WO1999042828A2

WO1999042828A2 - Treating cancer

Info

Publication number: WO1999042828A2
Application number: PCT/GB1999/000503
Authority: WO
Inventors: Hilmar Meek Warenius
Original assignee: Theryte Ltd
Current assignee: Theryte Ltd
Priority date: 1998-02-18
Filing date: 1999-02-18
Publication date: 1999-08-26
Anticipated expiration: 2000-08-18
Also published as: EP1057028B1; DE69907156D1; EP1057027A2; AU2538299A; EP1057032B1; US20030134315A1; WO1999042839A3; AU2538499A; JP2002504688A; WO1999042828A3; DE69907155T2; CA2321482A1; WO1999042834A2; AU2630099A; WO1999042837A1; EP1057029A2; US6521407B1; AU739001B2; ATE238556T1; CA2321467A1

Abstract

Provided is a method for measuring the resistance of p53 mutant cancer cells to the cytotoxic effects of a chemotherapeutic agent, which method comprises testing a sample comprising p53 mutant cells or an extract therefrom for the level of expression of Cyclin D1 or for the abundance of Cyclin D1 protein. Also provided is a kit for measuring the resistance of p53 mutant cancer cells to the cytotoxic effects of a chemotherapeutic agent, which kit comprises: i) a means for testing for the level of expression of Cyclin D1 or for the abundance of Cyclin D1 protein; and ii) a means for identifying p53 mutant cells.

Description

TREATING CANCER

The present application concerns methods of selecting the most appropriate therapy for patients suffering from cancer. The application is particularly concerned with measuring the resistance of cancer cells to chemotherapeutic agents

Although radiotherapy and chemotherapy have been responsible for curing many people of cancer m the latter half of this century, there still remain a large number of tumours which either show little response to treatment, or respond initially only to recur later. In particular, women treated for ovarian cancer with platinatmg agents often show encouraging initial responses to chemotherapy (which often involves the use of cis- diammmedichloroplatmum (CDDP) as the drug of first choice), but by 5 years after diagnosis, 2/3 of them have succumbed to their disease. Similarly lung cancer patients may respond favourably to combination chemotherapy regimens containing CDDP at the outset of treatment but very few experience long term survival. A better understanding of the mechanisms underlying the responsiveness of cancers to CDDP could help predict which patients are most likely to benefit from CDDP or whether alternative cytotoxic agents such as taxol or different therapies such as radiotherapy might be appropπate. Understanding treatment response mechanisms also holds the possibility of selectively modulating these mechanisms to improve the treatment of human cancer using CDDP

It has become increasingly apparent that certain oncogenes and tumour suppressor genes may not only be implicated m carcmogenesis, but can also influence the sensitivity of malignant cells to therapeutic agents. Attempts have therefore been made to use these and other genes to try and predict the therapeutic response of human cancer to the presently available treatment modalities such as radiotherapy and/or cytotoxic chemotherapy. Research up to the present time, however, has generally attempted to only examine the expression of single tumour related genes as methods of predicting therapeutic response Research m the public domain has suggested that mutations m the p53 tumour suppressor gene, which can be found in around 50% of common cancers such as those of the breast, lung and ovary, are associated with resistance to treatment with cytotoxic drugs or radiation. Despite a considerable body of work, however, there are at present no successful clinical tests by which the detection of mutations m the p53 gene alone can be used to predict with an acceptable degree of certainty whether or not a patient's cancer is likely to respond to chemotherapy with, for example, platmatmg agents or the newer cytotoxic agents such as taxanes (e g. taxol)

The expression of single genes alone on the response of human cancer cell lines to treatment with cytotoxic drugs such as CDDP has been studied in human in vitro cell lines because these present a model system relevant to the response of human cancer in the clinic In particular, they exhibit the range of sensitivities to cytotoxic drugs and ionising radiation usually encountered in the clmic. Discoveπes m human in vitro cell lines, therefore, have a strong possibility of being able to be translated into clinically useful tests for how well cancers may be expected to respond to treatment.

The progress of cells through the cell cycle is governed by holoenzymes formed by a combination of proteins called cychns, whose levels fluctuate throughout the cell cycle, and cyclin dependent kmases (CDKs) which become active when they join with cychns The cychn/CDK complexes can be inhibited by proteins termed cyclm dependent kmase inhibitors (CDKIs) which include the protein p21 WAF1/CIP1 (ρ21)

The protein products of the Cyclin Dl and Bl genes and their respective cychn- dependent kmase partners CDK4 and CDK1 have been studied Cyclin Dl and CDK4 control the progress of cells through the cell cycle checkpoint between Gl and S-phase (the phase of DNA synthesis). Cyclin Bl and CDK1 control the cell cycle checkpoint just before mitosis. The expression of Cyclm Dl protein m a seπes of 16 human cancer cell lines has been shown to be related to their intrinsic resistance to the cytotoxic drug CDDP (Waremus et al , 1996) Cyclm Dl protein levels, however, showed no relationship with radiosensitivity, another treatment modality. The relationship between Cyclm Dl and CDDP resistance is not, however, strong enough on its own to provide the basis of clinically useful predictive assays

Thus, there are no indicators that measuπng the mutational status or levels of expression of the protein products of single oncogenes, proto-oncogenes or tumour suppressor genes in human cancer cells would be able to provide the basis of a reliable clinical test for whether clinical tumours were likely to respond to treatment with chemotherapeutic agents, including platinating agents and CDDP.

This invention provides methods of predicting whether human cancer cells are likely to respond to anticancer therapy agents (chemotherapeutic agents, such as platinating agents e.g. CDDP) by contemporaneously measuring the properties of two or more cancer-related genes. Moreover the co-relationship between certain independently expressed cancer genes identified in this invention also provides previously undescribed targets against which to potentially direct therapy that is more cancer specific.

In particular, this invention provides a method for measuring the resistance of p53 mutant cancer cells to the cytotoxic effects of chemotherapeutic agents, which method comprises testing a sample comprising p53 mutant cells or an extract therefrom for the level of expression of Cyclin Dl or for the abundance of Cyclin Dl protein.

This invention also provides a kit for measuring the resistance of p53 mutant cancer cells to the cytotoxic effects of chemotherapeutic agents, which kit comprises:

(i) a means for testing for the level of expression of Cyclin Dl or for the abundance of Cyclin Dl protein; and

(ii) a means for identifying p53 mutant cells.

Thus, this application preferably deals with measuring the levels of Cyclin D 1 protein, in cells whose p53 mutational status has been determined (e.g. by DNA sequencing) to determine the resistance of a tumour to (for example) CDDP. High Cyclin Dl levels or high Cyclin Dl expression together with p53 mutation is strongly associated with resistance to chemotherapeutic agents, e.g. CDDP in human cancer cells.

The over-expression of Cyclin Dl, or the elevation of Cyclin Dl protein levels can be measured by any appropriate method, e.g. Western blotting. The point at which it is considered that the level is elevated or that the expression is over-expression is clear to the skilled person in this field, according to general teaching from the literature regarding usual levels of Cyclin Dl in human cell lines (see Oncogene, 1993, vol. 8, 2127-2133; and Oncogene, 1995, vol. 10, 775-778. This point can be determined according to the judgement of the individual carrying out the present method, depending on the particular cancer cells and patient involved.

The present invention will be described in further detail by way of example only with reference to the accompanying drawings, in which:

Figure 1 shows the relationship between the level of Cyclin Dl protein and relative resistance to CDDP in mutant p53 cell lines; and

Figure 2 shows the corresponding relationship in wild-type p53 cell lines.

Human cancer cell lines with a combination of p53 mutation and high levels of expression of the Cyclin Dl protein are resistant to CDDP. This finding carries important clinical possibilities with regard to providing a potentially new parameter for predictive assays for CDDP responsiveness or a new target for modulating CDDP responsiveness.

The high correlation of p53 mutations with high Cyclin Dl levels or Cyclin Dl over- expression also provides a potential target for drug development. Efforts are being made to develop drugs against mutant forms of p53 and independently, against Cyclin Dl . Such drugs are likely to be more effective when used together to treat cancers with the above p53 mutations and Cyclin Dl over-expression. Such drugs might also be used in combination with other agents such as CDDP as potentiators of its effectiveness.

Figure 1 shows that in p53 mutant human cell lines there is a strong relationship between the level of Cyclin Dl protein and relative resistance to CDDP as measured by the D0.1 values. The implication is that human cancer cells with p53 mutations and high levels of Cyclin Dl protein are unlikely to respond to CDDP and an alternative therapy such as radiotherapy or taxol should be considered. It is possible that taxol sensitivity is not influenced by a combination of p53 mutation and Cyclin Dl protein over-expression. The Cyclin Dl/p53 mutation test may also detect resistance to other cytotoxic drugs such as etoposide. Thus the test will indicate situations where radiation might be a viable alternative to CDDP, or whether other cytotoxic agents might be more appropπate.

A clinical test may be developed for CDDP sensitivity based on the dual measurement of Cyclm Dl protein expression and the presence of mutations m the p53 gene. Cyclm Dl protein is typically measured by Western blotting or lmmunocytochemistry m a research environment but for diagnostic purposes cheaper and more rapid methods are preferable.

The determination of the mutational status of p53 can be effected by sequencing the genomic locus bearing the gene from the patient or by sequencing the expressed mRNA after conversion to cDNA Various nucleic acid sequencing methodologies are available at present, all of which are appropriate for use with this diagnostic assay. The typical method would be based on incorporation of terminating nucleotides into polymerase generated copies of a template, using the method of Sanger et al, 1977 Many alternatives have arisen recently including adaptor sequencing (PCT US95/12678), ligation based sequencing (PCT US96/05245), sequencing by hybridisation (A.D. Mirzabekov, TIBTech 12: 27 - 32, 1994) to list a few. Various methods for testing for specific mutations are known m the art, such as the TaqMan assay, oligonucleotide ligase assays, single strand conformational polymorphisms and assays based on hybridisation of template nucleic acids to oligonucleotide arrays

Because Cyclm Dl is a relatively short lived protein under cyclical transcπptional control, it is likely that mRNA levels for Cyclin Dl will follow the same pattern as the Cyclm Dl protein and show a similar strong relationship to CDDP resistance. This would make it possible to carry out a functional assay for resistance to CDDP by extracting mRNA from tumour samples and using this to determine the relative abundance of Cyclin Dl mRNA and to detect mutations in the p53 mRNA.

Oligonucleotide Arrays

Determination of mRNA levels can be effected m a number of ways One can readily convert poly-A bearing mRNA to cDNA using reverse transcription - a method is descπbed m the example illustrating this invention. Reverse Transcπptase PCR (RTPCR) methods allow the quantity of single RNAs to be determined, but with a relatively low level of accuracy. Arrays of oligonucleotides are a relatively novel approach to nucleic acid analysis, allowing mutation analysis, sequencing by hybridisation and mRNA expression analysis. Methods of construction of such arrays have been developed, (see for example: A.C. Pease et al. Proc. Natl. Acad. Sci. USA. 91,

5022 - 5026, 1994; U. Maskos and E.M. Southern, Nucleic Acids Research 21, 2269 -

2270, 1993; E.M. Southern et al, Nucleic Acids Research 22, 1368 - 1373, 1994) and further methods are envisaged. Arrays that measure expression levels of mRNAs and detect mutations in those RNAs are being developed and these offer an attractive embodiment of the diagnostic test proposed by this invention.

lmmunocytochemistry

An alternative embodiment of this invention can measure Cyclin Dl protein levels by immunocytochemistry using confocal laser fluorescence microscopy. Preferably a scanning system is used such as those described in PCT US91/09217, PCT NL/00081 and PCT/US95/01886. Additionally, it is desirable that the microscopy system is also able to analyse multiple fluorescent dyes. In a preferred embodiment, antibodies against mutant forms of p53 are labelled with one dye, an antibody against Cyclin Dl (sc-6281, Santa Cruz Biotechnology, CA) is labelled with a second dye whilst a third DNA binding dye can be used to select for aneuploid cells. DNA binding dyes such as Hoechst 33258 dye, which binds AT-rich DNA or Chromomycin A₃, which binds GC-rich DNA, are appropriate. Antibodies exist against a number of known mutant forms of the p53 protein. A diagnostic test may comprise the steps of:

• Extracting a biopsy of the tumour from a patient.

• Optionally micro-dissecting that material to separate normal tissue from tumour material.

• Preparing the biopsy material for microscopy which includes the steps of:

♦ Labelling the biopsy material with the above fluorescently labelled antibody probes against Cyclin Dl . The biopsy material may also, optionally be labelled with antibody probes against p53 mutant proteins and with a DNA binding dye.

♦ Separating the labelled cells from unbound labelled probes. • Placing the labelled biopsy material in a scanning confocal microscope to count cells that:

♦ Over-express or show elevated levels of Cyclin Dl , i.e. are labelled with at least a threshold quantity of antibody against Cyclin Dl.

♦ Optionally, express mutant forms of p53, i.e. are labelled with at least the threshold quantity of antibodies against p53 mutants. Alternatively, p53 mutational status might be determined by analysis of the mRNA or genomic DNA as discussed above.

♦ Optionally, have chromosomal amplifications as detected by the intensity of fluorescence from DNA binding fluorescent dyes.

Fluorescence Activated Cell Sorting

A further embodiment of the diagnostic test can exploit Fluorescence Activated Cell Sorting (FACS). A FACS instrument separates cells in a suspension in a manner dependent on the cells being labelled with a fluorescent marker. A typical FACS device operates as follows. Cells in a suspension travelling in single file are passed through a vibrating nozzle which causes the formation of droplets containing a single cell or none at all. The droplets pass through a laser beam. Fluorescence excited from each individual cell in its droplet by the laser is measured. After the detector the stream of cells in suspension pass through an electrostatic collar which gives the droplets a surface charge. The cells carrying droplets are given a positive or negative charge. If the drop contains a cell that fluoresces with an intensity above a particular threshold, the drop gets a charge of one polarity. Unlabelled cells get a charge of the opposite polarity. The charged droplets are then deflected by an electric field and depending on their surface charge are directed into separate containers and are counted Droplets that contain more than one cell scatter light more than individual cells which is readily detected and so these are left uncharged and enter a third disposal container. Multi-channel fluorescent detection devices have been constructed that can separate cells on the basis of labelling with multiple different fluorescent labels. These have multiple lasers which can excite fluorescence at different frequencies and the detector will detect different emission frequencies. A three label system is appropriate for this test. The same labelled probes as those described above for use in a confocal scanning fluorescence microscope would be appropriate. A diagnostic test might comprise the steps of:

• Extracting a biopsy of the tumour from a patient.

• Disrupting intracellular adhesion to form a single cell suspension.

• Labelling the suspended cells with the above fluorescently labelled probes against Cyclin D 1. The biopsy material may also, optionally be labelled with antibody probes against p53 mutant proteins and with a DNA binding dye.

• Separating the labelled cells from unbound labelled probes.

• Passing the labelled cell suspension through a FACS device to count cells that:

♦ Over-express or show elevated levels of Cyclin Dl, i.e. are labelled with the anti- Cyclin D 1 antibody above a threshold for 'normal' expression.

♦ Optionally, express a mutant form of p53, i.e. are labelled with at least a threshold quantity of antibody against mutant forms of p53.

Modulation of Cyclin Dl Expression in p53 Mutant Human Cancers At present many attempts are being made to develop drugs which inhibit Cyclin Dl . As this molecule has a vital function in controlling the progress of normal cells through the 'start' component of the Gl/S checkpoint such inhibitors would be likely to be extremely non-selective and very toxic to normal cells. The more specific relationship of resistance to CDDP and sensitivity to taxanes in p53 mutant human cancer cells having elevated Cyclin Dl levels described here provides a much more defined target for novel therapeutic agents which could potentially used in conjunction with taxanes, this being an agent with a proven track record of curing many (though by no means all) cancers. This approach is based on a concept of starting with therapeutic agents which already work to some extent and using techniques such as gene targeting to enhance the efficacy of already available therapeutic agents. In the case of patients who have mutant forms of p53, it may be possible to increase their responsiveness to platinating agents by decreasing their levels of Cyclin Dl. Cyclin Dl inhibitors are likely to be non-selectively toxic, but if administered at low doses in conjunction with an agent such as a taxane, the combination may be more effective against tumours than either alone, particularly to cells over-expressing Cyclin Dl .

Example 1

Human in vitro cell lines of different histological origin which exhibit a range of intrinsic sensitivity to cytotoxic drugs as measured by clonogenic cell survival assays, have been shown to provide appropriate models of the response of clinical tumours to chemotherapy. In particular, these cell lines exhibit the range of sensitivities to cytotoxic drugs and ionising radiation usually encountered in the clinic. These human in vitro cancer cell lines are now widely recognised as relevant models for the clinical response of tumours to chemotherapy. Intrinsic sensitivity to cytotoxic agents is measured by clonogenic assays of a range of human cancer cell lines. It is therefore possible to identify genes whose expression and/or mutational status is related to intrinsic sensitivity to cytotoxic agents in a wide range of human in vitro cell lines by measuring the expression of target genes and/or determining their mutational status and correlating these parameters to cell line sensitivity to cytotoxic agents. This procedure has identified genes relevant to clinical responsiveness to CDDP. Discoveries in human in vitro cell lines, such as those leading to this invention, therefore, have a strong possibility of being able to be translated into clinically useful tests for how well cancers may be expected to respond to treatment. The body of work that has been carried out to measure the clonogenic cell survival of a wide range of human in vitro cell lines of different histology after exposure to CDDP is described below.

Materials and Methods

Cell lines and clonogenic cell survival assays

The growth characteristics clonogenic assay procedures of the human in vitro cell lines used in this analysis have already been reported (Warenius et al 1994). The cell lines are listed, with their histological classification m Table 1. All are well established; many having been growing in vitro for several years. Cell lines were either donations or purchased by our laboratories. On receipt all were grown for 5 passages to provide sufficient cells for batch storage m liquid nitrogen. Duπng this peπod contamination was excluded by at least one passage in antibiotic free medium and mycoplasma testing was carried out on all lines. For clonogenic assays, cells were taken from a designated primary liquid nitrogen batch and grown for 3-6 passages until there were sufficient well-growing cells. Further batches from these cells were frozen m liquid nitrogen. Cells were routinely maintained m DMEM medium except RT112 and H322, which were grown m RPMI1640 and MGHU-1 which were grown in Ham's F12 medium. All lines were supplemented with 10% heat-mactivated fetal calf serum (HIFCS).

Table 1. p53 mutational status

c

CD

C H m

</) x m m

H c r- m σ>

In order to assay CDDP sensitivity 10²-10⁵ cells were plated m 3 ml of Ham's F12 medium supplemented with 10% FCS m 6 well plates and incubated at 37°C m an atmosphere of 5% C0₂ for 8 hours. Dilutions of 0.02-2.0 μg/ml from a 1 mg/ml stock solution of CDDP (light protected) were then made and 1 ml of the appropriate dilution were added to each plate to give a final volume of 4 ml. The plates were then incubated at

37°C in an atmosphere of 5% C0₂ in darkness for 14 days in the presence of the CDDP.

The medium was then removed, the cells were fixed m 70 % ethanol and stained with

10% Giemsa and colonies of > 100 cells counted. One 6 well plate was used for each drug dilution. The data points from all the assays were pooled to provide means and SEMs. A minimum of 3 separate clonogenic assays with 6 points/drug dose/assay were necessary for each cell line. CDDP cell survival was determined at the 10% clonogenic cell survival level (DO 1) by interpolation of the fitted regression curve

Identification of mutations in thep53 gene by PCR and DNA sequencing Material for PCR and DNA sequencing of p53 and Western blotting for Cyclm-Dl protein, was obtained from the same liquid nitrogen batches used to provide cells for clonogenic cell survival data. Cells were grown for up to three passages pπor to being subjected to the following procedures:

Nucleic Acid Isolation

RNA and genomic DNA were prepared from the cell lines descπbed here by the guamdimum isothiocyanate CsCl gradient method (Chirgwm et al, 1979, Barraclough et al, 1987). Bnefly, the cells were collected in ice-cold phosphate-buffered salme (PBS) and homogenised m guamdimum isothiocyanate buffer (4M guamdimum isothiocyanate, 50mM Tπs pH 7.5, 25mM EDTA pH 8.0, 0.5% (w/v) sodium lauryl sarcosme and 8% (v v) 2-mercaptoethanol added just prior to use. The homogenate was cleared by centπfugation at 8,000 rpm for 10 rams at 4°C (SS34 rotor, Sorvall RC-5B centrifuge) and the RNA pelleted by centπfugation of the homogenate through a cushion of 5.7M caesium chlonde/O.lM EDTA at 32,000 rpm for 20hr at 20°C (TST 41.14 rotor, Kontron Centπkon T20 60 ultracentnfuge). The pellet of RNA was redissolved m 0.1% (w/v) SDS and precipitated with ethanol overnight at -20°C before quantitation Polymerase Chain Reaction, cDNA synthesis and nucleotide sequencing

PCR (for exons 2-8 and for exons 9-11) was performed on DNA and RNA extracted from the human carcinoma cell lines. Each exon was then examined by DNA sequencing. PCR

Pπmers were designed flanking each exon and synthesised on an Applied Biosystems

381 A DNA synthesiser Each exon was amplified separately with the exceptions of exons

2 and 3 which were amplified as a unit, and exons 9, 10 and 11 which were amplified together by reverse transcπption polymerase chain reaction (RTPCR). The following pπmers were used:

Exon 2/3 sense 5'-CCC ACT TTT CCT CTT GCA GC-3'

Exon 2/3 antisense 5'-AGC CCA ACC CTT GTC CTT AC-3'

Exon 4 sense 5'-CTG CTC TTT TCA CCC ATC TA-3'

Exon 4 antisense 5'-GCA TTG AAG TCT CAT GGA AG-3'

Exon 5 sense 5'-TGT TCA CTT GTG CCC TGA CT-3'

Exon 5 antisense 5'-CAG CCC TGT CGT CTC TCC AG-3'

Exon 6 sense 5'-GCC TCT GAT TCC TCA CTG AT-3'

Exon 6 antisense 5'-TTA ACC CCT CCT CCC AGA GA-3'

Exon 7 sense 5'-ACT GGC CTC ATC TTG GGC CT-3'

Exon 7 antisense 5'-TGT GCA GGG TGG CAA GTG GC-3^*

Exon 8 sense 5'-T ATC CTG AGT AGT GG-3'

Exon 8 antisense 5'-T GCT TGC TTA CCT CG-3'

Exon 9/10/11 sense 5'-AGA AAG GGG AGC CTC ACC AC-3'

Exon 9/10/11 antisense 5'-CTG ACG CAC ACC TAT TGC AA-3'

Genomic DNA was digested with EcoRl and precipitated with ethanol and resuspended in 50μl of water (Sigma) before being subjected to PCR amplification. The DNA (l μg) was amplified m 50μl PCR reactions containing 20 pmoles of each pπmer. A 'hot start' PCR protocol was used with the dNTP's and Taq enzyme initially separated from the rest of the reaction components on a wax cushion. The reactions were placed m a pre-heated PCR block at 95°C for 2 minutes before undergoing thirty cycles of denaturation (30s at 95°C), annealing (30s at 60°C for exons 2-3, 4 and 6; 65°C for exons 5 and 8; 67°C for exon 7, and 68°C for exon 9-1 1) and extension (1 mm at 72°C). The PCR products were checked on a 0.8% (w/v) agarose gel before being purified using a Wizard minicolumn

(Promega), and used directly in sequencing reactions.

cDNA synthesis and RTPCR

Complementary DNA was synthesised from approximately 5μg of total RNA using oligo (dT) as a primer. Total RNA (5μg), human placental ribonuclease inhibitor (HPRI) 20U and l μg oligo (dT) were heated at 70°C for 10 minutes, chilled on ice, added to lx first strand buffer (50mM Tris-HCl, pH 8.3, 75mM potassium chloride and 3mM magnesium chloride), 0.01M DTT, dNTPs (0.5mM for each deoxyribonucleoside triphosphate), 400U of Superscript Reverse Transcriptase (Gibco) and incubated at 37°C for 1 hour. PCR for exons 9 to 1 1 was carried out using 5μl of the above incubation in a 50μl of PCR reaction as described in the previous section.

Nucleotide Sequencing

Sequencing primers (10 pmoles) were radioactively labelled at their 5' ends with ³²P-ATP (45μCi) at 37°C for 30 min in a reaction containing T4 Polynucleotide Kinase (PNK) (9.7U, Pharmacia) and lx T4 PNK buffer (lOmM Tris-acetate, lOmM magnesium acetate and 50mM potassium acetate). The primers used were identical to those employed in the PCR reactions except for exon 5 for which a separate sense sequencing primer was designed as follows: 5'-TAC TCC CCT GCC CTC-3'. Sequencing was carried out by the dideoxynucleotide enzymatic method (Sanger et al, 1977), using the fmol DNA Sequencing System (Promega). Any putative sequence mutations identified were confirmed by additional sequencing of the exon in the antisense direction as well as by carrying out a repeat PCR and sequencing of the cell line.

Western Blotting for Cyclin Dl

Two independent Western blottings with lysates for each cell line loaded in pairs on each gel were carried out. Standard conditions were used for the preparation of cells for lysates for Western blotting on each of the cell lines; 10⁷ cells were grown in 162 cm^" tissue culture flasks (Costar Ltd., High Wycombe, Bucks) until they were pre-confluent but still growing exponentially as confirmed by flow cytometry. Cells were then removed by trypsinisation, resuspended in complete medium + 10% FCS and washed 3 times by serial centπfugation and resuspension in PBS without serum. 1-3 x 10⁸ viable cells were then pelleted by centπfugation and resuspended at 3x10⁷ cells per ml of lysate buffer (Stock solution. 10% SDS 10ml., 0.5M Tπs pH 6.8, glycerol 10 ml., Double distilled water 62 ml. To 10 ml. of stock solution were added 100 ml of 10 mM Leupeptm + 10 ml 100 mM

PMSF) Protein estimations were performed and the final concentration of the lysates adjusted to 300 μg total cellular protein per 100 μl. To measure Cyclm Dl protein, 150 μg of total cellular protein in 50 μl of lysate buffer was added per lane well to a 7.5%

Laemmh separating gel and electrophoresis carried out at 16°C using 60V over 16 hours and a constant cuπent of 500mA Blots were transferred to nitrocellulose at 22°C over 16 hours using to a semi-dry blotting apparatus (Biorad, Richmond, CA), incubated with the a mouse IgGj monoclonal antibody to mammalian Cychns (Gl 24-259.5, Pharmmgen) and then incubated with rabbit anti-mouse conjugated antibodies (Dako, UK) at 1/1000 and developed in alkaline phosphatase buffer containing Nitroblue Tetrazohum and 5-

Bromo-4-Chloro-3-Indoyl Phosphate, (Sigma, Poole, Dorset, UK) (50mg/ml m dimethylformamide) for 1 hr at room temperature m darkness. Colour development was arrested with double distilled water, and the blots were dπed flat. Cychns were clearly resolved as distinct bands, Cyclm Dl having the lowest mobility.

Quantitation of the protein product of the Cyclm Dl gene was earned out by measurement of optical density on a Schimadzu scanning densitometer with tungsten light and expressed as O D. units per 150 μg of total cellular protein. Titration curves obtained by loading different amounts of total cellular protein have previously shown that linear relationships for optical density (O.D.) could be obtained over the range found for Cyclm Dl protein across the cell lines (Waremus et al 1994, Browning 1997). In order to compare different Cyclm Dl protein levels between the cell lines, the mean O D. value for all the lines was calculated and the relative O.D. for Cyclin Dl protein in each individual cell line was normalised to the mean O D. and multiplied by an arbitrary value of 5.0

Results

Mutations were found m mRNA expressed from the p53 gene in a number of the cell lines (see Table 1) The mutations identified m the cell lines descπbed here were in exons 5-8 which are known to contain the majoπty of p53 mutations (Hollstem et al,

1991) All these mutations have been previously described apart from the nonsense mutation identified m codon 166 of the RPMI7951 line. This along with the G to T transversion m codon 298 of H417 did not he withm the most highly conserved region of the p53 gene In the OAW42 ovarian carcinoma cell line the single base missense mutation from CGA to CGG was silent, so that the mutant triplet still coded for the same amino acid (Arg) as is present in wild-type p53 (wtp53) protein. A normal p53 protein was thus expressed in half of the cell lines The mRNA of the other half of the cell lines coded for abnormal p53 protein. RPMI7951 and H417 possessed stop mutations resulting in 165 and 297 amino acid truncated proteins respectively. COLO320 and H322 independently exhibited a missense G:C to A:T mutation at the same site resulting in an ammo-acid substitution from Arg to Tryp. RT112 and HT29/5 also had mutations coding for changes in Arg (to Gly and His respectively) COLO320, H322 and RT112 were homozygous for p53 mutations. The other three mutant lines showed evidence of retention of heterozygosity HT29/5 and RPMI7951 both expressed small amounts of wild-type p53 mRNA though H417 expressed relatively high levels.

The relationship between Cyclm Dl levels and CDDP sensitivity was examined for all cell lines and then independently m the wtp53 and mp53 cells. The ranges of Cyclm-Dl protein levels m wtp53 cells and mp53 cells overlapped (3.33-10.39 and 3.58-8.46 respectively) Only m p53 mutant cells was a useful correlation found between Cyclm Dl protein levels and resistance to CDDP.

Thus, m mutant p53 cell lines, the higher the Cyclm Dl levels, the more likely it is that the cells are resistant to CDDP (Figure 1). This correlation is not found in wild-type p53 cell lines (Figure 2). References

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Claims

CLAIMS:

1. A method for measuring the resistance of p53 mutant cancer cells to the cytotoxic effects of a chemotherapeutic agent, which method comprises testing a sample comprising p53 mutant cells or an extract therefrom for the level of expression of Cyclin Dl or for the abundance of Cyclin Dl protein.

2. A method according to claim 1, wherein the sample is extracted from a subject.

3. A method according to claim 1 or claim 2, wherein the chemotherapeutic agent is a platinating agent.

4. A method according to claim 3, wherein the platinating agent is CDDP.

5. A method according to any preceding claim, wherein the testing for the abundance of Cyclin Dl protein comprises measuring the abundance of Cyclin Dl mRNA.

6. A method according to claim 5, wherein the measurement of the abundance of Cyclin Dl mRNA comprises contacting the sample with a probe for Cyclin Dl mRNA.

7. A method according to any of claims 1-4, wherein the testing is carried out using Western blotting.

8. A method according to any of claims 1-4, wherein the testing comprises contacting the sample with a labelled antibody against Cyclin D 1 protein.

9. A method according to claim 8, wherein the antibody against Cyclin Dl protein is 14841 C (from clone number G- 124-259.5, Pharmingen USA).

10. A method according to any preceding claim, wherein p53 mutant cells are identified by contacting the sample with a labelled antibody against mutant p53.

11. A method according to any of claims 8-10, wherein at least one antibody is labelled with a fluorescent label.

12. A method according to any preceding claim, further comprising contacting the sample with a DNA binding dye for labelling aneuploid cells.

13. A method according to claim 12, wherein the DNA binding dye is Hoechst 33258, or Chromomycin A₃ dye.

14. A method according to any preceding claim, wherein the sample is a sample of cells.

15. A method according to claim 14, wherein the testing is carried out by performing a cell count.

16. A method according to claim 15, wherein the cell count is performed using multi- parameter flow cytometry.

17. A method according to claim 15, wherein the cell count is performed using scanning confocal microscopy.

18. A method according to claim 15, wherein the cell count is performed using fluorescence activated cell sorting.

19. A method according to any of claims 15-18, wherein the sample of cells is micro- dissected prior to performing the cell count, to separate normal tissue from tumour tissue.

20. A method according to any of claims 15-19, wherein prior to performing the cell count, intracellular adhesion in the sample of cells is disrupted, to form a single cell suspension.

21. A method for selecting an agent for treating cancer, which method comprises:

(a) testing a sample comprising p53 mutant cells, or an extract therefrom, for the level of expression of Cyclin Dl or for the abundance of Cyclin Dl protein, and

(b) if Cyclin Dl is over-expressed, and/or Cyclin Dl protein is present at elevated levels, selecting for treatment an agent other than a platinating agent;

(c) if Cyclin Dl is not over-expressed and/or Cyclin Dl protein is substantially not present at elevated levels, selecting for treatment a chemotherapeutic agent comprising a platinating agent.

22. A method according to claim 21, wherein the selection for treatment is carried out according to step (b) and the agent other than a platinating agent is ionising radiation, or is a taxane.

23. A method according to claim 21, wherein the selection for treatment is carried out according to step (c) and the agent comprising a platinating agent is an agent comprising CDDP.

24. A kit for measuring the resistance of p53 mutant cancer cells to the cytotoxic effects of a chemotherapeutic agent, which kit comprises:

(i) a means for testing for the level of expression of Cyclin Dl or for the abundance of Cyclin Dl protein; and (ii) a means for identifying p53 mutant cells.

25. A kit according to claim 24, wherein the means for testing for the abundance of Cyclin Dl protein comprises a probe for Cyclin Dl mRNA.

26. A kit according to claim 24, wherein the means for testing for the abundance of Cyclin Dl protein comprises a labelled antibody against Cyclin Dl protein.

27. A kit according to claim 26, wherein the antibody against Cyclin Dl protein is

14841 C (from clone number G-124-259.5, Pharmingen USA).

28. A kit according to any of claims 24-27, wherein the means for identifying p53 mutant cells comprises a labelled antibody against mutant p53.

29. A kit according to any of claims 26-28, wherein at least one antibody is labelled with a fluorescent label.

30. A kit according to any of claims 24-29, further comprising a DNA binding dye, for labelling aneuploid cells.

31. A kit according to claim 30, wherein the DNA binding dye is Hoechst 33258, or Chromomycin A₃ dye.

32. Use of a means for testing for the level of expression of Cyclin Dl or for the abundance of Cyclin Dl protein, for measuring the resistance of cancer cells to the cytotoxic effects of a chemotherapeutic agent.

33. Use of a means for identifying p53 mutant cells, for measuring the resistance of cancer cells to the cytotoxic effects of a chemotherapeutic agent.