WO2000044940A2 - Nucleic acid sequences for detecting genetic markers for cancer in a biological sample - Google Patents
Nucleic acid sequences for detecting genetic markers for cancer in a biological sample Download PDFInfo
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- WO2000044940A2 WO2000044940A2 PCT/US2000/002270 US0002270W WO0044940A2 WO 2000044940 A2 WO2000044940 A2 WO 2000044940A2 US 0002270 W US0002270 W US 0002270W WO 0044940 A2 WO0044940 A2 WO 0044940A2
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- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
- C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/158—Expression markers
Definitions
- This invention relates to detection of nucleic acids that serve as cancer markers in biological samples, and specifically relates to methods for specifically detecting nucleic acids encoding prostate-specific antigen (PSA), prostate-specific membrane antigen (PSMA), and/or human glandular kallikrein (hK2) which, when present individually or together in a biological sample are indicative of the presence of cancer in the organism, particularly prostate and breast cancers.
- PSA prostate-specific antigen
- PSMA prostate-specific membrane antigen
- hK2 human glandular kallikrein
- Prostate cancer is a leading cause of death in men, particularly in men over 60 years of age.
- the biological aggressiveness of the cancer varies greatly between individuals, with some cancers remaining as latent tumors which do not progress to clinical significance, and others rapidly progressing and metastasizing to a fatal disease within a few years.
- Clinical diagnosis and staging of prostate tumors has relied on digital rectal examination (DRE), computed tomography (CT) scans and/or endorectal magnetic resonance imaging (MRI).
- DRE digital rectal examination
- CT computed tomography
- MRI endorectal magnetic resonance imaging
- detection of cells bearing molecular markers specific to or highly expressed in prostate tissue has been used diagnostically.
- Prostate specific antigen is a protease made in high concentrations in prostatic epithelial cells and secreted into ducts of the prostate gland.
- PSA is a molecular marker for detection of prostate cancer (prostatic adenocarcinoma).
- Prostatic acid phosphatase (PAP) is another secreted enzyme that has been used as a serum marker for detection of prostatic metastases.
- Human glandular kallikrein-2 (hK2) is another prostate-associated protein that has been linked to prostate cancer (Partin A.W. et al., 1999, Urology 54(5): 839-845; Darson M.F. et al., 1999, Urology 53(5): 939-944).
- a cancer such as prostate or breast cancer
- a cancer such as prostate or breast cancer
- locally invasive i.e., for prostate cancer, penetrating the capsule or seminal vesicle
- RT-PCR reverse transcriptase-polymerase chain reaction
- Prostate cancer cells are also presumed to be shed into the bloodstream, permitting them to disseminate to distant sites where the cells may become established as metastases.
- PSA prostate-specific antigen
- PSA-synthesizing cells in circulating blood is an abnormal situation indicative of potential prostate cancer metastases (sometimes referred to as "hematogenous micrometastasis"), although only about 0.01% of circulating solid tumor cells eventually result in a metastatic deposit (Moreno, J.G. et al., 1992, Cancer Res. 52: 6110-6112).
- detecting abnormal amounts of PSA in females may indicate the presence of breast cancer (Yu H. & Berkel H., 1999, J. La. State Med. Soc. 151 (4): 209-213).
- Monoclonal antibody-based immunoassays for measuring total PSA, free PSA (unbound to alp a-1 -antichymotrypsin or "ACT"), and PSA-ACT complexes in body fluids have been disclosed for diagnostic methods to distinguish between patients with benign prostatic hyperplasia (BHP) and those with prostatic carcinoma (US Pat. No. 5,614,372 to Lilja et al.; US Pat. Nos. 5,698,402 and 5,710,007 to Luderer et al.).
- Other known immunoassays measure total serum PSA and distinguish between free PSA in serum and PSA-protein complexes which tend to be in higher concentrations in sera from prostate cancer patients (US Pat. No.
- RT-PCR detection of PSA-synthesizing cells in peripheral blood has also been correlated with stage D1 to D3 pathology, and with capsular penetration by prostate tumor cells (Moreno, J.G. et al., 1992, Cancer Res. 52: 6110-6112; Katz, A.E. et al., 1994, Urology 43: 765-775; US Pat. Nos.
- RT- PCR assays rely on obtaining RNA from a blood sample, reverse transcribing the RNA into cDNA, amplifying the cDNA using a pair of primers complementary to separate regions of the PSA gene, and demonstrating the presence of the amplified DNA by observing a particular size DNA on a gel.
- PCR amplification of DNA requires a repeated series of thermal denaturation, primer annealing and synthesis steps (US Pat. Nos. 4,683,195, 4,683,202, and 4,800159 to Mullis et al.).
- the amplified DNA may be further characterized by restriction endonuclease digestion, probing with a PSA-specific oligonucleotide (e.g., Southern blotting), and/or DNA sequencing.
- Micrometastasis of other types of solid tumors (melanoma, neuroblastoma, breast cancer, cervical cancer) has also been detected using RT-PCR assays for other cell markers (Wu, A. et al., 1990, US & Can. Acad. Pathol. Ann.
- PSA is a member of a group of serine proteases known as glandular kallikreins.
- the human kallikreins include pancreatic/renal kallikrein (hK1), prostate-specific glandular kallikrein (hK2 or HPSK), and PSA (also known as hK2) which are encoded by related genes (hKLK1 , hKLK2 and hKLK3 or PSA, respectively). Because of the chemical and structural similarities of these proteins and genes, it is important to be able to distinguish the individual proteins in immunoassays and the individual genes or their corresponding mRNA in nucleic acid detection methods. Expression of hK2 has been associated with prostate and breast cancers (Black M.H. et al., 2000, Br. J. Cancer 82(2):361 -367; Partin A.W.
- nucleic acid sequences useful for amplification of PSA mRNA in RT-PCR assays and detection of DNA products have been described (e.g., in Deguchi, T. et al., 1993, Cancer Res. 53: 5350-5354; Katz, A.E. et al., 1994, Urology 43: 765-775; Moreno, J.G. et al., 1992, Cancer Res. 52: 6110-6112; US Pat. Nos. 5,506,106, 5,688,649 and 5,674,682 to Croce et al.).
- prostate-associated genetic markers e.g., PSA, PSMA and/or hK2
- Detection of prostate-associated genetic markers is useful for detecting cancer metastases, particularly prostate cancer in men and breast cancer in men and women, thereby indicating appropriate treatment.
- nucleic acid sequences and methods that are used to specifically detect the presence of genetic expression of prostate-associated genetic markers, i.e., specific mRNA sequences that provide diagnostic information.
- detecting these prostate-associated marker mRNA at levels useful for detecting relatively few cells containing the mRNA in a biological sample, such as occur in micrometastases.
- the present invention is directed to assay methods for detecting and/or quantifying nucleic acids that encode prostate-specific antigen (PSA), particularly mRNA, in a non-prostate biological sample.
- PSA prostate-specific antigen
- the present invention includes preferred nucleic acid sequences useful for amplifying and hybridizing to amplified PSA-specific nucleic acids.
- an oligonucleotide having the sequence of any one of SEQ ID NO:1 to SEQ ID NO:43.
- Another aspect of the invention is an oligonucleotide comprising a target-binding sequence consisting of the sequence of any one of SEQ ID NO:15 to SEQ ID NO:43, and optionally a contiguous sequence required for an amplification reaction.
- the contiguous sequence required for an amplification reaction is a sequence that is a polymerase binding sequence, and more preferably, the polymerase binding sequence binds a T7 RNA polymerase.
- Preferred embodiments are oligonucleotides having the sequence is any one of SEQ ID NO:1 to SEQ ID NO:14.
- Another aspect of the invention is a combination of oligonucleotides used in a detection assay specific for a prostate specific antigen (PSA) target nucleic acid sequence.
- the combination comprises a first oligonucleotide that serves as a first amplification primer that hybridizes specifically to a first PSA-specific sequence contained in an exon of a PSA expressed gene sequence, or that spans a joining point linking two exons of a PSA expressed gene sequence; a second oligonucleotide that serves as a second amplification primer that specifically hybridizes to a different, non-overlapping second PSA-specific sequence contained in an exon of a PSA expressed gene sequence, or that spans a joining point linking two exons of a PSA expressed gene sequence; and a third oligonucleotide that serves as a detection probe that specifically hybridizes to a third PSA-specific sequence contained in one or more exons of a PSA expressed gene sequence.
- PSA prostate specific antigen
- the first PSA-specific sequence is contained in PSA exon 2, exon 3 or exon 4, or is a sequence that spans a joining point linking exons 2 and 3 or exons 3 and 4.
- the second PSA-specific sequence is contained in PSA exon 3, exon 4 or exon 5, or is a sequence that spans a joining point linking exons 3 and 4 or exons 4 and 5.
- the third PSA-specific sequence is contained within PSA exon 2, exon 3, exon 4 or exon 5, or spans a joining point that links PSA exons 2 and 3, exons 3 and 4, or exons 4 and 5.
- oligonucleotides are a first oligonucleotide comprising a sequence selected from the group consisting of SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:18, SEQ ID NO:20, SEQ ID NO:21 and SEQ ID NO:26; the second oligonucleotide comprising a sequence selected from the group consisting of SEQ ID NO:30, SEQ ID NO:31 , SEQ ID NO:32, SEQ ID NO:33, SEQ ID NO:34, SEQ ID NO:35, SEQ ID NO:37, SEQ ID NO:38, SEQ ID NO:40 and SEQ ID NO:41 ; and the third oligonucleotide comprises a sequence selected from the group consisting of SEQ ID NO:1 , SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:14. Additional preferred combinations of first, second and
- SEQ ID NO:18, SEQ ID NO:30 and SEQ ID NO:6 SEQ ID NO:16, SEQ ID NO:31 and SEQ ID NO:2 SEQ ID NO:16, SEQ ID NO:31 and SEQ ID NO:3 SEQ ID NO:16, SEQ ID NO:33 and SEQ ID NO:2 SEQ ID NO:16, SEQ ID NO:33 and SEQ ID NO:3 SEQ ID NO:16, SEQ ID NO:32 and SEQ ID NO:2 SEQ ID N0:16 SEQ ID NO:32 and SEQ ID N0:3
- SEQ ID NO:26 SEQ ID NO:40 and SEQ ID N0:8; or SEQ ID NO:26, SEQ ID NO:41 and SEQ ID NO:8.
- first, second and third oligonucleotides in that order, have sequences of: SEQ ID NO:17, SEQ ID NO:30 and SEQ ID NO:1 ;
- the combination of first, second and third oligonucleotides further includes at least one helper probe oligonucleotide.
- Preferred helper probe oligonucleotides included in a combination consist of an oligonucleotide having the sequence of SEQ ID NO:27 or SEQ ID NO:28, or a combination of oligonucleotides having those sequences.
- first, second and third oligonucleotides and helper probe oligonucleotides in that order, have the sequences of: SEQ ID NO:21 , SEQ ID NO:41 , SEQ ID NO:8 and SEQ ID NO:27;
- SEQ ID NO:26 SEQ ID N0.41, SEQ ID NO:8, SEQ ID NO:27 and SEQ ID NO:28.
- One aspect of the invention is a method of detecting a prostate-associated target nucleic acid in a biological sample containing nucleic acid, comprising the steps of providing a nucleic acid sample containing a target nucleic acid that includes at least a portion of at least one expressed gene sequence encoding prostate-specific antigen (PSA), prostate-specific membrane antigen (PSMA) or human kallikrein 2 (hK2); then hybridizing to the target nucleic acid at least one primer oligonucleotide containing a sequence that hybridizes specifically to the target nucleic acid or a complement thereof; producing a plurality of amplification products of the target nucleic acid by using at least one polymerase activity; providing a probe oligonucleotide that hybridizes specifically to at least one amplification product of the target nucleic acid; and detecting a signal resulting from the probe hybridized to the amplification product.
- PSA prostate-specific antigen
- PSMA prostate-specific membrane antigen
- the at least one primer oligonucleotide comprises the sequence of any one of SEQ ID NO:15 to SEQ ID NO:29, SEQ ID NO:46, SEQ ID NO:48, or a target-binding sequence of any one of SEQ ID NO:30 to SEQ ID NO:43, SEQ ID NO:47 or SEQ ID NO:49.
- the target nucleic acid is a PSA mRNA
- the at least one primer oligonucleotide comprises a promoter-primer oligonucleotide consisting of a sequence complementary to at least a portion of the PSA mRNA and a sequence that is a promoter sequence, and at least one primer oligonucleotide that hybridizes specifically to a nucleic acid strand complementary to the PSA mRNA
- the probe oligonucleotide hybridizes specifically to amplification products of a sense that is the same as that of the PSA mRNA.
- the promoter-primer oligonucleotide comprises the sequence of any one of SEQ ID NO:30 to SEQ ID NO:43
- the primer oligonucleotide that hybridizes specifically to a nucleic acid strand complementary to the PSA mRNA comprises the sequence of any one of SEQ ID NO:15 to SEQ ID NO:29.
- the target nucleic acid is a PSMA mRNA
- the at least one primer oligonucleotide comprises a promoter-primer oligonucleotide consisting of a sequence complementary to at least a portion of the PSMA mRNA and a sequence that is a promoter sequence, and at least one primer oligonucleotide that hybridizes specifically to a nucleic acid strand complementary to the PSMA mRNA
- the probe oligonucleotide hybridizes specifically to amplification products of a sense that is the same as that of the PSMA mRNA.
- the promoter-primer oligonucleotide comprises the sequence of SEQ ID NO:49
- the primer oligonucleotide that hybridizes specifically to amplification products of a sense that is the same as that of the PSMA mRNA comprises the sequence of SEQ ID NO:48.
- the target nucleic acid is a hK2 mRNA
- the at least one primer oligonucleotide comprises a promoter-primer oligonucleotide consisting of a sequence complementary to at least a portion of the hK2 mRNA and a sequence that is a promoter sequence, and at least one primer oligonucleotide that hybridizes specifically to a nucleic acid strand complementary to the hK2 mRNA
- the probe oligonucleotide hybridizes specifically to amplification products of a sense that is the same as that of the hK2 mRNA.
- the method of Claim 14 wherein the promoter-primer oligonucleotide comprises the sequence of SEQ ID NO:47, and the primer oligonucleotide that hybridizes specifically to amplification products of a sense that is the same as that of the hK2 mRNA comprises the sequence of SEQ ID NO:46.
- the detecting step uses at least one probe oligonucleotide consisting of a sequence of any one of SEQ ID NO:1 to SEQ ID NO:14, SEQ ID NO:27, SEQ ID NO:28 or SEQ ID NO:50.
- One embodiment of the method comprises assaying for the expressed gene sequence encoding PSA and at least one expressed gene sequence encoding PSMA or hK2.
- the nucleic acid sample is RNA, more preferably mRNA, isolated from human prostate tissue, peripheral blood, breast tissue, kidney tissue, small intestine, lung tissue, liver tissue or lymph node.
- the detecting step detects a signal in a homogeneous detection assay.
- FIG. 1 is a schematic drawing showing the PSA gene structure and alignment of various PSA and kallikrein-1 sequences available from GenBank and or EMBL using the accession numbers (Ace. No.) provided below, where the closed boxes (-) indicate exons 1 to 5 ("E1 ", “E2”, “E3”, “E4" and “E5") and the open boxes ( ⁇ ) indicate introns ("11", “12", “13” and “14” are specifically labeled, whereas introns preceding the first exon or following the last exon are not labeled), presented over a scale representing the number of bases from 0 to 6,800 to show the relative positions of the introns and exons.
- the diagramed known PSA gene sequences are labeled: "HSPSAR” (1 ,466 bp; Ace. No. X05332), ⁇ UMAPS” (1 ,446 bp; Ace. No. M26663), ⁇ SPSA” (1 ,729 bp; Ace. No. X07730), "HUMPAA” (1 ,415 bp; Ace. No. M21895), “HUMPAB” (1 ,654 bp; Ace. No. M21896), “HUMPAC” (658 bp; Ace. No. M21897), "S75755" (569 bp; Ace. No. S75755), "HSU17040" (990 bp; Ace. No. U17040), "HSPSA1 "
- FIG. 2 is a schematic drawing showing the relative locations of various probes of the present invention (listed on the left using SEQ ID NO.) over a solid line representing the majority of the expressed PSA gene (based on the 1 ,466 bp sequence of HSPSAR, Ace. No. X05332) with the locations of exons 1 -5 (labeled E1 , E2, E3, E4, and E5) shown above the solid line and the splice junctions of deleted introns 1-4 (labeled 11 , 12, 13, and 14) shown below the solid line.
- FIG. 3 is a schematic drawing showing the relative locations of various probes of the present invention (listed on the left using SEQ ID NO.) over a solid line representing the majority of the expressed PSA gene (based on the 1 ,466 bp sequence of HSPSAR, Ace. No. X05332) with the locations of exons 1-5 (labeled E1 , E2, E3, E4, and E5) shown above the solid line and the splice junctions of deleted introns 1-4 (labeled 11 , 12, 13, and 14) shown below the solid line.
- FIG. 4 is a schematic drawing showing the relative locations of various probes of the present invention (listed on the left using SEQ ID NO.) over a solid line labeled "HSPSAR" representing the majority of the expressed PSA gene (based on the 1 ,466 bp sequence of HSPSAR, Ace. No. X05332) with the locations of exons 1-5 (labeled E1 , E2, E3, E4, and E5) shown above the solid line and the splice junctions of deleted introns 1-4 (labeled 11 , 12, 13, and 14) shown below the solid line.
- HSPSAR solid line labeled "HSPSAR" representing the majority of the expressed PSA gene (based on the 1 ,466 bp sequence of HSPSAR, Ace. No. X05332) with the locations of exons 1-5 (labeled E1 , E2, E3, E4, and E5) shown above the solid line and the splice junctions of deleted introns 1-4 (labeled 11 , 12, 13,
- FIG. 5 is a diagram showing the linearity of PSA-specific target amplification and detection of chemiluminescence (Net Mean RLU) in assays containing 10, 5, 1 , 0.5, 0.1 , 0.05, 0.01 or 0.005 pg of prostate total RNA per reaction, in which the experimental results are shown as a dotted line and dotted symbols and the calculated linear regression line is solid.
- Net Mean RLU chemiluminescence
- the present invention includes nucleic acid sequences specific for segments of a human PSA gene which are used in methods of detecting PSA-specific sequences in nucleic acids prepared from a biological sample that is not taken from prostate tissue.
- the invention further includes nucleic acid sequences specific for segments of other prostate-associated genetic markers, a human PSMA gene and hK2 gene, which are used in methods of detecting prostate-associated sequences that are useful cancer detection markers in nucleic acids prepared from a biological sample of non-prostate tissue, including breast tissue.
- the non-prostate tissue can include, for example, blood, lymph node, breast or breast cyst, kidney, liver, lung, muscle, stomach or intestinal tissue.
- the invention also includes preferred methods that combine nucleic acid sequences for amplifying and detecting PSA-specific sequences, PSMA and/or hK2 sequences, individually or in combination, in non-prostate tissue.
- the preferred methods amplify PSA, PSMA and/or hK2 mRNA sequences without requiring thermal cycling and detect the amplified sequences in a homogeneous assay system.
- the methods may optionally include a simplified method of preparing RNA samples derived from non-prostate tissue samples, such as peripheral blood, lymph nodes or bone marrow, although other non-prostate tissues may be used.
- the preferred RNA preparation method is relatively simple and provides RNA suitable for analysis and detection of mRNA species that occur in relatively low abundance in the biological samples.
- the sequence of the human PSA gene is known and is available in a number of databases (GenBank and EMBL databases, in Accession Nos. AF007544, X05332, M26663, X07730, M21895, M21896, M21897, S75755, U17040, X13942, X14810, M24543, M27274; accession numbers beginning with "X” indicate sequences in the EMBL database).
- the sequence of the related gene for the human glandular kallikrein-1 is known (Ace. No. S39329) as is the human prostate-specific membrane antigen sequence (GenBank Ace. No. M99487). As shown in FIG.
- the PSA and kallikrein-1 genes share similar structural characteristics, which include five exons (labeled E1 to E5) separated by four internal introns (labeled 11 to 14).
- Preferred probes, primers and promoter-primers of the present invention used for detecting PSA-specific sequences are shown in Table 1 (with their SEQ ID NOs). Table 1
- FIGS. 2 to 4 show the relative locations of these sequences compared to the expressed human PSA gene sequences (1 ,466 bp sequence of HSPSAR, Ace. No. X05332), diagramed with the relative locations of the exons and intron splice sites at the bottoms of the figures.
- FIG. 2 the relative locations of probes having sequences of SEQ ID NO:1 to SEQ ID NO:5 and SEQ ID N0:7 to SEQ ID NO:14 are shown. These preferred probes are specific for PSA sequences in exons 2, 3 and 4.
- a probe specific for a PSA intron 3 sequence (SEQ ID NO:6) is not shown on FIG. 2. Referring to FIG.
- primers having sequences of SEQ ID NO:15 to SEQ ID NO:29 are shown. These preferred primers are specific for PSA sequences in exons 2, 3, 4, and spanning exons 2 and 3, including the splice junction (SEQ ID NO:28).
- SEQ ID NO:28 the relative locations of primers having sequences of SEQ ID NO:30 to SEQ ID NO:43 are shown. These preferred target-binding sequences are specific for PSA sequences in exons 3, 4 and 5.
- a preferred primer has the sequence GTCAGAGCCTGCCAAGATCACAG (SEQ ID NO:46) and a preferred promoter-primer has the sequence TAAA ⁇ AATACGACTCACTATAGGGAGACCACCAGCACACAACATGAACTCTGTC (SEQ ID NO:46) and a preferred promoter-primer has the sequence TAAA ⁇ AATACGACTCACTATAGGGAGACCACCAGCACACAACATGAACTCTGTC (SEQ ID NO:46) and a preferred promoter-primer has the sequence TAAA ⁇ AATACGACTCACTATAGGGAGACCACCAGCACACAACATGAACTCTGTC (SEQ ID NO:46) and a preferred promoter-primer has the sequence TAAA ⁇ AATACGACTCACTATAGGGAGACCACCAGCACACAACATGAACTCTGTC (SEQ ID NO:46) and a preferred promoter-primer has the sequence TAAA ⁇ AATACGACTCACTATAGGGAGACCACCAGCACACAACATGAACTCTGTC
- a labeled probe suitable for detecting the amplified hK2 sequences uses the sequence of SEQ ID NO:1 shown in Table 1.
- a preferred primer has the sequence CAGATATGTCATTCTGGGAGGTC (SEQ ID NO:48) and a preferred promoter-primer has the sequence TAAA ⁇ AATACGACTCACTATAGGGAGACCAAA ⁇ C ⁇ CTGCATCCCAGC ⁇ GC (SEQ ID NO:48) and a preferred promoter-primer has the sequence TAAA ⁇ AATACGACTCACTATAGGGAGACCAAA ⁇ C ⁇ CTGCATCCCAGC ⁇ GC (SEQ ID NO:48) and a preferred promoter-primer has the sequence TAAA ⁇ AATACGACTCACTATAGGGAGACCAAA ⁇ C ⁇ CTGCATCCCAGC ⁇ GC (SEQ ID NO:48) and a preferred promoter-primer has the sequence TAAA ⁇ AATACGACTCACTATAGGGAGACCAAA ⁇ C ⁇ CTGCATCCCAGC ⁇ GC (SEQ ID NO:48) and a preferred promoter-primer has the sequence TAAA ⁇ AATACGACTCACTATAGGGAGACCAAA ⁇ C ⁇ CTGCATCC
- the present invention also includes a method for detecting and quantifying the PSA-specific RNA species, which is particularly important because these mRNA species occur in relatively low abundance in RNA samples prepared from non-prostate tissues.
- Other embodiments of the invention include methods for detecting prostate-associated PSMA and hK2 RNA species, which when detected individually or in combination with each other or PSA sequences, are important because these also are cancer markers for prostate and breast cancer when found in non-prostate tissues.
- prostate-associated markers PSA, PSMA and hK2
- PSA, PSMA and hK2 are clinically important because cancers from individual patients may express one or more of the markers, such that detecting one or more of the markers decreases the potential of false negatives during diagnosis that might otherwise result if the presence of only one marker was tested.
- These methods are useful for medical diagnoses without requiring a prostate biopsy and for clinically monitoring a patient's response to therapy for prostate cancer. Because the methods are sufficiently sensitive to detect the presence of relatively low levels of prostate-associated RNA, such as PSA- specific mRNA, they are useful for detecting recurrence or metastasis of prostate and/or breast cancer.
- Another advantage of the present methods is that amplification primers specific for different exons of a target sequence will amplify only mRNA that have been spliced to link the exons in proximity, thereby eliminating amplification and false positive detection that might result from contaminating genomic DNA in the biological sample.
- detection of genomic DNA is precluded because the exons in the genomic sequence are separated by intron sequence(s) such that the entire region between the two primer binding sites will not be efficiently amplified and, therefore, will not be detected.
- the invention also includes preferred combinations of nucleic acid sequences for amplifying and detecting human prostate-associated genetic markers, including those specific for PSA, PSMA and hK2 nucleic acid sequences.
- nucleotide sequence or “nucleic acid sequence” is meant the sequence of nitrogenous bases along a linear information-containing molecule that is capable of hydrogen-bonding with another nucleic acid strand of DNA or RNA having a complementary base sequence.
- the terms are not meant to limit such information-containing molecules to polymers of nucleotides perse but also include molecule structures containing one or more nucleotide analogs or abasic units in the polymer.
- the polymers may include base subunits containing a sugar moiety or a substitute for ribose or deoxyribose (for example, 2' halide- or methoxy-substituted pentose sugars), and may be linked by linkages other than phosphodiester bonds, such as phosphorothioate, methylphosphonate, and peptide linkages.
- oligonucleotide is meant a polymeric chain of two or more chemical subunits, each subunit comprising a nucleotide base moiety, a sugar moiety, and a linking moiety which joins the subunits in a linear spacial configuration.
- An oligonucleotide may contain up to thousands of such subunits, but generally contains subunits in a range having a lower limit of between about 5 to about 10 subunits, and an upper range between about 20 to about 1 ,000 subunits.
- the most common nucleotide base moieties are guanine (G), adenine (A), cytosine (C), thymine (T) and uracil (U), although other rare or modified nucleotide bases able to form hydrogen bonding (e.g., inosine or I) are well known to those skilled in the art.
- the most common sugar moieties are ribose and deoxyribose, although 2'-0-methyl ribose, halogenated sugars, and other modified and different sugars are well known.
- the linking group is usually a phosphorus-containing moiety, commonly a phosphodiester linkage, although other known phosphate-containing linkages (e.g., phosphorothioates, methylphosphonates) and non-phosphorus- containing linkages (e.g. peptide-like linkages found in "peptide nucleic acids" or PNA) known in the art are included.
- PNA are intended to fall within this definition of an oligonucleotide.
- an oligonucleotide includes one in which at least one base moiety has been modified, for example, by the addition of propyne groups, so long as (1) the modified base moiety retains the ability to form a non- covalent association with G, A, C, T or U, and (2) an oligonucleotide comprising at least one modified nucleotide base moiety is not sterically prevented from hybridizing with a complementary single- stranded nucleic acid.
- An oligonucleotide's ability to hybridize with a complementary nucleic acid strand under particular conditions e.g., temperature, salt concentration
- amplification is meant production of multiple copies of a target nucleic acid that contains at least a portion of a the intended specific target nucleic acid sequence (PSA, PSMA or hK2).
- the multiple copies may be referred to as amplicons or amplification products.
- the amplified target contains less than the complete target gene sequence (introns and exons) or an expressed target gene sequence (spliced transcript of exons and flanking untranslated sequences).
- PSA-specific amplicons may be produced by amplifying a portion of the PSA target polynucleotide by using amplification primers which hybridize to, and initiate polymerization from, internal positions of the PSA target polynucleotide.
- the amplified portion contains a detectable target sequence which may be detected using any of a variety of well known methods.
- nucleic acid amplification conditions environmental conditions including salt concentration, temperature, the presence or absence of temperature cycling, the presence of a nucleic acid polymerase, nucleoside triphosphates, and cofactors which are sufficient to permit the production of multiple copies of a target nucleic acid or its complementary strand using a nucleic acid amplification method.
- Many well-known methods of nucleic acid amplification require thermocycling to alternately denature double-stranded nucleic acids and hybridize primers. For example, the polymerase chain reaction or PCR (US Pat. Nos.
- RT-PCR reverse transcriptase
- cDNA complementary DNA
- LCR ligase chain reaction
- Thermophilic SDA or tSDA uses thermophilic endonucleases and polymerases at higher temperatures in essentially the same method (European Pat. App. 0 684,315).
- Other amplification methods include nucleic acid based sequence amplification or NASBA (US Pat No. 5,130,238), one that uses an RNA replicase (Q ⁇ replicase) to amplify the probe molecule itself (Lizardi, P. et al., 1988, BioTechnol. 6: 1197-1202), a transcription based amplification method (Kwoh, D. et al, 1989, Proc. Natl. Acad. Sci.
- RNA polymerase to make many RNA transcripts of a target region
- RNA polymerase uses a promoter-primer that hybridizes to a target nucleic acid in the presence of a reverse transcriptase and an RNA polymerase to form a double stranded promoter. Then, RNA polymerase activity produces RNA transcripts that can become templates for further rounds of TMA in the presence of a second primer capable of hybridizing to the RNA transcripts.
- TMA is an isothermal method that uses an RNAse H activity to digest the RNA strand of an RNA-DNA hybrid, thereby making the DNA strand available for hybridization with a primer or promoter-primer.
- RNAse H activity associated with a retroviral reverse transcriptase provided for amplification is used.
- primer an oligonucleotide capable of binding to a region of a target nucleic acid or its complement and promoting nucleic acid amplification of the target nucleic acid. In most cases a primer will have a free 3' end which can be extended by a nucleic acid polymerase. All amplification primers include a base sequence capable of hybridizing via complementary base interactions either directly with at least one strand of the target nucleic acid or with a strand that is complementary to the target sequence. Amplification primers serve as substrates for enzymatic activity that produces a longer nucleic acid product.
- amplification primers anneal to opposite strands of a double stranded target DNA that has been denatured and the primers are extended by a thermostable DNA polymerase to produce double-stranded DNA products which are denatured with heat, cooled and annealed to the amplification primers, and the primers are extended by polymerase activity during multiple cycles (e.g., about 20 to about 50 thermic cycles).
- one amplification primer is a "promoter-primer" that hybridizes to a target RNA and reverse transcriptase (RT) produces a cDNA copy of the target RNA, while RNase H activity degrades the target RNA.
- the promoter-primer is an oligonucleotide that comprises a promoter sequence (which become functional when double stranded) located to 5' of a target-binding sequence which is capable of hybridizing to the target sequence.
- the target-binding sequence is capable of hybridizing to a binding site of the target RNA at a location 3' to the sequence to be amplified.
- the promoter sequence When made double-stranded, the promoter sequence is capable of binding an RNA polymerase to begin transcription of the target sequence to which the promoter primer is hybridized.
- a promoter-primer may be referred to as a 'T7-primer" when it is specific for T7 RNA polymerase recognition. Under certain circumstances the 3' end of a promoter-primer, or a subpopulation of such promoter-primers, may be modified to block or reduce primer extension.
- a second amplification primer then binds to the cDNA and RT produces another DNA strand resulting in a double-stranded DNA containing a functional RNA promoter at one end.
- the second amplification primer comprises a target-binding sequence capable of hybridizing to the complement (i.e., the cDNA strand) of the target RNA. It may be referred to as a "non-T7 primer” to distinguish it from a "T7-primer”.
- An RNA polymerase uses this promoter sequence to produce multiple RNA transcripts (i.e., amplicons), generally about 100 to 1 ,000 copies. Each newly-synthesized amplicon can anneal with the second amplification primer which is extended by RT to produce a DNA copy, while the RNase H activity degrades the RNA of this RNA:DNA duplex.
- the promoter-primer then binds to the newly synthesized DNA and RT creates a double-stranded DNA from which the RNA polymerase produces multiple amplicons. A billion-fold isothermic amplification can thus be achieved using two amplification primers.
- a "target-binding sequence" of an amplification primer is the portion that determines target specificity because that portion is capable of annealing to the a target nucleic acid strand or its complementary strand.
- the complementary target sequence to which the target-binding sequence hybridizes is referred to as a primer-binding sequence.
- the primer sequence consists essentially of a target-binding sequence, whereas other methods (e.g., TMA or SDA) include additional specialized sequences adjacent to the target-binding sequence (e.g., an RNA polymerase promoter sequence adjacent to a target-binding sequence in a promoter-primer or a restriction endonuclease recognition sequence for an SDA primer).
- SEQ IN NO:15 to SEQ ID NO:29 are amplification primers that do not include additional functional sequences
- SEQ ID NO:30 to SEQ ID NO:43 are T7 promoter-primers that include additional functional sequences (underlined) besides the target-binding sequences (not underlined); the underlined sequences are preferred T7 polymerase promoter sequences.
- all of the primer and probe sequences of the present invention may be synthesized using standard in vitro synthetic methods.
- primer sequences disclosed herein using routine methods to add additional specialized sequences (e.g., promoter or restriction endonuclease recognition sequences) to make primers suitable for use in a variety of amplification methods.
- additional specialized sequences e.g., promoter or restriction endonuclease recognition sequences
- promoter-primer sequences described herein can be modified by removing the promoter sequences to produce amplification primers that are essentially target-binding sequences, suitable for amplification procedures that do not use these additional functional sequences, such as PCR.
- the PSA-specific sequences of the primers and probes of SEQ ID NO:1 to SEQ ID NO:43 and the hK2-specific sequences of primers of SEQ ID NO;46 AND 47 were selected by aligning the known sequences of PSA exons with the known sequences of HSPSAR and human kallikrien exon sequences (HUMKAL2, HUMKAL2a, HUMKAL2b, HUMKAL2c, HUMKAL2d, HSKALLI, and
- HUMPSAA using the an alignment algorithm using default parameters of the algorithm, such as, for example, the BLASTN algorithm available from the National Center for Biotechnology Information at the National Library of Medicine, or using the Multiple Alignment Construction and Analysis Workbench ("MACAW") algorithm as described in detail previously (Shuler et al, 1991 , Proteins 9(3):180-190).
- MACAW Multiple Alignment Construction and Analysis Workbench
- regions of the PSA exon or hK2 region for which a primer or probe sequence was desired which contained the least amount of identity with the other sequences were identified. From those sequences, oligonucleotide sequences of the appropriate length and GC content for a primer or probe were selected and synthesized for tested.
- the predicted secondary structure of the selected primer or probe sequence was determined by using an algorithm that calculates RNA secondary structure, as previously described in detail (Matzura and Wennborg, Complete Applications in the Biosciences, 1996, Vol. 12, No. 3, pp 247-9).
- the primers of SEQ ID NO:48 and SEQ ID NO:49 and the probe of SEQ ID NO:50 for the human PSMA were similarly designed and selected. Although algorithms were used to aid in sequence alignment and predicting secondary structure, those skilled in the art could readily perform these steps manually.
- target sequence is meant the nucleotide base sequence of a nucleic acid strand, at least a portion of which is capable of being detected using a labeled oligonucleotide probe. Primers bind to a portion of a target sequence, which includes both complementary strands when the target sequence is a double-stranded nucleic acid.
- RNA ribonucleic acid having the same nucleotide base sequence as a deoxyribonucleic acid (DNA), with the appropriate U for T substitution(s).
- DNA deoxyribonucleic acid
- DNA DNA having the same nucleotide base sequence as an RNA but with the appropriate T for U substitution(s).
- nucleic acid and oligonucleotide refer to molecular structures having either a DNA or RNA base sequence or a synthetic combination of DNA and RNA base sequences, including analogs thereof, which include “abasic” residues.
- solid support is meant a material that is essentially insoluble under the solvent and temperature conditions of the assay method, comprising free chemical groups available for joining an oligonucleotide or nucleic acid.
- the solid support is covalently coupled to an oligonucleotide designed to directly or indirectly bind a target nucleic acid.
- the oligonucleotide attached to the solid support is preferably a poly-T sequence.
- a preferred solid support is a particle, such as a micron- or submicron-sized bead or sphere.
- solid support materials such as, for example, silica, polyacrylate, polyacrylamide, a metal, polystyrene, latex, nitrocellulose, polypropylene, nylon or combinations thereof. More preferably, the solid support is capable of being attracted to a location by means of a magnetic field, such as a solid support having a magnetite core. Particularly preferred supports are monodisperse magnetic spheres (i.e., uniform size ⁇ about 5%).
- detecting an amplification product is meant any of a variety of methods for determining the presence of an amplified nucleic acid, such as, for example, hybridizing a labeled probe to a portion of the amplified product.
- a labeled probe is an oligonucleotide that specifically binds to another sequence and contains a detectable group which may be, for example, a fluorescent moiety, a chemiluminescent moiety, a radioisotope, biotin, avidin, enzyme, enzyme substrate, or other reactive group.
- a labeled probe includes an acridinium ester (AE) moiety that can be detected chemiluminescently under appropriate conditions (as described in US Pat. No. 5,283,174).
- AE acridinium ester
- the detecting step may either be qualitative or quantitative, although quantitative detection of PSA-specific or other prostate-associated genetic amplicons is preferred for determining the level of prostate-associated gene expression (e.g., PSA-specific mRNA) in a non-prostate sample, which indicates the degree of metastasis or recurrence of prostate and/or breast cancer.
- PSA-specific mRNA e.g., PSA-specific mRNA
- Assays for purifying and detecting a target polynucleotide often involve capturing a target polynucleotide onto a solid support.
- the solid support retains the target polynucleotide during one or more washing steps of the target polynucleotide purification procedure.
- One hybridization sandwich technique for capturing and for detecting the presence of a target polynucleotide involves the capture of the target polynucleotide by a probe bound to a solid support and hybridization of a detection probe to the captured target polynucleotide (US Pat. No. 4,486,539 to Ranki et al.). Detection probes not hybridized to the target polynucleotide are readily washed away from the solid support.
- Another method uses a mediator polynucleotide that hybridizes to both a target polynucleotide and to a polynucleotide fixed on a solid support such that the mediator polynucleotide joins the target polynucleotide to the solid support to produce a bound target (US Pat. No. 4,751 ,177 to Stabinsky).
- a labeled probe can be hybridized to the bound target and unbound labeled probe can be washed away from the solid support.
- RNA and/or mRNA require extensive purification of RNA and/or mRNA prior to amplification and detection, often involving harsh chemicals such as guanidinium thiocyanate (Sambrook, J. et al, 1989, Molecular Cloning, A Laboratory Manual, 2 nd ed. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY), pp. 7.37- 7.57; Lin, L. et al, 1993, "Simple and Rapid Sample Preparation Methods for Whole Blood and Blood Plasma” in Diagnostic Molecular Microbiology, Principles and Applications (Persing, D.H. et al, Eds, American Society for Microbiology, Washington, DC), pp 605-616).
- harsh chemicals such as guanidinium thiocyanate
- Non-prostate biological samples may be hematopoietic tissue such as peripheral blood or bone marrow, plasma, non-prostate biopsy tissue including lymph nodes, respiratory tissue or exudates, gastrointestinal tissue, urine, feces, semen or other body fluids or materials.
- the preferred sample preparation method requires a minimum of technical expertise and uses standard laboratory equipment and relatively low cost reagents to yield target mRNA suitable for amplification, while avoiding false positives that may result from potentially cross-reactive sequences found in chromosomal DNA.
- the preferred simplified sample preparation method eliminates extensive extraction and shearing of chromosomal DNA (to reduce viscosity), avoids use of potentially harmful reagents (e.g., guanidinium compounds, phenol or chloroform) and minimizes the number of steps, thus minimizing sample loss and increasing detection of low abundance mRNA species.
- the methods invention includes a method of detecting or quantifying prostate-associated genetic markers, such as PSA-specific nucleic acids, particularly mRNA.
- the methods include contacting a non-prostate biological sample that potentially contains a prostate-associated genetic marker target sequence with a first primer or promoter-primer capable of specifically hybridizing to the target gene sequence (PSA, PSMA and/or hK2), and providing at least one nucleic acid polymerase activity, under nucleic acid amplification conditions to produce target-specific amplification products ("amplicons").
- the target-specific amplification products are a plurality of a nucleic acid strands comprising a region complementary to the specific target sequence and at least one probe binding site capable of hybridizing under hybridization conditions with a labeled oligonucleotide probe specific for the amplified target sequences, thereby forming a probe:target hybrid.
- the method also includes detecting the labeled probe:target hybrid as an indication of the presence of the prostate- associated genetic marker nucleic acid in the non-prostate biological sample.
- Preferred embodiments further include preparation of the target nucleic acid substrate from the biological sample using a relatively simple sample preparation procedure.
- the detecting step may further include one or more helper probes specific for a portion of the amplified target nucleic acid to enhance detection of the target in the assay.
- helper probes hybridize to the amplified target sequences to remove secondary structure or otherwise enhance the capability of the other probes to bind to the detected sequence.
- the prostate-associated genetic marker target sequence is RNA
- the labeled oligonucleotide probe is of the same sense.
- only a promoter-primer is used in the amplifying step and the probe is targeted to a portion of the amplicon.
- the target RNA is detected using a probe of the same sense as the target RNA and capable of hybridizing with a base sequence region located within the amplified complementary nucleic acid (as previously described in detail in U.S. Pat. No. 5,554,516 to Kacian et al.).
- selected primers specific for human PSA, PSMA and/or hK2 gene sequences are used in a transcription mediated amplification that uses both a promoter-primer and an amplification primer without promoter sequence, and the amplified products are detected with a probe capable of being detected in a homogeneous assay (see US Pat. Nos. 5,480,784 and 5,399,491 to Kacian & Fultz; US Pat. No. 5,554,516 to Kacian et al.; US Pat. No. 5,283,174 to Arnold et al.; European Pat. App. No. EP 0709466). These general amplification and detection methods are well known in the art.
- the preferred amplification method produces an amplified nucleic acid or amplicon that is an RNA, and even more preferably produces predominantly amplified RNA that is complementary to the target sequence (i.e., the opposite sense as the target).
- the target is mRNA, arbitrarily designated (+) sense strands
- the amplicons are preferably (-) sense strands.
- the probes for detecting such amplicons are any sequence capable of hybridizing specifically to an amplified sequence (i.e., are complementary to a portion of the amplicon).
- 'TMA transcription-mediated amplification
- the promoter-primer is of the (-) sense
- the template target nucleic acid is of the (+) sense
- the produced amplicons are of the (-) sense.
- one of the two primers used in the amplification step is a T7 (- sense) promoter-primer that binds to the prostate-associated genetic marker mRNA and one of the two primers is a non-T7 (+ sense) primer that binds to the cDNA product produced from the activity of reverse transcriptase extending the T7 promoter-primer that uses the mRNA as a template.
- the T7 promoter-primer contains a T7 RNA polymerase recognition sequence at the 5' end of the target-binding sequence, whereas the non-T7 primer does not contain a T7 RNA polymerase recognition sequence and consists essentially of a target-binding sequence.
- Preferred promoter-primers have a length range having a lower limit of between about 35-45 nt and an upper limit between about 45-100 nt.
- promoter-primers are about 40-70 nt long, and more preferably are about 45-55 nt long.
- a T7 promoter sequence of a promoter-primer is about 25-30 nt long; particularly preferred T7 promoter sequences include SEQ ID NO:44 or SEQ ID NO:45.
- Preferred target-binding regions of a PSA- specific promoter-primer hybridize specifically to a human PSA gene exon sequence, preferably within any one of exons 3, 4 or 5.
- Primers used in transcription mediated amplification in conjunction with promoter primers consist essentially of target-binding sequences specific for human PSA, PSMA or hK2 gene sequences.
- Preferred PSA-specific bind to PSA sequences within an exon or spanning a splice junction of two exons, and more preferably have target-binding sequences specific for any one of exons 2, 3 or 4, or span the exon 2 and 3 splice junction of the human PSA gene.
- Primers preferably have a length within a range having a lower limit of about 15-20 nt and an upper limit within a range of about 25-100 nt, more preferably in a range of about 15-30 nt, and most preferably in a range of about 20-25 nt in length.
- preferred PSA-specific primers have the sequences of SEQ ID NO:15 to SEQ ID NO:29 and preferred PSA-specific promoter-primers have the sequences of SEQ ID NO:30 to SEQ ID NO:43, where the promoter sequence is underlined and the target-binding sequence is not underlined.
- One aspect of the present invention is a method of amplifying a PSA-specific target sequence in mRNA present in a sample taken from non-prostate tissue and detecting the amplified product as an measure of prostate or breast cancer cells present in non-prostate tissue, thus indicating the presence of breast cancer or metastasis of prostate cancer.
- chemiluminescent detection assay for detecting the nucleic acid probe
- those skilled in the art could readily use other labels and detection methods well known in the art, such as labels based on enzymes, enzyme substrates, fluorescent, luminescent, chemiluminescent and electrochemiluminescent molecules, radionuclides, and fluorescent atoms to detect a hybridized probe; the amplification product may be detected using standard methods such as by gel electrophoresis or filtration, increased light absorption, hyperchromatic shift, or HPLC.
- Preferred homogeneous assays have advantages over heterogeneous assays (i.e., those necessitating physical separation to differentiate signal of hybridized probe from signal due to unhybridized probe), but the homogeneous detection aspect is not critical to the present invention.
- a fluorescent or chemiluminescent label is incorporated into the probe, and more preferably the label is a chemiluminescent acridinium ester (AE).
- Probes for use in the methods of the present invention may be targeted to any region of the amplicon to be detected, and preferably the probe is of the same sense as the target nucleic acid.
- a PSA-specific probe may hybridize to either on intron or exon sequence, and preferably hybridizes to a sequence within a PSA gene exon (e.g., in exon 2, 3 or 4), or spanning an exon splice site (e.g., spanning the 3' end of exon 3 and the 5' end of exon 4), or within a PSA gene intron (e.g., within intron 3).
- Probe sequences may be within a range of about 5-100 nt long, and preferably are within about 10-50 nt long, more preferably about 20-25 nucleotides long.
- Preferred probe sequences include those having SEQ ID NO:1 to SEQ ID NO:14 (with their general location in the human PSA gene shown in Table 1) and SEQ ID NO:50.
- the probes are AE-labeled and hybridize to the amplified RNA products of a TMA reaction.
- the primers and probes of the present invention may be used in amplification and detection methods that use nucleic acid substrates isolated by any of a variety of well known methods.
- the target mRNA may prepared by the following relatively simple procedure to yield mRNA suitable for use in TMA.
- cells in a biological sample were lysed by contacting the cell suspension with a lysing solution containing at least about 150 mM of a soluble salt, preferably a lithium halide salt, a chelating agent and a non-ionic detergent in an effective amount to lyse the cellular cytoplasmic membrane without causing substantial release of nuclear DNA or RNA.
- a lysing solution containing at least about 150 mM of a soluble salt, preferably a lithium halide salt, a chelating agent and a non-ionic detergent in an effective amount to lyse the cellular cytoplasmic membrane without causing substantial release of nuclear DNA or RNA.
- the cell suspension and lysing solution were mixed at a ratio of about 1 :1 to 1 :3, and the detergent concentration in the lysing solution was between about 0.5% to 1.5% (v/v).
- any of a variety of known non-ionic detergents are effective in the lysing solution (e.g,TRITON ® -type, TWEEN ®" - type and NP-type); typically the lysing solution contained an octylphenoxy polyethoxyethanol detergent, preferably 1% TRITON ® X-102.
- This procedure has been used primarily with biological samples that contain cell suspensions (e.g., blood and bone marrow), but it works equally well on other tissues if the cells are separated using standard mincing, screening and/or proteolysis methods to separate cells individually or into small clumps.
- RNA After cell lysis, the released total RNA was stable, and may be stored at room temperature for at least 2 hr without significant RNA degradation without additional RNAse inhibitors.
- Total RNA may be used in amplification without further purification, or mRNA may be isolated using standard methods, generally dependent on affinity binding to the poly-A portion of mRNA.
- mRNA isolation used capture particles consisting essentially of poly-dT oligonucleotides attached to insoluble particles that were added to the above-described lysis mixture, the poly-dT moieties annealed to the poly-A mRNA, and the particles were separated physically from the mixture.
- superparamagnetic particles were used and separated by applying a magnetic field to the outside of the container.
- a suspension of about 300 ⁇ g of particles in a standard phosphate buffered saline (PBS), pH 7.4, of 140 mM NaCI) having either dT 14 or dT 30 linked at a density of about 1 to 100 pmoles per mg (preferably 10-100 pmols/mg, more preferably 10-50 pmols/mg) were added to about 1 ml of lysis mixture.
- PBS phosphate buffered saline
- Any superparamagnetic particles may be used, although typically the particles were a magnetite core coated with latex or silica (e.g., commercially available from Serodyn or Dynal) to which poly-dT oligonucleotides were attached using standard procedures (Lund et al., Nuc.
- the lysis mixture containing the particles was gently mixed and incubated at about 22°C to 42°C for about 30 min, when a magnetic field was applied to the outside of the tube to separate the particles with attached mRNA from the mixture and the supernatant was removed.
- the particles were washed one or more times, generally three, using standard resuspension methods and magnetic separation as described above. Then, the particles were suspended in a buffer solution and used immediately in amplification or stored frozen.
- a number of parameters may be varied without substantially affecting the sample preparation.
- the number of particle washing steps may be varied and the particles may be separated from the supernatant by other means (e.g., filtration, precipitation, centrifugation).
- the solid support may have nucleic acid capture probes joined thereto that are complementary to the specific target sequence or any particle or solid support that non-specifically binds the target nucleic acid may be used (e.g., polycationic supports as described in U.S. Pat. No. 5,599,667 to Arnold et al.).
- the isolated RNA was released from the capture particles using a standard low salt elution process or amplified while retained on the particles by using primers that bind to regions of the RNA not involved in base pairing with the poly-dT or in other interactions with the solid phase matrix.
- the exact volumes and proportions described above are not critical and may be varied so long as significant release of nuclear material does not occur. Vortex mixing is preferred for small scale preparations but other mixing procedures may be substituted.
- the ionic strength of the lysing solution be at least about 150 mM, preferably 150 mM to 1 M, because lower ionic strengths lead to nuclear material contamination (e.g., DNA) that increases viscosity and may interfere with amplification and/or detection steps to produce false positives.
- Lithium salts are preferred in the lysing solution tor prevent RNA degradation, although other soluble salts (e.g., NaCI) combined with one or more known RNAse inhibitors would be equally effective.
- Table 2 lists preferred combinations of primers and probes used for amplification and detection of PSA, PSMA and hK2 genetic markers, with or without helper probe(s), using TMA essentially as described previously in US Pat. Nos.5,399,491 , 5,480,784, and 5,554,516, and detection in a homogeneous protection assay, essentially as described previously in US Pat. No. 5,283,174.
- Each row represents a preferred combination. Of these, particularly preferred combinations for amplifying and detecting PSA mRNA are indicated with an asterisk (*) in each box of the row in Table 2.
- the last two entries in Table 2 are primers and probes for amplifying and detecting specifically hK2 target (SEQ ID NOS 46, 47 and 1) and PSMA target (SEQ ID NOS 48, 49 and 50).
- Nucleic acids from a variety of biological samples have been used in testing the methods of prostate-associated marker mRNA amplification and detection with the primers and probes described herein, including in vitro transcripts of a PSA cDNA, whole blood spiked with in vitro transcripts of a PSA cDNA, total RNA isolated from a prostate cancer cell line (LNCaP cells, Horoszewicz J.S. et al, 1983, Cancer Res. 43: 1809-1818; ATCC No. CRL-10995), whole blood spiked with LNCaP cells, peripheral blood, breast tissue cells, lung cells, poly-A RNA isolated and tested individually from prostate cancer cells, lymph nodes, breast tissue cells, kidney cells, small intestine tissue cells and white blood cell genomic DNA.
- LNCaP cells Horoszewicz J.S. et al, 1983, Cancer Res. 43: 1809-1818; ATCC No. CRL-10995
- LNCaP cells Horoszewicz J.S. et al
- Total RNA from lung, mammary gland and prostate
- poly-A RNA from kidney, liver, lymph node, mammary gland, small intestine and prostate
- RNA and poly-A RNA were prepared using standard methods (derived from the method of Chirgwin et al, 1979, Biochem. 18:5294, with poly-A RNA selected using oligo(dT) cellulose; commercially available from Clontech Laboratories, Inc., Palo Alto, CA).
- Total RNA and poly-A RNA were prepared from peripheral blood from normal human donors using substantially the same methods.
- In vitro transcripts of a PSA cDNA were prepared using a PSA cDNA clone (obtained from the ATCC, Accession No. 106527) present in a vector (pBluscript SK-; Adams et al, 1985, Nature 377(3): 174) or the PSA cDNA fragment of about 1.2 kb was subcloned into another vector (pSP64 poly(A) vector) for use in preparing in vitro transcripts.
- the plasmid DNA was prepared and purified using standard methods, linearized by enzymatic digestion at a point 3' of the cDNA insert, and transcribed using an RNA polymerase. Transcripts were prepared using standard methods and reagents (supplied in an AMPLISCRIBE Translation Kit, from Epicenter Technologies, Corp, Madison, WI).
- uncoagulated peripheral blood or bone marrow was added to about 750 ⁇ of the lysing solution.
- the proportions of each of these two components is not critical, and generally a 1 :1 ratio to 1 :3 ratio of the components is capable of lysing the samples.
- the lysing solution used most commonly consisted of 50 mM HEPES (pH 7.5), 1 M LiCI, 5 mM EDTA, and 1% TRITON ® X-102.
- uncoagulated is meant that the blood or bone marrow was treated upon collection with about 2mM to about 20 mM EDTA, or an effective amount of heparin or similar anticoagulant known in the art.
- the particles were washed one to three times by resuspending them in about 1 ml of a wash solution (50 mM HEPES, pH 7.5, 5 mM EDTA, 150 mM NaCI and 0.1% (w/v) sodium dodecyl sulfate (SDS)) with mixing by vortexing for about 3 to 5 seconds to suspend the beads, which were separated from the supernatant as described above, and the supernatant wash was discarded. Following washing, the particles were suspended in 250 ⁇ of a buffer (10 mM HEPES, pH 7.5,1 mM EDTA) and either stored at -30°C for later use or used immediately.
- a wash solution 50 mM HEPES, pH 7.5, 5 mM EDTA, 150 mM NaCI and 0.1% (w/v) sodium dodecyl sulfate (SDS)
- SDS sodium dodecyl sulfate
- the particles with attached RNA were used directly or, occasionally, the attached RNA was released from the capture particles using a standard elution procedures (e.g., with heat).
- a standard elution procedures e.g., with heat.
- the presence of solid particles did not impair amplification and the simplicity of using the particles with attached RNA was preferred to an additional RNA isolation step.
- EXAMPLE 2 Amplification and Detection of PSA-specific mRNA
- individual combinations of a non- T7(+) primer and a T7(-) promoter-primer were used to amplify an in vitro transcript (as described above) of PSA gene sequences.
- the amplification products were detected in a homogeneous protection assay essentially as described in US Pat. No. 5,283,174 , to Arnold et al, using a single probe labeled with acridinium ester, in which the chemiluminescent signal is detected as relative light units ("RLU").
- RLU relative light units
- the T7 promoter-primer (SEQ ID NO:30) is specific for PSA exon 4, the primers are specific for PSA exon 3 (SEQ ID NO:15, SEQ ID NO:17 and SEQ ID NO:18), and the probe is specific for PSA exon 3 (SEQ ID NO:1).
- a solution containing different numbers of in vitro transcripts (10 3 , 10 4 , or 10 5 molecules, or a negative control containing no transcripts) was added to a tube containing 25 ⁇ of an amplification reagent containing 160 mM Tris-HCl (pH 7.5), 100 mM MgCI 2 70 mM KCI, 20% (w/v) polyvinylpyrrolidone, 16 mM each of the four ribonucleoside triphosphates ATP, GTP, CTP, and UTP, 4 mM each of the four deoxyribonucleoside triphosphates dATP, dGTP, dCTP, and dTTP, 400 nM (15 pmoles).
- the T7 promoter-primer at 15 pmols/reaction had the sequence of SEQ ID NO:30
- the non-T7 primer at 400 nM (15 pmoles) had the sequence of SEQ ID NO:15, SEQ ID NO:17, or SEQ ID NO:18.
- Each reaction was incubated at 60°C for 10 min, although any temperature capable of melting intramolecular base pairing in the target nucleic acid is suitable (e.g., between about 60° C and 70° C, more preferably between about 65°C and about 67°C).
- each reaction was incubated at about 42° C for 5 min, after which an enzyme reagent (25 ⁇ l containing 2000 units of recombinant MMLV reverse transcriptase, 2000 units recombinant T7 RNA polymerase, 8 mM HEPES (pH 7.5), 50 mM N- acetyl-L-cysteine, 0.04 mM zinc acetate, 80 mM trehalose, 140 mM Tris-HCl (pH 8.0), 70 mM KCI, 1mM EDTA, 0.01% (w/v) phenol red, 10% (v/v) TRITON ® X-102 and 20% (v/v) glycerol) was added and the reaction was gently mixed and incubated for about 1 hr at 42° C.
- This amplification method produced amplified RNA of a sense opposite to that of the target RNA.
- RNA was detected using 100 ⁇ of a probe reagent containing 100 mM lithium succinate (pH 4.7), 1.2 M LiCI, 15 mM aldrithiol-2, 2% (w/v) lithium lauryl sulfate (LLS), 20 mM EDTA, 20 mM ethylene glycol-bis-( ⁇ -amino ethyl ether) N, N, N', N'-tetracetic acid (EGTA), 3% ethanol, and 7.5 nM of a hybridization probe having SEQ ID NO:1 , labeled with a chemiluminescent acridinium ester (AE) linked via non-nucleotide linkers using methods essentially a described in US Pat. No. 5,585,481 to Arnold er a/.
- the detection solution was added to the reaction and incubated at 60°C for 30 min to permit hybridization of the probe to the amplified target.
- the probe (SEQ ID NO:1) was detected in a homogeneous protection assay (HPA) which included the following steps.
- HPA homogeneous protection assay
- 300 ⁇ of an alkaline solution 600 mM sodium borate, pH 8.5, and 1 % (v/v) TRITON ® X-100 was added to the mixture described above.
- the AE label on hybridized probe is protected from hydrolysis by its association with a double helix, whereas the AE label on unhybridized probe is not protected from hydrolysis, making unhybridized probe undetectable.
- the solution was incubated at 60° C for 10 min, cooled at room temperature for 5 min, and mixed with 200 ⁇ l of a solution containing 30 mM hydrogen peroxide and 1 mM nitric acid, followed immediately by addition of 200 ⁇ l of a solution containing 1 M NaOH and 2% (w/v) ZWITTERGENT ® 3-14.
- Chemiluminescence was detected using a luminometer (e.g., LEADER ® 50), with the output measured in relative light units (“RLU").
- Table 3 show that the three combinations of primers and promoter- primers tested in this example gave varying levels of amplification, all detected with the same probe, and all provided a signal above background when 10 3 copies of the target RNA were included in the assay. Of these three combinations, the combination of SEQ ID NO:18 and SEQ ID NO:30 gave the best results, and the system became saturated for detection when 10 4 copies of the target RNA were included in the assay.
- EXAMPLE 3 Amplification and Detection of PSA mRNA in Total and Poly-A RNA from Prostate Tissue
- a number of combinations of primer, promoter-primer and probe were used to amplify and detect PSA-specific mRNA contained within a sample of total RNA prepared from prostate tissue as described above.
- RNA in the tested samples was equivalent to a calculated numbers of cells as follows: 1 pg is equivalent to less than 1 cell (about 0.1 cell), 10 pg is equivalent to about 1 cell, 100 pg is equivalent to about 10 cells, 1 ,000 pg (1 ng) is equivalent to about 100 cells, and 10,000 pg (10 ng) is equivalent to about 100 cells. In some experiments, the total range of RNA concentrations were not tested.
- the prostate poly-A RNA was isolated using poly-dT hybridization in which the poly-dT oligonucleotides were about dT 14 to dT 30 in length and covalently linked to magnetic particles; the purification steps used (magnetic separation and washing) were substantially as described in Example 1. It was expected that total prostate RNA would contain about 5% PSA-specific mRNA, and the amount of poly-A RNA (i.e., purified mRNA) added to the amplification and detection samples was reduced accordingly.
- poly-A RNA i.e., purified mRNA
- poly-A RNA from prostate tissue was added to triplicate tubes at 5 pg or 0.5 pg per reaction, which were amplified and detected using the combination of SEQ ID NO:18 and SEQ ID NO:30 as primers, and SEQ ID NO:1 as probe, substantially as described for the results presented in Table 4.
- the mean RLU detected were 1 ,404,286 and for 0.5 pg the mean RLU detected were 392,558.
- helper probes may increase the signal detected, allowing detection of PSA-specific sequences present in less than 0.1 pg of total RNA isolated from prostate tissue using the preferred amplification and detection system.
- amplification was performed substantially as described in Examples 2 and 3, except that about 100 pmol of helper probe oligonucleotides were added to the amplification reaction along with the AE- labeled probe using in the detection step. Amplification then proceeded as described above, followed by detection of chemiluminescence as described above.
- the PSA-specific target was provided in total RNA isolated from prostate tissue as described in Example 3, tested at concentrations ranging from 0.016 pg to 10 pg.
- the helper probes in these experiments were SEQ ID NO:27 (in PSA exon 2) and SEQ ID NO:28 (spanning the joining point of PSA exons 2 and 3). The results of these tests are shown in Table 5, with the signal representing the mean of triplicate samples for each RNA concentration tested.
- RNA isolated from prostate tissue obtained from Clonetech, Palo Alto, CA
- WBC white blood cells
- Helper probes SEQ ID NO:27 and SEQ ID NO:28
- the prostate total RNA was used at 10 pg or 1 pg per reaction, whereas at least 10,000-f old more WBC total RNA was used for comparison (1 ⁇ g or 100 ng per reaction).
- a negative control with no added RNA was included, and all reactions were tested in triplicate, with the results presented as the mean of the three reactions (Mean RLU). The results are presented in Table 6.
- each of the four combinations of primers and probes tests specifically amplified and detected PSA-specific target RNA in prostate total RNA.
- the results were essentially negative for the samples under the same conditions that included WBC total RNA from a normal donor which would not be expected to contain PSA-specific target mRNA. That is, despite the use of 10,000-fold to 1 ,000,000-fold more WBC total RNA in the reactions compared to prostate total RNA, no false positives were observed (i.e., none gave results equivalent to those obtained with 1 pg of prostate RNA).
- the linearity of detection of PSA-specific target sequence was measured in an amplification and detection assay in which the combination of non-T7(+) primer of SEQ ID NO:26, T7 promoter primer of SEQ ID NO:40 and probe of SEQ ID NO:8 was used with prostate total RNA over a range of 10 pg to 0.001 pg per reaction (i.e., using 10, 5, 1 , 0.5, 0.1 , 0.05, 0.01 or 0.005 pg per reaction).
- test aliquots were prepared from the 10 pg aliquot by diluting 1 :2 and 1 :10 to obtain a 5 pg and 1 pg aliquots; the 5 pg aliquot was then serially diluted 1 :10 to obtain the 0.5, 0.05 and 0.005 pg aliquots and the 1 pg aliquot was similarly diluted to obtain the 0.1 and 0.01 pg aliquots. All assays were performed in triplicate, and the negative control contained no prostate total RNA in the reaction. The results of these assays are shown graphically in FIG.
- EXAMPLE 5 Amplification and Detection of PSA Target Sequences in Denatured Genomic DNA
- amplification and chemiluminescent detection assays were performed using denatured and undenatured genomic DNA obtained from peripheral WBC.
- the genomic DNA is expected to contain normal PSA gene sequences, which would be inaccessible to primers for amplification or probe for detection in its undenatured state.
- the non-T7 (+) primer was SEQ ID NO:18
- the T7 promoter-primer was SEQ ID NO:30
- the AE-labeled probe was SEQ ID NO:30.
- the positive control was PSA gene in vitro transcripts prepared substantially as in Example 2 and used as 100 copies per reaction, 10 copies per reaction and 1 copy per reaction.
- the negative control was a reaction run without addition of nucleic acid target (DNA or RNA).
- the WBC genomic DNA was isolated using standard DNA isolation procedures, with shearing to decrease viscosity in solution (Sambrook et al. Molecular Cloning, A Laboratory Manual (2nd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1989), and used with or without prior denaturation at about 5 ⁇ g, 0.5 ⁇ g and 0.05 ⁇ g per reaction.
- the DNA was denatured by heating to 95 °C for about 10 min and then cooled immediately. Amplification and detection assays were performed substantially as described in Examples 2 and 3, and the results of triplicate tests for each sample are presented as mean RLU in Table 7.
- Amplification of Prostate Polv-A RNA and PSA In Vitro Transcripts This example compares amplification and detection results using a preferred combination of primers and probe, for which the target nucleic acid was either poly-A RNA isolated from prostate tissue or in vitro transcripts of a PSA cDNA sequence.
- the prostate poly-A RNA was isolated using hybridization to poly-dT oligomers immobilized to a solid support, substantially as described in Examples 1 and 3, and the in vitro transcripts were prepared substantially as described in Example 2.
- the amplification and detection methods were performed substantially as described in Examples 2-4, using as a non-T7(+) primer an oligonucleotide having SEQ ID NO:16, as a T7(-) promoter-primer an oligonucleotide having SEQ ID NO:32 and as a probe an oligonucleotide having SEQ ID NO:2, labeled with AE.
- the target sequences were added to the amplification reactions, which were performed in triplicate for each combination, at a calculated concentration of 10,000 copies of in vitro transcript per tube or 0.875 ng of poly-A-containing prostate RNA per tube, or no added RNA in the negative control tubes.
- peripheral blood samples were tested from individuals suspected of having either benign prostate hyperplasia or prostate cancer.
- Peripheral blood samples were collected shortly before prostate surgery (pre-surgery) and soon after surgical removal of the prostate gland (post-surgery).
- known numbers of cells of a prostate cancer cell line (LNCaP cells; ATCC No. CRLI-10995) or PSA-specific in vitro transcripts (as described in Example 2) were mixed with peripheral blood obtained from a normal individual.
- the clinical or control blood samples were lysed and the mRNA was isolated using the system of poly-dT oligomers attached to magnetic particles substantially as described in Example 1.
- amplification and detection methods were performed substantially as described in Examples * 2-4, using as a non-T7(+) primer an oligonucleotide having SEQ ID NO:18, as a T7(-) promoter-primer an oligonucleotide having SEQ ID NO:30 and as a probe an oligonucleotide having SEQ ID NO:1 , labeled with AE.
- the target sequences were added to the amplification reactions, which were performed in triplicate for each sample, at: (1) about 50 to 100 ng of total RNA, equivalent to about 2.5 to 5 ng of mRNA per reaction for each clinical sample, (2) a calculated concentration of 2,000 or 200 or 20 copies of in vitro transcript per reaction, and (3) the calculated equivalent of about 10 cells, 1 cell or 0.1 LNCaP cell per reaction. Negative control reactions contained no added RNA.
- the mean RLU results for the triplicate samples for each set of reactions, or mean RLU of nine reactions for the negative controls, are presented in Table 8.
- the primers and probe are capable of detecting PSA- specific target RNA less than the equivalent of one cancer cell in a volume of about 1.0 ml peripheral blood as detected in the sample containing the equivalent of one LNCaP cell.
- the assay is capable of detecting as little as 20 copies of transcript in a blood sample.
- PSA prostate specific antigen
- amplification and detection assays were performed on RNA isolated from other human tissues to determine the relative levels of PSA-specific target detected in those tissues. Unless otherwise indicated, all tissues were obtained from normal donors (i.e., non-cancerous tissue).
- the assays were performed in triplicate for each sample using either total RNA or poly-A RNA isolated from human tissue samples substantially as described in previous examples using a non-T7(+) primer an oligonucleotide having SEQ ID NO:18, a T7(-) promoter-primer an oligonucleotide having SEQ ID NO:30 and an AE-labeled probe have the oligonucleotide sequence of SEQ ID NO:1.
- the results of these assays are presented in Table 9, with the negative control results being the mean of 12 reactions performed without adding target RNA.
- poly-A RNA isolated from human prostate tissue, peripheral blood, breast tissue, kidney tissue, liver tissue, small intestine and lymph node were compared in similar amplification and detection assays, using the same combination of primers and probe as above.
- the mRNA for prostate tissue was assayed at 5 fg or 0.5 fg per reaction, and the mRNA from the other biological sources was assayed at 5 ng and 0.5 ng per reaction.
- PSA-specific target sequences were detected in the prostate tissue, breast tissue, kidney tissue, small intestine and lymph node, but no signal above the negative control (i.e., reactions without added RNA) was detected in liver tissue or blood.
- the relative signal (mean RLU of duplicate assays) detected indicated that the PSA target nucleic acid present in breast tissue, kidney tissue, small intestine and lymph node was about 10 5 -fold to 10 6 -fold less than present in prostate tissue.
- the PSA target detection system can detect even relatively small amounts of target in tissues other than prostate tissue. Because some tested tissues (liver and peripheral blood) were negative for PSA-specific target in these assays indicates that the PSA gene is not merely expressed at a lower level in all human tissues besides prostate. Therefore, the PSA target may be a general marker for cancerous or pre-cancerous conditions in selected other human tissues. An increase in detectable PSA-specific target (e.g., in peripheral blood) may then be an indication of metastasized prostate cancer or other types of cancer.
- PSMA and hK2 Targets in Various Biological Samples
- the other prostate-associated cancer marker targets PSMA and hK2 are also useful for detecting the presence of these target mRNA in non-prostate tissue.
- amplification and detection assays were performed on total and poly(A) RNA isolated from human tissues to determine the relative levels of PSA, PSMA and hK2 specific target in those tissues. All tissues were obtained from normal donors (i.e., non-cancerous tissue) and the assays were performed in triplicate for each sample, substantially as described in Example 8.
- RNA or poly(A) RNA was as indicated in Table 10, where 5 ng of poly(A) RNA is equivalent to about 100 ng of total RNA.
- transcription-mediated amplification was performed using a non-T7(+) primer having SEQ ID NO:18, a T7(-) promoter-primer having SEQ ID NO:30 and an AE- labeled probe having SEQ ID NO:1.
- transcription-mediated amplification was performed using a non-T7(+) primer having SEQ ID NO:48, a T7(-) promoter-primer having SEQ ID NO:49 and an AE-labeled probe having SEQ ID NO:50.
- the results shown in Table 10 indicate that the amplification and detection methods used here detected PSA-specific RNA in a prostate sample containing at least 10 fg of total RNA, in a breast sample containing at least 1 ng of total RNA, in a lung sample containing at least 100 ng of total RNA, and in samples containing at least 50 pg poly(A) RNA isolated from lymph node, kidney and small intestine.
- the assays detected this genetic marker RNA in prostate total RNA (at least 10 pg/sample), breast total RNA (at least 100 ng/sample), and lymph node poly(A) RNA (at least 500 pg/sample).
- the assays detected this genetic marker RNA in prostate total RNA (at least 10 pg/sample), breast total RNA (at least 1 ng/sample), lung (at least 1 ng/sample) and in poly(A) RNA isolated from lymph node (at least 50 pg/sample), kidney (at least 50 pg/sample) and small intestine (at least 5 pg/sample). None of the primer and probe combinations detected the genetic marker (PSA, hK2, PSMA) in RNA isolated from normal blood, and generally hK2 was detected in lower amounts in the other tissues relative to PSA or PSMA.
- Table 10 results also show that assays are quantitative, detecting RLU that are relatively proportional to the amount of target-specific RNA in the sample, up to the saturation point of detection (about 2.5 x 10 s RLU in these experiments). Thus standard titration experiments could be used to quantitatively determine the relative amounts of target RNA in a sample.
- EXAMPLE 10 Amplification and Detection of PSA, PSMA and hK2 Targets in Clinical Samples
- clinical samples peripheral blood drawn from patients having benign prostate hyperplasia (BPH) or prostate carcinoma (CaP), or blood drawn from normal controls
- BPH benign prostate hyperplasia
- CaP prostate carcinoma
- Total RNA was isolated from the clinical samples using standard guanidium isothiocyanate extraction methods (Sambrook, J. et al, 1989, Molecular Cloning, A Laboratory Manual, 2 nd ed. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY), pp. 7.37-7.57).
- each sample was assayed in duplicate using 500 ng for detection of PSA RNA, 500 ng for detection of hK2 RNA and 100 ng for detection of PSMA. Positive samples were those that produced detectable signal above a cutoff point of greater than 5,000 RLU for PSA detection, greater than 10,000 RLU for hK2 detection, and greater than 1 ,500 RLU for PSMA detection; negative samples were those that produced signal below the cutoff points for each target.
- the primers and probes were the same as used in the assays described in Example 9 (for PSA, SEQ ID Nos 18, 30 and 1 ; for PSMA, SEQ ID NOs 48, 49 and 50; and for hK2, SEQ ID NOs 46, 47 and 1).
- the results of these assays are shown in Table 11 , with the specimens grouped according to the disease state of the person from whom the sample was taken.
- the results of Table 11 show a generally positive correlation between the clinical status of the sample donor and the detection of PSA. Eleven of fourteen prostate cancer patients were positive, only one of ten BPH patients was positive and none of the normal controls was positive in the assay. Detection of hK2 also showed a positive correlation to prostate carcinoma status (7 of 14 were positive), although one normal control was positive and three BPH patients of ten were positive. Detection of PSMA showed no strong correlation with the clinical status of the donor, but for two of the three prostate cancer patients that tested positive for PSMA, they were also positive for PSA. One prostate cancer patient (specimen 10) was positive only for PSMA and two prostate cancer patients were positive only for hK2.
- the assays specifically detect the individual cancer genetic markers in RNA isolated from clinical samples and that each marker individually, or in combination with one or two other prostate-associated genetic cancer marker, is useful for detecting a molecular marker that correlates with prostate cancer.
- a molecular marker that correlates with prostate cancer For patients that show symptoms of prostate cancer but test negative with one genetic marker (e.g., PSA), another marker (e.g., hK2) may result in a positive signal, thus decreasing the potential of a false negative diagnosis that would result from reliance on results of only one marker.
- a positive result obtain for another genetic marker may be used to further add support to the positive diagnosis or to provide an indication of the extent of tumor growth.
- the results may support the diagnosis that metastasis has occurred.
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WO2002042463A2 (en) * | 2000-11-21 | 2002-05-30 | Diadexus, Inc. | Compositions and methods relating to prostate specific genes and proteins |
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EP1757705A3 (en) * | 2003-05-01 | 2007-08-01 | Veridex LLC | Intraoperative lymph node assay |
EP1953246A3 (en) * | 2003-05-01 | 2008-11-19 | Veridex, LLC | Intraoperative lymph node assay |
EP2199406A1 (en) * | 2003-05-01 | 2010-06-23 | Veridex, LLC | Intraoperative lymph node assay |
CN111518170A (en) * | 2020-05-09 | 2020-08-11 | 新乡医学院 | FRET-based PSA fluorescent probe, preparation method and application thereof |
Also Published As
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JP4495349B2 (en) | 2010-07-07 |
US7267956B2 (en) | 2007-09-11 |
EP1151142A2 (en) | 2001-11-07 |
WO2000044940A3 (en) | 2000-12-07 |
US20090035773A1 (en) | 2009-02-05 |
US20030104448A1 (en) | 2003-06-05 |
US20080026398A1 (en) | 2008-01-31 |
AU767587B2 (en) | 2003-11-20 |
CA2360073C (en) | 2011-01-18 |
JP2002535014A (en) | 2002-10-22 |
CA2360073A1 (en) | 2000-08-03 |
US20050118630A1 (en) | 2005-06-02 |
AU3475500A (en) | 2000-08-18 |
US6551778B1 (en) | 2003-04-22 |
US6811985B2 (en) | 2004-11-02 |
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