US20050100931A1

US20050100931A1 - Methods and compositions for the identification and assessment of prostate cancer therapies and the diagnosis of prostate cancer

Info

Publication number: US20050100931A1
Application number: US10/831,704
Authority: US
Inventors: Andrew Shyjan
Original assignee: Millennium Pharmaceuticals Inc
Current assignee: Millennium Pharmaceuticals Inc
Priority date: 1997-12-24
Filing date: 2004-04-23
Publication date: 2005-05-12
Also published as: US6506607B1

Abstract

The invention concerns two classes of differentially regulated genes: 1) genes that are more highly expressed in prostate cancer cells treated with testosterone than in untreated prostate cancer cells; and 2) genes that are more highly expressed in prostate cancer cells treated with bicalutamide, an anti-androgenic compound, than in untreated prostate cancer cells. Disclosed are methods for selecting and monitoring the effectiveness of therapeutic agents used for the treatment of prostate cancer. Also disclosed are methods for identifying novel therapeutic agents for the treatment of prostate cancer and methods and compositions for preventing, treating, and diagnosing prostate cancer.

Description

RELATED APPLICATION INFORMATION

This application claims priority from provisional application Ser. No. 60/079,303, filed Mar. 25, 1998, and from provisional application Ser. No. 60/068,821, filed Dec. 24, 1997.

BACKGROUND OF THE INVENTION

Prostate cancer is the most commonly diagnosed cancer in American men and the second most common cause of death from cancer in American men.
Androgen withdrawal, by castration or through the use of an anti-androgenic drug, is the preferred treatment method for prostate cancer.
Bicalutamide (casodex) is a relatively potent, orally active anti-androgenic drug. Approximately 80% of the prostate cancer patients treated with bicalutamide respond to the treatment; however, most patients eventually relapse.
Prostate cancer, like other cancers, can be viewed as a breakdown in the communication between tumor cells and their environment, including their normal neighboring cells. Growth-stimulatory and growth-inhibitory signals are routinely exchanged between cells within a tissue. Normally, cells do not divide in the absence of stimulatory signals, and, likewise, will cease dividing in the presence of inhibitory signals. In a cancerous or neoplastic state, a cell acquires the ability to “override” these signals and to proliferate under conditions in which a normal cell would not grow.
In general, tumor cells must acquire a number of distinct aberrant traits in order to proliferate in an abnormal manner. Reflecting this requirement is the fact that the genomes of certain well-studied tumors carry several different independently altered genes, including activated oncogenes and inactivated tumor suppressor genes.
In addition to abnormal cell proliferation, cells must acquire several other traits for tumor progression to occur. For example, early on in tumor progression, cells must evade the host immune system. Further, as tumor mass increases, the tumor must acquire vasculature to supply nourishment and remove metabolic waste. Additionally, cells must acquire an ability to invade adjacent tissue. In many cases cells ultimately acquire the capacity to metastasize to distant sites.
It is apparent that the complex process of tumor development and growth must involve multiple gene products. It is therefore important to define the role of specific genes involved in tumor development and growth and identify those genes and gene products that can serve as targets for the diagnosis, prevention and treatment of cancers.
In the realm of cancer therapy it often happens that a therapeutic agent that is initially effective for a given patient becomes, overtime, ineffective or less effective for that patient. The very same therapeutic agent may continue to be effective over a long period of time for a different patient. Further, a therapeutic agent which is effective, at least initially, for some patients is completely ineffective or even harmful for other patients. Accordingly, it would be useful to identify genes and/or gene products that represent prognostic markers with respect to a given therapeutic agent or class of therapeutic agents. It then may be possible to determine which patients will benefit from particular therapeutic regimen and, importantly, determine when, if ever, the therapeutic regime begins to lose its effectiveness. The ability to make such predictions would make it possible to cease a therapeutic regime which has lost its effectiveness well before its loss of effectiveness becomes apparent by conventional measures.

SUMMARY OF THE INVENTION

The invention features methods for selecting and monitoring the effectiveness of therapeutic agents used for the treatment of prostate cancer. The invention also features methods for identifying novel therapeutic agents for the treatment of prostate cancer. The invention also features methods and compositions diagnosing prostate cancer and methods and compositions for preventing, treating, and diagnosing prostate cancer.
The invention is based, in part, on the identification of two classes of differentially regulated genes: 1) genes that are more highly expressed in prostate cancer cells treated with testosterone than in untreated prostate cancer cells; and 2) genes that are more highly expressed in prostate cancer cells treated with bicalutamide, an anti-androgenic compound, than in untreated prostate cancer cells. Genes which are more highly expressed in testosterone-treated prostate cancer cells than untreated prostate cancer cells are listed in Table 1 (SEQ ID NOS:1-40, 86-130 and FIGS. 1-40, 86-130). Genes which are more highly expressed in bicalutamide-treated prostate cancer cells than untreated prostate cancer cells are listed in Table 2 (SEQ ID NOS:41-85, 131-191 and FIGS. 41-85, 131-191).
By examining the expression of one or more of these identified genes in a sample of prostate cancer cells, it is possible to determine whether a selected compound, e.g., an anti-androgenic compound, can be used to treat the prostate cancer. Importantly, this determination can be made on a patient by patient basis. Thus, one can determine whether or not a particular prostate cancer treatment is likely to benefit a particular patient. The invention also features methods for determining whether a particular prostate cancer has become refractory to treatment with an anti-androgenic compound or other therapeutic agent.
The invention also features diagnostic methods and prognostic methods which can be used to identify patients having or at risk for developing prostate cancer. The identified differentially expressed genes whose expression is increased in the presence of testosterone and/or the products of such genes can be used to identify cells exhibiting or predisposed development of prostate cancer thereby diagnosing individuals having, or at high risk for developing, prostate cancer. The detection of the differential expression of identified genes can be used to select therapies before the benign cells attain a malignant state and to design a preventive intervention in pre-neoplastic cells in individuals at high risk.
In the various methods of the invention, gene expression can be measured at the mRNA or protein level. Alternatively, expression can be measured indirectly by measuring the activity of the protein encoded by the identified gene.
The differentially expressed genes identified herein are potential targets for the development of therapeutic compounds. Genes that are expressed at a higher level in prostate cancer cells in the presence of testosterone than in the absence of testosterone are identified. Because testosterone is required for growth and survival of prostate cancer cells, genes whose expression is increased in the presence of testosterone are potential therapeutic targets. Thus, identifying compounds which reduce the expression of such a gene or reduce the activity of the product of such a gene forms the basis for the development of new therapeutic agents. In addition, as noted above, increased expression of these genes can serve as a prognostic or diagnostic indicator of prostate cancer. Moreover, where increased expression of these genes is observed during the course of a therapy, it can be expected that the therapy is or has become relatively ineffective.
Also identified are genes that are expressed in prostate cancer cells at a high level in the presence of the anti-androgenic drug bicalutamide than in the absence of bicalutamide. Because bicalutamide is known to inhibit the growth of prostate cancer cells, genes whose expression is increased in the presence of bicalutamide are potential therapeutic targets. Thus, identifying compounds which increase the expression of such a gene or increase the activity of the product of such a gene forms the basis for the development of new therapeutic agents. In addition, increased expression of these genes can serve as a indicator that a given therapy is effective.
The invention provides methods for the identification of compounds that modulate the expression of genes or the activity of gene products involved in prostate cancer as well as methods for the treatment of prostate cancer. Such methods can, for example, involve the administration of such modulatory compounds to individuals exhibiting symptoms or markers of prostate cancer.
This invention is based, in part, on systematic search strategies coupled with sensitive and high throughput gene expression assays, to identify genes differentially expressed in prostate tumor cells treated with different drugs. The search strategies and assays used herein permit the identification of all genes, whether known or novel, which are differentially expressed in, e.g., testosterone-treated prostate cancer cells relative to untreated prostate cancer cells.
This comprehensive approach and evaluation permits the discovery of novel genes and gene products, as well as the identification of an array of genes and gene products (whether novel or known) that are influenced by drugs and natural products which are known to influence the growth and survival of prostate cancer cells. Thus, the present invention makes possible the identification and characterization of targets useful for rationale drug design and for the prognosis, diagnosis, monitoring, treatment, and prevention of prostate cancer.
In some respects the differentially expressed genes described herein can be used in the same manner and prostate specfic antigen, a commonly used marker for prostate cancer and pre-cancerous conditions related to prostate cancer.
“Differential expression,” as used herein, refers to both quantitative, as well as qualitative, differences in the expression pattern of a gene in tumor cells treated with a particular drug and untreated tumor cells. Differentially expressed genes can represent “fingerprint genes,” and/or “target genes.”
“Fingerprint gene,” as used herein, refers to a differentially expressed gene whose expression pattern can be utilized as part of a prognostic or diagnostic marker for the evaluation of prostate cancer or which, alternatively, can be used in methods for identifying compounds useful for the treatment of prostate cancer or evaluating the effectiveness of a prostate cancer treatment. For example, the effect of the compound on the fingerprint gene expression pattern normally displayed in connection with prostate cancer can be used to evaluate the efficacy of the compound as a treatment for prostate cancer or can, additionally, be used to monitor patients undergoing clinical evaluation for the treatment of prostate cancer.
A “fingerprint pattern,” as described herein, is the pattern generated when the expression pattern of a series (which can range from two up to all the fingerprint genes which exist for a given state) of fingerprint genes is determined. A fingerprint pattern can be used in the same diagnostic, prognostic and compound identification methods as the expression of a single fingerprint gene.
A “target gene,” as described herein, is a differentially expressed gene involved in prostate cancer such that modulation of the level of target gene expression or of target gene product activity can act to prevent and/or ameliorate symptoms of the prostate cancer. Compounds that modulate the expression of the target gene or the activity of the target gene product can be used in the treatment of prostate cancer. Still further, compounds that modulate the expression of the target gene or activity of the target gene product can be used in treatments to deter benign cells from developing into prostate cancer cells. Still further, compounds that modulate the expression of the target gene or activity of the target gene product can be used to design a preventive intervention in pre-neoplastic cells in individuals at high risk.

DESCRIPTION OF THE FIGURES

FIGS. 1-191 are the nucleotide sequences of SEQ ID NOS:1-191.

DETAILED DESCRIPTION OF THE INVENTION

The invention is based, in part, on the identification of genes that are differentially expressed in prostate cancer cells treated with selected compounds. By evaluating the expression pattern of a variety of genes in the presence and absence of a selected compound it is possible to create a profile of the response of prostate cancer cells to the selected compound.
I. Identification of Differentially Expressed Genes
Described below are examples of methods which can be used to identify differentially expressed genes, i.e., genes whose expression in prostate cancer cells is altered by a selected compound, e.g., testosterone.
Differential expression refers to both quantitative, as well as qualitative differences the expression pattern of a gene or group of genes. Thus, a differentially expressed gene can qualitatively have its expression increased or decreased in, for example, testosterone-treated prostate cancer cells versus untreated prostate cancer cells.
In some cases, the difference in expression between treated and untreated (control) cells may be qualitative rather than quantitative. Thus, the expression of a selected gene might be detectable using a certain assay method in the presence of a given drug and undetectable using the same assay in the absence of the drug.
Alternatively, a differentially expressed gene can exhibit an expression level which differs, i.e., is quantitatively increased or decreased in treated cells versus control cells.
The degree to which expression differs need only be large enough to be visualized via standard characterization techniques, such as, for example, a differential display technique. Other standard, well-known characterization techniques by which expression differences can be visualized include, but are not limited to, quantitative reverse transcriptase (RT)-coupled PCR and Northern analyses and RNase protection techniques and methods which employ arrays of nucleic acid molecules, e.g., cDNAs linked to a solid support, e.g., a Gene Expression Micro-Array™ (Synteni, Inc.; Fremont, Calif.).
a) Approaches to the Identification of Differentially Expressed Genes
There are a variety of approaches (or paradigms) which can be used to identify differentially expressed genes. In all cases, drug-treated and untreated cells (or cells treated with different drugs) are compared. The paradigms differ in the source of the cells that are differentially treated. Thus, the cells can be differentially treated in vitro prostate cancer cells, e.g., a cells of a prostate cancer cell line (an “in vitro paradigm”), differentially treated representatives of an animal model of prostate cancer (an “in vivo paradigm”), or differentially treated prostate cancer patients (a “clinical paradigm”).
Once a particular differentially expressed gene has been identified through the use of one paradigm, its expression pattern can be further characterized, for example, by studying its expression in a different paradigm. A gene can, for example, be regulated one way, i.e., can exhibit one differential gene expression pattern, in a given paradigm, but can be regulated differently in another paradigm. The use, therefore, of multiple paradigms can be helpful in distinguishing the roles and relative importance of particular genes in prostate cancer.
In an in vitro paradigm, differentially expressed genes are detected by comparing the pattern of gene expression between the experimental (drug-treated) prostate cancer cells and control (untreated or treated with a different drug) prostate cancer cells.
In an in vivo paradigm, animal models of prostate cancer can be utilized to discover differentially expressed genes. A variety of animal models can be used in an in vivo paradigms. Matched animal are treated with a drug or left untreated (or treated with a different drug).
In a clinical paradigm samples from surgical and biopsy specimens are used. Such specimens can represent normal tissue, primary, secondary or metastasized tumors obtained from patients. Surgical specimens can be procured under standard conditions involving freezing and storing in liquid nitrogen (see, for example, Karmali et al., 1983, Br. J. Cancer 48:689-696.) RNA from specimen cells is isolated by, for example, differential centrifugation of homogenized tissue, and analyzed for differential expression relative to other specimen cells, preferably cells obtained from the same patient at a different time, e.g., before drug treatment, during treatment with a different drug, or at an earlier time during treatment with the same drug.
b) Methods for Identifying Differentially Expressed Genes
In order to identify differentially expressed genes, RNA, either total or mRNA, can be isolated from cells utilized in paradigms such as those described above. Any RNA isolation technique which does not select against the isolation of mRNA can be utilized for the purification of such RNA samples (see, e.g., Ausubel et al., eds., 1987-1997, Current Protocols in Molecular Biology, John Wiley & Sons, Inc. New York). Additionally, large numbers of tissue samples can readily be processed using techniques well known to those of skill in the art, such as, for example, the single-step RNA isolation process of Chomczynski (1989, U.S. Pat. No. 4,843,155).
Transcripts within the collected RNA samples which represent RNA produced by differentially expressed genes can be identified by utilizing a variety of methods which are well known to those of skill in the art. For example, differential screening (Tedder et al., 1988, Proc. Natl. Acad. Sci. USA 85:208-212), subtractive hybridization (Hedrick et al., 1984, Nature 308:149-153; Lee et al., 1984, Proc. Natl. Acad. Sci. USA 88:2825), and, preferably, differential display (Liang and Pardee 1993, U.S. Pat. No. 5,262,311), can be utilized to identify nucleic acid sequences derived from genes that are differentially expressed.
Differential screening involves the duplicate screening of a cDNA library in which one copy of the library is screened with a total cell cDNA probe corresponding to the mRNA population of sample while a duplicate copy of the cDNA library is screened with a total cDNA probe corresponding to the mRNA population of a second sample. For example, one cDNA probe can correspond to a total cell cDNA probe of a cell or tissue derived from a control sample, while the second cDNA probe can correspond to a total cell cDNA probe of the same cell type derived from an experimental (e.g, drug-treated) sample. Those clones which hybridize to one probe but not to the other potentially represent clones derived from genes differentially expressed in the cell of interest in control versus experimental samples.
Subtractive hybridization techniques generally involve the isolation of mRNA taken from two different sources, e.g., treated and untreated cells, the hybridization of the mRNA or single-stranded cDNA reverse-transcribed from the isolated mRNA, and the removal of all hybridized, and therefore double-stranded, sequences. The remaining non-hybridized, single-stranded cDNAs, potentially represent clones derived from genes that are differentially expressed in the two mRNA sources. Such single-stranded cDNAs are then used as the starting material for the construction of a library comprising clones derived from differentially expressed genes.
Differential display is a procedure which, utilizing the well-known polymerase chain reaction (PCR; the experimental embodiment set forth in Mullis 1987, U.S. Pat. No. 4,683,202), allows for the identification of sequences derived from genes which are differentially expressed. First, isolated RNA is reverse-transcribed into single-stranded cDNA, utilizing standard techniques which are well known to those of skill in the art. Primers for the reverse transcriptase reaction can include, but are not limited to, oligo dT-containing primers, preferably of the 3′ primer type of oligonucleotide described below. Next, this technique uses pairs of PCR primers, as described below, which allow for the amplification of clones representing a random subset of the RNA transcripts present within any given cell. Utilizing different pairs of primers allows each of the mRNA transcripts present in a cell to be amplified. Among such amplified transcripts can be identified those which have been produced from differentially expressed genes.
The 3′ oligonucleotide primer of the primer pairs can contain an oligo dT stretch of 10-13 dT nucleotides at its 5′ end, preferably 11, which hybridizes to the poly(A) tail of mRNA or to the complement of a cDNA reverse transcribed from an mRNA poly(A) tail. Second, in order to increase the specificity of the 3′ primer, the primer can contain one or more, preferably two, additional nucleotides at its 3′ end. Because, statistically, only a subset of the mRNA derived sequences present in the sample of interest will hybridize to such primers, the additional nucleotides allow the primers to amplify only a subset of the mRNA derived sequences present in the sample of interest. This is preferred in that it allows more accurate and complete visualization and characterization of each of the bands representing amplified sequences.
The 5′ primer can contain a nucleotide sequence expected, statistically, to have the ability to hybridize to cDNA sequences derived from the tissues of interest. The nucleotide sequence can be an arbitrary one, and the length of the 5′ oligonucleotide primer can range from about 9 to about 15 nucleotides, with about 13 nucleotides being preferred.
Additionally, arbitrary primer sequences cause the lengths of the amplified partial cDNAs produced to be variable, thus allowing different clones to be separated by using standard denaturing sequencing gel electrophoresis.
PCR reaction conditions should be chosen which optimize amplified product yield and specificity, and, additionally, produce amplified products of lengths which can be resolved utilizing standard gel electrophoresis techniques. Such reaction conditions are well known to those of skill in the art, and important reaction parameters include, for example, length and nucleotide sequence of oligonucleotide primers as discussed above, and annealing and elongation step temperatures and reaction times.
The pattern of clones resulting from the reverse transcription and amplification of the mRNA of two different cell types is displayed via sequencing gel electrophoresis and compared. Differences in the two banding patterns indicate potentially differentially expressed genes.
Once potentially differentially expressed gene sequences have been identified via bulk techniques such as, for example, those described above, the differential expression of such putatively differentially expressed genes should be corroborated. Corroboration can be accomplished via, for example, such well-known techniques as Northern analysis, quantitative RT-coupled PCR or RNase protection.
Upon corroboration, the differentially expressed genes can be further characterized, and can be identified as target and/or fingerprint genes.
Amplified sequences of differentially expressed genes obtained through differential display can be used to isolate the full length clones of the corresponding gene. The full-length coding portion of the gene can readily be isolated, without undue experimentation, by molecular biological techniques well known in the art. For example, the isolated differentially expressed amplified fragment can be labeled and used to screen a cDNA library. Alternatively, the labeled fragment can be used to screen a genomic library.
PCR technology can also be utilized to isolate full-length cDNA sequences. Thus, the isolated amplified gene fragments (of about at least 10 nucleotides, preferably longer, of about 15 nucleotides) obtained through differential display have their 5′ terminal end at some random point within the gene and have 3′ terminal ends at a position corresponding to the 3′ end of the transcribed portion of the gene. Once nucleotide sequence information from an amplified fragment is obtained, the remainder of the gene (i.e., the 5′ end of the gene, when utilizing differential display) can be obtained using, for example, RT-PCR.
A reverse transcription reaction can then be performed on the RNA using an oligonucleotide primer complementary to the mRNA that corresponds to the amplified cloned fragment, for the priming of first strand synthesis. Because the primer is anti-parallel to the mRNA, extension will proceed toward the 5′ end of the mRNA. The resulting RNA/DNA hybrid can then be “tailed” with guanines using a standard terminal transferase reaction, the hybrid can be digested with RNAase H, and second strand synthesis can then be primed with a poly-C primer. Using the two primers, the 5′ portion of the gene is then amplified using PCR. Sequences obtained can then be isolated and recombined with previously isolated sequences to generate a full-length cDNA of the differentially expressed gene. For a review of cloning strategies and recombinant DNA techniques which can be used, see, e.g., Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, Cold Springs Harbor Press, N.Y.; and Ausubel et al., supra.
II. Examples of the Identification of Differentially Expressed Genes
Described below is the identification of two classes of genes which are differentially expressed in prostate cancer cells.
The first example concerns the identification of 40 genes whose expression is increased in prostate cancer cells in the presence of testosterone. It is known that testosterone is required for the growth and survival of prostate cancer cells. Accordingly, genes whose expression is increased in the presence of testosterone can be used as markers to identify prostate cancers which might be successfully treated by the use of an anti-androgenic drug. In addition, these genes can be used as markers to identify prostate cancers which may have become refractory to anti-androgenic treatment. Because higher expression of these genes is associated with testosterone-exposed prostate cancer cells, they can be used as diagnostic and prognostic markers to identify individuals suffering from or at risk for developing prostate cancer. These genes and the proteins they encode can also be used to identify novel therapeutic agents for treatment of prostate cancer and as diagnostic markers.
The second example concerns the identification of 45 genes whose expression is increased in prostate cancer cells in the presence of bicalutamide, an anti-androgenic compound that is commonly used to treat prostate cancer. Because the increased expression of these genes in prostate cancer cells is associated with a successful treatment for prostate cancer, these genes can be used as markers to identify novel therapeutic compounds and to monitor the course/effectiveness of a therapy, particularly an anti-androgenic therapy.

a) EXAMPLE 1

Identification of Genes Whose Expression is Increased in the Presence of Testosterone

LNCaP cells were grown T162 flasks coated with Matrigel in RPMI-1640 medium supplemented with 10% FBS and 50 nM testosterone. Prior to testosterone treatment, the cells were pre-incubated for 24.5 hours in dye-free RPMI-1640 containing 2% charcoal stripped serum.
Five T162 flasks of pretreated cells were treated with testosterone-containing medium (dye-free RPMI-1640, 2% CSS, 100 nM testosterone, 0.09% DMSO). After 25 hours of incubation in testosterone-containing medium, the cells were detached from the flasks with trypsin and pelleted. Five T162 flasks of pretreated cells were used as a control. Untreated cells were collected in the same manner.
Total RNA was prepared from the cell pellets using the RNeasy protocol (Qiagen). Approximately 260 μg of total RNA was obtained from each cell pellet. Next, polyA+ RNA was prepared form approximately 240 μg of each total RNA sample using the Oligotex protocol (Qiagen), approximately 6 μg of polyA+ RNA was obtaining from each 240 μg total RNA sample, and 2 μg of each polyA+ RNA sample was used for the generation of subtraction libraries using the PCR-select protocol. (Clontech; Palo Alto, Calif.).
The PCR products representing partial cDNAs of putatively differentially expressed mRNAs were subcloned into pCR2.1 (InVitrogen) and transformed into INValphaF¹cells.
The differentially expressed genes were then identified by screening on a Gene Expression Micro-Array™ (Synteni, Inc.; Fremont, Calif.).

Table 1 is a list of identified genes whose expression is greater in testosterone-treated prostate cancer cells than untreated prostate cancer cells. Generally the genes are listed in ranked order. In some cases only a partial sequence is presented in the corresponding figure. The various methods described herein can employ complete sequences or fragments thereof.

TABLE 1


	Fold
	Increase	SEQ
	In	ID
Gene	mRNA	NO.

Monoamine oxidase	5.5	1
Neprilysin	2.8	2
Cell division control protein 2 homolog (X05360)	*	3
Cell division protein kinase 6	3.1	4
5-hydroxytryptamine 2C receptor	*	5
Aryl hydrocarbon receptor nuclear translocator	4.6	6
Guanine nucleotide exchange factor MSS4 (U74324)	2.7	7
(−76 nucleotide)
DNA mismatch repair protein MSH2	*	8
HEK2 protein tyrosine kinase receptor	2.6	9
Ras-like GTP-binding protein RAN	2.6	10
UDP glucuronosyltransferase precursor (UGT2B15)	2.8	11
BM28 mRNA/DNA replication licensing factor	2.4	12
(huMCM2)
Yeast guanine nucleotide-binding protein beta subunit-	2.4	13
like protein
Thyroid receptor interactor (TRIP7) (L40357)	2.4	14
(−92 nucleotide)
Pyruvate kinase (M26252) = human TCB gene encoding	2.3	15
cytosolic thyroid hormone-binding protein
EXT1 = putative tumor suppressor/hereditary mult.	2.4	16
exostoses candidate gene
Phospholipase A2 (M22430)	2.7	17
UDP-glucuronosyltransferase 2B7 precursor	3.9	18
WILMS' tumor protein (X51630)	*	19
Apolipoprotein B-100 precursor (XO4506)	*	20
Forkhead protein FREAC-2	*	21
S-adenosylmethionine decarboxylase	2.3	22
Kinesin-related protein	4.8	23
Spectrin alpha chain	3.5	24
KIAA0018 gene (D13643)	3.3	25
Myeloblast KIAA0130 gene (D50920)	3.3	26
Brain-expressed HHCPA78 homolog (S73591)	3	27
Vacuolar ATP synthase subunit AC39; or bovine	3.1	28
(P17694) NADH-ubiquinone oxidoreductase 49 kD
subunit
Gelsolin precursor	2.8	29
Ankyrin G (ANK-3) (U13616)	2.7	30
High mobility group protein HMG1 (X12597)	2.6	31
S-adenosylmethionine decarboxylase proenzyme	2.5	32
(M21154)
p0071 protein (X81889)	2.4	33
F02A9.5 homolog	*	34
Eukaryotic inititaion factor 1A	2.4	35
L-lactate dehydrogenase M chain (X02152, M17516)	3	36
Cytochrome b5	3.3	37
Fibronectin (S00848, transformation-associated human	2.8	38
fragment)
Tubulin beta 1 chain	2.8	39
Histone H2AZ	2.5	40
STS (WI 12919)	7.7	86
ESTs {344156}	5.9	87
STS (WI-8530)	5	88
ESTs {128990}	5	89
ESTs {26259}	5	90
ESTs {48537}	4.5	91
ESTs {221118}	4.4	92
ESTs {195079}	4.3	93
ESTs {242643}	4.1	94
ESTs {41700}	4	95
ESTs {301487}	3.8	96
ESTs {469725}	3.7	97
Immunoglobulin rearranged H-chain V-region	3.6	98
(C-D-J Hg)
ESTs {249347}	3.5	99
ESTs {135326}	3.4	100
ESTs {177150}	3.1	101
ESTs {375900}	3.1	102
ESTs {46287}	3	103
ESTs {264293}	3	104
ESTs {429349}	3	105
ESTs {128055}	2.8	106
ESTs {415795}	2.8	107
ESTs {364618}	2.7	108
ESTs {52371}	2.6	109
ESTs {471083}	2.6	110
ESTs {23605}	2.5	111
ESTs {32161}	2.5	112
ESTs {364477}	2.5	113
54 kDa progesterone receptor-associated immunophilin	2.5	114
FKBP54
ESTs {488092}	2.5	115
ESTs {151339}	2.4	116
ESTs {174787}	2.4	117
ESTs {230447}	2.4	118
ESTs {131591}	2.3	119
ESTs {141115}	2.3	120
Simian T-cell lymphotropic virus type I DNA for tax/rex	2.3	121
region
ESTs {51591}	2.3	122
ESTs {297463}	2.3	123
ESTs {180082}	2.1	124
ESTs {133211}	*	125
Thymopoietin alpha	*	126
ESTs {52092}	*	127
ESTs {238656}	*	128
ESTs {428502}	*	129
Zinc finger protein	*	130

b) EXAMPLE 2

Identification of Genes Whose Expression is Increased in the Presence of Bicalutamide

LNCaP cells were grown in T162 flasks coated with Matrigel in RPMI-1640 medium supplemented with 10% FBS and 50 nM testosterone. Prior to bicalutamide treatment, cells were preincubated for 24.5 hours in dye-free RPMI-1640 containing 2% charcoal stripped serum.
Five T162 flasks of pretreated cells were treated with bicalutamide-containing medium (dye-free RPMI-1640, 2% CSS, 100 nM bicalutamide in DMSO). After 25 hours of incubation in bicalutamide-containing medium, LNCaP cells were detached from the flasks with trypsin and pelleted. Five T162 flasks of pretreated cells were used as a control. Untreated cells were collected in the same manner.
Total RNA was prepared from the cell pellets using the RNeasy protocol (Qiagen). Approximately 260 μg of total RNA was obtained form each cell pellet. Next, polyA+ RNA was prepared form approximately 240 μg of each total RNA sample using the Oligotex protocol (Qiagen), approximately 6 μg of polyA+ RNA was obtaining from each 240 μg total RNA sample, and 2 μg of each polyA+ RNA sample was used for the generation of subtraction libraries using the PCR-select protocol (Clontech; Palo Alto, Calif.).
The PCR products representing partial cDNAs of putatively differentially expressed mRNAs were subcloned into pCR2.1 (InVitrogen) and transformed into INValphaF¹cells.
The diffentially expressed genes were then identified by screening on a Gene Expression Micro-Array™ (Synteni, Inc.; Fremont, Calif.).

Table 2 is a list of identified genes whose expression is greater in bicalutamide-treated prostate cancer cells than untreated prostate cancer cells. Generally the genes are listed in ranked order. In some cases only a partial sequence is presented in the corresponding figure. The various methods described herein can employ complete sequences or fragments thereof.

TABLE 2


	FOLD	SEQ
	INCREASE	ID
GENE	IN mRNA	NO.

Cyclin-dependent kinase inhibitor 1 {268652}	4.5	41
Activating transcription factor 3 (ATF3) {428248}	11.5	42
Defender against cell death 1 {488974}	2.9	43
Transcription factor ITF-2 {380738}	*	44
CCAAT/Enhancer binding protein BETA {357095}	*	45
CLCN3 {346749}	2.4	46
Phosphotyrosine independent ligand p62 for the Lck	5.8	47
SH2 domain {510278}
Seryl-tRNA synthetase {510431}	4.3	48
D53 (hD53) {510461}	3.8	49
Unknown human protein {512334}	3.5	50
Thioredoxin reductase {510377}	2.6	51
Tryptophanyl-tRNA synthetase {510220}	*	52
ORF and HepG2 (identical sequence) {510258}	5.3	53
4F2 cell-surface antigen heavy chain {510504}	8.1	54
Asparagine synthetase {510206}	2.8	55
pM5 {509550}	2.3	56
Archain {488510}	2.3	57
Gravin {488106}	2.8	58
Metallothionein-II (mt-II) {484963}	*	59
Signal recognition particle receptor alpha subunit	2.6	60
{358710}
Phosphoenolpyruvate carboxykinase {363272}	3.4	61
Protein translation factor SUI1 homolog {365542}	2.7	62
NADPH-flavin reductase {365775}	3.7	63
Peptidyl-prolyl CIS-trans isomerase B precursor	2.5	64
{376399}
Aspartate aminotransferase {417270}	3.1	65
OS-9 precursor {417136}	2.7	66
KIAA0025 and PIGHEP3 homologous region	5.3	67
{418227}
Glucosamine-fructose-6-phosphate aminotransferase	3.2	68
{469633}
ADP-ribosylation factor 1 {471384}	3.1	69
Glycyl-tRNA synthetase {471164}	3.6	70
Prion protein (PrP) {470074}	3.1	71
Mitochondrial serine hydroxymethyltransferase	2.4	72
{344080}
Alanyl-TRNA synthetase {343998}	3.8	73
bZIP protein NF-IL3A {343273}	*	74
Interleukin-8 precursor {328692}	*	75
Translocon-associated protein {324179}	2.5	76
Proto-oncogene tyrosine-protein kinase FYN	*	77
{323555}
Translation initiation factor 5 (elF5) {299843}	2.3	78
RESTIN {291620}	2.3	79
Transcription elongation factor S-II {257458}	2.8	80
Human clone 137308 {252491}	2.6	81
Glutamate-cysteine ligase regulatory subunit	4.1	82
{245939}
Fatty aldehyde dehydrogenase {208950}	3.1	83
MHC class 1 HLA-Bw58 gene {203448}	2.3	84
Mitochondrial NDA (P)+ dependent malic enzyme	2.5	85
{109375}
ESTs {44552}	*	131
ESTs {381626}	*	132
ESTs {486242}	*	133
Tryptophanyl tRNA sythestase (IFNWRS)	*	134
{489453}
AU-rich element RNA-binding protein AUF1	*	135
{510536}
GADD 153 = Growth arrest and DNA-damage	11.1	136
inductor gene {362009}
KIAA0025 gene {30476}	6.7	137
Phosphotyrosine independent ligand p62 for the Lck	6.4	138
SH2 domain {471392}
150 kDa oxygen-regulated protein ORP150	5.9	139
{486858}
78 KD Glucose regulated protein precursor	4	140
{366350}
Smad 1 {345928}	3.9	141
EST28g11 WATM1 {486703}	3.8	142
ESTs {322080}	3.7	143
Seryl-tRNA sythetase {129892}	3.6	144
HU-K4 {470677}	3.6	145
ESTs {126530}	3.5	146
ESTs {429327}	3.5	147
Vascular endothelial growth factor (VEGF (165))	3.2	148
{488697}
ESTs {50914}	3.1	149
ESTs {279847}	3.1	150
ESTs {361548}	3.1	151
ESTs {364730}	3.1	152
ESTs {470212}	3.1	153
ESTs {471210}	3.1	154
ESTs {289300}	3	155
ESTs {427725}	3	156
ESTs {428217}	2.9	157
rfp transforming protein {485268}	2.8	158
ESTs {487420}	2.8	159
60S RIBOSOMAL PROTEIN L18A {509699}	2.8	160
ESTs {31943}	2.7	161
ESTs {376271}	2.7	162
ESTs {469642}	2.7	163
ESTs {471826}	2.7	164
KIAA0262 {485008}	2.7	165
ESTs {292082}	2.6	166
ESTs {365557}	2.6	167
Immunogloblin light chain (lambda) {119218}	2.5	168
ELP-1 {147979}	2.5	169
TRAMP protein {149355}	2.5	170
ESTs {294078}	2.5	171
ESTs {291005}	2.5	172
ESTs {365907}	2.5	173
ESTs {427801}	2.5	174
ESTs {469515}	2.5	175
Tral mRNA for human homologue of murine tumor	2.5	176
rejection antigen gp96 {509486}
Biotin-[propionyl-CoA-carboxylase (ATP-	2.4	177
hydrolysing)] {176590}
Tral mRNA for human homologue of murine tumor	2.4	178
rejection antigen gp96 {242829}
Cancellous bone osteoblast mRNA for GS3786	2.4	179
{486005}
ESTs {509583}	2.4	180
ESTs {44551}	2.3	181
ESTs {245853}	2.3	182
ESTs {306075}	2.3	183
ESTs {322143}	2.3	184
ESTs {322749}	2.3	185
ESTs {359877}	2.3	186
ESTs {360446}	2.3	187
ESTs {360789}	2.3	188
Protein tyrosine kinase t-Rorl {418257}	2.3	189
ESTs {486712}	2.3	190
ESTs {489106}	2.3	191

III. The Use of Differentially Expressed Genes in Selecting and Monitoring Prostate Cancer Therapies

The expression level of identified differentially expressed genes may be used to assess patients undergoing clinical evaluation for the treatment of prostate cancer. Thus, the identified genes can be used to select an appropriate therapy for an individual and to monitor an ongoing therapy. They may also be utilized as surrogate markers to monitor clinical human trials of a drug being tested for their efficacy as a prostate cancer treatment. In either case, one or more of the identified differentially expressed genes may be utilized as a marker.
One can determine whether a given patient will benefit from anti-androgenic therapy by examining the expression level of one or more of the differentially expressed genes identified herein as being expressed at a higher level in prostate cancer-cells in the presence of testosterone than in the absence of testosterone. If one or more of these genes is more highly expressed in the patient's prostate cancer cells than in normal prostate cells, the prostate cancer cells are more likely to respond to anti-androgenic therapy. As used herein, “anti-androgenic therapy” refers broadly to any therapy which interferes with or blocks the synthesis or action of an androgen. Similarly, “anti-testosterone therapy” refers broadly to any therapy which interferes with or blocks the synthesis or action of testosterone. Such therapies can, for example, block ligand receptor binding (e.g., binding of testosterone to its receptor), receptor signalling (e.g., signal transduction mediated by the binding of testosterone to its receptor), or the activity or expression of a downstream regulated gene.
Accordingly, the invention features a method for determining whether a compound, e.g., an anti-androgenic compound can be used to treat prostate cancer in a patient. The method includes:

- a) obtaining a patient biological sample;
- b) determining the normalized expression level of one or more genes selected from the group consisting of SEQ ID NOS:1-40, 86-130 in the patient sample;
- c) comparing the normalized expression level of the selected one or more genes determined in step b) with the normalized expression level of the selected one or more genes in a non-prostate cancer biological sample; and
- d) identifying that a compound can be used to treat prostate cancer in the patient when the normalized expression level of the selected one or more genes in the patient sample is greater than the normalized expression level of the selected one or more genes in the non-prostate cancer sample.

A non-prostate cancer biological sample is a sample of prostate cells, serum, interstitial fluid, blood, or seminal fluid from an individual which is not suffering from prostate cancer or a cell line, e.g., a prostate cell line which is not a prostat cancer cell line.
If the normalized expression of the selected one or more genes in the patient sample is not greater than the normalized expression of the selected one or more genes in the non-prostate cancer cell sample, it is less likely that an anti-androgenic therapy will be successful.
The invention also features a method for determining whether a compound, e.g., an anti-androgenic compound, can be used to treat prostate cancer in a patient, which method includes:

- a) obtaining a patient biological sample;
- b) determining the normalized expression level of one or more genes selected from the group consisting of SEQ ID NOS:1-40, 86-130 in the patient sample;
- c) comparing the normalized expression level of the selected one or more genes determined in step b) with the normalized expression level of the selected one or more genes in a non-prostate cancer sample; and
- d) identifying that a compound cannot be used to treat prostate cancer in the patient when the normalized expression level of the selected one or more genes in the patient sample is equal to or less than the normalized expression level of the selected one or more genes in the non-prostate cancer biological sample.

Generally, it is preferable to assess the expression of two, five or more, or even ten or more of the genes that are expressed at a higher level in prostate cancer cells treated with testosterone. Thus, it is preferable to assess the expression of a panel of differentially expressed genes.
In these assays, as well as other assays involving comparison of “normalized” expression levels, normalization refers to correcting the expression level of a differentially expressed gene by comparing its expression to the expression of a gene which is not differentially expressed in response to the selected compound, e.g., a gene that is not differentially expressed in prostate cancer cells in response to testosterone. Suitable genes for nromalization include housekeeping genes, e.g., the actin gene. This normalization allows one to compare the expression level in one sample, e.g., a patient sample, to another sample, e.g., a non-prostate cancer sample.
The expression level can be measured in a number of ways, including: measuring the mRNA encoded by each of the selected one or more genes; measuring the amount of protein encoded by each of the selected one or more genes; and measuring the activity of the protein encoded by each of the selected one or more genes.
Preferably, the expression level of several different selected genes from the group consisting of SEQ ID NOS:1-40, 86-130 are compared. For example, the expression of the gene of SEQ ID NO: 1 is compared in the two samples, and the expression of the gene of SEQ ID NO:2 is compared in the two samples. Preferably the selected genes are five or more genes selected from the group consisting of SEQ ID NOS:1-40, 86-130 or ten or more genes selected from the group consisting of SEQ ID NOS:1-40, 86-130.
The patient biological sample can be derived from, e,g., patient prostate cells, patient serum, patient interstitial fluid, patient blood, or patient seminal fluid. A sample of prostate cancer cells can be obtained by needle biopsy or other method used to biopsy or sample prostate cells.
As discussed above, the identified genes can also be used as markers to assess whether a prostate tumor has become refractory to an ongoing treatment (e.g., anti-androgenic treatment). When a tumor is no longer responding to a treatment the expression profile of the tumor cells is more closely resemble the expression profile of testosterone-treated prostate cancer cells than bicalutamide-treated prostate cancer cells.
Accordingly, the invention features methods for determining whether an anti-androgen treatment should be continued in a prostate cancer patient. One such method includes:

- a) obtaining a patient biological sample;
- b) determining the normalized expression level of one or more genes selected from the group consisting of SEQ-ID NOS:1-40, 86-130 in the patient sample;
- c) comparing the normalized expression level of the selected one or more genes determined in step b) with the normalized expression level of the selected one or more genes in a non-prostate cancer biological sample; and
- d) discontinuing treatment when the normalized expression level of the selected one or more genes in the patient sample is greater than the normalized expression level of the selected one or more genes in the non-prostate cancer sample.

Another method for determining whether an anti-androgen treatment should be continued in a prostate cancer patient includes:

- a) obtaining a patient biological sample;
- b) determining the normalized expression level of one or more genes selected from the group consisting of SEQ ID NOS:1-40, 86-130 in the patient sample;
- c) comparing the normalized expression level determined in step b) with the normalized expression level of the selected one or more genes in a non-prostate cancer biological sample; and
- d) continuing treatment when the normalized expression of the selected one or more genes in the patient sample is equal to or less than the normalized expression of the selected one or more genes in the non-prostate cancer sample.

Preferably, the expression level of several different selected genes from the group consisting of SEQ ID NOS: 1-40, 86-130 are compared. For example, the expression of the gene of SEQ ID NO: 1 is compared in the two samples, and the expression of the gene of SEQ ID NO:2 is compared in the two samples. Preferably the selected genes are five or more genes selected from the group consisting of SEQ ID NOS:1-40, 86-130 or ten or more genes selected from the group consisting of SEQ ID NOS:1-40, 86-130.
The patient biological sample can be derived from, e,g., patient prostate cells, patient serum, patient interstitial fluid, patient blood, or patient seminal fluid.
In the context of clinical trials, test patients can be administered compounds suspected of being effective for treatment of prostate cancer. Control patients can be given a placebo. Tumor cells or biopsies can be drawn from each patient after a determined period of treatment. RNA can be isolated and subjected to expression analysis as described above.
Yet another method for determining whether a treatment should be continued in a prostate cancer patient includes:

- a) obtaining a patient biological sample;
- b) determining the normalized expression level of one or more genes selected from the group consisting of SEQ ID NOS:41-85, 131-191 in the patient sample;
- c) comparing the normalized expression level of the selected one or more genes determined in step b) with the normalized expression level of the selected one or more genes in a non-prostate cancer biological sample; and
- d) discontinuing treatment when the normalized expression level of the selected one or more genes in the patient sample is less than or equal to the normalized expression level of the selected one or more genes in the non-prostate cancer sample.

Yet another method for determining whether a treatment should be continued in a prostate cancer patient incldues:

- a) obtaining a patient biological sample;
- b) determining the normalized expression level of one or more genes selected from the group consisting of SEQ ID NOS:41-85, 131-191 in the patient sample;
- c) comparing the normalized expression level determined in step b) with the normalized expression level of the selected one or more genes in a non-prostate cancer biological sample; and
- d) continuing treatment when the normalized expression of the selected one or more genes in the patient sample is greater than the normalized expression of the selected one or more genes in the non-prostate cancer sample.

Preferably, the expression level of several different selected genes from the group consisting of SEQ ID NOS: 41-85, 131-191 are compared. For example, the expression of the gene of SEQ ID NO: 41 is compared in the two samples, and the expression of the gene of SEQ ID NO:42 is compared in the two samples. Preferably the selected genes are five or more genes selected from the group consisting of SEQ ID NOS:41-85, 131-191 or ten or more genes selected from the group consisting of SEQ ID NOS:41-85, 131-191.
The patient biological sample can be derived from, e,g., patient prostate cells, patient serum, patient interstitial fluid, patient blood, or patient seminal fluid.
In the context of clinical trials, test patients can be administered compounds suspected of being effective for treatment of prostate cancer. Control patients can be given a placebo. Tumor cells or biopsies can be drawn from each patient after a determined period of treatment. RNA can be isolated and subjected to expression analysis as described above.
The identified differentially expressed genes can also be used to determine whether a compound can be used to treat prostate cancer either generally or in a specific patient. In this approach the expression of one or more of the differentially expressed genes identified herein is measured in prostate cancer cells in the presence and absence of the candidate therapeutic compound.
If the gene(s) whose expression is assessed is of the class that is expressed at a higher level in the in the presence bicalutamide than in the absence of bicalutamide (SEQ ID NOS:41-85, 131-191), and it is observed that the gene(s) is more highly expressed in the presence of the candidate compound than in the absence of the candidate compound, then the candidate compound is likely to be a useful therapeutic agent. Thus, the invention features methods for determining whether a compound can be used to treat prostate cancer. The method includes:

- a) measuring the expression level of one or more genes selected from the group consisting of SEQ ID NOS:41-85, 131-191 in a prostate cancer cell sample in the presence and absence of the compound; and
- b) identifying the compound as useful for treating prostate cancer when the expression level of the selected one or more genes in the presence of the compound is greater than the expression level of the selected one or more genes in the absence of the compound.

If the gene(s) whose expression is assessed in the screening assay is of the class that is expressed at a higher level in the in the presence testosterone than in the absence of testosterone (SEQ ID NOS:1-40, 86-130), and it is observed that the gene(s) is not more highly expressed in the presence of the candidate compound than in the absence of the candidate compound, then the candidate compound is likely to be a useful therapeutic. Thus, the invention features a method for determining whether a compound can be used to treat prostate cancer, which method includes:

- a) measuring the expression level of one or more genes selected from the group consisting of SEQ ID NOS:1-40, 86-130 in prostate cancer cell sample in the presence and absence of the compound; and
- b) identifying the compound as useful for treating prostate cancer when the expression level of the selected one or more genes in the presence of the compound is less than the expression level of the selected one or more genes in the absence of the compound.

Of course, the above-described screening method can entail measuring gene expression in a prostate cancer cell line or in prostate cancer cells isolated from a selected patient. Thus, the method can be used to identify therapeutic compounds which are expected to be generally useful as well and to identify therapeutic compounds which are expected to be beneficial for a particular patient.
It should also be recognized that there can be considerable benefit in assessing the expression of two or more, five or more, or even ten or more identified differentially expressed genes when screening candidate therapeutic agents.
IV. The Use of Differentially Expressed Genes in Diagnosing Prostate Cancer
A variety of methods can be employed for the diagnosis of prostate cancer. Such methods can, for example, utilize reagents such as fingerprint gene nucleotide sequences and antibodies directed against differentially expressed fingerprint gene products. Specifically, such reagents can be used, for example, for the detection of the detection of either over- or under-expression a differentially expressed gene or the presence of a mutation in a differentially expressed gene that is a target gene.
An identified differentially expressed gene which is expressed at a higher level in prostate cancer cells in the presence of testosterone than the absence of testosterone can be used as diagnostic markers. Thus, the invention features a method for determining whether a person has or is at risk of developing prostate cancer, which method includes:
A method for determining whether an individual has or at risk for developing prostate cancer, comprising:

- a) obtaining a biological sample from the individual;
- b) determining the normalized expression level of one or more genes selected from the group consisting of SEQ ID NOS:1-40, 86-130 in the individual sample;
- c) comparing the normalized expression level of the selected one or more genes determined in step b) with the normalized expression level of the selected one or more genes in a non-prostate cancer biological sample; and
- d) indentifying the individual as having or being at risk for developing prostate cancer when the normalized expression level of the selected one or more genes in the individual sample is greater than the normalized expression level of the selected one or more genes in the non-prostate cancer sample.

The methods described herein can be performed, for example, by utilizing pre-packaged diagnostic kits comprising at least one specific fingerprint gene nucleic acid or anti-fingerprint gene antibody reagent described herein, which can be conveniently used, e.g., in clinical settings, to diagnose patients exhibiting symptoms of prostate cancer.
a) Detection of Fingerprint Gene Nucleic Acids
DNA or RNA from the cell type or tissue to be analyzed can easily be isolated using procedures which are well known to those in the art. Diagnostic procedures can also be performed in situ directly upon tissue sections (fixed and/or frozen) of patient tissue obtained from biopsies or resections, such that no nucleic acid purification is necessary. Nucleic acid reagents such as those described above can be used as probes and/or primers for such in situ procedures (see, for example, Nuovo, 1992, PCR in situ Hybridization: Protocols and Applications, Raven Press, NY).
Fingerprint gene nucleotide sequences, either RNA or DNA, can, for example, be used in hybridization or amplification assays of biological samples to detect genes and expression patterns associated with prostate cancer. Such assays can include, but are not limited to, Southern or Northern analyses, single stranded conformational polymorphism analyses, in situ hybridization assays, and, polymerase chain reaction analyses. Such analyses can reveal both quantitative aspects of the expression pattern of the fingerprint gene, and qualitative aspects of the fingerprint gene expression and/or gene composition. That is, such techniques can include, for example, point mutations, insertions, deletions, chromosomal rearrangements, and/or activation or inactivation of gene expression.
Preferred diagnostic methods for the detection of fingerprint gene-specific nucleic acid molecules can involve for example, contacting and incubating nucleic acids, derived from the cell type or tissue being analyzed, with one or more labeled nucleic acid reagents under conditions favorable for the specific annealing of these reagents to their complementary sequences within the nucleic acid molecule or interest. Preferably, the lengths of these nucleic acid reagents are at least 15 to 30 nucleotides. After incubation, all non-annealed nucleic acids are removed from the nucleic acid:fingerprint RNA molecule hybrid. The presence of nucleic acids from the target tissue which have hybridized, if any such molecules exist, is then detected. Using such a detection scheme, the nucleic acid from the tissue or cell type of interest can be immobilized, for example, to a solid support such as a membrane, or a plastic surface such as that on a microtiter plate or polystyrene beads. In this case, after incubation, non-annealed, labeled fingerprint nucleic acid reagents are easily removed. Detection of the remaining, annealed, labeled nucleic acid reagents is accomplished using standard techniques well-known to those in the art.
Alternative diagnostic methods for the detection of fingerprint gene specific nucleic acid molecules can involve their amplification, e.g., by PCR (the experimental embodiment set forth in Mullis, 1987, U.S. Pat. No. 4,683,202), ligase chain reaction (Barany, 1991, Proc. Natl. Acad. Sci. USA 88:189-193), self sustained sequence replication (Guatelli et al., 1990, Proc. Natl. Acad. Sci. USA 87:1874-1878), transcriptional amplification system (Kwoh et al., 1989, Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta Replicase (Lizardi et al., 1988, Bio/Technology 6:1197), or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers.
In one embodiment of such a detection scheme, a cDNA molecule is obtained from an RNA molecule of interest (e.g., by reverse transcription of the RNA molecule into cDNA). Cell types or tissues from which such RNA can be isolated include any tissue in which wild type fingerprint gene is known to be expressed. A sequence within the cDNA is then used as the template for a nucleic acid amplification reaction, such as a PCR amplification reaction, or the like. The nucleic acid reagents used as synthesis initiation reagents (e.g., primers) in the reverse transcription and nucleic acid amplification steps of this method are chosen from among the fingerprint gene nucleic acid reagents. The preferred lengths of such nucleic acid reagents are at least 19-30 nucleotides. For detection of the amplified product, the nucleic acid amplification can be performed using radioactively or non-radioactively labeled nucleotides. Alternatively, enough amplified product can be made such that the product can be visualized by standard ethidium bromide staining or by utilizing any other suitable nucleic acid staining method.
In addition to methods which focus primarily on the detection of one nucleic acid sequence, fingerprint profiles can also be assessed in such detection schemes. Fingerprint profiles can be generated, for example, by utilizing a differential display procedure, as discussed above, Northern analysis, and/or RT-PCR. Any of the fingerprint gene sequences described above can be used as probes and/or PCR primers for the generation and corroboration of such fingerprint profiles.
b) Detection of Fingerprint Gene Products
Antibodies directed against wild-type or mutant fingerprint gene products can also be used in prostate cancer diagnostics and prognostics. Such diagnostic methods, can be used to detect abnormalities in the level of fingerprint gene protein expression, or abnormalities in the structure and/or tissue, cellular, or subcellular location of fingerprinting gene protein. Structural differences can include, for example, differences in the size, electronegativity, or antigenicity of the mutant fingerprint gene protein relative to the normal fingerprint gene protein.
Protein from the tissue or cell type to be analyzed can easily be isolated using techniques which are well known to those of skill in the art. The protein isolation methods employed herein can, for example, be such as those described in Harlow and Lane (Harlow and Lane, 1988, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.), which is incorporated herein by reference in its entirety.
Preferred diagnostic methods for the detection of wild-type or mutant fingerprint gene peptide molecules can involve, for example, immunoassays wherein fingerprint gene peptides are detected by their interaction with an anti-fingerprint gene specific peptide antibody.
For example, antibodies, or fragments of antibodies, useful in the present invention can be used to quantitatively or qualitatively detect the presence of wild-type or mutant fingerprint gene peptides. This can be accomplished, for example, by immunofluorescence techniques employing a fluorescently labeled antibody (see below) coupled with light microscopic, flow cytometric, or fluorimetric detection. Such techniques are especially preferred if the fingerprint gene peptides are expressed on the cell surface.
The antibodies (or fragments thereof) useful in the present invention can, additionally, be employed histologically, as in immunofluorescence or immunoelectron microscopy, for in situ detection of target gene peptides. In situ detection can be accomplished by removing a histological specimen from a patient, and applying thereto a labeled antibody of the present invention. The antibody (or fragment) is preferably applied by overlaying the labeled antibody (or fragment) onto a biological sample. Through the use of such a procedure, it is possible to determine not only the presence of the fingerprint gene peptides, but also their distribution in the examined tissue. Using the present invention, those of ordinary skill will readily perceive that any of a wide variety of histological methods (such as staining procedures) can be modified in order to achieve such in situ detection.
Immunoassays for wild-type or mutant fingerprint gene peptides typically comprise incubating a biological sample, such as a biological fluid, a tissue extract, freshly harvested cells, or cells which have been incubated in tissue culture, in the presence of a detectably labeled antibody capable of identifying fingerprint gene peptides, and detecting the bound antibody by any of a number of techniques well-known in the art.
The biological sample can be brought in contact with and immobilized onto a solid phase support or carrier such as nitrocellulose, or other solid support which is capable of immobilizing cells, cell particles or soluble proteins. The support can then be washed with suitable buffers followed by treatment with the detectably labeled fingerprint gene specific antibody. The solid phase support can then be washed with the buffer a second time to remove unbound antibody. The amount of bound label on solid support can then be detected by conventional means.
Suitable solid phase supports or carriers include any support capable of binding an antigen or an antibody. Well-known supports or carriers include glass, polystyrene, polypropylene, polyethylene, dextran, nylon, amylases, natural and modified celluloses, polyacrylamides, gabbros, and magnetite. The nature of the carrier can be either soluble to some extent or insoluble for the purposes of the present invention. The support material can have virtually any possible structural configuration so long as the coupled molecule is capable of binding to an antigen or antibody. Thus, the support configuration can be spherical, as in a bead, or cylindrical, as in the inside surface of a test tube, or the external surface of a rod. Alternatively, the surface can be flat such as a sheet, test strip, etc. Preferred supports include polystyrene beads. Those skilled in the art will know many other suitable carriers for binding antibody or antigen, or will be able to ascertain the same by use of routine experimentation.
The binding activity of a given lot of anti-wild type or mutant fingerprint gene peptide antibody can be determined according to well-known methods. Those skilled in the art will be able to determine operative and optimal assay conditions for each determination by employing routine experimentation.
One of the ways in which the fingerprint gene peptide-specific antibody can be detectably labeled is by linking the same to an enzyme and use in an enzyme immunoassay (EIA). The enzyme which is bound to the antibody will react with an appropriate substrate, preferably a chromogenic substrate, in such a manner as to produce a chemical moiety which can be detected, for example, by spectrophotometric, fluorimetric or by visual means. Enzymes which can be used to detectably label the antibody include, but are not limited to, malate dehydrogenase, staphylococcal nuclease, delta-5-steroid isomerase, yeast alcohol dehydrogenase, alpha-glycerophosphate, dehydrogenase, triose phosphate isomerase, horseradish peroxidase, alkaline phosphatase, asparaginase, glucose oxidase, beta-galactosidase, ribonuclease, urease, catalase, glucose-6-phosphate dehydrogenase, glucoamylase and acetylcholinesterase. The detection can be accomplished by calorimetric methods which employ a chromogenic substrate for the enzyme. Detection can also be accomplished by visual comparison of the extent of enzymatic reaction of a substrate in comparison with similarly prepared standards.
Detection can also be accomplished using any of a variety of other immunoassays. For example, by radioactively labeling the antibodies or antibody fragments, it is possible to detect fingerprint gene wild type or mutant peptides through the use of a radioimmunoassay (RIA). The radioactive isotope can be detected by such means as the use of a gamma counter or a scintillation counter or by autoradiography.
It is also possible to label the antibody with a fluorescent compound. When the fluorescently labeled antibody is exposed to light of the proper wave length, its presence can then be detected due to fluorescence. Among the most commonly used fluorescent labeling compounds are fluorescein isothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin, o-phthaldehyde and fluorescamine.
The antibody can also be detectably labeled using fluorescence emitting metals such as ¹⁵²Eu, or others of the lanthanide series. These metals can be attached to the antibody using such metal chelating groups as diethylenetriaminepentacetic acid (DTPA) or ethylenediaminetetraacetic acid (EDTA).
The antibody also can be detectably labeled by coupling it to a chemiluminescent compound. The presence of the chemiluminescent-tagged antibody is then determined by detecting the presence of luminescence that arises during the course of a chemical reaction. Examples of particularly useful chemiluminescent labeling compounds are luminol, isoluminol, theromatic acridinium ester, imidazole, acridinium salt and oxalate ester.
Likewise, a bioluminescent compound can be used to label the antibody of the present invention. Bioluminescence is a type of chemiluminescence found in biological systems in, which a catalytic protein increases the efficiency of the chemiluminescent reaction. The presence of a bioluminescent protein is determined by detecting the presence of luminescence. Important bioluminescent compounds for purposes of labeling are luciferin, luciferase and aequorin.
V. Characterization of Differentially Expressed Genes
Differentially expressed genes can be further characterized by using techniques known to those skilled in the art.
Such characterization can yield information regarding the biological function of the identified genes. An assessment of the biological function of the differentially expressed genes, in addition, will allow for their designation as target and/or fingerprint genes.
Specifically, any of the differentially expressed genes whose further characterization indicates that a modulation of the gene's expression or a modulation of the gene product's activity can reduce symptoms of prostate cancer are designated “target genes.” Such target genes and target gene products can be used to identify therapeutics. A differentially expressed genes whose further characterization indicates that it does not influence growth or viability of prostate cancer cells, but whose expression pattern contributes to a gene expression “fingerprint” pattern correlative of, for example, the effectiveness of a drug is designated a “fingerprint gene.” Such genes can be used as diagnostic markers and as markers for assessing the effectiveness or potential effectiveness of a therapeutic agent.
A variety of techniques can be utilized to further characterize the identified genes. First, the nucleotide sequence of the identified genes, which can be obtained by utilizing standard techniques well known to those of skill in the art, can be used to further characterize such genes. For example, the sequence of the identified genes can reveal homologies to one or more known sequence motifs which can yield information regarding the biological function of the identified gene product.
Second, an analysis of the tissue and/or cell type distribution of the mRNA produced by the identified genes can be conducted, utilizing standard techniques well known to those of skill in the art. Such techniques can include, for example, Northern analyses, RT-coupled PCR and RNase protection techniques. Such analyses provide information as to whether the identified genes are expressed in tissues expected to contribute to prostate cancer. Such analyses can also provide quantitative information regarding steady state mRNA regulation, yielding data concerning which of the identified genes exhibits a high level of regulation in, preferably, tissues which can be expected to contribute to prostate cancer. Additionally, standard in situ hybridization techniques can be utilized to provide information regarding which cells within a given tissue express the identified gene. Such an analysis can provide information regarding the biological function of an identified gene in instances wherein only a subset of the cells within the tissue is thought to be relevant to prostate cancer.
Third, the sequences of the identified genes can be used, utilizing standard techniques, to place the genes onto genetic maps, e.g., mouse (Copeland and Jenkins 1991, Trends in Genetics 7:113-118) and human genetic maps (Cohen et al., 1993, Nature 366:698-701). Such mapping information can yield information regarding the genes' importance to human disease by, for example, identifying genes which map within genetic regions to which predisposition to prostate cancer also maps.
Fourth, the biological function of the identified genes can be more directly assessed by utilizing relevant in vivo and in vitro systems. In vivo systems can include, but are not limited to, animal systems which naturally exhibit symptoms of prostate cancer or ones which have been engineered to exhibit such symptoms.
The role of identified gene products can be determined by transfecting cDNAs encoding these gene products into appropriate cell lines, such as, for example, a prostate cancer cell line and analyzing the effect of the gene product on cell growth.
In further characterizing the biological function of the identified genes, the expression of these genes can be modulated within the in vivo and/or in vitro systems, i.e., either over-expressed or under-expressed, and the subsequent effect on the system then assayed. Alternatively, the activity of the product of the identified gene can be modulated by either increasing or decreasing the level of activity in the in vivo and/or in vitro system of interest, and assessing the effect of such modulation.
The information obtained through such characterizations can suggest relevant methods for the treatment of prostate cancer. For example, treatment can include a modulation of gene expression and/or gene product activity. Characterization procedures such as those described herein can indicate where such modulation should involve an increase or a decrease in the expression or activity of the gene or gene product of interest.
a) Expression of Proteins Encoded by Differentially Expressed Genes
A variety of host-expression vector systems can be utilized to express the differentially expressed gene coding sequences of the invention. Such host-expression systems represent vehicles by which the coding sequences of interest can be produced and subsequently purified, but also represent cells which can, when transformed or transfected with the appropriate nucleotide coding sequences, exhibit the differentially expressed gene protein in situ. These include but are not limited to microorganisms such as bacteria (e.g., E. coli and B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing differentially expressed gene protein coding sequences; yeast (e.g., Saccharomyces and Pichia) transformed with recombinant yeast expression vectors containing the differentially expressed gene protein coding sequences; insect cell systems infected with recombinant virus-expression vectors (e.g., baculovirus) containing the differentially expressed gene protein coding sequences; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing differentially expressed gene protein coding sequences; or mammalian cell systems (e.g., COS, CHO, BHK, 293, 3T3) harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells (e.g., metallothionein promoter) or from mammalian viruses (e.g., the adenovirus late promoter; the vaccinia virus 7.5K promoter).
In bacterial systems, a number of expression vectors can be advantageously selected depending upon the use intended for the differentially expressed gene protein being expressed. For example, when a large quantity of such a protein is to be produced, for the generation of antibodies or to screen peptide libraries, for example, vectors which direct the expression of high levels of fusion protein products that are readily purified can be desirable. Such vectors include, but are not limited, to the E. coli expression vector pUR278 (Ruther et al., 1983, EMBO J. 2:1791), in which the differentially expressed-gene protein coding sequence can be ligated individually into the vector in frame with the lacZ coding region so that a fusion protein is produced; pIN vectors (Inouye & Inouye, 1985, Nucleic Acids Res. 13:3101-3109; Van Heeke & Schuster, 1989, J. Biol. Chem. 264:5503-5509); and the like. pGEX vectors can also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption to glutathione-agarose beads followed by elution in the presence of free glutathione. The pGEX vectors are designed to include thrombin or factor Xa protease cleavage sites so that the cloned target gene protein can be released from the GST moiety.
In an insect system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes. The virus grows in Spodoptera frugiperda cells. The differentially expressed gene coding sequence can be cloned individually into non-essential regions (for example the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (for example, the polyhedrin promoter). Successful insertion of differentially expressed gene coding sequence will result in inactivation of the polyhedrin gene and production of non-occluded recombinant virus (i.e., virus lacking the proteinaceous coat coded for by the polyhedrin gene). These recombinant viruses are then used to infect Spodoptera frugiperda cells in which the inserted gene is expressed (e.g., see Smith et al., 1983, J. Viol. 46:584; Smith, U.S. Pat. No. 4,215,051).
In mammalian host cells, a number of viral-based expression systems can be utilized. In cases where an adenovirus is used as an expression vector, the differentially expressed gene coding sequence of interest can be ligated to an adenovirus transcription/translation control complex, e.g., the late promoter and tripartite leader sequence. This chimeric gene can then be inserted in the adenovirus genome by in vitro or in vivo recombination. Insertion in a non-essential region of the viral genome (e.g., region E1 or E3) will result in a recombinant virus that is viable and capable of expressing differentially expressed gene protein in infected hosts (e.g., see Logan & Shenk, 1984, Proc. Natl. Acad. Sci. USA 81:3655-3659). Specific initiation signals can also be required for efficient translation of inserted differentially expressed gene coding sequences. These signals include the ATG initiation codon and adjacent sequences. In cases where an entire identified gene, including its own initiation codon and adjacent sequences, is inserted into the appropriate expression vector, no additional translational control signals can be needed. However, in cases where only a portion of the identified coding sequence is inserted, exogenous translational control signals, including, perhaps, the ATG initiation codon, must be provided. Furthermore, the initiation codon must be in phase with the reading frame of the desired coding sequence to ensure translation of the entire insert. These exogenous translational control signals and initiation codons can be of a variety of origins, both natural and synthetic. The efficiency of expression can be enhanced by the inclusion of appropriate transcription enhancer elements, transcription terminators, etc., (see Bittner et al., 1987, Methods in Enzymol. 153:516-544).
In addition, a host cell strain can be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Such modifications (e.g., glycosylation) and processing (e.g., cleavage) of protein products can be important for the function of the protein. Different host cells have characteristic and specific mechanisms for the post-translational processing and modification of proteins. Appropriate cell lines or host systems can be chosen to ensure the correct modification and processing of the foreign protein expressed. To this end, eukaryotic host cells which possess the cellular machinery for proper processing of the primary transcript, glycosylation, and phosphorylation of the gene product can be used. Such mammalian host cells include but are not limited to CHO, VERO, BHK, HeLa, COS, MDCK, 293, 3T3, WI38, etc.
For long-term, high-yield production of recombinant proteins, stable expression is preferred. For example, cell lines which stably express the differentially expressed gene protein can be engineered. Rather than using expression vectors which contain viral origins of replication, host cells can be transformed with DNA controlled by appropriate expression control elements (e.g., promoter, enhancer, sequences, transcription terminators, polyadenylation sites, etc.), and a selectable marker. Following the introduction of the foreign DNA, engineered cells can be allowed to grow for 1-2 days in an enriched media, and then are switched to a selective media. The selectable marker in the recombinant plasmid confers resistance to the selection and allows cells to stably integrate the plasmid into their chromosomes and grow to form foci which in turn can be cloned and expanded into cell lines. This method can advantageously be used to engineer cell lines which express the identified gene protein. Such engineered cell lines can be particularly useful in screening and evaluation of compounds that affect the endogenous activity of the differentially expressed gene protein.
A number of selection systems can be used, including, but not limited to, the herpes simplex virus thymidine kinase (Wigler et al., 1977, Cell 11:223), hypoxanthine-guanine phosphoribosyltransferase (Szybalska & Szybalski, 1962, Proc. Natl. Acad. Sci. USA 48:2026), and adenine phosphoribosyltransferase (Lowy et al., 1980, Cell 22:817) genes in tk⁻, hgprt⁻ or aprt⁻ cells, respectively. Also, antimetabolite resistance can be used as the basis of selection for dhfr, which confers resistance to methotrexate (Wigler et al., 1980, Natl. Acad. Sci. USA 77:3567; O'Hare et al., 1981, Proc. Natl. Acad. Sci. USA 78:1527); gpt, which confers resistance to mycophenolic acid (Mulligan & Berg, 1981, Proc. Natl. Acad. Sci. USA 78:2072); neo, which confers resistance to the aminoglycoside G-418 (Colberre-Garapin et al., 1981, J. Mol. Biol. 150:1); and hygro, which confers resistance to hygromycin (Santerre et al., 1984, Gene 30:147) genes.
An alternative fusion protein system allows for the ready purification of non-denatured fusion proteins expressed in human cell lines (Janknecht et al., 1991, Proc. Natl. Acad. Sci. USA 88:8972-8976). In this system, the gene of interest is subcloned into a vaccinia recombination plasmid such that the gene's open reading frame is translationally fused to an amino-terminal tag consisting of six histidine residues. Extracts from cells infected with recombinant vaccinia virus are loaded onto ni2+ nitriloacetic acid-agarose columns and histidine-tagged proteins are selectively eluted with imidazole-containing buffers.
When used as a component in assay systems such as that described herein, the differentially expressed gene protein can be labeled, either directly or indirectly, to facilitate detection of a complex formed between the differentially expressed gene protein and a test substance. Any of a variety of suitable labeling systems can be used including but not limited to radioisotopes such as ¹²⁵I; enzyme labeling systems that generate a detectable colorimetric signal or light when exposed to substrate; and fluorescent labels.
Where recombinant DNA technology is used to produce the differentially expressed gene protein for such assay systems, it can be advantageous to engineer fusion proteins that can facilitate labeling, solubility, immobilization and/or detection.
Indirect labeling involves the use of a third protein, such as a labeled antibody, which specifically binds to either a differentially expressed gene product. Such antibodies include but are not limited to polyclonal, monoclonal, chimeric, single chain, Fab fragments and fragments produced by a Fab expression library.
b) Antibodies Specific for Differentially Expressed Gene Products
Described below are methods for the production of antibodies capable of specifically recognizing one or more differentially expressed gene products. Such antibodies can include, but are not limited to polyclonal antibodies, monoclonal antibodies (mAbs), humanized or chimeric antibodies, single chain antibodies, Fab fragments, F(ab′)₂fragments, fragments produced by a FAb expression library, anti-idiotypic (anti-Id) antibodies, and epitope-binding fragments of any of the above. Such antibodies can be used, for example, in the detection of a fingerprint or target gene product in a biological sample, or, alternatively, as a method for the inhibition of abnormal target gene activity. Thus, such antibodies can be utilized as treatment methods, and/or can be used as part of diagnostic techniques whereby patients can be tested for abnormal levels of fingerprint or target gene proteins, or for the presence of abnormal forms of the such proteins.
For the production of antibodies to a differentially expressed gene, various host animals can be immunized by injection with a differentially expressed gene protein, or a portion thereof. Such host animals can include but are not limited to rabbits, mice, and rats, to name but a few. Various adjuvants can be used to increase the immunological response, depending on the host species, including but not limited to Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, dinitrophenol, and potentially useful human adjuvants such as BCG (Bacilli Calmette-Guerin) and Corynebacterium parvum.
Polyclonal antibodies are heterogeneous populations of antibody molecules derived from the sera of animals immunized with an antigen, such as target gene product, or an antigenic functional derivative thereof. For the production of polyclonal antibodies, host animals such as those described above, can be immunized by injection with differentially expressed gene product supplemented with adjuvants as also described above.
Monoclonal antibodies, which are homogeneous populations of antibodies to a particular antigen, can be obtained by any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to the hybridoma technique of Kohler and Milstein, (1975, Nature 256:495-497; and U.S. Pat. No. 4,376,110), the human B-cell hybridoma technique (Kosbor et al., 1983, Immunology. Today 4:72; Cole et al., 1983, Proc. Natl. Acad. Sci. USA 80:2026-2030), and the BV-hybridoma technique (Cole et al., 1985, Monoclonal Antibodies And Cancer Therapy, Alan R. Liss, Inc., pp. 77-96). Such antibodies can be of any immunoglobulin class including IgG, IgM, IgE, IgA, IgD and any subclass thereof. The hybridoma producing the mAb of this invention can be cultivated in vitro or in vivo. Production of high titers of mAbs in vivo makes this the presently preferred method of production.
In addition, techniques developed for the production of “chimeric antibodies” (Morrison et al., 1984, Proc. Natl. Acad. Sci., 81:6851-6855; Neuberger et al., 1984, Nature, 312:604-608; Takeda et al., 1985, Nature, 314:452-454; U.S. Pat. No. 4,816,567) by splicing the genes from a mouse antibody molecule of appropriate antigen specificity together with genes from a human antibody molecule of appropriate biological activity can be used. A chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a murine mAb and a human immunoglobulin constant region.
Alternatively, techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778; Bird, 1988, Science 242:423-426; Huston et al., 1988, Proc. Natl. Acad. Sci. USA 85:5879-5883; and Ward et al., 1989, Nature 334:544-546) and for making humanized monoclonal antibodies (U.S. Pat. No. 5,225,539, which is incorporated herein by reference in its entirety) can be utilized to produce anti-differentially expressed gene product antibodies.
Antibody fragments which recognize specific epitopes can be generated by known techniques. For example, such fragments include but are not limited to: the F(ab′)₂fragments which can be produced by pepsin digestion of the antibody molecule and the Fab fragments which can be generated by reducing the disulfide bridges of the F(ab′)₂fragments. Alternatively, Fab expression libraries can be constructed (Huse et al., 1989, Science, 246:1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity.
c) In Vitro and In Vivo Systems for Gene Characterization
Described below are in vitro and in vivo systems which can be used to further characterize differentially Expressed Genes. These system can also be used as part of screening strategies designed to identify compounds which are capable of preventing and/or ameliorating symptoms of prostate cancer. Thus, these systems can be used to identify drugs, pharmaceuticals, therapies and interventions which can be effective in treating prostate cancer and to determine the in vivo efficacy of drugs, pharmaceuticals, therapies and interventions.
1) In Vitro Systems
Cells that contain and express target gene sequences and exhibit cellular phenotypes associated with prostate cancer, can be utilized to identify compounds that exhibit an ability to prevent and/or treat prostate cancer.
Further, the fingerprint pattern of gene expression of cells of interest can be analyzed and compared to the normal fingerprint pattern. Those compounds which cause cells exhibiting cellular phenotypes of prostate cancer to produce a fingerprint pattern more closely resembling a normal fingerprint pattern for the cell of interest can be considered candidates for further testing regarding an ability to ameliorate the symptoms of prostate cancer.
Cells which will be utilized for such assays can, for example, include LNCap cells. In addition, purified primary or secondary tumor cells derived from either transgenic or non-transgenic tumor cells can be used.
Further, cells which can be used for such assays can also include recombinant, transgenic cell lines. While primary cultures derived from the metastasis in transgenic animals can be utilized, the generation of continuous cell lines is preferred. For examples of techniques which can be used to derive a continuous cell line from a transgenic animal, see Small et al., 1985, Mol. Cell Biol. 5:642-648.
Alternatively, cells of a cell type known to be involved in prostate cancer can be transfected with sequences capable of increasing or decreasing the amount of target gene expression within the cell. For example, target gene sequences can be introduced into, and over expressed in, the genome of the cell of interest, or, if endogenous target gene sequences are present, they can either be overexpressed or, alternatively, be disrupted in order to underexpress or inactivate target gene expression.
In order to overexpress a target gene sequence, the coding portion of the target gene sequence can be ligated to a regulatory sequence which is capable of driving gene expression in the cell type of interest. Such regulatory regions will be well known to those of skill in the art.
For under expression of an endogenous target gene sequence, such a sequence can be isolated and engineered such that when reintroduced into the genome of the cell type of interest, the endogenous target gene alleles will be inactivated. Preferably, the engineered target gene sequence is introduced via gene targeting such that the endogenous target sequence is disrupted upon integration of the engineered target gene sequence into the cell's genome.
Transfection of target gene sequence nucleic acid can be accomplished by utilizing standard techniques (see, e.g., Ausubel, supra). Transfected cells should be evaluated for the presence of the recombinant target gene sequences, for expression and accumulation of target gene mRNA, and for the presence of recombinant target gene protein production. In instances wherein a decrease in target gene expression is desired, standard techniques can be used to demonstrate whether a decrease in endogenous target gene expression and/or in target gene product production is achieved.
2) In Vivo Systems
In vivo systems of prostate cancer can be either non-recombinant animals or recombinantly engineered transgenic animals. Such models may be generated, for example, by introducing tumor cells into syngeneic mice using techniques such as implanting prostatic cancer cells into the prostate gland. After an appropriate period of time, the tumors which result from these injections can be counted and analyzed.
For the generation of animal models of prostate cancer, cells derived from, for example, a prostate cancer cell line may be implanted into the prostate of an animal and the resulting tumors may be analyzed and compared to, for example, normal tissue.
The role of identified gene products (i.e., those encoded by target genes) can be determined by transfecting cDNAs encoding such gene products into the appropriate cell line and analyzing its effect on the cells' ability to induce prostate cancer in animal models such as these. The role of the identified gene products may be further analyzed by, for example, culturing cells derived from the tumors which develop in the animal models, introducing these cultured cells into animals, and subsequently measuring the level of identified gene product present in the resulting tumor cells. In this manner, cell line variants are developed which can be useful in analyzing the role of quantitative and/or qualitative differences in the expression of the identified genes on the cells' ability to induce prostate cancer.
Recombinant animal models for prostate cancer can be engineered by utilizing, for example, target gene sequences such as those described herein in conjunction with techniques for producing transgenic animals that are well known to those of skill in the art. For example, target gene sequences can be introduced into, and overexpressed in, the genome of the animal of interest, or, if endogenous target gene sequences are present, they can either be overexpressed or, alternatively, can be disrupted in order to underexpress or inactivate target gene expression.
In order to overexpress a target gene sequence, the coding portion of the target gene sequence can be ligated to a regulatory sequence which is capable of driving gene expression in the animal and cell type of interest. Such regulatory regions will be well known to those of skill in the art.
In order to obtain underexpression of an endogenous target gene sequence, such a sequence can be introduced into the genome of the animal of interest such that the endogenous target gene alleles will be inactivated. Preferably, an engineered sequence comprising at least part of the target gene sequence is utilized and is introduced, via gene targeting, such that the endogenous target sequence is disrupted upon integration of the engineered target gene sequence into the animal's genome.
Animals of any species, including, but not limited to, mice, rats, rabbits, guinea pigs, pigs, micro-pigs, goats, and non-human primates, e.g., baboons, monkeys, and chimpanzees can be used to generate animal models of prostate cancer.
Any technique known in the art can be used to introduce a target gene transgene into animals to produce the founder lines of transgenic animals. Such techniques include, but are not limited to pronuclear microinjection (Hoppe and Wagner, 1989, U.S. Pat. No. 4,873,191); retrovirus mediated gene transfer into germ lines (Van der Putten et al., 1985, Proc. Natl. Acad. Sci., USA 82:6148-6152); gene targeting in embryonic stem cells (Thompson et. al., 1989, Cell 56:313-321); electroporation of embryos (Lo, 1983, Mol Cell. Biol. 3:1803-1814); and sperm-mediated gene transfer (Lavitrano et al., 1989, Cell 57:717-723).
The present invention provides for transgenic animals that carry the transgene in all their cells, as well as animals which carry the transgene in some, but not all their cells, i.e., mosaic animals. The transgene can be integrated, either as a single transgene or in concatamers, e.g., head-to-head tandems or head-to-tail tandems. The transgene can also be selectively introduced into and activated in a particular cell type using known techniques (Lasko et al., 1992, Proc. Natl. Acad. Sci. USA 89:6232-6236). The regulatory sequences required for such a cell-type specific activation will depend upon the particular cell type of interest, and will be apparent to those of skill in the art.
When it is desired that the target gene transgene be integrated into the chromosomal site of the endogenous target gene, gene targeting is preferred. Briefly, when such a technique is to be utilized, vectors containing some nucleotide sequences homologous to the endogenous target gene of interest are designed for the purpose of integrating, via homologous recombination with chromosomal sequences, into and disrupting the function of, the nucleotide sequence of the endogenous target gene. The transgene can also be selectively introduced into a particular cell type, thus inactivating the endogenous gene of interest in only that cell type, by following, for example, the teaching of Gu et al. (1994, Science 265:103-106). The regulatory sequences required for such a cell-type specific inactivation will depend upon the particular cell type of interest, and will be apparent to those of skill in the art.
Once transgenic animals have been generated, the expression of the recombinant target gene and protein can be assayed utilizing standard techniques. Initial screening can be accomplished by Southern blot analysis or PCR techniques to analyze animal tissues to assay whether integration of the transgene has taken place. The level of mRNA expression of the transgene in the tissues of the transgenic animals can also be assessed using techniques which include, but are not limited to, Northern blot analysis of tissue samples obtained from the animal, in situ hybridization analysis, and RT-coupled PCR. Samples of target gene-expressing tissue, can also be evaluated immunocytochemically using antibodies specific for the transgenic product of interest.
The target gene transgenic animals that express target gene mRNA or target gene transgene peptide (detected immunocytochemically, using antibodies directed against target gene product epitopes) at easily detectable levels should then be further evaluated to identify those animals which display prostate cancer characteristics.
Additionally, specific cell types within the transgenic animals can be analyzed for cellular phenotypes characteristic of prostate cancer. Such cellular phenotypes can include, for example, differential gene expression characteristic of prostate cancer cells. Further, such cellular phenotypes can include as assessment of a particular cell type fingerprint profile and its comparison to known fingerprint profiles of the particular cell type in animals exhibiting prostate cancer. Such transgenic animals serve as suitable model systems for prostate cancer.
Once target gene transgenic founder animals are produced (i.e., those animals which express target gene proteins in cells or tissues of interest, and which, preferably, exhibit prostate cancer characteristics), they can be bred, inbred, outbred, or crossbred to produce colonies of the particular animal. Examples of such breeding strategies include but are not limited to: outbreeding of founder animals with more than one integration site in order to establish separate lines; inbreeding of separate lines in order to produce compound target gene transgenics that express the target gene transgene of interest at higher levels because of the effects of additive expression of each target gene transgene; crossing of heterozygous transgenic animals to produce animals homozygous for a given integration site in order to both augment expression and eliminate the possible need for screening of animals by DNA analysis; crossing of separate homozygous lines to produce compound heterozygous or homozygous lines; breeding animals to different inbred genetic backgrounds so as to examine effects of modifying alleles on expression of the target gene transgene and the development of symptoms of prostate cancer. One such approach is to cross the target gene transgenic founder animals with a wild-type strain to produce an F1 generation that exhibits symptoms of prostate cancer. The F1 generation can then be inbred in order to develop a homozygous line, if it is found that homozygous target gene transgenic animals are viable.
d) Identification of Compounds That Interact with a Target Gene Product
The following assays are designed to identify compounds that bind to target gene products, compounds that bind to other cellular proteins that interact with a target gene product, and compounds that interfere with the interaction of the target gene product with other cellular proteins.
Such compounds can include, but are not limited to, other cellular proteins. Specifically, such compounds can include, but are not limited to, peptides, such as, for example, soluble peptides, including, but not limited to Ig-tailed fusion peptides, comprising extracellular portions of target gene product transmembrane receptors, and members of random peptide libraries (see, e.g., Lam et al., 1991, Nature 354:82-84; Houghton et al., 1991, Nature 354:84-86), made of D-and/or L-configuration amino acids, phosphopeptides (including, but not limited to, members of random or partially degenerate phosphopeptide libraries; see, e.g., Songyang et al., 1993, Cell 72:767-778), antibodies (including, but not limited to, polyclonal, monoclonal, humanized, anti-idiotypic, chimeric or single chain antibodies, and FAb, F(ab′)₂and FAb expression libary fragments, and epitope-binding fragments thereof), and small organic or inorganic molecules.
Compounds identified via assays such as those described herein can be useful, for example, in elaborating the biological function of the target gene product, and for ameliorating symptoms of prostate cancer. For example, in instances in which prostate cancer is associated with lower expression of a target gene product, and/or lower target gene product activity, compounds that interact with the target gene product can include ones which increase the activity of the target gene product. Such compounds would bring about an effective increase in the level of target gene activity, thus ameliorating symptoms of prostate cancer. Conversely, in instances in which a mutation within a target gene cause aberrant target gene products to be made which have a deleterious effect that leads to prostate cancer, compounds that bind target gene product can be identified that inhibit the activity of the target gene product.
1) Screening Assays for Compounds and Cellular Proteins That Bind to a Target Gene Product
In vitro systems can be designed to identify compounds capable of binding the target gene products of the invention. Compounds identified can be useful, for example, in modulating the activity of wild type and/or mutant target gene products, preferably mutant target gene proteins, can be useful in elaborating the biological function of the target gene product, can be utilized in screens for identifying compounds that disrupt normal target gene interactions, or can in themselves disrupt such interactions.
The principle of the assays used to identify compounds that bind to the target gene product involves preparing a reaction mixture of the target gene protein and the test compound under conditions and for a time sufficient to allow the two components to interact and bind, thus forming a complex which can be removed and/or detected in the reaction mixture. These assays can be conducted in a variety of ways. For example, one method to conduct such an assay would involve anchoring target gene product or the test substance onto a solid phase and detecting target gene product/test compound complexes anchored on the solid phase at the end of the reaction. In one embodiment of such a method, the target gene product can be anchored onto a solid surface, and the test compound, which is not anchored, can be labeled, either directly or indirectly.
In practice, microtiter plates can conveniently be utilized as the solid phase. The anchored component can be immobilized by non-covalent or covalent attachments. Non-covalent attachment can be accomplished by simply coating the solid surface with a solution of the protein and drying. Alternatively, an immobilized antibody, preferably a monoclonal antibody, specific for the protein to be immobilized can be used to anchor the protein to the solid surface. The surfaces can be prepared in advance and stored.
In order to conduct the assay, the nonimmobilized component is added to the coated surface containing the anchored component. After the reaction is complete, unreacted components are removed (e.g., by washing) under conditions such that any complexes formed will remain immobilized on the solid surface. The detection of complexes anchored on the solid surface can be accomplished in a number of ways. Where the previously immobilized component is pre-labeled, the detection of label immobilized on the surface indicates that complexes were formed. Where the previously nonimmobilized component is not pre-labeled, an indirect label can be used to detect complexes anchored on the surface; e.g., using a labeled antibody specific for the immobilized component (the antibody, in turn, can be directly labeled or indirectly labeled with a labeled anti-Ig antibody).
Alternatively, a reaction can be conducted in a liquid phase, the reaction products separated from unreacted components, and complexes detected; e.g., using an immobilized antibody specific for target gene or the test compound to anchor any complexes formed in solution, and a labeled antibody specific for the other component of the possible complex to detect anchored complexes.
Any method suitable for detecting protein-protein interactions can be employed for identifying novel target product-cellular or extracellular protein interactions. In such a case, the target gene serves as the known “bait” gene.
2) Assays for Compounds That Interfere with the Binding of a Target Gene Product to a Second Cellular Protein
The target gene products of the invention can, in vivo, interact with one or more cellular or extracellular macromolecules, such as proteins. For the purposes of this discussion, such cellular and extracellular macromolecules are referred to herein as “binding partners.” Compounds that disrupt such interactions can be useful in regulating the activity of the target gene product, especially mutant target gene products. Such compounds can include, but are not limited to molecules such as antibodies, peptides, and small molecules.
The basic principle of the assay systems used to identify compounds that interfere with the interaction between the target gene product and its cellular or extracellular binding partner or partners involves preparing a reaction mixture containing the target gene product, and the binding partner under conditions and for a time sufficient to allow the two products to interact and bind, thus forming a complex. In order to test a compound for inhibitory activity, the reaction mixture is prepared in the presence and absence of the test compound. The test compound can be initially included in the reaction mixture, or can be added at a time subsequent to the addition of target gene and its cellular or extracellular binding partner. Control reaction mixtures are incubated without the test compound or with a placebo. The formation of any complexes between the target gene product and the cellular or extracellular binding partner is then detected. The formation of a complex in the control reaction, but not in the reaction mixture containing the test compound, indicates that the compound interferes with the interaction of the target gene product and the interactive binding partner. Additionally, complex formation within reaction mixtures containing the test compound and normal target gene product can also be compared to complex formation within reaction mixtures containing the test compound and mutant target gene product. This comparison can be important in those cases wherein it is desirable to identify compounds that disrupt interactions of mutant but not normal target gene products.
The assay for compounds that interfere with the interaction of the target gene products and binding partners can be conducted in a heterogeneous or homogeneous format. Heterogeneous assays involve anchoring either the target gene product or the binding partner onto a solid phase and detecting complexes anchored on the solid phase at the end of the reaction. In homogeneous assays, the entire reaction is carried out in a liquid phase. In either approach, the order of addition of reactants can be varied to obtain different information about the compounds being tested. For example, test compounds that interfere with the interaction between the target gene products and the binding partners, e.g., by competition, can be identified by conducting the reaction in the presence of the test substance; i.e., by adding the test substance to the reaction mixture prior to or simultaneously with the target gene product and interactive cellular or extracellular binding partner. Alternatively, test compounds that disrupt preformed complexes, e.g., compounds with higher binding constants that displace one of the components from the complex, can be tested by adding the test compound to the reaction mixture after complexes have been formed. The various formats are described briefly below.
In a heterogeneous assay system, either the target gene product or the interactive cellular or extracellular binding partner, is anchored onto a solid surface, while the non-anchored species is labeled, either directly or indirectly. In practice, microtitre plates are conveniently utilized. The anchored species can be immobilized by non-covalent or covalent attachments. Non-covalent attachment can be accomplished simply by coating the solid surface with a solution of the target gene product or binding partner and drying. Alternatively, an immobilized antibody specific for the species to be anchored can be used to anchor the species to the solid surface. The surfaces can be prepared in advance and stored.
In order to conduct the assay, the partner of the immobilized species is exposed to the coated surface with or without the test compound. After the reaction is complete, unreacted components are removed (e.g., by washing) and any complexes formed will remain immobilized on the solid surface. The detection of complexes anchored on the solid surface can be accomplished in a number of ways. Where the non-immobilized species is pre-labeled, the detection of label immobilized on the surface indicates that complexes were formed. Where the non-immobilized species is not pre-labeled, an indirect label can be used to detect complexes anchored on the surface; e.g., using a labeled antibody specific for the initially non-immobilized species (the antibody, in turn, can be directly labeled or indirectly labeled with a labeled anti-Ig antibody). Depending upon the order of addition of reaction components, test compounds which inhibit complex formation or which disrupt preformed complexes can be detected.
Alternatively, the reaction can be conducted in a liquid phase in the presence or absence of the test compound, the reaction products separated from unreacted components, and complexes detected; e.g., using an immobilized antibody specific for one of the binding components to anchor any complexes formed in solution, and a labeled antibody specific for the other partner to detect anchored complexes. Again, depending upon the order of addition of reactants to the liquid phase, test compounds which inhibit complex or which disrupt preformed complexes can be identified.
In an alternate embodiment of the invention, a homogeneous assay can be used. In this approach, a preformed complex of the target gene product and the interactive cellular or extracellular binding partner product is prepared in which either the target gene products or their binding partners are labeled, but the signal generated by the label is quenched due to complex formation (see, e.g., U.S. Pat. No. 4,109,496 which utilizes this approach for immunoassays). The addition of a test substance that competes with and displaces one of the species from the preformed complex will result in the generation of a signal above background. In this way, test substances which disrupt target gene product-cellular or extracellular binding partner interaction can be identified.
In a particular embodiment, the target gene product can be prepared for immobilization using recombinant DNA techniques. For example, the target gene coding region can be fused to a glutathione-S-transferase (GST) gene using a fusion vector such as pGEX-5X-1, in such a manner that its binding activity is maintained in the resulting fusion product. The interactive cellular or extracellular product can be purified and used to raise a monoclonal antibody, using methods routinely practiced in the art. This antibody can be labeled with the radioactive isotope ¹²⁵I, for example, by methods routinely practiced in the art. In a heterogeneous assay, e.g., the GST-Target gene fusion product can be anchored to glutathione-agarose beads. The interactive cellular or extracellular binding partner product can then be added in the presence or absence of the test compound in a manner that allows interaction and binding to occur. At the end of the reaction period, unbound material can be washed away, and the labeled monoclonal antibody can be added to the system and allowed to bind to the complexed components. The interaction between the target gene product and the interactive cellular or extracellular binding partner can be detected by measuring the amount of radioactivity that remains associated with the glutathione-agarose beads. A successful inhibition of the interaction by the test compound will result in a decrease in measured radioactivity.
Alternatively, the GST-target gene fusion product and the interactive cellular or extracellular binding partner product can be mixed together in liquid in the absence of the solid glutathione-agarose beads. The test compound can be added either during or after the binding partners are allowed to interact. This mixture can then be added to the glutathione-agarose beads and unbound material is washed away. Again the extent of inhibition of the binding partner interaction can be detected by adding the labeled antibody and measuring the radioactivity associated with the beads.
These same techniques can be employed using peptide fragments that correspond to the binding domains of the target gene product and the interactive cellular or extracellular binding partner (in case where the binding partner is a product), in place of one or both of the full length products. Any number of methods routinely practiced in the art can be used to identify and isolate the protein's binding site. These methods include, but are not limited to, mutagenesis of one of the genes encoding one of the products and screening for disruption of binding in a co-immunoprecipitation assay. Compensating mutations in the gene encoding the second species in the complex can be selected. Sequence analysis of the genes encoding the respective products will reveal the mutations that correspond to the region of the product involved in interactive binding. Alternatively, one product can be anchored to a solid surface using methods described above, and allowed to interact with and bind to its labeled binding partner, which has been treated with a proteolytic enzyme, such as trypsin. After washing, a short, labeled peptide comprising the binding domain can remain associated with the solid material, which can be isolated and identified by amino acid sequencing. Also, once the gene coding for the cellular or extracellular binding partner product is obtained, short gene segments can be engineered to express peptide fragments of the product, which can then be tested for binding activity and purified or synthesized.
VI. Treatment of Prostate Cancer by Modulation of Differentially Expressed Genes or Gene Products
Prostate cancer can be treated by modulating the expression of a target gene or the activity of a target gene product. The modulation can be of a positive or negative nature, depending on the specific situation involved, but each modulatory event yields a net result in which prostate cancer symptoms are ameliorated.
“Negative modulation,” refers to a reduction in the level and/or activity of target gene product relative to the level and/or activity of the target gene product in the absence of the modulatory treatment.
“Positive modulation,” refers to an increase in the level and/or activity of target gene product relative to the level and/or activity of target gene product in the absence of modulatory treatment.
It is possible that prostate cancer can be caused, at least in part, by an abnormal level of gene product, or by the presence of a gene product exhibiting abnormal activity. As such, the reduction in the level and/or activity of such gene products would bring about the amelioration of prostate cancer symptoms.
Alternatively, it is possible that prostate cancer can be brought about, at least in part, by the absence or reduction of the level of gene expression, or a reduction in the level of a gene product's activity. As such, an increase in the level of gene expression and/or the activity of such gene products would bring about the amelioration of prostate cancer symptoms.
a) Negative Modulatory Techniques
As discussed, above, successful treatment of prostate cancer can be brought about by techniques which serve to inhibit the expression or activity of target gene products.
For example, compounds, e.g., a compound identified using an assays described above, which proves to exhibit negative modulatory activity, can be used in accordance with the invention to prevent and/or ameliorate symptoms of prostate cancer. Such molecules can include, but are not limited to peptides, phosphopeptides, small organic or inorganic molecules, or antibodies (including, for example, polyclonal, monoclonal, humanized, anti-idiotypic, chimeric or single chain antibodies, and FAb, F(ab′)₂and FAb expression library fragments, and epitope-binding fragments thereof).
Further, antisense and ribozyme molecules which inhibit expression of the target gene can also be used in accordance with the invention to reduce the level of target gene expression, thus effectively reducing the level of target gene activity. Still further, triple helix molecules can be utilized in reducing the level of target gene activity.
Among the compounds which can exhibit the ability to prevent and/or ameliorate symptoms of prostate cancer are antisense, ribozyme, and triple helix molecules. Such molecules can be designed to reduce or inhibit either wild type, or if appropriate, mutant target gene activity. Techniques for the production and use of such molecules are well known to those of skill in the art.
Anti-sense RNA and DNA molecules act to directly block the translation of mRNA by hybridizing to targeted mRNA and preventing protein translation. With respect to antisense DNA, oligodeoxyribonucleotides derived from the translation initiation site, e.g., between the −10 and +10 regions of the Target gene nucleotide sequence of interest, are preferred.
Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA. (For a review, see, for example, Rossi, 1994, Current Biology 4:469-471.) The mechanism of ribozyme action involves sequence specific hybridization of the ribozyme molecule to complementary target RNA, followed by a endonucleolytic cleavage. The composition of ribozyme molecules must include one or more sequences complementary to the target gene mRNA and must include the well-known catalytic sequence responsible for mRNA cleavage. For this sequence, see U.S. Pat. No. 5,093,246, which is incorporated by reference herein in its entirety. As such within the scope of the invention are engineered hammerhead motif ribozyme molecules that specifically and efficiently catalyze endonucleolytic cleavage of RNA sequences encoding target gene proteins.
Specific ribozyme cleavage sites within any potential RNA target are initially identified by scanning the molecule of interest for ribozyme cleavage sites which include the following sequences, GUA, GUU, and GUC. Once identified, short RNA sequences of between 15 and 20 ribonucleotides corresponding to the region of the target gene containing the cleavage site can be evaluated for predicted structural features, such as secondary structure, that can render the oligonucleotide sequence unsuitable. The suitability of candidate sequences can also be evaluated by testing their accessibility to hybridization with complementary oligonucleotides, using ribonuclease protection assays.
Nucleic acid molecules to be used in triplex helix formation for the inhibition of transcription should be single stranded and composed of deoxynucleotides. The base composition of these oligonucleotides must be designed to promote triple helix formation via Hoogsteen base pairing rules, which generally require sizeable stretches of either purines or pyrimidines to be present on one strand of a duplex. Nucleotide sequences can be pyrimidine-based, which will result in TAT and CGC⁺ triplets across the three associated strands of the resulting triple helix. The pyrimidine-rich molecules provide base complementarily to a purine-rich region of a single strand of the duplex in a parallel orientation to that strand. In addition, nucleic acid molecules can be chosen that are purine-rich, for example, contain a stretch of G residues. These molecules will form a triple helix with a DNA duplex that is rich in GC pairs, in which the majority of the purine residues are located on a single strand of the targeted duplex, resulting in GGC triplets across the three strands in the triplex.
Alternatively, the potential sequences that can be targeted for triple helix formation can be increased by creating a so called “switchback” nucleic acid molecule. Switchback molecules are synthesized in an alternating 5′-3′,3′-5′ manner, such that they base pair with first one strand of a duplex and then the other, eliminating the necessity for a sizeable stretch of either purines or pyrimidines to be present on one strand of a duplex.
In instances wherein the antisense, ribozyme, and/or triple helix molecules described herein are utilized to reduce or inhibit mutant gene expression, it is possible that the technique utilized can also efficiently reduce or inhibit the transcription (triple helix) and/or translation (antisense, ribozyme) of mRNA produced by normal target gene alleles such that the possibility can arise wherein the concentration of normal target gene product present can be lower than is necessary for a normal phenotype. In such cases, to ensure that substantially normal levels of target gene activity are maintained, nucleic acid molecules that encode and express target gene polypeptides exhibiting normal target gene activity can be introduced into cells via gene therapy method. Alternatively, in instances in which the target gene encodes an extracellular protein, it can be preferable to co-administer normal target gene protein into the cell or tissue in order to maintain the requisite level of cellular or tissue target gene activity.
Anti-sense RNA and DNA, ribozyme and triple helix molecules of the invention can be prepared by any method known in the art for the synthesis of DNA and RNA molecules. These include techniques for chemically synthesizing oligodeoxyribonucleotides and oligoribonucleotides well known in the art such as, for example, solid phase phosphoramidite chemical synthesis. Alternatively, RNA molecules can be generated by in vitro and in vivo transcription of DNA sequences encoding the antisense RNA molecule. Such DNA sequences can be incorporated into a wide variety of vectors which incorporate suitable RNA polymerase promoters such as the T7 or SP6 polymerase promoters. Alternatively, antisense cDNA constructs that synthesize antisense RNA constitutively or inducibly, depending on the promoter used, can be introduced stably into cell lines.
Various well-known modifications to the DNA molecules can be introduced as a means of increasing intracellular stability and half-life. Possible modifications include but are not limited to the addition of flanking sequences of ribo- or deoxy-nucleotides to the 5′ and/or 3′ ends of the molecule or the use of phosphorothioate or 2′ O-methyl rather than phosphodiesterase linkages within the oligodeoxyribonucleotide backbone.
Antibodies can be generated which are both specific for target gene product and which reduce target gene product activity. Such antibodies may, therefore, by administered in instances whereby negative modulatory techniques are appropriate for the treatment of prostate cancer. Antibodies can be generated using standard techniques against the proteins themselves or against peptides corresponding to portions of the proteins. The antibodies include but are not limited to polyclonal, monoclonal, Fab fragments, single chain antibodies, chimeric antibodies, and the like.
In instances where the target gene protein to which the antibody is directed is intracellular and whole antibodies are used, internalizing antibodies can be preferred. However, lipofectin or liposomes can be used to deliver the antibody or a fragment of the Fab region which binds to the target gene epitope into cells. Where fragments of the antibody are used, the smallest inhibitory fragment which binds to the target protein's binding domain is preferred. For example, peptides having an amino acid sequence corresponding to the domain of the variable region of the antibody that binds to the target gene protein can be used. Such peptides can be synthesized chemically or produced via recombinant DNA technology using methods well known in the art (e.g., see Creighton, 1983, supra; and Sambrook et al., 1989, supra). Alternatively, single chain neutralizing antibodies which bind to intracellular target gene product epitopes can also be administered. Such single chain antibodies can be administered, for example, by expressing nucleotide sequences encoding single-chain antibodies within the target cell population by utilizing, for example, techniques such as those described in Marasco et al. (1993, Proc. Natl. Acad. Sci. USA 90:7889-7893).
b) Positive Modulatory Techniques
As discussed above, successful treatment of prostate cancer symptoms can be brought about by techniques which serve to increase the level of target gene expression or to increase the activity of a target gene product.
For example, compounds, e.g., compounds identified through assays described, which prove to exhibit positive modulatory activity can be used in accordance with the invention to ameliorate prostate cancer symptoms. Such molecules can include, but are not limited to, peptides, phosphopeptides, small organic or inorganic molecules, or antibodies (including, for example, polyclonal, monoclonal, humanized, anti-idiotypic, chimeric or single chain antibodies, and FAb, F(ab′)₂and FAb expression library fragments, and epitope-binding fragments thereof).
For example, a target gene protein, at a level sufficient to ameliorate prostate cancer symptoms can be administered to a patient exhibiting such symptoms. One of skill in the art will readily know how to determine the concentration of effective, non-toxic doses of the normal target gene protein.
In instances wherein the compound to be administered is a peptide compound, DNA sequences encoding the peptide-compound can, alternatively, be directly administered to a patient exhibiting prostate cancer symptoms, at a concentration sufficient to generate the production of an amount of target gene product adequate to ameliorate prostate cancer symptoms. The DNA molecules can be produced, for example, by well-known recombinant techniques.
In the case of peptide compounds which act extracellularly, the DNA molecules encoding such peptides can be taken up and expressed by any cell type, so long as a sufficient circulating concentration of peptide results for the elicitation of a reduction in prostate cancer symptoms.
In the case of compounds which act intracellularly, the DNA molecules encoding such peptides must be taken up and expressed by cells involved in the prostate cancer at a sufficient level to bring about the reduction of prostate cancer symptoms.
Any technique which serves to selectively administer DNA molecules to a cell involved in prostate cancer is, therefore, preferred for the DNA molecules encoding intracellularly acting peptides.
Further, patients can be treated for symptoms of prostate cancer by gene replacement therapy. One or more copies of a normal target gene or a portion of the gene that directs the production of a normal target gene protein with target gene function can be inserted into cells, using vectors which include, but are not limited to adenovirus, adeno-associated virus, and retrovirus vectors, in addition to other particles that introduce DNA into cells, such as liposomes. Techniques such as those described above can be utilized for the introduction of normal target gene sequences into human cells.
In instances wherein the target gene encodes an extracellular, secreted gene product, such gene replacement techniques may be accomplished either in vivo or in vitro. For such cases, the cell types expressing the target gene is less important than achieving a sufficient circulating concentration of the extracellular molecules for the amelioration of prostate cancer symptoms to occur. In vitro, target gene sequences can be introduced into autologous cells. Those cells expressing the target gene sequence of interest can then be reintroduced, preferably by intravenous administration, into the patient such that there results an amelioration of prostate cancer symptoms.
In instances wherein the gene replacement involves a gene which encodes a product which acts intracellularly, it is preferred that gene replacement be accomplished in vivo. Further, because the cell type in which the gene replacement must occur is the cell type involved in prostate cancer, such techniques must successfully target such prostate cancer cells.
VII. Therapeutic Treatment
The identified compounds that inhibit target gene expression, synthesis and/or activity can be administered to a patient at therapeutically effective doses to prevent, treat or ameliorate prostate cancer. A therapeutically effective dose refers to that amount of the compound sufficient to result in amelioration of symptoms of prostate cancer.
a) Effective Dose
Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD₅₀(the dose lethal to 50% of the population) and the ED₅₀(the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD₅₀/ED₅₀. Compounds which exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects can be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects.
The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED₅₀with little or no toxicity. The dosage can vary within this range depending upon the dosage form employed and the route of administration utilized. For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC₅₀(i.e., the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma can be measured, for example, by high performance liquid chromatography.
b) Formulations and Use
Pharmaceutical compositions for use in accordance with the present invention can be formulated in conventional manner using one or more physiologically acceptable carriers or excipients.
Thus, the compounds and their physiologically acceptable salts and solvates can be formulated for administration by inhalation or insufflation (either through the mouth or the nose) or oral, buccal, parenteral or rectal administration.
For oral administration, the pharmaceutical compositions can take the form of, for example, tablets or capsules prepared by conventional means with pharmaceutically acceptable excipients such as binding agents (e.g., pregelatinised maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose); fillers (e.g., lactose, microcrystalline cellulose or calcium hydrogen phosphate); lubricants (e.g., magnesium stearate, talc or silica); disintegrants (e.g., potato starch or sodium starch glycolate); or wetting agents (e.g., sodium lauryl sulphate). The tablets can be coated by methods well known in the art. Liquid preparations for oral administration can take the form of, for example, solutions, syrups or suspensions, or they can be presented as a dry product for constitution with water or other suitable vehicle before use. Such liquid preparations can be prepared by conventional means with pharmaceutically acceptable additives such as suspending agents (e.g., sorbitol syrup, cellulose derivatives or hydrogenated edible fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles (e.g., almond oil, oily esters, ethyl alcohol or fractionated vegetable oils); and preservatives (e.g., methyl or propyl-p-hydroxybenzoates or sorbic acid). The preparations can also contain buffer salts, flavoring, coloring and sweetening agents as appropriate.
Preparations for oral administration can be suitably formulated to give controlled release of the active compound.
For buccal administration the compositions can take the form of tablets or lozenges formulated in conventional manner.
For administration by inhalation, the compounds for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit can be determined by providing a valve to deliver a metered amount. Capsules and cartridges of e.g., gelatin for use in an inhaler or insufflator can be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.
The compounds can be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion. Formulations for injection can be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative. The compositions can take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and can contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Alternatively, the active ingredient can be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.
The compounds can also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides.
In addition to the formulations described previously, the compounds can also be formulated as a depot preparation. Such long acting formulations can be administered by implantation (for example, subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, the compounds can be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.
The compositions can, if desired, be presented in a pack or dispenser device which can contain one or more unit dosage forms containing the active ingredient. The pack can for example comprise metal or plastic foil, such as a blister pack. The pack or dispenser device can be accompanied by instructions for administration.

OTHER EMBODIMENTS

The present invention is not to be limited in scope by the specific embodiments described which are intended as single illustrations of individual aspects of the invention and functionally equivalent methods and components are within the scope of the invention, in addition to those shown and described herein will become apparent to those skilled in the art from the foregoing description and accompanying drawings. Such modifications are intended to fall within the scope of the appended claims.

Claims

1. A method for determining whether a compound can be used to treat prostate cancer in a patient, comprising:

a) obtaining a patient biological sample;

b) determining the normalized expression level of one or more genes selected from the group consisting of SEQ ID NOS:1-40, 86-130 in the patient sample; c)

comparing the normalized expression level of the selected one or more genes determined in step b) with the normalized expression level of the selected one or more genes in a non-prostate cancer biological sample; and

d) identifying that a compound can be used to treat prostate cancer in the patient when the normalized expression level of the selected one or more genes in the patient sample is greater than the normalized expression level of the selected one or more genes in the non-prostate cancer biological sample.

2. (canceled)

3. A method for determining whether a treatment should be continued in a prostate cancer patient, comprising:

a) obtaining a patient biological sample;

d) discontinuing treatment when the normalized expression level of the selected one or more genes in the patient sample is greater than the normalized expression level of the selected one or more genes in the non-prostate cancer sample.

4-6. (canceled)

7. The method of claim 1 wherein the normalized expression level of the selected one or more genes is determined by measuring the mRNA encoded by each of the selected one or more genes.

8. The method of claim 1 wherein the normalized expression level of the selected one or more genes is determined by measuring the amount of protein encoded by each of the selected one or more genes.

9. The method of claim 1 wherein the normalized expression level of the selected one or more genes is determined by measuring the activity of the protein encoded by each of the selected one or more genes.

10. The method of claim 1 wherein the selected genes are five or more genes selected from the group consisting of SEQ ID NOS:1-40, 86-130.

11. The method of claim 1 wherein the selected genes are ten or more genes selected from the group consisting of SEQ ID NOS:1-40, 86-130.

12. The method of claim 1 wherein the compound is an anti-androgenic compound.

13. (canceled)

14. The method of claim 1 wherein the patient biological sample is derived from patient prostate cells, serum, interstitial fluid, blood, or seminal fluid.

15-18. (canceled)

19. A method for determining whether a compound can be used to treat prostate cancer, comprising:

a) measuring the expression level of one or more genes selected from the group consisting of SEQ ID NOS:41-85, 131-191 in a prostate cancer cell sample in the presence and absence of the compound; and

b) identifying the compound as useful for treating prostate cancer when the expression level of the selected one or more genes in the presence of the compound is greater than the expression level of the selected one or more genes in the absence of the compound.

20. A method for determining whether a compound can be used to treat prostate cancer, comprising:

a) measuring the expression level of one or more genes selected from the group consisting of SEQ ID NOS:1-40, 86-130 in prostate cancer cell sample in the presence and absence of the compound; and

b) identifying the compound as useful for treating prostate cancer when the expression level of the selected one or more genes in the presence of the compound is less than the expression level of the selected one or more genes in the absence of the compound.

21. The method of claim 19 wherein the expression level of the selected one or more genes is determined by measuring the mRNA encoded by each of the selected one or more genes; measuring the amount of protein encoded by each of the selected one or more genes, or by measuring the activity of the protein encoded by each of the selected one or more genes.

22-23. (canceled)

24. The method of claim 19 wherein the selected genes are five or more genes selected from the group consisting of SEQ ID NOS:41-85, 131-191.

25. The method of claim 19 wherein the selected genes are ten or more genes selected from the group consisting of SEQ ID NOS:41-85, 131-191.

26-27. (canceled)

28. A method for determining whether a treatment should be continued in a prostate cancer patient, comprising:

a) obtaining a patient biological sample;

b) determining the normalized expression level of one or more genes selected from the group consisting of SEQ ID NOS:41-85, 131-191 in the patient sample;

c) comparing the normalized expression level of the selected one or more genes determined in step b) with the normalized expression level of the selected one or more genes in a non-prostate cancer biological sample; and

d) discontinuing treatment when the normalized expression level of the selected one or more genes in the patient sample is less than or equal to the normalized expression level of the selected one or more genes in the non-prostate cancer sample.

29. (canceled)

30. The method of claim 28 wherein the treatment is an anti-androgenic treatment.

31. The method of claim 28 wherein the patient biological sample is derived from patient prostate cells, serum, interstitial fluid, blood, or seminal fluid.

32-37. (canceled)

38. A method for determining whether an individual has or at risk for developing prostate cancer, comprising:

a) obtaining a biological sample from the individual;

b) determining the normalized expression level of one or more genes selected from the group consisting of SEQ ID NOS:1-40, 86-130 in the individual sample;

d) indentifying the individual as having or being at risk for developing prostate cancer when the normalized expression level of the selected one or more genes in the individual sample is greater than the normalized expression level of the selected one or more genes in the non-prostate cancer sample.