AU7067498A - Brca2 transcriptional activator domain and uses thereof - Google Patents

Description

WO98/48013 PCT/GB98/01181 1 BRCA2 TRANSCRIPTIONAL ACTIVATOR DOMAIN AND USES THEREOF The present invention provides polypeptides, nucleic acid encoding the polypeptides, substances which interact 5 with the polypeptides, oligonucleotide probes and primers, and various methods and uses thereof. In particular it relates to transcriptional activator polypeptides and substances which modulate their activity. It is founded on the surprising discovery, supported by clear experimental 10 data, that portions of the polypeptide encoded by the tumour suppressor gene, BRCA2 (Tavtigian, S.V., Simard, J., Rommens, J., Couch, F. Shattuck-Eidens, D., et al. (1996), Nat. Genet. 12, 333-337), have transcriptional activation capacity, and that these portions are flanked in full-length polypeptide by 15 regions which interact with inhibitor molecules which inhibit transcriptional activation. Experimental evidence is also provided showing that a mutation that is associated with familial breast cancer and is within the transcriptional activator domain severely reduces activation of 20 transcription. Furthermore, molecules (polypeptide domains) which interact with this region of the BRCA2 polypeptide have been identified experimentally and may be used to modulate transcriptional activation.

WO98/48013 PCT/GB98/01181 2 Figure 1 shows that sequences within exon 3 of BRCA2 show sequence similarity to the activation domain of c-jun. Below the alignment is the exon structure of the BRCA2 protein. Various portions of BRCA2 are shown below, along 5 with relative figures for transcription activation when fused to the GAL4 DNA binding domain (1-147), compared with the activity of the GAL4 DNA binding domain alone. The results represent an average of several independent experiments, of which details are provided below. 10 Figure 2 shows the protein and DNA sequence of residues 1-197 of BRCA2, including the various domains and regions employed in aspects and embodiments of the present invention. A mutation of tyr to cys at residue 42 is indicated, such mutation being associated with familial breast cancers (3). 15 Nordling et al.(10) have also reported (after the priority date of the present invention) that a large deletion which disrupts the exon 3 transcription activator domain of BRCA2 is the disease-causing mutation in a Swedish breast/ovarian cancer family. 20 Figure 3 shows the amino acid and DNA sequence of a portion of the protein named "BBPl" (BRCA2 Binding Protein-l) found to interact with the BRCA2 TAD and to modulate its transcriptional activation.

WO98/48013 PCT/GB98/01181 3 Figure 4 shows a portion of the BBP1 protein and encoding DNA expressed and demonstrated to interact with BRCA2 TAD, modulating its transcriptional activation. 5 According to a first aspect of the present invention there is provided a polypeptide which has the amino acid sequence of a fragment of BRCA2 protein and which is able to act as transcriptional activator. Further aspects provide use of such a polypeptide in activating transcription and 10 methods of activating transcription which employ such a polypeptide. A fragment of BRCA2 according to the present invention may in some embodiments have less than about 300 amino acids, less than about 200 amino acids, less than about 150 amino 15 acids, less than about 120 amino acids, less than about 100 amino acids, or less than about 70 amino acids. Generally in order for a polypeptide to have transcriptional activator function requires a DNA binding domain which recognises a site within a promoter sequence. 20 Thus, polypeptides according to this aspect of the present invention may include or be fused or otherwise operably linked to a DNA binding domain, which may be heterologous or foreign to BRCA2, e.g. being of a polypeptide such as GAL4, WO98/48013 PCT/GB98/01181 4 or LexA or any suitable example, of which many are known and in standard use in the art. See e.g. "Gene regulation" by David Latchman, published by Unwin Hyman Ltd (1990). There are many examples of transcription activation 5 domains being fused to DNA binding domains of polypeptides such as GAL4, in order to study and/or manipulate transcriptional activation. For instance, Martin et al. (Nature (1995) 375: 691-694) fused activation domain portions of E2F1 to the DNA binding domain of GAL4, to study 10 interaction with MDM2, while Brown et al. (The EMBO J. (1995) 14 (1): 124-131) fused portions of c-Fos protein to the DNA binding domain of GAL4, to investigate transcriptional activation and particularly silencing of such activation on inclusion of inhibitory domains within the fusion protein. 15 A polypeptide according to the present invention may include or consist essentially of amino acids 18-105 or 23 105 of the human BRCA2 polypeptide (residue 23 is the boundary of exon 3), the sequences of which are shown in Figure 2, or an amino acid sequence which is a fragment, 20 mutant, variant, allele or derivative thereof. For instance, particular embodiments of the present invention may make individual use of the two fragments of the exon 3 activation domain demonstrated experimentally as described below to have WO98/48013 PCT/GB98/01181 5 the ability to activate transcription, i.e. the fragment which is amino acids 18 to 60 (shown to be a primary activating region) and the fragment which is amino acids 60 to 105 (shown to be an auxiliary activating region). Other 5 fragments within the fragment of BRCA2 residues 18-105 may be employed as transcription activators provided they retain the ability to so function. Alanine scanning and other techniques of systematic alteration and/or fragmentation of a polypeptide may be used to identify regions and/or residues 10 functionally involved or required. Instead of using a wild-type BRCA2 fragment, the polypeptide may include an amino acid sequence which differs by one or more amino acid residues from the wild-type amino acid sequence, by one or more of addition, insertion, 15 deletion and substitution of one or more amino acids. Thus, variants, derivatives, alleles, mutants and homologues, e.g. from other organisms, are included. Preferably, the amino acid sequence shares homology with the sequence or Figure 2, preferably at least about 30%, or 20 40%, or 50%, or 60%, or 70%, or 75%, or 80%, or 85% homology, or at least about 90% or 95% homology. As is well-understood, homology at the amino acid level is generally in terms of amino acid similarity or identity.

WO98/48013 PCT/GB98/01181 6 Similarity allows for "conservative variation", i.e. substitution of one hydrophobic residue such as isoleucine, valine, leucine or methionine for another, or the substitution of one polar residue for another, such as 5 arginine for lysine, glutamic for aspartic acid, or glutamine for asparagine. Similarity may be as defined and determined by the TBLASTN program, of Altschul et al. (1990) J. Mol. Biol. 215: 403-10, which is in standard use in the art, or more preferably using the algorithm GAP (Genetics Computer 10 Group, Madison, WI). GAP uses the Needleman and Wunsch algorithm to align two complete sequences that maximizes the number of matches and minimizes the number of gaps. Generally, the default parameters are used, with a gap creation penalty = 12 and gap extension penalty = 4. Use of 15 either of the terms "homology" and "homologous" herein does not imply any necessary evolutionary relationship between compared sequences, in keeping for example with standard use of terms such as "homologous recombination" which merely requires that two nucleotide sequences are sufficiently 20 similar to recombine under the appropriate conditions. Homology may be over the full-length of the relevant polypeptide or may more preferably be over a contiguous sequence of about 15, 20, 25, 30, 40, 50 or more amino acids, WO98/48013 PCTGB98/01181 7 compared with the relevant wild-type amino acid sequence. Preferred polypeptides may include a transcriptional activation domain with at least about 50%, 60%, 70%, 80%, 85%, 90% or 95% identity with that of BRCA2 exon 3, as shown 5 in Figure 2, or the fragment which is amino acids 18 to 60, or the fragment which is amino acids 60 to 105. At the nucleic acid level sequence identity may be assessed by means of hybridization of molecules under stringent conditions. The present invention extends to 10 nucleic acid that hybridizes with any one or more of the specific sequences disclosed herein under stringent conditions. Suitable conditions include, e.g. for detection of sequences that are about 80-90% identical, hybridization overnight at 42 0 C in 0.25M Na 2

HPO

4 , pH 7.2, 6.5% SDS, 10% 15 dextran sulfate and a final wash at 55 0 C in 0.1X SSC, 0.1% SDS. For detection of sequences that are greater than about 90% identical, suitable conditions include hybridization overnight at 65 0 C in 0.25M Na 2

HPO

4 , pH 7.2, 6.5% SDS, 10% dextran sulfate and a final wash at 60 0 C in 0.1X SSC, 0.1% 20 SDS. For convenience herein, the residues 18-105 fragment of BRCA2 polypeptide is referred to as the BRCA2 transcription activation domain ("TAD"), the residues 18-60 fragment as the WO98/48013 PCT/GB98/01181 8 BRCA2 primary activating region or "PAR", and the residues 60-105 as the BRCA2 auxiliary activating region or "AAR", bearing in mind that mutants, alleles, variants, derivatives and smaller fragments may be employed in the present 5 invention and are therefore generally encompassed by use of such terms in the description unless e.g. context requires otherwise. One or more additional portions of the BRCA2 polypeptide may be included, if desired. One such embodiment includes 10 the portion from residues 126 to 197, or a fragment, mutant, allele, variant or derivative thereof. In further embodiments of various aspects of the present invention, a polypeptide includes or consists essentially of the fragment of BRCA2 at residues 126 to 197, which may be used for 15 instance in looking for and/or obtaining substances which interact with it and which may have an effect on a BRCA2 function. Further experimental evidence included below indicates that within the BRCA2 polypeptide the transcription 20 activation domain of the invention, the TAD including the PAR and the AAR, is flanked by two "inhibitory regions" which are bound by molecules which inhibit activation of transcription by the TAD, as demonstrated experimentally and described WO98/48013 PCT/GB98/01181 9 below. The position of the two inhibitory regions is shown - in Figure 1 ("IR1" and "IR2"), with sequence information being given in Figure 2. Further polypeptides according to the present invention 5 include IR1 and/or IR2 in addition to the TAD. Of course, mutant, allele, derivative or variant sequences, or fragments, may be used instead of the wild-type sequence shown. As discussed below, a polypeptide which includes IR1 and/or IR2 with the BRCA2 TAD may be used in the 10 identification and isolation of molecules which interact with or bind the inhibitory regions to inhibit transcriptional activation by the TAD, and substances which interfere with such interaction or binding and/or inhibition of transcriptional activation. Also, peptides including or 15 consisting essentially of all or part of the IR1 and IR2 sequences may be used similarly in the identification and isolation of molecules which interact or bind, preferably which inhibit transcriptional activation by the TAD upon interaction or binding, and in the identification and 20 isolation of molecules which interfere with such interaction or binding to modulate inhibition of activation of transcription by the TAD. Inhibitor domains have been shown to be present in a WO98/48013 PCT/GB98/01181 10 number of transcription factors (references 4, 5, 6 below). - In c-Fos and others there is evidence that the inhibitor is functioning by binding a protein or proteins to mediate repression of transcriptional activation. This evidence 5 comes from "squelching" experiments in which the inhibitor domain was added in excess to compete away any potential repressor protein (4). Similar experiments may be performed using polypeptides and peptides of the present invention. Addition of BRCA2 IR1 and/or IR2 peptides in excess may 10 increase the activation capacity of inactive BRCA2 fragment residues 1-125. There are other instances where an inhibitor domain functions via intra-molecular interaction which "masks" the activation domain. As discussed more fully below, assay methods and means, for example using a high 15 throughput screen, may be used to find molecules which activate BRCA2 transcriptional activation, which may do this by binding the inhibitor domain and preventing an intra molecular interaction. A peptide according to a further aspect of the invention 20 may include or consist essentially of the IR1 and/or IR2 sequences shown in Figure 2. Where additional amino acids are included, which amino acids may be from BRCA2 (so that the peptide is a larger fragment of BRCA2) or may be WO98/48013 PCT/GB98/01181 11 heterologous or foreign to BRCA2, the peptide may be about -20, 25, 30 or 35 amino acids in length. A peptide according to this aspect may be included within a larger fusion protein, particularly where the peptide is fused to a non 5 BRCA2 (i.e. heterologous or foreign) sequence, such as a polypeptide or protein domain. Further similar aspects relate in the same or similar terms to peptides including or consisting essentially of fragments of BBP1 (see below). 10 Various screening and assay formats employing polypeptides and peptides according to the present invention are discussed below. A convenient way of producing a polypeptide or peptide 15 according to the present invention is to express nucleic acid encoding it, by use of nucleic acid in an expression system. Accordingly the present invention also provides in various aspects nucleic acid encoding the polypeptides and peptides of the invention. (This includes "BBPl" (BRCA2 20 Binding Protein 1) discussed further below.) Generally, nucleic acid according to the present invention is provided as an isolate, in isolated and/or purified form, or free or substantially free of material with WO98/48013 PCT/GB98/01181 12 which it is naturally associated, such as free or substantially free of nucleic acid flanking the gene in the human genome, except possibly one or more regulatory sequence(s) for expression. Nucleic acid may be wholly or 5 partially synthetic and may include genomic DNA, cDNA or RNA. Where nucleic acid according to the invention includes RNA, reference to the sequence shown should be construed as encompassing the RNA equivalent, with U substituted for T. Nucleic acid sequences encoding a polypeptide in 10 accordance with the present invention can be readily prepared by the skilled person using the information and references contained herein and techniques known in the art (for example, see Sambrook, Fritsch and Maniatis, "Molecular Cloning, A Laboratory Manual, Cold Spring Harbor Laboratory 15 Press, 1989, and Ausubel et al, Short Protocols in Molecular Biology, John Wiley and Sons, 1992), given the nucleic acid sequence and clones available (e.g. Tavtigian, S.V., Simard, J., Rommens, J., Couch, F. Shattuck-Eidens, D., et al. (1996), Nat. Genet. 12, 333-337). These techniques include 20 (i) the use of the polymerase chain reaction (PCR) to amplify samples of such nucleic acid, e.g. from genomic sources, (ii) chemical synthesis, or (iii) preparing cDNA sequences. Modifications to the BRCA2 sequences can be made, e.g. using WO98/48013 PCT/GB98/01181 13 site directed mutagenesis, to lead to the expression of - modified BRCA2 polypeptide or to take account of codon preference in the host cells used to express the nucleic acid. 5 In order to obtain expression of the nucleic acid sequences, the sequences can be incorporated in a vector having one or more control sequences operably linked to the nucleic acid to control its expression. The vectors may include other sequences such as promoters or enhancers to 10 drive the expression of the inserted nucleic acid, nucleic acid sequences so that the polypeptide or peptide is produced as a fusion and/or nucleic acid encoding secretion signals so that the polypeptide produced in the host cell is secreted from the cell. Polypeptide can then be obtained by 15 transforming the vectors into host cells in which the vector is functional, culturing the host cells so that the polypeptide is produced and recovering the polypeptide from the host cells or the surrounding medium. Prokaryotic and eukaryotic cells are used for this purpose in the art, 20 including strains of E. coli, yeast, and eukaryotic cells such as COS or CHO cells. Thus, the present invention also encompasses a method of WO98/48013 PCT/GB98/01181 14 making a polypeptide or peptide (as disclosed), the method -including expression from nucleic acid encoding the polypeptide or peptide (generally nucleic acid according to the invention). This may conveniently be achieved by growing 5 a host cell in culture, containing such a vector, under appropriate conditions which cause or allow expression of the polypeptide. Polypeptides and peptides may also be expressed in in vitro systems, such as reticulocyte lysate. Systems for cloning and expression of a polypeptide in a 10 variety of different host cells are well known. Suitable host cells include bacteria, eukaryotic cells such as mammalian and yeast, and baculovirus systems. Mammalian cell lines-available in the art for expression of a heterologous polypeptide include Chinese hamster ovary cells, HeLa cells, 15 baby hamster kidney cells, COS cells and many others. A common, preferred bacterial host is E. coli. Suitable vectors can be chosen or constructed, containing appropriate regulatory sequences, including promoter sequences, terminator fragments, polyadenylation 20 sequences, enhancer sequences, marker genes and other sequences as appropriate. Vectors may be plasmids, viral e.g. 'phage, or phagemid, as appropriate. For further details see, for example, Molecular Cloning: a Laboratory WO98/48013 PCT/GB98/01181 15 Manual: 2nd edition, Sambrook et al., 1989, Cold Spring Harbor Laboratory Press. Many known techniques and protocols for manipulation of nucleic acid, for example in preparation of nucleic acid constructs, mutagenesis, sequencing, 5 introduction of DNA into cells and gene expression, and analysis of proteins, are described in detail in Current Protocols in Molecular Biology, Ausubel et al. eds., John Wiley & Sons, 1992. Thus, a further aspect of the present invention provides 10 a host cell containing heterologous nucleic acid as disclosed herein. The nucleic acid of the invention may be integrated into the genome (e.g. chromosome) of the host cell. Integration may be promoted by inclusion of sequences which promote 15 recombination with the genome, in accordance with standard techniques. The nucleic acid may be on an extra-chromosomal vector within the cell, or otherwise identifiably heterologous or foreign to the cell. A still further aspect provides a method which includes 20 introducing the nucleic acid into a host cell. The introduction, which may (particularly for in vitro introduction) be generally referred to without limitation as "transformation", may employ any available technique. For WO98/48013 PCT/GB98/01181 16 eukaryotic cells, suitable techniques may include calcium -phosphate transfection, DEAE-Dextran, electroporation, liposome-mediated transfection and transduction using retrovirus or other virus, e.g. vaccinia or, for insect 5 cells, baculovirus. For bacterial cells, suitable techniques may include calcium chloride transformation, electroporation and transfection using bacteriophage. As an alternative, direct injection of the nucleic acid could be employed. Marker genes such as antibiotic resistance or 10 sensitivity genes may be used in identifying clones containing nucleic acid of interest, as is well known in the art. The introduction may be followed by causing or allowing expression from the nucleic acid, e.g. by culturing host 15 cells (which may include cells actually transformed although more likely the cells will be descendants of the transformed cells) under conditions for expression of the gene, so that the encoded polypeptide (or peptide) is produced. If the polypeptide is expressed coupled to an appropriate signal 20 leader peptide it may be secreted from the cell into the culture medium. Following production by expression, a polypeptide or peptide may be isolated and/or purified from the host cell and/or culture medium, as the case may be, and WO98/48013 PCT/GB98/01181 17 subsequently used as desired, e.g. in the formulation of a Composition which may include one or more additional components, such as a pharmaceutical composition which includes one or more pharmaceutically acceptable excipients, 5 vehicles or carriers (e.g. see below). Introduction of nucleic acid may take place in vivo by way of gene therapy, as discussed below. A host cell containing nucleic acid according to the present invention, e.g. as a result of introduction of the 10 nucleic acid into the cell or into an ancestor of the cell and/or genetic alteration of the sequence endogenous to the cell or ancestor (which introduction or alteration may take place in vivo or ex vivo), may be comprised (e.g. in the soma) within an organism which is an animal, particularly a 15 mammal, which may be human or non-human, such as rabbit, guinea pig, rat, mouse or other rodent, cat, dog, pig, sheep, goat, cattle or horse, or which is a bird, such as a chicken. Genetically modified or transgenic animals or birds comprising such a cell are also provided as further aspects 20 of the present invention. This may have a therapeutic aim. (Gene therapy is discussed below.) Also, the presence of a mutant, allele, derivative or variant sequence within cells of an organism, WO98/48013 PCT/GB98/01181 18 particularly when in place of a homologous endogenous sequence, may allow the organism to be used as a model in testing and/or studying substances which modulate activity of the encoded polypeptide in vitro or are otherwise indicated 5 to be of therapeutic potential. Conveniently, however, assays for such substances may be carried out in vitro, within host cells or in cell-free systems. A polypeptide according to the present invention may be 10 used in screening for molecules which affect or modulate its activity or function. Such molecules may be useful in a therapeutic (possibly including prophylactic) context. Combinatorial library technology provides an efficient way of testing a potentially vast number of different substances for 15 ability to modulate bind to and/or activity of a polypeptide. Such libraries and their use are known in the art. The use of peptide libraries may be preferred in certain circumstances. In various further aspects the present invention relates 20 to screening and assay methods and means, and substances identified thereby. Thus, further aspects of the present invention provide WO98/48013 PCT/GB98/01181 19 the use of a polypeptide or peptide of the invention as disclosed, and/or encoding nucleic acid therefor, in screening or searching for and/or obtaining/identifying a substance, e.g. peptide or chemical compound, which interacts 5 and/or binds with the polypeptide or peptide and/or interferes with its function or activity or that of another substance, e.g. polypeptide or peptide, which interacts and/or binds with the polypeptide or peptide of the invention. For instance, a method according to one aspect of 10 the invention includes providing a polypeptide or peptide of the invention and bringing it into contact with a substance, which contact may result in binding between the polypeptide or peptide and the substance. Binding may be determined by any of a number of techniques available in the art, both 15 qualitative and quantitative. In various aspects the present invention is concerned with provision of assays for substances which inhibit interaction between the BRCA2 IR1 and IR2 peptide motifs (discussed above) and the inhibitory molecule or molecules 20 which bind these regions to inhibit transcriptional activation by the TAD. Further assays are for substances which interact with or bind the TAD and/or modulate its ability to activate WO98/48013 PCT/GB98/01181 20 transcription. A protein termed "BBP1" (BRCA2 Binding Protein-1) has been found to interact with the BRCA2 TAD, specifically the PAR. A domain of BBP1 was expressed (see experimental 5 section) and shown to repress activity of the BRCA2 TAD. Assays of the invention may therefore use the BRCA2 TAD, or suitable fragment thereof, and BBP1, or suitable fragment thereof, in obtaining substances able to interfere with their interaction and/or modulate the effect of BBP1 on BRCA2 10 transcription activation. As noted, the IR1 and IR2 peptides of the invention and polypeptides including one or more of these may be used in screening for and obtaining the inhibitory molecules which interact or bind IR1 and/or IR2 within BRCA2 in vivo to 15 inhibit transcriptional activation. A substance which binds the TAD may inhibit transcriptional activation, or may stimulate and/or enhance it. For instance, it is known that c-Jun transcriptional activator function is stimulated by phosphorylation of the 20 active site by a kinase (Jun N-terminal kinase, Jnk). A phosphorylase removes the phosphate to deactivate the transcriptional activator function. A molecule that inhibits or prevents the dephosphorylation may be used to enhance WO98/48013 PCT/GB98/01181 21 transcriptional activation. Such a molecule may include a binding portion of the kinase. As discussed elsewhere herein, the BRCA2 TAD has significant sequence homology with the TAD of Jun and a kinase is able to bind it. Thus, a 5 kinase which operates on the BRCA2 TAD, or a BRCA2 TAD binding portion of the kinase, has been obtained and used to modulate transcriptional activation. Phosphorylation may be determined for example by immobilising a BRCA2 fragment, mutant, variant or derivative 10 thereof, e.g. on a bead or plate, and detecting phosphorylation using an antibody or other binding molecule which binds the relevant site of phosphorylation with a different affinity when the site is phosphorylated from when the site is not phosphorylated. Such antibodies may be 15 obtained by means of any standard technique as discussed elsewhere herein, e.g. using a phosphorylated peptide (such as a fragment of BRCA2). Binding of a binding molecule which discriminates between the phosphorylated and non phosphorylated form of BRCA2 or relevant fragment, mutant, 20 variant or derivative thereof may be assessed using any technique available to those skilled in the art, which may involve determination of the presence of a suitable label, such as fluorescence. Phosphorylation may be determined by WO98/48013 PCT/GB98/01181 22 immobilisation of BRCA2 or a fragment, mutant, variant or derivative thereof, on a suitable substrate such as a bead or plate, wherein the substrate is impregnated with scintillant, such as in a standard scintillation proximetry assay, with 5 phosphorylation being determined via measurement of the incorporation of radioactive phosphate. Phosphate incorporation into BRCA2 or a fragment, mutant, variant or derivative thereof, may be determined by precipitation with acid, such as trichloroacetic acid, and collection of the 10 precipitate on a suitable material such as nitrocellulose filter paper, followed by measurement of incorporation of radiolabeled phosphate. SDS-PAGE separation of substrate may be employed followed by detection of radiolabel. 15 As described below, the present inventors have obtained in their experimental work substances, in particular polypeptide domains, which interact with BRCA2 polypeptide fragments in accordance with the present invention. 20 Another aspect of the present invention provides an assay (A) which includes: (a) bringing into contact a polypeptide or peptide according to the invention including BRCA2 IR1 and/or IR2 as WO98/48013 PCT/GB98/01181 23 disclosed, and a putative binding molecule or other test substance; and (b) determining interaction or binding between the polypeptide or peptide and the test substance. 5 A substance which interacts with or binds to the BRCA2 TAD, IR1 and/or IR2 may be isolated and/or purified, manufactured and/or used to modulate transcriptional activation as discussed. 10 In another aspect, the present invention provides an assay (B) which includes: (a) bringing into contact a polypeptide according to the present invention, including a BRCA2 TAD and optionally a 15 IR1 and/or IR2 and a DNA binding domain capable of binding a nucleotide sequence within a promoter, and a putative inhibitor compound under conditions where the polypeptide, in the absence of inhibitor, is capable of binding the nucleotide sequence within the promoter to activate 20 transcription; (b) providing a nucleic acid molecule which includes a promoter which includes the nucleotide sequence to which the polypeptide is capable of binding to activate transcription WO98/48013 PCT/GB98/01181 24 of a sequence operably linked to the promoter; and (c) measuring the degree of modulation or alteration of transcriptional activation caused by said inhibitor compound. 5 A compound which increases the level of transcriptional activation, particularly, when IR1 and IR2 are not included may be useful in enhancing transcriptional activation by BRCA2 TAD, which has therapeutic potential given BRCA2's role as a tumour suppressor and the experimental evidence 10 described below on the effect of a mutation within the BRCA2 TAD which is associated with familial breast cancer on decreasing BRCA2 TAD transcriptional activation. A compound which binds IR1 and/or IR2 may inhibit transcriptional activation by the polypeptide. Thus, 15 inhibition of transcriptional activation allows for identification of molecules which bind IR1 and/or IR2, including a natural ligand. A molecule which binds IR1 and/or IR2 in vivo, e.g. a molecule naturally present in a mammalian, e.g. human, tumour 20 (e.g. breast tumour) or non-tumour cell, and preferably a molecule which inhibits transcriptional activation by the BRCA2 TAD, obtainable using assay (A) or assay (B) may be isolated and may be manufactured, and may be subsequently WO98/48013 PCT/GB98/01181 25 used to assay for substances which interfere with its binding to IR1 and/or IR2 within BRCA2 polypeptide and/or ability to inhibit BRCA2 TAD transcriptional activation. 5 Thus, a further aspect of the invention employs a peptide or polypeptide which includes BRCA2 IR1 and/or IR2 (bearing in mind these terms always, unless context requires otherwise, allow for the use of a mutant, variant, derivative, allele or fragment) and a molecule obtainable by 10 assay (A) or assay (B) which binds IR1 or IR2 in an assay for substances which interfere with such binding and may therefore inhibit inhibition of the transcriptional activation capacity of the BRCA2 TAD. Such an assay may include bringing into contact a 15 peptide or polypeptide including a IR1 or IR2 sequence and a binding molecule for the IR1 or IR2 sequence (such as obtainable by means of assay (A) or assay (B)) in the presence of a test substance, wherein the test conditions are such that in the absence of a substance able to interfere 20 with binding between the IR1 and/or IR2 sequence and the binding molecule such binding occurs, and determining binding between the IR1 and/or IR2. This may be followed by isolation and/or manufacture and/or use of a substance which WO98/48013 PCT/GB98/01181 26 tests positive for ability to interefere with the binding of interest. It is not necessary to use the entire proteins for 5 assays of the invention which test for binding between two molecules. Fragments may be generated and used in any suitable way known to those of skill in the art. Suitable ways of generating fragments include, but are not limited to, recombinant expression of a fragment from encoding DNA. Such 10 fragments may be generated by taking encoding DNA, identifying suitable restriction enzyme recognition sites either side of the portion to be expressed, and cutting out said portion from the DNA. The portion may then be operably linked to a suitable promoter in a standard commercially 15 available expression system. Another recombinant approach is to amplify the relevant portion of the DNA with suitable PCR primers. Small fragments (up to about 20 or 30 amino acids) may also be generated using peptide synthesis methods which are well known in the art. 20 For example, in a preferred embodiment of the invention a polypeptide may be fused to a heterologous DNA binding domain such as that of the yeast transcription factor GAL 4. The GAL 4 transcription factor includes two functional WO98/48013 PCTGB98/01181 27 domains. These domains are the DNA binding domain (GAL4DBD) and the GAL4 transcriptional activation domain (GAL4TAD). By fusing one polypeptide or peptide to one of those domains and another polypeptide or peptide to the respective counterpart, 5 a functional GAL 4 transcription factor is restored only when two polypeptides or peptides of interest interact. Thus, interaction of the polypeptides or peptides may be measured by the use of a reporter gene probably linked to a GAL 4 DNA binding site which is capable of activating transcription of 10 said reporter gene. This assay format is described by Fields and Song, 1989, Nature 340A; 245-246. This type of assay format can be used in both mammalian cells and in yeast. Other combinations of DNA binding domain and transcriptional activation domain are available in the art and may be 15 preferred, such as the LexA DNA binding domain and the VP60 transcriptional activation domain. The precise format of the assay of the invention may be varied by those of skill in the art using routine skill and knowledge. For example, the interaction between the 20 polypeptides may be studied in vitro by labelling one with a detectable label and bringing it into contact with the other which has been immobilised on a solid support. Suitable detectable labels include 35 S-methionine which may be WO98/48013 PCT/GB98/01181 28 incorporated into recombinantly produced peptides and polypeptides. Recombinantly produced peptides and polypeptides may also be expressed as a fusion protein containing an epitope which can be labelled with an antibody. 5 The protein which is immobilized on a solid support may be immobilized using an antibody against that protein bound to a solid support or via other technologies which are known per se. A preferred in vitro interaction may utilise a fusion protein including glutathione-S-transferase (GST). 10 This may be immobilized on glutathione agarose beads. In an in vitro assay format of the type described above a test compound can be assayed by determining its ability to diminish the amount of labelled peptide or polypeptide which binds to the immobilized GST-fusion polypeptide. This may be 15 determined by fractionating the glutathione-agarose beads by SDS-polyacrylamide gel electrophoresis. Alternatively, the beads may be rinsed to remove unbound protein and the amount of protein which has bound can be determined by counting the amount of label present in, for example, a suitable 20 scintillation counter. An assay according to the present invention may also take the form of an in vivo assay. The in vivo assay may be performed in a cell line such as a yeast strain in which the WO98/48013 PCT/GB98/01181 29 relevant polypeptides or peptides are expressed from one or more vectors introduced into the cell. A further assay according to the present invention tests 5 for ability of a substance to modulate transcriptional activation by BRCA2 TAD, e.g. by inhibiting interaction of IR1 and/or IR2 with a binding molecule or respective binding molecules (such as one or more ligands obtainable by assay (A) or assay (B)) which inhibit such transcriptional 10 activation. Such an assay may involve: (a) bringing into contact a polypeptide according to the present invention, including a BRCA2 TAD and a IR1 and/or IR2 and a DNA binding domain capable of binding a nucleotide 15 sequence within a promoter, a binding molecule or molecules for IR1 and/or IR2 which inhibit(s) transcriptional activation by the BRCA2 TAD, and a test compound, under conditions in which the binding molecule or molecule(s) for IR1 and/or IR2 inhibit(s) transcriptional activation of the 20 promoter by the BRCA2 TAD,; (b) providing a nucleic acid molecule which includes a promoter which includes the nucleotide sequence to which the polypeptide is capable of binding to activate transcription WO98/48013 PCT/GB98/01181 30 of a sequence operably linked to the promoter when the polypeptide is not bound by the IR1 and/or IR2 binding molecule or molecules; and (c) measuring the degree of modulation or alteration of 5 transcriptional activation caused by said test compound. A reporter gene construct including a promoter which includes a nucleotide sequence to which the DNA binding domain binds, operably linked to a reporter gene, may be 10 introduced into an expression system such as a cell together with one or more expression vectors encoding polypeptide or peptide components of an assay according to the present invention. Two or more binding sites (for example 3, 4 or 5) may be present in the nucleic acid construct and this may 15 enhance sensitivity of the assay. By "promoter" is meant a sequence of nucleotides from which transcription may be initiated of DNA operably linked downstream (i.e. in the 3' direction on the sense strand of double-stranded DNA). 20 "Operably linked" in the context of a sequence of interest and a promoter means joined as part of the same nucleic acid molecule, suitably positioned and oriented for transcription to be initiated from the promoter. DNA WO98/48013 PCT/GB98/01181 31 operably linked to. a promoter is "under transcriptional -initiation regulation" of the promoter. "Promoter activity" is used to refer to ability to initiate transcription. The level of promoter activity is 5 quantifiable for instance by assessment of the amount of mRNA produced by transcription from the promoter or by assessment of the amount of protein product produced by translation of mRNA produced by transcription from the promoter. The amount of a specific mRNA present in an expression system may be 10 determined for example using specific oligonucleotides which are able to hybridise with the mRNA and which are labelled or may be used in a specific amplification reaction such as the polymerase chain reaction. Use of a reporter gene facilitates determination of promoter activity by reference 15 to protein production. Generally, the gene may be transcribed into mRNA which may be translated into a peptide or polypeptide product which may be detected and preferably quantitated following expression. A gene whose encoded product may be assayed 20 following expression is termed a "reporter gene", i.e. a gene which "reports" on promoter activity. A reporter gene preferably encodes an enzyme which catalyses a reaction which produces a detectable signal, WO98/48013 PCT/GB98/01181 32 preferably a visually detectable signal, such as a coloured -product. Many examples are known, including P-galactosidase and luciferase. P-galactosidase activity may be assayed by production of blue colour on substrate, the assay being by 5 eye or by use of a spectrophotometer to measure absorbance. Fluorescence, for example that produced as a result of luciferase activity, may be quantitated using a spectrophotometer. Radioactive assays may be used, for instance using chloramphenicol acetyltransferase, which may 10 also be used in non-radioactive assays. The presence and/or amount of gene product resulting from expression from the reporter gene may be determined using a molecule able to bind the product, such as an antibody or fragment thereof. The binding molecule may be labelled directly or indirectly using 15 any standard technique. Those skilled in the art are well aware of a multitude of possible reporter genes and assay techniques which may be used to determine gene activity. Any suitable reporter/assay may be used and it should be appreciated that no particular 20 choice is essential to or a limitation of the present invention. A method of screening for ability of a substance to modulate activity of a promoter may include contacting an WO98/48013 PCT/GB98/01181 33 expression system, such as a host cell, containing assay components as herein disclosed with a test or candidate substance and determining expression of the heterologous gene. 5 The level of expression in the presence of the test substance may be compared with the level of expression in the absence of the test substance. A difference in expression in the presence of the test substance indicates ability of the substance to modulate gene expression. An increase in 10 expression of the gene compared with expression of another gene not linked to a promoter as disclosed herein indicates specificity of the substance for modulation of the promoter. A promoter construct may be introduced into a cell line using any technique previously described to produce a stable 15 cell line containing the reporter construct integrated into the genome. The cells may be grown and incubated with test compounds for varying times. The cells may be grown in 96 well plates to facilitate the analysis of large numbers of compounds. The cells may then be washed and the reporter 20 gene expression analysed. For some reporters, such as luciferase the cells will be lysed then analysed. Following identification of a substance which modulates or affects promoter activity, the substance may be WO98/48013 PCT/GB98/01181 34 investigated further. Furthermore, it may be manufactured - and/or used in preparation, i.e. manufacture or formulation, of a composition such as a medicament, pharmaceutical composition or drug. These may be administered to 5 individuals. The amount of test substance or compound which may be added to an assay of the invention will normally be determined by trial and error depending upon the type of 10 compound used. Typically, from about 0.01 to 100 nM concentrations of putative inhibitor compound may be used, for example from 0.1 to 10 nM. Greater concentrations may be used when a peptide is the test substance. Compounds which may be used may be natural or synthetic 15 chemical compounds used in drug screening programmes. Extracts of plants which contain several characterised or uncharacterised components may also be used. A further class of putative inhibitor compounds can be derived from the BRCA2 polypeptide and/or a ligand which binds IR1 and/or IR2. 20 Peptide fragments of from 5 to 40 amino acids, for example from 6 to 10 amino acids from the region of the relevant polypeptide responsible for interaction, may be tested for their ability to disrupt such interaction.

WO98/48013 PCT/GB98/01181 35 The skilled person can use the techniques described herein and others well known in the art to produce large amounts of peptides, for instance by expression from encoding nucleic acid. 5 Peptides can also be generated wholly or partly by chemical synthesis. The compounds of the present invention can be readily prepared according to well-established, standard liquid or, preferably, solid-phase peptide synthesis methods, general descriptions of which are broadly available 10 (see, for example, in J.M. Stewart and J.D. Young, Solid Phase Peptide Synthesis, 2nd edition, Pierce Chemical Company, Rockford, Illinois (1984), in M. Bodanzsky and A. Bodanzsky, The Practice of Peptide Synthesis, Springer Verlag, New York (1984); and Applied Biosystems 430A Users 15 Manual, ABI Inc., Foster City, California), or they may be prepared in solution, by the liquid phase method or by any combination of solid-phase, liquid phase and solution chemistry, e.g. by first completing the respective peptide portion and then, if desired and appropriate, after removal 20 of any protecting groups being present, by introduction of the residue X by reaction of the respective carbonic or sulfonic acid or a reactive derivative thereof.

WO98/48013 PCT/GB98/01181 36 Antibodies directed to the site of interaction in either protein form a further class of putative inhibitor compounds. Candidate inhibitor antibodies may be characterised and their binding regions determined to provide single chain antibodies 5 and fragments thereof which are responsible for disrupting the interaction. Antibodies in accordance with the present invention which discriminate between BRCA2 which is wild-type and BRCA2 which is mutated in the region of interest, are useful in screening procedures as discussed further below. 10 Antibodies may be obtained using techniques which are standard in the art. Methods of producing antibodies include immunising a mammal (e.g. mouse, rat, rabbit, horse, goat, sheep or monkey) with the protein or a fragment thereof. 15 Antibodies may be obtained from immunised animals using any of a variety of techniques known in the art, and screened, preferably using binding of antibody to antigen of interest. For instance, Western blotting techniques or immunoprecipitation may be used (Armitage et al., 1992, 20 Nature 357: 80-82). Isolation of antibodies and/or antibody producing cells from an animal may be accompanied by a step of sacrificing the animal. As an alternative or supplement to immunising a mammal WO98/48013 PCUGB98/01181 37 with a peptide, an antibody specific for a protein may be - obtained from a recombinantly produced library of expressed immunoglobulin variable domains, e.g. using lambda bacteriophage or filamentous bacteriophage which display 5 functional immunoglobulin binding domains on their surfaces; for instance see WO92/01047. The library may be naive, that is constructed from sequences obtained from an organism which has not been immunised with any of the proteins (or fragments), or may be one constructed using sequences 10 obtained from an organism which has been exposed to the antigen of interest. Antibodies according to the present invention may be modified in a number of ways. Indeed the term "antibody" should be construed as covering any binding substance having 15 a binding domain with the required specificity. Thus the invention covers antibody fragments, derivatives, functional equivalents and homologues of antibodies, including synthetic molecules and molecules whose shape mimics that of an antibody enabling it to bind an antigen or epitope. 20 Example antibody fragments, capable of binding an antigen or other binding partner are the Fab fragment consisting of the VL, VH, Cl and CH1 domains; the Fd fragment consisting of the VH and CH1 domains; the Fv fragment WO98/48013 PCT/GB98/01181 38 consisting of the.VL and VH domains of a single arm of an -antibody; the dAb fragment which consists of a VH domain; isolated CDR regions and F(ab')2 fragments, a bivalent fragment including two Fab fragments linked by a disulphide 5 bridge at the hinge region. Single chain Fv fragments are also included. A hybridoma producing a monoclonal antibody according to the present invention may be subject to genetic mutation or other changes. It will further be understood by those 10 skilled in the art that a monoclonal antibody can be subjected to the techniques of recombinant DNA technology to produce other antibodies or chimeric molecules which retain the specificity of the original antibody. Such techniques may involve introducing DNA encoding the immunoglobulin 15 variable region, or the complementarity determining regions (CDRs), of an antibody to the constant regions, or constant regions plus framework regions, of a different immunoglobulin. See, for instance, EP184187A, GB 2188638A or EP-A-0239400. Cloning and expression of chimeric antibodies 20 are described in EP-A-0120694 and EP-A-0125023. Hybridomas capable of producing antibody with desired binding characteristics are within the scope of the present invention, as are host cells, eukaryotic or prokaryotic, WO98/48013 PCT/GB98/01181 39 containing nucleic acid encoding antibodies (including Antibody fragments) and capable of their expression. The invention also provides methods of production of the antibodies including growing a cell capable of producing the 5 antibody under conditions in which the antibody is produced, and preferably secreted. The reactivities of antibodies on a sample (e.g. the subject of a diagnostic test) may be determined by any 10 appropriate means. Tagging with individual reporter molecules is one possibility. The reporter molecules may directly or indirectly generate detectable, and preferably measurable, signals. The linkage of reporter molecules may be directly or indirectly, covalently, e.g. via a peptide 15 bond or non-covalently. Linkage via a peptide bond may be as a result of recombinant expression of a gene fusion encoding antibody and reporter molecule. One favoured mode is by covalent linkage of each antibody with an individual fluorochrome, phosphor or laser 20 dye with spectrally isolated absorption or emission characteristics. Suitable fluorochromes include fluorescein, rhodamine, phycoerythrin and Texas Red. Suitable chromogenic dyes include diaminobenzidine.

WO98/48013 PCT/GB98/01181 40 Other reporters include macromolecular colloidal -particles or particulate material such as latex beads that are coloured, magnetic or paramagnetic, and biologically or chemically active agents that can directly or indirectly 5 cause detectable signals to be visually observed, electronically detected or otherwise recorded. These molecules may be enzymes which catalyse reactions that develop or change colours or cause changes in electrical properties, for example. They may be molecularly excitable, 10 such that electronic transitions between energy states result in characteristic spectral absorptions or emissions. They may include chemical entities used in conjunction with biosensors. Biotin/avidin or biotin/streptavidin and alkaline phosphatase detection systems may be employed. 15 The mode of determining binding is not a feature of the present invention and those skilled in the art are able to choose a suitable mode according to their preference and general knowledge. 20 Antibodies in accordance with the present invention may be used in screening for the presence of a particular polypeptide, for example in a test sample containing cells or cell lysate as discussed, such as a BRCA2 polypeptide WO98/48013 PCT/GB98/01181 41 including a mutation in the TAD, IR1 and/or IR2, where such mutation is reflected in an alteration in one or more epitopes allowing discrimination between the mutant and wild type regions of BRCA2. Screening methods using antibodies 5 are discussed further below. Antibodies may also be used in purifying and/or isolating a polypeptide according to the present invention, for instance following production of the polypeptide by expression from encoding nucleic acid therefor. Antibodies 10 may modulate the activity of the polypeptide to which they bind and so, if that polypeptide has a deleterious effect in an individual, may be useful in a therapeutic context (which may include prophylaxis). 15 An antibody may be provided in a kit, which may include instructions for use of the antibody, e.g. in determining the presence of a particular substance in a test sample. One or more other reagents may be included, such as labelling molecules, buffer solutions, elutants and so on. Reagents 20 may be provided within containers which protect them from the external environment, such as a sealed vial. Other candidate inhibitor compounds may be based on WO98/48013 PCT/GB98/01181 42 modelling the 3-dimensional structure of a polypeptide or peptide fragment and using rational drug design to provide potential inhibitor compounds with particular molecular shape, size and charge characteristics. 5 In a further aspect, the invention provides compounds obtainable by an assay according to the present invention, for example peptide compounds based on portions of the BRCA2 polypeptide. 10 A compound found to have the ability to modulate transcriptional activity of BRCA2 TAD, with therapeutic potent-ial in anti-tumour treatment, may be used in combination with any other anti-tumour compound. In such a 15 case, the assay of the invention, when conducted in vivo, need not measure the degree of inhibition of binding or transcriptional activation caused by the inhibitor compound being tested. Instead the effect on tumorigenicity may be measured. It may be that such a modified assay is run in 20 parallel or subsequent to the main assay of the invention in order to confirm that any effect on tumorigenicity is as a result of the inhibition of binding or transcriptional activation caused by said inhibitor compound and not merely a WO98/48013 PCT/GB98/01181 43 general toxic effect. The present invention extends in various aspects not only to a substance identified as a modulator of BRCA2 5 transcriptional activity, in accordance with what is disclosed herein, but also a pharmaceutical composition, medicament, drug or other composition including such a substance, a method including administration of such a composition to a patient, e.g. for anti-tumour or other anti 10 proliferative treatment, which may include preventative treatment, use of such a substance in manufacture of a composition for administration, e.g. for anti-tumour or other anti-proliferative treatment, and a method of making a pharmaceutical composition including admixing such a 15 substance with a pharmaceutically acceptable excipient, vehicle or carrier, and optionally other ingredients. Also encompassed within the scope of the present invention are functional mimetics of peptide fragments of 20 BRCA2 polypeptide TAD, IR1 or IR2, or the binding ligand or ligands for IR1 and/or IR2, which interfere with interaction between these polypeptides, and/or transcriptional activation by BRCA2 TAD. The term "functional mimetic" means a WO98/48013 PCT/GB98/01181 44 substance which may not contain an active portion of the - relevant amino acid sequence, and probably is not a peptide at all, but which retains the relevant interfering activity. The design and screening of candidate mimetics is described 5 in detail below. A substance identified using the present invention may be peptide or non-peptide in nature. Non-peptide "small molecules" are often preferred for many in vivo 10 pharmaceutical uses. Accordingly, a mimetic or mimick of the substance (particularly if a peptide) may be designed for pharmaceutical use. The designing of mimetics to a known pharmaceutically active compound is a known approach to the development of 15 pharmaceuticals based on a "lead" compound. This might be desirable where the active compound is difficult or expensive to synthesise or where it is unsuitable for a particular method of administration, e.g. peptides are not well suited as active agents for oral compositions as they tend to be 20 quickly degraded by proteases in the alimentary canal. Mimetic design, synthesis and testing may be used to avoid randomly screening large number of molecules for a target property.

WO98/48013 PCTGB98/01181 45 There are several steps commonly taken in the design of - a mimetic from a compound having a given target property. Firstly, the particular parts of the compound that are critical and/or important in determining the target property 5 are determined. In the case of a peptide, this can be done by systematically varying the amino acid residues in the peptide, e.g. by substituting each residue in turn. These parts or residues constituting the active region of the compound are known as its "pharmacophore". 10 Once the pharmacophore has been found, its structure is modelled to according its physical properties, e.g. stereochemistry, bonding, size and/or charge, using data from a range of sources, e.g. spectroscopic techniques, X-ray diffraction data and NMR. Computational analysis, similarity 15 mapping (which models the charge and/or volume of a pharmacophore, rather than the bonding between atoms) and other techniques can be used in this modelling process. In a variant of this approach, the three-dimensional structure of the ligand and its binding partner are modelled. 20 This can be especially useful where the ligand and/or binding partner change conformation on binding, allowing the model to take account of this the design of the mimetic. A template molecule is then selected onto which chemical WO98/48013 PCT/GB98/01181 46 groups which mimic the pharmacophore can be grafted. The -template molecule and the chemical groups grafted on to it can conveniently be selected so that the mimetic is easy to synthesise, is likely to be pharmacologically acceptable, and 5 does not degrade in vivo, while retaining the biological activity of the lead compound. The mimetic or mimetics found by this approach can then be screened to see whether they have the target property, or to what extent they exhibit it. Further optimisation or modification can then be carried out 10 to arrive at one or more final mimetics for in vivo or clinical testing. Whether it is a polypeptide, antibody, peptide, nucleic acid molecule, small molecule, mimetic or other 15 pharmaceutically useful compound according to the present invention that is to be given to an individual, administration is preferably in a "prophylactically effective amount" or a "therapeutically effective amount" (as the case may be, although prophylaxis may be considered therapy), this 20 being sufficient to show benefit to the individual. The actual amount administered, and rate and time-course of administration, will depend on the nature and severity of what is being treated. Prescription of treatment, e.g.

WO98/48013 PCT/GB98/01181 47 decisions on dosage etc, is within the responsibility of -general practitioners and other medical doctors. A composition may be administered alone or in combination with other treatments, either simultaneously or 5 sequentially dependent upon the condition to be treated. Pharmaceutical compositions according to the present invention, and for use in accordance with the present invention, may include, in addition to active ingredient, a pharmaceutically acceptable excipient, carrier, buffer, 10 stabiliser or other materials well known to those skilled in the art. Such materials should be non-toxic and should not interfere with the efficacy of the active ingredient. The precise nature of the carrier or other material will depend on the route of administration, which may be oral, or by 15 injection, e.g. cutaneous, subcutaneous or intravenous. Pharmaceutical compositions for oral administration may be in tablet, capsule, powder or liquid form. A tablet may include a solid carrier such as gelatin or an adjuvant. Liquid pharmaceutical compositions generally include a liquid 20 carrier such as water, petroleum, animal or vegetable oils, mineral oil or synthetic oil. Physiological saline solution, dextrose or other saccharide solution or glycols such as ethylene glycol, propylene glycol or polyethylene glycol may WO98/48013 PCT/GB98/01181 48 be included. For intravenous, cutaneous or subcutaneous injection, or injection at the site of affliction, the active ingredient will be in the form of a parenterally acceptable aqueous 5 solution which is pyrogen-free and has suitable pH, isotonicity and stability. Those of relevant skill in the art are well able to prepare suitable solutions using, for example, isotonic vehicles such as Sodium Chloride Injection, Ringer's Injection, Lactated Ringer's Injection. 10 Preservatives, stabilisers, buffers, antioxidants and/or other additives may be included, as required. A polypeptide, peptide or other substance able to interfere with the interaction of the relevant polypeptide, 15 peptide or other substance as disclosed herein may be provided in a kit, e.g. sealed in a suitable container which protects its contents from the external environment. Such a kit may include instructions for use. 20 The experimental evidence included below demonstrates that a mutation within the BRCA2 TAD which is associated with familial breast cancer severely reduces the ability of the TAD to activate transcription.

WO98/48013 PCT/GB98/01181 49 Given such experimental evidence, oligonucleotides -designed to hybridise to a region within the TAD or IR1 or IR2 may be used in diagnostic and prognostic screening. Oligonucleotide probes or primers, as well as the full 5 length BRCA2 TAD (optionally including IR1 and/or IR2) sequence (and mutants, alleles, variants and derivatives) are useful in screening a test sample containing nucleic acid for the presence of alleles, mutants and variants, especially those that confer susceptibility or predisposition to 10 proliferative disorders, including cancers, the probes hybridising with a target sequence from a sample obtained from the individual being tested. The conditions of the hybridisation can be controlled to minimise non-specific binding, and preferably stringent to moderately stringent 15 hybridisation conditions are preferred. The skilled person is readily able to design such probes, label them and devise suitable conditions for the hybridisation reactions, assisted by textbooks such as Sambrook et al (1989) and Ausubel et al (1992). 20 Nucleic acid isolated and/or purified from one or more cells (e.g. human) or a nucleic acid library derived from nucleic acid isolated and/or purified from cells (e.g. a cDNA library derived from mRNA isolated from the cells), may be WO98/48013 PCT/GB98/01181 50 probed under conditions for selective hybridisation and/or -subjected to a specific nucleic acid amplification reaction such as the polymerase chain reaction (PCR). A method may include hybridisation of one or more (e.g. 5 two) probes or primers to target nucleic acid. Where the nucleic acid is double-stranded DNA, hybridisation will generally be preceded by denaturation to produce single stranded DNA. The hybridisation may be as part of a PCR procedure, or as part of a probing procedure not involving 10 PCR. An example procedure would be a combination of PCR and low stringency hybridisation. A screening procedure, chosen from the many available to those skilled in the art, is used to identify successful hybridisation events and isolated hybridised nucleic acid. 15 Binding of a probe to target nucleic acid (e.g. DNA) may be measured using any of a variety of techniques at the disposal of those skilled in the art. For instance, probes may be radioactively, fluorescently or enzymatically labelled. Other methods not employing labelling of probe 20 include examination of restriction fragment length polymorphisms, amplification using PCR, RNAase cleavage and allele specific oligonucleotide probing. Probing may employ the standard Southern blotting WO 98/48013 PCT/GB98/01181 51 technique. For instance DNA may be extracted from cells and -digested with different restriction enzymes. Restriction fragments may then be separated by electrophoresis on an agarose gel, before denaturation and transfer to a 5 nitrocellulose filter. Labelled probe may be hybridised to the DNA fragments on the filter and binding determined. DNA for probing may be prepared from RNA preparations from cells. Those skilled in the art are well able to employ suitable conditions of the desired stringency for selective 10 hybridisation, taking into account factors such as oligonucleotide length and base composition, temperature and so on. PCR techniques for the amplification of nucleic acid are described in US Patent No. 4,683,195. In general, such 15 techniques require that sequence information from the ends of the target sequence is known to allow suitable forward and reverse oligonucleotide primers to be designed to be identical or similar to the polynucleotide sequence that is the target for the amplification. PCR includes steps of 20 denaturation of template nucleic acid (if double-stranded), annealing of primer to target, and polymerisation. The nucleic acid probed or used as template in the amplification reaction may be genomic DNA, cDNA or RNA. PCR can be used to WO98/48013 PCT/GB98/01181 52 amplify specific sequences from genomic DNA, specific RNA -sequences and cDNA transcribed from mRNA, bacteriophage or plasmid sequences. References for the general use of PCR techniques include Mullis et al, Cold Spring Harbor Symp. 5 Quant. Biol., 51:263, (1987), Ehrlich (ed), PCR technology, Stockton Press, NY, 1989, Ehrlich et al, Science, 252:1643 1650, (1991), "PCR protocols; A Guide to Methods and Applications", Eds. Innis et al, Academic Press, New York, (1990). 10 On the basis of amino acid sequence information, oligonucleotide probes or primers may be designed, taking into account the degeneracy of the genetic code, and, where appropriate, codon usage of the organism from the candidate nucleic acid is derived. An oligonucleotide for use in 15 nucleic acid amplification may have about 10 or fewer codons (e.g. 6, 7 or 8), i.e. be about 30 or fewer nucleotides in length (e.g. 18, 21 or 24). Generally specific primers are upwards of 14 nucleotides in length, but generally need not be more than 18-20. Those skilled in the art are well versed 20 in the design of primers for use processes such as PCR. A further aspect of the present invention provides an oligonucleotide or polynucleotide fragment of the nucleotide WO98/48013 PCT/GB98/01181 53 sequence shown for the BRCA2 TAD, IR1 and IR2 regions in Figure 2 or a complementary sequence, in particular for use in a method of obtaining and/or screening nucleic acid. The sequences referred to above may be modified by addition, 5 substitution, insertion or deletion of one or more nucleotides, but preferably without abolition of ability to hybridise selectively with nucleic acid with the sequence shown for the BRCA2 region in Figure 2, that is wherein the degree of homology of the oligonucleotide or polynucleotide 10 with the sequence given is sufficiently high. In some preferred embodiments, oligonucleotides according to the present invention that are fragments of the sequences shown for regions of BRCA2 in Figure 2, or any allele associated with susceptibility to cancer or other 15 disorder of cell proliferation, are at least about 10 nucleotides in length, more preferably at least about 15 nucleotides in length, more preferably at least about 20 nucleotides in length. Such fragments themselves individually represent aspects of the present invention. 20 Fragments and other oligonucleotides may be used as primers or probes as discussed but may also be generated (e.g. by PCR) in methods concerned with determining the presence in a test sample of a sequence indicative of susceptibility to WO98/48013 PCT/GB98/01181 54 cancer or other disorder of cell-cycle regulation. - Preferred probes or primers according to certain embodiments of this aspect of the present invention are designed to hybridise with and/or amplify a fragment of the 5 BRCA2 TAD, shown in Figure 2, including the codon for residue 42, mutation at which is associated with cancer susceptibility and is demonstrated herein to severely reduce transcriptional activation by the BRCA2 TAD. This is as a result of a change in the coding nucleotide sequence from TAT 10 to TGT. Thus, suitable oligonucleotides for probing or priming around codon 42 or other codon associated with disease susceptibility in the coding sequence shown in Figure 2 may be about 20 nucleotides in length, or may include a 15 contiguous sequence of about 20 nucleotides of the coding sequence shown (either sense strand or anti-sense strand, also known as coding and non-coding strands respectively). The oligonucleotide sequence may be designed so that it anneals to the sense or anti-sense strand with the codon of 20 interest (e.g. 42) towards the middle of the oligonucleotide, or at or adjacent the 3' or 5' end, different possibilities being preferred for different purposes. Exemplary sequences of oligonucleotides designed to WO98/48013 PCT/GB98/01181 55 anneal around codon .42 of the wild-type sequence shown in Figure 2 thus include: 5'-TATAATTCTGAACCTGCAGA-3' (corresponding to a portion of the sense strand, and thus 5 complementary to the anti-sense strand with codon 42 at the 5' end) 5'-ATAATTCTGAACCTGCAGAT-3' (corresponding to a portion of the sense strand, and thus complementary to the anti-sense strand with the nucleotide 10 (A) that is changed (to T) in the mutation discussed herein at the 5' end) 5'-ATAGGGTGGAGCTTCTGAAG-3' (corresponding to a portion of the anti-sense strand, and thus complementary to the sense strand with the anti-codon 15 for codon 42 at the 5' end of the oligonucleotide) 5'-TAGGGTGGAGCTTCTGAAGA-3' (corresponding to a portion of the anti-sense strand, and thus complementary to the sense strand with the nucleotide complementary to the A that is changed in the mutation 20 discussed herein at the 5' end of the oligonucleotide) 5'-GCTCCACCCTATAATTCTG-3' 5'-CAGAATTATAGGGTGGAGC-3 (respectively complementary to the anti-sense and sense WO98/48013 PCT/GB98/01181 56 strands having codon 42 (or its complement) towards the middle of the oligonucleotides). These oligonucleotides will anneal without mismatch to the wild-type sequence but will include a mismatch where the 5 TAT at codon 42 is mutated to TGT. Oligonucleotides that will anneal to the mutated sequence including TGT at codon 42 without mismatch, and the wild-type sequence with mismatch, include 5' -TGTAATTCTGAACCTGCAGA-3' 10 5' -ACAATTCTGAACCTGCAGAT-3' 5' -GTAGGGTGGAGCTTCTGAAG-3' 5' -CAGGGTGGAGCTTCTGAAGA-3' 5' -GCTCCACCCTGTAATTCTG-3' 5' -CAGAATTACAGGGTGGAGC-3 15 (corresponding to the oligonucleotides given above which anneal without mismatch to the wild-type sequence, but with the requisite change at the position corresponding to codon 42). Similarly designed oligonucleotides may be employed for 20 any mutation or other sequence alteration within a BRCA2 fragment according to the present invention. Detection of mismatches and other techniques useful for screening of mutations are discussed further below.

WO98/48013 PCT/GB98/01181 57 Other oligonucleotides useful in accordance with various aspects of the present invention, such as methods involving amplification of sequences encoding particular BRCA2 fragments, include: 5 5'-ATGCCTATTGGATCCAAAGA-3' (complementary to the 3' end of the antisense strand of the coding sequence shown in Figure 2) 5'-GAACTTGACCAAGACATATC-3' (complementary to the 3' end of the sense strand of the 10 coding sequence shown in Figure 2) 5'-ATCCATTTTAGTTTTCACTG-3' (complementary to the sense strand of the coding sequence at the 3' end of the region encoding IR2, ending with codon 125 in Figure 2) 15 5'-TAAGTCTAATTTGAATTTAT-3' (complementary to the sense strand of the coding sequence at the 3' end of the region encoding the TAD AAR, ending with codon 105) 5'-AACCTATTTAAACTCCACAA-3' 20 (complementary to the anti-sense strand of the coding sequence at its 3' end corresponding to the 5' end of the region of the sense strand encoding the TAD AAR, beginning with codon 60) WO 98/48013 PCT/GB98/01181 58 5'-GTTTGGTTCGTAATTGTTGT-3' (complementary to the sense strand of the coding sequence at the 3' end of the region encoding the TAD PAR, ending with codon 60) 5 5'-CGCTGCAACAAAGCAGATTT-3' (complementary to the anti-sense strand of the coding sequence at its 3' end corresponding to the 5' end of the region of the sense strand encoding the TAD PAR, beginning at codon 18). 10 These and other oligonucleotides may be used in various combinations to amplify particular regions of the BRCA2 fragment, including the whole fragment for which the sequence is shown in Figure 2, the TAD, the TAD AAR, the TAD PAR, and the TAD plus IR1 and/or IR2. 15 Methods involving use of nucleic acid in diagnostic and/or prognostic contexts, for instance in determining susceptibility to, e.g., cancer, and other methods concerned with determining the presence of sequences indicative of, e.g., cancer susceptibility 20 A number of methods are known in the art for analysing biological samples from individuals to determine whether the individual carries an BRCA2 allele with a mutation within the WO98/48013 PCT/GB98/01181 59 region for which the sequence is shown in Figure 2 predisposing them to disease. The purpose of such analysis may be used for diagnosis or prognosis, and serve to detect the presence of, e.g., an existing cancer, to help identify 5 the type of cancer, to assist a physician in determining the severity or likely course of the cancer and/or to optimise treatment of it. The methods may be used to detect alleles that are statistically associated with a susceptibility to cancer or other proliferative disorder in the future, e.g. 10 early onset cancer, identifying individuals who would benefit from regular screening to provide early diagnosis of cancer. Broadly, the methods divide into those screening for the presence of nucleic acid sequences and those that rely on detecting the presence or absence of polypeptide. The 15 methods make use of biological samples from individuals that are suspected of contain the nucleic acid sequences or polypeptide. Examples of biological samples include blood, plasma, serum, tissue samples, tumour samples, saliva and urine. 20 Exemplary approaches for detecting nucleic acid or polypeptides include: (a) comparing the sequence of nucleic acid in the sample WO98/48013 PCT/GB98/01181 60 with an BRCA2 nucleic acid sequence to determine whether the - sample from the patient contains one or more mutations in a region for which the sequence is shown in Figure 2; or, (b) determining the presence in a sample from a patient 5 of the polypeptide encoded by BRCA2 and, if present, determining whether the polypeptide is includes a region corresponding to that shown in Figure 2 (e.g. including TAD, IR1 and/or IR2), and/or is mutated in such a region; or, (c) using DNA fingerprinting to compare the restriction 10 pattern produced when a restriction enzyme cuts a sample of nucleic acid from the patient with the restriction pattern obtained from a region corresponding to that shown in Figure 2 for normal gene or from known mutations thereof; or, (d) using a specific binding member capable of binding 15 to a nucleic acid sequence (either a normal sequence or a known mutated sequence) encoding a fragment of BRCA2 corresponding to a region for which the sequence is shown in Figure 2 (e.g. including TAD, IRl and/or IR2), the specific binding member including nucleic acid hybridisable with the 20 BRCA2 sequence, or substances including an antibody domain with specificity for a native or mutated BRCA2 fragment nucleic acid sequence or the polypeptide encoded by it, the specific binding member being labelled so that binding of the WO98/48013 PCT/GB98/01181 61 specific binding member to its binding partner is detectable; -or, (e) using PCR involving one or more primers based on normal or mutated BRCA2 gene sequence to screen for normal or 5 mutant sequences within the region of BRCA2 corresponding to a region for which the sequence is shown in Figure 2 (e.g. including TAD, IR1 and/or IR2) in a sample from a patient. A "specific binding pair" includes a specific binding member (sbm) and a binding partner (bp) which have a 10 particular specificity for each other and which in normal conditions bind to each other in preference to other molecules. Examples of specific binding pairs are antigens and antibodies (see above), molecules and receptors and complementary nucleotide sequences. The skilled person will 15 be able to think of many other examples and they do not need to be listed here. Further, the term "specific binding pair" is also applicable where either or both of the specific binding member and the binding partner include a part of a larger molecule. In embodiments in which the specific 20 binding pair are nucleic acid sequences, they will be of a length to hybridise to each other under the conditions of the assay, preferably greater than 10 nucleotides long, more preferably greater than 15 or 20 nucleotides long.

WO98/48013 PCT/GB98/01181 62 In most embodiments for screening for susceptibility alleles, the BRCA2 nucleic acid in the sample will initially be amplified, e.g. using PCR, to increase the amount of the analyte as compared to other sequences present in the sample. 5 This allows the target sequences to be detected with a high degree of sensitivity if they are present in the sample. This initial step may be avoided by using highly sensitive array techniques that are becoming increasingly important in the art. 10 To reiterate in further detail, the identification of a significant region of the BRCA2 gene and its implication with disorders of cell proliferation paves the way for aspects of the present invention to provide the use of materials and 15 methods, such as are disclosed and discussed above, for establishing the presence or absence in a test sample of an variant form of the gene, in particular an allele or variant specifically associated with cancer. This may be for diagnosing a predisposition of an individual to cancer. It 20 may be for diagnosing cancer of a patient with the disease as being associated with the gene. This allows for planning of appropriate therapeutic and/or prophylactic treatment, permitting stream-lining of WO98/48013 PCT/GB98/01181 63 treatment by targeting those most likely to benefit. A variant form of the gene may contain one or more insertions, deletions, substitutions and/or additions of one or more nucleotides compared with the wild-type sequence 5 which may or may not disrupt the transcriptional activation function of the region examined herein. Differences at the nucleic acid level are not necessarily reflected by a difference in the amino acid sequence of the encoded polypeptide. However, a mutation or other difference in a 10 gene may result in a frame-shift or stop codon, which could seriously affect the nature of the polypeptide produced, or a point mutation or gross mutational change to the encoded polypeptide, including insertion, deletion, substitution and/or addition of one or more amino acids or regions in the 15 polypeptide, which may affect transcriptional activation. There are various methods for determining the presence or absence in a test sample of a particular nucleic acid sequence, such as the sequence shown for a BRCA2 fragment in 20 Figure 2 or a mutant, variant or allele thereof. Tests may be carried out on preparations containing genomic DNA, cDNA and/or mRNA. Testing cDNA or mRNA has the advantage of the complexity of the nucleic acid being reduced WO98/48013 PCT/GB98/01181 64 by the absence of intron sequences, but the possible disadvantage of extra time and effort being required in making the preparations. RNA is more difficult to manipulate than DNA because of the wide-spread occurrence of RN'ases. 5 Nucleic acid in a test sample may be sequenced and the sequence compared with the sequence shown in Figure 2 to determine whether or not a difference is present. If so, the difference can be compared with known susceptibility alleles to determine whether the test nucleic acid contains one or 10 more of the variations indicated, or the difference can be investigated for association with cancer. Since it will not generally be time- or labour-efficient to sequence all nucleic acid in a test sample or even the whole BRCA2 gene fragment corresponding to the region shown 15 in Figure 2, a specific amplification reaction such as PCR using one or more pairs of primers may be employed to amplify the region of interest in the nucleic acid. The amplified nucleic acid may then be sequenced as above, and/or tested in any other way to determine the presence or absence of a 20 particular feature. Nucleic acid for testing may be prepared from nucleic acid removed from cells or in a library using a variety of other techniques such as restriction enzyme digest and electrophoresis.

WO98/48013 PCT/GB98/01181 65 Nucleic acid may be screened using a variant- or allele specific probe. Such a probe corresponds in sequence to a region of the BRCA2 gene, or its complement, containing a sequence alteration known to be associated with 5 susceptibility to cancer or other proliferative disorder. Under suitably stringent conditions, specific hybridisation of such a probe to test nucleic acid is indicative of the presence of the sequence alteration in the test nucleic acid. For efficient screening purposes, more than one probe may be 10 used on the same test sample. Allele- or variant-specific oligonucleotides may similarly be used in PCR to specifically amplify particular sequences if present in a test sample. Assessment of whether a PCR band contains a gene variant may be carried out in a 15 number of ways familiar to those skilled in the art. The PCR product may for instance be treated in a way that enables one to display the mutation or polymorphism on a denaturing polyacrylamide DNA sequencing gel, with specific bands that are linked to the gene variants being selected. 20 An alternative or supplement to looking for the presence of variant sequences in a test sample is to look for the presence of the normal sequence, e.g. using a suitably specific oligonucleotide probe or primer.

WO98/48013 PCT/GB98/01181 66 Use of oligonucleotide probes and primers has been discussed in more detail above. Approaches which rely on hybridisation between a probe and test nucleic acid and subsequent detection of a mismatch 5 may be employed. Under appropriate conditions (temperature, pH etc.), an oligonucleotide probe will hybridise with a sequence which is not entirely complementary. The degree of base-pairing between the two molecules will be sufficient for them to anneal despite a mis-match. Various approaches are 10 well known in the art for detecting the presence of a mis match between two annealing nucleic acid molecules. For instance, RN'ase A cleaves at the site of a mis match. Cleavage can be detected by electrophoresing test nucleic acid to which the relevant probe or probe has 15 annealed and looking for smaller molecules (i.e. molecules with higher electrophoretic mobility) than the full length probe/test hybrid. Other approaches rely on the use of enzymes such as resolvases or endonucleases. Thus, an oligonucleotide probe that has the sequence of 20 a region of the normal BRCA2 gene (either sense or anti-sense strand) corresponding to the fragment shown in Figure 2 in which at least one mutation associated with, e.g., cancer susceptibility is known to occur, may be annealed to test WO98/48013 PCT/GB98/01181 67 nucleic acid and the presence or absence of a mis-match determined. Detection of the presence of a mis-match may indicate the presence in the test nucleic acid of a mutation associated with, e.g., cancer susceptibility. On the other 5 hand, an oligonucleotide probe that has the sequence of a region of the BRCA2 gene including a mutation associated with, e.g., cancer susceptibility may be annealed to test nucleic acid and the presence or absence of a mis-match determined. The presence of a mis-match may indicate that 10 the nucleic acid in the test sample has the normal sequence. In either case, a battery of probes to different regions of the gene may be employed. The presence of differences in sequence of nucleic acid molecules may be detected by means of restriction enzyme 15 digestion, such as in a method of DNA fingerprinting where the restriction pattern produced when one or more restriction enzymes are used to cut a sample of nucleic acid is compared with the pattern obtained when a sample containing the normal gene or a variant or allele is digested with the same enzyme 20 or enzymes. A test sample of nucleic acid may be provided for example by extracting nucleic acid from cells, e.g. in saliva or preferably blood, or for pre-natal testing from the WO98/48013 PCT/GB98/01181 68 amnion, placenta or foetus itself. Nucleic acid according to the present invention, such as a full-length coding sequence or oligonucleotide probe or 5 primer, may be provided as part of a kit, e.g. in a suitable container such as a vial in which the contents are protected from the external environment. The kit may include instructions for use of the nucleic acid, e.g. in PCR and/or a method for determining the presence of nucleic acid of 10 interest in a test sample. A kit wherein the nucleic acid is intended for use in PCR may include one or more other reagents required for the reaction, such as polymerase, nucleosides, buffer solution etc. The nucleic acid may be labelled. A kit for use in determining the presence or 15 absence of nucleic acid of interest may include one or more articles and/or reagents for performance of the method, such as means for providing the test sample itself, e.g. a swab for removing cells from the buccal cavity or a syringe for removing a blood sample (such components generally being 20 sterile). In a further aspect, the present invention provides an apparatus for screening for BRCA2 TAD, IR1 and/or IR2 nucleic acid, the apparatus including storage means including the BRCA2 nucleic acid sequence as set out in WO98/48013 PCT/GB98/01181 69 Figure 2, or a fragment thereof, the stored sequence being used to compare the sequence of the test nucleic acid to determine the presence of mutations. 5 There are various methods for determining the presence or absence in a test sample of a particular polypeptide, such as a polypeptide including a fragment of BRCA2 corresponding to a region for which the amino acid sequence is shown in Figure 2 or an amino acid sequence mutant, variant or allele 10 thereof. A sample may be tested for the presence of a binding partner for a specific binding member such as an antibody (or mixture of antibodies), specific for one or more particular variants of the BRCA2 polypeptide shown in the figures, or a 15 mutant, variant or allele thereof. A sample may be tested for the presence of a binding partner for a specific binding member such as an antibody (or mixture of antibodies), specific for the BRCA2 polypeptide shown in the figures. 20 In such cases, the sample may be tested by being contacted with a specific binding member such as an antibody under appropriate conditions for specific binding, before binding is determined, for instance using a reporter system WO98/48013 PCT/GB98/01181 70 as discussed. Where a panel of antibodies is used, different reporting labels may be employed for each antibody so that binding of each can be determined. A specific binding member such as an antibody may be 5 used to isolate and/or purify its binding partner polypeptide from a test sample, to allow for sequence and/or biochemical analysis of the polypeptide to determine whether it has the sequence and/or properties of the BRCA2 polypeptide whose sequence is shown in the figures, or if it is a mutant or 10 variant form. Amino acid sequence is routine in the art using automated sequencing machines. Nucleic acid according to the present invention, encoding a polypeptide functional as a transcriptional 15 activator, may be used in methods of gene therapy, for instance in treatment of individuals with the aim of preventing or curing (wholly or partially) cancer or other disorder involving loss of proper regulation of the cell cycle and/or cell growth. 20 Nucleic acid encoding an authentic biologically active BRCA2 fragment polypeptide, i.e. with ability to activate transcription, may be used in a method of gene therapy, to treat a patient who is unable to synthesize the active WO98/48013 PCT/GB98/01181 71 polypeptide or unable to synthesize it at the normal level, thereby providing the effect provided by wild-type and suppressing the occurrence of cancer and/or reduce the size or extent of existing defects in cell-cycle and/or growth 5 regulation in the target cells. Vectors such as viral vectors have been used in the prior art to introduce genes into a wide variety of different target cells. Typically the vectors are exposed to the target cells so that transfection can take place in a 10 sufficient proportion of the cells to provide a useful therapeutic or prophylactic effect from the expression of the desired polypeptide. The transfected nucleic acid may be permanently incorporated into the genome of each of the targeted tumour cells, providing long lasting effect, or 15 alternatively the treatment may have to be repeated periodically. A variety of vectors, both viral vectors and plasmid vectors, are known in the art, see US Patent No. 5,252,479 and WO 93/07282. In particular, a number of viruses have 20 been used as gene transfer vectors, including papovaviruses, such as SV40, vaccinia virus, herpesviruses, including HSV and EBV, and retroviruses. Many gene therapy protocols in the prior art have used disabled murine retroviruses.

WO98/48013 PCT/GB98/01181 72 As an alternative to the use of viral vectors other known methods of introducing nucleic acid into cells includes electroporation, calcium phosphate co-precipitation, mechanical techniques such as microinjection, transfer 5 mediated by liposomes and direct DNA uptake and receptor mediated DNA transfer. As mentioned above, the aim of gene therapy using nucleic acid encoding an BRCA2 polypeptide, or an active portion thereof, is to increase the amount of the expression 10 product of the nucleic acid in cells in which the level of the wild-type polypeptide is absent or present only at reduced levels. Such treatment may be therapeutic in the treatment of cells which are already cancerous or pre cancerous or prophylactic in the treatment of individuals 15 known through screening to have an BRCA2 susceptibility allele and hence a predisposition to cancer. Receptor-mediated gene transfer, in which the nucleic acid is linked to a protein ligand via polylysine, with the ligand being specific for a receptor present on the surface 20 of the target cells, is an example of a technique for specifically targeting nucleic acid to particular cells. As noted, a polypeptide termed "BBPI" (BRCA2 Binding WO98/48013 PCT/GB98/01181 73 Protein 1) has been found to interact with the PAR of BRCA2 and a portion of it able to repress transcriptional activation by BRCA2 TAD. The isolated polypeptide, isolated nucleic acid encoding 5 it, vectors and host cells including the nucleic acid, and methods of making the polypeptide all represent further aspects of the present invention. Thus in one aspect the present invention provides a polypeptide including the amino acid sequence shown in Figure 10 3 or the amino acid sequence shown in Figure 4. In one embodiment a polypeptide according to the present invention may be approximately up to about 2000 amino acids, or as encoded by the approximately 7.5kb mRNA discussed below. In one embodiment a polypeptide according to the invention 15 includes the amino acid sequence of Figure 3 or Figure 4, is able to bind BRCA2 TAD and is obtainable from human ovary or testis cells. Antibodies directed against the amino acid sequence of Figure 3 or Figure 4, or a suitable fragment thereof, may be used in isolation and/or purification of the 20 polypeptide from ovary or testis cells. The polypeptide may be provided in isolated form and may be formulated into a composition containing at least one additional component, such as a pharmaceutically acceptable excipient.

WO98/48013 PCT/GB98/01181 74 Nucleic acid encoding the BBP1 polypeptide is also provided as an aspect of the present invention. The invention provides a nucleic acid molecule including the encoding nucleotide sequence shown in Figure 3 or Figure 4. 5 The nucleic acid molecule may be RNA of approximately 7.5 kb including said encoding sequence (the RNA equivalent) or a cDNA copy of such RNA and obtainable by probing a cDNA library or RNA generated from human ovary or testes. Nucleic acid according to this aspect of the present 10 invention is obtainable using one or more oligonucleotide probes or primers designed to hybridise with one or more fragments of the nucleic acid sequence shown in Figure 3 or Figure 4, particularly fragments of relatively rare sequence, based on codon usage or statistical analysis. A primer 15 designed to hybridise with a fragment of the nucleic acid sequence shown in Figure 3 or Figure 4 may be used in conjunction with one or more oligonucleotides designed to hybridise to a sequence in a cloning vector within which target nucleic acid has been cloned, or in so-called "RACE" 20 (rapid amplification of cDNA ends) in which cDNA's in a library are ligated to an oligonucleotide linker and PCR is performed using a primer which hybridises with the sequence shown in Figure 3 or Figure 4 and a primer which hybridises WO98/48013 PCT/GB98/01181 75 to the oligonucleotide linker. In the context of cloning, it may be necessary for one or more gene fragments to be ligated to generate a full length coding sequence. Also, where a full-length encoding 5 nucleic acid molecule has not been obtained, a smaller molecule representing part of the full molecule, may be used to obtain full-length clones. Inserts may be prepared from partial cDNA clones and used to screen cDNA libraries. The full-length clones isolated may be subcloned into expression 10 vectors and activity assayed by transfection into suitable host cells, e.g. with a reporter plasmid. A method may include hybridisation of one or more (e.g. two) probes or primers to target nucleic acid. Where the nucleic acid is double-stranded DNA, hybridisation will 15 generally be preceded by denaturation to produce single stranded DNA. The hybridisation may be as part of a PCR procedure, or as part of a probing procedure not involving PCR. An example procedure would be a combination of PCR and low stringency hybridisation. A screening procedure, chosen 20 from the many available to those skilled in the art, is used to identify successful hybridisation events and isolated hybridised nucleic acid. Binding of a probe to target nucleic acid (e.g. DNA) may WO98/48013 PCT/GB98/01181 76 be measured using any of a variety of techniques at the disposal of those skilled in the art. For instance, probes may be radioactively, fluorescently or enzymatically labelled. Other methods not employing labelling of probe 5 include examination of restriction fragment length polymorphisms, amplification using PCR, RNAase cleavage and allele specific oligonucleotide probing. Probing may employ the standard Southern blotting technique. For instance DNA may be extracted from cells and 10 digested with different restriction enzymes. Restriction fragments may then be separated by electrophoresis on an agarose gel, before denaturation and transfer to a nitrocellulose filter. Labelled probe may be hybridised to the DNA fragments on the filter and binding determined. DNA 15 for probing may be prepared from RNA preparations from cells. Preliminary experiments may be performed by hybridising under low stringency conditions various probes to Southern blots of DNA digested with restriction enzymes. Suitable conditions would be achieved when a large number of 20 hybridising fragments were obtained while the background hybridisation was low. Using these conditions nucleic acid libraries, e.g. cDNA libraries representative of expressed sequences, may be searched.

WO98/48013 PCT/GB98/01181 77 Those skilled in the art are well able to employ suitable conditions of the desired stringency for selective hybridisation, taking into account factors such as oligonucleotide length and base composition, temperature and 5 so on. The BBP1 polypeptide, fragments, mutants, variants and derivatives thereof, and encoding nucleic acid may be used in the same or similar terms as fragments of BRCA2 as discussed above, e.g. in assays. Peptide fragments may be used to 10 modulate transcriptional activation by BRCA2. Further aspects and embodiments will be apparent to those of ordinary skill in the art upon consideration of the above disclosure and the following experimental report, 15 presented by way of illustration of embodiments of the present invention and without limitation. All documents mentioned in this specification are hereby incorporated herein by reference. 20 EXPERIMENTAL EXEMPLIFICATION The BRCA2 gene encodes a large 3418 residue protein of WO98/48013 PCT/GB98/01181 78 unknown function which is found mutated in 45% of familial breast cancers (1). The present inventors have scrutinised the BRCA2 protein sequence for any similarity to proteins of known function. It has surprisingly been found that exon 3 5 sequences at the N-terminus of BRCA2 (within a region highly conserved between human and mouse) show sequence similarity to the activation domain of c-jun (Figure 1). The homology overlaps the delta region of c-jun which contains the binding site for the Jun N-terminal Kinase (JNK, (2)). In view of 10 the similarity of exon 3 sequences to a transcriptional activation domain, the inventors investigated whether this region of BRCA2 has transcriptional activation capacity. Surprisingly, it has been found that BRCA2 sequences spanning exon 3 (23-105) are able to activate transcription 15 in yeast, when linked to the lexA DNA binding domain. In contrast, all the other highly conserved domains of BRCA2 (919-1171, 1500-1589, 2034-2223 and 3200-3326) do not show any activation potential in this assay. These various domains were fused to the lexA DNA binding domain and used to 20 drive the activity of a promoter including a lexA binding site, which was linked to the B-gal gene. The results are shown in Table 1. BRCA2 exon 3 sequences (18-105) also have potent WO98/48013 PCT/GB98/01181 79 activation potential in two different mammalian cell lines, U20S (Figure 1) and NMuMG (data not shown) when these sequences are linked to the GAL4 DNA binding domain. Fusions of portions of the BRCA2 protein and the DNA 5 binding domain of GAL4 (1-147) were co-transfected into U20S cells along with a target promoter 5GAL4EIBCAT and CAT activity was then measured 24 h following transfection. The activity shown represents the relative value compared to the activity of the GAL4 DNA binding domain alone. The results 10 represent an average of several independent experiments.- The expression levels of the different constructs were established by western blotting using a GAL4 specific antibody. The c-jun homology region (60-105) contributes to this 15 activation potential but has relatively little independent activity, whereas the adjacent region (18-60) remains significant, although reduced activation capacity. Residues 18-60 therefore represent a primary activating region (PAR) whereas residues (60-105) represent an auxiliary activating 20 region (AAR). Within the PAR lies a tyr residue at position 42 which is found mutated to cys in familial breast cancers (3) (shown in Figure 2). Introduction of this tyr to cys mutation into WO98/48013 PCT/GB98/01181 80 PAR severely compromises its activation potential. Further characterisation of this region reveals that the activation potential within exon 3 is under negative control of inhibitory regions (IR1 and IR2) present directly N- and 5 C-terminal to exon 3. Together these small regions completely mask the activation potential of BRCA2. This type of regulation by inhibitor regions has been shown to be operational in a number of transcription factors (4,5,6) and in the case of c-Fos, inhibitor function has been 10 demonstrated in the context of the intact protein assayed on its natural binding site (4). These results provide the first insight into the potential function and regulation of the BRCA2 protein. They provide indication that (a) BRCA2 has the ability to 15 stimulate transcription, (b) its activation potential is under negative control by inhibitory sequences and (c) signal transduction pathways culminating in the stimulation of JNK like kinases may regulate BRCA2 activity. To date two genes, BRAC1 and BRCA2, have been implicated 20 in the generation of familial breast cancers. Although these two proteins have no apparent sequence similarity, circumstantial evidence relating mainly to their size and overlapping expression patterns, has raised the possibility WO98/48013 PCT/GB98/01181 81 that their functions may be related (7). Our finding that BRCA2, like BRACI (8,9) has transcriptional activation potential provides the first functional evidence to support this. Indeed, the fact that the mutations found naturally in 5 breast cancers disrupt the activation potential of both BRAC1 or BRCA2, argues that compromising this activity may be an important step in the generation of familial breast cancers. This is further supported by the Nordling et al. finding noted above, i.e. that a large deletion disrupting the exon 3 10 transcription activator domain of BRCA2 is the disease causing mutation in a Swedish breast/ovarian cancer family. Using two hybrid screens, polypeptide regions which interact with BRCA2 fragments according to the present 15 invention are identified. Polypeptides or peptides including such regions may be included in screens and assays as discussed above and may be used to modulate BRCA2 transcriptional activation. Furthermore, they may themselves be built into screens and assays such as two hybrid assays to 20 obtain and/or identify molecules which modulate or interfere with their interaction with BRCA2 and/or their action on BRCA2 transcriptional activation.

WO98/48013 PCT/GB98/01181 82 Identification of a protein which binds the BRCA2 PAR and modulates its transcriptional activity, and cloning of encoding nucleic acid In two hybrid screens (see below) using the BRCA2 PAR a 5 protein was identified which binds the PAR. The protein has been termed "BBPI" - BRCA2 Binding Protein 1. An initial partial encoding sequence was obtained and is shown in Figure 4. 10 More encoding sequence of 2.2kb was obtained. Northerns showed that the BBP1 message is about 7.5kb, and expressed highly in ovary and testes, where BRCA2 is also highly expressed (comparisons with other tissues). 15 Demonstration that BBP1 modulates transcription activity of the BRCA2 TAD A portion of the BBP1 protein as shown in Figure 4 was expressed in mammalian cells as above and shown to repress activity of the BRCA2 activation domain. 20 The BRCA2 TAD was linked to the GAL4 DNA binding domain and a reporter gene under control of a promoter including GAL4 sites included in the cells. Titration in of increasing concentrations of the BBP1 WO98/48013 PCT/GB98/01181 83 expression vector gave increasing repression of expression of -the reporter construct. Mapping of interaction site for BBPI1 in BRCA2 5 Overlapping fragments of BRCA2 TAD were used to map the BBP1 binding site to within amino acids 18-46 of BRCA2. The overlap is a highly conserved region in BRCA2 between human and mouse and is where the noted mutation associated with breast cancer lies (residue 42). 10 This provides ample basis for screens and assays for substances which interfere with interaction between BBP1 and BRCA2 and have an effect on BRCA2 transcriptional activation. 15 The following describes two hybrid assay techniques for yeast. When performing a two hybrid assay to look for substances which interfere with the interaction between two polypeptides or peptides it may be preferred to use mammalian cells instead of yeast cells. The same principles apply and 20 similar methods are well known to the person skilled in the art. Two Hybrid Screens for Interacting Molecules WO98/48013 PCT/GB98/01181 84 The following method is used to isolate molecules which interact with a BRCA2 polypeptide or peptide in accordance with the present invention. The yeast two hybrid system is based on a protein 5 interaction assay in yeast (Fields and Song. 1989. Nature 340, 245-246). The following protocol contains several modifications of the original Fields strategy and facilitates large scale library screens. It has been designed and optimised and was first used by Ann Vojtek to isolate c-raf 10 and a-raf clones (Vojtek et al. 1993. Cell 74, 205-214).- The method described below is essentially identical to the one outlined in Vojtek et al. It uses the same set of vectors (the different bait constructs are described below) and yeast strains. The Two Hybrid System is based on an in vivo yeast 15 protein interaction assay. In general yeast are transformed with a reporter gene construction which expresses a selective marker protein (e.g. encoding B-galactosidase). The promoter of that gene has been designed such that it contains binding site for the LexA 20 DNA-binding protein. Gene expression from that plasmid is usually very low. Two more expression vectors are transformed into the yeast containing the selectable marker expression plasmid. The first of those two vectors is based WO 98/48013 PCT/GB98/01181 85 on pBTM116. It contains the coding sequence for the full length LexA gene linked to a multiple cloning site. This multiple cloning site is used to clone a gene of interest, i.e. encoding a BRCA2 polypeptide or peptide in accordance 5 with the present invention, in frame on to the LexA coding region. The second yeast expression vector contains the activation domain of the herpes simplex transactivator VP16 fused to random sequences of a cDNA library or a library of sequences encoding peptides with diverse e.g. random 10 sequences (depending on whether the aim is to obtain a naturally occurring ligand for the BRCA2 polypeptide or peptide or to screen for peptides which interact). Those two plasmids facilitate expression from the reporter construct containing the selectable marker only when the LexA fusion 15 construct (bait) interacts with a polypeptide or peptide sequence derived from the cDNA or peptide library. A modification of this when looking for peptides which interfere with interaction between a BRCA2 polypeptide or peptide and a ligand or other binding molecule, e.g. for the 20 TAD or for IR1 and/or IR2, employs the BRCA2 polypeptide or peptide as a fusion with the LexA DNA binding domain, and the binding molecule as a fusion with VP60, and involves a third expression cassette, which may be on a separate expression WO98/48013 PCT/GB98/01181 86 vector, from which a peptide or a library of peptides of diverse and/or random sequence may be expressed. A reduction in reporter gene expression (e.g. in the case of P galactosidase a weakening of the blue colour) results from 5 the presence of a peptide which disrupts the interaction between the BRCA1 polypeptide or peptide and the binding molecule, which interaction is required for transcriptional activation of the P-galactosidase gene. As noted, instead of using LexA and VP60, other similar 10 combinations of proteins which together form a functional transcriptional activator may be used, such as the GAL4 DNA binding domain and the GAL4 transcriptional activation domain. 15 Two Hybrid Plasmids Amino Acids 1-197 of a human BRCA2 clone are amplified by PCR and cloned as in frame with the LexA gene in pBTM116, which contains the TRP1 gene which allows selection of transformed yeast on tryptophan negative plates. 20 The pVPl6 library vector carries the LEU2 gene which allows selection on Leucine negative plates. A human cDNA library cloned next to the activation domain of VP16 is generated by random primed synthesis of poly A+ RNA. The WO98/48013 PCT/GB98/01181 87 vast majority of inserts have a length of 400 - 600 nucleotides. Two reporter constructs are in use and both are provided by the yeast strain L40. The first construct has a 5 selectable marker, the LYS2 gene, which allows growth on Lysine negative plates. It contains the coding region for the histidine gene under the control of a promoter containing four binding sites for the LexA operator. The second reporter gene has a URA3 gene as selectable marker which 10 allows growth on uracil negative plates. It contains the coding region for the lacZ gene controlled by a promoter containing eight binding sites for the lexA protein. Yeast Transformation 15 Small Scale Transformation 10 ml of YPAD are inoculated with a colony of L40 and incubated overnight at 30 0 C. Thereafter, the culture is diluted to an OD600 of around 0.4 in 50 ml YPAD and grown for an additional 2-4 hours. Cells are then pelleted at 2500 rpm 20 at room temperature and re-suspended in 40 ml TE. Yeast are then repelleted at 2500 rpm and resuspended in 2 ml of 100 mM LiAc in 0.5 x TE. This yeast suspension is incubated at room temperature for 10 minutes. 1 Ag of plasmid DNA together WO98/48013 PCT/GB98/01181 88 with 100 jg of sonicated sheared salmon sperm DNA is mixed with 100 Al of the yeast suspension. After a further addition of a buffer of 700 p4l containing 100 mM (LiAc), 40% PEG-3350 in 1 x TE, the solution is mixed well and incubated 5 at 30 0 C for 30 minutes. To stop the transformation process 88 p4l DMSO is added and the mixture heat- shocked at 40 0 C for 7 minutes. Cells are pelletted in a microfuge for 10 seconds and re-suspended in 1 ml TE. Cells are then re-washed in 1 ml TE and re-suspended in 50-100 il TE and plated on 10 selective plates. Plates are incubated at 30 0 C and colonies picked after 2-3 days. Small scale transformation may be used to test the induction of the beta-galactosidase activity by the LexA/BRCA2 fragment fusion plasmid. The beta-galactosidase 15 filter assay is described below. Large Scale Library Transformation The LexA/BRCA2 fragment fusion plasmid is introduced into L40 by selecting for growth on tryptophan minus plates 20 after a small scale transformation. The resulting strain is used to grow a 2 ml overnight culture in yeast selective medium minus tryptophan and minus uracil. Thereafter, the culture is diluted with 100 ml of the same medium. The next WO98/48013 PCT/GB98/01181 89 day the mid log phase culture is used to inoculate 1 litre of YPAD medium (pre-warmed to 30 0 C). The optical density at 600 nm should be about 0.3. This culture is grown at 30 0 C for 3 hours. During this time the cells should roughly double in 5 number. Yeast are pelletted at 2500 rpm for 5 minutes at room temperature and re-suspended in 500 ml of TE. After a re-spin the cells are taken up in 10 ml of 100 mM Li Ac in 0.5 x TE. To this a mixture of 0.5 ml of 10 mg/ml denatured salmon sperm DNA and 200 pg of library plasmid is added. The 10 suspension is mixed well. After this 70 ml of a solution containing 100 mM LiAc, 40% PEG-3350 in 1 x TBE is added and mixed well. This mixture is incubated for 30 minutes at 30 0 C. The transformation mixture is then transferred to a sterile 2 litre beaker and 8.8 ml of DMSO was added. After 15 mixing the suspension is heat shocked at 42 0 C in a water bath for 6 minutes. Thereafter, the suspension is diluted with 200 ml of YPA and rapidly cooled to room temperature in a water bath. Cells are then pelletted at 2500 rpm for 5 minutes at room temperature, washed with 250 ml YPA medium 20 and re-suspended in 1 litre of pre-warmed YPAD medium. At this stage incubation at 30 0 C is allowed for 1 hour with gentle shaking. The culture is then pelletted at 2500 rpm for 5 minutes at room temperature and re-suspended in 500 ml WO98/48013 PCT/GB98/01181 90 of selective medium omitting uracil, tryptophan leucine ( UTL). After a further respin cells are resuspended in 1 litre of pre-warmed -UTL medium with shaking at 30 0 C for about 4 hours. Thereafter, cells are pelletted at 2500 rpm 5 for 5 minutes at room temperature and washed twice with selective medium omitting tryptophan, histidine, uracil and leucine (-THULL). The final pellet is resuspended in 10 ml of -THULL medium and plated in aliquots of 100 pl on plates made from -THULL media. If the bait alone can activate the 10 B-galactosidase gene, this is suppressed by the inclusion of 3 amino 124-triazole at an appropriate concentration (e.g. 50mM). After 2-3 days colonies are picked to a grid. A nitrocellulose filter lift is used in a beta-galactosidase filter assay for analysis of lacZ induction. 15 Beta-galactosidase Filter Assay Filters are removed from the plates and immersed for 3-5 seconds in liquid nitrogen. Filters are then placed, colony side up, at room temperature until thawed. The beta 20 galactosidase assay is performed in the lid of a petri dish. 3 ml of Z-buffer (60 mM Na 2

HPO

4 , 40 mM NaH 2

PO

4 , 10 mM KC1, 1 mM MgSO 4 , pH7.0) containing 30 ml of 50 mg/ml X-gal. Circularised Whatman filters (#1) are placed into the buffer, WO98/48013 PCT/GB98/01181 91 followed by the nitrocellulose filters, colonies facing up. The lid is then covered with the bottom of the petri dish and placed at 30 0 C. Interactions are detectable by the appearance of a blue colour after 20 to 40 minutes. 5 Recovering of Plasmids from Yeast and Shuttling into E.coli Viable cells are recovered from colonies and grown in a 50 ml overnight culture with the appropriate selection. The next morning cells are pelletted at 2500 rpm for 5 minutes at 10 room temperature. Pellets are resuspended in 0.3 ml of lysis buffer (2.5 M LiC1, 50 mM Tris-Cl (pH 8.0), 4% Triton X-100, 62.5 mM EDTA). At this stage solution is transferred to 1.5 ml tubes and 150 ml of glass beads (0.45 - 0.50 mm) together with 0.3 ml phenol/chloroform are added. After vigorous 15 shaking for 1 minute samples are centrifuged for 1 minute and the aqueous phase transferred to a new tube. DNA is precipitated twice with ethanol and resuspended in 25 ml TE followed by electroporation of DNA into E.coli. 20 Verification of Interacting Partners Recovered library plasmids from positive yeast colonies are retransformed into the L40 strain containing the LexA/BRCA2 fragment bait vector using the small scale WO98/48013 PCT/GB98/01181 92 transformation procedure. Using the beta-galactosidase filter assay positive colonies are identified with the LexA/BRCA2 fragment bait. No induction of beta-galactosidase activity is detected in colonies transformed with a LexA 5 instead of a LexA/BRCA 2 fragment clone. The underlying protein interactions of the positive colonies are significant and consequently further analysed. Identification of a Full Length cDNA of A BRCA2 Binding 10 Molecule In order to isolate a full length cDNA clone of a molecule which binds BRCA2 TAD, IR1 and/or IR2, a plasmid cDNA library is plated on ampicillin resistant plates. Nitrocellulose filter lifts of those plates are hybridised to 15 DNA sequences obtained through the yeast two hybrid screen. Washes are done at high stringency and positive signals are identified. Isolated DNA is sequenced and if necessary partial clones are ligated to provide a full length coding sequence. A full length sequence may be verified as such by 20 primer walking sequencing in both directions. Identification of a kinase able to bind the activation domain of BRCA2 WO 98/48013 PCT/GB98/01181 93 Using residues 18-141 of BRCA2 as an affinity column a kinase has been purified from HeLa nuclear extracts which phosphorylates within amino acids 60-105 of BRCA2, specifically the region of BRCA2 which is homologous to the 5 JNK binding site in c-jun. This was demonstrated by deletion of residues 80-107 in BRCA2, which abolished binding of the kinase. This mutation also reduced the activation capacity of BRCA2. The region of BRCA2 residues 60-105 is phosphorylated in vivo. 10 The kinase was found not to be stimulated by uv and is therefore not JNK. This was confirmed by experiments in which recombinant JNK was found not to bind the region of BRCA2. REFERENCES 15 1. Wooster, R. et al. (1994). Science, 265, 2088-2090. 2. Derijard, B. et al. (1994). Cell, 76, 1025-1037. 3. Friend, S. and the Breast Cancer Information Core Steering Committee (1995). Breast cancer information on the web. Nature Genetics 11: 238-239. 20 4. Brown, H.J. et al. (1995). EMBO J., 14, 124-131. 5. Dennig, J. et al. (1996). EMBO J., 15, 5659-5667. 6. Dubendorff, J.W., et al. (1992). Genes & Development, 6, 2524-2535.

WO98/48013 PCT/GB98/01181 94 7. Thakur, S. et al. (1997). Mol & Cell. Biol. 17, 444 452. 8. Chapman, M.S. and Verma, I.M. (1996). Nature, 382, 678 679. 5 9. Varo, A. et al. PNAS, 93, 13595-13599. 10. Nordling, M., et al., Cancer Research, 58, 1372-1375, April 1, 1998 TABLE 1 shows the results of a B-galactosidase liquid assay 10 using various fragments of BRCA2 fused to the DNA binding domain of lexA. TABLE 1 bait activity [U1 15 18-105 112+2 919-1171 (BRC1) 0 1500-1589 (BRC4) 0 2034-2223 (BRC8) 0 3200-3326 0

Claims (32)

1. A fragment of BRCA2 which is able to act as transcriptional activator when operably linked to a heterologous DNA binding domain. 5

2. A fragment according to claim 1 which is of less than about 200 amino acids.

3. A fragment according to claim 1 or claim 2 which 10 includes amino acids 23-105 of the human BRCA2 polypeptide the sequence of which is shown in Figure 2.

4. A fragment according to claim 3 which includes amino acids 18-105 of the human BRCA2 polypeptide the sequence of 15 which is shown in Figure 2.

5. A fragment according to claim 1 or claim 2 which includes amino acids 18 to 60 of the human BRCA2 polypeptide the sequence of which is shown in Figure 2. 20

6. A fragment according to claim 1 or claim 2 which includes amino acids 60 to 105 of the human BRCA2 polypeptide the sequence of which is shown in Figure 2. WO 98/48013 PCT/GB98/01181 96

7. A fragment according to any of claims 1 to 6 including amino acids 1-17 and/or amino acids 106-125 of the human BRCA2 polypeptide the sequence of which is shown in Figure 2. 5

8. A mutant, variant or derivative of a BRCA2 fragment according to any of claims 1 to 7, which mutant, variant or derivative is able to act as transcriptional activator when operably linked to a heterologous DNA binding domain and has at least 80% sequence similarity with said fragment. 10

9. A fragment according to any of claims 1 to 7 or a mutant, variant or derivative thereof according to claim 8 fused to a sequence of amino acids heterologous to BRCA2. 15

10. A substance including a fragment according to any of claims 1 to 7 or a mutant, variant or derivative thereof according to claim 8 operably linked to a heterologous DNA binding domain. 20

11. An isolated nucleic acid molecule encoding a fragment according to any of claims 1 to 7 or a mutant, variant or derivative thereof according to claim 8. WO98/48013 PCT/GB98/01181 97

12. Nucleic acid according to claim 11 wherein said fragment, mutant, variant or derivative is fused to a sequence of amino acids heterologous to BRCA2. 5

13. Nucleic acid according to claim 11 or claim 12 operably linked to regulatory sequences for expression of the encoded product.

14. A host cell transformed with nucleic acid according to 10 claim 13.

15. A method for production of a fragment according to any of claims 1 to 7 or a mutant, variant or derivative thereof according to claim 8, the method including causing expression 15 from nucleic acid according to claim 13.

16. A method according to claim 15 including culturing a host cell transformed with said nucleic acid under conditions for expression of the encoded product. 20

17. A method according to claim 15 or claim 16 wherein said fragment, mutant, variant or derivative is isolated and/or purified. WO 98/48013 PCT/GB98/01181 98

18. A method according to claim 17 including formulating said fragment, mutant, variant or derivative into a composition including at least one additional component. 5

19. A method of producing a transcription factor, the method including operably linking a fragment according to any of claims 1 to 7 or a mutant, variant or derivative according to claim 8 to a DNA binding domain to form a transcription factor. 10

20. A method of activating transcription from a promoter including a motif for a DNA binding domain, the method including bringing into contact the promoter and a substance according to claim 10 wherein said heterologous DNA binding 15 domain is able to bind said motif, under conditions wherein the DNA binding domain binds said motif and transcription from the promoter is activated.

21. An assay method which includes: 20 (a) bringing into contact a substance including a fragment according to any of claims 1 to 6 or a mutant, variant or derivative thereof according to claim 8 and a test compound; and WO98/48013 PCT/GB98/01181 99 (b) determining interaction between said substance and said test compound.

22. An assay method which includes: 5 (a) bringing into contact a substance including a fragment according to any of claims 1 to 5 or a mutant, variant or derivative thereof according to claim 8, or a fragment of BRCA2 including amino acids 18-46 as shown in Figure 2, a substance including a fragment of BBP1 of which 10 the amino acid sequence is shown in Figure 3 or Figure 4, or a mutant, variant or derivative thereof which is able to bind BRCA2; and a test compound, under conditions in which in the absence of the test compound being an inhibitor, the two said substances interact; 15 (b) determining interaction between said substance.

23. An assay method which includes: (a) bringing into contact a substance according to claim 10 including a DNA binding domain able to bind a motif 20 within a promoter, the method including bringing into contact a substance according to claim 10 and a putative inhibitor compound under conditions where the substance, in the absence of inhibitor, is capable of binding the nucleotide sequence WO98/48013 PCTGB98/01181 100 within the promoter to activate transcription; (b) providing a nucleic acid molecule which includes a promoter which includes the motif to which said DNA binding domain is capable of binding to activate transcription of a 5 sequence operably linked to the promoter; and (c) measuring the degree of modulation or alteration of transcriptional activation caused by said inhibitor compound.

24. An assay method which includes: 10 (a) bringing into contact a substance including a fragment according to any of claims 1 to 6 or a mutant, variant or derivative thereof according to claim 8 and a test compound in the presence of a kinase under conditions in which the kinase normally phosphorylates said fragment, 15 mutant, variant or derivative; and (b) determining phosphorylation of said fragment, mutant, variant or derivative.

25. An assay method which includes: 20 (a) bringing into contact a substance including amino acids 1-17 and/or 106-125, and a putative binding molecule or other test compound; and (b) determining interaction or binding between the WO98/48013 PCT/GB98/01181 101 substance and the test compound.

26. An assay method according to any of claims 21 to 25 wherein the test compound is a peptide fragment of BRCA2 or 5 BBP1 or a mimetic thereof.

27. A method wherein a test compound identified as testing positive in a method according to any of claims 21 to 26 is formulated into a composition including at least one 10 additional component.

28. Use of a fragment according to any of claims 1 to 7 or a mutant, variant or derivative thereof according to claim 8 in an assay to identify a compound which is able to modulate 15 transcriptional activation by BRCA2.

29. A peptide which is a fragment of a fragment according to any of claims 1 to 7 or a mutant, variant or derivative thereof according to claim 8 or a fragment of BBP1 the amino 20 acid sequence of which is shown in Figure 3 or Figure 4, or a non-peptidyl mimetic of said peptide, which peptide or mimetic thereof is able to modulate transcriptional activation by BRCA2. WO98/48013 PCT/GB98/01181 102

30. A peptide according to claim 29 including residues 18-46 of the amino acid sequence of human BRCA2 polypeptide which is shown in Figure 2. 5

31. A peptide which includes amino acids 1-17 of the human BRCA2 polypeptide the sequence of which is shown in Figure 2.

32. A peptide which includes amino acids 106-125 of the human BRCA2 polypeptide the sequence of which is shown in 10 Figure 2.