Nucleic acid molecules encoding CASPR/p190

Abstract

The 190 kDa Contactin ASsociated PRotein (CASPR/p190) is identified and is implicated as the bridge between contactin and intracellular second messenger systems for the signal caused by the binding of the carboxy anhydrase domain of RPTP&bgr; to contactin and resulting in neurite growth, differentiation or survival. Mammalian CASPR/p190 cDNAs and proteins are described, including those from human and rat. In addition, particular domains of the proteins are characterized.

Description

[0001] The present application claims priority under 35 U.S.C. §119(e) to provisional application serial No. 60/014,199, filed Mar. 27, 1996, the entire contents of which is incorporated herein by reference in its entirety.

1. INTRODUCTION

[0002] The present invention relates to the 190 Kd neuronal protein (hereinafter “p190”, “CASPR” or “CASPR/p190”) that interacts with contactin, and with the carbonic anhydrase (“CAH”) domain of the receptor-type tyrosine phosphatase RPTP-&bgr;, specific peptides thereof and nucleic acid molecules encoding such p190 proteins and peptides. The protein is also referred to as CASPR, for Contactin ASsociated PRotein. The CAH domain of RPTP&bgr; has previously been identified as a ligand for contactin, and the binding of the CAH domain of RPTP&bgr; to the contactin on neural cells results in neurite growth, differentiation and survival. CASPR/p190 has been identified as a potential bridge that couples contactin, a GPI-linked protein, with intracellular second messenger systems. The invention also relates to compounds that mimic, enhance, or suppress the effects of p190, including those molecules which act downstream in the signal transduction pathway that results from the binding of the ligand to contactin. In addition, the invention also relates to the use of such compounds to treat neurologic diseases including those characterized by insufficient, aberrant, or excessive neurite growth, differentiation or survival.

2. BACKGROUND OF THE INVENTION

[0003] The ability of cells to respond to signals from their microenvironment is a fundamental feature of development. In the developing nervous system, neurons migrate and extend axons to establish their intricate network of synaptic connections (Goodman and Shatz, 1993, Cell/Neuron (Suppl.), 72/10:77-98). During migration and axonal pathfinding, cells are guided by both attractive and repulsive signals (Hynes and Lander, 1992, Cell, 68:303-322; Keynes and Cook, 1992, Lurr. Opin. Neurobiol., 2:55-59). The ability of the neuron to respond to these signals requires cell surface molecules that are able to receive the signal and to transmit it to the cell interior resulting in specific biological responses.

[0004] It is well established that protein tyrosine phosphorylation is responsible for the regulation of many cellular responses to external stimuli crucial for cell growth, proliferation and differentiation (Schlessinger and Ullrich, 1992, Neuron, 9:383-391). Tyrosine phosphorylation has been implicated in several developmental processes in the nervous system. For example, receptor tyrosine kinases were shown to effect neuronal survival (Chao, 1992, Neuron, 9:583-593), and cell fate determination (Zipursky and Rubin, 1994, Annu. Rev. Neurosci., 17:373-397). Non-receptor tyrosine kinases have been shown to be downstream elements in signaling-via cell recognition molecules that play a role in cell guidance and migration (Ignelzi et al., 1994, Neuron, 12:873-884; Umemori et al., 1994, Nature, 367-572-586).

[0005] The transient nature of signaling by phosphorylation requires specific phosphatases for control and regulation (Hunter, 1995, Cell, 80:225-236). Indeed, many protein tyrosine phosphatases have been shown to be expressed in specific regions of the developing brain, including the olfactory neuroepithelium (Walton et al., 1993, Neuron, 11:387-400), the cortex (Sahin et al., 1995, J. Comp. Neurol., 351:617-631), and in retinal Müller glia (Shock et al., 1995, Mol. Brain Res., 28:110-116). Furthermore, expression of several tyrosine phosphatases, such as PTP&agr; (den Hertog et al., 1993, EMBO J., 12:3789-3798), PC12-PTP1 (Sharama and Lombroso, 1995, J. Biol. Chem., 270:49-53) and several forms of LAR (Zhang and Longo, 1995, J. Cell. Biol., 128:415-431) have been found to be regulated during neural differentiation of P19 or PC12 cells.

[0006] Receptor-type tyrosine phosphatases (RPTPs) have been subdivided into several groups based on structural characteristics of their extracellular domains (Charbonneau and Tonks, 1992, Annu. Rev. Cell Biol., 8:463-493; Barnea et al., 1993, Mol. Cell. Biol., 13:1497-1506). RPTP&bgr;/&zgr; and RPTP&ggr; are members of a distinct group of phosphatases, characterized by the presence of a carbonic anhydrase-like domains (CAH), fibronectin type III repeats (FNIII), and a long cysteine free region (spacer domain) in their extracellular domain (Barnea et al., 1993, Mol. Cell. Biol., 13:1497-1506; Krueger et al., 1992, Proc. Natl. Acad. Sci. USA, 89:7417-7421; Levy et al., 1993, J. Biol. Chem., 268:10573-10581). The expression of RPTP&bgr; is restricted to the central and peripheral nervous system, while RPTP&ggr; is expressed both in the developing nervous system, as well as, in a variety of other tissues in adult rat (Canoll et al., 1993, Dev. Brain Res., 75:293-298; Barnea et al., 1993, Mol. Cell. Biol., 13:1497-1506). RPTP&bgr; exists in three forms, one secreted form and two membrane bound forms, that differ by the absence of 860 residues from the spacer domain (Levy et al., 1993, J. Biol. Chem., 268:1053-10582; Maurel et al., 1994, Proc. Natl. Acad. Sci. USA, 91:2512-2516). The secreted form has been identified as a chondroitin sulfate proteoglycan from rat brain called phosphocan (3F8 proteoglycan) (Barnea et al., 1994, Cell, 76:205; Maurel et al., 1994, Proc. Natl. Acad. Sci. USA, 91:2512-2516; Shitara et al., 1994, J. Biol. Chem. 269:20189-20193). The transmembrane form has also been shown to be expressed in a form of a chondroitin sulfate proteoglycan (Barnea et al., 1994, J. Biol. Chem., 269:14349-14352). Purified phosphocan can interact in vitro with the extracellular matrix protein tenascin, and with the adhesion molecules, N-CAM and Ng-CAM (Barnea et al., 1994, J. Biol. Chem., 269:14349-14352; Grumet et al., 1993, J. Cell. Biol., 120:815-824; Grumet et al., 1994, J. Biol. Chem., 269:12142-12146; Milev et al., 1994, J. Cell. Biol., 127:2512-2516).

3. SUMMARY OF THE INVENTION

[0007] The present invention relates to the 190 Kd neuronal protein (hereinafter “p190”, “CASPR” or “CASPR/p190”) that interacts with contactin, and with the carbonic anhydrase (“CAH”) domain of the receptor-type tyrosine phosphatase RPTP-&bgr;, specific peptides thereof and nucleic acid molecules encoding such p190 proteins and peptides.

[0008] The invention further relates to the use of p190 and related compounds to treat neurologic diseases including those characterized by insufficient, aberrant, or excessive neurite growth, differentiation or survival. More specifically, the invention relates to the use of compounds that mimic, enhance or suppress the effects of p190 on neurite growth, differentiation and survival.

[0009] The invention is based, in part, on the discovery that the CAH domain of RPTP&bgr; (RPTP&bgr;-CAH) is the ligand for contactin and that its binding results in neurite growth, differentiation and survival, and on the further discovery that p190 acts as the bridge between contactin and intracellular second messenger systems.

[0010] In the examples described infra, it is shown that receptor phosphatase RPTP&bgr; specifically interacts with two ligands, one on the surface of glial cells, and the other on the surface of neuronal cells. Using expression cloning in COS7 cells and bioaffinity purification, the neuronal ligand was identified to be the rat homologue of the cell recognition molecule contactin (F11/F3). Using combinations of soluble and membrane bound forms of RPTP&bgr; and contactin it is demonstrated that the reciprocal interaction between the two molecules is mediated by the CAH domain of the phosphatase. Moreover, it is found that when used as a substrate, the CAH domain of RPTP&bgr; induced neurite growth, differentiation and survival of primary neurons and IMR-32 neuroblastoma cells. Using antibody perturbation experiments, the contactin ligand was found to be a neuronal receptor for the CAH domain of RPTP&bgr;. The data indicate that the interactions between contactin, a cell recognition molecule, and RPTB&bgr;, a transmembrane protein tyrosine phosphatase, plays an important role in neuronal development and differentiation. As explained more fully in Section 5.2, the further experiments of the examples were conducted to elucidate the interaction between contactin and intracellular second messenger systems. Binding experiments revealed that the interaction between p190 and contactin is important for the role of contactin and RPTP&bgr;-CAH in neuronal growth, development and differentiation.

[0011] 3.1. Definitions

[0012] As used herein, the following terms and abbreviations shall have the meanings indicated below: 1 TABLE 1 base pair(s) bp carbonic anhydrase CAH carbonic anhydrase domain of RPTP&bgr; RPTP&bgr; complementary DNA cDNA counts per minute cpm deoxyribonucleic acid DNA fibronectin type III FNIII glycosyl-phosphatedylinositol GPI kilobase pairs kb kilodation kDa micrograms &mgr;g micrometer &mgr;m nanograms ng nanometer nm nucleotide nt phospholipase C PI-PLC polyacrylamide gel electrophoresis PAGE polymerase chain reaction PCR receptor type tyrosine phosphatase beta RPTP&bgr; ribonucleic acid RNA sodium dodecyl sulfate SDS units u

[0013] As used herein, the word “modulate” shall have its usual meaning, but shall also encompass the meanings of the words enhance, inhibit, and mimic. In addition, as used herein, the word “expression”, when used in connection with a gene such as p190, shall have its usual meaning, but shall also encompass the transcription of the gene, the longevity of the functional mRNA transcribed from the gene, the translation of that mRNA, and the activity of the gene product.

4. DESCRIPTION OF THE DRAWINGS

[0014] FIG. 1 shows the homology between human and rat CASPR/p190 proteins. Also shown are the important domains of the proteins as more fully described infra at Section 5.3.

5. DETAILED DESCRIPTION OF THE INVENTION

[0015] A large group of protein tyrosine phosphatases have structural characteristics suggesting that they function as cell surface receptors. Receptor type tyrosine phosphatase &bgr; (RPTP&bgr;) is expressed in the developing nervous system and it contains a carbonic anhydrase (CAH) domain as well as a fibronectin type III (FNIII) repeat in its extracellular domain. A variety of experiments were conducted to search for ligands of RPTP&bgr;. These experiments led to the surprising recognition that the CAH domain of RPTP&bgr; is a functional ligand for contactin, a GPI-membrane anchored neuronal cell recognition molecule that functions as a receptor on neurons. The CAH domain of RPTP&bgr; (RPTP&bgr;-CAH) induces cell adhesion and neurite growth of primary tectal neurons, and differentiation of neuroblastoma cells. Further experiments led to the recognition that the interaction between p190 and contactin is important in mediating the effects of contactin and RPTP&bgr;-CAH. The assays of the invention identify compounds that mimic, enhance, or inhibit the p190 mediated effects of contactin/RPTP&bgr;-CAH on neural cells including, but not limited to, agonists and antagonists of contactin/RPTP&bgr;-CAH. Therapeutic uses of compounds so identified are also provided. The invention is described in detail in the following subsections and examples for purposes of clarity and not by way of limitation.

[0016] 5.1. Biology of the Interaction Between Contactin and the CAH Domain of RPTP&bgr;

[0017] During development of the nervous systems, neurons are guided by secreted and cell bound molecules that provide both negative and positive cues. The experiments described in the examples of Sections 6.1 and 6.2 show that RPTP&bgr;, a receptor type protein tyrosine phosphatase, may provide such a signal by interacting with the axonal recognition molecule contactin. RPTP&bgr; is a developmentally regulated protein that exists in three forms, one secreted and two membrane bound. The extracellular region of RPTP&bgr; has a multidomain structure consisting of a CAH-like domain, a single FNIII repeat, and a long cysteine free spacer region. The complex structural nature of its extracellular region may result in a multifunctional protein that is able to interact with different proteins. As documented by the data shown herein, the CAH and the FNIII domains bind to at least two potential ligands present on neurons or glial cells. Functional expression cloning in COS7 cells and affinity purification with a specific affinity matrix followed by microsequencing enabled unequivocal identification of the cell recognition molecule contactin (F3/F11) as a neuronal ligand of RPTP&bgr;. The interaction between contactin and RPTP&bgr; is mediated via the CAH domain of the phosphatase, while the FNIII domain appears to bind to another molecule expressed on the surface of glial cells. It was previously shown that the secreted proteoglycan form of RPTP&bgr; interacts with tenascin, N-CAM and Ng-CAM (Grumet et al., 1994, J. Biol. Chem., 269:12142-12146; Barnea et al., 1994, J. Biol. Chem., 269:14349-14352; Grumet et al., 1993, J. Cell. Biol., 120:815-724; Milev et al., 1994, J. Cell. Biol., 127:1703-1715). Since N-CAM and Ng-CAM do not bind directly to the CAH or the FNIII domain of RPTP&bgr;, they may interact with the large spacer domain of the phosphatase. Alternatively, they could interact with RPTP&bgr; through a third component. Contactin may fulfill this function since it has been shown to interact with Ng-CAM, Nr-CAM, and the matrix proteins tenascin and restriction (Brümmendorf et al., 1993, Neuron, 10:711-727; Morales et al., 1993, Neuron, 11:1113-1122; Zisch et al., 1992, J. Cell. Biol., 119:203-213). The various subdomains of the extracellular region of RPTP&bgr; are able to interact with several distinct proteins that are expressed on diverse cell types in the central nervous system.

[0018] In contrast to other cell recognition molecules that are widely expressed in the nervous system, members of the contactin subgroup appear to be expressed in a restricted manner on specific axons during development (Dodd et al., 1988, Neuron, 1:105-116; Faivre-Sarrailh et al., 1992, J. Neurosci., 12:257-267). The spatial and temporal expression pattern of these proteins indicates they play an important role during development of the nervous system. Contactin was found to be exclusively expressed on neurons during development in fiber-rich areas of the retina, tectum, spinal cord and cerebellum (Ranscht, 1988, J. Cell. Biol, 107:1561-1573). It was found to be localized in the postnatal and adult mouse cerebellum in axonal extensions of the granule cells in the parallel layer (Faivre-Sarrailh et al., 1992, J. Neurosci., 12:257-267). This pattern of expression is overlapping with the expression pattern of RPTP&bgr; in the rat. RPTP&bgr; was shown to be expressed in fiber-rich regions such as the parallel fibers of the cerebellum and the spinal cord (Canoll et al., 1993, Dev. Brain Res., 75:293-298; Milev et al., 1994, J. Cell. Biol., 127:1703-1715). RPTP&bgr; is also expressed on glial and radial glial cells, and its secreted form is produced by astrocytes. Therefore, both forms of RPTP&bgr; may modulate neuronal function via interactions with contactin.

[0019] The contactin subgroup of glycoproteins all share structural similarity in that they are, glycosyl-phosphatidylinositol (GPI)-anchored proteins. They also exist in soluble forms generated as a result of membrane release or by expression of alternative spliced forms (Brümmendorf and Rathjen, 1993, J. Neurochem., 61:1207-1219). Differential expression of the membrane-bound and soluble forms of contactin was found in the hypothalamus-hypophyseal system (Rougon et al., 1994, Braz. J. Med. Biol. Res., 2:409-414). RPTP&bgr; also exists in either membrane bound or secreted forms that are developmentally regulated. Therefore, both RPTP&bgr; and contactin may act as either a ligand or a receptor for each other. Hence, the classical notion of ligand receptor interaction does not fully explain this system since both components might switch roles at different stages of development. For example, the soluble form of RPTP&bgr; produced by glial cells may act as a ligand for the membrane bound form of contactin expressed on the surface of neuronal cells. Conversely, the soluble form of contactin may act as ligand for the membrane bound form of RPTP&bgr; expressed on the surface of glial cells. Moreover, interaction between the membrane bound forms of contactin expressed on the surface of neurons with the membrane form of RPTP&bgr; expressed on the surface of glial cells may lead to bidirectional signals between these two cell types. Such complex interactions between the various forms of RPTP&bgr; and contactin may generate developmentally regulated unidirectional and bidirectional signals.

[0020] While not being limited to any theory or explanation of how the invention works, the following is hypothesized to explain how the CAH domain of RPTB&bgr; binds to contactin. Carbonic anhydrases are highly efficient enzymes that catalyze the hydration of CO2. Yet, the CAH domain of PTPases were not thought to be endowed with enzymatic activity due to substitution of two of the three key histidine residues that are essential for enzymatic activity (Barnea et al., 1993, Mol. Cell. Biol., 13:1497-1506). In contradistinction, the highly packed hydrophobic core as well as the hydrophobic residues that are exposed on the surface of carbonic anhydrase structure and which are conserved in the CAH domains of RPTP&ggr; and &bgr; may be involved in protein-protein interaction and thus function as a ligand binding domain (Barnea et al., 1993, Mol. Cell. Biol., 13:1497-1506). It is of note that Vaccinia virus contains a transmembrane protein with a CAH-like domain in its extracellular domain, which was thought to be involved in binding of the virion to host proteins (Maa et al., 1990, J. Biol. Chem., 265: 1669-1577). Therefore, in theory but not by way of limitation, compounds exhibiting effects which mimic, enhance, or inhibit the contactin mediated effects of RPTP&bgr;-CAH on neuronal cells may do so via other members of the contactin family of glycoproteins, and may do so even if lacking in CAH activity.

[0021] A number of models may be proposed for how contactin, a GPI-linked protein that is inserted into the outer leaflet of the plasma membrane, transmits a signal into the cells to promote neurite outgrowth. In theory, and not by way of limitation, one possibility is that contactin is able to interact with a transmembrane signaling component. The p190 (also referred to as p180) protein that was coprecipitated with contactin has been a candidate for such a signaling protein. p190 may be membrane-associated since it may not be released by phospholipase C treatment. Another potential signal transducer may be L1/Ng-CAM or a related molecule. This transmembrane CAM was shown to interact with contactin (Brümmendorf et al., 1993, Neuron, 10:711-727), and to initiate second messenger cascade via its cytoplasmic domain (Doherty and Walsh, 1994, Curr. Opin. Neurobiol., 4:49-55). The best characterized GPI linked signaling protein is the ciliary neurotrophic factor receptor (CNTF receptor). Following ligand binding, the CNTFR interacts with the signal transducer gp130. The gp130 protein that is shared by several lymphokines and cytokines such as IL-6, LIF and Oncostatin, undergoes dimerization followed by recruitment of the cytoplasmic Jak protein tyrosine kinases. Stimulation of the Jak kinases leads to activation of both the Ras/MAP kinase and the Stat signaling pathways that relay signals from the cell surface to the nucleus. A contactin associated protein such as p190 may have a function similar to the function of gp130.

[0022] As demonstrated by the examples infra, the binding of the CAH domain of RPTP&bgr; to contactin leads to cell adhesion and neurite outgrowth. It seems unlikely that the induction of neurite growth is a default response resulting from cell adhesion per se. Neurons were found to adhere to extracellular matrix proteins such as tenascin and restriction in short term binding assays, but these substrates did not promote further neurite extension (Schachner et al., 1994, Perspect. Dev. Neurobiol., 1:33-41). It was recently reported that the FNIII domain of contactin is responsible for adhesion, while the neurite promoting activity was attributed to the Ig domains (Durbec et al., 1994, Eur. J. Neuro., 6:461-472). Another study demonstrated that contactin can mediate the repulsion of neurons by restriction (Pesheva et al., 1993, Neuron, 10:69-82). Again, this effect was proposed to occur in a stepwise manner, first an adhesion step that was followed by a signal that was transduced to the cells leading to retraction. Therefore, in light of the results presented herein, it may be that in response to different stimuli, the same molecule can transmit opposite signals depending on the context or milieu. Whatever the mechanism, the results presented here demonstrate that a receptor type tyrosine phosphatase serves as a functional ligand for a GPI-anchored cell adhesion molecule.

[0023] Contactin may also serve as a functional ligand for RPTP&bgr;. Modulation of phosphatase activity by neuronal contactin may result in signaling to glial cells. If this does occur, this kind of bidirectional flow of information should allow the interacting cells to respond quickly to local environmental changes during development. Two other receptor type tyrosine phosphatases RPTP&mgr; and RPTP&kgr; were shown to mediate cell-cell interaction in a hemophilic manner (Brady-Kalany et al., 1993, J. Cell. Biol., 122:961-972; Gebbink et al., 1993, J. Biol. Chem., 268:16101-16104; Sap et al., 1994, Mol. Cell. Biol., 14:1-9). However, changes in catalytic activity as a result of these interactions could not be detected. These phosphatases are joining a growing family of proteins that are involved in cellular recognition that contain intrinsic enzymatic activities, including kinases (Dtrk; Pulido et al., 1992), EMBO J., 11:391-404, &bgr; subunit of Na+, K+-ATPase (AMOG; Gloor et al., 1990, J. Cell. Biol., 109:755-788), and &bgr; subunit of prolyl 4-hydroxylase (cognin; Rao and Hausman, 1993, Proc. Natl. Acad. Sci. USA, 90:2950-2954).

[0024] In summary, the experiments and data described herein demonstrate that RPTP&bgr; is a functional ligand for the GPI-anchored cell recognition molecule contactin. The interactions between these two proteins is mediated by the CAH domain of the phosphatase. In addition, the FNIII of RPTP&bgr; repeat is required for interaction with glia cells, demonstrating that the multidomain structure of RPTP&bgr; enables interactions with different proteins, and indicates that other potential ligands may modulate these interactions.

[0025] 5.2 Biology of the p190 Interaction

[0026] Applicants have discovered that contactin functionally interacts with p190, a novel mammalian protein described herein. In light of this information, p190 may play an important role as the link between contactin mediated neurite growth, differentiation and survival and the intracellular second messenger signalling responsible for this contactin mediated effect.

[0027] Cell recognition molecules that contain immunoglobulin (Ig)-like domains and fibronectin type III repeats (FNIII) mediate the interaction of neurons with their local environment during development (Edelman et al., 1991, Annu. Rev. Biochem., 60:155-190; Rathjen et al., 1991, Semin. Neurosci., 3:297-307; Sonderegger et al., 1991, J. Cell. Biol., 119:1387-1394). Based on structural similarity they are subdivided to three groups. The first is represented by NCAM that exist in several alternatively spliced forms (Cunningham et al., 1987, Science, 236:799-805). The second is the L1/Ng-CAM subgroup that also contains Nr-CAM and Neurofascin (Grumet, 1992, J. Neurosci. Res., 31:1-13). The third group contains contactin and its mouse and chicken homologues F3 and F11 (Ranscht, 1988, J. Cell. Biol., 107:1561-1573; Brummendorf et al., 1989, Neuron, 2:1351-1361; Gennarini et al., 1989, J. Cell. Biol., 109:755-788; Reid et al., 1994, Brain Res. Mol. Brain Res., 21:1-8; Berglund et al., 1994, Genomics, 21:571-582), TAG-1 and its chick and human homologues Axonin 1 and TAX-1 (Furley et al., 1990, Cell 61:157-170; Hasler et al., 1993, Eur. J. Biochem., 211:329-339; Zuellig et al., 1992, Eur. J. Biochem., 204:453-463) and BIG-1 (Yoshihara et al., 1994, Neuron, 13:415-426).

[0028] The glycoproteins from the contactin subgroup are all glycosylphosphatydylinositol (GPI)-anchored proteins composed of six C2 type Ig-like domains and four fibronectin type III repeats. They can also be found as secreted proteins as a result of membrane release and shedding or by alternative splicing that generate soluble forms (Brümmendorf et al., 1993, J. Neurochem., 61:1207-1219). In contrast to other cell recognition molecules that are widely expressed in the nervous system, members of the contactin subgroup are expressed in a more restricted manner on specific axons during development (Dodd et al., 1985, Neuron, 1:105-116; Faivre-Sarrailh et al., 1992, J. Neurosci., 12:257-267; Yoshihara et al., 1994, Neuron, 13:415-426). This spatial and temporal expression pattern suggests that they play a key role during axonal guidance and synapse formation.

[0029] Contactin interacts with other members of the Ig superfamily and with extracellular matrix components. Direct interaction was demonstrated between contactin and NgCAM and NrCAM, the extracellular matrix proteins tenascin and restrictin and with the carbonic anhydrase domain of the receptor type tyrosine phosphatase &bgr; (RPTP&bgr;) (Brümmendorf et al, 1993, Neuron, 10:711-727; Zisch et al., 1992, J. Cell. Biol., 119:203-213; Zisch et al., 1992, J. Mol. Neurosci.; Pesheva et al., 1993, Neuron, 10:69-82; Peles et al., 1995, Cell, 82:251-260). These interactions are mediated by different Ig-like domains, the first and second domains bind to tenascin and Ng-CAM while the second and third mediate its interaction with restrictin (Zisch et al., 1992, J. Cell. Biol., 119:203-213; Zisch et al., 1992, J. Mol. Neurosci.; Brümmendorf et al, 1993, Neuron, 10:711-727.). Moreover, contactin has been shown to be involved in both positive and negative responses of neurons to various stimuli (Peles et al., 1995, Cell, 82:251-260; Pesheva et al., 1993, Neuron, 10:69-82). When presented as a ligand to neurons, either as a membrane-bound or a soluble form, contactin induces axonal growth (Clarke et al., 1993, Eur. J. Cell. Biol., 61:108-115; Durbec et al., 1992, J. Cell. Biol., 117:877-887; Gennarini et al., 1989, J. Cell. Biol., 109:755-788). Its neuronal receptor has been identified as the recognition molecule Nr-CAM (Morales et al., 1993, Neuron, 11:1113-1122). Contactin itself functions as a receptor present on neurons. It mediates their repulsion by the extracellular matrix protein restrictin and neurite outgrowth induced by the CAH domain of RPTP&bgr; (Pesheva et al., 1993, Neuron, 10:69-82; Peles et al., 1995, Cell, 82:251-260). Thus, depending on the cellular context and ligand, contactin can mediate two opposite cellular responses (e.g. repulsion vs. adhesion and outgrowth).

[0030] The function of cell recognition molecules involves two stages, first an adhesion step and then a signal transduction step. Signaling by these molecules has been shown to utilize different second messenger systems including GTP-binding proteins, calcium influx and tyrosine kinases (Reviewed in Doherty et al., 1994, Curr. Opin. Neurobiol., 4:49-55). Non-receptor tyrosine kinases of the src family connect different external signals with intracellular signaling pathways. They are highly expressed in developing neurons and are enriched in the nerve growth cones (Bare et al., 1993, Oncogene, 8:1429-1436; Maness et al., 1994, J. Biol. Chem., 193:5001-5005; Sudol et al., 1988, Oncogene Res., 2:345-355.). There is increasing evidence that links these kinases to signaling pathways that are utilized by neural cell recognition molecules. Recently, the potential role for Src and Fyn kinases as a downstream component in L1 and N-CAM signaling was demonstrated using cerebellar neurons from src and fyn-knockout mice (Beggs et al., 1993, J. Cell Biol. 127:825-833; Ignelzi et al., 1994, Neuron, 12:873-884). In addition, activation of Fyn by the cell adhesion molecule MAG in oligodendrocytes was implicated as a regulatory signaling event during myelination (Umemori et al., 1994, Nature, 367:572-576). Finally, Fyn has been shown to associate with contactin in mouse cerebellum and in chick neurons in culture (Olive et al., 1995, J. Neurochem., 65; Zisch et al., 1992, J. Cell. Biol., 119:203-213; Zisch et al., 1992, J. Mol. Neurosci.

[0031] The method by which contactin, a GPI-linked protein, associates with a cytoplasmic kinases is unclear. One possibility is that contactin interacts with a transmembrane protein that acts as a “bridge” to the cell interior.

[0032] The experiments described herein by the Examples of Section 8 describe the cloning of such candidate molecules termed CASPR/p190 (for Contactin ASsociated PRotein). These 190 kDa proteins are found in a complex with contactin and the CAH domain of RPTP&bgr;, but only when both p190 and RPTP&bgr; are present on the same surface of the membrane. The cytoplasmic tail of CASPR/p190 contains a proline rich sequence that interacts with the SH3 domain of Src family kinases. Therefore this molecule could be a potential bridge that couples contactin, a GPI-linked protein, with intracellular second messenger systems.

[0033] 5.3 Mammalian p190 Genes and Gene Products

[0034] The present invention includes, but is not limited to CASPR/p190 peptides, polypeptides, polypeptide fragments and fusion proteins as described herein. The present invention further includes CASPR/p190 nucleic acid molecules are described herein.

[0035] In one embodiment, such CASPR/p190 genes and gene products are mammalian, preferably human or rodent, genes and gene products. In another embodiment, such genes and gene products are naturally occurring genes and gene products.

[0036] The purification and sequencing of p190 protein and the cloning of mammalian p190 cDNA may be conducted as described for human and rat p190 cDNA in the Examples of Section 8.

[0037] The human and rat CASPR/p190 transcripts have open reading frames that encode for 1384 and 1381 amino acids, respectively, and share 93% identity at the amino acid level. CASPR/p190 is a putative type I transmembrane protein with a short proline-rich cytoplasmic domain. (The transmembrane domain is marked as TMD in FIG. 1).

[0038] A description of the CASPR/p190 gene product follows. Such CASPR/p190 gene products include, but are not limited to gene products containing the amino acid sequence depicted in SEQ ID NOS:2 or 4, or the amino acid sequence of at least one of the domains depicted in SEQ ID NOS:2 or 4 and/or as depicted in FIG. 1 and/or as described below.

[0039] The first CASPR/p190 methionine is followed by a stretch of 19-20 amino acid residues rich in hydrophobic residues, which probably acts as a signal sequence. The extracellular domains of rat and human CASPR/p190 contain 1281 and 1282 amino acid residues, respectively. The extracellular region of CASPR/p190 contains 16 potential N-linked glycosylation sites followed by a second hydrophobic stretch that is a typical transmembrane domain.

[0040] The CASPR/p190 extracellular domain is a novel mosaic of several motifs that to mediate protein-protein interactions. Near the N-terminus of mature CASPR/p190 (109 amino acid residues) is a domain with 31-33% amino acid identity to the C1 and C2 terminal domains of coagulation factors V and VIII, 26% identity with the neuronal adhesion molecule neurophilin (previously known as the neuronal A5 antigen) and 20% identity to a region of discoidin I, a lectin from the slime mold Dictyostelium discoideum. The domain is marked as DISC in FIG. 1.

[0041] The extracellular domain of CASPR/p190 also contains four repeats, of approximately 140 amino acid residues each, with homology to neurexins, a family of polymorphic neuronal cell surface proteins. These domains are marked as NX1-NX4 in FIG. 1.

[0042] CASPR/p190 also contains two epidermal growth factor (EGF)-like modules (marked as EGF1-EGF2 in FIG. 1).

[0043] A single domain related to the C-terminal region of fibrinogen beta/gamma (marked as FIB in FIG. 1) is flanked by an EGF and neurexin motif.

[0044] CASPR/p190 contains a stretch of 47 amino acids that is identical between human and rat CASPR/p190, and contains seven copies of Pro-Gly-Tyr-X1-2 and three additional imperfect repeats of this sequence (marked as PGY in FIG. 1).

[0045] The cytoplasmic domain of human and rat CASPR/p190 contain 78 and 74 amino acids, respectively. These include a 38-42 amino acid proline-rich motif (38% proline), the majority of which consists of proline residues alternating with alanine, glycine, or threonine residues (marked as PRO in FIG. 1).

[0046] In addition to full length CASPR/p190 gene products, CASPR/p190 polypeptide fragments are also included within the scope of the invention. In this sense, the term “CASPR/p190 polypeptide fragments” encompasses polypeptides that comprise p190 fragments, deletions, including internal deletions or any combination of p190 fragments or deletions. In particular, p190 polypeptides are those that specifically include or lack any of the domains listed in Table 2, below, or any combination thereof. 2 TABLE 2 CASPR/p190 AMINO ACID RESIDUES AS SHOWN IN FIG. 1 AND IN SEQ DOMAIN NAME ID NOS:1 or 3 DISC  40-168 (SEQ ID NO:1)  41-169 (SEQ ID NO:3) NX1  199-330 (SEQ ID NO:1)  200-331 (SEQ ID NO:3) NX2  362-486 (SEQ ID NO:1)  363-487 (SEQ ID NO:3) EGF1  544-576 (SEQ ID NO:1)  544-577 (SEQ ID NO:3) FIB  582-739 (SEQ ID NO:1)  583-740 (SEQ ID NO:3) NX3  809-938 (SEQ ID NO:1)  810-939 (SEQ ID NO:3) EGF2  961-985 (SEQ ID NO:1)  962-986 (SEQ ID NO:3) PGY 1031-1077 (SEQ ID NO:1) 1032-1078 (SEQ ID NO:3) NX4 1083-1218 (SEQ ID NO:1) 1084-1219 (SEQ ID NO:3) TMD 1282-1306 (SEQ ID NO:1) 1283-1307 (SEQ ID NO:3) PRO 1328-1369 (SEQ ID NO:1) 1329-1366 (SEQ ID NO:3)

[0047] In a further embodiment of the invention, the p190 DNA or a modified sequence thereof may be ligated to a heterologous sequence to encode a CASPR/p190 fusion protein. For example, for screening peptide libraries it may be useful to encode a chimeric p190 protein expressing a heterologous epitope that is recognized by a commercially available antibody. A fusion protein may also be engineered to contain a cleavage site located between the p190 sequence and the heterologous protein sequence, so that the p190 protein or protein fragment can be cleaved away from the heterologous moiety. In another embodiment, DNA sequences encoding a fusion protein comprising all or a portion of the p190 protein fused to another protein with a desired activity are within the scope of the invention; e.g., enzymes such as GUS (&bgr;-glucuronidase), &bgr;-galactosidase, luciferase, etc.

[0048] With respect to nucleic acid molecules, the invention contemplates nucleic acid molecules containing: 1) any DNA sequence that encodes the same amino acid sequence as encoded by the DNA sequences shown in SEQ ID NO:1 and SEQ ID NO:3; 2) any DNA sequence that hybridize to the complement of the coding sequences disclosed herein under highly stringent conditions, e.g., washing in 0.1×SSC/0.1% SDS at 68° C. (Ausubel, et al., eds., 1989, Current Protocols in Molecular Biology, Vol. I, Green Publishing Associates, Inc., and John Wiley & sons, Inc., New York, at p. 2.10.3; see also Sambrook, J. et al., (1989) Molecular cloning, Colo. Spring Harbor Press, USA, pp. 9.47-9.55), and which can encode a functionally equivalent gene product; and/or 3) any DNA sequence that hybridizes to the complement of the coding sequences disclosed therein under less stringent conditions, such as moderately stringent conditions, e.g., washing in 0.2×SSC/0.1% SDS at 42° C. (Ausubel, et al., 1989, supra; Sambrook, et al., 1989, supra), yet which encodes a functionally equivalent gene product.

[0049] As used herein, the term “functionally equivalent gene product” refers to a gene product that exhibits at least one of the biological functions of the gene product depicted in SEQ ID NOS: 2 and/or 4. Such biological functions can include, but are not limited to, a function (e.g., a protein-protein interaction function) as exhibited by at least one of the domains of the SEQ ID NO:2 or 4 gene products.

[0050] In another embodiment, DNAs that encode mutant forms of p190 are also included within the scope of the invention. Such mutant p190 DNA sequences encompass deletions, additions and/or substitutions of nucleotide residues, or of regions coding for domains within the p190 protein. These mutated p190 DNAs may encode gene products that are functionally equivalent or which display properties very different from the native forms of p190.

[0051] The invention also encompasses 1) DNA vectors that contain any of the coding sequences disclosed herein (see SEQ ID NO:1 and SEQ ID NO:3), and/or their complements (i.e., antisense); 2) DNA expression vectors that contain any of the coding sequences disclosed therein, and/or their complements (i.e., antisense), operatively associated with a regulatory element that directs the expression of the coding and/or antisense sequences; and 3) genetically engineered host cells that contain any of the coding sequences disclosed therein, and/or their complements (i.e., antisense), operatively associated with a regulatory element that directs the expression of the coding and/or antisense sequences in the host cell. Regulatory element includes but is not limited to inducible and non-inducible promoters, enhancers, operators and other elements known to those skilled in the art that drive and regulate expression. The invention includes fragments of any of the DNA sequences disclosed herein.

[0052] p190 sequence can be obtained from a variety of sources including cDNA libraries. For example, appropriate cDNA libraries which are good sources of p190 can be obtained from (Clonetech (Palo Alto, Calif.), Stratagene (La Jolla, Calif.) the ATCC Repository (Rockville, Md.). In addition, cDNA libraries may be prepared from mRNA pools collected from mammalian cells which express p190 either constitutively or inducibly. By way of example but not by way of limitation, such cells include rat GH3 cells, as well as CHO, VERO, BHK, HeLa, COS, MDWCK, -293, WI38, etc. The collection of mRNA pools and construction of cDNA libraries from these cells are set forth more fully in the examples described infra.

[0053] Any of the cDNA libraries described above may be screened by hybridization or PCR using the p190 sequences described herein as oligonucleotide probes. Screening can be performed using those portions of the p190 sequence as discussed in the Examples of Section 8, infra.

[0054] In addition to cDNA libraries, partial p190 sequence can be obtained from any genomic library by library screening or from genomic DNA by PCR. Full cDNA sequences can be obtained by PCR of total RNA isolated from any cell or tissue that expresses p190 including, but not limited to, neuronal tissue. Cellular sources also include, but are not limited to, hematopoietic, fetal, and embryonal tissues.

[0055] Alternatively, the cDNA libraries described above can be used to construct expression libraries in a cell line such as CHO, VERO, BHK, HeLa, COS, MDWCK, -293, WI38, etc., or other cells known in the art to contain little or no autologous p190 activity. These expression libraries can then be screened using antibodies which are specific to p190. Expression libraries for antibody screening may also be made in bacteria, such as E. coli, using phage vectors, such as lambda. These expression libraries may also be screened for p190 enzyme activity as set forth in the examples which are described in more detail infra.

[0056] Other isoforms of p190 may exist and may be cloned using the p190 gene sequence.

[0057] 5.4 Expressing the p190 Gene Product

[0058] In order to express a biologically active p190, the coding sequence for the enzyme, a function equivalent, or a modified sequence, as, e.g., described in Section 5.3., supra, is inserted into an appropriate eukaryotic expression vector, i.e., a vector which contains the necessary elements for transcription and translation of the inserted coding sequence in appropriate eukaryotic host cells which possess the cellular machinery and elements for the proper processing, i.e., signal cleavage, glycosylation, phosphorylation, sialylation, and protein sorting. Mammalian host cell expression systems are preferred for the expression of biologically active enzymes that are properly folded and processed. When administered in humans such expression products may also exhibit tissue targeting.

[0059] The invention also encompasses peptide fragments of the p190 gene product. The p190 gene product or peptide fragments thereof, can be linked to a heterologous peptide or protein as a fusion protein. In addition, chimeric p190 expressing a heterologous epitope that is recognized by a commercially available antibody is also included in the invention. A durable fusion protein may also be engineered; i.e., a fusion protein which has a cleavage site located between the p190 sequence and the heterologous protein sequence, so that the p190 gene product, or fragment thereof, can be cleaved away from the heterologous moiety. For example, a collagenase cleavage recognition consensus sequence may be engineered between the p190 gene product, or fragment thereof, the heterologous peptide or protein. The p190 domain can be released from this fusion protein by treatment with collagenase.

[0060] 5.4.1 Construction of Expression Vectors and Preparation of Transfectants

[0061] Methods which are well-known to those skilled in the art can be used to construct expression vectors containing the p190 coding sequence and appropriate transcriptional/translational control signals. These methods include in vitro recombination/genetic recombination. See, for example, the techniques described in Sambook et al., 1987, Molecular Cloning A Laboratory Manual, Cold Spring Harbor Laboratory, N.Y., Chapter 12.

[0062] p190 proteins produced by these methods would be useful for in vitro studies on the mechanism of action of p190 and particularly for further studies on the mechanism of action of any inhibitors that are selective for p190 that are identified by drug screening with the stably expressing p190 cell lines, as infra, or for investigating the mechanism of action of existing drugs or of inhibitors that may be identified by other means. The purified p190 proteins would also be useful for the production of crystals suitable for X-ray crystallography. Such crystals would be extremely beneficial for the rational design of drugs based on molecular structure. Expression of these chimeric DNA constructs in a baculovirus or yeast system and subsequent crystallization of the proteins would yield such data.

[0063] A variety of eukaryotic host-expression systems may be used to express the p190 coding sequence. Although prokaryotic systems offer the distinct advantage of ease of manipulation and low cost of scale-up, their major drawback in the expression of p190 is their lack of proper post-translational modifications of expressed mammalian proteins. Eukaryotic systems, and preferably mammalian expression systems, allow for proper modification to occur. Eukaryotic cells which possess the cellular machinery for proper processing of the primary transcript glycosylation, phosphorylation, and, advantageously secretion of the gene product should be used as host cells for the expression of p190. Mammalian cell lines are preferred. Such host cell lines may include but are not limited to CHO, VERO, BHK, HeLa, COS, MDWCK, -293, WI38, etc. Alternatively, eukaryotic host cells which possess some but not all of the cellular machinery required for optional processing of the primary transcript and/or post-translational processing and/or secretion of the gene product may be modified to enhance the host cell's processing capabilities. For example, a recombinant nucleotide sequence encoding a peptide product that performs a processing function the host cell had not previously been capable of performing, may be engineered into the host cell line. Such a sequence may either be co-transfected into the host cell along with the gene of interest, or included in the recombinant construct encoding the gene of interest. Alternatively, cell lines containing this sequence may be produced which are then transfected with the gene of interest.

[0064] Appropriate eukaryotic expression vectors should be utilized to direct the expression of p190 in the host cell chosen. For example, at least two basic approaches may be followed for the design of vectors based on SV40. The first is to replace the SV40 early region with the gene of interest while the second is to replace the late region (Hammarskjold, et al., 1986, Gene, 43:41-50. Early and late region replacement vectors can also be complemented in vitro by the appropriate SV40 mutant lacking the early or late region. Such complementation will produce recombinants which are packaged into infectious capsids and which contain the p190 gene. A permissive cell line can then be infected to produce the recombinant protein. SV40-based vectors can also be used in transient expression studies, where best results are obtained when they are introduced into COS (CV-1, origin of SV40) cells, a derivative of CV-1 (green monkey kidney cells) which contain a single copy of an origin defective SV40 genome integrated into the chromosome. These cells actively synthesize large T antigen (SV40), thus initiating replication from any plasmid containing an SV40 origin of replication.

[0065] In addition to SV40, almost every molecularly cloned virus or retrovirus may be used as a cloning or expression vehicle. Viral vectors based on a number of retroviruses (avian and murine), adenoviruses, vaccinia virus (Cochran, et al., 1985, Proc. Natl. Acad. Sci. USA, 82:19-23) and polyoma virus may be used for expression. Other cloned viruses, such as J C (Howley, et al., 1980, J. Virol, 36:878-882), BK and the human papilloma viruses (Heilmsan, et al., 1980, J. Virol, 36:395-407), offer the potential of being used as eukaryotic expression vectors. For example, when using adenovirus expression vectors, the p190 coding sequence may be ligated to an adenovirus transcription/translation control complex, e.g., the late promoter and tripartite leader sequence. This chimeric gene may then be inserted in the adenovirus genome by in vitro or in vivo recombination. Insertion in a non-essential region of the viral genome (e.g., region E1 or E3) will result in a recombinant virus that is viable and capable of expressing the human enzyme in infected hosts (e.g., see Logan & Shenk, 1984, Proc. Natl. Acad. Sci. USA, 81:3655-3659). Alternatively, the vaccinia virus 7.5K promoter may be used. (e.g., see, Hackett et al., 1982, Proc. Natl. Acad. Sci. USA, 79:7415-7419; Hackett et al., 1994, J. Virol. 49:857-864, Panicali et al., 1982, Proc. Natl. Acad. Sci. USA, 79:4927-4931). Of particular interest are vectors based on bovine papilloma virus (Sarver, et al., 1981, Mol. Cell. Biol., 1:486-496), or Semliki Forest Virus, which provides large quantities of active protein in induced cells (Olkkohnen et al., 1994, Meth. Cell. Biol., 43 part A:43-53; Lundstrum et al., 1994, Eur. J. Biochem., 224:917-921). These vectors have the ability to replicate as extrachromosomal elements. Shortly after entry of this DNA into mouse cells, the plasmid replicates to about 100 to 200 copies per cell. Transcription of the inserted cDNA does not require integration of the plasmid into the host's chromosome, thereby yielding a high level of expression. These vectors can be used for stable expression by including a selectable marker in the plasmid, such as the neo gene. High level expression may also be achieved using inducible promoters such as the metallothionine IIA promoter, heat shock promoters, etc.

[0066] For long-term, high-yield production of recombinant proteins, stable expression is preferred. For example, following the introduction of foreign DNA, engineered cells may be allowed to grow for 1-2 days an enriched media, and then are switched to a selective media. Rather than using expression vectors which contain viral origins of replication, host cells can be transformed with the p190 DNA controlled by appropriate expression control elements (e.g., promoter, enhancer, sequences, transcription terminators, polyadenylation sites, etc.), and a selectable marker. The selectable marker in the recombinant plasmid confers resistance to the selection and allows cells to stably integrate the plasmid into their chromosomes and grow to form foci which in turn can be cloned and expanded into cell lines. A number of selection systems may be used, including but not limited to the herpes simplex virus thymidine kinase (Wigler, et al., 1977, Cell, 11:223-232), hypoxanthine-guanine phosphoribosylatransferase (Szybalska & Szybalski, 1962, Proc. Natl. Acad. Sci. USA, 48:2026), and adenine phosphoribosyltransferase (Lowy, et al., 1980, Cell, 22:817-823) genes can be employed in tk−, hgprt− or aprt− cells respectively. Also, antimetabolite resistance can be used as the basis of selection for dhfr, which confers resistance to methotrexate (Wigler, et al., 1980, Natl. Acad. Sci. USA 77:3567-3570; O'Hare, et al., 1981, Proc. Natl. Acad. Sci. USA 78:1527-1531); ygpt, which confers resistance to mycophenolic acid (Mulligan & Berg, 1981, Proc. Natl. Acad. Sci. USA, 78:2072-2076); neo, which confers resistance to the aminoglycoside G-418 (Colberre-Garapin, et al., 1981, J. Mol. Biol., 150:1-14); and hygro, which confers resistance to hygromycim (Santerre, et al., 1994, Gene, 30:147-156) genes. Recently, additional selectable genes have been described, namely trpB, which allows cells to utilize indole in place of tryptophan; hisD, which allows cells to utilize histinol in place of histidine (Hartman & Mulligan, 1988, Proc. Natl. Acad. Sci. USA, 85:8047-8051), and ODC (ornithine decarboxylase) which confers resistance to the ornithine decarboxylase inhibitor, 2-(difluromethyl)-DL-ornithine, DFMO (McConlogue L., 1987, In: Current Communications in Molecular Biology, Cold Spring Harbor Laboratory ed.).

[0067] Alternative eukaryotic expression systems which may be used to express the p190 enzymes are yeast transformed with recombinant yeast expression vectors containing the p190 coding sequence; insect cell system infected with recombinant virus expression vectors (e.g., baculovirus) containing the p190 coding sequence; or plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic, TMV) or transformed with recombinant plasmid expression vectors (e.g., Ti plasmid) containing the p190 coding sequence.

[0068] In yeast, a number of vectors containing constitutive or inducible promoters may be used. For a review see, Current Protocols in Molecular Biology,-Vol. 2, 1988, Ed. Ausubel et al., Greene Publish. Assoc. & Wiley Interscience, Ch. 13; Grant et al., 1987, Expression and Secretion Vectors for Yeast, in Methods in Enzymology, Eds. Wu & Grossman, 31987, Acad. Press, N.Y., Vol. 153, pp. 516-544; Glover, 1986, DNA Cloning, Vol. II, IRL Press, Wash., D.C., Ch. 3; Bitter, 1987, Heterologous Gene Expression in Yeast, Methods in Enzymology, Eds. Berger & Kimmel Acad. Press, N.Y., Vol. 152, pp. 673-694; and The Molecular Biology of the Yeast Saccharomyces, 1982, Eds. Strathem et al., Cold Spring Harbor Press, Vols. I and II. For complementation assays in yeast, cDNAs for p190 may be cloned into yeast episomal plasmids (YEp) which replicate autonomously in yeast due to the presence of the yeast 2&mgr; circle. The cDNA may be cloned behind either a constitutive yeast promoter such as ADH or LEU2 or an inducible promoter such as GAL (Cloning in Yeast, Chpt. 3, R. Rothstein In: DNA Cloning Vol. 11, A Practical Approach, Ed. D M Glover, 1986, IRL Press, Wash., D.C.). Constructs may contain the 5′ and 3′ non-translated regions of the cognate p190 mRNA or those corresponding to a yeast gene. YEp plasmids transform at high efficiency and the plasmids are extremely stable. Alternatively, vectors may be used which promote integration of foreign DNA sequences into the yeast chromosome.

[0069] Alternately, active, post-translationally modified p190 proteins can be obtained using a yeast expression system such as the Pichia pastoris expression system marketed by Invitrogen (Pichia pastoris is owned and licensed by Research Corporation Technologies, Tucson, Ariz.; however, all components are available from Invitrogen, San Diego, Calif.). In this example, cDNAs encoding human p190 are independently cloned into the pHIL-D2 Pichia expression vector. After linearization with a restriction endonuclease, these constructs are transfected into spheroblasts of the his4 Pichia pastoris strain, GS115, and recombinant yeast carrying the cloned p190 DNA sequences are identified by screening for yeast clones that grow in the absence of histidine (now supplied by the recombinant vector), but do not efficiently utilize methanol as the sole carbon source (due to the presence of p190 in the place of AOXI gene sequence coding for methanol utilization). After expansion of such clones in the presence of an alternative carbon source such as glycerol, large quantities of cells would be transferred to liquid media containing methanol where replication ceases. However, cells remain viable for many days during which time human p190 proteins are specifically expressed at high levels under control of the AOXI promoter. The advantages of this system include very high protein yields and lower expense in the production and maintenance of cultures.

[0070] In cases where plant expression vectors are used, the expression of the p190 coding sequence may be driven by any of a number of promoters. For example, viral promoters such as the 35S RNA and 19S RNA promoters of CaMV (Brisson et al., 1984, Nature, 310:511-514), or the coat protein promoter of TMV (Takamatsu et al., 1987, EMBO J., 6:307-311) may be used; alternatively, plant promoters such as the small subunit of RUBISCO (Coruzzi et al., 1994, EMBO J., 3:1671-1680; Broglie et al., 1984, Science, 224:838-843); or heat shock promoters, eg., soybean hsp 17.5-E or hsp 17.3-B (Gurley et al., 1986, Mol. Cell. Biol., 6:559-565) may be used. These constructs can be introduced into plant cells using Ti plasmids, Ri plasmids, plant virus vectors; direct DNA transformation; microinjection, electroporation, etc. For reviews of such techniques see, for example, Weissbach & Weissbach, 1988, Methods for Plant Molecular Biology, Academic Press, NY, Section VIII, pp. 421-463; and Grierson & Corey, 1988, Plant Molecular Biology, 2d Ed., Blackie, London, Ch. 7-9.

[0071] An alternative expression system which could be used to express p190 is an insect system. In one such system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes. The virus grows in Spodoptera frugiperda cells. The p190 sequence may be cloned into non-essential regions (for example the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (for example the polyhedrin promoter). Successful insertion of the coding sequence will result in inactivation of the polyhedrin gene and production of non-occluded recombinant virus (i.e., virus lacking the proteinaceous coat coded for by the polyhedrin gene). These recombinant viruses are then used to infect Spodoptera frugiperda cells in which the inserted gene is expressed. (e.g., see Smith et al., 1983, J. Virol., 46:584, Smith, U.S. Pat. No. 4,215,051).

[0072] In a specific embodiment of an insect system, the DNA encoding p190 can be independently cloned into the pBlueBacIII recombinant transfer vector (Invitrogen, San Diego, Calif.) downstream of the polyhedrin promoter and transfected into Sf9 insect cells (derived from Spodoptera frugiperda ovarian cells, available from Invitrogen, San Diego, Calif.) to generate recombinant virus containing p190. After plaque purification of the recombinant virus high-titer viral stocks are prepared that in turn would be used to infect Sf9 or High Five™ (BTI-TN-5B1-4 cells derived from Trichoplusia ni egg cell homogenates; available from Invitrogen, San Diego, Calif.) insect cells, to produce large quantities of appropriately post-translationally modified p190 proteins. Although it is possible that these cells themselves could be directly useful for drug assays, the p190 proteins prepared by this method can be used for in vitro assays of drug potency and selectivity.

[0073] 5.4.2 Identification of Transfectants or Transformants Expressing the p190 Gene Product

[0074] The host cells which contain the p190 coding sequence and which express the biologically active gene product may be identified by at least four general approaches: (a) DNA-DNA or DNA-RNA hybridization; (b) the presence or absence of “marker” gene functions; (c) assessing the level of transcription as measured by the expression of p190 mRNA transcripts in the host cell; and (d) detection of the gene product as measured by immunoassay or by its biological activity.

[0075] In the first approach, the presence of the p190 coding sequence inserted in the expression vector can be detected by DNA-DNA or DNA-RNA hybridization or PCR using probes comprising nucleotide sequences that are homologous the p190 coding sequence or portions or derivatives thereof.

[0076] In the second approach, the recombinant expression vector/host system can be identified and selected based upon the presence or absence of certain “marker” gene functions (e.g., resistance to antibiotics, resistance to methotrexate, transformation phenotype, occlusion body formation in baculovirus, etc.). For example, if the p190 coding sequence is within a marker gene sequence of the vector, recombinants containing the p190 coding sequence can be identified by the absence of the marker gene function. Alternatively, a marker gene can be placed in tandem with the p190 sequence under the control of the same or different promoter used to control the expression of the p190 coding sequence. Expression of the marker in response to induction or selection indicates expression of the p190 coding sequence. In addition, the marker gene may be identified by DNA-DNA or DNA-RNA hybridization or PCR.

[0077] In the third approach, transcriptional activity for the p190 coding region can be assessed by hybridization or PCR assays. For example, RNA can be isolated and analyzed by Northern blot using a probe homologous to the p190 coding sequence or particular portions thereof. Alternatively, total nucleic acids of the host cell may be extracted and assayed for hybridization to such probes.

[0078] In the fourth approach, the expression of the p190 protein product can be assessed immunologically, for example by Western blots, immunoassays such as radioimmuno-precipitation, enzyme-linked immunoassays and the like. The ultimate test of the success of the expression system, however, involves the detection of the biologically active p190 gene product. Where the host cell secretes the gene product, the cell free media obtained from the cultured transfectant host cell may be assayed for p190 activity. Where the gene product is not secreted, cell lysates may be assayed for such activity. In either case, a number of assays can be used to detect p190 activity, including but not limited to, those described in the examples infra or those known in the art.

[0079] 5.4.3 Cell Lines Expressing p190

[0080] The present invention also relates to cell lines containing recombinant DNA sequence, preferably a chromosomally integrated recombinant DNA sequence, which comprises the gene encoding p190 which cell lines further do not express autologous p190, apart from that encoded by the recombinant DNA sequence.

[0081] A specific embodiment of the present invention is an engineered mammalian cell line which contains a chromosomally integrated, genetically-engineered (“recombinant”) DNA sequence, which DNA sequence expresses mammalian p190, and wherein said cell line also does not express autologous p190. The cell line is preferably of human or primate origin, such as the exemplified monkey kidney COS cell line, but cell lines derived from other species may be employed, including chicken, hamster, murine, ovine and the like; the CHO (Chinese hamster ovary) cell line for example, may be particularly preferred for large scale production.

[0082] Any cell or cell line, the genotype of which has been altered by the presence of a recombinant DNA sequence is encompassed by the invention. The recombinant DNA sequence may also be referred to herein as “heterologous DNA,” “exogenous DNA,” “genetically engineered” or “foreign DNA,” indicating that the DNA was introduced into the genotype or genome of the cell or cell line by a process of genetic engineering.

[0083] The invention includes, but is not limited to, a cell or cell line wherein the native p190 DNA sequence has been removed or replaced as a result of interaction with a recombinant DNA sequence. Such cells are called p190 knockouts, herein, if the resulting cell is left without a native DNA that encodes a functional p190 gene product.

[0084] As used herein, the term “recombinant DNA sequence” refers to a DNA sequence that has been derived or isolated from any source, that may be subsequently chemically altered, and later introduced into mammalian cells. An example of a recombinant DNA sequence “derived” from a source, would be a DNA sequence that is identified as a useful fragment within a given organism, and which is then chemically synthesized in essentially pure form. An example of such DNA sequence “isolated” from a source would be a DNA sequence that is excised or removed from said source by chemical means, e.g., by the use of restriction endonucleases, so that it can be further manipulated, e.g., amplified, for use in the invention, by the methodology of genetic engineering.

[0085] Therefore, “recombinant DNA sequence” includes completely synthetic DNA, semi-synthetic DNA, DNA isolated from biological sources, and DNA derived from introduced RNA. Generally, the recombinant DNA sequence is not originally resident in the genotype which is the recipient of the DNA sequence, or it is resident in the genotype but is not expressed.

[0086] The isolated recombinant DNA sequence used for transformation herein may be circular or linear, double-stranded or single-stranded. Generally, the DNA sequence is chimeric linear DNA, or is a plasmid or viral expression vector, that can also contain coding regions flanked by regulatory sequences which promote the expression of the recombinant DNA present in the resultant cell line. For example, the recombinant DNA sequence may itself comprise or consist of a promoter that is active in mammalian cells, or may utilize a promoter already present in the genotype that is the transformation target. Such promoters include, but are not limited to, the CMV promoter, SV 40 late promoter and retroviral LTRs (long terminal repeat elements).

[0087] The general methods for constructing recombinant DNA which can transform target cells are well known to those skilled in the art, and the same compositions and methods of construction may be utilized to produce the DNA useful herein. For example, J. Sambrook et al., Molecular Cloning; A Laboratory Manual, Cold Spring Harbor Laboratory Press (2d ed., 1989), provides suitable methods of construction.

[0088] Aside from recombinant DNA sequence that serve as transcription units for p190 or other portions thereof, a portion of the recombinant DNA may be untranscribed, serving a regulatory or a structural function.

[0089] The recombinant DNA sequence to be introduced into the cells further will generally contain either a selectable marker gene or a reporter gene or both to facilitate identification and selection of transformed cells. Alternatively, the selectable marker may be carried on a separate piece of DNA and used in a co-transformation procedure. Both selectable markers and reporter genes may be flanked with appropriate regulatory sequences to enable expression in mammalian cells. Useful selectable markers are well known in the art and include, for example, anti-biotic and herbicide resistance genes.

[0090] Sources of DNA sequences useful in the present invention include Poly-A RNA from mammalian cells, from which the mRNA encoding p190 can be derived and used for the synthesis of the corresponding cDNA by methods known to the art. Such sources include cDNA libraries and mRNA pools made from neuronal, neuroblastoma, embryonic, fetal, and hematopoietic tissues of human, rat or other mammalian origin.

[0091] Selectable marker genes encoding enzymes which impart resistance to biocidal compounds are listed in Table 1, below. 3 TABLE 3 Selectable Marker Genes Resistance Confers Gene or Enzyme Resistance to: Reference Neomycin phospho- G-418, neomycin, Southern et transferase (neo) kanamycin al., 1982, J. Mol. Appl. Gen., 1:327-341 Hygromycin Hygromycin B Shimizu et al., 1986, phosphotrans- Mol. Cell Biol., ferase (hpt or 6:1074-1087 hyg) Dihydrofolate Methotrexate Kwok et al., 1986, reductase (dhfr) Proc. Nat'l. Acad. Sci. USA, 4552-4555 Phosphinothricin Phosphinothricin DeBlock et al., 1987, acetyltransferase EMBO J., 6:2513-2518 (bar) 2,2-Dichloropro- 2-2,Dichloropro- Buchanan-Wollaston et pionic acid pionic acid al., 1989, J. Cell. dehalogenase (Dalapon) Biochem., Supp. 13D, 330 Acetohydroxyacid Sulfonylurea, Anderson et al. (U.S. synthase imidazolinone and Pat. No. triazolopyrimidine 4,761,373); G. W. herbicides Haughn et al., 1988 Mol. Gen. Genet., 211:266-271 5-Enolpyruvyl- Glyphosate Comai et al., 1985 shikimatephos- Nature, 317:741-744 phate synthase (aroA) Haloarylnitrilase Bromoxynil Stalker et al., published PCT appln. W087/04181 Acetyl-coenzyme A Sethoxydim, Parker et al., 1990 carboxylase haloxyfop Plant Physiol., 92:1220 Dihydropteroate Sulfonamide Guerineau et al., synthase (sul I) herbicides 1990, Plant Molec. Biol., 15:127-136 32 kD photosystem Triazine herbicides Hirschberg et al., II polypeptide 1983, Science, (psbA) 222:1346-1349 Anthranilate 5-Methyltryptophan Hibberd et al. (U.S. synthase Pat. No. 4,581,847) Dihydrodipicolin- Aminoethyl cysteine Glassman et al., ic acid synthase published PCT (dap A) application No. W089/11789

[0092] Reporter genes are used for identifying potentially transformed cells and for evaluating the functionality of regulatory sequences. Reporter genes which encode for easily assayable marker proteins are well known in the art. In general, a reporter gene is a gene which is not present in or expressed by the recipient organism or tissue and which encodes a protein whose expression is manifested by some easily detectable property, e.g., enzymatic activity. Preferred genes includes the chloramphenicol acetyl transferase gene (cat) from Tn9 of E. coli, the beta-galactosidase gene of E. coli, the beta-glucuronidase gene (gus) of the uidA locus of E. coli, and the luciferase gene from firefly Photinus pyralis. Expression of the reporter gene is assayed at a suitable time after the DNA has been introduced into the recipient cells.

[0093] Other elements such as introns, enhancers, polyadenylation sequences and the like, may also be a part of the recombinant DNA sequence. Such elements may or may not be necessary for the function of the DNA, but may provide improved expression of the DNA by affecting transcription, stability of the mRNA, or the like. Such elements may be included in the DNA as desired to obtain the optimal performance of the transforming DNA in the cell.

[0094] The recombinant DNA sequence can be readily introduced into the target cells by transfection with an expression vector, such as a viral expression vector, comprising cDNA encoding p190 by the modified calcium phosphate precipitation procedure of Chen et al., 1987, Mol. Cell. Biol., 7:2745-2752. Transfection can also be accomplished by other methods, including lipofection, using commercially available kits, e.g., provided by Life Technologies.

[0095] In a preferred embodiment of the invention, the cell lines of the invention are able to express a stable p190 gene product or analog, homologue, or deletion thereof after several passages through cell culture.

[0096] 5.4.4 Purification of the p190 Gene Product

[0097] Once a cell that produces high levels of biologically active p190 is identified, the cell may be clonally expanded and used to produce large quantities of the enzyme, which may be purified using techniques well-known in the art including, but not limited to, immunoaffinity purification, chromatographic methods including high performance liquid chromatography and the like. Where the enzyme is secreted by the cultured cells, p190 may be readily recovered from the culture medium.

[0098] Where the p190 coding sequence, or fragment thereof, has been engineered to encode a cleavable fusion protein, the purification of the p190 gene product, or fragment thereof, may be readily accomplished using affinity purification techniques. For example, an antibody specific for the heterologous peptide or protein can be used to capture the durable fusion protein; for example, on a solid surface, a column etc. The p190 moiety can be released by treatment with the appropriate enzyme that cleaves the linkage site. cDNA construction using the polymerase chain reaction accompanied by transfection and purification of the expressed protein permits the isolation of sufficient quantities of p190 for characterization of the enzyme's physical and kinetic properties. Using site-directed mutagenesis or naturally occurring mutant sequences, this system provides a reasonable approach to determine the effects of the altered primary structure on the function of the protein. Fusion constructs of the p190 protein domain with the marker peptide preceding the amino terminus of p190 or following the carboxy terminus of p190 may also be engineered to evaluate which fusion construct will interfere the least, if at all, with the protein's biologic function and the ability to be purified.

[0099] Using this aspect of the invention, any cleavage site or enzyme cleavage substrate may be engineered between the p190 sequence and a second peptide or protein that has a binding partner which could be used for purification, e.g, any antigen for which an immunoaffinity column can be prepared.

[0100] 5.5 Antibodies to the p190 Gene Product

[0101] For the production of antibodies, various host animals may be immunized by injection with the p190 gene product, or a portion thereof including, but not limited to, portions of the p190 gene product in a recombinant protein. Such host animals may include but are not limited to rabbits, mice, and rats, to name but a few. Various adjuvants may be used to increase the immunological response, depending on the host species, including but not limited to Freund's (complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, dinitrophenol, and potentially useful human adjuvants such as BCG (bacille Calmette-Guerin) and Corynebacterium parvum.

[0102] Monoclonal antibodies may be prepared by using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include but are not limited to the hybridoma technique originally described by Kohler and Milstein, 1975, Nature, 256:495-497, the human B-cell hybridoma technique (Kosbor et al., 1983, Immunology Today, 4:72, Cote et al., 1983, Proc. Natl. Acad. Sci., 80:2026-2030) and the EBV-hybridoma technique (Cole et al., 1985, Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96). In addition, techniques developed for the production of “chimeric antibodies” (Morrison et al., 1984, Proc. Natl. Acad. Sci., 81:6851-6855; Neuberger et al., 1984, Nature, 312:604-608; Takeda et al., 1985, Nature, 314:452-454) by splicing the genes from a mouse antibody molecule of appropriate antigen specificity together with genes from a human antibody molecule of appropriate biological activity can be used. Alternatively, techniques described for the production of single chain antibodies (U.S. Pat. No. 4,946,778) can be adapted to produce single chain antibodies specific to one of the binding partners.

[0103] Antibody fragments which recognize specific epitopes may be generated by known techniques. For example, such fragments include but are not limited to: the F(ab′)2 fragments which can be produced by pepsin digestion of the antibody molecule and the Fab fragments which can be generated by reducing the disulfide bridges of the F(ab′)2 fragments. Alternatively, Fab expression libraries may be constructed (Huse et al., 1989, Science, 246:1275-1281) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity.

[0104] 5.6 Gene Therapies Based on the p190 Gene

[0105] A variety of gene therapy approaches may be used in accordance with the invention to modulate expression of the p190 gene in vivo. For example, antisense DNA molecules may be engineered and used to block translation of p190 mRNA in vivo. Alternatively, ribozyme molecules may be designed to cleave and destroy the p190 mRNAs in vivo. In another alternative, oligonucleotides designed to hybridize to the 5′ region of the p190 gene (including the region upstream of the coding sequence) and form triple helix structures may be used to block or reduce transcription of the p190 gene. In yet another alternative, nucleic acid encoding the full length wild-type p190 message may be introduced in vivo into cells which otherwise would be unable to produce the wild-type p190 gene product in sufficient quantities or at all.

[0106] In a preferred embodiment, the antisense, ribozyme and triple helix nucleotides are designed to inhibit the translation or transcription of p190. To accomplish this, the oligonucleotides used should be designed on the basis of relevant sequences unique to p190. For example, and not by way of limitation, the oligonucleotides should not fall within those regions where the nucleotide sequence of p190 is most homologous to that of other known proteins.

[0107] Instead, it is preferred that the oligonucleotides fall within the regions of p190, which diverge from the sequence of other known proteins.

[0108] In the case of antisense molecules, it is preferred that the sequence be chosen from those divergent sequences just mentioned above. It is also preferred that the sequence be at least 18 nucleotides in length in order to achieve sufficiently strong annealing to the target mRNA sequence to prevent translation of the sequence. Izant and Weintraub, 1984, Cell, 36:1007-1015; Rosenberg et al., 1985, Nature, 313:703-706.

[0109] In the case of the “hammerhead” type of ribozymes, it is also preferred that the target sequences of the ribozymes be chosen from the above-mentioned divergent sequences. Ribozymes are RNA molecules which possess highly specific endoribonuclease activity. Hammerhead ribozymes comprise a hybridizing region which is complementary in nucleotide sequence to at least part of the target RNA, and a catalytic region which is adapted to cleave the target RNA. The hybridizing region contains nine (9) or more nucleotides. Therefore, the hammerhead ribozymes of the present invention have a hybridizing region which is complementary to the sequences listed above and is at least nine nucleotides in length. The construction and production of such ribozymes is well known in the art and is described more fully in Haseloff and Gerlach, 1988, Nature, 334:585-591.

[0110] The ribozymes of the present invention also include RNA endoribonucleases (hereinafter “Cech-type ribozymes”) such as the one which occurs naturally in Tetrahymena Thermophila (known as the IVS, or L-19 IVS RNA) and which has been extensively described by Thomas Cech and collaborators (Zaug, et al., 1984, Science, 224:574-578; Zaug and Cech, 1986, Science, 231:470-475; Zaug, et al., 1986, Nature, 324:429-433; published International patent application No. WO 88/04300 by University Patents Inc.; Been and Cech, 1986, Cell, 47:207-216). The Cech endoribonucleases have an eight base pair active site which hybridizes to a target RNA sequence whereafter cleavage of the target RNA takes place. The invention encompasses those Cech-type ribozymes which target eight base-pair active site sequences that are exclusive to p190.

[0111] In the case of oligonucleotides that hybridize to and form triple helix structures at the 5′ terminus of the p190 gene and can be used to block transcription, it is preferred that they be complementary to those sequences in the 5′ terminus of p190 which are not present in other related proteins. However, it is preferred that the sequences not include those regions of the p190 promoter which are even slightly homologous to that of other known proteins.

[0112] The foregoing compounds can be administered by a variety of methods which are known in the art including, but not limited to the use of liposomes as a delivery vehicle. Naked DNA or RNA molecules may also be used where they are in a form which is resistant to degradation such as by modification of the ends, by the formation of circular molecules, or by the use of alternate bonds including phosphothionate and thiophosphoryl modified bonds. In addition, the delivery of nucleic acid may be by facilitated transport where the nucleic acid molecules are conjugated to poly-lysine or transferrin. Nucleic acid may also be transported into cells by any of the various viral carriers, including but not limited to, retrovirus, vaccinia, AAV, and adenovirus.

[0113] Alternatively, a recombinant nucleic acid molecule which encodes, or is, such antisense, ribozyme, triple helix, or p190 molecule can be constructed. This nucleic acid molecule may be either RNA or DNA. If the nucleic acid encodes an RNA, it is preferred that the sequence be operatively attached to a regulatory element so that sufficient copies of the desired RNA product are produced. The regulatory element may permit either constitutive or regulated transcription of the sequence. In vivo, that is, within the cells or cells of an organism, a transfer vector such as a bacterial plasmid or viral RNA or DNA, encoding one or more of the RNAs, may be transfected into cells e.g. (Llewellyn et al., 1987, J. Mol. Biol., 195:115-123; Hanahan et al. 1983, J. Mol. Biol., 166:557-580). Once inside the cell, the transfer vector may replicate, and be transcribed by cellular polymerases to produce the RNA or it may be integrated into the genome of the host cell. Alternatively, a transfer vector containing sequences encoding one or more of the RNAs may be transfected into cells or introduced into cells by way of micromanipulation techniques such as microinjection, such that the transfer vector or a part thereof becomes integrated into the genome of the host cell.

[0114] 5.7 Drug Screening Assays

[0115] The present invention provides a simple in vitro system for the screening of drug actions on p190, which will be useful for the development of drugs that modulate the growth, differentiation or survival of neurons. Assays can be performed on living mammalian cells, which more closely approximate the effects of a particular serum level of drug in the body, or on microsomal extracts prepared from the cultured cell lines. Studies using microsomal extracts offer the possibility of a more rigorous determination of direct drug/enzyme interactions.

[0116] The p190-synthesizing cell lines are useful for evaluating the activity of potential bioactive agents on p190.

[0117] The present invention also provides a second mammalian cell line which contains a chromosomally integrated, recombinant DNA sequence, wherein said DNA sequence expresses mammalian, p190, and wherein said cell line also preferably does not express autologous p190 activity. This second cell line is also preferably a primate, murine or human cell line.

[0118] Thus, the present invention also provides a method to evaluate.

[0119] The invention also relates to methods for the identification of genes, termed “pathway genes”, which are associated with the p190 gene product or with the biochemical pathways which extend therefrom. “Pathway gene”, as used herein, refers to a gene whose gene product exhibits the ability to interact with the p190 gene product.

[0120] Any method suitable for detecting protein-protein interactions may be employed for identifying pathway gene products by identifying interactions between gene products and the p190 gene product. Such known gene products may be cellular or extracellular proteins. Those gene products which interact with such known gene products represent pathway gene products and the genes which encode them represent pathway genes.

[0121] Among the traditional methods which may be employed are co-immunoprecipitation, crosslinking and co-purification through gradients or chromatographic columns. Utilizing procedures such as these allows for the identification of pathway gene products. Once identified, a pathway gene product may be used, in conjunction with standard techniques, to identify its corresponding pathway gene. For example, at least a portion of the amino acid sequence of the pathway gene product may be ascertained using techniques well known to those of skill in the art, such as via the Edman degradation technique (see, e.g., Creighton, 1983, Proteins: Structures and Molecular Principles, W. H. Freeman & Co., N.Y., pp. 34-49). The amino acid sequence obtained may be used as a guide for the generation of oligonucleotide mixtures that can be used to screen for pathway gene sequences. Screening made be accomplished, for example by standard hybridization or PCR techniques. Techniques for the generation of oligonucleotide mixtures and screening are well-known. (See, e.g., Ausubel et al., eds., 1987-1993, Current Protocols in Molecular Biology, John Wiley & Sons, Inc. New York, and PCR Protocols: A Guide to Methods and Applications, 1990, Innis, M. et al., eds. Academic Press, Inc., New York).

[0122] Additionally, methods may be employed which result in the simultaneous identification of pathway genes which encode the protein interacting with the p190 gene product. These methods include, for example, probing expression libraries with labeled protein known or suggested to be involved in cardiovascular disease, using this protein in a manner similar to the well known technique of antibody probing of &lgr;gt11 libraries.

[0123] One such method which detects protein interactions in vivo, the two-hybrid system, is described in detail for illustration only and not by way of limitation. One version of this system has been described (Chien et al., 1991, Proc. Natl. Acad. Sci. USA, 88:9578-9582) and is commercially available from Clontech (Palo Alto, Calif.).

[0124] Briefly, utilizing such a system, plasmids are constructed that encode two hybrid proteins: one consists of the DNA-binding domain of a transcription activator protein fused to a known protein, and the other consists of the activator protein's activation domain fused to an unknown protein that is encoded by a cDNA which has been recombined into this plasmid as part of a cDNA library. The plasmids are transformed into a strain of the yeast Saccharomyces cerevisiae that contains a reporter gene (e.g., lacZ) whose regulatory region contains the activator's binding sites. Either hybrid protein alone cannot activate transcription of the reporter gene: the DNA-binding domain hybrid because it does not provide activation function and the activation domain hybrid because it cannot localize to the activator's binding sites. Interaction of the two proteins reconstitutes the functional activator protein and results in expression of the reporter gene, which is detected by an assay for the reporter gene product.

[0125] The two-hybrid system or related methodology may be used to screen activation domain libraries for proteins that interact with the p190 gene product, herein also called the known “bait” gene protein. Total genomic or cDNA sequences may be fused to the DNA encoding an activation domain. Such a library and a plasmid encoding a hybrid of the bait gene protein fused to the DNA-binding domain may be cotransformed into a yeast reporter strain, and the resulting transformants may be screened for those that express the reporter gene. These colonies may be purified and the library plasmids responsible for reporter gene expression may be isolated. DNA sequencing may then be used to identify the proteins encoded by the library plasmids.

[0126] For example, and not by way of limitation, the bait gene may be cloned into a vector such that it is translationally fused to the DNA encoding the DNA-binding domain of the GAL4 protein.

[0127] A cDNA library of the cell line from which proteins that interact with bait gene are to be detected can be made using methods routinely practiced in the art. According to the particular system described herein, for example, the cDNA fragments may be inserted into a vector such that they are translationally fused to the activation domain of GAL4. This library may be co-transformed along with the bait gene-GAL4 fusion plasmid into a yeast strain which contains a lacZ gene driven by a promoter which contains the GAL4 activation sequence. A cDNA encoded protein, fused to the GAL4 activation domain, that interacts with bait gene will reconstitute an active GAL4 protein and thereby drive expression of the lacZ gene. Colonies which express lacZ may be detected by their blue color in the presence of X-gal. The cDNA may then be purified from these strains, and used to produce and isolate the bait gene-interacting protein using techniques routinely practiced in the art.

[0128] Once a pathway gene has been identified and isolated, it may be further characterized as, for example, discussed herein.

[0129] The proteins identified as products of pathway genes may be used to modulate p190 gene expression, as defined herein, or may themselves be targets for modulation to in turn modulate symptoms associated with p190 expression.

[0130] 5.8 Compounds Identified in the Screens

[0131] The compounds identified in the screen will demonstrate the ability to selectively modulate the expression of p190. These compounds include but are not limited to nucleic acid encoding p190 and homologues, analogues, and deletions thereof, as well as antisense, ribozyme, triple helix, antibody, and polypeptide molecules and small inorganic molecules.

[0132] 5.9 Pharmaceutical Formulations and Routes of Administration

[0133] Any of the identified compounds can be administered to an animal host, including a human patient, by itself, or in pharmaceutical compositions where it is mixed with suitable carriers or excipient(s) at doses therapeutically effective to treat or ameliorate a variety of disorders, including those characterized by insufficient, aberrant, or excessive p190 activity or neurite growth, differentiation or survival, including but not limited to: ALS; general ataxia; Parkinson's disease; Alzheimer's disease; Huntington's disease; general neuropathy; cerebral palsy; neurologic trauma; and mental retardation. A therapeutically effective dose further refers to that amount of the compound sufficient to result in amelioration of symptoms associated with such disorders. Techniques for formulation and administration of the compounds of the instant application may be found in “Remington's Pharmaceutical Sciences,” Mack Publishing Co., Easton, Pa., latest edition.

[0134] A number of disorders may be characterized by insufficient, aberrant, or excessive p190 activity. In addition, several physiological states which may, from time to time be considered undesired, may also be associated with p190 activity. By way of example, but not by way of limitation, such disorders and physiological states which may be treated with the compounds of the invention include but are not limited to those characterized by insufficient, aberrant, or excessive neurite growth, differentiation or survival, including but not limited to: ALS; general ataxia; Parkinson's disease; Alzheimer's disease; Huntington's disease; general neuropathy; cerebral palsy; neurologic trauma; and mental retardation.

[0135] The compounds of the invention may be designed or administered for tissue specificity. If the compound comprises a nucleic acid molecule, including those comprising an expression vector, it may be linked to a regulatory sequence which is specific for the target tissue, such as the brain, skin, joints, bladder, kidney, liver, ovary, etc. by methods which are known in the art including those set forth in Hart, 1994, Ann. Oncol., 5 Suppl 4: 59-65; Dahler et al., 1994, Gene, 145: 305-310; DiMaio et al., 1994, Surgery, 116:205-213; Weichselbaum et al., Cancer Res., 54:4266-4269; Harris et al., 1994, Cancer, 74 (Suppl. 3):1021-1025; Rettinger et al., Proc. Nat'l. Acad. Sci. USA, 91:1460-1464; and Xu et al, Exp. Hematol., 22:223-230; Brigham et al., 1994, Prog. Clin. Biol. Res., 388:361-365. The compounds of the invention may be targeted to specific sites of inflammation by direct injection to those sites, such as joints, in the case of arthritis. Compounds designed for use in the central nervous system should be able to cross the blood brain barrier or be suitable for administration by localized injection. Similarly, compounds specific for the bladder can be directly injected therein. Compounds may also be designed for confinement in the gastrointestinal tract for use against disorders such as colorectal carcinoma. In addition, the compounds of the invention which remain within the vascular system may be useful in the treatment of vascular inflammation which might arise as a result of arteriosclerosis, balloon angioplasty, catheterization, myocardial infarction, vascular occlusion, and vascular surgery and which have already been associated with p190 by Pritchard et al., 1994, J. Biol. Chem., 269, 8504-8509. Such compounds which remain within the bloodstream may be prepared by methods well known in the art including those described more fully in McIntire, 1994, Annals Biomed. Engineering, 22:2-13.

[0136] 5.9.1 Effective Dosage

[0137] Pharmaceutical compositions suitable for use in the present invention include compositions wherein the active ingredients are contained in an effective amount to achieve its intended purpose. More specifically, a therapeutically effective amount means an amount effective to prevent development of or to alleviate the existing symptoms of the subject being treated. Determination of the effective amounts is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein.

[0138] For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from cell culture assays. For example, a dose can be formulated in animal models to achieve a circulating concentration range that includes the IC50 (the dose where 50% of the cells show the desired effects) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans.

[0139] A therapeutically effective dose refers to that amount of the compound that results in amelioration of symptoms or a prolongation of survival in a patient. Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio between LD50 and ED50. Compounds which exhibit high therapeutic indices are preferred. The data obtained from these cell culture assays and animal studies can be used in formulating a range of dosage for use in human. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. (See e.g. Fingl et al., 1975, in “The Pharmacological Basis of Therapeutics”, Ch. 1 p1). Dosage amount and interval may be adjusted individually to provide plasma levels of the active moiety which are sufficient to maintain the desired effects.

[0140] In cases of local administration or selective uptake, the effective local concentration of the drug may not be related to plasma concentration.

[0141] The amount of composition administered will, of course, be dependent on the subject being treated, on the subject's weight, the severity of the affliction, the manner of administration and the judgment of the prescribing physician.

[0142] 5.9.2 Composition and Formulation

[0143] The pharmaceutical compositions of the present invention may be manufactured in a manner that is itself known, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes.

[0144] Pharmaceutical compositions for use in accordance with the present invention thus may be formulated in conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries which facilitate processing of the active compounds into preparations which can be used pharmaceutically. Proper formulation is dependent upon the route of administration chosen.

[0145] For injection, the agents of the invention may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks's solution, Ringer's solution, or physiological saline buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.

[0146] For oral administration, the compounds can be formulated readily by combining the active compounds with pharmaceutically acceptable carriers well known in the art. Such carriers enable the compounds of the invention to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like, for oral ingestion by a patient to be treated. Pharmaceutical preparations for oral use can be obtained 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, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carboxymethylcellulose, and/or polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.

[0147] Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used, which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.

[0148] 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 plasticizer, such as glycerol or sorbitol. The push-fit capsules can contain the active ingredients in admixture with filler such as lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active compounds may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added. All formulations for oral administration should be in dosages suitable for such administration.

[0149] For buccal administration, the compositions may take the form of tablets or lozenges formulated in conventional manner.

[0150] For administration by inhalation, the compounds for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas. In the case of a pressurized aerosol the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of e.g. gelatin for use in an inhaler or insufflator may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

[0151] The compounds may be formulated for parenteral administration by injection, e.g., by bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multi-dose containers, with an added preservative. The compositions may take such forms as suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.

[0152] Pharmaceutical formulations for parenteral administration include aqueous solutions of the active compounds in water-soluble form. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. Aqueous injection suspensions may contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions.

[0153] Alternatively, the active ingredient may be in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.

[0154] The compounds may also be formulated in rectal compositions such as suppositories or retention enemas, e.g., containing conventional suppository bases such as cocoa butter or other glycerides.

[0155] In addition to the formulations described previously, the compounds may also be formulated as a depot preparation. Such long acting formulations may be administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, the compounds may be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.

[0156] A pharmaceutical carrier for the hydrophobic compounds of the invention is a cosolvent system comprising benzyl alcohol, a nonpolar surfactant, a water-miscible organic polymer, and an aqueous phase. Naturally, the proportions of a co-solvent system may be varied considerably without destroying its solubility and toxicity characteristics. Furthermore, the identity of the co-solvent components may be varied.

[0157] Alternatively, other delivery systems for hydrophobic pharmaceutical compounds may be employed. Liposomes and emulsions are well known examples of delivery vehicles or carriers for hydrophobic drugs. Certain organic solvents such as dimethylsulfoxide also may be employed, although usually at the cost of greater toxicity. Additionally, the compounds may be delivered using a sustained-release system, such as semipermeable matrices of solid hydrophobic polymers containing the therapeutic agent. Various of sustained-release materials have been established and are well known by those skilled in the art. Sustained-release capsules may, depending on their chemical nature, release the compounds for a few weeks up to over 100 days. Depending on the chemical nature and the biological stability of the therapeutic reagent, additional strategies for protein stabilization may be employed.

[0158] The pharmaceutical compositions also may comprise suitable solid or gel phase carriers or excipients. Examples of such carriers or excipients include but are not limited to calcium carbonate, calcium phosphate, various sugars, starches, cellulose derivatives, gelatin, and polymers such as polyethylene glycols.

[0159] Many of the compounds of the invention may be provided as salts with pharmaceutically compatible counterions. Pharmaceutically compatible salts may be formed with many acids, including but not limited to hydrochloric, sulfuric, acetic, lactic, tartaric, malic, succinic, etc. Salts tend to be more soluble in aqueous or other protonic solvents that are the corresponding free base forms.

[0160] 5.9.3 Routes of Administration

[0161] Suitable routes of administration may, for example, include oral, rectal, transmucosal, transdermal, or intestinal administration; parenteral delivery, including intramuscular, subcutaneous, intramedullary injections, as well as intrathecal, direct intraventricular, intravenous, intraperitoneal, intranasal, or intraocular injections.

[0162] Alternately, one may administer the compound in a local rather than systemic manner, for example, via injection of the compound directly into an affected area, often in a depot or sustained release formulation.

[0163] Furthermore, one may administer the drug in a targeted drug delivery system, for example, in a liposome coated with an antibody specific for affected cells. The liposomes will be targeted to and taken up selectively by the cells.

[0164] 5.9.4 Packaging

[0165] The compositions may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient. The pack may for example comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration. Compositions comprising a compound of the invention formulated in a compatible pharmaceutical carrier may also be prepared, placed in an appropriate container, and labelled for treatment of an indicated condition. Suitable conditions indicated on the label may include treatment of a disease such as one characterized by insufficient, aberrant, or excessive neurite growth, differentiation, or survival.

6. EXAMPLE

The Interaction Between Contactin and the CAH Domain of RPTP&bgr;

[0166] The subsections below describe the biological interaction between contactin and the CAH domain of RPTP&bgr;. The data demonstrate that ligands for RPTP&bgr; are differentially expressed in. neuronal and glial cell lines. In addition, it is shown that a 140 kDa protein from these cell lines interacts with the CAH domain of RPTP&bgr;, and that this 140 kDa protein is contactin. The data also demonstrate that RPTP&bgr; interacts with both membrane-bound and soluble contactin.

[0167] 6.1. Materials and Methods

[0168] 6.1.1. Cell Culture

[0169] SF763T and SF767T human astrocytoma cell lines were grown in athymic nu/nu mice to create a tumor derived cell line. The parental lines (SF763 and SF767) were generously provided by Dr. Michael E. Bernes (The Barrow Neurological Institute, Phoenix, Ariz.). All other cell line used were supplied by the American Type Culture Collection (Rockville, Md.). For culturing of rat sensory neuron, spinal sensory ganglia were dissected from newborn rat pups and dissociated by incubation with trypsin (0.05% for 10 minutes). The ganglia were washed several times in L15+10% fetal calf serum, and triturated with a pasteur pipette. The resulting single cell suspension was not subjected to preplating. The cells were plated at 15,000 cells per well in an eight-well chamber slide (Nunc) precoated with 10 mg/ml laminin in PBS. The medium was L15/CO2 with supplements as described (Hawrot and Patterson, 1979, Meth. Enzymol., 58:547-584), and nerve growth factor was added at 50 ng/ml. The cells were cultured for two days prior to staining.

[0170] 6.1.2. Generation and Production of Fc-Fusions

[0171] To construct the Fc-fusion molecule, different subdomains of RPTP&bgr; extracellular region were amplified using pfu (Stratagene, La Jolla, Calif.) and cloned into a unique BamHI site upstream from the hinge region of human IgG1-Fc. For the construction of &bgr;C and &bgr;CF fusions a DNA fragment was amplified from position -20, within the Bluescript sequence to position 939 and 1245 respectively (&bgr;C-Fc aa 1-313, &bgr;CF-Fc aa 1-415) (Levy et al., 1993, J. Biol. Chem., 268:10573-10581). In frame fusion was made by creating a BamHI site in the 3′ primer maintaining the original amino acids sequence in the fusion junction. These fragments were further cloned into HindIII-BamHI linearized pC&ggr;1 vector, a modified version of pIG1 that contained a cDNA form instead of the genomic fragment of human IgG (Simmons, 1993, in Cellular Interactions in Development. A Practical Approach, Hartley (ed.), IRL Press). The same strategy was used to construct human contactin-Fc (Hcon-Fc) fusion molecule. Briefly, total RNA was prepared from Y79 retinoblastoma cells and converted to single strand cDNA using SuperScript II reveres transcriptase (Gibco-BRL) following the suppliers protocol. This cDNA was use as a template to clone human contactin by three overlapping PCR reactions into EcoRI-BamHI sites of pC&ggr;1 vector. In order to use these sites, the EcoRI site at position 3173 (Reid et al., 1994, Brain Res. Mol. Brain Res., 21:1-8), was eliminated by changing a single base during the PCR reaction. The final construct contained amino acids 1-1020 of human contactin fused to the IgG region. To construct &bgr;F-Fc the region between nucleotides 901 to 1242 was amplified with a set of primers that introduced SacII and BamHI sites in the ends of the fragment. This fragment was cloned into pCN&ggr;1 between the globulin gene and a sequence encoding a signal peptide derived from TGF&bgr; gene (Plowman et al., 1992, J. Biol. Chem., 267:13073-13078). The integrity of all the above constructs was checked by complete nucleotide sequence determination or by restriction enzyme analysis. Fusion proteins were produced transiently in COS7 cells or by cotransfection with pN1012-Neo into 293 cells and selecting for individual G418 resistant clones as described (Peles et al., 1991, EMBO J., 10:2077-2086). Purification of fusion proteins was achieved by affinity chromatography on Protein-A Sepharose CL 4B (Pharmacia). Bound proteins were eluted with 100 mM sodium citrate PH 2.5, 1M MgCl2, followed by buffer exchange on a PD-10 desalting column (Pharmacia). The proteins were analyzed by gel electrophoresis followed by silver staining (ICN, Costa Mesa, Calif.). Concentration of the purified proteins was determined by bradford reagent (BioRad, Richmond, Calif.), and by an ELISA assay using peroxidase coupled antibody against human IgG (Pierce, Roxford, Ill.). The same antibody was used to detect the fusion proteins by western blotting followed by chemiluminescence reagent (ECL; Amersham) as described previously (Peles et al., 1992, Cell, 69:205-216).

[0172] 6.1.3. Expression Cloning in COS Cells

[0173] Total cellular RNA was prepared from GH3 cells using acid guanidinium thiocyanate extraction (Chomczynski and Sacchi, 1987, Anal. Biochem., 162:156-159), and Poly(A) RNA was isolated by two passages over an oligo dT cellulose column (Pharmacia). cDNA was synthesized using the Superscript kit (Gibco BRL, Bethesda, Md.) by priming with a random primer that contained a HindIII site. Following the addition of EcoRI adaptors the double-stranded cDNA was size selected on agarose gel. cDNAs larger then 2 kb were ligated into a EcoRl and HindIII-digested pcMP1 plasmid vector, a derivative of the pCMV-1 vector (Lammers et al., 1993, J. Biol. Chem., 168:24456-22462). E. coli DH10B cells (GIBCO BRL) were transformed by electroporation REF. This procedure generated a cDNA library with 2×106 independent clones. Pools of 3000 bacterial clones were grown for 24 hours and scraped from plates using, LB containing 15% glycerol. Twenty percent of the cultures were saved as glycerol stocks at −70° C. and plasmid DNA was prepared from the rest using the Wizard plasmid purification kit (Promega).

[0174] Plasmid DNA (10 &mgr;g) was transfected into COS7 cell grown on chamber slides (Nunc) with lipofectamin (GIBCO BRL). After 72 hours cells were incubated for one hour with medium containing 0.5 &mgr;g/ml &bgr;CF-Fc. Unbound Fc-fusion proteins were removed by three washes with cold DMEM/F12 and the cells were fixed with 4% paraformaldehyd in PBS. Immunostaining was performed with ABC staining system (Vector Lab), using biotinylated anti-human IgG antibodies (Fc specific; Jackson Labs, West Grove, Pa.) following by streptavidin alkaline phosphatase and NBT/BCIP as substrate according to the protocol provided by the manufacturer. One positive pool (#54) was subdivided and rescreened until a single clone (F8) was isolated.

[0175] DNA sequence determination was carried out using the dideoxy-chain termination method (Sanger et al., 1977, Proc. Natl. Acad. Sci., USA 74:5463), with Sequenase 2.0 (United States Biochemical Corporation, Cleveland, Ohio). Sequencing was performed on both strands by priming with synthetic oligonucleotides.

[0176] 6.1.4. Construction of RPTP&bgr;/EGF-Receptor Chimeras

[0177] To generate a plasmid for the expression of &bgr;CF/EK chimeras, a portion of the extracellular domain of RPTP&bgr; containing the CAH and the FINIII domains (&bgr;CF, aa 1-418) was fused to the human EGF receptor at position 634, twelve amino acids after the transmembrane domain in its extracellular region. These fragments were amplified using pfu (Stratagene, La Jolla, Calif.) with a specific set of primers that introduce a BstBI site at the junction between the two genes. The resulting fragments were ligated into Bluescript (Stratagene, La Jolla, Calif.). Proper fusion between the two molecules was verified by nucleotide sequence analysis. This chimeric gene was then subcloned into a NotI site in the reteroviral vector SR&agr;-SL and viral stocks where prepared by cotransfecting COS-7 cells with this vector along with a helper virus plasmid (Muller et al., 1991, Mol. Cell. Biol., 11:1785-1792). These viruses where used to infect NIH 3T3 (clone 2.2), which lack endogenous EGF-receptor. Following infection, cells where selected in a medium containing 1 mg/ml G418 (Gibco-BRL) and resistant colonies were individually grown and assayed for the expression of the chimeric receptor by Western blotting with antibodies against the carboxyl terminus of the EGF-R (Kris et al., 1985, Cell, 40:619-625) as described previously (Peles et al., 1992, Cell, 69:205-216).

[0178] 6.1.5. Binding of Fc-Fusion Proteins

[0179] Confluent monolayer of cells were incubated for one hour with conditioned medium containing 0.25-0.5 mg/ml Fc-fusion protein. The unbound proteins were removed by three washes with binding medium (0.1% BSA, 0.2% none fat dry milk in DMEM/F12) and the cells were further incubated with 1 ng/ml [125I]-Protein A (Amersham), for 30 minutes at 4° C. Plates were washed three times with cold binding medium and cell bound radioactivity was determined as described previously (Peles et al., 1993, EMBO J., 12:961-971). Cellular staining using the Fc-fusion proteins was done using the procedure described above for expression cloning.

[0180] 6.1.6. Chemical Crosslinking Experiments

[0181] Cells were incubated for four hours with medium containing, the different Fc-fusion proteins. Following three washes with cold PBS/Ca (1 mM CaCl2 in PBS), the cells were incubated for additional 30 minutes with PBS/Ca containing 1 mM DTSSP (3,3′-Dithiobis[sulfosuccinimidyl--propionate], Pierce, Rockford, Ill.). Free cross-linker was removed by additional PBS wash followed by quenching with 100 mM glycine in TBS for 10 minutes at 4° C. Cell lysates were made in SBN lysis buffer (Peles et al., 1991, EMBO J., 10:2077-2086), and Sepharose-protein A was added to the cleared lysates. Following two hours incubation at 4° C., the beads were washed three times with HNTG buffer (Peles et al., 1991, EMBO J., 10:2077-2086), and the bound proteins were eluted by adding SDS PAGE sample buffer containing 5% &bgr;-mercaptoethanol and further incubation for 10 minutes at 95° C.

[0182] 6.1.7. Protein Purification and Sequencing

[0183] Cellular membranes were prepared from 5×108 GH3 cells by homogenization in hypotonic buffer that included 10 mM Hepes pH 7.5, 1 mM EGTA, 1 mM MgCl2, 10 &mgr;g/ml aprotinin, 10 &mgr;g/ml leupeptin and 2 mM PMSF. Nuclei and unbroken cells were removed by low speed centrifugation (1000 g×10 minutes at 4° C.), and the supernatant was then subjected to high speed centrifugation at 40000 g (30 minutes at 4° C.). The membrane pellet was resuspended in SML solubilization buffer (2% Sodium monolaurate, 2 mM MgCl2, 2 mM PMSF in PBS). After one hour incubation on ice the detergent-insoluble materials was removed by centrifugation, and the sample was diluted tenfold with PBS containing 2 mM MgCl2. This sample was loaded on a column of &bgr;CF-FC bound to Sepharose Protein A (200 &mgr;g &bgr;CF-Fc/ml beads) at 4° C. The column was washed with SML buffer containing 0.15% detergent and the bound proteins were eluted by adding SDS sample buffer and heating to 95° C. Proteins were separated on 7.5% gel and electroblotted in CAPS buffer (100 mM CAPS, 10% MeOH) to ProBlott membrane (Applied Biosystems). The membrane was stained with coomassie R-250 and the 140 kDa band was excised and subjected to direct microsequencing analysis. Microsequencing was performed with an Applied Biosystems Model 494 sequencer, run using standard reagents and programs from the manufacturer.

[0184] To obtain internal peptide sequence the blotted band was moistened with neat acetonitrile, then reduced by the addition of 200 ul of 0.1 M Tris pH 8.5, 10 mM dithiothreitol, 10% acetonitrile. After incubation at 55° C. for 30′ the sample was cooled to room temperature and 20 ul of 0.25M 4-vinylpyridine in acetonitrile added. After 30 minutes at room temperature the blots were washed 5 times with 10% acetonitrile. Digestion was performed for 16 hours with 1 ug modified trypsin (Promega) in 50 ul of 0.1M Tris pH 8.0, 10% acetonitrile, 1% octylglucoside. Digestion was stopped by the addition of 2 ul of neat trifluoroacetic acid (TFA). Peptides were separated on a 1 mm×200 mm Reliasil C-18 reverse phase column on a Michrom UMA HPLC run at 50 ul per minute. Solvents used were 0.1% TFA in water and 0.085% TFA in 95% acetonitrile/5% water. A linear gradient of 5 to 65% B was run over 60 minutes. Absorbance was monitored at 214 nm and peaks were collected manually into a 96 well polyethylene microtitre plate. Purified peptides were sequenced as described above.

[0185] 6.1.8. Treatment with PI-PLC

[0186] Cells grown to confluency in 90 mm dishes were metabolically labeled with 100&mgr; Ci/ml [35S]-methionine and cysteine mix (NEN, Boston, Mass.) for four hours at 37° C. Labeled cells were washed three times with MEM and incubated with 250 mU of phosphatidylinositol specific phospholipase C (PI-PLC, Boehringer Mannheim or a kind gift from Dr. J. Salzer) for 50 minutes at 37° C. The supernatant was collected and cleared by centrifugation (1000 g), membranes were prepared from the cells and further solubilized in SML buffer as described above. &bgr;CF-Fc bound to Sepharose-protein A beads was added to the supernatant and the membrane fractions for one hour at 4° C. The beads were washed twice with 0.15% sodium monolaurate in PBS and once in PBS before the addition of SDS sample buffer. The precipitated proteins were separated on 7.5% cell and subjected to autoradiography.

[0187] For binding experiments, cell were treated with different amounts of PI-PLC (as indicated in the legend to the figures) in MEM containing 0.5% BSA for 30-60 minutes at 37° C. Cells were briefly washed and binding of &bgr;CF-Fc was performed as described above.

[0188] 6.2. Results

[0189] 6.2.1. The CAH Domain of RPTP&bgr; Mediates an Interaction with Neurons

[0190] To identify cellular ligands for RPTP&bgr;, fusion proteins were constructed between different subdomains of RPTP&bgr; and the Fc portion of human IgG. Three chimeric constructs were made, one containing both the carbonic anhydrase and the fibronectin domains (&bgr;CF-Fc) and two others carrying each domain by itself (&bgr;C-FC or &bgr;F-FC). Initially, &bgr;CF-Fc was used to screen for a membrane bound ligand on the surface of different neuronal and glial cell lines. Several cell lines that bind this fusion protein were identified. These were the IMR-32 neuroblastoma cells, the two closely related neuroendocrine derived cell lines GH3 and GH1, and five different glioblastoma cell lines.

[0191] The fact that these positive cell lines were derived from glial and neuronal origins raised the possibility that RPTP&bgr; may interact with two different membrane-associated ligands. Alternatively, a single ligand may exist which is expressed by both neurons and glia cells. To explore these two possibilities it was examined whether a fusion protein that contained only the CAH domain of RPTP&bgr; (&bgr;C-Fc) will retain the same cell specificity observed with &bgr;CF-FC. It was reasoned that in a multidomain receptor like RPTP&bgr;, each domain might function as an independent unit in terms of its interaction with a specific ligand. Thus, the use of a single domain in binding experiments might allow the identification of a cell type specific ligand. As depicted in FIG. 2A, this fusion protein, indeed, binds to the same neuronal and neuroendocrine cell lines. In contrast, none of the glioblastomas were positive, suggesting that there are at least two ligands for RPTP&bgr; that are differentially expressed on neuronal or glial cells. This result also implied that the CAH domain mediates the interaction of RPTP&bgr; with a specific ligand present in neurons but not in glia cells.

[0192] Accordingly, if the binding of &bgr;C-FC to neuronal ligand reflects the interactions occurring in vivo, one would expect to see similar binding specificity on cultures of primary neurons. The binding of the different fusion proteins to cultured dorsal root ganglion cells (DRG), followed by detection of the bound proteins by immunostaining, was analyzed. &bgr;C-FC and &bgr;CF-FC bound to GH3 cells, as well as to the primary neurons. A fusion protein containing the fibronectin domain alone (&bgr;F-Fc) failed to bind to either GH3 cells or DRG neurons. In other experiments, binding of &bgr;F-FC to several glial cell lines was detected, but no binding of this domain to neuronal derived cell lines or neurons derived from rat DRGs and chick cortex was detected. In addition, it was examined whether the binding specificity observed with the CAH domain of RPTP&bgr; is unique to this receptor by comparing it with the related phosphatase RPTP&ggr; (Barnea et al., 1993, Mol. Cell. Biol., 13:1497-1506). A fusion protein made with the CAH domain of this highly homologous family member did not bind to GH3 cells or to primary neurons.

[0193] Altogether these results suggests that specific ligands for RPTP&bgr; exist on the surface of cells from neuronal and glial origin. Different subdomains of the receptor mediate its interaction with those distinct ligands. The CAH mediates an interaction with neurons while the FNIII enables the interaction of RPTP&bgr; with glia cells. In the work presented here, the identification and molecular characterization of the ligand for the CAH domain is described.

[0194] 6.2.2. Covalent Crosslinking Experiments Reveal a 140 kDa Protein that Interacts with the CAH Domain of RPTP&bgr;

[0195] To characterize ligands for RPTP&bgr;, a reversible cross-linker (DSSTP) was used, and proteins were sought that specifically bound to &bgr;C-Fc. Two of the cell lines that bound &bgr;C-Fc (IMR32 and GH3), as well as COS7 cells as a control, were allowed to react with the fusion proteins containing the FNIII or the CAH domains followed by cross-linking and precipitation of the complexes. As shown in FIG. 3, a protein of about 140 kilodalton specifically reacted with &bgr;C-Fc in the rat GH3 and human IMR-32 cells. No reactivity was detected in control cells or in cells incubated with &bgr;F-Fc. The cross-linker (DSSTP) used, undergoes cleavage in the reducing SDS PAGE conditions and, therefore, permits the identification of the true molecular weight of the putative ligand. This result suggested that the same ligand is expressed in the rat GH3 and the human IMR-32 lines.

[0196] 6.2.3. Molecular Cloning of a Candidate Ligand for RPTP&bgr; from Rat GH3 Cells Reveals the Rat Homologue of Contactin

[0197] An expression cloning strategy was employed in an effort to clone the gene that encodes the 140 kDa candidate ligand. we have employed. Plasmid pools made from a GH3-cDNA library were transfected into COS7 cells and the cells were screened for their ability to bind &bgr;CF-Fc. Positive cells were detected by immunostaining with biotinylated anti-human IgG antibodies and sterptavidin alkaline phosphatase. One positive pool was identified that when transfected yielded several stained cells on the slide. This pool was subdivided and rescreened four times until a single clone (F8) was isolated. Transfection of COS7 cells with this plasmid resulted in positive staining of approximately 25%-50% of the cells, a number that correlates well with the maximum transfection efficiency in our system. DNA sequence analyses of clone F8 showed that it contained a 3.9 kb insert and a single long open reading frame of 3063 nucleotides. The deduced 1021 amino acid sequence encoded by this clone has been presented elsewhere. Data bank search with this sequence showed that it shares 95% and 99% identity at the amino acid level with human and mouse contactin respectively (Berglund and Ranscht, 1994, Genomics, 21:571-582; Gennarini et al., 1989, J. Cell. Biol., 109:755-788; Reid et al., 1994, Brain Res. Mol. Brain Res., 21:1-8). It was therefore concluded that the ligand for RPTP&bgr; cloned from GH3 cells is the rat homologue of contactin. Structurally, this protein consists of six C2 type Ig domains, four fibronectin type III repeats and an hydrophobic region that mediates its attachment to the membrane by a GPI linkage (Gennarini et al., 1989, J. Cell. Biol., 109:755-788; Reid et al., 1994, Brain Res. Mol. Brain Res., 21:1-8). Functionally, it is a neural cell adhesion molecule that has been suggested to play a morphogenic role during the development of the nervous system (Rathjen et al., 1987, J. Cell. Biol., 104:343-353; Walsh and Doherty, 1991, Cell. Biol. Int. Rep., 15:1151-1166).

[0198] In parallel to the expression cloning strategy, and as a complementary approach, a biochemical procedure was employed that utilized the CAH domain as an affinity reagent for protein purification. p140 was purified from solubilized membranes prepared from GH3 cells on a column of &bgr;CF-Fc. After resolving the eluted protein on SDS/PAGE, the 140 kDa species was subject directly to N-terminal sequencing, or was digested with trypsin. Two peptide sequences obtained, one from the N-terminus and the other from an internal peptide after tryptic digest. Both sequences matched the translated F8 sequence and confirmed that contactin is indeed a ligand for the CAH domain of RPTP&bgr;.

[0199] 6.2.4. Binding Analysis of RPTPB and Contactin

[0200] The binding specificity of different subdomains of RPTP&bgr; towards contactin was examined. COS7 cells were transfected with rat contactin (clone F8) and analyzed for their ability to bind fusion proteins containing the CAH, FNIII or both domains. As expected, expression of contactin enabled the binding of the CAH domain of RPTP&bgr; to the cells. The FNIII domain alone did not bind to contactin expressing cells. In addition, similar results were obtained with a fusion protein that carries most of the extracellular region of the short form of RPTP&bgr; (aa 1-644; data not shown).

[0201] The reciprocal interaction, namely, whether soluble contactin molecules are able to bind specifically to cells expressing RPTP&bgr;, was explored next. In these experiments, COS7 cells were transfected with chimeric receptor constructs that consist of the entire extracellular region of the short form of RPTP&bgr; (&bgr;CFS/EK), the CAH domain plus the FNIII repeat (&bgr;CF/EK), or the CAH domain alone (&bgr;C/EK) fused to the transmembrane and intracellular domains of the EGF receptor. A chimeric receptor was used instead of the wild type phosphatase because the wild type phosphatase was not able to be expressed in heterologous cells. Human contactin-Fc fusion protein binds to cells transfected with these chimeric receptors but not to control cells. Taken together, these results demonstrate that expression of contactin is both necessary and sufficient for binding to the CAH domain RPTP&bgr;.

[0202] 6.2.5. Soluble Contactin Released from the Membrane by Phospholipase C Treatment Interacts with RPTP&bgr;

[0203] Contactin belongs to a family of recognition molecules that TAG-1 and BIG-1, all of which are anchored to the plasma membrane via a glycosyl-phosphatidylinositol (GPI). Therefore, it was of interest to see how phospholipase C (PI-PLC) treatment would effect the interaction between contactin and RPTP&bgr;. When incubated with COS7 cells expressing contactin (clone F8), PI-PLC completely abolished the binding of &bgr;CF-Fc to the cells. Similar results were obtained also with GH3 cells.

[0204] It has been demonstrated that members of this family and other GPI-linked proteins may exist either in a membrane bound or a secreted soluble form that is released from the cell surface (Furley et al., 1990, Cell, 61:157-170; Théveniau et al., 1992, J. Cell. Biochem., 48:61-72). Hence, it was examined whether the different forms of contactin, including those released after PI-PLC treatment, could interact with RPTP&bgr;. To this aim, GPI-linked proteins were released from metabolically labeled GH3 cells with the enzyme and purified contactin by bioaffinity precipitation from membrane extracts of the cells or the cell supernatants. Without PI-PLC treatment, two proteins p140 and p190 from the membrane fraction could specifically associate with &bgr;C-Fc. These proteins were not present in the supernatant and they were not detected with &bgr;F-Fc. However, after PI-PLC treatment, p140/contactin could be precipitated from the medium of the cells, indicating that the soluble form produced by phospholipase treatment interacts with RPTP&bgr;. This result may suggest that, in addition to the interaction between the membrane bound forms of these proteins, soluble contactin could potentially interact in vivo with RPTP&bgr;. &bgr;C-Fc could precipitate the 190 kilodaltons protein only from membrane fraction and not from the cell supernatant. PI-PLC treatment did not release this protein from the cells suggesting that it is either an integral membrane protein or a cytoskeletal protein associated with contactin complexes. Since contactin by itself is sufficient to mediate the interaction with RPTP&bgr;, the 190 kDa protein may be associated with contactin in the cells and coprecipitated with it during the bioaffinity procedure. One intriguing possibility is that p190 is a signaling unit used by contactin on the surface of neurons (see below).

7. EXAMPLE

The CAH Domain of RPTP&bgr; Induces Contactin Mediated Neurite Outgrowth

[0205] The subsections below describe the induction, by the CAH domain of RPTP&bgr;, of contactin mediated neurite outgrowth. It is shown that the CAH domain of RPTP&bgr; is a permissive substrate for neuronal adhesion and neurite growth. In addition, it is also shown that the neurite growth, differentiation and survival induced by the carbonic anhydrase-like domain of RPTP&bgr; is mediated by neuronal contactin.

[0206] 7.1. Materials and Methods

[0207] The materials and methods for this example were the same as those set forth in the example described in section 6.1 above, except as supplemented or amended below.

[0208] 7.1.1. Neurite Outgrowth Assays

[0209] Neurite outgrowth assays using IMR 32 cells were performed as described previously (Friedlander et al., 1994, J. Cell. Biol., 125:669-680) using 35 mm petri dishes coated with different proteins adsorbed on the substrate. After blocking the dishes with 1% BSA/PBS, the blocking solution was replaced with 3×104 cells suspended in 140 &mgr;l of DMEM/F12/ITS. Following incubation for 3 hrs at 37° C. during which time most of the cells adhered to the dish, the medium was removed and replaced with DMEM/FI2/ITS medium containing antibodies (Ig fraction purified by ammonium sulfate precipitation and DE52 chromatography). Dishes were incubated for 48 hrs and fixed with Hanks/0.3% sucrose 2.5% paraformaldehyde. For PI-PLC treatment, primary tectal neurons (5×104 cells/250 ml) were prepared from E9 chick embryos (Grumet et al., 1984, Proc. Natl. Acad. Sci. USA, 81:267-271) and incubated with 0.25 &mgr;l of PIPLC (1.7 U/ml) in DMEM/F12/ITS+ at 37° C. for 30 min. The cell suspension was then incubated on dishes coated with different substrates without changing the medium.

[0210] 7.2. Results

[0211] 7.2.1. Neurite Outgrowth Induced by the CAH Domain of RPTP&bgr; is Mediated Through Contactin

[0212] Contactin has been shown to be involved in both positive and negative responses of neurons to various stimuli (Brümmendorf and Rathjen, 1993, J. Neurochem., 61:127-1219). When presented as a ligand to neurons, either as a membrane-bound or a soluble form, contactin induces axonal growth (Brümmendorf et al., 1993, Neuron, 10:711-727; Clarke et al., 1993, Eur. J. Cell. Biol., 61:108-115; Durbec et al., 1992, J. Cell. Biol., 117:877-887; Gennarini et al., 1989, J. Cell. Biol., 109:755-788). Its neural receptor has been identified as the recognition molecule Nr-CAM (Morales et al., 1993, Neuron 11:1113-1122). On the other hand, contactin itself is a receptor present on neurons and mediates their repulsion by the extracellular matrix protein janusin (Pesheva et al., 1993, Neuron, 10:69-82). The results described in the example of Section 6.1 indicate that the CAH domain of RPTP&bgr; can bind to contactin on cells. To analyze effects of this binding on neurons, chick tectal cells, known to express contactin, were plated on dishes previously coated with &bgr;CF-Fc fusion protein or with Ng-CAM or laminin as controls. Cells attached and grow processes on both of these substrates. Treatment of the cells with PI-PLC prior to plating completely abolished cell attachment and neurite extension on RPTP&bgr;. In contrast, PI-PLC did not have a dramatic effect on cells growing on Ng-CAM or laminin as substrate. Thus, it was concluded that the CAH domain of RPTP&bgr; is a permissive substrate for neuronal adhesion and neurite growth. Moreover, the cell adhesion and axonal elongation induced by RPTP&bgr; is mediated through a GPI-anchored receptor.

[0213] Next it was investigated whether contactin could be the neuronal receptor for the CAH domain of RPTP&bgr;. To this aim, a human neuroblastoma cell line IMR-32 was used that has the capacity to differentiate and to elaborate neurites in response to different stimuli (Lüdecke and Unnsicker, 1990, Cancer, 65:2270-2278). These cells have fibroblastic morphology when crown on petri dishes coated with fibronectin, but on laminin substrates they assume a neuronal phenotype and extend processes with growth cones. A similar morphologic differentiation was seen after plating the cells on the CAH domain of RPTP&bgr;. In contrast, the CAH domain of RPTP&ggr; had no effect on cell adhesion and differentiation. These results show that IMR-32 cells respond specifically to the carbonic anhydrase domain of RPTP&bgr;. To determine whether contactin could be acting as a receptor on the IMR-32 cells for RPTP&bgr;, the effects of antibodies against contactin on the growth of cells on different substrates were tested. Antibodies against contactin inhibited the growth of processes on &bgr;C-Fc and &bgr;CF-Fc but not on laminin. In the presence of these antibodies, the IMR-32 cells also retracted their processes and many cells lifted off the dish yielding fewer cells after 2 days of incubation. No effect was observed with control antibodies. Thus, the neurite growth, differentiation and survival induced by the carbonic anhydrase-like domain of RPTP&bgr; is mediated by contactin present in the neurons.

8. EXAMPLE

The Cloning of p190 and the Interaction Between it and Contactin

[0214] The subsections below describe the purification and sequencing of p190 protein and the subsequent cloning of rat and human p190 cDNA. The interaction between p190 and contactin is also demonstrated.

[0215] 8.1 Materials and Methods

[0216] 8.1.1 Protein Purification and Sequencing

[0217] Solubilized membrane lysate was prepared from 3×109 GH3 cells and loaded on a column of &bgr;CF-Fc bound to Sepharose protein A (Pharmacia) as described previously (Peles et al., 1995, Cell, 82:251-260). Bound proteins were separated on 6.5% SDS gel, blotted to ProBlot membrane (Applied Biosystem, Inc.) and stained with Coomassie R-250. To obtain internal peptide sequence, the blotted 190 kDa band was moistened with neat acetonitrile and then reduced by the addition of 200 ul of 0.1M Tris pH 8.5, 10 mM dithiothreitol, 10% acetonitrile. Digestion was performed for 16 hours with 1 &mgr;g modified trypsin (Promega) in 50 &mgr;l of 0.1M Tris pH 8.0, 10% acetonitrile, 1% octylglucoside. Digestion was stopped by the addition of 2 &mgr;l of neat trifluoroacetic acid (TFA). Peptides were separated on a 1 mm×200 mm Reliasil C-18 reverse phase column on a Michrom UMA HPLC run at 50 ul per minute. Solvents used were 0.1% TFA in water and 0.085% TFA in 95% acetonitrile/5% water. A linear gradient of 5 to 65% B was run over 60 minutes. Absorbance was monitored at 214 nm and peaks were collected manually into a 96 well polyethylene microtiter plate. Purified peptides were sequenced as described (Peles et al., 1995, Cell, 82:251-260).

[0218] 8.1.2 Cloning of Rat and Human CASPR/p190 cDNA

[0219] The sequence of one tryptic peptide obtained from the purified protein (QNLPQILEES) was found in a 900 bp EST fragment B102/LF98 from the BRCA1 region on chromosome 17q21 (Friedman et al., 1994, Cancer Res., 54:6374-6382). Primers corresponding to this region (5′ primer: TCG CAG GCT ATG AGC CTG GCT ACA TCC; 3′ primer: GTG GGT AGG GGA GGT TTG CTG CCA GG) were use for RT-PCR to clone this DNA fragment from rat GH3 cells. A 600 bp DNA fragment derived from this region was further used as a probe to screen a ZAPEX-GH3 cDNA library. This cDNA library was constructed in ZAP-Express phage (Stratagene, San Diego, Calif.), using oligo dT priming. Plate hybridization and other cloning techniques were performed according to standard procedures (Sambrook et al., 1989, Molecular cloning: A Laboratory Manual, 2nd Edition (Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory)). Clone ZX5 had a 2.5 kb insert that contained in addition to the B102 fragment, a sequence downstream that matched additional peptide sequence. A second cDNA library was made from GH3 mRNA by priming with a specific oligonucleotide GGA GGT CTC CTT TAG according to the sequence that was found in the 5′ end of clone ZX5. This cDNA was cloned into ZAP-Express (Stratagene, San Diego, Calif.) to generate ZB-GH3 library. This library was use to isolate multiple clones that overlapped with ZX5 and contained the 5′ end of the gene. To clone the human gene a cDNA library was made from IMR32 neuroblastoma cells in ZAP-Express (ZX-IMR). Probes were generated by PCR from the 5′ ends of rat clone ZB181 and from IMR32 cDNA according to the B102 sequence as described above for the rat gene. Several clones had a 5 kb insert that contained the full length gene. DNA sequence determination was carried out using the dideoxy-chain termination method with Sequenase 2.0 (United States Biochemical Corporation, Cleveland, Ohio). Sequencing was performed on both strands by priming with synthetic oligonucleotides.

[0220] 8.1.3. Expression Constructs

[0221] An EcoRI-XhoI fragment containing the 5′ end of rat CASPR/p190 (from clone ZB161) was ligated with an XhoI-EcoRI fragment containing the 3′ end of the gene (from clone ZB181) and cloned into pCMP1 (Peles et al., 1995, Cell, 82:251-260) to generate pCM190R. An HA-tagged version of the gene was constructed by replacing an EcoRI-AccI fragment with a PCR-generated fragment containing the HA-tag sequence. This resulted in the addition of the HA sequence to the 3′ end of the coding region of rat CASPR/p190 to generate pCM190HA. Construction of contactin expression vectors was previously described (Peles et al., 1995, Cell, 82:251-260). The plasmids pSGT-cSRC and pSGT-fyn, containing human src and fyn genes and the plasmids used for generation of the GST-SH3s fusions were described previously (Erplel et al., 1995, EMBO J., 14:963-975). To generate a GST-fusion protein containing the cytoplasmic tail of rat CASPR/p190, the corresponding region (aa 1308-1380) was amplified by PCR and cloned into pGEX-4T (Pharmacia). The sequence of the final construct was verified by DNA sequencing.

[0222] 8.1.4. Northern Blot Analysis

[0223] Multiple tissue northern blots (MTN Blots, Clontech) were Used. A DNA fragment (position 3600-4232 of human CASPR/p190) was generated by RT-PCR from IMR32 mRNA. This fragment was labeled by random priming (“prime it”; Stratagene, San Diego, Calif.), purified using PCR-clean column (Qiagen) and used as a probe. Hybridization was carried out for 16 hours in a buffer containing 5×SSC, 5× Denhart's solution, 50% formamide, 0.2% SDS and 100 ug/ml denatured salmon sperm DNA at 42 oC. The blots were washed at 60 oC. twice in a buffer containing 0.5×SSC, 0.1% SDS and once with 0.1×SSC, 0.2% SDS. Signals were detected by autoradiography. The same membranes were reprobed with a 2 kb human &bgr;-actin cDNA as a control probe (Clontech, Palo Alto, Calif.).

[0224] 8.1.5. Immunohistochemistry and Ig-Fusion Binding

[0225] Production of different Ig-fusion chimeric proteins and cell binding experiments were done exactly as described previously (Peles et al., 1995, Cell, 82:251-260). Staining of tissue sections with antibodies was done essentially as described (Milev et al., 1994, J. Cell Biol., 127:1703-1715).

[0226] 8.1.6. Generation of Antibodies

[0227] Polyclonal antibodies against CASPR/p190 were generated according to standard procedures (Harlow, 1990, Antibodies: A Laboratory Manual). Ab60 was obtained by immunizing rabbits with a GST-fusion protein containing all the cytoplasmic domain of rat CASPR/p190 (GST-190CT). Affinity purification was achieved first by passing the serum on a column of Sepharose-GST. Then, the unbound material was loaded on a column of GST-190CT Sepharose. Bound antibodies were eluted with 100 mM sodium citrate pH 2.8 and 1.5 M MgCl2. Eluted material was precipitated with ammonium sulfate, resuspended in DDW and extensively dialysis against PBS. Antibody 87AP was generated against an eight aa long peptide corresponding to the C-terminal sequence of rat CASPR/p190. Affinity purification on a Sepharose-peptide column was done essentially as described above for Ab60. Antibodies against F3 were previously described (Faivre-Sarrailh et al., 1992, J. Neurosci., 12:257-267). Antibody CST1 that recognize Src, Fyn and Yes was previously described (Erplel et al., 1995, EMBO J., 14:963-975). Ab18 against Src and Ab16 against Fyn were purchased from Santa Cruz Antibodies (Santa Cruz, Calif.). Monoclonal antibody against HA-tag was purchase from Boehringer. Mouse polyclonal antibody against contactin was generated by immunization of mice with purified human contactin-Ig fusion protein according to Yoshihara et al, 1994, Neuron, 13:415-426.

[0228] 8.1.7. Generation of Anti HCon-Ig Sera

[0229] Immunoprecipitation and Western blot analysis: COS transfection protocol using Lipofectamine (Gibco-BRL) was previously described (Peles et al., 1995, Cell, 82:251-260). To detect the association between Contactin and CASPR/p190 the cells were grown to subconfluency and were metabolically labeled with 100 mCi/ml [35S]-methionine and cysteine mix (NEN, Boston, Mass.) for four hours at 37° C. Membranes were prepared from the cells and further solubilized in SML buffer (2% Sodium monolaurate, 2 mM MgCl2, 2 mM PMSF in PBS). &bgr;C-Fc bound to Sepharose-protein A beads was added to a tenfold diluted supernatant and incubated for two hours at 4° C. The beads were washed twice with 0.15% sodium monolaurate in PBS and once in PBS before the addition of SDS sample buffer. The precipitated proteins were separated on 7.5% gel and subjected to autoradiography.

[0230] Preparation of rat brain membranes: five P7 rat brains were pooled and homogenized in a glass homogenizer in a buffer containing 20 mM Hepes pH 7.4, 0.32 M sucrose, 1 mM EGTA, 1.5 mM MgSO4, 10 &mgr;g/ml Aprotinin and Leupeptin and 1 mM PMSF. Nuclei and heavy cell debris were removed by low speed centrifugation (3000 g×10 minutes at 4° C.), and the supernatant was then subjected to high speed centrifugation at 40,000 g for 60 minutes. The membrane pellet was resuspended in SML solubilization buffer. After one hour incubation on ice the detergent-insoluble materials was removed by centrifugation. The sample was diluted four to tenfold with PBS containing 2 mM MgCl2 and subjected to precipitation with antibodies or Ig-fusions.

[0231] Biotinylation of cell surface molecules was carried out for 20 minutes at 23° C. using 50 &mgr;g/ml Biotin-LC-NHS (Pierce). The reaction was stopped by adding NH4Cl to final concentration of 10 mM followed by two washes with TBS-glycine buffer (50 mM Tris pH 7.4, 150 mM NaCl and 50 mM glycine) on ice prior to solubilization.

[0232] Immunoprecipitation and western blotting was performed as described previously (Peles et al, 1992, Cell, 69:205-216). Blots were reacted with streptavidin-linked peroxidase (Amersham) and detected using chemiluminescence reagent (Pierce).

[0233] 8.2. Results

[0234] 8.2.1. CASPR/p190 Gene and Gene Products

[0235] The 190 kD protein which associates with the CAH-contactin complex was purified using affinity chromatography with &bgr;C-Fc, utilizing the techniques described, above, in Section 8.1. Briefly, membrane lysates from GH3 cells were applied to a &bgr;C-Fc column and bound proteins were separated by SDS-PAGE. The protein believed to correspond to p190 was excised and subjected to trypsin digestion. The amino acid sequences of two tryptic peptides were determined using a gas-phase microsequencer. The amino acid sequences obtained were then utilized to identify corresponding DNA fragments encoding such sequences, as described, above, in Section 8.1. The DNA fragments thus obtained were in turn used to isolate cDNA molecules encoding the full length p190 gene products of both human and rat.

[0236] The human CASPR/p190 nucleic acid sequence is depicted in SEQ ID NO:1, and the human CASPR/p190 amino acid sequence is depicted in SEQ ID NO:2. The rat CASPR/p190 nucleic acid sequence is depicted in SEQ ID NO:3, and the rat CASPR/p190 amino acid sequence is depicted in SEQ ID NO:4.

[0237] The human and rat CASPR/p190 transcripts have open reading frames that encode for 1384 and 1381 amino acids, respectively, and share 93% identity at the amino acid level. CASPR/p190 is a putative type I transmembrane protein with a short proline-rich cytoplasmic domain. (The transmembrane domain is marked as TMD in FIG. 1).

[0238] The first p190 methionine is followed by a stretch of 19-20 amino acid residues rich in hydrophobic residues, which probably acts as a signal sequence. The extracellular domains of rat and human CASPR/p190 contain 1281 and 1282 amino acid residues, respectively. The extracellular region of CASPR/p190 contains 16 potential N-linked glycosylation sites followed by a second hydrophobic stretch that is a typical transmembrane domain.

[0239] The CASPR/p190 extracellular domain is a mosaic of several motifs known to mediate protein-protein interactions. Near the N-terminus of mature CASPR/p190 (109 amino acid residues) is a domain with 31-33% amino acid identity to the C1 and C2 terminal domains of coagulation factors V and VIII (Jenny et al., 1987, Proc. Natl. Acad. Sci. U.S.A., 84:4846-50; Wood et al., 1984, Nature, 312:330-37) and 26% identity with the neuronal adhesion molecule neurophilin (previously known as the neuronal A5 antigen) and 20% identity to a region of discoidin I, a lectin from the slime mold Dictyostelium discoideum (Takagi et al., 1991, Neuron, 7:295-307). The domain is marked as DISC in FIG. 1. The extracellular domain of CASPR/p190 also contains four repeats, of approximately 140 amino acid residues each, with homology to neurexins, a family of polymorphic neuronal cell surface proteins. These domains are marked as NX1-NX4 in FIG. 1. There are 6 copies of the motif in the &agr;-neurexins, one in the &bgr;-neurexins, and one to five in the C-terminal portions of laminin A, agrin, slit, and perlecan (Ushkaryov et al., 1992, Science, 257:50-56). Together, the five motifs in the basement membrane protein laminin A are referred to as the G domain, a region suggested to mediate cell adhesion. The first three neurexin motifs of CASPR/p190 share 29-32% amino acid identity to regions of rat neurexinIII-&agr; and neurexinII-&agr;, whereas the fourth motif is most similar to agrin (34% identity). CASPR/p190 also contains two epidermal growth factor (EGF)-like modules (marked as EGF1-EGF2 in FIG. 1); both of which are most related to repeats within the drosophila neurogenic proteins Notch and slit (39-46% identity) (Rothberg et al., 1988, Cell, 55:1047-59; Wharton et al., 1985, Cell, 43:567-81). A single domain related to the C-terminal region of fibrinogen beta/gamma (marked as FIB in FIG. 1) is flanked by an EGF and neurexin motif. Finally, there is a stretch of 47 amino acids, that is identical between human and rat CASPR/p190, and contains seven copies of Pro-Gly-Tyr-X1-2 and three additional imperfect repeats of this sequence (marked as PGY in FIG. 1). The Pro-Gly-Tyr repeat is found in a molluscan adhesive protein (SW:A61077, and a putative chicken prior protein (SW:A46280), whereas the Pro-X-Tyr repeat is present in multiple copies in a soybean cell wall protein (SW:A29324) and the X-Gly-Tyr repeat in heterogeneous nuclear RNP proteins (SW:B41732). The cytoplasmic domain of human and rat CASPR/p190 contain 78 and 74 amino acids, respectively. These include a 38-42 amino acid proline-rich motif (38% proline), the majority of which consists of proline residues alternating with alanine, glycine, or threonine residues (marked as PRO in FIG. 1). Alignment of this region with the non-redundant protein database revealed several proteins containing such “PAPA” motifs. Proline-rich domains can serve as binding sites for SH3-containing protein, yet none of the proteins that align with this domain of CASPR/p190 are known to interact with an SH3 motif.

[0240] 8.2.2. CASPR/p190 Expression

[0241] Northern blot analysis of mRNA isolated from human tissues reveals that CASPR/p190 was expressed predominantly in the brain as a 6.2 kb transcript. Weak expression of CASPR/p190 was detected in ovary, as well as in the pancreas, colon, lung, heart, intestine and testis. Similar results wee obtained for rat tissue hybridized with a rat CASPR/p190 probe.

[0242] A high level of CASPR/p190 was detected in different regions of the adult human nervous system, including high expression in the cortex, cerebellum and in the thalamus, while weaker expression is detected in the spinal cord and in the corpus callosum. These analyses demonstrated that the CASPR/p190 gene was expressed predominantly in the central nervous system.

[0243] Polyclonal rabbit antibodies raised against a GST fusion protein containing the CASPR/p190 cytoplasmic domain were raised and used to stain permeabilized human IMR-32 neuroblastoma and rat GH3 neuroendocrine cell lines found to express CASPR/p190. These studies revealed recognition of a 190 kD protein.

[0244] Similar results were obtained staining COS7 cell lysates that had been transfected with an expression vector directing the synthesis of CASPR/p190. No CASPR/p190 was detected in mock-transfected or untransfected cells.

[0245] Immunohistochemistry studies were then performed which demonstrated that CASPR/p190 and contactin localized in the rat retina. Specific CASPR/p190 staining was seen in the ganglion cell fiber layer and in the inner plexiform layers. Similar staining was observed for contactin, with the highest expression in the nerve fiber layer containing the axons that project from the ganglion cells into the optic nerve. Thus, CASPR/p190 and contactin colocalize on neurons in fiber-rich areas of the retina. Further, increased CASPR/p190 staining was detected in membrane preparations from rat brains from E18 to post-natal day eight, a period of extensive axonal outgrowth and synaptogenesis. A similar temporal expression pattern was detected in this tissue in the same period (Gennarini et al., 1989, J. Cell Biol. 109:755-788).

[0246] 8.2.3. Lateral Interaction in the Plasma Membrane Between CASPR/p190 and Contactin

[0247] The interaction between contactin, RPTP&bgr; and CASPR/p190 was then investigated using soluble and membrane-associated variants of these proteins. Specifically, the possibility that the interaction between contactin and CASPR/p190 requires that both proteins be present on the same cell (cis interaction) was studied.

[0248] To examine this possibility, COS7 cells were transfected with expression vectors that expressed either CASPR/p190 alone or together with contactin. Lysates of transfected cells were subject to precipitation analysis with the CAH domain of RPTP&bgr; (&bgr;C-Fc). The CAH domain of RPTP&bgr; only precipitated CASPR/p190 from cells co-expressing contactin. Thus, it appears that the CAH domain of RPTP&bgr; can form a ternary complex with contactin and CASPR/p190 proteins. Similar results were obtained using an expression vector expressing tagged CASPR/p190.

[0249] Moreover, soluble contactin molecules did not associate with CASPR/p190 when RPTP&bgr; and CASPR/p190 were co-expressed in the same cells.

[0250] On the basis of these experiments, it appears that the CAH domain of RPTP&bgr; does not bind directly to CASPR/p190 and that contactin and CASPR/p190 are complexed by means of lateral interactions (cis) in the membrane, thus explaining the reason why the protein is referred to as CASPR (i.e., Contactin-associated protein).

[0251] 8.2.4. Complex Formation Between CASPR/p190 and Contactin

[0252] The role of RPTP&bgr; in formation of the CASPR/p190-contactin complex was next examined. IMR-32 cell lysates were subjected to immunoprecipitation with CASPR/p190 antibodies followed by immunoblotting with contactin antibodies. These experiments demonstrated that contactin and CASPR/p190 were constitutively associated on the surface of the IMR-32 cells. In this cell line, it appeared that virtually all CASPR/p190 molecules were associated with contactin.

[0253] The existence of an in vivo contactin-CASPR/p190 complex was also demonstrated using rat brain tissue. Lysates of P7 rat brain membranes were subjected to precipitation with &bgr;C-Fc followed by immunoblotting with antibodies specific to either contactin of CASPR/p190.

[0254] Taken together, these data demonstrate that contactin and CASPR/p190 are constitutively complexed in neuronal cell lines and tissues and that complex formation between these two proteins does not require RPTP&bgr;.

[0255] 8.2.5. Interaction Between CASPR/p190 and SH3 Domains of Signaling Molecules

[0256] Experiments described herein demonstrated that the CASPR/p190 cytoplasmic domain can serve as a binding site for SH3 domains of signalling molecules which will transmit the signal initiated by RPTP&bgr; binding to the contactin-CASPR/p190 complex.

[0257] Specifically, four of seven GST-SH3 domains of signalling molecules were able to bind selectively to the CASPR/p190 protein, including the SH3 domains of Src, Fyn, p85 and PLC&ggr;. Association was not detected with Csk, Grb2 or Gap SH3 domains. CASPR/p190 did not bind to a mutant Src SH3 domain in which a conserved Trp at position 118 was replaced with an Ala residue.

[0258] Next it was determined that c-Src could associate with CASPR/p190 fusion proteins in transiently infected COS7 cells. Specifically, lysates of transfected cells were subjected to immunoprecipitation with antibodies against c-Src, followed by immunoblotting with anti-fusion antibodies.

[0259] Further, the association between endogenous c-Src and CASPR/p190 in IMR-32 or GH3 cells was investigated using a similar immunoprecipitation/immunoblotting strategy with Src and CASPR/p190 antibodies. Results of such experiments detected no association between c-Src and CASPR/p190.

[0260] These experiments raise the possibility that the cytoplasmic domain of CASPR/p190 can serve as a target for SH3 domains of signalling molecules.

Claims

1. An isolated nucleic acid molecule having a nucleotide sequence that:

(a) encodes the amino acid sequence SEQ ID NO:2;

(b) encodes the amino acid sequence SEQ ID NO:4; or

(c) is the complement of the nucleotide sequence of (a) or (b).

2. An isolated nucleic acid molecule having a nucleotide sequence that hybridizes under highly stringent conditions to the nucleic acid molecule of claim 1, and encodes a naturally occurring p190 polypeptide.

3. A nucleic acid molecule which comprises (a) a nucleotide sequence that encodes a polypeptide having the amino acid sequence shown in SEQ ID NO:2 from amino acid residues 40-168, 199-330, 362-486, 544-576, 582-739, 809-938, 961-985, 1031-1077, 1083-1218, 1282-1306, or 1328-1369; or (b) the complement of the nucleotide sequence of (a).

4. A nucleic acid molecule which comprises (a) a nucleotide sequence that encodes a p190 polypeptide lacking at least one domain which has an amino acid sequence shown in SEQ ID NO:2 from amino acid residues 40-168, 199-330, 362-486, 544-576, 582-739, 809-938, 961-985, 1031-1077, 1083-1218, 1282-1306, or 1328-1369; or (b) the complement of the nucleotide sequence of (a).

5. A recombinant vector containing the nucleic acid molecule of claims 1, 2, 3, or 4.

6. The recombinant vector of claim 5 wherein the nucleic acid molecule is operatively associated with an element that controls the expression of the nucleic acid molecule in a host cell.

7. An engineered host cell containing the nucleic acid molecule of claim 1, 2, 3, or 4.

8. An engineered host cell containing the nucleic acid molecule of claim 1, 2, 3, or 4 operatively associated with an element that controls the expressing of the nucleic acid molecule by the engineered host cell.

9. The engineered host cell of claim 8 which is eukaryotic.

10. The engineered host cell of claim 8 which is prokaryotic.

11. An isolated polypeptide comprising an amino acid sequence encoded by the nucleic acid molecule of claim 1, 2, 3 or 4.

12. The isolated polypeptide of claim 11, wherein the polypeptide comprises the amino acid sequence of SEQ ID NO:2 or SEQ ID NO:4.

13. A method for preparing a p190 polypeptide comprising:

(a) culturing a eukaryotic host cell which contains the nucleotide sequence of claim 1, 2, 3, or 4 operatively associated with an element that controls expression of the DNA sequence so that a p190 polypeptide is expressed by the host cell; and

(b) recovering the p190 polypeptide from the culture.

14. A method for preparing a p190 polypeptide comprising:

(a) culturing a prokaryotic host cell which contains the nucleotide sequence of claim 1, 2, 3, or 4 operatively associated with an element that controls expression of the DNA sequence so that a p190 polypeptide is expressed by the host cell; and

(b) recovering the p190 polypeptide from the culture.

15. The isolated nucleic acid molecule of claim 1 wherein the nucleotide sequence comprises the nucleotide sequence of SEQ ID NO:1 or SEQ ID NO:3.