AU2001288405A1 - Amino acid substitution mutants of interleukin 13 - Google Patents

Description

AMINO ACID SUBSTITUTION MUTANTS OF INTERLEUKIN 13

CROSS- REFERENCE TO RELATED APPLICATIONS The present application claims the benefit of U.S. Provisional patent application number 60/229,194 filed August 30, 2000. STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER

FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT This invention was made in part with U.S. government support under grant CA741145 awarded by the National Institutes of Health. The U.S . government may have certain rights in the invention. BACKGROUND OF THE INVENTION

Human interleu in 13 (ML 13) is a 114 amino acid cytokine secreted by activated T cells. Mintyetal. (1993) Nature, 362:248-250; and McKenzie etal. (1993)Proc.Natl. Acad. Sci.USA, 90:3735-3739. HL13 is involved in regulating several different physiological responses. Among these, hIL13 has been shown to downregulate the production of cytokines involved in inflammation. Minty et al, supra; and de Waal Malefyt et al. (1993) J. Immunol., 151:6370-

6381. It has also been shown to upregulate expression of major histocompatibility class II molecules and CD23 on monocytes, and to regulate various aspects of B cell function De Waal Malefyt et al. (1993) Res. Immunol. 144:629-633; McKenzie et al., supra; and de Waal Malefyt et al. (1993) J. Immunol., 151:6370-6381. In addition to regulating cells of the immune system, IL-13 has also been shown to act on other cell types. For example, IL13 has been shown to modulate expression of vascular cell adhesion molecule- 1 (VCAM-1) on endothelial cells. Sironi et al. (1994) Blood, 84:1913-1921; Bochner et al. (1995) J. Immunol., 154:799-803; and Schnyder et al. (1996) Blood, 87:4286-4295.

Based on its predicted secondary structure, hIL 13 has been added to a growing family of growth hormone-like cytokines that all exhibit bundled alpha-helical core topology.

Bamborough et al. (1994) Prot. Engin., 7:1077-1082. Structural analyses indicated that ML 13 is a globular protein comprised mainly of four alpha-helical regions (helices A, B, C, and D) arranged in a "bundled core." Miyajima et al. (1992) Ann. Rev. Immunol., 10, 295-331.

While dissimilar at the primary amino acid level, ML 13 and human interleukin 4 (hIL4) bind and signal through a shared receptor complex. Zurawski et al. (1993) EMBO J., 12:2663- 2670; and Tony et al. (1994) Eur. J. Biochem., 225:659-66. This shared receptor is a heterodimer that includes a first subunit of approximately 140 kDa termed pi 40, and a second subunit of approximately 52 kDa tenned a' or IL13Ral. Idzerda et al. (1990) J. Exp. Med., 173:861-873; Obiri et al. (1995) J. Biol. Chem., 270:8797-8804; Hilton et al. (1996) Proc. Natl. Acad. Sci. USA, 93 :497-501; andMilou etal. (1997) FEBS Letters, 401:163-166. Unlike ML4,

ML13 does not bind pl40 in the absence of a'. Vita etal. (1995) J. Biol. Chem., 270:3512-3517. In addition to the shared receptor, another ML 13 receptor termed the restricted (IL4 independent) receptor exists. In contrast to the shared receptor, the latter receptor binds ML 13 but not ML4. The restricted receptor is also sometimes called the glioma-associated receptor because it is preferentially expressed at high levels in certain malignant cells, including those in high grade human gliomas. Debinski et al. (1995) Clin. Cancer Res., 1:1253-1258; and Debinski et al. (1996) J. Biol. Chem., 271, 22428-22433. In addition to being associated with malignancies, ML13 has also been associated with other pathological conditions. Notably, IL13 has been shown to be involved in pathways that regulate airway inflammation, suggesting that this cytokine might play an important role in asthma and perhaps other allergic pathologies. Webb et al., (2000) J. Immunol.165: 108-113; and Djukanovic, R. (2000) Clin. Exp. Allergy 30 Suppl 1:46-50.

SUMMARY OF THE INVENTION The invention relates to the development and characterization of several mutants of ML 13. Using these mutants, three regions of native ML 13 were identified as being required for signaling through the shared receptor. These regions were localized to alpha-helices A, C and D and were generally separated from the regions involved in binding to the restricted receptor. Glutamic acids at positions 13 and 16 in ML 13 alpha-helix A, arginine and serine at positions 66 and 69 in helix C, and arginine at position 109 in helix D were found to be important in inducing biological signaling because these mutations resulted in the loss and/or gain of functional phenomena.

Mutants within the invention include those having one or more of the native amino acids ofML13 at positions 13, 16, 17, 66, 69, 99, 102, 104, 105, 106, 107, 108, 109, 112, 113, and 114 replaced with a different amino acid. These mutants are expressed herein as hIL13.X,PX₂, where P is a number corresponding to the position of the mutated amino acid in hIL13, X, is the letter abbreviation of the amino acid that was replaced, and X₂ is the letter abbreviation of the replacement amino acid. Mutants with multiple mutations are indicated in the same fashion as ML13X₁PX₂.X₃PιX₄for a double amino acid substitution mutant. ML13XιPX₂.X₃P₁X₄.X₅P₂X₆ for a triple amino acid substitution mutant; and hIL13X₁PX₂.X₃P₁X₄.X₅P₂X₆.X₇P₃X₈ or a quadruple amino acid substitution mutant. For example, ML13.E13K represents a mutant form of ML13 that has the glutamic acid residue that naturally occurs at position 13 in native ML13 replaced with a lysine residue; and ML 13.E13K.S69D represents a mutant form of ML 13 that has the glutamic acid residue that naturally occurs at position 13 in native ML 13 replaced with a lysine residue and the serine residue that naturally occurs at position 69 in native Ll 3 replaced with an aspartic acid residue. Representative single amino acid substitution mutants within the invention include ML13.E13K, ML13.E13I, ML13.E13C, ML13.E13S, ML13.E13R,

ML13.E13Y,hIL13.E13D,ML13.E16K,ML13.E17K,ML13.R66D,hIL13.S69D₎ML13.D99K, ML13.L102A, ML13.L104A, ML13.K105D, ML13.K106D, ML13.L107A, ML13.F108Y, ML13.R109D, ML13.R112D, ML13.F113D, and ML13.N114D. The invention also includes double, triple, and quadruple amino acid substitution mutants including: ML13.E13K.S69D (SEQ ID NO:2); ML13.E13K.R109D (SEQ ID NO:3); ML13.E13K.R112D (SEQ ID NO:4); hIL13.E13Y.R66D (SEQ ID NO:5); hIL13.E13Y.S69D (SEQ ID NO:6); ML13.E13K.R66D.S69D (SEQ ID NO:7); ML13.E13Y.R66D.S69D (SEQ ID NO:8); and ML13.E13K.R66D.S69D.R112D (SEQ ID NO:9).

Accordingly, the invention features a purified mutant hIL 13 molecule including an amino acid sequence (a) having at least 90% sequence identity to the native MLl 3 sequence (SEQ ID

NO : 1 ) and (b) differing from the native ML 13 sequence by at least a first amino acid substitution occurring in the A alpha helix and a second amino acid substitution occurring in the D alpha helix.

Also within the invention is a purified mutant ML 13 molecule including an amino acid sequence (a) having at least 90% sequence identity to the native ML13 sequence (SEQ ID NO: 1) and (b) differing from the native ML 13 sequence by at least three amino acid substitutions. In one variation of the foregoing, the amino acid sequence differs from the native ML13 sequence by at least a first amino acid substitution occurring in the A alpha helix, a second amino acid substitution occurring in the D alpha helix, and a third amino acid substitution occurring in the C alpha helix. In another variation of the foregoing, the amino acid sequence differs from the native ML 13 sequence by at least four amino acid substitutions, e.g., with at least a first amino acid substitution occurring in the A alpha helix, a second amino acid substitution occurring in the D alpha helix, and a third amino acid substitution occurring in the C alpha helix.

The invention further includes a purified mutant hIL13 molecule that includes a polypeptide having or consisting of an amino acid sequence of one of SEQ ID NOs: 2-9. The purified mutant ML 13 molecule of the invention can further include a pharmaceutically acceptable carrier and/or can be conjugated to an effector molecule such as a cytotoxin (e.g., a Pseudomonas exotoxin such as PE38QQR, PE1E, and PE4E, Diptheria toxin, ricin, abrin, saporin, and pokeweed viral protein), a detectable label, an antibody, a liposome, and a lipid. The effector molecule can also be a radionuclide. In another aspect, the invention features a purified nucleic acid encoding a polypeptide including or consisting of an amino acid sequence of one of SEQ ID NOs: 2-9.

The invention additionally features an antibody that specifically binds an ML 13 mutant but not a native ML13. The ML13 mutant can be one of the above-described mutant ML13 molecules such as one that includes an amino acid sequence of one of SEQ ID NOs: 2-9. In still another aspect, the invention includes a method of delivering a ML 13 mutant to a cell. This method includes the steps of: (a) providing a ML 13 mutant (such as one described above) (b) providing the cell; and (c) contacting the cell with the ML 13 mutant. In the method, the ML13 mutant can be conjugated to an effector molecule. The step (c) of contacting the cell with the ML13 mutant can takes place in an animal, e.g., by administering the mutant to the animal by injection or other means. 51. Also in another variation of the method, the cell can form part of a tumor in an animal such that the tumor is growing at a measurable rate in the animal. In this variation, the rate is decreased subsequent to the step (c) of contacting the cell with the ML 13 mutant.

Unless otherwise defined, all technical terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.

Commonly understood definitions of molecular biology terms can be found in Rieger et al., Glossary of Genetics: Classical and Molecular, 5th edition, Springer- Verlag: New York, 1991; and Lewin, Genes V, Oxford University Press: New York, 1994.

As used herein, the phrase "native MLl 3" means the mature form of human interleukin 13 , the amino acid sequence of which is shown herein as SEQ ID NO : 1.

The phrase "ML13 mutant," "mutant ML13," or a "mutant ML13 molecule" means an hIL 13 in which one or more of the amino acids differ from the corresponding amino acids in the native ML13. Thus, for example, where a native ML 13 has a glutamic acid at position 13, a mutant hIL 13 can have an amino acid other than glutamic acid at position 13 (e.g., glutamic acid is substituted with lysine). It will appreciated that mutant IL13 molecules of this invention include mutant IL13 molecules of other mammalian species (e.g., rat, murine, porcine, ovine, goats, non-human primates, bovine, canus, and the like) and this invention contemplates the use of mutant IL13 in veterinary as well as human medical conditions.

As used herein, the terms "protein" and "polypeptide" are used synonymously to mean any peptide-linked chain of amino acids, regardless of length or post-translational modification, e.g., glycosylation or phosphorylation. An "purified" polypeptide is one that has been substantially separated or isolated away from other polypeptides in a cell, organism, or mixture in which the polypeptide occurs (e.g., 30, 40, 50, 60, 70, 80, 90, 95, 96, 97, 98, 99, 100% free of contaminants).

As used herein, a "nucleic acid" or a "nucleic acid molecule" means a chain of two or more nucleotides such as RNA (ribonucleic acid) and DNA (deoxyribonucleic acid). A "purified" nucleic acid molecule is one that has been substantially separated or isolated away from other nucleic acid sequences in a cell or organism in which the nucleic acid naturally occurs (e.g., 30, 40, 50, 60, 70, 80, 90, 95, 96, 97, 98, 99, 100% free of contaminants). The term includes, e.g., a recombinant nucleic acid molecule incorporated into a vector, a plasmid, a virus, or a genome of a prokaryote or eukaryote. Examples of purified nucleic acids include cDNAs, fragments of genomic nucleic acids, nucleic acids produced polymerase chain reaction (PCR), nucleic acids formed by restriction enzyme treatment of genomic nucleic acids, recombinant nucleic acids, and chemically synthesized nucleic acid molecules. A "recombinant" nucleic acid molecule is one made by an artificial combination of two otherwise separated segments of sequence, e.g., by chemical synthesis or by the manipulation of isolated segments of nucleic acids by genetic engineering techniques.

As used herein, "sequence identity" means the percentage of identical subunits at corresponding positions in two sequences when the two sequences are aligned to maximize subunit matching, i.e., taking into account gaps and insertions. When a subunit position in both of the two sequences is occupied by the same monomeric subunit, e.g., if a given position is occupied by an alanine in each of two polypeptide molecules, then the molecules are identical at that position. For example, if 7 positions in a sequence 10 amino acids in length are identical to the corcesponding positions in a second 10 amino acid sequence, then the two sequences have 70% sequence identity. Sequence identity is typically measured using sequence analysis software (e.g., Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, WI 53705).

By the term "antibody" is meant an immunoglobulin as well as any portion or fragment of an immunoglobulin whether made by enzymatic digestion of intact immunoglobulin or by techniques in molecular biology. The term also refers to a mixture containing an immunoglobulin (or portion or fragment thereof) such as an antiserum.

The term "specifically binds" , as used herein, when referring to a polypeptide (including antibodies) or receptor, refers to a binding reaction which is determinative of the presence of the protein or polypeptide or receptor in a heterogeneous population of proteins and other biologies.

Thus, under designated conditions (e.g. immunoassay conditions in the case of an antibody), the specified ligand or antibody binds to its particular "target" (e.g. an IL13 specifically binds to an I 13 receptor) and does not bind in a significant amount to other proteins present in the sample or to other proteins to which the ligand or antibody may come in contact in an organism. Generally, a first molecule that "specifically binds" a second molecule has a binding affinity greater than about 10^s (e.g., 10⁶, 10⁷, 10⁸, 10⁹, 10¹⁰, 10^u, and 10¹² or more) moles/liter for that second molecule.

A "mutation" in a polypeptide refers to the substitution of an amino acid at a particular position in a polypeptide with a different amino acid at that position. Thus, for example, the mutation hIL 13.E 13K.S69D indicates that the native amino acids at positions 13 and 69 in IL 13

(glutamic acid, E; and serine, S) are replaced with lysine (K) and aspartic acid (D) respectively. In some cases, a mutation can be the deletion, addition, or substitution of more than one amino acid in a polypeptide. The mutation does not require an actual removal and substitution of the amino acid(s) in question. The protein can be created de novo with the replacement amino acid in the position(s) of the desired mutation(s) so the net result is equivalent to the replacement of the amino acid in question.

Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In the case of conflict, the present specification, including definitions will control. In addition, the particular embodiments discussed below are illustrative only and not intended to be limiting. BRIEF DESCRIPTION OF THE DRAWINGS The invention is pointed out with particularity in the appended claims. The above and further advantages of this invention may be better understood by referring to the following description taken in conjunction with the accompanying drawings, in which: Figure 1 A is a graph showing the cytotoxicity of IL13.E13K-PE38QQR mutant-based constructs on U-251 MG cells. Standard error of the mean is shown by a vertical bar. Numbers (n) of experiments for each cytotoxin were: IL13.E13K-PE38QQR (n =2), IL13.E13K.R66D- PE38QQR (n =4), IL13.E13K.S69D-PE38QQR (n =5), IL13.E13K.R66D.S69D-PE38QQR (n =7). *** = pO.OOl by ANOVA. Figure IB is a graph showing the cytotoxicity of IL13.E13K-PE38QQR mutant-based constmcts on HUVEC. Standard error of the mean is shown by a vertical bar. Numbers (n) of experiments for each cytotoxin were: IL13.E13K-PE38QQR (n =3), IL13.E13K.R66D- PE38QQR(n=3), IL13.E13K.S69D-PE38QQR(n=4),andIL13.E13K.R66D.S69D-PE38QQR (n =5). Figure 2A is a graph showing the cytotoxicity of IL 13.E 13 Y-PE38QQR mutant-based constructs on U-251 MG cells. Standard error of the mean is shown by a vertical bar. Numbers (n) of experiments for each cytotoxin were: IL13.E13Y-PE38QQR (N=2), IL13.E13Y.R66D- PE38QQR (n =2) and IL13.E13Y.S69D-PE38QQR (n =2).

Figure 2B is a graph showing the cytotoxicity of IL13.E13Y-PE38QQR mutant based constructs on HUVEC cells. Standard error of the mean is shown by a vertical bar. Numbers

(n) of experiments for each cytotoxin were: IL13.E13Y-PE38QQR (n =2), IL13.E13Y.R66D- PE38QQR (n =2) and IL13.E13Y.S69D-PE38QQR (n =2).

Figure 3A is a graph showing the cytotoxicity of IL13.E13K-PE1E mutant based constructs on U-251 MG cells. Standard error of the mean is shown by a vertical bar. Numbers (n) of experiments for each cytotoxin were: IL13.E13K-PE1E (n =2), IL13.E13K.R66D-PE1E

(n =2), IL13.E13K.S69D-PE1E (n=2) andIL13.E13K.R66D.S69D-PElE (n=2). PElEmutant based constructs on U-251 MG cells.

Figure 3B is a graph showing the cytotoxicity of IL13.E13K-PE1E mutant based constructs on HUVEC cells. Standard error of the mean is shown by a vertical bar. Numbers (n) of experiments for each cytotoxin were: IL13.E13K-PE1E (n =1), LL13.E13K.R66D-PE1E

(n =2), IL13.E13K.S69D-PE1E (n =2) and IL13.E13K.R66D.S69D-PE1E (n =2).

Figure 4 A is a graph showing the IL13 receptor-mediated cytotoxicity of IL13.E13K.R66D.S69D-PE38QQR on U-251 MG cells. A neutralizing cytokine (IL13, IL13.E13K, or IL4) was added at a final concentration of 1 ng/ml. Standard error of the mean is shown by a vertical bar. Cytotoxicity of IL13.E13K.R66D.S69D-PE38QQR was significantly lower in the presence of IL13 or IL13.E13K (*** = pO.OOl) and significantly increased in the presence of IL4 (* = p<0.05) by ANOVA.

Figure 4B is a graph showing the cytotoxicity of IL13.E13K.R66D.S69D-PE38QQRvs. non-specific toxicity of PE38QQR on U-251 MG cells. Standard error of the mean is shown by a vertical bar. Numbers (n) of experiments for each cytotoxin were: IL13.E13K.R66D.S69D- PE38QQR (0.01 to 10 ng/ml values pooled from Figure 1, 1000 ad 5000 ng/ml values n =2), and PE38QQR (n =3). IL13.E13K.R66D.S69D-PE38QQR was significantly more cytotoxic to U-

251 MG cells than PE38QQR itself (*** = pθ.0001 by ANOVA).

Figure 5A is a graph showing the cytotoxicity of IL13.E13K.R66D.S69D-PE38QQRvs. non-specific toxicity of PE38QQR on HUVEC. Standard error of the mean is shown by a vertical bar. Numbers (n) of experiments for each cytotoxin were: IL13.E13K.R66D.S69D- PE38QQR (n =2) and PE38QQR (n =2).

Figure 5B is a graph showing the cytotoxicity of IL13.E13K.R66D.S69D-PE38QQR and PE38QQR on glial cells. Standard error of the mean is shown by a vertical bar. Numbers (n) of experiments for each cytotoxin were: IL13.E13K.R66DS69D-PE38QQR (n =3) and PE38QQR (n =3). Figure 6 is a graph showing the ability of IL13.E1 Y.R66D.S69D-PE1E to inhibit the growth of a tumor in an animal.

DETAILED DESCRIPTION This invention encompasses compositions and methods relating to hIL13 mutants. The below described preferred embodiments illustrate adaptations of these compositions and methods. Nonetheless, from the description of these embodiments, other aspects of the invention can be made and/or practiced based on the description provided below.

Biological Methods

Methods involving conventional molecular biology techniques are described herein. Such techniques are generally known in the art and are described in detail in methodology treatises such as Molecular Cloning: A Laboratory Manual, 2nd ed., vol. 1-3, ed. Sambrook et al., Cold

Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989; and Current Protocols in

Molecular Biology, ed. Ausubel et al., Greene Publishing and Wiley-Interscience, New York, 1992 (with periodic updates). Various techniques using polymerase chain reaction (PCR) are described, e.g., in Innis et al., PCR Protocols: A Guide to Methods and Applications, Academic Press: San Diego, 1990. PCR-primer pairs can be derived from known sequences by known techniques such as using computer programs intended for that purpose (e.g., Primer, Version 0.5, ©1991, Whitehead Institute for Biomedical Research, Cambridge, MA.). The Reverse

Transcriptase Polymerase Chain Reaction (RT-PCR) method used to identify and amplify certain polynuleotide sequences within the invention was performed as described in Elek et al., In Vivo, 14: 172- 182, 2000). Methods for chemical synthesis of nucleic acids are discussed, for example, in Beaucage and Carruthers, Tetra. Letts. 22:1859-1862, 1981, and Matteucci et al., J, Am. Chem. Soc. 103:3185, 1981. Chemical synthesis of nucleic acids can be performed, for example, on commercial automated oligonucleotide synthesizers. Immunological methods (e.g., preparation of antigen-specific antibodies, immunoprecipitation, and imrnunoblotting) are described, e.g., in Current Protocols in Immunology, ed. Coligan et al., John Wiley & Sons, New York, 1991; andMethods of Immunological Analysis, ed. Masseyef etal., John Wiley & Sons, New York, 1992.

Mutant ML 13 Molecules The mutant ML 13 molecules of the invention are based on the amino acid sequence of native L 13 (SEQ ID NO:l). The ML 13 mutants within the invention differ by two or more amino acids from native hIL 13. For example, hIL 13 mutants within the invention can have 90% or more (e.g., 91, 92, 93, 94, 95, 96, 97, 98, and 99%) sequence identity with native ML13. Examples of ML 13 mutants within the invention are those having the amino acid sequences of SEQ ID NOs:2-9. These mutants each have a mutation in a domain corresponding to either the A (residues 9-25 of SEQ ID NO:l), C (residues 59-71 of SEQ ID NO: 1), and/or D (residues 97- 113 of SEQ ID NO: 1) alpha-helices of native ML13. Each of these features a substitution of at least two (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) of the amino acid residues that occurs in native

ML13. Other ML13 mutants within the invention are those with deletion (e.g., truncation) and addition (i.e., those with additional amino acids added to the native ML13 sequence) mutations.

Mutants of MLl 3 can be made in a number of ways by adapting techniques well known in the art. See, e.g., Sambrook et al., supra; and Ausubel et al., supra. For example, starting with the known amino acid sequence of ML13 (i.e., SEQ ID NO:l), the skilled artisan can chemically synthesize various mutant L 13 molecules using, e.g, automated commercial polypeptide synthesizers. Techniques for solid phase synthesis of polypeptides are well known. See, e.g., Barany and Merrifield, Solid-Phase Peptide Synthesis; pp. 3-284 in The Peptides: Analysis, Synthesis, Biology. Vol. 2: Special Methods in Peptide Synthesis, Part A., Merrifield, et al., J. Am. Chem. Soc, 85: 2149-2156 (1963), and Stewart et al., Solid Phase Peptide Synthesis, 2nd ed. Pierce Chem. Co., Rockford, IL (1984). Using this technique, ML13 mutants can be synthesized as a single polypeptide. Alternatively, shorter oligopeptide portions of the mutant

ML 13 molecule can first be synthesized and then fused together to form the full length mutant by condensation of the amino terminus of one oligopeptide portion with the carboxyl terminus of the another oligopeptide portion to forming a peptide bond. The fusions can then be purified by standard protein chemistry techniques. Mutants of ML 13 can also be produced through recombinant expression of ML 13- encoding nucleic acids (see below) in which the nucleic acid is modified, randomly or in a site- specific manner, to change (substitute), add to, or delete, some or all of the amino acids in the encoded polypeptide. Site-specific mutations can be introduced into the IL13-encoding nucleic acid by a variety of conventional techniques well described in the scientific and patent literature. Illustrative examples include : site-directed mutagenesis by overlap extension polymerase chain reaction (OE-PCR), as in Urban (1997) Nucleic Acids Res. 25: 2227-2228; Ke (1997) Nucleic Acids Res., 25: 3371-3372, and Chattopadhyay (1997) Biotechniques 22: 1054- 1056, describing PCR-based site-directed mutagenesis "megaprimer" method; Bohnsack (1997) Mol. Biotechnol. 7: 181-188; Ailenberg (1997) Biotechniques 22: 624-626, describing site-directed mutagenesis using a PCR-based staggered re-annealing method without restriction enzymes; Nicolas (1997)

Biotechniques 22: 430-434, site-directed mutagenesis using long primer-unique site elimination and exonuclease III. Unique-site elimination mutagenesis can also be used (see, e.g., Dang et al. (1992) Anal. Biochem., 200: 81). The production of mutants of biologically active proteins such as IFN-beta and IL-2 is described in detail in U.S. Patent No. 4,853,332 and the mutation of ML 13 is described in Example 1 below.

Other ML 13 mutants can be prepared by chemically modifying native MLl 3 according to known chemical modification methods. See, e.g., Belousov (1997) Nucleic Acids Res. 25:3440-3444; Frenkel (1995) Free Radic. Biol. Med. 19: 373-380; Blommers (1994) Biochemistry 33: 7886- 7896. Likewise, ML13 mutants made by chemical synthesis or by expression of nucleic acids as described above can be chemically modified to make additional

ML 13 mutants. Characterizing ML 13 Mutants Mutants of ML 13 can have characteristics that differ from those native ML 13. For example, native hIL 13 has the functional characteristics of binding both shared receptor and the restrictive receptor. Native ML 13 also has the characteristic of inducing transmembrane signals through binding shared receptors expressed on a cell surface. Such signaling can result in a measurable change in the cell's physiology. Changes can be the production of second messengers- e.g, an increase in intracellular [Ca²⁺], activation of protein kinases and/or phosphorylases, changes in phosphorylation of a substrate, changes in signal transducers and activators of transcription, etc. They can also be changes in the cell proteome, e.g., from increased or decreased transcription or translation. Or they can be changes in a functional or phenotypic characteristic of the cell. For instance, adding native ML 13 to TF- 1 cells can increase their rate of proliferation. As another example, adding native ML 13 can cause HUVEC to increase their expression of VCAM-1.

Characteristics of a given mutant ML 13 molecule can therefore be assessed by examining the ability of the molecule to bind the shared receptor and/or the restrictive receptor. Similarly, the ability of the mutant molecule to induce transmembrane signaling can be assessed by examining whether contacting a cell expressing an IL13 receptor with the mutant molecule results in a change in the cell's physiology. By these methods, ML13 mutants can be characterized as those that bind both the shared receptor and/or the restrictive receptor, those that bind only one of the receptors, and those that do not bind either receptor. By quantifying the affinity of a mutant hIL 13 molecule, it can also be characterized as one that binds with less, about equal, or more affinity than native ML13. Mutants of ML 13 can also be characterized as having or lacking the ability to cause a transmembrane signal and/or a change in a cell's function or phenotype. The changes caused by a mutant ML 13 molecule can also be quantified to further characterize the molecule as one that causes such changes less than (of less magnitude), about equal to, ormore than (of greater magnitude) those caused by native MLl 3. For instance mutants of ML 13 that specifically bind to an ML 13 receptor associated with a cell in a manner that induces a measurable change in the cell's physiology can be those that modulate the proliferation rate of a cell line that expresses an IL13 receptor such as TF- 1 cells. Antagonistic MLl 3 mutants are those that reduce the proliferation rate of the cell line compared to that induced by native

ML13; agonistic ML13 mutants are those that induce about same (e.g., 50-150% or 75-125% of) proliferation rate of the cell line as that induced by native ML13; and superagonistic ML 13 mutants are those that increase the proliferation rate of the cell line compared to that induced by native Ll 3.

Chimeric Molecules of Mutant ML 13 and Effector Molecules The invention also provides a chimeric molecule including a mutant L 13 molecule conjugated to an effector molecule. The effector molecule can be any molecule that can be conjugated to an ML 13 mutant and exert a particular function. Examples of effector molecules include cytotoxins, drugs, detectable labels, targeting ligands, and delivery vehicles.

A mutant L 13 molecule conjugated with a one or more cytotoxins can be used to kill cells expressing a receptor to which the mutant binds. Cytotoxins for use in the invention can be any cytotoxic agent (i.e., molecule that can kill a cell after contacting the cell) that can be conjugated to ML 13 or an ML 13 mutant. Examples of cytotoxins include, without limitation, radionuclides (e.g.,³⁵S, ^,4C, ³²P,¹²⁵I, ^,3,I, ⁹⁰Y, ⁸⁹Zr, ²⁰¹T1, ¹⁸⁵Re, ¹⁸⁸Re, ⁵⁷Cu, ^2I3Bi, ²¹¹At, etc.), conjugated radionuclides, and chemotherapeutic agents. Further examples of cytotoxins include, but are not limited to, antimetabolites (e.g., 5-ftourouricil (5-FU), methotrexate (MTX), fludarabine, etc.), anti-microtubule agents (e.g., vincristine, vinblastine, colchicine, taxanes (such as paclitaxel and docetaxel), etc.), alkylating agents (e.g., cyclophasphamide, melphalan, bischloroethylnitrosurea (BCNU), etc.), platinum agents (e.g., cisplatin (also termed cDDP), carboplatin, oxaliplatin, JM-216, CI-973, etc.), anthracyclines (e.g., doxorubicin, daunorubicin, etc.), antibiotic agents (e.g., mitomycin-C), topoisomerase inhibitors (e.g., etoposide, tenoposide, and camptothecins), or other cytotoxic agents such as ricin, diptheria toxin (DT), Pseudomonas exotoxin (PE) A, PE40, abrin, saporin, pokeweed viral protein, ethidium bromide, glucocorticoid, and others. See, e.g. U.S. Patent No. 5,932, 188. Useful variations of PE and DT include PE38QQR (see, U.S. Patent No. 5,614,191), PE IE and PE4E (see, e.g., Chaudhary et al. (1995) J. Biol. Chem., 265:16306), and DT388 and DT398 (Chaudhary, et al. (1991) Bioch. Biophys. Res. Comm., 180: 545-551) can also be used.

Mutant ML 13 molecules conjugated with one or more detectable labels can be used to detect the presence of a receptor to which the mutant binds, e.g., in diagnostic assays (e.g., in the detection of shed tumor cells overexpression the IL13 receptor) and/or in the in vivo localization of tumor cells. Detectable labels for use in the invention can be any substance that can be conj ugated to ML 13 or an ML 13 mutant and detected. Suitable detectable labels are those that can be detected, for example, by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Useful detectable labels in the present invention include biotin or streptavidin, magnetic beads (e.g., Dynabeads™), fluorescent dyes (e.g., fluorescein isothiocyanate, texas red, rhodamine, green fluorescent protein, and the like), radiolabels (e.g., ³H, ¹²⁵I, ³⁵S, ¹⁴C, ²P, ^{l u}In, ⁹⁷Ru, ⁶⁷Ga, ⁶⁸Ga, or ⁷²As,), radioopaque substances such as metals for radioimaging, paramagnetic agents for magnetic resonance imaging, enzymes (e.g., horseradish peroxidase, alkaline phosphatase and others commonlyused in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic (e.g. polystyrene, polypropylene, latex, etc.) beads.

Means of detecting such labels are well known to those of skill in the art. Thus, for example, radiolabels may be detected using photographic film or scintillation counters, fluorescent markers may be detected using a photo detector to detect emitted illumination.

Enzymatic labels are typically detected by providing the enzyme with a substrate and detecting the reaction product produced by the action of the enzyme on the substrate, and colorimetric labels are detected by simply visualizing the colored label, and so forth.

Mutant ML13 molecules conjugated with one or more targeting ligands (i.e., molecules that can bind a particular receptor) can be used to mediate binding of the mutants to a particular receptor or cell expressing the receptor. Any targeting ligand that can be conjugated to ML 13 or an ML13 mutant can be used. Examples of such targeting ligands includes antibodies (or the antigen-binding portion of antibodies); and chemokines, growth factors, soluble cytokine receptors (e.g., those lacking a transmembrane domain), superantigens, or other molecules that bind a particular receptor. A large number of these molecules are known, e.g., IL-2, IL-4, IL-6, IL-7, tumor necrosis factor (TNF), anti-Tac, TGF-alpha., SEA, SEB, and the like. As a representative example, an L 13 mutant can be conjugated with a soluble form of a ML 13 receptor. This conjugate, for example, could be used to both antagonize an endogenous ML 13 receptor on a cell and neutralize any L 13 present in the vicinity of the cell. Mutant ML 13 molecules conjugated with one or more nucleic acids can be used to specifically target delivery of the nucleic acid(s) to a target cell (e.g., one expressing an receptor to which the mutant binds). Any nucleic acid that can be conjugated to ML 13 or an ML 13 mutant can be used. The nucleic acids can be attached directly to the mutant ML 13 , attached via a linker, or complexed with or encapsulated in another moiety (e.g., a lipid, a liposome, a viral coat, or the like) that is attached to the mutant IL13 molecule. The nucleic acid can provide any of number of effector functions. For example, a nucleic acid encoding one or more proteins can be used to deliver a particular enzymatic activity, substrate, and/or epitope to a target cell. For these applications or others where expression (e.g. transcription or translation) of the nucleic acid is desired, the nucleic acid is preferably a component of an expression cassette that includes all the regulatory sequences necessary to express the nucleic acid in the cell. Suitable expression cassettes typically include promoter initiation and termination codons, and are selected to optimize expression in the target cell. Methods of constructing suitable expression cassettes are well known to those of skill in the art. See, e.g., Sambrook et al., supra.

A mutant ML 13 molecule conjugated with a one or more drugs can be used to deliver such drug(s) to cells expressing a receptor to which the mutant binds. Any drug which can be conjugated to ML 13 or an ML 13 mutant can be used. Examples of such drugs include sensitizing agents that render a target (e.g., tumor) cell susceptible to various cancer therapeutics. The sensitizing agent can be a small molecule drug or a gene (under the control of a promoter in an appropriate expression cassette to induce expression in the target cell). For example, it has been proposed that expression of the herpes simplex virus (HSV) thymidine kinase (TK) gene in proliferating cells, renders the cells sensitive to the deoxynucleoside analog, ganciclovir. Moolten et at. (1986) Cancer Res. 46:5276-5281; Moolten et al. (1990) Hum. Gene Ther. 1: 125-134;

Moolten et al. (1990) J. Natl. Cancer Inst. 82: 297-300; Short et al. (1990) J. Neurosci. Res. 27:427-433; Ezzedine et al. (1991) New Biol. 3: 608-614, Boviatsis et al. (1994) Hum. Gene Ther. 5: 183- 191. HSV-TK mediates the phosphorylation of ganciclovir, which is incorporated into DNA strands during DNA replication (S-phase) in the cell cycle, leading to chain termination and cell death. Elion (1983) Antimicr. Chemother. 12, sup. B:9-17. A second example of a gene with a drug-conditional "killing" function is the bacterial cytosine deaminase gene, which confers chemosensitivity to the relatively non-toxic 5-fluorouracil precursor 5- fluorocytosine. Mullen et al. (1992) Proc. Natl. Acad. Sci. USA 89: 33-37; Huber et al. (1993) Cancer Res. 53: 4619-4626; Mullen et al. (1994) Cancer Res. 54: 1503-1506. Still another example of a gene with a drug-conditional "killing" function is a cytochrome P450 gene.

Expression, of the gene product renders tumor cells sensitive to a chemofherapeutic agent, in particular, cyclophosphamide or ifosphamide. See, U.S. Patent No. 5,688,773. The drug employed need not be a gene. For example, it can be one of the compounds that can treat multiple drug resistance of susceptible tumor cells described in U.S. Patent No.4,282,233. Other drugs can also be used. For example, chemotherapy drugs such as doxorubicin, vinblastine, genistein, and other described above can be conjugated to the mutant ML 13 molecule.

A mutant ML 13 molecule conjugated to a one or more delivery vehicles is also within the invention. Such conjugates can be used to deliver other substances such as a drug to cells expressing a receptor to which the mutant binds. Any delivery vehicle that can be conjugated to ML 13 or an ML 13 mutant can be used. Examples of such delivery vehicles include liposomes and lipids (e.g., micelles). Liposomes encapsulating drugs or micelles including drugs may also be used. Methods for preparing liposomes attached to proteins are well known to those of skill in the art. See, for example, U.S. Patent No.4,957,735; and Connor etal.,Pharm. Ther., 28: 341- 365 (1985).

Effector molecules can be conjugated (e.g., covalently bonded) to a mutant hIL 13 by any method known in the art for conjugating two such molecules together. For example, the mutant ML 13 can be chemically derivatized with an effector molecule either directly or using a linker

(spacer). Several methods and reagents (e.g., cross-linkers) for mediating this conjugation are known. See, e.g., catalog of Pierce Chemical Company; and Means and Feeney, Chemical Modification of Proteins, Holden-Day Inc., San Francisco, CA 1971. Various procedures and linker molecules for attaching various compounds including radionuclide metal chelates, toxins, and drugs to proteins (e.g., to antibodies) are described, for example, in European Patent

Application No. 188,256; U.S. Patent Nos. 4,671,958; 4,659,839; 4,414,148; 4,699,784; 4,680,338; 4,569,789; and 4,589,071; and Borlinghaus etal. Cancer Res.47: 4071-4075 (1987). In particular, production of various immunotoxins is well-known within the art and can be found, for example in "Monoclonal Antibody- Toxin Conjugates: Aiming the Magic Bullet," Thorpe et al., Monoclonal Antibodies in Clinical Medicine, Academic Press, pp. 168-190 (1982);

Waldmann (1991) Science, 252: 1657; and U.S. Patent Nos. 4,545,985 and 4,894,443.

Where the effector molecule is a polypeptide, the chimeric molecule including the ML 13 mutant and the effector can be a fusion protein. Fusion proteins can be prepared using conventional techniques in molecular biology to join the two genes in frame into a single nucleic acid, and then expressing the nucleic acid in an appropriate host cell under conditions in which the fusion protein is produced.

A mutant L 13 may be conjugated to one or more effector molecule(s) in various orientations. For example, the effector molecule may be joined to either the amino or carboxy termini of the mutant ML13. The mutant IL13 molecule may also be joined to an internal region of the effector molecule, or conversely, the effector molecule may be joined to an internal location of the mutant IL13 molecule.

In some circumstances, it is desirable to free the effector molecule from the mutant ML 13 molecule when the chimeric molecule has reached its target site. Therefore, chimeric conjugates comprising linkages that are cleavable in the vicinity of the target site may be used when the effector is to be released at the target site. Cleaving of the linkage to release the effector molecule from the mutant IL1 molecule may be prompted by enzymatic activity or conditions to which the conjugate is subjected either inside the target cell or in the vicinity of the target site.

When the target site is a tumor, a linker which is cleavable under conditions present at the tumor site (e.g. when exposed to tumor-associated enzymes or acidic pH) may be used. A number of different cleavable linkers are known to those of skill in the art. See, e.g., U.S. Patent Nos. 4,618,492; 4,542,225; and 4,625,014. The mechanisms for release of an agent from these linker groups include, for example, irradiation of aphotolabilebond and acid-catalyzed hydrolysis. U.S.

Patent No. 4,671,958, for example, includes a description of irnrnunoconjugates comprising linkers which are cleaved at the target site in vivo by the proteolytic enzymes of the patient's complement system. In view of the large number of methods that have been reported for attaching a variety of radiodiagnostic compounds, radiotherapeutic compounds, drugs, toxins, and other agents to antibodies one skilled in the art will be able to determine a suitable method for attaching a given effector molecule to a mutant ML 13 molecule.

Nucleic Acids Encoding Mutant ML 13 Molecules and Methods of Making Mutant ML 13 Molecules Using Nucleic Acids The invention also provides purified nucleic acids encoding the mutant ML 13 molecules and the fusion proteins described above. Starting with a known protein sequence, DNA encoding the mutant ML 13 molecules or the fusion proteins may be prepared by any suitable method, including, for example, cloning and restriction of appropriate sequences or direct chemical synthesis by methods such as the phosphotriester method of Narang et al. (1979) Meth. Enzymol. 68: 90-99; the phosphodiester method of Brown et al. (1979) Meth. Enzymol. 68: 109-151; the diethylphosphoramidite method of Beaucage et al. (1981) Tetra. Lett., 22: 1859-1862; and the solid support method of U.S. Patent No. 4,458,066. Because of the degeneracy of the genetic code, a large number of different nucleic acids will encode the mutant ML 13 molecules and the fusion proteins. Each of these is included within the invention.

Chemical synthesis produces a single stranded oligonucleotide. This may be converted into double stranded DNA by hybridization with a complementary sequence, or by polymerization with a DNA polymerase using the single strand as a template. Longer DNA sequences maybe obtained by the ligation of shorter sequences. Alternatively, subsequences may be cloned and the appropriate subsequences cleaved using appropriate restriction enzymes. The fragments may then be ligated to produce the desired DNA sequence.

DNA encoding the mutant ML 13 molecules or the fusion proteins may be cloned using DNA amplification methods such as polymerase chain reaction (PCR). Thus, in a preferred embodiment, the gene for ML 13 is PCR amplified, using primers that introduce one or more mutations. The primers preferably include restrictions sites, e.g., a sense primer containing the restriction site for Ndel and an antisense primer containing the restriction site for Hindlll. In one embodiment, the primers are selected to amplify the nucleic acid starting at position 19, as described by McKenzie et al. (1987), supra. This produces a nucleic acid encoding the mature IL13 sequence (or mutant ML13 molecules) and having terminal restriction sites.

For making DNA encoding the fusion proteins, the DNA encoding the effector molecule can be obtained from available sources. For example, the PE38QQR fragment may be excised from the plasmid pWDMH4-38QQR or plasmid pSGC242FdNl as described by Debinski et al. Int. J. Cancer, 58: 744-748 (1994), and by Debinski et al. ( 1994) Clin. Cancer Res. 1:1015-1022 respectively. Ligation of the mutant IL13 molecule and a Pseudomonas exotoxin (e.g.,

PE38QQR) sequences and insertion into a vector produces a vector encoding the mutant IL13 joined to the terminus of the Pseudomonas exotoxin (e.g., joined to the amino terminus of PE38QQR, PE1E, or PE4E (position 253)). In a preferred embodiment, the two molecules are joined directly. Alternatively there canbe an intervening peptide linker (e.g., a three amino acid junction consisting of glutamic acid, alanine, and phenylalanine introduced by the restriction site).

While the two molecules are preferably essentially directly joined together, one of skill will appreciate that the molecules may be separated by a peptide spacer consisting of one or more amino acids. Generally the spacer will have no specific biological activity other than to join the proteins or to preserve some minimum distance or other spatial relationship between them. However, the constituent amino acids of the spacer may be selected to influence some property of the molecule such as the solubility, folding, net charge, or hydrophobicity.

The nucleic acid sequences encoding the mutant ML 13 molecules or the fusion proteins may be expressed in a variety of host cells, including E. coli, other bacterial hosts, yeast, and various higher eukaryotic cells such as the COS, CHO and HeLa cells lines and myeloma cell lines. The recombinant protein gene will be operably linked to appropriate expression control sequences for each host. F or E. coli this includes a promoter such as the T7, tip, or lambda promoters, a ribosome binding site and preferably a transcription termination signal. For eukaryotic cells, the control sequences will include a promoter and preferably an enhancer derived from immunoglobulin genes, SV 40, cytomegalovirus, etc., and a polyadenylation sequence, and may include splice donor and acceptor sequences. Plasmid vectors of the invention made as described above can be transferred into the chosen host cell by well-known methods such as calcium chloride, or heat shock, transformation for E. coli and calcium phosphate treatment or electroporation for mammalian cells. Cells transformed by the plasmids can be selected by resistance to antibiotics conferred by genes contained on the plasmids, such as the amp, gpt, neo and hyg genes. Once expressed, the recombinant mutant ML 13 molecules or fusion proteins can be purified according to standard procedures of the art, including ammonium sulfate precipitation, affinity columns, column chromatography, gel electrophoresis and the like. See, generally, R.¹ Scopes, Protein Purification, Springer- Verlag, N.Y. (1982); and Deutscher, Methods in Enzymology Vol. 182: Guide to Protein Purification, Academic Press, Inc. N.Y. (1990). Substantially pure compositions of at least about 90 to 95% homogeneity are preferred, and 98 to 99% or more homogeneity are most preferred for pharmaceutical uses. Once purified, partially or to homogeneity as desired, the polypeptides may then be used therapeutically.

After chemical synthesis, biological expression, or purification, the mutant ML 13 molecules or the fusion proteins may possess a conformation substantially different than the native conformations of the constituent polypeptides. In this case, it may be necessary to denature and reduce the polypeptide and then to cause the polypeptide to re-fold into the preferred conformation. Methods of reducing and denaturing proteins and inducing re-folding are well known to those of skill in the art. See, Debinski et al. (1993) J. Biol. Chem., 268: 14065-14070; Kreitman and Pastan (1993) Bioconjug. Chem., 4: 581-585; and Buchner, et al. (1992) Anal. Biochem., 205: 263-270.

Modifications can be made to the IL13 receptor targeted fusion proteins without diminishing their biological activity. Some modifications may be made to facilitate the cloning, expression, or incorporation of the targeting molecule into a fusion protein. Such modifications are well known to those of skill in the art and include, for example, a methionine added at the amino terminus to provide an initiation site, or additional amino acids placed on either terminus to create conveniently located restriction sites or termination codons. Antibodies Mutants of ML 13 (or immunogenic fragments or analogs thereof) can be used to raise antibodies useful in the invention. Such polypeptides can be produced by recombinant techniques or synthesized as described above. In general, ML 13 mutants can be coupled to a carrier protein, such as KLH, as described in Ausubel et al., supra, mixed with an adjuvant, and inj ected into a host mammal. Antibodies produced in that animal can then be purified by peptide antigen affinity chromatography. In particular, various host animals can be immunized by injection with an ML 13 mutant or an antigenic fragment thereof. Commonly employed host animals include rabbits, mice, guinea pigs, and rats. Various adjuvants that can be used to increase the immunological response depend on the host species and include Freund's adjuvant

(complete and incomplete), mineral gels such as aluminum hydroxide, surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin, and dinitrophenol. Other potentially useful adjuvants include BCG (bacille Calmette-Guerin) and Corynebacterium parvum. Polyclonal antibodies are heterogeneous populations of antibody molecules that are contained in the sera of the immunized animals. Antibodies within the invention therefore include polyclonal antibodies and, in addition, monoclonal antibodies, single chain antibodies, Fab fragments, F(ab')₂ fragments, and molecules produced using a Fab expression library. Monoclonal antibodies, which are homogeneous populations of antibodies to a particular antigen, can be prepared using the mutants of ML 13 described above and standard hybridoma technology (see, for example, Kohler et al., Nature 256:495, 1975; Kohler et al., Eur. J. Immunol. 6:511, 1976; Kohler et al., Eur. J. Immunol. 6:292, 1976; Hammerling et al, "Monoclonal Antibodies and T Cell Hybridomas," Elsevier, N.Y., 1981; Ausubel et al., supra). In particular, monoclonal antibodies can be obtained by any technique that provides for the production of antibody molecules by continuous cell lines in culture such as described in Kohler et al., Nature 256:495,

1975, and U.S. Pat. No. 4,376,110; the human B-cell hybridoma technique (Kosbor et al., Immunology Today 4:72, 1983; Cole etal., Proc. Natl. Acad. Sci. USA 80:2026, 1983), and the EBV-hybridoma technique (Cole et al, "Monoclonal Antibodies and Cancer Therapy," Alan R. Liss, Inc., pp.77-96, 1983). Such antibodies canbe of any immunoglobulin class including IgG, IgM, IgE, IgA, IgD and any subclass thereof. A hybridoma producing a mAb of the invention may be cultivated in vitro or in vivo. The ability to produce high titers of mAbs in vivo makes this a particularly useful method of production. Once produced, polyclonal or monoclonal antibodies can be tested for specific recognition of the mutants by Western blot or immunoprecipitation analysis by standard methods, for example, as described in Ausubel et al., supra. Antibodies that specifically recognize and bind to ML 13 mutants are useful in the invention. For example, such antibodies can be used to monitor the amount of an MLl 3 mutant associated with a cell or to block binding of a particular mutant a receptor.

Antibodies of the invention can be produced using fragments of the ML 13 mutants that lie outside highly conserved regions and appear likely to be antigenic, by criteria such as high frequency of charged residues. Cross-reactive anti-ML13 mutant antibodies are produced using a fragment of a L 13 mutant that is conserved amongst members of this family of proteins. In one specific example, such fragments are generated by standard techniques of PCR, and are then cloned into the pGEX expression vector (Ausubel et al., supra). Fusion proteins are expressed in E.coli and purified using a glutathione agarose affinity matrix as described in Ausubel, et al., supra. Non-cross reactive antibodies can be prepared by adsorbing the antibody with the antigen(s) that the antibody is desired not to react with. For example, antisera prepared against a particular MLl 3 mutant can be adsorbed with other ML 13 mutants and/or native ML 13 to reduce or eliminate cross-reactivity.

In some cases it may be desirable to minimize the potential problems of low affinity or specificity of antisera. In such circumstances, two or three fusions can be generated for each protein, and each fusion can be injected into at least two rabbits. Antisera can be raised by injections in a series, preferably including at least three booster injections. Antiserum is also checked for its ability to immunoprecipitate recombinant mutants of ML13 or control proteins, such as glucocorticoid receptor, CAT, or luciferase.

Techniques described for the production of single chain antibodies (U.S. Pat. Nos. 4,946,778, 4,946,778, and 4,704,692) can be adapted to produce single chain antibodies against an MLl 3 mutant, or a fragment thereof. Single chain antibodies are formed by linking the heavy and light chain fragments of the Fv region via an amino acid bridge, resulting in a single chain polypeptide.

Antibody fragments that recognize and bind to specific epitopes can be generated by known techniques. For example, such fragments include but are not limited to F(ab')₂ fragments that can be produced by pepsin digestion of the antibody molecule, and Fab fragments that can be generated by reducing the disulfide bridges of F(ab')₂ fragments. Alter-natively, Fab expression libraries can be constructed (Huse et al., Science 246: 1275, 1989) to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity.

The antibodies of the invention can be used, for example, in the detection of a ML 13 mutant in a biological sample. Antibodies can also be used to interfere with the interaction of an ML 13 mutant and other molecules that bind the mutant (e.g., an ML 13 receptor).

Methods of Delivering a Mutant ML 13 Molecule to a Cell The invention also provides a method of delivering an IL 13 mutant to a cell. This method is useful, among other things, for directing a chimeric molecule including the ML13 mutant and an effector molecule to a cell so that the effector molecule can exert its function. For example, an L 13 mutant conjugated to a cytotoxin can be delivered to a target cell to be killed by mixing a composition containing the chimeric molecule with the target cell expressing a receptor that binds the mutant. As another example, an ML 13 mutant conjugated to a detectable label can be directed to a target cell to be labeled by mixing a composition containing the chimeric molecule with the target cell expressing a receptor that binds the mutant. Mutant ML 13 molecules can be delivered to a cell by any known method. For example, a composition containing the ML 13 mutant can be added to cells suspended in medium. Alternatively, a mutant ML13 can be administered to an animal (e.g., by a parenteral route) having a cell expressing a receptor that binds the mutant so that the mutant binds to the cell in situ. The mutant ILI3 molecules of this invention are particularly well suited as targeting moieties for binding tumor cells because tumor cells overexpress ILI3 receptors. In particular, carcinoma tumor cells (e.g. renal carcinoma cells) overexpress ILI3 receptors at levels ranging from about 2100 sites/cell to greater than 150,000 sites per cell. Similarly, gliomas and other transformed cells also overexpress ILI3 receptors (ILI3R). Thus, the methods of this invention can be used to target an effector molecule to a variety of cancers. Such cancers are well known to those of skill in the art and include, but are not limited to, cancers of the skin (e.g., basal or squamous cell carcinoma, melanoma, Kaposi's sarcoma, etc.), cancers of the reproductive system (e.g.^', testicular, ovarian, cervical), cancers of the gastrointestinal tract (e.g., stomach, small intestine, large intestine, colorectal, etc.), cancers of the mouth and throat (e.g. esophageal, larynx, oropharynx, nasopharynx, oral, etc.), cancers of the head and neck, bone cancers, breast cancers, liver cancers, prostate cancers (e.g., prostate carcinoma), thyroid cancers, heart cancers, retinal cancers (e.g., melanoma), kidney cancers, lung cancers (e.g., mesothelioma), pancreatic cancers, brain cancers (e.g. gliomas, medulloblastomas, meningiomas, etc.) and cancers of the lymph system (e.g. lymphoma). In a particularly preferred embodiment, the methods of this invention are used to target effector molecules to brain cancers (especially gliomas).

One of skill in the art will appreciate that identification and confirmation of ILI3 overexpression by other cells requires only routine screening using well-known methods. Typically this involves providing a labeled molecule that specifically binds to the ILI3 receptor

(e.g., a native or mutant ILI3). The cells in question are then contacted with this molecule and washed. Quantifying the amount of label remaining associated with the test cell provides a measure of the amount of ILI3 receptor (ILI3R) present on the surface of that cell. In a preferred embodiment, IL13 receptor may be quantified by measuring the binding of ^,25I-labeled IL 13 (¹²⁵I- ILI3) to the cell in question. Details of such a binding assay are provided in U.S. Patent

5,614,191.

As IL13 has been implicated in playing an important regulatory role in allergic hyperactivity reactions such as asthma (Webb et al. (2000) J. Immunol. 165:108-113), the invention also provides a method of modulating an allergic response by contacting a cell important in the response (e.g., a lymphocyte such as a B cell, an eosinophil, a mast cell, and/or any other cells involved in Th₂-dominated inflammatory responses) with one or more ML 13 mutants. Thus, for example, where interaction of native hIL 13 with an ML 13 receptor expressed on a cell causes transmembrane signals that contribute to the cell's role in an allergic reaction (e.g., inducing inflammation), a mutant ML13 can be used to block this interaction and inhibit the allergic reaction. The interaction between native ML 13 and the IL13 receptor can be blocked, for example, by contacting the cell 1 can with an ML 13 mutant that binds to the IL13 receptor (in some cases with more affinity than native L 13) but does not cause the transmembrane signaling through the receptor. For asthma, such an ML 13 mutant could be administered by inhalation of a pharmaceutical composition containing the mutant. Pharmaceutical Compositions

The mutant L 13 molecules (including those conjugated with an effector molecule) of this invention can be prepared for parenteral, topical, oral, or local administration, such as by aerosol or transdermally, for prophylactic and/or therapeutic treatment. The pharmaceutical compositions can be administered in a variety of unit dosage forms depending upon the method of administration. For example, unit dosage forms suitable for oral administration include powder, tablets, pills, capsules and lozenges. It some cases it may be desirable to protect the fusion proteins and pharmaceutical compositions of this invention, from being digested (e.g., when administered orally). This can be accomplished either by complexing the protein with a composition that renders it resistant to acidic and enzymatic hydrolysis, or by packaging the protein in an appropriately resistant carrier such as a liposome. Means of protecting compounds from digestion are well known in the art (see, e.g., U.S. Patent 5,391,377 describing lipid compositions for oral delivery of therapeutic agents).

The pharmaceutical compositions can also be delivered to an animal by inhalation by any presently known suitable technique. For example, the ML 13 mutants of the invention can be delivered in the form of an aerosol spray produced from pressurized packs or a nebulizer, with the use of a suitable propellant such as dichlorodifluromethane, trichlorotri-fluoromethane, dichlorotetrafiurorefhane, carbon dioxide, or any other suitable gas. In the case of a pressurized aerosol, the dosage unit may be controlled using a valve to deliver a metered amount. Capsules and cartridges (e.g., of gelatin) containing a powder mix of the ML 13 mutant and a suitable base (e.g., lactose or starch) can be used in an inhaler or insufflator to deliver the mutant to the respiratory tract of an animal. The pharmaceutical compositions of this invention are particularly useful for parenteral administration, such as intravenous administration or administration into a body cavity or lumen of an organ. The compositions for administration will commonly comprise a solution of the mutant ML 13 molecule dissolved in a pharmaceutically acceptable carrier, preferably an aqueous carrier. A variety of aqueous carriers can be used, e.g. , buffered saline and the like, These solutions are sterile and generally free of undesirable matter (e.g., pyrogens). These compositions may be sterilized by conventional, well known sterilization techniques. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions such as pH adjusting and buffering agents, toxicity adjusting agents and the like, for example, sodium acetate, sodium chloride, potassium chloride, calcium chloride, sodium lactate and the like. The concentration of the mutant ML 13 in these formulations can vary widely, and will be selected primarily based on fluid volumes, viscosities, body weight and the like in accordance with the particular mode of administration selected and the patient's needs. Actual methods for preparing parenterally administrable compositions will be known or apparent to those skilled in the art and are described in more detail in such publications as Remington's Pharmaceutical Science, 15th ed., Mack Publishing Company, Easton, Pennsylvania (1980). Toxicity and therapeutic efficacy of the pharmaceutical compositions utilized in the invention can be determined by standard pharmaceutical procedures, using either cells in culture or experimental animals to determine the LD₅₀ (the dose lethal to 50% of the population) and the ED₅₀ (the dose therapeutically effective in 50% of the population). The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio LD₅₀/ED₅₀.

Doses that exhibit large therapeutic indices are preferred. While those that exhibit toxic side effects may be used, care should be taken to design a delivery system that targets the pharmaceutical composition to the site of affected tissue in order to minimize potential damage to uninfected cells and, thereby, reduce side effects. The data obtained from cell culture assays and animal studies can be used in fonnulating a range of dosage for use in humans. The dosage of such pharmaceutical compositions lies preferably within a range of circulating concentrations that include an ED₅₀ with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. For any pharmaceutical composition used in a method of the invention, the therapeutically effective dose can be estimated initially from cell culture assays. A dose can be formulated in animal models to achieve an IC₅₀ (that is, the concentration of the test compound which achieves a half-maximal inhibition of symptoms) as determined in cell culture. Such information can be used to more accurately determine useful doses in humans. Levels in plasma can be measured, for example, by high performance liquid chromatography. Although dosage should be determined for each particular application, it is expected that a dose of a typical pharmaceutical composition for intravenous administration would be about 0, 1 to 10 mg per patient per day. Dosages from 0.1 up to about 100 mg per patient per day may be used, particularly when the pharmaceutical compositions is administered to a secluded site and not into the blood stream, such as into a body cavity or into a lumen of an organ. The compositions containing the present ML13 mutants, or a cocktail thereof (i.e., with other proteins), can be administered for therapeutic treatments. In therapeutic applications, compositions are administered to a patient suffering from a disease, in an amount sufficient to cure or at least partially arrest the disease and its complications. An amount adequate to accomplish this is defined as a "therapeutically effective dose." Amounts effective for this use will depend upon the severity of the disease and the general state of the patient's health. Single or multiple administrations of the compositions may be administered depending on the dosage and frequency as required and tolerated by the patient. In any event, the composition should provide a sufficient quantity of the proteins of this invention to effectively treat the patient.

Among various uses of the cytotoxic fusion proteins of the present invention are included a variety of disease conditions caused by specific human cells that may be eliminated by the toxic action of the protein. One preferred application is the treatment of cancer (e.g., a glioma), such as by the use of an mutant IL13 ligand attached to a cytotoxin (e.g., PE or a PE derivative).

It will be appreciated by one of skill in the art that there are some regions that are not heavily vascularized or that are protected by cells joined by tight junctions and/or active transport mechanisms which reduce or prevent the entry of macromolecules present in the blood stream. For example, systemic administration of therapeutics to treat gliomas, or other brain cancers, is constrained by the blood-brain barrier which resists the entry of macro-molecules into the subarachnoid space. Thus, the therapeutic compositions of this invention can be administered directly to the tumor site. For instance, brain tumors (e.g., gliomas) can be treated by administering the therapeutic composition directly to the tumor site (e.g., through a surgically implanted catheter). Where the fluid delivery through the catheter is pressurized, small molecules ( e.g. the therapeutic molecules of this invention) will typically infiltrate as much as two to three centimeters beyond the tumor margin.

Alternatively, the therapeutic composition canbe placed at the target site in a slow release formulation (e.g., a thrornbin-fibrinogen mixture). Such formulations can include, for example, a biocompatible sponge or other inert or resorbable matrix material impregnated with the therapeutic composition, slow dissolving time release capsules or microcapsules, and the like.

Typically the catheter, or catheters, ortime release formulation will be placed at the tumor site as part of a surgical procedure. Thus, for example, where major tumor mass is surgically debulked, the perfusing catheter or time release formulation can be emplaced at the tumor site as an adjunct therapy. Of course, surgical removal of the tumor mass may be undesired, not required, or impossible, in which case, the delivery of the therapeutic compositions of this invention may comprise the primary therapeutic modality.

Imaging

The invention also provides a method of imaging a cell expressing a receptor that binds an ML13 mutant in vivo. In an exemplary method, an ML13 mutant conjugated to a label detectable by the chosen imaging technique is administered to an animal having the cell expressing a receptor that binds the particular hIL 13 mutant. The animal is then imaged using the chosen imaging technique. Examples of labels useful for diagnostic imaging include radiolabels such as ¹³¹1, ^mIn, ¹²³I, ⁹⁹mTc, ³²P, ¹²⁵1, ³H,¹⁴C, and ^I88Rh; fluorescent labels such as fluorescein and rhodamine; nuclear magnetic resonance active labels; positron emitting isotopes detectable by a positron emission tomography ("PET") scanner; chemiluminescent labels such as luciferin; and enzymatic markers such as peroxidase or phosphatase. Mutants of ML 13 can be labeled with such reagents as described above or using techniques known in the art. Those mutants having one or more amino acids substituted with a tyrosine are preferred for iodine- labeling as the extra tyrosine residue(s) should allow better labeling.

Any imaging technique compatible with the labeled-hlL 13 mutant can be used. Examples of such techniques include immunoscintigraphy where a gamma camera is used to detect the location and distribution of gamma-emitting radioisotopes; MRI where a paramagnetic labeled- ML13 mutant is used; PET where an ML 13 mutant is conjugated with a positron emitting label; and X-ray imaging where an ML13 mutant is conjugated with a radioopaque label (e.g., a metal particle). A more detailed description of such techniques is provided in Handbook of Targeted Delivery of Imaging Agents (Handbook of Pharmacology and Toxicology), ed. V. Torchilin,

CRC Press, 1995; Armstrong et al., Diagnostic Imaging, Blackwell Science Inc., 1998; and Diagnostic Nuclear Medicine, ed. C. Schiepers, Springer Verlag, 2000.

As an illustrative example, the location of glioma tumor cells in an animal can be detennined by injecting (e.g., parenterally or in situ) an animal with a composition including native ML13 or an ML13 mutant conjugated to a detectable label (e.g., a gamma emitting radioisotope). The composition is then allowed to equilibrate in the animal, and to bind to the glioma cells. The animal is then subjected to imaging (e.g., using a gamma camera) to image where the glioma cells are.

Diagnostic Kits In another embodiment, this invention provides for kits for the treatment of tumors or for the detection of cells overexpressing IL 13 receptors. Kits will typically comprise a chimeric molecule of the present invention (e.g., a mutant ML13 conjugated to a detectable label, a mutant ML 13 conjugated to cytotoxin, a mutant IL 13 conjugated to a targeting ligand, etc.). In addition the kits will typically include instructional materials disclosing means of use of chimeric molecule ( e.g., as a cytotoxin, for detection of tumor cells, to augment an immune response, etc.). The kits may also include additional components to facilitate the particular application for which the kit is designed. Thus, for example, where a kit contains a chimeric molecule in which the effector molecule is a detectable label, the kit may additionally contain means of detecting the label (e.g. enzyme substrates for enzymatic labels, filter sets to detect fluorescent labels, appropriate secondary labels such as a sheep anti-mouse-HRP , or the like). The kits may additionally include buffers and other reagents routinely used for the practice of a particular method. Such kits and appropriate contents are well known to those of skill in the art.

EXAMPLES The present invention is further illustrated by the following specific examples. The examples are provided for illustration only and are not to be construed as limiting the scope or content of the invention in any way. Example 1- Materials and Methods

Materials. IL13.E13K-PE1E, IL13.E13K-PE38QQR, and PE38QQR cDNA templates were cloned as previously described. Debinski et al., J. Biol. Chem 1996;271:22428-22433; Debinski et al., Nature Biotech 1998;16:449-453. Human umbilical vein endothelial cells (HUVEC), U-251 MG human glioblastoma cells, and SVG-pl2 normal human glial cells were obtained from ATCC (Rockville, MD). Unique site elimination mutagenesis kit, fast protein liquid chromatographic system, columns (FPLC), and media were obtained from Amersham Pharmacia LKB Biotechnology (Piscataway, NJ). Oligonucleotide primers were synthesized at the Macromolecular Core Laboratory, Perm State College of Medicine (Hershey, PA). A polymerase chain reaction kit was purchased from Perkin Elmer Cetus (Norwalk, CT). MTS/PMS reagents for cell titer 96 aqueous non-radioactive cell proliferation assay and BL21

(1DE3) E. coli cells were obtained from Promega (Madison, WI). DH5a E. coli cells, Luria Bertani (LB) media for E. coli culture, dialysis tubing, phosphate buffered saline (PBS), tissue culture media, fetal calf serum and DNA standards were purchased from Gibco BRL Life Technologies (Gaithersburg, MD). SDS-PAGE supplies and ethidium bromide were purchased from Bio-Rad (Hercules, CA). Maxi, Mini, and Gel Extraction DNA purification kits were purchased from Qiagen, Inc. (Santa Clara, CA). X-Omat film was purchased from Eastman Kodak Co. (Rochester, NY). All enzymes and buffers, DTT, and protein standards were obtained from New England Biolabs (Beverly, MA). Ampicillin, lysozyme, and phenol/chloroform/isoamyl alcohol were obtained from Boehringer Mannheim (Indianapolis, IN). Mouse albumin, dithioerythritol (DTE), oxidized glutathione, L-arginine, urea, and cyclohexamide were purchased from Sigma (St.. Louise, MO). IPTG was purchased from Inalco Spa (Milano, Italy). 0.5 ml tuberculin syringes and needles were obtained from Becton

Dickinson (Franklin Lakes, NJ).

Methods. Design of Mutant Primers. Using Vector NTI Suite software (Bethesda, MD.), mutation primers were designed to eliminate unique restriction sites while changing the amino acid of interest in order to enhance selection and yield of mutant plasmids , Four separate mutant primers were designed to introduce mutations at positions 13, 66, and 69 of IL13. The mutant primer for position 13 of IL13 changed lysine to aspartic acid while eliminating a Bsu361 site.

Three mutant primers were designed to introduce glutamic acids at position 66, 69, and 66 and

69 together while eliminating a Blp I site. A construct encoding IL 13.E 13K/R66D/S69D/R112D was made using the cDNA for IL13.E13K/R66D/S69D and a unique site mutagenesis kit with a primer containing both Rl 12D mutation and a stop codon.

Mutagenesis. Unique site elimination mutagenesis was performed as described by

Amersham Pharmacia Biotech according to the method by Deng and Nickoloff (Anal. Biochem.

1992;200:81-88.). Restriction digests were performed on the isolated DNA from single colonies in order to identify plasmids containing the incorporated mutations. The DNA was then both amplified and purified with Qiagen Maxi-prep or Mini-prep kits. Purified DNA was then sequence-verified.

Polymerase Chain Reaction. Forward and reverse primers were designed to amplify the

Pseudomonas exotoxin variant PEIE. The fusion cDNA construct of IL13.E13K-PE1E served as the template for the PCR reaction. See, Debinski et al., J. Biol. Chem ., 1996, 271 :22428-

22433. The PCR product was digested with appropriate restriction endonucleases and ligated into a multi-cloning vector that contained an ampicillin resistant gene. cDNAs that displayed the appropriate size bands after restriction digests were then sequence-verified. The plasmid shown to contain the PEIE insert was then used in a prokaryotic IPTG-inducible protein expression system as described below.

Production and purification of recombinant fusion proteins. E. coli strain BL21 (1DE3) cells, which contain an IPTG-inducible T7 RNA polymerase gene, were transformed with plasmids of interest and cultured in 1 liter of LB Broth (Gibco/Life Technologies). Once the E. coli reached logarithmic growth, the plasmids were induced to express the chimeric fusion proteins. The cells were incubated with IPTG for 1.5 hours. The proteins were localized to the inclusion bodies denatured and renatured as previously described. Thompson, J.P. andDebinski

W., J.Biol. Chem., 1999,274:29944-29950. After Dialysis, the renatured proteins werepurified on two ion exchange columns (Q-Sepharose and Mono Q) using FPLC. Samples of fractions were taken after each column and run on SDS polyacrylamide gels (SDS-PAGE) to assess purity and appropriate size of proteins after each column. Concentrations were determined for fractions containing the purest representation of the proteins of interest. Protein concentrations were assessed by the Bradford assay (Pierce "Plus," Rockford, IL) using bovine serum albumin (BS A) as a standard. Proteins were then filter-sterilized and used for in vitro analyses.

Cytotoxicity assays. The cytotoxic activity of the cytotoxins was tested primarily on U- 251 MG, HUVEC, and transformed fetal glial cell line, SVG pl2. The cells were grown under controlled conditions in a Steri-cult 200 cell culture incubator (Marietta, Ohio) at 37°c, 5% C0₂, and 90% humidity. The cells were harvesteorand centrifuged when confluent and cell number was determined with a hemocytometer. Trypan blue exclusion was used to identify dead cells. 4.5xl0⁵ HUVEC, lxlO⁵ U-251 MG, and 2.5xl0⁵ SVG pl2 viable cells per well were plated in 96 well tissue culture plates in 150 ml of GIBCO-BRL minimum essential media per well. The cells were then allowed 24 hrs to adhere and proliferate before cytotoxins were added. The various concentrations of the chimeric toxins were diluted in 0.1% BSA/PBS, and 25 ml of each dilution was added to the cells after 24 hrs. 25 ml of excess of IL13, IL13.E13K, or IL4 was added to wells (4 mg/ml final concentration) for neutralization experiments. In neutralization experiments, cytotoxins were added to cells 1 hr after an excess of IL13 or IL4 was added. In both types of experiments, four wells from each 96 well plate were treated with cycloheximide to serve as a positive control and 4 wells received only 0.1% BSA/PBS to serve as a negative control. In addition, 25 ml of 0.1% BSA/PBS was added to the wells not receiving toxin or blocker to maintain a final volume of 200 ml in each well. Cells were incubated at 37 °C for another 48 hrs. The cytotoxicity was determined using a colorimetric MTS (3-(4,5- dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt)/ PMS (phenazine methasulfate) cell proliferation assay. MTS/PMS was added at half concentration as recommended by the manufacturer. The cells were incubated with the dye for 2-6 hrs, and the absorbance was measured at 490 nm for each well using a microplate reader (Cambridge Technology, Inc., Watertown, MA.).

IC₅₀ determination. The absorbency values obtained from the microplate reader for each assay were used. The mean absorbency was taken from three wells containing cells that were treated with cycloheximide. This value then served as the background for the assay. The three control absorbency readings had the background subtracted from them and the mean was taken. All triplicate experimental values also had the background subtracted from them. However, each experimental absorbency value was then divided by the mean control absorbency value. Therefore, each of the three cell viability values generated by the experimental groups were expressed as % of the control. (A₄₉₀ experimental - Mean A₄₉₀ of cyclohexamide)

% viability =

Mean (A₄₉₀ Control - Mean A₄₉₀ of cyclohexamide)

Example 2- Results

Generation of multiply-mutated IL13-based cytotoxins. All mutants made in this study are listed in Table 1. All cDNA plasmids were confirmed by sequence analysis to have the correct mutations incorporated in both IL13 and PE genes. However, through careful sequence verification of parental templates (IL13.E13K-PE4E and IL13.E13K-PE38QQR) before performing mutagenesis, sequencing showed that the PE4E template was really PEIE. Therefore, PE4E was subsequently made as well by site directed mutagenesis (Table 1).

Table 1. List of multiply mutated IL 13 -based cytotoxins containing either PE38QQR or PE 1 E derivative of Pseudomonas exotoxin. PE3800R template PEIE template

IL13.E13K.R66D-PE38QQR IL13.E13K.R66D-PE1E IL13.E13K.S69D-PE38QQR IL13.E13K.S69D-PE1E

IL13.E13K.R66D.S69D-PE38QQR IL13.E13K. R66D.S69D-PE1E IL13.E13Y-PE38QQR IL13.E13Y-PE1E IL13.E13Y.R66D-PE38QQR IL13.E13Y.R66D-PE1E IL13.E13Y.S69D-PE38QQR IL13.E13Y.S69D-PE1E IL13.E13Y.R66D.S69D-PE38QQR IL13.E13Y.R66D.S69D-PE1E

IL13.E13K-PE4E

The constructions listed in Table 1 were successfully used to generate and purify recombinant fusion proteins. As verified by SDS-PAGE, the IL13-based PE38QQR mutant constructs were approximately 50 kDa and the IL13-based PEIE mutant constructs were approximately 78 kDa in size. Proteins eluted from a Mono Q column showed that all were significantly enriched and about 95% free of any contaminating proteins, with a notable exception of IL13.E13Y.R66D.S69D-PE38QQR, as judged by SDS-PAGE. This protein repeatedly had a high background level of contaminating bacterial proteins.

Cytotoxic activity of novel anti-glioma cytotoxins. The cytotoxicity of IL13 mutant- based PE-containing cytotoxins on U-251 MG, HUVEC and normal glial SVG-pl2 cells was determined. IL13.E13K-based PE38QQR-containing constructs were highly cytotoxic and displayed IC₅₀ values ranging from 0.08 - 0.25 ng/ml on U-251 MG glioma cells (Fig. 1A). Double mutant IL13 cytotoxin, IL13.E13K.R66D-PE38QQR, tended to be the most active

(statistically significant at 1 ng/ml) when compared with other cytotoxins within this group. These double- and triple-mutated IL13 -based cytotoxins were also tested on normal endothelial cells. In sharp contrast to results obtained on glioma cells, more than 80% of HUVEC were still viable when treated with these same cytotoxins at concentrations as high as 1000 ng/ml (Fig. IB). IL13.E13Y-basedPE38QQRmutant constructs (Table 1) were somewhatmore cytotoxic than E13K mutant-containing fusion proteins and the IC₅₀s ranged from 0.05 to 0.14 ng/ml on U-251 MG glioma cells (Fig. 2A). Thus, different amino acid substitution at position 13 alone or in double-mutated IL 13 did not prevent the cytokine from an effective delivery of PE to cancer cells. Importantly, more than 75% of HUVEC treated with this group of cytotoxins were still viable at concentrations as high as 1000 ng/ml (Fig. 2B).

Another group of cytotoxins examined were by IL13.E13K-based PEIE derivative- containing constructs (Table 1). These cytotoxins showed remarkable cytotoxicity to U-251 MG glioma cells with IC₅₀ values ranging from 0.04 to 0.07 ng/ml (Fig. 3A). However, the gain in cytotoxic activity on glioma cells was compromised by a measurable low toxicity to normal endothelial cells (Fig. 3B) exhibited by these cytotoxins. E13K.S69D and E13K.R66D.S69D

XL 13 mutant-based cytotoxins, were the least active within this group of cytotoxins and they displayed IC₅₀ values ranging from 500 to 600 ng/ml on HUVEC (Fig. 3B). IL13.E13Y-based PEIE constructs showed similar cytotoxicity to U-251 MGglioma cells astheIL13.E13K-based PEIE constructs with IC₅₀ values ranging from 0.04 to 0.06 ng/ml (Table 2 and data not shown). However, the same group of IL 13.El 3 Y cytotoxins was consistently more toxic to HUVEC with

IC₅₀ values ranging from 160 to 240 ng/ml (Table 2 and unshown data). Table 2. IC₅₀ for cytotoxins on glioma cells (U-251 MG) and normal cells (HUVEC and SVG- pl2). * - % viable at 5000 ng/ml

Cytotoxin U-251 MG HUVEC SVG-pl2

[IC₅₀ values (ng/ml) or % viable at 1000 ng/ml] PE38QQR 3 30000 > >7700 %%** 1050

IL13.E13K-PE38QQR 0.13 >80 % IL13.E13K.R66D-PE38QQR 0.08 >80 % IL13.E13K.S69D-PE38QQR 0.23 >80 %

IL13.E13K.R66D.S69D-PE38QQR 0 0..2233 > >8800 %%** 1150 IL13.E13Y-PE38QQR 0.06 >70 %

IL13.E13Y.R66D-PE38QQR 0.14 >70 % IL13.E13Y.S69D-PE38QQR 0.06 >70 % PEIE 3 34400 > >9900%% 1150

IL13.E13K-PE1E 0.04 180 IL13.E13K.R66D-PE1E 0.04 300

IL13.E13K.S69D-PE1E 0.04 630

IL13.E13K.R66D.S69D-PE1E 00..0077 550000 130

IL13.E13Y-PE1E 0.04 240

IL13.E13Y.R66D-PE1E 0.06 240 IL13.E13Y.S69D-PE1E 0.05 190

IL13.E13Y.R66D.S69D-PE38QQR 0.04 160

IL13.E13K-PE4E 1.0 100 %

The experiments with a variety of IL13 mutant-based cytotoxins with different forms of PE provided evidence that it is feasible to extensively re-engineer the ligand (IL13) in a molecularly targeted anti-glioma cytotoxin, while retaining its potent cytotoxic activity toward cancer cells.

Restrictive 1X13 receptor-mediated cytotoxicity of mutated IL 13 -based cytotoxic proteins. One of the extensively mutagenized constructs that showed a favorable profile of the ratio of its cytotoxic activity on glioma cells vs. toxicity to normal cells, IL13.E13K.R66D.S69D- PE38QQR, was used in further experiments. The specificity of this cytotoxin interaction with the IL4-independent IL13 receptor on these cells was analyzed. Neutralization assays were performed on U-251 MG glioma cells in order to determine whether the cytotoxicity of IL 13.E 13K.R66D. S69D-PE38QQR could be blocked in the presence of an excess of IL 13 or IL4. In this assay, IL13.E13K.R66D.S69D-PE38QQR showed again a potent cytotoxicity to U-251 MG glioma cells. This cytotoxicity was neutralized with an excess of either IL 13 orIL13.E13K (Fig. 4A). At a cytotoxin concentration of 100 ng/ml, an excess of IL13 or IL13.E13K allowed more than 80% of the U-251 MG cells to survive while only 5% of the cells were viable when treated with the cytotoxin alone (Fig.4A). However, in sharp contrast, an excess of IL4 was not only unsuccessful in blocking IL13.E13K.R66D.S69D-PE38QQR's cytotoxicity to U-251 MG glioma cells, but actually made the cytotoxin more cytotoxic to cancer cells (Fig.4A). Also, at a cytotoxin' s concentration of 100 ng/ml virtually all U-251 MG glioma cells were killed in the presence of an excess of IL4 (Fig. 4A).

Cytotoxicity of IL13-based PE-containing derivatives vs. cytotoxicity of PE derivatives alone. To further demonstrate the receptor-dependent cytotoxicity of PE derivatives on the cells that were examined, the cytotoxicity of 1X13 mutant-based PE-containing constructs was compared to the relative cytotoxicity of the recombinant PEs alone. Cytotoxicity assays were performed on U-251 MG glioma, HUVEC and SVG pl2 cells. IL13.E13K.R66D.S69D- PE38QQR was very potent at killing U-251 MG glioma cells (IC₅₀ of 0.24 ng/ml) while the PE38QQR toxin alone had an IC₅₀ of only 300 ng/ml on these. cells (Fig. 4B). Further, the IL13.E13K.R66D.S69D-PE1E cytotoxin was very active on glioma cells (IC₅₀ of 0.052 ng/ml) while the PEIE toxin alone had an IC₅₀ of only 340 ng/ml on U-251 MG cells (Table 2 and unshown data). On normal endothelial cells, however, there was no significant difference in cytotoxicity between IL13.E13K.R66D.S69D-PE38QQR and the PE38QQR toxin alone and approximately 70% of the HUVEC were still viable at concentrations of 5000 ng/ml of either toxin or cytotoxin (Fig. 5A). A cytotoxin from another group studied, IL13.E13K.R66D.S69D-

PE1E, had an IC₅₀ value of approximately 500 ng/ml, as seen in Fig. 3B, but the PEIE alone exhibited very little cytotoxicity to HUVEC.

Experimentation on normal cells derived from the central nervous system. An established fetal glial cell line was used. The IL13.E13K.R66D.S69D-based cytotoxins showed some toxicity to those cells however with low IC₅₀ values. The IC₅₀ value of IL13.E13K.R66D.S69D-

PE38QQR was determined to be 1150 ng/ml while the PE38QQR toxin alone had an IC₅₀ of 1050 ng/ml on glial cells (Fig. 5B). The IC₅₀ value of IL13.E13K.R66D.S69D-PE1E was determined to be 130 ng/ml while the PEIE toxin alone had an IC₅₀ of 1150 ng/ml on glial cells. IL13.E13K-PE4E, which displayed distinctly different cytotoxicity characteristics from that of IL13.E13K-PE1E, was also examined. IL13.E13K-PE4EhadanIC₅₀value of 1 ng/ml on U-251

MG glioma cells while approximately 100% of HUVEC cells were viable at concentrations of 1000 ng/ml. Multiply mutated IL13-based cytotoxins are potent and specific anti-glioma agents. Table 2 summarizes the results of several experiments. In general, PE38QQR-containing cytotoxins were very active on glioma cells and very poorly active on normal cells. Their non-specific toxicity, if detectable, was in parallel to that of the toxin's alone. PEIE-containing cytotoxins were even more active on glioma cells than the fusion proteins with PE38QQR, but their toxicity to nonnal cells was more pronounced.

Example 3- In vivo experiment.

IL13.E13K.R66D.S69D-PE38QQR cytotoxin was used in an experiment in mice. 5.0, 1.0, and 0.2 mg per mouse was injected four times into test animals (limited with the available amount of the cytotoxin). All animals survived all the injections, and none showed any signs of toxicity. In comparison to previous experiments using different cytotoxins, this is the first time that a potent in vitro cytotoxin was observed to not be toxic to animals at this dosage range. Cf., Debinski et al., Nature Biotech., 1998;16:449-453. This result is especially promising because it provides evidence to suggest that the three mutations that were incorporated into IL 13 - PE38QQR (IL13.E13K.R66D.S69D) were successful in diminishing non-specific host organ interactions of the cytotoxin. This result suggests that rational design has produced more specific (less toxic) cytotoxins.

Example 4- Inhibition of Tumor Growth in an Animal

Referring to Figure 6, murine malignant glioma cells (ML13Rα2 positive G-26 cells) were implanted subcutaneously into 5 to 6- week old male BL57/J6 mice (6 X 10⁶ cells/mouse). After large established tumors formed, IL13.E13Y.R66D.S69D-PE1E cytotoxin (1.0 or 0.2 ug per mouse) or vehicle (PBS/BSA) was administered to the animals by 5 intratumoral injections every other day and tumor volumes were recorded starting on Day 0. At various time points thereafter, tumor volume was measured in the animals. The tumors grew rapidly in the vehicle- treated animals, however tumors regressed in IL13 cytotoxin receiving animals only (complete regression was seen at some time points) at several time points after day 0 (see Fig. 6).

Other Embodiments This description has been by way of example of how the compositions and methods of invention can be made and carried out. Those of ordinary skill in the art will recognize that various details may be modified in arriving at the other detailed embodiments, and that many of these embodiments will come within the scope of the invention.

Therefore, to apprise the public of the scope of the invention and the embodiments covered by the invention, the following claims are made. What is claimed is:

Claims (1)

1. 1. A purified mutant ML 13 molecule comprising an amino acid sequence (a) having at least 90% sequence identity to the native ML13 sequence (SEQ ID NO: 1) and (b) differing from the native ML13 sequence by at least a first amino acid substitution occurring in the A alpha helix and a second amino acid substitution occurring in the D alpha helix.

   2. A purified mutant ML 13 molecule comprising an amino acid sequence (a) having at least 90% sequence identity to the native ML 13 sequence (SEQ ID NO:l) and (b) differing from the native ML13 sequence by at least three amino acid substitutions.

   3. The purified mutant ML 13 molecule of claim 2, wherein the amino acid sequence differs from the native ML 13 sequence by at least a first amino acid substitution occurring in the A alpha helix, a second amino acid substitution occurring in the D alpha helix, and a third amino acid substitution occurring in the C alpha helix.

   4. The purified mutant ML 13 molecule of claim 2, wherein the amino acid sequence differs from the native ML13 sequence by at least four amino acid substitutions.

   5. The purified mutant ML13 molecule of claim 4, wherein the amino acid sequence differs from the native ML13 sequence by at least a first amino acid substitution occurring in the A alpha helix, a second amino acid substitution occurring in the D alpha helix, and a third amino acid substitution occurring in the C alpha helix.

   6. A purified mutant ML 13 molecule, wherein the molecule comprises a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NOs: 2-9.

   7. A purified mutant MLl 3 molecule, wherein the molecule consists of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NOs: 2-9.

   8. The purified mutant hIL 13 molecule of claim 6, wherein the molecule comprises a polypeptide having the amino acid sequence of SEQ ID NO: 2.

   9. The purified mutant ML 13 molecule of claim 6, wherein the molecule comprises a polypeptide having the amino acid sequence of SEQ ID NO: 3.

   10. The purified mutant ML 13 molecule of claim 6, wherein the molecule comprises a polypeptide having the amino acid sequence of SEQ ID NO: 4.

   11. The purified mutant ML 13 molecule of claim 6, wherein the molecule comprises a polypeptide having the amino acid sequence of SEQ ID NO: 5.

   12. The purified mutant ML 13 molecule of claim 6, wherein the molecule comprises a polypeptide having the amino acid sequence of SEQ ID NO: 6.

   13. The purified mutant MLl 3 molecule of claim 6, wherein the molecule comprises a polypeptide having the amino acid sequence of SEQ ID NO: 7.

   14. The purified mutant ML 13 molecule of claim 6, wherein the molecule comprises a polypeptide having the amino acid sequence of SEQ ID NO: 8.

   15. The purified mutant ML 13 molecule of claim 1 , further comprising a pharmaceutically acceptable carrier.

   16. The purified mutant ML13 molecule of claim 2, further comprising a pharmaceutically acceptable carrier.

   17. The purified mutant MLl 3 molecule of claim 6, further comprising a pharmaceutically acceptable carrier.

   18. The purified mutant ML 13 molecule of claim 1 , wherein the molecule is conjugated to an effector molecule.

   19. The purified mutant ML13 molecule of claim 2, wherein the molecule is conjugated to an effector molecule.

   20. The purified mutant ML 13 molecule of claim 6, wherein the molecule is conjugated to an effector molecule.

   21. The purified mutant ML13 molecule of claim 18, wherein the effector molecule is selected from the group consisting of a cytotoxin, a detectable label, an antibody, a liposome, and a lipid.

   22. The purified mutant ML13 molecule of claim 21, wherein the effector molecule is a cytotoxin selected from the group consisting of a Pseudomonas exotoxin, Diptheria toxin, ricin, abrin, saporin, and pokeweed viral protein.

   23. The purified mutant ML13 molecule of claim 22, wherein the cytotoxin is selected from the group consisting of PE38QQR, PEIE, and PE4E.

   24. The purified mutant ML 13 molecule of claim 21 , wherein the effector molecule comprises a radionuclide.

   25. The purified mutant hIL 13 molecule of claim 19, wherein the effector molecule is selected from the group consisting of a cytotoxin, a detectable label, an antibody, a liposome, and a lipid.

   26. The purified mutant ML 13 molecule of claim 25, wherein the effector molecule is a cytotoxin selected from the group consisting of a Pseudomonas exotoxin, Diptheria toxin, ricin, abrin, saporin, and pokeweed viral protein.

   27. The purified mutant ML 13 molecule of claim 26, wherein the cytotoxin is selected from the group consisting of PE38QQR, PEIE, and PE4E,

   28. The purified mutant ML13 molecule of claim 25, wherein the effector molecule comprises a radionuclide.

   29. The purified mutant MLl 3 molecule of claim 20, wherein the effector molecule is selected from the group consisting of a cytotoxin, a detectable label, an antibody, a liposome, and a lipid.

   30. The purified mutant ML13 molecule of claim 29, wherein the effector molecule is a cytotoxin selected from the group consisting of a Pseudomonas exotoxin, Diptheria toxin, ricin, abrin, saporin, and pokeweed viral protein.

   31. The purified mutant ML13 molecule of claim 30, wherein the cytotoxin is selected from the group consisting of PE38QQR, PEIE, and PE4E.

   32. The purified mutant ML13 molecule of claim 29, wherein the effector molecule comprises a radionuclide.

   33. A purified nucleic acid encoding a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 2-9.

   34. The purified nucleic acid of claim 33, wherein the polypeptide consists of a sequence selected from the group consisting of SEQ ID NOs: 2-9.

   35. A purified antibody that specifically binds an ML 13 mutant but not a native ML 13 , the ML 13 mutant being selected from the group consisting of the mutant ML 13 molecules of claims 1, 2, and 6.

   36. The antibody of claim 35, wherein the ML 13 mutant comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 2-9.

   37. A method of delivering a ML 13 mutant to a cell comprising the steps of: (a) providing a ML 13 mutant selected from the group consisting of the mutant ML 13 molecules of claims 1, 2, and 6. (b) providing the cell; and (c) contacting the cell with the ML 13 mutant.

   38. The method of claim 37, wherein the ML13 mutant is a polypeptide comprising a sequence selected from the group consisting of SEQ ID NOs: 2-9.

   39. The method of claim 38, wherein the ML 13 mutant is conjugated to an effector molecule.

   43. The method of claim 40, wherein the effector molecule is selected from the group consisting of a cytotoxin, a detectable label, an antibody, a liposome, and a lipid.

   44. The method of claim 43, wherein the effector molecule is a cytotoxin selected from the group consisting of a Pseudomonas exotoxin, Diptheria toxin, ricin, abrin, saporin, and pokeweed viral protein.

   45. The method of claim 44, wherein the cytotoxin is selected from the group consisting of PE38QQR, PE 1 E, and PE4E.

   46. The method of claim 40, wherein the effector molecule comprises a radionuclide.

   47. The method of claim 37, wherein the step (c) of contacting the cell with the hIL13 mutant takes place in an animal.

   48. The method of claim 47, wherein the ML13 mutant is conjugated to an effector molecule.

   49. The method of claim 47, further comprising the step of administering the ML 13 mutant to the animal.

   50. The method of claim 49, wherein the step of administering the ML 13 mutant to the animal is performed by injection.

   51. The method of claim 37, wherein the cell forms part of a tumor in an animal; the tumor is growing at a measurable rate in the animal; and the rate is decreased subsequent to the step (c) of contacting the cell with the ML 13 mutant.