uric acid, Xanthine, Xylitol, and any combination thereof;panel 15 is selected from the group consisting of (22S,23S,25R)-3β-methoxy-16β,23:22,26-diepoxy-5α-cholestane, 1-Methoxymethyl-2-phenylthioindole-3-carbaldehyde, 1-Stearoyl-rac-glycerol, 2,4-Dihydroxybutanoic acid, 2,5-Dipropyltetrahydrofuran, 4-hydroxymandelic acid, Acetamide, Arabinofuranose, Beta-Alanine, Daidzein, D-Allose, DL-isoleucine, D-tagatofuranose, Ethanolamine, Galangin, Guanidinoacetic acid, L-Arabinitol, Levulinic acid, L-Lactic acid, Monopalmitin, Palmitic acid, Pseudouridine, Quinic acid, Stearic acid, Sucrose, Tartronic acid, Xanthine, and any combination thereof; andpanel 16 is selected from the group consisting of (4RS,5SR)-5-hydroperoxy-4-decanol, 2,5-Dipropyltetrahydrofuran, 3,4,5-Trihydroxypentanoic acid, 4-Hydroxybenzoic acid, 6-ethoxyiminohexane-1,2,3,4,5-pentol, Acetamide, Arabinofuranose, Beta-Alanine, D-Allose, DL-4-Hydroxy-3-methoxymandelic acid, Ethyl 1-penten-3-ynesulfonate, Galacturonic acid, Galangin, Glyceric acid, Guanidinoacetic acid, Hippuric Acid, Levulinic acid, L-Pyroglutamic acid, Pantothenic acid, Pseudouridine, Pyruvic acid, Quinic acid, Tartronic acid, Uric acid, Xanthine, and any combination thereof.
  • 13. A method for monitoring a prostate cancer subject on active surveillance (AS), comprising detecting a level of a prostate cancer marker in a biological sample from the subject, wherein the prostate cancer marker is selected from the group consisting of markers in Tables 1, 2, 5 and 6.
Provisional Applications (1)
Number Date Country
63580581 Sep 2023 US