AGONISTIC ANTI-TUMOR NECROSIS FACTOR RECEPTOR 2 ANTIBODIES
The invention provides agonistic TNFR2 antibodies and antigen-binding fragments thereof and encompasses the use of these antibodies as therapeutics to promote the proliferation of regulatory T cells (T-reg) for the treatment of immunological diseases. Antibodies of the invention can be used to potentiate the T-reg-mediated deactivation of self- and allergen-reactive T- and B-eases. Antibodies and can thus be used to treat a wide variety of indications, including autoimmune diseases, allergic reactions, asthma, graft-versus-host disease, and allograft rejection, among others.
The invention relates to antibodies capable of potentiating tumor necrosis factor receptor 2 signalling and their use for modulating the activity of T-reg cells, and provides therapies for immunological disorders or conditions, such as multiple sclerosis, asthma, allergic reactions, graft-versus-host disease, and transplantation graft rejection.
BACKGROUND OF THE INVENTIONMaintaining control of the cell-mediated and humoral immune responses is an important facet of healthy immune system activity. The aberrant regulation of T-cell and B-cell driven immune reactions has been associated with a wide array of human diseases, as the inappropriate mounting of an immune response against various self and foreign antigens plays a causal role in such pathologies as autoimmune disorders, asthma, allergic reactions, graft-versus-host disease, transplantation graft rejection, and a variety of other immunological disorders. These diseases are mediated by T- and B-lymphocytes that exhibit reactivity against self antigens and those derived from non-threatening sources, such as allergens or transplantation allografts. T-reg cells (T-reg cells) have evolved in order to inhibit the activity of immune cells that are cross-reactive with “self” major histocompatability complex (MHC) proteins and other benign antigens. T-reg cells represent a heterogeneous class of T-cells that can be distinguished based on their unique surface protein presentation. The most well-understood populations of T-reg cells include CD4+, CD25+, FoxP3+T-reg cells and CD17+T-reg cells. The precise mechanisms by which these cells mediate suppression of autoreactive T-cells is the subject of ongoing investigations, though it has been shown that certain classes of T-reg cells inhibit production of the proliferation-inducing cytokine IL-2 in target T-cells and may additionally sequester IL-2 from autoreactive cells by virtue of the affinity of CD25 (a subdomain of the IL-2 receptor) for IL-2 (Josefowicz et al., Ann. Rev. Immun., 30:531-564 (2012)). Moreover, it has been shown that CD4+, CD25+, FoxP3+T-reg cells are also present in B-cell-rich areas and are capable of directly suppressing immunoglobulin production independent of their ability to attenuate TH2-cell activity (Lim et al., J. Immunol., 175:4180-4183 (2005)).
Tumor necrosis factor receptor (TN FR) subtypes 1 and 2 have been identified on the T-reg cell surface as signal transduction molecules that dictate cell fate. The activation of TNFR1, for instance, potentiates the caspase signaling cascade and terminates in T-reg apoptosis, while activation of TNFR2 induces signaling through the mitogen-activated protein kinase (MAPK) signaling pathway, which orchestrates the TRAF2/3- and NFκB-mediated transcription of genes that promote cell proliferation and escape from apoptosis. Due to its role in directing cell survival and growth, TNFR2 represents an attractive target for expanding populations of T-reg cells as a strategy for treating immunological disorders. There is currently a need for therapies that can augment T-reg cell survival and proliferation for use in treatments targeting such diseases as autoimmune disorders, graft-versus-host disease, allograft rejection, allergic reactions, and asthma, among others.
SUMMARY OF THE INVENTIONThe invention provides TNFR2 agonist antibodies and antigen-binding fragments thereof capable of binding TNFR2 and promoting TNFR2 signaling, as well as methods of producing such antibodies and antigen-binding fragments thereof, and methods of treating a subject suffering from an immunological disease by administering such antibodies and antigen-binding fragments thereof.
In a first aspect, the invention provides a TNFR2 agonist antibody or antigen-binding fragment thereof capable of specifically binding TNFR2 (e.g., human TNFR2), e.g., in a human or in a non-human animal. The antibody or antigen-binding fragment thereof specifically binds an epitope containing amino acids 56-60 of SEQ ID NO: 366 (KCSPG) and does not specifically bind an epitope containing amino acids 142-146 of SEQ ID NO: 366 (KCRPG). The antibody or antigen-binding fragment thereof may also lack specific binding for another tumor necrosis factor receptor (TNFR) superfamily member, such as TNFR1, RANK, CD30, CD40, Lymphotoxin beta receptor (LT-PR), OX40, Fas receptor, Decoy receptor 3, CD27, 4-1 BB, Death receptor 4, Death receptor 5, Decoy receptor 1, Decoy receptor 2, Osteoprotegrin, TWEAK receptor, TACI, BAFF receptor, Herpesvirus entry mediator, Nerve growth factor receptor, B-cell maturation antigen, Glucocorticoid-induced TNFR-related, TROY, Death receptor 6, Death receptor 3, and Ectodysplasin A2 receptor. TNFR2 agonist antibodies and antigen-binding fragments thereof that specifically bind non-human TNFR2 exhibit specific binding to an epitope containing amino acids KCPPG, but do not specifically bind an epitope containing amino acids KCGPG and/or KCSPG. In addition, TNFR2 agonist antibodies and antigen-binding fragments thereof that specifically bind non-human TNFR2 may also lack specific binding to a TNFR superfamily member other than TNFR2.
In an additional aspect, the invention provides a TNFR2 agonist antibody or antigen-binding fragment thereof capable of specifically binding TNFR2, such as human TNFR2, that specifically binds an epitope containing amino acids 56-60 of SEQ ID NO: 366 (KCSPG) and does not specifically bind another TNFR superfamily member. In certain embodiments, the antibody or antigen-binding fragment thereof does not bind an epitope containing amino acids 142-146 of SEQ ID NO: 366 (KCRPG). In additional cases, the antibody or antigen-binding fragment thereof does not specifically bind any other epitope within TNFR2.
The invention also provides a TNFR2 agonist antibody or antigen-binding fragment thereof capable of specifically binding TNFR2, such as human TNFR2, that specifically binds an epitope containing amino acids 56-60 of SEQ ID NO: 366 (KCSPG) and is capable of promoting the proliferation of a population of T-regulatory (T-reg) cells. In another aspect, the invention encompasses a TNFR2 agonist antibody or antigen-binding fragment thereof capable of specifically binding TNFR2, such as human TNFR2, that specifically binds an epitope containing amino acids 56-60 of SEQ ID NO: 366 (KCSPG) and is capable of promoting the death of one or more CD8+ T-cells. In yet another aspect, the invention provides a TNFR2 agonist antibody or antigen-binding fragment thereof capable of specifically binding TNFR2, such as human TNFR2, that specifically binds an epitope containing amino acids 56-60 of SEQ ID NO: 366 (KCSPG) and is capable of promoting an increase in the level of one or more mRNA molecules encoding a protein selected from the group consisting of cIAP2, TRAF2, Etk, VEGFR2, PI3K, Akt, a protein involved in the angiogenic pathway, an IKK complex, RIP, NIK, MAP3K, a protein involved in the NFkB pathway, NIK, JNK, AP-1, a MEK (e.g., MEK1, MEK7), MKK3, NEMO, IL2R, Foxp3, IL2, TNF, and lymphotoxin (e.g., lymphotoxin α and lymphotoxin β). In another aspect, the invention provides a TNFR2 agonist antibody or antigen-binding fragment thereof capable of specifically binding TNFR2, such as human TNFR2, that specifically binds an epitope amino acids 56-60 of SEQ ID NO: 366 (KCSPG) and is capable of promoting an increase in the level of one or more proteins selected from the group consisting of cIAP2, TRAF2, Etk, VEGFR2, PI3K, Akt, a protein involved in the angiogenic pathway, an IKK complex, RIP, NIK, MAP3K, a protein involved in the NFkB pathway, NIK, JNK, AP-1, a MEK (e.g., MEK1, MEK7), MKK3, NEMO, IL2R, Foxp3, IL2, TNF, and lymphotoxin (e.g., lymphotoxin α and lymphotoxin β).
The TNFR2 agonist antibody or antigen-binding fragment thereof of the invention specifically binds an epitope within human TNFR2 containing at least five discontinuous or continuous residues within amino acids 96-154 of SEQ ID NO: 366 (CGSRCSSDQVETQACTREONRICTCRPGWYCALSKQESCRLCAPLRKCRPGFGVARPGT). Additionally or alternatively, the antibody or antigen-binding fragment thereof binds an epitope within amino acids 111-150 of SEQ ID NO: 366 (TREQNRICTCRPGWYCALSKQEGCRLCAPLRKCRPGFGVA). In other cases, the antibody or antigen-binding fragment thereof binds an epitope within amino acids 115-142 of SEQ ID NO: 366 (NRICTCRPGWYCALSKQEGCRLCAPLRK). Antibodies and antigen-binding fragments of the invention may also bind an epitope within amino acids 122-136 of SEQ ID NO: 366 (PGWYCALSKQEGCRL), and/or an epitope within amino acids 101-107 of SEQ ID NO: 366 (SSDQVET). In further embodiments, the antibody or antigen-binding fragment thereof of the invention binds an epitope within amino acids 48-67 of SEQ ID NO: 366 (QTAQMCCSKCSPGQHAKVFC). In some cases, the antibody or antigen-binding fragment thereof of the invention specifically binds the epitope containing amino acids 56-60 of SEQ ID NO: 366 (KCSPG) with a KD of less than about 10 nM.
In another aspect, the invention provides a TNFR2 agonist antibody or antigen-binding fragment thereof that specifically binds to an epitope within or containing the amino acid sequence of any one of SEQ ID NOs: 1-341, 346, and 367 and that is capable of specifically binding human TNFR2 but does not specifically bind another TNFR superfamily member.
The TNFR2 agonist antibody or antigen-binding fragment thereof may activate TNFR2 signaling. The antibody or antigen-binding fragment thereof may also bind TNFR2 with a KD of no greater than about 10 nM (e.g., with a KD of no greater than about 1 nM). Additionally or alternatively, the antibody or antigen-binding fragment thereof binds TNFR2 to form an antibody-antigen complex with a kon of at least about 104 M−1s−1 (e.g., with a kon of at least about 105 M−1s−1). In some cases, the antibody or antigen-binding fragment thereof binds TNFR2 to form an antibody-antigen complex, in which the complex dissociates with a koff of no greater than about 10−3 s−1 (e.g., with a koff of no greater than about 10−4 s−1). In additional embodiments, the antibody or antigen-binding fragment thereof is capable of promoting the proliferation of a population of T-regulatory (T-reg) cells (e.g., in the presence of TNFα).
In some embodiments, the antibody or antigen-binding fragment thereof has a non-native constant region. For instance, the antibody may be a monoclonal antibody that has a non-native constant region. In some embodiments, the antibody or antigen-binding fragment thereof is an isolated, non-murine antibody.
In another aspect, the invention provides a method of identifying a TNFR2 agonist antibody or antigen-binding fragment thereof, the method including the steps of:
(a) contacting a mixture of antibodies or fragments thereof with at least one peptide having the amino acid sequence of any one of SEQ ID NOs: 1-341, 346, and 367; and
(b) separating antibodies or fragments thereof that specifically bind the peptide from the mixture, thereby producing an enriched antibody mixture comprising at least one TNFR2 agonist antibody or antigen-binding fragment thereof.
In some cases, the method includes the step of determining the amino acid sequence of one or more of the antibodies or antigen-binding fragments thereof in the enriched antibody mixture. In certain embodiments, the peptide is bound to a surface. Additionally or alternatively, the antibody or antigen-binding fragment thereof is expressed on the surface of a phage, bacterial cell, or yeast cell. In other cases, the antibody or antigen-binding fragment thereof is expressed as one or more polypeptide chains non-covalently bound to ribosomes or covalently bound to mRNA or cDNA. The peptide may be conjugated to a detectable label, such as a fluorescent molecule (e.g., green fluorescent protein, cyan fluorescent protein, yellow fluorescent protein, red fluorescent protein, phycoerythrin, allophycocyanin, hoescht, 4′,6-diamidino-2-phenylindole (DAPI), propidium iodide, fluorescein, coumarin, rhodamine, tetramethylrhoadmine, and cyanine) or an epitope tag (e.g., maltose-binding protein, glutathione-S-transferase, a poly-histidine tag, a FLAG-tag, a myc-tag, human influenza hemagglutinin (HA) tag, biotin, and streptavidin). In some embodiments, steps (a) and (b) described above are sequentially repeated one or more times.
In additional embodiments of the invention, the method further includes the steps of:
i) exposing the enriched antibody mixture to at least one peptide containing the amino acid sequence of a TNFR superfamily member other than TNFR2; and retaining antibodies or fragments thereof that do not specifically bind the peptide, thereby producing a TNFR2-specific antibody mixture containing at least one TNFR2 agonist antibody or antigen-binding fragment thereof that does not specifically bind a TNFR superfamily member other than TNFR2; and/or
ii) exposing the enriched antibody mixture to at least one peptide containing amino acids 142-146 of SEQ ID NO: 366 (KCRPG); and retaining antibodies or fragments thereof that do not specifically bind the peptide, thereby producing an antibody mixture containing at least one TNFR2 agonist antibody or antigen-binding fragment thereof that does not specifically bind a peptide containing amino acids 142-146 of SEQ ID NO: 366 (KCRPG).
In some cases, the method includes performing steps (i) and (ii) in either order.
In another aspect, the invention provides a method of producing a TNFR2 agonist antibody or antigen-binding fragment thereof by immunizing a non-human mammal with a peptide containing the sequence of any one of SEQ ID NOs: 1-341, 346, and 367 and collecting serum containing the TNFR2 agonist antibody or antigen-binding fragment thereof, such that the antibody or antigen-binding fragment thereof is capable of specifically binding an epitope containing amino acids 56-60 of SEQ ID NO: 366 (KCSPG). In some cases, the non-human mammal is selected from the group consisting of a rabbit, mouse, rat, goat, guinea pig, hamster, horse, primate, and sheep. Additionally or alternatively, the peptide contains the amino acid sequence PGWYCALSKQEGCRL (SEQ ID NO: 11).
In a further aspect, the invention provides a TNFR2 agonist antibody or antigen-binding fragment thereof produced by any of the above-described methods. In some cases, the antibody or antigen-binding fragment thereof specifically binds an epitope containing amino acids 56-60 of SEQ ID NO: 366 (KCSPG) and does not specifically bind an epitope containing amino acids 142-146 of SEQ ID NO: 366 (KCRPG). Additionally or alternatively, the antibody or antigen-binding fragment thereof specifically binds an epitope containing amino acids 56-60 of SEQ ID NO: 366 (KCSPG) and does not specifically bind a TNFR superfamily member other than TNFR2. In some cases, the antibody or antigen-binding fragment thereof activates TNFR2 signaling. In additional embodiments, the antibody or antigen-binding fragment thereof binds TNFR2 with a KD of no greater than about 10 nM (e.g., with a KD of no greater than about 1 nM). Additionally or alternatively, the antibody or antigen-binding fragment thereof binds TNFR2 to form an antibody-antigen complex with a kon of at least about 104 M−1s−1 (e.g., with a kon of at least about 105 M−1s−1). In some cases, the antibody or antigen-binding fragment thereof binds TNFR2 to form an antibody-antigen complex, in which the complex dissociates with a koff of no greater than about 10−3s−1 (e.g., with a koff of no greater than about 10−4s−1). In additional embodiments, the antibody or antigen-binding fragment thereof is capable of promoting the proliferation of a population of T-regulatory (T-reg) cells (e.g., in the presence of TNFα).
In some cases, the TNFR2 agonist antibody or antigen-binding fragment thereof of the invention is a monoclonal antibody or antigen-binding fragment thereof, a polyclonal antibody or antigen-binding fragment thereof, a human antibody or antigen-binding fragment thereof, a humanized antibody or antigen-binding fragment thereof, a primatized antibody or antigen-binding fragment thereof, a bispecific antibody or antigen-binding fragment thereof, or a multi-specific antibody or antigen-binding fragment thereof. In other embodiments, the antibody or antigen-binding fragment thereof of the invention is a dual-variable immunoglobulin domain, a monovalent antibody or antigen-binding fragment thereof, a chimeric antibody or antigen-binding fragment thereof, a single-chain Fv molecule (scFv), a diabody, a triabody, a nanobody, an antibody-like protein scaffold, a domain antibody, a Fv fragment, a Fab fragment, a F(ab′)2 molecule, or a tandem scFv (taFv).
In further embodiments, the TNFR2 agonist antibody of the invention may contain an immunoglobulin, such as an immunoglobulin of subtype IgG, IgM, IgA, IgD, or IgE.
In some embodiments, the antibody or antigen-binding fragment thereof has a non-native constant region. For instance, the antibody may be a monoclonal antibody that has a non-native constant region. In some embodiments, the antibody or antigen-binding fragment thereof is an isolated, non-murine antibody.
In another aspect, the invention provides a pharmaceutical composition containing a TNFR2 agonist antibody or antigen-binding fragment thereof of the invention and a pharmaceutically acceptable carrier or excipient. The pharmaceutical composition of the invention may also contain an additional therapeutic agent, such as TNFα or BCG, or an immunotherapy agent, such as an anti-CTLA-4 agent, an anti-PD-1 agent, an anti-PD-L1 agent, an anti-PD-L2 agent, a TNF-α cross-linking agent, a TRAIL cross-linking agent, a CD27 agent, a CD30 agent, a CD40 agent, a 4-1 BB agent, a GITR agent, an OX40 agent, a TRAILR1 agent, a TRAILR2 agent, or a TWEAKR agent.
The invention also provides a polynucleotide encoding a TNFR2 agonist antibody or antigen-binding fragment thereof of the invention, as well as a vector containing such a polynucleotide. In some embodiments, the vector is an expression vector, such as a eukaryotic expression vector. In other embodiments, the expression vector is a viral vector, such as an adenovirus (Ad, e.g., a serotype 5, 26, 35, or 48 adenovirus), retrovirus (e.g., a γ-retrovirus or a lentivirus), poxvirus, adeno-associated virus, baculovirus, herpes simplex virus, or a vaccinia virus (e.g., a modified vaccinia Ankara (MVA)).
In a further aspect, the invention encompasses a host cell containing a vector of the invention. In some cases, the host cell is a prokaryotic cell. In other embodiments, the vector is a eukaryotic cell, such as a mammalian cell (e.g., a CHO cell, a DHFR CHO cell, a NSO myeloma cell, a COS cell, a 293 cell, or a SP2/0 cell.).
The invention additionally provides a method of producing a TNFR2 agonist antibody or antigen-binding fragment described above, the method including the steps of expressing a polynucleotide encoding the antibody or antigen-binding fragment thereof in a host cell and recovering the antibody or antigen-binding fragment thereof from host cell medium.
In another aspect, the invention provides a method of inhibiting an immune response mediated by a B cell or a CD8+ T cell in a subject and a method of treating an immunological disease in a subject, the methods individually including the step of administering to the subject a TNFR2 agonist antibody or antigen binding fragment of the invention, a pharmaceutical composition of the invention, a polynucleotide of the invention, a vector of the invention, or a host cell of the invention.
In some embodiments, the antibody or antigen-binding fragment thereof has a non-native constant region. For instance, the antibody may be a monoclonal antibody that has a non-native constant region. In some embodiments, the antibody or antigen-binding fragment thereof is an isolated, non-murine antibody.
In some cases, the subject is in need of tissue or organ repair or regeneration (e.g., repair or regeneration of a pancreas, salivary gland, pituitary gland, kidney, heart, lung, hematopoietic system, cranial nerves, heart, aorta, olfactory gland, ear, nerves, structures of the head, eye, thymus, tongue, bone, liver, small intestine, large intestine, gut, lung, brain, skin, peripheral nervous system, central nervous system, spinal cord, breast, embryonic structures, embryos, and testes). Administration of a TNFR2 agonist antibody or antigen-binding fragment thereof stimulates or allows repair and/or regeneration of the tissue or organ.
The immunological disease to be treated may be selected from the group consisting of an autoimmune disease, a neurological condition, an allergy, asthma, macular degeneration, muscular atrophy, a disease related to miscarriage, atherosclerosis, bone loss, a musculoskeletal disease, obesity, a graft-versus-host disease, and an allograft rejection. In other embodiments, the autoimmune disease is selected from the group consisting of type I diabetes, Alopecia Areata, Ankylosing Spondylitis, Antiphospholipid Syndrome, Autoimmune Addison's Disease, Autoimmune Hemolytic Anemia, Autoimmune Hepatitis, Behcet's Disease, Bullous Pemphigoid, Cardiomyopathy, Celiac Sprue-Dermatitis, Chronic Fatigue Immune Dysfunction Syndrome (CFIDS), Chronic Inflammatory Demyelinating Polyneuropathy, Churg-Strauss Syndrome, Cicatricial Pemphigoid, CREST Syndrome, Cold Agglutinin Disease, Crohn's Disease, Essential Mixed Cryoglobulinemia, Fibromyalgia-Fibromyositis, Graves' Disease, Guillain-Barré, Hashimoto's Thyroiditis, Hypothyroidism, Idiopathic Pulmonary Fibrosis, Idiopathic Thrombocytopenia Purpura (ITP), IgA Nephropathy, Juvenile Arthritis, Lichen Planus, Lupus, Meniere's Disease, Mixed Connective Tissue Disease, Multiple Sclerosis, Myasthenia Gravis, Pemphigus Vulgaris, Pernicious Anemia, Polyarteritis Nodosa, Polychondritis, Polyglandular Syndromes, Polymyalgia Rheumatica, Polymyositis and Dermatomyositis, Primary Agammaglobulinemia, Primary Biliary Cirrhosis, Psoriasis, Raynaud's Phenomenon, Reiter's Syndrome, Rheumatic Fever, Rheumatoid Arthritis, Sarcoidosis, Scleroderma, Sjögren's Syndrome, Stiff-Man Syndrome, Takayasu Arteritis, Temporal Arteritis/Giant Cell Arteritis, Ulcerative Colitis, Uveitis, Vasculitis, Vitiligo, and Wegener's Granulomatosis.
In other embodiments, the neurological condition is selected from the group consisting of a brain tumor, a brain metastasis, a spinal cord injury, schizophrenia, epilepsy, Amyotrophic lateral sclerosis (ALS), Parkinson's disease, Alzheimer's disease, Huntington's disease, and stroke.
In some cases, the allergy is selected from the group consisting of food allergy, seasonal allergy, pet allergy, hives, hay fever, allergic conjunctivitis, poison ivy allergy oak allergy, mold allergy, drug allergy, dust allergy, cosmetic allergy, and chemical allergy.
In other embodiments, the allograft rejection is selected from the group consisting of skin graft rejection, bone graft rejection, vascular tissue graft rejection, ligament graft rejection (e.g., cricothyroid ligament graft rejection, periodontal ligament graft rejection, suspensory ligament of the lens graft rejection, palmar radiocarpal ligament graft rejection, dorsal radiocarpal ligament graft rejection, ulnar collateral ligament graft rejection, radial collateral ligament graft rejection, suspensory ligament of the breast graft rejection, anterior sacroiliac ligament graft rejection, posterior sacroiliac ligament graft rejection, sacrotuberous ligament graft rejection, sacrospinous ligament graft rejection, inferior pubic ligament graft rejection, superior pubic ligament graft rejection, anterior cruciate ligament graft rejection, lateral collateral ligament graft rejection, posterior cruciate ligament graft rejection, medial collateral ligament graft rejection, cranial cruciate ligament graft rejection, caudal cruciate ligament graft rejection, and patellar ligament graft rejection), and organ graft rejection.
In still other embodiments, the graft-versus-host disease arises from a bone marrow transplant or one or more blood cells selected from the group consisting of hematopoietic stem cells, common myeloid progenitor cells, common lymphoid progenitor cells, megakaryocytes, monocytes, basophils, eosinophils, neutrophils, macrophages, T-cells, B-cells, natural killer cells, and dendritic cells.
In some cases, the above-described methods include administering to the subject an additional therapeutic agent, such as TNFα or BCG. Additionally or alternatively, the subject may be administered an immunotherapy agent, such as an anti-CTLA-4 agent, an anti-PD-1 agent, an anti-PD-L1 agent, an anti-PD-L2 agent, a TNF-α cross-linking agent, a TRAIL cross-linking agent, a CD27 agent, a CD30 agent, a CD40 agent, a 4-1 BB agent, a GITR agent, an OX40 agent, a TRAILR1 agent, a TRAILR2 agent, or a TWEAKR agent.
In certain embodiments of the above-described methods, the subject is a mammal (e.g., a human). Additionally or alternatively, the antibody may be 8E6.D1 or a humanized antibody or antigen-binding fragment thereof containing one or more (or all) heavy chain and/or light chain CDRs of 8E6.D1.
The invention also provides a kit containing an agent, such as a TNFR2 agonist antibody or antigen binding fragment of the invention, a pharmaceutical composition of the invention, a polynucleotide of the invention, a vector of the invention, and/or a host cell of the invention. In some cases, the kit includes instructions for transfecting a vector of the invention into a host cell. Additionally, the kit may include instructions for expressing a TNFR2 agonist antibody or antigen-binding fragment thereof of the invention in the host cell, and/or a reagent that can be used to express the antibody or antigen-binding fragment thereof in the host cell. In other embodiments, the kit includes instructions for administering the agent to a subject (e.g., a mammalian subject, such as a human) in order to treat an immunological disease. In other embodiments, the kit includes instructions for making or using the agent.
DefinitionsAs used herein, the term “about” refers to a value that is no more than 10% above or below the value being described. For example, the term “about 5 nM” indicates a range of from 4.5 nM to 5.5 nM.
As used herein, the terms “agonist TNFR2 antibody” and “agonistic TNFR2 antibody” refer to TNFR2 antibodies that are capable of promoting or increasing activation of TNFR2 and/or potentiating one or more signal transduction pathways mediated by TNFR2. For example, agonistic TNFR2 antibodies of the invention can promote or increase the proliferation of a population of T-reg cells. Agonistic TNFR2 antibodies of the invention may promote or increase TNFR2 activation by binding TNFR2, e.g., so as to induce a conformational change that renders the receptor biologically active. For instance, agonistic TNFR2 antibodies may nucleate the trimerization of TNFR2 in a manner similar to the interaction between TNFR2 and its cognate ligand, TNFα, thus inducing TNFR2-mediated signalling. Agonistic TNFR2 antibodies of the invention may be capable of inducing the proliferation of CD4+, CD25+, FOXP3+T-reg cells. Agonistic TNFR2 antibodies of the invention may also be capable of suppressing the proliferation of cytotoxic T lymphocytes (e.g., CD8+ T-cells), e.g., through activation of immunomodulatory T-reg cells or by directly binding TNFR2 on the surface of an autoreactive cytotoxic T-cell and inducing apoptosis. Unless otherwise noted, the terms “agonist TNFR2 antibody” and “agonistic TNFR2 antibody” also include antibody fragments, e.g., those described below, that retain the ability to bind TNFR2 and potentiate TNFR2 signal transduction. An agonist TNFR2 antibody or fragment thereof may specifically bind TNFR2 without exhibiting specific binding for another receptor of the tumor necrosis factor receptor (TNFR) superfamily.
As used herein, the term “antibody” (Ab) refers to an immunoglobulin molecule that specifically binds to, or is immunologically reactive with, a particular antigen, and includes polyclonal, monoclonal, genetically engineered and otherwise modified forms of antibodies, including but not limited to chimeric antibodies, humanized antibodies, heteroconjugate antibodies (e.g., bi- tri- and quad-specific antibodies, diabodies, triabodies, and tetrabodies), and antigen-binding fragments of antibodies, including e.g., Fab′, F(ab′)2, Fab, Fv, recombinant IgG (rIgG) fragments, and scFv fragments. Moreover, unless otherwise indicated, the term “monoclonal antibody” (mAb) is meant to include both intact molecules, as well as antibody fragments (such as, for example, Fab and F(ab′)2 fragments) that are capable of specifically binding to a target protein. Fab and F(ab′)2 fragments lack the Fc fragment of an intact antibody, clear more rapidly from the circulation of the animal, and may have less non-specific tissue binding than an intact antibody (see Wahl et al., J. Nucl. Med. 24:316, 1983; incorporated herein by reference).
The term “antigen-binding fragment,” as used herein, refers to one or more fragments of an antibody that retain the ability to specifically bind to a target antigen. The antigen-binding function of an antibody can be performed by fragments of a full-length antibody. The antibody fragments can be, e.g., a Fab, F(ab′)2, scFv, SMIP, diabody, a triabody, an affibody, a nanobody, an aptamer, or a domain antibody. Examples of binding fragments encompassed by the term “antigen-binding fragment” of an antibody include, but are not limited to: (i) a Fab fragment, a monovalent fragment consisting of the VL, VH, CL, and CH1 domains; (ii) a F(ab′)2 fragment, a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region; (iii) a Fd fragment consisting of the VH and CH1 domains; (iv) a Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb including VH and VL domains; (vi) a dAb fragment (Ward et al., Nature 341:544-546, 1989), which consists of a VH domain; (vii) a dAb which consists of a VH or a VL domain; (viii) an isolated complementarity determining region (CDR); and (ix) a combination of two or more isolated CDRs which may optionally be joined by a synthetic linker. Furthermore, although the two domains of the Fv fragment, VL and VH, are coded for by separate genes, they can be joined, using recombinant methods, by a linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv (scFv); see, e.g., Bird et al., Science 242:423-426, 1988, and Huston et al., Proc. Natl. Acad. Sci. USA 85:5879-5883, 1988). These antibody fragments can be obtained using conventional techniques known to those of skill in the art, and the fragments can be screened for utility in the same manner as intact antibodies. Antigen-binding fragments can be produced by recombinant DNA techniques, enzymatic or chemical cleavage of intact immunoglobulins, or, in certain cases, by chemical peptide synthesis procedures known in the art.
As used herein, the terms “anti-tumor necrosis factor receptor 2 antibody,” “TNFR2 antibody,” “anti-TNFR2 antibody portion,” and/or “anti-TNFR2 antibody fragment” and the like include any protein or peptide-containing molecule that includes at least a portion of an immunoglobulin molecule, such as but not limited to at least one complementarity determining region (CDR) of a heavy or light chain or a ligand binding portion thereof, a heavy chain or light chain variable region, a heavy chain or light chain constant region, a framework region, or any portion thereof, that is capable of specifically binding to TNFR2. TNFR2 antibodies also include antibody-like protein scaffolds, such as the tenth fibronectin type III domain (10Fn3), which contains BC, DE, and FG structural loops similar in structure and solvent accessibility to antibody CDRs. The tertiary structure of the 10Fn3 domain resembles that of the variable region of the IgG heavy chain, and one of skill in the art can graft, e.g., the CDRs of a TNFR2 monoclonal antibody onto the fibronectin scaffold by replacing residues of the BC, DE, and FG loops of 10Fn3 with residues from the CDRH-1, CDRH-2, or CDRH-3 regions of a TNFR2 monoclonal antibody. The use of 10Fn3 domains as scaffolds for epitope grafting is described, e.g., in WO 2000/034784, the disclosure of which is incorporated herein by reference. Additional scaffold proteins encompassed by the term “anti-tumor necrosis factor receptor 2 antibody,” “TNFR2 antibody,” and the like include peptide-Fc fusion proteins (described, e.g., in WO 2012/122378; as well as in U.S. Pat. No. 8,633,297; the disclosures of each of which are incorporated herein by reference).
As used herein, the term “bispecific antibodies” refers to monoclonal, often human or humanized antibodies that have binding specificities for at least two different antigens. Bispecific TNFR2 antibodies of the invention may have binding specificities that are directed towards TNFR2 and any other antigen, e.g., for a cell-surface protein, receptor, receptor subunit, tissue-specific antigen, virally derived protein, virally encoded envelope protein, bacterially derived protein, or bacterial surface protein, etc. A bispecific antibody may also be an antibody or antigen-binding fragment thereof that includes two separate antigen-binding domains (e.g., two scFvs joined by a linker). The scFvs may bind the same antigen or different antigens.
As used herein, the term “chimeric” antibody refers to an antibody having variable sequences derived from an immunoglobulin of one source organism, such as rat or mouse, and constant regions derived from an immunoglobulin of a different organism (e.g., a human). Methods for producing chimeric antibodies are known in the art. See, e.g., Morrison, 1985, Science 229(4719): 1202-7; Oi et al, 1986, BioTechniques 4:214-221; Gillies et al, 1985, J. Immunol. Methods 125:191-202; U.S. Pat. Nos. 5,807,715; 4,816,567; and 4,816,397; the disclosures of each of which are incorporated herein by reference.
As used herein, the term “complementarity determining region” (CDR) refers to a hypervariable region found both in the light chain and the heavy chain variable domains. The more highly conserved portions of variable domains are called the framework regions (FRs). As is appreciated in the art, the amino acid positions that delineate a hypervariable region of an antibody can vary, depending on the context and the various definitions known in the art. Some positions within a variable domain may be viewed as hybrid hypervariable positions in that these positions can be deemed to be within a hypervariable region under one set of criteria while being deemed to be outside a hypervariable region under a different set of criteria. One or more of these positions can also be found in extended hypervariable regions. The invention includes antibodies comprising modifications in these hybrid hypervariable positions. The variable domains of native heavy and light chains each comprise four framework regions that primarily adopt a β-sheet configuration, connected by three CDRs, which form loops that connect, and in some cases form part of, the β-sheet structure. The CDRs in each chain are held together in close proximity by the FR regions in the order FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4 and, with the CDRs from the other antibody chains, contribute to the formation of the target binding site of antibodies (see Kabat et al, Sequences of Proteins of Immunological Interest (National Institute of Health, Bethesda, Md. 1987; incorporated herein by reference). As used herein, numbering of immunoglobulin amino acid residues is done according to the immunoglobulin amino acid residue numbering system of Kabat et al, unless otherwise indicated.
As used herein, the terms “conservative mutation,” “conservative substitution,” or “conservative amino acid substitution” refer to a substitution of one or more amino acids for one or more different amino acids that exhibit similar physicochemical properties, such as polarity, electrostatic charge, and/or steric volume. These properties are summarized for each of the twenty naturally-occurring amino acids in Table 1 below.
From this table it is appreciated that the conservative amino acid families include (i) G, A, V, L and I; (ii) D and E; (iii) A, S and T; (iv) H, K and R; (v) N and Q; and (vi) F, Y and W. A conservative mutation or substitution is therefore one that substitutes one amino acid for a member of the same amino acid family (e.g., a substitution of Ser for Thr or Lys for Arg).
As used herein, the term “conjugate” refers to a compound formed by the chemical bonding of a reactive functional group of one molecule with an appropriately reactive functional group of another molecule. Conjugates may additionally be produced, e.g., as two polypeptide domains covalently bound to one another as part of a single polypeptide chain that is synthesized by the translation of a single RNA transcript encoding both polypeptides in frame with one another.
As used herein, the term “derivatized antibodies” refers to antibodies that are modified by a chemical reaction so as to cleave residues or add chemical moieties not native to an isolated antibody. Derivatized antibodies can be obtained, e.g., by glycosylation, acetylation, pegylation, phosphorylation, amidation, derivatization by addition of known chemical protecting/blocking groups, proteolytic cleavage, linkage to a cellular ligand or other protein. Any of a variety of chemical modifications can be carried out by known techniques, including, without limitation, specific chemical cleavage, acetylation, formylation, metabolic synthesis of tunicamycin, etc. using established procedures. Additionally, the derivative can contain one or more non-natural amino acids, e.g., using amber suppression technology (see, e.g., U.S. Pat. No. 6,964,859; incorporated herein by reference). In certain cases, it may be desirable to include one or more non-natural amino acids within an antibody of the invention in order to provide a reactive functional group that can be used to conjugate the antibody to another molecule. Examples of unnatural amino acids that exhibit this functionality include those that contain, e.g., one or more azide, alkyne, ketone, aniline, alkene, tetrazole, 1,2-aminothiol, phosphine, norbornene, or tetrazine moieties. The reactivity of these functional groups is known to those of skill in the art and is described, e.g., in US 2015/0005481; U.S. Pat. No. 7,807,619; de Araújo, et al., Chemistry 12:6095-6109 (2006); and Köhn, et al., Angew Chem Int Ed Engl, 43:3106-3116 (2004); the disclosures of each of which are incorporated herein by reference. Other examples of non-natural amino acids that may desirably be incorporated into an antibody of the invention include D-amino acids and other those containing other non-natural side-chain moieties so as to reduce the susceptibility of the antibody to proteolytic degradation by evading recognition by endogenous proteases and endopeptidases.
As used herein, the term “diabodies” refers to bivalent antibodies comprising two polypeptide chains, in which each polypeptide chain includes VH and VL domains joined by a linker that is too short (e.g., a linker composed of five amino acids) to allow for intramolecular association of VH and VL domains on the same peptide chain. This configuration forces each domain to pair with a complementary domain on another polypeptide chain so as to form a homodimeric structure. Accordingly, the term “triabodies” refers to trivalent antibodies comprising three peptide chains, each of which contains one VH domain and one VL domain joined by a linker that is exceedingly short (e.g., a linker composed of 1-2 amino acids) to permit intramolecular association of VH and VL domains within the same peptide chain. In order to fold into their native structure, peptides configured in this way typically trimerize so as to position the VH and VL domains of neighboring peptide chains spatially proximal to one another to permit proper folding (see Holliger et al., Proc. Natl. Acad. Sci. USA 90:6444-48, 1993; incorporated herein by reference).
As used herein, a “dual variable domain immunoglobulin” (“DVD-Ig”) refers to an antibody that combines the target-binding variable domains of two monoclonal antibodies via linkers to create a tetravalent, dual-targeting single agent. (Gu et al., Meth. Enzymol., 502:25-41, 2012; incorporated by reference herein). Suitable linkers for use in the light chains of the DVDs of the invention include those identified on Table 2.1 on page 30 of Gu et al.: the short K chain linkers ADAAP (SEQ ID NO: 380) (murine) and TVAAP (SEQ ID NO: 381) (human); the long K chain linkers ADAAPTVSIFP (SEQ ID NO: 382) (murine) and TVAAPSVFIFPP (SEQ ID NO: 383) (human); the short A chain linker QPKAAP (SEQ ID NO: 384 (human); the long A chain linker QPKAAPSVTLFPP (SEQ ID NO: 385) (human); the GS-short linker GGSGG (SEQ ID NO: 386), the GS-medium linker GGSGGGGSG (SEQ ID NO: 387), and the GS-long linker GGSGGGGSGGGGS (SEQ ID NO: 388) (all GS linkers are murine and human). Suitable linkers for use in the heavy chains of the DVDs include those identified on Table 2.1 on page 30 of Gu & Ghayur, 2012, Methods in Enzymology 502:25-41, incorporated by reference herein: the short linkers AKTTAP (SEQ ID NO: 389) (murine) and ASTKGP (SEQ ID NO: 390) (human); the long linkers AKTTAPSVYPLAP (SEQ ID NO: 391) (murine) and ASTKGPSVFPLAP (SEQ ID NO: 392) (human); the GS-short linker GGGGSG (SEQ ID NO: 393), the GS-medium linker GGGGSGGGGS (SEQ ID NO: 394), and the GS-long linker GGGGSGGGGSGGGG (SEQ ID NO: 395) (all GS linkers are murine and human).
As used herein, the term “endogenous” describes a molecule (e.g., a polypeptide, protein, antibody, enzyme, cofactor, or nucleic acid) that is found naturally in a particular organism (e.g., a human) or in a particular location within an organism (e.g., an organ, a tissue, or a cell, such as a human cell).
As used herein, the term “exogenous” describes a molecule (e.g., a polypeptide, protein, antibody, enzyme, cofactor, or nucleic acid) that is not found naturally in a particular organism (e.g., a human) or in a particular location within an organism (e.g., an organ, a tissue, or a cell, such as a human cell). Exogenous materials include those that are provided from an external source to an organism or to cultured matter extracted there from.
As used herein, the term “framework region” or “FR” includes amino acid residues that are adjacent to the CDRs. FR residues may be present in, for example, human antibodies, rodent-derived antibodies (e.g., murine antibodies), humanized antibodies, primatized antibodies, chimeric antibodies, antibody fragments (e.g., Fab fragments), single chain antibody fragments (e.g., scFv fragments), antibody domains, and bispecific antibodies, among others.
As used herein, the term “fusion protein” refers to a protein that is joined via a covalent bond to another molecule. A fusion protein can be chemically synthesized by, e.g., an amide-bond forming reaction between the N-terminus of one protein to the C-terminus of another protein. Alternatively, a fusion protein containing one protein or protein domain covalently bound to another protein or protein domain can be expressed recombinantly in a cell (e.g., a eukaryotic cell or prokaryotic cell) by expression of a polynucleotide encoding the fusion protein, for example, from a vector or the genome of the cell. A fusion protein may contain one protein that is covalently bound to a linker, which in turn is covalently bound to another molecule. Examples of linkers that can be used for the formation of a fusion protein include peptide-containing linkers, such as those that contain naturally occurring or non-naturally occurring amino acids. In certain cases, it may be desirable to include D-amino acids in the linker, as these residues are not present in naturally-occurring proteins and are thus more resistant to degradation by endogenous proteases. Linkers can be prepared using a variety of strategies that are well known in the art, and depending on the reactive components of the linker, can be cleaved by enzymatic hydrolysis, photolysis, hydrolysis under acidic conditions, hydrolysis under basic conditions, oxidation, disulfide reduction, nucleophilic cleavage, or organometallic cleavage. These and other linker modalities are described, e.g., in Leriche et al., Bioorg. Med. Chem., 20:571-582, (2012), the disclosure of which is incorporated herein by reference.
As used herein, the term “heterospecific antibodies” refers to monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. Traditionally, the recombinant production of heterospecific antibodies is based on the co-expression of two immunoglobulin heavy chain-light chain pairs, where the two heavy chains have different specificities (as described, e.g., in Milstein et al., Nature 305:537, (1983), the disclosure of which is incorporated herein by reference). Similar procedures for generating heterospecific antibodies are disclosed, e.g., in WO 93/08829; WO 91/00360, WO 92/00373; EP 03089; U.S. Pat. Nos. 6,210,668; 6,193,967; 6,132,992; 6,106,833; 6,060,285; 6,037,453; 6,010,902; 5,989,530; 5,959,084; 5,959,083; 5,932,448; 5,833,985; 5,821,333; 5,807,706; 5,643,759, 5,601,819; 5,582,996; 5,496,549; 4,676,980; as well as in Traunecker et al., EMBO J. 10:3655 (1991); and Suresh et al., Methods in Enzymology 121:210 (1986); the disclosures of each of which are incorporated herein by reference. Heterospecific antibodies can include Fc mutations that enforce correct chain association in multi-specific antibodies, as described, e.g., by Klein et al, mAbs 4(6):653-663, (2012); the disclosure of which is incorporated herein by reference.
As used herein, the term “human antibody” refers to an antibody in which substantially every part of the protein (e.g., CDR, framework, CL, CH domains (e.g., CH1, CH2, CH3), hinge, (VL, VH)) is derived from a human germline immonglobulin sequence. A human antibody can be produced in a human cell (e.g., by recombinant expression), or by a non-human animal or a prokaryotic or eukaryotic cell that is capable of expressing functionally rearranged human immunoglobulin (e.g., heavy chain and/or light chain) genes. Human antibodies can be made by a variety of methods known in the art including phage display methods using antibody libraries derived from human immunoglobulin sequences. See U.S. Pat. Nos. 4,444,887 and 4,716,111; and PCT publications WO 1998/46645; WO 1998/50433; WO 1998/24893; WO 1998/16654; WO 1996/34096; WO 1996/33735; and WO 1991/10741; the disclosure of each of which is incorporated herein by reference. Human antibodies can also be produced using transgenic mice that are incapable of expressing functional endogenous immunoglobulins, but which can express human immunoglobulin genes. See, e.g., PCT publications WO 98/24893; WO 92/01047; WO 96/34096; WO 96/33735; U.S. Pat. Nos. 5,413,923; 5,625,126; 5,633,425; 5,569,825; 5,661,016; 5,545,806; 5,814,318; 5,885,793; 5,916,771; and 5,939,598; the disclosure of each of which is incorporated by reference herein.
As used herein, the term “humanized” antibodies refers to forms of non-human (e.g., primate, murine, rabbit, goat, rodent, or other non-human mammal) antibodies that are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab′, F(ab′)2 or other target-binding subdomains of antibodies) which contain minimal sequences derived from non-human immunoglobulin. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin. All or substantially all of the FR regions may also be those of a human immunoglobulin sequence. The humanized antibody can also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin consensus sequence. Methods of antibody humanization are known in the art. See, e.g., Riechmann et al., Nature 332:323-7, 1988; U.S. Pat. Nos. 5,530,101; 5,585,089; 5,693,761; 5,693,762; and U.S. Pat. No. 6,180,370 to Queen et al; EP239400; PCT publication WO 91/09967; U.S. Pat. No. 5,225,539; EP592106; and EP519596; incorporated herein by reference.
As used herein, the term “monoclonal antibody” refers to an antibody that is derived from a single clone, including any eukaryotic, prokaryotic, or phage clone, and not the method by which it is produced.
As used herein, the term “multi-specific antibodies” refers to antibodies that exhibit affinity for more than one target antigen. Multi-specific antibodies can have structures similar to full immunoglobulin molecules and include Fc regions, for example IgG Fc regions. Such structures can include, but not limited to, IgG-Fv, IgG-(scFv)2, DVD-Ig, (scFv)2-(scFv)2-Fc and (scFv)2-Fc-(scFv)2. In case of IgG-(scFv)2, the scFv can be attached to either the N-terminal or the C-terminal end of either the heavy chain or the light chain. Exemplary multi-specific molecules that include Fc regions and into which TNFR2 antibodies or antigen-binding fragments thereof can be incorporated have been reviewed, e.g., by Kontermann, 2012, mAbs 4(2):182-197, Yazaki et al, 2013, Protein Engineering, Design & Selection 26(3):187-193, and Grote et al, 2012, in Proetzel & Ebersbach (eds.), Antibody Methods and Protocols, Methods in Molecular Biology vol. 901, chapter 16:247-263; incorporated herein by reference. In certain cases, antibody fragments can be components of multi-specific molecules without Fc regions, based on fragments of IgG or DVD or scFv. Exemplary multi-specific molecules that lack Fc regions and into which antibodies or antibody fragments can be incorporated include scFv dimers (diabodies), trimers (triabodies) and tetramers (tetrabodies), Fab dimers (conjugates by adhesive polypeptide or protein domains) and Fab trimers (chemically conjugated), are described by Hudson and Souriau, 2003, Nature Medicine 9:129-134; incorporated herein by reference.
As used herein, the term “non-native constant region” refers to an antibody constant region that is derived from a source that is different from that of the antibody variable region or that is a human-generated synthetic polypeptide having an amino sequence that is different from the native antibody constant region sequence. For instance, an antibody containing a non-native constant region may have a variable region derived from a non-human source (e.g., a mouse, rat, or rabbit) and a constant region derived from a human source (e.g., a human antibody constant region).
As used herein, the term “percent (%) sequence identity” refers to the percentage of amino acid (or nucleic acid) residues of a candidate sequence that are identical to the amino acid (or nucleic acid) residues of a reference sequence after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity (e.g., gaps can be introduced in one or both of the candidate and reference sequences for optimal alignment and non-homologous sequences can be disregarded for comparison purposes). Alignment for purposes of determining percent sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software, such as BLAST, ALIGN, or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. For example, a reference sequence aligned for comparison with a candidate sequence may show that the candidate sequence exhibits from 50% to 100% sequence identity across the full length of the candidate sequence or a selected portion of contiguous amino acid (or nucleic acid) residues of the candidate sequence. The length of the candidate sequence aligned for comparison purposes may be, for example, at least 30%, (e.g., 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%) of the length of the reference sequence. When a position in the candidate sequence is occupied by the same amino acid residue as the corresponding position in the reference sequence, then the molecules are identical at that position.
As used herein, the term “primatized antibody” refers to an antibody comprising framework regions from primate-derived antibodies and other regions, such as CDRs and constant regions, from antibodies of a non-primate source. Methods for producing primatized antibodies are known in the art. See e.g., U.S. Pat. Nos. 5,658,570; 5,681,722; and 5,693,780; incorporated herein by reference.
As used herein, the term “operatively linked” in the context of a polynucleotide fragment is intended to mean that the two polynucleotide fragments are joined such that the amino acid sequences encoded by the two polynucleotide fragments remain in-frame.
As used herein, the term “pharmacokinetic profile” refers to the absorption, distribution, metabolism, and clearance of a drug (e.g., an antibody) over time following administration of the drug to a patient.
As used herein, the term “regulatory sequence” includes promoters, enhancers and other expression control elements (e.g., polyadenylation signals) that control the transcription or translation of the antibody chain genes. Such regulatory sequences are described, for example, in Goeddel, Gene Expression Technology: Methods in Enzymology 185 (Academic Press, San Diego, Calif., 1990); incorporated herein by reference.
As used herein, the term “scFv” refers to a single chain Fv antibody in which the variable domains of the heavy chain and the light chain from an antibody have been joined to form one chain. scFv fragments contain a single polypeptide chain that includes the variable region of an antibody light chain (VL) (e.g., CDR-L1, CDR-L2, and/or CDR-L3) and the variable region of an antibody heavy chain (VH) (e.g., CDR-H1, CDR-H2, and/or CDR-H3) separated by a linker. The linker that joins the VL and VH regions of a scFv fragment can be a peptide linker composed of proteinogenic amino acids. Alternative linkers can be used to so as to increase the resistance of the scFv fragment to proteolytic degradation (e.g., linkers containing D-amino acids), in order to enhance the solubility of the scFv fragment (e.g., hydrophilic linkers such as polyethylene glycol-containing linkers or polypeptides containing repeating glycine and serine residues), to improve the biophysical stability of the molecule (e.g., a linker containing cysteine residues that form intramolecular or intermolecular disulfide bonds), or to attenuate the immunogenicity of the scFv fragment (e.g., linkers containing glycosylation sites). scFv molecules are known in the art and are described, e.g., in U.S. Pat. No. 5,892,019; Flo et al., (Gene 77:51, 1989); Bird et al., (Science 242:423, 1988); Pantoliano et al., (Biochemistry 30:10117, 1991); Milenic et al., (Cancer Research 51:6363, 1991); and Takkinen et al., (Protein Engineering 4:837, 1991). The VL and VH domains of an scFv molecule can be derived from one or more antibody molecules. It will also be understood by one of ordinary skill in the art that the variable regions of the scFv molecules of the invention can be modified such that they vary in amino acid sequence from the antibody molecule from which they were derived. For example, in one embodiment, nucleotide or amino acid substitutions leading to conservative substitutions or changes at amino acid residues can be made (e.g., in CDR and/or framework residues). Alternatively or in addition, mutations are made to CDR amino acid residues to optimize antigen-binding using art-recognized techniques. ScFv fragments are described, for example, in WO 2011/084714; incorporated herein by reference.
As used herein, a small modular immunopharmaceutical (SMIP) protein refers to a protein that contains one or more of the following immunoglobulin domains: an antigen-binding domain, an immunoglobulin hinge region or a domain derived there from, an immunoglobulin heavy chain CH2 constant region or a domain derived there from, and an immunoglobulin heavy chain CH3 constant region or a domain derived there from. Polypeptides containing one or more of these domains can be obtained using methods known in the art or described herein, e.g., by recombinant expression of a polynucleotide encoding one or more of these domains or by chemical synthesis techniques (e.g., solid phase peptide synthesis, see Solid Phase Peptide Synthesis, 2nd ed., 1984 The Pierce Chemical Co., Rockford, 111; the disclosure of which is incorporated herein by reference in its entirety).
As used herein, the phrase “specifically binds” refers to a binding reaction which is determinative of the presence of an antigen in a heterogeneous population of proteins and other biological molecules that is recognized, e.g., by an antibody or antigen-binding fragment thereof, with particularity. An antibody or antigen-binding fragment thereof that specifically binds to an antigen will bind to the antigen or an epitope(s) thereof with a KD of less than 100 nM (e.g., between 1 pM and 100 nM). An antibody or antigen-binding fragment thereof that does not exhibit specific binding to a particular antigen or epitope thereof will exhibit a KD of greater than 100 nM (e.g., greater than 500 nM, 1 μM, 100 μM, 500 μM, or 1 mM) for that particular antigen or epitope thereof. A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein or carbohydrate. For example, solid-phase ELISA immunoassays are routinely used to select antibodies specifically immunoreactive with a protein or carbohydrate. See, e.g., Harlow & Lane, Antibodies, A Laboratory Manual, Cold Spring Harbor Press, New York (1988); and Harlow & Lane, Using Antibodies, A Laboratory Manual, Cold Spring Harbor Press, New York (1999), for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity.
As used herein, the terms “subject” and “patient” refer to an organism that receives treatment (e.g., by administration of an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention) for a particular disease or condition as described herein (such as an immunological disorder, e.g., an autoimmune disease). Examples of subjects and patients include mammals, such as humans, primates, pigs, goats, rabbits, hamsters, cats, dogs, guinea pigs, members of the bovidae family (such as cattle, bison, buffalo, and yaks, among others), cows, sheep, horses, and bison, among others, receiving treatment for diseases or conditions, for example, immunological disorders, such as autoimmune disorders, graft-versus-host disease, allograft rejection, allergic reactions, and asthma, among others. A patient that is eligible for treatment with the compositions and methods of the invention may have an established disease (e.g., an established immunological disorder, such as an autoimmune disease), in which case the patient has been diagnosed as having the disease and has shown symptoms of the disease for a prolonged period of time (e.g., over the course of days, weeks, months, or years). Alternatively, a patient may be symptomatic for a particular disease, such as an immunological disorder described herein, but has yet to be diagnosed with the disease by a physician. Other patients eligible for treatment with the compositions and methods of the invention include those that have been diagnosed as having an immunological disorder, and may or may not be showing symptoms of the disease as of yet. For example, a patient eligible for treatment with the compositions and methods of the invention may be described as diagnosed but asymptomatic if the patient has received a diagnosis of an immunological disorder, such as multiple sclerosis, e.g., by detection of depleted myelin sheath around one or more neurons of the patient due to the activity of autoreactive T-cells, even though the patient may not yet be showing symptoms of multiple sclerosis (e.g., lack of balance, reduced cognitive performance, blurred vision, or attenuated coordination, among others). Another example of a patient that has been diagnosed with an immunological condition but is asymptomatic as of yet includes a patient that has been diagnosed with rheumatoid arthritis, e.g., by the detection of autoreactive T-cells in a lymph sample isolated from the patient, even though the patient has not yet presented with the symptoms associated with this disease, such as joint pain, joint stiffness, and a decrease in the muscle range or movement, among others.
As used herein, the terms “tumor necrosis factor receptor superfamily,” “TNFR superfamily,” or “TNFRSF” refer to a group of type I transmembrane proteins, with a carboxy-terminal intracellular domain and an amino-terminal extracellular domain characterized by a common cysteine rich domain (CRD). The TNFR superfamily includes receptors that mediate cellular signaling as a consequence of binding to one or more ligands in the TNF superfamily. The TNFR superfamily can be divided into two subgroups: receptors containing the intracellular death domain and those lacking this domain. The death domain is an 80 amino acid motif that propagates apoptotic signal transduction cascades following receptor activation. Exemplary TNFR super family members that contain the intracellular death domain include TNFR1, while TNFR2 represents a TNFR super family protein that does not contain this domain. Members of the TNFR superfamily include TNFR1, TNFR2, RANK, CD30, CD40, Lymphotoxin beta receptor (LT-PR), OX40, Fas receptor, Decoy receptor 3, CD27, 4-1 BB, Death receptor 4, Death receptor 5, Decoy receptor 1, Decoy receptor 2, Osteoprotegrin, TWEAK receptor, TACI, BAFF receptor, Herpesvirus entry mediator, Nerve growth factor receptor, B-cell maturation antigen, Glucocorticoid-induced TNFR-related, TROY, Death receptor 6, Death receptor 3, and Ectodysplasin A2 receptor.
As used herein, the term “transfection” refers to any of a wide variety of techniques commonly used for the introduction of exogenous DNA into a prokaryotic or eukaryotic host cell, e.g., electroporation, heat shock, lipofection, calcium phosphate precipitation, DEAE-dextran transfection and the like.
As used herein, the terms “treat” or “treatment” refer to therapeutic treatment, in which the object is to inhibit or slow down (lessen) an undesired physiological change or disorder, such as an immunological disorder (e.g., autoimmune disease, allergic reaction, graft-versus-host disease, or allograft rejection). Beneficial or desired clinical results of treatment include, without limitation, alleviation of symptoms, diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, and remission (whether partial or total), whether detectable or undetectable. Those in need of treatment include those already with the condition or disorder, as well as those prone to have the condition or disorder or those in which the condition or disorder is to be inhibited.
As used herein the term “variable region CDR” includes amino acids in a CDR or complementarity determining region as identified using sequence- or structure-based methods. As used herein, the term “CDR” or “complementarity determining region” refers to the noncontiguous antigen-binding sites found within the variable regions of both heavy and light chain polypeptides. These particular regions have been described by Kabat et al., J. Biol. Chem. 252:6609-6616 (1977); Kabat, et al., Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242, 1991; Chothia et al., J. Mol. Biol. 196:901-917 (1987); and by MacCallum et al., J. Mol. Biol. 262:732-745 (1996); the disclosures of each of which are incorporated herein by reference. For agonistic TNFR2 antibodies of the invention, a CDR, as defined by Kabat, may be based on sequence comparisons.
As used herein, the term “vector” includes a nucleic acid vector, e.g., a DNA vector, such as a plasmid, a RNA vector, virus or other suitable replicon (e.g., viral vector). A variety of vectors have been developed for the delivery of polynucleotides encoding exogenous proteins into a prokaryotic or eukaryotic cell. Examples of such expression vectors are disclosed in, e.g., WO 1994/11026, the disclosure of which is incorporated herein by reference. Expression vectors of the invention contain a polynucleotide sequence, as well as, e.g., additional sequence elements used for the expression of proteins and/or the integration of these polynucleotide sequences into the genome of a cell, such as a mammalian cell (e.g., a human cell). Vectors that can be used for the expression of antibodies and antibody fragments of the invention include plasmids that contain regulatory sequences, such as promoter and enhancer regions, which direct gene transcription. Other useful vectors for expression of antibodies and antibody fragments contain polynucleotide sequences that enhance the rate of translation of these genes or improve the stability or nuclear export of the mRNA that results from gene transcription. These sequence elements include, e.g., 5′ and 3′ untranslated regions, an internal ribosomal entry site (IRES), and polyadenylation signal site in order to direct efficient transcription of the gene carried on the expression vector. The expression vectors of the invention may also contain a polynucleotide encoding a marker for selection of cells that contain such a vector. Examples of a suitable marker include genes that encode resistance to antibiotics, such as ampicillin, chloramphenicol, kanamycin, or nourseothricin.
As used herein, the term “VH” refers to the variable region of an immunoglobulin heavy chain of an antibody, including, e.g., the heavy chain of an Fv, scFv, Fab, F(ab′)2, Fd, scFv, SMIP, diabody, triabody, affibody, or nanobody. References to “VL” refer to the variable region of an immunoglobulin light chain, including, e.g., the light chain of an Fv, scFv, Fab, F(ab′)2, Fd, scFv, SMIP, diabody, triabody, affibody, or nanobody. Antibodies and immunoglobulins are glycoproteins having the same structural characteristics. While antibodies exhibit binding specificity to a specific target, immunoglobulins include both antibodies and other antibody-like molecules which lack target specificity. Native antibodies and immunoglobulins are typically heterotetrameric glycoproteins of about 150,000 Daltons, composed of two identical light (L) chains and two identical heavy (H) chains. Each heavy chain of a native antibody has at the amino terminus a variable domain (VH) followed by a number of constant domains. Each light chain of a native antibody has a variable domain at the amino terminus (VL) and a constant domain at the carboxy terminus.
Agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention potentiate the activation of TNFR2 by binding this receptor (e.g., on the exterior surface of a T-reg cell) and inducing a TNFR2-mediated signal transduction cascade. Agonistic TNFR2 antibodies may promote TNFR2 signaling by nucleating a trimer of TNFR2 proteins at the T-reg cell surface. This is the spatial configuration induced by binding of TNFR2 to its cognate ligand, TNFα. This trimerization event brings individual TNFR2 proteins into close proximity and initiates signaling via the MAPK/NFκB/TRAF2/3 pathway, which ultimately leads to cell growth and escape from apoptosis. Agonistic TNFR2 antibodies of the invention may emulate the TNFR2-TNFα interaction by binding the receptor and triggering this structural change.
Antibodies or antigen-binding fragments thereof of the invention can be used to promote the proliferation of a population of T-reg cells and thus enhance the immunomodulatory activity of these cells. Agonistic TNFR2 antibodies and antigen-binding fragments thereof can therefore be used to attenuate an aberrant cell-mediated or humoral immune response associated with a variety of human diseases, such as autoimmune disorders, asthma, allergic reactions, and diseases associated with allograft tolerance. For instance, agonistic TNFR2 antibodies of the invention may be administered to suppress cytotoxic T-cell and B-cell activity, thereby attenuating the response of a patient to a self or benign antigen. Agonistic TNFR2 antibodies and antigen-binding fragments thereof can be administered to a mammalian subject, such as a human (e.g., by any of a number of routes of administration described herein) in order to attenuate an aberrant immune response, such as a response against a self or non-threatening antigen. Alternatively, agonistic TNFR2 antibodies of the invention can be used to expand a population of T-reg cells ex vivo that have been extracted, e.g., from a patient or an MHC-matched donor. After inducing proliferation of these T-reg cells in culture by treatment with an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention, these cells can subsequently be administered to a patient, e.g., using standard cellular administration techniques known in the art or described herein. In this way, agonistic TNFR2 antibodies of the invention may synergize with existing techniques to suppress humoral and cell-mediated immune responses as a treatment modality for patients suffering from a variety of immunological disorders.
Agonistic TNFR2 AntibodiesAgonistic TNFR2 antibodies of the invention include antigen-binding fragments, such as an scFv, Fab, F(ab′)2, diabody, triabody, or antibody-like scaffold protein as described above, and may be of any immunoglobulin subtype, such as IgG, IgM, IgA, IgD, and IgE. The anti-TNFR2 antibodies of the invention are capable of interacting with and promoting signal transduction events mediated by TNFR2. Thus, the TNFR2 antibodies of the invention can selectively potentiate TNFR2-mediated T-reg cell growth. Without being limited to any particular mechanism, this phenotype may be achieved due to the ability of an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention to induce conformational changes within TNFR2 that lead to receptor trimerization. This spatial configuration has been shown to render TNFR2 active for MAPK/TRAF 2/3 signal transduction, which subsequently leads to activation of NFκB-mediated transcription of genes involved in T-reg cell growth and escape from apoptosis (Faustman, et al., Nat. Rev. Drug Disc., 9:482-493 (2010), the disclosure of which is incorporated herein by reference).
Agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention may be capable of inducing the proliferation of a population of T-reg cells, (e.g., levels of CD4+, CD25+, FOXP3+ T cells) e.g., by 0.00001 to 100.0% (e.g., 0.00001%, 0.00002%, 0.00003%, 0.00004%, 0.00005%, 0.00006%, 0.00007%, 0.00008%, 0.00009%, 0.0001%, 0.0002%, 0.0003%, 0.0004%, 0.0005%, 0.0006%, 0.0007%, 0.0008%, 0.0009%, 0.001%, 0.002%, 0.003%, 0.004%, 0.005%, 0.006%, 0.007%, 0.008%, 0.009%, 0.01%, 0.02%, 0.03%, 0.04%, 0.05%, 0.06%, 0.07%, 0.08%, 0.09%, 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.6%, 0.7%, 0.8%, 0.9%, 1.0%, 2.0%, 3.0%, 4.0%, 5.0%, 6.0%, 7.0%, 8.0%, 9.0%, 10.0%, 20.0%, 30.0%, 40.0%, 50.0%, 60.0%, 70.0%, 80.0%, 90.0%, or 100%), e.g., in vivo in a subject administered the antibody or antigen-binding fragment thereof, or in vitro in a sample containing the T-reg cells that are contacted with the antibody or antigen-binding fragment thereof, as measured, e.g., by FACS analysis, relative to a subject or sample containing a population of cells not treated with an agonistic TNFR2 antibody or fragment thereof of the invention.
Agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention can therefore be used to promote T-reg cell proliferation and can be administered to a mammalian subject, such as a human patient, with an autoimmune disorder, in order to attenuate the magnitude and duration of an immune response (e.g., quantity of CD8+ cytotoxic T lymphocytes produced in vivo in response to a self or non-threatening foreign antigen) in the patient. For instance, administration of an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention to a human patient, or a population of T-reg cells expanded ex vivo by treatment with the antibody or antigen-binding fragment thereof of the invention, can cause a reduction in the amount of secreted immunoglobulin (e.g., IgG) that is cross-reactive with a self or non-threatening antigen, e.g., by 0.00001 mg/mL to 10.0 mg/mL (e.g., 0.00001 mg/mL, 0.0001 mg/mL, 0.001 mg/mL, 0.01 mg/mL, 0.1 mg/mL, 1.0 mg/mL, or 10.0 mg/mL), or by 0.001 to 1.0 mg/mL (e.g., 0.001 mg/mL, 0.005 mg/mL, 0.010 mg/mL, 0.050 mg/mL, 0.10 mg/mL, 0.20 mg/mL, 0.30 mg/mL, 0.40 mg/mL, 0.50 mg/mL, 0.60 mg/mL, 0.70 mg/mL, 0.80 mg/mL, 0.90 mg/mL, or 1.0 mg/mL) relative to a subject not treated with an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention. Additionally or alternatively, agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention may be capable of diminishing cytotoxic T-cell counts (e.g., levels of CD8+ T cells) e.g., by 0.00001 to 100.0% (e.g., 0.00001%, 0.00002%, 0.00003%, 0.00004%, 0.00005%, 0.00006%, 0.00007%, 0.00008%, 0.00009%, 0.0001%, 0.0002%, 0.0003%, 0.0004%, 0.0005%, 0.0006%, 0.0007%, 0.0008%, 0.0009%, 0.001%, 0.002%, 0.003%, 0.004%, 0.005%, 0.006%, 0.007%, 0.008%, 0.009%, 0.01%, 0.02%, 0.03%, 0.04%, 0.05%, 0.06%, 0.07%, 0.08%, 0.09%, 0.1%, 0.2%, 0.3%, 0.4%, 0.5%, 0.6%, 0.7%, 0.8%, 0.9%, 1.0%, 2.0%, 3.0%, 4.0%, 5.0%, 6.0%, 7.0%, 8.0%, 9.0%, 10.0%, 20.0%, 30.0%, 40.0%, 50.0%, 60.0%, 70.0%, 80.0%, 90.0%, or 100%) in a subject as measured, e.g., by FACS analysis relative to a subject not treated with an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention. For instance, an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention can be administered to a subject (e.g., a mammalian subject, such as a human) in order to treat, e.g., an immunological disease described herein. Treatment of a subject in this manner may reduce the quantity of autoreactive CD8+ T-cells within the subject.
Agonistic TNFR2 antibodies of the invention may additionally attenuate the secretion of IFNγ, an immunostimulatory cytokine, in a subject, e.g., by 0.00001 mg/mL to 10.0 mg/mL (e.g., 0.00001 mg/mL, 0.0001 mg/mL, 0.001 mg/mL, 0.01 mg/mL, 0.1 mg/mL, 1.0 mg/mL, or 10.0 mg/mL), or by 0.001 to 1.0 mg/mL (e.g., 0.001 mg/mL, 0.005 mg/mL, 0.010 mg/mL, 0.050 mg/mL, 0.10 mg/mL, 0.20 mg/mL, 0.30 mg/mL, 0.40 mg/mL, 0.50 mg/mL, 0.60 mg/mL, 0.70 mg/mL, 0.80 mg/mL, 0.90 mg/mL, or 1.0 mg/mL) relative to a subject not treated with an agonistic TNFR2 antibody of the invention.
Additionally or alternatively, agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention may be capable of stimulating the transcription of various genes. For instance, an agonistic TNFR2 antibody or antigen-binding fragment thereof may induce the expression of one or more of cIAP2, TRAF2, Etk, VEGFR2, PI3K, Akt, genes encoding proteins involved in the angiogenic pathway, IKK complexes, RIP, NIK, MAP3K, genes encoding proteins involved in the NFkB pathway, NIK, JNK, AP-1, a MEK (e.g., MEK1, MEK7), MKK3, NEMO, IL2R, Foxp3, IL2, TNF, and lymphotoxin (e.g., lymphotoxin α and lymphotoxin β). For instance, an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention may be capable of inducing the transcription of one or more of these genes, thus resulting in an increase in the level of the mRNA transcripts derived from the one or more genes and/or an increase in the level of protein encoded by the one or more genes. The increase in expression of these genes can be detected using established molecular biology techniques known in the art, e.g., by detecting an increase in mRNA levels by Northern blot analysis or reverse-transcription PCT (RT-PCR) methods, or by detecting an increase in protein levels by immunoblot analysis or ELISA-based techniques. Additionally or alternatively, an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention may be capable of promoting the activity of one or more proteins associated with the TNFR2 signal transduction cascade (or related signaling pathways that are activated as a result of TNFR2 signaling). For instance, an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention may be capable of promoting an increase in the phosphorylation of one or more proteins, such as cIAP2, TRAF2, Etk, VEGFR2, PI3K, Akt, genes encoding proteins involved in the angiogenic pathway, IKK complexes, RIP, NIK, MAP3K, genes encoding proteins involved in the NFkB pathway, NIK, JNK, AP-1, a MEK (e.g., MEK1, MEK7), MKK3, NEMO, IL2R, Foxp3, IL2, TNF, and lymphotoxin (e.g., lymphotoxin α and lymphotoxin β). An increase in the phosphorylation of one or more proteins that occurs, e.g., as a result of treatment of a subject or of a sample of cells isolated from a subject can be detected using standard molecular biology techniques known in the art, such as by immunoblot analysis or ELISA-based techniques.
Agonistic TNFR2 antibodies of the invention are capable of discriminating among the members of the tumor necrosis factor receptor superfamily (TNFRSF). Preferred agonistic TNFR2 antibodies and antigen-binding fragments thereof are those that do not specifically bind a TNFRSF member other than TNFR2. The TNFR superfamily includes receptors that mediate cellular signaling as a consequence of binding to one or more ligands in the TNF superfamily. The TNFR superfamily can be divided categorically into two types of receptors on the basis of whether the receptor contains an intracellular death domain, an 80-amino acid motif that propagates apoptotic signal transduction cascades following receptor activation. Exemplary TNFR super family members that contain the intracellular death domain include TNFR1, while TNFR2 represents a TNFR super family protein that does not contain this domain. Members of the TNFR superfamily include TNFR1, TNFR2, RANK, CD30, CD40, Lymphotoxin beta receptor (LT-8R), OX40, Fas receptor, Decoy receptor 3, CD27, 4-1 BB, Death receptor 4, Death receptor 5, Decoy receptor 1, Decoy receptor 2, Osteoprotegrin, TWEAK receptor, TACI, BAFF receptor, Herpesvirus entry mediator, Nerve growth factor receptor, B-cell maturation antigen, Glucocorticoid-induced TNFR-related, TROY, Death receptor 6, Death receptor 3, and Ectodysplasin A2 receptor.
Agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention can be assessed to determine whether they lack specific binding for another TNFR superfamily member using a variety of in vitro binding assays, such as ELISA-based methods. For instance, agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention may specifically bind human TNFR2 or a TNFR2-derived peptide, such as the peptide fragment defined by residues 48-67 of SEQ ID NO: 366 within human TNFR2 (QTAQMCCSKCSPGQHAKVFC, SEQ 10 NO: 346), with an affinity that is, e.g., at least 5-fold greater (e.g., 5-fold greater, 6-fold greater, 7-fold greater, 8-fold greater, 9-fold greater, 10-fold greater, 20-fold greater, 30-fold greater, 40-fold greater, 50-fold greater, 60-fold greater, 60-fold greater, 70-fold greater, 80-fold greater, 90-fold greater, 100-fold greater, 200-fold greater, 300-fold greater, 400-fold greater, 500-fold greater, 600-fold greater, 700-fold greater, 800-fold greater, 900-fold greater, 1,000-fold greater, 2,000-fold greater, 3,000-fold greater, 4,000-fold greater, 5,000-fold greater, 6,000-fold greater, 7,000-fold greater, 8,000-fold greater, 9,000-fold greater, 10,000-fold greater, or more) than the affinity of the same antibody for another TNFR superfamily member. For instance, agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention may bind the peptide defined by SEQ ID NO: 346 with an affinity that is, e.g., 5-fold greater. 6-fold greater, 7-fold greater, 8-fold greater, 9-fold greater, 10-fold greater, 20-fold greater, 30-fold greater, 40-fold greater, 50-fold greater, 60-fold greater, 60-fold greater, 70-fold greater, 80-fold greater, 90-fold greater, 100-fold greater, 200-fold greater, 300-fold greater, 400-fold greater, 500-fold greater, 600-fold greater, 700-fold greater, 800-fold greater, 900-fold greater, 1,000-fold greater, 2,000-fold greater, 3,000-fold greater, 4,000-fold greater, 5,000-fold greater, 6,000-fold greater, 7,000-fold greater, 8,000-fold greater, 9,000-fold greater, or 10,000-fold greater than the affinity of the same antibody for another TNFR superfamily member, such as TNFR1, RANK, CD30, CD40, Lymphotoxin beta receptor (LT-PR), OX40, Fas receptor, Decoy receptor 3, CD27, 4-1 BB, Death receptor 4, Death receptor 5, Decoy receptor 1, Decoy receptor 2, Osteoprotegrin, TWEAK receptor, TACI, BAFF receptor, Herpesvirus entry mediator, Nerve growth factor receptor, B-cell maturation antigen, Glucocorticoid-induced TNFR-related, TROY, Death receptor 6, Death receptor 3, or Ectodysplasin A2 receptor.
Additionally, agonistic TNFR2 antibodies and antigen-binding fragments of the invention may, but preferably do not, bind an epitope containing residues 142-146 of SEQ ID NO: 366 within human TNFR2 (KCRPG, SEQ ID NO: 375). For instance, agonistic TNFR2 antibodies of the invention may bind an epitope containing residues 130-149 of SEQ ID NO: 366 (KQEGCRLCAPLRKCRPGFGV, SEQ ID NO: 357).
Preferred agonistic TNFR2 antibodies and antigen-binding fragments of the invention are those that specifically bind the KCSPG epitope of TNFR2, but do not specifically bind the KCRPG epitope of TNFR2 (i.e., the agonistic TNFR2 antibodies and antigen-binding fragments can distinguish between these two epitopes). For instance, an agonistic TNFR2 antibody or antigen-binding fragment of the invention may bind an epitope containing one or more residues within the KCSPG motif of TNFR2 with an affinity that is, e.g., 5-fold greater, 6-fold greater, 7-fold greater, 8-fold greater, 9-fold greater, 10-fold greater, 20-fold greater, 30-fold greater, 40-fold greater, 50-fold greater, 60-fold greater, 60-fold greater, 70-fold greater, 80-fold greater, 90-fold greater, 100-fold greater, 200-fold greater, 300-fold greater, 400-fold greater, 500-fold greater, 600-fold greater, 700-fold greater, 800-fold greater, 900-fold greater, 1,000-fold greater, 2,000-fold greater, 3,000-fold greater, 4,000-fold greater, 5,000-bold greater, 6,000-fold greater, 7,000-fold greater, 8,000-fold greater, 9,000-fold greater, or 10,000-fold greater than the affinity of the same antibody or antigen-binding fragment for a peptide that contains the KCRPG sequence of human TNFR2 (SEQ ID NO: 375). For example, agonistic TNFR2 antibodies and antigen-binding fragments of the invention may bind an epitope containing one or more residues of the KCSPG motif, such as the peptide defined by residues 48-67 of human TNFR2 (QTAQMCCSKCSPGQHAKVFC, SEQ ID NO: 346) with an affinity that is, e.g., 5-fold greater, 6-fold greater, 7-fold greater, 8-fold greater, 9-fold greater, 10-fold greater, 20-fold greater, 30-fold greater, 40-fold greater, 50-fold greater, 60-fold greater, 60-fold greater, 70-fold greater, 80-fold greater, 90-fold greater, 100-fold greater, 200-fold greater, 300-fold greater, 400-fold greater, 500-fold greater, 600-fold greater, 700-fold greater, 800-fold greater, 900-fold greater, 1,000-fold greater, 2,000-fold greater, 3,000-fold greater, 4,000-fold greater, 5,000-fold greater, 6,000-fold greater, 7,000-fold greater, 8,000-fold greater, 9,000-fold greater, or 10,000-fold greater than the affinity of the same antibody or antigen-binding fragment for a peptide that contains the KCRPG sequence (SEQ ID NO: 375) of human TNFR2, such as a peptide defined by residues 130-149 of SEQ ID NO: 366 (KQEGCRLCAPLRKCRPGFGV, SEQ ID NO: 357).
Specific Binding Properties of Agonistic TNFR2 AntibodiesThe specific binding of an antibody or antibody fragment of the invention to TNFR2 (e.g., human TNFR2) can be determined by any of a variety of established methods. The affinity can be represented quantitatively by various metrics, including the concentration of antibody needed to achieve half-maximal potentiation of TNFR2 signalling in vitro (EC50) and the equilibrium constant (KD) of the antibody-TNFR2 complex dissociation. The equilibrium constant, KD, which describes the interaction of TNFR2 with an antibody or antigen-binding fragment thereof of the invention is the chemical equilibrium constant for the dissociation reaction of a TNFR2-antibody complex into solvent-separated TNFR2 and antibody molecules that do not interact with one another.
Antibodies of the invention are those that specifically bind to TNFR2 with a KD value of less than 100 nM (e.g., 95 nM, 90 nM, 85 nM, 80 nM, 75 nM, 70 nM, 65 nM, 60 nM, 55 nM, 50 nM, 45 nM, 40 nM, 35 nM, 30 nM, 25 nM, 20 nM, 15 nM, 10 nM, 5 nM, 4 nM, 3 nM, 2 nM, or 1 nM). In certain cases, antibodies of the invention are those that specifically bind to TNFR2 with a KD value of less than 1 nM (e.g., 990 pM, 980 pM, 970 pM, 960 pM, 950 pM, 940 pM, 930 pM, 920 pM, 910 pM, 900 pM, 890 pM, 880 pM, 870 pM, 860 pM, 850 pM, 840 pM, 830 pM, 820 pM, 810 pM, 800 pM, 790 pM, 780 pM, 770 pM, 760 pM, 750 pM, 740 pM, 730 pM, 720 pM, 710 pM, 700 pM, 690 pM, 680 pM, 670 pM, 660 pM, 650 pM, 640 pM, 630 pM, 620 pM, 610 pM, 600 pM, 590 pM, 580 pM, 570 pM, 560 pM, 550 pM, 540 pM, 530 pM, 520 pM, 510 pM, 500 pM, 490 pM, 480 pM, 470 pM, 460 pM, 450 pM, 440 pM, 430 pM, 420 pM, 410 pM, 400 pM, 390 pM, 380 pM, 370 pM, 360 pM, 350 pM, 340 pM, 330 pM, 320 pM, 310 pM, 300 pM, 290 pM, 280 pM, 270 pM, 260 pM, 250 pM, 240 pM, 230 pM, 220 pM, 210 pM, 200 pM, 190 pM, 180 pM, 170 pM, 160 pM, 150 pM, 140 pM, 130 pM, 120 pM, 110 pM, 100 pM, 90 pM, 80 pM, 70 pM, 60 pM, 50 pM, 40 pM, 30 pM, 20 pM, 10 pM, 5 pM, or 1 pM).
Antibodies of the invention can also be characterized by a variety of in vitro binding assays. Examples of experiments that can be used to determine the KD or EC50 of a TNFR2 antibody include, e.g., surface plasmon resonance, isothermal titration calorimetry, fluorescence anisotropy, and ELISA-based assays, among others. ELISA represents a particularly useful method for analyzing antibody activity, as such assays typically require minimal concentrations of antibodies. A common signal that is analyzed in a typical ELISA assay is luminescence, which is typically the result of the activity of a peroxidase conjugated to a secondary antibody that specifically binds a primary antibody (e.g., a TNFR2 antibody of the invention). Antibodies of the invention are capable of binding TNFR2 and epitopes derived thereof, such as epitopes containing one or more, or all, of residues 56-60 of SEQ ID NO: 366 within human TNFR2 (KCSPG, SEQ ID NO: 367), as well as isolated peptides derived from TNFR2 that structurally pre-organize various residues in a manner that may simulate the conformation of these amino acids in the native protein. For instance, antibodies of the invention may bind peptides containing one or more, or all, amino acids of this KCSPG motif and one or more additional amino acids of residues 48-67 of SEQ ID NO: 366 within human TNFR2 (SEQ ID NO: 346). Such peptides may pre-dispose one or more residues of the KCSPG motif towards binding an agonistic TNFR2 antibody or antigen-binding fragment thereof, e.g., by selectively presenting a conformation of the KCSPG epitope that is similar to the conformation this epitope exhibits in native human TNFR2. Exemplary peptides capable of stabilizing short sequence motifs include cyclic and bicyclic peptides, e.g., that feature an amide bond between the N- and C-terminal residues of the peptide and/or intramolecular cross-links formed by reaction of a side-chain functional group (e.g., a cysteine thiolate) with a scaffolding molecule (e.g., a multivalent electrophile, such as 2,6-bis(bromomethyl)pyridine or 1,3,5-tris(bromomethyl)benzene). Other intramolecular cross-links, such as olefin-containing linkers formed by ring-closing metathesis, saturated alkyl linkers formed by olefin reduction, disulfide bridges formed by cysteine oxidation, and triazole-containing linkers formed by azide-alkyne cycloaddition reactions are known in the art and can be used to produce a peptide that restricts the conformation of an epitope within TNFR2, such as the KCSPG motif, to that which is presented in the native protein (see, e.g., WO 2014/190257; WO 2008/040833; WO 2012/057624; U.S. Pat. Nos. 7,999,068; and 8,778,844; the disclosures of each of which are incorporated herein by reference).
The binding of an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention to TNFR2 or a constrained peptide containing one or more, or all, of the residues of the KCSPG motif can be quantified, e.g., via an ELISA-based technique. For instance, one can determine whether a TNFR2 antibody binds to a particular epitope within TNFR2 by analyzing the luminescence that occurs upon incubation of an HRP substrate (e.g., 2,2′-azino-di-3-ethylbenzthiazoline sulfonate) with a complex containing an antigen (e.g., a TNFR2-derived peptide) and a TNFR2 antibody when the complex is bound to a HRP-conjugated secondary antibody. For instance, TNFR2 antibodies of the invention may induce a luminescence response of about 150 absorbance units or more when incubated with surface-immobilized antigen and a HRP-conjugated secondary antibody in the presence of an HRP substrate. In certain cases, the luminescence observed can be from about 150 to about 1,400 absorbance units (e.g., 200-1,000 absorbance units, 300-900 absorbance units, or 400-800 absorbance units). In particular cases, the luminescence observed can be from about 150 to about 300 absorbance units (e.g., 150-200 absorbance units or 200-250 absorbance units).
Agonistic TNFR2 Antibodies that Bind TNFR2 from Non-Human Animals
In addition to binding one or more, or all, of the residues of the KCSPG motif, or polypeptides containing the KCSPG motif, agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention also include those that specifically bind epitopes containing the equivalent TNFR2 motif of non-human animals, such as non-human mammals, e.g., in a cow, bison, boar, mouse, or rat, among others. In these non-human mammals, the TNFR2 sequence features a KCPPG motif (SEQ ID NO: 396) in place of a KCSPG motif. Agonistic TNFR2 antibodies and antigen-binding fragments of the invention also include those that are capable of specifically binding epitopes that contain one or more, or all, of the residues KCPPG in TNFR2 derived from a non-human animal. These agonistic TNFR2 antibodies and antigen-binding fragments may be administered, e.g., to non-human mammals.
Sequences within non-human TNFR2 that are equivalent to the KCSPG motif in human TNFR2 are shown in Table 2 below.
Agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention may be capable of binding epitopes surrounding the KCPPG motif in TNFR2 derived from non-human animals. For instance, agonistic TNFR2 antibodies and antigen-binding fragments thereof may be capable of binding epitopes such as QKIQMCCSKCPPGYRVQSLC in TNFR2 derived from cattle (SEQ ID NO: 402), HKIQMCCSKCPPGYRVQSLC in TNFR2 derived from bison (SEQ ID NO: 403), TKAQMCCSKCPPGFRIQTSC in TNFR2 derived from boar (SEQ ID NO: 404), RKAQMCCAKCPPGQYVKHFC in TNFR2 derived from a mouse (SEQ ID NO: 405), and/or KKAQMCCAKCPPGQYAKHFC in TNFR2 derived from a rat (SEQ ID NO: 406), as well as sequences that exhibit at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 99%, or 100% sequence identity) to these sequences and epitopes that contain conservative amino acid substitutions relative to these sequences (e.g., so long as the amino acids KCPPG are present in the epitope).
Agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention may be capable of binding epitopes surrounding downstream of the KCPPG motif in TNFR2 derived from non-human animals. For instance, agonistic TNFR2 antibodies and antigen-binding fragments thereof may be capable of binding epitopes such as SSDQVET in TNFR2 derived from cattle, bison, and boar (SEQ ID NO: 368), TTDQVEI in TNFR2 derived from mice (SEQ ID NO: 407), and/or SDDQVET in TNFR2 derived from rats (SEQ ID NO: 408), as well as sequences that exhibit at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 99%, or 100% sequence identity) to these sequences and epitopes that contain conservative amino acid substitutions relative to these sequences.
Agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention may be capable of binding additional epitopes downstream of the KCPPG motif in TNFR2 derived from non-human animals. For instance, agonistic TNFR2 antibodies and antigen-binding fragments thereof may be capable of binding epitopes such as TTKQNRICTCKPGWYCTLGRQEGCRLCVALRKCGPGFGVA in TNFR2 derived from cattle and bison (SEQ ID NO: 409), TPKQNRICSCKPGWYCTLGRQEGCRLCMALRKCSPGFGVT in TNFR2 derived from boar (SEQ ID NO: 410), TKQQNRVCACEAGRYCALKTHSGSCRQCMRLSKCGPGFGVA in TNFR2 derived from mice (SEQ ID NO: 411), and/or TKKQNRVCACNADSYCALKLHSGNCRQCMKLSKCGPGFGVA in TNFR2 derived from rats (SEQ ID NO: 412), as well as sequences that exhibit at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 99%, or 100% sequence identity) to these sequences and epitopes that contain conservative amino acid substitutions relative to these sequences.
In certain cases, agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention are capable of specifically binding epitopes that contain one or more, or all of the residues KCPPG in TNFR2 derived from a non-human animal and do not specifically bind a member of the TNFR superfamily other than TNFR2 (e.g., TNFR1, RANK, CD30, CD40, Lymphotoxin beta receptor (LT-PR), OX40, Fas receptor, Decoy receptor 3, CD27, 4-1 BB, Death receptor 4, Death receptor 5, Decoy receptor 1, Decoy receptor 2, Osteoprotegrin, TWEAK receptor, TACI, BAFF receptor, Herpesvirus entry mediator, Nerve growth factor receptor, B-cell maturation antigen, Glucocorticoid-induced TNFR-related, TROY, Death receptor 6, Death receptor 3, and Ectodysplasin A2 receptor).
Additionally or alternatively, agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention for use in non-human mammals are capable of specifically binding epitopes containing one or more, or all, of the residues KCPPG in TNFR2 derived from a non-human animal, but do not specifically bind an epitope in TNFR2 derived from a non-human animal containing a sequence equivalent to the KCRPG motif present in human TNFR2 (e.g., KCGPG or KCSPG, see Table 3 and sequence alignment below).
Sequences in TNFR2 derived from a non-human animal that are equivalent to the KCRPG motif in human TNFR2 include the KCGPG motif (SEQ ID NO: 413) in cattle, bison, mice, and rats. The sequence in TNFR2 derived from a boar that is equivalent to KCRPG found in human TNFR2 is KCSPG, located at amino acids 144-148 within boar TNFR2. Sequences within TNFR2 derived from non-human animals that are equivalent to the KCRPG motif in human TNFR2 are shown in Table 3 below.
Epitopes within TNFR2 derived from the non-human mammals discussed above that may be bound by agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention are summarized in the sequence alignment below. This sequence alignment shows partial sequences of TNFR2 derived from human, cattle, bison, boar, mouse, and rat, as well as epitopes (shown in bold font) that may be bound by agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention.
In addition to the thermodynamic parameters of a TNFR2-antibody interaction, it is also possible to quantitatively characterize the kinetic association and dissociation of an antibody or antibody fragment of the invention with TNFR2. This can be done by monitoring the rate of antibody-antigen complex formation according to established procedures. For example, one can use surface plasmon resonance (SPR) to determine the rate constants for the formation (kon) and dissociation (koff) of an antibody-TNFR2 complex. These data also enable calculation of the equilibrium constant of (KD) of antibody-TNFR2 complex dissociation, since the equilibrium constant of this unimolecular dissociation can be expressed as the ratio of the koff to kon values. SPR is a technique that is particularly advantageous for determining kinetic and thermodynamic parameters of receptor-antibody interactions since the experiment does not require that one component be modified by attachment of a chemical label. Rather, the receptor is typically immobilized on a solid metallic surface which is treated in pulses with solutions of increasing concentrations of antibody. Antibody-receptor binding induces distortion in the angle of reflection of incident light at the metallic surface, and this change in refractive index over time as antibody is introduced to the system can be fit to established regression models known in the art in order to calculate the association and dissociation rate constants of an antibody-receptor interaction.
Antibodies of the invention exhibit high kon and low koff values upon interaction with TNFR2, consistent with high-affinity receptor binding. For example, antibodies of the invention may exhibit kon values in the presence of TNFR2 of greater than 104 M−1s−1 (e.g., 1.0×104 M−1s−1, 1.5×104 M−1s−1, 2.0×104 M−1s−1, 2.5×104 M−1s−1, 3.0×104 M−1s−1, 3.5×104 M−1s−1, 4.0×104 s 4.5×104 M−1s−1, 5.0×104 M−1s−1, 5.5×104 M−1s−1, 6.0×104 M−1s−1, 6.5×104 M−1s−1, 7.0×104 M−1s−1, 7.5×104 M−1s−1, 8.0×104 M−1s−1, 8.5×104 M−1s−1, 9.0×104 M−1s−1, 9.5×104 M−1s−1, 1.0×105 M−1s−1, 1.5×105 M−1s−1, 2.0×105 M−1s−1, 2.5×105 M−1s−1, 3.0×105 M−1s−1, 3.5×105 M−1s−1, 4.0×105 M−1s−1, 4.5×105 M−1s−1, 5.0×105 M−1s−1, 5.5×105 M−1s−1, 6.0×105 M−1s−1, 6.5×105 M−1s−1, 7.0×105 M−1s−1, 7.5×105 M−1s−1, 8.0×105 M−1s−1, 8.5×105 M−1s−1, 9.0×105 M−1s−1, 9.5×105 M−1s−1, or 1.0×106 M−1s−1). Antibodies of the invention exhibit low koff values when bound to TNFR2, since antibodies are capable of interacting with distinct TNFR2 epitopes containing one or more of residues 56-60 of SEQ ID NO: 366 within human TNFR2 with a high affinity. Epitopes containing one or more of these residues form strong intermolecular contacts with agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention, which serve to slow the dissociation of the antibody-TNFR2 complex. This high receptor affinity is manifested in low koff values. For instance, antibodies of the invention may exhibit koff values of less than 10−3s−1 when complexed to TNFR2 (e.g., 1.0×10−3s−1, 9.5×10−4s−1, 9.0×10−4s−1, 8.5×10−4s−1, 8.0×10−4s−1, 7.5×10−4s−1, 7.0×10−4s−1, 6.5×10−4 s−1, 6.0×10−4s−1, 5.5×10−4 s−1, 5.0×10−4s−1, 4.5×10−4 s−1, 4.0×10−4s−1, 3.5×10−4s−1, 3.0×10−4s−1, 2.5×10−4s−1, 2.0×10−4s−1, 1.5×10−4s−1, 1.0×10−4s−1, 9.5×10−5s−1, 9.0×10−5s−1, 8.5×10−5s−1, 8.0×10−5s−1, 7.5×10−5s−1, 7.0×10−5s−1, 6.5×10−5s−1, 6.0×10−5s−1, 5.5×10−5s−1, 5.0×10−5s−1, 4.5×10−5s−1, 4.0×10−5 s−1, 3.5×10−5s−1, 3.0×10−5 s−1, 2.5×10−5s−1, 2.0×10−5 s−1, 1.5×10−5 s−1, or 1.0×10−5s−1).
Epitopes within TNFR2 Bound by Agonistic TNFR2 Antibodies
The high affinities of antibodies of the invention for TNFR2 coupled with the rapid onset of antibody-TNFR2 complex formation and the slow dissociation of these complexes render these antibodies well-suited for therapeutic applications as activators of T-reg cell proliferation. The high kon values, for instance, indicate that antibodies of the invention are capable of localizing to the surface of a TNFR2-expressing cell (e.g., a T-reg cell) and rapidly associating with TNFR2, thereby inducing receptor activation, e.g., in a fashion similar to that of TNFα. Moreover, the slow dissociation of the antibody-TNFR2 complex can be indicative of a long half-life of the complex in vivo, which results in stable, sustained up-regulation of the growth of the TNFR2-expressing cell (e.g., sustained up-regulation of T-reg growth, such as a CD4+, CD25+, FOXP3+ T-cell). These ideal thermodynamic and kinetic parameters of TNFR2 binding are consistent with the strong intermolecular contacts that are established upon association of antibodies and antibody fragments of the invention with TNFR2.
Among the difficulties in developing TNFR2 antibodies that are capable of inducing TNFR2 signal transduction stimulating the propagation of T-reg cells has been the elucidation of epitopes within TNFR2 that promote agonistic receptor-binding. Particular, discrete peptide fragments found within the TNFR2 primary structure may bind agonistic antibodies of the invention by virtue of the spatial orientation of these residues in the native conformation of the receptor. Significantly, these residues have been difficult to identify, as many isolated linear TNFR2-derived peptides do not appear to interact with agonistic TNFR2 antibodies due to the different conformations these peptides exhibit when structurally pre-organized within the full-length protein and when isolated in solution. Epitope mapping analysis using linear peptides, as well as constrained cyclic and bicyclic peptides, derived from various regions of TNFR2 indicates that agonistic TNFR2 antibodies of the invention bind epitopes from distinct regions of the TNFR2 amino acid sequence, and may bind these epitopes in a conformation-dependent manner. Particularly important epitopes that bind agonistic TNFR2 antibodies of the invention and promote receptor activation are those that contain one or more, or all, of the residues of the KCSPG motif (SEQ ID NO: 367), located at positions 56-60 of SEQ ID NO: 366 within human TNFR2. One or more of these residues may reside within larger epitopes, such as residues 48-67 of SEQ ID NO: 366, which may interact with agonistic TNFR2 antibodies of the invention. The knowledge of those residues that selectively bind TNFR2 antibodies in a manner that promotes receptor activation, and thus, T-reg cell proliferation, can be used to identify and design a wide array of agonistic TNFR2 antibodies and antigen-binding fragments thereof using library screening techniques, such as those described herein or known in the art. For instance, structurally rigidified peptides containing one or more, or all, of the residues within the KCSPG sequence (e.g., a cyclic or bicyclic peptide that presents the KCSPG motif in a conformation similar to that observed in native human TNFR2) can be used to screen and select for antibodies, antigen-binding fragments, and antibody-like scaffolds that bind these epitopes with high affinity and selectivity.
Several distinct residues within TNFR2 bind agonistic TNFR2 antibodies and antibody fragments of the invention and establish strong intermolecular contacts with these antibodies. Notably, functional agonistic TNFR2 antibodies and antibody fragments of the invention selectively bind an epitope containing one or more, or all, of amino acids 56-60 of SEQ ID NO: 366 within human TNFR2 (KCSPG, SEQ ID NO: 367). The spatial orientation of this epitope is shown in
In addition to interacting with the KCSPG motif (SEQ ID NO: 367), agonistic TNFR2 antibodies of the invention may also specifically bind an epitope within human TNFR2 that includes at least five continuous or discontinuous residues from positions 96-154 of SEQ ID NO: 366 within human TNFR2 (CGSRCSSDQVETQACTREQNRICTCRPGWYCALSKQEGCRLCAPLRKCRPSFGVARPGT, SEQ ID NO: 371), as well as epitopes that exhibit at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 99%, or 100% sequence identity) to this sequence and epitopes that contain conservative amino acid substitutions relative to this sequence.
Agonistic TNFR2 antibodies of the invention may also specifically bind an epitope containing at least five continuous or discontinuous residues from positions 96-112 of SEQ ID NO: 366 within TNFR2 (CGSRCSSDQVETQACTR, SEQ ID NO: 372), or an epitope that exhibits at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 99%, or 100% sequence identity) to this sequence or contains conservative amino acid substitutions relative to this sequence. For example, in certain cases, agonistic TNFR2 antibodies of the invention may specifically bind an epitope that includes one or more residues from positions 101-107 of SEQ ID NO: 366 within TNFR2 (SSDQVET, SEQ ID NO: 368), as well as epitopes that exhibit at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 99%, or 100% sequence identity) to this sequence and epitopes that contain conservative amino acid substitutions relative to this sequence.
Additionally, agonistic TNFR2 antibodies of the invention may specifically bind an epitope containing at least five continuous or discontinuous residues from positions 110-147 of SEQ ID NO: 366 within TNFR2 (CTREQNRICTCRPGWYCALSKQEGCRLCAPLRKCRPGF, SEQ ID NO: 373), or an epitope that exhibits at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 99%, %, or 100% sequence identity) to this sequence or contains conservative amino acid substitutions relative to this sequence. For example, in certain cases, agonistic TNFR2 antibodies of the invention may specifically bind an epitope that includes one or more residues from positions 115-142 of SEQ ID NO: 366 within TNFR2 (NRICTCRPGWYCALSKQEGCRLCAPLRK, SEQ ID NO: 369), as well as epitopes that exhibit at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 99%, %, or 100% sequence identity) to this sequence and epitopes that contain conservative amino acid substitutions relative to this sequence.
Agonistic TNFR2 antibodies of the invention may also specifically bind an epitope containing at least five continuous or discontinuous residues from positions 106-155 of SEQ ID NO: 366 within TNFR2 (ETQACTREQNRICTCRPGWYCALSKQEGCRLCAPLRKCRPGFGVARPGTE, SEQ ID NO: 374), or an epitope that exhibits at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 99%, or 100% sequence identity) to this sequence or contains conservative amino acid substitutions relative to this sequence. For example, in certain cases, agonistic TNFR2 antibodies of the invention may specifically bind an epitope that includes one or more residues from positions 111-150 of SEQ ID NO: 366 within TNFR2 (TREQNRICTCRPGWYCALSKQEGCRLCAPLRKCRPGFGVA, SEQ ID NO: 370), as well as epitopes that exhibit at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 99%, or 100% sequence identity) to this sequence and epitopes that contain conservative amino acid substitutions relative to this sequence.
In certain cases, an agonistic TNFR2 antibody of the invention may bind an epitope that includes one or more residues from positions 122-136 of SEQ ID NO: 366 within TNFR2 (PGWYCALSKQEGCRL, SEQ ID NO: 11), as well as epitopes that exhibit at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 99%, or 100% sequence identity) to this sequence and epitopes that contain conservative amino acid substitutions relative to this sequence.
In addition to binding epitopes within TNFR2 that contain one or more residues of the KCSPG motif, agonistic TNFR2 antibodies of the invention may also bind epitopes containing one or more residues of the KCRPG motif (positions 142-146 within TNFR2, SEQ ID NO: 375). Preferably, however, agonistic TNFR2 antibodies or antigen-binding fragments thereof bind an epitope containing the KCRPG sequence with a KD that is substantially higher (e.g., at least 10-fold higher, 15-fold higher, 20-fold higher, 25-fold higher, 50-fold higher, 100-fold higher, 200-fold higher, 300-fold higher, 400-fold higher, 500-fold higher, 600-fold higher, 700-fold higher, 800-fold higher, 900-fold higher, 1,000-fold higher, or 10,000-fold higher) than that of the same antibody or antigen-binding fragment thereof for an epitope containing the KCSPG sequence. For instance, agonistic TNFR2 antibodies of the invention may bind an epitope containing at least five continuous or discontinuous residues from positions 130-149 of SEQ ID NO: 366 (KQEGCRLCAPLRKCRPGFGV, SEQ ID NO: 357), or an epitope that exhibits at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 99%, or 100% sequence identity) to this sequence or contains conservative amino acid substitutions relative to this sequence. In certain cases, agonistic TNFR2 antibodies of the invention may bind an epitope containing one or more residues from positions 137-144 of SEQ ID NO: 366 (CAPLRKCR, SEQ ID NO: 376) and/or an epitope containing one or more residues from positions 141-149 of SEQ ID NO: 366 (KCRPGFGV; SEQ ID NO: 377), as well as epitopes that exhibit at least 85% sequence identity (e.g., 85%, 90%, 95%, 97%, 99%, or 100% sequence identity) to these sequences and epitopes that contain conservative amino acid substitutions relative to these sequences. In preferred embodiments, agonistic TNFR2 antibodies or antigen-binding fragments thereof do not exhibit specific binding for an epitope containing the KCRPG sequence.
Agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention also include those that can discriminate among members of the TNFR superfamily and specifically bind TNFR2 but do not specifically bind other receptors within this family. For instance, in various embodiments, the invention provides agonistic TNFR2 antibodies that are capable of binding and activating TNFR2 while not exhibiting specific binding for a TNFR superfamily member, such as TNFR1, RANK, CD30, CD40, Lymphotoxin beta receptor (LT-PR), OX40, Fas receptor, Decoy receptor 3, CD27, 4-1BB, Death receptor 4, Death receptor 5, Decoy receptor 1, Decoy receptor 2, Osteoprotegrin, TWEAK receptor, TACI, BAFF receptor, Herpesvirus entry mediator, Nerve growth factor receptor, B-cell maturation antigen, Glucocorticoid-induced TNFR-related, TROY, Death receptor 6, Death receptor 3, and Ectodysplasin A2 receptor.
Agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention include those that are capable of specifically binding an epitope within human TNFR2 containing one or more, or all, or residues 48-67 of SEQ ID NO: 366 (QTAQMCCSKCSPGQHAKVFC, SEQ ID NO: 346), and do not bind any other epitope within TNFR2 or within another TNFR superfamily member. For instance, agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention may specifically bind an epitope within human TNFR2 containing residues 56-60 of SEQ ID NO: 366 (KCSPG, SEQ ID NO: 367) and may not specifically bind any other epitope within TNFR2 or another TNFR superfamily member (e.g., an epitope containing residues 142-146 of human TNFR2 (KCRPG, SEQ ID NO: 375), or an epitope containing the residues KCPPG (SEQ ID NO: 396) of another TNFR superfamily member).
Agonistic TNFR2 Antibody MR2-1One example of an agonistic TNFR2 antibody is MR2-1, which binds TNFR2 and potentiates TNFR2-mediated T-reg cell proliferation (
A representative agonistic TNFR2 antibody of the invention is 8E6.D1, which is a murine antibody that binds TNFR2 and potentiates TNFR2-mediated T-reg cell proliferation (
Agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention exhibit an affinity for TNFR2 that is the same as or similar to that of 8E6.D1. The high affinity of 8E6.D1 for TNFR2 coupled with the rapid formation and the slow dissociation of the 8E6.D1-TNFR2 complex is consistent with the strong intermolecular contacts that underlie this protein-protein interaction. 8E6.D1 binds to distinct epitopes within the primary structure of TNFR2 that are spatially aligned in the native conformation of the receptor. The KCSPG motif (SEQ ID NO: 367) has been identified as a particularly important functional epitope that establishes strong intermolecular contacts with 8E6.D1 as determined by epitope mapping analysis (
Antibodies of the invention include human, humanized, primatized, and chimeric antibodies that contain one or more of the CDRs of 8E6.D1, or a CDR that exhibits at least 85% sequence identity (e.g., 90%, 95%, 97%, 99%, or 100% sequence identity) to any of these CDRs or sequences that contain conservative mutations relative to these CDRs. Antibodies of the invention also include human, humanized, primatized, and chimeric antibodies that contain one or more CDRs that are identical to those of 8E6.D1 except for conservative amino acid substitutions. For example, agonistic TNFR2 antibodies of the invention can be generated by incorporating any of the CDRs of 8E6.D1 into the framework regions (e.g., FR1, FR2, FR3, and FR4) of a human antibody. Exemplary framework regions that can be used for the development of a humanized TNFR2 antibody containing one or more of the CDRs of 8E6.D1 include, without limitation, those described in U.S. Pat. Nos. 7,732,578, 8,093,068, and WO 2003/105782; the disclosures of which are incorporated herein by reference.
One strategy that can be used to design humanized antibodies of the invention is to align the sequences of the heavy chain variable region and light chain variable region of 8E6.D1 with the heavy chain variable region and light chain variable region of a consensus human antibody. Consensus human antibody heavy chain and light chain sequences are known in the art (see e.g., the “VBASE” human germline sequence database; see also Kabat, et al., Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242 (1991); Tomlinson et al., J. Mol. Biol., 227:776-98 (1992); and Cox et al, Eur. J. Immunol., 24:827-836 (1994); the disclosures of each of which are incorporated herein by reference). In this way, the variable domain framework residues and CDRs can be identified by sequence alignment (see Kabat, supra). One can substitute one or more CDRs of the heavy chain and/or light chain variable domains of a consensus human antibody with one or more corresponding CDRs of an agonistic TNFR2 antibody of the invention in order to produce a humanized TNFR2 antibody. Exemplary variable domains of a consensus human antibody include the heavy chain variable domain EVQLVESGGGLVQPGGSLRLSCAASGFTFSDYAMSWVRQAPGKGLEWVAVISENGSDTYYADSVKGR FTISRDDSKNTLYLQMNSLRAEDTAVYYCARDRGGAVSYFDVWGQGTLVTVSS (SEQ ID NO: 378) and the light chain variable domain DIQMTQSPSSLSASVGDRVTITCRASQDVSSYLAWYQQKPGKAPKLLIYAASSLESGVPSRFSGSGSGT DFTLTISSLQPEDFATYYCQQYNSLPYTFGQGTKVEIKRT (SEQ ID NO: 379), identified in U.S. Pat. No. 6,054,297; the disclosure of which is incorporated herein by reference (CDRs are shown in bold were determined according to the method of Chothia, et al., J. Mol. Biol., 196:901-917 (1987), the disclosure of which is incorporated herein by reference). These amino acid substitutions can be made, for example, by recombinant expression of polynucleotides encoding the heavy and light chains of a humanized antibody in a host cell using methods known in the art or described herein. For instance, the heavy chain and light chain CDRs of 8E6.D1 can be inserted into the consensus human antibody heavy and light chain variable domain sequences in place of the CDRs native to these sequences (shown in bold above) in order to produce a humanized agonistic TNFR2 antibody of the invention.
Similarly, this strategy can also be used to produce primatized TNFR2 antibodies, as one can substitute the CDRs of the heavy and/or light chain variable domains of a primate antibody consensus sequence with one or more corresponding CDRs of 8E6.D1. Consensus primate antibody sequences known in the art (see e.g., U.S. Pat. Nos. 5,658,570; 5,681,722; and 5,693,780; the disclosures of each of which are incorporated herein by reference).
In certain cases, it may be desirable to import particular framework residues in addition to CDR sequences from a TNFR2 antibody, such as 8E6.D1, into the heavy and/or light chain variable domains of a human antibody. For instance, U.S. Pat. No. 6,054,297 identifies several instances when it may be advantageous to retain certain framework residues from a particular antibody heavy chain or light chain variable region in the resulting humanized antibody. In certain cases, framework residues may engage in non-covalent interactions with the antigen and thus contribute to the affinity of the antibody for the target antigen. In other cases, individual framework residues may modulate the conformation of a CDR, and thus indirectly influence the interaction of the antibody with the antigen. Alternatively, certain framework residues may form the interface between VH and VL domains, and may therefore contribute to the global antibody structure. In other cases, framework residues may constitute functional glycosylation sites (e.g., Asn-X-Ser/Thr) which may dictate antibody structure and antigen affinity upon attachment to carbohydrate moieties. In cases such as those described above, it may be beneficial to retain certain framework residues of an agonistic TNFR2 antibody (e.g., 8E6.D1) in the resulting humanized or primatized antibodies and antigen-binding fragments thereof of the invention, as various framework residues may promote high epitope affinity and improved biochemical activity of the antibody or antigen-binding fragment thereof.
Antibodies of the invention also include antibody fragments, Fab domains, F(ab′)2 molecules, single chain variable fragments (scFvs), tandem scFv fragments, diabodies, triabodies, dual variable domain immunoglobulins, multi-specific antibodies, bispecific antibodies, SMIP proteins, and heterospecific antibodies that contain one or more of the CDRs of 8E6.D1, or a CDR that exhibits at least 85% sequence identity (e.g., 90%, 95%, 97%, 99%, or 100% sequence identity) to any of these CDRs. Antibodies and antigen-binding fragments thereof of the invention include those that also contain CDRs having between one and three amino acid substitutions (e.g., conservative or nonconservative substitutions) relative to the CDR sequences of 8E6.D1. These molecules can be expressed recombinantly, e.g., by incorporating polynucleotides encoding these proteins into expression vectors for transfection in a eukaryotic or prokaryotic cell using techniques described herein or known in the art, or synthesized chemically, e.g., by solid phase peptide synthesis methods described herein or known in the art.
Antibodies of the invention additionally include antibody-like scaffolds that contain one or more of the CDRs of 8E6.D1, or a CDR that exhibits at least 85% sequence identity (e.g., 90%, 95%, 97%, 99%, or 100% sequence identity) to any of these CDRs or sequences that contain between one and three amino acid substitutions (e.g., conservative or nonconservative substitutions) relative to the CDR sequences of 8E6.D1. Examples of antibody-like scaffolds include proteins that contain a tenth fibronectin type III domain (10Fn3), which contains BC, DE, and FG structural loops analogous to canonical antibodies. It has been shown that the tertiary structure of the 10Fn3 domain resembles that of the variable region of the IgG heavy chain, and one of skill in the art can graft, e.g., the CDRs of 8E6.D1 or sequences containing conserved amino acid substitutions relative to these CDRs onto the fibronectin scaffold by replacing residues of the BC, DE, and FG loops of 10Fn3 with residues of 8E6.D1 CDRs. This can be achieved by recombinant expression of a modified 10Fn3 domain in a prokaryotic or eukaryotic cell (e.g., using the vectors and techniques described herein). Examples of using the 10Fn3 domain as an antibody-like scaffold for the grafting of CDRs from antibodies onto the BC, DE, and FG structural loops are reported in WO 2000/034784; WO 2009/142773; WO 2012/088006; and U.S. Pat. No. 8,278,419; the disclosures of each of which are incorporated herein by reference.
Nucleic Acids and Expression SystemsAgonistic TNFR2 antibodies of the invention can be prepared by any of a variety of established techniques. For instance, an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention can be prepared by recombinant expression of immunoglobulin light and heavy chain genes in a host cell. To express an antibody recombinantly, a host cell can be transfected with one or more recombinant expression vectors carrying DNA fragments encoding the immunoglobulin light and heavy chains of the antibody such that the light and heavy chains are expressed in the host cell and, optionally, secreted into the medium in which the host cells are cultured, from which medium the antibodies can be recovered. Standard recombinant DNA methodologies are used to obtain antibody heavy and light chain genes, incorporate these genes into recombinant expression vectors and introduce the vectors into host cells, such as those described in Molecular Cloning; A Laboratory Manual, Second Edition (Sambrook, Fritsch and Maniatis (eds), Cold Spring Harbor, N. Y., 1989), Current Protocols in Molecular Biology (Ausubel et al., eds., Greene Publishing Associates, 1989), and in U.S. Pat. No. 4,816,397; the disclosures of each of which are incorporated herein by reference.
Vectors for Expression of Agonistic TNFR2 Antibodies and Antibody FragmentsViral genomes provide a rich source of vectors that can be used for the efficient delivery of exogenous genes into the genome of a cell (e.g., a eukaryotic or prokaryotic cell). Viral genomes are particularly useful vectors for gene delivery because the polynucleotides contained within such genomes are typically incorporated into the genome of a target cell by generalized or specialized transduction. These processes occur as part of the natural viral replication cycle, and do not require added proteins or reagents in order to induce gene integration. Examples of viral vectors include a retrovirus, adenovirus (e.g., Ad5, Ad26, Ad34, Ad35, and Ad48), parvovirus (e.g., adeno-associated viruses), coronavirus, negative strand RNA viruses such as orthomyxovirus (e.g., influenza virus), rhabdovirus (e.g., rabies and vesicular stomatitis virus), paramyxovirus (e.g. measles and Sendai), positive strand RNA viruses, such as picornavirus and alphavirus, and double stranded DNA viruses including adenovirus, herpes virus (e.g., Herpes Simplex virus types 1 and 2, Epstein-Barr virus, cytomegalovirus), and poxvirus (e.g., vaccinia, modified vaccinia Ankara (MVA), fowlpox and canarypox). Other viruses useful for delivering polynucleotides encoding antibody light and heavy chains or antibody fragments of the invention include Norwalk virus, togavirus, flavivirus, reoviruses, papovavirus, hepadnavirus, and hepatitis virus, for example. Examples of retroviruses include: avian leukosis-sarcoma, mammalian C-type, B-type viruses, D-type viruses, HTLV-BLV group, lentivirus, spumavirus (Coffin, J. M., Retroviridae: The viruses and their replication, In Fundamental Virology, Third Edition, B. N. Fields, et al., Eds., Lippincott-Raven Publishers, Philadelphia, 1996, the disclosure of which is incorporated herein by reference). Other examples of viral genomes useful in conjunction with the compositions and methods of the invention include murine leukemia viruses, murine sarcoma viruses, mouse mammary tumor virus, bovine leukemia virus, feline leukemia virus, feline sarcoma virus, avian leukemia virus, human T-cell leukemia virus, baboon endogenous virus, Gibbon ape leukemia virus, Mason Pfizer monkey virus, simian immunodeficiency virus, simian sarcoma virus, Rous sarcoma virus, and lentiviruses. Other examples of vectors are described, for example, in U.S. Pat. No. 5,801,030; the disclosure of which is incorporated herein by reference.
Genome Editing TechniquesIn addition to viral vectors, a variety of additional methods have been developed for the incorporation of genes, e.g., those encoding antibody light and heavy chains, single chain variable fragments (scFvs), tandem scFvs, Fab domains, F(ab′)2 domains, diabodies, and triabodies, among others, into the genomes of target cells for antibody expression. One such method that can be used for incorporating polynucleotides encoding agonistic TNFR2 antibodies or antigen-binding fragments thereof into prokaryotic or eukaryotic cells includes transposons. Transposons are polynucleotides that encode transposase enzymes and contain a polynucleotide sequence or gene of interest flanked by excision sites at the 5′ and 3′ positions. Once a transposon has been delivered into a cell, expression of the transposase gene commences and results in active enzymes that cleave the gene of interest from the transposon. This activity is mediated by the site-specific recognition of transposon excision sites by the transposase. In certain cases, these excision sites may be terminal repeats or inverted terminal repeats. Once excised from the transposon, the gene of interest can be integrated into the genome of a prokaryotic or eukaryotic cell by transposase-catalyzed cleavage of similar excision sites that exist within nuclear genome of the cell. This allows the gene encoding a TNFR2 antibody or fragment or domain thereof to be inserted into the cleaved nuclear DNA at the excision sites, and subsequent ligation of the phosphodiester bonds that join the gene of interest to the DNA of the prokaryotic or eukaryotic cell genome completes the incorporation process. In certain cases, the transposon may be a retrotransposon, such that the gene encoding the antibody is first transcribed to an RNA product and then reverse-transcribed to DNA before incorporation in the prokaryotic or eukaryotic cell genome. Exemplary transposon systems include the piggybac transposon (described in detail in WO 2010/085699) and the sleeping beauty transposon (described in detail in US20050112764); the disclosures of each of which are incorporated herein by reference.
Another useful method for the integration of nucleic acid molecules encoding agonistic TNFR2 antibodies or antigen-binding fragments thereof into the genome of a prokaryotic or eukaryotic cell utilizes clustered regularly interspaced short palindromic repeats (CRISPR)/Cas technology, which is derived from a system that originally evolved as an adaptive defense mechanism in bacteria and archaea against infection by viruses. The CRISPR/Cas system consists of palindromic repeat sequences within plasmid DNA and an associated Cas9 nuclease. This ensemble of DNA and protein directs site specific DNA cleavage of a target sequence by first incorporating foreign DNA into CRISPR loci. Polynucleotides containing these foreign sequences and the repeat-spacer elements of the CRISPR locus are in turn transcribed in a host cell to create a guide RNA, which can subsequently anneal to a target sequence and localize the Cas9 nuclease to this site. In this manner, highly site-specific cas9-mediated DNA cleavage can be engendered in a foreign polynucleotide because the interaction that brings cas9 within close proximity of the target DNA molecule is governed by RNA:DNA hybridization. As a result, one can theoretically design a CRISPR/Cas system to cleave any target DNA molecule of interest. This technique has been exploited in order to edit eukaryotic genomes (Hwang et al., Nat. Biotech., 31:227-229 (2013), the disclosure of which is incorporated herein by reference) and can be used as an efficient means of site-specifically editing eukaryotic or prokaryotic genomes in order to cleave DNA prior to the incorporation of a polynucleotide encoding a TNFR2 antibody or antigen-binding fragment thereof of the invention. The use of CRISPR/Cas to modulate gene expression has been described in U.S. Pat. No. 8,697,359; the disclosure of which is incorporated herein by reference.
Alternative methods for site-specifically cleaving genomic DNA prior to the incorporation of a polynucleotide encoding a TNFR2 antibody or antibody fragment of the invention include the use of zinc finger nucleases and transcription activator-like effector nucleases (TALENs). Unlike the CRISPR/Cas system, these enzymes do not contain a guiding polynucleotide to localize to a specific target sequence. Target specificity is instead controlled by DNA binding domains within these enzymes. Zinc finger nucleases and TALENs for use in genome editing applications are described, e.g., in Urnov et al., Nat. Rev. Genet., 11:636-646 (2010); and in Joung et al., Nat. Rev. Mol. Cell. Bio., 14:49-55 (2013); the disclosures of each of which are incorporated herein by reference. Additional genome editing techniques that can be used to incorporate polynucleotides encoding antibodies of the invention into the genome of a prokaryotic or eukaryotic cell include the use of ARCUS™ meganucleases that can be rationally designed so as to site-specifically cleave genomic DNA. The use of these enzymes for the incorporation of polynucleotides encoding agonistic TNFR2 antibodies or antibody fragments of the invention into the genome of a prokaryotic or eukaryotic cell is particularly advantageous in view of the structure-activity relationships that have been established for these enzymes. Single chain meganucleases can thus be modified at certain amino acid positions in order to create nucleases that selectively cleave DNA at desired locations. These single-chain nucleases have been described extensively, e.g., in U.S. Pat. Nos. 8,021,867 and 8,445,251; the disclosures of each of which are incorporated herein by reference.
Polynucleotide Sequence ElementsTo express agonistic TNFR2 antibodies or antibody fragments of the invention, polynucleotides encoding partial or full-length light and heavy chains, e.g., obtained as described above, can be inserted into expression vectors such that the genes are operatively linked to transcriptional and translational control sequences. The expression vector and expression control sequences are chosen to be compatible with the expression host cell used. Polynucleotides encoding the light chain gene and the heavy chain of a TNFR2 antibody can be inserted into separate vectors, or, optionally, both polynucleotides can be incorporated into the same expression vector using established techniques described herein or known in the art.
In addition to polynucleotides encoding the heavy and light chains of an antibody (or a polynucleotide encoding an antibody fragment, such as a scFv molecule), the recombinant expression vectors of the invention may carry regulatory sequences that control the expression of the antibody chain genes in a host cell. The design of the expression vector, including the selection of regulatory sequences, may depend on such factors as the choice of the host cell to be transformed or the level of expression of protein desired. For instance, suitable regulatory sequences for mammalian host cell expression include viral elements that direct high levels of protein expression in mammalian cells, such as promoters and/or enhancers derived from cytomegalovirus (CMV) (such as the CMV promoter/enhancer), Simian Virus 40 (SV40) (such as the SV40 promoter/enhancer), adenovirus, (e.g., the adenovirus major late promoter (AdMLP)) and polyoma. For further description of viral regulatory elements, and sequences thereof, see e.g., U.S. Pat. Nos. 5,168,062; 4,510,245; and 4,968,615; the disclosures of each of which are incorporated herein by reference.
In addition to antibody heavy and light chain genes and regulatory sequences, recombinant expression vectors of the invention may carry additional sequences, such as sequences that regulate replication of the vector in host cells (e.g., origins of replication) and selectable marker genes. A selectable marker gene facilitates selection of host cells into which the vector has been introduced (see e.g., U.S. Pat. Nos. 4,399,216; 4,634,665; and 5,179,017; the disclosures of each of which are incorporated herein by reference). For example, typically the selectable marker gene confers resistance to cytotoxic drugs, such as G418, puromycin, blasticidin, hygromycin or methotrexate, to a host cell into which the vector has been introduced. Suitable selectable marker genes include the dihydrofolate reductase (DHFR) gene (for use in DHFR″ host cells with methotrexate selection/amplification) and the neo gene (for G418 selection). In order to express the light and heavy chains of a TNFR2 antibody or a TNFR2 antibody fragment, the expression vector(s) containing polynucleotides encoding the heavy and light chains can be transfected into a host cell by standard techniques known in the art or described herein.
Polynucleotides Encoding Modified Agonistic TNFR2 Antibodies and Antibody FragmentsIn certain cases, agonistic TNFR2 antibodies or antibody fragments of the invention can be produced that are similar to a particular agonistic TNFR2 antibody but feature differences in the sequence of one or more CDRs. In other cases, the antibodies of the invention may be similar feature differences in one or more framework regions relative to another agonistic TNFR2 antibody. For instance, one or more framework regions of an agonistic TNFR2 antibody derived from a non-human mammal may be substituted with the framework region of a human antibody. Exemplary framework regions include, for example, human framework regions described in U.S. Pat. No. 7,829,086, and primate framework regions as described in EP 1945668; the disclosures of each of which are incorporated herein by reference. Alternatively, antibodies of the invention may be similar to another agonistic TNFR2 antibody but exhibit differences in the sequence of one or more CDRs and differences in one or more framework regions. To generate nucleic acids encoding such agonistic TNFR2 antibodies, DNA fragments encoding, e.g., at least one, or both, of the light chain variable regions and the heavy chain variable regions can be produced by chemical synthesis (e.g., by solid phase polynucleotide synthesis techniques), in vitro gene amplification (e.g., by polymerase chain reaction techniques), or by replication of the polynucleotide in a host organism. For instance, nucleic acids encoding agonistic TNFR2 antibodies of the invention may be obtained by amplification and modification of germline DNA or cDNA encoding light and heavy chain variable sequences so as to incorporate the CDRs of an agonistic TNFR2 antibody into the framework residues of a consensus antibody. This can be achieved, for example, by performing site-directed mutagenesis of germline DNA or cDNA and amplifying the resulting polynucleotides using the polymerase chain reaction (PCR) according to established procedures. Germline DNA sequences for human heavy and light chain variable region genes are known in the art (see, e.g., the “VBASE” human germline sequence database; see also Kabat et al., Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242 (1991); Tomlinson et al., J. Mol. Biol., 227:776-798 (1992); and Cox et al., Eur. J. Immunol., 24:827-836 (1994); the disclosures of each of which are incorporated herein by reference). Additionally, a polynucleotide encoding the heavy or light chain variable region of an agonistic TNFR2 antibody can be synthesized and used as a template for mutagenesis to generate a variant as described herein using routine mutagenesis techniques. Alternatively, a DNA fragment encoding the variant can be directly synthesized (e.g., by established solid phase nucleic acid chemical synthesis procedures).
The isolated DNA encoding the VH region of an agonistic TNFR2 antibody of the invention can be converted to a full-length heavy chain gene (as well as a Fab heavy chain gene) by operatively linking the VH-encoding DNA to another DNA molecule encoding heavy chain constant region domains (CH1, CH2, CH3, and, optionally, CH4). The sequences of human heavy chain constant region genes are known in the art (see e.g., Kabat et al., Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242, 1991, the disclosure of which is incorporated herein by reference) and DNA fragments encompassing these regions can be obtained by standard PCR amplification. The heavy chain constant region can be an IgG1, IgG2, IgG3, IgG4, IgA, IgE, IgM or IgD constant region, but in certain embodiments is an IgG1 constant region. For a Fab fragment heavy chain gene, the VH-encoding DNA can be operatively linked to another DNA molecule encoding only the heavy chain CH1 domain.
The isolated DNA encoding the VL region of an agonistic TNFR2 antibody of the invention can be converted to a full-length light chain gene (as well as a Fab light chain gene) by operatively linking the VL-encoding DNA to another DNA molecule encoding the light chain constant region, CL. The sequences of human light chain constant region genes are known in the art (see e.g., Kabat et al., Sequences of Proteins of Immunological Interest, Fifth Edition (U.S. Department of Health and Human Services, NIH Publication No. 91-3242, 1991)) and DNA fragments encompassing these regions can be obtained, e.g., by amplification in a prokaryotic or eukaryotic cell of a polynucleotide encoding these regions, by PCR amplification, or by chemical polynucleotide synthesis. The light chain constant region can be a kappa (κ) or lambda (A) constant region. To create a scFv gene, the VH and VL-encoding DNA fragments are operatively linked to another fragment encoding a flexible linker, e.g., a polynucleotide encoding a flexible, hydrophilic amino acid sequence, such as the amino acid sequence (Gly4Ser)3, such that the VH and VL sequences can be expressed as a contiguous single-chain protein, with the VL and VH regions joined by the linker (see e.g., Bird et al., Science 242:423-426 (1988); Huston et al., Proc. Natl. Acad. Sci. USA 85:5879-5883 (1988); McCafferty et al., Nature 348:552-554 (1990); the disclosures of each of which are incorporated herein by reference).
Recombinant DNA technology can also be used to remove some or all of the DNA encoding either or both of the light and heavy chains that is not necessary for binding to TNFR2. The molecules expressed from such truncated DNA molecules are also encompassed by the antibodies of the invention. In addition, bifunctional antibodies can be produced in which one heavy and one light chain are derived from an agonistic TNFR2 antibody and the other heavy and light chain are specific for an antigen other than TNFR2. Such antibodies can be generated, e.g., by crosslinking a heavy chain and light chain derived from an agonistic TNFR2 antibody to a heavy chain and light chain of a second antibody by standard chemical crosslinking methods (e.g., by disulfide bond formation). Bifunctional antibodies can also be made by expressing a nucleic acid molecule engineered to encode a bifunctional antibody in a prokaryotic or eukaryotic cell.
In certain cases, dual specific antibodies, i.e., antibodies that bind TNFR2 and a different antigen using the same binding site, can be produced by mutating amino acid residues in the light chain and/or heavy chain CDRs. In various embodiments, dual specific antibodies that bind two antigens, such as TNFR2 and a second cell-surface receptor, can be produced by mutating amino acid residues in the periphery of the antigen-binding site. (Bostrom et al., Science 323: 1610-1614 (2009); the disclosure of which is incorporated herein by reference). Dual functional antibodies can be made by expressing a polynucleotide engineered to encode a dual specific antibody.
Modified agonistic TNFR2 antibodies and antibody fragments of the invention can also be produced by chemical synthesis (e.g., by the methods described in Solid Phase Peptide Synthesis, 2nd ed., 1984 The Pierce Chemical Co., Rockford, 111; the disclosure of which is incorporated herein by reference). Variant antibodies can also be generated using a cell-free synthetic platform (see, e.g., Chu et al., Biochemia No. 2, 2001 (Roche Molecular Biologicals); the disclosure of which is incorporated herein by reference).
The above-described methods can be applied to antibody 8E6.D1 so as to produce an agonistic TNFR2 antibody or antigen-binding fragment thereof with altered properties. For instance, agonistic TNFR2 antibodies of the invention can be based on the heavy chain or light chain amino acid sequences or one or more CDRs of 8E6.D1. Using techniques described herein or known in the art, one can modify one or more amino acid sequences of 8E6.D1, e.g., so as to improve the affinity of the resulting antibody for TNFR2. Full-length antibodies and antibody fragments can also be produced using the amino acid sequences of 8E6.D1 as a starting point for the design of other TNFR2 agonistic antibodies or antigen-binding fragments of the invention. For instance, using standard techniques known in the art, one can produce DNA fragments encoding the VH and/or VL segments of 8E6.D1, e.g., by chemical synthesis or by PCR-based methods. These DNA fragments can be further manipulated by standard recombinant DNA techniques, e.g., to convert the variable region genes to full-length antibody chain genes or to fragment genes, such as those that encode a Fab fragment, F(ab′)2 fragment, scFv, diabody, triabody, or antibody-like scaffold protein. In these manipulations, a VL- or VH-encoding DNA fragment is operatively linked to another DNA fragment encoding another protein, such as an antibody constant region, a flexible linker, or a scaffold protein (e.g., a 10Fn3 domain).
Host Cells for Expression of Agonistic TNFR2 Antibodies and Antibody FragmentsAgonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention may be expressed in either prokaryotic or eukaryotic host cells. In certain embodiments, expression of antibodies or antigen-binding fragments thereof is performed in eukaryotic cells, e.g., mammalian host cells, for optimal secretion of a properly folded and immunologically active antibody. Exemplary mammalian host cells for expressing the recombinant antibodies or antigen-binding fragments thereof of the invention include Chinese Hamster Ovary (CHO cells) (including DHFR CHO cells, described in Urlaub and Chasin, Proc. Natl. Acad. Sci. USA, 77:4216-4220 (1980), used with a DHFR selectable marker, e.g., as described in Kaufman and Sharp, Mol. Biol., 159:601-621, (1982), NSO myeloma cells, COS cells, 293 cells, and SP2/0 cells. Additional cell types that may be useful for the expression of antibodies and fragments thereof include bacterial cells, such as BL-21(DE3) E. coli cells, which can be transformed with vectors containing foreign DNA according to established protocols. Additional eukaryotic cells that may be useful for expression of antibodies include yeast cells, such as auxotrophic strains of S. cerevisiae, which can be transformed and selectively grown in incomplete media according to established procedures known in the art. When recombinant expression vectors encoding antibody genes are introduced into mammalian host cells, the antibodies are produced by culturing the host cells for a period of time sufficient to allow for expression of the antibody in the host cells or secretion of the antibody into the culture medium in which the host cells are grown.
Antibodies can be recovered from the culture medium using standard protein purification methods. Host cells can also be used to produce portions of intact antibodies, such as Fab fragments or scFv molecules. The invention also includes methods in which the above procedure is varied according to established protocols known in the art. For example, it can be desirable to transfect a host cell with DNA encoding either the light chain or the heavy chain (but not both) of an agonistic TNFR2 antibody of this invention in order to produce an antigen-binding fragment of the antibody.
Once an agonistic TNFR2 antibody or antigen-binding fragments thereof of the invention has been produced by recombinant expression, it can be purified by any method known in the art for purification of an immunoglobulin molecule, for example, by chromatography (e.g., ion exchange, affinity, particularly by affinity for TNFR2 after Protein A or Protein G selection, and sizing column chromatography), centrifugation, differential solubility, or by any other standard technique for the purification of proteins. Further, the agonistic TNFR2 antibodies of the invention or fragments thereof can be fused to heterologous polypeptide sequences described herein or otherwise known in the art to facilitate purification or to produce therapeutic conjugates (see “Antibody conjugates,” below).
Once isolated, an agonistic TNFR2 antibody or antigen-binding fragments thereof can, if desired, be further purified, e.g., by high performance liquid chromatography (see, e.g., Fisher, Laboratory Techniques in Biochemistry and Molecular Biology (Work and Burdon, eds., Elsevier, 1980); the disclosure of which is incorporated herein by reference), or by gel filtration chromatography, such as on a Superdex™ 75 column (Pharmacia Biotech AB, Uppsala, Sweden).
Platforms for Generating and Affinity-Maturing Agonistic TNFR2 Antibodies and Antigen-Binding FragmentsMapping Epitopes of TNFR2 that Promote Receptor Activation
Agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention can be produced by screening libraries of antibodies and antigen-binding fragments thereof for functional molecules that are capable of binding epitopes within TNFR2 that selectively promote receptor activation. Linear peptides isolated from the TNFR2 protein may not adopt the same three dimensional conformations as those peptide sequences located within the protein. TNFR2 provides a structurally rigidified framework that biases the conformations of individual peptide fragments and reinforces these spatial orientations by establishing intramolecular contacts (e.g., hydrogen bonds, dipole-dipole interactions, salt bridges) and by differentially positioning various regions for exposure to solvent depending on the relative hydrophilicity and lipophilicity of these areas (Mukai et al., Sci. Signal., 3:ra83-ra83 (2010); the disclosure of which is incorporated herein by reference). The conformational constraint of a peptide fragment within TNFR2 can be achieved by incorporating the amino acid residues of a TNFR2 epitope (e.g., an epitope that promotes receptor activation) into a structurally pre-organized peptide scaffold, such as a cyclic, bicyclic, tricyclic, or tetrayclic peptide. Cyclic and polycyclic peptides such as these confine a peptide fragment to a distinct three-dimensional conformation. This can be achieved, e.g., by synthesizing peptide epitopes isolated from TNFR2 by established chemical synthetic methods (e.g., by solid phase peptide synthesis as described herein) and incorporating cysteine residues into the sequence at the N- and C-terminal positions or at various internal positions within the peptide chain. It may be advantageous to incorporate cysteine residues that are chemically protected at the thiol moiety with a protecting group that can be removed under conditions different from those used to remove other protecting groups within the peptide being synthesized and different from those used to assemble the peptide chain. Exemplary orthogonal protecting groups for the cysteine thiol include the 4-methyltrityl group and 4-methoxtrityl group, each of which can be removed using dilute trifluoracetic acid (examples are described, e.g., in Isidro-Llobet et al., Chem Rev., 109:2455-2504 (2009); the disclosure of which is incorporated herein by reference).
After introducing a cysteine residue into a synthetic peptide fragment derived from an epitope within TNFR2, the peptide can be cyclized by treating the peptide with a multivalent electrophile, such as a bis(bromomethyl) or tris(bromomethyl)arene derivative. Alternative multivalent thiol-reactive electrophiles can be used, e.g., 1,5-difluoro-2,4-dinitrobenzene, acyclic dibromoalkanes, and others (see, e.g., Jo et al., J. Am. Chem. Soc., 134:17704-17713 (2012); the disclosure of which is incorporated herein by reference). In certain cases, it may be advantageous to prevent the participation of a cysteine residue in the synthetic peptide fragment in a cyclization reaction. For instance, it may be desirable to synthesize a polycyclic peptide containing multiple cysteine residues such that only select cysteine thiols participate in the intramolecular crosslinking process. To prevent unwanted participation of these additional Cys thiol groups in the coupling reaction, a simple approach is, for instance, to use Fmoc-Cys(Acm) (Fmoc-acetamidomethyl-L-cysteine) for the introduction of a protected Cys residue during the course of peptide synthesis. Alternatively, Fmoc-Cys(StBu)-OH can be used, and/or the corresponding t-butyloxycarbonyl (Boc)-protected amino acids. The Acm or StBu group is not removed during the course of a normal TFA deprotection-cleavage reaction, and instead requires oxidative treatment (e.g., with iodine, 12) in the case of the Acm group, or reductive treatment (e.g., β-mercaptoethanol or 1,4-dithiothreiotol) in the case of the StBu group to yield the reduced sulfhydryl form of the peptide, which can either be used directly or subsequently oxidized to the corresponding cystinyl peptide. In one embodiment, a peptide is used which contains at least one Cys derivative, such as Cys(Acm) or Cys(StBu), to allow selective deprotection of a Cys-thiol group. Selective deprotection of a Cys-thiol group renders the Cys-thiol group available for reacting at a desired moment, such as following completion of peptide chain assembly and prior to the deprotection of other residues within the peptide (see, e.g., WO 2008/013454; the disclosure of which is incorporated herein by reference).
As an example, libraries of cyclic and polycyclic peptides containing individual fragments isolated from TNFR2 and combinations of fragments from distinct regions of TNFR2 can be synthesized by techniques such as those described above in order to incorporate cysteine residues at various positions within the peptide scaffold and using different electrophilic crosslinking reagents (see, e.g., Example 1 and
Methods for high throughput screening of antibody libraries for molecules capable of binding epitopes within TNFR2 (e.g., epitopes presented by peptides having the sequence of any one of SEQ ID NOs: 1-341, such as SEQ ID NOs: 3, 11, 61, or 87, and particularly those that contain the KCSPG motif, as in SEQ ID NOs: 53, 69, 75, 118, and 233) include, without limitation, display techniques including phage display, bacterial display, yeast display, mammalian display, ribosome display, mRNA display, and cDNA display. The use of phage display to isolate ligands that bind biologically relevant molecules has been reviewed, e.g., in Felici et al., Biotechnol. Annual Rev. 1:149-183 (1995); Katz, Annual Rev. Biophys. Biomol. Struct. 26:27-45 (1997); and Hoogenboom et al., Immunotechnology 4:1-20, (1998); the disclosures of each of which are incorporated herein by reference. Several randomized combinatorial peptide libraries have been constructed to select for polypeptides that bind different targets, e.g., cell surface receptors or DNA (reviewed by Kay, Perspect. Drug Discovery Des. 2, 251-268 (1995); and Kay et al., Mol. Divers. 1:139-140 (1996). Proteins and multimeric proteins have been successfully phage-displayed as functional molecules (see EP 0349578A, EP 4527839A, EP 0589877A; Chiswell and McCafferty, Trends Biotechnol. 10, 80-84 (1992)). In addition, functional antibody fragments (e.g. Fab, single chain Fv [scFv]) have been expressed (see, e.g., McCafferty et al., Nature 348: 552-554 (1990); Barbas et al., Proc. Natl. Acad Sci. USA 88:7978-7982 (1991); and Clackson et al., Nature 352:624-628 (1991). These references are hereby incorporated by reference in their entirety.
Phage Display TechniquesAs an example, phage display techniques can be used in order to screen libraries of antibodies and antigen-binding fragments thereof for functional molecules capable of binding cyclic or polycyclic peptides containing epitopes within TNFR2 that promote receptor activation (e.g., peptides having the sequence of any one of SEQ ID NOs: 1-341, such as SEQ ID NOs: 3, 11, 61, or 87, and particularly those that contain the KCSPG motif, as in SEQ ID NOs: 53, 69, 75, 118, and 233). For instance, libraries of polynucleotides encoding single chain antibody fragments, such as scFv fragments, that contain randomized hypervariable regions can be obtained using established procedures (e.g., solid phase polynucleotide synthesis or error-prone PCR techniques, see McCullum et al., Meth. Mol. Biol., 634:103-(2010); incorporated herein by reference). These randomized polynucleotides can subsequently be incorporated into a viral genome such that the randomized antibody chains encoded by these genes are expressed on the surface of filamentous phage, e.g., by a covalent bond between the antibody chain and a coat protein (e.g., pill coat protein on the surface of M13 phage). This provides a physical connection between the genotype and phenotype of the antibody chain. In this way, libraries of phage that display diverse antibody chains containing random mutations in hypervariable regions can be screened for the ability of the exterior antibody chains to bind TNFR2 epitopes (e.g., peptides having the sequence of any one of SEQ ID NOs: 1-341) that are immobilized to a surface using established procedures. For instance, cyclic peptides such as those represented by SEQ ID NOs: 53, 69, 75, 118, and 233, which contain the KCSPG motif, can be physically bound to the surface of a microtiter plate by forming a covalent bond between the peptide and an epitope tag (e.g., biotin) and incubating the peptide in wells of a microtiter plate that have been previously coated with a complementary tag (e.g., avidin) that binds the tag attached to the peptide with high affinity. Suitable epitope tags include, without limitation, maltose-binding protein, glutathione-S-transferase, a poly-histidine tag, a FLAG-tag, a myc-tag, human influenza hemagglutinin (HA) tag, biotin, streptavidin. Peptides containing the epitopes presented by these molecules are capable of being immobilized on surfaces containing such complementary molecules as maltose, glutathione, a nickel-containing complex, an anti-FLAG antibody, an anti-myc antibody, an anti-HA antibody, streptavidin, or biotin, respectively. In this way, phage can be incubated with a surface containing an immobilized TNFR2-derived peptide for a time suitable to allow binding of the antibody to the constrained peptide and in the presence of an appropriate buffer system (e.g., one that contains physiological salt concentration, ionic strength, and is maintained at physiological pH by a buffering agent). The surface can then be washed (e.g., with phosphate buffer containing 0.1% Tween-20) so as to remove phage that do not present antibody chains that interact with the TNFR2-derived peptides with an affinity greater than a particular threshold value.
The affinity of the antibodies that remain after this initial panning (i.e., screening) step can be modulated by adjusting the conditions of the washing step (e.g., by including mildly acidic or basic components, or by including other TNFR2-derived peptides at a low concentration in order to compete with immobilized peptides for antigen-binding sites). In this way, the population of phage that remains bound to the surfaces of the microtiter plate following the washing step is enriched for phage that bind TNFR2-derived peptide epitopes that promote receptor activation. The remaining phage can then be amplified by eluting the phage from the surface containing these peptides (e.g., by altering the ambient pH, ionic strength, or temperature) so as to diminish protein-protein interaction strength. The isolated phage can then be amplified, e.g., by infecting bacterial cells, and the resulting phage can optionally be subjected to panning by additional iterations of screening so as to further enrich the population of phage for those harboring higher-affinity TNFR2 antibodies. Following these panning stages, phage that display high-affinity antibodies or antigen-binding fragments thereof can subsequently be isolated and the genomes of these phage can be sequenced in order to identify the polynucleotide and polypeptide sequences of the encoded antibodies. Phage display techniques such as this can be used to generate, e.g., antibody chains, such as scFv fragments, tandem scFv fragments, and other antigen-binding fragments of the invention that can be used as agonists of TNFR2. Exemplary phage display protocols for the identification of antibody chains and antigen-binding fragments thereof that bind a particular antigen with high affinity are well-established and are described, e.g., in U.S. Pat. No. 7,846,892; WO 1997/002342; U.S. Pat. No. 8,846,867; and WO 2007/132917; the disclosures of which are incorporated herein by reference. Similar phage display techniques can be used to generate antibody-like scaffolds (e.g., 10Fn3 domains) of the invention that bind epitopes within TNFR2 that promote receptor activation (e.g., epitopes presented by peptides with the sequence of any one of SEQ ID NOs: 1-341, such as SEQ ID NOs: 3, 11, 61, or 87, and particularly those that contain the KCSPG motif, as in SEQ ID NOs: 53, 69, 75, 118, and 233). Exemplary phage display protocols for the identification of antibody-like scaffold proteins are described, e.g., in WO 2009/086116; the disclosure of which is incorporated herein by reference).
(ii) Cell-Based Display Techniques
Other in vitro display techniques that exploit the linkage between genotype and phenotype of a solvent-exposed antibody or antigen-binding fragment thereof include yeast and bacterial display. Yeast display techniques are established in the art and are often advantageous in that high quantities of antibodies (often up to 30,000) can be presented on the surface of an individual yeast cell (see, e.g., Boder et al., Nat Biotechnol. 15:553 (1997); the disclosure of which is incorporated herein by reference). The larger size of whole cells (e.g., yeast cells or bacterial cells) over filamentous phage enables an additional screening strategy, as one can use flow cytometry to both analyze and sort libraries of labeled cells. For instance, established procedures can be used to generate libraries of bacterial cells or yeast cells that express antibodies containing randomized hypervariable regions (see, e.g., see U.S. Pat. No. 7,749,501 and US 2013/0085072; the disclosures of each which are incorporated herein by reference). For instance, large libraries of yeast cells that express polynucleotides encoding naïve scFv fragments can be made using established procedures (de Bruin et al., Nat Biotechnol 17:397, (1999); the disclosure of which is incorporated herein by reference). Yeast cells expressing these polynucleotides can then be incubated with two different fluorescent molecules during the panning steps: one dye that binds conserved residues within the antibody and thus reflects the amount of antibody displayed, and another dye that fluoresces at a different wavelength and binds the antigen, thus indicating the amount of antigen bound. In these cases, it is useful to use a cyclic or polycyclic peptide containing the sequence of any one of SEQ ID NOs: 1-341, such as SEQ ID NOs: 3, 11, 61, or 87 (and particularly those that contain the KCSPG motif, as in SEQ ID NOs: 53, 69, 75, 118, and 233) that has been conjugated to an epitope tag (e.g., biotin), optionally at a residue that is not expected to interfere with antibody-antigen-binding. This enables a fluorescent dye labeled with a complementary tag (e.g., avidin) to localize to the antibody-antigen complex. This results in great flexibility and immediate feedback on the progress of a selection. In contrast to phage display, by normalizing to antibody display levels, antibodies with higher affinities, rather than greater expression levels can easily be selected. In fact, it is possible to distinguish and sort antibodies whose affinities differ by only two-fold (see, e.g., VanAntwerp and Wittrup, Biotechnol. Prog., 16:31, (2000); the disclosure of which is incorporated herein by reference).
(iii) Nucleotide Display Techniques
Display techniques that utilize in vitro translation of randomized polynucleotide libraries also provide a powerful approach to generating agonistic TNFR2 antibodies of the invention. For instance, randomized DNA libraries encoding antibodies or antigen-binding fragments thereof that contain mutations within designated hypervariable regions can be obtained, e.g., using established PCR-based mutagenesis techniques as described herein. The polynucleotides of these libraries may contain transcription regulating sequences, such as promoters and transcription terminating sequences, and may additionally encode sequences that increase the rate of translation of the resulting mRNA construct (e.g., RES sequences, 5′ and 3′ UTRs, a poly-adenylation tract, and other elements known in the art to promote translation of an RNA transcript). These polynucleotide libraries can be incubated in an appropriately buffered solution containing RNA polymerase and RNA nucleoside triphosphates (NTPs) in order to enable transcription of the DNA sequences to competent mRNA molecules, which can subsequently be translated by large and small ribosomal subunits, aminoacyl tRNA molecules, and translation initiation and elongation factors present in solution (e.g., using the PURExpress® In Vitro Protein Synthesis Kit, New England Biolabs®). Designed mRNA modifications can enable the antibody product to remain covalently bound to the mRNA template by a chemical bond to puromycin (e.g., see Keefe, Curr. Protoc. Mol. Biol., Chapter 24, Unit 24.5 (2001); the disclosure of which is incorporated herein by reference). This genotype-phenotype linkage can thus be used to select for antibodies that bind a TNFR2-derived peptide (e.g., a peptide that has the sequence of any one of SEQ ID NOs: 1-341, such as SEQ ID NOs: 3, 11, 61, or 87, and particularly those that contain the KCRPG motif, as in SEQ ID NOs: 53, 69, 75, 118, and 233) by incubating mRNA:antibody fusion constructs with a peptide immobilized to a surface and panning in a fashion similar to phage display techniques (see, e.g., WO 2006/072773; the disclosure of which is incorporated herein by reference).
Optionally, antibodies of the invention can be generated using a similar technique, except the antibody product may be bound non-covalently to the ribosome-mRNA complex rather than covalently via a puromycin linker. This platform, known as ribosome display, has been described, e.g., in U.S. Pat. No. 7,074,557; the disclosure of which is incorporated herein by reference. Alternatively, antibodies can be generated using cDNA display, a technique that is analogous to mRNA display methodology with the exception that cDNA, rather than mRNA, is covalently bound to an antibody product via a puromycin linker. cDNA display techniques offer the advantage of being able to perform panning steps under increasingly stringent conditions, e.g., under conditions in which the salt concentration, ionic strength, pH, and/or temperature of the environment is adjusted in order to screen for antibodies with particularly high affinity for TNFR2-derived peptides. This is due to the higher natural stability of double-stranded cDNA over single-stranded mRNA. cDNA display screening techniques are described, e.g., in Ueno et al., Methods Mol. Biol., 805:113-135 (2012); the disclosure of which is incorporated herein by reference.
In addition to generating agonistic TNFR2 antibodies of the invention, in vitro display techniques (e.g., those described herein and those known in the art) also provide methods for improving the affinity of a TNFR2 antibody of the invention. For instance, rather than screening libraries of antibodies and fragments thereof containing completely randomized hypervariable regions, one can screen narrower libraries of antibodies and antigen-binding fragments thereof that feature targeted mutations at specific sites within hypervariable regions. This can be accomplished, e.g., by assembling libraries of polynucleotides encoding antibodies or antigen-binding fragments thereof that encode random mutations only at particular sites within hypervariable regions. These polynucleotides can then be expressed in, e.g., filamentous phage, bacterial cells, yeast cells, mammalian cells, or in vitro using, e.g., ribosome display, mRNA display, or cDNA display techniques in order to screen for antibodies or antigen-binding fragments thereof that specifically bind TNFR2 epitopes that promote receptor activation (e.g., peptides containing the sequence of any one of SEQ ID NOs: 1-341, such as SEQ ID NOs: 3, 11, 61, or 87, and particularly those that contain the KCSPG motif, as in SEQ ID NOs: 53, 69, 75, 118, and 233) with improved binding affinity. Yeast display is particularly well-suited for affinity maturation, and has been used previously to improve the affinity of a single chain antibody to a KD of 48 fM (see Boder et al., Proc Natl Acad Sci USA 97:10701 (2000)); the disclosure of which is incorporated herein by reference.
Additional in vitro techniques that can be used for the generation and affinity maturation of agonistic TNFR2 antibodies of the invention include the screening of combinatorial libraries of antibodies or antigen-binding fragments thereof for functional molecules capable of specifically binding TNFR2-derived peptides (e.g., a peptide having the amino acid sequence of any one of SEQ ID NOs: 1-341, such as SEQ ID NOs: 3, 11, 61, or 87, and particularly a peptide containing the KCSPG motif, such as a peptide having the amino acid sequence of any one of SEQ ID NOs: 53, 69, 75, 118, and 233). Combinatorial antibody libraries can be obtained, e.g., by expression of polynucleotides encoding randomized hypervariable regions of an antibody or antigen-binding fragment thereof in a eukaryotic or prokaryotic cell. This can be achieved, e.g., using gene expression techniques described herein or known in the art. Heterogeneous mixtures of antibodies can be purified, e.g., by Protein A or Protein G selection, sizing column chromatography), centrifugation, differential solubility, and/or by any other standard technique for the purification of proteins. Libraries of combinatorial libraries thus obtained can be screened, e.g., by incubating a heterogeneous mixture of these antibodies with a peptide derived from TNFR2 that has been immobilized to a surface (e.g., a peptide having the amino acid sequence of any one of SEQ ID NOs: 1-341 immobilized to the surface of a solid-phase resin or a well of a microtiter plate) for a period of time sufficient to allow antibody-antigen-binding. Non-binding antibodies or fragments thereof can be removed by washing the surface with an appropriate buffer (e.g., a solution buffered at physiological pH (approximately 7.4) and containing physiological salt concentrations and ionic strength, and optionally containing a detergent, such as TWEEN-20). Antibodies that remain bound can subsequently be detected, e.g., using an ELISA-based detection protocol (see, e.g., U.S. Pat. No. 4,661,445; the disclosure of which is incorporated herein by reference).
Additional techniques for screening combinatorial libraries of antibodies for those that specifically bind TNFR2-derived peptides (e.g., a peptide containing the amino acid sequence of any one of SEQ ID NOs: 1-341, such as SEQ ID NOs: 3, 11, 61, or 87, and particularly a peptide containing the KCSPG motif, such as a peptide having the amino acid sequence of any one of SEQ ID NOs: 53, 69, 75, 118, and 233) include the screening of one-bead-one-compound libraries of antibody fragments. Antibody fragments can be chemically synthesized on a bead (e.g., using established split-and-pool solid phase peptide synthesis protocols) composed of a hydrophilic, water-swellable material such that each bead displays a single antibody fragment. Heterogeneous bead mixtures can then be incubated with a TNFR2-derived peptide that is optionally labeled with a detectable moiety (e.g., a fluorescent dye) or that is conjugated to an epitope tag (e.g., biotin, avidin, FLAG tag, HA tag) that can later be detected by treatment with a complementary tag (e.g., avidin, biotin, anti-FLAG antibody, anti-HA antibody, respectively). Beads containing antibody fragments that specifically bind a TNFR2-derived peptide (e.g., a peptide containing the amino acid sequence of any one of SEQ ID NOs: 1-341, such as SEQ ID NOs: 3, 11, 61, or 87, and particularly a peptide containing the KCSPG motif, such as a peptide having the amino acid sequence of any one of SEQ ID NOs: 53, 69, 75, 118, and 233) can be identified by analyzing the fluorescent properties of the beads following incubation with a fluorescently-labeled antigen or complementary tag (e.g., by confocal fluorescent microscopy or by fluorescence-activated bead sorting; see, e.g., Muller et al., J. Biol. Chem., 16500-16505 (1996); the disclosure of which is incorporated herein by reference). Beads containing antibody fragments that specifically bind TNFR2-derived peptides can thus be separated from those that do not contain high-affinity antibody fragments. The sequence of an antibody fragment that specifically binds a TNFR2-derived peptide can be determined by techniques known in the art, including, e.g., Edman degradation, tandem mass spectrometry, matrix-assisted laser-desorption time-of-flight mass spectrometry (MALDI-TOF MS), nuclear magnetic resonance (NMR), and 2D gel electrophoresis, among others (see, e.g., WO 2004/062553; the disclosure of which is incorporated herein by reference).
Negative Screens of Antibodies or Antigen-Binding FragmentsIn addition to the above-described methods for screening for an antibody or antibody fragment that specifically binds to an epitope derived from human TNFR2 containing the KCSPG motif (or an equivalent of this epitope in a non-human mammal TNFR2), one can additionally perform negative screens in order to eliminate antibodies or antibody fragments that may also bind an epitope that contains the KCRPG motif (e.g., a peptide containing residues 130-149 of SEQ ID NO: 366 (KQEGCRLCAPLRKCRPGFGV, SEQ ID NO: 357; or an equivalent of this epitope in a non-human mammal TNFR2).
In addition, antibodies or antibody fragments can also be screened to eliminate antibodies or antigen-binding fragments that specifically bind to a TNFR superfamily member other than TNFR2, such as TNFR1, RANK, CD30, CD40, Lymphotoxin beta receptor (LT-PR), OX40, Fas receptor, Decoy receptor 3, CD27, 4-1 BB, Death receptor 4, Death receptor 5, Decoy receptor 1, Decoy receptor 2, Osteoprotegrin, TWEAK receptor, TACI, BAFF receptor, Herpesvirus entry mediator, Nerve growth factor receptor, B-cell maturation antigen, Glucocorticoid-induced TNFR-related, TROY, Death receptor 6, Death receptor 3, or Ectodysplasin A2 receptor. This can be accomplished using any of the above-described methods or variations thereof, e.g., such that the antibodies or antibody fragments being screened are those that were previously identified as being capable of specifically binding a peptide containing one or more residues of the KCSPG sequence (e.g., at least the KCS sequence). Exemplary techniques useful for a negative screen include those described above or known in the art, such as phage display, yeast display, bacterial display, ribosome display, mRNA display, cDNA display, or surface-based combinatorial library screens (e.g., in an ELISA format). This screening technique represents a useful strategy for identifying an agonistic TNFR2 antibody or antibody fragment of the invention that does not bind, e.g., another TNFR superfamily member or an epitope within TNFR2 that contains the KCRPG sequence.
Immunization of a Non-Human MammalAnother strategy that can be used to produce agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention includes immunizing a non-human mammal with an antigen that contains the KCSPG motif (or an equivalent of this epitope in a non-human mammal TNFR2). Examples of non-human mammals that can be immunized in order to produce agonistic TNFR2 antibodies and fragments thereof of the invention include rabbits, mice, rats, goats, guinea pigs, hamsters, horses, and sheep, as well as non-human primates. For instance, established procedures for immunizing primates are known in the art (see, e.g., WO 1986/6004782; the disclosure of which is incorporated herein by reference). Immunization represents a robust method of producing monoclonal antibodies by exploiting the antigen specificity of B lymphocytes.
For example, monoclonal antibodies can be prepared by the Kohler-Millstein procedure (described, e.g., in EP 0110716; the disclosure of which is incorporated herein by reference), in which spleen cells from a non-human animal (e.g., a primate) immunized with a peptide that presents a TNFR2-derived antigen that promotes receptor activation (e.g., a peptide containing the amino acid sequence of any one of SEQ ID NOs: 1-341, such as SEQ ID NOs: 3, 11, 61, or 87, and particularly a peptide containing the KCSPG motif, such as a peptide having the amino acid sequence of any one of SEQ ID NOs: 53, 69, 75, 118, and 233). A clonally-expanded B lymphocyte produced by immunization can be isolated from the serum of the animal and subsequently fused with a myeloma cell in order to form a hybridoma. Hybridomas are particularly useful agents for antibody production, as these immortalized cells can provide a lasting supply of an antigen-specific antibody. Antibodies from such hybridomas can subsequently be isolated using techniques known in the art, e.g., by purifying the antibodies from the cell culture medium by affinity chromatography, using reagents such as Protein A or Protein G.
Antibody ConjugatesPrior to administration of agonistic TNFR2 antibodies or fragments thereof of the invention to a mammalian subject (e.g., a human), it may be desirable to conjugate the antibody or fragment thereof to a second molecule, e g., to modulate the activity of the antibody in vivo. Agonistic TNFR2 antibodies and fragments thereof can be conjugated to other molecules at either the N-terminus or C-terminus of a light or heavy chain of the antibody using any one of a variety of established conjugation strategies that are well-known in the art. Examples of pairs of reactive functional groups that can be used to covalently tether an agonistic TNFR2 antibody or fragment thereof to another molecule include, without limitation, thiol pairs, carboxylic acids and amino groups, ketones and amino groups, aldehydes and amino groups, thiols and α,β-unsaturated moieties (such as maleimides or dehydroalanine), thiols and alpha-halo amides, carboxylic acids and hydrazides, aldehydes and hydrazides, and ketones and hydrazides.
Agonistic TNFR2 antibodies and fragments thereof of the invention can be covalently appended directly to another molecule by chemical conjugation as described. Alternatively, fusion proteins containing agonistic TNFR2 antibodies and fragments thereof of the invention can be expressed recombinantly from a cell (e.g., a eukaryotic cell or prokaryotic cell). This can be accomplished, for example, by incorporating a polynucleotide encoding the fusion protein into the nuclear genome of a cell (e.g., using techniques described herein or known in the art). Optionally, antibodies and fragments thereof of the invention can be joined to a second molecule by forming a covalent bond between the antibody and a linker. This linker can then be subsequently conjugated to another molecule, or the linker can be conjugated to another molecule prior to ligation to the TNFR2 antibody or fragment thereof. Examples of linkers that can be used for the formation of a conjugate include polypeptide linkers, such as those that contain naturally occurring or non-naturally occurring amino acids. In certain cases, it may be desirable to include D-amino acids in the linker, as these residues are not present in naturally-occurring proteins and are thus more resistant to degradation by endogenous proteases. Fusion proteins containing polypeptide linkers can be made using chemical synthesis techniques, such as those described herein, or through recombinant expression of a polynucleotide encoding the fusion protein in a cell (e.g., a prokaryotic or eukaryotic cell). Linkers can be prepared using a variety of strategies that are well known in the art, and depending on the reactive components of the linker, can be cleaved by enzymatic hydrolysis, photolysis, hydrolysis under acidic conditions, hydrolysis under basic conditions, oxidation, disulfide reduction, nucleophilic cleavage, or organometallic cleavage (see, e.g., Leriche et al., Bioorg. Med. Chem., 20:571-582 (2012)).
Drug-Antibody ConjugatesAn agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention can additionally be conjugated to, admixed with, or administered separately from a therapeutic agent, such as a cytotoxic molecule. Such conjugates of the invention may be applicable to, e.g., the treatment or prevention of a disease associated with autoreactive cytotoxic T-cell activity. In these cases, antibody-drug conjugates of the invention may bind a TNFR2 receptor on the surface of an autoreactive T-cell and induce cell death due to the activity of the conjugated cytotoxic agent. Exemplary cytotoxic agents that can be conjugated to, admixed with, or administered separately from an agonistic TNFR2 antibody include, without limitation, antineoplastic agents such as: acivicin; aclarubicin; acodazole hydrochloride; acronine; adozelesin; adriamycin; aldesleukin; altretamine; ambomycin; a. metantrone acetate; aminoglutethimide; amsacrine; anastrozole; anthramycin; asparaginase; asperlin; azacitidine; azetepa; azotomycin; batimastat; benzodepa; bicalutamide; bisantrene hydrochloride; bisnafide dimesylate; bizelesin; bleomycin sulfate; brequinar sodium; bropirimine; busulfan; cactinomycin; calusterone; camptothecin; caracemide; carbetimer; carboplatin; carmustine; carubicin hydrochloride; carzelesin; cedefingol; chlorambucil; cirolemycin; cisplatin; cladribine; combretestatin a-4; crisnatol mesylate; cyclophosphamide; cytarabine; dacarbazine; daca (n-[2-(dimethyl-amino) ethyl] acridine-4-carboxamide); dactinomycin; daunorubicin hydrochloride; daunomycin; decitabine; dexormaplatin; dezaguanine; dezaguanine mesylate; diaziquone; docetaxel; dolasatins; doxorubicin; doxorubicin hydrochloride; droloxifene; droloxifene citrate; dromostanolone propionate; duazomycin; edatrexate; eflornithine hydrochloride; ellipticine; elsamitrucin; enloplatin; enpromate; epipropidine; epirubicin hydrochloride; erbulozole; esorubicin hydrochloride; estramustine; estramustine phosphate sodium; etanidazole; ethiodized oil i 131; etoposide; etoposide phosphate; etoprine; fadrozole hydrochloride; fazarabine; fenretinide; floxuridine; fludarabine phosphate; fluorouracil; 5-fdump; flurocitabine; fosquidone; fostriecin sodium; gemcitabine; gemcitabine hydrochloride; gold au 198; homocamptothecin; hydroxyurea; idarubicin hydrochloride; ifosfamide; ilmofosine; interferon alfa-2a; interferon alfa-2b; interferon alfa-nl; interferon alfa-n3; interferon beta-i a; interferon gamma-i b; iproplatin; irinotecan hydrochloride; lanreotide acetate; letrozole; leuprolide acetate; liarozole hydrochloride; lometrexol sodium; lomustine; losoxantrone hydrochloride; masoprocol; maytansine; mechlorethamine hydrochloride; megestrol acetate; melengestrol acetate; melphalan; menogaril; mercaptopurine; methotrexate; methotrexate sodium; metoprine; meturedepa; mitindomide; mitocarcin; mitocromin; mitogillin; mitomalcin; mitomycin; mitosper; mitotane; mitoxantrone hydrochloride; mycophenolic acid; nocodazole; nogalamycin; ormaplatin; oxisuran; paclitaxel; pegaspargase; peliomycin; pentamustine; peploycinsulfate; perfosfamide; pipobroman; piposulfan; piroxantrone hydrochloride; plicamycin; plomestane; porfimer sodium; porfiromycin; prednimustine; procarbazine hydrochloride; puromycin; puromycin hydrochloride; pyrazofurin; rhizoxin; rhizoxin d; riboprine; rogletimide; safingol; safingol hydrochloride; semustine; simtrazene; sparfosate sodium; sparsomycin; spirogermanium hydrochloride; spiromustine; spiroplatin; streptonigrin; streptozocin; strontium chloride sr 89; sulofenur; talisomycin; taxane; taxoid; tecogalan sodium; tegafur; teloxantrone hydrochloride; temoporfin; teniposide; teroxirone; testolactone; thiamiprine; thioguanine; thiotepa; thymitaq; tiazofurin; tirapazamine; tomudex; top53; topotecan hydrochloride; toremifene citrate; trestolone acetate; triciribine phosphate; trimetrexate; trimetrexate glucuronate; triptorelin; tubulozole hydrochloride; uracil mustard; uredepa; vapreotide; verteporfin; vinblastine; vinblastine sulfate; vincristine; vincristine sulfate; vindesine; vindesine sulfate; vinepidine sulfate; vinglycinate sulfate; vinleurosine sulfate; vinorelbine tartrate; vinrosidine sulfate; vinzolidine sulfate; vorozole; zeniplatin; zinostatin; zorubicin hydrochloride; 2-chlorodeoxyadenosine; 2′ deoxyformycin; 9-aminocamptothecin; raltitrexed; N-propargyl-5,8-dideazafolic acid; 2chloro-2′-arabino-fluoro-2′-deoxyadenosine; 2-chloro-2′-deoxyadenosine; anisomycin; trichostatin A; hPRL-G129R; CEP-751; linomide; sulfur mustard; nitrogen mustard (mechlor ethamine); cyclophosphamide; melphalan; chlorambucil; ifosfamide; busulfan; N-methyl-Nnitrosourea (MNU); N, N′-Bis (2-chloroethyl)-N-nitrosourea (BCNU); N-(2-chloroethyl)-N′ cyclohexyl-N-nitrosourea (CCNU); N-(2-chloroethyl)-N′-(trans-4-methylcyclohexyl-N-nitrosourea (MeCCNU); N-(2-chloroethyl)-N′-(diethyl) ethylphosphonate-N-nitrosourea (fotemustine); streptozotocin; diacarbazine (DTIC); mitozolomide; temozolomide; thiotepa; mitomycin C; AZQ; adozelesin; cisplatin; carboplatin; ormaplatin; oxaliplatin; C1-973; DWA 2114R; JM216; JM335; Bis (platinum); tomudex; azacitidine; cytarabine; gemcitabine; 6-mercaptopurine; 6-thioguanine; hypoxanthine; teniposide 9-amino camptothecin; topotecan; CPT-11; Doxorubicin; Daunomycin; Epirubicin; darubicin; mitoxantrone; losoxantrone; Dactinomycin (Actinomycin D); amsacrine; pyrazoloacridine; all-trans retinol; 14-hydroxy-retro-retinol; all-trans retinoic acid; N-(4-hydroxyphenyl) retinamide; 13-cis retinoic acid; 3-methyl TTNEB; 9-cis retinoic acid; fludarabine (2-F-ara-AMP); or 2-chlorodeoxyadenosine (2-Cda).
Other cytotoxic agents that can be conjugated to, admixed with, or administered separately from an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention in order to treat or prevent, e.g., the progression of a disease associated with aberrant cytotoxic T-cell proliferation include, but are not limited to, 20-pi-1,25 dihydroxyvitamin D3; 5-ethynyluracil; abiraterone; acylfulvene; adecypenol; adozelesin; aldesleukin; ALL-TK antagonists; altretamine; ambamustine; amidox; amifostine; aminolevulinic acid; amrubicin; amsacrine; anagrelide; anastrozole; andrographolide; angiogenesis inhibitors; antagonist D; antagonist G; antarelix; anti-dorsalizing morphogenetic protein-1; antiandrogen, prostatic carcinoma; antiestrogen; antineoplaston; antisense oligonucleotides; aphidicolin glycinate; apoptosis gene modulators; apoptosis regulators; apurinic acid; ara-CDP-DL-PTBA; argininedeaminase; asulacrine; atamestane; atrimustine; axinastatin 1; axinastatin 2; axinastatin 3; azasetron; azatoxin; azatyrosine; baccatin III derivatives; balanol; batimastat; BCR/ABL antagonists; benzochlorins; benzoylstaurosporine; beta lactam derivatives; beta-alethine; betaclamycin B; betulinic acid; bFGF inhibitor; bicalutamide; bisantrene; bisaziridinylspermine; bisnafide; bistratene A; bizelesin; breflate; bleomycin A2; bleomycin B2; bropirimine; budotitane; buthionine sulfoximine; calcipotriol; calphostin C; camptothecin derivatives (e.g., 10-hydroxy-camptothecin); canarypox IL-2; capecitabine; carboxamide-amino-triazole; carboxyamidotriazole; CaRest M3; CARN 700; cartilage derived inhibitor; carzelesin; casein kinase inhibitors (ICOS); castanospermine; cecropin B; cetrorelix; chlorins; chloroquinoxaline sulfonamide; cicaprost; cis-porphyrin; cladribine; clomifene analogues; clotrimazole; collismycin A; collismycin B; combretastatin A4; combretastatin analogue; conagenin; crambescidin 816; crisnatol; cryptophycin 8; cryptophycin A derivatives; curacin A; cyclopentanthraquinones; cycloplatam; cypemycin; cytarabine ocfosfate; cytolytic factor; cytostatin; dacliximab; decitabine; dehydrodidemnin B; 2′deoxycoformycin (DCF); deslorelin; dexifosfamide; dexrazoxane; dexverapamil; diaziquone; didemnin B; didox; diethylnorspermine; dihydro-5-azacytidine; dihydrotaxol, 9-; dioxamycin; diphenyl spiromustine; discodermolide; docosanol; dolasetron; doxifluridine; droloxifene; dronabinol; duocarmycin SA; ebselen; ecomustine; edelfosine; edrecolomab; eflornithine; elemene; emitefur; epirubicin; epothilones (A, R=H; B, R=Me); epithilones; epristeride; estramustine analogue; estrogen agonists; estrogen antagonists; etanidazole; etoposide; etoposide 4′-phosphate (etopofos); exemestane; fadrozole; fazarabine; fenretinide; filgrastim; finasteride; flavopiridol; flezelastine; fluasterone; fludarabine; fluorodaunorunicin hydrochloride; forfenimex; formestane; fostriecin; fotemustine; gadolinium texaphyrin; gallium nitrate; galocitabine; ganirelix; gelatinase inhibitors; gemcitabine; glutathione inhibitors; hepsulfam; heregulin; hexamethylene bisacetamide; homoharringtonine (HHT); hypericin; ibandronic acid; idarubicin; idoxifene; idramantone; ilmofosine; ilomastat; imidazoacridones; imiquimod; immunostimulant peptides; insulin-like growth factor-1 receptor inhibitor; interferon agonists; interferons; interleukins; iobenguane; iododoxorubicin; ipomeanol; irinotecan; iroplact; irsogladine; isobengazole; isohomohalicondrin B; itasetron; jasplakinolide; kahalalide F; lamellarin-N triacetate; lanreotide; leinamycin; lenograstim; lentinan sulfate; leptolstatin; letrozole; leukemia inhibiting factor; leukocyte alpha interferon; leuprolide+estrogen+progesterone; leuprorelin; levamisole; liarozole; linear polyamine analogue; lipophilic disaccharide peptide; lipophilic platinum compounds; lissoclinamide 7; lobaplatin; lombricine; lometrexol; lonidamine; losoxantrone; lovastatin; loxoribine; lurtotecan; lutetium texaphyrin; lysofylline; lytic peptides; maytansine; mannostatin A; marimastat; masoprocol; maspin; matrilysin inhibitors; matrix metalloproteinase inhibitors; menogaril; rnerbarone; meterelin; methioninase; metoclopramide; MIF inhibitor; ifepristone; miltefosine; mirimostim; mismatched double stranded RNA; mithracin; mitoguazone; mitolactol; mitomycin analogues; mitonafide; mitotoxin fibroblast growth factor-saporin; mitoxantrone; mofarotene; molgramostim; monoclonal antibody, human chorionic gonadotrophin; monophosphoryl lipid A+myobacterium cell wall sk; mopidamol; multiple drug resistance gene inhibitor; multiple tumor suppressor 1-based therapy; mustard anticancer agent; mycaperoxide B; mycobacterial cell wall extract; myriaporone; N-acetyldinaline; N-substituted benzamides; nafarelin; nagrestip; naloxone+pentazocine; napavin; naphterpin; nartograstim; nedaplatin; nemorubicin; neridronic acid; neutral endopeptidase; nilutamide; nisamycin; nitric oxide modulators; nitroxide antioxidant; nitrullyn; 06-benzylguanine; octreotide; okicenone; oligonucleotides; onapristone; ondansetron; ondansetron; oracin; oral cytokine inducer; ormaplatin; osaterone; oxaliplatin; oxaunomycin; paclitaxel analogues; paclitaxel derivatives; palauamine; palmitoylrhizoxin; pamidronic acid; panaxytriol; panomifene; parabactin; pazelliptine; pegaspargase; peldesine; pentosan polysulfate sodium; pentostatin; pentrozole; perflubron; perfosfamide; perillyl alcohol; phenazinomycin; phenylacetate; phosphatase inhibitors; picibanil; pilocarpine hydrochloride; pirarubicin; piritrexim; placetin A; placetin B; plasminogen activator inhibitor; platinum complex; platinum compounds; platinum-triamine complex; podophyllotoxin; porfimer sodium; porfiromycin; propyl bis-acridone; prostaglandin J2; proteasome inhibitors; protein A-based immune modulator; protein kinase C inhibitor; protein kinase C inhibitors, microalgal; protein tyrosine phosphatase inhibitors; purine nucleoside phosphorylase inhibitors; purpurins; pyrazoloacridine; pyridoxylated hemoglobin polyoxyethylene conjugate; raf antagonists; raltitrexed; ramosetron; ras farnesyl protein transferase inhibitors; ras inhibitors; ras-GAP inhibitor; retelliptine demethylated; rhenium Re 186 etidronate; rhizoxin; ribozymes; RII retinamide; rogletimide; rohitukine; romurtide; roquinimex; rubiginone B 1; ruboxyl; safingol; saintopin; SarCNU; sarcophytol A; sargramostim; Sdi 1 mimetics; semustine; senescence derived inhibitor 1; sense oligonucleotides; signal transduction inhibitors; signal transduction modulators; single chain antigen-binding protein; sizofiran; sobuzoxane; sodium borocaptate; sodium phenylacetate; solverol; somatomedin binding protein; sonermin; sparfosic acid; spicamycin D; spiromustine; splenopentin; spongistatin 1; squalamine; stem cell inhibitor; stem-cell division inhibitors; stipiamide; stromelysin inhibitors; sulfinosine; superactive vasoactive intestinal peptide antagonist; suradista; suramin; swainsonine; synthetic glycosaminoglycans; tallimustine; tamoxifen methiodide; tauromustine; tazarotene; tecogalan sodium; tegafur; tellurapyrylium; telomerase inhibitors; temoporfin; temozolomide; teniposide; tetrachlorodecaoxide; tetrazomine; thaliblastine; thalidomide; thiocoraline; thrombopoietin; thrombopoietin mimetic; thymalfasin; thymopoietin receptor agonist; thymotrinan; thyroid stimulating hormone; tin ethyl etiopurpurin; tirapazamine; titanocene dichloride; topotecan; topsentin; toremifene; totipotent stem cell factor; translation inhibitors; tretinoin; triacetyluridine; triciribine; trimetrexate; triptorelin; tropisetron; turosteride; tyrosine kinase inhibitors; tyrphostins; UBC inhibitors; ubenimex; urogenital sinus-derived growth inhibitory factor; urokinase receptor antagonists; vapreotide; variolin B; vector system, erythrocyte gene therapy; velaresol; veramine; verdins; verteporfin; vinorelbine; vinxaltine; vitaxin; vorozole; zanoterone; zeniplatin; zilascorb; and zinostatin stimalamer.
Labeled TNFR2 Antibodies or Antigen-Binding FragmentsAgonistic TNFR2 antibodies or antigen-binding fragments thereof may be conjugated to another molecule, such as an epitope tag, e.g., for the purpose of purification or detection. Examples of such molecules that are useful in protein purification include those that present structural epitopes capable of being recognized by a second molecule. This is a common strategy that is employed in protein purification by affinity chromatography, in which a molecule is immobilized on a solid support and exposed to a heterogeneous mixture containing a target protein conjugated to a molecule capable of binding the immobilized compound. Examples of epitope tag molecules that can be conjugated to agonistic TNFR2 antibodies or fragments thereof, e.g., for the purposes of molecular recognition include, without limitation, maltose-binding protein, glutathione-S-transferase, a poly-histidine tag, a FLAG-tag, a myc-tag, human influenza hemagglutinin (HA) tag, biotin, streptavidin. Conjugates containing the epitopes presented by these molecules are capable of being recognized by such complementary molecules as maltose, glutathione, a nickel-containing complex, an anti-FLAG antibody, an anti-myc antibody, an anti-HA antibody, streptavidin, or biotin, respectively. For example, one can purify an agonistic TNFR2 antibody or fragment thereof of the invention that has been conjugated to an epitope tag from a complex mixture of other proteins and biomolecules (e.g., DNA, RNA, carbohydrates, phospholipids, etc) by treating the mixture with a solid phase resin containing an complementary molecule that can selectively recognize and bind the epitope tag of the TNFR2 antibody or fragment thereof. Examples of solid phase resins include agarose beads, which are compatible with purifications in aqueous solution.
A TNFR2 antibody or antigen-binding fragment thereof of the invention can also be covalently appended to a fluorescent molecule, e.g., to detect the antibody or antigen-binding fragment thereof by fluorimetry and/or by direct visualization using fluorescence microscopy. Exemplary fluorescent molecules that can be conjugated to antibodies of the invention include green fluorescent protein, cyan fluorescent protein, yellow fluorescent protein, red fluorescent protein, phycoerythrin, allophycocyanin, hoescht, 4′,6-diamidino-2-phenylindole (DAPI), propidium iodide, fluorescein, coumarin, rhodamine, tetramethylrhoadmine, and cyanine. Additional examples of fluorescent molecules suitable for conjugation to antibodies of the invention are well-known in the art and have been described in detail in, e.g., U.S. Pat. Nos. 7,417,131 and 7,413,874; the disclosures of each of which are incorporated by reference herein.
Agonistic TNFR2 antibodies or antigen-binding fragments thereof containing a fluorescent molecule are particularly useful for monitoring the cell-surface localization properties of antibodies and fragments thereof of the invention. For instance, one can expose cultured mammalian cells (e.g., T-reg cells) to agonistic TNFR2 antibodies or fragments thereof of the invention that have been covalently conjugated to a fluorescent molecule and subsequently analyze these cells using conventional fluorescent microscopy techniques known in the art. Confocal fluorescent microscopy is a particularly powerful method for determining cell-surface localization of TNFR2 antibodies or fragments thereof, as individual planes of a cell can be analyzed in order to distinguish antibodies or fragments thereof that have been internalized into a cell's interior, e.g., by receptor-mediated endocytosis, from those that are bound to the external face of the cell membrane. Additionally, cells can be treated with TNFR2 antibodies of the invention conjugated to a fluorescent molecule that emits visible light of a particular wavelength (e.g., fluorescein, which fluoresces at about 535 nm) and an additional fluorescent molecule that is known to localize to a particular site on the T-reg cell surface and that fluoresces at a different wavelength (e.g., a molecule that localizes to CD25 and that fluoresces at about 599 nm). The resulting emission patterns can be visualized by confocal fluorescence microscopy and the images from these two wavelengths can be merged in order to reveal information regarding the location of the TNFR2 antibody or antigen-binding fragment thereof on the T-reg cell surface with respect to other receptors.
Bioluminescent proteins can also be incorporated into a fusion protein for the purposes of detection and visualization of an agonistic TNFR2 antibody or fragment thereof. Bioluminescent proteins, such as Luciferase and aequorin, emit light as part of a chemical reaction with a substrate (e.g., luciferin and coelenterazine). Exemplary bioluminescent proteins suitable for use as a diagnostic sequence and methods for their use are described in, e.g., U.S. Pat. Nos. 5,292,658; 5,670,356; 6,171,809; and 7,183,092; the disclosures of each of which are incorporated herein by reference. Agonistic TNFR2 antibodies or fragments thereof labeled with bioluminescent proteins are a useful tool for the detection of antibodies of the invention following an in vitro assay. For instance, the presence of an agonistic TNFR2 antibody that has been conjugated to a bioluminescent protein can be detected among a complex mixture of additional proteins by separating the components of the mixture using gel electrophoresis methods known in the art (e.g., native gel analysis) and subsequently transferring the separated proteins to a membrane in order to perform a Western blot. Detection of the TNFR2 antibody among the mixture of other proteins can be achieved by treating the membrane with an appropriate Luciferase substrate and subsequently visualizing the mixture of proteins on film using established protocols.
The antibodies and fragments thereof of the invention can also be conjugated to a molecule comprising a radioactive nucleus, such that an antibody or fragment thereof of the invention can be detected by analyzing the radioactive emission pattern of the nucleus. Alternatively, an agonistic TNFR2 antibody or fragment thereof can be modified directly by incorporating a radioactive nucleus within the antibody during the preparation of the protein. Radioactive isotopes of methionine (35S), nitrogen (15N), or carbon (13C) can be incorporated into antibodies or fragments thereof of the invention by, e.g., culturing bacteria in media that has been supplemented with nutrients containing these isotopes. Optionally, tyrosine derivatives containing a radioactive halogen can be incorporated into an agonistic TNFR2 antibody or fragment thereof, e.g., by culturing bacterial cells in media supplemented with radiolabeled tyrosine. It has been shown that tyrosine functionalized with a radioactive halogen at the C2 position of the phenol system are rapidly incorporated into elongating polypeptide chains using the endogenous translation enzymes in vivo (see U.S. Pat. No. 4,925,651; the disclosure of which is incorporated herein by reference). The halogens include fluorine, chlorine, bromine, iodine, and astatine. Additionally, agonistic TNFR2 antibodies or fragments thereof can be modified following isolation and purification from cell culture by functionalizing antibodies or fragments thereof of the invention with a radioactive isotope. The halogens represent a class of isotopes that can be readily incorporated into a purified protein, e.g., by aromatic substitution at tyrosine or tryptophan via reaction of one or more of these residues with an electrophilic halogen species. Examples of radioactive halogen isotopes include 18F, 75Br, 77Br, 122I, 123I, 124I, 125I, 129I, 131I, or 211At.
An alternative strategy for the incorporation of a radioactive isotope is the covalent attachment of a chelating group to the agonistic TNFR2 antibody or fragment thereof. Chelating groups can be covalently appended to an agonistic TNFR2 antibody or fragment thereof by attachment to a reactive functional group, such as a thiol, amino group, alcohol, or carboxylic acid. The chelating groups can then be modified to contain any of a variety of metallic radioisotopes, including, without limitation, such radioactive nuclides as 125I, 67Ga, 111In, 99Tc, 169Yb, 186Re, 123I, 124I, 125I, 131I, 99mTc, 111In, 64Cu, 67Cu, 186Re, 188Re, 177Lu, 90Y, 77As, 72As, 86Y, 88Zr, 211At, 212Bi, 213Bi, or 225Ac.
In certain cases, it may be desirable to covalently conjugate the antibodies or fragments thereof of the invention with a chelating group capable of binding a metal ion from heavy elements or rare earth ions, such as Gd3+, Fe3+, Mn3+, or Cr2+. Conjugates containing chelating groups that are coordinated to such paramagnetic metals are useful as in MRI imaging applications. Paramagnetic metals include, but are not limited to, chromium (III), manganese (II), iron (II), iron (III), cobalt (II), nickel (II), copper (II), praseodymium (III), neodymium (III), samarium (III), gadolinium (III), terbium (III), dysprosium (III), holmium (III), erbium (III), and ytterbium (III). In this way, agonistic TNFR2 antibodies can be detected by MRI spectroscopy. For instance, one can administer agonistic TNFR2 antibodies or fragments thereof conjugated to chelating groups bound to paramagnetic ions to a mammalian subject (e.g., a human patient) in order to monitor the distribution of the antibody following administration. This can be achieved by administration of the antibody to a patient by any of the administration routes described herein, such as intravenously, and subsequently analyzing the location of the administered antibody by recording an MRI of the patient according to established protocols.
Agonistic TNFR2 antibodies or fragments thereof can additionally be conjugated to other molecules for the purpose of improving the solubility and stability of the protein in aqueous solution. Examples of such molecules include PEG, PSA, bovine serum albumin (BSA), and human serum albumin (HSA), among others. For instance, one can conjugate an agonistic TNFR2 antibody or fragment thereof to carbohydrate moieties in order to evade detection of the antibody or fragment thereof by the immune system of the patient receiving treatment. This process of hyperglycosylation reduces the immunogenicity of therapeutic proteins by sterically inhibiting the interaction of the protein with B-cell receptors in circulation. Alternatively, agonistic TNFR2 antibodies or fragments thereof can be conjugated to molecules that prevent clearance from human serum and improve the pharmacokinetic profile of antibodies of the invention. Exemplary molecules that can be conjugated to or inserted within agonistic TNFR2 antibodies or fragments thereof of the invention so as to attenuate clearance and improve the pharmacokinetic profile of these antibodies and fragments include salvage receptor binding epitopes. These epitopes are found within the Fc region of an IgG immunoglobulin and have been shown to bind Fc receptors and prolong antibody half life in human serum. The insertion of salvage receptor binding epitopes into TNFR2 antibodies or fragments thereof can be achieved, e.g., as described in U.S. Pat. No. 5,739,277; the disclosure of which is incorporated herein by reference.
Modified Agonistic TNFR2 Antibodies and Antigen-Binding Fragments ThereofIn addition to conjugation to other therapeutic agents and labels for identification or visualization, agonistic TNFR2 antibodies and fragments thereof of the invention can also be modified so as to improve their pharmacokinetic profile, biophysical stability, or inhibitory capacity. For instance, any cysteine residue not involved in maintaining the bioactive conformation of the agonistic TNFR2 antibody or fragment thereof may be substituted with an isosteric or isolectronic amino acid (e.g., serine) in order to improve the oxidative stability of the molecule and prevent aberrant crosslinking. Conversely, cystine bond(s) may be added to the antibody or fragment thereof to improve its stability (particularly where the antibody is an antibody fragment, such as an Fv fragment). This can be accomplished, e.g., by altering a polynucleotide encoding the antibody heavy and light chains or a polynucleotide encoding an antibody fragment so as to encode one or more additional pairs of cysteine residues that can form disulfide bonds under oxidative conditions in order to reinforce antibody tertiary structure (see, e.g., U.S. Pat. No. 7,422,899; the disclosure of which is incorporated herein by reference).
Another useful modification that can be made to agonistic TNFR2 antibodies and fragments thereof of the invention includes altering the glycosylation profile of these antibodies and fragments thereof. This can be achieved, e.g., by substituting, inserting, or deleting amino acids in an agonistic TNFR2 antibody so as to insert or remove a glycosylation site. Glycosylation of antibodies typically occurs in N-linked or O-linked fashion. N-linked glycosylation is a process whereby the attachment of a carbohydrate moiety to an antibody occurs at the side chain of an asparagine residue. Consensus amino acid sequences for N-linked glycosylation include the tripeptide sequences asparagine-X-serine (NXS) and asparagine-X-threonine (NXT), where X is any amino acid except proline. The insertion of either of these tripeptide sequences in a polypeptide (e.g., an agonistic TNFR2 antibody) creates a potential glycosylation site. O-linked glycosylation refers to the attachment of one of the sugars N-acetylgalactosamine, galactose, or xylose to a hydroxyamino acid, most commonly serine or threonine, although 5-hydroxyproline and 5-hydroxylysine are also competent substrates for glycoside formation. Addition of glycosylation sites to a TNFR2 antibody can thus be accomplished by altering the amino acid sequence of the antibody (e.g., using recombinant expression techniques as described herein) such that it contains one or more of the above-described tripeptide sequences to promote N-linked glycosylation, or one or more serine or threonine residues to the sequence of the original antibody engender O-linked glycosylation (see, e.g., U.S. Pat. No. 7,422,899; the disclosure of which is incorporated herein by reference).
In alternative cases, it may be desirable to modify the antibody or fragment thereof of the invention with respect to effector function, e.g., so as to enhance antigen-dependent cell-mediated cytotoxicity (ADCC) and/or complement dependent cytotoxicity (CDC) of the antibody. This may be achieved by introducing one or more amino acid substitutions in an Fc region of the antibody. For instance, cysteine residues may be introduced in the Fc region of an agonistic TNFR2 antibody or fragment thereof (e.g., by recombinant expression techniques as described herein), so as to facilitate additional inter-chain disulfide bond formation in this region. The homodimeric antibody thus generated may have increased conformational constraint, which may foster improved internalization capability and/or increased complement-mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). Homodimeric antibodies with enhanced anti-tumor activity may also be prepared using heterobifunctional cross-linkers as described, for example, in Wolff et al., Canc. Res., 53:2560-2565 (1993); the disclosure of which is incorporated herein by reference. Alternatively, 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-Canc. Drug Des., 3:219-230 (1989); the disclosure of which is incorporated herein by reference).
The serum half life of agonistic TNFR2 antibodies and fragments thereof of the invention can be improved in certain cases by incorporating one more amino acid modifications, such as by altering the CH1 or CL region of the Fab domain to introduce a salvage receptor motif, e.g., that found in the two loops of a CH2 domain of an Fc region of an IgG. Such alterations are described, for instance, in U.S. Pat. Nos. 5,869,046 and 6,121,022; the disclosures of which are incorporated herein by reference.
Methods of TreatmentAgonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention are useful therapeutics for the treatment of a wide array of immunological disorders. Agonistic TNFR2 antibodies and fragments thereof can be administered to a subject, e.g., a mammalian subject, such as a human, in order to treat such conditions as autoimmune diseases, neurological diseases, metabolic diseases (e.g., diabetes), macular diseases (e.g., macular degeneration), muscular atrophy, diseases related to miscarriage, vascular diseases (e.g., atherosclerosis), diseases related to bone loss (e.g., bone loss as a result of menopause or osteoporosis), allergies, asthma, a blood disorder (e.g., hemophilia), a musculoskeletal disorder, a disease related to growth receptor expression or activity, obesity, graft-versus-host disease (GVHD), or an allograft rejection. Agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention can also be used to treat a patient in need of organ repair or regeneration, e.g., by inducing the proliferation of cells within a damaged tissue or organ. Agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention can be administered to a mammalian subject, such as a human, to stimulate the proliferation of T-reg cells (e.g., CD4+, CD25+, FOXP3+T-reg cells). This response can have the effect of reducing populations of cytotoxic T-lymphocytes (e.g., CD8+ T-cells) that are often associated with mounting an inappropriate immune response that can cause an immunological disorder. In addition, antibodies of the invention may synergize with existing T-reg proliferating agents, such as IL-2 and TNFα. For instance, antibodies or antigen-binding fragments thereof of the invention may be capable of stimulating the proliferation of a population of T-reg cells by between 1% and 100% relative to untreated cells (e.g., 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, and 100%) as described in Examples 5 and 6. In certain cases, antibodies of the invention may be capable of reducing the growth of a population of CD8+ T-cells, e.g., by about 50% to about 200% relative to untreated cells (e.g., 50%, 75%, 100%, 125%, 150%, 175%, or 200%).
Agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention can be administered to a subject, e.g., a mammalian subject, such as a human, suffering from a graft rejection. Agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention may treat graft rejections, e.g., by binding TNFR2 receptors on the surface of autoreactive CD8+ T-cells that bind antigens presented on the surface of the graft and inducing apoptosis in these CD8+ T-cells, or by inducing the expansion of T-reg cells that may subsequently eliminate autoreactive CD8+ T-cells. Examples of graft rejections that can be treated by administration of agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention include, without limitation, skin graft rejection, bone graft rejection, vascular tissue graft rejection, ligament graft rejection (e.g., cricothyroid ligament graft rejection, periodontal ligament graft rejection, suspensory ligament of the lens graft rejection, palmar radiocarpal ligament graft rejection, dorsal radiocarpal ligament graft rejection, ulnar collateral ligament graft rejection, radial collateral ligament graft rejection, suspensory ligament of the breast graft rejection, anterior sacroiliac ligament graft rejection, posterior sacroiliac ligament graft rejection, sacrotuberous ligament graft rejection, sacrospinous ligament graft rejection, inferior pubic ligament graft rejection, superior pubic ligament graft rejection, anterior cruciate ligament graft rejection, lateral collateral ligament graft rejection, posterior cruciate ligament graft rejection, medial collateral ligament graft rejection, cranial cruciate ligament graft rejection, caudal cruciate ligament graft rejection, patellar ligament graft rejection) and organ graft rejection (e.g., heart, lung, kidney, liver, pancreas, intestine, and thymus graft rejection, among others).
Agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention may be administered to a subject, e.g., a mammalian subject, such as a human) suffering from a graft-versus-host disease (GVHD). Exemplary graft-versus-host diseases that can be treated using the compositions and methods of the invention include those that arises from a bone marrow transplant, as well as from the transplantation of blood cells, such as hematopoietic stem cells, common myeloid progenitor cells, common lymphoid progenitor cells, megakaryocytes, monocytes, basophils, eosinophils, neutrophils, macrophages, T-cells, B-cells, natural killer cells, and/or dendritic cells.
Agonistic TNFR2 antibodies of the invention can be administered to a subject, e.g., a mammalian subject, such as a human, suffering from an immunological disease, e.g., in order to bind a TNFR2 receptor on the surface of an autoreactive T-cell and induce apoptosis, and/or to promote T-reg cell growth and thus suppress the activity of inappropriately reactive cytotoxic T-lymphocytes and B-lymphocytes in the patient. Antibodies of the invention can be administered to a subject, e.g., via any of the routes of administration described herein.
Immunological diseases that can be treated by administration of antibodies or antigen-binding fragments thereof of the invention include allergies, such as food allergy, seasonal allergy, pet allergy, hives, hay fever, allergic conjunctivitis, poison ivy allergy oak allergy, mold allergy, drug allergy, dust allergy, cosmetic allergy, and chemical allergy.
Diseases that can be treated by administration of an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention include autoimmune diseases, such as type I diabetes, alopecia areata, ankylosing spondylitis, antiphospholipid syndrome, autoimmune Addison's Disease, autoimmune hemolytic anemia, autoimmune hepatitis, Behcet's Disease, bullous pemphigoid, cardiomyopathy, celiac sprue-dermatitis, chronic fatigue immune dysfunction syndrome (CFIDS), chronic inflammatory demyelinating polyneuropathy, Churg-Strauss Syndrome, cicatricial pemphigoid, limited scleroderma (CREST Syndrome), cold agglutinin disease, Crohn's Disease, discoid lupus, essential mixed cryoglobulinemia, fibromyalgia-fibromyositis, Graves' Disease, Guillain-Barré Syndrome, Hashimoto's Thyroiditis, hypothyroidism, Inflammatory Bowel Disease, autoimmune lymphoproliferative syndrome (ALPS), idiopathic pulmonary fibrosis, idiopathic thrombocytopenia purpura (ITP), IgA nephropathy, juvenile arthritis, lichen planus, lupus, Meniere's Disease, mixed connective tissue disease, multiple sclerosis, myasthenia gravis, pemphigus vulgaris, pernicious anemia, polyarteritis nodosa, polychondritis, polyglandular syndromes, polymyalgia rheumatica, polymyositis, dermatomyositis, primary agammaglobulinemia, primary biliary cirrhosis, psoriasis, Raynaud's Phenomenon, Reiter's Syndrome, rheumatic fever, rheumatoid arthritis, sarcoidosis, scleroderma, Sjögren's Syndrome, Stiff-Man syndrome, Takayasu Arteritis, temporal arteritis/giant cell arteritis, ulcerative colitis, uveitis, vasculitis, vitiligo, and Wegener's Granulomatosis.
Agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention can additionally be used to treat patients in need of organ repair or regeneration. For instance, agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention may be used to stimulate organ repair or regeneration, e.g., by binding TNFR2 on the surface of cells within damaged tissue so as to induce TRAF2/3- and/or NFκB-mediated cell proliferation. Examples of tissues and organs that may be induced to regenerate by administration of an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention to a subject (e.g., a mammalian subject, such as a human) include the pancreas, salivary gland, pituitary gland, kidney, heart, lung, hematopoietic system, cranial nerves, heart, blood vessels including the aorta, olfactory gland, ear, nerves, structures of the head, eye, thymus, tongue, bone, liver, small intestine, large intestine, gut, lung, brain, skin, peripheral nervous system, central nervous system, spinal cord, breast, embryonic structures, embryos, and testes.
Agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention can also be administered to a subject (e.g., a mammalian subject, such as a human) in order to treat a neurological disease or condition, such as a brain tumor, a brain metastasis, a spinal cord injury, schizophrenia, epilepsy, Amyotrophic lateral sclerosis (ALS), Parkinson's disease, Alzheimer's disease, Huntington's disease, or stroke.
An agonistic TNFR2 antibody of the invention may also be admixed, conjugated, or administered with, or administered separately from, another agent that promotes T-reg cell proliferation. Additional agents that can be used to promote T-reg cell expansion include, e.g., IL-2 and TNFα, the cognate ligand for TNFR2.
Additionally or alternatively, an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention may be admixed, conjugated, or administered with, or administered separately from, an immunotherapy agent. Exemplary immunotherapy agents useful in conjunction with the compositions and methods of the invention include an anti-CTLA-4 agent, an anti-PD-1 agent, an anti-PD-L1 agent, an anti-PD-L2 agent, a TNF-α cross-linking agent, a TRAIL cross-linking agent, a CD27 agent, a CD30 agent, a CD40 agent, a 4-1BB agent, a GITR agent, an OX40 agent, a TRAILR1 agent, a TRAILR2 agent, a TWEAKR agent, and, e.g., agents directed toward the immunological targets described in Table 1 of Mahoney et al., Cancer Immunotherapy, 14:561-584 (2015), the disclosure of which is incorporated herein by reference. For example, immunological target 4-1BB ligand may be targeted with an anti-4-1BB ligand antibody; immunological target OX40L may be targeted with an anti-OX40L antibody; immunological target GITR may be targeted with an anti-GITR antibody; immunological target CD27 may be targeted with an anti-CD27 antibody; immunological target TL1A may be targeted with an anti-TL1A antibody; immunological target CD40L may be targeted with an anti-CD40L antibody; immunological target LIGHT may be targeted with an anti-LIGHT antibody; immunological target BTLA may be targeted with an anti-BTLA antibody; immunological target LAG3 may be targeted with an anti-LAG3 antibody; immunological target TIM3 may be targeted with an anti-TIM3 antibody; immunological target Singlecs may be targeted with an anti-Singlecs antibody; immunological target ICOS ligand may be targeted with an anti-ICOS ligand antibody; immunological target B7-H3 may be targeted with an anti-B7-H3 antibody; immunological target B7-H4 may be targeted with an anti-B7-H4 antibody; immunological target VISTA may be targeted with an anti-VISTA antibody; immunological target TMIGD2 may be targeted with an anti-TMIGD2 antibody; immunological target BTNL2 may be targeted with an anti-BTNL2 antibody; immunological target CD48 may be targeted with an anti-CD48 antibody; immunological target KIR may be targeted with an anti-KIR antibody; immunological target LIR may be targeted with an anti-LIR antibody; immunological target ILT may be targeted with an anti-ILT antibody; immunological target NKG2D may be targeted with an anti-NKG2D antibody; immunological target NKG2A may be targeted with an anti-NKG2A antibody; immunological target MICA may be targeted with an anti-MICA antibody; immunological target MICB may be targeted with an anti-MICB antibody; immunological target CD244 may be targeted with an anti-CD244 antibody; immunological target CSF1R may be targeted with an anti-CSF1R antibody; immunological target IDO may be targeted with an anti-IDO antibody; immunological target TGFβ may be targeted with an anti-TGFβ antibody; immunological target CD39 may be targeted with an anti-CD39 antibody; immunological target CD73 may be targeted with an anti-CD73 antibody; immunological target CXCR4 may be targeted with an anti-CXCR4 antibody; immunological target CXCL12 may be targeted with an anti-CXCL12 antibody; immunological target SIRPA may be targeted with an anti-SIRPA antibody; immunological target CD47 may be targeted with an anti-CD47 antibody; immunological target VEGF may be targeted with an anti-VEGF antibody; and immunological target neuropilin may be targeted with an anti-neuropilin antibody (see, e.g., Table 1 of Mahoney et al.).
A physician of ordinary skill in the art can readily determine an effective amount of an agonistic TNFR2 antibody or antibody fragment for administration to a mammalian subject (e.g., a human) in need thereof. For example, a physician could start prescribing doses of an antibody of the invention at levels lower than that required to achieve the desired therapeutic effect and gradually increase the dosage until the desired effect is achieved. Alternatively, a physician may begin a treatment regimen by administering an agonistic TNFR2 antibody or antibody fragment at a high dose and subsequently administer progressively lower doses until a therapeutic effect is achieved (e.g., a reduction in the proliferation of a population of CD8+ T-cells or a decrease in the peripheral secretion of IFNγ). In general, a suitable daily dose of an antibody or antigen-binding fragment thereof of the invention will be an amount of the antibody which is the lowest dose effective to produce a therapeutic effect. An antibody or antigen-binding fragment thereof of the invention may be administered by injection, e.g., by intravenous, intramuscular, intraperitoneal, or subcutaneous injection, optionally proximal to the site of a target tissue. A daily dose of a therapeutic composition of an antibody or antigen-binding fragment thereof of the invention may be administered as a single dose or as two, three, four, five, six or more doses administered separately at appropriate intervals throughout the day, week, month, or year, optionally, in unit dosage forms. While it is possible for an antibody or fragment thereof of the invention to be administered alone, it may also be administered as a pharmaceutical formulation in combination with excipients, carriers, and optionally, additional therapeutic agents.
Antibodies or fragments thereof of the invention can be monitored for their ability to attenuate the progression of an immunological disease, such as an autoimmune disease, by any of a variety of methods known in the art. For instance, a physician may monitor the response of a mammalian subject (e.g., a human) to treatment with an antibody of the invention by analyzing the quantity of IFNγ secreted by CD8+ T-cells within a particular patient. For example, antibodies of the invention may be capable of reducing IFNγ secretion by between 1% and 100% (e.g., 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, or 100%). Alternatively, a physician may monitor the responsiveness of a subject (e.g., a human) to treatment with agonisticTNFR2 antibodies or antigen-binding fragments thereof of the invention by analyzing the T-reg cell population in the lymph of a particular subject. For instance, a physician may withdrawn a sample of blood from a mammalian subject (e.g., a human) and determine the quantity or density of a population of T-reg cells (e.g., CD4+CD25+ FOXP3+T-reg cells or CD17+T-reg cells) using established procedures, such as fluorescence activated cell sorting. In these cases, high counts of T-reg cells is indicative of efficacious therapy, while lower T-reg cell counts may indicate that the patient is to be prescribed or administered higher dosages of the TNFR2 antibody of the invention until, e.g., an ideal T-reg cell count is achieved. In addition, a physician of skill in the art may monitor the effect of treatment by administration of agonistic TNFR2 antibodies of antigen-binding fragments thereof to a patient suffering from an immunological disorder, such as an autoimmune disease described herein, by analyzing the quantity of autoreactive CD8+ T-cells within a lymph sample isolated from the patient. Agonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention may attenuate the proliferation of autoreactive T-cells, e.g., by binding TNFR2 at the surface of an autoreactive T-cell and inducing apoptosis, and/or by stimulating the expansion of T-reg cells that subsequently eliminate autoreactive T lymphocytes. Treatment with agonistic TNFR2 antibodies or antigen-binding fragments thereof can lead to reduced quantities of autoreactive T-cells within the lymph isolated from a patient receiving treatment, and a rapid decline in the population of autoreactive T-cells in a lymph sample isolated from such a patient indicates effective treatment. In cases where a lymph sample isolated from a patient exhibits an autoreactive T-cell count that has not declined in response to agonistic TNFR2 antibody therapy, a physician may prescribe the patient higher doses of the antibody or an antigen-binding fragment thereof or may administer the agonistic TNFR2 antibody or antigen-binding fragment thereof with higher frequency, e.g., multiple times per day, week, or month.
Pharmaceutical CompositionsTherapeutic compositions containing an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention can be prepared using methods known in the art. For example, such compositions can be prepared using, e.g., physiologically acceptable carriers, excipients or stabilizers (Remington's Pharmaceutical Sciences 16th edition, Osol, A. Ed. (1980); incorporated herein by reference), and in a desired form, e.g., in the form of lyophilized formulations or aqueous solutions. The compositions can also be prepared so as to contain the active agent (e.g., an agonistic TNFR2 antibody or fragment thereof) at a desired concentration. For example, a pharmaceutical composition of the invention may contain at least 10% (e.g., 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.5%, 99.9%, or 100%) active agent by weight (w/w).
Additionally, an active agent (e.g., an agonistic TNFR2 antibody or fragment thereof of the invention) that can be incorporated into a pharmaceutical formulation can itself have a desired level of purity. For example, an antibody or antigen-binding fragment thereof of the invention may be characterized by a certain degree of purity after isolating the antibody from cell culture media or after chemical synthesis, e.g., of a single chain antibody fragment (e.g., scFv) by established solid phase peptide synthesis methods or native chemical ligation as described herein. An agonistic TNFR2 antibody of the invention may be at least 10% pure prior to incorporating the antibody into a pharmaceutical composition (e.g., 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 97%, 98%, 99%, 99.5%, 99.9%, 99.99%, or 100% pure).
Pharmaceutical compositions of agonistic TNFR2 antibodies of the invention can be prepared for storage as lyophilized formulations or aqueous solutions by mixing the antibody having the desired degree of purity with optional pharmaceutically acceptable carriers, excipients or stabilizers typically employed in the art, e.g., buffering agents, stabilizing agents, preservatives, isotonifiers, non-ionic detergents, antioxidants, and other miscellaneous additives. See, e.g., Remington's Pharmaceutical Sciences, 16th edition (Osol, ed. 1980; incorporated herein by reference). Such additives must be nontoxic to the recipients at the dosages and concentrations employed.
Buffering AgentsBuffering agents help to maintain the pH in the range which approximates physiological conditions. They can be present at concentration ranging from about 2 mM to about 50 mM. Suitable buffering agents for use with TNFR2 antibodies and antigen-binding fragments thereof of the invention include both organic and inorganic acids and salts thereof such as citrate buffers {e.g., monosodium citrate-disodium citrate mixture, citric acid-trisodium citrate mixture, citric acid-monosodium citrate mixture, etc.), succinate buffers {e.g., succinic acid-monosodium succinate mixture, succinic acid-sodium hydroxide mixture, succinic acid-disodium succinate mixture, etc.), tartrate buffers (e.g., tartaric acid-sodium tartrate mixture, tartaric acid-potassium tartrate mixture, tartaric acid-sodium hydroxide mixture, etc.), fumarate buffers {e.g., fumaric acid-monosodium fumarate mixture, fumaric acid-disodium fumarate mixture, monosodium fumarate-disodium fumarate mixture, etc.), gluconate buffers {e.g., gluconic acid-sodium glyconate mixture, gluconic acid-sodium hydroxide mixture, gluconic acid-potassium glyuconate mixture, etc.), oxalate buffer {e.g., oxalic acid-sodium oxalate mixture, oxalic acid-sodium hydroxide mixture, oxalic acid-potassium oxalate mixture, etc.), lactate buffers {e.g., lactic acid-sodium lactate mixture, lactic acid-sodium hydroxide mixture, lactic acid-potassium lactate mixture, etc.) and acetate buffers {e.g., acetic acid-sodium acetate mixture, acetic acid-sodium hydroxide mixture, etc.). Additionally, phosphate buffers, histidine buffers and trimethylamine salts such as Tris can be used.
PreservativesPreservatives can be added to a composition of the invention to retard microbial growth, and can be added in amounts ranging from 0.2%-1% (w/v). Suitable preservatives for use with TNFR2 antibodies and antigen-binding fragments thereof of the invention include phenol, benzyl alcohol, meta-cresol, methyl paraben, propyl paraben, octadecyldimethylbenzyl ammonium chloride, benzalconium halides {e.g., chloride, bromide, and iodide), hexamethonium chloride, and alkyl parabens such as methyl or propyl paraben, catechol, resorcinol, cyclohexanol, and 3-pentanol. Isotonicifiers sometimes known as “stabilizers” can be added to ensure isotonicity of liquid compositions of the invention and include polhydric sugar alcohols, for example trihydric or higher sugar alcohols, such as glycerin, arabitol, xylitol, sorbitol and mannitol. Stabilizers refer to a broad category of excipients which can range in function from a bulking agent to an additive which solubilizes the therapeutic agent or helps to prevent denaturation or adherence to the container wall. Typical stabilizers can be polyhydric sugar alcohols (enumerated above); amino acids such as arginine, lysine, glycine, glutamine, asparagine, histidine, alanine, ornithine, L-leucine, 2-phenylalanine, glutamic acid, threonine, etc., organic sugars or sugar alcohols, such as lactose, trehalose, stachyose, mannitol, sorbitol, xylitol, ribitol, myoinisitol, galactitol, glycerol and the like, including cyclitols such as inositol; polyethylene glycol; amino acid polymers; sulfur containing reducing agents, such as urea, glutathione, thioctic acid, sodium thioglycolate, thioglycerol, a-monothioglycerol and sodium thio sulfate; low molecular weight polypeptides (e.g., peptides of 10 residues or fewer); proteins such as human serum albumin, bovine serum albumin, gelatin or immunoglobulins; hydrophylic polymers, such as polyvinylpyrrolidone monosaccharides, such as xylose, mannose, fructose, glucose; disaccharides such as lactose, maltose, sucrose and trisaccharides such as raffinose; and polysaccharides such as dextran. Stabilizers can be present in the range from 0.1 to 10,000 weights per part of weight active protein.
DetergentsNon-ionic surfactants or detergents (also known as “wetting agents”) can be added to help solubilize the therapeutic agent as well as to protect the therapeutic protein against agitation-induced aggregation, which also permits the formulation to be exposed to shear surface stressed without causing denaturation of the protein. Suitable non-ionic surfactants include polysorbates (20, 80, etc.), polyoxamers (184, 188 etc.), Pluronic polyols, polyoxyethylene sorbitan monoethers (TWEEN®-20, TWEEN®-80, etc.). Non-ionic surfactants can be present in a range of about 0.05 mg/mL to about 1.0 mg/mL, for example about 0.07 mg/mL to about 0.2 mg/mL.
Additional miscellaneous excipients include bulking agents (e.g., starch), chelating agents (e.g., EDTA), antioxidants (e.g., ascorbic acid, methionine, vitamin E), and cosolvents.
Other Pharmaceutical CarriersAlternative pharmaceutically acceptable carriers that can be incorporated into a composition of the invention may include dextrose, sucrose, sorbitol, mannitol, starch, rubber arable, potassium phosphate, arginate, gelatin, potassium silicate, microcrystalline cellulose, polyvinylpyrrolidone, cellulose, water, syrups, methyl cellulose, methylhydroxy benzoate, propylhydroxy benzoate, talc, magnesium stearate, and mineral oils, but not limited to. A composition containing a TNFR2 antibody of the invention may further include a lubricant, a humectant, a sweetener, a flavoring agent, an emulsifier, a suspending agent, and a preservative. Details of suitable pharmaceutically acceptable carriers and formulations can be found in Remington's Pharmaceutical Sciences (19th ed., 1995), which is incorporated herein by reference.
Compositions for Combination TherapyPharmaceutical compositions of the invention may optionally include more than one active agent. For instance, compositions of the invention may contain an agonistic TNFR2 antibody or fragment thereof conjugated to, admixed with, or administered separately from another pharmaceutically active molecule, e.g., T-reg cell, or an additional agent that is useful for induction of T-reg cell expansion. For instance, an agonistic TNFR2 antibody or antigen-binding fragment thereof may be admixed with one or more additional active agents, such as IL-2 or TNFα, in order to treat an immunological disease, e.g., a disorder described herein. Alternatively, pharmaceutical compositions of the invention may be formulated for co-administration or sequential administration with one or more additional active agents that can be used to attenuate CD8+ T-cell growth. Examples of additional active agents that can be used to attenuate cytotoxic T-cell proliferation and that can be conjugated to, admixed with, or administered separately from an agonistic TNFR2 antibody or antibody fragment of the invention include cytotoxic agents, e.g., those described herein.
Agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention can also be admixed with, co-administered with, or administered separately from Bacillus Calmette-Guérin (BCG), a bacterial strain that has been used to treat a variety of immunological disorders, such as type I diabetes, multiple sclerosis, scleroderma, Sjogren's disease, systemic lupus erythematosus, Grave's disease, hypothyroidism, Crohn's disease, colititis, an autoimmune skin disease, and rheumatoid arthritis, among others. For instance, a physician of skill in the art may prescribe a patient presenting with an immunological disorder (e.g., one of those described above, such as type I diabetes or rheumatoid arthritis) a therapeutic regimen that includes an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention in combination with BCG. The agonistic TNFR2 antibody or antigen-binding fragment thereof may be co-administered with BCG, e.g., by an injection route described herein. Alternatively, the agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention may be administered separately from a BCG-containing composition. The use of BCG to treat immunological disorders has been described, e.g., in U.S. Pat. No. 6,660,487; and in U.S. Pat. No. 6,599,710; the disclosures of each of which are incorporated herein by reference.
Blood-Brain Barrier PenetrationIn certain embodiments, agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention can be formulated to ensure proper distribution in vivo. For example, the blood-brain barrier (BBB) excludes many highly hydrophilic compounds. To ensure that the therapeutic compositions of the invention cross the BBB (if desired), they can be formulated, for example, in liposomes. Methods of manufacturing liposomes have been described, e.g., U.S. Pat. Nos. 4,522,811; 5,374,548; and 5,399,331. The liposomes may comprise one or more moieties that are selectively transported into specific cells or organs, thereby enhancing targeted drug delivery (see, e.g., V. V. Ranade, J. Clin. Pharmacol. 29:685, 1989)). Exemplary targeting moieties include, e.g., folate or biotin (see, e.g., U.S. Pat. No. 5,416,016); mannosides (Umezawa et al. (Biochem. Biophys. Res. Commun. 153:1038, 1988)); antibodies (P. G. Bloeman et al. (FEBS Lett. 357:140, 1995); M. Owais et al. (Antimicrob. Agents Chemother. 39:180, 1995)); surfactant protein A receptor (Briscoe et al. (Am. J. Physiol. 1233:134, 1995)); the disclosures of each of which are incorporated herein by reference.
Routes of Administration and DosingAgonistic TNFR2 antibodies and antigen-binding fragments thereof of the invention can be administered to a mammalian subject (e.g., a human) by a variety of routes such as orally, transdermally, subcutaneously, intranasally, intravenously, intramuscularly, intraocularly, intratumorally, parenterally, topically, intrathecally and intracerebroventricularly. The most suitable route for administration in any given case will depend on the particular antibody or antigen-binding fragment administered, the patient, pharmaceutical formulation methods, administration methods (e.g., administration time and administration route), the patient's age, body weight, sex, severity of the diseases being treated, the patient's diet, and the patient's excretion rate.
The effective dose of an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention can range from about 0.0001 to about 100 mg/kg of body weight per single (e.g., bolus) administration, multiple administrations or continuous administration, or to achieve a serum concentration of 0.0001-5000 pg/mL serum concentration per single (e.g., bolus) administration, multiple administrations or continuous administration, or any effective range or value therein depending on the condition being treated, the route of administration and the age, weight, and condition of the subject. In certain embodiments, e.g., for the treatment of cancer, each dose can range from about 0.0001 mg to about 500 mg/kg of body weight. For instance, a pharmaceutical composition of the invention may be administered in a daily dose in the range of 0.001-100 mg/kg (body weight). The dose may be administered one or more times (e.g., 2-10 times) per day, week, month, or year to a mammalian subject (e.g., a human) in need thereof.
Therapeutic compositions can be administered with medical devices known in the art. For example, in an embodiment, a therapeutic composition of the invention can be administered with a needleless hypodermic injection device, such as the devices disclosed in U.S. Pat. Nos. 5,399,163; 5,383,851; 5,312,335; 5,064,413; 4,941,880; 4,790,824; or U.S. Pat. No. 4,596,556. Examples of well-known implants and modules useful in the invention include those described in U.S. Pat. No. 4,487,603; which discloses an implantable micro-infusion pump for dispensing medication at a controlled rate; U.S. Pat. No. 4,486,194; which discloses a therapeutic device for administering medicaments through the skin; U.S. Pat. No. 4,447,233; which discloses a medication infusion pump for delivering medication at a precise infusion rate; U.S. Pat. No. 4,447,224; which discloses a variable flow implantable infusion apparatus for continuous drug delivery; U.S. Pat. No. 4,439,196; which discloses an osmotic drug delivery system having multi-chamber compartments; and U.S. Pat. No. 4,475,196; which discloses an osmotic drug delivery system. These patents are incorporated herein by reference. Many other such implants, delivery systems, and modules are known to those skilled in the art.
Kits Containing Agonistic TNFR2 Antibodies and Antigen-Binding Fragments ThereofThis invention also includes kits that contain agonistic TNFR2 antibodies or antigen-binding fragments thereof. The kits provided herein may contain any of the agonistic TNFR2 antibodies and fragments thereof described above, as well as any of the polynucleotides encoding these antibodies, vectors containing these polynucleotides, or cells engineered to express and secrete antibodies of the invention (e.g., prokaryotic or eukaryotic cells). A kit of this invention may include reagents that can be used to produce the compositions of the invention (e.g., agonistic TNFR2 antibodies, conjugates containing agonistic TNFR2 antibodies, polynucleotides encoding agonistic TNFR2 antibodies, and vectors containing these polynucleotides). Optionally, kits of the invention may include reagents that can induce the expression of agonistic TNFR2 antibodies within cells (e.g., mammalian cells), such as doxycycline or tetracycline. In other cases, a kit of the invention may contain a compound capable of binding and detecting a fusion protein that contains an agonistic TNFR2 antibody and an epitope tag. For instance, in such cases a kit of the invention may contain maltose, glutathione, a nickel-containing complex, an anti-FLAG antibody, an anti-myc antibody, an anti-HA antibody, biotin, or streptavidin.
Kits of the invention may also include reagents that are capable of detecting an agonistic TNFR2 antibody or fragment thereof directly. Examples of such reagents include secondary antibodies that selectively recognize and bind particular structural features within the Fc region of an agonistic TNFR2 antibody of the invention. Kits of the invention may contain secondary antibodies that recognize the Fc region of an agonistic TNFR2 antibody and that are conjugated to a fluorescent molecule. These antibody-fluorophore conjugates provide a tool for analyzing the localization of agonistic TNFR2 antibodies, e.g., in a particular tissue or cultured mammalian cell using established immunofluorescence techniques. In certain cases, kits of the invention may include additional fluorescent compounds that exhibit known sub-cellular localization patterns. These reagents can be used in combination with another antibody-fluorophore conjugate, e.g., one that specifically recognizes a different receptor on the cell surface in order to analyze the localization of an agonistic TNFR2 antibody relative to other cell-surface proteins.
Kits of the invention may also contain a reagent that can be used for the analysis of a patient's response to treatment by administration of agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention. For instance, kits of the invention may include an agonistic TNFR2 antibody and one or more reagents that can be used to determine the quantity of T-reg cells in a blood sample withdrawn from a subject (e.g., a human) that is undergoing treatment with an antibody of the invention. Such a kit may contain, e.g., antibodies that selectively bind cell-surface antigens presented by T-reg cells, such as CD4 and CD25. Optionally, these antibodies may be labeled with a fluorescent dye, such as fluorescein or tetramethylrhodamine, in order to facilitate analysis of a population of T-reg cells by fluorescence-activated cell sorting (FACS) methods known in the art. Kits of the invention may optionally contain one or more reagents that can be used to quantify a population of cytotoxic T-lymphocytes, e.g., in order to determine the effectiveness of an agonistic TNFR2 antibody of the invention in attenuating CD8+ T-cell proliferation. For instance, kits of the invention may contain an antibody that selectively binds cell-surface markers on the surface of a cytotoxic T-cell, such as CD8 or CD3. Optionally, these antibodies may be labeled with fluorescent molecules so as to enable quantitation by FACS analysis.
A kit of the invention may also contain one or more reagents useful for determining the affinity and selectivity of an agonistic TNFR2 antibody or antigen-binding fragment thereof of the invention for one or more peptides derived from TNFR2 (e.g., a peptide containing the sequence of any one of SEQ ID NOs: 1-341, such as SEQ ID NOs: 3, 11, 61, or 87, and particularly those that contain the KCSPG motif, as in SEQ ID NOs: 53, 69, 75, 118, and 233). For instance, a kit may contain an agonistic TNFR2 antibody and one or more reagents that can be used in an ELISA assay to determine the KD of an antibody of the invention for one or more peptides that present a TNFR2 epitope in a conformation similar to that of the epitope in the native protein. A kit may contain, e.g., a microtiter plate containing wells that have been previously conjugated to avidin, and may contain a library of TNFR2-derived peptides, each of which conjugated to a biotin moiety. Such a kit may optionally contain a secondary antibody that specifically binds to the Fc region of an agonistic TNFR2 antibody of the invention, and the secondary antibody may be conjugated to an enzyme (e.g., horseradish peroxidase) that catalyzes a chemical reaction that results in the emission of luminescent light.
Kits of the invention may also contain agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention and reagents that can be conjugated to such an antibody, including those previously described (e.g., a cytotoxic agent, a fluorescent molecule, a bioluminescent molecule, a molecule containing a radioactive isotope, a molecule containing a chelating group bound to a paramagnetic ion, etc). These kits may additionally contain instructions for how the conjugation of an agonistic TNFR2 antibody of the invention to a second molecule, such as those described above, can be achieved.
A kit of the invention may also contain a vector containing a polynucleotide that encodes an agonistic TNFR2 antibody or fragment thereof, such as any of the vectors described herein. Alternatively, a kit may include mammalian cells (e.g., CHO cells) that have been genetically altered to express and secrete agonistic TNFR2 antibodies or fragments thereof from the nuclear genome of the cell. Such a kit may also contain instructions describing how expression of the agonistic TNFR2 antibody or fragment thereof from a polynucleotide can be induced, and may additionally include reagents (such as, e.g., doxycycline or tetracycline) that can be used to promote the transcription of these polynucleotides. Such kits may be useful for the manufacture of agonistic TNFR2 antibodies or antigen-binding fragments thereof of the invention.
Other kits of the invention may include tools for engineering a prokaryotic or eukaryotic cell (e.g., a CHO cell or a BL21(DE3) E. coli cell) so as to express and secrete an agonistic TNFR2 antibody or fragment thereof of the invention from the nuclear genome of the cell. For example, a kit may contain CHO cells stored in an appropriate media and optionally frozen according to methods known in the art. The kit may also provide a vector containing a polynucleotide that encodes a nuclease (e.g., such as the CRISPER/Cas, zinc finger nuclease, TALEN, ARCUS™ nucleases described herein) as well as reagents for expressing the nuclease in the cell. The kit can additionally provide tools for modifying the polynucleotide that encodes the nuclease so as to enable one to alter the DNA sequence of the nuclease in order to direct the cleavage of a specific target DNA sequence of interest. Examples of such tools include primers for the amplification and site-directed mutagenesis of the polynucleotide encoding the nuclease of interest. The kit may also include restriction enzymes that can be used to selectively excise the nuclease-encoding polynucleotide from the vector and subsequently re-introduce the modified polynucleotide back into the vector once the user has modified the gene. Such a kit may also include a DNA ligase that can be used to catalyze the formation of covalent phosphodiester linkages between the modified nuclease-encoding polynucleotide and the target vector. A kit of the invention may also provide a polynucleotide encoding an agonistic TNFR2 antibody or fragment thereof, as well as a package insert describing the methods one can use to selectively cleave a particular DNA sequence in the genome of the cell in order to incorporate the polynucleotide encoding an agonistic TNFR2 antibody into the genome at this site. Optionally, the kit may provide a polynucleotide encoding a fusion protein that contains an agonistic TNFR2 antibody or fragment thereof and an additional polypeptide, such as, e.g., those described herein.
EXAMPLESThe following examples are put forth so as to provide those of ordinary skill in the art with a description of how the compositions and methods claimed herein may be performed, made, and evaluated, and are intended to be purely exemplary of the invention and are not intended to limit the scope of what the inventor regard as her invention.
Example 1. Mapping the Discrete Epitopes within TNFR2 that Interact with MR2-1Libraries of linear, cyclic, and bicyclic peptides derived from human TNFR2 were screened for distinct sequences within the protein that exhibit high affinity for TNFR2 antibody MR2-1. In order to screen conformational epitopes within TNFR2, peptides from distinct regions of the primary protein sequence were conjugated to one another to form chimeric peptides. These peptides contained cysteine residues at strategic positions within their primary sequences (see, e.g.,
The “Constrained Libraries of Peptides on Surfaces” (CLIPS) platform used for this analysis begins with the conversion of the target protein, e.g., TNFR2, into a library of up to 10,000 overlapping peptide constructs, using a combinatorial matrix design (Timmerman et al., J. Mol. Recognit., 20: 283-29 (2007)). On a solid carrier, a matrix of linear peptides is synthesized, which are subsequently shaped into spatially defined CLIPS constructs. Constructs representing multiple parts of the discontinuous epitope in the correct conformation bind the antibody with high affinity, which is detected and quantified. Constructs presenting the incomplete epitope bind the antibody with lower affinity, whereas constructs not containing the epitope do not bind at all. Affinity information is used in iterative screens to define the sequence and conformation of epitopes in detail.
Peptide SynthesisTo reconstruct epitopes of the target molecule a library of peptides was synthesized. An amino functionalized polypropylene support was obtained by grafting a proprietary hydrophilic polymer formulation via reaction with t-butyloxycarbonyl-hexamethylenediamine (BocHMDA) using dicyclohexylcarbodiimide (DCC) with N-hydroxybenzotriazole (HOBt) and subsequent cleavage of the Boc-groups using trifluoroacetic acid (TFA). Standard Fmoc-peptide synthesis was used to synthesize peptides on the amino-functionalized solid support by custom modified JANUS® liquid handling stations (Perkin Elmer). CLIPS technology allows one to structure peptides into single loops, double-loops, triple loops, sheet-like folds, helix-like folds and combinations thereof. CLIPS templates are coupled to cysteine residues. The side-chains of multiple cysteines in the peptides are coupled to one or two CLIPS templates. For example, a 0.5 mM solution of the CLIPS template (2,6-bis(bromomethyl)pyridine) is dissolved in ammonium bicarbonate (20 mM, pH 7.8)/acetonitrile (1:3(v/v)). This solution is added to a surface-bound peptide array. The CLIPS template will react with side-chains of two cysteines as present in the solid-phase bound peptides of the peptide-arrays (455 wells plate with 3 μl wells). The peptide arrays are gently shaken in the solution for 30 to 60 minutes while completely covered in solution. Finally, the peptide arrays are washed extensively with excess of H2O and sonicated in disrupt-buffer containing 1% SDS/0.1% beta-mercaptoethanol in PBS (pH 7.2) at 70° C. for 30 minutes, followed by sonication in H2O for another 45 minutes.
ELISA ScreeningThe binding of antibody to each of the synthesized peptides was tested in an ELISA format. Surface-immobilized peptide arrays were incubated with primary antibody solution (overnight at 4° C.). After washing, the peptide arrays were incubated with a 1/1000 dilution of an appropriate antibody peroxidase conjugate (SBA) for one hour at 25° C. After washing, the peroxidase substrate 2,2′-azino-di-3-ethylbenzthiazoline sulfonate (ABTS) and 2 μl/ml of 3 percent H2O2 were added. After one hour, the color development was measured. The color development was quantified with a charge coupled device (CCD)—camera and an image processing system. The values obtained from the CCD camera range from 0 to 3000 mAU, similar to a standard 96-well plate ELISA-reader. The results are quantified and stored into the Peplab database. Occasionally a well contains an air-bubble resulting in a false-positive value, the cards are manually inspected and any values caused by an air-bubble are scored as 0.
Peptides that bound MR2-1 with high affinity are highlighted in
-
- HUMAN T-REG FLOW™ Kit (BioLegend, Cat. No. 320401)
- Cocktail Anti-human CD4 PE-Cy5/CD25 PE (BioLegend, Part No. 78930)
- ALEXA FLUOR® 488 Anti-human FOXP3, Clone 259D (BioLegend, Part No. 79467)
- ALEXA FLUOR® 488 Mouse IgG1, k Isotype Ctrl (ICFC), Clone MOPC-21 (BioLegend, Part No. 79486)
- FOXP3 Fix/Perm Buffer (4×) (BioLegend, Cat. No. 421401)
- FOXP3 Perm Buffer (10×) (BioLegend, Cat. No. 421402)
- PE anti-human CD25, Clone: BC96 (BioLegend, Cat. No. 302606)
- ALEXA FLUOR® 488 Anti-human FOXP3, Clone 259D (BioLegend, Cat. No. 320212)
- PBS pH 7.4 (1×) (Gibco Cat. No. 10010-023)
- HBSS (1×) (Gibco Cat. No. 14175-095)
- FBS (heat inactivated)
- 15 ml tubes
- Bench top centrifuge with swing bucket rotor for 15 ml tubes (set speed 1100 rpm or 200 g)
- HUMAN T-REG FLOW™ Kit (BioLegend, Cat. No. 320401)
Agonistic TNFR2 antibodies (MR2-1 and 8E6.D1) were tested for the ability to induce the proliferation of T-reg cells. Cultured T-reg cells were treated with varying concentrations of the agonistic TNFR2 antibodies in the presence and absence of stimulatory growth factors (e.g., TNFα) for set periods of time. T-reg cells were also cultured in the presence of MR2-1 at various concentrations ranging, e.g., from 0-250 μg/ml in the presence and absence of TNFα. As controls, T-reg cells were also incubated with TNFα alone at concentrations ranging from 0-100 ng/ml. Additionally, control T-reg cells were cultured in the presence of IL-2 alone.
Following the incubation of T-reg cells under the conditions described above, the cell counts were determined using flow cytometry analysis. T-reg cells at a density of 0.2-1×106 cells/100 μl were distributed into a 15-ml conical tube and centrifuged for 5 minutes in order to pellet the cells. The supernatant was discarded and cells were resuspended in 100 μl of wash buffer (1×HBSS containing 2% FBS). 5 μl of PE anti-human CD25 fluorophore-antibody conjugate were added to this mixture, and the cells were subsequently vortexed and incubated in the dark for 25 minutes. The cells were then washed by adding 1 ml of wash buffer and subsequently centrifuging for 5 minutes. The supernatant was then discarded and 1 ml of FoxP3 fixation/permeabilization buffer (1:4 dilution of 4×FOXP3 Fix/Perm buffer in PBS) was added to the cells. The cells were then vortexed and incubated in the dark for 20 minutes. Cells were subsequently centrifuged for 5 minutes and supernatant was discarded. Cells were then resuspended in 1 ml of fresh wash buffer, vortexed, and centrifuged for 5 minutes. Cells were subsequently resuspended in 1 ml of 1×FOXP3 Perm Buffer (1:10 dilution of 10×FOXP3 Perm Buffer in PBS), vortexed, and incubated in the dark for 15 minutes. Following incubation, cells were centrifuged for 5 minutes and supernatant was subsequently discarded. The cell pellet was then resuspended in 100 μl of 1×FOXP3 Perm Buffer. At this point, 5 μl of either ALEXA FLUOR® 488 anti-human FOXP3 or ALEXA FLUOR® 488 mouse IgG1, k isotype control were added to the cells. Cells were then vortexed and incubated in the dark for 35 minutes. Following incubation, cells were washed by adding 1 ml of fresh wash buffer to the cells, vortexing the cells and centrifuging for 5 minutes. The supernatant was then discarded and the cell pellet was resuspended in 0.2-0.5 ml of 1×HBSS free of FBS. Cell counts were then determined by flow cytometry analysis,
As seen in
An exemplary method for in vitro protein evolution of agonistic TNFR2 antibodies of the invention is phage display, a technique which is well known in the art. Phage display libraries can be created by making a designed series of mutations or variations within a coding sequence for the CDRs of an antibody or the analogous regions of an antibody-like scaffold (e.g., the BC, CD, and DE loops of 10Fn3 domains). The template antibody-encoding sequence into which these mutations are introduced may be, e.g., a naive human germline sequence as described herein. These mutations can be performed using standard mutagenesis techniques described herein or known in the art. Each mutant sequence thus encodes an antibody corresponding in overall structure to the template except having one or more amino acid variations in the sequence of the template. Retroviral and phage display vectors can be engineered using standard vector construction techniques as described herein or known in the art. P3 phage display vectors along with compatible protein expression vectors, as is well known in the art, can be used to generate phage display vectors for antibody diversification as described herein.
The mutated DNA provides sequence diversity, and each transformant phage displays one variant of the initial template amino acid sequence encoded by the DNA, leading to a phage population (library) displaying a vast number of different but structurally related amino acid sequences. Due to the well-defined structure of antibody hypervariable regions, the amino acid variations introduced in a phage display screen are expected to alter the binding properties of the binding peptide or domain without significantly altering its structure.
In a typical screen, a phage library is contacted with and allowed to bind a TNFR2-derived peptide (e.g., a peptide having the sequence of any one of SEQ ID NOs: 1-341, such as SEQ ID NOs: 3, 11, 61, or 87, and particularly those that contain the KCSPG motif, as in SEQ ID NOs: 53, 69, 75, 118, and 233), or a particular subcomponent thereof. To facilitate separation of binders and non-binders, it is convenient to immobilize the target on a solid support. Phage bearing a TNFR2-binding moiety can form a complex with the target on the solid support whereas non-binding phage remain in solution and can be washed away with excess buffer. Bound phage can then liberated from the target by changing the buffer to an extreme pH (pH 2 or pH 10), changing the ionic strength of the buffer, adding denaturants, or other known means. To isolate the binding phage exhibiting the polypeptides of the present invention, a protein elution is performed.
The recovered phage can then be amplified through infection of bacterial cells and the screening process can be repeated with the new pool that is now depleted in non-binding antibodies and enriched for antibodies that bind the target peptide. The recovery of even a few binding phage is sufficient to amplify the phage for a subsequent iteration of screening. After a few rounds of selection, the gene sequences encoding the antibodies or antigen-binding fragments thereof derived from selected phage clones in the binding pool are determined by conventional methods, thus revealing the peptide sequence that imparts binding affinity of the phage to the target. During the panning process, the sequence diversity of the population diminishes with each round of selection until desirable peptide-binding antibodies remain. The sequences may converge on a small number of related antibodies or antigen-binding fragments thereof, typically 10-50 out of about 109 to 1010 original candidates from each library. An increase in the number of phage recovered at each round of selection is a good indication that convergence of the library has occurred in a screen. After a set of binding polypeptides is identified, the sequence information can be used to design other secondary phage libraries, biased for members having additional desired properties (see, e.g., WO 2014/152660; the disclosure of which is incorporated herein by reference).
Example 4. Producing a scFv TNFR2 AgonistAntibody fragments of the invention include scFv fragments, which consist of the antibody variable regions of the light and heavy chains combined in a single peptide chain. A TNFR2 antibody can be used as a framework for the development of an scFv antibody fragment by recombinantly expressing a polynucleotide encoding the variable region of a light chain of the TNFR2 antibody (e.g., 8E6.D1) operatively linked to the variable region of a heavy chain of that antibody. This can be accomplished using established mutagenesis protocols as described herein or known in the art. This polynucleotide can then be expressed in a cell (e.g., a CHO cell) and the scFv fragment can subsequently be isolated from the cell culture media.
Alternatively, scFv fragments derived from an agonistic TNFR2 antibody can be produced by chemical synthetic methods (e.g., by Fmoc-based solid-phase peptide synthesis, as described herein). One of skill in the art can chemically synthesize a peptide chain consisting of the variable region of a light chain of the TNFR2 antibody (e.g., 8E6.D1) operatively linked to the variable region of a heavy chain of that antibody. Native chemical ligation can be used as a strategy for the synthesis of long peptides (e.g., greater than 50 amino acids). Native chemical ligation protocols are known in the art and have been described, e.g., by Dawson et al., Science, 266:776-779 (1994); the disclosure of which is incorporated herein by reference.
Example 5. Treatment of Type I Diabetes in a Human Patient by Administration of Agonistic TNFR2 AntibodiesThe agonistic TNFR2 antibodies of the invention (e.g., a humanized version of 8E6-D1 or an antigen-binding fragment thereof) can be administered to a human patient in order to treat type I diabetes. For instance, a human patient suffering from type I diabetes can be treated by administering an agonistic TNFR2 antibody of the invention by an appropriate route (e.g., intravenously) at a particular dosage (e.g., between 0.001 and 100 mg/kg/day) over a course of days, weeks, months, or years. If desired, the agonistic TNFR2 antibody can be co-administered with, admixed with, or administered separately from, another therapeutic effective for treating type I diabetes, such as BCG.
The progression of type I diabetes that is treated with an agonistic TNFR2 antibody of the invention can be monitored by any one or more of several established methods. A physician can monitor the patient by direct observation in order to evaluate how the symptoms exhibited by the patient have changed in response to treatment. A urine sample isolated from the patient may be analyzed in order to determine the content of glucose in the sample, which can indicate the effectiveness of the TNFR2 antibody therapy. For instance, if the content of glucose in the urine sample is high, may indicate that the patient is to be administered higher dosages of an agonistic TNFR2 antibody of the invention until a minimal urine glucose concentration has been maintained.
Example 6. Treatment of Allograft Rejection in a Human Patient by Administration of Agonistic TNFR2 AntibodiesThe agonistic TNFR2 antibodies of the invention (e.g., a humanized version of 8E6-D1 or an antigen-binding fragment thereof) can be administered to a human patient in order to treat allograft rejection. Administration of these antibodies induces the proliferation of a population of T-reg cells, which attenuates immune responses mounted by self-reactive cytotoxic T-cells that are associated with the rejection of a tissue graft following transplantation. For instance, a human patient presenting with allograft rejection can be treated by administering an agonistic TNFR2 antibody of the invention (e.g., a TNFR2 antibody that specifically binds an epitope containing one or more residues of the KCSPG sequence of TNFR2 (residues 56-60 of SEQ ID NO: 366) by an appropriate route (e.g., intravenously) at a particular dosage (e.g., between 0.001 and 100 mg/kg/day) over a course of days, weeks, months, or years. If desired, the agonistic TNFR2 antibody can be modified, e.g., by hyperglycosylation or by conjugation with PEG, so as to evade immune recognition and/or to improve the pharmacokinetic profile of the antibody.
The progression of the allograft rejection that is treated with an agonistic TNFR2 antibody of the invention can be monitored by any one or more of several established methods. A physician can monitor the patient by direct observation in order to evaluate how the symptoms exhibited by the patient have changed in response to treatment. A blood sample can also be withdrawn from the patient in order to analyze the cell count of one or more CD8+ T-cells in order to determine if the quantity of cells has changed (e.g., decreased) in response to treatment with an agonistic TNFR2 antibody of the invention. A physician may also monitor the fluctuation in the volume of the allograft within the patient during the course of TNFR2 antibody therapy. Based on the results of these analyses, a physician may prescribe higher/lower dosages or more/less frequent dosing of the agonistic TNFR2 antibody in subsequent rounds of treatment in order to preserve the allograft.
Example 7. Treatment of Rheumatoid Arthritis in a Human Patient by Administration of Agonistic TNFR2 AntibodiesThe agonistic TNFR2 antibodies of the invention (e.g., a humanized version of 8E6-D1 or an antigen-binding fragment thereof) can be administered to a human patient in order to treat rheumatoid arthritis. For instance, a human patient suffering from rheumatoid arthritis can be treated by administering an agonistic TNFR2 antibody of the invention by an appropriate route (e.g., intravenously) at a particular dosage (e.g., between 0.001 and 100 mg/kg/day) over a course of days, weeks, months, or years. If desired, the agonistic TNFR2 antibody can be co-administered with, admixed with, or administered separately from, another therapeutic effective for treating rheumatoid arthritis, such as BCG.
The progression of rheumatoid arthritis that is treated with an agonistic TNFR2 antibody of the invention can be monitored by any one or more of several established methods. A physician can monitor the patient by direct observation in order to evaluate how the symptoms exhibited by the patient have changed in response to treatment. For instance, a physician of skill in the art may monitor the level of joint pain, joint stiffness, or muscle range exhibited by the patient in response to TNFR2 antibody therapy. Additionally, a lymph sample isolated from the patient may be analyzed in order to determine the quantity of autoreactive CD8+ T-cells in the sample, e.g., by FACS analysis, which can indicate the effectiveness of the TNFR2 antibody therapy. For instance, if the count of autoreactive CD8+ T-cells in the lymph sample is high, may indicate that the patient is to be administered higher dosages of an agonistic TNFR2 antibody of the invention, e.g., until the autoreactive T-cell population within the patient has been eliminated.
Example 8. Treatment of Multiple Sclerosis in a Human Patient by Administration of Agonistic TNFR2 AntibodiesThe agonistic TNFR2 antibodies of the invention (e.g., a humanized version of 8E6-D1 or an antigen-binding fragment thereof) can be administered to a human patient in order to treat multiple sclerosis. For instance, a human patient suffering from multiple sclerosis can be treated by administering an agonistic TNFR2 antibody of the invention by an appropriate route (e.g., intravenously) at a particular dosage (e.g., between 0.001 and 100 mg/kg/day) over a course of days, weeks, months, or years. If desired, the agonistic TNFR2 antibody can be co-administered with, admixed with, or administered separately from, another therapeutic effective for treating multiple sclerosis, such as BCG.
The progression of multiple sclerosis that is treated with an agonistic TNFR2 antibody of the invention can be monitored by any one or more of several established methods. A physician can monitor the patient by direct observation in order to evaluate how the symptoms exhibited by the patient have changed in response to treatment. For instance, a physician of skill in the art may monitor the patient to determine if he or she is exhibiting improved vision and/or coordination, faster reflexes, increased motor activity, and/or improved cognitive performance in response to TNFR2 antibody therapy. If improvements in these traits are not observed, a physician may prescribe the patient higher doses or more frequent administration of the agonistic TNFR antibody or antigen-binding fragment thereof. Additionally, a lymph sample isolated from the patient may be analyzed in order to determine the quantity of autoreactive CD8+T-cells in the sample, e.g., by FACS analysis, which can indicate the effectiveness of the TNFR2 antibody therapy. For instance, if the count of autoreactive CD8+ T-cells in the lymph sample that recognize myelin sheath-producing cells is high, this may indicate that the patient is to be administered higher dosages of an agonistic TNFR2 antibody of the invention, e.g., until the autoreactive T-cell population within the patient has been eliminated.
Other EmbodimentsAll publications, patents, and patent applications mentioned in this specification are incorporated herein by reference to the same extent as if each independent publication or patent application was specifically and individually indicated to be incorporated by reference.
While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the invention that come within known or customary practice within the art to which the invention pertains and may be applied to the essential features hereinbefore set forth, and follows in the scope of the claims.
Other embodiments are within the claims.
Claims
1. An antibody or antigen-binding fragment thereof that specifically binds human TNFR2, wherein said antibody or antigen-binding fragment thereof specifically binds:
- (a) an epitope within human TNFR2 comprising amino acids 56-60 of SEQ ID NO: 366; and/or
- (b) a polypeptide having the amino acid sequence of any one of SEQ ID NOs: 1-341, 346, and 367;
- and wherein said antibody or antigen-binding fragment thereof does not specifically bind an epitope within human TNFR2 comprising amino acids 142-146 of SEQ ID NO: 366.
2-5. (canceled)
6. The antibody or antigen-binding fragment thereof of claim 1, wherein said antibody or antigen-binding fragment thereof:
- (a) promotes proliferation of a population of T-regulatory (T-reg) cells, optionally in the presence of TNFα;
- (b) promotes cell death in a population of CD8+ T-cells;
- (c) promotes an increase in the level of one or more mRNA molecules encoding a protein selected from the group consisting of cIAP2, TRAF2, Etk, VEGFR2, PI3K, Akt, a protein involved in the angiogenic pathway, an IKK complex, RIP, NIK, MAP3K, a protein involved in the NFkB pathway, NIK, JNK, AP-1, a MEK, MKK3, NEMO, IL2R, Foxp3, IL2, TNF, and lymphotoxin;
- (d) promotes an increase in the level of one or more proteins selected from the group consisting of cIAP2, TRAF2, Etk, VEGFR2, PI3K, Akt, a protein involved in the angiogenic pathway, an IKK complex, RIP, NIK, MAP3K, a protein involved in the NFkB pathway, NIK, JNK, AP-1, a MEK, MKK3, NEMO, IL2R, Foxp3, IL2, TNF, and lymphotoxin;
- (e) activates TNFR2 signaling;
- (f) specifically binds TNFR2 with a KD of no greater than about 10 nM;
- (g) specifically binds TNFR2 to form an antibody-antigen complex with a kon of at least about 104 M−1s−1;
- (h) specifically binds TNFR2 to form an antibody-antigen complex, and wherein said complex dissociates with a koff of no greater than about 10−3s−1; and/or
- (i) does not specifically bind another tumor necrosis factor receptor (TNFR) superfamily member.
7-9. (canceled)
10. The antibody or antigen-binding fragment thereof of claim 1, wherein said antibody or antigen-binding fragment thereof specifically binds:
- (a) an epitope within human TNFR2 comprising at least five discontinuous or continuous residues within amino acids 96-154 of SEQ ID NO: 366
- (b) an epitope within amino acids 111-150 of SEQ ID NO: 366;
- (c) an epitope within amino acids 115-142 of SEQ ID NO: 366;
- (d) an epitope within amino acids 122-136 of SEQ ID NO: 366;
- (e) an epitope within amino acids 101-107 of SEQ ID NO: 366;
- (f) an epitope within amino acids 48-67 of SEQ ID NO: 366; and/or
- (g) said epitope comprising amino acids 56-60 of SEQ ID NO: 366 with a KD of less than about 10 nM.
11-26. (canceled)
27. A method of identifying a TNFR2 agonist antibody or antigen-binding fragment thereof comprising:
- (a) contacting a mixture of antibodies or fragments thereof with at least one peptide having the amino acid sequence of any one of SEQ ID NOs: 1-341, 346, and 367; and
- (b) separating antibodies or fragments thereof that specifically bind said peptide from said mixture, thereby producing an enriched antibody mixture comprising at least one said TNFR2 agonist antibody or antigen-binding fragment thereof.
28. The method of claim 27, wherein:
- (a) said method comprises determining the amino acid sequence of one or more of the antibodies or antigen-binding fragments thereof in said enriched antibody mixture;
- (b) said peptide is bound to a surface;
- (c) said antibody or antigen-binding fragment thereof is expressed on the surface of a phage, bacterial cell, or yeast cell or said antibody or antigen-binding fragment thereof is expressed on the surface of a phage, bacterial cell, or yeast cell;
- (d) said peptide is conjugated to a detectable label;
- (e) steps (a) and (b) are sequentially repeated one or more times; and/or
- (f) the method further comprises: i) exposing said enriched antibody mixture to at least one peptide comprising the amino acid sequence of a TNFR superfamily member other than TNFR2, and retaining antibodies or fragments thereof that do not specifically bind said peptide, thereby producing a TNFR2-specific antibody mixture comprising at least one TNFR2 agonist antibody or antigen-binding fragment thereof that does not specifically bind a TNFR superfamily member other than TNFR2; and/or ii) exposing said enriched antibody mixture to at least one peptide comprising amino acids 142-146 of SEQ ID NO: 366, and retaining antibodies or fragments thereof that do not specifically bind said peptide, thereby producing an antibody mixture comprising at least one TNFR2 agonist antibody or antigen-binding fragment thereof that does not specifically bind a peptide comprising amino acids 142-146 of SEQ ID NO: 366.
29-38. (canceled)
39. A method of producing a TNFR2 agonist antibody or antigen-binding fragment thereof comprising immunizing a non-human mammal with a peptide comprising the sequence of any one of SEQ ID NOs: 1-341, 346, and 367 and collecting serum comprising said TNFR2 agonist antibody or antigen-binding fragment thereof, wherein said antibody or antigen-binding fragment thereof is capable of specifically binding an epitope comprising amino acids 56-60 of SEQ ID NO: 366.
40. The method of claim 39, wherein:
- (a) said non-human mammal is selected from the group consisting of a rabbit, mouse, rat, goat, guinea pig, hamster, horse, and sheep; and/or
- (b) said peptide comprises the amino acid sequence of SEQ ID NO: 11.
41. (canceled)
42. An antibody or antigen-binding fragment thereof that is produced by the method of claim 39.
43-53. (canceled)
54. The antibody or antigen-binding fragment thereof of claim 1, wherein said antibody or antigen-binding fragment thereof is a monoclonal antibody or antigen-binding fragment thereof, a polyclonal antibody or antigen-binding fragment thereof, a human antibody or antigen-binding fragment thereof, a humanized antibody or antigen-binding fragment thereof, a primatized antibody or antigen-binding fragment thereof, a bispecific antibody or antigen-binding fragment thereof, a multi-specific antibody or antigen-binding fragment thereof, a dual-variable immunoglobulin domain, a monovalent antibody or antigen-binding fragment thereof, a chimeric antibody or antigen-binding fragment thereof, a single-chain Fv molecule (scFv), a diabody, a triabody, a nanobody, an antibody-like protein scaffold, a domain antibody, a Fv fragment, a Fab fragment, a F(ab′)2 molecule, or a tandem scFv (taFv).
55. (canceled)
56. The antibody of claim 1, wherein said antibody comprises an immunoglobulin subtype selected from the group consisting of IgG, IgM, IgA, IgD, and IgE.
57. A pharmaceutical composition comprising the antibody or antigen-binding fragment thereof of claim 1 and a pharmaceutically acceptable carrier or excipient.
58. The pharmaceutical composition of claim 57, wherein said pharmaceutical composition further comprises an additional therapeutic agent, optionally wherein said additional therapeutic agent is selected from the group consisting of TNFα and BCG.
59-61. (canceled)
62. A polynucleotide encoding the antibody or antigen-binding fragment thereof of claim 1.
63. A vector comprising the polynucleotide of claim 62.
64-70. (canceled)
71. An isolated host cell comprising the vector of claim 63.
72. The host cell of claim 71, wherein said host cell is:
- (a) a prokaryotic cell; or
- (b) a eukaryotic cell; optionally wherein said eukaryotic cell is a CHO cell, a DHFR CHO cell, a NSO myeloma cell, a COS cell, a 293 cell, or a SP2/0 cell.
73-75. (canceled)
76. A method of producing the antibody or antigen-binding fragment thereof of claim 1, said method comprising expressing a polynucleotide encoding said antibody or antigen-binding fragment thereof in a host cell and recovering the antibody or antigen-binding fragment thereof from host cell medium.
77. A method of inhibiting an immune response mediated by a B cell or CD8+ T cell in a subject, said method comprising administering to the subject the antibody or antigen-binding fragment thereof of claim 1.
78. A method of treating an immunological disease in a subject, said method comprising administering to the subject the antibody or antigen-binding fragment thereof of claim 1.
79. The method of claim 78, wherein said subject is in need of a tissue or organ regeneration.
80. The method of claim 79, wherein said tissue or organ is selected from the group consisting of a pancreas, salivary gland, pituitary gland, kidney, heart, lung, hematopoietic system, cranial nerves, heart, aorta, olfactory gland, ear, nerves, structures of the head, eye, thymus, tongue, bone, liver, small intestine, large intestine, gut, lung, brain, skin, peripheral nervous system, central nervous system, spinal cord, breast, embryonic structures, embryos, and testes.
81. The method of claim 78, wherein said immunological disease is selected from the group consisting of an autoimmune disease, a neurological condition, an allergy, asthma, macular degeneration, muscular atrophy, a disease related to miscarriage, atherosclerosis, bone loss, a musculoskeletal disease, obesity, a graft-versus-host disease, and an allograft rejection.
82. The method of claim 81, wherein:
- (a) said autoimmune disease is selected from the group consisting of type I diabetes, Alopecia Areata, Ankylosing Spondylitis, Antiphospholipid Syndrome, Autoimmune Addison's Disease, Autoimmune Hemolytic Anemia, Autoimmune Hepatitis, Behcet's Disease, Bullous Pemphigoid, Cardiomyopathy, Celiac Sprue-Dermatitis, Chronic Fatigue Immune Dysfunction Syndrome (CFIDS), Chronic Inflammatory Demyelinating Polyneuropathy, Churg-Strauss Syndrome, Cicatricial Pemphigoid, CREST Syndrome, Cold Agglutinin Disease, Crohn's Disease, Essential Mixed Cryoglobulinemia, Fibromyalgia-Fibromyositis, Graves' Disease, Guillain-Barré, Hashimoto's Thyroiditis, Hypothyroidism, Idiopathic Pulmonary Fibrosis, Idiopathic Thrombocytopenia Purpura (ITP), IgA Nephropathy, Juvenile Arthritis, Lichen Planus, Lupus, Meniere's Disease, Mixed Connective Tissue Disease, Multiple Sclerosis, Myasthenia Gravis, Pemphigus Vulgaris, Pernicious Anemia, Polyarteritis Nodosa, Polychondritis, Polyglandular Syndromes, Polymyalgia Rheumatica, Polymyositis and Dermatomyositis, Primary Agammaglobulinemia, Primary Biliary Cirrhosis, Psoriasis, Raynaud's Phenomenon, Reiter's Syndrome, Rheumatic Fever, Rheumatoid Arthritis, Sarcoidosis, Scleroderma, Sjögren's Syndrome, Stiff-Man Syndrome, Takayasu Arteritis, Temporal Arteritis/Giant Cell Arteritis, Ulcerative Colitis, Uveitis, Vasculitis, Vitiligo, and Wegener's Granulomatosis;
- (b) said neurological condition is selected from the group consisting of a brain tumor, a brain metastasis, a spinal cord injury, schizophrenia, epilepsy, Amyotrophic lateral sclerosis (ALS), Parkinson's disease, Alzheimer's disease, Huntington's disease, and stroke;
- (c) said allergy is selected from the group consisting of food allergy, seasonal allergy, pet allergy, hives, hay fever, allergic conjunctivitis, poison ivy allergy oak allergy, mold allergy, drug allergy, dust allergy, cosmetic allergy, and chemical allergy;
- (d) said graft-versus-host disease arises from a bone marrow transplant or one or more blood cells selected from the group consisting of hematopoietic stem cells, common myeloid progenitor cells, common lymphoid progenitor cells, megakaryocytes, monocytes, basophils, eosinophils, neutrophils, macrophages, T-cells, B-cells, natural killer cells, and dendritic cells; and/or
- (e) said allograft rejection is selected from the group consisting of skin graft rejection, bone graft rejection, vascular tissue graft rejection, ligament graft rejection, and organ graft rejection, optionally wherein: (i) said ligament graft rejection is selected from the group consisting of cricothyroid ligament graft rejection, periodontal ligament graft rejection, suspensory ligament of the lens graft rejection, palmar radiocarpal ligament graft rejection, dorsal radiocarpal ligament graft rejection, ulnar collateral ligament graft rejection, radial collateral ligament graft rejection, suspensory ligament of the breast graft rejection, anterior sacroiliac ligament graft rejection, posterior sacroiliac ligament graft rejection, sacrotuberous ligament graft rejection, sacrospinous ligament graft rejection, inferior pubic ligament graft rejection, superior pubic ligament graft rejection, anterior cruciate ligament graft rejection, lateral collateral ligament graft rejection, posterior cruciate ligament graft rejection, medial collateral ligament graft rejection, cranial cruciate ligament graft rejection, caudal cruciate ligament graft rejection, and patellar ligament graft rejection; and/or (ii) said organ graft rejection is selected from the group consisting of heart graft rejection, lung graft rejection, kidney graft rejection, liver graft rejection, pancreas graft rejection, intestine graft rejection, and thymus graft rejection.
83-88. (canceled)
89. The method of claim 78, wherein said method further comprises administering to said subject an additional therapeutic agent.
90. The method of claim 89, wherein said additional therapeutic agent is selected from the group consisting of TNFα and BCG.
91-92. (canceled)
93. The method of claim 78, wherein said subject is a mammal.
94. The method of claim 93, wherein said mammal is a human.
95. The method of claim 78, wherein said antibody is 8E6.D1 or a humanized antibody or antigen-binding fragment thereof comprising one or more heavy chain or light chain CDRs of 8E6.D1.
96. (canceled)
97. A kit comprising the antibody or antigen-binding fragment thereof of claim 1, a polynucleotide encoding the antibody or antigen-binding fragment thereof, a vector comprising the polynucleotide, or a host cell comprising the vector or polynucleotide, wherein the kit optionally comprises a package insert that instructs a user of said kit to administer said antibody or antigen-binding fragment thereof, polynucleotide, vector, or host cell to a human patient suffering from an immunological disease.
98-129. (canceled)
130. The antibody or antigen-binding fragment thereof of claim 1, wherein said antibody or antigen-binding fragment thereof comprises a non-native constant region.
131. The antibody or antigen-binding fragment thereof of claim 1, wherein said antibody or antigen-binding fragment thereof is an isolated, non-murine antibody.
132-133. (canceled)
Type: Application
Filed: Aug 26, 2016
Publication Date: May 9, 2019
Inventor: Denise L. FAUSTMAN (Boston, MA)
Application Number: 15/755,404
