# Patent

## Title
PCA3, PCA3 genes, and methods of use

## Abstract

The present invention relates, in general, to a prostate-specific antigen, PCA3. In particular, the present invention relates to nucleic acid molecules coding for the PCA3 protein; purified PCA3 proteins and polypeptides; recombinant nucleic acid molecules; cells containing the recombinant nucleic acid molecules; antibodies having binding affinity specifically to PCA3 proteins and polypeptides; hybridomas containing the antibodies; nucleic acid probes for the detection of nucleic acids encoding PCA3 proteins; a method of detecting nucleic acids encoding PCA3 proteins or polypeptides in a sample; kits containing nucleic acid probes or antibodies; bioassays using the nucleic acid sequence, protein or antibodies of this invention to diagnose, assess or prognose a mammal afflicted with prostate cancer; therapeutic uses; and methods of preventing prostate cancer in an animal.

## Background
This application is a divisional application of U.S. patent application Ser. No. 09/402,713, filed Jun. 13, 2000 (allowed) and claims priority to international Application Number PCT/CA98/00346 filed Apr. 9, 1998, and to U.S. Provisional Application No. 60/041,836 filed Apr. 10, 1997. All documents above are herein incorporated by reference in their entirety.


STATEMENT REGARDING FEDERALLY-SPONSORED RESEARCH AND DEVELOPMENT
Statement under MPEP 310. The U.S. government has a paid-up license in this invention and the right in limited circumstances to require the patent owner to license others on reasonable terms as provided for by the terms of Grant No. CA 58236 awarded by the U.S. Department of Health and Human Services National Institutes of Health.
Part of the work performed during development of this invention utilized U.S. Government funds. The U.S. Government has certain rights in this invention.


FIELD OF THE INVENTION
The present invention relates, in general, to a prostate cancer antigen, PCA3. In particular, the present invention relates to nucleic acid molecules coding for the PCA3 protein; purified PCA3 proteins and polypeptides; recombinant nucleic acid molecules; cells containing the recombinant nucleic acid molecules; antibodies having binding affinity specifically to PCA3 proteins and polypeptides; hybridomas containing the antibodies; nucleic acid probes for the detection of nucleic acids encoding PCA3 proteins; a method of detecting nucleic acids encoding PCA3 proteins or polypeptides in a sample; kits containing nucleic acid probes or antibodies; bioassays using the nucleic acid sequence, protein or antibodies of this invention to diagnose, assess, or prognose a mammal afflicted with prostate cancer; therapeutic uses; and methods of preventing prostate cancer in an animal.
BACKGROUND OF THE INVENTION
Prostate cancer is the most commonly diagnosed malignancy and the second leading cause of cancer-related deaths in the western male population. When this carcinoma has locally or distantly spread, no curative therapy can be offered. Therefore, efforts to control the disease (i.e., to decrease prostate cancer mortality) have focused on increasing detection of the cancer while it is still locally confined and potentially curable. Studies aimed at the early detection of prostate cancer have demonstrated an appreciable increase in the detection of organ-confined potentially curable prostate cancers. However, it has not yet been demonstrated that the increased detection rate will decrease the prostate cancer-specific mortality rates. On the other hand, there is also no evidence that early diagnosis will decrease the mortality rates. Both in the United States and in Europe, discussions on the efficacy and acceptability of screening programs, the issue of overdiagnosis and overtreatment and the chances that early treatment will lead to reduced prostate cancer morbidity and mortality, are still ongoing and make early detection of prostate cancer a controversial issue (Schröder, Urology 46: 6270 (1995)).
Measurements of serum concentrations of prostatic marker enzymes have recognized value in the clinical detection, diagnosis and management of prostate cancer. The two most widely used prostatic marker enzymes are prostatic acid phosphatase (PAP) and prostate-specific antigen (PSA). Normally, both enzymes are secreted from the prostatic epithelial cells into the seminal fluid, but in patients with prostatic disease they leak into the circulation, where they can be detected by means of immunological assays (Armbruster, Clin. Che. 39: 181-95 (1993)).
Prostatic acid phosphatase, one of the earliest serum markers for prostate, has an as yet undetermined function and is one of the most predominant protein components in human prostatic secretions. The use of PAP as a marker for prostatic tumors is complicated by the reported structural similarities between the prostate-specific acid phosphatase and the lysosomal acid phosphatase occurring in all tissues. Furthermore, there is a tendency towards lower PAP mRNA and protein levels in prostate cancer in comparison with benign prostatic hyperplasia (BPH). In recent years, PAP measurements were superseded by serum PSA measurements in the clinical management of prostate cancer.
Prostate-specific antigen was identified by several groups in the 1970's as a prostate-specific protein from the seminal fluid. In 1979, it was purified as an antigen from prostate cancer tissue. Further research showed that PSA is produced exclusively by the columnar epithelial cells of the prostate and periuretural glands. Normal prostate epithelium and benign hyperplastic tissue actually produce more PSA mRNA and protein than does prostate cancer tissue. Furthermore, it was shown that loss of differentiation of prostatic carcinomas is associated with a decrease in the level of intraprostatic PSA.
Abnormalities in prostate architecture occurring as a result of prostatic disease lead to an increased leakage of PSA (and PAP) into the serum and make serum PSA measurements a marker for prostate cancer. Despite the fact that early studies have indicated that diagnostic PSA testing would be hampered by the fact that it lacked specificity in differentiating between BPH and prostate cancer, PSA testing was introduced in 1986 and revolutionized the management of patients with prostate cancer. Increased knowledge on the organ specificity of PSA and the relationship of elevated serum PSA levels to prostate disease as well as improvement of biopsy techniques and histological evaluation, led to a appreciation of the clinical value of PSA testing, a utility not yet achieved by any other (prostate) tumor marker. Cloning of the gene that encodes PSA revealed that it is a member of the human kallikrein gene family and resulted in the development of new approaches to the use of PSA as a marker: the very sensitive reverse transcriptaske polymerase chain reaction (RT-PCR) method is used to detect extremely small numbers of malignant prostate cells in blood samples from prostate cancer patients and might provide a sensitive tool to identify patients with micrometastatic disease (Moreno et al., Cancer Res. 52: 6110-12 (1992); and Katz et al, Urology 43: 765-75 (1994)).
Prostate-specific membrane antigen (PSM) was originally identified using an antibody developed by immunizing mice with the membrane fraction of LNCaP human prostatic adenocarcinoma cells. Like PAP and PSA, PSM can be detected in normal prostate, BPH and prostate cancer and is absent from most other tissues. Also for PSM, RT-PCR studies have been developed to detect circulating prostate cancer cells, however, further investigations are required to establish the usefulness of PSM as marker for prostatic cancer.
In summary, PSA is currently recognized as the premier marker for prostatic cancer, being useful for screening selected populations of patients with symptoms indicative of prostate cancer and for monitoring patients after therapy, especially after surgical prostatectomy (measurable levels of PSA indicate residual disease or metastasis and increasing PSA concentrations indicate recurrent disease). The significant weaknesses of PSA as a tumor marker are that (1) PSA is not able to always distinguish prostate cancer from BPH; and (2) that its expression decreases with loss of differentiation of carcinomas.
In view of the fact that advanced prostate cancer remains a life threatening disease reaching a very significant proportion of the male population, there remains a need for the development of new treatment and diagnostic modalities for (late stage) prostate cancer.
The present invention seeks to meet these and other needs.
The present description refers to a number of documents, the content of which is herein incorporated by reference.
SUMMARY OF THE INVENTION
The invention provides, in general, isolated nucleic acid molecules coding for PCA3 or fragments thereof.
The invention further provides purified polypeptides encoding PCA3 or an epitope binding portion thereof.
The invention also provides nucleic acids for the specific detection of the presence of nucleic acids encoding PCA3 proteins or polypeptides in a sample.
The invention further provides a method of detecting nucleic acid encoding PCA3 in a sample.
The invention also provides a kit for detecting the presence of nucleic acid encoding PCA3 in a sample.
The invention further provides a recombinant nucleic acid molecule comprising, 5′ to 3′, a promoter effective to initiate transcription in a host cell and the above-described isolated nucleic acid molecule.
The invention also provides a recombinant nucleic acid molecule comprising a vector and the above-described isolated nucleic acid molecule.
The invention further provides an antisense PCA3 nucleic acid molecule.
The invention also provides a cell that contains the above-described recombinant nucleic acid molecule.
The invention further provides a non-human organism that contains the above-described recombinant nucleic acid molecule.
The invention also provides an antibody having binding affinity specifically to PCA3 or an epitope-bearing portion thereof.
The invention further provides a method of detecting PCA3 in a sample.
The invention also provides a method of measuring the amount of PCA3 in a sample.
The invention in addition provides immunogenic reagents to induce protection against PCA3-expressing prostate cancer cells. Preferably, such immunogenic reagents are polypeptides encoding PCA3, an antigenic portion thereof, fusion proteins encoding PCA3 or fusion protein encoding antigenic portions of PCA3. In such an embodiment, these immunogenic reagents would function as vaccine agents.
The invention further provides a method of detecting antibodies having binding affinity specifically to PCA3.
The invention further provides a diagnostic kit comprising a first container means containing the above-described antibody, and a second container means containing a conjugate comprising a binding partner of the monoclonal antibody and a label.
The invention also provides a hybridoma which produces the above-described monoclonal antibody.
The invention further provides diagnostic methods for human disease, in particular, prostate cancer. Preferably, a method of diagnosing the presence or predisposition to develop prostate cancer in a patient is provided herein.
The invention also provides methods for therapeutic uses involving all or part of (1) a nucleic acid sequence encoding PCA3, (2) antisense PCA3 nucleic acid molecules, (2) PCA3 protein, or (4) PCA3 antibodies.
Further objects and advantages of the present invention will be clear from the description that follows.
Definitions
In the description that follows, a number of terms used in recombinant DNA (rDNA) technology are extensively utilized. In order to provide a clear and consistent understanding of the specification and claims, including the scope to be given such terms, the following definitions are provided.
Isolated Nucleic Acid Molecule. An “isolated nucleic acid molecule”, as is generally understood and used herein, refers to a polymer of nucleotides, and includes but should not be limited to DNA and RNA. The “isolated” nucleic acid molecule is purified from its natural in vivo state.
Recombinant DNA. Any DNA molecule formed by joining DNA segments from different sources and produced using recombinant DNA technology (aka. molecular genetic engineering).
DNA Segment. A DNA segment, as is generally understood and used herein, refers to a molecule comprising a linear stretch of nucleotides wherein the nucleotides are present in a sequence that can encode, through the genetic code, a molecule comprising a linear sequence of amino acid residues that is referred to as a protein, a protein fragment or a polypeptide.
Gene. A DNA sequence related to a single polypeptide chain or protein, and as used herein includes the 5′ and 3′ untranslated ends. The polypeptide can be encoded by a full-length sequence or any portion of the coding sequence, so long as the functional activity of the protein is retained.
Complementary DNA (cDNA). Recombinant nucleic acid molecules synthesized by reverse transcription of messenger RNA (“mRNA”).
Structural Gene. A DNA sequence that is transcribed into mRNA that is then translated into a sequence of amino acids characteristic of a specific polypeptide.
Restriction Endonuclease. A restriction endonuclease (also restriction enzyme) is an enzyme that has the capacity to recognize a specific base sequence (usually 4, 5, or 6 base pairs in length) in a DNA molecule, and to cleave the DNA molecule at every place where this sequence appears. For example, EcoRI recognizes the double-stranded palindromic base sequence 5′-GAATTC-3′/3′-CTTAAG-5′.
Restriction Fragment. The DNA molecules produced by digestion with a restriction endonuclease are referred to as restriction fragments. Any given genome can be digested by a particular restriction endonuclease into a discrete set of restriction fragments.
Agarose Gel Electrophoresis. To detect a polymorphism in the length of restriction fragments, an analytical method for fractionating double-stranded DNA molecules on the basis of size is required. The most commonly used technique (though not the only one) for achieving such a fractionation is agarose gel electrophoresis. The principle of this method is that DNA molecules migrate through the gel as though it were a sieve that retards the movement of the largest molecules to the greatest extent and the movement of the smallest molecules to the least extent. Note that the smaller the DNA fragment, the greater the mobility under electrophoresis in the agarose gel.
The DNA fragments fractionated by agarose gel electrophoresis can be visualized directly by a staining procedure if the number of fragments included in the pattern is small. The DNA fragments of genomes can be visualized successfully. However, most genomes, including the human genome, contain far too many DNA sequences to produce a simple pattern of restriction fragments. For example, the human genome is digested into approximately 1,000,000 different DNA fragments by EcoRI. In order to visualize a small subset of these fragments, a methodology referred to as the Southern hybridization procedure can be applied.
Southern Transfer Procedure. The purpose of the Southern transfer procedure (also referred to as blotting) is to physically transfer DNA fractionated by agarose gel electrophoresis onto a nitrocellulose filter paper or another appropriate surface or method, while retaining the relative positions of DNA fragments resulting from the fractionation procedure. The methodology used to accomplish the transfer from agarose gel to nitrocellulose involves drawing the DNA from the gel into the nitrocellulose paper by capillary action.
Nucleic Acid Hybridization. Nucleic acid hybridization depends on the principle that two single-stranded nucleic acid molecules that have complementary base sequences will reform the thermodynamically favored double-stranded structure if they are mixed under the proper conditions. The double-stranded structure will be formed between two complementary single-stranded nucleic acids even if one is immobilized on a nitrocellulose filter. In the Southern hybridization procedure, the latter situation occurs. As noted previously, the DNA of the individual to be tested is digested with a restriction endonuclease, fractionated by agarose gel electrophoresis, converted to the single-stranded form, and transferred to nitrocellulose paper, making it available for reannealing to the hybridization probe. Examples of hybridization conditions can be found in Ausubel, F. M. et al., Current protocols in Molecular Biology, John Wily & Sons, Inc., New York, N.Y. (1989). A nitrocellulose filter is incubated overnight at 68° C. with labeled probe in a solution containing 50% formamide, high salt (either 5×SSC[20×:3M NaCl/0.3M trisodium citrate] or 5×SSPE [20×:3.6M NaCl/0.2M NaH2PO4/0.02M EDTA, pH 7.7]), 5× Denhardt's solution, 1% SDS, and 100 μg/ml denatured salmon sperm DNA. This is followed by several washes in 0.2×SSC/0.1% SDS at a temperature selected based on the desired stringency: room temperature (low stringency), 42° C. (moderate stringency) or 68° C. (high stringency). The temperature selected is determined based on the melting temperature (Tm) of the DNA hybrid.
Hybridization Probe. To visualize a particular DNA sequence in the Southern hybridization procedure, a labeled DNA molecule or hybridization probe is reacted to the fractionated DNA bound to the nitrocellulose filter. The areas on the filter that carry DNA sequences complementary to the labeled DNA probe become labeled themselves as a consequence of the reannealing reaction. The areas of the filter that exhibit such labeling are visualized. The hybridization probe is generally produced by molecular cloning of a specific DNA sequence.
Oligonucleotide or Oligomer. A molecule comprised of two or more deoxyribonucleotides or ribonucleotides, preferably more than three. Its exact size will depend on many factors, which in turn depend on the ultimate function or use of the oligonucleotide. An oligonucleotide can be derived synthetically or by cloning.
Sequence Amplification. A method for generating large amounts of a target sequence. In general, one or more amplification primers are annealed to a nucleic acid sequence. Using appropriate enzymes, sequences found adjacent to, or in between the primers are amplified.
Amplification Primer. An oligonucleotide which is capable of annealing adjacent to a target sequence and serving as an initiation point for DNA synthesis when placed under conditions in which synthesis of a primer extension product which is complementary to a nucleic acid strand is initiated.
Antisense nucleic acid molecule. An “antisense nucleic acid molecule” refers herein to a molecule capable of forming a stable duplex or triplex with a portion of its targeted nucleic acid sequence (DNA or RNA). The use of antisense nucleic acid molecules and the design and modification of such molecules is well known in the art as described for example in WO 96/32966, WO 96/11266, WO 94/15646, WO 93/08845, and U.S. Pat. No. 5,593,974. Antisense nucleic acid molecules according to the present invention can be derived from the nucleic acid sequences of the present invention and modified in accordance to well known methods. For example, some antisense molecules can be designed to be more resistant to degradation, to increase their affinity to their targeted sequence, to affect their transport to chosen cell types or cell compartments, and/or to enhance their lipid solubility by using nucleotide analogs and/or substituting chosen chemical fragments thereof, as commonly known in the art.
Vector. A plasmid or phage DNA or other DNA sequence into which DNA can be inserted to be cloned. The vector can replicate autonomously in a host cell, and can be further characterized by one or a small number of endonuclease recognition sites at which such DNA sequences can be cut in a determinable fashion and into which DNA can be inserted. The vector can further contain a marker suitable for use in the identification of cells transformed with the vector. Markers, for example, are tetracycline resistance or ampicillin resistance. The words “cloning vehicle” are sometimes used for “vector.”
Expression. Expression is the process by which a structural gene produces a polypeptide. It involves transcription of the gene into mRNA, and the translation of such mRNA into polypeptide(s).
Expression Vector. A vector or vehicle similar to a cloning vector but which is capable of expressing a gene which has been cloned into it, after transformation into a host. The cloned gene is usually placed under the control of (i.e., operably linked to) certain control sequences such as promoter sequences.
Expression control sequences will vary depending on whether the vector is designed to express the operably linked gene in a prokaryotic or eukaryotic host and can additionally contain transcriptional elements such as enhancer elements, termination sequences, tissue-specificity elements, and/or translational initiation and termination sites.
Functional Derivative. A “functional derivative” of a sequence, either protein or nucleic acid, is a molecule that possesses a biological activity (either functional or structural) that is substantially similar to a biological activity of the protein or nucleic acid sequence. A functional derivative of a protein can contain post-translational modifications such as covalently linked carbohydrate, depending on the necessity of such modifications for the performance of a specific function. The term “functional derivative” is intended to include the “fragments,” “segments,” “variants,” “analogs,” or “chemical derivatives” of a molecule.
As used herein, a molecule is said to be a “chemical derivative” of another molecule when it contains additional chemical moieties not normally a part of the molecule. Such moieties can improve the molecule's solubility, absorption, biological half life, and the like. The moieties can alternatively decrease the toxicity of the molecule, eliminate or attenuate any undesirable side effect of the molecule, and the like. Moieties capable of mediating such effects are disclosed in Remington's Pharmaceutical Sciences (1980). Procedures for coupling such moieties to a molecule are well known in the art.
Variant. A “variant” of a protein or nucleic acid is meant to refer to a molecule substantially similar in structure and biological activity to either the protein or nucleic acid. Thus, provided that two molecules possess a common activity and can substitute for each other, they are considered variants as that term is used herein even if the composition or secondary, tertiary, or quaternary structure of one of the molecules is not identical to that found in the other, or if the amino acid or nucleotide sequence is not identical.
Allele. An “allele” is an alternative form of a gene occupying a given locus on the chromosome.
Mutation. A “mutation” is any detectable change in the genetic material which can be transmitted to daughter cells and possibly even to succeeding generations giving rise to mutant cells or mutant individuals. If the descendants of a mutant cell give rise only to somatic cells in multicellular organisms, a mutant spot or area of cells arises. Mutations in the germ line of sexually reproducing organisms can be transmitted by the gametes to the next generation resulting in an individual with the new mutant condition in both its somatic and germ cells. A mutation can be any (or a combination of detectable, unnatural change affecting the chemical or physical constitution, mutability, replication, phenotypic function, or recombination of one or more deoxyribonucleotides; nucleotides can be added, deleted, substituted for, inverted, or transposed to new positions with and without inversion. Mutations can occur spontaneously and can be induced experimentally by application of mutagens. A mutant variation of a nucleic acid molecule results from a mutation. A mutant polypeptide can result from a mutant nucleic acid molecule.
Species. A “species” is a group of actually or potentially interbreeding natural populations. A species variation within a nucleic acid molecule or protein is a change in the nucleic acid or amino acid sequence that occurs among species and can be determined by DNA sequencing of the molecule in question.
Polyacrylamide Gel Electrophoresis (PAGE). The most commonly used technique (though not the only one) for achieving a fractionation of polypeptides on the basis of size is polyacrylamide gel electrophoresis. The principle of this method is that polypeptide molecules migrate through the gel as though it were a sieve that retards the movement of the largest molecules to the greatest extent and the movement of the smallest molecules to the least extent. Note that the smaller the polypeptide fragment, the greater the mobility under electrophoresis in the polyacrylamide gel. Both before and during electrophoresis, the polypeptides typically are continuously exposed to the detergent sodium dodecyl sulfate (SDS), under which conditions the polypeptides are denatured. Native gels are run in the absence of SDS. The polypeptides fractionated by polyacrylamide gel electrophoresis can be visualized directly by a staining procedure if the number of polypeptide components is small.
Western Transfer Procedure. The purpose of the Western transfer procedure (also referred to as blotting) is to physically transfer polypeptides fractionated by polyacrylamide gel electrophoresis onto a nitrocellulose filter paper or another appropriate surface or method, while retaining the relative positions of polypeptides resulting from the fractionation procedure. The blot is then probed with an antibody that specifically binds to the polypeptide of interest.
Purified. A “purified” protein or nucleic acid is a protein or nucleic acid that has been separated from a cellular component. “Purified” proteins or nucleic acids have been purified to a level of purity not found in nature.
Substantially Pure. A “substantially pure” protein or nucleic acid is a protein or nucleic acid preparation that is lacking in all other cellular components.



BRIEF DESCRIPTION OF THE DRAWINGS
Having thus generally described the invention, reference will now be made to the accompanying drawings, showing by way of illustration a preferred embodiment thereof, and in which:
FIG. 1 shows the genomic structure of the PCA3 gene.
FIG. 2A-J, (A) a PCA3 cDNA structure; (B)-(J) a PCA3 nucleotide and amino acid cDNA sequence (SEQ ID NOs:1 and 2).
FIG. 3 is a schematic representation comparing cDNA clones pMB9 and λDD3.6.
FIG. 4 shows the location of a transcription start site (TSS) of PCA3. The transcription start site was determined by primer extension (PB), S1-nuclease mapping (S1), and 5′ Rapid Amplification of cDNA Ends (RACE) assays. The sequence in FIG. 4 (SEQ ID NO: 9) is as set forth between nucleotides 1 and 120 of SEQ ID NO:6 with a “g” nucleotide and a “gt” dinucleotide at the 5′ and 3′ ends respectively.
FIG. 5A-F (A) a PCA3 cDNA structure; (B)-(F) a PCA3 nucleotide and amino acid cDNA sequence (SEQ ID NOs:6 and 7); putative poly-adenylation signals are underlined.



Other objects, advantages and features of the present invention will become more apparent upon reading of the following non-restrictive description of preferred embodiments with reference to the accompanying drawings which are exemplary and should not be interpreted as limiting the scope of the present invention.
DESCRIPTION OF THE PREFERRED EMBODIMENT
For purposes of clarity of disclosure, and not by way of limitation, the detailed description of the invention is divided into the following subsections:

    I. Isolated Nucleic Acid Molecules Coding for PCA3 Polypeptides.
    II. Purified PCA3 Polypeptides.
    III. A Nucleic Acid for the Specific Detection of PCA3 Nucleic Acid.
    IV. A Method of Detecting the Presence of PCA3 Nucleic Acid in a Sample.
    V. A Kit for Detecting the Presence of PCA3 Nucleic Acid in a Sample.
    VI. DNA Constructs Comprising a PCA3 Nucleic Acid Molecule and Cells Containing These Constructs.
    VII. An Antibody Having Binding Affinity to a PCA3 Polypeptide and a Hybridoma Containing the Antibody.
    VIII. A Method of Detecting a PCA3 Polypeptide or Antibody in a Sample.
    IX. A Diagnostic Kit Comprising a PCA3 Protein or Antibody.
    X. Diagnostic Screening.
    XI. Therapeutic Treatments.
    XII. Transgenic PCA3 Non-human Animals.

I. Isolated Nucleic Acid Molecules Coding for PCA3 Polypeptides



In one embodiment, the present invention relates to isolated (purified) PCA3 nucleic acid molecules. Preferably, the PCA3 nucleic acid molecule comprises a polynucleotide sequence at least 90% identical (more preferably, 95%, 96%, 97%, 98%, 99% or 100% identical) to a sequence selected from the group consisting of:
(a) a nucleotide sequence encoding a PCA3 polypeptide comprising the complete amino acid sequence in SEQ ID NO:2 or SEQ ID NO:7;
(b) a nucleotide sequence encoding a PCA3 polypeptide comprising the complete amino acid sequence encoded by the polynucleotide clone contained in the deposit at the Centraal voor Schimmelcultures as accession number CBS 682.97;
(c) a nucleotide sequence encoding a PCA3 polypeptide comprising the complete amino acid sequence encoded by the polynucleotide clone contained in the deposit at the Centraal voor Schimmelcultures as accession number CBS 100521; and
(d) a nucleotide sequence complementary to any of the nucleotide sequences in (a), (b), or (c).
pMB9 is a PCA3 cDNA clone which contains exons 1, 2, 3, 4a and 4b of the PCA3 gene. pMB9 was deposited at the Phabagen Collection, University of Utrecht, Padualaan 8, 3584 CH Utrecht (which is a division of the Centraalbureau voor Schimmelcultures, Oosterstrattl, Postbus 273, 3740 AG Baarn) under the regulations of the Budapest Treaty on Apr. 10, 1997 as accession number CBS 682.97.
λDD3.6 is a PCA3 cDNA clone which contains exons 3, 4a, 4b, 4c, and 4d. λDD3.6 was deposited at the Phabagen Collection, University of Utrecht, Padualaan 8, 3584 CH Utrecht (which is a division of the Centraalbureau voor Schimmelcultures, Oosterstratt1, Postbus 273, 3740 AG Baam) under the regulations of the Budapest Treaty on Mar. 27, 1998 as accession number CBS 100521.
In one preferred embodiment, the isolated nucleic acid molecule comprises a PCA3 nucleotide sequence with greater than 90% identity or similarity to the nucleotide sequence present in SEQ ID NO:1 (preferably greater than 95%, 96%, 97%, 98%, 99% or 100%). In another preferred embodiment, the isolated nucleic acid molecule comprises the PCA3 coding sequence present in SEQ ID NO:1. In another embodiment, the isolated nucleic acid molecule encodes the PCA3 amino acid sequence present in SEQ ID NO:2 or SEQ ID NO:7. In yet another embodiment, the isolated nucleic acid molecule comprises a PCA3 nucleotide sequence with greater than 90% identity or similarity to the nucleotide sequence present in SEQ ID NO:6 (preferably greater than 95%, 96%, 97%, 98%, 99% or 100%). In another preferred embodiment, the isolated nucleic acid molecule comprises the PCA3 coding sequence present in SEQ ID NO:6.
Also included within the scope of this invention are isolated nucleic acids comprising cDNA splice variants of PCA3 or polynucleotide sequences which are at least 90% identical thereto, preferably at least 95% identical thereto. In view of the fact that virtually all combinations of exons are possible, non-limiting examples of such splice variants include isolated PCA3 nucleic acids comprising exons 1, 2, 3, 4a and 4b (SEQ ID NO:1); exons 1, 3, 4a, 4b, and 4c (SEQ ID NO:3 and region 4c which is contiguous to region 4b, see FIG. 1); exons 1, 3, 4a, 4b, 4c, and 4d (SEQ ID NO:3 and region 4c which is contiguous to region 4b and region 4d which is contiguous to region 4c, see FIG. 1); exons 1, 3, 4a, and 4b (SEQ ID NO:3); exons 1, 3, and 4a (SEQ ID NO:4); exons 1, 2, 3, 4a, 4b, 4c, and 4d (SEQ ID NO:6) Preferably, the PCA3 nucleic acid molecule comprises a polynucleotide sequence at least 90% identical (more preferably, 95%, 96%, 97%, 98%, 99% or 100% identical) to one of the above-described splice variants.
Also included within the scope of this invention are the functional equivalents of the herein-described isolated nucleic acid molecules and derivatives thereof. For example, the nucleic acid sequences depicted in SEQ ID NO:1 or SEQ ID NO:6 can be altered by substitutions, additions or deletions that provide for functionally equivalent molecules. Due to the degeneracy of nucleotide coding sequences, other DNA sequences which encode substantially the same amino acid sequence as depicted in SEQ ID NO:2 and SEQ ID NO:7 can be used in the practice of the present invention. These include but are not limited to nucleotide sequences comprising all or portions of PCA3 nucleic acid depicted in SEQ ID NO:1, 3, 4 or 6, which are altered by the substitution of different codons that encode a functionally equivalent amino acid residue within the sequence.
In addition, the nucleic acid sequence can comprise a nucleotide sequence which results from the addition, deletion or substitution of at least one nucleotide to the 5′-end and/or the 3′-end of the nucleic acid formula shown in SEQ ID NO:1, 3, 4, or 6 or a derivative thereof. Any nucleotide or polynucleotide can be used in this regard, provided that its addition, deletion or substitution does not substantially alter the amino acid sequence of SEQ ID NO:2, or SEQ ID NO:7 which is encoded by the nucleotide sequence. Moreover, the nucleic acid molecule of the present invention can, as necessary, have restriction endonuclease recognition sites added to its 5′-end and/or 3′-end. All variations of the nucleotide sequence of the PCA3 nucleotide coding sequence and fragments thereof permitted by the genetic code are, therefore, included in this invention.
Further, it is possible to delete codons or to substitute one or more codons by codons other than degenerate codons to produce a structurally modified polypeptide, but one which has substantially the same utility or activity of the polypeptide produced by the unmodified nucleic acid molecule. As recognized in the art, the two polypeptides are functionally equivalent, as are the two nucleic acid molecules which give rise to their production, even though the differences between the nucleic acid molecules are not related to degeneracy of the genetic code.
A. Isolation of Nucleic Acid
In one aspect of the present invention, isolated nucleic acid molecules coding for polypeptides having amino acid sequences corresponding to PCA3 are provided. In particular, the nucleic acid molecule can be isolated from a biological sample containing PCA3 RNA or DNA.
The nucleic acid molecule can be isolated from a biological sample containing PCA3 RNA using the techniques of cDNA cloning and subtractive hybridization. The nucleic acid molecule can also be isolated from a cDNA library using a homologous probe.
The nucleic acid molecule can be isolated from a biological sample containing genomic DNA or from a genomic library. Suitable biological samples include, but are not limited to, whole organisms, organs, tissues, blood and cells. The method of obtaining the biological sample will vary depending upon the nature of the sample.
One skilled in the art will realize that genomes can be subject to slight allelic variations between individuals. Therefore, the isolated nucleic acid molecule is also intended to include allelic variations, so long as the sequence is a functional derivative of the PCA3 coding sequence. When a PCA3 allele does not encode the identical sequence to that found in SEQ ID NO:1 or 6, it can be isolated and identified as PCA3 using the same techniques used herein, and especially PCR techniques to amplify the appropriate gene with primers based on the sequences disclosed herein.
One skilled in the art will realize that organisms other than humans will also contain PCA3 genes (for example, eukaryotes; more specifically, mammals, birds, fish, and plants; more specifically, gorillas, rhesus monkeys, and chimpanzees). The invention is intended to include, but not be limited to, PCA3 nucleic acid molecules isolated from the above-described organisms.
B. Synthesis of Nucleic Acid
Isolated nucleic acid molecules of the present invention are also meant to include those chemically synthesized. For example, a nucleic acid molecule with the nucleotide sequence which codes for the expression product of a PCA3 gene can be designed and, if necessary, divided into appropriate smaller fragments. Then an oligomer which corresponds to the nucleic acid molecule, or to each of the divided fragments, can be synthesized. Such synthetic oligonucleotides can be prepared, for example, by the triester method of Matteucci et al., J. Am. Chem. Soc. 103:3185-3191 (1981) or by using an automated DNA synthesizer.
An oligonucleotide can be derived synthetically or by cloning. If necessary, the 5′-ends of the oligomers can be phosphorylated using T4 polynucleotide kinase. Kinasing of single strands prior to annealing or for labeling can be achieved using an excess of the enzyme. If kinasing is for the labeling of probe, the ATP can contain high specific activity radioisotopes. Then, the DNA oligomer can be subjected to annealing and ligation with T4 ligase or the like.
II. Purified PCA3 Polypeptides
In another embodiment, the present invention relates to a purified polypeptide (preferably, substantially pure) having an amino acid sequence corresponding to PCA3, or a functional derivative thereof. In a preferred embodiment, the polypeptide has the amino acid sequence set forth in SEQ ID NO:2 or 7 or mutant or species variation thereof, or at least 80% identity or at least 90% similarity thereof (preferably, at least 90%, 95%, 96%, 97%, 98%, or 99% identity or at least 95%, 96%, 97%, 98%, or 99% similarity thereof, or at least 6 contiguous amino acids thereof (preferably, at least 10, 15, 20, 25, or 50 contiguous amino acids thereof).
In a preferred embodiment, the invention relates to PCA3 epitopes. The epitope of these polypeptides is an immunogenic or antigenic epitope. An immunogenic epitope is that part of the protein which elicits an antibody response when the whole protein is the immunogen. An antigenic epitope is a fragment of the protein which can elicit an antibody response. Methods of selecting antigenic epitope fragments are well known in the art. See, Sutcliffe et al., Science 219:660-666 (1983). Antigenic epitope-bearing peptides and polypeptides of the invention are useful to raise an immune response that specifically recognizes the polypeptides. Antigenic epitope-bearing peptides and polypeptides of the invention comprise at least 7 amino acids (preferably, 9, 10, 12, 15 or 20 amino acids) of the proteins of the invention. An example of a antigenic peptide is HTQEAQKEAQR (SEQ ID NO:5).
Amino acid sequence variants of PCA3 can be prepared by mutations in the DNA. Such variants include, for example, deletions from, or insertions or substitutions of, residues within the amino acid sequence shown in SEQ ID NO:2 or 7. Any combination of deletion, insertion, and substitution can also be made to arrive at the final construct, provided that the final construct possesses the desired activity.
While the site for introducing an amino acid sequence variation is predetermined, the mutation per se need not be predetermined. For example, to optimize the performance of a mutation at a given site, random mutagenesis can be conducted at the target codon or region and the expressed PCA3 variants screened for the optimal combination of desired activity. Techniques for making substitution mutations at predetermined sites in DNA having a known sequence are well known, for example, site-specific mutagenesis.
Preparation of a PCA3 variant in accordance herewith is preferably achieved by site-specific mutagenesis of DNA that encodes an earlier prepared variant or a nonvariant version of the protein. Site-specific mutagenesis allows the production of PCA3 variants through the use of specific oligonucleotide sequences that encode the DNA sequence of the desired mutation. In general, the technique of site-specific mutagenesis is well known in the art, as exemplified by publications such as Adelman et al., DNA 2:183 (1983) and Ausubel et al. “Current Protocols in Molecular Biology”, J. Wiley & Sons, NY, N.Y., 1996.
Amino acid sequence deletions generally range from about 1 to 30 residues, more preferably 1 to 10 residues, and typically are contiguous.
Amino acid sequence insertions include amino and/or carboxyl-terminal fusions of from one residue to polypeptides of essentially unrestricted length, as well as intrasequence insertions of single or multiple amino acid residues. Intrasequence insertions (i.e., insertions within the complete PCA3 sequence) can range generally from about 1 to 10 residues, more preferably 1 to 5.
The third group of variants are those in which at least one amino acid residue in the PCA3 molecule, and preferably, only one, has been removed and a different residue inserted in its place. Such substitutions preferably are made in accordance with the following Table 1 when it is desired to modulate finely the characteristics of PCA3.










TABLE 1







Original Residue
Exemplary Substitutions









Ala
gly; ser



Arg
lys



Asn
gln; his



Asp
glu



Cys
ser



Gln
asn



Glu
asp



Gly
ala; pro



His
asn; gln



Ile
leu; val



Leu
ile; val



Lys
arg; gln; glu



Met
leu; tyr; ile



Phe
met; leu; tyr



Ser
thr



Thr
ser



Trp
tyr



Tyr
trp; phe



Val
ile; leu










Substantial changes in functional or immunological identity are made by selecting substitutions that are less conservative than those in Table 1, i.e., selecting residues that differ more significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain. The substitutions that in general are expected are those in which (a) glycine and/or proline is substituted by another amino acid or is deleted or inserted; (b) a hydrophilic residue, e.g., seryl or threonyl, is substituted for (or by) a hydrophobic residue, e.g., leucyl, isoleucyl, phenylalanyl, valyl, or alanyl; (c) a cysteine residue is substituted for (or by) any other residue; (d) a residue having an electropositive side chain, e.g., lysyl, arginyl, or histidyl, is substituted for (or by) a residue having an electronegative charge, e.g., glutamyl or aspartyl; or (e) a residue having a bulky side chain, e.g., phenylalanine, is substituted for (or by) one not having such a side chain, e.g., glycine.
Some deletions and insertions, and substitutions are not expected to produce radical changes in the characteristics of PCA3. However, when it is difficult to predict the exact effect of the substitution, deletion, or insertion in advance of doing so, one skilled in the art will appreciate that the effect will be evaluated by routine screening assays. For example, a variant typically is made by site-specific mutagenesis of the native PCA3 encoding-nucleic acid, expression of the variant nucleic acid in recombinant cell culture, and, optionally, purification from the cell culture, for example, by immunoaffinity adsorption on a column (to absorb the variant by binding it to at least one remaining immune epitope). The activity of the cell lysate or purified PCA3 molecule variant is then screened in a suitable screening assay for the desired characteristic. For example, a change in the immunological character of the PCA3 molecule, such as affinity for a given antibody, is measured by a competitive type immunoassay. Changes in immunomodulation activity are measured by the appropriate assay. Modifications of such protein properties as redox or thermal stability, hydrophobicity, susceptibility to proteolytic degradation or the tendency to aggregate with carriers or into multimers are assayed by methods well known to the ordinarily skilled artisan.
A variety of methodologies known in the art can be utilized to obtain the peptide of the present invention. In one embodiment, the peptide is purified from tissues or cells which naturally produce the peptide. Alternatively, the above-described isolated nucleic acid fragments can be used to express the PCA3 protein in any organism. The samples of the present invention include cells, protein extracts or membrane extracts of cells, or biological fluids. The sample will vary based on the assay format, the detection method and the nature of the tissues, cells or extracts used as the sample.
Any organism can be used as a source for the peptide of the invention, as long as the source organism naturally contains such a peptide. As used herein, “source organism” refers to the original organism from which the amino acid sequence of the subunit is derived, regardless of the organism the subunit is expressed in and ultimately isolated from.
One skilled in the art can readily follow known methods for isolating proteins in order to obtain the peptide free of natural contaminants. These include, but are not limited to: immunochromotography, size-exclusion chromatography, HPLC, ion-exchange chromatography, and immuno-affinity chromatography.
In a preferred embodiment, the purification procedures comprise ion-exchange chromatography and size exclusion chromatography. Any one of a large number of ion-exchange resins known in the art can be employed, including for example, monoQ, sepharose Q, macro-prepQ, AG1-X2, or HQ. Examples of suitable size exclusion resins include, but are not limited to, Superdex 200, Superose 12, and Sephycryl 200. Elution can be achieved with aqueous solutions of potassium chloride or sodium chloride at concentrations ranging from 0.01M to 2.0M.
III. A Nucleic Acid for the Specific Detection of PCA3 Nucleic Acid
In another embodiment, the present invention relates to a nucleic acid for the specific detection of the presence of PCA3 nucleic acid in a sample comprising the above-described nucleic acid molecules or at least a fragment thereof which binds under stringent conditions to PCA3 nucleic acid.
In one prefered embodiment, the present invention relates to an isolated nucleic acid consisting of 10 to 1000 nucleotides (prefererably, 10 to 500, 10 to 100, 10 to 50, 10 to 35, 20 to 1000, 20 to 500, 20 to 100, 20 to 50, or 20 to 35) which hybridizes preferentially to RNA or DNA encoding PCA3 or to a PCA3 gene but not to RNA or DNA of which is not related to PCA3, wherein said nucleic acid probe is or is complementary to a nucleotide sequence consisting of at least 10 consecutive nucleotides (preferably, 15, 18, 20, 25, or 30) from the nucleic acid molecule comprising a polynucleotide sequence at least 90% identical to a sequence selected from the group consisting of:
(a) a nucleotide sequence encoding the PCA3 polypeptide comprising the complete amino acid sequence in SEQ ID NO:2 or 7;
(b) a nucleotide sequence encoding the PCA3 polypeptide comprising the complete amino acid sequence encoded by the polynucleotide clone contained in the deposit at the Centraal voor Schimmelcultures as accession number CBS 682.97, respectively;
(c) a nucleotide sequence encoding the PCA3 polypeptide comprising the complete amino acid sequence encoded by the polynucleotide clone contained in the deposit at the Centraal voor Schimmelcultures as accession number CBS 100521, respectively;
(d) a nucleotide sequence encoding the PCA3 gene comprising the nucleotide sequence in SEQ ID NO:1, 3, 4, or 6; (e) a nucleotide sequence encoding an exon of the PCA3 gene comprising nucleotides 1-98, 99-263, 264-446, 447-985 or 986-2037 as set forth in SEQ ID NO:1;
(f) a nucleotide sequence encoding an exon of the PCA3 gene comprising nucleotides 1-120,121-285,286-468,469-1007, 1008-2066, 2067-2622 or 2623-3582 as set forth in SEQ ID NO:6;
(g) a nucleotide sequence complementary to any of the nucleotide sequences in (a), (b), (c), (d), (e) or (f);
(h) a nucleotide sequence as previously described above.
Preferably, the nucleic acid does not specifically hybridize to nucleotides 511-985 of SEQ ID NO:1, to nucleotides 567-961 of SEQ ID NO:1, to nucleotides 533-1007 of SEQ ID NO:6, or to nucleotides 589-983 of SEQ ID NO:6.
Complementary sequences are also known as antisense nucleic acids when they comprise sequences which are complementary to the coding strand.
Examples of specific nucleic acid probes which can be used in the present invention are set forth in Table 2, below.







TABLE 2







NUCLEIC ACID PROBES










Size (no. of bases)
Nucleotides













Exon 1
98
1-98 of SEQ ID NO: 1


Exon 2
165
99-263 of SEQ ID NO: 1


Exon 3
183
264-446 of SEQ ID NO: 1


Exon 4a
539
447-985 of SEQ ID NO: 1


Exon 4b
1052
986-2037 of SEQ ID NO: 1


Probe 1
20
1-20 of SEQ ID NO: 1


Probe 2
30
1-30 of SEQ ID NO: 1


Probe 3
40
1-40 of SEQ ID NO: 1


Probe 4
20
381-400 of SEQ ID NO: 1


Probe 5
30
381-410 of SEQ ID NO: 1


Probe 6
20
401-420 of SEQ ID NO: 1


Probe 7
30
401-430 of SEQ ID NO: 1


Probe 8
20
511-530 of SEQ ID NO: 1


Probe 9
30
501-530 of SEQ ID NO: 1


Probe 10
20
77-98 of SEQ ID NO: 1


Probe 11
20
99-118 of SEQ ID NO: 1


Probe 12
20
244-263 of SEQ ID NO: 1


Probe 13
20
264-283 of SEQ ID NO: 1


Probe 14
20
427-446 of SEQ ID NO: 1


Probe 15
20
447-466 of SEQ ID NO: 1


Exon 1
120
1-120 of SEQ ID NO: 6


Exon 2
165
121-285 of SEQ ID NO: 6


Exon 3
183
286-468 of SEQ ID NO: 6


Exon 4a
539
469-1007 of SEQ ID NO: 6


Exon 4b
1059
1008-2066 of SEQ ID NO: 6


Exon 4c
556
2067-2622 of SEQ ID NO: 6


Exon 4d
960
2623-3582 of SEQ ID NO: 6









Of course, as will be understood by the person of ordinary skill, a multitude of additional probes can be designed from the same or other region of SEQ ID NO:1 as well as from SEQ ID NO:6 and other sequences of the present invention.
The nucleic acid probe can be used to probe an appropriate chromosomal or cDNA library by usual hybridization methods to obtain another nucleic acid molecule of the present invention. A chromosomal DNA or cDNA library can be prepared from appropriate cells according to recognized methods in the art (cf. Molecular Cloning: A Laboratory Manual, second edition, edited by Sambrook, Fritsch, & Maniatis, Cold Spring Harbor Laboratory, 1989).
In the alternative, chemical synthesis is carried out in order to obtain nucleic acid probes having nucleotide sequences which correspond to N-terminal and C-terminal portions of the PCA3 amino acid sequence. Thus, the synthesized nucleic acid probes can be used as primers in a polymerase chain reaction (PCR) carried out in accordance with recognized PCR techniques, essentially according to PCR Protocols, A Guide to Methods and Applications, edited by Michael et al., Academic Press, 1990, utilizing the appropriate chromosomal, cDNA or cell line library to obtain the fragment of the present invention.
One skilled in the art can readily design such probes based on the sequence disclosed herein using methods of computer alignment and sequence analysis known in the art (cf. Molecular Cloning: A Laboratory Manual, second edition, edited by Sambrook, Fritsch, & Maniatis, Cold Spring Harbor Laboratory, 1989).
The hybridization probes of the present invention can be labeled by standard labeling techniques such as with a radiolabel, enzyme label, fluorescent label, biotin-avidin label, chemiluminescence, and the like. After hybridization, the probes can be visualized using known methods.
The nucleic acid probes of the present invention include RNA, as well as DNA probes, such probes being generated using techniques known in the art.
In one embodiment of the above described method, a nucleic acid probe is immobilized on a solid support. Examples of such solid supports include, but are not limited to, plastics such as polycarbonate, complex carbohydrates such as agarose and sepharose, and acrylic resins, such as polyacrylamide and latex beads. Techniques for coupling nucleic acid probes to such solid supports are well known in the art.
The test samples suitable for nucleic acid probing methods of the present invention include, for example, cells or nucleic acid extracts of cells, or biological fluids. The sample used in the above-described methods will vary based on the assay format, the detection method and the nature of the tissues, cells or extracts to be assayed. Methods for preparing nucleic acid extracts of cells are well known in the art and can be readily adapted in order to obtain a sample which is compatible with the method utilized.
IV. A Method of Detecting the Presence of PCA3 Nucleic Acid in a Sample
In another embodiment, the present invention relates to a method of detecting the presence of PCA3 nucleic acid in a sample comprising a) contacting the sample with the above-described nucleic acid probe, under specific hybridization conditions such that hybridization occurs, and b) detecting the presence of the probe bound to the nucleic acid molecule. One skilled in the art would select the nucleic acid probe according to techniques known in the art as described above. Samples to be tested include but should not be limited to RNA or DNA samples from human tissue.
V. A Kit for Detecting the Presence of PCA3 Nucleic Acid in a Sample
In another embodiment, the present invention relates to a kit for detecting the presence of PCA3 nucleic acid in a sample comprising at least one container means having disposed therein the above-described nucleic acid probe. In a preferred embodiment, the kit further comprises other containers comprising one or more of the following: wash reagents and reagents capable of detecting the presence of bound nucleic acid probe. Examples of detection reagents include, but are not limited to radiolabelled probes, enzymatic labeled probes (horse radish peroxidase, alkaline phosphatase), and affinity labeled probes (biotin, avidin, or steptavidin).
In detail, a compartmentalized kit includes any kit in which reagents are contained in separate containers. Such containers include small glass containers, plastic containers or strips of plastic or paper. Such containers allow the efficient transfer of reagents from one compartment to another compartment such that the samples and reagents are not cross-contaminated and the agents or solutions of each container can be added in a quantitative fashion from one compartment to another. Such containers will include a container which will accept the test sample, a container which contains the probe or primers used in the assay, containers which contain wash reagents (such as phosphate buffered saline, Tris-buffers, and the like), and containers which contain the reagents used to detect the hybridized probe, bound antibody, amplified product, or the like.
One skilled in the art will readily recognize that the nucleic acid probes described in the present invention can readily be incorporated into one of the established kit formats which are well known in the art.
VI. DNA Constructs Comprising a PCA3 Nucleic Acid Molecule and Cells Containing These Constructs
In another embodiment, the present invention relates to a recombinant DNA molecule comprising, 5′ to 3′, a promoter effective to initiate transcription in a host cell and the above-described nucleic acid molecules. In another embodiment, the present invention relates to a recombinant DNA molecule comprising a vector and an above-described nucleic acid molecule.
In another embodiment, the present invention relates to a nucleic acid molecule comprising a transcriptional control region functional in a cell, a sequence complimentary to an RNA sequence encoding an amino acid sequence corresponding to the above-described polypeptide, and a transcriptional termination region functional in the cell.
Preferably, the above-described molecules are isolated and/or purified DNA molecules.
In another embodiment, the present invention relates to a cell or non-human organism that contains an above-described nucleic acid molecule.
In another embodiment, the peptide is purified from cells which have been altered to express the peptide.
As used herein, a cell is said to be “altered to express a desired peptide” when the cell, through genetic manipulation, is made to produce a protein which it normally does not produce or which the cell normally produces at low levels. One skilled in the art can readily adapt procedures for introducing and expressing either genomic, cDNA, or synthetic sequences into either eukaryotic or prokaryotic cells.
A nucleic acid molecule, such as DNA, is said to be “capable of expressing” a polypeptide if it contains nucleotide sequences which contain transcriptional and translational regulatory information and such sequences are “operably linked” to nucleotide sequences which encode the polypeptide. An operable linkage is a linkage in which the regulatory DNA sequences and the DNA sequence sought to be expressed are connected in such a way as to permit gene sequence expression. The precise nature of the regulatory regions needed for gene sequence expression can vary from organism to organism, but shall in general include a promoter region which, in prokaryotes, contains both the promoter (which directs the initiation of RNA transcription) as well as the DNA sequences which, when transcribed into RNA, will signal synthesis initiation. Such regions will normally include those 5′-non-coding sequences involved with initiation of transcription and translation, such as the TATA box, capping sequence, CMT sequence, and the like.
If desired, the non-coding region 3′ to the PCA3 coding sequence can be obtained by the above-described methods. This region can be retained for its transcriptional termination regulatory sequences, such as termination and polyadenylation. Thus, by retaining the 3′-region naturally contiguous to the DNA sequence encoding a PCA3 gene, the transcriptional termination signals can be provided. Where the transcriptional termination signals are not satisfactorily functional in the expression host cell, then a 3′ region functional in the host cell can be substituted.
Two DNA sequences (such as a promoter region sequence and a PCA3 coding sequence) are said to be operably linked if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter region sequence to direct the transcription of a PCA3 coding sequence, or (3) interfere with the ability of the PCA3 coding sequence to be transcribed by the promoter region sequence. Thus, a promoter region would be operably linked to a DNA sequence if the promoter were capable of effecting transcription of that DNA sequence.
The present invention encompasses the expression of the PCA3 coding sequence (or a functional derivative thereof in either prokaryotic or eukaryotic cells. Prokaryotic hosts are, generally, the most efficient and convenient for the production of recombinant proteins and, therefore, are preferred for the expression of the PCA3 coding sequence.
Prokaryotes most frequently are represented by various strains of E. coli. However, other microbial strains can also be used, including other bacterial strains. In prokaryotic systems, plasmid vectors that contain replication sites and control sequences derived from a species compatible with the host can be used. Examples of suitable plasmid vectors include pBR322, pUC18, pUC19, pUC118, pUC119 and the like; suitable phage or bacteriophage vectors include λgt10, λgt11 and the like; and suitable virus vectors include pMAM-neo, pKRC and the like. Preferably, the selected vector of the present invention has the capacity to replicate in the selected host cell.
Recognized prokaryotic hosts include bacteria such as E. coli, Bacillus, Streptomyces, Pseudomonas, Salmonella, Serratia, and the like. However, under such conditions, the peptide will not be glycosylated. The prokaryotic host must be compatible with the replicon and control sequences in the expression plasmid.
To express PCA3 in a prokaryotic cell, it is necessary to operably link the PCA3 coding sequence to a functional prokaryotic promoter. Such promoters can be either constitutive or, more preferably, regulatable (i.e., inducible or derepressible). Examples of constitutive promoters include the int promoter of bacteriophage λ, the bla promoter of the β-lactamase gene sequence of pBR322, and the CAT promoter of the chloramphenicol acetyl transferase gene sequence of pBR325, and the like. Examples of inducible prokaryotic promoters include the major right and left promoters of bacteriophage λ (PL and PR), the trp, recA, lacZ, lac, and gal promoters of E. coli, the α-amylase (Ulmanen et al., J. Bacteriol. 162:176-182 (1985)) and the ç-28-specific promoters of B. subtilis (Gilman et al., Gene sequence 32:11-20 (1984)), the promoters of the bacteriophages of Bacillus (Gryczan, In: The Molecular Biology of the Bacilli, Academic Press, Inc., NY (1982)), and Streptomyces promoters (Ward et al., Mol. Gen. Genet. 203:468-478 (1986)). Prokaryotic promoters are reviewed by Glick (J. Ind. Microbiol. 1:277-282 (1987)); Cenatiempo (Biochimie 68:505-516 (1986)); and Gottesman (Ann. Rev. Genet. 18:415-442 (1984)).
Proper expression in a prokaryotic cell also requires the presence of a ribosome binding site upstream of the gene sequence-encoding sequence. Such ribosome binding sites are disclosed, for example, by Gold et al. (Ann. Rev. Microbiol. 35:365-404 (1981)).
The selection of control sequences, expression vectors, transformation methods, and the like, are dependent on the type of host cell used to express the gene. As used herein, “cell”, “cell line”, and “cell culture” can be used interchangeably and all such designations include progeny. Thus, the words “transformants” or “transformed cells” include the primary subject cell and cultures derived therefrom, without regard to the number of transfers. It is also understood that all progeny can not be precisely identical in DNA content, due to deliberate or inadvertent mutations. However, as defined, mutant progeny have the same functionality as that of the originally transformed cell.
Host cells which can be used in the expression systems of the present invention are not strictly limited, provided that they are suitable for use in the expression of the PCA3 peptide of interest. Suitable hosts include eukaryotic cells.
Preferred eukaryotic hosts include, for example, yeast, fungi, insect cells, mammalian cells either in vivo, or in tissue culture. Preferred mammalian cells include HeLa cells, cells of fibroblast origin such as VERO or CHO-K1, or cells of lymphoid origin and their derivatives.
In addition, plant cells are also available as hosts, and control sequences compatible with plant cells are available, such as the cauliflower mosaic virus 35S and 19S, and nopaline synthase promoter and polyadenylation signal sequences.
Another preferred host is an insect cell, for example Drosophila larvae. Using insect cells as hosts, the Drosophila alcohol dehydrogenase promoter can be used, Rubin, Science 240:1453-1459 (1988). Alternatively, baculovirus vectors can be engineered to express large amounts of PCA3 in insect cells (Jasny, Science 238:1653 (1987); Miller et al., In: Genetic Engineering (1986), Setlow, J. K., et al., eds., Plenum, Vol. 8, pp. 277-297).
Different host cells have characteristic and specific mechanisms for the translational and post-translational processing and modification (e.g., glycosylation, cleavage) of proteins. Appropriate cell lines or host systems can be chosen to ensure the desired modification and processing of the foreign protein expressed.
Any of a series of yeast gene sequence expression systems can be utilized which incorporate promoter and termination elements from the actively expressed gene sequences coding for glycolytic enzymes. These enzymes are produced in large quantities when yeast are grown in mediums rich in glucose. Known glycolytic gene sequences can also provide very efficient transcriptional control signals.
Yeast provides substantial advantages in that it can also carry out post-translational peptide modifications. A number of recombinant DNA strategies exist which utilize strong promoter sequences and high copy number of plasmids which can be utilized for production of the desired proteins in yeast. Yeast recognizes leader sequences on cloned mammalian gene sequence products and secretes peptides bearing leader sequences (i.e., pre-peptides). For a mammalian host, several possible vector systems are available for the expression of PCA3.
A wide variety of transcriptional and translational regulatory sequences can be employed, depending upon the nature of the host. The transcriptional and translational regulatory signals can be derived from viral sources, such as adenovirus, bovine papilloma virus, simian virus, or the like, where the regulatory signals are associated with a particular gene sequence which has a high level of expression. Alternatively, promoters from mammalian expression products, such as actin, collagen, myosin, and the like, can be employed. Transcriptional initiation regulatory signals can be selected which allow for repression or activation, so that expression of the gene sequences can be modulated. Of interest are regulatory signals which are temperature-sensitive so that by varying the temperature, expression can be repressed or initiated, or are subject to chemical (such as metabolite) regulation.
As discussed above, expression of PCA3 in eukaryotic hosts requires the use of eukaryotic regulatory regions. Such regions will, in general, include a promoter region sufficient to direct the initiation of RNA synthesis. Preferred eukaryotic promoters include, for example, the promoter of the mouse metallothionein I gene sequence (Hamer et al., J. Mol. Appl. Gen. 1:273-288 (1982)); the TK promoter of Herpes virus (McKnight, Cell 31:355-365 (1982)); the SV40 early promoter (Benoist et al., Nature (London) 290:304-310 (1981)); the yeast gal4 gene sequence promoter (Johnston et al., Proc. Natl. Acad. Sci. (USA) 79:6971-6975 (1982); Silver et al., Proc. Natl. Acad. Sci. (USA) 81:5951-5955 (1984)) and the CMV immediate-early gene promoter (Thomsen et al, Proc. Natl. Acad. Sci (USA) 81:659-663 (1984).
As is widely known, translation of eukaryotic mRNA is initiated at the codon which encodes the first methionine. For this reason, it is preferable to ensure that the linkage between a eukaryotic promoter and a PCA3 coding sequence does not contain any intervening codons which are capable of encoding a methionine (i.e., AUG). The presence of such codons results either in a formation of a fusion protein (if the AUG codon is in the same reading frame as the PCA3 coding sequence) or a frame-shift mutation (if the AUG codon is not in the same reading frame as the PCA3 coding sequence).
A PCA3 nucleic acid molecule and an operably linked promoter can be introduced into a recipient prokaryotic or eukaryotic cell either as a non-replicating DNA (or RNA) molecule, which can either be a linear molecule or, more preferably, a closed covalent circular molecule. Since such molecules are incapable of autonomous replication, the expression of the gene can occur through the transient expression of the introduced sequence. Alternatively, permanent expression can occur through the integration of the introduced DNA sequence into the host chromosome.
In one embodiment, a vector is employed which is capable of integrating the desired gene sequences into the host cell chromosome. Cells which have stably integrated the introduced DNA into their chromosomes can be selected by also introducing one or more markers which allow for selection of host cells which contain the expression vector. The marker can provide for prototrophy to an auxotrophic host, biocide resistance, e.g., antibiotics, or heavy metals, such as copper, or the like. The selectable marker gene sequence can either be directly linked to the DNA gene sequences to be expressed, or introduced into the same cell by co-transfection. Additional elements can also be needed for optimal synthesis of single chain binding protein mRNA. These elements can include splice signals, as well as transcription promoters, enhancer signal sequences, and termination signals. cDNA expression vectors incorporating such elements include those described by Okayama, Molec. Cell. Biol. 3:280 (1983).
In a preferred embodiment, the introduced nucleic acid molecule will be incorporated into a plasmid or viral vector capable of autonomous replication in the recipient host. Any of a wide variety of vectors can be employed for this purpose. Factors of importance in selecting a particular plasmid or viral vector include: the ease with which recipient cells that contain the vector can be recognized and selected from those recipient cells which do not contain the vector; the number of copies of the vector which are desired in a particular host; and whether it is desirable to be able to “shuttle” the vector between host cells of different species. Preferred prokaryotic vectors include plasmids such as those capable of replication in E. coli (such as, for example, pBR322, ColE1, pSC101, pACYC 184, nVX. Such plasmids are, for example, disclosed by Sambrook (cf. Molecular Cloning: A Laboratory Manual, second edition, edited by Sambrook, Fritsch, & Maniatis, Cold Spring Harbor Laboratory, 1989). Bacillus plasmids include pC194, pC221, pT127, and the like. Such plasmids are disclosed by Gryczan (In: The Molecular Biology of the Bacilli, Academic Press, NY (1982), pp. 307-329). Suitable Streptomyces plasmids include pIJ101 (Kendall et al., J. Bacteriol. 169:4177-4183 (1987)), and streptomyces bacteriophages such as φC31 (Chater et al, In: Sixth International Symposium on Actinomycetales Biology, Akademiai Kaido, Budapest, Hungary (1986), pp. 45-54). Pseudomonas plasmids are reviewed by John et al. (Rev. Infect. Dis. 8:693-704 (1986)), and Izaki (Jpn. J. Bacteriol. 33:729-742 (1978)).
Preferred eukaryotic plasmids include, for example, BPV, vaccinia, SV40, 2-micron circle, and the like, or their derivatives. Such plasmids are well known in the art (Botstein et al., Miami Wntr. Symp. 19:265-274 (1982); Broach, In: The Molecular Biology of the Yeast Saccharomyces: Life Cycle and Inheritance, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., p. 445-470 (1981); Broach, Cell 28:203-204 (1982); Bollon et al., J. Clin. Hematol. Oncol. 10:39-48 (1980); Maniatis, In: Cell Biology: A Comprehensive Treatise, Vol. 3, Gene Sequence Expression, Academic Press, NY, pp. 563-608 (1980)).
Once the vector or nucleic acid molecule containing the construct(s) has been prepared for expression, the DNA construct(s) can be introduced into an appropriate host cell by any of a variety of suitable means, i.e., transformation, transfection, conjugation, protoplast fusion, electroporation, particle gun technology, calcium phosphate-precipitation, direct microinjection, and the like. After the introduction of the vector, recipient cells are grown in a selective medium, which selects for the growth of vector-containing cells. Expression of the cloned gene molecule(s) results in the production of PCA3. This can take place in the transformed cells as such, or following the induction of these cells to differentiate (for example, by administration of bromodeoxyuracil to neuroblastoma cells or the like).
VII. An Antibody Having Binding Affinity to a PCA3 Polypeptide and a Hybridoma Containing the Antibody
In another embodiment, the present invention relates to an antibody having binding affinity specifically to a PCA3 polypeptide as described above or specifically to a PCA3 polypeptide binding fragment thereof. An antibody binds specifically to a PCA3 polpeptide or binding fragment thereof if it does not bind to non-PCA3 polypeptides. Those which bind selectively to PCA3 would be chosen for use in methods which could include, but should not be limited to, the analysis of altered PCA3 expression in tissue containing PCA3.
The PCA3 proteins of the present invention can be used in a variety of procedures and methods, such as for the generation of antibodies, for use in identifying pharmaceutical compositions, and for studying DNA/protein interaction.
The PCA3 peptide of the present invention can be used to produce antibodies or hybridomas. One skilled in the art will recognize that if an antibody is desired, such a peptide would be generated as described herein and used as an immunogen.
The antibodies of the present invention include monoclonal and polyclonal antibodies, as well as fragments of these antibodies. The invention further includes single chain antibodies. Antibody fragments which contain the idiotype of the molecule can be generated by known techniques. For example, such fragments include but are not limited to: the F(ab′)2 fragment; the Fab′ fragments, Fab fragments, and Fv fragments.
Of special interest to the present invention are antibodies to PCA3 which are produced in humans, or are “humanized” (i.e. non-immunogenic in a human) by recombinant or other technology: Humanized antibodies can be produced, for example by replacing an immunogenic portion of an antibody with a corresponding, but non-immunogenic portion (i.e. chimeric antibodies) (Robinson, R. R. et al., International Patent Publication PCT/US86/02269; Akira, K. et al., European Patent Application 184,187; Taniguchi, M., European Patent Application 171,496; Morrison, S. L. et al., European Patent Application 173,494; Neuberger, M. S. et al., PCT Application WO 86/01533; Cabilly, S. et al., European Patent Application 125,023; Better, M. et al, Science 240:1041-1043 (1988); Liu, A. Y. et al., Proc. Natl. Acad. Sci. USA 84:3439-3443 (1987); Liu, A. Y. et al., J. Immunol. 139:3521-3526 (1987); Sun, L. K. et al., Proc. Natl. Acad. Sci. USA 84:214-218 (1987); Nishimura, Y. et al., Canc. Res. 47:999-1005 (1987); Wood, C. R. et al., Nature 314:446-449 (1985)); Shaw et al., J. Natl. Cancer Inst 80:1553-1559 (1988). General reviews of “humanized” chimeric antibodies are provided by Morrison, S. L. (Science, 229:1202-1207 (1985)) and by Oi, V. T. et al., BioTechniques 4:214 (1986)). Suitable “humanized” antibodies can be alternatively produced by CDR or CEA substitution (Jones, P. T. et al., Nature 321:552-525 (1986); Verhoeyan et al., Science 239:1534 (1988); Beidler, C. B. et al., J. Immunol. 141:4053-4060 (1988)).
In another embodiment, the present invention relates to a hybridoma which produces the above-described monoclonal antibody. A hybridoma is an immortalized cell line which is capable of secreting a specific monoclonal antibody.
In general, techniques for preparing monoclonal antibodies and hybridomas are well known in the art (Campbell, “Monoclonal Antibody Technology: Laboratory Techniques in Biochemistry and Molecular Biology,” Elsevier Science Publishers, Amsterdam, The Netherlands (1984); St. Groth et al., J. Immunol. Methods 35:1-21 (1980)).
Any animal (mouse, rabbit, and the like) which is known to produce antibodies can be immunized with the selected polypeptide. Methods for immunization are well known in the art. Such methods include subcutaneous or interperitoneal injection of the polypeptide. One skilled in the art will recognize that the amount of polypeptide used for immunization will vary based on the animal which is immunized, the antigenicity of the polypeptide and the site of injection.
The polypeptide can be modified or administered in an adjuvant in order to increase the peptide antigenicity. Methods of increasing the antigenicity of a polypeptide are well known in the art. Such procedures include coupling the antigen with a heterologous protein (such as globulin or β-galactosidase) or through the inclusion of an adjuvant during immunization.
For monoclonal antibodies, spleen cells from the immunized animals are removed, fused with myeloma cells, and allowed to become monoclonal antibody producing hybridoma cells.
Any one of a number of methods well known in the art can be used to identify the hybridoma cell which produces an antibody with the desired characteristics. These include screening the hybridomas with an ELISA assay, western blot analysis, or radioimmunoassay (Lutz et al., Exp. Cell Res. 175:109-124 (1988)).
Hybridomas secreting the desired antibodies are cloned and the class and subclass is determined using procedures known in the art (Campbell, Monoclonal Antibody Technology: Laboratory Techniques in Biochemistry and Molecular Biology, supra (1984)).
For polyclonal antibodies, antibody containing antisera is isolated from the immunized animal and is screened for the presence of antibodies with the desired specificity using one of the above-described procedures.
In another embodiment of the present invention, the above-described antibodies are detectably labeled. Antibodies can be detectably labeled through the use of radioisotopes, affinity labels (such as biotin, avidin, and the like), enzymatic labels (such as horse radish peroxidase, alkaline phosphatase, and the like) fluorescent labels (such as FITC or rhodamine, and the like), paramagnetic atoms, and the like. Procedures for accomplishing such labeling are well-known in the art, for example, see (Sternberger et al., J. Histochem. Cytochem. 18:315 (1970); Bayer et al., Meth. Enzym. 62:308 (1979); Engval et al., Immunol. 109:129 (1972); Goding, J. Immunol. Meth. 13:215 (1976)). The labeled antibodies of the present invention can be used for in vitro, in vivo, and in situ assays to identify cells or tissues which express a specific peptide.
In another embodiment of the present invention the above-described antibodies are immobilized on a solid support. Examples of such solid supports include plastics such as polycarbonate, complex carbohydrates such as agarose and sepharose, acrylic resins and such as polyacrylamide and latex beads. Techniques for coupling antibodies to such solid supports are well known in the art (Weir et al., “Handbook of Experimental Immunology” 4th Ed., Blackwell Scientific Publications, Oxford, England, Chapter 10 (1986); Jacoby et al., Meth. Enzym. 34 Academic Press, N.Y. (1974)). The immobilized antibodies of the present invention can be used for in vitro, in vivo, and in situ assays as well as in immunochromatography.
Furthermore, one skilled in the art can readily adapt currently available procedures, as well as the techniques, methods and kits disclosed above with regard to antibodies, to generate peptides capable of binding to a specific peptide sequence in order to generate rationally designed antipeptide peptides, for example see Hurby et al., “Application of Synthetic Peptides: Antisense Peptides”, In Synthetic Peptides, A User's Guide, W.H. Freeman, NY, pp. 289-307 (1992), and Kaspczak et al., Biochemistry 28:9230-8 (1989).
Anti-peptide peptides can be generated in one of two fashions. First, the anti-peptide peptides can be generated by replacing the basic amino acid residues found in the PCA3 peptide sequence with acidic residues, while maintaining hydrophobic and uncharged polar groups. For example, lysine, arginine, and/or histidine residues are replaced with aspartic acid or glutamic acid and glutamic acid residues are replaced by lysine, arginine or histidine.
VIII. A Method of Detecting a PCA3 Polypeptide or Antibody in a Sample
In another embodiment, the present invention relates to a method of detecting a PCA3 polypeptide in a sample, comprising: a) contacting the sample with an above-described antibody (or protein), under conditions such that immunocomplexes form, and b) detecting the presence of the antibody bound to the polypeptide. In detail, the methods comprise incubating a test sample with one or more of the antibodies of the present invention and assaying whether the antibody binds to the test sample. Altered levels of PCA3 in a sample as compared to normal levels can indicate a specific disease (ex. prostate cancer).
In a further embodiment, the present invention relates to a method of detecting a PCA3 antibody in a sample, comprising: a) contacting the sample with an above-described PCA3 protein, under conditions such that immunocomplexes form, and b) detecting the presence of the protein bound to the antibody or antibody bound to the protein. In detail, the methods comprise incubating a test sample with one or more of the proteins of the present invention and assaying whether the antibody binds to the test sample.
Conditions for incubating an antibody with a test sample vary. Incubation conditions depend on the format employed in the assay, the detection methods employed, and the type and nature of the antibody used in the assay. One skilled in the art will recognize that any one of the commonly available immunological assay formats (such as radioimmunoassays, enzymelinked immunosorbent assays, diffusion based Ouchterlony, or rocket immunofluorescent assays) can readily be adapted to employ the antibodies of the present invention. Examples of such assays can be found in Chard, An Introduction to Radioimmunoassay and Related Techniques, Elsevier Science Publishers, Amsterdam, The Netherlands (1986); Bullock et al., Techniques in Immunocytochemistry, Academic Press, Orlando, Fla. Vol. 1 (1982), Vol. 2 (1983), Vol. 3 (1985); Tijssen, Practice and Theory of Enzyme Immunoassays: Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1985).
The immunological assay test samples of the present invention include cells, protein or membrane extracts of cells, or biological fluids such as blood, serum, plasma, or urine. The test sample used in the above-described method will vary based on the assay format, nature of the detection method and the tissues, cells or extracts used as the sample to be assayed. Methods for preparing protein extracts or membrane extracts of cells are well known in the art and can be readily be adapted in order to obtain a sample which is capable with the system utilized.
IX. A Diagnostic Kit Comprising PCA3 Protein or Antibody
In another embodiment of the present invention, a kit is provided which contains all the necessary reagents to carry out the previously described methods of detection.
The kit can comprise: i) a first container means containing an above-described antibody, and ii) second container means containing a conjugate comprising a binding partner of the antibody and a label.
The kit can comprise: i) a first container means containing an above-described protein, and preferably, ii) second container means containing a conjugate comprising a binding partner of the protein and a label. More specifically, a diagnostic kit comprises PCA3 protein as described above, to detect antibodies in the serum of potentially infected animals or humans.
In another preferred embodiment, the kit further comprises one or more other containers comprising one or more of the following: wash reagents and reagents capable of detecting the presence of bound antibodies. Examples of detection reagents include, but are not limited to, labeled secondary antibodies, or in the alternative, if the primary antibody is labeled, the chromophoric, enzymatic, or antibody binding reagents which are capable of reacting with the labeled antibody. The compartmentalized kit can be as described above for nucleic acid probe kits.
One skilled in the art will readily recognize that the antibodies described in the present invention can readily be incorporated into one of the established kit formats which are well known in the art.
X. Diagnostic Screening
It is to be understood that although the following discussion is specifically directed to human patients, the teachings are also applicable to any animal that expresses PCA3.
The diagnostic and screening methods of the invention are especially useful for a patient suspected of being at risk for developing a disease associated with an altered expression level of PCA3 based on family history, or a patient in which it is desired to diagnose a PCA3-related disease (ex. prostate cancer).
According to the invention, presymptomatic screening of an individual in need of such screening is now possible using DNA encoding the PCA3 protein or the PCA3 gene of the invention or fragments thereof. The screening method of the invention allows a presymptomatic diagnosis, including prenatal diagnosis, of the presence of a missing or aberrant PCA3 gene in individuals, and thus an opinion concerning the likelihood that such individual would develop or has developed a PCA3-associated disease. This is especially valuable for the identification of carriers of altered or missing PCA3 genes, for example, from individuals with a family history of a PCA3-associated disease. Early diagnosis is also desired to maximize appropriate timely intervention.
In one preferred embodiment of the method of screening, a tissue sample would be taken from such individual, and screened for (1) the presence of the “normal” PCA3 gene; (2) the presence of PCA3 mRNA and/or (3) the presence of PCA3 protein. The normal human gene can be characterized based upon, for example, detection of restriction digestion patterns in “normal” versus the patients DNA, including RFLP analysis, using DNA probes prepared against the PCA3 sequence (or a functional fragment thereof taught in the invention. Similarly, PCA3 mRNA can be characterized and compared to normal PCA3 mRNA (a) levels and/or (b) size as found in a human population not at risk of developing PCA3-associated disease using similar probes. Lastly, PCA3 protein can be (a) detected and/or (b) quantitated using a biological assay for PCA3 activity or using an immunological assay and PCA3 antibodies. When assaying PCA3 protein, the immunological assay is preferred for its speed. An (1) aberrant PCA3 DNA size pattern, and/or (2) aberrant PCA3 mRNA sizes or levels and/or (3) aberrant PCA3 protein levels would indicate that the patient is at risk for developing a PCA3-associated disease.
More specifically, a method of diagnosing the presence or predisposition to develop prostate cancer in a patient is provided herein.
The screening and diagnostic methods of the invention do not require that the entire PCA3 DNA coding sequence be used for the probe. Rather, it is only necessary to use a fragment or length of nucleic acid that is sufficient to detect the presence of the PCA3 gene in a DNA preparation from a normal or affected individual, the absence of such gene, or an altered physical property of such gene (such as a change in electrophoretic migration pattern). Preferably, any of the probes as described above are used.
Prenatal diagnosis can be performed when desired, using any known method to obtain fetal cells, including amniocentesis, chorionic villous sampling (CVS), and fetoscopy. Prenatal chromosome analysis can be used to determine if the portion of the chromosome possessing the normal PCA3 gene is present in a heterozygous state.
XI. Therapeutic Treatments
A. Therapeutic Nucleic Acids
A therapeutic nucleic acid as a therapeutic agent can have, but is not limited to, at least one of the following therapeutic effects on a target cell: inhibiting transcription of a DNA sequence; inhibiting translation of an RNA sequence; inhibiting reverse transcription of an RNA or DNA sequence; inhibiting a post-translational modification of a protein; inducing transcription of a DNA sequence; inducing translation of an RNA sequence; inducing reverse transcription of an RNA or DNA sequence; inducing a post-translational modification of a protein; transcription of the nucleic acid as an RNA; translation of the nucleic acid as a protein or enzyme; and incorporating the nucleic acid into a chromosome of a target cell for constitutive or transient expression of the therapeutic nucleic acid.
Therapeutic effects of therapeutic nucleic acids can include, but are not limited to: turning off a defective gene or processing the expression thereof, such as antisense RNA or DNA; inhibiting viral replication or synthesis; gene therapy as expressing a heterologous nucleic acid encoding a therapeutic protein or correcting a defective protein; modifying a defective or underexpression of an RNA such as an hnRNA, an mRNA, a tRNA, or an rRNA; encoding a drug or prodrug, or an enzyme that generates a compound as a drug or prodrug in pathological or normal cells expressing the chimeric receptor; and any other known therapeutic effects.
In the method of treating a PCA3-associated disease (preferably, prostate cancer) in a patient in need of such treatment, a PCA3 gene which is not indicative of a disease state can be provided to the cells of such patient in a manner and amount that permits the expression of the PCA3 protein provided by such gene, for a time and in a quantity sufficient to treat such patient. Preferably, gene replacement (“knock out”) technology is used that would replace the disease causing PCA3 gene with a PCA3 gene which does not cause disease (specifically, prostate cancer).
Included as well in the invention are pharmaceutical compositions comprising an effective amount of at least one PCA3 antisense oligonucleotide, in combination with a pharmaceutically acceptable carrier. Such antisense oligos include, but are not limited to, at least one nucleotide sequence of 12-500 bases in length which is complementary to PCA3 exons 1, 2, 3, 4a-4d; a DNA sequence of SEQ ID NO:1, 3, 4, or 6; or a DNA sequence encoding at least 4 amino acids of SEQ ID NO:2 or SEQ ID NO:7.
Alternatively, the PCA3 nucleic acid can be combined with a lipophilic carrier such as any one of a number of sterols including cholesterol, cholate and deoxycholic acid. A preferred sterol is cholesterol.
The PCA3 gene therapy nucleic acids and the pharmaceutical compositions of the invention can be administered by any means that achieve their intended purpose. For example, administration can be by parenteral, subcutaneous, intravenous, intramuscular, intra-peritoneal, or transdermal routes. The dosage administered will be dependent upon the age, health, and weight of the recipient, kind of concurrent treatment, if any, frequency of treatment, and the nature of the effect desired.
Compositions within the scope of this invention include all compositions wherein the PCA3 antisense oligonucleotide is contained in an amount effective to achieve decreased expression of at least one PCA3 gene. While individual needs vary, determination of optimal ranges of effective amounts of each component is within the skill of the art. Typically, the PCA3 nucleic acid can be administered to mammals, e.g. humans, at a dose of 0.005 to 1 mg/kg/day, or an equivalent amount of the pharmaceutically acceptable salt thereof, per day of the body weight of the mammal being treated.
Suitable formulations for parenteral administration include aqueous solutions of the PCA3 nucleic acid in water-soluble form, for example, water-soluble salts. In addition, suspensions of the active compounds as appropriate oily injection suspensions can be administered. Suitable lipophilic solvents or vehicles include fatty oils, for example, sesame oil, or synthetic fatty acid esters, for example, ethyl oleate or triglycerides. Aqueous injection suspensions can contain substances which increase the viscosity of the suspension include, for example, sodium carboxymethyl cellulose, sorbitol, and/or dextran. Optionally, the suspension can also contain stabilizers.
Many vector systems are known in the art to provide such delivery to human patients in need of a gene or protein missing from the cell. For example, retrovirus systems can be used, especially modified retrovirus systems and especially herpes simplex virus systems (Gage et al, U.S. Pat. No. 5,082,670). Such methods are provided for, in, for example, the teachings of Breakefield, X. A. et al., The New Biologist 3:203-218 (1991); Huang, Q. et al., Experimental Neurology 115:303-316 (1992); WO93/03743; WO90/0944; Taylor, WO 92/06693; Mulligan, R. C., Science 260:926-932 (1993); and Brown et al., “Retroviral Vectors,” in DNA Cloning: A Practical Approach, Volume 3, IRL Press, Washington, D.C. (1987). Delivery of a DNA sequence encoding a normally expressed PCA3 protein will effectively replace the PCA3 gene responsible for the disease state (ex. prostate cancer).
The means by which the vector carrying the nucleic acid can be introduced into the cell include but is not limited to, microinjection, electroporation, transduction, or transfection using DEAE-Dextran, lipofection, calcium phosphate or other procedures known to one skilled in the art (Molecular Cloning, A Laboratory Manual, Sambrook et al, eds., Cold Spring Harbor Press, Plainview, N.Y. (1989)).
In another embodiment of this invention, a normal PCA3 gene is expressed as a recombinant gene in a cell, so that the cells can be transplanted into a mammal, preferably a human in need of gene therapy. To provide gene therapy to an individual, a genetic sequence which encodes for all or part of the PCA3 gene is inserted into a vector and introduced into a host cell.
Further gene therapy methods which can be used to transfer nucleic acid to a patient are set forth in Chatterjee and Wong, Current Topics in Microbiol and Immuno., 218: 61-73 (1996); Zhang, J. Mol. Med. 74:191-204 (1996); Schmidt-Wolf and Schmidt-Wolf, J. of Hematotherapy 4:551-561 (1995); Shaughnessy et al., Seminars in Oncology 23(1): 159-171 (1996); and Dunbar Annu. Rev. Med. 47:11-20 (1996).
Specificity for gene expression in prostate cancer cells can be conferred by using appropriate cell-specific regulatory sequences, such as cell-specific enhancers and promoters.
Thus, gene therapy can be used to alleviate PCA3 related pathology by inhibiting the inappropriate expression of a particular form of PCA3. Moreover, gene therapy can be used to alleviate such pathologies by providing the appropriate expression level of a particular form of PCA3. In this case, particular PCA3 nucleic acid sequences can be coded by DNA or RNA constructs which are administered in the form of viruses, as described above.
B. Antagonists and Agonists of PCA3
The ability of antagonists and agonists of PCA3 to interfere or enhance the activity of PCA3 can be evaluated with cells containing PCA3. An assay for PCA3 activity in cells can be used to determine the functionality of the PCA3 protein in the presence of an agent which may act as antagonist or agonist, and thus, agents that interfere or enhance the activity of PCA3 are identified.
The agents screened in the assays can be, but are not limited to, antibodies, peptides, carbohydrates, vitamin derivatives, or other pharmaceutical agents. These agents can be selected and screened 1) at random, 2) by a rational selection or 3) by design using for example, protein or ligand modeling techniques (preferably, computer modeling).
For random screening, agents such as antibodies, peptides, carbohydrates, pharmaceutical agents and the like are selected at random and are assayed for their ability to bind to or stimulate/block the activity of the PCA3 protein.
Alternatively, agents may be rationally selected or designed. As used herein, an agent is said to be “rationally selected or designed” when the agent is chosen based on the configuration of the PCA3 protein.
In one embodiment, the present invention relates to a method of screening for an antagonist or agonist which stimulates or blocks the activity of PCA3 comprising:
(a) incubating a cell expressing PCA3 with an agent to be tested; and
(b) assaying the cell for the activity of the PCA3 protein by measuring the agents effect on ATP binding of PCA3.
Any cell may be used in the above assay so long as it expresses a functional form of PCA3 and the PCA3 activity can be measured. The preferred expression cells are eukaryotic cells or organisms. Such cells can be modified to contain DNA sequences encoding PCA3 using routine procedures known in the art. Alternatively, one skilled in the art can introduce mRNA encoding the PCA3 protein directly into the cell.
Using PCA3 ligands (ligands including antagonists and agonists as described above) the present invention further provides a method for modulating the activity of the PCA3 protein in a cell. In general, ligands (antagonists and agonists) which have been identified to block or stimulate the activity of PCA3 can be formulated so that the ligand can be contacted with a cell expressing a PCA3 protein in vivo. The contacting of such a cell with such a ligand results in the in vivo modulation of the activity of the PCA3 proteins. So long as a formulation barrier or toxicity barrier does not exist, ligands identified in the assays described above will be effective for in vivo use.
In another embodiment, the present invention relates to a method of administering PCA3 or a PCA3 ligand (including PCA3 antagonists and agonists) to an animal (preferably, a mammal (specifically, a human)) in an amount sufficient to effect an altered level of PCA3 in the animal. The administered PCA3 or PCA3 ligand could specifically effect PCA3 associated functions. Further, since PCA3 is expressed in prostatic cancer cells, administration of PCA3 or PCA3 ligand could be used to alter PCA3 levels in such cells.
One skilled in the art will appreciate that the amounts to be administered for any particular treatment protocol can readily be determined. The dosage should not be so large as to cause adverse side effects, such as unwanted cross-reactions, anaphylactic reactions, and the like. Generally, the dosage will vary with the age, condition, sex and extent of disease in the patient, counter indications, if any, and other such variables, to be adjusted by the individual physician. Dosage can vary from 0.001 mg/kg to 50 mg/kg of PCA3 or PCA3 ligand, in one or more administrations daily, for one or several days. PCA3 or PCA3 ligand can be administered parenterally by injection or by gradual perfusion over time. It can be administered intravenously, intraperitoneally, intramuscularly, or subcutaneously.
Preparations for parenteral administration include sterile or aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers, such as those based on Ringer's dextrose, and the like. Preservatives and other additives can also be present, such as, for example, antimicrobials, antioxidants, chelating agents, inert gases and the like. See, generally, Remington's Pharmaceutical Science, 16th Ed., Mack Eds. (1980).
In another embodiment, the present invention relates to a pharmaceutical composition comprising PCA3 or PCA3 ligand in an amount sufficient to alter PCA3 associated activity, and a pharmaceutically acceptable diluent, carrier, or excipient. Appropriate concentrations and dosage unit sizes can be readily determined by one skilled in the art as described above (See, for example, Remington's Pharmaceutical Sciences (16th ed., Osol, A., Ed., Mack, Easton Pa. (1980) and WO 91/19008).
C. Immunotherapy
The present invention provides the above-described PCA3 antibodies (preferably, PCA3 murine antibodies and chimeric PCA3 murine-human antibodies, and fragments and regions thereof) which inhibit or neutralize PCA3 biological activity in vivo and are specific for PCA3. These antibodies can be used for therapeutic purposes in subjects having pathologies or conditions associated with the presence of aberrant PCA3 expression. Antibodies, and fragments, regions and derivatives thereof, of the present invention preferably contain at least one region which recognizes an epitope of PCA3 which has inhibiting and/or neutralizing biological activity in vivo.
Treatment comprises parenterally administering a single or multiple doses of the antibody, fragment or derivative. Preferred for human pharmaceutical use are high affinity potent PCA3-inhibiting and/or neutralizing murine and chimeric antibodies, fragments and regions of this invention.
Monoclonal antibodies of the present invention may be administered by any means that enables the active agent to reach the agent's site of action in the body of a mammal. Because proteins are subject to being digested when administered orally, parenteral administration, i.e., intravenous, subcutaneous, intramuscular, would ordinarily be used to optimize absorption.
Monoclonal antibodies of the present invention may be administered either as individual therapeutic agents or in combination with other therapeutic agents. They can be administered alone, but are generally administered with a pharmaceutical carrier selected on the basis of the chosen route of administration and standard pharmaceutical practice.
The dosage administered will, of course, vary depending upon known factors such as the pharmacodynamic characteristics of the particular agent, and its mode and route of administration; age, health, and weight of the recipient; nature and extent of symptoms, kind of concurrent treatment, frequency of treatment, and the effect desired. Usually a daily dosage of active ingredient can be about 0.1 to 100 milligrams per kilogram of body weight. Ordinarily 0.5 to 50, and preferably 1 to 10 milligrams per kilogram per day given in divided doses 1 to 6 times a day or in sustained release form is effective to obtain desired results.
Dosage forms (composition) suitable for internal administration generally contain from about 1 milligram to about 500 milligrams of active ingredient per unit. In these pharmaceutical compositions the active ingredient will ordinarily be present in an amount of about 0.5-95% by weight based on the total weight of the composition.
For parenteral administration, the antibody can be formulated as a solution, suspension, emulsion or lyophilized powder in association with a pharmaceutically acceptable parenteral vehicle. Examples of such vehicles are water, saline, Ringer's solution, dextrose solution, and 5% human serum albumin. Liposomes and nonaqueous vehicles such as fixed oils may also be used. The vehicle or lyophilized powder may contain additives that maintain isotonicity (e.g., sodium chloride, mannitol) and chemical stability (e.g., buffers and preservatives). The formulation is sterilized by commonly used techniques.
Suitable pharmaceutical carriers are described in the most recent edition of Remington's Pharmaceutical Sciences, A. Osol, a standard reference text in this field.
The murine and chimeric antibodies, fragments and regions of this invention, their fragments, and derivatives can be used therapeutically as immunoconjugates (see for review: Dillman, R. O., Ann. Int. Med. 111:592-603 (1989)). They can be coupled to cytotoxic proteins, including, but not limited to Ricin-A, Pseudomonas toxin, and Diphtheria toxin. Toxins conjugated to antibodies or other ligands, are known in the art (see, for example, Olsnes, S. et al., Immunol. Today 10:291-295 (1989)). Plant and bacterial toxins typically kill cells by disrupting the protein synthetic machinery.
The antibodies of this invention can be conjugated to additional types of therapeutic moieties including, but not limited to, radionuclides, cytotoxic agents and drugs. Examples of radionuclides which can be coupled to antibodies and delivered in vivo to sites of antigen include 212Bi, 131I, 186Re, and 90Y, which list is not intended to be exhaustive. The radionuclides exert their cytotoxic effect by locally irradiating the cells, leading to various intracellular lesions, as is known in the art of radiotherapy.
Cytotoxic drugs which can be conjugated to antibodies and subsequently used for in vivo therapy include, but are not limited to, daunorubicin, doxorubicin, methotrexate, and Mitomycin C. Cytotoxic drugs interfere with critical cellular processes including DNA, RNA, and protein synthesis. For a fuller exposition of these classes of drugs which are known in the art, and their mechanisms of action, see Goodman, A. G., et al., Goodman and Gilman's THE PHARMACOLOGICAL BASIS OF THERAPEUTICS, 7th Ed., Macmillan Publishing Co., 1985.
The antibodies of this invention may be advantageously utilized in combination with other monoclonal or murine and chimeric antibodies, fragments and regions, or with lymphokines or hemopoietic growth factors, etc., which serve to increase the number or activity of effector cells which interact with the antibodies.
XII. Transgenic PCA3 Non-Human Animals
Methods of Generating Transgenic Non-Human Animals
The non-human animals of the invention comprise any animal having a transgenic interruption or alteration of the endogenous gene(s) (knock-out animals) and/or into the genome of which has been introduced one or more transgenes that direct the expression of human PCA3. Also prefered are the introduction of antisense PCA3 nucleic acids.
Such non-human animals include vertebrates such as rodents, non-human primates, sheep, dog, cow, amphibians, reptiles, etc. Preferred non-human animals are selected from non-human mammalian species of animals, most preferably, animals from the rodent family including rats and mice, most preferably mice.
The transgenic animals of the invention are animals into which has been introduced by nonnatural means (i.e., by human manipulation), one or more genes that do not occur naturally in the animal, e.g., foreign genes, genetically engineered endogenous genes, etc. The nonnaturally introduced genes, known as transgenes, may be from the same or a different species as the animal but not naturally found in the animal in the configuration and/or at the chromosomal locus conferred by the transgene. Transgenes may comprise foreign DNA sequences, i.e., sequences not normally found in the genome of the host animal. Alternatively or additionally, transgenes may comprise endogenous DNA sequences that are abnormal in that they have been rearranged or mutated in vitro in order to alter the normal in vivo pattern of expression of the gene, or to alter or eliminate the biological activity of an endogenous gene product encoded by the gene. (Watson, J. D., et al., in Recombinant DNA, 2d Ed., W.H. Freeman & Co., New York (1992), pages 255-272; Gordon, J. W., Intl. Rev. Cytol. 115:171-229 (1989); Jaenisch, R., Science 240:1468-1474 (1989); Rossant, J., Neuron 2:323-334 (1990)).
The transgenic non-human animals of the invention are produced by introducing transgenes into the germline of the non-human animal. Embryonic target cells at various developmental stages are used to introduce the transgenes of the invention. Different methods are used depending on the stage of development of the embryonic target cell(s).
1. Microinjection of zygotes is the preferred method for incorporating transgenes into animal genomes in the course of practicing the invention. A zygote, a fertilized ovum that has not undergone pronuclei fusion or subsequent cell division, is the preferred target cell for microinjection of transgenic DNA sequences. The murine male pronucleus reaches a size of approximately 20 micrometers in diameter, a feature which allows for the reproducible injection of 1-2 picoliters of a solution containing transgenic DNA sequences. The use of a zygote for introduction of transgenes has the advantage that, in most cases, the injected transgenic DNA sequences will be incorporated into the host animal's genome before the first cell division (Brinster, et al., Proc. Natl. Acad. Sci. (USA) 82:4438-4442 (1985)). As a consequence, all cells of the resultant transgenic animals (founder animals) stably carry an incorporated transgene at a particular genetic locus, referred to as a transgenic allele. The transgenic allele demonstrates Mendelian inheritance: half of the offspring resulting from the cross of a transgenic animal with a non-transgenic animal will inherit the transgenic allele, in accordance with Mendel's rules of random assortment.
2. Viral integration can also be used to introduce the transgenes of the invention into an animal. The developing embryos are cultured in vitro to the developmental stage known as a blastocyst. At this time, the blastomeres may be infected with appropriate retroviruses (Jaenich, R., Proc. Natl. Sci. (USA) 73:1260-1264 (1976)). Infection of the blastomeres is enhanced by enzymatic removal of the zona pellucida (Hogan, et al., in Manipulating the Mouse Embryo, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1986)). Transgenes are introduced via viral vectors which are typically replication-defective but which remain competent for integration of viral-associated DNA sequences, including transgenic DNA sequences linked to such viral sequences, into the host animal's genome (Jahner, et al., Proc. Natl. Acad. Sci. (USA) 82:6927-6931 (1985); Van der Putten, et al., Proc. Natl. Acad. Sci. (USA) 82:6148-6152 (1985)). Transfection is easily and efficiently obtained by culture of blastomeres on a mono-layer of cells producing the transgene-containing viral vector (Van der Putten, et al., Proc. Natl. Acad. Sci. (USA) 82:6148-6152 (1985); Stewart, et al., EMBO Journal 6:383-388 (1987)). Alternatively, infection may be performed at a later stage, such as a blastocoele (Jahner, D., et al., Nature 298:623-628 (1982)). In any event, most transgenic founder animals produced by viral integration will be mosaics for the transgenic allele; that is, the transgene is incorporated into only a subset of all the cells that form the transgenic founder animal. Moreover, multiple viral integration events may occur in a single founder animal, generating multiple transgenic alleles which will segregate in future generations of offspring. Introduction of transgenes into germline cells by this method is possible but probably occurs at a low frequency (Jahner, D., et al., Nature 298:623-628 (1982)). However, once a transgene has been introduced into germline cells by this method, offspring may be produced in which the transgenic allele is present in all of the animal's cells, i.e., in both somatic and germline cells.
3. Embryonic stem (ES) cells can also serve as target cells for introduction of the transgenes of the invention into animals. ES cells are obtained from pre-implantation embryos that are cultured in vitro (Evans, M. J., et al., Nature 292:154-156 (1981); Bradley, M. O., et al., Nature 309:255-258 (1984); Gossler, et al., Proc. Natl. Acad. Sci. (USA) 83:9065-9069 (1986); Robertson et al., Nature 322:445-448 (1986); Robertson, E. J., in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, Robertson, E. J., ed., IRL Press, Oxford (1987), pages 71-112). ES cells, which are commercially available (from, e.g., Genome Systems, Inc., St. Louis, Mo.), can be transformed with one or more transgenes by established methods (Lovell-Badge, R. H., in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, Robertson, E. J., ed., IRL Press, Oxford (1987), pages 153-182). Transformed ES cells can be combined with an animal blastocyst, whereafter the ES cells colonize the embryo and contribute to the germline of the resulting animal, which is a chimera (composed of cells derived from two or more animals) (Jaenisch, R., Science 240:1468-1474 (1988); Bradley, A., in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach, Robertson, E. J., ed., IRL Press, Oxford (1987), pages 113-151). Again, once a transgene has been introduced into germline cells by this method, offspring may be produced in which the transgenic allele is present in all of the animal's cells, i.e., in both somatic and germline cells.
However it occurs, the initial introduction of a transgene is a Lamarckian (non-Mendelian) event. However, the transgenes of the invention may be stably integrated into germ line cells and transmitted to offspring of the transgenic animal as Mendelian loci. Other transgenic techniques result in mosaic transgenic animals, in which some cells carry the transgenes and other cells do not. In mosaic transgenic animals in which germ line cells do not carry the transgenes, transmission of the transgenes to offspring does not occur. Nevertheless, mosaic transgenic animals are capable of demonstrating phenotypes associated with the transgenes.
Transgenes may be introduced into non-human animals in order to provide animal models for human diseases. Transgenes that result in such animal models include, e.g., transgenes that encode mutant gene products associated with an inborn error of metabolism in a human genetic disease and transgenes that encode a human factor required to confer susceptibility to a human pathogen (i.e., a bacterium, virus, or other pathogenic microorganism) (Leder et al., U.S. Pat. No. 5,175,383 (Dec. 29, 1992); Kindt et al., U.S. Pat. No. 5,183,949 (Feb. 2, 1993); Small et al., Cell 46:13-18 (1986); Hooper et al., Nature 326:292-295 (1987); Stacey et al., Nature 332:131-136 (1988); Windle et al., Nature 343:665-669 (1990); Katz et al., Cell 74:1089-1100 (1993)). Transgenically introduced mutations comprise null (“knock-out”) alleles in which a DNA sequence encoding a selectable and/or detectable marker is substituted for a genetic sequence normally endogenous to a non-human animal. Resultant transgenic non-human animals that are predisposed to a disease, or in which the transgene causes a disease, may be used to identify compositions that induce the disease and to evaluate the pathogenic potential of compositions known or suspected to induce the disease (Berns, A. J. M., U.S. Pat. No. 5,174,986 (Dec. 29, 1992)), or to evaluate compositions which may be used to treat the disease or ameliorate the symptoms thereof (Scott et al., WO 94/12627 (1994)).
Offspring that have inherited the transgenes of the invention are distinguished from littermates that have not inherited transgenes by analysis of genetic material from the offspring for the presence of biomolecules that comprise unique sequences corresponding to sequences of, or encoded by, the transgenes of the invention. For example, biological fluids that contain polypeptides uniquely encoded by the selectable marker of the transgenes of the invention may be immunoassayed for the presence of the polypeptides. A more simple and reliable means of identifying transgenic offspring comprises obtaining a tissue sample from an extremity of an animal, e.g., a tail, and analyzing the sample for the presence of nucleic acid sequences corresponding to the DNA sequence of a unique portion or portions of the transgenes of the invention, such as the selectable marker thereof. The presence of such nucleic acid sequences may be determined by, e.g., hybridization (“Southern”) analysis with DNA sequences corresponding to unique portions of the transgene, analysis of the products of PCR reactions using DNA sequences in a sample as substrates and oligonucleotides derived from the transgene's DNA sequence, etc.
The present invention is described in further detail in the following non-limiting examples.
EXAMPLE 1
Isolation and Characterization of PCA3 cDNA and Genomic DNA
In order to identify new markers for prostate cancer, a differential display analysis (Liang et al., Science 257: 967-971 (1992)) was used to identify genes overexpressed in prostatic carcinomas in comparison to normal prostate; total RNA from normal, benign hyperplastic and malignant prostatic tissue from the same patients was extracted. Using twenty different combinations of primers (four anchored primers, five arbitrary primers), eleven apparently differentially expressed mRNAs were identified (i.e., consistently overexpressed in all carcinomas studied and not expressed in normal or BPH tissue). The complementary DNA (cDNA) fragments were used as probes for Northern blot analysis to confirm the consistent overexpression in the prostatic tumors used for the differential display. One of the probes (named DD3, a 486 bp cDNA) detected two major transcripts (2.3 and 4.0 kb) that are highly overexpressed in 47 of 50 human prostatic tumors studied, whereas no (or very low levels of) expression of these transcripts was found in normal or BPH tissue from the same patients.
To obtain a full length cDNA clone, a cDNA library was constructed using mRNA isolated from human primary prostatic tumor tissue. 250 positive DD3 related clones were obtained from screening this library. 80 clones were purified and the nucleotide sequence of these clones was determined by automated sequence analysis.
A genomic library constructed of human placenta genomic DNA cloned in λFIX2 was screened using DD3 as a probe. Four different clones were obtained, two of them located towards the 5′ end of the gene (λFIX-ME3 and -ME4) and two clones located towards the 3′ end of the gene (λFIX-ME1 and -ME2). The 5′ end of λFIX-ME4 was subcloned and used as a probe to screen the genomic library. Three new, unique clones were isolated (λFIX-IH1, IH2, and IH6).
From the 80 analyzed cDNA clones, at least four different transcripts were shown to be present due to alternative splicing or alternative polyadenylation. Sequence analysis of the genomic clones as compared to the cDNA clones revealed the genomic structure of the PCA3 gene. Three introns and 4 exons are present. The first intron is approximately 20 kb in length.
The first cDNA species is found in approximately 5% of the cDNA clones and contains exons 1, 2, 3, 4a and 4b (poly-adenylation after 4b is preceeded by a real consensus poly-A-addition signal)(FIG. 1).
The second cDNA species, found in approximately 15% of the cDNA cloned, contains exons 1, 3, 4a, 4b and 4c, arises by alternative splicing of the second exon (not present in this cDNA) and terminates at a different (real consensus) poly-A-addition signal (FIG. 1).
The third cDNA species contains exons 1, 3, 4a, and 4b and is the most common one found (approximately 65% of 80 clones) (FIG. 1). This cDNA is most likely responsible for the most prominent transcript seen by Northern blot analysis (2 kb).
The fourth cDNA species detected contains exons 1, 3, and 4a representing about 15% of clones, and terminates after 4a, which is the original DD3 clone stop site (FIG. 1). The poly-A-addition signal present here is close to the consensus sequence.
PCA3 is a gene wherein significant alternative splicing (as well as alternative poly-adenylation) occurs, as evidenced by the differently sized transcripts observed on Northern blots and the different types of clones identified. As mentioned previously, other splicing variants can be identified, as virtually every combination of exons is possible. For instance, a cDNA clone having exons 2, 3, 4a, 4b, and 4c has recently been identified. Indeed, it appears that clones representing virtually all possible exon combinations have been isolated.
One such splicing variant was identified by sequencing a clone named λDD3.6. λDD3.6 is a λgt11 clone identified and isolated upon screening of a cDNA library made from prostate RNA of a 25 year old male (obtained from Clonetech) with a PCA3 probe. λDD3.6 contains exon 3, 4a, 4b, 4c, and 4d. However, this cDNA clone also contains intron sequences (part of intron 2, as well as intron 3).
A comparison of the two deposited clones PMB9 and λDD3.6 is shown in FIG. 3.
Different combinations of exons were examined by computer analysis to identify open reading frames (ORFs) and to predict the protein encoding region. The longest ORF was also the most highly likely protein encoding region. The longest ORF of 153 nucleotides encodes a small peptide of 51 amino acids, PCA3. PCA3 is encoded by part of exon 3 and 4a. The small size of the protein suggests that the protein most likely functions as a messenger molecule and has the potential to be secreted from the cells. The nucleotide sequence of exons 1-4a-d and the amino acid sequence of PCA3 are shown in FIG. 2 and FIG. 5 (SEQ ID NO:1 and 6 and 2 and 7, respectively).
It will be recognized by the person of ordinary skill, that a cDNA clone comprising the nucleic acid sequence presented in SEQ ID NO:6 and shown in FIG. 5 can be obtained as previously described by isolating and characterizing PCA3 cDNA clones. For example, and as commonly known in the art, probes which are specific to at least one of the 5′ end, exon 1, 2, 3, 4a, 4b, 4c and 4d can be further used to increase the probability of having a full-length PCA3 cDNA clone. 96-well plates, for example, can be used to screen a large number of PCA3 positive cDNA clones, using the probes mentioned above. Of course, PCA3 positive clones can also be sequenced, as commonly known and as described herein, until a desired cDNA clone is obtained.
In addition it is also possible to obtain a cDNA clone comprising the sequence shown in SEQ ID NO:6 and shown in FIG. 5, using PCA3 specific primers and an amplifying method such as PCR. For example, PCR technology with primers specific for the ultimate 5′ and 3′ end of the PCA3 cDNA, could be used to amplify a desired product (almost 4 kb) from RNA, isolated for example from prostatic tumors, and clone the PCR products. However, since PCR amplification may introduce mistakes, a sequencing of the complete cDNA would most likely be required.
As well known to the person of ordinary skill, a cDNA clone comprising the sequence shown in SEQ ID NO:6 and shown in FIG. 5 can also be constructed using the clones described herein (or newly isolated ones) and conventional genetic engineering methods.
For example, such a full length cDNA clone can be constructed using the deposited clones pMB9 and λDD3.6. A non-limiting example of a strategy to construct such a cDNA clone comprising the nucleic acid sequence of SEQ ID NO:6 and FIG. 5, is described below.
λDD3.6 phage DNA is digested to completion with NdeI, and the approximately 2 kb NdeI fragment isolated from an agarose gel. This fragment contains part of PCA3 exon 4b, exons 4c+4d and about 50 nucleotides of phage DNA. The ends of this 2 kb fragment are then filled in with Klenow-fragment DNA polymerase and dNTPs, the blunt-ended fragment are then ligated into the HincII/SmaI sites of Bluescript SK. The loss of the HindIII site of Bluescript by the HincII and SmaI digestion is essential for further cloning steps in this particular strategy (see below). It is to be noted that NdeI sites are also present in phage λgt11, giving rise to several additional fragments, some of which are close to 2 kb (i.e., a 1.8 kb and a 2.5 kb fragment). Nevertheless, it is straight forward to separate these different bands on an agarose gel. The correct orientation of insertion of the blunt-ended 2 kb NdeI fragment of λDD3.6 into Bluescript (termed construct PCA3-X) can be verified by a single SacI digestion, which should yield a  ̃0.45 and  ̃4.5 kb fragment by Ethidium-bromide staining of agarose gels. Sequence analysis may be performed to confirm the identity of the PCA3 insert.
The PCA3-X construct is then digested to completion with HindIII and BamHI and a 4.8 kb vector-insert isolated from an agarose gel. This results in the removal of −0.2 kb of DNA from the insert. pMB9 can be simultaneously digested to completion with BamHI and HindIII and the 1.9 kb insert (containing PCA3 exons 1, 2, 3, 4a and most of exon 4b) isolated from an agarose gel. The pMB9-derived insert is ligated into the BamHI/HindIII site of the PCA3-X construct. The resulting construct, PCA3-Y contains the complete cDNA of PCA3, except for the first 22 nucleotides of exon 1 (see below and FIG. 4). These 22 nucleotides can be added to the PCA3 cDNA by cutting the PCA3-Y construct and the oligo-(74)-mer (SEQ ID NO:8) to completion with BamHI and PstI and ligating the oligomer in construct PCA3-Y, resulting in construct PCA3-Z. Nucleotide sequence analysis can be performed to verify that the oligo was properly ligated (i.e. to confirm that just one oligo was ligated and not a whole array of oligos). Of course, a sequencing of the resulting cDNA in PCA3-Z, can be performed to verify the integrity of the nucleic acid sequence.
Screening of a somatic cell hybrid panel revealed that the gene encoding PCA3 is located on human chromosome 9. Using a mixture of four PCA3-related genomic clones as a probe to hybridize to metaphase chromosomes of human lymphocytes, PCA3 was mapped to 9q21-22 (See also, FIG. 1).
The conservation of PCA3 gene during evolution was studied by Southern blot analysis and revealed that a homolog of this gene is present in monkey, cow, horse, sheep, goat and pig. The gene is also present in dog and cat. By comparison, the gene encoding PSA is only found in primates.
EXAMPLE 2
Prostate Specific Expression of PCA3
Upon developing PCA3 specific primers, RT-PCR analysis was performed using RNA from several normal human tissues. At 40 cycles of PCR, PCA3 related products in normal prostate and BPH tissues were amplified. PCA3 expression is very prostate specific since no PCA3 product could be amplified under these conditions in the following normal human tissues: artery, brain, breast, bladder, colon, duodenum, heart, liver, lung, ovary, pancreas, placenta, seminal vesicles, skeletal muscle, skin, spinal cord, spleen and testis. Also in the human prostate cancer cell lines ALVA-31, DU145, JCA-1, PPC-1, PC3, and TSU-Pr1 no PCA3 related PCR product could be detected. In the cell line LNCaP a product can be obtained after 40 cycles of PCR (whereas under the same conditions a product can be obtained in prostatic tumors within 20 cycles). The technology used to assess the prostate specific expression of PCA3 can be adapted in a diagnostic test for prostate cancer. In addition, it can be adapted to the identification of the prostatic origin of a metastase.
Furthermore, a semi-quantitative RT-PCR analysis to compare the expression of PCA3 to that of PSA (prostate-specific antigen) and PSM (prostate-specific membrane antigen) and to establish if PCA3-RT-PCR analysis can be used to distinguish malignant from benign prostatic specimens was performed. After quantification of the RT-reaction, 10 ng of cDNA was used for the PCR reaction and as a control, beta-2 microglobulin was also examined. PCA3 products found allowed a clear distinction between benign and malignant specimens in 23 of 25 cases studied whereas PSA and PSM could not make this distinction: approximately equal amounts of product were found in normal and tumor samples. The expression of PSA and PCA3 was also compared by Northern blot analysis, which clearly shows the higher tumor-specificity of PCA3. At least a 20-fold overexpression of PCA3 in prostatic carcinomas as compared to normal or BPH tissues is observed. This is distinctly different from expression of PSM and PSA, both of which are decreased in malignant versus benign tissues. Thus, PCA3 appears to be a good marker for diagnostic of prostate cancer.
An ideal tumor marker for prostate cancer should not only be able to positively distinguish between benign and malignant tissues but also be able to predict clinical outcome (cure or progression) of patients afflicted with this disease. Data has shown that indeed, the level of expression of PCA3 tends to be positively correlated with tumor grade.
RISH (and eventually immunohistochemistry) is used to establish whether or not there is correlation beween overexpression of PCA3, tumor grade, stage, and clinical outcome. For both the paraffin-embedded and frozen specimens, long-term clinical follow-up is available. Using computer-assisted image analysis, quantitation of PCA3 expression levels as detected by RISH is performed and this is normalized to an external reference (Tamimi et al., Cancer Res. 53: 5512-16 (1993); Tamimi et al., B. J. Cancer (1996)). A multivariate regression analysis including Gleason: grade, pathological tumor stage, clinical tumor stage, PSA levels and PCA3 expression will be used to establish whether PCA3 is an accurate predictor of progression and has (additional) prognostic value.
Reverse transcriptase polymerase chain reaction (RT-PCR) assays have been developed to detect occult hematogenous micrometastatic cells that might otherwise have gone undetected by presently available staging modalities. Such RT-PCR assays have already been performed in patients with prostate cancer and other malignancies. A highly sensitive (nested) RT-PCR assay (or other types of amplification assays including without being limited to NASBA, PCR, QB rep., SOA, TMA, and LCR (Winn-Deen, J. Clin., Liquid Assay 19: 21-26 (1996)) can be used to detect prostate cancer cells in the circulating blood of prostate: cancer patients to identify patients at risk for having or developing metastases. Experiments will include appropriate controls (e.g. β-2-microglobulin) and will be performed in a semi-quantitative way (i.e., quantify the cDNA synthesis and use equal amounts of input for the PCR analysis).
The molecular staging studies will be performed in the larger context of the BIOMED II program (Markers for Prostate Cancer). In this extensive collaborative study, PSA and PSM will be studied as well as other potentially interesting markers for prostate cancer. Blood samples are already being collected from patients that are diagnosed with prostatic disease in the participating institutions. An optimization of the collecting and handling of blood samples from patients for the detection of circulating tumor cells has been initiated. The use for example of vacutainerTM CPT-tubes (BecktonDickinson) for blood collection and purification of peripheral blood leukocytes in combination with a TrizolTM RNA-extraction procedure (guanidinium thiocyanate based) resulted in the preparation of RNA qualitatively and quantitatively suitable for PCR analysis. The use of PCA3-specific primers, to amplify PCA3 transcripts in RNA extracted from blood from prostate cancer patients, revealed that the presence of prostate cancer cells in the blood circulation, of not only patients with proven metastases, but also of patients with assumed localized disease, could be detected. More extensive studies on a larger patient population and a correlation with clinical data and follow-up will be carried out to determine the prognostic value of PCA3 for the individual prostate cancer patient.
Nested RT-PCR analysis (or similar amplification methods) should prove instrumental in determining whether there are any organs (not yet tested) that express PCA3. For example, Cowper's gland (same embryonic origin as the prostate) and also skene's gland (female “homologue” to the prostate) will be tested for PCA3.
In one “normal” prostate tissue specimen that contained 10% of tumor cells, PCA3 expression was detected indicating the high sensitivity of PCA3 as a tumor marker. In this manner, PCA3 expression was also detected in a few BPH samples that were subsequently found to contain small areas of tumor cells. The level of expression of PCA3 in prostatic cancers shows a trend towards a positive correlation with tumor grade. These data are based on analysis of autoradiographs resulting from Northern blot hybridization.
The observation that PCA3 expression seems to increase with loss of differentiation is different from what is reported for PSA, since PSA expression levels decrease with loss of differentiation (Hakalahti et al., Int J. Cancer 55:590-597 (1993)). There is at least 20-fold overexpression of PCA3 in prostatic carcinomas in comparison to normal or BPH tissues. This is distinctly different from the expression of PSA which is reported to decrease in malignant versus benign tissues. PCA3 expression was detected in 4 of 4 metastases studied.
EXAMPLE 3
Identification of a Transcription Start Site of PCA3
In order to determine the transcription start site of PCA3 primer extension analysis, S1-nuclease mapping and 5′RACE (rapid amplification of cDNA ends) assays were performed. The major transcription start site was found to be located within a range of 4 nucleotides (FIG. 4).
The results of these experiments further lengthen the size of the cDNA in a 5′ direction by a further 22 nt with respect to the cDNA sequence of pMB9 (SEQ ID NO:1 and FIG. 2). This additional 5′ polynucleotide sequence is also shown in SEQ ID NO:6 and FIG. 5)
All publications mentioned hereinabove are hereby incorporated in their entirety by reference.
While the foregoing invention has been described in some detail for purposes of clarity and understanding, it will be appreciated by one skilled in the art from a reading of this disclosure that various changes in form and detail can be made without departing from the true scope of the invention and appended claims.
Although the present invention has been described hereinabove by way of preferred embodiments thereof, it can be modified, without departing from the spirit and nature of the subject invention as defined in the appended claims.

## Claims

1. A method of detecting a PCA3 nucleic acid in a sample comprising:
a) contacting said PCA3 nucleic acid with an isolated nucleic acid molecule comprising from 10 to 500 nucleotides under conditions such that hybridization occurs, wherein said nucleic acid molecule specifically hybridizes to a PCA3 nucleic acid sequence selected from the group consisting of:
i) a nucleotide sequence contained in the deposit at the Centraal voor Schimmelcultures as accession number CBS 682.97;
ii) a nucleotide sequence contained in the deposit at the Centraal voor Schimmelcultures as accession number CBS 100521;
iii) a nucleotide sequence set forth in SEQ ID NO:1, 3, 4 or 6, wherein said nucleotide sequence is over-expressed in prostate cancer tissue as compared to normal human tissues;
iv) a nucleotide sequence fully complementary to any of the nucleotide sequences in (i), (ii) or (iii); and
b) detecting the presence of said PCA3 nucleic acid.

2. The method of claim 1, wherein said nucleic acid molecule comprises at least 12 to 500 nucleotides.

3. The method of claim 1, wherein said nucleic acid molecule comprises at least 15 nucleotides.

4. The method of claim 1, wherein said isolated nucleic acid molecule specifically hybridizes to the PCA3 nucleic acid sequence selected from:
i) the nucleotide sequence set forth in SEQ ID NO:1, 3, 4 or 6, wherein said nucleotide sequence is over-expressed in prostate cancer tissue as compared to normal human tissues; and
ii) the nucleotide sequence fully complementary to the nucleotide sequence in (i).

5. The method of claim 4, wherein said nucleic acid molecule comprises at least 12 to 500 nucleotides.

6. The method of claim 4, wherein said nucleic acid molecule comprises at least 15 nucleotides.

7. The method of claim 4, wherein said nucleic acid molecule comprises at least 18 nucleotides.

8. The method of claim 4, wherein said nucleic acid molecule comprises at least 20 nucleotides.

9. The method of claim 4, wherein said nucleic acid molecule comprises from 20 to 35 nucleotides.

10. The method of claim 4, wherein said nucleic acid molecule comprises from 20 to 50 nucleotides.

11. The method of claim 1, wherein said nucleic acid molecule is or is complementary to a nucleotide sequence consisting of at least 10 consecutive nucleotides from a PCA3 exon selected from the group consisting of:
a) nucleotides of exon 1, from positions 1-98 of SEQ ID NO: 1 or positions 1-120 of SEQ ID NO: 6;
b) nucleotides of exon 3 from positions 264-446 of SEQ ID NO: 1 or positions 286-468 of SEQ ID NO: 6;
c) nucleotides of exon 4a from positions 447-985 of SEQ ID NO: 1 or positions 469-1007 of SEQ ID NO: 6;
d) nucleotides of exon 4b from positions 986-2037 of SEQ ID NO: 1 or positions 1008-2066 of SEQ ID NO: 6;
e) nucleotides of exon 4c from positions 2067-2622 of SEQ ID NO: 6; and
f) of exon 4d from positions 2623-3582 of SEQ ID NO: 6.

12. The method of claim 5, wherein said nucleic acid molecule is or is complementary to a nucleotide sequence consisting of at least 12 to 500 consecutive nucleotides from a PCA3 exon selected from the group consisting of:
a) nucleotides of exon 1, from positions 1-98 of SEQ ID NO: 1 or positions 1-120 of SEQ ID NO: 6;
b) nucleotides of exon 3 from positions 264-446 of SEQ ID NO: 1 or positions 286-468 of SEQ ID NO: 6;
c) nucleotides of exon 4a from positions 447-985 of SEQ ID NO: 1 or positions 469-1007 of SEQ ID NO: 6;
d) nucleotides of exon 4b from positions 986-2037 of SEQ ID NO: 1 or positions 1008-2066 of SEQ ID NO: 6;
e) nucleotides of exon 4c from positions 2067-2622 of SEQ ID NO: 6; and
f) nucleotides of exon 4d from positions 2623-3582 of SEQ ID NO: 6.

13. The method of claim 6, wherein said nucleic acid molecule is or is complementary to a nucleotide sequence consisting of at least 15 consecutive nucleotides from a PCA3 exon selected from the group consisting of:
a) nucleotides of exon 1, from positions 1-98 of SEQ ID NO: 1 or positions 1-120 of SEQ ID NO: 6;
b) nucleotides of exon 3 from positions 264-446 of SEQ ID NO: 1 or positions 286-468 of SEQ ID NO: 6;
c) nucleotides of exon 4a from positions 447-985 of SEQ ID NO: 1 or positions 469-1007 of SEQ ID NO: 6;
d) nucleotides of exon 4b from positions 986-2037 of SEQ ID NO: 1 or positions 1008-2066 of SEQ ID NO: 6;
e) nucleotides of exon 4c from positions 2067-2622 of SEQ ID NO: 6; and
f) nucleotides of exon 4d from positions 2623-3582 of SEQ ID NO: 6.

14. The method of claim 5, 7, 8, 9 or 10 wherein said nucleic acid molecule is or is complementary to the polynucleotide sequence set forth from nucleotides 401 to 553 of SEQ ID NO:6.

15. The method of claim 6, wherein said nucleic acid molecule is or is complementary to the polynucleotide sequence set forth from nucleotides 401 to 553 of SEQ ID NO:6.

16. The method of claim 1, wherein said isolated nucleic acid molecule does not hybridize to nucleotides 511-985 of SEO ID NO:1 or nucleotides 533-1007 of SEQ ID NO:6.

17. The method of claim 1, wherein said sample is selected from the group consisting of: an organ, a tissue, a cell, an extract of cells, and a biological fluid.

18. The method of claim 1, wherein said PCA3 nucleic acid is PCA3 RNA.

19. The method of claim 18, comprising an amplification of said PCA3 nucleic acid.

20. The method of claim 19, wherein said amplification is polymerase chain reaction (PCR).

21. The method of claim 19, wherein said PCA3 nucleic acid is detected with a nucleic acid probe that specifically hybridizes thereto.

22. The method of claim 21, wherein said detecting comprises a visualization.

23. The method of claim 21, wherein said detecting comprises a detection of a radiolabel, an enzyme label, a fluorescent label, a biotin-avidin label or chemiluminescence.

24. The method of claim 15, wherein said sample is selected from the group consisting of: an organ, a tissue, a cell, an extract of cells, and a biological fluid.

25. The method of claim 24, wherein said PCA3 nucleic acid is PCA3 RNA.

26. The method of claim 25, comprising an amplification of said PCA3 nucleic acid.

27. The method of claim 26, wherein said amplification is polymerase chain reaction (PCR).

28. The method of claim 25, wherein said PCA3 nucleic acid is detected with a nucleic acid probe that specifically hybridizes thereto.

29. The method of claim 11, 12 or 13 wherein said nucleic acid molecule does not hybridize to nucleotides 511-985 of SEQ ID NO:1 or to nucleotides 533-1007 of SEQ ID NO:6.