HUMAN NETRIN-1

Abstract: Specific netrin proteins, nucleic acids which encode netrin proteins and hybridization reagents, probes and primers capable of hybridizing with netrin genes and methods for screening chemical libraries for lead compounds for pharmacological agents useful in the diagnosis or treatment of disease associated undesirable cell growth are provided. An exemplary screen involves forming a mixture comprising a recombinant netrin protein, a natural intracellular netrin protein binding target and a candidate pharmacological agent; incubating the mixture under conditions whereby, but for the presence of said candidate pharmacological agent, said netrin protein selectively binds said binding target; and detecting the presence or absence of specific binding of said netrin protein to said binding target.

Description: Human Netrin- 1 INTRODUCTION Field ofthe Invention The field of this invention is human netrin proteins and genes. Background In the developing nervous system, axons project considerable distances along stereotyped pathways to reach their targets. Axon growth and guidance depends partly on the recognition of cell-surface and extracellular matrix cues along these pathways. The identification of such nerve cell growth and guidance cues is the holy grail of neurobiology. These are the compounds that tell neurons when to grow, where to grow, and when to stop growing. The medical applications of such compounds are enormous and include modulating neuronal growth regenerative capacity, treating neurodegenerative disease, and mapping (e.g. diagnosing) genetic neurological defects. Over decades of concentrated research, various hypotheses involving chemo- attractants and repellents, labeled pathways, cell adhesion molecules, etc. have been invoked to explain guidance. Molecules such as N-CAM and N-cadherin have been reported to provide favorable substrates for axon growth and certain sensory axons may be responsive to NGF and NGF-like factors. Recent reports suggest the existence of diffusible chemotropic molecule(s) which influence the pattern and orientation of commissural axon growth. Relevant Literature Ishii et al. (1992) Neuron 9, 873-881 disclose a gene, unc-6, derived from C. elegans, which has sequence similarity to the disclosed netrins. Serafini et al (1994) Cell 78, 409-424 and Kennedy et al (1994) Cell 78, 425-435 at page 5, column 1 describe related vertebrate netrins. The work was also reported in The New York Times, Section B7, Tuesday, August 16, 1994 and more recently (May 19, 1995) described in Science 268, 971-973 (see also references cited therein). SUMMARY OF THE INVENTION The invention provides methods and compositions relating to a human netrin protein and gene. Netrins are a class of proteins which are naturally involved in neural axon guidance. The subject compositions include nucleic acids which encode the specified netrin protein and hybridization probes and primers capable of hybridizing with the specified netrin gene. The netrin proteins finds particular use in modulating neural axon outgrowth. The disclosed compositions also find use variously in screening chemical libraries for regulators of axon outgrowth and orientation, in genetic mapping, as probes for netrin genes, as diagnostic reagents for genetic neurological disease and in the production of specific cellular and animal systems for the development of neurological disease therapy. DETAILED DESCRIPTION OF THE INVENTION The invention provides methods and compositions relating to a human netrin- 1 protein and gene; including methods and compositions for identifying, purifying, characterizing, and producing the subject proteins and for identifying, characterizing, cloning, expressing, inhibiting the expression of and amplifying the subject nucleic acids. The subject proteins may be incomplete translates ofthe disclosed netrin cDNA sequence or deletion mutants ofthe corresponding conceptual translates, which translates or deletion mutants have the human netrin- 1 binding activity and specificity described herein. The netrins are isolated, partially pure or pure and are typically recombinantly produced. An "isolated" protein for example, is unaccompanied by at least some ofthe material with which it is associated in its natural state; generally constituting at least about 0.5%, preferably at least about 2%, and more preferably at least about 10% by weight ofthe total protein in a given sample; and a pure protein constitutes at least about 50%, preferably at least about 90%, and more preferably at least about 99% by weight ofthe total protein in a given sample. A wide variety of molecular and biochemical methods are available for generating and expressing the subject compositions, see e.g. Molecular Cloning, A Laboratory Manual (Sambrook, et al. Cold Spring Harbor Laboratory), Current Protocols in Molecular Biology (Eds. Ausubel, et al., Greene Publ. Assoc, Wiley-Interscience, NY) or that are otherwise known in the art. The disclosed netrin compositions may be used to generate human netrin- 1 specific antibodies, to modulate axon outgrowth or guidance in situ or in vivo, etc. For in vivo applications, the compositions are added to a retained physiological fluid such as blood or synovial fluid. For CNS administration, a variety of techniques are available for promoting transfer ofthe therapeutic 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. Netrins may also be amenable to direct injection or infusion, topical, intratracheal/nasal administration e.g. through aerosol, intraocularly, or within/on implants e.g. fibers e.g. collagen, osmotic pumps, grafts comprising appropriately transformed cells, etc. A particular method of administration involves coating, embedding or derivatizing fibers, such as collagen fibers, protein polymers, etc. with therapeutic proteins. Other useful approaches are described in Otto et al. (1989) J Neuroscience Research 22, 83-91 and Otto and Unsicker (1990) J Neuroscience 10, 1912-1921. Generally, the amount administered will be empirically determined, typically in the range of about 10 to 1000 μg/kg ofthe recipient and the concentration will generally be in the range of about 50 to 500 μg/ml in the dose administered. Other additives may be included, such as stabilizers, bactericides, etc. will be present in conventional amounts. The invention provides netrin-specific binding agents including isolated binding targets such as membrane-bound netrin receptors and netrin-specific antibodies and binding agents identified in screens of natural and synthetic chemical libraries, and methods of identifying and making such agents, and their use in diagnosis, therapy and pharmaceutical development. Generally, netrin-specificity ofthe binding agent is shown by binding equilibrium constants. Such agents are capable of selectively binding the specified netrin, i.e. with an equilibrium constant at least about 10 7 M ', preferably at least about 10 8 M "1 , more preferably at least about IO 9 M" 1 . A wide variety of cell-based and cell-free assays may be used to demonstrate netrin-specific binding; preferred are rapid in vitro, cell-free assays such as mediating or inhibiting netrin-cell/protein binding, immunoassays, etc. The invention also provides nucleic acids encoding the subject proteins, which nucleic acids may be part of netrin-expression vectors and may be incoφorated into recombinant cells for expression and screening, transgenic animals for functional studies (e.g. the efficacy of candidate drugs for neural disease or injury), etc. and nucleic acid hybridization probes and replication/amplification primers having a disclosed netrin cDNA specific sequence. The hybridization probes contain a sequence common or complementary to the corresponding netrin gene sufficient to make the probe capable of specifically hybridizing to the corresponding netrin gene, and only to the corresponding netrin gene, in the presence of other netrin genes. Hence, the subject probes and primers are uniquely specific to the disclosed cDNA. Hybridization probes having in excess of 100 continuous bases of netrin gene sequence are generally capable of hybridizing to the corresponding netrin cDNA and remaining bound at a reduced final wash stringency of 0.2 X SSC (0.9 M saline/0.09 M sodium citrate) and 0.1% SDS buffer at a temperature of 65 °C. The subject nucleic acids are isolated, meaning they comprise a sequence joined to a nucleotide other than that which it is joined to on a natural chromosome, and usually constitute at least about 0.5% , preferably at least about 2%, and more preferably at least about 5% by weight of total nucleic acid present in a given fraction. A pure nucleic acid constitutes at least about 50%, preferably at least about 90%, and more preferably at least about 95% by weight of total nucleic acid present in a given fraction. The subject nucleic acids find a wide variety of applications including use as translatable transcripts, hybridization probes, PCR primers, therapeutic nucleic acids, etc.; use in detecting the presence of netrin genes and gene transcripts, e.g. allele-specific oligonucleotide (ASO) probes use to identify wild-type and mutant netrin alleles in clinical and laboratory samples, in detecting or amplifying nucleic acids encoding other netrins, and in gene therapy applications, e.g. antisense oligonucleotides capable of inhibiting the intracellular expression of a targeted netrin transcript. The invention provides efficient methods of identifying pharmacological agents or lead compounds for agents capable of mimicking or modulating netrin function (e.g. bioactive netrin deletion mutants and netrin peptides). A wide variety of screens may be used; for example, cell-based assays may be used for monitoring netrin function and in vitro binding assays may be used to identify netrin-specific binding agents. Kennedy et al. (1994) Cell 78, 425-435 describe a particularly convenient COS cell-based netrin expression assay. Preferred methods are amenable to automated, cost-effective high throughput screening of natural and synthetic chemical libraries for lead compounds. Identified reagents find use in the pharmaceutical industries for animal and human trials; for example, the reagents may be derivatized and rescreened in in vitro and in vivo assays to optimize activity and minimize toxicity for pharmaceutical development. EXAMPLES Human Netrin 1 (SEQ ID NO:2^ and cDNA fSEO ID NO: R We isolated chicken netrin 1 and 2 cDNAs as described in Serafini et al. (1974) Cell 78:409-424. Based on the chick netrin 1 and 2 cDNA sequences, we designed degenerate oligonucleotide primers and used these primers to amplify a cDNA encoding mouse netrin 1 from a murine cDNA library. We then isolated a human netrin cDNA using degenerate oligonucleotide primers constructed using amino acid sequences conserved in chick and mouse netrin sequences as a guide. The starting material for PCR was 100 ng of human genomic DNA. Two rounds of PCR amplification were used. In the first round, the following program and conditions were used: 1. 94°C 30 sec; 2. 50°C 45 sec; 3. 72°C, 1 minute; 4. go to 1, 30 times; 5. 4°C; 6. end. In the second round of PCR amplification, nested PCR and the following conditions and program were used: 1. 94 °C 1 minute; 2. 42 °C 1 minute; 3. increments of 1 °C every 5 seconds to 72°C; 4. 72°C for 3 minutes; 5. go to 1, 2 times; 6. 94°C for 1 minute; 7. 46°C for 1 minute; 8. increments of 1 °C every 6 seconds until 72°C; 9. 72°C 2 minutes; 10. go to 6, 7 times; 11. 94°C for 1 minute; 12. 55 °C for 1 minute; 13. 72 °C 2 minute; 14. go to 11, 24 times; 15. 94°C for 1 minute; 16. 55°C for 1 minute; 17. 72°C for 10 minutes; 18. 4°C; 19. end. PCR products were subcloned and individual clones containing inserts corresponding to human netrin sequence isolated using a Grunstein and Hogness screen (Sambrook, 1989). 32 P was incorporated into a probe using PCR with a portion ofthe mouse netrin- 1 cDNA clone as a template. The final wash of the filters was at a reduced stringency of IX SSC and 0.1%SDS at 65 °C (Sambrook et al., 1989). This screen isolated an approximately 140 base pair human netrin cDNA clone. This cDNA fragment was used to isolate a longer human netrin cDNA from a Human fetal brain cDNA library (Stratagene cat#936206). The -140 base pair human netrin cDNA was used as a template and 32 P incorporated into a human netrin cDNA probe using PCR. 1X10 6 clones were screened at high stringency (Sambrook et al., 1989) identifying a single approximately 7 kb netrin cDNA (HBC-1, deposited with ATCC June 7, 1995, as plasmid HN-1, deposit number 97204). Sequence analysis determined that an EcoRI subclone ofthe 7 kb HBC-1 clone corresponded to a splice variant of human netrin- 1. The first 1086 base pairs of sequence show high homology to mouse netrin- 1 and the remaining 626 base pairs are highly divergent. A potential splice donor site is identified at the junction of the netrin and the divergent sequence. A clone that corresponds to the 3' end of human netrin- 1 was isolated using reverse transcription and PCR with a 5' primer at position 999 ofthe human sequence and a 3' degenerate primer to the last 15 base pairs ofthe mouse netrin sequence. Three additional independent clones were isolated to confirm the sequence of the PCR reaction product. The region of overlap between this new clone and the HBC-1 Eco clone is 46 base pairs and is identical in sequence. To verify the overlap, an additional clone was isolated using a 5' primer at position 818 and a 3' primer at position 1582 ofthe human netrin- 1 sequence. Two independent clones isolated using these primers confirm the structure ofthe cDNA. Finally, the sequence encoding the C-terminal 5 amino acids was confirmed. A primer was designed to a region within the 3' untranslated region that is conserved between chicken and mouse netrin- 1. A PCR product was generated using this primer and a 5' primer in the human sequence at position 1568 and the sequence was verified. RT-PCR procedures were as follows: fetal brain RNA (19-23 weeks) was obtained from Clontech. RT-PCR was performed using the GeneAmp Thermostable rTth Reverse Transcriptase RNA PCR Kit from Perkin Elmer. A hot start technique was used to denature the RNA by mixing 50 ng with 30 pmol degenerate primer deg-1, 1 μl 10X rTth Reverse Transcriptase Buffer (Perkin Elmer) and water in a total volume of 7.2 μl; this mixture was heated to 95° C for 2 minutes, followed by a 5 minute incubation at 70 °C. The reaction was cooled to 60 °C and reverse transcription was begun by adding a mixture containing 1 μl 10 mM MnCl 2 , 1 μl rTth DNA polymerase (Perkin Elmer, 2.5 U), and 0.2 μl each lOmM dATP, dCTP, dGTP, and dTTP . The 60 °C incubation was continued for 5 minutes, followed by two 5 minute incubations at 65 °C and 70°C. The reaction was then chilled on ice. To amplify the human netrin- 1 fragment by PCR, a mixture containing 2 μl DMSO, 3 μl 25 mM MgCl 2 , 4 μl 10X Chelating Buffer (Perkin Elmer) and 34.5 μl water was added to the reverse transcription reaction. 30 pmol of a human netrin-specific primer, h-net- 5'999, was added (0.5 μl) to the mixture and PCR was carried out in an MJ Research PTC- 200 Peltier Thermal Cycler using the "Calculated" temperature control method and the following conditions: 1) 95° C for 2 minutes; 2) 55° C for 25 seconds; 3) 95° C for 10 seconds; 4) Repeat steps 2-3, 34 times; 5) 60° C for 7 minutes; and 6) 4° C hold. The reaction was analyzed by gel electrophoresis and transferred to nylon membrane. Netrin-specific products were detected by Southern hybridization using a mouse netrin probe corresponding to sequence from position 1342 to position 1875 of mouse netrin. A plug of agarose corresponding to the cross hybridizing fragment (migrating at approximately 850 bp) was extracted with a Pasteur pipet and reamplified as follows: the agarose plug was combined with a reaction mixture containing 1.25 μl formamide, 5 μl of 10X PCR Buffer II (Perkin Elmer), 5 μl of 25 mM MgCl 2 , 30 pmol human netrin-specific primer h-net-5'999, 30 pmol degenerate netrin primer deg-1, 5 U AmpliTaq DNA Polymerase (Perkin Elmer), and sterile water in a total volume of 49 μl. PCR was carried out in an MJ Research PTC- 200 Peltier Thermal Cycler using the "Block" temperature control method and the following conditions: 1) 95° C for 2 minutes; 2) 50° C for 1 minute; 3) 75° C for 1 minute, 30 seconds; 4) 95 ° C for 20 seconds; 5) Repeat steps 2- 4, 39 times; 6) 75° C for 10 minutes; and 7) 4° C hold. The reaction was analyzed by gel electrophoresis and a band of DNA at approximately 850 bp was purified using the BioRad Prep-A-Gene system, ligated with the TA cloning vector (InVitroGen), and transformed into DH5α competent bacterial cells. Colonies were analyzed for the correct size insert by colony PCR, grown overnight at 37° C in LB media containing lOOμg/ml ampicillin, and DNA was prepared from the culture using a Qiagen Tip- 100 column. The inserts were confirmed by restriction digests and the sequence was generated using an ABI 377 automated sequencer. To confirm the last 15 nucleotides ofthe human netrin- 1 clone, the 3' end ofthe clone was amplified from first strand cDNA using a 5' primer to known sequence and a 3' primer to sequence in the 3' untranslated region ofthe mouse netrin- 1 clone. First, cDNA was synthesized as described in "Rapid Amplification of cDNA Ends," by Michael Frohman (In: PCR Primer: A Laboratory Manual, C.W. Dieffenbach and G.S. Dveksler, eds., Cold Spring Harbor Laboratory Press, 1995) using the protocol described in the section "3 '-End cDNA Amplification" (pp. 388-389), and 1 μg fetal brain poly A+ RNA (Clontech). 1 μl of the diluted cDNA was amplified in a 50 μl reaction containing 67 mM Tris HCI, pH 9.0, 6.7 mM magnesium chloride, 16.6 mM ammonium sulfate, 0.17 mg/ml BSA, 10 % DMSO, 1.5 mM each dNTP, 30 pmol 5' primer "h-net 5' 1449" and 30 pmol 3' primer "m-net 3' UT 2238". The primer "h-net 5 '1449" corresponds to sequence beginning at position 1449 in the human netrin- 1 clone. The primer "m-net 3' UT 2238" corresponds to sequence in the 3' untranslated region of mouse netrin- 1, with the addition of an Xba I restriction site sequence at the 5' end. Taq DNA polymerase, 1 μl, (Perkin Elmer) was combined with 0.5 μl TaqStart Antibody (ClonTech) and 2.5 μl TaqStart Antibody Dilution Buffer, incubated at room temperature for 10 minutes, and added to the PCR reaction mixture. The reaction was amplified in an MJ Research PTC-200 Peltier Thermal Cycler using the "Calculated" temperature control method and the following conditions: 1) 95° C for 2 minutes; 2) 62° C for 30 seconds; 3) 57° C for 30 seconds; 4) 52° C for 10 seconds; 5) 72° C for 40 minutes; 6) 94° C for 10 seconds; 7) 62° C for 1 minute; 8) 72° C for 3 minutes; 9) Repeat steps 6-8, 4 times; 10) 94° C for 10 seconds; 11) 57° C for 1 minute; 12) 72° C for 3 minutes; 13) Repeat steps 10-12, 4 times; 14) 94° C for 10 seconds; 15) 52° C for 1 minute; 16) 72° C for 3 minutes; 17) Repeat steps 14-16, 24 times; 18) 75° C for 10 minutes; 19) 4° C hold. The reaction was diluted 1 :20 in TE, and 1 μl was re-amplified in a 50 μl reaction containing 67 mM Tris HCI, pH 9.0, 6.7 mM magnesium chloride, 16.6 mM ammonium sulfate, 0.17 mg/ml BSA, 10 % DMSO, 1.5 mM each dNTP, 30 pmol ofthe 5' primer "h-net 5' 1702," 30 pmol ofthe 3' primer "m-net 3' UT 2238" and 0.25 ul Taq DNA Polymerase. The primer "m-net 5' 1702" corresponds to sequence beginning at position 1568 in the human netrin- 1 clone. The reaction was amplified in an MJ Research PTC -200 Peltier Thermal Cycler using the "Calculated" temperature control method and the following conditions: 1) 95° C for 2 minutes; 2) 94° C for 10 seconds; 3) 58° C for 1 minute; 4) 72° C for 3 minutes; 5) Repeat steps 2-4, 4 times; 6) 94° C for 10 seconds; 7) 54° C for 45 seconds; 8) 72° C for 3 minutes; 9) Repeat steps 6-8, 4 times; 10) 94° C for 10 seconds; 11) 50° C for 30 seconds; 12) 72° C for 3 minutes; 13) Repeat steps 10-12, 24 times; 14) 75° C for 5 minutes; and 15) 4° C hold. The reaction was analyzed by gel electrophoresis and a 530 bp product was isolated from the gel using the Prep-A-Gene System (BioRad). The product was ligated into pCR 2.1 (InVitroGen) overnight at 14° C. Transformants were cultured overnight in LB media containing 100 μg/ml ampicillin and DNA was purified from cultures using Easy Pure Plasmid Preps (Super Mini, Primm Labs). DNA sequence was generated using an ABI 377 automated sequencer. To confirm the 3' end sequence, two additional fragments spanning the 3' end of human netrin were generated by PCR using the m-net 5' 1702 primer and a 3' primer, h-net 3' 1959 corresponding to sequence in the 3 1 untranslated region of human netrin- 1. Amplification with these primers generated products of approximately 390 base pairs in duplicate reactions. The fragments were amplified in an MJ Research PTC-200 Peltier Thermal Cycler using the "Calculated" temperature control method and the following conditions: 1) 95° C for 2 minutes; 2) 94° C for 10 seconds; 3) 58° C for 1 minute; 4) 72° C for 3 minutes; 5) Repeat steps 2-4, 4 times; 6) 94° C for 10 seconds; 7) 54° C for 45 seconds; 8) 72° C for 3 minutes; 9) Repeat steps 6-8, 4 times; 10) 94° C for 10 seconds; 11) 50° C for 30 seconds; 12) 72° C for 3 minutes; 13) Repeat steps 10-12, 19 times; 14) 75° C for 5 minutes; and 15) 4° C hold. The reactions were analyzed by gel electrophoresis to confirm their size, and directly sequenced using an ABI 377 automated sequencer. All publications and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incoφorated by reference. Although the foregoing invention has been described in some detail by way of illustration and example for puφoses of clarity of understanding, it will be readily apparent to those of ordinary skill in the art in light ofthe teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope ofthe appended claims. SEQUENCE LISTING (1) GENERAL INFORMATION: (i) APPLICANTS: EXELIXIS PHARMACEUTICALS AND THE REGENTS OF THE UNIVERSITY OF CALIFORNIA (ii) TITLE OF INVENTION: HUMAN NETRIN-1 (iii) NUMBER OF SEQUENCES: 2 (iv) CORRESPONDENCE ADDRESS: (A) ADDRESSEE: SCIENCE & TECHNOLOGY LAW GROUP (B) STREET: 268 BUSH STREET, SUITE 3200 (C) CITY: SAN FRANCISCO (D) STATE: CALIFORNIA (E) COUNTRY: USA (F) ZIP: 94104 (v) COMPUTER READABLE FORM: (A) MEDIUM TYPE: Floppy disk (B) COMPUTER: IBM PC compatible (C) OPERATING SYSTEM: PC-DOS/MS-DOS (D) SOFTWARE: Patentln Release #1.0, Version #1.30 (vi) CURRENT APPLICATION DATA: (A) APPLICATION NUMBER: (B) FILING DATE: (C) CLASSIFICATION: (viii) ATTORNEY/AGENT INFORMATION: (A) NAME: OSMAN, RICHARD A (B) REGISTRATION NUMBER: 36,627 (C) REFERENCE/DOCKET NUMBER: UC93-300-6PCT (ix) TELECOMMUNICATION INFORMATION: (A) TELEPHONE: (415) 343-4341 (B) TELEFAX: (415) 343-4342 (2) INFORMATION FOR SEQ ID NO: 1 : (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 1848 base pairs (B) TYPE: nucleic acid (C) STRANDEDNESS: single (D) TOPOLOGY: linear (ii) MOLECULE TYPE: CDNA (ix) FEATURE: (A) NAME/KEY: CDS (B) LOCATION: 34..1845 (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 1 : GGCGCGGCAG GGCCGGGGCA AGCTGGACGC AGC ATG ATG CGC GCA GTG TGG GAG 54 Met Met Arg Ala Val Trp Glu 1 5 GCG CTG GCG GCG CTG GCG GCG GTG GCG TGC CTG GTG GGC GCG GTG CGC 102 Ala Leu Ala Ala Leu Ala Ala Val Ala Cys Leu Val Gly Ala Val Arg 10 15 20 GGC GGG CCC GGG CTC AGC ATG TTC GCG GGC CAG GCG GCG CAG CCC GAT 150 Gly Gly Pro Gly Leu Ser Met Phe Ala Gly Gin Ala Ala Gin Pro Asp 25 30 35 CCC TGC TCG GAC GAG AAC GGC CAC CCG CGC CGC TGC ATC CCG GAC TTT 198 Pro Cys Ser Asp Glu Asn Gly His Pro Arg Arg Cys lie Pro Asp Phe 40 45 50 55 GTC AAT GCG GCC TTC GGC AAG GAC GTG CGC GTG TCC AGC ACC TGC GGC 246 Val Asn Ala Ala Phe Gly Lys Asp Val Arg Val Ser Ser Thr Cys Gly 60 65 70 CGG CCC CCG GCG CGC TAC TGC GTG GTG AGC GAG CGC GGC GAG GAG CGG 294 Arg Pro Pro Ala Arg Tyr Cys Val Val Ser Glu Arg Gly Glu Glu Arg 75 80 85 CTG CGC TCG TGC CAC CTC TGC AAC GCG TCC GAC CCC AAG AAG GCG CAC 342 Leu Arg Ser Cys His Leu Cys Asn Ala Ser Asp Pro Lys Lys Ala His 90 95 100 CCG CCC GCC TTC CTC ACC GAC CTC AAC AAC CCG CAC AAC CTG ACG TGC 390 Pro Pro Ala Phe Leu Thr Asp Leu Asn Asn Pro His Asn Leu Thr Cys 105 110 115 TGG CAG TCC GAG AAC TAC CTG CAG TTC CCG CAC AAC GTC ACG CTC ACA 438 Trp Gin Ser Glu Asn Tyr Leu Gin Phe Pro His Asn Val Thr Leu Thr 120 125 130 135 CTG TCC CTC GGC AAG AAG TTC GAA GTG ACC TAC GTG AGC CTG CAG TTC 486 Leu Ser Leu Gly Lys Lys Phe Glu Val Thr Tyr Val Ser Leu Gin Phe 140 145 150 TGC TCG CCG CGG CCC GAG TCC ATG GCC ATC TAC AAG TCC ATG GAC TAC 534 Cys Ser Pro Arg Pro Glu Ser Met Ala lie Tyr Lys Ser Met Asp Tyr 155 160 165 GGG CGC ACG TGG GTG CCC TTC CAG TTC TAC TCC ACG CAG TGC CGC AAG 582 Gly Arg Thr Trp Val Pro Phe Gin Phe Tyr Ser Thr Gin Cys Arg Lys 170 175 180 ATG TAC AAC CGG CCG CAC CGC GCG CCC ATC ACC AAG CAG AAC GAG CAG 630 Met Tyr Asn Arg Pro His Arg Ala Pro lie Thr Lys Gin Asn Glu Gin 185 190 195 GAG GCC GTG TGC ACC GAC TCG CAC ACC GAC ATG CGC CCG CTC TCG GGC 678 Glu Ala Val Cys Thr Asp Ser His Thr Asp Met Arg Pro Leu Ser Gly 200 205 210 215 GGC CTC ATC GCC TTC AGC ACG CTG GAC GGG CGG CCC TCG GCG CAC GAC 726 Gly Leu lie Ala Phe Ser Thr Leu Asp Gly Arg Pro Ser Ala His Asp 220 225 230 TTC GAC AAC TCG CCC GTG CTG CAG GAC TGG GTC ACG GCC ACA GAC ATC 774 Phe Asp Asn Ser Pro Val Leu Gin Asp Trp Val Thr Ala Thr Asp lie 235 240 245 CGC GTG GCC TTC AGC CGC CTG CAC ACG TTC GGC GAC GAG AAC GAG GAC 822 Arg Val Ala Phe Ser Arg Leu His Thr Phe Gly Asp Glu Asn Glu Asp 250 255 260 GAC TCG GAG CTG GCG CGC GAC TCG TAC TTC TAC GCG GTG TCC GAC CTG 870 Asp Ser Glu Leu Ala Arg Asp Ser Tyr Phe Tyr Ala Val Ser Asp Leu 265 270 275 CAG GTG GGC GGC CGG TGC AAG TGC AAC GGC CAC GCG GCC CGC TGC GTG 918 Gin Val Gly Gly Arg Cys Lys Cys Asn Gly His Ala Ala Arg Cys Val 280 285 290 295 CGC GAC CGC GAC GAC AGC CTG GTG TGC GAC TGC AGG CAC AAC ACG GCC 966 Arg Asp Arg Asp Asp Ser Leu Val Cys Asp Cys Arg His Asn Thr Ala 300 305 310 GGC CCG GAG TGC GAC CGC TGC AAG CCC TTC CAC TAC GAC CGG CCC TGG 1014 Gly Pro Glu Cys Asp Arg Cys Lys Pro Phe His Tyr Asp Arg Pro Trp 315 320 325 CAG CGC GCC ACA GCC CGC GAA GCC AAC GAG TGC GTG GCC TGT AAC TGC 1062 Gin Arg Ala Thr Ala Arg Glu Ala Asn Glu Cys Val Ala Cys Asn Cys 330 335 340 AAC CTG CAT GCC CGG CGC TGC CGC TTC AAC ATG GAG CTC TAC AAG CTT 1110 Asn Leu His Ala Arg Arg Cys Arg Phe Asn Met Glu Leu Tyr Lys Leu 345 350 355 TCG GGG CGC AAG AGC GGA GGT GTC TGC CTC AAC TGT CGC CAC AAC ACC 1158 Ser Gly Arg Lys Ser Gly Gly Val Cys Leu Asn Cys Arg His Asn Thr 360 365 370 375 GCC GGC CGC CAC TGC CAT TAC TGC AAG GAG GGC TAC TAC CGC GAC ATG 1206 Ala Gly Arg His Cys His Tyr Cys Lys Glu Gly Tyr Tyr Arg Asp Met 380 385 390 GGC AAG CCC ATC ACC CAC CGG AAG GCC TGC AAA GCC TGT GAT TGC CAC 1254 Gly Lys Pro lie Thr His Arg Lys Ala Cys Lys Ala Cys Asp Cys His 395 400 405 CCT GTG GGT GCT GCT GGC AAA ACC TGC AAC CAA ACC ACC GGC CAG TGT 1302 Pro Val Gly Ala Ala Gly Lys Thr Cys Asn Gin Thr Thr Gly Gin Cys 410 415 420 CCC TGC AAG GAC GGC GTG ACG GGT ATC ACC TGC AAC CGC TGC GCC AAA 1350 Pro Cys Lys Asp Gly Val Thr Gly lie Thr Cys Asn Arg Cys Ala Lys 425 430 435 GGC TAC CAG CAG AGC CGC TCT CCC ATC GCC CCC TGC ATA AAG ATC CCT 1398 Gly Tyr Gin Gin Ser Arg Ser Pro lie Ala Pro Cys lie Lys lie Pro 440 445 450 455 GTA GCG CCG CCG ACG ACT GCA GCC AGC AGC GTG GAG GAG CCT GAA GAC 1446 Val Ala Pro Pro Thr Thr Ala Ala Ser Ser Val Glu Glu Pro Glu Asp 460 465 470 TGC GAT TCC TAC TGC AAG GCC TCC AAG GGG AAG CTG AAG ATT AAC ATG 1494 Cys Asp Ser Tyr Cys Lys Ala Ser Lys Gly Lys Leu Lys lie Asn Met 475 480 485 AAA AAG TAC TGC AAG AAG GAC TAT GCC GTC CAG ATC CAC ATC CTG AAG 1542 Lys Lys Tyr Cys Lys Lys Asp Tyr Ala Val Gin lie His lie Leu Lys 490 495 500 GCG GAC AAG GCG GGG GAC TGG TGG AAG TTC ACG GTG AAC ATC ATC TCC 1590 Ala Asp Lys Ala Gly Asp Trp Trp Lys Phe Thr Val Asn lie lie Ser 505 510 515 GTG TAT AAG CAG GGC ACG AGC CGC ATC CGC CGC GGT GAC CAG AGC CTG 1638 Val Tyr Lys Gin Gly Thr Ser Arg lie Arg Arg Gly Asp Gin Ser Leu 520 525 530 535 TGG ATC CGC TCG CGG GAC ATC GCC TGC AAG TGT CCC AAA ATC AAG CCC 1686 Trp lie Arg Ser Arg Asp lie Ala Cys Lys Cys Pro Lys lie Lys Pro 540 545 550 CTC AAG AAG TAC CTG CTG CTG GGC AAC GCG GAG GAC TCT CCG GAC CAG 1734 Leu Lys Lys Tyr Leu Leu Leu Gly Asn Ala Glu Asp Ser Pro Asp Gin 555 560 565 AGC GGC ATC GTG GCC GAT AAA AGC AGC CTG GTG ATC CAG TGG CGG GAC 1782 Ser Gly lie Val Ala Asp Lys Ser Ser Leu Val lie Gin Trp Arg Asp 570 575 580 ACG TGG GCG CGG CGG CTG CGC AAG TTC CAG CAG CGT GAG AAG AAG GGC 1830 Thr Trp Ala Arg Arg Leu Arg Lys Phe Gin Gin Arg Glu Lys Lys Gly 585 590 595 AAG TGC AAG AAG GCC TAG 1848 Lys Cys Lys Lys Ala 600 (2) INFORMATION FOR SEQ ID NO:2 : (i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 604 amino acids (B) TYPE: amino acid (D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2 : Met Met Arg Ala Val Trp Glu Ala Leu Ala Ala Leu Ala Ala Val Ala 1 5 10 15 Cys Leu Val Gly Ala Val Arg Gly Gly Pro Gly Leu Ser Met Phe Ala 20 25 30 Gly Gin Ala Ala Gin Pro Asp Pro Cys Ser Asp Glu Asn Gly His Pro 35 40 45 Arg Arg Cys lie Pro Asp Phe Val Asn Ala Ala Phe Gly Lys Asp Val 50 55 60 Arg Val Ser Ser Thr Cys Gly Arg Pro Pro Ala Arg Tyr Cys Val Val 65 70 75 80 Ser Glu Arg Gly Glu Glu Arg Leu Arg Ser Cys His Leu Cys Asn Ala 85 90 95 Ser Asp Pro Lys Lys Ala His Pro Pro Ala Phe Leu Thr Asp Leu Asn 100 105 110 Asn Pro His Asn Leu Thr Cys Trp Gin Ser Glu Asn Tyr Leu Gin Phe 115 120 125 Pro His Asn Val Thr Leu Thr Leu Ser Leu Gly Lys Lys Phe Glu Val 130 135 140 Thr Tyr Val Ser Leu Gin Phe Cys Ser Pro Arg Pro Glu Ser Met Ala 145 150 155 160 He Tyr Lys Ser Met Asp Tyr Gly Arg Thr Trp Val Pro Phe Gin Phe 165 170 175 Tyr Ser Thr Gin Cys Arg Lys Met Tyr Asn Arg Pro His Arg Ala Pro 180 185 190 He Thr Lys Gin Asn Glu Gin Glu Ala Val Cys Thr Asp Ser His Thr 195 200 205 Asp Met Arg Pro Leu Ser Gly Gly Leu He Ala Phe Ser Thr Leu Asp 210 215 220 Gly Arg Pro Ser Ala His Asp Phe Asp Asn Ser Pro Val Leu Gin Asp 225 230 235 240 Trp Val Thr Ala Thr Asp He Arg Val Ala Phe Ser Arg Leu His Thr 245 250 255 Phe Gly Asp Glu Asn Glu Asp Asp Ser Glu Leu Ala Arg Asp Ser Tyr 260 265 270 Phe Tyr Ala Val Ser Asp Leu Gin Val Gly Gly Arg Cys Lys Cys Asn 275 280 285 Gly His Ala Ala Arg Cys Val Arg Asp Arg Asp Asp Ser Leu Val Cys 290 295 300 Asp Cys Arg His Asn Thr Ala Gly Pro Glu Cys Asp Arg Cys Lys Pro 305 310 315 320 Phe His Tyr Asp Arg Pro Trp Gin Arg Ala Thr Ala Arg Glu Ala Asn 325 330 335 Glu Cys Val Ala Cys Asn Cys Asn Leu His Ala Arg Arg Cys Arg Phe 340 345 350 Asn Met Glu Leu Tyr Lys Leu Ser Gly Arg Lys Ser Gly Gly Val Cys 355 360 365 Leu Asn Cys Arg His Asn Thr Ala Gly Arg His Cys His Tyr Cys Lys 370 375 380 Glu Gly Tyr Tyr Arg Asp Met Gly Lys Pro He Thr His Arg Lys Ala 385 390 395 400 Cys Lys Ala Cys Asp Cys His Pro Val Gly Ala Ala Gly Lys Thr Cys 405 410 415 Asn Gin Thr Thr Gly Gin Cys Pro Cys Lys Asp Gly Val Thr Gly He 420 425 430 Thr Cys Asn Arg Cys Ala Lys Gly Tyr Gin Gin Ser Arg Ser Pro He 435 440 445 Ala Pro Cys He Lys He Pro Val Ala Pro Pro Thr Thr Ala Ala Ser 450 455 460 Ser Val Glu Glu Pro Glu Asp Cys Asp Ser Tyr Cys Lys Ala Ser Lys 465 470 475 480 Gly Lys Leu Lys He Asn Met Lys Lys Tyr Cys Lys Lys Asp Tyr Ala 485 490 495 Val Gin He His He Leu Lys Ala Asp Lys Ala Gly Asp Trp Trp Lys 500 505 510 Phe Thr Val Asn He He Ser Val Tyr Lys Gin Gly Thr Ser Arg He 515 520 525 Arg Arg Gly Asp Gin Ser Leu Trp He Arg Ser Arg Asp He Ala Cys 530 535 540 Lys Cys Pro Lys He Lys Pro Leu Lys Lys Tyr Leu Leu Leu Gly Asn 545 550 555 560 Ala Glu Asp Ser Pro Asp Gin Ser Gly He Val Ala Asp Lys Ser Ser 565 570 575 Leu Val He Gin Trp Arg Asp Thr Trp Ala Arg Arg Leu Arg Lys Phe 580 585 590 Gin Gin Arg Glu Lys Lys Gly Lys Cys Lys Lys Ala 595 600

Claims: WHAT IS CLAIMED IS: 1. An isolated netrin comprising the amino acid sequence of SEQ ID NO:2. 2. Isolated human netrin- 1. 3. An isolated nucleic acid encoding a netrin according to claim 1. 4. An isolated nucleic acid according to claim 3, having the nucleotide sequence of SEQ ID NO: l . 5. An isolated hybridization probe having complementarity to a nucleic acid according to claim 4 sufficient to specifically hybridize with said nucleic acid. 6. A method of modulating the growth, differentiation or moφhology of a neuron, said method comprising contacting said neuron with a composition according to claim 1. 7. A method of modulating the growth, differentiation or moφhology of a neuron, said method comprising contacting said neuron with a composition according to claim 5 under conditions whereby said probe hybridizes with an endogenous human netrin-encoding gene or transcript in said neuron. 8. A method of determining the presence of a human netrin gene in sample comprising a nucleic acid, said method comprising contacting said sample with a probe according to claim 5 and detecting the presence of specific hybridization of said probe to said nucleic acid. 9. A method of determining the presence of a human netrin having the amino acid sequence of SEQ ID NO:2 in a sample, said method comprising contacting said sample with an agent which specifically binds said netrin and detecting the presence of specific binding of said agent to said netrin. 10. A method of screening for candidate drugs, said method comprising the steps of: contacting a prospective agent with a mixture comprising a netrin according to claim 1 and a netrin binding target under conditions wherein, but for the presence of said prospective agent, said netrin and said netrin binding target have a first association; detecting a second association between said netrin and said netrin binding target; comparing said first and second association; wherein a difference between said first and second association identifies said prospective agent as a lead pharmaceutical compound which modulates the interaction of said netrin and said netrin binding target.

Inventors: KENNEDY TIMOTHY, LEONARDO DAVID, SERAFINI TITO, SHYIAN ANNE, SWIMMER CANDACE, TESSIER-LAVIGNE MARC, ZHANG YUAN, KENNEDY, TIMOTHY, LEONARDO, DAVID, SERAFINI, TITO, SHYIAN, ANNE, SWIMMER, CANDACE, TESSIER-LAVIGNE, MARC, ZHANG, YUAN
Applicants: EXELIXIS PHARMACEUTICALS INC, UNIV CALIFORNIA, EXELIXIS PHARMACEUTICALS, INC., THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
Application year: 1997
Main classification: C07K1
IPC codes: A61K31, A61K38, A61K45, A61P25, C07K14, C12N15, C12Q1, G01N33