Biomarkers useful for diagnosing prostate cancer, and methods thereof

Abstract

The present invention describes a method for predicting a health-state indicative of the presence of prostate cancer. The method measures the intensities of specific small biochemicals, called metabolites, in a blood sample from a patient with an undetermined health-state, and compares these intensities to the intensities observed in a population of healthy individuals and/or to the intensities previously observed in a population of confirmed prostate cancer-positive individuals. The method enables a practitioner to determine the probability that a screened patient is positive for prostate cancer.

What is claimed is: 
     
         1 . A method for determining a change in prostate cancer in a patient, the method comprising the steps of:
 a) analyzing at least one blood sample from said patient by high resolution mass spectrometry to obtain accurate mass intensity data;   b) comparing the accurate mass intensity data to corresponding data obtained from one or more than one reference blood sample to identify an increase or decrease in accurate mass intensity; and   c) using said increase or decrease in accurate mass intensity to determine change in prostate cancer in said patient,   wherein the accurate mass intensity is measured at one or more of the following hydrogen and electron adjusted accurate masses or neutral accurate masses, in Daltons, ±5 ppm,   wherein the hydrogen and electron adjusted accurate masses or neutral accurate masses at which intensity decreases are: 174.1408, 188.1566, 194.0804, 232.9133, 242.2251, 252.2096, 258.2482, 268.2412, 272.2357, 276.2096, 278.2256, 279.2287, 280.2414, 281.2448, 283.2602, 292.204, 296.2358, 298.2519, 299.2558, 300.2098, 300.2676, 302.2256, 304.2394, 304.241, 305.243, 305.2439, 306.257, 308.2715, 310.2154, 310.2884, 312.2313, 312.304, 314.2464, 320.2358, 326.2262, 327.0326, 329.2426, 329.2445, 330.2568, 340.2977, 342.2198, 368.3437, 369.3474, 371.3538, 392.294, 411.3186, 430.3083, 430.3818, 431.3861, 432.3686, 452.2536, 481.3171, 481.3172, 482.3216, 484.3792, 492.4184, 494.4344, 495.3328, 495.4376, 496.336, 501.2848, 505.3227, 506.3213, 507.3317, 509.3493, 517.3148, 518.3182, 518.4345, 519.332, 519.3328, 520.4502, 521.348, 521.4526, 522.464, 523.364, 523.4678, 524.4725, 529.3167, 531.3123, 534.4645, 538.501, 541.3148, 541.3422, 541.3433, 542.3453, 542.3461, 545.346, 548.4817, 549.4848, 552.4048, 555.3101, 565.3393, 565.3394, 566.3433, 566.3434, 567.3546, 567.3548, 568.3573, 568.3574, 569.3687, 569.3691, 570.3726, 570.4653, 570.4915, 579.5322, 580.5345, 587.3228, 589.3401, 589.3404, 590.343, 590.4597, 596.4794, 599.4932, 601.5077, 604.5441, 605.5469, 609.3242, 612.5004, 615.4797, 622.4973, 623.4918, 623.5003, 624.5134, 625.5078, 625.5163, 626.5109, 626.5285, 627.5204, 627.5306, 628.5236, 628.5426, 629.5453, 630.5582, 632.5752, 635.5246, 641.4915, 646.5709, 647.574, 647.6063, 648.5865, 649.5056, 649.5898, 655.5509, 660.5005, 660.6082, 663.4864, 670.5688, 670.5711, 671.5723, 672.5865, 673.5893, 673.6185, 673.6224, 675.6359, 675.6375, 676.6393, 680.5625, 684.5487, 685.5543, 686.5126, 688.5294, 690.4849, 690.547, 692.5571, 693.611, 695.647, 696.5856, 696.651, 699.5205, 702.5675, 705.6083, 707.6256, 708.6308, 710.4923, 716.4982, 721.6388, 722.6423, 723.5194, 723.5198, 724.5247, 724.5496, 725.5375, 726.5456, 727.5565, 728.562, 729.5724, 731.4913, 732.4938, 733.6425, 735.6555, 736.6584, 737.5354, 738.5449, 741.5307, 742.5354, 743.5469, 744.4942, 745.4972, 746.556, 747.5201, 747.5234, 748.5279, 748.5722, 749.5346, 749.5354, 749.5364, 749.5402, 749.5763, 750.5403, 750.5434, 751.551, 751.5529, 751.5548, 752.5565, 752.5578, 753.5674, 755.4866, 756.4905, 757.5017, 757.5618, 758.5089, 758.5654, 759.516, 759.578, 760.5223, 760.5816, 761.5269, 765.5665, 766.5701, 767.5821, 768.4944, 768.5507, 769.4957, 770.5109, 771.5809, 772.5269, 772.5856, 773.5337, 774.5404, 775.553, 775.5533, 776.5563, 776.6057, 777.5679, 779.5438, 779.5831, 780.5474, 781.5612, 782.5087, 782.5649, 783.5141, 783.578, 784.5235, 784.5813, 785.5295, 785.5936, 786.5404, 786.5967, 787.5447, 793.5387, 794.5126, 794.5424, 795.5555, 796.5292, 798.6776, 803.5436, 803.5685, 804.547, 804.5717, 804.7208, 804.7219, 805.5606, 805.5834, 805.7267, 806.5643, 806.5863, 807.5761, 808.5795, 809.5937, 810.5401, 810.597, 811.5733, 812.5767, 813.5888, 814.592, 816.5591, 816.7297, 817.5376, 819.5553, 821.5718, 822.5751, 824.689, 825.5545, 825.5548, 826.5579, 826.7053, 827.5439, 827.5698, 827.5699, 827.7084, 828.5734, 828.5741, 828.7206, 829.5597, 829.5857, 829.7239, 829.7244, 830.5887, 830.6537, 830.7359, 831.575, 831.5999, 831.6002, 831.7409, 832.5765, 832.6028, 832.6039, 835.6996, 836.7063, 837.5884, 837.7182, 838.7227, 839.7321, 847.5955, 850.703, 851.5689, 851.7111, 852.5725, 852.7198, 852.7242, 853.5854, 853.7252, 854.5887, 855.6013, 856.6046, 856.6697, 857.617, 857.6733, 858.6847, 859.6877, 861.5265, 861.7174, 861.7808, 862.7228, 863.6874, 863.7339, 864.738, 865.7482, 866.7527, 867.7576, 871.5528, 872.5556, 873.5684, 876.7223, 877.7271, 878.7381, 879.598, 879.742, 880.7528, 880.7555, 881.7568, 881.7609, 882.7673, 882.7717, 883.7715, 884.7817, 884.7873, 885.7867, 885.7919, 886.5582, 886.8027, 887.5625, 887.8022, 893.774, 894.7273, 894.7813, 895.5578, 895.559, 895.7335, 895.7873, 896.745, 897.573, 897.75, 898.7605, 899.5871, 899.7663, 900.5897, 902.737, 903.7407, 904.7535, 905.7573, 906.769, 907.7735, 908.708, 908.7842, 908.7843, 909.7153, 909.7892, 910.7248, 910.7979, 911.7326, 912.7412, 913.7502, 914.7577, 915.7673, 916.774, 917.7836, 918.7901, 919.7981, 920.747, 920.8054, 921.753, 921.8145, 922.7656, 922.8229, 923.5884, 923.7675, 924.7826, 926.7371, 928.7519, 930.7673, 931.7691, 931.793, 932.7819, 934.7235, 935.7299, 936.7387, 937.7457, 938.7553, 939.7616, 940.7709, 941.7779, 942.7876, 943.7931, 944.8033, 945.8085, 946.8187, 950.7385, 952.7568, 952.7759, 954.7905, 962.7616, 964.7764, 965.7839, 966.7933, 967.7981, 968.8072, 1016.929, 1017.934, 1018.943, 1019.95, 1040.934, 1225.093, 1226.098, 1227.107, 1228.113, 1229.118, 1251.115, and 1253.129, and a decrease in the accurate mass intensity at one or more of said accurate masses in the blood sample from the patient relative to the reference indicates that the patient has prostate cancer or is at risk of prostate cancer; and   wherein the hydrogen and electron adjusted accurate masses or neutral accurate masses at which intensity increases are: 202.0454, 205.8867, 216.0401, 218.0372, 226.0687, 228.1476, 243.0719, 244.056, 247.9578, 273.874, 283.9028, 317.9626, 326.2476, 328.2628, 331.8326, 339.9964, 341.8614, 351.8906, 354.1668, 382.2903, 472.3925, 473.3957, 552.3825, 582.2469, 583.2504, 736.2234, 776.6069, 783.6349, 997.3968, 1176.777 and 1373.744, and an increase in the accurate mass intensity at one or more of said accurate masses in the blood sample from the patient relative to the reference indicates that the patient has prostate cancer or is at risk of prostate cancer.   
     
     
         2 . The method of  claim 1 , wherein the accurate mass intensities represent ionized metabolites. 
     
     
         3 . The method of  claim 1 , further comprising
 analyzing at least one sample from said patient by mass spectrometry to obtain accurate mass intensity data for one or more than one internal control metabolite; and   calculating a ratio for each of the accurate mass intensities obtained in step (a) to the accurate mass intensities obtained for the one or more than one internal control metabolite;   wherein the comparing step (b) comprises comparing each ratio to one or more corresponding ratios obtained for one or more than one reference sample.   
     
     
         4 . The method of  claim 1 , wherein the hydrogen and electron adjusted accurate mass, or neutral accurate mass, is selected from the group consisting of: a) 495.3328, b) 517.3148, c) 519.3328, d) 521.3480, e) 523.3640, f) 541.3148, g) 545.3460, h) 481.3171, i) 531.3123, j) 541.3422, k) 555.3101, l) 565.3394, m) 567.3546, n) 569.3687 and combinations thereof, and a decrease in accurate mass intensity at one or more of said accurate masses in the blood sample from the patient relative to the reference indicates that the patient has prostate cancer or is at risk of prostate cancer. 
     
     
         5 . The method of  claim 1 , wherein the accurate mass intensity data is obtained using a Fourier transform ion cyclotron resonance, time of flight, orbitrap, quadrupole or triple quadrupole mass spectrometer. 
     
     
         6 . The method of  claim 1 , wherein the blood sample is a whole blood sample, a blood serum sample, or a plasma sample. 
     
     
         7 . The method of  claim 1 , wherein a liquid/liquid extraction is performed on the blood samples whereby non-polar metabolites are dissolved in an organic solvent and polar metabolites are dissolved in an aqueous solvent. 
     
     
         8 . The method of  claim 1 , wherein said one or more than one reference blood sample is a plurality of blood samples obtained from control individuals; one or more than one baseline sample obtained from the patient at an earlier date; or a combination thereof. 
     
     
         9 . A method for determining prostate cancer, a change in prostate cancer, or the risk of prostate cancer in a patient, the method comprising the steps of:
 a) analyzing at least one blood sample from said patient to obtain quantifying data for one or more than one metabolite marker using an analytical device or system;   b) comparing the quantifying data for said one or more than one metabolite marker to corresponding data obtained for one or more than one reference blood sample to identify a decrease in the level of said one or more than one metabolite marker in said blood sample; and   c) using said decrease in the level of said one or more than one metabolite marker in said at least one sample for determining prostate cancer, change in prostate cancer, or the risk of prostate cancer in said patient,   wherein the one or more than one metabolite marker comprises one or more lysophospholipid selected from the group consisting of: lysophosphatidylcholines, lysophosphatidylethanolamines, lysophosphatidyldimethylethanolamines, lysophosphatidylserines, lysosphingosylphosphoryl-cholines, lysophosphatidylglycerols, lysophosphatidylinositols, platelet activating factors (PAFs), and combinations thereof,   and wherein a decrease in the level of said one or more than one metabolite marker in the blood sample from the patient relative to the reference indicates that patient has prostate cancer or is at risk of prostate cancer.   
     
     
         10 . The method of  claim 9 , wherein step a) comprises analyzing the blood sample by liquid chromatography mass spectrometer (LC-MS). 
     
     
         11 . The method of  claim 9 , wherein the method is a high-throughput method and step a) comprises analyzing the blood sample by direct injection or liquid chromatography and linear ion trap tandem mass spectrometry. 
     
     
         12 . The method of  claim 9 , further comprising:
 analyzing at least one sample from said patient to obtain quantifying data for one or more than one internal control metabolite; and   obtaining a ratio for each of the levels of said one or more than one metabolite marker to the level obtained for the one or more than one internal control metabolite;   wherein the comparing step (b) comprises comparing each ratio to one or more corresponding ratios obtained for the one or more than one reference sample.   
     
     
         13 . The method of  claim 9 , wherein said one or more than one reference blood sample is a plurality of blood samples obtained from control individuals; one or more than one baseline blood sample obtained from the patient at an earlier date; or a combination thereof. 
     
     
         14 . The method of  claim 9 , wherein said lysophospholipids are lysophosphatidylcholine-related compounds. 
     
     
         15 . The method of  claim 9 , wherein said lysophospholipids are N,N-dimethyl-lysophosphoethanolamine-related compounds. 
     
     
         16 . The method of  claim 14 , wherein the one or more than one metabolite is characterized by
 a) at least one MS/MS transition detected in [M+H]+ mode selected from 496, 478, 419, 313, 283, 258, 239, 184, 166, 104, or 86 for molecular formula C24H51NO7P+;   b) at least one MS/MS transition detected in [M+H]+ mode selected from 518, 459, 415, 359, 341, 281, 221, 104, or 86 for molecular formula C26H49NO7P+;   c) at least one MS/MS transition detected in [M+H]+ mode selected from 520, 502, 461, 445, 281, 221, 184, 166, 124, or 86 for molecular formula C26H51NO7P+;   d) at least one MS/MS transition detected in [M+H]+ mode selected from 522, 504, 478, 357, 258, 221, 184, 124, 104 or 86 for molecular formula C26H53NO7P+;   e) at least one MS/MS transition detected in [M+H]+ mode selected from 524, 506, 496, 478, 331, 313, 258, 285, 184, 166, 124, 104 or 86 for molecular formula C26H55NO7P+;   f) at least one MS/MS transition detected in [M+H]+ mode selected from 542, 483, 284, 225, 184, 104, or 86 for molecular formula C28H49NO7P+; or   g) at least one MS/MS transition detected in [M+H]+ mode selected from 546, 528, 514, 487, 104, or 86 for molecular formula C28H53NO7P+.   
     
     
         17 . The method of  claim 15 , wherein the one or more than one metabolite is characterized by:
 j) at least one MS/MS transition detected in [M−H]− mode selected from 540, 480, 255, 242, 224, 168, 153 or 79 for molecular formula C25H51NO9P−;   l) at least one MS/MS transition detected in [M−H]− mode selected from 564, 504, 454, 279, 242, 224, 168, 153, or 79 for molecular formula C27H51NO9P−;   m) at least one MS/MS transition detected in [M−H]− mode selected from 566, 506, 281, 242, 224, 168, 153, or 79 for molecular formula C27H53NO9P−; or   n) at least one MS/MS transition detected in [M−H]− mode selected from 568, 508, 283, 242, 224, 168, 153 or 79 for molecular formula C27H55NO9P−.   
     
     
         18 . The method of  claim 9 , wherein the one or more than one metabolite is characterized by the structure 
       
         
           
           
               
               
           
         
       
     
     
         19 . The method of  claim 9 , wherein the quantifying data is obtained using a Fourier transform ion cyclotron resonance, time of flight, orbitrap, quadrupole or triple quadrupole mass spectrometer. 
     
     
         20 . The method of  claim 19 , wherein the mass spectrometer is equipped with a chromatographic system. 
     
     
         21 . The method of  claim 20 , wherein the chromatographic system is a liquid or gas chromatographic system. 
     
     
         22 . The method of  claim 9 , wherein the blood sample is a whole blood sample, a blood serum sample, or a blood plasma sample. 
     
     
         23 . The method of  claim 9 , wherein a liquid/liquid extraction is performed on the blood samples whereby non-polar metabolites are dissolved in an organic solvent and polar metabolites are dissolved in an aqueous solvent. 
     
     
         24 . The method of  claim 23 , wherein the extracted samples are analyzed by positive or negative electrospray ionization, positive or negative atmospheric pressure chemical ionization, or a combination thereof. 
     
     
         25 . The method of  claim 1 , wherein the accurate mass intensity is measured at the hydrogen and electron adjusted accurate mass or neutral accurate mass, in Daltons, ±1 ppm. 
     
     
         26 . The method of  claim 9 , wherein the decrease in the level of said one or more than one metabolite marker in said sample is identified in the comparing step (b) using a colorimetric chemical assay, an antibody-based enzyme-linked immunosorbant assay (ELISA), a dipstick chemical assay, or a mass spectrometry-based system. 
     
     
         27 . The method of  claim 9 , wherein the method is for determining prostate cancer in a patient. 
     
     
         28 . The method of  claim 9 , wherein the method is for determining a change in prostate cancer in a patient. 
     
     
         29 . The method of  claim 9 , wherein the method is for determining the risk of prostate cancer in a patient. 
     
     
         30 . A method for determining a change in prostate cancer in a patient, the method comprising the steps of:
 a) analyzing at least one blood sample from said patient by high resolution mass spectrometry to obtain accurate mass intensity data;   b) comparing the accurate mass intensity data to corresponding data obtained from one or more than one reference blood sample to identify an increase or decrease in accurate mass intensity; and   c) using said increase or decrease in accurate mass intensity to determine a change in prostate cancer in said patient,   wherein the accurate mass intensity is measured at a hydrogen and electron adjusted accurate mass or neutral accurate mass of 519.3328, in Daltons, ±5 ppm and wherein a decrease in the accurate mass intensity of 519.3328 in the blood sample from the patient relative to a reference blood sample indicates that patient has prostate cancer or is at risk of prostate cancer.