# Patent

## Title
Antibodies to Toso

## Abstract

The present invention provides methods and compositions for modulating Toso activity and treating diseases and disorders in which Toso is implicated. Such methods and compositions include the use of one or more antibodies that bind to a Toso protein or to a ligand of a Toso protein.

## Background
CROSS REFERENCES TO RELATED APPLICATIONS
The present application claims the benefit of U.S. Provisional Application No. 61/842,766, filed Jul. 3, 2013, the content of which is expressly incorporated herein by reference in its entirety for all purposes.


BACKGROUND OF THE INVENTION
Toso or Faim3 (Fas Apoptotic inducing molecule 3) is a single membrane spanning cell surface receptor originally characterized through a retroviral overexpression screen in Jurkat cells, a T cell leukemic line, as a mediator of Fas-induced apoptotic cell death (Hitoshi, Y., et al., Toso, a cell surface, specific regulator of Fas-induced apoptosis in T cells. Immunity, 1998. 8(4): p. 461-71). Subsequent studies have suggested that Toso is the elusive receptor for IgM. The expression of Toso also seems to correlate with particularly aggressive forms of Chronic Lymphocytic Leukemia, or CLL. Modulation of Toso activity may also affect immune system disorders.
There is a need for molecules that are able to modulate Toso activity.
SUMMARY OF THE INVENTION
Accordingly, the present invention provides methods and compositions for modulating Toso activity and treating diseases and disorders in which Toso is implicated.
In one aspect, the present invention provides antibodies that bind to Toso or to a ligand of Toso.
In a further aspect, the present invention provides an antibody comprising a heavy chain variable region comprising any one of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57.
In a further embodiment, the present invention provides an antibody comprising a heavy chain variable region having a sequence with at least about 95% sequence identity to any one of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, wherein the antibody binds Toso.
In a further aspect, the present invention provides an antibody comprising a light chain variable region comprising any one of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58.
In a further embodiment, the present invention provides an antibody comprising a light chain variable region having a sequence with at least about 95% sequence identity to any one of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, wherein the antibody binds Toso.
In a further aspect, the present invention provides an antibody comprising: a first heavy chain CDR comprising any of the CDR1 sequences listed in Table 1, a second heavy chain CDR comprising any of the CDR2 sequences listed in Table 1, a third heavy chain CDR comprising any of the CDR3 sequences listed in Table 1, a first light chain CDR comprising any of the CDR1 sequences listed in Table 2, a second light chain CDR comprising any of the CDR2 sequences listed in Table 2, and a third light chain CDR comprising any of the CDR3 sequences listed in Table 2, wherein said antibody binds Toso.
In a still further aspect, the antibodies described herein encompass humanized antibodies.
In a still further aspect, the present invention provides a nucleic acid encoding an antibody in accordance with any of the above-described antibodies.
In a yet further aspect, the present invention provides an expression vector, that encodes an antibody in accordance with any of the above-described antibodies.
In a still further aspect, the present invention provides a method of making an antibody in accordance with any of the above-described antibodies, where the method includes the step of providing a cell comprising a nucleic acid encoding the antibody, where the cell is cultured under conditions suitable for expression of the antibody.
In a yet further aspect, the present invention provides methods for treating a Toso-associated disease that include treating a subject in need thereof with an antibody in accordance with any of the above-described antibodies



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 provides sequences of antibodies that bind to Toso. Asterisks denote stop codons, which can in some embodiments be removed by protein engineering methods known in the art to allow for expression of the full length sequence.
FIG. 2 provides sequences of antibodies that do not bind to Toso. Asterisks denote stop codons, which can in some embodiments be removed by protein engineering methods known in the art to allow for expression of the full length sequence.



DETAILED DESCRIPTION OF THE INVENTION
The practice of the present invention may employ, unless otherwise indicated, conventional techniques and descriptions of organic chemistry, polymer technology, molecular biology (including recombinant techniques), cell biology, biochemistry, and immunology, which are within the skill of the art. Such conventional techniques include polymer array synthesis, hybridization, ligation, phage display, and detection of hybridization using a label. Specific illustrations of suitable techniques can be had by reference to the example herein below. However, other equivalent conventional procedures can, of course, also be used. Such conventional techniques and descriptions can be found in standard laboratory manuals such as Genome Analysis: A Laboratory Manual Series (Vols. I-IV), Using Antibodies: A Laboratory Manual, Cells: A Laboratory Manual, PCR Primer: A Laboratory Manual, and Molecular Cloning: A Laboratory Manual (all from Cold Spring Harbor Laboratory Press), Stryer, L. (1995) Biochemistry (4th Ed.) Freeman, New York, Gait, “Oligonucleotide Synthesis: A Practical Approach” 1984, IRL Press, London, Nelson and Cox (2000), Lehninger, Principles of Biochemistry 3rd Ed., W. H. Freeman Pub., New York, N.Y. and Berg et al. (2002) Biochemistry, 5th Ed., W. H. Freeman Pub., New York, N.Y., all of which are herein incorporated in their entirety by reference for all purposes.
Note that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a polymerase” refers to one agent or mixtures of such agents, and reference to “the method” includes reference to equivalent steps and methods known to those skilled in the art, and so forth.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. All publications mentioned herein are incorporated herein by reference for the purpose of describing and disclosing devices, compositions, formulations and methodologies which are described in the publication and which might be used in connection with the presently described invention.
Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges is also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either both of those included limits are also included in the invention.
In the following description, numerous specific details are set forth to provide a more thorough understanding of the present invention. However, it will be apparent to one of skill in the art that the present invention may be practiced without one or more of these specific details. In other instances, well-known features and procedures well known to those skilled in the art have not been described in order to avoid obscuring the invention.
In order that the application may be more completely understood, several definitions are set forth below. Such definitions are meant to encompass grammatical equivalents.
As used herein, the term “comprising” is intended to mean that the compositions and methods include the recited elements, but not excluding others. “Consisting essentially of” when used to define compositions and methods, shall mean excluding other elements of any essential significance to the composition or method. “Consisting of” shall mean excluding more than trace elements of other ingredients for claimed compositions and substantial method steps. Embodiments defined by each of these transition terms are within the scope of this invention. Accordingly, it is intended that the methods and compositions can include additional steps and components (comprising) or alternatively including steps and compositions of no significance (consisting essentially of) or alternatively, intending only the stated method steps or compositions (consisting of).
All numerical designations, e.g., pH, temperature, time, concentration, and molecular weight, including ranges, are approximations which are varied (+) or (−) by increments of 0.1. It is to be understood, although not always explicitly stated that all numerical designations are preceded by the term “about”. The term “about” also includes the exact value “X” in addition to minor increments of “X” such as “X+0.1” or “X−0.1.” It also is to be understood, although not always explicitly stated, that the reagents described herein are merely exemplary and that equivalents of such are known in the art.
A “composition” may include any substance comprising an agent or compound and is also intended to encompass any combination of an agent or compound and other substances, including a carrier, e.g., compound or composition, inert (for example, a detectable agent or label) or active, such as an adjuvant, diluent, binder, stabilizer, buffers, salts, lipophilic solvents, preservative, adjuvant or the like. Carriers also include pharmaceutical excipients and additives proteins, peptides, amino acids, lipids, and carbohydrates (e.g., sugars, including monosaccharides, di-, tri-, tetra-, and oligosaccharides; derivatized sugars such as alditols, aldonic acids, esterified sugars and the like; and polysaccharides or sugar polymers), which can be present singly or in combination, comprising alone or in combination 1-99.99% by weight or volume. Exemplary protein excipients include serum albumin such as human serum albumin (HSA), recombinant human albumin (rHA), gelatin, casein, and the like. Representative amino acid/antibody components, which can also function in a buffering capacity, include alanine, glycine, arginine, betaine, histidine, glutamic acid, aspartic acid, cysteine, lysine, leucine, isoleucine, valine, methionine, phenylalanine, aspartame, and the like. Carbohydrate excipients are also intended within the scope of this invention, examples of which include but are not limited to monosaccharides such as fructose, maltose, galactose, glucose, D-mannose, sorbose, and the like; disaccharides, such as lactose, sucrose, trehalose, cellobiose, and the like; polysaccharides, such as raffinose, melezitose, maltodextrins, dextrans, starches, and the like; and alditols, such as mannitol, xylitol, maltitol, lactitol, xylitol sorbitol (glucitol) and myoinositol.
The term pharmaceutically acceptable carrier (or medium), which may be used interchangeably with the term biologically compatible carrier or medium, refers to reagents, cells, compounds, materials, compositions, and/or dosage forms that are not only compatible with the cells and other agents to be administered therapeutically, but also are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other complication commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable carriers suitable for use in the present invention include liquids, semi-solid (e.g., gels) and solid materials (e.g., cell scaffolds and matrices, tubes sheets and other such materials as known in the art and described in greater detail herein). These semi-solid and solid materials may be designed to resist degradation within the body (non-biodegradable) or they may be designed to degrade within the body (biodegradable, bioerodable). A biodegradable material may further be bioresorbable or bioabsorbable, i.e., it may be dissolved and absorbed into bodily fluids (water-soluble implants are one example), or degraded and ultimately eliminated from the body, either by conversion into other materials or breakdown and elimination through natural pathways.
As used herein, the term “patient” or “subject” intends an animal, a mammal or yet further a human patient. For the purpose of illustration only, a mammal includes but is not limited to a human, a simian, a murine, a bovine, an equine, a porcine or an ovine.
As used herein, the term “oligonucleotide” or “polynucleotide” refers to a short polymer composed of deoxyribonucleotides, ribonucleotides or any combination thereof. Oligonucleotides are generally at least about 10, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100 or more nucleotides in length. An oligonucleotide may be used as a primer or as a probe.
The term “amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, γ-carboxyglutamate, and O-phosphoserine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that function in a manner similar to a naturally occurring amino acid.
The term “isolated” as used herein refers to molecules or biological or cellular materials being substantially free from other materials, e.g., greater than 70%, or 80%, or 85%, or 90%, or 95%, or 98%. In one aspect, the term “isolated” refers to nucleic acid, such as DNA or RNA, or protein or polypeptide, or cell or cellular organelle, or tissue or organ, separated from other DNAs or RNAs, or proteins or polypeptides, or cells or cellular organelles, or tissues or organs, respectively, that are present in the natural source and which allow the manipulation of the material to achieve results not achievable where present in its native or natural state, e.g., recombinant replication or manipulation by mutation. The term “isolated” also refers to a nucleic acid or peptide that is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized. Moreover, an “isolated nucleic acid” is meant to include nucleic acid fragments which are not naturally occurring as fragments and would not be found in the natural state. The term “isolated” is also used herein to refer to polypeptides which are isolated from other cellular proteins and is meant to encompass both purified and recombinant polypeptides, e.g., with a purity greater than 70%, or 80%, or 85%, or 90%, or 95%, 98%, or 99%. The term “isolated” is also used herein to refer to cells or tissues that are isolated from other cells or tissues and is meant to encompass both cultured and engineered cells or tissues.
A “recombinant” nucleic acid refers an artificial nucleic acid that is created by combining two or more sequences that would not normally occur together. In one embodiment, it is created through the introduction of relevant DNA into an existing organismal DNA, such as the plasmids of bacteria, to code for or alter different traits for a specific purpose, such as antibiotic resistance. A “recombinant” polypeptide is a polypeptide that is derived from a recombinant nucleic acid.
As used herein, the term “promoter” refers to a nucleic acid sequence sufficient to direct transcription of a gene. Also included in the invention are those promoter elements which are sufficient to render promoter dependent gene expression controllable for cell type specific, tissue specific or inducible by external signals or agents.
In some embodiments, a promoter is an inducible promoter or a discrete promoter. Inducible promoters can be turned on by a chemical or a physical condition such as temperature or light. Examples of chemical promoters include, without limitation, alcohol-regulated, tetracycline-regulated, steroid-regulated, metal-regulated and pathogenesis-related promoters. Examples of discrete promoters can be found in, for examples, Wolfe et al. Molecular Endocrinology 16(3): 435-49.
As used herein, the term “regulatory element” refers to a nucleic acid sequence capable of modulating the transcription of a gene. Non-limiting examples of regulatory element include promoter, enhancer, silencer, poly-adenylation signal, transcription termination sequence. Regulatory element may be present 5′ or 3′ regions of the native gene, or within an intron.
Various proteins are also disclosed herein with their GenBank Accession Numbers for their human proteins and coding sequences. However, the proteins are not limited to human-derived proteins having the amino acid sequences represented by the disclosed GenBank Accession Nos, but may have an amino acid sequence derived from other animals, particularly, a warm-blooded animal (e.g., rat, guinea pig, mouse, chicken, rabbit, pig, sheep, cow, monkey, etc.).
As used herein, the term “Toso”, “FAIM3” or “Fas apoptotic inhibitory molecule 3” refers to a protein having an amino acid sequence substantially identical to any of the representative Toso sequences, including any and all versions of GenBank Accession Nos. NP_001135945 (human isoform b), NP_001180267 (human isoform c), NP_005440 (human isoform a), NP_081252 (mouse) or NP_001014843 (rat). Suitable cDNA encoding Toso are provided at GenBank Accession Nos. NM_001142473, NM_001193338, NM_005449, NM_026976, and NM_001014843.
As used herein, the term “biological activity of Toso” or “Toso activity” refers to any biological activity associated with the full length native Toso protein. In some embodiments, the biological activity of Toso refers to binding to an IgM antibody. In further embodiments, the biological activity of Toso refers to inhibiting CD11b or CD18 activity. In yet further embodiments, the biological activity of Toso refers to increasing the activation threshold of granulocytes. Activation threshold can be measured by number of activated granulocytes from bone marrow. In further embodiments, the biological activity of Toso includes the activation of dendritic cells and their ability to present antigen to T cells. In further embodiments, the biological activity of Toso includes inhibition of apoptosis or enhancement of TNF signaling. In some embodiments, the Toso biological activity is equivalent to the activity of a protein having an amino acid sequence represented by GenBank Accession No. NP_001135945, NP_001180267, NP_005440, NP_081252 or NP_001014843, including any and all versions of these accession numbers.
As used herein, the term “treating” refers to administering a pharmaceutical composition for the purpose of improving the condition of a patient by reducing, alleviating, reversing, or preventing at least one adverse effect or symptom of a disease or disorder.
As used herein, the term “preventing” refers to identifying a subject (i.e., a patient) having an increased susceptibility to a disease but not yet exhibiting symptoms of the disease, and administering a therapy according to the principles of this disclosure. The preventive therapy is designed to reduce the likelihood that the susceptible subject will later become symptomatic or that the disease will be delay in onset or progress more slowly than it would in the absence of the preventive therapy. A subject may be identified as having an increased likelihood of developing the disease by any appropriate method including, for example, by identifying a family history of the disease or other degenerative brain disorder, or having one or more diagnostic markers indicative of disease or susceptibility to disease.
As used herein, the term “sample” or “test sample” refers to any liquid or solid material containing nucleic acids. In suitable embodiments, a test sample is obtained from a biological source (i.e., a “biological sample”), such as cells in culture or a tissue sample from an animal, most preferably, a human.
As used herein, the term “substantially identical”, when referring to a protein or polypeptide, is meant one that has at least 80%, 85%, 90%, 95%, or 99% sequence identity to a reference amino acid sequence. The length of comparison is preferably the full length of the polypeptide or protein, but is generally at least 10, 15, 20, 25, 30, 40, 50, 60, 80, or 100 or more contiguous amino acids. A “substantially identical” nucleic acid is one that has at least 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to a reference nucleic acid sequence. The length of comparison is preferably the full length of the nucleic acid, but is generally at least 20 nucleotides, 30 nucleotides, 40 nucleotides, 50 nucleotides, 75 nucleotides, 100 nucleotides, 125 nucleotides, or more.
As used herein, an “amino acid substitution” or “substitution” refers to the replacement of an amino acid at a particular position in a starting polypeptide sequence with another amino acid. For example, the substitution M23Y refers to a variant polypeptide in which the methionine at position 23 is replaced with a tyrosine.
A “biological equivalent” of a protein or nucleic acid refers to a protein or nucleic acid that is substantially identical to the protein or nucleic acid by amino acid or nucleic acid sequence or that has an equivalent biological activity.
As used herein, the term “effective amount” refers to a quantity of compound (e.g., an antibody or biologically active fragment thereof) delivered with sufficient frequency to provide a medical benefit to the patient. In one embodiment, an effective amount of a protein is an amount sufficient to treat or ameliorate a symptom of a disease.
A “population” of cells refers to a collection of more than one cell that is identical (clonal) or non-identical in phenotype and/or genotype.
“Substantially homogeneous” describes a population of cells in which more than about 50%, or alternatively more than about 60%, or alternatively more than 70%, or alternatively more than 75%, or alternatively more than 80%, or alternatively more than 85%, or alternatively more than 90%, or alternatively, more than 95%, of the cells are of the same or similar phenotype. Phenotype can be determined by a pre-selected cell surface marker or other marker.
The terms autologous transfer, autologous transplantation, autograft and the like refer to treatments wherein the cell donor is also the recipient of the cell replacement therapy. The terms allogeneic transfer, allogeneic transplantation, allograft and the like refer to treatments wherein the cell donor is of the same species as the recipient of the cell replacement therapy, but is not the same individual. A cell transfer in which the donor's cells and have been histocompatibly matched with a recipient is sometimes referred to as a syngeneic transfer. The terms xenogeneic transfer, xenogeneic transplantation, xenograft and the like refer to treatments wherein the cell donor is of a different species than the recipient of the cell replacement therapy.
As used herein, an “antibody” includes whole antibodies and any antigen binding fragment or a single chain thereof. Thus the term “antibody” includes any protein or peptide containing molecule that comprises at least a portion of an immunoglobulin molecule. Examples of such include, but are not limited to a 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 (FR) region, or any portion thereof, or at least one portion of a binding protein. In general, the term “antibody” includes any polypeptide that includes at least one constant domain, including, but not limited to, CH1, CH2, CH3 and CL. Antibodies that find use in the present invention can take on a number of formats as described herein, including traditional antibodies as well as antibody derivatives, fragments and mimetics.
The antibodies can be polyclonal or monoclonal and can be isolated from any suitable biological source, e.g., murine, rat, sheep and canine.
A monoclonal antibody is an antibody produced by a single clone of cells or a hybridoma, and therefore is a single pure homogeneous type of antibody.
A hybridoma is a cell that is produced in the laboratory from the fusion of an antibody-producing lymphocyte and a non-antibody producing cancer cell, usually a myeloma or lymphoma. A hybridoma proliferates and produces a continuous supply of a specific monoclonal antibody.
The term “human antibody” as used herein, is intended to include antibodies having variable and constant regions derived from human germline immunoglobulin sequences. The human antibodies of the invention may include amino acid residues not encoded by human germline immunoglobulin sequences (e.g., mutations introduced by random or site-specific mutagenesis in vitro or by somatic mutation in vivo). However, the term “human antibody” as used herein, is not intended to include antibodies in which CDR sequences derived from the germline of another mammalian species, such as a mouse, have been grafted onto human framework sequences. Thus, 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 substantially non-immunogenic in humans, with only minor sequence changes or variations. Similarly, antibodies designated primate (monkey, baboon, chimpanzee, etc.), rodent (mouse, rat, rabbit, guinea pig, hamster, and the like) and other mammals designate such species, sub-genus, genus, sub-family, family specific antibodies. Further, chimeric antibodies include any combination of the above. Such changes or variations optionally and preferably retain or reduce the immunogenicity in humans or other species relative to non-modified antibodies. Thus, a human antibody is distinct from a chimeric or humanized antibody. It is pointed out that a human antibody can be produced by a non-human animal or prokaryotic or eukaryotic cell that is capable of expressing functionally rearranged human immunoglobulin (e.g., heavy chain and/or light chain) genes. Further, when a human antibody is a single chain antibody, it can comprise a linker peptide that is not found in native human antibodies. For example, an Fv can comprise a linker peptide, such as two to about eight glycine or other amino acid residues, which connects the variable region of the heavy chain and the variable region of the light chain. Such linker peptides are considered to be of human origin.
As used herein, a human antibody is “derived from” a particular germline sequence if the antibody is obtained from a system using human immunoglobulin sequences, e.g., by immunizing a transgenic mouse carrying human immunoglobulin genes or by screening a human immunoglobulin gene library. A human antibody that is “derived from” a human germline immunoglobulin sequence can be identified as such by comparing the amino acid sequence of the human antibody to the amino acid sequence of human germline immunoglobulins. A selected human antibody typically is at least 90% identical in amino acids sequence to an amino acid sequence encoded by a human germline immunoglobulin gene and contains amino acid residues that identify the human antibody as being human when compared to the germline immunoglobulin amino acid sequences of other species (e.g., murine germline sequences). In certain cases, a human antibody may be at least 95%, or even at least 96%, 97%, 98%, or 99% identical in amino acid sequence to the amino acid sequence encoded by the germline immunoglobulin gene. Typically, a human antibody derived from a particular human germline sequence will display no more than 10 amino acid differences from the amino acid sequence encoded by the human germline immunoglobulin gene. In certain cases, the human antibody may display no more than 5, or even no more than 4, 3, 2, or 1 amino acid difference from the amino acid sequence encoded by the germline immunoglobulin gene.
The term “recombinant human antibody”, as used herein, includes all human antibodies that are prepared, expressed, created or isolated by recombinant means, such as antibodies isolated from an animal (e.g., a mouse) that is transgenic or transchromosomal for human immunoglobulin genes or a hybridoma prepared therefrom, antibodies isolated from a host cell transformed to express the antibody, e.g., from a transfectoma, antibodies isolated from a recombinant, combinatorial human antibody library, and antibodies prepared, expressed, created or isolated by any other means that involve splicing of human immunoglobulin gene sequences to other DNA sequences. Such recombinant human antibodies have variable and constant regions derived from human germline immunoglobulin sequences. In certain embodiments, however, such recombinant human antibodies can be subjected to in vitro mutagenesis (or, when an animal transgenic for human Ig sequences is used, in vivo somatic mutagenesis) and thus the amino acid sequences of the VH and VL regions of the recombinant antibodies are sequences that, while derived from and related to human germline VH and VL sequences, may not naturally exist within the human antibody germline repertoire in vivo. Methods to making these antibodies are described herein.
“Isotype” as used herein is meant any of the subclasses of immunoglobulins defined by the chemical and antigenic characteristics of their constant regions. It should be understood that therapeutic antibodies can also comprise hybrids of isotypes and/or subclasses.
The terms “polyclonal antibody” or “polyclonal antibody composition” as used herein refer to a preparation of antibodies that are derived from different B-cell lines. They are a mixture of immunoglobulin molecules secreted against a specific antigen, each recognizing a different epitope.
The terms “monoclonal antibody” or “monoclonal antibody composition” as used herein refer to a preparation of antibody molecules of single molecular composition. A monoclonal antibody composition displays a single binding specificity and affinity for a particular epitope.
As used herein, the term “label” intends a directly or indirectly detectable compound or composition that is conjugated directly or indirectly to the composition to be detected, e.g., N-terminal histidine tags (N-His), magnetically active isotopes, e.g., 115Sn, 117Sn and 119Sn, a non-radioactive isotopes such as 13C and 15N, polynucleotide or protein such as an antibody so as to generate a “labeled” composition. The term also includes sequences conjugated to the polynucleotide that will provide a signal upon expression of the inserted sequences, such as green fluorescent protein (GFP) and the like. The label may be detectable by itself (e.g. radioisotope labels or fluorescent labels) or, in the case of an enzymatic label, may catalyze chemical alteration of a substrate compound or composition which is detectable. The labels can be suitable for small scale detection or more suitable for high-throughput screening. As such, suitable labels include, but are not limited to magnetically active isotopes, non-radioactive isotopes, radioisotopes, fluorochromes, chemiluminescent compounds, dyes, and proteins, including enzymes. The label may be simply detected or it may be quantified. A response that is simply detected generally comprises a response whose existence merely is confirmed, whereas a response that is quantified generally comprises a response having a quantifiable (e.g., numerically reportable) value such as an intensity, polarization, and/or other property. In luminescence or fluorescence assays, the detectable response may be generated directly using a luminophore or fluorophore associated with an assay component actually involved in binding, or indirectly using a luminophore or fluorophore associated with another (e.g., reporter or indicator) component.
Examples of luminescent labels that produce signals include, but are not limited to bioluminescence and chemiluminescence. Detectable luminescence response generally comprises a change in, or an occurrence of, a luminescence signal. Suitable methods and luminophores for luminescently labeling assay components are known in the art and described for example in Haugland, Richard P. (1996) Handbook of Fluorescent Probes and Research Chemicals (6th ed.). Examples of luminescent probes include, but are not limited to, aequorin and luciferases.
Examples of suitable fluorescent labels include, but are not limited to, fluorescein, rhodamine, tetramethylrhodamine, eosin, erythrosin, coumarin, methyl-coumarins, pyrene, Malacite green, stilbene, Lucifer Yellow, Cascade BIueTM, and Texas Red. Other suitable optical dyes are described in the Haugland, Richard P. (1996) Handbook of Fluorescent Probes and Research Chemicals (6th ed.).
In another aspect, the fluorescent label is functionalized to facilitate covalent attachment to a cellular component present in or on the surface of the cell or tissue such as a cell surface marker. Suitable functional groups, including, but not are limited to, isothiocyanate groups, amino groups, haloacetyl groups, maleimides, succinimidyl esters, and sulfonyl halides, all of which may be used to attach the fluorescent label to a second molecule. The choice of the functional group of the fluorescent label will depend on the site of attachment to either a linker, the agent, the marker, or the second labeling agent.
By “ADCC” or “antibody dependent cell-mediated cytotoxicity” as used herein is meant the cell-mediated reaction wherein nonspecific cytotoxic cells that express FcγRs recognize bound antibody on a target cell and subsequently cause lysis of the target cell. ADCC is correlated with binding to FcγRIIIa; increased binding to FcγRIIIa leads to an increase in ADCC activity.
By “ADCP” or antibody dependent cell-mediated phagocytosis as used herein is meant the cell-mediated reaction wherein nonspecific cytotoxic cells that express FcγRs recognize bound antibody on a target cell and subsequently cause phagocytosis of the target cell.
By “modification” herein is meant an amino acid substitution, insertion, and/or deletion in a polypeptide sequence or an alteration to a moiety chemically linked to a protein. For example, a modification may be an altered carbohydrate or PEG structure attached to a protein. By “amino acid modification” herein is meant an amino acid substitution, insertion, and/or deletion in a polypeptide sequence. For clarity, unless otherwise noted, the amino acid modification is always to an amino acid coded for by DNA, e.g. the 20 amino acids that have codons in DNA and RNA.
By “amino acid substitution” or “substitution” herein is meant the replacement of an amino acid at a particular position in a parent polypeptide sequence with a different amino acid. In particular, in some embodiments, the substitution is to an amino acid that is not naturally occurring at the particular position, either not naturally occurring within the organism or in any organism. For example, the substitution E272Y refers to a variant polypeptide, in which the glutamic acid at position 272 is replaced with tyrosine. For clarity, a protein which has been engineered to change the nucleic acid coding sequence but not change the starting amino acid (for example exchanging CGG (encoding arginine) to CGA (still encoding arginine) to increase host organism expression levels) is not an “amino acid substitution”; that is, despite the creation of a new gene encoding the same protein, if the protein has the same amino acid at the particular position that it started with, it is not an amino acid substitution.
By “amino acid insertion” or “insertion” as used herein is meant the addition of an amino acid sequence at a particular position in a parent polypeptide sequence. For example, −233E or 233E designates an insertion of glutamic acid after position 233 and before position 234. Additionally, −233ADE or A233ADE designates an insertion of AlaAspGlu after position 233 and before position 234.
By “amino acid deletion” or “deletion” as used herein is meant the removal of an amino acid sequence at a particular position in a parent polypeptide sequence. For example, E233- or E233# designates a deletion of glutamic acid at position 233. Additionally, EDA233- or EDA233# designates a deletion of the sequence GluAspAla that begins at position 233.
By “variant protein” or “protein variant”, or “variant” as used herein is meant a protein that differs from that of a parent protein by virtue of at least one amino acid modification. Protein variant may refer to the protein itself, a composition comprising the protein, or the amino sequence that encodes it. Preferably, the protein variant has at least one amino acid modification compared to the parent protein, e.g. from about one to about seventy amino acid modifications, and preferably from about one to about five amino acid modifications compared to the parent. In some embodiments the parent polypeptide, for example an Fc parent polypeptide, is a human wild type sequence, such as the Fc region from IgG1, IgG2, IgG3 or IgG4, although human sequences with variants can also serve as “parent polypeptides”. The protein variant sequence herein will preferably possess at least about 80% identity with a parent protein sequence, and most preferably at least about 90% identity, more preferably at least about 95-98-99% identity. Variant protein can refer to the variant protein itself, compositions comprising the protein variant, or the DNA sequence that encodes it. Accordingly, by “antibody variant” or “variant antibody” as used herein is meant an antibody that differs from a parent antibody by virtue of at least one amino acid modification, “IgG variant” or “variant IgG” as used herein is meant an antibody that differs from a parent IgG (again, in many cases, from a human IgG sequence) by virtue of at least one amino acid modification, and “immunoglobulin variant” or “variant immunoglobulin” as used herein is meant an immunoglobulin sequence that differs from that of a parent immunoglobulin sequence by virtue of at least one amino acid modification. “Fc variant” or “variant Fc” as used herein is meant a protein comprising an amino acid modification in an Fc domain. The Fc variants of the present invention are defined according to the amino acid modifications that compose them. Thus, for example, N434S or 434S is an Fc variant with the substitution serine at position 434 relative to the parent Fc polypeptide, wherein the numbering is according to the EU index. Likewise, M428L/N434S defines an Fc variant with the substitutions M428L and N434S relative to the parent Fc polypeptide. The identity of the WT amino acid may be unspecified, in which case the aforementioned variant is referred to as 428L/434S. It is noted that the order in which substitutions are provided is arbitrary, that is to say that, for example, 428L/434S is the same Fc variant as M428L/N434S, and so on. For all positions discussed in the present invention that relate to antibodies, unless otherwise noted, amino acid position numbering is according to the EU index. The EU index or EU index as in Kabat or EU numbering scheme refers to the numbering of the EU antibody (Edelman et al., 1969, Proc Natl Acad Sci USA 63:78-85, hereby entirely incorporated by reference.) The modification can be an addition, deletion, or substitution. Substitutions can include naturally occurring amino acids and, in some cases, synthetic amino acids. Examples include U.S. Pat. No. 6,586,207; WO 98/48032; WO 03/073238; U52004-0214988A1; WO 05/35727A2; WO 05/74524A2; J. W. Chin et al., (2002), Journal of the American Chemical Society 124:9026-9027; J. W. Chin, & P. G. Schultz, (2002), Chem Bio Chem 11:1135-1137; J. W. Chin, et al., (2002), PICAS United States of America 99:11020-11024; and, L. Wang, & P. G. Schultz, (2002), Chem. 1-10, all entirely incorporated by reference.
As used herein, “protein” herein is meant at least two covalently attached amino acids, which includes proteins, polypeptides, oligopeptides and peptides. The peptidyl group may comprise naturally occurring amino acids and peptide bonds, or synthetic peptidomimetic structures, i.e. “analogs”, such as peptoids (see Simon et al., PNAS USA 89(20):9367 (1992), entirely incorporated by reference). The amino acids may either be naturally occurring or synthetic (e.g. not an amino acid that is coded for by DNA); as will be appreciated by those in the art. For example, homo-phenylalanine, citrulline, ornithine and noreleucine are considered synthetic amino acids for the purposes of the invention, and both D- and L-(R or S) configured amino acids may be utilized. The variants of the present invention may comprise modifications that include the use of synthetic amino acids incorporated using, for example, the technologies developed by Schultz and colleagues, including but not limited to methods described by Cropp & Shultz, 2004, Trends Genet. 20(12):625-30, Anderson et al., 2004, Proc Natl Acad Sci USA 101 (2):7566-71, Zhang et al., 2003, 303(5656):371-3, and Chin et al., 2003, Science 301(5635):964-7, all entirely incorporated by reference. In addition, polypeptides may include synthetic derivatization of one or more side chains or termini, glycosylation, PEGylation, circular permutation, cyclization, linkers to other molecules, fusion to proteins or protein domains, and addition of peptide tags or labels.
By “residue” as used herein is meant a position in a protein and its associated amino acid identity. For example, Asparagine 297 in IgG1 (also referred to as Asn297 or N297) is a residue at position 297 in the human antibody IgG1.
By “Fab” or “Fab region” as used herein is meant the polypeptide that comprises the VH, CH1, VL, and CL immunoglobulin domains. Fab may refer to this region in isolation, or this region in the context of a full length antibody, antibody fragment or Fab fusion protein. By “Fv” or “Fv fragment” or “Fv region” as used herein is meant a polypeptide that comprises the VL and VH domains of a single antibody.
By “non-naturally occurring modification” as used herein is meant an amino acid modification that is not isotypic. For example, because none of the IgGs comprise a serine at position 434, the substitution 434S in IgG1, IgG2, IgG3, or IgG4 (or hybrids thereof) is considered a non-naturally occurring modification.
By “effector function” as used herein is meant a biochemical event that results from the interaction of an antibody Fc region with an Fc receptor or ligand. Effector functions include but are not limited to ADCC, ADCP, and CDC.
By “parent polypeptide” as used herein is meant a starting polypeptide that is subsequently modified to generate a variant. The parent polypeptide may be a naturally occurring polypeptide, or a variant or engineered version of a naturally occurring polypeptide. Parent polypeptide may refer to the polypeptide itself, compositions that comprise the parent polypeptide, or the amino acid sequence that encodes it. Accordingly, by “parent immunoglobulin” as used herein is meant an unmodified immunoglobulin polypeptide that is modified to generate a variant, and by “parent antibody” as used herein is meant an unmodified antibody that is modified to generate a variant antibody. It should be noted that “parent antibody” includes known commercial, recombinantly produced antibodies as outlined below.
By “position” as used herein is meant a location in the sequence of a protein. Positions may be numbered sequentially, or according to an established format, for example the EU index for antibody numbering.
By “target antigen” as used herein is meant the molecule that is bound specifically by the variable region of a given antibody. A target antigen may be a protein, such as the Toso protein, carbohydrate, lipid, or other chemical compound.
By “target cell” as used herein is meant a cell that expresses a target antigen.
By “variable region” as used herein is meant the region of an immunoglobulin that comprises one or more Ig domains substantially encoded by any of the V.kappa., V.lamda., and/or VH genes that make up the kappa, lambda, and heavy chain immunoglobulin genetic loci respectively.
By “wild type or WT” herein is meant an amino acid sequence or a nucleotide sequence that is found in nature, including allelic variations. A WT protein has an amino acid sequence or a nucleotide sequence that has not been intentionally modified.
Although the present invention is described primarily with reference to specific embodiments, it is also envisioned that other embodiments will become apparent to those skilled in the art upon reading the present disclosure, and it is intended that such embodiments be contained within the present inventive methods.
I. Overview of the Invention
The present invention is directed to methods and compositions for modulating the activity of the Toso protein (which is also interchangeably referred to herein as “Toso” or “Toso receptor” or “Faim3” or “FCMR”). Methods and compositions of the present invention may be used in accordance with and in some embodiments in combination with other known methods of modulating activity of the Toso protein, such as those described in, for example, U.S. Ser. No. 13/831,031, filed on Mar. 14, 2013, which is hereby incorporated by reference in its entirety for all purposes and in particular for any disclosure, claims, figures, or other teachings related to methods and compositions for modulating activity of the Toso protein.
In some embodiments, the methods and compositions of the invention increase activity of the Toso protein. In other embodiments, the methods and compositions of the invention inhibit activity of the Toso protein.
In certain aspects, compositions for modulating the activity of the Toso protein include agents that bind to the Toso protein or to a ligand of the Toso protein. In further embodiments, the compositions of the invention include an antibody that binds to the Toso protein or to a ligand of the Toso protein.
The present invention is further directed to methods of treating disorders and diseases by administering an antibody that modulates the activity of Toso in a subject. As will be discussed in further detail herein, antibodies of the invention can be used to treat subjects suffering from without limitation Type II diabetes, an autoimmune disorder (including without limitation Type 1 diabetes, multiple sclerosis, or rheumatoid arthritis), asthma, allergy, chronic obstructive pulmonary disease (“COPD”), hyper-IgM syndrome, CLL, lupus, or a neutrophilia-associated disorder (including without limitation neutropenia, severe congenital neutropenia, cyclical neutropenia, antibody mediated neutropenia, reticular dysgenesis, leukocyte adhesion deficiency, familiar myeloproliferative disease, chronic myelogenous leukemia, familiar cold urticaria and leukocytosis, and chronic granulomatous disease).
II. Antibodies to Toso
Antibodies of the invention modulate Toso activity. In some embodiments, antibodies of the invention increase Toso activity. In other embodiments, antibodies of the invention decrease Toso activity. In some embodiments, antibodies of the invention bind directly to the Toso protein. In other embodiments, antibodies of the invention bind to a ligand of the Toso protein. In further embodiments, antibodies of the invention bind or otherwise interact with an intermediate protein or other molecule and indirectly affect Toso activity through that interaction with the intermediate protein or other molecule.
Methods of preparing antibodies are generally known in the art. For example, U.S. Pat. No. 6,727,350 discusses Toso antibodies and methods for preparing the same, and is hereby incorporated by reference in its entirety for all purposes and in particular for all teachings related to antibodies directed to the Toso protein.
In some embodiments, antibodies of the invention are identified by phage display screening using methods known in the art and described in further detail herein. Such methods will in further embodiments include producing a fully human antibody by cloning the results of the phage display screening into an expression vector for human IgG.
Antibodies that find use in the present invention can take on a number of formats as described herein, including traditional antibodies as well as antibody derivatives, fragments and mimetics, described below. In general, the term “antibody” includes any polypeptide that includes at least one constant domain, including, but not limited to, CH1, CH2, CH3 and CL.
Traditional antibody structural units typically comprise a tetramer. Each tetramer is typically composed of two identical pairs of polypeptide chains, each pair having one “light” (typically having a molecular weight of about 25 kDa) and one “heavy” chain (typically having a molecular weight of about 50-70 kDa). Human light chains are classified as kappa and lambda light chains. The present invention is directed to the IgG class, which has several subclasses, including, but not limited to IgG1, IgG2, IgG3, and IgG4. Thus, “isotype” as used herein is meant any of the subclasses of immunoglobulins defined by the chemical and antigenic characteristics of their constant regions. It should be understood that therapeutic antibodies can also comprise hybrids of isotypes and/or subclasses.
The amino-terminal portion of each chain includes a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition, generally referred to in the art and herein as the “Fv domain” or “Fv region”. In the variable region, three loops are gathered for each of the V domains of the heavy chain and light chain to form an antigen-binding site. Each of the loops is referred to as a complementarity-determining region (hereinafter referred to as a “CDR”), in which the variation in the amino acid sequence is most significant. “Variable” refers to the fact that certain segments of the variable region differ extensively in sequence among antibodies. Variability within the variable region is not evenly distributed. Instead, the V regions consist of relatively invariant stretches called framework regions (FRs) of 15-30 amino acids separated by shorter regions of extreme variability called “hypervariable regions” that are each 9-15 amino acids long or longer.
Each VH and VL is composed of three hypervariable regions (“complementary determining regions,” “CDRs”) and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4.
The hypervariable region generally encompasses amino acid residues from about amino acid residues 24-34 (LCDR1; “L” denotes light chain), 50-56 (LCDR2) and 89-97 (LCDR3) in the light chain variable region and around about 31-35B (HCDR1; “H” denotes heavy chain), 50-65 (HCDR2), and 95-102 (HCDR3) in the heavy chain variable region; Kabat et al., SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991) and/or those residues forming a hypervariable loop (e.g. residues 26-32 (LCDR1), 50-52 (LCDR2) and 91-96 (LCDR3) in the light chain variable region and 26-32 (HCDR1), 53-55 (HCDR2) and 96-101 (HCDR3) in the heavy chain variable region; Chothia and Lesk (1987) J. Mol. Biol. 196:901-917. Specific CDRs of the invention are described below.
Throughout the present specification, the Kabat numbering system is generally used when referring to a residue in the variable domain (approximately, residues 1-107 of the light chain variable region and residues 1-113 of the heavy chain variable region) (e.g, Kabat et al., supra (1991)).
The CDRs contribute to the formation of the antigen-binding, or more specifically, epitope binding site of antibodies. “Epitope” refers to a determinant that interacts with a specific antigen binding site in the variable region of an antibody molecule known as a paratope. Epitopes are groupings of molecules such as amino acids or sugar side chains and usually have specific structural characteristics, as well as specific charge characteristics. A single antigen may have more than one epitope.
The epitope may comprise amino acid residues directly involved in the binding (also called immunodominant component of the epitope) and other amino acid residues, which are not directly involved in the binding, such as amino acid residues which are effectively blocked by the specifically antigen binding peptide; in other words, the amino acid residue is within the footprint of the specifically antigen binding peptide.
Epitopes may be either conformational or linear. A conformational epitope is produced by spatially juxtaposed amino acids from different segments of the linear polypeptide chain. A linear epitope is one produced by adjacent amino acid residues in a polypeptide chain. Conformational and nonconformational epitopes may be distinguished in that the binding to the former but not the latter is lost in the presence of denaturing solvents.
An epitope typically includes at least 3, and more usually, at least 5 or 8-10 amino acids in a unique spatial conformation. Antibodies that recognize the same epitope can be verified in a simple immunoassay showing the ability of one antibody to block the binding of another antibody to a target antigen, for example “binning.”
In some embodiments, the antibodies are full length. By “full length antibody” herein is meant the structure that constitutes the natural biological form of an antibody, including variable and constant regions, including one or more modifications as outlined herein.
Alternatively, the antibodies can be a variety of structures, including, but not limited to, antibody fragments, monoclonal antibodies, bispecific antibodies, minibodies, domain antibodies, synthetic antibodies (sometimes referred to herein as “antibody mimetics”), chimeric antibodies, humanized antibodies, antibody fusions (sometimes referred to as “antibody conjugates”), and fragments of each, respectively.
Antibody Fragments
In one embodiment, the antibody is an antibody fragment. Of particular interest are antibodies that comprise Fc regions, Fc fusions, and the constant region of the heavy chain (CH1-hinge-CH2-CH3), again also including constant heavy region fusions.
Specific antibody fragments include, but are not limited to, (i) the Fab fragment consisting of VL, VH, CL and CH1 domains, (ii) the Fd fragment consisting of the VH and CH1 domains, (iii) the Fv fragment consisting of the VL and VH domains of a single antibody; (iv) the dAb fragment (Ward et al., 1989, Nature 341:544-546, entirely incorporated by reference) which consists of a single variable, (v) isolated CDR regions, (vi) F(ab′)2 fragments, a bivalent fragment comprising two linked Fab fragments (vii) single chain Fv molecules (scFv), wherein a VH domain and a VL domain are linked by a peptide linker which allows the two domains to associate to form an antigen binding site (Bird et al., 1988, Science 242:423-426, Huston et al., 1988, Proc. Natl. Acad. Sci. U.S.A. 85:5879-5883, entirely incorporated by reference), (viii) bispecific single chain Fv (WO 03/11161, hereby incorporated by reference) and (ix) “diabodies” or “triabodies”, multivalent or multispecific fragments constructed by gene fusion (Tomlinson et. al., 2000, Methods Enzymol. 326:461-479; WO94/13804; Holliger et al., 1993, Proc. Natl. Acad. Sci. U.S.A. 90:6444-6448, all entirely incorporated by reference). The antibody fragments may be modified. For example, the molecules may be stabilized by the incorporation of disulphide bridges linking the VH and VL domains (Reiter et al., 1996, Nature Biotech. 14:1239-1245, entirely incorporated by reference).
Chimeric and Humanized Antibodies
In some embodiments, the scaffold components can be a mixture from different species. As such, if the protein is an antibody, such antibody may be a chimeric antibody and/or a humanized antibody. In general, both “chimeric antibodies” and “humanized antibodies” refer to antibodies that combine regions from more than one species. For example, “chimeric antibodies” traditionally comprise variable region(s) from a mouse (or rat, in some cases) and the constant region(s) from a human. “Humanized antibodies” generally refer to non-human antibodies that have had the variable-domain framework regions swapped for sequences found in human antibodies. Generally, in a humanized antibody, the entire antibody, except the CDRs, is encoded by a polynucleotide of human origin or is identical to such an antibody except within its CDRs. The CDRs, some or all of which are encoded by nucleic acids originating in a non-human organism, are grafted into the beta-sheet framework of a human antibody variable region to create an antibody, the specificity of which is determined by the engrafted CDRs. The creation of such antibodies is described in, e.g., WO 92/11018, Jones, 1986, Nature 321:522-525, Verhoeyen et al., 1988, Science 239:1534-1536, all entirely incorporated by reference. “Backmutation” of selected acceptor framework residues to the corresponding donor residues is often required to regain affinity that is lost in the initial grafted construct (U.S. Pat. Nos. 5,530,101; 5,585,089; 5,693,761; 5,693,762; 6,180,370; 5,859,205; 5,821,337; 6,054,297; 6,407,213, all entirely incorporated by reference). The humanized antibody optimally also will comprise at least a portion of an immunoglobulin constant region, typically that of a human immunoglobulin, and thus will typically comprise a human Fc region. Humanized antibodies can also be generated using mice with a genetically engineered immune system. Roque et al., 2004, Biotechnol. Prog. 20:639-654, entirely incorporated by reference. A variety of techniques and methods for humanizing and reshaping non-human antibodies are well known in the art (See Tsurushita & Vasquez, 2004, Humanization of Monoclonal Antibodies, Molecular Biology of B Cells, 533-545, Elsevier Science (USA), and references cited therein, all entirely incorporated by reference). Humanization methods include but are not limited to methods described in Jones et al., 1986, Nature 321:522-525; Riechmann et al., 1988; Nature 332:323-329; Verhoeyen et al., 1988, Science, 239:1534-1536; Queen et al., 1989, Proc Natl Acad Sci, USA 86:10029-33; He et al., 1998, J. Immunol. 160: 1029-1035; Carter et al., 1992, Proc Natl Acad Sci USA 89:4285-9, Presta et al., 1997, Cancer Res. 57(20):4593-9; Gorman et al., 1991, Proc. Natl. Acad. Sci. USA 88:4181-4185; O'Connor et al., 1998, Protein Eng 11:321-8, all entirely incorporated by reference. Humanization or other methods of reducing the immunogenicity of nonhuman antibody variable regions may include resurfacing methods, as described for example in Roguska et al., 1994, Proc. Natl. Acad. Sci. USA 91:969-973, entirely incorporated by reference. In one embodiment, the parent antibody has been affinity matured, as is known in the art. Structure-based methods may be employed for humanization and affinity maturation, for example as described in U.S. Ser. No. 11/004,590. Selection based methods may be employed to humanize and/or affinity mature antibody variable regions, including but not limited to methods described in Wu et al., 1999, J. Mol. Biol. 294:151-162; Baca et al., 1997, J. Biol. Chem. 272(16):10678-10684; Rosok et al., 1996, J. Biol. Chem. 271(37): 22611-22618; Rader et al., 1998, Proc. Natl. Acad. Sci. USA 95: 8910-8915; Krauss et al., 2003, Protein Engineering 16(10):753-759, all entirely incorporated by reference. Other humanization methods may involve the grafting of only parts of the CDRs, including but not limited to methods described in U.S. Ser. No. 09/810,510; Tan et al., 2002, J. Immunol. 169:1119-1125; De Pascalis et al., 2002, J. Immunol. 169:3076-3084, all entirely incorporated by reference.
In one embodiment, the antibody is a minibody. Minibodies are minimized antibody-like proteins comprising a scFv joined to a CH3 domain. Hu et al., 1996, Cancer Res. 56:3055-3061, entirely incorporated by reference. In some cases, the scFv can be joined to the Fc region, and may include some or the entire hinge region.
Toso Antibodies and Variants
As used herein, the term “Toso antibody” refers to any antibody that binds to Toso or binds to a ligand of Toso, including antibodies comprising any of the sequences described herein and variants thereof.
In certain aspects, Toso antibodies of the invention include antibodies comprising CDR sequences as provided in FIG. 1 and below in Tables 1 and 2.







TABLE 1







CDR sequences of Toso antibodies-heavy chain










Clone
CDR1
CDR2
CDR3





3kr7
DFIFNNYN
IDTSTYTT
ARDRYGSSYWGGHYFHAMDV



(SEQ ID NO: 71)
(SEQ ID NO: 72)
(SEQ ID NO: 73)


 


k-2-5
GFSFSDFG
VRYDGSKE
AKDEMARWAYVDWLPHLHHSYGMDV



(SEQ ID NO: 74)
(SEQ ID NO: 75)
(SEQ ID NO: 76)


 


5/7k5
GFSFSDFG
VRYDGSKE
AKDEMARWAYVDWLPHLHHSYGMDV



(SEQ ID NO: 77)
(SEQ ID NO: 78)
(SEQ ID NO: 79)


 


5/7k1
GFTFSNHW
IKRDATST
VREGGYTYGGVYYYNGMDV



(SEQ ID NO: 80)
(SEQ ID NO: 81)
(SEQ ID NO: 82)


 


5/7k6
DFIFNNYN
IDTSTYTT
ARDRYGSSYWGGHYFHAMDV



(SEQ ID NO: 83)
(SEQ ID NO: 84)
(SEQ ID NO: 85)


 


5/15kL24
GFTFSSYD
ISGSGGSP
AKPYTSGWYVGCDS



(SEQ ID NO: 86)
(SEQ ID NO: 87)
(SEQ ID NO: 88)


 


5/15kL26
GFTFSDCA
ISGSGLST
TKAPWDYYGSGNTDHFDH



(SEQ ID NO: 89)
(SEQ ID NO: 90)
(SEQ ID NO: 91)


 


5/15kL30
GFTFSSHA
ISGRGSSI
AKGLADFDY



(SEQ ID NO: 92) 
(SEQ ID NO: 93)
(SEQ ID NO: 94)


 


k-4.15
GYDFANFW
IYPDDSDV
TRRYSGAQLGVDS



(SEQ ID NO: 95) 
(SEQ ID NO: 96) 
(SEQ ID NO: 97)


 


k-4.16
GYTFTSYG
ISVYNGNT
ARDGLRWLRPTGMDV



(SEQ ID NO: 98) 
(SEQ ID NO: 99)
(SEQ ID NO: 100)


 


k-4.18
GFTFSSYA
ISSSGTNT
VKGSGVGYQYYYGMDV



(SEQ ID NO: 101)
(SEQ ID NO: 102)
(SEQ ID NO: 103)


 


k-4.20
GYSLSDYS
INPKTGGT
ARPGFCTIDNCHDFFDS



(SEQ ID NO: 104)
(SEQ ID NO: 105)
(SEQ ID NO: 106)


 


k-4.17
GYTFSDYY
INPKTGGT
ARRSLNLYYDYGMDV



(SEQ ID NO: 107)
(SEQ ID NO: 108)
(SEQ ID NO: 109)


 


L-1-13
GALVTNTAYY
IYANGRT
VRLVPKRTATLHYYIDV



(SEQ ID NO: 110)
(SEQ ID NO: 111)
(SEQ ID NO: 112)


 


1R2kr3
GDTSSIYA
INPIPRIT
ARDCSGGSCFRQDAFDI



(SEQ ID NO: 113)
(SEQ ID NO: 114)
(SEQ ID NO: 115)


 


K3-22
GDTSSIYA
INPIPRIT
ARDCSGGSCFRQDAFDI



(SEQ ID NO: 116)
(SEQ ID NO: 117)
(SEQ ID NO: 118)


 


k-2-48
GYTLTSYD
MNPNSGNT
ARGRSIINHYYGLDV



(SEQ ID NO: 119)
(SEQ ID NO: 120)
(SEQ ID NO: 121)


 


K3-24
DFIFNNYN
IDTSTYTT
ARDRYGSSYWGGHYFHAMDV



(SEQ ID NO: 122)
(SEQ ID NO: 123)
(SEQ ID NO: 124)


 


5/15L28
GFSFSSYN
ISSGSSYI
TRDRYYHDSDEYYDADGFDV



(SEQ ID NO: 125)
(SEQ ID NO: 126)
(SEQ ID NO: 127)


 


5/15kL19
GFTFNTYA
ISANGGTT
ARDHLWFGEYIFDC



(SEQ ID NO: 128)
(SEQ ID NO: 129)
(SEQ ID NO: 130)


 


k-5.10
GFTFTDAW
IKSRTGGGTT
VWSGRNWFGH



(SEQ ID NO: 131)
(SEQ ID NO: 132)
(SEQ ID NO: 133)


 


k-2-42
GYTLTSYD
MNPNSGNT
ARGRSIINHYYGLDV



(SEQ ID NO: 134)
(SEQ ID NO: 135)
(SEQ ID NO: 136)


 


1R2kr30
DFIFNNYN
IDTSTYTT
ARDRYGSSYWGATISTLWT



(SEQ ID NO: 137)
(SEQ ID NO: 138)
(SEQ ID NO: 139)


 


K1
GYIFTDYW
IYPGDSET
ARHGRGYCGGGSCQGTLIDN



(SEQ ID NO: 140)
(SEQ ID NO: 141)
(SEQ ID NO: 142)


 


L1
GYIFTDYW
IYPGDSET
ARHGRGYCGGGSCQGTLIDN



(SEQ ID NO: 143)
(SEQ ID NO: 144)
(SEQ ID NO: 145)


 


k-2-32
GYTLTSYD
MNPNSGNT
ARGRSIINHYYGLDV



(SEQ ID NO: 146)
(SEQ ID NO: 147)
(SEQ ID NO: 148)


 


L-8.2
GYIFTDYW
IYPGDSET
ARHGRGYCGGGSCQGTLIDN



(SEQ ID NO: 149)
(SEQ ID NO: 150)
(SEQ ID NO: 151)


 


L-8.6
GYIFTDYW
IYPGDSET
ARHGRGYCGGGSCQGTLIDN



(SEQ ID NO: 152)
(SEQ ID NO: 153)
(SEQ ID NO: 154)


 


L-8.17
GYIFTDYW
IYPGDSET
ARHGRGYCGGGSCQGTLIDN



(SEQ ID NO: 155)
(SEQ ID NO: 156)
(SEQ ID NO: 157)
















TABLE 2







CDR sequences of Toso antibodies-light chain










Clone
CDR1
CDR2
CDR3





3kr7
QSVGTS
DAS
QQRSNGPPSWT



(SEQ ID NO: 158)
(SEQ ID NO: 159)
(SEQ ID NO: 160)


 


k-2-5
QSVSSN
GAS
QQYNNWPYT



(SEQ ID NO: 161)
(SEQ ID NO: 162)
(SEQ ID NO: 163)


 


5/7k5
QSVSSN
GAS
QQYNNWPYT



(SEQ ID NO: 164)
(SEQ ID NO: 165)
(SEQ ID NO: 166)


 


5/7k1
QSVFSSSYSEDY
WAS
QYYITPIT



(SEQ ID NO: 167)
(SEQ ID NO: 168)
(SEQ ID NO: 169)


 


5/7k6
QSVGTS
DAS
QQRSTGLRVGR



(SEQ ID NO: 170)
(SEQ ID NO: 171)
(SEQ ID NO: 172)


 


5/15kL24
QSVSSSY
GAS
QQYGSSPWT



(SEQ ID NO: 173)
(SEQ ID NO: 174)
(SEQ ID NO: 175)


 


5/15kL26
QSVRSY
DAT
QQRNNWPLT



(SEQ ID NO: 176)
(SEQ ID NO: 177)
(SEQ ID NO: 178)


 


5/15kL30
QSVSSY
DAS
QQRSNWPPYS



(SEQ ID NO: 179)
(SEQ ID NO: 180)
(SEQ ID NO: 181)


 


k-4.15
QRVNTGY
GAS
QQHGTSPYT



(SEQ ID NO: 182)
(SEQ ID NO: 183)
(SEQ ID NO: 184)


 


k-4.16
QDITHS
DAS
QQYDNVPIT



(SEQ ID NO: 185)
(SEQ ID NO: 186)
(SEQ ID NO: 187)


 


k-4.18
QNVLYNSNKKNY
WAS
QQYYGTPLT



(SEQ ID NO: 188)
(SEQ ID NO: 189)
(SEQ ID NO: 190)


 


k-4.20
QRLVYSDGNTY
KVS
MQSSTDWPWT



(SEQ ID NO: 191)
(SEQ ID NO: 192)
(SEQ ID NO: 193)


 


k-4.17
RSVLYTSTNRYL
WAS
QQYYNPPVYT



(SEQ ID NO: 194)
(SEQ ID NO: 195)
(SEQ ID NO: 196)


 


L-1-13
SGHSSYAI
LNSDGSH
QTWGTGIHWV



(SEQ ID NO: 197)
(SEQ ID NO: 198)
(SEQ ID NO: 199)


 


1R2kr3
QSVSDY
AAS
XQSYTTAYT



(SEQ ID NO: 200)
(SEQ ID NO: 201)
(SEQ ID NO: 202)


 


K3-22
QSVSDY
AAS
QQSYTTAYT



(SEQ ID NO: 203)
(SEQ ID NO: 204)
(SEQ ID NO: 205)


 


k-2-48
QSVSSY
DAS
QQRSNWPWT



(SEQ ID NO: 206)
(SEQ ID NO: 207)
(SEQ ID NO: 208)


 


K3-24
QSVGTS
DAS
QQRSNGPPSWT



(SEQ ID NO: 209)
(SEQ ID NO: 210)
(SEQ ID NO: 211)


 


5/15L28
QSISSY
AAS
QQSYSTLSL



(SEQ ID NO: 212)
(SEQ ID NO: 213)
(SEQ ID NO: 214)


 


5/15kL19
QSVFSSSYSEDY
WAS
QQYYITPIT



(SEQ ID NO: 215)
(SEQ ID NO: 216)
(SEQ ID NO: 217)


 


k-5.10
QSLVHSDGNTY
KIS
CKLHNFLTL



(SEQ ID NO: 218)
(SEQ ID NO: 219)
(SEQ ID NO: 220)


 


k-2-42
QSISNY
AAS
QQSYSTPET



(SEQ ID NO: 221)
(SEQ ID NO: 222)
(SEQ ID NO: 223)


 


1R2kr30
QSISSY
AAS
QQSYSTPCT



(SEQ ID NO: 224)
(SEQ ID NO: 225)
(SEQ ID NO: 226)


 


K1
QSVFSSSYSEDY
WAS
QQYYITPIT



(SEQ ID NO: 227)
(SEQ ID NO: 228)
(SEQ ID NO: 229)


 


L1
SLRTYY
AKT
NSRDSSDNLW



(SEQ ID NO: 230)
(SEQ ID NO: 231)
(SEQ ID NO: 232)


 


k-2-32
QDISNY
DAS
QQYDNLPPGSP



(SEQ ID NO: 233)
(SEQ ID NO: 234)
(SEQ ID NO: 235)


 


L-8.2
SLRTYY
AKN
NSRDSSDNLW



(SEQ ID NO: 236)
(SEQ ID NO: 237)
(SEQ ID NO: 238)


 


L-8.6
SLRTYY
AKT
NSRDSSDNLW



(SEQ ID NO: 239)
(SEQ ID NO: 240)
(SEQ ID NO: 241)


 


L-8.17
SLRTYY
AKN
NSRDSSDNLW



(SEQ ID NO: 242)
(SEQ ID NO: 243)
(SEQ ID NO: 244)









In further embodiments, Toso antibodies of the invention comprise variants of the CDR sequences as provided in FIG. 1. In general, variants can include any number of modifications, as long as the function of the protein is still present, as described herein. That is, in the case of amino acid variants generated with the CDRs of any of the antibodies comprising sequences as provided in FIG. 1, for example, the antibody should still specifically bind to Toso or a ligand of Toso. Similarly, if amino acid variants are generated with the Fc region, for example, the variant antibodies should maintain the required receptor binding functions for the particular application or indication of the antibody.
However, in general, from 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 amino acid substitutions are generally utilized as often the goal is to alter function with a minimal number of modifications. In some cases, there are from 1 to 5 modifications, with from 1-2, 1-3 and 1-4 also finding use in many embodiments.
In some embodiments, one or more amino acid modifications are made in one or more of the CDRs of the Toso antibodies of the invention as provided in FIG. 1 and Tables 1 and 2. In general, only 1 or 2 or 3-amino acids are substituted in any single CDR, and generally no more than from 4, 5, 6, 7, 8 9 or 10 changes are made within a set of CDRs. However, it should be appreciated that any combination of no substitutions, 1, 2 or 3 substitutions in any CDR for a particular antibody can be independently and optionally combined with any other substitution.
In some cases, amino acid modifications in the CDRs are referred to as “affinity maturation”. An “affinity matured” antibody is one having one or more alteration(s) in one or more CDRs which results in an improvement in the affinity of the antibody for antigen, compared to a parent antibody which does not possess those alteration(s). In some cases, although rare, it may be desirable to decrease the affinity of an antibody to its antigen, but this is generally not preferred.
Affinity maturation can be done to increase the binding affinity of the antibody for the antigen by at least about 10% to 50-100-150% or more, or from 1 to 5 fold as compared to the “parent” antibody. Preferred affinity matured antibodies will have nanomolar or even picomolar affinities for the target antigen. Affinity matured antibodies are produced by known procedures. See, for example, Marks et al., 1992, Biotechnology 10:779-783 that describes affinity maturation by variable heavy chain (VH) and variable light chain (VL) domain shuffling. Random mutagenesis of CDR and/or framework residues is described in: Barbas, et al. 1994, Proc. Nat. Acad. Sci, USA 91:3809-3813; Shier et al., 1995, Gene 169:147-155; Yelton et al., 1995, J. Immunol. 155:1994-2004; Jackson et al., 1995, J. Immunol. 154(7):3310-9; and Hawkins et al, 1992, J. Mol. Biol. 226:889-896, for example.
Alternatively, amino acid modifications can be made in one or more of the CDRs of the antibodies of the invention that are “silent”, e.g. that do not significantly alter the affinity of the antibody for the antigen. These can be made for a number of reasons, including optimizing expression (as can be done for the nucleic acids encoding the antibodies of the invention).
Thus, included within the definition of the CDRs and antibodies of the invention are variant CDRs and antibodies; that is, the antibodies of the invention can include amino acid modifications in one or more of the CDRs of antibodies 3kr7, k-2-5, 5/7k5, 5/7k1, 5/7k6, 5/15kL24, 5/15kL26, 5/15kL30, k-4.15, k-4.16, k-4.18, k-4.20, k-4.17, L-1-13, 1R2kr3, K3-22, k-2-48, K3-24, 5/15L28, 5/15kL19, k-5.10, k-2-42, 1R2kr30, K1, L1, k-2-32, L-8.2, L-8.6, L-8.17, for which sequences of the heavy and light chains are provided in FIG. 1. In addition, amino acid modifications can also independently and optionally be made in any region outside the CDRs, including framework and constant regions.
In some embodiments, the Toso antibodies (also referred to herein as “anti-Toso” or “anti-Toso antibodies”) of the invention are composed of a variant Fc domain. As is known in the art, the Fc region of an antibody interacts with a number of Fc receptors and ligands, imparting an array of important functional capabilities referred to as effector functions. These Fc receptors include, but are not limited to, (in humans) FcγRI (CD64) including isoforms FcγRIa, FcγRIb, and FcγRIc; FcγRII (CD32), including isoforms FcγRIIa (including allotypes H131 and R131), FcγRIIb (including FcγRIIb-1 and FcγRIIb-2), and FcγRIIc; and FcγRIII (CD16), including isoforms FcγRIIIa (including allotypes V158 and F158, correlated to antibody-dependent cell cytotoxicity (ADCC)) and FcγRIIIb (including allotypes FcγRIIIb-NA1 and FcγRIIIb-NA2), FcRn (the neonatal receptor), C1q (complement protein involved in complement dependent cytotoxicity (CDC)) and FcRn (the neonatal receptor involved in serum half-life). Suitable modifications can be made at one or more positions as is generally outlined, for example in US 2004/013210, US 2005/0054832, US 2006/0024298, US 2006/0121032, US 2006/0235208, US 2007/0148170, U.S. Pat. No. 6,737,056, 7,670,600, 6,086,875 all of which are expressly incorporated by reference in their entirety, and in particular for specific amino acid substitutions that increase binding to Fc receptors.
In further aspects, Toso antibodies of the invention comprise any of the full length heavy or light chain sequences provided in FIG. 1. In further embodiments, Toso antibodies of the invention comprise sequences with a sequence identity of about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% and 100% identity to any of the full length heavy or light chain sequences provided in FIG. 1.
In still further aspects, Toso antibodies of the invention comprise consensus sequences that encompass CDR sequences as provided in FIG. 1 and Tables 1 and 2. Such consensus sequences can be identified through alignments of the CDR sequences and through the use of tools available on public databases.
In exemplary embodiments, Toso antibodies of the invention comprise a heavy chain CDR1 comprising the following consensus sequence: G-X1-TFS-X2-Y-X3, wherein X1 is F, D or Y, X2 is N, D or S, and X3 is A, G, W or N.
In further embodiments, Toso antibodies of the invention comprise a heavy chain CDR2 comprising the following consensus sequence: I-X1-PSG-X2-T-X3, wherein X1 is S, D, or Y, X2 is G or D, and X3 is T or P.
In still further embodiments, Toso antibodies of the invention comprise a light chain CDR1 comprising the following consensus sequence: Q-S-X1-S-X2-Y, wherein X1 is V or I, and X2 is S, D or N.
In still further embodiments, Toso antibodies of the invention comprise a light chain CDR3 comprising the following consensus sequence: QQ-X1-Y-X2-TP-X3-T, wherein X1 is Y, R or S, X2 is N, G, T, S or I, and X3 is L, I, E, or C.
As will be appreciated, although methods are known in the art for identifying antibodies to a particular protein, not all antibodies identified in such methods will bind to the protein of interest. Thus, one aspect of the present invention is the identification of antibodies that bind to Toso as distinguished from antibodies that do not bind to Toso—see for example the heavy and light chain sequences of the antibodies of FIG. 1, which are from antibodies that do bind to Toso, as opposed to the heavy and light chain sequences of the antibodies in FIG. 2, which do not bind to Toso.
In further aspects, the present invention provides an expression vector encoding an antibody or protein according to any of the sequences described herein and in accordance with any of the sequences provided in FIG. 1.
In still further aspects, the present invention provides a method of making an antibody or protein according to any of the sequences described herein and in accordance with any of the sequences provided in FIG. 1, the method comprising providing a cell comprising a nucleic acid encoding that antibody or protein, where the cell is cultured under conditions suitable for expression of the antibody or protein.
In still further aspects, the present invention provides a method of treating a Toso-associated disease, the method comprising treating a subject in need thereof with an antibody or protein according to any of the sequences described herein and in accordance with any of the sequences provided in FIG. 1.
In yet further aspects, the antibodies of the invention find use in a variety of applications, including diagnosis of Toso-related diseases and treatment thereof.
Additional Modifications to Toso Antibodies
In addition to any of the modifications and variants outlined above, other modifications can be made. For example, the molecules may be stabilized by the incorporation of disulphide bridges linking the VH and VL domains (Reiter et al., 1996, Nature Biotech. 14:1239-1245, entirely incorporated by reference for all purposes and in particular for all teachings regarding modifications of molecules, including antibodies). In addition, there are a variety of covalent modifications of antibodies that can be made as outlined below.
Covalent modifications of antibodies are included within the scope of this invention, and are generally, but not always, done post-translationally. For example, several types of covalent modifications of the antibody are introduced into the molecule by reacting specific amino acid residues of the antibody with an organic derivatizing agent that is capable of reacting with selected side chains or the N- or C-terminal residues.
Cysteinyl residues most commonly are reacted with α-haloacetates (and corresponding amines), such as chloroacetic acid or chloroacetamide, to give carboxymethyl or carboxyamidomethyl derivatives. Cysteinyl residues may also be derivatized by reaction with bromotrifluoroacetone, α-bromo-β-(5-imidozoyl)propionic acid, chloroacetyl phosphate, N-alkylmaleimides, 3-nitro-2-pyridyl disulfide, methyl 2-pyridyl disulfide, p-chloromercuribenzoate, 2-chloromercuri-4-nitrophenol, or chloro-7-nitrobenzo-2-oxa-1,3-diazole and the like.
In addition, modifications at cysteines are particularly useful in antibody-drug conjugate (ADC) applications, further described below. In some embodiments, the constant region of the antibodies can be engineered to contain one or more cysteines that are particularly “thiol reactive”, so as to allow more specific and controlled placement of the drug moiety. See for example U.S. Pat. No. 7,521,541, incorporated by reference in its entirety herein.
Histidyl residues are derivatized by reaction with diethylpyrocarbonate at pH 5.5-7.0 because this agent is relatively specific for the histidyl side chain. Para-bromophenacyl bromide also is useful; the reaction is preferably performed in 0.1M sodium cacodylate at pH 6.0.
Lysinyl and amino terminal residues are reacted with succinic or other carboxylic acid anhydrides. Derivatization with these agents has the effect of reversing the charge of the lysinyl residues. Other suitable reagents for derivatizing alpha-amino-containing residues include imidoesters such as methyl picolinimidate; pyridoxal phosphate; pyridoxal; chloroborohydride; trinitrobenzenesulfonic acid; O-methylisourea; 2,4-pentanedione; and transaminase-catalyzed reaction with glyoxylate.
Arginyl residues are modified by reaction with one or several conventional reagents, among them phenylglyoxal, 2,3-butanedione, 1,2-cyclohexanedione, and ninhydrin. Derivatization of arginine residues requires that the reaction be performed in alkaline conditions because of the high pKa of the guanidine functional group. Furthermore, these reagents may react with the groups of lysine as well as the arginine epsilon-amino group.
The specific modification of tyrosyl residues may be made, with particular interest in introducing spectral labels into tyrosyl residues by reaction with aromatic diazonium compounds or tetranitromethane. Most commonly, N-acetylimidizole and tetranitromethane are used to form 0-acetyl tyrosyl species and 3-nitro derivatives, respectively. Tyrosyl residues are iodinated using 1251 or 1311 to prepare labeled proteins for use in radioimmunoassay, the chloramine T method described above being suitable.
Carboxyl side groups (aspartyl or glutamyl) are selectively modified by reaction with carbodiimides (R′—N═C═N—R′), where R and R′ are optionally different alkyl groups, such as 1-cyclohexyl-3-(2-morpholinyl-4-ethyl) carbodiimide or 1-ethyl-3-(4-azonia-4,4-dimethylpentyl) carbodiimide. Furthermore, aspartyl and glutamyl residues are converted to asparaginyl and glutaminyl residues by reaction with ammonium ions.
Derivatization with bifunctional agents is useful for crosslinking antibodies to a water-insoluble support matrix or surface for use in a variety of methods, in addition to methods described below. Commonly used crosslinking agents include, e.g., 1,1-bis(diazoacetyl)-2-phenylethane, glutaraldehyde, N-hydroxysuccinimide esters, for example, esters with 4-azidosalicylic acid, homobifunctional imidoesters, including disuccinimidyl esters such as 3,3′-dithiobis(succinimidylpropionate), and bifunctional maleimides such as bis-N-maleimido-1,8-octane. Derivatizing agents such as methyl-3-[(p-azidophenyl)dithio]propioimidate yield photoactivatable intermediates that are capable of forming crosslinks in the presence of light. Alternatively, reactive water-insoluble matrices such as cynomolgusogen bromide-activated carbohydrates and the reactive substrates described in U.S. Pat. Nos. 3,969,287; 3,691,016; 4,195,128; 4,247,642; 4,229,537; and 4,330,440, all entirely incorporated by reference, are employed for protein immobilization.
Glutaminyl and asparaginyl residues are frequently deamidated to the corresponding glutamyl and aspartyl residues, respectively. Alternatively, these residues are deamidated under mildly acidic conditions. Either form of these residues falls within the scope of this invention.
Other modifications include hydroxylation of proline and lysine, phosphorylation of hydroxyl groups of seryl or threonyl residues, methylation of the α-amino groups of lysine, arginine, and histidine side chains (T. E. Creighton, Proteins: Structure and Molecular Properties, W. H. Freeman & Co., San Francisco, pp. 79-86 [1983], entirely incorporated by reference), acetylation of the N-terminal amine, and amidation of any C-terminal carboxyl group.
In addition, as will be appreciated by those in the art, labels (including fluorescent, enzymatic, magnetic, radioactive, etc. can all be added to the antibodies (as well as the other compositions of the invention).
Another type of covalent modification is alterations in glycosylation. In another embodiment, the antibodies disclosed herein can be modified to include one or more engineered glycoforms. By “engineered glycoform” as used herein is meant a carbohydrate composition that is covalently attached to the antibody, wherein said carbohydrate composition differs chemically from that of a parent antibody. Engineered glycoforms may be useful for a variety of purposes, including but not limited to enhancing or reducing effector function.
Engineered glycoforms may be generated by a variety of methods known in the art (Umana et al., 1999, Nat Biotechnol 17:176-180; Davies et al., 2001, Biotechnol Bioeng 74:288-294; Shields et al., 2002, J Biol Chem 277:26733-26740; Shinkawa et al., 2003, J Biol Chem 278:3466-3473; U.S. Pat. No. 6,602,684; U.S. Ser. No. 10/277,370; U.S. Ser. No. 10/113,929; PCT WO 00/61739A1; PCT WO 01/29246A1; PCT WO 02/31140A1; PCT WO 02/30954A1, all entirely incorporated by reference; (Potelligent® technology [Biowa, Inc., Princeton, N.J.]; GlycoMAb® glycosylation engineering technology [Glycart Biotechnology AG, Zurich, Switzerland]). Many of these techniques are based on controlling the level of fucosylated and/or bisecting oligosaccharides that are covalently attached to the Fc region, for example by expressing an IgG in various organisms or cell lines, engineered or otherwise (for example Lec-13 CHO cells or rat hybridoma YB2/0 cells, by regulating enzymes involved in the glycosylation pathway (for example FUT8 [α1,6-fucosyltranserase] and/or β1-4-N-acetylglucosaminyltransferase III [GnTIII]), or by modifying carbohydrate(s) after the IgG has been expressed. For example, the “sugar engineered antibody” or “SEA technology” of Seattle Genetics functions by adding modified saccharides that inhibit fucosylation during production; see for example 20090317869, hereby incorporated by reference in its entirety. Engineered glycoform typically refers to the different carbohydrate or oligosaccharide; thus an antibody can include an engineered glycoform.
Alternatively, engineered glycoform may refer to the IgG variant that comprises the different carbohydrate or oligosaccharide. As is known in the art, glycosylation patterns can depend on both the sequence of the protein (e.g., the presence or absence of particular glycosylation amino acid residues, discussed below), or the host cell or organism in which the protein is produced. Particular expression systems are discussed below.
Glycosylation of polypeptides is typically either N-linked or O-linked. N-linked refers to the attachment of the carbohydrate moiety to the side chain of an asparagine residue. The tri-peptide sequences asparagine-X-serine and asparagine-X-threonine, where X is any amino acid except proline, are the recognition sequences for enzymatic attachment of the carbohydrate moiety to the asparagine side chain. Thus, the presence of either of these tri-peptide sequences in a polypeptide 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 or 5-hydroxylysine may also be used.
Addition of glycosylation sites to the antibody is conveniently accomplished by altering the amino acid sequence such that it contains one or more of the above-described tri-peptide sequences (for N-linked glycosylation sites). The alteration may also be made by the addition of, or substitution by, one or more serine or threonine residues to the starting sequence (for O-linked glycosylation sites). For ease, the antibody amino acid sequence is preferably altered through changes at the DNA level, particularly by mutating the DNA encoding the target polypeptide at preselected bases such that codons are generated that will translate into the desired amino acids.
Another means of increasing the number of carbohydrate moieties on the antibody is by chemical or enzymatic coupling of glycosides to the protein. These procedures are advantageous in that they do not require production of the protein in a host cell that has glycosylation capabilities for N- and O-linked glycosylation. Depending on the coupling mode used, the sugar(s) may be attached to (a) arginine and histidine, (b) free carboxyl groups, (c) free sulfhydryl groups such as those of cysteine, (d) free hydroxyl groups such as those of serine, threonine, or hydroxyproline, (e) aromatic residues such as those of phenylalanine, tyrosine, or tryptophan, or (f) the amide group of glutamine. These methods are described in WO 87/05330 and in Aplin and Wriston, 1981, CRC Crit. Rev. Biochem., pp. 259-306, both entirely incorporated by reference.
Removal of carbohydrate moieties present on the starting antibody (e.g. post-translationally) may be accomplished chemically or enzymatically. Chemical deglycosylation requires exposure of the protein to the compound trifluoromethanesulfonic acid, or an equivalent compound. This treatment results in the cleavage of most or all sugars except the linking sugar (N-acetylglucosamine or N-acetylgalactosamine), while leaving the polypeptide intact. Chemical deglycosylation is described by Hakimuddin et al., 1987, Arch. Biochem. Biophys. 259:52 and by Edge et al., 1981, Anal. Biochem. 118:131, both entirely incorporated by reference. Enzymatic cleavage of carbohydrate moieties on polypeptides can be achieved by the use of a variety of endo- and exo-glycosidases as described by Thotakura et al., 1987, Meth. Enzymol. 138:350, entirely incorporated by reference. Glycosylation at potential glycosylation sites may be prevented by the use of the compound tunicamycin as described by Duskin et al., 1982, J. Biol. Chem. 257:3105, entirely incorporated by reference. Tunicamycin blocks the formation of protein-N-glycoside linkages.
Another type of covalent modification of the antibody comprises linking the antibody to various non proteinaceous polymers, including, but not limited to, various polyols such as polyethylene glycol, polypropylene glycol or polyoxyalkylenes, in the manner set forth in, for example, 2005-2006 PEG Catalog from Nektar Therapeutics (available at the Nektar website) U.S. Pat. Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337, all entirely incorporated by reference. In addition, as is known in the art, amino acid substitutions may be made in various positions within the antibody to facilitate the addition of polymers such as PEG. See for example, U.S. Publication No. 2005/0114037A1, entirely incorporated by reference.
III. Methods of Modulating Toso Activity
In one aspect, the present invention is directed to methods of modulating Toso activity. In one embodiment, methods of modulating Toso activity comprise inhibiting Toso activity. In other embodiments, methods of modulating Toso activity comprise increasing Toso activity.
In some embodiments, methods of the present invention involve directly modulating Toso activity. In an exemplary embodiment, such methods include applying an agent that binds to Toso, such as an antibody.
In further embodiments, Toso activity is modulated by a combination of mechanisms, for example by administering a composition comprising an agent that binds to Toso in combination with a composition comprising an agent that binds to cognate ligands of Toso or with a second agent that binds to Toso. In an exemplary embodiment, such a combination may include without limitation a Toso antibody and a soluble Toso protein, such as the soluble Toso protein described in U.S. Ser. No. 13/831,031, filed on Mar. 14, 2013, which is hereby incorporated by reference in its entirety for all purposes and in particular for any disclosure, claims, figures, or other teachings related to a soluble Toso protein.
As will be appreciated, methods of modulating Toso activity can include the use of any of the compositions described herein in any combination, including an antibody comprising any one or more of SEQ ID NOs. 1-62 as well as any variants or modifications thereof as described herein.
V. Methods of Treating Disorders
In one aspect and in accordance with any of the above, the present invention provides methods of treating disorders by treating subjects in need thereof with a composition that modulates Toso activity, where in preferred embodiments that composition includes one or more Toso antibodies.
In a specific embodiment and in accordance with any of the above, the present invention provides methods of treating disorders by treating subjects in need thereof with a composition that includes a Toso antibody. Without being limited by theory, one potential mechanism by which the Toso antibody is an effective treatment for these disorders is through modulating Toso activity. In certain embodiments, methods of treating disorders in accordance with the present invention includes administering a therapeutically effective amount of any of the Toso antibodies described herein, including antibodies comprising any one or more of SEQ ID NOs: 1-62 or any variants thereof. In further embodiments, the soluble Toso proteins used to treat disorders, including diabetes, multiple sclerosis, asthma, and cancer include an antibody comprising a heavy or light chain sequence with about 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identity to any one of SEQ ID NOs: 1-28. Such antibodies may further be modified in accordance with the methods described herein, including chemical modifications, for the treatment of any of the disorders described herein.
In further aspects, the present invention is directed to methods of treating disorders and diseases by administering a Toso antibody or variant thereof to a subject. Antibodies of the invention can be used to treat subjects suffering from without limitation: an autoimmune disorder (including without limitation Type 1 diabetes, multiple sclerosis, or rheumatoid arthritis), Type 2 diabetes, asthma, allergy chronic obstructive pulmonary disease (“COPD”), hyper-IgM syndrome, lupus, cancer, or a neutrophilia-associated disorder (including without limitation neutropenia, severe congenital neutropenia, cyclical neutropenia, antibody mediated neutropenia, reticular dysgenesis, leukocyte adhesion deficiency, familiar myeloproliferative disease, chronic myelogenous leukemia, familiar cold urticaria and leukocytosis, and chronic granulomatous disease). As will be appreciated, any of the Toso antibodies described herein, singly or in any combination, can be used to treat any of these disorders or diseases.
As discussed above, in some embodiments, soluble Toso proteins of the invention are used to treat cancer. In further embodiments, methods of treating cancer in accordance with the invention include methods of inhibiting tumor invasion and/or metastasis by modulating Toso activity. In exemplary embodiments, compositions of the invention are used to treat any one of the group of an adenocarcinoma, a leukemia, a lymphoma, a melanoma, a myeloma, a sarcoma or a teratocarcinoma in subjects in need thereof. In further embodiments, compositions of the invention are used to treat subjects suffering from a cancer in one or more of adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid or uterus.
EXAMPLE 1
Human Naïve Phage scFv Library Construction
Peripheral blood mononuclear cells (PBMCs) were obtained from donated and commercially available blood samples. PBMCs were separated using Ficoll-PaqueTM PLUS (GE Healthcare). Total RNA was then isolated from the separated PBMCs using Trizol and mRNA was then purified from the Total RNA using Dynabeads® mRNA Purification Kit for mRNA Purification from Total RNA Preps (Ambion).
First strand cDNA synthesis from the mRNA was conducted using SuperScript III First-Strand Synthesis System for RT-PCR (Invitrogen). The cDNA library was pooled and the concentration measured.
Variable kappa-, lambda- and gamma-chain genes were amplified separately using 60-90 ng of cDNA as template and 2.5 μl each of the provided constant and available region DNA primer set 1 (F2000, Progen), 25 μl of 2×terra PCR buffer, 1 μl of terra polymerase mix, at a total volume of 50 μl. PCR conditions: 95° C. for 30 sec (denatureation), 55° C. 1 min (annealing), and 75° C. for 1 min (extension), total 30 cycles. At the beginning of the first cycle, the reaction mixture was incubated at 95° C. for 3 min and at the end of the last cycle incubated at 75° C. for 5 min.
To introduce restriction sites, PCRs were performed in a total of 50 μl containing: 1 μl of the PCR product of variable gene (kappa-, lambda- and gamma-chain genes were used as templates respectively), 2.5 μl each of the provided constant and variable region DNA primer set 2 (F2000, Progen), 25 μl of 2×terra PCR buffer, 1 μl of terra polymerase mix. PCR conditions: 95° C. for 30 sec (denaturation), 57° C. for 1 min (annealing), and 75° C. for 1 min (extension), total 14 cycles. At the beginning of the first cycle, incubation at 95° C. for 3 min and at the end of the last cycle incubation at 75° C. for 5 min. The PCR product was purified using gel DNA extraction kit (Clontech). The purified kappa, lambda and gamma DNA respectively were pooled.
Light chain DNA was cloned into phagemid vector pSEX81 by: digesting 10 μg phagemid vector pSEX81 (Progen) by adding 25 μl of Buffer H, 6 μl of NotI (40 u/μl) and 0.5 μl of RNase A (10 μg) at a total volume of 224 μl·mix and incubating for 8 min at 37° C., then adding 20 μl of MluI (10 u/μl), incubated for 6 minutes at 37° C. Following that, alkaline phosphatase (CIP) was added, and incubation continued for 15 minutes at 37° C. Then, 0.25 μl of 0.5M pH8.0 EDTA was added, followed by incubation for 20 min at 65° C. The mixture was run out on a gel and the gel band containing the MluI/NotI-pSEX81-fragment was cut and extracted using a gel DNA extraction kit. 1.5 μg of the pooled kappa- and the pooled lambda-chain PCR products, respectively were then digested by adding 7.5 μl of buffer H, 0.9 μl of NotI (40 u/μl), incubating for 20 min at 37° C., and then adding 3 μl of MluI (10 u/μl), followed by further incubation for 40 minutes at 37° C. A 1.5% agarose gel was run with the reaction products and the band at 400 bp was cut and purified using a gel DNA extraction kit. The digested vector (pSEX81) and insert (kappa- or lambda-variable chain genes) were ligated using a molar ratio between 1:1 and 1:3. The reaction mixture included 50 ng DNA, 1 U of T4 ligase, ligation buffer and H2O to a final volume of 15 μl. Overnight incubation at 16° C. was followed by precipitation of the DNA by adding 1/10 volume of 3M sodium acetate, 20 μg glycogen, 2.5× volume of absolute ethanol. Incubation for 1.5 hour at −20° C. was followed by sedimenting of the precipitate by centrifugation for 30 minutes at 13,000 rpm. The pellet was washed with 80% ethanol at least twice, and then the pellet was allowed to dry at room temperature. The dried pellet was resuspended in 2-5 μl H2O.
Heavy chain DNA was then cloned into the pSEX81 vectors containing the light chain DNA by: digesting 10 μg of light chain containing vectors (kappa-pSEX81 and lambda-pSEX81) respectively with 10 μl of HindIII (10 u/μl), 25 μl of Buffer H, 0.5 μl of RNAse A (10 μg) in a total volume 230 μl, incubating for 20 min at 37° C., then, adding 10 μl of NcoI (10 u/μl), then incubating 90 minutes at 37° C. The remaining procedures for digesting the vectors are the same as described above. For digesting the heavy chain insert, 1 μg of the pooled gamma chain PCR products was digested with 7.5 ul of 10× buffer H, 2.7 ul of HindIII (10 u/ul), 4 ul of NcoI (10 u/ul) at a total volume of 75 μl, followed by incubation for 4 hours at 37° C., and then by incubation for 20 min at 65° C. The digested DNA was purified using a gel DNA extraction kit. Ligation and precipitation of the DNA was completed as described above.
Library stocks were created by: 1.5 μl of one ligation reaction was used for the electroporation of 40 μl electrocompetent E. coli XL-blue (Stratagene). Each transformation of the ligated DNA library was plated onto SOB-GA agar plates and incubated 30° C. overnight. 6 ml 2×YT-GA medium was added to each plate and the bacteria were scraped into the medium. The cells were pooled and made into glycerol stocks.
EXAMPLE 2
Biopanning of library
An inoculated culture was grown at 37° C. with shaking at 250 rpm until an A600 Of 0.1 was reached. M13K07 helper phage was added, and then the culture was incubated for 15 minutes at 37° C. without shaking, then 1 hour at 37° C. with shaking at 250 rpm. Cells were pelleted for 10 min at 1500 g and then resuspended in 400 ml of 2×YT-AK medium. The suspension was grown overnight at 30° C. with shaking at 250 rpm. The culture was spun and phage was then precipitated using a PEG solution. Phage was titerated. Glycerol stocks could be made or the libraries could be used directly for panning.
Two wells in a nunc 96-well plate were coated with 200 μl/well, 100 μg/ml of purified Toso-Fc in PBS; two wells were coated with 200 μl of 100 μg/ml rhIgG Fc (Sino Biological Inc.); 200 μl of 5% milk PBS (MPBS) was added to another 2 wells (without antigen), and the plate was incubated overnight at 4° C.
0.6 ml of 1012 pfu/ml phages was removed from the naïve libraries to a 1.5 ml tubes, protein G beads were added to the tubes, and then tubes were incubated on a rotary for overnight at 4° C.
The Toso-Fc coated wells were emptied the next morning and washed 3 times with PBST and block with 250 ul of 5% MPBS, followed by incubation for 2 hours at room temperature.
The rhIgG Fc (Sino Biological Inc.) coated wells were emptied. The phage-protein G beads solution was centrifuged and 100 μl supernatant was transferred to each of the two rhIgG Fc coated wells. 100 ug/ml rhIgG Fc, 100 μl/well was added (Sino Biological Inc.), and incubated at room temperature for 1 hour.
The non-protein coated wells were emptied and the phage solution was transferred to non-protein coated wells separately and incubated for 1 hour at room temperature.
The blocking buffer was removed from the Toso-Fc-coated wells and then washed several times with PBST. The 200 μl phage solution was transferred to the Toso-Fc-coated wells and incubated for 1.5 hours at room temperature.
The Toso-Fc-coated wells were emptied and washed several times with PBST. The phage was eluted by adding 200 μl 100 mM triethylamine to each of the two wells follow by 10 minutes of incubation.
The eluted phage was transferred to 2×1.5 ml tubes containing 800 ul of 1M Tris-HCl (pH7.5) to neutralize the pH.
2×10 ul of eluted phage was used to do titration. The remaining eluted phage was used to infect 10 ml fresh TG1 cells (OD600=0.4). 200 ul of this sample was spread on a 2×YT agar plate containing 100 ul/ml of ampicillin and 1% glucose, grown overnight at 32° C. The remaining infected cells were incubated at 37° C. with shaking at 250 rpm for 1 hour, following which the volume was increased to 110 ml with 2×YT medium containing 100 ug/ml amp, followed by incubation at 37° C. with shaking at 250 rpm.
M13KO7 helper phages (100 μl of 1012 pfu) were added to the infected culture and grown at 37° C., also. Kanamycin was added to the culture at a final concentration of 50 μg/ml. This culture was incubated overnight at 37° C., with shaking at 250 rpm for the next round of panning.
Although various aspects of this technology have been described above with a certain degree of particularity, or with reference to one or more individual aspects, those skilled in the art could make numerous alterations to the disclosed aspects without departing from the spirit or scope of the technology hereof. Since many aspects can be made without departing from the spirit and scope of the presently described technology, the appropriate scope resides in the claims hereinafter appended. Other aspects are therefore contemplated. Furthermore, it should be understood that any operations may be performed in any order, unless explicitly claimed otherwise or a specific order is inherently necessitated by the claim language. It is intended that all matter contained in the above description and shown in the accompanying drawings shall be interpreted as illustrative only of particular aspects and are not limiting to the embodiments shown. Unless otherwise clear from the context or expressly stated, any concentration values provided herein are generally given in terms of admixture values or percentages without regard to any conversion that occurs upon or following addition of the particular component of the mixture. To the extent not already expressly incorporated herein, all published references and patent documents referred to in this disclosure are incorporated herein by reference in their entirety for all purposes. Changes in detail or structure may be made without departing from the basic elements of the present technology as defined in the following claims.

## Claims

1. An antibody comprising a heavy chain comprising the amino acid sequence of SEQ ID NO: 1 and a light chain comprising the amino acid sequence of SEQ ID NO: 2.

2. An antibody comprising a heavy chain comprising the amino acid sequence of SEQ ID NO: 3 and a light chain comprising the amino acid sequence of SEQ ID NO: 4.

3. An antibody comprising a heavy chain comprising the amino acid sequence of SEQ ID NO: 5 and a light chain comprising the amino acid sequence of SEQ ID) NO: 6.

4. An antibody comprising a heavy chain comprising the amino acid sequence of SEQ ID NO: 7 and a light chain comprising the amino acid sequence of SEQ ID NO: 8.

5. An antibody comprising a heavy chain comprising the amino acid sequence of SEQ ID NO: 9 and a light chain comprising the amino acid sequence of SEQ ID NO: 10.