WO2008121813A2

WO2008121813A2 - Modulation of cytokine production

Info

Publication number: WO2008121813A2
Application number: PCT/US2008/058648
Authority: WO
Inventors: Vishva Dixit; Nobuhiko Kayagaki
Original assignee: Genentech, Inc.
Priority date: 2007-03-30
Filing date: 2008-03-28
Publication date: 2008-10-09
Also published as: WO2008121813A3

Abstract

Methods of using DUBA polypeptides and nucleic acids in modulating cytokine production and in modulating immune response are provided. Methods of diagnosing and treating certain pathophysiological conditions using the DUBA polypeptides and nucleic acids of the invention are also provided.

Description

MODULATION OF CYTOKINE PRODUCTION

FIELD OF THE INVENTION

This invention relates to the field of methods of using DUBA polypeptides and nucleic acids in modulating cytokine production and in modulating immune response.

BACKGROUND

Innate immune responses are initiated when host cellular pattern recognition receptors encounter pathogen-associated molecular patterns (PAMPs) (Akira et al., Cell 124, 783 (2006)). Double and single strand RNAs are virus-derived PAMPs that trigger the intracellular PAMP sensors toll-like receptor 3 (TLR3), retinoic acid-inducible protein I (RIG-I), and melanoma differentiation-associated gene 5 (MD A5) (Alexopoulou et al.,

Nature 413, 732 (2001); Yamamoto et al, Science 301, 640 (2003); Kato et al, Nature 441, 101 (2006)). Activation of these intracellular sensors leads to the recruitment of specific adaptor proteins for interferon (IFN)-I (type I interferon) production: TRIF interacts with TLR3, whereas IPS-1/Cardif/MAVS/VISA is recruited by RIG-I and MDA5 (Akira et al., Cell 124, 783 (2006); Yamamoto et al, Science 301, 640 (2003); Meylan & Tschopp, MoI. Cell 22, 561 (2006)). These adaptors mediate the assembly of a signaling complex composed of the ubiquitin ligase TNF receptor-associated factor (TRAF3) and the kinases TANK- binding kinase (TBK)I and IKB kinase (IKK)-ε/IKK-/ (Hacker et al, Nature 439, 204 (2006); Oganesyan et al, Nature 439, 208 (2006)). This complex then activates the downstream transcription factors, IFN regulatory factors IRF-3 and IRF-7 to switch on IFN-I expression (Honda et al., Immunity 25, 349 (2006)). The type I interferons (IFNs) are cytokines which have pleiotropic effects on a wide variety of cell types. IFNs are best known for their antiviral activity, but they also have anti-bacterial, anti-protozoal, immunomodulatory, and cell- growth regulatory functions (van den Broek et al., Immunol Rev. 148: 5-18 (1995); Pfeffer et al., Cancer Res. 58: 2489-99 (1998)). The type I interferons include interferon-α (IFN-α) and interferon-β (IFN-β).

The important molecular functions ascribed to interferons and, by extension, the interferon regulatory response pathways described above, suggest that such pathways represent significant therapeutic targets. It would therefore be beneficial to elucidate a means for selectively modulating those pathways and provide compositions and methods therefor. The present invention provides this and other benefits.

DISCLOSURE OF THE INVENTION Methods of using DUBA polypeptides and nucleic acids in modulating cytokine production are provided. Methods of using DUBA polypeptides and nucleic acids in treating or detecting certain diseases are also provided.

In one embodiment, the invention provides a method of modulating interferon production in a cell, comprising administering to the cell at least one modulator of DUBA expression and/or DUBA activity. In one aspect, the interferon is a type I interferon. In another aspect, the interferon is selected from IFN-α and IFN-β. In another aspect, the at least one modulator of DUBA expression modulates DUBA transcription. In another aspect, the at least one modulator of DUBA expression modulates DUBA translation. In another aspect, the modulator of DUBA expression and/or DUBA activity modifies DUBA expression and/or DUBA activity such that signaling through the TLR3, RIG-I, or MDA5 signaling pathways is modulated. In another such aspect, the modulator of DUBA expression and/or DUBA activity, modifies DUBA expression and/or DUBA activity such that TRAF3 activity is modulated. In another such aspect, the TRAF3 activity is modulated due to an increase or decrease in the amount of K63 -linked polyubiquitination of TRAF3. In another embodiment, the invention provides a method of increasing interferon production in a cell, comprising administering to the cell at least one compound that decreases or blocks DUBA expression and/or DUBA activity. In one aspect, the compound that decreases or blocks DUBA expression and/or DUBA activity is a DUBA antagonist. In another such aspect, the DUBA antagonist is selected from an antibody, an antigen-binding fragment, an aptamer, an interfering RNA, a small molecule, a peptide, and an antisense molecule. In another such aspect, the interfering RNA is selected from the silencing RNAs set forth in SEQ ID NOs: 36, 50, 64, and 78. In another aspect, the interferon is a type I interferon. In another aspect, the interferon is selected from IFN-α and IFN-β. In another aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA transcription. In another aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA translation. In another aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA expression and/or DUBA activity such that signaling through the TLR3, RIG-I, or MDA5 signaling pathways is increased. In another such aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA expression and/or DUBA activity such that TRAF3 activity is increased. In another such aspect, the TRAF3 activity is increased due to an increase in the amount of K63 -linked polyubiquitination of TRAF3. In another embodiment, the invention provides a method for the treatment of a disease or condition caused by, exacerbated by, or prolonged by decreased levels of interferon in a subject relative to interferon levels in a healthy subject, comprising administering to the subject an effective amount of at least one compound that decreases or blocks DUBA expression and/or DUBA activity in the subject. In one aspect, the compound that decreases or blocks DUBA expression and/or DUBA activity is a DUBA antagonist. In another such aspect, the DUBA antagonist is selected from an antibody, an antigen-binding fragment, an aptamer, an interfering RNA, a small molecule, a peptide, and an antisense molecule. In another such aspect, the interfering RNA is selected from the silencing RNAs set forth in SEQ ID NOs: 36, 50, 64, and 78. In another aspect, the interferon is a type I interferon. In another aspect, the interferon is selected from IFN-α and IFN-β. In another aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA transcription. In another aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA translation. In another aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA expression and/or DUBA activity such that signaling through the TLR3, RIG-I, or MDA5 signaling pathways is increased. In another such aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA expression and/or DUBA activity such that TRAF3 activity is increased. In another such aspect, the TRAF3 activity is increased due to an increase in the amount of K63 -linked polyubiquitination of TRAF3. In another aspect, the disease or condition is selected from at least one of a cell proliferative disorder, an infection, an immune/inflammatory disorder, and an interferon-related disorder.

In another embodiment, the invention provides a method for increasing interferon production in a cell, comprising inhibiting DUBA expression and/or DUBA activity in the cell. In one aspect, DUBA expression and/or DUBA activity is inhibited by administration of at least one compound that decreases or blocks DUBA expression and/or DUBA activity. In another such aspect, the at least one compound is a DUBA antagonist. In another such aspect, the DUBA antagonist is selected from an antibody, an antigen-binding fragment, an aptamer, an interfering RNA, a small molecule, a peptide, and an antisense molecule. In another such aspect, the interfering RNA is selected from the silencing RNAs set forth in SEQ ID NOs: 36, 50, 64, and 78. In another aspect, the interferon is a type I interferon. In another aspect, the interferon is selected from IFN-α and IFN-β. In another aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA transcription. In another aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA translation. In another aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA expression and/or DUBA activity such that signaling through the TLR3, RIG-I, or MDA5 signaling pathways is increased. In another such aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA expression and/or DUBA activity such that TRAF3 activity is increased. In another such aspect, the TRAF3 activity is increased due to an increase in the amount of K63 -linked polyubiquitination of TRAF3. In another aspect, the cell is in vitro. In another aspect, the cell is in vivo.

In another embodiment, the invention provides a method for increasing interferon production in a mammal, comprising inhibiting DUBA expression and/or DUBA activity in the mammal. In one aspect, DUBA expression and/or DUBA activity is inhibited by administration of at least one compound that decreases or blocks DUBA expression and/or DUBA activity. In another such aspect, the at least one compound is a DUBA antagonist. In another such aspect, the DUBA antagonist is selected from an antibody, an antigen-binding fragment, an aptamer, an interfering RNA, a small molecule, a peptide, and an antisense molecule. In another such aspect, the interfering RNA is selected from the silencing RNAs set forth in SEQ ID NOs: 36, 50, 64, and 78. In another aspect, the interferon is a type I interferon. In another aspect, the interferon is selected from IFN-α and IFN-β. In another aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA transcription. In another aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA translation. In another aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA expression and/or DUBA activity such that signaling through the TLR3, RIG-I, or MDA5 signaling pathways is increased. In another such aspect, the at least one compound that decreases or blocks DUBA expression and/or DUBA activity decreases or blocks DUBA expression and/or DUBA activity such that TRAF3 activity is increased. In another such aspect, the TRAF3 activity is increased due to an increase in the amount of K63 -linked polyubiquitination of TRAF3. In one aspect, the mammal is a human. In another embodiment, the invention provides a method of decreasing interferon production in a cell, comprising administering to the cell at least one compound that increases DUBA expression and/or DUBA activity. In one aspect, the at least one compound that increases DUBA expression and/or DUBA activity is a DUBA agonist. In another such aspect, the DUBA agonist is selected from an antibody, an antigen-binding fragment, an aptamer, an interfering RNA, a small molecule, a peptide, an antisense molecule, and another binding polypeptide. In one such aspect, the aptamer, interfering RNA, or antisense molecule interferes with the transcription and/or translation of a DUB A-inhibitory molecule. In another such aspect, the antibody, antigen-binding fragment, small molecule, peptide, or other binding polypeptide specifically binds DUBA in such a manner as to enhance and/or strengthen binding of DUBA to its target ligand. In another such aspect, the antibody, antigen-binding fragment, small molecule, peptide, or other binding polypeptide specifically binds DUBA in such a manner as to inhibit or block the binding of DUBA by an inhibitory molecule. In another aspect, the interferon is a type I interferon. In another aspect, the interferon is selected from IFN-α and IFN-β. In another aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA transcription. In another aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA translation. In another aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA expression and/or DUBA activity such that signaling through the TLR3, RIG-I, or MDA5 signaling pathways is decreased. In another such aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA expression and/or DUBA activity such that TRAF3 activity is decreased. In another such aspect, the TRAF3 activity is decreased due to a decrease in the amount of K63 -linked polyubiquitination of TRAF3.

In another embodiment, the invention provides a method for the treatment of a disease or condition caused by, exacerbated by, or prolonged by increased levels of interferon in a subject relative to interferon levels in a healthy subject, comprising administering to the subject an effective amount of at least one compound that increases DUBA expression and/or DUBA activity in the subject. In one aspect, the at least one compound that increases DUBA expression and/or DUBA activity is a DUBA agonist. In another such aspect, the DUBA agonist is selected from an antibody, an antigen-binding fragment, an aptamer, an interfering RNA, a small molecule, a peptide, an antisense molecule, and another binding polypeptide. In one such aspect, the aptamer, interfering RNA, or antisense molecule interferes with the transcription and/or translation of a DUBA-inhibitory molecule. In another such aspect, the antibody, antigen-binding fragment, small molecule, peptide, or other binding polypeptide specifically binds DUBA in such a manner as to enhance and/or strengthen binding of DUBA to its target ligand. In another such aspect, the antibody, antigen-binding fragment, small molecule, peptide, or other binding polypeptide specifically binds DUBA in such a manner as to inhibit or block the binding of DUBA by an inhibitory molecule. In another aspect, the interferon is a type I interferon. In another aspect, the interferon is selected from IFN-α and IFN-β. In another aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA transcription. In another aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA translation. In another aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA expression and/or DUBA activity such that signaling through the TLR3, RIG-I, or MDA5 signaling pathways is decreased. In another such aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA expression and/or DUBA activity such that TRAF3 activity is decreased. In another such aspect, the TRAF3 activity is decreased due to a decrease in the amount of K63- linked polyubiquitination of TRAF3. In another aspect, the disease or condition is selected from at least one of a cell proliferative disorder, an infection, an immune/inflammatory disorder, and an interferon-related disorder. In another such aspect, the disease or condition is systemic lupus erythematosus.

In another embodiment, the invention provides a method for decreasing interferon production in a cell, comprising stimulating DUBA expression and/or DUBA activity in the cell. In one aspect, DUBA expression and/or DUBA activity is stimulated by administration of at least one compound that increases DUBA expression and/or DUBA activity. In another such aspect, the at least one compound that increases DUBA expression and/or DUBA activity is a DUBA agonist. In another such aspect, the DUBA agonist is selected from an antibody, an antigen- binding fragment, an aptamer, an interfering RNA, a small molecule, a peptide, an antisense molecule, and another binding polypeptide. In one such aspect, the aptamer, interfering RNA, or antisense molecule interferes with the transcription and/or translation of a DUB A-inhibitory molecule. In another such aspect, the antibody, antigen-binding fragment, small molecule, peptide, or other binding polypeptide specifically binds DUBA in such a manner as to enhance and/or strengthen binding of DUBA to its target ligand. In another such aspect, the antibody, antigen-binding fragment, small molecule, peptide, or other binding polypeptide specifically binds DUBA in such a manner as to inhibit or block the binding of DUBA by an inhibitory molecule. In another aspect, the interferon is a type I interferon. In another aspect, the interferon is selected from IFN-α and IFN-β. In another aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA transcription. In another aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA translation. In another aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA expression and/or DUBA activity such that signaling through the TLR3, RIG-I, or MDA5 signaling pathways is decreased. In another such aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA expression and/or DUBA activity such that TRAF3 activity is decreased. In another such aspect, the TRAF3 activity is decreased due to a decrease in the amount of K63 -linked polyubiquitination of TRAF3. In one aspect, the cell is in vitro. In another aspect, the cell is in vivo.

In another embodiment, the invention provides a method for decreasing interferon production in a mammal, comprising stimulating DUBA expression and/or DUBA activity in the mammal. In one aspect, DUBA expression and/or DUBA activity is stimulated by administration of at least one compound that increases DUBA expression and/or DUBA activity. In another such aspect, the at least one compound that increases DUBA expression and/or DUBA activity is a DUBA agonist. In another such aspect, the DUBA agonist is selected from an antibody, an antigen-binding fragment, an aptamer, an interfering RNA, a small molecule, a peptide, an antisense molecule, and another binding polypeptide. In one such aspect, the aptamer, interfering RNA, or antisense molecule interferes with the transcription and/or translation of a DUBA- inhibitory molecule. In another such aspect, the antibody, antigen-binding fragment, small molecule, peptide, or other binding polypeptide specifically binds DUBA in such a manner as to enhance and/or strengthen binding of DUBA to its target ligand. In another such aspect, the antibody, antigen-binding fragment, small molecule, peptide, or other binding polypeptide specifically binds DUBA in such a manner as to inhibit or block the binding of DUBA by an inhibitory molecule. In another aspect, the interferon is a type I interferon. In another aspect, the interferon is selected from IFN-α and IFN-β. In another aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA transcription. In another aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA translation. In another aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA expression and/or DUBA activity such that signaling through the TLR3, RIG-I, or MDA5 signaling pathways is decreased. In another such aspect, the at least one compound that increases DUBA expression and/or DUBA activity increases DUBA expression and/or DUBA activity such that TRAF3 activity is decreased. In another such aspect, the TRAF3 activity is decreased due to a decrease in the amount of K63- linked polyubiquitination of TRAF3. In one aspect, the mammal is human.

In another embodiment, the invention provides methods for detecting a predisposition to or the presence or extent of a disease or condition relating to abnormal interferon levels in a subject, comprising detecting the amount and/or activity of DUBA in the subject. In another aspect, the interferon is a type I interferon. In another aspect, the interferon is selected from IFN-α and IFN- β. In another aspect, the disease or condition is selected from at least one of a cell proliferative disorder, an infection, an immune/inflammatory disorder, and an interferon-related disorder. In another such aspect, the disease or condition is systemic lupus erythematosus. In another aspect, detecting the amount of DUBA comprises detecting DUBA polynucleotide. In another such aspect, detecting the amount of DUBA comprises detecting DNA encoding DUBA. In another such aspect, detecting the amount of DUBA comprises detecting RNA encoding DUBA. In another such aspect, the RNA is mRNA. In another such aspect, the detecting comprises a Northern or Southern blot. In another aspect, detecting the amount of DUBA comprises detecting DUBA polypeptide. In another such aspect, the detecting comprises a Western blot analysis. In another aspect, detecting the activity of DUBA comprises detecting DUBA deubiquitination activity. In another such aspect, the deubiquitination activity is deubiquitinylation of K63 -linked polyubiquitinated TRAF3. In another such aspect, such detecting is by means of a reporter assay. In another such aspect, the K63 -linked polyubiquitin chain is labeled. In another embodiment, the invention provides a method for selectively deubiquitinylating a K63-linked polyubiquitinated polypeptide while not deubiquitinylating a polypeptide that is polyubiquitinated with a polyubiquitin comprising one or more lysine linkages other than K63, comprising treating the K63-linked polyubiquitinated polypeptide with DUBA. In one aspect, the polyubiquitinated polypeptide is TRAF3. In another aspect, the lysine linkage other than K63 is K48-linkage.

In another embodiment, the invention provides a method for selectively deubiquitinylating only one or more K63 -linked polyubiquitin chains but not polyubiquitin chains comprising one or more lysine linkages other than K63 in a polyubiquitinated polypeptide comprising treating the polypeptide with DUBA. In one aspect, the polyubiquitinated polypeptide is TRAF3. In another aspect, the lysine linkage other than K63 is K48-linkage. BRIEF DESCRIPTION OF THE DRAWINGS

Figure IA shows schematic representations of certain members of the OTU- containing family of deubiquitinases. Figures IB, 1C, and ID depict the results of siRNA- based high-throughput screening experiments described in Example IA. The data represent the average of two experiments, and similar results were also obtained from three independent experiments. The ability of the various deubiquitinases to stimulate NF-κB (Figure IB), IFN-β (Figure 1C), and IFN-α4 (Figure ID) production are shown.

Figure 2A shows the protein sequence alignment of OTU domain-containing members of the DUB family. Conserved amino acid residues are highlighted, and asterisks identify predicted catalytic residues. Figure 2B shows a schematic representation of the 571- amino acid DUBA protein depicting the N-terminal proline/glycine-rich region, the central OTU domain, three conserved catalytic cysteine protease residues (D221, C224, and H334), and the C-terminal ubiquitin-interacting motif ("UIM"). Figure 2C depicts a Northern blot showing the tissue distribution of DUBA mRNA in human tissues, as described in Example IB(I). Figures 2D and 2E depict the results of experiments assessing the relative effect of DUBA knockdown with DUBA siRNA #1 or DUBA siRNA #2 versus a control siRNA on activation of NF-κB and IFN-α4 production in TLR3/293 cells treated with polyLC, as described in Example 1(B)(2). Figure 2F shows a Western blot depicting DUBA protein levels in HEK293 cells three days after transfection with the indicated siRNAs with actin detection as a control, as described in Example 1(B)(2). Figure 2G depicts the results of experiments assessing the activity of different forms of DUBA siRNA#l in activating IFN-α4 signaling in TLR3/293 cells treated with polyLC, as described in Example 1(B)(2). The data shown represent the average of two experiments. Similar results were also obtained from three independent experiments. Figure 3 A depicts a schematic pathway for IFN-I production mediated by TLR3,

RIG-I, or MDA5. Figure 3B shows the results of experiments described in Example 2 assessing relative activation of various signaling pathway components upon DUBA siRNA#l or control siRNA treatment in HEK293 cells or TLR3/293 cells in the context of NF-κB (left panel), IFN-β (middle panel) or IFN-α4 (right panel) production. Figure 3 C shows the results of experiments to determine the effect of DUBA siRNA#l or DUBA siRNA#2 treatment upon actual production of IL-8, IFN-α, and RANTES in polyLC-treated TLR3/293 cells, as described in Example 2. Figure 3D depicts the results of siRNA experiments conducted in RAW264.3 cells to identify the impact of DUBA knockdown on cytokine production from those cells, as described in Example 2. Figure 3E shows the results of experiments examining the impact of DUBA knockdown on signaling via certain intracellular adaptor molecules in HEK293 cells, as described in Example 2.

Figure 4 depicts the results of experiments assessing the effect of DUBA or DUBA- C224S expression on NF-κB (left panel), IFN-β (middle panel), or IFN-α4 (right panel) production in cells upon coexpression of the indicated activator (TLR3, RIG-I CARD domain, MDA5 CARD domain, or IRF7), as described in Example 3. The data represents the mean +/- standard deviation of triplicated samples.

Figure 5 A depicts the results of experiments assessing the ubiquitin isopeptidase activity of DUBA on K48-linked or K63-linked tetraubiquitin chains, as described in Example 4A. Figure 5B shows the amino acid sequence of TRAF3 with the peptides identified by mass spectrometry indicated in bold text, as described in Example 4B. Figure 5 C depicts Western blots showing that DUBA and TRAF3 co immunoprecipitate, as described in Example 4B. Figure 5D shows Western blots depicting the results of experiments described in Example 4C. The leftmost panel shows the relative ability of DUBA to deubiquitinate TRAF3 and TRAF6. The center panel shows the relative ability of DUBA to deubiquitinate TRAF3 ubiquitinated with a K48-linked polyubiquitin (center lane) or a K63-linked polyubiquitin (right lane). The rightmost panel shows the relative ability of wild-type DUBA (center lane) or DUBA C224S (right lane) to deubiquitinate TRAF3 labeled with K63 -linked polyubiquitin. Figure 5 E depicts Western blots showing the results of endogenous TRAF3 ubiquitination experiments described in Example 4C. Figure 5F depicts Western blots from experiments described in Example 4C indicating that DUBA dissociates TRAF3 from TBKl.

Figure 6 A depicts a protein sequence alignment of UIM domains from several deubiquitinases. Conserved amino acid residues are highlighted. Figure 6B depicts Western blots showing the results of experiments described in Example 4D indicating that the GST-UIM fusion, but not the GST-UIM mutant (L542A/S549A) is able to interact with both K48-linked and K63-linked ubiquitin chains. Figure 6C depicts graphs depicting the results of experiments described in Example 4D, showing that both the OTU and UIM domains contribute to DUBA activity. Figure 6D depicts Western blots showing the results of experiments described in Example 4D indicating that UIM or OTU-impaired or deleted DUBA mutants have correspondingly impaired ability to deubiquitinate Myc-TRAF3.

Figure 7A shows Western blots depicting the results of experiments described in Example 4D indicating that DUBA has activity in the Baff-R/LT-betaR signaling pathway, shown in Figure 7B. "N. S." indicates a nonspecific band. Other data herein and in the preceding figures demonstrates that DUBA is a negative regulator of the TLR3/RIG-I/MDA5 signaling pathway (Figure 7A).

Figures 8 A and 8B depict the results of experiments assessing the relative activities of DUBA and DUBA truncation mutants in stimulating IFN-β production in the MDA5 and RIG-I pathways in HEK293 cells, as described in Example 4. Figure 8 A provides schematics of wild-type DUBA (wt) and the DUBA truncation mutants: the isolated DUBA OTU domain (amino acids 172-351, OTU), the N-terminal portion of DUBA including the OTU domain (amino acids 1-351, N+0TU), and the OTU domain through the C-terminus of DUBA (amino acids 172-571, OTU+C). Figure 8 A also provides graphs showing that OTU and N+OTU significantly stimulate IFN-β production while OTU+C inhibits IFN-β production. Figure 8B is a Western blot showing that wild-type DUBA and the DUBA truncation mutants were all strongly expressed in 293 cells.

MODES FOR CARRYING OUT THE INVENTION

General Techniques

The practice of the present invention will employ, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature, such as, "Molecular Cloning: A Laboratory Manual", third edition (Sambrook et al, 2001); "Oligonucleotide Synthesis" (M. J. Gait, ed., 1984); "Animal Cell Culture" (R. I. Freshney, ed., 1987); "Methods in Enzymology" (Academic Press, Inc.); "Current Protocols in Molecular Biology" (F. M. Ausubel et al., eds., 1987, and periodic updates); "PCR: The Polymerase Chain Reaction", (Mullis et al., ed., 1994); PCR 2: A Practical Approach (M. J. MacPherson, B. D. Hames and G. R. Taylor eds. (1995)); Harlow and Lane, eds. (1988) Antibodies, A Laboratory Manual; "A Practical Guide to Molecular Cloning" (Perbal Bernard V., 1988); and "Phage Display: A Laboratory Manual" (Barbas et al., 2001).

Definitions As used herein, the terms "OTU domain containing 5", "OTUD5", "deubiquitinating enzyme A" and "DUBA" are used interchangeably, and are defined as all species of native and synthetic polypeptides of DUBA, including, but not limited to, the full-length DUBA polypeptide, the mature form of the DUBA polypeptide in which the signal sequence has been removed, and soluble forms of the DUBA polypeptide.

A "DUBA-binding compound" and a "DUBA-binding molecule" are used interchangeably herein, and are molecules of the invention that specifically bind to DUBA polypeptide. Such molecules include, but are not limited to, anti-DUBA antibodies, DUBA- binding fragments of anti-DUBA antibodies, DUBA-specific aptamers, DUBA-binding small molecules, DUBA-binding peptides, and other polypeptides that specifically bind DUBA (including, but not limited to, DUBA-binding fragments of one or more DUBA ligands, optionally fused to one or more additional domains (e.g., TRAF3-Fc)). The human nucleic acid sequence of DUBA is:

CCGGGTTCTCTCCCGGCGTGCCCCGCGCCGGGTTTGTTGGGGGGTACTCGGCAGT GCAGCCATGACTATACTCCCCAAAAAGAAGCCGCCGCCTCCCGACGCCGACCCC GCCAACGAGCCGCCGCCGCCCGGGCCGATGCCCCCGGCGCCGCGGCGCGGCGGA GGTGTGGGCGTGGGCGGCGGCGGCACGGGCGTGGGCGGCGGCGATCGCGACCGT GACTCCGGCGTCGTGGGGGCCCGTCCGCGAGCTTCGCCACCGCCTCAAGGCCCGC TACCAGGACCGCCGGGCGCTCTTCATCGCTGGGCGCTGGCCGTGCCGCCTGGTGC AGTGGCGGGTCCCCGGCCACAACAGGCTTCTCCACCTCCTTGCGGGGGCCCAGGT GGTCCCGGCGGCGGTCCCGGCGACGCGCTGGGCGCAGCGGCGGCGGGTGTGGGT GCCGCGGGCGTGGTGGTGGGTGTGGGTGGTGCCGTAGGCGTGGGCGGCTGCTGC TCCGGGCCTGGGCACAGCAAGCGGCGACGTCAAGCTCCCGGGGTTGGCGCGGTT GGCGGGGGCAGTCCCGAGCGTGAGGAGGTCGGCGCAGGCTACAACAGTGAGGA CGAGTATGAGGCGGCTGCAGCACGCATCGAGGCTATGGACCCTGCCACTGTCGA GCAGCAGGAGCATTGGTTTGAAAAGGCCCTACGAGACAAGAAGGGCTTCATCAT CAAGCAGATGAAGGAGGATGGCGCCTGTCTCTTCCGGGCTGTAGCTGACCAGGT GTATGGAGACCAGGACATGCATGAGGTTGTGCGAAAGCATTGCATGGACTATCT GATGAAGAATGCCGACTACTTCTCCAACTATGTCACAGAGGACTTTACCACCTAC ATTAACAGGAAGCGGAAAAACAATTGCCATGGCAACCACATTGAGATGCAGGCC ATGGCAGAGATGTACAACCGTCCTGTGGAGGTGTACCAGTACAGCACAGGTACT TCTGCAGTGGAACCCATCAACACATTCCATGGGATACATCAAAACGAGGACGAA CCCATTCGTGTTAGCTACCATCGGAATATCCACTATAATTCAGTGGTGAATCCTA ACAAGGCCACCATTGGTGTGGGGCTGGGCCTGCCATCATTCAAACCAGGGTTTGC AGAGCAGTCTCTGATGAAGAATGCCATAAAAACATCGGAGGAGTCATGGATTGA ACAGCAGATGCTAGAAGACAAGAAACGGGCCACAGACTGGGAGGCCACAAATG AAGCCATCGAGGAGCAGGTGGCTCGGGAATCCTACCTGCAGTGGTTGCGGGATC AGGAGAAACAGGCTCGCCAGGTCCGAGGCCCCAGCCAGCCCCGGAAAGCCAGC GCCACATGCAGTTCGGCCACAGCAGCAGCCTCCAGTGGCCTGGAGGAGTGGACT AGCCGGTCCCCGCGGCAGCGGAGTTCAGCCTCGTCACCTGAGCACCCTGAGCTGC ATGCTGAATTGGGCATGAAGCCCCCTTCCCCAGGCACTGTTTTAGCTCTTGCCAA ACCTCCTTCGCCCTGTGCGCCAGGTACAAGCAGTCAGTTCTCGGCAGGGGCCGAC CGGGCAACTTCCCCCCTTGTGTCCCTCTACCCTGCTTTGGAGTGCCGGGCCCTCAT TCAGCAGATGTCCCCCTCTGCCTTTGGTCTGAATGACTGGGATGATGATGAGATC CTAGCTTCGGTGCTGGCAGTGTCCCAACAGGAATACCTAGACAGTATGAAGAAA AACAAAGTGCACAGAGACCCGCCCCCAGACAAGAGTTGATGGAGACCCAGGGAT TGGACACCATCTCCCAACCCCAGTACTCCTGCTCTCCGGTGCCACCTCACCTTCTT TGGCTTCTTCCCTCTTGCCTCCTTCTGTTCTTTCTGCTCTCCCCTCTTTTCCCTCCTC CTCACTTCCCTCTGGCTAGCCCACCCCTGCACTCTCTCTCATTGCCGCTGCCACTA TCACCTGTCTCTCTGCCAGCTGATGTGCCCTGTTGCCCCCCACCCCATCCCGCACA GAACCATCCCTGCATTCCACAGGGGACTCGGGCAAGGGTGCCGAAGATAGACAA GAGGCACACAGAGACAGACCAACTGGCAGCCAGGCAGCCCCAGAGGAGAGAGA CATTCAGACAGAGGAAAGTCTCCCTGCCCCTCATTCCTTCCAAGATGAGAAAAAC TTGCCGCCACCCCCCGACACTGATGCCAGGGAGGTGGGAGGAAGAAGTGGGAAA TTTCCCTTCCCAGTACCCCCAAGAACGTCTGAGCCTTCAATGTTGAATTTTTTCTT TATTAAAATTACTTTTATCTTATAAAATCAACTAATCAAAAATGATATAGACGAC AGCACTGGCTCTGTGAAGGTGGCATCTTTCTGGGCAGGCAGGCCATGGGGCATG GAGGAGGGTGCAAAGATATGGGTTGCTGTCTTCTGGCCTCCAGCTGCATGGAGG CCGGCCCAGGGTCTAGGGTGTGCACTGGGCAAGGGCAGGGCGGCAGGTGTCAGG CCGGCTTGGACAATGAAACCCTGACCTTGCTGCATTCCTTTTGCTTCCACCACCAC TAGCTTCTTTGGAATCTTGGGGTGGGGGTCATCTTTGGGGATTATGGCTGCCACC CGGGATTTGAGTGTAGGGAGTGTGGGAGCAGCCTTGGCAGATGGGGCACCCGTG CCCTGCAGGTGTTGACAAGATCCGCCATCTGTAATGTCCTTGGCACAATAAAACC AAATGTCAGTTTCAAAAAAAAAAAAAAAAAAA (SEQ ID NO: 100).

The amino acid sequence of human DUBA polypeptide is: MTILPKKKPPPPDADPANEPPPPGPMPPAPRRGGGVGVGGGGTGVGGGDRDRDSGV VGARPRASPPPQGPLPGPPGALHRWALAVPPGAVAGPRPQQASPPPCGGPGGPGGGP GDALGAAAAGVGAAGVVVGVGGAVGVGGCCSGPGHSKRRRQAPGVGAVGGGSPE REEVGAGYNSEDEYEAAAARIEAMDPATVEQQEHWFEKALRDKKGFIIKQMKEDG ACLFRAVADQ VYGDQDMHEVVRKHCMD YLMKNAD YFSNYVTEDFTTYINRKRKN NCHGNHIEMQAMAEMYNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSYHRNI HYNSVVNPNKATIGVGLGLPSFKPGFAEQSLMKNAIKTSEESWIEQQMLEDKKRATD WEATNEAIEEQVARESYLQWLRDQEKQARQVRGPSQPRKASATCSSATAAASSGLE EWTSRSPRQRSSASSPEHPELHAELGMKPPSPGTVLALAKPPSPCAPGTSSQFSAGAD RATSPLVSLYPALECRALIQQMSPSAFGLNDWDDDEILASVLAVSQQEYLDSMKKNK VHRDPPPDKS (SEQ ID NO: 101).

The term "aptamer" refers to a nucleic acid molecule that is capable of binding to a target molecule, such as a polypeptide. For example, an aptamer of the invention can specifically bind to a DUBA polypeptide, or to a molecule in a signaling pathway that modulates the expression of DUBA. The generation and therapeutic use of aptamers are well established in the art. See, e.g., U.S. Pat. No. 5,475,096, and the therapeutic efficacy of Macugen® (Eyetech, New York) for treating age-related macular degeneration.

The terms "DUBA antagonist" and "antagonist of DUBA activity or DUBA expression" are used interchangeably and refer to a compound that interferes with the normal functioning of DUBA, either by decreasing transcription or translation of DUBA-encoding nucleic acid, or by inhibiting or blocking DUBA polypeptide activity, or both. Examples of DUBA antagonists include, but are not limited to, antisense polynucleotides, interfering RNAs (including, but not limited to, the anti-DUBA siRNAs set forth in SEQ ID NOs: 36, 50, 64, and 78), catalytic RNAs, RNA-DNA chimeras, DUBA-specific aptamers, anti-DUBA antibodies, DUBA-binding fragments of anti-DUBA antibodies, DUBA-binding small molecules, DUBA-binding peptides, and other polypeptides that specifically bind DUBA (including, but not limited to, DUBA-binding fragments of one or more DUBA ligands, optionally fused to one or more additional domains (e.g., TRAF3-Fc)), such that the interaction between the DUBA antagonist and DUBA results in a reduction or cessation of DUBA activity or expression.

The terms "DUBA agonist" and "agonist of DUBA activity or DUBA expression" are used interchangeably and refer to a compound that enhances or stimulates the normal functioning of DUBA, by increasing transcription or translation of DUBA-encoding nucleic acid, and/or by inhibiting or blocking activity of a molecule that inhibits DUBA expression or DUBA activity, and/or by enhancing normal DUBA activity (including, but not limited to, enhancing the stability of DUBA or enhancing binding of DUBA to one or more target ligands). For example, the DUBA agonist can be selected from an antibody, an antigen- binding fragment, an aptamer, an interfering RNA, a small molecule, a peptide, an antisense molecule, and another binding polypeptide. In another example, the DUBA agonist can be a polynucleotide selected from an aptamer, interfering RNA, or antisense molecule that interferes with the transcription and/or translation of a DUB A-inhibitory molecule.

The term "small molecule" is defined herein as an organic or inorganic molecule having a molecular weight below about 1000 Daltons. In certain embodiments, a small molecule has a molecular weight below about 500 Daltons. Small molecules can be nucleic acids, peptides, polypeptides, peptidomimetics, carbohydrates, lipids or other organic or inorganic molecules.

An "isolated" or "purified" peptide, polypeptide, antibody, or biologically active fragment thereof is separated and/or recovered from a component of its natural environment. Contaminant components include materials that would typically interfere with diagnostic or therapeutic uses for the polypeptide, and may include enzymes, hormones, and other proteinaceous or non-proteinaceous materials. Preparations having preferably less than 30% by dry weight of non-desired contaminating material (contaminants), preferably less than 20%, 10%, and preferably less than 5% contaminants are considered to be substantially isolated. An isolated, recombinantly-produced peptide/polypeptide or biologically active portion thereof is preferably substantially free of culture medium, i.e., culture medium represents preferably less than 20%, preferably less than about 10%, and preferably less than about 5% of the volume of a peptide/polypeptide preparation. Examples of contaminants include cell debris, culture media, and substances used and produced during in vitro synthesis of the peptide/polypeptide. In one embodiment, the polypeptide will be purified (1) to greater than 95% by weight as determined by, for example, the Lowry method, and in some embodiments more than 99% by weight, (2) to a degree sufficient to obtain at least 15 residues of N-terminal or internal amino acid sequence by use of, for example, a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under reducing or nonreducing conditions using, for example, Coomassie blue or silver stain. Isolated polypeptide includes the polypeptide in situ within recombinant cells since at least one component of the polypeptide's natural environment will not be present. Ordinarily, however, isolated polypeptide will be prepared by at least one purification step. As used herein, the term "anti-DUBA antibody" refers to an antibody that is capable of specifically binding to DUBA.

The phrase "substantially similar," "substantially the same", "equivalent", or "substantially equivalent", as used herein, denotes a sufficiently high degree of similarity between two numeric values (for example, one associated with a molecule and the other associated with a reference/comparator molecule) such that one of skill in the art would consider the difference between the two values to be of little or no biological and/or statistical significance within the context of the biological characteristic measured by said values (e.g., Kd values). The difference between said two values is, for example, less than about 50%, less than about 40%, less than about 30%, less than about 20%, and/or less than about 10% as a function of the value for the reference/comparator molecule.

The phrase "substantially reduced," or "substantially different", as used herein, denotes a sufficiently high degree of difference between two numeric values (generally one associated with a molecule and the other associated with a reference/comparator molecule) such that one of skill in the art would consider the difference between the two values to be of statistical significance within the context of the biological characteristic measured by said values (e.g., Kd values). The difference between said two values is, for example, greater than about 10%, greater than about 20%, greater than about 30%, greater than about 40%, and/or greater than about 50% as a function of the value for the reference/comparator molecule. "Binding affinity" generally refers to the strength of the sum total of noncovalent interactions between a single binding site of a molecule (e.g., an antibody) and its binding partner (e.g., an antigen). Unless indicated otherwise, as used herein, "binding affinity" refers to intrinsic binding affinity which reflects a 1:1 interaction between members of a binding pair (e.g., antibody and antigen). The affinity of a molecule X for its partner Y can generally be represented by the dissociation constant (Kd). Affinity can be measured by common methods known in the art, including those described herein. Low-affinity antibodies generally bind antigen slowly and tend to dissociate readily, whereas high-affinity antibodies generally bind antigen faster and tend to remain bound longer. A variety of methods of measuring binding affinity are known in the art, any of which can be used for purposes of the present invention. Specific illustrative embodiments are described in the following.

In one embodiment, the "Kd" or "Kd value" according to this invention is measured by a radiolabeled antigen binding assay (RIA) performed with the Fab version of an antibody of interest and its antigen as described by the following assay. Solution binding affinity of

Fabs for antigen is measured by equilibrating Fab with a minimal concentration of (125 j)_ labeled antigen in the presence of a titration series of unlabeled antigen, then capturing bound antigen with an anti-Fab antibody-coated plate (Chen, et al, (1999) J MoI Biol 293:865-881). To establish conditions for the assay, microtiter plates (as one example, those available from Dynex) are coated overnight with 5 μg/ml of a capturing anti-Fab antibody (Cappel Labs) in 50 mM sodium carbonate (pH 9.6), and subsequently blocked with 2% (w/v) bovine serum albumin in PBS for two to five hours at room temperature (approximately 23°C). In a non- adsorbent plate (Nunc #269620), 100 pM or 26 pM [125j]__antig_{en are m}i_xed _wlth serial dilutions of a Fab of interest (e.g., consistent with assessment of an anti-VEGF antibody, Fab- 12, in Presta et al., (1997) Cancer Res. 57:4593-4599). The Fab of interest is then incubated overnight; however, the incubation may continue for a longer period (e.g., 65 hours) to insure that equilibrium is reached. Thereafter, the mixtures are transferred to the capture plate for incubation at room temperature (e.g., for one hour). The solution is then removed and the plate washed eight times with 0.1% Tween-20 in PBS. When the plates have dried, 150 μl/well of scintillant (MicroScint-20; Packard) is added, and the plates are counted on a Topcount gamma counter (Packard) for ten minutes. Concentrations of each Fab that give less than or equal to 20% of maximal binding are chosen for use in competitive binding assays. According to another embodiment the Kd or Kd value is measured by using surface plasmon resonance assays using a BIAcoreTM_2000 or a BIAcoreTM.βQOO (BIAcore, Inc., Piscataway, NJ) at 25°C with immobilized antigen CM5 chips at ~10 response units (RU). Briefly, carboxymethylated dextran biosensor chips (CM5, BIAcore Inc.) are activated with N-ethyl-N'- (3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) and N- hydroxysuccinimide (NHS) according to the supplier's instructions. Antigen is diluted with 10 mM sodium acetate, pH 4.8, to 5 μg/ml (~0.2 μM) before injection at a flow rate of 5 μl/minute to achieve approximately 10 response units (RU) of coupled protein. Following the injection of antigen, 1 M ethanolamine is injected to block unreacted groups. For kinetics measurements, two-fold serial dilutions of Fab (0.78 nM to 500 nM) are injected in PBS with 0.05% Tween 20 (PBST) at 25°C at a flow rate of approximately 25 μl/min. Association rates (k_on) and dissociation rates (k_off) are calculated using a simple one-to-one Langmuir binding model (see, for example, BIAcore Evaluation Software version 3.2) by simultaneously fitting the association and dissociation sensorgrams. The equilibrium dissociation constant (Kd) is calculated as the ratio koff^^on. S^ee _> ^e-8-_> Chen, Y., et al.,

(1999) J MoI Biol 293:865-881. If the on-rate exceeds 10⁶ M"¹ s"¹ by the surface plasmon resonance assay above, then the on-rate can be determined by using a fluorescent quenching technique that measures the increase or decrease in fluorescence emission intensity

(excitation = 295 nm; emission = 340 nm, 16 nm band-pass) at 25⁰C of a 20 nM anti-antigen antibody (Fab form) in PBS, pH 7.2, in the presence of increasing concentrations of antigen as measured in a spectrometer, such as a stop-flow equipped spectrophometer (Aviv Instruments) or a 8000-series SLM-Aminco spectrophotometer (ThermoSpectronic) with a stirred cuvette.

An "on-rate" or "rate of association" or "association rate" or "k_on" according to this invention can also be determined with the same surface plasmon resonance technique described above using a BIAcore™-2000 or a BIAcore™-3000 (BIAcore, Inc., Piscataway, NJ) at 25°C with immobilized antigen CM5 chips at ~10 response units (RU). Briefly, carboxymethylated dextran biosensor chips (CM5, BIAcore Inc.) are activated with N-ethyl-N'- (3-dimethylaminopropyl)-carbodiimide hydrochloride (EDC) and N- hydroxysuccinimide (NHS) according to the supplier's instructions. Antigen is diluted with 10 mM sodium acetate, pH 4.8, to 5 μg/ml (~0.2 μM) before injection at a flow rate of 5 μl/minute to achieve approximately 10 response units (RU) of coupled protein. Following the injection of antigen, IM ethanolamine is injected to block unreacted groups. For kinetics measurements, two-fold serial dilutions of Fab (0.78 nM to 500 nM) are injected in PBS with 0.05% Tween 20 (PBST) at 25°C at a flow rate of approximately 25 μl/min. Association rates (k_on) and dissociation rates (k_off) are calculated using a simple one-to-one Langmuir binding model (BIAcore Evaluation Software version 3.2) by simultaneously fitting the association and dissociation sensorgram. The equilibrium dissociation constant (Kd) was calculated as the ratio k_off/k_on See, e.g., Chen, Y., et al., (1999) J. MoI Biol 293:865-881.

However, if the on-rate exceeds 10^ M^~l s^~l by the surface plasmon resonance assay above, then the on-rate can be determined by using a fluorescent quenching technique that measures the increase or decrease in fluorescence emission intensity (excitation = 295 nm; emission =

340 nm, 16 nm band-pass) at 25⁰C of a 20 nM anti-antigen antibody (Fab form) in PBS, pH 7.2, in the presence of increasing concentrations of antigen as measured in a spectrometer, such as a stop-flow equipped spectrophometer (Aviv Instruments) or a 8000-series SLM- Aminco spectrophotometer (ThermoSpectronic) with a stirred cuvette.

The term "vector," as used herein, is intended to refer to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. One type of vector is a "plasmid", which refers to a circular double stranded DNA loop into which additional DNA segments may be ligated. Another type of vector is a phage vector. Another type of vector is a viral vector, wherein additional DNA segments may be ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) can be integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome. Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as "recombinant expression vectors" (or simply, "recombinant vectors"). In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, "plasmid" and "vector" may be used interchangeably as the plasmid is the most commonly used form of vector.

"Polynucleotide," or "nucleic acid," as used interchangeably herein, refer to polymers of nucleotides of any length, and include DNA and RNA. The nucleotides can be deoxyribonucleotides, ribonucleotides, modified nucleotides or bases, and/or their analogs, or any substrate that can be incorporated into a polymer by DNA or RNA polymerase, or by a synthetic reaction. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and their analogs. If present, modification to the nucleotide structure may be imparted before or after assembly of the polymer. The sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may be further modified after synthesis, such as by conjugation with a label. Other types of modifications include, for example, "caps," substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoamidates, carbamates, etc.) and with charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.), those containing pendant moieties, such as, for example, proteins (e.g., nucleases, toxins, antibodies, signal peptides, ply-L-lysine, etc.), those with intercalators (e.g., acridine, psoralen, etc.), those containing chelators (e.g., metals, radioactive metals, boron, oxidative metals, etc.), those containing alkylators, those with modified linkages (e.g., alpha anomeric nucleic acids, etc.), as well as unmodified forms of the polynucleotides(s). Further, any of the hydroxyl groups ordinarily present in the sugars may be replaced, for example, by phosphonate groups, phosphate groups, protected by standard protecting groups, or activated to prepare additional linkages to additional nucleotides, or may be conjugated to solid or semi-solid supports. The 5 ' and 3 ' terminal OH can be phosphorylated or substituted with amines or organic capping group moieties of from 1 to 20 carbon atoms. Other hydroxyls may also be derivatized to standard protecting groups. Polynucleotides can also contain analogous forms of ribose or deoxyribose sugars that are generally known in the art, including, for example, 2'-O-methyl-, 2'-O-allyl, 2'-fluoro- or 2'-azido-ribose, carbocyclic sugar analogs, α-anomeric sugars, epimeric sugars such as arabinose, xyloses or lyxoses, pyranose sugars, furanose sugars, sedoheptuloses, acyclic analogs and basic nucleoside analogs such as methyl riboside. One or more phosphodiester linkages may be replaced by alternative linking groups. These alternative linking groups include, but are not limited to, embodiments wherein phosphate is replaced by P(O)S ("thioate"), P(S)S ("dithioate"), "(O)NR₂ ("amidate"), P(O)R, P(O)OR', CO or CH2 ("formacetal"), in which each R or R' is independently H or substituted or unsubstituted alkyl (1-20 C) optionally containing an ether (-O-) linkage, aryl, alkenyl, cycloalkyl, cycloalkenyl or araldyl. Not all linkages in a polynucleotide need be identical. The preceding description applies to all polynucleotides referred to herein, including RNA and DNA.

"Oligonucleotide," as used herein, generally refers to short, generally single-stranded, generally synthetic polynucleotides that are generally, but not necessarily, less than about 200 nucleotides in length. The terms "oligonucleotide" and "polynucleotide" are not mutually exclusive. The description above for polynucleotides is equally and fully applicable to oligonucleotides.

"Antibodies" (Abs) and "immunoglobulins" (Igs) are glycoproteins having the same structural characteristics. While antibodies exhibit binding specificity to a specific antigen, immunoglobulins include both antibodies and other antibody-like molecules which generally lack antigen specificity. Polypeptides of the latter kind are, for example, produced at low levels by the lymph system and at increased levels by myelomas. The terms "antibody" and "immunoglobulin" are used interchangeably in the broadest sense and include monoclonal antibodies (e.g., full length or intact monoclonal antibodies), polyclonal antibodies, monovalent, multivalent antibodies, multispecific antibodies (e.g., bispecific antibodies so long as they exhibit the desired biological activity) and may also include certain antibody fragments (as described in greater detail herein). An antibody can be chimeric, human, humanized and/or affinity matured.

The "variable region" or "variable domain" of an antibody refers to the amino- terminal domains of heavy or light chain of the antibody. These domains are generally the most variable parts of an antibody and contain the antigen-binding sites. The term "variable" refers to the fact that certain portions of the variable domains differ extensively in sequence among antibodies and are used in the binding and specificity of each particular antibody for its particular antigen. However, the variability is not evenly distributed throughout the variable domains of antibodies. It is concentrated in three segments called complementarity-determining regions (CDRs) or hypervariable regions both in the light-chain and the heavy-chain variable domains. The more highly conserved portions of variable domains are called the framework (FR). The variable domains of native heavy and light chains each comprise four FR regions, largely adopting a beta-sheet configuration, connected by three CDRs, which form loops connecting, and in some cases forming part of, the beta-sheet structure. The CDRs in each chain are held together in close proximity by the FR regions and, with the CDRs from the other chain, contribute to the formation of the antigen-binding site of antibodies (see Kabat et al., Sequences of Proteins of Immunological Interest, Fifth Edition, National Institute of Health, Bethesda, MD (1991)). The constant domains are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody-dependent cellular toxicity.

Papain digestion of antibodies produces two identical antigen-binding fragments, called "Fab" fragments, each with a single antigen-binding site, and a residual "Fc" fragment, whose name reflects its ability to crystallize readily. Pepsin treatment yields an F(ab')₂ fragment that has two antigen-combining sites and is still capable of cross-linking antigen. "Fv" is the minimum antibody fragment which contains a complete antigen- recognition and -binding site. In a two-chain Fv species, this region consists of a dimer of one heavy- and one light-chain variable domain in tight, non-covalent association. In a single-chain Fv species, one heavy- and one light-chain variable domain can be covalently linked by a flexible peptide linker such that the light and heavy chains can associate in a "dimeric" structure analogous to that in a two-chain Fv species. It is in this configuration that the three CDRs of each variable domain interact to define an antigen-binding site on the surface of the VH-VL dimer. Collectively, the six CDRs confer antigen-binding specificity to the antibody. However, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) has the ability to recognize and bind antigen, although at a lower affinity than the entire binding site.

The Fab fragment also contains the constant domain of the light chain and the first constant domain (CHl) of the heavy chain. Fab' fragments differ from Fab fragments by the addition of a few residues at the carboxy terminus of the heavy chain CHl domain including one or more cysteines from the antibody hinge region. Fab '-SH is the designation herein for Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group. F(ab')₂ antibody fragments originally were produced as pairs of Fab' fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments are also known. The "light chains" of antibodies (immunoglobulins) from any vertebrate species can be assigned to one of two clearly distinct types, called kappa (K) and lambda (λ), based on the amino acid sequences of their constant domains.

Depending on the amino acid sequences of the constant domains of their heavy chains, antibodies (immunoglobulins) can be assigned to different classes. There are five major classes of immunoglobulins: IgA, IgD, IgE, IgG and IgM, and several of these may be further divided into subclasses (isotypes), e.g., IgG₁, IgG₂, IgG₃, IgG₄, IgA₁, and IgA₂ . The heavy chain constant domains that correspond to the different classes of immunoglobulins are called α, δ, ε, γ, and μ, respectively. The subunit structures and three-dimensional configurations of different classes of immunoglobulins are well known and described generally in, for example, Abbas et al. Cellular and MoI. Immunology, 4th ed. (2000). An antibody may be part of a larger fusion molecule, formed by covalent or non-covalent association of the antibody with one or more other proteins or peptides.

The terms "full length antibody," "intact antibody" and "whole antibody" are used herein interchangeably, to refer to an antibody in its substantially intact form, not antibody fragments as defined below. The terms particularly refer to an antibody with heavy chains that contain the Fc region.

"Antibody fragments" comprise only a portion of an intact antibody, wherein the portion retains at least one, and as many as most or all, of the functions normally associated with that portion when present in an intact antibody. In one embodiment, an antibody fragment comprises an antigen binding site of the intact antibody and thus retains the ability to bind antigen. In another embodiment, an antibody fragment, for example one that comprises the Fc region, retains at least one of the biological functions normally associated with the Fc region when present in an intact antibody, such as FcRn binding, antibody half life modulation, ADCC function and complement binding. In one embodiment, an antibody fragment is a monovalent antibody that has an in vivo half life substantially similar to an intact antibody. For example, such an antibody fragment may comprise on antigen binding arm linked to an Fc sequence capable of conferring in vivo stability to the fragment.

The term "monoclonal antibody" as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Thus, the modifier "monoclonal" indicates the character of the antibody as not being a mixture of discrete antibodies. Such monoclonal antibody typically includes an antibody comprising a polypeptide sequence that binds a target, wherein the target-binding polypeptide sequence was obtained by a process that includes the selection of a single target binding polypeptide sequence from a plurality of polypeptide sequences. For example, the selection process can be the selection of a unique clone from a plurality of clones, such as a pool of hybridoma clones, phage clones or recombinant DNA clones. It should be understood that the selected target binding sequence can be further altered, for example, to improve affinity for the target, to humanize the target binding sequence, to improve its production in cell culture, to reduce its immunogenicity in vivo, to create a multispecific antibody, etc., and that an antibody comprising the altered target binding sequence is also a monoclonal antibody of this invention. In contrast to polyclonal antibody preparations which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody of a monoclonal antibody preparation is directed against a single determinant on an antigen. In addition to their specificity, the monoclonal antibody preparations are advantageous in that they are typically uncontaminated by other immunoglobulins. The modifier "monoclonal" indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, the monoclonal antibodies to be used in accordance with the present invention may be made by a variety of techniques, including, for example, the hybridoma method (e.g., Kohler et al., Nature, 256: 495 (1975); Harlow et al., Antibodies: A Laboratory Manual, (Cold Spring Harbor Laboratory Press, 2^nd ed. 1988); Hammerling et al., in: Monoclonal Antibodies and T-CeIl hybridomas 563-681 (Elsevier, N.Y., 1981)), recombinant DNA methods (see, e.g., U.S. Patent No. 4,816,567), phage display technologies (See, e.g., Clackson et al, Nature, 352: 624-628 (1991); Marks et al, J. MoI. Biol. 222: 581-597 (1992); Sidhu et al., J. MoI. Biol. 338(2): 299-310 (2004); Lee et al., J. MoI. Biol. 340(5): 1073-1093 (2004); Fellouse, Proc. Natl. Acad. Sci. USA 101(34): 12467-12472 (2004); and Lee et al., J. Immunol. Methods 284(1-2): 119-132(2004), and technologies for producing human or human-like antibodies in animals that have parts or all of the human immunoglobulin loci or genes encoding human immunoglobulin sequences (see, e.g., WO98/24893; WO96/34096; WO96/33735; WO91/10741; Jakobovits et al., Proc. Natl. Acad. Sci. USA 90: 2551 (1993); Jakobovits et al., Nature 362: 255-258 (1993); Bruggemann et al., Year in Immunol. 7:33 (1993); U.S. Patent Nos. 5,545,807; 5,545,806; 5,569,825; 5,625,126; 5,633,425; 5,661,016; Marks et al., Bio/Technology 10: 779-783 (1992); Lonberg et al., Nature 368: 856-859 (1994); Morrison, Nature 368: 812-813 (1994); Fishwild et al., Nature Biotechnol. 14: 845- 851 (1996); Neuberger, Nature Biotechnol. 14: 826 (1996) and Lonberg and Huszar, Intern. Rev. Immunol. 13: 65-93 (1995).

The monoclonal antibodies herein specifically include "chimeric" antibodies in which a portion of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (U.S. Patent No. 4,816,567; and Morrison et al, Proc. Natl. Acad. Sci. USA 81:6851-6855 (1984)).

"Humanized" forms of non-human {e.g., murine) antibodies are chimeric antibodies that contain minimal sequence derived from non-human immunoglobulin. In one embodiment, a humanized antibody is a human immunoglobulin (recipient antibody) in which residues from a hypervariable region of the recipient are replaced by residues from a hypervariable region of a non-human species (donor antibody) such as mouse, rat, rabbit or nonhuman primate having the desired specificity, affinity, and/or capacity. In some instances, framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues. Furthermore, humanized antibodies may comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance. In general, the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the hypervariable loops correspond to those of a non- human immunoglobulin and all or substantially all of the FRs are those of a human immunoglobulin sequence. The humanized antibody optionally will also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. For further details, see Jones et al, Nature 321:522-525 (1986);

Riechmann et al, Nature 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol. 2:593-596 (1992). See also the following review articles and references cited therein: Vaswani and Hamilton, Ann. Allergy, Asthma & Immunol. 1:105-115 (1998); Harris, Biochem. Soc. Transactions 23:1035-1038 (1995); Hurle and Gross, Curr. Op. Biotech. 5:428-433 (1994). The term "hypervariable region", "HVR", or "HV", when used herein refers to the regions of an antibody variable domain which are hypervariable in sequence and/or form structurally defined loops. Generally, antibodies comprise six hypervariable regions; three in the VH (Hl, H2, H3), and three in the VL (Ll, L2, L3). A number of hypervariable region delineations are in use and are encompassed herein. The Kabat Complementarity Determining Regions (CDRs) are based on sequence variability and are the most commonly used (Kabat et al, Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, MD. (1991)). The letters "HC" and "LC" preceding the term "CDR" refer, respectively, to a CDR of a heavy chain and a light chain. Chothia refers instead to the location of the structural loops (Chothia and Lesk J. MoI Biol. 196:901-917 (1987)). The AbM hypervariable regions represent a compromise between the Kabat CDRs and Chothia structural loops, and are used by Oxford Molecular's AbM antibody modeling software. The "contact" hypervariable regions are based on an analysis of the available complex crystal structures. The residues from each of these hypervariable regions are noted below.

Loop Kabat AbM Chothia Contact

Ll L24-L34 L24-L34 L26-L32 L30-L36

L2 L50-L56 L50-L56 L50-L52 L46-L55

L3 L89-L97 L89-L97 L91-L96 L89-L96 Hl H31-H35B H26-H35B H26-H32 H30-H35B

(Kabat Numbering)

Hl H31-H35 H26-H35 H26-H32 H30-H35

(Chothia Numbering) H2 H50-H65 H50-H58 H53-H55 H47-H58 H3 H95-H102 H95-H102 H96-H101 H93-H101

Hypervariable regions may comprise "extended hypervariable regions" as follows: 24-36 or 24-34 (Ll), 46-56 or 50-56 (L2) and 89-97 or 89-96 (L3) in the VL and 26-35 (Hl), 50-65 or 49-65 (H2) and 93-102, 94-102, or 95-102 (H3) in the VH. The variable domain residues are numbered according to Kabat et al, supra, for each of these definitions.

"Framework" or "FR" residues are those variable domain residues other than the hypervariable region residues as herein defined. The term "variable domain residue numbering as in Kabat" or "amino acid position numbering as in Kabat," and variations thereof, refers to the numbering system used for heavy chain variable domains or light chain variable domains of the compilation of antibodies in Kabat et al., Sequences of Proteins of Immunological Interest, 5^th Ed. Public Health Service, National Institutes of Health, Bethesda, MD (1991). Using this numbering system, the actual linear amino acid sequence may contain fewer or additional amino acids corresponding to a shortening of, or insertion into, a FR or HVR of the variable domain. For example, a heavy chain variable domain may include a single amino acid insert (residue 52a according to Kabat) after residue 52 of H2 and inserted residues (e.g. residues 82a, 82b, and 82c, etc. according to Kabat) after heavy chain FR residue 82. The Kabat numbering of residues may be determined for a given antibody by alignment at regions of homology of the sequence of the antibody with a "standard" Kabat numbered sequence.

"Single-chain Fv" or "scFv" antibody fragments comprise the VH and VL domains of antibody, wherein these domains are present in a single polypeptide chain. Generally, the scFv polypeptide further comprises a polypeptide linker between the VH and VL domains which enables the scFv to form the desired structure for antigen binding. For a review of scFv see Pluckthun, in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds., Springer-Verlag, New York, pp. 269-315 (1994).

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; WO93/1161; and Hollinger et al., Proc. Natl. Acad. Sci. USA 90: 6444-6448 (1993). A "human antibody" is one which possesses an amino acid sequence which corresponds to that of an antibody produced by a human and/or has been made using any of the techniques for making human antibodies as disclosed herein. This definition of a human antibody specifically excludes a humanized antibody comprising non-human antigen-binding residues.

An "affinity matured" antibody is one with one or more alterations in one or more HVRs thereof which result in an improvement in the affinity of the antibody for antigen, compared to a parent antibody which does not possess those alteration(s). In one embodiment, an affinity matured antibody has nanomolar or even picomolar affinities for the target antigen. Affinity matured antibodies are produced by procedures known in the art.

Marks et al Bio/Technology 10:779-783 (1992) describes affinity maturation by VH and VL domain shuffling. Random mutagenesis of CDR and/or framework residues is described by: Barbas et al Proc Nat. Acad. ScL USA 91:3809-3813 (1994); Schier et al Gene 169:147-155 (1995); Yelton et al J. Immunol 155:1994-2004 (1995); Jackson et al, J. Immunol 154(7):3310-9 (1995); and Hawkins et al, J. MoI Biol 226:889-896 (1992).

A "blocking" antibody or an "antagonist" antibody is one which inhibits or reduces biological activity of the antigen it binds. Certain blocking antibodies or antagonist antibodies substantially or completely inhibit the biological activity of the antigen.

An "agonist antibody", as used herein, is an antibody which mimics at least one of the functional activities of a polypeptide of interest.

A "disorder" is any condition that would benefit from treatment with an antibody of the invention. This includes chronic and acute disorders or diseases including those pathological conditions which predispose the mammal to the disorder in question. Non- limiting examples of disorders to be treated herein include infection, cell proliferative disorders, immune/inflammatory disorders (including, but not limited to autoimmune disorders), and other interferon-related disorders.

The term "infection" refers to diseases caused by one or more other organisms invading or impinging upon the normal physiology of the mammal having the infection. Examples of infections include, but are not limited to, viral infections, bacterial infections, parasitic infections (e.g., infections caused by worms and nematodes), and fungal infections. The terms "cell proliferative disorder" and "proliferative disorder" refer to disorders that are associated with some degree of abnormal cell proliferation. In one embodiment, the cell proliferative disorder is cancer. The terms "cancer" and "cancerous" refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth/proliferation and, e.g., tumor formation. Examples of cancer include, but are not limited to, carcinoma, lymphoma (e.g., Hodgkin's and non-Hodgkin's lymphoma), blastoma, sarcoma, and leukemia. More particular examples of such cancers include squamous cell cancer, small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung, squamous carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastrointestinal cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, colorectal cancer, endometrial or uterine carcinoma, salivary gland carcinoma, kidney cancer, liver cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma, leukemia and other lymphoproliferative disorders, and various types of head and neck cancer. Cell proliferative disorders also include, but are not limited to, pre-leukemic disorders, such as myelodysplastic syndromes (MDS).

"Tumor," as used herein, refers to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues. The terms "cancer," "cancerous," "cell proliferative disorder," "proliferative disorder" and "tumor" are not mutually exclusive as referred to herein.

The term "interferon-related disorder" refers to or describes a disorder that is typically characterized by or contributed to by aberrant amounts or activities of one or more interferons. The terms "inflammatory disorder" and "immune disorder" refer to or describe disorders caused by aberrant immunologic mechanisms and/or aberrant cytokine signaling (e.g., aberrant interferon signaling). Examples of inflammatory and immune disorders include, but are not limited to, autoimmune diseases, immunologic deficiency syndromes, and hypersensitivity. An "autoimmune disease" herein is a non-malignant disease or disorder arising from and directed against an individual's own tissues. The autoimmune diseases herein specifically exclude malignant or cancerous diseases or conditions, especially excluding B cell lymphoma, acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), Hairy cell leukemia and chronic myeloblasts leukemia. Examples of autoimmune diseases or disorders include, but are not limited to, inflammatory responses such as inflammatory skin diseases including psoriasis and dermatitis (e.g. atopic dermatitis); systemic scleroderma and sclerosis; responses associated with inflammatory bowel disease (such as Crohn's disease and ulcerative colitis); respiratory distress syndrome (including adult respiratory distress syndrome; ARDS); dermatitis; meningitis; encephalitis; uveitis; colitis; glomerulonephritis; allergic conditions such as eczema and asthma and other conditions involving infiltration of T cells and chronic inflammatory responses; atherosclerosis; leukocyte adhesion deficiency; rheumatoid arthritis; systemic lupus erythematosus (SLE) (including but not limited to lupus nephritis, cutaneous lupus); diabetes mellitus (e.g. Type I diabetes mellitus or insulin dependent diabetes mellitus); multiple sclerosis; Reynaud's syndrome; autoimmune thyroiditis; Hashimoto's thyroiditis; allergic encephalomyelitis;

Sjogren's syndrome; juvenile onset diabetes; and immune responses associated with acute and delayed hypersensitivity mediated by cytokines and T-lymphocytes typically found in tuberculosis, sarcoidosis, polymyositis, granulomatosis and vasculitis; pernicious anemia (Addison's disease); diseases involving leukocyte diapedesis; central nervous system (CNS) inflammatory disorder; multiple organ injury syndrome; hemolytic anemia (including, but not limited to cryoglobinemia or Coombs positive anemia) ; myasthenia gravis; antigen-antibody complex mediated diseases; anti-glomerular basement membrane disease; antiphospholipid syndrome; allergic neuritis; Graves' disease; Lambert-Eaton myasthenic syndrome; pemphigoid bullous; pemphigus; autoimmune polyendocrinopathies; Reiter's disease; stiff- man syndrome; Behcet disease; giant cell arteritis; immune complex nephritis; IgA nephropathy; IgM polyneuropathies; immune thrombocytopenic purpura (ITP) or autoimmune thrombocytopenia, etc.

Examples of immunologic deficiency syndromes include, but are not limited to, ataxia telangiectasia, leukocyte-adhesion deficiency syndrome, lymphopenia, dysgammaglobulinemia, HIV or deltaretrovirus infections, common variable immunodeficiency, severe combined immunodeficiency, phagocyte bactericidal dysfunction, agammaglobulinemia, DiGeorge syndrome, and Wiskott-Aldrich syndrome. Examples of hypersensitivity include, but are not limited to, allergies, asthma, dermatitis, hives, anaphylaxis, Wissler's syndrome, and thrombocytopenic purpura. As used herein, "treatment" refers to clinical intervention in an attempt to alter the natural course of the individual or cell being treated, and can be performed either for prophylaxis or during the course of clinical pathology. Desirable effects of treatment include preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing or decreasing inflammation and/or tissue/organ damage, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis. In some embodiments, treatments of the invention are used to delay development of a disease or disorder. An "individual" is a vertebrate. In certain embodiments, the vertebrate is a mammal. Mammals include, but are not limited to, farm animals (such as cows), sport animals, pets (such as cats, dogs, and horses), primates, mice and rats. In certain embodiments, the vertebrate is a human. "Mammal" for purposes of treatment refers to any animal classified as a mammal, including humans, domestic and farm animals, and zoo, sports, or pet animals, such as dogs, horses, cats, cows, etc. In certain embodiments, the mammal is human.

An "effective amount" refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired therapeutic or prophylactic result. A "therapeutically effective amount" of a substance/molecule of the invention may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the substance/molecule, to elicit a desired response in the individual. A therapeutically effective amount is also one in which any toxic or detrimental effects of the substance/molecule are outweighed by the therapeutically beneficial effects. A "prophylactically effective amount" refers to an amount effective, at dosages and for periods of time necessary, to achieve the desired prophylactic result. Typically but not necessarily, since a prophylactic dose is used in subjects prior to or at an earlier stage of disease, the prophylactically effective amount would be less than the therapeutically effective amount.

The term "cytotoxic agent" as used herein refers to a substance that inhibits or prevents the function of cells and/or causes destruction of cells. The term is intended to include radioactive isotopes (e.g., At²¹¹, 1¹³¹, 1¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³, Bi²¹², P³², Pb²¹² and radioactive isotopes of Lu), chemotherapeutic agents (e.g., methotrexate, adriamicin, vinca alkaloids (vincristine, vinblastine, etoposide), doxorubicin, melphalan, mitomycin C, chlorambucil, daunorubicin or other intercalating agents, enzymes and fragments thereof such as nucleolytic enzymes, antibiotics, and toxins such as small molecule toxins or enzymatically active toxins of bacterial, fungal, plant or animal origin, including fragments and/or variants thereof, and the various antitumor or anticancer agents disclosed below. Other cytotoxic agents are described below. A tumoricidal agent causes destruction of tumor cells. A "chemotherapeutic agent" is a chemical compound useful in the treatment of cancer. Examples of chemotherapeutic agents include alkylating agents such as thiotepa and CYTOXAN® cyclosphosphamide; alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); delta-9-tetrahydrocannabinol (dronabinol, MARINOL®); beta-lapachone; lapachol; colchicines; betulinic acid; a camptothecin (including the synthetic analogue topotecan (HYCAMTIN®), CPT-11 (irinotecan, CAMPTOSAR®), acetylcamptothecin, scopolectin, and 9-aminocamptothecin); bryostatin; callystatin; CC- 1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); podophyllotoxin; podophyllinic acid; teniposide; cryptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CBl-TMl); eleutherobin; pancratistatin; a sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine; antibiotics such as the enediyne antibiotics (e. g., calicheamicin, especially calicheamicin gammall and calicheamicin omegall (see, e.g., Agnew, Chem Intl. Ed. Engl., 33: 183-186 (1994)); dynemicin, including dynemicin A; an esperamicin; as well as neocarzinostatin chromophore and related chromoprotein enediyne antibiotic chromophores), aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, carminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6- diazo-5-oxo-L-norleucine, ADRIAMYCIN® doxorubicin (including morpholino- doxorubicin, cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogues such as denopterin, methotrexate, pteropterin, trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine; androgens such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti- adrenals such as aminoglutethimide, mitotane, trilostane; folic acid replenisher such as frolinic acid; aceglatone; aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diaziquone; elfornithine; elliptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenamet; pirarubicin; losoxantrone; 2-ethylhydrazide; procarbazine; PSK® polysaccharide complex (JHS Natural Products, Eugene, OR); razoxane; rhizoxin; sizofiran; spirogermanium; tenuazonic acid; triaziquone; 2,2',2"-trichlorotriethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine (ELDISINE®, FILDESIN®); dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside ("Ara-C"); thiotepa; taxoids, e.g., TAXOL® paclitaxel (Bristol-Myers Squibb Oncology, Princeton, NJ.), ABRAXANETM Cremophor-free, albumin-engineered nanoparticle formulation of paclitaxel (American Pharmaceutical Partners, Schaumberg, Illinois), and TAXOTERE® doxetaxel (Rhδne-Poulenc Rorer,

Antony, France); chloranbucil; gemcitabine (GEMZAR®); 6-thioguanine; mercaptopurine; methotrexate; platinum analogs such as cisplatin and carboplatin; vinblastine (VELBAN®); platinum; etoposide (VP- 16); ifosfamide; mitoxantrone; vincristine (ONCOVIN®); oxaliplatin; leucovovin; vinorelbine (NAVELBINE®); novantrone; edatrexate; daunomycin; aminopterin; ibandronate; topoisomerase inhibitor RFS 2000; difluorometlhylornithine (DMFO); retinoids such as retinoic acid; capecitabine (XELOD A®); pharmaceutically acceptable salts, acids or derivatives of any of the above; as well as combinations of two or more of the above such as CHOP, an abbreviation for a combined therapy of cyclophosphamide, doxorubicin, vincristine, and prednisolone, and FOLFOX, an abbreviation for a treatment regimen with oxaliplatin (ELOXATINTM) combined with 5 -FU and leucovovin.

Also included in this definition are anti-hormonal agents that act to regulate, reduce, block, or inhibit the effects of hormones that can promote the growth of cancer, and are often in the form of systemic, or whole-body treatment. They may be hormones themselves. Examples include anti-estrogens and selective estrogen receptor modulators (SERMs), including, for example, tamoxifen (including NOLVADEX® tamoxifen), EVISTA® raloxifene, droloxifene, 4-hydroxytamoxifen, trioxifene, keoxifene, LYl 17018, onapristone, and FARESTON® toremifene; anti-pro gesterones; estrogen receptor down-regulators (ERDs); agents that function to suppress or shut down the ovaries, for example, leutinizing hormone-releasing hormone (LHRH) agonists such as LUPRON® and ELIGARD® leuprolide acetate, goserelin acetate, buserelin acetate and tripterelin; other anti-androgens such as flutamide, nilutamide and bicalutamide; and aromatase inhibitors that inhibit the enzyme aromatase, which regulates estrogen production in the adrenal glands, such as, for example, 4(5)-imidazoles, aminoglutethimide, MEGASE® megestrol acetate, AROMASIN® exemestane, formestanie, fadrozole, RIVISOR® vorozole, FEMARA® letrozole, and ARIMID EX® anastrozole. In addition, such definition of chemotherapeutic agents includes bisphosphonates such as clodronate (for example, BONEFOS® or OSTAC®), DIDROCAL® etidronate, NE-58095, ZOMETA® zoledronic acid/zoledronate, FOSAMAX® alendronate, AREDIA® pamidronate, SKELID® tiludronate, or ACTONEL® risedronate; as well as troxacitabine (a 1,3-dioxolane nucleoside cytosine analog); antisense oligonucleotides, particularly those that inhibit expression of genes in signaling pathways implicated in abherant cell proliferation, such as, for example, PKC-alpha, Raf, H-Ras, and epidermal growth factor receptor (EGF-R); vaccines such as THERATOPE® vaccine and gene therapy vaccines, for example, ALLOVECTIN® vaccine, LEUVECTIN® vaccine, and VAXID® vaccine; LURTOTECAN® topoisomerase 1 inhibitor; ABARELIX® rmRH; lapatinib ditosylate (an ErbB-2 and EGFR dual tyrosine kinase small-molecule inhibitor also known as GW572016); and pharmaceutically acceptable salts, acids or derivatives of any of the above. As used herein, the terms "ubiquitin" and "monoubiquitin" are used interchangeably, and are defined as all species of native human and synthetic ubiquitin substantially similar to a 76-amino acid protein having at least one lysine residue at amino acid 6, amino acid 22, amino acid 27, amino acid 29, amino acid 33, amino acid 48, and/or amino acid 63.

As used herein, the term "polyubiquitin" is defined as all species of native human and synthetic polymeric chains of ubiquitin which fall within human and synthetic classes of different polymeric linkages of ubiquitin, including, but not limited to, K6-linked polyubiquitin, K22-linked polyubiquitin, K27-linked polyubiquitin, K29-linked polyubiquitin, K33-linked polyubiquitin, K48-linked polyubiquitin and K63-linked polyubiquitin. Polyubiquitin may be of any length, and includes at least two ubiquitin moieties. Polyubiquitin is distinguished from tandem repeats of ubiquitin that are originally expressed as a single protein.

As used herein, the terms "K* -linked polyubiquitin" and "Lys* -linked polyubiquitin" are interchangeable, and refer to a polyubiquitin molecule comprising at least one isopeptide bond between the C-terminus of one ubiquitin moiety and a lysine at position * in another ubiquitin moiety. For example, a "K63 -linked polyubiquitin" is used interchangeably with a "Lys63 -linked polyubiquitin", and both terms refer to a polyubiquitin molecule comprising an isopeptide bond between the C-terminus of one of the ubiquitin moieties in the molecule and the lysine at position 63 in another ubiquitin moiety in the molecule.

As used herein, a statement that a first lysine linkage "differs" from a second lysine linkage indicates that the first lysine linkage between one ubiquitin moiety and another ubiquitin moiety involves a different lysine residue (e.g., K6, K22, K27, K29, K33, K48, and/or K63) than the second lysine linkage between one ubiquitin moiety and another ubiquitin moiety.

Compositions and Methods of Making Same

The present invention provides antibodies that bind specifically to DUBA. In one embodiment, an antibody of the invention comprises In one embodiment, anti-DUBA antibodies of the invention are monoclonal. Also encompassed within the scope of the invention are antibody fragments such as Fab, Fab', Fab'-SH and F(ab')₂ fragments, and variations thereof, of the anti-DUBA antibodies provided herein. These antibody fragments can be created by traditional means, such as enzymatic digestion, or may be generated by recombinant techniques. Such antibody fragments may be chimeric, human or humanized. These fragments are useful for the experimental, diagnostic, and therapeutic purposes set forth herein. Monoclonal antibodies can be obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Thus, the modifier "monoclonal" indicates the character of the antibody as not being a mixture of discrete antibodies. The anti-DUBA monoclonal antibodies of the invention can be made using a variety of methods known in the art, including the hybridoma method first described by Kohler et ah, Nature, 256:495 (1975), or alternatively they may be made by recombinant DNA methods (e.g., U.S. Patent No. 4,816,567).

Some embodiments of antibodies of the invention comprise a light chain variable domain of humanized 4D5 antibody (huMAb4D5-8) (HERCEPTIN®, Genentech, Inc., South San Francisco, CA, USA) (also referred to in U.S. Pat. No. 6,407,213 and Lee et al, J. MoI. Biol. (2004), 340(5): 1073-93) as depicted in SEQ ID NO: 1 below.

1 Asp He GIn Met Thr GIn Ser Pro Ser Ser Leu Ser Ala Ser VaI GIy Asp Arg VaI Thr He Thr Cys Arg Ala Ser GIn Asp VaI Asn Thr Ala VaI Ala Trp Tyr GIn GIn Lys Pro GIy Lys Ala Pro Lys Leu Leu He

Tyr Ser Ala Ser Phe Leu Tyr Ser GIy VaI Pro Ser Arg Phe Ser GIy Ser Arg Ser GIy Thr Asp Phe Thr Leu Thr He Ser Ser Leu GIn Pro GIu Asp Phe Ala Thr Tyr Tyr Cys GIn GIn His Tyr Thr Thr Pro Pro Thr Phe GIy GIn GIy Thr Lys VaI GIu He Lys 107 (SEQ ID NO: 1) (HVR residues are underlined)

In one embodiment, the huMAb4D5-8 light chain variable domain sequence is modified at one or more of positions 30, 66 and 91 (Asn, Arg and His as indicated in bold/italics above, respectively). In one embodiment, the modified huMAb4D5-8 sequence comprises Ser in position 30, GIy in position 66 and/or Ser in position 91. Accordingly, in one embodiment, an antibody of the invention comprises a light chain variable domain comprising the sequence depicted in SEQ ID NO: 2 below:

1 Asp He GIn Met Thr GIn Ser Pro Ser Ser Leu Ser Ala Ser VaI GIy Asp Arg VaI Thr He Thr Cys Arg Ala Ser GIn Asp VaI Ser Thr Ala

VaI Ala Trp Tyr GIn GIn Lys Pro GIy Lys Ala Pro Lys Leu Leu He Tyr Ser Ala Ser Phe Leu Tyr Ser GIy VaI Pro Ser Arg Phe Ser GIy Ser GIy Ser GIy Thr Asp Phe Thr Leu Thr He Ser Ser Leu GIn Pro GIu Asp Phe Ala Thr Tyr Tyr Cys GIn GIn Ser Tyr Thr Thr Pro Pro Thr Phe GIy GIn GIy Thr Lys VaI GIu He Lys 107 (SEQ ID NO: 2) (HVR residues are underlined) Substituted residues with respect to huMAb4D5-8 are indicated in bold/italics above.

Antibodies of the invention can comprise any suitable framework variable domain sequence, provided binding activity to DUBA is substantially retained. For example, in some embodiments, antibodies of the invention comprise a human subgroup III heavy chain framework consensus sequence. In one embodiment of these antibodies, the framework consensus sequence comprises substitution at position 71, 73 and/or 78. In some embodiments of these antibodies, position 71 is A, 73 is T and/or 78 is A. In one embodiment, these antibodies comprise heavy chain variable domain framework sequences of huMAb4D5-8 (HERCEPTIN^®, Genentech, Inc., South San Francisco, CA, USA) (also referred to in U.S. Pat. Nos. 6,407,213 & 5,821,337, and Lee et al, J. MoI. Biol. (2004), 340(5): 1073-93). In one embodiment, these antibodies further comprise a human DI light chain framework consensus sequence. In one embodiment, these antibodies comprise light chain HVR sequences of huMAb4D5-8 as described in U.S. Pat. Nos. 6,407,213 & 5,821,337.) In one embodiment, these antibodies comprise light chain variable domain sequences of huMAb4D5-8 (SEQ ID NO: 1 and 2) (HERCEPTIN^®, Genentech, Inc., South San Francisco, CA, USA) (also referred to in U.S. Pat. Nos. 6,407,213 & 5,821,337, and Lee et al., J. MoI. Biol. (2004), 340(5): 1073-93). In one embodiment, an antibody of the invention is affinity matured to obtain the target binding affinity desired.

In one aspect, the invention provides an antibody that competes with any of the above-mentioned antibodies for binding to DUBA. In one aspect, the invention provides an antibody that binds to the same antigenic determinant on DUBA as any of the above- mentioned antibodies.

Compositions comprising at least one anti-DUBA antibody or at least one polynucleotide comprising sequences encoding an anti-DUBA antibody are provided. In certain embodiments, a composition may be a pharmaceutical composition. As used herein, compositions comprise one or more antibodies that bind to DUBA and/or one or more polynucleotides comprising sequences encoding one or more antibodies that bind to DUBA. These compositions may further comprise suitable carriers, such as pharmaceutically acceptable excipients including buffers, which are well known in the art.

Isolated antibodies and polynucleotides are also provided. In certain embodiments, the isolated antibodies and polynucleotides are substantially pure.

In one embodiment, anti-DUBA antibodies are monoclonal. In another embodiment, fragments of the anti-DUBA antibodies (e.g., Fab, Fab'-SH and F(ab')2 fragments) are provided. These antibody fragments can be created by traditional means, such as enzymatic digestion, or may be generated by recombinant techniques. Such antibody fragments may be chimeric, humanized, or human. These fragments are useful for the diagnostic and therapeutic purposes set forth below. Generation of anti-DUBA antibodies using a phage display library

A variety of methods are known in the art for generating phage display libraries from which an antibody of interest can be obtained. One method of generating antibodies of interest is through the use of a phage antibody library as described in Lee et al., J. MoI. Biol. (2004), 340(5): 1073-93.

The anti-DUBA antibodies of the invention can be made by using combinatorial libraries to screen for synthetic antibody clones with the desired activity or activities. In principle, synthetic antibody clones are selected by screening phage libraries containing phage that display various fragments of antibody variable region (Fv) fused to phage coat protein. Such phage libraries are panned by affinity chromatography against the desired antigen. Clones expressing Fv fragments capable of binding to the desired antigen are adsorbed to the antigen and thus separated from the non-binding clones in the library. The binding clones are then eluted from the antigen, and can be further enriched by additional cycles of antigen adsorption/elution. Any of the anti-DUBA antibodies of the invention can be obtained by designing a suitable antigen screening procedure to select for the phage clone of interest followed by construction of a full length anti-DUBA antibody clone using the Fv sequences from the phage clone of interest and suitable constant region (Fc) sequences described in Kabat et al, Sequences of Proteins of Immunological Interest, Fifth Edition, NIH Publication 91-3242, Bethesda MD (1991), vols. 1-3.

The antigen-binding domain of an antibody is formed from two variable (V) regions of about 110 amino acids, one each from the light (VL) and heavy (VH) chains, that both present three hypervariable loops or complementarity-determining regions (CDRs). Variable domains can be displayed functionally on phage, either as single-chain Fv (scFv) fragments, in which VH and VL are covalently linked through a short, flexible peptide, or as Fab fragments, in which they are each fused to a constant domain and interact non-covalently, as described in Winter et al., Ann. Rev. Immunol, 12: 433-455 (1994). As used herein, scFv encoding phage clones and Fab encoding phage clones are collectively referred to as "Fv phage clones" or "Fv clones".

Repertoires of VH and VL genes can be separately cloned by polymerase chain reaction (PCR) and recombined randomly in phage libraries, which can then be searched for antigen-binding clones as described in Winter et al, Ann. Rev. Immunol, 12: 433-455 (1994). Libraries from immunized sources provide high-affinity antibodies to the immunogen without the requirement of constructing hybridomas. Alternatively, the naive repertoire can be cloned to provide a single source of human antibodies to a wide range of non-self and also self antigens without any immunization as described by Griffiths et al, EMBO J 12: 725-734 (1993). Finally, naive libraries can also be made synthetically by cloning the unrearranged V-gene segments from stem cells, and using PCR primers containing random sequence to encode the highly variable CDR3 regions and to accomplish rearrangement in vitro as described by Hoogenboom and Winter, J MoI Biol, 227: 381-388 (1992).

Filamentous phage is used to display antibody fragments by fusion to the minor coat protein pill. The antibody fragments can be displayed as single chain Fv fragments, in which VH and VL domains are connected on the same polypeptide chain by a flexible polypeptide spacer, e.g. as described by Marks et al, J. MoI Biol, 222: 581-597 (1991), or as Fab fragments, in which one chain is fused to pill and the other is secreted into the bacterial host cell periplasm where assembly of a Fab-coat protein structure which becomes displayed on the phage surface by displacing some of the wild type coat proteins, e.g. as described in Hoogenboom et al, Nucl Acids Res., 19: 4133-4137 (1991). In general, nucleic acids encoding antibody gene fragments are obtained from immune cells harvested from humans or animals. If a library biased in favor of anti-DUBA clones is desired, the subject is immunized with DUBA to generate an antibody response, and spleen cells and/or circulating B cells or other peripheral blood lymphocytes (PBLs) are recovered for library construction. In one embodiment, a human antibody gene fragment library biased in favor of anti-human DUBA clones is obtained by generating an anti-human DUBA antibody response in transgenic mice carrying a functional human immunoglobulin gene array (and lacking a functional endogenous antibody production system) such that DUBA immunization gives rise to B cells producing human antibodies against DUBA. The generation of human antibody-producing transgenic mice is described in Section (III)(b) below.

Additional enrichment for anti-DUBA reactive cell populations can be obtained by using a suitable screening procedure to isolate B cells expressing DUBA-specific membrane bound antibody, e.g., by cell separation with DUBA affinity chromatography or adsorption of cells to fluorochrome-labeled DUBA followed by flow-activated cell sorting (FACS).

Alternatively, the use of spleen cells and/or B cells or other PBLs from an unimmunized donor provides a better representation of the possible antibody repertoire, and also permits the construction of an antibody library using any animal (human or non-human) species in which DUBA is not antigenic. For libraries incorporating in vitro antibody gene construction, stem cells are harvested from the subject to provide nucleic acids encoding unrearranged antibody gene segments. The immune cells of interest can be obtained from a variety of animal species, such as human, mouse, rat, lagomorpha, luprine, canine, feline, porcine, bovine, equine, and avian species, etc.

Nucleic acid encoding antibody variable gene segments (including VH and VL segments) are recovered from the cells of interest and amplified. In the case of rearranged VH and VL gene libraries, the desired DNA can be obtained by isolating genomic DNA or mRNA from lymphocytes followed by polymerase chain reaction (PCR) with primers matching the 5' and 3' ends of rearranged VH and VL genes as described in Orlandi et ah, Proc. Natl Acad. ScL (USA), 86: 3833-3837 (1989), thereby making diverse V gene repertoires for expression. The V genes can be amplified from cDNA and genomic DNA, with back primers at the 5' end of the ex on encoding the mature V-domain and forward primers based within the J-segment as described in Orlandi et al. (1989) and in Ward et ah, Nature, 341: 544-546 (1989). However, for amplifying from cDNA, back primers can also be based in the leader exon as described in Jones et al., Biotechnol, 9: 88-89 (1991), and forward primers within the constant region as described in Sastry et al, Proc. Natl. Acad. Sci. (USA), 86: 5728-5732 (1989). To maximize complementarity, degeneracy can be incorporated in the primers as described in Orlandi et al. (1989) or Sastry et al (1989). In certain embodiments, the library diversity is maximized by using PCR primers targeted to each V-gene family in order to amplify all available VH and VL arrangements present in the immune cell nucleic acid sample, e.g. as described in the method of Marks et al, J. MoI Biol, 222: 581-597 (1991) or as described in the method of Orum et al, Nucleic Acids Res., 21: 4491-4498 (1993). For cloning of the amplified DNA into expression vectors, rare restriction sites can be introduced within the PCR primer as a tag at one end as described in Orlandi et al (1989), or by further PCR amplification with a tagged primer as described in Clackson et al, Nature, 352: 624-628 (1991).

Repertoires of synthetically rearranged V genes can be derived in vitro from V gene segments. Most of the human VH-gene segments have been cloned and sequenced (reported in Tomlinson et al, J. MoI Biol, 227: 776-798 (1992)), and mapped (reported in Matsuda et al, Nature Genet., 3: 88-94 (1993); these cloned segments (including all the major conformations of the Hl and H2 loop) can be used to generate diverse VH gene repertoires with PCR primers encoding H3 loops of diverse sequence and length as described in Hoogenboom and Winter, J MoI Biol, 227: 381-388 (1992). VH repertoires can also be made with all the sequence diversity focused in a long H3 loop of a single length as described in Barbas et al, Proc. Natl. Acad. Sci. USA, 89: 4457-4461 (1992). Human VK and Vλ segments have been cloned and sequenced (reported in Williams and Winter, Eur. J. Immunol, 23: 1456-1461 (1993)) and can be used to make synthetic light chain repertoires. Synthetic V gene repertoires, based on a range of VH and VL folds, and L3 and H3 lengths, will encode antibodies of considerable structural diversity. Following amplification of V- gene encoding DNAs, germline V-gene segments can be rearranged in vitro according to the methods of Hoogenboom and Winter, J MoI Biol, 111: 381-388 (1992).

Repertoires of antibody fragments can be constructed by combining VH and VL gene repertoires together in several ways. Each repertoire can be created in different vectors, and the vectors recombined in vitro, e.g., as described in Hogrefe et al, Gene, 128: 119-126 (1993), or in vivo by combinatorial infection, e.g., the loxP system described in Waterhouse et al, Nucl Acids Res., 21: 2265-2266 (1993). The in vivo recombination approach exploits the two-chain nature of Fab fragments to overcome the limit on library size imposed by E. coli transformation efficiency. Naive VH and VL repertoires are cloned separately, one into a phagemid and the other into a phage vector. The two libraries are then combined by phage infection of phagemid-containing bacteria so that each cell contains a different combination and the library size is limited only by the number of cells present (about 10¹² clones). Both vectors contain in vivo recombination signals so that the VH and VL genes are recombined onto a single replicon and are co-packaged into phage virions. These huge libraries provide large numbers of diverse antibodies of good affinity (K_d ^" of about 10^" M).

Alternatively, the repertoires may be cloned sequentially into the same vector, e.g. as described in Barbas et al, Proc. Natl. Acad. ScL USA, 88: 7978-7982 (1991), or assembled together by PCR and then cloned, e.g. as described in Clackson et al., Nature, 352: 624-628 (1991). PCR assembly can also be used to join VH and VL DNAs with DNA encoding a flexible peptide spacer to form single chain Fv (scFv) repertoires. In yet another technique, "in cell PCR assembly" is used to combine VH and VL genes within lymphocytes by PCR and then clone repertoires of linked genes as described in Embleton et al., Nucl. Acids Res., 20: 3831-3837 (1992).

Screening of the libraries can be accomplished by any art-known technique. For example, DUBA can be used to coat the wells of adsorption plates, expressed on host cells affixed to adsorption plates or used in cell sorting, or conjugated to biotin for capture with streptavidin-coated beads, or used in any other art-known method for panning phage display libraries.

The phage library samples are contacted with immobilized DUBA under conditions suitable for binding of at least a portion of the phage particles with the adsorbent. Normally, the conditions, including pH, ionic strength, temperature and the like are selected to mimic physiological conditions. The phages bound to the solid phase are washed and then eluted by acid, e.g. as described in Barbas et al, Proc. Natl. Acad. Sci USA, 88: 7978-7982 (1991), or by alkali, e.g. as described in Marks et al, J. MoI Biol, 111: 581-597 (1991), or by DUBA antigen competition, e.g. in a procedure similar to the antigen competition method of

Clackson et al, Nature, 352: 624-628 (1991). Phages can be enriched 20-1,000-fold in a single round of selection. Moreover, the enriched phages can be grown in bacterial culture and subjected to further rounds of selection.

The efficiency of selection depends on many factors, including the kinetics of dissociation during washing, and whether multiple antibody fragments on a single phage can simultaneously engage with antigen. Antibodies with fast dissociation kinetics (and weak binding affinities) can be retained by use of short washes, multivalent phage display and high coating density of antigen in solid phase. The high density not only stabilizes the phage through multivalent interactions, but favors rebinding of phage that has dissociated. The selection of antibodies with slow dissociation kinetics (and good binding affinities) can be promoted by use of long washes and monovalent phage display as described in Bass et ah, Proteins, 8: 309-314 (1990) and in WO 92/09690, and a low coating density of antigen as described in Marks et al, Biotechnol, 10: 779-783 (1992). It is possible to select between phage antibodies of different affinities, even with affinities that differ slightly, for DUBA. However, random mutation of a selected antibody (e.g. as performed in some of the affinity maturation techniques described above) is likely to give rise to many mutants, most binding to antigen, and a few with higher affinity. With limiting DUBA, rare high affinity phage could be competed out. To retain all the higher affinity mutants, phages can be incubated with excess biotinylated DUBA, but with the biotinylated DUBA at a concentration of lower molarity than the target molar affinity constant for DUBA. The high affinity-binding phages can then be captured by streptavidin- coated paramagnetic beads. Such "equilibrium capture" allows the antibodies to be selected according to their affinities of binding, with sensitivity that permits isolation of mutant clones with as little as two-fold higher affinity from a great excess of phages with lower affinity. Conditions used in washing phages bound to a solid phase can also be manipulated to discriminate on the basis of dissociation kinetics.

Anti-DUBA clones may be activity selected. In one embodiment, the invention provides anti-DUBA antibodies that increase production of IFN-I from cells when such antibodies or antigen-binding fragments thereof are present in the cells. In another embodiment, the invention provides anti-DUBA antibodies that lessen or prevent the deubiquitination of K63-linked polyubiquitinylated TRAF3 by DUBA. Fv clones corresponding to such anti-DUBA antibodies can be selected by (1) isolating anti-DUBA clones from a phage library as described in Section B(I)(2) above, and optionally amplifying the isolated population of phage clones by growing up the population in a suitable bacterial host; (2) selecting DUBA and a second protein against which blocking and non-blocking activity, respectively, is desired; (3) adsorbing the anti-DUBA phage clones to immobilized DUBA; (4) using an excess of the second protein to elute any undesired clones that recognize DUBA-binding determinants which overlap or are shared with the binding determinants of the second protein; and (5) eluting the clones which remain adsorbed following step (4).

Optionally, clones with the desired blocking/non-blocking properties can be further enriched by repeating the selection procedures described herein one or more times.

DNA encoding the Fv clones of the invention is readily isolated and sequenced using conventional procedures (e.g. by using oligonucleotide primers designed to specifically amplify the heavy and light chain coding regions of interest from hybridoma or phage DNA template). Once isolated, the DNA can be placed into expression vectors, which are then transfected into host cells such as E. coli cells, simian COS cells, Chinese hamster ovary (CHO) cells, or myeloma cells that do not otherwise produce immunoglobulin protein, to obtain the synthesis of the desired monoclonal antibodies in the recombinant host cells. Review articles on recombinant expression in bacteria of antibody-encoding DNA include Skerra et al, Curr. Opinion in Immunol, 5: 256 (1993) and Pluckthun, Immunol. Revs, 130: 151 (1992).

DNA encoding the Fv clones of the invention can be combined with known DNA sequences encoding heavy chain and/or light chain constant regions (e.g. the appropriate DNA sequences can be obtained from Kabat et al. , supra) to form clones encoding full or partial length heavy and/or light chains. It will be appreciated that constant regions of any isotype can be used for this purpose, including IgG, IgM, IgA, IgD, and IgE constant regions, and that such constant regions can be obtained from any human or animal species. A Fv clone derived from the variable domain DNA of one animal (such as human) species and then fused to constant region DNA of another animal species to form coding sequence(s) for "hybrid", full length heavy chain and/or light chain is included in the definition of "chimeric" and "hybrid" antibody as used herein. In one embodiment, a Fv clone derived from human variable DNA is fused to human constant region DNA to form coding sequence(s) for all human, full or partial length heavy and/or light chains.

The antibodies produced by naive libraries (either natural or synthetic) can be of moderate affinity (K_d ^"1 of about 10⁶ to 10⁷ M^"1), but affinity maturation can also be mimicked in vitro by constructing and reselecting from secondary libraries as described in Winter et al (1994), supra. For example, mutation can be introduced at random in vitro by using error- prone polymerase (reported in Leung et al, Technique, 1: 11-15 (1989)) in the method of Hawkins et al, J. MoI Biol, 226: 889-896 (1992) or in the method of Gram et al, Proc. Natl. Acad. Sci USA, 89: 3576-3580 (1992). Additionally, affinity maturation can be performed by randomly mutating one or more CDRs, e.g. using PCR with primers carrying random sequence spanning the CDR of interest, in selected individual Fv clones and screening for higher affinity clones. WO 9607754 (published 14 March 1996) described a method for inducing mutagenesis in a complementarity determining region of an immunoglobulin light chain to create a library of light chain genes. Another effective approach is to recombine the VH or VL domains selected by phage display with repertoires of naturally occurring V domain variants obtained from unimmunized donors and screen for higher affinity in several rounds of chain reshuffling as described in Marks et al, Biotechnol, 10: 779-783 (1992). This technique allows the production of antibodies and antibody fragments with affinities in the 10^~9 M range.

Other methods of generating anti-DUBA antibodies

Other methods of generating and assessing the affinity of antibodies are well known in the art and are described, e.g., in Kohler et al, Nature 256: 495 (1975); U.S. Patent No. 4,816,567; Goding, Monoclonal Antibodies: Principles and Practice, pp. 59-103 (Academic Press, 1986; Kozbor, J Immunol, 133:3001 (1984); Brodeur et al, Monoclonal Antibody Production Techniques and Applications, pp. 51-63 (Marcel Dekker, Inc., New York, 1987; Munson et al, Anal Biochem., 107:220 (1980); Engels et al, Agnew. Chem. Int. Ed. Engl, 28: 716-734 (1989); Abrahmsen et al, EMBOJ., 4: 3901 (1985); Methods in Enzymology, vol. 44 (1976); Morrison et al, Proc. Natl. Acad. Sci. USA, 81: 6851-6855 (1984).

Generation of candidate antibodies can be achieved using routine skills in the art, including those described herein, such as the hybridoma technique and screening of phage displayed libraries of binder molecules. These methods are well-established in the art.

Briefly, the anti-DUBA antibodies of the invention can be made by using combinatorial libraries to screen for synthetic antibody clones with the desired activity or activities. In principle, synthetic antibody clones are selected by screening phage libraries containing phage that display various fragments of antibody variable region (Fv) fused to phage coat protein. Such phage libraries are panned by affinity chromatography against the desired antigen. Clones expressing Fv fragments capable of binding to the desired antigen are adsorbed to the antigen and thus separated from the non-binding clones in the library. The binding clones are then eluted from the antigen, and can be further enriched by additional cycles of antigen adsorption/elution. Any of the anti-DUBA antibodies of the invention can be obtained by designing a suitable antigen screening procedure to select for the phage clone of interest followed by construction of a full length anti-DUBA antibody clone using the Fv sequences from the phage clone of interest and suitable constant region (Fc) sequences described in Kabat et al , Sequences of Proteins of Immunological Interest, Fifth Edition, NIH Publication 91-3242, Bethesda MD (1991), vols. 1-3. See also PCT Pub. WO03/102157, and references cited therein.

In one embodiment, anti-DUBA antibodies of the invention are monoclonal. Also encompassed within the scope of the invention are antibody fragments such as Fab, Fab', Fab'-SH and F(ab')₂ fragments, and variations thereof, of the anti-DUBA antibodies provided herein. These antibody fragments can be created by traditional means, such as enzymatic digestion, or may be generated by recombinant techniques. Such antibody fragments may be chimeric, human or humanized. These fragments are useful for the experimental, diagnostic, and therapeutic purposes set forth herein. Monoclonal antibodies can be obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Thus, the modifier "monoclonal" indicates the character of the antibody as not being a mixture of discrete antibodies. The anti-DUBA monoclonal antibodies of the invention can be made using a variety of methods known in the art, including the hybridoma method first described by Kohler et ah, Nature, 256:495 (1975), or alternatively they may be made by recombinant DNA methods (e.g., U.S. Patent No. 4,816,567).

General Methods

In general, the invention provides methods and compositions for modulating DUBA expression and/or activity. In one embodiment, such methods and compositions for modulating DUBA expression and/or activity are useful for treatment of interferon-mediated disorders. In another embodiment, the methods and compositions of the invention are used to treat cell proliferative disorders. In another embodiment, the methods and compositions of the invention are used to treat an infection. In another embodiment, the methods and compositions of the invention are used to treat immune disorders. In another embodiment, the methods and compositions of the invention are used to treat other interferon-related disorders. As shown herein, DUBA is a negative regulator for TRAF3 -mediated type I interferon production. DUBA is herein shown to deubiquitinate TRAF3. More specifically, DUBA removes K63-linked polyubiquitin chains from TRAF3, but does not remove K48- linked polyubiquitin chains from TRAF3. TRAF3 is a molecule in the TLR3 signaling cascade, and is also a member of the RIG-I and MDA5 signaling cascades. The K63-linked polyubiquitinated form of TRAF3 signals for the production of IFN through those pathways, while the K48-linked polyubiquitinated form of TRAF3 results in the production of other cytokines (see Figure 7B). Thus, the methods and compositions of the invention may be used to either stimulate the deubiquitinylation of TRAF3 by DUBA (agonizing DUBA activity) and thereby decreasing interferon production, or may be used to inhibit or block the deubiquitinylation of TRAF3 by DUBA (antagonizing DUBA activity) and thereby increasing interferon production. Both agonizing and antagonizing methods and compositions are provided by the invention. In one nonlimiting example, as exemplified herein, antagonizing DUBA expression using siRNA specific for DUBA resulted in increased production of interferon. In another nonlimiting example, as exemplified herein, agonizing DUBA expression by constitutively expressing DUBA resulted in decreased activation of interferon production via the TLR3, RIG-I and MDA-5 pathways.

The invention therefore provides compounds that antagonize DUBA expression that may be used in the methods of the invention. Such antagonists are described herein, and include, but are not limited to, antisense polynucleotides, catalytic RNA, RNA-DNA hybrids, and interfering RNA molecules. The invention also provides compounds that antagonize DUBA activity that may be used in the methods of the invention. Such antagonists are described herein, and include, but are not limited to, anti-DUBA antibodies or DUBA- binding fragments thereof, DUBA-binding peptides, DUBA-specific small molecules, DUBA-specific aptamers, and other polypeptides that specifically bind DUBA. Mutant DUBA comprising a mutation in one or more regions necessary for DUBA activity (i.e., a catalytically inactive DUBA, including, but not limited to DUBA comprising a C224S mutation, as described herein) may also antagonize the activity of normal DUBA by, e.g., competing for binding to one or more DUBA ligands such that wild-type DUBA cannot readily deubiquitinylate those ligands, or can do so only at a greatly reduced rate. The invention also provides compounds that agonize DUBA expression that may be used in the methods of the invention. Such agonists are described herein, and include, but are not limited to, polynucleotides and polypeptides that interfere with one or more molecules that normally inhibit or repress DUBA expression. The invention also provides compounds that agonize DUBA activity that may be used in the methods of the invention. Such agonists are described herein, and include, but are not limited to polypeptides, small molecules, antibodies and antibody fragments, peptides, and aptamers that interfere with one or more DUBA inhibitors, or that enhance binding of DUBA to a DUBA ligand.

In another aspect, the compositions of the invention find utility as reagents for detection and isolation of DUBA, such as detection of DUBA in various cell types and tissues, including, but not limited to, the determination of DUBA density and distribution in cell populations and within a given sample of cells. The compositions of the invention can also be used in assays to screen for other agonists or antagonists of DUBA expression or activity. In a nonlimiting example, blocking anti-DUBA antibodies may be used in screens to identify small molecule antagonists of DUBA-mediated deubiquitinylation of K63-linked polyubiquitinated TRAF3. For example, the activity of one or more potential small molecule antagonists may be compared to the activity of the antagonistic anti-DUBA antibodies in suppressing such TRAF3 deubiquitinylation. DUBA may also be used as a reagent to selectively remove K63 -linked polyubiquitin chains from a polyubiquitinated protein.

The invention provides methods of increasing IFN-α and/or IFN-β production by inhibiting DUBA expression and/or activity. Similarly, the invention provides methods of decreasing IFN-α and/or IFN-β production by stimulating DUBA expression and/or activity. Such inhibiting or stimulating can take place in reconstituted molecular systems in vitro, or in vivo.

Small Molecule DUBA Modulators

Small molecules can be useful modulators of DUBA-ligand interaction. Small molecules that inhibit such an interaction are potentially useful inhibitors of DUBA activity. Examples of small molecule modulators include small peptides, peptide-like molecules (preferably soluble), and synthetic, non-peptidyl organic or inorganic compounds. Libraries of chemical and/or biological mixtures, such as fungal, bacterial, or algal extracts, are known in the art and can be readily screened.. Libraries of compounds may be presented in solution (Houghten et al, Biotechniques. 13:412-21 (1992)) or on beads (Lam et al, Nature. 354:82- 84 (1991)), on chips (Fodor et al., Nature. 364:555-6 (1993)), bacteria, spores (Ladner et al., US Patent No. 5,223,409, 1993), plasmids (Cull et al., Proc Natl Acad Sci USA. 89:1865-9 (1992)) or on phage (Cwirla et al., Proc Natl Acad Sci USA. 87:6378-82 (1990); Devlin et al., Science. 249:404-6 (1990); Felici et al., J MoI Biol. 222:301-10 (1991); Ladner et al., US Patent No. 5,223,409, 1993; Scott and Smith, Science. 249:386-90 (1990)). An exemplary but nonlimiting cell-free assay comprises contacting DUBA with a ligand (i.e., K63- polyubiquitinated TRAF3) to form an assay mixture, contacting the assay mixture with a test compound, and determining the ability of the test compound to interact with DUBA or the ligand, where determining the ability of the test compound to interact with DUBA or the ligand comprises determining whether a detectable characteristic of the DUBA/ligand complex is modulated. For example, the binding interaction of DUBA and the ligand, as determined by the amount of complex that is formed, can be indicative of whether the test compound is able to modulate the interaction between DUBA and the ligand when present in the assay system. The amount of complex can be assessed by methods known in the art, some of which are described herein, for example ELISA (including competitive binding ELISA), yeast two-hybrid, Biacore® assays, and proximity (e.g., fluorescent resonance energy transfer, enzyme-substrate) assays.

Vectors, Host Cells and Recombinant Methods For recombinant production of a protein of the invention (i.e., an anti-DUBA antibody or antigen-binding fragment thereof, a peptide, or another polypeptide DUBA-binding molecule, the nucleic acid encoding it is isolated and inserted into a replicable vector for further cloning (amplification of the DNA) or for expression. DNA encoding the polypeptide is readily isolated and sequenced using conventional procedures (e.g. , in one embodiment by using oligonucleotide probes that are capable of binding specifically to genes encoding the heavy and light chains of the anti-DUBA antibody). Many vectors are available. The choice of vector depends in part on the host cell to be used. Host cells include, but are not limited to, cells of either prokaryotic or eukaryotic (generally mammalian) origin. It will be appreciated that constant regions of any isotype can be used for this purpose, including IgG, IgM, IgA, IgD, and IgE constant regions, and that such constant regions can be obtained from any human or animal species.

Generating Polypeptides of the Invention Using Prokaryotic Host Cells

Vector Construction Polynucleotide sequences encoding polypeptides of the invention can be obtained using standard recombinant techniques. Desired polynucleotide sequences may be isolated and sequenced. For example, polynucleotide sequences may be isolated and sequenced from antibody producing cells such as hybridoma cells. Alternatively, polynucleotides can be synthesized using nucleotide synthesizer or PCR techniques. Once obtained, sequences encoding the polypeptides are inserted into a recombinant vector capable of replicating and expressing heterologous polynucleotides in prokaryotic hosts. Many vectors that are available and known in the art can be used for the purpose of the present invention. Selection of an appropriate vector will depend mainly on the size of the nucleic acids to be inserted into the vector and the particular host cell to be transformed with the vector. Each vector contains various components, depending on its function (amplification or expression of heterologous polynucleotide, or both) and its compatibility with the particular host cell in which it resides. The vector components generally include, but are not limited to: an origin of replication, a selection marker gene, a promoter, a ribosome binding site (RBS), a signal sequence, the heterologous nucleic acid insert and a transcription termination sequence.

In general, plasmid vectors containing replicon and control sequences which are derived from species compatible with the host cell are used in connection with these hosts. The vector ordinarily carries a replication site, as well as marking sequences which are capable of providing phenotypic selection in transformed cells. For example, E. coli is typically transformed using pBR322, a plasmid derived from an E. coli species. pBR322 contains genes encoding ampicillin (Amp) and tetracycline (T et) resistance and thus provides easy means for identifying transformed cells. pBR322, its derivatives, or other microbial plasmids or bacteriophage may also contain, or be modified to contain, promoters which can be used by the microbial organism for expression of endogenous proteins. Examples of pBR322 derivatives used for expression of particular antibodies are described in detail in Carter et al, U.S. Patent No. 5,648,237.

In addition, phage vectors containing replicon and control sequences that are compatible with the host microorganism can be used as transforming vectors in connection with these hosts. For example, bacteriophage such as λGEM.TM.-l 1 may be utilized in making a recombinant vector which can be used to transform susceptible host cells such as E. coli LE392.

The expression vector of the invention may comprise two or more promoter-cistron pairs, encoding each of the polypeptide components (e.g., one promoter-cistron pair for each of the light and heavy chains of an antibody of the invention). A promoter is an untranslated regulatory sequence located upstream (5') to a cistron that modulates its expression. Prokaryotic promoters typically fall into two classes, inducible and constitutive. Inducible promoter is a promoter that initiates increased levels of transcription of the cistron under its control in response to changes in the culture condition, e.g. the presence or absence of a nutrient or a change in temperature.

A large number of promoters recognized by a variety of potential host cells are well known. The selected promoter can be operably linked to cistron DNA encoding the light or heavy chain by removing the promoter from the source DNA via restriction enzyme digestion and inserting the isolated promoter sequence into the vector of the invention. Both the native promoter sequence and many heterologous promoters may be used to direct amplification and/or expression of the target genes. In some embodiments, heterologous promoters are utilized, as they generally permit greater transcription and higher yields of expressed target gene as compared to the native target polypeptide promoter.

Promoters suitable for use with prokaryotic hosts include the PhoA promoter, the β- galactamase and lactose promoter systems, a tryptophan (trp) promoter system and hybrid promoters such as the tac or the trc promoter. However, other promoters that are functional in bacteria (such as other known bacterial or phage promoters) are suitable as well. Their nucleotide sequences have been published, thereby enabling a skilled worker operably to ligate them to cistrons encoding the target light and heavy chains (Siebenlist et al. (1980) Cell 20: 269) using linkers or adaptors to supply any required restriction sites. In one aspect of the invention, each cistron within the recombinant vector comprises a secretion signal sequence component that directs translocation of the expressed polypeptides across a membrane. In general, the signal sequence may be a component of the vector, or it may be a part of the target polypeptide DNA that is inserted into the vector. The signal sequence selected for the purpose of this invention should be one that is recognized and processed (i.e. cleaved by a signal peptidase) by the host cell. For prokaryotic host cells that do not recognize and process the signal sequences native to the heterologous polypeptides, the signal sequence is substituted by a prokaryotic signal sequence selected, for example, from the group consisting of the alkaline phosphatase, penicillinase, Ipp, or heat-stable enterotoxin II (STII) leaders, LamB, PhoE, PeIB, OmpA and MBP. In one embodiment of the invention, the signal sequences used in both cistrons of the expression system are STII signal sequences or variants thereof.

In another aspect, the production of the polypeptides according to the invention can occur in the cytoplasm of the host cell, and therefore does not require the presence of secretion signal sequences within each cistron. In that regard, in one embodiment, anti- DUBA immunoglobulin light and heavy chains are expressed, folded and assembled to form functional immunoglobulins within the cytoplasm. Certain host strains (e.g., the E. coli trxB^~ strains) provide cytoplasm conditions that are favorable for disulfide bond formation, thereby permitting proper folding and assembly of expressed protein subunits. Proba and Pluckthun Gene, 159:203 (1995). Polypeptides (i.e., antibodies) of the invention can also be produced by using an expression system in which the quantitative ratio of expressed polypeptide components can be modulated in order to maximize the yield of secreted and properly assembled polypeptides of the invention. Such modulation is accomplished at least in part by simultaneously modulating translational strengths for the polypeptide components.

One technique for modulating translational strength is disclosed in Simmons et al., U.S. Pat. No. 5,840,523. It utilizes variants of the translational initiation region (TIR) within a cistron. For a given TIR, a series of amino acid or nucleic acid sequence variants can be created with a range of translational strengths, thereby providing a convenient means by which to adjust this factor for the desired expression level of the specific chain. TIR variants can be generated by conventional mutagenesis techniques that result in codon changes which can alter the amino acid sequence. In certain embodiments, changes in the nucleotide sequence are silent. Alterations in the TIR can include, for example, alterations in the number or spacing of Shine-Dalgarno sequences, along with alterations in the signal sequence. One method for generating mutant signal sequences is the generation of a "codon bank" at the beginning of a coding sequence that does not change the amino acid sequence of the signal sequence (i.e., the changes are silent). This can be accomplished by changing the third nucleotide position of each codon; additionally, some amino acids, such as leucine, serine, and arginine, have multiple first and second positions that can add complexity in making the bank. This method of mutagenesis is described in detail in Yansura et al. (1992) METHODS: A Companion to Methods in Enzymol 4:151-158.

In one embodiment, a set of vectors is generated with a range of TIR strengths for each cistron therein. This limited set provides a comparison of expression levels of each chain as well as the yield of the desired antibody products under various TIR strength combinations. TIR strengths can be determined by quantifying the expression level of a reporter gene as described in detail in Simmons et al. U.S. Pat. No. 5, 840,523. Based on the translational strength comparison, the desired individual TIRs are selected to be combined in the expression vector constructs of the invention.

Prokaryotic host cells suitable for expressing polypeptides of the invention include Archaebacteria and Eubacteria, such as Gram-negative or Gram-positive organisms. Examples of useful bacteria include Escherichia (e.g., E. colϊ), Bacilli (e.g., B. subtilis), Enterobacteria, Pseudomonas species (e.g., P. aeruginosa), Salmonella typhimurium, Serratia marcescans, Klebsiella, Proteus, Shigella, Rhizobia, Vitreoscilla, or Paracoccus. In one embodiment, gram-negative cells are used. In one embodiment, E. coli cells are used as hosts for the invention. Examples of E. coli strains include strain W3110 (Bachmann, Cellular and Molecular Biology, vol. 2 (Washington, D. C: American Society for Microbiology, 1987), pp. 1190-1219; ATCC Deposit No. 27,325) and derivatives thereof, including strain 33D3 having genotype W3110 AfhuA (AtonA) ptr3 lac Iq lacL8 AompTA(nmpc-fepE) degP41 kan^R (U.S. Pat. No. 5,639,635). Other strains and derivatives thereof, such as E. coli 294 (ATCC 31,446), E. coli B, E. coli_λ 1776 (ATCC 31,537) and E. coli RV308(ATCC 31,608) are also suitable. These examples are illustrative rather than limiting. Methods for constructing derivatives of any of the above-mentioned bacteria having defined genotypes are known in the art and described in, for example, Bass et al., Proteins, £:309-314 (1990). It is generally necessary to select the appropriate bacteria taking into consideration replicability of the replicon in the cells of a bacterium. For example, E. coli, Serratia, or Salmonella species can be suitably used as the host when well known plasmids such as pBR322, pBR325, pACYC177, or pKN410 are used to supply the replicon. Typically the host cell should secrete minimal amounts of proteolytic enzymes, and additional protease inhibitors may desirably be incorporated in the cell culture.

Production of the Polypeptides of the Invention Host cells are transformed with the above-described expression vectors and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.

Transformation means introducing DNA into the prokaryotic host so that the DNA is replicable, either as an extrachromosomal element or by chromosomal integrant. Depending on the host cell used, transformation is done using standard techniques appropriate to such cells. The calcium treatment employing calcium chloride is generally used for bacterial cells that contain substantial cell-wall barriers. Another method for transformation employs polyethylene glycol/DMSO. Yet another technique used is electroporation.

Prokaryotic cells used to produce the polypeptides of the invention are grown in media known in the art and suitable for culture of the selected host cells. Examples of suitable media include luria broth (LB) plus necessary nutrient supplements. In some embodiments, the media also contains a selection agent, chosen based on the construction of the expression vector, to selectively permit growth of prokaryotic cells containing the expression vector. For example, ampicillin is added to media for growth of cells expressing ampicillin resistant gene.

Any necessary supplements besides carbon, nitrogen, and inorganic phosphate sources may also be included at appropriate concentrations introduced alone or as a mixture with another supplement or medium such as a complex nitrogen source. Optionally the culture medium may contain one or more reducing agents selected from the group consisting of glutathione, cysteine, cystamine, thioglycollate, dithioerythritol and dithiothreitol.

The prokaryotic host cells are cultured at suitable temperatures. For E. coli growth, for example, growth occurs at a temperature range including, but not limited to, about 20⁰C to about 39°C, about 25°C to about 37°C, and at about 30⁰C. The pH of the medium may be any pH ranging from about 5 to about 9, depending mainly on the host organism. For E. coli, the pH can be from about 6.8 to about 7.4, or about 7.0.

If an inducible promoter is used in the expression vector of the invention, protein expression is induced under conditions suitable for the activation of the promoter. In one aspect of the invention, PhoA promoters are used for controlling transcription of the polypeptides. Accordingly, the transformed host cells are cultured in a phosphate-limiting medium for induction. In one embodiment, the phosphate-limiting medium is the C.R.A.P. medium (see, e.g., Simmons et al., J Immunol. Methods (2002), 263:133-147). A variety of other inducers may be used, according to the vector construct employed, as is known in the art.

In one embodiment, the expressed polypeptides of the present invention are secreted into and recovered from the periplasm of the host cells. Protein recovery typically involves disrupting the microorganism, generally by such means as osmotic shock, sonication or lysis. Once cells are disrupted, cell debris or whole cells may be removed by centrifugation or filtration. The proteins may be further purified, for example, by affinity resin chromatography. Alternatively, proteins can be transported into the culture media and isolated therein. Cells may be removed from the culture and the culture supernatant being filtered and concentrated for further purification of the proteins produced. The expressed polypeptides can be further isolated and identified using commonly known methods such as polyacrylamide gel electrophoresis (PAGE) and Western blot assay.

In one aspect of the invention, polypeptide production is conducted in large quantity by a fermentation process. Various large-scale fed-batch fermentation procedures are available for production of recombinant proteins. Large-scale fermentations have at least 1000 liters of capacity, for example about 1,000 to 100,000 liters of capacity. These fermentors use agitator impellers to distribute oxygen and nutrients, especially glucose (a common carbon/energy source). Small scale fermentation refers generally to fermentation in a fermentor that is no more than approximately 100 liters in volumetric capacity, and can range from about 1 liter to about 100 liters.

In a fermentation process, induction of protein expression is typically initiated after the cells have been grown under suitable conditions to a desired density, e.g., an OD₅₅O of about 180-220, at which stage the cells are in the early stationary phase. A variety of inducers may be used, according to the vector construct employed, as is known in the art and described above. Cells may be grown for shorter periods prior to induction. Cells are usually induced for about 12-50 hours, although longer or shorter induction time may be used.

To improve the production yield and quality of the polypeptides of the invention, various fermentation conditions can be modified. For example, to improve the proper assembly and folding of the secreted polypeptides (for example, antibody polypeptides), additional vectors overexpressing chaperone proteins, such as Dsb proteins (DsbA, DsbB, DsbC, DsbD and or DsbG) or FkpA (a peptidylprolyl cis,trans-isomerase with chaperone activity) can be used to co-transform the host prokaryotic cells. The chaperone proteins have been demonstrated to facilitate the proper folding and solubility of heterologous proteins produced in bacterial host cells. Chen et al. (1999) J Bio Chem 274: 19601-19605; Georgiou et al., U.S. Patent No. 6,083,715; Georgiou et al., U.S. Patent No. 6,027,888; Bothmann and Pluckthun (200O) J Biol. Chem. 275: 17100-17105; Ramm and Pluckthun (200O) J Biol. Chem. 275: 17106-17113; Arie et al. (2001) MoI. Microbiol. 39: 199-210. To minimize proteolysis of expressed heterologous proteins (especially those that are proteolytically sensitive), certain host strains deficient for proteolytic enzymes can be used for the present invention. For example, host cell strains may be modified to effect genetic mutation(s) in the genes encoding known bacterial proteases such as Protease III, OmpT, DegP, Tsp, Protease I, Protease Mi, Protease V, Protease VI and combinations thereof. Some E. coli protease-deficient strains are available and described in, for example, JoIy et al.

(1998), supra; Georgiou et al., U.S. Patent No. 5,264,365; Georgiou et al., U.S. Patent No. 5,508,192; Hara et al., Microbial Drug Resistance, 2:63-72 (1996).

In one embodiment, E. coli strains deficient for proteolytic enzymes and transformed with plasmids overexpressing one or more chaperone proteins are used as host cells in the expression system of the invention. Antibody Purification

In one embodiment, the antibody protein produced herein is further purified to obtain preparations that are substantially homogeneous for further assays and uses. Standard protein purification methods known in the art can be employed. The following procedures are exemplary of suitable purification procedures: fractionation on immunoaffinity or ion- exchange columns, ethanol precipitation, reverse phase HPLC, chromatography on silica or on a cation-exchange resin such as DEAE, chromatofocusing, SDS-PAGE, ammonium sulfate precipitation, and gel filtration using, for example, Sephadex G-75.

In one aspect, Protein A immobilized on a solid phase is used for immunoaffinity purification of the antibody products of the invention. Protein A is a 4IkD cell wall protein from Staphylococcus aureas which binds with a high affinity to the Fc region of antibodies. Lindmark et al (1983) J Immunol. Meth. 62:1-13. The solid phase to which Protein A is immobilized can be a column comprising a glass or silica surface, or a controlled pore glass column or a silicic acid column. In some applications, the column is coated with a reagent, such as glycerol, to possibly prevent nonspecific adherence of contaminants.

As the first step of purification, the preparation derived from the cell culture as described above can be applied onto a Protein A immobilized solid phase to allow specific binding of the antibody of interest to Protein A. The solid phase would then be washed to remove contaminants non-specifically bound to the solid phase. Finally the antibody of interest is recovered from the solid phase by elution.

Generating polypeptides using eukaryotic host cells

The vector components generally include, but are not limited to, one or more of the following: a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence. (i) Signal sequence component

A vector for use in a eukaryotic host cell may also contain a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide of interest. The heterologous signal sequence selected generally is one that is recognized and processed {i.e., cleaved by a signal peptidase) by the host cell. In mammalian cell expression, mammalian signal sequences as well as viral secretory leaders, for example, the herpes simplex gD signal, are available. The DNA for such precursor region is ligated in reading frame to DNA encoding the polypeptide.

(H) Origin of replication

Generally, an origin of replication component is not needed for mammalian expression vectors. For example, the SV40 origin may typically be used only because it contains the early promoter.

(Ui) Selection gene component

Expression and cloning vectors may contain a selection gene, also termed a selectable marker. Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, where relevant, or (c) supply critical nutrients not available from complex media.

One example of a selection scheme utilizes a drug to arrest growth of a host cell. Those cells that are successfully transformed with a heterologous gene produce a protein conferring drug resistance and thus survive the selection regimen. Examples of such dominant selection use the drugs neomycin, mycophenolic acid and hygromycin.

Another example of suitable selectable markers for mammalian cells are those that enable the identification of cells competent to take up the antibody nucleic acid, such as DHFR, thymidine kinase, metallothionein-I and -II (e.g., primate metallothionein genes), adenosine deaminase, ornithine decarboxylase, etc.

For example, cells transformed with the DHFR selection gene may first be identified by culturing all of the transformants in a culture medium that contains methotrexate (Mtx), a competitive antagonist of DHFR. Appropriate host cells when wild-type DHFR is employed include, for example, the Chinese hamster ovary (CHO) cell line deficient in DHFR activity (e.g., ATCC CRL-9096).

Alternatively, host cells (particularly wild-type hosts that contain endogenous DHFR) transformed or co-transformed with DNA sequences encoding an antibody, wild-type DHFR protein, and another selectable marker such as aminoglycoside 3 '-phosphotransferase (APH) can be selected by cell growth in medium containing a selection agent for the selectable marker such as an aminoglycosidic antibiotic, e.g., kanamycin, neomycin, or G418. See U.S. Patent No. 4,965,199. (iv) Promoter component

Expression and cloning vectors usually contain a promoter that is recognized by the host organism and is operably linked to nucleic acid encoding a polypeptide of interest (e.g., an antibody). Promoter sequences are known for eukaryotes. Virtually all eukaryotic genes have an AT -rich region located approximately 25 to 30 bases upstream from the site where transcription is initiated. Another sequence found 70 to 80 bases upstream from the start of transcription of many genes is a CNCAAT region where N may be any nucleotide. At the 3' end of most eukaryotic genes is an AATAAA sequence that may be the signal for addition of the poly A tail to the 3' end of the coding sequence. All of these sequences are suitably inserted into eukaryotic expression vectors.

Antibody polypeptide transcription from vectors in mammalian host cells can be controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus, adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, or from heat-shock promoters, provided such promoters are compatible with the host cell systems.

The early and late promoters of the S V40 virus are conveniently obtained as an S V40 restriction fragment that also contains the SV40 viral origin of replication. The immediate early promoter of the human cytomegalovirus is conveniently obtained as a HindIII E restriction fragment. A system for expressing DNA in mammalian hosts using the bovine papilloma virus as a vector is disclosed in U.S. Patent No. 4,419,446. A modification of this system is described in U.S. Patent No. 4,601,978. See also Reyes et al, Nature 297:598-601

(1982) on expression of human β-interferon cDNA in mouse cells under the control of a thymidine kinase promoter from herpes simplex virus. Alternatively, the Rous Sarcoma

Virus long terminal repeat can be used as the promoter.

(v) Enhancer element component

Transcription of DNA encoding a polypeptide of the invention by higher eukaryotes can often be increased by inserting an enhancer sequence into the vector. Many enhancer sequences are now known from mammalian genes (globin, elastase, albumin, α-fetoprotein, and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus. Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers. See also Yaniv, Nature 297:17-18 (1982) on enhancing elements for activation of eukaryotic promoters. The enhancer may be spliced into the vector at a position 5' or 3' to the antibody polypep tide-encoding sequence, but is generally located at a site 5' from the promoter. (vi) Transcription termination component

Expression vectors used in eukaryotic host cells will typically also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5' and, occasionally 3', untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of the mRNA encoding an antibody. One useful transcription termination component is the bovine growth hormone polyadenylation region. See WO94/11026 and the expression vector disclosed therein. (vii) Selection and transformation of host cells Suitable host cells for cloning or expressing the DNA in the vectors herein include higher eukaryote cells described herein, including vertebrate host cells. Propagation of vertebrate cells in culture (tissue culture) has become a routine procedure. Examples of useful mammalian host cell lines are monkey kidney CVl 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); Chinese hamster ovary cellsΛDHFR (CHO, Urlaub et al, Proc. Natl. Acad. ScL USA 77:4216 (1980)); mouse Sertoli cells (TM4, Mather, Biol. Reprod. 23:243-251 (1980)); monkey kidney cells (CVl ATCC CCL 70); African green monkey kidney cells (VERO-76, ATCC CRL- 1587); human cervical carcinoma cells (HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo rat liver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL 75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT 060562, ATCC CCL51); TRI cells (Mather et al., Annals NY. Acad. Sci. 383:44-68 (1982)); MRC 5 cells; FS4 cells; and a human hepatoma line (Hep G2).

Host cells are transformed with the above-described expression or cloning vectors for antibody production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences. (viii) Culturing the host cells

The host cells used to produce a polypeptide of this invention may be cultured in a variety of media. Commercially available media such as Ham's FlO (Sigma), Minimal Essential Medium ((MEM), (Sigma), RPMI- 1640 (Sigma), and Dulbecco's Modified Eagle's Medium ((DMEM), Sigma) are suitable for culturing the host cells. In addition, any of the media described in Ham et ah, Meth. Enz. 58:44 (1979), Barnes et ah, Anal. Biochem. \02:255 (1980), U.S. Pat. Nos. 4,767,704; 4,657,866; 4,927,762; 4,560,655; or 5,122,469; WO 90/03430; WO 87/00195; or U.S. Patent Re. 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. (ix) Purification of Polypeptide When using recombinant techniques, the polypeptide of the invention can be produced intracellularly, 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, are generally removed, for example, by centrifugation or ultrafiltration. Where the polypeptide is secreted into the medium, supernatants from such expression systems are generally first concentrated using a commercially available protein concentration filter, for example, an

Amicon or Millipore Pellicon ultrafiltration unit. A protease inhibitor such as PMSF may be included in any of the foregoing steps to inhibit proteolysis and antibiotics may be included to prevent the growth of adventitious contaminants.

The polypeptide composition prepared from the cells can be purified using, for example, hydroxylapatite chromatography, gel electrophoresis, dialysis, and affinity chromatography, with affinity chromatography being a generally acceptable purification technique. The suitability of affinity reagents is understood in the art. For example, the suitability of affinity reagents such as protein A as an affinity ligand for an antibody of the invention depends on the species and isotype of any immunoglobulin Fc domain that is present in the antibody. Protein A can be used to purify antibodies that are based on human γl, γ2, or γ4 heavy chains (Lindmark et ah, J. Immunol. Meth. 62: 1-13 (1983)). Protein G is recommended for all mouse isotypes and for human γ3 (Guss et ah, 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, NJ) is useful for purification. Other techniques for protein purification such as fractionation on an ion-exchange column, ethanol precipitation, Reverse Phase HPLC, chromatography on silica, chromatography on heparin SEPHAROSE™ chromatography on an anion or cation exchange resin (such as a polyaspartic acid column), chromatofocusing, SDS-PAGE, and ammonium sulfate precipitation are also available depending on the antibody to be recovered.

Following any preliminary purification step(s), the mixture comprising the polypeptide of interest and contaminants may be subjected to further purification steps, as necessary. For example, a mixture comprising the antibody of interest and contaminants may be subjected to further purification steps, e.g. low pH hydrophobic interaction chromatography using an elution buffer at a pH between about 2.5-4.5, generally performed at low salt concentrations {e.g., from about 0-0.25M salt).

It should be noted that, in general, techniques and methodologies for preparing polypeptides (for example, antibodies) for use in research, testing and clinical use are well- established in the art, consistent with the above and/or as deemed appropriate by one skilled in the art for the particular polypeptide of interest.

Activity Assays Binding polypeptides of the invention (e.g., antibodies and other DUBA-binding polypeptides) can be characterized for their physical/chemical properties and biological functions by various assays known in the art.

Purified polypeptides of the invention can be further characterized by a series of assays including, but not limited to, N-terminal sequencing, amino acid analysis, non- denaturing size exclusion high pressure liquid chromatography (HPLC), mass spectrometry, ion exchange chromatography and papain digestion. Where necessary, the polypeptides of the invention are analyzed for their biological activity. In some embodiments, antibodies of the invention are tested for their antigen binding activity. The antigen binding assays that are known in the art and can be used herein include without limitation any direct or competitive binding assays using techniques such as western blots, radioimmunoassays, ELISA (enzyme linked immunosorbent assay),

"sandwich" immunoassays, immunoprecipitation assays, fluorescent immunoassays, and protein A immunoassays.

In one embodiment, the invention contemplates an altered antibody that possesses some but not all effector functions, which make it a desirable candidate for many applications in which the half life of the antibody in vivo is important yet certain effector functions (such as complement and ADCC) are unnecessary or deleterious. In certain embodiments, the Fc activities of the antibody are measured to ensure that only the desired properties are maintained. In vitro and/or in vivo cytotoxicity assays can be conducted to confirm the reduction/depletion of CDC and/or ADCC activities. For example, Fc receptor (FcR) binding assays can be conducted to ensure that the antibody lacks FcγR binding (hence likely lacking ADCC activity), but retains FcRn binding ability. The primary cells for mediating ADCC, NK cells, express FcγRIII only, whereas monocytes express FcγRI, FcγRII and FcγRIII. FcR expression on hematopoietic cells is summarized in Table 3 on page 464 of Ravetch and Kinet, Annu. Rev. Immunol 9:457-92 (1991). An example of an in vitro assay to assess ADCC activity of a molecule of interest is described in U.S. Patent No. 5,500,362 or

5,821,337. Useful effector cells for such assays include peripheral blood mononuclear cells (PBMC) and Natural Killer (NK) cells. Alternatively, or additionally, ADCC activity of the molecule of interest may be assessed in vivo, e.g., in a animal model such as that disclosed in Clynes et al. PNAS (USA) 95:652-656 (1998). CIq binding assays may also be carried out to confirm that the antibody is unable to bind CIq and hence lacks CDC activity. To assess complement activation, a CDC assay, e.g. as described in Gazzano-Santoro et al., J. Immunol. Methods 202: 163 (1996), may be performed. FcRn binding and in vivo clearance/half life determinations can also be performed using methods known in the art. Antibody Fragments The present invention encompasses antibody fragments. In certain circumstances there are advantages of using antibody fragments, rather than whole antibodies. The smaller size of the fragments allows for rapid clearance, and may lead to improved access to solid tumors. Various techniques have been developed for the production of antibody fragments. Traditionally, these fragments were derived via proteolytic digestion of intact antibodies (see, e.g., Morimoto et al., Journal of Biochemical and Biophysical Methods 24:107-117 (1992); and Brennan et al., Science, 229:81 (1985)). However, these fragments can now be produced directly by recombinant host cells. Fab, Fv and ScFv antibody fragments can all be expressed in and secreted from E. coli, thus allowing the facile production of large amounts of these fragments. Antibody fragments can be isolated from the antibody phage libraries discussed above. Alternatively, Fab'-SH fragments can be directly recovered from E. coli and chemically coupled to form F(ab')₂ fragments (Carter et al., Bio/Technology 10:163-167 (1992)). According to another approach, F(ab')₂ fragments can be isolated directly from recombinant host cell culture. Fab and F(ab')₂ fragment with increased in vivo half-life comprising salvage receptor binding epitope residues are described in U.S. Pat. No. 5,869,046. Other techniques for the production of antibody fragments will be apparent to the skilled practitioner. In other embodiments, the antibody of choice is a single chain Fv fragment (scFv). See WO 93/16185; U.S. Pat. Nos. 5,571,894; and 5,587,458. Fv and sFv are the only species with intact combining sites that are devoid of constant regions; thus, they are suitable for reduced nonspecific binding during in vivo use. sFv fusion proteins may be constructed to yield fusion of an effector protein at either the amino or the carboxy terminus of an sFv. See Antibody Engineering, ed. Borrebaeck, supra. The antibody fragment may also be a "linear antibody", e.g., as described in U.S. Pat. No. 5,641,870 for example. Such linear antibody fragments may be monospecific or bispecific. Humanized Antibodies

The invention encompasses humanized antibodies. Various methods for humanizing non-human antibodies are known in the art. For example, a humanized antibody can have one or more amino acid residues introduced into it from a source which is non-human. These non-human amino acid residues are often referred to as "import" residues, which are typically taken from an "import" variable domain. Humanization can be essentially performed following the method of Winter and co-workers (Jones et al (1986) Nature 321:522-525; Riechmann et al (1988) Nature 332:323-327; Verhoeyen et al (1988) Science 239:1534- 1536), by substituting hypervariable region sequences for the corresponding sequences of a human antibody. Accordingly, such "humanized" antibodies are chimeric antibodies (U.S. Patent No. 4,816,567) wherein substantially less than an intact human variable domain has been substituted by the corresponding sequence from a non-human species. In practice, humanized antibodies are typically human antibodies in which some hypervariable region residues and possibly some FR residues are substituted by residues from analogous sites in rodent antibodies.

The choice of human variable domains, both light and heavy, to be used in making the humanized antibodies can be important to reduce antigenicity. According to the so-called "best-fit" method, the sequence of the variable domain of a rodent antibody is screened against the entire library of known human variable-domain sequences. The human sequence which is closest to that of the rodent is then accepted as the human framework for the humanized antibody (Sims et al. (1993) J Immunol. 151:2296; Chothia et al. (1987) J MoI. Biol. 196:901. Another method uses a particular framework derived from the consensus sequence of all human antibodies of a particular subgroup of light or heavy chains. The same framework may be used for several different humanized antibodies (Carter et al. (1992) Proc. Natl. Acad. ScL USA, 89:4285; Presta et al. (1993) J Immunol, 151:2623.

It is further generally desirable that antibodies be humanized with retention of high affinity for the antigen and other favorable biological properties. To achieve this goal, according to one method, humanized antibodies are prepared by a process of analysis of the parental sequences and various conceptual humanized products using three-dimensional models of the parental and humanized sequences. Three-dimensional immunoglobulin models are commonly available and are familiar to those skilled in the art. Computer programs are available which illustrate and display probable three-dimensional conformational structures of selected candidate immunoglobulin sequences. Inspection of these displays permits analysis of the likely role of the residues in the functioning of the candidate immunoglobulin sequence, i.e., the analysis of residues that influence the ability of the candidate immunoglobulin to bind its antigen. In this way, FR residues can be selected and combined from the recipient and import sequences so that the desired antibody characteristic, such as increased affinity for the target antigen(s), is achieved. In general, the hypervariable region residues are directly and most substantially involved in influencing antigen binding.

Human antibodies

Human anti-DUBA antibodies of the invention can be constructed by combining Fv clone variable domain sequence(s) selected from human-derived phage display libraries with known human constant domain sequences(s) as described above. Alternatively, human monoclonal anti-DUBA antibodies of the invention can be made by the hybridoma method. Human myeloma and mouse-human heteromyeloma cell lines for the production of human monoclonal antibodies have been described, for example, by Kozbor J Immunol, 133: 3001 (1984); Brodeur et al, Monoclonal Antibody Production Techniques and Applications, pp. 51-63 (Marcel Dekker, Inc., New York, 1987); and Boerner et al, J. Immunol, 147: 86 (1991). It is now possible to produce transgenic animals (e.g. mice) that are capable, upon immunization, of producing a full repertoire of human antibodies in the absence of endogenous immunoglobulin production. For example, it has been described that the homozygous deletion of the antibody heavy-chain joining region (JH) gene in chimeric and germ-line mutant mice results in complete inhibition of endogenous antibody production. Transfer of the human germ-line immunoglobulin gene array in such germ-line mutant mice will result in the production of human antibodies upon antigen challenge. See, e.g., Jakobovits et al, Proc. Natl Acad. Sci USA, 90: 2551 (1993); Jakobovits et al, Nature, 362: 255 (1993); Bruggermann et al, Year in Immunol, 7: 33 (1993).

Gene shuffling can also be used to derive human antibodies from non-human, e.g. rodent, antibodies, where the human antibody has similar affinities and specificities to the starting non-human antibody. According to this method, which is also called "epitope imprinting", either the heavy or light chain variable region of a non-human antibody fragment obtained by phage display techniques as described above is replaced with a repertoire of human V domain genes, creating a population of non-human chain/human chain scFv or Fab chimeras. Selection with antigen results in isolation of a non-human chain/human chain chimeric scFv or Fab wherein the human chain restores the antigen binding site destroyed upon removal of the corresponding non-human chain in the primary phage display clone, i.e. the epitope governs (imprints) the choice of the human chain partner. When the process is repeated in order to replace the remaining non-human chain, a human antibody is obtained (see PCT WO 93/06213 published April 1, 1993). Unlike traditional humanization of non- human antibodies by CDR grafting, this technique provides completely human antibodies, which have no FR or CDR residues of non-human origin. Bispecific Antibodies

Bispecific antibodies are monoclonal antibodies that have binding specificities for at least two different antigens. In certain embodiments, bispecific antibodies are human or humanized antibodies. In certain embodiments, one of the binding specificities is for DUBA and the other is for any other antigen. Bispecific antibodies can be prepared as full length antibodies or antibody fragments {e.g. F(ab')₂ bispecific antibodies). Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy chain-light chain pairs, where the two heavy chains have different specificities (Milstein and Cuello, Nature, 305: 537 (1983)). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of 10 different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule, which is usually done by affinity chromatography steps, is rather cumbersome, and the product yields are low. Similar procedures are disclosed in WO 93/08829 published May 13, 1993, and in Traunecker et al, EMBO J., 10: 3655 (1991).

According to a different embodiment, antibody variable domains with the desired binding specificities (antibody-antigen combining sites) are fused to immunoglobulin constant domain sequences. The fusion, for example, is with an immunoglobulin heavy chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. In certain embodiments, the first heavy-chain constant region (CHl), containing the site necessary for light chain binding, is present in at least one of the fusions. DNAs encoding the immunoglobulin heavy chain fusions and, if desired, the immunoglobulin light chain, are inserted into separate expression vectors, and are co-transfected into a suitable host organism. This provides for great flexibility in adjusting the mutual proportions of the three polypeptide fragments in embodiments when unequal ratios of the three polypeptide chains used in the construction provide the optimum yields. It is, however, possible to insert the coding sequences for two or all three polypeptide chains in one expression vector when the expression of at least two polypeptide chains in equal ratios results in high yields or when the ratios are of no particular significance. In one embodiment of this approach, the bispecific antibodies are composed of a hybrid immunoglobulin heavy chain with a first binding specificity in one arm, and a hybrid immunoglobulin heavy chain-light chain pair (providing a second binding specificity) in the other arm. It was found that this asymmetric structure facilitates the separation of the desired bispecific compound from unwanted immunoglobulin chain combinations, as the presence of an immunoglobulin light chain in only one half of the bispecific molecule provides for a facile way of separation. This approach is disclosed in WO 94/04690. For further details of generating bispecific antibodies see, for example, Suresh et al, Methods in Enzymology, 121 :210 (1986). According to another approach, the interface between a pair of antibody molecules can be engineered to maximize the percentage of heterodimers which are recovered from recombinant cell culture. The 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.

Bispecific 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. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (US Patent No. 4,676,980), and for treatment of HIV infection (WO 91/00360, WO 92/00373, and EP 03089). 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 US Patent No. 4,676,980, along with a number of cross-linking techniques.

Techniques for generating bispecific antibodies from antibody fragments have also been described in the literature. For example, bispecific antibodies can be prepared using chemical linkage. Brennan et ah, Science, 229: 81 (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate F(ab')₂ fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation. The Fab' fragments generated are then converted to thionitrobenzoate (TNB) derivatives. One of the Fab'-TNB derivatives is then reconverted to the Fab'-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab'-TNB derivative to form the bispecific antibody. The bispecific antibodies produced can be used as agents for the selective immobilization of enzymes. Recent progress has facilitated the direct recovery of Fab'-SH fragments from E. coli, which can be chemically coupled to form bispecific antibodies. Shalaby et ah, J. Exp. Med., 175: 217-225 (1992) describe the production of a fully humanized bispecific antibody F(ab')₂ molecule. Each Fab' fragment was separately secreted from E. coli and subjected to directed chemical coupling in vitro to form the bispecific antibody. 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 antibody fragments directly from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers. 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. The "diabody" technology described by Hollinger et al, Proc. Natl. Acad. Sci. USA, 90:6444- 6448 (1993) has provided an alternative mechanism for making bispecific antibody fragments. The fragments comprise a heavy-chain variable domain (VH) connected to a light-chain variable domain (VL) by a linker which is too short to allow pairing between the two domains on the same chain. Accordingly, the VH and VL domains of one fragment are forced to pair with the complementary VL and VH domains of another fragment, thereby forming two antigen-binding sites. Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) dimers has also been reported. See Gruber et al, J. Immunol, 152:5368 (1994). Antibodies with more than two valencies are contemplated. For example, trispecific antibodies can be prepared. Tutt et al J. Immunol 147: 60 (1991). Multivalent Antibodies

A multivalent antibody may be internalized (and/or catabolized) faster than a bivalent antibody by a cell expressing an antigen to which the antibodies bind. The antibodies of the present invention can be multivalent antibodies (which are other than of the IgM class) with three or more antigen binding sites (e.g. tetravalent antibodies), which can be readily produced by recombinant expression of nucleic acid encoding the polypeptide chains of the antibody. The multivalent antibody can comprise a dimerization domain and three or more antigen binding sites. The dimerization domain comprises (or consists of), for example, an Fc region or a hinge region. In this scenario, the antibody will comprise an Fc region and three or more antigen binding sites amino-terminal to the Fe region. In one embodiment, a multivalent antibody comprises (or consists of), for example, three to about eight, or four antigen binding sites. The multivalent antibody comprises at least one polypeptide chain (for example, two polypeptide chains), wherein the polypeptide chain(s) comprise two or more variable domains. For instance, the polypeptide chain(s) may comprise VDl-(Xl)n -VD2- (X2)n -Fc, wherein VDl is a first variable domain, VD2 is a second variable domain, Fc is one polypeptide chain of an Fc region, Xl and X2 represent an amino acid or polypeptide, and n is 0 or 1. For instance, the polypeptide chain(s) may comprise: VH-CHl -flexible linker-VH-CHl-Fc region chain; or VH-CHl -VH-CHl -Fc region chain. The multivalent antibody herein may further comprise at least two (for example, four) light chain variable domain polypeptides. The multivalent antibody herein may, for instance, comprise from about two to about eight light chain variable domain polypeptides. The light chain variable domain polypeptides contemplated here comprise a light chain variable domain and, optionally, further comprise a CL domain.

Polypeptide Variants

In some embodiments, amino acid sequence modification(s) of the polypeptides described herein are contemplated. For example, it may be desirable to improve the binding affinity and/or other biological properties of an antibody of the invention. Amino acid sequence variants of the antibody are prepared by introducing appropriate nucleotide changes into the antibody nucleic acid, or by peptide synthesis. Such modifications include, for example, deletions from, and/or insertions into and/or substitutions of, residues within the amino acid sequences of the antibody. Any combination of deletion, insertion, and substitution can be made to arrive at the final construct, provided that the final construct possesses the desired characteristics. The amino acid alterations may be introduced in the subject antibody amino acid sequence at the time that sequence is made.

The invention also provides variant versions of the proteins of the invention (including, but not limited to, anti-DUBA antibodies or fragments thereof, peptides, and other DUBA-binding polypeptides). In such variant proteins, any residues may be changed from the corresponding residues of the protein, while still encoding a protein that maintains modulatory activity. In one embodiment, a variant of an anti-DUBA antibody or fragment thereof, a peptide, or another DUBA-binding polypeptide has at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, 99% amino acid sequence identity with the sequence of a reference anti- DUBA antibody or fragment thereof, peptide, or other DUBA-binding polypeptide. In general, the variant exhibits substantially the same or greater binding affinity than the reference anti-DUBA antibody or fragment thereof, peptide, or other DUBA-binding polypeptide, e.g., at least 0.75X, 0.8X, 0.9X, 1.0X, 1.25X or 1.5X the binding affinity of the reference anti-DUBA antibody or fragment thereof, peptide, or other DUBA-binding polypeptide, based on an art-accepted binding assay quantitation unit/metric.

In general, variants of the invention include variants in which residues at a particular position in the sequence have been substituted by other amino acids, and further includes the possibility of inserting an additional residue or residues between two residues of the parent protein/peptide as well as the possibility of deleting one or more residues from the parent sequence or adding one or more residues to the parent sequence. Any amino acid substitution, insertion, or deletion is encompassed by the invention. In certain circumstances, the substitution is a conservative substitution as described herein. "Percent (%) amino acid sequence identity" is defined as the percentage of amino acid residues that are identical with amino acid residues in a reference (parent) polypeptide sequence when the two sequences are aligned. To determine % amino acid identity, sequences are aligned and if necessary, gaps are introduced to achieve the maximum % sequence identity; conservative substitutions are not considered as part of the sequence identity. Amino acid sequence alignment procedures to determine percent identity are well known to those of skill in the art. Often publicly available computer software such as BLAST, BLAST2, ALIGN2 or Megalign (DNASTAR) software is used to align peptide sequences. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.

When amino acid sequences are aligned, the % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B (which can alternatively be phrased as a given amino acid sequence A that has or comprises a certain % amino acid sequence identity to, with, or against a given amino acid sequence B) can be calculated as:

% amino acid sequence identity = X/Y ^' 100 where

X is the number of amino acid residues scored as identical matches by the sequence alignment program's or algorithm's alignment of A and B and Y is the total number of amino acid residues in B. If the length of amino acid sequence A is not equal to the length of amino acid sequence B, the % amino acid sequence identity of A to B will not equal the % amino acid sequence identity of B to A.

A useful method for identification of certain residues or regions of the polypeptides of the invention that are preferred locations for mutagenesis is called "alanine scanning mutagenesis" as described by Cunningham and Wells (1989) Science, 244: 1081-1085. Here, a residue or group of target residues are identified (e.g., charged residues such as arg, asp, his, lys, and glu) and replaced by a neutral or negatively charged amino acid (e.g., alanine or polyalanine) to affect the interaction of the amino acids with antigen. Those amino acid locations demonstrating functional sensitivity to the substitutions then are refined by introducing further or other variants at, or for, the sites of substitution. Thus, while the site for introducing an amino acid sequence variation is predetermined, the nature of the mutation per se need not be predetermined. For example, to analyze the performance of a mutation at a given site, ala scanning or random mutagenesis is conducted at the target codon or region and the expressed polypeptides are screened for the desired activity.

Amino acid sequence insertions include amino- and/or carboxyl-terminal fusions ranging in length from one residue to polypeptides containing a hundred or more residues, as well as intrasequence insertions of single or multiple amino acid residues. Examples of terminal insertions include an antibody with an N-terminal methionyl residue or the antibody fused to a cytotoxic polypeptide. Other insertional variants of the antibody molecule include the fusion to the N- or C-terminus of the antibody to an enzyme (e.g. for ADEPT) or a polypeptide which increases the serum half-life of the antibody.

Another type of variant is an amino acid substitution variant. These variants have at least one amino acid residue in the polypeptide molecule replaced by a different residue. The sites of greatest interest for substitutional mutagenesis in the antibodies of the invention include the hypervariable regions, but FR alterations are also contemplated. Conservative substitutions are shown in Table A under the heading of "preferred substitutions". If such substitutions result in a change in biological activity, then more substantial changes, denominated "exemplary substitutions" in Table A, or as further described below in reference to amino acid classes, may be introduced and the products screened. TABLE A

Substantial modifications in the biological properties of the polypeptide are accomplished by selecting substitutions that differ significantly in their effect on maintaining (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a sheet or helical conformation, (b) the charge or hydrophobicity of the molecule at the target site, or (c) the bulk of the side chain. Amino acids may be grouped according to similarities in the properties of their side chains (in A. L. Lehninger, in Biochemistry, second ed., pp. 73- 75, Worth Publishers, New York (1975)): (1) non-polar: Ala (A), VaI (V), Leu (L), He (I), Pro (P), Phe (F), Trp (W), Met (M) (2) uncharged polar: GIy (G), Ser (S), Thr (T), Cys (C), Tyr (Y), Asn (N), GIn (Q)

(3) acidic: Asp (D), GIu (E)

(4) basic: Lys (K), Arg (R), His(H)

Alternatively, naturally occurring residues may be divided into groups based on common side-chain properties:

(1) hydrophobic: Norleucine, Met, Ala, VaI, Leu, He;

(2) neutral hydrophilic: Cys, Ser, Thr, Asn, GIn;

(3) acidic: Asp, GIu;

(4) basic: His, Lys, Arg; (5) residues that influence chain orientation: GIy, Pro;

(6) aromatic: Trp, Tyr, Phe.

Non-conservative substitutions will entail exchanging a member of one of these classes for another class. Such substituted residues also may be introduced into the conservative substitution sites or, into the remaining (non-conserved) sites.

One type of substitutional variant involves substituting one or more hypervariable region residues of a parent antibody (e.g. a humanized or human antibody). Generally, the resulting variant(s) selected for further development will have modified (e.g., improved) biological properties relative to the parent antibody from which they are generated. A convenient way for generating such substitutional variants involves affinity maturation using phage display. Briefly, several hypervariable region sites (e.g. 6-7 sites) are mutated to generate all possible amino acid substitutions at each site. The antibodies thus generated are displayed from filamentous phage particles as fusions to at least part of a phage coat protein (e.g., the gene III product of M13) packaged within each particle. The phage-displayed variants are then screened for their biological activity (e.g. binding affinity) as herein disclosed. In order to identify candidate hypervariable region sites for modification, scanning mutagenesis (e.g., alanine scanning) can be performed to identify hypervariable region residues contributing significantly to antigen binding. Alternatively, or additionally, it may be beneficial to analyze a crystal structure of the antigen-antibody complex to identify contact points between the antibody and antigen. Such contact residues and neighboring residues are candidates for substitution according to techniques known in the art, including those elaborated herein. Once such variants are generated, the panel of variants is subjected to screening using techniques known in the art, including those described herein, and antibodies with superior properties in one or more relevant assays may be selected for further development.

Nucleic acid molecules encoding amino acid sequence variants of the polypeptides of the invention are prepared by a variety of methods known in the art. These methods include, but are not limited to, isolation from a natural source (in the case of naturally occurring amino acid sequence variants) or preparation by oligonucleotide-mediated (or site-directed) mutagenesis, PCR mutagenesis, and cassette mutagenesis of an earlier prepared variant or a non- variant version of the polypeptide.

It may be desirable to introduce one or more amino acid modifications in an Fc region of antibodies of the invention, thereby generating an Fc region variant. The Fc region variant may comprise a human Fc region sequence (e.g., a human IgGl, IgG2, IgG3 or IgG4 Fc region) comprising an amino acid modification (e.g. a substitution) at one or more amino acid positions including that of a hinge cysteine.

In accordance with this description and the teachings of the art, it is contemplated that in some embodiments, an antibody of the invention may comprise one or more alterations as compared to the wild type counterpart antibody, e.g. in the Fc region. These antibodies would nonetheless retain substantially the same characteristics required for therapeutic utility as compared to their wild type counterpart. For example, it is thought that certain alterations can be made in the Fc region that would result in altered (i.e., either improved or diminished) CIq binding and/or Complement Dependent Cytotoxicity (CDC), e.g., as described in WO99/51642. Such variants may comprise an amino acid substitution at one or more of amino acid positions 270, 322, 326, 327, 329, 331, 333 or 334 of the Fc region. See also Duncan & Winter Nature 322:738-40 (1988); U.S. Patent No. 5,648,260; U.S. Patent No. 5,624,821; and WO94/29351 concerning other examples of Fc region variants. In one aspect, the invention provides antibodies comprising modifications in the interface of Fc polypeptides comprising the Fc region, wherein the modifications facilitate and/or promote heterodimerization. These modifications comprise introduction of a protuberance into a first Fc polypeptide and a cavity into a second Fc polypeptide, wherein the protuberance is positionable in the cavity so as to promote complexing of the first and second Fc polypeptides. Methods of generating antibodies with these modifications are known in the art, e.g., as described in U.S. Pat. No. 5,731,168. Immunoconjugates

In another aspect, the invention provides immunoconjugates, or antibody-drug conjugates (ADC), comprising an antibody conjugated to a cytotoxic agent such as a chemotherapeutic agent, a drug, a growth inhibitory agent, a toxin (e.g., an enzymatically active toxin of bacterial, fungal, plant, or animal origin, or fragments thereof), or a radioactive isotope (i.e., a radioconjugate).

The use of antibody-drug conjugates for the local delivery of cytotoxic or cytostatic agents, i.e. drugs to kill or inhibit tumor cells in the treatment of cancer (Syrigos and Epenetos (1999) Anticancer Research 19:605-614; Niculescu-Duvaz and Springer (1997) Adv. Drg Del. Rev. 26: 151-172; U.S. patent 4,975,278) allows targeted delivery of the drug moiety to tumors, and intracellular accumulation therein, where systemic administration of these unconjugated drug agents may result in unacceptable levels of toxicity to normal cells as well as the tumor cells sought to be eliminated (Baldwin et al., (1986) Lancet pp. (Mar. 15, 1986):603-05; Thorpe, (1985) "Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Review," in Monoclonal Antibodies '84: Biological And Clinical Applications, A. Pinchera et al. (eds.), pp. 475-506). Maximal efficacy with minimal toxicity is sought thereby. Both polyclonal antibodies and monoclonal antibodies have been reported as useful in these strategies (Rowland et al., (1986) Cancer Immunol. Immunother., 21 : 183-87). Drugs used in these methods include daunomycin, doxorubicin, methotrexate, and vindesine (Rowland et al., (1986) supra). Toxins used in antibody-toxin conjugates include bacterial toxins such as diphtheria toxin, plant toxins such as ricin, small molecule toxins such as geldanamycin (Mandler et al (2000) Jour, of the Nat. Cancer Inst. 92(19): 1573-1581; Mandler et al (2000) Bioorganic & Med. Chem. Letters 10: 1025-1028; Mandler et al (2002) Bioconjugate Chem. 13:786-791), maytansinoids (EP 1391213; Liu et al., (1996) Proc. Natl. Acad. Sci. USA 93:8618-8623), and calicheamicin (Lode et al (1998) Cancer Res. 58:2928; Hinman et al (1993) Cancer Res. 53:3336-3342). The toxins may effect their cytotoxic and cytostatic effects by mechanisms including tubulin binding, DNA binding, or topoisomerase inhibition. Some cytotoxic drugs tend to be inactive or less active when conjugated to large antibodies or protein receptor ligands. ZEVALIN® (ibritumomab tiuxetan, Biogen/Idec) is an antibody-radioisotope conjugate composed of a murine IgGl kappa monoclonal antibody directed against the CD20 antigen found on the surface of normal and malignant B lymphocytes and ¹¹¹In or ⁹⁰Y radioisotope bound by a thiourea linker-chelator (Wiseman et al (2000) Eur. Jour. Nucl. Med. 27(7):766-77; Wiseman et al (2002) Blood 99(12):4336-42; Witzig et al (2002) J. Clin. Oncol. 20(10):2453-63; Witzig et al (2002) J. Clin. Oncol. 20(15):3262-69). Although ZEVALIN has activity against B-cell non-Hodgkin's Lymphoma (NHL), administration results in severe and prolonged cytopenias in most patients. MYLOTARG™ (gemtuzumab ozogamicin, Wyeth Pharmaceuticals), an antibody drug conjugate composed of a hu CD33 antibody linked to calicheamicin, was approved in 2000 for the treatment of acute myeloid leukemia by injection (Drugs of the Future (2000) 25(7):686; U.S. Patent Nos. 4970198; 5079233; 5585089; 5606040; 5693762; 5739116; 5767285; 5773001). Cantuzumab mertansine (Immunogen, Inc.), an antibody drug conjugate composed of the huC242 antibody linked via the disulfide linker SPP to the maytansinoid drug moiety, DMl, is tested for the treatment of cancers that express CanAg, such as colon, pancreatic, gastric, and others. MLN-2704 (Millennium Pharm., BZL Biologies, Immunogen Inc.), an antibody drug conjugate composed of the anti-prostate specific membrane antigen (PSMA) monoclonal antibody linked to the maytansinoid drug moiety, DMl, is tested for the potential treatment of prostate tumors. The auristatin peptides, auristatin E (AE) and monomethylauristatin

(MMAE), synthetic analogs of dolastatin, were conjugated to chimeric monoclonal antibodies cBR96 (specific to Lewis Y on carcinomas) and cAClO (specific to CD30 on hematological malignancies) (Doronina et al (2003) Nature Biotechnology 21 (7):778-784) and are under therapeutic development. Chemotherapeutic agents useful in the generation of immunoconjugates are described herein (above). Enzymatically active toxins and fragments thereof that can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes. See, e.g., WO 93/21232 published October 28, 1993. A variety of radionuclides are available for the production of radioconjugated antibodies. Examples include ²¹²Bi, ¹³¹I, ¹³¹In, ⁹⁰Y, and ¹⁸⁶Re. Conjugates of the antibody and cytotoxic agent are made using a variety of bifunctional protein-coupling agents such as N-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCl), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis- azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as toluene 2,6- diisocyanate), and bis-active fluorine compounds (such as l,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin can be prepared as described in Vitetta et al., Science, 238: 1098 (1987). Carbon- 14-labeled l-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See WO94/11026.

Conjugates of an antibody and one or more small molecule toxins, such as a calicheamicin, maytansinoids, dolostatins, aurostatins, a trichothecene, and CC 1065, and the derivatives of these toxins that have toxin activity, are also contemplated herein. Maytansine and maytansinoids

In some embodiments, the immunoconjugate comprises an antibody of the invention conjugated to one or more maytansinoid molecules.

Maytansinoids are mitotic inhibitors which act by inhibiting tubulin polymerization. Maytansine was first isolated from the east African shrub Maytenus serrata (U.S. Patent No. 3,896,111). Subsequently, it was discovered that certain microbes also produce maytansinoids, such as maytansinol and C-3 maytansinol esters (U.S. Patent No. 4,151,042). Synthetic maytansinol and derivatives and analogues thereof are disclosed, for example, in U.S. Patent Nos. 4,137,230; 4,248,870; 4,256,746; 4,260,608; 4,265,814; 4,294,757; 4,307,016; 4,308,268; 4,308,269; 4,309,428; 4,313,946; 4,315,929; 4,317,821; 4,322,348; 4,331,598; 4,361,650; 4,364,866; 4,424,219; 4,450,254; 4,362,663; and 4,371,533.

Maytansinoid drug moieties are attractive drug moieties in antibody drug conjugates because they are: (i) relatively accessible to prepare by fermentation or chemical modification, derivatization of fermentation products, (ii) amenable to derivatization with functional groups suitable for conjugation through the non-disulfide linkers to antibodies, (iii) stable in plasma, and (iv) effective against a variety of tumor cell lines.

Exemplary embodiments of maytansinoid drug moieties include: DMl; DM3; and DM4. Immunoconjugates containing maytansinoids, methods of making same, and their therapeutic use are disclosed, for example, in U.S. Patent Nos. 5,208,020, 5,416,064 and European Patent EP 0 425 235 Bl, the disclosures of which are hereby expressly incorporated by reference. Liu et al., Proc. Natl. Acad. Sci. USA 93:8618-8623 (1996) described immunoconjugates comprising a maytansinoid designated DMl linked to the monoclonal antibody C242 directed against human colorectal cancer. The conjugate was found to be highly cytotoxic towards cultured colon cancer cells, and showed antitumor activity in an in vivo tumor growth assay. Chari et al., Cancer Research 52:127-131 (1992) describe immunoconjugates in which a maytansinoid was conjugated via a disulfide linker to the murine antibody A7 binding to an antigen on human colon cancer cell lines, or to another murine monoclonal antibody TA.1 that binds the HER-2/neu oncogene. The cytotoxicity of the TA.l-maytansonoid conjugate was tested in vitro on the human breast cancer cell line SK-BR-3, which expresses 3 x 10⁵ HER-2 surface antigens per cell. The drug conjugate achieved a degree of cytotoxicity similar to the free maytansinoid drug, which could be increased by increasing the number of maytansinoid molecules per antibody molecule. The A7-maytansinoid conjugate showed low systemic cytotoxicity in mice.

Antibody-maytansinoid conjugates can be prepared by chemically linking an antibody to a maytansinoid molecule without significantly diminishing the biological activity of either the antibody or the maytansinoid molecule. See, e.g., U.S. Patent No. 5,208,020 (the disclosure of which is hereby expressly incorporated by reference). An average of 3-4 maytansinoid molecules conjugated per antibody molecule has shown efficacy in enhancing cytotoxicity of target cells without negatively affecting the function or solubility of the antibody, although even one molecule of toxin/antibody would be expected to enhance cytotoxicity over the use of naked antibody. Maytansinoids are well known in the art and can be synthesized by known techniques or isolated from natural sources. Suitable maytansinoids are disclosed, for example, in U.S. Patent No. 5,208,020 and in the other patents and nonpatent publications referred to hereinabove. Maytansinoids include, but are not limited to, maytansinol and maytansinol analogues modified in the aromatic ring or at other positions of the maytansinol molecule, such as various maytansinol esters.

There are many linking groups known in the art for making antibody-maytansinoid conjugates, including, for example, those disclosed in U.S. Patent No. 5,208,020 or EP Patent 0 425 235 Bl, Chari et al, Cancer Research 52:127-131 (1992), and U.S. Patent Application No. 10/960,602, filed Oct. 8, 2004, the disclosures of which are hereby expressly incorporated by reference. Antibody-maytansinoid conjugates comprising the linker component SMCC may be prepared as disclosed in U.S. Patent Application No. 10/960,602, filed Oct. 8, 2004. The linking groups include disulfide groups, thioether groups, acid labile groups, photolabile groups, peptidase labile groups, or esterase labile groups, as disclosed in the above-identified patents. Additional linking groups are described and exemplified herein.

Conjugates of the antibody and maytansinoid may be made using a variety of bifunctional protein coupling agents such as N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP), succinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCl), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis- azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as toluene 2,6- diisocyanate), and bis-active fluorine compounds (such as l,5-difluoro-2,4-dinitrobenzene). Coupling agents include, but are not limited to, N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP) (Carlsson et al, Biochem. J. 173:723-737 (1978)) and N-succinimidyl-4- (2-pyridylthio)pentanoate (SPP) to provide for a disulfide linkage.

The linker may be attached to the maytansinoid molecule at various positions, depending on the type of the link. For example, an ester linkage may be formed by reaction with a hydroxyl group using conventional coupling techniques. The reaction may occur at the C-3 position having a hydroxyl group, the C- 14 position modified with hydroxym ethyl, the C- 15 position modified with a hydroxyl group, and the C-20 position having a hydroxyl group. In one embodiment, the linkage is formed at the C-3 position of maytansinol or a maytansinol analogue.

Auristatins and dolostatins

In some embodiments, the immunoconjugate comprises an antibody of the invention conjugated to dolastatins or dolostatin peptidic analogs and derivatives, the auristatins (U.S. Patent Nos. 5635483; 5780588). Dolastatins and auristatins have been shown to interfere with microtubule dynamics, GTP hydrolysis, and nuclear and cellular division (Woyke et al (2001) Antimicrob. Agents and Chemother. 45(12):3580-3584) and have anticancer (U.S. 5663149) and antifungal activity (Pettit et al (1998) Antimicrob. Agents Chemother. 42:2961-2965). The dolastatin or auristatin drug moiety may be attached to the antibody through the N (amino) terminus or the C (carboxyl) terminus of the peptidic drug moiety (WO 02/088172).

Exemplary auristatin embodiments include the N-terminus linked monomethylauristatin drug moieties DE and DF, disclosed in "Monomethylvaline Compounds Capable of Conjugation to Ligands", U.S. Ser. No. 10/983,340, filed Nov. 5, 2004, the disclosure of which is expressly incorporated by reference in its entirety. Exemplary auristatin embodiments include MMAE and MMAF. Additional exemplary embodiments comprising MMAE or MMAF and various linker components (described further herein) include Ab-MC-vc-P AB-MMAF, Ab-MC-vc-P AB-MMAE, Ab- MC-MMAE and Ab-MC-MMAF. Typically, peptide-based drug moieties can be prepared by forming a peptide bond between two or more amino acids and/or peptide fragments. Such peptide bonds can be prepared, for example, according to the liquid phase synthesis method (see E. Schroder and K. Lubke, "The Peptides", volume 1, pp 76-136, 1965, Academic Press) that is well known in the field of peptide chemistry. The auristatin/dolastatin drug moieties may be prepared according to the methods of: U.S. 5,635,483; U.S. 5,780,588; Pettit et al (1989) J. Am. Chem. Soc. 111:5463-5465; Pettit et al (1998) Anti-Cancer Drug Design 13:243-277; Pettit, G.R., et al. Synthesis, 1996, 719-725; and Pettit et al (1996) J. Chem. Soc. Perkin Trans. 1 5:859-863. See also Doronina (2003) Nat Biotechnol 21(7):778-784; "Monomethylvaline Compounds Capable of Conjugation to Ligands", U.S. Ser. No. 10/983,340, filed Nov. 5, 2004, hereby incorporated by reference in its entirety (disclosing, e.g., linkers and methods of preparing monomethylvaline compounds such as MMAE and MMAF conjugated to linkers).

Calicheamicin

In other embodiments, the immunoconjugate comprises an antibody of the invention conjugated to one or more calicheamicin molecules. The calicheamicin family of antibiotics is capable of producing double-stranded DNA breaks at sub-picomolar concentrations. For the preparation of conjugates of the calicheamicin family, see U.S. patents 5,712,374, 5,714,586, 5,739,116, 5,767,285, 5,770,701, 5,770,710, 5,773,001, and 5,877,296 (all to American Cyanamid Company). Structural analogues of calicheamicin which may be used include, but are not limited to, γ/, (X₂ ¹, 01₃ ¹, N-acetyl-γ/, PSAG and θ\ (Hinman et al., Cancer Research 53:3336-3342 (1993), Lode et al., Cancer Research 58:2925-2928 (1998) and the aforementioned U.S. patents to American Cyanamid). Another anti-tumor drug to which the antibody can be conjugated is QFA, which is an antifolate. Both calicheamicin and QFA have intracellular sites of action and do not readily cross the plasma membrane. Therefore, cellular uptake of these agents through antibody mediated internalization greatly enhances their cytotoxic effects.

Other cytotoxic agents

Other antitumor agents that can be conjugated to the antibodies of the invention include BCNU, streptozoicin, vincristine and 5-fluorouracil, the family of agents known collectively LL-E33288 complex described in U.S. patents 5,053,394, 5,770,710, as well as esperamicins (U.S. patent 5,877,296).

Enzymatically active toxins and fragments thereof which can be used include diphtheria A chain, nonbinding active fragments of diphtheria toxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII, and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin, enomycin and the tricothecenes. See, for example, WO 93/21232 published October 28, 1993. The present invention further contemplates an immunoconjugate formed between an antibody and a compound with nucleolytic activity (e.g., a ribonuclease or a DNA endonuclease such as a deoxyribonuclease; DNase).

For selective destruction of the tumor, the antibody may comprise a highly radioactive atom. A variety of radioactive isotopes are available for the production of radioconjugated antibodies. Examples include At²¹¹, 1¹³¹, 1¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³, Bi²¹², P³², Pb²¹² and radioactive isotopes of Lu. When the conjugate is used for detection, it may comprise a radioactive atom for scintigraphic studies, for example Tc^99m or I¹²³, or a spin label for nuclear magnetic resonance (NMR) imaging (also known as magnetic resonance imaging, MRI), such as iodine- 123 again, iodine-131, indium-I l l, fluorine- 19, carbon-13, nitrogen- 15, oxygen- 17, gadolinium, manganese or iron.

The radio- or other labels may be incorporated in the conjugate in known ways. For example, the peptide may be biosynthesized or may be synthesized by chemical amino acid synthesis using suitable amino acid precursors involving, for example, fluorine- 19 in place of hydrogen. Labels such as Tc^99m or I¹²³, Re¹⁸⁶, Re¹⁸⁸ and In¹¹¹ can be attached via a cysteine residue in the peptide. Yttrium-90 can be attached via a lysine residue. The IODOGEN method (Fraker et al (1978) Biochem. Biophys. Res. Commun. 80: 49-57) can be used to incorporate iodine- 123. "Monoclonal Antibodies in Immunoscintigraphy" (Chatal,CRC Press 1989) describes other methods in detail.

Conjugates of the antibody and cytotoxic agent may be made using a variety of bifunctional protein coupling agents such as N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP), succinimidyl-4-(N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC), iminothiolane (IT), bifunctional derivatives of imidoesters (such as dimethyl adipimidate HCl), active esters (such as disuccinimidyl suberate), aldehydes (such as glutaraldehyde), bis- azido compounds (such as bis (p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such as bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such as toluene 2,6- diisocyanate), and bis-active fluorine compounds (such as l,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin can be prepared as described in Vitetta et al., Science 238:1098 (1987). Carbon- 14-labeled l-isothiocyanatobenzyl-3-methyldiethylene triaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent for conjugation of radionucleotide to the antibody. See WO94/11026. The linker may be a "cleavable linker" facilitating release of the cytotoxic drug in the cell. For example, an acid-labile linker, peptidase-sensitive linker, photolabile linker, dimethyl linker or disulfide-containing linker (Chari et al, Cancer Research 52:127-131 (1992); U.S. Patent No. 5,208,020) may be used. The compounds of the invention expressly contemplate, but are not limited to, ADC prepared with cross-linker reagents: BMPS, EMCS, GMBS, HBVS, LC-SMCC, MBS, MPBH, SBAP, SIA, SIAB, SMCC, SMPB, SMPH, sulfo-EMCS, sulfo-GMBS, sulfo-KMUS, sulfo-MBS, sulfo-SIAB, sulfo-SMCC, and sulfo-SMPB, and SVSB (succinimidyl-(4- vinylsulfone)benzoate) which are commercially available (e.g., from Pierce Biotechnology, Inc., Rockford, IL., U.S.A). See pages 467-498, 2003-2004 Applications Handbook and Catalog.

Preparation of antibody drug conjugates

In the antibody drug conjugates (ADC) of the invention, an antibody (Ab) is conjugated to one or more drug moieties (D), e.g. about 1 to about 20 drug moieties per antibody, through a linker (L). The ADC of Formula I may be prepared by several routes, employing organic chemistry reactions, conditions, and reagents known to those skilled in the art, including: (1) reaction of a nucleophilic group of an antibody with a bivalent linker reagent, to form Ab-L, via a covalent bond, followed by reaction with a drug moiety D; and (2) reaction of a nucleophilic group of a drug moiety with a bivalent linker reagent, to form D-L, via a covalent bond, followed by reaction with the nucleophilic group of an antibody. Additional methods for preparing ADC are described herein.

Ab-(L-D)_p I

The linker may be composed of one or more linker components. Exemplary linker components include 6-maleimidocaproyl ("MC"), maleimidopropanoyl ("MP"), valine- citrulline ("val-cit"), alanine-phenylalanine ("ala-phe"), p-aminobenzyloxycarbonyl ("PAB"), N-Succinimidyl 4-(2-pyridylthio) pentanoate ("SPP"), N-Succinimidyl 4-(N- maleimidomethyl) cyclohexane-1 carboxylate ("SMCC), and N-Succinimidyl (4-iodo- acetyl) aminobenzoate ("SIAB"). Additional linker components are known in the art and some are described herein. See also "Monomethylvaline Compounds Capable of Conjugation to Ligands", U.S. Ser. No. 10/983,340, filed Nov. 5, 2004, the contents of which are hereby incorporated by reference in its entirety.

In some embodiments, the linker may comprise amino acid residues. Exemplary amino acid linker components include a dipeptide, a tripeptide, a tetrapeptide or a pentapeptide. Exemplary dipeptides include: valine-citrulline (vc or val-cit), alanine- phenylalanine (af or ala-phe). Exemplary tripeptides include: glycine-valine-citrulline (gly- val-cit) and glycine-glycine-glycine (gly-gly-gly). Amino acid residues which comprise an amino acid linker component include those occurring naturally, as well as minor amino acids and non-naturally occurring amino acid analogs, such as citrulline. Amino acid linker components can be designed and optimized in their selectivity for enzymatic cleavage by a particular enzyme, for example, a tumor-associated protease, cathepsin B, C and D, or a plasmin protease.

Exemplary linker component structures are shown below (wherein the wavy line indicates sites of covalent attachment to other components of the ADC):

Additional exemplary linker components and abbreviations include (wherein the antibody (Ab) and linker are depicted, and p is 1 to about 8):

Nucleophilic groups on antibodies include, but are not limited to: (i) N-terminal amine groups, (ii) side chain amine groups, e.g. lysine, (iii) side chain thiol groups, e.g. cysteine, and (iv) sugar hydroxyl or amino groups where the antibody is glycosylated. Amine, thiol, and hydroxyl groups are nucleophilic and capable of reacting to form covalent bonds with electrophilic groups on linker moieties and linker reagents including: (i) active esters such as NHS esters, HOBt esters, haloformates, and acid halides; (ii) alkyl and benzyl halides such as haloacetamides; (iii) aldehydes, ketones, carboxyl, and maleimide groups. Certain antibodies have reducible interchain disulfides, i.e. cysteine bridges. Antibodies may be made reactive for conjugation with linker reagents by treatment with a reducing agent such as DTT (dithiothreitol). Each cysteine bridge will thus form, theoretically, two reactive thiol nucleophiles. Additional nucleophilic groups can be introduced into antibodies through the reaction of lysines with 2-iminothiolane (Traut's reagent) resulting in conversion of an amine into a thiol. Reactive thiol groups may be introduced into the antibody (or fragment thereof) by introducing one, two, three, four, or more cysteine residues (e.g., preparing mutant antibodies comprising one or more non-native cysteine amino acid residues).

Antibody drug conjugates of the invention may also be produced by modification of the antibody to introduce electrophilic moieties, which can react with nucleophilic substituents on the linker reagent or drug. The sugars of glycosylated antibodies may be oxidized, e.g. with periodate oxidizing reagents, to form aldehyde or ketone groups which may react with the amine group of linker reagents or drug moieties. The resulting imine Schiff base groups may form a stable linkage, or may be reduced, e.g. by borohydride reagents to form stable amine linkages. In one embodiment, reaction of the carbohydrate portion of a glycosylated antibody with either galactose oxidase or sodium meta-periodate may yield carbonyl (aldehyde and ketone) groups in the protein that can react with appropriate groups on the drug (Hermanson_^ Bioconjugate Techniques). In another embodiment, proteins containing N-terminal serine or threonine residues can react with sodium meta-periodate, resulting in production of an aldehyde in place of the first amino acid (Geoghegan & Stroh, (1992) Bioconjugate Chem. 3:138-146; U.S. 5362852). Such aldehyde can be reacted with a drug moiety or linker nucleophile.

Likewise, nucleophilic groups on a drug moiety include, but are not limited to: amine, thiol, hydroxyl, hydrazide, oxime, hydrazine, thiosemicarbazone, hydrazine carboxylate, and arylhydrazide groups capable of reacting to form covalent bonds with electrophilic groups on linker moieties and linker reagents including: (i) active esters such as NHS esters, HOBt esters, haloformates, and acid halides; (ii) alkyl and benzyl halides such as haloacetamides; (iii) aldehydes, ketones, carboxyl, and maleimide groups.

Alternatively, a fusion protein comprising the antibody and cytotoxic agent may be made, e.g., by recombinant techniques or peptide synthesis. The length of DNA may comprise respective regions encoding the two portions of the conjugate either adjacent to one another or separated by a region encoding a linker peptide which does not destroy the desired properties of the conjugate.

In yet another embodiment, the antibody may be conjugated to a "receptor" (such streptavidin) for utilization in tumor pre-targeting wherein the antibody-receptor conjugate is administered to the patient, followed by removal of unbound conjugate from the circulation using a clearing agent and then administration of a "ligand" (e.g., avidin) which is conjugated to a cytotoxic agent (e.g., a radionucleotide).

Antibody (Ab)-MC-MMAE may be prepared by conjugation of any of the antibodies provided herein with MC-MMAE as follows. Antibody, dissolved in 500 mM sodium borate and 500 mM sodium chloride at pH 8.0 is treated with an excess of 100 mM dithiothreitol (DTT). After incubation at 37 ⁰C for about 30 minutes, the buffer is exchanged by elution over Sephadex G25 resin and eluted with PBS with 1 mM DTPA. The thiol/ Ab value is checked by determining the reduced antibody concentration from the absorbance at 280 nm of the solution and the thiol concentration by reaction with DTNB (Aldrich, Milwaukee, WI) and determination of the absorbance at 412 nm. The reduced antibody dissolved in PBS is chilled on ice. The drug linker reagent, maleimidocaproyl-monomethyl auristatin E (MMAE), i.e. MC-MMAE, dissolved in DMSO, is diluted in acetonitrile and water at known concentration, and added to the chilled reduced antibody 2H9 in PBS. After about one hour, an excess of maleimide is added to quench the reaction and cap any unreacted antibody thiol groups. The reaction mixture is concentrated by centrifugal ultrafiltration and 2H9-MC-

MMAE is purified and desalted by elution through G25 resin in PBS, filtered through 0.2 μm filters under sterile conditions, and frozen for storage.

Antibody-MC-MMAF may be prepared by conjugation of any of the antibodies provided herein with MC-MMAF following the protocol provided for preparation of Ab-MC- MMAE.

Antibody-MC-val-cit-P AB-MMAE is prepared by conjugation of any of the antibodies provided herein with MC-val-cit-P AB-MMAE following the protocol provided for preparation of Ab-MC-MMAE.

Antibody-MC-val-cit-P AB-MMAF is prepared by conjugation of any of the antibodies provided herein with MC-val-cit-P AB-MMAF following the protocol provided for preparation of Ab-MC-MMAE.

Antibody-SMCC-DMl is prepared by conjugation of any of the antibodies provided herein with SMCC-DMl as follows. Purified antibody is derivatized with (Succinimidyl 4- (N-maleimidomethyl) cyclohexane-1-carboxylate (SMCC, Pierce Biotechnology, Inc) to introduce the SMCC linker. Specifically, antibody is treated at 20 mg/mL in 50 mM potassium phosphate/ 50 mM sodium chloride/ 2 mM EDTA, pH 6.5 with 7.5 molar equivalents of SMCC (20 mM in DMSO, 6.7 mg/mL). After stirring for 2 hours under argon at ambient temperature, the reaction mixture is filtered through a Sephadex G25 column equilibrated with 5OmM potassium phosphate/ 50 mM sodium chloride/ 2 mM EDTA, pH 6.5. Antibody-containing fractions are pooled and assayed.

Antibody-SMCC prepared thusly is diluted with 5OmM potassium phosphate/50 mM sodium chloride/2 mM EDTA, pH 6.5, to a final concentration of about 10 mg/ml, and reacted with a 10 mM solution of DMl in dimethylacetamide. The reaction is stirred at ambient temperature under argon for 16.5 hours. The conjugation reaction mixture is filtered through a Sephadex G25 gel filtration column (1.5 x 4.9 cm) with 1 x PBS at pH 6.5. The DMl drug to antibody ratio (p) may be about 2 to 5, as measured by the absorbance at 252 nm and at 280 nm. Ab-SPP-DMl is prepared by conjugation of any of the antibodies provided herein with SPP-DMl as follows. Purified antibody is derivatized with N-succinimidyl-4-(2- pyridylthio)pentanoate to introduce dithiopyridyl groups. Antibody (376.0 mg, 8 mg/mL) in 44.7 mL of 50 mM potassium phosphate buffer (pH 6.5) containing NaCl (50 mM) and EDTA (1 mM) is treated with SPP (5.3 molar equivalents in 2.3 mL ethanol). After incubation for 90 minutes under argon at ambient temperature, the reaction mixture is gel filtered through a Sephadex G25 column equilibrated with a 35 mM sodium citrate, 154 mM NaCl, 2 mM EDTA buffer. Antibody-containing fractions were pooled and assayed. The degree of modification of the antibody is determined as described above.

Antibody-SPP-Py (about 10 μmoles of releasable 2-thiopyridine groups) is diluted with the above 35 mM sodium citrate buffer, pH 6.5, to a final concentration of about 2.5 mg/mL. DMl (1.7 equivalents, 17 μmoles) in 3.0 mM dimethylacetamide (DMA, 3% v/v in the final reaction mixture) is then added to the antibody solution. The reaction proceeds at ambient temperature under argon for about 20 hours. The reaction is loaded on a Sephacryl S300 gel filtration column (5.0 cm x 90.0 cm, 1.77 L) equilibrated with 35 mM sodium citrate, 154 mM NaCl, pH 6.5. The flow rate may be about 5.0 niL/min and 65 fractions (20.0 mL each) are collected. The number of DMl drug molecules linked per antibody molecule (p') is determined by measuring the absorbance at 252 nm and 280 nm, and may be about 2 to 4 DMl drug moieties per 2H9 antibody.

Antibody-BMPEO-DMl is prepared by conjugation of any of the antibodies provided herein with BMPEO-DMl as follows. The antibody is modified by the bis-maleimido reagent BM(PEO)4 (Pierce Chemical), leaving an unreacted maleimido group on the surface of the antibody. This may be accomplished by dissolving BM(PEO)4 in a 50% ethano I/water mixture to a concentration of 10 mM and adding a tenfold molar excess to a solution containing antibody in phosphate buffered saline at a concentration of approximately 1.6 mg/ml (10 micromolar) and allowing it to react for 1 hour to form an antibody-linker intermediate, 2H9-BMPEO. Excess BM(PEO)4 is removed by gel filtration (HiTrap column, Pharmacia) in 30 mM citrate, pH 6 with 150 mM NaCl buffer. An approximate 10 fold molar excess DMl is dissolved in dimethyl acetamide (DMA) and added to the 2H9-BMPEO intermediate. Dimethyl formamide (DMF) may also be employed to dissolve the drug moiety reagent. The reaction mixture is allowed to react overnight before gel filtration or dialysis into PBS to remove unreacted DMl. Gel filtration on S200 columns in PBS is used to remove high molecular weight aggregates and to furnish purified 2H9-BMPEO-DM1.

Antibody Derivatives

Antibodies of the invention can be further modified to contain additional nonproteinaceous moieties that are known in the art and readily available. In one embodiment, the moieties suitable for derivatization of the antibody are water soluble polymers. Non-limiting examples of water soluble polymers include, but are not limited to, polyethylene glycol (PEG), copolymers of ethylene glycol/propylene glycol, carboxymethylcellulose, dextran, polyvinyl alcohol, polyvinyl pyrrolidone, poly-1, 3- dioxolane, poly-1, 3, 6-trioxane, ethylene/maleic anhydride copolymer, polyaminoacids (either homopolymers or random copolymers), and dextran or poly(n-vinyl pyrrolidone)polyethylene glycol, propropylene glycol homopolymers, prolypropylene oxide/ethylene oxide co- polymers, polyoxyethylated polyols (e.g., glycerol), polyvinyl alcohol, and mixtures thereof. Polyethylene glycol propionaldehyde may have advantages in manufacturing due to its stability in water. The polymer may be of any molecular weight, and may be branched or unbranched. The number of polymers attached to the antibody may vary, and if more than one polymer is attached, the polymers can be the same or different molecules. In general, the number and/or type of polymers used for derivatization can be determined based on considerations including, but not limited to, the particular properties or functions of the antibody to be improved, whether the antibody derivative will be used in a therapy under defined conditions, etc.

In another embodiment, conjugates of an antibody and nonproteinaceous moiety that may be selectively heated by exposure to radiation are provided. In one embodiment, the nonproteinaceous moiety is a carbon nanotube (Kam et al., Proc. Natl. Acad. Sci. 102: 11600- 11605 (2005)). The radiation may be of any wavelength, and includes, but is not limited to, wavelengths that do not harm ordinary cells, but which heat the nonproteinaceous moiety to a temperature at which cells proximal to the antibody-nonproteinaceous moiety are killed.

Pharmaceutical Formulations

Therapeutic formulations comprising one or more of the compounds of the invention are prepared for storage by mixing the one or more compounds having the desired degree of purity with optional physiologically acceptable carriers, excipients or stabilizers {Remington 's Pharmaceutical Sciences 16th edition, Osol, A. Ed. (1980)), in the form of aqueous solutions, lyophilized or other dried formulations. Acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate, histidine and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt-forming counter-ions such as sodium; metal complexes (e.g., Zn-protein complexes); and/or non-ionic surfactants such as TWEEN™, PLURONICS™ or polyethylene glycol (PEG).

The formulation herein may also contain more than one active compound as necessary for the particular indication being treated, including, but not limited to those with complementary activities that do not adversely affect each other. Such molecules are suitably present in combination in amounts that are effective for the purpose intended.

The active ingredients may also be entrapped in microcapsule prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsule and poly-(methylmethacylate) microcapsule, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules) or in macroemulsions.

Such techniques are disclosed in Remington's Pharmaceutical Sciences 16th edition, Osol, A. Ed. (1980). The formulations to be used for in vivo administration must be sterile. This is readily accomplished, for example, by filtration through sterile filtration membranes.

Sustained-release preparations may be prepared. Suitable examples of sustained- release preparations include semipermeable matrices of solid hydrophobic polymers containing a therapeutic compound of the invention, which matrices are in the form of shaped articles, e.g., films, or microcapsule. Examples of sustained-release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides (U.S. Pat. No. 3,773,919), copolymers of L-glutamic acid and γ ethyl-L-glutamate, non-degradable ethylene-vinyl acetate, degradable lactic acid- glycolic acid copolymers such as the LUPRON DEPOT™ (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate), and poly-D-(-)-3- hydroxybutyric acid. While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogels release proteins for shorter time periods. When encapsulated proteinaceous compounds (for example, binding polypeptides of the invention such as antibodies) remain in the body for a long time, they may denature or aggregate as a result of exposure to moisture at 37°C, resulting in a loss of biological activity and possible changes in immunogenicity. Rational strategies can be devised for stabilization depending on the mechanism involved. For example, if the aggregation mechanism is discovered to be intermolecular S-S bond formation through thio- disulfide interchange, stabilization may be achieved by modifying sulfhydryl residues, lyophilizing from acidic solutions, controlling moisture content, using appropriate additives, and developing specific polymer matrix compositions.

Uses

The compositions of the invention may be used in, for example, in vitro, ex vivo and in vivo therapeutic methods. For example, the DUBA binding polypeptides, polynucleotides and small molecules of the invention can be used as an antagonist to partially or fully block the specific antigen activity in vitro, ex vivo and/or in vivo. Moreover, at least some of the compositions of the invention can neutralize DUBA activity from other species. Accordingly, the compositions of the invention can be used to inhibit a specific DUBA activity, e.g., in a cell culture containing the antigen, in human subjects or in other mammalian subjects having the antigen with which an antibody of the invention cross-reacts (e.g. chimpanzee, baboon, marmoset, cynomolgus and rhesus, pig or mouse). In one embodiment, an antibody of the invention can be used for inhibiting antigen activities by contacting the antibody with the antigen such that antigen activity is inhibited. In one embodiment, the antigen is a human protein molecule. In another embodiment, the antigen is DUBA. In another embodiment, a DUBA-binding polypeptide, polynucleotide, or small molecule of the invention inhibits a deubiquitination activity of DUBA.

In one embodiment, a binding compound of the invention can be used in a method for inhibiting an antigen in a subject suffering from a disorder in which the antigen activity is detrimental, comprising administering to the subject a binding compound of the invention such that the antigen activity in the subject is inhibited. In one embodiment, the antigen is a human protein molecule and the subject is a human subject. Alternatively, the subject can be a mammal expressing the antigen with which a binding compound of the invention binds. Still further the subject can be a mammal into which the antigen has been introduced (e.g., by administration of the antigen or by expression of an antigen trans gene). A binding compound of the invention can be administered to a human subject for therapeutic purposes. Moreover, a binding compound of the invention can be administered to a non-human mammal expressing an antigen with which the antibody cross-reacts (e.g., a primate, pig or mouse) for veterinary purposes or as an animal model of human disease. Regarding the latter, such animal models may be useful for evaluating the therapeutic efficacy of the binding compounds of the invention (e.g., testing of dosages and time courses of administration). Binding compounds of the invention can be used to treat, inhibit, delay progression of, prevent/delay recurrence of, ameliorate, or prevent diseases, disorders or conditions associated with abnormal expression and/or activity of DUBA , including but not limited to cell proliferative disorders, infections, immune/inflammatory disorders, and other interferon- related disorders. In one aspect, a blocking binding compound of the invention specifically binds to

DUBA such that it inhibits normal DUBA activity by blocking or interfering with the interaction between DUBA and one or more DUBA ligands, thereby inhibiting the corresponding signaling pathway and other associated molecular or cellular events.

In another aspect, an agonising binding compound of the invention specifically binds to DUBA such that it stimulates and/or enhances normal DUBA activity by stimulating or enhancing the interaction between DUBA and one or more DUBA ligands, thereby inhibiting the corresponding signaling pathway and other associated molecular or cellular events. In certain embodiments, an immunoconjugate comprising an antibody conjugated with a cytotoxic agent is administered to the patient. In certain embodiments, the immunoconjugate is internalized by the cell, resulting in increased therapeutic efficacy of the immunoconjugate in killing the cell. In one embodiment, the cytotoxic agent targets or interferes with nucleic acid in the target cell. In another embodiment, the immunoconjugate is multivalent, binding to an antigen expressed on the surface of a target cell and facilitating internalization of the immunoconjugate into the cell such that the immunoconjugate can specifically interact with DUBA. Examples of such cytotoxic agents include any of the chemotherapeutic agents noted herein (such as a maytansinoid or a calicheamicin), a radioactive isotope, or a ribonuclease or a DNA endonuclease.

Compounds of the invention can be used either alone or in combination with other compositions in a therapy. For instance, an antibody of the invention may be co-administered with another antibody, and/or adjuvant/therapeutic agents (e.g., steroids). In another example, an antibody of the invention may be combined with an anti-inflammatory and/or antiseptic in a treatment scheme, e.g. in treating any of the diseases described herein, including cell proliferative disorders, infections, immune/inflammatory disorders, and other interferon-related disorders. Such combined therapies noted above include combined administration (where the two or more agents are included in the same or separate formulations), and separate administration, in which case, administration of the antibody of the invention can occur prior to, and/or following, administration of the adjunct therapy or therapies.

A compound of the invention (and adjunct therapeutic agent) can be administered by any suitable means, including parenteral, subcutaneous, intraperitoneal, intrapulmonary, and intranasal, and, if desired for local treatment, intralesional administration. Parenteral infusions include intramuscular, intravenous, intraarterial, intraperitoneal, or subcutaneous administration. In addition, the antibody is suitably administered by pulse infusion, particularly with declining doses of the antibody. Dosing can be by any suitable route, e.g. by injections, such as intravenous or subcutaneous injections, depending in part on whether the administration is brief or chronic. The location of the binding target of a binding compound of the invention may be taken into consideration in preparation and administration of the antibody. When the binding target is an intracellular molecule, certain embodiments of the invention provide for the antibody or antigen-binding fragment thereof to be introduced into the cell where the binding target is located. In one embodiment, an antibody of the invention can be expressed intracellularly as an intrabody. The term "intrabody," as used herein, refers to an antibody or antigen-binding portion thereof that is expressed intracellularly and that is capable of selectively binding to a target molecule, as described in Marasco, Gene Therapy 4: 11-15 (1997); Kontermann, Methods 34: 163-170 (2004); U.S. Patent Nos. 6,004,940 and

6,329,173; U.S. Patent Application Publication No. 2003/0104402, and PCT Publication No. WO2003/077945. Intracellular expression of an intrabody is effected by introducing a nucleic acid encoding the desired antibody or antigen-binding portion thereof (lacking the wild-type leader sequence and secretory signals normally associated with the gene encoding that antibody or antigen-binding fragment) into a target cell. Any standard method of introducing nucleic acids into a cell may be used, including, but not limited to, microinjection, ballistic injection, electroporation, calcium phosphate precipitation, liposomes, and transfection with retroviral, adenoviral, adeno-associated viral and vaccinia vectors carrying the nucleic acid of interest. One or more nucleic acids encoding all or a portion of an anti-DUBA antibody or an antigen-binding fragment thereof of the invention can be delivered to a target cell, such that one or more intrabodies are expressed which are capable of intracellular binding to DUBA and modulation of one or more DUBA-mediated cellular pathways.

In another embodiment, the compounds of the invention are provided in a form that can be internalized into cells. For example, internalizing antibodies are provided. Antibodies can possess certain characteristics that enhance delivery of antibodies into cells, or can be modified to possess such characteristics. Techniques for achieving this are known in the art. For example, cationization of an antibody is known to facilitate its uptake into cells (see, e.g., U.S. Patent No. 6,703,019). Lipofections or liposomes can also be used to deliver the antibody into cells. Where antibody fragments are used, the smallest inhibitory fragment that specifically binds to the binding domain of the target protein is generally advantageous. For example, based upon the variable-region sequences of an antibody, peptide molecules can be designed that retain the ability to bind the target protein sequence. Such peptides can be synthesized chemically and/or produced by recombinant DNA technology. See, e.g., Marasco et al, Proc. Natl. Acad. Sci. USA, 90: 7889-7893 (1993).

Entry of modulator polypeptides into target cells can be enhanced by methods known in the art. For example, certain sequences, such as those derived from HIV Tat or the Antennapedia homeodomain protein are able to direct efficient uptake of heterologous proteins across cell membranes. See, e.g., Chen et al., Proc. Natl. Acad. Sci. USA (1999), 96:4325-4329.

When the binding target is located in the brain, certain embodiments of the invention provide for the antibody, antigen binding fragment, or other binding polypeptide, polynucleotide, or small molecule of the invention to traverse the blood-brain barrier. Certain neurodegenerative diseases are associated with an increase in permeability of the blood-brain barrier, such that the antibody or antigen-binding fragment can be readily introduced to the brain. When the blood-brain barrier remains intact, several art-known approaches exist for transporting molecules across it, including, but not limited to, physical methods, lipid-based methods, and receptor and channel-based methods.

Physical methods of transporting the antibody, antibody fragment, other binding polypeptide, polynucleotide, or small molecule of the invention across the blood-brain barrier include, but are not limited to, circumventing the blood-brain barrier entirely, or by creating openings in the blood-brain barrier. Circumvention methods include, but are not limited to, direct injection into the brain (see, e.g., Papanastassiou et al., Gene Therapy 9: 398-406 (2002)) and implanting a delivery device in the brain (see, e.g., Gill et al., Nature Med. 9: 589-595 (2003); and Gliadel Wafers™, Guildford Pharmaceutical). Methods of creating openings in the barrier include, but are not limited to, ultrasound (see, e.g., U.S. Patent Publication No. 2002/0038086), osmotic pressure (e.g., by administration of hypertonic mannitol (Neuwelt, E. A., Implication of the Blood-Brain Barrier and its Manipulation, VoIs 1 & 2, Plenum Press, N. Y. (1989))), permeabilization by, e.g., bradykinin or permeabilizer A- 7 (see, e.g., U.S. Patent Nos. 5,112,596, 5,268,164, 5,506,206, and 5,686,416), and transfection of neurons that straddle the blood-brain barrier with vectors containing polynucleotides that either bind DUBA or nucleic acid encoding DUBA, or which encode a polypeptide of the invention that specifically binds DUBA (see, e.g., U.S. Patent Publication No. 2003/0083299).

Lipid-based methods of transporting the antibody or other binding polypeptide, polynucleotide, or small molecule of the invention across the blood-brain barrier include, but are not limited to, encapsulating the antibody or other binding polypeptide, polynucleotide, or small molecule of the invention in liposomes that are coupled to antibody binding fragments that bind to receptors on the vascular endothelium of the blood-brain barrier (see, e.g., U.S. Patent Application Publication No. 20020025313), and coating the antibody or other binding polypeptide, polynucleotide, or small molecule of the invention n low-density lipoprotein particles (see, e.g., U.S. Patent Application Publication No. 20040204354) or apolipoprotein E (see, e.g., U.S. Patent Application Publication No. 20040131692).

Receptor and channel-based methods of transporting the antibody or other binding polypeptide, polynucleotide, or small molecule of the invention across the blood-brain barrier include, but are not limited to, using glucocorticoid blockers to increase permeability of the blood-brain barrier (see, e.g., U.S. Patent Application Publication Nos. 2002/0065259, 2003/0162695, and 2005/0124533); activating potassium channels (see, e.g., U.S. Patent Application Publication No. 2005/0089473), inhibiting ABC drug transporters (see, e.g., U.S. Patent Application Publication No. 2003/0073713); coating a compound of the invention with a transferrin and modulating activity of the one or more transferrin receptors (see, e.g., U.S. Patent Application Publication No. 2003/0129186), and cationizing the antibodies (see, e.g., U.S. Patent No. 5,004,697).

The compound of the invention would be formulated, dosed, and administered in a fashion consistent with good medical practice. Factors for consideration in this context include the particular disorder being treated, the particular mammal being treated, the clinical condition of the individual patient, the cause of the disorder, the site of delivery of the agent, the method of administration, the scheduling of administration, and other factors known to medical practitioners. The compound of the invention need not be, but is optionally formulated with one or more agents currently used to prevent or treat the disorder in question. The effective amount of such other agents depends on the amount of the compound of the invention present in the formulation, the type of disorder or treatment, and other factors discussed above. These are generally used in the same dosages and with administration routes as described herein, or about from 1 to 99% of the dosages described herein, or in any dosage and by any route that is empirically/clinically determined to be appropriate. For the prevention or treatment of disease, the appropriate dosage of a compound of the invention (when used alone or in combination with other agents such as chemotherapeutic agents) will depend on the type of disease to be treated, the type of compound, the severity and course of the disease, whether the compound is administered for preventive or therapeutic purposes, previous therapy, the patient's clinical history and response to the compound, and the discretion of the attending physician. The compound is suitably administered to the patient at one time or over a series of treatments. Depending on the type and severity of the disease, about 1 μg/kg to 15 mg/kg (e.g. 0.1mg/kg-10mg/kg) of a compound of the invention (i.e., an antibody) can be an initial candidate dosage for administration to the patient, whether, for example, by one or more separate administrations, or by continuous infusion. One typical daily dosage might range from about 1 μg/kg to 100 mg/kg or more, depending on the factors mentioned above. For repeated administrations over several days or longer, depending on the condition, the treatment would generally be sustained until a desired suppression of disease symptoms occurs. One exemplary dosage of an antibody of the invention would be in the range from about 0.05 mg/kg to about 10 mg/kg. Thus, one or more doses of about 0.5 mg/kg, 2.0 mg/kg, 4.0 mg/kg or 10 mg/kg (or any combination thereof) may be administered to the patient. Such doses may be administered intermittently, e.g. every week or every three weeks (e.g. such that the patient receives from about two to about twenty, or e.g. about six doses of the antibody). An initial higher loading dose, followed by one or more lower doses may be administered. An exemplary dosing regimen comprises administering an initial loading dose of about 4 mg/kg, followed by a weekly maintenance dose of about 2 mg/kg of the antibody. However, other dosage regimens may be useful. The progress of this therapy is easily monitored by conventional techniques and assays.

Articles of Manufacture

In another aspect of the invention, an article of manufacture containing materials useful for the treatment, prevention and/or diagnosis of the disorders described above is provided. The article of manufacture comprises a container and a label or package insert on or associated with the container. Suitable containers include, for example, bottles, vials, syringes, etc. The containers may be formed from a variety of materials such as glass or plastic. The container holds a composition which is by itself or when combined with another composition effective for treating, preventing and/or diagnosing the condition and may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle). In certain embodiments, at least one active agent in the composition is an antibody of the invention. The label or package insert indicates that the composition is used for treating the condition of choice. Moreover, the article of manufacture may comprise (a) a first container with a composition contained therein, wherein the composition comprises an antibody of the invention; and (b) a second container with a composition contained therein, wherein the composition comprises a further cytotoxic or otherwise therapeutic agent. The article of manufacture in this embodiment of the invention may further comprise a package insert indicating that the compositions can be used to treat a particular condition. Alternatively, or additionally, the article of manufacture may further comprise a second (or third) container comprising a pharmaceutically-accep table buffer, such as bacteriostatic water for injection (BWFI), phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, and syringes.

The following are examples of the methods and compositions of the invention. It is understood that various other embodiments may be practiced, given the general description provided above. All references cited herein, including patent applications and publications, are incorporated by reference in their entirety.

EXAMPLES

EXAMPLE 1: EFFECT OF DEUBIQUITINASE KNOCKDOWN ON CYTOKINE PRODUCTION THROUGH THE TLR3 PATHWAY

Ubiquitin is a 76 amino acid protein found in all eukaryotic cells that is covalently linked to various proteins by ubiquitin ligase enzymes (Pickart, Cell 116, 181 (2004);

Hershko & Ciechanover, Annu. Rev. Biochem. 67, 425 (1998)). The C-terminus of ubiquitin typically links to a lysine residue within a target protein, but lysines within ubiquitin itself can also be modified such that polyubiquitin chains are formed. Polyubiquitin chains formed through linkages that utilize lysine 48 in ubiquitin often mark target proteins for proteasome- mediated proteolytic destruction. Polyubiquitin chains that are linked through lysine 63 in ubiquitin, however, can direct other outcomes. These chains have been implicated, for example, in the activation of signaling pathways that impact DNA repair or the transcription factor nuclear factor KB (NF-KB) (Hershko & Ciechanover, Annu. Rev. Biochem. 67, 425 (1998); Pickart, Cell 116, 181 (2004); Chen, Nat. Cell Biol. 7, 758 (2005)). As one example, TLRs use the ubiquitin ligase TRAF6 to recruit downstream kinases TAKl and IKK-β for the activation of NF-κB (Chen, Nat Cell Biol 7, 758 (2005); Wullaert et al, Trends Immunol. 27, 533 (2006)). Deubiquitinating enzymes (DUBs) are proteases that specifically cleave ubiquitin linkages and can thereby oppose the action of ubiquitin ligases (Nijman et al, Cell 123, 773 (2005)). The DUB A20, for example, acts as a negative regulator of the classical NF-κB activation pathway. Mice that lack A20 exhibit spontaneous inflammation and perinatal lethality due to unchecked NF-κB activation (Boone et al, Nat. Immunol. 5, 1052 (2004)). A20 belongs to a subfamily of 14 DUBs characterized by an OTU domain (Fig. IA). To date, the physiological function of only a few members is known. A. IDENTIFICATION OF DEUBIQUITINASES INVOLVED IN TLR3 SIGNALING.

In response to exposure to various bacterial/viral signals (i.e., the presence of lipopolysaccharide ("LPS"), polyLC, or muramyldipeptide), one or more signaling cascades in mammalian cells become activated and result in the production of one or more cytokines. Ubiquitination and deubiquitination have been shown to be involved in modulating the signal transmitted through such pathways (see, e.g., Hershko & Ciechanover, Annu. Rev. Biochem. 67, 425 (1998); Pickart, Cell 116, 181 (2004); Chen, Nat. Cell Biol. 7, 758 (2005)). To assess the importance of deubiquitination for interferon production in response to stimulation by bacterial/viral signals, known deubiquitinases were knocked-down in cells using a silencing RNA approach. Several known ovarian tumor domain ("OTU")-containing deubiquitinases are schematically shown in Figure IA.

Nineteen-mer siRNAs specifically targeted to OTU-containing deubiquitinases and having 3 ' dTdT overhangs were constructed, and are shown in Table 1.

TABLE 1: OTU Domain-Containing Protein siRNAs mRNA

Name RefSeq ORF siRNA# 1 siRNA# 2 siRNA# 3 siRNA# 4 bp

CAGUGGUGAAUCCUAA CGUCUGAGCCUUCAAU CGGAAUAUCCACUAUAA CUGGGCCUGCCAUCAUUC

DUBA NM_017602 2759 571 CAATT(SEQIDNO 36) GUUTT(SEQIDNO 50) UUTT(SEQIDNO 64) ATT(SEQIDNO 78) CGCACCGCCAGCUACA CGACAGUAGCAUUGAA GCUACGACGACUUCAUG GGUGGGAAACGAAAUUCG

DUBA-2 NM_207320 1689 288 UGATT(SEQIDNO 37) UCUTT(SEQIDNO 51) AUTT(SEQIDNO 65) ATT(SEQIDNO 79) CAUGGUUACCCUUAAG GGGUUUCCUCCUAAAG CAUGGCGACAGAAUUAC CCCCAUUGGUCCUGAUGU

DUBA-3 NM_025054 8192 1222 UCUTT(SEQIDNO 38) AGUTT(SEQIDNO 52) AATT(SEQIDNO 66) UTT(SEQIDNO 80) CGACCUGAGAGAUGAA GGCAGGACCGAAAACA CCUUCGCCGCUCUCAACA CAGUGGUGCCAGAAUCUU

DUBA-4 XM_375697 6615 473 GUATT(SEQIDNO 39) AUATT(SEQIDNO 53) UTT(SEQIDNO 67) UTT(SEQIDNO 81)

DUBA-5 NM_016023 3166 293 GAUAAUACAGGCAGAU CUAGACAGUUAGAAAU CAAUUGAAGCUGACUAC GACCGCUGAGUAUAUGCA UCUTT(SEQIDNO 40) UAATT(SEQIDNO 54) UATT(SEQIDNO 68) ATT(SEQIDNO 82) GGACAUAGUCAGUUGG CACAUUGGAGAAUAUU GAGGACCUACCUAAAGA GGGAGAUCGAGCCAUUGU

DUBA-6 NM_199324 6980 1048 AUATT(SEQIDNO 41) ACUTT(SEQIDNO 55) UATT(SEQIDNO 69) ATT(SEQIDNO 83) CGGUGUCUACCAUGAU CAGUAACGGACACUAU CAACUGGUGCAAACAAA CUGAAUGUGAAUAUCCAU

DUBA-7 XM_166659 3389 638 UCATT(SEQIDNO 42) GAUTT(SEQIDNO 56) CUTT(SEQIDNO 70) UTT(SEQIDNO 84) GCCUCAUAGCACAAAU GCAAUAGAGAUAUCGA CUGGGCAUACGAUUGAG GCCUCGUGUUUUAAUGCA

DUBA-8 NM_018566 6265 348 UGUTT(SEQIDNO 43) UUUTT(SEQIDNO 57) AUTT(SEQIDNO 71) ATT(SEQIDNO 85) GGGAAGAUUUGAAGAC GCACCAUGUUUGAAGG GCGGAAAGCUGUGAAGA CAGCAUGAGUACAAGAAA

A20 NM_006290 4446 790 UUATT(SEQIDNO 44) AUATT(SEQIDNO 58) UATT(SEQIDNO 72) UTT(SEQIDNO 86) GGACAUGGAUGCUGUU GAAUCUAUCUGCCUUU GAAGGAGAAUACCAAGG UGAAAGUACUUGAGGAUC

Cezanne NM_020205 3159 858 CUGTT(SEQIDNO 45) GGATT(SEQIDNO 59) AATT(SEQIDNO 73) ATT(SEQIDNO 87) GGGCAGCACUUCUACA UGUCCUAGCCCAUAUA GGACGACAUUGCCCAAG GCACACACUUCAGCAAGA

Cezanne2 NM_130901 3042 926 UGATT(SEQIDNO 46) UUATT(SEQIDNO 60) AATT(SEQIDNO 74) ATT(SEQIDNO 88)

OTUBl NM_017670 GAGCUCUCGGUCCUAU GGCCUGACGGCAACUG CUGGACACUACGAUAUC GGGCUUCACUGAAUUCAC 1747 271 ACATT(SEQIDNO 47) UUUTT(SEQIDNO 61) CUTT(SEQIDNO 75) ATT(SEQIDNO 89) GGAUUUACCGGAGGAA CCGUUUACCUGCUCUA CGUUUACCUGCUCUAUA CUUCCGGCACUUCAUUGA

0TUB2 NM_023112 3890 234 AAUTT(SEQIDNO 48) UAATT(SEQIDNO 62) AATT(SEQIDNO 76) UTT(SEQIDNO 90) GAAUCUCCAAUUAUUA

Trabid NM 017580 2710 708 CCCAAGUUAUCUUUCU GACGACCAAUUAUAGUU CUCAGGAGCUAGGUAAUG ACUTT(SEQIDNO 49) GUUTT(SEQIDNO 63) UATT(SEQIDNO 77) ATT(SEQIDNO 91)

siRNA# 1 siRNA# 2 siRNA# 3 siRNA# 4 murine CGGAAUAUCCACUAUA GAAUACCUAGACAGUA CCCCCAGACAAGAGUUG GCAUGGACUAUCUGAUGA DUBA AUUTT(SEQIDNO 92) UGATT(SEQIDNO 94) AUTT(SEQIDNO 96) ATT(SEQIDNO 98) GFP GGAGAAGAACUCUUUA GGAGAUGCAACUUAUG GGAGAGGACAAUCUUCU GAAUUGAGCUGAAAGGCA (control) CUGTT(SEQIDNO 93) GAATT(SEQIDNO 95) UUTT(SEQIDNO 97) UTT(SEQIDNO 99)

For high-throughput screening, four siRNAs targeting one individual DUB gene were pooled and used together, or a control siRNA (siCONTROL non-targeting siRNA) (Dharmacon) was used. HEK293 cells were purchased from ATCC. HEK293 cells stably expressing toll-like receptor 3 ("TLR3") ("TLR3/293 cells") were established by the transfection of the cells with the TLR3/pUNO plasmid (Invitrogen). Both HEK293 cells and TLR3/293 cells were transfected with 20 nM of individual or control siRNA or 80 nM of pooled siRNA in Lipofectamine 2000 (Invitrogen) in a 96- well plate on day 0. The plates were incubated for 48 hours at 37 ⁰C. The cells were then transfected with either 20 ng of an NF -KB- or IFN-α4-luciferase reporter plasmid together with 30 ng of control plasmid and incubated for an additional 24 hours at 37 ⁰C. The cells were co-cultured with the TLR3 ligand 20 μg/mL polyLC (Biochemica) for 24 hours at 37 ⁰C. Reporter gene (luciferase) activity was subsequently measured by a dual reporter assay (Promega kit El 980) following the manufacturer's instructions. The results are shown in Figure IB. siRNA-based knockdown of most OTU-containing deubiquitinases had no effect on the normal inability of the cell to produce NF-κB or IFN-β through the TLR3 pathway in response to challenge with polyLC (a synthetic analog of ds RNA and known ligand of TLR3). However, knockdown of A20 expression by pooled siRNA oligos resulted in a marked increase in TLR3- induced NF-κB-dependent gene transcription (Figure IB), consistent with previous studies (Boone et al, Nat. Immunol. 5, 1052 (2004)). Activated TLR3 is known to simultaneously promote production of IFN-α4 through the transcription factors IRF-3 and IRF-7 (Honda et al., Immunity 25, 349 (2006)). The impact of A20 in this assay appeared to be limited to NF-κB activation only, likely because A20 knockdown had negligible effect on TLR3 -induced activation of either an IFN-α4 promoter or an IFN-β promoter (Figures 1C and ID). Knockdown of another negative regulator of NF-κB signaling, CYLD (a non-OTU-containing deubiquitinase known to be a tumor suppressor and a member of the ubiquitin specific protease (USP) subfamily of DUBs (Nijman et al, Cell 123, 773 (2005); Bignell et al, Nat. Genet. 25, 160 (2000)), also resulted in a marked increase in NF-κB production by the cells (Figure IB). As observed with A20, knockdown of CYLD did not increase activation of either an IFN-α4 promoter or an IFN-β promoter (Figures 1C and ID). Knockdown of DUBA significantly increased TLR3 -induced activation of IFN-α4 and IFN-β production by the cells (Figures 1C and ID), without altering activation of an NF-κB -dependent reporter (Figure IB). This result supported the idea that ubiquitination of one or more TLR3 pathway components is necessary for activation of IFN- α4 and IFN-β production. No significant effects on NF-κB, IFN-α4, or IFN-β activation were observed upon knockdown of any of the other DUBs tested.

B. CHARACTERIZATION OF DUBA ACTIVITY AND FUNCTION

The role of DUBA in production of interferons through the TLR3 -mediated pathway was further investigated. The structure of DUBA is shown in Figure 2B. DUBA contains an OTU domain in the middle of its predicted 571 amino acid full-length sequence. The catalytic triad, essential for cysteine protease activity, is conserved in DUBA as well (Asp221, Cys224, and His334). DUBA additionally has a unique glycine and proline-rich sequence at its N-terminus and a ubiquitin- interacting motif ("UIM") embedded in a conserved C-terminal helix. 1. Tissue Distribution of DUBA

The tissue distribution of DUBA was analyzed by Northern blot. A human multiple tissue RNA blot (Clontech) was hybridized with a ³²P-labeled human DUBA probe (nucleotides 601-1200) obtained by PCR using human genomic DNA as a template, and visualized following the manufacturer's instructions. As shown in Figure 2C, an approximately 2.7 kb transcript corresponding to DUBA mRNA was found in several human tissues, including liver, placenta, and peripheral blood leukocytes. 2. Further Characterization of DUBA RNA Silencing

The data for DUBA in Figures IB- ID was obtained using pooled DUBA siRNA, so the experiment was repeated using individual DUBA siRNAs (siRNA #1, siRNA #2, or a control siRNA) using the protocol described above to determine whether a particular siRNA was more or less effective than any other DUBA siRNA. As shown in Figures 2D and 2E, pretreatment of cells with either siRNA#l or siRNA#2 coupled with stimulation by polyLC resulted in significant activation of IFN-α4 production, but no significant activation of NF-κB production as compared to pretreatment with a control siRNA.

The effects of DUBA siRNA treatment on DUBA protein levels in cells were also assessed. Rabbit anti-DUBA antibodies were obtained from rabbits immunized with synthetic human DUBA peptides (amino acids 18-32, amino acids 165-180, and amino acids 450-463). The antibodies were mixed and the mixture was used for immunoprecipitation experiments. Hamster anti-DUBA antibodies were obtained from Armenian hamsters immunized with recombinant full-length mouse DUBA purified from baculovirus-infected Sf-9 insect cells. Cross-reactivity of the hamster antibodies with human DUBA was confirmed by Western blot using human DUBA-transfected cells. To confirm that the DUBA siRNAs were blocking DUBA protein production, HEK293 cells were transfected with siRNA#l, siRNA#2, or a control siRNA as described above and incubated for three days at 37 ⁰C. At the end of the incubation, DUBA protein was immunoprecipitated with rabbit anti-human DUBA polyclonal antibody and subjected to SDS page analysis, followed by Western blot analysis using hamster anti-DUBA antibody as a probe. One percent of the lysate was subjected to Western blotting with anti-β-actin antibody as a control for general protein expression. After electrophoresis, samples were transferred to nitrocellulose membrane using an Invitrogen transfer apparatus. The membrane was blocked with 4% skimmed milk, stained with primary antibody (1 μg/mL) for 16 hours at 4 ⁰C. The membrane was washed with TBST for 30 minutes, and stained with HRP-labeled anti-hamster secondary antibody (Jackson). After washing with TBST for an additional 30 minutes, the membrane was developed with PIERCE Supersignal™ and exposed to film. Both DUBA siRNA#l and siRNA#2 decreased to about the same extent the amount of DUBA protein immunoprecipitated from the cells as compared to cells treated with a control siRNA (Figure 2F). Thus, both in terms of stimulating IFN-α4 production and in terms of decreasing DUBA protein production, DUBA siRNA#l and siRNA#2 behaved equivalently.

To better understand the action of the DUBA siRNA in cells, TLR3/293 cells were transfected with 20 nM of a double-stranded or a non-annealed single-stranded form of DUBA siRNA#l . After two days incubation at 37 ⁰C, the cells were transfected with an IFN-α4 luciferase reporter construct and incubated for 24 hours. Cells were then stimulated with 20 μg/mL polyLC for 36 hours, and relative promoter activation was calculated based on the dual reporter assay described above in Example IA. The data represent the average of two independent experiments.

The results are shown in Figure 2G. The double-stranded form of DUBA siRNA#l was the only active form of the siRNA in TLR3/293 cells. Without TLR3 engagement by polyLC, neither DUBA siRNA could influence basal NF-κB and IFN-α responses. These results thus excluded possible non-specific activation of IFN-α4 and NF-κB by siRNA, as has been previously observed in TLR7/8-expressing plasmacytoid dendritic cells upon exposure to contaminated ssRNA (Hornung et al, Nat. Med. 11, 263 (2005)).

EXAMPLE 2: ROLE OF DUBA IN OTHER INTERFERON-RELATED SIGNALING PATHWAYS

Knockout mice studies have shown that RNA virus recognition resulting in IFN-I production is mediated in part by RIG-I and MDA5, two caspase activation and recruitment domain ("CARD")- containing DExD/H box RNA helicases, in addition to the TLR3 -mediated pathway described above (see Figure 3A). These helicases detect invading RNA viruses and engage the IFN-I response through the adaptor protein IPS-I (Akira et al., Cell 124, 783 (2006); Meylan & Tschopp, MoI. Cell 22, 561 (2006); Yoneyama et al, Nat Immunol. 5, 730 (2004)). The role of DUBA in the RIG-I and MDA5 pathways was therefore investigated. FLAG-, Myc-, and His-tagged DUBA genes and related mutant genes were amplified by PCR and subcloned into the vector pCDNA3(-) (Invitrogen). To avoid possible engagement of the RNA helicase domains of RIG-I and MDA5 by the siRNAs, the CARD domains of RIG-I and MDA5 were isolated. A RIG-I CARD domain polynucleotide (encoding amino acids 1-229 of RIG-I) was subcloned into the vector pCDNA3(-) (Invitrogen). The MDA5 CARD domain construct (amino acids 1-207 cloned into the vector pCMV) was obtained from Origene. TBK-I and IKK-ε/I were subcloned into pCDNA3(-) by PCR using standard methods. HEK293 cells were transfected with 20 nM control or DUBA siRNA on day 0 and then NF-κB, IFN-β or IFN-α4 luciferase reporter gene together with the indicated activators on day 2. For MDA5, RIG-I, TBK+IKK-ε, and IRF-7 plasmid transfections, 30 ng of the plasmids were transfected together with 20 ng luciferase reporter plasmid at 72 hours post siRNA treatment. After a further 24 hour incubation, one of the following ligands was added to the culture to engage the corresponding receptor: Pam3CSK4 (10 μg/mL), polyLC (20 μg/mL), LPS (10 μg/mL), muramyldipeptide (10 μg/mL), IL-I (50 ng/mL), or TNF-α (50 ng/mL), and the culture was incubated for another 24 hours. At the end of that period, reporter gene activation was measured. The data shown represents the mean +/- standard deviation of triplicated samples.

The results are shown in Figure 3B. DUBA knockdown increased activation of IFN-β and IFN-α4 promoters in response to RIG-I_CARD and MDA5_CARD expression, and the magnitude of the effect was similar to that seen when polyLC was used to stimulate TLR3 (Figure 3B, middle and right panels). RIG-I- and MD A5 -induced NF-κB responses were only slightly increased in response to DUBA gene knockdown, although all of the other tested receptor-engaged NF-κB responses were not affected (Figure 3B, leftmost panel). The results suggested that of the pathways tested, the observed negative regulatory role of DUBA was in the TLR3, RIG-I, and MDA5 pathways. For the cotransfection with DUBA plasmid, HEK293 cells were transfected with control,

FLAG-DUB A/pCDNA3, or FLAG-DUBA C/S mt/pCDNA3 (30 ng) together with control, MDA5CARD or RIG-ICARD plasmid (5 ng) and luciferase reporter plasmids (20 ng). After a 36- hour incubation at 37 ⁰C, luciferase activity was measured by dual reporter assay.

The preceding experiments relied on reporter gene measurement to assess activation of production of IFN-α. The experiments were repeated, but instead of reporter gene measurement, the amount of cytokine produced by the cells was measured directly. TLR3/293 cells (Figure 3 C, left and center upper panels and right panel) or HEK293 cells (Figure 3 C, left and center lower panels), were transfected with DUBA siRNA #1 or #2 or a control siRNA as described above and incubated for 72 hours at 37 ⁰C. Cells were subsequently stimulated with 20 μg/mL polyLC or 20 U/well of Sendai virus ("SeV")(Cantell strain, obtained from ATCC) or 50 ng/mL TNF-α for 24 hours at 37 ⁰C. The supernatants from the cell cultures were collected and the secreted IL-8, IFN-α and RANTES content measured (IFN-α was measured by an Amersham ELISA kit according to the manufacturer's directions; IL8- and RANTES proteins were measured by a luminex (LINCO Research) according to the manufacturer's directions). Data represents the mean +/- standard deviation of triplicated samples. The results are shown in Figure 3C. The increased transcriptional response to polyLC after

DUBA knockdown was concomitant with increased secretion of IFN-α and RANTES, both of which are reportedly under the control of IRF-3 and IRF-7 (Honda et al., Immunity 25, 349 (2006)). IFN-α protein production triggered by polyLC-induced TLR3 stimulation was about 14-fold increased in the DUBA knockdown cells (upper left panel). RANTES, an IFN-I-induced chemokine, was also overproduced (upper center panel). While DUBA knockdown consistently led to a slight increase in the activity of anNF-κB-dependent reporter gene in response to RIG-I_CARD and MDA5_CARD overexpression, it did not alter NF-κB activation by TNF, IL-I NOD2, or TLRs 2-4 (Figure 3B). In agreement with these findings, DUBA knockdown did not alter NF-κB-dependent TNF -induced IL-8 secretion (Figure 3C, right panel). Thus the impact of DUBA on NF -KB signaling appears confined to that triggered by the RNA helicases RIG-I and MDA5.

Sendai virus was also used instead of polyLC in order to activate endogenous, cytosolic RIG-I (Kato et al., Nature 441, 101 (2006)) in a more physiologically relevant manner. DUBA knockdown significantly augmented secretion of both IFN-α and RANTES in Sendai virus-infected 293 cells

(Figure 3 C, bottom left and center panels).

DUBA knockdown also increased IFN-β secretion from the RAW264.3 macrophage cell line after treatment with ligands for TLR4 or TLR7 (Figure 3D, two left panels) (siRNA treatment of RAW264.3 cells was according to the methods described in Amarzguioui et α/., Nature Protocols 1,

508 (2006)), but it did not affect TLR2-induced NF-κB-dependent IL-6 production (Figure 3D, right panel).

Enforced expression of the adaptors TRIF, IPS-I, and IRAK-4 was used to bypass activation of TLR3, RIG-I/MDA5, and TLR7, TLR8, and TLR9, respectively, while still inducing IFN-I expression. The experimental protocol was according to that described in Example 1. Briefly,

HEK293 cells were transfected with either a control siRNA or DUBA siRNA#l . After three days, the cells were transfected with an IFN-α4 reporter gene construct and the indicated activator. Luciferase activity was measured after a 36 hour period of stimulation. Data represent the mean +/- standard deviation of triplicate samples. The results are shown in Figure 3E. In each instance, DUBA knockdown enhanced activation of an IFN-α4 promoter. Taken together with the above findings, the data show that DUBA is a negative regulator of IFN-I expression downstream of multiple pathogen recognition systems. Moreover, the data suggests that a common signaling component utilized by these receptors may be deubiquitinated by DUBA.

EXAMPLE 3: EFFECTS OF DUBA PROTEIN OVEREXPRESSION

The preceding results showed that DUBA gene knockdown augmented IFN-I production in HEK293 cells expressing TLR3. Experiments were also undertaken to determine whether increased DUBA activity might decrease or inhibit IFN-I production in response to the same stimuli. Full- length DUBA was amplified by PCR using standard techniques and subcloned into pCDNA3(-) (Invitrogen). The forward primer was ATGACTAT ACTCCCCAAAAA (SEQ ID NO: 3) and the reverse primer was TCAACTCTTGTCTGGGGGCG (SEQ ID NO: 4). DUBA containing a serine at position 224 instead of cysteine ("DUBA C224S") was created using a mutagenesis kit (Stratagene), a forward primer with the sequence GAGGATGGCGCCAGTCTCTTCCGGG (SEQ ID NO: 5), and a reverse primer with the sequence CCCGGAAGAGACTGGCGCCATCCTC (SEQ ID NO: 6), following the manufacturer's directions. Constructs comprising wild-type DUBA or a DUBA C224S were transfected together with TLR3, the CARD domain of RIG-I (see Example 2), the CARD domain of MDA5 (see Example 2), or IRF-7 into HEK293 cells. Specifically, HEK293 cells were transfected with control, FLAG-DUB A/pCDNA3, or FLAG-DUBA C224S/pCDNA3 (30 ng) together with control, MD A5 -CARD or RIG-I CARD plasmid (10 ng) and the luciferase reporter plasmid (20 ng). After 36 hours, luciferase activity was measured by a dual reporter assay, as described in Example IA. Data shown represent the mean +/- standard deviation of triplicated samples. As shown in Figure 4 (middle and right panels), ectopic wild-type DUBA expression significantly inhibited activation of IFN-α and IFN-β production through pathways mediated by TLR3, RIG-Ic_ARD, and MDA5_CARD- However, no such inhibitory activity was observed when wild- type DUBA was ectopically expressed in conjunction with IRF-7, suggesting that DUBA does not play a suppressive role in that signaling pathway (Figure 4, middle and right panels). This suppressive effect relied on DUBA enzymatic activity, since the DUBA C224S mutant exhibited only a slight effect on IFN-I responses to signaling through TLR3, RIG-I_CARD, and MDA5_CARD (Figure 4, middle and right panels). Activation of RIG-I and MD A5 -mediated NF-κB production was also decreased by overexpression of wild-type DUBA (Figure 4, left panel). No such significant effect was observed in the TLR3 -expressing cells, in accord with the results obtained in Examples 1 and 2 (Figure 4, left panel). Taken together, these data strongly support the hypothesis that DUBA plays a negative regulatory role in NF-κB production in the MDA5 and RIG-I-mediated signaling pathways, but not in the TLR3 -mediated pathway.

The downstream signaling machinery that is common to multiple receptors that induce IFN-I expression includes the ubiquitin ligase TRAF3, the kinases TBKl and IKK-e, and the transcription factors IRF-3 and IRF-7 (Akira et al., Cell 124, 783 (2006); Meylan & Tschopp, MoI. Cell 22, 561 (2006); Hacker et al, Nature 439, 204 (2006); Oganesyan et al, Nature 439, 208 (2006); Honda et al., Immunity 25, 349 (2006)). DUBA knockdown did not affect activation of IFN-β or IFN-α4 promoters in response to overexpressed IRF7 or coexpressed TBKl plus IKK-e (Figure 4), indicating that DUBA must act upstream of the TBKl/IKK-ε kinases. Consistent with these observations, overexpression of DUBA failed to inhibit IFN-α4 and IFN-β promoter activation by overexpressed IRF7 (Figure 4).

EXAMPLE 4: DUBA AND DEUBIOUITINATION A. LINKAGE-SPECIFIC DEUBIQUITINATION

The conserved catalytic triad within the OTU domain of DUBA suggests that DUBA has deubiquitinating activity. To obtain direct evidence for this enzymatic activity, recombinant DUBA was purified from E. coli and tested for deubiquitination activity. DUBA constructs with an N- terminal unizyme tag were expressed utilizing a phoA promoter-driven construct in BL21 RIL E. coli (Stratagene). Cultures were grown at 30 ⁰C to an OD_60O of 0.5 and the temperature was lowered to 10 ⁰C for 65 hours. Resulting pellets were microfluidized in a buffer containing 50 mM HEPES-NaOH pH 8.0, 300 mM NaCl, 10% glycerol, 5 mM 2-mercaptoethanol, 5 mM imidazole and 0.1% Brij35. The supernatant was then bound to Talon Resin™ (Clontech), washed in the same buffer, and eluted with 150 mM imidazole. The recombinant purified wild-type DUBA protein was incubated with lysine 48- or lysine

63-linked tetraubiquitin chains to assess the deubiquitination ability of the proteins. K48- or K63- linked tetraubiquitin chains (0.5 μg) (Boston Biochem) were mixed with wild-type DUBA or isopeptidase T (BostonBiochem) (1 μg) in DUBA assay buffer (50 mM HEPES pH 8.0, 0.01% Brij35, 10% glycerol, and 3 mM DTT) and incubated with or without 20 μM NEM at 37 ⁰C for 16 hours. Cysteine protease activity was blocked with 20 μM NEM in the reactions indicated. Samples were prepared for immunoblot analysis with anti-ubiquitin antibodies (Sigma). The results are shown in Figure 5. DUBA degraded lysine 63 -linked tetraubiquitin chains as effectively as known deubiquitinase isopeptidase T (IsoT), but, unlike IsoT, did not degrade lysine 48- linked tetraubiquitin chains (Figure 5A). DUBA has a conserved cysteine protease motif, and the cysteine protease inhibitor N-ethylmaleimide (NEM) also abrogated the ability of DUBA to degrade K63 -linked tetraubiquitin chains (compare DUBA+NEM to DUBA lanes in Figure 5 A, right panel). B. IDENTIFYING DUBA-INTERACTING PROTEINS

To further understand the role DUBA plays in the negative regulation of IFN-I expression, studies were performed to identify other proteins that may interact with DUBA intracellularly. FLAG epitope-tagged DUBA was transfected into HEK293 cells. After 48 hours, the cells were lysed with DISC buffer (30 mM Tris-HCl pH 7.5, 150 mM NaCl, 1% Triton X-100, 10% glycerol) containing complete protease inhibitor cocktail (Roche) and 10 μM NEM (Sigma). DUBA and any complexed proteins were immunoprecipitated with anti-FLAG beads (Sigma), followed by elution with 500 μg/mL FLAG peptide (Sigma). The resulting eluent was subjected to two-dimensional gel electrophoresis in combination with nano liquid-chromatography tandem mass spectrometry (GeLC- MS/MS) (Schirle, M. A. Heurtier, B. Kuster, MoI. Cell Proteomics 2, 1297 (2003)) and ion trap mass spectrometry (LTQ; Thermo Electron) with Mascot database search and the Scaffold program (Proteome Software) for visualization and validation of results.

Multiple peptides were detected in the immunoprecipitated DUBA complex, including three peptides from TRAF3 (see Figure 5B). TRAF3 is a RING finger-type ubiquitin ligase that is essential for IFN-I expression downstream of TLRs and the helicase receptors RIG-I and MDA5, and presumably functions upstream of TBKl (Hacker et al, Nature 439, 204 (2006); Oganesyan et al., Nature 439, 208 (2006)). The binding of DUBA to TRAF3 was thus investigated. HEK293 cells stably expressing TLR3 were stimulated with 20 μg/mL polyLC and lysates were prepared at 0, 60, and 180 minutes. Immunoprecipitation was performed using an anti-DUBA antibody according to the methods described previously, and co-precipitating endogenous TRAF3 was detected by Western blotting with anti-TRAF3 antibody (Santa Cruz). As shown in Figure 5C, increased binding of endogenous DUBA to endogenous TRAF3 was observed after polyLC stimulation of TLR3, confirming a probable direct DUBA/TRAF3 interaction. C. DUBA AND TRAF3 The finding that DUBA is likely associated with TRAF3 in vivo, taken together with the DUBA knockdown studies above finding that DUBA likely targets a common signaling protein upstream of TKBl and IKK-ε, suggested that DUBA might suppress IFN-I expression by deubiquitinating TRAF3. To test this, FLAG-tagged TRAF3 and HA-tagged ubiquitin were coexpressed with or without DUBA in HEK293 cells, and the extent of TRAF3 ubiquitination was determined. Briefly, HEK293 cells were co-transfected with FLAG-TRAF3, HA-Ub, and either empty vector, Myc -tagged wild-type DUBA, or DUBA C224S. After 24 hours growth, the cells were incubated with 25 μM MG-132 for four hours. The cells were lysed with RIPA buffer (50 mM Tris- HCl pH 7.4, 150 mM NaCl, 2 mM EDTA, 1 % NP-40, 0.1 % SDS) containing protease inhibitor cocktail and 10 μM NEM. Non-covalently bound proteins were dissociated by boiling in 1% SDS (v/v) and samples were diluted 1:10 in lysis buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 2 mM EDTA, 1 % NP-40) containing protease inhibitor cocktail and 10 μM NEM. TRAF3 proteins were immunoprecipitated by standard procedures using rabbit anti-TRAF3 antibodies (Santa Cruz) and HRP-labeled anti-rabbit antibodies (TrueBlot). After heat denaturation in 1% SDS, TRAF3 was immunoprecipitated with anti-FLAG antibody after 24 hours and Western blotting was performed using anti-HA or anti-FLAG antibody as indicated in Figure 5. The in vivo ubiquitination assay was performed as previously described (Wertz et α/., Nature 430, 694 (2004)). Wild type ubiquitin or mutants retaining only a single lysine (K48 or K63) were employed in the center panel of Figure 5. 1% of input lysate was subjected to Western blotting with anti-Myc antibody, as described above.

When overexpressed FLAG-TRAF3 was immunoprecipitated from lysates (after boiling in SDS to remove associated proteins), a smear corresponding to ubiquitinated TRAF3 was detected with anti-HA antibody (Figure 5D, left panel). Wild-type DUBA but not the catalytic site mutant DUBA C224S reduced the amount of ubiquitinated TRAF3 detected. Neither DUBA nor DUBA C224S deubiquitinated TRAF6 (Figure 5D, left panel, three rightmost lanes), indicating that the deubiquitination of TRAF3 was specific. Using HA-tagged ubiquitin mutants where only lysine 48 or lysine 63 is available to form polyubiquitin chains, TRAF3 mainly acquired lysine 63 -linked polyubiquitin chains (Figure 5D, middle panel). This modification was reduced by coexpression of DUBA (Figure 5D, right panel). TRAF3 is known to interact with the downstream TLR3 signaling pathway component TBK-

1 in vivo. To determine whether DUBA can interfere with the TRAF3-TBK-1 interaction, co- immunoprecipitation experiments were performed. Briefly, HEK293 cells were transfected with FLAG-TRAF3 together with control plasmid, Myc-tagged DUBA, or DUBA C224S as described above. After a 48 hour incubation, the TRAF3 complex was immunoprecipitated with anti-FLAG beads, and subjected to immunoblot with anti-TBKl and anti-FLAG. 1% of input lysate was subjected to Western blotting with anti-Myc and anti-TBKl antibody. As shown in Figure 5F, DUBA coexpression significantly decreased the amount of co-immunoprecipitated TRAF3/TBK-1 as compared to control (non-DUBA) levels, while the DUBA catalytic mutant had a lesser effect. Experiments described herein indicated that DUBA interacts with the RIG-I signaling pathway. The ability of DUBA to deubiquitinate RIG-I was thus also investigated. HEK293 cells were transfected with 20 nM control or DUBA siRNA #1. After 36 hours, the cells were co- transfected with control or FLAG-tagged RIG-I_CARD and HA-Ub constructs and incubated for 24 hours. After heat denaturation in 1% SDS, endogenous TRAF3 was immunoprecipitated with anti- TRAF3 and subjected to immunoblot with anti-HA or anti-TRAF3 antibodies. 1% of input lysate was subjected to Western blot analysis with anti-FLAG antibody. 50% of the input lysate was subjected to Western blot analysis for DUBA as described above. The results are shown in Figure 5E. Ubiquitination of endogenous TRAF3 was detected upon overexpression of RIG-I_CARD and this ubiquitination was increased by knockdown of DUBA (Figure 5E).

Taken together, these data indicated that DUBA is able to promote the removal of lysine 63- linked polyubiquitin chains from TRAF3. Without being limited by any one theory, this may explain the evidence herein that DUBA is able to negatively control IFN-I production. Similar mechanisms exist in the NF-κB pathway, where A20 and CYLD reportedly deubiquitinate TRAF2 and TRAF6, respectively, to switch off classical NF-κB signaling by TLRs and the TNF receptor (Chen, Nat. Cell Biol. 7, 758 (2005); Wullaert et al, Trends Immunol. 27, 533 (2006); Boone et al, Nat. Immunol. 5, 1052 (2004)). As is the case with TRAF6 (Lamothe et al, J. Biol. Chem. 282, 4102 (2007)), TRAF3 autoubiquitination by lysine 63 -linked polyubiquitin chains is likely to be important for downstream signaling events. Without being bound by one particular interpretation, TRAF3 ubiquitination may facilitate the recruitment of downstream signaling components. The experiments herein showed that DUBA overexpression resulted in a partial but significant reduction in the interaction of TRAF3 with TBKl, and this reduction was dependent on the catalytic activity of DUBA (Figure 5F). D. ROLE OF DUBA DOMAINS (1). Ubiquitin-binding domains

Ubiquitin-binding domains (UBDs) such as the ubiquitin-associated domain (UBA) and ubiquitin-interacting motif (UIM) can influence various cellular events through binding to ubiquitinated proteins (Hicke, H. L. Schubert, C. P. Hill, Nat. Rev. MoI. Cell Biol. 6, 610 (2005); Hurley, S. Lee, G. Prag, Biochem. J. 399, 361 (2006)). Some DUBs, including USP5 and USP25, reportedly have one or more putative UBDs, but the function of UBDs in the deubiquitination reaction remains to be elucidated. A Hidden Markov Model analysis using the Pfam model indicated that DUBA has a putative UIM embedded in a conserved C-terminal helix (Figure 6A).

To assess the function of the putative DUBA UIM, the ability of the region to bind specifically to polyubiquitin chains was assessed. GST, GST-DUBA UIM (amino acids 534-571 of DUBA), or GST-DUBA UIM L542A/S549A mutant proteins were purified from HEK293 cells by glutathione column, and incubated with CNBr-activated agarose beads (Pharmacia) coated with K48 Ub₃.₇, K63 Ub₃.₇ (both from BostonBiochem), or BSA in 1% Triton X-100, 50 mM Tris-HCl pH 7.5, 150 mM NaCl buffer for two hours at 4 ⁰C. Immunoprecipitations were performed as described herein using anti-ubiquitin antibodies (Sigma). Bound material was analyzed by Western blotting with anti-GST antibody (Sigma). GST-S5a was used as a positive control. As shown in Figure 6B, both lysine 48- and lysine 63-linked polyubiquitin chains could bind to GST fused to the DUBA UIM in coimmunoprecipitation studies. Mutation of conserved residues in the DUBA UIM domain (L542A/S549A) prevented this binding. These results indicated that the DUBA UIM is indeed capable of interacting with polyubiquitin chains.

DUBA UIM mutants were used to determine the role of the UIM in the negative regulation of IFN-I expression by DUBA. Hek293 cells were transfected with IFN-β reporter construct and the indicated activator (RIG-IC_ARD or MDAC_ARD) together with either empty vector or the indicated version of DUBA, as described above. Reporter activity was measured after 36 hours. The data represent the mean +/- standard deviation of triplicate samples. Expression of wild-type and mutant DUBA protein was assessed by Western blotting. Both DUBA ΔUIM and DUBA L542A/S549A UIM retained some ability to attenuate RIG-I_CARD- or MDA5c_ARD-induced activation of an IFN-β promoter, although they were much less effective than wild-type DUBA (Figure 6C). Experiments were also performed to assess the impact of the DUBA mutants on the ubiquitination of Myc-TRAF3 using the methodology described in Example 2, above. Compared to wild-type DUBA, both UIM mutants were also consistently less effective at reducing the level of ubiquitinated TRAF3 in cells (Figure 6D). These results suggested an important role for the DUBA UIM in DUBA function, but left the possibility that the UIM might not be the sole substrate recognition site. The binding affinity between ubiquitin and UIMs is typically very low (Kd>100 μM) (Hicke et al., Nat. Rev. MoI. Cell Biol. 6, 610 (2005); Hurley et al., Biochem. J. 399, 361 (2006)), so the DUBA UIM was predicted to play a supportive but not necessarily controlling role by capturing and presenting ubiquitinated substrates to the catalytic domain. The results described herein indicate that DUBA likely shuts down IFN-I expression through deubiquitination of TRAF3. TRAF3 also regulates non-classical NF-κB/NFκB2 signaling by controlling the NIK kinase level, which in turn activates downstream kinase IKK-α (Bonizzi & Karin, Trends Immunol. 25, 280 (2004); He et al, J. Exp. Med. 203, 2413 (2006); Liao et al., J. Biol. Chem. 279, 26243 (2004)). Several cell surface receptors, including Baff-receptor and LT-beta receptor, preferentially engage TRAF3 for eventual proteolytic processing of latent NF -κB2 pi 00 to active p52 (Bonizzi & Karin, Trends Immunol. 25, 280 (2004)) . That signaling pathway is essential for B-cell survival and lymphoid organogenesis (Bonizzi & Karin, Trends Immunol. 25, 280 (2004)). Accordingly, experiments were undertaken to assess whether DUBA impacts the pl00/p52 signaling pathway. Briefly, 293 cells stably expressing Baff receptor were transfected with either a control siRNA or DUBA siRNA#l using the methods described in Example 2. Three days later, the cells were co-cultured with or without 500 ng/ml Blys for 24 hours. The cells were lysed, and the lysates were immunoprecipitated with anti-pl00/p52 antibodies, and blotted with NF-κB2 antibodies (Cell Signaling). Intriguingly, knockdown of DUBA did not affect pl00/p52 status, either with or without Baff-receptor engagement by Blys ligand (Figure 7A). This finding suggests that DUBA impacts only one aspect of TRAF3 signaling, namely that required for IFN-I expression. How TRAF3 exerts distinct dual functions remains to be elucidated. Given that DUBA preferentially cleaves lysine 63- linked polyubiquitin chains (Figure 5A), it is possible that the lysine 63 -linked polyubiquitination of TRAF3 selectively stimulates IFN-I production. Lysine 48-lmked polyubiquitination mediated by TRAF3, which is less influenced by DUBA, is likely required for non-classical NF -KB signaling. This is consistent with previous reports showing that non-classical NF -KB signaling is governed by TRAF3 -mediated degradation of NIK (Liao et al., J. Biol. Chem. 279, 26243 (2004)). Diseases such as systemic lupus erythematosis (SLE), where excess IFN-I production leads to inflammatory pathogenesis (Pascual et al., Curr. Opin. Immunol. 18, 676 (2006)), stress the importance of negatively regulating IFN-I. The results indicate that DUBA likely has a critical role in switching off IFN-I responses and thereby helps prevent unchecked innate immunity. (2). OTU domain The contribution of another DUBA domain, the OTU domain (see Figure 2A), to the suppressive activity of DUBA was investigated. A series of OTU-containing DUBA truncation mutants was constructed (see Figure 8A for schematic representations), including the OTU domain itself (amino acids 172-351), the N-terminal portion of DUBA terminating immediately after the OTU domain (amino acids 1-351), and the OTU domain through the C-terminus (amino acids 172-571). A reporter assay for each mutant and wild-type DUBA was performed as described in Example IA, with the exception that a low dose (10 ng) of each construct and wild-type was used. For the DUBA co- transfection, HEK293 cells were transfected with control, DUBA wild-type and UIM mutants (30 ng) together with control MDA5_CARD or RIG-I_CARD plasmid (5 ng) and luciferase reporter plasmids (20 ng). After 36 hours at 37 ⁰C, luciferase activity was measured by the dual reporter assay as described above. Expression of DUBA proteins and truncation mutants in transfected cells was evaluated by Western blot using standard methods and an anti-FLAG antibody as a probe.

As shown in Figure 8B, wild-type DUBA and each DUBA truncation mutant were strongly expressed in the transfected 293 cells, and thus the functional activity of each mutant could be reasonably assessed by reporter assay (Figure 8A). Wild-type DUBA and, to a lesser extent, the DUBA OTU domain alone inhibited MDA5 and RIG-I-induced IFN-β promoter activation (Figure 8A). When the OTU domain was fused with the DUBA N-terminus, DUBA inhibitory activity was severely impaired. In contrast, the DUBA OTU-C terminal truncation exhibited the strongest inhibitor effect. Together, these results indicated that the OTU domain alone has the ability to suppress IFN-I responses, and that the N-terminus and the C-terminus have opposite regulatory roles (negative, and positive, respectively) in DUBA function.

Claims

WE CLAIM:

1. A method of modulating interferon production in a cell, comprising administering to the cell at least one modulator of DUBA expression and/or DUBA activity.

2. A method of increasing interferon production in a cell, comprising administering to the cell at least one compound that decreases or blocks DUBA expression and/or DUBA activity.

3. A method of decreasing interferon production in a cell, comprising administering to the cell at least one compound that increases DUBA expression and/or DUBA activity.

4. A method for the treatment of a disease or condition caused by, exacerbated by, or prolonged by decreased levels of interferon in a subject relative to interferon levels in a healthy subject, comprising administering to the subject an effective amount of at least one compound that decreases or blocks DUBA expression and/or DUBA activity in the subject.

5. A method for the treatment of a disease or condition caused by, exacerbated by, or prolonged by increased levels of interferon in a subject relative to interferon levels in a healthy subject, comprising administering to the subject an effective amount of at least one compound that increases DUBA expression and/or DUBA activity in the subject.

6. A method for increasing interferon production in a cell, comprising inhibiting DUBA expression and/or DUBA activity in the cell.

7. A method for decreasing interferon production in a cell, comprising stimulating DUBA expression and/or DUBA activity in the cell.

8. A method for increasing interferon production in a mammal, comprising inhibiting DUBA expression and/or DUBA activity in the mammal.

9. A method for decreasing interferon production in a mammal, comprising stimulating DUBA expression and/or DUBA activity in the mammal.

10. A method for detecting a predisposition to or the presence or extent of a disease or condition relating to abnormal interferon levels in a subject, comprising detecting the amount and/or activity of

DUBA in the subject.

11. The method of claim 10, wherein the disease or condition is selected from at least one of a cell proliferative disorder, an infection, an immune/inflammatory disorder, and an interferon-related disorder.

12. The method of any of claims 1-10, wherein the interferon is a type I interferon.

13. The method of claim 12, wherein the interferon is selected from IFN-α and IFN-β.

14. The method of claim 2 or 4, wherein the compound that decreases or blocks DUBA expression and/or DUBA activity is a DUBA antagonist.

15. The method of claim 14, wherein the DUBA antagonist is selected from an antibody, an antigen- binding fragment, an aptamer, an interfering RNA, a small molecule, a peptide, and an antisense molecule.

16. The method of claim 15, wherein the interfering RNA is selected from the silencing RNAs set forth in SEQ ID NOs: 36, 50, 64, and 78.

17. The method of claim 3 or 5, wherein the compound that increases DUBA expression and/or DUBA activity is a DUBA agonist.

18. The method of claim 17, wherein the DUBA agonist is selected from an antibody, an antigen- binding fragment, an aptamer, an interfering RNA, a small molecule, a peptide, and an antisense molecule.

19. The method of claim 1 , wherein the at least one modulator of DUBA expression modulates DUBA transcription.

20. The method of claim 1 , wherein the at least one modulator of DUBA expression modulates DUBA translation.

21. The methods of any of claims 1-10, wherein the modulator of DUBA expression and/or DUBA activity, the compound that increases DUBA expression and/or DUBA activity, or the compound that decreases or blocks DUBA expression and/or DUBA activity modifies DUBA expression and/or DUBA activity such that signaling through the TLR3, RIG-I, or MDA5 signaling pathways is modulated TRAF3 activity is modulated.

22. The method of claim 21 , wherein the modulator of DUBA expression and/or DUBA activity, the compound that increases DUBA expression and/or DUBA activity, or the compound that decreases or blocks DUBA expression and/or DUBA activity modifies DUBA expression and/or DUBA activity such that TRAF3 activity is modulated.

23. The method of claim 22, wherein the TRAF3 activity is modulated due to an increase or decrease in the amount of K63 -linked polyubiquitination of TRAF3.

24. A method for selectively deubiquitinylating a K63-linked polyubiquitinated polypeptide while not deubiquitinylating a polypeptide that is polyubiquitinated with a polyubiquitin comprising one or more lysine linkages other than K63, comprising treating the K63 -linked polyubiquitinated polypeptide with DUBA.

25. A method for selectively deubiquitinylating only one or more K63 -linked polyubiquitin chains but not polyubiquitin chains comprising one or more lysine linkages other than K63 in a polyubiquitinated polypeptide comprising treating the polypeptide with DUBA.

26. The method of claim 24 or 25, wherein the polyubiquitinated polypeptide is TRAF3.