WO1999042090A2

WO1999042090A2 - Treating cancer

Info

Publication number: WO1999042090A2
Application number: PCT/GB1999/000502
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: EP1057032B1; US6878526B1; DE69907154D1; DE69907156T2; JP2002504688A; AU2538599A; DE69907155T2; AU2630099A; WO1999042090A3; WO1999042821A2; EP1057029B1; ATE238554T1; CA2321481A1; JP2002504496A; EP1057030B1; JP2002503822A; WO1999042834A2; WO1999042837A1; AU2538099A; EP1057033A1

Abstract

Provided is a method for selecting a chemotherapeutic 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 D1 or for the abundance of Cyclin D1 protein; and (b) if Cyclin D1 is over-expressed, and/or Cyclin D1 protein is present at elevated levels, selecting for treatment a chemotherapeutic agent comprising a taxane; (c) if Cyclin D1 is not overexpressed and/or Cyclin D1 protein is substantially not present at elevated levels, selecting for treatment a chemotherapeutic agent comprising an agent other than a taxane. Also provided is a kit for selecting a chemotherapeutic agent for treatment, which kit comprises: (a) a means for identifying p53 mutant cells; and (b) a means for testing for the level of expression of Cyclin D1 or for the abundance of Cyclin D1 protein in cells or in a sample therefrom.

Description

TREATING CANCER

The present invention concerns a method for selecting the most appropriate therapy for patients suffering from cancer. The invention is particularly concerned with selecting a chemotherapeutic agent for treating cancer. The invention is particularly useful for choosing between a treatment agent comprising a platinating agent and a treatment agent comprising a taxane such as Paclitaxel (taxol).

Although radiotherapy and chemotherapy have been responsible for curing many people of cancer in 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 platinating agents often show encouraging initial responses to chemotherapy (which often involves the use of cis- diamminedichloroplatinum (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 taxanes (e.g. taxol) or different therapies such as radiotherapy might be appropriate. 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, and genes responsible for the molecular control of proliferating cells proceeding through the cell division cycle (cell cycle), may not only be implicated in carcinogenesis, 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 in the public domain has suggested that mutations in 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 in 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, platinating agents or the newer cytotoxic agents such as taxanes.

The effect of 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 clinic. Discoveries in 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 cyclins, whose levels fluctuate throughout the cell cycle, and cyclin dependent kinases (CDKs) which become active when they join with cyclins. The cyclin/CDK complexes can be inhibited by proteins termed cyclin dependent kinase inhibitors (CDKIs) which include the protein p21 WAF1/CIP1 (p21).

The protein products of the Cyclin Dl and Bl genes and their respective cyclin- dependent kinase 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 Cyclin Dl protein in a series of 16 human cancer cell lines has been shown to be related to their intrinsic resistance to the cytotoxic drug CDDP (Warenius et al., 1996). Cyclin Dl protein levels, however, showed no relationship with radiosensitivity, another treatment modality. The relationship between Cyclin Dl and CDDP resistance is not, however, strong enough on its own to provide the basis of clinically useful predictive assays.

Paclitaxel, which is a member of the class of anti-cancer drugs known as taxanes, has been shown clinically to be of benefit when added to treatment with platinating agents in the clinical treatment of ovarian cancer. It has been reported that cells can become more sensitive to Paclitaxel when they lose normal p53 function as a result of infection with human papilloma virus constructs or SV40 virus constructs (Wahl et al, Nature Medicine, vol. 2, No. 1, 72-79, 1996). This is thought to result from increasing G2/M arrest and apoptosis. However, it is not the case that all p53 mutant cancer cells are sensitive to taxol. Accordingly, based on this correlation on its own these studies have not been able to engender a reliable predictive method for determining a likely effective treatment in specific cases.

It is an aim of the present invention to solve the problems associated with the prior art and to provide a method which can be used to predict a specific treatment which is likely to be successful in specific cases.

Thus, this invention provides methods of predicting whether human cancer cells are best treated with taxanes such as taxol or with other agents such as 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 to which a therapy that is more cancer specific can potentially be directed.

In particular, this invention provides a method for selecting a chemotherapeutic 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 a chemotherapeutic agent comprising a taxane;

(c) if Cyclin Dl is not overexpressed and/or Cyclin Dl protein is substantially not present at elevated levels, selecting for treatment a chemotherapeutic agent comprising an agent other than a taxane.

This application also provides a kit for selecting a chemotherapeutic agent for treatment, which kit comprises:

(a) a means for identifying p53 mutant cells; and

(b) a means for testing for the level of expression of Cyclin Dl or for the abundance of Cyclin D 1 protein in cells or in a sample therefrom.

The present invention is advantageous, since previously there were no indicators that simultaneously measuring the mutational status and/or levels of expression of the protein products of two or more 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 best treated with taxanes, or with alternative agents.

Thus using the present invention, in appropriate cases chemotherapeutic agents other than taxanes, such as CDDP, can be ruled out of the treatment regime before treatment begins and replaced with taxanes, such as taxol. This has the advantage of avoiding unnecessary treatment which might be harmful to the patient and also saves money by finding the correct treatment more quickly. In addition, the patient receives the right treatment earlier in the procedure, saving time which is vital for the patient's chances of recovery.

The over-expression of Cyclin Dl, or the elevation of Cyclin Dl protein levels can be measured by any appropriate method. The point at which it is considered that the level is elevated or that the expression is overexpression is well known to the skilled person in this field, according to general teaching from the literature (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 specifically deals with measuring the levels of Cyclin Dl protein, in cells whose p53 mutational status has been determined (e.g. by DNA sequencing). High Cyclin Dl levels or high Cyclin Dl expression together with p53 mutation is indicative of a resistance to the cytotoxic effects of a chemotherapeutic agent other than a taxane (e.g. platinating agents such as CDDP) and is also strongly associated with a sensitivity to taxanes. Thus, as Cyclin Dl levels rise, whilst the cells are more likely to be resistant to platinating agents, they remain highly likely to be sensitive to taxanes (see Figure 1).

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 resistance to Cisplatin (black points) and resistance to taxanes (white points) in mutant p53 cell lines, as the Cyclin Dl levels increase; 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 the cytotoxic effects of chemotherapeutic agents such as CDDP, but are sensitive to taxanes. These findings carry important clinical possibilities with regard to providing a potentially new parameter for predictive assays for taxane responsiveness or a new target for modulating taxane responsiveness.

The high correlation of taxane sensitivity to CDDP resistance in cells with p53 mutations, and 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 taxol as potentiators of its effectiveness.

Figure 1 shows that in p53 mutant human cell lines with high Cyclin Dl levels or Cyclin Dl over-expression there is a strong relationship between resistance to CDDP and sensitivity to taxol, as measured by the D0.1 values (the dose of the drug which reduces clonogenic survival to 10% of the control, untreated cells). Thus human cancer cells with p53 mutations and high levels of Cyclin Dl protein which do not respond to CDDP will very likely respond to taxanes as an alternative therapy. The Cyclin Dl/p53 mutation test may also indicate a correlation of taxane sensitivity to resistance to other cytotoxic drugs such as etoposide.

A clinical test may be developed for taxane sensitivity based on the measurement of Cyclin Dl protein expression and the presence of mutations in the p53 gene. Cyclin Dl protein is typically measured by Western blotting or immunocytochemistry.

A specific example of a chemotherapeutic agent, the resistance against which is often compared with taxane sensitivity, is CDDP. Thus using the present invention, in appropriate cases CDDP can be ruled out of the treatment regime before treatment begins and replaced with taxol. Further examples of agents which can be replaced with taxanes include other platinating agents, such as carboplatin and paraplatin as well as other chemotherapeutic agents, for example alkylating agents, DNA intercalating agents such as Doxorubicin, topoisomerase inhibitors, anti-metabolites such as methotrexate, 5- fluorouracil, DNA synthesis inhibitors such as cytosine arabinoside, and mitotic inhibitors such as the vinca alkaloids.

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 is 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 in 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 Cyclin Dl is a relatively short lived protein under cyclical transcriptional control, it is likely that mRNA levels for Cyclin Dl follow the same pattern as the Cyclin Dl protein and show a similar strong relationship to CDDP resistance. This makes 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 in a number of ways. One can readily convert poly-A bearing mRNA to cDNA using reverse transcription - a method is described in the example illustrating this invention. Reverse Transcriptase 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. Immunocytochemistry

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. 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 Dl 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.

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

Modulation of Cyclin Dl Expression inp5S 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 overexpressing Cyclin Dl.

Example 1

Human in vitro cell lines of different histological origin which exhibit a range of intrinsic sensitivities to cytotoxic drugs as measured by clonogenic cell survival assays, have been shown to provide appropriate models for 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, can be translated into clinically useful tests for how well cancers may be expected to respond to treatment. The experimentation that has been undertaken to measure the clonogenic cell survival of a wide range of human in vitro cell lines of different histology after exposure to taxanes is described below.

Materials and Methods

Cell lines and clonogenic cell survival assays

The growth characteristics clonogenic assay procedures of the 11 human in vitro cell lines used in this analysis have already been reported e.g. in Britten R.A. and Warenius H., Eur. J. Cane. 29A, 1315-1320 (1993). The cell lines are listed, with their histological classification in Table 2. 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 in liquid nitrogen. During this period 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 in liquid nitrogen. Cells were routinely maintained in DMEM medium. All lines were supplemented with 10% heat- inactivated foetal calf serum (HIFCS). Table 1 also shows relative values for Cyclin Dl levels in five p53 mutant and six p53 wild-type human in vitro cell lines. Also shown are the absolute and relative DO.l values (i.e. the dose of the drug that reduces the clonogenic cell survival to

10% of the untreated control cells) for CDDP and taxol. The DO.l values were obtained by several independent clonogenic assays and the data fitted by linear regression analysis.

The clonogenic assays were repeated until statistically satisfactory fits were achieved on linear regression. The DO.l values were obtained by interpolation of the linear regression lines. The cytotoxic drug DO.l values have been normalised and expressed as relative

DO.1 values, to enable the relative sensitivity of each cell to each of the drugs to be compared. In order to normalise the values, the mean DO.1 was calculated independently for CDDP and taxol; each absolute DO.l value was then adjusted by dividing by the mean value to give a relative DO.1 value for each drug for each cell line.

The results set out in Table 1 are plotted in the graphs shown in Figures 1 and 2. Figure 1 shows relative DO.l values for CDDP and taxol in five p53 mutant cell lines. Three of the cell lines are relatively resistant to CDDP, but not to taxol. The remaining two cell lines which are less relatively resistant to CDDP are only slightly more sensitive to taxol than to CDDP. There would thus be an advantage in using taxol rather than cisplatin in the former three cell lines, but not in the latter two.

Figure 2 shows that there is no relationship between Cyclin Dl protein levels and relative sensitivity to CDDP in wild type p53 cells. Moreover, some cell lines are relatively more resistant to taxol than CDDP. Thus, in wild-type p53 cell lines, Cyclin Dl is not a useful indicator either of resistance to CDDP or of whether the cell that would preferentially respond to taxol rather than CDDP.

Table 1

*(±1 S.E.M.)

The Histology of the cell lines used in the above investigations is shown below in Table 2.

Table 2

In order to assay CDDP sensitivity 10²-10⁵ cells were plated in 3 ml of Ham's F12 medium supplemented with 10% FCS in 6 well plates and incubated at 37°C in an atmosphere of 5% CO₂ 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% CO₂ in darkness for 14 days in the presence of the CDDP. The medium was then removed, the cells were fixed in 70% ethanol and stained with 10% Giemsa and colonies of > 100 cells counted. One 6 well plate was used for each drug dilution. 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.l) by interpolation of the fitted regression curve.

To measure taxol sensitivity, the same protocol as described above for CDDP was employed, except an amphiphilic solubilising agent was added with the taxol.

Identification of mutations in thep53 gene by PCR and DNA sequencing

Material for PCR and DNA sequencing of p53 and Western blotting for Cyclin-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 prior to being subjected to the following procedures:

Nucleic Acid Isolation

RNA and genomic DNA were prepared from the cell lines described here by the guanidinium isothiocyanate CsCl gradient method (Chirgwin et al, 1979, Barraclough et al, 1987). Briefly, the cells were collected in ice-cold phosphate-buffered saline (PBS) and homogenised in guanidinium isothiocyanate buffer (4M guanidinium isothiocyanate, 50mM Tris pH 7.5, 25mM EDTA pH 8.0, 0.5% (w/v) sodium lauryl sarcosine and 8% (v/v) 2-mercaptoethanol added just prior to use. The homogenate was cleared by centrifugation at 8,000 rpm for 10 mins at 4°C (SS34 rotor, Sorvall RC-5B centrifuge) and the RNA pelleted by centrifugation of the homogenate through a cushion of 5.7M caesium chloride/O.lM EDTA at 32,000 rpm for 20hr at 20°C (TST 41.14 rotor, Kontron Centrikon T20 60 ultracentrifuge). The pellet of RNA was re-dissolved in 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 Primers were designed flanking each exon and synthesised on an Applied Biosy stems 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 transcription polymerase chain reaction (RTPCR). The following primers 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 re-suspended in 50μl of water (Sigma) before being subjected to PCR amplification. The DNA (l μg) was amplified in 50μl PCR reactions containing 20 pmoles of each primer. 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 in 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 exons 9-11) and extension (1 min 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 lμg 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 11 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 16 cell lines; 10⁷ cells were grown in 162 cm² 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, re-suspended in complete medium +10% FCS and washed 3 times by serial centrifugation and re-suspension in PBS without serum. l-3xl0⁸ viable cells were then pelleted by centrifugation and re-suspended at 3x10⁷ cells per ml of lysate buffer (Stock solution: 10% SDS 10ml., 0.5M Tris pH 6.8, glycerol 10 ml., Double distilled water 62 ml. To 10 ml. of stock solution were added 100 ml of 10 mM Leupeptin + 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 Cyclin Dl protein, 150μg of total cellular protein in 50μl of lysate buffer were added per lane well to a 7.5% Laemmli separating gel and electrophoresis carried out at 16°C using 60V over 16 hours and a constant current 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 IgG_! monoclonal antibody to mammalian cyclins (Gl 24-259.5, Pharmingen) and then incubated with rabbit anti-mouse conjugated antibodies (Dako, UK) at 1/1000 and developed in alkaline phosphatase buffer containing Nitroblue Tetrazolium and 5-Bromo-4-Chloro-3-Indoyl Phosphate, (Sigma, Poole, Dorset, UK) (50mg/ml in dimethylformamide) for 1 hr at room temperature in darkness. Colour development was arrested with double distilled water, and the blots were dried flat. Cyclins were clearly resolved as distinct bands, Cyclin Dl having the lowest mobility.

Quantitation of the protein product of the Cyclin Dl gene was carried out by measurement of optical density on a Schimadzu scanning densitometer with tungsten light and expressed as O.D. units per 150μg 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 Cyclin Dl protein across the cell lines (Warenius et al 1994, Browning 1997). In order to compare different Cyclin 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 in mRNA expressed from the p53 gene in 5 of the 11 cell lines. The mutations identified in the cell lines described here were in exons 5-8 which are known to contain the majority of p53 mutations (Hollstein et al, 1991). All these mutations have been previously described. 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 6 of the 11 cell lines. The mRNA of the other 5 cell lines coded for abnormal p53 protein. RT112 and HT29 also had mutations coding for changes in Arg (to Gly and His respectively). RT112 was homozygous for p53 mutations.

The relationship between Cyclin Dl levels and CDDP sensitivity was examined for all 11 cell lines and then independently in the wtp53 and mp53 cells. The ranges of Cyclin-Dl protein levels in wtp53 cells and mp53 cells overlapped (0.28-6.65 and 3.21-9.39 respectively). In p53 mutant cells having elevated Cyclin Dl protein levels a useful correlation was found between taxane sensitivity and resistance to CDDP (see Figure 1). In mutant p53 cell lines, the more elevated the Cyclin Dl levels, the more resistant the cells are to the cytotoxic effects of chemotherapeutic agents other than taxanes (e.g.

CDDP), but it is likely that these cells are instead sensitive to taxanes. In other words, in p53 mutant cell lines, Cyclin Dl over expression or elevated Cyclin Dl protein levels is an indicator that cells which are resistant to platinating agents will remain responsive to taxanes, whereas cell lines with low Cyclin Dl expression are likely to benefit from treatment with either taxanes or platinating agents (see Figure 1). However, the same correlation is not found in wild-type p53 cells, in which some cell lines which are relatively resistant to CDDP are also resistant to taxanes, whilst others which are also relatively resistant to CDDP are sensitive to taxanes.

Accordingly, the present invention allows selection of an appropriate treatment for certain cancers by identifying the p53 mutational status, and Cyclin Dl expression or Cyclin Dl protein level elevation in tumour cells; if platinating agents are ineffective for such cells, then a taxane is likely to be an effective agent for treatment of the cancer instead.

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Claims

CLAIMS:

1. A method for selecting a chemotherapeutic 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 a chemotherapeutic agent comprising a taxane;

2. A method according to claim 1, wherein the chemotherapeutic agent is selected according to step (b), and the taxane comprises taxol.

3. A method according to claim 1, wherein the chemotherapeutic agent is selected according to step (c), and the agent other than a taxane comprises a platinating agent.

4. A method according to claim 2, wherein the chemotherapeutic agent selected for treatment further comprises a platinating agent.

5. A method according to claim 3, wherein the chemotherapeutic agent selected for treatment further comprises a taxane.

6. A method according to any preceding claim, wherein the sample is extracted from a subject.

7. 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.

8. A method according to claim 7, wherein the measurement of the abundance of

Cyclin Dl mRNA comprises contacting the sample with a probe for Cyclin Dl mRNA.

9. A method according to any of claims 1-6, wherein the testing for the abundance of Cyclin Dl protein is carried out using Western blotting.

10. A method according to any of claims 1-6, wherein the testing for the abundance of Cyclin Dl protein comprises contacting the sample with a labelled antibody against Cyclin Dl protein.

11. A method according to claim 10, wherein the antibody against Cyclin Dl protein is 14841 C (from clone number G-124-259.5, Pharmingen USA).

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

13. A method according to any of claims 10-12, wherein at least one antibody is labelled with a fluorescent label.

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

15. A method according to claim 14, wherein the DNA binding dye is Hoechst 33258, or Chromomycin A₃ dye.

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

17. A method according to claim 16, wherein the testing is carried out by performing a cell count.

18. A method according to claim 17, wherein the cell count is performed using multi- parameter flow cytometry.

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

20. A method according to claim 17, wherein the cell count is performed using fluorescence activated cell sorting.

21. A method according to any of claims 17-20, wherein the sample of cells is micro- dissected prior to performing the cell count, to separate normal tissue from tumour tissue.

22. A method according to any of claims 17-21, wherein prior to performing the cell count, intracellular adhesion in the sample of cells is disrupted, to form a single cell suspension.

23. A method according to any preceding claim, for selecting either an agent comprising a taxane, or an agent comprising a platinating agent, for treating cancer.

24. A kit for selecting a chemotherapeutic agent for treatment, which kit comprises:

(a) a means for identifying p53 mutant cells; and

(b) a means for testing for the level of expression of Cyclin Dl or for the abundance of Cyclin Dl protein in cells or in a sample therefrom.

25. A kit according to claim 24, for selecting either an agent comprising a taxane, or an agent comprising a compound other than a taxane such as a platinating agent, for treating cancer.

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

27. A kit according to claim 24 or claim 25, wherein the means for testing for the abundance of Cyclin Dl protein comprises a labelled antibody against Cyclin Dl protein.

28. A kit according to claim 27, wherein the antibody against Cyclin Dl protein is 14841 C (from clone number G-124-259.5, Pharmingen USA).

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

30. A kit according to any of claims 27-29, wherein at least one antibody is labelled with a fluorescent label.

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

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

33. Use of a means for identifying p53 mutant cells, for selecting either an agent comprising a taxane, or an agent comprising a platinating agent, for treating cancer.

34. Use of a means for testing for the abundance of Cyclin Dl protein in cells or in a sample therefrom, for selecting either an agent comprising a taxane, or an agent comprising a platinating agent, for treating cancer.