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  • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
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  • C07K2317/00—Immunoglobulins specific features
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  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
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  • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
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  • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
  • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding

Definitions

• the present invention relates generally to neural development and neurological disorders.
• the invention specifically concerns identification of novel modulators of the myelin-associated inhibitory system and various uses of the modulators so identified.
• axons of the adult mammalian CNS neurons have very limited capacity to regenerate following injury, whereas axons in the peripheral nervous system (PNS) regenerate rapidly.
• PNS peripheral nervous system
• CNS neuron's limited capacity to regenerate is in part to an intrinsic property of CNS axons, but also due to an impermissible environment.
• the CNS myelin while it is not the only source of inhibitory cues for neurite growth, contains numerous inhibitory molecules that actively block axonal growth and therefore constitutes a significant barrier to regeneration.
• Nogo also known as NogoA
• MAG myelin-associated glycoprotein
• OMgp leucine rich repeat (LRR) protein with a glycosylphosphatidylinositol (GPI) anchor.
• NogoA has been described as a 66-amino acid extracellular polypeptide that is found in all three isoforms of Nogo.
• NgR Nogo Receptor- 1
• NgRl Nogo Receptor- 1
• NgR2 and NgR3 Two NgRl homologs (NgR2 and NgR3) have also been identified. US 2005/0048520 Al (Strittmatter et al.), published March 3, 2005.
• NgR is a GPI- anchored cell surface protein, it is unlikely to be a direct signal transductor (Zheng et al., i Proc. Natl. Acad. Sci. USA 102: 1205-1210 (2005)).
• Others have suggested that the neurotrophin receptor p75 NTR acts as a co-receptor for NgR and provides the signal- transducing moiety in a receptor complex (Wang et al., Nature 420:74-78 (2002); Wong et al., Nat. Neurosci. 5: 1302-1308 (2002)).
• MHC class I The major histocompatibility complex (MHC) class I was originally identified as a region encoding a family of molecules that are important for the immune system. Recent evidences have indicated that MHC class I molecules have additional functions in the development and adult CNS. Boulanger and Shatz, Nature Rev Neurosci. 5:521-531 (2004); US 2003/0170690 (Shatz and Syken), published September 11 , 2003. Many of the MHC class I members and their binding partners are found to be expressed in CNS neurons.
• MHC class I molecules might be involved in activity-dependent synaptic plasticity, a process during which the strength of existing synaptic connections increases or decreases in response to neuronal activity, followed by long term structural alterations to circuits.
• MHC class I encoding region has also been genetically linked to a wide variety of disorders with neurological symptoms, and abnormal functions of MHC class I molecules are thought to contribute to the disruption of normal brain development and plasticity.
• PirB a murine polypeptide that was first described by Kubagawa et al, Proc. Nat. Acad. Sci.
• Mouse PirB has several human orthologs, which are members of the leukocyte immunoglobulin-like receptor, subfamily B (LILRB), and are also referred to as "immunoglobulin-like transcripts" (ILTs)
• LILRB leukocyte immunoglobulin-like receptor
• ILTs immunoglobulin-like transcripts
• the human orthologs show significant homology to the murine sequence, from highest to lowest in the following order: LILRB3/ILT5,
• LILRB 1/ILT2, LILRB5/ILT3, LILRB2/ILT4, and, just as PirB, are all inhibitory receptors.
• LILRB3/ILT5 (NP 006855) and LILRB 1/ILT2 (NPJ)06660) were first described by Samaridis and Colonna, Eur. J. Immunol. 27(3):660-665 (1997) LILRB5/ILT3 (NP_006831) has been identified by Borges et al., J. Immunol. 159(1 1):5192-5196 (1997).
• LILRB2/ILT4 also known as MIRl 0
• PirB and its human orthologs show a great degree of structural variability.
• the sequences of various alternatively spliced forms are available from EMBL/GenBank, including, for example, the following accession numbers for human ILT4 cDNA: ILT4-cl 1 AF009634; ILT4-cl 17 AFl 1566; ILT4-cl26 AFl 1565.
• the PirB/LILRB polypeptides are MHC Class I (MHCI) inhibitory receptors, and are known for their role in regulating immune cell activation (Kubagawa et al., supra; Hayami et al., JL Biol. Chem.
• the present invention is based, at least in part, on the finding that interfering with PirB activity using function-blocking anti-PirB antibodies helps rescuing neurite outgrowth inhibition by Nogo66 and myelin, and that blocking PirB and NgR activities concurrently leads to a near-complete release from myelin inhibition.
• the invention concerns an isolated anti-PirB/LILRB antibody that binds essentially to the same epitope on human PirB (LILRB) as an antibody selected from the group consisting of YW259.2, YW259.9 and YW259.12.
• the invention concerns an isolated anti-PirB/LILRB antibody that competes for binding to human PirB (LILRB) with an antibody selected from the group consisting of YW259.2, YW259.9 and YW259.12.
• the invention concerns an isolated anti-PirB/LILRB antibody that comprises one, two, or three, hypervariable region sequences from a heavy chain selected from the group consisting of: YW259.2 heavy chain (SEQ ID NO: 4 or 1 1),
• YW259.9 heavy chain (SEQ ID NO: 5 or 12), and YW259.12 heavy chain (SEQ ID NO: 6 or 13).
• the antibody comprises all hypervariable region sequences of the YW259.2 antibody heavy chain (SEQ ID NO: 4 or 11). In another embodiment, the antibody comprises all hypervariable region sequences of the YW259.9 antibody heavy chain (SEQ ID NO: 5 or 12).
• the antibody comprises all hypervariable region sequences of the YW259.12 antibody heavy chain (SEQ ID NO: 6 or 13). In a further embodiment, the antibody comprises a light chain.
• the antibody comprises one, two or three hypervariable region sequences of a light chain from the polypeptide sequence of SEQ ID NO: 7.
• the antibody comprises all hypervariable region sequences of a light chain comprising the polypeptide sequence of SEQ ID NO: 7 or 15.
• the antibody comprises both a heavy and a light chain, where the heavy chain comprises one, two, or three, hypervariable region sequences from a heavy chain selected from the group consisting of: YW259.2 heavy chain (SEQ ID NO: 4 or 11), YW259.9 heavy chain (SEQ ID NO: 5 or 12), and YW259.12 heavy chain (SEQ ID NO: 6 or 13), and/or the light chain comprises one, two or three hypervariable region sequences of a light chain from the polypeptide sequence of SEQ ID NO: 7 or 15.
• the antibody is selected from the group consisting of antibodies YW259.2, YW259.9, and YW259.12.
• the invention concerns an isolated anti-PirB antibody wherein the full-length IgG form of the antibody specifically binds human PirB with a binding affinity of 5nM or better, or 1 nM or better.
• the antibody promotes axonal regeneration, such as regeneration of CNS neurons.
• the antibody at least partially, rescues neurite outgrowth inhibition by Nogo66 and myelin.
• the antibody preferably is a monoclonal antibody, which may, for example, be a chimeric antibody, a humanized antibody, an affinity matured antibody, a human antibody, or a bispecific antibody, an antibody fragment or an immunoconjugate.
• the invention concerns a polynucleotide encoding an anti- PirB/LILRB antibody herein.
• the invention concerns vectors and host cells comprising a polynucleotide encoding an antibody (including coding sequences of one or more antibody chains) herein.
• the host cells include prokaryotic, eukaryotic and mammalian hosts.
• the invention concerns a method for making an anti-PirB/LILRB antibody, comprising (a) expressing a vector comprising nucleic acid encoding the antibody in a suitable host cell, and (b) recovering the antibody.
• the invention concerns a composition
• a composition comprising an anti- PirB/LILRB antibody herein, and a pharmaceutically acceptable excipient.
• the composition comprises a second medicament, wherein the anti-PirB/LILRB antibody is a first medicament.
• the second medicament may, for example, be a NgR inhibitor, such as an anti-NgR antibody.
• the invention concerns a kit comprising an anti-PirB/LILRB antibody herein.
• the invention concerns a method for promoting axon regeneration comprising administering to a subject in need an effective amount of an anti-PirB/LILRB antibody herein.
• the subject is a human patient.
• the treatment method herein enhances survival or neurons and/or induces the outgrowth of neurons
• the invention concerns a method of treating a neurodegenerative disease, comprising administering to a subject in need an effective amount of an anti-PirB/LILRB antibody herein.
• the neurodegenerative disease may, for example, be characterized by physical damage to the central nervous system, and includes, without limitation, brain damage associated with stroke.
• the neurodegenerative disease is selected from the group consisting of trigeminal neuralgia, glossopharyngeal neuralgia, Bell's Palsy, myasthenia gravis, muscular dystrophy, amyotrophic lateral sclerosis (ALS), multiple sclerosis (MS), progressive muscular atrophy, progressive bulbar inherited muscular atrophy, peripheral nerve damage caused by physical injury (e.g., burns, wounds) or disease states such as diabetes, kidney dysfunction or by the toxic effects of chemotherapeutics used to treat cancer and AIDS, herniated, ruptured or prolapsed invertebrate disk syndromes, cervical spondylosis, plexus disorders, thoracic outlet destruction syndromes, peripheral neuropathies such as those caused by lead, dapsone, ticks, prophyria, Gullain-Barre syndrome, Alzheimer's disease, Huntington's Disease, and Parkinson's disease.
• trigeminal neuralgia e.g., glossopharyngeal neuralgia
• the invention further concerns an anti-idiotype antibody that specifically binds an anti-PirB antibody herein.
• LILRB2 sequence (SEQ ID NO: 2).
• FIGS. 2 A and 2B Blocking PirB reverses inhibition of CGN outgrowth on AP- Nogo66 or myelin.
• Dissociated mouse P7 CGN were plated on PDL/laminin (control), AP- Nogo66, or myelin to test inhibition by these substrates.
• A Representative photomicrographs
• B a graph measuring average neurite length ( ⁇ SE) from one representative experiment. Neurons grown on PDL/laminin, AP-Nogo66, or myelin were cultured in the presence or absence of function-blocking antibodies to PirB (aPBl; 50 ⁇ g/ml). aPBl significantly reduced inhibition by either substrate.
• aPBl significantly reduced inhibition by either substrate.
• FIGS 3A-3D Blocking PirB reverses inhibition of CGN outgrowth on AP-Nogo66 or myelin.
• Dissociated mouse P7 CGN were plated on PDL/laminin (control), AP-Nogo66, or myelin to test inhibition by these substrates.
• Representative photomicrographs are shown in Figures 3 A and 3C and a graph measuring average neurite length ( ⁇ SE) from one representative experiment is shown in Figures 3B and 3D.
• Neurons grown on PDL/laminin, AP-Nogo66, or myelin were cultured in the presence or absence of function-blocking antibodies to PirB (aPBl ; 50 ⁇ g/ml). aPBl significantly reduced inhibition by either substrate.
• FIGS. 4A and 4B Both PirB and NgR are required to mediate growth cone collapse by myelin inhibitors. Growth cones of postnatal DRG axons were treated with medium alone (control), myelin (3 ⁇ g/ml), or AP-Nogo66 (100 nM) for 30 minutes to stimulate collapse, and stained with Rhodamine-phalloidin to visualize growth cones.
• A Representative photomicrographs
• B a graph measuring percent growth cone collapse ( ⁇ SEM) from cumulative experiments.
• FIGS 5A-5D Blocking PirB partially disinhibits neurite outgrowth in DRG neurons and on the substrate MAG. Representative photomicrographs are shown in Figures 5A and 5C; graphs showing the average neurite length ( ⁇ SE) from one representative experiment are shown in Figures 5B and 5D.
• Figure 8 DNA sequence of anti-PirB antibody YW259.12 heavy chain (SEQ ID NO:
• Figure 1 Protein sequence of anti-PirB antibody YW259.12 heavy chain (SEQ ID NO: 6).
• Figure 13 Ability of anti-PirB antibody YW259.2(IgG) to inhibit the activity of His- tagged mouse PirB.
• Figure 14 Ability of anti-PirB antibody YW259.9 (IgG) to inhibit the activity of His-tagged mouse PirB.
• Figure 15 Ability of anti-PirB antibody YW259.12 (IgG) to inhibit the activity of His-tagged mouse PirB.
• FIGS 17A-17C Alignment of heavy chain sequences of anti-PirB antibodies YW259.2 (SEQ ID NO: 1 1); YW259.9 (SEQ ID NO: 12) and YW259.12 (SEQ ID NO 13).
• the CDR Hl , CDR H2 and CDR H3 sequences are boxed, along with the CDR H domains according to Kabat, Chothia and the contact CDR H domains.
• Hum III is disclosed as SEQ ID NO: 10.
• Figures 18A-18C Alignment of light chain sequences of anti-PirB antibodies YW259.2 (SEQ ID NO: 15) ; YW259.9 (SEQ ID NO: 15) and YW259.12 (SEQ ID NO: 15), and HUKI (SEQ ID NO: 14).
• the CDR Ll , CDR L2 and CDR L3 sequences are boxed, along with the CDR L domains according to Kabat, Chothia and the contact CDR L domains.
• Hum III is disclosed as SEQ ID NO: 10.
• C1QTNF5 (CTRP5; NP_05646) inhibits neurite outgrowth of dorsal root ganglion neurons, and this inhibition is reduced when PirB is blocked by PirB function- blocking antibody YW259.2.
• paired-immunoglobulin-like receptor B and “PirB” are used herein interchangeably, and refer to a native-sequence, 841 -amino acid mouse inhibitory protein of SEQ ID NO: 1 ( Figure 1) (NP 035225), and its native-sequence homologues in rat and other non-human mammals, including all naturally occurring variants, such as alternatively spliced and allelic variants and isoforms, as well as soluble forms thereof.
• Figure 1 NP 035225
• NP 035225 native-sequence homologues in rat and other non-human mammals, including all naturally occurring variants, such as alternatively spliced and allelic variants and isoforms, as well as soluble forms thereof.
• LILRB leukocyte immunoglobulin-like receptor, subfamily B
• all naturally occurring variants such as alternatively spliced and allelic variants and isoforms, as well as soluble forms thereof.
• LILRB3/ILT5 LILRB 1/ILT2, LILRB5/ILT3, and ILIRB2/ILT4
• a reference to any individual member also includes reference to all naturally occurring variants, such as alternatively spliced and allelic variants and isoforms, as well as soluble forms thereof.
• LILRB2 LIR2
• MIRlO 598-amino acid polypeptide of SEQ ID NO:2 ( Figure 1) (NP 005865), and its naturally occurring variants, such as alternatively spliced and allelic variants and isoforms, as well as soluble forms thereof.
• Figure 1 NP 005865
• NP 005865 598-amino acid polypeptide of SEQ ID NO:2
• its naturally occurring variants such as alternatively spliced and allelic variants and isoforms, as well as soluble forms thereof.
• PrB/LILRB is used herein to jointly refer to the corresponding mouse and human proteins and native sequence homologues in other non-human mammals, including all naturally occurring variants, such as alternatively spliced and allelic variants and isoforms, as well as soluble forms thereof.
• myelin-associated protein is used in the broadest sense and includes all proteins present in CNS myelin that inhibit neuronal regeneration, including Nogo, MAG and OMgp.
• Isolated when used to describe the various proteins disclosed herein, means protein that has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials that would typically interfere with diagnostic or therapeutic uses for the protein, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous solutes.
• the protein will be purified (1) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (2) to homogeneity by SDS-PAGE under non-reducing or reducing conditions using Coomassie blue or, preferably, silver stain, or (3) to homogeneity by mass spectroscopic or peptide mapping techniques.
• Isolated protein includes protein in situ within recombinant cells, since at least one component of the natural environment of the protein in question will not be present. Ordinarily, however, isolated protein will be prepared by at least one purification step.
• nucleic acid molecule is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the nucleic acid in question.
• An isolated nucleic acid molecule is other than in the form or setting in which it is found in nature. Isolated nucleic acid molecules therefore are distinguished from the nucleic acid molecules as they exist in natural cells.
• an isolated nucleic acid molecule includes nucleic acid molecules contained in cells that ordinarily express such nucleic acid where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.
• the term "PirB/LILRB antagonist” is used to refer to an agent capable of blocking, neutralizing, inhibiting, abrogating, reducing or interfering with PirB/LILRB activities.
• the PirB/LILRB antagonist interferes with myelin associated inhibitory activities, thereby enhancing neurite outgrowth, and/or promoting neuronal growth, repair and/or regeneration.
• the PirB/LILRB antagonist inhibits the binding of PirB/LILRB to Nogo66 and/or MAG and/or OMgp by binding to PirB/LILRB.
• PirB/LILRB antagonists include, for example, antibodies to PirB/LILRB and antigen binding fragments thereof, truncated or soluble fragments of PirB/LILRB, Nogo 66, MAG or OMgp that are capable of sequestering the binding between PirB/LILRB and Nogo 66, or between PirB/LILRB and MAG, or between PirB/LILRB and OMgp and small molecule inhibitors of the PirB/LILRB related inhibitory pathway.
• PirB/LILRB antagonists also include short-interfering RNA (siRNA) molecules capable of inhibiting or reducing the expression of PirB/LILRB mRN A.
• siRNA short-interfering RNA
• a preferred PirB/LILRB antagonist is an anti- PirB/LILRB antibody.
• antibody herein is used in the broadest sense and specifically covers intact antibodies, monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g. bispecific antibodies) formed from at least two intact antibodies, and antibody fragments, so long as they exhibit the desired biological activity.
• monoclonal antibody refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to polyclonal antibody preparations which include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen. In addition to their specificity, the monoclonal antibodies are advantageous in that they may be synthesized uncontaminated by other antibodies.
• the modifier "monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method.
• the monoclonal antibodies to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler el al, Nature, 256:495 (1975), or may be made by recombinant DNA methods (see, e.g., U.S. Patent No. 4,816,567).
• the “monoclonal antibodies” may also be isolated from phage antibody libraries using the techniques described in Clackson et al, Nature, 352:624-628 (1991) and Marks et al, J. MoI Biol , 222:581-597 (1991), for example.
• Antibodies specifically include "chimeric" antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (U.S. Patent No. 4,816,567; and Morrison et al, Proc. Natl. Acad. ScL USA, 81 :6851-6855 (1984)).
• Chimeric antibodies of interest herein include primatized antibodies comprising variable domain antigen-binding sequences derived from a non- human primate (e.g. Old World Monkey, Ape etc) and human constant region sequences.
• Antibody fragments comprise a portion of an intact antibody, preferably comprising the antigen-binding or variable region thereof.
• antibody fragments include Fab, Fab', F(ab') 2 , and Fv fragments; diabodies; linear antibodies; single-chain antibody molecules; and multispecific antibodies formed from antibody fragment(s).
• an “intact” antibody is one which comprises an antigen-binding variable region as well as a light chain constant domain (CL) and heavy chain constant domains, CH I , CH2 and CH3.
• the constant domains may be native sequence constant domains (e.g. human native sequence constant domains) or amino acid sequence variant thereof.
• the intact antibody has one or more effector functions.
• Humanized forms of non-human (e.g., rodent) antibodies are chimeric antibodies that contain minimal sequence derived from non-human immunoglobulin.
• humanized antibodies are human immunoglobulins (recipient antibody) in which residues from a hypervariable region of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and capacity.
• donor antibody such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and capacity.
• framework region (FR) residues of the human immunoglobulin are replaced by corresponding non- human residues.
• humanized antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance.
• the humanized antibody will comprise substantially all of at least one, and typically two, variable domains (Fab, Fab', F(ab') 2 , Fabc, Fv), in which all or substantially all of the hypervariable loops correspond to those of a non- human immunoglobulin and all or substantially all of the FRs are those of a human immunoglobulin sequence.
• the humanized antibody optionally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin.
• Fc immunoglobulin constant region
• hypervariable region when used herein refers to the regions of an antibody variable domain which are hypervariable in sequence and/or form structurally defined loops.
• the hypervariable region comprises amino acid residues from a "complementarity determining region" or "CDR" (i.e. residues 24-34, 50-56, and 89-97 in the light chain variable domain and 31 -35, 50-65, and 95-102 in the heavy chain variable domain; Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, MD. (1991)) and/or those residues from a "hypervariable loop" (i.e.
• variable domain residues are numbered according to Kabat et al., supra, as discussed in more detail below.
• “Framework” or "FR" residues are those variable domain residues other than the residues in the hypervariable regions as herein defined.
• a "parent antibody” or "wild-type” antibody is an antibody comprising an amino acid sequence which lacks one or more amino acid sequence alterations compared to an antibody variant as herein disclosed.
• the parent antibody generally has at least one hypervariable region which differs in amino acid sequence from the amino acid sequence of the corresponding hypervariable region of an antibody variant as herein disclosed.
• the parent polypeptide may comprise a native sequence (i.e. a naturally occurring) antibody
• antibody variant refers to an antibody which has an amino acid sequence which differs from the amino acid sequence of a parent antibody.
• the antibody variant comprises a heavy chain variable domain or a light chain variable domain having an amino acid sequence which is not found in nature. Such variants necessarily have less than 100% sequence identity or similarity with the parent antibody.
• the antibody variant will have an amino acid sequence from about 75% to less than 100% amino acid sequence identity or similarity with the amino acid sequence of either the heavy or light chain variable domain of the parent antibody, more preferably from about 80% to less than 100%, more preferably from about 85% to less than 100%, more preferably from about 90% to less than 100%, and most preferably from about 95% to less than 100%.
• the antibody variant is generally one which comprises one or more amino acid alterations in or adjacent to one or more hypervariable regions thereof.
• amino acid alteration refers to a change in the amino acid sequence of a predetermined amino acid sequence. Exemplary alterations include insertions, substitutions and deletions.
• amino acid substitution refers to the replacement of an existing amino acid residue in a predetermined amino acid sequence; with another different amino acid residue.
• a “replacement” amino acid residue refers to an amino acid residue that replaces or substitutes another amino acid residue in an amino acid sequence.
• the replacement residue may be a naturally occurring or non-naturally occurring amino acid residue.
• amino acid insertion refers to the introduction of one or more amino acid residues into a predetermined amino acid sequence.
• the amino acid insertion may comprise a "peptide insertion” in which case a peptide comprising two or more amino acid residues joined by peptide bond(s) is introduced into the predetermined amino acid sequence.
• the inserted peptide may be generated by random mutagenesis such that it has an amino acid sequence which does not exist in nature.
• an amino acid alteration "adjacent a hypervariable region” refers to the introduction or substitution of one or more amino acid residues at the N-terminal and/or C- terminal end of a hypervariable region, such that at least one of the inserted or replacement amino acid residue(s) form a peptide bond with the N-terminal or C-terminal amino acid residue of the hypervariable region in question.
• a "naturally occurring amino acid residue” is one encoded by the genetic code, generally selected from the group consisting of: alanine (Ala); arginine (Arg); asparagine (Asn); aspartic acid (Asp); cysteine (Cys); glutamine (GIn); glutamic acid (GIu); glycine (GIy); histidine (His); isoleucine (He): leucine (Leu); lysine (Lys); methionine (Met); phenylalanine (Phe); proline (Pro); serine (Ser); threonine (Thr); tryptophan (Trp); tyrosine (Tyr); and valine (VaI).
• non-naturally occurring amino acid residue herein is an amino acid residue other than those naturally occurring amino acid residues listed above, which is able to covalently bind adjacent amino acid residues(s) in a polypeptide chain.
• non-naturally occurring amino acid residues include norleucine, ornithine, norvaline, homoserine and other amino acid residue analogues such as those described in Ellman et al. Meth. Enzym. 202:301-336 (1991).
• the procedures of Noren et al. Science 244: 182 (1989) and Ellman et al., supra can be used. Briefly, these procedures involve chemically activating a suppressor tRNA with a non- naturally occurring amino acid residue followed by in vitro transcription and translation of the RNA.
• the candidate sequence is aligned with any immunoglobulin sequence or any consensus sequence in Kabat. Alignment may be done by hand, or by computer using commonly accepted computer programs; an example of such a program is the Align 2 program. Alignment may be facilitated by using some amino acid residues which are common to most Fab sequences.
• the light and heavy chains each typically have two cysteines which have the same residue numbers; in VL domain the two cysteines are typically at residue numbers 23 and 88, and in the VH domain the two cysteine residues are typically numbered 22 and 92.
• Framework residues generally, but not always, have approximately the same number of residues, however the CDRs will vary in size.
• an antibody with a "high-affinity” is an antibody having a Kp, or dissociation constant, in the nanomolar (nM) range or better.
• a KD in the "nanomolar range or better” may be denoted by XnM, where X is a number less than about 10.
• affinity matured antibody is one with one or more alterations in one or more CDRs thereof which result an improvement in the affinity of the antibody for antigen, compared to a parent antibody which does not possess those alteration(s).
• Preferred affinity matured antibodies will have nanomolar or even picomolar affinities for the target antigen.
• Affinity matured antibodies are produced by procedures known in the art. Marks et al. Bio/Technology 10:779-783 (1992) describes affinity maturation by V H and VL domain shuffling. Random mutagenesis of CDR and/or framework residues is described by: Barbas et al. Proc Nat. Acad. Sci, USA 91 :3809-3813 (1994); Schier et al.
• a “functional antigen binding site” of an antibody is one which is capable of binding a target antigen.
• the antigen binding affinity of the antigen binding site is not necessarily as strong as the parent antibody from which the antigen binding site is derived, but the ability to bind antigen must be measurable using any one of a variety of methods known for evaluating antibody binding to an antigen.
• An antibody having a "biological characteristic" of a designated antibody is one which possesses one or more of the biological characteristics of that antibody which distinguish it from other antibodies that bind to the same antigen.
• filamentous phage refers to a viral particle capable of displaying a heterogenous polypeptide on its surface, and includes, without limitation, fl , fd, PfI , and M13.
• the filamentous phage may contain a selectable marker such as tetracycline (e.g., "fd- tet”).
• Various filamentous phage display systems are well known to those of skill in the art (see, e.g., Zacher et al. Gene 9: 127-140 (1980), Smith et al. Science 228: 1315-1317 (1985); and Parmley and Smith Gene 73: 305-318 (1988)).
• panning is used to refer to the multiple rounds of screening process in identification and isolation of phages carrying compounds, such as antibodies, with high affinity and specificity to a target.
• siRNA short-interfering RNA
• siRNAs are an intermediate of RNA interference, the process double-stranded RNA silences homologous genes.
• siRNAs typically are comprised of two single-stranded RNAs of about 15-25 nucleotides in length that form a duplex, which may include single-stranded overhang(s). Processing of the double-stranded RNA by an enzymatic complex, for example by polymerases, results in the cleavage of the double- stranded RNA to produce siRNAs.
• RNA interference RNA interference
• siRNAs RNA interference silencing complexes
• the term "interfering RNA (RNAi)" is used herein to refer to a double-stranded RNA that results in catalytic degradation of specific mRNAs, and thus can be used to inhibit/lower expression of a particular gene.
• polymorphism is used herein to refer to more than one forms of a gene or a portion (e.g., allelic variant) thereof.
• a portion of a gene of which there are at least two different forms is referred to as a "polymorphic region" of the gene.
• a specific genetic sequence at a polymorphic region of a gene is an "allele.”
• a polymorphic region can be a single nucleotide, which differs in different alleles, or can be several nucleotides long.
• disorders in general refers to any condition that would benefit from treatment with an antagonists of PirB/LILRB2, such as an anti-PirB antibody, including any condition that is expected to benefit from axon regeneration therapy, and/or an improvement of synaptic plasticity in the nervous system.
• disorders to be treated herein include, without limitation, diseases and conditions benefiting from the enhancement of neurite outgrowth, promotion of neuronal growth, repair or regeneration, including neurological disorders, such as physically damaged nerves and neurodegenerative diseases.
• disorders specifically include physical damage to the central nervous system (e.g.
• brain damage associated with stroke and neurological disorders relating to neurodegeneration, such as, for example, trigeminal neuralgia, glossopharyngeal neuralgia, Bell's Palsy, myasthenia gravis, muscular dystrophy, amyotrophic lateral sclerosis (ALS), progressive muscular atrophy, progressive bulbar inherited muscular atrophy, multiple sclerosis (MS), herniated, ruptured or prolapsed invertebrate disk syndromes, cervical spondylosis, plexus disorders, thoracic outlet destruction syndromes, peripheral nerve damage caused by physical injury or disease states such as diabetes, peripheral neuropathies such as those caused by lead, dapsone, ticks, prophyria, Gullain-Barre syndrome, Alzheimer's disease, Huntington's Disease, or Parkinson's disease.
• neurodegeneration such as, for example, trigeminal neuralgia, glossopharyngeal neuralgia, Bell's Palsy, myasthenia gravis, muscular dystrophy, am
• treating refers to curative therapy, prophylactic therapy, and preventative therapy.
• Consecutive treatment or administration refers to treatment on at least a daily basis without interruption in treatment by one or more days.
• Intermittent treatment or administration, or treatment or administration in an intermittent fashion refers to treatment that is not consecutive, but rather cyclic in nature.
• preventing neurodegeneration includes (1) the ability to inhibit or prevent neurodegeneration in patients newly diagnosed as having a neurodegenerative disease or at risk of developing a new neurodegenerative disease and (2) the ability to inhibit or prevent further neurodegeneration in patients who are already suffering from, or have symptoms of, a neurodegenerative disease.
• mammal refers to any mammal classified as a mammal, including humans, higher non-human primates, rodents, domestic and farm animals, such as cows, horses, dogs and cats. In a preferred embodiment of the invention, the mammal is a human.
• Administration "in combination with” one or more further therapeutic agents includes simultaneous (concurrent) and consecutive administration in any order.
• an “effective amount” is an amount sufficient to effect beneficial or desired therapeutic (including preventative) results.
• An effective amount can be administered in one or more administrations.
• progeny As used herein, the expressions "cell,” “cell line,” and “cell culture” are used interchangeably and all such designations include progeny. Thus, the words “transformants” and “transformed cells” include the primary subject cell and cultures derived therefrom without regard for the number of transfers. It is also understood that all progeny may not be precisely identical in DNA content, due to deliberate or inadvertent mutations. The term “progeny” refers to any and all offspring of every generation subsequent to an originally transformed cell or cell line. Mutant progeny that have the same function or biological activity as screened for in the originally transformed cell are included. Where distinct designations are intended, it will be clear from the context.
• Percent (%) amino acid sequence identity with respect to the sequences identified herein is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in a reference sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art can determine appropriate parameters for measuring alignment, including assigning algorithms needed to achieve maximal alignment over the full-length sequences being compared. For purposes herein, percent amino acid identity values can be obtained using the sequence comparison computer program, ALIGN-2, which was authored by Genentech, Inc.
• ALIGN-2 program is publicly available through Genentech, Inc., South San Francisco, CA. All sequence comparison parameters are set by the ALIGN-2 program and do not vary. "Stringency" of hybridization reactions is readily determinable by one of ordinary skill in the art, and generally is an empirical calculation dependent upon probe length, washing temperature, and salt concentration. In general, longer probes require higher temperatures for proper annealing, while shorter probes need lower temperatures. Hybridization generally depends on the ability of denatured DNA to re-anneal when complementary strands are present in an environment below their melting temperature.
• High stringency conditions are identified by those that: (1) employ low ionic strength and high temperature for washing; 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 5O 0 C; (2) employ during hybridization a denaturing agent; 50% (v/v) formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/5 OmM sodium phosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodium citrate at 42 0 C; or (3) employ 50% formamide, 5 x SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5 x Denhardt's solution, sonicated salmon sperm DNA (50 ⁇ g/ml), 0.1% SDS, and 10% dextran sulfate at 42 0 C, with washes at 42 0 C
• Modely stringent conditions may be identified as described by Sambrook et al, Molecular Cloning: A Laboratory Manual New York: Cold Spring Harbor Press, 1989, and include overnight incubation at 37 0 C in a solution comprising: 20% formamide, 5 x SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH 7.6), 5 x Denhardt's solution, 10% dextran sulfate, and 20 mg/ml denatured sheared salmon sperm DNA, followed by washing the filters in 1 x SSC at about 37-5O 0 C.
• the skilled artisan will recognize how to adjust the temperature, ionic strength, etc. as necessary to accommodate factors such as probe length and the like.
• control sequences refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism.
• the control sequences that are suitable for prokaryotes include a promoter, optionally an operator sequence, and a ribosome binding site.
• Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
• Nucleic acid is "operably linked" when it is placed into a functional relationship with another nucleic acid sequence.
• DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide;
• a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or
• a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation.
• "operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
• a "small molecule” is defined herein to have a molecular weight below about 1000 Daltons, preferably below about 500 Daltons.
• anti-PirB antibodies of the present invention can be produced by methods known in the art, including techniques of recombinant DNA technology. i) Antigen Preparation
• Soluble antigens or fragments thereof, optionally conjugated to other molecules, can be used as immunogens for generating antibodies.
• immunogens for transmembrane molecules, such as receptors, fragments of these (e.g. the extracellular domain of a receptor) can be used as the immunogen.
• cells expressing the transmembrane molecule can be used as the immunogen.
• Such cells can be derived from a natural source (e.g. cancer cell lines) or may be cells which have been transformed by recombinant techniques to express the transmembrane molecule.
• Other antigens and forms thereof useful for preparing antibodies will be apparent to those in the art.
• a protein that is immunogenic in the species to be immunized e.g., keyhole limpet hemocyanin, serum albumin, bovine thyrog
• Animals are immunized against the antigen, immunogenic conjugates, or derivatives by combining, e.g., 100 ⁇ g or 5 ⁇ g of the protein or conjugate (for rabbits or mice, respectively) with 3 volumes of Freund's complete adjuvant and injecting the solution intradermally at multiple sites.
• the animals are boosted with 1/5 to 1/10 the original amount of peptide or conjugate in Freund's complete adjuvant by subcutaneous injection at multiple sites.
• Seven to 14 days later the animals are bled and the serum is assayed for antibody titer. Animals are boosted until the titer plateaus.
• the animal is boosted with the conjugate of the same antigen, but conjugated to a different protein and/or through a different cross-linking reagent.
• Conjugates also can be made in recombinant cell culture as protein fusions.
• aggregating agents such as alum are suitably used to enhance the immune response.
• Monoclonal antibodies may be made using the hybridoma method first described by Kohler et al., Nature, 256:495 (1975), or may be made by recombinant DNA methods (U.S. Pat. No. 4,816,567).
• a mouse or other appropriate host animal such as a hamster or macaque monkey, is immunized as hereinabove described to elicit lymphocytes that produce or are capable of producing antibodies that will specifically bind to the protein used for immunization.
• lymphocytes may be immunized in vitro.
• Lymphocytes then are fused with myeloma cells using a suitable fusing agent, such as polyethylene glycol, to form a hybridoma cell (Goding, Monoclonal Antibodies: Principles and Practice, pp.59-103 (Academic Press, 1986)).
• a suitable fusing agent such as polyethylene glycol
• the hybridoma cells thus prepared are seeded and grown in a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, parental myeloma cells.
• a suitable culture medium that preferably contains one or more substances that inhibit the growth or survival of the unfused, parental myeloma cells.
• the culture medium for the hybridomas typically will include hypoxanthine, aminopterin, and thymidine (HAT medium), which substances prevent the growth of HGPRT-deficient cells.
• Preferred myeloma cells are those that fuse efficiently, support stable high-level production of antibody by the selected antibody-producing cells, and are sensitive to a medium such as HAT medium.
• preferred myeloma cell lines are murine myeloma lines, such as those derived from MOPC-21 and MPC-11 mouse tumors available from the SaIk Institute Cell Distribution Center, San Diego, Calif. USA, and SP-2 or X63- Ag8-653 cells available from the American Type Culture Collection, Rockville, Md. USA.
• Human myeloma and mouse-human heteromyeloma cell lines also have been described for the production of human monoclonal antibodies (Kozbor, J. Immunol., 133:3001 (1984); Brodeur et al, Monoclonal Antibody Production Techniques and Applications, pp. 51 -63 (Marcel Dekker, Inc., New York, 1987)).
• Culture medium in which hybridoma cells are growing is assayed for production of monoclonal antibodies directed against the antigen.
• the binding specificity of monoclonal antibodies produced by hybridoma cells is determined by immunoprecipitation or by an in vitro binding assay, such as radioimmunoassay (RIA) or enzyme-linked immunoabsorbent assay (ELISA).
• RIA radioimmunoassay
• ELISA enzyme-linked immunoabsorbent assay
• the clones may be subloned by limiting dilution procedures and grown by standard methods (Goding, MonoclonalAntibodies: Principles and Practice, pp.59- 103 (Academic Press, 1986)). Suitable culture media for this purpose include, for example, D-MEM or RPMI- 1640 medium.
• the hybridoma cells may be grown in vivo as ascites tumors in an animal.
• the monoclonal antibodies secreted by the subclones are suitably separated from the culture medium, ascites fluid, or serum by conventional immunoglobulin purification procedures such as, for example, protein A-Sepharose, hydroxylapatite chromatography, gel electrophoresis, dialysis, or affinity chromatography.
• DNA encoding the monoclonal antibodies is readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the monoclonal antibodies).
• the hybridoma cells serve as a preferred source of such DNA.
• the DNA may be placed into expression vectors, which are then transfected into host cells such as E. coli cells, simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of monoclonal antibodies in the recombinant host cells. Recombinant production of antibodies will be described in more detail below.
• antibodies or antibody fragments can be isolated from antibody phage libraries generated using the techniques described in McCafferty et al., Nature, 348:552-554 (1990).
• the DNA also may be modified, for example, by substituting the coding sequence for human heavy- and light-chain constant domains in place of the homologous murine sequences (U.S. Pat. No. 4,816,567; Morrison, et al., Proc. Natl. Acad. Sci. USA, 81 :6851 (1984)), or by covalently joining to the immunoglobulin coding sequence all or part of the coding sequence for a non-immunoglobulin polypeptide.
• non-immunoglobulin polypeptides are substituted for the constant domains of an antibody, or they are substituted for the variable domains of one antigen- combining site of an antibody to create a chimeric bivalent antibody comprising one antigen- combining site having specificity for an antigen and another antigen-combining site having specificity for a different antigen.
• a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human. These non-human amino acid residues are often referred to as "import" residues, which are typically taken from an "import” variable domain. Humanization can be essentially performed following the method of Winter and co-workers (Jones et al., Nature, 321 :522-525 (1986); Riechmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science, 239:1534-1536 (1988)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody. Accordingly, such "humanized” antibodies are chimeric antibodies (U.S. Pat.
• humanized antibodies are typically human antibodies in which some CDR residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.
• variable domains both light and heavy
• sequence of the variable domain of a rodent antibody is screened against the entire library of known human variable-domain sequences.
• the human sequence which is closest to that of the rodent is then accepted as the human framework (FR) for the humanized antibody (Sims et al., J. Immunol., 151 :2296 (1993); Chothia et al, J. MoI. Biol, 196:901 (1987)).
• Another method uses a particular framework derived from the consensus sequence of all human antibodies of a particular subgroup of light or heavy chains.
• the same framework may be used for several different humanized antibodies (Carter et al., Proc. Natl. Acad Sci. USA, 89:4285 (1992); Presta et al., J. ImmnoL, 151 :2623 (1993)).
• humanized antibodies are prepared by a process of analysis of the parental sequences and various conceptual humanized products using three-dimensional models of the parental and humanized sequences.
• Three-dimensional immunoglobulin models are commonly available and are familiar to those skilled in the art.
• Computer programs are available which illustrate and display probable three-dimensional conformational structures of selected candidate immunoglobulin sequences. Inspection of these displays permits analysis of the likely role of the residues in the functioning of the candidate immunoglobulin sequence, i.e., the analysis of residues that influence the ability of the candidate immunoglobulin to bind its antigen.
• FR residues can be selected and combined from the recipient and import sequences so that the desired antibody characteristic, such as increased affinity for the target antigen(s), is achieved.
• the CDR residues are directly and most substantially involved in influencing antigen binding.
• transgenic animals e.g., mice
• J.sub.H antibody heavy-chain joining region
• Human antibodies can also be derived from phage-display libraries (Hoogenboom et al, J. MoI. Biol, 227:381 (1991); Marks et al, J. MoL Biol., 222:581-597 (1991); Vaughan et al. Nature Biotech 14:309 (1996)). Generation of human antibodies from antibody phage display libraries is further described below. (v) Antibody Fragments
• antibody fragments Traditionally, these fragments were derived via proteolytic digestion of intact antibodies (see, e.g., Morimoto et al., Journal of Biochemical and Biophysical Methods 24: 107-1 17 (1992) and Brennan et al., Science, 229:81 (1985)). However, these fragments can now be produced directly by recombinant host cells. For example, the antibody fragments can be isolated from the antibody phage libraries discussed above. Alternatively, Fab'-SH fragments can be directly recovered from E. coli and chemically coupled to form F(ab') 2 fragments (Carter et al., Bio/Technology 10:163-167 (1992)).
• the F(ab') 2 is formed using the leucine zipper GCN4 to promote assembly of the F(ab') 2 molecule.
• F(ab') 2 fragments can be isolated directly from recombinant host cell culture. Other techniques for the production of antibody fragments will be apparent to the skilled practitioner.
• the antibody of choice is a single chain Fv fragment (scFv). See WO 93/16185.
• Multispecific antibodies have binding specificities for at least two different epitopes, where the epitopes are usually from different antigens. While such molecules normally will only bind two different epitopes (i.e. bispecific antibodies, BsAbs), antibodies with additional specificities such as trispecific antibodies are encompassed by this expression when used herein. Examples of BsAbs include those with one arm directed against
• BsABs include those with one arm directed against PirB/LILRB2 and another arm directed against NgR.
• Methods for making bispecific antibodies are known in the art. Traditional production of full length bispecific antibodies is based on the coexpression of two immunoglobulin heavy chain-light chain pairs, where the two chains have different specificities (Millstein et al., Nature, 305:537-539 (1983)). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of 10 different antibody molecules, of which only one has the correct bispecific structure.
• antibody variable domains with the desired binding specificities are fused to immunoglobulin constant domain sequences.
• the fusion preferably is with an immunoglobulin heavy chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant region (CHl) containing the site necessary for light chain binding, present in at least one of the fusions.
• DNAs encoding the immunoglobulin heavy chain fusions and, if desired, the immunoglobulin light chain are inserted into separate expression vectors, and are co-transfected into a suitable host organism. This provides for great flexibility in adjusting the mutual proportions of the three polypeptide fragments in embodiments when unequal ratios of the three polypeptide chains used in the construction provide the optimum yields. It is, however, possible to insert the coding sequences for two or all three polypeptide chains in one expression vector when the expression of at least two polypeptide chains in equal ratios results in high yields or when the ratios are of no particular significance.
• the bispecific antibodies are composed of a hybrid immunoglobulin heavy chain with a first binding specificity in one arm, and a hybrid immunoglobulin heavy chain-light chain pair (providing a second binding specificity) in the other arm. It was found that this asymmetric structure facilitates the separation of the desired bispecific compound from unwanted immunoglobulin chain combinations, as the presence of an immunoglobulin light chain in only one half of the bispecific molecule provides for a facile way of separation. This approach is disclosed in WO 94/04690. For further details of generating bispecific antibodies see, for example, Suresh et al., Methods in Enzvmology. 121 :210 (1986).
• the interface between a pair of antibody molecules can be engineered to maximize the percentage of heterodimers which are recovered from recombinant cell culture.
• the preferred interface comprises at least a part of the CH3 domain of an antibody constant domain.
• one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains (e.g. tyrosine or tryptophan).
• Compensatory "cavities" of identical or similar size to the large side chain(s) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones (e.g. alanine or threonine).
• Bispecific antibodies include cross-linked or "heteroconjugate" antibodies.
• one of the antibodies in the heteroconjugate can be coupled to avidin, the other to biotin.
• Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Pat. No. 4,676,980), and for treatment of HIV infection (WO 91/00360, WO 92/200373).
• Heteroconjugate antibodies may be made using any convenient cross- linking methods. Suitable cross-linking agents are well known in the art, and are disclosed in U.S. Pat. No. 4,676,980, along with a number of cross-linking techniques.
• bispecific antibodies can be prepared using chemical linkage.
• Brennan et al, Science 229: 81 (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate F(ab') 2 fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation.
• the Fab' fragments generated are then converted to thionitrobenzoate (TNB) derivatives.
• One of the Fab'-TNB derivatives is then reconverted to the Fab'-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab'-TNB derivative to form the bispecific antibody.
• the bispecific antibodies produced can be used as agents for the selective immobilization of enzymes.
• Fab'-SH fragments can also be directly recovered from E. coli, and can be chemically coupled to form bispecific antibodies.
• Shalaby et al., J. Exp. Med., 175: 217-225 (1992) describe the production of a fully humanized bispecific antibody F(ab') 2 molecule.
• Each Fab' fragment was separately secreted from E. coli and subjected to directed chemical coupling in vitro to form the bispecific antibody.
• bispecific antibodies have been produced using leucine zippers.
• the leucine zipper peptides from the Fos and Jun proteins were linked to the Fab' portions of two different antibodies by gene fusion.
• the antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers. This method can also be utilized for the production of antibody homodimers.
• the fragments comprise a heavy-chain variable domain (VFI) connected to a light-chain variable domain (VL) by a linker which is too short to allow pairing between the two domains on the same chain. Accordingly, the VH and VL domains of one fragment are forced to pair with the complementary VL and VH domains of another fragment, thereby forming two antigen-binding sites.
• VFI heavy-chain variable domain
• VL light-chain variable domain
• Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) dimers has also been reported. See Gruber et al, J. Immunol, 152:5368 (1994).
• Antibodies with more than two valencies are contemplated.
• trispecific antibodies can be prepared.
• Effector Function Engineering It may be desirable to modify the antibody of the invention with respect to effector function, so as to enhance the effectiveness of the antibody.
• cysteine residue(s) may be introduced in the Fc region, thereby allowing interchain disulfide bond formation in this region.
• the homodimeric antibody thus generated may have improved internalization capability and/or increased complement-mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See Caron et al., J. Exp Med. 176: 1 191 -1 195 (1992) and Shopes, B. J. Immunol.
• Homodimeric antibodies with enhanced antitumor activity may also be prepared using heterobifunctonal cross-linkers as described in Wolff et al. Cancer Research 53:2560-2565 (1993).
• an antibody can be engineered which has dual Fc regions and may thereby have enhanced complement lysis and ADCC capabilities. See Stevenson et al Anti-Cancer Drug Design 3:219-230 (1989).
• an antibody fragment rather than an intact antibody, to increase tumor penetration, for example.
• the salvage receptor binding epitope preferably constitutes a region wherein any one or more amino acid residues from one or two loops of a Fc domain are transferred to an analogous position of the antibody fragment.
• the epitope is taken from the CH2 domain of the Fc region (e.g., of an IgG) and transferred to the CHl, CH3, or V.sub.H region, or more than one such region, of the antibody.
• the epitope is taken from the CH2 domain of the Fc region and transferred to the CL region or VL region, or both, of the antibody fragment.
• Covalent modifications of antibodies are included within the scope of this invention. They may be made by chemical synthesis or by enzymatic or chemical cleavage of the antibody, if applicable. Other types of covalent modifications of the antibody are introduced into the molecule by reacting targeted amino acid residues of the antibody with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C- terminal residues. Examples of covalent modifications are described in U.S. Pat. No. 5,534,615, specifically incorporated herein by reference.
• a preferred type of covalent modification of the antibody comprises linking the antibody to one of a variety of nonproteinaceous polymers, e.g., polyethylene glycol, polypropylene glycol, or polyoxyalkylenes, in the manner set forth in U.S. Pat. Nos. 4,640,835; 4,496,689; 4,301 ,144; 4,670,417; 4,791,192 or 4,179,337. (x) Generation of Antibodies From Synthetic Antibody Phage Libraries
• the invention provides a method for generating and selecting novel antibodies using a unique phage display approach.
• the approach involves generation of synthetic antibody phage libraries based on single framework template, design of sufficient diversities within variable domains, display of polypeptides having the diversified variable domains, selection of candidate antibodies with high affinity to target the antigen, and isolation of the selected antibodies.
• the antibody libraries used in the invention can be generated by mutating the solvent accessible and/or highly diverse positions in at least one CDR of an antibody variable domain. Some or all of the CDRs can be mutated using the methods provided herein. In some embodiments, it may be preferable to generate diverse antibody libraries by mutating positions in CDRHl, CDRH2 and CDRH3 to form a single library or by mutating positions in CDRL3 and CDRH3 to form a single library or by mutating positions in CDRL3 and CDRHl, CDRH2 and CDRH3 to form a single library.
• a library of antibody variable domains can be generated, for example, having mutations in the solvent accessible and/or highly diverse positions of CDRHl, CDRH2 and CDRH3.
• Another library can be generated having mutations in CDRLl, CDRL2 and CDRL3.
• These libraries can also be used in conjunction with each other to generate binders of desired affinities. For example, after one or more rounds of selection of heavy chain libraries for binding to a target antigen, a light chain library can be replaced into the population of heavy chain binders for further rounds of selection to increase the affinity of the binders.
• a library is created by substitution of original amino acids with variant amino acids in the CDRH3 region of the variable region of the heavy chain sequence.
• the resulting library can contain a plurality of antibody sequences, wherein the sequence diversity is primarily in the CDRH3 region of the heavy chain sequence.
• the library is created in the context of the humanized antibody 4D5 sequence, or the sequence of the framework amino acids of the humanized antibody 4D5 sequence.
• the library is created by substitution of at least residues 95-10Oa of the heavy chain with amino acids encoded by the DVK codon set, wherein the DVK codon set is used to encode a set of variant amino acids for every one of these positions.
• An example of an oligonucleotide set that is useful for creating these substitutions comprises the sequence (DVK) 1 .
• a library is created by substitution of residues 95-10Oa with amino acids encoded by both DVK and NNK codon sets.
• an oligonucleotide set that is useful for creating these substitutions comprises the sequence (DVK) ⁇ (NNK).
• a library is created by substitution of at least residues 95-10Oa with amino acids encoded by both DVK and NNK codon sets.
• An example of an oligonucleotide set that is useful for creating these substitutions comprises the sequence (DVK) 5 (NNK).
• Another example of an oligonucleotide set that is useful for creating these substitutions comprises the sequence (NNK)(,.
• suitable oligonucleotide sequences can be determined by one skilled in the art according to the criteria described herein.
• CDRH3 designs are utilized to isolate high affinity binders and to isolate binders for a variety of epitopes.
• the range of lengths of CDRH3 generated in this library is 1 1 to 13 amino acids, although lengths different from this can also be generated.
• H3 diversity can be expanded by using NNK, DVK and NVK codon sets, as well as more limited diversity at N and/or C-terminal.
• CDRHl and CDRH2 Diversity can also be generated in CDRHl and CDRH2.
• the designs of CDR-Hl and H2 diversities follow the strategy of targeting to mimic natural antibodies repertoire as described with modification that focus the diversity more closely matched to the natural diversity than previous design.
• multiple libraries can be constructed separately with different lengths of H3 and then combined to select for binders to target antigens.
• the multiple libraries can be pooled and sorted using solid support selection and solution sorting methods as described previously and herein below. Multiple sorting satrategies may be employed. For example, one variation involves sorting on target bound to a solid, followed by sorting for a tag that may be present on the fusion polypeptide (eg. anti-gD tag) and followed by another sort on target bound to solid.
• the libraries can be sorted first on target bound to a solid surface, the eluted binders are then sorted using solution phase binding with decreasing concentrations of target antigen. Utilizing combinations of different sorting methods provides for minimization of selection of only highly expressed sequences and provides for selection of a number of different high affinity clones.
• High affinity binders for the target antigen can be isolated from the libraries. Limiting diversity in the H1/H2 region decreases degeneracy about 10 4 to 10 5 fold and allowing more H3 diversity provides for more high affinity binders. Utilizing libraries with different types of diversity in CDRH3 (eg. utilizing DVK or NVT) provides for isolation of binders that may bind to different epitopes of a target antigen.
• CDRLl amino acid position 28 is encoded by RDT; amino acid position 29 is encoded by RKT; amino acid position 30 is encoded by RVW; amino acid position 31 is encoded by ANW; amino acid position 32 is encoded by THT; optionally, amino acid position 33 is encoded by CTG ; in CDRL2: amino acid position 50 is encoded by KBG; amino acid position 53 is encoded by AVC; and optionally, amino acid position 55 is encoded by GMA ; in CDRL3: amino acid position 91 is encoded by TMT or SRT or both; amino acid position 92 is encoded by DMC; amino acid position 93 is encoded by RVT; amino acid position 94 is encoded by NHT; and amino acid position 96 is encoded by TWT or YKG or both.
• a library or libraries with diversity in CDRHl, CDRH2 and CDRH3 regions is generated.
• diversity in CDRH3 is generated using a variety of lengths of H3 regions and using primarily codon sets XYZ and NNK or NNS.
• Libraries can be formed using individual oligonucleotides and pooled or oligonucleotides can be pooled to form a subset of libraries.
• the libraries of this embodiment can be sorted against target bound to solid. Clones isolated from multiple sorts can be screened for specificity and affinity using ELISA assays. For specificity, the clones can be screened against the desired target antigens as well as other nontarget antigens.
• binders to the target antigen can then be screened for affinity in solution binding competition ELISA assay or spot competition assay.
• High affinity binders can be isolated from the library utilizing XYZ codon sets prepared as described above. These binders can be readily produced as antibodies or antigen binding fragments in high yield in cell culture.
• High affinity binders isolated from the libraries of these embodiments are readily produced in bacterial and eukaryotic cell culture in high yield.
• the vectors can be designed to readily remove sequences such as gD tags, viral coat protein component sequence, and/or to add in constant region sequences to provide for production of full length antibodies or antigen binding fragments in high yield.
• a library with mutations in CDRH3 can be combined with a library containing variant versions of other CDRs, for example CDRLl, CDRL2, CDRL3, CDRHl and/or CDRH2.
• a CDRH3 library is combined with a CDRL3 library created in the context of the humanized 4D5 antibody sequence with variant amino acids at positions 28, 29, 30,31, and/or 32 using predetermined codon sets.
• a library with mutations to the CDRH3 can be combined with a library comprising variant CDRHl and/or CDRH2 heavy chain variable domains.
• the CDRHl library is created with the humanized antibody 4D5 sequence with variant amino acids at positions 28, 30, 31, 32 and 33.
• a CDRH2 library may be created with the sequence of humanized antibody 4D5 with variant amino acids at positions 50, 52, 53, 54, 56 and 58 using the predetermined codon sets.
• the novel antibodies generated from phage libraries can be further modified to generate antibody mutants with improved physical, chemical and or biological properties over the parent antibody.
• the assay used is a biological activity assay
• the antibody mutant preferably has a biological activity in the assay of choice which is at least about 10 fold better, preferably at least about 20 fold better, more preferably at least about 50 fold better, and sometimes at least about 100 fold or 200 fold better, than the biological activity of the parent antibody in that assay.
• an anti-PirB/LILRB antibody mutant preferably has a binding affinity for PirB/LILRB which is at least about 10 fold stronger, preferably at least about 20 fold stronger, more preferably at least about 50 fold stronger, and sometimes at least about 100 fold or 200 fold stronger, than the binding affinity of the parent antibody.
• one or more amino acid alterations are introduced in one or more of the hypervariable regions of the parent antibody.
• one or more alterations (e.g. substitutions) of framework region residues may be introduced in the parent antibody where these result in an improvement in the binding affinity of the antibody mutant for the antigen from the second mammalian species.
• framework region residues to modify include those which non-covalently bind antigen directly (Amit et al. (1986) Science 233:747-753); interact with/effect the conformation of a CDR (Chothia et al. (1987) J MoI. Biol.
• modification of one or more of such framework region residues results in an enhancement of the binding affinity of the antibody for the antigen from the second mammalian species. For example, from about one to about five framework residues may be altered in this embodiment of the invention. Sometimes, this may be sufficient to yield an antibody mutant suitable for use in preclinical trials, even where none of the hypervariable region residues have been altered. Normally, however, the antibody mutant will comprise additional hypervariable region alteration(s).
• hypervariable region residues which are altered may be changed randomly, especially where the starting binding affinity of the parent antibody is such that such randomly produced antibody mutants can be readily screened.
• hypervariable region residue(s) are replaced by alanine or polyalanine residue(s) to affect the interaction of the amino acids with the antigen from the second mammalian species.
• Those hypervariable region residue(s) demonstrating functional sensitivity to the substitutions then are refined by introducing further or other mutations at or for the sites of substitution.
• the site for introducing an amino acid sequence variation is predetermined, the nature of the mutation per se need not be predetermined.
• the ala-mutants produced this way are screened for their biological activity as described herein.
• hydrophobic norleucine, met, ala, val, leu, ile
• neutral hydrophilic cys, ser, thr, asn, gin
• the sites selected for modification are affinity matured using phage display (see above).
• Nucleic acid molecules encoding amino acid sequence mutants are prepared by a variety of methods known in the art. These methods include, but are not limited to, oligonucleotide-mediated (or site-directed) mutagenesis, PCR mutagenesis, and cassette mutagenesis of an earlier prepared mutant or a non-mutant version of the parent antibody.
• the preferred method for making mutants is site directed mutagenesis (see, e.g., Kunkel
• the antibody mutant will only have a single hypervariable region residue substituted. In other embodiments, two or more of the hypervariable region residues of the parent antibody will have been substituted, e.g. from about two to about ten hypervariable region substitutions. Ordinarily, the antibody mutant with improved biological properties will have an amino acid sequence having at least 75% amino acid sequence identity or similarity with the amino acid sequence of either the heavy or light chain variable domain of the parent antibody, more preferably at least 80%, more preferably at least 85%, more preferably at least 90%, and most preferably at least 95%.
• Identity or similarity with respect to this sequence is defined herein as the percentage of amino acid residues in the candidate sequence that are identical (i.e same residue) or similar (i.e. amino acid residue from the same group based on common side-chain properties, see above) with the parent antibody residues, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity. None of N-terminal, C-terminal, or internal extensions, deletions, or insertions into the antibody sequence outside of the variable domain shall be construed as affecting sequence identity or similarity.
• the biological activity of that molecule relative to the parent antibody is determined. As noted above, this may involve determining the binding affinity and/or other biological activities of the antibody.
• a panel of antibody mutants is prepared and screened for binding affinity for the antigen or a fragment thereof.
• One or more of the antibody mutants selected from this initial screen are optionally subjected to one or more further biological activity assays to confirm that the antibody mutant(s) with enhanced binding affinity are indeed useful, e.g. for preclinical studies.
• the antibody mutant(s) so selected may be subjected to further modifications, oftentimes depending on the intended use of the antibody. Such modifications may involve further alteration of the amino acid sequence, fusion to heterologous polypeptide(s) and/or covalent modifications such as those elaborated below. With respect to amino acid sequence alterations, exemplary modifications are elaborated above. For example, any cysteine residue not involved in maintaining the proper conformation of the antibody mutant also may be substituted, generally with serine, to improve the oxidative stability of the molecule and prevent aberrant cross linking. Conversely, cysteine bond(s) may be added to the antibody to improve its stability (particularly where the antibody is an antibody fragment such as an Fv fragment). Another type of amino acid mutant has an altered glycosylation pattern.
• glycosylation sites may be achieved by deleting one or more carbohydrate moieties found in the antibody, and/or adding one or more glycosylation sites that are not present in the antibody.
• Glycosylation of antibodies is typically either N-linked or 0-linked.
• N-linked refers to the attachment of the carbohydrate moiety to the side chain of an asparagine residue.
• the tripeptide sequences asparagine-X-serine and asparagine-X-threonine, where X is any amino acid except proline, are the recognition sequences for enzymatic attachment of the carbohydrate moiety to the asparagine side chain.
• X is any amino acid except proline
• O-linked glycosylation refers to the attachment of one of the sugars N-aceylgalactosamine, galactose, or xylose to a hydroxyamino acid, most commonly serine or threonine, although 5-hydroxyproline or 5- hydroxylysine may also be used. Addition of glycosylation sites to the antibody is conveniently accomplished by altering the amino acid sequence such that it contains one or more of the above-described tripeptide sequences (for N-linked glycosylation sites).
• the alteration may also be made by the addition of, or substitution by, one or more serine or threonine residues to the sequence of the original antibody (for O-linked glycosylation sites), (xii) Recombinant Production of Antibodies
• the nucleic acid encoding it is isolated and inserted into a replicable vector for further cloning (amplification of the DNA) or for expression.
• DNA encoding the monoclonal antibody is readily isolated and sequenced using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the antibody). Many vectors are available.
• the vector components generally include, but are not limited to, one or more of the following: a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence (e.g. as described in U.S. Pat. No. 5,534,615, specifically incorporated herein by reference).
• Suitable host cells for cloning or expressing the DNA in the vectors herein are the prokaryote, yeast, or higher eukaryote cells described above.
• Suitable prokaryotes for this purpose include eubacteria, such as Gram-negative or Gram-positive organisms, for example, Enterobacteriaceae such as Escherichia, e.g., E. coli, Enterobacter, Erwinia, Klebsiella, Proteus, Salmonella, e.g., Salmonella typhimurium, Serrafia, e.g, Serratia marcescans, and Shigeila, as well as Bacilli such as B. subtilis and B. licheniformis (e.g., B.
• E. coli 294 ATCC 31,446
• E. coli B E. coli X 1776
• E coil W3110 ATCC 27,325
• eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for antibody-encoding vectors.
• Saccharomyces cerevisiae or common baker's yeast, is the most commonly used among lower eukaryotic host microorganisms.
• Kluyveromyces hosts such as, e.g., K. lactis, K. fragilis (ATCC 12,424), K. bulgaricus (ATCC 16,045), K. wickeramii (ATCC 24,178), K. waltii (ATCC 56,500), K.
• drosophilarum ATCC 36,906), K. thermotolerans, and K. marxianus; yarrowia (EP 402,226); Pichia pastoris (EP 183,070); Candida; Trichoderma reesia (EP 244,234); Neurospora crassa; Schwanniomyces such as Schwanniomyces occidentalis; and filamentous fungi such as, e.g., Neurospora, Penicillium, Tolypocladium, and Aspergillus hosts such as A. nidulans and A. niger.
• Suitable host cells for the expression of glycosylated antibody are derived from multicellular organisms.
• invertebrate cells include plant and insect cells.
• Numerous baculoviral strains and variants and corresponding permissive insect host cells from hosts such as Spodoptera frugiperda (caterpillar), Aedes aegypti (mosquito), Aedes albopictus (mosquito), Drosophila melanogaster (fruitfly), and Bombyx mori have been identified.
• a variety of viral strains for transfection are publicly available, e.g., the L-I variant of Autographa californica NPV and the Bm-5 strain of Bombyx mori NPV, and such viruses may be used as the virus herein according to the present invention, particularly for transfection of Spodoptera frugiperda cells.
• Plant cell cultures of cotton, corn, potato, soybean, petunia, tomato, and tobacco can also be utilized as hosts.
• vertebrate cells have been greatest in vertebrate cells, and propagation of vertebrate cells in culture (tissue culture) has become a routine procedure.
• useful mammalian host cell lines are monkey kidney CVl line transformed bySV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subloned for growth in suspension culture, Graham et al, J. Gen Virol. 36:59 (1977)); baby hamster kidney cells (BHK, ATCC CCL 10); Chinese hamster ovary cells/-DHFR (CHO, Urlaub et al., Proc. Natl. Acad. Sci. USA 77:4216 (1980)); mouse Sertoli cells (TM4, Mather, Biol. Reprod.
• COS-7 monkey kidney CVl line transformed bySV40
• human embryonic kidney line (293 or 293 cells subloned for growth in suspension culture, Graham et al, J. Gen Virol. 36:59 (1977)
• baby hamster kidney cells BHK, ATCC CCL
• monkey kidney cells (CVl ATCC CCL 70); African green monkey kidney cells (VERO-76, ATCC CRL-1587); human cervical carcinoma cells (HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells (Wl 38, ATCC CCL 75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT 060562, ATCC CCL51); TRI cells (Mather et al., Annals N. Y. Acad. Sci. 383:44-68 (1982)); MRC 5 cells; FS4 cells; and a human hepatoma line (Hep G2).
• Host cells are transformed with the above-described expression or cloning vectors for antibody production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
• the host cells used to produce the antibody of this invention may be cultured in a variety of media.
• Commercially available media such as Ham's FlO (Sigma), Minimal Essential Medium ((MEM), (Sigma), RPMI- 1640 (Sigma), and Dulbecco's Modified Eagle's Medium ((DMEM), Sigma) are suitable for culturing the host cells.
• any of these media may be supplemented as necessary with hormones and/or other growth factors (such as insulin, transferrin, or epidermal growth factor), salts (such as sodium chloride, calcium, magnesium, and phosphate), buffers (such as HEPES), nucleotides (such as adenosine and thymidine), antibiotics (such as GENTAMYCINTM), trace elements (defined as inorganic compounds usually present at final concentrations in the micromolar range), and glucose or an equivalent energy source. Any other necessary supplements may also be included at appropriate concentrations that would be known to those skilled in the art.
• the culture conditions such as temperature, pH, and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan.
• the antibody can be produced intracellularly, in the periplasmic space, or directly secreted into the medium. If the antibody is produced intracellularly, as a first step, the particulate debris, either host cells or lysed cells, is removed, for example, by centrifugation or ultrafiltration. Where the antibody is secreted into the medium, supernatants from such expression systems are generally first concentrated using a commercially available protein concentration filter, for example, an Amicon or Millipore Pellicon ultrafiltration unit. A protease inhibitor such as PMSF may be included in any of the foregoing steps to inhibit proteolysis and antibiotics may be included to prevent the growth of adventitious contaminants.
• a protease inhibitor such as PMSF may be included in any of the foregoing steps to inhibit proteolysis and antibiotics may be included to prevent the growth of adventitious contaminants.
• the antibody composition prepared from the cells can be purified using, for example, hydroxyl apatite chromatography, gel electrophoresis, dialysis, and affinity chromatography, with affinity chromatography being the preferred purification technique.
• affinity chromatography is the preferred purification technique.
• the suitability of protein A as an affinity ligand depends on the species and isotype of any immunoglobulin Fc domain that is present in the antibody. Protein A can be used to purify antibodies that are based on human .gamma.1, .gamma.2, or .gamma.4 heavy chains (Lindmark et al., J. Immunol. Meth. 62: 1-13 (1983)).
• Protein G is recommended for all mouse isotypes and for human .gamma.3 (Guss et al., EMBO J. 5: 1567-1575 (1986)).
• the matrix to which the affinity ligand is attached is most often agarose, but other matrices are available. Mechanically stable matrices such as controlled pore glass or poly(styrenedivinyl)benzene allow for faster flow rates and shorter processing times than can be achieved with agarose.
• the antibody comprises a CH 3 domain
• the Bakerbond ABXTM resin J. T. Baker, Phillipsburg, NJ.
• anti-PirB/LILRB antibodies of the present invention are believed to find use as agents for enhancing the survival or inducing the outgrowth of nerve cells. They are, therefore, useful in the therapy of degenerative disorders of the nervous system
• neurodegenerative diseases including, for example, physical damage to the central nervous system (spinal cord and brain); brain damage associated with stroke; and neurological disorders relating to neurodegeneration, such as, for example, trigeminal neuralgia, glossopharyngeal neuralgia, Bell's Palsy, myasthenia gravis, muscular dystrophy, amyotrophic lateral sclerosis (ALS), multiple sclerosis (MS), progressive muscular atrophy, progressive bulbar inherited muscular atrophy, peripheral nerve damage caused by physical injury (e.g., burns, wounds) or disease states such as diabetes, kidney dysfunction or by the toxic effects of chemotherapeutics used to treat cancer and AIDS, herniated, ruptured or prolapsed invertebrate disk syndromes, cervical spondylosis, plexus disorders, thoracic outlet destruction syndromes, peripheral neuropathies such as those caused by lead, dapsone, ticks, prophyria, Gullain-Barre syndrome, Alzheimer's disease, Huntington
• anti-PirB/LILRB antibodies herein are also useful as components of culture media for use in culturing nerve cells in vitro.
• preparations comprising the anti-PirB/LILRB antibodies herein are useful as standards in competitive binding assays when labeled with radioiodine, enzymes, fluorophores, spin labels, and the like.
• Therapeutic formulations of the anti-PirB/LILRB antibodies herein are prepared for storage by mixing the compound identified (such as an antibody) having the desired degree of purity with optional physiologically acceptable carriers, excipients or stabilizers (Remington's Pharmaceutical Sciences, supra), in the form of lyophilized cake or aqueous solutions.
• Acceptable carriers, excipients or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate and other organic acids; antioxidants including ascorbic acid; low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone, amino acids such as glycine, glutamine, asparagine, arginine or lysine; monosaccharides, disaccharides and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugar alcohols such as mannitol or sorbitol; salt-forming counterions such as sodium; and/or nonionic surfactants such as Tween, Pluronics or PEG.
• buffers such as phosphate, citrate and other organic acids
• antioxidants including ascorbic acid
• the anti-PirB/LILRB antibodies to be used for in vivo administration must be sterile. This is readily accomplished by filtration through sterile filtration membranes, prior to or following lyophilization and reconstitution.
• Therapeutic compositions may be placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle.
• the anti-PirB/LILRB antibodies of the present invention may be optionally combined with or administered in combination with neurotrophic factors including NGF, NT-3, and/or BDNF and used with other conventional therapies for degenerative nervous disorders.
• the anti-PirB/LILRB antibodies of the present invention can be advantageously administered in combination with NgR inhibitors, such as antibodies, small molecules or peptides, blocking the binding of Nogo-66, MAG and/or OMgp to NgR.
• the route of administration is in accord with known methods, e.g. injection or infusion by intravenous, intraperitoneal, intracerebral, intramuscular, intraocular, intraarterial or intralesional routes, topical administration, or by sustained release systems as noted below.
• the compounds may be administered continuously by infusion into the fluid reservoirs of the CNS, although bolus injection is acceptable.
• the compounds are preferably administered into the ventricles of the brain or otherwise introduced into the CNS or spinal fluid.
• Administration may be performed by an indwelling catheter using a continuous administration means such as a pump, or it can be administered by implantation, e.g., intracerebral implantation, of a sustained-release vehicle.
• the compounds can be injected through chronically implanted cannulas or chronically infused with the help of osmotic minipumps.
• Subcutaneous pumps are available that deliver proteins through a small tubing to the cerebral ventricles.
• Suitable administration protocols and delivery systems involving a subcutaneous pump device or continuous intracerebroventricular infusion through a totally implanted drug delivery system are those used for the administration of dopamine, dopamine agonists, and cholinergic agonists to Alzheimer patients and animal models for Parkinson's disease described by Harbaugh, J. Neural Transm. Suppl., 24:271 (1987); and DeYebenes, et al., Mov. Disord. 2: 143 (1987).
• sustained release preparations include semipermeable polymer matrices in the form of shaped articles, e.g. films, or microcapsules.
• Sustained release matrices include polyesters, hydrogels, polylactides (U.S. Pat. No. 3,773,919, EP 58,481), copolymers of L-glutamic acid and gamma ethyl-L-glutamate (Sidman, et al., 1983,
• the liposomes are of the small (about 200-800 Angstroms) unilamelar type in which the lipid content is greater than about 30 mol. % cholesterol, the selected proportion being adjusted for the optimal therapy.
• An effective amount of an active compound to be employed therapeutically will depend, for example, upon the therapeutic objectives, the route of administration, and the condition of the patient. Accordingly, it will be necessary for the therapist to titer the dosage and modify the route of administration as required to obtain the optimal therapeutic effect.
• a typical daily dosage might range from about 1 ⁇ g/kg to up to 100 mg/kg or more, depending on the factors mentioned above.
• the clinician will administer an active compound until a dosage is reached that repairs, maintains, and, optimally, reestablishes neuron function.
• the progress of this therapy is easily monitored by conventional assays. Further details of the invention are illustrated by the following non-limiting examples.
• the cDNA library used in the screen was comprised of full-length human cDNA clones in expression-ready vectors generated by Origene. These cDNAs were compiled, arrayed, and pooled. Pools of approximately 100 cDNA's were transiently transfected into COS7 cells. In particular, on Day 1, COS7 cells were plated at a density of 85, 000 cells per well in 12-well plates. On Day 2, 1 mg of pooled cDNA's were transfected per well using the lipid-based transfection reagent FuGENE 6 (Roche). On Day 4, screening was performed. Briefly, culture medium was removed from cells and replaced with 0.5 ml of 293 cell- conditioned medium containing AP-fusion bait proteins (20-50 nM).
• LILRB2 leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2 (LILRB2), mRNA" (SEQ ID NO: 2). This gene is also known by multiple alternative nomenclatures, including MIGlO, ILT4, and LIR2
• PirB function-blocking antibodies Preparation and testing of PirB function-blocking antibodies PirB function-blocking antibodies
• Antibodies against PirB were generated by panning a synthetic phage antibody library against the PirB extracellular domain (W. C. Liang et al., J MoI Biol 366, 815 (2007)). Antibody clones (10 ⁇ g/ml) were then tested in vitro for their ability to block binding of AP-Nogo66 (50 nM) to PirB-expressing COS7 cells.
• the nucleotide and amino acid sequences of the heavy and light chain sequences of various YW259 anti-mouse PirB (anti-mPirB) antibodies are shown in Figures 6-16, and 17 and 18.
• Figures 17 and 18 also show the hypervariable region sequences within the heavy and light chains of YW259.2, YW250.9 and YW259.12, respectively. Neurite Outgrowth Assay
• 96- well plates pre-coated with poly-D-lysine (Biocoat, BD) were coated with myelin (0.75 ⁇ g/ml) overnight or with AP-Nogo66 or MAG-Fc (150-300 ng/spot) for two hours, and then treated with laminin (10 ⁇ g/ml in F- 12) for 2 hours (CGN cultures) or 4 hours (DRG cultures).
• Mouse P7 cerebellar neurons were cultured as previously described (B. Zheng et al, Proc Natl Acad Sci USA 102, 1205 (2005)) and plated at -2X10 4 cells per well.
• Mouse PlO DRG neurons were cultured as previously described (Zheng et al., 2005, supra) and plated at -5X10 3 cells per well. Cultures were grown for 22 hours at 37°C with 5% CO 2 , and then fixed with 4% paraformaldehyde/ 10% sucrose and stained with anti- ⁇ lll-tubulin (TuJl, Covance). For each experiment, all conditions were performed in six replicate wells, from which maximum neurite lengths were measured and averages were determined between the six wells. Each experiment was performed at least three times with similar results, p- values were determined using Student's t test. Growth Cone Collapse Assay
• DRG explants were isolated by dissecting out DRG from 3 -week-old mice and slicing them into thirds. Each DRG explant was then cultured in an individual PDL (100 ⁇ g/ml)- and laminin QO ⁇ g/ml)-coated well from an eight- well plate. At 72-hours-post-plating, explants were incubated with AP-Nogo66 (100 nM) or myelin (3 ⁇ g/ml) for 30 minutes to stimulate collapse. Cultures were fixed with 4%paraformaldehyde/10% sucrose, and growth cones were then visualized by rhodamine-phalloidin (Molecular Probes) staining and scored for collapse. Average growth cone collapse was determined by averaging at least 3 replicate wells. Results
• PirB is a functional receptor for Nogo66
• P7 cerebellar granule neurons (CGN), for which neurite outgrowth is inhibited when grown on AP-Nogo66
• CGN cerebellar granule neurons
• adult CGN have been shown to express PirB (J. Syken et al., Science 313,1795 (2006)), and we found that is also the case for juvenile CGN as assessed by RT-PCR, immunohistochemistry and in situ hybridization (data not shown).
• PirB can bind the functionally inhibitory domain of Nogo66, but do not address whether endogenous PirB in CGN mediates inhibition by AP-Nogo66.
• NgR has previously been described as a receptor for myelin inhibitors, it is possible that PirB and NgR function together to mediate inhibition of neurite outgrowth.
• both PirB and NgR function were blocked together in CGN's by culturing neurons from NgR-null mice in the presence of anti-PirB.
• NgR-/- CGN neurite outgrowth is inhibited by AP- Nogo66 or myelin to the same extent as that in WT neurons (50% and 49%; Figure 3).
• aPB 1 antibody treatment of NgR+/- neurons partially reversed inhibition by either AP-Nogo66 or myelin, as seen above for aPBl treatment of WT neurons.
• aPBl treatment of NgR-/- neurons partially reversed inhibition by AP-Nogo66, but did not provide any further rescue than that seen with aPB l treatment of NgR+/- neurons or WT neurons.
• aPBl treatment of NgR-/- neurons restored neurite outgrowth on myelin to nearly control levels.
• PirB but not NgR, is required for substrate inhibition by APNogo66 in CGN, but only in part.
• both PirB and NgR together contribute to the substrate inhibition imparted by myelin.
• NgR is thought to be required for growth cone collapse in response to various myelin inhibitors (J. E. Kim et al, Neuron 44, 439 (2004), O.Chivatakarn et al, J. Neurosci. 27, 71 17 (2007)), it is possible that PirB is also involved in this more acute response.
• C1QTNF5 inhibited neurite outgrowth of cereberral granule neurone (CGN), and this inhibition was reversed by PirB function-blocking antibody YW259.2.
• CGN cereberral granule neurone
• PirB function-blocking antibody YW259.2 The results are shown in Figure 19. Together, these results support a novel role for PirB as a necessary receptor for neurite inhibition by myelin extracts, and more specifically by the myelin-associated inhibitors Nogo66 and MAG. Indeed, PirB appears to be a more significant mediator of substrate inhibition than NgR, since removal of PirB function alone (either genetically or using antibodies) partially disinhibits growth on both myelin extracts- and myelin inhibitors, whereas genetic removal of NgR alone does not disinhibit on any of these substrates.
• NgR appears to play an adjunct role in mediating inhibition by myelin extracts (but not Nogo66), since genetic removal of NgR can augment the disinhibition caused by anti-PirB antibodies on myelin (but not on Nogo66).
• Our findings may help to explain the surprising lack of enhanced CST regeneration in NgR knockout mice (J.E. Kim et al., supra, B. Zheng et al., Proc. Natl. Acad. Sci. USA 102, 1205 (2005)), despite the reported regeneration or sprouting seen in rodents infused with the NgR ectodomain (S. Li et al., J. Neurosci. 24, 1051 1 (2004)).
• PirB appears to be a more significant receptor for substrate inhibition than NgR, inactivation of either PirB or NgR alone is sufficient to block the acute growth cone collapse caused by addition of myelin inhibitors. This observation suggests that collapse is a more demanding process, requiring both PirB and NgR activities, acting either in parallel or together.
• PirB and NgR receptors have recently been shown to play similar roles in limiting plasticity of synaptic connections in the visual cortex: in mice lacking either receptor, eye closure during a critical developmental period results in excessive strengthening of connections via the open eye (J. Syken et al, 2006, supra, A. W. McGee et al., Science 309, 2222 (2005), supra).
• the mechanisms responsible for the effect of both receptors in mediating growth cone collapse could also underlie the commonality of their role in ocular dominance plasticity.

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• 2009
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