WO2003091390A2

WO2003091390A2 - Regulation of gene expression by neuromodulators and discovery of a novel ngf-induced protein termed pincher

Info

Publication number: WO2003091390A2
Application number: PCT/US2002/036628
Authority: WO
Inventors: Simon Halegoua; Brian S. Hilbush; Karl W. Hasel
Original assignee: Digital Gene Technologies, Inc.
Priority date: 2001-11-14
Filing date: 2002-11-14
Publication date: 2003-11-06
Also published as: WO2003091390A3; AU2002367786A8; AU2002367786A1

Abstract

Polynucleotides, polypeptides, kits and methods are provided related to regulated genes characteristic of response of PC12 cells to the neuromodulators NGF and IFNg.

Description

REGULATION OF GENE EXPRESSION BY NEUROMODULATORS AND DISCOVERY OF A NOVEL NGF-INDUCED PROTEIN TERMED PINCHER

RELATED APPLICATION

The present application claims priority to U.S. Provisional Patent Application No. 60/335,985, filed November 14, 2001, which is hereby incoφorated by reference.

BACKGROUND OF THE INVENTION

Nerve Growth Factor (NGF) is the prototypic and best-studied member of the neurotrophin family of neuronal growth factors. NGF controls the survival and development of certain populations of peripheral neurons and influences neuronal phenotype throughout life (Levi-Montalcini, 1987; Snider, 1994) (Halegoua et al., Curr. Top. Microbiol. Immunol. 165:119-70 (1991)). NGF actions which are seen during embryogenesis and in the adult include control of neuronal precursor cell proliferation, differentiation and modulation of neuronal morphology, regulation of neurotransmitter synthesis and secretion, the cessation of cell division and prevention of cell death, the expression of neuronal-specific proteins, synaptogenesis and control of synaptic efficacy (synaptic modulation), and the expression of electrical excitability. The latter includes the specific expression of voltage dependent sodium, calcium and potassium channels, as well as modulation of their activities.

The PC 12 cell line has provided a valuable model for the analysis of the molecular events associated with and which mediate the actions of NGF (Halegoua et al., Curr.Top. Microbiol. Immunol. 165:119-70 (1991)). NGF treatment of PC12 cells results in the promotion and establishment of a neuronal phenotype resembling that of sympathetic and sensory neurons. These neuronal characteristics include the cessation of cell division, the morphological elaboration of neuritic processes, the prevention of cell death in serum-free medium, the synthesis and secretion of catecholaminergic and cholinergic neurotransmitters and their receptors, the expression of neuronal-specific proteins, increased expression of genes encoding various voltage-dependent ion channels and the establishment of a sodium-based action potential mechanism. Studies on the mechanism of NGF actions in PC 12 cells have revealed a complex signal transduction pathway involving various proto-oncogene products (Halegoua et al, Curr.Top. Microbiol. Immunol. 165:119-70 (1991)). The major functional receptor for NGF is the proto-oncoprotein Trk, a receptor tyrosine kinase. The activation of Trie by NGF has been shown to lead to a sequence of proto-oncoprotein activations involving the Src-Ras-Raf-MAP kinase pathway, which mediates the elaboration of phenotypes including neurite growth, inductions of a variety of genes including those for neuronal specific proteins and ion channels such as voltage-dependent calcium channels, the cessation of cell division and regulation of neurotransmitter synthesis. Branch points along the signaling pathway have been shown to differentially modulate the promotion of specific phenotypes (D'Arcangelo and Halegoua, Mol. Cell. Biol. 13(6):3146-55 (1993)). For example, Ras, but not Raf, leads to the induction of the neuronal gene SCG-10, and the induction of the thy-1 gene is stimulated by Src independently of Ras-Raf-MAP kinase activations. The establishment of electrical excitability in response to NGF-treatment of PC 12 cells occurs through the induction of the type II and PNl voltage-dependent sodium channel genes (Mandel et al., Proc. Natl. Acad. Sci. USA 85(3):924-28 (1988); D'Arcangelo et al., J. Cell. Biol. 122(4):915-21 (1993)). The induction of PNl, the peripheral neuron-specific sodium channel, is mediated by Trk through a signaling pathway which is independent of Src-Ras-Raf-MAP kinase signaling (D'Arcangelo and Halegoua, Mol. Cell. Biol. 13(6):3146-55 (1993)). The induction of the PNl gene after 5-24 hours has been found to occur in a triggered manner, in response to a brief (one minute) pulse of NGF, an event which can be mimicked by pulsatile treatment with interferon-gamma (IFN-γ; Toledo-Aral et al., Neuron 14(3):607-11 (1995)). Thus, three aspects of signaling can be used to classify the unique mechanism of PNl gene induction, Ras-independence, triggered induction by NGF, and triggered induction by IFN-γ. Using these criteria, a second gene induction event, for the neuronal intermediate filament protein peripherin, has been similarly classified in PC 12 cells.

The demonstration that two functionally diverse proteins are similarly classified according to the new induction criteria has led to the hypothesis that a wider subset of neuronal phenotypes induced by NGF and IFN-γ are mediated in a Ras-independent and triggered manner (Toledo-Aral et al., Neuron 14(3):607-11 (1995)). This unique mode of signaling could allow for the long-term manipulation of specific neuronal phenotypes by transient stimulation (or inhibition) of the signaling components. Given the importance of PNl and peripherin to neuronal physiology, additional important phenotypic markers might be expected to be similarly classified.

The principal site of NGF action is at the synapse where it is released from the neuronal postsynaptic target, internalized into the presynaptic terminal and transported retrogradely to the neuronal cell body (Reynolds et al., 2000). The retrograde transport of NGF, and/or an NGF-generated signal, has been postulated to mediate both neuronal survival (Hendry et al., 1974) and changes in gene expression (Hendry and Bonyhady, 1980; Toma et al., 1997; Riccio et al., 1999; Watson et al, 1999).

Although retrograde transport of NGF would appear to be important for NGF actions, the mechanisms for NGF internalization, formation of the transport vehicle and its interaction with the transport machinery have been elusive. NGF is internalized after binding to its plasma membrane receptors, p75^NTR and TrkA. In sympathetic neurons internalization is mediated primarily by the receptor tyrosine kinase TrkA (Curtis et al., 1995). NGF and TrkA have been reported to be associated with and/or stimulate different types of endocytic machinery in PC 12 cells, including clathrin-coated vesicles (Grimes et al., 1996), raffling and pinocytosis (Connolly et al., 1987), and calveolae (Huang et al., 1999; Peiro et al., 2000). The means by which NGF and TrkA are internalized may involve any combination of these processes or alternatively may involve a novel process that uses a blend of these features. Evidence obtained from sympathetic neurons supports the idea that internalized NGF is retrogradely transported from neuronal terminals in endosomes, presumed to be contained within multivesicular bodies (Weible et al., 2001). As opposed to the well-defined modes for processing receptor-mediated endosomes (see review, Mellman, 1996), a remarkable feature of NGF-containing endosomes in neuronal terminals is that they can avoid degradation or recycling, and instead can be directed to the retrograde transport machinery. Whether they are resistant to degradation due to the unusual nature of the vesicle formation process, or simply by the rapid sorting and trafficking of the endosomal vesicle to the transport machinery, is unknown. The goals of this work are to provide a better understanding and identification of the genes that are associated with and/or which mediate the actions of NGF. More specifically, the basic mechanisms regarding how the NGF received at the neuronal terminal mediate signaling at the cell body have yet to be elucidated. It has been proposed that NGF-filled endosomes with the capacity for receptor-mediated intracellular signal transduction function during and after retrograde transport (see Halegoua et al., 1991). Putative signaling endosomes containing NGF and TrkA have since been identified and isolated from PC12 cells (Grimes et al, 1996; Grimes et al., 1997). Although signaling pathways activated by retrogradely transported NGF and TrkA have only recently been investigated, TrkA signaling at the plasma membrane is well documented and is mediated through multiple pathways initiated by specific TrkA autophosphorylation sites (see review, Kaplan and Miller, 2000). The two best studied signaling sites on TrkA are P-Y490 that binds to the cytoplasmic scaffolding protein She, and P-Y785 that binds to the membrane effector phospholipase C-gamma (PLC-γ). She mediates stimulation of Ras-MAP kinase (Rozakis-Adcock et al., 1992; Thomas et al., 1992), and PI-3-kinase (Holgado-Madruga et al, 1997) signaling pathways. PLC-γ mediates signaling pathways through metabolites generated from its action on phosphatidylinositol turnover (see Carpenter and Ji, 1999). These signaling pathways are further branched, leading to differential control of gene expression (D'Arcangelo and Halegoua, 1993) and survival (see review, Kaplan and Miller, 2000). Retrograde axonally transported TrkA has also been shown to be autophosphorylated (Ehlers et al., 1995; Riccio et al., 1997), particularly on Y490, the She-binding site (Bhattacharyya et al., 1997). The retrograde transport of the activated NGF/TrkA complex has been shown to mediate the phosphorylation and activation of the transcription factor CREB, in the cell body (Riccio et al., 1997; Watson et al., 1999), which is in part necessary for neuronal survival (Bonni et al., 1999; Riccio et al, 1999). Recent findings have suggested that internalized TrkA may signal differently from the plasma membrane receptor, although a consensus on the different signaling parameters has not yet been reached (Saragovi et al., 1998; Zhang et al., 2000; Wu et al., 2001). Understanding the mechanisms for the formation and processing of, and signaling from the endosomal NGF/TrkA complex have been hampered by a lack of tools with which to specifically manipulate internalization of the NGF/TrkA complex and generation of the signaling endosome.

What is needed therefore, is an understanding and identification of the genes that are associated with and/or which mediate the actions of NGF. More specifically, the basic mechanisms regarding how the NGF received at the neuronal terminal mediate signaling at the cell body have yet to be elucidated. Such genes may be associated with a disorder of neuronal differentiation, such as Alzheimer's Disease, diabetic neuropathy, congenital insensitivity to pain with anhidrosis, or a side effect of NGF therapy, such as myalgia or hyperalgesia. We have identified a novel NGF-induced protein in PC 12 cells, termed Pincher that functions as a pinocytic chaperone for NGF and TrkA. Pincher facilitates both the NGF-induced internalization of TrkA by a pinocytic process, and the sorting of long-lived endosomal vesicles with NGF-signaling capabilities. Pincher function may shed light on the process of retrograde endosomal NGF signaling.

Further, preliminary studies have investigated the role of Pincher in the retina. Recently it has been found that Pincher is expressed in the photoreceptor outer segment of the retina, which is normally continually shed and phagocytosed by macrophage-like retinal pigment epithelial (RPE) cells. It was recently demonstrated that a deletion in the gene for receptor tyrosine kinase Mertk is associated with this disease (D'Cruz PM, et al., Hum Mol Genet 2000 9:645-51; Vollrath D, et al., Proc Natl Acad Sci U S A 2001 98: 12584-9). Further, Mertk mutations have been discovered in humans with retinitis pigmentosa. Given that phagocytosis by RPE cells is driven by Mertk, as pinocytosis driven by Trk, it is possible that Pincher may play a role in that pathway as well. Defects in this process, either in phagocytosis or in shedding, results in photoreceptor degeneration, which is relevant to the diseases retinitis pigmentosa and macular degeneration.

In order to examine how gene expression is regulated by various neuromodulators, such as NGF and IFN-G, the TOGA^® method of gene expression analysis was used to identify and analyze mRNA expression. The Total Gene Expression Analysis (TOGA^®) method, described in Sutcliffe et al., Proc. Natl. Acad. Sci. USA 97(5): 1976-81 (2000), International published application WO 00/26406, U.S. Patent No. 5,459,037, U.S. Patent No. 5,807,680, U.S. Patent No. 6,030,784, U.S. Patent No. 6,096,503, U.S. Patent No. 6,110,680, and U.S. Patent 6,309,834, all of which are incorporated herein by reference, is a tool used to identify and analyze mRNA expression. The TOGA^® method is an improved method for the simultaneous sequence-specific identification of mRNAs in an mRNA population which allows the visualization of nearly every mRNA expressed by a tissue as a distinct band on a gel whose intensity corresponds roughly to the concentration of the mRNA. The method can identify changes in expression of mRNA associated with the administration of drugs or agents such as neuronal growth factor, or changes in expression of mRNA associated with the pathways associated with and/or which mediate the actions of NGF. In addition, the method can identify such changes in expression of mRNA that may be associated with physiological or pathological conditions, such as a disorder of neuronal differentiation, such as Alzheimer's Disease, diabetic neuropathy, congenital insensitivity to pain with anhidrosis, retinitis pigmentosa and macular degeneration, or a side effect of NGF therapy, such as myalgia or hyperalgesia.

SUMMARAY OF THE INVENTION

The PC 12 cell line has served as a useful model in studies examining the mechanisms by which NGF regulates the neuronal phenotype. Such studies have identified some proteins and genes that are associated with and/or which mediate the actions of NGF. Such molecules are useful in therapeutic and diagnostic applications in the treatment of disorders or diseases affecting the control of neuronal precursor cell proliferation, differentiation and modulation of neuronal morphology, regulation of neurotransmitter synthesis and secretion, the cessation of cell division and prevention of cell death, the expression of neuronal-specific proteins, synaptogenesis and control of synaptic efficacy (synaptic modulation), and the expression of electrical excitability. In one embodiment, the invention is useful for adjusting the number of NGF receptors on a cell surface, for modulating the sensitivity of cells to NGF and for modulating the cell's response to NGF.

Particularly, novel and previously known polynucleotides and polypeptides of the present invention that effectively modulate NGF metabolism can be used therapeutically and diagnostically in diseases and conditions involving altered target cell metabolism of NGF. Such diseases and conditions include those involving reduced or elevated number of trkA NGF receptors. Also included would be diseases or conditions involving reduced or elevated sensitivity of target cells to NGF due to alterations in internalization of NGF, trkA, or NGF-trkA complex or alternation in intracellular messenger metabolism. Such diseases include forms of Alzheimer's disease characterized by altered trkA numbers and expression (Dubus, P., et al., Expression of trk isoforms in brain regions and in the striatum of patients with Alzheimer's disease, Exp Neurol 2000 Oct., 165(2): 285-294; Hock, C.H., et al., Alterations in neurotrophins and neurotrophin receptors in Alzheimer's disease, J. Neural Transm. Suppl. 2000; 59:171-174; Hock, C.H., et al., Decreased trkA neurotrophin receptor expression in the parietal cortex of patients with Alzheimer's disease, Neurosci Lett 1998 Jan 30; 241(2-3): 151-154.). Other diseases include diabetic neuropathy (Freeman, R., Human studies of recombinant human nerve growth factor and diabetic peripheral neuropathy, Eur. Neurol. 1999; 41 Suppl 1:20-26) and congenital insensitivity to pain with anhidrosis (CEP A) (Miura, Y., et al, Mutation and polymorphism analysis of the trkA (NTRK1) gene encoding a high-affinity receptor for nerve growth factor in congenital insensitivity to pain with anhidrosis (CEP A) families, Hum Genet 2000 Jan; 106(1): 116-24; Shatzky, S., et al., Congenital insensitivity to pain with anhidrosis (CIP A) in Israeli-Bedouins: genetic heterogeneity, novel mutations in the trkA/NGF receptor gene, clinical findings, and results of nerve conduction studies, Am. J. Med. Genet. 2000 Jun 19;92(5):353-60.). The subcutaneous and system administration of nerve growth factor is known to produce painful side effects such as myalgia and hyperalgesia (Rogers, B.C., Development of recombinant human nerve growth factor (rhNGF) as a treatment for peripheral neuropathic disease, Neurotoxicology 1996 Fall- Winter; 17(3-4): 865-70; Petty, B.G., The effect of systemically administered recombinant human nerve growth factor in healthy human subjects, Ann. Neurol. 1994 Aug; 36(2): 244-246.). Native and modified polynucleotides and polypeptides of the present invention that effectively modulate NGF metabolism can be used therapeutically as an adjunct to NGF therapy to ameliorate such side effects.

One embodiment of the invention provides a method for preventing, treatmg, modulating, or ameliorating a medical condition, such as disorders of altered target cell metabolism of NGF, comprising administering to a mammalian subject a therapeutically effective amount of a polypeptide of the invention or a polynucleotide of the invention.

In other embodiments, the disorder can be, Alzheimer's disease, retinitis pigmentosum, macular degeneration, diabetic neuropathy, congenital insensitivity to pain with anhidrosis, or a side effect of NGF therapy, such as myalgia or hyperalgesia.

A further embodiment of the invention provides an isolated antibody that binds specifically to the isolated polypeptide of the invention. A preferred embodiment of the invention provides a method for preventing, treating, modulating, or ameliorating a medical condition, such as disorders of neuronal differentiation comprising administering to a mammalian subject a therapeutically effective amount of the antibody.

An additional embodiment of the invention provides a method of diagnosing a pathological condition or a susceptibility to a pathological condition in a subject. The method comprises determining the presence or absence of a mutation in a polynucleotide of the invention. A pathological condition or a susceptibility to a pathological condition, such as diseases and conditions involving altered target cell metabolism of NGF, is diagnosed based on the presence or absence of the mutation. Even another embodiment of the invention provides a method of diagnosing a pathological condition or a susceptibility to a pathological condition in a subject, such as diseases and conditions involving altered target cell metabolism of NGF. The method comprises detecting an alteration in expression of a polypeptide encoded by the polynucleotide of the invention, wherein the presence of an alteration in expression of the polypeptide is indicative of the pathological condition or susceptibility to the pathological condition. The alteration in expression can be an increase in the amount of expression or a decrease in the amount of expression. Ln a preferred embodiment a first biological sample is obtained from a patient suspected of having a disease or condition involving altered target cell metabolism of NGF and a second sample from a suitable comparable control source is obtained. The amount of at least one polypeptide encoded by a polynucleotide of the invention is determined in the first and second sample. The amount of the polypeptide in the first and second samples is determined. A patient is diagnosed as having a disorder of altered target cell metabolism of NGF if the amount of the polypeptide in the first sample is greater than or less than the amount of the polypeptide in the second sample.

Where a polynucleotide of the invention is down-regulated and exacerbates a pathological condition, such as diseases and conditions involving altered target cell metabolism of NGF, the expression of the polynucleotide can be increased or the level of the intact polypeptide product can be increased in order to treat, prevent, ameliorate, or modulate the pathological condition. This can be accomplished by, for example, administering a polynucleotide or polypeptide of the invention to the mammalian subject. Alzheimer's disease is an example of a disorder characterized by reduced trkA numbers and expression (Dubus, P., et al, Exp Neurol 2000; 165:285-294; Hock, C.H., et al, J. Neural Transm. Suppl. 2000; 59: 171-174; Hock, C.H., et al., Neurosci Lett 1998;

241:151-154.). Polynucleotides of the present invention that effectively modulate NGF metabolism, such as HAL_18 (SEQ ID NO: 12), can be used therapeutically to elevate the number of trkA NGF receptors.

Where a polynucleotide of the invention is up-regulated and exacerbates a pathological condition in a mammalian subject, such as a disease involving altered target cell metabolism of NGF, the expression of the polynucleotide can be blocked or reduced or the level of the intact polypeptide product can be reduced in order to treat, prevent, ameliorate, or modulate the pathological condition. HAL_18 (SEQ JD NO: 12) is an example of such an up-regulated molecule, which showed increased expression in PC 12 cells in response to treatment with nerve growth factor. NGF is administered as a treatment for peripheral neuropathic disease and in some individuals produces painful side effects such as myalgia and hyperalgesia. Thus HAL_18 could be used to modulate NGF metabolism as an adjunct to NGF therapy to ameliorate such side effects. This can be accomplished by, for example, the use of antisense oligonucleotides, triple helix base pairing methodology or ribozymes. Alternatively, drugs or antibodies that bind to and inactivate the polypeptide product can be used.

The present invention also provides novel polynucleotides and the encoded polypeptides to that are regulated by neuromodulators in the control of neuronal precursor cell proliferation, differentiation and modulation of neuronal morphology. Such genes may be associated with Alzheimer's Disease, retinitis pigmentosum, macular degeneration, diabetic neuropathy, congemtal insensitivity to pain with anhidrosis, or a side effect of NGF therapy, such as myalgia or hyperalgesia. Moreover, the present invention relates to vectors, host cells, antibodies, and recombinant methods for producing the polynucleotides and the polypeptides. One embodiment of the invention provides an isolated nucleic acid molecule comprising a polynucleotide chosen from the group consisting of SEQ ID NO:l, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ED NO:5, SEQ ID NO:6, SEQ ED NO:7, SEQ ID NO:8, SEQ ED NO:9, SEQ ID NO: 10, SEQ ID NO:ll, SEQ ID NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ED NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ED NO:24, SEQ ED NO:25, SEQ ID NO:26, SEQ ED NO:27, SEQ ED NO:28 and SEQ ID NO:29. Also provided is an isolated nucleic acid molecule comprising a polynucleotide at least 95% identical to any one of these isolated nucleic acid molecules and an isolated nucleic acid molecule at least ten bases in length that is hybridizable to any one of these isolated nucleic acid molecules under stringent conditions. Any one of these isolated nucleic acid molecules can comprise sequential nucleotide deletions from either the 5 '-terminus or the 3 '-terminus. Further provided is a recombinant vector comprising any one of these isolated nucleic acid molecules and a recombinant host cell comprising any one of these isolated nucleic acid molecules. Also provided is the gene corresponding to the cDNA sequence of any one of these isolated nucleic acids.

Another embodiment of the invention provides an isolated polypeptide encoded by a polynucleotide chosen from the group consisting of SEQ ID NO: 1 , SEQ ED NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ED NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ED NO:10, SEQ ED NO:l l, SEQ ID NO:12, SEQ ED NO:13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ED NO: 16, SEQ ID NO: 17, SEQ ED NO: 18, SEQ ID NO: 19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ID NO:23, SEQ ID NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ID NO:27, SEQ ID NO:28 and SEQ ID NO:29. Also provided is an isolated nucleic acid molecule encoding any of these polypeptides, an isolated nucleic acid molecule encoding a fragment of any of these polypeptides, an isolated nucleic acid molecule encoding a polypeptide epitope of any of these polypeptides, and an isolated nucleic acid encoding a species homologue of any of these polypeptides. Preferably, any one of these polypeptides has biological activity. Optionally, any one of the isolated polypeptides comprises sequential amino acid deletions from either the C-terminus or the N-terminus. Further provided is a recombinant host cell that expresses any one of these isolated polypeptides.

Yet another embodiment of the invention comprises an isolated antibody that binds specifically to an isolated polypeptide encoded by a polynucleotide chosen from the group consisting of SEQ ID NO:l, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ED NO:6, SEQ ID NO:7, SEQ ED NO:8, SEQ ID NO:9, SEQ ED NO:10, SEQ ID NO:ll, SEQ ED NO:12, SEQ ID NO:13, SEQ ID NO:14, SEQ ID NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ED NO:19, SEQ LD NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ED NO:23, SEQ ID NO:24, SEQ ED NO:25, SEQ ID

NO:26, SEQ ID NO:27, SEQ ID NO:28 and SEQ ID NO:29. The isolated antibody can be a monoclonal antibody or a polyclonal antibody.

Another embodiment of the invention provides a method for identifying a binding partner to a polypeptide of the invention. A polypeptide of the invention is contacted with a binding partner and it is determined whether the binding partner effects an activity of the polypeptide. Yet another embodiment of the invention is a method of identifying an activity of an expressed polypeptide in a biological assay. A polypeptide of the invention is expressed in a cell and isolated. The expressed polypeptide is tested for an activity in a biological assay and the activity of the expressed polypeptide is identified based on the test results.

Still another embodiment of the invention provides a substantially pure isolated DNA molecule suitable for use as a probe for genes regulated in a disorder of altered target cell metabolism of NGF, chosen from the group consisting of the DNA molecules shown in SEQ ED NO: 1, SEQ ID NO:2, SEQ ED NO:3, SEQ ID NO:4, SEQ JD NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO:l l, SEQ ED NO: 12, SEQ ID NO:13, SEQ ID NO:14, SEQ ED NO:15, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:18, SEQ ID NO:19, SEQ ID NO:20, SEQ ID NO:21, SEQ ID NO:22, SEQ ED NO:23, SEQ JD NO:24, SEQ ID NO:25, SEQ ID NO:26, SEQ ED NO:27, SEQ ID NO:28 and SEQ ID NO:29, their corresponding genes or regions thereof, and DNA molecules at least 95% similar to the foregoing molecules. Even another embodiment of the invention provides a kit for detecting the presence of a polypeptide of the invention in a mammalian tissue sample. The kit comprises a first antibody that immunoreacts with a mammalian protein encoded by a gene corresponding to the polynucleotide of the invention or with a polypeptide encoded by the polynucleotide in an amount sufficient for at least one assay and suitable packaging material. The kit can further comprise a second antibody that binds to the first antibody. The second antibody can be labeled with enzymes, radioisotopes, fluorescent compounds, colloidal metals, chemiluminescent compounds, phosphorescent compounds, or bioluminescent compounds. Another embodiment of the invention provides a kit for detecting the presence of genes encoding a protein comprising a polynucleotide of the invention, or fragment thereof having at least 10 contiguous bases, in an amount sufficient for at least one assay, and suitable packaging material.

Yet another embodiment of the invention provides a method for detecting the presence of a nucleic acid encoding a protein in a mammalian tissue sample. A polynucleotide of the invention or fragment thereof having at least 10 contiguous bases is hybridized with the nucleic acid of the sample. The presence of the hybridization product is detected.

Additional embodiments of the invention provide a method for using a polynucleotide of the invention, a polypeptide of the invention, an antibody of the invention, or a gene of the invention or a region thereof for the manufacture of a medicament useful in the treatment of a medical condition, such as, for example, a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIP A, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy. An additional embodiment of the invention provides a method of diagnosing a pathological condition or a susceptibility to a pathological condition in a subject. The method comprises determining the presence or absence of a mutation in a polynucleotide or gene of the invention or a region thereof. A pathological condition or a susceptibility to a medical condition, such as, for example, a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIP A, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy is diagnosed based on the presence or absence of the mutation.

Even other embodiments of the invention provide methods of diagnosing a pathological condition or a susceptibility to a pathological condition, such as, for example, a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIP A, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy in a subject. The methods comprise detecting an alteration in expression of a polynucleotide, gene or region thereof, or a polypeptide encoded by the polynucleotide or gene of the invention, wherein the presence of an alteration in expression of the polypeptide is indicative of the pathological condition or susceptibility to the pathological condition. The alteration in expression can be an increase in the amount of expression or a decrease in the amount of expression. In a preferred embodiment, a first biological sample is obtained from a patient suspected of having a medical condition, such as, for example, a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIP A, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy and a second sample from a suitable comparable control source is obtained. The amount of at least one polypeptide, polynucleotide or gene of the invention or a region thereof is determined in the first and second sample. A patient is diagnosed as having the medical condition if the amount of the polypeptide, polynucleotide or gene or region thereof in the first sample is greater than or less than the amount of the polypeptide, polynucleotide or gene or region thereof in the second sample. Yet other embodiments of the invention involve assessing the stage of a medical condition, such as, for example, a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIP A, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy by testing for regulation of at least one polynucleotide, polypeptide, antibody or gene of the invention or a region thereof. Further embodiments of the invention involve assessing the efficacy or toxicity of a therapeutic treatment of a medical condition, such as, for example, a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CEP A, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy, by testing for regulation of at least one polynucleotide, polypeptide, antibody or gene of the invention or a region thereof.

Another embodiment of the present invention provides a method of using a polynucleotide, polypeptide, antibody or gene of the invention or a region thereof for delivering to a patient in need thereof, genes, DNA vaccines, diagnostic reagents, peptides, proteins or macromolecules. Another embodiment of the invention provides a method of using a polypeptide or antibody of the invention to identify a binding partner to a polypeptide of the invention. In a preferred embodiment, a polypeptide of the invention is contacted with a binding partner and it is determined whether the binding partner affects an activity of the polypeptide. Additionally, the present invention provides novel polynucleotides, genes and their encoded polypeptides. One embodiment of the invention provides an isolated nucleic acid molecule comprising a polynucleotide chosen from the group consisting of SEQ ID NOs: 5, 16 and 29. Also provided is an isolated nucleic acid molecule comprising a polynucleotide at least 95% identical to any one of the isolated nucleic acid molecules of the invention, an isolated nucleic acid molecule at least ten bases in length that is hybridizable to any one of the isolated nucleic acid molecules of the invention under stringent conditions, and an isolated nucleic acid molecule that is a homolog, ortholog, or paralog of any one of the isolated nucleic acid molecules of the invention. Any one of the isolated nucleic acid molecules of the invention can comprise sequential nucleotide deletions from either the 5 '-terminus or the 3 '-terminus. Also provided is the gene corresponding to the cDNA sequence of any one of the isolated nucleic acids of the invention, an isolated nucleic acid molecule hybridizable to such gene under stringent conditions, and an isolated nucleic acid molecule or gene that is a homolog, paralog or ortholog of such gene.

Another embodiment of the invention provides an isolated or purified polypeptide encoded by a polynucleotide chosen from the group consisting of SEQ ED NOs: 5, 16 and 29, a polynucleotide at least 95% identical to said polynucleotide or a gene corresponding to one of the foregoing polynucleotides and the complements and degenerate variants thereof. Also provided is an isolated or purified polypeptide 90% identical to one of the foregoing polypeptides, a fragment of one the foregoing polypeptides, and the homologs, paralogs, and orthologs of the foregoing polypeptides. Also provided is an isolated nucleic acid molecule or gene encoding any of the polypeptides or polypeptide fragments of the invention. Optionally, any one of the isolated polypeptides of the invention comprises sequential amino acid deletions from either the C-terminus or the N-terminus. Yet another embodiment of the invention comprises an isolated antibody that binds specifically to an isolated polypeptide encoded by a polynucleotide chosen from the group consisting of SEQ JD NOs: 5, 16 and 29, a polynucleotide at least 95% identical to said polynucleotide or a gene corresponding to one of the foregoing polynucleotides and the complements and degenerate variants thereof. The isolated antibody can be a monoclonal antibody or a polyclonal antibody. An additional embodiment of the invention involves a method for identifying biomolecules associated with a medical condition, such as, for example, a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CEP A, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy, comprising the steps of: developing a cellular experiment specific for the medical condition, harvesting the RNA from the cells used in the experiment, obtaining a gene expression profile, and using the gene expression profile for identifying biomolecules whose expression was altered during the experiment. The biomolecules identified may be polynucleotides, polypeptides or genes.

In another embodiment, the present invention provides a method for assessing the efficacy of a test compound for treating a medical condition, such as, for example, a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CEP A, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with

NGF therapy. The method involves comparing a level of expression of a molecule of the present invention (i.e., a marker) in a first sample obtained from a patient. The test compound is administered to the first sample. The level of expression of the same marker is then measured in a second sample obtained from the patient, which same was not exposed to the test compound. The levels of expression are compared from the first and second samples and a substantially increased or decreased level of expression in the first sample, relative to the second sample, is an indication that the test compound is efficacious in treating the medical condition.

In yet another embodiment, the present invention provides a method for assessing the efficacy of a test compound for modulating endocytosis, pinocytosis or receptor internalization. The method involves generating a recombinant cell line that overexpresses the Pincher protein (i.e., the polypeptide expressed by the polynucleotide listed in SEQ ID NO: 29) and a control cell line. Contacting one population of recombinant cells with the test compound and monitoring the level of expression of the Pincher protein in the recombinant cell line and the control cell line. Monitoring the level of Pincher expression may be carried out via immunodetection methods well known to those of skill in the art, such as, for example, by using antibodies directed against Pincher in immunoflourescense staining.

The foregoing merely summarizes certain aspects of the invention and is not intended, nor should it be construed as limiting the invention in any way.

BRIEF DESCRIPTION OF THE DRAWINGS

These and other features, aspects, and advantages of the present invention will become better understood with reference to the following description, appended claims, and accompanying drawings where: Figure 1 is a graphical representation of the results of TOGA^® runs using a 5'

PCR primer with parsing bases GCAC (SEQ ED NO: 35) and the universal 3' PCR primer (SEQ ED NO: 33) showing PCR products produced from mRNA extracted from PC 12 cells treated as follows: Panel A: control wash (CW), Panel B: 1 hour with NGF (lhr NGF), Panel C: 1 hour with IFN-γ (lhr IFN), Panel D: 5 hours with NGF (5hr NGF), Panel E: 5 hours with IFN-γ (5hr IFN), and Panel F: 24 hours with NGF (24hr NGF), where the vertical index line indicates a PCR product of about 349 b.p. that is present in the 1 hr NGF and 1 hr IFN samples and enriched in 5 hr NGF, 5 hr IFN, and 24 hr NGF samples. The horizontal axis represents the number of base pairs of the molecules in these samples and the vertical axis represents the fluorescence measurement in the TOGA^® analysis (which corresponds to the relative expression of the molecule of that address). The results of the TOGA^® runs have been normalized using the methods described in pending U.S. Patent Application Serial No. 09/318,699/U.S., and PCT Application Serial No. PCT/USOO/14159, both entitled Methods and System for Amplitude Normalization and Selection of Data Peaks (Dennis Grace, Jay son Durham); and U.S. Patent 6,334,099, PCT Application Serial No. PCT/US00/14123 and pending U.S. Patent Application Serial Nos. 09/940,987/U.S., 09/940,581/U.S., 09/940,746/U.S., all entitled Methods for Nonnalization of Experimental Data (Dennis Grace, Jayson Durham) all of which are incorporated herein by reference. The vertical line drawn through the six panels represents the DST molecule identified as HAL_18 (SEQ ID NO: 12).

Figure 2 presents a graphical example of the results obtained when a DST is verified by the Extended TOGA^® method using a primer generated from a cloned product. The PCR product corresponding to SEQ JD NO: 12 (HAL_18) was cloned and a 5' PCR primer was built from the cloned DST (SEQ ID NO:36). The product obtained from PCR with this primer (SEQ ID NO:36) and the universal 3' PCR primer (SEQ ID NO: 33) (as shown in the top panel, A) was compared to the length of the original PCR product that was produced in the TOGA^® reaction with mRNA extracted from PC 12 cells treated for 5 hr with NGF using a 5' PCR primer with parsing bases GCAC (SEQ ID

NO:35) and the universal 3' PCR primer (SEQ ID NO:33) (as shown in the middle panel, B). For all panels, the number of base pairs is shown on the horizontal axis, and fluorescence intensity (which corresponds to relative expression) is found on the vertical axis, h the bottom panel (panel C), the traces from the top and middle panels are overlaid, demonstrating that the peak found using an extended primer from the cloned

DST is the same number of base pairs as the original PCR product obtained through TOGA^® as HAL_18 (SEQ JD NO:12). The bottom panel thus illustrates that HAL_18 (SEQ ID NO: 12) was the DST amplified in Extended TOGA^®. Interestingly, more than one peak was observed, suggesting the presence of two mRNAs, one of which could be an alternatively spliced product. Northern analysis described below confirmed the presence of more than one mRNA as well, consistent with an alternatively spliced product.

Figure 3 represents the results of Northern Blot analysis of clone HAL_18 (GCAC 349), where an agarose gel containing polyA enriched mRNA from PC12 cells treated with NGF as well as size standards was blotted after electrophoresis and probed with either radiolabeled HAL_18 (nucleotides 1-454) (panel A) or cyclophilin (panel B). PC 12 cells were treated as follows: 1 hour NGF pulse followed by 2-6 hour chase

(samples l'2hr, l'3hr, l'4hr, l'5hr, and l'6hr), continuous NGF treatment for 2-6 hours (samples 2hr, 3hr, 4hr, 5hr, and 6hr), and no NGF treatment (control) (Panel A). The indicated two alternatively spliced forms of HAL_18 transcripts (4kb and 3kb) confirmed results using an antisense RNA probe from HAL_18 template. Both the bands were inducible by NGF and IFN-γ, verifying the results obtained using TOGA^®. Panels C and D show the time-course of HAL_18 induction by NGF in PC12 cells. Total cellular RNA (10 μg) was prepared from PC12 cells incubated with NGF (100 μg/ml) for the indicated time (hours). The RNA was hybridized with a DNA probe generated from HAL_18 cDNA fragment. Re-hybridization with a cyclophilin pEB15probe (lkb) (Panel D) provided an internal control for the amount of RNA in each lane. HAL_18 expression reaches a peak of 4-fold induction at 4 hours after NGF treatment and then returns to the basal level after 24 hours of NGF treatment.

Figure 4 Panel A (left) shows a Northern blot hybridized with an antisense RNA probe generated from HAL_18 template and cyclophilin probe (internal control) using total RNA (10 μg) isolated from GSrasDN6 cells treated with dexamethasone (DEX) (0.5 μM) for sixteen hours to induce dominant inhibitory ras^N17 or DMSO (DM) carrier and

NGF (100 μg/ g, 4 hr) or FGF as indicated. 17N-2 cells constitutively expressing ras^N17 were then treated or not with NGF for 1 minute or 5 hours as indicated and RNA analyzed by Northern blot (Figure 4 Panel A, right). The two alternatively spliced forms of HAL_18 transcripts (4kb and 3kb) are indicated. In Figure 4 Panel B (left), GSrasl cells were treated with 0.5μM dexamethasone for the indicated times, to induce ra^⁶¹ oncogene expression. Expression of rasL61 in these cells stimulated the expression of the two mRNAs by five-fold in a prolonged time course over 72 hours (Fig. 4 Panel B, left). Fig. 4 Panel B, right, GSrasl cells or GSΔB-raf cells were treated with 0.5 μM dexamethasone for the indicated times to induce ra^⁶¹ or truncated, activated b-raf, respectively. Total cellular RNA was isolated and subjected to real-time RT-PCR using HAL_18- or GAPDH-specific primers. Data was processed and is shown as a histogram for the induction of HAL_18 after normalization to GAPDH. In summary, the expression of activated forms of Ras andb-Raf is sufficient to induce sustained HAL_18 gene expression.

Figure 5 further investigates the role of Ras-independent and -dependent pathways. Total RNA (10 μg) was isolated from the PC12 mutant nnr5 (lacking TrkA), and the following nnr5 stable transfectants expressing wild type or mutant TrkAs, T14 (wild type TrkA), Y490 (Y490F mutant), Y785 (Y785F mutant), Y490/785 (double mutant) after a four-hour treatment with NGF (100 μg/ml). RNA was blotted and hybridized with an antisense RNA probe generated from a HAL_18 template. The two alternatively spliced forms of HAL_18 transcripts (4kb and 3kb) are indicated. Re- hybridization with a cyclophilin pEB15probe (lkb) provided an internal control for the amount of RNA in each lane. As expected, HAL_18 mRNAs were induced by NGF- treatment of the PC12 nnr5 lines expressing TrkA but not in the lines lacking TrkA (T14 and nnr, respectively, Fig. 5). Lower levels of induction could be seen in cells expressh g each of the TrkA single mutants (Y490F or Y785F, Fig. 5). NGF-treated cells expressing the TrkA double mutant, Y490F/Y785F did not show HAL_18 mRNA induction, indicating that both TrkA autophosphorylation sites contribute to the induction.

Figure 6 shows the results of an experiment demonstrating the tissue specific expression of the HAL_18 gene, (left) Rat tissue polyA+mRNA (Clontech) and (right) total cellular RNA (10 μg) isolated from rat dorsal root ganglia (DRG), lung and heart was hybridized with an antisense RNA probe generated from HAL_18 template. The two alternatively spliced forms of HAL__18 transcripts (4kb and 3kb) are indicated. HAL_18 RNA was found to be primarily expressed in the heart, with moderate expression in the lung and detectable expression in the kidney and brain.

Figure 7 shows the results of an experiment demonstrating that the induction of HAL_18 gene expression does not require de novo synthesis of protein. PC 12 cells treated with NGF (100 μg/ml) were cultured in the absence or presence of the translational inhibitor cycloheximide (CHX, 10 μg/ml). CHX was applied at the indicated times (minutes) after NGF addition. Total RNA was isolated from the cells at 4 hours after the addition of NGF to the medium and analyzed by Northern blotting. The two alternatively spliced forms of HAL_18 transcripts (4kb and 3kb) are indicated. The blot was re-hybridized with an antisense RNA probe for PN1(1 lkb) as a positive control for CHX. The cyclophilin was re-probed as an internal control for RNA loading. Figure 8 depicts the predicted Pincher amino acid sequence illustrating domains of interest. The EH domain is a protein-protein interaction domain found in other proteins involved in membrane trafficking. A second protein-protein interaction domain is a coiled-coiled domain that is often found in proteins that form homomers. A third domain is distantly related to AAA type ATPases that contains an intact P-loop ATP/GTP- binding motif.

Figure 9 represents the results of immunoprecipitation followed by Western blot analysis. Pincher was immunoprecipitated from cell extracts, blotted onto nitrocellulose, and the blots probed with anti-Pincher antibody or anti-HA antibody. The left panel represents PC12 cells treated with NGF for the indicated times and blots probed with the anti-Pincher antibody. The right panel represents PC 12 cells transfected with a CMN- driven expression plasmid encoding HA-tagged-Pincher. Western blot of the immunoprecipitate was first probed with anti-Pincher antibody (shown in left lane of the right panel) and re-probed with anti-HA antibody (shown in right lane of the right panel). The more slowly migrating position of HA-Pincher is indicated.

Figure 10 demonstrates Pincher overexpression enhances NGF-induced internalization and sorting of TrkA. In this study, TrkA-overexpressing TrkA-PC12 cell cultures were transfected with a CMV-HA-Pincher construct. Double immunofluorescence staining of fixed, permeabilized cells with anti-HA mAb (Alexa 488, green) and anti-TrkA polyclonal antibody (Cy5, red) was visualized using a Zeiss LSM510 confocal microscope using a 100X objective and LSM510 software. The photographic images are negatives of black and white images; in the original photographs, TrkA antibodies were labeled with a red fiuorophore and HA antibodies were labeled with a green fiuorophore. Figure 10A depicts cells expressing HA-Pincher ( + HA-Pincher) or not ( - HA-Pincher) are indicated. Cells were treated or not with NGF for the indicated times. The bar in the top left panel represents 5 μm. Figure 10B shows Zeiss LSM510 deconvolution software was used to create a 3-D reconstruction of the HA-Pincher expressing cell shown in the NGF lOmin overlay.

For the studies represented in Figure 11, TrkA-overexpressing TrkA-PC12 cell cultures were transfected with a CMN-HA-Pincher construct and treated with ΝGF as in Fig 10. Cells were processed for immunogold electron microscopy using anti-Pincher antibody. Figure 11 Panel A shows immunogold labeled Pincher associated with complex ruffling formations (arrowheads) localized at the peripheral membrane, twenty minutes after exposure to ΝGF. Figure 11 Panel B represents immunogold labeled Pincher associated with a complex ruffling formation at the peripheral membrane ten minutes after exposure to ΝGF, where arrowheads indicate the locations of cytoskeletal structures. Figure 11 Panel C depicts immunogold labeled Pincher associated with a complex ruffling formation at the peripheral membrane ten minutes after exposure to ΝGF.

Figure 12 represents low power electron micrograph of a portion of a TrkA-PC12 cell overexpressing Pincher ten minutes after exposure to ΝGF. Immunogold labeled Pincher is associated with at least two different intracellular structures. The arrowheads point to Pincher immunogold labeled structures that appear to be internalized complex ruffling formations. The small arrows point to a few (of the many present) examples of intracellular vesicles and tubules that are immunogold labeled for Pincher. The boxed region is shown at higher power in Figure 13, lower panel.

Figure 13 (upper panel) shows an example of an internalized complex ruffling formation apparently 'delivering' membrane bound vesicles to a large vesicle accumulating body (NAB). Note the absence of Pincher immunogold labeling of vesicles within the NAB. The lower panel is a higher power electron micrograph of the boxed region in Figure 12; immunogold Pincher labeled tubules are highlighted with arrowheads. The sections in both panels are taken from Trk-PC12 cells overexpressing Pincher 10 min after exposure to ΝGF.

Figure 14 represents an electron micrograph showing immunogold labeling of Pincher associated with vesicles and tubules (arrows) and the peripheral membrane (arrowheads). The section is from a TrkA-PC12 cell overexpressing Pincher one hour after exposure to ΝGF. Figure 15 demonstrates Pincher overexpression enhances fluid-phase uptake of

ΝGF in PC12 cells. TrkA-overexpressing TrkA-PC12 cell cultures were transfected with a CMN-HA-Pincher construct as in Fig 10. Panel A: To examine fluid-phase uptake by confocal fluorescence microscopy, cells were incubated with media containing fluorescent Alexa488-conjugated-10kd-dextran for 15 min (-ΝGF) or also treated with NGF for 15 min at 37°C. Pincher-transfected cells were stained with anti-Pincher polyclonal antibody (Alexa 546). The photographic images are negatives of black and white images; in the original photographs, Pincher antibodies were labeled with a red fiuorophore and dextran was labeled with a green fiuorophore. No Pincher staining was observed when anti-Pincher antibody was pre-blocked with GST-Pincher fusion protein (not shown). In the cells overexpressing Pincher, a massive accumulation of dextran- containing cytoplasmic structures could be seen, in large part surrounded by an array of Pincher containing tubular/vesicular structures (Fig. 15 Panel A, bottom right of panel, see arrow). Panel B: cells were treated with myc-tagged NGF for the times indicated in Figure 15 Panel B at 4°C (to prevent uptake) and at 37°C. NGF-myc was visualized by confocal fluorescence microscopy after anti-myc monoclonal antibody staining (Alexa 546) and Pincher staining using polyclonal anti-Pincher antibody (Alexa 488). The photographic images are negatives of black and white images; in the original photographs, Pincher antibodies were labeled with a green fiuorophore and myc antibodies were labeled with a red fiuorophore. Cells expressing HA-Pincher ( + HA- Pincher) or not ( - HA-Pincher) are indicated. The bar in the upper left corner box in Panels A and B represents 5μm.

Figure 16 shows Pincher overexpression enhances NGF-stimulated internalization and sorting of autophosphorylated TrkA. TrkA-overexpressing TrkA-PC12 cell cultures were transfected with a CMN-HA-Pincher construct as in Fig 10. Double immunofluorescence staining of fixed, permeabilized cells was carried out using anti-HA mAb (Alexa 488) and anti-phospho-Y490TrkA polyclonal antibody (Cy5). The photographic images are negatives of black and white images; in the original photographs, HA antibodies were labeled with a green fiuorophore and the phospho- Y490TrkA antibodies were labeled with a red fiuorophore. Cells were treated with ΝGF for the times indicated in Figure 16. Cells expressing HA-Pincher ( + HA-Pincher) or not ( - HA-Pincher) are also indicated. In transfected cells, HA-Pincher and phospho-TrkA are localized to the plasma membrane in untreated cells, co-internalized within five minutes ΝGF treatment, differentially sorted within fifteen minutes ΝGF treatment, and HA-Pincher is selectively recycled to the plasma membrane by one hour ΝGF treatment with phospho-Trk remaining accumulated in the cytoplasm. The bar in the upper left corner box represents 5 μm.

Figure 17 shows ΝGF-induced vesicles in Pincher-overexpressing cells associate with activated MAP kinases. TrkA-overexpressing TrkA-PC12 cells were transfected with a CMV-HA-Pincher construct as in Fig 10. Immunofluorescence staining was carried out using anti-HA monoclonal antibody (Alexa 488) and anti-phospho-MAP kinase polyclonal antibody (Cy5). The photographic images are negatives of black and white images; in the original photographs, HA antibodies were labeled with a red fiuorophore and the phospho-MAP kinase antibodies were labeled with a green fiuorophore. Cells were treated with ΝGF for the indicated times. Phospho-MAP kinase showed dim and diffuse cytoplasmic staining before ΝGF-treatment and bright staining after treatment. In transfected cells expressing HA-Pincher (+ HA-Pincher), within five minutes of treatment bright phospho-MAP kinase staining was seen together with intracellular Pincher, after 15 minutes of NGF-treatment bright phospho-MAP kinase staining was seen clustered within a surrounding pattern of Pincher staining, and after 60 minutes, Pincher returned to the plasma membrane. The NGF-treated cells not expressing HA-Pincher (-HA-Pincher) are brightly but diffusely stained with anti-phospho-MAP kinase antibody. The bar in the upper left corner box represents 5 μm.

Figure 18 shows the results of an experiment using confocal microscopy showing that an EH domain deletion mutant of Pincher (PincherΔEH) localizes to novel intracellular structures and is unresponsive to NGF. The TrkA-PC12 cells were transiently transfected with HA-PincherΔEH and treated with NGF for the indicated times. After fixation and permeabihzation, cells were stained using antibodies to TrkA and HA. HA-PincherΔEH labeling is shown on the left, TrkA labeling is shown in the center and an overlay of both labels are shown on the right. The photographic images are negatives of black and white images; in the original photographs, TrkA antibodies were labeled with a green fiuorophore and HA antibodies were labeled with a red fiuorophore. In the absence of NGF ("control"), TrkA staining is on the plasma membrane (Figure 18 A) and with some staining in the juxtanuclear region (Figure 18B), while HA- PincherΔEH labeling is only shown clustering in large structures, not appearing on the plasma membrane (Figure 18B). After NGF treatment for 5 minutes at 37 degrees Celsius ("NGF 5 min"), TrkA labeling is seen both on the plasma membrane (Figure 18 A) and in the cytosol (Figure 18B), but no change in the localization of HA- pincherΔEH labeling is observed. After 1 hour of NGF treatment at 37 degrees Celsius ("NGF 1 hour"), TrkA labeling is present on the plasma membrane (panel A) and in the cytosol. HA-PincherΔEH labeling remains clustered in large structures, and shows no localization change caused by NGF. Figure 19 shows that the Pincher ATP/GTP-binding site mutant is dominant inhibitory for NGF-induced pinocytosis and endocytic signaling. Panel A shows that overexpression of Pincher G68E blocks NGF-induced fluid phase pinocytosis of dextran- Alexa488 in PC12 cells. The photographic images are negatives of black and white images; in the original photographs, Pincher G68E antibodies were labeled with a red fiuorophore and dextran-Alexa488 was labeled with a green fiuorophore. Panel B demonsfrates that overexpressing Pincher G68E cells block phospho-TrkA internalization after NGF treatment. P-TrkA accumulates at cell surface ruffles and blebs where G68E is expressed. The photographic images are negatives of black and white images; in the original photographs, Pincher G68E antibodies were labeled with a green fluorophore and phospho-TrkA antibodies were labeled with a red fluorophore. Panel C shows Pincher G68E overexpression results in accumulation of phospho-MAPK at the plasma membrane, thus preventing activated map kinase from going to the cytoplasm and nucleus. The photographic images are negatives of black and white images; in the original photographs, Pincher G68E antibodies were labeled with a green fluorophore and phospho-MAPK antibodies were labeled with a red fluorophore. Figure 20 shows that expression of the Pincher ATP/GTP binding site mutant results in accumulation of cell surface blebs. Panel A shows a lower power election micrograph of immunogold Δ-Pincher labeled TrkA-PC12 cell overexpressing Pincher G68E mutant. As shown, blebs accumulate at the cell surface. Panel B represents a higher magnification of the electron micrograph of a portion of the cell surface in order to show the fine structure of blebs formation. We believe that this accumulation of plasma membrane blebs is due to the prevention of pinocytosis, thus preventing ruffles from internalizing. Pincher may also play a role in organizing the cytoskeleton at the ruffling membrane - a loss of cytoskeletal function there might result in bleb formation. Thus, these studies suggest that Pincher is a major mediator of macropinocytosis in cells. Figure 21 shows that Pincher overexpression enhances the formation of TrkA endosomes by NGF in sympathetic neuron somata that were isolated from superior cervical ganglion neurons from newborn rat pups that were dissociated and cultured in vitro with NGF. After 5 days the neurons were double transfected with plasmids encoding HA-Pincher and TrkA. Two days later, the cells were fixed in 4% paraformaldehyde and stained with a combination of anti-phospho-TrkA antibody (B, middle panel) and anti-HA antibody (A, left panel), as observed using confocal immunofluorescence microscopy. The accumulation of endosomes containing activated, phospho-TrkA can be seen in the cells expressing HA-Pincher, which surrounds the accumulations. The merging of the two signals is seen in panel C. Figure 22 shows that Pincher enhances and mutant G68E-Pincher inhibits the cytoplasmic accumulation of activated phospho-erk5 in sympathetic neurons treated with NGF. Superior cervical ganglion neurons from newborn rat pups were dissociated and cultured in vitro with NGF. After 1 day the neurons were infected with adeno viruses encoding either HA-Pincher or HA-G68E-Pincher, as well as Green Fluorescent Protein (GFP). Two days later, the cells were fixed in 4% paraformaldehyde and stained with anti-phospho-erk5 antibody (B and E, middle panel), and observed using confocal immunofluorescence microscopy. The accumulation of endosomes associated with phospho-erk5 can be seen in the cytoplasm of cells expressing HA-Pincher, and limited to the plasma membrane in cells expressing HA-G68E-Pincher. The infected cells are indicated by the presence of GFP (A and D, left panel). The merged images are shown in C andF.

Figure 23 shows that Pincher enhances and mutant G68E-Pincher inhibits the internalization and cytoplasmic accumulation of TrkB in sympathetic neurons treated with NGF. Superior cervical ganglion neurons from newborn rat pups were dissociated and cultured in vitro with NGF and BDNF (NT-2). After 1 day the neurons were doubly infected with adenoviruses encoding either HA-Pincher or HA-G68E-Pincher, and adenoviruses encoding TrkB-GFP. Two days later, the cells were fixed in 4% paraformaldehyde and stained with anti-TrkB antibody (A or D), and anti-HA antibody (B or E), and observed using confocal immunofluorescence microscopy. The accumulation of endosomes associated with TrkB can be seen in the cytoplasm of cells expressing HA-Pincher, and limited to the plasma membrane in cells expressing HA-

G68E-Pincher. Panel C shows the merged images of A and B; Panel F shows the merged images of D and E.

Figure 24 shows that Pincher is concentrated at neurite terminals. Superior cervical ganglion neurons from newborn rat pups were dissociated and cultured in vitro with NGF. After 1 day the neurons were infected with adenovirus encoding HA-Pincher and GFP. Two days later, the cells were fixed in 4% paraformaldehyde and stained with anti-HA antibody (Panel A), and observed using confocal immunofluorescence microscopy. The infected cells are indicated by the presence of GFP (Panel B). Shown are two neurite terminal growth cones. Pincher is concentrated at the ruffling growth cone membranes (relative to the cytoplasmic GFP). Panel C shows the merged imaged of Panel A and B. Figure 25 shows that Pincher and TrkB are co-internalized at the neuronal terminal and along the neurite and retrogradely transported in response to neurotrophin treatment. Superior cervical ganglion neurons from newborn rat pups were dissociated and cultured in vitro with the neurotrophins NGF and BDNF (NT-2). After 1 day the neurons were doubly infected with adenoviruses encoding HA-Pincher, and adenoviruses encoding TrkB-GFP. Two days later, the media of three cultures was exchanged with media lacking neurotrophin and incubated for five hours. After NT starvation, the second culture was treated with the NTs for ten minutes and the third culture was treated for one hour. All the cells were fixed in 4% paraformaldehyde and stained with anti-TrkB antibody (Panel A,D,H), and anti-HA antibody (Panel B,C,E,F,I,J), and observed using confocal immunofluorescence microscopy. Co-internalization of both TrkB and HA- Pincher was observed after ten minutes of NT treatment. The terminals were largely devoid of co-internalized TrkB and Pincher after one hour of NT treatment, but they were co-localized in puncti along the neurites. Figure 26 shows that expression of HA-G68E-Pincher prevented NT-mediated internalization and retrograde transport of TrkB at neurite terminals. Superior cervical ganglion neurons from newborn rat pups were dissociated and cultured in vitro with NGF and BDNF (NT-2). After 1 day the neurons were doubly infected with adenoviruses encoding HA-G68E-Pincher, and adenoviruses encoding TrkB-GFP. Two days later, the cells were fixed in 4% paraformaldehyde and stained with anti-TrkB antibody (Panel A), and anti-HA antibody (Panel B), and observed using confocal immunofluorescence microscopy. Shown is a neurite terminal in which HA-G68E-Pincher and TrkB are co- localized and concentrated at two foci at the growth cone tip. No internalized foci could be seen. Panel C shows the merged image of A and B.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

The present invention and the methods of obtaining and using the present invention will be described in detail after setting forth some preliminary definitions, which are provided to facilitate understanding of certain terms used in the present invention. Many of the techniques described herein are described in Dracopoli et al., Current Protocols in Human Genetics, John Wiley and Sons, New York (1999), and Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, New York (2000), both of which are incorporated herein by reference. Definitions

"Isolated" refers to material removed from its original environment (e.g., the natural environment if it is naturally occurring), and thus is altered "by the hand of man" from its natural state.

"Stringent hybridization conditions" refers to an overnight incubation at 42°C in a solution comprising 50% formamide, 5X SSC (5X SSC = 750 mM NaCl, 75 mM sodium citrate, 50 mM sodium phosphate pH 7.6), 5X Denhardt's solution, 10% dextran sulfate, and 20 μg/ml denatured, sheared salmon sperm DNA, followed by washing the filters in 0.1X SSC at about 65°C. Changes in the stringency of hybridization and signal detection are primarily accomplished through the manipulation of formamide concentration (lower percentages of formamide result in lowered stringency); salt conditions, or temperature. For example, lower stringency conditions include an overnight incubation at 37°C in a solution comprising 6X SSPE (20X SSPE = 3M NaCl; 0.2M NaH₂PO₄; 0.02M EDTA, pH 7.4), 0.5% SDS, 30% formamide, 100 μg/ml salmon sperm blocking DNA; followed by washes at 50°C with IX SSPE, 0.1% SDS. In addition, to achieve even lower stringency, washes performed following stringent hybridization can be done at higher salt concentrations (e.g. 5X SSC). Note that variations in the above conditions may be accomplished through the inclusion and/or substitution of alternate blocking reagents used to suppress background in hybridization experiments. Typical blocking reagents include Denhardt's reagent, BLOTTO (5% w/v non-fat dried milk in phosphate buffered saline ("PBS"), heparin, denatured salmon sperm DNA, and other commercially available proprietary formulations. The inclusion of specific blocking reagents may require modification of the hybridization conditions described above, due to problems with compatibility. Of course, a polynucleotide which hybridizes only to polyA+ sequences (such as any 3' terminal polyA÷ tract of a cDNA shown in the sequence listing), or to a complementary stretch of T (or U) residues, would not be included in the definition of "polynucleotide," since such a polynucleotide would hybridize to any nucleic acid molecule containing a poly (A) stretch or the complement thereof (e.g., practically any double-stranded cDNA clone). "Conservative amino acid substitution" refers to a substitution between similar amino acids that preserves an essential chemical characteristic of the original polypeptide.

"Identity" per se has an art-recognized meaning and can.be calculated using published techniques. (See, e.g., Lesk, Ed., Computational Molecular Biology, Oxford University Press, New York, (1988); Smith, Ed., Biocomputing: Informatics And Genome Projects, Academic Press, New York, (1993); Griffin and Griffin, Eds., Computer Analysis Of Sequence Data, Part I, Humana Press, New Jersey, (1994); von Heinje, Sequence Analysis In Molecular Biology, Academic Press, (1987); and Gribskov and Devereux, Eds., Sequence Analysis Primer, M Stockton Press, New York, (1991)). While there exists a number of methods to measure identity between two polynucleotide or polypeptide sequences, the term "identity" is well known to skilled artisans (Carillo et al, SIAM J Applied Math., 48:1073 (1988)). Methods commonly employed to determine identity or similarity between two sequences include, but are not limited to, those disclosed in "Guide to Huge Computers," Martin J. Bishop, Ed., Academic Press, San Diego, (1994) and Carillo et al, (1988), Supra.

"EST" refers to an Expressed Sequence Tag, i.e. a short sequence of a gene made from cDNA, typically in the range of 200 to 500 base pairs. Since an EST corresponds to a specific region of a gene, it can be used as a tool to help identify unknown genes and map their position in the genome. "DST" refers to a Digital Sequence Tag, i.e., a polynucleotide that is an expressed sequence tag of the 3' end of an mRNA.

Other terms used in the fields of biotechnology and molecular and cell biology as used herein will be as generally understood by one of ordinary skill in the applicable arts.

Treatment of Diseases and Conditions Involving Altered Target Cell Metabolism of NGF

Where a polynucleotide, polypeptide or gene of the invention or region thereof is down-regulated and is associated with a pathological condition, such as diseases and conditions involving altered target cell metabolism of NGF, the expression of the polynucleotide or gene or region thereof can be increased or the level of the intact polypeptide product can be increased in order to freat, prevent, ameliorate, or modulate the pathological condition. This can be accomplished by, for example, administering a polynucleotide, polypeptide or gene of the invention or region thereof (or a set of polynucleotides, polypeptides, genes or regions thereof, including those of the invention) to the mammalian subject. Alzheimer's disease is an example of a disorder characterized by reduced trkA numbers and expression (Dubus, P., et al., Exp Neurol 2000; 165:285- 294; Hock, C.H., et al, J. Neural Transm. Suppl. 2000;59:171-174; Hock, C.H., et al., Neurosci Lett 1998;241:151-154.). Polynucleotides of the present invention that effectively modulate NGF metabolism, such as HAL_18 (SEQ ED NO: 12), can be used therapeutically to elevate the number of trkA NGF receptors. A polynucleotide or gene of the invention or region thereof can be admimstered to a mammalian subject alone or with other polynucleotides or genes by a recombinant expression vector comprising the polynucleotide or gene or region thereof. As used herein, a mammalian subject can be a human, baboon, chimpanzee, macaque, cow, horse, sheep, pig, dog, cat, rabbit, guinea pig, rat or mouse. Preferably, the recombinant vector comprises a polynucleotide shown in SEQ ID NOs: 1-29 inclusive or a polynucleotide which is at least 98% identical to a nucleic acid sequence shown in SEQ ID NOs: 1-29 inclusive or a gene corresponding to one of the foregoing polynucleotides or a region thereof. Also, preferably, the recombinant vector comprises a variant polynucleotide that is at least 80%, 90%, or 95% identical to a polynucleotide comprising at least one of SEQ ID NOs: 1-29 inclusive, a polynucleotide at least ten bases in length hybridizable to polynucleotide comprising at least one of SEQ ID NOs: 1-29 inclusive, a polynucleotide comprising at least one SEQ ID NOs: 1-29 inclusive with sequential nucleotide deletions from either the 5' terminus or the 3' terminus, or a species homolog of a polynucleotide comprising at least one of SEQ ID NOs: 1-29 inclusive or gene corresponding to any one of the foregoing polynucleotides of a region thereof.

The administration of a polynucleotide or gene of the invention, or region thereof or recombinant expression vector containing such polynucleotide, gene or region thereof to a mammalian subject can be used to express a polynucleotide in said subject for the treatment of, for example, a condition involving altered target cell metabolism of NGF. Expression of a polynucleotide or gene in target cells would effect greater production of the encoded polypeptide. In some cases, where the encoded polypeptide is a nuclear protein, the regulation of other genes may be secondarily up- or down-regulated. Alzheimer's disease is an example of a disorder characterized by reduced trkA numbers and expression (Dubus, P., et al., Exp Neurol 2000;165:285-294; Hock, C.H., et al., J. Neural Transm. Suppl. 2000;59:171-174; Hock, C.H., et al., Neurosci Lett 1998;241:151- 154.). Polynucleotides of the present invention that effectively modulate NGF metabolism, such as HAL_18 (SEQ ED NO: 12), can be used therapeutically to elevate the number of trkA NGF receptors.

There are available to one skilled in the art multiple viral and non- viral methods suitable for introduction of a nucleic acid molecule into a target cell, as described above. In addition, a naked polynucleotide, gene or region thereof can be administered to target cells. Polynucleotides and genes of the invention or regions thereof and recombinant expression vectors of the invention can be administered as a pharmaceutical composition (including, without limitation, genes delivered by vectors such as adeno-associated virus, liposomes, PLGA, canarypox virus, adenovirus, retroviruses including IL-1 and GM-CSF antagonists). Such a composition comprises an effective amount of a polynucleotide, gene or region thereof or recombinant expression vector, and a pharmaceutically acceptable formulation agent selected for suitability with the mode of administration. Suitable formulation materials preferably are non-toxic to recipients at the concentrations employed and can modify, maintain, or preserve, for example, the pH, osmolarity, viscosity, clarity, color, isotonicity, odor, sterility, stability, rate of dissolution or release, adsorption, or penetration of the composition. See Remington 's Pharmaceutical Sciences (18th Ed., A.R. Gennaro, ed., Mack Publishing Company 1990).

The pharmaceutically active compounds (i.e., a polynucleotide, gene or region thereof or a vector) can be processed in accordance with conventional methods of pharmacy to produce medicinal agents for administration to patients, including humans and other mammals. Thus, the pharmaceutical composition comprising a polynucleotide, gene or region thereof or a recombinant expression vector may be made up in a solid form (including granules, powders or suppositories) or in a liquid form (e.g., solutions, suspensions, or emulsions). The dosage regimen for treating a disease with a composition comprising a polynucleotide, gene or region thereof or expression vector is based on a variety of factors, including the type or severity of the condition involving altered target cell metabolism of NGF, the age, weight, sex, medical condition of the patient, the route of administration, and the particular compound employed. Thus, the dosage regimen may vary widely, but can be determined routinely using standard methods. A typical dosage may range from about 0.1 mg/kg to about 100 mg/kg or more, depending on the factors mentioned above.

The frequency of dosing will depend upon the pharmacokinetic parameters of the polynucleotide, gene or region thereof or vector in the formulation being used. Typically, a clinician will administer the composition until a dosage is reached that achieves the desired effect. The composition may therefore be administered as a single dose, as two or more doses (which may or may not contain the same amount of the desired molecule) over time, or as a continuous infusion via implantation device or catheter. Further refinement of the appropriate dosage is routinely made by those of ordinary skill in the art and is within the ambit of tasks routinely performed by them. Appropriate dosages may be ascertained through use of appropriate dose-response data.

The cells of a mammalian subject may be transfected in vivo, ex vivo, or in vitro. Administration of a polynucleotide, gene or region thereof or a recombinant vector containing a polynucleotide, gene or region thereof to a target cell in vivo may be accomplished using any of a variety of techniques well known to those skilled in the art. For example, U.S. Patent No. 5,672,344 describes an in vivo viral-mediated gene transfer system involving a recombinant neurotropliic HSN-1 vector. The above-described compositions of polynucleotides, genes and regions thereof and recombinant vectors can be transfected in vivo by oral, buccal, parenteral, rectal, or topical administration as well as by inhalation spray. The term "parenteral" as used herein includes, subcutaneous, intravenous, intramuscular, intrasternal, infusion techniques or intraperitoneally.

While the nucleic acids and/or vectors of the invention can be administered as the sole active pharmaceutical agent, they can also be used in combination with one or more vectors of the invention or other agents. When administered as a combination, the therapeutic agents can be formulated as separate compositions that are given at the same time or different times, or the therapeutic agents can be given as a single composition. Another delivery system for polynucleotides or genes of the invention and regions thereof is a "non- viral" delivery system. Techniques that have been used or proposed for gene therapy include DNA-ligand complexes, adenovirus-ligand-DNA complexes, direct injection of DNA, CaPO₄ precipitation, gene gun techniques, electroporation, lipofection, and colloidal dispersion (Mulligan, R., (1993) Science, 260 (5110):926-32). Any of these methods are widely available to one skilled in the art and would be suitable for use in the present invention. Other suitable methods are available to one skilled in the art, and it is to be understood that the present invention may be accomplished using any of the available methods of transfection. Several such methodologies have been utilized by those skilled in the art with varying success. Id.

Where a polynucleotide or gene of the invention is up-regulated and exacerbates a pathological condition in a mammalian subject, such as a disease involving altered target cell metabolism of NGF, the expression of the polynucleotide or gene can be blocked or reduced or the level of the intact polypeptide product can be reduced in order to freat, prevent, ameliorate, or modulate the pathological condition. HAL_18 (SEQ ID NO: 12) is an example of such an up-regulated molecule, which showed increased expression in PC 12 cells in response to treatment with nerve growth factor. NGF is administered as a treatment for peripheral neuropathic disease and in some individuals produces painful side effects such as myalgia and hyperalgesia. Thus HAL_18 could be used to modulate NGF metabolism as an adjunct to NGF therapy to ameliorate such side effects. This can be accomplished by, for example, the use of antisense oligonucleotides, triple helix base pairing methodology or ribozymes. Alternatively, drugs or antibodies that bind to and inactivate the polypeptide product can be used.

Antisense oligonucleotides are nucleotide sequences that are complementary to a specific DNA or RNA sequence. Once introduced into a cell, the complementary nucleotides combine with natural sequences produced by the cell to form complexes and block either transcription or translation. Preferably, an antisense oligonucleotide is at least 11 nucleotides in length, but can be at least 12, 15, 20, 25, 30, 35, 40, 45, or 50 or more nucleotides long. Longer sequences also can be used. Antisense oligonucleotide molecules can be provided in a DNA construct and introduced into a cell as described above to decrease the level of gene products of the invention in the cell. Antisense oligonucleotides can be deoxyribonucleotides, ribonucleotides, or a combination of both. Oligonucleotides can be synthesized manually or by an automated synthesizer, by covalently linking the 5' end of one nucleotide with the 3' end of another nucleotide with non-phosphodiester internucleotide linkages such alkylphosphonates, phosphorothioates, phosphorodithioates, alkylphosphonotliioates, alkylphosphonates, phosphoramidates, phosphate esters, carbamates, acetamidate, carboxymethyl esters, carbonates, and phosphate triesters. See Brown, (1994) Meth. Mol. Biol, 20:1-8; Sonveaux, (1994) Meth. Mol. Biol, 26:1-72; Uhlmann et al., (1990) Chem. Rev., 90:543- 583. Modifications of gene expression can be obtained by designing antisense oligonucleotides that will form duplexes to the control, 5', or regulatory regions of a gene of the invention. Oligonucleotides derived from the transcription initiation site, e.g., between positions -10 and +10 from the start site, are preferred.

Similarly, inhibition can be achieved using "triple helix" base-pairing methodology. Triple helix pairing causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or chaperons. Therapeutic advances using triplex DNA have been described in the literature (e.g., Gee et al., in Huber & Carr, Molecular and Immulogic Approaches, Futura Publishing Co., Mt. Kisco, N.Y., 1994). An antisense oligonucleotide also can be designed to block translation of mRNA by preventing the transcript from binding to ribosomes.

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

Antisense oligonucleotides can be modified without affecting their ability to hybridize to a polynucleotide or gene of the invention or regions thereof. These modifications can be internal or at one or both ends of the antisense molecule. For example, internucleoside phosphate linkages can be modified by adding cholesteryl or diamine moieties with varying numbers of carbon residues between the amino groups and terminal ribose. Modified bases and/or sugars, such as arabinose instead of ribose, or a 3', 5 '-substituted oligonucleotide in which the 3' hydroxyl group or the 5' phosphate group are substituted, also can be employed in a modified antisense oligonucleotide.

These modified oligonucleotides can be prepared by methods well known in the art. See, e.g., Agrawal et al., (1992) Trends Biotechnol, 10:152-158; Uhlmann et al., (1990) Chem. Rev., 90:543-584; Uhlmann et al., (1987) Tetrahedron. Lett, 215:3539-3542. Ribozymes are RNA molecules with catalytic activity. See, e.g., Cech, (1987) Science, 236:1532-1539; Cech, (1990) Ann. Rev. Biochem., 59:543-568; Cech, (1992) Curr. Opin. Struct. Biol, 2:605-609; Couture & Stinchcomb, (1996) Trends Genet., 12:510-515. Ribozymes can be used to inhibit gene function by cleaving an RNA sequence, as is known in the art (e.g., Haseloff et al., U.S. Patent No. 5,641,673). The mechanism of ribozyme action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA, followed by endonucleolytic cleavage. Examples include engineered hammerhead motif ribozyme molecules that can specifically and efficiently catalyze endonucleolytic cleavage of specific nucleotide sequences.

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

Specific ribozyme cleavage sites within a RNA target can be identified by scanning the target molecule for ribozyme cleavage sites which include the following sequences: GUA, GUU, and GUC. Once identified, short RNA sequences of between 15 and 20 ribonucleotides corresponding to the region of the target RNA containing the cleavage site can be evaluated for secondary structural features which may render the target inoperable. Suitability of candidate RNA targets also can be evaluated by testing accessibility to hybridization with complementary oligonucleotides using ribonuclease protection assays. The nucleotide sequences shown in SEQ ED NOs: 1-29 inclusive, their complements and their corresponding genes and regions thereof provide sources of suitable hybridization region sequences. Longer complementary sequences can be used to increase the affinity of the hybridization sequence for the target. The hybridizing and cleavage regions of the ribozyme can be integrally related such that upon hybridizing to the target RNA through the complementary regions, the catalytic region of the ribozyme can cleave the target.

Ribozymes can be introduced into cells as part of a DNA construct. Mechanical methods, such as microinjection, liposome-mediated transfection, electroporation, or calcium phosphate precipitation, can be used to introduce a ribozyme-containing DNA construct into cells in which it is desired to decrease polynucleotide expression.

Alternatively, if it is desired that the cells stably retain the DNA construct, the construct can be supplied on a plasmid and maintained as a separate element or integrated into the genome of the cells, as is known in the art. A ribozyme-encoding DNA construct can include transcriptional regulatory elements, such as a promoter element, an enhancer or UAS element, and a transcriptional terminator signal, for controlling transcription of ribozymes in the cells.

As taught in Haseloff et al., U.S. Patent No. 5,641,673, ribozymes can be engineered so that ribozyme expression will occur in response to factors that induce expression of a target gene. Ribozymes also can be engineered to provide an additional level of regulation, so that destruction of mRNA occurs only when both a ribozyme and a target gene are induced in the cells. Polypeptides or antibodies to the polypeptides of the invention can also be used directly as therapeutics to prevent, treat, modulate, or ameliorate disease. The mammalian subject (preferably a human) can be given a recombinant or synthetic form of the polypeptide in one of many possible different formulations, including, but not limited to, subcutaneous, intravenous, intramuscular, intraperitoneal, or intracranial injections of a solution of the polypeptide or antibody, or a suspension of a crystallized form of the polypeptide or antibody; topical creams or slow release cutaneous patch containing the polypeptide; encapsulated forms for oral or other gastrointestinal delivery of the polypeptide or antibody. In some cases, delivery of the polypeptide or antibody may be in the form of injection or transplantation of cells or tissues containing an expression vector such that a recombinant form of the polypeptide will be secreted by the cells or tissues, as described above for transfected cells.

The frequency and dosage of the administration of the polypeptides or antibodies will be determined by factors such as the biological activity of the pharmacological preparation, the persistence and clearance of the active protein, and the goals of treatment. In the case of antibody therapies, the frequency and dosage will also depend on the ability of the antibody to bind and neutralize the target molecules in the target tissues. Diagnostic Tests Pathological conditions or susceptibility to pathological conditions, such as diseases and conditions involving altered target cell metabolism of NGF, can be diagnosed using methods of the invention. Testing for expression of a polynucleotide or gene of the invention or regions thereof or for the presence of the polynucleotide or gene product can correlate with the severity of the condition and can also indicate appropriate treatment. Furthermore, testing for regulation of a polynucleotide or gene of the invention or regions thereof or a panel of polynucleotides or genes of the invention or regions thereof can be used in drug development studies to assess the efficacy or toxicity of any experimental therapeutic. For example, the presence or absence of a mutation in a polynucleotide or gene of the invention or regions thereof can be determined through sequencing techniques known to those skilled in the art and a pathological condition or a susceptibility to a pathological condition can be diagnosed based on the presence or absence of the mutation. Further, an alteration in expression of a polypeptide encoded by a polynucleotide or gene of the invention can be detected, where the presence of an alteration in expression of the polypeptide is indicative of the pathological condition or susceptibility to the pathological condition. The alteration in expression can be an increase in the amount of expression or a decrease in the amount of expression, i.e. a modulation in expression. Examples exist of diseases or conditions involving both reduced or elevated sensitivity of target cells to NGF.

The use of diagnostic tests is not limited to determining the presence of or susceptibility to disease. In many cases, the diagnostic test can be used to assess disease stage, especially in situations where such an objective lab test has no alternative reliable subjective test available. These tests can be used to follow the course of disease, help predict the future course of disease, or determine the possible reversal of the disease condition. For example, the level of expression of polynucleotides, genes, polypeptides of the invention or regions thereof may be indicative of disease stage or progression.

In drug development studies, these tests can be useful as efficacy markers, so that the ability of any new therapeutics to treat disease can be evaluated on the basis of these objective assays. The utility of these diagnostic tests will first be determined by developing statistical information correlating the specific lab test values with several clinical parameters so that the lab test values can be known to reliably predict certain clinical conditions. In many cases, the diagnostic lab tests based on the polynucleotides, genes, antibodies or polypeptides of the invention, i.e., gene expression profiles of polynucleotides or polypeptides encoded by the polynucleotides identified in SEQ ID NOs: 1-29, will be important markers of drug or disease toxicity. The markers of toxicity versus drug efficacy will be determined by studies correlating the effects of known toxins or pathological conditions with specific alterations in gene regulation. Toxicity markers generated in this fashion will be useful to distinguish the various therapeutic versus deleterious effects on cells or tissues in the patient.

As an additional method of diagnosis, a first biological sample from a patient suspected of having a pathological condition, such as as diseases and conditions involving altered target cell metabolism of NGF, is obtained along with a second sample from a suitable comparable control source. A biological sample can comprise saliva, blood, cerebrospinal fluid, amniotic fluid, urine, feces, tissue, or the like, such as brain tissue. A suitable control source can be obtained from one or more mammalian subjects that do not have the pathological condition. For example, the average concentration and distribution of a polynucleotide, gene, or polypeptide of the invention or a region thereof can be determined from biological samples taken from a representative population of mammalian subjects, wherein the mammalian subjects are the same species as the subject from which the test sample was obtained. The amount of at least one polypeptide, gene, polynucleotide of the invention or region thereof is determined in the first and second sample. The amounts of the polypeptide in the first and second samples are compared. A patient is diagnosed as having the pathological condition if the amount of the polypeptide, gene, polynucleotide of the invention or a region thereof in the first sample is greater than or less than the amount of the polypeptide, gene, polynucleotide of the invention or a region thereof in the second sample. Preferably, the amount of polypeptide, gene, polynucleotide of the invention or a region thereof in the first sample falls in the range of samples taken from a representative group of patients with the pathological condition.

The method for diagnosing a pathological condition can comprise a step of detecting nucleic acid molecules comprising a nucleotide sequence in a panel of at least two nucleotide sequences, wherein at least one sequence in said panel is at least 95% identical to a sequence of at least 50 contiguous nucleotides in a sequence selected from said group.

The present invention also includes a diagnostic system, preferably in kit form, for assaying for the presence of the polypeptide of the present invention in a body sample, including, but not limited to brain tissue, cell suspensions or tissue sections; or a body fluid sample, such as CSF, blood, plasma or serum, where it is desirable to detect the presence, and preferably the amount, of the polypeptide of this invention in the sample according to the diagnostic methods described herein.

In a related embodiment, the discovery of differential expression patterns for the molecules of the invention allows for screening of test compounds with an eye to modulating a particular expression pattern; for example, screening can be done for compounds that will convert an expression profile for a poor prognosis to a better prognosis. These methods can also be done on the protein basis; that is, protein expression levels of the molecules of the invention, such as, for example, polypeptides encoded by the polynucleotides identified in SEQ ED NOs: 1-29, can be evaluated for diagnostic and prognostic purposes or to screen test compounds. In addition, the invention provides methods of conducting high-throughput screening for test compounds capable of inhibiting activity of proteins encoded by the polynucleotides of the invention, i.e., SEQ JD NOs: 1-29. The method of high-throughput screening involves combining test compounds and the polypeptide and measuring an effect of the test compound on the encoded polypeptide. Functional assays such as cytosensor microphysiometer, calcium flux assays such as FLIPR (Molecular Devices Corp, Sunnyvale, CA), or the TUNEL assay may be employed to measure cellular activity.

The invention also provides a method of screening test compounds for inl ibitors of diseases and conditions involving altered target cell metabolism of NGF and the pharmaceutical compositions comprising the test compounds. The method for screening comprises obtaining samples from subjects afflicted with diseases and conditions involving altered target cell metabolism of NGF, maintaining separate aliquots of the samples with a plurality of test compounds, and comparing expression of a molecules of the invention, i.e., SEQ JD NOs: 1-29, in each of the aliquots to determine whether any of the test compounds provides a substantially modulated level of expression relative to samples with other test compounds or to an untreated sample. In addition, methods of screening may be devised by combining a test compound with a protein and thereby determining the effect of the test compound on the polypeptide.

In a related embodiment, a nucleic acid molecule can be used as a probe (i.e., an oligonucleotide) to detect the presence of a polynucleotide of the present invention, a gene corresponding to a polynucleotide of the present invention or a region thereof, or a mRNA in a cell that is diagnostic for the presence or expression of a polypeptide of the present invention in the cell. The nucleic acid molecule probes can be of a variety of lengths from at least about 10 to about 5000 nucleotides long, although they will typically be about 20 to 500 nucleotides in length. The probe can be used to detect the polynucleotide, gene, gene region or mRNA through hybridization methods that are well lαiown in the art.

In a related embodiment, detection of genes corresponding to the polynucleotides of the present invention can be conducted by primer extension reactions such as the polymerase chain reaction (PCR). To that end, PCR primers are utilized in pairs, as is well known, based on the nucleotide sequence of the gene to be detected. Preferably, the nucleotide sequence is a portion of the nucleotide sequence of a polynucleotide of the present invention. Particularly preferred PCR primers can be derived from any portion of a DNA sequence encoding a polypeptide of the present invention, but are preferentially from regions that are not conserved in other cellular proteins.

Preferred PCR primer pairs useful for detecting the genes corresponding to the polynucleotides of the present invention and expression of these genes are described below. Nucleotide primers from the corresponding region of the polypeptides of the present invention described herein are readily prepared and used as PCR primers for detection of the presence or expression of the corresponding gene in any of a variety of tissues.

In another embodiment, a diagnostic system, preferably in kit form, is contemplated for assaying for the presence of the polypeptide of the present invention or an antibody immunoreactive with the polypeptide of the present invention in a body fluid sample. Such diagnostic kit would be useful for monitoring the fate of a therapeutically admimstered polypeptide of the present invention or an antibody immunoreactive with the polypeptide of the present invention. The system includes, in an amount sufficient for at least one assay, a polypeptide of the present invention and/or a subject antibody as a separately packaged immunochemical reagent. Instructions for use of the packaged reagent(s) are also typically included.

A diagnostic system of the present invention preferably also includes a label or indicating means capable of signaling the formation of an immunocomplex containing a polypeptide or antibody molecule of the present invention.

Any label or indicating means can be linked to or incorporated in an expressed protein, polypeptide, or antibody molecule that is part of an antibody or monoclonal antibody composition of the present invention or used separately, and those atoms or molecules can be used alone or in conjunction with additional reagents. Such labels are themselves well-known in clinical diagnostic chemistry and constitute a part of this invention only insofar as they are utilized with otherwise novel proteins methods and/or systems. The labeling means can be a fluorescent labeling agent that chemically binds to antibodies or antigens without denaturing them to form a fluorochrome (dye) that is a useful immunofluorescent tracer. Suitable fluorescent labeling agents are fluorochromes such as fluorescein isocyanate (FIC), fluorescein isothiocyanate (FITC), 5- dimethylamine-1-naphthalenesulfonyl chloride (DANSC), tetramethylrhodamine isothiocyanate (TRITC), hssamine, rhodamine 8200 sulphonyl chloride (RB 200 SC) and the like. A description of immunofluorescence analysis techniques is found in DeLuca, "Immunofluorescence Analysis", in Antibody As a Tool, Marchalonis et al., Eds., John Wiley & Sons, Ltd., pp. 189-231 (1982), which is incorporated herein by reference. Other suitable labeling agents are known to those skilled in the art. In preferred embodiments, the indicating group is an enzyme, such as horseradish peroxidase (HRP), glucose oxidase, or the like. In such cases where the principal indicating group is an enzyme such as HRP or glucose oxidase or a vitamin, such as biotin, additional reagents are required to visualize the formation of the receptor-ligand complex. Such additional reagents for HRP include hydrogen peroxide and an oxidation dye precursor, such as diaminobenzidine. Such additional reagents for biotin include streptavidin. An additional reagent useful with glucose oxidase is 2,2'-amino-di-(3-ethyl- benzthiazoline-G-sulfonic acid) (ABTS).

Radioactive elements are also useful labeling agents and are used illustratively herein. An exemplary radiolabeling agent is a radioactive element that produces gamma ray emissions. Elements which themselves emit gamma rays, such as ¹²⁴1, ¹²⁵1, ¹²⁸1, ¹³²I and ⁵¹Cr represent one class of gamma ray emission-producing radioactive element indicating groups. Particularly preferred is ¹²⁵I. Another group of useful labeling means are those elements such as ^πC, ^1SF, ¹⁵O and ¹³N which themselves emit positrons. The positrons so emitted produce gamma rays upon encounters with electrons present in the animal's body. Also useful is a beta emitter, such ⁿ 'indium or ³H. The linking of labels or labeling of polypeptides and proteins is well known in the art. For instance, antibody molecules produced by a hybridoma can be labeled by metabolic incorporation of radioisotope-containing amino acids provided as a component in the culture medium (see, e.g., Galfre et al., Meth. Enzymol, 73:3-46 (1981)). The techniques of protein conjugation or coupling through activated functional groups are particularly applicable (see, e.g., Aurameas, et al., Scand. J. Immunol, Vol. 8 Suppl. 7:7- 23 (1978); Rodwell et al., Biotech., 3:889-894 (1984); and U.S. Patent No. 4,493,795).

The diagnostic systems can also include, preferably as a separate package, a specific binding agent. Exemplary specific binding agents are second antibody molecules, complement proteins or fragments thereof, such as, S. aureus protein A, and the like. Preferably the specific binding agent binds the reagent species when that species is present as part of a complex.

In preferred embodiments, the specific binding agent is labeled. However, when the diagnostic system includes a specific binding agent that is not labeled, the agent is typically used as an amplifying means or reagent. In these embodiments, the labeled specific binding agent is capable of specifically binding the amplifying means when the amplifying means is bound to a reagent species-containing complex.

The diagnostic kits of the present invention can be used in an "ELISA" format to detect the quantity of the polypeptide of the present invention in a sample. A description of the ELISA technique is found in Sites et al., Basic and Clinical Immunology, 4th Ed., Chap. 22, Lange Medical Publications, Los Altos, CA (1982) and in U.S. Patent No. 3,654,090; U.S. Patent No. 3,850,752; and U.S. Patent No. 4,016,043, which are all incorporated herein by reference.

Thus, in some embodiments, a polypeptide of the present invention, an antibody or a monoclonal antibody of the present invention can be affixed to a solid matrix to form a solid support that comprises a package in the subject diagnostic systems.

A reagent is typically affixed to a solid matrix by adsorption from an aqueous medium, although other modes of affixation applicable to proteins and polypeptides can be used that are well known to those skilled in the art. Exemplary adsorption methods are described herein. Useful solid matrices are also well known in the art. Such materials are water insoluble and include the cross-linked dextran available under the trademark SEPHADEX from Pharmacia Fine Chemicals (Piscataway, NJ), agarose, polystyrene beads of about 1 micron (μm) to about 5 millimeters (mm) in diameter available from several suppliers (e.g., Abbott Laboratories, Chicago, IL), polyvinyl chloride, polystyrene, cross-linked polyacrylamide, nitrocellulose- or nylon-based webs (sheets, strips or paddles) or tubes, plates or the wells of a microtiter plate, such as those made from polystyrene or polyvinylchloride.

The reagent species, labeled specific binding agent, or amplifying reagent of any diagnostic system described herein can be provided in solution, as a liquid dispersion or as a substantially dry power, e.g., in lyophilized form. Where the indicating means is an enzyme, the enzyme's substrate can also be provided in a separate package of a system. A solid support such as the before-described microtiter plate and one or more buffers can also be included as separately packaged elements in this diagnostic assay system. The packaging materials discussed herein in relation to diagnostic systems are those customarily utilized in diagnostic systems.

Novel Polynucleotides

The present invention also is directed to certain novel polynucleotides identified as SEQ ID NOs: 5, 16 and 29. Searches were performed against the Genbank and EST databases and showed no significant homology between the polynucleotides identified as SEQ ID NOs: 5, 16 and 29.

Genes

The present invention also relates to the genes corresponding to SEQ ID NOs:l- 29, and the polypeptides encoded by the polynucleotides or genes or regions thereof of SEQ ED NOs: 1-29. The corresponding gene can be isolated in accordance with lαiown methods using the sequence information disclosed herein. Such methods include preparing probes or primers from the disclosed sequence and identifying or amplifying the corresponding gene from appropriate sources of genomic material. Homologs, Paralogs and Orthologs

Also provided in the present invention are homologs of the polynucleotides, polypeptides and genes of the invention and regions thereof, including paralogous genes and orthologous genes. Nucleic acid homologs may be isolated and identified using suitable probes or primers from the sequences provided herein and screening a suitable nucleic acid source for the desired homolog. Studies of gene and protein evolution often involve the comparison of homologs, which are sequences that have common origins but may or may not have common activity. Sequences that share an arbitrary level of similarity determined by alignment of matching bases are called homologous. There are many cases in which genes have duplicated, assumed somewhat different functions and been moved to other regions of the genome (e.g. alpha and beta globin). Such related genes in the same species are referred to as paralogs (e.g., Lundin, 1993, who refers to Fitch, 1976 for this distinction). They must be distinguished from orthologs (homologous genes in different species, such as beta globin in human and mouse) if any sensible comparisons are to be made. These terms as relate to genes are formally defined as follows:

As used herein, "paralogous genes" are genes within the same species produced by gene duplication in the course of evolution. They may be arranged in clusters or distributed on different chromosomes, an arrangement which is usually conserved in a wide range of vertebrates.

As used herein, "orthologous genes" describes homologous genes in different species that are descended from the same gene in the nearest common ancestor. Orthologs tend to have similar function.

In reports of previous Human Gene Mapping Workshops, the Comparative Gene Mapping Committee recommended explicit criteria for establishing homology between genes mapped in different species, as well as urging inclusion of specific criteria in comparative gene mapping publications (O'Brien and Graves, 1991). The evidence for gene homology might also be recorded in The Comparative Animal Genome database (TCAGdb). Revised criteria for determining homology can include any of the following (the most stringent are asterixed): Gene or other nucleotide sequence:

• similar nucleotide sequence*

• cross-hybridization to the same molecular probe*

• conserved map position*

Protein or polypeptide:

• similar amino acid sequence*

• similar subunit structure and formation of functional heteropolymer

• immunological cross-reaction • similar expression profile

• similar subcellular location

• similar substrate specificity

• similar response to specific inhibitors

Phenotype:

• similar mutant phenotype

• complementation of function*

Two new criteria have recently been added. Because of the accumulation of overwhelming evidence for linkage conservation among mammal and vertebrate species, conserved map position may now itself constitute an important criterion of homology, and is particularly valuable in distinguishing between members of a gene family. Complementation of function has also been added, because it is now possible to establish complementation of function by transfection across even the widest species barriers. More recent studies have also demonstrated that some of these criteria are much more stringent than others. A strong basis for homology would be a demonstration of high DNA or amino acid sequence similarity, plus in addition to conservation of map position between flanking homologous markers. Less robust immunological and biochemical criteria for gene homology would need to be confirmed at least by gene position. The assumption of gene homology must be considered a working hypothesis, and may later be further confirmed when further scientific criteria are applied.

Preferred embodiments of the present invention include homologs, paralogs and orthologs of the polynucleotides, polypeptides and genes of the invention and regions thereof. Polypeptides

The polypeptides of the invention can be prepared in any suitable manner. Such polypeptides include isolated naturally occurring polypeptides, recombinantly produced polypeptides, synthetically produced polypeptides, or polypeptides produced by a combination of these methods. Means for preparing such polypeptides are well understood in the art. See, e.g., Curr. Prot. Mol. Bio., Chapter 16.

The polypeptides may be in the form of the secreted protein, including the mature form, or may be a part of a larger protein, such as a fusion protein (see below). It is often advantageous to include an additional amino acid sequence that contains secretory or leader sequences, pro-sequences, sequences which aid in purification (such as multiple histidine residues), or an additional sequence for stability during recombinant production.

The polypeptides of the present invention are preferably provided in an isolated form, and preferably are substantially purified. A recombinantly produced version of a polypeptide, including the secreted polypeptide, can be substantially purified by the one- step method described in Smith & Jolmson (Gene, 67:31-40, 1988). Polypeptides of the invention also can be purified from natural or recombinant sources using antibodies of the invention raised against the secreted protein according to methods that are well known in the art.

Signal Sequences Methods for predicting whether a protein has a signal sequence, as well as the cleavage point for that sequence, are available. For instance, the method of McGeoch uses the information from a short N-terminal charged region and a subsequent uncharged region of the complete (uncleaved) protein (Virus Res., 3:271-286 (1985)). The method of von Heinje uses the information from the residues surrounding the cleavage site, typically residues -13 to +2, where +1 indicates the amino terminus of the secreted protein (Nucleic Acids Res., 14:4683-4690 (1986)). Therefore, from a deduced amino acid sequence, a signal sequence and mature sequence can be identified.

The deduced amino acid sequence of a secreted polypeptide can be analyzed by a computer program called Signal P (Nielsen et al., Protein Engineering, 10:1-6 (1997), which predicts the cellular location of a protein based on the amino acid sequence. As part of this computational prediction of localization, the methods of McGeoch and von Heinje are incorporated.

As one of ordinary skill in the art will appreciate, however, cleavage sites sometimes vary from organism to organism and cannot be predicted with absolute certainty. Accordingly, the present invention provides secreted polypeptides having a sequence corresponding to the translations of SEQ JD NOs: 1-29 and their corresponding genes which have an N-terminus beginning within 5 residues (i.e., + or - 5 residues) of the predicted cleavage point. Similarly, it is also recognized that in some cases, cleavage of the signal sequence from a secreted protein is not entirely uniform, resulting in more than one secreted species. These polypeptides, and the polynucleotides and genes encoding such polypeptides, are contemplated by the present invention.

Moreover, the signal sequence identified by the above analysis may not necessarily predict the naturally occurring signal sequence. For example, the naturally occurring signal sequence may be further upstream from the predicted signal sequence. However, it is likely that the predicted signal sequence will be capable of directing the secreted protein to the ER. These polypeptides, and the polynucleotides and genes encoding such polypeptides, are contemplated by the present invention. Polynucleotide, Polypeptide and Gene Variants Polynucleotide, polypeptide and gene variants differ from the polynucleotides, polypeptides and genes of the present invention, but retain essential properties thereof. In general, variants have close similarity overall and are identical in many regions to the polynucleotide or polypeptide of the present invention.

Further embodiments of the present invention include polynucleotides having at least 80% identity, more preferably at least 90% identity, and most preferably at least 95%, 96%, 97%, 98% or 99% identity to a sequence contained in SEQ ID NOs: 1-29. Of course, due to the degeneracy of the genetic code, one of ordinary skill in the art will immediately recognize that a large number of the polynucleotides having at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity, polynucleotides at least ten bases in length hybridizable to polynucleotide comprising at least one of SEQ ED NOs: 1-29 inclusive, polynucleotides comprising at least one SEQ ID NOs: 1-29 inclusive with sequential nucleotide deletions from either the 5' terminus or the 3' terminus, or a species homolog of polynucleotides comprising at least one of SEQ ED NOs: 1-29 inclusive will encode a polypeptide identical to an amino acid sequence contained in the translations of SEQ JD NOs:l-29.

Further embodiments of the present invention include genes and regions thereof having at least 80% identity, more preferably at 90% identity, and most preferably at least 95%, 96%, 97%, 98% or 99% identity to genes corresponding to a sequence contained in SEQ ID NOs: 1-29 and regions thereof. Of course, due to the degeneracy of the genetic code, one of ordinary skill in the art will immediately recognize that a large number of the genes having at least 85%, 90%, 95%, 96%, 97%, or 99% identity respectively to genes of the invention, genes hybridizable to genes of the invention, genes of the invention with sequential nucleotide deletions from either the 5' terminus or the 3' terminus, or a species homolog of genes of the invention will encode a polypeptide identical to an amino acid sequence contained in the translations of genes of the invention. Further embodiments of the present invention also include polypeptides having at least 80% identity, more preferably at least 85% identity, more preferably at least 90% identity, and most preferably at least 95%, 96%, 97%, 98% or 99% identity to an amino acid sequence contained in translations of SEQ ED NOs: 1-29 and their corresponding genes. Preferably, the above polypeptides should exhibit at least one biological activity of the protein. In a preferred embodiment, polypeptides of the present invention include polypeptides having at least 90% similarity, more preferably at least 95% similarity, and still more preferably at least 96%, 97%, 98%, or 99% similarity to an amino acid sequence contained in translations of SEQ JD NOs: 1-29 and their corresponding genes. Methods for aligning polynucleotides, polypeptides, genes or regions thereof are codified in computer programs, including the GCG program package (Devereux et al., Nuc. Acids Res. 12:387 (1984)), BLASTP, BLASTN, FASTA (Atschul et al., J Molec. Biol. 215:403 (1990)), and Bestfit program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, 575 Science Drive, Madison, WI 53711) which uses the local homology algorithm of Smith and Waterman (Adv. in App. Math., 2:482-489 (1981)). When using any of the sequence alignment programs to determine whether a particular sequence is, for instance, 95% identical to a reference sequence, the parameters are set such that the percentage of identity is calculated over the full length of the reference polynucleotide or gene that gaps in identity of up to 5% of the total number of nucleotides in the reference polynucleotide or gene are allowed.

A preferred method for determining the best overall match between a query sequence (a sequence of the present invention) and a subject sequence, also referred to as a global sequence alignment, can be determined using the FASTDB computer program based on the algorithm of Brutlag et al. (Comp. App. Biosci., 6:237-245 (1990)). The term "sequence" includes nucleotide and amino acid sequences. In a sequence alignment the query and subject sequences are either both nucleotide sequences or both amino acid sequences. The result of said global sequence alignment is presented in terms of percent identity. Preferred parameters used in a FASTDB search of a DNA sequence to calculate percent identity are: Matrix=Unitary, k-tuple=4, Mismatch Penalty=l, Joining Penalty=30, Randomization Group Length=0, and Cutoff Score=l, Gap Penalty=5, Gap Size Penalty 0.05, and Window Size=500 or query sequence length in nucleotide bases, whichever is shorter. Preferred parameters employed to calculate percent identity and similarity of an amino acid alignment are:

150, k-tuple=2, Mismatch Penalty= 1, Joining Penalty=20, Randomization Group

Cutoff Score=l, Gap Penalty=5, Gap Size Penalty=0.05, and Window Size=500 or query sequence length in amino acid residues, whichever is shorter.

For example, a polynucleotide having a nucleotide sequence of at least 95% "identity" to a sequence contained in SEQ ED NOs: 1-29 means that the polynucleotide is identical to a sequence contained in SEQ ED NOs: 1-29 or the cDNA except that the polynucleotide sequence may include up to five point mutations per each 100 nucleotides of the total length (not just within a given 100 nucleotide stretch). In other words, to obtain a polynucleotide having a nucleotide sequence at least 95% identical to SEQ JD NOs:l-29, up to 5% of the nucleotides in the sequence contained in SEQ ID NOs:l-29 or the cDNA can be deleted, inserted, or substituted with other nucleotides. These changes may occur anywhere throughout the polynucleotide. Similarly, a polypeptide having an amino acid sequence having at least, for example, 95% "identity" to a reference polypeptide, means that the amino acid sequence of the polypeptide is identical to the reference polypeptide except that the polypeptide sequence may include up to five amino acid alterations per each 100 amino acids of the total length of the reference polypeptide. In other words, to obtain a polypeptide having an amino acid sequence at least 95% identical to a reference amino acid sequence, up to 5% of the amino acid residues in the reference sequence may be deleted or substituted with another amino acid, or a number of amino acids up to 5% of the total amino acid residues in the reference sequence may be inserted into the reference sequence. These alterations of the reference sequence may occur at the amino or carboxy terminal positions of the reference amino acid sequence or anywhere between those terminal positions, interspersed either individually among residues in the reference sequence or in one or more contiguous groups within the reference sequence.

The variants may contain alterations in the coding regions, non-coding regions, or both. Especially preferred are polynucleotide variants containing alterations that produce silent substitutions, additions, or deletions, but do not alter the properties or activities of the encoded polypeptide. Nucleotide variants produced by silent substitutions due to the degeneracy of the genetic code are preferred. Moreover, variants in which 5-10, 1-5, or 1-2 amino acids are substituted, deleted, or added in any combination are also preferred. Polynucleotide variants can be produced for a variety of reasons. For instance, a polynucleotide variant may be produced to optimize codon expression for a particular host (i.e., codons in the human mRNA may be changed to those preferred by a bacterial host, such as E. coli). Variants may also arise by the process of ribosomal frameshifting, by franslational read-through at naturally occurring stop codons, and by decoding of in- frame franslational stop codons UGA tlirough insertion of selanocysteine (See The RNA World, 2^nd edition, ed: Gesteland, R.F., Cech, T.R., & Atkins, J.F.; Cold Spring Harbor Laboratory Press, 1999).

The variants may be allelic variants. Naturally occurring variants are called "allelic variants," and refer to one of several alternate forms of a gene occupying a given locus on a chromosome of an organism (Lewin, Ed., Genes II, John Wiley & Sons, New York (1985)). These allelic variants can vary at either the polynucleotide and/or polypeptide level. Alternatively, non-naturally occurring variants may be produced by mutagenesis techniques or by direct synthesis. See, e.g., Curr. Prot. Mol. Bio., Chapter 8.

Using known methods of protein engineering and recombinant DNA technology, variants may be generated to improve or alter the characteristics of the polypeptides of the present invention. For example, polypeptide variants containing amino acid substitutions of charged amino acids with other charged or neutral amino acids may produce proteins with improved characteristics, such as decreased aggregation. As known, aggregation of pharmaceutical formulations both reduces activity and increases clearance due to the aggregate's immunogenic activity (see, e.g., Pinckard et al., Clin. Exp. Immunol. 2:331-340 (1967); Robbins et al., Diabetes, 36: 838-845 (1987); Cleland et al., Crit. Rev. Therap. Drug Carrier Sys., 10:307-377 (1993)). Similarly, interferon gamma exhibited up to ten times higher activity after deleting 8-10 amino acid residues from the carboxy terminus of this protein (Dobeli et al., J. Biotechnology, 7:199-216 (1988)). Moreover, ample evidence demonstrates that variants often retain a biological activity similar to that of the naturally occurring protein. For example, Gayle et al. conducted extensive mutational analysis of human cytokine IL-la (J. Biol. Chem., 268:22105-22111 (1993)). These investigators used random mutagenesis to generate over 3,500 individual IL- 1 a mutants that averaged 2.5 amino acid changes per variant over the entire length of the molecule. Multiple mutations were examined at every possible amino acid position. The investigators concluded that "most of the molecule could be altered with little effect on either binding or biological activity." In fact, only 23 unique amino acid sequences, out of more than 3,500 amino acid sequences examined, produced a protein that differed significantly in activity from the wild-type sequence. Another experiment demonstrated that one or more amino acids can be deleted from the N-terminus or C-terminus of the secreted protein without substantial loss of biological function. Ron et al. reported variant KGF proteins having heparin binding activity even after deleting 3, 8, or 27 amino-terminal amino acid residues (J. Biol. Chem. 268: 2984- 2988 (1993)). Furthermore, even if deleting one or more amino acids from the N-terminus or C- terminus of a polypeptide results in modification or loss of one or more biological functions, other biological activities may still be retained. For example, the ability of a deletion variant to induce and/or to bind antibodies which recognize the secreted form will likely be retained when less than the majority of the residues of the secreted form are removed from the N-terminus or C-terminus. Whether a particular polypeptide lacking N- or C-terminal residues of a protein retains such immunogenic activities can readily be determined by routine methods described herein and otherwise known in the art.

Thus, the invention further includes polypeptide variants that show substantial biological activity. Such variants include deletions, insertions, inversions, repeats, frameshifting, read-through franslational variants, and substitutions selected according to general rules known in the art so as have little effect on activity. For example, guidance concerning how to make phenotypically silent amino acid substitutions is provided in Bowie et al., Science, 247:1306-1310 (1990), wherein the authors indicate that there are two main strategies for studying the tolerance of an amino acid sequence to change. The first strategy exploits the tolerance of amino acid substitutions by natural selection during the process of evolution. By comparing amino acid sequences in different species, the amino acid positions that have been conserved between species can be identified. These conserved amino acids are likely important for protein function. In contrast, the amino acid positions in which substitutions have been tolerated by natural selection indicate positions which are not critical for protein function. Thus, positions tolerating amino acid substitution may be modified while still maintaining biological activity of the protein.

The second strategy uses genetic engineering to introduce amino acid changes at specific positions of a cloned gene to identify regions critical for protein function. For example, site-directed mutagenesis or alanine-scanning mutagenesis (the introduction of single alanine mutations at every residue in the molecule) can be used (Cunningham et al., Science, 244:1081-1085 (1989)). The resulting mutant molecules can then be tested for biological activity.

According to Bowie et al., these two strategies have revealed that proteins are surprisingly tolerant of amino acid substitutions. The authors further indicate which amino acid changes are likely to be permissive at certain amino acid positions in the protein. For example, the most buried or interior (within the tertiary structure of the protein) amino acid residues require nonpolar side chains, whereas few features of surface or exterior side chains are generally conserved. Moreover, tolerated conservative amino acid substitutions involve replacement of the aliphatic or hydrophobic amino acids Ala, Val, Leu and He; replacement of the hydroxyl residues Ser and Thr; replacement of the acidic residues Asp and Glu; replacement of the amide residues Asn and Gin; replacement of the basic residues Lys, Arg, and His; replacement of the aromatic residues Phe, Tyr, and Trp; and replacement of the small-sized amino acids Ala, Ser, Thr, Met, and Gly.

Besides conservative amino acid substitution, variants of the present invention include: (i) substitutions with one or more of the non-conserved amino acid residues, where the substituted amino acid residues may or may not be one encoded by the genetic code; (ii) substitution with one or more of amino acid residues having a substituent group; (iii) fusion of the mature polypeptide with another compound, such as a compound to increase the stability and/or solubility of the polypeptide (e.g., polyethylene glycol); (iv) fusion of the polypeptide with additional amino acids, such as an IgG Fc fusion region peptide, a leader or secretory sequence, or a sequence facilitating purification. Such variant polypeptides are deemed to be within the scope of those skilled in the art from the teachings herein.

Polynucleotide and Polypeptide Fragments In the present invention, a "polynucleotide fragment" and "region of a gene" refers to a short polynucleotide having a nucleic acid sequence contained in SEQ ED NOs: 1-29. The short nucleotide fragments are preferably at least about 15 nucleotides (nt), and more preferably at least about 20 nt, still more preferably at least about 30 nt, and even more preferably, at least about 40 nt in length. A fragment "at least 20 nt in length," for example, is intended to include 20 or more contiguous bases from the cDNA sequence contained in that shown in SEQ ID NOs: 1-29. These nucleotide fragments are useful as diagnostic probes and primers as discussed herein. Of course, larger fragments (e.g., 50, 150, and greater than 150 nucleotides) are preferred.

Moreover, representative examples of polynucleotide fragments of the invention, include, for example, fragments having a sequence from about nucleotide number 1-50, 51-100, 101-150, 151-200, 201-250, 251-300, 301-350, 351-400, 401-450, to the end of SEQ ID NOs: 1-29. In this context " about" includes the particularly recited ranges, larger or smaller by several nucleotides (i.e., 5, 4, 3, 2, or 1 nt) at either terminus or at both termini. Preferably, these fragments encode a polypeptide that has biological activity. In the present invention, a "polypeptide fragment" refers to a short amino acid sequence contained in the translations of SEQ ID NOs: 1-29. Protein fragments may be "free-standing," or comprised within a larger polypeptide of which the fragment forms a part or region, most preferably as a single continuous region. Representative examples of polypeptide fragments of the invention include, for example, fragments from about amino acid number 1-20, 21-40, 41-60, or 61 to the end of the coding region. Moreover, polypeptide fragments can be about 20, 30, 40, 50, or 60 amino acids in length. In this context "about" includes the particularly recited ranges, larger or smaller by several amino acids (5, 4, 3, 2, or 1) at either extreme or at both extremes.

In situations where a DST of the present invention is not a translatable polypeptide, i.e., where the DST is in whole or in part of the 3 ' untranslated region of its corresponding gene, the translation product or region of the translation product of the gene corresponding to the DST is intended to be encompassed by the terms "polypeptide" or "polypeptide fragment" as used herein.

Preferred polypeptide fragments include the secreted protein as well as the mature form. Further preferred polypeptide fragments include the secreted protein or the mature form having a continuous series of deleted residues from the amino or the carboxy terminus, or both. For example, any number of amino acids ranging from 1-60, can be deleted from the amino terminus of either the secreted polypeptide or the mature form. Similarly, any number of amino acids ranging from 1-30, can be deleted from the carboxy terminus of the secreted protein or mature form. Furthermore, any combination of the above amino and carboxy terminus deletions are preferred. Similarly, polynucleotide fragments encoding these polypeptide fragments are also preferred.

Also preferred are polypeptide and polynucleotide fragments characterized by structural or functional domains, such as fragments that comprise alpha-helix and alpha- helix-forming regions, beta-sheet and beta-sheet-forming regions, turn and turn-forming regions, coil and coil-forming regions, hydrophilic regions, hydrophobic regions, alpha amphipathic regions, beta amphipathic regions, flexible regions, surface-forming regions, substrate binding region, and high antigenic index regions. Polypeptide fragments of the translations of SEQ ID NOs: 1-29 and their corresponding genes falling within conserved domains are specifically contemplated by the present invention. Moreover, polynucleotide fragments encoding these domains are also contemplated.

Other preferred fragments are biologically active fragments or the polynucleotide or gene encoding biologically active fragments. Biologically active fragments are those exhibiting activity similar, but not necessarily identical, to an activity of the polypeptide of the present invention. The biological activity of the fragments may include an improved desired activity, or a decreased undesirable activity. Epitopes And Antibodies Or Binding Partners To Tiem Fragments which function as epitopes may be produced by any conventional means. (See, e.g., Houghten, R. A., Proc. Natl. Acad. Sci. USA, 82:5131-5135 (1985), further described in U.S. Patent No. 4,631,211). In the present invention, immunogenic epitopes preferably contain a sequence of at least seven, more preferably at least nine, and most preferably between about 15 to about 30 amino acids. Antigenic epitopes are useful to raise antibodies, including monoclonal antibodies, which specifically bind the epitope. (See, e.g., Wilson et al., Cell, 37:767-778 (1984); Sutcliffe et al., Science, 219:660-666 (1983)). Similarly, immunogenic epitopes can be used to induce antibodies or to select binding partners according to methods well known in the art. (See, e.g., Sutcliffe et al., (1983) supra; Wilson et al., (1984) supra; Chow et al., Proc. Natl. Acad. Sci., USA, 82:910-914; and Bittle et al., J. Gen. Virol, 66:2347-2354 (1985)). A preferred immunogenic epitope includes the secreted protein. The immunogenic epitope may be presented together with a carrier protein, such as an albumin, to an animal system (such as rabbit or mouse). Alternatively, the immunogenic epitope may be prescribed without a carrier, if the sequence is of sufficient length (at least about 25 amino acids). However, immunogenic epitopes comprising as few as 8 to 10 amino acids have been shown to be sufficient to raise antibodies capable of binding to, at the very least, linear epitopes in a denatured polypeptide (e.g., in Western blotting.) As used herein, the term "antibody" (Ab) or "monoclonal antibody" (mAb) is meant to include intact molecules as well as antibody fragments (such as, for example, Fab and F(ab')2 fragments) which are capable of specifically binding to protein. Fab and F(ab')2 fragments lack the Fc fragment of intact antibody, clear more rapidly from the circulation, and may have less non-specific tissue binding than an intact antibody (Wahl et al, J Nucl. Med., 24:316-325, 1983). Thus, these fragments are preferred, as well as the products of a Fab or other immunoglobulin expression library. Moreover, antibodies of the present invention include chimeric, single chain, and human and humanized antibodies. The antibodies may be chimeric antibodies, e.g., humanized versions of murine monoclonal antibodies. Such humanized antibodies may be prepared by known techniques, and offer the advantage of reduced immunogenicity when the antibodies are administered to humans. See, e.g., Co et al, Nature, 351:501-2 (1991). In one embodiment, a humanized monoclonal antibody comprises the variable region of a murine antibody (or just the antigen binding site thereof) and a constant region derived from a human antibody. Alternatively, a humanized antibody fragment may comprise the antigen binding site of a murine monoclonal antibody and a variable region fragment (lacking the antigen-binding site) derived from a human antibody. Procedures for the production of chimeric and further engineered monoclonal antibodies include those described in Riechmann et al, Nature, 332:323, 1988, Liu et al, PNAS, 84:3439, 1987, Larrick et al, Bio/Technology, 7:934, 1989, and Winter and Harris, TIPS, 14:139, May, 1993, Zou et al, Science 262:1271-4, 1993, Zou et al, Curr. Biol, 4:1099-103, 1994, and Walls et al, Nucleic Acids Res., 21:2921-9, 1993.

One method for producing a human antibody comprises immunizing a non-human animal, such as a transgenic mouse, with a polypeptide translated from a nucleotide sequence chosen from SEQ JD NOs: 1-29 or their corresponding genes, whereby antibodies directed against the polypeptide translated from a nucleotide sequence chosen from SEQ ED NOs: 1-29 or their corresponding genes are generated in said animal. Procedures have been developed for generating human antibodies in non-human animals. The antibodies may be partially human, or preferably completely human. For example, mice have been prepared in which one or more endogenous immunoglobulin genes are inactivated by various means and human immunoglobulin genes are introduced into the mice to replace the inactivated mouse genes. Such transgenic mice may be genetically altered in a variety of ways. The genetic manipulation may result in human immunoglobulin polypeptide chains replacing endogenous immunoglobulin chains in at least some (preferably virtually all) antibodies produced by the animal upon immunization. Examples of techniques for production and use of such transgenic animals are described in U.S. Patent Nos. 5,814,318, 5,569,825, and 5,545,806, which are incorporated by reference herein. Antibodies produced by immunizing transgenic animals with a polypeptide translated from a nucleotide sequence chosen from SEQ ID NOs: 1-29 or their corresponding genes and methods of using such antibodies are provided herein.

Monoclonal antibodies may be produced by conventional procedures, e.g., by immortalizing spleen cells harvested from the transgenic animal after completion of the immunization schedule. The spleen cells may be fused with myeloma cells to produce hybridomas by conventional procedures. Examples of such techniques are described in U.S. Patent No. 4,196,265, which is incorporated by reference herein.

A method for producing a hybridoma cell line comprises immunizing such a transgenic animal with an immunogen comprising at least seven contiguous amino acid residues of a polypeptide translated from a nucleotide sequence chosen from SEQ ED NOs:l-29 or their corresponding genes; harvesting spleen cells from the immunized animal; fusing the harvested spleen cells to a myeloma cell line, thereby generating hybridoma cells; and identifying a hybridoma cell line that produces a monoclonal antibody that binds a polypeptide translated from a nucleotide sequence chosen from SEQ ID NOs: 1-29 or their corresponding genes. Such hybridoma cell lines, and monoclonal antibodies produced therefrom, are encompassed by the present invention. Monoclonal antibodies secreted by the hybridoma cell line are purified by conventional techniques. Examples of such techniques are described in U.S. Patent No. 4,469,630 and U.S. Patent No. 4,361,549.

Antibodies are only one example of binding partners to epitopes or receptor molecules. Other examples include, but are not limited to, synthetic peptides, which can be selected as a binding partner to an epitope or receptor molecule. The peptide may be selected from a peptide library as described by Appel et al, Biotechniques, 13, 901-905; and Dooley et zd. . Biol Chem. 273, 18848-18856, 1998.

Binding assays can select for those binding partners (antibody, synthetic peptide, or other molecule) with highest affinity for the epitope or receptor molecule, using methods known in the art. Such assays may be done by immobilizing the epitope or receptor on a solid support, allowing binding of the library of antibodies or other molecules, and washing away those molecules with little or no affinity. Those binding partners or antibodies with highest affinity for the epitope or receptor will remain bound to the solid support. Alternatively, arrays of candidate binding partners may be immobilized, and a labeled soluble receptor molecule is allowed to interact with the array, followed by washing unbound receptors. High affinity binding is detectable by the presence of bound label.

Antibodies or other binding partners may be employed in an in vitro procedure, or administered in vivo to inhibit biological activity induced by a polypeptide translated from a nucleotide sequence chosen from SEQ JD NOs: 1 -29 or their corresponding genes. Disorders caused or exacerbated (directly or indirectly) by the interaction of such polypeptides of the present invention with cell surface receptors thus may be treated. For example, a patient suffering a disorder of altered target cell metabolism of NGF could be treated with such an antibody to block these effects. A therapeutic method involves in vivo administration of a blocking antibody to a mammal in an amount effective for reducing a biological activity induced by a polypeptide translated from a nucleotide sequence chosen from SEQ JD NOs: 1-29 or their corresponding genes. For example, NGF is administered as a treatment for peripheral neuropathic disease and in some individuals produces painful side effects such as myalgia and hyperalgesia. Thus an antibody could be used to modulate NGF metabolism as an adjunct to NGF therapy to ameliorate such side effects.

Generally, antibodies or binding partners to receptors or cell surface polypeptides also can be linked to moieties, such as, for example, drug-loaded particles, antigens, DNA vaccines, immune modulators, other peptides, proteins for specific binding, and the like to the cells for targeting and enhanced delivery of the drug-loaded particles, antigens,

DNA vaccines, immune modulators, other peptides, proteins for specific binding, and the like. Exemplary vaccines that can be specifically targeted to particular cells include, but are not limited to, rotavirus, influenza, diptheria, tetanus, pertussis, Hepatitis A, B and C, as well as conjugate vaccines, including S. pneumonia. Similarly, exemplary drugs that may be specifically targeted to particular cells include, but are not limited to, insulin, LHRH, buserlein, vasopressin and recombinant interleukins, such as IL-2 and IL-12.

Additionally, exemplary vectors, such as, for example, adeno-associated virus, canarypox virus, adenovirus, retrovirus, and other delivery vehicles, such as, for example, liposomes and PLGA may be used to specifically target therapeutic moieties, such as, for example, IL-1 antagonist, GM-CSF antagonists, and the like, to particular cells. As is apparent to one skilled in the art, numerous other vaccines, drugs, and vectors may be useful in targeting and delivering therapeutic agents to particular cells.

Also provided herein are conjugates comprising a detectable (e.g., diagnostic) or therapeutic agent, attached to an antibody directed against a polypeptide translated from a nucleotide sequence chosen from SEQ JD NOs: 1-29 or their corresponding genes. Examples of such agents are well known, and include, but are not limited to diagnostic radionuclides, therapeutic radionuclides, and cytotoxic drugs. See, e.g., Thrush et al, Annu.Rev.Immunol, 14:49-71, 1996. The conjugates may be useful in in vitro or in vivo procedures.

Fusion Proteins Any polypeptide of the present invention can be used to generate fusion proteins.

For example, the polypeptides of the present invention, when fused to a second protein, can be used as an antigenic tag. Antibodies raised against the polypeptides of the present invention can be used to indirectly detect the second protein by binding to the polypeptide. Moreover, because secreted proteins target cellular locations based on trafficking signals, the polypeptides of the present invention can be used as targeting molecules once fused to other proteins.

Examples of domains that can be fused to polypeptides of the present invention include not only heterologous signal sequences, but also other heterologous functional regions. The fusion does not necessarily need to be direct, but may occur through linker sequences. Moreover, fusion proteins may also be engineered to improve characteristics of the polypeptide of the present invention. For instance, a region of additional amino acids, particularly charged amino acids, may be added to the N-terminus of the polypeptide to improve stability and persistence during purification from the host cell or subsequent handling and storage. Also, peptide moieties may be added to the polypeptide to facilitate purification. Such regions may be removed prior to final preparation of the polypeptide. The addition of peptide moieties to facilitate handling of polypeptides is a familiar and routine technique in the art.

In addition, polypeptides of the present invention, including fragments and, specifically, epitopes, can be combined with parts of the constant domain of immunoglobulins (IgG), resulting in chimeric polypeptides. These fusion proteins facilitate purification and show an increased half-life in vivo. One reported example describes chimeric proteins consisting of the first two domains of the human CD4- polypeptide and various domains of the constant regions of the heavy or light chains of mammalian immunoglobulins (EP A 394,827; Traunecker et al, Nature, 331:84-86, 1988). Fusion proteins having disulfide-linked dimeric structures (due to the IgG) can also be more efficient in binding and neutralizing other molecules, than the monomeric secreted protein or protein fragment alone (Fountoulakis et al, J. Biochem., 270:3958- 3964 (1995)). Similarly, EP A 0 464 533 (Canadian counterpart 2045869) discloses fusion proteins comprising various portions of constant region of immunoglobulin molecules together with another human protein or part thereof. In many cases, the Fc part in a fusion protein is beneficial in therapy and diagnosis, and thus can result in, for example, improved pharmacokinetic properties (see, e.g., EP A 0 232 262). Alternatively, deleting the Fc part after the fusion protein has been expressed, detected, and purified, would be desired. For example, the Fc portion may hinder therapy and diagnosis if the fusion protein is used as an antigen for immunizations. In drug discovery, for example, human proteins, such as hIL-5, have been fused with Fc portions for the purpose of high- throughput screening assays to identify antagonists of hIL-5 (See, Bennett et al, J. Mol. Recognition 8:52-58 (1995); Johanson et al, J. Biol. Chem., 270:9459-9471,1995). Moreover, the polypeptides of the present invention can be fused to marker sequences, such as a peptide that facilitates purification of the fused polypeptide. In preferred embodiments, the marker amino acid sequence is a hexa-histidine peptide, such as the tag provided in a pQE vector (QIAGEN, Inc., Chatsworth, CA), among others, many of which are commercially available. As described in Gentz et al, for instance, hexa-histidine provides for convenient purification of the fusion protein (Proc. Natl. Acad. Sci. USA 86:821-824 (1989)). Another peptide tag useful for purification, the "HA" tag, corresponds to an epitope derived from the influenza hemagglutinin protein (Wilson et al, Cell, 37:767 (1984)). Other fusion proteins may use the ability of the polypeptides of the present invention to target the delivery of a biologically active peptide. This might include focused delivery of a toxin to tumor cells, or a growth factor to stem cells.

Thus, any of these above fusions can be engineered using the polynucleotides or the polypeptides of the present invention. See, e.g., Curr. Prot. Mol Bio., Chapter 9.6. Vectors, Host Cells, and Protein Production

The present invention also relates to vectors containing the polynucleotide or gene of the present invention or regions thereof, host cells, and the production of polypeptides by recombinant techniques. The vector may be, for example, a phage, plasmid, viral, or retroviral vector. Retroviral vectors may be replication competent or replication defective. In the latter case, viral propagation generally will occur only in complementing host cells.

The polynucleotides, genes or regions thereof may be joined to a vector containing a selectable marker for propagation in a host. Generally, a plasmid vector is introduced in a precipitate, such as a calcium phosphate precipitate, or in a complex with a charged lipid. If the vector is a virus, it may be packaged in vitro using an appropriate packaging cell line and then transduced into host cells. See, e.g., Curr. Prot. Mol. Bio., Chapters 9.9, 16.15.

The polynucleotide or gene or gene region insert should be operatively linked to an appropriate promoter, such as the phage lambda PL promoter, the E. coli lac, trp, phoA and tac promoters, the SV40 early and late promoters and promoters of retroviral LTRs, to name a few. Other suitable promoters will be known to the skilled artisan. The expression constructs will further contain sites for transcription initiation, termination, and, in the transcribed region, a ribosome binding site for translation. The coding portion of the transcripts expressed by the constructs will preferably include a translation initiating codon at the beginning and a termination codon (UAA, UGA or UAG) appropriately positioned at the end of the polypeptide to be translated.

As indicated, the expression vectors will preferably include at least one selectable marker. Such markers include dihydrofolate reductase, G418 or neomycin resistance for eukaryotic cell culture and tefracycline, kanamycin or ampicillin resistance genes for culturing inE. coli and other bacteria. Representative examples of appropriate hosts include, but are not limited to, bacterial cells, such as E. coli, Streptomyces and Salmonella typhimurium cells; fungal cells, such as yeast cells; insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, 293, and Bowes melanoma cells, and plant cells. Appropriate culture mediums and conditions for the above-described host cells are known in the art. Vectors preferred for use in bacteria include pQΕ70, pQE60 and pQE-9, available from QIAGEN, Inc.; pBluescript vectors, Phagescript vectors, pNH8A, PNH16A, PNH18A, pNH46A, available from Stratagene Cloning Systems, Inc.; and ptrc99a, ρKK223-3, pKK233-3, pDR540, pRIT5 available from Pharmacia Biotech, Inc. Among preferred eukaryotic vectors are pWLNEO, pSV2CAT, pOG44, pXTl and pSG available from Stratagene; and pSVK3, pBPV, pMSG and pSVL available from Pharmacia. Other suitable vectors will be readily apparent to the skilled artisan. introduction of the construct into the host cell can be effected by calcium phosphate transfection, DEAE-dexfran mediated transfection, cationic lipid-mediated transfection, electroporation, transduction, infection, or other methods. Such methods are described in many standard laboratory manuals, such as Davis et al, Basic Methods In Molecular Biology (1986). It is specifically contemplated that the polypeptides of the present invention may, in fact, be expressed by a host cell lacking a recombinant vector. A polypeptide of this invention can be recovered and purified from recombinant cell cultures by well-known methods, including ammonium sulfate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, hydrophobic interaction chromatography, affinity chromatography, hydroxylapatite chromatography, and lectin chromatography. Most preferably, high performance liquid chromatography ("HPLC") is employed for purification.

Depending upon the host employed in a recombinant production procedure, the polypeptides of the present invention may be glycosylated or may be non-glycosylated. In addition, polypeptides of the invention may also include an initial modified methionine residue, in some cases as a result of host-mediated processes. Thus, it is well lαiown in the art that the N-terminal methionine encoded by the translation initiation codon generally is removed with high efficiency from any protein after translation in all eukaryotic cells. While the N-terminal methionine on most proteins also is efficiently removed in most prokaryotes, for some proteins, this prokaryotic removal process is inefficient, depending on the nature of the amino acid to which the N-terminal methionine is covalently linked.

Polypeptides of the present invention, and preferably the secreted form, can also be recovered from products purified from natural sources, including bodily fluids, tissues and cells, whether directly isolated or cultured; products of chemical synthetic procedures; and products produced by recombinant techniques from a prokaryotic or eukaryotic host, including, for example, bacterial, yeast, higher plant, insect, and mammalian cells.

Other Uses of the Polynucleotides of the Invention

Each of the polynucleotides and genes of the present invention and regions thereof identified herein can be used in numerous ways as reagents. The following description should be considered exemplary and utilizes known techniques. The polynucleotides and genes of the present invention and regions thereof are useful for chromosome identification. There exists an ongoing need to identify new chromosome markers, since few chromosome marking reagents based on actual sequence data (repeat polymorphisms) are presently available. Disorders in which receptor mediated endocytosis is implicated, such as retinitis pigmentosum, would benefit from use of a polynucleotide such as HAL_18 (SEQ ID NO: 12) as a diagnostic marker. Briefly, sequences can be mapped to chromosomes by preparing PCR primers (preferably 15-25 bp) from the sequences shown in SEQ JD NOs: 1-29 or their corresponding genes or regions thereof. Primers can be selected using computer analysis so that primers do not span more than one predicted exon in the genomic DNA. These primers may then be used for PCR screening of somatic cell hybrids containing individual human chromosomes. Only those hybrids containing the human gene corresponding to the SEQ ID NOs: 1-29 or their corresponding genes or regions thereof will yield an amplified fragment.

Similarly, somatic hybrids provide a rapid method of PCR mapping the polynucleotides to particular chromosomes. Moreover, sublocalization of the polynucleotides can be achieved with panels of specific chromosome fragments. Other gene-mapping strategies that can be used include in situ hybridization, prescreening with labeled flow-sorted chromosomes, and preselection by hybridization to construct chromosome specific-cDNA libraries. Precise chromosomal location of the polynucleotides, genes of the invention or regions thereof can also be achieved using fluorescence in situ hybridization (FISH) of a metaphase chromosomal spread. This technique uses polynucleotides as short as 500 or 600 bases; however, polynucleotides of 2,000-4,000 bp are preferred. For a review of this technique, see Verma et al, Human Chromosomes: a Manual of Basic Techniques, Pergamon Press, New York (1988).

For chromosome mapping, the polynucleotides, genes of the invention or regions thereof can be used individually (to mark a single chromosome or a single site on that chromosome) or in panels (for marking multiple sites and/or multiple chromosomes). Preferred polynucleotides correspond to the noncoding regions of the cDNAs because the coding sequences are more likely conserved within gene families, thus increasing the chance of cross-hybridization during chromosomal mapping.

Once a polynucleotide, gene of the invention or region thereof has been mapped to a precise chromosomal location, the physical position of the polynucleotide, gene or region thereof can be used in linkage analysis. Linkage analysis establishes coinheritance between a chromosomal location and presentation of a particular disease. Disease mapping data are found, for example, in V. McKusick, Mendelian Inheritance in Man (available on line tlirough Johns Hopkins University Welch Medical Library), Kruglyak et al. (Am. J. Hum. Genet, 56:1212-23, 1995); Curr. Prot. Hum. Genet. Assuming one megabase mapping resolution and one gene per 20 kb, a cDNA precisely localized to a chromosomal region associated with the disease could be one of 50-500 potential causative genes. Thus, once coinheritance is established, differences in the polynucleotide and the corresponding gene or region thereof between affected and unaffected individuals can be examined.

The polynucleotides of SEQ ID NOs: 1-29 and their corresponding genes or regions thereof can be used for this analysis of individuals. The disorders retinitis pigmentosum, macular degeneration, and congenital insensitivity to pain with anhidrosis have genetic etiology and also are disorders where receptor mediated endocytosis is implicated. Thus, a polynucleotide, such as HAL_18 (SEQ ID NO: 12), can be used to support or diagnose such disorders.

First, visible structural alterations in the chromosomes, such as deletions or translocations, are examined in chromosome spreads or by PCR. If no structural alterations exist, the presence of point mutations is ascertained. Mutations observed in some or all affected individuals, but not in normal individuals, indicates that the mutation may cause the disease. However, complete sequencing of the polypeptide and the corresponding gene from several normal individuals is required to distinguish the mutation from a polymorphism. If a new polymorphism is identified, this polymorphic polypeptide can be used for further linkage analysis.

Furthermore, increased or decreased expression of the gene in affected individuals as compared to unaffected individuals can be assessed using polynucleotides or genes of the present invention or regions thereof. Any of these alterations (altered expression, chromosomal rearrangement, or mutation) can be used as a diagnostic or prognostic marker.

In addition to the foregoing, a polynucleotide or gene of the invention or regions thereof can be used to control gene expression tlirough triple helix formation or antisense DNA or RNA. Both methods rely on binding of the polynucleotide or gene or gene region to DNA or RNA. For these techniques, preferred polynucleotides are usually 20 to 40 bases in length and complementary to either the region of the gene involved in transcription (see, Lee et al, Nuc. Acids Res., 6:3073 (1979); Cooney et al, Science, 241:456 (1988); and Dervan et al, Science, 251:1360 (1991) for discussion of triple helix formation) or to the mRNA itself (see, Okano, J. Neurochem, 56:560 (1991); and Oligodeoxy-nucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, FL (1988) for a discussion of antisense technique). Triple helix formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA molecule into polypeptide. Both techniques are effective in model systems, and the information disclosed herein can be used to design antisense or triple helix polynucleotides in an effort to treat disease.

Other Uses of the Polypeptides and Antibodies of the Invention

Each of the polypeptides identified herein can be used in numerous ways. The following description should be considered exemplary and utilizes known techniques. A polypeptide of the present invention can be used to assay protein levels in a biological sample using antibody-based techniques. For example, protein expression in tissues can be studied with classical immunohistological methods (Jalkanen, et al, J. Cell Biol, 101:976-985, 1985; Jalkanen et al, J Cell. Biol, 105:3087-3096, 1987). Other antibody-based methods useful for detecting protein gene expression include immunoassays, such as the enzyme linked immunosorbent assay (ELISA) and the radioimmunoassay (RIA). See, e.g., Curr. Prot. Mol. Bio., Chapter 11. Suitable antibody assay labels are known in the art and include enzyme labels, such as glucose oxidase; and radioisotopes, such as iodine (¹²⁵1, ¹²¹I), carbon (¹⁴C), sulfur (³⁵S), tritium (³H), indium (¹¹²In), and technetium (^99mTc); fluorescent labels, such as fluorescein and rhodamine; and organic moieties, such as biotin. In addition to assaying secreted protein levels in a biological sample, proteins can also be detected in vivo by imaging. Antibody labels or markers for in vivo imaging of protein include those detectable by X-radiography, nuclear magnetic resonance (NMR), or electron spin resonance (ESR). For X-radiography, suitable labels include radioisotopes such as barium or cesium, which emit detectable radiation but are not overtly harmful to the subject. Suitable markers for NMR and ESR include those with a detectable characteristic spin, such as deuterium, which may be incorporated into the antibody by labeling of nutrients for the relevant hybridoma. '

A protein-specific antibody or antibody fragment that has been labeled with an appropriate detectable imaging moiety such as a radioisotope (e.g., ¹³¹1, ¹¹²In, ^99mTc), a radio-opaque substance, or a material detectable by NMR, is introduced (e.g., parenterally, subcutaneously, or intraperitoneally) into the mammal. It will be understood in the art that the size of the subject and the imaging system used will determine the quantity of imaging moiety needed to produce diagnostic images. In the case of a radioisotope moiety, the quantity of radioactivity necessary for a human subject will normally range from about 5 to 20 millicuries of ^99mTc. The labeled antibody or antibody fragment will then preferentially accumulate at the location of cells which contain the specific protein. In vivo tumor imaging is described in Burchiel et al, "Immunophaπnacokinetics of Radiolabeled Antibodies and Their Fragments" (Chapter 13 in Tumor Imaging: The Radiochemical Detection of Cancer, Burchiel and Rhodes, Eds., Masson Publishing Inc. (1982)).

Thus, the invention provides a method of diagnosing a disorder, which involves (a) assaying the expression of a polypeptide of the present invention in cells or body fluid of an individual; and (b) comparing the level of gene expression with a standard gene expression level, whereby an increase or decrease in the assayed polypeptide gene expression level compared to the standard expression level is indicative of a disorder.

Moreover, polypeptides of the present invention can be used to treat disease. For example, patients can be administered a polypeptide of the present invention in an effort to replace absent or decreased levels of the polypeptide (e.g., insulin); to supplement absent or decreased levels of a different polypeptide (e.g., hemoglobin S for hemoglobin B); to inhibit the activity of a polypeptide (e.g., an oncogene); to activate the activity of a polypeptide (e.g., by binding to a receptor); to reduce the activity of a membrane bound receptor by competing with it for free ligand (e.g., soluble tumor necrosis factor (TNF) receptors used in reducing inflammation); or to bring about a desired response (e.g., blood vessel growth). Similarly, antibodies directed to a polypeptide of the present invention can also be used to freat disease. For example, administration of an antibody directed to a polypeptide of the present invention can bind and reduce overproduction of the polypeptide. Similarly, administration of an antibody can activate the polypeptide, such as by binding to a polypeptide bound to a membrane (receptor). Polypeptides can be used as antigens to trigger immune responses. For example, NGF is administered as a treatment for peripheral neuropathic disease and in some individuals produces painful side effects such as myalgia and hyperalgesia. Thus an antibody could be used to modulate NGF metabolism as an adjunct to NGF therapy to ameliorate such side effects.

A mammalian subject (preferably a human) can be given a recombinant or synthetic form of a polypeptide or antibody in one of many possible different formulations, preferably encapsulated and other forms for oral or other gastrointestinal delivery of the polypeptide or antibody. In some cases, delivery of the polypeptide or antibody may be in the form of injection or transplantation of cells or tissues containing an expression vector such that a recombinant form of the polypeptide will be secreted by the cells or tissues, as described above for transfected cells. The frequency and dosage of the administration of the polypeptides or antibodies will be determined by factors such as the biological activity of the pharmacological preparation and the goals in the treatment of diseases and conditions involving altered target cell metabolism of NGF. En the case of antibody deliveries, the frequency of dosage will also depend on the ability of the antibody to bind and neutralize the target molecules in the target tissues.

Polypeptides can also be used to raise antibodies, which in turn are used to measure protein expression from a recombinant cell, as a way of assessing transformation of the host cell. See, e.g., Curr. Prot Mol Bio., Chapter 11.15. Moreover, the polypeptides of the present invention can be used to test the following biological activities.

Biological Activities

The polynucleotides, polypeptides and genes of the present invention and regions thereof can be used in assays to test for one or more biological activities. If these polynucleotides, polypeptides and genes or gene regions exhibit activity in a particular assay, it is likely that these molecules may be involved in the diseases associated with the biological activity. Thus, the polynucleotides, polypeptides, genes and gene regions can be used to prevent or treat the associated disease or pathological condition. Examples of the disease or pathological conditions that may be prevented or treated according to the methods described herein include, but are not limited to, diseases and conditions involving altered target cell metabolism of NGF. Nervous System Activity

A polypeptide, polynucleotide or gene of the present invention or region thereof may be useful in treating deficiencies or disorders of the central nervous system or peripheral nervous system by activating or inhibiting the proliferation, differentiation, or mobilization (chemotaxis) of neurob lasts, stem cells, or glial cells. Also, a polypeptide, polynucleotide or gene of the present invention may be useful in treating deficiencies or disorders of the central nervous system or peripheral nervous system by activating or inl ibiting the mechanisms of synaptic transmission, synthesis, metabolism and inactivation of neural transmitters, neuromodulators and trophic factors, and by activating or inhibiting the expression and incoφoration of enzymes, structural proteins, membrane channels, and receptors in neurons and glial cells.

The etiology of these deficiencies or disorders may be genetic, somatic (such as cancer or some autoimmune disorder), acquired (e.g., by chemotherapy or toxins), or infectious. Moreover, a polynucleotide, polypeptide or gene of the present invention or region thereof can be used as a marker or detector of a particular nervous system disease or disorder. The disorder or disease can be any of Alzheimer's Disease, Pick's disease, Binswanger's disease, other senile dementia, Parkinson's disease, parkinsonism, obsessive compulsive disorders, epilepsy, encephaolopathy, ischemia, alcohol addiction, drug addiction, schizophrenia, amyotrophic lateral sclerosis, multiple sclerosis, depression, and bipolar manic-depressive disorder. Alternatively, the polypeptide, polynucleotide or gene of the present invention or region thereof can be used to study circadian variation, aging, or long-term potentiation, the latter affecting the hippocampus. Additionally, particularly with reference to mRNA species occurring in particular structures within the central nervous system, the polypeptide, polynucleotide or gene of the present invention or region thereof can be used to study brain regions that are known to be involved in complex behaviors, such as learning and memory, emotion, drug addiction, glutamate neurotoxicity, feeding behavior, olfaction, viral infection, vision, and movement disorders. Immune Activity

A polypeptide, polynucleotide or gene of the present invention or region thereof may be useful in treating deficiencies or disorders of the immune system, by activating or inhibiting the proliferation, differentiation, or mobilization (chemotaxis) of immune cells. Immune cells develop through a process called hematopoiesis, producing myeloid (platelets, red blood cells, neutrophils, and macrophages) and lymphoid (B and T lymphocytes) cells from pluripotent stem cells. The etiology of these immune deficiencies or disorders may be genetic, somatic (such as cancer or some autoimmune disorders) acquired (e.g., by chemotherapy or toxins), or infectious. Moreover, a polynucleotide, polypeptide or gene of the present invention or region thereof can be used as a marker or detector of a particular immune system disease or disorder.

A polynucleotide, polypeptide or gene of the present invention or region thereof may be useful in treating or detecting deficiencies or disorders of hematopoietic cells. A polypeptide, polynucleotide or gene of the present invention or region thereof could be used to increase differentiation and proliferation of hematopoietic cells, including the pluripotent stem cells, in an effort to treat those disorders associated with a decrease in certain (or many) types hematopoietic cells. Examples of immunologic deficiency syndromes include, but are not limited to blood protein disorders (e.g. agammaglobulinemia, dysgammaglobulinemia), ataxia telangiectasia, common variable immunodeficiency, Di George's Syndrome, HIV infection, HTLV-BLV infection, leukocyte adhesion deficiency syndrome, lymphopenia, phagocyte bactericidal dysfunction, severe combined immunodeficiency (SCIDs), Wiskott- Aldrich Disorder, anemia, thrombocytopenia, or hemoglobinuria.

Moreover, a polypeptide, polynucleotide or gene of the present invention or region thereof could also be used to modulate hemostatic (bleeding cessation) or thrombolytic activity (clot formation). For example, by increasing hemostatic or thrombolytic activity, a polynucleotide, polypeptide or gene of the present invention or region thereof could be used to treat blood coagulation disorders (e.g., afibrinogenemia, factor deficiencies), blood platelet disorders (e.g. thrombocytopenia), or wounds resulting from trauma, surgery, or other causes. Alternatively, a polynucleotide, polypeptide or gene of the present invention or region thereof that can decrease hemostatic or thrombolytic activity could be used to inhibit or dissolve clotting. These molecules could be important in the treatment of heart attacks (infarction), strokes, or scarring. A polynucleotide, polypeptide or gene of the present invention or region thereof may also be useful in the treatment or detection of autoimmune disorders. Many autoimmune disorders result from inappropriate recognition of self as foreign material by immune cells. This inappropriate recognition results in an immune response leading to the destruction of the host tissue. Therefore, the administration of a polypeptide, polynucleotide or gene of the present invention or region a thereof that inhibits an immune response, particularly the proliferation, differentiation, or chemotaxis of T-cells, or in some way results in the induction of tolerance, may be an effective therapy in preventing autoimmune disorders.

Examples of autoimmune disorders that can be treated or detected by the present invention include, but are not limited to: Addison's Disease, hemolytic anemia, antiphospholipid syndrome, rheumatoid arthritis, dermatitis, allergic encephalomyelitis, glomerulonephritis, Goodpasture's Syndrome, Graves' Disease, Multiple Sclerosis, Myasthenia Gravis, Neuritis, Ophthalmia, Bullous Pemphigoid, Pemphigus, Polyendocrinopathies, Purpura, Reiter's Disease, Stiff-Man Syndrome, Autoimmune Thyroiditis, Systemic Lupus Erythematosus, Autoimmune Pulmonary Inflammation, Guillain-Barre Syndrome, insulin dependent diabetes mellitis, and autoimmune inflammatory eye disease.

Similarly, allergic reactions and conditions, such as asthma (particularly allergic asthma) or other respiratory problems, may also be treated by a polypeptide, polynucleotide or gene of the present invention or a region thereof. Moreover, these molecules can be used to treat anaphylaxis, hypersensitivity to an antigenic molecule, or blood group incompatibility.

A polynucleotide, polypeptide or gene of the present invention or a region thereof may also be used to treat and/or prevent organ rejection or graft- versus-host disease (GVHD). Organ rejection occurs by host immune cell destruction of the transplanted tissue through an immune response. Similarly, an immune response is also involved in GVHD, but, in this case, the foreign transplanted immune cells destroy the host tissues. The administration of a polypeptide, polynucleotide or gene of the present invention or a region thereof that inhibits an immune response, particularly the proliferation, differentiation, or chemotaxis of T-cells, may be an effective therapy in preventing organ rej ection or GVHD .

Similarly, a polypeptide, polynucleotide or gene of the present invention or a region thereof may also be used to modulate inflammation. For example, the polypeptide, polynucleotide gene or a region thereof may inhibit the proliferation and differentiation of cells involved in an inflammatory response. These molecules can be used to freat inflammatory conditions, both chronic and acute conditions, including inflammation associated with infection (e.g., septic shock, sepsis, or systemic inflammatory response syndrome (SIRS)), ischemia-reperfusion injury, endotoxin lethality, arthritis, complement-mediated hyperacute rejection, nephritis, cytokine or chemokine induced lung injury, inflammatory bowel disease, Crohn's disease, or resulting from over production of cytokines (e.g., TNF or IL-1.) Hyperprohferative Disorders

A polypeptide, polynucleotide or gene of the invention or a region thereof can be used to treat or detect hyperprohferative disorders, including neoplasms. A polypeptide, polynucleotide or gene of the present invention or a region thereof may inhibit the proliferation of the disorder tlirough direct or indirect interactions. Alternatively, a polypeptide, polynucleotide or gene of the present invention or region thereof may proliferate other cells that can inhibit the hyperprohferative disorder.

For example, by increasing an immune response, particularly increasing antigenic qualities of the hyperprohferative disorder or by inducing the proliferation, differentiation, or mobilization of T-cells, hyperprohferative disorders can be treated. This immune response may be increased by either enhancing an existing immune response, or by initiating a new immune response. Alternatively, decreasing an immune response may also be a method of treating hyperprohferative disorders, such as by administering the polypeptide, polynucleotide, gene or region thereof, as a chemotherapeutic agent. Examples of hyperprohferative disorders that can be treated or detected by a polynucleotide, polypeptide or gene of the present invention or a region thereof include, but are not limited to neoplasms located in the abdomen, bone, breast, digestive system, liver, pancreas, peritoneum, endocrine glands (adrenal, parathyroid, pituitary, testicles, ovary, thymus, thyroid), eye, head and neck, nervous system (central and peripheral), lymphatic system, pelvic region, skin, soft tissue, spleen, thoracic region, and urogenital system.

Similarly, other hyperprohferative disorders can also be treated or detected by a polynucleotide or polypeptide of the present invention. Examples of such hyperprohferative disorders include, but are not limited to hypergammaglobulinemia, lymphoproliferative disorders, paraproteinemias, purpura, sarcoidosis, Sezary Syndrome, Waldenstron's Macroglobulinemia, Gaucher's Disease, histiocytosis, and any other hyperprohferative disease, besides neoplasia, located in an organ system listed above. Infectious Disease A polypeptide, polynucleotide or gene of the present invention or region thereof can be used to treat or detect infectious agents. For example, by increasing the immune response, particularly increasing the proliferation and differentiation of B and/or T cells, infectious diseases may be treated. The immune response may be increased by either enhancing an existing immune response, or by initiating a new immune response. Alternatively, the polypeptide, polynucleotide or gene of the present invention or region thereof may also directly inhibit the infectious agent, without necessarily eliciting an immune response.

Vimses are one example of an infectious agent that can cause disease or symptoms that can be treated or detected by a polynucleotide, polypeptide or gene of the present invention or region thereof. Examples of vimses include, but are not limited to, the following DNA and RNA viral families: Arbovirus, Adenoviridae, Arenaviridae, Arterivirus, Birnaviridae, Bunyaviridae, Caliciviridae, Circoviridae, Coronaviridae, Flaviviridae, Hepadnaviridae (Hepatitis), Heφesviridae (such as Cytomegaloviras, Heφes Simplex, Heφes Zoster), Mononegavirus (e.g., Paramyxoviridae, Morbillivirus, Rhabdoviridae), Orthomyxoviridae (e.g., Influenza), Papovaviridae, Parvoviridae,

Picornaviridae, Poxviridae (such as Smallpox or Vaccinia), Reoviridae (e.g., Rotavirus), Refroviridae (HTLV-I, HTLV-II, Lentivims), and Togaviridae (e.g., Rubivirus). Vimses falling within these families can cause a variety of diseases or symptoms, including, but not limited to, arthritis, bronchiollitis, encephalitis, eye infections (e.g., conjunctivitis, keratitis), chronic fatigue syndrome, hepatitis (A, B, C, E, Chronic Active, Delta), meningitis, opportunistic infections (e.g., AIDS), pneumonia, Burkitt's Lymphoma, chickenpox, hemorrhagic fever, Measles, Mumps, Parainfluenza, Rabies, the common cold, Polio, leukemia, Rubella, sexually transmitted diseases, skin diseases (e.g., Kaposi's, warts), and viremia. A polypeptide, polynucleotide or gene of the present invention or region thereof can be used to treat or detect any of these symptoms or diseases.

Similarly, bacterial or fungal agents that can cause disease or symptoms and that can be treated or detected by a polynucleotide or polypeptide of the present invention include, but are not limited to, the following Gram-Negative and Gram-positive bacterial families and fungi: Actinomycetales (e.g., Corynebacterium, Mycobacterium, Norcardia), Aspergillosis, Bacillaceae (e.g., Anthrax, Clostridium), Bacteroidaceae, Blastomycosis, Bordetella, Borrelia, Brucellosis, Candidiasis, Campylobacter, Coccidioidomycosis, Cryptococcosis, Dermatocycoses, Enterobacteriaceae (Klebsielia, Salmonella, Serratia, Yersinia), Erysipelothrix, Helicobacter, Legionellosis, Leptospirosis, Listeria, Mycoplasmatales, Neisseriaceae (e.g., Acinetobacter, Gonorrhea, Menigococcal), Pasteurellacea infections (e.g., Actinobacillus, Heamophilus, Pasteurella), Pseudomonas, Rickettsiaceae, Chlamydiaceae, Syphilis, and Staphylococcus. These bacterial or fungal families can cause numerous diseases or symptoms, including, but not limited to, bacteremia, endocarditis, eye infections (conjunctivitis, tuberculosis, uveitis), gingivitis, opportunistic infections (e.g., AIDS related infections), paronychia, prosthesis-related infections, Reiter's Disease, respiratory tract infections (such as whooping Cough or empyema), sepsis, Lyme Disease, Cat-Scratch Disease, Dysentery, Paratyphoid Fever, food poisoning, Typhoid, pneumonia, Gonorrhea, meningitis, Chlamydia, Syphilis, Diphtheria, Leprosy, Paratuberculosis, Tuberculosis, Lupus, Botulism, gangrene, tetanus, impetigo, Rheumatic Fever, Scarlet Fever, sexually-transmitted diseases, skin diseases (e.g., celluhtis, dermatocycoses), toxemia, urinary fract infections, and wound infections. A polypeptide, polynucleotide or gene of the present invention or region thereof can be used to treat or detect any of these symptoms or diseases.

Moreover, parasitic agents causing disease or symptoms that can be treated or detected by a polynucleotide, polypeptide or gene of the present invention or region thereof include, but are not limited to, the following families: Amebiasis, Babesiosis, Coccidiosis, Cryptosporidiosis, Dientamoebiasis, Dourine, Ectoparasitic, Giardiasis, Helminthiasis, Leishmaniasis, Theileriasis, Toxoplasmosis, Trypanosomiasis, and Trichomonas. These parasites can cause a variety of diseases or symptoms, including, but not limited to, Scabies, Trombiculiasis, eye infections, intestinal disease (e.g., dysentery, giardiasis), liver disease, lung disease, opportunistic infections (e.g., AIDS related), Malaria, pregnancy complications, and toxoplasmosis. A polypeptide, polynucleotide or gene of the present invention or region thereof can be used to treat or detect any of these symptoms or diseases.

Preferably, treatment using a polypeptide, polynucleotide or gene of the present invention or region thereof could either be by administering an effective amount of a polypeptide to the patient, or by removing cells from the patient, supplying the cells with a polynucleotide or gene or gene region of the present invention, and returning the engineered cells to the patient (ex vivo therapy). Moreover, the polypeptide, polynucleotide or gene of the present invention or region thereof can be used as an antigen in a vaccine to raise an immune response against infectious disease. Regeneration

A polynucleotide, polypeptide or gene of the present invention or region thereof can be used to differentiate, proliferate, and attract cells, leading to the regeneration of tissues (see, Science, 276:59-87 (1997)). The regeneration of tissues could be used to repair, replace, or protect tissue damaged by congenital defects, trauma (wounds, burns, incisions, or ulcers), age, disease (e.g. osteoporosis, osteocarthritis, periodontal disease, liver failure), surgery (including cosmetic plastic surgery), fibrosis, reperfusion injury, or systemic cytokine damage.

Similarly, nerve and brain tissue could also be regenerated by using a polynucleotide, polypeptide or gene of the present invention or a region thereof to proliferate and differentiate nerve cells. Diseases that could be treated using this method include central and peripheral nervous system diseases, neuropathies, or mechanical and traumatic disorders (e.g., spinal cord disorders, head trauma, cerebrovascular disease, and stroke). Specifically, diseases associated with peripheral nerve injuries, peripheral neuropathy (e.g., resulting from chemotherapy or other medical therapies), localized neuropathies, and central nervous system diseases (e.g., Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis, and Shy-Drager syndrome), could all be treated using the polynucleotide, polypeptide or gene of the present invention or a region thereof.

Binding Activity A polypeptide of the present invention may be used to screen for molecules that bind to the polypeptide or for molecules to which the polypeptide binds. The binding of the polypeptide and the molecule may activate (i.e., an agonist), increase, inhibit (i.e., an antagonist), or decrease activity of the polypeptide or the molecule bound. Examples of such molecules include antibodies, oligonucleotides, proteins (e.g., receptors), or small molecules.

Preferably, the molecule is closely related to the natural ligand of the polypeptide, e.g., a fragment of the ligand, or a natural substrate, a ligand, a structural or functional mimetic (see, e.g., Coligan et al, Current Protocols in Immunology 1(2), Chapter 5 (1991)). Similarly, the molecule can be closely related to the natural receptor to which the polypeptide binds or, at least, related to a fragment of the receptor capable of being bound by the polypeptide (e.g., an active site). In either case, the molecule can be rationally designed using known techniques.

Preferably, the screening for these molecules involves producing appropriate cells which express the polypeptide, either as a secreted protein or on the cell membrane. Preferred cells include cells from mammals, yeast, Drosophila, or E. coli. Cells expressing the polypeptide (or cell membrane containing the expressed polypeptide) are then preferably contacted with a test compound potentially containing the molecule to observe binding, stimulation, or inhibition of activity of either the polypeptide or the molecule. The assay may simply test binding of a test compound to the polypeptide, wherein binding is detected by a label, or in an assay involving competition with a labeled competitor. Further, the assay may test whether the test compound results in a signal generated by binding to the polypeptide.

Alternatively, the assay can be carried out using cell-free preparations, polypeptide/molecule affixed to a solid support, chemical libraries, or natural product mixtures. The assay may also simply comprise the steps of mixing a test compound with a solution containing a polypeptide, measuring polypeptide/molecule activity or binding, and comparing the polypeptide/molecule activity or binding to a standard.

Preferably, an ELISA assay can measure polypeptide level or activity in a sample (e.g., biological sample) using a monoclonal or polyclonal antibody. The antibody can measure polypeptide level or activity by either binding, directly or indirectly, to the polypeptide or by competing with the polypeptide for a substrate.

All of these above assays can be used as diagnostic or prognostic markers. The molecules discovered using these assays can be used to treat disease or to bring about a particular result in a patient (e.g., blood vessel growth) by activating or inhibiting the polypeptide/molecule. Moreover, the assays can discover agents that may inhibit or enhance the production of the polypeptide from suitably manipulated cells or tissues.

Therefore, the invention includes a method of identifying compounds which bind to a polypeptide of the invention comprising the steps of: (a) incubating a candidate binding compound with a polypeptide of the invention; and (b) determining if binding has occurred. Moreover, the invention includes a method of identifying agonists/antagonists comprising the steps of: (a) incubating a candidate compound with a polypeptide of the invention, (b) assaying a biological activity, and (c) determining if a biological activity of the polypeptide has been altered.

Other Activities A polypeptide, polynucleotide or gene of the present invention or a region thereof may also increase or decrease the differentiation or proliferation of embryonic stem cells from a lineage other than the above-described hemopoietic lineage.

A polypeptide, polynucleotide or gene of the present invention or a region thereof may also be used to modulate mammalian characteristics, such as body height, weight, hair color, eye color, skin, percentage of adipose tissue, pigmentation, size, and shape (e.g., cosmetic surgery). Similarly, a polypeptide, polynucleotide, or gene of the present invention or region thereof may be used to modulate mammalian metabolism affecting catabolism, anabolism, processing, utilization, and storage of energy.

A polypeptide, polynucleotide or gene of the present invention or a region thereof may be used to change a mammal's mental state or physical state by influencing biorhythms, circadian rhythms, depression (including depressive disorders), tendency for violence, tolerance for pain, the response to opiates and opioids, tolerance to opiates and opioids, withdrawal from opiates and opioids, reproductive capabilities (preferably by activin or inhibin-like activity), hormonal or endocrine levels, appetite, libido, memory, stress, or other cognitive qualities. A polypeptide, polynucleotide or gene of the present invention or a region thereof may also be used as a food additive or preservative, such as to increase or decrease storage capabilities, fat content, lipid, protein, carbohydrate, vitamins, minerals, cofactors, or other nutritional components.

The following examples are intended to illustrate the invention, and are not to be construed as limiting the scope of the invention.

EXAMPLE 1

Identification and Characterization of Polynucleotides

Regulated by Neuromodulators

In order to examine how gene expression is regulated by various neuromodulators, polyA-mRNA was isolated from PC 12 cells before and at different times after triggered induction by NGF or IFN-γ. PC 12 cells were pulse treated with either NGF (100 ng/ml) for two minutes, IFN-γ (1000 units/ml) for three minutes, or with control medium (Dulbecco's modified Eagles (DME) medium; CW) containing fresh serum (5% fetal calf serum, 10% horse semm) for two minutes. The cells were then washed two times with DME and incubated at 37 degrees Celsius in an atmosphere of 10% CO₂/ 90% air in DME containing semm for varying lengths of time. After incubations for one hour (for NGF, IFN-γ, and CW), 5 hours (for NGF and IFN-γ) and 24 hours (for NGF), the cells were washed with phosphate buffered saline (PBS) and harvested. Cells were lysed in lysis solution containing 0.14 M NaCl, 1.5 mM MgCl₂, 10 mM Tris-HCl (pH 8.6), 1 mM DTT, 1000 U/ml RNAsin, and 0.5% NP-40. The nuclei were removed by centrifugation and the cytoplasmic RNA was isolated by the LiCl method. Poly-A containing RNA was isolated by oligo dT chromatography.

The TOGA^® Process Isolated RNA from PC 12 cells was analyzed using a method of simultaneous sequence-specific identification of mRNAs known as TOGA^® (TOtal Gene expression Analysis) described in Sutcliffe, et al. Proc. Natl Acad. Sci. USA, 97(5): 1976-1981 (2000); International published application WO 00/26406; U.S. Patent No. 5,459,037; U.S. Patent No. 5,807,680; U.S. Patent No. 6,030,784; U.S. Patent No. 6,096,503, U.S. Patent 6,110,680, and U.S. Patent 6,309,834, hereby incoφorated herein by reference. Preferably, prior to the application of the TOGA^® technique, the isolated RNA was enriched to form a starting polyA-containing mRNA population by methods known in the art. In a preferred embodiment, the TOGA^® method further comprised an additional PCR step performed using four 5' PCR primers in four separate reactions and cDNA templates prepared from a population of antisense cRNAs. A final PCR step that used 256 5 ' PCR primers in separate reactions produced PCR products that were cDNA fragments that corresponded to the 3 '-region of the starting mRNA population. The produced PCR products were then identified by: a) the initial 5' sequence comprising the sequence remainder of the recognition site of the restriction endonuclease used to cut and isolate the 3' region plus the sequence of the preferably four parsing bases immediately 3' to the remainder of the recognition site, preferably the sequence of the entire fragment, and b) the length of the fragment. These two parameters, sequence and fragment length, were used to compare the obtained PCR products to a database of known polynucleotide sequences. Since the length of the obtained PCR products includes known vector sequences at the 5' and 3' ends of the insert, the sequence of the insert provided in the sequence listing is shorter than the fragment length that forms part of the digital address. The method yields Digital Sequence Tags (DSTs), that is, polynucleotides that are expressed sequence tags of the 3' end of mRNAs. DSTs that showed changes in relative levels following exposure to NGF or EFN-γ were selected for further study. The intensities of the laser-induced fluorescence of the labeled PCR products were compared across samples isolated from PC 12 cells treated with NGF for 1, 5, or 24 hours or with IFN-γ for 1 or 5 hours.

In general, double-stranded cDNA is generated from poly(A)-enriched cytoplasmic RNA extracted from the tissue samples of interest using an equimolar mixture or set of all 48 5'-biotinylated anchor primers to initiate reverse transcription. One such suitable set is G-A-A-T-T-C-A-A-C-T-G-G-A-A-G-C-G-G-C-C-G-C-A-G-G-A-A-T-T-T-T-T-T-T- T-T-T-T-T-T-T-T-T-T-T-V-N-N (SEQ JD NO: 30), where V is A, C or G and N is A, C, G or T. One member of this mixture of 48 anchor primers initiates synthesis at a fixed position at the 3' end of all copies of each mRNA species in the sample, thereby defining a 3 ' endpoint for each species, resulting in biotinylated double-stranded cDNA.

Each biotinylated double-stranded cDNA sample was cleaved with the restriction endonuclease Mspl, which recognizes the sequence CCGG. The resulting fragments of cDNA corresponding to the 3' region of the starting mRNA were then isolated by capture of the biotinylated cDNA fragments on a streptavidin-coated substrate. Suitable streptavidin-coated substrates include microtifre plates, PCR tubes, polystyrene beads, paramagnetic polymer beads, and paramagnetic porous glass particles. A preferred streptavidin-coated substrate is a suspension of paramagnetic polymer beads (Dynal, Inc., Great Neck, NY).

After washing the streptavidin-coated substrate and captured biotinylated cDNA fragments, the cDNA fragment product was released by digestion with Notl, which cleaves at an 8 -nucleotide sequence within the anchor primers but rarely within the niRNA-derived portion of the cDNAs. The 3' Mspl-Notl fragments, which are of uniform length for each mRNA species, were directionally ligated into Clal- Notl-cleaved plasmid pBC SK+ (Stratagene, La Jolla, CA) in an antisense orientation with respect to the vector's T3 promoter, and the product used to transform Escherichia coli SURE cells (Stratagene). The ligation regenerates the Notl site, but not the Mspl site, leaving CGG as the first 3 bases of the 5' end of all PCR products obtained. Each library contained in excess of 5 x 10⁵ recombinants to ensure a high likelihood that the 3' ends of all mRNAs with concentrations of 0.001% or greater were multiply represented. Plasmid preps (Qiagen) were made from the cDNA library of each sample under study. An aliquot of each library was digested with Mspl, which effects linearization by cleavage at several sites within the parent vector while leaving the 3' cDNA inserts and their flanking sequences, including the T3 promoter, intact. The product was incubated with T3 RNA polymerase (MEGAscript kit, Ambion) to generate antisense cRNA transcripts of the cloned inserts containing known vector sequences abutting the Mspl and Notl sites from the original cDNAs.

At this stage, each of the cRNA preparations was processed in a three-step fashion. In step one, 250 ng of cRNA was converted to first-strand cDNA using the 5' RT primer (A-G-G-T-C-G-A-C-G-G-T-A-T-C-G-G, (SEQ ID NO: 31). In step two, 400 pg of cDNA product was used as PCR template in four separate reactions with each of the four 5' PCR primers of the form G-G-T-C-G-A-C-G-G-T-A-T-C-G-G-N (SEQ ID NO: 32), each paired with a "universal" 3' PCR primer G-A-G-C-T-C-C-A-C-C-G-C-G-G-T (SEQ JD NO: 33) to yield four sets of PCR reaction products ("NI reaction products"). In step three, the product of each subpool was further divided into 64 subsubpools (2ng in 20μl) for the second PCR reaction. This PCR reaction comprised adding 100 ng of the fluoresceinated "universal" 3' PCR primer (SEQ JD NO: 33) conjugated to 6- FAM and 100 ng of the appropriate 5' PCR primer of the form C-G-A-C-G-G-T-A-T-C- G-G-N-N-N-N (SEQ ID NO: 34), and using a program that included an annealing step at a temperature X slightly above the Tm of each 5' PCR primer to minimize artifactual mispriming and promote high fidelity copying. Each polymerase chain reaction step was performed in the presence of TaqStart antibody (Clonetech).

The products ("N4 reaction products") from the final polymerase chain reaction step for each of the tissue samples were resolved on a series of denaturing DNA sequencing gels using the automated ABI Prizm 377 sequencer. Data were collected using the GeneScan software package (ABI) and normalized for amplitude and migration. Complete execution of this series of reactions generated 64 product subpools for each of the four pools established by the 5' PCR primers of the first PCR reaction, for a total of 256 product subpools for the entire 5' PCR primer set of the second PCR reaction.

The mRNA samples extracted from timepoint as described above were analyzed. Table 1 is a summary of the expression levels of 102 mRNAs determined from cDNA. These cDNA molecules are identified by their digital address, that is, a partial 5' terminus nucleotide sequence coupled with the length of the molecule, as well as the relative amount of the molecule produced at different time intervals after treatment. The 5' terminus partial nucleotide sequence is determined by the recognition site for Mspl (CC GG) and the nucleotide sequence of the parsing bases of the 5' PCR primer used in the final PCR step. The digital address length of the fragment was determined by inteφolation on a standard curve and, as such, may vary ± 1-2 b.p. from the actual length as determined by sequencing.

For example, the entry in Table 1 that describes a DNA molecule identified by the digital address Mspl GCAC 349, is further characterized as having a 5' terminus partial nucleotide sequence of CGGGCAC and a digital address length of 349 b.p. The DNA molecule identified as Mspl GCAC 349 (HAL_18; SEQ JD NO: 12) is further described as being expressed at increasing levels after treatment with NGF. In contrast, treatment with NGF results in a marked decrease of the expression of Mspl GACT 280 (HAL_17; SEQ ED NO: 11). Similarly, the other DNA molecules identified in Table 1 by their Mspl digital addresses are further characterized by 1) the level of gene expression in PC 12 cells following wash with control solution, 2) the level of gene expression in PC 12 cells following treatment with NGF for 1 hour, 3) the level of gene expression in PC 12 cells following treatment with IFN-γ for 1 hour, 4) the level of gene expression in PC 12 cells following treatment with NGF for 5 hours, 5) the level of gene expression in PC 12 cells following treatment with EFN-γ for 5 hours, and 6) the level of gene expression in PC 12 cells following treatment with NGF for 24 hours. Several of the isolated clones were further characterized in Table 2 and their nucleotide sequences are provided in the Sequence Listing below. The isolated clones chosen showed between about two-fold and about 27-fold changes in expression, and were induced by both NGF and IFNγ, IFNγ alone, or NGF alone.

The ligation of the sequence into a vector does not regenerate the Mspl site; the experimentally determined sequence reported herein has C-G-G as the first bases of the 5' end. The data shown in Figure 1 were generated with a 5'-PCR primer (C-G-A-C-G-G-

T-A-T-C-G-G-G-C-A-C, SEQ JD NO: 35) paired with the "universal" 3' primer (SEQ ID NO: 33) labeled with 6-carboxyfluorescein (6FAM, ABI) at the 5' terminus. PCR reaction products were resolved by gel electrophoresis on 4.5% acrylamide gels and fluorescence data acquired on ABI377 automated sequencers. Data were analyzed using GeneScan software (Perkin-Elmer). Figure 1 is a graphical representation of the results of TOGA^® runs using a 5'

PCR primer with parsing bases GCAC (SEQ ED NO:35) and the universal 3' PCR primer (SEQ ID NO: 33) showing PCR products produced from mRNA extracted from PC 12 cells treated as follows: A: control wash (CW), B: 1 hour with NGF (IhrNGF), C: 1 hour with IFN-γ (lhrlFN), D: 5 hours with NGF (5hrNGF), E: 5 hours with IFN-γ (5hrIFN), and F: 24 hours with NGF (24hrNGF), where the vertical index line indicates a PCR product of about 349 b.p. that is present in the lhr NGF and lhr IFN-γ samples and enriched in 5hr NGF, 5hr EFN-γ, and 24hr NGF samples. The horizontal axis represents the number of base pairs of the molecules in these samples and the vertical axis represents the fluorescence measurement in the TOGA^® analysis (which corresponds to the relative expression of the molecule of that address). The results of the TOGA^® mns have been normalized using the methods described in pending U.S. Patent Application Serial No. 09/318,699/U.S., and PCT Application Serial No. PCT/USOO/14159, both entitled Methods and System for Amplitude Normalization and Selection of Data Peaks (Dennis Grace, Jayson Durham); and U.S. Patent 6,334,099, PCT Application Serial No. PCT/USOO/14123 and pending U.S. Patent Application Serial Nos. 09/940,987/U.S., 09/940,581/U.S., 09/940,746/U.S., all entitled Methods for Normalization of Experimental Data (Dennis Grace, Jayson Durham) all of which are incoφorated herein by reference. The vertical line drawn tlirough the six panels represents the DST molecule identified as HAL_18 (SEQ JD NO: 12). Some products, which were differentially represented, appeared to migrate in positions that suggest that the products were novel based on comparison to data extracted from GenBank. The sequences of such products were determined by the following method: cloning.

Cloning of TOGA^® Generated PCR Products In suitable cases, the PCR product was isolated, cloned into a TOPO vector (Invitrogen) and sequenced on both strands. The database matches for each cloned DST sequence are listed in Table 2. DST HAL_18 (SEQ JD NO: 12), the DNA molecule identified by Mspl GCAC 349, was one such cloned product. In order to verify that the cloned product corresponds to the TOGA^® peak of interest, the extended TOGA^® assay was performed for each DST.

Verification Using the Extended TOGA^® Method

In order to verify that the TOGA^® peak of interest corresponds to the identified DST, an extended TOGA^® assay was performed for each DST as described below. PCR primers ("Extended TOGA^® primers") were designed from the sequence determined from cloning.

PCR was performed using the Extended TOGA^® primers and the NI PCR reaction products as a substrate. Oligonucleotides were synthesized with the sequence G- A-T-C-G-A-A-T-C extended at the 3 ' end with a partial Mspl site (C-G-G), and an additional 18 adjacent nucleotides from the determined sequence of the DST. For example, for the PCR product with the TOGA^® address GCAC 349 (DST HAL_18; SEQ ID NO: 12) , the 5' PCR primer was G-A-T-C-G-A-A-T-C-C-G-G-G-C-A-C-T-G-C-C-T- C-C-T-T-G-C-A-T-T (SEQ JD NO:36). This 5' PCR primer was paired with the fluorescence labeled universal 3 ' PCR primer (SEQ JD NO:33) in a PCR reaction using the PCR NI reaction product as substrate.

Figure 2 presents a graphical example of the results obtained when a DST is verified by the Extended TOGA^® method using a primer generated from a cloned product. The PCR product corresponding to SEQ JD NO: 12 (HAL_18) was cloned and a 5 ' PCR primer was built from the cloned DST (SEQ ID NO:36). The product obtained from PCR with this primer (SEQ ID NO:36) and the universal 3' PCR primer (SEQ ED NO:33) (as shown in the top panel, A) was compared to the length of the original PCR product that was produced in the TOGA^® reaction with mRNA extracted from PC 12 cells treated for 5 hr with NGF using a 5' PCR primer with parsing bases GCAC (SEQ JD NO:35) and the universal 3 ' PCR primer (SEQ DD NO:33) (as shown in the middle panel, B). For all panels, the number of base pairs is shown on the horizontal axis, and fluorescence intensity (which corresponds to relative expression) is found on the vertical axis. In the bottom panel (panel C), the traces from the top and middle panels are overlaid, demonstrating that the peak found using an extended primer from the cloned DST is the same number of base pairs as the original PCR product obtained tlirough TOGA^® as HAL_18 (SEQ ID NO: 12). The bottom panel thus illustrates that HAL_18 (SEQ ID NO: 12) was the DST amplified in Extended TOGA^®. Interestingly, more than one peak was observed, suggesting the presence of two mRNAs, one of which could be an alternatively spliced product. Northern analysis described below confirmed the presence of more than one mRNA as well, consistent with an alternatively spliced product.

The length of the PCR product generated with the Extended TOGA^® primer was compared to the length of the original PCR product that was produced in the TOGA^® reaction.

Assignment of Identities to DSTs

Digital Sequence Tags (DSTs) can be easily associated with the gene encoding the full-length mRNA transcript including both 5' and 3' untranslated regions by methods known to those skilled in the art. For example, searches of the public databases of expressed sequences (e.g., GenBank) can identify cDNA sequences that overlap with the DST. Statistically significant sequence matches with greater than 95% nucleotide sequence matches across the overlap region can be used to generate a contiguous sequence ("contig") and serial searches with the accumulated contig sequence can be used to assemble extended sequence associated with the DST. In cases where the assembled contig includes an open reading frame (a nucleotide sequence encoding a continuous sequence of amino acids), the polypeptide encoded by the expressed mRNA can be predicted.

In other cases, extended sequence can also be generated by making a probe containing the DST sequence. The probe would then be used to select cDNA clones by hybridization methods known in the art. These cDNA clones may be selected from libraries of cDNA clones developed from the original RNA sample, from other RNA samples, from fractionated mRNA samples, or from other widely available cDNA libraries, including those available from commercial sources. Sequences from the selected cDNA clones can be assembled into contigs in the same manner described for database sequences. The cDNA molecules can also be isolated directly from the mRNA by the rapid analysis of cDNA ends (RACE) and long range PCR. This method can be used to isolate the entire full-length cDNA or the intact 5' and 3' ends of the cDNA.

Methods for alignment of biological sequences for pairwise comparison are well known in the art. Local alignments between a query sequence and a subject sequence can be derived by using the algorithm of Smith (J Mol Biol, 1981), by the homology alignment algorithm of Needleman (JMol Biol, 1970), or by the similarity search algorithm of Pearson (Proc Natl Acad Sci, 1988). A preferred method for determining the best overall match between a query sequence (a sequence of the present invention) and a subject sequence, also referred to as a sequence database, can be determined using the BLAST computer program based on the algorithm of Altschul and colleagues (Altschul, JMol Biol; 1990; Altschul, Nucleic Acids Res, 1997). The term "sequence" includes nucleotide and amino acid sequences. In a sequence alignment, the query sequence can be either protein or nucleic acid or any combination thereof. BLAST is a statistically driven search method that finds regions of similarity between a query and database sequences. These are called segment pairs, and consist of gapless alignments of any part of two sequences. Within these aligned regions, the sum of the scoring matrix values of their constituent symbol pairs is higher than a level expected to occur by chance alone. The scores obtained in a BLAST search can be inteφreted by the experienced investigator to determine real relationships versus random similarities. The BLAST program supports four different search mechanisms: • Nucleotide Query Searching a Nucleotide Database- Each database sequence is compared to the query in a separate nucleotide-nucleotide pairwise comparison. • Protein Query Searching a Protein Database- Each database sequence is compared to the query in a separate protein-protein pairwise comparison. • Nucleotide Query Searching a Protein Database- The query is translated, and each of the six products is compared to each database sequence in a separate protein-protein pairwise comparison.

• Protein Query Searching a Nucleotide Database- Each nucleotide database sequence is translated, and each of the six products is compared to the query in a separate protein-protein pairwise comparison.

By using the BLAST program to search for matches between a sequence of the present invention and sequences in GenBank and EST databases, identities were assigned whenever possible. A portion of these results is listed in Table 2.

EXAMPLE 2

Characterization of a Novel NGF Induced Polynucleotide and Protein Identification and Regulation of Pincher, a Gene Induced by Pulsatile NGF-treatment Unlike most genes whose induction requires continual NGF treatment, the PNl voltage-dependent sodium channel gene is maximally induced at five hours after as little as one minute of exposure of PC12 cells to NGF (Toledo-Aral et al, 1995). PNl induction requires the surface TrkA receptor and is activated through a "triggered", Ras- independent pathway mediated by PLC-γ signaling (Toledo- Aral et al, 1995; Choi et al, 2001). To determine if other genes were induced through this unusual pathway, we examined gene inductions after pulsatile NGF-treatment using the TOGA^® technology. Following TOGA^® analysis of mRNA samples from control and NGF-treated cells, 108 RNAs (approximately 1% of total) appeared differentially up regulated by 2-fold or greater in response to NGF. The TOGA PCR fragments representing the induced transcripts were cloned and sequenced to obtain gene identities. The regulation of about 30 corresponding mRNAs was assessed further by Northern blot analysis. One cDNA, HAL_18 (SEQ ED NO: 12), represented an mRNA that was induced three- to five-fold by NGF-treatment of PC12 cells.

As described in Example 1, TOGA^® analysis using a 5' PCR primer with parsing bases GCAC (SEQ ID NO:35) identified the DST molecule known as HAL_18 (SEQ ID NO: 12) that significantly increased in expression after 5 hours of NGF treatment (Figure 1). Verification of this peak by extended TOGA^® (as described in Example 1) is shown in Figure 2. The extended TOGA^® verification suggested that two mRNAs were produced from this PCR primer, suggesting an alternatively spliced form. Northern analysis, as described below, confirmed the presence of two mRNAs. As described in Table 2, HAL_18 (SEQ ID NO: 12) was identified as an EST (Accession number AI103599). To further confirm these changes, Northern Blot analysis was performed.

Figure 3 represents the results of Northern Blot analysis of clone HAL_18 (GCAC 349), where an agarose gel containing polyA enriched mRNA from PC12 cells treated with NGF as well as size standards was blotted after electrophoresis and probed with either radiolabeled HAL_18 (nucleotides 1-454) (SEQ ID NO: 29) (panel A) or cyclophilin (panel B). PC12 cells were treated as follows: 1 hour NGF pulse followed by 2-6 hour chase (samples l'21ιr, l'3hr, l'4hr, l'5hr, and l'6hr), continuous NGF treatment for 2-6 hours (samples 2hr, 3hr, 4hr, 5hr, and 6hr), and no NGF treatment (control) (Panel A). The indicated two alternatively spliced forms of HAL_18 transcripts (4kb and 3kb) confirmed results using an antisense RNA probe from HAL_18 template. Both the bands were inducible by NGF and IFN-γ, verifying the results obtained using TOGA^®. Panels C and D show the time-course of HAL_18 induction by NGF in PC 12 cells. Total cellular RNA (10 μg) was prepared from PC12 cells incubated with NGF (100 μg/ml) for the indicated time (hours). The RNA was hybridized with a DNA probe generated from HAL_18 cDNA fragment. Re-hybridization with a cyclophilin pIB 15probe (lkb) (Panel D) provided an internal control for the amount of RNA in each lane. Expression reaches a peak of 4-fold induction at 4 hours after NGF treatment and then returns to the basal level after 24 hours of NGF treatment. To determine if the HAL_18 mRNAs were induced like the PNl gene in a Ras- independent manner, NGF induction was examined in the GSrasDN6 cell line (Thomas et al, 1992; D'Arcangelo and Halegoua, 1993), which inducibly expresses a dominant- inhibitory form of Ras (ras^N17) (in response to dexamethasone). Figure 4 Panel A (left) shows a Northern blot hybridized with an antisense RNA probe generated from HAL_18 template and cyclophilin probe (internal control) using total RNA (10 μg) isolated from GSrasDN6 cells treated with dexamethasone (DEX) (0.5 μM) for sixteen hours to induce dominant inhibitory ras^m? or DMSO (DM) carrier and NGF (100 μg/mg, 4 hr) or FGF as indicated. Suφrisingly, NGF-mediated induction of HAL_18 mRNAs was inhibited after expression of ras^N17 (Fig. 4 Panel A), suggesting the existence of a Ras-dependent pathway for induction of this gene. Further, we found that pulsatile freatment of 17N-2 cells with NGF results in a significant (two-fold) induction of HAL_18 mRNAs (Fig. 4 Panel A, right). 17N-2 cells constitutively expressing ras^my were then treated or not with NGF for 1 minute or 5 hours as indicated and RNA analyzed by Northern blot (Figure 4 Panel A, right). The two alternatively spliced forms of HAL_18 transcripts (4kb and 3kb) are indicated. Two-fold induction by NGF of HAL_18 gene expression is detected with both 1 -minute treatment and continuous treatment (Fig. 4 Panel A, right). Thus, Figure 4 Panel A illustrates that this induction can occur in a rαs-independent manner.

The ability of Ras to mediate induction of the mRNAs was examined further using GSrasl cells in which the activated ras oncogene, ras¹⁶¹ could be inducibly expressed (Thomas et al, 1992; D'Arcangelo and Halegoua, 1993). hi Figure 4 Panel B (left) GSrasl cells were treated with 0.5μM dexamethasone for the indicated times, to induce ras¹⁶¹ oncogene expression. Expression of rasL61 in these cells stimulated the expression of the two mRNAs by five-fold in a prolonged time course over 72 hours (Fig. 4 Panel B, left). A similar level of mRNA induction was seen, as determined by real-time quantitative PCR, after inducible expression of an activated form of B-Raf in GSΔB-raf PC12 cells (Fig. 4 Panel B, right), the Ras effector that mediates activation of MAP kinase. GSrasl cells or GSΔB-raf cells were treated with 0.5μM dexamethasone for the indicated times to induce ras¹⁶¹ or truncated, activated b-raf, respectively. Total cellular RNA was isolated and subjected to real-time RT-PCR using HAL_18- or GAPDH- specific primers. Data was processed and is shown as a histogram for the induction of HAL_18 after normalization to GAPDH. h summary, the expression of activated forms of Ras and b-Raf is sufficient to induce sustained HAL_18 gene expression.

The above results suggested that HAL_ 18 mRNAs is induced tlirough both Ras- independent and -dependent pathways. To further test this idea we explored the HAL_18 gene induction by NGF by wild type and mutant Trks. Total RNA (10 μg) was isolated from the PC 12 mutant nnr5 (lacking TrkA), and the following nnr5 stable fransfectants expressing wild type or mutant TrkAs, T14 (wild type TrkA), Y490 (Y490F mutant), Y785 (Y785F mutant), Y490/785 (double mutant) after a four-hour treatment with NGF (100 μg/ml). RNA was blotted and hybridized with an antisense RNA probe generated from a HAL_18 template. The two alternatively spliced forms of HAL_18 transcripts (4kb and 3kb) are indicated. Re-hybridization with a cyclophilin pIB15probe (lkb) provided an internal control for the amount of RNA in each lane. As expected, HAL_18 mRNAs were induced by NGF-treatment of the PC 12 nnr5 lines expressing TrkA but not in the lines lacking TrkA (T14 and nnr, respectively, Fig. 5). Lower levels of induction could be seen in cells expressing each of the TrkA single mutants (Y490F or Y785F, Fig. 5). NGF-treated cells expressing the TrkA double mutant, Y490F/Y785F did not show HAL_18 mRNA induction, indicating that both TrkA autophosphorylation sites contribute to the induction.

In summary, the studies described in Figures 4 and 5 demonstrated that HAL_ 18 induction is mediated by Ras-dependent and Ras-independent pathways via multiple TrkA autophosphorylation sites. As HAL_18 was discovered in NGF treated rat PC 12 cells, it was of interest to determine whether HAL_18 was expressed in normal rat tissues, and compare the level of expression in different tissue types. Figure 6 shows the results of an experiment demonstrating the tissue specific expression of the HAL_18 gene, (left) Rat tissue polyA+mRNA (Clontech) and (right) total cellular RNA (10 μg) isolated from rat dorsal root ganglia (DRG), lung and heart was hybridized with an antisense RNA probe generated from HAL_18 template. The two alternatively spliced forms of HAL_18 transcripts (4kb and 3kb) are indicated. HAL_18 RNA was found to be primarily expressed in the heart, with moderate expression in the lung and detectable expression in the kidney and brain. Figure 7 shows the results of an experiment demonstrating that the induction of .

HAL_18 gene expression does not require de novo synthesis of protein. PC 12 cells treated with NGF (100 μg/ml) were cultured in the absence or presence of the franslational inhibitor cycloheximide (CHX, 10 μg/ml). CHX was applied at the indicated times (minutes) after NGF addition. Total RNA was isolated from the cells at 4 hours after the addition of NGF to the medium and analyzed by Northern blotting. The two alternatively spliced forms of HAL_18 transcripts (4kb and 3kb) are indicated. The blot was re-hybridized with an antisense RNA probe for PN1(1 lkb) as a positive control for CHX. The cyclophilin was re-probed as an internal control for RNA loading.

Since HAL_18 was identified as an EST (Accession number All 03599), full- length cloning and sequencing was utilized in order to determine its identity and function. Using a HAL_18 clone as a probe, a PC 12 cDNA library was screened in order to obtain a full-length cDNA clone for the gene containing the HAL_18 sequence. The same PC 12 Poly(A)+ mRNA isolated from PC 12 cells 5 hours after NGF freatment as used above for TOGA^® analysis, was also used to construct both random primed and oligo (dT)-primed λ ZAPII cDNA libraries (Stratagene). A pooled library consisted of 1.0X10⁶ independent clones prior to amplification. Screening of 10⁶ recombinants with a ³²P-labeled HAL_18 cDNA probe (oligo labeling kit, Pharmacia) resulted in the isolation of 15 positive clones. All 15 clones were sequenced and the overlapping sequences revealed a single full-length coding region.

BLAST searching showed that the cDNA clone encodes a new member of a protein family originally defined by PAST-1 in the Drosophila gene bank. The full- length sequence was found to have a high degree of homology with genes identified in C. elegans, Drosophilia, and Plasmodium, and to human, mouse, and rat EST clones. Thus, the full-length cDNA corresponding to the HAL_18 clone encodes the rat homolog of PAST-1. Studies described below elucidating the function of the protein demonstrate that the protein product of HAL_18 is a pinocytic chaperone for TrkA, and thus was named Pincher (SEQ ID NO:29).

The predicted open reading frame is shown in Figure 8. The only difference noted between comparisons of multiple clones was the length of 3' untranslated sequence, suggesting that the two mRNAs detected on Northern blots and in the extended TOGA^® verification represent alternate splice forms. Analysis of the predicted Pincher amino acid sequence revealed several interesting domains (Fig. 8). The first domain is an EH domain, a protein-protein interaction domain found in other proteins involved in membrane trafficking. A second protein-protein interaction domain is a coiled-coiled domain that is often found in proteins that form homomers. A third domain is distantly related to AAA type ATPases that contains an intact P-loop ATP/GTP-binding motif. Because of these structural features, and its induction by NGF, we decided to examine whether Pincher was involved in TrkA trafficking.

An EH domain is found in many membrane trafficking proteins (Santolini et al, 1999). Pincher is a member of a subfamily of EH-domain-containing proteins first defined by the PAST-1 gene contained in the Drosophila gene bank. Recently, both mammalian and nematode homologues of PAST-1 have been identified. The human PAST genes comprise a family with four members (EHD-1 to EHD-4, Mintz et al, 1999; Pohl et al, 2000), of which EHD-1 is the human homologue to the single PAST-1 Drosophila gene and the recently identified nematode gene RME-1 (Grant et al, 2001). Pincher sequence is nearly identical to the partial sequence of EHD-4 gene (Pohl et al, 2000) and thus appears to be its homologue. In addition to the EH domain, these genes are also distantly related to AAA ATPases, including a conserved ATP/GTP-binding P- loop, which is essential for RME-1 function (Grant et al, 2001).

Although the PAST-1 family members have no known function, recent reports have implicated PAST-1 in events underlying receptor-mediated endocytosis. The mouse homologue for PAST-1, mRME-1 has been suggested to mediate recycling of receptor- containing endocytic vesicles and was found to be localized to an endosome recycling compartment in Chinese hamster ovary cells (Lin et al, 2001). EHD-1, the human homologue of mRME-1, has recently been suggested to mediate receptor-induced endocytosis of IGF-1 (Rotem-Yehudar et al, 2001). Due to a co-localization of transferring with EHD-1 in a small number of vesicles (Mintz, et al, 1999), and the retention of clathrin-containing complexes by a EHD-1 affinity column (Rotem-Yehudar et al, 2001), the authors suggested that EHD-1 participated in a clathrin-mediated endocytic process that would lead to endosome recycling and degradation. To further characterize the function of this novel protein, recombinant cDNA constracts were prepared, recombinant protein was expressed and isolated, and antibodies were generated. The methods for protein expression are as follows. A mammalian expression vector encoding HA-tagged Pincher was generated by sub-cloning full length Pincher cDNA from a pBlueScript vector into the pCGN-HA vector between Xbal and Kpnl restriction sites. A bacterial expression vector encoding GST-Pincher was generated by sub-cloning full length Pincher cDNA into pGEX-3X vector at the EcoRl and BamHl sites. GST-Pincher was expressed in XLl-Blue (Stratagene) cells and purified using glutathione-agarose beads (Sigma-Aldrich), and dialyzed. Rabbit anti- Pincher polyclonal antibody was generated by Research Genetics, Inc. after immunizing rabbits with GST-Pincher coupled to KLH. Pincher protein levels were measured by immunoprecipitation followed by Western blot analysis (Figure 9). Protein extracts were isolated and quantified by Coomassie Plus protein assay reagent (Pierce). About 500μg of cell lysate was diluted in lysis buffer and incubated at 4°C for 4 hours with 5μg of primary anti-Pincher antibody. Immune complexes were isolated using 50μl of protein G-agarose suspension (GIBCO-BRL). The immunoprecipitates were washed, eluted from protein G-agarose beads by treatment with SDS-PAGE sampling buffer, denatured in a boiling bath for 5 min, and subjected to SDS- 10% PAGE and analyzed by Western blotting. The anti-Pincher antibody was used at a 1 :5000 dilution and an anti-HA antibody was used at 1 :200 dilution. Protein levels were detected using the ECL kit (Amersham). Figure 9 shows the induction of Pincher protein levels over time. The left panel represents PC 12 cells treated with NGF for the indicated times and blots probed with the anti-Pincher antibody. The right panel represents PC 12 cells transfected with a CMV-driven expression plasmid encoding HA- tagged-Pincher. As shown in Figure 9, Pincher was induced by NGF freatment of PC12 cells over a time course that corresponded in magnitude and followed the time of induction of the HAL_18 mRNAs detected on Northern blots. No Pincher protein could be detected in blots prepared from immunoprecipitates using anti-Pincher antibody that was pre-blocked with GST-Pincher (not shown). HA-Pincher expression was also confirmed in Western blots of cell extracts from fransfected cultures (panel on the right). While the GST-tagged Pincher was ideal for protein production, purification, and antibody production, the HA-tagged Pincher was ideal for localizing Pincher in the cell and its association with TrkA.

Pincher Enhances NGF-induced TrkA Endocytosis

In order to examine whether Pincher was involved in TrkA trafficking TrkA-PC12 cells that overexpress TrkA were transfected with a mammalian expression vector encoding a HA-tagged Pincher. Pincher localization was examined by confocal immunofluorescence microscopy using an anti-HA antibody. Figure 10 demonstrates Pincher overexpression enhances NGF-induced internalization and sorting of TrkA. In this study, TrkA-overexpressing TrkA-PC12 cell cultures were transfected with a CMV- HA-Pincher constmct. Double immunofluorescence staining of fixed, permeabilized cells with anti-HA mAb (Alexa 488, green) and anti-TrkA polyclonal antibody (Cy5, red) was visualized using a Zeiss LSM510 confocal microscope using a 100X objective and LSM510 software. The photographic images are negatives of black and white images; in the original photographs, TrkA antibodies were labeled with a red fluorophore and HA antibodies were labeled with a green fluorophore. Figure 10A depicts cells expressing HA-Pincher ( + HA-Pincher) or not ( - HA-Pincher) are indicated. Cells were treated or not with NGF for the indicated times. The bar in the top left panel represents 5 μm. Figure 10B shows Zeiss LSM510 deconvolution software was used to create a 3-D reconstruction of the HA-Pincher expressing cell shown in the NGF lOmin overlay.

As seen in Figure 10, in untreated cells Pincher is localized primarily to the plasma membrane, but can be occasionally visualized intracellularly. Plasma membrane localization was confirmed by co-staining with wheat germ agglutinin, which showed a greatly overlapping staining pattern (not shown). The distribution of Pincher did not appear to depend on the level of Pincher expression as indicated by the similar pattern of staining for both dimly and brightly stained cells. TrkA, visualized in the same cells by double-labeling using anti-TrkA antibody, was also primarily localized to the plasma membrane in a pattern that partially overlapped with that of Pincher (Fig. 10). The small level of intracellular TrkA staining was presumably associated with the endoplasmic reticulum in the TrkA-PC12 cells. After NGF treatment, both Pincher and TrkA migrated away from the peripheral plasma membrane in a time-dependent manner. After two minutes of NGF-treatment, both Pincher and TrkA became preferentially associated with NGF-induced raffles and blebs at the plasma membrane (Fig. 10). Within three minutes of NGF-treatment cells were also seen in which Pincher and TrkA were both dramatically associated with intracellular vesicle-like structures in largely overlapping patterns (Fig. 10). Although NGF-treatment rapidly caused an apparent co-localization and internalization of Pincher and TrkA, within ten minutes of NGF-treatment Pincher and TrkA localization became differentially reorganized. Pincher was associated predominantly with an unusual array of intracellular structures (see NGF 10 min, Fig. 10). The Pincher-containing arrays were sorted away from a centralized collection of TrkA-containing structures. Pincher arrays were often found surrounding the TrkA- containing structures, as shown in the 3-D reconstruction of the cell in Fig 10B. Within one hour of NGF-treatment, Pincher was again found predominantly at plasma membrane and juxtamembrane locations, but rarely in internal structures, while TrkA was observed to have accumulated mainly in a dense collection of intracellular vesicle-like stmctures (Fig. 10), which were never seen to be associated with the nucleus. In many cells, as depicted in Figure 10, TrkA was extensively internalized and was barely detected at the plasma membrane.

As described above a massive internalization of TrkA, accumulation of intracellular TrkA-containing structures in the cytoplasm, and apparent depletion of TrkA from the plasma membrane, was seen after NGF-treatment of Pincher-overexpressing cells. Although an overall similar reorganization of TrkA occurred in TrkA-PC12 cells in response to NGF, the reorganization of TrkA in Pincher-overexpressing cells was dramatically enhanced. Although not described previously, TrkA became concentrated at sites of raffling plasma membrane within two minutes of NGF treatment (Fig. 10). However, the appearance of TrkA at raffling membranes appeared to affect a greater proportion of the TrkA in Pincher-overexpressing cells (see example shown in Fig. 10). The normal sequence of TrkA internalization after NGF treatment, as reported (Grimes et al, 1996) and as seen in the untransfected cells in the same slides (Fig. 10), affected a much smaller percentage of TrkA in the one-hour time frame, leaving TrkA predominantly plasma membrane associated. TrkA internalization could well be seen, as has been described (Grimes et al, 1996), associated with intracellular vesicle-like structures formed after NGF treatment, but the accumulations were relatively fewer in number, and distributed in smaller clusters throughout the cytoplasm (Fig. 10). Large accumulations of cytoplasmic TrkA seen in Pincher-overexpressing cells were quite stable and were often present even after 24 hours of NGF-treatment (not shown), although these cells were poorly adherent and granular and as such did not appear healthy. Unfortunately, we could not detect endogenous Pincher by immunocytochemistry, because our anti-Pincher antibody did not stain the untransfected cells, although it did detect endogenous Pincher in Western blots (Fig. 9). However, an apparent dosage effect of ectopic Pincher expression on the NGF-induced pattern of reorganization of both TrkA and Pincher was observed. All patterns of TrkA reorganization were most dramatic in the brightly stained Pincher-transfected cells, and were less dramatic in the lightly stained cells (not shown).

The confocal observations on Pincher localization and translocation with NGF treatment were verified and extended by EM immunogold analyses. For the studies represented in Figure 11, TrkA-overexpressing TrkA-PC12 cell cultures were transfected with a CMV-HA-Pincher construct and treated with NGF as in Fig 10. Cells were processed for immunogold electron microscopy using anti-Pincher antibody. Figure 11 Panel A shows immunogold labeled Pincher associated with complex raffling formations (arrowheads) localized at the peripheral membrane, twenty minutes after exposure to NGF. Figure 11 Panel B represents immunogold labeled Pincher associated with a complex raffling formation at the peripheral membrane ten minutes after exposure to NGF, where arrowheads indicate the locations of cytoskeletal stmctures. Figure 11 Panel C depicts immunogold labeled Pincher associated with a complex raffling formation at the peripheral membrane ten minutes after exposure to NGF.

As depicted in Figure 11, between two and ten minutes of NGF-treatment, immunogold-labeled Pincher was associated with plasma membrane-associated complex raffling formations. The peripheral membrane localization corresponded well with the NGF-induced blebs observed by confocal microscopy. Notably, these complex raffling formations exhibited fibrous structures indicative of cytoskeletal arrangements (see Fig. 11 Panel B), which is consistent with the notion that macropinocytotic raffling was being observed. The complex raffling structures appear to be an infolded matrix of multiple raffling membrane edges (see Fig. 11 Panel C).

Figure 12 represents low power electron micrograph of a portion of a TrkA-PC12 cell overexpressing Pincher ten minutes after exposure to NGF. Immunogold labeled Pincher is associated with at least two different intracellular structures. The arrowheads point to Pincher immunogold labeled structures that appear to be internalized complex raffling formations. The small arrows point to a few (of the many present) examples of intracellular vesicles and tubules that are immunogold labeled for Pincher. The boxed region is shown at higher power in Figure 13, lower panel. Figure 13 (upper panel) shows an example of an internalized complex raffling formation apparently 'delivering' membrane bound vesicles to a large vesicle accumulating body (VAB). Note the absence of Pincher immunogold labeling of vesicles within the VAB. The lower panel is a higher power electron micrograph of the boxed region in Figure 12; immunogold Pincher labeled tubules are highlighted with arrowheads. The sections in both panels are taken from Trk-PC12 cells overexpressing Pincher 10 min after exposure to NGF. To summarize the studies depicted in Figures 12 and 13, at ten minutes of NGF- treatment, similar complex stractures were occasionally seen in the cytoplasm (Figs. 12 and 13). These internal stractures would appear to be "remnants" of the complex ruffling stractures, suggesting that they can be internalized en mass. Pincher was never found to be associated with clathrin-coated invaginations of the plasma membrane or vesicles, but was frequently associated with intracellular endosomal vesicles and tubules (Figs. 12 and 13). The Pincher-containing complex ruffling stractures as well as the vesicular and tubular stractures were seen to surround and associate with accumulations of large Pincher-free bodies filled with vesicles (Fig. 12 and 13). This pattern of Pincher staining was strikingly similar to the pattern seen by immunofluorescence confocal microscopy (see Fig. 10, NGF 10 min). Elecfron microscopically, examples were seen in which the internalized Pincher-containing complex ruffling structures and tubules were fused with the vesicle-filled bodies and many of these raffling stractures and tubules were found to contain vesicular stractures within them (Fig. 13). The pattern of vesicle-filled bodies also appeared to closely match that observed for TrkA-containing stractures using confocal immunocytochemistry (Fig. 10). Immunogold EM analyses could not provide further substantiation, as we were not successful with the available anti-TrkA antibodies. Figure 14 represents an elecfron micrograph showing immunogold labeling of Pincher associated with vesicles and tubules (arrows) and the peripheral membrane (arrowheads). The section is from a TrkA-PC12 cell overexpressing Pincher one hour after exposure to NGF. At one hour after NGF-treatment Pincher was again associated with the plasma membrane and with vesicles and tubules near the cell periphery (Fig. 14). That the tubules and their "cores" were elecfron lucent (Fig. 14) suggested they were contiguous with the extracellular fluid. Pincher-generated vesicles contain extracellular fluid and NGF

The internalization of TrkA and Pincher, enhanced by Pincher overexpression, appeared to be caused by a NGF-induced, fluid-phase macropinocytotic process, occurring at membrane ruffles. To further test this possibility, we examined whether the fluid-phase uptake of media-soluble fluorescent Alexa488-10kd-dextran was stimulated by NGF-treatment of Pincher-transfected TrkA-PC12 cell cultures (Figure 15). In this case, overexpressed Pincher was visualized using anti-Pincher antibody. TrkA- overexpressing TrkA-PC12 cell cultures were transfected with a CMV-HA-Pincher construct as in Fig 10. To examine fluid-phase uptake by confocal fluorescence microscopy, cells were incubated with media containing fluorescent Alexa488- conjugated-lOkd-dexfran for 15 min (-NGF) or also treated with NGF for 15 min at 37°C (Panel A). Pincher-transfected cells were stained with anti-Pincher polyclonal antibody (Alexa 546). The photographic images are negatives of black and white images; in the original photographs, Pincher antibodies were labeled with a red fluorophonre and dexfran was labeled with a green fluorophore. No Pincher staining was observed when anti-Pincher antibody was pre-blocked with GST-Pincher fusion protein (not shown). As seen in Figure 15 Panel A, dexfran was not significantly taken up by the cells whether or not they overexpressed Pincher after transfection. However, NGF-treatment caused an uptake of dexfran into cells. In cells that did not overexpress Pincher, an expected pattern of dexfran uptake was observed after fifteen minutes of NGF-treatment, consisting of a scattered array of cytoplasmic vesicular stractures containing dexfran. However, in the cells overexpressing Pincher, a massive accumulation of dextran-containing cytoplasmic stractures could be seen, in large part surrounded by an array of Pincher containing tubular/vesicular stractures (Fig. 15 Panel A, bottom right of panel, see arrow). The pattern of dexfran surrounded by Pincher structures was similar to the pattern obtained with TrkA-labeling described above. Interestingly, dexfran localization also overlapped with the Pincher stractures, suggesting that they also contained extracellular fluid. Because the NGF that is added to the culture medium would be expected to be internalized together with TrkA, we examined the pattern of NGF uptake in Pincher- transfected cells. For this puφose, myc-tagged NGF (Moller et al, 1998) was isolated from the media of COS cell cultures that were transfected with a myc-NGF expression construct. Cells were treated with myc-tagged NGF for the times indicated in Figure 15B at 4°C (to prevent uptake) and at 37°C. NGF-myc was visualized by confocal fluorescence microscopy after anti-myc monoclonal antibody staining (Alexa 546) and Pincher staining using polyclonal anti-Pincher antibody (Alexa 488). The photographic images are negatives of black and white images; in the original photographs, Pincher antibodies were labeled with a green fluorophore and myc antibodies were labeled with a red fluorophore. Cells expressing HA-Pincher ( + HA-Pincher) or not ( - HA-Pincher) are indicated. The bar in the upper left hand corner box of Panels A and B represents 5 μm.

To summarize the results from Figure 15B, cells were treated with myc-NGF at 4°C to allow binding to TrkA without internalization. Under these conditions, as seen in Figure 15B, myc-NGF was not internalized, even in Pincher-expressing cells, and some anti-myc staining could be seen at the cell surface. When myc-NGF-treatment was carried out at 37°C, myc-NGF was found with Pincher at raffling membrane blebs, and co-internalization could be seen within five minutes of treatment (Fig. 15B). By one hour of treatment, myc-NGF was found to be concentrated in a dense accumulation of cytoplasmic vesicles (Fig. 15B), as described above for TrkA and for dexfran, while Pincher was localized to the plasma membrane. This pattern of myc-NGF staining contrasts with that seen in untransfected cells, in which NGF-treatment resulted in a sparse distribution of intracellular punctate staining (Fig 15B).

Pincher-generated Vesicles Mediate NGF/TrkA Signaling

The above results indicated that NGF was internalized together with TrkA. We thus expected that the internalized TrkA might remain activated and autophosphorylated (Bhattacharyya et al, 1997). To test this possibility, we used an anti-phospho-Y490TrkA antibody in confocal immunofluorescence microscopy of Pincher-transfected, TrkA- PC12 cell cultures (Figure 16). TrkA-overexpressing TrkA-PC12 cell cultures were transfected with a CMV-HA-Pincher construct as in Fig 10. Double immunofluorescence staining of fixed, permeabilized cells was carried out using anti-HA mAb (Alexa 488) and anti-phospho-Y490TrkA polyclonal antibody (Cy5). The photographic images are negatives of black and white images; in the original photographs, HA antibodies were labeled with a green fluorophore and the phospho-Y490TrkA antibodies were labeled with a red fluorophore. Cells were treated with NGF for the times indicated in Figure 16. Cells expressing HA-Pincher ( + HA-Pincher) or not ( - HA-Pincher) are also indicated. As expected, before NGF freatment, Pincher overexpressing cells detected with anti-HA antibody did not stain well with anti- phospho-Y490TrkA antibody (Fig. 16). However, after NGF treatment, a time-dependent pattern of anti-phospho-Y490TrkA staining was observed that was remarkably similar to that described above using anti-TrkA antibody. Within five minutes of NGF-treatment, anti-phospho-Y490TrkA staining could be seen at the plasma membrane concentrated together with Pincher at membrane raffles and blebs (Fig. 16). Pincher overexpression was found to increase both the appearance of phospho- TrkA in raffles after NGF-treatment (see Fig. 16), and the level of TrkA autophosphorylation. Staining of phosphorylated TrkA was seen in 67% of the Pincher- overexpressing cells (47 out of 70 cells examined) compared to 28% (28 out of 100 cells examined) of the cells not overexpressing Pincher, when assayed at ten minutes of NGF- treatment. By fifteen minutes of NGF-treatment, a massive internalization of both Pincher and phospho-Y490TrkA was seen accumulated in the cytoplasm in both overlapping and non-overlapping patterns (Fig. 16). Cytoplasmic staining of internalized phospho- Y490TrkA was seen in 89% of those Pincher-overexpressing cells compared to 34% of the phospho-TrkA stained cells not overexpressing Pincher. In addition, the extent of internalization per positive cell appeared dramatically higher in the Pincher- overexpressing cells compared to untransfected cells (see Fig. 16). After one hour NGF- treatment, Pincher was found predominantly on the cell surface, while phospho-Y490- TrkA staining was bright and in a concentrated array of cytoplasmic vesicles in a distribution that was not seen in untransfected cells (Fig. 16), as was seen for TrkA and myc-NGF. In many cells, as shown in Figure 16, little phosphorylated TrkA was seen at the cell surface, suggesting that the internalization was sufficient to significantly deplete activated TrkA from the cell surface. Dense accumulations of phosphorylated TrkA, similar to that seen at one hour NGF-treatment, were often seen even after 24 hours of NGF treatment (not shown). The persistence of TrkA autophosphorylation in intracellular vesicles suggested that they would have the capacity to mediate downstream signaling events in the cytoplasm. To test this possibility, we examined the distribution of NGF-activated MAP kinases, whose activation is mediated through phospho-Y490 TrkA signaling (Stephens et al, 1994). MAP kinase phosphorylation has been shown to be persistently stimulated in PC12 cells and is initiated within five minutes of NGF-treatment (Qui and Green, 1992). MAP kinase phosphorylation was examined using an anti-phospho-MAP kinase antibody in immunofluorescence staining of TrkA-PC12 cells transfected with a Pincher expression plasmid (Figure 17). TrkA-overexpressing TrkA-PC12 cells were fransfected with a CMV-HA-Pincher construct as in Fig 10. Immunofluorescence staining was carried out using anti-HA monoclonal antibody (Alexa 488) and anti-phospho-MAP kinase polyclonal antibody (Cy5). The photographic images are negatives of black and white images; in the original photographs, HA antibodies were labeled with a red fluorophore and the phospho-MAP kinase antibodies were labeled with a green fluorophore. Cells were treated with NGF for the times indicated in Figure 17.

As shown in Figure 17, before NGF treatment, Pincher overexpressing cells detected with anti-HA antibody, showed low level staining with the anti-phospho-MAP kinase antibody (Fig. 17). However, after NGF freatment, a time-dependent pattern of phospho-MAP kinase staining was observed that was remarkably similar to that described above using the anti-phospho-Y490TrkA antibody. Within five minutes NGF-treatment, bright phospho-MAP kinase staining could be seen just below the plasma membrane concentrated under Pincher at membrane ruffles and co-localized with Pincher upon internalization (Fig. 17). By fifteen minutes of NGF-freatment, phospho-MAP kinase staining was seen in large concentrated punctate formations in the cytoplasm. As was seen with phospho-TrkA-staining, the bright cytoplasmic staining of phospho-MAP kinase was often surrounded by the Pincher tubular arrays (Fig. 17). As recently reported (Wu et al. 2001), the pattern of phospho-MAP kinase staining after NGF-freatment in untransfected cells was punctate and diffusely distributed throughout the cytoplasm (Fig 17). Within one hour NGF freatment, Pincher was again seen associated predominantly with the plasma membrane while phospho-MAP kinase remained concentrated in the cytoplasm (Fig. 17). This staining pattern was still seen after two hours of NGF-treatment (not shown). As exemplified in Figure 17, although bright staining of phospho-MAP kinase was seen diffusely throughout the cytoplasm of non-transfected cells, the patterns of concentrated formations of phospho-MAP kinase were only seen in Pincher- overexpressing cells. In order to characterize the stmcture/function of Pincher, the EH domain was deleted. This deletion mutant is referred to as PincherΔEH. Figure 18 shows the results of an experiment using confocal microscopy showing that an EH domain deletion mutant of Pincher localizes to novel intracellular stmctures and is unresponsive to NGF. The TrkA-PC12 cells were transiently transfected with HA-PincherΔEH and treated with NGF for the times indicated in Figure 18. After fixation and permeabihzation, cells were stained using antibodies to TrkA and HA. HA-PincherΔEH labeling is shown on the left, TrkA labeling is shown in the center and an overlay of both labels are shown on the right. The photographic images are negatives of black and white images; in the original photographs, TrkA antibodies were labeled with a green fluorophore and HA antibodies were labeled with a red fluorophore. In the absence of NGF ("confrol"), TrkA staining is on the plasma membrane (Figure 18 A) and with some staining in the juxtanuclear region (Figure 18B), while HA-PincherΔEH labeling is only shown clustering in large structures, not appearing on the plasma membrane (Figure 18B). After NGF treatment for 5 minutes at 37 degrees Celsius ("NGF 5 min"), TrkA labeling is seen both on the plasma membrane (Figure 18 A) and in the cytosol (Figure 18B), but no change in the localization of HA-pincherΔEH labeling is observed. After 1 hour of NGF treatment at 37 degrees Celsius ("NGF 1 hour"), TrkA labeling is present on the plasma membrane (Figure 18 A) and in the cytosol. HA-PincherΔEH labeling remains clustered in large structures, and shows no localization change caused by NGF. Thus, deletion of the EH domain of Pincher results in a complete relocalization to novel intracellular vesicular structures, a loss of Pincher from the plasma membrane and no relocalization in response to NGF.

In order to characterize the stmcture/function of Pincher, an additional mutant was created, involving the ATP/GTP -binding domain. Figure 19 shows that the Pincher ATP/GTP -binding site mutant is dominant inhibitory for NGF-induced pinocytosis and endocytic signaling. Panel A shows that overexpression of Pincher G68E blocks NGF- induced fluid phase pinocytosis of dexfran- Alexa488 in PC12 cells. The photographic images are negatives of black and white images; in the original photographs, Pincher G68E antibodies were labeled with a red fluorophore and dexfran- Alexa488 was labeled with a green fluorophore. Panel B demonstrates that overexpressing Pincher G68E cells block phospho-TrkA internalization after NGF treatment. P-TrkA accumulates at cell surface raffles and blebs where G68E is expressed. The photographic images are negatives of black and white images; in the original photographs, Pincher G68E antibodies were labeled with a green fluorophore and phospho-TrkA antibodies were labeled with a red fluorophore. Panel C shows Pincher G68E overexpression results in accumulation of phospho-MAPK at the plasma membrane, thus preventing activated map kinase from going to the cytoplasm and nucleus. The photographic images are negatives of black and white images; in the original photographs, Pincher G68E antibodies were labeled with a green fluorophore and phospho-MAPK antibodies were labeled with a red fluorophore. Further characterization of the Pincher ATP/GTP -binding domain by electron microscopy is shown in Figure 20. Figure 20 shows that expression of the Pincher ATP/GTP binding site mutant results in accumulation of cell surface blebs. Panel A shows a lower power election micrograph of immunogold Δ-Pincher labeled TrkA-PC12 cell overexpressing Pincher G68E mutant. As shown, blebs accumulate at the cell surface. Panel B represents a higher magnification of the electron micrograph of a portion of the cell surface in order to show the fine structure of blebs formation. We believe that this accumulation of plasma membrane blebs is due to the prevention of pinocytosis, thus preventing raffles from internalizing. Pincher may also play a role in organizing the cytoskeleton at the raffling membrane - a loss of cytoskeletal function there might result in bleb formation. Thus, these studies suggest that Pincher is a major mediator of macropinocytosis in cells.

Pincher and NGF/TrkA Signaling in Sympathetic Neurons

Figure 21 demonstrates that Pincher overexpression enhances the formation of TrkA endosomes by NGF in sympathetic neuron somata that were isolated from superior cervical ganglion neurons taken from newborn rat pups that were dissociated and cultured in vitro with NGF. After 5 days the neurons were double fransfected with plasmids encoding HA-Pincher and TrkA. Two days later, the cells were fixed in 4% paraformaldehyde and stained with a combination of anti-phospho-TrkA antibody (B, middle panel) and anti-HA antibody (A, left panel), as observed using confocal immunofluorescence microscopy. The accumulation of endosomes containing activated, phospho-TrkA can be seen in the cells expressing HA-Pincher, which surrounds the accumulations. The merging of the two signals is seen in panel C. These data demonstrate that Pincher has the ability to perform a similar functional role in NGF/TrkA signaling for NGF-dependent neurons taken from superior cervical ganglia as was shown above for PC12 cells.

To investigate the ability of Pincher to trigger NGF/TrkA signaling events in neurons, the cellular localization of phospho-erk5 was examined following expression of HA-Pincher or an inactive mutant (HA-G68E-Pincher) in individual neurons in culture. Superior cervical ganglion neurons from newborn rat pups were dissociated and cultured in vitro with NGF. After 1 day the neurons were infected with adenoviruses encoding either HA-Pincher or HA-G68E-Pincher, as well as Green Fluorescent Protein (GFP). Two days later, the cells were fixed in 4% paraformaldehyde and stained with anti- phospho-erk5 antibody (Figure 22 B and E, middle panel), and observed using confocal immunofluorescence microscopy. The accumulation of endosomes associated with phospho-erk5 can be seen in the cytoplasm of cells expressing HA-Pincher, and limited to the plasma membrane in cells expressing HA-G68E-Pincher. The infected cells are indicated by the presence of GFP (Figure 22 A and D, left panel). The merged images are shown in Figure 22 C and F. The results demonstrate that Pincher enhances, and mutant G68E-Pincher inhibits, the cytoplasmic accumulation of activated phospho-erk5 in sympathetic neurons treated with NGF.

Pincher Induces BDNF /TrkB Signaling Endosome Formation in Sympathetic Neurons

Figure 23 shows that Pincher enhances and mutant G68E-Pincher inhibits the internalization and cytoplasmic accumulation of TrkB in sympathetic neurons treated with NGF and BDNF. Superior cervical ganglion neurons from newborn rat pups were dissociated and cultured in vitro with NGF and BDNF (NT-2). After 1 day the neurons were doubly infected with adenovirases encoding either HA-Pincher or HA-G68E- Pincher, and adenovirases encoding TrkB-GFP. Two days later, the cells were fixed in 4% paraformaldehyde and stained with anti-TrkB antibody (Figure 23 A or D), and anti- HA antibody (Figure 23 B or E), and observed using confocal immunofluorescence microscopy. The accumulation of endosomes associated with TrkB can be seen in the cytoplasm of cells expressing HA-Pincher, and limited to the plasma membrane in cells expressing HA-G68E-Pincher. Figure 23 C shows the merged images of A and B; Panel F shows the merged images of D and E. These data demonstrate that Pincher overexpression can enhance the intemahzation of signaling endosomes for two members of the neurotrophin family, NGF and BDNF, in neurons.

Pincher Localization at Neurite Terminals in Sympathetic Neurons

The cellular localization of Pincher was determined in superior cervical ganglion neurons isolated from iiewbom rat pups and infected with adenoviruses encoding HA- Pincher. Superior cervical ganglion neurons were dissociated and cultured in vitro with NGF. After 1 day the neurons were infected with adenovirus encoding HA-Pincher and GFP. Two days later, the cells were fixed in 4% paraformaldehyde and stained with anti- HA antibody (Figure 24 A), and observed using confocal immunofluorescence microscopy. The infected cells are indicated by the presence of GFP (Figure 24 B).

Shown are two neurite terminal growth cones. Figure 24 C shows the merged imaged of Panel A and B. The data indicate that Pincher is concentrated at raffling growth cone membranes (relative to the cytoplasmic GFP), a predominate site of pinocytosis in neurons.

Neurotrophin-Induced Internalization and Retrograde Transport of Pincher and TrkB in Sympathetic Neurons

Figure 25 shows that Pincher and TrkB are co-intemalized at the neuronal terminal and along the neurite and retrogradely transported in response to neurotrophin treatment. Superior cervical ganglion neurons from newborn rat pups were dissociated and cultured in vitro with the neurotrophins NGF and BDNF (NT-2). After 1 day the neurons were doubly infected with adenovirases encoding HA-Pincher, and adenovirases encoding TrkB-GFP. Two days later, the media of the three cultures was exchanged with media lacking neurotrophin and incubated for five hours. After neurotrophin starvation, the second culture was treated with the neurotrophins for ten minutes and the third culture was treated for one hour. All the cells were fixed in 4% paraformaldehyde and stained with anti-TrkB antibody (Figure 25 A,D,H), and anti-HA antibody (Figure 25 B,C,E,F,I,J), and observed using confocal immunofluorescence microscopy. Co- intemalization of both TrkB and HA-Pincher was observed after ten minutes of NT treatment. The terminals were largely devoid of co-internalized TrkB and Pincher after one hour of NT treatment, but they were co-localized in puncti along the neurites.

To determine whether Pincher is required for neurotrophin-induced internalization and retrograde transport of TrkB, the expression of TrkB was examined in sympathetic neurons harboring the dominant negative mutant of Pincher, HA-G68E-Pincher. In Figure 26, superior cervical ganglion neurons from newborn rat pups were dissociated and cultured in vitro with NGF and BDNF (NT-2). After 1 day the neurons were doubly infected with adenovirases encoding HA-G68E-Pincher, and adenovirases encoding TrkB-GFP. Two days later, the cells were fixed in 4% paraformaldehyde and stained with anti-TrkB antibody (Figure 26 A), and anti-HA antibody (Figure 26 B), and observed using confocal immunofluorescence microscopy. Shown is a neurite terminal in which HA-G68E-Pincher and TrkB are co-localized and concentrated at two foci at the growth cone tip. No internalized foci could be seen. Figure 26 C shows the merged image of A and B. These results demonstrate that expression of HA-G68E-Pincher prevented neurotrophin-mediated intemahzation and retrograde transport of TrkB at neurite terminals. The data above taken together indicate that Pincher is likely to be required, in neurons, for neurotrophin receptor internalization following receptor occupancy. Furthermore, the demonstration that the retrograde transport of neurotrophin signaling endosomes is blocked by the dominant negative Pincher mutant indicates that Pincher-driven endosome formation leads to signaling complexes whose downstream actions are essential for neuronal survival.

Summary and Significance Using the TOGA^® technology, we have identified a cDNA, HAL_18, encoding a novel NGF-induced protein in PC 12 cells. HAL_18 expression was characterized by Northern analysis, which confirmed the regulation predicted by TOGA^® analysis. Northern blot analysis also demonstrated that HAL_18 induction was mediated by Ras- dependent and Ras-independent pathways via multiple TrkA autophosphroylation sites. HAL_18 was shown to encode a tissue-specific mRNA, and the protein product was termed Pincher (Pinocytic Chaperone), because of its ability to drive endocytosis and trafficking of NGF and its receptor TrkA. Additional studies of Pincher characterized the signaling pathways to Pincher induction, and the role of Pincher in TrkA endocytosis and signaling. TrkA and Pincher endocytosis were visualized by confocal immunofluorescence microscopy in PC 12 cells overexpressing HA-tagged-Pincher. Immuno-EM analysis, demonstrated unequivocally that Pincher was associated with NGF-stimulated fluid phase macropinocytosis. The activation state of TrkA, examined using myc-tagged NGF, and a phospho-TrkA specific antibody, indicated that the internalized TrkA vesicles contained NGF and TrkA that was continually autophosphorylated. Immunostaining using phosphorylation state-specific antibodies indicated that the internalized vesicles retained autophosphorylated TrkA and were associated with activated MAP kinases. From both gain-of-function and loss-of-function experiments in PC 12 cells and sympathetic neurons, we conclude that Pincher mediates both the NGF-induced intemahzation of TrkA by a pinocytic process, and the sorting of long-lived endosomal vesicles with NGF-signaling capabilities. The function of Pincher in growth factor signaling pathways extends across the neurotrophin family, as BDNF and its receptor, TrkB, utilize a Pincher-mediated mechanism for intemahzation and retrograde transport. Pincher is a member of a family of closely related proteins that are known in humans as EHD-1 to EHD-4. Although the family members have no known function, recent reports have implicated a Drosphophila homolog, PAST-1, in events underlying receptor-mediated endocytosis. The mouse homologue for PAST-1, mRME-1 has been suggested to mediate recycling of receptor-containing endocytic vesicles and was found to be localized to an endosome recycling compartment in Chinese hamster ovary cells (Lin et al, 2001). This function is unlike that for Pincher, which did not mediate recycling of the Trl A-containing vesicles that persisted in the cytoplasm. Furthennore, mRME-1 overexpressed in TrkA-PC12 cells did not act like Pincher to enhance NGF- induced TrkA intemahzation (Shao and Halegoua, unpublished). EHD-1, the human homologue of mRME-1, has recently been suggested to mediate receptor-induced endocytosis of IGF- 1 (Rotem-Yehudar et al, 2001). Due to a co-localization of transferring with EHD-1 in a small number of vesicles (Mintz, et al, 1999), and the retention of clathrin-containing complexes by a EHD-1 affinity column (Rotem-Yehudar et al, 2001), the authors suggested that EHD-1 participated in a clathrin-mediated endocytic process that would lead to endosome recycling and degradation. The primary involvement of Pincher appears to be in clathrin-independent pinocytic processes because we did not observe any significant co-localization of Pincher with clathrin in immunofluorescence labeling of PC 12 cells (Shao and Halegoua, unpublished data), and have never found Pincher to be associated with clathrin-coated stractures by electron microscopy. The differences between Pincher and mRME-1 or EHD-1 suggest that the different PAST-1 family members may have different functions in vesicle transport. It is tempting to speculate that a common functionality of Pincher and PAST-1 homologues lies in the ability to pinch membrane, which in the case of mRME-1 results in the formation of recycling vesicles and in the case of Pincher results in macropinocytotic stractures. The tissue distribution of Pincher mRNA is similar to that of mRME-1 and EHD-1 , with high levels of expression in heart and lung, suggesting that Pincher may also be involved in a broader spectrum of receptor-mediated pinocytic events.

HAL_18 served as an example of the mechanisms by which NGF regulates the neuronal phenotype. These TOGA^® studies have identified some proteins and genes, such as HAL_18 (Pincher), that are associated with and/or which mediate the actions of NGF. Such molecules are useful in therapeutic and diagnostic applications in the treatment of disorders or diseases affecting the control of neuronal precursor cell proliferation, differentiation and modulation of neuronal moφhology, regulation of neurotransmitter synthesis and secretion, the cessation of cell division and prevention of cell death, the expression of neuronal-specific proteins, synaptogenesis and confrol of synaptic efficacy (synaptic modulation), and the expression of electrical excitability. Molecules described in the invention are also useful for adjusting the number of NGF receptors on a cell surface, for modulating the sensitivity of cells to NGF and for modulating the cell's response to NGF. Further, polynucleotides in the present invention that effectively modulate NGF metabolism can be used therapeutically and diagnostically in diseases and conditions involving altered target cell metabolism of NGF. Such diseases and conditions include those involving reduced or elevated number of trkA NGF receptors. Also included would be diseases or conditions involving reduced or elevated sensitivity of target cells to NGF due to alterations in intemahzation of NGF, trkA, or NGF-trkA complex or alternation in intracellular messenger metabolism. Such diseases include forms of Alzheimer's disease characterized by altered trkA numbers and expression (Dubus, P., et al, Expression of trk isoforms in brain regions and in the striatum of patients with Alzheimer's disease, Exp Neurol 2000, 165:285-294; Hock, C.H., et al, Alterations in neurofrophins and neurotrophin receptors in Alzheimer's disease, J. Neural Transm. Suppl. 2000;59:171-174; Hock, C.H., et al, Decreased trkA neurotrophin receptor expression in the parietal cortex of patients with Alzheimer's disease, Neurosci Lett 1998;241(2-3):151-154). Other diseases include diabetic neuropathy (Freeman, R., Human studies of recombinant human nerve growth factor and diabetic peripheral neuropathy, Eur. Neurol. 1999;41 Suppl 1:20-26) and congenital insensitivity to pain with anhidrosis (CEP A) (Miura, Y., et al, Mutation and polymoφhism analysis of the trkA (NTRK1) gene encoding a high-affinity receptor for nerve growth factor in congenital insensitivity to pain with anhidrosis (CEP A) families, Hum Genet 2000;106:116-24; Shatzky, S., et al, Congenital insensitivity to pain with anhidrosis (CIP A) in Israeli-Bedouins: genetic heterogeneity, novel mutations in the til A NGF receptor gene, clinical findings, and results of nerve conduction studies, Am. J. Med. Genet. 2000;92:353-60.). The subcutaneous and system administration of nerve growth factor is known to produce painful side effects such as myalgia and hyperalgesia (Rogers, B.C., Development of recombinant human nerve growth factor (rhNGF) as a treatment for peripheral neuropathic disease, Neurotoxicology 1996 Fall- Winter; 17(3- 4):865-70; Petty, B.G., The effect of systemically administered recombinant human nerve growth factor in healthy human subjects, Ann. Neurol. 1994 Aug; 36(2):244-246.). Native and modified polynucleotides and polypeptides of the present invention that effectively modulate NGF metabolism can be used therapeutically as an adjunct to NGF therapy to ameliorate such side effects.

The polynucleotides, polypeptides, kits and methods of the present invention may be embodied in other specific forms without department from the teachings or essential characteristics of the invention. The described embodiments are therefore to be considered in all respects as illustrative and not restrictive, the scope of the invention being indicated by the appended claims rather than the foregoing description, and all changes which come within the meaning and range of equivalency of the claims are, therefore, to be embraced within.

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TABLE 2

Digital Nucleotide homology

Seq ID DST ID Address Database Match (Accession #) % Homology

NO (Mspl)

DST nucleotide range Database nucleotide range ( p#) (bp#)

1 HAL_1 ACCT 376 Rat NICER element (GL5-14) 5' long 97% 1-317 183-499 terminal repeat (M59028)

2 HAL_4 AGAC 442 Rat endogenous retroviral sequence, 95% 133-389 5767 - 6023 5'and3'LTR(D90005)

3 HAL_5 AGGA 379 EST205638 Normalized rat ovary, 97% 99-307 1-209

Bento Soares rattus sp. cDNA clone

ROVAQ573' end (AI011187)

4 HAL_6 AGGG 417 EST UI-R-AO-ar-g-05-O-UI.sl UI-R- 100% 1-179 202-380 AO Rattus norvegicus cDNA/UI-R-

AO-ar-g-05-0-UI3' similar to gb/J03161/HUMSRF (AA818844)

5 HAL 7 AGTG 421 NOVEL N/A N/A N/A

6 HAL_9 ATCT 377 Rat NICER element (GL5-14) 5' long 94% 1-195 183-377 terminal repeat (M59028)

7 HAL_11 CCTG 483 EST UI-R-Cl-kp-e-08-0-UI.sl UI-R- 99% 61 -436 11-386

Cl Rattus norvegicus cDNA/UI-R-

Cl-kp-e-08-0-UI3' (AI058661)

8 HAL_14 CGGA 369 Mus Musculus mRNA for poly(A) 96% 1-317 438-754 binding protein (X65553) and

EST 111483 Rat PC-12 cells, NGF- 98% 9-314 1-307 treated (9 days) Rattus sp. Clone

RPNCB12 similar to Polyadenylate- binding protein (H35169)

9 HAL_15 CGTA 468 EST UI-R-C2-nd-a-05-0-UI-.sl UI-R- 99% 42-308 11-277

C2 Rattus norvegicus cDNA/UI-R-

C2_nd-a-05-0-UI 3' (AI071985)

10 HAL_16 GAAG 125 EST va66c04.rl Soares mouse 93% 10-73 262 - 325

3NME125 Mus musculus cDNA clone 7363265' (AA270492)

TABLE 2 (continued)

Digital Nucleotide homology

SeqH⁾ DST ID Address Database Match (Accession #) % Homology

NO (Mspl)

DST nucleotide range Database nucleotide range

(bp#) (bp#)

20 HAL_27 TACC210 EST mz59gl2.xl Soares mouse 87% 80 - 157 1-78 lymph node NbMLN Mus musculus cDNA clone (AI661103.1)

21 HAL_28 TGTT 245 EST w52c08.rl Soares 2NbMT Mus 94% 1-126 19 - 144 musculus cDNA clone 1226030

5' (AA739300)

22 HAL_29 GATT 266 Rat hepatic steroid hydroxylase IIA2 97% 1-209 3999-4208

(CYP2A2) gene, exons 1 and 2

(M33313)

23 HAL_30 GTCC 279 Rat C/EBP-related protein 2 (CRP2) 96% 1-53 1378 - 1429 gene, complete eds. (M84011) 100% 106-221 1483 - 1598

24 HAL_31 TCAC291 Rat dihydropyridine-sensitive L-type 98% 1-237 1761-2000 calcium channel alpha-2 subunit

(CCHL2A) gene, complete eds.

(M86621)

25 HAL_32 TGCA 297 EST193533 Normalized rat ovary, 96% 1-241 17-257

Bento Soares Rattus sp. cDNA clone

ROVAK533' end (AA850765)

26 HAL_34 GTAT 308 EST mt58gll.rl Soares 2NbMT Mus 89% 154-256 215-318 musculus cDNA clone 6341485'

(AA184704)

27 HAL_35 GGCA 356 EST UI-R-AAl-zz-d-08-O-UI.sl UI- 100% 229 - 305 196-272

R-AA1 Rattus norvegicus cDNA cloneUI-R-AAl-zz-d-08-0-UI 3', mRNA sequence (AI710081.1)

28 HAL_36 AGAG 365 Mus musculus Sid3177 mRNA, 98% 1-313 36-348 complete eds (AB024935.1)

EST = Expressed Sequence ' fag, N/A = Not Applicable

Claims

We claim:

1. A method for preventing or treating a medical condition, comprising administering to a mammalian subject a therapeutically effective amount of at least one nucleic acid molecule comprising a polynucleotide chosen from the group consisting of SEQ ID NOs: 1-29, wherein the medical condition is selected from the group consisting of a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIP A, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy.

2. A method for preventing or treating a medical condition comprising administering to a mammalian subject a therapeutically effective amount of at least one polypeptide encoded by a polynucleotide chosen from the group consistmg of SEQ ID NOs: 1-29, wherein the medical condition is selected from the group consisting of a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIP A, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy.

3. A method for preventing or treating a medical condition comprising administering to a mammalian subject a therapeutically effective amount of at least one antibody that binds specifically to a polypeptide encoded by a polynucleotide chosen from the group consisting of SEQ ID NOs: 1-29, wherein the medical condition is selected from the group consisting of a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIPA, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy.

4. A method of diagnosing a medical condition or a susceptibility to a medical condition in a subject comprising:

(a) determining the presence of a mutation in one or more of polynucleotides chosen from the group consistmg of SEQ ID NOs: 1-29; and

(b) diagnosing a medical condition or a susceptibility to a medical condition based on the presence of said mutation, wherein the medical condition is selected from the group consisting of a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIPA, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy.

5. A method for diagnosing a medical condition or a susceptibility to the medical condition in a patient, wherein the medical condition is selected from the group consistmg of a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIPA, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy, the method comprising the steps of:

(a) obtaining a first biological sample from a patient suspected of having the medical condition;

(b) obtaining a second sample from a suitable comparable control source;

(c) determining in the first and second samples a level of expression of at least one of:

(i) a first polypeptide encoded by a polynucleotide selected from the group consisting of SEQ ID NOs: 1-29;

(ii) a second polypeptide encoded by a gene corresponding to any of the foregoing polynucleotides or another gene at least 95% identical to said gene;

(iii) a third polypeptide at least 90% identical to one of the foregoing polypeptides;

(iv) a fragment of one of the foregoing polypeptides; or

(v) a polynucleotide selected from the group consisting of SEQ ID NOs: 1-29; and

(d) comparing the level of expression of the at least one polypeptide or the polynucleotide in the first and second samples, wherein the patient is diagnosed as having the medical condition or is susceptible to having the medical condition if the level of expression of the at least one polypeptide or the polynucleotide in the first sample is substantially modulated relative to the level of expression of the at least one polypeptide or the polynucleotide in the second sample.

6. A method for manufacturing a medicament for the treatment of a medical condition, wherein the medical condition is selected from the group consisting of a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIPA, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy, the method using at least one of:

(a) a first polynucleotide selected from the group consisting of SEQ ID NOs: 1-29;

(b) a second polynucleotide at least 95% identical to the first polynucleotide;

(c) a third polynucleotide at least ten bases in length that is hybridizable to the first polynucleotide under stringent conditions;

(d) a gene corresponding to any of the foregoing polynucleotides, another gene at least 95% identical to the gene, or a region of any of the foregoing genes;

(e) a first polypeptide encoded by a polynucleotide selected from the group consisting of SEQ ID NOs: 1-29;

(f) a second polypeptide encoded by a gene corresponding to any of the foregoing polynucleotides or another gene at least 95% identical to said gene;

(g) a third polypeptide at least 90% identical to one of the foregoing polypeptides; or

(h) a fragment of one of the foregoing polypeptides.

7. A method for manufacturing a medicament for the treatment of a medical condition, wherein the medical condition is selected from the group consisting of a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIPA, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy, the method using an antibody that binds specifically to at least one of:

(a) a first polypeptide encoded by a polynucleotide selected from the group consistmg of SEQ ID NOs: 1-29;

(b) a second polypeptide encoded by a gene corresponding to any of the foregoing polynucleotides or another gene at least 95% identical to said gene;

(c) a third polypeptide at least 90% identical to one of the foregoing polypeptides; or

(d) a fragment of one of the foregoing polypeptides.

8. A method for identifying a binding partner to a polypeptide encoded by a polynucleotide chosen from the group consisting of SEQ ID NOs: 1-29, the method comprising:

(a) contacting said polypeptide with a binding partner; and

(b) determining whether the binding partner effects an activity of the polypeptide.

9. A method for identifying an activity of an expressed polypeptide in a biological assay, the method comprising:

(a) expressing in a cell a polypeptide encoded by a polynucleotide chosen from the group consisting of SEQ ID NOs: 1-29;

(b) isolating the expressed polypeptide;

(c) testing the expressed polypeptide for an activity in a biological assay; and

(d) identifying the activity of the expressed polypeptide based on the test results.

10. A substantially pure isolated DNA molecule suitable for use as a probe for genes regulated in a medical condition, chosen from the group consisting of SEQ ID NOs:l- 29, wherem the medical condition is selected from the group consisting of a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIPA, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy.

11. A kit for detecting the presence of a polypeptide encoded by a polynucleotide selected from the group consisting of SEQ ID NOs: 1-29 in a mammalian tissue sample comprising a first antibody, wherein said first antibody immunoreacts with a mammalian protein encoded by a gene corresponding to a polypeptide encoded by a polynucleotide selected from the group consisting of SEQ ID NOs: 1-29 in an amount sufficient for at least one assay and suitable packaging material.

12. The kit of claim 11 further comprising a second antibody that binds to the first antibody.

13. The kit of claim 12, wherein the second antibody is labeled, and wherein the label is selected from the group consisting of enzymes, radioisotopes, fluorescent compounds, colloidal metals, chemiluminescent compounds, phosphorescent compounds, and bioluminescent compounds.

14. A kit for detecting the presence of a gene encoding a protein comprising a polynucleotide chosen from the group consisting of SEQ ID NOs: 1-29, or fragment thereof having at least 10 contiguous bases, in an amount sufficient for at least one assay, and suitable packaging material.

15. A method for detecting the presence of a nucleic acid encoding a protein in a mammalian tissue sample, comprising the steps of:

(a) hybridizing a polynucleotide chosen from the group consisting of SEQ ID NOs: 1-29, or fragment thereof having at least 10 contiguous bases, with the nucleic acid of the sample; and

(b) detecting the presence of the hybridization product.

16. A method for identifying biomolecules associated with a medical condition, the method comprising the steps of:

(a) developing a cellular experiment specific for a disorder of neuronal differentiation;

(b) harvesting the RNA from the cells used in the experiment;

(c) obtaining a gene expression profile; and

(d) using the gene expression profile for identifying biomolecules which expression was altered during the experiment, wherein the medical condition is selected from the group consisting of a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIPA, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy

17. A method for assessing the efficacy of a treatment for treating a medical condition in a subject, wherein the medical condition is selected from the group consisting of a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIPA, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy, the method comprising the steps of comparing:

(a) a level of expression of a polynucleotide selected from the group consisting of SEQ ID NOs: 1-29, or a polypeptide encoded by a polynucleotide selected from the group consisting of SEQ ID NOs: 1-29, in a first sample obtained from the subject prior to providing at least a portion of the treatment to the subject; and

(b) a level of expression of the same polynucleotide or polypeptide in a second sample following provision of the portion of the treatment, wherein a modulated level of expression of the polynucleotide or polypeptide in the second sample relative to the first sample, is an indication that the treatment is efficacious for treating the medical condition.

18. An isolated nucleic acid molecule comprising a polynucleotide listed in SEQ ID NOs: 5, 16 and 29, or a second isolated nucleic acid molecule at least 95%> identical to said first isolated nucleic acid, wherein expression of the polynucleotide is modulated, relative to a control sample, in a patient afflicted with a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIPA, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, or hyperalgesia associated with NGF therapy.

19. An isolated polypeptide encoded by:

(a) a first polynucleotide listed in SEQ ID NOs: 5, 16 and 29; or

(b) a second polynucleotide at least 95% identical to said first polynucleotide; or

(c) a gene or region thereof corresponding to any of the foregoing polynucleotides or another gene at least 95% identical to said gene; or

(d) the complements and degenerate variants of any of the foregoing polynucleotides or genes, wherein the expression of the polypeptide is modulated, relative to a control sample, in a patient afflicted with a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIPA, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, or hyperalgesia associated with NGF therapy.

20. An isolated nucleic acid molecule at least ten bases in length that is hybridizable to the isolated nucleic acid molecule of claim 18 under stringent conditions.

21. An isolated nucleic acid molecule encoding a fragment of the polypeptide of claim 19.

22. The isolated nucleic acid of claim 21, wherein the nucleic acid encodes an epitope.

23. The polypeptide of claim 19, wherein the polypeptide has biological activity.

24. An isolated nucleic acid encoding a species homolog of the polypeptide of claim 19.

25. The isolated nucleic acid molecule of claim 1, wherein the nucleotide sequence comprises sequential nucleotide deletions from either the 5' end or the 3 'end.

26. An isolated fragment of any polypeptide of claim 19.

27. An isolated polypeptide that is a homolog, paralog or ortholog of any polypeptide of claim 19.

28. A recombinant vector comprising:

(a) the isolated nucleic acid molecule of claim 19 operably linked to a promoter;

(b) an origin of replication; and

(c) a selectable marker.

29. A recombinant host cell comprising the recombinant vector of claim 28.

30. A method for making a recombinant host cell comprising:

(a) introducing the recombinant vector of claim 28 into a host cell.

31. The isolated polypeptide of claim 19, wherein the isolated polypeptide comprises sequential amino acid deletions from either the C-terminus or the N-terminus.

32. An isolated antibody that binds specifically to the isolated polypeptide of claim 19, wherein said isolated antibody is a polyclonal or monoclonal antibody.

33. A recombinant host cell that expresses the isolated polypeptide of claim 19.

34. An isolated polypeptide produced by the steps of:

(a) culturing the recombinant host cell of claim 29 under conditions such that said polypeptide is expressed; and

(b) isolating the polypeptide.

35. A method for assessing the efficacy of a test compound for treating a medical condition in a mammalian subject, the method comprising the step of comparing:

(a) a level of expression of a marker in a first sample obtained from the subject, wherein the first sample is exposed to the test compound and wherein the marker is selected from the group consisting of polynucleotides listed in SEQ ID NO: 1-29; polypeptides encoded by the polynucleotides listed in SEQ ID NO: 1-29; and fragments thereof; and

(b) a level of expression of the same marker in a second sample obtained from the subject, wherein the second sample is not exposed to the test compound, and wherein a substantially increased or decreased level of expression of the marker in the first sample, relative to the second sample, is an indication that the test compound is efficacious in treating the medical condition, wherein the medical condition is selected from the group consisting of a disorder of altered target cell growth, differentiation, response to NGF, internalization of NGF, Alzheimer's Disease, diabetic neuropathy, CIPA, retinitis pigmentosum, congenital macular degeneration, a side effect of NGF therapy, and hyperalgesia associated with NGF therapy.

36. A method for assessing the efficacy of a test compound for modulating endocytosis, pinocytosis or receptor internalization, the method comprising:

(a) isolating recombinant cell line comprising a recombinant vector capable of expressing the polynucleotide listed in SEQ ID NO: 29;

(b) separating the recombinant cell line into a control population and a test population;

(c) contacting the test population with the test compound;

(d) monitoring a level of expression of the polypeptide expressed by the polynucleotide listed in SEQ ID NO: 29 in both the control and test populations, wherein a modulated level of expression of the polypeptide expressed by the polynucleotide listed in SEQ ID NO: 29 is an indication that the test compound is efficacious for modulating endocytosis, pinocytosis or receptor internalization.

37. The method of claim 36, wherein the level of expression of the polypeptide expressed by the polynucleotide listed in SEQ ID NO: 29 is monitored by immunodetection.