WO2000050061A1

WO2000050061A1 - Detecting the expression of the desc1 gene in squamous cell carcinoma

Info

Publication number: WO2000050061A1
Application number: PCT/IB1999/001818
Authority: WO
Inventors: Jas C. Lang
Original assignee: Ohio State University Research Foundation
Current assignee: Ohio State University Research Foundation
Priority date: 1999-02-26
Filing date: 1999-11-11
Publication date: 2000-08-31
Anticipated expiration: 2001-08-26
Also published as: AU1068900A

Abstract

The present invention provides a novel method for diagnosing squamous cell carcinoma or prostate cancer in a tissue sample. The method does not involve visual examination of morphology. The method comprises providing a sample from the subject and assaying for the presence, or absence or reduced level of expression of a novel gene, hereinafter referred to as the 'DESC1 gene'. The method comprises isolating RNA, preferably mRNA from tissue samples, and detecting the mRNA which encodes all or part of DESC1 protein. Preferably the detection comprises amplifying the mRNA, preferably by reverse transcriptase-PCR using primers specific to a region in the DESC1 gene; and detecting the presence or absence of the amplified product to determine whether DESC1 mRNA is present or absent in the tissue sample. Alternatively the detection comprises separating the RNA which encodes all or part of DESC1 protein from the total RNA, preferably by separating on an agarose gel, and detecting the mRNA encoding DESC1, preferably by using a probe specific for such mRNA. Optionally, the DESC1 mRNA when present, is also quantified using conventional techniques. The present invention also relates to polynucleotides which encode the DESC1 protein, to the DESC 1 protein, and to antibodies to the DESC1 protein. The present invention also relates to hybridization probes, and to primers useful in the method of detecting DESC1 mRNA.

Description

DETECTING THE EXPRESSION OF THE DESCl GENE

IN SQUAMOUS CELL CARCINOMA

This invention was made in part with government support under CA63134 and DEI 2704 awarded by the National Institutes of Health. The U.S. government has certain rights in the invention.

Background of the Invention

Typically, morphological examination of the tissues is performed to characterize squamous cell carcinomas of the head and neck and tissues adjacent to such tumor tissue. The morphological examination usually involves the sectioning and staining of an excised tissue sample followed by microscopic examination by a cytologist or pathologist. However, visual examination does result in some errors, particularly by pathologists who do not routinely encounter such tissue samples.

Accordingly, it is desirable to have a technique which does not require visual examination of morphological characteristics to diagnose or confirm a pathologist' s diagnosis of squamous cell carcinoma of the head and neck.

Summary of the Invention

The present invention provides a novel method for diagnosing squamous cell carcinoma or prostate cancer in a tissue sample. The method does not involve visual examination of morphology. The method comprises providing a sample from the subject and assaying for the presence, or absence or reduced level of expression of a novel gene, hereinafter referred to as the "DESCl gene". The method comprises isolating RNA, preferably mRNA from tissue samples, and detecting the mRNA which encodes all or part of DESCl protein. Preferably the detection comprises amplifying the mRNA, preferably by reverse transcriptase-PCR using primers specific to a region in the DESCl gene; and detecting the presence or absence of the amplified product to determine whether DESCl mRNA is present or absent in the tissue sample. Alternatively the detection comprises separating the RNA which encodes all or part of DESCl protein from the total RNA, preferably by separating on an agarose gel, and detecting the mRNA encoding DESCl, preferably by using a probe specific for such mRNA. Optionally, the DESCl mRNA when present, is also quantified using conventional techniques. The present invention also relates to polynucleotides which encode the DESCl protein, to the DESC 1 protein, and to antibodies to the DESCl protein. The present invention also relates to hybridization probes, and to primers useful in the method of detecting DESCl mRNA.

Brief Description of the Figures

FIGURE 1A is the nucleotide sequence, SEQ.ID.NO. 1, of a cDNA which encodes a DESCl protein, with the predicted amino acid sequence of the amino acid sequence, SEQ. ID. NO. 2 encoded by the nucleotide sequence. Putative initiation and termination codons are boxed, as are residues predicted to represent conserved amino acids of the catalytic triad. Suggested location of catalytic cleavage site is shown by vertical arrow. Consensus polyadenylation signals are double underlined. The predicted hydrophobic transmembrane sequence or signal peptide is located at about amino acids 18-37 and is underlined.

FIGURE IB is an alternate nucleotide sequence, SEQ.ID.NO. 3, of a cDNA which encodes a DESCl protein, with the predicted amino acid sequence of the amino acid sequence, SEQ. ID. NO. 4 encoded by the nucleotide sequence.

Figure 2. DESCl expression in normal tissue and metastatic neck node used for RDA analysis and in primary carcinoma from the same patient. RT-PCR analysis. Primers utilized: D10. DI 1. Size of RT-PCR product, 555 bp.

Figure 3. Expression of DESCl in squamous cell carcinoma of the head and neck (SSCHN) and matched normal tissues. A, RT-PCR analysis of DESC l expression in SCCHN and matched normal tissue. Primers utilized: D3, D4. Size of RT-PCR product 149 bp. Low molecular weight band seen in negative control lane and some sample lanes represents unincorporated [α P]dCTP. B, Northern analysis of DESCl expression in SCCHN, matched normal tissue and metastatic neck node. PHA, pharynx; TSL, tonsil; FOM, floor of mouth; TON, tongue; EPI, epiglotis; LAR, larynx; R T, retromolar trigone; T B, tongue base.

Figure 4. Expression of DESCl in epithelial cell lines and human tissues. RT-PCR analysis using total RNA derived from epithelial cell lines and human tissues. Primers utilized, D10 and Dl l .

Figure 5. Expression of DESCl in multiple human tissues. Northern analysis using A total RNA (Human Normal Tissue Blot III) and B, polyadenylated RNA (Human Multiple Tissue Northern Blot II). Detailed Description of the Invention

A novel gene has been discovered which is expressed in significant levels in epithelial derived tissues, specifically epithelial tissues of the head, neck, oral mucosa, tonsils, prostate, testes, and skin in healthy individuals, i.e. individuals who do not have squamous cell carcinoma or prostate carcinoma. However, in tumor tissue samples taken from patients with squamous cell carcinoma, particularly of the head and neck, the expression of the DESCl gene is absent or significantly reduced. The differential expression permits the identification of squamous cell carcinoma of the head and neck.

Similarly, expression of the DESCl gene is reduced or absent in prostate carcinoma and, thus, permits identification of prostate carcinoma. Polynucleotides

The present invention provides isolated polynucleotides which encode a DESCl protein. One embodiment of a polynucleotide which encodes a DESCl protein is shown in Fig. 1 A. another embodiment is shown in Fig. IB

Due to the known degeneracy of the genetic code wherein more than one codon can encode the same amino acid, a DNA sequence may vary from that shown in Fig 1A and still encode a DESCl protein having the amino acid sequences shown in Fig. 1A. Similarly, a DNA sequence may vary from that shown in Fig. 1A and IB and still encode the amino acid sequence shown in Fig. IB.

The present invention also encompasses polynucleotides having sequences that are capable of hybridizing to the nucleotide sequences of Figs 1A and IB under stringent conditions, preferably highly stringent conditions. Hybridization conditions are based on the melting temperature TM of the nucleic acid binding complex or probe, as described in Berger and Kimmel (1987) Guide to Molecular Cloning Techniques, Methods in Enzymology, Vol. 152, Academic Press. The term "stringent conditions, as used herein, is the "stringency" which occurs within a range from about Tm-5 (5° below the melting temperature of the probe) to about 20° C below Tm. . "Highly Stringent hybridization conditions" refers to an overnight incubation at 42 degree C in a solution comprising 50% formamide. 5x SSC (750 mM NaCl, 75 mM sodium citrate), 50 mM sodium phosphate (pH 7.6), 5x Denhardt's solution, 10% dextran sulfate, and 20 μg/ml denatured, sheared salmon sperm DNA. followed by washing the filters in 0.2x SSC at about 65 degree C. As recognized in the art, stringency conditions can be attained by varying a number of factors such as the length and nature, i.e., DNA or RNA, of the probe; the length and nature of the target sequence, the concentration of the salts and other components, such as formamide, dextran sulfate. and polyethylene glycol, of the hybridization solution. All of these factors may be varied to generate conditions of stringency which are equivalent to the conditions listed above.

Changes in the stringency of hybridization and signal detection are primarily accomplished through the manipulation of formamide concentration (lower percentages of formamide result in lower stringency); salt conditions, or temperature. For example, moderately high stringency conditions include an overnight incubation at 37 degree C in a solution comprising 6X SSPE (20X SSPE = 3M NaCl; 0.2 M NaH₂PO₄; 0.02M EDTA, pH 7.4), 0.5% SDS, 30% formamide, 100 ug/ml salmon sperm blocking DNA; followed by washes at 50 degree C with 1XSSPE, 0.1% SDS. In addition, to achieve even lower stringency, washes performed following stringent hybridization can be done at higher salt concentrations (e.g. 5X SSC).

Note that variations in the above conditions may be accomplished through the inclusion and/or substitution of alternate blocking reagents used to suppress background in hybridization experiments. Typical blocking reagents include Denhardt^'s reagent, BLOTTO, heparin, denatured salmon sperm DNA, and commercially available proprietary formulations. The inclusion of specific blocking reagents may require modification of the hybridization conditions described above, due to problems with compatibility.

The present invention also encompasses alleles of the DESCl protein encoding sequences. As used herein, the term an "allele" or "allelic sequence" is an alternative form of an DESCl encoding sequence. The allele may result from one or more mutations in the DESCl encoding sequence. Such mutations typically arise from natural addition, deletion of substitution of nucleotides in the open reading frame sequences. Any gene which encodes a DESC 1 protein may have none, one, or several allelic forms. Such alleles are identified using conventional techniques, such as, for example, screening libraries with probes.

The present invention also encompasses altered polynucleotides which encode a DESCl protein. Such alterations include deletions, additions, or substitutions. Such alterations may produce a silent change and result in a DESCl protein having the same amino acid sequence as the DESCl protein encoded by the unaltered polynucleotide. Such alterations may produce a nucleotide sequence possessing non-naturally occurring codons. For example, codons preferred by a particular prokaryotic or eucaryotic host may be incorporated into the nucleotide sequences shown in Figs 1A and IB to increase the rate of expression of the polypeptides encoded by such sequences. Such alterations, conventionally, are accomplished using site-directed mutagenesis. The polynucleotides are useful for producing DESCl protein. For example, an RNA molecule encoding a DESCl protein is used in a cell-free translation systems to prepare such polypeptide. Alternatively, a DNA molecule encoding a DESCl protein is introduced into an expression vector and used to transform cells. Examples of expression vectors are chromosomal, nonchromosomal and synthetic DNA sequences, e.g., derivatives of SV40, bacterial plasmids, phage DNAs; yeast plasmids, vectors derived from combinations of plasmids and phage DNAs, viral DNA such as vaccinia, adenovirus, fowl pox virus, pseudorabies, baculovirus, and retrovirus. The DNA sequence is introduced into the expression vector by conventional procedures.

Accordingly, the present invention also relates to recombinant constructs comprising one or more of the polynucleotide sequences. Examples of constructs are vectors, such as a plasmid, phagemid, or viral vector, into which a sequence that encodes the DESCl protein has been inserted. In the expression vector, the DNA sequence which encodes the DESCl protein is operatively linked to an expression control sequence, i.e., a promoter, which directs mRNA synthesis. Representative examples of such promoters, include the LTR or SV40 promoter, the E. coli lac or trp, the phage lambda PL promoter and other promoters known to control expression of genes in prokaryotic or eukaryotic cells or in viruses. The promoter may also be the natural promoter of the DESCl encoding sequence. The expression vector, preferably, also contains a ribosome binding site for translation initiation and a transcription terminator. Preferably, the recombinant expression vectors also include an origin of replication and a selectable marker, such as for example, the ampicillin resistance gene of E. coli to permit selection of transformed cells, i.e. cells that are expressing the heterologous DNA sequences. The polynucleotide sequence encoding the DESCl protein is incorporated into the vector in frame with translation initiation and termination sequences.

The polynucleotides encoding a DESCl protein are used to express recombinant protein using conventional techniques. Such techniques are described in Sambrook, J. et al (1989) Molecular Cloning A Laboratory Manual, Cold Spring Harbor Press, Plainview. N.Y. and Ausubel, F. M. et al. (1989) Current Protocols in Molecular Biology, John wile & Sons. New York, NY.

Polynucleotides encoding a DESCl protein or fragments thereof, are also useful for designing hybridization probes for isolating and identifying cDNA clones and genomic clones encoding a DESCl protein or allelic forms thereof. Such hybridization techniques are conventional. The sequences that encode the DESCl proteins or fragments thereof, are also useful for designing primers for polymerase chain reaction (PCR), a technique useful for obtaining large quantities of cDNA molecules that encode the DESCl proteins.

Also encompassed by the present invention, are single stranded polynucleotides, hereinafter referred to as antisense polynucleotides, having sequences which are complementary to the DNA and RNA sequences which encode the DESCl proteins. The term "complementary" as used herein refers to the natural binding of the polynucleotides under permissive salt and temperature conditions by base pairing.

Isolated polynucleotides encoding a DESCl protein are also useful as chromosome markers to map related gene positions. DESCl polynucleotide probes are preferably labeled with radioisotopes, fluorescent labels or enzymatic labels.

Polynucleotides encoding an DESCl protein are useful to detect DESCl gene expression in biopsied tissue samples. DESCl polynucleotides or fragments thereof are also useful as probes or primers to identify tissues or cells in which the corresponding DESCl gene transcript is expressed. Proteins

The DESCl protein possesses four regions of conserved homology with members of the serine protease gene family. The sequence identity between DESC 1 protein and the serine protease, Human Airway Trypsin-like Protease (HAT)(Fig. IB) at the amino acid level is 38%o overall and 51% when the serine protease catalytic domain only is compared (DESCl residues 191-422). This information suggests that DESCl protein is a novel member of the serine-protease gene family.

DESC 1 protein has the following conserved domains: (a) a predicted hydrophobic transmembrane domain located at about amino acids 18-37; (b) a predicted catalytic cleavage site located at about amino acids 190-191 ; and (c) a predicted catalytic domain located at about amino acids 191-422, containing conserved residues comprising the serine protease catalytic triad at about amino acids 231 (histidine), 276 (aspartic acid) and 372 (serine). As shown in Figure 1, the predicted mature protein encompasses about 422 amino acids, while the predicted secreted and cleaved form of DESCl, which may be membrane-bound or soluble, encompasses about 232 amino acids (residues 191-422).

DESCl may, similar to HAT, be a transmembrane serine protease possessing an extracellular COOH-terminal catalytic region. Accordingly, DESCl protein may be used to cleave naturally occurring substrate proteins and by amino acid substitutions, to cleave proteins which are substrates of other serine proteases. Thus DESCl polypeptides can be used to cleave a peptide for usage in microsequencing or for peptide mapping of proteins. DESCl serine protease activity may be assayed utilizing standard methodologies used to demonstrate the activity of other serine proteases, as described for example by Smyth et al., J. Biol. Chem., 267: 24418-24425 and utilizing commercially available serine protease substrates including, but not limited to, Benzoyl-prolyl-phenyl-alanyl-arginine-4-nitril-anilide acetate; Tosyl-glycyl-prolyl-lysine-4-ntranilide acetate; Carbobenzoxy-valyl-glycyl-arginine- 4-nitril-analide acetate and N-Methoxycarobonyl-D-norleucyl-glycl-L-arginine-4-nitranilide acetate (Boehringer Mannheim). Additionally, assay of serine protease activity of DESCl can be utilized to identify inhibitors of DESCl activity, by addition of known protease inhibitors to the assay, such as alpha2-macroglobulin, 2-(2-Aminoethyl)-benzyensulfonyl fluoride hydrochloride and Leupeptin (Boehringer Mannheim).

The term DESCl protein in addition to encompassing the amino acid sequences of the reference amino acid sequences shown in Figures 1A and IB, also encompasses variant DESCl proteins whose amino acid sequence is similar to one of the reference amino acid sequences, but does not have 100% identity with the reference amino acid sequences. Such variant DESCl protein has an altered sequence in which one or more of the amino acids is deleted or substituted, or one or more amino acids are inserted, as compared to the reference amino acid sequence. Such variant DESC 1 proteins have an amino acid sequence which is at least 90% identical, preferably, at least 95% identical, more preferably at least 98% identical, most preferably at least 99% identical to the reference amino acid sequence. Sequences which are at least 90% identical have no more than 5 alterations, i.e. any combination of deletions, insertions or substitutions, per 100 amino acids of the reference amino acid sequence. Percent identity may be determined by comparing the amino acid sequence of the variant DESCl protein with the reference sequence using MEGALIGN project in the DNA STAR program. The variant sequences and reference sequences are aligned for identity calculations using the method of the software basic local alignment search tool in the BLAST network service (the National Center for Biotechnology Information, Bethesda, MD) which employs the method of Altschul. S. F., Gish. W., Miller, W„ Myers, E. W. & Lipman, D. J. (1990) J. Mol. Biol. 215, 403-410. Identities are calculated, for example, by the Align program (DNAstar, Inc.) In all cases, internal gaps and amino acid insertions in the candidate sequence as aligned are not ignored when making the identity calculation.

While variant DESCl proteins have non-conservative amino acid substitutions, it is preferred that variant DESCl proteins have the conservative amino acid substitutions. In conservative amino acid substitutions, the substituted amino acid has similar structural or chemical properties with the corresponding amino acid in the reference sequence. By way of example, conservative amino acid substitutions involve substitution of one aliphatic or hydrophobic amino acids, e.g. alanine, valine, leucine and isoleucine, with another; substitution of one hydroxyl-containing amino acid, e.g. serine and threonine, with another; substitution of one acidic residue, e.g. glutamic acid or aspartic acid, with another; replacement of one amide-containing residue, e.g. asparagine and glutamine, with another; replacement of one aromatic residue, e.g. phenylalanine and tyrosine, with another; replacement of one basic residue, e.g. lysine, arginine and histidine, with another; and replacement of one small amino acid, e.g., alanine, serine, threonine, methionine, and glycine, with another.

Preferably, the variant DESCl protein is immunoreactive with antibodies that bind to the reference DESCl protein. Guidance in determining which amino acid residues may be substituted, inserted or deleted without abolishing immunoreactivity of the variant protein with an antibody specific for the respective reference protein are found using computer programs well known in the art, for example, DNASTAR software.

The present invention also relates to fusion proteins comprising a DESCl protein and a tag, i.e.. a second protein or one or more amino acids, preferably from about 2 to 65 amino acids, more preferably from about 34 to about 62 amino acids, which are added to the amino or carboxy terminus of the DESCl PROTEIN. Typically, such additions are made to stabilize the fusion protein or to simplify purification of an expressed recombinant form of the corresponding DESCl protein Such tags are known in the art. Representative examples of such tags include sequences which encode a series of histidine residues, the epitope tag FLAG, the Herpes simplex glycoprotein D. beta-galactosidase. maltose binding protein, or glutathione S-transferase.

The present invention also encompasses DESC 1 proteins in which one or more amino acids, preferably no more than 10 amino acids, are altered by post-translation processes or synthetic methods. Examples of such modifications include, but are not limited to, acetylation. amidation. ADP-ribosylation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or a lipid, cross-linking gamma- carboxylation, glycosylation. hydroxylation, iodination, methylation. myristoylation. oxidation, pegylation, proteolytic processing, phosphorylation, prenylation, racemization. sulfation, and transfer-RNA mediated additions of amino acids to proteins such as arginylation and ubiquitination.

The DESCl protein and fragments thereof, particularly extracellular fragments thereof, are useful as immunogens to produce antibodies immunospecific for the DESCl protein. The term "immunospecific" means the antibodies have substantially greater affinity for the DESCl protein than for other proteins. Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain, and Fab fragments. Polyclonal antibodies are generated using conventional techniques, such as by administering the DESCl protein or fragment thereof to a host animal. Depending on the host species, various adjuvants are preferably used to increase immunological response. Among adjuvants used in humans, BCG (bacilli Calmette-Guerin, and Corynebacterium parvum are especially preferable). Conventional techniques are also used to collect blood from the immunized animals and to isolate the serum and/or the IgG fraction from the blood.

For preparation of monoclonal antibodies, conventional hybridoma techniques are used. Such antibodies are produced by continuous cell lines in culture. Suitable techniques for preparing monoclonal antibodies include, but are not limited to, the hybridoma technique, the human B-cell hybridoma technique, and the EBV hybridoma technique.

Various immunoassays may be used for screening to identify antibodies having the desired specificity. These include conventional techniques which involve competitive binding or immunoradiometric assays and typically involve the measurement of complex formation between the DESCl protein and the antibody. Antibodies to the DESCl protein

Antibodies which are specific for and bind to the DESCl protein or the extracellular domain of the DESC 1 protein, are useful research tools for identifying tissues that contain reduced levels of the DESCl protein and also for purifying the DESCl protein, from cell or tissue extracts, or medium of cultured cells, or partially purified preparations of intracellular and extracellular protein. Such purification is accomplished by conventional techniques such as by affinity chromatography.

Method of Assaying for DESCl mRNA in Tissue Samples

Expression of the DESCl transcript in a tissue sample or cell sample is determined using conventional procedures including, but not limited to DNA-RNA hybridization or PCR amplification.

A sample of the subject's tissue is obtained from a site which is suspected as being a tumor site. Preferably, one or more tissue samples from the area adjoining or preferably distal to the putative tumor site are also obtained from the subject. More preferably, samples are also obtained from matched normal, unaffected epithelial tissue of the subject. Preferably, all tissue samples are snap-frozen in liquid nitrogen immediately following resection. RNA is isolated from the tissue samples by conventional techniques such as a TRIzol extraction procedure see for example, Gramza et. al. "Efficient Method for Preparing Normal and Tumor Tissue for RNA Extraction" BioTechniques, volume 18, page 218 (1995) which is fully incorporated herein by reference.

The presence of DESCl mRNA is detected by RT-PCR technology using a forward primer that anneals to a region on the antisense strand of the DESCl gene and reverse primer which anneal to a region on the sense strand of the DESCl gene. Preferably, the forward and reverse primers anneal to regions of the DESCl gene which are separated by between 149 to 1471 base pairs, more preferably 300 to 400 base pairs. Preferably, the primers comprise 18- 36 nucleotides, more preferably 22-31 nucleotides. Preferably, the primers have a G+C content of 40% or greater. More preferably the forward and reverse primers comprise the following sequences, respectively:

DESCl antisense , DI 1, 5'-TGCATCAAGCAAACAGTTTATTGAGATC-3';

DESCl sense, D10, 5'CCTGTTCCCTACACAAATHCAGTAC-3'. The size of the PCR product produced using such primers is 555 bp.

Optionally, a normalization standard, such as a housekeeping gene, is included in the PCR reaction. The expression of the preferred housekeeping gene is the same level in normal squamous cells and in cells derived from squamous cell carcinoma tumor tissue. For example, suitable housekeeping genes are HPRT or genes encoding actin or tubulin. Primers to the normalization standard are selected such that the length of the PCR amplification product of the normalization standard will vary from the length of the PCR amplification product of DESC 1 mRNA to allow separation of the two PCR amplification products on an agarose gel.

Preferably, an internal standard comprising a double-stranded nucleic acid fragment which competes with the DESCl gene for the primers is added to the PCR reaction mixture. Preferably, the PCR product that results from amplification of the internal standard is of a different size from that of the PCR product that results from amplification of the DESC 1 mRNA to enable separation of the two products on an agarose gel.

Optimum cycle number for PCR amplification is preferably pre-determined for each primer set using a mixture of RT reactions from ten random samples selected from specimens of tumor RNA and matched normal RNA. This step is necessary to ensure that PCR amplification remains in the linear range and that production of PCR product does not plateau. Under the reaction conditions used, the quantity of PCR product is directly proportional to the amount of radioactivity incorporated into the DNA. This method allows a comparative analysis of gene expression between samples through direct comparison of radioactivity incorporated into each PCR product.

Preferably, the presence of the primer-specific PCR product is detected by separating the PCR products on an agarose gel. The presence of the primer-specific product is detected by ethidium bromide staining of the agarose gel. More preferably, the primer-specific product contains alpha- P-deoxynucleotide as a result of incorporating alpha-^J~-p- deoxynucleotide into the PCR reaction mixture. Detection of such PCR product is accomplished by measuring the amount of radiolabeled deoxynucleotide incorporated into the PCR product by gel scanning using autoradiograms, or by liquid scintillation counting of excised portions of the gel. Band intensity of DESCl RT-PCR product is then compared and intensity is directly proportional to the level of expression of DESCl RNA in the original tissue sample.

Alternatively the mRNA is extracted, separated, preferably on an agarose gel. and the mRNA encoding DESCl is detected preferably using a probe specific for such mRNA.

DESCl RNA is expressed in normal human epithelial tissue. DESCl RNA is also expressed in normal human epidermal keratinocytes undergoing exponential growth in tissue culture (NEHK cells; Clonetics, San Diego. CA). DESCl RNA expression is reduced or absent in squamous cell carcinoma (SCC). Thus, in one embodiment, reduced DESCl expression in neoplastic tissue of epithelial origin may be considered to be a diagnostic indicator of SCC.

Isolation and Sequence Analysis of DESCl cDNA

Representational Difference Analysis (RDA) was performed on mRNA isolated from the normal oral buccal mucosa and from an squamous cell carcinoma -positive metastatic neck node from an individual who presented with a primary squamous cell carcinoma of the tongue which was metastatic to regional neck nodes. Representational Difference Analysis was performed with carcinoma RNA as driver in the reaction, allowing selection of genes expressed in normal tissue but not in tumor tissue. Representational Difference Analysis (RDA) was performed by utilizing PCR-Select cDNA subtraction methodologies (CLONTECH, Palo Alto, CA) as described in the manufacturer's protocol. 0.5% of the Representational Difference Analysis final reaction was subject to PCR amplification. The PCR amplification products thus obtained were cloned directly into mammalian expression vector pCMV-Script (Stratagene, La Jolla, CA). All recombinant clones were screened for inserts by PCR analysis and positive clones subjected to sequence analysis using vector-specific T3 primers. BLASTN sequence analysis was then performed, using the GenBank sequence database. One recombinant clone designated "C35", carrying a 581 bp insert, possessed an open reading frame spanning the full length of the clone. The putative gene represented by this clone was designated Differential Expressed in Squamous Cell Carcinoma Gene 1 (DESCl). The C35 clone was devoid of consensus polyadenylation signals. In order to obtain the 3' end of the gene, 3 'RACE analysis was performed on the remaining normal tissue mRNA used previously for RDA analysis. Sequence analysis of 3 'RACE products allowed identification of two consensus polyadenylation signal sequences separated by 633 bp (Fig. 1A). In order to obtain additional 5' sequence, 5 'RACE was also performed.

A full-length DESCl cDNA clone (pDESCl) was constructed following analysis of DESCl sequence information obtained from overlapping pCMV-Script, 5' and 3' RACE clones. pDESCl was generated by RT-PCR amplification of normal skin RNA (Invitrogen, Carlsbad, CA) utilizing DESCl primers Dl l and D12. primers Dl l and D12 have the following sequence:

Dl l, 5'-TGCATCAAGCAAACAGTTTATTGAGATC-3'; D 12, 5 GACTTGGATGTAGACCTCGACCTTC AC-3 ' .

The PCR product was then cloned into TOPO TA cloning vector pCDNA3.1/V5/His- Topo (Invitrogen, Carlsbad, CA).The sequence of pDESCl was determined by cycle sequencing using a Thermo Sequenase system (Amersham, Cleveland. OH), followed by electrophoresis using the CastAway sequencing system (Stratagene, La Jolla, CA) according to the manufacturer^'s instructions.

The full-length nucleotide sequence(SEQ ID NOT) of one cDNA encoding DESC 1 protein is shown in Fig. 1A. An alternate full-length nucleotide sequence, SEQ.ID.NO. 3 is shown in Figure IB. The cDNA comprises a contiguous sequence of 1461 nucleotides which encodes a predicted open reading frame of 422 or 423 amino acid residues (SEQ ID NO:2). The open reading frame begins at an N-terminal methionine located at nucleotide position 53 or 56, and ends at a stop codon at nucleotide position 1322. The predicted molecular weight of the DESCl protein is about 44 kDa. Tissue Expression of DESCl

In order to characterize the tissue-specific expression pattern of DESCl, Northern analysis was performed on total RNA from multiple human tissue samples and cell lines. The results are shown in Figure 5 and demonstrate a high degree of tissue specificity of DESCl expression. Under these conditions two predominant transcripts of 2.2 kb and 1.6 kb in size were detected in tonsil tissue. Under these conditions no significant level of DESCl expression was detected in any other tissue examined, that is thymus. appendix, lymph node, gall bladder, ovary, spleen, colon small intestine, leukocyte, heart, brain, placenta, lung, liver, skeletal muscle, kidney prostate and testes. However, when Northern analysis was performed with a higher degree of sensitivity, utilizing polyadenylated RNA rather than total RNA, DESCl expression was detected in prostate and testes. A single 1.6 kb transcript is seen in testes. The three transcripts detected in prostate include a 1.6 kb transcript a 2.2 kb transcript and an additional transcript of approximately 4.4kb, which is observed exclusively in prostate tissue. In addition, expression of DESCl was detected at a minimal level in pancreas. No expression of DESCl was detected in thymus, appendix, lymph node, gall bladder, ovary, spleen, colon small intestine, leukocyte, heart, brain, placenta, lung, liver, skeletal muscle. and kidney. Thus, the DESCl gene is strongly tissue-specific in its pattern of expression.

To determine whether DESCl expression was epithelial-specific, the levels of DESCl transcripts in epithelial cell lines and tissue were determined using RT-PCR analysis. The results, shown in Fig 4 established that DESCl is expressed in neonatal (NHEKNeo) adult (NHEKAd) and prostate (PrEC) epithelial cells, confirming that the expression of the DESCl gene is epithelial specific. Figure 4 also shows DESCl expression in human skin and confirms expression in prostate and testes.

The RT-PCR analysis utilized primers D10 and Dl l, specific to the 3^" end of DESCl , and produced a product that does not encompass the internal polyadenylation consensus site. This analysis allows detection of DESCl expression in testes. Since testes exhibits only the smaller 1.6 kb transcript, the data is consistent with identification of the 1.6 kb RNA as the transcript which encodes the DESCl polypeptide. A second 3' RACE product isolated demonstrates processing of a DESCl RNA at the internal polyadenylation site (nucleotides 802-807). This transcript terminates at nucleotide 823 and demonstrates that the internal site is functional. Chromosomal Mapping Using a DESC 1 probe.

Chromosomal mapping of DESCl gene was performed using a Human/Rodent Somatic Cell Hybrid Panel from Oncor, Gaithersburg, MD, with hybridization conditions for DESCl probe as described above. The DESCl probe hybridized to only the lane containing human chromosome 4. Chromosomal mapping of DESCl was additionally performed using the Genebridge 4 Radiation Hybrid Panel (Research Genetics Inc., Huntsville. AL) according to the manufacturer's instructions by PCR amplification using primers Dl l and D18, with normal human placental DdnA (Sigma, St. Louis, MO) as template. D18 primer has the following sequence, 5'-GGAATAGTGAGCTCGGGAGATG-3\

The chromosomal location of DESCl was then determined by accessing Whitehead Institute/MIT Center for Genome Research radiation hybrid map of the human genome. DESCl is located on the long arm of chromosome 4, positioned 20.21cR from marker WI- 5548, and between markers D4S1619 and WI-7844. D4S1619 and WI-7844 have been mapped by FISH analysis to 4ql2 and 4ql3. Thus DESCl is at 4ql2 - 4ql3 within a region about 10Mb in size

The following examples, which describe in greater detail the procedures for determining DESCl gene expression levels in tissue samples, are intended to illustrate but not limit the procedures. Example 1

Ten squamous cell carcinoma specimens, and matched normal tissue, selected from diverse sites in the head and neck region were obtained. All normal tissue specimens were harvested from clinically appearing normal tissue located at least 3 cm. from the tumor margin. RNA was extracted from the samples and subjected to RT-PCR analysis. of expression of DESCl was conducted in the samples.

1.0 μg of total RNA was used for first strand cDNA synthesis in a total volume of 25 μl and reactions otherwise performed according to manufacturer's instructions (ProSTAR. Stratagene, La Jolla, CA). PCR amplification was performed in the presence of 2 units of Taq 2000 DNA polymerase (Stratagene, La Jolla, CA), with reaction conditions: 1 OmM Tris- HCI (pH 8.8), 50 mM KCI. 1.5 mM MgCl₂, 0.01% gelatin, 400 nM each primer. 200μM dNTPs, and where appropriate. 0.25μl [α³²P]dCTP (3000Ci/mmol) in a final volume of 25μl. Separate reactions were performed for each primer pair with reaction conditions; 96°C 3min followed by 94°C 30s. 55°C 30's, 72°C 1 min for 31 cycles (HPRT) or 33 cycles (DESCl) and a final 5 min extension at 72°C. PCR amplification of full-length DESCl was performed utilizing the above cycling conditions, with an additional 1 min extension time for each cycle at 72°C, and using the Advantage HF PCR kit (CLONTECH Laboratories Ind. Palo Alto, CA). PCR samples were then run through 22% agarose gels and presence of amplified product and correct product size verified by ethidium bromide fluorescence in the presence of 100 bp size markers (Gibco BRL, Gaithersburg, MD). PCR products generated were then electroblotted using a Bio-Rad Semi-Dri Electroblotter SD and transferred at 12V/110 mA for 10 min. The membrane was removed and exposed to BioMax film (Eastman Kodak, Rochester, NY). Primers utilized in PCR reactions comprise: hypoxanthine phosphoribosyl transferase (HPRT) primers HPtl , 5'-GTAATGACCAGTCAACA-3' and HPRT2, 5^'- CCAGCAAGCTTGCGACCTTGACCA-3' and DESCl primers

D3 , 5 ' -TC ACTGTTC ATTATGTGAG ATAT AATC A-3 ' ;

D4, 5'-CACCATTGATTCAAGTCTCTGGCTCAT-3';

D 10, 5 '-CCTGTTCCCTACACAAATGCAGTAC-3 ' ;

Dl l, 5'-TGCATCAAGCAAACAGTTTATTGAGATC-3';

D12, 5'-TGACTTGGATGTAGACCTCGACCTTCAC-3' and

D18, 5'-GGAATAGTGAGCTCGGGAGATG-3'.

PCR amplification of the HPRT gene was performed as a control to demonstrate equal loading and to determine integrity of RNA. Primers sets were designed by computer analysis (Oligo 4.0; NBI, Hamel, MN) of available DNA sequences for each gene and, with the exception of set Dl l. D18, are intron-spanning precluding PCR amplification of any residual DNA present in RNA samples. Optimum cycle number for PCR amplification was pre-determined for each primer set using a mixture of RT reactions from ten random tumor samples. This step is necessary to ensure that PCR amplification remains in the linear range and that production of PCR product does not plateau. Under reaction conditions used, quantity of PCR product is therefore directly proportional to the amount of radioactivity incorporated into the DNA.

The results, shown in Figure 3 A, showed lower levels of expression of DESCl in 9 of the 10 primary carcinomas relative to the high level of expression in matched normal tissue. It has been discovered that in non cancerous epithelial tissue, DESCl is expressed at a high level, yet in squamous cell carcinoma, DESCl is not expressed or only expressed at a very low level, i.e., at levels less than 10% of the levels found in matched normal tissue Example 2

Six specimens of squamous cell carcinoma of the head and neck, matched normal tissue and metastatic regional neck nodes were obtained. The mRNA extraction was conducted as in Example 1. A northern blot containing squamous cell carcinoma specimens was generated by electrophoresis of 10 μg total RNA on a 1% glyoxal agarose gel according to manufacturer's instructions (Northern Max-Gly, Ambion. Austin, TX). Blots were hybridized with [α^j2P]dCTP-labeled DESCl cDNA probe spanning 581 nucleotides of the DESC l coding sequence (nucleotides 165-746), or control β-actin cDNA (CLONTECH Laboratories Inc., Palo Alto, CA), according to manufacturer^'s protocol. Blots were then washed in 0.5 x SSC, 0.1% SDS for 30 min. at room temperature, followed by 0.1 x SSC, 0.1% SDS for 1 hr. at 50°C with two changes of solution. The blots were then exposed to BioMax film.

As shown in Fig. 3B, expression of DESCl was lower in squamous cell carcinoma specimens relative to matched normal specimens. Additionally, DESC 1 expression was not detected in any metastatic nodal tissue samples, with the exception of minimal expression in a pharyngeal carcinoma metastatic to regional neck nodes.

Example 3

Specimens for analysis comprising primary carcinoma, metastatic node and matched normal tissue were obtained from an individual who presented with a primary squamous cell carcinoma of the tongue which was metastatic to regional neck nodes. The mRNA extraction, amplification and analysis for expression of DESC 1 was conducted as in Example 1. As shown in Figure 2, DESCl was expressed at a high level in normal tissue sample but. in contrast, was expressed at a very low level in the primary tongue carcinoma and absent from the metastatic nodal tissue derived from the same individual.

Notably, little to no DESCl PCR transcripts were detected in the tumor samples of Examples 1-3. These results show that the present method is useful for determining the levels of DESCl mRNA in tumor tissue from individuals with squamous cell carcinoma and for distinguishing squamous cell carcinoma tissue from healthy tissue. Such method is also useful to determine whether expression is absent, present, or altered. Thus, the present method is also useful for research purposes to determine whether therapeutic agents modulate expression of the DESC- 1 gene. Example 4

The DESCl gene has been cloned into mammalian expression vector pcDNA3.1/V5/His-TOPO, in both the sense and anti-sense direction. These constructs and the empty vector alone were transfected into NIH3T3 cells and stable colonies were obtained via use of the neomycin resistance gene present on the sample plasmid. Colonies obtained were counted. Total colony count for two flasks transfected with DESCl sense construct is 128. Total colony count for two flasks transfected with anti-sense DESCl construct is 301. Total colony count for two flasks transfected with empty vector alone is 245. Additionally, colonies from DESCl sense construct were smaller, suggesting that the growth rate of the colonies was slower. Thus, the present invention also relates to a method altering replication or growth of host cells by introducing a polynucleotide which encodes the DESC 1 into such cells and then expressing the polynucleotide.

Example 5 Expression of DESCl in prostate cancer specimens and cell lines.

Expression of DESCl was assayed in specimens of human prostate cancer and prostate cancer cell lines. RT-PCR analysis of DESCl expression was performed using PCR primers D10 and Dl l previously used to assay for epxression of DESCl in squamous cell carcinomas of the head and neck. The results show lack of DESCl expression in 2/3 human prostate cancer xenografts grown in mice. Expression of DESCl is also undetectable in human prostate cancer cell lines DU145 and PC3. However, expression of DESCl can be detected in normal human prostate tissue, normal human prostate epithelial cells (PrEC cells, Clonetics) and in normal prostate cells immortalized with HPV (PZ HPV-7).

Example 6

Western Analysis of DESCl Expression in Transfected Human Embryonal Kidney Epithelial Cells

The DESCl cDNA was cloned into ecdysone-inducible mammalian expression vector pIND Topo TA to produce recombinant clone pDESCl/IND C4. In this clone, the DESCl polypeptide is expressed as a fusion protein with a carboxy- terminal tag containing the V5 epitope from the paramyxovirus SV5. When expressed in mammalian cells, DESCl can then be detected by Western analysis utilizing an antibody to the V5 epitope. PDESCl/InD C4 was transfected into human embroyonal kidney epithelial calls (293 cells) previously engineered to express the insect ecdysone receptor. Transfection of pDESCl /InD C4 was performed using Effectene (Qiagen) transfection reagent. Expression of DESCl from this recombinant clone was accomplished by addition of Ponasterone (a synethetic analog of ecdysone) which allows binding of the ecdysone receptor to its response element in the promoter controlling DESCl expression according to the manufacturer's instructions (Invitrogen). 72 hours post transfection, cell lysates were made from 293 cells both treated and untreated with Ponasterone. Lysates were then run on NuPAGE acrylamide gels (Novex) and Western analysis performed utilizing a chemiluminescent Western blotting immunodetection system (Novex). The results are shown below and demonstrate presence of a polypeptide approximately 52kd in lanes 1 and 3 (ponasterone induced) but not in lanes 2 and 4 (ponasterone negative). The molecular weight of 52kd is consistent with the predicted size of the fusion polypeptide produced by DESCl (47kd) and the fused V4/HIS Tag epitopes (5kd).

DESCl

1 2 3 4 Example 7

Expression of DESCl in COS cells, Purification of Recombinant Protein and Assay for Protease Activity

DESCl full length cDNa was cloned into mammalian expression vector pcDNA4/HisMax (Invitrogen). In this recombinant construct, the DESCl polypeptide is expressed as a fusion protein with an amino-terminal His tag. DNA was transfected into COS cells utilizing Superfect transfection reagent. 72 hours after transfection, cells were lysed and recombinant DESCl polypeptide purified utilizing the Xpress protein purification system (Invitrogen) according to the manufacturer's instructions. Purification was accomplished via binding of the His tag to ProBond resin and subsequent elution of the recombinant polypeptide. Protease activity was then tested by incubation of DESCl recombinant polypeptide in a PepTag Protease Assay. In this assay, presence of protease activity is demonstrated by proteolysis of small dye-linked peptides. Digestion of the peptides alters the size and charge, and these changes can be detected by agarose gel electrophoresis. DESCl polypeptide was incubated with PepTag peptide Cl, with sequence: Dye-Pro-Leu-Ser-Arg-Thr-Leu-Ser-Val-Ala-Ala-Lys. Proteolytic cleavage between the C-terminal lysine and the internal arginine yields fragments with a neutral charge which remain in the well on electrophoresis. Intact peptide has a net positive charge and migrates towards the negative electrode. Protease activity was measured according to the manufacturer's p_{tpep y}rotocol (Promega). The results are shown below and demonstrate proteolytic cleavage of Cl peptide by fractions containing DESCl polypeptide eluted from the ProBond resin. Results show increasing activity within fractions 1-6, while peptide incubated with elution buffer alone (lane 7) shows no protease activity (peptide intact). Positive control alkaline protease demonstrates protease activity (lane 8) similar to that of DESCl fractions.

Cleaved Peptide Intact Peptide

Claims

CLAIMS What is claimed is:

1. A method for detecting DESCl gene expression in a sample from a subject comprising the following steps: providing a tissue sample from the subject; assaying for expression of DESCl gene in said sample.

2. An isolated nucleic acid comprising a polynucleotide encoding a protein having at least 90% identity to the DESCl protein shown in Figure 1 A or B.

3. The isolated nucleic acid of claim 2 having wherein the polynucleotide encodes a mature from or a soluble form of the DESCl protein.

4. A recombinant vector comprising the nucleic acid of claim 2.

5. A recombinant host comprising the recombinant vecotor of claim 4.

6. An isolated DESCl protein comprising a sequence having at least 90% identity to the amino acid sequence in Figure 1A or IB.

7. An antibody that binds specifically to the DESCl protein.

8. The isolated DESC 1 protein of claim 6 comprising the amino acid sequence set forth in Figure 1A or IB.

9. The isolated nucleic acid of claim 2 wherein the polynucleotide hybridizes under stringent conditions with the nucleotide sequence shown in Figure 1 A or IB.