WO2012112953A2

WO2012112953A2 - Molecular switch for neuronal outgrowth

Info

Publication number: WO2012112953A2
Application number: PCT/US2012/025738
Authority: WO
Inventors: John G FLANAGAN; Yingjie Shen; Edith Yvonne JONES; Alexandru Radu ARICESCU; Charlotte Hannah COLES
Original assignee: President And Fellows Of Harvard College; The Chancellor, Masters And Scholars Of The University Of Oxford
Priority date: 2011-02-18
Filing date: 2012-02-17
Publication date: 2012-08-23
Also published as: AU2012219323A1; WO2012112953A3; US20140045762A1; EP2675895A4; EP2675895A2; CA2827383A1; US9744188B2

Abstract

Disclosed herein are methods of inducing neuronal outgrowth of a neuron. The methods comprise contacting the neuron with an agent that binds receptor protein tyrosine phosphatase δ (RPTPδ), to thereby induce neuronal outgrowth of the neuron. The agent may induces clustering of RPTPδ and/or inhibit binding of chondroitin sulfate proteoglycan (CSPG) to RPTPδ. Examples of suitable agents are heparan sulfate proteoglycan, heparan sulfate, heparan sulfate oligosaccharides, or heparin oligosaccharides. Additional agents are also disclosed. The neuron can be a CNS neuron or peripheral neuron. Also disclosed herein are methods of treating neuronal injury in a subject comprising, administering to the subject an agent that binds RPTPδ. Administration may be to a site of neuronal injury, to thereby induce neuronal outgrowth at the site of neuronal injury.

Description

MOLECULAR SWITCH FOR NEURONAL OUTGROWTH

RELATED APPLICATIONS

[0001] This application claims the benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application No. 61/444,620, filed February 18, 2011, the contents of which are incorporated herein by reference in their entirety.

GOVERNMENT SUPPORT

[0002] This invention was supported by the National Institutes for Health (NIH) Grant No. EY11559 and HD29417 and the Government of the United States has certain rights thereto.

FIELD OF THE INVENTION [0003] The invention relates to the treatment of neuronal injury.

BACKGROUND

[0004] Type Ila receptor protein tyrosine phosphatases (RPTPs) are cell surface receptors important for nervous system development, function and repair (1-3). Vertebrate family members (RPTPa, LAR and RPTP5) and invertebrate orthologues (e.g. Drosophila DLAR) localise to axonal growth cones, regulating neuronal growth and guidance and participating in excitatory synapse formation and maintenance (1, 4-8). RPTPa^A mice exhibit neurological and neuroendocrine defects (9-10) as well as increased nerve regeneration (11-15), while RPTP5-deficient mice show impaired learning and memory (16); RPTPa and δ double- mutant mice have a developmental loss of motor neurons leading to paralysis (17).

[0005] Type Ila RPTP extracellular regions interact with HSPGs and CSPGs (5, 7, 12, 18). These proteoglycans modulate neuronal growth, guidance and connectivity, typically with CSPGs inhibiting and HSPGs promoting axon extension (19-23). Up-regulation of CSPGs in glial scar tissue after neural injury is an important factor limiting CNS axon sprouting and regeneration (2, 21, 24-25). In adult mouse dorsal root ganglion (DRG) sensory axons, this CSPG inhibitory effect is mediated, at least in part, by RPTPa (12). In contrast, in developing chick retinal ganglion cell axons, RPTPa was reported to promote growth in response to basal lamina (26). These observations posed a potential conundrum, namely that of RPTPa interactions eliciting opposing effects on neuronal outgrowth. SUMMARY

[0006] One aspect of the invention relates to a method of inducing neuronal outgrowth of a neuron comprising, contacting the neuron with an agent that binds receptor protein tyrosine phosphatase σ (RPTPa), to thereby induce neuronal outgrowth of the neuron. In one embodiment, the agent induces clustering of RPTPa. In one embodiment, the agent inhibits binding of chondroitin sulfate proteoglycan (CSPG) to RPTPa. In one embodiment, the agent is heparan sulfate proteoglycan, heparan sulfate, heparin oligosaccharide, or heparan sulfate oligosaccharide. In one embodiment, the heparin oligosaccharide or heparan sulfate oligosaccharide contains 8 or more saccharide units and less than 67 saccharide units. In one embodiment, the heparin oligosaccharide or heparan sulfate oligosaccharide contains 10 or more saccharide units and less than 67 saccharide units. In one embodiment, the heparan sulfate proteoglycan is glypican 2 or a derivative thereof. In one embodiment, the agent binds to the first immunoglobulin-like domain of RPTPa. In one embodiment, the agent is in solution. In one embodiment, the agent is contained in a matrix. Contacting can occur in vitro or in vivo. In one embodiment, the neuron is located at a site of injured or diseased tissue. In one embodiment, the method further comprises contacting said neuron with a second agent that promotes neuronal outgrowth. In one embodiment, the second agent reduces inhibition of neuronal outgrowth. The neuron contacted can be either a central nervous system neuron or a peripheral nervous system neuron.

[0007] Another aspect of the invention relates to a method of treating neuronal injury in a subject comprising, administering to the subject an agent that binds RPTPa to thereby induce neuronal outgrowth. In one embodiment, the method further comprises selecting a subject in need of treatment for neuronal injury. In one embodiment, the agent is administered at a site of neuronal injury, to thereby induce neuronal outgrowth at the site of neuronal injury. In one embodiment, the agent induces clustering of the RPTPa. In one embodiment, the agent inhibits binding of chondroitin sulfate proteoglycan (CSPG) to the RPTPa. In one embodiment, the neuronal injury is selected from the group consisting of stroke, spinal cord injury, traumatic brain injury, peripheral nerve injury, skin burn, and eye injury (e.g,.

affecting optic nerve fibers or corneal nerves). In one embodiment, the neuronal injury is acute. In one embodiment, the agent is heparan sulfate proteoglycan, heparan sulfate, heparin oligosaccharide, or heparan sulfate oligosaccharide. In one embodiment, the heparin oligosaccharide or heparan sulfate oligosaccharide contains 8 or more saccharide units and less than 67 saccharide units. In one embodiment, the heparin oligosaccharide or heparan sulfate oligosaccharide contains 10 or more saccharide units and less than 67 saccharide units. In one embodiment, the heparan sulfate proteoglycan is glypican 2 or a derivative thereof. In one embodiment, the method further comprises contacting said neuron with a second agent that promotes neuronal outgrowth. In one embodiment, the agent is in solution. In one embodiment, the agent is contained in a matrix. In one embodiment, the agent directly binds to the RPTPa. In one embodiment, the agent binds to the first immunoglobulin-like domain of RPTPa. Administration of the agent can be systemic or localized. In one embodiment, administration is by method selected from the group consisting of oral, intramuscular injection, subcutaneous or intradermal injection, intravenous injection, buccal administration, transdermal, rectal, colonic, vaginal, intranasal, and inhalation. In one embodiment, localized administration is by implantation of a matrix that contains the agent. In one embodiment, implantation is by injection and the matrix is a gel that solidifies in the body of the subject.

[0008] Another aspect of the invention relates to a method of promoting neural outgrowth in the nervous system of a subject, comprising administering to the subject an agent that binds RPTPa, to contact a neuron and thereby induce neural (axonal) outgrowth of the neuron. In one embodiment, the agent induces clustering of the RPTPa. In one embodiment, the method further comprises selecting a subject in need of treatment for neuronal injury. In one embodiment, the agent inhibits binding of chondroitin sulfate proteoglycan (CSPG) to the RPTPa. In one embodiment, the agent is heparan sulfate proteoglycan, heparan sulfate, heparin oligosaccharide, or heparan sulfate oligosaccharide. In one embodiment, the heparin oligosaccharide or heparan sulfate oligosaccharide contains 8 or more saccharide units and less than 67 saccharide units. In one embodiment, the heparin oligosaccharide or heparan sulfate oligosaccharide contains 10 or more saccharide units and less than 67 saccharide units. In one embodiment, the heparan sulfate proteoglycan is glypican 2 or a derivative thereof. In one embodiment, the agent is in solution. In one embodiment, the agent is contained in a matrix. In one embodiment, the CNS neuron is located at or adjacent to a site of diseased or injured tissue. In one embodiment, the injured tissue results from an injury selected from the group consisting of stroke, spinal cord injury, traumatic brain injury, peripheral nerve injury, skin burn, and eye injury. In one embodiment, the injured tissue results from an acute injury. In one embodiment, the injury injured tissue results from a chronic injury. In one embodiment, the diseased tissue is at a site of neuronal degeneration. In one embodiment, the diseased tissue results from a neurodegenerative disease.

Administration can be either systemic or localized. In one embodiment, administration is by method selected from the group consisting of oral, intramuscular injection, subcutaneous or intradermal injection, intravenous injection, buccal administration, transdermal, rectal, colonic, vaginal, intranasal, and inhalation. In one embodiment, localized administration is by implantation of a matrix that contains the agent. In one embodiment, implantation is by injection and the matrix is a gel that solidifies in the body of the subject.

[0009] In one embodiment of any of the above therapeutic methods, the method further comprises selecting a subject in need of treatment for neuronal injury or in need of neuronal outgrowth, prior to administration of the agent.

Definitions

[0010] As used herein, the term axonal "growth" or "outgrowth" (also referred to herein as "neuronal outgrowth") includes the process by which axons or dendrites extend from a neuron. The outgrowth can result in a new neuritic projection or in the extension of a previously existing cellular process. Axonal outgrowth may include linear extension of an axonal process by five cell-diameters or more. Neuronal growth processes, including neuritogenesis, can be evidenced by detection of neuronal growth markers such as GAP-43 (e.g., detected by methods such as immunostaining for GAP-43). "Stimulating axonal growth" means promoting axonal outgrowth. The term neurite outgrowth may also be used in place of axonal outgrowth throughout the application.

[0011] "Central nervous system (CNS) neurons" include the neurons of the brain, the cranial nerves and the spinal cord. The term CNS neuron is not intended to include support- cells or protection-cells such as astrocytes, oligodentrocytes, microglia, ependyma and the like, nor is it intended to include peripheral nervous system (e.g., somatic, autonomic, sympathetic or parasympathetic nervous system) neurons. Although, in some embodiments, such cells are also, contacted with the agents described herein.

[0012] "Peripheral nervous system (PNS) neurons" includes the neurons which reside or extend outside of the CNS. PNS is intended to include the neurons commonly understood as categorized in the peripheral nervous system, including sensory neurons and motor neurons. The term PNS neuron is not intended to include support or protection cells such as Schwann cells, satellite glia, enteric glia, and the like, nor is it intended to include CNS nervous system neurons, although, in some embodiments, such cells are also contacted with the agents described herein.

[0013] The term "patient" or "subject" or "animal" or "host" may be used

interchangeably herein, and refers to any animal. The animal can be a human or a non- human animal. The subject may be a human, but can also be a mammal in need of veterinary treatment, e.g., domestic animals or game animals, farm animals, and laboratory animals (e.g., rats, mice, guinea pigs, primates, and the like). Usually the animal is a mammal or vertebrate such as a primate, rodent, lagomorph, domestic animal or game animal. Primates include human and non-human primates, Non-human primates include chimpanzees, cynomologous monkeys, spider monkeys, and macaques, e.g., Rhesus or Pan. Rodents and lagomorphs include mice, rats, woodchucks, ferrets, rabbits and hamsters. Domestic and game animals include cows, horses, pigs, sheep, deer, bison, buffalo, mink, felines, e.g., domestic cat, canines, e.g., dog, wolf and fox, avian species, e.g., chicken, turkey, emu and ostrich, and fish, e.g., trout, catfish and salmon. Subject includes any subset of the foregoing, e.g., all of the above, but excluding one or more groups or species such as humans, primates or rodents. Other subsets of subjects include subjects of a given species or group of species of varying ages, e.g., young humans, e.g., about 1 week of age to about 9 years of age, adolescent humans, e.g., about 10-19 years of age, adult humans, e.g., about 20-100 years of age, and mature adult or elderly humans, e.g., at least about 55 years of age, at least about 60 years of age, at least about 65 years of age or a range of ages such as about 60-100 years of age. Thus, as used herein, prevention or treatment of a disease, condition or symptom may include or exclude any subset of subjects that are grouped by age. A subject can be male or female.

[0014] A subject can be one who has been diagnosed with or identified as suffering from neuronal injury or having a disorder characterized by neuronal injury or degeneration (e.g., atrophy/wasting). A subject can be one who is not currently being treated with an agent described herein (e.g., heparin oligosaccharide). A subject can be one who has been previously diagnosed with a disease that is being treated with a therapeutic regimen comprising an agent described herein (e.g., heparin oligosaccharide) wherein the disease is not a disease characterized by neuronal injury or degeneration. A subject can be one who has suffered a traumatic neuronal injury.

[0015] "Contacting" as the term is used herein with respect to a cell (e.g., a neuron) refers to any mode of agent delivery or "administration," either to cells or to whole organisms, in which the agent is brought into contact with one or more cells, in sufficient amount to exhibit its effect on the cell. "Contacting" includes both in vivo and in vitro methods of bringing an agent described herein into proximity with a cell. For example, when neuronal outgrowth of a neuron is stimulated in vitro, agents can be administered, for example, by transfection, lipofection, electroporation, viral vector infection, or by addition to growth medium. In vivo contacting is achieved by administration to a subject, as described herein. Suitable modes of administration can be determined by those skilled in the art and such modes of administration may vary between agents.

[0016] The term "antibody" refers to an immunoglobulin protein that is capable of binding an antigen. Antibody as used herein is meant to include antibody fragments, e.g. F(ab')2, Fab', Fab, capable of binding the antigen or antigenic fragment of interest.

[0017] The term "humanized antibody" is used herein to describe complete antibody molecules, i.e. composed of two complete light chains and two complete heavy chains, as well as antibodies consisting only of antibody fragments, e.g. Fab, Fab', F (ab') 2, and Fv, wherein the CDRs are derived from a non-human source and the remaining portion of the Ig molecule or fragment thereof is derived from a human antibody, preferably produced from a nucleic acid sequence encoding a human antibody.

[0018] The terms "human antibody" and "humanized antibody" are used herein to describe an antibody of which all portions of the antibody molecule are derived from a nucleic acid sequence encoding a human antibody. Such human antibodies are most desirable for use in antibody therapies, as such antibodies would elicit little or no immune response in the human subject. The term "chimeric antibody" is used herein to describe an antibody molecule as well as antibody fragments, as described above in the definition of the term "humanized antibody." The term "chimeric antibody" encompasses humanized antibodies. Chimeric antibodies have at least one portion of a heavy or light chain amino acid sequence derived from a first mammalian species and another portion of the heavy or light chain amino acid sequence derived from a second, different mammalian species.

[0019] Preferably, the variable region is derived from a non-human mammalian species and the constant region is derived from a human species. Specifically, the chimeric antibody is preferably produced from a nucleotide sequence from a non-human mammal encoding a variable region and a nucleotide sequence from a human encoding a constant region of an antibody.

BRIEF DESCRIPTION OF THE DRAWINGS

[0020] This patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.

Figure 1A-Figure 1H show the results of experiments that demonstrate RPTPo-GAG interactions modulate contrasting growth responses of sensory neurons. Figures 1A-1F are photographs of immunostained mouse DRG neurons in culture following the indicated treatment. Figures 1A, lC,and IE are wild-type DRG neurons. Figures IB, ID and IF are RPTP&^/~ ¥'& mouse DRG neurons. Neurons were grown on a poly-D-lysine/laminin mixture alone (control) or supplemented with either neurocan or glypican-2 proteoglycans and imaged 48 hours later by GAP-43 immunostaining. Figure 1G is a bar graph of data obtained from neurite measurements of representative cells from experiments referred to in Figure 1A to IF. The data indicate statistically significant neurocan inhibition and glypican-2 promotion of outgrowth. Figure 1H is a bar graph of data from experiments that indicate these effects are largely mediated via RPTPo, and the proteoglycan GAG chains are essential for their interactions with RPTPo. Pre -treatment of neurocan with chondroitinase ABC (ChABC) or glypican-2 with heparitinase III (HPNIII) dramatically reduced binding to RPTPo in solid phase binding assays, n = 3 mice for each genotype, except RPTPa'^' on neurocan, where n = 4. ***P < 0.001, **P < 0.01, Student's t-test. Scale bar, 100 μπι.

Figure 2A - Figure 2F show the structure of the proteoglycan binding region of type Ila RPTPs. Figure 2A is a schematic of the domain organisation of the type Ila RPTP family. N, amino terminus (extracellular); SP, secretion signal peptide; TM, transmembrane helix; C, carboxy terminus (intracellular); Ig, immunoglobulin-like domain; FN3, fibronectin type III domain. The ectodomain may be remodelled by alternative splicing, yielding multiple receptor isoforms with distinct expression patterns (1). Protein constructs illustrated here were used in subsequent biophysical assays and crystallographic studies. Residue numbering corresponds to chicken RPTPa. Figure 2B is a ribbon diagram of chicken RPTPa Igl-2. Six residues have previously been shown to be important for binding to HSPGs and CSPGs (12, 18) and are illustrated as blue sticks. Figure 2C is a solvent-accessible surface representations of Igl-2 crystal structures from chicken RPTPa, human RPTPa, human RPTP5, human LAR and Drosophila LAR, coloured by the electrostatic potential contoured at + 5 kT/e (red, acidic; blue, basic). Figure 2D is a model that shows how sucrose octasulfate (SOS) induces movement of the proteoglycan binding Lys-loop in human LAR (green) relative to the apo-protein (wheat); the R76-D100 salt bridge is disrupted to allow this conformational change. R76, together with K67 and K68, are involved in binding to the sulfate substituents from the five-membered ring of the SOS ligand. Surface representations of the boxed region in Figure 2C are shown for apo-LAR in Figure 2E, and for SOS-bound LAR in Figure 2F, crystal structures highlight the malleability of the proteoglycan binding surface; colors as in Figure 2C.

Figure 3A-Figure 3H show results from experiments which indicate GAG-induced oligomerisation of RPTPa. Figure 3A models the dimensions of the RPTPa proteoglycan binding surface taken from the chicken RPTPa Igl-2 crystal structure. Figure 3B and Figure 3C are graphs of data which indicate that Neurocan-alkaline phosphatase (NC-AP, a representative CSPG) and Glypican-2- AP (Glyp2-AP, a representative HSPG) bind to immobilised mouse RPTPa sEcto-Fc with comparable affinities. Kd values were obtained from the binding curves, assuming a one-to-one binding event. Figures 3D-3G are graphs of data collected from size-exclusion chromatography coupled to multi-angle light scattering (SEC-MAL, used to investigate the oligomerisation state of human RPTPa Igl-FN3 in solution with an excess of varying length GAGs. The data indicate that heparin dp8 is the minimum length of heparin oligosaccharide required to promote oligomerisation. Figure 3D shows the results of experiments where the protein was incubated alone (red), with dp4 (orange), dp6 (purple), dp8 (green) dplO (blue), dp20 (light green) or dp30 (grey). The data in Figure 3E indicate that the addition of longer heparin oligosaccharides results in the formation of larger RPTP oligomers. The data in Figure 3F indicate that the oligomerisation state of a quadruple K67A/K68A/K70A/K71A mutant of human RPTPa Igl-FN3 (Igl-FN3 ΔΚ) was insensitive to the addition of heparin. Figure 3G shows the results of experiments where heparan sulfate but not chondroitin sulfate induces oligomerisation of human RPTPa Igl-FN3; "x5" indicate increased GAG amounts (28). Refractive index traces (scaled within each panel) and measured molecular weights are represented by bold and dashed lines respectively. Refractive index peaks indicated by an asterisk correspond to excess glycan ligand. Figure 3H is a proposed model for RPTPa clustering along the highly sulfated domains of heparan sulfate. An unperturbed helical structure for heparin (PDB accession code 1HPN) is used in this model, which is scaled relative to the Igl-2 molecule.

Figure 4A-Figure 4T is a collection of photographs and an illustration of a model. The collection presents experimental results that indicate immunolocalization of endogenous HS, CS and RPTPo in DRG neuron cultures. Figures 4A-F show immunolocalization of CS (red), with GAP43 neuronal marker (green) and DAPI nuclear stain (blue). Colors are merged in E and F. Boxed areas in A and E are enlarged in B and F. Filled arrowheads point tohigh CS labeling over ECM adjacent to non-neuronal cells. Open arrowheads point to dark areas of low CS labeling overlap with cell bodies and axons. GAP43 labeled axon in F grows over a non-neuronal cell at lower left. Figures 4G-L show HS (red), with GAP43 (green) and DAPI (blue). Colors are merged in Figure 4K and L. Boxed areas are enlarged in H and L. Arrowheads point to HS labeling over GAP43 labeled neuronal processes. Figures 4M-S show immunolocalization of HS (red) with RPTPo (green). Figures 4M-0 show labeling of a neuron, including cell body and neurites (arrowheads). Figures 4P-4S show a growth cone (arrowhead) with axon shaft (arrow) at higher magnification. DIC image is in Figure 4S. Both HS and RPTPo show punctate labeling, in similar although not identical patterns. Scale bar: 60 μπι (Figures 4A, C-E, G, TK, M-O) and 6 μπι (Figures 4P-S). Figure 4T shows an illustration of a model for type Ila RPTP-proteoglycan interactions and their distinct functional consequences. Islands of high/intermediate sulfation on HS chains (shown in pink/yellow) stabilise receptor oligomers, causing an uneven distribution of tyrosine phosphatase activity, formation of microdomains with high phosphotyrosine levels and supporting neuronal extension. Conversely, secreted CS (blue chains), present in glial scar tissues, is unable to induce tight RPTPa oligomerization, competing with HS and inhibiting axon growth. Regulatory mechanisms might include shedding (i); crystal structure of human RPTPa Igl-3 reveals an exposed furin-like protease cleavage site in the Ig2-3 linker (scissors; Figure 17).

Figure 5 is a bar graph of data from experiments that indicate Glypican-2 induced neurite outgrowth is largely dependent upon the presence of its heparan sulfate moieties. Wild-type P8 mouse dorsal root ganglion (DRG) neurons were grown on substrates containing a poly-D-lysine/laminin mixture (control) or supplemented with glypican-2, either with or without heparitinase III (HPNIII) treatment. The outgrowth of DRG neurons, relative to the control (assigned 100 % outgrowth) was quantified. Treatment with HPNIII did not completely eliminate the growth promoting effect of the glypican-2 substrate, which may reflect either novel interactions involving the deglycosylated glypican core or incomplete enzymatic digestion of the heparan sulfate chains. Error bars show SEMs. **p<0.005 and *p<0.05, Student's t-test. The necessity of the chondroitin sulfate groups of neurocan for CSPG-mediated inhibition of DRG outgrowth, has been reported previously (S2).

Figure 6 is a sequence alignment of the two N-terminal Ig domains of the type Ila RPTP family members across species. Sequences correspond to the RPTP isoforms lacking the MeA and MeB exons, based on amino acid sequences taken from the following sources: RPTPa human (NM_130854.2), mouse (BC052462.1), chicken (NM_205407.1), xenopus (NM_001141992.1) and zebrafish (XP_002666198.1); RPTP6 human (BC106713.1), mouse (EDL31049.1), chick (NP_990738.1), xenopus (NM_001090381.1) and zebrafish

(NP_001159520.1); RPTP LAR human (NM_002840.3), mouse (NM_011213.2), chicken (XP_001233494.1), xenopus (NP_001081987) and zebrafish (NP_001077045.1); Drosophila LAR (NM_078880.3), leech HmLARl (AF017084.1) and HmLAR2 (AF017083.1), C.

elegans PTP-3A (AF316539.1) and Nematostella RPTP (XP_001639024.1). Numbers above the sequence alignment correspond to amino acid residue numbers relative to the chicken RPTPa sequence, where residue 1 is the initial methionine. Black arrows above the sequence alignment indicate the location of the β- strands within the two immunoglobulin domains, based on the structure of chick Igl-2, assigned using ksdssp (29). Blue boxes highlight the lysine loop between β strands C-D (containing K67, K68, K70 and K71) and the arginine loop between β strands E-F (containing R96 and R99). Black asterisks above the alignments highlight R76 and D100, the two residues forming the salt bridge which is disrupted upon binding of human LAR Igl-2 to sucrose octasulfate.

Figure 7A-Figure 7C is a collection of illustrations and tables which indicate the structural alignment of the type Ila RPTPs illustrates the conserved architecture of the two N- terminal domains across the type Ila RPTP family. (A) Igl domains from human RPTP LAR (P3₂21) and RPTP6 (P3₂21) crystal structures were aligned with the Igl domain from human RPTPa (I4i22) using SHP (S22), to obtain an overlay of the human RPTP structures. (B) Igl from the chicken RPTPa (I4i22) and DLAR (C2) structures were similarly aligned with the Igl from l human RPTPa (I4i22). (C) Structural comparison of the Igl-Ig2 domain interface for the type Ila RPTPs. Igl-Ig2 angle deviation represents the angle required to realign the Ig2 domains (containing the residues listed) from the Igl-2 structures on human RPTPa Ι4χ22 Ig2 after having first superposed each Igl-2 structure to align with human RPTPa Ι4χ22 Igl and was calculated from the rotation matrix obtained for the Ig2 domain transformation in SHP. Interface surface areas per domain and the change in free energy for the Igl-Ig2 interaction were estimated for each structure (using residues equivalent to 29-130 and 131- 226 as molecule A and molecule B respectively), in the PISA prediction program (EBI, EMBL) and the surface complementarity was calculated using SC (S30). Although the buried surface area at the Igl-Ig2 domain interface is comparable and the interdomain angle variation is small across the structures, the AG value and surface complementarity score for this domain arrangement in the DLAR structure are both notably less favorable.

Figure 8A-Figure 8F is a collection of illustrations that show comparison of the Igl- Ig2 interdomain interactions observed in chicken RPTPa and Drosophila LAR (DLAR) Igl-2 crystal structures. Chicken RPTPa: (A) Ribbon representation of the Igl-2 crystal structure, highlighting the linker region (solid box) and the domain interface (dashed box). (B)

Sidechains of hydrophobic residues L124, L129, P130 and F133, which lie on the Igl-Ig2 Pro-rich loop, also pack closely with 142, V44 and A212 in a hydrophobic interdomain region, (C) Two salt bridges R91-E205 and E126-R215 and a network of hydrogen bonds involving the hydroxyl groups of S50 and Y216, the sidechain amide of Q41, the backbone carbonyls of 142 and F171, the backbone amide of V214 and two water molecules (purple spheres), hold Igl and Ig2 in a rigid arrangement. The interdomain interactions, including the two highlighted water molecules, observed in the chick RPTPa Igl-2 structure are present in the three human RPTP structures and the residues involved are also highly conserved across species (Fig. 6). DLAR: (D) Ribbon representation of the Igl-2 crystal structure, highlighting the linker region (solid box) and the domain interface (dashed box), (E) Sidechains of P130 and F133 from the Igl-Ig2 loop, pack with the carbon backbones of the Y124 and R44 sidechains, but this hydrophobic region is less extensive than in the chicken RPTPa structure. (F) Two salt bridges R91-E205 and R44-E215 and a network of hydrogen bonds involving the backbone carbonyl of G42, the backbone amide of T214, the sidechain amide of Q41, the carboxyl group of E209, the imidazole group of H216, the hydroxyl groups of S50, Y52, Y166 and T214 and four water molecules, hold Igl and Ig2 in a similarly rigid arrangement. Interdomain interactions directly between protein residues and through water molecules are illustrated with black and grey dashed lines respectively. Blue and red atoms represent nitrogen and oxygen. Notably, there is a charge swap in residue 215 between the vertebrate (R215) and Drosophila (D215) crystal structures, which forms an interdomain salt bridge in all proteins.

Figure 9 is a Sequence alignment of the two N-terminal Ig domains of the type Ila RPTP family members across species (sequences from Fig. 6). Hydrophobic amino acids (AVFMILWY) are coloured green, acidic (DE) are red, basic (RKH) are blue and residues (STCNGQP) are magenta. The bold and dashed lines represent interdomain salt bridges that are either conserved or nonconserved between RPTP Igl -2 crystal structures. Residues highlighted with black asterisks appear to be involved in interdomain hydrogen bonding interactions and those indicated with black arrows pack in a hydrophobic region near to the rigid interdomain linker.

Figure 10A-Figure 10D is a collection of schematics that show model building for o

the 2.05 A human LAR Igl-2-sucrose octasulfate (SOS) crystal structure. (A) and (B):

SigmaA- weighted electron density maps from refinement of the initial human LAR Igl -2 model after molecular replacement in Phaser (SI 6). 2F o - F_c maps (blue) and F o - F_c maps (green and red) are contoured at 1 σ and + 3 σ respectively. Unmodelled features in the electron density maps are highlighted by white dashed lines. (C) and (D): SigmaA- weighted electron density maps after refinement in Phenix (SI 8) prior to addition of the SOS ligand to the model. 2F o -F_cmaps (purple) and F_c -F o maps (green and red) are contoured at σ and + 3 σ respectively. Asterisks mark the density into which three sulfate groups of the SOS ligand were initially placed, and onto which a full SOS molecule was superposed. The five- membered ring appeared to fit well into the electron density, but this left the six-membered ring of the ligand pointing into the solvent and consequently without electron density.

Therefore the SOS ring was split at the disaccharide linker and just the five-membered ring was included in the model for refinement in Phenix (S18). The R wo* and R&_∞ decreased from 20.0 % and 23.4 % to 19.5 % and 22.5 % respectively upon addition of the five-membered ring from SOS to the model, supporting the inclusion of the ligand in the final crystal structure. Extensive co-crystallization attempts with fragments of chondroitin sulfate or heparin (widely-used to mimic highly sulfated regions of heparan sulfate) and various type Ila RPTP constructs did not produce interpretable electron density maps for the glycans, presumably due to their structural heterogeneity.

o

Figure 11 is an illustration of an electron density map for the 2.05 A crystal structure of human LAR Igl-2 in complex with sucrose octasulfate (SOS). The flexible proteoglycan binding loop is coloured in purple while the remainder of the LAR protein is coloured in pink. The carbon backbone of the SOS ligand is shown in grey. Non-carbon atoms are highlighted as follows: nitrogen, blue; oxygen, red; sulphur, yellow. The sidechains of K67, K68 and R76 are well ordered in the SOS-bound LAR crystal structure and are suitably positioned to form electrostatic interactions with the negatively charged sulfate groups of the o

SOS ligand (distances less than 3.6 A between oppositely charged groups are indicated by black dashed lines). R96 and R99 which lie on the Arg-loop are also well ordered, but play no role in SOS-binding in this crystal structure. R99 instead assumes the role of R76 in the apo-LAR crystal structure, by forming a salt bridge with DlOO after the R76-D100 salt bridge is broken and R76 becomes involved in ligand binding. K70 is disordered and clear density is not visible for the sidechain. Blue mesh represents the SigmaA weighted 2Fo -F_c electron density map contoured at 1 σ, after the final round of structure refinement in Phenix (SI 8).

Figure 12A-12F is a collection of illustrations that show conformational flexibility of the proteoglycan binding loop across type Ila RPTP structures. (A) Ribbon representation of the chicken RPTPa Igl backbone. The "Lys"-loop and "Arg"-loop which harbour the crucial heparin binding residues, are highlighted in blue. The rmsd between the Igl C_a positions of chicken RPTPa (Ι4χ22 space group) and either (B) human RPTP5 (P3₂21 space group), (C) human LAR (P3₂21 space group), (D) human RPTPa ( A∑2 space group), (E) human RPTPa (C2 space group) or (F) DLAR (C2 space group) was measured using SHP (S22) and is plotted upon the chicken RPTPa Igl structure; increasing rmsd values are shown using a rainbow scale (blue, low rmsd; red, high rmsd) and the increasing thickness of the protein backbone. The Lys-loop displays the greatest movement across crystal structures, indicating that this region has an inherent flexibility, which may facilitate binding of the type Ila RPTP receptors to different GAG ligands.

Figure 13A- Figure 13D are graphical representations of data from experiments that indicate Heparin-induced dimerisation of human RPTPa ectodomain constructs. A series of human RPTPa constructs were incubated with (blue) and without (red) a two-fold molar excess of heparin dplO before SEC-MALS (size-exclusion chromatography-multi-angle light scattering) analysis; (A) Igl-2, (B) Igl-3, (C) Igl-FN3, (D) sEcto. Refractive index traces (scaled within each panel) are shown by bold lines and the measured molecular weights are shown by dotted lines. Peaks in the refractive index that are indicated by an asterisk correspond to excess dplO ligand. A Superdex 75 column (1 cm x 30 cm) was used for the Igl-2 construct (A) while all other constructs (B-D) were analysed using a Superdex 200 (1 cm x 30 cm) column.

Figure 14A- Figure 14E present graphical respresentation of data from experiments for investigation of type Ila RPTP clustering in solution. After incubation of human RPTPa alone or with heparin dp 10 (Iduron H010), electrospray ionisation-mass spectrometry (ESI- MS) and analytical ultracentrifugation (AUC) were used to analyse the oligomerisation state of the protein. The mass of human RPTPa Igl-2 alone was confirmed using ESTMS under denaturing conditions; (A) an ion series corresponding to different charge states of the proteins was obtained and (B) this ion series was deconvoluted to give the molecular weight of the protein 23,660 Da (estimated molecular weight based on sequence is 23,676 Da). (C) Human RPTPa Igl-2 in complex with heparin dplO and analysed using ESI-MS under native conditions. Two main ion series are observed; a series at lower m/z values corresponding to the protein alone (red) with a deconvoluted mass of 23, 672 Da and a series at higher m/z values (blue) with a deconvoluted mass of 53,104 Da which would correspond to a protein- dplO complex. Further ion series at higher m/z values still are also present, which most likely represent higher order oligomers, but these series couldn't be deconvoluted to obtain mass values due to the overlapping arrangement and low abundance of the peaks. A series of sedimentation velocity AUC experiments were performed with the human RPTPa Igl-2 protein either alone (D) or in complex with heparin dp 10 (E). The coloured circles represent the measured data points, while the black lines represent the fit of the data (the normal black lines correspond to the individual species included in the model and the bold lines to the fit of the overall model to the data). A single homogeneous species, with a Svedberg value indicating a monomeric protein was observed in the sample containing the protein alone. However the protein-hep arin complex sample appears to contain three different species, which may match the monomeric, dimeric and higher order oligomeric states also observed in the native ESTMS experiments.

Figure 15 is a graphical presentation of experimental results that measured the ability of the type Ila RPTPs to bind to a heparin affinity column. Purified Igl-2 constructs of human RPTPa (blue), RPTP LAR (red) and RPTP5 (yellow) were sequentially injected over the column and eluted upon addition of 550 mM, 490 mM and 600 mM sodium chloride respectively. All proteins were freshly purified by SEC, then desalted in 50 mM HEPES, 50 mM sodium chloride, pH 7.5 prior to injection onto a 1 ml heparin column, before elution with a gradient of 50 mM HEPES, 2M sodium chloride, pH 7.5 (black).

Figure 16A-Figure 16F are graphical representations of experimental results that indicate GAG-induced oligomerisation of the type Ila RPTP family. Alone (red), or after incubation with a five-fold molar excess of heparin dp 10 (blue) or an equivalent amount of chondroitin sulfate (yellow), human RPTPa Igl-FN3 (A), RPTP5 Igl-dFN3 (B) or LAR Igl- dFN3 (C) were analysed by SEC-MALS. Similarly to RPTPa, RPTP5 was observed to oligomerise upon addition of heparin dplO, however a longer oligosaccharide (dp30 in a fivefold molar excess, grey) was required to induce oligomerisation of LAR. In contrast to heparin, the introduction of chondroitin sulfate did not induce the oligomerisation of any of the human type Ila family members. Heparin promotes the oligomerisation of DLAR Igl- FN3 (D), but this protein also requires a longer minimal heparin unit than RPTPa. Incubating human RPTPa Igl - FN3 with a mixture of either heparin dp 10 and a five-fold greater amount of chondroitin sulfate (E) or heparan sulfate and a five-fold greater amount of chondroitin sulfate (F) resulted in oligomers of reduced mass relative to the addition of heparin dp 10 or heparan sulfate alone. Refractive index traces (scaled within each panel) are shown by bold lines and the measured molecular weights are shown by dotted lines. Peaks in the refractive index that are indicated by an asterisk correspond to excess oligosaccharide ligand. A

Superdex 200 (1 cm x 30 cm) column was used for all constructs.

Figure 17A-Figure 17B are illustrations of the crystal structure of human RPTPa Igl -3. (A) Ribbon representation of the three Nterminal Ig domains of a human RPTPa R227Q+R228N double mutant. Only after introduction of these two point mutations to disrupt a potential furin cleavage motif RVRR, could crystals of intact Igl -3 protein be obtained. The structure reveals that this motif is located in an exposed, flexible linker (black) between Ig domains 2 and 3. Residues 67-73 of the "Lys"-loop are not included in the structure as they were not well resolved in the electron density; they are indicated here by a dashed black line. (B) An overlay of human RPTPo Igl-2 (pink) and Igl-3 illustrates the preserved architecture of the first two Ig domains in the Igl-3 structure. Removal of Igl-2, which contains the glycosaminoglycan binding site, either at or prior to arrival at the cell surface, could represent an additional mode of regulation of the type Ila RPTPs. However, RPTP isoforms which contain the MeB exon (which encodes four amino acid residues, ELRE, and lies within the RVRR motif), would be unable to utilise such a regulatory mechanism. For example, an isoform of RPTP6 lacking MeB is found to be expressed in the kidney, while an isoform with the MeB insert is expressed in the brain (S31, S32), therefore isoform expression patterns would determine whether this proteolytic cleavage event occurs in specific tissues. Additional membrane proximal and non-isoform dependent protease cleavage sites have been identified for type Ila RPTPs (S33), which result in the shedding of almost the entire ectodomain and would also desensitise the receptors to proteoglycans. A novel RPTPo isoform lacking Ig3 has been identified in human ulcerative colitis patients (S34). The deletion of this domain may result in disruption of RPTPa-ligand interactions, though as yet no binding partner for the Ig3 has been identified. Alternatively, it is possible that the resultant direct fusion of the rigid Igl-2 unit onto the remainder of the ectodomain, limits the range of movement of the Igl-2 unit, hampering efficient proteoglycan binding and receptor clustering.

Figure 18A- Figure 18G is a collection of photographs that show

immunolocalization of endogenous HS, CS and RPTPa in DRG neuron cultures. Treatments are as described in Fig. 4 and (27), with additional controls shown here. (A and B)

Immunolocalization of CS (red), with GAP43 neuronal marker (green) and DAPI nuclear stain (blue). Colors are merged in the right-hand panel. Figure 18 A, shows strong CS labeling over the ECM, whereas areas corresponding to cells showed little or no CS labeling above background. Figure 18 B shows a control treated with chondroitinase ABC to remove CS. (C and D) Immunolocalization of HS (red), with GAP43 (green) and DAPI (blue). Colors are merged in the right-hand panel. Figure 18C, shows strong HS labeling over cells including neurites, with additional faint labeling above background over the ECM. Figure 18 D shows a control treated with combined heparinase I, II and III, to remove HS. (E-G)

Immunolocalization of RPTPa (green), combined with HS labeling (red) in Figures 18 E and F, or GAP43 neuronal marker (red) in Figure 18 G. The right-hand Figures show DIC images. Figure 18G shows a negative control for RPTPa labeling with secondary antibody only. RPTP and HS overlapped in similar although not identical patterns in cells, as well as in puncta within the growth cone. Some additional scattered dots were seen outside the cells and may be cell fragments based on DIC and DAPI images. A similar pattern, with punctate labeling in the growth cone and scattered dots outside the cell, was reported for RPTPa previously (35). Scale bar: 60 μπι (Figures 18 A-E), 6 μπι (Figures 18F and G).

Figure 19 is a bar graph of experimental results that show CSPG competition for HSPG-induced neurite outgrowth. Wild-type P10 mouse dorsal root ganglion (DRG) neurons were grown on substrates containing a poly-Dlysine/ laminin mixture (control), or supplemented with either 5 μg/ml glypican-2, or with a mixture of 5 μg/ml glypican-2 plus 125 μg/ml CSPG. The outgrowth of DRG neurons, relative to control (assigned 100 % outgrowth) was quantified. Treatment with glypican-2 promoted outgrowth to a lesser extent than the higher concentration (30 μg/ml) of glypican-2 used in Figs. 1 and 5. CSPG out- competed the outgrowth promoting effect of glypican-2, leading to outgrowth inhibition relative to the control. Error bars show SEM. ***p<0.001, **p<0.01, Student's t-test.

Figure 20 is a graphical representation of data from experiments that indicate Heparin 30-mer and 67-mer inhibited interaction of the CSPG neurocan to PTPs-Fc in a solid phase binding assay. Heparin 8-mer produced little or no inhibition. IC50 values for Heparin30 and Heparin67 were 21 nM and 15 nM respectively.

Figure 21 is a bar graph of data from experiments that indicate Heparin 30-mer promoted neurite outgrowth in presence or absence of CSPG. *** p<0.001

Figure 22 is a bar graph of data from experiments that indicate Heparin8, in contrast to heparin 30, did not promote neurite outgrowth on CSPG. *p<0.5, **p<0.01.

Figure 23A and Figure 23B are the results of experiments showing that heparin oligosaccharides bind to the extracellular domain of ΡΤΡσ, and compete for binding with CSPG. Figure 23A shows, on the left hand side, a graph of biotin-labeled heparin oligosaccharide 67-mer (HS67) binding to the ΡΤΡσ extracellular domain fused to an Fc tag. The measured dissociation constant (K_D) was 2.3 nM. The graph on the right hand side shows the ability of unlabeled HS67 to outcompete the CSPG neurocan, fused to an AP tag, for binding to the ΡΤΡσ extracellular domain, fused to an Fc tag. The inhibition constant (Ki), calculated from the Cheng-Prusoff equation, was 2.2 nM, very consistent with the K_D for this oligosaccharide. Figure 23B shows the results of competition experiments with heparin oligosaccharides of a range of different lengths (HS6 through HS67, corresponding to 6 through 67 monosaccharide units). All lengths tested showed evidence of competition with CSPG. Lengths of HS17 and above showed the strongest ability to compete, with Ki values in the low nanomolar range.

Figure 24 shows that a heparin oligosaccharide can overcome CSPG inhibition and promote neurite extension, in a dose-dependent manner. Neurite outgrowth of dissociated mouse DRG neurons with or without CSPGs (60μg/ml), and with HS23 at the indicated concentrations, was measured and normalized against control without CSPG or HS23.

Increasing doses of HS23 incrementally reversed the CSPG inhibitory effect on neurite extension. As with the HSPG glypican 2 (Fig. 1), higher concentrations of HS23 promoted axon extension relative to control. *p<0.05, ***p<0.001.

Figure 25 shows that the effect of heparin oligosaccharides in reversing CSPG inhibition and promoting neurite outgrowth is dependent on the length of the

oligosaccharides. The neurite outgrowth of dissociated mouse DRG neurons in the presence of CSPGs (6C^g/ml) and heparin oligosaccharides of indicated lengths was measured and normalized against control with CSPG and without HS. The results showed that heparin oligosaccharides with lengths greater than 10 saccharide units overcame the inhibitory effect of CSPG and promoted neurite extension; these were the same oligosaccharide lengths that were found to compete strongly with CSPG for binding to ΡΤΡσ in Figure 23B. Shorter heparin oligosaccharides did not overcome CSPG inhibition, but rather were found to further inhibit neurite extension. *p<0.05, ***p<0.001.

Figure 26 shows the human PTPsigma transcript variant 4, amino acid sequence.

Figure 27 shows the human PTPsigma transcript variant 4, nucleotide sequence.

Figure 28 shows the human ΡΤΡσ transcript variant 3 amino acid.

Figure 29 shows the human ΡΤΡσ transcript variant 3 nucleotide sequence.

Figure 30 shows the human ΡΤΡσ transcript variant 1 amino acid sequence.

Figure 31 shows the human ΡΤΡσ transcript variant 1 nucleotide .

Figure 32 shows the murine ΡΤΡσ amino acid sequence.

Figure 33 shows the murine ΡΤΡσ nucleotide sequence.

Figure 34 is a schematic representation of a pentasaccharide which comprises the anti-thrombin binding domain and is responsible for the anticoagulant (From Gandhi, N.S., Mancera, R.L., 2010, 15: 1058-69).

Figure 35 is a table showing the crystallization conditions and freezing methods used. Crystallisation trials were set up with human RPTPa Igl-3 wildtype protein. Crystals were obtained within 80 days. Subsequent structure determination showed clear density for Igl-2, but no space within the crystal lattice for a third Ig domain. This suggested a proteolytic cleavage of the protein within the flexible linker between Ig domains two and three, which contains a putative 225 RVRR 228 furin motif. To obtain crystals of human RPTPa Igl-3 a double point mutation R227Q+R228N was necessary to disrupt this motif.

Figure 36 is a table showing crystallographic data collection and refinement statistics.

Figure 37 is a table showing the summary of MALS experiments. Heparin

experiments were performed with different batches of heparin oligomers and tested at 1:2 and 1:5 protein:heparin ratios respectively. The approximate molecular weight of heparin dplO is -3.3 kDa, dp20 is -6.6 kDa and dp30 -10 kDa. CS (Sigma, C4384) and HS (Huron, GAG- HS01) mixtures used in these experiments contain GAG fragments 10-50 kDa in mass. All Igl-FN3 proteins were injected at -10 μΜ. The molecular weight values listed in this table (MALS MW) were measured at the peak in the refractive index trace for a given experiment. The error in the measured molecular weights is the uncertainty statistic provided by the Astra software (Wyatt Technologies).

DETAILED DESCRIPTION

[0021] Aspects of the present invention relate to the findings that certain agents that bind to receptor protein tyrosine phosphatase σ (RPTPa) on a neuron, can induce neuronal outgrowth of that neuron. Examples of such agents are described herein.

[0022] In one respect, the present invention relates to a method of inducing neuronal outgrowth of a neuron. This is achieved, for example, by contacting the neuron with an effective amount of an agent that binds RPTPa, to thereby induce neuronal outgrowth of the neuron. Contact can be to the cell body or cell process. Such agents are described herein. The contacting can occur in vitro or in vivo. In vitro, the agent, for example, can be added to a cell culture containing the neuron. In vivo, the agent can be administered to a subject, such that an effective amount of the agent comes in contact with the neuron (herein referred to as the target neuron), to thereby induce the neuronal outgrowth. In one embodiment, the neuron is a central nervous system neuron. In one embodiment, the neuron is a peripheral nervous system neuron.

[0023] Without being bound by theory, it is thought that the agent induces neuronal outgrowth by inducing the clustering of RPTPa and/or inhibiting CSPG binding to the RPTPa of the neuron.

[0024] The neuron can further be contacted with a second agent that promotes neuronal outgrowth, as discussed herein.

[0025] When the method is performed in vivo, by administration of the agent to a subject, neuronal outgrowth in the subject is promoted. As such, another aspect of the present invention relates to a method of promoting neural outgrowth in the nervous system of a subject (e.g, CNS or PNS). The method comprises administering a therapeutically effective amount of the agent to contact the neuron, and thereby induce neural outgrowth of the contacted neuron(s). [0026] The neuron contacted in vivo may be located at a site of injured or diseased tissue. Such injury or disease can impair normal neuronal function by disrupting normal neural connections. Examples of specific types of injury or disease that can disrupt normal neural connections are provided herein. The induction of neuronal outgrowth at such sites can have therapeutic effects. As such, another aspect of the present invention relates to a method of treating neuronal injury in a subject. The method comprises administering an agent that binds RPTPa to a site of neuronal injury in the subject, to thereby induce neuronal outgrowth at the site of neuronal injury.

[0027] In one embodiment, the treatment comprises adjusting an already ongoing therapeutic regimen of the subject such that at least one symptom of neuronal damage is reduced. Without limitation, a therapeutic regime can be adjusted by modulating the frequency of administration of the agent (e.g., heparin oligosaccharide) and/or by altering the site or mode of administration.

[0028] In one embodiment, the method further comprises diagnosing a subject for neuronal injury (e.g,. acute and/or traumatic injury) and/or neuronal degeneration, prior to treating the subject as described herein. In one embodiment of the methods described herein, the method further comprises selecting a subject with neuronal injury or degeneration before treating the subject as described herein. The method may further comprise selecting a subject in need of treatment of neuronal injury, degeneration or disease, prior to such treatment. Such selection may involve identification within a subject of such nerve damage, or the site of the nerve damage.

[0029] In one embodiment, neuronal outgrowth induced is sufficient to at least partially restore nerve function to an injured area (e.g., through an injured spinal cord). The restored function can be achieved by either 1) promoting regeneration of damaged neurons (axons) to restore the injured neural pathway, 2) promoting sprouting or plasticity of new connections that can compensate functionally (possibly distinct from the damaged connections, and 3) a combination of the two.

[0030] The methods herein utilize an "effective amount" of the agent. An "effective amount" of an agent refers to an amount sufficient to achieve a desired effect, as described herein (e.g., neuronal outgrowth of a contacted neuron). In one embodiment, the effective amount is sufficient to cause clustering of RPTPa when contacted to a cell expressing that receptor. In one embodiment, the effective amount is sufficient to compete with CSPG for binding of RPTPa when contacted to a cell expressing that receptor. [0031] The methods of treating or treatment of a subject, described herein, utilize a therapeutically effect amount of the agent. The term "therapeutically effective amount" refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic result in a subject. As used herein, the term "therapeutically effective amount" refers to an amount of agent such that treatment of a patient with that amount can be associated with a medically desirable change (a therapeutic result) in neuronal outgrowth, nerve function, or that can reduce, or ameliorate neuronal damage. A therapeutic result in the subject may be, e.g., lessening of symptoms, prolonged survival, improved mobility, and the like. A therapeutic result need not be a "cure." A therapeutically effective amount of an agent as defined herein may vary according to factors such as the disease state, age, and weight of the subject, and the ability of the agent to elicit a desired response in the subject. Dosage regimens may be adjusted to provide the optimum therapeutic response. A

therapeutically effective amount is also one in which any toxic or detrimental effects of the active compound are outweighed by the therapeutically beneficial effects.

Agents that bind to Receptor Protein Tyrosine Phosphatase σ (RPTPa) to induce Neuronal Outgrowth

[0032] In one embodiment the agent binds RPTPa to inhibit the binding of CSPG. In one embodiment the agent binds the first immunoglobulin-like domain of RPTPa (e.g., via the IglGAG binding site ).

[0033] In one embodiment the agent binds RPTPa to induce clustering of the receptor. In one embodiment the agent that induces clustering binds the first immunoglobulin-like domain of RPTPa (e.g., via the IglGAG binding site ). In one embodiment, the agent is multivalent. Without being bound by theory, it is expected that agents which bind RPTPa multivalently will thereby induce clustering.

[0034] Agents that promote clustering of RPTPa useful in the methods described herein include heparan sulfate proteoglycans, heparan sulfates, heparin oligosaccharides and heparan sulfate oligosaccharides. In one embodiment the heparan sulfate proteoglycan is glypican 2 or a derivative or modification thereof. In one embodiment, the heparin oligosaccharide or heparan sulfate oligosaccharide contains 8 or more saccharide units. In one embodiment, the heparin oligosaccharide or heparan sulfate oligosaccharide contains less than 67 oligosaccharide units. Such agents are described in more detail below.

[0035] Additional agents that specifically bind to one or more sites of RPTPa (e.g., to thereby induce clustering and/or inhibit binding of CSPG) are also known or can be generated by the skilled practitioner. In one embodiment, the agent is an antibody or comprises a functional fragment of an antibody that binds to the RPTPa. Examples of a functional fragment of an antibody include, without limitation, F(ab')2, Fab', Fab, capable of binding the RPTPa. The antibody or functional fragment thereof may be humanized for use in a human subject. The antibody or functional fragment thereof may be chimeric.

[0036] When obtained or otherwise derived from a natural source, the agent for use in the methods described herein can be obtained from a whole animal or alternatively cell culture. In one embodiment, the agent is obtained or derived from a natural source that is of the same species as the subject on which the method is performed. In one embodiment, the agent is obtained or derived from a natural source that is of a different species as the subject on which the method is performed. The various animal species described herein for a "subject" also provide suitable sources of the agent.

[0037] One such agent that can be used in the methods of the invention is a

glycosaminoglycan. The glycosaminoglycan can arise in and be purified from natural sources. The agent may be a fragment of the natural glycoasminoglycan (e.g., those described herein), and/or it may be further chemically modified. In some embodiments, the oligosaccharides described herein may be derived from a larger glycosaminoglycan (e.g,. by purification, fragmentation, and/or modification). Several classes of glycosaminoglycans exist, including 1) heparan sulfate and heparin, 2) chondroitin sulfate, and 3) dermatan sulfate and keratan sulfates.

[0038] Another example of an agent that can be used to induce neuronal outgrowth is a heparin oligosaccharide. A variety of heparin oligosaccharides are known in the art and commercially available. Heparin oligosaccharides are typically described by virtue of the number of repeated unit or alternatively by their molecular weight. For example,

octasaccharide have a molecular weight of about 2400 Da. Decasaccharides have a molecular weight of about 3000 Da. In one embodiment, the heparin oligosaccharide contains 8 or more saccharide units (this may also be referred to as having 4 or more di- saccharide units). In one embodiment, the heparin oligosaccharide contains 10 or more saccharide units (5 or more di-saccharide units). In one embodiment, the heparin

oligosaccharide contains 20 or more saccharide units (10 or more di-saccharide units). In one embodiment, the heparin oligosaccharide contains about 30 or more saccharide units (15 or more di-saccharide units; approximately 9000 Da). Larger heparin polymers (e.g. heparin polysaccharides that contain about 67 or more saccharide units, approximately 20,000 Da) are also expected to induce neuronal outgrowth when used in the methods described herein. Such larger heparin oligosaccharides are typically referred to in the art as heparin polysaccharides. In one embodiment, the heparin oligosaccharide contains about 17, 23, 30, or 67 monosaccharide units. In one embodiment, the heparin olidosaccharide has a molecular weight of 1800, 2400, 3000, 5000, 7000, 9000, or 20,000 Da.

[0039] Another example of an agent that can be used to induce neuronal outgrowth is a heparan sulfate or a heparan sulfate oligosaccharide. Heparan sulfate oligosaccharides can be described by virtue of the number of repeated unit or alternatively by their molecular weight. In one embodiment, the heparan sulfate oligosaccharide contains 8 or more saccharide units (this may also be referred to as having 4 or more di- saccharide units). In one embodiment, the heparan sulfate oligosaccharide contains 10 or more saccharide units (5 or more di- saccharide units). In one embodiment, the heparan sulfate oligosaccharide contains 20 or more saccharide units (10 or more di- saccharide units). In one embodiment, the heparan sulfate oligosaccharide contains about 30 or more saccharide units (15 or more di-saccharide units). Larger heparan sulfate polymers (e.g. heparan sulfate polysaccharides that contain about 67 or more saccharide units) are also expected to induce neuronal outgrowth when used in the methods described herein. Such larger heparan sulfate oligosaccharides are typically referred to in the art as heparan sulfate polysaccharides. In one embodiment, the heparin sulfate oligosaccharide contains about 17, 23, 30, or 67 monosaccharide units.

[0040] The heparin oligosaccharide or heparan sulfate oligosaccharide can be derived from a natural or synthetic source, as described herein. In one embodiment, the heparin oligosaccharide or heparan sulfate oligosaccharide is derived by degradation (e.g., chemical) of HSPG. The heparin oligosaccharide may be further chemically modified, (e.g,. to facilitate storage or administration).

[0041] In addition to length, a variety of carbohydrates of different structures (referred to as structural variants) are expected to exhibit the same activity as the heparin

oligosaccharides described herein. Such carbohydrates are described below, by way of non- limiting example. Many such structural variants are available commercially (e.g., from Seikagaku, Neoparin, Northstar, Iduron). For heparan sulfate, five positions can be modified to produce the structural variants: 2- sulfation of the uronic acid, and N-deacetylation, N- sulphation, 3-sulfation and 6-sulfation of the glucosamine. Chondroitin sulfate also exists in forms denoted A, C, D and E, referring to differential sulfation at C2 of the uronic acid, or C4 or C6 of the GalNAc. Heparan sulfate and chondroitin sulfate carbohydrates are available with each of these positions oversulfated or desulfated (Gallagher, J.T. Biochem Soc Trans, 2006. 34: 438 41;Lepenies, B et al.,. Applications of synthetic carbohydrates to chemical biology. Curr Opin Chem Biol, 2010. 14: 404-11; Mulloy, B. Adv Pharmacol, 2006. 53: 49- 67; Seeberger, P.H. Nature, 2007. 446: 1046-51). In addition to HS and CS, other

saccharides expected to exhibit similar function include dermatan and keratin sulfates ( DSPGs and KSPGs) since they are reported to inhibit axon regeneration (Smith-Thomas, et al.,J Cell Sci, 1995. 108: 1307-15), as well as synthetic polymers such as dextran sulfate.

[0042] One model to explain the opposing effects of HSPG and chondroitinsulfate proteoglycan (CSPG) mediated by ΡΤΡσ is that the distribution of sulfate groups (typically 1- 2 per disaccharide) along an individual chondroitin sulfate chain is relatively uniform, while heparan sulfate has a distinct modular composition, with regions of high sulfation (3 groups per disaccharide), flanked by intermediately modified transition zones and variably spaced by largely unmodified sections almost devoid of sulfation (Murphy,et al. J Biol Chem, 2004. 279: 27239-45). Although other chemical differences between heparan sulfate and chondroitin sulfate may contribute to differential effects on RPTPa, these observations suggest a model where the islands of high sulfation present in heparan sulfate, but not chondroitin sulfate, may promote close packing of RPTPa molecules along these regions. Therefore, oligosaccharides that mimic these islands of high sulfation density may be predicted to have particularly high effectiveness in promoting neurite growth. As such, a highly sulfated carbohydrate mimetic of heparin, heparan sulfate, chondroitin sulfate, dermatan sulfate or keratan sulfate is also envisioned for use in the methods described herein.

[0043] Heparin is well known to be an anticoagulant, and since this may create undesirable side effects, polymers with reduced or absent anticoagulant activity that also envisioned for use in the methods and formulations described herein. Anticoagulation by heparin is mediated mostly through its binding to anti-thrombin, and structural features of the saccharide chain that cause anticoagulant activity of heparin are known (Avci, et al., Curr Pharm Des, 2003. 9: 2323-35; Gandhi et al, Drug Discov Today, 2010. 15: 1058-69; Lever et al., Nat Rev Drug Discov, 2002. 1: 140-8.7-9). In particular, most of the anticoagulant activity of heparin resides in a specific 5-mer saccharide sequence,

[0044] Structural and functional studies have shown that a unique pentasaccharide (sometimes referred to as AGA*IA, DEFGH, or antithormbin binding domain (ABD)) comprises the anti-thrombin binding domain and is responsible for the anticoagulant activity of heparin. This pentasaccharide sequence is composed on three glucosamine residues (D, F, and H), a glucuronic acid residue E, and an iduronic acid residue (G). The sulfo group at C-3 of the central glucosamine residue (F) is a marker for the anti-thrombin bind site. The actual sequence of ABD is GlcNAc/NS6S→ GlcA→ GlcNS3S6S→ IdoA2S→ GlcNS6S (where GlcNS6S is a glucosamine comprising a sulfo group on the nitrogen and a sulfate group on C6, GlcA is glucoronic acid, GlcNS3S6S is a glucosamine comprising a sulfo group on the nitrogen and a sulfate group on C3 and C6, and IdoA2S is iduronic acid comprising a sulfate group on C2) and is shown in Figure 34. See for example, Avci, F.Y., Karst, N.A., Linhardt, R.J., Curr Pharm Des, 2003, 9: 2323-35; Gandhi, N.S., Mancera, R.L., 2010, 15: 1058-69; and Lever, R. and Page, CP., Nat Rev Drug Discov, 2002, 1: 140-8. The structural requirements for the binding of heparin to anti-thrombin are shown in Figure 34. As shown in Figure 34, charged sulfate groups (highlighted in the full boxes) are essential for activation of anti-thrombin while other charged sulfate groups (highlighted in the dashed boxes) are required to increase the biological activity. Moreover, hydrophobic interactions between the heparin pentasaccharide and anti-thrombin can also contribute to increasing the binding affinity. It is well known in the art that removal of N-sulfo groups in residue D results in a 50% loss of anti-Xa activity; removal of either of the O-sulfo groups in residues G or H results in a 75% loss of activity; and removal of any one of the 6-O-sulfo groups on residue D, carboxyl on residue E, 3-O-sulfo or N-sulfo on residue F, carboxyl on residue G, or N- sulfo group on residue H results in a 95% loss of activity.

[0045] A heparin or heparin derivative with reduced anticoagulant activity can be obtained by making one or more modification in the anti-thrombin binding pentasaccharide. Modifications can include one or more of changing, modifying, replacing, or substituting a charged sulfate group that is considered to be essential or required for anticoagulant activity. Exemplary modifications can include one or more of removing one or more of the sulfo groups, replacing one or more of the sulfo groups with a phospho group, replacing one or more of the sulfo groups with carboxylic group or carbonyl group, replacing one or more of the sulfo groups with an alkyl group (e.g., methyl, ethyl, propyl, butyl, isopropyl, pentyl, t- butyl, hexyl, and the like), alkylating one or more of the sulfate groups (e.g. with a methyl, ethyl, propyl, butyl, isopropyl, pentyl, t-butyl, or hexyl group), replacing the sulfo group on one or more of the nitrogens with an acyl (e.g., acetyl) group, replacing one or more of the saccharides with another saccharide (e.g., by a modified or unmodified allose, altrose, glucose, mannose, gulose, idose, galactose, or talose), replacing one or more of the saccharides with a non- saccharide linker, removing one or more of the saccharides, replacing the sodium cation from one or more of the sulfate groups with a different cation, replacing one or more of the sulfate groups with a 1,1-dihalogen alkyl group (e.g., 1,1-difluoroalkyl), replacing one or more of the sulfate groups with a 1,1-difluoromethylesulfate group, replacing one or more of the sulfate groups with a 1,1-difluoromethyletetazole group, and the like.

[0046] A heparin comprising a modified ABD can have anticoagulant activity that is at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80% or 90% less than the anticoagulant activity of an heparin comprising a unmodified ABD. While not crucial, a heparin comprising a modified ABD can be free of any anticoagulant activity. Methods for determining anticoagulant activity are well known in the art and can be used to determine the anticoagulant activity of a heparin comprising a modified ABD.

[0047] Some exemplary non-anticoagulant heparin and heparin sulfates mimetics include, but are not limited to, Pentosan polysulfate, and Heparin tetrasaccharide.

[0048] Non-linear branched sulfated carbohydrates are also envisioned for use in the methods described herein, including without limitation, heparin-BSA, as well as

glycodendrimers which can be produced with defined branched structures using click chemistry by methods known in the art (Lepenies, et al., Curr Opin Chem Biol, 2010. 14: 404-1 1). ΡΤΡσ activation may require higher-oligomerization, than dimerization, to promote neurite extension (Figure 25), reminiscent of the requirement of Eph receptors for large scale clustering (Flanagan, et al.,Annu. Rev. Neurosci., 1998. 21: 309-345; Vearing, et al., Growth Factors, 2005. 23: 67-76). Therefore, the branched polymers that can cluster receptors in an extended two-dimensional array are also envisioned.

Heparan Sulfate Proteoglycan (HSPG)

[0049] One type of glycosaminoglycan is heparan sulfate proteoglycan (HSPG). The biosynthesis of HSPGs leads to the production of molecules with great structural

heterogeneity with respect to the size of the polysaccharide chain, the ratio of iduronic (IdoA) to glucuronic acid (GlcA) units, and the amount and distribution of sulfate groups along the carbohydrate backbone.

[0050] Different HSPG's associate with the cell surface by a variety of mechanisms. HSPGs can link to the plasma membrane through a hydrophobic transmembrane domain of their core protein or through a glycosyl-phosphatidylinositol (GPI) anchor covalently bound to the core protein (transmembrane HSPGs). Also, HSPGs can interact with the cell by non- covalent linkage to different cell- surface macromolecules (peripheral membrane HSPGs). Transmembrane HSPGs are glypican (Doolittle, R. F. (1992) Protein Sci. 1, 191-200.), cerebroglycan (Stipp, et al. (1994) J. Cell Biol. 124, 149-160), betaglycan (Massague, J. (1992) Cell 69, 1067-1070), CD44 (Brown, et al. (1991) J. Cell Biol. 113, 207-221), and the members of the syndecan family (Bernfield, M., Kokenyesi, (1992) Annu. Rev. Cell Biol. 8, 165-193): syndecan 1, fibroglycan (syndecan 2), N-syndecan (syndecan 3) and ryudocan (syndecan 4). Glypican and cerebroglycan are typical GPI-anchored HSPGs. Syndecans and betaglycan are typical transmembrane HSPGs characterized by a core protein composed of an extracellular domain, a single membrane- spanning domain and a short cytoplasmic domain (28 to 34 amino acid residues). In the extracellular domain are present the consensus sequences for glycosylation and a conserved putative proteolytic cleavage site. The cytoplasmic domain of syndecans can interact with the cytoskeleton and contains four conserved tyrosine residues, one of them hypothesized to be substrate for enzymatic phosphorylation. Perleccan and dystroglycan are associated with the extracellular matrix. Perlecan is a typical peripheral membrane HSPG that interacts with the cell surface through its core protein (Lopez-Casillas et al. (1991) Cell 67, 785-795). The cell-adhesion motif Arg- Gly-Asp within the core protein of perlecan binds integrins bl or b3 present on endothelial cell surface (Hayashi et al. (1992) J. Cell Biol. 119, 945-959). However, HSPGs may associate to the cell surface and/or ECM also through their GAG-chain, as demonstrated by the observation that half of the total content of HSPGs in endothelial cells can be released after incubation with soluble heparin (Lowe-Krentz, et al. (1992) Mol. Cell. Biochem. 109, 51-60). Agrin and collagen XVIII are two other HSPGs that are found in the brain.

[0051] HSPGs exist also in soluble form following their mobilization from the cell surface. Transmembrane HSPGs are released after proteolytic digestion of their core protein (Saksela et al. (1988) J. Cell Biol. 107, 743-751). GAG-chain-associated HSPGs are released by exogenous GAGs by a simple law mass action (Lowe-Krentz, et al. (1992) Mol. Cell. Biochem. 109, 51-60) or by enzymatic digestion of their polysaccharide backbone (Bashkin et al. (1989) Biochemistry 28, 1737-1743). GPI-anchored HSPGs can be released by action of endogenous phospholipase (Brunner et al. (1991) J. Cell Biol. 114, 1275-1283).

[0052] In one embodiment, the agent used in the methods of the invention is purified and/or isolated prior to its use. Purified materials are typically "substantially pure", meaning that a molecule or fragment thereof has been separated from the components that naturally accompany it. Typically, the polypeptide is substantially pure when it is at least 60%, 70%, 80%, 90%, 95%, or even 99%, by weight, free from the proteins and other organic molecules with which it is associated naturally. For example, a substantially pure molecule may be obtained by extraction from a natural source or by chemical synthesis. "Isolated" as the term is used herein, refers to the molecule or a mixture of molecules, having been removed from its natural location and environment. In the case of an isolated or purified domain or fragment of a naturally occurring molecule, the domain or fragment is substantially free from flanking portions that occur naturally.

[0053] The use of combinations of 2 or more agents (e.g., those described herein) is also envisioned. For example, combinations of different lengths of heparin oligosaccharides, combinations of different HSPGs, or derivatives thereof, etc. In one embodiment, the agent used is a mixture of unfractionated heparin.

Other Agents

[0054] The methods described herein can further include administration or contacting a cell (e.g., a neuron) with a second agent that acts to enhance neuronal outgrowth, e.g. an agent that blocks other regeneration inhibitors (e.g., a compound that blocks myelin- associated inhibition of neurite growth). Known inhibitors of neuronal outgrowth (e.g., of regeneration at a CNS injury site) are myelin-derived inhibitors (e.g., Nogo-A, MAG, OMgp, Ehprin B3, Sema 4D and Sema 5A), astrocyte derived inhibitors (e.g., CSPG, KSPG, Ephrin B2 and Slit), fibroblast derived inhibitors (e.g., Sema 3A). The second agent may be an antagonist to any of these inhibitors. In one embodiment, the cell is further contacted with one or more such second agents. In one embodiment, the agent inhibits a myelin inhibitor of neural regeneration (e.g., myelin-associated glycoprotein (MAG), Nogo, oligodendrocyte myelin glycoprotein (OMgp)). Inhibitors of MAG are disclosed in U.S. Patent No. 5,932,542. Inhibitors of Nogo are disclosed in U.S. Patent Application Pub No. 2009/0215691. Inhibitors of OMgp are disclosed in U.S. Patent Application Pub. No. 2008/0188411. The cell can be contacted with this second agent before, after, and/or concurrently with the agent that inhibits the interaction of CSPG with ΡΤΡσ. The second agent can be formulated in a pharmaceutical composition with the first agent.

[0055] The second agent may be an agent that stimulates neuronal outgrowth. Such agents promote the intrinsic growth capability of a neuron. Such agents which promote neuronal outgrowth are known in the art. Such agents include, without limitation, agents that activate the growth pathway of neurons (e.g., CNS) are agents that are capable of producing a neurosalutary effect. As used herein, a "neurosalutary effect" means a response or result favorable to the health or function of a neuron, of a part of the nervous system, or of the nervous system generally. Examples of such effects include improvements in the ability of a neuron or portion of the nervous system to resist insult, to regenerate, to maintain desirable function, to grow or to survive. The phrase "producing a neurosalutary effect" includes producing or effecting such a response or improvement in function or resilience within a component of the nervous system. For example, examples of producing a neurosalutary effect would include stimulating axonal outgrowth after injury to a neuron; rendering a neuron resistant to apoptosis; rendering a neuron resistant to a toxic compound such as β-amyloid, ammonia, or other neurotoxins; reversing age-related neuronal atrophy or loss of function; or reversing age-related loss of cholinergic innervation.

[0056] Any agent that activates the growth pathway of neurons (e.g., CNS) is suitable for use in the methods of the present invention as a second agent. Examples of second agents include, but are not limited to, neurotrophic factors such as inosine, mannose, gulose, or glucose-6-phosphate, as described in Li et al., 23 J. Neurosci. 7830 (2003); Chen et al., 99 PNAS 1931 (2002); and Benowitz et al., 273 J. Biol. Chem. 29626 (1998). TGF-β, and oncomodulin as described in Yin et al., 23 J. Neurosci. 2284 (2003), are also such agents. In addition, polypeptide growth factors such as BDNF, NGF, NT-3, CNTF, LIF, and GDNF can be used. In one embodiment the methods of the present invention which comprise an agent that stimulates neuronal outgrowth further comprise contacting neurons (e.g., CNS) with a cAMP modulator that increases the concentration of intracellular cAMP (e.g., cAMP), and/or polyamines (Cai et al., 35 Neuron 711 (2002)). For example, the ability of mature rat retinal ganglionic cells to respond to mannose requires elevated cAMP (Li et. al., 2003).

[0057] Combinations of an agent (referred to herein as second agents) that blocks regeneration inhibitors, and an agent that stimulates neuronal outgrowth can also be used in conjunction with the agent that binds RPTPa (referred to herein as the first agent). The cell can be contacted with one or more second agents before, after, and/or concurrently with the first agent, and/or before, after, and/or concurrently with the second agent. Administration to a subject to achieve the desired order of contacting the agents with the target cells is within the ability of the skilled artisan.

[0058] The agents described herein may further be modified (e.g., chemically modified). Such modification may be designed to facilitate manipulation or purification of the molecule, to increase solubility of the molecule, to facilitate administration, targeting to the desired location, to increase or decrease half life. A number of such modifications are known in the art and can be applied by the skilled practitioner.

[0059] In one embodiment, the agent is obtained or isolated from a source exogenouse to the subject to which it is being administered.

Targeted Cells [0060] The agents and therapeutic pharmaceutical compositions described herein may be delivered to neurons of the CNS and/or the PNS to thereby stimulate neuronal outgrowth. In general, the targeted cell(s) will express RPTPa. Such neurons may be injured or diseased. Such neurons may alternatively be healthy, uninjured neurons. Such neurons may be located at the site of injury or diseased tissue, or at a site incident to the injury or diseased tissue. The neurons to be targeted for therapeutic administration, delivery/contact of the agents and compositions described herein will be neurons from which neuronal outgrowth is thought to prove beneficial to the subject. Such determination is within the ability of the skilled practitioner through no more than routine experimentation. In one embodiment, the targeted cells are the actual injured neurons (e.g, to promote re-generation). In another embodiment, the targeted cells are neurons whose outgrowth produces compensatory neuronal function with respect to the neuronal injury. In another embodiment, both types of neurons (injured and compensatory) are targeted.

Treatments of Neuronal Disorders

[0061] In one embodiment, the agent described herein is administered to a subject for therapeutic purposes to promote neuronal outgrowth to thereby treat a neuronal disorder in the subject. As used herein, the term "neuronal disorder" includes a disease, disorder, or condition which directly or indirectly affects the normal functioning or anatomy of a subject's nervous system. The disorder may be an injury, or degeneration of the central nervous system and/or of peripheral nerves. The neuronal disorder may result from injury (e.g., traumatic injury) or from disease (e.g., neurodegenerative disease). Such injuries include stroke, traumatic brain injury, peripheral nerve injury, spinal cord injury, skin burn, and eye injury.

[0062] The term "stroke" is art-recognized and includes sudden diminution or loss of consciousness, sensation and voluntary motion caused by rupture or obstruction (for example, by a blood clot) of an artery of the brain. "Traumatic brain injury" is art-recognized and includes the condition in which a traumatic blow to the head causes damage to the brain or connecting spinal cord, with or without penetrating the skull. Usually, the initial trauma can result in expanding hematoma, subarachnoid hemorrhage, cerebral edema, raised intracranial pressure, and cerebral hypoxia, which can, in turn, lead to severe secondary events due to low cerebral blood flow. [0063] The neuronal injury can be acute or chronic. Examples of acute injury are those that results from surgery, trauma, compression, contusion, transection or other physical injury, vascular pharmacologic or other insults including hemorrhagic or ischemic damage. Chronic neuronal injury may results from repetitive stress, inflammation/oxidative stress within a neural tissue caused by disease, neurodegenerative or other neurological diseases.

[0064] Neuronal degenerative diseases include, without limitation, amyotrophic lateral sclerosis (ALS), retinitis pigmentosa, glaucoma, multiple sclerosis, mild cognitive impairment, Alzheimer's disease, Pick's disease, senile dementia, progressive supranuclear palsy, subcortical dementias, Wilson disease, multiple infarct disease, arteriosclerotic dementia, AIDS associated dementia, cerebellar degeneration, spinocerebellar degeneration syndromes, Friedreichs ataxia, ataxia telangiectasia, epilepsy-related brain damage, spinal cord injury, restless legs syndrome, Huntington's disease, Parkinson's disease, striatonigral degeneration, cerebral vasculitis, mitochondrial encephalomyopathies, neuronal ceroid lipofuscinosis, spinal muscular atrophies, lysosomal storage disorders with central nervous system involvement, leukodystrophies, urea cycle defect disorders, hepatic encephalopathies, renal encephalopathies, metabolic encephalopathies, porphyria, bacterial meningitis, viral meningitis, meningoencephalitis, prion diseases, poisonings with neurotoxic compounds, Guillain Barre syndrome, chronic inflammatory neuropathies, polymyositis, dermatomyositis and radiation-induced brain damage. Included in the aspect is neurodegeneration including peripheral neuropathy due to therapeutic administration of cranial irradiation or

chemotherapeutic agents.

Peripheral nerve damage

[0065] In one embodiment, the agent is administered to a subject to treat damage associated with peripheral neuropathies including, but not limited to, the following: diabetic neuropathies, virus-associated neuropathies, including acquired immunodeficiency syndrome (AIDS) related neuropathy, infectious mononucleosis with polyneuritis, viral hepatitis with polyneuritis; Guillian-Barre syndrome; botulism-related neuropathy; toxic polyneuropathies including lead and alcohol-related neuropathies; nutritional neuropathies including subacute combined degeneration; angiopathic neuropathies including neuropathies associated with systemic lupus erythematosis; sarcoid-associated neuropathy; carcinomatous neuropathy; compression neuropathy (e.g. carpal tunnel syndrome) and hereditary neuropathies, such as Charcot-Marie-Tooth disease. The agent is administered to thereby contact a peripheral nerve and induce neuronal outgrowth. The nerve may be an injured peripheral nerve, or a compensatory peripheral nerve.

[0066] Peripheral nerves such as dorsal root ganglia, otherwise known as spinal ganglia, are known to extend down the spinal column. These nerves can be injured as a result of spinal injury. Such peripheral nerve damage associated with spinal cord injury can also be treated using the present methods. The subject is treated in accordance with the present method for peripheral nerve damage as the result of peripheral neuropathies. The injury for treatment can be acute or chronic. The spinal cord injury may be a complete severing of the spinal cord, a partial severing of the spinal cord, or a crushing or compression injury of the spinal cord.

Transmembrane Protein Tyrosine Phosphatases (PTPs)

[0067] Transmembrane PTPs form a large and diverse molecular family, and have a structure typical of transmembrane cell surface receptors (Chagnon et al., Biochem Cell Biol 82, 664 (2004); Johnson et al., Physiol Rev 83, 1 (2003). ΡΤΡσ is a receptor type protein- tyrosine phosphatase that has been cloned and identified in mouse, in rat, and in human (Pulido et al., Proc. Nat. Acad. Sci. 92: 11686-11690, 1995; PubMed ID : 8524829). ΡΤΡσ and other PTPs in the LAR subfamily can act as receptors for heparan sulfate proteoglycans (HSPGs), and these PTPs are involved in axon guidance and synapse formation during development. In the adult, ΡΤΡσ gene disruption enhances regeneration in sciatic, facial and optic nerves.

[0068] ΡΤΡσ has two intracellular PTPase domains and an extracellular region having Ig- like and fibronectin type III- like domains. The specific location of the various domains of the ΡΤΡσ molecule are known in the art. Pulido et al., 92 PNAS 11686 (1995); PubMed ID: 8524829. Alternative splicing of ΡΤΡσ generates four isoforms; the long isoforms 1 and 2, which are expressed in a range of human tissues, contain an additional four fibronectin type III domains compared with the short isoforms 3 and 4, which are predominantly found in the brain (Naoto et al., J Bone Miner. Res. 11, 535 (1996)). Amino acid and nucleotide sequences for human and mouse ΡΤΡσ are shown in the Examples section below.

Administration

[0069] For the therapeutic methods described herein, the agent is administered to the subject to be treated. The term "administered" or "administering" to a subject includes dispensing, delivering or applying the agent to the subject by any suitable route for delivery of the agent to a site in the body where neuronal outgrowth is desired (e.g., the site of neuronal injury or neuronal degeneration) to thereby contact a neuron at that site. Contact can be to the cell body or cell process. The route of administration and the dosage regimen will be determined by skilled clinicians, based on factors such as the exact nature of the condition being treated, the severity of the condition, and the age and general physical condition of the patient. In one embodiment, administration is to thereby contact injured and/or non-injured neurons proximal to the injury site. In one embodiment, administration is such as to deliver the agent across the blood brain barrier. Pharmaceutical compositions described herein comprising one or more of the specific agents described herein are also envisioned as other aspects of the invention.

[0070] Typically the agent is administered in the context of a pharmaceutical

composition. A pharmaceutical composition typically comprises the agent and a

pharmaceutically acceptable carrier. A pharmaceutically acceptable carrier is one that is physiologically compatible with the intended route of administration, to deliver the agent in active form (e.g., not degraded). In one embodiment, the agent/pharmaceutical composition is in solution. In another embodiment, the agent is in a solid or in a semi-solid form (e.g., contained in a matrix). In one embodiment, the agent is in a liquid matrix that changes phase once injected into the body. In one embodiment, the pharmaceutical composition is a slow release implant that can be deposited at the site of injury or target site of contacting the neuron.

[0071] As the term is used herein, a matrix is a composition designed to localize/hold the agent in a specific desired location of the subject once administered. Such a matrix can be a gel, a paste, or a solid substance, that has the agent incorporated therein. The agent may be available in the matrix, or released from the matrix over time to thereby contact the neurons in the general location of the matrix. In one embodiment, the matrix is liquid at room temperature and more solid (e.g., a gel, paste, solid) once in the body. In one embodiment, the temperature of the body induces the phase shift. One such matrix is an injectable hydrogel. A variety of such hydrogels and routes/ methods of administration are disclosed in Macaya et al., (Biomed. Mater. 7 (2012) 012001 (22pp)). In one embodiment, the hydrogel is a thermogel (an aqueous monomer/polymer solution which has the ability to form a gel upon temperature change) such as is disclosed in Klouda et al., (Eur. J. Pharm. Biopharm. (2008) 68: 34-45). [0072] Administration can be systemic or local. Local administration can be into the site of nerve or brain or cord injury, into a site of pain or neural degeneration, or intraocularly to contact neuroretinal cells. Administration can be directly into the neural tissue (e.g., the injured neural tissue). Routes of administration including delivery by either the parenteral or oral route, intramuscular injection, extradural, intramedullary, injection directly into neural tissue, subcutaneous/intradermal injection, intravenous injection, buccal administration, transdermal delivery and administration by the rectal, colonic, vaginal, intranasal or respiratory tract route. The agent can also be administered, topically, by inhalation (e.g., intrabronchial, intranasal, oral inhalation or intranasal drops). Other examples of local administration include delivery to the eye, such as by eyedrops, creams or erodible formulations to be placed under the eyelid, intraocular injection into the aqueous or the vitreous humor, injection into the external layers of the eye, such as via subconjunctival injection or sub tenon injection.

[0073] A form of administration suitable for treatment of spinal cord injury is localized delivery (e.g., injection) into the spinal column or spinal canal. In certain aspects of the invention, the agent is introduced into the cerebrospinal fluid, a cerebral ventricle, the lumbar area, or the cistema magna of a subject. The term "lumbar region" is intended to include the area between the third and fourth lumbar (lower back) vertebrae. The term "cistema magna" is intended to include the area where the skull ends and the spinal cord begins at the back of the head. The term "cerebral ventricle" is intended to include the cavities in the brain that are continuous with the central canal of the spinal cord. Administration may be at the vertebrae closest to the injury site.

[0074] In another embodiment of the invention, the agent is administered to a subject intrathecally (e.g., to treat stroke). As used herein, the term "intrathecal administration" is intended to include delivering an active compound formulation directly into the cerebrospinal fluid of a subject, by techniques including lateral cerebroventricular injection through a burrhole or cisternal or lumbar puncture or the like (described in Lazorthes et al., 1991, and Ommaya A.K., 1984, the contents of which are incorporated herein by reference). In one embodiment, the administration is by way of deposition of a slow-release implant at the target site. In one embodiment, administration is by injection into the brain parenchyma.

[0075] Injections described herein can be, for example, rapid volume injection or slow infusion. [0076] An additional means of administration is to intracranial tissue by application of the agent to the olfactory epithelium, with subsequent transmission to the olfactory bulb and transport to more proximal portions of the brain. Such administration can be by nebulized or aerosolized preparations.

[0077] Administration of the agent to any of the above mentioned sites can be achieved by direct implantation or injection of the agent or by the use of infusion pumps. Implantable or external pumps and catheter may be used.

[0078] For injection, the agent of the invention can be formulated in liquid solutions, preferably in physiologically compatible buffers such as Hank's solution or Ringer's solution. In addition, the agent may be formulated in solid form and re-dissolved or suspended immediately prior to use. Lyophilized forms are also included. The injection can be, for example, in the form of a bolus injection or continuous infusion (such as using infusion pumps) of the agent formulation.

[0079] Another method of administration is delivery of the agent contained within a matrix. Implantation of the matrix at the desired site results in delivery of the agent to the neurons to thereby promote outgrowth. The matrix can be a gel or a semi-solid or solid matrix. In one embodiment, the agent is dispersed from the matrix to the surrounding area. In one embodiment, the agent is present in the matrix in the absence of any extraneous agents e.g., a DNA encoding therapeutic agent. The matrix can be implanted via surgical implantation, or by topical application or injection into the injury site, such as with a matrix in the form of a gel or paste.

[0080] In one embodiment, the agent described herein is administered to the subject in the period from the time of, for example, an injury to the nervous system up to about 100 hours after the injury has occurred, for example within 24, 12, or 6 hours from the time of injury. In another embodiment of the invention, the active compound formulation is administered to a subject (e.g., at the site of injury), usually within 100 hours of when an injury occurs.

[0081] Another method of administration is via cells that express the agent described herein. Such cells are implanted at the administration sites described herein by the methods described herein (e.g,. contained in a gel for implantation).

Dosage and Levels of Administration [0082] Toxicity and therapeutic efficacy can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50% of the population) and the ED50 (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD50/ED50. Compositions that exhibit large therapeutic indices, are preferred. As used herein, the term ED denotes effective dose and is used in connection with animal models. The term EC denotes effective concentration and is used in connection with in vitro models. The data obtained from the cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED50 with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized.

[0083] The therapeutically effective dose can be estimated initially from cell culture assays. A dose may be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of the therapeutic which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Levels in plasma may be measured, for example, by high performance liquid chromatography. Levels within neural tissue of an experimental animal can be determined by procedures such as immunolocalization, or Western blot of tissue extracts, or by fluorescently tagging the therapeutic compound prior to administration. Once an appropriate level is effected in an experimental animal, the corresponding dose for a human subject can be extrapolated therefrom. The effects of any particular dosage can be monitored by a suitable bioassay, for example neuronal outgrowth or increased nerve function. Restoration of nerve function can be evidenced by restoration of nerve impulse conduction, a detectable increase in conduction action potentials, observation of anatomical continuity, restoration of more than one spinal root level, an increase in behavior or sensitivity, or a combination thereof.

[0084] In some embodiments the amount of neuronal outgrowth or increased nerve function produced by the in vitro contacting or in vivo administration of the agent, described herein, is increased by at least 5%, at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60 %, at least 70%, at least 80%, at least 90 %, at least, 1-fold, 2-fold, 3- fold, 4-fold, 5-fold, 10-fold, 50-fold, or 100-fold or more, relative to reference level. A reference level an be obtained, for example, by using an appropriate control to generate a reference level, and can be, for example, a similar or identical subject who has experienced similar or identical conditions, but in the absence of the added agent.

[0085] The agent can be administered to a subject for an extended period of time to produce optimum axonal outgrowth. Sustained contact with the active compound can be achieved, for example, by repeated administration of the agent over a period of time, such as one week, several weeks, one month or longer. The pharmaceutically acceptable formulation used to administer the active compound(s) can also be formulated to provide sustained delivery of the active compound to a subject. For example, the formulation may deliver the active compound for at least one, two, three, or four weeks, inclusive, following initial administration to the subject. For example, a subject to be treated in accordance with the present invention is treated with the active compound for at least 30 days (either by repeated administration or by use of a sustained delivery system, or both).

Detecting Neuro generative Effect

[0086] Neuronal outgrowth induced by the methods described herein can be determined by a variety of methods, such as by determination of the formation of axons (e.g., detecting the formation of neuronal branching microscopically, or by showing cytoplasmic transport of dyes). Neuronal outgrowth can also be detected by determination of the formation of neural connectivity. Outgrowth can also be determined by an increase or a restoration of function of the neuron. Neuronal function can be measured by standard assays such as detection of action potential or nerve impulse condition by standard assays.

[0087] The promotion of neural generation in a subject by the methods described herein may be assessed using any of a variety of known procedures and assays. For example, the determination of the establishment, or re-establishment of neural connectivity, and/or function after an injury. Such neural connectivity and/or function, may be determined visually (e.g., histologically by slicing neuronal tissue and looking at neuronal branching, or by showing cytoplasmic transport of dyes). Functional assays can also be used to determine neural generation, such as by detecting full or partial restoration of a neural function.

Examples of such assays are, without limitation, use of an electroretinogram to detect restoration of function after damage to the neural retina or optic nerve; or measurement of the pupillary response to light in the damaged eye to detect restoration of the response. [0088] Other tests that may be used include standard tests of neurological function in human subjects or in animal models of spinal injury (such as standard reflex testing, urologic tests, urodynamic testing, tests for deep and superficial pain appreciation, proprioceptive placing of the hind limbs, ambulation, and evoked potential testing). In addition, nerve impulse conduction can be measured in a subject, such as by measuring conduct action potentials, as an indication of restoration of neuronal function.

[0089] Animal models suitable for use in the assays of the present invention include the rat model of partial transaction (see Weidner et al., 2001), that tests how well a compound can enhance the survival and sprouting of the intact remaining fragment of an almost fully- transected cord. Another injury model is the rodent model for contusion which closely mimics the injury seen in the majority of human spinal cord injury patients. Accordingly, after administration of a candidate agent these animals may be evaluated for recovery of a certain function, such as how well the rats may manipulate food pellets with their forearms (to which the relevant cord had been cut 97%).

[0090] Another animal model suitable for use in the assays of the present invention includes the rat model of stroke (see Kawamata et al., 1997, for various tests that may be used to assess sensori motor function in the limbs as well as vestibulomotor function after an injury). Administration to these animals of the agents of the invention can be used to assess whether a given compound, route of administration, or dosage provides a neuroregenerative effect, such as increasing the level of function, or increasing the rate of regaining function or the degree of retention of function in the test animals.

[0091] Standard neurological evaluations used to assess progress in human patients after a stroke may also be used to evaluate the ability of an agent to produce a neurosalutary effect in a subject. Such standard neurological evaluations are routine in the medical arts, and are described in, for example, "Guide to Clinical Neurobiology" Edited by Mohr and Gautier (Churchill Livingstone Inc. 1995).

[0092] Another aspect of the present invention relates to a method for identifying an agent that induces neuronal outgrowth. The method comprises identifying a molecule that induces clustering of RPTPa (e.g., through direct binding) by screening candidate agents. A candidate agent identified as inducing clustering of RPTPa is expected to be an agent that will induce neuronal outgrowth, and thus be useful in the methods described herein. Such an identified candidate agent can further be verified as an agent useful in the methods described herein by determining its ability to induce neuronal outgrowth (e.g., by subjecting it to a neuronal outgrowth assay) as described herein.

[0093] Also encompassed by the present invention is an article of manufacture (e.g., a kit) comprising packaging material and compositions comprising the agents described herein (e.g. pharmaceutical compositions) contained within the packaging material. The packaging material comprises a label which indicates that the pharmaceutical may be administered, for a sufficient term at an effective dose, for inducing neuronal outgrowth in a subject, and/or treating neuronal injury or neurodegenerative diseases described herein. The present invention also encompasses pharmaceutical compositions described herein.

[0094] Unless otherwise defined herein, scientific and technical terms used in connection with the present application shall have the meanings that are commonly understood by those of ordinary skill in the art. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular.

[0095] It should be understood that this invention is not limited to the particular methodology, protocols, and reagents, etc., described herein and as such may vary. The terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention, which is defined solely by the claims.

[0096] Other than in the operating examples, or where otherwise indicated, all numbers expressing quantities of ingredients or reaction conditions used herein should be understood as modified in all instances by the term "about." The term "about" when used to described the present invention, in connection with percentages means ±1%, or ±5%.

[0097] In one respect, the present invention relates to the herein described compositions, methods, and respective component(s) thereof, as essential to the invention, yet open to the inclusion of unspecified elements, essential or not ("comprising). In some embodiments, other elements to be included in the description of the composition, method or respective component thereof are limited to those that do not materially affect the basic and novel characteristic(s) of the invention ("consisting essentially of). This applies equally to steps within a described method as well as compositions and components therein. In other embodiments, the inventions, compositions, methods, and respective components thereof, described herein are intended to be exclusive of any element not deemed an essential element to the component, composition or method ("consisting of). [0098] All patents, patent applications, and publications identified are expressly incorporated herein by reference for the purpose of describing and disclosing, for example, the methodologies described in such publications that might be used in connection with the present invention. These publications are provided solely for their disclosure prior to the filing date of the present application. Nothing in this regard should be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention or for any other reason. All statements as to the date or representation as to the contents of these documents is based on the information available to the applicants and does not constitute any admission as to the correctness of the dates or contents of these documents.

[0099] The present invention may be as defined in any one of the following numbered paragraphs.

1. A method of inducing neuronal outgrowth of a neuron comprising, contacting the neuron with an agent that binds receptor protein tyrosine phosphatase σ (RPTPa), to thereby induce neuronal outgrowth of the neuron.

2. The method of paragraph 1, wherein the agent induces clustering of RPTPa.

3. The method of paragraph 1, wherein the agent inhibits binding of chondroitin sulfate proteoglycan (CSPG) to RPTPa.

4. The method of any one of paragraphs 1-3, wherein the agent is selected from the group consisting of heparan sulfate proteoglycan, heparan sulfate, heparin

oligosaccharide, and heparan sulfate oligosaccharide.

5. The method of paragraph 4, wherein the heparin oligosaccharide or the heparan

sulfate oligosaccharide contains 8 or more saccharide units and less than 67 saccharide units.

6. The method of any one of paragraphs 1-5, wherein the heparin oligosaccharide or the heparan sulfate oligosaccharide contains 10 or more saccharide units and less than 67 saccharide units. The method of paragraph 4, wherein the heparan sulfate proteoglycan is glypican 2 or a derivative thereof. The method of any one of paragraphs 1-7, said agent binds to the first

immunoglobulin-like domain of RPTPa. The method of any one of paragraphs 1-7 wherein the agent is in solution. The method of any one of paragraphs 1-8, wherein the agent is contained in a matrix. The method of any one of paragraphs 1-10, wherein the contacting occurs in vitro. The method of any one of paragraphs 1-10, wherein the contacting occurs in vivo. The method of paragraph 12, wherein said neuron is located at a site of injured or diseased

tissue. The method of any one of paragraphs 1-13, further comprising contacting said neuron with a second agent that promotes neuronal outgrowth. The method of paragraph 14, wherein the second agent reduces inhibition of neuronal outgrowth. The method of any one of paragraphs 1-15, wherein the neuron is a central nervous system neuron. The method of any one of paragraphs 1-15, wherein the neuron is a peripheral nervous system neuron. A method of treating neuronal injury in a subject comprising, administering to the subject an agent that binds RPTPa to thereby induce neuronal outgrowth. The method of paragraph 18, further comprising selecting a subject in need of treatment for neuronal injury prior to the administering. The method of any one of paragraphs 18 or 19, wherein the agent is administered at a site of neuronal injury, to thereby induce neuronal outgrowth at the site of neuronal injury. The method of any one of paragraphs 18-20 wherein the agent induces clustering of the RPTPa. The method of any one of paragraphs 18 -20, wherein the agent inhibits binding of chondroitin sulfate proteoglycan (CSPG) to the RPTPa. The method of any one of paragraphs 18-22, wherein the neuronal injury is selected from the group consisting of stroke, spinal cord injury, traumatic brain injury, peripheral nerve injury, skin burn, and eye injury. The method of any one of paragraphs 16-22 wherein the neuronal injury is acute. The method of any one of paragraphs 16-22 wherein the neuronal injury is chronic. The method of any one of paragraphs 16-22, wherein the agent is selected from the group consisting of heparan sulfate proteoglycan, heparan sulfate, heparin

oligosaccharide, and heparan sulfate oligosaccharide. The method of paragraph 26, wherein the heparin oligosaccharide or the heparan sulfate oligosaccharide contains 8 or more saccharide units and less than 67 saccharide units. The method of any one of paragraphs 26 or 27, wherein the the heparin

oligosaccharide or the heparan sulfate oligosaccharide contains 10 or more saccharide units and less than 67 saccharide units. The method of paragraph 26, wherein the heparan sulfate proteoglycan is glypican 2 or a derivative thereof. The method of any one of paragraphs 19-20, further comprising contacting said neuron with a second agent that promotes neuronal outgrowth. The method of any one of paragraphs 18-30 wherein the agent is soluble. The method of any one of paragraphs 18-30 wherein the agent is contained in a matrix. The method of any one of paragraphs 18-32 wherein the agent directly binds to the RPTPa. The method of any one of paragraphs 18-33, wherein the agent binds to the first immunoglobulin-like domain of RPTPa. The method of any one of paragraphs 18-34, wherein administering is systemic or localized. The method of paragraph 35, wherein administration is by method selected from the group consisting of oral, intramuscular injection, subcutaneous or intradermal injection, intrathecal, extradural, intramedullary, injection directly into neural tissue, intravenous injection, buccal administration, transdermal, rectal, colonic, vaginal, intranasal, and inhalation. The method of paragraph 35, wherein localized administration is by implantation of a matrix that contains the agent. The method of paragraph 36, wherein implantation is by injection and the matrix is a gel that solidifies in the body of the subject. A method of promoting neural outgrowth in the nervous system of a subject, comprising administering to the subject an agent that binds RPTPa, to contact a neuron and thereby induce neural outgrowth of the neuron. The method of paragraph 39, further comprising selecting a subject in need of promotion of neural outgrowth prior to the administering. The method of any one of paragraphs 39-40, wherein the agent induces clustering of the RPTPa. The method of paragraph 39, wherein the agent inhibits binding of chondroitin sulfate proteoglycan (CSPG) to the RPTPa. The method of paragraph 39, wherein the agent is heparan sulfate proteoglycan, heparan sulfate, heparin oligosaccharide or heparan sulfate oligosaccharide . The method of paragraph 43, wherein the heparin oligosaccharide or the heparan sulfate oligosaccharide contains 8 or more saccharide units and less than 67 saccharide units. The method of paragraph 43, wherein the heparin oligosaccharide or the heparan sulfate oligosaccharide contains 10 or more saccharide units and less than 67 saccharide units. The method of paragraph 43, wherein the heparan sulfate proteoglycan is glypican 2 or a derivative thereof. The method of any one of paragraphs 39-46 wherein the agent is in solution. The method of any one of paragraphs 39-46 wherein the agent is contained in a matrix. The method of any one of paragraphs 39-48, wherein the neuron is located at or adjacent to a site of diseased or injured tissue. The method of paragraph 49, wherein the injured tissue results from an injury selected from the group consisting of stroke, spinal cord injury, traumatic brain injury, peripheral nerve injury, skin burn, and eye injury affecting optic nerve fibers. The method of paragraph 49, wherein the injured tissue results from an acute injury. The method of paragraph 49, wherein the diseased tissue is a site of neuronal degeneration. The method of paragraph 49, wherein the diseased tissue results from a

neurodegenerative

disease. The method of any one of paragraphs 39-53, wherein administering is systemic or localized. The method of paragraph 54, wherein administration is by method selected from the group consisting oral, intramuscular injection, subcutaneous or intradermal injection, intrathecal, extradural, intramedullary, injection directly into neural tissue, intravenous injection, buccal administration, transdermal, rectal, colonic, vaginal, intranasal, and inhalation. The method of paragraph 54, wherein localized administration is by implantation of a matrix that contains the agent.

The method of paragraph 56, wherein implantation is by injection and the matrix is a gel that solidifies in the body of the subject. [00100] The present invention is further illustrated by the following Examples. These Examples are provided to aid in the understanding of the invention and are not construed as a limitation thereof.

EXAMPLES

Example 1 - Proteoglycan-Specific Molecular Switch for RPTPa Clustering and Neuronal Extension

[00101] Previous results led to alternative predictions for the potential effects, if any, of HSPGs acting via RPTPa in DRG neurons: these might inhibit outgrowth, like CSPGs, or promote outgrowth, as suggested by the response of retinal ganglion cells to basal lamina. Neurocan, a CSPG, reduced outgrowth of wild- type DRG neurons by approximately 60%, as described previously (12), and this inhibitory effect was decreased in RPTPa ^A neurons (P<0.001; Figure 1, A-D and G). In contrast, glypican-2, an HSPG, strongly promoted outgrowth of wild-type neurons. This promoting effect was reduced to undetectable levels in RPTPa ^A neurons, showing a requirement for RPTPa (P<0.01; Figure 1, E to G). Heparitinase III treatment of the glypican-2 significantly reduced its growth-promoting ability (P<0.005; Figure 5), indicating that its glycosaminoglycan (GAG) chains are involved. Chondroitinase ABC and heparitinase III reduced RPTPa binding by neurocan and glypican-2 respectively, confirming the specific presence of HS and CS on these proteoglycans and the role of GAG chains in mediating interactions with RPTPa (Figure 1H).

[00102] The observed dichotomy in CSPG/HSPG function, apparently mediated through a common receptor, RPTPa, is intriguing given that mutagenesis studies indicate a common binding site for the two proteoglycan classes (12, 18). To investigate the structural basis of proteoglycan recognition in RPTPa and type Ila RPTPs in general, crystallographic studies were undertaken. The type Ila RPTP ectodomain is predicted to consist of three I-set immunoglobulin (Ig)-like domains followed by either five or nine fibronectin (FN) type III repeats (Figure 2A). A series of RPTPa, RPTP5 and LAR deletion constructs were generated for structural and functional assays (27), all including the N-terminal Ig domain harbouring the putative GAG binding site (Figure 2A) (12, 18). Crystal structures were determined of the two N-terminal Ig domains (Igl-2), which formed the minimal stable unit, for examples across family members and species (chicken and human RPTPa, human RPTP5 and LAR, Drosophila DLAR; see (28), Tables 1 and 2 and Figure 6). A V-shape arrangement of Igl and Ig2 is stabilized by conserved interactions, irrespective of the crystallization conditions and packing (Figure 2B and Figure 7 to 9).

[00103] RPTPa residues previously shown to mediate GAG binding (K67, K68, K70, K71, R96 and R99) lie on loops between Igl β-strands C-D and E-F, forming an extended positively-charged surface (Figure 2, B and C). The determined crystal structures, supplemented by sequence comparisons, show this site is highly conserved across family members and species (Figure 2C and Figure 6) suggesting a common GAG binding mode. A

2.05 A resolution crystal structure of human LAR Igl -2 in complex with sucrose octasulfate (SOS), a synthetic heparin-mimic, confirmed the GAG-binding site location and revealed a conformational plasticity of the C-D ("Lys") loop (residues K67-F77; Figure 2D, Figure 10- 12 and Figure 36 and Figure 37). SOS binding triggered an outwards movement of residues V72-F77, following rupture of the R76-D100 salt bridge. K67, K68 and R76 form

electrostatic interactions with SOS whilst R99 interacts with D100, resulting in a modified topology of the GAG-binding surface but maintaining the overall positive charge (Figure 2, E and F). Thus, the combination of basic side chains deployed by the type Ila RPTP GAG- binding site may vary to match the sulfate chemistry of a particular disaccharide unit, conferring the ability to accommodate chemically diverse GAGs.

[00104] Interaction affinities of RPTPa sEcto with neurocan and glypican-2, in solid phase binding assays, were in the same range (10-20 nM K^; Figure 3B and C), similar to those determined in previous studies of CSPGs or HSPGs binding to type Ila RPTPs (7, 12), although weaker than measured previously for heparin-BSA (0.3nM) (18). The glycan binding surface on Igl forms an elliptical area of ~35Ax24A (Figure 3A). Comparisons with a compact heparin structure, a helix with a 4 saccharide pitch of 17.5A (29), suggested that GAG chains could assemble RPTPa oligomers. A series of size-defined heparin fragments were then incubated with a RPTPa construct containing the six N-terminal domains (Igl- FN3; Figure 2A). Heparin fragments containing four [degree of polymerization 4 (dp4)] or six (dp6) saccharide residues did not alter the Igl-FN3 oligomeric state, as assessed by size- exclusion chromatography coupled with multi-angle light scattering (MALS) (Figure 3D to 3G and Figure 37). However, fragments containing eight (dp8) or ten (dplO) saccharides induced a shift towards a dimeric Igl-FN3 species (Figure 3D and Figure 37). This trend continued as heparin fragments of increasing length were tested; Igl-FN3 mixed with dp20 and dp30 formed tri and tetrameric clusters, respectively (Figure 3E and Figure 37). A quadruple K67, K68, K70, K71 mutation to alanine, previously shown to impair binding to both CSPGs and HSPGs (12, 18), abolished the heparin-induced clustering effects (Figure 3F and Figure 37). The clustering behaviour was reproduced in MALS measurements for an RPTPa domain deletion series (Figure 2 A and Figure 13) and validated for Igl-2 by analytical ultracentrifugation and native mass spectrometry (Figure 14). These data provide compelling evidence that the Igl GAG-binding site is necessary and sufficient for receptor clustering dependent on heparin fragment length (Figure 13, 14 and Figure 37). Similar heparin-induced oligomerisation characteristics were demonstrated for other type Ila RPTPs, albeit with some variation (Figure 15, 16 and Figure 37).

[00105] MALS was then used to compare the ability of chondroitin sulfate (CS) and heparan sulfate (HS) GAGs to induce oligomerization. HS (30-150 saccharide units) induced tetrameric clustering of RPTPa Igl-FN3, analogous to dp30 heparin fragments (Figure 3G and Figure 37). In striking contrast to heparin or HS, comparable CS (30-150 saccharide units) quantities did not induce clustering of any type Ila RPTP construct (Figure 3E and Figure 16). Using five-fold higher CS concentrations we were able to detect evidence of binding to RPTPa Igl-FN3, but the molecular mass did not shift to the levels seen for stable GAG-induced oligomers (Figure 3G and Figure 37). Since in our solid state assay CSPGs and HSPGs had shown comparable binding affinities to RPTPa we tested whether CS could compete with HS in the MALS assay. Excess CS inhibited both HS- and heparin dplO- induced clustering (Figure 16 and Figure 37). Thus differences in GAG chemical structure must be responsible for the contrasting effects of HS and CS on RPTPa oligomerisation (Figure 3H).

[00106] The competing effects of CS and HS on RPTPo oligomerization suggest axon outgrowth may be determined by relative amounts, rather than independent effects, of HSPG and CSPG acting on RPTPo. To investigate this model, DRG neuron cultures were assessed for expression of endogenous HS and CS. Immunofluorescence showed both CS and HS are endogenously produced by these cultures. CS labeling was seen primarily over the extracellular matrix (ECM), where it was highest adjacent to non-neuronal cells, suggesting production of CSPG by these cells, whereas cell bodies and GAP43-labeled neurites showed little or no evidence of CS labeling and were typically aligned with dark areas in the immunofluorescence (Figures 4A-F and 18). HS labeling, in contrast, was highest over cell bodies and neurites, where RPTPo labeling was also seen (Figs. 4G-0 and 18). At higher magnification, RPTPo labeling revealed a punctate distribution over the growth cone, as described previously (15), and was similar (although not identical) to the HS pattern (Figure 4P-S). These results thus support a model where endogeneous HSPGs in these cultures act predominantly in cis on the cell surface, while CSPGs are presented in trans by the ECM (Figure 4T). Exogenous HSPG or CSPG addition (Figure 1) would shift the HSPG:CSPG ratio. Consistent with this interpretation, and with the ability of CS to compete HS-mediated RPTPa oligomerization (Figure 16), addition of CSPG to DRG cultures could block the outgrowth-promoting effect of exogenous HSPG (P<0.001; Figure 19).

[00107] Mechanistic parallels can be drawn for proteoglycan- specific regulation of other cell surface receptor systems. HS is known to play an essential role in fibroblast growth factor (FGF) signalling (30), and the number of FGF-FGFR protomers in a supramolecular assembly directly correlates with the size of the GAG chain (31). Opposing HSPG and CSPG effects have been reported in semaphorin-mediated axon guidance (22). HSPGs and CSPGs differ in the chemical composition of their GAG chains. The distribution of sulfate groups (typically 1-2 per disaccharide) along CS chains is relatively uniform, while HS has a distinct modular composition, with high sulfation regions (3 groups per disaccharide), flanked by intermediately modified transition zones and variably spaced by largely unmodified sections almost devoid of sulfation (32). Without being bound by theory, the observations reported herein suggest a model where islands of high sulfation present in HS, but not CS, may promote close packing of RPTPa molecules.

[00108] RPTPa clustering would translate into an uneven distribution of phosphatase activity on the cell surface, consistent with localization-based models for receptor action (33). Small regions depleted in phosphatase activity could enhance the extent and duration of a phosphorylated state for proteins stimulating neuronal extension (1, 34-35). The solution and cellular data presented herein are consistent with a model whereby increasing the

CSPG:HSPG ratio shifts the balance away from growth-promoting RPTPa clusters, stalling neuronal growth cones (Figure 4T). This model predicts that molecules able to promote RPTPa oligomerization may prove beneficial in strategies to facilitate plasticity and regeneration following nervous system injury. More generally, proteoglycan-binding is a common property of many cell surface signalling systems involved in normal biology and disease. Results presented herein point to a mechanism by which differences in the structure of GAG chains can serve as a stop/go molecular switch for cell motility and may provide a general paradigm in the biology of cell surface signalling.

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36. Coordinates and structure factors are deposited in the Protein Data Bank (seeFigure 37).

Materials and Methods

Construct design and cloning. [00109] A series of type Ila RPTP constructs were cloned into the pHLsec vector (SI), introducing an N-terminal secretion signal sequence and a C-terminal hexahistadine tag. Human RPTPa short isoform (NCBI Ref. Seq. NM_130853.2): Igl-2 (amino acids 30-231), Igl-3 (30-321), Igl-FN3 (30-602), sEcto (30-839). Human RPTP LAR (NCBI Ref. Seq. NM_002840.3): Igl-2 (30-231), Igl-FN3 (30-602). Human RPTP5 (NCBI Ref. Seq.

BC106713.1): Igl-2 (21-220), Igl-FN3 (21-594). Drosophila RPTP LAR (NCBI Ref. Seq. NM_078880.3): Igl-2 (33-232), Igl-FN3 (33-606). Chick RPTPa (NCBI Ref. Seq.

NM_205407.1) Igl-2 29-226. A human RPTPa Igl-3 R227Q+R228N mutant construct was designed to prevent proteolytic cleavage during Igl-3 crystallisation trials. This construct was generated by two-step overlapping PCRs. The Glypican2-AP construct was generated by subcloning the coding sequence for amino acids 1-555 of mouse Glypican-2 (NCBI Ref. Seq. BC083180) into the APTag5 vector. Mouse RPTPa sEcto-Fc and Neurocan-AP fusion proteins were generated as described previously (S2).

Protein purification and crystallisation.

[00110] All Igl-2 constructs were expressed in HEK-293T cells following transient transfection using polyethylenimine (SI). Human RPTPa Igl-3 R227Q+R228N was expressed in HEK-293T cells, in the presence of kifunensine (Toronto Research Chemicals), a specific inhibitor of a-mannosidase (S3, S4). Igl-FN3 and sEcto constructs were expressed in either HEK-293T cells in the presence of kifunensine or in GnTT HEK293S cells (S5). All proteins were purified from filtered cell culture media by immobilised nickel affinity chromatography (Chelating Sepharose Fast Flow, GE Healthcare) followed by heparin affinity chromatography (HiTrap Heparin HP column, GE Healthcare) and finally gel filtration (Superdex resin, GE Healthcare) in 10 mM HEPES, 150 mM NaCl, pH 7.5. In addition, the human RPTPa Igl-3 R227Q+R228N protein, which contains two N-linked glycosylation sites, was incubated for 3 hours at 37 °C with endoglycosidase Fl (S4, S6) to cleave the N-linked Man₉GlcNAc₂ oligosaccharides to a single GlcNAc residue prior to the heparin affinity chromatography step of the purification. Expression of selenomethionine labelled protein was carried out as described previously (SI) and the protein was

subsequently purified as described for native proteins.

[00111] Crystallisation trials, using 100 nl protein solution plus lOOnl reservoir solution in sitting drop vapour diffusion format were set up in 96-well Greiner plates using a Cartesian Technologies robot (S7). Crystallisation plates were maintained at 20.5 °C in a TAP Homebase storage vault and imaged via a Veeco visualisation system (S8). Crystallisation conditions for all proteins are provided in Figure 35.

Data collection and processing.

[00112] All crystals obtained were cryo-protected as stated (Figure 35) and then flash frozen at 100 K. X-ray diffraction data was collected at the Diamond Light Source,

Oxfordshire, UK or the European Synchotron Radiation Facility, France as indicated. The diffraction images were indexed, integrated, scaled and merged using either the HKL2000 (S9) or the xia2 (S10) data processing suites. The chick RPTPa Igl-2 structure was determined by SAD analysis, using images collected from a selenomethionine labelled protein crystal at the selenium peak wavelength (λ = 0.9783 A). Using SHELXD (Sll) via the autoSHARP interface (S12), the positions of two selenium atoms were determined, before subsequent phase calculation, improvement and preliminary model building was performed.

These preliminary models were used together with a high resolution (1.65 A) native dataset in iterative rounds of automatic model building using RESOLVE (S13), ARP/wARP (S14) and manual building using Coot (S15). The data obtained for all subsequent type Ila RPTP proteins were phased by molecular replacement using the chicken RPTPa Igl-2 solution as a search model in Phaser (S16). The resulting electron density maps were of high quality and enabled manual model adjustment in Coot (SI 5) and refinement in Refmac (SI T), Phenix (S18) and Buster (S19). For structural validation PROCHECK (S20) and MolProbity (S21) were used to assess the stereochemical properties of the models and refinement statistics are given in Table S2. The superimposition of atomic models to compare the domain architecture between different structures, was performed using SHP (S22), based on Ca positions.

Crystallographic figures were created using PyMOL (S23) and APBS was used to calculate the electrostatic potential of solvent accessible surfaces (S24).

Multi-angle light scattering (MALS).

[00113] MALS experiments were carried out on a Wyatt MALS/AFFFF System (Wyatt Technologies). All proteins were purified as described above, and samples were incubated alone or with an oligosaccharide ligand for an hour at room temperature prior to use in MALS analysis. For size defined heparin fragments (Iduron dp4-dp30; product codes HO04- HO30) a five-fold molar excess of oligosaccharide to protein was used, except for the series of experiments presented in Figure 13, where a range of RPTPa constructs were tested with a separate batch of dplO at a two-fold molar excess (Figure 37, highlighted in blue). Equivalent amounts (equal mg/ml concentrations) of HS (Iduron, GAG-HS01) and CS (Sigma, C4384) were used for MALS experiments as had been for heparin dp 10 (in giving a five-fold molar excess). "x5" indicates that a five-fold greater quantity of HS or CS was used. All Igl-FN3 proteins were injected at approximately 10 μΜ. Size exclusion chromatography was performed in 10 mM Tris, 50 mM NaCl, pH 7.5 on a Superdex75 or Superdex200 HR10/30 column (GE Healthcare), attached to an Agilent chromatography system. An Optilab rEX Refractive Index detector and a Dawn Helios II Multi- Angle Light Scattering (MALS) detector recorded the refractive index and light scattering of the samples upon elution from the size exclusion column. The Wyatt software ASTRA was used to analyse all the data collected.

Native Mass Spectrometry.

[00114] 10 μΜ human RPTPa Igl-2 (desalted previously into 100 mM ammonium acetate pH 7.5) and 50 μΜ dplO (ammonium salt) were incubated in a final volume of 500 μΐ for an hour. Gel filtration in 100 mM ammonium acetate pH 7.5 was carried out with this complex sample and the Igl-2 protein alone, and fractions taken from the peaks on the UV traces and diluted to a concentration of 8 μΜ were used for analysis. Electrospray ionisation-mass spectrometry (ESI-MS) was carried out on a Waters Quadrupole Time-of-Flight (Q-Tof) Micro instrument with direct infusion of the protein samples. For native analysis, the protein- heparin complex spectrum was obtained using a cone voltage of 200 V.

Analytical Ultracentrifugation.

[00115] Sedimentation equilibrium and velocity experiments were carried out at 20 °C in an Optima XL-I analytical ultracentrifuge (Beckman Instruments) utilising a scanning absorbance of 280 nm and interference optics. Samples of human RPTPa Igl-2 alone and in complex to heparin dplO, were taken directly from gel filtration in 20 mM Tris, 50 mM NaCl pH 7.5. Sedimentation velocity experiments were performed and analysed using the time derivative g(s*) method (25). Samples were equilibrated at 20 °C in the rotor, before the velocity was sequentially increased through speeds of 12, 18, 25, 35 and 50 krpm, 50 scans being made at each speed. ProFit (QuantumSoft) was used to fit Gaussian curves to the g(s*) plots obtained, and to describe the distribution of individual species.

Solid phase binding assays.

[00116] Analysis of binding between RPTPa sEcto-Fc and Glypican-2 or Neurocan alkaline phosphate (AP) fusion proteins was performed as described previously (S2, S26). All fusion proteins were produced in transiently transfected 293T cells. Briefly, the RPTPa Fc- fusion protein was immobilised on 96-well Reactibind Protein A-coated plates (Pierce) and incubated with soluble proteoglycan- AP proteins which had been normalised for equal input AP activity. AP activity was determined by measuring substrate turnover on a microplate reader as described (S27, S28). For experiments involving treatment with chondroitinase ABC (Sigma) or heparitinase III (HPNIII, Sigma), chondoitinase-treated, heparitinase-treated or mock-treated proteoglycan- APs were incubated at 37 °C for 2 hours prior to addition to the RPTPa-Fc coated plates. In Figure 23, the binding between RPTPa-Fc and heparin-derived size-fractionated oligosaccharides with different lengths (HS6, HS8, HS10, HS17, HS23, HS30 and HS67, corresponding to hexasaccharide, octasaccharide, decasaccharide, or approximately 17, 23, 30 and 67 saccharide units; molecular weights 1,800 Da, 3,000 Da, 5,000 Da, 7,000 Da, 9,000 Da, and 20,000 Da; Neoparin) was analyzed with RPTPa-Fc immobilised on 96-well Reactibind Protein A-coated plates (Pierce) and incubated with soluble biotinalated HS. The bound HS was quantified by AP enzyme activity following incubation with streptavidin-AP (Promega). The effect of HS oligosaccharides on Neurocan- AP binding to RPTPa-Fc was tested by adding HS oligosaccharides of various lengths as described above.

DRG neurite outgrowth assay and immunofluorescence.

[00117] DRGs of P8-12 RPTPo^+/+ or RPTPa^^' mice were cut off from all roots. Neurons were dissociated and subjected to neurite outgrowth assays and analysis as described previously (S2). For experiments in Figure 1, recombinant mouse Neurocan (5800-NC, R&D Systems) was used at 5 μg/ml and recombinant mouse Glypican-2 (2355-GP, R&D Systems) at 30 μg/ml. In Figure 5, 30 g/ml of Glypican-2 was pre-incubated with 1 unit/ml of Heparitinase III (HPNIII, H8891, Sigma) at 37 °C for 4 hrs where indicated, prior to use in outgrowth assays. For experiments in Figure 19, recombinant mouse glypican-2 was used at 5 μg/ml, and Chondroitin Sulfate Proteoglycan mixture (CSPG, CO 17, Millipore) was at 125 μg/ml. For experiments in Figure 24 and 25, Chondroitin Sulfate Proteoglycan mixture (CSPG, CO 17, Millipore) was at 60 aglm\, with or without the addition of HS at indicated length and concentration (1 μΜ for all HS in Figure 21). Proteoglycans and heparin oligosaccharides were added to neuronal cultures 30 min after seeding and were replenished 24 hrs later. At 48 hrs after seeding, cells were fixed and immunostained with anti-GAP43 antibody (NB300-143, Novus). The whole of each well was scanned with a fluorescence microscope and the images were then analyzed for total neurite outgrowth using the

Metamorph program. [00118] For immunolocalization, dissociated DRG neurons were cultured without treatment then fixed and permeabilized, to allow co-staining with the cytoplasmic marker GAP43, at about 48 hrs after seeding. Where indicated, the fixed samples were then treated at 37 °C for 2 hrs with either 1 unit/ml of Chondroitinase ABC (C3667, Sigma) or a mixture of Heparinase I, II and III (H2519, H6512, H8891, Sigma), each at 1 unit/ml. Subsequently, samples were subjected to immuno staining using anti-chondroitin sulfate antibody (C8035, Sigma), anti-heparin/heparan sulfate antibody (OBT1698, AbD Serotec), anti-RPTPo antibody (AF3430, R&D Systems) and anti-GAP43 antibody (NB300-143, Novus).

Statistics

[00119] Error bars show SEMs; P values were calculated by Student's t-test. References for Materials and Methods, Example 1, and Figures 5-19, and Tables 1-3

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57. T. S. Walter et al., Acta Crystallogr. D Biol. Crystallogr. 61, 651 (2005).

58. C. J. Mayo et al., Structure 13, 175 (2005).

59. Z. Otwinowski, Minor, Wladek, Methods Enzymol. , 307 (1997).

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527. J. G. Flanagan, H.-J. Cheng, Methods Enzymol. 327, 198 (2000).

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[00120] Additional information and sequences regarding ΡΤΡσ and its functional domains (e.g., first immunoglobulin-like domain) are available in Aricescu et al., 22 Mol. Cell Biol. 1881 (2002), as well as the following GENBANK Accession Numbers: NM 130855, NM 130854, NM 130853, NM 002850 for human; and NM 011218 for mouse. For example, a purified ΡΤΡσ fragment that includes a first immunoglobulin-like domain comprises residues 47-109 or 33-123 of the amino acid sequence of NM 002850.

[00121]

Example 2 - Defined-Length Heparin Oligosaccharides Compete with CSPG and Promote Neurite Outgrowth

[00122] The observed dichotomy in CSPG/HSPG function, mediated through a common receptor, ΡΤΡσ, is even more intriguing given that mutagenesis studies point towards a common binding site for the two proteoglycan classes [1, 2] . The affinities for the interaction of ΡΤΡσ sEcto with Neurocan and Glypican-2, as representative CSPGs and HSPGs, were measured in solid phase binding assays (data not shown). The affinities were in the same range as one another (10-20 nM K_d), and also similar to those determined in previous studies of CSPGs or HSPGs binding to type Ila PTPs [1, 4], although weaker than measured previously for heparin-BSA (0.3 nM) [2] .

[00123] The ability of defined length heparin oligosaccharides to compete with CSPGs and promote neurite outgrowth was tested. If heparins compete with CSPGs, they would have to bind to ΡΤΡσ with comparable affinity. In initial binding experiments, heparin oligosaccharides were seen to bind to ΡΤΡσ with affinities (K_D) of approximately 10 nM (data not shown). This is similar to the affinity of HSPGs and CSPGs binding to ΡΤΡσ, indicating that oligosaccharides should be capable of competing effectively with endogenous proteoglycans. In further experiments, the ability of heparin oligosaccharides to act as competitive inhibitors for the binding of CSPG to ΡΤΡσ was directly tested. Heparin oligosaccharides were seen to inhibit binding of the CSPG neurocan to ΡΤΡσ (Figure 20). For heparin 30-mer and 67-mer, the IC50 for inhibition of neurocan-ΡΤΡσ binding in a solid phase assay was approximately 20 nM, very consistent with their affinity of binding to ΡΤΡσ. When a heparin 30-mer was tested in DRG neuron culture, it was observed to promote neurite outgrowth (p=0.001). Furthermore, it completely counteracted CSPG inhibition of outgrowth (p<0.001) (Figure 21). Interestingly, a heparin 8-mer did not promote outgrowth or counteract CSPG inhibition (data not shown). As described in the previous section, heparin 8-mers were able to promote dimerization of the ΡΤΡσ ectodomain. It may be that these in vitro assays are not sensitive enough to detect neurite outgrowth induction by heparin 8-mers, or alternatively ΡΤΡσ signaling that promotes neurite outgrowth is not triggered by receptor dimerization, and instead may require higher-order clustering of the receptor. Given that heparin is in wide therapeutic use for other purposes already, defined length heparin oligosaccharides provide useful therapeutics to promote neural regeneration. These results indicate that heparin oligosaccharides can be used to promote of recovery from neuronal (e.g., CNS) injury in vivo.

References for Example 2

1. Shen, Y., Tenney, A. P., Busch, S.A., Horn, K.P., Cuascut, F.X., Liu, K., He, Z., Silver, J., and Flanagan, J.G. PTPsigma is a receptor for Chondroitin Sulfate Proteoglycan, an inhibitor of neural regeneration. Science, 2009. 326: p. 592-6.

2. Aricescu, A.R., McKinnell, I.W., Halfter, W., and Stoker, A.W. Heparan sulfate proteoglycans are ligands for receptor protein tyrosine phosphatase sigma. Mol Cell Biol, 2002. 22(6): p. 1881-92.

3. Ledig, M.M., Haj, F., Bixby, J.L., Stoker, A.W., and Mueller, B.K. The receptor tyrosine phosphatase CRYP alpha promotes intraretinal axon growth. Journal of Cell Biology, 1999. 147(2): p. 375-388. 4. Johnson, K.G., Tenney, A.P., Ghose, A., Duckworth, A.M., Higashi, M.E., Parfitt, K.,

Marcu, O., Heslip, T.R., Marsh, J.L., Schwarz, T.L., Flanagan, J.G., and Van Vactor, D. The HSPGs Syndecan and Dailylike bind the receptor phosphatase LAR and exert distinct effects on synaptic development. Neuron, 2006. 49(4): p. 517-31.

Example 3- Defined-length heparin oligosaccharides compete with CSPG and promote axon extension

[00124] The finding that HSPG can promote axon extension through ΡΤΡσ in a manner competitive with CSPG raised a question: is the core protein of the HSPG necessary for a functional effect on axons, or might it be possible to achieve promotion of axon growth using sulfated carbohydrate chains alone? To investigate this, binding experiments were initially performed, reasoning that if heparin oligosaccharides are to reverse the functional effects of CSPG, they would need to bind to ΡΤΡσ with high affinity. The results of these experiments indeed showed that heparin oligosaccharides bound to ΡΤΡσ with high affinity, and that they inhibited the binding of CSPG to ΡΤΡσ (Figure 23). Moreover, the affinities of oligosaccharides for ΡΤΡσ were up to 5-10 fold tighter than observed for HSPG or CSPG (Figure 23 A). This high affinity is very promising in regard to therapeutic applications, since it indicates that oligosaccharides should be capable of competing effectively with endogenous proteoglycans. The ability of oligosaccharides to compete with CSPG was dependent on length, with chains greater than 10 saccharide units showing strong competition, with inhibition constants (Κ;) in the low nanomolar range, whereas shorter oligosaccharides competed with CSPG more weakly (Figure 23B).

[00125] The functional effect of heparin oligosaccharides on axon extension of cultured dorsal root ganglion (DRG) neurons were then tested. The results showed that heparin oligosaccharide could completely overcome the inhibition of outgrowth caused by CSPG, in a dose-dependent manner (Figure 24). This effect on axon outgrowth was found to be strongly dependent on chain length.

Oligosaccharide chains greater than 10 saccharide units in length were found to promote axon extension (Figure 25). This length dependence is very consistent with the ability of these same oligosaccharide chains to compete at high affinity with CSPG for ΡΤΡσ binding (Figure 23). The strongest growth promoting effects were seen for HS23 and HS30, while a promoting effect was also seen with HS67 although less strongly than HS23 in this assay (p<0.05 for HS23 versus HS67). In contrast, heparin chains less than or equal to 10 saccharide units in length were not found to reverse the inhibitory effects of CSPG, and instead caused further inhibition of axon extension (Figure 25). It is interesting that heparin chains of 8 and 10 saccharide units did not promote axon growth, considering that chains of this length were able to cause dimerization of the ΡΤΡσ ectodomain (Figure 3). These results imply that dimerization of ΡΤΡσ may not be sufficient to promote axon growth, and that higher- order oligomerization or large-scale clustering of the receptor may be required to transduce a growth- promoting signal. Given that heparin is in wide therapeutic use for other purposes already, defined length heparin oligosaccharides provide useful therapeutics to promote neural regeneration. These results indicate that heparin oligosaccharides can be used to promote of recovery from neuronal (e.g., CNS) injury in vivo.

Claims

What is claimed is:

2. The method of claim 1, wherein the agent induces clustering of RPTPa.

3. The method of claim 1, wherein the agent inhibits binding of chondroitin sulfate proteoglycan (CSPG) to RPTPa.

4. The method of any one of claims 1-3, wherein the agent is selected from the group consisting of heparan sulfate proteoglycan, heparan sulfate, heparin oligosaccharide, and heparan sulfate oligosaccharide.

5. The method of claim 4, wherein the heparin oligosaccharide or the heparan sulfate oligosaccharide contains 8 or more saccharide units and less than 67 saccharide units.

6. The method of any one of claims 1-5, wherein the heparin oligosaccharide or the heparan sulfate oligosaccharide contains 10 or more saccharide units and less than 67 saccharide units.

7. The method of claim 4, wherein the heparan sulfate proteoglycan is glypican 2 or a derivative thereof.

8. The method of any one of claims 1-7, said agent binds to the first immunoglobulin- like domain of RPTPa.

9. The method of any one of claims 1-7 wherein the agent is in solution.

10. The method of any one of claims 1-8, wherein the agent is contained in a matrix.

11. The method of any one of claims 1-10, wherein the contacting occurs in vitro.

12. The method of any one of claims 1-10, wherein the contacting occurs in vivo.

13. The method of claim 12, wherein said neuron is located at a site of injured or diseased tissue.

14. The method of any one of claims 1-13, further comprising contacting said neuron with a second agent that promotes neuronal outgrowth.

15. The method of claim 14, wherein the second agent reduces inhibition of neuronal outgrowth.

16. The method of any one of claims 1-15, wherein the neuron is a central nervous system neuron.

17. The method of any one of claims 1-15, wherein the neuron is a peripheral nervous system neuron.

18. A method of treating neuronal injury in a subject comprising, administering to the subject an agent that binds RPTPa to thereby induce neuronal outgrowth.

19. The method of claim 18, further comprising selecting a subject in need of treatment for neuronal injury prior to the administering.

20. The method of any one of claims 18 or 19, wherein the agent is administered at a site of neuronal injury, to thereby induce neuronal outgrowth at the site of neuronal injury.

21. The method of any one of claims 18-20 wherein the agent induces clustering of the RPTPa.

22. The method of any one of claims 18 -20, wherein the agent inhibits binding of

chondroitin sulfate proteoglycan (CSPG) to the RPTPa.

23. The method of any one of claims 18-22, wherein the neuronal injury is selected from the group consisting of stroke, spinal cord injury, traumatic brain injury, peripheral nerve injury, skin burn, and eye injury.

24. The method of any one of claims 16-22 wherein the neuronal injury is acute.

25. The method of any one of claims 16-22 wherein the neuronal injury is chronic.

26. The method of any one of claims 16-22, wherein the agent is selected from the group consisting of heparan sulfate proteoglycan, heparan sulfate, heparin oligosaccharide, and heparan sulfate oligosaccharide.

27. The method of claim 26, wherein the heparin oligosaccharide or the heparan sulfate oligosaccharide contains 8 or more saccharide units and less than 67 saccharide units.

28. The method of any one of claims 26 or 27, wherein the the heparin oligosaccharide or the heparan sulfate oligosaccharide contains 10 or more saccharide units and less than 67 saccharide units.

29. The method of claim 26, wherein the heparan sulfate proteoglycan is glypican 2 or a derivative thereof.

30. The method of any one of claims 19-20, further comprising contacting said neuron with a second agent that promotes neuronal outgrowth.

31. The method of any one of claims 18-30 wherein the agent is soluble.

32. The method of any one of claims 18-30 wherein the agent is contained in a matrix.

33. The method of any one of claims 18-32 wherein the agent directly binds to the

RPTPa.

34. The method of any one of claims 18-33, wherein the agent binds to the first

immunoglobulin-like domain of RPTPa.

35. The method of any one of claims 18-34, wherein administering is systemic or localized.

36. The method of claim 35, wherein administration is by method selected from the group consisting of oral, intramuscular injection, subcutaneous or intradermal injection, intrathecal, extradural, intramedullary, injection directly into neural tissue, intravenous injection, buccal administration, transdermal, rectal, colonic, vaginal, intranasal, and inhalation.

37. The method of claim 35, wherein localized administration is by implantation of a matrix that contains the agent.

38. The method of claim 36, wherein implantation is by injection and the matrix is a gel that solidifies in the body of the subject.

39. A method of promoting neural outgrowth in the nervous system of a subject,

comprising administering to the subject an agent that binds RPTPa, to contact a neuron and thereby induce neural outgrowth of the neuron.

40. The method of claim 39, further comprising selecting a subject in need of promotion of neural outgrowth prior to the administering.

41. The method of any one of claims 39-40, wherein the agent induces clustering of the RPTPa.

42. The method of claim 39, wherein the agent inhibits binding of chondroitin sulfate proteoglycan (CSPG) to the RPTPa.

43. The method of claim 39, wherein the agent is heparan sulfate proteoglycan, heparan sulfate, heparin oligosaccharide or heparan sulfate oligosaccharide .

44. The method of claim 43, wherein the heparin oligosaccharide or the heparan sulfate oligosaccharide contains 8 or more saccharide units and less than 67 saccharide units.

45. The method of claim 43, wherein the heparin oligosaccharide or the heparan sulfate oligosaccharide contains 10 or more saccharide units and less than 67 saccharide units.

46. The method of claim 43, wherein the heparan sulfate proteoglycan is glypican 2 or a derivative thereof.

47. The method of any one of claims 39-46 wherein the agent is in solution.

48. The method of any one of claims 39-46 wherein the agent is contained in a matrix.

49. The method of any one of claims 39-48, wherein the neuron is located at or adjacent to a site of diseased or injured tissue.

50. The method of claim 49, wherein the injured tissue results from an injury selected from the group consisting of stroke, spinal cord injury, traumatic brain injury, peripheral nerve injury, skin burn, and eye injury affecting optic nerve fibers.

51. The method of claim 49, wherein the injured tissue results from an acute injury.

52. The method of claim 49, wherein the diseased tissue is a site of neuronal

degeneration.

53. The method of claim 49, wherein the diseased tissue results from a neurodegenerative disease.

54. The method of any one of claims 39-53, wherein administering is systemic or

localized.

55. The method of claim 54, wherein administration is by method selected from the group consisting oral, intramuscular injection, subcutaneous or intradermal injection, intrathecal, extradural, intramedullary, injection directly into neural tissue, intravenous injection, buccal administration, transdermal, rectal, colonic, vaginal, intranasal, and inhalation.

The method of claim 54, wherein localized administration is by implantation of a matrix that contains the agent.

The method of claim 56, wherein implantation is by injection and the matrix is a gel that solidifies in the body of the subject.