# Patent

## Title
Modulating Robo: ligand interactions

## Abstract

Disclosed are methods and compositions for identifying agents which modulate the interaction of Robo and a Robo ligand and for modulating the interaction of Robo and a Robo ligand. The methods for identifying Robo:ligand modulators find particular application in commercial drug screens. These methods generally comprise (1) combining a Robo polypeptide, a Slit polypeptide and a candidate agent under conditions whereby, but for the presence of the agent, the Robo and Slit polypeptides engage in a first interaction, and (2) determining a second interaction of the Robo and Slit polypeptides in the presence of the agent, wherein a difference between the first and second interactions indicates that the aget modulates the interaction of the Robo and Slit polypeptides. The subject methods of modulating the interaction of Robo and a Robo ligand involve combining a Robo polypeptide, a Slit polypeptide and a modulator under conditions whereby, but for the presence of the modulator, the Robo and Slit polypeptides engage in a first interaction, whereby the Robo and Slit polypeptides engage in a second interaction different from the first interaction. In a particular embodiment, the modulator is dominant negative form of the Robo or Slit polypeptide.

## Background
This application is a continuation of and claims the benefit of U.S. application Ser. No. 09/922,600, filed Aug. 3, 2001, abandoned which is a continuation of and claims the benefit of U.S. application Ser. No. 09/540,245, filed Mar. 31, 2000, now U.S. Pat. No. 6,270,984, which is a divisional of and claims the benefit of U.S. application Ser. No. 09/191,647, filed Nov. 13, 1998, now U.S. Pat. No. 6,046,015 which claims the benefit of U.S. Provisional Application No. 60/081,057 filed Apr. 07, 1998 and U.S. Provisional Application No. 60/065,544, filed Nov. 14, 1997, all of which are incorporated herein by reference.


The research carried out in the subject application was supported in part by NIH grant NS18366. The government may have rights in any patent issuing on this application.


INTRODUCTION
Field of the Invention
The field of this invention is methods for modulating nerve cell function.
BACKGROUND
In the developing CNS, most growth cones confront the midline at one or multiple times during their journey and make the decision of whether to cross or not to cross. This decision is not a static one but rather changes according to the growth cone's history. For example, in the Drosophila ventral nerve cord, about 10% of the interneurons project their axons only on their own side, in some cases extending near the midline without crossing it. The other 90% of the interneurons first project their axons across the midline and then turn to project longitudinally on the other side, often extending near the midline. These growth cones, having crossed the midline once, never cross it again, in spite of their close proximity to the midline and the many commissural axons crossing it. This decision to cross or not to cross is not unique to Drosophila but is common to a variety of midline structures in all bilaterally symmetric nervous systems.
What midline signals and growth cone receptors control whether growth cones do or do not cross the midline? After crossing once, what mechanism prevents these growth cones from crossing again? A related issue concerns the nature of the midline as an intermediate target. If so many growth cones find the midline such an attractive structure, why do they cross over it rather than linger? Why do they leave the midline?
One approach to find the genes encoding the components of such a system is to screen for mutations in which either too many or too few axons cross the midline. Such a large-scale mutant screen was previously conducted in Drosophila, and led to the identification of two key genes: commissureless (comm) and roundabout (robo) (Seeger et al., 1993; reviewed by Tear et al., 1993). In comm mutant embryos, commissural growth cones initially orient toward the midline but then fail to cross it and instead recoil and extend on their own side. robo mutant embryos, on the other hand, display the opposite phenotype in that too many axons cross the midline; many growth cones that normally extend only on their own side instead now project across the midline and axons that normally cross the midline only once instead appear to cross and recross multiple times (Seeger et al, 1993; present disclosure). Double mutants of comm and robo display a robo-like phenotype.
How do comm and robo function to control midline crossing? Neither the initial paper on these genes (Seeger et al., 1993) nor the cloning of comm (Tear et al., 1996) resolved this question. comm encodes a novel surface protein expressed on midline cells. In fact, the comm paper (Tear et al., 1996) ended with the hope that future work would “ . . . help shed some light on the enigmatic function of Comm.”
U.S. Ser. No. 08/971,172 (Robo, A Novel Family of Polypeptides and Nucleic Acids, by inventors: Corey S. Goodman, Thomas Kidd, Kevin J. Mitchell and Guy Tear, now abandoned) discloses the cloning and characterization of robo in various species including Drosophila; Robo polypeptides and polypeptide-encoding nucleic acids are also disclosed and their genbank accession numbers referenced in Kidd et al. (1998) Cell 92, 205-215. robo encodes a new class of guidance receptor with 5 immunoglobulin (Ig) domains, 3 fibronectin type III domains, a transmembrane domain, and a long cy subfamily of Ig superfamily proteins that is highly conserved from fruit flies to mammals. The Robo ectodomains, and in particular the first two Ig domains, are highly conserved from fruit fly to human, while the cytoplasmic domains are more divergent. Nevertheless, the cytoplasmic domains contain three highly conserved short proline-rich motifs which may represent binding sites for SH3 or other binding domains in linker or signaling molecules.
For those axons that never cross the midline, Robo is expressed on their growth cones from the outset; for the majority of axons that do cross the midline, Robo is expressed at high levels on their growth cones only after they cross the midline. Transgenic rescue experiments in Drosophila reveal that Robo can function in a cell autonomous fashion, consistent with it functioning as a receptor. Thus, in Drosophila, Robo appears to function as the gatekeeper controlling midline crossing; growth cones expressing high levels of Robo are prevented from crossing the midline. Robo proteins in mammals function in a similar manner in controlling axon guidance.
U.S. Ser. No. 60/065,54 (Methods for Modulating Nerve Cell Function, by inventors: Corey S. Goodman, Thomas Kidd, Guy Tear, Claire Russell and Kevin Mitchell) discloses ectopic and overexpression studies revealing that Comm down-regulates Robo expression, demonstrating that Comm functions to suppress the Robo-mediated midline repulsion. These results show that the levels of Comm at the midline and Robo on growth cones are tightly intertwined and dynamically regulated to assure that only certain growth cones cross the midline, that those growth cones that cross do not linger at the midline, and that once they cross they never do so again.
Relevant Literature
Seeger, M., Tear, G., Ferres-Marco, D. and Goodman C. S. (1993) Neuron 10,409-426; Tear G., et al. (1996) Neuron 16, 501-514; Rothberg et al. (1990) Genes Dev 4, 2169-2187; Kidd et al. (1998) Cell 92, 205-215.
SUMMARY OF THE INVENTION
The invention provides methods and compositions relating to vertebrate Slit1 and Slit2, collectively vertebrate Slit) polypeptides, related nucleic acids, polypeptide domains thereof having vertebrate Slit-specific structure and activity, and modulators of vertebrate Slit function. Vertebrate Slit polypeptides can regulate cell, especially nerve cell, function and morphology. The polypeptides may be produced recombinantly from transformed host cells from the subject vertebrate Slit polypeptide encoding nucleic acids or purified from mammalian cells. The invention provides isolated vertebrate Slit hybridization probes and primers capable of specifically hybridizing with natural vertebrate Slit genes, vertebrate Slit-specific binding agents such as specific antibodies, and methods of making and using the subject compositions in diagnosis (e.g. genetic hybridization screens for vertebrate Slit transcripts), therapy (e.g. to modulate nerve cell growth) and in the biopharmaceutical industry (e.g. as immunogens, reagents for isolating vertebrate Slit genes and polypeptides, reagents for screening chemical libraries for lead pharmacological agents, etc.).
The invention also provides methods and compositions for identifying agents which modulate the interaction of Robo and a Robo ligand and for modulating the interaction of Robo and a Robo ligand. The methods for identifying Robo:ligand modulators find particular application in commercial drug screens. These methods generally comprise (1) combining a Robo polypeptide, a Slit polypeptide and a candidate agent under conditions whereby, but for the presence of the agent, the Robo and Slit polypeptides engage in a first interaction, and (2) determining a second interaction of the Robo and Slit polypeptides in the presence of the agent, wherein a difference between the first and second interactions indicates that the aget modulates the interaction of the Robo and Slit polypeptides. The subject methods of modulating the interaction of Robo and a Robo ligand involve combining a Robo polypeptide, a Slit polypeptide and a modulator under conditions whereby, but for the presence of the modulator, the Robo and Slit polypeptides engage in a first interaction, whereby the Robo and Slit polypeptides engage in a second interaction different from the first interaction. In a particular embodiment, the modulator is dominant negative form of the Robo or Slit polypeptide.


DETAILED DESCRIPTION OF THE INVENTION
The subject methods include screens for agents which modulate Robo:ligand interactions and methods for modulating Robo:ligand interactions. Robo activation is found to regulate a wide variety of cell functions, including cell-cell interactions, cell mobility, morphology, etc. Slit polypeptides are disclosed as specific activators and inactivators of Robo polypeptides. Accordingly, the invention provides methods for modulating targeted cell function comprising the step of modulating Robo activation by contacting the cell with a modulator of a Robo:Slit interaction.
The targeted Robo polypeptide is generally naturally expressed on the targeted cells. The nucleotide sequences of exemplary natural cDNAs encoding drosophila 1, drosophila 2, C. elegans, human 1, human 2 and mouse 1 Robo polypeptides and their translates are described in Kidd et al. (1998) Cell 92, 205-215 and U.S. Ser. No. 08/971,172. The targeted Robo polypeptides comprise at least a functional Robo domain, which domain has Robo-specific amino acid sequence and binding specificity or function. Preferred Robo domains comprise at least 8, preferably at least 16, more preferably at least 32, most preferably at least 64 consecutive residues of a natural full length Robo. In a particular embodiment, the domains comprise one or more structural/functional Robo immunoglobulin, fibronectin or cytoplasmic motif domains described herein. The subject domains provide Robo-specific antigens and/or immunogens, especially when coupled to carrier proteins. For example, peptides corresponding to Robo- and human Robo-specific domains are covalently coupled to keyhole limpet antigen (KLH) and the conjugate is emulsified in Freunds complete adjuvant. Laboratory rabbits are immunized according to conventional protocol and bled. The presence of Robo-specific antibodies is assayed by solid phase immunosorbant assays using immobilized Robo polypeptides. Generic Robo-specific peptides are readily apparent as conserved regions in aligned Robo polypeptide sequences. In addition, species-specific antigenic and/or immunogenic peptides are readily apparent as diverged extracellular or cytosolic regions in alignments Human Robo-specific antibodies are characterized as uncross-reactive with non-human Robo polypeptides.
The subject domains provide Robo domain specific activity or function, such as Robo-specific cell, especially neuron modulating or modulating inhibitory activity, Robo-ligand-binding or binding inhibitory activity. Robo-specific activity or function may be determined by convenient in vitro, cell-based, or in vivo assays: e.g. in vitro binding assays, cell culture assays, in animals (e.g. gene therapy, transgenics, etc.), etc. The binding target may be a natural intracellular binding target, a Robo regulating protein or other regulator that directly modulates Robo activity or its localization; or non-natural binding target such as a specific immune protein such as an antibody, or a Robo specific agent such as those identified in screening assays such as described below. Robo-binding specificity may be assayed by binding equilibrium constants (usually at least about 107 M−1, preferably at least about 108 M−1, more preferably at least about 109 M−1), by the ability of the subject polypeptide to function as negative mutants in Robo-expressing cells, to elicit Robo specific antibody in a heterologous host (e.g a rodent or rabbit), etc.
Similarly, the Slit polypeptide is conveniently selected from Slit polypeptides which specifically activate or inhibit the activation of the Robo polypeptide. Exemplary suitable Slit polypeptides (a) comprises a vertebrate Slit sequence disclosed herein, especially human Slit-1 (SEQ ID NO:02), or a deletion mutant thereof which specifically modulates Robo expression or a sequence about 60-70%, preferably about 70-80%, more preferably about 80-90%, more preferably about 90-95%, most preferably about 95-99% similar to a vertebrate Slit sequence disclosed herein as determined by Best Fit analysis using default settings and is other than a natural drosophila Slit sequence, preferably other than a natural invertebrate Slit sequence, and/or (b) is encoded by a nucleic acid comprising a natural Slit encoding sequence (such as a natural human Slit-1 encoding sequence, SEQ ID NO:01) or a fragment thereof at least 36, preferably at least 72, more preferably at least 144, most preferably at least 288 nucleotides in length which specifically hybridizes thereto. Suitable deletion mutants are readily screened in Robo binding or activation assays as described herein. Preferred Slit domains/deletion mutants/fragments comprise at least 8, preferably at least 16, more preferably at least 32, most preferably at least 64 consecutive residues of a disclosed vertebrate Slit sequences and provide a Slit specific activity, such as Slit-specific antigenicity and/or immunogenicity, especially when coupled to carrier proteins as described above for Robo above. Suitable natural Slit encoding sequence fragments are of length sufficient to encode such Slit domains. In a particular embodiment, the Slit fragments comprise species specific fragments; such fragments are readily discerned from alignments of the disclosed sequences, see, e.g. shown as unboxed sequences in Tables 1 and 2.







TABLE 1





Alignment of human Slit-1 (SEQ ID NO:02), human Slit-2 (SEQ ID NOS:03-06), Drosophila


Slit-1 (SEQ ID NO:07), C. elegans Slit-1 (SEQ ID NOS:08-09), mouse Slit-2 (SEQ ID NOS:10-


11) and mouse Slit-1 (SEQ ID NOS:12-14).




























































































































































































































































































































TABLE 2





Alignment of human Slit-1 (SEQ ID NO:02) and Drosophila Slit-1 (SEQ ID NO:07)














































































































































































































































































































Exemplary such human Slit-1 immunogenic and/or antigenic peptides are shown in Table 3.








TABLE 3







Immunogenic human Slit-1 polypeptides eliciting Slit-1 specific


rabbit polyclonal antibody: Slit polypeptide-KLH conjugates


immunized per protocol described above.










Slit Polypeptide
Immunogenicity







SEQ ID NO:02, res. 1-10
+++



SEQ ID NO:02, res. 29-41
+++



SEQ ID NO:02, res. 75-87
+++



SEQ ID NO:02, res. 92-109
+++



SEQ ID NO:02, res. 132-141
+++



SEQ ID NO:02, res. 192-205
+++



SEQ ID NO:02, res. 258-269
+++



SEQ ID NO:02, res. 295-311
+++



SEQ ID NO:02, res. 316-330
+++



SEQ ID NO:02, res. 373-382
+++



SEQ ID NO:02, res. 403-422
+++



SEQ ID NO:02, res. 474-485
+++



SEQ ID NO:02, res. 561-576
+++



SEQ ID NO:02, res. 683-697
+++



SEQ ID NO:02, res. 768-777
+++



SEQ ID NO:02, res. 798-813
+++



SEQ ID NO:02, res. 882-894
+++



SEQ ID NO:02, res. 934-946
+++



SEQ ID NO:02, res. 1054-1067
+++



SEQ ID NO:02, res. 1181-1192
+++



SEQ ID NO:02, res. 1273-1299
+++



SEQ ID NO:02, res. 1383-1397
+++



SEQ ID NO:02, res. 1468-1477
+++



SEQ ID NO:02, res. 1508-1517
+++










The subject domains provide Slit domain specific activity or function, such as Slit-specific cell, especially neuron modulating or modulating inhibitory activity, Slit-ligand-binding or binding inhibitory activity. Slit-specific activity or function may be determined by convenient in vitro, cell-based, or in vivo assays: e.g. in vitro binding assays, cell culture assays, in animals (e.g. gene therapy, transgenics, etc.), etc. The binding target may be a natural intracellular binding target, a Slit regulating protein or other regulator that directly modulates Slit activity or its localization; or non-natural binding target such as a specific immune protein such as an antibody, or a Slit specific agent such as those identified in screening assays such as described below. Slit-binding specificity may be assayed by binding equilibrium constants (usually at least about 107 M−1, preferably at least about 108 M−1, more preferably at least about 109 M−1), by the ability of the subject polypeptide to function as negative mutants in Slit-expressing cells, to elicit Slit specific antibody in a heterologous host (e.g a rodent or rabbit), etc.
In one embodiment, the Slit polypeptides are encoded by a nucleic acid comprising SEQ ID NO:01 or a fragment thereof which hybridizes with a full-length strand thereof, preferably under stringent conditions. Such nucleic acids comprise at least 36, preferably at least 72, more preferably at least 144 and most preferably at least 288 nucleotides of SEQ ID NO:01. Demonstrating specific hybridization generally requires stringent conditions, for example, hybridizing in a buffer comprising 30% formamide in 5×SSPE (0.18 M NaCl, 0.01 M NaPO4, pH 7.7, 0.001 M EDTA) buffer at a temperature of 42° C. and remaining bound when subject to washing at 42° C. with 0.2×SSPE (Conditions I); preferably hybridizing in a buffer comprising 50% formamide in 5×SSPE buffer at a temperature of 42° C. and remaining bound when subject to washing at 42° C. with 0.2×SSPE buffer at 42° C. (Conditions II). Exemplary nucleic acids which hybridize with a strand of SEQ ID NO:01 are shown in Table 4.







TABLE 4







Exemplary nucleic acids which hybridize with a strand of


SEQ ID NO:01 under Conditions I and/or II.










Slit Nucleic Acid
Hybridization







SEQ ID NO:01, nucl. 1-47
+



SEQ ID NO:01, nucl. 58-99
+



SEQ ID NO:01, nucl. 95-138
+



SEQ ID NO:01, nucl. 181-220
+



SEQ ID NO:01, nucl. 261-299
+



SEQ ID NO:01, nucl. 274-315
+



SEQ ID NO:01, nucl. 351-389
+



SEQ ID NO:01, nucl. 450-593
+



SEQ ID NO:01, nucl. 524-546
+



SEQ ID NO:01, nucl. 561-608
+



SEQ ID NO:01, nucl. 689-727
+



SEQ ID NO:01, nucl. 708-737
+



SEQ ID NO:01, nucl. 738-801
+



SEQ ID NO:01, nucl. 805-854
+



SEQ ID NO:01, nucl. 855-907
+



SEQ ID NO:01, nucl. 910-953
+



SEQ ID NO:01, nucl. 1007-1059
+



SEQ ID NO:01, nucl. 1147-1163
+



SEQ ID NO:01, nucl. 1258-1279
+



SEQ ID NO:01, nucl. 1375-1389
+



SEQ ID NO:01, nucl. 1581-1595
+



SEQ ID NO:01, nucl. 1621-1639
+



SEQ ID NO:01, nucl. 1744-1755
+



SEQ ID NO:01, nucl. 1951-1969
+



SEQ ID NO:01, nucl. 2150-2163
+



SEQ ID NO:01, nucl. 2524-2546
+



SEQ ID NO:01, nucl. 2761-2780
+



SEQ ID NO:01, nucl. 2989-2999
+



SEQ ID NO:01, nucl. 3108-3117
+



SEQ ID NO:01, nucl. 3338-3351
+



SEQ ID NO:01, nucl. 3505-3514
+



SEQ ID NO:01, nucl. 3855-3867
+



SEQ ID NO:01, nucl. 4010-4025
+



SEQ ID NO:01, nucl. 4207-4219
+



SEQ ID NO:01, nucl. 4333-4345
+



SEQ ID NO:01, nucl. 4521-4529
+










A wide variety of cell types express Robo polypeptides subject to regulation by the disclosed methods, including many neuronal cells, transformed cells, infected (e.g. virus) cells, etc. Ascertaining Robo binding or activation is readily effected by binding assays or cells function assays as disclosed herein or in the cited copending applications. Accordingly, indications for the subject methods encompass a wide variety of cell types and function, including axon outgrowth, tumor cell invasion or migration, etc. The target cell may reside in culture or in situ, i.e. within the natural host. For in situ 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 of the 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. Slit polypeptides 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 polypeptides. 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 of the 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.
In one embodiment, the invention provides administering the subject Slit polypeptides in combination with a pharmaceutically acceptable excipient such as sterile saline or other medium, gelatin, an oil, etc. to form pharmaceutically acceptable compositions. The compositions and/or compounds may be administered alone or in combination with any convenient carrier, diluent, etc. and such administration may be provided in single or multiple dosages. Useful carriers include solid, semi-solid or liquid media including water and non-toxic organic solvents. In another embodiment, the invention provides the subject compounds in the form of a pro-drug, which can be metabolically converted to the subject compound by the recipient host. A wide variety of pro-drug formulations for polypeptide-based therapeutics are known in the art. The compositions may be provided in any convenient form including tablets, capsules, troches, powders, sprays, creams, etc. As such the compositions, in pharmaceutically acceptable dosage units or in bulk, may be incorporated into a wide variety of containers. For example, dosage units may be included in a variety of containers including capsules, pills, etc. The compositions may be advantageously combined and/or used in combination with other therapeutic or prophylactic agents, different from the subject compounds. In many instances, administration in conjunction with the subject compositions enhances the efficacy of such agents, see e.g. Goodman & Gilman's The Pharmacological Basis of Therapeutics, 9th Ed., 1996, McGraw-Hill.
In another aspect, the invention provides methods of screening for agents which modulate Robo-Slit interactions. These methods generally involve forming a mixture of a Robo-expressing cell, a Slit polypeptide and a candidate agent, and determining the effect of the agent on the amount of Robo expressed by the cell. The methods are amenable to automated, cost-effective high throughput screening of 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. Cell and animal based neural guidance/repulsion assays are described in detail in the experimental section below.
The amino acid sequences of the disclosed vertebrate Slit polypeptides are used to back-translate Slit polypeptide-encoding nucleic acids optimized for selected expression systems (Holler et al. (1993) Gene 136, 323-328; Martin et al. (1995) Gene 154, 150-166) or used to generate degenerate oligonucleotide primers and probes for use in the isolation of natural Slit-encoding nucleic acid sequences (“GCG” software, Genetics Computer Group, Inc, Madison Wis.). Slit-encoding nucleic acids used in Slit-expression vectors and incorporated into recombinant host cells, e.g. for expression and screening, transgenic animals, e.g. for functional studies such as the efficacy of candidate drugs for disease associated with Slit-modulated cell function, etc.
The invention also provides nucleic acid hybridization probes and replication/amplification primers having a vertebrate Slit cDNA specific sequence comprising a fragment of a disclosed vertebrate cDNA sequence, and sufficient to effect specific hybridization thereto. Such primers or probes are at least 12, preferably at least 24, more preferably at least 36 and most preferably at least 96 nucleotides in length. Demonstrating specific hybridization generally requires stringent conditions, for example, hybridizing in a buffer comprising 30% formamide in 5×SSPE (0.18 M NaCl, 0.01 M NaPO4, pH 7.7, 0.001 M EDTA) buffer at a temperature of 42° C. and remaining bound when subject to washing at 42° C. with 0.2×SSPE; preferably hybridizing in a buffer comprising 50% formamide in 5×SSPE buffer at a temperature of 42° C. and remaining bound when subject to washing at 42° C. with 0.2×SSPE buffer at 42° C. Slit nucleic acids can also be distinguished using alignment algorithms, such as BLASTX (Altschul et al. (1990) Basic Local Alignment Search Tool, J Mol Biol 215, 403-410). In addition, the invention provides nucleic acids having a sequence about 60-70%, preferably about 70-80%, more preferably about 80-90%, more preferably about 90-95%, most preferably about 95-99% similar to a vertebrate Slit sequence disclosed herein as determined by Best Fit analysis using default settings and is other than a natural drosophila Slit sequence, preferably other than a natural invertebrate Slit sequence. In a particular embodiment, the Slit polynucleotide fragments comprise species specific fragments; such fragments are readily discerned from alignments of the disclosed sequences.
The subject nucleic acids are of synthetic/non-natural sequences and/or are recombinant, meaning they comprise a non-natural sequence or a natural sequence joined to nucleotide(s) other than that which it is joined to on a natural chromosome. The subject recombinant nucleic acids comprising the nucleotide sequence of disclosed vertebrate Slit nucleic acids, or fragments thereof, contain such sequence or fragment at a terminus, immediately flanked by (i.e. contiguous with) a sequence other than that which it is joined to on a natural chromosome, or flanked by a native flanking region fewer than 10 kb, preferably fewer than 2 kb, more preferably fewer than 500 bp, which is at a terminus or is immediately flanked by a sequence other than that which it is joined to on a natural chromosome. While the nucleic acids are usually RNA or DNA, it is often advantageous to use nucleic acids comprising other bases or nucleotide analogs to provide modified stability, etc.
The subject nucleic acids find a wide variety of applications including use as translatable transcripts, hybridization probes, PCR primers, diagnostic nucleic acids, etc.; use in detecting the presence of Slit genes and gene transcripts and in detecting or amplifying nucleic acids encoding additional Slit homologs and structural analogs. In diagnosis, Slit hybridization probes find use in identifying wild-type and mutant Slit alleles in clinical and laboratory samples. Mutant alleles are used to generate allele-specific oligonucleotide (ASO) probes for high-throughput clinical diagnoses. In therapy, therapeutic Slit nucleic acids are used to modulate cellular expression or intracellular concentration or availability of active Slit. Exemplary human Slit-1 probes and primers are shown in Table 5 and Table 6.







TABLE 5





Hybridization Probes for Regions of Human Slit-1.
















Hybridization probe for first
SEQ ID NO:01, nucleotides 82-828


leucine rich repeat region


Hybridization probe for second
SEQ ID NO:01, nucleotides 829-1503


leucine rich repeat region


Hybridization probe for third
SEQ ID NO:01, nucleotides 1504-2166


leucine rich repeat region


Hybridization probe for fourth
SEQ ID NO:01, nucleotides 2167-2751


leucine rich repeat region


Hybridization probe for EGF
SEQ ID NO:01, nucleotides 2752-3327


repeats one to five


Hybridization probe for the sixth
SEQ ID NO:01, nucleotides 3328-3461


EGF repeat and preceding spacer


region


Hybridization probe for the 99aa
SEQ ID NO:01, nucleotides 3462-3987


spacer/G-loop region


Hybridization probe for EGF
SEQ ID NO:01, nucleotides 3988-4341


repeats seven to nine


Hybridization probe for the
SEQ ID NO:01, nucleotides 4342-4575


cysteine knot region
















TABLE 6





PCR Primers for regions of Human Slit.
















PCR Primers for first
Forward: SEQ ID NO:01, nucleotides 82-111


leucine rich repeat
Reverse: reverse complement of SEQ ID NO:01,


region
nucleotides 799-828


PCR Primers for
Forward: SEQ ID NO:01, nucleotides 829-858


second leucine rich
Reverse: reverse complement of SEQ ID NO:01,


repeat region
nucleotides 1474-1503


PCR Primers for third
Forward: SEQ ID NO:01, nucleotides 1504-1533


leucine rich repeat
Reverse: reverse complement of SEQ ID NO:01,


region
nucleotides 2137-2166


PCR Primers for
Forward: SEQ ID NO:01, nucleotides 2167-2196


fourth leucine rich
Reverse: reverse complement of SEQ ID NO:01,


repeat region
nucleotides 2722-2751


PCR Primers for EGF
Forward: SEQ ID NO:01, nucleotides 2752-2781


repeats one to five
Reverse: reverse complement of SEQ ID NO:01,



nucleotides 3298-3327


PCR Primers for the
Forward: SEQ ID NO:01, nucleotides 3328-3357


sixth EGF repeat and
Reverse: reverse complement of SEQ ID NO:01,


preceding spacer
nucleotides 3432-3461


region


PCR Primers for the
Forward: SEQ I:01, nucleotides 3462-3491


99aa spacer/G-loop
Reverse: reverse complement of SEQ ID NO:01,


region
nucleotides 3958-3987


PCR Primers for EGF
Forward: SEQ ID NO:01, nucleotides 3988-4017


repeats seven to nine
Reverse: reverse complement of SEQ ID NO:01,



nucleotides 4312-4341


PCR Primers for the
Forward: SEQ ID NO:01, nucleotides 4342-4371


cysteine knot region
Reverse: reverse complement of SEQ ID NO:01,



nucleotides 4546-4575









Leucine rich repeats (LRRs) are predicted by comparison with known proteins and by the presence of a leucine rich core sequence. In slit proteins, the LRRs are flanked by conserved sequences referred to as the amino- and carboxy-flanking regions. These flanking regions are found in other known proteins, but only in a few instances are both the amino- and carboxy-flank regions present in a single protein. The so called “99aa spacer” is actually  ̃200 amino acids in the Drosophila protein and 174 amino acids in Human Slit-1. This region shows homology to the G-loops of laminin A chains.
Cysteine knots are dimerisation domains defined by the presence of six cysteine residues between which disulphide bridges form. The only absolutely conserved residues are the six cysteines, and spacing between them is highly variable, apart from between cysteines 2 and 3, and 5 and 6. The glycine between cysteines 2 and 3 is only present in a subset of cysteine knots. Drosophila slit and Human slit-1 both have an extra cysteine after cysteines 5 and 6: this may serve as an intermolecular bond. Human Slit-1 gene displays the overall structure of the Drosophila gene, and amino acid conservation is found along the entire length of the protein (48% homology at the amino acid sequence excluding the signal sequence; see below). The Human gene has an extra LRR between LRR2 and LRR3 of the first set of LRRs; in the third set, the Human gene has an extra LRR between LRR3 and LRR4. The Human gene has two extra EGF repeats, on either side of the seventh EGF repeat in Drosophila slit.
Isolation of Human Slit-1
Searching of the EST database revealed an EST, ab16g10.r1, with homology to the 99aa spacer region of Drosophila slit. This EST was used to probe a Human fetal brain library (Stratagene), and clones for Human slit-1 were isolated.
Features of Human Slit Predicted Protein













Signal sequence
SEQ ID NO:02, residues 7-24


First amino-flanking sequence
SEQ ID NO:02, residues 28-59


First set of Leucine Rich Repeats
SEQ ID NO:02, residues 60-179



(6 repeats)


First carboxy-flanking sequence
SEQ ID NO:02, residues 180-276


Second amino-flanking sequence
SEQ ID NO:02, residues 277-308


Second set of Leucine Rich
SEQ ID NO:02, residues 309-434


Repeats
(5 repeats)


Second carboxy-flanking sequence
SEQ ID NO:02, residues 435-501


Third amino-flanking sequence
SEQ ID NO:02, residues 502-533


Third set of Leucine Rich Repeats
SEQ ID NO:02, residues 534-560



(5 repeats)


Third carboxy-flanking sequence
SEQ ID NO:02, residues 661-722


Fourth amino-flanking sequence
SEQ ID NO:02, residues 723-754


Fourth set of Leucine Rich Repeats
SEQ ID NO:02, residues 755-855



(4 repeats)


Fourth carboxy-flanking sequence
SEQ ID NO:02, residues 856-917


First EGF repeat
SEQ ID NO:02, residues 918-952


Second EGF repeat
SEQ ID NO:02, residues 953-993


Third EGF repeat
SEQ ID NO:02, residues 994-1031


Fourth EGF repeat
SEQ ID NO:02, residues 1032-1071


Fifth EGF repeat
SEQ ID NO:02, residues 1072-1109


Spacer
SEQ ID NO:02, residues 1110-1116


Sixth EGF repeat
SEQ ID NO:02, residues 1117-1153


“99aa spacer”
SEQ ID NO:02, residues 1155-1329


Seventh EGF repeat
SEQ ID NO:02, residues 1330-1366


Eighth EGF repeat
SEQ ID NO:02, residues 1367-1404


Ninth EGF repeat
SEQ ID NO:02, residues 1405-1447


Cysteine knot motif
SEQ ID NO:02, residues 1448-1525









Amino Acid Identity Between Drosophila and Human Slit-1














First amino-flanking sequence
53%


First set of Leucine Rich Repeats
52%



(54%, 67%, NA, 38%, 54%, 50%)


First carboxy-flanking sequence
42%


Second amino-flanking sequence
50%


Second set of Leucine Rich Repeats
60%



(54%, 58%, 67%, 71%, 50%)


Second carboxy-flanking sequence
62%


Third amino-flanking sequence
56%


Third set of Leucine Rich Repeats
49%



(46%, 46%, 42%, NA, 58%)


Third carboxy-flanking sequence
36%


Fourth amino-flanking sequence
53%


Fourth set of Leucine Rich Repeats
48%



(25%, 58%, 46%, 63%)


Fourth carboxy-flanking sequence
63%


First EGF repeat
34%


Second EGF repeat
46%


Third EGF repeat
46%


Fourth EGF repeat
35%


Fifth EGF repeat
47%


Spacer
22%


Sixth EGF repeat
40%


“99aa spacer”
38%


Seventh EGF repeat
11%/NA


Eighth EGF repeat
44%


Nineth EGF repeat
29%/NA


Cysteine knot motif
34%





NA: not applicable due to absence of homologous repeat. 






Figures for Individual LLRs are Shown in Brackets.

The following examplary assay is offered by way of illustration and not by way of limitation:
EXAMPLES
Protocol for Ligand Screening of Transfected COS Cells
I. Prepare the Ligand
Expression Construct: cDNAs encoding targeted Slit polypeptides are tagged with the Fc portion of human IgG and subcloned into a 293 expression vector (pCEP4: In Vitrogen).
Transfection: 293 EBNA cells are transfected (CaPO4 method) with the Slit expression constructs. After 24 h recovery, transfected cells are selected with G418 (geneticin, 250 ug/ml, Gibco) and hygromycin (200 ug/ml). Once the selection process is complete, cells are maintained in Dulbecco's Modified Eagles medium (DME)/10% FCS under selection.
Preparation of Conditioned Medium: Serum-containing media is replaced with Optimem with glutamax-1 (Gibco) and 300 ng/ml heparin (Sigma), and the cells are conditioned for 3 days. The media is collected and spun at 3,000×g for 10 minutes. The supernatant is filtered (0.45 um) and stored with 0.1% azide at 4° C. for no more than 2 weeks.
II. Prepare Truncated Receptor (Positive Control)
Expression Construct: cDNA encoding a corresponding Robo C-terminal deletion mutant comprising the extracellular domain (truncated immediately N-terminal to the transmembrane region) is subcloned into a 293 expression vector (pCEP4: In Vitrogen).
Transfection: 293 EBNA cells are transfected (CaPO4 method) with the receptor mutant expression construct. After 24 h recovery, transfected cells are selected with G418 (geneticin, 250 ug/ml, Gibco) and hygromycin (200 ug/ml). Once the selection process is complete, cells are maintained in Dulbecco's Modified Eagles medium (DME)/10% FCS under selection.
Preparation of Conditioned Medium: Serum-containing media is replaced with Optimem with glutamax-1 (Gibco) and 300 ng/ml heparin (Sigma), and the cells are conditioned for 3 days. The media is collected and spun at 3,000×g for 10 minutes. The supernatant is filtered (0.45 um) and stored with 0.1% azide at 4° C. for no more than 2 weeks.
II. Transfect COS Cells
Seed COS cells (250,000) on 35 mm dishes in 2 ml DME/10% FCS.
18-24 h later, dilute 1 ug of Robo-encoding DNA (cDNA cloned into pMT21 expression vector) into 200 ul serum-free media and add 6 ul of Lipofectamine (Gibco). Incubate this solution at room temperature for 15-45 min.
Wash the cells 2× with PBS. Add 800 ul serum-free media to the tube containing the lipid-DNA complexes. Overlay this solution onto the washed cells.
Incubate for 6 h. Stop the reaction by adding 1 ml DMA/20% FCS. Refeed cells. Assay cells 12 hr later.
III. Ligand Binding Assay
Wash plates of transfected COS cells 1× with cold PBS (plus Ca/Mg)/1% goat serum. Add 1 ml conditioned media neat and incubate 90 min at room temp.
Wash plates 3× with PBS (plus Ca/Mg). On the 4th wash, add 1 ml 50% methanol to 1 ml PBS. Then add 1 ml methanol. Evacuate and add 1 ml methanol.
Wash 1× with PBS. Wash 1× PBS/1% goat serum.
Add secondary antibody (1-to-2,000 anti-human Fc conjugated to alkaline phosphatase (Jackson Lab)) in PBS/1% goat serum. Incubate 30-40 min room temp.
Wash 3× with PBS. Wash 1× alkaline phosphatase buffer (100 mM Tris-Cl, pH 9.5, 100 mM NaCl, 5 mM MgCl2). Prepare alkaline phosphatase reagents: 4.5 ul/ml NBT and 3.5 ul/ml BCIP (Gibco) in alkaline phosphatase buffer.
Incubate 10-30 min, quench with 20 mM EDTA in PBS. Cells that have bound Slit polypeptides are visible by the presence of a dark purple reaction product.
In parallel incubations, positive controls are provided by titrating Slit binding with serial dilutions of the mutant receptor conditioned medium.
IV. Results: Binding of Slit to Robo
Cell expressing mammalian Slit polypeptides were shown to bind Robo. No reactivity was observed with control COS cells or with receptor-expressing COS cells in the presence of the secondary antibody but in the absence of the Slit-Fc fusion. Binding was observed to receptor-expression cells using a construct in which a Slit polypeptide is fused directly to alkaline phosphatase, for which a secondary antibody is not required. Receptor deletion mutants titrate the Slit-Robo binding, serving as a positive control for inhibition assays.
Protocol for High Throughput Robo-Slit Binding Assay
A. Reagents:


    
    
        Neutralite Avidin: 20 μg/ml in PBS.
        Blocking buffer: 5% BSA, 0.5% Tween 20 in PBS; 1 hour at room temperature.
        Assay Buffer: 100 mM KCl, 20 mM HEPES pH 7.6, 1 mM MgCl2, 1% glycerol, 0.5% NP-40, 50 mM β-mercaptoethanol, 1 mg/ml BSA, cocktail of protease inhibitors.
        33P Robo polypeptide 10× stock: 10−8−10−6 M “cold” Robo polypeptide specific Robo domain supplemented with 200,000-250,000 cpm of labeled Robo (Beckman counter). Place in the 4° C. microfridge during screening.
        Protease inhibitor cocktail (1000×): 10 mg Trypsin Inhibitor (BMB # 109894), 10 mg Aprotinin (BMB # 236624), 25 mg Benzamidine (Sigma # B-6506), 25 mg Leupeptin (BMB # 1017128), 10 mg APMSF (BMB # 917575), and 2 mM NaVO3(Sigma # S-6508) in 10 ml of PBS.
        Slit: 10−7−10−5 M biotinylated Slit in PBS.

B. Preparation of Assay Plates:

        Coat with 120 μl of stock N-Avidin per well overnight at 4° C.
        Wash 2 times with 200 μl PBS.
        Block with 150 μl of blocking buffer.
        Wash 2 times with 200 μl PBS.

C. Assay:

        Add 40 μl assay buffer/well.
        Add 10 μl compound or extract.
        Add 10 μl 33P-Robo (20-25,000 cpm/0.1-10 pmoles/well=10−9−10−7 M final conc).
        Shake at 25° C. for 15 minutes.
        Incubate additional 45 minutes at 25° C.
        Add 40 μM biotinylated Slit (0.1-10 pmoles/40 ul in assay buffer)
        Incubate 1 hour at room temperature.
        Stop the reaction by washing 4 times with 200 μM PBS.
        Add 150 μM scintillation cocktail.
        Count in Topcount.

D. Controls for All Assays (Located on Each Plate):

        a. Non-specific binding
        b. Soluble (non-biotinylated Slit) at 80% inhibition.
    
    


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 incorporated by reference. Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to those of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims.

## Claims

1. An isolated antibody that specifically binds a slit protein comprising the sequence of SEQ. ID NO:2.

2. The antibody of claim 1 which is a polyclonal antibody.

3. The antibody of claim 1 which is a monoclonal antibody.

4. The antibody of claim 1, wherein the antibody is produced using an immunogenic fragment of SEQ. ID NO:2.

5. The antibody of claim 4, wherein the immunogenic fragment of SEQ ID NO:2 is selected from the group consisting of residues 1-10, 29-41, 75-87, 92-109, 132-141, 192-205, 258-269, 295-311, 316-330, 373-382, 403-422, 474-485, 561-576, 683-697, 768-777, 798-813, 882-894, 934-946, 1054-1067, 1181-1192, 1273-1299, 1383-1397, 1468-1477, 1508-1517, of SEQ ID NO:2.

6. A composition comprising an antibody that specifically binds a slit protein comprising the sequence of SEQ ID NO:2.

7. The composition of claim 6, wherein the antibody is a polyclonal antibody.

8. The composition of claim 6, wherein the antibody is a monoclonal antibody.

9. The composition of claim 6, wherein the antibody is produced using an immunogenic fragment of SEQ ID NO:2.

10. The composition of claim 6, wherein the immunogenic fragment of SEQ ID NO:2 is selected from the group consisting of residues 1-10, 29-41, 75-87, 92-109, 132-141, 192-205, 258-269, 295-311, 316-330, 373-382, 403-422, 474-485, 561-576, 683-697, 768-777, 798-813, 882-894, 934-946, 1054-1067, 1181-1192, 1273-1299, 1383-1397, 1468-1477, 1508-1517, of SEQ ID NO:2.

11. The composition of claim 6, further comprising a pharmaceutically acceptable excipient.

12. An isolated antibody that specifically binds a Slit polypeptide comprising SEQ ID NO:2, or a subsequence thereof having at least 16 consecutive amino acids residues thereof and comprising one or more unboxed amino acid residues of SEQ ID NO:2 in at least one table selected from the group consisting of Table 1 and Table 2.

13. An isolated antibody that specifically binds a Slit polypeptide according to claim 12, wherein the Slit polypeptide comprises SEQ ID NO:2, or a subsequence thereof having at least 64 consecutive amino acid residues thereof and comprising one or more unboxed amino acid residues of the corresponding sequence in at least one table selected from the group consisting of Table 1 and Table 2.

14. An isolated antibody that specifically binds a Slit polypeptide consisting of SEQ ID NO:2.

15. An isolated antibody that specifically binds a Slit polypeptide according to claim 12, wherein the Slit polypeptide comprises SEQ ID NO:2, or a subsequence thereof having at least 16 consecutive amino acid residues thereof and comprising one or more unboxed amino acid residues of the corresponding sequence in Table 2.

16. An isolated antibody that specifically binds a Slit polypeptide according to claim 12, wherein the Slit polypeptide comprises SEQ ID NO:2, or a subsequence thereof having at least 64 consecutive amino acid residues thereof and comprising one or more unboxed amino acid residues of the corresponding sequence in Table 2.

17. The antibody of claim 12, wherein the antibody is produced using an immunogenic fragment of SEQ ID NO:2.

18. The antibody of claim 17, wherein the immunogenic fragment of SEQ ID NO:2 is selected from the group of residues 1-10, 29-41, 75-87, 92-109, 132-141, 192-205, 258-269, 295-311, 316-330, 373-382, 403-422, 474-485, 561-576, 683-697, 768-777, 798-813, 882-894, 934-946, 1054-1067, 1181-1192, 1273-1299, 1383-1397, 1468-1477, and 1508-1517 of SEQ ID NO:2.

19. An isolated antibody that specifically binds a fragment of Slit polypeptide SEQ ID NO:2 having one or more Slit domain selected from the group of a leucine rich repeat, an EGF repeat and cysteine knot motif.

20. The antibody of claim 19, wherein the leucine rich repeat is selected from the group of one or more of residues 60-179, 309-434, 534-560, and 755-855 of SEQ ID NO:2.

21. The antibody of claim 19, wherein the EGF repeat is selected from the group of one or more of residues 918-952, 953-993, 994-1031, 1032-1071, 1072-1109, 1117-1153, 1330-1366, 1367-1404, and 1405-1447 of SEQ ID NO:2.

22. The antibody of claim 19, wherein the cysteine knot motif is residues 1448-1525 of SEQ ID NO:2.

23. The antibody of claim 19, wherein the antibody is produced using a leucine rich repeat or EGF repeat fragment of SEQ ID NO:2.

24. The antibody of claim 23, wherein the leucine rich repeat of SEQ ID NO:2 is selected from the group of residues 60-179, 309-434, 534-560, and 755-855 of SEQ ID NO:2.

25. The antibody of claim 23, wherein the EGF repeat of SEQ ID NO:2 is selected from the group of residues 918-952, 953-993, 994-1031, 1032-1071, 1072-1109, 1117-1153, 1330-1366, 1367-1404, and 1405-1447 of SEQ ID NO:2.

26. The antibody of any of claims 12-25 which is a polyclonal antibody.

27. The antibody of any of claims 12-25 which is a monoclonal antibody.

28. A composition comprising an antibody that specifically binds a Slit polypeptide comprising the sequence of SEQ ID NO:2, or a subsequence thereof having at least 16 consecutive amino acid residues thereof and comprising one or more unboxed amino acid residues of SEQ ID NO:2 in at least one table selected from the group consisting of Table 1 and Table 2, further comprising a pharmaceutically acceptable excipient.

29. The composition of claim 28, wherein the antibody is polyclonal antibody.

30. The composition of claim 28, wherein the antibody is a monoclonal antibody.

31. A method of screening for an antibody that modulates Robo/Slit interaction comprising:
(a) forming a mixture of a Robo-expressing cell, a Slit polypeptide comprising the sequence of SEQ ID NO:2, and a candidate antibody; and 
(b) determining the effect of the antibody on the amount of Robo expressed by the cell or on the activity of the Robo expressed by the cell, 

wherein a change in the amount of Robo expressed by the cell or in the activity of the Robo expressed by the cell in the presence of the candidate antibody indicates that the antibody modulates Robo/Slit interaction.