WO2004094607A2

WO2004094607A2 - Methods of therapy and diagnosis using targeting of cells that express a human transporter-like protein

Info

Publication number: WO2004094607A2
Application number: PCT/US2004/012170
Authority: WO
Inventors: Peter C.R. Emtage
Original assignee: Nuvelo, Inc.
Priority date: 2003-04-21
Filing date: 2004-04-20
Publication date: 2004-11-04
Also published as: WO2004094607A3

Abstract

Certain cells, including types of cancer cells such as prostate cancer, are capable of expressing P-type ATPase-like (ATPHy1) mRNA and protein. Targeting using ATPHy1 polypeptides, nucleic acids encoding for ATPHy1 polypeptides and anti-ATPHy1 antibodies provides a method of killing or inhibiting that growth of cancer cells that express the ATPHy1 protein. Methods of therapy and diagnosis of disorders associated with ATPHy1 protein-expressing cells, such as breast, colon, lung, and prostate cancer, are described.

Description

METHODS OF THERAPY AND DIAGNOSIS USING TARGETING OF CELLS THAT EXPRESS A HUMAN TRANSPORTER-LIKE PROTEIN

1. BACKGROUND 1.1 CROSS REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of priority to and is a continuation-in-part application of U.S. Patent Application Serial No. 10/420,268 filed April 21, 2003 entitled "Methods of Therapy and Diagnosis Using Targeting of Cells that Express a Human Transporter-like Protein," Attorney Docket No. NUVO-03, herein incoφorated by reference in its entirety.

1.2 TECHNICAL FIELD

This invention relates to compositions and methods for targeting P-type ATPase-like protein (herein denoted ATPHyl)-expressing cells using antibodies, polypeptides, polynucleotides, peptides, and small molecules and their use in the therapy and diagnosis of various pathological states, including cancer.

1.3 SEQUENCE LISTING

The sequences of the polynucleotide and polypeptide of the invention are listed in the sequence listing and are submitted on a compact disc containing the file labeled "NUVO- 03CP PCT.txt"-^18.0 KB (49,152 bytes), which was created on an IBM PC, Windows 2000 operating system on Monday April 19, 2004 at 12:08:14 PM. The sequence listing entitled "NUVO-03CP PCT.txt" is herein incoφorated by reference in its entirety. A computer readable format ("CRF") and three duplicate copies ("Copy 1," "Copy 2" and "Copy 3") of the Sequence Listing "NUVO-03CP PCT.txt" are submitted herein. Applicants hereby state that the content of the CRF and Copies 1, 2 and 3 of the Sequence Listing, submitted in accordance with 37 CFR § 1.821(c) and (e), respectively, are the same.

1.4 BACKGROUND ART Immunotherapy provides a method of harnessing the immune system to treat various pathological states, including cancer, autoimmune disease, transplant rejection, hypeφroliferative conditions, allergic reactions, emphysema, and wound healing. Antibody therapy for cancer involves the use of antibodies, or antibody fragments, against a tumor antigen to target antigen-expressing cells. Antibodies, or antibody fragments, may have direct or indirect cytotoxic effects or may be conjugated or fused to cytotoxic moieties. Direct effects include the induction of apoptosis, the blocking of growth factor receptors, and anti-idiotype antibody formation. Indirect effects include antibody- dependent cell-mediated cytotoxicity (ADCC) and complement-mediated cellular cytotoxicity (CMCC). When conjugated or fused to cytotoxic moieties, the antibodies, or fragments thereof, provide a method of targeting the cytotoxicity towards the tumor antigen expressing cells. (Green, et al, Cancer Treatment Reviews, 26:269-286 (2000), incoφorated herein by reference in its entirety).

Because antibody therapy targets cells expressing a particular antigen, there is a possibility of cross-reactivity with normal cells or tissue. Although some cells, such as hematopoietic cells, are readily replaced by precursors, cross-reactivity with many tissues can lead to detrimental results. Thus, considerable research has gone towards finding tumor- specific antigens. Such antigens are found almost exclusively on tumors or are expressed at a greater level in tumor cells than the corresponding normal tissue. Tumor-specific antigens provide targets for antibody targeting of cancer, or other disease-related cells, expressing the antigen. Antibodies specific to such tumor-specific antigens can be conjugated to cytotoxic compounds or can be used alone in immunotherapy. Immunotoxins target cytotoxic compounds to induce cell death. For example, anti-CD22 antibodies conjugated to deglycosylated ricin A may be used for treatment of B cell lymphoma that has relapsed after conventional therapy (Amlot, et al., Blood 82:2624-2633 (1993), incoφorated herein by reference in its entirety) and has demonstrated encouraging responses in initial clinical studies. The immune system functions to eliminate organisms or cells that are recognized as non-self, including microorganisms, neoplasms and transplants. A cell-mediated host response to tumors includes the concept of immunologic surveillance, by which cellular mechanisms associated with cell-mediated immunity destroy newly transformed tumor cells after recognizing tumor-associated antigens (antigens associated with tumor cells that are not apparent on normal cells). Furthermore, a humoral response to tumor-associated antigens enables destruction of tumor cells through immunological processes triggered by the binding of an antibody to the surface of a cell, such as antibody-dependent cellular cytotoxicity (ADCC) and complement mediated lysis. Recognition of an antigen by the immune system triggers a cascade of events including cytokine production, B-cell proliferation, and subsequent antibody production.

Often tumor cells have reduced capability of presenting antigen to effector cells, thus impeding the immune response against a tumor-specific antigen. In some instances, the tumor-specific antigen may not be recognized as non-self by the immune system, preventing an immune response against the tumor-specific antigen from occurring. In such instances, stimulation or manipulation of the immune system provides effective techniques of treating cancers expressing one or more tumor-specific antigens.

For example, Rituximab (Rituxan®) is a chimeric antibody directed against CD20, a B cell-specific surface molecule found on >95% of B-cell non-Hodgkin's lymphoma (Press, et al, Blood 69:584-591 (1987); Malony, et al, Blood 90:2188-2195 (1997), both of which are incoφorated herein in their entirety). Rituximab induces ADCC and inhibits cell proliferation through apoptosis in malignant B cells in vitro (Maloney, et al, Blood 88:637a (1996), incoφorated herein by reference in its entirety). Rituximab is currently used as a therapy for advanced stage or relapsed low-grade non-Hodgkin's lymphoma, which has not responded to conventional therapy.

Active immunotherapy, whereby the host is induced to initiate an immune response against its own tumor cells can be achieved using therapeutic vaccines. One type of tumor- specific vaccine uses purified idiotype protein isolated from tumor cells, coupled to keyhole limpet hemocyanin (KLH) and mixed with adjuvant for injection into patients with low- grade follicular lymphoma (Hsu, et al, Blood 89:3129-3135 (1997), incoφorated herein by reference in its entirety). Another type of vaccine uses antigen-presenting cells (APCs), which present antigen to naϊve T cells during the recognition and effector phases of the immune response. Dendritic cells, one type of APC, can be used in a cellular vaccine in which the dendritic cells are isolated from the patient, co-cultured with tumor antigen and then reinfused as a cellular vaccine (Hsu, et al, Nat. Med. 2:52-58 (1996), incoφorated herein by reference in its entirety). Immune responses can also be induced by injection of naked DNA. Plasmid DNA that expresses bicistronic mRNA encoding both the light and heavy chains of tumor idiotype proteins, such as those from B cell lymphoma, when injected into mice, are able to generate a protective, anti-tumor response (Singh, et al, Vaccine 20:1400-1411 (2002)).

Cancer of the colon, breast, lung, pancreas and ovary as well as other cancers are treatable and often curable diseases when localized to the respective organs. Surgery is the primary form of treatment and results in cure in many patients. However, recurrence following surgery is a major problem and often is the ultimate cause of death. Systemic adjuvant chemotherapy reduces the recurrence rate and prolongs the survival of patients that present with late stage disease. However, the toxic effects of therapeutic outcomes, and the presence of drug refractoriness remain considerable problems that need to be overcome to improve the quality of life and reduce the death rate of cancer patients. A number of approaches using vaccines and antibodies as adjuvant therapy are being studied, and mounting evidence indicates that many cancers are immunogenic, and that they may reasonably be considered as targets for immunotherapy. Antibody-based therapy has been effective in the treatment of certain cancers. For example, HERCEPTIN ® (Genetech, CA) antibodies have been used successfully to treat some cancers of the breast, and edrecolomab (Panorex®) has been shown to be a less toxic and adequate alternative to chemotherapy for patients with stage II colon cancer (Yves Dencausse etal, Annals of Oncology, Vol 11, Suppl.4 October 2000, page 47). In spite of these advances, the deployment of immunotherapy as a treatment option against cancers remains hampered by the lack of tumor associated antigens that are tumor- specific, strongly immunogenic and that are shared among different patients (Dalerba et al, Clin Rev Oncol Hematol 46:33-57 (2003)). Therefore, there exists a need in the art to identify antigens that are clearly and specifically expressed on the surface of cancer cells that could serve as targets for various targeting strategies. Accordingly, Applicants have identified a molecular target useful for therapeutic intervention in colon, breast, lung, and prostate cancers, and provide herein methods for the diagnosis and therapy of said cancers.

2. SUMMARY OF THE INVENTION The invention provides therapeutic and diagnostic methods of targeting cells expressing a P-type ATPase-like protein (herein denoted as ATPHyl) by using targeting elements such as ATPHyl polypeptides, nucleic acids encoding ATPHyl protein, and anti- ATPHyl antibodies, including fragments or other modifications thereof, peptides and small molecules. The ATPHyl protein is highly expressed in breast, prostate, colon and lung cancer cells relative to its expression in healthy cells. Thus, targeting of cells that express ATPHyl will have a minimal effect on healthy tissues while destroying or inhibiting the growth of the cancer cells. Similarly, other cancers can be targeted if they bear the ATPHyl antigen. For example, inhibition of growth and/or destruction of ATPHyl -expressing cancer cells results from targeting such cells with anti-ATPHyl antibodies. One embodiment of the invention is a method of destroying ATPHyl -expressing cells by conjugating anti- ATPHyl antibodies with cytocidal materials such as radioisotopes or other cytotoxic compounds. The present invention provides a variety of targeting elements and compositions.

One such embodiment is a composition comprising an anti-ATPHyl antibody preparation. Exemplary antibodies include a single anti-ATPHyl antibody, a combination of two or more anti-ATPHyl antibodies, a combination of an anti-ATPHyl antibody with a non- ATPHyl antibody, a combination of an anti-ATPHyl antibody and a therapeutic agent, a combination of an anti-ATPHyl antibody and a cytocidal agent, a bispecific anti-ATPHyl antibody, Fab ATPHyl antibodies or fragments thereof, including any fragment of an antibody that retains one or more complementary determining regions (CDRs) that recognize ATPHyl, humanized anti-ATPHyl antibodies that retain all or a portion of a CDR that recognizes ATPHyl, anti-ATPHyl conjugates, and anti-ATPHyl antibody fusion proteins. Another targeting embodiment of the invention is a composition comprising an

ATPHyl antigen, for example, an ATPHyl polypeptide, or a fragment or variant thereof and optionally comprising a suitable adjuvant.

Yet another targeting embodiment is a composition comprising a nucleic acid encoding ATPHyl, or a fragment or variant thereof, optionally within a recombinant vector. A further targeting embodiment of the present invention is a composition comprising an antigen-presenting cell transformed with a nucleic acid encoding ATPHyl, or a fragment or variant thereof, optionally within a recombinant vector.

Yet another targeting embodiment of the invention is a preparation comprising an ATPHyl polypeptide or peptide fragment or variant thereof. A further targeting embodiment of the present invention is a non- ATPHyl polypeptide or peptide that binds an ATPHyl polypeptide or polynucleotide of the invention.

Another targeting embodiment of the invention is a preparation comprising a small molecule that recognizes or binds to an ATPHyl polypeptide or polynucleotide of the invention. The present invention further provides a method of targeting ATPHyl -expressing cells, which comprises administering a targeting element or composition in an amount effective to target ATPHyl -expressing cells. Any one of the targeting elements or compositions described herein may be used in such methods, including an anti-ATPHyl antibody preparation, an ATPHyl antigen comprising a ATPHyl polypeptide, or a fragment or variant thereof or a composition of a nucleic acid encoding ATPHyl, or a fragment or variant thereof, optionally within a recombinant vector or a composition of an antigen- presenting cell transformed with a nucleic acid encoding ATPHyl, or fragment or variant thereof, optionally within a recombinant vector.

The present invention further provides a method of targeting ATPHyl -expressing cells, which comprises administering a targeting element or composition in an amount effective to target ATPHyl -expressing cells. Any one of the targeting elements or compositions described herein may be used in such methods, including an anti-ATPHyl antibody preparation, an ATPHyl antigen comprising an ATPHyl polypeptide, or a fragment or variant thereof or a composition of a nucleic acid encoding ATPHyl, or a fragment or variant thereof, optionally with a recombinant vector or a composition of an antigen-presenting cell transformed with a nucleic acid encoding ATPHyl, or fragment or variant thereof, optionally within a recombinant vector, or an ATPHyl polypeptide, peptide fragment or variant thereof, or a binding polypeptide, peptide or small molecule that binds to an ATPHyl polypeptide or polynucleotide of the invention.

The invention also provides a method of inhibiting the growth of cancer cells, including breast, lung, prostate, and colon cancer cells, ATPHyl -expressing cancer cells, which comprises administering a targeting element or a targeting composition in an amount effective to inhibit the growth of said cancer cells. Any one of the targeting elements or compositions described herein may be used in such methods, including an anti-ATPHyl antibody preparation, an ATPHyl antigen comprising an ATPHyl polypeptide, fragment, or variant thereof, composition of a nucleic acid encoding ATPHyl, or fragment or variant thereof, optionally within a recombinant vector, or a composition of an antigen-presenting cell transformed with a nucleic acid encoding ATPHyl, or fragment or variant thereof, optionally within a recombinant vector, or an ATPHyl polypeptide, peptide fragment, or variant thereof, or a binding polypeptide, peptide or small molecule that binds to an ATPHyl polypeptide or polynucleotide of the invention.

The present invention further provides a method of treating disorders associated with the proliferation of ATPHyl -expressing cells in a subject in need thereof, comprising the step of administering a targeting element or targeting composition in a therapeutically effective amount to treat disorders associated with ATPHyl -expressing cells. Any one of the targeting elements or compositions described herein may be used in such methods, including an anti-ATPHyl antibody preparation, an ATPHyl antigen comprising an ATPHyl polypeptide, fragment, or variant thereof, a composition of a nucleic acid encoding ATPHyl, or fragment or variant thereof, optionally within a recombinant vector, or a composition of an antigen-presenting cell comprising a nucleic acid encoding ATPHyl, or fragment or variant thereof, optionally within a recombinant vector, or an ATPHyl polypeptide, peptide fragment, or variant thereof, or a binding polypeptide, peptide or small molecule that binds to or recognizes an ATPHyl polypeptide or polynucleotide of the invention.

Examples of disorders associated with the proliferation of ATPHyl -expressing cells include cancers, such as breast, colon, prostate, and lung cancers. Other cancers that bear the ATPHyl antigen, such as stomach, thymus, epithelial and squamous cell carcinomas, as well as other cancers including gastrointestinal cancers including esophageal cancer, stomach cancer, colorectal cancer, polyps associated with colorectal neoplasms, pancreatic cancer and gallbladder cancer, cancer of the adrenal cortex, ACTH-producing tumor, bladder cancer, brain cancer including intrinsic brain tumors, neuroblastomas, astrocytic brain tumors, gliomas, and metastatic tumor cell invasion of the central nervous system, Ewing's sarcoma, head and neck cancer including mouth cancer and larynx cancer, kidney cancer including renal cell carcinoma, liver cancer, lung cancer including small and non- small cell lung cancers, malignant peritoneal effusion, malignant pleural effusion, skin cancers including malignant melanoma, tumor progression of human skin keratinocytes, squamous cell carcinoma, basal cell carcinoma, and hemangiopericytoma, mesothelioma, Kaposi's sarcoma, bone cancer including osteomas and sarcomas such as fibrosarcoma and osteosarcoma, cancers of the female reproductive tract including uterine cancer, endometrial cancer, ovarian cancer, ovarian (germ cell) cancer and solid tumors in the ovarian follicle, vaginal cancer, cancer of the vulva, and cervical cancer; breast cancer (small cell and ductal), penile cancer, retinoblastoma, testicular cancer, thyroid cancer, trophoblastic neoplasms, and Wilms' tumor, and hematopoietic-based cancers can also be targeted. The invention further provides a method of modulating the immune system by either suppression or stimulation of growth factors and cytokines, by administering the targeting elements or compositions of the invention. The invention also provides a method of modulating the immune system through activation of immune cells (such as natural killer cells, T cells, B cells and myeloid cells), through the suppression of activation, or by stimulating or suppressing proliferation of these cells by ATPHyl peptide fragments or ATPHyl antibodies.

The present invention also provides a method of diagnosing disorders associated with ATPHyl -expressing cells comprising the step of measuring the expression patterns of ATPHyl protein and/or its associated mRNA. Yet another embodiment of a method of diagnosing disorders associated with ATPHyl -expressing cells comprising the step of detecting ATPHyl expression using anti-ATPHyl antibodies. Expression levels or patterns may then be compared with a suitable standard indicative of the desired diagnosis. Such methods of diagnosis include compositions, kits and other approaches for determining whether a patient is a candidate for ATPHyl therapy in which said ATPHyl is targeted.

The present invention also provides a method of enhancing the effects of therapeutic agents and adjunctive agents used to treat and manage disorders associated with ATPHyl - expressing cells, by administering ATPHyl preparations of said ATPHyl with therapeutic and adjuvant agents commonly used to treat such disorders.

3. BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1 depicts a BLASTP amino acid sequence alignment between the protein encoded by SEQ ID NO: 1 (i.e. SEQ ID NO: 2) ATPHyl and rabbit Type IV P-type ATPase (also known as RTNG-finger binding protein) (SEQ ID NO: 3), indicating that the two sequences share 88% similarity and 85% identity over 1173 amino acids of SEQ ID NO: 2. Figure 2 depicts a BLASTP amino acid sequence alignment between the protein encoded by SEQ ID NO: 1 (i.e. SEQ ID NO: 2) ATPHyl and human potential phospholipids-transporting ATPase IR (SEQ ID NO: 4), indicating that the two sequences share 100% identity over 672 amino acids of SEQ ID NO: 2. Figure 3 shows the relative expression of ATPHyl mRNA (as determined by RT-

PCR) derived from healthy tissues, a cell line derived from acute mylogenous leukemia (KG1), and tumor tissues derived from B cell lymphoma (H02-85T, H02-86T), follicular lymphoma (H02-74T, H02-76T, H02-77T), myeloma (H02-79T), colon tumor (CO7554T, CO7932T, CO8067T) and normal adjacent colon tissue (CO7554N, CO7932N), lung tumor (LU7981T, LU7987T, LU8044T) and normal adjacent lung tissue (LU7981N, LU7987N, LU8044N), prostate and normal adjacent prostate tissue, and breast tumor (H02-39T, H02- 41T, H02-43T, H02-45T) and normal adjacent breast tissue (H02-40N, H02-42N, H02-44N). 4. DETAILED DESCRIPTION OF THE INVENTION

The present invention relates to methods of targeting cells that express ATPHyl using targeting elements, such as polypeptides, nucleic acids, antibodies, binding polypeptides, peptides and small molecules, including fragments or other modifications of any of these elements.

The present invention provides a novel approach for diagnosing and treating diseases and disorders associated with said ATPHyl . The method comprises administering an effective dose of targeting preparations such as antigens, antigen presenting cells, or pharmaceutical compositions comprising the targeting elements, ATPHyl polypeptides, nucleic acids encoding ATPHyl, anti-ATPHyl antibodies, or binding polypeptides, peptides and small molecules that bind to ATPHyl polypeptides or polynucleotides, described below. Targeting of ATPHyl on the cell membranes is expected to inhibit the growth of or destroy such cells. An effective dose will be the amount of such targeting preparations necessary to target the cell surface ATPHyl and inhibit the growth of or destroy the cells expressing ATPHyl and/or metastasis.

A further embodiment of the present invention is to enhance the effects of therapeutic agents and adjunctive agents used to treat and manage disorders associated with said ATPHyl, by administering targeting preparations that recognize ATPHyl with therapeutic and adjuvant agents commonly used to treat such disorders. Chemotherapeutic agents useful in treating neoplastic disease and antiproliferative agents and drugs used for immunosuppression include alkylating agents, such as nitrogen mustards, alkyl sulfonates, nitrosoureas, triazenes; antimetabolites, such as folic acid analogs, pyrimidine analogs, and purine analogs; natural products, such as vinca alkaloids, epipodophyllotoxins, antibiotics, and enzymes; miscellaneous agents such as polatinum coordination complexes, substituted urea, methyl hydrazine derivatives, and adrenocortical suppressant; and hormones and antagonists, such as adrenocorticosteroids, progestins, estrogens, androgens, and anti-estrogens (Calebresi and Parks, pp. 1240-1306 in, Eds. A.G Goodman, L.S. Goodman, T.W. Rail, andF. Murad, The Pharmacological Basis of Therapeutics, Seventh Edition, MacMillan Publishing Company, New York, (1985), incoφorated herein by reference in its entirety).

Adjunctive therapy used in the management of such disorders includes, for example, radiosensitizing agents, coupling of antigen with heterologous proteins, such as globulin or beta-galactosidase, or inclusion of an adjuvant during immunization. High doses may be required for some therapeutic agents to achieve levels to effectuate the target response, but may often be associated with a greater frequency of dose- related adverse effects. Thus, combined use of the targeting therapeutic methods of the present invention with agents commonly used to treat disorders associated with expression of ATPHyl allows the use of relatively lower doses of such agents resulting in a lower frequency of adverse side effects associated with long-term administration of the conventional therapeutic agents. Thus another indication for the targeting therapeutic methods of this invention is to reduce adverse side effects associated with conventional therapy of these disorders. 4.1 TARGETING OF ATPHyl

P-type ATPases comprise a well-studied family of proteins involved in the active transport of charged substrates across biological membranes (reviewed in Dunbar and Caplan, J. Biol. Chem. 276:29617-29620 (2001) herein incoφorated by reference in its entirety). Members of this family include the sodium/potassium- (Na /K -), proton/potassium- (H⁺/K⁺-), and calcium- (Ca²⁺-) ATPases, as well as aminophospholipid transporters, which are responsible for maintaining cellular homeostasis via osmotic balance and intracellular ionic composition. Furthermore, almost every transport operation performed by the cells of epithelial tissues is coupled in some fashion to the action of a P- type ATPase (Caplan, Am. J. Physiol. 272:G1304-G1313 (1997) herein incoφorated by reference in its entirety). The enzymatic activities of these pumps constitute some of the principle means by which animal cells convert the energy within ATP into electrochemical gradients that can be exploited by all manner of metabolic pathways. The physiologic function of an ion transport protein is determined in part by its subcellular localization and the cellular mechanisms that modulate its activity. A human homolog of the P-type ATPases, herein termed ATPHyl , has been found to be upregulated in breast, colon, lung and prostate cancer (as determined by mRNA and protein expression) when compared to healthy tissue as well as normal tissue obtained from a position adjacent to the tumor (see Examples 1 and 3 and Figure 3), with the exception of normal breast and prostate tissue. ATPHyl polypeptides and polynucleotides encoding such polypeptides are disclosed in co-owned U.S. Patent Application Serial No. 09/488,725, 09/552,317 (corresponding to PCT Publication No. WO 01/53455 and WO 01/52616), 09/620,312 (corresponding to PCT Publication No. WO 01/53312), and U.S. Provisional Patent Application Serial No. 60/458,824. These and all other U.S. patents and patent applications, foreign patents and PCT publications cited herein are hereby incoφorated by reference in their entirety. U.S. Patent Application Serial No. 09/488,725 and 09/552,317 incoφorated by reference herein in their entirety relate, in general to a collection or library of at least one novel nucleic acid sequences, specifically contigs, assembled from expressed sequence tags (ESTs). U.S. Patent Application Serial No. 09/620,312 and 60/458,824, incoφorated by reference herein in their entirety, (specifically including all sequences in the sequence listing) discloses ATPHyl polypeptides, isolated polynucleotides encoding such polypeptides, including recombinant molecules, cloned genes or degenerate variants thereof, especially naturally occurring variants such as allelic variants, fragments or analogs or variants of such polynucleotides or polypeptides, antisense polynucleotide molecules, and antibodies that specifically recognize one or more epitopes present on such polypeptides, including polyclonal, monoclonal, single chain, bispecific, fragment, human and humanized antibodies, as well as hybridomas producing monoclonal antibodies, and diagnostic and therapeutic uses and screening assays associated with such polynucleotides, polypeptides and antibodies.

The ATPHyl polypeptide of SEQ ID NO: 2 is an approximately 1177 amino acid protein with a predicted molecular weight of 353 kD unglycosylated. The initial methionine starts at position 273 and the putative stop codon begins at position 3804 of SEQ LD NO: 1. Using TMpred (Hofmann and Stoffel, Biol. Chem. Hoppe-Seyler 374:166 (1993) herein incoφorated by reference in its entirety), nine (9) transmembrane domains are predicted to span residues 66-81, 88-103, 289-307, 342-361, 910-923, 960-973, 999-1015, 1030-1050, and 1069-1086 of SEQ ID NO: 2. One of skill in the art will recognize that the actual domains may be different than those predicted by the computer program. Using the eMATRTX software package (Stanford University, Stanford, CA; Wu et al, J. Comp. Biol. 6:219-235 (1999) herein incoφorated by reference in its entirety) ATPHyl is expected to have a Na⁺/K⁺-transporting ATPase signature IV (accession number PR00121D) at residues 398-419, an E1-E2 ATPases domain (accession number IPB001757B) at residues 404-838, a P-type cation-transporting ATPase superfamily signature II (accession number PROOl 19B) at residues 405-419, a P-type cation-transporting ATPase superfamily signature TV (accession number PROOl 19D) at residues 698-708, and a P-type cation-transporting ATPase superfamily signature V (accession number PROOl 19E) at residues 819-838. Using the pfam families database (Washington University School of Medicine, St. Louis, MO; Bateman et al, Nucl Acids Res. 30:276-280 (2002) herein incoφorated by reference in its entirety), SEQ ID NO: 2 is predicted to contain two (2) haloacid dehalogenase-like hydrolase domains at residues 401-747 and residues 816-842, as well as two (2) binding-protein-dependent transport system domains at residues 918-941 and residues 1038-1099.

Using a pfam model near the C-terminus, which is typically intracellular in other family members, the topology of ATPHyl was determined to predict the extracellular domains of ATPHyl. The following regions of ATPHyl are predicted to be extracellular: amino acids 82-87, 308-341, 924-959, 1016-1029, and 1087-1177. One of skill in the art will recognize that the actual domains may be different than those predicted.

Protein database searches with the BLASTP algorithm (Altschul et al, J. Mol. Evol 36:290-300 (1993); Altschul et al, J. Mol. Biol. 21:403-410 (1990) both of which are herein incoφorated by reference in their entirety) indicate that SEQ ID NO: 2 is homologous to the rabbit type IV P:type ATPase that binds to the RTNG motif of the RUSH transcription factor (gi 7715417) and the human potential phospholipids-transporting ATPase IR (gi 8134330). An alignment of SEQ ID NO: 2 with the rabbit P-type ATPase (SEQ ID NO: 3) is shown in Figure 1 indicating that the two sequences share 88% similarity and 85% identity over 1173 amino acids of SEQ ID NO: 2, wherein A=Alanine, C=Cysteine, D=Aspartic Acid, E= Glutamic Acid, F=Phenylalanine, G=Glycine, H=Histidine, I=Isoleucine, K=Lysine, L=Leucine, M=Methionine, N=Asparagine, P=Proline, Q=Glutamine, R=Arginine, S=Serine, T=Threonine, V=Valine, W=Tryptophan, Y=Tyrosine. Gaps are presented as dashes. An alignment of SEQ ID NO: 2 with the human potential phospholipid-transporting ATPase (SEQ ID NO: 4) is shown in Figure 2, indicating that the two sequences share 100% identity over 672 amino acids of SEQ ID NO: 2, wherein A= Alanine, C=Cysteine, D^Aspartic Acid, E= Glutamic Acid, F=Phenylalanine, G=Glycine, H=Histidine, I=Isoleucine, K=Lysine, L=Leucine, M=Methionine, N=Asparagine, P=Proline, Q=Glutamine, R=Arginine, S=Serine, T=Threonine, V= Valine, W=Tryptophan, Y=Tyrosine. Gaps are presented as dashes. ATPHyl is expressed in certain cancers including breast, colon, lung, and prostate cancer while most healthy cells fail to express ATPHyl or express it at low levels (see Figure 3). Thus, targeting ATPHyl will be useful in treating these cancers. The ATPHyl peptide itself may be used to target toxins or radioisotopes to tumor cells in vivo. The extracellular domain(s) of ATPHyl, or a fragment of this domain, may be able to bind to ATPHyl expressed on tumor cells. This peptide fragment then may be used as a means to deliver cytotoxic agents to ATPHyl bearing tumor cells. Much like an antibody, these fragments may specifically target cells expressing this antigen. Targeted delivery of these cytotoxic agents to the tumor cells would result in cell death and suppression of tumor growth. An example of the ability of an extracellular fragment binding to and activating its intact receptor (by homophilic binding) has been demonstrated with the

CD84 receptor (Martin, et al, J. Immunol, 161:3668-3616 (2001), incoφorated herein by reference in its entirety).

Extracellular fragments of the ATPHyl receptor may also be used to modulate immune cells expressing the protein. Extracellular domain fragments of the receptor may bind to and activate its own receptor expressed on the cell surface. On cells bearing the ATPHyl receptor (such as NK cells, T cells, B cells and myeloid cells) this may result in stimulating the release of cytokines (such as interferon gamma for example) that may enhance or suppress the immune system. Additionally, binding of these fragments to cells bearing the ATPHyl receptor may result in the activation of these cells and also may stimulate proliferation. Some fragments may bind to the intact ATPHyl receptor and block activation signals and cytokine release by immune cells. These fragments would then have an immune suppressive effect. Fragments that activate and stimulate the immune system may have anti-tumor properties. These fragments may stimulate an immunological response that can result in immune mediated tumor cell killing. The same fragments may result in stimulating the immune system to mount an enhance response to foreign invaders such as virus and bacteria. Fragments that suppress the immune response may be useful in treating lymphoprohferative disorders, auto-immune disease, graft-vs-host disease, and inflammatory disorders such as emphysema.

4.2 DEFINITIONS

The term "fragment" of a nucleic acid refers to a sequence of nucleotide residues which are at least 5 nucleotides, more preferably at least 7 nucleotides, more preferably at least 9 nucleotides, more preferably at least 11 nucleotides and most preferably at least 17 nucleotides. The fragment is preferably less than 500 nucleotides, preferably less than 200 nucleotides, more preferably less than 100 nucleotides, more preferably less than 50 nucleotides and most preferably less than 30 nucleotides. Preferably the fragments can be used in polymerase chain reaction (PCR), various hybridization procedures or microarray procedures to identify or amplify identical or related parts of mRNA or DNA molecules. A fragment or segment may uniquely identify each polynucleotide sequence of the present mvention. Preferably the fragment comprises a sequence substantially similar to a portion of

SEQ ID NO: 1. A polypeptide "fragment " is a stretch of amino acid residues of at least 5 amino acids, preferably at least 7 amino acids, more preferably at least 9 amino acids and most preferably at least 17 or more amino acids. The peptide preferably is not greater than

200 amino acids, more preferably less than 150 amino acids and most preferably less than 100 amino acids. Preferably the peptide ranges in size from 5 to 200 amino acids. To be active, any polypeptide must have sufficient length to display biological and/or immunological activity. The term "immunogenic" refers to the capability of the natural, recombinant or synthetic ATPHyl peptide, or any peptide thereof, to induce a specific immune response in appropriate animals or cells and to bind with specific antibodies. The term "ATPHyl antigen" refers to a molecule that when introduced into an animal is capable of stimulating an immune response in said animal specific to the ATPHyl polypeptide or fragment thereof, of the present invention.

The term "variant"(or "analog") refers to any polypeptide differing from naturally occurring polypeptides by amino acid insertions, deletions, and substitutions, created using, e g., recombinant DNA techniques. Guidance in determining which amino acid residues may be replaced, added or deleted without abolishing activities of interest, may be found by comparing the sequence of the particular polypeptide with that of homologous peptides and minimizing the number of amino acid sequence changes made in regions of high homology (conserved regions) or by replacing amino acids with consensus sequence.

Alternatively, recombinant variants encoding these same or similar polypeptides may be synthesized or selected by making use of the "redundancy" in the genetic code. Various codon substitutions, such as the silent changes which produce various restriction sites, may be introduced to optimize cloning into a plasmid or viral vector or expression in a particular prokaryotic or eukaryotic system. Mutations in the polynucleotide sequence may be reflected in the polypeptide or domains of other peptides added to the polypeptide to modify the properties of any part of the polypeptide, to change characteristics such as ligand-binding affinities, interchain affinities, or degradation/turnover rate. 4.3 TARGETING USING ATPHYl ANTIGENS

One embodiment of the present invention provides a composition comprising an ATPHyl polypeptide to stimulate the immune system against ATPHyl, thus targeting ATPHyl -expressing cells. Use of a tumor antigen in a composition for generating cellular and humoral immunity for the puφose of anti-cancer therapy is well known in the art. For example, one type of tumor-specific antigen composition uses purified idiotype protein isolated from tumor cells, coupled to keyhole limpet hemocyanin (KLH) and mixed with adjuvant for injection into patients with low-grade follicular lymphoma (Hsu, et al, Blood 89: 3129-3135 (1997), herein incoφorated by reference in its entirety). U.S. Patent No. 6,312,718, herein incoφorated by reference in its entirety, describes methods for inducing immune responses against malignant B cells, in particular lymphoma, chronic lymphocytic leukemia, and multiple myeloma. The methods described therein utilize compositions that include liposomes having (1) at least one B-cell malignancy-associated antigen, (2) IL-2 alone, or in combination with at least one other cytokine or chemokine, and (3) at least one lipid molecule. Methods of targeting ATPHyl using an ATPHyl antigen typically employ an ATPHyl polypeptide, including fragments, analogs and variants.

As another example, dendritic cells, one type of antigen-presenting cell, can be used in a cellular composition in which the dendritic cells are isolated from the patient, co- cultured with tumor antigen and then reinfused as a cellular composition (Hsu, et al, Nat. Med. 2:52-58 (1996), herein incoφorated by reference in its entirety).

Combining this antigen targeting therapy with other types of therapeutic agents in treatments such as chemotherapy or radiotherapy is also contemplated.

4.4 TARGETING USING NUCLEIC ACIDS 4.4.1 DIRECT DELIVERY OF NUCLEIC ACIDS

In some embodiments, a nucleic acid encoding ATPHyl, or encoding a fragment, analog or variant thereof, within a recombinant vector is utilized. Such methods are known in the art. For example, immune responses can be induced by injection of naked DNA. Plasmid DNA that expresses bicistronic mRNA encoding both the light and heavy chains of tumor idiotype proteins, such as those from B cell lymphoma, when injected into mice, are able to generate a protective, anti-tumor response (Singh, et al, Vaccine 20:1400-1411 (2002), herein incoφorated by reference in its entirety). ATPHyl viral vectors are particularly useful for delivering nucleic acids encoding ATPHyl of the invention to cells. Examples of vectors include those derived from influenza, adenovirus, vaccinia, heφes symplex virus, fowlpox, vesicular stomatitis virus, canarypox, poliovirus, adeno-associated virus, and lentivirus and sindbus virus. Of course, non- viral vectors, such as liposomes or even naked DNA, are also useful for delivering nucleic acids encoding ATPHyl of the invention to cells.

Combining this type of therapy with other types of therapeutic agents or treatments such as chemotherapy or radiation is also contemplated.

4.4.2 NUCLEIC ACIDS EXPRESSED IN CELLS In some embodiments, a vector comprising a nucleic acid encoding the ATPHyl polypeptide (including a fragment, analog or variant) is introduced into a cell, such as a dendritic cell or a macrophage. When expressed in an antigen-presenting cell (APC), the ATPHyl cell surface antigens are presented to T cells eliciting an immune response against ATPHyl . Such methods are also known in the art. Methods of introducing tumor antigens into APCs and vectors useful therefore are described in U.S. Patent No. 6,300,090, herein incoφorated by reference in its entirety. The vector encoding ATPHyl may be introduced into the APCs in vivo. Alternatively, APCs are loaded with ATPHyl or a nucleic acid encoding ATPHyl ex vivo and then introduced into a patient to elicit an immune response against ATPHyl . In another alternative, the cells presenting ATPHyl antigen are used to stimulate the expansion of anti-ATPHyl cytotoxic T lymphocytes (CTL) ex vivo followed by introduction of the stimulated CTL into a patient. (U.S. Patent No. 6,306,388, herein incoφorated by reference in its entirety).

4.4.3 ANTISENSE NUCLEIC ACIDS

Another aspect of the invention pertains to isolated antisense nucleic acid molecules that can hybridize to, or are complementary to, the nucleic acid molecule comprising the ATPHyl nucleotide sequence, or fragments, analogs or derivatives thereof. An "antisense" nucleic acid comprises a nucleotide sequence that is complementary to a "sense" nucleic acid encoding a protein (e.g., complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA sequence). In specific aspects, antisense nucleic acid molecules are provided that comprise a sequence complementary to at least 10, 25, 50, 100, 250 or 500 nucleotides or an entire ATPHyl coding strand, or to only a portion thereof.

Nucleic acid molecules encoding fragments, homologs, derivatives and analogs of a

ATPHyl or antisense nucleic acids complementary to a ATPHyl nucleic acid sequence of are additionally provided. In one embodiment, an antisense nucleic acid molecule is antisense to a "coding region" of the coding strand of a nucleotide sequence encoding an ATPHyl protein. The term "coding region" refers to the region of the nucleotide sequence comprising codons which are translated into amino acid residues. In another embodiment, the antisense nucleic acid molecule is antisense to a "conceding region" of the coding strand of a nucleotide sequence encoding the ATPHyl protein. The term "conceding region" refers to 5' and 3' sequences which flank the coding region that are not translated into amino acids (i.e., also referred to as 5' and 3' untranslated regions).

Given the coding strand sequences encoding the ATPHyl protein disclosed herein, antisense nucleic acids of the invention can be designed according to the rules of Watson and Crick or Hoogsteen base pairing. The antisense nucleic acid molecule can be complementary to the entire coding region of ATPHyl mRNA, but more preferably is an oligonucleotide that is antisense to only a portion of the coding or noncoding region of ATPHyl mRNA. For example, the antisense oligonucleotide can be complementary to the region surrounding the translation start site of ATPHyl mRNA. An antisense oligonucleotide can be, for example, 5, 10, 15, 20, 25, 30, 35, 40, 45, or 50 nucleotides in length. An antisense nucleic acid of the invention can be constructed using chemical synthesis or enzymatic ligation reactions using procedures known in the art. For example, an antisense nucleic acid (e.g., an antisense oligonucleotide) can be chemically synthesized using naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acids (e.g., phosphorothioate derivatives and acridine substituted nucleotides can be used).

Examples of modified nucleotides that can be used to generate the antisense nucleic acid include: 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil, 5- carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6-isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2-methylguanine, 3- methylcytosine, 5-methylcytosine, N6-adenine, 7-methylguanine, 5- methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D-mannosylqueosine, 5'-methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-N6-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2-thiocytosine, 5-methyl- 2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and 2,6-diaminopurine. Alternatively, the antisense nucleic acid can be produced biologically using an expression vector into which a nucleic acid has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest, described further in the following section).

The antisense nucleic acid molecules of the invention are typically administered to a subject or generated in situ such that they hybridize with or bind to cellular mRNA and/or genomic DNA encoding a ATPHyl protein to thereby inhibit expression of the protein (e.g., by inhibiting transcription and/or translation). The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid molecule that binds to DNA duplexes, through specific interactions in the major groove of the double helix. An example of a route of administration of antisense nucleic acid molecules of the invention includes direct injection at a tissue site. Alternatively, antisense nucleic acid molecules can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense molecules can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface (e.g., by linking the antisense nucleic acid molecules to peptides or antibodies that bind to cell surface receptors or antigens). The antisense nucleic acid molecules can also be delivered to cells using the vectors described herein. To achieve sufficient nucleic acid molecules, vector constructs in which the antisense nucleic acid molecule is placed under the control of a strong pol II or pol III promoter are preferred.

In yet another embodiment, the antisense nucleic acid molecule of the invention is an alpha-anomeric nucleic acid molecule. An alpha-anomeric nucleic acid molecule forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual alpha-units, the strands run parallel to each other. See, e.g., Gaultier, et al, Nucl Acids Res. 15: 6625-6641 (1987). The antisense nucleic acid molecule can also comprise a 2'-o- methylribonucleotide (see, e.g., Inoue, et al, Nucl. Acids Res. 15: 6131 -6148 (1987)) or a chimeric RNA-DNA analogue (see, e.g., ioue, et al, FEBSLett. 215: 327-330 (1987), all of which are herein incoφorated by reference in their entirety.

4.4.4 RIBOZYMES AND PNA MOIETIES In still another embodiment, an antisense nucleic acid of the invention is a ribozyme.

Ribozymes are catalytic RNA molecules with ribonuclease activity that are capable of cleaving a single-stranded nucleic acid, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334:585-591)) can be used to catalytically cleave mRNA transcripts to thereby inhibit translation of an mRNA. A ribozyme having specificity for a nucleic acid of the invention can be designed based upon the nucleotide sequence of a DNA disclosed herein (i.e., SEQ ID NO: 1). For example, a derivative of Tetrahymena L-19 IVS RNA can be constructed in which the nucleotide sequence of the active site is complementary to the nucleotide sequence to be cleaved in a mRNA. See, e.g., Cech et al. U.S. Pat. No. 4,987,071; and Cech et al. U.S. Pat. No. 5,116,742. Alternatively, mRNA of the invention can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules. See, e.g., Bartel et al., (1993) Science 261:1411-1418.

Alternatively, gene expression can be inhibited by targeting nucleotide sequences complementary to the regulatory region (e.g., promoter and/or enhancers) to form triple helical structures that prevent transcription of the gene in target cells. See generally, Helene. (1991) Anticancer Drug Des. 6: 569-84; Helene. et al. (1992) Ann. N.Y. Acad. Sci. 660:27-36; and Maher (1992) Bioassays 14: 807-15.

In various embodiments, the nucleic acids of the invention can be modified at the base moiety, sugar moiety or phosphate backbone to improve, e.g., the stability, hybridization, or solubility of the molecule. For example, the deoxyribose phosphate backbone of the nucleic acids can be modified to generate peptide nucleic acids (see Hyrup et al. (1996) BioorgMed Chem 4: 5-23). As used herein, the terms "peptide nucleic acids" or "PNAs" refer to nucleic acid mimics, e.g., DNA mimics, in which the deoxyribose phosphate backbone is replaced by a pseudopeptide backbone and only the four natural nucleobases are retained. The neutral backbone of PNAs has been shown to allow for specific hybridization to DNA and RNA under conditions of low ionic strength. The synthesis of PNA oligomers can be performed using standard solid phase peptide synthesis protocols as described in Hyrup et al. (1996) above; Perry-O'Keefe et al. (1996) PNAS 93:

14670-675.

PNAs of the mvention can be used in therapeutic and diagnostic applications. For example, PNAs can be used as antisense or antigene agents for sequence-specific modulation of gene expression by, e.g. , inducing transcription or translation arrest or inliibiting replication. PNAs of the invention can also be used, e.g., in the analysis of single base pair mutations in a gene by, e.g., PNA directed PCR clamping; as artificial restriction enzymes when used in combination with other enzymes, e.g., SI nucleases (Hyrup B. (1996) above); or as probes or primers for DNA sequence and hybridization (Hyrup et al. (1996), above; Perry-O'Keefe (1996), above).

In another embodiment, PNAs of the invention can be modified, e.g., to enhance their stability or cellular uptake, by attaching lipophilic or other helper groups to PNA, by the formation of PNA-DNA chimeras, or by the use of liposomes or other techniques of drug delivery known in the art. For example, PNA-DNA chimeras can be generated that may combine the advantageous properties of PNA and DNA. Such chimeras allow DNA recognition enzymes, e.g. , RNase H and DNA polymerases, to interact with the DNA portion while the PNA portion would provide high binding affinity and specificity. PNA-DNA chimeras can be linked using linkers of appropriate lengths selected in terms of base stacking, number of bonds between the nucleobases, and orientation (Hyrup (1996) above). The synthesis of PNA-DNA chimeras can be performed as described in Hyrup

(1996) above and Finn et al. (1996) Nucl Acids Res 24: 3357-63. For example, a DNA chain can be synthesized on a solid support using standard phosphoramidite coupling chemistry, and modified nucleoside analogs, e.g., 5'-(4-methoxytrityl)amino-5^,-deoxy-thymidine phosphoramidite, can be used between the PNA and the 5' end of DNA (Mag et al. (1989) Nucl Acid Res 17: 5973-88). PNA monomers are then coupled in a stepwise manner to produce a chimeric molecule with a 5' PNA segment and a 3' DNA segment (Finn et al. (1996) above). Alternatively, chimeric molecules can be synthesized with a 5' DNA segment and a 3' PNA segment. See, Petersen et al. (1975) BioorgMed Chem Lett 5: 1119-11124. In other embodiments, the oligonucleotide may include other appended groups such as peptides (e.g., for targeting host cell receptors in vivo), or agents facilitating transport across the cell membrane (see, e.g., Letsinger et al, 1989, Proc. Natl Acad. Sci. U.S.A. 86:6553-6556; Lemaitre et al, 1987, Proc. Natl. Acad. Sci. 84:648-652; PCT Publication No. WO 88/09810) or the blood-brain barrier (see, e.g., PCT Publication No. W089/10134). In addition, oligonucleotides can be modified with hybridization triggered cleavage agents (See, e.g., Krol et al, 1988, BioTechniques 6:958-976) or intercalating agents. (See, e.g., Zon, 1988, Pharm. Res. 5: 539-549). To this end, the oligonucleotide maybe conjugated to another molecule, e.g., a peptide, a hybridization triggered cross-linking agent, a transport agent, a hybridization-triggered cleavage agent, etc.

4.4.5 GENE THERAPY

Mutations in the polynucleotides of the invention gene may result in loss of normal function of the encoded protein. The invention thus provides gene therapy to restore normal activity of the polypeptides of the invention; or to treat disease states involving polypeptides of the invention. Delivery of a functional gene encoding polypeptides of the invention to appropriate cells is effected ex vivo, in situ, or in vivo by use of vectors, and more particularly viral vectors (e.g., adenovirus, adeno-associated virus, or a retrovirus), or ex vivo by use of physical DNA transfer methods (e.g., liposomes or chemical treatments). See, for example, Anderson, Nature, 392(Suppl):25-20 (1998). For additional reviews of gene therapy technology see Friedmann, Science, 244: 1275-1281 (1989); Verma, Scientific American: 68-84 (1990); and Miller, Nature, 357: 455-460 (1992), all of which are herein incoφorated by reference in their entirety. Introduction of any one of the nucleotides of the present invention or a gene encoding the polypeptides of the present invention can also be accomplished with extrachromosomal substrates (transient expression) or artificial chromosomes (stable expression). Cells may also be cultured ex vivo in the presence of proteins of the present invention in order to proliferate or to produce a desired effect on or activity in such cells. Treated cells can then be introduced in vivo for therapeutic pvnposes. Alternatively, it is contemplated that in other human disease states, preventing the expression of or inhibiting the activity of polypeptides of the invention will be useful in treating the disease states. It is contemplated that antisense therapy or gene therapy could be applied to negatively regulate the expression of polypeptides of the invention.

Other methods inhibiting expression of a protein include the introduction of antisense molecules to the nucleic acids of the present invention, their complements, or their translated RNA sequences, by methods known in the art. Further, the polypeptides of the present invention can be inhibited by using targeted deletion methods, or the insertion of a negative regulatory element such as a silencer, which is tissue specific. The present invention still further provides cells genetically engineered in vivo to express the polynucleotides of the invention, wherein such polynucleotides are in operative association with a regulatory sequence heterologous to the host cell which drives expression of the polynucleotides in the cell. These methods can be used to increase or decrease the expression of the polynucleotides of the present invention.

Knowledge of DNA sequences provided by the invention allows for modification of cells to permit, increase, or decrease, expression of endogenous polypeptide. Cells can be modified (e.g., by homologous recombination) to provide increased polypeptide expression by replacing, in whole or in part, the naturally occurring promoter with all or part of a heterologous promoter so that the cells express the protein at higher levels. The heterologous promoter is inserted in such a manner that it is operatively linked to the desired protein encoding sequences. See, for example, PCT International Publication No. WO 94/12650, PCT International Publication No. WO 92/20808, and PCT International Publication No. WO 91/09955, all of which are incoφorated by reference in their entirety. It is also contemplated that, in addition to heterologous promoter DNA, amplifiable marker DNA (e.g., ada, dhfr, and the multifunctional CAD gene which, encodes carbamyl phosphate synthase, aspartate transcarbamylase, and dihydroorotase) and/or intron DNA may be inserted along with the heterologous promoter DNA. If linked to the desired protein coding sequence, amplification of the marker DNA by standard selection methods results in co- amplification of the desired protein coding sequences in the cells.

In another embodiment of the present invention, cells and tissues may be engineered to express an endogenous gene comprising the polynucleotides of the invention under the control of inducible regulatory elements, in which case the regulatory sequences of the endogenous gene may be replaced by homologous recombination. As described herein, gene targeting can be used to replace a gene's existing regulatory region with a regulatory sequence isolated from a different gene or a novel regulatory sequence synthesized by genetic engineering methods. Such regulatory sequences may be comprised of promoters, enhancers, scaffold-attachment regions, negative regulatory elements, transcriptional initiation sites, regulatory protein binding sites or combinations of said sequences. Alternatively, sequences which affect the structure or stability of the RNA or protein produced may be replaced, removed, added, or otherwise modified by targeting. These sequences include polyadenylation signals, mRNA stability elements, splice sites, leader sequences for enhancing or modifying transport or secretion properties of the protein, or other sequences which alter or improve the function or stability of protein or RNA molecules.

The targeting event may be a simple insertion of the regulatory sequence, placing the gene under the control of the new regulatory sequence, e.g., inserting a new promoter or enhancer or both upstream of a gene. Alternatively, the targeting event may be a simple deletion of a regulatory element, such as the deletion of a tissue-specific negative regulatory element. Alternatively, the targeting event may replace an existing element; for example, a tissue-specific enhancer can be replaced by an enhancer that has broader or different cell- type specificity than the naturally occurring elements. Here, the naturally occurring sequences are deleted and new sequences are added. In all cases, the identification of the targeting event may be facilitated by the use of one or more selectable marker genes that are contiguous with the targeting DNA, allowing for the selection of cells in which the exogenous DNA has integrated into the cell genome. The identification of the targeting event may also be facilitated by the use of one or more marker genes exhibiting the property of negative selection, such that the negatively selectable marker is linked to the exogenous DNA, but configured such that the negatively selectable marker flanks the targeting sequence, and such that a correct homologous recombination event with sequences in the host cell genome does not result in the stable integration of the negatively selectable marker. Markers useful for this puφose include the Heφes Simplex Virus thymidine kinase (TK) gene or the bacterial xanthine-guanine phosphoribosyl-transferase (gpt) gene.

The gene targeting or gene activation techniques which can be used in accordance with this aspect of the invention are more particularly described in U.S. Patent No. 5,272,071 to Chappel; U.S. Patent No. 5,578,461 to Sherwin et al; International Application No. PCT/US92/09627 (WO 93/09222) by Selden et al.; and International Application No. PCT/US90/06436 (WO 91/06667) by Skoultchi et al., each of which is incoφorated by reference herein in its entirety.

4.5 ANTI-ATPHYl ANTIBODIES

Alternatively, immunotargeting involves the administration of components of the immune system, such as antibodies, antibody fragments, or primed cells of the immune system against the target. Methods of immunotargeting cancer cells using antibodies or antibody fragments are well known in the art. U.S. Patent No. 6,306,393 describes the use of anti-CD22 antibodies in the immunotherapy of B-cell malignancies, and U.S. Patent No. 6,329,503 describes immunotargeting of cells that express seφentine transmembrane antigens (both U.S. patents are herein incoφorated by reference in their entirety).

ATPHyl antibodies (including humanized or human monoclonal antibodies or fragments or other modifications thereof, optionally conjugated to cytotoxic agents) may be introduced into a patient such that the antibody binds to ATPHyl expressed by cancer cells and mediates the destruction of the cells and the tumor and/or inhibits the growth of the cells or the tumor. Without intending to limit the disclosure, mechanisms by which such antibodies can exert a therapeutic effect may include complement-mediated cytolysis, antibody-dependent cellular cytotoxicity (ADCC), modulating the physiologic function of ATPHyl , inhibiting binding or signal transduction pathways, modulating tumor cell differentiation, altering tumor angiogenesis factor profiles, modulating the secretion of immune stimulating or tumor suppressing cytokines and growth factors, modulating cellular adhesion, and/or by inducing apoptosis. ATPHyl antibodies conjugated to toxic or therapeutic agents, such as radioligands or cytosolic toxins, may also be used therapeutically to deliver the toxic or therapeutic agent directly to ATPHyl -bearing tumor cells.

ATPHyl antibodies may be used to suppress the immune system in patients receiving organ transplants or in patients with autoimmune diseases such as arthritis. Healthy immune cells would be targeted by these antibodies leading their death and clearance from the system, thus suppressing the immune system. ATPHyl antibodies may be used as antibody therapy for solid tumors which express this action. Cancer immunotherapy using antibodies provides a novel approach to treating cancers associated with cells that specifically express ATPHyl . As described above, ATPHyl mRNA is expressed in breast, lung, colon, and prostate tumor tissues indicating that ATPHyl may be used as a therapeutic antibody target and a diagnostic marker for certain cell types or disorders (e.g., breast, colon, lung, and prostate cancer). Cancer immunotherapy using antibodies has been previously described for other types of cancer, including but not limited to colon cancer (Arlen et al, Crit. Rev. Immunol. 18:133-138 (1998)), multiple myeloma (Ozaki et al, Blood 90:3179-3186 (1997); Tsunenari et al, Blood 90:2437-2444 (1997)), gastric cancer (Kasprzyk et al, Cancer Res. 52:2771-2776 (1992)), B cell lymphoma (Funakoshi et al, J. Immunother. Emphasisi Tumor Immunol.

19:93-101 (1996)), leukemia (Zhong et al, Leuk. Res. 20:581-589 (1996)), colorectal cancer (Moun et /., Cancer Res. 54:6160-6166 (1994); Velders et al, Cancer Res. 55:4398-4403 (1995)), and breast cancer (Shepard et al, J. Clin. Immunol. 11:117-127 (1991), all of the above listed references are herein incoφorated by reference in their entirety).

Although ATPHyl antibody therapy may be useful for all stages of the foregoing cancers, antibody therapy may be particularly appropriate in advanced or metastatic cancers. Combining the antibody therapy method with a chemotherapeutic, radiation or surgical regimen may be preferred in patients that have not received chemotherapeutic treatment, whereas treatment with the antibody therapy may be indicated for patients who have received one or more chemotherapies. Additionally, antibody therapy can also enable the use of reduced dosages of concomitant chemotherapy, particularly in patients that do not tolerate the toxicity of the chemotherapeutic agent very well. Furthermore, treatment of cancer patients with ATPHyl antibody with tumors resistant to chemotherapeutic agents might induce sensitivity and responsiveness to these agents in combination.

Prior to anti-ATPHyl immunotargeting, a patient may be evaluated for the presence and level of ATPHyl expression by the cancer cells, preferably using immunohistochemical assessments of tumor tissue, quantitative ATPHyl imaging, quantitative RT-PCR, or other techniques capable of reliably indicating the presence and degree of ATPHyl expression. For example, a blood or biopsy sample may be evaluated by immunohistochemical methods to determine the presence of ATPHyl -expressing cells or to determine the extent of ATPHyl expression on the surface of the cells within the sample. Methods for immunohistochemical analysis of tumor tissues or released fragments of ATPHyl in the serum are well known in the art.

Anti-ATPHyl antibodies useful in treating cancers include those, which are capable of initiating a potent immune response against the tumor and those, which are capable of direct cytotoxicity. In this regard, anti-ATPHyl mAbs may elicit tumor cell lysis by either complement-mediated or ADCC mechanisms, both of which require an intact Fc portion of the immunoglobulin molecule for interaction with effector cell Fc receptor sites or complement proteins. In addition, anti-ATPHyl antibodies that exert a direct biological effect on tumor growth are useful in the practice of the invention. Potential mechanisms by which such directly cytotoxic antibodies may act include inhibition of cell growth, modulation of cellular differentiation, modulation of tumor angiogenesis factor profiles, and the induction of apoptosis. The mechanism by which a particular anti-ATPHyl antibody exerts an anti-tumor effect may be evaluated using any number of in vitro assays designed to determine ADCC, ADMMC, complement-mediated cell lysis, and so forth, as is generally known in the art.

The anti-tumor activity of a particular anti-ATPHyl antibody, or combination of anti-ATPHyl antibody, may be evaluated in vivo using a suitable animal model. For example, xenogenic prostate cancer models wherein human prostate cells are introduced into immune compromised animals, such as nude or SCID mice. Efficacy may be predicted using assays which measure inhibition of tumor formation, tumor regression or metastasis, and the like.

It should be noted that the use of murine or other non-human monoclonal antibodies, human/mouse chimeric mAbs may induce moderate to strong immune responses in some patients. In the most severe cases, such an immune response may lead to the extensive formation of immune complexes, which, potentially, can cause renal failure. Accordingly, preferred monoclonal antibodies used in the practice of the therapeutic methods of the invention are those which are either fully human or humanized and which bind specifically to the target ATPHyl antigen with high affinity but exhibit low or no antigenicity in the patient.

The method of the invention contemplates the administration of single anti-ATPHyl monoclonal antibodies (mAbs) as well as combinations, or "cocktails", of different mAbs. Two or more monoclonal antibodies that bind to ATPHyl may provide an improved effect compared to a single antibody. Alternatively, a combination of an anti-ATPHyl antibody with an antibody that binds a different antigen may provide an improved effect compared to a single antibody. Such mAb cocktails may have certain advantages inasmuch as they contain mAbs, which exploit different effector mechanisms or combine directly cytotoxic mAbs with mAbs that rely on immune effector functionality. Such mAbs in combination may exhibit synergistic therapeutic effects. In addition, the administration of anti-ATPHyl mAbs may be combined with other therapeutic agents, including but not limited to various chemotherapeutic agents, androgen-blockers, and immune modulators (e.g., IL-2, GM-CSF). The anti-ATPHyl mAbs may be administered in their "naked" or unconjugated form, or may have therapeutic agents conjugated to them. Additionally, bispecific antibodies may be used. Such an antibody would have one antigemc binding domain specific for ATPHyl and the other antigenic binding domain specific for another antigen (such as CD20 for example). Finally, Fab ATPHyl antibodies or fragments of these antibodies (including fragments conjugated to other protein sequences or toxins) may also be used as therapeutic agents. Antibodies that specifically bind ATPHyl are useful in compositions and methods for targeting cells expressing ATPHyl and for diagnosing a disease or disorder wherein cells involved in the disorder express ATPHyl. Such antibodies include monoclonal and polyclonal antibodies, single chain antibodies, chimeric antibodies, bifunctional/bispecific antibodies, humanized antibodies, human antibodies, and complementary determining region (CDR)-grafted antibodies, including compounds that include CDR and/or antigen-binding sequences, which specifically recognize ATPHyl. Antibody fragments, including Fab, Fab', F(ab')₂, and F_v, are also useful.

The term "specific for" indicates that the variable regions of the antibodies recognize and bind ATPHyl exclusively (i.e., able to distinguish ATPHyl from other similar polypeptides despite sequence identity, homology, or similarity found in the family of polypeptides), but may also interact with other proteins (for example, S. aureus protein A or other antibodies in ELIS A techniques) through interactions with sequences outside the variable region of the antibodies, and in particular, in the constant region of the molecule. Screening assays in which one can determine binding specificity of an anti-ATPHyl antibody are well known and routinely practiced in the art. (Chapter 6, Antibodies A Laboratory Manual, Eds. Harlow, et al, Cold Spring Harbor Laboratory; Cold Spring Harbor, NY (1988), herein incoφorated by reference in its entirety).

ATPHyl polypeptides can be used to immunize animals to obtain polyclonal and monoclonal antibodies that specifically react with ATPHyl . Such antibodies can be obtained using either the entire protein or fragments thereof as an immunogen. The peptide immunogens additionally may contain a cysteine residue at the carboxyl terminus, and are conjugated to a hapten such as keyhole limpet hemocyanin (KLH). Methods for synthesizing such peptides have been previously described (Merrifield, J. Amer. Chem. Soc. 85, 2149-2154 (1963); Krstenansky, et al, FEBS Lett. 211: 10 (1987), both of which are incoφorated by reference in their entirety). Techniques for preparing polyclonal and monoclonal antibodies as well as hybridomas capable of producing the desired antibody have also been previously disclosed (Campbell, Monoclonal Antibodies Technology: Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1984); St. Groth, et al, J. Immunol. 35:1-21 (1990); Kohler and Milstein, Nature 256:495-497 (1975)), the trioma technique, the human B-cell hybridoma technique (Kozbor, et al, Immunology Today 4:72 (1983); Cole, et al, in, Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96 (1985), all of which are incoφorated by reference in their entirety).

Any animal capable of producing antibodies can be immunized with an ATPHyl peptide or polypeptide. Methods for immunization include subcutaneous or intraperitoneal injection of the polypeptide. The amount of the ATPHyl peptide or polypeptide used for immunization depends on the animal that is immunized, antigenicity of the peptide and the site of injection. The ATPHyl peptide or polypeptide used as an immunogen may be modified or administered in an adjuvant in order to increase the protein's antigenicity.

Methods of increasing the antigenicity of a protein are well known in the art and include, but are not limited to, coupling the antigen with a heterologous protein (such as globulin or β- galactosidase) or through the inclusion of an adjuvant during immunization.

For monoclonal antibodies, spleen cells from the immunized animals are removed, fused with myeloma cells, such as SP2/0-Agl4 myeloma cells, and allowed to become monoclonal antibody producing hybridoma cells. Any one of a number of methods well known in the art can be used to identify the hybridoma cell that produces an antibody with the desired characteristics. These include screening the hybridomas with an ELISA assay, Western blot analysis, or radioimmunoassay (Lutz, et al, Exp. Cell Res. 175:109-124 (1988), herein incoφorated by reference in its entirety). Hybridomas secreting the desired antibodies are cloned and the class and subclass is determined using procedures known in the art (Campbell, A.M., Monoclonal Antibody Technology: Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1984), herein incoφorated by reference in its entirety). Techniques described for the production of single chain antibodies can be adapted to produce single chain antibodies to ATPHyl (U.S. Patent 4,946,778, herein incoφorated by reference in its entirety).

For polyclonal antibodies, antibody-containing antiserum is isolated from the immunized animal and is screened for the presence of antibodies with the desired specificity using one of the above-described procedures.

Because antibodies from rodents tend to elicit strong immune responses against the antibodies when administered to a human, such antibodies may have limited effectiveness in therapeutic methods of the invention. Methods of producing antibodies that do not produce a strong immune response against the administered antibodies are well known in the art. For example, the anti-ATPHyl antibody can be a nonhuman primate antibody. Methods of making such antibodies in baboons are disclosed in PCT publication No. WO 91/11465 and

Losman et al, Int. J. Cancer 46:310-314 (1990), both of which are herein incoφorated by reference in their entirety. In one embodiment, the anti-ATPHyl antibody is a humanized monoclonal antibody. Methods of producing humanized antibodies have been previously described. (U.S. Patent Nos. 5,997,867 and 5,985,279, Jones et al, Nature 321 :522 (1986);

Riechmann et al, Nature 332:323(1988); Verhoeyen et al, Science 239:1534-1536 (1988);

Carter et al, Proc. Nat'lAcad. Sci. USA 89:4285-4289 (1992); Sandliu, Crit. Rev. Biotech.

12:437-462 (1992); and Singer, et al, J. Immun. 150:2844-2857 (1993), all of which are herein incoφorated by reference in their entirety). In another embodiment, the anti-ATPHyl antibody is a human monoclonal antibody. Humanized antibodies are produced by transgenic mice that have been engineered to produce human antibodies. Hybridomas derived from such mice will secrete large amounts of human monoclonal antibodies. Methods for obtaining human antibodies from transgenic mice are described in Green et al, Nature Genet. 7:13-21(1994), Lonberg, et al, Nature 368:856 (1994), and Taylor, et al, Int. Immun. 6:519 (1994), all of which are herein incoφorated by reference in their entirety. The present invention also includes the use of anti-ATPHyl antibody fragments. Antibody fragments can be prepared by proteolytic hydrolysis of an antibody or by expression in E. coli of the DNA coding for the fragment. Antibody fragments can be obtained by pepsin or papain digestion of whole antibodies. For example, antibody fragments can be produced by enzymatic cleavage of antibodies with pepsin to provide a 5S fragment denoted F(ab')₂. This fragment can be further cleaved using a thiol reducing agent, and optionally a blocking group for the sulfhydryl groups resulting from cleavage of disulfide linkages, to produce 3.5S Fab' monovalent fragments. Alternatively, an enzymatic cleavage using pepsin produces two monovalent Fab fragments and an Fc fragment directly. These methods have been previously described (U.S. Patent Nos. 4,036,945 and 4,331,647, Nisonoff, et al, Arch Biochem. Biophys. 89:230 (1960); Porter, Biochem. J. 73:119 (1959), Edelman, et al, Meth. Enzymol 1:422 (1967), all of which are herein incoφorated by reference in their entirety). Other methods of cleaving antibodies, such as separation of heavy chains to form monovalent light-heavy chain fragments, further cleavage of fragments, or other enzymatic, chemical or genetic techniques may also be used, so long as the fragments bind to the antigen that is recognized by the intact antibody. For example, Fv fragments comprise an association of V_H and V_L chains, which can be noncovalent (Inbar et al, Proc. Nat'l Acad. Sci. USA 69:2659 (1972), herein incoφorated by reference in its entirety). Alternatively, the variable chains can be linked by an intermolecular disulfide bond or cross-linked by chemicals such as glutaraldehyde.

In one embodiment, the Fv fragments comprise VH and V_L chains that are connected by a peptide linker. These single-chain antigen binding proteins (sFv) are prepared by constructing a structural gene comprising DNA sequences encoding the V_H and V_L domains which are connected by an oligonucleotide. The structural gene is inserted into an expression vector, which is subsequently introduced into a host cell, such as E. coli. The recombinant host cells synthesize a single polypeptide chain with a linker peptide bridging the two V domains. Methods for producing sFvs have been previously described (U.S. Patent No. 4,946,778, Whitlow, et al, Methods: A Companion to Methods in Enzymology

2:97 (1991), Bird, et al, Science 242:423 (1988), Pack, et al, Bio/Technology 11:1271

(1993), all of which are herein incoφorated by reference in their entirety).

Another form of an antibody fragment is a peptide coding for a single complementarity-determining region (CDR). CDR peptides ("minimal recognition units") can be obtained by constructing genes encoding the CDR of an antibody of interest. Such genes are prepared, for example, by using the polymerase chain reaction to synthesize the variable region from RNA of antibody-producing cells (Larrick, et al., Methods: A Companion to Methods in Enymology 2:106 (1991); Courtenay-Luck, pp. 166-179 in, Monoclonal Antibodies Production, Engineering and Clinical Applications, Eds. Ritter et al, Cambridge University Press (1995); Ward, et al, pp. 137-185 in, Monoclonal Antibodies Principles and Applications, Eds. Birch et al, Wiley-Liss, Inc. (1995), all of which are herein incoφorated by reference in their entirety).

The present invention further provides the above-described antibodies in detectably labeled form. Antibodies can be detectably labeled through the use of radioisotopes, affinity labels (such as biotin, avidin, etc.), enzymatic labels (such as horseradish peroxidase, alkaline phosphatase, etc.) fluorescent labels (such as FITC or rhodamine, etc.), paramagnetic atoms, etc. Procedures for accomplishing such labeling have been previously disclosed (Sternberger, et al, J. Histochem. Cytochem. 18:315 (1970); Bayer, et al, Meth. Enzym. 62:308 (1979); Engval, et al, Immunol. 109:129 (1972); Goding, J Immunol. Meth. 13:215 (1976), all of which are herein incoφorated by reference in their entirety).

The labeled antibodies can be used for in vitro, in vivo, and in situ assays to identify cells or tissues in which ATPHyl is expressed. Furthermore, the labeled antibodies can be used to identify the presence of secreted ATPHyl in a biological sample, such as a blood, urine, and saliva samples.

4.5.1 ANTI-ATPHYl ANTIBODY CONJUGATES The present invention contemplates the use of "naked" anti-ATPHyl antibodies, as well as the use of immunoconjugates. Immnunoconjugates can be prepared by indirectly conjugating a therapeutic agent such as a cytotoxic agent to an antibody component. Toxic moieties include, for example, plant toxins, such as abrin, ricin, modeccin, viscumin, pokeweed anti-viral protein, saporin, gelonin, momoridin, trichosanthin, barley toxin; bacterial toxins, such as Diptheria toxin, Pseudomonas endotoxin and exotoxin,

Staphylococcal enterotoxin A; fungal toxins, such as α-sarcin, restrictocin; cytotoxic RNases, such as extracellular pancreatic RNases; DNase I (Pastan, et al, Cell 47:641 (1986); Goldenberg, Cancer Journal for Clinicians 44:43 (1994), herein incoφorated by reference in their entirety), calicheamicin, and radioisotopes, such as ³²P, ⁶⁷Cu, ⁷⁷As, ¹⁰⁵Rh, ¹⁰⁹Pd, ^mAg, ¹²¹Sn, ¹³¹L ¹⁶⁶Ho, ¹⁷⁷Lu, ¹⁸⁶Re, ¹⁸⁸Re, ¹⁹⁴Ir, ¹⁹⁹Au (Illidge and Brock, Curr Pharm. Design

6:1399 (2000), herein incoφorated by reference in its entirety). In humans, clinical trials are underway utilizing a yttrium-90 conjugated anti-CD20 antibody for B cell lymphomas (Cancer Chemother Pharmacol 48(Suppl 1):S91-S95 (2001), herein incoφorated by reference in its entirety). General techniques have been previously described (U.S. Patent Nos. 6,306,393 and

5,057,313, Shih, et al, Int. J. Cancer 41:832-839 (1988); Shih, et al, Int. J. Cancer 46: 1101-1106 (1990), all of which are herein incoφorated by reference in their entirety). The general method involves reacting an antibody component having an oxidized carbohydrate portion with a carrier polymer that has at least one free amine function and that is loaded with a plurality of drug, toxin, chelator, boron addends, or other therapeutic agent. This reaction results in an initial Schiff base (imine) linkage, which can be stabilized by reduction to a secondary amine to form the final conjugate.

The carrier polymer is preferably an aminodextran or polypeptide of at least 50 amino acid residues, although other substantially equivalent polymer carriers can also be used. Preferably, the final immunoconjugate is soluble in an aqueous solution, such as mammalian serum, for ease of administration and effective targeting for use in therapy. Thus, solubilizing functions on the carrier polymer will enhance the serum solubility of the final immunoconjugate. In particular, an aminodextran will be preferred. The process for preparing an inmmunoconjugate with an aminodextran carrier typically begins with a dextran polymer, advantageously a dextran of average molecular weight of about 10,000-100,000. The dextran is reacted with an oxidizing agent to affect a controlled oxidation of a portion of its carbohydrate rings to generate aldehyde groups. The oxidation is conveniently effected with glycolytic chemical reagents such as NaIO₄, according to conventional procedures. The oxidized dextran is then reacted with a polyamine, preferably a diamine, and more preferably, a mono- or polyhydroxy diamine.

Suitable amines include ethylene diamine, propylene diamine, or other like polymethylene diamines, diethylene triamine or like polyamines, l,3-diamino-2-hydroxypropane, or other like hydroxylated diamines or polyamines, and the like. An excess of the amine relative to the aldehyde groups of the dextran is used to ensure substantially complete conversion of the aldehyde functions to Schiff base groups. A reducing agent, such as NaBH₄, NaBH CN or the like, is used to effect reductive stabilization of the resultant Schiff base intermediate. The resultant adduct can be purified by passage through a conventional sizing column or ultrafiltration membrane to remove cross-linked dextrans. Other conventional methods of derivatizing a dextran to introduce amine functions can also be used, e.g., reaction with cyanogen bromide, followed by reaction with a diamine.

The amninodextran is then reacted with a derivative of the particular drug, toxin, chelator, immunomodulator, boron addend, or other therapeutic agent to be loaded, in an activated form, preferably, a carboxyl-activated derivative, prepared by conventional means, e.g., using dicyclohexylcarbodiimide (DCC) or a water soluble variant thereof, to form an intermediate adduct. Alternatively, polypeptide toxins such as pokeweed antiviral protein or ricin A-chain, and the like, can be coupled to aminodextran by glutaraldehyde condensation or by reaction of activated carboxyl groups on the protein with amines on the aminodextran. Chelators for radiometals or magnetic resonance enhancers are well-known in the art.

Typical are derivatives of ethylenediaminetetraacetic acid (EDTA) and diethylenetriaminepentaacetic acid (DTP A). These chelators typically have groups on the side chain by which the chelator can be attached to a carrier. Such groups include, e.g., benzylisothiocyanate, by which the DTPA or EDTA can be coupled to the amine group of a carrier. Alternatively, carboxyl groups or amine groups on a chelator can be coupled to a carrier by activation or prior derivatization and then coupling, all by well-known means. Boron addends, such as carboranes, can be attached to antibody components by conventional methods. For example, carboranes can be prepared with carboxyl functions on pendant side chains, as is well known in the art. Attachment of such carboranes to a carrier, e.g., aminodextran, can be achieved by activation of the carboxyl groups of the carboranes and condensation with amines on the carrier to produce an intermediate conjugate. Such intermediate conjugates are then attached to antibody components to produce therapeutically useful immunoconjugates, as described below.

A polypeptide carrier can be used instead of aminodextran, but the polypeptide carrier should have at least 50 amino acid residues in the chain, preferably 100-5000 amino acid residues. At least some of the amino acids should be lysine residues or glutamate or aspartate residues. The pendant amines of lysine residues and pendant carboxylates of glutamine and aspartate are convenient for attaching a drug, toxin, immunomodulator, chelator, boron addend or other therapeutic agent. Examples of suitable polypeptide carriers include polylysine, polyglutamic acid, polyaspartic acid, co-polymers thereof, and mixed polymers of these amino acids and others, e.g., serines, to confer desirable solubility properties on the resultant loaded carrier and immunoconjugate. Conjugation of the intermediate conjugate with the antibody component is effected by oxidizing the carbohydrate portion of the antibody component and reacting the resulting aldehyde (and ketone) carbonyls with amine groups remaining on the carrier after loading with a drug, toxin, chelator, immunomodulator, boron addend, or other therapeutic agent. Alternatively, an intermediate conjugate can be attached to an oxidized antibody component via amine groups that have been introduced in the intermediate conjugate after loading with the therapeutic agent. Oxidation is conveniently effected either chemically, e.g., with NaIO₄ or other glycolytic reagent, or enzymatically, e.g., with neuraminidase and galactose oxidase. In the case of an aminodextran carrier, not all of the amines of the aminodextran are typically used for loading a therapeutic agent. The remaining amines of aminodextran condense with the oxidized antibody component to form Schiff base adducts, which are then reductively stabilized, normally with a borohydride reducing agent.

Analogous procedures are used to produce other immunoconjugates according to the invention. Loaded polypeptide carriers preferably have free lysine residues remaining for condensation with the oxidized carbohydrate portion of an antibody component. Carboxyls on the polypeptide carrier can, if necessary, be converted to amines by, e.g., activation with DCC and reaction with an excess of a diamine. The final immunoconjugate is purified using conventional techniques, such as sizing chromatography on Sephacryl S-300 or affinity chromatography using one or more ATPHyl epitopes.

Alternatively, immunoconjugates can be prepared by directly conjugating an antibody component with a therapeutic agent. The general procedure is analogous to the indirect method of conjugation except that a therapeutic agent is directly attached to an oxidized antibody component. It will be appreciated that other therapeutic agents can be substituted for the chelators described herein. Those of skill in the art will be able to devise conjugation schemes without undue experimentation. As a further illustration, a therapeutic agent can be attached at the hinge region of a reduced antibody component via disulfide bond formation. For example, the tetanus toxoid peptides can be constructed with a single cysteine residue that is used to attach the peptide to an antibody component. As an alternative, such peptides can be attached to the antibody component using a heterobifunctional cross-linker, such as N-succinyl 3-(2- pyridyldithio)proprionate (SPDP) (Yu, et al, Int. J. Cancer 56:244 (1994), herein incoφorated by reference in its entirety). General techniques for such conjugation have been previously described (Wong, Chemistry of Protein Conjugation and Cross-linking, CRC Press (1991); Upeslacis, et al, pp. 187-230 in, Monoclonal Antibodies Principles and Applications, Eds. Birch et al, Wiley-Liss, Inc. (1995); Price, pp. 60-84 in, Monoclonal Antibodies: Production, Engineering and Clinical Applications Eds. Ritter, et al, Cambridge University Press (1995), all of which are herein incoφorated by reference in their entirety).

As described above, carbohydrate moieties in the Fc region of an antibody can be used to conjugate a therapeutic agent. However, the Fc region may be absent if an antibody fragment is used as the antibody component of the immunoconjugate. Nevertheless, it is possible to introduce a carbohydrate moiety into the light chain variable region of an antibody or antibody fragment (Leung, et al, J. Immunol. 154:5919-5926 (1995); U.S. Pat. No. 5,443,953), both of which are herein incoφorated by reference in their entirety. The engineered carbohydrate moiety is then used to attach a therapeutic agent.

In addition, those of skill in the art will recognize numerous possible variations of the conjugation methods. For example, the carbohydrate moiety can be used to attach polyethyleneglycol in order to extend the half-life of an intact antibody, or antigen-binding fragment thereof, in blood, lymph, or other extracellular fluids. Moreover, it is possible to construct a "divalent immunoconjugate" by attaching therapeutic agents to a carbohydrate moiety and to a free sulfhydryl group. Such a free sulfhydryl group may be located in the hinge region of the antibody component.

4.5.2 ANTI-ATPHYl ANTIBODY FUSION PROTEINS When the therapeutic agent to be conjugated to the antibody is a protein, the present invention contemplates the use of fusion proteins comprising one or more anti- ATPHyl antibody moieties and an immunomodulator or toxin moiety. Methods of making antibody fusion proteins have been previously described (U.S. Patent No. 6,306,393, herein incoφorated by reference in its entirety). Antibody fusion proteins comprising an interleukin-2 moiety have also been previously disclosed (Boleti, et al, Ann. Oncol. 6:945 (1995), Nicolet, et al, Cancer Gene Ther. 2:161 (1995), Becker, et al, Proc. Nat'lAcad. Sci. USA 93:7826 (1996), Hank, et al, Clin. Cancer Res. 2:1951 (1996), Hu, et al, Cancer Res. 56:4998 (1996) all of which are herein incoφorated by reference in their entirety). In addition, Yang, et al, Hum. Antibodies Hybridomas 6:129 (1995), herein incoφorated by reference in its entirety, describe a fusion protein that includes an F(ab')₂ fragment and a tumor necrosis factor alpha moiety.

Methods of making antibody-toxin fusion proteins in which a recombinant molecule comprises one or more antibody components and a toxin or chemotherapeutic agent also are known to those of skill in the art. For example, antibody-Pseudomonas exotoxin A fusion proteins have been described (Chaudhary, et al, Nature 339:394 (1989), Brinkmann, et al, Proc. Nat'lAcad. Sci. USA 88:8616 (1991), Barra, et al, Proc. Natl. Acad. Sci. USA 89:5867 (1992), Friedman, et al, J. Immunol. 150:3054 (1993), Wels, et al, Int. J. Can. 60:137 (1995), Fominaya et al, J. Biol. Chem. 271:10560 (1996), Kuan, et al, Biochemistry 35:2872 (1996), Schmidt, et al, Int. J. Can. 65:538 (1996), all of which are herein incoφorated by reference in their entirety). Antibody-toxin fusion proteins containing a diphtheria toxin moiety have been described (Kreitman, et al, Leukemia 7:553 (1993), Nicholls, et al, J. Biol. Chem. 268:5302 (1993), Thompson, et al, J. Biol. Chem. 270:28037 (1995), and Vallera, et al, Blood 88:2342 (1996). Deonarain et al. (Tumor Targeting 1:177 (1995)), have described an antibody-toxin fusion protein having an RNase moiety, while Linardou, et al. (Cell Biophys. 24-25:243 (1994), all of which are herein incoφorated by reference in their entirety), produced an antibody-toxin fusion protein comprising a DNase I component. Gelonin and Staphylococcal enterotoxin-A have been used as the toxin moieties in antibody-toxin fusion proteins (Wang, et al, Abstracts of the 209th ACS National Meeting, Anaheim, Calif., Apr. 2-6, 1995, Part 1, BIOT005; Dohlsten, et al, Proc. Nat'l Acad. Sci. USA 91 :8945 (1994), both of which herein incoφorated by reference in their entirety).

4.5.3 FAB FRAGMENTS AND SINGLE CHAIN ANTIBODIES

According to the invention, techniques can be adapted for the production of single-chain antibodies specific to ATPHyl (see e.g., U.S. Patent No. 4,946,778). In addition, methods can be adapted for the construction of F_a expression libraries (see e.g., Huse, et ah, Science 246: 1275-1281 (1989)) to allow rapid and effective identification of monoclonal F_a fragments with the desired specificity for a protein or derivatives, fragments, analogs or homologs thereof. Antibody fragments that contain the idiotypes to a protein antigen may be produced by techniques known in the art including, but not limited to: (i) an F(_ab')2 fragment produced by pepsin digestion of an antibody molecule; (ii) an F_ab fragment generated by reducing the disulfide bridges of an F(_ab_')₂ fragment; (iii) an F_ab fragment generated by the treatment of the antibody molecule with papain and a reducing agent and (iv) F_v fragments.

4.5.4 BISPECIFIC ATPHYI ANTIBODIES

Bispecific antibodies are monoclonal, preferably human or humanized, antibodies that have binding specificities for at least two different antigens. In the present case, one of the binding specificities is for an antigenic protein of the invention. The second binding target is any other antigen, and advantageously is a cell-surface protein or receptor or receptor subunit.

Methods for making bispecific antibodies are known in the art. Traditionally, the recombinant production of bispecific antibodies is based on the co-expression of two immunoglobulin heavy-chain/light-chain pairs, where the two heavy chains have different specificities (Milstein and Cuello, Nature, 305:537-539 (1983)). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture often different antibody molecules, of which only one has the correct bispecific structure. The purification of the correct molecule is usually accomplished by affinity chromatography steps. Similar procedures are disclosed in WO 93/08829, published 13 May 1993, and in Traunecker et al, 1991 EMBOJ., 10, 3655-3659. Antibody variable domains with the desired binding specificities (antibody-antigen combining sites) can be fused to immunoglobulin constant domain sequences. The fusion preferably is with an immunoglobulin heavy-chain constant domain, comprising at least part of the hinge, CH2, and CH3 regions. It is preferred to have the first heavy-chain constant region (CHI) containing the site necessary for light-chain binding present in at least one of the fusions. DNAs encoding the immunoglobulin heavy-chain fusions and, if desired, the immunoglobulin light chain, are inserted into separate expression vectors, and are co- transfected into a suitable host organism. For further details of generating bispecific antibodies see, for example, Suresh et al, Methods in Enzymology, 121: 210 (1986). According to another approach described in WO 96/27011 , the interface between a pair of antibody molecules can be engineered to maximize the percentage of heterodimers that are recovered from recombinant cell culture. The preferred interface comprises at least a part of the CH3 region of an antibody constant domain. In this method, one or more small amino acid side chains from the interface of the first antibody molecule are replaced with larger side chains (e.g. tyrosine or tryptophan). Compensatory "cavities" of identical or similar size to the large side chain(s) are created on the interface of the second antibody molecule by replacing large amino acid side chains with smaller ones (e.g. alanine or threonine). This provides a mechanism for increasing the yield of the heterodimer over other unwanted end-products such as homodimers. Bispecific antibodies can be prepared as full-length antibodies or antibody fragments

(e.g. F(ab') bispecific antibodies). Techniques for generating bispecific antibodies from antibody fragments have been described in the literature. For example, bispecific antibodies can be prepared using chemical linkage. Brennan et al, Science 229:81 (1985) describe a procedure wherein intact antibodies are proteolytically cleaved to generate F(ab') fragments. These fragments are reduced in the presence of the dithiol complexing agent sodium arsenite to stabilize vicinal dithiols and prevent intermolecular disulfide formation. The Fab' fragments generated are then converted to thionitrobenzoate (TNB) derivatives. One of the Fab' -TNB derivatives is then reconverted to the Fab'-thiol by reduction with mercaptoethylamine and is mixed with an equimolar amount of the other Fab'-TNB derivative to form the bispecific antibody. The bispecific antibodies produced can be used as agents for the selective immobilization of enzymes.

Additionally, Fab' fragments can be directly recovered from E. coli and chemically coupled to form bispecific antibodies. Shalaby et al, J. Exp. Med. 175:217-225 (1992) describe the production of a fully humanized bispecific antibody F(ab')₂ molecule. Each

Fab' fragment was separately secreted fromE. coli and subjected to directed chemical coupling in vitro to form the bispecific antibody. The bispecific antibody thus formed was able to bind to cells overexpressing the ErbB2 receptor and normal human T cells, as well as trigger the lytic activity of human cytotoxic lymphocytes against human breast tumor targets.

Various techniques for making and isolating bispecific antibody fragments directly from recombinant cell culture have also been described. For example, bispecific antibodies have been produced using leucine zippers. Kostelny et al, J. Immunol. 148:1547-1553

(1992). The leucine zipper peptides from the Fos and Jun proteins were linked to the Fab' portions of two different antibodies by gene fusion. The antibody homodimers were reduced at the hinge region to form monomers and then re-oxidized to form the antibody heterodimers. This method can also be utilized for the production of antibody homodimers. The "diabody" technology described by Hollinger et al, Proc. Natl. Acad. Sci. USA 90:6444-6448 (1993) has provided an alternative mechanism for making bispecific antibody fragments. The fragments comprise a heavy-chain variable domain (V_H) connected to a light-chain variable domain (V_L) by a linker which is too short to allow pairing between the two domains on the same chain. Accordingly, the V_H and V_L domains of one fragment are forced to pair with the complementary V and V_H domains of another fragment, thereby forming two antigen-binding sites. Another strategy for making bispecific antibody fragments by the use of single-chain Fv (sFv) dimers has also been reported. See, Gruber et al, J. Immunol. 152:5368 (1994).

Antibodies with more than two valencies are contemplated. For example, trispecific antibodies can be prepared. Tutt et al, J. Immunol 147:60 (1991).

Exemplary bispecific antibodies can bind to two different epitopes, at least one of which originates in the protein antigen of the invention. Alternatively, an anti-antigenic arm of an immunoglobulin molecule can be combined with an arm which binds to a triggering molecule on a leukocyte such as a T-cell receptor molecule (e.g. CD2, CD3, CD28, or B7), or Fc receptors for IgG (FC R), such as FcγRI (CD64), FC7RII (CD32) and FcγRIII (CD16) so as to focus cellular defense mechanisms to the cell expressing the particular antigen. Bispecific antibodies can also be used to direct cytotoxic agents to cells which express a particular antigen. These antibodies possess an antigen-binding arm and an arm which binds a cytotoxic agent or a radionuclide chelator, such as EOTUBE, DPTA, DOTA, or TETA. Another bispecific antibody of interest binds the protein antigen described herein and further binds tissue factor (TF).

4.5.5 HETEROCONJUGATE ATPHY1 ANTIBODIES Heteroconjugate antibodies are also within the scope of the present invention.

Heteroconjugate antibodies are composed of two covalently joined antibodies. Such antibodies have, for example, been proposed to target immune system cells to unwanted cells (U.S. Patent No. 4,676,980), and for treatment of HTV infection (WO 91/00360; WO 92/200373; EP 03089). It is contemplated that the antibodies can be prepared in vitro using known methods in synthetic protein chemistry, including those involving crosslinking agents. For example, immunotoxins can be constructed using a disulfide exchange reaction or by fonning a thioether bond. Examples of suitable reagents for this puφose include iminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, for example, in U.S. Patent No. 4,676,980.

4.5.6 EFFECTOR FUNCTION ENGINEERING

It can be desirable to modify the antibody of the invention with respect to effector function, so as to enhance, e.g., the effectiveness of the antibody in treating cancer. For example, cysteine residue(s) can be introduced into the Fc region, thereby allowing interchain disulfide bond formation in this region. The homodimeric antibody thus generated can have improved internalization capability and/or increased complement- mediated cell killing and antibody-dependent cellular cytotoxicity (ADCC). See Caron et al, J. Exp Med., 176:1191-1195 (1992) and Shopes, J. Immunol, 148:2918-2922 (1992). Homodimeric antibodies with enhanced anti-tumor activity can also be prepared using heterobifunctional cross-linkers as described in Wolff et al. Cancer Research, 53:2560-

2565 (1993). Alternatively, an antibody can be engineered that has dual Fc regions and can thereby have enhanced complement lysis and ADCC capabilities. See Stevenson et al, Anti-Cancer Drug Design, 3:219-230 (1989).

4.6 PEPTIDES

ATPHyl peptides, such as fragments of the extracellular region, may be used to target toxins or radioisotopes to tumor cells in vivo by binding to or interacting with the cell surface antigens of the invention expressed on tumor or diseased cells. Much like an antibody, these fragments may specifically target cells expressing this antigen. Targeted delivery of these cytotoxic agents to the tumor cells would result in cell death and suppression of tumor growth. An example of the ability of an extracellular fragment binding to and activating its intact receptor (by homophilic binding) has been demonstrated with the CD84 receptor (Martin et al, J. Immunol. 167:3668-3676 (2001), herein incoφorated by reference in its entirety).

Extracellular fragments of ATPHyl may also be used to modulate immune cells expressing the protein. Extracellular domain fragments of ATPHyl may bind to and activate its own receptor on the cell surface, which may result in stimulating the release of cytokines (such as interferon gamma from NK cells, T cells, B cells or myeloid cells, for example) that may enhance or suppress the immune system. Additionally, binding of these fragments to cells bearing ATPHyl of the invention may result in the activation of these cells and also may stimulate proliferation. Some fragments may bind to the intact ATPHyl and block activation signals and cytokine release by immune cells. These fragments would then have an immunosuppressive effect. Fragments that activate and stimulate the immune system may have anti-tumor properties. These fragments may stimulate an immunological response that can result in immune-mediated tumor cell killing. The same fragments may result in stimulating the immune system to mount an enhanced response to foreign invaders such as viruses and bacteria. Fragments that suppress the immune response may be useful in treating lymphoproliferative disorders, auto-immune diseases, graft-vs-host disease, and inflammatory diseases, such as emphysema.

4.7 OTHER BINDING PEPTIDES OR SMALL MOLECULES

Screening of organic compound or peptide libraries with recombinantly expressed ATPHyl protein of the invention may be useful for identification of therapeutic molecules that function to specifically bind to or even inhibit the activity of ATPHyl . Synthetic and naturally occurring products can be screened in a number of ways deemed routine to those of skill in the art. Random peptide libraries are displayed on phage (phage display) or on bacteria, such as on E. coli. These random peptide display libraries can be used to screen for peptides which interact with a known target which can be a protein or a polypeptide, such as a ligand or receptor, a biological or synthetic macromolecule, or organic or inorganic substances. By way of example, diversity libraries, such as random or combinatorial peptide or non-peptide libraries can be screened for molecules that specifically bind to ATPHyl polypeptides. Many libraries are known in the art that can be used, i.e. chemically synthesized libraries, recombinant (i.e. phage display libraries), and in vitro translation- based libraries. Techniques for creating and screening such random peptide display libraries are known in the art (Ladner et al, U.S. Patent No. 5,223, 409; Ladner et al, U.S. Patent No. 4,946,778; Ladner et al, U.S. Patent No. 5,403,484; Ladner et al, U.S. Patent No.

5,571,698, all of which are herein incoφorated by reference in their entirety) and random peptide display libraries and kits for screening such libraries are available commercially, for instance from Clontech (Palo Alto, CA), Invitrogen Inc. (San Diego, CA), New England Biolabs, hie. (Beverly, MA), and Pharmacia KLB Biotechnology Inc. (Piscataway, NJ). Random peptide display libraries can be screened using the ATPHyl sequences disclosed herein to identify proteins which bind to ATPHyl .

Examples of chemically synthesized libraries are described in Fodor et al, Science 251:161-113 (1991); Houghten et al, Nature 354:84-86 (1991); Lam et al, Nature 354:82- 84 (1991); Medynski, Bio/Technology 12:709-710 (1994); Gallop et al, J. Med. Chem. 37:1233-1251 (1994); Ohlmeyer et al, Proc. Natl. Acad. Sci. USA 90:10922-10926 (1993); Erb et al, Proc. Natl. Acad. Sci. USA 91:11422-11426 (1994); Houghten et al, Biotechniques 13:412 (1992); Jayawickreme et al, Proc. Natl. Acad. Sci. USA 91:1614-1618 (1994); Salmon et al, Proc. Natl. Acad. Sci. USA 90:11708-11712 (1993); PCT Publication No. WO 93/20242; Brenner and Lerner, Proc. Natl. Acad. Sci. USA 89:5381-5383 (1992), all of which are herein incoφorated by reference in their entirety.

Examples of phage display libraries are described in Scott and Smith, Science 249:386-390 (1990); Devlin et al, Science 249:404-406 (1990); Christian et al, J. Mol. Biol. 227:711-718 (1992); Lenstra, J Immunol Meth. 152:149-157 (1992); Kay et al, Gene 128:59-65 (1993); PCT Publication No. WO 94/18318, all of which are herein incoφorated by reference in their entirety.

In vitro translation-based libraries include but are not limited to those described in PCT Publication No. WO 91/05058, and Mattheakis et al, Proc. Natl. Acad. Sci. USA 91 :9022-9026 (1994), both of which are herein incoφorated by reference in their entirety. Byway of examples of non-peptide libraries, a benzodiazepine library (see for example, Bunin et al, Proc. Natl. Acad. Sci. USA 91 :4708-4712 (1994), herein incoφorated by reference in its entirety) can be adapted for use. Peptoid libraries (Simon et al, Proc. Natl. Acad. Sci. USA 89:9367-9371 (1992), herein incoφorated by reference in its entirety) can also be used. Another example of a library that can be used, in which the amide functionalities in peptides have been permethylated to generate a chemically transformed combinatorial library, is described by Ostresh et al. (Proc. Nad. Acad. Sci. USA 91:11138- 11142 (1994), herein incoφorated by reference in its entirety).

Screening the libraries can be accomplished by any of a variety of commonly known methods. See, for example, the following references which disclose screening of peptide libraries: Parmley and Smith, Adv. Exp. Med. Biol 251:215-218 (1989); Scott and Smith, Science 249:386-390 (1990); Fowlkes etal, Biotechniques 13:422-427 (1992); Oldenburg et al, Proc. Natl. Acad. Sci. USA 89:5393-5397 (1992); Yu et al, Cell 76:933-945 (1994); Staudt et al, Science 241:577-580 (1988); Bock et al, Nature 355:564-566 (1992); Tuerk et al, Proc. Natl. Acad. Sci. USA 89:6988-6992 (1992); Ellington et al, Nature 355:850-852 (1992); Rebar and Pabo, Science 263:671-673 (1993); and PCT Publication No. WO 94/18318, all of which are herein incoφorated by reference in their entirety.

In a specific embodiment, screening can be carried out by contacting the library members with an ATPHyl protein (or nucleic acid or derivative) immobilized on a solid phase and harvesting those library members that bind to the protein (or nucleic acid or derivative). Examples of such screening methods, termed "panning" techniques are described by way of example in Parmley and Smith, Gene 73:305-318 (1988); Fowlkes et al, Biotechniques 13:422-427 (1992); PCT Publication No. WO 94/18318, all of which are herein incoφorated by reference in their entirety, and in references cited hereinabove. In another embodiment, the two-hybrid system for selecting interacting protein in yeast (Fields and Song, Nature 340:245-246 (1989); Chien et al, Proc. Natl. Acad. Sci. USA 88:9578-9582 (1991), both of which are herein incoφorated by reference in their entirety) can be used to identify molecules that specifically bind to ATPHyl or an ATPHyl derivative. These "binding polypeptides" or small molecules which interact with ATPHyl polypeptides can be used for tagging or targeting cells; for isolating homolog polypeptides by affinity purification; they can be directly or indirectly conjugated to drugs, toxins, radionuclides and the like. These binding polypeptides or small molecules can also be used in analytical methods such as for screening expression libraries and neutralizing activity, i.e., for blocking interaction between ligand and receptor, or viral binding to a receptor. The binding polypeptides or small molecules can also be used for diagnostic assays for determining circulating levels of ATPHyl polypeptides of the invention; for detecting or quantitating soluble ATPHyl polypeptides as marker of underlying pathology or disease. These binding polypeptides or small molecules can also act as ATPHyl "antagonists" to block ATPHyl binding and signal transduction in vitro and in vivo. These anti-ATPHyl binding polypeptides or small molecules would be useful for inhibiting ATPHyl activity or protein binding. Binding polypeptides can also be directly or indirectly conjugated to drugs, toxins, radionuclides and the like, and these conjugates used for in vivo diagnostic or therapeutic applications. Binding peptides can also be fused to other polypeptides, for example an immunoglobulin constant chain or portions thereof, to enhance their half-life, and can be made multivalent (through, e.g. branched or repeating units) to increase binding affinity for ATPHyl. For instance, binding polypeptides of the present invention can be used to identify or treat tissues or organs that express a corresponding anti-complementary molecule (receptor or antigen, respectively, for instance). More specifically, binding polypeptides or bioactive fragments or portions thereof, can be coupled to detectable or cytotoxic molecules and delivered to a mammal having cells, tissues or organs that express the anti- complementary molecule.

Suitable detectable molecules may be directly or indirectly attached to the binding polypeptide, and include radionuclides, enzymes, substrates, cofactors, inhibitors, fluorescent markers, chemiluminescent markers, magnetic particles and the like. Suitable cytotoxic molecules may be directly or indirectly attached to the binding polypeptide, and include bacterial or plant toxins (for instance, diphtheria toxin, Pseudomonas exotoxin, ricin, abrin and the like), as well as therapeutic radionuclides, such as iodine-131, rhenium-188, or yttrium-90 (either directly attached to the binding polypeptide, or indirectly attached through a means of a chelating moiety, for instance). Binding polypeptides may also be conjugated to cytotoxic drugs, such as adriamycin. For indirect attachment of a detectable or cytotoxic molecule, the detectable or cytotoxic molecule can be conjugated with a member of a complementary/anticomplementary pair, where the other member is bound to the binding polypeptide. For these puφoses, biotin/streptavidin is an exemplary complementary/anticomplementarypair.

In another embodiment, binding polypeptide-toxin fusion proteins can be used for targeted cell or tissue inhibition or ablation (for instance, to treat cancer cells or tissues).

Alternatively, if the binding polypeptide has multiple functional domains (i.e., an activation domain or a ligand binding domain, plus a targeting domain), a fusion protein including only the targeting domain may be suitable for directing a detectable molecule, a cytotoxic molecule, or a complementary molecule to a cell or tissue type of interest. In instances where the domain only fusion protein includes a complementary molecule, the anti- complementary molecule can be conjugated to a detectable or cytotoxic molecule. Such domain-complementary molecule fusion proteins thus represent a generic targeting vehicle for cell/tissue-specific delivery of generic anti-complementary-detectable/cytotoxic molecule conjugates.

4.8 DISEASES AMENABLE TO ANTI-ATPHYl TARGETING

In one aspect, the present invention provides reagents and methods useful for treating diseases and conditions wherein cells associated with the disease or disorder express

ATPHyl such as breast, prostate, colon, and lung cancers. In addition, these diseases can include cancers, and other hypeφroliferative conditions, such as hypeφlasia, psoriasis, contact dermatitis, immunological disorders, wound healing, arthritis, and autoimmune disease. Whether the cells associated with a disease or condition express ATPHyl can be - determined using the diagnostic methods described herein.

Comparisons of ATPHyl mRNA and protein expression levels between diseased cells, tissue or fluid (blood, lymphatic fluid, etc.) and corresponding normal samples are made to determine if the patient will be responsive to therapy targeting ATPHyl antigens of the invention. Methods for detecting and quantifying the expression of ATPHyl mRNA or protein use standard nucleic acid and protein detection and quantitation techniques that are well known in the art and are described in Sambrook, et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, NY (1989) or Ausubel, et al, Current Protocols in Molecular Biology, John Wiley & Sons, New York, NY (1989), both of which are incoφorated herein by reference in their entirety. Standard methods for the detection and quantification of ATPHyl mRNA include in situ hybridization using labeled ATPHyl riboprobes (Gemou-Engesaeth, et al., Pediatrics 109: E24-E32 (2002), herein incoφorated by reference in its entirety), Northern blot and related techniques using ATPHyl polynucleotide probes (Kunzli, et al, Cancer 94: 228 (2002), herein incoφorated by reference in its entirety), RT-PCR analysis using ATPHyl -specific primers (Angchaiskisiri, et al., Blood 99: 130 (2002), herein incoφorated by reference in its entirety), and other amplification detection methods, such as branched chain DNA solution hybridization assay (Jardi, et al, J. Viral Hepat. 8:465-471 (2001), herein incoφorated by reference in its entirety), transcription-mediated amplification (Kimura, et al, J. Clin. Microbiol 40:439- 445 (2002), herein incoφorated by reference in its entirety), microarray products, such as oligos, cDNAs, and monoclonal antibodies, and real-time PCR (Simpson, et al, Molec.

Vision, 6:178-183 (2000), herein incoφorated by reference in its entirety). Standard methods for the detection and quantification of ATPHyl protein include western blot analysis (Sambrook, 1989 supra, Ausubel, 1989 supra)), immunocytochemistry (Racila, et al, Proc. Natl. Acad. Sci. USA 95:4589-4594 (1998), herein incoφorated by reference in its entirety), and a variety of immunoassays, including enzyme-linked immunosorbant assay

(ELISA), radioimmuno assay (RIA), and specific enzyme immunoassay (EIA) (Sambrook,

1989 supra, Ausubel, 1989 supra). Peripheral blood cells can also be analyzed for ATPHyl expression using flow cytometry using, for example, immunomagnetic beads specific for ATPHyl (Racila, 1998 supra) or biotinylated ATPHyl antibodies (Soltys, et al, J. Immunol. 168:1903 (2002), herein incoφorated by reference in its entirety).

Yet another related aspect of the invention is directed to methods for gauging tumor aggressiveness by determining the levels of ATPHyl protein or mRNA in tumor cells compared to the corresponding normal cells (Orlandi, et al, Cancer Res. 62:567 (2002), herein incoφorated by reference in its entirety). In one embodiment, the disease or disorder is a cancer.

The diseases treatable by methods of the present invention preferably occur in mammals. Mammals include, for example, humans and other primates, as well as pet or companion animals such as dogs and cats, laboratory animals such as rats, mice and rabbits, and farm animals such as horses, pigs, sheep, and cattle.

Tumors or neoplasms include growths of tissue cells in which the multiplication of the cells is uncontrolled and progressive. Some such growths are benign, but others are termed "malignant" and may lead to death of the organism. Malignant neoplasms or "cancers" are distinguished from benign growths in that, in addition to exhibiting aggressive cellular proliferation, they may invade surrounding tissues and metastasize. Moreover, malignant neoplasms are characterized in that they show a greater loss of differentiation (greater "dedifferentiation"), and greater loss of their organization relative to one another and their surrounding tissues. This property is also called "anaplasia." Neoplasms treatable by the present invention also include solid phase tumors/malignancies, i.e., carcinomas, locally advanced tumors and human soft tissue sarcomas. Carcinomas include those malignant neoplasms derived from epithelial cells that infiltrate (invade) the surrounding tissues and give rise to metastastic cancers, including lymphatic metastases. Adenocarcinomas are carcinomas derived from glandular tissue, or which form recognizable glandular structures. Another broad category or cancers includes sarcomas, which are tumors whose cells are embedded in a fibrillar or homogeneous substance like embryonic connective tissue. The invention also enables treatment of cancers of the myeloid or lymphoid systems, including leukemias, lymphomas and other cancers that typically do not present as a tumor mass, but are distributed in the vascular or lymphoreticular systems.

The type of cancer or tumor cells that may be amenable to treatment according to the invention include, for example, breast, colon, lung, and prostate cancers (as shown in the Examples), gastrointestinal cancers including esophageal cancer, stomach cancer, colorectal cancer, polyps associated with colorectal neoplasms, pancreatic cancer and gallbladder cancer, cancer of the adrenal cortex, ACTH-producing tumor, bladder cancer, brain cancer including intrinsic brain tumors, neuroblastomas, astrocytic brain tumors, gliomas, and metastatic tumor cell invasion of the central nervous system, Ewing's sarcoma, head and neck cancer including mouth cancer and larynx cancer, kidney cancer including renal cell carcinoma, liver cancer, lung cancer including small and non-small cell lung cancers, malignant peritoneal effusion, malignant pleural effusion, skin cancers including malignant melanoma, tumor progression of human skin keratinocytes, squamous cell carcinoma, basal cell carcinoma, and hemangiopericytoma, mesothelioma, Kaposi's sarcoma, bone cancer including osteomas and sarcomas such as fibrosarcoma and osteosarcoma, cancers of the female reproductive tract including uterine cancer, endometrial cancer, ovarian cancer, ovarian (germ cell) cancer and solid tumors in the ovarian follicle, vaginal cancer, cancer of the vulva, and cervical cancer; breast cancer (small cell and ductal), penile cancer, retinoblastoma, testicular cancer, thyroid cancer, trophoblastic neoplasms, and Wilms' tumor.

The invention is particularly illustrated herein in reference to treatment of certain types of experimentally defined cancers. In these illustrative treatments, standard state-of- the-art in vitro and in vivo models have been used. These methods can be used to identify agents that can be expected to be efficacious in in vivo treatment regimens. However, it will be understood that the method of the invention is not limited to the treatment of these tumor types, but extends to any cancer derived from any organ system. Leukemias can result from uncontrolled B cell proliferation initially within the bone marrow before disseminating to the peripheral blood, spleen, lymph nodes and finally to other tissues. Uncontrolled B cell proliferation also may result in the development of lymphomas that arise within the lymph nodes and then spread to the blood and bone marrow.

Therapeutic compositions of the invention may be effective in adult and pediatric oncology including in solid phase tumors/malignancies, locally advanced tumors, human soft tissue sarcomas, metastatic cancer, including lymphatic metastases, blood cell malignancies, including multiple myeloma, acute and chronic leukemias and lymphomas, head and neck cancers, including mouth cancer, larynx cancer, and thyroid cancer, lung cancers including small cell carcinoma and non-small cell cancers, breast cancers including small cell carcinoma and ductal carcinoma, gastrointestinal cancers including esophageal cancer, stomach cancer, colon cancer, colorectal cancer and polyps associated with colorectal neoplasia, pancreatic cancers, liver cancer, urologic cancers including bladder cancer and prostate cancer, malignancies of the female genital tract including ovarian carcinoma, uterine (including endometrial) cancers, and solid tumor in the ovarian follicle, kidney cancers including renal cell carcinoma, brain cancers including intrinsic brain tumors, neuroblastoma, astrocytic brain tumors, gliomas, metastatic tumor cell invasion in the central nervous system, bone cancers including osteomas, sarcomas including fibrosarcoma and osteosarcoma, skin cancers including malignant melanoma, tumor progression of human skin keratinocytes, squamous cell carcinoma, basal cell carcinoma, hemangiopericytoma, and Kaφosi's sarcoma. Targeting ATPHyl may also be possible to modulate immune responses, in a number of ways. Down regulation may be in the form of inhibiting or blocking an immune response already in progress or may involve preventing the induction of an immune response. Down regulating or preventing one or more antigen functions (including without limitation B lymphocyte antigen functions, e.g., modulating or preventing high level lymphokine synthesis by activated T cells, will be useful in situations of tissue, skin and organ transplantation and in graft- versus-host disease (GVHD). For example, blockage of T cell function should result in reduced tissue destruction in tissue transplantation. Typically, in tissue transplants, rejection of the transplant is initiated through its recognition as foreign by T cells, followed by an immune reaction that destroys the transplant. The administration of a therapeutic composition of the invention may prevent cytokine synthesis by immune cells, such as T cells, and thus acts as an immunosuppressant. Moreover, a lack of costimulation may also be sufficient to anergize the T cells, thereby inducing tolerance in a subject. Induction of long-term tolerance by B lymphocyte antigen-blocking reagents may avoid the necessity of repeated adininistration of these blocking reagents. To achieve sufficient immunosuppression or tolerance in a subject, it may also be necessary to block the function of a combination of B lymphocyte antigens.

The efficacy of particular therapeutic compositions in preventing organ transplant rejection or GVHD can be assessed using animal models that are predictive of efficacy in humans. Examples of appropriate systems which can be used include allogeneic cardiac grafts in rats and xenogeneic pancreatic islet cell grafts in mice, both of which have been used to examine the immunosuppressive effects of CTLA4Ig fusion proteins in vivo as described in Lenschow et al, Science 257:789-792 (1992) and Turka et al, Proc. Natl. Acad. Sci USA, 89:11102-11105 (1992), both of which are herein incoφorated by reference. In addition, murine models of GVHD (see Paul ed., Fundamental Immunology, Raven Press, New York, 1989, pp. 846-847, herein incoφorated by reference) can be used to determine the effect of therapeutic compositions of the invention on the development of that disease.

4.9 ADMINISTRATION

The anti-ATPHyl monoclonal antibodies used in the practice of a method of the invention may be formulated into pharmaceutical compositions comprising a carrier suitable for the desired delivery method. Suitable carriers include any material which when combined with the anti-ATPHyl antibodies retains the anti-tumor function of the antibody and is nonreactive with the subject's immune systems. Examples include, but are not limited to, any of a number of standard pharmaceutical carriers such as sterile phosphate buffered saline solutions, bacteriostatic water, and the like.

The anti-ATPHyl antibody formulations may be administered via any route capable of delivering the antibodies to the tumor site. Potentially effective routes of administration include, but are not limited to, intravenous, intraperitoneal, intramuscular, intratumor, intradermal, and the like. The preferred route of administration is by intravenous injection. A preferred formulation for intravenous injection comprises anti-ATPHyl mAbs in a solution of preserved bacteriostatic water, sterile unpreserved water, and/or diluted in polyvinylchloride or polyethylene bags containing 0.9% sterile sodium chloride for Injection, USP. The anti-ATPHyl mAb preparation may be lyophilized and stored as a sterile powder, preferably under vacuum, and then reconstituted in bacteriostatic water containing, for example, benzyl alcohol preservative, or in sterile water prior to injection. Treatment will generally involve the repeated administration of the anti-ATPHyl antibody preparation via an acceptable route of administration such as intravenous injection (IV), typically at a dose in the range of about 0.1 to about 10 mg/kg body weight; however other exemplary doses in the range of 0.01 mg/kg to about 100 mg/kg are also contemplated. Doses in the range of 10-500 mg mAb per week may be effective and well tolerated. Rituximab (Rituxan®), a chimeric CD20 antibody used to treat B-cell lymphoma, non- Hodgkin's lymphoma, and relapsed indolent lymphoma, is typically administered at 375 mg/m by IV infusion once a week for 4 to 8 doses. Sometimes a second course is necessary, but no more than 2 courses are allowed. An effective dosage range for Rituxan® would be 50 to 500 mg/m² (Maloney, et al, Blood 84: 2457-2466 (1994); Davis, et al, J. Clin. Oncol. 18: 3135-3143 (2000), both of which are herein incoφorated by reference in their entirety). Based on clinical experience with Trastuzumab (Herceptin®), a humanized monoclonal antibody used to treat HER2(human epidermal growth factor 2)-positive metastatic breast cancer (Slamon, et al, Mol Cell Biol. 9: 1165 (1989), herein incoφorated by reference in its entirety), an initial loading dose of approximately 4 mg/kg patient body weight IV followed by weekly doses of about 2 mg/kg TV of the anti-ATPHyl mAb preparation may represent an acceptable dosing regimen (Slamon, et al, N. Engl J. Med. 344: 783(2001), herein incoφorated by reference in its entirety). Preferably, the initial loading dose is administered as a 90 minute or longer infusion. The periodic maintenance dose may be administered as a 30 minute or longer infusion, provided the initial dose was well tolerated. However, as one of skill in the art will understand, various factors will influence the ideal dose regimen in a particular case. Such factors may include, for example, the binding affinity and half life of the mAb or mAbs used, the degree of ATPHyl overexpression in the patient, the extent of circulating shed ATPHyl antigen, the desired steady-state antibody concentration level, frequency of treatment, and the influence of chemotherapeutic agents used in combination with the treatment method of the invention. Treatment can also involve anti-ATPHyl antibodies conjugated to radioisotopes. Studies using radiolabeled-anti-carcinoembryonic antigen (anti-CEA) monoclonal antibodies, provide a dosage guideline for tumor regression of 2-3 infusions of 30-80 mCi/m² (Behr, et al. Clin, Cancer Res. 5(10 Suppl.): 3232s-3242s (1999), Juweid, et al, J. Nucl. Med. 39:34-42 (1998), both of which are herein incoφorated in their entirety).

Alternatively, dendritic cells transfected with mRNA encoding ATPHyl can be used as a vaccine to stimulate T-cell mediated anti-tumor responses. Studies with dendritic cells transfected with prostate-specific antigen mRNA suggest a 3 cycles of intravenous administration of l^χ10⁷ - 5*10⁷ cells for 2-6 weeks concomitant with an intradermal injection of 10⁷ cells may provide a suitable dosage regimen (Heiser, et al, J. Clin. Invest.

109:409-417 (2002); Hadzantonis and O'Neill, Cancer Biother. Radiopharm. 1:11-22 (1999), both of which are herein incoφorated in their entirety). Other exemplary doses of between 1x10 ⁵ to lxlO⁹ or lxlO⁶ to lxlO⁸ cells are also contemplated.

Naked DNA vaccines using plasmids encoding ATPHyl can induce an immunologic anti-tumor response. Administration of naked DNA by direct injection into the skin and muscle is not associated with limitations encountered using viral vectors, such as the development of adverse immune reactions and risk of insertional mutagenesis (Hengge, et al, J. Invest. Dermatol 116:919 (2001) herein incoφorated in its entirety). Studies have shown that direct injection of exogenous cDNA into muscle tissue results in a strong immune response and protective immunity (Han, Curr. Opin. Mol. Ther. 1:116-120 (1999), herein incoφorated in its entirety). Physical (gene gun, electroporation) and chemical (cationic lipid or polymer) approaches have been developed to enhance efficiency and target cell specificity of gene transfer by plasmid DNA (Nisbikawa and Huang, Hum. Gene Ther. 12:861-870 (2001) herein incoφorated in its entirety). Plasmid DNA can also be administered to the lungs by aerosol delivery (Densmore, et αl., Mol. Ther. 1:180-188 (2000)). Gene therapy by direct injection of naked or lipid - coated plasmid DNA is envisioned for the prevention, treatment, and cure of diseases such as cancer, acquired immunodeficiency syndrome, cystic fibrosis, cerebrovascular disease, and hypertension (Prazeres, et αl., Trends Biotechnol 17:169-174 (1999); Weihl, et αl., Neurosurgery 44:239- 252 (1999), both of which are herein incoφorated in their entirety). HIV-1 DNA vaccine dose-escalating studies indicate administration of 30-300 μg/dose as a suitable therapy (Weber, et α , Eur. J. Clin. Microbiol. Infect. Dis. 20: 800 (2001), herin incoφorated in its entirety. Naked DNA injected intracerebrally into the mouse brain was shown to provide expression of a reporter protein, wherein expression was dose-dependent and maximal for 150 μg DNA injected (Schwartz, et αl., Gene Ther. 3:405-411 (1996), herein incoφorated in its entirety). Gene expression in mice after intramuscular injection of nanospheres containing 1 micro gram of beta-galactosidase plasmid was greater and more prolonged than was observed after an injection with an equal amount of naked DNA or DNA complexed with Lipofectamine (Truong, et αl., Hum. Gene Ther. 9:1709-1717 (1998), herein incoφorated in its entirety). In a study of plasmid-mediated gene transfer into skeletal muscle as a means of providing a therapeutic source of insulin, wherein four plasmid constructs comprising a mouse furin cDNA transgene and rat proinsulin cDNA were injected into the calf muscles of male Balb/c mice, the optimal dose for most constructs was 100 micrograms plasmid DNA (Kon, et al. J. Gene Med. 1:186-194 (1999), herein incoφorated in its entirety). Other exemplary doses of 1-1000 μg/dose or 10-500 g/dose are also contemplated.

Optimally, patients should be evaluated for the level of circulating shed ATPHyl antigen in serum in order to assist in the determination of the most effective dosing regimen and related factors. Such evaluations may also be used for monitoring puφoses throughout therapy, and may be useful to gauge therapeutic success in combination with evaluating other parameters.

4.9.1 ATPHYI TARGETING COMPOSITIONS

Compositions for targeting ATPHyl -expressing cells are within the scope of the present invention. Pharmaceutical compositions comprising antibodies are described in detail in, for example, US Patent No. 6,171,586, herein incoφorated in its entirety. Such compositions comprise a therapeutically or prophylactically effective amount an antibody, or a fragment, variant, derivative or fusion thereof as described herein, in admixture with a pharmaceutically acceptable agent. Typically, the ATPHyl immunotargeting agent will be sufficiently purified for administration to an animal.

The pharmaceutical composition may contain formulation materials for modifying, maintaining or preserving, for example, the pH, osmolarity, viscosity, clarity, color, isotonicity, odor, sterility, stability, rate of dissolution or release, adsoφtion or penetration of the composition. Suitable formulation materials include, but are not limited to, amino acids (such as glycine, glutamine, asparagine, arginine or lysine); antimicrobials; antioxidants (such as ascorbic acid, sodium sulfite or sodium hydrogen-sulfite); buffers (such as borate, bicarbonate, Tris-HCl, citrates, phosphates, other organic acids); bulking agents (such as mannitol or glycine), chelating agents [such as ethylenediamine tetraacetic acid (EDTA)]; complexing agents (such as caffeine, polyvinylpyrrolidone, beta-cyclodextrin or hydroxypropyl-beta-cyclodextrin); fillers; monosaccharides; disaccharides and other carbohydrates (such as glucose, mannose, or dextrins); proteins (such as serum albumin, gelatin or immunoglobulins); coloring; flavoring and diluting agents; emulsifying agents; hydrophilic polymers (such as polyvinylpyrrolidone); low molecular weight polypeptides; salt-forming counterions (such as sodium); preservatives (such as benzalkonium chloride, benzoic acid, salicylic acid, thimerosal, phenethyl alcohol, methylparaben, propylparaben, chlorhexidine, sorbic acid or hydrogen peroxide); solvents (such as glycerin, propylene glycol or polyethylene glycol); sugar alcohols (such as mannitol or sorbitol); suspending agents; surfactants or wetting agents (such as pluronics, PEG, sorbitan esters, polysorbates such as polysorbate 20, polysorbate 80, triton, tromethamine, lecithin, cholesterol, tyloxapal); stability enhancing agents (sucrose or sorbitol); tonicity enhancing agents (such as alkali metal halides (preferably sodium or potassium chloride, mannitol sorbitol); delivery vehicles; diluents; excipients and/or pharmaceutical adjuvants. (Remington's Pharmaceutical Sciences, 18th Edition, Ed. A.R. Gennaro, Mack Publishing Company, (1990), herein incoφorated in its entirety).

The optimal pharmaceutical composition will be determined by one skilled in the art depending upon, for example, the intended route of administration, delivery format, and desired dosage. See, for example, Remington 's Pharmaceutical Sciences, supra. Such compositions may influence the physical state, stability, rate of zn vivo release, and rate of in vivo clearance of the ATPHyl targeting agent.

The primary vehicle or carrier in a pharmaceutical composition may be either aqueous or non-aqueous in nature. For example, a suitable vehicle or carrier may be water for injection, physiological saline solution or artificial cerebrospinal fluid, possibly supplemented with other materials common in compositions for parenteral administration. Neutral buffered saline or saline mixed with serum albumin are further exemplary vehicles. Other exemplary pharmaceutical compositions comprise Tris buffer of about pH 7.0-8.5, or acetate buffer of about pH 4.0-5.5, which may further include sorbitol or a suitable substitute therefor. In one embodiment of the present invention, ATPHyl targeting agent compositions may be prepared for storage by mixing the selected composition having the desired degree of purity with optional formulation agents (Remington's Pharmaceutical Sciences, supra) in the form of a lyophilized cake or an aqueous solution. Further, the binding agent product may be formulated as a lyophilizate using appropriate excipients such as sucrose. The pharmaceutical compositions can be selected for parenteral delivery.

Alternatively, the compositions may be selected for inhalation or for delivery through the digestive tract, such as orally. The preparation of such pharmaceutically acceptable compositions is within the skill of the art. The formulation components are present in concentrations that are acceptable to the site of administration. For example, buffers are used to maintain the composition at physiological pH or at slightly lower pH, typically within a pH range of from about 5 to about 8. When parenteral adniinistration is contemplated, the therapeutic compositions for use in this invention may be in the form of a pyrogen-free, parenterally acceptable aqueous solution comprising the ATPHyl immunotargeting agent in a pharmaceutically acceptable vehicle. A particularly suitable vehicle for parenteral injection is sterile distilled water in which an ATPHyl targeting agent is formulated as a sterile, isotonic solution, properly preserved. Yet another preparation can involve the formulation of the desired molecule with an agent, such as injectable microspheres, bio-erodible particles, polymeric compounds (polylactic acid, polyglycolic acid), beads, or liposomes, which provides for the controlled or sustained release of the product which may then be delivered via a depot injection. Hyaluronic acid may also be used, and this may have the effect of promoting sustained duration in the circulation. Other suitable means for the introduction of the desired molecule include implantable drug delivery devices.

In another aspect, pharmaceutical formulations suitable for parenteral administration may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hanks' solution, Ringer's solution, or physiologically buffered saline. Aqueous injection suspensions may contain substances that increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Additionally, suspensions of the active compounds may be prepared as appropriate oily injection suspensions. Suitable ripopbilic solvents or vehicles include fatty oils, such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate, triglycerides, or liposomes. Non-lipid polycationic amino polymers may also be used for delivery. Optionally, the suspension may also contain suitable stabilizers or agents to increase the solubility of the compounds and allow for the preparation of highly concentrated solutions.

In another embodiment, a pharmaceutical composition may be formulated for inhalation. For example, an ATPHyl immunotargeting agent may be formulated as a dry powder for inhalation. Polypeptide or nucleic acid molecule inhalation solutions may also be formulated with a propellant for aerosol delivery. In yet another embodiment, solutions may be nebulized. Pulmonary administration is further described in PCT Application No. PCT/US94/001875, herein incoφorated in its entirety, which describes pulmonary delivery of chemically modified proteins. It is also contemplated that certain formulations may be administered orally. In one embodiment of the present invention, ATPHyl targeting agents that are administered in this fashion can be formulated with or without those carriers customarily used in the compounding of solid dosage forms such as tablets and capsules. For example, a capsule may be designed to release the active portion of the formulation at the point in the gastrointestinal tract when bioavailability is maximized and pre-systemic degradation is minimized. Additional agents can be included to facilitate absoφtion of the binding agent molecule. Diluents, flavorings, low melting point waxes, vegetable oils, lubricants, suspending agents, tablet disintegrating agents, and binders may also be employed. Pharmaceutical compositions for oral administration can also be formulated using pharmaceutically acceptable carriers well known in the art in dosages suitable for oral administration. Such carriers enable the pharmaceutical compositions to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for ingestion by the patient. Pharmaceutical preparations for oral use can be obtained through combining active compounds with solid excipient and processing the resultant mixture of granules (optionally, after grinding) to obtain tablets or dragee cores. Suitable auxiliaries can be added, if desired. Suitable excipients include carbohydrate or protein fillers, such as sugars, including lactose, sucrose, mannitol, and sorbitol; starch from corn, wheat, rice, potato, or other plants; cellulose, such as methyl cellulose, hydroxypropylmethyl-cellulose, or sodium carboxymethylcellulose; gums, including arabic and tragacanth; and proteins, such as gelatin and collagen. If desired, disintegrating or solubilizing agents may be added, such as the cross-linked polyvinyl pyrrolidone, agar, and alginic acid or a salt thereof, such as sodium alginate. Dragee cores may be used in conjunction with suitable coatings, such as concentrated sugar solutions, which may also contain gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for product identification or to characterize the quantity of active compound, i.e., dosage.

Pharmaceutical preparations that can be used orally also include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a coating, such as glycerol or sorbitol. Push-fit capsules can contain active ingredients mixed with fillers or binders, such as lactose or starches, lubricants, such as talc or magnesium stearate, and, optionally, stabilizers, hi soft capsules, the ATPHyl targeting agent may be dissolved or suspended in suitable liquids, such as fatty oils, liquid, or liquid polyethylene glycol with or without stabilizers. Another pharmaceutical composition may involve an effective quantity of ATPHyl targeting agent in a mixture with non-toxic excipients that are suitable for the manufacture of tablets. By dissolving the tablets in sterile water, or other appropriate vehicle, solutions can be prepared in unit dose form. Suitable excipients include, but are not limited to, inert diluents, such as calcium carbonate, sodium carbonate or bicarbonate, lactose, or calcium phosphate; or binding agents, such as starch, gelatin, or acacia; or lubricating agents such as magnesium stearate, stearic acid, or talc.

Additional pharmaceutical compositions will be evident to those skilled in the art, including formulations involving ATPHyl targeting agents in sustained- or controlled- delivery formulations. Techniques for formulating a variety of other sustained- or controUed-delivery means, such as liposome carriers, bio-erodible microparticles or porous beads and depot injections, are also known to those skilled in the art. See, for example, PCT/US93/00829, herein incoφorated in its entirety, that describes controlled release of porous polymeric microparticles for the delivery of pharmaceutical compositions. Additional examples of sustained-release preparations include semipermeable polymer matrices in the form of shaped articles, e.g. films, or microcapsules. Sustained release matrices may include polyesters, hydrogels, polylactides (U.S. Patent No. 3,773,919; European Patent No. EP 58,481), copolymers of L-glutamic acid and gamma ethyl-L- glutamate (Sidman et al, Biopolymers, 22:547-556 (1983)), poly (2-hydroxyethyl- methacrylate) (Langer et al, J Biomed Mater Res, 15:167-277, (1981)) and (Langer et al, Chem Tech, 12:98-105(1982)), ethylene vinyl acetate (Langer et al, supra) or poly-D (-)-3- hydroxybutyric acid (European Patent No. EP 133,988, all of which are herein incoφorated in their entirety). Sustained-release compositions also include liposomes, which can be prepared by any of several methods known in the art. See e.g., Epstein, et al, Proc Natl Acad Sci (USA), 82:3688-3692 (1985); European Patent Nos. EP 36,676, EP 88,046, and EP 143,949, all of which are herein incoφorated by reference in their entirety.

The pharmaceutical composition to be used for in vivo administration typically must be sterile. This may be accomplished by filtration through sterile filtration membranes. Where the composition is lyophilized, sterilization using this method may be conducted either prior to or following lyophilization and reconstitution. The composition for parenteral administration may be stored in lyophilized form or in solution. In addition, parenteral compositions generally are placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle.

Once the pharmaceutical composition has been formulated, it may be stored in sterile vials as a solution, suspension, gel, emulsion, solid, or a dehydrated or lyophilized powder. Such formulations may be stored either in a ready-to-use form or in a form (e.g., lyophilized) requiring reconstitution prior to administration. In a specific embodiment, the present invention is directed to kits for producing a single-dose administration unit. The kits may each contain both a first container having a dried ATPHyl targeting agent and a second container having an aqueous formulation. Also included within the scope of this invention are kits containing single and multi-chambered pre-filled syringes (e.g., liquid syringes and lyosyringes).

4.9.2 DOSAGE An effective amount of a pharmaceutical composition to be employed therapeutically will depend, for example, upon the therapeutic context and objectives. One skilled in the art will appreciate that the appropriate dosage levels for treatment will thus vary depending, in part, upon the molecule delivered, the indication for which ATPHyl targeting agent is being used, the route of administration, and the size (body weight, body surface or organ size) and condition (the age and general health) of the patient. Accordingly, the clinician may titer the dosage and modify the route of administration to obtain the optimal therapeutic effect. A typical dosage may range from about 0.1 mg/kg to up to about 100 mg/kg or more, depending on the factors mentioned above. In other embodiments, the dosage may range from 0.1 mg/kg up to about 100 mg/kg; or 0.01 mg/kg to 1 g/kg; or 1 mg/kg up to about 100 mg/kg or 5 mg/kg up to about 100 mg/kg. In other embodiments, the dosage may range from 10 mCi to 100 mCi per dose for radioimmunotherapy, from about lxl 0⁷ - 5x10⁷ cells or lxl0⁵to 1x10⁹cells or lxlO⁶ to lxlO⁸ cells per injection or infusion, or from 30 μg to 300 μg naked DNA per dose or 1-1000 μg/dose or 10-500 μg/dose, depending on the factors listed above.

For any compound, the therapeutically effective dose can be estimated initially either in cell culture assays or in animal models such as mice, rats, rabbits, dogs, or pigs. An animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.

The exact dosage will be detennined in light of factors related to the subject requiring treatment. Dosage and administration are adjusted to provide sufficient levels of the active compound or to maintain the desired effect. Factors that may be taken into account include the severity of the disease state, the general health of the subject, the age, weight, and gender of the subject, time and frequency of administration, drug combination(s), reaction sensitivities, and response to therapy. Long-acting pharmaceutical compositions may be administered every 3 to 4 days, every week, or biweekly depending on the half-life and clearance rate of the particular formulation.

The frequency of dosing will depend upon the pharmacokinetic parameters of the ATPHyl targeting agent in the formulation used. Typically, a composition is administered until a dosage is reached that achieves the desired effect. The composition may therefore be administered as a single dose, or as multiple doses (at the same or different concentrations/dosages) over time, or as a continuous infusion. Further refinement of the appropriate dosage is routinely made. Appropriate dosages may be ascertained through use of appropriate dose-response data.

Pharmaceutical compositions suitable for use in the present invention include compositions wherein the active ingredients are contained in an effective amount to achieve its intended puφose. More specifically, a therapeutically effective amount means an amount effective to prevent development of or to alleviate the existing symptoms of the subject being treated. Determination of the effective amount is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein. For any compound used in the method of the invention, the therapeutically effective dose can be estimated initially from appropriate in vitro assays. For example, a dose can be fonnulated in animal models to achieve a circulating concentration range that can be used to more accurately determine useful doses in humans. For example, a dose can be formulated in animal models to achieve a circulating concentration range that includes the IC₅₀ as determined in cell culture (i.e., the concentration of the test compound which achieves a half-maximal inhibition of the protein's biological activity). Such information can be used to more accurately determine useful doses in humans. A therapeutically effective dose refers to that amount of the compound that results in amelioration of symptoms or a prolongation of survival in a patient. Toxicity and therapeutic efficacy of such compounds can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD₅₀ (the dose lethal to 50% of the population) and the ED₅₀ (the dose therapeutically effective in 50% of the population).

The dose ratio between toxic and therapeutic effects is the therapeutic index and it can be expressed as the ratio between LD5₀ and ED₅₀. Compounds which exhibit high therapeutic indices are preferred. The data obtained from these cell culture assays and animal studies can be used in formulating a range of dosage for use in human. The dosage of such compounds lies preferably within a range of circulating concentrations that include the ED₅₀ with little or no toxicity. The dosage may vary within this range depending upon the dosage form employed and the route of administration utilized. The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. See, e.g., Fingl et al, 1975, in "The Pharmacological Basis of Therapeutics", Ch. 1 p.1. Dosage amount and interval may be adjusted individually to provide plasma levels of the active moiety which are sufficient to maintain the desired effects, or minimal effective concentration (MEC). The MEC will vary for each compound but can be estimated from in vitro data. Dosages necessary to achieve the MEC will depend on individual characteristics and route of administration. However, HPLC assays or bioassays can be used to determine plasma concentrations.

Dosage intervals can also be determined using MEC value. Compounds should be administered using a regimen which maintains plasma levels above the MEC for 10-90% of the time, preferably between 30-90% and most preferably between 50-90%. In cases of local administration or selective uptake, the effective local concentration of the drug may not be related to plasma concentration.

An exemplary dosage regimen for polypeptides or other compositions of the invention will be in the range of about 0.01 μg/kg to 100 mg/kg of body weight daily, with the preferred dose being about 0.1 μg/kg to 25 mg/kg of patient body weight daily, varying in adults and children. Dosing may be once daily, or equivalent doses may be delivered at longer or shorter intervals.

The amount of composition administered will, of course, be dependent on the subject being treated, on the subject's age and weight, the severity of the affliction, the manner of administration and the judgment of the prescribing physician. 4.9.3 ROUTES OF ADMINISTRATION

The route of administration of the pharmaceutical composition is in accord with known methods, e.g. orally, through injection by intravenous, intraperitoneal, intracerebral

(intra-parenchymal), intracerebroventricular, intramuscular, intra-ocular, intra-arterial, intraportal, intralesional routes, intrameduUary, intrathecal, intraventricular, transdermal, subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, urethral, vaginal, or rectal means, by sustained release systems, by implantation devices, or through inhalation.

Where desired, the compositions may be administered by bolus injection or continuously by infusion, or by implantation device. Alternatively or additionally, the composition may be administered locally via implantation of a membrane, sponge, or another appropriate material on to which the ATPHyl targeting agent has been absorbed or encapsulated. Where an implantation device is used, the device may be implanted into any suitable tissue or organ, and delivery of the ATPHyl targeting agent may be via diffusion, timed-release bolus, or continuous administration.

In some cases, it may be desirable to use pharmaceutical compositions in an ex vivo manner, hi such instances, cells, tissues, or organs that have been removed from the patient are exposed to the pharmaceutical compositions after which the cells, tissues and/or organs are subsequently implanted back into the patient. In other cases, an ATPHyl targeting agent can be delivered by implanting certain cells that have been genetically engineered to express and secrete the polypeptide. Such cells may be animal or human cells, and may be autologous, heterologous, or xenogeneic. Optionally, the cells may be immortalized. In order to decrease the chance of an immunological response, the cells may be encapsulated to avoid infiltration of surrounding tissues. The encapsulation materials are typically biocompatible, semi-permeable polymeric enclosures or membranes that allow the release of the protein product(s) but prevent the destruction of the cells by the patient's immune system or by other detrimental factors from the surrounding tissues.

4.10 COMBINATION THERAPY

ATPHyl targeting agents of the invention can be utilized in combination with other therapeutic agents, and may enhance the effect of these other therapeutic agents such that a lesser daily amount, lesser total amount or reduced frequency of administration is required in order to achieve the same therapeutic effect at reduced toxicity. For cancer, these other therapeutics include, for example radiation treatment, chemotherapeutic agents, as well as other growth factors. For transplant rejection or autoimmune diseases, these other therapeutics include for example immunosuppressants such as cyclosporine, azathioprine corticosteroids, tacrolimus or mycophenolate mofetil.

In one embodiment, anti-ATPHyl antibody is used as a radiosensitizer. i such embodiments, the anti-ATPHyl antibody is conjugated to a radiosensitizing agent. The term "radiosensitizer," as used herein, is defined as a molecule, preferably a low molecular weight molecule, administered to animals in therapeutically effective amounts to increase the sensitivity of the cells to be radiosensitized to electromagnetic radiation and/or to promote the treatment of diseases that are treatable with electromagnetic radiation. Diseases that are treatable with electromagnetic radiation include neoplastic diseases, benign and malignant tumors, and cancerous cells.

The terms "electromagnetic radiation" and "radiation" as used herein include, but are not limited to, radiation having the wavelength of 10^" to 100 meters. Preferred embodiments of the present invention employ the electromagnetic radiation of: gamma- radiation (10^"2° to 10^"13 m), X-ray radiation (10^"12 to 10^"9 m), ultraviolet light (10 nm to 400 nm), visible light (400 nm to 700 nm), infrared radiation (700 nm to 1.0 mm), and microwave radiation (1 mm to 30 cm). Radiosensitizers are known to increase the sensitivity of cancerous cells to the toxic effects of electromagnetic radiation. Many cancer treatment protocols currently employ radiosensitizers activated by the electromagnetic radiation of X-rays. Examples of X-ray activated radiosensitizers include, but are not limited to, the following: metronidazole, misonidazole, desmethylmisonidazole, pimonidazole, etanidazole, nimorazole, mitomycin C, RSU 1069, SR 4233, EO9, RB 6145, nicotinamide, 5-bromodeoxyuridine (BUdR),

5-iododeoxyuridine (IUdR), bromodeoxycytidine, fluorodeoxyuridine (FUdR), hydroxyurea, cisplatin, and therapeutically effective analogs and derivatives of the same.

Photodynamic therapy (PDT) of cancers employs visible light as the radiation activator of the sensitizing agent. Examples of photodynamic radiosensitizers include the following, but are not limited to: hematopoφhyrin derivatives, Photofrin(r), benzopoφhyrin derivatives, NPe6, tin etiopoφhyrin (SnET2), pheoborbide-a, bacteriochlorophyll-a, naphthalocyanines, phthalocyanines, zinc phthalocyanine, and therapeutically effective analogs and derivatives of the same. Chemotherapy treatment can employ anti-neoplastic agents including, for example, alkylating agents including: nitrogen mustards, such as mechlorethamine, cyclophosphamide, ifosfamide, melphalan and chlorambucil; nitrosoureas, such as carmustine (BCNU), lomustine (CCNU), and semustine (methyl-CCNU); ethylenimines/methylmelamine such as thriethylenemelamine (TEM), triethylene, thiophosphoramide (thiotepa), hexamethylmelamine (HMM, altretamine); alkyl sulfonates such as busulfan; triazines such as dacarbazine (DTIC); antimetabolites including folic acid analogs such as methotrexate and trimetrexate, pyrimidine analogs such as 5-fluorouracil, fluorodeoxyuridine, gemcitabine, cytosine arabinoside (AraC, cytarabine), 5-azacytidine, 2,2'-difluorodeoxycytidine, purine analogs such as 6-mercaptopurine, 6-thioguanine, azathioprine, 2'-deoxycoformycin (pentostatin), erythrohydroxynonyladenine (EHNA), fludarabine phosphate, and 2-chlorodeoxyadenosine (cladribine, 2-CdA); natural products including antimitotic drugs such as paclitaxel, vinca alkaloids including vinblastine (VLB), vincristine, and vinorelbine, taxotere, estramustine, and estramustine phosphate; ppipodophylotoxins such as etoposide and teniposide; antibiotics such as actimomycin D, daunomycin (rubidomycin), doxorubicin, mitoxantrone, idarubicin, bleomycins, plicamycin (mithramycin), mitomycinC, and actinomycin; enzymes such as L-asparaginase; biological response modifiers such as interferon-alpha, IL-2, G-CSF and GM-CSF; miscellaneous agents including platinium coordination complexes such as cisplatin and carboplatin, anthracenediones such as mitoxantrone, substituted urea such as hydroxyurea, methylhydrazine derivatives including N-methylhydrazine (MIH) and procarbazine, adrenocortical suppressants such as mitotane (o,p'-DDD) and aminoglutetliimide; hormones and antagonists including adrenocorticosteroid antagonists such as prednisone and equivalents, dexamethasone and aminoglutethimide; progestin such as hydroxyprogesterone caproate, medroxyprogesterone acetate and megestrol acetate; estrogen such as diethylstilbestrol and ethinyl estradiol equivalents; antiestrogen such as tamoxifen; androgens including testosterone propionate and fluoxymesterone/equivalents; antiandrogens such as flutamide, gonadotropin-releasing hormone analogs and leuprolide; and non-steroidal antiandrogens such as flutamide. Combination therapy with growth factors can include cytokines, lymphokines, growth factors, or other hematopoietic factors such as M-CSF, GM-CSF, TNF, IL-1, IL-2, IL-3, IL-4, IL-5, LL-6, IL-7, LL-8, IL-9, IL-10, IL-11, IL-12, IL-13, LL-14, IL-15, IL-16, IX- 17, IL-18, IFN, TNFO, TNFl, TNF2, G-CSF, Meg-CSF, GM-CSF, thrombopoietin, stem cell factor, and erythropoietin. Other compositions can include known angiopoietins, for example, vascular endothelial growth factor (VEGF). Growth factors include angiogenin, bone moφhogenic protein- 1, bone moφhogenic protein-2, bone moφhogenic protein-3, bone moφhogenic protein-4, bone moφhogenic protein-5, bone moφhogenic protein-6, bone moφhogenic protein-7, bone moφhogenic protein-8, bone moφhogenic protein-9, bone moφhogenic protein- 10, bone moφhogenic protein- 11, bone moφhogenic protein- 12, bone moφhogenic protein-13, bone moφhogenic protein-14, bone moφhogenic protein-15, bone moφhogenic protein receptor IA, bone moφhogenic protein receptor IB, brain derived neurotrophic factor, ciliary neutrophic factor, ciliary neutrophic factor receptor, cytokine- induced neutrophil chemotactic factor 1, cytokine-induced neutrophil chemotactic factor 2, endothelial cell growth factor, endothelin 1, epidermal growth factor, epithelial-derived neutrophil attractant, fibroblast growth factor 4, fibroblast growth factor 5, fibroblast growth factor 6, fibroblast growth factor 7, fibroblast growth factor 8, fibroblast growth factor 8b, fibroblast growth factor 8c, fibroblast growth factor 9, fibroblast growth factor 10, fibroblast growth factor acidic, fibroblast growth factor basic, glial cell line-derived neutrophic factor receptor 2, growth related protein, heparin binding epidermal growth factor, hepatocyte growth factor, hepatocyte growth factor receptor, insulin-like growth factor I, insulin-like growth factor receptor, insulin-like growth factor II, insulin-like growth factor binding protein, keratinocyte growth factor, leukemia inhibitory factor, leukemia inhibitory factor receptor, nerve growth factor, nerve growth factor receptor, neurotrophin-3, neurotiophin-4, placenta growth factor, placenta growth factor 2, platelet-derived endothelial cell growth factor, platelet derived growth factor, platelet derived growth factor A chain, platelet derived growth factor AA, platelet derived growth factor AB, platelet derived growth factor B chain, platelet derived growth factor BB, platelet derived growth factor receptor, pre-B cell growth stimulating factor, stem cell factor, stem cell factor receptor, transforming growth factor, transforming growth factor 1, transforming growth factor 1.2, transforming growth factor 2, transforming growth factor 3, transforming growth factor 5, latent transforming growth factor 1, transforming growth factor binding protein I, transforming growth factor binding protein II, transforming growth factor binding protein III, tumor necrosis factor receptor type I, tumor necrosis factor receptor type II, urokinase-type plasminogen activator receptor, vascular endothelial growth factor, and chimeric proteins and biologically or immunologically active fragments thereof. 4.11 DIAGNOSTIC USES OF ATPHYl

4.11.1 ASSAYS FOR DETERMINING ATPHyl-EXPRESSION

STATUS

Determining the status of ATPHyl expression patterns in an individual may be used to diagnose cancer and may provide prognostic information useful in defining appropriate therapeutic options. Similarly, the expression status of ATPHyl may provide information useful for predicting susceptibility to particular disease stages, progression, and/or tumor aggressiveness. The mvention provides methods and assays for determining ATPHyl expression status and diagnosing cancers that express ATPHyl . Li one aspect, the invention provides assays useful in determining the presence of cancer in an individual, comprising detecting a significant increase or decrease, as applicable, in ATPHyl mRNA or protein expression in a test cell or tissue or fluid sample relative to expression levels in the corresponding normal cell or tissue. In one embodiment, the presence of ATPHyl mRNA is evaluated in tissue samples of a breast cancer tumor. The presence of significant ATPHyl expression may be useful to indicate whether the breast cancer tissue is susceptible to ATPHyl targeting using a targeting composition of the invention, hi a related embodiment, ATPHyl expression status may be determined at the protein level rather than at the nucleic acid level. For example, such a method or assay would comprise determining the level of ATPHyl expressed by cells in a test tissue sample and comparing the level so determined to the level of ATPHyl expressed in a corresponding normal sample. In one embodiment, the presence of ATPHyl is evaluated, for example, using immunohistochemical methods. ATPHyl antibodies capable of detecting ATPHyl expression may be used in a variety of assay formats well known in the art for this puφose. Peripheral blood may be conveniently assayed for the presence of cancer cells, including lymphomas and leukemias, using RT-PCR to detect ATPHyl expression. The presence of RT-PCR amplifiable ATPHyl mRNA provides an indication of the presence of one of these types of cancer. A sensitive assay for detecting and characterizing carcinoma cells in blood maybe used (Racila, et al, Proc. Natl. Acad. Sci. USA 95: 4589-4594 (1998), herein incoφorated by reference in its entirety). This assay combines immunomagnetic enrichment with multiparameter flow cytometric and immunohistochemical analyses, and is highly sensitive for the detection of cancer cells in blood, reportedly capable of detecting one epithelial cell in 1 ml of peripheral blood. A related aspect of the mvention is directed to predicting susceptibility to developing cancer in an individual. In one embodiment, a method for predicting susceptibility to cancer comprises detecting ATPHyl mRNA or ATPHyl protein in a tissue sample, its presence indicating susceptibility to cancer, wherein the degree of ATPHyl mRNA or protein expression present is proportional to the degree of susceptibility.

Yet another related aspect of the invention is directed to methods for assessment of tumor aggressiveness (Orlandi, et al, Cancer Res. 62:567 (2002), herein incoφorated by reference in its entirety). In one embodiment, a method for gauging aggressiveness of a tumor comprises determining the level of ATPHyl mRNA or ATPHyl protein expressed by cells in a sample of the tumor, comparing the level so determined to the level of ATPHyl mRNA or ATPHyl protein expressed in a corresponding normal tissue taken from the same individual or a normal tissue reference sample, wherein the degree of ATPHyl mRNA or ATPHyl protein expression in the tumor sample relative to the normal sample indicates the degree of aggressiveness. Methods for detecting and quantifying the expression of ATPHyl mRNA or protein are described herein and use standard nucleic acid and protein detection and quantification technologies well known in the art. Standard methods for the detection and quantification of ATPHyl mRNA include in situ hybridization using labeled ATPHyl riboprobes (Gemou- Engesaeth, et al, Pediatrics, 109:E24-E32 (2002)), Northern blot and related techniques using ATPHyl polynucleotide probes (Kunzii, et al, Cancer 94:228 (2002)), RT-PCR analysis using primers specific for ATPHyl (Angchaiskisiri, et al, Blood 99:130 (2002)), and other amplification type detection methods, such as, for example, branched DNA (Jardi, et al, J. Viral Hepat. 8:465-471 (2001)), SISBA, TMA (Kimura, et al, J Clin. Microbiol. 40:439-445 (2002)), and microarray products of a variety of sorts, such as oligos, cDNAs, and monoclonal antibodies. In a specific embodiment, real-time RT-PCR may be used to detect and quantify ATPHyl mRNA expression (Simpson, et al, Molec. Vision 6:178-183 (2000)). Standard methods for the detection and quantification of protein may be used for this puφose. In a specific embodiment, polyclonal or monoclonal antibodies specifically reactive with the wild-type ATPHyl may be used in an immunohistochemical assay of biopsied tissue (Ristimaki, et al, Cancer Res. 62:632 (2002), herein incoφorated by reference in its entirety). 4.11.2 DIAGNOSTIC ASSAYS AND KITS

The present invention further provides methods to identify the presence or expression of ATPHyl, or homolog thereof, in a test sample, using a nucleic acid probe or antibodies of the present invention, optionally conjugated or otherwise associated with a suitable label. In general, methods for detecting an ATPHyl polynucleotide can comprise contacting a sample with a compound that binds to and forms a complex with the polynucleotide for a period sufficient to form the complex, and detecting the complex, so that if a complex is detected, a polynucleotide of the invention is detected in the sample. Such methods can also comprise contacting a sample under stringent hybridization conditions with nucleic acid primers that anneal to a polynucleotide of the invention under such conditions, and amplifying annealed polynucleotides, so that if a polynucleotide is amplified, a polynucleotide of the invention is detected in the sample.

The term "stringent" is used to refer to conditions that are commonly understood in the art as stringent. Stringent conditions can include highly stringent conditions (i.e., hybridization to filter-bound DNA in 0.5 M NaHPO₄, 7% sodium dodecyl sulfate (SDS), 1 mM EDTA at 65°C, and washing in 0.1* SSC/0.1% SDS at 68°C), and moderately stringent conditions (i.e., washing in 0.2x SSC/0.1% SDS at 42°C). Other exemplary hybridization conditions are described herein in the examples.

In instances of hybridization of deoxyoligonucleotides, additional exemplary stringent hybridization conditions include washing in 6x SSC/0.05% sodium pyrophosphate at 37°C (for 14-base oligonucleotides), 48°C (for 17-base oligonucleotides), 55°C (for 20- base oligonucleotides), and 60°C (for 23-base oligonucleotides).

In general, methods for detecting a polypeptide of the invention can comprise contacting a sample with a compound that binds to and forms a complex with the polypeptide for a period sufficient to form the complex, and detecting the complex, so that if a complex is detected, a polypeptide of the invention is detected in the sample.

In detail, such methods comprise incubating a test sample with one or more of the antibodies or one or more of the nucleic acid probes of the present invention and assaying for binding of the nucleic acid probes or antibodies to components within the test sample. Conditions for incubating a nucleic acid probe or antibody with a test sample vary.

Incubation conditions depend on the format employed in the assay, the detection methods employed, and the type and nature of the nucleic acid probe or antibody used in the assay. One skilled in the art will recognize that any one of the commonly available hybridization, amplification or immunological assay formats can readily be adapted to employ the nucleic acid probes or antibodies of the present invention. Examples of such assays can be found in Chard, T., An Introduction to Radioimmunoassay and Related Techniques, Elsevier Science Publishers, Amsterdam, The Netherlands (1986); Bullock, G.R. et al, Techniques in Immunocytochemistry, Academic Press, Orlando, FL Vol. 1 (1982), Vol. 2 (1983), Vol. 3 (1985); Tijssen, P., Practice and Theory ofimmunoassays: Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1985). The test samples of the present invention include cells, protein or membrane extracts of cells, or biological fluids such as sputum, blood, serum, plasma, or urine. The test sample used in the above-described method will vary based on the assay format, nature of the detection method and the tissues, cells or extracts used as the sample to be assayed. Methods for preparing protein extracts or membrane extracts of cells are well known in the art and can be readily be adapted in order to obtain a sample which is compatible with the system utilized. In another embodiment of the present invention, kits are provided which contain the necessary reagents to carry out the assays of the present invention. Specifically, the invention provides a compartment kit to receive, in close confinement, one or more containers which comprises: (a) a first container comprising one of the probes or antibodies of the present invention; and (b) one or more other containers comprising one or more of the following: wash reagents, reagents capable of detecting presence of a bound probe or antibody. h detail, a compartment kit includes any kit in which reagents are contained in separate containers. Such containers include small glass containers, plastic containers or strips of plastic or paper. Such containers allows one to efficiently transfer reagents from one compartment to another compartment such that the samples and reagents are not cross-contaminated, and the agents or solutions of each container can be added in a quantitative fashion from one compartment to another. Such containers will include a container which will accept the test sample, a container which contains the antibodies used in the assay, containers which contain wash reagents (such as phosphate buffered saline, Tris-buffers, etc), and containers which contain the reagents used to detect the bound antibody or probe. Types of detection reagents include labeled nucleic acid probes, labeled secondary antibodies, or in the alternative, if the primary antibody is labeled, the enzymatic, or antibody binding reagents which are capable of reacting with the labeled antibody. One skilled in the art will readily recognize that the disclosed probes and antibodies of the present invention can be readily incoφorated into one of the established kit formats which are well known in the art.

4.11.3 MEDICAL IMAGING

ATPHyl antibodies that recognize ATPHyl and fragments thereof are useful in medical imaging of sites expressing ATPHyl. Such methods involve chemical attachment of a labeling or imaging agent, such as a radioisotope, which include Cu, Y, I, I, ¹⁸⁶Re, ¹⁸⁸Re, ²¹¹At, and²¹²Bi, administration of the labeled antibody and fragment to a subject in a pharmaceutically acceptable carrier, and imaging the labeled antibody and fragment in vivo at the target site. Radiolabelled anti-ATPHyl antibodies or fragments thereof may be particularly useful in in vivo imaging of ATPHyl expressing cancers, such as lymphomas or leukemias. Such antibodies may provide highly sensitive methods for detecting metastasis of ATPHyl -expressing cancers. Upon consideration of the present disclosure, one of skill in the art will appreciate that many other embodiments and variations may be made in the scope of the present invention. Accordingly, it is intended that the broader aspects of the present invention not be limited to the disclosure of the following examples.

5. EXAMPLES

EXAMPLE 1

ATPHYI MRNA IS EXPRESSED IN BREAST, COLON, LUNG, AND PROSTATE CANCER

TISSUES

Figure 3 shows the relative expression of mRNA derived from B-cell cell lines, healthy tissues, and tumor tissues derived from B cell lymphomas, follicular lymphomas, myelomas and colon, lung, and prostate tumor tissues and their corresponding normal adjacent tissue.

Total mRNA derived from tissues and cells lines was subjected to quantitative realtime PCR (TaqMan) (Simpson, et al, Molec. Vision, 6:178-183 (2000) herein incoφorated by reference) to determine the relative expression of ATPHyl mRNA. Total mRNA derived from cell lines (obtained from ATCC, Manassas, VA) was isolated using standard protocols. The cell line was derived from acute myelogenous leukemia (KG1).

The mRNA derived from the tumor tissues (Clinomics Biosciences, Inc., Pittsfield, MA) was prepared from malignant B cells and other cells that had been isolated from the tumors. Tumor samples were obtained from different patients suffering from B cell lymphomas (H02-85T, H02-86T), follicular lymphoma (H02-74T, H02-76T, H02-77T), and myeloma (H02-79T), as well as patients suffering from colon cancer (CO7554T, CO7932T, CO8067T; normal adjacent colon tissue (CO7554N, CO7932N)), lung cancer (LU7981T, LU7987T, LU8044T; normal adjacent lung tissue (LU7981N, LU7987N, LU8044N)), prostate cancer and normal adjacent prostate tissue, and breast cancer (H02-39T, H02-41T, H02-43T, H02-45T ; normal adjacent breast tissue (H02-40N, H02-42N, H02-44N)). DNA sequences encoding Elongation Factor 1 were used as a positive control and normalization factors in all samples. All assays were performed in duplicate with the resulting values averaged. The y-axis shows the relative expression of the ATPHyl mRNA, wherein the lowest expression was set as equal to 1 and the rest of the values are expressed as relative to 1.

Figure 3 shows that relatively little expression of the ATPHyl gene was found in healthy tissues with the exception of breast and prostate tissue. The results show that ATPHyl is upregulated in breast, colon, lung, and prostate cancer tumors, indicating that ATPHyl may be used as a therapeutic target or as a diagnostic marker for these types of disorders.

EXAMPLE 2 PRODUCTION OF ATPHYI -SPECIFIC ANTIBODIES

Cells expressing ATPHyl are identified using antibodies to ATPHyl . Polyclonal antibodies are produced by DNA vaccination or by injection of peptide antigens into rabbits or other hosts. An animal, such as a rabbit, is immunized with a peptide from the extracellular region of ATPHyl conjugated to a carrier protein, such as BSA (bovine serum albumin) or KLH (keyhole limpet hemocyanin). The rabbit is initially immunized with conjugated peptide in complete Freund's adjuvant, followed by a booster shot every two weeks with injections of conjugated peptide in incomplete Freund's adjuvant. Anti-ATPHyl antibody is affinity purified from rabbit serum using ATPHyl peptide coupled to Affi-Gel 10 (Bio-Rad), and stored in phosphate-buffered saline with 0.1% sodium azide. To determine that the polyclonal antibodies are ATPHyl -specific, an expression vector encoding ATPHyl is introduced into mammalian cells. Western blot analysis of protein extracts of non-transfected cells and the ATPHyl -containing cells is performed using the polyclonal antibody sample as the primary antibody and a horseradish peroxidase-labeled anti-rabbit antibody as the secondary antibody. Detection of an approximately 353 kD band in the ATPHyl -containing cells and lack thereof in the control cells indicates that the polyclonal antibodies are specific for ATPHyl .

One such polyclonal antibody was made using KLH conjugated to an immunogenic ATPHyl peptide having the amino acid sequence Ser-Ala-Ser-Asp-Pro-Phe-Tyr-Thr-Asn-

Asp-Arg-Ser (SEQ ID NO: 5) that corresponds to amino acid residues 649 to 660 of SEQ ID

NO: 2. The anti-ATPHyl polyclonal antibody is herein denoted as 18835a. To determine that 18835a was ATPHyl -specific, an expression vector encoding a V5/His tagged ATPHyl

(plntron- ATPHyl, Nuvelo, Inc.) was introduced into mammalian COS-7 cells. Western blot analysis of protein extracts of non-transfected cells and the ATPHyl -containing transfected cells was performed using 18835a as the primary antibody and a horseradish peroxidase- labeled anti-rabbit antibody as the secondary antibody. Detection of an approximately 353 kD band in the ATPHyl -containing cells and lack thereof in the control cells indicated that 18835a was specific for ATPHyl. Monoclonal antibodies are produced by injecting mice with an ATPHyl peptide, with or without adjuvant. Subsequently, the mouse is boosted every 2 weeks until an appropriate immune response has been identified (typically 1-6 months), at which point the spleen is removed. The spleen is minced to release splenocytes, which are fused (in the presence of polyethylene glycol) with murine myeloma cells. The resulting cells (hybridomas) are grown in culture and selected for antibody production by clonal selection. The antibodies are secreted into the culture supernatant, facilitating the screening process, such as screening by an enzyme-linked immunosorbent assay (ELISA). Alternatively, humanized monoclonal antibodies are produced either by engineering a chimeric murine/human monoclonal antibody in which the murine-specific antibody regions are replaced by the human counteφarts and produced in mammalian cells, or by using transgenic "knock out" mice in which the native antibody genes have been replaced by human antibody genes and immunizing the transgenic mice as described above.

EXAMPLE 3 DIAGNOSTIC METHODS USING ATPHYI -SPECIFIC ANTIBODIES TO DETECT

ATPHYI EXPRESSION

Expression of ATPHyl in tissue samples isolated from various adenocarcinomas including breast, ovarian, melanoma, colon and prostate tissues was detected using the anti- ATPHyl polyclonal antibody (see Example 2 for details). Samples were prepared for immunohistochemical (LHC) analysis (LifeSpan Biosciences Inc., Seattle, WA) by fixing the tissue in 10% formalin embedding in paraffin, and sectioning using standard techniques. Sections were stained using the ATPHyl -specific antibody followed by incubation with a secondary horseradish peroxidase (HRP)-conjugated antibody and visualized by the product of the HRP enzymatic reaction. Data as seen in Table 1 shows that ATPHyl is expressed in breast, colon and prostate tumor tissues. In addition, breast, ovarian, melanoma, colon and prostate adenocarcinoma tumor tissues stained positive for ATPHyl protein by LHC analysis (data not shown). The IHC date is consistent with the mRNA data (see Example 1) indicating that ATPHyl targeting therapy can be useful to treat breast, colon, prostate and lung cancers.

Table 1

Additionally, antibody blocking assays were performed and analyzed by IHC. Normal and breast cancer tumor tissue samples were prepared for LHC as stated above; however, before the samples were incubated with the anti-ATPHyl antibody 18835a, 18835a was pre-treated with an excess of SEQ ID NO: 5, herein denoted at blocking peptide 18835b, and then processed as stated above. In the samples tested, SEQ ID NO: 5 blocked the reactivity of 18835a in the breast cancer tumor tissues. Expression of ATPHyl on the surface of cells within a blood sample is detected by flow cytometry. Peripheral blood mononuclear cells (PBMC) are isolated from a blood sample using standard techniques. The cells are washed with ice-cold PBS and incubated on ice with the ATPHyl -specific polyclonal antibody for 30 min. The cells are gently pelleted, washed with PBS, and incubated with a fluorescent anti-rabbit antibody for 30 min. on ice. After the incubation, the cells are gently pelleted, washed with ice cold PBS, and resuspended in PBS containing 0.1% sodium azide and stored on ice until analysis. Samples are analyzed using a FACScalibur flow cytometer (Becton Dickinson) and CELLQuest software (Becton Dickinson). Instrument settings are determined using FACS-Brite calibration beads (Becton-Dickinson). Tumors expressing ATPHyl is imaged using ATPHyl -specific antibodies conjugated to a radionuclide, such as ¹²³I, and injected into the patient for targeting to the tumor followed by X-ray or magnetic resonance imaging.

EXAMPLE 4

IN VITRO ANTIBODY-DEPENDENT CYTOTOXICITY ASSAY

The ability of an ATPHyl-specific antibody to induce antibody-dependent cell- mediated cytoxicity (ADCC) is determined in vitro. ADCC is performed using the CytoTox 96 Non-Radioactive Cytoxicity Assay (Promega; Madison, WI) (Hornick et al, Blood 89:4437-4447, (1997)) as well as effector and target cells. Peripheral blood mononuclear cells (PBMC) or neutrophilic polymoφhonuclear leukocytes (PMN) are two examples of effector cells that can be used in this assay. PBMC are isolated from healthy human donors by Ficoll-Paque gradient centrifugation, and PMN are purified by centrifugation through a discontinuous percoll gradient (70% and 62%) followed by hypotonic lysis to remove residual erythrocytes. Prostate cancer cells (for example) are used as target cells.

The target cells are suspended in RPMI 1640 medium supplemented with 2% fetal bovine serum and plated in 96-well V-bottom microtitier plates at 2 10⁴ cells/well. ATPHyl-specific antibody is added in triplicate to individual wells at 1 μg/ml, and effector cells are added at various effector.target cell ratios (12.5:1 to 50:1). The plates are incubated for 4 hours at 37°C. The supematants are then harvested, lactate dehydrogenase release determined, and percent specific lysis calculated using the manufacture's protocols.

EXAMPLE 5 TOXIN-CONJUGATED ATPHYI -SPECIFIC ANTIBODIES Antibodies to ATPHyl are conjugated to toxins and the effect of such conjugates in animal models of cancer is evaluated. Chemotherapeutic agents, such as calicheamycin and carboplatin, or toxic peptides, such as ricin toxin, are used in this approach. Antibody-toxin conjugates are used to target cytotoxic agents specifically to cells bearing the antigen. The antibody-toxin binds to these antigen-bearing cells, becomes internalized by receptor- mediated endocytosis, and subsequently destroys the targeted cell. In this case, the antibody-toxin conjugate targets ATPHyl -expressing cells, such as prostate cancer cells, and deliver the cytotoxic agent to the tumor resulting in the death of the tumor cells. One such example of a toxin that may be conjugated to an antibody is carboplatm. The mechanism by which this toxin is conjugated to antibodies is described in Ota et al, Asia-Oceania J. Obstet. Gynaecol. 19: 449-457 (1993). The cytotoxicity of carboplatin- conjugated ATPHyl-specific antibodies is evaluated in vitro, for example, by incubating ATPHyl -expressing target cells (such as the prostate cancer cell line, for example) with various concentrations of conjugated antibody, medium alone, carboplatin alone, or antibody alone. The antibody-toxin conjugate specifically targets and kills cells bearing the ATPHyl antigen, whereas, cells not bearing the antigen, or cells treated with medium alone, carboplatin alone, or antibody alone, show no cytotoxicity. The antitumor efficacy of carboplatin-conjugated ATPHyl -specific antibodies is demonstrated in in vivo murine tumor models. Five to six week old, athymic nude mice are engrafted with tumors subcutaneously or through intravenous injection. Mice are treated with the ATPHyl -carboplatin conjugate or with a non-specific antibody-carboplatin conjugate. Tumor xenografts in the mouse bearing the ATPHyl antigen are targeted and bound to by the ATPHyl -carboplatin conjugate. This results in tumor cell killing as evidenced by tumor necrosis, tumor shrinkage, and increased survival of the treated mice.

Other toxins are conjugated to ATPHyl-specific antibodies using methods known in the art. An example of a toxin conjugated antibody in human clinical trials is CMA-676, an antibody to the CD33 antigen in AML which is conjugated with calicheamicin toxin (Larson, Semin. Hematol 38(Suppl 6):24-31 (2001)).

EXAMPLE 6 RADIO-IMMUNOTHERAPY USING ATPHYI -SPECIFIC ANTIBODIES

Animal models are used to assess the effect of antibodies specific to ATPHyl as vectors in the delivery of radionuclides in radio-immunotherapy to treat lymphoma, hematological malignancies, and solid tumors. Human tumors are propagated in 5-6 week old athymic nude mice by injecting a carcinoma cell line or tumor cells subcutaneously. Tumor-bearing animals are injected intravenously with radio-labeled anti-ATPHyl antibody (labeled with 30-40 μCi of ¹³¹I, for example) (Behr, et al, Int. J. Cancer 11: 787-795 (1988)). Tumor size is measured before injection and on a regular basis (i.e. weekly) after injection and compared to tumors in mice that have not received treatment. Anti-tumor efficacy is calculated by correlating the calculated mean tumor doses and the extent of induced growth retardation. To check tumor and organ histology, animals are sacrificed by cervical dislocation and autopsied. Organs are fixed in 10% formalin, embedded in paraffin, and thin sectioned. The sections are stained with hematoxylin-eosin.

EXAMPLE 7 THERAPY USING ATPHYI-SPECIFIC ANTIBODIES

Animal models are used to evaluate the effect of ATPHyl-specific antibodies as targets for antibody-based targeting therapy using monoclonal antibodies. Human myeloma cells are injected into the tail vein of 5-6 week old nude mice whose natural killer cells have been eradicated. To evaluate the ability of ATPHyl-specific antibodies in preventing tumor growth, mice receive an intraperitoneal injection with ATPHyl-specific antibodies either 1 or 15 days after tumor inoculation followed by either a daily dose of 20 μg or 100 μg once or twice a week, respectively (Ozaki, et al, Blood 90:3179-3186 (1997)). Levels of human IgG (from the immune reaction caused by the human tumor cells) are measured in the murine sera by ELIS A. The effect of ATPHyl-specific antibodies on the proliferation of cancer cells is examined in vitro using a H-thymidine incoφoration assay (Ozaki et al, supra). Cells are cultured in 96-well plates at 1 10^s cells/ml in 100 μl/well and incubated with various amounts of ATPHyl antibody or control IgG (up to 100 μg/ml) for 24 h. Cells are incubated with 0.5 μCi ³H-thymidine (New England Nuclear, Boston, MA) for 18 h and harvested onto glass filters using an automatic cell harvester (Packard, Meriden, CT). The incoφorated radioactivity is measured using a liquid scintillation counter.

The cytotoxicity of the ATPHyl monoclonal antibody is examined by the effect of complements on cancer cells using a ⁵¹Cr-release assay (Ozaki et al., supra). Myeloma cells are labeled with 0.1 mCi ⁵¹Cr-sodium chromate at 37°C for 1 h. ⁵¹Cr-labeled cells are incubated with various concentrations of ATPHyl monoclonal antibody or control IgG on ice for 30 min. Unbound antibody is removed by washing with medium. Cells are distributed into 96-well plates and incubated with serial dilutions of baby rabbit complement at 37°C for 2 h. The supematants are harvested from each well and the amount of ⁵¹Cr released is measured using a gamma counter. Spontaneous release of ⁵¹Cr is measured by incubating cells with medium alone, whereas maximum ⁵¹Cr release is measured by treating cells with 1% NP-40 to disrupt the plasma membrane. Percent cytotoxicity is measured by dividing the difference of experimental and spontaneous ⁵¹Cr release by the difference of maximum and spontaneous Cr release. Antibody-dependent cell-mediated cytotoxicity (ADCC) for the ATPHyl monoclonal antibody is measured using a standard 4 h ⁵¹Cr-release assay (Ozaki et al, supra). Splenic mononuclear cells from SCID mice are used as effector cells and cultured with or without recombinant interleukin-2 (for example) for 6 days. ⁵¹Cr-labeled target myeloma cells (1 x 10⁴ cells) are placed in 96-well plates with various concentrations of anti- ATPHyl monoclonal antibody or control IgG. Effector cells are added to the wells at various effector to target ratios (12.5:1 to 50:1). After 4 h, culture supematants are removed and counted in a gamma counter. The percentage of cell lysis is determined as above.

EXAMPLE 8

ATPHYI-SPECIFIC ANTIBODIES AS IMMUNOSUPPRESSANTS

Animal models are used to assess the effect of ATPHyl-specific antibodies block signaling through the ATPHyl receptor to suppress autoimmune diseases, such as arthritis or other inflammatory conditions, or rejection of organ transplants. Immunosuppression is tested by injecting mice with horse red blood cells (HRBCs) and assaying for the levels of HRBC-specific antibodies (Yang, et al, Int. Immunopharm. 2:389-397 (2002)). Animals are divided into five groups, three of which are injected with anti-ATPHyl antibodies for 10 days, and 2 of which receive no treatment. Two of the experimental groups and one control group are injected with either Earle's balanced salt solution (EBSS) containing 5-10 x 10⁷ HRBCs or EBSS alone. Anti-ATPHyl antibody treatment is continued for one group while the other groups receive no antibody treatment. After 6 days, all animals are bled by retro- orbital puncture, followed by cervical dislocation and spleen removal. Splenocyte suspensions are prepared and the serum is removed by centrifugation for analysis.

Immunosupression is measured by the number of B cells producing HRBC-specific antibodies. The lg isotype (for example, IgM, IgGl, IgG2, etc.) is determined using the IsoDetect™ Isotyping kit (Stratagene, La Jolla, CA). Once the lg isotype is known, murine antibodies against HRBCs are measured using an ELISA procedure. 96-well plates are coated with HRBCs and incubated with the anti-HRBC antibody-containing sera isolated from the animals. The plates are incubated with alkaline phosphatase-labeled secondary antibodies and color development is measured on a microplate reader (SPECTRAmax 250, Molecular Devices) at 405 nm using -nitrophenyl phosphate as a substrate.

Lymphocyte proliferation is measured in response to the T and B cell activators concanavalin A and lipopolysaccharide, respectively (Jiang, et al, J. Immunol. 154:3138- 3146 (1995). Mice are randomly divided into 2 groups, 1 receiving anti-ATPHyl antibody therapy for 7 days and 1 as a control. At the end of the treatment, the animals are sacrificed by cervical dislocation, the spleens are removed, and splenocyte suspensions are prepared as above. For the ex vivo test, the same number of splenocytes are used, whereas for the in vivo test, the anti-ATPHyl antibody is added to the medium at the beginning of the experiment. Cell proliferation is also assayed using the ³H-thymidine incoφoration assay described above (Ozaki, et al, Blood 90: 3179 (1997)).

EXAMPLE 9 CYTOKINE SECRETION IN RESPONSE TO ATPHYI PEPTIDE FRAGMENTS

Assays are carried out to assess activity of fragments of the ATPHyl protein, such as the lg domain, to stimulate cytokine secretion and to stimulate immune responses in NK cells, B cells, T cells, and myeloid cells. Such immune responses can be used to stimulate the immune system to recognize and/or mediate tumor cell killing or suppression of growth. Similarly, this immune stimulation can be used to target bacterial or viral infections.

Alternatively, fragments of the ATPHyl that block activation through the ATPHyl receptor may be used to block immune stimulation in natural killer (NK), B, T, and myeloid cells.

Fusion proteins containing fragments of the ATPHyl, such as the lg domain (ATPHyl -lg), are made by inserting a CD33 leader peptide, followed by a ATPHyl domain fused to the Fc region of human IgGl into a mammalian expression vector, which is stably transfected into NS-1 cells, for example. The fusion proteins are secreted into the culture supernatant, which is harvested for use in cytokine assays, such as interferon-γ (LFN-γ) secretion assays (Martin, et al, J. Immunol. 167:3668-3676 (2001)).

PBMCs are activated with a suboptimal concentration of soluble CD3 and various concentrations of purified, soluble anti-ATPHyl monoclonal antibody or control IgG. For ATPHyl -lg cytokine assays, anti-human Fc lg at 5 or 20 μg/ml is bound to 96-well plates and incubated overnight at 4°C. Excess antibody is removed and either ATPHyl -lg or control lg is added at 20-50 μg/ml and incubated for 4 h at room temperature. The plate is washed to remove excess fusion protein before adding cells and anti-CD3 to various concentrations. Supematants are collected after 48 h of culture and IFN-γ levels are measured by sandwich ELISA, using primary and biotinylated secondary anti-human LFN-γ antibodies as recommended by the manufacturer. EXAMPLE 10

TUMOR IMAGING USING ATPHYI-SPECIFIC ANTIBODIES

ATPHyl-specific antibodies are used for imaging ATPHyl -expressing cells in vivo. Six- week-old athymic nude mice are irradiated with 400 rads from a cesium source. Three days later the irradiated mice are inoculated with 4x 10⁷ RA1 cells and 4 10⁶ human fetal lung fibroblast feeder cells subcutaneously in the thigh. When the tumors reach approximately 1 cm in diameter, the mice are injected intravenously with an inoculum containing 100 μCi/10 μg of ¹³¹I-labeled ATPHyl-specific antibody. At 1, 3, and 5 days postinjection, the mice are anesthetized with a subcutaneous injection of 0.8 mg sodium pentobarbital. The immobilized mice are then imaged in a prone position with a Spectrum 91 camera equipped with a pinhole collimator (Raytheon Medical Systems; Melrose Park, IL) set to record 5,000 to 10,000 counts using the Nuclear MAX Plus image analysis software package (MEDX Inc.; Wood Dale, IL) (Hornick, et al, Blood 89:4437-4447 (1997)).

EXAMPLE 11 IN VIVO TUMOR MODELS The tumor suppressing activity of ATPHyl targeting molecules is tested by taking groups of 4-10 nude, athymic male mice are injected subcutaneously with 10⁶ cells, either a control (M12pcDNA), ATPHyl expressing clones, or low expressing clones (Spenger et al, Cancer Research 59:2370-2375 (1999), incoφorated herein by reference in its entirety). The clones the lowest levels of ATPHyl are used as the comparison benchmark. Mice are monitored for 8 weeks for weight gain/loss and tumor formation. Tumor volume is calculated using the formula (/ x w² )/2 (where / = length and w = width of the tumor) (Id.). Statistical analysis using the Kruskal-Wallis method for comparing tumor formation, and the Mann- Whitney [/test for comparing tumor volume are performed to detennine any statistical significance amongst groups.

After 8 weeks, the mice are sacrificed, and the tumors removed and digested with 0.1% collagenase (Type I) and 50 μg/ml DNase (Worthington Biochemical Coφ., Freehold, NJ). Dispersed cells are plated in ITS medium/5% FBS at %% CO₂ at 37°C for 24 hours to allow attachment. After 24 hours, the cultures are switched to serum-free medium. The cells are split, the media and RNA collected, and Western immunoblots and Northern blots are done to detect ATPHyl . EXAMPLE 12

IN VITRO ASSAY OF CELL PROLIFERATION AND MIGRATION

The effect of ATPHyl-specific antibodies or therapeutic peptides on the proliferation of cancer cells is examined in vitro usmg a H-thymidme incoφoration assay (Ozaki et al, Blood 90:3179-3186 (1997), herein incoφorated by reference in its entirety. Tumor cells are cultured in 96-well plates at 1 x 10⁵ cells/ml in 100 μl/well and incubated with various amounts of antibody or control IgG (up to 100 μg/ml) for 24 h. Cells are incubated with 0.5 μCi ³H-thymidine (New England Nuclear, Boston, MA) for 18 h and harvested onto glass filters using an automatic cell harvester (Packard, Meriden, CT). The incoφorated radioactivity is measured using a liquid scintillation counter.

Cell migration is conducted in 24-well, 6.5-mm internal diameter Transwell cluster plates (Coming Costar, Cambridge, MA). Briefly, 10⁵ cells/75 μl are loaded onto fibronectin (5 μM)-coated polycarbonate membranes (8-μm pore size) separating two chambers of a transwell (Tai et al, Blood 99:1419-1427 (2002), herein incoφorated by reference in its entirety. Medium with or without anti-ATPHyl antibodies is added to the lower chamber of the Transwell cluster plates. After 8-16 h, cells migrating to the lower chamber are counted using a Coulter counter ZBII (Beckman Coulter) and by hemacytometer.

Claims

WE CLAIM:

1. A pharmaceutical composition comprising an anti-ATPHyl antibody specific for cells that cause cancer selected from the group consisting of breast, colon, lung, and prostate cancer, wherein said antibody specifically binds to a polypeptide having an amino acid sequence of SEQ LD. NO: 2 or extracellular portion thereof.

2. The pharmaceutical composition of claim 1, wherein said antibody is a monoclonal anti-ATPHyl antibody or antigen-binding fragment thereof.

3. The pharmaceutical composition of claim 1, wherein said antibody is administered in an amount effective to kill or inhibit the growth of cells that cause a cancer selected from the group consisting of breast, colon, lung, and prostate cancer.

4. A method of targeting ATPHyl protein on cells that cause a cancer selected from the group consisting of breast, colon, lung, and prostate cancer, comprising the step of administering a composition to said cells in an amount effective to target said ATPHyl - expressing cells, wherein said composition is an anti-ATPHyl antibody that specifically binds to a polypeptide having an amino acid sequence of SEQ ID NO: 2 or extracellular portion thereof.

5. A method of killing or inhibiting the growth of ATPHyl -expressing cells that cause a cancer selected from the group consisting of breast, colon, lung, and prostate cancer, comprising the step of administering a composition to said cells in an amount effective to kill or inhibit the growth of said cancer cells, wherein said composition is an anti-ATPHyl antibody that specifically binds to a polypeptide having an amino acid sequence of SEQ ID. NO: 2 or extracellular portion thereof.

6. A method of killing or inhibiting the growth of ATPHyl -expressing cells that cause a cancer selected from the group consisting of breast, colon, lung, and prostate cancer, comprising the step of administering a composition to said cells in an amount effective to kill or inhibit the growth of said cancer cells, wherein said composition comprises an ATPHyl antigen.

7. A method of killing or inhibiting the growth of ATPHyl -expressing cells that cause a cancer selected from the group consisting of breast, colon, lung, and prostate cancer, comprising the step of administering a composition to said cells in an amount effective to kill or inhibit the growth of said cancer cells, wherein said composition comprises a nucleic acid of SEQ LD NO: 1 encoding ATPHyl, or immunogenic fragment thereof, within a recombinant vector.

8. A method of killing or inhibiting the growth of ATPHyl -expressing cells that cause a cancer selected from the group consisting of breast, colon, lung, and prostate cancer, comprising the step of administering a composition to said cells in an amount effective to kill or inhibit the growth of said cancer cells, wherein said composition comprises an antigen-presenting cell comprising a nucleic acid of SEQ ID NO: 1 encoding ATPHyl, or immunogenic fragment thereof, within a recombinant vector.

9. The method according to claims 4, 5, 6, 7, or 8, wherein said cells are contacted with as second therapeutic agent.

10. The method according to claim 4 or 5, wherein said anti-ATPHyl antibody composition is administered in an amount effective to achieve a dosage range from about 0.1 to about 10 mg/kg body weight.

11. The method according to claims 4, 5, 6, 7, or 8, wherein said pharmaceutical composition is administered in a sterile preparation together with a pharmaceutically acceptable carrier therefor.

12. A method of diagnosing cancer selected from the group consisting of breast, colon, lung, and prostate cancer comprising the steps of: detecting or measuring the expression of ATPHyl protein on a cell; and comparing said expression to normal tissue.

13. The method according to claim 12, wherein said expression is ATPHyl mRNA expression.

14. The method according to claim 12, wherein said expression is detected or measured using anti-ATPHyl antibodies.

15. Use of an anti-ATPHyl antibody in preparation of a medicament for killing or inhibiting the growth of ATPHyl -expressing cells that cause a cancer selected from the group consisting of breast, colon, lung, and prostate cancer, wherein said antibody specifically binds to a polypeptide having the amino acid sequence of SEQ LD NO: 2 or extracellular portion thereof.

16. Use of an ATPHyl antigen in preparation of a medicament for killing or inhibiting the growth of ATPHyl -expressing cells that cause a cancer selected from the group consisting of breast, colon, lung, and prostate cancer.

17. Use of a nucleic acid of SEQ JJD NO: 1 encoding ATPHyl or immunogenic fragment thereof, within a recombinant vector, in preparation of a medicament for killing or inhibiting the growth of ATPHyl -expressing cells that cause a cancer selected from the group consisting of breast, colon, lung, and prostate cancer.

18. Use of an antigen-presenting cell comprising a nucleic acid of SEQ LD NO : 1 encoding ATPHyl or immunogenic fragment thereof, within a recombinant vector, in preparation of a medicament for killing or inhibiting the growth of ATPHyl -expressing cells that cause a cancer selected from the group consisting of breast, colon, lung, and prostate cancer.

19. An isolated polypeptide comprising the amino acid sequence of SEQ LD NO:

20. A pharmaceutical composition comprising the isolated polypeptide of claim

19.

21. An antibody that specifically binds to SEQ LD NO: 5.

22. The antibody of claim 21, wherein said antibody is a monoclonal antibody or antibody fragment thereof.

23. The antibody of claim 21 , wherein said antibody is a polyclonal antibody of antibody fragment thereof.

24. The antibody of claim 21, wherein said antibody is 18835a.