WO2003087831A2

WO2003087831A2 - Proteins involved in breast cancer

Info

Publication number: WO2003087831A2
Application number: PCT/GB2003/001559
Authority: WO
Inventors: Lyndsey J Hudson; Alasdair Craig Stamps; Jonathan Alexander Terrett
Original assignee: Oxford Glycosciences (Uk) Ltd
Priority date: 2002-04-11
Filing date: 2003-04-10
Publication date: 2003-10-23
Also published as: AU2003222604A1; WO2003087831A3; AU2003222604A8; GB0208331D0

Abstract

The present invention provides methods and compositions for the screening, diagnosis and therapy of breast cancer, for monitoring the effectiveness of breast cancer treatment, and for drug development.

Description

PROTEINS INVOLVED IN BREAST CANCER

The present invention relates to breast cancer membrane proteins (BCMPs). The invention also relates to the use of these BCMPs, compositions comprising the BCMPs, including vaccines and antibodies that are immunospecific for the BCMPs in the diagnosis, prophylaxis and treatment of breast cancer.

Breast cancer is one of the leading causes of cancer death for women in the Western world. The major challenges in breast cancer treatment are to improve early detection rates, to find new non-invasive markers that can be used to follow disease progression and identify relapse, and to find improved and less toxic therapies, especially for more advanced disease where 5 year survival is still very poor. Thus, there is a great need to identify targets which are more specific to the cancer cells, ideally ones which are expressed on the surface of the tumour cells so that they can be attacked by promising new approaches like immunotherapeutics and targeted toxins.

The present invention is based on the finding of polypeptides which represent novel diagnostic markers for or therapreutic targets for the treatment of breast cancer.

Accordingly, provided is a method of screening for and/or diagnosis of breast cancer in a subject, and/or monitoring the effectiveness of breast cancer therapy, which comprises the step of detecting and/or quantifying in a biological sample obtained from said subject a BCMP polypeptide which: a) comprises an amino acid sequence of any one of SEQ ID NOS: 1-547; b) is a derivative of a) having one or more amino acid substitutions, modifications, deletions or insertions, and which retains the activity of the BCMP polypeptide; or c) is a fragment of a polypeptide of a) or b), which is at least ten amino acids long and has at least 70% homology over the length of the fragment.

These methods of the invention are suitable for monitoring the effectiveness of breast cancer treatment, for identifying patients most likely to respond to a particular therapeutic treatment, for drug development and discovery of new targets for drug treatment.

In a further aspect, the present invention provides a method for identifying the presence or absence of metastatic breast cancer cells in a biological sample obtained from a human subject, which comprises the step of identifying the presence or absence of one or more BCMP polypeptides.

The above polypeptides described in a) to c) above are hereinafter referred to as "BCMP polypeptides". The term "polypeptides" includes peptides, polypeptides and proteins. These are used interchangeably unless otherwise specified. "Active" as used herein refers to material displaying one or more functional activities associated with a full-length or mature BCMP polypeptide, e.g. binding to a BCMP polypeptide substrate or BCMP polypeptide binding partner, antigenicity (binding to an anti-BCMP antibody), immunogenicity, enzymatic activity etc. BCMP polypeptides may be in the form of a 'mature' protein or may be part of a larger protein such as a fusion protein. For example, a BCMP polypeptide may be fused with the constant domain of immunoglobulins (IgA, IgE, IgG, IgM), or portions thereof (CH1 , CH2, CH3, or any combination thereof and portions thereof) resulting in chimeric polypeptides. Such fusion proteins may facilitate purification, increase half-life in vivo, and enhance the delivery of an antigen across an epithelial barrier to the immune system. An increase in the half-life in vivo and facilitated purification has been shown for chimeric proteins consisting of the first two domains of the human CD-polypeptide and various domains of the constant regions of the heavy or light chains of mammalian immunoglobulins (see, e.g. EP 394827; Traunecker et al., 1988 Nature, 331 :84-86). Enhanced delivery of an antigen across the epithelial barrier to the immune system has been demonstrated for antigens (e.g, insulin) conjugated to an FcRn binding partner such as IgG or Fc fragments (see e.g. WO 96/22024 and WO 99/04813).

It is often advantageous to include an additional amino acid sequence which contains secretory or leader sequences, a pre-, pro- or prepro-protein sequence, or a sequence which aids in purification such as an affinity tag, for example, but without limitation, multiple histidine residues, a FLAG tag, HA tag or myc tag. An additional sequence which may provide stability during recombinant production may also be used. Such sequences may be optionally removed as required by incorporating a cleavable sequence as an additional sequence or part thereof. Thus, a BCMP polypeptide may be fused to other moieties including other polypeptides. Such additional sequences and affinity tags are well known in the art.

Amino acid substitutions may be conservative or semi-conservative as known in the art and preferably do not significantly affect the desired activity of the polypeptide. Substitutions may be naturally occurring or may be introduced for example using mutagenesis (e.g. Hutchinson et al., 1978, J. Biol. Chem. 253:6551 ). Thus, the amino acids glycine, alanine, valine, leucine and isoleucine can often be substituted for one another (amino acids having aliphatic side chains). Of these possible substitutions, it is preferred that glycine and alanine are used to substitute for one another (since they have relatively short side chains) and that valine, leucine and isoleucine are used to substitute for one another (since they have larger aliphatic side chains which are hydrophobic). Other amino acids which can often be substituted for one another include but are not limited to:

- phenylalanine, tyrosine and tryptophan (amino acids having aromatic side chains);

- lysine, arginine and histidine (amino acids having basic side chains);

- aspartate and glutamate (amino acids having acidic side chains);

- asparagine and glutamine (amino acids having amide side chains);

- cysteine and methionine (amino acids having sulphur-containing side chains); and

- aspartic acid and glutamic acid can substitute for phospho-serine and phospho- threonine, respectively (amino acids with acidic side chains).

In one particular embodiment, the substituted amino acid(s) do significantly affect the activity of the BCMP polypeptide and may be selected specifically to render dominant negative activity upon the peptide. In another embodiment, the substituted amino acid(s) may be selected specifically to render the polypeptide constitutively active.

Modifications include naturally occurring modifications such as, and without limitation, post-translational modifications and also non-naturally occurring modifications such as may be introduced by mutagenesis. Preferably a derivative according to b) has at least 70% identity to an amino acid sequence as defined in a), more preferably it has at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 98% identity. Percentage identity is a well known concept in the art and can be calculated using, for example but without limitation, the BLAST™ software available from NCBI (Altschul, S.F. etal., 1990, J. Mol. Biol. 215:403-410; Gish, W. & States, D.J. 1993, Nature Genet. 3:266-272. Madden, T.L. et al., 1996, Meth. Enzymol. 266:131-141 ; Altschul, S.F. et al., 1997, Nucleic Acids Res. 25:3389-3402); Zhang, J. & Madden, T.L. 1997, Genome Res. 7:649-656).

Fragments of BCMP polypeptides as described in c) above are at least 10 amino acids in length, preferably they are at least 20, at least 30, at least 50 or at least 100 amino acids in length. A fragment has at least 70% identity over its length to an amino acid sequence as defined in a) or b), more preferably it has at least 75%, at least 80%, at least 85%, at least 90%, at least 95% or at least 98% identity.

A BCMP polypeptide can be identified in a biological sample from any source such as a serum sample or a tissue sample, e.g. breast tissue. For instance, when looking for evidence of metastatic breast cancer, one would look at major sites of breast metastasis, e.g. lymph nodes, liver, lung and/or bone. As used herein, breast tissue refers to the breast itself, as well as the tissue adjacent to and/or within the strata underlying the breast.

For clarity of disclosure, and not by way of limitation, the invention will be described with respect to the analysis of breast tissue samples. However, as one skilled in the art will appreciate, the assays and techniques described below can be applied to other types of patient samples, including a body fluid (e.g. blood, serum, plasma or saliva), a tissue sample from a patient at risk of having breast cancer (e.g. a biopsy such as a breast tissue biopsy) or homogenate thereof. The methods and compositions of the present invention are specially suited for screening, diagnosis and prognosis of a living subject, but may also be used for postmortem diagnosis in a subject, for example, to identify if family members are at risk of developing the same disease.

Preferably, the methods of the present invention are not based on looking for the presence of all of the BCMPs, but rather on a single BCMP or "clusters" or groups thereof. A cluster or group may comprise two or more BCMPs.

For any given BCMP, the detected level obtained upon analysing breast tissue from subjects having breast cancer relative to the detected level obtained upon analysing breast tissue from subjects free from breast cancer will depend upon the particular analytical protocol and detection technique that is used, provided that such BCMP is differentially expressed between normal and disease tissue. Thus, the present invention contemplates that each laboratory will establish a reference range for each BCMP in subjects free from breast cancer according to the analytical protocol and detection technique in use, as is conventional in the diagnostic art. Preferably, at least one control positive breast tissue sample from a subject known to have breast cancer or at least one control negative breast tissue sample from a subject known to be free from breast cancer (and more preferably both positive and negative control samples) are included in each batch of test samples analysed, wherein a change in abundance of the BCMP polypeptide or BCMP polypeptides in the breast tissue from the subject relative to breast tissue from a subject or subjects free from breast cancer (e.g. a control sample or a previously determined reference range) indicates the presence of breast cancer.

In one embodiment, a change in the abundance of one or more BCMP polypeptides in a test sample relative to a control sample (from a subject or subjects free from breast cancer) or a previously determined reference range indicates the presence of breast cancer. In another embodiment, the relative abundance of one or more BCMP polypeptides in a test sample compared to a control sample or a previously determined reference range indicates a subtype of breast cancer (e.g. primary or metastatic breast cancer). In yet another embodiment, the relative abundance of one or more BCMP polypeptides in a test sample relative to a control sample or a previously determined reference range indicates the degree or severity of breast cancer (e.g. the likelihood for metastasis). In any of the aforesaid methods, detection of one or more BCMP polypeptides herein may optionally be combined with detection of one or more additional biomarkers for breast cancer. Any suitable method in the art can be employed to measure the level of BCMP polypeptides, including but not limited to 2D-gel electrophoresis, kinase assays, immunoassays to detect and/or visualize the BCMP polypeptides (e.g. Western blot, immunoprecipitation followed by sodium dodecyl sulfate polyacrylamide gel electrophoresis, immunocytochemistry, etc.). In cases where a BCMP polypeptide has a known function, an assay for that function may be used to measure BCMP expression.

The BCMPs of the invention can be assayed by any method known to those skilled in the art, including but not limited to, 1 D-gel electrophoresis described herein, 2D gel- electrophoresis (see for example US 6,278,794), kinase assays, phosphatase assays, enzyme assays, binding assays or other functional assays, immunoassays, and Western blotting.

In one aspect of the invention, two-dimensional electrophoresis is used to analyse breast tissue from a subject, preferably a living subject, in order to measure the expression of one or more BCMPs for screening, prognosis or diagnosis of breast cancer, to monitor the effectiveness of breast cancer therapy, or for drug development. Two-dimensional electrophoresis may be performed using any means known in the art, for example but not limited to, methods described in US 6,278,794 and EP 0941477.

In a further aspect, the method of detecting/quantifying the presence of a BCMP polypeptide comprises detecting a captured BCMP polypeptide using a directly or indirectly labelled detection reagent, e.g. a detectable marker such as, without limitation, a chemiluminescent, enzymatic, fluorescent, or radioactive moiety.

In one preferred embodiment, a BCMP polypeptide or BCMP polypeptides are detected in an immunoassay. For example but without limtation, an immunoassay can be performed by contacting a sample from a subject to be tested with an anti-BCMP antibody under conditions such that immunospecific binding can occur if the BCMP polypeptide is present, and detecting or measuring the amount of any immunospecific binding by the antibody. Anti-BCMP antibodies can be produced by the methods and techniques taught herein.

In another embodiment, binding of antibody in tissue sections can be used to detect aberrant BCMP polypeptide localization or an aberrant level of one or more BCMP polypeptides. In a specific embodiment, antibody to a BCMP polypeptide can be used to assay a patient tissue (e.g. a breast tissue biopsy) for the level of the BCMP polypeptide where an aberrant level of said BCMP polypeptide is indicative of breast cancer. As used herein, an "aberrant level" includes a level that is increased or decreased compared with the level in a subject free from breast cancer or a reference level. If desired, the comparison can be performed with a matched sample from the same subject, taken from a portion of the body not affected by breast cancer.

Any suitable immunoassay can be used, including, without limitation, competitive and non-competitive assay systems using techniques such as Western blots, radioimmunoassays, ELISA (enzyme linked immunosorbent assay), "sandwich" immunoassays, immunoprecipitation assays, precipitin reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, complement-fixation assays, immunoradiometric assays, fluorescent immunoassays and protein A immunoassays.

For example, a BCMP polypeptide can be detected in a fluid sample (e.g. blood, urine, or breast tissue homogenate) by means of a two-step sandwich assay. In the first step, a capture reagent (e.g. an anti-BCMP antibody) is used to capture the BCMP polypeptide. The capture reagent can optionally be immobilized on a solid phase. In the second step, a directly or indirectly labeled detection reagent is used to detect the captured BCMP polypeptide. In one embodiment, the detection reagent is a lectin. Any lectin can be used for this purpose that preferentially binds to the BCMP polypeptide rather than to other isoforms that have the same core protein as the BCMP polypeptide or to other proteins that share the antigenic determinant recognized by the antibody. In a preferred embodiment, the chosen lectin binds to the BCMP polypeptide with at least 2-fold greater affinity, more preferably at least 5-fold greater affinity, still more preferably at least 10-fold greater affinity, than to said other isoforms that have the same core protein as the BCMP polypeptide or to said other proteins that share the antigenic determinant recognized by the antibody. Based on the present description, a lectin that is suitable for detecting a given BCMP polypeptide can readily be identified by methods well known in the art, for instance upon testing one or more lectins enumerated in Table I on pages 158-159 of Sumar et al., Lectins as Indicators of Disease-Associated Glycoforms, In: Gabius H-J & Gabius S (eds.), 1993, Lectins and Glycobiology, at pp. 158-174. In an alternative embodiment, the detection reagent is an antibody, e.g. an antibody that immunospecifically detects other post-translational modifications, such as an antibody that immunospecifically binds to phosphorylated amino acids. Examples of such antibodies include those that bind to phosphotyrosine (BD Transduction Laboratories, catalog nos.: P11230-050/P11230-150; P11120; P38820; P39020), those that bind to phosphoserine (Zymed Laboratories Inc., South San Francisco, CA, catalog no. 61 -8100) and those that bind to phosphothreonine (Zymed Laboratories Inc., San Francisco, CA, catalogue nos. 71-8200, 13-9200).

The invention also provides diagnostic kits, comprising a capture reagent (e.g. an antibody) against a BCMP polypeptide as defined above. In addition, such a kit may optionally comprise one or more of the following:

(1 ) instructions for using the capture reagent for diagnosis, prognosis, therapeutic monitoring or any combination of these applications;

(2) a labelled binding partner to the capture reagent;

(3) a solid phase (such as a reagent strip) upon which the capture reagent is immobilised; and

(4) a label or insert indicating regulatory approval for diagnostic, prognostic or therapeutic use or any combination thereof.

If no labelled binding partner to the capture reagent is provided, an anti-BCMP polypeptide capture reagent itself can be labelled with a detectable marker (see above).

Domains of some BCMP polypeptides are known in the art and have been described in the scientific literature. Moreover, domains of a BCMP polypeptide can be identified using techniques known to those of skill in the art. For example, one or more domains of a BCMP polypeptide can be identified by using one or more of the following programs: ProDom, TMpred, and SAPS. ProDom compares the amino acid sequence of a polypeptide to a database of compiled domains (see, e.g. http://www.toulouse.inra.fr/prodom.html; Corpet F. et al., 1999, Nucleic Acids Res., 27:263-267). TMpred predicts membrane-spanning regions of a polypeptide and their orientation. This program uses an algorithm that is based on the statistical analysis of TMbase, a database of naturally occuring transmembrane proteins (see, e.g. www.ch.embnet.org/software TMPRED_form.html; Hofmann & Stoffel, 1993, Biol. Chem. Hoppe-Seyler 347:166). The SAPS program analyses polypeptides for statistically significant features like charge-clusters, repeats, hydrophobic regions, compositional domains (see, e.g. Brendel et al., 1992, Proc. Natl. Acad. Sci. USA 89: 2002-2006). Thus, based on the present description, the skilled artisan can identify domains of a BCMP polypeptide having enzymatic or binding activity, and further can identify nucleotide sequences encoding such domains. These nucleotide sequences can then be used for recombinant expression of a BCMP polypeptide that retains the enzymatic or binding activity of the mature or full length BCMP polypeptide.

Based on the present description, the skilled artisan can identify domains of a BCMP polypeptide having enzymatic or binding activity, and further can identify nucleotide sequences encoding such domains. These nucleotide sequences can then be used for recombinant expression of a BCMP polypeptide that retain the enzymatic or binding activity of the mature or full length BCMP.

In one embodiment, a BCMP polypeptide has an amino acid sequence sufficiently similar to domain of a known polypeptide. As used herein, the term "sufficiently similar" refers to a first amino acid or nucleotide sequence which contains a sufficient number of identical or equivalent (e.g. with a similar side chain) amino acid residues or nucleotides to a second amino acid or nucleotide sequence such that the first and second amino acid or nucleotide sequences have or encode a common structural domain or common functional activity or both.

A BCMP polypeptide domain can be assessed for its function using techniques well known to those of skill in the art. For example, a domain can be assessed for its kinase activity or phosphatase activity or for its ability to bind to DNA using techniques known to the skilled artisan. Kinase or phosphatase activity can be assessed, for example, by measuring the ability of a polypeptide to phosphorylate or dephosphorylate, respectively, a substrate. DNA binding activity can be assessed, for example, by measuring the ability of a polypeptide to bind to a DNA binding element in an electromobility shift assay.

It is well known that is possible to screen an antigenic protein or polypeptide to identify epitopic regions, i.e. those regions which are responsible for the protein or polypeptide's antigenicity or immunogenicity. Amino acid and peptide characteristics well known to the skilled person can be used to predict the antigenic index (a measure of the probability that a region is antigenic) of a BCMP polypeptide. For example, but without limitation, the 'Peptidestructure' program (Jameson and Wolf, 1988, CABIOS, 4(1 ):181) and a technique referred to as Threading' (Altuvia Y. et al., 1995, J. Mol. Biol. 249:244) can be used. Thus, the BCMP polypeptides may include one or more such epitopes or be sufficiently similar to such regions so as to retain their antigenic/immunogenic properties. Methods well known to the skilled person can be used to test fragments and/or homologues and/or derivatives of a polypeptide for antigenicity. Thus, the fragments for use in the present invention may include one or more such epitopic regions or be sufficiently similar to such regions to retain their antigenic/immunogenic properties. Thus, for fragments for use according to the present invention the degree of identity is perhaps irrelevant, since they may be 100% identical to a particular part of a protein or polypeptide, homologue or derivative as described herein. The key issue may be that the fragment retains the antigenic/immunogenic properties of the protein from which it is derived. If the BCMP polypeptide is a fusion protein it may or may not be necessary to remove the tag such that the BCMP polypeptide retains its antigenicity.

The skilled person will appreciate that homologues or derivatives of the BCMPs will also find use as antigenic/immunogenic material. Thus, for instance proteins that include one or more additions, deletions, substitutions or the like are encompassed by the present invention. In addition, it may be possible to replace one amino acid with another of similar "type"; for instance, replacing one hydrophobic amino acid with another. One can use a program such as the CLUSTAL program to compare amino acid sequences. This program compares amino acid sequences and finds the optimal alignment by inserting spaces in either sequence as appropriate. It is possible to calculate amino acid identity or similarity (identity plus conservation of amino acid type) for an optimal alignment. A program like BLASTx will align the longest stretch of similar sequences and assign a value to the fit. It is thus possible to obtain a comparison where several regions of similarity are found, each having a different score. Both types of analysis are contemplated in the present invention. BCMP derivatives preferably possess at least a degree of the antigenicity and/or immunogenicity of the protein or polypeptide from which they are derived. Thus, in a further aspect, the invention provides an antigen composition comprising one or more BCMP polypeptides of the invention and/or one or more antigenic fragments thereof. Such a composition can be used for the detection and/or diagnosis of breast cancer.

Accordingly, the present invention provides a method of detecting and/or diagnosing breast cancer which comprises:

(i) bringing into contact with a sample to be tested an antigenic BCMP polypeptide; and (ii) detecting the presence of antibodies to said polypeptide.

In particular, the protein, antigenic fragment thereof or antigen composition of the present invention can be used to detect IgA, IgM or IgG antibodies. Suitably, the sample to be tested will be a biological sample, for example but not limited to, a sample of blood, breast tissue, lymph node, bone or lung.

One or more antigenic BCMP polypeptides can be provided as a kit for use in the in vitro detection and/or diagnosis of breast cancer. Thus, in a still further aspect, the present invention provides a kit for use in the detection and/or diagnosis of breast cancer, which kit comprises an antigenic BCMP polypeptide. In addition, such a kit may optionally comprise one or more of the following:

(1 ) instructions for using the BCMP polypeptide for diagnosis, prognosis, therapeutic monitoring or any combination of these applications;

(2) a labelled binding partner to the captured antibody;

(3) a solid phase (such as a reagent strip) upon which the BCMP polypeptide is immobilised; and

As will be discussed below, BCMP polypeptides are of use in an immunotherapeutic approach to breast cancer. The skilled person will appreciate that for the preparation of one or more such polypeptides, the preferred approach will be based on recombinant DNA techniques. In addition, nucleic acid molecules encoding the polypeptides or fragments thereof may be used in their own right. Thus, the invention also provides a method of screening for and/or diagnosis of breast cancer in a subject, and/or monitoring the effectiveness of breast cancer therapy which comprises the step of detecting and/or quantifying the amount of a nucleic acid molecule in a biological sample obtained from said subject, wherein the nucleic acid molecule: d) comprises a DNA sequence which codes for a BCMP polypeptide as defined in a), or its RNA equivalent; e) has a sequence which is complementary to the sequences of d); f) has a sequence which codes for a polypeptide as defined in b) to c) above; g) has a sequence which shows substantial identity with any of those of d), e) and f); or h) is a fragment of d), e), f) or g), which is at least ten nucleotides in length.

Unless the context indicates otherwise, BCMP nucleic acids include those nucleic acid molecules defined in d) to h) above and may have one or more of the following characteristics:

1 ) they may be DNA or RNA;

2) they may be single or double stranded;

3) they may be in substantially pure form. Thus, they may be provided in a form which is substantially free from contaminating proteins and/or from other nucleic acids; and

4) they may be with introns or without introns (e.g. as cDNA).

Fragments of BCMP nucleic acids as described in h) above are preferably at least 20, at least 30, at least 50, at least 100 or at least 250 nucleotides in length. The nucleic acid molecule may be in isolated, recombinant or chemically synthetic form.

The invention also provides the use of nucleic acids which are complementary to the BCMP nucleic acids described in d)-h) above, and can hybridise to said BCMP nucleic acids. Such nucleic acid molecules are referred to as "hybridising" nucleic acid molecules. For example, but without limitation, hybridising nucleic acid molecules can be useful as probes or primers. Hybridising nucleic acid molecules may have a high degree of sequence identity along its length with a nucleic acid molecule within the scope of d)-h) above (e.g. at least 50%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 98% sequence identity). The use of hybridising nucleic acid molecules that can hybridise to any of the BCMP nucleic acid molecules discussed above, e.g. in hybridising assays, is also covered by the present invention. As will be appreciated by the skilled person, the higher the sequence identity a given single stranded nucleic acid molecule has with another nucleic acid molecule, the greater the likelihood that it will hybridise to a nucleic acid molecule which is complementary to that other nucleic acid molecule under appropriate conditions.

Hybridisation assays can be used for detection, prognosis, diagnosis, or monitoring of conditions, disorders, or disease states, associated with aberrant expression of genes encoding a BCMP polypeptide, or for differential diagnosis of patients with signs or symptoms suggestive of breast cancer. In particular, such a hybridisation assay can be carried out by a method comprising contacting a patient sample containing nucleic acid with a nucleic acid probe capable of hybridising to a BCMP DNA or RNA that encodes a BCMP polypeptide as defined herein, under conditions such that hybridisation can occur, and detecting or measuring any resulting hybridisation. Accordingly, such a hybridisation assay comprises: i) contacting a biological sample, obtained from a subject, containing nucleic acid with a nucleic acid probe capable of hybridising to a BCMP nucleic acid molecule, under conditions such that hybridisation can occur; and ii) detecting or measuring any resulting hybridisation.

In one embodiment, a change in the abundance of mRNA encoding one or more BCMP polypeptides in a test sample relative to a control sample or a previously determined reference range indicates the presence of breast cancer. Any suitable hybridization assay can be used to detect BCMP expression by detecting and/or visualizing mRNA encoding the BCMP polypeptide (e.g. Northern assays, dot blots, in situ hybridization, etc.).

Desirably such hybridising molecules are at least 10 nucleotides in length and preferably are at least 25 or at least 50 nucleotides in length. The hybridising nucleic acid molecules preferably hybridise to nucleic acids within the scope of d), e), f), g) or h) above, specifically.

Desirably the hybridising molecules will hybridise to such molecules under stringent hybridisation conditions. One example of stringent hybridisation conditions is where attempted hybridisation is carried out at a temperature of from about 35°C to about 65°C using a salt solution which is about 0.9M. However, the skilled person will be able to vary such conditions as appropriate in order to take into account variables such as probe length, base composition, type of ions present, etc. For a high degree of selectivity, relatively stringent conditions are used to form the duplexes, such as low salt or high temperature conditions. As used herein, "highly stringent conditions" means hybridisation to filter-bound DNA in 0.5 M NaHPO₄, 7% sodium dodecyl sulphate (SDS), 1 mM EDTA at 65°C, and washing in 0.1xSSC/0.1% SDS at 68°C (Ausubel F.M. et al., eds., 1989, Current Protocols in Molecular Biology, Vol. I, Green Publishing Associates, Inc., and John Wiley & Sons, Inc., New York, at p. 2.10.3). For some applications, less stringent conditions for duplex formation are required. As used herein "moderately stringent conditions" means washing in 0.2xSSC/0.1 % SDS at 42°C (Ausubel ef al., 1989, supra). Hybridisation conditions can also be rendered more stringent by the addition of increasing amounts of formamide, to destabilise the hybrid duplex. Thus, particular hybridisation conditions can be readily manipulated, and will generally be chosen depending on the desired results. In general, convenient hybridisation temperatures in the presence of 50% formamide are: 42°C for a probe which is 95 to 100% identical to the fragment of a gene encoding a polypeptide as defined herein, 37°C for 90 to 95% identity and 32°C for 70 to 90% identity.

The invention also provides a kit comprising a nucleic acid probe capable of hybridizing to RNA encoding a BCMP. In a specific embodiment, a kit comprises in one or more containers a pair of primers (e.g. each in the size range of 6-30 nucleotides, more preferably 10-30 nucleotides and still more preferably 10-20 nucleotides) that under appropriate reaction conditions can prime amplification of at least a portion of a nucleic acid encoding a BCMP, such as by polymerase chain reaction (see, e.g. Innis et al., 1990, PCR Protocols, Academic Press, Inc., San Diego, CA), ligase chain reaction (see EP 320308) use of Qβ replicase, cyclic probe reaction, or other methods known in the art).

Kits are also provided which allow for the detection of a plurality of BCMPs or a plurality of nucleic acids each encoding a BCMP. A kit can, optionally, further comprise a predetermined amount of an isolated BCMP protein or a BCMP nucleic acid, e.g. for use as a standard or control. Cell types that express or overexpress RNA encoding a BCMP polypeptide can be identified by various methods known in the art. Such cell types include but are not limited to leukocytes (e.g. neutrophils, macrophages, monocytes) and resident cells (e.g. astrocytes, glial cells, neuronal cells, and ependymal cells). Such methods include, but are not limited to, hybridization with a specific nucleic acid (e.g. by Northern hybridization, dot blot hybridization, in situ hybridization), observing the ability of RNA from the cell type to be translated in vitro into a BCMP polypeptide, immunoassay, etc. In a preferred aspect, primary tissue from a subject can be assayed for BCMP polypeptide or nucleic acid expression prior to treatment, e.g. by immunocytochemistry or in situ hybridization.

If desired, a gene encoding a BCMP polypeptide, a related gene, or related nucleic acid sequences or subsequences, including complementary sequences, can also be used in hybridization assays. A nucleotide encoding a BCMP polypeptide, or subsequences thereof comprising at least 8 nucleotides, preferably at least 12 nucleotides, and most preferably at least 15 nucleotides can be used as a hybridization probe. Hybridization assays can be used for detection, prognosis, diagnosis, or monitoring of conditions, disorders, or disease states, associated with aberrant expression of genes encoding BCMP polypeptides, or for differential diagnosis of subjects with signs or symptoms suggestive of breast cancer. In particular, such a hybridization assay can be carried out by a method comprising contacting a subject's sample containing nucleic acid with a nucleic acid probe capable of hybridizing to a DNA or RNA that encodes a BCMP polypeptide, under conditions such that hybridization can occur, and detecting or measuring any resulting hybridization.

In another aspect, the present invention provides a method for the prophylaxis and/or treatment of breast cancer in a subject, which comprises administering to said subject a therapeutically effective amount of at least one BCMP polypeptide.

Recombinant BCMP polypeptides may be prepared by processes well known in the art from genetically engineered host cells comprising expression systems. Accordingly, the present invention also relates to expression systems which comprise a BCMP polypeptide or BCMP nucleic acid, to host cells which are genetically engineered with such expression systems and to the production of BCMP polypeptides by recombinant techniques. Cell-free translation systems systems can also be employed to produce recombinant polypeptides (e.g. rabbit reticulocyte lysate, wheat germ lysate, SP6/T7 in vitro T&T and RTS 100 E. Coli HY transcription and translation kits from Roche Diagnostics Ltd., Lewes, UK and the TNT Quick coupled Transcription/Translation System from Promega UK, Southampton, UK.

For recombinant BCMP polypeptide production, host cells can be genetically engineered to incorporate expression systems or portions thereof for BCMP nucleic acids. Such incorporation can be performed using methods well known in the art, such as, calcium phosphate transfection, DEAD-dextran mediated transfection, transvection, microinjection, cationic lipid-mediated transfection, electroporation, transduction, scrape loading, ballistic introduction or infection (see e.g. Davis et al., Basic Methods in Molecular Biology, 1986 and Sambrook etal., Molecular Cloning: A Laboratory Manual, 2^nd Ed., Cold Spring Harbour laboratory Press, Cold Spring Harbour, NY, 1989).

Representative examples of host cells include bacterial cells e.g. E. Coli, Streptococci, Staphylococci, Streptomyces and Bacillus subtilis cells; fungal cells, such as yeast cells and Aspergillus cells; insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, HeLa, C127, 3T3, HEK 293, BHK and Bowes melanoma cells; and plant cells.

A wide variety of expression systems can be used, such as and without limitation, chromosomal, episomal and virus-derived systems, e.g. vectors derived from bacterial plasmids, from bacteriophage, from transposons, from yeast episomes, from insertion elements, from yeast chromosomal elements, from viruses such as baculoviruses, papova viruses such as SV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabies viruses and retroviruses, and vectors derived from combinations thereof, such as those derived from plasmid and bacteriophage genetic elements, such as cosmids and phagemids. The expression systems may contain control regions that regulate as well as engender expression. Generally, any system or vector which is able to maintain, propagate or express a nucleic acid to produce a polypeptide in a host may be used. The appropriate BCMP nucleic acid sequence may be inserted into an expression system by any variety of well- known and routine techniques, such as those set forth in Sambrook et al., supra. Appropriate secretion signals may be incorporated into the BCMP polypeptide to allow secretion of the translated protein into the lumen of the endoplasmic reticulum, the periplasmic space or the extracellular environment. These signals may be endogenous to the BCMP polypeptide or they may be heterologous signals.

In one embodiment, BCMP polypeptides are provided in isolated form and include BCMP polypeptides that have been purified to at least some extent and may be fused to other moieties. BCMP polypeptides can be produced using recombinant methods, synthetically produced or produced by a combination of these methods. In particular, fusions of the BCMP polypeptides with localisation-reporter proteins such as the Green Fluorescent Protein (US 5,625,048, 5,777,079, 6,054,321 and 5,804,387) or the DsRed fluorescent protein (Matz, et al., 1999, Nature Biotech. 17:969-973) are specifically contemplated. BCMP polypeptides may be provided in substantially pure form, that is to say free, to a substantial extent, from other proteins. Thus, a BCMP polypeptide may be provided in a composition in which it is the predominant component present (i.e. it is present at a level of at least 50%; preferably at least 75%, at least 80%, at least 85%, at least 90%, or at least 95%; when determined on a weight weight basis excluding solvents or carriers).

If a BCMP polypeptide is to be expressed for use in cell-based screening assays, it is preferred that the polypeptide be produced at the cell surface. In this event, the cells may be harvested prior to use in the screening assay. If the BCMP polypeptide is secreted into the medium, the medium can be recovered in order to isolate said polypeptide. If produced intracellularly, the cells must first be lysed before the BCMP polypeptide is recovered.

BCMP polypeptides can be recovered and purified from recombinant cell cultures by well-known methods including, ammonium sulphate or ethanol precipitation, acid extraction, anion or cation exchange chromatography, phosphocellulose chromatography, affinity chromatography, hydrophobic interaction chromatography, hydroxylapatite chromatography, molecular sieving chromatography, centrifugation methods, electrophoresis methods and lectin chromatography. In one embodiment, a combination of these methods is used. In another embodiment, high performance liquid chromatography is used. In a further embodiment, an antibody which specifically binds to a BCMP polypeptide can be used to deplete a sample comprising a BCMP polypeptide of said polypeptide or to purify said polypeptide. Techniques well-known in the art may be used for refolding to regenerate native or active conformations of the BCMP polypeptides when the polypeptides have been denatured during isolation and or purification.

In another alternative embodiment, native BCMPs can be purified from natural sources, by standard methods such as those described above (e.g. immunoaffinity purification). Alternatively, a BCMP polypeptide may be chemically synthesized.

In a further aspect, the present invention provides a method for the prophylaxis and/or treatment of breast cancer in a subject, which comprises administering to said subject a therapeutically effective amount of at least one BCMP nucleic acid. In one embodiment, the present invention provides the use of at least one BCMP nucleic acid in the preparation of a pharmaceutical composition for use in the treatment of breast cancer. Preferably, the BCMP nucleic acid is administered via gene therapy (see for example Hoshida, T. et al., 2002, Pancreas, 25:111-121 ; Ikuno, Y. 2002, Invest. Ophthalmol. Vis. Sci. 2002 43:2406-2411 ; Bollard, O, 2002, Blood 99:3179-3187; Lee E., 2001 , Mol. Med. 7:773-782).

Gene therapy refers to administration to a subject of an expressed or expressible nucleic acid. In this embodiment, the nucleic acid produces its encoded BCMP polypeptide that mediates a therapeutic effect by promoting BCMP polypeptide function. Any of the methods for gene therapy available in the art can be used according to the present invention. Exemplary methods are described below.

For general reviews of the methods of gene therapy, see Goldspiel ef al., 1993, Clinical Pharmacy 12:488-505; Wu and Wu, 1991 , Biotherapy 3:87-95; Tolstoshev, 1993, Ann. Rev. Pharmacol. Toxicol. 32:573-596; Mulligan, 1993, Science 260:926-932; and Morgan and Anderson, 1993, Ann. Rev. Biochem. 62:191 -217; May, 1993, TIBTECH 11 (5):155-215. Methods commonly known in the art of recombinant DNA technology which can be used are described in Ausubel et al., 1993, Current Protocols in Molecular Biology, John Wiley & Sons, eds., NY; and Kriegler, 1990, Gene Transfer and Expression, A Laboratory Manual, Stockton Press, NY.

In a preferred aspect, the pharmaceutical composition comprises a BCMP nucleic acid, said nucleic acid being part of an expression vector that expresses a BCMP polypeptide in a suitable host. In particular, such a nucleic acid has a promoter operably linked to the coding region, said promoter being inducible or constitutive (and, optionally, tissue-specific). In another particular embodiment, a nucleic acid molecule is used in which the coding sequences and any other desired sequences are flanked by regions that promote homologous recombination at a desired site in the genome, thus providing for intrachromosomal expression of the BCMP nucleic acid (Koller and Smithies, 1989, Proc. Natl. Acad. Sci. USA 86:8932-8935; Zijlstra et al., 1989, Nature 342:435-438).

Delivery of the nucleic acid into a subject may be direct, in which case the subject is directly exposed to the nucleic acid or nucleic acid-carrying vector; this approach is known as in vivo gene therapy. Alternatively, delivery of the nucleic acid into the subject may be indirect, in which case cells are first transformed with the nucleic acid in vitro and then transplanted into the subject; this approach is known as ex vivo gene therapy.

In a specific embodiment, the nucleic acid is directly administered in vivo, where it is expressed to produce the encoded product. This can be accomplished by any of numerous methods known in the art, e.g. by constructing it as part of an appropriate nucleic acid expression vector and administering it so that it becomes intracellular, e.g. by infection using a defective or attenuated retroviral or other viral vector (see US 4,980,286); by direct injection of naked DNA; by use of microparticle bombardment (e.g. a gene gun; Biolistic, Dupont); by coating with lipids, cell-surface receptors or transfecting agents; by encapsulation in liposomes, microparticles or microcapsules; by administering it in linkage to a peptide which is known to enter the nucleus; or by administering it in linkage to a ligand subject to receptor- mediated endocytosis (see, e.g. Wu & Wu, 1987, J. Biol. Chem. 262:4429-4432), which can be used to target cell types specifically expressing the receptors. In another embodiment, a nucleic acid-ligand complex can be formed in which the ligand comprises a fusogenic viral peptide to disrupt endosomes, allowing the nucleic acid to avoid lysosomal degradation. In yet another embodiment, the nucleic acid can be targeted in vivo for cell specific uptake and expression, by targeting a specific receptor (see, e.g. WO 92/06180, WO 92/22635; WO92/20316, WO93/14188 and WO 93/20221). Alternatively, the nucleic acid can be introduced intracellularly and incorporated within host cell DNA for expression, by homologous recombination (Koller & Smithies, 1989, Proc. Natl. Acad. Sci. USA 86:8932- 8935; Zijlstra et al., 1989, Nature 342:435-438).

In a specific embodiment, a viral vector that contains a nucleic acid encoding a BCMP polypeptide is used. For example, a retroviral vector can be used (see Miller et al., 1993, Meth. Enzymol. 217:581-599). In general, retroviral vectors have been modified to delete retroviral sequences that are not necessary for packaging of the viral genome and integration into host cell DNA. The nucleic acid encoding the BCMP polypeptide to be used in gene therapy is cloned into the vector, which facilitates delivery of the gene into a subject. More detail about retroviral vectors can be found in Boesen et al. (1994, Biotherapy 6:291 -302) which describes the use of a retroviral vector to deliver the mdrl gene to hematopoietic stem cells in order to make the stem cells more resistant to chemotherapy. Other references illustrating the use of retroviral vectors in gene therapy are: Clowes et al., 1994, J. Clin. Invest. 93:644-651 ; Kie et al., 1994, Blood 83:1467-1473; Salmons and Gunzberg, 1993, Human Gene Therapy 4:129-141 ; and Grossman & Wilson, 1993, Curr. Opin. Genetics and Devel. 3:110-114.

Adenoviruses are other viral vectors that can be used in gene therapy. Adenoviruses are especially attractive vehicles for delivering genes to respiratory epithelia. Adenoviruses naturally infect respiratory epithelia where they cause a mild disease. Other targets for adenovirus-based delivery systems are liver, the central nervous system, endothelial cells, and muscle. Adenoviruses have the advantage of being capable of infecting non-dividing cells. Kozarsky and Wilson, 1993, Current Opinion in Genetics and Development 3:499-503 present a review of adenovirus-based gene therapy. Bout et al., 1994, Human Gene Therapy 5:3-10 demonstrated the use of adenovirus vectors to transfer genes to the respiratory epithelia of rhesus monkeys. Other instances of the use of adenoviruses in gene therapy can be found in Rosenfeld etal., 1991 , Science 252:431 -434; Rosenfeld et al., 1992, Cell 68:143-155; Mastrangeli et al., 1993, J. Clin. Invest. 91 :225-234; WO 94/12649; and Wang, et al., 1995, Gene Therapy 2:775-783.

Adeno-associated virus (AAV) has also been proposed for use in gene therapy (Walsh et al., 1993, Proc. Soc. Exp. Biol. Med. 204:289-300; US 5,436,146).

Another approach to gene therapy involves transferring a gene to cells in tissue culture by such methods as electroporation, lipofection, calcium phosphate mediated transfection, or viral infection. Usually, the method of transfer includes the transfer of a selectable marker to the cells. The cells are then placed under selection to isolate those cells that have taken up and are expressing the transferred gene. Those cells are then delivered to a subject.

In this embodiment, the nucleic acid is introduced into a cell prior to administration in vivo, of the resulting recombinant cell. Such introduction can be carried out by any method known in the art, including but not limited to transfection, electroporation, microinjection, infection with a viral or bacteriophage vector containing the nucleic acid sequences, cell fusion, chromosome-mediated gene transfer, microcell-mediated gene transfer, spheroplast fusion, etc. Numerous techniques are known in the art for the introduction of foreign genes into cells (see, e.g. Loeffler and Behr, 1993, Meth. Enzymol. 217:599-618; Cohen et al., 1993, Meth. Enzymol. 217:618-644; Cline, 1985, Pharmac. Ther. 29:69-92) and may be used in accordance with the present invention, provided that the necessary developmental and physiological functions of the recipient cells are not disrupted. The technique should provide for the stable transfer of the nucleic acid to the cell, so that the nucleic acid is expressible by the cell and preferably heritable and expressible by its cell progeny.

The resulting recombinant cells can be delivered to a subject by various methods known in the art. In a preferred embodiment, epithelial cells are injected, e.g. subcutaneously. In another embodiment, recombinant skin cells may be applied as a skin graft onto the subject. Recombinant blood cells (e.g. hematopoietic stem or progenitor cells) are preferably administered intravenously. The amount of cells envisioned for use depends on the desired effect, the condition of the subject, etc., and can be determined by one skilled in the art.

Cells into which a nucleic acid can be introduced for purposes of gene therapy encompass any desired, available cell type, and include but are not limited to neuronal cells, glial cells (e.g. oligodendrocytes or astrocytes), epithelial cells, endothelial cells, keratinocytes, fibroblasts, muscle cells, hepatocytes; blood cells such as T lymphocytes, B- lymphocytes, monocytes, macrophages, neutrophils, eosinophils, megakaryocytes, granulocytes; various stem or progenitor cells, in particular hematopoietic stem or progenitor cells, e.g. as obtained from bone marrow, umbilical cord blood, peripheral blood or fetal liver.

In a preferred embodiment, the cell used for gene therapy is autologous to the subject that is treated. In an embodiment in which recombinant cells are used in gene therapy, a nucleic acid encoding a BCMP polypeptide is introduced into the cells such that it is expressible by the cells or their progeny, and the recombinant cells are then administered in vivo for therapeutic effect. In a specific embodiment, stem or progenitor cells are used. Any stem or progenitor cells which can be isolated and maintained in vitro can be used in accordance with this embodiment of the present invention (see e.g. WO 94/08598; Stemple and Anderson, 1992, Cell 71 :973-985; Rheinwald, 1980, Meth. Cell Bio. 21A:229; and Pittelkow and Scott, 1986, Mayo Clinic Proc. 61 :771).

In a specific embodiment, the BCMP nucleic acid to be introduced for purposes of gene therapy comprises an inducible promoter operably linked to the coding region, such that expression of the nucleic acid is controllable by controlling the presence or absence of the appropriate inducer of transcription.

Direct injection of a DNA coding for a BCMP polypeptide may also be performed according to, for example, the techniques described in US 5,589,466. These techniques involve the injection of "naked DNA", i.e. isolated DNA molecules in the absence of liposomes, cells, or any other material besides a suitable carrier. The injection of DNA encoding a protein and operably linked to a suitable promoter results in the production of the protein in cells near the site of injection and the elicitation of an immune response in the subject to the protein encoded by the injected DNA. In a preferred embodiment, naked DNA comprising (a) DNA encoding a BCMP polypeptide and (b) a promoter are injected into a subject to elicit an immune response to the BCMP polypeptide.

In a specific embodiment, hybridising nucleic acid molecules are used as anti-sense molecules, to alter the expression of BCMP polypeptides by binding to complementary BCMP nucleic acids and can be used in the treatment or prevention of breast cancer. An anti-sense nucleic acid includes a BCMP nucleic acid capable of hybridising by virtue of some sequence complementarity to a portion of an RNA (preferably mRNA) encoding a BCMP polypeptide. The anti-sense nucleic acid can be complementary to a coding and/or non-coding region of an mRNA encoding such a polypeptide. Most preferably, expression of a BCMP polypeptide is inhibited by use of anti-sense nucleic acids. Thus, the present invention provides the therapeutic or prophylactic use of nucleic acids comprising at least eight nucleotides that are anti-sense to a gene or cDNA encoding a BCMP polypeptide.

In a specific embodiment, BCMP expression is inhibited by use of BCMP anti-sense nucleic acids. The present invention provides the therapeutic or prophylactic use of nucleic acids comprising at least six nucleotides that are anti-sense to a gene or cDNA encoding a BCMP or a portion thereof. As used herein, a BCMP "anti-sense" nucleic acid refers to a nucleic acid capable of hybridizing by virtue of some sequence complementarity to a portion of an RNA (preferably mRNA) encoding a BCMP. The anti-sense nucleic acid may be complementary to a coding and/or noncoding region of an mRNA encoding a BCMP polypeptide. Such anti-sense nucleic acids have utility as compounds that inhibit BCMP polypeptide expression, and can be used in the treatment or prevention of breast cancer.

The anti-sense nucleic acids of the invention are double-stranded or single-stranded oligonucleotides, RNA or DNA or a modification or derivative thereof, and can be directly administered to a cell or produced intracellularly by transcription of exogenous, introduced sequences.

The anti-sense nucleic acids are of at least six nucleotides and are preferably oligonucleotides ranging from 6 to about 500 oligonucleotides. In specific aspects, the oligonucleotide is preferably 6-50 nucleotides. The oligonucleotides can be DNA or RNA or chimeric mixtures or derivatives or modified versions thereof and can be single-stranded or double-stranded. The oligonucleotide can be modified at the base moiety, sugar moiety, or phosphate backbone. The oligonucleotide may include other appended groups such as peptides; agents that facilitate transport across the cell membrane (see, e.g. Letsinger et al., 1989, Proc. Natl. Acad. Sci. USA 86:6553-6556; Lemaitre et al., 1987, Proc. Natl. Acad. Sci. 84:648-652; WO 88/09810) or blood-brain barrier (see, e.g. WO 89/10134); 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).

In a preferred aspect of the invention, an anti-sense oligonucleotide is provided, preferably of single-stranded DNA. The oligonucleotide may be modified at any position on its structure with substituents generally known in the art.

The anti-sense oligonucleotide may comprise at least one of the following modified base moieties: 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine, 5-(carboxyhydroxyl methyl) 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, wybutoxosine, pseudouracil, queosine, 2- thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid, 3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, 2,6-diaminopurine, and other base analogs.

In another embodiment, the oligonucleotide comprises at least one modified sugar moiety, e.g. one of the following sugar moieties: arabinose, 2-fluoroarabinose, xylulose, and hexose.

In yet another embodiment, the oligonucleotide comprises at least one of the following modified phosphate backbones: a phosphorothioate, a phosphorodithioate, a phosphoramidothioate, a phosphoramidate, a phosphordiamidate, a methylphosphonate, an alkyl phosphotriester, a formacetal, or an analog of formacetal.

In yet another embodiment, the oligonucleotide is an alpha-anomeric oligonucleotide. An alpha-anomeric oligonucleotide forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual beta-units, the strands run parallel to each other (Gautier et al., 1987, Nucl. Acids Res. 15:6625-6641).

The oligonucleotide may be conjugated to another molecule, e.g. a peptide, hybridization triggered cross-linking agent, transport agent, or hybridization-triggered cleavage agent. Oligonucleotides of the invention may be synthesized by standard methods known in the art, e.g. by use of an automated DNA synthesizer (such as are commercially available from Biosearch, Applied Biosystems, etc). As examples, phosphorothioate oligonucleotides may be synthesized by the method of Stein et al. (1988, Nucl. Acids Res. 16:3209), and methylphosphonate oligonucleotides can be prepared by use of controlled pore glass polymer supports (Sarin et al., 1988, Proc. Natl. Acad. Sci. USA, 85:7448-7451 ).

In a specific embodiment, the BCMP anti-sense nucleic acid of the invention is produced intracellularly by transcription from an exogenous sequence. For example, a vector can be introduced in vivo, such that it is taken up by a cell; within the cell the vector or a portion thereof is transcribed, producing an anti-sense nucleic acid (RNA) of the invention. Such a vector would contain a sequence encoding the BCMP anti-sense nucleic acid. Such a vector can remain episomal or become chromosomally integrated, as long as it can be transcribed to produce the desired anti-sense RNA. Such vectors can be constructed by recombinant DNA technology standard in the art. Vectors can be plasmid, viral, or others known in the art, used for replication and expression in mammalian cells. Expression of the sequence encoding the BCMP anti-sense RNA can be by any promoter known in the art to act in mammalian, preferably human, cells. Such promoters can be inducible or constitutive. Examples of such promoters are outlined above.

The anti-sense nucleic acids of the invention comprise a sequence complementary to at least a portion of an RNA transcript of a gene encoding a BCMP, preferably a human gene encoding a BCMP. However, absolute complementarity, although preferred, is not required. A sequence "complementary to at least a portion of an RNA," as referred to herein, means a sequence having sufficient complementarity to be able to hybridize, under stringent conditions or moderately stringent conditions as described above, with the RNA thus forming a stable duplex; in the case of double-stranded BCMP anti-sense nucleic acids, a single strand of the duplex DNA may thus be tested, or triplex formation may be assayed. The ability to hybridize will depend on both the degree of complementarity and the length of the anti-sense nucleic acid. Generally, the longer the hybridizing nucleic acid, the more base mismatches with an RNA encoding a BCMP it may contain and still form a stable duplex (or triplex, as the case may be). One skilled in the art can ascertain a tolerable degree of mismatch by use of standard procedures to determine the melting point of the hybridized complex.

The BCMP anti-sense nucleic acids can be used to treat or prevent breast cancer when the target BCMP polypeptide is overexpressed in the breast tissue of subjects suspected of having or suffering from breast cancer. In a preferred embodiment, a single- stranded DNA anti-sense BCMP oligonucleotide is used.

In another embodiment, symptoms of breast cancer may be ameliorated by decreasing the level of a BCMP or BCMP activity by using gene sequences encoding the BCMP in conjunction with well-known gene "knock-out," ribozyme or triple helix methods to decrease gene expression of a BCMP. In this approach ribozyme or triple helix molecules are used to modulate the activity, expression or synthesis of the gene encoding the BCMP, and thus to ameliorate the symptoms of breast cancer. Such molecules may be designed to reduce or inhibit expression of a mutant or non-mutant target gene. Techniques for the production and use of such molecules are well known to those of skill in the art.

Ribozyme molecules designed to catalytically cleave gene mRNA transcripts encoding a BCMP can be used to prevent translation of target gene mRNA and, therefore, expression of the gene product (see, e.g. WO90/1 1364; Sarver et al., 1990, Science 247:1222-1225).

Ribozymes are enzymatic RNA molecules capable of catalyzing the specific cleavage of RNA (for a review, see Rossi, 1994, Current Biology 4:469-471 ). The mechanism of ribozyme action involves sequence specific hybridization of the ribozyme molecule to complementary target RNA, followed by an endonucleolytic cleavage event. The composition of ribozyme molecules must include one or more sequences complementary to the target gene mRNA, and must include the well known catalytic sequence responsible for mRNA cleavage (for this sequence, see, e.g. US 5,093,246).

While ribozymes that cleave mRNA at site specific recognition sequences can be used to destroy mRNAs encoding a BCMP, the use of hammerhead ribozymes is preferred. Hammerhead ribozymes cleave mRNAs at locations dictated by flanking regions that form complementary base pairs with the target mRNA. The sole requirement is that the target mRNA have the following sequence of two bases: 5'-UG-3'. The construction and production of hammerhead ribozymes is well known in the art and is described more fully in Myers, 1995, Molecular Biology and Biotechnology: A Comprehensive Desk Reference, VCH Publishers, New York (see especially Figure 4, page 833) and in Haseloff & Gerlach, 1988, Nature, 334, 585-591.

Preferably the ribozyme is engineered so that the cleavage recognition site is located near the 5' end of the mRNA encoding the BCMP, i.e. to increase efficiency and minimize the intracellular accumulation of non-functional mRNA transcripts.

The ribozymes of the present invention also include RNA endoribonucleases (hereinafter "Cech-type ribozymes") such as the one that occurs naturally in Tetrahymena thermophila (known as the IVS, or L-19 IVS RNA) and that has been extensively described by Thomas Cech and collaborators (Zaug, et al., 1984, Science, 224, 574-578; Zaug and Cech, 1986, Science, 231 , 470-475; Zaug, et al., 1986, Nature, 324, 429-433; WO 88/04300; Been and Cech, 1986, Cell, 47, 207-216). The Cech-type ribozymes have an eight base pair active site which hybridizes to a target RNA sequence whereafter cleavage of the target RNA takes place. The invention encompasses those Cech-type ribozymes which target eight base-pair active site sequences that are present in the gene encoding the BCMP.

As in the anti-sense approach, the ribozymes can be composed of modified oligonucleotides (e.g. for improved stability, targeting, etc.) and should be delivered to cells that express the BCMP in vivo. A preferred method of delivery involves using a DNA construct "encoding" the ribozyme under the control of a strong constitutive pol III or pol II promoter, so that transfected cells will produce sufficient quantities of the ribozyme to destroy endogenous mRNA encoding the BCMP and inhibit translation. Because ribozymes, unlike anti-sense molecules, are catalytic, a lower intracellular concentration is required for efficacy. Endogenous BCMP expression can also be reduced by inactivating or "knocking out" the gene encoding the BCMP, or the promoter of such a gene, using targeted homologous recombination (e.g. see Smithies, et al., 1985, Nature 317:230-234; Thomas and Capecchi, 1987, Cell 51 :503-512; Thompson et al., 1989, Cell 5:313-321 ; and Zijlstra et al., 1989, Nature 342:435-438). For example, a mutant gene encoding a non-functional BCMP (or a completely unrelated DNA sequence) flanked by DNA homologous to the endogenous gene (either the coding regions or regulatory regions of the gene encoding the BCMP) can be used, with or without a selectable marker and/or a negative selectable marker, to transfect cells that express the target gene in vivo. Insertion of the DNA construct, via targeted homologous recombination, results in inactivation of the target gene. Such approaches are particularly suited in the agricultural field where modifications to ES (embryonic stem) cells can be used to generate animal offspring with an inactive target gene (e.g. see Thomas and Capecchi, 1987 and Thompson, 1989, supra). However this approach can be adapted for use in humans provided the recombinant DNA constructs are directly administered or targeted to the required site in vivo using appropriate viral vectors.

Alternatively, the endogenous expression of a gene encoding a BCMP can be reduced by targeting deoxyribonucleotide sequences complementary to the regulatory region of the gene (i.e. the gene promoter and/or enhancers) to form triple helical structures that prevent transcription of the gene encoding the BCMP in target cells in the body (see generally, Helene, 1991 , Anticancer Drug Des. 6:569-584; Helene, et al., 1992, Ann. NN. Acad. Sci., 660, 27-36; and Maher, 1992, Bioassays 14:807-815).

Nucleic acid molecules to be used in triplex helix formation for the inhibition of transcription should be single stranded and composed of deoxynucleotides. The base composition of these oligonucleotides must be designed to promote triple helix formation via Hoogsteen base pairing rules, which generally require sizeable stretches of either purines or pyrimidines to be present on one strand of a duplex. Nucleotide sequences may be pyrimidine-based, which will result in TAT and CGC triplets across the three associated strands of the resulting triple helix. The pyrimidine-rich molecules provide base complementarity to a purine-rich region of a single strand of the duplex in a parallel orientation to that strand. In addition, nucleic acid molecules that are purine-rich, for example containing a stretch of G residues, may be chosen. These molecules will form a triple helix with a DNA duplex that is rich in GC pairs, in which the majority of the purine residues are located on a single strand of the targeted duplex, resulting in GGC triplets across the three strands in the triplex.

Alternatively, the potential sequences that can be targeted for triple helix formation may be increased by creating a so called "switchback" nucleic acid molecule. Switchback molecules are synthesized in an alternating 5'-3', 3'-5' manner, such that they base pair with first one strand of a duplex and then the other, eliminating the necessity for a sizeable stretch of either purines or pyrimidines to be present on one strand of a duplex.

In instances wherein the anti-sense, ribozyme, or triple helix molecules described herein are utilized to inhibit mutant gene expression, it is possible that the technique may so efficiently reduce or inhibit the transcription (triple helix) or translation (anti-sense, ribozyme) of mRNA produced by normal gene alleles of a BCMP that the situation may arise wherein the concentration of BCMP present may be lower than is necessary for a normal phenotype. In such cases, to ensure that substantially normal levels of activity of a gene encoding a BCMP are maintained, gene therapy may be used to introduce into cells nucleic acid molecules that encode and express the BCMP that exhibit normal gene activity and that do not contain sequences susceptible to whatever anti-sense, ribozyme, or triple helix treatments are being utilized. Alternatively, in instances whereby the gene encodes an extracellular protein, normal BCMPs can be co-administered in order to maintain the requisite level of BCMP activity.

Anti-sense RNA and DNA, ribozyme, and triple helix molecules of the invention may be prepared by any method known in the art for the synthesis of DNA and RNA molecules, as discussed above. These include techniques for chemically synthesizing oligodeoxyribonucleotides and oligoribonucleotides well known in the art such as for example solid phase phosphoramidite chemical synthesis. Alternatively, RNA molecules may be generated by in vitro and in vivo transcription of DNA sequences encoding the anti-sense RNA molecule. Such DNA sequences may be incorporated into a wide variety of vectors that incorporate suitable RNA polymerase promoters such as the T7 or SP6 polymerase promoters. Alternatively, anti-sense cDNA constructs that synthesize anti-sense RNA constitutively or inducibly, depending on the promoter used, can be introduced stably into cell lines.

The nucleotide sequences of the present invention, including DNA and RNA, and comprising a sequence encoding a BCMP polypeptide may be synthesized using methods known in the art, such as using conventional chemical approaches or polymerase chain reaction (PCR) amplification. The nucleotide sequences of the present invention also permit the identification and cloning of the gene encoding a BCMP polypeptide for example, by screening cDNA libraries, genomic libraries or expression libraries. Specific embodiments for the cloning of a gene encoding a BCMP polypeptide are presented below by way of example and not of limitation.

For example, to clone a gene encoding a BCMP polypeptide by PCR techniques, anchored degenerate oligonucleotides (or a set of most likely oligonucleotides) can be designed for all BCMP peptide fragments identified as part of the same protein. PCR reactions under a variety of conditions can be performed with relevant cDNA and genomic DNAs (e.g. from breast tissue or from cells of the immune system) from one or more species. Also vectorette reactions can be performed on any available cDNA and genomic DNA using the oligonucleotides (which preferably are nested) as above. Vectorette PCR is a method that enables the amplification of specific DNA fragments in situations where the sequence of only one primer is known. Thus, it extends the application of PCR to stretches of DNA where the sequence information is only available at one end (Arnold C, 1991 , PCR Methods Appl. 1 :39-42; Dyer KD, Biotechniques, 1995, 19:550-552). Vectorette PCR may be performed with probes that are, for example, anchored degenerate oligonucleotides (or most likely oligonucleotides) coding for BCMP polypeptide fragments, using as a template a genomic library or cDNA library pools. Anchored degenerate oligonucleotides (and most likely oligonucleotides) can be designed for all BCMP polypeptide fragments. These oligonucleotides may be labeled and hybridized to filters containing cDNA and genomic DNA libraries. Oligonucleotides to different peptides from the same protein will often identify the same members of the library. The cDNA and genomic DNA libraries may be obtained from any suitable or desired mammalian species, for example from humans.

Nucleotide sequences comprising a nucleotide sequence encoding a BCMP polypeptide are useful for their ability to hybridize selectively with complementary stretches of genes encoding other proteins. Depending on the application, a variety of hybridization conditions may be employed to obtain nucleotide sequences at least 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% identical, or 100% identical, to the sequence of a nucleotide encoding a BCMP polypeptide.

For a high degree of selectivity, relatively stringent conditions are used to form the duplexes, such as low salt or high temperature conditions; such conditions are described above.

In the preparation of genomic libraries, DNA fragments are generated, some of which will encode parts or the whole of a BCMP polypeptide. Any suitable method for preparing DNA fragments may be used in the present invention. For example, the DNA may be cleaved at specific sites using various restriction enzymes. Alternatively, one may use DNAse in the presence of manganese to fragment the DNA, or the DNA can be physically sheared, as for example, by sonication. The DNA fragments can then be separated according to size by standard techniques, including but not limited to agarose and polyacrylamide gel electrophoresis, column chromatography and sucrose gradient centrifugation. The DNA fragments can then be inserted into suitable vectors, including but not limited to plasmids, cosmids, bacteriophages lambda or T₄, and yeast artificial chromosome (YAC; See, e.g. Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York; Glover, D.M. (ed.), 1985, DNA Cloning: A Practical Approach, MRL Press, Ltd., Oxford, U.K. Vol. I, II; Ausubel F.M. et al., eds., 1989, Current Protocols in Molecular Biology, Vol. I, Green Publishing Associates, Inc., and John Wiley & sons, Inc., New York). The genomic library may be screened by nucleic acid hybridization to labeled probe (Benton and Davis, 1977, Science 196:180; Grunstein and Hogness, 1975, Proc. Natl. Acad. Sci. USA. 72: 3961 ).

Based on the present description, the genomic libraries may be screened with labeled degenerate oligonucleotide probes corresponding to the amino acid sequence of any peptide of the BCMP using optimal approaches well known in the art. Any probe used is preferably at least 10 nucleotides, at least 15 nucleotides, at least 20 nucleotides, at least 25 nucleotides, at least 30 nucleotides, at least 40 nucleotides, at least 50 nucleotides, at least 60 nucleotides, at least 70 nucleotides, at least 80 nucleotides, or at least 100 nucleotides.

Some BCMP polypeptides disclosed herein were found to correspond to previously identified proteins encoded by genes whose sequences are publicly known (sequence analysis and protein identification of BCMP polypeptides was carried out using the methods described in Examples). To screen such a gene, any probe may be used that is complementary to the gene or its complement; preferably the probe is 10 nucleotides or longer, more preferably 15 nucleotides or longer. The SWISS-PROT and trEMBL databases (held by the Swiss Institute of Bioinformatics (SIB) and the European Bioinformatics Institute (EBI) which are available at http://www.expasy.ch/ and the GenBank database (held by the National Institute of Health (NIH) which is available at http://www.ncbi.nlm.nih.gov/) provide protein sequences for the BCMP polypeptides listed in Tables 1 and 2.

When a library is screened, clones with inserted DNA encoding a BCMP polypeptide will hybridize to one or more members of the corresponding set of degenerate oligonucleotide probes (or their complement). Hybridization of such oligonucleotide probes to genomic libraries is carried out using methods known in the art. For example, hybridization with one of the above-mentioned degenerate sets of oligonucleotide probes, or their complement (or with any member of such a set, or its complement) can be performed under highly stringent or moderately stringent conditions as defined above, or can be carried out in 2X SSC, 1.0% SDS at 50°C and washed using the washing conditions described supra for highly stringent or moderately stringent hybridization.

Clones containing nucleotide sequences encoding a BCMP polypeptide may also be obtained by screening expression libraries. For example, DNA from the relevant source is isolated and random fragments are prepared and ligated into an expression vector (e.g. a bacteriophage, plasmid, phagemid or cosmid) such that the inserted sequence in the vector is capable of being expressed by the host cell into which the vector is then introduced. Various screening assays can then be used to select for the expressed BCMP polypeptide. In one embodiment, the various anti-BCMP antibodies of the invention can be used to identify the desired clones using methods known in the art (see, for example, Harlow and Lane, 1988, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, Appendix IV). Colonies or plaques from the library are brought into contact with the antibodies to identify those clones that bind antibody.

In an embodiment, colonies or plaques containing DNA that encode a BCMP polypeptide can be detected using DYNA Beads according to Olsvick et al., 29th ICAAC, Houston, Tex. 1989. Anti-BCMP antibodies are crosslinked to tosylated DYNA Beads M280, and these antibody-containing beads are then contacted with colonies or plaques expressing recombinant polypeptides. Colonies or plaques expressing a BCMP polypeptide are identified as any of those that bind the beads.

Alternatively, the anti-BCMP antibodies can be nonspecifically immobilized to a suitable support, such as silica or Celite® resin. This material is then used to adsorb to bacterial colonies expressing the BCMP polypeptide.

In another aspect, PCR amplification may be used to isolate from genomic DNA a substantially pure DNA (i.e. a DNA substantially free of contaminating nucleic acids) encoding the BCMP polypeptide. Preferably such a DNA is at least 95% pure, more preferably at least 99% pure. Oligonucleotide sequences, degenerate or otherwise, that correspond to peptide sequences of BCMP polypeptides can be used as primers. PCR can be carried out, e.g. by use of a Perkin-Elmer Cetus thermal cycler and Taq polymerase (Gene Amp® or AmpliTaq DNA polymerase). One can choose to synthesize several different degenerate primers, for use in the PCR reactions. It is also possible to vary the stringency of hybridization conditions used in priming the PCR reactions, to allow for greater or lesser degrees of nucleotide sequence similarity between the degenerate primers and the corresponding sequences in the DNA. After successful amplification of a segment of the sequence encoding a BCMP polypeptide, that segment may be molecularly cloned and sequenced, and utilized as a probe to isolate a complete genomic clone. This, in turn, will permit the determination of the gene's complete nucleotide sequence, the analysis of its expression, and the production of its protein product for functional analysis, as described infra.

The gene encoding a BCMP polypeptide can also be identified by mRNA selection by nucleic acid hybridization followed by in vitro translation. In this procedure, fragments are used to isolate complementary mRNAs by hybridization. Such DNA fragments may represent available, purified DNA encoding a BCMP polypeptide of another species (e.g. mouse, human). Immunoprecipitation analysis or functional assays (e.g. aggregation ability in vitro; binding to receptor) of the in vitro translation products of the isolated products of the isolated mRNAs identifies the mRNA and, therefore, the complementary DNA fragments that contain the desired sequences. In addition, specific mRNAs may be selected by adsorption of polysomes isolated from cells to immobilized antibodies that specifically recognize a BCMP polypeptide. A radiolabeled cDNA encoding a BCMP polypeptide can be synthesized using the selected mRNA (from the adsorbed polysomes) as a template. The radiolabeled mRNA or cDNA may then be used as a probe to identify the DNA fragments encoding a BCMP polypeptide from among other genomic DNA fragments.

Alternatives to isolating genomic DNA encoding a BCMP polypeptide include, but are not limited to, chemically synthesizing the gene sequence itself from a known sequence or making cDNA to the mRNA which encodes the BCMP polypeptide. For example, RNA for cDNA cloning of the gene encoding a BCMP polypeptide can be isolated from cells which express the BCMP polypeptide. Those skilled in the art will understand from the present description that other methods may be used and are within the scope of the invention.

Any suitable eukaryotic cell can serve as the nucleic acid source for the molecular cloning of the gene encoding a BCMP polypeptide. The nucleic acid sequences encoding a BCMP polypeptide can be isolated from vertebrate, mammalian, primate, human, porcine, bovine, feline, avian, equine, canine or murine sources. The DNA may be obtained by standard procedures known in the art from cloned DNA (e.g. a DNA "library"), by chemical synthesis, by cDNA cloning, or by the cloning of genomic DNA, or fragments thereof, purified from the desired cell (see, e.g. Sambrook et al., 1989, Molecular Cloning, A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York; Glover, D.M., ed., 1985, DNA Cloning: A Practical Approach, MRL Press, Ltd., Oxford, U.K. Vol. I & II). Clones derived from genomic DNA may contain regulatory and intron DNA regions in addition to coding regions; clones derived from cDNA will contain only exon sequences. One skilled in the art will understand that, in many cases, an isolated cDNA sequence will be incomplete, in that the region coding for the polypeptide is cut short at the 5' end of the cDNA. This is a consequence of reverse transcriptase, an enzyme with inherently low processivity (a measure of the ability of the enzyme to remain attached to the template during the polymerization reaction), failing to complete a DNA copy of the mRNA template during 1^st strand cDNA synthesis.

Methods to obtain full length cDNAs or to extend short cDNAs are well known in the art, for example RACE (Rapid amplification of cDNA ends; e.g. Frohman et al., 1988, Proc. Natl. Acad. Sci USA 85:8998-9002). Recent modifications of the technique, exemplified by the Marathon™ technology (Clontech Laboratories Inc.) have significantly simplified the search for longer cDNAs. This technology uses cDNAs prepared from mRNA extracted from a chosen tissue followed by the ligation of an adaptor sequence onto each end. PCR is then carried out to amplify the missing 5'end of the cDNA using a combination of gene specific and adaptor specific oligonucleotide primers. The PCR reaction is then repeated using nested primers which have been designed to anneal with the amplified product, typically an adaptor specific primer that anneals further 3' in the adaptor sequence and a gene specific primer that anneals further 5' in the known gene sequence. The products of this reaction can then be analysed by DNA sequencing and a full length cDNA constructed either by joining the product directly to the existing cDNA to give a complete sequence, or carrying out a separate full length PCR using the new sequence information for the design of the 5' primer.

The identified and isolated gene or cDNA can then be inserted into any suitable cloning vector. A large number of vector-host systems known in the art may be used. As those skilled in the art will appreciate, the only limitation is that the vector system chosen be compatible with the host cell used. Such vectors include, but are not limited to, bacteriophages such as lambda derivatives, plasmids such as PBR322 or pUC plasmid derivatives or the Bluescript™ vector (Stratagene) or modified viruses such as adenoviruses, adeno-associated viruses or retroviruses. The insertion into a cloning vector can be accomplished, for example, by ligating the DNA fragment into a cloning vector which has complementary cohesive termini. However, if the complementary restriction sites used to fragment the DNA are not present in the cloning vector, the ends of the DNA molecules may be enzymatically modified. Alternatively, any site desired may be produced by ligating nucleotide sequences (linkers) onto the DNA termini; these ligated linkers may comprise specific chemically synthesized oligonucleotides encoding restriction endonuclease recognition sequences. In an alternative method, the cleaved vector and the gene encoding a BCMP polypeptide may be modified by homopolymeric tailing. Recombinant molecules can be introduced into host cells via transformation, transfection, infection, electroporation, etc., so that many copies of the gene sequence are generated.

In specific embodiments, transformation of host cells with recombinant DNA molecules that incorporate the isolated gene encoding the BCMP polypeptide, cDNA, or synthesized DNA sequence enables generation of multiple copies of the gene. Thus, the gene may be obtained in large quantities by growing transformants, isolating the recombinant DNA molecules from the transformants and, when necessary, retrieving the inserted gene from the isolated recombinant DNA.

In a specific embodiment, an isolated nucleic acid molecule that encodes a BCMP derivative can be created by introducing one or more nucleotide substitutions, additions or deletions into the BCMP nucleic acid sequence such that one or more amino acid substitutions, additions or deletions are introduced into the encoded protein. Standard techniques known to those of skill in the art can be used to introduce mutations, including, for example, site-directed mutagenesis and PCR-mediated mutagenesis. Alternatively, mutations can be introduced randomly along all or part of the coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened for biological activity to identify mutants that retain activity. Following mutagenesis, the encoded protein can be expressed and the activity of the protein can be determined.

The nucleotide sequence coding for a BCMP polypeptide can be inserted into an appropriate expression vector, i.e. a vector which contains the necessary elements for the transcription and translation of the inserted protein-coding sequence. The necessary signals for transcription and translation can also be supplied by the native gene encoding a BCMP polypeptide or its flanking regions, or the native gene encoding a BCMP polypeptide or its flanking regions. A variety of host-vector systems may be utilized in the present invention to express the protein-coding sequence. These include but are not limited to mammalian cell systems infected with virus (e.g. vaccinia virus, adenovirus, etc.); insect cell systems infected with virus (e.g. baculovirus); microorganisms such as yeast containing yeast vectors; or bacteria transformed with bacteriophage, DNA, plasmid DNA, or cosmid DNA. The expression elements of vectors vary in their strengths and specificities. Depending on the host-vector system utilized, any one of a number of suitable transcription and translation elements may be used. In specific embodiments, a nucleotide sequence encoding a human gene (or a nucleotide sequence encoding a functionally active portion of a human BCMP polypeptide) is expressed. In yet another embodiment, a fragment of a BCMP polypeptide comprising a domain of the BCMP is expressed.

Any of the methods previously described for the insertion of DNA fragments into a vector may be used to construct expression vectors containing a chimeric gene consisting of appropriate transcriptional and translational control signals and the protein coding sequences. These methods may include in vitro recombinant DNA and synthetic techniques and in vivo recombinants (genetic recombination). Expression of a BCMP nucleic acid sequence encoding a BCMP polypeptide may be regulated by a second nucleic acid sequence so that the BCMP polypeptide is expressed in a host transformed with the recombinant DNA molecule. For example, expression of a BCMP polypeptide may be controlled by any promoter or enhancer element known in the art. Promoters which may be used to control the expression of the gene encoding a BCMP polypeptide include, but are not limited to, the SV40 early promoter region (Bernoist and Chambon, 1981 , Nature 290:304- 310), the promoter contained in the 3'-long terminal repeat of Rous sarcoma virus (Yamamoto, et al., 1980, Cell 22:787-797), the herpes thymidine kinase promoter (Wagner et al., 1981 , Proc. Natl. Acad. Sci. USA. 78:1441-1445), the regulatory sequences of the metallothionein gene (Brinster et al., 1982, Nature 296:39-42), the tetracycline (Tet) promoter (Gossen et al., 1995, Proc. Nat. Acad. Sci. USA 89:5547-5551); prokaryotic expression vectors such as β-lactamase promoter (Villa-Kamaroff, et al., 1978, Proc. Natl. Acad. Sci. USA. 75:3727-3731 ), or the tac promoter (DeBoer, et al., 1983, Proc. Natl. Acad. Sci. USA. 80: 21 -25; see also "Useful proteins from recombinant bacteria" in Scientific American, 1980, 242 :74-94); plant expression vectors comprising the nopaline synthetase promoter region (Herrera-Estrella et al., Nature 303:209-213) or the cauliflower mosaic virus 35S RNA promoter (Gardner, et al., 1981 , Nucl. Acids Res. 9: 2871 ), and the promoter of the photosynthetic enzyme ribulose biphosphate carboxylase (Herrera-Estrella etal., 1984, Nature 310:115-120); promoter elements from yeast or other fungi such as the Gal 4 promoter, the ADC (alcohol dehydrogenase) promoter, PGK (phosphoglycerol kinase) promoter, alkaline phosphatase promoter, and the following animal transcriptional control regions, which exhibit tissue specificity and have been utilized in transgenic animals: elastase I gene control region which is active in pancreatic acinar cells (Swift et al., 1984, Cell 38:639- 646; Ornitz etal., 1986, Cold Spring Harbor Symp. Quant. Biol. 50:399-409; MacDonald, 1987, Hepatology 7:425-515); insulin gene control region which is active in pancreatic beta cells (Hanahan, 1985, Nature 315:115-122), immunoglobulin gene control region which is active in lymphoid cells (Grosschedl etal., 1984, Cell 38:647-658; Adames et al., 1985, Nature 318:533-538; Alexander et al., 1987, Mol. Cell. Biol. 7: 1436-1444), mouse mammary tumor virus control region which is active in testicular, breast, lymphoid and mast cells (Leder et al., 1986, Cell 45:485-495), albumin gene control region which is active in liver (Pinkert et al., 1987, Genes and Devel. 1 : 268-276), alpha-fetoprotein gene control region which is active in liver (Krumlauf et al., 1985, Mol. Cell. Biol. 5:1639-1648; Hammer et al., 1987, Science 235:53-58), alpha 1 -antitrypsin gene control region which is active in the liver (Kelsey et al., 1987, Genes and Devel. 1 :161 -171 ), beta-globin gene control region which is active in myeloid cells (Mogram et al., 1985, Nature 315:338-340; Kollias et al., 1986, Cell 46:89-94; myelin basic protein gene control region which is active in oligodendrocyte cells in the brain (Readhead et al., 1987, Cell 48:703-712); myosin light chain-2 gene control region which is active in skeletal muscle (Sani, 1985, Nature 314:283-286); neuronal-specific enolase (NSE) which is active in neuronal cells (Morelli et al., 1999, Gen. Virol. 80: 571 -83); brain-derived neurotrophic factor (BDNF) gene control region which is active in neuronal cells (Tabuchi et al., 1998, Biochem. Biophys. Res. Com. 253:818-823); glial fibrillary acidic protein (GFAP) promoter which is active in astrocytes (Gomes et al., 1999, Braz J Med Biol Res 32(5): 619-631 ; Morelli et al., 1999, Gen. Virol. 80:571 -83) and gonadotropic releasing hormone gene control region which is active in the hypothalamus (Mason et al., 1986, Science 234:1372-1378).

In a specific embodiment, a vector is used that comprises a promoter operably linked to a nucleic acid encoding a BCMP polypeptide, one or more origins of replication, and, optionally, one or more selectable markers (e.g. an antibiotic resistance gene).

In a specific embodiment, an expression construct is made by subcloning a BCMP nucleic acid encoding a BCMP polypeptide into the EcoRI restriction site of each of the three pGEX vectors (Glutathione S-Transferase expression vectors; Smith and Johnson, 1988, Gene 7:31 -40). This allows for the expression of the BCMP polypeptide from the subclone in the correct reading frame.

In mammalian host cells, a number of viral-based expression systems may be utilized. In cases where an adenovirus is used as an expression vector, the BCMP nucleic acid encoding sequence a BCMP polypeptide may be ligated to an adenovirus transcription/translation control complex, e.g. the late promoter and tripartite leader sequence. This chimeric gene may then be inserted in the adenovirus genome by in vitro or in vivo recombination. Insertion in a non-essential region of the viral genome (e.g. region E1 or E3) will result in a recombinant virus that is viable and capable of expressing the antibody molecule in infected hosts (see e.g. Logan & Shenk, 1984, Proc. Natl. Acad. Sci. USA 81 :355-359). Specific initiation signals may also be required for efficient translation of inserted antibody coding sequences. These signals include the ATG initiation codon and adjacent sequences. Furthermore, the initiation codon must be in phase with the reading frame of the desired coding sequence to ensure translation of the entire insert. These exogenous translational control signals and initiation codons can be of a variety of origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of appropriate transcription enhancer elements, transcription terminators, etc. (see Bittner et al., 1987, Methods in Enzymol. 153:51 -544).

Expression vectors containing inserts of a gene encoding a BCMP polypeptide can be identified by three general approaches: (a) nucleic acid hybridization, (b) presence or absence of "marker" gene functions, and (c) expression of inserted sequences. In the first approach, the presence of a gene encoding a BCMP polypeptide inserted in an expression vector can be detected by nucleic acid hybridization using probes comprising sequences that are homologous to an inserted gene encoding a BCMP polypeptide. In the second approach, the recombinant vector/host system can be identified and selected based upon the presence or absence of certain "marker" gene functions (e.g. thymidine kinase activity, resistance to antibiotics, transformation phenotype, occlusion body formation in baculovirus, etc.) caused by the insertion of a gene encoding a BCMP polypeptide in the vector. For example, if the gene encoding a BCMP polypeptide is inserted within the marker gene sequence of the vector, recombinants containing the gene encoding the BCMP insert can be identified by the absence of the marker gene function. In the third approach, recombinant expression vectors can be identified by assaying the gene product (i.e. the inserted BCMP sequence) expressed using the recombinant expression system. Such assays can be based, for example, on the physical or functional properties of the BCMP polypeptide in an in vitro assay system, e.g. binding with an anti-BCMP antibody.

In addition, a host cell strain may be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Expression from certain promoters can be elevated in the presence of certain inducers; thus, expression of the genetically engineered BCMP or BCMP derivative, fragment or fusion protein may be controlled. Furthermore, different host cells have characteristic and specific mechanisms for the translational and post-translational processing and modification (e.g. glycosylation, phosphorylation of proteins). Appropriate cell lines or host systems can be chosen to ensure the desired modification and processing of the foreign protein expressed. For example, expression in a bacterial system will produce an unglycosylated product and expression in yeast will produce a glycosylated product. Eukaryotic host cells that possess the cellular machinery for proper processing of the primary transcript, glycosylation, and phosphorylation of the gene product may be used. Such mammalian host cells include but are not limited to CHO, VERY, BHK, Hela, COS, MDCK, 293, 3T3, and WI38. Furthermore, different vector/host expression systems may effect processing reactions to different extents.

For long-term, high-yield production of recombinant proteins, stable expression is preferred. For example, cell lines which stably express the differentially expressed or pathway gene protein may be engineered. Rather than using expression vectors that contain viral origins of replication, host cells can be transformed with DNA controlled by appropriate expression control elements (e.g. promoter, enhancer, sequences, transcription terminators, polyadenylation sites, etc.), and a selectable marker. Following the introduction of the foreign DNA, engineered cells may be allowed to grow for 1-2 days in an enriched medium, and then are switched to a selective medium. The selectable marker in the recombinant plasmid confers resistance to the selection and allows cells to stably integrate the plasmid into their chromosomes and grow to form foci which in turn can be cloned and expanded into cell lines. This method may advantageously be used to engineer cell lines which express the differentially expressed or pathway gene protein. Such engineered cell lines may be particularly useful in screening and evaluation of compounds that affect the endogenous activity of the differentially expressed or pathway gene protein.

A number of selection systems may be used, including but not limited to the herpes simplex virus thymidine kinase (Wigler, et al., 1977, Cell 11 :223), hypoxanthine-guanine phosphonbosyltransferase (Szybalska & Szybalski, 1962, Proc. Natl. Acad. Sci. USA 48:2026), and adenine phosphonbosyltransferase (Lowy, et al., 1980, Cell 22:817) genes can be employed in tk-, hgprt- or aprt- cells, respectively. Also, antimetabolite resistance can be used as the basis of selection for dhfr, which confers resistance to methotrexate (Wigler, ef al., 1980, Proc. Natl. Acad. Sci. USA 77: 3567; O'Hare, et al., 1981 , Proc. Natl. Acad. Sci. USA 78:1527); gpt, which confers resistance to mycophenolic acid (Mulligan & Berg, 1981 , Proc. Natl. Acad. Sci. USA 78: 2072); neo, which confers resistance to the aminoglycoside G-418 (Colberre-Garapin, et al., 1981 , J. Mol. Biol. 150: 1) and hygro genes, which confer resistance to hygromycin (Santerre, et al., 1984, Gene 30:147).

Nucleic acids encoding a BCMP polypeptide can be fused to an epitope tag (e.g. the hemaglutinin ("HA") tag or flag tag) to aid in detection and purification of the expressed polypeptide. For example, a system described by Janknecht et al. allows for the ready purification of non-denatured fusion proteins expressed in human cell lines (Janknecht et al., 1991 , Proc. Natl. Acad. Sci. USA 88:8972-897). Fusion proteins can be made by ligating the appropriate nucleic acid sequences encoding the desired amino acid sequences to each other by methods known in the art, in the proper coding frame, and expressing the chimeric product by methods commonly known in the art.

A further aspect of the invention relates to a vaccine composition of use in the treatment of breast cancer. Thus, a BCMP polypeptide or BCMP nucleic acid may be useful as antigenic and /or immunogenic material, and may be used in the production of vaccines for treatment or prophylaxis of breast cancer. In this context, "antigenic" is taken to mean that the protein or nucleic acid is capable of being used to raise antibodies or indeed is capable of inducing an antibody response in a subject. "Immunogenic" is taken to mean that the protein or nucleic acid is capable of eliciting a protective immune response in a subject. Thus, the BCMP polypeptide or nucleic acid may be capable of not only generating an antibody response but, in addition, non-antibody based immune responses.

Thus, in a further aspect, the present invention provides the use of a BCMP polypeptide or a BCMP nucleic acid in the production of a pharmaceutical composition for the treatment or prophylaxis of breast cancer, wherein the composition is a vaccine. The vaccine optionally comprises one or more suitable adjuvants. Examples of adjuvants well- known in the art include inorganic gels, such as aluminium hydroxide, and water-in-oil emulsions, such as incomplete Freund's adjuvant. Other useful adjuvants will be well known to the skilled person.

Since a polypeptide or a nucleic acid may be broken down in the stomach, the vaccine composition is preferably administered parenterally (e.g. subcutaneous, intramuscular, intravenous or intradermal injection).

Accordingly, the present invention provides:

(a) the use of a BCMP polypeptide or BCMP nucleic acid in the preparation of an immunogenic composition, preferably a vaccine;

(b) the use of such an immunogenic composition in inducing an immune response in a subject; and

(c) a method for the treatment or prophylaxis of breast cancer in a subject, or of vaccinating a subject against breast cancer which comprises the step of administering to the subject an effective amount of a BCMP polypeptide, preferably as a vaccine.

According to the invention, a BCMP polypeptide may also be used as an immunogen to generate antibodies which immunospecifically bind such an immunogen. Such immunogens can be isolated by any convenient means, including the methods described above. Antibodies of the invention include, but are not limited to polyclonal, monoclonal, bispecific, humanized or chimeric antibodies, single chain antibodies, Fab fragments and F(ab') fragments, fragments produced by a Fab expression library, anti-diotypic (anti-Id) antibodies, and epitope-binding fragments of any of the above.

In one embodiment, antibodies that recognize gene products of genes encoding BCMP polypeptides are publicly available. In another embodiment, methods known to those skilled in the art are used to produce antibodies that recognize a BCMP polypeptide. In another embodiment, antibodies to a specific domain of a BCMP polypeptide are produced. In a specific embodiment, hydrophilic fragments of a BCMP polypeptide are used as immunogens for antibody production.

The term "antibody" as used herein refers to immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, i.e. molecules that contain an antigen binding site that specifically binds an antigen. The immunoglobulin molecules of the invention can be of any class (e.g. IgG, IgE, IgM, IgD and IgA) or subclass of immunoglobulin molecule capable of immunospecific binding to a BCMP polypeptide.

In the production of antibodies, screening for the desired antibody can be accomplished by techniques known in the art, e.g. EL1SA (enzyme-linked immunosorbent assay). For example, to select antibodies that recognize a specific domain of a BCMP polypeptide, one may assay generated hybridomas for a product which binds to a BCMP polypeptide comprising said domain. For selection of an antibody that specifically binds a first BCMP polypeptide but which does not specifically bind to (or binds less avidly to) a second BCMP polypeptide, one can select on the basis of positive binding to the first BCMP polypeptide and a lack of binding to (or reduced binding to) the second BCMP polypeptide; for example differential binding to different BCMP polypeptide homologues. Similarly, for selection of an antibody that specifically binds a BCMP polypeptide but which does not specifically bind to (or binds less avidly to) a different isoform of the same BCMP polypeptide (such as a different glycosylated form which has the same core peptide as the BCMP polypeptide), one can select on the basis of positive binding to the BCMP polypeptide and a lack of binding to (or reduced binding to) the different isoform (e.g. a different glycosylated form). Thus, the present invention provides an antibody (preferably a monoclonal antibody) that binds with greater affinity (preferably at least 2-fold, more preferably at least 5-fold still more preferably at least 10-fold greater affinity) to a BCMP polypeptide than to a different isoform or isoforms (e.g. glycosylated forms) of the BCMP.

Polyclonal antibodies which may be used in the methods of the invention are heterogeneous populations of antibody molecules derived from the sera of immunized animals. Unfractionated immune serum can also be used. Various procedures known in the art may be used for the production of polyclonal antibodies to a BCMP polypeptide. In a particular embodiment, rabbit polyclonal antibodies to an epitope of a BCMP polypeptide can be obtained. For example, for the production of polyclonal or monoclonal antibodies, various host animals can be immunized by injection with the native or a synthetic (e.g. recombinant) version of a BCMP polypeptide, including but not limited to rabbits, mice, rats, etc. The invention described herein provides isolated BCMP polypeptides suitable for such immunization. If a BCMP polypeptide is purified by gel electrophoresis, the BCMP polypeptide can be used for immunization with or without prior extraction from the polyacrylamide gel. Various adjuvants may be used to enhance the immunological response, depending on the host species, including, but not limited to, complete or incomplete Freund's adjuvant, a mineral gel such as aluminum hydroxide, surface active substance such as lysolecithin, pluronic polyol, a polyanion, a peptide, an oil emulsion, keyhole limpet hemocyanin, dinitrophenol, and an adjuvant such as BCG (bacille Calmette-Guerin) or corynebacterium parvum. Additional adjuvants are also well known in the art.

For preparation of monoclonal antibodies (mAbs) directed toward a BCMP polypeptide any technique which provides for the production of antibody molecules by continuous cell lines in culture may be used. For example, the hybridoma technique originally developed by Kohler and Milstein (1975, Nature 256:495-497), as well as the trioma technique, the human B-cell hybridoma technique (Kozbor et al., 1983, Immunology Today 4:72), and the EBV-hybridoma technique to produce human monoclonal antibodies (Cole et al., 1985, in Monoclonal Antibodies and Cancer Therapy, Alan R. Liss, Inc., pp. 77-96). Such antibodies may be of any immunoglobulin class including IgG, IgM, IgE, IgA, IgD and any subclass thereof. The hybridoma producing the mAbs of the invention may be cultivated in vitro or in vivo. In an additional embodiment of the invention, monoclonal antibodies can be produced in germ-free animals utilizing known technology.

The monoclonal antibodies include but are not limited to human monoclonal antibodies and chimeric monoclonal antibodies (e.g. human-mouse chimeras). A chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a human immunoglobulin constant region and a variable region derived from a murine mAb (see, e.g. US 4,816,567 and US 4,816397) Humanized antibodies are antibody molecules from non-human species having one or more complementarily determining regions (CDRs) from the non-human species and a framework region from a human immunoglobulin molecule (see, e.g. US 5,585,089)

Chimeric and humanized monoclonal antibodies can be produced by recombinant DNA techniques known in the art, for example using methods described in WO 87/02671 ; EP 184187; EP 171496; EP 173494; WO 86/01533; US 4,816,567; EP 125023; Better et al., 1988, Science 240:1041-1043; Liu et al., 1987, Proc. Natl. Acad. Sci. USA 84: 3439-3443; Liu et al., 1987, J. Immunol. 139:3521-3526; Sun et al., 1987, Proc. Natl. Acad. Sci. USA 84:214-218; Nishimura et al., 1987, Cane. Res. 47:999-1005; Wood et al., 1985, Nature 314:446-449; and Shaw et al., 1988, J. Natl. Cancer Inst. 80:1553-1559; Morrison, 1985, Science 229:1202-1207; Oi et al., 1986, Bio Techniques 4:214; US 5,225,539; Jones et al., 1986, Nature 321 :552-525; Verhoeyan et al., 1988, Science 239:1534; and Beidler et al., 1988, J. Immunol. 141 :4053-4060.

Completely human antibodies are particularly desirable for therapeutic treatment of human subjects. Such antibodies can be produced using transgenic mice which are incapable of expressing endogenous immunoglobulin heavy and light chain genes, but which can express human heavy and light chain genes. The transgenic mice are immunized in the normal fashion with a selected antigen, e.g. all or a portion of a BCMP polypeptide. Monoclonal antibodies directed against the BCMP polypeptide can be obtained using conventional hybridoma technology. The human immunoglobulin transgenes harbored by the transgenic mice rearrange during B-cell differentiation, and subsequently undergo class switching and somatic mutation. Thus, using such a technique, it is possible to produce therapeutically useful IgG, IgA, IgM and IgE antibodies. For an overview of this technology for producing human antibodies, see Lonberg and Huszar (1995, Int. Rev. Immunol. 13:65- 93). For a detailed discussion of this technology for producing human antibodies and human monoclonal antibodies and protocols for producing such antibodies, see, e.g. US 5,625,126; 5,633,425; 5,569,825; 5,661 ,016 and 5,545,806. In addition, companies such as Abgenix, Inc. (Freemont, CA) and Genpharm (San Jose, CA) can be engaged to provide human antibodies directed against a selected antigen using technology similar to that described above. Completely human antibodies that recognize a selected epitope can be generated using a technique referred to as "guided selection." In this approach a selected non-human monoclonal antibody, e.g. a mouse antibody, is used to guide the selection of a completely human antibody recognizing the same epitope (Jespers et al., 1994, Bio/technology 12:899- 903).

The antibodies of the present invention can also be generated using various phage display methods known in the art. In phage display methods, functional antibody domains are displayed on the surface of phage particles which carry the polynucleotide sequences encoding them. In a particular, such phage can be utilized to display antigen binding domains expressed from a repertoire or combinatorial antibody library (e.g, human or murine). Phage expressing an antigen binding domain that binds the antigen of interest can be selected or identified with antigen, e.g. using labeled antigen or antigen bound or captured to a solid surface or bead. The phage used in these methods are typically filamentous phage including fd and M13 binding domains expressed from phage with Fab, Fv or disulfide stabilized Fv antibody domains recombinantly fused to either the phage gene III or gene VIII protein. Phage display methods that can be used to make the antibodies of the present invention include those disclosed in Brinkman et al., 1995, J. Immunol. Methods 182:41 -50; Ames et al., 1995, J. Immunol. Methods 184:177-186; Kettleborough etal., 1994, Eur. J. Immunol. 24:952-58; Persic et al., 1997, Gene 187 9-18; Burton et al., 1994, Advances in Immunol, 57:191 -280; EP0589877; WO 90/02809; WO 91/10737; WO 92/01047; WO 92/18619; WO 93/11236; WO 95/15982; WO 95/20401 ; and US 5,698,426; 5,223,409; 5,403,484; 5,580,717; 5,427,908; 5,750,753; 5,821 ,047; 5,571 ,698; 5,427,908; 5,516,637; 5,780,225; 5,658,727; 5,733,743 and 5,969,108.

As described in the above references, after phage selection, the antibody coding regions from the phage can be isolated and used to generate whole antibodies, including human antibodies, or any other desired antigen binding fragment, and expressed in any desired host, including mammalian cells, insect cells, plant cells, yeast, and bacteria, e.g. as described in detail below. For example, techniques to recombinantly produce Fab, Fab' and F(ab')₂ fragments can also be employed using methods known in the art such as those disclosed in WO 92/22324; Mullinax et al., 1992, BioTechniques 12(6):864-869; and Sawai et al., 1995, AJRI 34:26-34; and Better et al., 1988, Science 240:1041-1043.

Examples of techniques that can be used to produce single-chain Fvs and antibodies include those described in US 4,946,778 and 5,258,498; Huston et al., 1991 , Methods in Enzymology 203:46-88; Shu et al., 1993, 90: 7995-999; and Skerra et al., 1998, Science 240:1038-1040.

The invention further provides for the use of bispecific antibodies, which can be made by methods known in the art. Traditional production of full-length bispecific antibodies is based on the coexpression of two immunoglobulin heavy chain-light chain pairs, where the two chains have different specificities (Milstein et al., 1983, Nature 305:537-539). Because of the random assortment of immunoglobulin heavy and light chains, these hybridomas (quadromas) produce a potential mixture of 10 different antibody molecules, of which only one has the correct bispecific structure. Purification of the correct molecule, which is usually done by affinity chromatography steps, is rather cumbersome, and the product yields are low. Similar procedures are disclosed in WO 93/08829, and Traunecker et al., 1991 , EMBO J. 10:3655-3659.

According to a different and more preferred approach, antibody variable domains with the desired binding specificities (antibody-antigen combining sites) are 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 (CH1 ) 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. This provides for great flexibility in adjusting the mutual proportions of the three polypeptide fragments in embodiments when unequal ratios of the three polypeptide chains used in the construction provide the optimum yields. It is, however, possible to insert the coding sequences for two or all three polypeptide chains in one expression vector when the expression of at least two polypeptide chains in equal ratios results in high yields or when the ratios are of no particular significance.

In a preferred embodiment of this approach, the bispecific antibodies are composed of a hybrid immunoglobulin heavy chain with a first binding specificity in one arm, and a hybrid immunoglobulin heavy chain-light chain pair (providing a second binding specificity) in the other arm. It was found that this asymmetric structure facilitates the separation of the desired bispecific compound from unwanted immunoglobulin chain combinations, as the presence of an immunoglobulin light chain in only one half of the bispecific molecule provides for a facile way of separation. This approach is disclosed in WO 94/04690. For further details for generating bispecific antibodies (see, for example, Suresh et al., Methods in Enzymology, 1986, 121 :210).

The invention provides functionally active fragments, derivatives or analogs of the anti-BCMP immunoglobulin molecules. Functionally active means that the fragment, derivative or analogue is able to elicit anti-idiotype antibodies (i.e. tertiary antibodies) that recognize the same antigen that is recognized by the antibody from which the fragment, derivative or analog is derived. Specifically, in a preferred embodiment the antigenicity of the idiotype of the immunoglobulin molecule may be enhanced by deletion of framework and CDR sequences that are C-terminal to the CDR sequence that specifically recognizes the antigen. To determine which CDR sequences bind the antigen, synthetic peptides containing the CDR sequences can be used in binding assays with the antigen by any binding assay method known in the art.

The present invention provides antibody fragments such as, but not limited to, F(ab')₂ fragments and Fab fragments. Antibody fragments that recognize specific epitopes may be generated by known techniques. F(ab')₂ fragments consist of the variable region, the light chain constant region and the CH1 domain of the heavy chain and are generated by pepsin digestion of the antibody molecule. Fab fragments are generated by reducing the disulfide bridges of the F(ab')₂ fragments. The invention also provides heavy chain and light chain dimers of the antibodies of the invention, or any minimal fragment thereof such as Fvs or single chain antibodies (SCAs) (e.g. as described in US 4,946,778; Bird, 1988, Science 242:423-42; Huston et al., 1988, Proc. Natl. Acad. Sci. USA 85:5879-5883; and Ward et al., 1989, Nature 334:544-54), or any other molecule with the same specificity as the antibody of the invention. Single chain antibodies are formed by linking the heavy and light chain fragments of the Fv region via an amino acid bridge, resulting in a single chain polypeptide. Techniques for the assembly of functional Fv fragments in E. coli may be used (Skerra et al., 1988, Science 242:1038-1041).

In other embodiments, the invention provides fusion proteins of the immunoglobulins of the invention (or functionally active fragments thereof), for example in which the immunoglobulin is fused via a covalent bond (e.g. a peptide bond), at either the N-terminus or the C-terminus to an amino acid sequence of another protein (or portion thereof, preferably at least 10, 20 or 50 amino acid portion of the protein) that is not the immunoglobulin. Preferably the immunoglobulin, or fragment thereof, is covalently linked to the other protein at the N-terminus of the constant domain. As stated above, such fusion proteins may facilitate purification, increase half-life in vivo, and enhance the delivery of an antigen across an epithelial barrier to the immune system.

The immunoglobulins of the invention include analogs and derivatives that are either modified, i.e. by the covalent attachment of any type of molecule as long as such covalent attachment that does not impair immunospecific binding. For example, but not by way of limitation, the derivatives and analogues of the immunoglobulins include those that have been further modified, e.g. by glycosylation, acetylation, pegylation, phosphylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to a cellular ligand or other protein, etc. Any of numerous chemical modifications may be carried out by known techniques, including, but not limited to specific chemical cleavage, acetylation, formylation, etc. Additionally, the analogue or derivative may contain one or more non- classical amino acids.

The foregoing antibodies can be used in methods known in the art relating to the localization and activity of a BCMP polypeptide, e.g. for imaging these proteins, measuring levels thereof in appropriate physiological samples, in diagnostic methods, etc.

The antibodies of the invention can be produced by any method known in the art for the synthesis of antibodies, in particular, by chemical synthesis or by recombinant expression, and are preferably produced by recombinant expression techniques.

Recombinant expression of antibodies, or fragments, derivatives or analogs thereof, requires construction of a nucleic acid that encodes the antibody. If the nucleotide sequence of the antibody is known, a nucleic acid encoding the antibody may be assembled from chemically synthesized oligonucleotides (e.g. as described in Kutmeier et al., 1994, BioTechniques 17:242), which, briefly, involves the synthesis of overlapping oligonucleotides containing portions of the sequence encoding antibody, annealing and ligation of those oligonucleotides, and then amplification of the ligated oligonucleotides by PCR.

Alternatively, the nucleic acid encoding the antibody may be obtained by cloning the antibody. If a clone containing the nucleic acid encoding the particular antibody is not available, but the sequence of the antibody molecule is known, a nucleic acid encoding the antibody may be obtained from a suitable source (e.g. an antibody cDNA library, or cDNA library generated from any tissue or cells expressing the antibody) by PCR amplification using synthetic primers hybridizable to the 3' and 5' ends of the sequence or by cloning using an oligonucleotide probe specific for the particular gene sequence.

If an antibody molecule that specifically recognizes a particular antigen is not available (or a source for a cDNA library for cloning a nucleic acid encoding such an antibody), antibodies specific for a particular antigen may be generated by any method known in the art, for example, by immunizing an animal, such as a rabbit, to generate polyclonal antibodies or, more preferably, by generating monoclonal antibodies. Alternatively, a clone encoding at least the Fab portion of the antibody may be obtained by screening Fab expression libraries (e.g. as described in Huse et al., 1989, Science 246:1275-1281 ) for clones of Fab fragments that bind the specific antigen or by screening antibody libraries (see, e.g. Clackson et al., 1991 , Nature 352:624; Hane et al., 1997 Proc. Natl. Acad. Sci. USA 94:4937).

Once a nucleic acid encoding at least the variable domain of the antibody molecule is obtained, it may be introduced into a vector containing the nucleotide sequence encoding the constant region of the antibody molecule (see, e.g. WO 86/05807; WO 89/01036; and US 5,122,464). Vectors containing the complete light or heavy chain for co-expression with the nucleic acid to allow the expression of a complete antibody molecule are also available. Then, the nucleic acid encoding the antibody can be used to introduce the nucleotide substitution(s) or deletion(s) necessary to substitute (or delete) the one or more variable region cysteine residues participating in an intrachain disulfide bond with an amino acid residue that does not contain a sulfhydyl group. Such modifications can be carried out by any method known in the art for the introduction of specific mutations or deletions in a nucleotide sequence, for example, but not limited to, chemical mutagenesis, in vitro site directed mutagenesis (Hutchinson et al., 1978, J. Biol. Chem. 253:6551 ), PCR based methods, etc.

In addition, techniques developed for the production of "chimeric antibodies" (Morrison et al., 1984, Proc. Natl. Acad. Sci. 81 :851-855; Neuberger et al., 1984, Nature 312:604-608; Takeda et al., 1985, Nature 314:452-454) by splicing genes from a mouse antibody molecule of appropriate antigen specificity together with genes from a human antibody molecule of appropriate biological activity can be used. As described supra, a chimeric antibody is a molecule in which different portions are derived from different animal species, such as those having a variable region derived from a murine mAb and a human antibody constant region, e.g. humanized antibodies.

Once a nucleic acid encoding an antibody molecule of the invention has been obtained, the vector for the production of the antibody molecule may be produced by recombinant DNA technology using techniques well known in the art. Thus, methods for preparing the protein of the invention by expressing nucleic acid containing the antibody molecule sequences are described herein. Methods well known to those skilled in the art can be used to construct expression vectors containing an antibody molecule coding sequences and appropriate transcriptional and translational control signals. These methods include, for example, in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. See, for example, the techniques described in Sambrook et al. (1990, Molecular Cloning, A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, NY) and Ausubel et al. (eds. 1998, Current Protocols in Molecular Biology, John Wiley & Sons, NY).

The expression vector is transferred to a host cell by conventional techniques and the transfected cells are then cultured by conventional techniques to produce an antibody of the invention. The host cells used to express a recombinant antibody of the invention may be either bacterial cells such as Escherichia coli, or, preferably, eukaryotic cells, especially for the expression of whole recombinant antibody molecule. In particular, mammalian cells, such as Chinese hamster ovary cells (CHO cells), in conjunction with a vector such as the major intermediate early gene promoter element from human cytomegalovirus, is an effective expression system for antibodies (Foecking et al., 1986, Gene 45:101 ; Cockett et al., 1990, Bio/Technology 8:2).

A variety of host-expression vector systems may be utilized to express an antibody molecule of the invention. Such host-expression systems represent vehicles by which the coding sequences of interest may be produced and subsequently purified, but also represent cells which may, when transformed or transfected with the appropriate nucleotide coding sequences, express the antibody molecule of the invention in situ. These include but are not limited to microorganisms such as bacteria (e.g. E. coli, B. subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vectors containing antibody coding sequences; yeast (e.g. Saccharomyces, Pichia) transformed with recombinant yeast expression vectors containing antibody coding sequences; insect cell systems infected with recombinant virus expression vectors (e.g. baculovirus) containing the antibody coding sequences; plant cell systems infected with recombinant virus expression vectors (e.g. cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors (e.g. Ti plasmid) containing antibody coding sequences; or mammalian cell systems (e.g. COS, CHO, BHK, 293, 3T3 cells) harboring recombinant expression constructs containing promoters derived from the genome of mammalian cells (e.g. metallothionein promoter) or from mammalian viruses (e.g. the adenovirus late promoter; the vaccinia virus 7.5K promoter).

In bacterial systems, a number of expression vectors may be advantageously selected depending upon the use intended for the antibody molecule being expressed. For example, when a large quantity of such a protein is to be produced, for the generation of pharmaceutical compositions comprising an antibody molecule, vectors that direct the expression of high levels of fusion protein products that are readily purified may be desirable. Such vectors include, but are not limited, to the E. coli expression vector pUR278 (Ruther et al., 1983, EMBO J. 2:1791 ), in which the antibody coding sequence may be ligated individually into the vector in frame with the lac Z coding region so that a fusion protein is produced; plN vectors (Inouye & Inouye, 1985, Nucleic Acids Res. 13:3101 -3109; Van Heeke & Schuster, 1989, J. Biol. Chem. 24:5503-5509); and the like. pGEX vectors may also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption and binding to a matrix such as glutathione-agarose beads followed by elution in the presence of free glutathione. The pGEX vectors are designed to include thrombin or factor Xa protease cleavage sites so that the cloned target gene product can be released from the GST moiety.

In an insect system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes. The virus grows in Spodoptera frugiperda cells. The antibody coding sequence may be cloned individually into non-essential regions (for example the polyhedrin gene) of the virus and placed under control of an AcNPV promoter (for example the polyhedrin promoter). In mammalian host cells, a number of viral-based expression systems (e.g. an adenovirus expression system) may be utilized.

As discussed above, a host cell strain may be chosen which modulates the expression of the inserted sequences, or modifies and processes the gene product in the specific fashion desired. Such modifications (e.g. glycosylation) and processing (e.g. cleavage) of protein products may be important for the function of the protein.

For long-term, high-yield production of recombinant antibodies, stable expression is preferred. For example, cells lines that stably express an antibody of interest can be produced by transfecting the cells with an expression vector comprising the nucleotide sequence of the antibody and the nucleotide sequence of a selectable (e.g. neomycin or hygromycin), and selecting for expression of the selectable marker. Such engineered cell lines may be particularly useful in screening and evaluation of compounds that interact directly or indirectly with the antibody molecule.

The expression levels of the antibody molecule can be increased by vector amplification (for a review, see Bebbington and Hentschel, The use of vectors based on gene amplification for the expression of cloned genes in mammalian cells in DNA cloning, Vol.3 (Academic Press, New York, 1987). When a marker in the vector system which expresses antibody is amplifiable, an increase in the level of inhibitor present in the culture of host cell will increase the number of copies of the marker gene. Since the amplified region is associated with the antibody gene, production of the antibody will also increase (Grouse et al., 1983, Mol. Cell. Biol. 3:257).

The host cell may be co-transfected with two expression vectors of the invention, the first vector encoding a heavy chain derived polypeptide and the second vector encoding a light chain derived polypeptide. The two vectors may contain identical selectable markers that enable equal expression of heavy and light chain polypeptides. Alternatively, a single vector may be used which encodes both heavy and light chain polypeptides. In such situations, the light chain should be placed before the heavy chain to avoid an excess of toxic free heavy chain (Proudfoot, 1986, Nature 322:52; Kohler, 1980, Proc. Natl. Acad. Sci. USA 77:2197). The coding sequences for the heavy and light chains may comprise cDNA or genomic DNA.

Once the antibody molecule of the invention has been recombinantly expressed, it may be purified by any method known in the art for purification of an antibody molecule, for example, by chromatography (e.g. ion exchange chromatography, affinity chromatography such as with protein A or specific antigen, and sizing column chromatography), centrifugation, differential solubility, or by any other standard technique for the purification of proteins.

Additionally, any fusion protein may be readily purified by utilizing an antibody specific for said fusion protein. For example, a system described by Janknecht allows for the ready purification of non-denatured fusion proteins expressed in human cell lines (Janknecht et al., 1991 , Proc. Natl. Acad. Sci. USA 88:8972-897). In this system, the gene of interest is subcloned into a vaccinia recombination plasmid such that the open reading frame of the gene is translationally fused to an amino-terminal tag consisting of six histidine residues. The tag serves as a matrix binding domain for the fusion protein. Extracts from cells infected with recombinant vaccinia virus are loaded onto Ni²⁺ nitriloacetic acid-agarose columns and histidine-tagged proteins are selectively eluted with imidazole-containing buffers.

An antibody optionally conjugated to a therapeutic moiety can be used as a therapeutic that is administered alone or in combination with cytotoxic factor(s) and/or cytokine(s). In particular, anti-BCMP antibodies or fragments thereof are conjugated to a diagnostic or therapeutic moiety to modify a given biological response. The therapeutic agent or drug moiety is not to be construed as limited to classical chemical therapeutic agents. For example, the drug moiety may be a protein or polypeptide possessing a desired biological activity. Such proteins may include, for example, a toxin such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin; a protein such as tumor necrosis factor, α- interferon, β-interferon, nerve growth factor, platelet derived growth factor, tissue plasminogen activator, a thrombotic agent or an anti-angiogenic agent, e.g. angiostatin or endostatin; or, a biological response modifier such as a lymphokine, interleukin-1 (IL-1), interleukin-2 (IL-2), interleukin-6 (IL-6), granulocyte macrophage colony stimulating factor (GM-CSF), granulocyte colony stimulating factor (G-CSF), nerve growth factor (NGF) or other growth factor. Other therapeutic moieties may include radionuclides such as ¹¹¹ln and ⁹⁰Y; antibiotics, e.g. calicheamicin; or drugs such as but not limited to, alkylphosphocholines, topoisomerase I inhibitors, taxoids and suramin.

The antibodies can be used for diagnosis or to determine the efficacy of a given treatment regimen. Detection can be facilitated by coupling the antibody to a detectable substance. Examples of detectable substances include various enzymes, prosthetic groups, fluorescent materials, luminescent materials, bioluminescent materials, radioactive nuclides, positron emitting metals (for use in positron emission tomography), and non radioactive paramagnetic metal ions (see generally US 4,741 ,900 for metal ions which can be conjugated to antibodies for use as diagnostics according to the present invention). Suitable enzymes include horseradish peroxidase, alkaline phosphatase, beta-galactosidase, or acetylcholinesterase; suitable prosthetic groups include streptavidin, avidin and biotin; suitable fluorescent materials include umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine, dichlorotriazinylamine fluorescein, dansyl chloride and phycoerythrin; suitable luminescent materials include luminol; suitable bioluminescent materials include luciferase, luciferin, and aequorin; and suitable radioactive nuclides include ¹²⁵l, ¹³¹l, ¹¹¹ln, "Tc. Anti-BCMP antibodies or fragments thereof can be conjugated to a therapeutic agent or drug moiety to modify a given biological response. The therapeutic agent or drug moiety is not to be construed as limited to classical chemical therapeutic agents. For example, the drug moiety may be a protein or polypeptide possessing a desired biological activity. Such proteins may include, for example, a toxin such as abrin, ricin A, pseudomonas exotoxin, or diphtheria toxin; a protein such as tumor necrosis factor, α-interferon, β-interferon, nerve growth factor, platelet derived growth factor, tissue plasminogen activator, a thrombotic agent or an anti-angiogenic agent, e.g. angiostatin or endostatin; or, a biological response modifier such as a lymphokine, interleukin-1 (IL-1), interleukin-2 (IL-2), interleukin-6 (IL-6), granulocyte macrophage colony stimulating factor (GM-CSF), granulocyte colony stimulating factor (G- CSF), nerve growth factor (NGF) or other growth factor.

Techniques for conjugating such therapeutic moiety to antibodies are well known, see, e.g. Arnon et al., "Monoclonal Antibodies For lmmunotargeting Of Drugs In Cancer Therapy", in Monoclonal Antibodies And Cancer Therapy, Reisfeld et al. (eds.), pp 243-56 (Alan R. Liss, Inc 1985); Hellstrom et al., "Antibodies For Drug Delivery", in Controlled Drug Delivery (2nd Ed.), Robinson et al. (eds.), pp 623-53 (Marcel Dekker, Inc. 1987); Thorpe, "Antibody Carriers Of Cytotoxic Agents In Cancer Therapy: A Review", in Monoclonal Antibodies '84: Biological And Clinical Applications, Pinchera et al. (eds.), pp. 475-506 (1985); "Analysis, Results, And Future Prospective Of The Therapeutic Use Of Radiolabeled Antibody In Cancer Therapy", in Monoclonal Antibodies For Cancer Detection And Therapy, Baldwin et al. (eds.), pp. 303-16 (Academic Press 1985), Thorpe et al., 1982, Immunol. Rev., 62:119-58 and Dubowchik etal., 1999, Pharmacology and Therapeutics, 83, 67-123).

Alternatively, an antibody can be conjugated to a second antibody to form an antibody heteroconjugate as described by Segal in US 4,676,980.

Breast cancer may be treated or prevented by administration to a subject suspected of having or known to have breast cancer or to be at risk of developing breast cancer of a compound that modulates (e.g. increases or decreases) the level or activity (e.g. function) of one or more BCMP polypeptides that are differentially present in the breast tissue of subjects having breast cancer compared with breast tissue of subjects free from breast cancer. In one embodiment, a compound is administered that downregulates the level or activity (i.e. function) of one or more BCMP polypeptides that are increased in the breast tissue of subjects having breast cancer.

Breast cancer is also treated or prevented by administration to a subject suspected of having or known to have breast cancer or to be at risk of developing breast cancer of a compound that downregulates the level or activity of one or more BCMP polypeptides that are increased in the breast tissue of subjects having breast cancer. In a preferred embodiment, therapy or prophylaxis is tailored to the needs of an individual subject.

Accordingly, the invention provides methods for identifying agents (e.g. candidate compounds or test compounds) that bind to a BCMP polypeptide or have a stimulatory or inhibitory effect on the expression or activity of a BCMP polypeptide. The invention also provides methods of identifying agents, candidate compounds or test compounds that bind to a BCMP polypeptide or have a stimulatory or inhibitory effect on the expression or activity of a BCMP polypeptide. Examples of agents, candidate compounds or test compounds include, but are not limited to, nucleic acids (e.g. DNA and RNA), carbohydrates, lipids, proteins, peptides, peptidomimetics, antibodies, small molecules (preferably molecules of 1000 daltons or less) and other drugs. Agents can be obtained using any of the numerous approaches in combinatorial library methods known in the art, including: biological libraries; spatially addressable parallel solid phase or solution phase libraries; synthetic library methods requiring deconvolution; the "one-bead one-compound" library method; and synthetic library methods using affinity chromatography selection. The biological library approach is limited to peptide libraries, while the other four approaches are applicable to peptide, non-peptide oligomer or small molecule libraries of compounds (Lam, 1997, Anticancer Drug Des. 12:145; US 5,738,996 and .5,807,683).

Examples of methods for the synthesis of molecular libraries can be found in the art, for example in: DeWitt etal., 1993, Proc. Natl. Acad. Sci. USA 90:6909; Erb etal., 1994, Proc. Natl. Acad. Sci. USA 91 :11422; Zuckermann et al., 1994, J. Med. Chem. 37:2678; Cho et al., 1993, Science 261 :1303; Carrell et al., 1994, Angew. Chem. Int. Ed. Engl. 33:2059; Carell et al., 1994, Angew. Chem. Int. Ed. Engl. 33:2061 ; and Gallop etal., 1994, J. Med. Chem. 37:1233.

Libraries of compounds may be presented, e.g. presented in solution (e.g. Houghten, 1992, Bio/Techniques 13:412-421), or on beads (Lam, 1991 , Nature 354:82-84), chips (Fodor, 1993, Nature 364:555-556), bacteria (US 5,223,409), spores (US 5,571 ,698; 5,403,484; and 5,223,409), plasmids (Cull et al., 1992, Proc. Natl. Acad. Sci. USA 89:1865- 1869) or phage (Scott and Smith, 1990, Science 249:386-390; Devlin, 1990, Science 249:404-406; Cwirla et al., 1990, Proc. Natl. Acad. Sci. USA 87:6378-6382; and Felici, 1991 , J. Mol. Biol. 222:301-310).

In one embodiment, agents that interact with (i.e. bind to) a BCMP polypeptide are identified in a cell-based assay system. In accordance with this embodiment, cells expressing a BCMP polypeptide are contacted with a candidate agent and the ability of the candidate agent to interact with the BCMP polypeptide is determined. Preferably, the ability of a candidate agent to interact with a BCMP polypeptide is compared to a reference range or control. In another embodiment, a first and second population of cells expressing a BCMP polypeptide are contacted with a candidate agent or a control agent and the ability of the candidate agent to interact with the polypeptide is determined by comparing the difference in interaction between the candidate agent and control agent. If desired, this assay may be used to screen a plurality (e.g. a library) of candidate compounds. The cell, for example, can be of prokaryotic origin (e.g. E. coli) or eukaryotic origin (e.g. yeast or mammalian). Further, the cells can express the BCMP polypeptide endogenously or be genetically engineered to express said BCMP polypeptides. In certain instances, the BCMP polypeptide or the candidate compound is labeled, for example with a radioactive label (such as ³²P, ³⁵S, and ¹²⁵l) or a fluorescent label (such as fluorescein isothiocyanate, rhodamine, phycoerythrin, phycocyanin, allophycocyanin, o-phthaldehyde or fluorescamine) to enable detection of an interaction between a BCMP polypeptide and a candidate compound. The ability of the candidate compound to interact directly or indirectly with a BCMP polypeptide can be determined by methods known to those of skill in the art. For example, the interaction can be determined by flow cytometry, a scintillation assay, immunoprecipitation or Western blot analysis.

In another embodiment, agents that interact with (i.e. bind to) a BCMP polypeptide are identified in a cell-free assay system where a native or recombinant BCMP polypeptide is contacted with a candidate agent and the ability of the candidate agent to interact with the polypeptide is determined. Preferably, the ability of a candidate agent to interact with a BCMP polypeptide is compared to a reference range or control. Alternatively, a first and second sample comprising native or recombinant BCMP polypeptide are contacted with a candidate agent or a control agent and the ability of the candidate agent to interact with the polypeptide is determined by comparing the difference in interaction between the candidate agent and control agent. If desired, this assay may be used to screen a plurality (e.g. a library) of candidate compounds. Preferably, the BCMP polypeptide is first immobilized, by, for example, contacting said BCMP polypeptide with an immobilized antibody which specifically recognizes and binds it, or alternatively by contacting a preparation of the BCMP polypeptide with a surface designed to bind proteins. The BCMP polypeptide may be partially or completely purified (e.g. partially or completely free of other polypeptides) or may be part of a cell lysate. As before, the ability of the candidate compound to interact with a BCMP polypeptide can be determined by methods known to those of skill in the art. These assays, whether cell-based or cell-free, can be used to screen a plurality (e.g. a library) of candidate compounds. In one embodiment, the BCMP polypeptide can be biotinylated using techniques well known to those of skill in the art (e.g. biotinylation kit, Pierce Chemicals; Rockford, IL). The ability of the candidate compound to interact with a BCMP polypeptide can be determined by methods known to those of skill in the art.

In a particular embodiment, agents that competitively interact with (i.e. competitively binding to) a BCMP polypeptide are identified in a competitive binding assay and the ability of the candidate agent to interact with the BCMP polypeptide is determined. Preferably, the ability of a candidate agent to interact with a BCMP polypeptide is compared to a reference range or control. In a preferred embodiment, a first and second population of cells expressing both a BCMP polypeptide and a protein which is known to interact with the BCMP polypeptide are contacted with a candidate agent or a control agent. The ability of the candidate agent to competitively interact with the BCMP polypeptide is then determined by comparing the interaction in the first and second population of cells. In another embodiment, an alternative second population or a further population of cells may be contacted with an agent which is known to competitively interact with a BCMP polypeptide. Alternatively, ' agents that competitively interact with a BCMP polypeptide are identified in a cell-free assay system by contacting a first and second sample comprising a BCMP polypeptide and a protein known to interact with the BCMP polypeptide with a candidate agent or a control agent. The ability of the candidate agent to competitively interact with the BCMP polypeptide is then determined by comparing the interaction in the first and second sample. In another embodiment, an alternative second sample or a further sample comprising a BCMP polypeptide may be contacted with an agent which is known to competitively interact with a BCMP polypeptide. In any case, the BCMP polypeptide and known interacting protein may be expressed naturally or may be recombinantly expressed; the candidate agent may be added exogenously, or be expressed naturally or recombinantly.

In one embodiment, a BCMP polypeptide is used as a "bait protein" in a two-hybrid assay or three hybrid assay to identify other proteins that bind to or interact with the BCMP polypeptide (see e.g. US 5,283,317; Zervos et al., 1993, Cell 72:223-232; Madura et al. 1993, J. Biol. Chem. 268:12046-12054; Bartel etal., 1993, Bio/Techniques 14:920-924; Iwabuchi et al., 1993, Oncogene 8:1693-1696; and WO 94/10300). As those skilled in the art will appreciate, such binding proteins are also likely to be involved in the propagation of signals by a BCMP polypeptide. For example, they may be upstream or downstream elements of a signalling pathway involving a BCMP polypeptide. Alternatively, polypeptides that interact with a BCMP polypeptide can be identified by isolating a protein complex comprising a BCMP polypeptide (i.e. a BCMP polypeptide which interacts directly or indirectly with one or more other polypeptides) and identifying the associated proteins using methods known in the art such as mass spectrometry or Western blotting (for examples see Blackstock, W. & Weir, M. 1999, Trends in Biotechnology, 17: 121-127; Rigaut, G. 1999, Nature Biotechnology, 17: 1030-1032; Husi, H. 2000, Nature Neurosci. 3:661 -669; Ho, Y. et al., 2002, Nature, 415:180-183; Gavin, A. et al., 2002, Nature, 415: 141-147).

In another embodiment, agents that modulate (i.e. upregulate or downregulate) the expression or activity of a BCMP polypeptide are identified in a cell-based assay system. Accordingly, the activity of a BCMP polypeptide is measured in a population of cells which naturally (endogenously) or recombinantly express a BCMP polypeptide, in the presence of a candidate agent. Preferably, the activity of a BCMP polypeptide is compared to a reference range or control. In a preferred embodiment, the activity of a BCMP polypeptide is measured in a first and second population of cells that naturally or recombinantly express a BCMP polypeptide, in the presence of agent or absence of a candidate agent (e.g. in the presence of a control agent) and the activity of the BCMP polypeptide is compared. The candidate agent can then be identified as a modulator of the activity of a BCMP polypeptide based on this comparison. It is understood that the expression of a BCMP polypeptide can be assessed by monitoring the expression of an mRNA encoding a BCMP polypeptide using the described assays. For example, when expression of the BCMP polypeptide or mRNA encoding said polypeptide is significantly greater in the presence of the candidate compound than in its absence, the candidate compound is identified as a stimulator of expression of the BCMP polypeptide or mRNA encoding said polypeptide. Alternatively, when expression of the BCMP polypeptide or mRNA encoding said polypeptide is significantly less in the presence of the candidate compound than in its absence, the candidate compound is identified as an inhibitor of the expression of the BCMP polypeptide or mRNA encoding said polypeptide. The level of expression of a BCMP polypeptide or its encoding mRNA can be determined by methods known to those of skill in the art. For example, mRNA expression can be assessed by Northern blot analysis or RT-PCR, and protein levels can be assessed by Western blot analysis. In another embodiment, a cell-based assay system is used to identify agents capable of modulating (i.e. stimulating or inhibiting) the activity of a BCMP polypeptide. Accordingly, the activity of a BCMP polypeptide is measured in a population of cells that naturally or recombinantly express a BCMP polypeptide, in the presence of a candidate agent. Preferably, the activity of a BCMP polypeptide is compared to a reference range or control. In a preferred embodiment, the activity of a BCMP polypeptide is measured in a first and second population of cells that naturally or recombinantly express a BCMP polypeptide, in the presence of agent or absence of a candidate agent (e.g. in the presence of a control agent) and the activity of the BCMP polypeptide is compared. The candidate agent can then be identified as a modulator of the activity of a BCMP polypeptide based on this comparison. Alternatively, the activity of a BCMP polypeptide can be measured in a cell-free assay system where the BCMP polypeptide is either natural or recombinant. Preferably, the activity of a BCMP polypeptide is compared to a reference range or control. In a preferred embodiment, the activity of a BCMP polypeptide is measured in a first and second sample in the presence or absence of a candidate agent and the activity of the BCMP polypeptide is compared. The candidate agent can then be identified as a modulator of the activity of a BCMP polypeptide based on this comparison.

The activity of a BCMP polypeptide can be assessed by detecting induction of a cellular signal transduction pathway (e.g. intracellular Ca²⁺, cAMP, cGMP, diacylglycerol, IP3, etc.), detecting catalytic or enzymatic activity of the target on a suitable substrate, detecting the induction of a reporter gene (e.g. a regulatory element that is responsive to a BCMP polypeptide and is operably linked to a nucleic acid encoding a detectable marker, e.g. luciferase), or detecting a cellular response, for example, cellular differentiation, transformation, or cell proliferation. Based on the present description, techniques known to those of skill in the art can be used for measuring these activities (see, e.g. US 5,401 ,639). The candidate compound can then be identified as a modulator of the activity of a BCMP polypeptide by comparing the effects of the candidate compound to the control compound. Suitable control compounds include phosphate buffered saline (PBS) and normal saline (NS).

In another embodiment, agents that modulate (e.g. upregulate or downregulate) the expression or activity, or both the expression and activity of a BCMP polypeptide are identified in an animal model. Examples of suitable animals include, but are not limited to, mice, rats, rabbits, monkeys, guinea pigs, dogs and cats. Preferably, the animal used represent a model of breast cancer (e.g. xenografts of human breast cancer cell lines such as MDA-MB-345 in oestrogen-deprived Severe Combined Immunodeficient (SCID) mice, Eccles et al. 1994, Cell Biophysics 24/25:279). These can be utilized to test compounds that modulate BCMP polypeptide or mRNA encoding said polypeptide levels, since the pathology exhibited in these models is similar to that of breast cancer. In accordance with this embodiment, the test compound or a control compound is administered (e.g. orally, rectally or parenterally such as intraperitoneally or intravenously) to a suitable animal and the effect on the expression, activity or both expression and activity of the BCMP polypeptide is determined. Changes in the expression of a polypeptide or nucleic acid can be assessed by the methods outlined above. Compounds able to restore BCMP polypeptide levels in a subject having breast cancer towards levels found in subjects free from breast cancer or to produce similar changes in experimental animal models of breast cancer can be used as lead compounds for further drug discovery, or used therapeutically. In a particular embodiment, a therapeutically effective amount of an agent can be determined by monitoring an amelioration or improvement in disease symptoms, to delay onset or slow progression of the disease, for example but without limitation, a reduction in tumour size. Techniques known to physicians familiar with breast cancer can be used to determine whether a candidate agent has altered one or more symptoms associated with the disease.

It is also apparent to the skilled artisan that, based upon the present disclosure, transgenic animals can be produced with "knock-out" mutations of the gene or genes encoding one or more BCMP polypeptides. A "knock-out" mutation of a gene is a mutation that causes the mutated gene to not be expressed, or expressed in an aberrant form or at a low level, such that the activity associated with the gene product is nearly or entirely absent. Preferably, the transgenic animal is a mammal, more preferably, the transgenic animal is a mouse.

Thus, an important feature of the present invention is the identification of genes encoding BCMP polypeptides which are involved in breast cancer. Breast cancer can be treated (e.g. to ameliorate symptoms or to retard onset or progression) or prevented by administration of a therapeutic compound that promotes function or expression of one or more BCMPs that are decreased in the breast tissue of subjects having breast cancer, or by administration of a therapeutic compound that reduces function or expression of one or more BCMPs that are increased in the breast tissue of subjects having breast cancer.

One skilled in the art will also appreciate that a BCMP polypeptide may also be used in a method for the structure-based design of an agent, in particular a small molecule which acts to modulate (e.g. stimulate or inhibit) the activity of said polypeptide, said method comprising:

1 ) determining the three-dimensional structure of a BCMP polypeptide;

2) deducing the three-dimensional structure within the BCMP polypeptide of the likely reactive or binding site(s);

3) synthesising candidate agents that are predicted to react or bind to the deduced reactive or binding site; and

4) testing whether the candidate agent is able to modulate the activity of the BCMP polypeptide.

It will be appreciated that the method described above is likely to be an iterative process.

In another embodiment, agents such as an enzyme, or a biologically active portion thereof, which is responsible for the production or degradation of a BCMP polypeptide or nucleic acid, or is responsible for the post-translational modification of a BCMP polypeptide can be identified. In a primary screen, substantially pure, native or recombinantly expressed BCMP polypeptides, nucleic acids or cellular extract or other sample comprising native or recombinantly expressed BCMP polypeptides or nucleic acids are contacted with a plurality of candidate agents (for example but without limitation, a plurality of agents presented as a library) that may be responsible for the processing of a BCMP polypeptide or nucleic acid, in order to identify such agents. The ability of the candidate agent to modulate the production, degradation or post-translational modification of a BCMP polypeptide or nucleic acid can be determined by methods known to those of skill in the art, including without limitation, flow cytometry, radiolabelling, a kinase assay, a phosphatase assay, immunoprecipitation and Western blot analysis, or Northern blot analysis.

In yet another embodiment, cells expressing a BCMP polypeptide are contacted with a plurality of candidate agents. The ability of such an agent to modulate the production, degradation or post-translational modification of a BCMP polypeptide can be determined by methods known to those of skill in the art, as described above.

This invention further provides agents identified by the above-described screening assays and uses thereof for treatments as described herein. Hereinafter, the agents identified by the above screening methods (including small molecules), antibodies specific for a BCMP polypeptide, BCMP polypeptides and BCMP nucleic acids of use in treatment are referred to as 'active agents'. The term 'treatment' includes either therapeutic or prophylactic therapy. When a reference is made herein to a method of treating or preventing a disease or condition using a particular active agent or combination of agents, it is to be understood that such a reference is intended to include the use of that active agent or combination of agents in the preparation of a medicament for the treatment or prevention of the disease or condition. The active agents of use in the invention may be given in combination with any other compound, including taxol, cyclophosphamide, tamoxifen, and doxorubacin.

Accordingly, the present invention provides a method for the prophylaxis and/or treatment of breast cancer, which comprises administering to said subject a therapeutically effective amount of at least one active agent of the invention.

In order to use active agents of the invention in therapy (human or veterinary), they will normally be formulated into a pharmaceutical composition in accordance with standard pharmaceutical practice, e.g. by admixing the active agent and a pharmaceutically acceptable carrier. Thus, according to a further aspect of the invention there is provided a pharmaceutical composition comprising at least one active agent of the invention and a pharmaceutically acceptable carrier. The pharmaceutical compositions are particularly useful in the prevention or treatment of breast cancer. In one aspect, the pharmaceutical composition is for use as a vaccine and so any additional components will be acceptable for vaccine use. In addition, the skilled person will appreciate that one or more suitable adjuvants may be added to such vaccine preparations.

Active agents of the invention may be administered to a subject by any of the routes conventionally used for drug administration, for example they may be administered parenterally, orally, topically (including buccal, sublingual or transdermal) or by inhalation. The most suitable route for administration in any given case will depend on the particular active agent, the breast cancer type, the subject, and the nature and severity of the disease and the physical condition of the subject. The active agents may be administered in combination, e.g. simultaneously, sequentially, or separately, with one or more other therapeutically active, e.g. anti-tumour, compounds.

The dosage to be administered of an active agent will vary according to the particular active agent, the breast cancer type, the subject, and the nature and severity of the disease and the physical condition of the subject, and the selected route of administration; the appropriate dosage can be readily determined by a person skilled in the art. For the treatment of breast cancer in humans and animals, the dosage may range from 0.01 mg/kg to 750 mg/kg. For prophylactic use in human and animals, the dosage may range from 0.01 mg/kg to 100 mg/kg.

The compositions may contain from 0.1 % by weight, preferably from 10-60% by weight, of the active agent of the invention, depending on the method of administration.

Pharmaceutical compositions may be conveniently presented in unit dose forms containing a predetermined amount of an active agent of the invention per dose. Such a unit may contain for example but without limitation, 10Omg/kg to 0.1 mg/kg depending on the condition being treated, the route of administration and the age, weight and condition of the subject. Preferred unit dosage compositions are those containing a daily dose or sub-dose, as recited above, or an appropriate fraction thereof, of the active agent.

It will be recognized by one of skill in the art that the optimal quantity and spacing of individual dosages of an active agent of the invention will be determined by the nature and extent of the condition being treated, the form, route and site of administration, and the particular subject being treated, and that such optimums can be determined by conventional techniques. It will also be appreciated by one of skill in the art that the optimal course of treatment, i.e. the number of doses of an active agent of the invention given per day for a defined number of days, can be ascertained by those skilled in the art using conventional course of treatment determination tests.

Dosage regimens are adjusted to provide the optimum desired response. For example, a single bolus may be administered, several divided doses may be administered over time or the dose may be proportionally reduced or increased as indicated by the exigencies of the therapeutic situation.

Pharmaceutically acceptable carriers for use in the invention may take a wide variety of forms depending, e.g. on the route of administration.

Compositions for oral administration may be liquid or solid. Oral liquid preparations may be in the form of, for example, aqueous or oily suspensions, solutions, emulsions, syrups or elixirs, or may be presented as a dry product for reconstitution with water or other suitable vehicle before use. Oral liquid preparations may contain suspending agents, for example sorbitol, methyl cellulose, glucose syrup, gelatin, hydroxyethyl cellulose, carboxymethyl cellulose, aluminium stearate gel or hydrogenated edible fats, emulsifying agents, for example lecithin, sorbitan monooleate, or acacia; water; non-aqueous vehicles (which may include edible oils), for example almond oil, oily esters such as glycerine, propylene glycol, or ethyl alcohol; preservatives, for example methyl or propyl p- hydroxybenzoate or sorbic acid; flavoring agents, preservatives, coloring agents and the like may be used.

In the case of oral solid preparations such as powders, capsules and tablets, carriers such as starches, sugars, microcrystalline cellulose, diluents, granulating agents, lubricants, binders, disintegrating agents, and the like may be included. Because of their ease of administration, tablets and capsules represent the most advantageous oral dosage unit form in which case solid pharmaceutical carriers are generally employed. In addition to the common dosage forms set out above, active agents of the invention may also be administered by controlled release means and/or delivery devices. Tablets and capsules may comprise conventional carriers or excipients such as binding agents for example, syrup, acacia, gelatin, sorbitol, tragacanth, or polyvinylpyrrolidone; fillers, for example lactose, sugar, maize-starch, calcium phosphate, sorbitol or glycine; tableting lubricants, for example magnesium stearate, talc, polyethylene glycol or silica; disintegrants, for example potato starch; or acceptable wetting agents such as sodium lauryl sulphate. The tablets may be coated by standard aqueous or non-aqueous techniques according to methods well known in normal pharmaceutical practice.

Pharmaceutical compositions of the present invention suitable for oral administration may be presented as discrete units such as capsules, cachets or tablets, each containing a predetermined amount of the active agent, as a powder or granules, or as a solution or a suspension in an aqueous liquid, a non-aqueous liquid, an oil-in-water emulsion or a water- in-oil liquid emulsion. Such compositions may be prepared by any of the methods of pharmacy but all methods include the step of bringing into association the active agent with the carrier, which constitutes one or more necessary ingredients. In general, the compositions are prepared by uniformly and intimately admixing the active agent with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product into the desired presentation. For example, a tablet may be prepared by compression or moulding, optionally with one or more accessory ingredients.

Compressed tablets may be prepared by compressing, in a suitable machine, the active agent in a free-flowing form such as a powder or granules, optionally mixed with a binder, lubricant, inert diluent, surface active or dispersing agent. Moulded tablets may be made by moulding, in a suitable machine, a mixture of the powdered compound moistened with an inert liquid diluent. Desirably, each tablet contains from about 1 mg to about 500 mg of the active agent and each cachet or capsule contains from about 1 to about 500 mg of the active agent.

Compositions comprising an active agent of the invention may also be prepared in powder or liquid concentrate form. Conventional water soluble excipients, such as lactose or sucrose, may be incorporated in the powders to improve their physical properties. Thus, particularly suitable powders of this invention comprise 50 to 100% w/w, and preferably 60 to 80% w/w of the combination and 0 to 50% w/w and preferably 20 to 40% w/w of conventional excipients. When used in a veterinary setting such powders may be added to animal feedstuffs, for example by way of an intermediate premix, or diluted in animal drinking water.

Liquid concentrates of this invention for oral administration suitably contain a water- soluble compound combination and may optionally include a veterinarily acceptable water miscible solvent, for example polyethylene glycol, propylene glycol, glycerol, glycerol formal or such a solvent mixed with up to 30% v/v of ethanol. The liquid concentrates may be administered to the drinking water of animals, particularly poultry.

Pharmaceutical compositions suitable for parenteral administration may be prepared as solutions or suspensions of the active agents of the invention in water suitably mixed with a surfactant such as hydroxypropylcellulose. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms.

The pharmaceutical forms suitable for injectable use include aqueous or non- aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the composition isotonic with the blood of the intended recipient, and aqueous and non-aqueous sterile suspensions which may include suspending agents and thickening agents. Extemporaneous injection solutions, dispersions and suspensions may be prepared from sterile powders, granules and tablets.

The compositions may be presented in unit-dose or multi-dose containers, for example in sealed ampoules and vials and to enhance stability, may be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example water for injections, immediately prior to use. The sterile liquid carrier may be supplied in a separate vial or ampoule and can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g. glycerol, propylene glycol and liquid polyethylene glycol), suitable mixtures thereof, and vegetable oils. Advantageously, agents such as a local anaesthetic, preservative and buffering agents can be included the sterile liquid carrier.

In certain embodiments, the active agents of the invention can be formulated to ensure proper distribution in vivo, for example, in liposomes. For methods of manufacturing liposomes, see, e.g. US 4,522,811 ; 5,374,548; and 5,399,331. The liposomes may comprise one or more moieties which are selectively transported into specific cells or organs, thus enhance targeted drug delivery (see, e.g. Ranade, V. 1989, J. Clin. Pharmacol. 29: 685). In a specific embodiment, it may be desirable to use liposomes targeted via antibodies to specific identifiable tumor antigens (Leonetti et al., 1990, Proc. Natl. Acad. Sci. USA, 87:2448-2451 ; Renneisen et al., 1990, J. Biol. Chem. 265:16337-16342). Exemplary targeting moieties include folate or biotin (see, e.g. US 5,416,016); mannosides (Umezawa et al., 1988, Biochem. Biophys. Res. Comm. 153:1038); antibodies (Bloeman, P. etal., 1995, FEBS Lett. 357:140; Owais, M. et al. (1995) Antimicrob. Agents Chemother. 39: 180); surfactant protein A receptor (Briscoe et al. (1995) Am. J. Physiol. 1233: 134), different species of which may comprise the compositions of the inventions, as well as components of the invented molecules; psi 20 (Schreier et al. (1994) J. Biol. Chem. 269: 9090); see also Keinanen, K. & Laukkanen, M., 1994, FEBS Lett. 346: 123; Killion, J. & Fidler, I., 1994, Immunomethods 4: 273. In a more preferred embodiment, the active agents formulated in liposomes include a targeting moiety. In a most preferred embodiment, the therapeutic compounds in the liposomes are delivered by bolus injection to a site proximal to the tumour.

Pharmaceutical compositions adapted for topical administration may be formulated as ointments, creams, suspensions, lotions, powders, solutions, pastes, gels, impregnated dressings, sprays, aerosols or oils, transdermal devices, dusting powders, and the like. These compositions may be prepared via conventional methods containing the active agent. Thus, they may also comprise compatible conventional carriers and additives, such as preservatives, solvents to assist drug penetration, emollients in creams or ointments and ethanol or oleyl alcohol for lotions. Such carriers may be present as from about 1 % up to about 98% of the composition. More usually they will form up to about 80% of the composition. As an illustration only, a cream or ointment is prepared by mixing sufficient quantities of hydrophilic material and water, containing from about 5-10% by weight of the compound, in sufficient quantities to produce a cream or ointment having the desired consistency.

Pharmaceutical compositions adapted for transdermal administration may be presented as discrete patches intended to remain in intimate contact with the epidermis of the recipient for a prolonged period of time. For example, the active agent may be delivered from the patch by iontophoresis.

For applications to external tissues, for example the mouth and skin, the compositions are preferably applied as a topical ointment or cream. When formulated in an ointment, the active agent may be employed with either a paraffinic or a water-miscible ointment base. Alternatively, the active agent may be formulated in a cream with an oil-in-water cream base or a water-in-oil base.

Pharmaceutical compositions adapted for topical administration in the mouth include lozenges, pastilles and mouth washes.

Pharmaceutical compositions adapted for topical administration to the eye include eye drops wherein the active agent is dissolved or suspended in a suitable carrier, especially an aqueous solvent. They also include topical ointments or creams as above.

Pharmaceutical compositions suitable for rectal administration wherein the carrier is a solid are most preferably presented as unit dose suppositories. Suitable carriers include cocoa butter or other glyceride or materials commonly used in the art, and the suppositories may be conveniently formed by admixture of the combination with the softened or melted carrier(s) followed by chilling and shaping moulds. They may also be administered as enemas.

Pharmaceutical compositions adapted for vaginal administration may be presented as pessaries, tampons, creams, gels, pastes, foams or spray compositions. These may comprise emollients or bases as commonly used in the art.

In one embodiment, the present invention provides the use of at least one BCMP polypeptide, in the preparation of a pharmaceutical composition for use in the treatment of breast cancer. In particular, a BCMP polypeptide may be fused to another polypeptide, such as the protein transduction domain of the HIV/Tat protein, which facilitates the entry of the fusion protein into a cell (Asoh, S. et al., 2002, Proc. Natl. Acad. Sci. USA, 99:17107-17112) is provided for use in the manufacture of a pharmaceutical composition for the treatment of breast cancer.

In a preferred embodiment, one or more antibodies each specifically binding to a BCMP polypeptide are administered, preferably as a pharmaceutical composition, alone or in combination with one or more additional therapeutic compounds or treatments. Examples of such therapeutic compounds or treatments include, but are not limited to, taxol, cyclophosphamide, tamoxifen, and doxorubacin. Preferably, such an antibody is allogeneic to the subject to which it is administered.

Most preferably, an active agent preferably as a pharmaceutical composition is administered to a human subject for therapy (e.g. to ameliorate symptoms or to retard onset or progression) or prophylaxis.

The invention also provides a pharmaceutical pack or kit comprising one or more containers filled with one or more of the pharmaceutical compositions comprising an active agent of the invention. Optionally associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects (a) approval by the agency of manufacture, use or sale for human administration, (b) directions for use, or both.

In summary, the invention further provides:

(i) the use of a BCMP polypeptide or BCMP nucleic acid in the manufacture of a medicament for the treatment of breast cancer; (ii) a method of treatment of breast cancer in a subject, which comprises administering to said subject a therapeutically effective amount of a BCMP polypeptide or a BCMP nucleic acid; (iii) a BCMP polypeptide or BCMP nucleic acid for use in the treatment of breast cancer; (iv) the use of an antibody that specifically binds to a BCMP polypeptide in the manufacture of a medicament for the treatment of breast cancer; (v) a method of treatment of breast cancer in a subject, which comprises administering to said subject a therapeutically effective amount of an antibody specific for a BCMP polypeptide; (vi) an antibody specific for a BCMP polypeptide for use in the treatment of breast cancer; (vii) the use of an agent which interacts with or modulates the expression or activity of a BCMP polypeptide or BCMP nucleic acid in the preparation of a medicament for the treatment of breast cancer; (viii) a method of treatment of breast cancer in a subject, which comprises administering to said subject a therapeutically effective amount of an agent which interacts with or modulates the expression or activity of a BCMP polypeptide or BCMP nucleic acid; and (ix) an agent which interacts with or modulates the expression or activity of a

BCMP polypeptide or BCMP nucleic acid for use in the treatment of breast cancer.

Preferred features of each aspect of the invention are as for each of the other aspects mutatis mutandis. All publications, including but not limited to patents and patent applications cited in this specification are herein incorporated by reference as if each individual publication were specifically and individually indicated to be incorporated by reference herein as though fully set forth.

The invention will now be described with reference to the following example, which is merely illustrative and should not in any way be construed as limiting the scope of the present invention.

EXAMPLE: Identification of Membrane Proteins Expressed in Breast Cancer Cell Lines

Proteins in breast cancer cell line membranes were separated by SDS-PAGE and analysed. Experimental 1a - Crude fractionation of adherent breast carcinoma cell lines

The human breast carcinoma cell lines MDA-MB-468 (ATCC:HB-132), T-47D (ATCC:HB-133), BT-474 (ATCC:HTB-20), and MCF-7 (ATCC:HTB-22) were cultured in DMF12 media containing 10% foetal calf serum , 2mM glutamine and 1% penicillin/streptomycin. The cells were maintained at 37°C in a humidified atmosphere of 95% air and 5 % CO₂.

1b - Cell fractionation and plasma membrane generation

Adherent cells (2 x 10⁸) were washed three times with PBS and scrapped using a plastic cell lifter. Cells were centrifuged at 1000 x g for 5min at 4°C and the cell pellet was resuspended in homogenization buffer (250 mM Sucrose, 10mM HEPES, 1 mM EDTA, 1 mM Vanadate and 0.02% azide, protease inhibitors). Cells were fractionated using a ball bearing homogeniser (8.002 mm ball, HGM Lab equipment) until approx. 95% of cells were broken. Membranes were fractionated using the method described by Pasquali et al. The fractionated cells were centrifuged at 3000 x g for 10min at 4°C and the postnuclear supernatant was layered onto a 60% sucrose cushion and centrifuged at 100 000 x g for 45min. The membranes were collected using a pasteur pipette and layered on a preformed 15 to 60% sucrose gradient and spun at 100 000 x g for 17hrs. Proteins from the fractionated sucrose gradient were run on a 4-20% 1 D gel (Novex) and subject to western blotting; those fractions containing alkaline phosphatase and transferrin immunoreactivity but not oxidoreductase II or calnexin immunoreactivity were pooled and represented the plasma membrane fraction.

1c - Preparation of plasma membrane fractions for 1D-gel analysis

Plasma membrane fractions were pooled and diluted at least four times with 10mM HEPES, 1 mM EDTA 1 mM Vanadate, 0.02% Azide. The diluted sucrose fraction was added to a SW40 or SW60 tube and centrifuged at 100 000 x g for 45min with slow acceleration and deceleration. The supernatant was removed from the membrane pellet and the pellet washed three times with PBS-CM. The membrane pellet was solubulized in 2% SDS in 63mM TrisHCI, pH 7.4. A protein assay was performed followed by the addition of mercaptoethanol (2% final), glycerol (10%) and bromopheneol blue (0.0025% final) was added. A final protein concentration of 1 μg/μl was used for 1 D-gel loading. 1d - 1 D-gel technology

Protein or membrane pellets were solubilised in 1 D-sample buffer (approximately 1 mg/ml) and the mixture heated to 95°C for 5min.

Samples were separated using 1 D-gel electrophoresis on pre-cast 8-16% gradient gels purchased from Bio-Rad (Bio-Rad Laboratories, Hemel Hempstead, UK). A sample containing 30-50 micrograms of the protein mixtures obtained from a detergent extract were applied to the stacking gel wells using a micro-pipette. A well containing molecular weight (10, 15, 25, 37, 50, 75, 100, 150 and 250 kDa) was included for calibration by interpolation of the separating gel after imaging. Separation of the proteins was performed by applying a current of 30mA to the gel for approximately 5hrs, or until the bromophenol blue marker dye had reached the bottom of the gel.

After electrophoresis the gel plates were prised open, the gel placed in a tray of fixer (10% acetic acid, 40% ethanol, 50% water) and shaken overnight. The gel was then primed for 30min by shaking in a primer solution (7.5% acetic acid, 0.05% SDS in Milli-Q water) followed by incubation with a fluorescent dye (0.06% OGS dye in 7.5% acetic acid) with shaking for 3 hrs. An example of a fluorescent dye is disclosed in US 6,335,446. Sypro Red (Molecular Probes, Inc., Eugene, Oregon) is a suitable alternative dye for this purpose.

A digital image of the stained gel was obtained by scanning on a Storm Scanner (Molecular Dynamics Inc, USA) in the blue fluorescence mode. The captured image was used to determine the area of the gel to excise for in-gel proteolysis.

1e - Recovery and analysis of selected proteins

Each vertical lane of the gel was excised using either a stainless steel scalpel blade or a PEEK gel cutter that cuts sequentially down the length of the gel lane with no attempt at collecting specific protein bands.

Proteins were processed using in-gel digestion with trypsin (Modified trypsin, Promega, Wisconsin, USA) to generate tryptic digest peptides. Recovered samples were divided into two. Prior to MALDI analysis samples were desalted and concentrated using C18 Zip Tips™ (Millipore, Bedford, MA). Samples for tandem mass spectrometry were purified using a nano LC system (LC Packings, Amsterdam, The Netherlands) incorporating C18 SPE material. Recovered peptide pools were analysed by MALDI-TOF-mass spectrometry (Voyager STR, Applied Biosystems, Framingham, MA) using a 337 nm wavelength laser for desorption and the reflectron mode of analysis. Pools were also analysed by nano-LC tandem mass spectrometry (LC/MS/MS) using a Micromass Quadrupole Time-of-Flight (Q-TOF) mass spectrometer (Micromass, Altrincham, UK). For partial amino acid sequencing and identification of BCMPs uninterpreted tandem mass spectra of tryptic peptides were searched against a database of public domain proteins constructed of protein entries in the non-redundant database held by the National Centre for Biotechnology Information (NCBI) which is accessible at http://www.ncbi.nlm.nih.gov/ using the SEQUEST search program (Eng et al., 1994, J. Am. Soc. Mass Spectrom. 5:976-989), version v.C.1. Criteria for database identification included: the cleavage specificity of trypsin; the detection of a suite of a, b and y ions in peptides returned from the database, and a mass increment for all Cys residues to account for carbamidomethylation. Following identification of proteins through spectral-spectral correlation using the SEQUEST program, masses detected in MALDI-TOF mass spectra were assigned to tryptic digest peptides within the proteins identified. In cases where no amino acid sequences could be identified through searching with uninterpreted MS/MS spectra of tryptic digest peptides using the SEQUEST program, tandem mass spectra of the peptides were interpreted manually, using methods known in the art. (In the case of interpretation of low-energy fragmentation mass spectra of peptide ions see Gaskell et al., 1992, Rapid Commun. Mass Spectrom. 6:658-662). The method described in WO 02/21139 was also used to interpret mass spectra.

RESULTS

The BCMPs disclosed herein have been identified in membrane protein extracts of human breast cancer-derived cell lines separated generally using 1 D-gel electrophoresis and tryptic digest of membrane protein extracts of human breast cancer-derived cell lines. Peptide sequences were compared to the SWISS-PROT and trEMBL databases (held by the Swiss Institute of Bioinformatics (SIB) and the European Bioinformatics Institue (EBI) which are available at http://www.expasy.com/) and the GenBank database (held by the National Institute of Health (NIH) which is available at http://www.ncbi.nlm.nih.gov/GenBank/) and corresponding genes identified. Published reports and databases, including databases of proteins expressed in normal human breast luminal epithelial cells (Page et al., Proc Natl Acad Sci U S A. 1999 96(22): 12589-94; EP1208381 ) were searched to establish whether the products of any of the identified genes had been previously demonstrated to be expressed in the membrane of human breast cells or human breast cancer cells. Two groups of BCMPs have been identified: (1) 416 BCMP polypeptides which matched known proteins not previously been described in breast cell membranes (Table 1 ); (2) 131 BCMP polypeptide sequences (Table 2) matching conceptual translations of cDNAs for which no protein or biological function has been described, for which the present invention defines the existence of the protein product and its localisation in the membranes of human breast cancer cells; and which the present invention shows may be additionally involved in human breast cancer. All of the BCMPs find utility as markers for breast cells, especially breast cancer cells. Each protein in Tables 1 and 2 is identified by a Swiss Prot or a Genbank Accession Number, or the sequences correspond to novel polypeptides. The apparent molecular weight and the amino acid sequences of tryptic digest peptides of these BCMPs identified by tandem mass spectrometry and database searching as described in the Examples, infra, are also listed in these Tables. Table 1. Known proteins which have not previouslv been described in breast cell membranes

Table 2. Protein sequences matching conceptual translations of cDNAs or genes for which no protein or biological function has been described

Claims

CLAIMS:

1. A method of screening for and/or diagnosis of breast cancer in a subject, and/or monitoring the effectiveness of breast cancer therapy, which comprises the step of detecting and/or quantifying in a biological sample obtained from said subject:

(i) a BCMP polypeptide which: a) comprises an amino acid sequence of any one of SEQ ID NOS: 1 -547; b) is a derivative of a) having one or more amino acid substitutions, modifications, deletions or insertions, and which retains the activity of the BCMP polypeptide; or c) is a fragment of a polypeptide of a) or b), which is at least ten amino acids long and has at least 70% homology over the length of the fragment; or

(ii) a nucleic acid molecule which: d) comprises a DNA sequence which codes for a BCMP polypeptide as defined in a), or its RNA equivalent; e) has a sequence which is complementary to the sequences of d); f) has a sequence which codes for a BCMP polypeptide as defined in b) or c); g) has a sequence which shows substantial identity with any of those of d), e) and f); or h) is a fragment of d), e), f) or g), which is at least ten nucleotides in length.

2. The method of claim 1 , wherein the level of said polypeptide or said nucleic acid is compared to a previously determined reference range or control.

3. The method according to claim 1 or 2, wherein the step of detecting comprises:

(a) contacting the sample with a capture reagent that is specific for a polypeptide as defined in claim 1 (i); and

(b) detecting whether binding has occurred between the capture reagent and said polypeptide in the sample.

4. The method according to claim 3, wherein step (b) comprises detecting the captured polypeptide using a directly or indirectly labelled detection reagent.

5. The method according to claim 3 or 4, wherein the capture reagent is immobilised on a solid phase.

6. An antibody, functionally-active fragment, derivative or analogue thereof, that specifically binds to one or more BCMP polypeptides as defined in claim 1 (i).

7. The method according to anyone of claims 1 to 5, wherein the polypeptide is detected and/ or quantified using an antibody that specifically binds to one or more BCMP polypeptides as defined in claim 1 (i).

8. An antibody according to claim 6 or the method of claim 7, wherein the antibody is monoclonal, polyclonal, chimeric, humanised or bispecific, or is conjugated to a therapeutic moiety, detectable label, second antibody or a fragment thereof, a cytotoxic agent or cytokine.

9. A diagnostic kit comprising a capture reagent specific for a BCMP polypeptide as defined in claim 1 (i), reagents and instructions for use.

10. The use of:

(i) a BCMP polypeptide as defined in claim 1 (i); (ii) a nucleic acid molecule as defined in claim 1 (ii); or (iii) an antibody as defined in claims 6 or 8; in the manufacture of a medicament for the treatment of breast cancer.

11. The use as claimed in claim 10(i), wherein the composition is a vaccine.

12. A method of screening for anti-breast cancer agents that interact with a BCMP polypeptide as defined in claim 1 (i), said method comprising:

(a) contacting said polypeptide with a candidate agent; and

(b) determining whether or not the candidate agent interacts with said polypeptide.

13. The method according to claim 12, wherein the determination of interaction between the candidate agent and BCMP polypeptide comprises quantitatively detecting binding of the candidate agent and said polypeptide.

14. A method of screening for anti-breast cancer agents that modulate:

(a) the expression or activity of a BCMP polypeptide as defined in claim 1 (i), or

(b) the expression of a nucleic acid molecule as defined in claim 1 (ii), comprising:

(i) comparing the expression or activity of said polypeptide, or the expression of said nucleic acid molecule, in the presence of a candidate agent with the expression or activity of said polypeptide, or the expression of said nucleic acid molecule, in the absence of the candidate agent or in the presence of a control agent; and

(ii) determining whether the candidate agent causes the expression or activity of said polypeptide, or the expression of said nucleic acid molecule, to change.

15. The method of claim 14, wherein the expression or activity level of said polypeptide, or the expression level of said nucleic acid molecule is compared with a predetermined reference range.

16. The method of claim 14 or 15, wherein part (ii) additionally comprises selecting an agent which modulates the expression or activity of said polypeptide, or the expression of said nucleic acid molecule for further testing, or therapeutic or prophylactic use as an anti- breast cancer agent.

17. An agent identified by the method of any of claims 12-14, which interacts with or causes the expression or activity of said polypeptide, or the expression of said nucleic acid molecule, to change.

18. The use of an agent which interacts with or causes a change in the expression or activity of a BCMP polypeptide or the expression of a BCMP nucleic acid as defined in claim 1 , in the manufacture of a medicament for the treatment of breast cancer.