WO1998011219A1

WO1998011219A1 - Disease associated membrane protein (damp)

Info

Publication number: WO1998011219A1
Application number: PCT/US1997/015924
Authority: WO
Inventors: Jennifer L. Hillman; Surya K. Goli
Original assignee: Incyte Pharmaceuticals, Inc.
Priority date: 1996-09-11
Filing date: 1997-09-10
Publication date: 1998-03-19
Also published as: AU4261297A

Abstract

The present invention provides a polynucleotide which identifies and encodes a novel human disease associated membrane protein (DAMP) and DAMP itself. The invention provides for genetically engineered expression vectors and host cells comprising the nucleic acid sequence encoding DAMP. The invention also provides pharmaceutical compositions containing DAMP and the use of such compositions for the treatment of cancer. The invention also provides diagnostic assays which utilize the polynucleotide to hybridize with the transcripts encoding DAMP or anti-DAMP antibodies which specifically bind to DAMP.

Description

DISEASE ASSOCIATED MEMBRANE PROTEIN (DAMP)

The present invention relates to nucleic acid and amino acid sequences of a novel disease associated membrane protein (DAMP) and to the use of these sequences in the diagnosis, study, prevention, and treatment of disease.

BACKGROUND ART Carbohydrates, proteins and lipids are all important constituents of cell membranes. Proteins, including glycoproteins, which span the lipid bilayer are called transmembrane proteins and may cross back and forth several times. While hydrophobic residues are relegated to the middle of the membrane, this crossing back and forth exposes hydrophihc residues to the internal and external milieu. (Unwin N et al (1984) Sci Am 250:78).

Membrane proteins participate in catalyzing reactions, transporting molecules in and out of cells, receiving and transmitting intercellular messages, anchoring cells to substratum, and providing tissue-identification tags. They are important in both paracrine and autocrine signaling and may react appropriately or inappropriately in response to growth factors. In fact, cells vary in identity, character and bioactivity largely as a result of variation in their membrane proteins.

Aberrant membrane proteins have been identified in a significant number of diseases and are intimately associated with cancers. Cells displaying these aberrant proteins are often locked in continuous cell division and are characterized by their altered gene transcription, decreased growth factor requirements, loss of anchorage, and cell moφhology. With aging, benign tumors arise with greater frequency even though they pose less risk. These tumors are often delineated by a fibrous capsule and contain cells that closely resemble and may function as normal cells. On the other hand, malignant cells are usually undifferentiated and characterized by their rapid proliferation and ability to metastasize. To improve tumor cell identification and provide opportunities for therapeutic intervention, it is essential to understand membrane protein expression and function. Peripheral myelin protein 22 (PMP22) provides such an opportunity. PMP22 is a hydrophobic protein of 160 residues having four predicted transmembrane domains which play a role in cell proliferation (Welcher AA et ai (1991) Proc Nat Acad Sci 88:7195-9). Tissue culture experiments using NIH 3T3 cells and primary dermal fibroblasts have shown that PMP22 is upregulated under growth arrest due to serum deprivation or high cell density. This suggests a . significant role for PMP22 in cell proliferation (Manfioletti G et al (1990) Mol Cell Biol 10:2924-30).

Furthermore, when PMP22 was transfected into cultured Schwann cells, the length of the growth (Gl) phase was extended (Zoidl G et al (1995) EMBO 14:1 122-28). The lack of PMP22 in dividing cells similarly emphasizes its influence on cell proliferation. Other proteins of this family, such as epithelial membrane protein 1 (EMP1; Taylor V et al (1995) J Biol Chem 270:28824-33) and a squamous cell-associated gene (CL-20; Marvin KW et al (1995) J Biol Chem 270:28910-16), are likely to serve similar functions related to cell proliferation and differentiation. In fact, EMP1 and PMP22 are co-expressed in most tissues although their relative expression levels differ. EMP1 and PMP22 mRNA levels are inversely regulated in the degenerating rat sciatic nerve after injury and by growth arrest in NIH 3T3 fibroblasts (Taylor, supra; Marvin, supra).

Identification and characterization of membrane proteins associated with various diseases such as metastatic tumors, squamous cell carcinoma, rheumatoid and osteoarthritis can provide the basis for the clinical diagnosis and therapeutic intervention. In addition, such molecules provide an opportunity for investigation of the molecular mechanisms governing the interactions between membrane proteins and disease.

DISCLOSURE OF THE INVENTION The present invention discloses a novel disease associated membrane protein, hereinafter referred to as DAMP, which shares features with four transmembrane spanning proteins involved in regulating cell proliferation. Accordingly, the invention features a substantially purified DAMP, as shown in the amino acid sequence of SEQ ID NO:l .

One aspect of the invention features isolated and substantially purified polynucleotides which encode DAMP. In a particular aspect, the polynucleotide is the nucleotide sequence of SEQ ID NO:2. In addition, the invention features polynucleotide sequences that hybridize under stringent conditions to SEQ ID NO:2.

The invention further relates to the nucleic acid sequence encoding DAMP, oligonucleotides, peptide nucleic acids, fragments, portions or antisense molecules thereof. The present invention also relates, in part, to the inclusion of the nucleic acid sequence encoding DAMP in an expression vector which can be used to transform host cells or organisms. The invention also provides for using similar vectors for the therapeutic transformation to prevent proliferation of cancerous cells or tissues.

The instant invention presents a method for producing DAMP or a fragment thereof. It contemplates the delivery of purified DAMP, alone or in a pharmaceutically acceptable excipient, to cancerous cells or tissues. It also encompasses antibodies which bind specifically to DAMP and can be used to examine prevalence of the protein in vivo.

BRIEF DESCRIPTION OF DRAWINGS Figures 1 A and IB shows the amino acid (SEQ ID NO:l) and nucleic acid sequences

(SEQ ID NO:2) of the novel DAMP of the present invention produced using MacDNAsis software (Hitachi Software Engineering Co Ltd, San Bruno CA).

Figures 2A and 2B shows the northern analysis for the consensus nucleotide sequence (SEQ ID NO:2) produced electronically using the LIFESEQ™ database (Incyte Pharmaceuticals, Palo Alto CA).

Figure 3 shows the amino acid sequence alignments among DAMP (SEQ ID NO: 1 ) and GI 1 171356, human tumor associated membrane protein homolog, and GI 951 124, mouse tumor associated membrane protein (Ben-Porath I and Benvenisty N et al 1996, in press). Sequences were aligned using the multisequence alignment program of DNAStar™ software (DNAStar Inc, Madison WI).

Figure 4 shows the hydrophobicity plot (generated using MacDNAsis software) for DAMP, SEQ ID NO: 1 ; the X axis reflects amino acid position, and the negative Y axis, hydrophobicity.

Figure 5 shows the isoelectric plot (generated using MacDNAsis software) for DAMP, SEQ ID NO: 1.

MODES FOR CARRYING OUT THE INVENTION Definitions

"Nucleic acid sequence" as used herein refers to an oligonucleotide, nucleotide or polynucleotide. and fragments or portions thereof, and to DNA or RNA of genomic or synthetic origin which may be single- or double-stranded, and represent the sense or antisense strand. Similarly, amino acid sequence as used herein refers to peptide or protein sequence.

"Peptide nucleic acid" as used herein refers to a molecule which comprises an oligomer to which an amino acid residue, such as lysine, and an amino group have been added. These small molecules, also designated anti-gene agents, stop transcript elongation by binding to their complementary (template) strand of nucleic acid (Nielsen PE et al (1993) Anticancer Drug Des 8:53-63).

A "deletion" is defined as a change in either nucleotide or amino acid sequence in which one or more nucleotides or amino acid residues, respectively, are absent.

An "insertion" or "addition" is that change in a nucleotide or amino acid sequence which has resulted in the addition of one or more nucleotides or amino acid residues, respectively, as compared to the naturally occurring DAMP. A "substitution" results from the replacement of one or more nucleotides or amino acids by different nucleotides or amino acids, respectively.

As used herein, DAMP refers to the amino acid sequence of substantially purified DAMP obtained from any species, particularly mammalian, including bovine, ovine, porcine, murine, equine, and preferably human, from any source whether natural, synthetic, semi-synthetic or recombinant.

A "variant" of DAMP is defined as an amino acid sequence differs by one or more amino acids. The variant may have "conservative" changes, wherein a substituted amino acid has similar structural or chemical properties, eg, replacement of leucine with isoleucine. More rarely, a variant may have "nonconservative" changes, eg, replacement of a glycine with a tryptophan. Similar minor variations may also include amino acid deletions or insertions, or both. Guidance in determining which and how many amino acid residues may be substituted, inserted or deleted without abolishing biological or immunological activity may be found using computer programs well known in the art, for example, DNAStar software.

The term "biologically active'¹ refers to DAMP having structural, regulatory or biochemical functions of a naturally occurring DAMP. Likewise, "immunologically active" defines the capability of the natural, recombinant or synthetic DAMP, or any oligopeptide thereof, to induce a specific immune response in appropriate animals or cells and to bind with specific antibodies.

The term "derivative" as used herein refers to the chemical modification of a nucleic acid encoding DAMP or the encoded DAMP. Illustrative of such modifications would be replacement of hydrogen by an alkyl, acyl, or amino group. A nucleic acid derivative would encode a polypeptide which retains essential biological characteristics of natural DAMP.

As used herein, the term "substantially purified" refers to molecules, either nucleic or amino acid sequences, that are removed from their natural environment, isolated or separated, and are at least 60% free, preferably 75% free, and most preferably 90% free from other components with which they are naturally associated.

The term "hybridization" as used herein shall include "any process by which a strand of nucleic acid joins with a complementary strand through base pairing" (Coombs J (1994) Dictionary of Biotechnology. Stockton Press, New York NY). Amplification is defined as the production of additional copies of a nucleic acid sequence and is generally carried out using polymerase chain reaction technologies well known in the art (Dieffenbach CW and GS Dveksler (1995) PCR Primer, a_. Laboratory Manual. Cold Spring Harbor Press, Plainview NY).

"Stringency" typically occurs in a range from about Tm-5°C (5°C below the Tm of the probe)to about 20°C to 25°C below Tm. As will be understood by those of skill in the art, stringent hybridization can be used to identify or detect identical polynucleotide sequences or to identify or detect similar or related polynucleotide sequences. Preferred Embodiment

The present invention relates to a novel human disease associated membrane protein (DAMP) identified among the cDNAS from a library constructed from synovial tissue of an individual with osteoarthritis and to the use of the nucleic acid and amino acid sequences in the study, diagnosis, prevention and treatment of disease. The consensus nucleotide sequence, disclosed herein, was extended and assembled from Incyte Clones 728086 (SYNOOAT01), 284708 (CARDNOT01), 319563, 407953, and 410362 (EOSIHET02), 388037 (THYMNOT02), 477554 (MMLR2DT01), 515270 (MMLR1DT01),615507 (MMLR2DT01),777006 (COLNNOT05), 851553 (NGANNOTOl), 983106 (TONGTUTOl ), 9951 12 (KIDNTUTOl ), and 1256428 (MENITUT03). As shown in Figures 2A and 2B, cDNAs encoding portions of DAMP were found in eosinophils and macrophages, and a variety of diseased tissues including rheumatoid and osteoarthritic synovia, cancerous and Crohn's colon, and tumors of the brain, heart, lung, tongue, prostate, ovary, stomach and kidney. It must be noted that naturally occurring expression of DAMP is not necessarily limited to these cells and tissues. The present invention also encompasses DAMP variants. A preferred DAMP variant is one having at least 80% amino acid sequence similarity to the amino acid sequence (SEQ ID NO:l), a more preferred DAMP variant is one having at least 90% amino acid sequence similarity to SEQ ID NO:l and a most preferred DAMP variant is one having at least 95% amino acid sequence similarity to SEQ ID NO: 1. Nucleic acid encoding the human DAMP of the present invention was first identified in cDNA, Incyte Clone 728086 (SEQ ID NO:2), through a computer- generated search for amino acid sequence alignments. The nucleic acid sequence, SEQ ID NO:2, encodes the 163 amino acid sequence, SEQ ID NO: 1. The present invention is based, in part, on the chemical and structural homology among DAMP, GI 1171356, human tumor associated membrane protein homolog, and GI 951 124, mouse tumor associated membrane protein (Ben-Porath I and Benvenisty N et al 1996, in press). DAMP residues 1-28, 62-90, 94-1 18, and 134-159 of SEQ ID NO: 1 represent four hydrophobic membrane spanning domains. In addition, potential N glycosylation sites are present at residues N_4g and N₅₇. The DAMP Coding Sequences

The extended and assembled nucleic acid and deduced amino acid sequences of DAMP are shown in Figures 1A and IB. In accordance with the invention, any nucleic acid sequence which encodes DAMP can be used to generate recombinant molecules which express DAMP. In a specific embodiment described herein, a partial sequence encoding DAMP was first isolated as Incyte Clone 728086 from a osteoarthritic synovium cDNA library (SYNOOAT01).

It will be appreciated by those skilled in the art that as a result of the degeneracy of the genetic code, a multitude of DAMP-encoding nucleotide sequences, some bearing minimal homology to the nucleotide sequences of any known and naturally occurring gene may be produced. The invention contemplates each and every possible variation of nucleotide sequence that could be made by selecting combinations based on possible codon choices. These combinations are made in accordance with the standard triplet genetic code as applied to the nucleotide sequence encoding naturally occurring DAMP, and all such variations are to be considered as being specifically disclosed.

Although nucleotide sequences which encode DAMP and its variants are preferably capable of hybridizing to the nucleotide sequence of the naturally occurring sequence under appropriately selected conditions of stringency, it may be advantageous to produce nucleotide sequences encoding DAMP or its derivatives possessing a substantially different codon usage. Codons may be selected to increase the rate at which expression of the peptide occurs in a particular prokaryotic or eukaryotic expression host in accordance with the frequency with which particular codons are utilized by the host. Other reasons for substantially altering the nucleotide sequence encoding DAMP and its derivatives without altering the encoded amino acid sequences include the production of RNA transcripts having more desirable properties, such as a greater half-life, than transcripts produced from the naturally occurring sequence.

A DNA sequence, or portions thereof, encoding DAMP or its derivative may be produced entirely by synthetic chemistry. After synthesis, the gene may be inserted into any of the many available DNA vectors and cell systems using reagents that generally available. Moreover, synthetic chemistry may be used to introduce mutations into a sequence encoding DAMP or any portion thereof.

Also included within the scope of the present invention are polynucleotide sequences that are capable of hybridizing to the nucleotide sequence of SEQ ID NO:2 under various conditions. Hybridization conditions are based on the melting temperature (Tm) of the nucleic acid binding complex or probe, as taught in Berger and Kimmel (1987, Guide to Molecular Cloning Techniques. Methods in Enzymologv. Vol 152, Academic Press, San Diego CA) incoφorated herein by reference, and on the salt concentrations under which the steps of the process are carried out .

Altered nucleic acid sequences encoding DAMP which may be used in accordance with the invention include deletions, insertions or substitutions of different nucleotides resulting in a polynucleotide that encodes the same or a functionally equivalent DAMP. The protein may also show deletions, insertions or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent DAMP. Deliberate amino acid substitutions may be made on the basis of similarity in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues as long as the biological activity of DAMP is retained. For example, negatively charged amino acids include aspartic acid and glutamic acid; positively charged amino acids include lysine and arginine; and amino acids with uncharged polar head groups having similar hydrophilicity values include leucine, isoleucine. valine; glycine. alanine; asparagine. glutamine; serine, threonine phenylalanine, and tyrosine.

Included within the scope of the present invention are alleles encoding DAMP. As used herein, an "allele" or "allelic sequence" is an alternative form of the nucleic acid sequence encoding DAMP. Alleles result from a mutation,- ie, a change in the nucleic acid sequence, and generally produce altered mRNAs or polypeptides whose structure or function may or may not be altered. Any given gene may have none, one or many allelic forms. Common mutational changes which give rise to alleles are generally ascribed to natural deletions, additions or substitutions of amino acids. Each of these types of changes may occur alone, or in combination with the others, one or more times in a given sequence. Methods for DNA sequencing may be used which are well known in the art and employ such enzymes as the Klenow fragment of DNA polymerase I, Sequenase® (US Biochemical Coφ, Cleveland OH)), Taq polymerase (Perkin Elmer, Norwalk CT), thermostable T7 polymerase (Amersham, Chicago IL), or combinations of recombinant polymerases and proofreading exonucleases such as the ELONGASE Amplification System marketed by Gibco BRL (Gaithersburg MD). Preferably, the process is automated with machines such as the Hamilton Micro Lab 2200 (Hamilton, Reno NV), Peltier Thermal Cycler (PTC200; MJ Research, Watertown MA) and the ABI 377 DNA sequencers (Perkin Elmer). Extending the Polynucleotide Sequence

The polynucleotide sequence encoding DAMP may be extended utilizing partial nucleotide sequence and various methods known in the art to detect upstream sequences such as promoters and regulatory elements. For example, Gobinda et al (1993; PCR Methods Applic 2:318-22) use "restriction-site" polymerase chain reaction (PCR) as a direct method which uses universal primers to retrieve unknown sequence adjacent to a known locus. First, genomic DNA is amplified in the presence of primer to a linker sequence and a primer specific to the known region. The amplified sequences are subjected to a second round of PCR with the same linker primer and another specific primer internal to the first one. Products of each round of PCR are transcribed with an appropriate RNA polymerase and sequenced using reverse transcriptase.

Inverse PCR can be used to amplify or extend sequences using divergent primers based on a known region (Triglia T et al (1988) Nucleic Acids Res 16:8186). The primers may be designed using OLIGO® 4.06 Primer Analysis Software (1992; National Biosciences Inc, Plymouth MN), or another appropriate program, to be 22-30 nucleotides in length, to have a GC content of 50% or more, and to anneal to the target sequence at temperatures about 68°-72° C. The method uses several restriction enzymes to generate a suitable fragment in the known region of a gene. The fragment is then circularized by intramolecular ligation and used as a PCR template.

Capture PCR (Lagerstrom M et al (1991) PCR Methods Applic 1 :11 1-19) is a method for PCR amplification of DNA fragments adjacent to a known sequence in human and yeast artificial chromosome DNA. Capture PCR also requires multiple restriction enzyme digestions and ligations to place an engineered double- stranded sequence into an unknown portion of the DNA molecule before PCR.

Another method which may be used to retrieve unknown sequence is walking PCR (Parker JD et al (1991 ) Nucleic Acids Res 19:3055-60), which involves targeted gene walking. Alternatively, PCR, nested primers. PromoterFinder™ (Clontech, Palo Alto CA) and PromoterFinder libraries can be used to walk in genomic DNA. This process avoids the need to screen libraries and is useful in finding intron/exon junctions.

Preferred libraries for screening for full length cDNAs are those which have been size-selected to include larger cDNAs. Also, random primed libraries are preferred in that they will contain more sequences which contain the 5' and upstream regions of genes. A randomly primed library may be particularly useful if an oligo d(T) library does not yield a full-length cDNA. Genomic libraries are useful for extension into the 5' nontranslated regulatory region.

Capillary electrophoresis may be used to analyze either the size or confirm the nucleotide sequence in sequencing or PCR products. Systems for rapid sequencing are available from Perkin Elmer, Beckman Instruments (Fullerton CA). and other companies. Capillary sequencing may employ flowable polymers for electrophoretic separation, four different fluorescent dyes (one for each nucleotide) which are laser activated, and detection of the emitted wavelengths by a charge coupled devise camera. Output/light intensity is converted to electrical signal using appropriate software (eg. Genotyper™ and Sequence Navigator™ from Perkin Elmer) and the entire process from loading of samples to computer analysis and electronic data display is computer controlled. Capillary electrophoresis is particularly suited to the sequencing of small pieces of DNA which might be present in limited amounts in a particular sample. The reproducible sequencing of up to 350 bp of Ml 3 phage DNA in 30 min has been reported (Ruiz-Martinez MC et al (1993) Anal Chem 65:2851-8). Expression of the Nucleotide Sequence In accordance with the present invention, polynucleotide sequences which encode DAMP, fragments of the polypeptide, fusion proteins or functional equivalents thereof may be used in recombinant DNA molecules that direct the expression of DAMP in appropriate host cells. Due to the inherent degeneracy of the genetic code, other DNA sequences which encode substantially the same or a functionally equivalent amino acid sequence, may be used to clone and express DAMP. As will be understood by those of skill in the art, it may be advantageous to produce DAMP-encoding nucleotide sequences possessing non-naturally occurring codons. Codons preferred by a particular prokaryotic or eukaryotic host (Murray E et al (1989) Nuc Acids Res 17:477-508) can be selected, for example, to increase the rate of DAMP expression or to produce recombinant RNA transcripts having desirable properties, such as a longer half-life, than transcripts produced from naturally occurring sequence.

The nucleotide sequences of the present invention can be engineered in order to alter DAMP-encoding sequence for a variety of reasons, including but not limited to, alterations which modify the cloning, processing and/or expression of the gene product. For example, mutations may be introduced using techniques which are well known in the art, eg, site-directed mutagenesis to insert new restriction sites, to alter glycosylation patterns, to change codon preference, to produce splice variants, etc. 5 In another embodiment of the invention, a natural, modified or recombinant DAMP- encoding sequence may be ligated to a heterologous sequence to encode a fusion protein. For example, for screening of peptide libraries for inhibitors of DAMP activity, it may be useful to encode a chimeric DAMP protein that is recognized by a commercially available antibody. A fusion protein may also be engineered to contain a cleavage site located between DAMP and the

10 heterologous protein sequence, so that the DAMP may be cleaved and substantially purified away from the heterologous moiety.

In an alternate embodiment of the invention, the sequence encoding DAMP may be synthesized, whole or in part, using chemical methods well known in the art (see Caruthers MH et al (1980) Nuc Acids Res Symp Ser 215-23, Horn T et al(1980) Nuc Acids Res Symp Ser

15 225-32, etc). Alternatively, the protein itself may be produced using chemical methods to synthesize an amino acid sequence for DAMP, whole or in part. For example, peptide synthesis can be performed using various solid-phase techniques (Roberge JY et al (1995) Science 269:202-204) and automated synthesis may be achieved, for example, using the ABI 431 A Peptide Synthesizer (Perkin Elmer) in accordance with the instructions provided by the 0 manufacturer.

The newly synthesized peptide can be substantially purified by preparative high performance liquid chromatography (eg, Creighton (1983) Proteins. Structures and Molecular Principles. WH Freeman and Co. New York NY). The composition of the synthetic peptides may be confirmed by amino acid analysis or sequencing (eg, the Edman degradation procedure; 5 Creighton, supra). Additionally the amino acid sequence of DAMP, or any part thereof, may be altered during direct synthesis and/or combined using chemical methods with sequences from other proteins, or any part thereof, to produce a variant polypeptide. Expression Systems

In order to express a biologically active DAMP, the nucleotide sequence encoding DAMP 0 or its functional equivalent, is inserted into an appropriate expression vector, ie, a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence. Methods which are well known to those skilled in the art can be used to construct expression vectors containing a sequence encoding DAMP and appropriate transcriptional or translational controls. These methods include in vitro recombinant DNA techniques, synthetic techniques and in vivo recombination or genetic recombination. Such techniques are described in Sambrook et al (1989) Molecular Cloning. A Laboratory Manual. Cold Spring Harbor Press, Plainview NY and Ausubel FM et al (1989) Current Protocols in Molecular Biology. John Wiley & Sons, New York NY.

A variety of expression vector/host systems may be utilized to contain and express a sequence encoding DAMP. These include but are not limited to microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (eg, baculovirus); plant cell systems transfected with virus expression vectors (eg, cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with bacterial expression vectors (eg, Ti or pBR322 plasmid); or animal cell systems. The "control elements" or "regulatory sequences" of these systems vary in their strength and specificities and are those nontranslated regions of the vector, enhancers, promoters, and 3' untranslated regions, which interact with host cellular proteins to carry out transcription and translation. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used. For example, when cloning in bacterial systems, inducible promoters such as the hybrid lacZ promoter of the Bluescript® phagemid (Stratagene, LaJolla CA) or pSportl (Gibco BRL) and ptφ-lac hybrids and the like may be used. The baculovirus polyhedrin promoter may be used in insect cells. Promoters or enhancers derived from the genomes of plant cells (eg, heat shock, RUBISCO; and storage protein genes) or from plant viruses (eg, viral promoters or leader sequences) may be cloned into the vector. In mammalian cell systems, promoters from the mammalian genes or from mammalian viruses are most appropriate. If it is necessary to generate a cell line that contains multiple copies of the sequence encoding DAMP, vectors based on SV40 or EBV may be used with an appropriate selectable marker.

In bacterial systems, a number of expression vectors may be selected depending upon the use intended for DAMP. For example, when large quantities of DAMP are needed for the induction of antibodies, vectors which direct high level expression of fusion proteins that are readily purified may be desirable. Such vectors include, but are not limited to, the multifunctional E. coli cloning and expression vectors such as Bluescript® (Stratagene), in which the sequence encoding DAMP may be ligated into the vector in frame with sequences for the amino-terminal Met and the subsequent 7 residues of β-galactosidase so that a hybrid protein is produced; pIN vectors (Van Heeke & Schuster (1989) J Biol Chem 264:5503-5509); and the like. pGEX vectors (Promega, Madison WI) may 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 adsoφtion to glutathione-agarose beads followed by elution in the presence of free glutathione. Proteins made in such systems are designed to include heparin, thrombin or factor XA protease cleavage sites so that the cloned polypeptide of interest can be released from the GST moiety at will.

In the yeast, Saccharomvces cerevisiae. a number of vectors containing constitutive or inducible promoters such as alpha factor, alcohol oxidase and PGH may be used. For reviews, see Ausubel et al (supra) and Grant et al (1987) Methods in Enzymology 153:516-544.

In cases where plant expression vectors are used, the expression of a sequence encoding DAMP may be driven by any of a number of promoters. For example, viral promoters such as the 35S and 19S promoters of CaMV (Brisson et al (1984) Nature 310:51 1-514) may be used alone or in combination with the omega leader sequence from TMV (Takamatsu et al (1987) EMBO J 6:307-31 1 ). Alternatively, plant promoters such as the small subunit of RUBISCO (Coruzzi et al (1984) EMBO J 3: 1671-1680; Brogue et al (1984) Science 224:838-843); or heat shock promoters (Winter J and Sinibaldi RM (1991) Results Probl Cell Differ 17:85-105) may be used. These constructs can be introduced into plant cells by direct DNA transformation or pathogen-mediated transfection. For reviews of such techniques, see Hobbs S or Murry LE in McGraw Hill Yearbook of Science and Technology H992 McGraw Hill New York NY, pp 191 - 196 or Weissbach and Weissbach (1988) Methods for Plant Molecular Biology. Academic Press, New York NY, pp 421 -463.

An alternative expression system which may be used to express DAMP is an insect system. In one such system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes in Spodoptera frugiperda cells or in Trichoplusia larvae. The sequence encoding DAMP may be cloned into a nonessential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter. Successful insertion of the sequence encoding DAMP will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein coat. The recombinant viruses are then used to infect £. frugiperda cells or Trichoplusia larvae in which DAMP is expressed (Smith et al (1983) J Virol 46:584; Engelhard EK et al ( 1994) Proc Nat Acad Sci 91 :3224-7).

In mammalian host cells, a number of viral-based expression systems may be utilized. In cases where an adenovirus is used as an expression vector, a sequence encoding DAMP may be ligated into an adenovirus transcription/ translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a nonessential El or E3 region of the viral genome will result in a viable virus capable of expressing in infected host cells (Logan and Shenk (1984) Proc Natl Acad Sci 81 :3655-59). In addition, transcription enhancers, such as the rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells. Specific initiation signals may also be required for efficient translation of a sequence encoding DAMP. These signals include the ATG initiation codon and adjacent sequences. In cases where the sequence encoding DAMP, its initiation codon and upstream sequences are inserted into the most appropriate expression vector, no additional translational control signals may be needed. However, in cases where only coding sequence, or a portion thereof, is inserted, exogenous transcriptional control signals including the ATG initiation codon must be provided. Furthermore, the initiation codon must be in the correct reading frame to ensure transcription of the entire insert. Exogenous transcriptional elements and initiation codons can be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers appropriate to the cell system in use (Scharf D et al (1994) Results Probl Cell Differ 20: 125-62; Bittner et al (1987) Methods in Enzymol 153:516-544).

In addition, a host cell strain may be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed protein in the desired fashion. Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation and acylation. Post-translational processing which cleaves a "prepro" form of the protein may also be important for correct insertion, folding and/or function. Different host cells such as CHO, HeLa, MDCK, 293, WI38, etc have specific cellular machinery and characteristic mechanisms for such post-translational activities and may be chosen to ensure the correct modification and processing of the introduced, foreign protein.

For long-term, high-yield production of recombinant proteins, stable expression is preferred. For example, cell lines which stably express DAMP may be transformed using expression vectors which contain viral origins of replication or endogenous expression elements and a selectable marker gene. Following the introduction of the vector, cells may be allowed to grow for 1 -2 days in an enriched media before they are switched to selective media. The puφose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells which successfully express the introduced sequences. Resistant clumps of stably transformed cells can be proliferated using tissue culture techniques appropriate to the cell type.

Any number of selection systems may be used to recover transformed cell lines. These include, but are not limited to, the heφes simplex virus thymidine kinase (Wigler M et al ( 1977) Cell 1 1 :223-32) and adenine phosphoribosyltransferase (Lowy I et al (1980) Cell 22:817-23) genes which can be employed in tk- or aprt- cells, respectively. Also, antimetabolite. antibiotic or herbicide resistance can be used as the basis for selection; for example, dhfr which confers resistance to methotrexate (Wigler M et al (1980) Proc Natl Acad Sci 77:3567-70); npt, which confers resistance to the aminoglycosides neomycin and G-418 (Colbere-Garapin F et al (1981 ) J Mol Biol 150: 1-14) and als or pat, which confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively (Murry, supra). Additional selectable genes have been described, for example, tφB, which allows cells to utilize indole in place of tryptophan, or hisD, which allows cells to utilize histinol in place of histidine (Hartman SC and RC Mulligan (1988) Proc Natl Acad Sci 85:8047-51 ). Recently, the use of visible markers has gained popularity with such markers as anthocyanins, β glucuronidase and its substrate, GUS, and luciferase and its substrate, luciferin, being widely used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system (Rhodes CA et al (1995) Methods Mol Biol 55:121-131). Identification of Transformants Containing the Polynucleotide Sequence

Although the presence/absence of marker gene expression suggests that the gene of interest is also present, its presence and expression should be confirmed. For example, if the sequence encoding DAMP is inserted within a marker gene sequence, recombinant cells containing the sequence encoding DAMP can be identified by the absence of marker gene function. Alternatively, a marker gene can be placed in tandem with the sequence encoding DAMP under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem sequence as well. Alternatively, host cells which contain the sequence encoding DAMP and expressing

DAMP may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridization and protein bioassay or immunoassay techniques which include membrane, solution, or chip based technologies for the detection and/or quantification of the nucleic acid or protein.

The presence of the polynucleotide sequence encoding DAMP can be detected by DNA-DNA or DNA-RNA hybridization or amplification using probes, portions or fragments of the sequence encoding DAMP. Nucleic acid amplification based assays involve the use of oligonucleotides or oligomers based on the nucleic acid sequence to detect transformants containing DNA or RNA encoding DAMP. As used herein "oligonucleotides" or "oligomers" refer to a nucleic acid sequence of at least about 10 nucleotides and as many as about 60 nucleotides, preferably about 15 to 30 nucleotides, and more preferably about 20-25 nucleotides which can be used as a probe or amplimer. A variety of protocols for detecting and measuring the expression of DAMP, using either polyclonal or monoclonal antibodies specific for the protein are known in the art. Examples include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA) and fluorescent activated cell sorting (FACS). A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes on DAMP is preferred, but a competitive binding assay may be employed. These and other assays are described, among other places, in Hampton R et al ( 1990, Serological Methods, a Laboratory Manual. APS Press, St Paul MN) and Maddox DE et al (1983, J Exp Med 158:1211). A wide variety of labels and conjugation techniques are known by those skilled in the art and can be used in various nucleic acid and amino acid assays. Means for producing labeled hybridization or PCR probes for detecting related sequences include oligolabeling, nick translation, end-labeling or PCR amplification using a labeled nucleotide. Alternatively, the DAMP-encoding sequence, or any portion of it, may be cloned into a vector for the production of an mRNA probe. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by addition of an appropriate RNA polymerase such as T7, T3 or SP6 and labeled nucleotides.

A number of companies such as Pharmacia Biotech (Piscataway NJ), Promega (Madison WI), and US Biochemical Coφ (Cleveland OH) supply commercial kits and protocols for these procedures. Suitable reporter molecules or labels include those radionuclides, enzymes, fluorescent, chemiluminescent, or chromogenic agents as well as substrates, cofactors, inhibitors, magnetic particles and the like. Patents teaching the use of such labels include US Patents 3,817,837; 3,850,752; 3,939,350; 3,996,345; 4,277,437; 4,275,149 and 4,366,241. Also, recombinant immunoglobulins may be produced as shown in US Patent No. 4,816,567 incoφorated herein by reference. Purification of DAMP

Host cells transformed with a nucleotide sequence encoding DAMP may be cultured under conditions suitable for the expression and recovery of the encoded protein from cell culture. The protein produced by a recombinant cell may be secreted or contained intracellularly depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing sequence encoding DAMP can be designed with signal sequences which direct secretion of DAMP through a prokaryotic or eukaryotic cell membrane. Other recombinant constructions may join the sequence encoding DAMP to nucleotide sequence encoding a polypeptide domain which will facilitate purification of soluble proteins (Kroll DJ et al (1993) DNA Cell Biol 12:441-53; cf discussion of vectors infra containing fusion proteins).

DAMP may also be expressed as a recombinant protein with one or more additional polypeptide domains added to facilitate protein purification. Such purification facilitating domains include, but are not limited to, metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilized metals, protein A domains that allow purification on immobilized immunoglobulin, and the domain utilized in the FLAGS extension affinity purification system (Immunex Coφ, Seattle WA). The inclusion of a cleavable linker sequences such as Factor XA or enterokinase (Invitrogen, San Diego CA) between the purification domain and DAMP is useful to facilitate purification. One such expression vector provides for expression of a fusion protein comprising the sequence encoding DAMP and nucleic acid sequence encoding 6 histidine residues followed by thioredoxin and an enterokinase cleavage site. The histidine residues facilitate purification while the enterokinase cleavage site provides a means for purifying DAMP from the fusion protein.

In addition to recombinant production, fragments of DAMP may be produced by direct peptide synthesis using solid-phase techniques (cf Stewart et al ( 1969) Solid-Phase Peptide

Synthesis. WH Freeman Co, San Francisco; Merrifield J (1963) J Am Chem Soc 85:2149-2154). In vitro protein synthesis may be performed using manual techniques or by automation. Automated synthesis may be achieved, for example, using Applied Biosystems 431 A Peptide Synthesizer (Perkin Elmer, Foster City CA) in accordance with the instructions provided by the manufacturer. Various fragments of DAMP may be chemically synthesized separately and combined using chemical methods to produce the full length molecule. Uses of DAMP DAMP appears to be associated with both inflammatory cells, autoimmune diseases and cancers. These diseases include rheumatoid and osteoarthritis, Crohn's diseases, melanoma and carcinomas of the brain, heart, lung, tongue, prostate, ovary, stomach and kidney.

DAMP has amino acid sequence homology with four other transmembrane proteins clearly associated with cell proliferation, and nucleotide homology with a growth arrest specific protein and an epithelial membrane protein. These homologies suggest that DAMP, or fragments or derivatives thereof, can be used in diagnostic methods for the detection of nucleotide sequences associated with tumors and other cancers. Furthermore, the nucleotide sequences of DAMP provide the basis for therapeutic molecules useful in the treatment of aberrant cell proliferation. Additionally, the sequences for DAMP will provide the basis for screening for agonists, antagonists or inhibitors that modulate the activity or products of DAMP

In another embodiment of the present invention, anti-DAMP antibodies capable of neutralizing the activity of DAMP may be used to prevent or treat diseases. Neri D et al (1995, Cell Biophys 27: 47- ) and Liberatore M et al (1995, Eur J Nucl Med 22: 1326-) describe simple methods for isotope labelling of cysteine-tagged antibodies resulting in more than 50% radionuclide incoφoration and full retention of immuoreactivity. DAMP-specific antibodies are also useful for the diagnosis of conditions and diseases associated with expression of the polypeptides.

The DAMP nucleic acid sequence of SEQ ID NO:2, can be incoφorated into effective eukaryotic expression vectors and directly administered into somatic cells for gene therapy. In like manner, RNA transcripts produced in vitro may be encapsulated in and administered via liposomes. Such vectors and transcripts may function transiently or may be incoφorated into the host chromosomal DNA for longer term expression.

In vivo delivery of genetic constructs into subjects is developed to the point of targeting specific cell types. The delivery to specific cells has been accomplished, for instance, by complexing nucleic acids with proteinous ligands that recognize cell specific receptors which mediate uptake (cf Wu GY et al (1991) J Biol Chem 266:14338-42). Alternatively, recombinant nucleic acid constructs may be injected directly for local uptake and integration (Jiao S et al (1992) Human Gene Therapy 3:21-33). DAMP Antibodies

DAMP-specific antibodies are useful for the diagnosis and treatment of conditions and diseases associated with expression of DAMP. Such antibodies include, but are not limited to, polyclonal, monoclonal, chimeric, single chain. Fab fragments and fragments produced by a Fab expression library. Neutralizing antibodies, ie, those which inhibit dimer formation, are especially preferred for diagnostics and therapeutics.

It is not necessary that the portion of DAMP used for antibody induction have biological activity; however, the protein fragment, or oligopeptide must be antigenic. Peptides used to induce specific antibodies may have an amino acid sequence consisting of at least five amino acids, and preferably at least 10 amino acids. Preferably, they should mimic a portion of the amino acid sequence of the natural protein and may contain the entire amino acid sequence of a small, naturally occurring molecule. Short stretches of DAMP amino acids may be fused with those of another protein such as keyhole limpet hemocyanin and antibody produced against the chimeric molecule. Procedures well known in the art can be used for the production of antibodies to DAMP.

For the production of antibodies, various hosts including goats, rabbits, rats, mice, etc may be immunized by injection with DAMP or any portion, fragment or oligopeptide which retains immunogenic properties. Depending on the host species, various adjuvants may be used to increase immunological response. Such adjuvants include but are not limited to Freund's, mineral gels such as aluminum hydroxide, and surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin. and dinitrophenol. BCG (bacilli Calmette-Guerin) and Corvnebacterium parvum are potentially useful human adjuvants.

Monoclonal antibodies to DAMP may be prepared using 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 originally described by Koehler and Milstein (1975 Nature 256:495-497), the human B-cell hybridoma technique (Kosbor et al (1983) Immunol Today 4:72; Cote et al (1983) Proc Natl Acad Sci 80:2026-2030) and the EBV-hybridoma technique (Cole et al ( 1985) Monoclonal Antibodies and ancer Therapy. Alan R Liss Inc, New York NY, pp 77-96).

In addition, techniques developed for the production of "chimeric antibodies", the splicing of mouse antibody genes to human antibody genes to obtain a molecule with appropriate antigen specificity and biological activity can be used (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). Alternatively, techniques described for the production of single chain antibodies (US Patent No. 4,946,778) can be adapted to produce DAMP-specific single chain antibodies

Antibodies may also be produced by inducing in vivo production in the lymphocyte population or by screening recombinant immunoglobulin libraries or panels of highly specific binding reagents as disclosed in Orlandi et al (1989, Proc Natl Acad Sci 86: 3833-3837), and Winter G and Milstein C (1991 ; Nature 349:293-299).

Antibody fragments which contain specific binding sites for DAMP may also be generated. For example, such fragments include, but are not limited to, the F(ab')2 fragments 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')2 fragments. Alternatively, Fab expression libraries may be constructed to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity (Huse WD et al (1989) Science 256:1275-1281).

A variety of protocols for competitive binding or immunoradiometric assays using either polyclonal or monoclonal antibodies with established specificities are well known in the art. Such immunoassays typically involve the formation of complexes between DAMP and its specific antibody and the measurement of complex formation. A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two noninterfering epitopes on a specific DAMP protein is preferred, but a competitive binding assay may also be employed. These assays are described in Maddox DE et al (1983, J Exp Med 158: 1211). Diagnostic Assays Using DAMP Specific Antibodies Particular DAMP antibodies are useful for the diagnosis of conditions or diseases characterized by expression of DAMP or in assays to monitor patients being treated with DAMP, its fragments, agonists or inhibitors. Diagnostic assays for DAMP include methods utilizing the antibody and a label to detect DAMP in human body fluids or extracts of cells or tissues. The polypeptides and antibodies of the present invention may be used with or without modification. Frequently, the polypeptides and antibodies will be labeled by joining them, either covalently or noncovalently, with a reporter molecule. A wide variety of reporter molecules are known, several of which were described above.

A variety of protocols for measuring DAMP, using either polyclonal or monoclonal antibodies specific for the respective protein are known in the art. Examples include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA) and fluorescent activated cell sorting (FACS). A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes on DAMP is preferred, but a competitive binding assay may be employed. These assays are described, among other places, in Maddox,

DE et al (1983, J Exp Med 158:1211).

In order to provide a basis for diagnosis, normal or standard values for DAMP expression must be established. This is accomplished by combining body fluids or cell extracts taken from normal subjects, either animal or human, with antibody to DAMP under conditions suitable for complex formation which are well known in the art. The amount of standard complex formation may be quantified by comparing various artificial membranes containing known quantities of

DAMP with both control and disease samples from biopsied tissues. Then, standard values obtained from normal samples may be compared with values obtained from samples from subjects potentially affected by disease. Deviation between standard and subject values establishes the presence of disease state.

Drug Screening

DAMP, its catalytic or immunogenic fragments or oligopeptides thereof, can be used for screening therapeutic compounds in any of a variety of drug screening techniques. The fragment employed in such a test may be free in solution, affixed to a solid support, borne on a cell surface, or located intracellularly. The formation of binding complexes, between DAMP and the agent being tested, may be measured.

Another technique for drug screening which may be used for high throughput screening of compounds having suitable binding affinity to the DAMP is described in detail in "Determination of Amino Acid Sequence Antigenicity" by Geysen HN, WO Application 84/03564, published on

September 13, 1984, and incoφorated herein by reference. In summary, large numbers of different small peptide test compounds are synthesized on a solid substrate, such as plastic pins or some other surface. The peptide test compounds are reacted with fragments of DAMP and washed. Bound DAMP is then detected by methods well known in the art. Substantially purified DAMP can also be coated directly onto plates for use in the aforementioned drug screening techniques. Alternatively, non-neutralizing antibodies can be used to capture the peptide and immobilize it on a solid support.

This invention also contemplates the use of competitive drug screening assays in which neutralizing antibodies capable of binding DAMP specifically compete with a test compound for binding DAMP. In this manner, the antibodies can be used to detect the presence of any peptide which shares one or more antigenic determinants with DAMP.

Uses of the Polynucleotide Encoding DAMP A polynucleotide sequence encoding DAMP or any part thereof may be used for diagnostic and/or therapeutic puφoses. For diagnostic puφoses, the sequence encoding DAMP of this invention may be used to detect and quantitate gene expression in biopsied tissues in which DAMP may be expressed in response to oncogenes. The diagnostic assay is useful to distinguish between absence, presence, and excess expression of DAMP and to monitor regulation of DAMP levels during therapeutic intervention. Included in the scope of the invention are oligonucleotide sequences, antisense RNA and DNA molecules, and peptide nucleic acids, (PNA).

Another aspect of the subject invention is to provide for hybridization or PCR probes which are capable of detecting polynucleotide sequences, including genomic sequences, encoding DAMP or closely related molecules. The specificity of the probe, whether it is made from a highly specific region, eg, 10 unique nucleotides in the 5' regulatory region, or a less specific region, eg, especially in the 3' region, and the stringency of the hybridization or amplification (maximal, high, intermediate or low) will determine whether the probe identifies only naturally occurring DAMP, alleles or related sequences.

Probes may also be used for the detection of related sequences and should preferably contain at least 50% of the nucleotides from any of these sequences encoding DAMP. The hybridization probes of the subject invention may be derived from the nucleotide sequence of SEQ ID NO:2 or from genomic sequence including promoter, enhancer elements and introns of the naturally occurring sequence encoding DAMP. Hybridization probes may be labeled by a variety of reporter groups, including radionuclides such as 32P or 35S, or enzymatic labels such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems, and the like.

Other means for producing specific hybridization probes for DNAs include the cloning of nucleic acid sequences encoding DAMP or DAMP derivatives into vectors for the production of mRNA probes. Such vectors are known in the art and are commercially available and may be used to synthesize RNA probes in vitro by means of the addition of the appropriate RNA polymerase as T7 or SP6 RNA polymerase and the appropriate radioactively labeled nucleotides. Diagnostic Use

Polynucleotide sequences encoding DAMP may be used for the diagnosis of conditions or diseases with which the expression of DAMP is associated. For example, polynucleotide sequences encoding DAMP may be used in hybridization or PCR assays of fluids or tissues from biopsies to detect DAMP expression. The form of such qualitative or quantitative methods may include Southern or northern analysis, dot blot or other membrane-based technologies; PCR technologies; dip stick, pin, chip and ELISA technologies. All of these techniques are well known in the art and are the basis of many commercially available diagnostic kits.

The DAMP-encoding nucleotide sequences disclosed herein provide the basis for assays that detect activation or induction associated with inflammation or disease. The nucleotide sequence may be labeled by methods known in the art and added to a fluid or tissue sample from a patient under conditions suitable for the formation of hybridization complexes. After an incubation period, the sample is washed with a compatible fluid which optionally contains a dye (or other label requiring a developer) if the nucleotide has been labeled with an enzyme. After the compatible fluid is rinsed off, the dye is quantitated and compared with a standard. If the amount of dye in the biopsied or extracted sample is significantly elevated over that of a comparable control sample, the nucleotide sequence has hybridized with nucleotide sequences in the sample, and the presence of elevated levels of nucleotide sequences encoding DAMP in the sample indicates the presence of the associated inflammation and/or disease. Such assays may also be used to evaluate the efficacy of a particular therapeutic treatment regime in animal studies, in clinical trials, or in monitoring the treatment of an individual patient. In order to provide a basis for the diagnosis of disease, a normal or standard profile for DAMP expression must be established. This is accomplished by combining body fluids or cell extracts taken from normal subjects, either animal or human, with DAMP, or a portion thereof, under conditions suitable for hybridization or amplification. Standard hybridization may be quantified by comparing the values obtained for normal subjects with a dilution series of DAMP run in the same experiment where a known amount of substantially purified DAMP is used. Standard values obtained from normal samples may be compared with values obtained from samples from patients affected by DAMP-associated diseases. Deviation between standard and subject values establishes the presence of disease.

Once disease is established, a therapeutic agent is administered and a treatment profile is generated. Such assays may be repeated on a regular basis to evaluate whether the values in the profile progress toward or return to the normal or standard pattern. Successive treatment profiles may be used to show the efficacy of treatment over a period of several days or several months. PCR, may be used as described in US Patent Nos. 4,683,195 and 4,965,188 provides additional uses for oligonucleotides based upon the sequence encoding DAMP. Such oligomers are generally chemically synthesized, but they may be generated enzymatically or produced from a recombinant source. Oligomers generally comprise two nucleotide sequences, one with sense orientation (5'->3') and one with antisense (3'<-5'), employed under optimized conditions for identification of a specific gene or condition. The same two oligomers, nested sets of oligomers, or even a degenerate pool of oligomers may be employed under less stringent conditions for detection and/or quantitation of closely related DNA or RNA sequences.

Additionally, methods which may be used to quantitate the expression of a particular molecule include radiolabeling (Melby PC et al 1993 J Immunol Methods 159:235-44) or biotinylating (Duplaa C et al 1993 Anal Biochem 229-36) nucleotides, coamplification of a control nucleic acid, and standard curves onto which the experimental results are inteφolated. Quantitation of multiple samples may be speeded up by running the assay in an ELISA format where the oligomer of interest is presented in various dilutions and a spectrophotometric or colorimetric response gives rapid quantitation. A definitive diagnosis of this type may allow health professionals to begin aggressive treatment and prevent further worsening of the condition. Similarly, further assays can be used to monitor the progress of a patient during treatment. Furthermore, the nucleotide sequences disclosed herein may be used in molecular biology techniques that have not yet been developed, provided the new techniques rely on properties of nucleotide sequences that are currently known such as the triplet genetic code, specific base pair interactions, and the like. Therapeutic Use Based upon its homology to EMAP-II and its expression profile, the polynucleotide encoding DAMP disclosed herein may be useful in the treatment of immune deficiency diseases.

Expression vectors derived from retroviruses, adenovirus, heφes or vaccinia viruses, or from various bacterial plasmids, may be used for delivery of nucleotide sequences to the targeted organ, tissue or cell population. Methods which are well known to those skilled in the art can be used to construct recombinant vectors which will express antisense of the sequence encoding DAMP. See, for example, the techniques described in Sambrook et al (supra) and Ausubel et al (supra).

The polynucleotides comprising full length cDNA sequence and/or its regulatory elements enable researchers to use the sequence encoding DAMP as an investigative tool in sense (Youssoufian H and HF Lodish 1993 Mol Cell Biol 13:98-104) or antisense (Eguchi et al (1991) Annu Rev Biochem 60:631-652) regulation of gene function. Such technology is now well known in the art, and sense or antisense oligomers, or larger fragments, can be designed from various locations along the coding or control regions.

Genes encoding DAMP can be turned off by transfecting a cell or tissue with expression vectors which express high levels of a desired DAMP fragment. Such constructs can flood cells with untranslatable sense or antisense sequences. Even in the absence of integration into the DNA, such vectors may continue to transcribe RNA molecules until all copies are disabled by endogenous nucleases. Transient expression may last for a month or more with a non-replicating vector (Mettler I, personal communication) and even longer if appropriate replication elements are part of the vector system.

As mentioned above, modifications of gene expression can be obtained by designing antisense molecules, DNA, RNA or PNA, to the control regions of the sequence encoding DAMP, ie, the promoters, enhancers, and introns. Oligonucleotides derived from the transcription initiation site, eg, between -10 and +10 regions of the leader sequence, are preferred. The antisense molecules may also be designed to block translation of mRNA by preventing the transcript from binding to ribosomes. Similarly, inhibition can be achieved using "triple helix" base-pairing methodology. Triple helix pairing compromises the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or regulatory molecules. Recent therapeutic advances using triplex DNA were reviewed by Gee JE et al (In: Huber BE and BI Carr (1994) Molecular and Immunologic Approaches. Futura Publishing Co, Mt Kisco NY).

Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA. The mechanism of ribozyme action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA. followed by endonucleolytic cleavage. Within the scope of the invention are engineered hammerhead motif ribozyme molecules that can specifically and efficiently catalyze endonucleolytic cleavage of the sequence encoding DAMP.

Specific ribozyme cleavage sites within any potential RNA target are initially identified by scanning the target molecule 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 may be evaluated for secondary structural features which may render the oligonucleotide inoperable. The suitability of candidate targets may also be evaluated by testing accessibility to hybridization with complementary oligonucleotides using ribonuclease protection assays.

Antisense molecules and ribozymes of the invention may be prepared by any method known in the art for the synthesis of RNA molecules. These include techniques for chemically synthesizing oligonucleotides such as solid phase phosphoramidite chemical synthesis. Alternatively, RNA molecules may be generated by in vitro and in vivo transcription of DNA sequences encoding DAMP. Such DNA sequences may be incoφorated into a wide variety of vectors with suitable RNA polymerase promoters such as T7 or SP6. Alternatively, antisense cDNA constructs that synthesize antisense RNA constitutively or inducibly can be introduced into cell lines, cells or tissues.

RNA molecules may be modified to increase intracellular stability and half-life. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5' and/or 3' ends of the molecule or the use of phosphorothioate or 2' O-methyl rather than phosphodiesterase linkages within the backbone of the molecule. This concept is inherent in the production of PNAs and can be extended in all of these molecules by the inclusion of nontraditional bases such as inosine, queosine and wybutosine as well as acetyl-, methyl-, thio- and similarly modified forms of adenine, cytidine, guanine, thymine, and uridine which are not as easily recognized by endogenous endonucleases. Methods for introducing vectors into cells or tissues include those methods discussed infra and which are equally suitable for in vivo, in vitro and ex vivo therapy. For ex vivo therapy, vectors are introduced into stem cells taken from the patient and clonally propagated for autologous transplant back into that same patient is presented in US Patent Nos. 5,399,493 and 5,437,994, disclosed herein by reference. Delivery by transfection and by liposome are quite well known in the art.

Furthermore, the nucleotide sequences encoding DAMP disclosed herein may be used in molecular biology techniques that have not yet been developed, provided the new techniques rely on properties of nucleotide sequences that are currently known, including but not limited to such properties as the triplet genetic code and specific base pair interactions. Detection and Mapping of Related Polynucleotide Sequences

The nucleic acid sequence encoding DAMP can also be used to generate hybridization probes for mapping the naturally occurring genomic sequence. The sequence may be mapped to a particular chromosome or to a specific region of the chromosome using well known techniques. These include in sim hybridization to chromosomal spreads, flow-sorted chromosomal preparations, or artificial chromosome constructions such as yeast artificial chromosomes, bacterial artificial chromosomes, bacterial PI constructions or single chromosome cDNA libraries as reviewed in Price CM (1993; Blood Rev 7:127-34) and Trask BJ (1991 ; Trends Genet 7:149-54).

The technique of fluorescent in situ hybridization of chromosome spreads has been described, among other places, in Verma et al ( 1988) Human Chromosomes: Manual of Basic Techniques. Pergamon Press, New York NY. Fluorescent in siiu hybridization of chromosomal preparations and other physical chromosome mapping techniques may be correlated with additional genetic map data. Examples of genetic map data can be found in the 1994 Genome Issue of Science (265 : 1981 f). Correlation between the location of a the sequence encoding DAMP on a physical chromosomal map and a specific disease (or predisposition to a specific disease) may help delimit the region of DNA associated with that genetic disease. The nucleotide sequences of the subject invention may be used to detect differences in gene sequences between normal, carrier or affected individuals.

In sil hybridization of chromosomal preparations and physical mapping techniques such as linkage analysis using established chromosomal markers are invaluable in extending genetic maps. A recent example of an STS based map of the human genome was recently published by the Whitehead-MIT Center for Genomic Research (Hudson TJ et al (1995) Science

270:1945-1954). Often the placement of a gene on the chromosome of another mammalian species such as mouse (Whitehead Institute/MIT Center for Genome Research, Genetic Map of the Mouse, Database Release 10, April 28, 1995) may reveal associated markers even if the number or arm of a particular human chromosome is not known. New sequences can be assigned to chromosomal arms, or parts thereof, by physical mapping. This provides valuable information to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once a disease or syndrome, such as ataxia telangiectasia (AT), has been crudely localized by genetic linkage to a particular genomic region, for example, AT to 1 lq22-23 (Gatti et al (1988) Nature 336:577-580), any sequences mapping to that area may represent associated or regulatory genes for further investigation. The nucleotide sequence of the subject invention may also be used to detect differences in the chromosomal location due to translocation, inversion, etc. among normal, carrier or affected individuals. Pharmaceutical Compositions

The present invention relates to pharmaceutical compositions which may comprise nucleotides, proteins, antibodies, agonists, antagonists, or inhibitors, alone or in combination with at least one other agent, such as stabilizing compound, which may be administered in any sterile, biocompatible pharmaceutical carrier, including, but not limited to, saline, buffered saline. dextrose, and water. Any of these molecules can be administered to a patient alone, or in combination with other agents, drugs or hormones, in pharmaceutical compositions where it is mixed with excipient(s) or pharmaceutically acceptable carriers. In one embodiment of the present invention, the pharmaceutically acceptable carrier is pharmaceutically inert. Administration of Pharmaceutical Compositions

Administration of pharmaceutical compositions is accomplished orally or parenterally. Methods of parenteral delivery include topical, intra-arterial (directly to the tumor), intramuscular, subcutaneous, intramedullary, intrathecal, intraventricular, intravenous, intraperitoneal, or intranasal administration. In addition to the active ingredients, these pharmaceutical compositions may contain suitable pharmaceutically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. Further details on techniques for formulation and administration may be found in the latest edition of "Remington's Pharmaceutical Sciences" (Maack Publishing Co, Easton PA). Pharmaceutical compositions for oral administration can be formulated using pharmaceutically acceptable carriers well known in the art in dosages suitable for oral administration. Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees. capsules, liquids, gels, syrups, slurries, suspensions and the like, for ingestion by the patient. Pharmaceutical preparations for oral use can be obtained through combination of active compounds with solid excipient, optionally grinding a resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are carbohydrate or protein fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; starch from corn, wheat, rice, potato, or other plants; cellulose such as methyl cellulose, hydroxypropylmethyl-cellulose, or sodium carboxymethylcellulose; and gums including arabic and tragacanth; and proteins such as gelatin and collagen. If desired, disintegrating or solubilizing agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, alginic acid, or a salt thereof, such as sodium alginate.

Dragee cores are provided with suitable coatings such as concentrated sugar solutions, which may also contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for product identification or to characterize the quantity of active compound, ie, dosage.

Pharmaceutical preparations which can be used orally include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a coating such as glycerol or sorbitol. Push-fit capsules can contain active ingredients mixed with a filler or binders such as lactose or starches, lubricants such as talc or magnesium stearate, and, optionally, stabilizers. In soft capsules, the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycol with or without stabilizers.

Pharmaceutical formulations for parenteral administration include aqueous solutions of active compounds. For injection, the pharmaceutical compositions of the invention may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiologically buffered saline. Aqueous injection suspensions may contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions.

For topical or nasal administration, penetrants appropriate to the particular barrier to be permeated are used in the formulation. Such penetrants are generally known in the art. Manufacture and Storage

The pharmaceutical compositions of the present invention may be manufactured in a manner that known in the art, eg, by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes. The pharmaceutical composition may be provided as a salt and can be formed with many acids, including but not limited to hydrochloric, sulfuric, acetic, lactic, tartaric, malic, succinic, etc. Salts tend to be more soluble in aqueous or other protonic solvents that are the corresponding free base forms. In other cases, the preferred preparation may be a lyophilized powder in lmM-50 mM histidine, 0.1%-2% sucrose, 2%-7% mannitol at a pH range of 4.5 to 5.5 that is combined with buffer prior to use.

After pharmaceutical compositions comprising a compound of the invention formulated in a acceptable carrier have been prepared, they can be placed in an appropriate container and labeled for treatment of an indicated condition. For administration of DAMP, such labeling would include amount, frequency and method of administration.

Therapeuticallv Effective Dose

Pharmaceutical compositions suitable for use in the present invention include compositions wherein the active ingredients are contained in an effective amount to achieve the intended puφose. The determination of an effective dose is well within the capability of those skilled in the art.

For any compound, the therapeutically effective dose can be estimated initially either in cell culture assays, eg, of neoplastic cells, or in animal models, usually mice, rabbits, dogs, or pigs. The animal model is also used to achieve a desirable concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.

A therapeutically effective dose refers to that amount of protein or its antibodies, antagonists, or inhibitors which ameliorate the symptoms or condition. Therapeutic efficacy and toxicity of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, eg, ED50 (the dose therapeutically effective in 50% of the population) and LD50 (the dose lethal to 50% of the population). The dose ratio between therapeutic and toxic effects is the therapeutic index, and it can be expressed as the ratio,

LD50/ED50. Pharmaceutical compositions which exhibit large therapeutic indices are preferred. The data obtained from cell culture assays and animal studies is used in formulating a range of dosage for human use. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage varies within this range depending upon the dosage form employed, sensitivity of the patient, and the route of administration. The exact dosage is chosen by the individual physician in view of the patient to be treated. Dosage and administration are adjusted to provide sufficient levels of the active moiety or to maintain the desired effect. Additional factors which may be taken into account include the severity of the disease state, eg, tumor size and location; age, weight and gender of the patient; diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy. Long acting pharmaceutical compositions might be administered every 3 to 4 days, every week, or once every two weeks depending on half-life and clearance rate of the particular formulation. Normal dosage amounts may vary from 0.1 to 100.000 micrograms, up to a total dose of about 1 g, depending upon the route of administration. Guidance as to particular dosages and methods of delivery is provided in the literature. See US Patent Nos. 4,657,760; 5,206,344; or 5,225,212. Those skilled in the art will employ different formulations for nucleotides than for proteins or their inhibitors. Similarly, delivery of polynucleotides or polypeptides will be specific to particular cells, conditions, locations, etc.

It is contemplated, for example, that DAMP can be used to screen for therapeutic molecules which would ameliorate the adverse effects of inflammatory cells in autoimmune diseases. The examples below are provided to illustrate the subject invention and are not included for the puφose of limiting the invention.

INDUSTRIAL APPLICABILITY I SYNOOAT01 cDNA Library Construction

The osteoarthritic joint from a 82 year-old female used for cDNA library construction was obtained from the University of California Davis. The frozen tissue was homogenized using a Brinkmann Homogenizer Polytron PT-3000 (Brinkmann Instruments, Westbury NJ) and lysed in a buffer containing guanidinium isothiocyanate. The lysate was centrifuged over a 5.7 M CsCl cushion using an Beckman SW28 rotor in a Beckman L8-70M Ultracentrifuge (Beckman Instruments) for 18 hours at 25,000 rpm at ambient temperature. The RNA was extracted twice with acid phenol pH 4.0 using the reagents and extraction procedures as supplied in the

Stratagene RNA Isolation Kit (Catalog #200345; Stratagene). RNA was precipitated using 0.3 M sodium acetate and 2.5 volumes of ethanol. resuspended in water and DNase treated for 15 min at 37iC. The RNA was isolated using the Qiagen Oligotex kit (QIAGEN Inc, Chatsworth CA). The poly-A+ RNA was handled according to the recommended protocols in the Superscript Plasmid System for cDNA Synthesis and Plasmid Cloning (Catalog #18248-013; Gibco/BRL). First strand cDNA synthesis was accomplished using oligo d(T) priming and second strand synthesis was performed using a combination of DNA polymerase I. E. coli ligase and RNase H. The cDNA was blunted with T4 polymerase, and a Sal I linker was added to the blunt ended cDNA. The Sal I adapted, double stranded cDNAs were the digested with Not I and fractionated on a Sepharose CL4B column (Catalog #275105, Pharmacia). Those cDNAs exceeding 400 bp were ligated into pSport I which was subsequently transformed into DHSa^-1 competent cells (Catalog #18258-012, Gibco/BRL). II Isolation and Sequencing of cDNA Clones

Plasmid DNA was released from the cells and purified using the Miniprep Kit (Catalog #77468; Advanced Genetic Technologies Coφoration, Gaithersburg MD). This kit consists of a 96-well block with reagents for 960 purifications. The recommended protocol was employed except for the following changes: 1) the 96 wells were each filled with only 1 ml of sterile Terrific Broth (Catalog #2271 1, LIFE TECHNOLOGIES™) with carbenicillin at 25 mg/L and glycerol at 0.4%; 2) the bacteria were cultured for 24 hours after the wells were inoculated and then lysed with 60 ml of lysis buffer; 3) a centrifugation step employing the Beckman GS-6R rotor at 2900 φm for 5 minutes was performed before the contents of the block were added to the primary filter plate; and 4) the optional step of adding isopropanol to TRIS buffer was not routinely performed. After the last step in the protocol, samples were transferred to a Beckman 96-well block for storage.

The cDNAs were sequenced by the method of Sanger F and AR Coulson ( 1975; J Mol Biol 94:44 If), using a Hamilton Micro Lab 2200 (Hamilton, Reno NV) in combination with four Peltier Thermal Cyclers (PTC200 from MJ Research, Watertown MA) and Applied Biosystems 377 or 373 DNA Sequencing Systems, and the reading frame was determined.

III Homology Searching of cDNA Clones and Their Deduced Proteins

Each cDNA was compared to sequences in GenBank using a search algorithm developed by Applied Biosystems and incoφorated into the INHERIT- 670 Sequence Analysis System. In this algorithm, Pattern Specification Language (TRW Inc, Los Angeles CA) was used to determine regions of homology. The three parameters that determine how the sequence comparisons run were window size, window offset, and error tolerance. Using a combination of these three parameters, the DNA database was searched for sequences containing regions of homology to the query sequence, and the appropriate sequences were scored with an initial value. Subsequently, these homologous regions were examined using dot matrix homology plots to distinguish regions of homology from chance matches. Smith- Waterman alignments were used to display the results of the homology search.

Peptide and protein sequence homologies were ascertained using the INHERIT^™ 670 Sequence Analysis System in a way similar to that used in DNA sequence homologies. Pattern Specification Language and parameter windows were used to search protein databases for sequences containing regions of homology which were scored with an initial value. Dot-matrix- homology plots were examined to distinguish regions of significant homology from chance matches.

BLAST, which stands for Basic Local Alignment Search Tool (Altschul SF (1993) J Mol Evol 36:290-300; Altschul, SF et al (1990) J Mol Biol 215:403-10), was used to search for local sequence alignments. BLAST produces alignments of both nucleotide and amino acid sequences to determine sequence similarity. Because of the local nature of the alignments, BLAST is especially useful in determining exact matches or in identifying homologs. BLAST is useful for matches which do not contain gaps. The fundamental unit of BLAST algorithm output is the High-scoring Segment Pair (HSP).

An HSP consists of two sequence fragments of arbitrary but equal lengths whose alignment is locally maximal and for which the alignment score meets or exceeds a threshold or cutoff score set by the user. The BLAST approach is to look for HSPs between a query sequence and a database sequence, to evaluate the statistical significance of any matches found, and to report only those matches which satisfy the user-selected threshold of significance. The parameter E establishes the statistically significant threshold for reporting database sequence matches. E is inteφreted as the upper bound of the expected frequency of chance occurrence of an HSP (or set of HSPs) within the context of the entire database search. Any database sequence whose match satisfies E is reported in the program output. IV Northern Analysis

Northern analysis is a laboratory technique used to detect the presence of a transcript of a gene and involves the hybridization of a labeled nucleotide sequence to a membrane on which RNAs from a particular cell type or tissue have been bound (Sambrook et al. supra).

Analogous computer techniques using BLAST (Altschul SF 1993 and 1990, supra) are used to search for identical or related molecules in nucleotide databases such as GenBank or the LIFESEQ™ database (Incyte, Palo Alto CA). This analysis is much faster than multiple, membrane- based hybridizations. In addition, the sensitivity of the computer search can be modified to determine whether any particular match is categorized as exact or homologous.

The basis of the search is the product score which is defined as:

% sequence identity x % maximum BLAST score

100 and it takes into account both the degree of similarity between two sequences and the length of the sequence match. For example, with a product score of 40, the match will be exact within a 1-

2% error; and at 70, the match will be exact. Homologous molecules are usually identified by selecting those which show product scores between 15 and 40, although lower scores may identify related molecules.

The results of the search shown in Fig 2 are reported as a list of libraries in which the DAMP encoding sequence occurs. Abundance and percentage abundance of the DAMP encoding sequence are also reported. Abundance directly reflects the number of times a particular transcript is represented in a cDNA library, and percent abundance is abundance divided by the total number of sequences examined in the cDNA library. V Extension of the Sequence Encoding DAMP

The nucleic acid sequence of SEQ ID NO:2 is used to design oligo-nucleotide primers for extending a partial nucleotide sequence to full length or for obtaining 5 'sequence from genomic libraries. One primer is synthesized to initiate extension in the antisense direction (XLR) and the other is synthesized to extend sequence in the sense direction (XLF). Primers allow the extension of the know sequence "outward" generating amplicons containing new, unknown nucleotide sequence for the region of interest (US Patent Application 08/487,1 12, filed June 7, 1995, specifically incoφorated by reference). The initial primers are designed from the cDNA using OLIGO^® 4.06 Primer Analysis Software (National Biosciences), or another appropriate program, to be 22-30 nucleotides in length, to have a GC content of 50% or more, and to anneal to the target sequence at temperatures about 68°-72° C. Any stretch of nucleotides which would result in haiφin structures and primer-primer dimerizations is avoided.

The original, selected cDNA libraries, or a human genomic library are used to extend the sequence; the latter is most useful to obtain 5' upstream regions. If more extension is necessary or desired, additional sets of primers are designed to further extend the known region.

By following the instructions for the XL-PCR kit (Perkin Elmer) and thoroughly mixing the enzyme and reaction mix, high fidelity amplification is obtained. Beginning with 40 pmol of each primer and the recommended concentrations of all other components of the kit, PCR is performed using the Peltier Thermal Cycler (PTC200; MJ Research, Watertown MA) and the following parameters:

Step 1 94° C for 1 min (initial denaturation)

Step 2 65° C for 1 min

Step 3 68° C for 6 min Step 4 94° C for 15 sec

Step 5 65° C for 1 min

Step 6 68° C for 7 min

Step 7 Repeat step 4-6 for 15 additional cycles

Step 8 94° C for 15 sec Step 9 65° C for 1 min Step 10 68° C for 7: 15 min

Step 1 1 Repeat step 8-10 for 12 cycles

Step 12 72° C for 8 min

Step 13 4° C (and holding) A 5-10 μ\ aliquot of the reaction mixture is analyzed by electrophoresis on a low concentration (about 0.6-0.8%) agarose mini-gel to determine which reactions were successful in extending the sequence. Bands thought to contain the largest products were selected and cut out of the gel. Further purification involves using a commercial gel extraction method such as

QIAQuick™ (QIAGEN Inc). After recovery of the DNA, Klenow enzyme was used to trim single-stranded, nucleotide overhangs creating blunt ends which facilitate religation and cloning. After ethanol precipitation, the products are redissolved in 13 μl of ligation buffer, lμl T4-DNA ligase (15 units) and \μ\ T4 polynucleotide kinase are added, and the mixture is incubated at room temperature for 2-3 hours or overnight at 16° C. Competent E coli cells (in 40 μ\ of appropriate media) are transformed with 3 μ\ of ligation mixture and cultured in 80 μl of SOC medium (Sambrook J et al, supra). After incubation for one hour at 37° C, the whole transformation mixture is plated on Luria Bertani (LB)-agar (Sambrook J et al, supra) containing 2xCarb. The following day, several colonies are randomly picked from each plate and cultured in 150 μl of liquid LB/2xCarb medium placed in an individual well of an appropriate, commercially-available, sterile 96-well microtiter plate. The following day, 5 μl of each overnight culture is transferred into a non-sterile 96-well plate and after dilution 1 : 10 with water, 5 μl of each sample is transferred into a PCR array.

For PCR amplification. 18 μl of concentrated PCR reaction mix (3.3x) containing 4 units of rTth DNA polymerase, a vector primer and one or both of the gene specific primers used for the extension reaction are added to each well. Amplification is performed using the following conditions:

Step 1 94° C for 60 sec

Step 2 94° C for 20 sec

Step 3 55° C for 30 sec

Step 4 72 ° C for 90 sec Step 5 Repeat steps 2-4 for an additional 29 cycles

Step 6 72° C for 180 sec

Step 7 4° C (and holding)

Aliquots of the PCR reactions are run on agarose gels together with molecular weight markers. The sizes of the PCR products are compared to the original partial cDNAs, and appropriate clones are selected, ligated into plasmid and sequenced. VI Labeling and Use of Hybridization Probes

Hybridization probes derived from SEQ ID NO:2 are employed to screen cDNAs, genomic DNAs or mRNAs. Although the labeling of oligonucleotides, consisting of about 20 base-pairs, is specifically described, essentially the same procedure is used with larger cDNA fragments. Oligonucleotides are designed using state-of-the-art software such as OLIGO 4.06 (National Biosciences), labeled by combining 50 pmol of each oligomer and 250 mCi of [γ-³²P] adenosine triphosphate (Amersham, Chicago IL) and T4 polynucleotide kinase (DuPont NEN^®, Boston MA). The labeled oligonucleotides are substantially purified with Sephadex G-25 super fine resin column (Pharmacia). A portion containing 10⁷ counts per minute of each of the sense and antisense oligonucleotides is used in a typical membrane based hybridization analysis of human genomic DNA digested with one of the following endonucleases (Ase I, Bgl II. Eco RI, Pst I. Xba 1. or Pvu II; DuPont NEN^®).

The DNA from each digest is fractionated on a 0.7 percent agarose gel and transferred to nylon membranes (Nytran Plus, Schleicher & Schuell, Durham NH). Hybridization is carried out for 16 hours at 40°C. To remove nonspecific signals, blots are sequentially washed at room temperature under increasingly stringent conditions up to 0.1 x saline sodium citrate and 0.5% sodium dodecyl sulfate. After XOMAT AR™ film (Kodak, Rochester NY) is exposed to the blots in a Phosphoimager cassette (Molecular Dynamics, Sunnyvale CA) for several hours, hybridization patterns are compared visually. VII Antisense Molecules

The sequence encoding DAMP, or any part thereof, is used to inhibit in vivo or in vitro expression of naturally occurring sequence. Although use of antisense oligonucleotides, comprising about 20 base-pairs, is specifically described, essentially the same procedure is used with larger cDNA fragments. An oligonucleotide complementary to a portion of the coding sequence of DAMP as shown in SEQ ID NO:2 is used to inhibit expression of naturally occurring sequence. The complementary oligonucleotide is designed from the most unique 5' sequence and used either to inhibit transcription by preventing promoter binding to the upstream nontranslated sequence or translation of a transcript encoding DAMP by preventing the ribosome from binding. Using an appropriate portion of the leader and 5' sequence of SEQ ID NO:2, an effective antisense oligonucleotide includes any 15-20 nucleotides spanning the region which translates into the signal or early coding sequence of the polypeptide as shown in Figures 1 A and IB. VIII Expression of DAMP Expression of DAMP is accomplished by subcloning the cDNAs into appropriate vectors and transfecting the vectors into host cells. In this case, the cloning vector, pSport, previously used for the generation of the cDNA library is used to express DAMP in £. coli. Upstream of the cloning site, this vector contains a promoter for ^β-galactosidase, followed by sequence containing 5 the amino-terminal Met and the subsequent 7 residues of β-galactosidase. Immediately following these eight residues is a bacteriophage promoter useful for transcription and a linker containing a number of unique restriction sites.

Induction of an isolated, transfected bacterial strain with IPTG using standard methods produces a fusion protein which consists of the first seven residues of β-galactosidase, about 5 to 10 15 residues of linker, and the full length DAMP. The signal sequence directs the secretion of DAMP into the bacterial growth media which can be used directly in the following assay for activity.

IX Assay for DAMP Activity

The chemotactic activity of DAMP is measured under agarose according to the method of 15 Nelson et al (1975; J Immunol 1 15: 1650). Mononuclear cells or granulocytes are exposed to serial dilutions of control media or media in which cells expressing recombinant DAMP were grown. After 2 hours incubation at 37°C, cells are fixed and stained. Spontaneous migration toward the control sample is compared to migration toward the test sample for various cell types. The specificity of the chemoattraction is determined by performing the agarose assay on 0 specific populations of cells. Blood cells obtained from venipuncture are fractionated by density gradient centrifugation and the chemotactic activity of DAMP is tested on enriched populations of neutrophils, peripheral blood mononuclear cells, granulocytes, monocytes and lymphocytes. Optionally, such enriched cell populations may be further fractionated using CD8⁺ and CD4⁺ specific antibodies for negative selection of CD4⁺ and CD8⁺ enriched T-cell populations, 5 respectively.

X Production of DAMP Specific Antibodies

DAMP is substantially purified using PAGE electrophoresis (Sambrook, supra) is used to immunize rabbits and to produce antibodies using standard protocols. The amino acid sequence translated from DAMP is analyzed using DNAStar software (DNAStar Inc) to determine regions 0 of high immunogenicity and a corresponding oligopeptide is synthesized and used to raise antibodies by means known to those of skill in the art. Analysis to select appropriate epitopes, such as those near the C-terminus or in hydrophilic regions (shown in Figure 4) is described by Ausubel FM et al (supra).

Typically, the oligopeptides are 15 residues in length, synthesized using an Applied Biosystems Peptide Synthesizer Model 431 A using fmoc-che istry, and coupled to keyhole limpet hemocyanin (KLH, Sigma) by reaction with M-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS; Ausubel FM et al, supra). Rabbits are immunized with the oligopeptide-KLH complex in complete Freund's adjuvant. The resulting antisera are tested for antipeptide activity, for example, by binding the peptide to plastic, blocking with 1% BSA, reacting with rabbit antisera, washing, and reacting with radioiodinated, goat anti-rabbit IgG. XI Purification of Naturally Occurring DAMP Using Specific Antibodies Naturally occurring or recombinant DAMP is substantially purified by immunoaffinity chromatography using antibodies specific for DAMP. An immunoaffinity column is constructed by covalently coupling DAMP antibody to an activated chromatographic resin such as CnBr-activated Sepharose (Pharmacia Biotech). After the coupling, the resin is blocked and washed according to the manufacturer's instructions. Membrane fractions from cells expressing DAMP are prepared by methods well known in the art. Alternatively, a recombinant DAMP fragment containing an appropriate signal sequence may be secreted in useful quantity into the medium in which transfected cells are grown.

The DAMP-containing preparation is passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of DAMP (eg, high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/DAMP binding (eg, a buffer of pH 2-3 or a high concentration of a chaotrope such as urea or thiocyanate ion), and DAMP is collected.

All publications and patents mentioned in the above specification are herein incoφorated by reference. Various modifications and variations of the described method and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in molecular biology or related fields are intended to be within the scope of the following claims. SEQUENCE LISTING

(1) GENERAL INFORMATION

(l) APPLICANT: INCYTE PHARMACEUTICALS, INC.

(li) TITLE OF THE INVENTION: NOVEL DISEASE ASSOCIATED MEMBRANE PROTEIN

(in) NUMBER OF SEQUENCES: 4

(IV) CORRESPONDENCE ADDRESS:

(A) ADDRESSEE: Incyte Pharmaceuticals, Inc.

(B) STREET: 3174 Porter Drive

(C) CITY: Palo Alto

(D) STATE: CA

(E) COUNTRY: U.S.

(F) ZIP: 94304

(v) COMPUTER READABLE FORM:

(A) MEDIUM TYPE: Diskette

(B) COMPUTER: IBM Compatible

(C) OPERATING SYSTEM: DOS

(D) SOFTWARE: FastSEQ Version 1.5

(vi) CURRENT APPLICATION DATA:

(A) PCT APPLICATION NUMBER: To Be Assigned

(B) FILING DATE: Filed Herewith

(vii) PRIOR APPLICATION DATA:

(A) APPLICATION NUMBER: US 08/714,027

(B) FILING DATE: ll-SEP-1997

(vni) ATTORNEY/AGENT INFORMATION:

(A) NAME: Billings, Lucy J.

(B) REGISTRATION NUMBER: 36,749

(C) REFERENCE/ DOCKET NUMBER: PF-0087 PCT

(ix) TELECOMMUNICATION INFORMATION:

(A) TELEPHONE: 650-855-0555

(B) TELEFAX: 650-845-4166

(2) INFORMATION FOR SEQ ID NO : 1 :

(l) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 163 ammo acids

(B) TYPE: amino acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear

(n) MOLECULE TYPE: peptide

(vii) IMMEDIATE SOURCE:

(A) LIBRARY: SYNOOAT01

(B) CLONE: 728068 (xi) SEQUENCE DESCRIPTION: SEQ ID NO:l:

Met Ser Leu Leu Leu Leu Val Val Ser Ala Leu His lie Leu lie Leu

1 5 10 15 lie Leu Leu Phe Val Ala Thr Leu Asp Lys Ser Trp Trp Thr Leu Pro

20 25 30

Gly Lys Glu Ser Leu Asn Leu Trp Tyr Asp Cys Thr Trp Asn Asn Asp

35 40 45

Thr Lys Thr Trp Ala Cys Ser Asn Val Ser Glu Asn Gly Trp Leu Lys

50 55 60

Ala Val Gin Val Leu Met Val Leu Ser Leu lie Leu Cys Cys Leu Ser 65 70 75 80

Phe lie Leu Phe Met Phe Gin Leu Tyr Thr Met Arg Arg Gly Gly Leu

85 90 95

Phe Tyr Ala Thr Gly Leu Cys Gin Leu Cys Thr Ser Val Ala Val Phe

100 105 110

Thr Gly Ala Leu lie Tyr Ala lie His Ala Glu Glu lie Leu Glu Lys

115 120 125

His Pro Arg Gly Gly Ser Phe Gly Tyr Cys Phe Ala Leu Ala Trp Val

130 135 140

Ala Phe Pro Leu Ala Leu Val Ser Gly lie lie Tyr lie His Leu Arg 145 150 155 160

Lys Arg Glu

(2) INFORMATION FOR SEQ ID NO: 2:

(l) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 838 base pairs

(B) TYPE: nucleic acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear

(n) MOLECULE TYPE: cDNA

(vii) IMMEDIATE SOURCE:

(A) LIBRARY: SYNOOAT01

(B) CLONE: 728068

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:2:

AAGGAAGCCC AGACAGTGTG GGCAGGAGGG AGAGAAGAGA CGCAGAAGGA GAGCGAGCGA 60

GAGAGAAAGG GTTCTGGATT GGAGGGGAGA GCAAGGGAGG GAGGAAGGCG GTGAGAGAGG 120

CGGGGGCCTC GGGAGGGTGA AAGGAGGGAG GAGAAGGGCG GGGCACGGAG GCCCGAACGA 180

GGGACAAGAC TCCGACTCCA GCTCTGACTT TTTTCGCGGC TCTCGGCTTC CACTGCAGCC 240

ATGTCACTCC TCTTGCTGGT GGTCTCAGCC CTTCACATCC TCATTCTTAT ACTGCTTTTC 300

GTGGCCACTT TGGACAAGTC CTGGTGGACT CTCCCTGGGA AAGAGTCCCT GAATCTCTGG 360

TACGACTGCA CGTGGAACAA CGACACCAAA ACATGGGCCT GCAGTAATGT CAGCGAGAAT 420

GGCTGGCTGA AGGCGGTGCA GGTCCTCATG GTGCTCTCCC TCATTCTCTG CTGTCTCTCC 480

TTCATCCTGT TCATGTTCCA GCTCTACACC ATGCGACGAG GAGGTCTCTT CTATGCCACC 540

GGCCTCTGCC AGCTTTGCAC CAGCGTGGCG GTGTTTACTG GCGCCTTGAT CTATGCCATT 600

CACGCCGAGG AGATCCTGGA GAAGCACCCG CGAGGGGGCA GCTTCGGATA CTGCTTCGCC 660

CTGGCCTGGG TGGCCTTCCC CCTCGCCCTG GTCAGCGGCA TCATCTACAT CCACCTACGG 720

AAGCGGGAGT GAGCGCCCCG CTTCGCTCGG CTGCCCCCGC CCCTTCCCGG CCCCCCTCGC 780

CGCGCGTCCT CCAAAAAATA AAACCTTAAC CGCGGANAAA AAAAAAAAAA CNAANGAA 838 (2) INFORMATION FOR SEQ ID NO : 3 :

(I) SEQUENCE CHARACTERISTICS:

(A) LENGTH: 157 amino acids

(B) TYPE: amino acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear

(II) MOLECULE TYPE: peptide

(vii) IMMEDIATE SOURCE:

(A) LIBRARY: GenBank

(B) CLONE: 1171356

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:

Met Leu Val Leu Leu Ala Gly He Tyr Val Val His He Ala Thr Val

1 5 10 15

He Met Leu Phe Val Ser Thr He Ala Asn Val Trp Leu Val Ser Ser

20 25 30

Thr Ala Asp Ala Ser Val Gly Leu Trp Lys Asn Cys Ser Asn Met Glu

35 40 45

Cys Ser Asp Ser Leu Ser Tyr Ala Ser Glu Asp Ala Leu Lys Thr Val

50 55 60

Gin Ala Phe Met He Leu Ser He He Phe Cys Val He Ala Leu Leu 65 70 75 80

Val Phe Ala Phe Gin Leu Phe Thr Met Glu Lys Gly Asn Arg Phe Phe

85 90 95

Leu Ser Gly Ala Thr Thr Leu Val Cys Trp Leu Cys He Leu Val Gly

100 105 110

Val Ser He Tyr Thr Ser His Tyr Ala Asn Arg Asp Gly Thr Gin Tyr

115 120 125

His His Gly Tyr Ser Tyr He Leu Gly Trp He Cys Phe Cys Phe Ser

130 135 140

Phe He He Gly Val Leu Tyr Leu Val Leu Arg Lys Lys 145 150 155

(2) INFORMATION FOR SEQ ID NO: :

(l) SEQUENCE CHARACTERISTICS.

(A) LENGTH: 160 amino acids

(B) TYPE: amino acid

(C) STRANDEDNESS: single

(D) TOPOLOGY: linear

(li) MOLECULE TYPE: peptide

(vii) IMMEDIATE SOURCE:

(A) LIBRARY: GenBank

(B) CLONE: 951124

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 4:

Met Leu Val Leu Leu Ala Gly Leu Phe Val Val His He Ala Thr Ala

1 5 10 15

He Met Leu Phe Val Ser Thr He Ala Asn Val Trp Met Val Ala Asp

20 25 30

Tyr Ala Asn Ala Ser Val Gly Leu Trp Lys Asn Cys Thr Gly Gly Asn

35 40 45

Cys Asp Gly Ser Leu Ser Tyr Gly Asn Glu Asp Ala He Lys Val Val 50 55 60 Gin Ala Phe Met He Leu Ser He He Phe Ser He He Ser Leu Val 65 70 75 80

Val Phe Val Phe Gin Leu Phe Thr Met Glu Lys Gly Asn Arg Phe Phe

85 90 95

Leu Ser Gly Ser Thr Met Leu Val Cys Trp Leu Cys He Leu Val Gly

100 105 110

Val Ser He Tyr Thr His His Tyr Ala His Ser Glu Gly Asn Phe Asn

115 120 125

Ser Ser Ser His Gin Gly Tyr Cys Phe He Leu Thr Trp He Cys Phe

130 135 140

Cys Phe Ser Phe He He Gly He Leu Tyr Met Val Leu Arg Lys Lys 145 150 155 160

Claims

1. A substantially purified polypeptide comprising the amino acid sequence of SEQ ID NO: 1 , or fragments thereof.

2. An isolated and purified polynucleotide sequence encoding the polypeptide of claim 1.

3. An isolated polynucleotide sequence comprising the nucleic acid sequence of SEQ ID

NO:2 or variants thereof.

4. An isolated polynucleotide sequence which is complementary to SEQ ID NO:2 or a variants thereof.

5. An isolated polynucleotide sequence which hybridizes under stringent conditions to SEQ ID NO.2.

6. A hybridization probe comprising SEQ ID NO:2, or fragments thereof.

7. A recombinant expression vector containing the polynucleotide sequence of claim 3.

8. A recombinant host cell containing the expression vector of claim 7.

9. A method for producing the polypeptide of SEQ ID NO: 1 , or fragments thereof, the method comprising the steps of: a) culturing the host cell of claim 8 under conditions suitable for the expression of the polypeptide; and b) recovering the polypeptide from the host cell culture.

10. A pharmaceutical composition comprising the polypeptide of SEQ ID NO:l in conjunction with a pharmaceutically acceptable excipient.

1 1. A method for the treatment of cancer, the method comprising administering to a subject in need of such treatment an amount of the pharmaceutical composition of claim 10 which is sufficient to treat the cancer.

12. A purified antibody which binds specifically to the polypeptide of claim 1.

13. A purified agonist which specifically modulates the activity of the polypeptide of claim 1.

14. A purified antagonist which specifically modulates the activity of the polypeptide of claim 1.

15. A hybridization probe comprising at least a portion of the polynucleotide of claim 1.

16. A method for the detection of polynucleotides encoding disease associated membrane protein in a biological sample comprising the steps of: a) hybridizing the probe of claim 15 to nucleic acid material, thereby forming a hybridization complex, and b) detecting said hybridization complex, wherein the presence of said complex correlates with the presence of a polynucleotide encoding disease associated membrane protein in said biological sample.