MONOCLONAL ANTIBODY 175 TARGETING THE EGF RECEPTOR AND DERIVATIVES AND USES THEREOF

FIELD OF THE INVENTION

[0001] The present invention relates to antibodies, particularly antibody 175, and fragments thereof, which bind to the EGF receptor, particularly to amplified or overexpressed epidermal growth factor receptor (EGFR) and to the de2-7 EGFR truncation of the EGFR. These antibodies are useful in the diagnosis and treatment of cancer. The antibodies of the present invention may also be used in therapy in combination with chemotherapeutics or anti-cancer agents and/or with other antibodies or fragments thereof.

BACKGROUND OF THE INVENTION

[0002] The treatment of proliferative disease, particularly cancer, by chemotherapeutic means often relies upon exploiting differences in target proliferating cells and other normal cells in the human or animal body. For example, many chemical agents are designed to be taken up by rapidly replicating DNA so that the process of DNA replication and cell division is disrupted. Another approach is to identify antigens on the surface of tumor cells or other abnormal cells which are not normally expressed in developed human tissue, such as tumor antigens or embryonic antigens. Such antigens can be targeted with binding proteins such as antibodies which can block or neutralize the antigen. In addition, the binding proteins, including antibodies and fragments thereof, may deliver a toxic agent or other substance which is capable of directly or indirectly activating a toxic agent at the site of a tumor.

[0003] The EGFR is an attractive target for tumor-targeted antibody therapy because it is overexpressed in many types of epithelial tumors (Voldborg, B. R., et al. (1997) Ann

Oncol 8:1197-206; den Eynde, B. and Scott, A. M. (1998) Tumor Antigens. In: P. J. Delves and I. M. Roitt (eds.), Encyclopedia of Immunology, Second Edition edition, pp. 2424-31.London: Academic Press). Moreover, expression of the EGFR is associated with poor prognosis in a number of tumor types including stomach, colon, urinary bladder, breast, prostate, endometrium, kidney and brain (e.g., glioma). Consequently, a number of EGFR antibodies have been reported in the literature with several undergoing clinical evaluation (Baselga, J., et al. (2000) J Clin Oncol. 18: 904; Faillot, T., et al. (1996) Neurosurgery 39: 478-83; Seymour, L. (1999) Cancer Treat Rev 25: 301-12). Results from studies using EGFR mAbs in patients with head and neck cancer, squamous cell lung cancer, brain gliomas and malignant astrocytomas have been encouraging. The antitumor activity of most EGFR antibodies is enhanced by their ability to block ligand binding (Sturgis, E. M., et al. (1994) Otolaryngol Head Neck Surg 111 : 633-43; Goldstein, N. L, et al. (1995) Clin Cancer Res 1 : 1311-8). Such antibodies may mediate their efficacy through both modulation of cellular proliferation and antibody dependent immune functions (e.g. complement activation). The use of these antibodies, however, may be limited by uptake in organs that have high endogenous levels of EGFR such as the liver and skin (Baselga, J., et al. (2000) J Clin Oncol. 18: 904; Faillot, T., et al. (1996) Neurosurgery 39: 478-83).

[0004] A significant proportion of tumors containing amplifications of the EGFR gene (i.e., multiple copies of the EGFR gene) also co-express a truncated version of the receptor (Wikstrand, C. J., et al. (1998) J Neurovirol 4: 148-58) known as de2-7 EGFR, δEGFR, or δ2-7 (terms used interchangeably herein) (Olapade-Olaopa, E. O., et al. (2000) Br J Cancer 82: 186-94). The rearrangement seen in the de2-7 EGFR results in an in-frame mature mRNA lacking 801 nucleotides spanning exons 2-7 (Wong, A. J., et al. (1992) Proc Natl Acad Sci U S A 89: 2965-9; Yamazaki, H., et al. (1990) Jpn J Cancer Res 81 : 773-9; Yamazaki, H., et al. (1998) MoI Cell Biol 8: 1816-20; Sugawa, N., et al. (1990) Proc Natl Acad Sci U S A 87: 8602-6). The corresponding EGFR protein has a 267 amino acid deletion comprising residues 6-273 of the extracellular domain and a novel glycine residue at the fusion junction (Sugawa, N., et al. (1990) Proc Natl Acad Sci USA 87: 8602-6). This deletion, together with the insertion of a glycine residue, produces

a unique junctional peptide at the deletion interface. The de2-7 EGFR has been reported in a number of tumor types including glioma, breast, lung, ovarian and prostate (Wikstrand, C. J., et al. (1997) Cancer Res. 57: 4130-40; Olapade-Olaopa, E. O., et al. (2000) Br J Cancer 82: 186-94; Wikstrand, C. J., et al. (1995) Cancer Res 55: 3140-8; Garcia de Palazzo, I. E., et al. (1993) Cancer Res 53: 3217-20). While this truncated receptor does not bind ligand, it possesses low constitutive activity and imparts a significant growth advantage to glioma cells grown as tumor xenografts in nude mice (Nishikawa, R., et al. (1994) Proc Natl Acad Sci USA 91: 7727-31, 1994.) and is able to transform NIH3T3 cells and MCF-7 cells (Batra, S. K., et al. (1995) Cell Growth Differ 6: 1251-9). The cellular mechanisms utilized by the de2-7 EGFR in glioma cells are not fully defined but are reported to include a decrease in apoptosis and a small enhancement of proliferation (Nagane, M., et al. (1996) Cancer Res 56: 5079-86).

[0005] As expression of this truncated receptor is restricted to tumor cells it represents a highly specific target for antibody therapy. Accordingly, a number of laboratories have reported the generation of both polyclonal and monoclonal antibodies specific to the unique peptide of de2-7 EGFR (Wikstrand, C. J., et al (1998) J Neurovirol 4: 148-58; Humphrey, P. A., et al (1990) Proc Natl Acad Sci USA 87: 4207-11; Okamoto, S., et al (1996) Br J Cancer 73: 1366-72; Hills, D., et al (1995) Int J Cancer 63: 537-43). A series of mouse mAbs, isolated following immunization with the unique de2-7 peptide, all showed selectivity and specificity for the truncated receptor and targeted de2-7 EGFR positive xenografts grown in nude mice (Wikstrand, C. J., et al (1995) Cancer Res 55: 3140-8; Reist, C. J., et al (1997) Cancer Res 57: 1510-5; Reist, C. J., et al (1995) Cancer Res 55: 4375-82).

[0006] However, one potential shortcoming of de2-7 EGFR antibodies is that only a proportion of tumors exhibiting amplification of the EGFR gene also express the de 2-7 EGFR. Therefore, de2-7 EGFR specific antibodies would be expected to be useful in only a percentage of EGFR positive tumors. Thus, while the extant evidence of activity of EGFR antibodies is encouraging, the observed limitations on range of applicability and efficacy reflected above remain. Accordingly, it would be desirable to have antibodies

and like agents that demonstrate efficacy with a broad range of tumors, and it is toward the achievement of that objective that the present invention is directed. In addition, antibodies which do not target normal tissues and EGFR in the absence of amplification, overexpression, or mutation, would be particularly useful. One such antibody, monoclonal antibody mAb806, has been previously described in WO02092771 and WO05081854. Additional such antibodies are needed and would be desirable.

[0007] The citation of references herein shall not be construed as an admission that such is prior art to the present invention.

SUMMARY OF THE INVENTION

[0008] The antibodies of the present invention, antibody 175 and fragments thereof or monomers, recombinant, or hybrid antibodies derived therefrom, recognize an EGFR epitope which is found in tumorigenic, hyperproliferative or abnormal cells and is not detectable in normal or wild type cells. The antibodies of the present invention are further exemplified by the antibody mAb 175 described herein.

[0009] This invention describes an antibody targeting the same EGF receptor epitope as the previously described monoclonal antibody (mAb) 806 (described in WO02092771 and WO05081854). The complementary determining regions (CDRs), the most important amino acids for antigen binding, of mAb 175 are highly homologous to the 806 antibody, with only a few amino acid differences.

[0010] The binding of an antibody to its target antigen is mediated through the complementarity-determining regions (CDRs) of its heavy and light chains, there being three CDR regions CDRl, CDR2, and CDR3. Accordingly, antibodies based on the CDR regions of the heavy or light chain, and preferably both, of mAb 175 will be useful antibodies for diagnostic and therapeutic applications, including in vivo therapy. Antibodies which are based on the CDRs of the mAb 175 antibody identified will be useful for targeting tumors with amplified EGFR regardless of their de2-7 EGFR status.

As mAb 175 does not bind significantly to normal, wild type receptor, there would be no significant uptake in normal tissue, a limitation of EGFR antibodies currently being developed.

[0011] The sequences of monoclonal antibody 175, targeting the EGF-receptor, have been determined and the CDR regions of the antibody have the amino acid sequences set out in Figure 1. The CDRs for each of the light chain and the heavy chain are provided herein. The AbI 75 light chain CDRs correspond to CDRl (SEQ ID NO: 1), CDR2 (SEQ ID NO: 2) and CDR3 (SEQ ID NO: 3). The AbI 75 heavy chain CDRs correspond to CDRl (SEQ ID NO: 4), CDR2 (SEQ ID NO: 5) and CDR3 (SEQ ID NO: 6).

[0012] Similar to antibody 806, the 175 antibodies of the invention also recognize amplified wild type EGFR and the de2-7 EGFR, yet bind to an epitope distinct from the unique junctional peptide of the de2-7 EGFR mutation (junctional peptide LEEKKGNYVVTDH (SEQ ID NO: 13). MAb 175 binds to the surface of A431 cells, which have an amplification of the EGFR gene but do not express the de2-7 EGFR. Importantly, mAb 175, like mAb 806, does not bind significantly to normal tissues such as liver and skin, which express levels of endogenous, wild type (wt) EGFR, but wherein EGFR is not aberrantly expressed or amplified.

[0013] While having very similar characteristics as mAb 806 with regard to the epitope binding, immunohistochemical staining etc., mAb 175 does show a higher potency than mAb 806 in treating human glioma xenografts expressing the de2-7 EGF-receptor.

[0014] In one aspect, the present invention provides an antibody capable of binding an antigen wherein said antibody comprises a polypeptide binding domain comprising an amino acid sequence substantially as set out in the CDRs of the light chain of Ab 175, comprising CDRl, CDR2, and/or CDR3, including as set out in SEQ ID NOs: 1-3. In a further aspect, the present invention provides an antibody capable of binding an antigen wherein said antibody comprises a polypeptide binding domain comprising an amino acid sequence substantially as set out in the CDRs of the heavy chain of Ab 175, comprising

CDRl, CDR2, and/or CDR3, including as set out in SEQ ID NOs: 4-6. Thus, the invention contemplates recombinant, humanized, chimeric, veneered, or other such antibodies, or antibody peptides, including domain peptides comprising the CDRs of the heavy and/or light chain of Ab 175. Such antibodies may comprise the sequences as set out in SEQ ID NOS: 1-3 for light chain, and SEQ ID NOs: 4-6 for heavy chain. In a preferred embodiment, the binding domains are carried by a human antibody framework.

[0015] In further aspects, the invention provides an isolated nucleic acid which comprises a sequence encoding an antibody as defined above, and methods of preparing antibodies of the invention which comprise expressing said nucleic acids under conditions to bring about expression of said binding member, and recovering the binding member.

[0016] Yet a further aspect of the invention are compositions of such antibodies with additional antibodies, such as antibodies which bind to EGFR, preferably inhibiting ligand binding thereto. Such compositions can be "one pot" cocktails, kits, and so forth, preferably formulated for ease of administration.

[0017] Antibodies or fragments thereof according to the invention may be used in a method of treatment or diagnosis of the human or animal body, such as a method of treatment of a tumor in a human patient which comprises administering to said patient an effective amount of an antibody of the invention.

[0018] The present invention also relates to a recombinant DNA molecule or cloned gene, or a degenerate variant thereof, which encodes an antibody of the present invention; preferably a nucleic acid molecule, in particular a recombinant DNA molecule or cloned gene, encoding the antibody VH CDR 1, 2, and/or 3 domains shown in FIGURE 1 (SEQ ID NOs: 4-6). In another embodiment, the present invention also relates to a recombinant DNA molecule or cloned gene, or a degenerate variant thereof, preferably a nucleic acid molecule, in particular a recombinant DNA molecule or cloned gene, encoding the antibody VL CDR 1, 2, and/or 3 domains shown in FIGURE 1 (SEQ ID NOs: 1-3).

[0019] In a further embodiment of the invention, the full DNA sequence of the recombinant DNA molecule or cloned gene encoding the sequences provided herein may be operatively linked to an expression control sequence which may be introduced into an appropriate host. The invention accordingly extends to unicellular hosts transformed with the cloned gene or recombinant DNA molecule comprising a DNA sequence encoding the present VH and/or VL CDRs, or portions thereof, of the antibody, and more particularly, a DNA sequence encoding the VH and/or VL CDRs set forth above and in Figure 1 and in SEQ ID NOs: 1, 2, 3, 4, 5 and/or 6.

[0020] The present invention naturally contemplates several means for preparation of the antibodies and active fragments thereof, including as illustrated herein known recombinant techniques, and the invention is accordingly intended to cover such synthetic or chimeric antibody preparations within its scope. The isolation of the nucleic acid and amino acid sequences disclosed herein facilitates the reproduction of the antibody of the present invention by such recombinant techniques, and accordingly, the invention extends to expression vectors prepared for expression in host systems by recombinant DNA techniques, and to the resulting transformed hosts.

[0021] The present invention provides drugs or other entities, including antibodies such as anti-idiotype antibodies, that are capable of binding to the antibody thereby modulating, inhibiting or potentiating the antibody activity. Such anti-idiotype antibodies would be useful in the development of drugs that would specifically bind the antibodies such as mAbl75 or its epitope or that would potentiate its activity.

[0022] The diagnostic utility of the present invention extends to the use of the antibodies of the present invention in assays to characterize tumors or cellular samples or to screen for tumors or cancer, including in vitro and in vivo diagnostic assays. In an immunoassay, a control quantity of the antibodies, or the like may be prepared and labeled with an enzyme, a specific binding partner and/or a radioactive element, and may then be introduced into a cellular sample. After the labeled material or its binding partner(s) has

had an opportunity to react with sites within the sample, the resulting mass may be examined by known techniques, which may vary with the nature of the label attached.

[0023] Antibodies of the invention may carry a detectable or functional label. The specific binding members may carry a radioactive label, such as the isotopes ³ H, ¹⁴ C, ³ P, ³⁵ S, ³⁶ Cl, ⁵¹ Cr, ⁵⁷ Co, ⁵⁸ Co, ⁵⁹ Fe, ⁹⁰ Y, ¹²¹ 1, ¹²⁴ I, ¹²⁵ I, ¹³¹ 1, ^{1 11} In, ²¹¹ At, ¹⁹⁸ Au, ⁶⁷ Cu, ²²⁵ Ac, ²¹³ Bi, ⁹⁹ Tc and ¹⁸⁶ Re. When radioactive labels are used, known currently available counting procedures may be utilized to identify and quantitate the antibodies. In the instance where the label is an enzyme, detection may be accomplished by any of the presently utilized colorimetric, spectrophotometric, fluorospectrophotometric, amperometric or gasometric techniques known in the art.

[0024] The radiolabeled antibodies and fragments thereof, are useful in in vitro diagnostics techniques and in in vivo radioimaging techniques. In a further aspect of the invention, radiolabeled antibodies and fragments thereof, particularly radioimmunoconjugates, are useful in radioimmunotherapy, particularly as radiolabeled antibodies for cancer therapy. In a still further aspect, the radiolabeled antibodies and fragments thereof, are useful in radioimmuno-guided surgery techniques, wherein they can identify and indicate the presence and/or location of cancer cells, precancerous cells, tumor cells, and hyperproliferative cells, prior to, during or following surgery to remove such cells.

[0025] Immunoconjugates or antibody fusion proteins of the present invention, wherein the antibodies and fragments thereof, of the present invention are conjugated or attached to other molecules or agents further include, but are not limited to binding members conjugated to a chemical ablation agent, toxin, immunomodulator, cytokine, cytotoxic agent, chemotherapeutic agent or drug.

[0026] The present invention includes an assay system which may be prepared in the form of a test kit for the quantitative analysis of the extent of the presence of, for instance, amplified EGFR or de2-7EGFR. The system or test kit may comprise a labeled

component prepared by one of the radioactive and/or enzymatic techniques discussed herein, coupling a label to the antibody, and one or more additional immunochemical reagents, at least one of which is a free or immobilized components to be determined or their binding partner(s).

[0027] In a further embodiment, the present invention relates to certain therapeutic methods which would be based upon the activity of the antibody, or active fragments thereof, or upon agents or other drugs determined to possess the same activity. A first therapeutic method is associated with the prevention or treatment of cancer, including but not limited to head and neck, breast, prostate and glioma.

[0028] In particular, the antibodies of the present invention, and in a particular embodiment the 175 antibody whose CDR domain region sequences are presented in Figure 1 and in SEQ ID NOS: 1-6 herein, or active fragments thereof, and chimeric (bispecific) or synthetic antibodies derived therefrom can be prepared in pharmaceutical compositions, including a suitable vehicle, carrier or diluent, for administration in instances wherein therapy is appropriate, such as to treat cancer. Such pharmaceutical compositions may also include methods of modulating the half-life of the antibodies or fragments by methods known in the art, such as pegylation. Such pharmaceutical compositions may further comprise additional antibodies or therapeutic agents.

[0029] Thus, a composition of the present invention may be administered alone or in combination with other treatments, therapeutics or agents, either simultaneously or sequentially dependent upon the condition to be treated. In addition, the present invention contemplates and includes compositions comprising the antibody or fragment thereof, herein described and other agents or therapeutics such as anti-cancer agents or therapeutics, anti-EGFR agents or antibodies, or immune modulators. More generally these anti-cancer agents may be tyrosine kinase inhibitors or phosphorylation cascade inhibitors, post-translational modulators, cell growth or division inhibitors (e.g. antimitotics), PDGFR inhibitors or signal transduction inhibitors. Other treatments or therapeutics may include the administration of suitable doses of pain relief drugs such as

non-steroidal anti-inflammatory drugs (e.g. aspirin, paracetamol, ibuprofen or ketoprofen) or opiates such as morphine, or anti-emetics. Thus, these agents may be anti-EGFR specific agents, such as AGl 478, or may be more general anti-cancer and anti-neoplastic agents, non limiting examples including doxorubicin, carboplatin and cisplatin. In addition, the composition may be administered with immune modulators, such as interleukins, tumor necrosis factor (TNF) or other growth factors, cytokines or hormones such as dexamethasone which stimulate the immune response and reduction or elimination of cancer cells or tumors. The composition may also be administered with, or may include combinations along with other anti-EGFR antibodies, including but not limited to the anti-EGFR antibodies mAb806; antibody 528; 225; SC-03; 108 (ATCC HB9764) U.S. Patent No. 6,217,866; 14El (U.S. Patent No. 5,942,602); DH8.3; L8A4; YlO; HuMAX-EGFr (Genmab/Medarex); ICR62; and ABX-EGF (Abgenix).

[0030] The present invention also includes antibodies and fragments thereof, which are covalently attached to or otherwise associated with other molecules or agents. These other molecules or agents include, but are not limited to, molecules (including antibodies or antibody fragments) with distinct recognition characteristics, toxins, ligands, and chemotherapeutic agents.

[0031] Other objects and advantages will become apparent to those skilled in the art from a review of the ensuing detailed description, which proceeds with reference to the following illustrative drawings, and the attendant claims.

BRIEF DESCRIPTION OF THE DRAWINGS

[0032] Figure 1: Alignment of amino acid sequences for CDR' s from mAb806 and mAbl75. Sequence differences between the two antibodies are bolded.

[0033] Figure 2: Immunohistochemical staining of cell lines and normal human liver with mAbl75. A: Biotinylated mAbl75 was used to stain sections prepared from blocks containing A431 cells (over-express the wtEGFR), U87MG.δ2-7 cells (express the δ2-7

EGFR) and U87MG cells (express the wtEGFR at modest levels). B; Staining of normal human liver (40Ox) with mAbl75 (left panel), isotype control (centre panel) and secondary antibody control (right panel). No specific sinusoidal or hepatocyte staining was observed.

[0034] Figure 3: Reactivity of mAb806 and mAbl75 with fragments of the EGFR displayed on yeast. A: Representative flow cytometry histograms depicting the mean fluorescence signal of mAbl75 and mAb806 labeling of yeast-displayed EGFR fragments. With yeast display a percentage of cells do not express protein on their surface resulting in 2 histogram peaks. The 9E10 antibody is used as a positive control as all fragments contain a linear C-terminal c-myc tag. B: Summary of antibody binding to various EGFR fragments. C: The EGFR fragments were denatured by heating yeast pellets to 80° C for 30 min. The c-myc tag was still recognized by the 9E10 anti-myc antibody in all cases, demonstrating that heat treatment does not compromise the yeast surface displayed protein. The conformation sensitive EGFR antibody mAb 225 was used to confirm denaturation.

[0035] Figure 4: Antitumor effects of mAb 175 on brain and prostate cancer xenografts. A: Mice (n=5) bearing U87MG.δ2-7 xenografts were injected i.p. with PBS, 1 mg of mAb 175 or mAb806 (positive control), three times weekly for two weeks on days 6, 8, 10, 13, 15 and 17 when the starting tumor volume was 100 mm ³ . Data are expressed as mean tumor volume ± SE. B: Cells were stained with two irrelevant antibodies (blue, solid and green, hollow), mAb 528 for total EGFR (pink, solid), mAb806 (light blue, hollow) and mAb 175 (orange, hollow) and then analyzed by FACS. C: DU 145 cells were lysed, subjected to IP with mAb 528, mAb806, mAbl75 or two independent irrelevant antibodies and then immunoblotted for EGFR. D: Mice (n=5) bearing DU 145 xenografts were injected i.p. with PBS, 1 mg of mAbl75 or mAb806, daily on days 18- 22, 25-29 and 39-43 when the starting tumor volume was 85 mm ³ . Data are expressed as mean tumor volume ± SE.

[0036] Figure 5: Crystal structures of EGFR peptide 287-302 bound to the Fab fragments (A) Cartoon of Fab 806, with the light chain, red; heavy chain, blue; bound peptide, yellow; and the superposed EGFR _287-3O2 from EGFR, purple. (B) Cartoon of Fab 175 with the light chain, yellow; heavy chain, green; bound peptide, lilac; and EGFR _287- 3 _O2 from EGFR(Dl -3), purple. (C) Detail from (B) showing the similarity Of EGFR _287-302 in the receptor to the peptide bound to FAb 175. Peptides backbones are shown as Ca traces and the interacting side chains as sticks. O atoms are coloured red; N, blue; S, orange and C, as for the main chain. (D) Superposition of EGFR with the Fabl75:peptide complex showing' spacial overlap. Colouring as in (C) with the suface of EGFRl 87-286 coloued turquoise. (E) Orthogonal view to (D) with EGFRl 87-286 shown in opaque blue and the surface of the light (orange) and heavy (green) chains transparent. (F) Detailed stereoview of 175 Fab complex looking into the antigen-binding site. Colouring as in (C) and side chain hydrogen bonds dotted in black. Water molecules buried upon complex formation are shown as red spheres.

[0037] Figure 6: Influence of the 271-283 cystine bond on mAb806 binding to the EGFR. A: Cells transfected with wtEGFR, EGFR-C271 A, EGFR-C283A or the C271A/C283A mutant were stained with mAb528 (solid pink histogram), mAb806 (blue line) or only the secondary antibody (purple) and then analyzed by FACS. The gain was set up using a class-matched irrelevant antibody.

B: BaF3 cells expressing the EGFR- C271A or or C271/283A EGFR were examined for their response to EGF in an MTT assay as described in Methods. EC ₅₀ S were derived using the Bolzman fit of the data points. Data represent mean and sd of triplicate measurements C: BaF3 cells expressing the wt or the EGFR- C271 A/C283A were IL-3 and serum starved, then exposed to EGF or vehicle control. Whole cell lyates were separated by SDS-PAGE and immunoblotted with anti-phosphotyrosine antibody (top panel) or anti-EGFR antibody (bottom panel). D: BaF3 cells expressing the wt (left panel) or the C271 A/C283A (right panel) EGFR were stimulated with increasing concentrations of EGF in the presence of no antibody (open symbols), mAb 528 (grey circles) or mAb806 (black triangles), both at lOμg/ml. Data are expressed as mean and sd of triplicate measurements.

[0038] Figure 7: A) Whole body gamma camera image of the biodistribution of ¹¹¹ In- ch806 in a patient with metastatic squamous cell carcinoma of the vocal cord, showing quantitative high uptake in tumour in the right neck (arrow). Blood pool activity, and minor catabolism of free ¹¹¹ In in liver, is also seen. B) Single Photon Computed Tomography (SPECT) image of the neck of this patient, showing uptake of ^{l u} In-ch806 in viable tumor (arrow), with reduced central uptake indicating necrosis. C) Corresponding CT scan of the neck demonstrating a large right neck tumour mass (arrow) with central necrosis.

[0039] Figure 8: A stereo model of the structure of the untethered EGFRl -621. The receptor backbone is traced in blue and the ligand TGF-α in red. The mAb806/175 epitope is drawn in turquoise and the disulfide bonds in yellow. The atoms of the disulfide bond which ties the epitope back into the receptor are shown in space-filling format. The model was constructed by docking the EGFR-ECD CR2 domain from the tethered conformation^ 5) onto the structure of an untethered EGFR monomer in the presence of its ligand (14).

[0040] Figure 9: Reactivity of mAb806 with fragments of the EGFR. Lysates from 293T cells transfected with vectors expressing the soluble 1-501 EGFR fragment or GH/EGFR fragment fusion proteins (GH-274-501, GH-282-501, GH-290-501 and GH- 298-501) were resolved by SDS-PAGE, transferred to membrane and immunoblotted with mAb806 (left panel) or the anti-myc antibody 9Bl 1 (right panel).

DETAILED DESCRIPTION

[0041] In accordance with the present invention there may be employed conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Sambrook et al, "Molecular Cloning: A Laboratory Manual" (1989); "Current Protocols in Molecular Biology" Volumes I-III [Ausubel, R. M., ed. (1994)]; "Cell Biology: A Laboratory

Handbook" Volumes I-III [J. E. Celis, ed. (1994))]; "Current Protocols in Immunology" Volumes I-III [Coligan, J. E., ed. (1994)]; "Oligonucleotide Synthesis" (MJ. Gait ed. 1984); "Nucleic Acid Hybridization" [B.D. Hames & SJ. Higgins eds. (1985)]; "Transcription And Translation" [B.D. Hames & SJ. Higgins, eds. (1984)]; "Animal Cell Culture" [R.I. Freshney, ed. (1986)]; "Immobilized Cells And Enzymes" [IRL Press, (1986)]; B. Perbal, "A Practical Guide To Molecular Cloning" (1984).

[0042] Therefore, if appearing herein, the following terms shall have the definitions set out below.

A. TERMINOLOGY

[0043] The term "aberrant expression" in its various grammatical forms may mean and include any heightened or altered expression or overexpression of a protein in a tissue, e.g. an increase in the amount of a protein, caused by any means including enhanced expression or translation, modulation of the promoter or a regulator of the protein, amplification of a gene for a protein, or enhanced half-life or stability, such that more of the protein exists or can be detected at any one time, in contrast to a non-overexpressed state. Aberrant expression includes and contemplates any scenario or alteration wherein the protein expression or post-translational modification machinery in a cell is taxed or otherwise disrupted due to enhanced expression or increased levels or amounts of a protein, including wherein an altered protein, as in mutated protein or variant due to sequence alteration, deletion or insertion, or altered folding is expressed.

[0044] It is important to appreciate that the term "aberrant expression" has been specifically chosen herein to encompass the state where abnormal (usually increased) quantities/levels of the protein are present, irrespective of the efficient cause of that abnormal quantity or level. Thus, abnormal quantities of protein may result from overexpression of the protein in the absence of gene amplification, which is the case e.g. in many cellular/tissue samples taken from the head and neck of subjects with cancer, while other samples exhibit abnormal protein levels attributable to gene amplification.

[0045] In this latter connection, certain of the work of the inventors that is presented herein to illustrate the invention includes the analysis of samples certain of which exhibit abnormal protein levels resulting from amplification of EFGR. This therefore accounts for the presentation herein of experimental findings where reference is made to amplification and for the use of the terms "amplification/amplified" and the like in describing abnormal levels of EFGR. However, it is the observation of abnormal quantities or levels of the protein that defines the environment or circumstance where clinical intervention as by resort to the binding members of the invention is contemplated, and for this reason, the present specification considers that the term "aberrant expression" more broadly captures the causal environment that yields the corresponding abnormality in EFGR levels.

[0046] Accordingly, while the terms "overexpression" and "amplification" in their various grammatical forms are understood to have distinct technical meanings, they are to be considered equivalent to each other, insofar as they represent the state where abnormal EFGR protein levels are present in the context of the present invention. Consequently, the term "aberrant expression" has been chosen as it is believed to subsume the terms "overexpression" and "amplification" within its scope for the purposes herein, so that all terms may be considered equivalent to each other as used herein.

[0047] The term "antibody "describes an immunoglobulin whether natural or partly or wholly synthetically produced. The term also covers any polypeptide or protein having a binding domain which is, or is homologous to, an antibody binding domain. CDR grafted antibodies are also contemplated by this term.

[0048] As antibodies can be modified in a number of ways, the term "antibody" should be construed as covering any specific binding member or substance having a binding domain with the required specificity. Thus, this term covers antibody fragments, derivatives, functional equivalents and homologues of antibodies, including any polypeptide comprising an immunoglobulin binding domain, whether natural or wholly or partially synthetic. Chimeric molecules comprising an immunoglobulin binding

domain, or equivalent, fused to another polypeptide are therefore included. Cloning and expression of chimeric antibodies are described in EP-A-0120694 and EP-A-0125023 and U.S. Patent Nos. 4,816,397 and 4,816,567.

[0049] It has been shown that fragments of a whole antibody can perform the function of binding antigens. Examples of binding fragments are (i) the Fab fragment consisting of VL, VH, CL and CHl domains; (ii) the Fd fragment consisting of the VH and CHl domains; (iii) the Fv fragment consisting of the VL and VH domains of a single antibody; (iv) the dAb fragment (Ward, E.S. et al., Nature 341, 544-546 (1989)) which consists of a VH domain; (v) isolated CDR regions; (vi) F(ab')2 fragments, a bivalent fragment comprising two linked Fab fragments (vii) single chain Fv molecules (scFv), wherein a VH domain and a VL domain are linked by a peptide linker which allows the two domains to associate to form an antigen binding site (Bird et al, Science, 242, 423-426, 1988; Huston et al, PNAS USA, 85, 5879-5883, 1988); (viii) multivalent antibody fragments (scFv dimers, trimers and/or tetramers (Power and Hudson, J Immunol. Methods 242: 193-204 9 (2000))(ix) bispecific single chain Fv dimers (PCT/US92/09965) and (x) "diabodies", multivalent or multispecific fragments constructed by gene fusion (WO94/13804; P. Holliger et al Proc. Natl. Acad. Sci. USA 90 6444-6448, (1993)).

[0050] An "antibody combining site" is that structural portion of an antibody molecule comprised of light chain or heavy and light chain variable and hypervariable regions that specifically binds antigen.

[0051] The phrase "antibody molecule" in its various grammatical forms as used herein contemplates both an intact immunoglobulin molecule and an immunologically active portion of an immunoglobulin molecule.

[0052] Exemplary antibody molecules are intact immunoglobulin molecules, substantially intact immunoglobulin molecules and those portions of an immunoglobulin molecule that contains the paratope, including those portions known in the art as Fab,

Fab', F(ab') ₂ and F(v), which portions are preferred for use in the therapeutic methods described herein.

[0053] Antibodies may also be bispecific, wherein one binding domain of the antibody is a specific binding member of the invention, and the other binding domain has a different specificity, e.g. to recruit an effector function or the like. Bispecific antibodies of the present invention include wherein one binding domain of the antibody is a specific binding member of the present invention, including a fragment thereof, and the other binding domain is a distinct antibody or fragment thereof, including that of a distinct anti- EGFR antibody, for instance antibody 528 (U.S. Patent No. 4,943,533), the chimeric and humanized 225 antibody (U.S. Patent No. 4,943,533 and WO/9640210), an anti-de2-7 antibody such as DH8.3 (Hills, D. et al (1995) Int. J. Cancer 63(4):537-543), antibody L8A4 and YlO (Reist, CJ et al (1995) Cancer Res. 55(19):4375-4382; Foulon CF et al. (2000) Cancer Res. 60(16):4453-4460), ICR62 (Modjtahedi H et al (1993) Cell Biophys. Jan- Jun;22(l-3): 129-46; Modjtahedi et al (2002) P.A.A.C.R. 55(14):3140-3148, or the antibody of Wikstrand et al (Wikstrand C. et al (1995) Cancer Res. 55(14):3140-3148). The other binding domain may be an antibody that recognizes or targets a particular cell type, as in a neural or glial cell-specific antibody. In the bispecific antibodies of the present invention the one binding domain of the antibody of the invention may be combined with other binding domains or molecules which recognize particular cell receptors and/or modulate cells in a particular fashion, as for instance an immune modulator (e.g., interleukin(s)), a growth modulator or cytokine (e.g. tumor necrosis factor (TNF), and particularly, the TNF bispecific modality demonstrated in U.S. S.N. 60/355,838 filed February 13, 2002 incorporated herein in its entirety) or a toxin (e.g., ricin) or anti-mitotic or apoptotic agent or factor.

[0054] Fab and F(ab') ₂ portions of antibody molecules may be prepared by the proteolytic reaction of papain and pepsin, respectively, on substantially intact antibody molecules by methods that are well-known. See for example, U.S. Patent No. 4,342,566 to Theofilopolous et al. Fab' antibody molecule portions are also well-known and are produced from F(ab') ₂ portions followed by reduction of the disulfide bonds linking the

two heavy chain portions as with mercaptoethanol, and followed by alkylation of the resulting protein mercaptan with a reagent such as iodoacetamide. An antibody containing intact antibody molecules is preferred herein.

[0055] The phrase "monoclonal antibody" in its various grammatical forms refers to an antibody having only one species of antibody combining site capable of immunoreacting with a particular antigen. A monoclonal antibody thus typically displays a single binding affinity for any antigen with which it immunoreacts. A monoclonal antibody may also contain an antibody molecule having a plurality of antibody combining sites, each immunospecific for a different antigen; e.g., a bispecific (chimeric) monoclonal antibody.

[0056] The term "antigen binding domain" describes the part of an antibody which comprises the area which specifically binds to and is complementary to part or all of an antigen. Where an antigen is large, an antibody may bind to a particular part of the antigen only, which part is termed an epitope. An antigen binding domain may be provided by one or more antibody variable domains. Preferably, an antigen binding domain comprises an antibody light chain variable region (VL) and an antibody heavy chain variable region (VH).

[0057] "Post-translational modification" may encompass any one of or combination of modification(s), including covalent modification, which a protein undergoes after translation is complete and after being released from the ribosome or on the nascent polypeptide cotranslationally. Post-translational modification includes but is not limited to phosphorylation, myristylation, ubiquitination, glycosylation, coenzyme attachment, methylation and acetylation. Post-translational modification can modulate or influence the activity of a protein, its intracellular or extracellular destination, its stability or half- life, and/or its recognition by ligands, receptors or other proteins Post-translational modification can occur in cell organelles, in the nucleus or cytoplasm or extracellularly.

[0058] The term "specific" may be used to refer to the situation in which one member of a specific binding pair will not show any significant binding to molecules other than its

specific binding partner(s). The term is also applicable where e.g. an antigen binding domain is specific for a particular epitope which is carried by a number of antigens, in which case the specific binding member carrying the antigen binding domain will be able to bind to the various antigens carrying the epitope.

[0059] The term "comprise" is generally used in the sense of include, that is to say permitting the presence of one or more features or components.

[0060] The term "consisting essentially of refers to a product, particularly a peptide sequence, of a defined number of residues which is not covalently attached to a larger product. In the case of the peptide of the invention referred to above, those of skill in the art will appreciate that minor modifications to the N- or C- terminal of the peptide may however be contemplated, such as the chemical modification of the terminal to add a protecting group or the like, e.g. the amidation of the C-terminus.

[0061] The term "isolated" refers to the state in which antibodies of the invention, or nucleic acid encoding such antibodies or CDRs thereof will be, in accordance with the present invention. Antibodies and nucleic acid will be free or substantially free of material with which they are naturally associated such as other polypeptides or nucleic acids with which they are found in their natural environment, or the environment in which they are prepared {e.g. cell culture) when such preparation is by recombinant DNA technology practised in vitro or in vivo. Antibodies and nucleic acid may be formulated with diluents or adjuvants and still for practical purposes be isolated - for example the members will normally be mixed with gelatin or other carriers if used to coat microtitre plates for use in immunoassays, or will be mixed with pharmaceutically acceptable carriers or diluents when used in diagnosis or therapy. Antibodies may be glycosylated, either naturally or by systems of heterologous eukaryotic cells, or they may be (for example if produced by expression in a prokaryotic cell) unglycosylated.

[0062] Also, as used herein, the terms "glycosylation" and "glycosylated" includes and encompasses the post-translational modification of proteins, termed glycoproteins, by

addition of oligosaccarides. Oligosaccharides are added at glycosylation sites in glycoproteins, particularly including N-linked oligosaccharides and O-linked oligosaccharides. N-linked oligosaccharides are added to an Asn residue, particularly wherein the Asn residue is in the sequence N-X-S/T, where X cannot be Pro or Asp, and are the most common ones found in glycoproteins. In the biosynthesis of N-linked glycoproteins, a high mannose type oligosaccharide (generally comprised of dolichol, N- Acetylglucosamine, mannose and glucose is first formed in the endoplasmic reticulum (ER). The high mannose type glycoproteins are then transported from the ER to the Golgi, where further processing and modification of the oligosaccharides occurs. O- linked oligosaccharides are added to the hydroxyl group of Ser or Thr residues. In O- linked oligosaccharides, N-Acetylglucosamine is first transferred to the Ser or Thr residue by N-Acetylglucosaminyltransferase in the ER. The protein then moves to the Golgi where further modification and chain elongation occurs. O-linked modifications can occur with the simple addition of the OGIcNAc monosaccharide alone at those Ser or Thr sites which can also under different conditions be phosphorylated rather than glycosylated.

[0063] As used herein, "pg" means picogram, "ng" means nanogram, "ug" or "μg" mean microgram, "mg" means milligram, "ul" or "μl" mean microliter, "ml" means milliliter, "1" means liter.

[0064] The terms "antibody 175", "175 antibody", "mAbl75", and any variants not specifically listed, may be used herein interchangeably, and as used throughout the present application and claims refer to proteinaceous material including single or multiple proteins, and extends to those proteins having the amino acid sequence data described herein and presented in Figure 1 and having or comprising the amino acid sequences as set out in SEQ ID NOs: 1, 2, 3, 4, 5, and/or 6 and the profile of activities set forth herein and in the Claims. Accordingly, proteins displaying substantially equivalent or altered activity are likewise contemplated. These modifications may be deliberate, for example, such as modifications obtained through site-directed mutagenesis, or may be accidental, such as those obtained through mutations in hosts that are producers of the complex or its

named subunits. Also, the terms "antibody 175", "175 antibody" and "mAbl75" are intended to include within their scope proteins specifically recited herein as well as all substantially homologous analogs and allelic variations.

[0065] The amino acid residues described herein are preferred to be in the "L" isomeric form. However, residues in the "D" isomeric form can be substituted for any L-amino acid residue, as long as the desired functional property of immunoglobulin-binding is retained by the polypeptide. NH ₂ refers to the free amino group present at the amino terminus of a polypeptide. COOH refers to the free carboxy group present at the carboxy terminus of a polypeptide. In keeping with standard polypeptide nomenclature, J. Biol. Chem., 243:3552-59 (1969), abbreviations for amino acid residues are shown in the following Table of Correspondence:

[0066] TABLE OF CORRESPONDENCE

SYMBOL AMINO ACID

1 -Letter 3 -Letter

Y Tyr tyrosine

G GIy glycine

F Phe phenylalanine

M Met methionine

A Ala alanine

S Ser serine

I He isoleucine

L Leu leucine

T Thr threonine

V VaI valine

P Pro proline

K Lys lysine

H His histidine

Q GIn glutamine

E GIu glutamic acid

W Trp tryptophan

R Arg arginine

D Asp aspartic acid

N Asn asparagine

C Cys cysteine

[0067] It should be noted that all amino-acid residue sequences are represented herein by formulae whose left and right orientation is in the conventional direction of amino- terminus to carboxy-terminus. Furthermore, it should be noted that a dash at the beginning or end of an amino acid residue sequence indicates a peptide bond to a further sequence of one or more amino-acid residues. The above Table is presented to correlate the three-letter and one-letter notations which may appear alternately herein.

[0068] A "replicon" is any genetic element (e.g., plasmid, chromosome, virus) that functions as an autonomous unit of DNA replication in vivo; i.e., capable of replication under its own control.

[0069] A "vector" is a replicon, such as plasmid, phage or cosmid, to which another DNA segment may be attached so as to bring about the replication of the attached segment.

[0070] A "DNA molecule" refers to the polymeric form of deoxyribonucleotides (adenine, guanine, thymine, or cytosine) in its either single stranded form, or a double- stranded helix. This term refers only to the primary and secondary structure of the molecule, and does not limit it to any particular tertiary forms. Thus, this term includes double-stranded DNA found, inter alia, in linear DNA molecules (e.g., restriction fragments), viruses, plasmids, and chromosomes. In discussing the structure of particular double-stranded DNA molecules, sequences may be described herein according to the normal convention of giving only the sequence in the 5' to 3' direction along the nontranscribed strand of DNA (i.e., the strand having a sequence homologous to the mRNA).

[0071] An "origin of replication" refers to those DNA sequences that participate in DNA synthesis.

[0072] A DNA "coding sequence" is a double-stranded DNA sequence which is transcribed and translated into a polypeptide in vivo when placed under the control of appropriate regulatory sequences. The boundaries of the coding sequence are determined by a start codon at the 5 ¹ (amino) terminus and a translation stop codon at the 3' (carboxyl) terminus. A coding sequence can include, but is not limited to, prokaryotic sequences, cDNA from eukaryotic mRNA, genomic DNA sequences from eukaryotic (e.g., mammalian) DNA, and even synthetic DNA sequences. A polyadenylation signal and transcription termination sequence will usually be located 3' to the coding sequence.

[0073] Transcriptional and translational control sequences are DNA regulatory sequences, such as promoters, enhancers, polyadenylation signals, terminators, and the like, that provide for the expression of a coding sequence in a host cell.

[0074] A "promoter sequence" is a DNA regulatory region capable of binding RNA polymerase in a cell and initiating transcription of a downstream (3 ¹ direction) coding sequence. For purposes of defining the present invention, the promoter sequence is bounded at its 3' terminus by the transcription initiation site and extends upstream (5' direction) to include the minimum number of bases or elements necessary to initiate transcription at levels detectable above background. Within the promoter sequence will be found a transcription initiation site (conveniently defined by mapping with nuclease Sl), as well as protein binding domains (consensus sequences) responsible for the binding of RNA polymerase. Eukaryotic promoters will often, but not always, contain "TATA" boxes and "CAT" boxes. Prokaryotic promoters contain Shine-Dalgarno sequences in addition to the -10 and -35 consensus sequences.

[0075] An "expression control sequence" is a DNA sequence that controls and regulates the transcription and translation of another DNA sequence. A coding sequence is "under

the control" of transcriptional and translational control sequences in a cell when RNA polymerase transcribes the coding sequence into mRNA, which is then translated into the protein encoded by the coding sequence.

[0076] A "signal sequence" can be included before the coding sequence. This sequence encodes a signal peptide, N-terminal to the polypeptide, that communicates to the host cell to direct the polypeptide to the cell surface or secrete the polypeptide into the media, and this signal peptide is clipped off by the host cell before the protein leaves the cell. Signal sequences can be found associated with a variety of proteins native to prokaryotes and eukaryotes.

[0077] The term "oligonucleotide," as used herein in referring to the probe of the present invention, is defined as a molecule comprised of two or more ribonucleotides, preferably more than three. Its exact size will depend upon many factors which, in turn, depend upon the ultimate function and use of the oligonucleotide. The term "primer" as used herein refers to an oligonucleotide, whether occurring naturally as in a purified restriction digest or produced synthetically, which is capable of acting as a point of initiation of synthesis when placed under conditions in which synthesis of a primer extension product, which is complementary to a nucleic acid strand, is induced, i.e., in the presence of nucleotides and an inducing agent such as a DNA polymerase and at a suitable temperature and pH. The primer may be either single-stranded or double-stranded and must be sufficiently long to prime the synthesis of the desired extension product in the presence of the inducing agent. The exact length of the primer will depend upon many factors, including temperature, source of primer and use of the method. For example, for diagnostic applications, depending on the complexity of the target sequence, the oligonucleotide primer typically contains 15-25 or more nucleotides, although it may contain fewer nucleotides. Primers are selected to be "substantially" complementary to different strands of a particular target DNA sequence. This means that the primers must be sufficiently complementary to hybridize with their respective strands. Therefore, the primer sequence need not reflect the exact sequence of the template. For example, a non- complementary nucleotide fragment may be attached to the 5' end of the primer, with the

remainder of the primer sequence being complementary to the strand. Alternatively, non- complementary bases or longer sequences can be interspersed into the primer, provided that the primer sequence has sufficient complementarity with the sequence of the strand to hybridize therewith and thereby form the template for the synthesis of the extension product.

[0078] As used herein, the terms "restriction endonucleases" and "restriction enzymes" refer to bacterial enzymes, each of which cut double-stranded DNA at or near a specific nucleotide sequence.

[0079] A cell has been "transformed" by exogenous or heterologous DNA when such DNA has been introduced inside the cell. The transforming DNA may or may not be integrated (covalently linked) into chromosomal DNA making up the genome of the cell. In prokaryotes, yeast, and mammalian cells for example, the transforming DNA may be maintained on an episomal element such as a plasmid. With respect to eukaryotic cells, a stably transformed cell is one in which the transforming DNA has become integrated into a chromosome so that it is inherited by daughter cells through chromosome replication.

[0080] This stability is demonstrated by the ability of the eukaryotic cell to establish cell lines or clones comprised of a population of daughter cells containing the transforming DNA. A "clone" is a population of cells derived from a single cell or common ancestor by mitosis. A "cell line" is a clone of a primary cell that is capable of stable growth in vitro for many generations.

[0081] Two DNA sequences are "substantially homologous" when at least about 75% (preferably at least about 80%, and most preferably at least about 90 or 95%) of the nucleotides match over the defined length of the DNA sequences. Sequences that are substantially homologous can be identified by comparing the sequences using standard software available in sequence data banks, or in a Southern hybridization experiment under, for example, stringent conditions as defined for that particular system. Defining

appropriate hybridization conditions is within the skill of the art. See, e.g., Maniatis et al., supra; DNA Cloning, VoIs. I & II, supra; Nucleic Acid Hybridization, supra.

[0082] It should be appreciated that also within the scope of the present invention are DNA sequences encoding antibodies of the invention which code for e.g. an antibody having a variable region domain having or comprising the same amino acid sequence as SEQ ID NO: 1, 2, 3, 4, 5, or 6, but which are degenerate to SEQ ID NO: 1, 2, 3, 4, 5, or 6. By "degenerate to" is meant that a different three-letter codon is used to specify a particular amino acid. It is well known in the art that the following codons can be used interchangeably to code for each specific amino acid:

Phenylalanine (Phe or F) UUU or UUC Leucine (Leu or L) UUA or UUG or CUU or CUC or CUA or CUG Isoleucine (He or I) AUU or AUC or AUA Methionine (Met or M) AUG Valine (VaI or V) GUU or GUC ofGUA or GUG Serine (Ser or S) UCU or UCC or UCA or UCG or AGU or AGC Proline (Pro or P) CCU or CCC or CCA or CCG Threonine (Thr or T) ACU or ACC or ACA or ACG Alanine (Ala or A) GCU or GCG or GCA or GCG Tyrosine (Tyr or Y) UAU or UAC Histidine (His or H) CAU or CAC Glutamine (GIn or Q) CAA or CAG Asparagine (Asn or N) AAU or AAC Lysine (Lys or K) AAA or AAG Aspartic Acid (Asp or D) GAU or GAC Glutamic Acid (GIu or E) GAA or GAG Cysteine (Cys or C) UGU or UGC Arginine (Arg or R) CGU or CGC or CGA or CGG or AGA or AGG Glycine (GIy or G) GGU or GGC or GGA or GGG Tryptophan (Trp or W) UGG

Termination codon UAA (ochre) or UAG (amber) or UGA (opal)

[0083] It should be understood that the codons specified above are for RNA sequences. The corresponding codons for DNA have a T substituted for U.

[0084] Mutations can be made in nucleic acid sequences encoding the antibody domains set out herein such that a particular codon is changed to a codon which codes for a different amino acid. Such a mutation is generally made by making the fewest nucleotide changes possible. A substitution mutation of this sort can be made to change an amino acid in the resulting protein in a non-conservative manner (i.e., by changing the codon from an amino acid belonging to a grouping of amino acids having a particular size or characteristic to an amino acid belonging to another grouping) or in a conservative manner (i.e., by changing the codon from an amino acid belonging to a grouping of amino acids having a particular size or characteristic to an amino acid belonging to the same grouping). Such a conservative change generally leads to less change in the structure and function of the resulting protein. A non-conservative change is more likely to alter the structure, activity or function of the resulting protein. The present invention should be considered to include sequences containing conservative changes which do not significantly alter the activity or binding characteristics of the resulting protein.

[0085] The following is one example of various groupings of amino acids:

Amino acids with nonpolar R groups

Alanine, Valine, Leucine, Isoleucine, Proline, Phenylalanine, Tryptophan, Methionine

Amino acids with uncharged polar R groups

Glycine, Serine, Threonine, Cysteine, Tyrosine, Asparagine, Glutamine

Amino acids with charged polar R groups (negatively charged at Ph 6.0) Aspartic acid, Glutamic acid

Basic amino acids (positively charged at pH 6.0) Lysine, Arginine, Histidine (at pH 6.0)

[0086] Another grouping may be those amino acids with phenyl groups: Phenylalanine, Tryptophan, Tyrosine

[0087] Another grouping may be according to molecular weight (i.e., size of R groups):

Glycine 75

Alanine 89

Serine 105

Proline 115

Valine 117

Threonine 119

Cysteine 121

Leucine 131

Isoleucine 131

Asparagine 132

Aspartic acid 133

Glutamine 146

Lysine 146

Glutamic acid 147

Methionine 149

Histidine (at pH 6.0) 155

Phenylalanine 165

Arginine 174

Tyrosine 181

Tryptophan 204

[0088] Particularly preferred substitutions are:

- Lys for Arg and vice versa such that a positive charge may be maintained;

- GIu for Asp and vice versa such that a negative charge may be maintained;

- Ser for Thr such that a free -OH can be maintained; and

- GIn for Asn such that a free NH ₂ can be maintained.

[0089] Amino acid substitutions may also be introduced to substitute an amino acid with a particularly preferable property. For example, a Cys may be introduced a potential site for disulfide bridges with another Cys. A His may be introduced as a particularly "catalytic" site (i.e., His can act as an acid or base and is the most common amino acid in biochemical catalysis). Pro may be introduced because of its particularly planar structure, which induces β-turns in the protein's structure.

[0090] Two amino acid sequences are "substantially homologous" when at least about 70% of the amino acid residues (preferably at least about 80%, and most preferably at least about 90 or 95%) are identical, or represent conservative substitutions.

[0091] A "heterologous" region of the DNA construct is an identifiable segment of DNA within a larger DNA molecule that is not found in association with the larger molecule in nature. Thus, when the heterologous region encodes a mammalian gene, the gene will usually be flanked by DNA that does not flank the mammalian genomic DNA in the genome of the source organism. Another example of a heterologous coding sequence is a construct where the coding sequence itself is not found in nature (e.g., a cDNA where the genomic coding sequence contains introns, or synthetic sequences having codons different than the native gene). Allelic variations or naturally-occurring mutational events do not give rise to a heterologous region of DNA as defined herein.

[0092] The phrase "pharmaceutically acceptable" refers to molecular entities and compositions that are physiologically tolerable and do not typically produce an allergic or similar untoward reaction, such as gastric upset, dizziness and the like, when administered to a human.

[0093] The phrase "therapeutically effective amount" is used herein to mean an amount sufficient to prevent, and preferably reduce by at least about 30 percent, preferably by at

least 50 percent, preferably by at least 70 percent, preferably by at least 80 percent, preferably by at least 90%, a clinically significant change in the growth or progression or mitotic activity of a target cellular mass, group of cancer cells or tumor, or other feature of pathology. For example, the degree of EGFR activation or activity or amount or number of EGFR positive cells, particularly of antibody or binding member reactive or positive cells may be reduced.

[0094] A DNA sequence is "operatively linked" to an expression control sequence when the expression control sequence controls and regulates the transcription and translation of that DNA sequence. The term "operatively linked" includes having an appropriate start signal (e.g., ATG) in front of the DNA sequence to be expressed and maintaining the correct reading frame to permit expression of the DNA sequence under the control of the expression control sequence and production of the desired product encoded by the DNA sequence. If a gene that one desires to insert into a recombinant DNA molecule does not contain an appropriate start signal, such a start signal can be inserted in front of the gene.

[0095] The term "standard hybridization conditions" refers to salt and temperature conditions substantially equivalent to 5 x SSC and 65 ⁰ C for both hybridization and wash. However, one skilled in the art will appreciate that such "standard hybridization conditions" are dependent on particular conditions including the concentration of sodium and magnesium in the buffer, nucleotide sequence length and concentration, percent mismatch, percent formamide, and the like. Also important in the determination of "standard hybridization conditions" is whether the two sequences hybridizing are RNA- RNA, DNA-DNA or RNA-DNA. Such standard hybridization conditions are easily determined by one skilled in the art according to well known formulae, wherein hybridization is typically 10-20 ⁰ C below the predicted or determined T _m with washes of higher stringency, if desired.

B. DETAILED DISCLOSURE.

[0096] The present invention provides a novel antibody 175 or fragment thereof, including immunogenic fragments, which recognizes an EGFR epitope, particularly the EGFR peptide ( ₂₈₇ CGADSYEMEEDGVRKC ₃₀₂ (SEQ ID NO: 14)), which is exposed in tumorigenic, hyperproliferative or abnormal cells wherein the epitope is enhanced, revealed, or evident and not detectable in normal or wild type cells. In a particular but non-limiting embodiment, the antibody recognizes an EGFR epitope which is enhanced or evident upon simple carbohydrate modification or early glycosylation and is reduced or not evident in the presence of complex carbohydrate modification or glycosylation. The antibody or fragment thereof does not bind to or recognize normal or wild type cells containing normal or wild type EGFR epitope in the absence of overexpression, amplification, or a tumorigenic event.

[0097] In a particular aspect of the invention and as stated above, the present inventors have discovered the novel monoclonal antibody 175, which specifically recognize amplified wild type EGFR and the de2-7 EGFR, yet bind to an epitope distinct from the unique junctional peptide of the de2-7 EGFR mutation. Additionally, while mAb 175 does not recognize the normal, wild type EGFR expressed on the cell surface of glioma cells, it does bind to the extracellular domain of the EGFR immobilized on the surface of ELISA plates, indicating a conformational epitope with a polypeptide aspect. Importantly, mAb 175 did not bind significantly to normal tissues such as liver and skin, which express levels of endogenous wt EGFR that are higher than in most other normal tissues, but wherein EGFR is not overexpressed or amplified. Thus, mAb 175 demonstrates novel and useful specificity, recognizing de2-7 EGFR and amplified EGFR, while not recognizing normal, wild type EGFR or the unique junctional peptide which is characteristic of de2-7 EGFR. In a preferred aspect the antibody 175 of the present invention comprises the VH and VL CDR domain amino acid sequences depicted in Figure 1 and in SEQ ID NOs: 1, 2, 3, 4, 5, and 6.

[0098] In another aspect, the invention provides an antibody capable of competing with the 175 antibody, under conditions in which at least 10% of an antibody having the VH and VL sequences of the 175 antibody is blocked from binding to de2-7EGFR by competition with such an antibody in an ELISA assay. As set forth above, anti-idiotype antibodies are contemplated herein.

Diagnostic and Therapeutic Uses

[0099] The unique specificity of the 175 antibodies or fragments thereof, of the present invention, provides diagnostic and therapeutic uses to identify, characterize, target and treat, reduce or eliminate a number of tumorigenic cell types and tumor types, for example head and neck, breast, lung, bladder or prostate tumors and glioma, without the problems associated with normal tissue uptake that may be seen with previously known EGFR antibodies. Thus, cells overexpressing EGFR (e.g. by amplification or expression of a mutant or variant EGFR), particularly those demonstrating aberrant post-translational modification may be recognized, isolated, characterized, targeted and treated or eliminated utilizing the 175 antibody(ies) or fragments thereof of the present invention.

[0100] The antibodies of the present invention can thus specifically categorize the nature of EGFR tumors or tumorigenic cells, by staining or otherwise recognizing those tumors or cells wherein EGFR overexpression, particularly amplification and/or EGFR mutation, particularly de2-7EGFR, is present. Further, the 175 antibodies of the present invention demonstrate significant in vivo anti-tumor activity against tumors containing amplified EGFR and against de2-7 EGFR positive xenografts. In a further aspect of the invention, there is provided a method of treatment of a tumor, a cancerous condition, a precancerous condition, and any condition related to or resulting from hyperproliferative cell growth comprising administration of an antibody 175 of the invention.

[0101] Antibodies of the present invention are designed to be used in methods of diagnosis and treatment of tumors in human or animal subjects, particularly epithelial

tumors. These tumors may be primary or secondary solid tumors of any type including, but not limited to, glioma, breast, lung, prostate, head or neck tumors.

Antibody Generation

[0102] The general methodology for making monoclonal antibodies by hybridomas is well known. Immortal, antibody-producing cell lines can also be created by techniques other than fusion, such as direct transformation of B lymphocytes with oncogenic DNA, or transfection with Epstein-Barr virus. See, e.g., M. Schreier et al., "Hybridoma Techniques" (1980); Hammerling et al., "Monoclonal Antibodies And T-cell Hybridomas" (1981); Kennett et al., "Monoclonal Antibodies" (1980); see also U.S. Patent Nos. 4,341,761; 4,399,121; 4,427,783; 4,444,887; 4,451,570; 4,466,917; 4,472,500; 4,491,632; 4,493,890. Panels of monoclonal antibodies produced against EFGR can be screened for various properties; i.e., isotype, epitope, affinity, etc. Of particular interest are monoclonal antibodies that mimic the activity of EFGR or its subunits. Such monoclonals can be readily identified in specific binding member activity assays. High affinity antibodies are also useful when immunoaffinity purification of native or recombinant specific binding member is possible. A monoclonal antibody useful in practicing the present invention can be produced by initiating a monoclonal hybridoma culture comprising a nutrient medium containing a hybridoma that secretes antibody molecules of the appropriate antigen specificity. The culture is maintained under conditions and for a time period sufficient for the hybridoma to secrete the antibody molecules into the medium. The antibody-containing medium is then collected. The antibody molecules can then be further isolated by well-known techniques.

[0103] Methods for producing monoclonal anti-EGFR antibodies are also well-known in the art. See Niman et al., Proc. Natl. Acad. Sci. USA, 80:4949-4953 (1983). Typically, the EGFR or a peptide analog is used either alone or conjugated to an immunogenic carrier, as the immunogen in the before described procedure for producing anti-EGFR monoclonal antibodies. The hybridomas are screened for the ability to produce an antibody that immunoreacts with the EGFR present in tumorigenic, abnormal or

hyperproliferative cells. Other anti-EGFR antibodies include but are not limited to the HuMAX-EGFr antibody from Genmab/Medarex, the 108 antibody (ATCC HB9764) and U.S. Patent No. 6,217,866, and antibody 14El from Schering AG (U.S. Patent No. 5,942,602).

RecombinantAntibodies, Chimerics, Bispecifics and Fragments

[0104] In general, the CDR regions, comprising amino acid sequences substantially as set out as the CDR regions of SEQ ID NOs: 1, 2, 3, 4, 5, and/or 6 will be carried in a structure which allows for binding of the CDR regions to an tumor antigen. By "substantially as set out" it is meant that that CDR regions of the invention will be either identical or highly homologous to the specified regions of SEQ ID NOs: 1, 2, 3, 4, 5, and/or 6. By "highly homologous" it is contemplated that only a few substitutions, preferably from 1 to 8, preferably from 1 to 5, preferably from 1 to 4, or from 1 to 3 or 1 or 2 substitutions may be made in the CDRs.

[0105] The structure for carrying the CDRs of the invention will generally be of an antibody heavy or light chain sequence or substantial portion thereof in which the CDR regions are located at locations corresponding to the CDR region of naturally occurring VH and VL antibody variable domains encoded by rearranged immunoglobulin genes. The structures and locations of immunoglobulin variable domains may be determined by reference to Kabat, E. A. et al, Sequences of Proteins of Immunological Interest. 4th Edition. US Department of Health and Human Services. 1987, and updates thereof, now available on the Internet (http://immuno.bme.nwu.edu)).

[0106] Preferably, the amino acid sequence substantially as set out as SEQ ID NO: 4, 5, and 6 are carried as the CDR 1 , 2, and 3 in a human heavy chain variable domain or a substantial portion thereof, and the amino acid sequences substantially as set out as SEQ ID NOs: 1, 2, and 3 are carried as the CDRs 1-3 respectively in a human light chain variable domain or a substantial portion thereof.

[0107] The variable domains may be derived from any germline or rearranged human variable domain, or may be a synthetic variable domain based on consensus sequences of known human variable domains. The CDR-derived sequences of the invention, as defined in the preceding paragraph, may be introduced into a repertoire of variable domains lacking CDR regions, using recombinant DNA technology. For example, Marks et al (Bio/Technology, 1992, 10:779-783) describe methods of producing repertoires of antibody variable domains in which consensus primers directed at or adjacent to the 5' end of the variable domain area are used in conjunction with consensus primers to the third framework region of human VH genes to provide a repertoire of VH variable domains lacking one or more CDR. Marks et al further describe how this repertoire may be combined with a CDR of a particular antibody. Using analogous techniques, the CDR-derived sequences of the present invention may be shuffled with repertoires of VH or VL domains lacking one or more CDR, and the shuffled complete VH or VL domains combined with a cognate VL or VH domain to provide antibodies of the invention. The repertoire may then be displayed in a suitable host system such as the phage display system of WO92/01047 so that suitable specific binding members may be selected. A repertoire may consist of from anything from 10 ⁴ individual members upwards, for example from 10 ⁶ to 10 ⁸ or 10 ¹⁰ members. Analogous shuffling or combinatorial techniques are also disclosed by Stemmer (Nature, 1994, 370:389-391), who describes the technique in relation to a β-lactamase gene but observes that the approach may be used for the generation of antibodies.

[0108] A further alternative is to generate novel VH or VL regions carrying the CDR- derived sequences of the invention using random mutagenesis of, for example, nucleic acid encoding the mAbl75 VH or VL CDRs to generate mutations within the domain(s). Such a technique is described by Gram et al (1992, Proc. Natl. Acad. ScL, USA, 89:3576- 3580), who used error-prone PCR. Another method which may be used is to direct mutagenesis to CDR regions of VH or VL genes. Such techniques are disclosed by Barbas et al, (1994, Proc. Natl. Acad. Sd., USA, 91 :3809-3813) and Schier et al (1996, J. MoI. Biol. 263:551-567). All the above described techniques are known as such in the art and in themselves do not form part of the present invention. The skilled person will be

able to use such techniques to provide specific binding members of the invention using routine methodology in the art.

[0109] A substantial portion of an immunoglobulin variable domain will comprise at least the three CDR regions. Additional residues at the N-terminal or C-terminal end of the substantial part of the variable domain may be those not normally associated with naturally occurring variable domain regions. For example, construction of antibodies of the present invention made by recombinant DNA techniques may result in the introduction of N- or C-terminal residues encoded by linkers introduced to facilitate cloning or other manipulation steps. Other manipulation steps include the introduction of linkers to join variable domains of the invention to further protein sequences including immunoglobulin heavy chains, other variable domains (for example in the production of diabodies) or protein labels as discussed in more detail below.

[0110] Although in a preferred aspect of the invention antibodies comprising one or more binding domains based on sequences substantially set out in SEQ ID NOs: 1, 2, 3, 4, 5, and/or 6 are preferred, single binding domains based on either of these sequences form further aspects of the invention. In the case of the binding domain based on the sequence substantially set out in SEQ ID NO:6, or the domains of SEQ ID NOS: 4-6, such binding domain(s) may be used as targeting agents for tumor antigens since it is known that immunoglobulin VH domains are capable of binding target antigens in a specific manner. In the case of either of the single chain specific binding domains, these domains may be used to screen for complementary domains capable of forming a two-domain specific binding member which has in vivo properties as good as or equal to the mAbl75 antibody disclosed herein.

[0111] This may be achieved by phage display screening methods using the so-called hierarchical dual combinatorial approach as disclosed in U.S. Patent 5,969,108 in which an individual colony containing either an H or L chain clone is used to infect a complete library of clones encoding the other chain (L or H) and the resulting two-chain specific

binding member is selected in accordance with phage display techniques such as those described in that reference. This technique is also disclosed in Marks et al, ibid.

[0112] Antibodies of the present invention may further comprise antibody constant regions or parts thereof. For example, antibodies based on SEQ ID NOs: 1-3 may be attached at their C-terminal end to antibody light chain constant domains including human CK or Cλ chains. Similarly, antibodies based on SEQ ID NOs: 4-6 may be attached at their C-terminal end to all or part of an immunoglobulin heavy chain derived from any antibody isotype, e.g. IgG, IgA, IgE, IgD and IgM and any of the isotype subclasses, particularly IgGl, IgG2b, and IgG4.

[0113] The application of molecular engineering to convert murine mAbs into chimeric mAbs (mouse V-region, human C-region) and humanised reagents where only the mAb complementarity-determining regions (CDR) are of murine origin has been critical to the clinical success of mAb therapy. The engineered mAbs have markedly reduced or absent immunogenicity, increased serum half-life and the human Fc portion of the mAb increases the potential to recruit the immune effectors of complement and cytotoxic cells. Investigations into the biodistribution, pharmacokinetics and any induction of an immune response to clinically administered mAbs requires the development of analyses to discriminate between the pharmaceutical and endogenous proteins.

[0114] The antibodies, or any fragments thereof, may also be conjugated or recombinantly fused to any cellular toxin, bacterial or other, e.g. pseudomonas exotoxin, ricin, or diphtheria toxin. The part of the toxin used can be the whole toxin, or any particular domain of the toxin. Such antibody-toxin molecules have successfully been used for targeting and therapy of different kinds of cancers, see e.g. Pastan, Biochim Biophys Acta. 1997 Oct 24; 1333(2):Cl-6; Kreitman et al., N Engl J Med. 2001 JuI 26;345(4):241-7; Schnell et al., Leukemia. 2000 Jan; 14(l):129-35; Ghetie et al., MoI Biotechnol. 2001 JuI; 18(3):251-68.

[0115] Bi- and tri-specific multimers can be formed by association of different scFv molecules and have been designed as cross-linking reagents for T-cell recruitment into tumors (immunotherapy), viral retargeting (gene therapy) and as red blood cell agglutination reagents (immunodiagnostics), see e.g. Todorovska et al., J Immunol Methods. 2001 Feb 1; 248(l-2):47-66; Tomlinson et al., Methods Enzymol. 2000; 326:461-79; McCaIl et al., J Immunol. 2001 May 15; 166(10):6112-7. Fully human antibodies can be prepared by immunizing transgenic mice carrying large portions of the human immunoglobulin heavy and light chains. These mice, examples of such mice are the Xenomouse™ (Abgenix, Inc.) (US Patent Nos. 6,075,181 and 6,150,584), the HuMAb-Mouse™ (Medarex, Inc./GenPharm) (US patent 5545806 and 5569825), the TransChromo Mouse™ (Kirin) and the KM Mouse™ (Medarex/Kirin), are well known within the art. Antibodies can then be prepared by, e.g. standard hybridoma technique or by phage display. These antibodies will then contain only fully human amino acid sequences. Fully human antibodies can also be generated using phage display from human libraries. Phage display may be performed using methods well known to the skilled artisan, as in Hoogenboom et al and Marks et al (Hoogenboom HR and Winter G. (1992) J MoI Biol. 227(2):381-8; Marks JD et al (1991) J MoI Biol. 222(3):581-97; and also U.S. Patents 5885793 and 5969108).

Therapeutic Antibodies and Uses

[0116] The in vivo properties, particularly with regard to tumor:blood ratio and rate of clearance, of antibodies of the invention will be at least comparable to mAbl75. Following administration to a human or animal subject such a specific binding member will show a peak tumor to blood ratio of > 1 :1. Preferably at such a ratio the specific binding member will also have a tumor to organ ratio of greater than 1 :1, preferably greater than 2:1, more preferably greater than 5:1. Preferably at such a ratio the specific binding member will also have an organ to blood ratio of < 1 : 1 in organs away from the site of the tumor. These ratios exclude organs of catabolism and secretion of the administered specific binding member.

[0117] Antibodies of the invention may be labelled with a detectable or functional label. Detectable labels include, but are not limited to, radiolabels such as the isotopes ³ H, C, ³² P, ³⁵ S, ³⁶ Cl, ⁵¹ Cr, ⁵⁷ Co, ⁵⁸ Co, ⁵⁹ Fe, ⁹⁰ Y, ¹²¹ I, ¹²⁴ I, ¹²⁵ 1, ¹³¹ I, ^{1 11} In, ²¹¹ At, ¹⁹⁸ Au, ⁶⁷ Cu, ²²⁵ Ac, ²¹³ Bi, ⁹⁹ Tc and ¹⁸⁶ Re, which may be attached to antibodies of the invention using conventional chemistry known in the art of antibody imaging. Labels also include fluorescent labels and labels used conventionally in the art for MRI-CT imagine. They also include enzyme labels such as horseradish peroxidase. Labels further include chemical moieties such as biotin which may be detected via binding to a specific cognate detectable moiety, e.g. labelled avidin. Functional labels include substances which are designed to be targeted to the site of a tumor to cause destruction of tumor tissue. Such functional labels include cytotoxic drugs such as 5-fluorouracil or ricin and enzymes such as bacterial carboxypeptidase or nitroreductase, which are capable of converting prodrugs into active drugs at the site of a tumor.

[0118] The 175 antibodies and/or their subunits may possess certain diagnostic applications and may for example, be utilized for the purpose of detecting and/or measuring conditions such as cancer, precancerous lesions, conditions related to or resulting from hyperproliferative cell growth or the like. The radiolabeled 175 antibodies and fragments thereof, are useful in in vitro diagnostics techniques and in in vivo radioimaging techniques and in radioimmunotherapy. In the instance of in vivo imaging, the antibodies of the present invention may be conjugated to an imaging agent rather than a radioisotope(s), including but not limited to a magnetic resonance image enhancing agent, wherein for instance an antibody molecule is loaded with a large number of paramagnetic ions through chelating groups. Examples of chelating groups include EDTA, porphyrins, polyamines crown ethers and polyoximes. Examples of paramagnetic ions include gadolinium, iron, manganese, rhenium, europium, lanthanium, holmium and ferbium. In a further aspect of the invention, radiolabeled 175 antibodies and fragments thereof, particularly radioimmunoconjugates, are useful in radioimmunotherapy, particularly as radiolabeled antibodies for cancer therapy. In a still further aspect, the radiolabeled 175 antibodies and fragments thereof, are useful in radioimmuno-guided surgery techniques, wherein they can identify and indicate the

presence and/or location of cancer cells, precancerous cells, tumor cells, and hyperproliferative cells, prior to, during or following surgery to remove such cells. Immunoconjugates or antibody fusion proteins of the present invention, wherein the 175 antibodies and fragments thereof, of the present invention are conjugated or attached to other molecules or agents further include, but are not limited to 175 antibodies conjugated to a chemical ablation agent, toxin, immunomodulator, cytokine, cytotoxic agent, chemotherapeutic agent or drug.

[0119] Radioimmunotherapy (RAIT) has entered the clinic and demonstrated efficacy using various antibody immunoconjugates. ¹³¹ I labeled humanized anti- carcinoembryonic antigen (anti-CEA) antibody hMN-14 has been evaluated in colorectal cancer (Behr TM et al (2002) Cancer 94(4Suppl): 1373-81) and the same antibody with ⁹⁰ Y label has been assessed in medullary thyroid carcinoma (Stein R et al (2002) Cancer 94(1):51-61). Radioimmunotherapy using monoclonal antibodies has also been assessed and reported for non-Hodgkin's lymphoma and pancreatic cancer (Goldenberg DM (2001) Crit Rev Oncol Hematol 39(1-2): 195-201; Gold DV et al (2001) Crit Rev Oncol Hematol 39 (1-2) 147-54). Radioimmunotherapy methods with particular antibodies are also described in U.S. Patent 6,306,393 and 6,331,175. Radioimmunoguided surgery (RIGS) has also entered the clinic and demonstrated efficacy and usefulness, including using anti-CEA antibodies and antibodies directed against tumor-associated antigens (Kim JC et al (2002) Int J Cancer 97(4):542-7; Schneebaum S et al (2001) World J Surg 25(12):1495-8; Avital S et al (2000) Cancer 89(8):1692-8; Mclntosh DG et al (1997) Cancer Biother Radiopharm 12 (4):287-94).

[0120] Antibodies of the present invention may be administered to a patient in need of treatment via any suitable route, usually by injection into the bloodstream or CSF, or directly into the site of the tumor. The precise dose will depend upon a number of factors, including whether the antibody is for diagnosis or for treatment, the size and location of the tumor, the precise nature of the antibody (whether whole antibody, fragment, diabody, etc), and the nature of the detectable or functional label attached to the antibody. Where a radionuclide is used for therapy, a suitable maximum single dose

is about 45 mCi/m ² , to a maximum of about 250 mCi/m ² . Preferable dosage is in the range of 15 to 40 mCi, with a further preferred dosage range of 20 to 30 mCi, or 10 to 30 mCi. Such therapy may require bone marrow or stem cell replacement. A typical antibody dose for either tumor imaging or tumor treatment will be in the range of from 0.5 to 40 mg, preferably from 1 to 4 mg of antibody in F(ab')2 form. Naked antibodies are preferable administered in doses of 20 to 1000 mg protein per dose, or 20 to 500 mg protein per dose, or 20 to 100 mg protein per dose. This is a dose for a single treatment of an adult patient, which may be proportionally adjusted for children and infants, and also adjusted for other antibody formats in proportion to molecular weight. Treatments may be repeated at daily, twice-weekly, weekly or monthly intervals, at the discretion of the physician. These formulations may include a second binding protein, such as the EGFR binding proteins described supra. In an especially preferred form, this second binding protein is a monoclonal antibody such as 528 or 225, discussed infra.

Pharmaceutical and Therapeutic Compositions

[0121] Antibodies of the present invention will usually be administered in the form of a pharmaceutical composition, which may comprise at least one component in addition to the specific binding member. Thus pharmaceutical compositions according to the present invention, and for use in accordance with the present invention, may comprise, in addition to active ingredient, a pharmaceutically acceptable excipient, carrier, buffer, stabiliser or other materials well known to those skilled in the art. Such materials should be non-toxic and should not interfere with the efficacy of the active ingredient. The precise nature of the carrier or other material will depend on the route of administration, which may be oral, or by injection, e.g. intravenous.

[0122] Pharmaceutical compositions for oral administration may be in tablet, capsule, powder or liquid form. A tablet may comprise a solid carrier such as gelatin or an adjuvant. Liquid pharmaceutical compositions generally comprise a liquid carrier such as water, petroleum, animal or vegetable oils, mineral oil or synthetic oil. Physiological

saline solution, dextrose or other saccharide solution or glycols such as ethylene glycol, propylene glycol or polyethylene glycol may be included.

[0123] For intravenous, injection, or injection at the site of affliction, the active ingredient will be in the form of a parenterally acceptable aqueous solution which is pyrogen-free and has suitable pH, isotonicity and stability. Those of relevant skill in the art are well able to prepare suitable solutions using, for example, isotonic vehicles such as Sodium Chloride Injection, Ringer's Injection, Lactated Ringer's Injection. Preservatives, stabilisers, buffers, antioxidants and/or other additives may be included, as required.

[0124] A composition may be administered alone or in combination with other treatments, therapeutics or agents, either simultaneously or sequentially dependent upon the condition to be treated. In addition, the present invention contemplates and includes compositions comprising the binding member, particularly antibody or fragment thereof, herein described and other agents or therapeutics such as anti-cancer agents or therapeutics, hormones, anti-EGFR agents or antibodies, or immune modulators. More generally these anti-cancer agents may be tyrosine kinase inhibitors or phosphorylation cascade inhibitors, post-translational modulators, cell growth or division inhibitors (e.g. anti-mitotics), or signal transduction inhibitors. Other treatments or therapeutics may include the administration of suitable doses of pain relief drugs such as non-steroidal anti -inflammatory drugs (e.g. aspirin, paracetamol, ibuprofen or ketoprofen) or opiates such as morphine, or anti-emetics. The composition can be administered in combination (either sequentially (i.e. before or after) or simultaneously) with tyrosine kinase inhibitors (including, but not limited to AG1478 and ZD1839, STI571, OSI-774, SU-6668), doxorubicin, temozolomide, cisplatin, carboplatin, nitrosoureas, procarbazine, vincristine, hydroxyurea, 5-fluoruracil, cytosine arabinoside, cyclophosphamide, epipodophyllotoxin, carmustine, lomustine, and/or other chemotherapeutic agents. Thus, these agents may be anti-EGFR specific agents, or tyrosine kinase inhibitors such as AG1478, ZDl 839, STI571, OSI-774, or SU-6668 or may be more general anti-cancer and anti-neoplastic agents such as doxorubicin,cisplatin, temozolomide, nitrosoureas, procarbazine, vincristine, hydroxyurea, 5-fluoruracil, cytosine arabinoside, cyclophosphamide,

epipodophyllotoxin, carmustine, or lomustine. In addition, the composition may be administered with hormones such as dexamethasone, immune modulators, such as interleukins, tumor necrosis factor (TNF) or other growth factors or cytokines which stimulate the immune response and reduction or elimination of cancer cells or tumors. An immune modulator such as TNF may be combined together with a member of the invention in the form of a bispecific antibody recognizing the 806 EGFR epitope as well as binding to TNF receptors. The composition may also be administered with, or may include combinations along with other anti-EGFR antibodies, including but not limited to the anti-EGFR antibodies 528, 225, SC-03, DR8.3, L8A4, YlO, ICR62 and ABX-EGF.

[0125] Previously the use of agents such as doxorubicin and cisplatin in conjunction with anti-EGFR antibodies have produced enhanced anti -tumor activity (Fan et al, 1993; Baselga et al, 1993). The combination of doxorubicin and mAb 528 resulted in total eradication of established A431 xenografts, whereas treatment with either agent alone caused only temporary in vivo growth inhibition (Baselga et al, 1993). Likewise, the combination of cisplatin and either mAb 528 or 225 also led to the eradication of well established A431 xenografts, which was not observed when treatment with either agent was used (Fan et al, 1993).

Conventional Radiotherapy

[0126] In addition, the present invention contemplates and includes therapeutic compositions for the use of the antibody in combination with conventional radiotherapy. It has been indicated that treatment with antibodies targeting EGF receptors can enhance the effects of conventional radiotherapy (Milas et al., Clin Cancer Res.2000 Feb: 6(2):701 8, Huang et al., Clin Cancer Res. 2000 Jun: 6(6):2166 74).

[0127] Combinations of the 175 antibody or fragment thereof and anti-cancer therapeutics are contemplated, particularly anti-EGFR therapeutics, including other anti- EGFR antibodies, demonstrate effective therapy, and particularly synergy, against xenografted tumors. The combination of AG 1478 and mAb 175 is such an exemplary

combination. AG 1478 (4-(3-chloroanilino)-6,7-dimethoxyquinazoline) is a potent and selective inhibitor of the EGF receptor kinase and is particularly described in United States Patent No. 5,457,105, incorporated by reference herein in its entirety (see also, Liu, W. et al (1999) J. Cell Sci. 112:2409; Eguchi, S. et al (1998) J. Biol. Chem. 273:8890; Levitsky, A. and Gazit, A. (1995) Science 267:1782). Therapeutic synergy of the 175 antibody with other anti-EGFR antibodies, particularly with the 528 anti-EGFR antibody is anticipated and contemplated.

[0128] The present invention further contemplates therapeutic compositions useful in practicing the therapeutic methods of this invention. A subject therapeutic composition includes, in admixture, a pharmaceutically acceptable excipient (carrier) and one or more antibody 175 or fragment thereof, as described herein as an active ingredient. In a preferred embodiment, the composition comprises an antigen capable of modulating the specific binding of the present binding member/antibody with a target cell.

[0129] The preparation of therapeutic compositions which contain polypeptides, analogs or active fragments as active ingredients is well understood in the art. Typically, such compositions are prepared as iηjectables, either as liquid solutions or suspensions. However, solid forms suitable for solution in, or suspension in, liquid prior to injection can also be prepared. The preparation can also be emulsified. The active therapeutic ingredient is often mixed with excipients which are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients are, for example, water, saline, dextrose, glycerol, ethanol, or the like and combinations thereof. In addition, if desired, the composition can contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents which enhance the effectiveness of the active ingredient. A polypeptide, analog or active fragment can be formulated into the therapeutic composition as neutralized pharmaceutically acceptable salt forms. Pharmaceutically acceptable salts include the acid addition salts (formed with the free amino groups of the polypeptide or antibody molecule) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed from the free

carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, procaine, and the like.

[0130] The therapeutic polypeptide-, analog- or active fragment-containing compositions are conventionally administered intravenously, as by injection of a unit dose, for example. The term "unit dose" when used in reference to a therapeutic composition of the present invention refers to physically discrete units suitable as unitary dosage for humans, each unit containing a predetermined quantity of active material calculated to produce the desired therapeutic effect in association with the required diluent; i.e., carrier, or vehicle.

[0131] The compositions are administered in a manner compatible with the dosage formulation, and in a therapeutically effective amount. The quantity to be administered depends on the subject to be treated, capacity of the subject's immune system to utilize the active ingredient, and degree of EFGR binding capacity desired. Precise amounts of active ingredient required to be administered depend on the judgment of the practitioner and are peculiar to each individual. However, suitable dosages may range from about 0.1 to 20, preferably about 0.5 to about 10, and more preferably one to several, milligrams of active ingredient per kilogram body weight of individual per day and depend on the route of administration. Suitable regimes for initial administration and booster shots are also variable, but are typified by an initial administration followed by repeated doses at one or more hour intervals by a subsequent injection or other administration. Alternatively, continuous intravenous infusion sufficient to maintain concentrations often nanomolar to ten micromolar in the blood are contemplated.

[0132] Pharmaceutical compositions for oral administration may be in tablet, capsule, powder or liquid form. A tablet may comprise a solid carrier such as gelatin or an adjuvant. Liquid pharmaceutical compositions generally comprise a liquid carrier such as water, petroleum, animal or vegetable oils, mineral oil or synthetic oil. Physiological saline solution, dextrose or other saccharide solution or glycols such as ethylene glycol,

propylene glycol or polyethylene glycol may be included. For intravenous, injection, or injection at the site of affliction, the active ingredient will be in the form of a parenterally acceptable aqueous solution which is pyrogen-free and has suitable pH, isotonicity and stability. Those of relevant skill in the art are well able to prepare suitable solutions using, for example, isotonic vehicles such as Sodium Chloride Injection, Ringer's Injection, Lactated Ringer's Injection. Preservatives, stabilisers, buffers, antioxidants and/or other additives may be included, as required.

Diagnostic Assays

[0133] The present invention also relates to a variety of diagnostic applications, including methods for detecting the presence of stimuli such as aberrantly expressed EGFR, by reference to their ability to be recognized by the present 175 antibody. Diagnostic applications of the antibody(ies) of the present invention include in vitro and in vivo applications well known and standard to the skilled artisan and based on the present description. Diagnostic assays and kits for in vitro assessment and evaluation of EGFR status, particularly with regard to aberrant expression of EGFR, may be utilized to diagnose, evaluate and monitor patient samples including those known to have or suspected of having cancer, a precancerous condition, a condition related to hyperproliferative cell growth or from a tumor sample. The assessment and evaluation of EGFR status is also useful in determining the suitability of a patient for a clinical trial of a drug or for the administration of a particular chemotherapeutic agent or specific binding member, particularly an antibody, of the present invention, including combinations thereof, versus a different agent or antibody. This type of diagnostic monitoring and assessment is already in practice utilizing antibodies against the HER2 protein in breast cancer (Hercep Test, Dako Corporation), where the assay is also used to evaluate patients for antibody therapy using Herceptin. In vivo applications include imaging of tumors or assessing cancer status of individuals, including radioimaging.

[0134] As suggested earlier, the diagnostic method of the present invention comprises examining a cellular sample or medium by means of an assay including an effective

amount of an antagonist to an EFGR /protein, such as an anti- EFGR antibody, preferably mAbl75 as provided herein. In addition, it is preferable for the anti- EFGR antibody molecules used herein be in the form of Fab, Fab', F(ab') ₂ or F(v) portions or whole antibody molecules. As previously discussed, patients capable of benefiting from this method include those suffering from cancer, a pre-cancerous lesion, a viral infection, pathologies involving or resulting from hyperproliferative cell growth or other like pathological derangement.

[0135] The presence of EGFR in cells can be ascertained by the usual in vitro or in vivo immunological procedures applicable to such determinations. A number of useful procedures are known. The procedures and their application are all familiar to those skilled in the art and accordingly may be utilized within the scope of the present invention. In such procedures the EGFR forms complexes with one or more antibody(ies) or binding partners and one member of the complex is labeled with a detectable label. The fact that a complex has formed and, if desired, the amount thereof, can be determined by known methods applicable to the detection of labels. The labels most commonly employed for these studies are radioactive elements, enzymes, chemicals which fluoresce when exposed to ultraviolet light, and others. A number of fluorescent materials are known and can be utilized as labels. These include, for example, fluorescein, rhodamine, auramine, Texas Red, AMCA blue and Lucifer Yellow. The EGFR or EGFR antibody 175 can also be labeled with a radioactive element or with an enzyme. The radioactive label can be detected by any of the currently available counting procedures. The preferred isotope may be selected from ³ H, ¹⁴ C, ³² P, ³⁵ S, ³⁶ Cl, ⁵¹ Cr, ⁵⁷ Co, ⁵⁸ Co, ⁵⁹ Fe, ⁹⁰ Y, ¹²¹ I, ¹²⁴ 1, ¹²⁵ 1, ¹³¹ I ₅ ¹¹¹ In, ²¹¹ At, ¹⁹⁸ Au, ⁶⁷ Cu, ²²⁵ Ac, ²¹³ Bi, ⁹⁹ Tc and ¹⁸⁶ Re. Enzyme labels are likewise useful, and can be detected by any of the presently utilized colorimetric, spectrophotometric, fluorospectrophotometric, amperometric or gasometric techniques. The enzyme is conjugated to the selected particle by reaction with bridging molecules such as carbodiimides, diisocyanates, glutaraldehyde and the like. Many enzymes which can be used in these procedures are known and can be utilized. The preferred are peroxidase, β-glucuronidase, β-D-glucosidase, β-D- galactosidase, urease, glucose oxidase plus peroxidase and alkaline phosphatase. U.S.

Patent Nos. 3,654,090; 3,850,752; and 4,016,043 are referred to by way of example for their disclosure of alternate labeling material and methods.

[0136] In a further embodiment of this invention, commercial test kits suitable for use by a medical specialist may be prepared to determine the presence or absence of aberrant expression of EGFR, including but not limited to amplified EGFR and/or an EGFR mutation, in suspected target cells. In accordance with the testing techniques discussed above, one class of such kits will contain at least the labeled EGFR or its binding partner, for instance an antibody specific thereto (antibody 175), and directions, of course, depending upon the method selected, e.g., "competitive," "sandwich," "DASP" and the like. The kits may also contain peripheral reagents such as buffers, stabilizers, etc.

[0137] Accordingly, a test kit may be prepared for the demonstration of the presence or capability of cells for aberrant expression or aberrant forms of EGFR, comprising:

(a) a predetermined amount of at least one labeled immunochemically reactive component obtained by the direct or indirect attachment of the 175 antibody or a specific binding partner thereto, to a detectable label;

(b) other reagents; and

(c) directions for use of said kit.

[0138] In accordance with the above, an assay system for screening potential drugs effective to modulate the activity of the EFGR, or the aberrant expression of EGFR, and/or the activity or binding of the antibody (particularly 175 antibody) may be prepared. The receptor or the antibody may be introduced into a test system, and the prospective drug may also be introduced into the resulting cell culture, and the culture thereafter examined to observe any changes in the S-phase activity of the cells, due either to the addition of the prospective drug alone, or due to the effect of added quantities of the known agent(s).

Nucleic Acids

[0139] The present invention further provides an isolated nucleic acid encoding an antibody 175 of the present invention. Nucleic acid includes DNA and RNA. In a preferred aspect, the present invention provides a nucleic acid which codes for a polypeptide of the invention as defined above, including a polypeptide as set out in SEQ ID NOs: 1, 2, 3, 4, 5, and/or 6. The present invention also provides constructs in the form of plasmids, vectors, transcription or expression cassettes which comprise at least one polynucleotide as above. The present invention also provides a recombinant host cell which comprises one or more constructs as above. A nucleic acid encoding any antibody 175 as provided itself forms an aspect of the present invention, as does a method of production of the antibody which method comprises expression from encoding nucleic acid therefore. Expression may conveniently be achieved by culturing under appropriate conditions recombinant host cells containing the nucleic acid. Following production by expression a specific binding member may be isolated and/or purified using any suitable technique, then used as appropriate.

[0140] Antibodies and encoding nucleic acid molecules and vectors according to the present invention may be provided isolated and/or purified, e.g. from their natural environment, in substantially pure or homogeneous form, or, in the case of nucleic acid, free or substantially free of nucleic acid or genes origin other than the sequence encoding a polypeptide with the required function. Nucleic acid according to the present invention may comprise DNA or RNA and may be wholly or partially synthetic. Systems for cloning and expression of a polypeptide in a variety of different host cells are well known. Suitable host cells include bacteria, mammalian cells, yeast and baculovirus systems. Mammalian cell lines available in the art for expression of a heterologous polypeptide include Chinese hamster ovary cells, HeLa cells, baby hamster kidney cells, NSO mouse melanoma cells and many others. A common, preferred bacterial host is E.coli. The expression of antibodies and antibody fragments in prokaryotic cells such as E.coli is well established in the art. For a review, see for example Plϋckthun, A. Bio/Technology 9: 545-551 (1991). Expression in eukaryotic cells in culture is also

available to those skilled in the art as an option for production of a specific binding member, see for recent reviews, for example Raff, M.E. (1993) Curr. Opinion Biotech. 4: 573-576; Trill JJ. et al. (1995) Curr. Opinion Biotech 6: 553-560. Suitable vectors can be chosen or constructed, containing appropriate regulatory sequences, including promoter sequences, terminator sequences, polyadenylation sequences, enhancer sequences, marker genes and other sequences as appropriate. Vectors may be plasmids, viral e.g. 'phage, or phagemid, as appropriate. For further details see, for example, Molecular Cloning: a Laboratory Manual: 2nd edition, Sambrook et al., 1989, Cold Spring Harbor Laboratory Press. Many known techniques and protocols for manipulation of nucleic acid, for example in preparation of nucleic acid constructs, mutagenesis, sequencing, introduction of DNA into cells and gene expression, and analysis of proteins, are described in detail in Short Protocols in Molecular Biology, Second Edition, Ausubel et al. eds., John Wiley & Sons, 1992. The disclosures of Sambrook et al. and Ausubel et al. are incorporated herein by reference.

[0141] Thus, a further aspect of the present invention provides a host cell containing nucleic acid encoding an antibody as disclosed herein. A still further aspect provides a method comprising introducing such nucleic acid into a host cell. The introduction may employ any available technique. The introduction may be followed by causing or allowing expression from the nucleic acid, e.g. by culturing host cells under conditions for expression of the gene. In one embodiment, the nucleic acid of the invention is integrated into the genome (e.g. chromosome) of the host cell. Integration may be promoted by inclusion of sequences which promote recombination with the genome, in accordance with standard techniques. The present invention also provides a method which comprises using a construct as stated above in an expression system in order to express an antibody or polypeptide as above.

[0142] As stated above, the present invention also relates to a recombinant DNA molecule or cloned gene, or a degenerate variant thereof, which encodes an antibody 175 or a fragment thereof, that possesses an amino acid sequence set forth in SEQ ID NOs: 1, 2, 3, 4, 5, and/or 6; preferably a nucleic acid molecule. As is well known in the art, DNA

sequences may be expressed by operatively linking them to an expression control sequence in an appropriate expression vector and employing that expression vector to transform an appropriate unicellular host.

[0143] In selecting an expression control sequence, a variety of factors will normally be considered. These include, for example, the relative strength of the system, its controllability, and its compatibility with the particular DNA sequence or gene to be expressed, particularly as regards potential secondary structures. Suitable unicellular hosts will be selected by consideration of, e.g., their compatibility with the chosen vector, their secretion characteristics, their ability to fold proteins correctly, and their fermentation requirements, as well as the toxicity to the host of the product encoded by the DNA sequences to be expressed, and the ease of purification of the expression products. Considering these and other factors a person skilled in the art will be able to construct a variety of vector/expression control sequence/host combinations that will express the DNA sequences of this invention on fermentation or in large scale animal culture.

[0144] Analogs, such as fragments, may be produced, for example, by pepsin digestion of antibody peptide(s) or material. Other analogs, such as muteins, can be produced by standard site-directed mutagenesis of specific binding member coding sequences. Analogs exhibiting antibody 175 -like activity such as small molecules, whether functioning as promoters or inhibitors, may be identified by known in vivo and/or in vitro assays. A DNA sequence encoding a 175 antibody can be prepared synthetically rather than cloned. The complete sequence is assembled from overlapping oligonucleotides prepared by standard methods and assembled into a complete coding sequence. See, e.g., Edge, Nature, 292:756 (1981); Nambair et al., Science, 223:1299 (1984); Jay et al., J. Biol. Chem., 259:6311 (1984). Synthetic DNA sequences allow convenient construction of genes which will express specific binding member analogs or "muteins". Alternatively, DNA encoding muteins can be made by site-directed mutagenesis of native specific binding member genes or cDNAs, and muteins can be made directly using conventional polypeptide synthesis. A general method for site-specific incorporation of

unnatural amino acids into proteins is described in Christopher J. Noren, Spencer J. Anthony-Cahill, Michael C. Griffith, Peter G. Schultz, Science, 244:182-188 (April 1989). This method may be used to create analogs with unnatural amino acids.

[0145] The invention may be better understood by reference to the following non-limiting Examples, which are provided as exemplary of the invention. The following examples are presented in order to more fully illustrate the preferred embodiments of the invention and should in no way be construed, however, as limiting the broad scope of the invention.

EXAMPLES

[0146] The invention may be better understood by reference to the following non-limiting Examples, which are provided as exemplary of the invention. The following examples are presented in order to more fully illustrate the preferred embodiments of the invention and should in no way be construed, however, as limiting the broad scope of the invention.

EXAMPLE 1

SUMMARY

[0147] The EGFR exists in two well-defined conformers - tethered and untethered. The tethered conformer, which has only been observed in ligand-free (and partly ligated) forms of the receptor, can be induced by a ligand to form the untethered, back-to-back dimer. mAb806 recognizes an epitope on some truncated, overexpressed or activated forms of the EGFR on the cell surface, but it does not recognize the EGFR on normal unstimulated cells. Another related antibody, mAbl75, also recognizes this unusual epitope. We have determined the 3D-structures of the EGFR ₂₈₇ - ₃₀ 2 peptide epitope bound to Fabs of antibodies mAb806 and mAbl75. In the presence of the antibody, the peptide epitope adopts a conformation very similar to that found in both forms of the receptor. However, binding the mAb806 or mAbl75 antibodies to the wtEGFR structure would be prohibited by significant steric clashes of the Fab with the CRl domain in both the tethered and untethered conformations. Examination of the 3D conformation of the CRl

domain suggested that breaking of a disulfide bond just before the epitope should allow the CRl domain to open up sufficiently to allow binding of either antibodies. The cystine mutant EGFRc _{27 IA/C} 2 _83A not only binds mAb806 and mAbl75, but the stoichiometry is 1 :1 (i.e. equivalent to mAb528 which recognizes the EGFR L2 ligand binding domain). Whereas mAb806 fails to inhibit the in vitro growth of cells expressing wild-type EGFR, mAb806 inhibits completely, ligand associated stimulation of BaF/3 cells expressing EGFRc27iA/C283A- Our results indicate that the mechanisms of binding of antibodies mAb806 and mAbl75 requires a form of the EGFR where the epitope is preferentially exposed either during receptor activation or through truncation or overexpression. Consequently, and in contrast to other EGFR antibodies, mAb806 preferentially localizes to the tumor in cancer patients overexpressing the EGFR. The mechanism of action suggests new approaches to the generation of antibodies for detection of tumors and for improving antibody/inhibitor killing of cancer cells with over-expressed, truncated or activated forms of receptors in the EGFR family

SIGNIFICANCE

[0148] The EGFR is involved in stimulating the growth of many human tumors. Although inhibitiors and antagonists have been used as therapeutic agents, success has been limited, in part by interfering with the EGFR on normal tissues and in part by the limited temporal action of some of the agents, ie Abs have longer action. The antibodies Mab806 and Mabl75 recognize an unusual conformation of the receptor, which often occurs on tumor cells, but not normal cells. The three dimensional binding site of these antibodies on the EGFR identifies the unusual conformation which explains their tumor specificity. These antibodies synergize with other anti-EGFR agents to induce profound tumor killing in mice. The intitial results in cancer patients using radiolabeled forms of the antibodies confirm the tumor selectivity.

INTRODUCTION

[0149] Understanding the activation of the EGFR by its family of ligands has been challenging but elegant genetic(i-J), biophysical(4-S) and more recently, crystallographic(P-77) studies have revealed many of the complex series of

conformational changes and aggregation events required to activate the EGFR intracellular tyrosine kinase domεάn(18). Amidst these complexities it is apparent that in solution the EGFR extracellular domain adopts at least two fundamental conformations: an inactive tethered conformation and an active untethered or extended, ligand-bound "back-to-back" dimer. The EGFR was the first growth factor receptor to be associated with cancer (19;20). The EGFR is activated by autocrine ligands(i 9;21;22) and, in a high proportion of advanced gliomas, the EGFR receptor extracellular domain is truncated(23;24) and consequentially activated. Often the activation of the EGFR is required for the maintenance of the malignant state. Conversely, except for a small number of cells in hair follicles and Brunner's gland, in adult organisms the EGFR is expressed at low levels and is inactive in adult life.

[0150] Two major classes of agents have been developed to target the EGFR: tyrosine kinase inhibitors (TKI' s) and monoclonal antibodies (mAb's). TKFs such as gefitinib (ZD 1839) and erlotinib (OSI-774) competitively bind to the ATP pocket of EGFR to inhibit its activation. In contrast, antibodies against EGFR, such as cetuximab (C225) and panitumumab (ABX-EGFR) competitively inhibit ligand binding and thereby prevent receptor activation. Both classes of the inhibitors and antibodies display significant antitumor activity in a range of EGFR-dependant mouse xenograft models(25-29) and both have been approved in select cancers including NSCL, pancreatic, head & neck and colon (30-32). While response rates to these EGFR therapeutics are modest, it is hoped that successful identification of patient sub-sets likely to respond to EGFR blockade will be able to improve on outcomes for the patients. In glioma for example, response to Tarceva appears largely restricted to a sub-set of patients who are double positive for δ2- 7EGFR (also called EGFRvIII), the extra-cellular truncation of the EGFR commonly expressed in glioma, and PTEN (33). While these therapeutics show promise, their use is restricted by dose limiting toxicities such as skin rash, which results from significant uptake of these agents in normal skin where EGFR expression is significant.

[0151] Many gliomas over-express EGεR(23;34), predominantly due to amplification of the EGFR gene. EGFR gene amplification in glioma is also associated with a mutation

event that leads to the excision of exons 2-7 (34) and the subsequent expression of a truncated, partially activated δ2-7 EGFR form of the EGFR(J5;5<5) mentioned above. The δ2-7 EGFR contains a unique fusion peptide at the N-terminus resulting from the splicing together of exons 1 and 8 and the insertion of an unique glycine. Several monoclonal antibodies directed to this junctional peptide have been described (34) and therefore represent potential therapeutics specific for the δ2-7 EGFR. We generated a panel of δ2-7 EGFR specific antibodies using NR6 cells (as variant of 3T3 devoid of endogenous EGFR family member) over-expressing this truncated EGFR. While showing robust binding to the δ2-7 EGFR, some of these antibodies also bind wtEGFR when over-expressed but not when it was expressed at physiological levels. The best described of these antibodies MAb806 (35; 37; 38), appears not to bind cells expressing less than 1 x 10 ⁵ EGFR on their surface, but only where higher expression levels lead to a distinct population of mAb806 reactive EGFR (5-10% of the total receptor population) (35,37,38).

[0152] Subsequent epitope mapping studies have shown that mAb806 binds to a short cysteine loop between amino acids 287-302 on the extracellular domain that is only exposed transiently as the EGFR moves from the tethered to the extended conformation (23,28). Thus, mAb806 reactivity is found only in cells with favorable conditions for receptor untethering, such as the presence of mutations (e.g. δ2-7 EGFR), over- expression or activation of the receptor. In the case of EGFR over-expression, there appears to be increased untethering as a result of both ligand-independent EGFR activation and changes in glycosylation(iP). These conditions are common in tumour cells but are rare in normal tissues, thereby allowing mAb806 to preferentially target tumour cells over normal tissues, such as the liver. Indeed, the results from our recently completed Phase I clinical trial with a chimeric version of mAb806 demonstrates that the epitope targeted by this antibody is not exposed on normal tissue but is accessible on a range of EGFR positive tumoτs(28;40). In xenografts mAb806 has shown robust antitumor activity against U87MG glioma cells expressing the δ2-7 EGFR, as well as a range of other models that over-express the wtEGFR in absence of the this mutaύon(28; 40). Furthermore, mAb806 shows synergistic anti-tumor activity in animal

models when used in combination with other EGFR therapeutics, including EGFR kinase inhibitors(27) and antibodies(47). with unrelated epitopes

[0153] The EGFR amino acid sequence between cysteine residues 287 and 302 is sufficient for the binding mAb806. However, while the truncation found in the δ2-7 EGFR clearly exposes this cysteine loop for binding by mAb806, the mechanism of mAb806- wtEGFR binding has only been partially resolved. The crystal structure of the EGFR has been solved for both the full length extracellular domain and EGFR-ECDi _-5 Oi fragment bound to ligand. Analysis of these structures make it evident that mAb806 could not bind to either the tethered EGFR as observed in the full length ECD structure(ii) or to the ligand-bound, untethered, back-to-back dimer seen with the EGFR-ECD _I-50I (74) or EGFR-ECD _1-62I (42) constructs. Therefore, we have proposed that mAb806 binds to a partially untethered form of the wtEGFR that exist between the inactive and active states. The inability of mAb806 to bind to the ligated, untethered EGFR was further confirmed by pre-incubating wtEGFR expressing BaF/3 cells with EGF under conditions that prevented receptor internalization. Under these conditions a larger percentage of the EGFR should form ligated back-to-back dimers, thus preventing mAb806 binding; an observation that was clearly confirmed(43). However, the effect of ligand on mAb806 binding in a steady state, such as might occur in cells with a robust EGFR/ligand autocrine loop, is unknown. Interestingly, while binding of mAb806 to cell surface wtEGFR is dependant on the conformation of the receptor, in the immunological sense, the epitope is not conformational as mAb806 is an excellent probe for EGFR in Western blots, i.e. it is capable of recognizing the denatured receptor. Clearly, accessibility to the epitope as determined by EGFR conformation, is the most critical factor with respect to mAb806 binding, not the conformation of the epitope itself. MAb806 also binds to EGFR immobilized on plastic and surface plasmon resonance chips(57).

[0154] In this report we also describe the biological activity, specificity and epitope of other antibodies, raised in the same manner as mAb806. In order to understand the unique specificity of these antibodies we determined the 3D structures for the mAb806

peptide epitope (EGFR _287-3O2 ) bound to the Fab fragment of mAb806 and mAbl75 and the free Fab fragments. The orientation OfEGFR _287-302 on the receptor and the conformation of this peptide bound to antibody confirmed that mAb806 must bind a specific form of the EGFR and that this form must be folded differently to the wtEGFR observed in either the tethered or extended conformation. Using point mutations we examine the influence of an adjacent cysteine loop (amino acids 271-283) on EGFR structure and mAb806/175 reactivity as this loop appears to severely restrict binding of these antibodies. We report the efficacy of mAb806 and 175 against DU 145 xenografts, a prostate cell line that possesses a robust TGF-α/EGFR autocrine stimulation loop, and the binding of radiolabeled-mAb806 to a head and neck cancer patient being treated in a Phase I setting(¥4).

RESULTS mAbl75 specificity

[0155] Preliminary binding studies suggested that mAbl75 displayed similar specificity for EGFR as mAb806. In the CDR regions of mAb806 (IgG2b) and maB175 (IgGl), the amino acid sequences are almost identical, with only one amino acid difference in each

(Figure 1). All these differences preserve the charge and size of the side-chains. Clearly, these antibodies have arisen independently.

[0156] We conducted a set of immunohistochemistry experiments to analyze the specificity of mAbl75 binding. mAbl75 stains sections of A431 xenografts that over- express the EGFR (Figure 2A) and sections of U87MG.δ2-7 glioma xenografts that express the δ2-7EGFR (Figure 2A). In contrast, mAbl75 does not stain U87MG xenograft sections. The U87MG cell line only expresses modest levels of the wild type EGFR (Figure IA) and has no detectable EGFR autocrine loop. Most importantly, mAbl75 does not bind to normal human liver sections (Figure 2B). Thus, mAbl75 appears to demonstrate the same specificity as mAb806: i.e. it detects over-expressed and truncated human EGFR, but not the wtEGFR expressed at modest levels.

Identification of the mAbl75 epitope

[0157] Since mAbl75 also binds the δ2-7EGFR, in which amino acids 6-273 are deleted, and EGFRi- _501, the mAbl75 epitope must be contained within residues 274-501. When determining the epitope of mAb806, we expressed a series of c-myc-tagged EGFR fragments fused to the carboxy terminus of human GH, all terminating at amino acid 50l(45;46). The mAbl75 also reacted with both the 274-501 and 282-501 EGFR fragments in Western blots, but did not detect fragments commencing at amino acid 290 or 298 (Supplemental Figure 9). The presence of all GH-EGFR fusion proteins was confirmed using the c-myc antibody, 9E10 (Supplemental Figure 9). Therefore, a critical determinant of the mAbl75 epitope is located near amino acid 290. Finally, a 274-501 EGFR fragment with the mAb806 epitope deleted (δ287-302) was also negative for mAbl75 binding (Figure 9), suggesting that this region similarly determined most of the mAbl75 binding.

[0158] We used a second approach to characterize the mAbl75 epitope further. Fragments encompassing extracellular domains of the EGFR were expressed on the surface of yeast and tested for mAbl75 binding by indirect immunofluorescence using flow cytometry. The mAbl75 recognized the yeast fragment 273-621, which corresponds to the extracellular domain of the δ2-7 EGFR, but not to fragments 1-176, 1- 294, 294-543 or 475-621 (Figure 3A and 3B). Thus, at least part of the mAbl75 epitope must be contained within the region between amino acids 274-294, agreeing with our immunoblotting data using EGFR fragments. Since mAbl75 binds to the denatured fragment of the 273-621 ( Figure 3C), the epitope must be linear in nature (Supplemental Figure 9). It is clear that mAb 806 and mAbl75 recognize a similar region and conformation of the EGFR.

[0159] Using surface plasmon resonance (BIAcore) we investigated the binding of mAbl 75 to the EGFR peptide (2 ₈₇ CGADSYEMEEDGVRKC ₃₀₂ (SEQ ID NO: 14)). The EGFR287-302 was immobilized on the biosensor surface using amine, thiol-disulfide exchange or Pms-Ser coupling chemistries. The latter method immobilizes the peptide exclusively through the N-terminal cysteine(¥7). mAb 175 bound the EGFR _28T-302 in all

orientations (Table 1). The affinity of mAbl75 for EGFR _2S7-302 ranged from 35 nM for Pms-serine coupling to 154 nM for amine coupling. In all cases the binding affinity of mAbl75 for EGFR _287-302 was lower than that obtained for mAb806 (Table 1). We also determined the affinity of mAbl75 to two different extracellular fragments of the EGFR. mAbl75 bound the 1-501 fragment with an affinity similar to that obtained using the peptide (16 nM versus 35 nM) (Table 1). As expected, the affinity of mAbl75 against the 1-621 full length extracellular domain, which can form the tethered conformation, was much lower (188 nM). Although mAb806 and mAb 175 have similar affinities for EGFR _287-302 , mAb 175 appears to display a higher affinity for the extra-cellular domain of the EGFR (Table 1). Clearly, the mAb 175 epitope is contained within the EGFR _287-302 and, like mAb806, the binding affinity to extra-cellular domain of the EGFR is dependent on conformation.

[0160] Table 1: BIAcore determination of antibody affinities for mAb806 and mAbl75 binding to EGFR epitopes

[0161] The panel of mutants of the 273-621 EGFR fragment, expressed on the surface of yeast (45; 46), was used to characterize the fine structure of the mAb 175 epitope. mAb 175 and mAb806 displayed a near identical pattern of reactivity to the mutants (Table 2). Disruption of the 287-302 disulfide bond only had a moderate effect on the epitope reactivity as the antibody bound to all mutants at C287 and to some but not all mutants at C302 (Table 2). Amino acids critical for mAb 175 binding include E293,

G298, V299, R300 and C302 (Table 2). mAbl75 appeared moderately more sensitive to mutations V299 and D297 but mAb806 also showed reduced binding to some mutations at these sites (Table 2). Again, the mAbl75 epitope appears to be essentially the same as the epitope recognized by mAb806.

[0162] Table 2: Display of EGFR Epitope 287-302 mutations on yeast and the binding scores for mAb806 and mAbl75

Efficacy of mAbl75 against tumor xenografts stimulated by δ2-7EGFR or an EGFR autocrine loop.

[0163] We examined the in vivo anti-tumor activity of mAb806 and mAbl75 against U87MG.δ2-7 glioma xenografts. Xenografts were allowed to establish for 6 days before antibody therapy (3 times a week for 2 weeks on days indicated) commenced. At this time the average tumor volume was 100 mm ³ (Figure 4A). mAbl75 treatment resulted in a reduction in overall tumor growth rate compared to treatment with vehicle or mAb806 and was highly significant at day 19 post-inoculation (P < 0.0001 versus control and P < 0.002 versus ma 806), when the control group was sacrificed for ethical reasons. The average tumor volume at this time was 1530, 300 and 100 mm ³ for the vehicle, mAb806 and mAbl75 treatment groups, respectively (Figure 4A), confirming mAbl75 is antitumor activity against xenografts expressing the δ2-7 EGFR.

[0164] Even though U87MG cells express approximately I X lO ⁵ EGFR per cell, mAb 806 is not able to recognize any of the surface EGFR, and not surprisingly, does not inhibit U87MG in vivo growth. Furthermore these cells do not co-express any EGFR

ligand. To test whether the EGFR epitope is transiently exposed and hence able to be recognized by mAb806 and mAbl75 in cells containing an EGFR autocrine loop. The prostate cell line DU 145 expresses the wtEGFR at levels similar to that observed in U87MG cells, however unlike the U87MG cells, the DU 145 cells contain an amplification of the TGF-α gene and thus exhibit an EGFR/TGF-α autocrine loop. Both mAbl75 and 806 bind to DU145 cells as determined by FACS analysis (Figure 4B) and both are able to immunoprecipitate a small proportion of the EGFR extracted from these cells (Figure 4C). Both techniques showed greater binding of mAbl75, however, when compared to mAb 528, which binds to the L2 domain, mAbl75 and mAb806 only bind a subset of EGFR on the surface of these cells (Figure 4B and 4C). Similar observations were seen with a second prostate cell line (LnCap); (data not shown) and a colon line (LIM1215) both of which also contain EGFR autocrine loops(22;48). Clearly, mAb806 and mAb 175 can recognize only a small proportion of the EGFR on cells in the presence of an autocrine stimulation loop.

[0165] Since mAb 175 and mAb806 bind more effectively to the EGFR expressed in DU 145 cells than U87MG cells, we conducted a study to analyse the anti -tumor activity of these antibodies in DU 145 xenografts grown in nude mice. Xenografts were allowed to establish for 18 days before therapy commenced (3 times a week for 3 weeks on days indicated). At this time the average tumor volume was 90 mm ³ (Figure 4D). Both mAb 175 and mAb806 inhibited the growth of DU 145 xenografts. The control group was sacrificed on day 67 and had a mean tumor volume of 1145 mm ³ compared with 605 and 815 mm ³ for the mAb806 and mAb 175 groups respectively (p < 0.007 and 0.02 respectively) (Figure 4D).

3D-Structure of EGFR2 ₈ 7- ₃₀ 2 in contact with the Fab fragments of mAb806 and mAbl75

[0166] In order to understand the molecular details of how mAb806 and mAbl75 could recognise EGFR in some, but not all conformations, the crystal structures of Fab fragments for both antibodies were determined in complex with the oxidized EGFR ₂₈₇ . ₃ o ₂ epitope (at 2.0 and 1.59 A resolution respectively, Figures 5 A & 5B) and alone (at 2.3 A

and 2.8 A resolution, respectively). In both cases, the free and complexed Fab structures were essentially the same and the conformations of the peptide and CDR loops of the antibodies were well defined (Figure 5). The epitope adopts a β-ribbon structure, with one edge of the ribbon pointing towards the Fab and V299 buried at the centre of the antigen-binding site (Figure 5C-E). Both ends of the epitope are exposed to solvent, consistent with these antibodies binding much longer polypeptides.

[0167] Of the 20 antibody residues in contact with the epitope, there are only two substitutions between mAb806 and mAbl75 (Figure 1). mAbl75 contact residues are: light-chain S30, S31, N32, Y49, H50, Y91, F94, W96 and heavy-chain D32, Y33, A34, Y51, S53, Y54, S55, N57, R59, A99, GlOO, RlOl; the mAb806 contact residues are the same, with sequence differences for the light-chain, N30 and heavy-chain, F33. EGFR ₂ 87- ₃ o2 binds to the Fab through close contacts between peptide residues 293-302, with most of the contacts being between residues 297 and 302. The only hydrogen bonds between main chain atoms OfEGFR _287-302 and the Fab are for residues 300 and 302 (Figure 5F). Recognition of the epitope sequence occurs through side-chain hydrogen bonds to residues E293 (to H50 and RlOl of the Fab), D297 (to Y51 and N57), R300 (to D32) and K301 (via water molecules to Y51 and W96). Hydrophobic contacts are made at G298, V299 and C302.

[0168] The conformation of the epitope backbone between 293 and 302 was essentially identical in the Fab806 and Fab 175 crystals (rms deviation = 0.4 A, for Ca atoms in these residues). Although constrained by the disulfide bond, the N-terminus of the peptide (287-292) does not make significant contact in either antibody structure and conformations in this region differ. However, this segment in the Fab806 complex appears rather disordered. More interestingly, the conformation of the EGFR _287-302 peptide in contact with the antibodies is quite closely related to the EGFR _287-3O2 conformation observed in the backbone of the tethered or untethered EGFR structures (Li et al., 2005; Garrett et al., 2002). For EGFR _287-302 from the Fabl75 complex, the rms deviations in Ca positions are 0.66 and 0.75 A, respectively (Figure 5).

[0169] To gain further insight into the recognition of EGFR by mAb806 and mAbl75, the conformation of ¹⁵ N labelled oxidized peptide EGFR2 ₈ 7- ₃ 02 was studied by NMR spectroscopy in solution, free and in the presence of 806 Fab (see Supplemental Data for details). For the free peptide, resonances were assigned and compared to those for random coil. Essentially, the free peptide adopted a random coil structure, not the beta ribbon as seen in the native EGFR(14). Upon addition of the Fab, resonance shifts were observed. However, due to the weak signal arising from significant line broadening upon addition of the Fab and successful crystallisation of the complexes, the solution structure of the Fab806-epitope complex was not pursued further. Clearly though, when the peptide binds to the Fab fragment of mAb806 (or mAbl75) it appears that the Fab selects or induces the conformation of the peptide which matches that peptide in the native receptor.

[0170] Why do mAb806 and mAbl75 recognise only some conformations of EGFR? We docked the Fab fragment of mAbl75 onto an extra-cellular domain of EGFR (tethered and untethered monomers) by superimposing EGFR2 ₈₇ - ₃₀ 2- For a δ2-7-like fragment there were no significant steric clashes with the receptor. In the untethered form there was substantially more accessible surface area of the Fab buried (920 A ² compared with 550 A ² in the tethered form). Therefore, this antigen may make additional contacts with non-CDR regions of the antibody, as has been indicated by yeast expression mutants(45). Conversely, docking the whole EGFR ectodomain onto the Fab, there is substantial spatial overlap with the part of the CRl domain preceding the epitope (residues 187-286) and running through the centre of the Fab (Figure SD, E). Hence, as the CRl domain has essentially the same structure in tethered or untethered conformations, mAb806 or mAbl 75 will be unable to bind to either form of EGFR. Clearly, there must be a difference between the orientation of the epitope with respect to the CRl domain in either known conformations of the wtEGFR and the orientation that permits epitope binding. Inspection of the CRl domain indicated that the disulfide bond (271-283) preceding EGFR2 ₈₇ - ₃₀₂ constrains the polypeptide which blocks access to the epitope; disruption of this disulfide, even though it is not involved in direct binding to the antibodies, would be

expected to allow partial unfolding of the CRl domain so that mAbl75 or mAb806 could gain access to the epitope.

Breaking of the EGFR 271-283 disulfide bond increases mAb806 binding [0171] Disulfide bonds in proteins provide increased structural rigidity but in some cell surface receptors, particularly those for cytokines and growth factors, transient breaking of disulfide bonds and disulfide exchange can control the receptor's function(4P). As this was one mechanism by which mAb806 and mAbl75 could gain access to their binding site, we attempted to increase the accessibility of the epitope by mutating either or both of the cysteine residues at positions 271 and 283 to alanine residues (C271 A/C283A). The vectors capable of expressing full length C271 A-, C283A- or C271 A/C283A- EGFR were transfected into the IL-3 dependent Ba/F3 cell line. Stable Ba/F3 clones, which expressed the C271 A- and C271 A/C283A- EGFR mutant at levels equivalent to the wtEGFR were selected (Figure 6A). Ba/F3 cells expressing high levels of mutant C283 A-EGFR were not observed. As previously described, the wtEGFR reacts poorly with mAb806; however, the mutant receptors reacted equally strongly with mAb528, mAb806 and the anti-FLAG antibody, suggesting that the receptor is expressed at the cell surface, is folded correctly and that the epitope for mAb806 is completely accessible in such cases. To confirm that mAb806 recognizes the C271 A/C283A mutant more efficiently than the wtEGFR, we determined the ratio of mAb806 binding to the binding of mAb528. Since both the wt and C271 A/C283A EGFR were N-terminally FLAG- tagged, we also determined the ratio of mAb806 and mAb528 binding to the M2 antibody. As reported previously, mAb806 only recognized a small proportion of the total wtEGFR expressed on the surface of Ba/F3 cells (the mAb806/528 binding ratio is 0.08) (Table 3). In contrast, mAb806 recognized virtually all of the C271 A/C283A mutant EGFR expressed on the cell surface (an mAb806/528 binding ratio of 1.01) (Figure 6 A and Table 3).

[0172] Table 3: mAb806 reactivity with cells expressing the wt or C271 A/C283A EGFR

* Average of four independent clones .

[0173] Mutation of the two cysteines did not compromise EGF binding or receptor function. BaF3 cells expressing the C271 A/C283 A EGFR mutant proliferate in the presence of EGF (Figure 6B). We have reproducibly observed a left-shift in the dose response curve for EGF in cells expressing the C271 A/C283A mutations, suggesting either higher affinity for the ligand, or enhanced signaling potential for the mutant receptor. Western blotting analysis confirmed that the C271 A/C283A mutant is expressed at similar levels to the wtEGFR and is tyrosine phosphorylated in response to EGF stimulation (Figure 6C). Consistent with previous studies in other cell lines, mAb806 has no effect on the in vitro EGF-induced proliferation of Ba/F3 cells expressing the wtEGFR, while the ligand blocking mAb 528 completely inhibits the EGF-induced proliferation of these cells (Figure 6D, left panel). In contrast, mAb806 totally ablated the EGF-induced proliferation in BaF3 cells expressing the C271/283A mutant (Figure 6D, right panel). When the 271-283 cysteine loop is disrupted, not only does mAb806 bind more effectively, but once bound, mAb806 prevents ligand induced proliferation.

Phase I Imaging study in Head and Neck Cancer

[0174] Eight patients [1 female and 7 male; mean age of 61 years (range 44-75)] completed this phase 1 trial as reported (44). All patients fulfilled inclusion criteria and, except for Patient 8 (who had a primary brain tumor), all had metastatic disease at study entry. Ab uptake by the tumor was seen in all patients, and ' ' 'ln-ch806, the chermerized version of mAb806, demonstrated prompt and high level uptake in tumor (Figure 7). The clearance of ^{i π} In-ch806 from normal organs (liver, lungs, kidney and spleen) showed no

difference between dose levels(44). In particular, liver clearance showed no difference between dose levels, indicating no saturable antigen compartment in the liver for ch806. Total liver uptake was a maximum of 14.45 ± 2.43 %ID immediately post infusion, and declined to 8.45 ± 1.63 %ID by 72 hours, and 3.18 ± 0.87 %ID by one week post infusion. This is in marked contrast to the uptake of antibodies to wtEGFR (eg 225), which have been shown to reach over 30 %ID in liver (for a 40mg dose) for over 3 days post infusion(50).

[0175] The measured peak tumor uptake of ^{π i} In-ch806 occurred 5-7 days post infusion. Calculation of quantitative tumor uptake in Patients 1 and 3 could not be accurately performed due to proximity of target lesion to cardiac blood pool and patient movement. Peak ch806 uptake in tumor ranged from 5.21 to 13.73 x 10 ^'3 %ID/gm tumor tissue. Calculation of actual ch806 concentration in tumor showed peak values of (mean ± SD) 0.85 ± 0 μg/gm (5mg/m ² ), 0.92 ± 0 μg/gm (lOmg/m ² ), 3.80 ± l.lOμg/gm (20mg/m ² ), and 7.05 ± 1.40μg/gm (40mg/m ² ).

DISCUSSION

[0176] When the levels or activity of the EGFR or the related erbB2 are perturbed, antibodies such as cetuximab and herceptin, that target EGFR family members, are important options for treating cancer. Determining the binding sites for these antibodies, the 3D-structures of both the target receptors and more recently, the antibody :receptor complexes, has improved our understanding of how these antibodies interfere with receptor activation. These studies have also suggested that targeting other epitopes on this receptor family may produce a new opportunities for using combinations of antibodies to improve cancer treatment.

[0177] Unfortunately, all of the currently available therapeutic anti-EGFR antibodies recognize the wtEGFR, which is expressed in virtually all normal tissues. Not only do the EGFR expressed in normal tissues represent a large sink for the antibodies, they are likely to be critical in the dose limiting toxicity (such as skin rash) observed and make use of antibody/cytotoxic conjugates impossible. Despite these problems, it should be

noted that most normal tissues appear to lack activated EGFR, thus neutralizing anti- EGFR antibodies appear not have a profound effect on vital homeostatic signaling. In contrast, many tumors contain activated EGFR, either through autocrine/paracrine mechanisms, truncation, mutation, gene amplification and/or over-expression. Importantly, activated EGFR seems to contribute to tumorgenicity by enhancing cell movement, proliferation, invasion, angiogenesis and survival of tumour cells. Consequently, the administration of anti-EGFR antibodies or EGFR kinase inhibitors can decrease the growth and survival of the tumor cells. Antibodies directed to the unique junctional peptide in the δ2-7 EGFR have the potential to target several tumors(57) without the difficulties associated with normal tissue uptake. In glioma, the expression of the δ2-7 EGFR is accompanied by over-expression of the wtEGFR which would not be inhibited by other δ2-7 EGFR antibodies, but should be inhibited by mAb806 or mAbl75.

[0178] Previously, we described an antibody, mAb806, which was raised against cells expressing δ2-7 EGFR. Not only does mAb806 bind this truncated receptor, but also binds to over-expressed wtEGFR. Mab806 recognizes an epitope contained within a cysteine loop (amino acids 287-302) that is accessible in the δ2-7 EGFR, but not in the wtEGFR when expressed at low to moderate levels on cells and in the absence of ligands. Similarly, purified, full-length extracellular domain of EGFR (EGFR _1-62 i). The epitope for this antibody was found to be near the hinge region of the EGFR extracellular domain that undergoes at change conformation during the formation of the active state. Furthermore, not only is the epitope buried in the inactive conformation, it also appeared to be inaccessible in the ligand bound back-to-back, untethered EGFR dimer. The intriguing properties of mAb806 prompted us to reanalyze other hybridomas expressing the monoclonal antibodies isolated from the initial fusion(5#). In preliminary screens, one of these mAbl75, appeared to have similar EGFR binding properties to mAb806. The amino acid sequences within their CDR loops are remarkably similar (90% sequence identity), and these differences preserve the size and charge of the relevant side chain. Like mAb806 the mAbl75 stains tumor cells which over-express the EGFR or which express the δ2-7 EGFR, but not cells with moderate levels of the wtEGFR, e.g. human

liver. Detailed epitope mapping showed that not only does mAbl75 bind the same cysteine loop as mAb806, but it also has a near identical binding profile to a series of mutants containing point mutations in this loop. Furthermore, neither antibody required the epitope disulfide bond to be intact for binding.

[0179] Both mAb806 and mAbl75 possess anti-tumor activity against human glioma xenografts that express the δ2-7 EGFR and both induce a significant delay in tumor growth, although mAbl75 appeared slightly more potent in this model. Interestingly, mAb806 and mAbl75 bind to the EGFR expressed on DU145 prostate cells, a cell line that expresses modest levels of EGFR but secretes significant amount of TGF-α(52) in an autocrine fashion. As with cell lines which over-express the EGFR, both antibodies only bind a small proportion of the surface EGFR on DU145 cells. However, both antibodies inhibit the growth of DU 145 xenografts in nude mice. Thus, it appears that the presence of ligand under physiological conditions increases the availability of the transitional form of the EGFR recognized by these antibodies and targeting this form is sufficient to downregulate EGFR driven cell growth.

[0180] This class of anti-EGFR antibodies may well have even wider anti-tumor action than first envisaged. Furthermore, the synergistic activity of mAb806, when used in combination with other EGFR therapeutics(47), suggests an immediate therapeutic role for antibodies of this class. mAb806 also binds to tumor cells that contain cancer- associated mutations which activate the EGFR kinase. mAb806 and mAbl75 selectively bind cells that have an activated EGFR and may be useful reagents for identifying and/or monitoring patients likely to respond to currently approved EGFR therapeutics.

[0181] Our structural studies with the EGFR _287-302 epitope indicate that both mAb806 and mAbl75 recognized the same 3D structural motif. The peptide residues in contact with mAb806 and mAbl75 exhibited almost identical structures in both cases, suggesting that this is the conformation of these amino acid, found in δ2-7 EGFR, the generating antigen. Indeed, the peptide backbone OfEGFR _287-302 seen in the antibody/peptide structures closely matches that occurring in both known conformations of EGFR

structure. However, the orientation of the epitope in these structures would prevent antibody access to the relevant amino acids: which is consistent with the experimental observation that antibody 806 does not bind wtEGFR. Detailed inspection of the EGFR structure raised another intriguing possibility. The EGFR _287-302 epitope hangs from a second disulfide bonded loop (amino acids 271-283) and disruption of this disulfide bond should allow access to the EGFR _287-302 loop without changing the backbone conformation of the epitope (see Figure 8). Our results with the C271A/C283A EGFR mutant indicate that the CRl domain must open up to allow mAb806 and 175 to bind stoichiometrically to the mutant receptor. This mutant receptor can still adopt a native conformation as it is fully responsive to EGF stimulation but, unlike the wtEGFR, is fully inhibited by mAb806.

[0182] On the surface of cells over-expressing the wtEGFR, there is clearly a sub- population of receptors in which the EGFR _287-302 epitope is accessible for mAb806 or mAbl75 binding. While access most readily occurs during receptor activation, it is not yet clear whether this sub-population of receptors are those in conformational transition to the untethered form, those in transition from the untethered form to the ligated activated state, or whether there is incomplete oxidation in a sub-set of the EGFR in which the disulfide bond between 271 and 283 has been damaged (reduced). If a reduced form of EGFR does exist on the surface of cancer cells, our data clearly shows it is likely to be active and capable of initiating cell signaling. The ability of mAb806 to inhibit the growth of xenografts over-expressing the wtEGFR, despite only binding a small sub- population of receptors and not inhibiting signaling downstream of the EGFR, remains an enigma. For this reason the concept that mAb806 binds a unique sub-set of EGFR that has unusual signaling properties has always been appealing, especially given its tremendous synergy with other EGFR therapeutics. If it exists on the cell surface of cancer cells, an EGFR reduced at the 271-283 disulfide could represent this unique form of the EGFR. Finally, it should be remembered that while the deletion in the δ2-7EGFR is very large, it does end at amino acid 273. The δ2-7 EGFR lacks this disulfide bond and is known to have different signaling properties to the wtEGFR. On the other hand, activating kinase mutations, autocrine loops and under-glycosylation of the EGFR also

enhance mAb806 reactivity by increasing activation of the receptor, presumably without the need of breaking the 271-283 disulfide. These observations support the concept that the CRl domain can kink to allow access to EGFR2 ₈ 7-302 at some point during EGFR activation, but is protected from kinking in the tethered and ligand-bound states. We are currently conducting on-going studies to determine if the EGFR recognized by mAb806 contains a reduced 271-283 disulfide bond.

[0183] The analysis of the results of our Phase I trial of chimerized 806 (ch806) confirmed that the epitope targeted by mAb806 is tumor specific. Quantitative biodistribution analysis clearly demonstrates the rapid and specific uptake of ch806 in tumor. These data are consistent with the highest quantitative targeting of antibodies to antigens expressed on cancer cells and markedly superior to values of wtEGFR antibodies at equivalent doses(44;50). The uptake of ch806 in all normal tissues (including liver) was low, indicating no evidence of binding to wtEGFR in normal tissue, and in liver represented only blood pool activity and minor catabolism of free ¹¹¹ In- chelate. This is in marked distinction to antibodies that target wtEGFR (eg 225; Cetuximab), which have been shown to have very high uptake (20-30% ID) in liver retained for over 72 hours post infusion, despite large protein doses being administered (up to 300mg)(50). In addition, antibodies to wtEGFR require large loading doses to saturate normal tissue before tumour uptake is evident(50), and also have dose limiting toxicity from antibody binding to wtEGFR in skin and gut(55). These results indicate that mAb806 does not target normal tissue in human, and quantitative analysis of biodistribution confirms the tumor specificity of the EGFR epitope targeted by mAb806 invivo.

[0184] Targeting the EGFR _287-3 Oi epitope with antibodies derived from mAb806 or mAbl75 is a way of attacking the activated EGFR in cancer cells with minimal uptake in normal tissue. Activation of the receptor can result from many of the mechanisms associated with cancer. Also, and possibly most importantly, these antibodies may be used to target cytotoxics, therapeutic nanoparticle, siRNA and radioisotopes directly to

the tumor site. Finally, these studies confirm that mAb806 and mAbl75 are valuable tools for helping map those events associated with EGFR activation on the cell surface.

[0185] In understanding, at a molecular level, how an antibody can recognise aberrant and activated forms of a growth factor receptor but not inactive wild-type receptor, this work can be used to generate antibodies to other targets for cancer therapeutics, for instance other members of the EGFR family. One method could use the disulfide mutant EGFR-C227A/C283A which binds antibodies mAb806 and mAbl75 stoichiometrically. If conformational perturbations seen for EGFR also occur when erbB2, erbB3 or erbB4 are overexpressed or activated continuously, then homologous disulfide mutants of these receptors may act as immunogens for creating other EGFR family member targeting antibodies with selectivity for tumors. Furthermore, when tumor cells overexpress other receptors, particularly those with disulfide rich domains such as Trk, a proportion of these receptors may be partially misfolded due to underglycosylation or transiently broken disulfide bonds. It is conceivable that disulfide mutant or truncated receptors could be used similarly as immunogens to potentially generate antibodies which recognise other aberrantly expressed receptors.

EXPERIMENTAL PROCEDURES Cell Lines

[0186] The δ2-7 EGFR transfected U87MG.δ2-7(5<) and the A431 cell lines(2) have been described previously. The hormone-independent prostate cell line DU 145(55) was obtained from the ATCC (atcc.org). See Supplemental Data for growth conditions of the cell lines.

Antibodies, Fabs and peptides

[0187] mAb806 and mAbl75 were produced and purified in the Biological Production Facility (Ludwig Institute for Cancer Research, Melbourne). For preparation and characterization of the antibodies, antibody fragments and peptide epitope see Supplemental Data

Mapping of m Ab 175 using EGFR fragments expressed in mammalian cells and yeast

[0188] The mapping was performed as described in the Supplemental Data.

Surface plasmon resonance (BIAcore)

[0189] A BIAcore 3000 was used for all experiments. The peptides containing the putative mAb806 epitope were immobilized on a CM5 sensor chip using amine, thiol or Pms coupling at a flow rate of 5μl/min(47). The mAb806 and mAbl75 were passed over the sensor surface at a flow rate of 5μl/min at 25°C. The surfaces were regenerated between runs by injecting 10 mM HCl at a flow rate of lOμl/min.

Immunoprecipitation and Western blotting

[0190] Cells were lysed with lysis buffer (1% Triton X-100, 30 mM HEPES, 150 mM NaCl, 500 mM 4-(2-aminoethyl) benzenesulfonylfluoride, 150 nM aprotinin, 1 mM E-64 protease inhibitor, 0.5 mM EDTA, and 1 mM leupeptin, pH 7.4) for 20 minutes, clarified by centrifugation at 14,000 x g for 30 minutes, immunoprecipitated with the relevant antibodies at a final concentration of 5 μg/ml for 60 minutes and captured by Sepharose- A beads overnight. Samples were then eluted with 2X NuPAGE SDS Sample Buffer (Invitrogen), resolved on NuPAGE gels (either 3-8% or 4-12%), electro-transferred onto Immobilon-P transfer membrane (Millipore) then probed with the relevant antibodies before detection by chemoluminescence radiography.

Immunohistochemistry

[0191] Frozen sections were stained with 5 μg/ml mAbl75 or irrelevant isotype control for 60 min at room temperature. Bound antibody was detected using the Dako Envision+ HRP detection system as per manufacturer's instructions. Sections were finally rinsed with water, counterstained with hematoxylin and mounted.

Xenograft Models

[0192] U87MG.δ2-7 cells ( (3x10 ⁶ ) in 100 μL of PBS were inoculated s.c. into both flanks of 4- to 6-week-old, female Balb/c nude mice (Animal Research Centre, Perth,

Australia). All studies were conducted using established tumor models as reported previously(^i). Treatment commenced once tumors had reached the mean volume indicated in the appropriate figure legend. Tumor volume in mm was determined using the formula (length x width ² )/2, where length was the longest axis and width was the perpendicular measurement. Data are expressed as mean tumor volume ± SE for each treatment group. All data was analyzed for significance by one-sided Student's t test where p < 0.05 was considered statistically significant. This research project was approved by the Animal Ethics Committee of the Austin Hospital.

Generation and characterization of stable cell lines expressing EGFR mutant constructs

[0193] Mutations of the (wt) EGFR were generated using a site-directed mutagenesis kit (Stratagene, La Jolla, CA). The template for each mutagenesis was the human EGFR cDNA (accession number x00588)(2). Automated nucleotide sequencing of each construct was performed to confirm the integrity of the EGFR mutations. Wild type and mutant (C173A/C281A) EGFR were transfected into BaF/3 cells by electroporation. Further details on the characterization of the cell lines are presented in the Supplemental Data.

Crystal structure determinations of Fab 175, and Fab 806, Fab-peptide complexes and the NMR structure of the 806 peptide epitope in solution

[0194] Crystallographic procedures for preparing and analyzing the Fab 806, Fab 175 and the individual Fab-peptide complexes and details on NMR studies of the ¹⁵ N-labelled 806 epitope peptide in solution are described in the Supplemental Data. Structures were determined by molecular replacement and refinement converged with R=0.225/Rfree=0.289 for Fab806 and R=0.226/Rfree=0.279 for Fab806:peptide; R=0.210/Rfree=0.305 for Fab806 and R=0.203/Rfree=0.257 for Fab806:peptide.

Biodistribution of chAb 806 Tumor in Patients

[0195] To demonstrate the tumor specificity of mAb806 invivo, a chimeric version

(ch806) was engineered and produced under cGMP conditions(5<5). A Phase I first-in-

man trial was conducted to evaluate the safety, biodistribution and immune response of ch806 in patients with 806 positive tumors, and the results of safety, biodistribution and pharmacokinetics have been reported previously (44). To define the specificity of ch806 in tumor compared to normal tissue (ie liver) in patients, the quantitative uptake of ch806 in tumor and liver was performed by calculation of % injected dose (ID) of ^m In-ch806 from whole body gamma camera images obtained over one week following injection of 5-7mCi (200-280MBq) ^{l u} In-ch806. Liver and tumor dosimetry calculations were performed based on regions of interest in each individual patient ^{i π} In-ch806 infusion image dataset, corrected for background and attenuation, allowing calculation of cumulated activity. Dosimetry calculation was performed to derive the concentration of ¹ ' 'in-chδOό in tumor and liver over a one week period post injection.

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EXAMPLE 2 SUPPLEMENTAL DATA

EXPERIMENTAL PROCEDURES Cell lines

[0197] All cell lines were maintained in DMEM (Life Technologies, Grand Island, NY) containing 10% FCS (CSL, Melbourne), 2 mM glutamine (Sigma Chemical Co, St. Louis), and penicillin/streptomycin (Life Technologies, Grand Island). In addition, the U87MG.δ2-7 cell line was maintained in 400mg/ml of Geneticin (Life Technologies, Inc, Grand Island). BaF/3(i) and BaF/3 cell lines expressing different EGF receptors(2) were maintained routinely in RPMI 1640 (GIBCO BRL) supplemented with 10% foetal calf serum (GIBCO BRL) and 10% WEHI-3B conditioned medium(5) as a source of IL-3. All cell lines were grown at 37°C in an air/CO ₂ (95%-5%) atmosphere.

Antibodies and peptides

[0198 Antibody generation. The murine fibroblast line NR6 _δEGFR was used as immunogen. Mouse hybridomas were generated by immunizing BALB/c mice five times subcutaneously at 2- to 3-week intervals, with 5xlO ⁵ - 2xlO ⁶ cells in adjuvant. Complete Freund's adjuvant was used for the first injection. Thereafter, incomplete Freund's adjuvant (Difco) was used. Spleen cells from immunized mice were fused with mouse myeloma cell line SP2/0. Supernatants of newly generated clones were screened in hemadsorption assays for reactivity with cell line NR6, NRόwtEGFR, and NR6 _δEGF R and then analyzed by hemadsorption assays with human glioblastoma cell lines U87MG, U87MGwtEGFR, and U87MG _δ EGFR.

[0199] Intact mAb's (50 mg) were digested in PBS with activated papain for 2-3 h at 37 ⁰ C at a ratio of 1 :20 and the papain was inactivated with iodoacetamide. The digestion was then passed over a column of Protein- A sepharose (Amersham) in 2OmM sodium phosphate buffer pH 8.0, with the flow-through further purified by cation exchange using on a Mono-S column (Amersham). Protein was then concentrated using a 10,000 MWCO centrifugal concentrator (Millipore). For Fab-peptide complexes a molar excess of lyophilised peptide was added directly to the Fab and incubated for 2 hours at 4°C before setting up crystallisation trials.

Mapping of mAb 175 using EGFR fragments expressed in mammalian cells

[0200] The day prior to transfection with these fragments, human 293T embryonic kidney fibroblasts were seeded at 8x10 ⁵ per well in 6-well tissue culture plates containing 2 ml of media. Cells were transfected with 3-4 μg of plasmid DNA complexed with Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions. 24 to 48 h after transfection, cell cultures were aspirated and cell monolayers lysed in 250 μl of lysis buffer (1% Triton X-100, 10% glycerol, 150 mM NaCl, 50 mM HEPES pH 7.4, 1 raM EGTA and Complete Protease Inhibitor mix (Roche). Aliquots of cell lysate (10-15 μl) were mixed with SDS sample buffer containing 1.5% β-mercaptoethanol, denatured by heating for 5 min at 100 ⁰ C and electrophoresed on 10% NuPAGE Bis-Tris polyacrylamide gels (Invitrogen). Samples were then electro-transferred to nitrocellulose membranes that were rinsed in TBST buffer (1OmM Tris-HCI, pH 8.0, 10OmM NaCl and 0.1% Tween-20) and blocked in TBST containing 2.5% skim milk for 30 min at room temperature. Membranes were incubated overnight at 4 ⁰ C with 0.5 μg/ml of mAb 175 in blocking buffer. Parallel membranes were probed overnight with mAb 9Bl 1 (1 :5000, Cell Signaling Technology, Danvers, Massachussets) to detect the c-myc epitope. Membranes were washed in TBST, and incubated in blocking buffer containing horseradish peroxidase-conjugated rabbit anti-mouse IgG (Biorad) at a 1 :5000 dilution for 2 h at room temperature. Blots were then washed in TBST, and developed using autoradiographic film following incubation with Western Pico Chemiluminescent Substrate (Pierce, Rockford, Illinois).

Mapping of mAb 175 using EGFR fragments expressed in mammalian cells and yeast

[0201] A series of overlapping c-myc-tagged EGFR ectodomain fragments, starting at residues 274, 282, 290 and 298 and all terminating at amino acid 501 and fused to growth hormone have been described previously(<5).

[0202] Expression of EGFR proteins on the yeast cell surface was performed as previously described(7). Briefly, transformed colonies were grown at 30°C in minimal media containing yeast nitrogen base, casein hydrolysate, dextrose, and phosphate buffer pH 7.4, on a shaking platform for approximately one day until an OD _60O of 5-6 was reached. Yeast cells were then induced for protein display by transferring to minimal media containing galactose, and incubated with shaking at 30°C for 24 h. Cultures were then stored at 4°C until analysis. Raw ascites fluid containing the c-myc monoclonal antibody 9E10 was obtained from Covance (Richmond, CA). 1 x 10 ⁶ yeast cells were washed with ice-cold FACS buffer (PBS containing 1 mg/ml BSA) and incubated with either anti-c-myc ascites (1 :50 dilution), or human EGFR monoclonal antibody (10 μg/ml) in a final volume of 50 μl, for 1 hr at 4 ⁰ C. The cells were then washed with ice cold FACS buffer and incubated with phycoerythrin-labelled anti-mouse IgG (1 :25 dilution), in a final volume of 50 μl for 1 h at 4 ⁰ C, protected from light. After washing the yeast cells with ice-cold FACS buffer, fluorescence data was obtained with a Coulter Epics XL flow cytometer (Beckman-Coulter), and analyzed with WinMDI cytometry software (J. Trotter, Scripps University). For determination of linear versus conformational epitopes, yeast cells were heated at 8O ⁰ C for 30 min, then chilled on ice 20 min prior to labelling with antibodies. The series of EGFR mutants listed in Table 2 have been described previously(#).

Generation and characterization of stable cell lines expressing EGFR mutant constructs

Generation of cell lines expressing EGFR mutants

[0203] Stable cell lines expressing the mutant EGFR were obtained by selection in neomycin-containing medium. After final selection, mRNA was isolated from each cell line, reverse transcribed and the EGFR sequence amplified by PCR. All mutations in the expressed EGFR were confirmed by sequencing the PCR products. The level of EGFR expression was determined by FACS analysis on a FACStar (Becton and Dickinson, Franklin Lakes, NJ) using the anti-EGFR antibody mAb52$(9;10) at 10 μg/ml in PBS, 5% FCS, 5 mM EDTA followed by Alexa 488-labeled anti-mouse Ig (1 :400 final dilution). Background fluorescence was determined by incubating the cells with an , irrelevant, class-matched primary antibody. All cells were routinely passaged in RPMI, 10% FCS, 10% WEHDB conditioned medium and 1.5 mg/ml G418. EGF -dependent activation of mutant EGFR

[0204] Cells expressing the wtEGFR or C271 A/C283 A-EGFR were washed and incubated for 3 hr in medium without serum or IL-3. Cells were collected by centrifugation and resuspended in medium containing EGF (100 ng/ml) or an equivalent volume of PBS. Cells were harvested after 15min, pelleted and lysed directly in SDS/PAGE sample buffer containing β-mercaptoethanol. Samples were separated on NuPAGE 4-12% gradient gels, transferred to Immobilon PVDF membrane and probed with anti-phosphotyrosine (4G10, Upstate Biotechnologies) or anti-EGFR antibodies (mAb806, produced at the LICR). Reactive bands were detected using chemiluminescence.

Effect of EGF and antibodies on cell proliferation

[0205]Cells growing in log phase were harvested and washed twice with PBS to remove residual IL-3. Cells were resuspended in RPMI 1640 plus 10% FCS and seeded into 96- well plates at 10 ⁵ cells/well with carrier only or with increasing concentrations of EGF. Where appropriate, a fixed concentration of mAb528 or mAb806 (2 μg/well) was also added to the cultures. Proliferation was determined using the MTT assay(77).

Reactivity with Conformation-specific Antibodies

[0206] Cells were collected by centrifugation and stained with the control or test antibodies (all at 10 μg/ml in FACS buffer for 40 min on ice, washed in FACS buffer) followed by Alexa 488-labeled anti-mouse Ig (1:400 final dilution, 20 min on ice). The cells were washed with ice-cold FACS buffer, collected by centrifugation, and analyzed on a FACScan; peak fluorescence channel and median fluorescence were determined for each sample using the statistical tool in CellQuest (Becton and Dickinson). Background (negative control) fluorescence was deducted from all measurements. The median fluorescence values were chosen as most representative of peak shape and fluorescence intensity and were used to derive the ratio of mAb 806 to mAb 528 binding.

Crystal structure determinations ofl 75, and 806 Fab, Fab-peptide complexes and the NMR structure of the 806 peptide epitope in solution

[0207] Crystals of native 806 Fab were grown by hanging drop vapour diffusion using 10mg/ml Fab and a reservoir containing 0.1M Sodium acetate buffer pH 4.6, 6-8% PEG6000 and 15-20% (Isopropanol. For data collection crystals were transferred to a cryoprotectant solution containing 0.1M Sodium acetate buffer pH 4.6, 10% PEG6000, 15-20% Isopropanol and 10% glycerol. Crystals were then mounted in a nylon loop and flash frozen directly into liquid nitrogen.

[0208] Crystals of 806 Fab-peptide complex were grown by hanging drop vapour diffusion using lOmg/ml Fab-peptide complex and a reservoir containing 0.2M ammonium acetate 16-18% PEG 5,000 monomethylether, crystals quality was then improved through seeding techniques. For data collection crystals were transfered to a cryoprotectant solution consisting of reservoir supplemented with 25% glycerol. Crystals were then mounted in a nylon loop and flash frozen directly into liquid nitrogen.

[0209] Crystals of 175 Fab-peptide complex were initially grown by free interface diffusion using a Topaz crystallisation system (Fluidigm, San Francisco). Microcrystals were grown by hanging drop vapour diffusion using 7mg/ml Fab with similar conditions 0.1M Bis-tris propane buffer, 0.2M ammonium acetate and 18% PEG 10,000. Microcrystals were then improved by streak seeding into 0.15m Sodium formate and

15% PEG 1500 to yield small plate shaped crystals. For data collection crystals were transferred to a cryoprotectant solution consisting of reservoir supplemented with 25% glycerol. Crystals were then mounted in a nylon loop and flash frozen directly into liquid nitrogen.

[0210] Diffraction data on 806 Fab and 175 Fab complex crystals were collected in-house using a R-AXIS IV detector on a Rigaku micromax-007 generator fitted with AXCO optics, these data were then processed using CrystalClear. 806 Fab-peptide complex data were collected on an ADSC quantum315 CCD detector at beamline X29, Brookhaven National Laboratory, these data were processed with HKL2000(72) (data collection statistics are shown in Table 1). Native 806 Fab was solved by molecular replacement using the program MOLREP(U) using the coordinates of the Fab structure 2E8 refinement of the structure was performed in REFMAC5(7¥) and model building in Coot(75). Both 806-peptide and 175 Fab-peptide structures were solved by molecular replacement using the program MOLREP using the coordinates of the 806 Fab structure, refinement and rebuilding were again performed in REFMAC5, and COOT and O. Validation of the final structures were performed with PROCHECK(Z 6) and WHATCHECK(Z 7).

NMR studies

[0211] For NMR studies, ¹⁵ N-labelled peptide was produced recombinantly as a fusion to the SH2 domain of SHP2 using the method previously described by Fairlie et al.(7#), except that the E. coli were grown in Neidhardt's minimal medium supplemented with ¹⁵ NH ₄ Cl(ZP). The peptide was cleaved from the fusion partner using CNBr, purified by reversed-phase HPLC and its identity confirmed by MALDI-TOF mass spectrometry and N-terminal sequencing. The methionine residue within the 806 antibody-binding sequence was mutated to leucine to enable cleavage from the fusion partner, but not within the peptide itself.

[0212] Samples used for NMR studies were prepared in H ₂ O solution containing 5% ² H ₂ O, 70 mM NaCl and 50 mM NaPO ₄ at pH 6.8. All spectra were acquired at 298K on a

Bruker Avance500 spectrometer using a cryoprobe. Sequential assignments of the peptide in the absence of m806Fab were established using standard 2D TOCSY and NOESY as well as ¹⁵ N-edited TOCSY and NOESY spectra. Interaction between the peptide and fAb806was examined by monitoring ¹⁵ N HSQC spectra of the peptide in the absence and presence of fAb806. Spectral perturbation of ¹⁵ N HSQC spectra of the peptide in the presence of f Ab806clearly indicates the peptide was able to bind to the fAb806under the presence solution conditions. Detailed conformation of the peptide in the complex form was, however, not determined.

[0213] Supplemental Table 1. Data Collection and Refinement Statistics

Data Collection

806(native) 806(peptide) 175(native) 175(peptide)

Space Group P2,2,2 P2, P2,2,2, P2,2,2

Cell Dimensions (A) α 140.37 35.92 36.37 83.17 b 74.62 83.16 94.80 69.26

C 83.87 72.21 β=92.43 108.90 71.47

Source in-house BNL X29 in-house in-house

Wavelength (A) 1.542 1.1 1.542 1.542

Resolution range (A) 29.7-2.2 50-2.0 50-2.8 14.18-1.59

(2.27-2.20) (2.07-2.0) (2.87-2.80) (1.65-1.59)

Emerge (%) 6.4 (26.7) 6.6 (28.2) 8.6 (30.0)

I/σl 12.2 (3.2) 22 (3.15) 10.2 (2.2)

Completeness (%) 98.3 (91.3) 96.6 (79.2) 98.4(90.5) 78.8 (1 1.8)

98.1 at 1.89 A

Total Reflections 156497 98374 205401

Unique reflections 44905 27692 9171 43879

Numbers in parentheses ar for the highest resolution shell.

Refinement

Resolution range (A) 20-2.3 72.17-2.00 50-2.6 14.18-1.6

Reflections 37397 26284 9171 41611

λ _ciyst 0.225 0.226 0.210 0.203

λ _free 0.289 0.279 0.305 0.257

Protein Atoms 6580 3294 3276 3390

Solvent Atoms 208 199 46 247 r.m.s.d bond length (A) 0.022 0.007 0.015 0.014 r.m.s.d bond angle (°) 1.70 1.12 1.77 1.48

Average B-factor (A ² ) 40.3 33.6 37.5 20.7 Overall anisotropic B-factors (A ² )

B I l -1.52 2.42 0.20 1.13

B22 2.22 -0.26 -1.022 -0.38

B33 -0.70 -2.1 1 1.03 -0.74

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