US20130018176A1

US20130018176A1 - Methods of producing hybridomas and monoclonal antibodies and antibodies produced thereby

Info

Publication number: US20130018176A1
Application number: US13/620,007
Authority: US
Inventors: Xiao-Juan Bi; Grace Ki Jeong LEE; Jackie Z. SHENG
Original assignee: Amgen Inc
Current assignee: Amgen Inc
Priority date: 2007-02-02
Filing date: 2012-09-14
Publication date: 2013-01-17

Abstract

Disclosed are a method of producing a hybridoma, a method of making an antibody involving the hybridoma, and an antibody made by the method.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a continuation of U.S. Nonprovisional application Ser. No. 12/022,515, filed 30 Jan. 30, 2008, which claims the benefit of priority of U.S. Provisional Application No. 60/888,059, filed Feb. 2, 2007, and U.S. Provisional Application No. 61/015,138, filed Dec. 19, 2007. Each of the priority applications are incorporated herein by reference in their entireties.
The instant application contains an ASCII “txt” compliant sequence listing, which serves as both the computer readable form (CRF) and the paper copy, and is hereby incorporated by reference in its entirety. The name of the “txt” file created on Aug. 30, 2012, is: A-1156-US-CON-OffPCT083012 ST25.txt, and is 241 kb in size.

FIELD OF THE INVENTION

The invention relates to a method of producing a hybridoma, a method of making an antibody involving the hybridoma, and an antibody made by the method.

BACKGROUND

Iron is an essential trace element required for growth and development of all living organisms. Iron content in mammals is regulated by controlling iron absorption, iron recycling, and release of iron from the cells in which it is stored. Iron is absorbed predominantly in the duodenum and upper jejunum by enterocytes. A feedback mechanism exists that enhances iron absorption in individuals who are iron deficient, and that reduces iron absorption in individuals with iron overload (Andrews Ann. Rev. Genomics Hum. Genet. 1:75 (2000); Philpott, Hepatology 35:993 (2002); Beutler et al., Drug-Metab. Dispos. 29:495 (2001)). Iron is recycled from degraded red cells by reticuloendothelial macrophages in bone marrow, hepatic Kupffer cells and spleen. Iron release is controlled by ferroportin, a major iron export protein located on the cell surface of enterocytes, macrophages and hepatocytes, the main cells capable of releasing iron into plasma. Hepcidin binds to ferroportin and decreases its functional activity by causing it to be internalized from the cell surface and degraded. (Nemeth et al., Science, 306:2090-3, 2004; De domenico et al., Mol. Biol. Cell., 8:2569-2578, 2007).
Hepcidin is the key signal regulating iron homeostasis (Philpott, Hepatology 35:993 (2002); Nicolas et al., Proc. Natl. Acad. Sci. USA 99:4396 (2002)). High levels of human hepcidin result in reduced iron levels, and vice versa. Mutations in the hepcidin gene which result in lack of hepcidin activity are associated with juvenile hemochromatosis, a severe iron overload disease (Roetto et al., Nat. Genet., 33:21-22, 2003). Studies in mice have demonstrated a role of hepcidin in control of normal iron homeostasis (Nicolas et al., Nat. Genet., 34:97-101, 2003; Nicolas et al., Proc. Natl. Acad. Sci. USA, 99:4596-4601, 2002; Nicolas et al., Proc. Natl. Acad. Sci. USA, 98:8780-8785, 2001.).
In addition, data is accumulating implicating hepcidin in iron sequestration during inflammation (See, e.g., Weinstein et al., Blood, 100:3776-36781, 2002; Kemna et al., Blood, 106:1864-1866, 2005; Nicolas et al., J. Clin. Invest., 110:1037-1044, 2002; Nemeth et al., J. Clin. Invest., 113:1271-1276, 2004; Nemeth et al., Blood, 101:2461-2463, 2003 and Rivera et al., Blood, 105:1797-1802, 2005). Hepcidin gene expression has been observed to be robustly upregulated after inflammatory stimuli, such as infections, which induce the acute phase response of the innate immune systems of vertebrates. In mice, hepcidin gene expression was shown to be upregulated by lipopolysaccharide (LPS), turpentine, Freund's complete adjuvant, and adenoviral infections. Hepcidin expression is induced by the inflammatory cytokine interleukin-6 (IL-6). A strong correlation between hepcidin expression and anemia of inflammation was also found in patients with chronic inflammatory diseases, including bacterial, fungal, and viral infections.
Human hepcidin, a 25 amino acid peptide with anti-microbial and iron-regulating activity, was discovered independently by two groups investigating novel anti-microbial peptides. (Krause et al., FEBS Lett. 480:147 (2000); Park et al., J. Biol. Chem. 276:7806 (2001)). It has also been referred to as LEAP-1 (liver-expressed antimicrobial peptide). A hepcidin cDNA encoding an 83 amino acid pre-propeptide in mice and an 84 amino acid pre-propeptide in rat and human were subsequently identified in a search for liver specific genes that were regulated by iron (Pigeon et al., J. Biol. Chem. 276:7811 (2001)). The 24 residue N-terminal signal peptide is first cleaved to produce pro-hepcidin, which is then further processed to produce mature hepcidin, found in both blood and urine. In human urine, the predominant form contains 25 amino acids, although shorter 22 and 20 amino acid peptides are also present.
The mature peptide is notable for containing eight cysteine residues linked as four disulfide bridges. The structure of hepcidin was studied by Hunter et al., J. Biol. Chem., 277:37597-37603 (2002), by NMR using chemically synthesized hepcidin with an identical HPLC retention time to that of native hepcidin purified from urine. Hunter et al. reported their determination that hepcidin folded into a hairpin loop structure containing a vicinal disulfide bond (C1-C8, C2-C7, C3-C6, C4-C5). More recently, determination of the structure of bass hepcidin was also reported, using the structural information of Hunter et al. and inferential NMR data to deduce an identical disulfide connectivity assignment (Lauth et al., J. Biol. Chem., 280:9272-9282 (2005). However, as discovered and disclosed herein by the present inventors, the structure of hepcidin was determined to have a disulfide bond connectivity that is different from that taught by the prior art.
U.S. Patent Publication Nos. 2003/0187228, 2004/0096987, 2004/0096990, 2005/0148025, 2006/0019339, 2005/0037971 and 2007/0224186; U.S. Pat. Nos. 7,232,892 and 7,294,690 and International Publication No. WO 02/98444 discuss hepcidin antibodies but fail to disclose or suggest the structural conformation of hepcidin disclosed herein.
Thus, the specification illustrates the determination of the structure of hepcidin, as well as the central role of hepcidin and its key functions in iron regulation and in the innate immune response to infection. Furthermore, the application provides, inter alia, bioactive hepcidin, monoclonal antibodies to the bioactive hepcidin, methods to produce the same, methods to determine bioactive hepcidin, and methods to modulate hepcidin activity or its expression, and methods for treating disorder of iron homeostasis as well as hepcidin antagonists and hepcidin agonists.

SUMMARY OF THE INVENTION

Various embodiments of the invention generally relate to purified, correctly folded human hepcidin, monoclonal antibodies thereto, hepcidin variants that retain one or more of the disulfide bonds of properly folded human hepcidin, methods for producing such materials, and methods for using such materials to detect hepcidin or to modulate hepcidin activity.
This application is believed to be the first report of bioactive human hepcidin disulfide connectivity in which disulfide bonds are formed between C1-C8, C2-C4, C3-C6 and C5-C7, and which predicts a compact and tightly folded molecule. In some embodiments, the invention provides for large scale production of hepcidin, expressed recombinantly or generated synthetically, which possesses identical disulfide connectivity and equivalent biological activity to native material. Such recombinant or synthetic material is useful for treatment of subjects in need of additional hepcidin, as well as for preparation of known hepcidin standards in detection methods and kits. The production of large batches of correctly-folded human hepcidin also permits the generation and testing of monoclonal antibodies that bind to hepcidin, especially monoclonal antibodies of high affinity and/or specificity. Such monoclonal antibodies are useful, for example, in hepcidin detection methods and in diagnostic and therapeutic methods.
In one aspect, the hepcidin activity antagonist is a monoclonal antibody that binds to mature, correctly-folded, bioactive human hepcidin (SEQ ID NO: 9), with the desired affinity. Also provided is a monoclonal antibody that binds hepcidin (SEQ ID NO: 9) and inhibits the iron-regulating activity of hepcidin. In one embodiment, the monoclonal antibody decreases intracellular iron concentration and/or increases circulating iron concentration at an EC₅₀of about 10⁻⁸M or less. In other embodiments, the monoclonal antibody exhibits the property in mammals of increasing red blood cell count (number) or hemoglobin or hematocrit levels, and/or normalizing reticulocyte count, reticulocyte mean cell volume and/or reticulocyte hemoglobin content.
In various embodiments, the monoclonal antibody binds to a conformational epitope of hepcidin, the conformational epitope comprising: any one of amino acids 1 through 5 (e.g., amino acid 1, 2, 3, 4 or 5) of SEQ ID NO: 9, and/or any one of amino acids 10 through 13 (e.g., amino acid 10, 11, 12 or 13) of SEQ ID NO: 9, and/or any one of amino acids 14 through 22 (e.g., amino acid 14, 15, 16, 17, 18, 19, 20, 21 or 22) of SEQ ID NO: 9. In a related aspect, the monoclonal antibody binds to a conformational loop comprising the Cys at position 10 and the Cys at position 13 of SEQ ID NO: 9 and/or a conformational loop comprising the Cys at position 14 and the Cys at position 22 of SEQ ID NO: 9.
In various embodiments monoclonal antibodies can include any of antibodies Ab43, 2.7, 2.41, R9, 1C9, 1S1, 1S2, 1S3, 1S4, 1S5, 3B3; 4E1, 7A3, 9D12, 12B9, 15E1, 18D8, 19C1, 19D12, 19H6, 23F11, and 26F11, or antibodies that retain any one, two, three, four, five, or six of CDRH1, CDRH2, CDRH3, CDRL1, CDRL2 or CDRL3 of such antibodies, optionally including one or two mutations in such CDR(s), or antibodies that retain a light or heavy chain variable region of any of such antibodies, or antibodies that bind to the same epitope on human hepcidin as antibodies Ab43, 2.7, 2.41, R9, 1C9, 1S1, 1S2, 1S3, 1S4, 1S5, 3B3; 4E1, 7A3, 9D12, 12B9, 15E1, 18D8, 19C1, 19D12, 19H6, 23F11, and 26F11, or that compete with such antibodies for binding to human hepcidin by at least 75%. Such competitive binding may be assessed by competitive ELISA or by the methods described for evaluating epitope specificity in Example 17 or by other methods described herein or known in the art.
Various embodiments also provide nucleic acids encoding any of the monoclonal antibodies described herein, vectors comprising such nucleic acid sequences, and host cells comprising such nucleic acids or vectors. In a related aspect, methods for recombinant production of such monoclonal antibodies are provided which include culturing the aforementioned host cell such that the nucleic acid is expressed to produce the antibody, and optionally recovering the antibody from the host cell or culture medium. In a related embodiment, an isolated antibody or agent produced by the aforementioned method is provided.
In another aspect, a method is provided of detecting human hepcidin in a sample, comprising contacting a sample from a human with any of the aforementioned antibodies under conditions that allow binding of the antibody to human hepcidin, and detecting the bound antibody. In one embodiment, a first antibody to hepcidin is immobilized on a solid support, as a capture reagent, and a second antibody to hepcidin is used as a detection reagent. In a related aspect, the amount of hepcidin in the sample is quantitated by measuring the amount of the bound antibody. The detection methods can be used in a variety of diagnostic, prognostic and monitoring methods, including methods of diagnosing a hepcidin-related disorder, methods of differentiating an inflammatory disease from a non-inflammatory disease and methods of monitoring therapy with a hepcidin antagonist. In such methods, a level of hepcidin above a certain threshold is correlated with the presence of hepcidin-related disorder, such as hepcidin-related anemia, while a level below said threshold indicates that the patient is unlikely to have hepcidin-related disorder. Similarly, a level of hepcidin above a certain threshold is correlated with the presence of an inflammatory disease, while a level below said threshold indicates that the patient is unlikely to have an inflammatory disease. In some embodiments, such methods will diagnose patients having iron deficiency anemia, anemia of inflammation or mixed anemia. For monitoring of therapy aimed at suppressing hepcidin levels, a level of hepcidin below a certain threshold indicates that the dose of hepcidin antagonist is therapeutically effective, and a level above said threshold indicates that the dose of hepcidin antagonist is not therapeutically effective.
In another aspect, pharmaceutical compositions are provided comprising a therapeutically effective amount of any of the antibodies described herein and a pharmaceutically acceptable carrier, diluent or excipient. Also provided is the use of such antibodies in preparation of a medicament for treatment of a human with an elevated level of hepcidin, a hepcidin-related disorder, a disorder of iron homeostasis or an anemia. It is understood that co-administration methods involving administration of antibodies with a second therapeutic agent, as described herein, encompass not only the use of the antibody in preparation of a medicament for co-administration with the second therapeutic agent, but also the use of the second therapeutic agent in preparation of a medicament for co-administration with the antibody.
Various embodiments further provide methods of using such antibodies, for example, to treat a mammal with an elevated level of hepcidin, or a hepcidin-related disorder, or a disorder of iron homeostasis, or a mammal with anemia, by administering a therapeutically effective amount of such antibody. In exemplary embodiments, the mammal is a human suffering from a condition selected from the group consisting of African iron overload, alpha thalassemia, Alzheimer's disease, anemia, anemia of cancer, anemia of chronic disease, anemia of inflammation, arteriosclerosis or atherosclerosis (including coronary artery disease, cerebrovascular disease or peripheral occlusive arterial disease), ataxias, ataxias related to iron, atransferrinemia, cancer, ceruloplasmin deficiency, chemotherapy-induced anemia, chronic renal/kidney disease (stage I, II, III, IV or V), including end stage renal disease or chronic renal/kidney failure, cirrhosis of liver, classic hemochromatosis, collagen-induced arthritis (CIA), conditions with hepcidin excess (elevated hepcidin), congenital dyserythropoietic anemia, congestive heart failure, Crohn's disease, diabetes, disorders of iron biodistribution, disorders of iron homeostasis, disorders of iron metabolism, ferroportin disease, ferroportin mutation hemochromatosis, folate deficiency, Friedrich's ataxia, funicular myelosis, gracile syndrome, H. pyelori infection or other bacterial infections, Hallervordan Spatz disease, hemochromatosis, hemochromatosis resulting from mutations in transferrin receptor 2, hemoglobinopathies, hepatitis, hepatitis (Brock), hepatitis C, hepatocellular carcinoma, hereditary hemochromatosis, HIV or other viral illnesses, Huntington's disease, hyperferritinemia, hypochromic microcytic anemia, hypoferremia, insulin resistance, iron deficiency anemia, iron deficiency disorders, iron overload disorders, iron-deficiency conditions with hepcidin excess, juvenile hemochromatosis (HFE2), multiple sclerosis, mutation in transferrin receptor 2, HFE, hemojuvelin, ferroportin or other genes of iron metabolism, neonatal hemochromatosis, neurodegenerative diseases related to iron, osteopenia, osteoporosis pancreatitis, Pantothenate kinase-associated neurodegeneration, Parkinson's disease, pellagra, pica, porphyria, porphyria cutanea tarda, pseudoencephalitis, pulmonary hemosiderosis, red blood cell disorders, rheumatoid arthritis, sepsis, sideroblastic anemia, systemic lupus erythematosus, thalassemia, thalassemia intermedia, transfusional iron overload, tumors, vasculitis, vitamin B6 deficiency, vitamin B12 deficiency, and/or Wilson's disease.
In yet another aspect, methods are provided for treating a mammal with anemia by administration of (a) a hepcidin activity antagonist or a hepcidin expression inhibitor and (b) an erythropoiesis stimulator, in therapeutically effective amounts. Exemplary hepcidin activity antagonists include antibodies that bind human hepcidin. Exemplary hepcidin expression inhibitors include polynucleotides or oligonucleotides that bind a human hepcidin nucleic acid. Exemplary erythropoiesis stimulators include erythropoietin, erythropoietin agonist variants, and peptides or antibodies that bind and activate erythropoietin receptor. Erythropoiesis stimulators include, but are not limited to, epoetin alfa, epoetin beta, epoetin delta, epoetin omega, epoetin iota, epoetin zeta, and analogs thereof, mimetic peptides, mimetic antibodies and HIF inhibitors (see U.S. Patent Publication No. 2005/0020487, the disclosure of which is incorporated by reference in its entirety). In particular, erythropoietin includes, but is not limited to, erythropoietin molecules or variants or analogs thereof as disclosed in the following patents or patent applications, which are each herein incorporated by reference in its entirety: U.S. Pat. Nos. 4,703,008; 5,441,868; 5,547,933; 5,618,698; 5,621,080; 5,756,349; 5,955,422 and 5,856,298; and WO 91/05867; WO 95/05465; WO 00/24893 and WO 01/81405. In certain exemplary embodiments, the erythropoiesis stimulator is selected from the group consisting of human erythropoietin (SEQ ID NO: 72) and darbepoetin alfa (SEQ ID NO: 73). Exemplary forms of anemia that may be treated according to such methods include anemia of inflammation, anemia of cancer, chemotherapy induced anemia, iron deficiency anemia, a disorder of iron homeostasis, ferroportin disease, or anemia resulting from kidney disease. Also provided are methods of treating a mammal with anemia that is hypo-responsive, or even resistant, to therapy with an erythropoiesis stimulator, comprising administering a therapeutically effective amount of a hepcidin activity antagonist, or alternatively a therapeutically effective amount of a hepcidin expression inhibitor.
In another related aspect, kits for treating a disorder associated with elevated hepcidin levels, or a hepcidin-related disorder, or a disorder of iron homeostasis, or a mammal with anemia, are also provided. In one exemplary embodiment, the kit includes (a) a hepcidin activity antagonist or a hepcidin expression inhibitor, and (b) an erythropoiesis stimulator, and optionally, iron. In another exemplary embodiment, the kit includes a hepcidin activity antagonist, or a hepcidin expression inhibitor, and a label attached to or packaged with the container, the label describing use of the hepcidin activity antagonist, or the hepcidin expression inhibitor, with an erythropoiesis stimulator. In yet another exemplary embodiment, the kit includes an erythropoiesis stimulator and a label attached to or packaged with the container, the label describing use of the erythropoiesis stimulator with a hepcidin activity antagonist, or a hepcidin expression inhibitor. Also provided is the use of a hepcidin activity antagonist or a hepcidin expression inhibitor in preparation of a medicament for administration with an erythropoiesis stimulator, as well as use of an erythropoiesis stimulator in preparation of a medicament for administration with a hepcidin activity antagonist or a hepcidin expression inhibitor. In any of these kits or uses, the hepcidin activity antagonist (or hepcidin expression inhibitor) and the erythropoiesis stimulator can be in separate vials or can be combined together in a single pharmaceutical composition. In yet another embodiment, the hepcidin activity antagonist (or hepcidin expression inhibitor) or the erythropoiesis stimulator, or both, can be combined with iron in a single pharmaceutical composition or can be in separate vials.
In a different aspect, a composition of purified, bioactive, correctly-folded, non-urinary human hepcidin is provided comprising SEQ ID NO: 96 wherein at least 80%, 85%, 90%, 95%, 98% or 99% of the human hepcidin in the composition has a C2-C4 disulfide bond, a C5-C7 disulfide bond, a C1-C8 disulfide bond, and a C3-C6 disulfide bond. In some embodiments, the human hepcidin has been chemically synthesized or produced in bacteria or other non-mammalian cells. The amount of a properly folded protein in a solution can be quantitated by methods known in the art (including heteronuclear single quantum correlation (HSQC), Morita et al., Protein Science, 12(6), 1216-1221 (2003)). In a related embodiment, methods of using such purified human hepcidin compositions are provided, for example, to generate or screen for monoclonal antibodies, to identify a hepcidin binding partner, or to test a composition comprising an antibody or specific binding agent for ability to bind human hepcidin. Generation of antibodies involves, e.g., contacting an immunoglobulin producing cell with the purified human hepcidin composition and isolating an immunoglobulin produced by said cell. Screening for antibodies or specific binding agents generally involve, for example, contacting a candidate hepcidin binding partner with the purified human hepcidin composition and detecting a complex formed between the candidate hepcidin binding partner and human hepcidin in the composition. In another related embodiment, the method further comprises administering the candidate hepcidin binding partner to a mammal. Testing an antibody or specific binding agent for ability to bind human hepcidin involves, e.g., contacting it with the purified human hepcidin composition or fragment thereof retaining proper folding, and detecting a complex formed between the human hepcidin and the antibody or specific binding agent.
In a related aspect, a method of refolding a human hepcidin polypeptide is provided comprising SEQ ID NO: 96 to a correctly-folded, bioactive form comprising (a) exposing a human hepcidin polypeptide to a chaotropic agent under conditions that promote denaturing, and (b) exposing the product of (a) to an oxidizing agent under conditions that promote renaturing into a properly folded and bioactive form, and (c) recovering a solution comprising the bioactive human hepcidin polypeptide, wherein at least 70%, at least 75%, at least 80%, at least 85%, at least 86%, at least 87%, at least 88%, at least 89%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% or more of the human hepcidin polypeptide has a C2-C4 disulfide-bond and a C5-C7 disulfide-bond. The amount of a properly folded protein in a solution can be quantitated by methods known in the art (including heteronuclear single quantum correlation (HSQC), Morita et al., Protein Science, 12(6), 1216-1221 (2003). In one embodiment, the correctly-folded bioactive hepcidin has an EC₅₀of <100 nM in a cell-based assay. In another embodiment, the correctly-folded bioactive hepcidin has an EC₅₀of <30 nM in a cell-based assay. In a related embodiment, (b) further comprises contacting the human hepcidin polypeptide with an oxidizing agent other than air. In another embodiment, the oxidizing takes place at a pH of greater than 8 and in a solution containing less than 0.1% acetic acid.
In a different aspect, a variant of human hepcidin is provided that retains the same or similar disulfide connectivity, and/or the same or similar predicted three-dimensional structure. In exemplary embodiments, the variant retains all eight cysteine residues and further retains the C2-C4 disulfide bond and/or the C5-C7 disulfide bond. Such variants may exhibit agonist or antagonist activity, i.e. retain or inhibit hepcidin biological activity (anti-microbial or iron-regulating activity). In exemplary embodiments, a hepcidin analog peptide is provided that comprises an amino acid sequence at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical over its length to SEQ ID NO: 96. Hepcidin variants may exhibit one or more of the following: retains ferroportin-binding activity (i.e., activates ferroportin or inhibits ferroportin iron transport), promotes or inhibits iron-regulating activity of mature human hepcidin (SEQ ID NO: 9) and/or decreases or increases circulating iron levels in vivo.
In another aspect, an antibody that detects purified mature human hepcidin of SEQ ID NO: 9 as a principal band having an approximate molecular weight of less than 6 kd (e.g., 3 kd±2) as determined by a sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) under reducing conditions is provided.
The foregoing summary is not intended to define every aspect of the invention, and additional aspects are described in other sections, such as the Detailed Description. The entire document is intended to be related as a unified disclosure, and it should be understood that all combinations of features described herein are contemplated, even if the combination of features are not found together in the same sentence, or paragraph, or section of this document.
In addition to the foregoing, the invention can include, as an additional aspect, all embodiments of the invention narrower in scope in any way than the variations defined by specific paragraphs herein. For example, certain aspects of the invention that are described as a genus, and it should be understood that every member of a genus is, individually, an aspect of the invention. Also, aspects described as a genus or selecting a member of a genus, should be understood to embrace combinations of two or more members of the genus.
It should be understood that while various embodiments in the specification are presented using “comprising” language, under various circumstances, a related embodiment may also be described using “consisting of” or “consisting essentially of” language. It is to be noted that the term “a” or “an”, refers to one or more, for example, “an immunoglobulin molecule,” is understood to represent one or more immunoglobulin molecules. As such, the terms “a” (or “an”), “one or more,” and “at least one” can be used interchangeably herein.
It should also be understood that when describing a range of values, the characteristic being described could be an individual value found within the range. For example, “a pH from about pH 4 to about pH 6,” could be, but is not limited to, pH 4, 4.2, 4.6, 5.1 5.5 etc. and any value in between such values. Additionally, “a pH from about pH 4 to about pH 6,” should not be construed to mean that the pH of a formulation in question varies 2 pH units in the range from pH 4 to pH 6 during storage, but rather a value may be picked in that range for the pH of the solution, and the pH remains buffered at about that pH. In some embodiments, when the term “about” is used, it means the recited number plus or minus 5%, 10%, 15% or more of that recited number. The actual variation intended is determinable from the context. Although the applicant(s) invented the full scope of the invention described herein, the applicants do not intend to claim subject matter described in the prior art work of others. Therefore, in the event that statutory prior art within the scope of a claim is brought to the attention of the applicants by a Patent Office or other entity or individual, the applicant(s) reserve the right to exercise amendment rights under applicable patent laws to redefine the subject matter of such a claim to specifically exclude such statutory prior art or obvious variations of statutory prior art from the scope of such a claim. Variations of the invention defined by such amended claims also are intended as aspects of the invention.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows an IRMPD FTMS spectra of all four preparations of human hepcidin demonstrating equivalence of all three synthetic and recombinant preparations to urinary hepcidin.

FIG. 2 shows 1D ¹H NMRspectra of the four preparations of human hepcidin demonstrating equivalence of all three synthetic and recombinant preparations to urinary hepcidin.

FIG. 3A shows HPLC analysis of partially reduced and alkylated hepcidin at pH2.

FIG. 3B shows HPLC analysis of partially reduced and alkylated hepcidin at pH3.

FIG. 4 shows a two-dimensional NOESY(dark)-TOCSY(light) overlay of backbone fingerprint region of recombinant human hepcidin showing backbone resonance assignments.

FIG. 5 shows an overlay of the ω₁-decoupled 2D TOCSY and ω₁-decoupled 2D TOCSY-NOESY experiments, as discussed in Example 8. The resonance positions of Ha protons are marked with the broken arrows. The asterisk denotes a folding artifact.

FIG. 6 is a schematic of human hepcidin polypeptide indicating the various disulfide bonds determined by two partial alkylative reduction techniques and confirmed by NMR.

FIG. 7 shows the average backbone structures of human hepcidin obtained by Hunter et al. (J. Biol. Chem., 277:37597-603, 2002) (left) and as determined in Example 8 (right).

FIG. 8 shows murine anti-hepcidin antibody Ab 43's functional ability to drive down intracellular iron concentrations in a beta-lactamase iron-response assay.

FIG. 9 shows murine anti-hepcidin antibody 2.7's functional ability to drive down intracellular iron concentrations in a beta-lactamase iron-response assay.

FIG. 10 shows murine anti-hepcidin antibody 2.41's functional ability to drive down intracellular iron concentrations in a beta-lactamase iron-response assay.

FIG. 11 demonstrates that an anti-hepcidin antibody neutralizes human hepcidin injected into mice.

FIG. 12 demonstrates that antibody neutralization of human hepcidin virally expressed mice restores normal early red cell characteristics.

FIG. 13A shows that viral overexpression of hepcidin causes hypo-responsiveness to erythropoietin.

FIG. 13B shows a titration of adenovirus-associated virus (AAV)-mediated hepcidin expression and resulting serum iron concentrations.

FIG. 14 shows that suppressing hepcidin restores responsiveness to Aranesp® (darbepoetin alfa) in an inflammatory anemia model.

FIG. 15A shows a schematic of the experimental procedure of Example 22.

FIGS. 15B-E demonstrate that an anti-hepcidin antibody restores responsiveness to erythropoietin in mice virally over-expressing hepcidin.

FIG. 16 shows that neutralization of hepcidin by anti-hepcidin antibody treatment restores responsiveness to erythropoietin in human hepcidin knock-in mice with anemia of inflammation.

FIG. 17A shows a decision tree of iron indices and disease states for assessment of a patient, in the absence of hepcidin measurement FIG. 17B shows a theoretical decision tree for assessment of a patient using measurement of hepcidin levels.

FIG. 18 demonstrates that hepcidin levels are elevated in anemia of cancer patients (AoC) and not in normal patients.

FIG. 19 demonstrates that hepcidin levels correlate with diagnosis of inflammatory anemia and not iron deficiency anemia.

FIG. 20 shows that the commercially available DRG prohepcidin ELISA is unable to detect mature hepcidin.

FIG. 21 shows prohepcidin concentration measured by a sandwich immunoassay, demonstrating that prohepcidin is not detectable in serum.

FIG. 22 shows a prohepcidin western blot, indicating that prohepcidin is degraded in serum unless protected by the presence of furin inhibitors

FIG. 23 shows that hepcidin and prohepcidin levels (as measured by the commercially available DRG prohepcidin ELISA) do not correlate in patient samples.

FIGS. 24A-B show that hepcidin levels are related to inflammatory status as assessed by C-reactive protein (A), and prohepcidin levels are not (B).

FIGS. 25A-B show that hepcidin levels aid in diagnosis of anemia of inflammation (A), and prohepcidin levels do not (B).

FIGS. 26A-B demonstrate that hepcidin levels correlate with diagnosis of inflammatory anemia (A), and prohepcidin levels do not (B).

FIG. 27 demonstrates that polyclonal antibodies raised against mature hepcidin can be used to construct a sandwich ELISA.

FIG. 28 shows a Biacore experiment demonstrating that two monoclonal antibodies can bind to hepcidin at once.

FIG. 29 demonstrates that a sandwich ELISA can be constructed with monoclonal antibodies raised against mature hepcidin.

FIG. 30 shows the concentration of hepcidin present in buffer, rabbit serum and pooled human serum as determined by a competitive binding assay.

FIG. 31 demonstrates the measurement of hepcidin in human sera.

FIG. 32 demonstrates the concentration of hepcidin present in normal human sera using a competitive binding assay.

FIG. 33 comparison of hepcidin levels detected in random human donors measured using the sandwich ELISA, competitive ELISA and mass spectrometric techniques.

FIG. 34 demonstrates that AoC patients with elevated hepcidin levels also have elevated C-reactive protein (CRP levels).

DETAILED DESCRIPTION OF THE INVENTION

The human hepcidin gene encodes an 84 residue pre-propeptide (SEQ ID NO: 8). The corresponding cDNA and genomic sequences are set forth in SEQ ID NOs: 7 and 100, respectively. The 24-residue N-terminal signal peptide (residues 1-24 of SEQ ID NO: 8) is first cleaved to produce pro-hepcidin, which is then further processed by cleavage of the prodomain (residues 25-59 of SEQ ID NO: 8) to produce the 25-residue mature hepcidin (residues 60-84 of SEQ ID NO: 8, set forth in SEQ ID NO: 9). In addition to the primary 25 amino acid form, further N-terminally truncated forms that are 20 or 22 amino acids in length can be identified in urine (20 amino acids, SEQ ID NO: 96; and 22 amino acids, SEQ ID NO: 98). Mature human hepcidin contains eight cysteine residues, which are referred to herein sequentially as C1 through C8 (numbered from the N-terminus to the C-terminus).
The novel disulfide connectivity reported herein and the corresponding modeled three-dimensional structure of hepcidin also permits the production of hepcidin variants that retain the same or similar disulfide connectivity and that are useful as modulators of hepcidin biological activity. For example, molecules that bind to and activate hepcidin receptor, molecules that bind to and cause internalization of ferroportin, or molecules that act as competitive inhibitors relative to hepcidin can be designed and produced.

I. Purified, Correctly-Folded Human Hepcidin Compositions

Hepcidin polypeptides may need to be “refolded” and oxidized into a proper tertiary structure and generating disulfide linkages in order to be biologically active. Refolding can be accomplished using the procedures described herein and others well known in the art. Such methods include, for example, exposing the solubilized polypeptide agent to a pH usually above 7 in the presence of a chaotropic agent. A chaotropic agent is a compound, including, without limitation, guanidine hydrochloride (guanidinium hydrochloride, GdnHCl), guanidine sulfate, urea, sodium thiocyanate, sarcosyl, sodium dodecyl sulfate, sodium octyl sulfate and/or other compounds which disrupt the noncovalent intermolecular bonding within the protein, permitting the polypeptide chain to assume a substantially random conformation.
In most cases, the refolding/oxidation solution will also contain a reducing agent plus its oxidized form in a specific ratio to generate a particular redox potential which allows for disulfide shuffling to occur for the formation of cysteine bridges. A reducing agent is capable of transferring electrons and, in so doing, “reducing” bonds between various atoms. In the context of various embodiments of the invention, a reducing agent will disrupt intra- and intermolecular interactions, in particular, those involving disulfide bridges. Exemplary reducing agents, according to the various embodiments of the invention include diothiothreitol, glutathione, dithioerythritol, or β-mercaptoethanol. Some commonly used redox couples include cysteine/cystamine, glutathione/dithiobisGSH, cupric chloride, dithiothreitol DTT/dithiane DTT, and 2-mercaptoethanol (bME)/dithio-bME. In many instances, a co-solvent may be used to increase the efficiency of the refolding. Commonly used cosolvents include glycerol, polyethylene glycol of various molecular weights, and arginine.
Once refolded, the disulfide connectivity of a hepcidin polypeptide can be assessed by a variety of techniques known in the art. In one aspect, the technique is NEM partial reductive alkylation; in another it is Fourier transform mass spectrometry (FT-MS). NEM partial reductive alkylation and FT-MS are discussed in more detail in Examples 1 and 4.
FT-MS (Fourier transform mass spectrometry) can be used to assess disulfide connectivity. As known in the art, FT-MS is based on the principle of a charged particle orbiting in a strong, stable magnetic field. By detecting the current generated by the orbiting ions, a Fourier transform may be used to determine the m/z of the ions. Advantageously, this procedure allows for very high mass resolution and the ability to perform convenient tandem mass spectroscopy experiments. Together, this allows for the unequivocal assignment of the proteolytic fragments under analysis. (See, e.g., Marshall et al., Mass Spectrometry Reviews, 17:1-35, 1998; Lewis et al., Proc Natl Acad Sci USA., 95:8596-601, 1998; Li et al., Anal Chem, 66:2077-83, 1994) FT-MS is discussed in more detail in Examples 1 and 4.
The amount of a properly folded protein in a solution can be quantitated by methods known in the art (including heteronuclear single quantum correlation (HSQC), Morita et al., Protein Science, 12(6), 1216-1221 (2003)). A misfolded protein such as hepcidin will have unique cross-peaks in an HSQC spectrum. By integrating these peaks, in principle, the percentage of misfolding is quantitated.

II. Hepcidin Antagonists

Various embodiments of the invention provide for the production and the use of two different categories of hepcidin antagonists: (a) hepcidin activity antagonists or (b) hepcidin expression inhibitors.
As used herein, “hepcidin activity antagonist” means a substance that inhibits human hepcidin's iron-regulating activity but that does not inhibit expression of the hepcidin gene or hepcidin mRNA.
As used herein, “hepcidin expression inhibitor” means a substance that inhibits expression of hepcidin gene or hepcidin mRNA.
Hepcidin activity antagonists and hepcidin expression inhibitors are mutually exclusive categories, although both fall under a general category of “hepcidin antagonist.”
In one aspect, the hepcidin activity antagonist can be a substance that inhibits the function of hepcidin, for example, by inhibiting binding between hepcidin and ferroportin, by inhibiting hepcidin-controlled cellular iron retention, or by facilitating ferroportin dependent iron transport. Hepcidin activity antagonists in this category include antibodies or peptide-based specific binding agents that bind hepcidin and inhibit its activity, including any of the antibodies described herein; hepcidin variants and derivatives thereof that bind to ferroportin but do not activate ferroportin iron transport; and small organic chemical compounds, optionally of less than about 1000 Daltons in molecular weight that bind hepcidin and inhibits its activity.
Hepcidin expression inhibitors include polynucleotides or oligonucleotides that bind to hepcidin DNA or mRNA and inhibit hepcidin expression, including antisense oligonucleotides, inhibitory RNA, DNA enzyme, ribozyme, an aptamer or pharmaceutically acceptable salts thereof that inhibit the expression of hepcidin.
A. Anti-Hepcidin Antibodies and Specific Binding Agents
Various embodiments of the invention provide antibodies, including monoclonal antibodies, that bind human hepcidin, methods of producing such antibodies, methods of using such antibodies for detecting hepcidin, pharmaceutical formulations including such antibodies, methods of preparing the pharmaceutical formulations, and methods of treating patients with the pharmaceutical formulations, including combination therapy with erythropoiesis stimulators as described below. Nucleic acids encoding such antibodies, vectors and recombinant host cells comprising such nucleic acids, and methods of producing such antibodies are also provided.
The term “antibody” is used in the broadest sense and includes fully assembled antibodies, monoclonal antibodies, polyclonal antibodies, multispecific antibodies (including bispecific antibodies), antibody fragments that can bind an antigen (including, Fab′, F′(ab)₂, Fv, single chain antibodies, diabodies), and recombinant peptides comprising the foregoing as long as they exhibit the desired biological activity. Multimers or aggregates of intact molecules and/or fragments, including chemically derivatized antibodies, are contemplated. Antibodies of any isotype class or subclass, including IgG, IgM, IgD, IgA, and IgE, IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2, or any allotype, are contemplated. Different isotypes have different effector functions; for example, IgG1 and IgG3 isotypes have antibody-dependent cellular cytotoxicity (ADCC) activity.
In some embodiments, the antibodies exhibit desirable characteristics such as binding affinity as measured by K_D(equilibrium dissociation constant) for hepcidin in the range of 1×10⁻⁶M or less, or ranging down to 10⁻¹⁶M or lower, (e.g., about 10⁻⁷, 10⁻⁸, 10⁻⁹, 10⁻¹⁰, 10⁻¹¹, 10⁻¹², 10⁻¹³, 10⁻¹⁴, 10⁻¹⁵, 10⁻¹⁶M or less). The equilibrium dissociation constant can be determined in solution equilibrium assay using BIAcore and/or KinExA, such as described in. Examples 13 and 14.
In other embodiments, the antibodies exhibit specificity for hepcidin. As used herein, an antibody is “specific for” human hepcidin when it has a significantly higher binding affinity for, and consequently is capable of distinguishing, human hepcidin compared to other unrelated proteins in different families. In some embodiments, such antibodies may also cross-react with hepcidin of other species, such as murine, rat, or primate hepcidin; while in other embodiments, the antibodies bind only to human or primate hepcidin and not significantly to rodent hepcidin. In exemplary embodiments, antibodies bind to human and cynomologous monkey hepcidin but not significantly to rodent hepcidin. In some embodiments, antibodies specific for hepcidin cross-react with other proteins in the same family, while in other embodiments, the antibodies distinguish hepcidin from other related family members, including defensins or mouse hepc2.
In yet other embodiments, the monoclonal antibodies inhibit (or neutralize) hepcidin iron-regulating activity, in vitro and preferably also in vivo. Such hepcidin-neutralizing antibodies are therapeutically useful for hepcidin-related disorders or disorders of iron homeostasis. Hepcidin neutralizing activity can be measured through a number of markers, for example, ferritin/iron levels, red blood cell count, red blood cell characteristics (hemoglobin content and/or cell volume), early red blood cell characteristics (reticulocyte numbers, hemoglobin content or cell volume) (Clinical Hematology, third edition, Lippincott, Williams and Wilkins; editor Mary L. Turgeon, 1999) ferroportin internalization, or iron transport. In an exemplary embodiment, the monoclonal antibody decreases intracellular iron concentration at an EC₅₀of about 10⁻⁸M or less and/or increases circulating iron concentration.
In some embodiments, a monoclonal antibody as described herein antagonizes the effect of human hepcidin or inhibits hepcidin iron-regulating activity. In some embodiments, a monoclonal antibody as described herein exerts an effect at an EC₅₀of about 1×10⁻⁸M or less, or about 1×10⁻⁷M or less. For example, an antibody may decrease the intracellular iron level in a cell at an EC₅₀of about 1×10⁻⁸M or less, or may reduce ferritin expression at an EC₅₀of about 1×10⁻⁸M or less, as determined by a ferritin assay. In other embodiments, a monoclonal antibody as described herein may reduce free serum hepcidin levels by at least about 20%, by at least about 30%, by at least about 40%, by at least about 50%, by at least about 60%, by at least about 70%, by at least about 80%, or by at least about 90%. In other embodiments, a monoclonal antibody as described herein may increase red blood cell count (number), red blood cell mean cell volume or red blood cell hemoglobin content, increase hemoglobin, increase hematocrit, increase Tsat, increase circulating (or serum) iron levels, and/or increase or normalize reticulocyte count, reticulocyte mean cell volume, reticulocyte hemoglobin content or reticulocyte numbers.
In specific exemplary embodiments, the invention contemplates:
1) a monoclonal antibody that retains any one, two, three, four, five, or six of CDRH1, CDRH2, CDRH3, CDRL1, CDRL2 or CDRL3 of any of antibody Ab43, 2.7, 2.41, R9, 1C9; 1S1, 1S2, 1S3, 1S4, 1S5, 3B3; 4E1, 7A3, 9D12, 12B9, 15E1, 18D8, 19C1, 19D12, 19H6, 23F11, and 26F11, optionally including one or two mutations in such CDR(s),
2) a monoclonal antibody that retains all of CDRH1, CDRH2, CDRH3, or the heavy chain variable region of any of antibody Ab43, 2.7, 2.41, R9, 1C9; 1S1, 1S2, 1S3, 1S4, 1S5, 3B3; 4E1, 7A3, 9D12, 12B9, 15E1, 18D8, 19C1, 19D12, 19H6, 23F11, and 26F11, optionally including one or two mutations in such CDR(s),
3) a monoclonal antibody that retains all of CDRL1, CDRL2, CDRL3, or the light chain variable region of any of antibody Ab43, 2.7, 2.41, R9, 1C9; 1S1, 1S2, 1S3, 1S4, 1S5, 3B3; 4E1, 7A3, 9D12, 12B9, 15E1, 18D8, 19C1, 19D12, 19H6, 23F11, and 26F11, optionally including one or two mutations in such CDR(s),
4) a monoclonal antibody that binds to the same epitope of mature human hepcidin as antibody Ab43, 2.7, 2.41, R9, 1C9; 1S1, 1S2, 1S3, 1S4, 1S5, 3B3; 4E1, 7A3, 9D12, 12B9, 15E1, 18D8, 19C1, 19D12, 19H6, 23F11, and 26F11, e.g. as determined through X-ray crystallography, or a conformational epitope comprising an amino acid within amino acids 1-5 of SEQ ID NO: 9 and/or an amino acid within a loop formed by amino acids 10-13 of SEQ ID NO: 9 and./or an amino acid within a loop formed by amino acids 14-22 of SEQ ID NO: 9; and
5) a monoclonal antibody that competes with antibody Ab43, 2.7, 2.41, R9, 1C9; 1S1, 1S2, 1S3, 1S4, 1S5, 3B3; 4E1, 7A3, 9D12, 12B9, 15E1, 18D8, 19C1, 19D12, 19H6, 23F11, and 26F11 for binding to mature human hepcidin by more than about 75%, more than about 80%, or more than about 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94% or 95%.
In one embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 16-21. In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 28-33 (2.7 CDRs). In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 40-45 (2.41 CDRs). In yet another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 52-57 (R9 CDRs). In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 111-116 (1C9 CDRs). In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 121-126 (3B3 CDRs). In yet another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 131-136 (4E1 CDRs). In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 141-146 (7A3 CDRs). In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 151-156 (9D12 CDRs). In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 161-166 (12B9 CDRs). In yet another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 171-176 (15E1 CDRs). In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 314-319 (18D8 CDRs). In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 324-329 (19C1 CDRs). In yet another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 294-299 (19D12 CDRs). In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 304-309 (19H6CDRs). In yet another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 181-186 (23F11 CDRs). In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 191-196 (26F11 CDRs). In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 203-205 and 131-133 (1S1 CDRs). In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 214-216 and 144-146 (1S2 CDRs). In yet another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 225-227 and 164-166 (1S3 CDRs). In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 236-238 and 174-176 (1S4 CDRs). In another embodiment, the antibody comprises at least one, two, three, four, five or all of the amino acid sequences selected from the group consisting of SEQ ID NOs: 247-249 and 184-186 (1S5 CDRs).
In some embodiments, the antibody comprises all three light chain CDRs, all three heavy chain CDRs, or all six CDRs. In some exemplary embodiments, two light chain CDRs from an antibody may be combined with a third light chain CDR from a different antibody. Alternatively, a CDRL1 from one antibody can be combined with a CDRL2 from a different antibody and a CDRL3 from yet another antibody, particularly where the CDRs are highly homologous. Similarly, two heavy chain CDRs from an antibody may be combined with a third heavy chain CDR from a different antibody; or a CDRH1 from one antibody can be combined with a CDRH2 from a different antibody and a CDRH3 from yet another antibody, particularly where the CDRs are highly homologous.
Consensus CDRs may also be used. In an exemplary embodiment, the antibody comprises one or more of the amino acid sequences set forth in SEQ ID NO: 74 (XASNLES), SEQ ID NO: 75 (XQSNEE) and SEQ ID NO: 76 (QQXNEX), SEQ ID NO: 28 (RASESVDSYGNSFMH), SEQ ID NO: 77 (WINTXSGVPTYADDFXG), SEQ ID NO: 78 (XXYYGX*A*Y), SEQ ID NO: 19 (TYGMS), SEQ ID NO: 284 (VIXYXXSNKYYADSVKG), SEQ ID NO: 285 (WIXAXNGXXXXAXXXQX), SEQ ID NO: 286 (AQEGXAPDAFDI), SEQ ID NO: 287 (QAWYSSTNVX), SEQ ID NO: 288 (QAWDSSTAXX), SEQ ID NO: 289 (QSDYSSXXX**), wherein X is any amino acid and * can be absent or any amino acid.
In yet another exemplary embodiment, the antibody comprises the light and/or heavy chain variable region of an antibody, e.g., SEQ ID NO: 15 (Ab43 heavy chain variable region), and/or SEQ ID NO: 13 (Ab43 light chain variable region); SEQ ID NO: 27 (2.7 heavy chain variable region), and/or SEQ ID NO: 25 (2.7 light chain variable region); SEQ ID NO: 39 (2.41 heavy chain variable region), and/or SEQ ID NO: 37 (2.41 light chain variable region); or SEQ ID NO: 51 (R9 heavy chain variable region), and/or SEQ ID NO: 49 (R9 light chain variable region), SEQ ID NO: 110 (1C9 heavy chain variable region) and/or SEQ ID NO: 108 (1C9 light chain variable region); or SEQ ID NO: 120 (3B3 heavy chain variable region) and/or SEQ ID NO: 118 (3B3 light chain variable region); SEQ ID NO: 130 (4E1 heavy chain variable region) and/or SEQ ID NO: 128 (4E1 light chain variable region); or SEQ ID NO: 140 (7A3 heavy chain variable region) and/or SEQ ID NO:138 (7A3 light chain variable region); or SEQ ID NO: 150 (9D12 heavy chain variable region) and/or SEQ ID NO: 148 (9D12 light chain variable region); SEQ ID NO: 160 (12B9 heavy chain variable region), and/or SEQ ID NO: 158 (12B9 light chain variable region); SEQ ID NO: 170 (15E1 heavy chain variable region) and/or SEQ ID NO: 168 (15E1 light chain variable region); SEQ ID NO: 313 (18D8 heavy chain variable region) and/or SEQ ID NO: 311 (18D8 light chain variable region); SEQ ID NO: 323 (19C1 heavy chain variable region) and/or SEQ ID NO: 321 (19C1 light chain variable region); SEQ ID NO: 293 (19D12 heavy chain variable region) and/or SEQ ID NO: 291 (19D12 light chain variable region); SEQ ID NO: 303 (19H6 heavy chain variable region) and/or SEQ ID NO: 301 (19H6 light chain variable region); SEQ ID NO: 180 (23F11 heavy chain variable region) and/or SEQ ID NO: 178 (23F11 light chain variable region); SEQ ID NO: 190 (26F11 heavy chain variable region) and/or SEQ ID NO: 188 (26F11 light chain variable region); or SEQ ID NO: 202 (1S1 heavy chain variable region) and/or SEQ ID NO: 128 (1S1 light chain variable region); SEQ ID NO: 213 (1S2 light chain variable region) and/or SEQ ID NO: 140 (1S2 heavy chain variable region); SEQ ID NO: 224 (1S3 light chain variable region) and/or SEQ ID NO: 160 (1S3 heavy chain variable region); SEQ ID NO: 235 (1S4 light chain variable region) and/or SEQ ID NO: 170 (1S4 heavy chain variable region; or SEQ ID NO: 246 (1S5 light chain variable region) and/or SEQ ID NO: 190 (1S5 heavy chain variable region.
In some embodiments, an antibody is provided that comprises a polypeptide having an amino acid sequence at least about 65%, 70%, 75%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to an amino acid sequence selected from the group consisting of SEQ ID NOs: 15 (Ab43 heavy chain variable region), 27 (2.7 heavy chain variable region), 39 (2.41 heavy chain variable region), 51 (R9 heavy chain variable region), 110 (1C9 heavy chain variable region), 120 (3B3 heavy chain variable region), 130 (4E1 heavy chain variable region), 140 (7A3 heavy chain variable region), 150 (9D12 heavy chain variable region), 160 (12B9 heavy chain variable region), 170 (15E1 heavy chain variable region), 313 (18D8 heavy chain variable region), 323 (19C1heavy chain variable region), 293 (19D12 heavy chain variable region), 303 (19H6 heavy chain variable region), 180 (23F11 heavy chain variable region), 190 (26F11 heavy chain variable region), 202 (1S1 heavy chain variable region), 13 (Ab43 light chain variable region), 25 (2.7 light chain variable region), 37 (2.41 light chain variable region), 49 (R9 light chain variable region), 108 (1C9 light chain variable region), 118 (3B3 light chain variable region), 128 (4E1 light chain variable region), 138 (7A3 light chain variable region), 148 (9D12 light chain variable region), 158 (12B9 light chain variable region), 168 (15E1 light chain variable region), 311 (18D8 light chain variable region), 321 (19C1 light chain variable region), 291 (19D12 light chain variable region), 301 (19H6 light chain variable region), 178 (23F11 light chain variable region), 188 (26F11 light chain variable region), 213 (1S2 light chain variable region), 224 (1S3 light chain variable region), 235 (1S4 light chain variable region), and 246 (1S5 light chain variable region) the polypeptide further comprising at least one or more of the amino acid sequences set forth in SEQ ID NOs: 16-21 (Ab43 CDRs), 28-33 (2.7CDRs), 40-45 (2.41 CDRs), 52-57 (R9 CDRs), 111-116 (1C9 CDRs), 121-126 (3B3 CDRs), 131-136 (4E1 CDRs), 141-146 (7A3 CDRs), 151-156 (9D12 CDRs), 161-166 (12B9 CDRs), 171-176 (15E1 CDRs), 314-319 (18D8 CDRs), 324-329 (19C1 CDRs), 294-299 (19D12 CDRs), 304-309 (19H6 CDRs), 181-186 (23F11 CDRs), 191-196 (26F11 CDRs), 203-205 and 131-133 (1S1 heavy chainCDRs), 214-216 and 144-146 (1S2 light chain CDRs), 225-227 and 164-166 (1S3 light chain CDRs), 236-238 and 174-176 (1S4 light chain CDRs) and 247-249 and 184-186 (1S5 light chain CDRs). In any of the foregoing embodiments, the polypeptide includes a sequence comprising one or two modifications to any of the amino acid sequences set forth in SEQ ID NOs: 16-21 (Ab43 CDRs), 28-33 (2.7CDRs), 40-45 (2.41 CDRs), 52-57 (R9 CDRs), 111-116 (1C9 CDRs), 121-126 (3B3 CDRs), 131-136 (4E1 CDRs), 141-146 (7A3 CDRs), 151-156 (9D12 CDRs), 161-166 (12B9 CDRs), 171-176 (15E1 CDRs), 314-319 (18D8 CDRs), 324-329 (19C1 CDRs), 294-299 (19D12 CDRs), 304-309 (19H6 CDRs), 181-186 (23F11 CDRs), 191-196 (26F11 CDRs), 203-205 and 131-133 (1S1 heavy chainCDRs), 214-216 and 144-146 (1S2 light chain CDRs), 225-227 and 164-166 (1S3 light chain CDRs), 236-238 and 174-176 (1S4 light chain CDRs) and 247-249 and 184-186 (1S5 light chain CDRs).
The cDNA and amino acid sequences for the full length light and heavy chains of each of antibodies 1C9, 3B3, 4E1, 7A3, 9D12, 12B9, 15E1, 23F11 and 26F11 are also provided. The cDNA sequences encoding the full length light chain of antibodies 1C9, 3B3, 4E1, 7A3, 9D12, 12B9, 15E1, 23F11, 26F11, 1S2, 1S3, 1S4 and 1S5, including the constant region, are set forth in SEQ ID NOs: 197, 208, 219, 230, 241, 252, 256, 260, 264, 217, 228, 239 and 250, respectively. The amino acid sequences of the full length light chain of antibodies 1C9, 3B3, 4E1, 7A3, 9D12, 12B9, 15E1, 23F11, 26F11, 1S2, 1S3, 1S4 and 1S5, including the constant region, are set forth in SEQ ID NOs: 198 (of which residues 1-20 correspond to the signal peptide and the remainder is the mature polypeptide), 209 (of which residues 1-19 correspond to the signal peptide and the remainder is the mature polypeptide), 220 (of which residues 1-20 correspond to the signal peptide and the remainder is the mature polypeptide), 231 (of which residues 1-20 correspond to the signal peptide and the remainder is the mature polypeptide), 242 (of which residues 1-19 correspond to the signal peptide and the remainder is the mature polypeptide), 253 (of which residues 1-20 correspond to the signal peptide and the remainder is the mature polypeptide), 257 (of which residues 1-20 correspond to the signal peptide and the remainder is the mature polypeptide), 261 (of which residues 1-19 correspond to the signal peptide and the remainder is the mature polypeptide), 265 (of which residues 1-19 correspond to the signal peptide and the remainder is the mature polypeptide), 218 (of which residues 1-22 correspond to the signal peptide and the remainder is the mature polypeptide), 229 (of which residues 1-22 correspond to the signal peptide and the remainder is the mature polypeptide), 240 (of which residues 1-22 correspond to the signal peptide and the remainder is the mature polypeptide) and 251 (of which residues 1-22 correspond to the signal peptide and the remainder is the mature polypeptide), respectively.
The cDNA sequences encoding the full length heavy chain of antibodies 1 C9, 3B3, 4E1, 7A3, 9D12, 12B9, 15E1, 23F11, 26F11 and 1S1, including the constant region, are set forth in SEQ ID NOs: 199, 210, 221, 232, 243, 254, 258, 262, 266 and 206, respectively. The amino acid sequences of the full length heavy chain of antibodies 1C9, 3B3, 4E1, 7A3, 9D12, 12B9, 15E1, 23F11, 26F11 and 1S1, including the constant region, are set forth in SEQ ID NOs: 200 (of which residues 1-19 correspond to the signal peptide and the remainder is the mature polypeptide), 211 (of which residues 1-19 correspond to the signal peptide and the remainder is the mature polypeptide), 222 (of which residues 1-19 correspond to the signal peptide and the remainder is the mature polypeptide), 233 (of which residues 1-19 correspond to the signal peptide and the remainder is the mature polypeptide), 244 (no signal peptide), 255 (of which residues 1-19 correspond to the signal peptide and the remainder is the mature polypeptide), 259 (of which residues 1-19 correspond to the signal peptide and the remainder is the mature polypeptide), 263 (of which residues 1-20 correspond to the signal peptide and the remainder is the mature polypeptide), 267 (of which residues 1-19 correspond to the signal peptide and the remainder is the mature polypeptide) and 207 (of which residues 1-19 correspond to the signal peptide and the remainder is the mature polypeptide), respectively.
In some embodiments of the invention, antibodies comprise amino acids 20-467 of SEQ ID NO: 207 (1S1 heavy chain) and amino acids 21-234 of SEQ ID NO: 220 (1S1 light chain); or amino acids 20-466 of SEQ ID NO: 233 (1S2 heavy chain) and amino acids 23-234 of SEQ ID NO: 218 (1S2 light chain); or amino acids 20-466 of SEQ ID NO: 255 (1S3 heavy chain) and amino acids 23-234 of SEQ ID NO: 229 (1S3 light chain); or amino acids 20-466 of SEQ ID NO: 259 (1S4 heavy chain) and wherein amino acids 23-234 of SEQ ID NO: 240 (1S4 light chain); or amino acids 20-466 of SEQ ID NO: 267 (1S5 heavy chain) and amino acids 23-234 of SEQ ID NO: 251 (1S5 light chain).
The term “monoclonal antibody” as used herein refers to an antibody, as that term is defined herein, obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations or alternative post-translational modifications that may be present in minor amounts, whether produced from hybridomas or recombinant DNA techniques. Nonlimiting examples of monoclonal antibodies include murine, rabbit, rat, chicken, chimeric, humanized, or human antibodies, fully assembled antibodies, multispecific antibodies (including bispecific antibodies), antibody fragments that can bind an antigen (including, Fab′, F′(ab)₂, Fv, single chain antibodies, diabodies), maxibodies, nanobodies, and recombinant peptides comprising the foregoing as long as they exhibit the desired biological activity, or variants or derivatives thereof. Humanizing or modifying antibody sequence to be more human-like is described in, e.g., Jones et al., Nature 321:522 525 (1986); Morrison et al., Proc. Natl. Acad. Sci., U.S.A., 81:6851 6855 (1984); Morrison and 01, Adv. Immunol., 44:65 92 (1988); Verhoeyer et al., Science 239:1534 1536 (1988); Padlan, Molec. Immun. 28:489 498 (1991); Padlan, Molec. Immunol. 31(3):169 217 (1994); and Kettleborough, C. A. et al., Protein Eng. 4(7):773 83 (1991); Co, M. S., et al. (1994), J. Immunol. 152, 2968-2976); Studnicka et al. Protein Engineering 7: 805-814 (1994); each of which is incorporated herein by reference in its entirety. One method for isolating human monoclonal antibodies is the use of phage display technology. Phage display is described in e.g., Dower et al., WO 91/17271, McCafferty et al., WO 92/01047, and Caton and Koprowski, Proc. Natl. Acad. Sci. USA, 87:6450-6454 (1990), each of which is incorporated herein by reference in its entirety. Another method for isolating human monoclonal antibodies uses transgenic animals that have no endogenous immunoglobulin production and are engineered to contain human immunoglobulin loci. See, e.g., Jakobovits et al., Proc. Natl. Acad. Sci. USA, 90:2551 (1993); Jakobovits et al., Nature, 362:255-258 (1993); Bruggermann et al., Year in Immuno., 7:33 (1993); WO 91/10741, WO 96/34096, WO 98/24893, or U.S. patent application publication nos. 20030194404, 20030031667 or 20020199213; each incorporated herein by reference in its entirety.
An “isolated” antibody refers to an antibody, as that term is defined herein, that has been identified and separated from a component of its natural environment. Contaminant components of its natural environment are materials that would interfere with diagnostic or therapeutic uses for the antibody, and may include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes. In certain embodiments, the antibody will be purified (1) to greater than 95% by weight of antibody, and most preferably more than 99% by weight, (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence, or (3) to homogeneity by SDS-PAGE under reducing or nonreducing conditions using Coomassie blue or, preferably, silver stain. Isolated naturally occurring antibody includes the antibody in situ within recombinant cells since at least one component of the antibody's natural environment will not be present. Ordinarily, however, isolated antibody will be prepared by at least one purification step.
An “immunoglobulin” or “native antibody” is a tetrameric glycoprotein. In a naturally-occurring immunoglobulin, each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kDa) and one “heavy” chain (about 50-70 kDa). The amino-terminal portion of each chain includes a “variable” (“V”) region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The carboxy-terminal portion of each chain defines a constant region primarily responsible for effector function. Immunoglobulins can be assigned to different classes depending on the amino acid sequence of the constant domain of their heavy chains. Heavy chains are classified as mu (μ), delta (Δ), gamma (γ), alpha (α), and epsilon (ε), and define the antibody's isotype as IgM, IgD, IgG, IgA, and IgE, respectively. Several of these may be further divided into subclasses or isotypes, e.g. IgG1, IgG2, IgG3, IgG4, IgA1 and IgA2. Different isotypes have different effector functions; for example, IgG1 and IgG3 isotypes have antibody-dependent cellular cytotoxicity (ADCC) activity. Human light chains are classified as kappa (κ) and lambda (λ) light chains. Within light and heavy chains, the variable and constant regions are joined by a “J” region of about 12 or more amino acids, with the heavy chain also including a “D” region of about 10 more amino acids. See generally, Fundamental Immunology, Ch. 7 (Paul, W., ed., 2nd ed. Raven Press, N.Y. (1989)).
Allotypes are variations in antibody sequence, often in the constant region, that can be immunogenic and are encoded by specific alleles in humans. Allotypes have been identified for five of the human IGHC genes, the IGHG1, IGHG2, IGHG3, IGHA2 and IGHE genes, and are designated as G1m, G2m, G3m, A2m, and Em allotypes, respectively. At least 18 Gm allotypes are known: nG1m(1), nG1m(2), G1m (1, 2, 3, 17) or G1m (a, x, f, z), G2m (23) or G2m (n), G3m (5, 6, 10, 11, 13, 14, 15, 16, 21, 24, 26, 27, 28) or G3m (b1, c3, b5, b0, b3, b4, s, t, g1, c5, u, v, g5). There are two A2m allotypes A2m(1) and A2m(2).
For a detailed description of the structure and generation of antibodies, see Roth, D. B., and Craig, N. L., Cell, 94:411-414 (1998), herein incorporated by reference in its entirety. Briefly, the process for generating DNA encoding the heavy and light chain immunoglobulin sequences occurs primarily in developing B-cells. Prior to the rearranging and joining of various immunoglobulin gene segments, the V, D, J and constant (C) gene segments are found generally in relatively close proximity on a single chromosome. During B-cell-differentiation, one of each of the appropriate family members of the V, D, J (or only V and J in the case of light chain genes) gene segments are recombined to form functionally rearranged variable regions of the heavy and light immunoglobulin genes. This gene segment rearrangement process appears to be sequential. First, heavy chain D-to-J joints are made, followed by heavy chain V-to-DJ joints and light chain V-to-J joints. In addition to the rearrangement of V, D and J segments, further diversity is generated in the primary repertoire of immunoglobulin heavy and light chains by way of variable recombination at the locations where the V and J segments in the light chain are joined and where the D and J segments of the heavy chain are joined. Such variation in the light chain typically occurs within the last codon of the V gene segment and the first codon of the J segment. Similar imprecision in joining occurs on the heavy chain chromosome between the D and J_Hsegments and may extend over as many as 10 nucleotides. Furthermore, several nucleotides may be inserted between the D and J_Hand between the V_Hand D gene segments which are not encoded by genomic DNA. The addition of these nucleotides is known as N-region diversity. The net effect of such rearrangements in the variable region gene segments and the variable recombination which may occur during such joining is the production of a primary antibody repertoire.
The term “hypervariable” region refers to amino acid residues from a complementarity determining region or CDR (i.e., residues 24-34 (L1), 50-56 (L2) and 89-97 (L3) in the light chain variable domain and 31-35 (H1), 50-65 (H2) and 95-102 (H3) in the heavy chain variable domain as described by Kabat et al., Sequences of Proteins of Immunological Interest, 5^thEd. Public Health Service, National Institutes of Health, Bethesda, Md. (1991)). Even a single CDR may recognize and bind antigen, although with a lower affinity than the entire antigen binding site containing all of the CDRs.
An alternative definition of residues from a hypervariable “loop” is described by Chothia et al., J. Mol. Biol. 196: 901-917 (1987) as residues 26-32 (L1), 50-52 (L2) and 91-96 (L3) in the light chain variable domain and 26-32 (H1), 53-55 (H2) and 96-101 (H3) in the heavy chain variable domain.
“Framework” or FR residues are those variable region residues other than the hypervariable region residues.
“Antibody fragments” comprise a portion of an intact immunoglobulin, preferably an antigen binding or variable region of the intact antibody, and include multispecific (bispecific, trispecific, etc.) antibodies formed from antibody fragments. Fragments of immunoglobulins may be produced by recombinant DNA techniques or by enzymatic or chemical cleavage of intact antibodies.
Nonlimiting examples of antibody fragments include Fab, Fab′, F(ab′)₂, Fv (variable region), domain antibodies (dAb, containing a VH domain) (Ward et al., Nature 341:544-546, 1989), complementarity determining region (CDR) fragments, single-chain antibodies (scFv, containing VH and VL domains on a single polypeptide chain) (Bird et al., Science 242:423-426, 1988, and Huston et al., Proc. Natl. Acad. Sci. USA 85:5879-5883, 1988, optionally including a polypeptide linker; and optionally multispecific, Gruber et al., J. Immunol. 152: 5368 (1994)), single chain antibody fragments, diabodies (VH and VL domains on a single polypeptide chain that pair with complementary VL and VH domains of another chain) (EP 404,097; WO 93/11161; and Hollinger et al., Proc. Natl. Acad. Sci. USA, 90:6444-6448 (1993)), triabodies, tetrabodies, minibodies (scFv fused to CH3 via a peptide linker (hingeless) or via an IgG hinge) (Olafsen, et al., Protein Eng Des Sel. 2004 April; 17(4):315-23), linear antibodies (tandem Fd segments (VH-CH1-VH-CH1) (Zapata et al., Protein Eng., 8(10):1057-1062 (1995)); chelating recombinant antibodies (crAb, which can bind to two adjacent epitopes on the sane antigen) (Neri et al., J Mol. Biol. 246:367-73, 1995), bibodies (bispecific Fab-scFv) or tribodies (trispecific Fab-(scFv)(2)) (Schoonjans et al., J. Immunol. 165:7050-57, 2000; Willems et al., J Chromatogr B Analyt Technol Biomed Life Sci. 786:161-76, 2003), intrabodies (Biocca, et al., EMBO J. 9:101-108, 1990; Colby et al., Proc Natl Acad Sci USA. 101:17616-21, 2004) which may also comprise cell signal sequences which retain or direct the antibody intracellularly (Mhashilkar et al, EMBO J. 14:1542-51, 1995; Wheeler et al., FASEB J. 17:1733-5, 2003), transbodies (cell-permeable antibodies containing a protein transduction domain (PTD) fused to scFv (Heng et al., Med Hypotheses. 64:1105-8, 2005), nanobodies (approximately 15 kDa variable domain of the heavy chain) (Cortez-Retamozo et al., Cancer Research 64:2853-57, 2004), small modular immunopharmaceuticals (SMIPs) (WO03/041600, U.S. Patent publication 20030133939 and US Patent Publication 20030118592), an antigen-binding-domain immunoglobulin fusion protein, a camelized antibody (in which VH recombines with a constant region that contains hinge, CH1, CH2 and CH3 domains) (Desmyter et al., J. Biol. Chem. 276:26285-90, 2001; Ewert et al., Biochemistry 41:3628-36, 2002; U.S. Patent Publication Nos. 20050136049 and 20050037421), a VHH containing antibody, heavy chain antibodies (HCAbs, homodimers of two heavy chains having the structure H2L2), or variants or derivatives thereof, and polypeptides that contain at least a portion of an immunoglobulin that is sufficient to confer specific antigen binding to the polypeptide, such as a CDR sequence, as long as the antibody retains the desired biological activity.
The term “variant” when used in connection with antibodies refers to a polypeptide sequence of an antibody that contains at least one amino acid substitution, deletion, or insertion in the variable region or the portion equivalent to the variable region, provided that the variant retains the desired binding affinity or biological activity. In addition, the antibodies as described herein may have amino acid modifications in the constant region to modify effector function of the antibody, including half-life or clearance, ADCC and/or CDC activity. Such modifications can enhance pharmacokinetics or enhance the effectiveness of the antibody in treating cancer, for example. See Shields et al., J. Biol. Chem., 276(9):6591-6604 (2001), incorporated by reference herein in its entirety. In the case of IgG1, modifications to the constant region, particularly the hinge or CH2 region, may increase or decrease effector function, including ADCC and/or CDC activity. In other embodiments, an IgG2 constant region is modified to decrease antibody-antigen aggregate formation. In the case of IgG4, modifications to the constant region, particularly the hinge region, may reduce the formation of half-antibodies.
The term “modification” when used in connection with antibodies or polypeptides described herein, includes but is not limited to, one or more amino acid change (including substitutions, insertions or deletions); chemical modifications that do not interfere with hepcidin-binding activity; covalent modification by conjugation to therapeutic or diagnostic agents; labeling (e.g., with radionuclides or various enzymes); covalent polymer attachment such as pegylation (derivatization with polyethylene glycol) and insertion or substitution by chemical synthesis of non-natural amino acids. In some embodiments, modified polypeptides (including antibodies) of the invention will retain the binding properties of unmodified molecules of the invention.
The term “derivative” when used in connection with antibodies or polypeptides of the invention refers to antibodies or polypeptides that are covalently modified by conjugation to therapeutic or diagnostic agents, labeling (e.g., with radionuclides or various enzymes), covalent polymer attachment such as pegylation (derivatization with polyethylene glycol) and insertion or substitution by chemical synthesis of non-natural amino acids. In some embodiments, derivatives of the invention will retain the binding properties of underivatized molecules of the invention.
Methods for making bispecific or other multispecific antibodies are known in the art and include chemical cross-linking, use of leucine zippers [Kostelny et al., J. Immunol. 148:1547-1553, 1992]; diabody technology [Hollinger et al., Proc. Natl. Acad. Sci. USA 90:6444-48, 1993]; scFv dimers [Gruber et al., J. Immunol. 152: 5368, 1994], linear antibodies [Zapata et al., Protein Eng. 8:1057-62, 1995]; and chelating recombinant antibodies [Neri et al., J Mol. Biol. 246:367-73, 1995].
Thus, a variety of compositions comprising one, two, and/or three CDRs of a heavy chain variable region or a light chain variable region of an antibody may be generated by techniques known in the art.
Recombinant Production of Antibodies
Isolated nucleic acids encoding monoclonal antibodies described herein are also provided, optionally operably linked to control sequences recognized by a host cell, vectors and host cells comprising the nucleic acids, and recombinant techniques for the production of the antibodies, which may comprise culturing the host cell so that the nucleic acid is expressed and, optionally, recovering the antibody from the host cell culture or culture medium.
Relevant amino acid sequence from an immunoglobulin of interest may be determined by direct protein sequencing, and suitable encoding nucleotide sequences can be designed according to a universal codon table. Alternatively, genomic or cDNA encoding the monoclonal antibodies may be isolated and sequenced from cells producing such antibodies using conventional procedures (e.g., by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the monoclonal antibodies).
Cloning is carried out using standard techniques (see, e.g., Sambrook et al. (1989) Molecular Cloning: A Laboratory Guide, Vols 1-3, Cold Spring Harbor Press, which is incorporated herein by reference). For example, a cDNA library may be constructed by reverse transcription of polyA+ mRNA, preferably membrane-associated mRNA, and the library screened using probes specific for human immunoglobulin polypeptide gene sequences. In one embodiment, however, the polymerase chain reaction (PCR) is used to amplify cDNAs (or portions of full-length cDNAs) encoding an immunoglobulin gene segment of interest (e.g., a light or heavy chain variable segment). The amplified sequences can be readily cloned into any suitable vector, e.g., expression vectors, minigene vectors, or phage display vectors. It will be appreciated that the particular method of cloning used is not critical, so long as it is possible to determine the sequence of some portion of the immunoglobulin polypeptide of interest.
One source for antibody nucleic acids is a hybridoma produced by obtaining a B cell from an animal immunized with the antigen of interest and fusing it to an immortal cell. Alternatively, nucleic acid can be isolated from B cells (or whole spleen) of the immunized animal. Yet another source of nucleic acids encoding antibodies is a library of such nucleic acids generated, for example, through phage display technology. Polynucleotides encoding peptides of interest, e.g., variable region peptides with desired binding characteristics, can be identified by standard techniques such as panning
The sequence encoding an entire variable region of the immunoglobulin polypeptide may be determined; however, it will sometimes be adequate to sequence only a portion of a variable region, for example, the CDR-encoding portion. Sequencing is carried out using standard techniques (see, e.g., Sambrook et al. (1989) Molecular Cloning: A Laboratory Guide, Vols 1-3, Cold Spring Harbor Press, and Sanger, F. et al. (1977) Proc. Natl. Acad. Sci. USA 74: 5463-5467, which is incorporated herein by reference). By comparing the sequence of the cloned nucleic acid with published sequences of human immunoglobulin genes and cDNAs, one of skill will readily be able to determine, depending on the region sequenced, (i) the germline segment usage of the hybridoma immunoglobulin polypeptide (including the isotype of the heavy chain) and (ii) the sequence of the heavy and light chain variable regions, including sequences resulting from N-region addition and the process of somatic mutation. One source of immunoglobulin gene sequence information is the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Md.
As used herein, an “isolated” nucleic acid molecule or “isolated” nucleic acid sequence is a nucleic acid molecule that is either (1) identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the natural source of the nucleic acid or (2) cloned, amplified, tagged, or otherwise distinguished from background nucleic acids such that the sequence of the nucleic acid of interest can be determined. An isolated nucleic acid molecule is other than in the form or setting in which it is found in nature. However, an isolated nucleic acid molecule includes a nucleic acid molecule contained in cells that ordinarily express the antibody where, for example, the nucleic acid molecule is in a chromosomal location different from that of natural cells.
Once isolated, the DNA may be operably linked to expression control sequences or placed into expression vectors, which are then transfected into host cells that do not otherwise produce immunoglobulin protein, to direct the synthesis of monoclonal antibodies in the recombinant host cells. Recombinant production of antibodies is well known in the art.
Expression control sequences refer to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotes, for example, include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
Nucleic acid is operably linked when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, operably linked means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading phase. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
Many vectors are known in the art. Vector components may include one or more of the following: a signal sequence (that may, for example, direct secretion of the antibody), an origin of replication, one or more selective marker genes (that may, for example, confer antibiotic or other drug resistance, complement auxotrophic deficiencies, or supply critical nutrients not available in the media), an enhancer element, a promoter, and a transcription termination sequence, all of which are well known in the art.
Cell, cell line, and cell culture are often used interchangeably and all such designations herein include progeny. Transformants and transformed cells include the primary subject cell and cultures derived therefrom without regard for the number of transfers. It is also understood that all progeny may not be precisely identical in DNA content, due to deliberate or inadvertent mutations. Mutant progeny that have the same function or biological activity as screened for in the originally transformed cell are included.
Exemplary host cells include prokaryote, yeast, or higher eukaryote cells (i.e., a multicellular organism). Prokaryotic host cells include eubacteria, such as Gram-negative or Gram-positive organisms, for example, Enterobacteriaceae such as Escherichia, e.g., E. coli, Enterobacter, Erwinia, Klebsiella, Proteus, Salmonella, e.g., Salmonella typhimurium, Serratia, e.g., Serratia marcescans, and Shigella, as well as Bacilli such as B. subtilis and B. lichenifonnis, Pseudomonas, and Streptomyces. Eukaryotic microbes such as filamentous fungi or yeast are suitable cloning or expression hosts for recombinant polypeptides or antibodies. Saccharomyces cerevisiae, or common baker's yeast, is the most commonly used among lower eukaryotic host microorganisms. However, a number of other genera, species, and strains are commonly available and useful herein, such as Pichia, e.g. P. pastoris, Schizosaccharomyces pombe; Kluyveromyces, Yarrowia; Candida; Trichoderma reesia; Neurospora crassa; Schwanniomyces such as Schwanniomyces occidentalis; and filamentous fungi such as, e.g., Neurospora, Penicillium, Tolypocladium, and Aspergillus hosts such as A. nidulans and A. niger.
Host cells for the expression of glycosylated polypeptide or antibody can be derived from multicellular organisms. Examples of invertebrate cells include plant and insect cells. Numerous baculoviral strains and variants and corresponding permissive insect host cells from hosts such as Spodoptera frugiperda (caterpillar), Aedes aegypti (mosquito), Aedes albopictus (mosquito), Drosophila melanogaster (fruitfly), and Bombyx mori have been identified. A variety of viral strains for transfection of such cells are publicly available, e.g., the L-1 variant of Autographa californica NPV and the Bm-5 strain of Bombyx mori NPV.
Vertebrate host cells are also suitable hosts, and recombinant production of polypeptide or antibody from such cells has become routine procedure. Examples of useful mammalian host cell lines are Chinese hamster ovary cells, including CHOK1 cells (ATCC CCL61), DXB-11, DG-44, and Chinese hamster ovary cells/−DHFR(CHO, Urlaub et al., Proc. Natl. Acad. Sci. USA 77: 4216 (1980)); monkey kidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); human embryonic kidney line (293 or 293 cells subcloned for growth in suspension culture, [Graham et al., J. Gen Virol. 36: 59 (1977)]; baby hamster kidney cells (BHK, ATCC CCL 10); mouse sertoli cells (TM4, Mather, Biol. Reprod. 23: 243-251 (1980)); monkey kidney cells (CV1 ATCC CCL 70); African green monkey kidney cells (VERO-76, ATCC CRL-1587); human cervical carcinoma cells (HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL 75); human hepatoma cells (Hep G2, HB 8065); mouse mammary tumor (MMT 060562, ATCC CCL51); TRI cells (Mather et al., Annals N.Y. Acad. Sci. 383: 44-68 (1982)); MRC 5 cells or FS4 cells; or mammalian myeloma cells.
Host cells are transformed or transfected with the above-described nucleic acids or vectors for antibody production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences. In addition, novel vectors and transfected cell lines with multiple copies of transcription units separated by a selective marker are particularly useful for the expression of antibodies.
The host cells used to produce an antibody described herein may be cultured in a variety of media. Commercially available media such as Ham's F10 (Sigma), Minimal Essential Medium ((MEM), (Sigma), RPMI-1640 (Sigma), and Dulbecco's Modified Eagle's Medium ((DMEM), Sigma) are suitable for culturing the host cells. In addition, any of the media described in Ham et al., Meth. Enz. 58: 44 (1979), Barnes et al., Anal. Biochem. 102: 255 (1980), U.S. Pat. No. 4,767,704; 4,657,866; 4,927,762; 4,560,655; or 5,122,469; WO90103430; WO 87/00195; or U.S. Pat. Re. No. 30,985 may be used as culture media for the host cells. Any of these media may be supplemented as necessary with hormones and/or other growth factors (such as insulin, transferrin, or epidermal growth factor), salts (such as sodium chloride, calcium, magnesium, and phosphate), buffers (such as HEPES), nucleotides (such as adenosine and thymidine), antibiotics (such as Gentamycin™ drug), trace elements (defined as inorganic compounds usually present at final concentrations in the micromolar range), and glucose or an equivalent energy source. Any other necessary supplements may also be included at appropriate concentrations that would be known to those skilled in the art. The culture conditions, such as temperature, pH, and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan.
Upon culturing the host cells, the antibody can be produced intracellularly, in the periplasmic space, or directly secreted into the medium. If the antibody is produced intracellularly, as a first step, the particulate debris, either host cells or lysed fragments, is removed, for example, by centrifugation or ultrafiltration.
The antibody can be purified using, for example, hydroxylapatite chromatography, cation or anion exchange chromatography, or preferably affinity chromatography, using the antigen of interest or protein A or protein G as an affinity ligand. Protein A can be used to purify antibodies that are based on human γ1, γ2, or γ4 heavy chains (Lindmark et al., J. Immunol. Meth. 62: 1-13 (1983)). Protein G is recommended for all mouse isotypes and for human γ3 (Guss et al., EMBO J. 5: 15671575 (1986)). The matrix to which the affinity ligand is attached is most often agarose, but other matrices are available. Mechanically stable matrices such as controlled pore glass or poly(styrenedivinyl)benzene allow for faster flow rates and shorter processing times than can be achieved with agarose. Where the antibody comprises a C_H3 domain, the Bakerbond ABX™resin (J. T. Baker, Phillipsburg, N.J.) is useful for purification. Other techniques for protein purification such as ethanol precipitation, Reverse Phase HPLC, chromatofocusing, SDS-PAGE, and ammonium sulfate precipitation are also possible depending on the antibody to be recovered.
Chimeric and Humanized Antibodies
Because chimeric or humanized antibodies are less immunogenic in humans than the parental rodent monoclonal antibodies, they can be used for the treatment of humans with far less risk of anaphylaxis. Thus, these antibodies are contemplated in therapeutic applications that involve in vivo administration to a human.
For example, a murine antibody on repeated in vivo administration in man either alone or as a conjugate will bring about an immune response in the recipient, sometimes called a HAMA response (Human Anti Mouse Antibody). The HAMA response may limit the effectiveness of the pharmaceutical if repeated dosing is required. The immunogenicity of the antibody may be reduced by chemical modification of the antibody with a hydrophilic polymer such as polyethylene glycol or by using the methods of genetic engineering to make the antibody binding structure more human like.
The phrase “chimeric antibody,” as used herein, refers to an antibody containing sequence derived from two different antibodies which typically originate from different species. Most typically, chimeric antibodies comprise variable Ig domains of a rodent monoclonal antibody fused to human constant Ig domains. Such antibodies can be generated using standard procedures known in the art (See Morrison, S. L., et al. (1984) Chimeric Human Antibody Molecules; Mouse Antigen Binding Domains with Human Constant Region Domains, Proc. Natl. Acad. Sci. USA 81, 6841-6855; and, Boulianne, G. L., et al, Nature 312, 643-646. (1984)). Although some chimeric monoclonal antibodies have proved less immunogenic in humans, the rodent variable Ig domains can still lead to a significant human anti-rodent response.
The phrase “humanized antibody” refers to an antibody derived from a non-human antibody, typically a rodent monoclonal antibody. Alternatively, a humanized antibody may be derived from a chimeric antibody.
Humanized antibodies may be achieved by a variety of methods including, for example: (1) grafting the non-human complementarity determining regions (CDRs) onto a human framework and constant region (a process referred to in the art as humanizing through “CDR grafting”), or, alternatively, (2) transplanting the entire non-human variable domains, but “cloaking” them with a human-like surface by replacement of surface residues (a process referred to in the art as “veneering”). These methods are disclosed in, e.g., Jones et al., Nature 321:522 525 (1986); Morrison et al., Proc. Natl. Acad. Sci., U.S.A., 81:6851 6855 (1984); Morrison and 01, Adv. Immunol., 44:65 92 (1988); Verhoeyer et al., Science 239:1534 1536 (1988); Padlan, Molec. Immun. 28:489 498 (1991); Padlan, Molec. Immunol. 31(3):169 217 (1994); and Kettleborough, C. A. et al., Protein Eng. 4(7):773 83 (1991) each of which is incorporated herein by reference in its entirety.
CDR grafting involves introducing one or more of the six CDRs from the mouse heavy and light chain variable Ig domains into the appropriate framework regions of a human variable Ig domain. This technique (Riechmann, L., et al., Nature 332, 323 (1988)), utilizes the conserved framework regions (FR1-FR4) as a scaffold to support the CDR loops which are the primary contacts with antigen. A significant disadvantage of CDR grafting, however, is that it can result in a humanized antibody that has a substantially lower binding affinity than the original mouse antibody, because amino acids of the framework regions can contribute to antigen binding, and because amino acids of the CDR loops can influence the association of the two variable Ig domains. To maintain the affinity of the humanized monoclonal antibody, the CDR grafting technique can be improved by choosing human framework regions that most closely resemble the framework regions of the original mouse antibody, and by site-directed mutagenesis of single amino acids within the framework or CDRs aided by computer modeling of the antigen binding site (e.g., Co, M. S., et al. (1994), J. Immunol. 152, 2968-2976).
One method of humanizing antibodies comprises aligning the non-human heavy and light chain sequences to human heavy and light chain sequences, selecting and replacing the non-human framework with a human framework based on such alignment, molecular modeling to predict the conformation of the humanized sequence and comparing to the conformation of the parent antibody. This process is followed by repeated back mutation of residues in the CDR region which disturb the structure of the CDRs until the predicted conformation of the humanized sequence model closely approximates the conformation of the non-human CDRs of the parent non-human antibody. Such humanized antibodies may be further derivatized to facilitate uptake and clearance, e.g., via Ashwell receptors (See, e.g., U.S. Pat. Nos. 5,530,101 and 5,585,089).
A number of humanizations of mouse monoclonal antibodies by rational design have been reported (See, for example, 20020091240 published Jul. 11, 2002, WO 92/11018 and U.S. Pat. No. 5,693,762, U.S. Pat. No. 5,766,866.
Human Engineered™ Antibodies
The phrase “Human Engineered™ antibody” refers to an antibody derived from a non-human antibody, typically a rodent monoclonal antibody or possibly a chimeric antibody. Human Engineering™ of antibody variable domains has been described by Studnicka [See, e.g., Studnicka et al. U.S. Pat. No. 5,766,886; Studnicka et al. Protein Engineering 7: 805-814 (1994)] as a method for reducing immunogenicity while maintaining binding activity of antibody molecules. According to the method, each variable region amino acid has been assigned a risk of substitution. Amino acid substitutions are distinguished by one of three risk categories: (1) low risk changes are those that have the greatest potential for reducing immunogenicity with the least chance of disrupting antigen binding; (2) moderate risk changes are those that would further reduce immunogenicity, but have a greater chance of affecting antigen binding or protein folding; (3) high risk residues are those that are important for binding or for maintaining antibody structure and carry the highest risk that antigen binding or protein folding will be affected. Due to the three-dimensional structural role of prolines, modifications at prolines are generally considered to be at least moderate risk changes, even if the position is typically a low risk position.
Variable regions of the light and heavy chains of a rodent antibody can be Human Engineered™ by substituting human amino acids at positions determined to be unlikely to adversely effect either antigen binding or protein folding, but likely to reduce immunogenicity in a human environment. Although any human variable region can be used, including an individual VH or VL sequence or a human consensus VH or VL sequence or an individual or consensus human germline sequence, generally a human sequence with highest identity or homology to the rodent sequence is used to minimize the number of substitutions. The amino acid residues at any number of the low risk positions, or at all of the low risk positions, can be changed. For example, at each low risk position where the aligned murine and human amino acid residues differ, an amino acid modification is introduced that replaces the rodent residue with the human residue. In addition, the amino acid residues at any number or all of the moderate risk positions can be changed. In exemplary embodiments, all of the low and moderate risk positions are changed from rodent to human sequence.
Synthetic genes containing modified heavy and/or light chain variable regions are constructed and linked to human γ heavy chain and/or kappa light chain constant regions. Any human heavy chain and light chain constant regions of any class or subclass may be used in combination with the Human Engineered™ antibody variable regions.
Antibodies from Transgenic Animals Engineered to Contain Human Immunoglobulin Loci
Antibodies to hepcidin can also be produced using transgenic animals that have no endogenous immunoglobulin production and are engineered to contain human immunoglobulin loci. For example, WO 98/24893 discloses transgenic animals having a human Ig locus wherein the animals do not produce functional endogenous immunoglobulins due to the inactivation of endogenous heavy and light chain loci. WO 91/741 also discloses transgenic non-primate mammalian hosts capable of mounting an immune response to an immunogen, wherein the antibodies have primate constant and/or variable regions, and wherein the endogenous immunoglobulin encoding loci are substituted or inactivated. WO 96/30498 discloses the use of the Cre/Lox system to modify the immunoglobulin locus in a mammal, such as to replace all or a portion of the constant or variable region to form a modified antibody molecule. WO 94/02602 discloses non-human mammalian hosts having inactivated endogenous Ig loci and functional human Ig loci. U.S. Pat. No. 5,939,598 discloses methods of making transgenic mice in which the mice lack endogenous heavy chains, and express an exogenous immunoglobulin locus comprising one or more xenogeneic constant regions.
Using a transgenic animal described above, an immune response can be produced to a selected antigenic molecule, and antibody producing cells can be removed from the animal and used to produce hybridomas that secrete human-derived monoclonal antibodies. Immunization protocols, adjuvants, and the like are known in the art, and are used in immunization of, for example, a transgenic mouse as described in WO 96/33735. The monoclonal antibodies can be tested for the ability to inhibit or neutralize the biological activity or physiological effect of the corresponding protein.
See also Jakobovits et al., Proc. Natl. Acad. Sci. USA, 90:2551 (1993); Jakobovits et al., Nature, 362:255-258 (1993); Bruggermann et al., Year in Immuno., 7:33 (1993); and U.S. Pat. No. 5,591,669, U.S. Pat. No. 5,589,369, U.S. Pat. No. 5,545,807; and U.S Patent Application No. 20020199213. U.S. Patent Application No. and 20030092125 describes methods for biasing the immune response of an animal to the desired epitope. Human antibodies may also be generated by in vitro activated B cells (see U.S. Pat. Nos. 5,567,610 and 5,229,275).
Antibody Production by Phage Display Techniques
The development of technologies for making repertoires of recombinant human antibody genes, and the display of the encoded antibody fragments on the surface of filamentous bacteriophage, has provided another means for generating human-derived antibodies. Phage display is described in e.g., Dower et al., WO 91/17271, McCafferty et al., WO 92/01047, and Caton and Koprowski, Proc. Natl. Acad. Sci. USA, 87:6450-6454 (1990), each of which is incorporated herein by reference in its entirety. The antibodies produced by phage technology are usually produced as antigen binding fragments, e.g. Fv or Fab fragments, in bacteria and thus lack effector functions. Effector functions can be introduced by one of two strategies: The fragments can be engineered either into complete antibodies for expression in mammalian cells, or into bispecific antibody fragments with a second binding site capable of triggering an effector function.
Typically, the Fd fragment (V_H-C_H1) and light chain (V_L-C_L) of antibodies are separately cloned by PCR and recombined randomly in combinatorial phage display libraries, which can then be selected for binding to a particular antigen. The antibody fragments are expressed on the phage surface, and selection of Fv or Fab (and therefore the phage containing the DNA encoding the antibody fragment) by antigen binding is accomplished through several rounds of antigen binding and re-amplification, a procedure termed panning Antibody fragments specific for the antigen are enriched and finally isolated.
Phage display techniques can also be used in an approach for the humanization of rodent monoclonal antibodies, called “guided selection” (see Jespers, L. S., et al., Bio/Technology 12, 899-903 (1994)). For this, the Fd fragment of the mouse monoclonal antibody can be displayed in combination with a human light chain library, and the resulting hybrid Fab library may then be selected with antigen. The mouse Fd fragment thereby provides a template to guide the selection. Subsequently, the selected human light chains are combined with a human Fd fragment library. Selection of the resulting library yields entirely human Fab.
A variety of procedures have been described for deriving human antibodies from phage-display libraries (See, for example, Hoogenboom et al., J. Mol. Biol., 227:381 (1991); Marks et al., J. Mol. Biol, 222:581-597 (1991); U.S. Pat. Nos. 5,565,332 and 5,573,905; Clackson, T., and Wells, J. A., TIBTECH 12, 173-184 (1994)). In particular, in vitro selection and evolution of antibodies derived from phage display libraries has become a powerful tool (See Burton, D. R., and Barbas III, C. F., Adv. Immunol. 57, 191-280 (1994); and, Winter, G., et al., Annu Rev. Immunol. 12, 433-455 (1994); U.S. patent application no. 20020004215 and WO92/01047; U.S. patent application no. 20030190317 published Oct. 9, 2003 and U.S. Pat. No. 6,054,287; U.S. Pat. No. 5,877,293.
Watkins, “Screening of Phage-Expressed Antibody Libraries by Capture Lift,” Methods in Molecular Biology, Antibody Phage Display: Methods and Protocols 178: 187-193, and U.S. Patent Application Publication No. 20030044772 published Mar. 6, 2003 describes methods for screening phage-expressed antibody libraries or other binding molecules by capture lift, a method involving immobilization of the candidate binding molecules on a solid support.
Antibody Fragments
As noted above, antibody fragments comprise a portion of an intact full length antibody, preferably an antigen binding or variable region of the intact antibody, and include linear antibodies and multispecific antibodies formed from antibody fragments. Nonlimiting examples of antibody fragments include Fab, Fab′, F(ab′)2, Fv, Fd, domain antibody (dAb), complementarity determining region (CDR) fragments, single-chain antibodies (scFv), single chain antibody fragments, diabodies, triabodies, tetrabodies, minibodies, linear antibodies, chelating recombinant antibodies, tribodies or bibodies, intrabodies, nanobodies, small modular immunopharmaceuticals (SMIPs), an antigen-binding-domain immunoglobulin fusion protein, a camelized antibody, a VHH containing antibody, or muteins or derivatives thereof, and polypeptides that contain at least a portion of an immunoglobulin that is sufficient to confer specific antigen binding to the polypeptide, such as a CDR sequence, as long as the antibody retains the desired biological activity. Such antigen fragments may be produced by the modification of whole antibodies or synthesized de novo using recombinant DNA technologies or peptide synthesis.
The term “diabodies” refers to small antibody fragments with two antigen-binding sites, which fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) in the same polypeptide chain (VH VL). By using a linker that is too short to allow pairing between the two domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create two antigen-binding sites. Diabodies are described more fully in, for example, EP 404,097; WO 93/11161; and Hollinger et al., Proc. Natl. Acad. Sci. USA, 90:6444-6448 (1993).
“Single-chain Fv” or “scFv” antibody fragments comprise the V_Hand V_Ldomains of antibody, wherein these domains are present in a single polypeptide chain, and optionally comprising a polypeptide linker between the V_Hand V_Ldomains that enables the Fv to form the desired structure for antigen binding (Bird et al., Science 242:423-426, 1988, and Huston et al., Proc. Natl. Acad. Sci. USA 85:5879-5883, 1988). An Fd fragment consists of the V_Hand C_H1 domains.
Additional antibody fragments include a domain antibody (dAb) fragment (Ward et al., Nature 341:544-546, 1989) which consists of a V_Hdomain.
“Linear antibodies” comprise a pair of tandem Fd segments (V_H-C_H1-V_H-C_H1) which form a pair of antigen binding regions. Linear antibodies can be bispecific or monospecific (Zapata et al. Protein Eng. 8:1057-62 (1995)).
A “minibody” consisting of scFv fused to CH3 via a peptide linker (hingeless) or via an IgG hinge has been described in Olafsen, et al., Protein Eng Des Sel. 2004 April; 17(4):315-23.
The term “maxibody” refers to bivalent scFvs covalently attached to the Fc region of an immunoglobulin, see, for example, Fredericks et al, Protein Engineering, Design & Selection, 17:95-106 (2004) and Powers et al., Journal of Immunological Methods, 251:123-135 (2001).
Functional heavy-chain antibodies devoid of light chains are naturally occurring in certain species of animals, such as nurse sharks, wobbegong sharks and Camelidae, such as camels, dromedaries, alpacas and llamas. The antigen-binding site is reduced to a single domain, the VH_Hdomain, in these animals. These antibodies form antigen-binding regions using only heavy chain variable region, i.e., these functional antibodies are homodimers of heavy chains only having the structure H₂L₂(referred to as “heavy-chain antibodies” or “HCAbs”). Camelized V_HHreportedly recombines with IgG2 and IgG3 constant regions that contain hinge, CH2, and CH3 domains and lack a CH1 domain. Classical V_H-only fragments are difficult to produce in soluble form, but improvements in solubility and specific binding can be obtained when framework residues are altered to be more VH_H-like. (See, e.g., Reichman, et al., J Immunol Methods 1999, 231:25-38.) Camelized V_HHdomains have been found to bind to antigen with high affinity (Desmyter et al., J. Biol. Chem. 276:26285-90, 2001) and possess high stability in solution (Ewert et al., Biochemistry 41:3628-36, 2002). Methods for generating antibodies having camelized heavy chains are described in, for example, in U.S. Patent Publication Nos. 20050136049 and 20050037421. Alternative scaffolds can be made from human variable-like domains that more closely match the shark V-NAR scaffold and may provide a framework for a long penetrating loop structure.
Because the variable domain of the heavy-chain antibodies is the smallest fully functional antigen-binding fragment with a molecular mass of only 15 kDa, this entity is referred to as a nanobody (Cortez-Retamozo et al., Cancer Research 64:2853-57, 2004). A nanobody library may be generated from an immunized dromedary as described in Conrath et al., (Antimicrob Agents Chemother 45: 2807-12, 2001).
Intrabodies are single chain antibodies which demonstrate intracellular expression and can manipulate intracellular protein function (Biocca, et al., EMBO J. 9:101-108, 1990; Colby et al., Proc Natl Acad Sci USA. 101:17616-21, 2004). Intrabodies, which comprise cell signal sequences which retain the antibody contruct in intracellular regions, may be produced as described in Mhashilkar et al (EMBO J 14:1542-51, 1995) and Wheeler et al. (FASEB J. 17:1733-5. 2003). Transbodies are cell-permeable antibodies in which a protein transduction domains (PTD) is fused with single chain variable fragment (scFv) antibodies Heng et al., (Med Hypotheses. 64:1105-8, 2005).
Further contemplated are antibodies that are SMIPs or binding domain immunoglobulin fusion proteins specific for target protein. These constructs are single-chain polypeptides comprising antigen binding domains fused to immunoglobulin domains necessary to carry out antibody effector functions. See e.g., WO03/041600, U.S. Patent publication 20030133939 and US Patent Publication 20030118592.
Multivalent Antibodies
In some embodiments, it may be desirable to generate multivalent or even a multispecific (e.g. bispecific, trispecific, etc.) monoclonal antibody. Such antibody may have binding specificities for at least two different epitopes of the target antigen, or alternatively it may bind to two different molecules, e.g. to the target antigen and to a cell surface protein or receptor. For example, a bispecific antibody may include an arm that binds to the target and another arm that binds to a triggering molecule on a leukocyte such as a T-cell receptor molecule (e.g., CD2 or CD3), or Fc receptors for IgG (FcγR), such as FcγRI (CD64), FcγRII (CD32) and FcγRIII (CD16) so as to focus cellular defense mechanisms to the target-expressing cell. As another example, bispecific antibodies may be used to localize cytotoxic agents to cells which express target antigen. These antibodies possess a target-binding arm and an arm which binds the cytotoxic agent (e.g., saporin, anti-interferon-60, vinca alkaloid, ricin A chain, methotrexate or radioactive isotope hapten). Multispecific antibodies can be prepared as full length antibodies or antibody fragments.
Additionally, the anti-hepcidin antibodies disclosed herein can also be constructed to fold into multivalent forms, which may improve binding affinity, specificity and/or increased half-life in blood. Multivalent forms of anti-hepcidin antibodies can be prepared by techniques known in the art.
Bispecific or multispecific antibodies include cross-linked or “heteroconjugate” antibodies. For example, one of the antibodies in the heteroconjugate can be coupled to avidin, the other to biotin. Heteroconjugate antibodies may be made using any convenient cross-linking methods. Suitable cross-linking agents are well known in the art, and are disclosed in U.S. Pat. No. 4,676,980, along with a number of cross-linking techniques. Another method is designed to make tetramers by adding a streptavidin-coding sequence at the C-terminus of the scFv. Streptavidin is composed of four subunits, so when the scFv-streptavidin is folded, four subunits associate to form a tetramer (Kipriyanov et al., Hum Antibodies Hybridomas 6(3): 93-101 (1995), the disclosure of which is incorporated herein by reference in its entirety).
According to another approach for making bispecific antibodies, the interface between a pair of antibody molecules can be engineered to maximize the percentage of heterodimers which are recovered from recombinant cell culture. One interface comprises at least a part of the C_H3 domain of an antibody constant domain. In this method, one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains (e.g., tyrosine or tryptophan). Compensatory “cavities” of identical or similar size to the large side chain(s) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones (e.g., alanine or threonine). This provides a mechanism for increasing the yield of the heterodimer over other unwanted end-products such as homodimers. See WO 96/27011 published Sep. 6, 1996.
Techniques for generating bispecific or multispecific antibodies from antibody fragments have also been described in the literature. For example, bispecific or trispecific antibodies can be prepared using chemical linkage. Brennan et al., Science 229:81 (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate F(ab′)₂fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation. The Fab′ fragments generated are then converted to thionitrobenzoate (TNB) derivatives. One of the Fab′-TNB derivatives is then reconverted to the Fab′-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab′-TNB derivative to form the bispecific antibody. The bispecific antibodies produced can be used as agents for the selective immobilization of enzymes. Better et al., Science 240: 1041-1043 (1988) disclose secretion of functional antibody fragments from bacteria (see, e.g., Better et al., Skerra et al. Science 240: 1038-1041 (1988)). For example, Fab′-SH fragments can be directly recovered from E. coli and chemically coupled to form bispecific antibodies (Carter et al., Bio/Technology 10:163-167 (1992); Shalaby et al., J. Exp. Med. 175:217-225 (1992)).
Shalaby et al., J. Exp. Med. 175:217-225 (1992) describe the production of a fully humanized bispecific antibody F(ab')₂molecule. Each Fab′ fragment was separately secreted from E. coli and subjected to directed chemical coupling in vitro to form the bispecfic antibody. The bispecific antibody thus formed was able to bind to cells overexpressing the HER2 receptor and normal human T cells, as well as trigger the lytic activity of human cytotoxic lymphocytes against human breast tumor targets.
Various techniques for making and isolating bispecific or multispecific antibody fragments directly from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers, e.g. GCN4. (See generally Kostelny et al., J. Immunol. 148(5):1547-1553 (1992).) The leucine zipper peptides from the Fos and Jun proteins were linked to the Fab′ portions of two different antibodies by gene fusion. The antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers. This method can also be utilized for the production of antibody homodimers.
Diabodies, described above, are one example of a bispecific antibody. See, for example, Hollinger et al., Proc. Natl. Acad. Sci. USA, 90:6444-6448 (1993). Bivalent diabodies can be stabilized by disulfide linkage.
Stable monospecific or bispecific Fv tetramers can also be generated by noncovalent association in (scFv₂)₂configuration or as bis-tetrabodies. Alternatively, two different scFvs can be joined in tandem to form a bis-scFv.
Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) dimers has also been reported. See Gruber et al., J. Immunol. 152: 5368 (1994). One approach has been to link two scFv antibodies with linkers or disulfide bonds (Mallender and Voss, J. Biol. Chem. 269:199-2061994, WO 94/13806, and U.S. Pat. No. 5,989,830, the disclosures of which are incorporated herein by reference in their entireties).
Alternatively, the bispecific antibody may be a “linear antibody” produced as described in Zapata et al. Protein Eng. 8(10):1057-1062 (1995). Briefly, these antibodies comprise a pair of tandem Fd segments (V_H-C_H1-V_H-C_H1) which form a pair of antigen binding regions. Linear antibodies can be bispecific or monospecific.
Antibodies with more than two valencies are also contemplated. For example, trispecific antibodies can be prepared. (Tutt et al., J. Immunol. 147:60 (1991)).
A “chelating recombinant antibody” is a bispecific antibody that recognizes adjacent and non-overlapping epitopes of the target antigen, and is flexible enough to bind to both epitopes simultaneously (Neri et al., J Mol Biol. 246:367-73, 1995).
Production of bispecific Fab-scFv (“bibody”) and trispecific Fab-(scFv)(2) (“tribody”) are described in Schoonjans et al. (J Immunol. 165:7050-57, 2000) and Willems et al. (J Chromatogr B Analyt Technol Biomed Life Sci. 786:161-76, 2003). For bibodies or tribodies, a scFv molecule is fused to one or both of the VL-CL (L) and VH-CH₁(Fd) chains, e.g., to produce a tribody two scFvs are fused to C-term of Fab while in a bibody one scFv is fused to C-term of Fab.
In yet another method, dimers, trimers, and tetramers are produced after a free cysteine is introduced in the parental protein. A peptide-based cross linker with variable numbers (two to four) of maleimide groups was used to cross link the protein of interest to the free cysteines (Cochran et al., Immunity 12(3): 241-50 (2000), the disclosure of which is incorporated herein in its entirety).
Antibody Screening Methods
Methods of identifying antibodies which bind hepcidin, which cross-block exemplary antibodies herein, and/or which inhibit hepcidin activity are also provided. Such methods may utilize the composition of highly purified, bioactive, correctly-folded, non-urinary human hepcidin (either chemically synthesized or produced in bacteria or non-mammalian cells) provided herein.
Antibodies may be screened for binding affinity by methods known in the art. For example, gel-shift assays, Western blots, radiolabeled competition assay, co-fractionation by chromatography, co-precipitation, cross linking, ELISA, and the like may be used, which are described in, for example, Current Protocols in Molecular Biology (1999) John Wiley & Sons, NY, which is incorporated herein by reference in its entirety.
To initially screen for antibodies which bind to the desired epitope on the target antigen, a routine cross-blocking assay such as that described in Antibodies, A Laboratory Manual, Cold Spring Harbor Laboratory, Ed Harlow and David Lane (1988), can be performed. Routine competitive binding assays may also be used, in which the unknown antibody is characterized by its ability to inhibit binding of target to a target-specific antibody of the invention. Intact antigen, fragments thereof such as the extracellular domain, or linear epitopes can be used. Epitope mapping is described in Champe et al., J. Biol. Chem. 270: 1388-1394 (1995).
In one variation of an in vitro binding assay, a method is provided comprising (a) contacting an immobilized hepcidin with a candidate antibody and (b) detecting binding of the candidate antibody to the hepcidin. In an alternative embodiment, the candidate antibody is immobilized and binding of hepcidin is detected. Immobilization is accomplished using any of the methods well known in the art, including covalent bonding to a support, a bead, or a chromatographic resin, as well as non-covalent, high affinity interaction such as antibody binding, or use of streptavidin/biotin binding wherein the immobilized compound includes a biotin moiety. Detection of binding can be accomplished (i) using a radioactive label on the compound that is not immobilized, (ii) using a fluorescent label on the non-immobilized compound, (iii) using an antibody immunospecific for the non-immobilized compound, (iv) using a label on the non-immobilized compound that excites a fluorescent support to which the immobilized compound is attached, as well as other techniques well known and routinely practiced in the art.
Antibodies that inhibit or neutralize human hepcidin activity may be identified by contacting hepcidin with an antibody, comparing hepcidin activity in the presence and absence of the test antibody, and determining whether the presence of the antibody decreases activity of the hepcidin. The biological activity of a particular antibody, or combination of antibodies, may be evaluated in vivo using a suitable animal model, including any of those described herein.
In exemplary embodiments, the invention includes high throughput screening (HTS) assays to identify antibodies that interact with or inhibit biological activity (i.e., inhibit phosphorylation, dimerization, ligand induced-receptor activation, or intracellular signaling, etc.) of target antigen. HTS assays permit screening of large numbers of compounds in an efficient manner. Cell-based HTS systems are contemplated to investigate the interaction between target antigen and its binding partners. HTS assays are designed to identify “hits” or “lead compounds” having the desired property, from which modifications can be designed to improve the desired property.
In another embodiment of the invention, high throughput screening for antibody fragments or CDRs with 1, 2, 3 or more modifications to amino acids within the CDRs having suitable binding affinity to a target antigen polypeptide is employed.
Specific Binding Agents
Other hepcidin-specific binding agents can be prepared, for example, based on CDRs from an antibody or by screening libraries of diverse peptides or organic chemical compounds for peptides or compounds that exhibit the desired binding properties for human hepcidin. Hepcidin specific binding agent include peptides containing amino acid sequences that are at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to one or more CDRs of murine antibody Ab43 (SEQ ID NOs: 16-21); murine antibody 2.7 (SEQ ID NOs: 28-33); murine antibody 2.41 (SEQ ID NOs: 40-45), rat antibody R9 (SEQ ID NOs: 52-57) or human antibody 1C9 (SEQ ID NOs: 111-116), human antibody 3B3 (SEQ ID NOs: 121-126), human antibody 4E1 (SEQ ID NOs: 131-136), human antibody 7A3 (SEQ ID NOs: 141-46), human antibody 9D12 (SEQ ID NOs: 151-156), human antibody 12B9 (SEQ ID NOs: 161-166), human antibody 15E1 (SEQ ID NOs: 171-176), human antibody 18D8 (SEQ ID NOs: 314-319), human antibody 19C1 (SEQ ID NOs: 324-329), human antibody 19D12 (SEQ ID NOs: 294-299), human antibody 19H6 (SEQ ID NOs: 304-309), human antibody 23F11 (SEQ ID NOs: 181-186), human antibody 26F11 (SEQ ID NOs: 191-196), or human antibody 1S1 (SEQ ID NOs: 203-205 and 131-133) or human antibody 1S2 (SEQ ID NOs: 214-216 and 144-146) or human antibody 1S3 (SEQ ID NOs: 225-227 and 164-166) or human antibody 1S4 (SEQ ID NOs: 236-238 and 174-176) or human antibody 1S5 (SEQ ID NO: 247-249 and 184-186).
Hepcidin-specific binding agents also include peptibodies. The term “peptibody” refers to a molecule comprising an antibody Fc domain attached to at least one peptide. The production of peptibodies is generally described in PCT publication WO 00/24782, published May 4, 2000. Any of these peptides may be linked in tandem (i.e., sequentially), with or without linkers. Peptides containing a cysteinyl residue may be cross-linked with another Cys-containing peptide, either or both of which may be linked to a vehicle. Any peptide having more than one Cys residue may form an intrapeptide disulfide bond, as well. Any of these peptides may be derivatized, for example, the carboxyl terminus may be capped with an amino group, cysteines may be cappe, or amino acid residues may substituted by moieties other than amino acid residues (see, e.g., Bhatnagar et al., J. Med. Chem. 39: 3814-9 (1996), and Cuthbertson et al., J. Med. Chem. 40: 2876-82 (1997), which are incorporated by reference herein in their entirety). The peptide sequences may be optimized, analogous to affinity maturation for antibodies, or otherwise altered by alanine scanning or random or directed mutagenesis followed by screening to identify the best binders. Lowman, Ann. Rev. Biophys. Biomol. Struct. 26: 401-24 (1997). Various molecules can be inserted into the specific binding agent structure, e.g., within the peptide portion itself or between the peptide and vehicle portions of the specific binding agents, while retaining the desired activity of specific binding agent. One can readily insert, for example, molecules such as an Fc domain or fragment thereof, polyethylene glycol or other related molecules such as dextran, a fatty acid, a lipid, a cholesterol group, a small carbohydrate, a peptide, a detectable moiety as described herein (including fluorescent agents, radiolabels such as radioisotopes), an oligosaccharide, oligonucleotide, a polynucleotide, interference (or other) RNA, enzymes, hormones, or the like. Other molecules suitable for insertion in this fashion will be appreciated by those skilled in the art, and are encompassed within the scope of the invention. This includes insertion of, for example, a desired molecule in between two consecutive amino acids, optionally joined by a suitable linker.
The development of hepcidin peptibodies is also contemplated. The interaction of a protein ligand with its receptor often takes place at a relatively large interface. However, as demonstrated for human growth hormone and its receptor, only a few key residues at the interface contribute to most of the binding energy. Clackson et al., Science 267: 383-6 (1995). The bulk of the protein ligand merely displays the binding epitopes in the right topology or serves functions unrelated to binding. Thus, molecules of only “peptide” length (generally 2 to 40 amino acids) can bind to the receptor protein of a given large protein ligand. Such peptides may mimic the bioactivity of the large protein ligand (“peptide agonists”) or, through competitive binding, inhibit the bioactivity of the large protein ligand (“peptide antagonists”).
Phage display technology has emerged as a powerful method in identifying such peptide agonists and antagonists. See, for example, Scott et al. Science 249: 386 (1990);
Devlin et al., Science 249: 404 (1990); U.S. Pat. No. 5,223,409, issued Jun. 29, 1993; U.S. Pat. No. 5,733,731, issued Mar. 31, 1998; U.S. Pat. No. 5,498,530, issued Mar. 12, 1996; U.S. Pat. No. 5,432,018, issued Jul. 11, 1995; U.S. Pat. No. 5,338,665, issued Aug. 16, 1994; U.S. Pat. No. 5,922,545, issued Jul. 13, 1999; WO 96/40987, published Dec. 19, 1996; and WO 98/15833, published Apr. 16, 1998 (each of which is incorporated by reference in its entirety). In peptide phage display libraries, random peptide sequences can be displayed by fusion with coat proteins of filamentous phage. The displayed peptides can be affinity-eluted against an antibody-immobilized extracellular domain of a receptor, if desired. The retained phage may be enriched by successive rounds of affinity purification and repropagation. The best binding peptides may be sequenced to identify key residues within one or more structurally related families of peptides. See, e.g., Cwirla et al., Science 276: 1696-9 (1997), in which two distinct families were identified. The peptide sequences may also suggest which residues may be safely replaced by alanine scanning or by mutagenesis at the DNA level. Mutagenesis libraries may be created and screened to further optimize the sequence of the best binders. Lowman, Ann. Rev. Biophys. Biomol. Struct. 26: 401-24 (1997).
Structural analysis of protein-protein interaction may also be used to suggest peptides that mimic the binding activity of large protein ligands. In such an analysis, the crystal structure may suggest the identity and relative orientation of critical residues of the large protein ligand, from which a peptide may be designed. See, e.g., Takasaki et al., Nature Biotech 15: 1266-70 (1997). These analytical methods may also be used to investigate the interaction between a receptor protein and peptides selected by phage display, which may suggest further modification of the peptides to increase binding affinity.
Other methods compete with phage display in peptide research. A peptide library can be fused to the carboxyl terminus of the lac repressor and expressed in E. coli. Another E. coli-based method allows display on the cell's outer membrane by fusion with a peptidoglycan-associated lipoprotein (PAL). Hereinafter, these and related methods are collectively referred to as “E. coli display.” In another method, translation of random RNA is halted prior to ribosome release, resulting in a library of polypeptides with their associated RNA still attached. Hereinafter, this and related methods are collectively referred to as “ribosome display.” Other methods employ chemical linkage of peptides to RNA. See, for example, Roberts and Szostak, Proc Natl Acad Sci USA, 94: 12297-303 (1997). Hereinafter, this and related methods are collectively referred to as “RNA-peptide screening.” Chemically derived peptide libraries have been developed in which peptides are immobilized on stable, non-biological materials, such as polyethylene rods or solvent-permeable resins. Another chemically derived peptide library uses photolithography to scan peptides immobilized on glass slides. Hereinafter, these and related methods are collectively referred to as “chemical-peptide screening.” Chemical-peptide screening may be advantageous in that it allows use of D-amino acids and other unnatural analogues, as well as non-peptide elements. Both biological and chemical methods are reviewed in Wells and Lowman, Curr. Opin. Biotechnol., 3: 355-62 (1992).
Conceptually, one may discover peptide mimetics of any protein using phage display and the other methods mentioned above. These methods have been used for epitope mapping, for identification of critical amino acids in protein-protein interactions, and as leads for the discovery of new therapeutic agents. See, e.g., Cortese et al., Curr. Opin. Biotech. 7: 616-21 (1996). Peptide libraries are now being used most often in immunological studies, such as epitope mapping. See Kreeger, The Scientist 10(13):19-20 (1996).
Sources for compounds that may be screened for ability to bind to or modulate (i.e., increase or decrease) the activity of the hepcidin polypeptides described herein include (1) inorganic and organic chemical libraries, (2) natural product libraries, and (3) combinatorial libraries comprised of either random or mimetic peptides, oligonucleotides or organic molecules.
Chemical libraries may be readily synthesized or purchased from a number of commercial sources, and may include structural analogs of known compounds or compounds that are identified as “hits” or “leads” via natural product screening.
The sources of natural product libraries are microorganisms (including bacteria and fungi), animals, plants or other vegetation, or marine organisms, and libraries of mixtures for screening may be created by: (1) fermentation and extraction of broths from soil, plant or marine microorganisms or (2) extraction of the organisms themselves. Natural product libraries include polyketides, non-ribosomal peptides, and (non-naturally occurring) variants thereof. For a review, see Science 282:63-68 (1998).
Combinatorial libraries are composed of large numbers of peptides, oligonucleotides or organic compounds and can be readily prepared by traditional automated synthesis methods, PCR, cloning or proprietary synthetic methods. Of particular interest are peptide and oligonucleotide combinatorial libraries. Still other libraries of interest include peptide, protein, peptidomimetic, multiparallel synthetic collection, recombinatorial, and polypeptide libraries. For a review of combinatorial chemistry and libraries created therefrom, see Myers, Curr. Opin. Biotechnol. 8:701-707 (1997). For reviews and examples of peptidomimetic libraries, see Al-Obeidi et al., Mol. Biotechnol, 9(3):205-23 (1998); Hruby et al., Curr Opin Chem Biol, 1(1):114-19 (1997); Dorner et al., Bioorg Med Chem, 4(5):709-15 (1996) (alkylated dipeptides).
Hepcidin-specific binding agents also include scaffolding proteins, as described by Hays et al. Trends In Biotechnology, 23(10):514-522 (2005), herein incorporated by reference in its entirety, and Avimer protein technology, as described in US Publication Nos. 2006-0286603 and 2006-0223114, both herein incorporated by reference in their entireties.
Screening Methods for Antibodies or Specific Binding Agents
Methods of identifying antibodies or specific binding agents which bind hepcidin and/or which cross-block exemplary antibodies described herein, and/or which inhibit hepcidin activity are also provided. Such methods may utilize the composition of highly purified, bioactive, correctly-folded, non-urinary human hepcidin (either chemically synthesized or produced in bacteria or non-mammalian cells) provided herein.
Antibodies or specific binding agents may be screened for binding affinity by methods known in the art. For example, gel-shift assays, Western blots, radiolabeled competition assay, co-fractionation by chromatography, co-precipitation, cross linking, ELISA, and the like may be used, which are described in, for example, Current Protocols in Molecular Biology (1999) John Wiley & Sons, NY, which is incorporated herein by reference in its entirety.
To initially screen for antibodies or specific binding agents which bind to the desired epitope on the target antigen, a routine cross-blocking assay such as that described in Antibodies, A Laboratory Manual, Cold Spring Harbor Laboratory, Ed Harlow and David Lane (1988), can be performed. Routine competitive binding assays may also be used, in which the unknown antibody is characterized by its ability to inhibit binding of target to a target-specific antibody of the invention. Intact antigen, fragments thereof such as the extracellular domain, or linear epitopes can be used. Epitope mapping is described in Champe et al., J. Biol. Chem. 270: 1388-1394 (1995).
In one variation of an in vitro binding assay, the invention provides a method comprising (a) contacting an immobilized hepcidin with a candidate antibody or specific binding agent and (b) detecting binding of the candidate antibody or specific binding agent to the hepcidin. In an alternative embodiment, the candidate antibody or specific binding agent is immobilized and binding of hepcidin is detected. Immobilization is accomplished using any of the methods well known in the art, including covalent bonding to a support, a bead, or a chromatographic resin, as well as non-covalent, high affinity interaction such as antibody binding, or use of streptavidin/biotin binding wherein the immobilized compound includes a biotin moiety. Detection of binding can be accomplished (i) using a radioactive label on the compound that is not immobilized, (ii) using a fluorescent label on the non-immobilized compound, (iii) using an antibody immunospecific for the non-immobilized compound, (iv) using a label on the non-immobilized compound that excites a fluorescent support to which the immobilized compound is attached, as well as other techniques well known and routinely practiced in the art.
In some embodiments, antibodies or specific binding agents that inhibit or neutralize human hepcidin activity may be identified by contacting hepcidin with the antibody (or specific binding agent), comparing hepcidin activity in the presence and absence of the test antibody (or specific binding agent), and determining whether the presence of the antibody (or specific binding agent) decreases activity of the hepcidin. The biological activity of a particular antibody, or specific binding agent, or combination of antibodies or specific binding agents, may be evaluated in vivo using a suitable animal model, including any of those described herein.
In some embodiments, the invention also contemplates high throughput screening (HTS) assays to identify antibodies that interact with or inhibit biological activity (i.e., inhibit phosphorylation, dimerization, ligand induced-receptor activation, or intracellular signaling, etc.) of target antigen. HTS assays permit screening of large numbers of compounds in an efficient manner. Cell-based HTS systems are contemplated to investigate the interaction between target antigen and its binding partners. HTS assays are designed to identify “hits” or “lead compounds” having the desired property, from which modifications can be designed to improve the desired property.
In another embodiment, high throughput screening for antibody fragments or CDRs with 1, 2, 3 or more modifications to amino acids within the CDRs having suitable binding affinity to a target antigen polypeptide is employed.
B. Inhibitory Oligonucleotides
Hepcidin expression inhibitors that may be used according to the methods described herein include inhibitor oligonucleotides or polynucleotides, including pharmaceutically acceptable salts thereof, e.g. sodium salts. Nonlimiting examples include: antisense oligonucleotides [Eckstein, Antisense Nucleic Acid Drug Dev., 10: 117-121 (2000); Crooke, Methods Enzymol., 313: 3-45 (2000); Guvakova et al., J. Biol. Chem., 270: 2620-2627 (1995); Manoharan, Biochim. Biophys. Acta, 1489: 117-130 (1999); Baker et al., J. Biol. Chem., 272: 11994-12000 (1997); Kurreck, Eur. J. Biochem., 270: 1628-1644 (2003); Sierakowska et al., Proc. Natl. Acad. Sci. USA, 93: 12840-12844 (1996); Marwick, J. Am. Med. Assoc. 280: 871 (1998); Tomita and Morishita, Curr. Pharm. Des., 10: 797-803 (2004); Gleave and Monia, Nat. Rev. Cancer, 5: 468-479 (2005) and Patil, AAPS J. 7: E61-E77 (2005], triplex oligonucleotides [Francois et al., Nucleic Acids Res., 16: 11431-11440 (1988) and Moser and Dervan, Science, 238: 645-650 (1987)], ribozymes/deoxyribozymes(DNAzymes) [Kruger et al., Tetrahymena. Cell, 31: 147-157 (1982); Uhlenbeck, Nature, 328: 596-600 (1987); Sigurdsson and Eckstein, Trends Biotechnol., 13 286-289 (1995); Kumar et al., Gene Ther., 12: 1486-1493 (2005); Breaker and Joyce, Chem. Biol., 1: 223-229 (1994); Khachigian, Curr. Pharm. Biotechnol., 5: 337-339 (2004); Khachigian, Biochem. Pharmacol., 68: 1023-1025 (2004) and Trulzsch and Wood, J. Neurochem., 88: 257-265 (2004)], small-interfering RNAs/RNAi [Fire et al., Nature, 391: 806-811 (1998); Montgomery et al., Proc. Natl. Acad. Sci. U.S.A., 95: 15502-15507 (1998); Cullen, Nat. Immunol., 3: 597-599 (2002); Hannon, Nature, 418: 244-251 (2002); Bernstein et al., Nature, 409: 363-366 (2001); Nykanen et al., Cell, 107: 309-321 (2001); Gilmore et al., J. Drug Target., 12: 315-340 (2004); Reynolds et al., Nat. Biotechnol., 22: 326-330 (2004); Soutschek et al., Nature, 432173-178 (2004); Ralph et al., Nat. Med., 11: 429-433 (2005); Xia et al., Nat. Med., 10816-820 (2004) and Miller et al., Nucleic Acids Res., 32: 661-668 (2004)], aptamers [Ellington and Szostak, Nature, 346: 818-822 (1990); Doudna et al., Proc. Natl. Acad. Sci. U.S.A., 92: 2355-2359 (1995); Tuerk and Gold, Science, 249: 505-510 (1990); White et al., Mol. Ther., 4: 567-573 (2001); Rusconi et al., Nature, 419: 90-94 (2002); Nimjee et al., Mol. Ther., 14: 408-415 (2006); Gragoudas et al., N. Engl. J. Med., 351: 3805-2816 (2004); Vinores, Curr. Opin. Mol. Ther., 5673-679 (2003) and Kourlas and Schiller et al., Clin. Ther., 28 36-44 (2006)] or decoy oligonucleotides [Morishita et al., Proc. Natl. Acad. Sci. U.S.A., 92: 5855-5859 (1995); Alexander et al., J. Am. Med. Assoc., 294: 2446-2454 (2005); Mann and Dzau, J. Clin. Invest., 106: 1071-1075 (2000) and Nimjee et al., Annu. Rev. Med., 56: 555-583 (2005). The foregoing documents are hereby incorporated by reference in their entirety herein, with particular emphasis on those sections of the documents relating to methods of designing, making and using inhibitory oligonucleotides. Commercial providers such as Ambion Inc. (Austin, Tex.), Darmacon Inc. (Lafayette, Colo.), InvivoGen (San Diego, Calif.), and Molecular Research Laboratories, LLC (Herndon, Va.) generate custom siRNA molecules. In addition, commercial kits are available to produce custom siRNA molecules, such as SILENCER™ siRNA Construction Kit (Ambion Inc., Austin, Tex.) or psiRNA System (InvivoGen, San Diego, Calif.).
Inhibitory oligonucleotides may be complementary to the coding portion of a target gene, 3′ or 5′ untranslated regions, or intronic sequences in a gene, or alternatively coding or intron sequences in the target mRNA. Intron sequences are generally less conserved and thus may provide greater specificity. In one embodiment, the inhibitory oligonucleotide inhibits expression of a gene product of one species but not its homologue in another species; in other embodiments, the inhibitory oligonucleotide inhibits expression of a gene in two species, e.g. human and primate, or human and murine.
In certain embodiments, the inhibitory oligonucleotide is capable of hybridizing to at least 8, 9, 10, 11, or 12 consecutive bases of the hepcidin gene or mRNA (SEQ ID NO: 99 (mouse) or SEQ ID NO: 100 (human) or the reverse strand thereof) under moderate or high stringency conditions. In some cases, depending on the length of the complementary region, one, two or more mismatches may be tolerated without affecting inhibitory function. In certain embodiments, the inhibitory oligonucleotide is an antisense oligonucleotide, an inhibitory RNA (including siRNA or RNAi, or shRNA), a DNA enzyme, a ribozyme (optionally a hammerhead ribozyme), an aptamer, or pharmaceutically acceptable salts thereof. In one embodiment, the oligonucleotide is complementary to at least 10 bases of SEQ ID NO: 104. In one embodiment, the oligonucleotide targets the nucleotides located in the vicinity of the 3′ untranslated region of the hepcidin mRNA.
Selection of mRNA Site to Target with Inhibitory Oligonucleotide
The specific sequence utilized in design of the oligonucleotides may be any contiguous sequence of nucleotides contained within the expressed gene message of the target. Programs and algorithms, known in the art, may be used to select appropriate target sequences. In addition, optimal sequences may be selected utilizing programs designed to predict the secondary structure of a specified single stranded nucleic acid sequence and allowing selection of those sequences likely to occur in exposed single stranded regions of a folded mRNA. Methods and compositions for designing appropriate oligonucleotides may be found, for example, in U.S. Pat. No. 6,251,588, the contents of which are incorporated herein by reference in its entirety.
Most mRNAs have been shown to contain a number of secondary and tertiary structures. Secondary structural elements in RNA are formed largely by Watson-Crick type interactions between different regions of the same RNA molecule. Important secondary structural elements include intramolecular double stranded regions, hairpin loops, bulges in duplex RNA and internal loops. Tertiary structural elements are formed when secondary structural elements come in contact with each other or with single stranded regions to produce a more complex three dimensional structure. A number of researchers have measured the binding energies of a large number of RNA duplex structures and have derived a set of rules which can be used to predict the secondary structure of RNA (see e.g. Jaeger et al., 1989, Proc. Natl. Acad. Sci. USA 86:7706; and Turner et al., 1988, Annu Rev. Biophys. Biophys. Chem. 17:167). The rules are useful in identification of RNA structural elements and, in particular, for identifying single stranded RNA regions which may represent segments of the mRNA to target for siRNA, ribozyme or antisense technologies.
Antisense Oligonucleotides
The constitutive expression of antisense oligonucleotides in cells has been shown to inhibit gene expression, possibly via the blockage of translation or prevention o