WO2001068841A2

WO2001068841A2 - Human dcc-like proteins

Info

Publication number: WO2001068841A2
Application number: PCT/EP2001/002784
Authority: WO
Inventors: Shyam Ramakrishnan
Original assignee: Bayer Aktiengesellschaft
Priority date: 2000-03-14
Filing date: 2001-03-13
Publication date: 2001-09-20
Also published as: AU2001260116A1; WO2001068841A3

Abstract

Reagents which regulate human Deleted in Colon Cancer (DCC)-like protein activity can be used to regulate axon outgrowth. Such regulation is particularly useful for modulating neuronal growth regenerative capacity, i.e. the regeneration of axons in adult nervous system after, for example, injury or trauma, for diagnosing genetic neurological defects, and for treating neurodegenerative disease.

Description

REGULATION OF HUMAN DCC-LIKE PROTEINS

TECHNICAL FIELD OF THE INVENTION

The invention relates to the area of regulation of nerve cell growth and guidance. More particularly, the invention relates to the regulation of human DCC-like protein activity to mediate axon outgrowth.

BACKGROUND OF THE INVENTION

Developing axons of the nervous system are guided along pathways to targets by attractive and repulsive extracellular matrix guidance cues. Nerve cell growth and guidance cues regulate the timing of neuron growth, the location of neuron growth, and the termination of neuron growth. For example, netrins are modulators of growth in developing axons and function as attractants for some axons and repellants for other axons. (Hinck et al. (1999) Cell 97:927; U.S. Patent Nos. 6,017,714 and 5,824,775). In Caenorhabditis elegans, unc-6 is a netrin and unc-5 and unc-40 are unc-6 receptors which are important in unc-6 dependant guidance of axons. Su et α/.(2000) Development 127:585. Unc-5 is a cell surface protein expressed on motile cells and pioneer axons and orients movement away from unc-6 sources. Unc-40 is a homolog of the cell surface proteins DCC and neogenin and is also expressed on motile cells and pioneer axons. Unc-40 orients movement toward unc-6 sources; however, where cells also coexpress unc-5, unc-40 orients movement away from unc-6 sources. Chan et al.(\996) Cell 87:187; U.S. Patent Nos. 5,747,262 and

5,939,271.

Deleted in Colorectal Cancer (DCC) and neogenin, homologs of unc-40, form a subgroup of the immunoglobulin superfamily which is characterized by the presence of four Ig domains and six fibronectin type II repeats in their extracellular domains.

See Keino-Masu et al.(\ 996) Cell 87: 175. DCC is a netrin receptor and mediates the effects of netrins on axons. Agents which can regulate neuron growth and guidance can be used to modulate neuronal growth regenerative capacity, i.e., the regeneration of axons in adult nervous system after, for example, injury or trauma, to diagnose genetic neurological defects, and to treat neurodegenerative disease. Such diseases include, for example, paralysis, Huntington's disease, Charcot-Marie-Tooth disease, Friedreich's ataxia, Hallervorden-Spatz disease, Leigh's disease, olivoponto- cerebellar atrophy, and Rett syndrome. Thus, there is a need in the art for substances and methods which can regulate the effect of netrin on axons and thus, neuron growth and guidance.

SUMMARY OF THE INVENTION

It is an object of the invention to provide reagents and methods of regulating axon outgrowth. These and other objects of the invention are provided by one or more of the embodiments described below.

One embodiment of the invention is a DCC-like polypeptide comprising an amino acid sequence selected from the group consisting of:

amino acid sequences which are at least about 50% identical to the amino acid sequence shown in SEQ ID NO. 2;

the amino acid sequence shown in SEQ ID NO. 2;

amino acid sequences which are at least about 50% identical to the amino acid sequence shown in SEQ ID NO. 4;

the amino acid sequence shown in SEQ ID NO. 4;

amino acid sequences which are at least about 50% identical to the amino acid sequence shown in SEQ ID NO. 6; and the amino acid sequence shown in SEQ ID NO. 6.

Yet another embodiment of the invention is a method of screening for agents which decrease the activity of a DCC-like protein. A test compound is contacted with a

DCC-like polypeptide comprising an amino acid sequence selected from the group consisting of:

the amino acid sequence shown in SEQ ID NO. 2;

the amino acid sequence shown in SEQ ID NO. 4;

amino acid sequences which are at least about 50% identical to the amino acid sequence shown in SEQ ID NO. 6; and

the amino acid sequence shown in SEQ ID NO. 6.

Binding between the test compound and the DCC-like polypeptide is detected. A test compound which binds to the DCC-like polypeptide is thereby identified as a potential agent for decreasing the activity of a DCC-like protein.

Another embodiment of the invention is a method of screening for agents which decrease the activity of a DCC-like protein. A test compound is contacted with a polynucleotide encoding a DCC-like polypeptide, wherein the polynucleotide comprises a nuclcotidc sequence selected from the group consisting of: nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO. 1;

the nucleotide sequence shown in SEQ ID NO. 1 ;

nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO. 3;

the nucleotide sequence shown in SEQ ID NO. 3;

nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO. 5; and

the nucleotide sequence shown in SEQ ID NO. 5.

Binding of the test compound to the polynucleotide is detected. A test compound which binds to the polynucleotide is identified as a potential agent for decreasing the activity of a DCC-like protein. The agent can work by decreasing the amount of the DCC-like protein through interacting with the DCC-like protein mRNA.

Another embodiment of the invention is a method of screening for agents which regulate the activity of a DCC-like protein. A test compound is contacted with a DCC-like polypeptide comprising an amino acid sequence selected from the group consisting of:

the amino acid sequence shown in SEQ ID NO. 2; amino acid sequences which are at least about 50% identical to the amino acid sequence shown in SEQ ID NO. 4;

the amino acid sequence shown in SEQ ID NO. 4;

the amino acid sequence shown in SEQ ID NO. 6.

A DCC-like protein activity of the polypeptide is detected. A test compound which increases DCC-like protein activity of the polypeptide relative to DCC-like protein activity in the absence of the test compound is thereby identified as a potential agent for increasing the activity of a DCC-like protein. A test compound which decreases DCC-like protein activity of the polypeptide relative to DCC-like protein activity in the absence of the test compound is thereby identified as a potential agent for decreasing the activity of a DCC-like protein.

Even another embodiment of the invention is a method of screening for agents which decrease the activity of a DCC-like protein. A test compound is contacted with a

DCC-like product of a polynucleotide which comprises a nucleotide sequence selected from the group consisting of:

nucleotide sequences which are at least about 50% identical to the nucleotide sequence shown in SEQ ID NO. 1 ;

the nucleotide sequence shown in SEQ ID NO. 1 ;

nucleotide sequences which arc at least about 50% identical to the nucleotide sequence shown in SEQ ID NO. 3; the nucleotide sequence shown in SEQ ID NO. 3;

the nucleotide sequence shown in SEQ ID NO. 5.

Binding of the test compound to the DCC-like product is detected. A test compound which binds to the DCC-like product is thereby identified as a potential agent for decreasing the activity of a DCC-like protein.

Still another embodiment of the invention is a method of reducing the activity of a DCC-like protein. A cell is contacted with a reagent which specifically binds to a polynucleotide encoding a DCC-like polypeptide or the product encoded by the polynucleotide, wherein the polynucleotide comprises a nucleotide sequence selected from the group consisting of:

the nucleotide sequence shown in SEQ ID NO. 1 ;

the nucleotide sequence shown in SEQ ID NO. 3;

the nucleotide sequence shown in SEQ ID NO. 5. DCC-like activity in the cell is thereby decreased.

The invention thus provides reagents and methods for regulating axon outgrowth. Such reagents and methods can be used ter alia, to modulate neuronal growth regenerative capacity, i.e., the regeneration of axons in adult nervous system after, for example, injury or trauma, to diagnose genetic neurological defects, and to treat neurodegenerative disease.

BRIEF DESCRIPTION OF THE DRAWINGS

Fig. 1 shows the DNA-sequence encoding a DCC-like polypeptide.

Fig. 2 shows the amino acid sequence of the DCC-like polypeptide of Fig. 1.

Fig. 3 shows the DNA-sequence encoding a DCC-like polypeptide. Fig. 4 shows the amino acid sequence of the DCC-like polypeptide of Fig. 3.

Fig. 5 shows the DNA-sequence encoding a DCC-like polypeptide.

Fig. 6 shows the amino acid sequence of the DCC-like polypeptide of Fig. 5.

DETAILED DESCRIPTION OF THE INVENTION

The invention relates to an isolated polynucleotide encoding a DCC-like polypeptide and being selected from the group consisting of:

a) a polynucleotide encoding a DCC-like polypeptide comprising an amino acid sequence selected from the group consisting of:

amino acid sequences which are at least about 50% identical to the amino acid sequence shown in SEQ ID NO. 2; the amino acid sequence shown in SEQ ID NO. 2; amino acid sequences which are at least about 50% identical to the amino acid sequence shown in SEQ ID NO. 4; the amino acid sequence shown in SEQ ID NO.4; amino acid sequences which are at least about 50% identical to the amino acid sequence shown in SEQ ID NO. 6; and the amino acid sequence shown in SEQ ID NO. 6.

b) a polynucleotide comprising the sequence of SEQ ID NOS: 1, 3 or 5;

c) a polynucleotide which hybridizes under stringent conditions to a polynucleotide specified in (a) and (b);

d) a polynucleotide the sequence of which deviates from the polynucleotide sequences specified in (a) to (c) due to the degeneration of the genetic code; and a polynucleotide which represents a fragment, derivative or allelic variation of a polynucleotide sequence specified in (a) to (d).

Furthermore, it has been discovered by the present applicant that the activity of a Deleted in Colorectal Cancer (DCC)-like protein can regulate the effect of netrin on axons and thus, neuron growth and guidance. Human DCC-like protein is a netrin receptor and can modulate, in humans, neuronal cell migration and axon guidance.

Human DCC-like protein can be used to develop treatments for various diseases and injuries, to develop diagnostic assays for these diseases and injuries, and to provide new tools for basic research especially in the fields of medicine and biology. Specifically, the present invention can be used to develop new drugs to modulate neuronal growth capacity, particularly regenerative capacity, and to modulate human DCC-like protein expression. Human DCC-like protein and regulators of human DCC-like protein thus can provide treatments for neural injury or trauma and neurodegenerative disease. DCC-Like Polypeptides

Human DCC-like polypeptides according to the invention comprise an amino acid sequence as shown in SEQ ID NOS:2, 4, or 6, a portion of one of those amino acid sequences, or a biologically active variant of an amino acid sequence shown in SEQ

ID NOS:2, 4, or 6 as defined below. The asterisks in SEQ ID NOS:2, 4, and 6 represent the positions of stop codons introduced into SEQ ID NOS:l, 3, and 5 by sequencing errors. The backslash in SEQ ID NO. 2 represents a frame shift from frame -2 to frame -1 introduced by sequencing errors. SEQ ID NO.l is complementary to the nucleotide sequence which encodes SEQ ID NO. 2. SEQ ID

NOS:3 and 5 encode SEQ ID NOS:4 and 6, respectively. DCC-like polypeptide can be a portion of a DCC-like protein, a full-length DCC-like protein, or a fusion protein comprising all or a portion of a DCC-like protein. Most preferably, a DCC-like polypeptide can bind to a netrin, can modulate the attractant or repellant activity of a netrin, and/or can regulate axon outgrowth. DCC-like activities can be measured, inter alia, as described in the specific examples, below.

Biologically Active Variants

DCC-like variants which are biologically active, i.e., retain a netrin binding activity, can modulate the attractant or repellant activity of a netrin, and/or regulate axon outgrowth, also are DCC-like polypeptides. Preferably, naturally or non-naturally occurring DCC-like variants have amino acid sequences which are at least about 50, preferably about 75, 90, 96, or 98% identical to an amino acid sequence shown in SEQ ID NO. 2, 4, or 6. Percent identity between a putative DCC-like variant and an amino acid sequence of SEQ ID NO. 2, 4, or 6 is determined using the Blast2 alignment program.

Variations in percent identity can be due, for example, to amino acid substitutions, insertions, or deletions. Amino acid substitutions arc defined as one for one amino acid replacements They are conscn atn c in nature \s hen the substituted ammo acid has similar structural and/or chemical properties. Examples of conservative replacements are substitution of a leucine with an isoleucine or valine, an aspartate with a glutamate, or a threonine with a serine.

Amino acid insertions or deletions are changes to or within an amino acid sequence.

They typically fall in the range of about 1 to 5 amino acids. Guidance in determining which amino acid residues can be substituted, inserted, or deleted without abolishing biological or immunological activity of a DCC-like polypeptide can be found using computer programs well known in the art, such as DNASTAR software. Whether an amino acid change results in a biologically active DCC-like polypeptide can readily be determined by assaying for DCC-like activity, as described, for example, in the specific examples, below.

Fusion Proteins

Fusion proteins can comprise at least 5, 6, 8, 10, 25, or 50 or more contiguous amino acids of an amino acid sequence shown in SEQ ID NO. 2, 4, or 6. Fusion proteins are useful for generating antibodies against DCC-like amino acid sequences and for use in various assay systems. For example, fusion proteins can be used to identify proteins which interact with portions of a DCC-like polypeptide. Protein affinity chromatography or library-based assays for protein-protein interactions, such as the yeast two-hybrid or phage display systems, can be used for this purpose. Such methods are well known in the art and also can be used as drug screens.

A DCC-like fusion protein comprises two protein segments fused together by means of a peptide bond. The first protein segment comprises at least 5, 6, 8, 10, 25, or 50 or more contiguous amino acids of a DCC-like polypeptide. Contiguous amino acids for use in a fusion protein can be selected from the amino acid sequences shown in SEQ ID NO. 2, 4, or 6 or from a biologically active variant of one of those se- quences, such as those described above. The first protein segment also can comprise full-length DCC-like protein. The second protein segment can be a full-length protein or a protein fragment or polypeptide. Proteins commonly used in fusion protein construction include β- galactosidase, β-glucuronidase, green fluorescent protein (GFP), autofluorescent proteins, including blue fluorescent protein (BFP), glutathione-S-transferase (GST), luciferase, horseradish peroxidase (HRP), and chloramphenicol acetyltransferase (CAT). Additionally, epitope tags are used in fusion protein constructions, including histidine (His) tags, FLAG tags, influenza hemagglutinin (HA) tags, Myc tags, VSV- G tags, and thioredoxin (Trx) tags. Other fusion constructions can include maltose binding protein (MBP), S-tag, Lex a DNA binding domain (DBD) fusions, GAL4

DNA binding domain fusions, and herpes simplex virus (HSV) BP16 protein fusions. A fusion protein also can be engineered to contain a cleavage site located between the DCC-like polypeptide-encoding sequence and the heterologous protein sequence, so that the DCC-like polypeptide can be cleaved and purified away from the heterologous moiety.

A fusion protein can be synthesized chemically, as is known in the art. Preferably, a fusion protein is produced by covalently linking two protein segments or by standard procedures in the art of molecular biology. Recombinant DNA methods can be used to prepare fusion proteins, for example, by making a DNA construct which comprises coding sequences selected from the complement of SEQ ID NO. 1 or from SEQ ID NOS:3 or 5 in proper reading frame with nucleotides encoding the second protein segment and expressing the DNA construct in a host cell, as is known in the art. Many kits for constructing fusion proteins are available from companies such as Promega Corporation (Madison, WI), Stratagene (La Jolla, CA), CLONTECH

(Mountain View, CA), Santa Cruz Biotechnology (Santa Cruz, CA), MBL International Corporation (MIC; Waterto n, MA), and Quantum Biotechnologies (Montreal, Canada; 1-888-DNA-KITS). Identification of Species Homologs

Species homologs of human DCC-like protein can be obtained using DCC-like poly- nucleotides (described below) to make suitable probes or primers for screening cDNA expression libraries from other species, such as mice, monkeys, or yeast, identifying cDNAs which encode homologs of DCC-like, and expressing the cDNAs as is known in the art.

DCC-like Polynucleotides

A DCC-like polynucleotide can be single- or double-stranded and comprises a coding sequence or the complement of a coding sequence for a DCC-like polypeptide. The complement of a partial nucleotide coding sequence for a DCC-like polypeptide is shown in SEQ ID NO. 1. Partial nucleotide coding sequences for DCC-like polypeptides are shown in SEQ ID NOS:3 and 5.

Degenerate nucleotide sequences encoding human DCC-like polypeptides, as well as homologous nucleotide sequences which are at least about 50, preferably about 75, 90, 96, or 98%) identical to the complement of the nucleotide sequences shown in SEQ ID NOS: l, 3, and 5 also are DCC-like polynucleotides. Percent sequence identity between the sequences of two polynucleotides is determined using computer programs such as ALIGN which employ the FASTA algorithm, using an affine gap search with a gap open penalty of -12 and a gap extension penalty of -2. Complementary DNA (cDNA) molecules, species homologs, and variants of DCC- like polynucleotides which encode biologically active DCC- like polypeptides also are DCC-like polynucleotides.

Identification of Variants and Homologs of DCC-like Polynucleotides

Variants and homologs of the DCC-like polynucleotides described above also are

DCC-like polynucleotides. Typically, homologous DCC-like polynucleotide sequences can be identified by hybridization of candidate polynucleotides to known DCC-like polynucleotides under stringent conditions, as is known in the art. For example, using the following wash conditions— 2X SSC (0.3 M NaCl, 0.03 M sodium citrate, pH 7.0), 0.1%o SDS, room temperature twice, 30 minutes each; then 2X SSC, 0.1% SDS, 50 _C once, 30 minutes; then 2X SSC, room temperature twice, 10 minutes each— homologous sequences can be identified which contain at most about 25-30% basepair mismatches. More preferably, homologous nucleic acid strands contain 15-25%> basepair mismatches, even more preferably 5-15% basepair mismatches.

Species homologs of the DCC-like polynucleotides disclosed herein also can be identified by making suitable probes or primers and screening cDNA expression libraries from other species, such as mice, monkeys, or yeast. Human variants of DCC-like polynucleotides can be identified, for example, by screening human cDNA expression libraries. It is well known that the T_m of a double-stranded DNA decreases by 1-1.5°C with every 1% decrease in homology (Bonner et al., J. Mol. Biol. 81, 123 (1973). Variants of human DCC-like polynucleotides or DCC-like polynucleotides of other species can therefore be identified by hybridizing a putative homologous DCC-like polynucleotide with a polynucleotide having a nucleotide sequence of SEQ ID NO. 1, 3, or 5 or the complements thereof to form a test hybrid.

The melting temperature of the test hybrid is compared with the melting temperature of a hybrid comprising DCC-like polynucleotides having perfectly complementary nucleotide sequences, and the number or percent of basepair mismatches within the test hybrid is calculated.

Nucleotide sequences which hybridize to DCC-like polynucleotides or their complements following stringent hybridization and/or wash conditions also are DCC-like polynucleotides. Stringent wash conditions are well known and understood in the art and are disclosed, for example, in Sambrook et al., MOLECULAR CLONING: A LAUORA I ORY MANUAL, 2d ed., 1989, at pages 9.50-9.51. Typically, for stringent hybridization conditions a combination of temperature and salt concentration should be chosen that is approximately 12-20°C below the calculated T_m of the hybrid under study. The T_m of a hybrid between a DCC-like polynucleotide having a nucleotide sequence shown in SEQ ID NO. 1, 3, or 5 or the complements thereof and a polynucleotide sequence which is at least about 50, preferably about 75, 90, 96, or 98% identical to one of those nucleotide sequences can be calculated, for example, using the equation of Bolton and McCarthy, Proc. Natl. Acad. Sci. U.S.A. 48, 1390 (1962):

T_m = 81.5°C - 16.6(logιo [Na⁺]) + 0.41(%G + C) - 0.63(%formamide) - 600//), where / = the length of the hybrid in basepairs.

Stringent wash conditions include, for example, 4X SSC at 65°C, or 50% formamide, 4X SSC at 42°C, or 0.5X SSC, 0.1% SDS at 65°C. Highly stringent wash conditions include, for example, 0.2X SSC at 65°C.

Preparation of DCC-like Polynucleotides

A naturally occurring DCC-like polynucleotide can be isolated free of other cellular components such as membrane components, proteins, and lipids. Polynucleotides can be made by a cell and isolated using standard nucleic acid purification techniques, or synthesized using an amplification technique, such as the polymerase chain reaction (PCR), or by using an automatic synthesizer. Methods for isolating polynucleotides are routine and are known in the art. Any such technique for obtaining a polynucleotide can be used to obtain isolated DCC-like polynucleotides. For example, restriction enzymes and probes can be used to isolate polynucleotide fragments which comprise DCC-like nucleotide sequences. Isolated polynucleotides are in preparations which are free or at least 70, 80, or 90% free of other molecules.

DCC-like cDNA molecules can be made with standard molecular biology techniques, using DCC-like mRNA as a template. DCC-like cDNA molecules can thereafter be replicated using molecular biology techniques known in the art and disclosed in manuals such as Sambrook et α/.(1989). An amplification technique, such as PCR, can be used to obtain additional copies of DCC-like polynucleotides using either human genomic DNA or cDNA as a template.

Alternatively, synthetic chemistry techniques can be used to synthesize DCC-like polynucleotides. The degeneracy of the genetic code allows alternate nucleotide sequences to be synthesized which will encode a DCC-like polypeptide having, for example, an amino acid sequence shown in SEQ ID NO. 2, 4, or 6 or a biologically active variant of one of those sequences.

Obtaining Full-Length DCC-like Polynucleotides

The nucleotide sequences of SEQ ID NOS:l, 3, or 5 can be used to identify the corresponding full length gene(s) from which they were derived. Nucleotide sequences can be nick-translated or end-labeled with ³²P using polynucleotide kinase using labeling methods known to those with skill in the art (BASIC METHODS IN MOLECULAR BIOLOGY, Davis et al., eds., Elsevier Press, N.Y., 1986). For example, a lambda library prepared from human tissue can be screened directly with the labeled sequences of interest or the library can be converted en masse to pBluescript (Stratagene Cloning Systems, La Jolla, Calif. 92037) to facilitate bacterial colony screening (see Sambrook et al., 1989, pg. 1.20).

Both methods are well known in the art. Briefly, filters with bacterial colonies containing the library in pBluescript or bacterial lawns containing lambda plaques are denatured, and the DNA is fixed to the filters. The filters are hybridized with the labeled probe using hybridization conditions described by Davis et al., 1986. The partial sequences, cloned into lambda or pBluescript, can be used as positive controls to assess background binding and to adjust the hybridization and washing stringencies necessary for accurate clone identification. The resulting auto- radiograms are compared to duplicate plates of colonies or plaques; each exposed spot corresponds to a positive colony or plaque. The colonies or plaques are selected and expanded, and the DNA is isolated from the colonies for further analysis and sequencing.

Positive cDNA clones are analyzed to determine the amount of additional sequence they contain using PCR with one primer from the partial sequence and the other primer from the vector. Clones with a larger vector-insert PCR product than the original partial sequence are analyzed by restriction digestion and DNA sequencing to determine whether they contain an insert of the same size or similar as the mRNA size determined from Northern blot Analysis.

Once one or more overlapping cDNA clones are identified, the complete sequence of the clones can be determined, for example after exonuclease III digestion (McCombie et ah, Methods 3, 33-40, 1991). A series of deletion clones is generated, each of which is sequenced. The resulting overlapping sequences are assembled into a single contiguous sequence of high redundancy (usually three to five overlapping sequences at each nucleotide position), resulting in a highly accurate final sequence.

Various PCR-based methods can be used to extend the nucleic acid sequences encoding the disclosed portions of human DCC-like protein to detect upstream sequences such as promoters and regulatory elements. For example, restriction-site

PCR uses universal primers to retrieve unknown sequence adjacent to a known locus (Sarkar, PCR Methods Applic. 2, 318-322, 1993). Genomic DNA is first amplified in the presence of a primer to a linker sequence and a primer specific to the known region. The amplified sequences are then 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 also can be used to amplify or extend sequences using divergent primers based on a known region (Triglia et al.. Nucleic Acids Res. 16, 8186, 1988). Primers can be designed using commercially available software, such as OLIGO 4.06 Primer Analysis software (National Biosciences Inc., Plymouth, Minn.), 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.

Another method which can be used is capture PCR, which involves PCR amplification of DNA fragments adjacent to a known sequence in human and yeast artificial chromosome DNA (Lagerstrom et al, PCR Methods Applic. 1, 111-119, 1991. In this method, multiple restriction enzyme digestions and ligations also can be used to place an engineered double-stranded sequence into an unknown fragment of the DNA molecule before performing PCR.

Another method which can be used to retrieve unknown sequences is that of Parker et al, Nucleic Acids Res. 19, 3055-3060, 1991. Additionally, PCR, nested primers, and PROMOTERFI DER libraries (CLONTECH, Palo Alto, Calif.) can be used to walk genomic DNA. This process avoids the need to screen libraries and is useful in finding intron/exon junctions.

When screening for full-length cDNAs, it is preferable to use libraries that have been size-selected to include larger cDNAs. Randomly-primed libraries are preferable, in that they will contain more sequences which contain the 5' regions of genes. Use of a randomly primed library may be especially preferable for situations in which an oligo d(T) library does not yield a full-length cDNA. Genomic libraries can be useful for extension of sequence into 5' non-transcribed regulatory regions.

Commercially available capillary electrophoresis systems can be used to analyze the size or confirm the nucleotide sequence of PCR or sequencing products. For example, capillary sequencing can employ fiowablc polymers for elcctrophoretic separation, four different fluorescent dyes (one for each nucleotide) which are laser activated, and detection of the emitted wavelengths by a charge coupled device camera. Output/light intensity can be converted to electrical signal using appropriate software (e.g. GENOTYPER and Sequence NAVIGATOR, Perkin Elmer), and the entire process from loading of samples to computer analysis and electronic data display can be computer controlled. Capillary electrophoresis is especially preferable for the sequencing of small pieces of DNA which might be present in limited amounts in a particular sample.

Obtaining DCC-like Polypeptides

DCC-like polypeptides can be obtained, for example, by purification from human neuronal cells, by expression of DCC-like polynucleotides, or by direct chemical synthesis.

Protein Purification

DCC-like polypeptides can be purified, for example, from human neuronal cells, including neuronal cell lines, as well as from transfected cells which express a DCC- like polypeptide. A purified DCC-like polypeptide is separated from other compounds which normally associate with the DCC-like polypeptide in the cell, such as certain proteins, carbohydrates, or lipids, using methods well-known in the art.

Such methods include, but are not limited to, size exclusion chromatography, ammonium sulfate fractionation, ion exchange chromatography, affinity chromatography, and preparative gel electrophoresis. A preparation of purified DCC-like polypeptides is at least 80% pure; preferably, the preparations are 90%, 95%, or 99% pure. Purity of the preparations can be assessed by any means known in the art, such as SDS-polyacrylamide gel electrophoresis. Activity of the purified preparations can be assayed, for example, as described in the specific examples, below. Expression of DCC-like Polynucleotides

To express a DCC-like polypeptide, a DCC-like polynucleotide can be inserted into an expression 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 sequences encoding DCC-like polypeptides and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Such techniques are described, for example, in Sambrook et α/.(1989) and in Ausubel et al., CURRENT

PROTOCOLS IN MOLECULAR BIOLOGY, John Wiley & Sons, New York, N.Y, 1989.

A variety of expression vector/host systems can be utilized to contain and express sequences encoding a DCC-like polypeptide. 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 (e.g., baculovirus), plant cell systems transformed with virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g. , Ti or pBR322 plasmids), or animal cell systems.

The control elements or regulatory sequences are those non-translated regions of the vector — enhancers, promoters, 5' and 3' untranslated regions — which interact with host cellular proteins to carry out transcription and translation. Such elements can vary in their strength and specificity. Depending on the vector system and host, any number of suitable transcription and translation elements, including constitutive and inducible promoters, can be used. For example, when cloning in bacterial systems, inducible promoters such as the hybrid lacZ promoter of the BLUESCRIPT phagemid (Stratagenc, LaJolla, Calif.) or pSPORTl plasmid (Life Technologies) and the like can be used. The baculovirus polyhedrin promoter can be used in insect cells. Promoters or enhancers derived from the genomes of plant cells (e.g., heat shock, RUBISCO, and storage protein genes) or from plant viruses (e.g., viral promoters or leader sequences) can be cloned into the vector. In mammalian cell systems, promoters from mammalian genes or from mammalian viruses are preferable. If it is necessary to generate a cell line that contains multiple copies of a nucleotide sequence encoding a DCC-like polypeptide, vectors based on SV40 or

EBV can be used with an appropriate selectable marker.

Bacterial and Yeast Expression Systems

In bacterial systems, a number of expression vectors can be selected depending upon the use intended for a DCC-like polypeptide. For example, when a large quantity of a DCC-like polypeptide is needed for the induction of antibodies, vectors which direct high level expression of fusion proteins that are readily purified can be used. Such vectors include, but are not limited to, multifunctional E. coli cloning and expression vectors such as BLUESCRIPT (Stratagene). In a BLUESCRIPT vector, a sequence encoding a DCC-like polypeptide can be ligated in frame with sequences for the amino-terminal Met and the subsequent 7 residues of -galactosidase so that a hybrid protein is produced. pIN vectors (Van Heeke & Schuster, J. Biol. Chem. 264, 5503-5509, 1989 or pGEX vectors (Promega, Madison, Wis.) also can be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST).

In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption to glutathione-agarose beads followed by elution in the presence of free glutathione. Proteins made in such systems can be 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 Saccluiromyces cerevisiae, a number of vectors containing constitutive or inducible promoters, such as alpha factor, alcohol oxidase, and PGH, can be used. For reviews, sec Ausubel et al. ( 1989) and Grant el al., Methods Enzymol. 153, 516- 544, 1987. Plant and Insect Expression Systems

If plant expression vectors are used, the expression of sequences encoding DCC-like polypeptides can be driven by any of a number of promoters. For example, viral promoters such as the 35S and 19S promoters of CaMV can be used alone or in combination with the omega leader sequence from TMV (Takamatsu, EMBO J. 6, 307-311, 1987). Alternatively, plant promoters such as the small subunit of RUBISCO or heat shock promoters can be used (Coruzzi et al., EMBO J. 3, 1671- 1680, 1984; Broglie et al, Science 224, 838-843, 1984; Winter et al, Results Probl. Cell Differ. 17, 85-105, 1991). These constructs can be introduced into plant cells by direct DNA transformation or by pathogen-mediated transfection. Such techniques are described in a number of generally available reviews (e.g., Hobbs or Murray, in MCGRAW HILL YEARBOOK OF SCIENCE AND TECHNOLOGY, McGraw Hill, New York, N.Y., pp. 191-196, 1992).

An insect system also can be used to express a DCC-like polypeptide. For example, in one such system Autographa calif or nica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes in Spodoptera frugiperda cells or in Trichoplusia larvae. Sequences encoding DCC-like polypeptides can be cloned into a non-essential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter. Successful insertion of DCC-like polypeptides will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein. The recombinant viruses can then be used to infect S. frugiperda cells or Trichoplusia larvae in which DCC-like polypeptides can be expressed (Engelhard et al, Proc. Nat. Acad. Sci. 91, 3224-3227, 1994).

Mammalian Expression Systems

A number of viral-based expression systems can be used to express DCC-like polypeptides in mammalian host cells. For example, if an adenovirus is used as an expression vector, sequences encoding DCC-like polypeptides can be ligated into an adenovirus transcription/translation complex comprising the late promoter and tripartite leader sequence. Insertion in a non-essential El or E3 region of the viral genome can be used to obtain a viable virus which is capable of expressing a DCC- like polypeptide in infected host cells (Logan & Shenk, Proc. Natl. Acad. Sci. 81, 3655-3659, 1984). If desired, transcription enhancers such as the Rous sarcoma virus

(RSV) enhancer can be used to increase expression in mammalian host cells.

Human artificial chromosomes (HACs) also can be used to deliver larger fragments of DNA than can be contained and expressed in a plasmid. HACs of 6M to 10M are constructed and delivered to cells via conventional delivery methods (e.g., liposomes, polycationic amino polymers, or vesicles).

Specific initiation signals also can be used to achieve more efficient translation of sequences encoding DCC-like polypeptides. Such signals include the ATG initiation codon and adjacent sequences. In cases where sequences encoding a DCC-like polypeptide, its initiation codon, and upstream sequences are inserted into the appropriate expression vector, no additional transcriptional or translational control signals may be needed. However, in cases where only coding sequence, or a fragment thereof, is inserted, exogenous translational control signals (including the ATG initiation codon) should be provided. The initiation codon should be in the correct reading frame to ensure translation of the entire insert. Exogenous translational elements and initiation codons can be of various origins, both natural and synthetic. The efficiency of expression can be enhanced by the inclusion of enhancers which are appropriate for the particular cell system which is used (see Scharf et al, Results Probl. Cell Differ. 20, 125- 162, 1994).

Host Cells

A host cell strain can be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed DCC-like polypeptide 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 polypeptide also can be used to facilitate correct insertion, folding, and/or function. Different host cells which have specific cellular machinery and characteristic mechanisms for post- translational activities (e.g., CHO, HeLa, MDCK, HEK293, and WI38), are available from the American Type Culture Collection (ATCC; 10801 University Boulevard, Manassas, VA 20110-2209) and can be chosen to ensure the correct modification and processing of the foreign protein.

Stable expression is preferred for long-term, high-yield production of recombinant proteins. For example, cell lines which stably express DCC-like polypeptides can be transformed using expression vectors which can contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells can be allowed to grow for 1-2 days in an enriched medium before they are switched to a selective medium. The purpose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells which successfully express the introduced DCC-like sequences. Resistant clones of stably transformed cells can be proliferated using tissue culture techniques appropriate to the cell type. See, for example, ANIMAL CELL CULTURE, R.I. Freshney, ed., 1986.

Any number of selection systems can be used to recover transformed cell lines. These include, but are not limited to, the herpes simplex virus thymidine kinase (Wigler et al, Cell 11, 223-32, 1977) and adenine phosphoribosyltransferase (Lowy et al, Cell 22, 817-23, 1980) genes which can be employed in tk^~ or aprf cells, respectively. Also, antimetabolite, antibiotic, or herbicide resistance can be used as the basis for selection. For example, dhfr confers resistance to methotrexate (Wigler et al, Proc. Natl. Acad. Sci. 77, 3567-70, 1980) npt confers resistance to the aminoglycosidcs ncomycin and G-418 (Colbere-Garapin et al, J. Mol. Biol. 150, 1 - 14, 1981 ), and als and pat confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively (Murray, 1992, supra). Additional selectable genes have been described. For example, trpB, allows cells to utilize indole in place of tryptophan; hisD, allows cells to utilize histinol in place of histidine (Hartman & Mulligan, Proc. Natl. Acad. Sci. 85, 8047-51, 1988). Visible markers such as anthocyanins, -glucuronidase and its substrate GUS, and luciferase and its substrate luciferin, can be used to identify transformants and to quantify the amount of transient or stable protein expression attributable to a specific vector system (Rhodes et al, Methods Mo Biol. 55, 121-131, 1995).

Detecting Expression of DCC-like Polypeptides

Although the presence of marker gene expression suggests that a DCC-like polynucleotide is also present, its presence and expression may need to be confirmed. For example, if a sequence encoding a DCC-like polypeptide is inserted within a marker gene sequence, transformed cells containing sequences which encode the DCC-like polypeptide can be identified by the absence of marker gene function.

Alternatively, a marker gene can be placed in tandem with a sequence encoding a DCC-like polypeptide under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of a DCC-like polynucleotide.

Alternatively, host cells which contain a DCC-like polynucleotide and which express a DCC-like polypeptide can 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 hybridizations and protein bioassay or immunoassay techniques which include membrane, solution, or chip-based technologies for the detection and or quantification of nucleic acid or protein. For example, the presence of a polynucleotide sequence encoding a DCC-like polypeptide can be detected by DNA- DNA or DNA-RNA hybridization or amplification using probes or fragments or fragments of polynucleotides encoding the DCC-like polypeptide. Nucleic acid amplification-based assays involve the use of oligonucleotides selected from sequences encoding the polypeptide to detect transformants which contain a DCC- like polynucleotide.

A variety of protocols for detecting and measuring the expression of a DCC-like polypeptide, using either polyclonal or monoclonal antibodies specific for the polypeptide, are known in the art. Examples include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), and fluorescence activated cell sorting (FACS). A two-site, monoclonal-based immunoassay using monoclonal antibodies reactive to two non-interfering epitopes on a DCC-like polypeptide can be used, or a competitive binding assay can be employed. These and other assays are described in

Hampton et al, SEROLOGICAL METHODS: A LABORATORY MANUAL, APS Press, St. Paul, Minn., 1990) and Maddox et al, J. Exp. Med. 158, 1211-1216, 1983).

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 sequences related to polynucleotides encoding DCC-like polypeptides include oligolabeling, nick translation, end-labeling, or PCR amplification using a labeled nucleotide. Alternatively, sequences encoding a DCC-like polypeptide can be cloned into a vector for the production of an mRNA probe. Such vectors are known in the art, are commercially available, and can be used to synthesize RNA probes in vitro by addition of labeled nucleotides and an appropriate RNA polymerase such as T7, T3, or SP6. These procedures can be conducted using a variety of commercially available kits (Amersham Pharmacia Biotech, Promega, and US Biochemical). Suitable reporter molecules or labels which can be used for ease of detection include radionuclides, enzymes, and fluorescent, chemiluminescent, or chromogenic agents, as well as substrates, cofactors, inhibitors, magnetic particles, and the like. Expression and Purification of DCC-like Polypeptides

Host cells transformed with nucleotide sequences encoding a DCC-like polypeptide can be cultured under conditions suitable for the expression and recovery of the protein from cell culture. The polypeptide produced by a transformed cell can 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 polynucleotides which encode DCC-like polypeptides can be designed to contain signal sequences which direct secretion of DCC-like polypeptides through a prokaryotic or eukaryotic cell membrane.

As discussed above, other constructions can be used to join a sequence encoding a DCC-like polypeptide to a nucleotide sequence encoding a polypeptide domain which will facilitate purification of soluble proteins. 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 Corp., Seattle, Wash.). Inclusion of cleavable linker sequences such as those specific for Factor XA or enterokinase (Invitrogen, San Diego, CA) between the purification domain and the DCC-like polypeptide also can be used to facilitate purification. One such expression vector provides for expression of a fusion protein containing a DCC- like polypeptide and 6 histidine residues preceding a thioredoxin or an enterokinase cleavage site. The histidine residues facilitate purification on IMAC (immobilized metal ion affinity chromatography, as described in Porath et al, Prot. Exp. Purif 3,

263-281. 1992), while the enterokinase cleavage site provides a means for purifying the DCC-like polypeptide from the fusion protein. Vectors which contain fusion proteins are disclosed in Kroll et al, DNA Cell Biυl. 12, 441 -453, 1993. Chemical Synthesis

Sequences encoding a DCC-like polypeptide can be synthesized, in whole or in part, using chemical methods well known in the art (see Caruthers et al, Nucl. Acids Res. Symp. Ser. 215-223, 1980; Horn et al. Nucl. Acids Res. Symp. Ser. 225-232, 1980).

Alternatively, a DCC-like polypeptide itself can be produced using chemical methods to synthesize its amino acid sequence, such as by direct peptide synthesis using solid-phase techniques (Merrifield, J Am. Chem. Soc. 85, 2149-2154, 1963; Roberge et al, Science 269, 202-204, 1995). Protein synthesis can be performed using manual techniques or by automation. Automated synthesis can be achieved, for example, using Applied Biosystems 431 A Peptide Synthesizer (Perkin Elmer). Optionally, fragments of DCC-like polypeptides can be separately synthesized and combined using chemical methods to produce a full-length molecule.

The newly synthesized peptide can be substantially purified by preparative high performance liquid chromatography (e.g., Creighton, PROTEINS: STRUCTURES AND MOLECULAR PRINCIPLES, WH Freeman and Co., New York, N.Y., 1983). The composition of a synthetic DCC-like polypeptide can be confirmed by amino acid analysis or sequencing (e.g., the Edman degradation procedure; see Creighton, supra). Additionally, any portion of the amino acid sequence of the DCC-like polypeptide can be altered during direct synthesis and/or combined using chemical methods with sequences from other proteins to produce a variant polypeptide or a fusion protein.

Production of Altered DCC-like Polypeptides

As will be understood by those of skill in the art, it may be advantageous to produce

DCC-like polypeptide-encoding nucleotide sequences possessing non-naturally occurring codons. For example, codons preferred by a particular prokaryotic or eukaryotic host can be selected to increase the rate of protein expression or to produce an RNA transcript having desirable properties, such as a half-life which is longer than that of a transcript generated from the naturally occurring sequence.

The nucleotide sequences disclosed herein can be engineered using methods generally known in the art to alter DCC-like polypeptide-encoding sequences for a variety of reasons, including but not limited to, alterations which modify the cloning, processing, and/or expression of the polypeptide or mRNA product. DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides can be used to engineer the nucleotide sequences. For example, site-directed mutagenesis can be used to insert new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, introduce mutations, and so forth.

Antibodies

Any type of antibody known in the art can be generated to bind specifically to an epitope of a DCC-like polypeptide. "Antibody" as used herein includes intact immunoglobulin molecules, as well as fragments thereof, such as Fab, F(ab')₂, and Fv, which are capable of binding an epitope of a DCC-like polypeptide. Typically, at least 6, 8, 10, or 12 contiguous amino acids are required to form an epitope.

However, epitopes which involve non-contiguous amino acids may require more, e.g., at least 15, 25, or 50 amino acids.

An antibody which specifically binds to an epitope of a DCC-like polypeptide can be used therapeutically, as well as in immunochemical assays, such as Western blots,

ELISAs, radioimmunoassays, immunohistochemical assays, immunoprecipitations, or other immunochemical assays known in the art. Various immunoassays can be used to identify antibodies having the desired specificity. Numerous protocols for competitive binding or immunoradiomelric assays are well known in the art. Such immunoassays typically involve the measurement of complex formation between an immunogen and an antibody which specifically binds to the immunogcn. Typically, an antibody which specifically binds to a DCC-like polypeptide provides a detection signal at least 5-, 10-, or 20-fold higher than a detection signal provided with other proteins when used in an immunochemical assay. Preferably, antibodies which specifically bind to DCC-like polypeptides do not detect other proteins in immunochemical assays and can immunoprecipitate a DCC-like polypeptide from solution.

DCC-like polypeptides can be used to immunize a mammal, such as a mouse, rat, rabbit, guinea pig, monkey, or human, to produce polyclonal antibodies. If desired, a

DCC- like polypeptide can be conjugated to a carrier protein, such as bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin. Depending on the host species, various adjuvants can be used to increase the immunological response. Such adjuvants include, but are not limited to, Freund's adjuvant, mineral gels (e.g., aluminum hydroxide), and surface active substances (e.g. lyso lecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol). Among adjuvants used in humans, BCG (bacilli Calmette-Guerin) and Corynebacterium parvum are especially useful.

Monoclonal antibodies which specifically bind to a DCC-like polypeptide can be prepared using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These techniques include, but are not limited to, the hybridoma technique, the human B-cell hybridoma technique, and the EBV-hybridoma technique (Kohler et al, Nature 256, 495-497, 1985; Kozbor et al, J. Immunol. Methods 81, 31-42, 1985; Cote et al, Proc. Natl Acad. Sci. 80, 2026-

2030, 1983; Cole et al, Mol. Cell Biol. 62, 109-120, 1984).

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,

Proc. Sail. Acad. Sci. 81, 6851 -6855, 1984; Neubergcr et al, Nature 312, 604-608, 1984; Takeda et al, Nature 314, 452-454, 1985). Monoclonal and other antibodies also can be "humanized" to prevent a patient from mounting an immune response against the antibody when it is used therapeutically. Such antibodies may be sufficiently similar in sequence to human antibodies to be used directly in therapy or may require alteration of a few key residues. Sequence differences between rodent antibodies and human sequences can be minimized by replacing residues which differ from those in the human sequences by site directed mutagenesis of individual residues or by grating of entire complementarity determining regions. Alternatively, humanized antibodies can be produced using recombinant methods, as described in GB2188638B. Antibodies which specifically bind to a DCC-like polypeptide can contain antigen binding sites which are either partially or fully humanized, as disclosed in U.S. 5,565,332.

Alternatively, techniques described for the production of single chain antibodies can be adapted using methods known in the art to produce single chain antibodies which specifically bind to DCC-like polypeptides. Antibodies with related specificity, but of distinct idiotypic composition, can be generated by chain shuffling from random combinatorial immunoglobin libraries (Burton, Proc. Natl. Acad. Sci. 88, 11120-23, 1991).

Single-chain antibodies also can be constructed using a DNA amplification method, such as PCR, using hybridoma cDNA as a template (Thirion et al, 1996, Eur. J. Cancer Prev. 5, 507-1 1). Single-chain antibodies can be mono- or bispecific, and can be bivalent or tetravalent. Construction of tetravalent, bispecific single-chain antibodies is taught, for example, in Coloma & Morrison, 1997, Nat. Biotechnol. 15,

159-63. Construction of bivalent, bispecific single-chain antibodies is taught in Mallender & Voss, 1994, J Biol Chem. 269, 199-206.

A nucleotide sequence encoding a single-chain antibody can be constructed using manual or automated nucleotide synthesis, cloned into an expression construct using standard recombinant DΝA methods, and introduced into a cell to express the coding sequence, as described below. Alternatively, single-chain antibodies can be produced directly using, for example, filamentous phage technology (Verhaar et al, 1995, Int. J. Cancer 61, 497-501; Nicholls et al, 1993, J Immunol. Meth. 165, 81- 91).

Antibodies which specifically bind to DCC-like polypeptides also can be produced by inducing in vivo production in the lymphocyte population or by screening immunoglobulin libraries or panels of highly specific binding reagents as disclosed in the literature (Oriandi et al, Proc. Natl. Acad. Sci. 86, 3833-3837, 1989; Winter et al, Nature 349, 293-299, 1991).

Other types of antibodies can be constructed and used therapeutically in methods of the invention. For example, chimeric antibodies can be constructed as disclosed in WO 93/03151. Binding proteins which are derived from immunoglobulins and which are multivalent and multispecific, such as the "diabodies" described in WO

94/13804, also can be prepared.

Antibodies according to the invention can be purified by methods well known in the art. For example, antibodies can be affinity purified by passage over a column to which a DCC-like polypeptide is bound. The bound antibodies can then be eluted from the column using a buffer with a high salt concentration.

Antisense Oligonucleotides

Antisense oligonucleotides are nucleotide sequences which are complementary to a specific DNA or RNA sequence. Once introduced into a cell, the complementary nucleotides combine with natural sequences produced by the cell to form complexes and block either transcription or translation. Preferably, an antisense oligonucleotide is at least 1 1 nucleotides in length, but can be at least 12, 15, 20, 25, 30, 35, 40, 45, or 50 or more nucleotides long. Longer sequences also can be used. Antisense oligonucleotide molecules can be provided in a DNA construct and introduced into a cell as described above to decrease the level of DCC-like gene products in the cell.

Antisense oligonucleotides can be deoxyribonucleotides, ribonucleotides, or a combination of both. Oligonucleotides can be synthesized manually or by an automated synthesizer, by covalently linking the 5' end of one nucleotide with the 3' end of another nucleotide with non-phosphodiester internucleotide linkages such alkylphosphonates, phosphorothioates, phosphorodithioates, alkylphosphonothioates, alkylphosphonates, phosphoramidates, phosphate esters, carbamates, acetamidate, carboxymethyl esters, carbonates, and phosphate triesters. See Brown, Meth. Mol.

Biol 20, 1-8, 1994; Sonveaux, Meth. Mol. Biol. 26, 1-72, 1994; Uhlmann et al, Chem. Rev. 90, 543-583, 1990.

Modifications of DCC-like gene expression can be obtained by designing antisense oligonucleotides which will form duplexes to the control, 5', or regulatory regions of a DCC-like gene. Oligonucleotides derived from the transcription initiation site, e.g., between positions -10 and +10 from the start site, are preferred. Similarly, inhibition can be achieved using "triple helix" base-pairing methodology. Triple helix pairing is useful because it causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or chaperons.

Therapeutic advances using triplex DNA have been described in the literature (e.g.,

Gee et al, in Huber & Carr, MOLECULAR AND I MUNOLOGIC APPROACHES, Futura

Publishing Co., Mt. Kisco, N.Y., 1994). An antisense oligonucleotide also can be designed to block translation of mRNA by preventing the transcript from binding to ribosomes.

Precise complementarity is not required for successful complex formation between an antisense oligonucleotide and the complementary sequence of a DCC-like polynucleotide. Antisense oligonucleotides which comprise, for example, 2, 3, 4, or 5 or more stretches of contiguous nucleotides which are precisely complementary to a DCC-hkc polynucleotide, each separated by a stretch of contiguous nucleotides which are not complementary to adjacent DCC-like nucleotides, can provide sufficient targeting specificity for DCC-like mRNA. Preferably, each stretch of complementary contiguous nucleotides is at least 4, 5, 6, 7, or 8 or more nucleotides in length. Non-complementary intervening sequences are preferably 1, 2, 3, or 4 nucleotides in length. One skilled in the art can easily use the calculated melting point of an antisense-sense pair to determine the degree of mismatching which will be tolerated between a particular antisense oligonucleotide and a particular DCC- like polynucleotide sequence.

Antisense oligonucleotides can be modified without affecting their ability to hybridize to a DCC-like polynucleotide. These modifications can be internal or at one or both ends of the antisense molecule. For example, internucleoside phosphate linkages can be modified by adding cholesteryl or diamine moieties with varying numbers of carbon residues between the amino groups and terminal ribose. Modified bases and/or sugars, such as arabinose instead of ribose, or a 3', 5'-substituted oligonucleotide in which the 3' hydroxyl group or the 5' phosphate group are substituted, also can be employed in a modified antisense oligonucleotide. These modified oligonucleotides can be prepared by methods well known in the art. See, e.g., Agrawal et al, Trends Biotechnol. 10, 152-158, 1992; Uhlmann et al, Chem. Rev. 90, 543-584, 1990; Uhlmann et al, Tetrahedron. Lett. 215, 3539-3542, 1987.

Ribozymes

Ribozymes are RNA molecules with catalytic activity. See, e.g., Cech, Science 236, 1532-1539; 1987; Cech, Ann. Rev. Biochem. 59, 543-568; 1990, Cech, Curr. Opin.

Struct. Biol. 2, 605-609; 1992, Couture & Stinchcomb, Trends Genet. 12, 510-515, 1996. Ribozymes can be used to inhibit gene function by cleaving an RNA sequence, as is known in the art (e.g., Haseloff et al, U.S. Patent 5,641,673). The mechanism of ribozymc action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA, followed by endonucleolytic cleavage.

Examples include engineered hammerhead motif ribozyme molecules that can specifically and efficiently catalyze endonucleolytic cleavage of specific nucleotide sequences.

The coding sequence of a DCC-like polynucleotide can be used to generate ribozymes which will specifically bind to mRNA transcribed from the DCC-like polynucleotide. Methods of designing and constructing ribozymes which can cleave RNA molecules in trans in a highly sequence specific manner have been developed and described in the art (see Haseloff et al .Nature 334, 585-591, 1988). For example, the cleavage activity of ribozymes can be targeted to specific RNAs by engineering a discrete "hybridization" region into the ribozyme. The hybridization region contains a sequence complementary to the target RNA and thus specifically hybridizes with the target (see, for example, Gerlach et al, EP 321,201).

Specific ribozyme cleavage sites within a DCC-like RNA target can be identified by scanning the DCC-like 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 RNA containing the cleavage site can be evaluated for secondary structural features which may render the target inoperable. Suitability of candidate DCC-like RNA targets also can be evaluated by testing accessibility to hybridization with complementary oligonucleotides using ribonuclease protection assays. The nucleotide sequences shown in SEQ ID NOS:l, 3, and 5 and their complements provide sources of suitable hybridization region sequences. Longer complementary sequences can be used to increase the affinity of the hybridization sequence for the target. The hybridizing and cleavage regions of the ribozyme can be integrally related such that upon hybridizing to the target RNA through the complementary regions, the catalytic region of the ribozyme can cleave the target.

Ribozymes can be introduced into cells as part of a DNA construct. Mechanical methods, such as microinjection, liposome-mediated transfection, electroporation, or calcium phosphate precipitation, can be used to introduce a ribozymc-containing DNA construct into cells in which it is desired to decrease DCC-like polypeptide expression. Alternatively, if it is desired that the cells stably retain the DNA construct, the construct can be supplied on a plasmid and maintained as a separate element or integrated into the genome of the cells, as is known in the art. A ribozyme-encoding DNA construct can include transcriptional regulatory elements, such as a promoter element, an enhancer or UAS element, and a transcriptional terminator signal, for controlling transcription of ribozymes in the cells.

As taught in Haseloff et al, U.S. Patent 5,641,673, ribozymes can be engineered so that ribozyme expression will occur in response to factors which induce expression of a target gene. Ribozymes also can be engineered to provide an additional level of regulation, so that destruction of mRNA occurs only when both a ribozyme and a target gene are induced in the cells.

Screening Methods

The invention provides methods for identifying modulators, i.e., candidate or test compounds which bind to DCC-like polypeptides or polynucleotides and/or have a stimulatory or inhibitory effect on, for example, expression or activity of the DCC- like polypeptide or polynucleotide, so as to mediates the effects of netrins on axons.

Both increased and decreased amounts of DCC-like polypeptides are useful, for example, for modulating netrin guidance of neuronal cell growth and cell migration and regulating axon outgrowth.

The invention provides assays for screening test compounds which bind to or modulate the activity of a DCC-like polypeptide or a DCC-like polynucleotide. A test compound preferably binds to a DCC-like polypeptide or polynucleotide. More preferably, a test compound increases or decreases a DCC-like activity of a DCC-like polypeptide or expression of an DCC-like polynucleotide by at least about 10, preferably about 50. more preferably about 75, 90, or 100% relative to the absence of the test compound. Test Compounds

Test compounds can be pharmacologic agents already known in the art or can be compounds previously unknown to have any pharmacological activity. The compounds can be naturally occurring or designed in the laboratory. They can be isolated from microorganisms, animals, or plants, and can be produced recombinantly, or synthesized by chemical methods known in the art. If desired, test compounds can be obtained using any of the numerous combinatorial library methods known in the art, including but not limited to, biological libraries, spatially addressable parallel solid phase or solution phase libraries, synthetic library methods requiring deconvolution, the "one-bead one-compound" library method, and synthetic library methods using affinity chromatography selection. The biological library approach is limited to polypeptide libraries, while the other four approaches are applicable to polypeptide, non-peptide oligomer, or small molecule libraries of compounds. See Lam, Anticancer Drug Des. 12, 145, 1997.

Methods for the synthesis of molecular libraries are well known in the art (see, for example, DeWitt et al, Proc. Natl. Acad. Sci. U.S.A. 90, 6909, 1993; Erb et al. Proc. Natl. Acad. Sci. U.S.A. 91, 1 1422, 1994; Zuckermann et al, J. Med. Chem. 37, 2678,

1994; Cho et al, Science 261, 1303, 1993; Carell et al, Angew. Chem. Int. Ed. Engl. 33, 2059, 1994; Carell et al, Angew. Chem. Int. Ed. Engl. 33, 2061; Gallop et al, J. Med. Chem. 37, 1233, 1994). Libraries of compounds can be presented in solution (see, e.g., Houghten, Biotechniques 13, 412-421, 1992), or on beads (Lam, Nature 354, 82-84, 1991), chips (Fodor, Nature 364, 555-556, 1993), bacteria or spores

(Ladner, U.S. Patent 5,223,409), plasmids (Cull et al, Proc. Natl. Acad. Sci. U.S.A. 89, 1865-1869, 1992), or phagc (Scott & Smith, Science 249, 386-390, 1990; Devlin, Science 249, 404-406, 1990); Cvvirla el al, Proc. Natl. Acad. Sci. 97, 6378-6382, 1990; Fclici, ./ Mol Biol 222, 301 -310, 1991 ; and Ladner, U.S. Patent 5,223,409). High Throughput Screening

Test compounds can be screened for the ability to bind to DCC-like polypeptides or polynucleotides or to affect DCC-like activity or DCC-like gene expression using high throughput screening. Using high throughput screening, many discrete compounds can be tested in parallel so that large numbers of test compounds can be quickly screened. The most widely established techniques utilize 96-well microtiter plates. The wells of the microtiter plates typically require assay volumes that range from 50 to 500 μl. In addition to the plates, many instruments, materials, pipettors, robotics, plate washers, and plate readers are commercially available to fit the 96- well format.

Alternatively, "free format assays," or assays that have no physical barrier between samples, can be used. For example, an assay using pigment cells (melanocytes) in a simple homogeneous assay for combinatorial peptide libraries is described by

Jayawickreme et al, Proc. Natl. Acad. Sci. U.S.A. 19, 1614-18 (1994). The cells are placed under agarose in petri dishes, then beads that carry combinatorial compounds are placed on the surface of the agarose. The combinatorial compounds are partially released the compounds from the beads. Active compounds can be visualized as dark pigment areas because, as the compounds diffuse locally into the gel matrix, the active compounds cause the cells to change colors.

Another example of a free format assay is described by Chelsky, "Strategies for Screening Combinatorial Libraries: Novel and Traditional Approaches," reported at the First Annual Conference of The Society for Biomolecular Screening in

Philadelphia, Pa. (Nov. 7-10, 1995). Chelsky placed a simple homogenous enzyme assay for carbonic anhydrase inside an agarose gel such that the enzyme in the gel would cause a color change throughout the gel. Thereafter, beads carrying combinatorial compounds via a photolinker were placed inside the gel and the compounds were partially released by UV-light. Compounds that inhibited the enzyme were observed as local zones of inhibition having less color change. Yet another example is described by Salmon et al, Molecular Diversity 2, 57-63 (1996). In this example, combinatorial libraries were screened for compounds that had cytotoxic effects on cancer cells growing in agar.

Another high throughput screening method is described in Beutel et al, U.S. Patent 5,976,813. In this method, test samples are placed in a porous matrix. One or more assay components are then placed within, on top of, or at the bottom of a matrix such as a gel, a plastic sheet, a filter, or other form of easily manipulated solid support. When samples are introduced to the porous matrix they diffuse sufficiently slowly such that the assays can be performed without the test samples running together.

Binding Assays

For binding assays, the test compound is preferably a small molecule which binds to and occupies the active site of a DCC-like polypeptide, thereby making the active site inaccessible to substrate such that normal biological activity is prevented. Examples of such small molecules include, but are not limited to, small peptides or peptide-like molecules. In binding assays, either the test compound or the DCC-like polypeptide can comprise a detectable label, such as a fluorescent, radioisotopic, chemiluminescent, or enzymatic label, such as horseradish peroxidase, alkaline phosphatase, or luciferase. Detection of a test compound which is bound to the DCC-like polypeptide can then be accomplished, for example, by direct counting of radioemmission, by scintillation counting, or by determining conversion of an appropriate substrate to a detectable product.

Alternatively, binding of a test compound to a DCC-like polypeptide can be determined without labeling either of the interactants. For example, a micro- physiomctcr can be used to detect binding of a test compound with a DCC-like polypeptide A microphysiometer (e g . Cytoscnsor™) is an analytical instrument that measures the rate at w hich a cell acidifies its environment using a light- addressable potentiometric sensor (LAPS). Changes in this acidification rate can be used as an indicator of the interaction between a test compound and a DCC-like polypeptide. (McConnell et al, Science 257, 1906-1912, 1992).

Determining the ability of a test compound to bind to a DCC-like polypeptide also can be accomplished using a technology such as real-time Bimolecular Interaction Analysis (BIA) (Sjolander & Urbaniczky, Anal. Chem. 63, 2338-2345, 1991, and Szabo et al, Curr. Opin. Struct. Biol. 5, 699-705, 1995). BIA is a technology for studying biospecific interactions in real time, without labeling any of the interactants (e.g., BIAcore™). Changes in the optical phenomenon surface plasmon resonance

(SPR) can be used as an indication of real-time reactions between biological molecules.

In yet another aspect of the invention, a DCC-like polypeptide can be used as a "bait protein" in a two-hybrid assay or three-hybrid assay (see, e.g., U.S. Patent 5,283,317;

Zervos et al, Cell 72, 223-232, 1993; Madura et al, J. Biol Chem. 268, 12046- 12054, 1993; Bartel et al, Biotechniques 14, 920-924, 1993; Iwabuchi et al, Oncogene 8, 1693-1696, 1993; and Brent W094/10300) to identify other proteins which bind to or interact with the DCC-like polypeptide and modulate its activity.

The two-hybrid system is based on the modular nature of most transcription factors, which consist of separable DNA-binding and activation domains. Briefly, the assay utilizes two different DNA constructs. For example, in one construct a polynucleotide encoding a DCC-like polypeptide can be fused to a polynucleotide encoding the DNA binding domain of a known transcription factor (e.g., GAL-4). In the other construct a DNA sequence that encodes an unidentified protein ("prey" or "sample") can be fused to a polynucleotide that codes for the activation domain of the known transcription factor. If the "bait" and the "prey" proteins are able to interact in vivo to form an protein-dependent complex, the DNA-binding and activation domains of the transcription factor are brought into close proximity. This proximity allows transcription of a reporter gene (e.g., LacZ), which is operably linked to a transcriptional regulatory site responsive to the transcription factor. Expression of the reporter gene can be detected, and cell colonies containing the functional transcription factor can be isolated and used to obtain the DNA sequence encoding the protein which interacts with the DCC-like polypeptide.

It may be desirable to immobilize either a DCC-like polypeptide (or polynucleotide) or the test compound to facilitate separation of bound from unbound forms of one or both of the interactants, as well as to accommodate automation of the assay. Thus, either the DCC-like polypeptide (or polynucleotide) or the test compound can be bound to a solid support. Suitable solid supports include, but are not limited to, glass or plastic slides, tissue culture plates, microtiter wells, tubes, silicon chips, or particles such as beads (including, but not limited to, latex, polystyrene, or glass beads). Any method known in the art can be used to attach the DCC-like polypeptide (or polynucleotide) or test compound to a solid support, including use of covalent and non-covalent linkages, passive absorption, or pairs of binding moieties attached respectively to the polypeptide or test compound and the solid support. Test compounds are preferably bound to the solid support in an array, so that the location of individual test compounds can be tracked. Binding of a test compound to a DCC- like polypeptide (or polynucleotide) can be accomplished in any vessel suitable for containing the reactants. Examples of such vessels include microtiter plates, test tubes, and microcentrifuge tubes.

In one embodiment, a DCC-like polypeptide is a fusion protein comprising a domain that allows the DCC-like polypeptide to be bound to a solid support. For example, glutathione-S-transferase fusion proteins can be adsorbed onto glutathione sepharose beads (Sigma Chemical, St. Louis, Mo ) or glutathione derivatized microtiter plates, which arc then combined with the test compound or the test compound and the non- adsorbed DCC-like polypeptide, the mixture is then incubated under conditions conduciv e to complex formation ( g , at physiological conditions for salt and pH) Following incubation, the beads or microtiter plate wells are washed to remove any unbound components Binding of the interactants can be determined cither directly or indirectly, as described above. Alternatively, the complexes can be dissociated from the solid support before binding is determined.

Other techniques for immobilizing proteins or polynucleotides on a solid support also can be used in the screening assays of the invention. For example, either a DCC-like polypeptide (or polynucleotide) or a test compound can be immobilized utilizing conjugation of biotin and streptavidin. Biotinylated DCC-like polypeptides, polynucleotides, or test compounds can be prepared from biotin-NHS(N-hydroxy- succinimide) using techniques well known in the art (e.g., biotinylation kit, Pierce Chemicals, Rockford, 111.) and immobilized in the wells of streptavidin-coated 96. well plates (Pierce Chemical). Alternatively, antibodies which specifically bind to a DCC-like polypeptide, polynucleotides, or a test compound, but which do not interfere with a desired binding site, such as the netrin binding site of the DCC-like polypeptide, can be derivatized to the wells of the plate. Unbound target or protein can be trapped in the wells by antibody conjugation.

Methods for detecting such complexes, in addition to those described above for the GST-immobilized complexes, include immunodetection of complexes using antibodies which specifically bind to a DCC-like polypeptide or test compound, enzyme-linked assays which rely on detecting a DCC-like activity of the DCC-like polypeptide, and SDS gel electrophoresis under non-reducing conditions.

Screening for test compounds which bind to a DCC-like polypeptide or polynucleotide also can be carried out in an intact cell. Any cell which comprises a DCC-like polynucleotide or polypeptide can be used in a cell-based assay system. A

DCC-like polynucleotide can be naturally occurring in the cell or can be introduced using techniques such as those described above. Either a primary culture or an established cell line, including cell lines such as the HCN-1A, HCN-2, CATH.a, Neuro-2a, and PC 12 (Clontech), can be used. An intact cell is contacted with a test compound. Binding of the test compound to a DCC-like polypeptide or polynucleotide is determined as described above, after lysing the cell to release the DCC-like polypeptide-or polynucleotide-test compound complex.

DCC-Like Gene Expression

In another embodiment, test compounds which increase or decrease DCC-like gene expression are identified. A DCC-like polynucleotide is contacted with a test compound, and the expression of an RNA or polypeptide product of the DCC-like polynucleotide is determined. The level of expression of DCC-like mRNA or polypeptide in the presence of the test compound is compared to the level of expression of DCC-like mRNA or polypeptide in the absence of the test compound. The test compound can then be identified as a modulator of expression based on this comparison. For example, when expression of DCC-like mRNA or polypeptide is greater in the presence of the test compound than in its absence, the test compound is identified as a stimulator or enhancer of DCC-like mRNA or polypeptide expression.

Alternatively, when expression of DCC-like mRNA or polypeptide is less in the presence of the test compound than in its absence, the test compound is identified as an inhibitor of DCC-like mRNA or polypeptide expression.

The level of DCC-like mRNA or polypeptide expression in the cells can be determined by methods well known in the art for detecting mRNA or polypeptides. Either qualitative or quantitative methods can be used. The presence of polypeptide products of a DCC-like polynucleotide can be determined, for example, using a variety of techniques known in the art, including immunochemical methods such as radioimmunoassay, Western blotting, and immunohistochemistry. Alternatively, polypeptide synthesis can be determined in vivo, in a cell culture, or in an in vitro translation system by detecting incorporation of labeled amino acids into a DCC-like polypeptide.

Such screening can be carried out either in a cell-free assay system or in an intact cell. Any cell which expresses a DCC-like polynucleotide can be used in a cell- based assay system. The DCC-like polynucleotide can be naturally occurring in the cell or can be introduced using techniques such as those described above. Either a primary culture or an established cell line, including cell lines such as HCN-1A, HCN-2, CATH.a, Neuro-2a, and PC 12 (Clontech), can be used, can be used.

Pharmaceutical Compositions

The invention also provides pharmaceutical compositions which can be administered to a patient to achieve a therapeutic effect. Pharmaceutical compositions of the invention can comprise, for example, a DCC-like polypeptide, DCC-like polynucleotide, antibodies which specifically bind to DCC-like proteins, or mimetics, agonists, antagonists, or inhibitors of DCC-like activity. The compositions can be administered alone or in combination with at least one other agent, such as stabilizing compound, which can be administered in any sterile, biocompatible pharmaceutical carrier, including, but not limited to, saline, buffered saline, dextrose, and water. The compositions can be administered to a patient alone, or in combination with other agents, drugs or hormones.

In addition to the active ingredients, these pharmaceutical compositions can contain suitable pharmaceutically-acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. Pharmaceutical compositions of the invention can be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, transdermal, subcutaneous, intraperitoneal, intranasal, parenteral, topical, sublingual, or rectal means. 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. Preferably, pharmaceutical compositions of the invention are provided to a retained physiological fluid such as blood or synovial fluid. For central nervous system (CNS) administration, a variety of techniques are available for promoting transfer of the composition across the blood brain barrier including disruption by surgery or injection, drugs which transiently open adhesion contact between CNS vasculature endothelial cells, and compounds which facilitate translocation through such cells.

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, hydroxy- propylmethyl-cellulose, or sodium carboxymethylcellulose; gums including arabic and tragacanth; and proteins such as gelatin and collagen. If desired, disintegrating or solubilizing agents can be added, such as the cross-linked polyvinyl pyrrolidone, agar, alginic acid, or a salt thereof, such as sodium alginate.

Dragee cores can be used in conjunction with suitable coatings, such as concentrated sugar solutions, which also can 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 can be added to the tablets or dragee coatings for product identification or to characterize the quantity of active compound, i.e., 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 can be dissolved or suspended in suitable liquids, such as fatty oils, liquid, or liquid polyethylene glycol with or without stabilizers.

Pharmaceutical formulations suitable for parenteral administration can be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks' solution, Ringer's solution, or physiologically buffered saline. Aqueous injection suspensions can contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Additionally, suspensions of the active compounds can 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. Non-lipid polycationic amino polymers also can be used for delivery. Optionally, the suspension also can 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.

The pharmaceutical compositions of the present invention can be manufactured in a manner that is known in the art, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping, or lyophilizing processes. The pharmaceutical composition can 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 than are the corresponding free base forms. In other cases, the preferred preparation can be a lyophilized powder which can contain any or all of the following: 1 -50 mM histidine, 0.1 %-2%> sucrose, and 2-7%> mannitol, at a pH range of 4.5 to 5.5, that is combined with buffer prior to use.

Further details on techniques for formulation and administration can be found in the latest edition of RΓ IISG I OVS PHARMACEUT ICAL Sen NCT.S (Maack Publishing Co., Easton, Pa.). After pharmaceutical compositions have been prepared, they can be placed in an appropriate container and labeled for treatment of an indicated condition. Such labeling would include amount, frequency, and method of administration.

Therapeutic Indications and Methods

DCC-like polypeptides and polynucleotides can be used to modulate nerve cell growth, especially axon outgrowth, and to regulate the location of neuron growth and the termination of neuron growth. DCC-like polypeptides and polynucleotides are therefore useful to modulate neuronal growth regenerative capacity, i.e. the regeneration of axons in adult nervous system after, for example, injury or trauma, to diagnose genetic neurological defects, and to treat neurodegenerative disease. Such diseases include, for example, paralysis, Huntington's disease, Charcot-Marie-Tooth disease, Friedreich's ataxia, Hallervorden-Spatz disease, Leigh's disease, olivopontocerebellar atrophy, and Rett syndrome.

This invention further pertains to the use of novel agents identified by the screening assays described above. Accordingly, it is within the scope of this invention to use a test compound identified as described herein in an appropriate animal model. For example, an agent identified as described herein (e.g., a modulating agent, an antisense nucleic acid molecule, a specific antibody, ribozyme, or a polypeptide- binding partner) can be used in an animal model to determine the efficacy, toxicity, or side effects of treatment with such an agent. Alternatively, an agent identified as described herein can be used in an animal model to determine the mechanism of action of such an agent. Furthermore, this invention pertains to uses of novel agents identified by the above-described screening assays for treatments as described herein.

A reagent which affects DCC-like activity can be administered to a mammalian cell, preferably to a human cell, cither ;^'/; vitro or in vivo, to reduce or increase a DCC-like function, such as netrin binding. The reagent can optionally bind to an expression product of a DCC-like gene. If the expression product is a polypeptide, for example, the reagent can be an antibody or a small chemical compound. For treatment of human cells ex vivo, a reagent can be added to a preparation of stem cells which have been removed from the body. The cells can then be replaced in the same or another human body, with or without clonal propagation, as is known in the art.

Alternatively, a reagent can be a DCC-like polynucleotide which can be supplied to a cell to increase a DCC-like function.

In one embodiment, the reagent is delivered using a liposome. Preferably, the liposome is stable in the animal into which it has been administered for at least about

30 minutes, more preferably for at least about 1 hour, and even more preferably for at least about 24 hours. A liposome comprises a lipid composition that is capable of targeting a reagent, particularly a polynucleotide, to a particular site in an animal, such as a human. Preferably, the lipid composition of the liposome is capable of targeting to a specific organ of an animal, such as the lung or liver.

A liposome useful in the present invention comprises a lipid composition that is capable of fusing with the plasma membrane of the targeted cell to deliver its contents to the cell. Preferably, the transfection efficiency of a liposome is about 0.5 g of DNA per 16 nmole of liposome delivered to about 10⁶ cells, more preferably about 1.0 g of DNA per 16 nmol of liposome delivered to about 10⁶ cells, and even more preferably about 2.0 g of DNA per 16 nmol of liposome delivered to about 10 cells. Preferably, a liposome is between about 100 and 500 nm, more preferably between about 150 and 450 nm, and even more preferably between about 200 and 400 nm in diameter.

Suitable liposomes for use in the present invention include those liposomes standardly used in, for example, gene delivery methods kno n to those of skill in the art. More preferred liposomes include liposomes

ιng a polycationic hpid composition and or liposomes having a cholesterol backbone conjugated to pol> - ethylene glycol Optionally, a liposome comprises a compound capable of targeting the liposome to a tumor cell, such as a tumor cell ligand exposed on the outer surface of the liposome.

Complexing a liposome with a reagent such as an antisense oligonucleotide or ribozyme can be achieved using methods which are standard in the art (see, for example, U.S. Patent 5,705,151). Preferably, from about 0.1 μg to about 10 μg of polynucleotide is combined with about 8 nmol of liposomes, more preferably from about 0.5 μg to about 5 μg of polynucleotides are combined with about 8 nmol liposomes, and even more preferably about 1.0 μg of polynucleotides is combined with about 8 nmol liposomes.

In another embodiment, antibodies can be delivered to specific tissues in vivo using receptor-mediated targeted delivery. Receptor-mediated DNA delivery techniques are taught in, for example, Findeis et al. Trends in Biotechnol. 11, 202-05 (1993); Chiou et al, GENE THERAPEUTICS: METHODS AND APPLICATIONS OF DIRECT GENE

TRANSFER (J.A. Wolff, ed.) (1994); Wu & Wu, J. Biol. Chem. 263, 621-24 (1988); Wu et al, J. Biol. Chem. 269, 542-46 (1994); Zenke et al, Proc. Natl. Acad. Sci. U.S.A. 87, 3655-59 (1990); Wu et al, J. Biol. Chem. 266, 338-42 (1991).

If the reagent is a single-chain antibody, a polynucleotide encoding the antibody can be constructed and introduced into a cell either ex vivo or in vivo using well- established techniques including, but not limited to, transferrin-polycation-mediated DNA transfer, transfection with naked or encapsulated nucleic acids, liposome- mediated cellular fusion, intracellular transportation of DNA-coated latex beads, protoplast fusion, viral infection, electroporation, "gene gun," and DEAE- or calcium phosphate-mediated transfection.

Effective in vivo dosages of an antibody are in the range of about 5 μg to about

50 μg kg. about 50 μg to about 5 g/kg, about 100 μg to about 500 μg kg of patient body weight, and about 200 to about 250 μg/kg of patient body weight. For administration of polynucleotides encoding single-chain antibodies, effective in vivo dosages are in the range of about 100 ng to about 200 ng, 500 ng to about 50 mg, about 1 μg to about 2 mg, about 5 μg to about 500 μg, and about 20 μg to about 100 μg of DNA.

If the expression product is mRNA, the reagent is preferably an antisense oligonucleotide or a ribozyme. Polynucleotides which express antisense oligonucleotides or ribozymes can be introduced into cells by a variety of methods, as described above.

Preferably, a reagent reduces or increases expression of a DCC-like gene or the activity of a DCC-like polypeptide by at least about 10, preferably about 50, more preferably about 75, 90, or 100% relative to the absence of the reagent. The effectiveness of the mechanism chosen to decrease the level of expression of a DCC- like gene or the activity of a DCC-like polypeptide can be assessed using methods well known in the art, such as hybridization of nucleotide probes to DCC-like- specific mRNA, quantitative RT-PCR, immunologic detection of a DCC-like polypeptide, or measurement of DCC-like activity.

In any of the embodiments described above, any of the pharmaceutical compositions of the invention can be administered in combination with other appropriate therapeutic agents. Selection of the appropriate agents for use in combination therapy can be made by one of ordinary skill in the art, according to conventional pharmaceutical principles. The combination of therapeutic agents can act synergistically to effect the treatment or prevention of the various disorders described above. Using this approach, one may be able to achieve therapeutic efficacy with lower dosages of each agent, thus reducing the potential for adverse side effects.

Determination of a Therapeutically Effective Dose

Determination of a therapeutically effective dose is well within the capability of those skilled in the art. A therapeutically effective dose refers to that amount of active ingredient which increases or decreases DCC-like activity relative to DCC-like activity which occurs in the absence of the therapeutically effective dose.

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

Therapeutic efficacy and toxicity, e g , ED₅₀ (the dose therapeutically effective in

50%) of the population) and LD₅₀ (the dose lethal to 50% of the population), can be determined by standard pharmaceutical procedures in cell cultures or experimental animals. The dose ratio of toxic to therapeutic effects is the therapeutic index, and it can be expressed as the ratio, LD₅₀/ED₅Q.

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 contained in such compositions is preferably within a range of circulating concentrations that include the ED₅o 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 will be determined by the practitioner, in light of factors related to the subject that requires treatment. Dosage and administration are adjusted to provide sufficient levels of the active ingredient or to maintain the desired effect.

Factors which can be taken into account include the severity of the disease state, general health of the subject, age, weight, and gender of the subject, diet, time and frequency of administration, drug combιnatιon(s), reaction sensitivities, and tolerance/response to therapy Long-acting pharmaceutical compositions can be administered every 3 to 4 days, every week, or once every two weeks depending on the half-life and clearance rate of the particular formulation. Normal dosage amounts of any particular reagent can 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 and generally available to practitioners in the art. Those skilled in the art will employ different formulations for nucleotides than for polypeptides or their inhibitors. Similarly, delivery of polynucleotides or polypeptides will be specific to particular cells, conditions, locations, etc.

Any of the therapeutic methods described above can be applied to any subject in need of such therapy, including, for example, mammals such as dogs, cats, cows, horses, rabbits, monkeys, and most preferably, humans.

The above disclosure generally describes the present invention, and all patents and patent applications cited in this disclosure are expressly incorporated herein. A more complete understanding can be obtained by reference to the following specific examples which are provided for purposes of illustration only and are not intended to limit the scope of the invention.

EXAMPLE 1

Detection of DCC-like protein activity

The polynucleotide of SEQ ID NO. 1 is inserted into the expression vector pCEV4 and the expression vector pCEV4-DCC-like polypeptide obtained is transfected into human embryonic kidney 293 cells. The cells are scraped from a culture flask into 5 ml of Tris HC1, 5 mM EDTA, pH 7.5, and lysed by sonication. Cell lysates are centrifuged at 1000 rpm for 5 minutes at 4 °C. The supernatant is centrifuged at 30,000 x g for 20 minutes at 4 °C. The pellet is suspended in binding buffer containing 50 mM Tris HC1, 5 mM MgSO₄, 1 mM EDTA, 100 mM NaCl, pH 7.5, supplemented with 0.1 % BSA, 2 μg/ml aprotinin, 0.5 mg/ml leupeptin, and 10 μg/ml phosphoramidon. Optimal membrane suspension dilutions, defined as the protein concentration required to bind less than 10 % of an added radioligand, i.e. ¹²⁵I-labeled netrin, are added to 96-well polypropylene microtiter plates containing ligand, non-labeled peptides, and binding buffer to a final volume of 250 ml.

In equilibrium saturation binding assays, membrane preparations are incubated in the presence of increasing concentrations (0.1 nM to 4 nM) of I ligand.

Binding reaction mixtures are incubated for one hour at 30°C. The reaction is stopped by filtration through GF/B filters treated with 0.5% polyethyleneimine, using a cell harvester. Radioactivity is measured by scintillation counting, and data are analyzed by a computerized non-linear regression program. Non-specific binding is defined as the amount of radioactivity remaining after incubation of membrane protein in the presence of 100 nM of unlabeled peptide. Protein concentration is measured by the Bradford method using Bio-Rad Reagent, with bovine serum albumin as a standard. The DCC-like protein activity of the polypeptide comprising the amino acid sequence of SEQ ID NO 2 is demonstrated. EXAMPLE 2

Radioligand binding assays

Human embryonic kidney 293 cells transfected with a polynucleotide which expresses human DCC-like receptor-like protein are scraped from a culture flask into 5 ml of Tris HC1, 5 mM EDTA, pH 7.5, and lysed by sonication. Cell lysates are centrifuged at 1000 rpm for 5 minutes at 4°C. The supernatant is centrifuged at 30,000 x g for 20 minutes at 4°C. The pellet is suspended in binding buffer containing 50 mM Tris HC1, 5 mM MgSO₄, 1 mM EDTA, 100 mM NaCl, pH 7.5, supplemented with 0.1 % BSA, 2 μg/ml aprotinin, 0.5 mg/ml leupeptin, and 10 μg/ml phosphoramidon. Optimal membrane suspension dilutions, defined as the protein concentration required to bind less than 10 % of the added radioligand, i.e. ¹²⁵I-labeled netrin, are added to 96-well polypropylene microtiter plates containing ligand or test compound, non-labeled peptides, and binding buffer to a final volume of 250 ml.

In equilibrium saturation binding assays, membrane preparations are incubated in the

1 ? presence of increasing concentrations (0.1 nM to 4 nM) of I ligand or test compound (specific activity 2200 Ci/mmol). The binding affinities of different test compounds are determined in equilibrium competition binding assays, using 0.1 nM

¹²⁵I-peptide in the presence of twelve different concentrations of each test compound.

Binding reaction mixtures are incubated for one hour at 30 °C. The reaction is stopped by filtration through GF/B filters treated with 0.5% polyethyleneimine, using a cell harvester. Radioactivity is measured by scintillation counting, and data are analyzed by a computerized non-linear regression program.

Non-specific binding is defined as the amount of radioactivity remaining after incubation of membrane protein in the presence of 100 nM of unlabeled peptide.

Protein concentration is measured by the Bradford method using Bio-Rad Reagent, with bovine serum albumin as a standard. A test compound which increases the radioactivity of membrane protein by at least 15%> relative to radioactivity of membrane protein which was not incubated with a test compound is identified as a compound which binds to a human DCC-like protein.

EXAMPLE 3

Identification of a test compound which binds to a DCC-like polypeptide

Purified DCC-like polypeptides comprising a glutathione-S-transferase protein are absorbed onto glutathione-derivatized wells of 96-well microtiter plates and are contacted with test compounds from a small molecule library at pH 7.0 in a physiological buffer solution. DCC-like polypeptides comprise an amino acid sequence shown in SEQ ID NO. , 4, or 6. The test compounds comprise a fluorescent tag. The samples are incubated for 5 minutes to one hour. Control samples are incubated in the absence of a test compound.

The buffer solution containing the test compounds is washed from the wells. Binding of a test compound to a DCC-like polypeptide is detected by fluorescence measurements of the contents of the wells. A test compound which increases the fluorescence in a well by at least 15% relative to fluorescence of a well in which a test compound was not incubated is identified as a compound which binds to a DCC- like polypeptide.

EXAMPLE 4

Regulation of axon outgrowth in an injured spinal cord

Synthesis of DCC-like antisense oligonucleotides comprising at least 1 1 contiguous nucleotides selected from SEQ ID NO. 1 or the complement of SEQ ID NOS: 3 or 5 is performed on a Pharmacia Gene Assembler series synthesizer using the phosphoramidite procedure (Uhlmann et al, Chem. Rev. 90, 534-83, 1990). Following assembly and deprotection, oligonucleotides are ethanol-precipitated twice, dried, and suspended in phosphate-buffered saline (PBS) at the desired concentration. Purity of these oligonucleotides is tested by capillary gel electrophoreses and ion exchange HPLC. Endotoxin levels in the oligonucleotide preparation are determined using the Limulus Amebocyte Assay (Bang, Biol. Bull. (Woods Hole, Mass.) 105, 361-362, 1953).

An aqueous composition containing the oligonucleotides or polypeptides at a concentration of 0.1-100 μM is injected, for example, directly into an injured spinal cord with a needle.

The injured spinal cord is monitored over a period of days or weeks. Additional injections of the oligonucleotides can be given during that time. Axon outgrowth from neurons in the injured spinal cord is increased.

EXAMPLE 5

Regulation of axon outgrowth

The effect of test compounds which bind to human DCC-like protein is tested by isolating and culturing explants of El l and E13 rat dorsal spinal cord in collagen gels. See Keino-Masu et al. (1996) Cell 87, 115. A test compound which binds to human DCC-like protein is added to explants at concentrations varying from 100 ng/ml, 300 ng/ml, 500 ng/ml, 1 μg/ml, to 10 μg/ml. Axon outgrowth from the explants in the presence of the test compound is determined by adding the lengths of all axons from each cxplant (regardless of bundle thickness), providing the "total axon length" for each cxplant. EXAMPLE 6

The effect of test compounds which bind to and block netrin binding of human DCC- like proteins is tested by isolating and culturing explants of El l and E13 rat dorsal spinal cord in collagen gels. See Keino-Masu et al.(\996) Cell 87:175. Blocking of axon outgrowth is accomplished by adding 0.1, 10, 100, or 1000 μg/ml of a monoclonal anti-DCC-like antibody to the cells. Axon outgrowth is measured as for Example 3.

EXAMPLE 7

The effect of test compounds on the binding of DCC-like polypeptides to netrin.

To screen test compounds for the ability to regulate DCC-like protein binding to netrin, cDNA encoding a DCC-like polypeptide is transfected into 293-EBNA cells using LipofectAMINE(GIBCO-BRL). See Keino-Masu et a/. (1996). Forty-eight hours after transfection, the cells are incubated with 2 μg/ml chick netrin protein in PBS supplemented with 10%> horse serum and 0.1 % sodium azide in the presence or absence of 2 μg/ml heparin at room temperature for 90 minutes. The cells are washed three times with PBS and fixed with methanol. Double staining of transfected gene products and bound netrin is carried out using antibodies to DCC- like protein and an anti-netrin antibody. Expression of the transfected proteins is detected using FITC-labeled secondary antibodies and bound netrin is visualized with a Cy3 -labeled secondary antibody. Test compounds are added to the cultured cells at varying concentrations, and binding of DCC-like protein to netrin is observed. A test compound which increases or decreases binding of DCC-like protein to netrin is identified as a potential agent for regulating axon outgrowth.

Claims

1. An isolated polynucleotide encoding a DCC-like polypeptide and being selected from the group consisting of:

amino acid sequences which are at least about 50% identical to the amino acid sequence shown in SEQ ID NO. 2; the amino acid sequence shown in SEQ ID NO. 2; amino acid sequences which are at least about 50% identical to the amino acid sequence shown in SEQ ID NO. 4; the amino acid sequence shown in SEQ ID NO. 4; amino acid sequences which are at least about 50% identical to the amino acid sequence shown in SEQ ID NO. 6; and the amino acid sequence shown in SEQ ID NO. 6.

b) a polynucleotide comprising the sequence of SEQ ID NOS: 1, 3 or 5;

d) a polynucleotide the sequence of which deviates from the poly- nucleotide sequences specified in (a) to (c) due to the degeneration of the genetic code; and

e) a polynucleotide which represents a fragment, derivative or allehc variation of a polynucleotide sequence specified in (a) to (d)

2. An expression vector containing any polynucleotide of claim 1.

3. A host cell containing the expression vector of claim 2.

4. A substantially purified DCC-like polypeptide encoded by a polynucleotide of claim 1.

5. A method for producing a DCC-like polypeptide, wherein the method comprises the following steps:

a) culturing the host cell of claim 3 under conditions suitable for the expression of the DCC-like polypeptide; and

b) recovering the DCC-like polypeptide from the host cell culture.

6. A method for detection of a polynucleotide encoding a DCC-like polypetide in a biological sample comprising the following steps:

a) hybridizing any polynucleotide of claim 1 to a nucleic acid material of a biological sample, thereby forming a hybridization complex; and

b) detecting said hybridization complex.

7. The method of claim 6, wherein before hybridization, the nucleic acid material of the biological sample is amplified.

8. A method for the detection of a polynucleotide of claim 1 or a DCC-like polypeptide of claim 5 comprising the steps of contacting a biological sample with a reagent which specifically interacts w ith the polynucleotide or the DCC-like polypeptide.

9. A diagnostic kit for conducting the method of any one of claims 6 to S.

10. A method of screening for agents which decrease the activity of a DCC-like protein, comprising the steps of:

contacting a test compound with any DCC-like polypeptide encoded by any polynucleotide of claim 1;

detecting binding of the test compound of the DCC-like polypeptide, wherein a test compound which binds to the polypeptide is identified as a potential therapeutic agent for decreasing the activity of a DCC-like protein.

11. A method of screening for agents which regulate the activity of a DCC-like protein, comprising the steps of:

contacting a test compound with a DCC-like polypeptide encoded by any polynucleotide of claim 1; and

detecting a DCC-like protein activity of the polypeptide, wherein a test compound which increases the DCC-like protein activity is identified as a potential therapeutic agent for increasing the activity of the DCC-like protein, and wherein a test compound which decreases the DCC-like protein activity of the polypeptide is identified as a potential therapeutic agent for decreasing the activity of the DCC-like protein.

12. A method of screening for agents which decrease the activity of a DCC-like protein, comprising the steps of:

contacting a test compound with any polynucleotide of claim 1 and detecting binding of the test compound to the polynucleotide, wherein a test compound which binds to the polynucleotide is identified as a potential therapeutic agent for decreasing the activity of DCC-like protein.

13. A method of reducing the activity of a DCC-like protein, comprising the steps of: contacting a cell with a reagent which specifically binds to any polynucleotide of claim 1 or any DCC-like polypeptide of claim 4, whereby the activity of a DCC-like protein is reduced.

14. A reagent that modulates the activity of a DCC-like polypeptide or a polynucleotide wherein said reagent is identified by the method of any of the claims 10 to 12.

15. A pharmaceutical composition, comprising: the expression vector of claim 2 or the reagent of claim 14 and a pharmaceutically acceptable carrier.

16. Use of the pharmaceutical composition of claim 15 for modulating the activity of a DCC-like protein in a disease.

17. Use of claim 16 wherein the disease is a neural injury, trauma or neurodegenerative disease.

18. Use of the pharmaceutical composition of claim 15 for mediating axon outgrowth.