Systems and Methods for Expression-Based Discrimination of Distinct Clinical Disease States in Prostate Cancer

Abstract

A system for expression-based discrimination of distinct clinical disease states in prostate cancer is provided that is based on the identification of sets of gene transcripts, which are characterized in that changes in expression of each gene transcript within a set of gene transcripts can be correlated with recurrent or non-recurrent prostate cancer. The Prostate Cancer Prognostic system provides for sets of “prostate cancer prognostic” target sequences and further provides for combinations of polynucleotide probes and primers derived there from. These combinations of polynucleotide probes can be provided in solution or as an array. The combination of probes and the arrays can be used for diagnosis. The invention further provides further methods of classifying prostate cancer tissue.

1 . A system for expression-based assessment of prostate cancer recurrence risk, said system comprising one or more polynucleotides, each of said polynucleotides capable of specifically hybridizing to a RNA transcript of a gene selected from the group of genes set forth in Table 3 and/or Table 6. 
     
     
         2 . The system of  claim 1 , wherein said one or more polynucleotides comprise one or more polynucleotide probes for the detection of the respective transcript. 
     
     
         3 . The system of  claim 1 , wherein said one or more polynucleotides comprise one or more primer pairs, each of said primer pairs capable of amplifying a portion of a sequence corresponding to the respective transcript. 
     
     
         4 . The system of any one of  claims 1 ,  2  and  3 , wherein said transcript comprises a sequence corresponding to one or more of the sequences set forth in SEQ ID NOs: 1-2114. 
     
     
         5 . The system of any one of  claims 1 ,  2  and  3 , wherein said transcript comprises a sequence corresponding to one or more of the sequences set forth in a SEQ ID NOs: 914-2114. 
     
     
         6 . The system according to any one of  claims 1  to  5 , wherein said system comprises at least 5 polynucleotides. 
     
     
         7 . The system according to any one of  claims 1  to  5 , wherein said system comprises at least 10 polynucleotides. 
     
     
         8 . The system according to any one of  claims 1  to  5 , wherein said system comprises at least 100 polynucleotides. 
     
     
         9 . The system of  claim 1 , wherein each of said one or more polynucleotides comprises a sequence corresponding to, or complementary to, one or more of the sequences set forth in Table 4 or a fragment thereof. 
     
     
         10 . The system of  claim 1 , wherein each of said one or more polynucleotides comprises a sequence corresponding to one or more nucleic acid molecules selected from the group consisting of:
 (a) a nucleic acid depicted in any one of SEQ ID NOs: 1-2114;   (b) an RNA form of any one of the nucleic acids depicted in SEQ ID NOs: 1-2114;   (c) a peptide nucleic acid form of any one of the nucleic acids depicted in SEQ ID NOs: 1-2114;   (d) a nucleic acid comprising at least 20 consecutive bases of any of (a-c);   (e) a nucleic acid comprising at least 25 consecutive bases having at least 90% sequence identity to any of (a-c); and   (f) a complement to any of (a-e).   
     
     
         11 . The system of  claim 1 , wherein said transcript comprises one or more of the sequences as set forth in SEQ ID NOs: 1, 4, 6, 9, 14-16, 18-21 915-917, 920, 922, 928, 929, 931, 935 and 936. 
     
     
         12 . The system of  claim 1 , wherein said transcript comprises one or more of the sequences as set forth in SEQ ID NOs: 3, 36, 60, 63, 926, 971, 978, 999, 1014 and 1022. 
     
     
         13 . The system of  claim 1 , wherein said transcript comprises one or more of the sequences as set forth in SEQ ID NOs 1-3, 32, 33, 36, 46, 60, 63, 66, 69, 88, 100, 241, 265, 334, 437, 920, 925, 934, 945, 947, 954, 971, 978, 999, 1004, 1014, 1022, 1023, 1032, 1080, 1093, 1101, 1164, 1248, 1304, 1311, 1330, 1402, 1425. 
     
     
         14 . Use of the system according to any one of  claims 1 ,  2  and  4  to  11  for the preparation of a nucleic acid array 
     
     
         15 . A nucleic acid array for expression-based assessment of prostate cancer recurrence risk, said array comprising at least ten probes immobilized on a solid support, each of said probes being between about 15 and about 500 nucleotides in length, each of said probes being derived from a sequence corresponding to, or complementary to, a transcript of a gene selected from the group of genes set forth in Table 3, or a portion of said transcript. 
     
     
         16 . The nucleic acid array according to  claim 15 , wherein each of said probes comprises a sequence as set forth in any one of SEQ ID NOs: 1-2114 or complement thereof. 
     
     
         17 . A method for expression-based assessment of prostate cancer recurrence risk, said method comprising: (a) determining the expression level of one or more transcripts of one or more genes in a test sample obtained from said subject to provide an expression pattern profile, said one or more genes selected from the group of genes set forth in Table 3, and (c) comparing said expression pattern profile with a reference expression pattern profile. 
     
     
         18 . The method of  claim 17 , wherein an increased relative level of expression of one or more transcripts, a decreased relative level of expression of one or more transcripts, or a combination thereof is used to classify a prostate cancer as recurrent. 
     
     
         19 . The method of  claim 17 , wherein an increased relative level of expression of one or more transcripts, a decreased relative level of expression of one or more transcripts, or a combination thereof is used to classify a prostate cancer as non-recurrent. 
     
     
         20 . The method of  claim 17 ; wherein said transcripts comprise a sequence as set forth in any one of SEQ ID NOs: 1-2114 or complement thereof. 
     
     
         21 . The method of  claim 17 , wherein said one or more transcripts comprise one or more sequences as set forth in any one of SEQ ID NOs: 1, 4, 6, 9, 14-16, 18-21 915-917, 920, 922, 928, 929, 931, 935 and 936. 
     
     
         22 . The method of  claim 17 , wherein said transcript comprises one or more of the sequences as set forth in SEQ ID NOs: 3, 36, 60, 63, 926, 971, 978, 999, 1014 and 1022. 
     
     
         23 . The method of  claim 17 , wherein said transcript comprises one or more of the sequences as set forth in SEQ ID NOs 1-3, 32, 33, 36, 46, 60, 63, 66, 69, 88, 100, 241, 265, 334, 437, 920, 925, 934, 945, 947, 954, 971, 978, 999, 1004, 1014, 1022, 1023, 1032, 1080, 1093, 1101, 1164, 1248, 1304, 1311, 1330, 1402, 1425. 
     
     
         24 . The method of  claim 17 , wherein the expression level of the one or more target sequences is determined by a method selected from the group consisting of RT-PCR, Northern blotting, ligase chain reaction, array hybridization, and a combination thereof. 
     
     
         25 . The method of any one of  claims 17  to  24 , further comprising measuring the expression level of at least one control nucleic acid in the sample. 
     
     
         26 . The method of any one of  claims 17  to  25 , wherein the sample is a fine needle aspirate biopsy [FNAB], cytology smear, cytology pellet, or a bulk tissue preparation. 
     
     
         27 . The method of any one of  claims 17  to  26 , wherein the sample is fresh-frozen or fixed. 
     
     
         28 . The method of any one of  claims 17  to  27 , wherein measuring the expression level utilizes a pattern recognition method. 
     
     
         29 . The method of  claim 28 , wherein the pattern recognition method comprises a linear combination of expression levels of the target sequences. 
     
     
         30 . The method of  claim 28  or  29 , wherein the pattern recognition method comprises a nonlinear combination of expression levels of the target sequences. 
     
     
         31 . A kit for characterizing the expression of one or more nucleic acid sequences depicted in SEQ ID NOs: 1-2114 comprising one or more nucleic acids selected from:
 (a) a nucleic acid depicted in any of SEQ ID NOs: 1-2114;   (b) an RNA form of any of the nucleic acids depicted in SEQ ID NOs: 1-2114;   (c) a peptide nucleic acid form of any of the nucleic acids depicted in SEQ ID NOs: 1-2114;   (d) a nucleic acid comprising at least 20 consecutive bases of any of (a-c);   (e) a nucleic acid comprising at least 25 consecutive bases having at least 90% sequence identity to any of (a-c); or   (f) a complement to any of (a-e); and   optionally instructions for correlating the expression level of said one or more nucleic acid sequences with the disease state of prostate cancer tissue.   
     
     
         32 . The kit of  claim 31 , wherein said one or more nucleic acids comprises one or more sequences as set forth in any one of SEQ ID NOs: 1, 4, 6, 9, 14-16, 18-21 915-917, 920, 922, 928, 929, 931, 935 and 936. 
     
     
         33 . The kit of  claim 31 , wherein said one or more nucleic acids comprises one or more of the sequences as set forth in SEQ ID NOs: 3, 36, 60, 63, 926, 971, 978, 999, 1014 and 1022. 
     
     
         34 . The kit of  claim 31 , wherein said one or more nucleic acids comprises one or more of the sequences as set forth in SEQ ID NOs 1-3, 32, 33, 36, 46, 60, 63, 66, 69, 88, 100, 241, 265, 334, 437, 920, 925, 934, 945, 947, 954, 971, 978, 999, 1004, 1014, 1022, 1023, 1032, 1080, 1093, 1101, 1164, 1248, 1304, 1311, 1330, 1402, 1425. 
     
     
         35 . The kit of any one of  claims 31  to  34 , wherein said one or more nucleic acids comprises labeled nucleic acids. 
     
     
         36 . The kit of any one of  claims 31  to  35 , wherein the kit comprises one or more primers or primer pairs that specifically amplify at least a portion of said nucleic acids. 
     
     
         37 . The kit of any of  claims 31  to  36 , wherein the kit further comprises one or more control samples comprising expressed RNA, an amplification product produced therefrom or a surrogate therefore, said control one or more control samples selected from:
 a sample from non-recurrent prostate cancer; and 
 a sample from recurrent prostate cancer. 
 
     
     
         38 . An array of probe nucleic acids certified for use in expression-based assessment of prostate cancer recurrence risk, wherein said array comprises at least two different probe nucleic acids that specifically hybridize to corresponding different target nucleic acids depicted in one of SEQ ID NOs: 1-2114, an RNA form thereof, or a complement to either thereof. 
     
     
         39 . The array of  claim 38 , further comprising one or more probe nucleic acids that specifically hybridize to house keeping genes. 
     
     
         40 . A device for classifying a biological sample from a prostate cancer as recurrent or non-recurrent, the device comprising:
 means for measuring the expression level of one or more transcripts of one or more genes selected from the group of genes set forth in Table 3 and/or 6;   means for correlating the expression level with a classification of prostate cancer status; and   means for outputting the prostate cancer status.   
     
     
         41 . The device of  claim 40 , wherein the machine utilizes an algorithm to characterize said expression level. 
     
     
         42 . A computer-readable medium comprising one or more digitally-encoded expression pattern profiles representative of the level of expression of one or more transcripts of one or more genes selected from the group of genes set forth in Table 3 and/or 6, each of said one or more expression pattern profiles being associated with a value wherein each of said values is correlated with the presence of recurrent or non-recurrent prostate cancer.