WO2005101013A2 - Substances et procedes pour le criblage de modulateurs de la regeneration neuronale - Google Patents

Substances et procedes pour le criblage de modulateurs de la regeneration neuronale Download PDF

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WO2005101013A2
WO2005101013A2 PCT/EP2005/003946 EP2005003946W WO2005101013A2 WO 2005101013 A2 WO2005101013 A2 WO 2005101013A2 EP 2005003946 W EP2005003946 W EP 2005003946W WO 2005101013 A2 WO2005101013 A2 WO 2005101013A2
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cell
c3ar
c5ar
igfbp
ofthe
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PCT/EP2005/003946
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WO2005101013A3 (fr
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Milos Pekny
Marcela Pekna
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Reglia Ab
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Priority to EP05739891A priority Critical patent/EP1782072A2/fr
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Publication of WO2005101013A3 publication Critical patent/WO2005101013A3/fr
Priority to US11/581,207 priority patent/US20070054325A1/en

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/502—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing non-proliferative effects
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/502—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing non-proliferative effects
    • G01N33/5029—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing non-proliferative effects on cell motility
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/502—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing non-proliferative effects
    • G01N33/5041—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics for testing non-proliferative effects involving analysis of members of signalling pathways
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
    • G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
    • G01N33/5044—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics involving specific cell types
    • G01N33/5058—Neurological cells
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/705—Assays involving receptors, cell surface antigens or cell surface determinants
    • G01N2333/72—Assays involving receptors, cell surface antigens or cell surface determinants for hormones
    • G01N2333/726—G protein coupled receptor, e.g. TSHR-thyrotropin-receptor, LH/hCG receptor, FSH
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2500/00—Screening for compounds of potential therapeutic value

Definitions

  • the present invention relates generally to material and methods used to identify modulators of neurogenesis and neuroregeneration, and use of said modulators in the treatment of neurodegenerative diseases and neurological injury.
  • astrocytes have been proposed to control both the number and the character of neuronal synapses. Little is known about function of astrocytes in CNS pathologies. In CNS trauma, tumor growth, brain ischemia or neurodegenerative diseases, astrocytes become reactive. Two hallmarks of this reaction, known as reactive gliosis (RG), are astroctye hypertrophy/prominent extension of cellular processes and upregulation of intermediate filaments (EFs), apart ofthe cytoskeleton, composed of three IF proteins - nestin, vimentin and GFAP.
  • RG reactive gliosis
  • RG is accompanied by an altered expression profile of many genes (Eng et al., Brain Pathol. 4: 229-237, 1994). The importance of RG in CNS pathologies remains poorly understood. It has been speculated that this reaction may be both positive and negative. RG may contribute to the healing process; stimulate proliferation of neural stem cells and thereby increase neurogenesis; reconstitute a locally damaged blood-brain barrier; or form a barrier against the migration of tumor cells. Alternatively, reactive astrocytes may constitute an obstacle to neuroregeneration by functioning as a physical and/or chemical barrier, or produce cytokines and components of extracellular matrix which can stimulate tumor cell migration and/or proliferation.
  • the regenerative capacity ofthe CNS is extremely limited despite the fact that neural stem cells are present in the CNS throughout life. Both endogenous neural stem cells and neural implants, grafted to replace lost neurons, fail to form functional connections to the extent that would influence the clinical outcome in conditions such as CNS trauma, stroke, or neurodegenerative diseases. The reason for the highly restricted regenerative capacity ofthe mammalian CNS remains unclear.
  • oligodendrocytes have been implicated as inhibitors of CNS regeneration (Chen et al, Nature 403: 434-439, 2001; GrandPre et al., Nature 403: 439-444, 2000; Fournier et al., Nature 409: 341-346, 2001), the role of astrocytes in this process remains incompletely understood.
  • the data available in the literature are contradictory and give a picture of a substantial complexity. Recently, it has been suggested that in the two regions ofthe adult CNS in which new neurons are generated, the dentate gyrus ofthe hippocampus and in the subventricular zone, astrocytes positively control neurogenesis (Song et al., Nature 417: 39- 44, 2002).
  • the present invention generally relates to materials and methods for identifying modulators of neurogenesis and neuroregeneration, and in particular, modulators that stimulate neurogenesis or neuroregeneration or modulate the central nervous system in a mammalian subject to create an environment more permissive or neurogenesis or neuroregeneration.
  • the modulators themselves also are aspects ofthe invention, as are mixtures ofthe modulators; mixtures of modulators with any other neurotropic factors; and compositions comprising the modulators in pharmaceutically acceptable carriers.
  • the invention also provides methods for using said modulators in the treatment or prevention of neurodegenerative diseases and neurological injury including modality which improves migration from the transplantation site, integration and/or survival of neural stem cells or immature neural or glial cells upon their transplantation into brain, retina, or spinal cord as a means of therapy.
  • the invention includes methods of using the modulators to improve cognitive function in any neurological disorder or following any neurological injury or slow the loss of such function due to aging or neurodegenerative disorder such as prion diseases, amyloidoses, Alzheimer's Disease, and the like.
  • the present invention provides a method of screening for a Complement 3 a receptor (C3aR) agonist comprising steps of (a) contacting a composition comprising a C3aR polypeptide in the presence and absence of a test agent; (b) measuring C3aR activation in the presence and absence ofthe test agent; and (c) selecting as a C3aR agonist a test agent that induces C3aR activation.
  • C3aR Complement 3 a receptor
  • the measuring step comprises steps of: (i) measuring binding between the test agent and the C3aR polypeptide; and (ii) measuring C3aR intemalization, wherein a test agent that binds C3aR and induces C3aR intemalization is identified as a C3aR agonist.
  • the measuring step comprises steps of: (i) measuring binding between the test agent and the C3aR polypeptide; and (ii) measuring C3aR signaling, wherein a test agent that binds C3aR and induces C3aR intracellular signaling is identified as a C3aR agonist.
  • a variety of techniques for measuring receptor signaling are described herein and/or known in the art.
  • the contacting step comprises contacting the C3aR polypeptide with a composition comprising a C3a polypeptide, and wherein binding between the test agent and the C3aR is measured by comparing C3a binding to C3aR in the presence and absence ofthe test agent, wherein decreased C3a binding to C3aR in the presence ofthe test agent indicates binding between the test agent and C3aR.
  • Any composition containing the receptor may be suitable for practice ofthe invention.
  • the C3aR is expressed on the surface of cells and preferred compositions include whole cells or membrane fractions ofthe cells, where the receptor is present in a non- denatured form in the membrane.
  • the invention includes a method of screening for a C3a receptor (C3aR) agonist, comprising steps of: (a)contacting a composition comprising a C3aR polypeptide with a composition comprising a C3a polypeptide in the presence and absence of a test agent; (b) measuring and comparing C3a binding to C3aR in the presence and absence ofthe test agent, wherein a test agent that inhibits C3a binding to C3aR is selected as a C3aR binding agent; (c) contacting a C3aR binding agent of step (b) to a cell that expresses C3aR on its surface; and (d) measuring and comparing receptor activation or receptor intemalization in the presence and absence ofthe C3aR binding agent, wherein increased receptor activation or intemalization in the presence of a C3aR binding agent compared to the absence identifies that C3aR binding agent as a C3aR agonist.
  • C3aR C3a receptor
  • the composition comprising C3aR polypeptide comprises a cell expressing the C3aR polypeptide on its surface.
  • the cell is recombinantly modified to express elevated levels of C3aR on its surface.
  • the cell is a cell transformed or transfected with a polynucleotide encoding C3aR and wherein the cell expresses C3aR encoded by the polynucleotide on its surface.
  • the composition comprising C3aR polypeptide comprises isolated cell membranes from cells that express C3aR polypeptide on their surfaces.
  • the contacting step generally comprises contacting a suspension of cell membranes from cells comprising C3aR with C3a and the test agent.
  • the binding between C3a and C3aR is detected by measuring a C3a-induced change to said cell.
  • the C3a-induced change in said cell is selected from the group consisting of a change in intracellular calcium ion concentration, a conversion of GTP to GDP, a change in cAMP concentration, cellular chemotaxis, and H O 2 production.
  • the C3aR polypeptide comprises an amino acid sequence at least 90% identical to the C3aR amino acid sequence selected from the group consisting of SEQ ID NOS: 5-7.
  • the C3a polypeptide comprises an amino acid sequence at least 90% identical to the C3a amino acid sequence selected from the group consisting of SEQ ID NOS: 2-3.
  • the present invention provides a method of screening for a complement 5a receptor (C5aR) agonist comprising the steps of (a) contacting a composition comprising a C5aR polypeptide in the presence and absence of a test agent; (b) measuring C5aR activation in the presence and absence ofthe test agent; and (c) selecting a test agent that induces C5aR activation.
  • C5aR complement 5a receptor
  • Such a measuring step generally comprises the steps of: (i) measuring binding between the test agent and the C5aR polypeptide; and (ii) measuring C5aR intemalization, wherein a test agent that binds C5aR and induces C5aR intemalization is identified as a C5aR agonist.
  • the measuring step comprises the steps of: (i) measuring binding between the test agent and the C5aR polypeptide; and (ii) measuring C5aR signaling, wherein a test agent that binds C5aR and induces C5aR intracellular signaling is identified as a C5aR agonist.
  • the contacting step comprises contacting the C5aR polypeptide with a composition comprising a C5a polypeptide, and wherein binding between the test agent and the C5aR is measured by comparing C5a binding to C5aR in the presence and absence ofthe test agent, wherein decreased C5a binding to C5aR in the presence ofthe test agent indicates binding between the test agent and C5aR.
  • the invention includes a method of screening for a C5a receptor (C5aR) agonist, comprising steps of: (a)contacting a composition comprising a C5aR polypeptide with a composition comprising a C5a polypeptide in the presence and absence of a test agent; (b) measuring and comparing C5a binding to C5aR in the presence and absence ofthe test agent, wherein a test agent that inhibits C5a binding to C5aR is selected as a C5aR binding agent; (c) contacting a C5aR binding agent of step (b) to a cell that expresses C5aR on its surface; and (d) measuring and comparing receptor activation or receptor intemalization in the presence and absence ofthe C5aR binding agent, wherein increased receptor activation or intemalization in the presence of a C5aR binding agent compared to the absence identifies that C5aR binding agent as a C5aR agonist.
  • C5aR C5a receptor
  • the composition comprising C5aR polypeptide comprises a cell expressing the C5aR polypeptide on its surface.
  • the cell is recombinantly modified to express elevated levels of C5aR on its surface.
  • the cell is a cell transformed or transfected with a polynucleotide encoding C5aR and wherein the cell expresses C5aR encoded by the polynucleotide on its surface.
  • the composition comprising C5aR polypeptide comprises isolated cell membranes from cells that express C5aR polypeptide on their surfaces.
  • the contacting step generally comprises contacting a suspension of cell membranes from cells comprising C5aR with C5a and the test agent.
  • the binding between C5a and C5aR is detected by measuring a C5a-induced change to said cell.
  • the C5a-induced change in said cell is selected from the group consisting of a change in intracellular calcium ion concentration, a conversion of GTP to GDP, a change in cAMP concentration, cellular chemotaxis, and H 2 O 2 production,
  • the C5aR polypeptide comprises an amino acid sequence at least 90% identical to the C5aR amino acid sequence selected from the group consisting of SEQ ID NOS: 12-16.
  • the C5a polypeptide comprises an amino acid sequence at least 90% identical to the C5a amino acid sequence selected from the group consisting of SEQ ID NOS: 9-10.
  • the present invention also includes methods of screening for an inhibitor of insulin-like growth factor binding protein 4 (IGFBP-4) comprising the steps of (a) contacting a cell or cell component expressing IGFBP-4 polypeptide in the presence and absence of a test agent; (b) measuring IGFBP-4 expression or activity in the presence and absence ofthe test agent; and (c) selecting a test agent that reduces IGFBP-4 expression or activity.
  • the cell is recombinantly modified to express elevated levels of IGFBP-4 polynucleotide or polypeptide.
  • the cell is transformed or transfected with a polynucleotide encoding IGFBP-4 and wherein the cell expresses IGFBP-4 messenger RNA or polypeptide encoded by the polynucleotide.
  • the IGFBP-4 polypeptide comprises an amino acid sequence at least 90% identical to the IGFBP-4 amino acid sequence selected from the group consisting of SEQ ID NOS: 18-20.
  • the invention includes a method of screening for an inhibitor of insulin-like growth factor binding protein 4 (IGFBP-4) comprising steps of: (a) contacting an IGFBP-4 polypeptide and an IGFBP-4 binding partner in the presence and absence of a test agent; (b) measuring and comparing binding between the IGFBP-4 polypeptide and the binding partner in the presence and absence ofthe test agent; and (c) selecting as an inhibitor a test agent that reduces IGFBP-4 binding to the binding partner.
  • IGFBP-4 binding partner for use in practicing the invention is a naturally occurring binding partner, such as an IGF polypeptide, for which sequences are known in the art and available from public databases such as the GenBank or SwissProt databases.
  • the IGFBP-4 polypeptide comprises: (1) an amino acid sequence at least 90% identical to the IGFBP-4 amino acid sequence selected from the group consisting of SEQ ID NOS: 13-15; or (2) a fragment of (1) that binds to an IGF polypeptide.
  • preferred variations include additional steps to verify that initial lead compounds are effective in cell based or animal (including human) environments.
  • such methods optionally include additional steps of culturing a neuron or neural stem cell or glial cell in the presence and absence ofthe inhibitor of IGFBP-4; measuring and comparing cell growth or survival or differentiation in the presence and absence ofthe inhibitor of IGFBP-4; and selecting an inhibitor of IGFBP-4 that promotes increased survival or growth or differentiation of said neuron or neural stem cell or glial cell.
  • the method further comprises a step of making an IGFBP-4 inhibitor composition comprising the inhibitor of IGFBP-4 and a pharmaceutically acceptable carrier.
  • the method may further comprise administering the IGFBP-4 inhibitor composition to a mammalian subject, and screening for neurological effects ofthe IGFBP-4 inhibitor on the subject.
  • the mammalian subject suffers from a neurological trauma, and wherein the mammalian subject is screened for neurological regeneration at a trauma site.
  • the mammalian subject suffers from neurological degeneration, and the mammalian subject is screened for inliibition ofthe degeneration.
  • the present invention also provides methods of screening for an inhibitor of UNC-51-Like Kinase (ULK) comprising the steps of (a) contacting a cell or cell component expressing ULK polypeptide in the presence and absence of a test agent; (b) measuring ULK expression or activity in the presence and absence ofthe test agent; and (c) selecting a test agent that reduces ULK expression or activity.
  • ULK UNC-51-Like Kinase
  • the cell is recombinantly modified to express elevated levels of ULK polynucleotide or polypeptide.
  • the cell is transformed or transfected with a polynucleotide encoding ULK and wherein the cell expresses ULK messenger RNA or polypeptide encoded by the polynucleotide.
  • the ULK polypeptide comprises an amino acid sequence at least 90% identical to the ULK amino acid sequence selected from the group consisting of SEQ ID NOS: 22-23.
  • the invention also includes a method of selecting an ETBR antagonist that promotes neurogenesis or neuroregeneration comprising steps of culturing a neuron or neural stem cell or glial cell in the presence and absence ofthe ETBR antagonist; measuring and comparing cell growth or survival or differentiation in the presence and absence ofthe ETBR antagonist; and selecting an ETBR antagonist that promotes increased survival or growth or differentiation of said neuron or neural stem cell or glial cell.
  • the methods ofthe invention comprise steps of culturing a neuron or neural stem cell in the presence and absence ofthe agonists or antagonists as set out above; measuring and comparing cell growth or survival or differentiation in the presence and absence ofthe agonist or antagonist; and selecting an agonist or antagonist that promotes increased survival or growth or differentiation of said neuron or neural stem cell.
  • the cell is selected from the group consisting of a hippocampal neuron or neural stem cell, a subventricular neuron or neuron stem cell, a cortical neuron or neuron stem cell, and a neuroblastoma cell.
  • the invention also includes methods of making compositions comprising the agonists or antagonists and pharmaceutically acceptable carriers.
  • compositions may also include the use of at least one additional factor which promotes neurogenesis or neuroregeneration selected from the group consisting of: NGF, BDNF, NT-3, 4, 5, or 6, CNTF, IGFI, IGFII, GDNF, GPA, bFGF, TGFB, and apolipoprotein E.
  • the invention includes administering the agonist or antagonist compositions to a mammalian subject, and screening for neurological effects ofthe agonist or antagonist on the subject.
  • the mammalian subject suffers from a neurological trauma and is screened for neurological regeneration at a trauma site.
  • the mammalian subject suffers from neurological degeneration and is screened for inhibition of the degeneration.
  • a mammalian subject is treated with a therapeutically effective amount of a modulator, which is an amount that is sufficient to induce a desired response in the treated subject.
  • a biologically or therapeutically effective amount of a modulator may be the amount that interferes with physiological activity ofthe treated mammal in a non-lethal manner.
  • a preferred modulator for use in the treatment methods is an agonist of C3aR, C5aR, or an antagonist of ETBR.
  • Another preferred modulator for use in the treatment methods is an inhibitor of IGFBP-4 or ULK expression or activity.
  • the invention is not limited to particular means for delivering the modulator to a mammal, nor is the invention limited as to the compositions comprising the modulator which may be delivered.
  • Modulators are identified as test compounds that alter, i.e., increase (agonist) or decrease (antagonist), a receptor function, such as a binding property of a receptor or an activity such as G protein-mediated signal transduction or membrane localization.
  • the composition may contain an isolated receptor; alternatively, the composition may contain a receptor in association with, e.g., an intact cell or cell portion, such as a membrane.
  • the methods ofthe invention embrace ligands that are attached to a label, such as a radiolabel (e.g., I, S, P, P, H), a fluorescence label, a chemiluminescence label, an enzymatic label and an immunogenic label.
  • assays may take the form of an ion flux assay, a yeast growth assay, a non-hydrolyzable GTP assay such as a [35S]-GTP ⁇ S assay, a cAMP assay, an inositol triphosphate assay, a diacylglycerol assay, a luciferase assay, a FLIPR assay for intracellular Ca2+ concentration, a mitogenesis assay, an ELISA, as well as other binding or function-based assays that are generally known in the art.
  • a non-hydrolyzable GTP assay such as a [35S]-GTP ⁇ S assay, a cAMP assay, an inositol triphosphate assay, a diacylglycerol assay, a luciferase assay, a FLIPR assay for intracellular Ca2+ concentration, a mitogenesis assay, an ELISA, as well as other binding or function
  • modulators of receptor activity may be identified as compounds that interfere with the expression of a receptor, either through inhibiting transcription ofthe DNA or translation ofthe corresponding mRNA.
  • Expression ofthe receptor can be monitored by any methods known in the art, including Western blot analysis using polyclonal or monoclonal antibodies to the receptor or Northern blot analysis or quantitative polymerase chain reaction (PCR) using suitable probes or primers based on the sequence ofthe receptor gene.
  • agents that interfere with the expression of gene products include anti- sense polynucleotides and ribozymes that are complementary to the gene sequences.
  • the invention further embraces methods to modulate transcription of gene products ofthe invention through use of oligonucleotide-directed triplet helix formation.
  • An additional aspect ofthe invention includes any compound or composition identified according to methods ofthe invention as a compound that stimulates neurogenesis or neuroregeneration. To the extent any such compound is already described in the literature, the invention nonetheless includes compositions comprising the compound as well as uses of the compound or compositions for therapeutic and prophylactic purposes described herein. Preferred compositions include the compound mixed with a pharmaceutically acceptable carrier, and or mixed with any other neural growth factor or other factor identified according to the invention as beneficial for neurogenesis or neuroregeneration. . Thus, the invention includes use of a C3aR agonist or a C5aR agonist in the manufacture of a medicament for the treatment or prevention of a neurological degeneration in a mammalian subject.
  • the invention also includes use of a C3aR agonist or a C5aR agonist in the manufacture of a medicament for the treatment of a neurological injury or trauma in a mammalian subject.
  • the invention includes a method of inhibiting neuronal degeneration comprising administering to a mammalian subject at risk for neuronal degeneration an agent selected from the group consisting of a C3aR agonist, a C5aR agonist, and combinations thereof.
  • the invention similarly includes a method of improving cognitive function or slowing loss of cognitive function comprising administering to a mammalian subject an agent selected from the group consisting of a C3aR agonist, a C5aR agonist, and combinations thereof.
  • the invention includes use of an IGFBP-4 antagonist, a ULK antagonist, or an ETBR antagonist in the manufacture of a medicament for the treatment or prevention of a neurological degeneration in a mammalian subject.
  • the invention further includes use of an IGFBP-4 antagonist, a ULK antagonist, or an ETBR antagonist in the manufacture of a medicament for the treatment of a neurological injury or trauma in a mammalian subject.
  • the invention provides a method of inhibiting neuronal degeneration comprising administering to a mammalian subject at risk for neuronal degeneration an agent selected from the group consisting of an IGFBP-4 antagonist, a ULK antagonist, an ETBR antagonist, and combinations thereof.
  • the invention includes a method of improving cognitive function or slowing loss of cognitive function comprising administering to a mammalian subject an agent selected from the group consisting of an IGFBP-4 antagonist, a ULK antagonist, an ETBR antagonist, and combinations thereof.
  • an agent selected from the group consisting of an IGFBP-4 antagonist, a ULK antagonist, an ETBR antagonist, and combinations thereof.
  • the invention also includes a variety of inhibitors that can be manufactured using known molecular biological techniques, based on knowledge ofthe protein, gene, cDNA, or mRNA structure of various targets described herein.
  • the invention includes antagonists such as the following (alone or in combination with each other): (a) antibody substances that bind to IGFBP-4, ULK, and ETBR; (b) antisense oligonucleotides that hybridize to IGFBP-4, ULK, or ETBR genomic DNA or mRNA and inhibit expression of IGFBP-4, ULK, or ETBR; (c) interfering RNA molecules that inhibit expression of IGFBP-4, ULK, or ETBR; and (d) aptamers that inhibit expression of IGFBP-4, ULK, or ETBR.
  • agonist antibody substances are contemplated as aspects ofthe invention. All ofthe foregoing modulators are useful for practicing the therapeutic methods ofthe invention.
  • the invention includes, as an additional aspect, all embodiments ofthe invention narrower in scope in any way than the variations specifically described herein.
  • the applicant(s) invented the full scope ofthe claims appended hereto, the claims appended hereto are not intended to encompass within their scope the prior art work of others. Therefore, in the event that statutory prior art within the scope of a claim is brought to the attention ofthe applicants by a Patent Office or other entity or individual, the applicant(s) reserve the right to exercise amendment rights under applicable patent laws to redefine the subject matter of such a claim to specifically exclude such statutory prior art or obvious variations of statutory prior art from the scope of such a claim. Variations ofthe invention defined by such amended claims also are intended as aspects ofthe invention.
  • the present invention includes materials and methods for screening for agents to regulate or manipulate neuroregeneration and neurogenesis.
  • the present invention also involves use of these agents in the treatment of neurodegenerative diseases and neurological injury.
  • DNA array technology was used to compare the gene expression profiles of wild-type mice (standard, regeneration-inhibiting) and GFAP -/- Vimentin -/- mice (regeneration- supporting model) to identify candidate genes to target to modulate in neurogenesis and neuroregeneration in the adult CNS. These molecular targets are useful to derive agents to promote neurogenesis and neuroregeneration. The same targets also may be useful to screen for agents to inhibit growth of CNS tumors.
  • agent that induces C3aR activation refers to any molecule or molecules (e.g., nucleic acid, peptide, polypeptide, binding agent, antibody, peptibody, small molecule, etc.) which can act directly or indirectly to upregulate expression or signaling of the C3aR polypeptide.
  • the term also encompasses agonists and other modulators which induce, stimulate, or enhance C3aR expression or signaling in cells that express C3aR.
  • agent that induces C5aR activation refers to any molecule or molecules (e.g., nucleic acid, peptide, polypeptide, binding agent, antibody, peptibody, small molecule, etc.) which can act directly or indirectly to upregulate expression or signaling of the C5aR polypeptide.
  • the term also encompasses agonists and other modulators which induce, stimulate, or enhance C5aR expression or signaling in cells that express C5aR.
  • agent that reduces IGFBP-4 expression or activity refers to any molecule or molecules (e.g., nucleic acid, peptide, polypeptide, binding agent, antibody, peptibody, small molecule, etc.) which can act directly or indirectly to downregulate or inhibit expression or activity ofthe IGFBP-4 polypeptide.
  • the term also encompasses antagonists and other modulators which reduce, inhibit, or decrease IGFBP-4 expression or activity.
  • agent that reduces ULK expression or activity refers to any molecule or molecules (e.g., nucleic acid, peptide, polypeptide, binding agent, antibody, peptibody, small molecule, etc.) which can act directly or indirectly to downregulate or inhibit expression or activity ofthe ULK polypeptide.
  • the term also encompasses antagonists and other modulators which reduce, inhibit, or decrease ULK expression or activity.
  • agent that reduces ETBR activation refers to any molecule or molecules (e.g., nucleic acid, peptide, polypeptide, binding agent, antibody, peptibody, small molecule, etc.) which can act directly or indirectly to downregulate or inhibit expression or signaling ofthe ETBR polypeptide.
  • nucleic acid construct refers to any nucleic acid molecule or molecules such as an isolated cDNA or genomic DNA protein encoding polynucleotide alone or in conjunction with a vector, promoter, enhancer, terminator, etc. This term includes, but is not limited to, DNA, RNA, oligonucleotides, including upstream and downstream regulators of nucleic acid expression.
  • therapeutically effective amount in the context of neurological diseases or conditions described herein refers to an amount effective to achieve measurable improvement (compared to an untreated control) as assessed by any relevant medical parameter used to evaluate subjects receiving treatment for the disease or condition.
  • expression vector refers to a vector which (when transformed or transfected into a suitable host cell) contains nucleic acid sequences which direct and/or control the expression, transcription, and/or translation of heterologous nucleic acid sequences that are inserted into the vector.
  • host cell is used to refer to a cell which has been transformed or transfected, or is capable of being transformed or transfected, with a nucleic acid. The term also includes the transgenic progeny ofthe transformed or transfected cell, whether or not the progeny is identical in morphology or in genetic make-up to the original parent.
  • pharmaceutically acceptable carrier refers to one or more formulation materials suitable for accomplishing or enhancing the delivery of a substance (as a pharmaceutical composition) to a mammalian (preferably a human) subject.
  • selective binding agent refers to a molecule or molecules having binding specificity for a selected target.
  • specific binding refers to the ability to bind to a target such as a polypeptide in vivo and no significantly cross-react with other molecules (e.g. other polypeptides in vivo).
  • Selective binding agents may also bind orthologs (species homologs) ofthe specifically identified polypeptides.
  • transduction is used to refer to the transfer of genes from one bacterium to another, usually by a phage.
  • Transduction also refers to the acquisition and transfer of eukaryotic cellular sequences by retroviruses.
  • transfection is used to refer to the uptake of foreign or exogenous DNA by a cell, and a cell has been "transfected" when the exogenous DNA has been introduced inside the cell membrane. A number of transfection techniques are well known in the art and are disclosed herein.
  • transformation refers to a change in a cell's genetic characteristics, and a cell has been transformed when it has been modified to contain new DNA. For example, a cell is transformed where it is genetically modified from its native state.
  • the transforming DNA may recombine with that ofthe cell by physically integrating into a chromosome ofthe cell, it may be maintained transiently as an episomal element without being replicated, or it may replicate independently as a plasmid.
  • a cell is considered to have been stably transformed when the DNA is replicated with the division ofthe cell.
  • vector is used to refer to any molecule (e.g. , nucleic acid, plasmid, or virus) used to transfer coding information to a host cell.
  • central nervous system or "CNS” includes the brain, spinal cord, and retina.
  • neurological regeneration includes CNS regeneration or neuroregeneration and refers to one of several types of events that lead to functional improvement ofthe CNS.
  • CNS improvement can manifest itself as an improvement, stabilization, or slowed-down deterioration of functions such as cognition, vision, etc.
  • the cellular basis for neuroregeneration can be e.g. increased proliferation (or slower death) of neural stem cells; generation of new neurons and/or glial cells (referred to as neurogenesis and gliogenesis, respectively); formation of new, or stabilization ofthe existing, neuronal synapses (synaptic regeneration); or re-growth of severed axons (axonal regeneration).
  • neurodegenerative disease includes CNS trauma and refers to one of several types of physical or pathological events including ischemic and hypoxic damage, toxic damage, and damage connected with a metabolic impairment (e.g. diabetes and diabetic retinopathy).
  • neurodegenerative diseases and disorders including e.g. Alzheimer's disease, Parkinson's disease, multiple sclerosis, Jacob-Creutzfelt's disease and other prion diseases), epilepsy, and aging.
  • A. C3aR and C5aR as Targets for Modulating Neurogenesis and Neuroregeneration includes a method of screening for complement 3 a receptor (C3aR) or complement 5 a receptor (C5aR) modulators to identify molecules useful to modulate neurogenesis and neuroregeneration and for using said modulators in the treatment of neurodegenerative diseases and neurological injury including modality, which improves migration from the transplantation site, integration and/or survival of neural stem cells, or immature neural or glial cells, upon their transplantation into the CNS as a means of therapy.
  • Complement a component ofthe humoral immune system, is involved in inflammation, opsonization, and cytolysis.
  • the complement cascade can be activated via the classical, lectin, or alternative pathway, resulting in the formation of C3-convertase, an enzymatic complex that activates the central molecule ofthe cascade, the third component, C3.
  • C3a The proteolytic activation of C3 generates C3a, a small fragment with anaphylatoxic properties, and C3b, a larger fragment that binds to an activating surface and triggers the terminal part of the cascade, culminating in the assembly ofthe terminal complement complex on the target surface and generating the most powerful complement-derived anapyhlatoxin, C5a.
  • the complement system has recently been proposed to participate in tissue regeneration in several different systems. Hippocampal and cortical neurons have also been shown to express receptors for complement fragments C3a and C5a (Davoust et al., Glia 26:201-211, 1999; O'Barr et al., J Immunol. 166:4154-4162, 2001.
  • C3aR and C5aR used immunohistochemistry and polyclonal antibodies against C3aR and C5aR on neural stem cells in vitro and in vivo (sections of mouse brain containing the main neurogenic zone (subventricular of lateral ventricles), and in a focal brain ischemia model in mice deficient in C3 (C3-/-) Pekna et al., Scan. J. Immunol. 47:25-29, 1998), to find that C3-/- mice had 30- 50% fewer neural progenitor cells and 25% fewer newly formed neurons in the prenumbra than controls, and larger infarct volumes.
  • C3-/- mice also had 24% fewer migrating neural progenitor cells in the subventricular zone (the main source of progenitor cells in the adult brain). These findings suggested that the complement system promotes neuroregeneration after cerebral ischemia. Therefore, the present invention contemplates the use of C3aR and C5aR agonists to stimulate neurogenesis or neuroregeneration and provides methods of screening for C3aR and C5aR agonists. Exemplary nucleotide and amino acid sequences for C3a, C5a, C3aR, and C5aR are set forth in the sequence listing and in Table 1 as summarized below: TABLE 1: C3A AND C3AR SEQUENCES
  • IGFBP-4 as a Target for Modulating Neurogenesis and Neuroregeneration
  • IGFBP-4 belongs to a family of six secreted IGF binding proteins. They all have similar domain organizations but differ in their ability to adhere to cellular surfaces and to their effect in the IGF regulating system.
  • IGF-I and IGF-II are two growth promoting peptides that have been shown to improve survival and growth of various cell types including neurons (Zhou et al., Endocrinol. 178:177-193, 2003).
  • IGF-I and IGF-II exert their functions through binding to the cellular receptors IGF-RII and IGF-RII, which are two transmembrane proteins with tyrosine kinase activity (Zhou et al., 2003, supra).
  • IGF-I and IGF-II in the extracellular environment are transported by IGF binding proteins.
  • the affinity between IGFs and IGF binding protein is always equal to or greater than IGF's affinity for its cellular receptors. The affinity is decreased and thereby regulated through phosphorylation, glycosylation, proteolysis or adherence to cell surface or extracellular matrix. This leads to local increase in IGF bioavailability (Zhou et al., 2003, supra).
  • IGFBP-4 is the smallest ofthe IGF binding proteins. IGFBP-4 exists in biological fluid as a doublet with a molecular weight of 24 kDa in its non-glycosylated form and 28 kDa in its glycosylated form (Zhou et al., 2003, supra). IGFBP-4 binds equally to IGF-I and IGF-II and it has solely shown inhibitory effects on the IGF system. IGFBP-4 binding to IGF makes IGFBP-4 a substrate for the protease PAPP-A. Upon a single site cleavage with PAPP-A, IGF is released to the local environment.
  • IGFBP-4 Because PAPP-A reversibly adheres to several different cell types, IGFBP-4's effect could be locally directed (Zhou et al., 2003, supra).
  • the genetic expression of IGFBP-4 is thought to be developmentally regulated and its expression has been shown to be regulated by hormones and cytokines in a tissue specific manner (Zhou et al., 2003, supra).
  • astrocytes hi the hippocampus ofthe uninjured control mouse brain, astrocytes were found to be highly positive for IGFBP-4.
  • reactive astrocytes were found to be highly positive for IGFBP-4.
  • IGFBP-4 anti-reactive astrocytes in GFAP-/-vim-/- (knockout) mice, that exhibit a regeneration-permissive environment. Therefore, the present invention contemplates the use of IGFBP-4 antagonists to stimulate neurogenesis or neuroregeneration and provides methods of screening for IGFBP-4 antagonists.
  • Exemplary nucleotide and amino acid sequences for IGFBP-4 are set forth in the sequence listing and in Table 2 as summarized below: TABLE 2: IGFBP-4 SEQUENCES
  • ULK ' UNC-51 -Like Kinase (ULK ' ) as a Target for Modulating Neuro enesis and Neuroregeneration ULKl has been shown to be involved in axonal elongation (Tomoda, Neuron
  • ULK and GABA-A receptor associated protein
  • the present invention contemplates the use of ULK antagonists to stimulate neurogenesis or neuroregeneration and provides methods of screening for ULK antagonists.
  • Exemplary nucleotide and amino acid sequences for ULK are set forth in the sequence listing and in Table 3 as summarized below: TABLE 3: ULK SEQUENCES
  • EBR Endothelin Receptor B
  • Endothelin receptor B belongs to a family of receptors that bind the endothelin peptides I, II, and III. ETBR is normally highly expressed by reactive astrocytes and weakly by endothelial cells (Ishikawa et al, Eur. J. Neurosci. 9:895-901, 1997; Baba, Life Sci. 62:1711-1715, 1998; Koyama et al., Glia 26:268-271, 1999; Peters et al., Exp. Neurol, 180:1-13, 2003).
  • ETBR antagonists with diversified specificity for the ETB and ETA receptors are known, such as those described in patent publications DE19858779, WO9911629, WO9857938, WO9711942, US5866568, and EP0562599, all incorporated herein by reference in their entireties.
  • Expression of ETBR was examined in GFAP-/-Nim-/- knockout mice (Wilhelmsson et al, J Neuroscience (in press), 2004).
  • Perfused brains were postfixed for one day at 4 C in paraformaldehyde and horizontal vibratome sections (50 ⁇ m) were made from the hippocampus, and stored in a cryoprotectant (50% 0.05M sodium phosphate, pH 7.3, 30% ethylene glycol, 20% glycerol) at -20 C. After several washes in PBS, the sections were incubated in 0.05% glycine in PBS for 1 h at room temperature and permeabilized overnight in PBS containing 0.5% Tween 20 and 1% BSA at 4° C.
  • a cryoprotectant 50% 0.05M sodium phosphate, pH 7.3, 30% ethylene glycol, 20% glycerol
  • Rabbit anti-ETBR antibody (Alomone Labs Ltd, Jerusalem, Israel), and mouse anti-GFAP antibody (clone GA5, Sigma-Aldrich), both diluted 1:100, followed by Alexa 488-conjugated anti-rabbit and Alexa 568-conjugated anti-mouse antibodies (Molecular Probes), both diluted 1 :500, were used for immunohistochemical staining.
  • ETBR protein was undetectable on reactive astrocytes, while very abundant on reactive astrocytes of normal mice (Wilhelmsson et al., 2004, supra).
  • ETBR was present on endothelial cells in both wild-type and knockout mice.
  • ETBR upregulation or activation of ETBR in reactive astrocytes requires an intermediate filament network, and in the absence of ETBR upregulation or activation, there is improved post- traumatic regeneration (Wilhelmsson et al., 2004, supra). Therefore, the present invention contemplates the use of ETBR antagonists to stimulate neurogenesis or neuroregeneration, and provides methods for identifying such antagonists.
  • Exemplary nucleotide and amino acid sequences for ETBR are set forth in the sequence listing and in Table 4 as summarized below: TABLE 4: ETBR SEQUENCES
  • C3aR C3a receptor
  • C5aR C5a receptor
  • ETBR endothelin receptor B
  • C3aR and C5aR are receptors for the chemotactic and anaphylactic peptides, C3a and C5a, which are mediators of complement inflammatory functions.
  • ETBR belongs to a family of receptors that bind the endothelin peptides I, II, and III.
  • Assays contemplated by the invention include both binding assays and activity assays; these assays may be performed in conventional or high throughput formats.
  • Modulator screens are designed to identify stimulatory and inhibitory agents.
  • the sources for potential agents to be screened include natural sources, such as a cell extract (e.g., invertebrate cells including, but not limited to, bacterial, fungal, algal, and plant cells) and synthetic sources, such as chemical compound libraries or biological libraries such as antibody substance or peptide libraries.
  • Agents are screened for the ability to either stimulate or inhibit the activity.
  • Binding assays are used to detect receptor binding activity to ligands. Both functional and binding assays of receptor activity are readily adapted to screens for modulators such as agonist (stimulatory) and antagonist (inhibitory) compounds.
  • the invention contemplates a multitude of assays to screen and identify modulators, such as agonists and antagonists, of ligand binding to receptors.
  • the receptor is immobilized and interaction with a binding partner is assessed in the presence and absence of a candidate modulator.
  • the binding partner is immobilized and the receptor is solubilized.
  • interaction between the receptor and its binding partner is assessed in a solution assay, both in the presence and absence of a candidate modulator.
  • An antagonist is identified as a compound that decreases binding between the receptor and its binding partner and/or decreases receptor signaling, while an agonist is identified as a compound that increases binding between the receptor and its binding partner and/or promotes receptor signaling.
  • Another contemplated assay involves a variation ofthe di-hybrid assay wherein a modulator of protein/protein interactions is identified by detection of a positive signal in a transformed or transfected host cell.
  • Candidate modulators for screening according to contemplated by the invention include any chemical compounds, including libraries of chemical compounds. There are a number of different libraries used for the identification of small molecule modulators, including: (1) chemical libraries, (2) natural product libraries, and (3) combinatorial libraries comprised of random peptides, oligonucleotides or organic molecules.
  • Natural product libraries consist of random chemical structures, or analogs of known compounds, or analogs of compounds that have been identified as “hits” or “leads” in prior drug discovery screens, some of which may be derived from natural products or from non-directed synthetic organic chemistry.
  • Natural product libraries are collections of microorganisms, animals, plants, or marine organisms which are used to create mixtures for screening by: (1) fermentation and extraction of broths from soil, plant or marine microorganisms or (2) extraction of plants or marine organisms. Natural product libraries include polyketides, non- ribosomal peptides, and variants (non-naturally occurring) thereof. For a review, see Science 282:63-68 (1998).
  • Combinatorial libraries are composed of large numbers of peptides, oligonucleotides, or organic compounds as a mixture. These libraries are relatively easy to prepare by traditional automated synthesis methods, PCR, cloning, or synthetic methods. Of particular interest are non-peptide combinatorial libraries. Still other libraries of interest include peptide, protein, peptidomimetic, multiparallel synthetic collection, recombinatorial, and polypeptide libraries. For a review of combinatorial chemistry and libraries created therefrom, see Myers, Curr. Opin. Biotechnol. 8:701-707 (1997).
  • Candidate modulators contemplated by the invention can be designed and include soluble forms of binding partners, as well as chimeric, or fusion, proteins thereof.
  • binding partner broadly encompasses non-peptide modulators, peptide modulators (e.g., neuropeptide variants), antibodies (including monoclonal and polyclonal antibodies, single chain antibodies, chimeric antibodies, bifunctional/bispecific antibodies, humanized antibodies, human antibodies, and complementary determining region (CDR)- grafted antibodies, including compounds which include CDR and/or antigen-binding sequences, which specifically recognize a polypeptide ofthe invention), antibody fragments, and modified compounds comprising antibody domains that are immunospecific for the expression product ofthe identified GPCR-like gene.
  • CDR complementary determining region
  • Such assays are useful, for example, in methods of identifying candidate modulators described herein, or in methods for identifying specific ligands of a receptor.
  • Assays that measure binding or interaction of compounds with target proteins include assays that identify compounds that inhibit unfolding or denaturation of a target protein, assays that separate compounds that bind to target proteins through affinity ultrafiltration followed by ion spray mass spectroscopy/HPLC methods or other physical and analytical methods, capillary electrophoresis assays and two-hybrid assays.
  • One such screening method to identify direct binding of test ligands to a target protein is described in U.S. Patent No. 5,585,277, incorporated herein by reference.
  • This method relies on the principle that proteins generally exist as a mixture of folded and unfolded states, and continually alternate between the two states.
  • a test ligand binds to the folded form of a target protein (i.e., when the test ligand is a ligand ofthe target protein)
  • the target protein molecule bound by the ligand remains in its folded state.
  • the folded target protein is present to a greater extent in the presence of a test ligand which binds the target protein, than in the absence of a ligand.
  • Binding ofthe ligand to the target protein can be determined by any method which distinguishes between the folded and unfolded states of the target protein.
  • the function ofthe target protein need not be known in order for this assay to be performed.
  • Virtually any agent can be assessed by this method as a test ligand, including, but not limited to, metals, polypeptides, proteins, lipids, polysaccharides, polynucleotides and small organic molecules.
  • Another method for identifying ligands of a target protein is described in Wieboldt et al., Anal. Chem., 69:1683-1691 (1997), incorporated herein by reference. This technique screens combinatorial libraries of 20-30 agents at a time in solution phase for binding to the target protein. Agents that bind to the target protein are separated from other library components by simple membrane washing.
  • the specifically selected molecules that are retained on the filter are subsequently liberated from the target protein and analyzed by HPLC and pneumatically assisted electrospray (ion spray) ionization mass spectroscopy.
  • This procedure selects library components with the greatest affinity for the target protein, and is particularly useful for small molecule libraries.
  • binding interactions are evaluated indirectly using the yeast two-hybrid system described in Fields et al., Nature, 340:245-246 (1989), and Fields et al., Trends in Genetics, 10:286-292 (1994), both of which are incorporated herein by reference.
  • the two-hybrid system is a genetic assay for detecting interactions between two proteins or polypeptides.
  • the two-hybrid system exploits the ability of a pair of interacting proteins to bring a transcription activation domain into close proximity with a DNA binding domain that binds to an upstream activation sequence (UAS) of a reporter gene, and is generally performed in yeast.
  • UAS upstream activation sequence
  • the assay requires the construction of two hybrid genes encoding (1) a DNA-binding domain that is fused to a first protein and (2) an activation domain fused to a second protein.
  • the DNA-binding domain targets the first hybrid protein to the UAS ofthe reporter gene; however, because most proteins lack an activation domain, this DNA-binding hybrid protein does not activate transcription ofthe reporter gene.
  • the second hybrid protein which contains the activation domain, cannot by itself activate expression ofthe reporter gene because it does not bind the UAS. However, when both hybrid proteins are present, the noncovalent interaction ofthe first and second proteins tethers the activation domain to the UAS, activating transcription of the reporter gene.
  • the yeast two-hybrid assay can be used to identify proteins that bind to the receptor.
  • a fusion polynucleotide encoding both a receptor or fragment (i.e., a first protein) and a UAS binding domain may be used.
  • a large number of hybrid genes each encoding a different second protein fused to an activation domain are produced and screened in the assay.
  • the second protein is encoded by one or more members of a total cDNA or genomic DNA fusion library, with each second protein coding region being fused to the activation domain. This system is applicable to a wide variety of proteins, and it is not even necessary to know the identity or function ofthe second binding protein.
  • the system is highly sensitive and can detect interactions not revealed by other methods; even transient interactions may trigger transcription to produce a stable mRNA that can be repeatedly translated to yield the reporter protein.
  • the receptor or fragment thereof is known to interact with another protein or nucleic acid
  • the two-hybrid assay can be used to detect agents that interfere with the binding interaction. Expression ofthe reporter gene is monitored as different test agents are added to the system. The presence of an inhibitory agent, for example, results in lack of or reduction in a reporter signal. 1.
  • Antibodies to Receptors as Modulators of Binding Standard techniques are employed to generate polyclonal or monoclonal antibodies to receptors, and to generate useful antigen-binding fragments thereof or variants thereof.
  • the antigen may be mixed with an adjuvant or linked to a hapten to increase antibody production.
  • Polyclonal and monoclonal antibodies, chimeric (e.g., humanized) antibodies, fragments of antibodies, and all other forms of antibody molecules disclosed herein are referred to collectively as antibody products.
  • a. Polyclonal or Monoclonal Antibodies As one exemplary protocol, a recombinant polypeptide or a synthetic fragment thereof is used to immunize a mouse for generation of monoclonal antibodies (or larger mammal, such as a rabbit, for polyclonal antibodies). To increase antigenicity, peptides are conjugated to Keyhole Lympet Hemocyanin (Pierce), according to the manufacturer's recommendations.
  • the antigen is emulsified with Freund's Complete Adjuvant and injected subcutaneously. At intervals of two to three weeks, additional aliquots of receptor antigen are emulsified with Freund's Incomplete Adjuvant and injected subcutaneously.
  • a serum sample is taken from the immunized mice and assayed by Western blot to confirm the presence of antibodies that immunoreact with a polypeptide. Serum from the immunized animals may be used as a polyclonal antisera or used to isolate polyclonal antibodies that recognize a receptor. Alternatively, the mice are sacrificed and their spleens are removed for generation of monoclonal antibodies. To generate monoclonal antibodies, the spleens are placed in 10 ml serum- free
  • RPMI 1640 and single-cell suspensions are formed by grinding the spleens in serum-free RPMI 1640, supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 100 Units/ml penicillin, and 100 ⁇ g/ml streptomycin (RPMI) (Gibco, Canada). The cell suspensions are filtered and washed by centrifugation and resuspended in serum-free RPMI. Thymocytes taken from three naive Balb/c mice are prepared in a similar manner and used as a Feeder Layer.
  • NS-1 myeloma cells kept in log phase in RPMI with 10% (FBS (Hyclone Laboratories, Inc., Logan, Utah) for three days prior to fusion, are centrifuged and washed as well.
  • FBS Hyclone Laboratories, Inc., Logan, Utah
  • spleen cells from the immunized mice are combined with NS-1 cells and centrifuged, and the supernatant is aspirated.
  • the cell pellet is dislodged by tapping the tube, and 2 ml of 37°C PEG 1500 (50% in 75 mM HEPES, pH 8.0) (Boehringer-Mannheim) is stirred into the pellet, followed by the addition of serum-free RPMI.
  • the cells are centrifuged and resuspended in RPMI containing 15% FBS, 100 ⁇ M sodium hypoxanthine, 0.4 ⁇ M aminopterin, 16 ⁇ M thymidine (HAT) (Gibco), 25 Units/ml IL-6 (Boehringer-Mannheim) and 1.5 x 106 thymocytes/ml and plated into 10 Corning flat-bottom 96-well tissue culture plates (Corning, Corning New York). On days 2, 4, and 6 after the fusion, 100 ⁇ l of medium is removed from the wells ofthe fusion plates and replaced with fresh medium.
  • Receptor-Neutralizing Antibodies from Phage Display Receptor-neutralizing antibodies are generated by phage display techniques such as those described in Aujame et al., Human Antibodies, 8(4):155-168 (1997); Hoogenboom, TIBTECH, 15:62-70 (1997); and Rader et al., Curr. Opin. Biotechnol, 8:503- 508 (1997), all of which are incorporated by reference.
  • antibody variable regions in the form of Fab fragments or linked single chain Fv fragments are fused to the amino terminus of filamentous phage minor coat protein pTfl. Expression ofthe fusion protein and incorporation thereof into the mature phage coat results in phage particles that present an antibody on their surface and contain the genetic material encoding the antibody.
  • a phage library comprising such constructs is expressed in bacteria, and the library is screened for target-specific phage-antibodies using a labeled or immobilized target peptide or polypeptide as antigen-probe. c.
  • Receptor-Neutralizing Antibodies from Transgenic Animals Receptor-neutralizing antibodies are generated in transgenic animals, such as mice, essentially as described in Braggemann et al., Immunol. Today 17(8):391-97 (1996) and Braggemann et al., Curr. Opin. Biotechnol. 8:455-58 (1997).
  • Transgenic mice carrying V-gene segments in germline configuration, and expressing the transgenes in their lymphoid tissue are immunized with a polypeptide composition using conventional immunization protocols.
  • Hybridomas are generated from B cells ofthe immunized mice using conventional protocols and screened to identify hybridomas secreting anti-receptor antibodies (e.g., as described above). 2.
  • HTS high throughput screening
  • the first approach involves measuring the binding of a known ligand, preferably labeled with a radiolabel, to a preparation that contains the receptor, either found in native tissue or based on expression ofthe gene encoding the receptor, typically in a heterologous system.
  • the recombinant system involves the expression of a recombinant receptor.
  • HTS binding screens It is also possible to screen for novel neuroregeneration compounds with radiolabeled ligands in HTS binding screens (Geary et al., 1999). Other reasons that recombinant receptors are preferred for HTS binding assays include better specificity (higher relative purity) and ability to generate large amounts of receptor material (see Hodgson, Bio/Technology 10:973-980 (1992)).
  • heterologous systems are available for expression of recombinant receptors and are well known to those skilled in the art. Such systems include bacteria (Sfrosberg et al., Trends in Pharm. Sci. 13:95-98 (1992)), yeast (Pausch, Trends in Biotech.
  • a receptor expressed in one ofthe described recombinant systems can be used for HTS binding assays in conjunction with its defined ligand.
  • the identified peptide is labeled with a suitable radioisotope, including, but not limited to, 125 I (preferred; see Geary et al., 1999), 3 H, 35 S or 32 P, by methods that are well known to those skilled in the art.
  • the peptides may be labeled by well-known methods with a suitable fluorescent label (Baindur et al., DrugDev. Res. 33:373-398 (1994); Rogers, Drug Disc. Today 2:156- 160 (1997)).
  • Radioactive ligand specifically bound to the receptor in membrane preparations made from cells expressing the recombinant protein can be detected in HTS assays in one of several standard ways, including filtration ofthe receptor-ligand complex to separate bound ligand from unbound ligand (Williams, 1991; Sweetnam et al., 1993).
  • Alternative methods include a scintillation proximity assay (SPA) or a FlashPlate format in which such separation is unnecessary (Nakayama et al., Drug Disc.
  • SPA scintillation proximity assay
  • FlashPlate format in which such separation is unnecessary
  • Binding of fluorescent ligands can be detected in various ways, including fluorescence energy transfer (FRET), direct spectrophotofluorometric analysis of bound ligand, or fluorescence polarization (see Rogers, 1997; Hill, Curr. Opin. Drug Disc. & Dev. 1:92-97 (1998)).
  • FRET fluorescence energy transfer
  • Activation of heterologous G-protein-coupled receptors expressed in recombinant systems results in a variety of biological responses, which are typically mediated by G proteins expressed in the host cells.
  • Agonist binding to a GPCR results in exchange of bound GDP for GTP at a binding site on the G subunit; one can use a radioactive, non- hydrolyzable derivative of GTP, such as [ 35 S]GTP ⁇ S, to measure binding of an agonist to the receptor. (Seifert et al., Eur. J. Biochem. 255:369-382 (1998).) One can also use this binding to measure the ability of antagonists to bind to the receptor by decreasing binding of GTP [ S] in the presence of a known agonist.
  • the G proteins required for functional expression of heterologous GPCRs can be native constituents ofthe host cell or can be introduced through well-known recombinant technology. The G proteins can be intact or chimeric.
  • G protein activation results in the stimulation or inhibition of other native proteins, events that can be linked to a measurable response.
  • biological responses include, but are not limited to, the following responses: the ability to survive in the absence of a limiting nutrient in specifically engineered yeast cells (Pausch, 1997); changes in intracellular Ca2+ concentration as measured by fluorescent dyes (Murphy et al., Curr. Opin. Drug Disc. &Dev. 1:192-199 (1998)).
  • Fluorescence changes can also be used to monitor ligand-induced changes in membrane potential or intracellular pH; an automated system suitable for HTS has been described for these purposes (Schroeder et al., J. Biomol. Screening 1:75-80 (1996)).
  • Melanophores prepared from Xenopus laevis show a ligand-dependent change in pigment organization in response to heterologous GPCR activation; this response is adaptable to HTS formats (Jayawickreme et al., 1997).
  • Assays are also available for the measurement of common second messengers, including cAMP, phosphoinositides and arachidonic acid.
  • modulators agonists and antagonists
  • the modulators that can be identified by these assays are natural ligand compounds ofthe receptor; synthetic analogs and derivatives of natural ligands; antibodies, antibody fragments, and/or antibody-like compounds derived from natural antibodies or from antibody-like combinatorial libraries; and/or synthetic compounds identified by high throughput screening of libraries; and other libraries known in the art. All modulators that bind GPCR-like receptors are useful for identifying GPCR-like polypeptides in tissue samples (e.g., for diagnostic purposes, pathological purposes, and other purposes known in the art).
  • Agonist and antagonist modulators are useful for up-regulating and down-regulating GPCR-like receptor activity, respectively, for purposes described herein.
  • GPCR-like receptor binding partners also may be used to deliver a therapeutic compound or a label to cells that express a GPCR-like receptor (e.g., by attaching the compound or label to the binding partner).
  • the assays may be performed using single putative modulators; they may also be performed using a known agonist in combination with candidate antagonists (or visa versa).
  • c. cAMP Assays In one type of assay, levels of cyclic adenosine monophosphate (cAMP) are measured in GPCR-like receptor-transfected cells that have been exposed to candidate modulator compounds. Protocols for cAMP assays have been described in the literature.
  • GPCR-like receptor coding sequence e.g., a cDNA or intronless genomic DNA
  • pzeoSN2 a commercial expression vector
  • transfected CHO cells are seeded into the 96-well microplates ofthe FlashPlate® assay kit, which are coated with solid scintillant to which antisera to cAMP has been bound.
  • some wells are seeded with wild type (untransfected) CHO cells.
  • Other wells on the plate receive various amounts of cAMP standard solution for use in creating a standard curve.
  • test compounds are added to the cells in each well, with water and/or compound-free medium/diluent serving as a control.
  • the test compound may be added to the wells prior to adding a known agonist/ligand, or the test compound may be premixed with a known agonist before adding the mixture to the wells.
  • cAMP is allowed to accumulate in the cells for exactly 15 minutes at room temperature. The assay is terminated by the addition of lysis buffer containing [ 125 I] -labeled cAMP, and the plate is counted using a Packard TopcountTM 96-well microplate scintillation counter.
  • Unlabeled cAMP from the lysed cells competes with the fixed amounts of [ 125 I]-cAMP for antibody bound to the plate.
  • a standard curve is constructed, and cAMP values for the unknowns are obtained by interpolation.
  • Changes in intracellular cAMP level of the cells in response to exposure to a test compound are indicative of GPCR receptor modulating activity.
  • Modulators that act as agonists at receptors which couple to the Gs subtype of G proteins will stimulate production of cAMP, leading to a measurable 3-10 fold increase.
  • Agonists of receptors which couple to the Gi/o subtype of G proteins will inhibit forskolin-stimulated cAMP production, leading to a measurable decrease of 50-100%.
  • Luciferase Reporter Gene Assay The photoprotein luciferase provides another useful tool for assaying for modulators of GPCR-like receptor activity.
  • Cells e.g., CHO cells or COS 7 cells
  • a GPCR-like receptor expression construct e.g., a
  • GPCR-like receptor in pzeoSN2 (Invitrogen, San Diego, CA)) and a reporter construct which includes a luciferase coding region downstream from a transcription factor, either the cAMP- response element (CRE), AP-1, or ⁇ F- ⁇ B.
  • CRE cAMP- response element
  • AP-1 AP-1
  • ⁇ F- ⁇ B cAMP- response element
  • Agonist binding to receptors coupled to the Gs subtype of G proteins leads to increases in cAMP, activating the CRE transcription factor and resulting in expression ofthe luciferase gene.
  • Agonist binding to receptors coupled to the Gq subtype of G proteins leads to production of diacylglycerol that activates protein kinase C, which activates the AP-1 or NF- ⁇ B transcription factors resulting in expression ofthe luciferase gene.
  • Luciferase activity may be quantitatively measured using, e.g., luciferase assay reagents that are commercially available from Promega (Madison, WI).
  • CHO cells are plated in 24-well culture dishes at a density of 100,000 cells/well one day prior to transfection and cultured at 37°C in ⁇ MEM (Gibco/BRL, Gaithersburg, MD) supplemented with 10% fetal bovine serum, 2 mM glutamine, 10 Units/ml penicillin and 10 ⁇ g/ml streptomycin.
  • Cells are transiently co- transfected with both a GPCR receptor expression construct and a reporter construct containing the luciferase gene.
  • the reporter plasmids CRE-luciferase, AP-1 -luciferase and NF-KB-luciferase may be purchased from Stratagene (LaJolla, CA).
  • Transfections are performed using FuGENE 6 transfection reagent (Boehringer-Mannheim), following the protocol provided in the product insert.
  • Cells transfected with the reporter construct alone are used as a control. Twenty-four hours after transfection, cells are washed once with phosphate buffered saline (PBS) pre-warmed to 37°C.
  • Seram-free ⁇ MEM is then added to the cells either alone (control) or with one or more candidate modulators and the cells are incubated at 37°C for five hours.
  • the candidate modulator may be added to the cell cultures prior to adding a known agonist/ligand or the candidate modulator may be pre- mixed with a known agonist before adding the mixture to the cells.
  • Receptors that are either constitutively active or activated by agonists typically give a 3-20 fold stimulation of luminescence compared to cells transfected with the reporter gene alone. Modulators that act as antagonists will reverse these effects at receptors that are either constitutively active or activated by known agonists.
  • Intracellular calcium measurement using FLIPR Changes in intracellular calcium levels are another recognized indicator of G protein-coupled receptor activity, and such assays can be employed to assay for modulators of GPCR-like receptor activity. For example, CHO cells stably transfected with a GPCR-like receptor expression constract are plated at a density of 4 x 104 cells/well in Packard black- walled 96-well plates specially designed to isolate fluorescent signals to individual wells.
  • D-PBS modified Dulbecco's PBS
  • fetal bovine serum containing 36 mg/L pyruvate and 1 g/L glucose
  • 1% fetal bovine serum and one of four calcium indicator dyes (Fluo-3TM AM, Fluo-4TM AM, Calcium GreenTM- 1 AM, or Oregon GreenTM 488 BAPTA-1 AM) at a concentration of 4 ⁇ M.
  • Plates are washed once with modified D-PBS without 1% fetal bovine serum and incubated for 10 minutes at 37°C to remove residual dye from the cellular membrane.
  • a series of washes with modified D-PBS without 1% fetal bovine serum is performed immediately prior to activation ofthe calcium response.
  • Calcium response is initiated by the addition of one or more candidate receptor agonist compounds, or a positive control such as a calcium ionophore A23187 (10 ⁇ M), or ATP (4 ⁇ M). Fluorescence is measured by Molecular Device's FLIPR with an argon laser, excitation at 488 nm. [See, e.g., Kuntzweiler et al., Drug Development Research, 44(1): 14- 20 (1998).] To screen for antagonists, a test compound or agent is added to the cell prior to adding a known agonist/ligand, or the test compound may be pre-mixed with a known agonist before adding the mixture to the cells.
  • the F-stop for the detector camera may be set at 2.5 and the length of exposure is about 0.4 msec.
  • Basal fluorescence of cells is measured for 20 seconds prior to addition of agonist, ATP, or A23187, and is subtracted from the response signal.
  • the calcium signal is measured for approximately 200 seconds, taking readings every two seconds.
  • the calcium ionophore and ATP increase the calcium signal 200% above baseline levels.
  • activated GPCRs increase the calcium signal approximately 10- 15% above baseline signal.
  • Antagonists inhibit or eliminate such activation.
  • Mitogenesis Assay In mitogenesis assays, the ability of candidate modulators to induce or inhibit GPCR-like receptor-mediated cell growth is determined. [See, e.g., Lajiness et al., J. Pharmacol. Exper. Ther.
  • CHO cells stably expressing a GPCR-like receptor are seeded into 96-well plates at a density of 5000 cells/well and grown at 37°C in ⁇ MEM with 10% fetal calf serum for 48 hours, at which time the cells are rinsed twice with seram-free ⁇ MEM. After rinsing, 80 ⁇ l of fresh ⁇ MEM, or ⁇ MEM containing a known mitogen, is added along with 20 ⁇ l ⁇ MEM containing varying concentrations of one or more test compounds diluted in seram-free medium. As controls, some wells on each plate receive serum-free medium alone, and some receive medium containing 10% fetal bovine serum.
  • Untransfected cells or cells transfected with the vector alone also may serve as controls. After culture for 16-18 hours, 1 ⁇ Ci/well of [3H]-thymidine is added to the wells and cells are incubated for an additional 2 hours at 37°C. The cells are trypsinized and harvested onto filter mats with a cell harvester (Tomtec) and the filters are counted in a
  • Betaplate counter The incorporation of [ H]-thymidine in seram-free test wells is compared to the results achieved in cells stimulated with serum.
  • Antagonists that bind to the receptor will inhibit the stimulation seen with a known agonist by up to 100%.
  • [ 35 S]GTPyS Binding Assay Because G protein-coupled receptors signal through intracellular G proteins whose activity involves GTP/GDP binding and hydrolysis, measurement of binding ofthe non-hydrolyzable GTP analog [ 35 S]GTP ⁇ S in the presence and absence of putative modulators provides another indicator of modulator activity.
  • cells stably transfected with a GPCR-like receptor expression constract are grown in 10 cm dishes to subconfluence, rinsed once with 5 ml of ice-cold Ca2+/Mg2+- free PBS, and scraped into 5 ml ofthe same buffer. Cells are pelleted by centrifugation (500 x g, 5 minutes), resuspended in 25 mM Tris, pH 7.5, 5 mM EDTA, 5 mM EDTA, pH 7.5 (TEE), and frozen in liquid nitrogen.
  • the cells are homogenized using a Dounce homogenizer (one ml TEE per plate of cells), and centrifuged at 1,000 x g for 5 minutes to remove nuclei and unbroken cells.
  • the homogenate supernatant is centrifuged at 20,000 x g for 20 minutes to isolate the membrane fraction, and the membrane pellet is washed once with TEE and resuspended in binding buffer (20 mM HEPES, pH 7.5, 150 mM NaCl, 10 mM MgC12, 1 mM EDTA).
  • the resuspended membranes can be frozen in liquid nitrogen and stored at - 70°C until use.
  • Nonspecific binding of [ 35 S]-GTP ⁇ S is measured in the presence of 100 ⁇ M GTP and subtracted from the total. Compounds are selected that modulate the amount of [ 35 S]-GTP ⁇ S binding in the cells, compared to untransfected control cells. Activation of receptors by agonists gives up to a five-fold increase in [ 35 S]GTP ⁇ S binding. This response is blocked by antagonists.
  • est molecule(s) refers to the molecule(s) that is/are under evaluation for the ability to modulate (i.e., increase or decrease) the activity of an IGFBP-4 and ULK polypeptide. Most commonly, a test molecule will interact directly with an IGFBP-4 and ULK polypeptide.
  • a test molecule may also modulate IGFBP-4 and ULK polypeptide activity indirectly, such as by affecting IGFBP-4 and ULK gene expression, or by binding to an IGFBP-4 and ULK binding partner (e.g., receptor, co-factor, or ligand).
  • a test molecule will bind to an IGFBP-4 and ULK polypeptide with an affinity constant of at least about 10 "6 M, preferably about 10 "8 M, more preferably about 10 "9 M, and even more preferably about 10 "10 M.
  • an IGFBP-4 and ULK polypeptide is incubated with a test molecule under conditions which permit the interaction ofthe test molecule with an IGFBP-4 and ULK polypeptide, and the extent ofthe interaction can be measured.
  • the test molecule(s) can be screened in a substantially purified form or in a crude mixture.
  • an IGFBP-4 or ULK antagonist may be a protein, peptide, carbohydrate, lipid, or small molecular weight molecule which interacts with an IGFBP-4 or ULK polypeptide or an IGFBP-4 or ULK polynucleotide to regulate its expression or activity.
  • Molecules which regulate IGFBP-4 or ULK polypeptide or IGFBP-4 or ULK polynucleotide expression or activity include nucleic acids which are complementary to nucleic acid encoding an IGFBP-4 and ULK polypeptide, or are complementary to nucleic acids sequences which direct or control the expression or activity of an IGFBP-4 and ULK polypeptide, and which act as antisense regulators of expression or activity.
  • test molecules may be carried out in several formats, including cell- based binding assays, membrane binding assays, solution-phase assays and immunoassays.
  • test molecules are incubated with an IGFBP-4 or ULK polypeptide or an IGFBP-4 or ULK polynucleotide for a specified period of time, and IGFBP-4 or ULK polypeptide activity is determined by one or more assays for measuring biological activity.
  • the interaction of test molecules with IGFBP-4 and ULK polypeptides may also be assayed directly using polyclonal or monoclonal antibodies in an immunoassay.
  • modified forms of IGFBP-4 and ULK polypeptides containing epitope tags as described herein may be used in immunoassays.
  • a binding partner e.g., IGF, a receptor, a ligand or a co-factor
  • in vitro assays may be used to measure the binding of an IGFBP-4 or ULK polypeptide to the corresponding binding partner (such as a selective binding agent, receptor, ligand, or co-factor).
  • binding partner e.g., IGF, a receptor, a ligand or a co-factor
  • an IGFBP-4 or ULK polypeptide is immobilized in the wells of a microtiter plate.
  • Radiolabeled an IGFBP-4 or ULK binding partner for example, iodinated IGFBP-4 or ULK binding partner
  • the test molecule(s) can then be added either one at a time (in either order) or simultaneously to the wells.
  • the wells can be washed and counted using a scintillation counter, for radioactivity to determine the extent to which the binding partner bound to an IGFBP-4 or ULK polypeptide.
  • the molecules will be tested over a range of concentrations, and a series of control wells lacking one or more elements ofthe test assays can be used for accuracy in the evaluation ofthe results.
  • An alternative to this method involves reversing the "positions" ofthe proteins, i.e., immobilizing an IGFBP-4 or ULK binding partner to the microtiter plate wells, incubating with the test molecule and radiolabeled IGFBP-4 or ULK polypeptide, and determining the extent of IGFBP-4 or ULK polypeptide binding. See, for example, Chapter 18, Current Protocols in Molecular Biology, Ausubel et al. , eds., John Wiley & Sons, New York, NY (1995).
  • an IGFBP-4 or ULK polypeptide or its binding partner may be conjugated to biotin and the presence of biotinylated protein can then be detected using streptavidin linked to an enzyme, such as horseradish peroxidase (HRP) or alkaline phosphatase (AP), that can be detected colorimetrically, or by fluorescent tagging of streptavidin.
  • an enzyme such as horseradish peroxidase (HRP) or alkaline phosphatase (AP)
  • HRP horseradish peroxidase
  • AP alkaline phosphatase
  • An antibody directed to an IGFBP-4 or ULK polypeptide or to an IGFBP-4 or ULK binding partner and conjugated to biotin may also be used and can be detected after incubation with enzyme-linked streptavidin linked to AP or HRP.
  • An IGFBP-4 or ULK polypeptide or an IGFBP-4 or ULK -like binding partner can also be immobilized by attachment to agarose beads, acrylic beads or other types of such inert solid phase substrates.
  • the substrate-protein complex can be placed in a solution containing the complementary protein and the test compound. After incubation, the beads can be precipitated by centrifugation, and the amount of binding between an IGFBP-4 or ULK polypeptide and its binding partner can be assessed using the methods described herein.
  • the substrate-protein complex can be immobilized in a column, and the test molecule and complementary protein are passed through the column.
  • the formation of a complex between an IGFBP-4 and ULK polypeptide and its binding partner can then be assessed using any ofthe techniques set forth herein, i.e., radiolabellmg, antibody binding or the like.
  • Another in vitro assay that is useful for identifying a test molecule which increases or decreases the formation of a complex between an IGFBP-4 or ULK polypeptide and an IGFBP-4 or ULK binding partner is a surface plasmon resonance detector system such as the BIAcore assay system (Pharmacia, Piscataway, NJ).
  • the BIAcore system may be carried out using the manufacturer's protocol.
  • This assay essentially involves the covalent binding of either (1) an IGFBP-4 or ULK polypeptide or (2) an IGFBP-4 or ULK binding partner to a dextran-coated sensor chip which is located in a detector.
  • the test compound and the other complementary protein can then be injected, either simultaneously or sequentially, into the chamber containing the sensor chip.
  • the amount of complementary protein that binds can be assessed based on the change in molecular mass which is physically associated with the dextran-coated side ofthe sensor chip; the change in molecular mass can be measured by the detector system.
  • test compounds it may be desirable to evaluate two or more test compounds together for their ability to increase or decrease the formation of a complex between a an IGFBP-4 or ULK polypeptide and an IGFBP-4 or ULK binding partner.
  • the assays set forth herein can be readily modified by adding such additional test compound(s) either simultaneous with, or subsequent to, the first test compound. The remainder ofthe steps in the assay are set forth herein .
  • In vitro assays such as those described herein may be used advantageously to screen large numbers of compounds for effects on complex formation by an IGFBP-4 or ULK polypeptide and an IGFBP-4 or ULK binding partner.
  • the assays may be automated to screen compounds generated in phage display, synthetic peptide, and chemical synthesis libraries.
  • Compounds which increase or decrease the formation of a complex between an IGFBP-4 or ULK polypeptide and an IGFBP-4 or ULK binding partner may also be screened in cell culture using cells and cell lines expressing either an IGFBP-4 or ULK polypeptide or an IGFBP-4 or ULK binding partner.
  • Cells and cell lines may be obtained from any mammal, but preferably will be from human or other primate, canine, or rodent sources.
  • the binding of an IGFBP-4 or ULK polypeptide to cells expressing an IGFBP-4 or ULK binding partner at the surface is evaluated in the presence or absence of test molecules, and the extent of binding may be determined by, for example, flow cytometry using a biotinylated antibody to an IGFBP-4 or ULK binding partner.
  • Cell culture assays can be used advantageously to further evaluate compounds that score positive in protein binding assays described herein.
  • Cell cultures can also be used to screen the impact of a drag candidate.
  • drag candidates may decrease or increase the expression or activity of an IGFBP-4 or ULK gene.
  • the amount of an IGFBP-4 or ULK polypeptide that is produced may be measured after exposure ofthe cell culture to the drag candidate.
  • one may detect the actual impact ofthe drag candidate on the cell culture.
  • the overexpression of a particular gene may have a particular impact on the cell culture. In such cases, one may test a drag candidate's ability to increase or decrease the expression ofthe gene or its ability to prevent or inhibit a particular impact on the cell culture.
  • the production of a particular metabolic product such as a fragment of a polypeptide
  • a yeast two hybrid system (Chien et al., Proc. Natl. Acad. Sci. USA, 88:9578- 9583, 1991) can be used to identify novel polypeptides that bind to, or interact with, IGFBP-4 or ULK polypeptides.
  • a yeast-two hybrid bait constract can be generated in a vector (such as the pAS2-l from Clontech) which encodes a yeast GAL4-DNA binding domain fused to the IGFBP-4 and ULK polynucleotide .
  • This bait constract may be used to screen human cDNA libraries wherein the cDNA library sequences are fused to GAL4 activation domains. Positive interactions will result in the activation of a reporter gene such as ⁇ -Gal. Positive clones emerging from the screening may be characterized further to identify interacting proteins.
  • the present invention also provides selective binding agents of polypeptides identified by the methods ofthe invention for the treatment of a pathological condition that would benefit from creating a regeneration-permissive environment to facilitate or stimulate neurogenesis or neuroregeneration.
  • the screening methods described herein identify suitable selective binding agents useful for therapeutic purposes and for formulation and modification by pharmaceutical chemists to improve serum half-life, reduce toxicity, and increase potency.
  • Suitable selective binding agents include, but are not limited to, antibodies and derivatives thereof, polypeptides, and small molecules. Suitable selective binding agents may be prepared using organic chemistry, biochemistry, molecular biology, and recombinant techniques.
  • An exemplary selective binding agent ofthe present invention is capable of binding a certain portion of an identified polypeptide thereby increasing the expression and/or signaling ofthe C3aR, C5aR; inhibiting the expression or activity of IGFBP-4 or ULK; and decreasing the expression and/or signaling of ETBR.
  • Selective binding agents such as antibodies and antibody fragments that bind polypeptides which increase the expression and/or signaling ofthe C3aR, C5aR; inhibit the expression or activity of IGFBP-4 or ULK; and decrease the expression and/or signaling of ETBR are within the scope ofthe present invention.
  • the antibodies may be polyclonal including monospecific polyclonal, monoclonal (MAbs), recombinant, chimeric, humanized such as CDR-grafted, human, single chain, and/or bispecific, as well as fragments, variants or derivatives thereof.
  • Antibody fragments include those portions ofthe antibody which bind to an epitope on the polypeptide which increases the expression and/or signaling ofthe C3aR, C5aR; inhibits the expression or activity of IGFBP-4 or ULK; and decreases the expression and/or signaling of ETBR. Examples of such fragments include Fab and F(ab') fragments generated by enzymatic cleavage of full-length antibodies.
  • binding fragments include those generated by recombinant DNA techniques, such as the expression of recombinant plasmids containing nucleic acid sequences encoding antibody variable regions.
  • Polyclonal antibodies directed toward a polypeptide which increases the expression and/or signaling ofthe C3aR, C5aR; inhibits the expression or activity of IGFBP- 4 or ULK; and decreases the expression and/or signaling of ETBR generally are produced in animals (e.g., rabbits or mice) by means of multiple subcutaneous or intraperitoneal injections of a polypeptide and an adjuvant.
  • a carrier protein such as keyhole limpet heocyanin, serum, albumin, bovine thyroglobulin, or soybean trypsin inhibitor.
  • aggregating agents such as alum are used to enhance the immune response. After immunization, the animals are bled and the serum is assayed for antibody titer.
  • Monoclonal antibodies directed toward polypeptides which increase the expression and/or signaling ofthe C3aR, C5aR; inhibit the expression or activity of IGFBP-4 or ULK; and decrease the expression and/or signaling of ETBR are within the scope ofthe present invention. These antibodies are produced using any method which provides for the production of antibody molecules by continuous cell lines in culture. Examples of suitable methods for preparing monoclonal antibodies include the hybridoma methods of Kohler et al. (Nature, 256: 495-497, 1975) and the human B-cell hybridoma method (Kozbor et al., J. Immunol, 133: 3001-3005, 1984; Brodeur et al., Monoclonal Antibody Production Techniques and Applications, pp.
  • hybridoma cell lines which produce monoclonal antibodies reactive with polypeptides which increase the expression and/or signaling ofthe C3aR, C5aR; inhibit the expression or activity of IGFBP-4 or ULK; and decrease the expression and/or signaling of ETBR.
  • Antibodies ofthe invention are screened in assays described herein for the desired agonist (C3aR or C5aR) or antagonist (IGFBP-4, ULK, and ETBR) activity.
  • antibodies which increase the expression and/or signaling ofthe C3aR or C5aR; inhibit the expression or activity of IGFBP-4 or ULK; and decrease the expression and/or signaling of ETBR typically will be labeled with a detectable moiety.
  • the detectable moiety can be any one which is capable of producing, either directly or indirectly, a detectable signal.
  • the detectable moiety may be a radioisotope, such as 3 H, 14 C, 32 P, 35 S, or 125 I, a fluorescent or chemiluminescent compound, such as fluorescein isothiocyanate, rhodamine, or luciferin; or an enzyme, such as alkaline phosphatase, b-galactosidase, or horseradish peroxidase (Bayer et al., Meth. Enz., 184: 138-163, 1990).
  • a radioisotope such as 3 H, 14 C, 32 P, 35 S, or 125 I
  • a fluorescent or chemiluminescent compound such as fluorescein isothiocyanate, rhodamine, or luciferin
  • an enzyme such as alkaline phosphatase, b-galactosidase, or horseradish peroxidase (Bayer et al., Meth. Enz., 184:
  • ком ⁇ онентs rely on the ability of a labeled standard (e.g., a polypeptide, or an immunologically reactive portion thereof) to compete with the test sample analyte for binding with a limited amount of antibody.
  • a labeled standard e.g., a polypeptide, or an immunologically reactive portion thereof
  • the amount of a polypeptide in the test sample is inversely proportional to the amount of standard that becomes bound to the antibodies.
  • the antibodies typically are insolubilized before or after the competition, so that the standard and analyte that are bound to the antibodies may conveniently be separated from the standard and analyte which remain unbound.
  • Sandwich assays typically involve the use of two antibodies, each capable of binding to a different immunogenic portion, or epitope, ofthe protein to be detected and/or quantitated.
  • the test sample analyte is typically bound by a first antibody which is immobilized on a solid support, and thereafter a second antibody binds to the analyte, thus forming an insoluble three-part complex.
  • the second antibody may itself be labeled with a detectable moiety (direct sandwich assays) or may be measured using an anti-immunoglobulin antibody that is labeled with a detectable moiety (indirect sandwich assays).
  • sandwich assay is an enzyme-linked immunosorbent assay (ELISA), in which case the detectable moiety is an enzyme.
  • Selective binding agents ofthe invention including antibodies which act as agonists (increase the expression and/or signaling) of C3aR or C5aR, or antagonists (inhibit the expression or activity (or signaling)) of IGFBP-4 or ULK or ETBR, may be used as therapeutics.
  • These therapeutic agents are generally agonists of a C3aR or a C5aR, or antagonists of IGFBP-4, ULK, or ETBR polypeptide.
  • antagonist antibodies ofthe invention are antibodies or binding fragments thereof which are capable of specifically binding to an IGFBP-4, ULK, or ETBR polypeptide and which are capable of inhibiting or eliminating the functional activity of an IGFBP-4, ULK, or ETBR polypeptide in vivo or in vitro.
  • the selective binding agent e.g., an antagonist antibody will inhibit the functional activity of an IGFBP-4, ULK, or ETBR polypeptide by at least about 50%, and preferably by at least about 80%.
  • the selective binging agent may be an antibody that is capable of interacting with an IGFBP-4, ULK, or ETBR binding partner (a ligand, co-factor, or receptor) thereby inhibiting or eliminating IGFBP-4, ULK, or ETBR activity in vitro or in vivo.
  • Selective binding agents including antagonist anti-IGFBP-4, -ULK, or -ETBR antibodies are identified by screening assays which are well known in the art.
  • the present invention also provides anti-ligand and anti-receptor compounds such as aptamer, antisense, and interference RNA techniques and therapies for the treatment of a pathological condition resulting from decreased expression or signaling of C3aR, C5aR; upregulated expression of IGFBP-4 or ULK; or increased expression or signaling of ETBR. 1. Aptamers Recent advances in the field of combinatorial sciences have identified short polymer sequences with high affinity and specificity to a given target.
  • SELEX technology has been used to identify DNA and RNA aptamers with binding properties that rival mammalian antibodies, the field of immunology has generated and isolated antibodies or antibody fragments which bind to a myriad of compounds and phage display has been utilized to discover new peptide sequences with very favorable binding properties. Based on the success of these molecular evolution techniques, it is certain that molecules can be created which bind to any target molecule.
  • a loop structure is often involved with providing the desired binding attributes as in the case of: aptamers which often utilize hairpin loops created from short regions without complimentary base pairing, naturally derived antibodies that utilize combinatorial arrangement of looped hyper- variable regions and new phage display libraries utilizing cyclic peptides that have shown improved results when compared to linear peptide phage display results.
  • aptamers which often utilize hairpin loops created from short regions without complimentary base pairing
  • naturally derived antibodies that utilize combinatorial arrangement of looped hyper- variable regions
  • new phage display libraries utilizing cyclic peptides that have shown improved results when compared to linear peptide phage display results.
  • the aptamer may be generated by preparing a library of nucleic acids; contacting the library of nucleic acids with a growth factor, wherein nucleic acids having greater binding affinity for the growth factor (relative to other library nucleic acids) are selected and amplified to yield a mixture of nucleic acids enriched for nucleic acids with relatively higher affinity and specificity for binding to the growth factor.
  • nucleic acids may be screened to select for molecules that bind to more than growth factor.
  • Antisense Molecules Another class of inhibitors that may be used in conjunction with the present invention is isolated antisense nucleic acid molecules that can hybridize to, or are complementary to, the nucleic acid molecule, nucleotide sequence, or fragments, analogs or derivatives thereof.
  • an “antisense” nucleic acid comprises a nucleotide sequence that is complementary to a "sense” nucleic acid encoding a protein (e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence).
  • antisense nucleic acid molecules are provided that comprise a sequence complementary to at least about 10, 25, 50, 100, 250 or 500 nucleotides or an entire receptor or ligand coding strand, or to only a portion thereof.
  • Nucleic acid molecules encoding fragments, homologs, derivatives and analogs of receptor or ligand or antisense nucleic acids complementary to a receptor or ligand nucleic acid sequence are additionally provided.
  • an antisense nucleic acid molecule is antisense to a "coding region" ofthe coding strand of a nucleotide sequence encoding a receptor or ligand protein (or fragments or fragment combination thereof).
  • the term "coding region” refers to the region ofthe nucleotide sequence comprising codons that are translated into amino acid residues.
  • the antisense nucleic acid molecule is antisense to a "conceding region" ofthe coding strand of a nucleotide sequence encoding the receptor or ligand protein.
  • antisense nucleic acids ofthe invention can be designed according to the rales of Watson and Crick or Hoogsteen base pairing.
  • the antisense nucleic acid molecule can be complementary to the entire coding region of a ligand or receptor mRNA, but more preferably is an oligonucleotide that is antisense to only a portion ofthe coding or noncoding region of receptor or ligand mRNA.
  • the antisense oligonucleotide can be complementary to the region surrounding the translation start site of receptor or ligand mRNA.
  • An antisense oligonucleotide can be, for example, about 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 nucleotides in length.
  • An antisense nucleic acid ofthe invention can be constructed using chemical synthesis or enzymatic ligation reactions using procedures known in the art.
  • an antisense nucleic acid e.g., an antisense oligonucleotide
  • an antisense nucleic acid can be chemically synthesized using naturally-occurring nucleotides or variously modified nucleotides designed to increase the biological stability ofthe molecules or to increase the physical stability ofthe duplex formed between the antisense and sense nucleic acids (e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used).
  • modified nucleotides that can be used to generate the antisense nucleic acid include: 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5- carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5-methylaminomethyluracil, 5- methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5'- methoxycar
  • the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following section).
  • the antisense nucleic acid molecules ofthe invention are typically administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a receptor or ligand to thereby inhibit expression of the protein (e.g. , by inhibiting transcription and/or translation).
  • the hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule that binds to DNA duplexes, through specific interactions in the major groove ofthe double helix.
  • An example of a route of administration of antisense nucleic acid molecules ofthe invention includes direct injection at a tissue site.
  • antisense nucleic acid molecules can be modified to target selected cells and then administered systemically.
  • antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface (e.g., by linking the antisense nucleic acid molecules to peptides or antibodies that bind to cell surface receptors or antigens).
  • the antisense nucleic acid molecules can also be delivered to cells using the vectors described herein.
  • vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter are preferred.
  • the antisense nucleic acid molecule ofthe invention is an alpha-anomeric nucleic acid molecule.
  • An alpha-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual alpha-units, the strands run parallel to each other. See, e.g., Gaultier, et al, Nucl. Acids Res., 15:6625-6641 (1987).
  • the antisense nucleic acid molecule can also comprise a 2'-o-methylribonucleotide (see, e.g., Inoue, et al. Nucl. Acids Res., 15:6131-6148 (1987)) or a chimeric RNA-DNA analogue (see, e.g., Inoue, et al, FEBS Lett, 215:327-330 (1987)).
  • Production and delivery of antisense molecules are facilitated by providing a vector comprising an anti-sense nucleotide sequence complementary to at least a part ofthe Receptor or ligand DNA sequence.
  • such a vector comprising an anti-sense sequence may be used to inhibit, or at least mitigate, Receptor or ligand expression.
  • the use of a vector of this type to inhibit Receptor or ligand expression is favored in instances where Receptor or ligand expression is associated with a particular disease state. 3.
  • RNA Interference Use of RNA Interference to inactivate or modulate receptor or ligand expression is also contemplated by this invention. RNA interference is described in U.S. Patent Appl. No. 2002-0162126, and Hannon, G., J Nature, 11:418:244-51 (2002).
  • RNA interference post-transcriptional gene silencing
  • quelling RNA interference
  • R ⁇ A interference offers a way of specifically and potently inactivating a cloned gene.
  • nucleic acids or proteins that can be delivered by gene therapy (e.g. delivery of a nucleic acid or a nucleic acid encoding a therapeutic polypeptide.
  • Additional embodiments ofthe present invention relate to cells and methods (e.g., homologous recombination and/or other recombinant production methods) for both the in vitro production of therapeutic polypeptides and for the production and delivery of therapeutic polypeptides by gene therapy or cell therapy.
  • Homologous and other recombination methods may be used to modify a cell that contains a normally transcriptionally silent gene, or an under expressed gene, and thereby produce a cell which expresses therapeutically efficacious amounts of polypeptides identified by the methods of the invention.
  • Homologous recombination is a technique originally developed for targeting genes to induce or correct mutations in transcriptionally active genes (Kucherlapati, Prog. Nucleic Acid Res. Mol. Biol. 36:301-310, 1989).
  • the DNA sequence to be inserted into the genome can be directed to a specific region ofthe gene of interest by attaching it to targeting DNA.
  • the targeting DNA is a nucleotide sequence that is complementary (homologous) to a region ofthe genomic DNA. Small pieces of targeting DNA that are complementary to a specific region ofthe genome are put in contact with the parental strand during the DNA replication process. It is a general property of DNA that has been inserted into a cell to hybridize, and therefore, recombine with other pieces of endogenous DNA through shared homologous regions.
  • this complementary strand is attached to an oligonucleotide that contains a mutation or a different sequence or an additional nucleotide, it too is incorporated into the newly synthesized strand as a result ofthe recombination.
  • the new sequence of DNA it is possible for the new sequence of DNA to serve as the template.
  • the transferred DNA is incorporated into the genome. Attached to these pieces of targeting DNA are regions of DNA which may interact with or control the expression of a polypeptide(s) identified by the methods ofthe invention, e.g., flanking sequences.
  • a promoter/enhancer element, a suppressor, or an exogenous transcription modulatory element is inserted in the genome ofthe intended host cell in proximity and orientation sufficient to influence the transcription of DNA encoding the desired polypeptide.
  • the control element controls a portion ofthe DNA present in the host cell genome.
  • the expression of a desired targeted gene in a cell is altered via homologous recombination into the cellular genome at a preselected site, by the introduction of DNA which includes at least a regulatory sequence, an exon and a splice donor site.
  • DNA which includes at least a regulatory sequence, an exon and a splice donor site.
  • These components are introduced into the chromosomal (genomic) DNA in such a manner that this, in effect, results in the production of a new transcription unit (in which the regulatory sequence, the exon and the splice donor site present in the DNA constract are operatively linked to the endogenous gene).
  • the expression ofthe desired endogenous gene is altered.
  • Altered gene expression encompasses activating (or causing to be expressed) a gene which is normally silent (unexpressed) in the cell as obtained, as well as increasing the expression of a gene which is not expressed at physiologically significant levels in the cell as obtained.
  • the embodiments further encompass changing the pattern of regulation or induction such that it is different from the pattern of regulation or induction that occurs in the cell as obtained, and reducing (including eliminating) the expression of a gene which is expressed in the cell as obtained.
  • homologous recombination can be used to increase, or cause, polypeptide production from a cell's endogenous gene involves first using homologous recombination to place a recombination sequence from a site-specific recombination system (e.g., Cre/loxP, FLP/FRT) (Sauer et al., Current Opinion In Biotechnology 5:521-527, 1994; Sauer et al., Methods In Enzymology 225:890-900, 1993) upstream (that is, 5' to) ofthe cell's endogenous genomic polypeptide coding region.
  • a site-specific recombination system e.g., Cre/loxP, FLP/FRT
  • upstream that is, 5' to
  • a plasmid containing a recombination site homologous to the site that was placed just upstream ofthe genomic polypeptide coding region is introduced into the modified cell line along with the appropriate recombinase enzyme.
  • This recombinase causes the plasmid to integrate, via the plasmid' s recombination site, into the recombination site located just upstream ofthe genomic polypeptide coding region in the cell line (Baubonis et al., Nucleic Acids Res. 27:2025-2029, 1993; O'Gorman et al., Science 257:1351-1355, 1991).
  • flanking sequences known to increase transcription e.g., enhancer/promoter, intron, translational enhancer
  • a further method to use the cell line in which the site specific recombination sequence had been placed just upstream ofthe cell's endogenous genomic polypeptide coding region is to use homologous recombination to introduce a second recombination site elsewhere in the cell line's genome.
  • the appropriate recombinase enzyme is then introduced into the two-recombination-site cell line, causing a recombination event (deletion, inversion, translocation) (Sauer et al., Current Opinion In Biotechnology, supra, 1994; Sauer, Methods Enzymol, supra, 1993) that would create a new or modified transcriptional unit resulting in de novo or increased polypeptide production from the cell's endogenous gene.
  • An additional approach for increasing, or causing, the expression of polypeptide(s) identified by the methods ofthe invention from a cell's endogenous gene(s) involves increasing, or causing, the expression of a gene or genes (e.g., transcription factors) and/or decreasing the expression of a gene or genes (e.g., transcriptional repressors) in a manner which results in de novo or increased polypeptide production from the cell's endogenous gene(s).
  • This method includes the introduction of a non-naturally occurring polypeptide (e.g., a polypeptide comprising a site specific DNA binding domain fused to a transcriptional factor domain) into the cell such that de novo or increased polypeptide production from the cell's endogenous gene(s) results.
  • the present ⁇ nvention further relates to DNA constructs useful in the method of altering expression of a target gene.
  • the exemplary DNA constructs comprise: (a) one or more targeting sequences; (b) a regulatory sequence; (c) an exon; and (d) an unpaired splice-donor site.
  • the targeting sequence in the DNA construct directs the integration of elements (a)-(d) into a target gene in a cell such that the elements (b)-(d) are operatively linked to sequences ofthe endogenous target gene.
  • the DNA constructs comprise: (a) one or more targeting sequences, (b) a regulatory sequence, (c) an exon, (d) a splice-donor site, (e) an intron, and (f) a splice- acceptor site, wherein the targeting sequence directs the integration of elements (a)-(f) such that the elements of (b)-(f) are operatively linked to the endogenous gene.
  • the targeting sequence is homologous to the preselected site in the cellular chromosomal DNA with which homologous recombination is to occur, hi the constract, the exon is generally 3' ofthe regulatory sequence and the splice-donor site is 3' ofthe exon.
  • sequence of a particular gene is known, such as the nucleic acid sequence of a polypeptide(s) identified by the methods of the invention presented herein
  • a piece of DNA that is complementary to a selected region ofthe gene can be synthesized or otherwise obtained, such as by appropriate restriction ofthe native DNA at specific recognition sites bounding the region of interest.
  • This piece serves as a targeting sequence(s) upon insertion into the cell and will hybridize to its homologous region within the genome. If this hybridization occurs during DNA replication, this piece of DNA, and any additional sequence attached thereto, will act as an Okazaki fragment and will be incorporated into the newly synthesized daughter strand of DNA.
  • the present invention includes nucleotides encoding polypeptide(s) identified by the methods ofthe invention, which nucleotides may be used as targeting sequences.
  • Polypeptide cell therapy e.g., the implantation of cells producing polypeptide(s) identified by the methods ofthe invention, is also contemplated. This embodiment involves implanting cells capable of synthesizing and secreting a biologically active form of a polypeptide(s) identified by the methods ofthe invention.
  • Such polypeptide- producing cells can be cells that are natural producers of said polypeptides or may be recombinant cells whose ability to produce polypeptides has been augmented by transformation with a gene encoding the desired polypeptide(s) identified by the methods of the invention or with a gene augmenting the expression of said polypeptide.
  • Such a modification may be accomplished by means of a vector suitable for delivering the gene as well as promoting its expression and secretion.
  • the natural cells producing the polypeptide(s) identified by the methods ofthe invention be of human origin and produce human polypeptide.
  • the recombinant cells producing polypeptide(s) identified by the methods ofthe invention be transformed with an expression vector containing a gene encoding a human polypeptide. Implanted cells may be encapsulated to avoid the infiltration of surrounding tissue.
  • Human or non-human animal cells may be implanted in patients in biocompatible, semipermeable polymeric enclosures or membranes that allow the release of polypeptide(s) identified by the methods ofthe invention, but prevent the destruction ofthe cells by the patient's immune system or by other detrimental factors from the surrounding tissue.
  • the patient's own cells, transformed to produce polypeptide(s) identified by the methods of the invention ex vivo may be implanted directly into the patient without such encapsulation.
  • Techniques for the encapsulation of living cells are known in the art, and the preparation ofthe encapsulated cells and their implantation in patients may be routinely accomplished. For example, Baetge et al.
  • WO95/05452 PCT/US94/09299
  • the capsules are biocompatible and are easily retrievable.
  • the capsules encapsulate cells transfected with recombinant DNA molecules comprising DNA sequences coding for biologically active molecules operatively linked to promoters that are not subject to down-regulation in vivo upon implantation into a mammalian host.
  • the devices provide for delivery ofthe molecules from living cells to specific sites within a recipient.
  • U.S. Patent Nos. 4,892,538, 5,011,472, and 5,106,627 A system for encapsulating living cells is described in PCT Application no.
  • PCT/US91/00157 of Aebischer et al. See also, PCT Application No. PCT/US91/00155 of Aebischer et al., Winn et al., Exper. Neurol. 113: 322-329, 1991, Aebischer et al., Exper. Neurol. 111:269-275, 1991; and Tresco et al, ASAIO 38:17-23, 1992.
  • polypeptide(s) identified by the methods ofthe invention are also envisioned.
  • a gene therapy technique is to use the gene (either genomic DNA, cDNA, and/or synthetic DNA) encoding a polypeptide(s) identified by the methods ofthe invention which may be operably linked to a constitutive or inducible promoter to form a "gene therapy DNA construct".
  • the promoter may be homologous or heterologous to the endogenous gene, provided that it is active in the cell or tissue type into which the construct will be inserted.
  • genes designed for site-specific integration e.g., endogenous sequences useful for homologous recombination
  • tissue-specific promoter e.g., tissue-specific promoter, enhancer(s) or silencer(s)
  • DNA molecules capable of providing a selective advantage over the parent cell DNA molecules useful as labels to identify transformed cells, negative selection systems, cell specific binding agents (as, for example, for cell targeting), cell- specific intemalization factors, and transcription factors to enhance expression by a vector as well as factors to enable vector manufacture.
  • a gene therapy DNA constract can then be introduced into cells (either ex vivo or in vivo) using viral or non- viral vectors.
  • One means for introducing the gene therapy DNA constract is by means of viral vectors as described herein.
  • vectors such as retro viral vectors
  • retro viral vectors will deliver the DNA constract to the chromosomal DNA ofthe cells, and the gene can integrate into the chromosomal DNA.
  • Other vectors will function as episomes, and the gene therapy DNA constract will remain in the cytoplasm.
  • regulatory elements can be included for the controlled expression ofthe identified gene in the target cell. Such elements are turned on in response to an appropriate effector. In this way, a therapeutic polypeptide can be expressed when desired.
  • One conventional confrol means involves the use of small molecule dimerizers or rapalogs (as described in WO9641865 (PCT/US96/099486); WO9731898 (PCT/US97/03137) and WO9731899 (PCT/US95/03157) used to dimerize chimeric proteins which contain a small molecule-binding domain and a domain capable of initiating biological process, such as a DNA-binding protein or transcriptional activation protein.
  • the dimerization ofthe proteins can be used to initiate transcription ofthe transgene.
  • An alternative regulation technology uses a method of storing proteins expressed from the gene of interest inside the cell as an aggregate or cluster.
  • the gene of interest is expressed as a fusion protein that includes a conditional aggregation domain which results in the retention ofthe aggregated protein in the endoplasmic reticulum.
  • the stored proteins are stable and inactive inside the cell.
  • the proteins can be released, however, by administering a drug (e.g., small molecule ligand) that removes the conditional aggregation domain and thereby specifically breaks apart the aggregates or clusters so that the proteins maybe secreted from the cell. See, Science 287:816-817, and 826-830 (2000).
  • a drug e.g., small molecule ligand
  • Other suitable control means or gene switches include, but are not limited to, the following systems.
  • Mifepristone (RU486) is used as a progesterone antagonist.
  • the binding of a modified progesterone receptor ligand-binding domain to the progesterone antagonist activates transcription by forming a dimer of two transcription factors which then pass into the nucleus to bind DNA.
  • the ligand-binding domain is modified to eliminate the ability ofthe receptor to bind to the natural ligand.
  • the modified steroid hormone receptor system is further described in U.S. 5,364,791; WO9640911; and WO9710337.
  • Yet another control system uses ecdysone (a fruit fly steroid hormone) which binds to and activates an ecdysone receptor (cytoplasmic receptor).
  • the receptor then translocates to the nucleus to bind a specific DNA response element (promoter from ecdysone-responsive gene).
  • the ecdysone receptor includes a transactivation domain/DNA- binding domain ligand-binding domain to initiate transcription.
  • the ecdysone system is further described in U.S. 5,514,578; WO9738117; WO9637609; and WO9303162.
  • Another control means uses a positive tetracycline-controllable transactivator.
  • This system involves a mutated tet repressor protein DNA-binding domain (mutated tet R- 4 amino acid changes which resulted in a reverse tetracycline-regulated transactivator protein, i.e., it binds to a tet operator in the presence of tetracycline) linked to a polypeptide which activates transcription.
  • mutated tet repressor protein DNA-binding domain mutated tet R- 4 amino acid changes which resulted in a reverse tetracycline-regulated transactivator protein, i.e., it binds to a tet operator in the presence of tetracycline
  • mutated tet R- 4 amino acid changes which resulted in a reverse tetracycline-regulated transactivator protein, i.e., it binds to a tet operator in the presence of tetracycline linked to a polypeptide which activates transcription.
  • In vivo gene therapy may be accomplished by introducing the gene encoding a polypeptide(s) identified by the methods ofthe invention into cells via local injection of an identified polypeptide's encoding nucleic acid molecule or by other appropriate viral or non- viral delivery vectors.
  • a nucleic acid molecule encoding a polypeptide may be contained in an adeno-associated virus (AAV) vector for delivery to the targeted cells (e.g., Johnson, International Publication No. WO95/34670; International Application No. PCT/US95/07178).
  • AAV adeno-associated virus
  • the recombinant AAV genome typically contains AAV inverted terminal repeats flanking a DNA sequence encoding a polypeptide(s) identified by the methods ofthe invention operably linked to functional promoter and polyadenylation sequences.
  • Alternative suitable viral vectors include, but are not limited to, retrovirus, adenovirus, herpes simplex viras, lentiviras, hepatitis viras, parvovirus, papovaviras, poxviras, alphaviras, coronaviras, rhabdoviras, paramyxoviras, and papilloma viras vectors.
  • U.S. Patent No. 5,399,346 provides examples of a process for providing a patient with a therapeutic protein by the delivery of human cells which have been treated in vitro to insert a DNA segment encoding a therapeutic protein. Additional methods and materials for the practice of gene therapy techniques are described in U.S. Patent No. 5,631,236 involving adenoviral vectors; U.S. Patent No. 5,672,510 involving retroviral vectors; and U.S. 5,635,399 involving retroviral vectors expressing cytokines.
  • Nonviral delivery methods include, but are not limited to, liposome-mediated transfer, naked DNA delivery (direct injection), receptor-mediated transfer (ligand-DNA complex), elecfroporation, calcium phosphate precipitation, and microparticle bombardment (e.g., gene gun).
  • Gene therapy materials and methods may also include the use of inducible promoters, tissue-specific enhancer-promoters, DNA sequences designed for site-specific integration, DNA sequences capable of providing a selective advantage over the parent cell, labels to identify transformed cells, negative selection systems and expression control systems (safety measures), cell-specific binding agents (for cell targeting), cell-specific intemalization factors, and transcription factors to enhance expression by a vector as well as methods of vector manufacture.
  • gene therapy or cell therapy can further include the delivery of one or more additional polypeptide(s) in the same or a different cell(s).
  • additional polypeptide(s) in the same or a different cell(s).
  • Such cells may be separately introduced into the patient, or the cells may be contained in a single implantable device, such as the encapsulating membrane described above, or the cells may be separately modified by means of viral vectors.
  • a means to increase endogenous expression of a polypeptide(s) identified by the methods ofthe invention in a cell via gene therapy is to insert one or more enhancer element(s) into the polypeptide promoter, where the enhancer element(s) can serve to increase transcriptional activity ofthe gene.
  • the enhancer element(s) used will be selected based on the tissue in which one desires to activate the gene(s); enhancer elements known to confer promoter activation in that tissue will be selected. For example, if a gene encoding a polypeptide(s) identified by the methods ofthe invention is to be "turned on" in T-cells, the lck promoter enhancer element may be used.
  • the functional portion ofthe transcriptional element to be added may be inserted into a fragment of DNA containing the identified polypeptide promoter (and optionally, inserted into a vector and/or 5! and/or 3! flanking sequence(s), etc.) using standard cloning techniques.
  • This constract can then be introduced into the desired cells either ex vivo or in vivo.
  • Gene therapy also can be used to decrease polypeptide expression by modifying the nucleotide sequence ofthe endogenous promoter(s). Such modification is typically accomplished via homologous recombination methods.
  • a DNA molecule containing all or a portion ofthe promoter ofthe gene(s) selected for inactivation can be engineered to remove and/or replace pieces ofthe promoter that regulate transcription.
  • the TATA box and/or the binding site of a transcriptional activator ofthe promoter may be deleted using standard molecular biology techniques; such deletion can inhibit promoter activity thereby repressing the transcription ofthe corresponding gene.
  • the deletion ofthe TATA box or the transcription activator binding site in the promoter may be accomplished by generating a DNA constract comprising all or the relevant portion of the polypeptide promoter(s) (from the same or a related species as the gene(s) to be regulated) in which one or more ofthe TATA box and/or transcriptional activator binding site nucleotides are mutated via substitution, deletion and/or insertion of one or more nucleotides.
  • the TATA box and/or activator binding site has decreased activity or is rendered completely inactive.
  • the construct will typically contain at least about 500 bases of DNA that correspond to the native (endogenous) 5' and 3' DNA sequences adjacent to the promoter segment that has been modified.
  • the construct may be introduced into the appropriate cells (either ex vivo or in vivo) either directly or via a viral vector as described herein.
  • the integration ofthe constract into the genomic DNA ofthe cells will be via homologous recombination, where the 5' and 3' DNA sequences in the promoter constract can serve to help integrate the modified promoter region via hybridization to the endogenous chromosomal DNA.
  • compositions are within the scope ofthe present invention.
  • Such pharmaceutical compositions may comprise a therapeutically effective amount of an identified agonist or antagonist/inhibitor in admixture with a pharmaceutically or physiologically acceptable formulation agent selected for suitability with the mode of administration.
  • they may also comprise a therapeutically effective amount of one or more selective binding agents in admixture with a pharmaceutically or physiologically acceptable formulation agent selected for suitability with the mode of administration.
  • Such compositions may be administered in therapeutically effective amounts depending on the application.
  • Acceptable formulation materials preferably are nontoxic to recipients at the dosages and concentrations employed.
  • the pharmaceutical composition may contain formulation materials for modifying, maintaining or preserving, for example, the pH, osmolarity, viscosity, clarity, color, isotonicity, odor, sterility, stability, rate of dissolution or release, adsorption or penetration ofthe composition.
  • Suitable formulation materials include, but are not limited to, amino acids (such as glycine, glutamine, asparagine, arginine or lysine); antimicrobials; antioxidants (such as ascorbic acid, sodium sulfite or sodium hydrogen-sulfite); buffers (such as borate, bicarbonate, Tris-HCl, citrates, phosphates, other organic acids); bulking agents (such as mannitol or glycine), chelating agents (such as ethylenediamine tefraacetic acid (EDTA)); complexing agents (such as caffeine, polyvinylpyrrolidone, beta-cyclodextrin or hydroxypropyl-beta-cyclodextrin); fillers; monosaccharides; disaccharides and other carbohydrates (such as glucose, mannose, or dextrins); proteins (such as serum albumin, gelatin or immunoglobulins); coloring; flavoring and diluting agents; emulsifying agents; hydro
  • the optimal pharmaceutical composition will be determined by one skilled in the art depending upon, for example, the intended route of administration, delivery format, and desired dosage. See for example, Remington's Pharmaceutical Sciences, supra. Such compositions may influence the physical state, stability, rate of in vivo release, and rate of in vivo clearance ofthe molecule.
  • the primary vehicle or carrier in a pharmaceutical composition may be either aqueous or non-aqueous in nature.
  • a suitable vehicle or carrier may be water for injection, physiological saline solution or artificial cerebrospinal fluid, possibly supplemented with other materials common in compositions for parenteral administration.
  • Neutral buffered saline or saline mixed with serum albumin are further exemplary vehicles.
  • Other exemplary pharmaceutical compositions comprise Tris buffer of about pH 7.0-8.5, or acetate buffer of about pH 4.0-5.5, which may further include sorbitol or a suitable substitute therefor.
  • polypeptide compositions may be prepared for storage by mixing the selected composition having the desired degree of purity with optional formulation agents (Remington's Pharmaceutical Sciences, supra) in the form of a lyophilized cake or an aqueous solution. Further, the polypeptide product may be formulated as a lyophilizate using appropriate excipients such as sucrose. Pharmaceutical compositions can be selected for parenteral delivery.
  • compositions may be selected for inhalation or for delivery through the digestive tract, such as orally.
  • the preparation of such pharmaceutically acceptable compositions is within the skill ofthe art.
  • the formulation components are present in concentrations that are acceptable to the site of administration.
  • buffers are used to maintain the composition at physiological pH or at slightly lower pH, typically within a pH range of from about 5 to about 8.
  • the therapeutic compositions for use in this invention may be in the form of a pyrogen-free, parenterally acceptable aqueous solution comprising the desired agonist or antagonist/inhibitor molecule in a pharmaceutically acceptable vehicle.
  • a particularly suitable vehicle for parenteral injection is sterile distilled water in which an agonist or antagonist/inhibitor molecule is formulated as a sterile, isotonic solution, properly preserved.
  • Yet another preparation can involve the formulation ofthe desired molecule with an agent, such as injectable microspheres, bio- erodible particles, polymeric compounds (polylactic acid, polyglycolic acid), beads, or liposomes, which provides for the controlled or sustained release ofthe product which may then be delivered via a depot injection.
  • Hyaluronic acid may also be used, and this may have the effect of promoting sustained duration in the circulation.
  • Other suitable means for the introduction ofthe desired molecule include implantable drag delivery devices.
  • a pharmaceutical composition may be formulated for inhalation.
  • an agonist or antagonist/inhibitor molecule may be formulated as a dry powder for inhalation.
  • Agonist or antagonist/inhibitor molecule inhalation solutions may also be formulated with a propellant for aerosol delivery.
  • solutions may be nebulized.
  • Pulmonary administration is further described in PCT Application No. PCT/US94/001875, which describes pulmonary delivery of chemically modified proteins. It is also contemplated that certain formulations may be administered orally.
  • agonist or antagonist/inhibitor molecules which are administered in this fashion can be formulated with or without those carriers customarily used in the compounding of solid dosage forms such as tablets and capsules.
  • a capsule may be designed to release the active portion ofthe formulation at the point in the gastrointestinal tract when bioavailability is maximized and pre-systemic degradation is minimized.
  • Additional agents can be included to facilitate absorption ofthe agonist or antagonist/inhibitor molecule.
  • Diluents, flavorings, low melting point waxes, vegetable oils, lubricants, suspending agents, tablet disintegrating agents, and binders may also be employed.
  • Another pharmaceutical composition may involve an effective quantity of an agonist or antagonist/inhibitor molecule in a mixture with non-toxic excipients which are suitable for the manufacture of tablets. By dissolving the tablets in sterile water, or other appropriate vehicle, solutions can be prepared in unit dose form.
  • Suitable excipients include, but are not limited to, inert diluents, such as calcium carbonate, sodium carbonate or bicarbonate, lactose, or calcium phosphate; or binding agents, such as starch, gelatin, or acacia; or lubricating agents such as magnesium stearate, stearic acid, or talc. Additional pharmaceutical compositions will be evident to those skilled in the art, including formulations involving identified agonist or antagonist/inhibitor molecules in sustained- or controlled-delivery formulations. Techniques for formulating a variety of other sustained- or controlled-delivery means, such as liposome carriers, bio-erodible microparticles or porous beads and depot injections, are also known to those skilled in the art.
  • sustained-release preparations include semipermeable polymer matrices in the form of shaped articles, e.g. films, or microcapsules.
  • Sustained release matrices may include polyesters, hydrogels, polylactides (U.S. 3,773,919, EP 58,481), copolymers of L-glutamic acid and gamma ethyl-L-glutamate (Sidman et al., Biopolymers, 22:547-556, 1983), poly (2- hydroxyethyl-methacrylate) (Langer et al., J.
  • Sustained-release compositions also include liposomes, which can be prepared by any of several methods known in the art. See e.g., Eppstein et al., Proc. Natl. Acad. Sci. USA, 52:3688-3692, 1985; EP 36,676; EP 88,046; EP 143,949. Formulations that facilitate delivery to the CNS are preferred for this invention.
  • the pharmaceutical composition to be used for in vivo administration typically must be sterile. This may be accomplished by filtration through sterile filtration membranes. Where the composition is lyophilized, sterilization using this method may be conducted either prior to or following lyophilization and reconstitution.
  • the composition for parenteral administration may be stored in lyophilized form or in solution.
  • parenteral compositions generally are placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle. Once the pharmaceutical composition has been formulated, it may be stored in sterile vials as a solution, suspension, gel, emulsion, solid, or a dehydrated or lyophilized powder.
  • kits for producing a single-dose administration unit may each contain both a first container having a dried protein and a second container having an aqueous formulation.
  • kits containing single and multi-chambered pre-filled syringes e.g., liquid syringes and lyosyringes.
  • a typical dosage may range from about O.Ol ⁇ g/kg to up to about 100 mg/kg or more, depending on the factors mentioned above. In other embodiments, the dosage may range from 0.1 mg/kg up to about 100 mg/kg; or lmg/kg up to about 100 mg/kg; or 5 mg/kg up to about 100 mg/kg.
  • the frequency of dosing will depend upon the pharmacokinetic parameters of the agonist or antagonist/inhibitor molecule in the formulation used. Typically, a clinician will administer the composition until a dosage is reached that achieves the desired effect.
  • the composition may therefore be admimstered as a single dose, or as two or more doses (which may or may not contain the same amount ofthe desired molecule) over time, or as a continuous infusion via implantation device or catheter. Further refinement ofthe 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 route of administration ofthe pharmaceutical composition is in accord with known methods, e.g.
  • compositions may be administered by bolus injection or continuously by infusion, or by implantation device.
  • the composition may be administered locally via implantation of a membrane, sponge, or another appropriate material on to which the desired molecule has been absorbed or encapsulated.
  • the device may be implanted into any suitable tissue or organ, and delivery ofthe desired molecule may be via diffusion, timed-release bolus, or continuous administration.
  • an agonist or antagonist/inhibitor molecule can be delivered by implanting certain cells that have been genetically engineered, using methods such as those described herein, to express and secrete the polypeptide ofthe identified agonist or antagonist/inhibitor.
  • Such cells may be animal or human cells, and may be autologous, heterologous, or xenogeneic.
  • the cells may be immortalized.
  • the cells may be encapsulated to avoid infiltration of surrounding tissues.
  • the encapsulation materials are typically biocompatible, semipermeable polymeric enclosures or membranes that allow the release ofthe protein product(s) but prevent the destruction ofthe cells by the patient's immune system or by other detrimental factors from the surrounding tissues.
  • the present invention includes the use of pharmaceutical compositions in neurogenesis and neuroregeneration (or in the manufacture of medicaments for treatment of conditions that benefit from neurogenesis or neuroregeneration).
  • compositions might affect these processes, it is important to understand some aspects of neuroregeneration, neurogenesis, and neurodegenerative diseases and disorders as set out below.
  • CNS Regeneration or Neuroregeneration and Neurogenesis refers to one of several types of events that lead to functional improvement ofthe CNS which can manifest itself as an improvement, stabilization, or slowed-down deterioration of functions such as cognition, vision, etc.
  • the cellular basis for CNS regeneration can be e.g.
  • CNS Regeneration and the Treatment of CNS Trauma and Neuorodegenerative Diseases and Disorders CNS regeneration is a desirable event that can slow down the progression or ameliorate consequences of many ofthe conditions that negatively affect the CNS and often lead to the loss of neuronal, astroglial, and other cells or causes their functional impairment.
  • Such conditions include CNS trauma, ischemic and hypoxic damage, toxic damage, damage connected with a metabolic impairment (e.g. diabetes and diabetic retinopathy), the whole range of neurodegenerative diseases (e.g. Alzheimer's disease, Parkinson's disease, multiple sclerosis, Jacob-Creutzfelt's disease and other prion diseases), epilepsy as well as aging.
  • the latter is not considered a disease (since it is inevitable and affects all individuals) but is associated with the same loss of neuronal and glial cells and deterioration of their function, albeit more discrete and with a comparably slow progression. 3.
  • Example 1 describes the identification of molecular targets by DNA arrays and protein analysis;
  • Example 2 provides a screening assay for complement 3 a receptor (C3aR) or complement 5a receptor (C5aR) agonists;
  • Example 3 discloses a screening assay for inhibitors of IGFBP-4;
  • Example 4 describes a screening assay for inhibitors of UNC-51- like kinase (ULK);
  • Example 5 provides a screening assay for effect(s) of endothelin receptor B (ETBR) antagonists in neurons, neuronal stem cells, and in animals after neural injury;
  • Example 6 describes entorhinal cortex lesion as a means of evaluating neuroregeneration;
  • Example 7 discloses neuronal cell cultures;
  • Example 8 discusses evaluation of astrocytic processes by immunohistochemistry;
  • Example 9 describes dye filling of astrocytes;
  • Example 10 provides a method for the quantification of proliferating cells in the brain;
  • Example 11 describes the quantification of newly generated neurons in
  • Example 1 Identification of Molecular Targets by DNA Arrays and Protein Analysis
  • DNA arrays, PCR (including quantitative RT-PCR), and subsequent protein analyses were used as a means to characterize gene and protein expression levels in normal mice and in the regeneration-supporting environment in GFAP-/-Vim-/- mice, to identify molecular targets that promote neurogenesis and regeneration in the adult CNS.
  • C3a Receptor C3aR
  • C5a Receptor C5a Receptor
  • Neural stem cells, migrating neuroblasts, immature neurons, and mature neurons all express receptors for complement fragments C3a and C5a.
  • mice deficient in the third complement component C3 -/-
  • C3 -/- mice had 30-50% fewer neural progenitor cells and 25% fewer newly formed neurons in the prenumbra than controls.
  • C3-/- mice also had larger infarct volumes and 24% fewer migrating neural progenitor cells in the subventricular zone.
  • the present invention includes a method of screening for C3aR or C5aR agonists.
  • Cells e.g., rat basophilic leukemia cell line, RBL-2H3 (ATCC no.
  • CRL-2256 stably expressing human C3aR (polynucleotide, SEQ ID NO: 4; polypeptide, SEQ ID NO: 5) or human C5aR (polynucleotide, SEQ ID NO: 11; polypeptide, SEQ ID NO: 12), are maintained under standard cell culture conditions in Eagle's MEM with Earle's salts, with L- glutamine and nonessential amino acids supplemented with FBS (10%) and G418 (400 ⁇ g/ml).
  • a radioligand binding assay based on the use of C3aR- or C5aR-expressing cells, or membranes of cells thereof, and 125 I-labelled human C3a (polynucleotide, SEQ ID NO: 1; polypeptide, SEQ ID NO: 2) or 125 I-labelled human C5a (polynucleotide, SEQ ID NO: 8; polypeptide, SEQ ID NO: 9), respectively, is performed in a 96-well microtiter plate format. Live cells, or membranes thereof, are bound to beads. Each plate well contains either I- C3a or 125 I-labelled C5a in binding buffer. Control wells, used to measure nonspecific binding, include an excess of unlabeled C3a or C5a.
  • Putative modulators of C3aR or C5aR such as non-peptide (e.g., small molecules from chemical libraries), or peptide, compounds are added. After incubation, the plates are washed and the plate-bound radioactivity is counted on a scintillation counter. The greater the binding of a test compound to the receptor (indicative of possible agonist or antagonist activity), the less ofthe radiolabelled ligand will bind to the cells or the cell membranes bound to the plate, which in turn results in a lower radioactivity count.
  • Compounds with high affinity binding to the respective receptor are further tested for an agonistic effect in another assay to distinguish agonists from antagonists, e.g., in a receptor intemalization assay, a chemotaxis assay, a H 2 O 2 production assay, a cell proliferation assay, a cell differentiation assay, and/or in an animal model of stroke or neural injury, etc.
  • a receptor intemalization assay uses human neutrophils which are stimulated by incubation with the natural ligands C3a or C5a, or with putative agonist compounds.
  • C3aR or C5aR are detected by polyclonal antibodies, and receptor intemalization is quantified by flow cytometry.
  • a chemotaxis assay uses human neutrophils which are fluorescein-labeled with 2',7'-bis-(2-carboxyethyl)-5-(and 6)-carboxyfluorescein acetoxymethyl ester) for 30 min at 37°C. After a washing step, labeled neutrophils (5 x 10 6 cells/ml) are loaded into the upper chamber of a 96-well mini chamber, separated by a polycarbonate filter with a porosity of 3 ⁇ m.
  • Lower chambers are loaded with different concentrations of C3a polypeptide, C5a polypeptide, or putative agonist compounds.
  • Cells are incubated for 30 min at 37°C, and the number of cells that migrate through the polycarbonate membrane to the lower surface is determined by cytofluorometry.
  • a H 2 O 2 production assay determines H 2 O production by isolated human neutrophils. In this assay, cells are pretreated for 1 h at 37°C with either C3a polypeptide or C5a polypeptide (@ 10 nM) or a putative agonist compound(s) in the presence of 1 mM sodium azide (to prevent endogenous catalases from destroying H O 2 ).
  • phorbol myristate acetate 25 ng/ml is added at the end ofthe preincubation and cell suspensions are incubated at 37°C for 15 min. The reaction is terminated by the addition of 0.1 ml of trichloroacetic acid (50% w/v). Samples are then centrifuged for 10 min at 500 x g, and ferrous ammonium sulfate and potassium thiocyanate are added to the supernatant at final concentrations of 1.5 mM and 0.25 M, respectively. The absorbance ofthe ferrithiocyanate complex is measured at 480 nm and is compared with a standard curve generated from dilutions of reference solutions of H O 2 .
  • a compound(s) identified as a putative C3aR or C5aR agonist(s) is also tested for its effect(s) on the in vitro proliferation and/or differentiation of neural stem cells, e.g., HCNA 94/GFPH (Palmer et al, Mol. Cell Neurosci. 6:389-404, 1997; Takahashi et al.,
  • the putative agonist(s) is also tested for its effect on neurogenesis in vivo.
  • the agonist(s) is administered orally or via an intraperitoneal, intravenous, intracranial, or subcutaneous injection.
  • the agonist's effect(s) on basal neurogenesis, as well as injury- induced neurogenesis, is determined by BrdU injections and immunostaining for Ki67, BrdU, NeuN, or doublecortin in various animal models of neural injury, e.g., middle cerebral artery occlusion (MCAO), electrical injury, and entorhinal cortex lesion.
  • MCAO middle cerebral artery occlusion
  • An increased number of Ki67-, BrdU-, NeuN-, or doublecortin-positive immunostained cells, compared to control (non-treated animals) indicates a positive effect on neurogenesis.
  • C3a and C5a ligands, fragments thereof, and the C3aR and C5aR agonist compounds, identified by the methods ofthe invention are then used to stimulate neurogenesis after cerebral ischemia and other types of brain injury, including neurodegenerative disorders, such as Alzheimer's disease, and to counteract the loss of neurons during aging.
  • Example 3 Screening Assay for IGFBP-4 Antagonists In the hippocampus ofthe uninjured control mouse brain, astrocytes were found to be highly positive for IGFBP-4 (SEQ ID NO: 20). Likewise, in the hippocampus of the injured control mouse brain (after entorhinal cortex lesions), reactive astrocytes were found to be highly positive for IGFBP-4. However, both non-reactive and reactive astrocytes in GFAP-/-Nim-/- (knockout) mice, that exhibit a regeneration-permissive environment, are negative for IGFBP-4. These data provide an indication to use IGFBP-4 inhibitors to create a regeneration-permissive environment to stimulate regeneration. The present invention contemplates a method of screening for IGFBP-4 inhibitors/antagonists. Primary mouse astrocytes or human astrocytoma cell lines, e.g. U-87 (ATCC
  • HTB-14 are maintained under standard cell culture conditions in Eagle's MEM with Earle's salts, with L-glutamine and nonessential amino acids supplemented with fetal calf serum (10%). Binding assays are performed in a 96-well microtiter plate format containing live cells. Each well is first coated with anti-IGFBP-4 antibody. Control wells without cells are included for non-specific binding ofthe secondary antibody. Non-peptide, as well as peptide, compounds (antagonists) are added and the cells are incubated. After incubation, the medium is removed from the wells and the cells are fixed with methanol.
  • Plate-bound/cell- bound IGFBP-4 is detected by the addition of a secondary anti-IGFBP-4 antibody that is either biotinylated or horse radish peroxidase (HRP)-conjugated. Plates containing biotinylated secondary antibody are further incubated with HRP- streptavidin. After development with a color substrate, the intensity of staining is quantified in a spectrophotometer. Compounds that lead to down-regulation of IGFBP-4 expression (antagonists) exhibit reduced optical density, in comparison with cells incubated without any test compound. Putative antagonists of IGFBP-4 are further tested for cell-toxicity.
  • HRP horse radish peroxidase
  • IGFBP-4 antagonists are further tested in vitro and in vivo as set out below. Astrocyte and neuron cultures from either postnatal day 0-2 mouse brains or postnatal day 6 cerebella are prepared either as explant cultures or by trypsinization (Pekny et al., Exp. Cell Res. 239: 332, 1998) and are allowed to grow into subconfluent state. Astrocytes are then plated on coverslips into 24-well culture plates, or alternatively, directly into 24 or 96-well plates.
  • Assays for neurite outgrowth are performed by culturing neurons on confluent monolayers of astrocytes in DMEM-F12 containing 5% fetal calf or bovine serum and 50 ng/ml NGF and various concentrations ofthe IGFBP-4 antagonist. After 6-24 hours, the cultures are fixed with 4% paraformaldehyde and immunostaining is perfomed by using antibodies against tubulin. The outgrowth of neurites is assessed from captured images. Neurite length is assessed as the distance from the center ofthe cell soma to the tip of its longest neurite.
  • a tested substance is considered to have an IGFBP-4 antagonistic effect (neuroregeneration-promoting effect), if in its presence, the average neurite length exceeds the average neurite length in cultures maintained without such a substance.
  • the IGFBP-4 antagonist(s) is then tested for its effect on neurogenesis in vivo.
  • the putative antagonist compound(s) is administered orally or via an intraperitoneal, intravenous, intracranial, or subcutaneous injection.
  • the antagonist's effect(s) on basal neurogenesis, as well as injury-induced neurogenesis is determined by BrdU injections and immunostaining for Ki67, BrdU, NeuN, or doublecortin in various animal models of neural injury, e.g., middle cerebral artery occlusion (MCAO), electrical injury, and entorhinal cortex lesion.
  • MCAO middle cerebral artery occlusion
  • IGFBP-4, fragments thereof, and the putative IGFBP-4 downregulating compounds (antagonists), identified by the methods ofthe invention are then used to stimulate neurogenesis after cerebral ischemia and other types of brain injury, including neurodegenerative disorders, such as Alzheimer's disease, and to counteract the loss of neurons during aging.
  • ULK UNC-51-Like Kinase
  • Primary mouse astrocytes or human astrocytoma cell lines, e.g. U-87 (ATCC no. HTB-14) are maintained under standard cell culture conditions in Eagle's MEM with Earle's salts, with L-glutamine and nonessential amino acids supplemented with fetal calf serum (10%).
  • Binding assays are performed in a 96-well microtiter plate format containing live cells. Each well is first coated with anti-ULK antibody. Control wells without cells are included for non-specific binding ofthe secondary antibody.
  • Non-peptide, as well as peptide, compoxmds (antagonists) are added and the cells are incubated. After incubation, the medium is removed from the wells and the cells are fixed with methanol. Plate-bound cell-bound ULK is detected by the addition of a secondary anti-ULK antibody that is either biotinylated or horse radish peroxidase (HRP)-conjugated. Plates containing biotinylated secondary antibody are further incubated with HRP- streptavidin. After development with a color substrate, the intensity of staining is quantified in a spectrophotometer.
  • HRP horse radish peroxidase
  • ULK antagonists Compounds that lead to down-regulation of ULK expression (antagonists) exhibit reduced optical density, in comparison with cells incubated without any test compound. Putative antagonists of ULK are further tested for cell-toxicity. Non-toxic compounds that induce a reduction in optical density in an assay as set out above (down- regulate ULK expression) by more than 50% are considered to be ULK antagonists. ULK antagonists are further tested in vitro and in vivo as set out below. Astrocyte and neuron cultures from either postnatal day 0-2 mouse brains or postnatal day 6 cerebella are prepared either as explant cultures or by trypsinization (Pekny et al, Exp. Cell Res. 239: 332, 1998) and are allowed to grow into subconfluent state.
  • Astrocytes are then plated on coverslips into 24-well culture plates, or alternatively, directly into 24 or 96-well plates.
  • Assays for neurite outgrowth are performed by culturing neurons on confluent monolayers of astrocytes in DMEM-F12 containing 5% fetal calf or bovine serum and 50 ng/ml NGF and various concentrations ofthe ULK antagonist. After 6-24 hours, the cultures are fixed with 4% paraformaldehyde and immunostaining is perfomed by using antibodies against tubulin.
  • the outgrowth of neurites is assessed from captured images. Neurite length is assessed as the distance from the center ofthe cell soma to the tip of its longest neurite.
  • a tested substance is considered to have an ULK antagonistic effect (neuroregeneration-promoting effect), if in its presence, the average neurite length exceeds the average neurite length in cultures maintained without such a substance.
  • the ULK antagonist(s) is then tested for its effect on neurogenesis in vivo.
  • the putative antagonist compound(s) is administered orally or via an intraperitoneal, intravenous, intracranial, or subcutaneous injection.
  • the antagonist's effect(s) on basal neurogenesis, as well as injury-induced neurogenesis is determined by BrdU injections and immunostaining for Ki67, BrdU, NeuN, or doublecortin in various animal models of neural injury, e.g., middle cerebral artery occlusion (MCAO), electrical injury, and entorhinal cortex lesion.
  • MCAO middle cerebral artery occlusion
  • ULK, fragments thereof, and the putative ULK downregulating compounds (antagonists), identified by the methods ofthe invention are then used to stimulate neurogenesis after cerebral ischemia and other types of brain injury, including neurodegenerative disorders, such as Alzheimer's disease, and to counteract the loss of neurons during aging.
  • Example 5 Screening Assay(s) for Effect(s) of Endothelin Receptor B (ETBR) Antagonists in Neurons, Neuronal Stem Cells, and in Animals after Neural Injury
  • ETBR Endothelin Receptor B
  • ETBR selective inhibitors (antagonists) of ETBR, such as BQ-788 (Calbiochem) and A-192621 (Abbott Laboratories) (Bagnato et al., Cancer Res. 64:1436- 1443, 2004; Rosano et al., Am J Pathol. 163:753-762, 2003), are tested for their effects in vitro and/or in vivo as set out below.
  • Astrocyte and neuron cultures from either postnatal day 0-2 mouse brains or postnatal day 6 cerebella are prepared either as explant cultures or by trypsinization (Pekny et al., Exp. Cell Res. 239: 332, 1998) and are allowed to grow into subconfluent state.
  • Astrocytes are then plated on coverslips into 24-well culture plates, or alternatively, directly into 24 or 96-well plates.
  • Assays for neurite outgrowth are performed by culturing neurons on confluent monolayers of astrocytes in DMEM-F12 containing 5% fetal calf or bovine serum and 50 ng/ml NGF and various concentrations ofthe ETBR antagonist. After 6-24 hours, the cultures are fixed with 4% paraformaldehyde and immunostaining is perfomed by using antibodies against tubulin.
  • the outgrowth of neurites is assessed from captured images. Neurite length is assessed as the distance from the center ofthe cell soma to the tip of its longest neurite.
  • a tested substance is considered to have an antagonistic effect, if in its presence, the average neurite length exceeds the average neurite length in cultures maintained without such a substance.
  • An ETBR antagonist is also tested for its effect on neurogenesis in vivo.
  • the ETBR antagonist(s) is administered orally or via an intraperitoneal injection intraperitoneal, intravenous, intracranial, or subcutaneous injection.
  • the antagonist's effect(s) on basal neurogenesis, as well as injury-induced neurogenesis is determined by BrdU injections and immunostaining for Ki67, BrdU, NeuN, or doublecortin in various animal models of neural injury, e.g., middle cerebral artery occlusion (MCAO), electrical injury, and entorhinal cortex lesion.
  • MCAO middle cerebral artery occlusion
  • ETBR antagonists are then used to stimulate neurogenesis after cerebral ischemia and other types of brain injury, including neurodegenerative disorders, such as Alzheimer's disease, and to counteract the loss of neurons during aging.
  • studies in which known connections are lesioned and changes in projection brain area are examined and used to explore structural plasticity in animal models.
  • the impact of entorhinal cortex lesions on the function ofthe hippocampal loop is widely studied.
  • modulators of the invention on neuroregeneration
  • entorhinal cortex lesion is performed on mice, and modulators of neuroregeneration (C3aR or C5aR agonists or IGFBP-4, ULK, or ETBR antagonists) are administered to induce neuroregeneration.
  • Unilateral entorhinal cortex lesion is performed as described previously (Stone et al., J. Neurosci. 18:3180-3185, 1998).
  • mice After 4 or 14 days, the mice are perfused transcardially with 4% paraformaldehyde (for immunohistochemistry) or 3% glutaraldehyde and 2% paraformaldehyde (for electron microscopy) and the brains are examined for neuroregeneration or neurogenesis by determining the 1) extension of astrocytic processes, 2) dye filling of asfrocytes, 3) quantification of newly proliferation cells, and 4) quantification of newly formed neurons (set out in Examples 8-11 below).
  • paraformaldehyde for immunohistochemistry
  • glutaraldehyde and 2% paraformaldehyde for electron microscopy
  • Example 7 Cell Culture Primary cultures, enriched in reactive astrocytes, are prepared from 2-day old mice as described by Pekny et al. (Exp. Cell. Res. 239:332-343, 1998). Cell cultures are prepared from 1) normal mice, 2) normal mice treated with a modulator of neuroregeneration (an agent identified as an agonist of C3aR or C5aR, or an antagonist of IGFBP-4, ULK, or ETBR), and optionally, 3) GFAP-/-Nim-/- mice.
  • a modulator of neuroregeneration an agent identified as an agonist of C3aR or C5aR, or an antagonist of IGFBP-4, ULK, or ETBR
  • Cultures are grown for 10 days in 96-well plates (Greiner Bio-One, Frickenhausen, Germany) containing Dulbecco's modified Eagle's medium (D5671 Sigma-Aldrich, St Louis, MO, USA), 10% fetal calf serum (Gibco BRL, Paisly, UK), L-glutamine (2 mM), and penicillin/streptomycin (Gibco BRL). Cultures are then evaluated for neurite outgrowth and extension of astrocytic process. Agents which promote neurite outgrowth and inhibit the extension of astrocytic processes are selected.
  • a cryoprotectant 50% 0.05M sodium phosphate, pH 7.3, 30% ethylene glycol, 20% glycerol
  • the sections are incubated in 0.05% glycine in PBS for 1 h at room temperature and permeabilized overnight in PBS containing 0.5% Tween 20 and 1% BSA at 4° C. Then, the sections are incubated with monoclonal antibody against glutamine synthase (Chemicon International; 1:100) or rabbit anti-cow SI 00 (DAKO, 1:200) in 0.01% Tween 20 and 1% BSA in PBS overnight.
  • glutamine synthase Chemicon International; 1:100
  • DAKO rabbit anti-cow SI 00
  • goat anti-mouse antibodies conjugated with Alexa 488 (Molecular Probes, Eugene, OR, USA; 1 :500) or goat anti-rabbit antibodies conjugated with Alexa 568 (Molecular Probes, 1:500) are incubated with the sections overnight at 4 C.
  • propidium iodide (Sigma-Aldrich) is added to the last wash before mounting.
  • mice are also examined using SI 00 immunostaining both at day 4 and 14.
  • Astrocytic processes are compared in 1) normal mice, 2) nonnal mice treated with a modulator of neuroregeneration (an agent identified as an agonist of C3aR or C5aR, or an antagonist of IGFBP-4, ULK, or ETBR), and optionally, 3) GFAP-/-Vim-/- mice.
  • a modulator of neuroregeneration an agent identified as an agonist of C3aR or C5aR, or an antagonist of IGFBP-4, ULK, or ETBR
  • Agents which inhibit astrocytic process length are selected.
  • Example 9 Dye Filling of Astrocytes
  • C3aR, C5aR, IGFBP-4, ULK, and ETBR dye-filling experiments are peformed, which allow 3D reconstraction of astrocytes in situ.
  • Intracellular injection of astrocytes in lightly fixed tissue slices is performed as described (Bushong et al., Neurosci. 22:183-92, 2002; Bushong et al, J. Camp. Neurol. 462:241-51, 2003).
  • mice On day 4 after entorhinal cortex lesion, the mice are transcardially perfused with oxygenated Ringer's solution (0.79% NaCl, 0.038% KC1, 0.02% MgC12* 6H2O, 0.018% Na 2HPO4, 0.125% NaHCO3, 0.03% CaC12» 2H2O, 0.2% dextrose, 0.02% xylocaine), followed by 4% paraformaldehyde in PBS (pH 7.4,) for 8-10 minutes, both at 37°C.
  • the brain is placed in ice- cold PBS and cut with a vibratome into 75 ⁇ m horizontal slices.
  • the slices are stored in PBS at 4°C and examined with an Olympus BX50WI microscope using infrared-DIC optics (Olympus, Melville, NY, 60x water objective NA 1.4).
  • Astrocytes in the medial outer molecular layer ofthe dentate gyms ofthe hippocampus are identified by the shape and size of their somata.
  • Glass micropipettes (OD 1.00 mm, ID 0.58 mm) are pulled on a vertical puller (David Kopf Instruments, Tujunga, CA) and backfilled with 5% aqueous lucifer yellow (Sigma-Aldrich).
  • Asfrocytes are impaled and iontophoretically injected with the dye using 1- second pulses of negative current (0.5 Hz) for 1-2 minutes. After several cells are filled, the slices are placed in ice-cold 4% paraformaldehyde for at least 1 hour.
  • the slices are repeatedly washed in PBS and permeabilized for 1 h at room temperature in PBS containing 1% BSA, 0,25% Triton X-l 00 and 3% normal donkey serum, followed by incubation with guinea pig antibodies against GFAP (Sigma-Aldrich, 1:100) for 48 h at 4° C in PBS containing 1% BSA, 0.1% Triton X- 100 and 0.3% normal donkey serum.
  • Quantification of neuropil volume reached by a dye-filled astrocyte is performed on 3D reconstructed cells in 3 wild-type and 3 GFAP-/-Nim-/- mice (in total 57 cells quantified) using Imaris 3.3 software.
  • the number and character of cell processes reaching outside a 40 ⁇ m wide circle, centered around the soma, are assessed by using ImageJ software on superimposed serial images in of 61 dye-filled astrocytes.
  • Astrocytic processes are compared in 1) normal mice, 2) normal mice treated with a modulator of neuroregeneration (an agent identified as an agonist of C3aR or C5aR, or an antagonist of IGFBP-4, ULK, or ETBR), and 3) GFAP-/-Vim-/- mice. Agents which inhibit extension of astrocytic processes are selected.
  • Example 10 Quantification of Proliferating Cells in the Brain Brains are immersion- fixed for 1 day in 4% buffered paraformaldehyde and paraffin-embedded. Horizontal microtome sections (8 ⁇ m) are taken between 2000 and 2500 ⁇ m below the upper surface ofthe hippocampus, which is the region showing most prominent signs of neurodegeneration and astrocyte activation after entorhinal cortex lesion. Sections are rehydrated and antigen-retrieved with 0.01 M citrate buffer, pH 6.0, in a microwave oven for 15 min.
  • the sections are incubated first with rat Ki67 antibodies (clone TEC-3, DAKO) diluted 1 :25 in PBS containing 0.1% BSA and 0.05% Triton X-l 00, and then with rabbit anti-cow SI 00 (DAKO) diluted 1:300, both for lh.
  • rat Ki67 antibodies clone TEC-3, DAKO
  • DAKO rabbit anti-cow SI 00
  • lectin buffer PBS, pH 6.8, containing 1% Triton X-l 00, 0.1 mM MgCl 2 , 0.1 mM MnCl 2 , and 0.1 mM CaCl 2
  • the sections are incubated with biotinylated lectin from Bandeiraea simplicifolia (isolectin, Sigma-Aldrich), diluted 1:10 in lectin buffer, for 1 h.
  • the secondary antibodies are Cy3-conjugated anti-rat (Jackson Immuno Research, West Grove, PA, USA), Alexa 488-conjugated anti-rabbit, and Alexa 633-conjugated streptavidin (both Molecular Probes).
  • Ki67 pos cells in the subventricular zone is made in four consecutive 8 ⁇ m sections per mouse using an epifluoresence microscope (Nikon Eclipse El 000, Nikon Instruments Europe B.V., Badhoevedorp, The Netherlands).
  • Cell proliferation is compared in 1) normal mice, 2) normal mice treated with a modulator of neuroregeneration (an agent identified as an agonist of C3aR or C5aR, or an antagonist of IGFBP-4, ULK, or ETBR), and 3) GFAP-/-Vim-/- mice.
  • a modulator of neuroregeneration an agent identified as an agonist of C3aR or C5aR, or an antagonist of IGFBP-4, ULK, or ETBR
  • Example 11 Quantification of Newly Generated Neurons in the Brain Mice are injected intraperitoneally with 5-bromo-2'-deoxyuridine (BrdU, 300 mg/kg body weight, Sigma-Aldrich), twice daily from day one to day seven after entorhinal cortex lesion and perfused six days after the last injection transcardially with 4% paraformaldehyde. Brains are fixed for one day at 4 C in paraformaldehyde and horizontal vibratome sections (50 ⁇ m) are obtained as set out above. Mouse anti-NeuN antibody (Chemicon International), diluted 1:100, followed by Alexa 568-conjugated anti-mouse (Molecular Probes), diluted 1:500 are used for immunohistochemical staining.
  • PrdU 300 mg/kg body weight, Sigma-Aldrich
  • the sections are processed as described above (in Quantification of astrocytic processes). To unmask the BrdU antigen, the sections are incubated in 2N HCl for 2 h, and then washed several times in PBS, before incubation with FITC-conjugated rat anti-BrdU antibody (clone BUI/75, Accurate Chemicals, Westbury, NY, USA), diluted 1:100.
  • FITC-conjugated rat anti-BrdU antibody clone BUI/75, Accurate Chemicals, Westbury, NY, USA
  • a laser-scanning confocal microscope and software (TCS NT, Leica) is used to quantify the number of BrdU p0S and BrdU pos NeuN pos cells in the granule cell layer ofthe dentate gyrus ofthe hippocampus on the injured side, on 25 optical sections covering the thickness of 50 ⁇ m and the whole granule cell layer ofthe dentate gyrus ofthe hippocampus.
  • Cell number is compared in 1) normal mice, 2) normal mice treated with a modulator of neuroregeneration (an agent identified as an agonist of C3 aR or C5aR, or an antagonist of IGFBP-4, ULK, or ETBR), and 3) GFAP-/- Vim-/- mice. Agents which promote generation of new neurons (neurogenesis or neuroregeneration) are identified.
  • mice are inflicted with neural injury, e.g., middle cerebral artery occlusion (MCAO), electrical injury, and entorhinal cortex lesion. After infliction of neural injury, animals are treated with one or more ofthe various modulators of neuroregeneration identified herein.
  • neural injury e.g., middle cerebral artery occlusion (MCAO)
  • electrical injury e.g., electrical injury
  • entorhinal cortex lesion e.g., electrical injury, and entorhinal cortex lesion.
  • entorhinal cortex lesion e.g., entorhinal cortex lesion.
  • MCAO middle cerebral artery occlusion
  • Improvement in cognitive function is compared in 1) normal mice, 2) normal mice treated with a modulator of neuroregeneration (an agent identified as an agonist of C3aR or C5aR, or an antagonist of IGFBP-4, ULK, or ETBR), and 3) GFAP-/-Vim-/- mice. Agents which promote improvement in cognitive function are selected.
  • a modulator of neuroregeneration an agent identified as an agonist of C3aR or C5aR, or an antagonist of IGFBP-4, ULK, or ETBR
  • Agents which promote improvement in cognitive function are selected.
  • Example 13 Optic Nerve Injury and Treatment with Modulators of Neuroregeneration Through their ability to become reactive and form scars after injury, mature astrocytes represent a key barrier to optic nerve regeneration in older mice.
  • Optic nerve injury is a standard model for studying CNS regeneration.
  • Rodent retinal ganglion cells whose axons form the optic nerve pathway, normally do not have the ability to regenerate their axons through an injured optic nerve.
  • RRCs retinal ganglion cells
  • optic nerve crash is performed on mice and modulators of neuroregeneration (C3aR or C5aR agonists or IGFBP-4, ULK, or ETBR antagonists) are administered to induce neuroregeneration.
  • modulators of neuroregeneration C3aR or C5aR agonists or IGFBP-4, ULK, or ETBR antagonists
  • IGFBP-4, ULK, or ETBR antagonists C3aR or C5aR agonists or IGFBP-4, ULK, or ETBR antagonists
  • FluoroGold is placed in the spinal cords(SCs) of mice immediately after optic nerve crush to label RGCs whose axons connect or regenerate to the SC.
  • RGCs with regenerated axons are counted in 1) normal mice, 2) normal mice treated with a modulator of neuroregeneration (an agent identified as an agonist of C3aR or C5aR, or an antagonist of IGFBP-4, ULK, or ETBR), and 3) GFAP- ⁇ -Nim-/- mice.
  • the number of RGCs with regenerated axons are expressed as a percentage of RGCs in the uninjured retina. Agents which promote regenerated axons are selected.
  • Example 14 C3aR and C5aR Expression on Neural Stem Cells and Neural Progenitors hnmunocytochemical analysis of clonally derived neural stem cells from adult rat hippocampus showed universal expression of C3aR and C5aR. Both receptors appeared to be localized in the cell membrane and were homogeneously distributed. The specificity of the anti-C3aR and anti-C5aR antibody, respectively was confirmed by the absence of immunostaining on brain sections from mice deficient in C3aR (Kildsgaard et al., J Immunol. 165:5406-5409, 2000) and C5aR (Hopken et al., Nature 383: 86-89, 1996), respectively.
  • Dcx is a marker of migrating neuroblasts, which are normally present in the SNZ and rostral migratory stream of adult brain ( ⁇ acher et al., Eur. J. Neurosci. 14:629-644, 2001). In both regions, all Dcx pos cells were also positive for C5aR, and many were positive for C3aR. Both C3aR and C5aR appeared to be membrane bound and homogeneously distributed, immunostaining for ⁇ eu ⁇ , a marker of differentiated neurons, showed that over 95% of ⁇ eu ⁇ pos cells were also positive for the C3aR and C5aR. Thus, neural stem cells, migrating neuroblasts, and mature nexxrons express C3aR and C5aR.
  • Example 15 Reduced Basal Neurogenesis in Mice Treated with a C3aR Antagonist
  • a nonpeptide antagonist ofthe C3aR SB290157 (Calbiochem, San Diego, CA, USA; 500 ⁇ g/mouse; Ames et al., J. Immunol. 166:6341-6348, 2001) diluted in PBS and DMSO (1.16% v/v) twice daily or vehicle for 10 days.
  • mice During the first 7 days, all the mice also received bromodeoxyuridine (BrdU) (Sigma-Aldrich; 200 mg/kg). On day 10 after the first injection, the mice were deeply anesthetized and perfused. Mouse brains were embedded in paraffin, cut into 8- ⁇ m sections, and stained with hematoxylin and erytrosin. For immunohistochemical evaluation, the sections were deparaffinized, permeabilized in 0.01 M citric acid (pH 6.0), heated twice for 5 min each in a microwave oven for antigen retrieval, and blocked with 0.1% BSA and 0.05% Triton-X-100 in PBS. Negative control was performed by omitting the primary antibody, unless stated otherwise.
  • PrdU bromodeoxyuridine
  • Newly formed neurons were visualized by staining with biotinylated mouse anti-NeuN monoclonal antibody (Chemicon, Temecula, CA, USA; 1:100) followed by Cy3- conjugated streptavidin (Sigma-Aldrich; 1:100) or Alexa633-conjugated streptavidin (Molecular Probes; 1 :500) in combination with FITC-conjugated rat anti-BrdU antibody (Accurate Chemical, Westbury, NY, USA; 1:75).
  • NeuN pos BrdU p0S cells were counted in the penumbra on 2-3 sections per mouse. BrdU pos cells were also counted in the SNZ.
  • the sections were further stained with mouse anti-BrdU antibody (DAKO; 1 :100) and Alexa 568 conjugated goat anti-mouse Ig (Molecular Probes; 1 :500).
  • BrdU pos and ⁇ eu ⁇ pos BrdU p0S cells were counted in one hemisphere on 4-12 sections 160 ⁇ m apart/region in the granular layer of the olfactory bulb (bregma 3.2 mm to 4.28 mm) and dentate gyrus sub granular zone (bregma -1.34 mm to -3.64 mm).
  • Migrating neural progenitor cells were detected with goat anti-doublecortin (Dcx) antibody (Santa Cruz Biotechnology, Santa Cruz, CA, USA; 1 :50) followed by
  • Dcx pos BrdU pos Proliferating migrating neuroblasts (Dcx pos BrdU pos ), newly formed neurons ( ⁇ eu ⁇ pos BrdU pos ) and BrdU p0S cells were counted in the two principal sites of adult neurogenesis, SNZ and the dentate gyrus subgranular zone ofthe hippocampus, as well as in the olfactory bulb, the final destination for the neuroblasts originating in SNZ under basal conditions. In all three regions, the number of Dcx pos BrdU pos cells was reduced in mice that received the C3aR antagonist.
  • Example 16 Reduced Number of Neuroblasts in the SVZ in the Injured Hemisphere of C3-/- Mice after Brain Ischemia
  • C3-/- mice and wild-type controls were subjected to middle cerebral artery occlusion (MCAO) or transection (MCAT).
  • MCAO middle cerebral artery occlusion
  • MCAT transection
  • the C3-/- mice had 24% fewer Dcx pos cells in the ipsilateral SVZ than wild-type mice (P ⁇ 0.05).
  • Example 17 C3-/- and Control Mice Respond to Brain Ischemia by Increased Cell Proliferation in the Ipsilateral SVZ
  • mice were injected with BrdU before and for 7 d after MCAT.
  • BrdU pos cells were more numerous in the ipsilateral than in the contralateral SVZ at 7 d (92.8 ⁇ 4.0 vs. 77.9 ⁇ 4.1, P ⁇ 0.05 for C3-I- mice and 90.0 ⁇ 3.9 vs. 70.7 ⁇ 4.4, P ⁇ 0.005 for wild-type mice) and 21 d after MCAT (14.5 ⁇ 1.0 vs.
  • Example 18 C3-/- Mice Have Fewer Proliferating Nonmicroglial/Nonendothelial Cells in the Penumbra
  • Ki-67 immxmostaining showed no difference in the number of proliferating cells in the penumbra of C3-/- and wild-type mice 7 d after MCAO (107 ⁇ 11.4 vs. 110 ⁇ 19.2/mm 3 ).
  • the fraction of proliferating nonmicroglial, nonendothelial cells Ki-67 pos isolectin neg
  • a cell population enriched in neural progenitor cells was 30% lower in the C3-/- mice (11.0 ⁇ 1.25 vs. 15.5 ⁇ 1.31%, P ⁇ 0.05) than in controls.
  • Example 19 C3-/- Mice Have Fewer Neural Progenitor Cells in the Penumbra and Infarct Area
  • brain sections were immunohistochemically stained for nestin, a marker of neural progenitor cells that is also expressed by reactive astrocytes (Lendahl et al., Cell
  • C3-/- mice had 50% fewer nestin os GFAP neg cells in the infarct area (3.6 ⁇ 0.97 vs. 8.3 ⁇ 1.76 cells/section, P ⁇ 0.05) and in the penumbra (15.9 ⁇ 2.02 vs. 28.4 ⁇ 2.22 cells/section, P ⁇ 0.005) 7 d after MCAO and 30% fewer nestin pos GFAP neg cells in the penumbra (11.3 ⁇ 0.2 vs. 16.1 ⁇ 0.5 cells/10 mm 2 , P ⁇ 0.00001) 7 d after MCAT.
  • Example 20 C3-/- Mice Have Fewer Newly Formed Neurons after Ischemia To determine if the reduction in the number of neural progenitor cells and migrating neuroblasts leads to reduced formation of new neurons, combined immunostaining for NeuN and BrdU was used. C3-/- mice had fewer newly-formed neurons (BrdU pos NeuN pos cells) in the penumbra both at 7 d (7.5 ⁇ 0.4 vs. 10.0 ⁇ 0.5 cells/10 mm 2 , P ⁇ 0.001) and at 21 d after MCAT (9.7 ⁇ 0.6 vs. 13.3 ⁇ 0.9 cells/10 mm 2 , P ⁇ 0.005) than controls.
  • the fraction of these cells among the BrdU pos cells was reduced in the C3-/- mice (3.4 ⁇ 0.2 vs. 4.76 ⁇ 0.3%, P ⁇ 0.005 and 4.9 ⁇ 0.4 vs. 6.5 ⁇ 0.4%, P ⁇ 0.05) compared to controls.
  • triple-label immunostaining was performed with antibodies against BrdU, NeuN, and activated caspase-3, the latter being expressed in association with delayed ischemic neuronal death (Namura et al., J. Neurosci. 18:3659-3668, 1998).
  • Example 22 Activation of Astrocytes and Microglia at the Infarct Border is Similar in C3-I- and Control Mice
  • activation of astrocytes and microglia was observed at 7 days after MCAO.
  • Reactive asfrocytes were identified by staining with polyclonal antibody against GFAP (DAKO; 1 : 100) and inflammatory cells by biotinylated lectin (Sigma-Aldrich; 1:10) followed by TRITC-conjugated swine anti-rabbit Ig and FITC-conjugated streptavidin (both from DAKO).
  • Staining intensity was assessed by measuring the width ofthe band of positive cells at the infarct border.
  • Immunostaining for GFAP showed a massive presence of highly GFAP p0S astrocytes at the infarct border in both C3N ⁇ and wild-type mice.
  • staining for isolectin a marker of microglia and endothelial cells, demonstrated a rim of activated microglial cells around the ischemic lesion and migration of these cells into the infarct area in both groups.
  • the width ofthe GFAP pos band was comparable in C3 ⁇ T and wild-type mice (456 ⁇ 62.3 and 440 ⁇ 25.1 ⁇ m), as was the width ofthe isolectin pos band (367 ⁇ 18.8 and 319 ⁇ 20.3 ⁇ m).
  • This study showed that reactive gliosis and infiltration with microglial cells was comparable in C3T and wild-type mice.
  • complement activation products, at least C3 do not appear to be critical for the recraitment of reactive astrocytes and microglia to the necrotic brain region.

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Abstract

La présente invention a trait à des substances et des procédés utilisés pour l'identification de modulateurs de la neurogenèse ou de la régénération neuronale, et l'utilisation desdits modulateurs dans le traitement de maladies neurodégénératives et la lésion neurologique.
PCT/EP2005/003946 2004-04-15 2005-04-14 Substances et procedes pour le criblage de modulateurs de la regeneration neuronale WO2005101013A2 (fr)

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EP1891438A2 (fr) * 2005-05-27 2008-02-27 Advanced Cell Technology, Inc. Méthodes destinées à l'identification de ligands pour des cellules souches et cellules dérivées de celles-ci
WO2009083185A2 (fr) * 2007-12-28 2009-07-09 Fovea Pharmaceuticals Sa Compositions et procédés pour la prophylaxie et le traitement de troubles ophtalmiques dégénératifs cellulaires
WO2012174591A1 (fr) * 2011-06-20 2012-12-27 The University Of Queensland Prévention et traitement de conditions inflammatoires aiguës
US11266715B2 (en) 2016-11-21 2022-03-08 Marcela Pekna C3A receptor agonists for use against ischemic brain injury, stroke, traumatic brain injury, spinal cord injury and neurodegenerative disorders

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Cited By (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP1891438A2 (fr) * 2005-05-27 2008-02-27 Advanced Cell Technology, Inc. Méthodes destinées à l'identification de ligands pour des cellules souches et cellules dérivées de celles-ci
EP1891438A4 (fr) * 2005-05-27 2008-12-10 Advanced Cell Tech Inc Méthodes destinées à l'identification de ligands pour des cellules souches et cellules dérivées de celles-ci
WO2009083185A2 (fr) * 2007-12-28 2009-07-09 Fovea Pharmaceuticals Sa Compositions et procédés pour la prophylaxie et le traitement de troubles ophtalmiques dégénératifs cellulaires
WO2009083185A3 (fr) * 2007-12-28 2010-01-14 Fovea Pharmaceuticals Sa Compositions et procédés pour la prophylaxie et le traitement de troubles ophtalmiques dégénératifs cellulaires
WO2012174591A1 (fr) * 2011-06-20 2012-12-27 The University Of Queensland Prévention et traitement de conditions inflammatoires aiguës
AU2012272550B2 (en) * 2011-06-20 2017-06-01 The University Of Queensland Prevention and treatment of acute inflammatory conditions
US11266715B2 (en) 2016-11-21 2022-03-08 Marcela Pekna C3A receptor agonists for use against ischemic brain injury, stroke, traumatic brain injury, spinal cord injury and neurodegenerative disorders

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