COMPOSITIONS AND METHODS FOR TREATING CANCER
This present invention compositions and methods of treating cancer and methods of accessing/monitoring the responsiveness of a cancer cell to a therapeutic compound.
This application a division of U.S. patent application Ser. No. 14/948,914, filed Nov. 23, 2015, which is a continuation of U.S. patent application Ser. No. 11/975,997, filed Oct. 22, 2007, which claims priority to U.S. Provisional Application No. 60/853,208, filed Oct. 20, 2006 and to U.S. Provisional Application No. 60/895,606, filed Mar. 19, 2007, the contents of each of which are incorporated by reference in their entireties.
STATEMENT AS TO FEDERALLY SPONSORED RESEARCHThis invention was made with U.S. government support under grant numbers RO1HL052725, RO1DK043889, PO1HL054785, and CA009361 awarded by The National Institutes of Health. The government has certain rights in the invention.
INCORPORATION-BY-REFERENCE OF SEQUENCE LISTINGThe contents of the file named “DFCI-070D01US_ST25.txt”, which was created on Aug. 5, 2019 and is 6 KB in size, are hereby incorporated by reference in their entirety.
FIELD OF THE INVENTIONThis invention relates generally to methods of methods of treating cancer. More specifically, the invention relates to methods of accessing the responsiveness of a cancer cell to a therapeutic compound.
BACKGROUND OF THE INVENTIONDNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light can cause DNA damage, resulting in as many as 1 million individual molecular lesions per cell per day. Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes. Other lesions induce potentially harmful mutations in the cell's genome, which will affect the survival of its daughter cells after it undergoes mitosis. Consequently, the DNA repair process must be constantly active so it can respond rapidly to any damage in the DNA structure.
The rate of DNA repair is dependent on many factors, including the cell type, the age of the cell, and the extracellular environment. A cell that has accumulated a large amount of DNA damage, or one that no longer effectively repairs damage incurred by its DNA, can enter one of three possible states: an irreversible state of dormancy, known as senescence; cell suicide, also known as apoptosis or programmed cell death or unregulated cell division, which can lead to the formation of a tumor.
SUMMARY OF THE INVENTIONThe present invention is based on the discovery that tumor cells have altered DNA repair and DNA damage response pathways and that loss of one of these pathways renders the cancer more sensitive to a particular class of DNA damaging agents. More particularly, the invention is based in part upon the discovery that a defect in two DNA repair pathways in a cell is lethal.
The present invention provides methods of treating cancer in a subject. In one embodiment, the method of treating cancer includes (a) determining whether the cancer cell is deficient in a DNA repair pathway and (b) administering a DNA damaging agent or inhibitor specific for at least one different DNA repair pathway than that identified in step (a) to the subject. In another embodiment, the method of treating cancer in a subject includes (a) determining whether the cancer cell is deficient in a DNA repair pathway, (b) identifying a DNA repair pathway protein or gene that is upregulated in the cancer cell and (c) administering a DNA damaging agent or inhibitor specific for the DNA repair pathway protein or gene identified in step (b) to the subject.
The present invention also provides methods for selecting a therapeutic agent for a particular cancer cell including (a) determining a deficiency in one or more DNA repair pathways in the cancer cell relative to a normal cell and (b) selecting a DNA damaging agent or inhibitor specific for at least one DNA repair pathway other than the DNA pathway identified in step (a).
The present invention also provides methods of determining the resistance or sensitivity of a cancer cell to a chemotherapeutic agent. In one embodiment, the method of determining the resistance of a cancer cell to a chemotherapeutic agent includes identifying a deficiency in a DNA repair pathway, where the presence of the deficiency indicates the cell is resistant to a chemotherapeutic agent specific for the DNA repair pathway. In another embodiment, the method of determining the sensitivity of a cancer cell to a chemotherapeutic agent includes identifying a deficiency in a DNA repair pathway, where the absence of the deficiency indicates the cell is sensitive to a chemotherapeutic agent specific for the DNA repair pathway.
The present invention also provides methods of identifying and modulating the responsiveness of a cancer cell to treatment. In one embodiment, the method of identifying the responsiveness of a cancer cell to a DNA crosslinking agent or ionizing radiation includes identifying a deficiency in the homologous recombination and crosslinking repair (FA/HR) DNA repair pathway, where the presence of the deficiency indicates the cell is sensitive to DNA cross linking agent or ionizing radiation, whereas an absence if the efficiency indicates the cell is resistant to DNA crosslinking agent or ionizing radiation. In another embodiment, a method of increasing the responsiveness of a cancer cell to a DNA crosslinking agent or ionizing radiation includes contacting the cancer cell with an inhibitor of the homologous recombination and crosslinking repair (FA/HR) DNA repair pathway. In another embodiment, the method of identifying the responsiveness of a cancer cell to a MAP2KAP2 inhibitor includes detecting phosphorylation of MAP2KAP2, where the presence of the phosphorylation indicates the cell is sensitive to a MAP2KAP2 inhibitor, whereas an absence of the phosphorylation indicates the cell is resistant to a MAP2KAP2 inhibitor. In another embodiment, the method of identifying the responsiveness of a cancer cell to a FA/HR DNA repair pathway inhibitor includes identifying a deficiency in the mismatch repair (MMR) DNA repair pathway, where the presence of the deficiency indicates the cell is sensitive to a FA/HR DNA repair pathway inhibitor whereas an absence if the efficiency indicates the cell is resistant to a FA/HR DNA repair pathway inhibitor.
The present invention also provides methods of assessing the effectiveness or monitoring the treatment of a subject with cancer. In one embodiment, the method of accessing the effectiveness of a treatment of a subject with cancer includes (a) measuring the level of an effective amount of two or more DNARMARKERS selected from DNARMARKERS 1-259 in a sample from the subject, and (b) comparing the level of the effective amount of the two or more DNARMARKERS to a reference value. In another embodiment, the method of monitoring the treatment of a subject with cancer includes (a) detecting the level of an effective amount of two or more DNARMARKERS from DNARMARKERS 1-259 in a first sample from the subject at a first period of time, (b) detecting the level of an effective amount of two or more DNARMARKERS in a second sample from the subject at a second period of time, and (c) comparing the level of the effective amount of the two or more DNARMARKERS detected in step (a) to the amount detected in step (b), or to a reference value. In another embodiment, the method of monitoring the treatment of a subject with cancer includes (a) determining whether the cancer cell is deficient in a DNA repair pathway at a first period of time, (b) determining whether the cancer cell is deficient in the DNA repair pathway identified in step (a) at a second period of time; where a decrease in the deficiency in the DNA repair pathway indicates the treatment is not efficacious, whereas a increase or no change in the DNA repair pathway indicates the treatment is efficacious
The present invention also provides a panel with at least two proteins from two or more DNA repair pathways including base excision repair (BER), homologous recombination and crosslinking repair (FA/HR), mismatch repair (MMR), non-homologous endjoining repair (NHEJ), nucleotide excision repair (NER), translesion DNA synthesis (TLS), and DNA damage responsiveness (DDR). In one embodiment, the panel includes at least one Fanconi Anemia protein and at least one Mismatch Repair protein. In another embodiment, the panel includes one or more DNARMARKERS that are indicative of a pathway associated to DNA repair or DNA damage recognition and regulatory proteins.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In the case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be limiting.
Other features and advantages of the invention will be apparent from the following detailed description and claims.
The invention relates to the observation that tumor cells have altered DNA repair and DNA damage response pathways and that loss of one of these pathways renders the cancer more sensitive to a particular class of DNA damaging agents. Cancer therapy procedures such as chemotherapy and radiotherapy work by overwhelming the capacity of the cell to repair DNA damage, resulting in cell death. More particularly, the invention is based in part upon the discovery that a defect in two DNA repair pathways in a cell is lethal. Thus, radiation and drug responsiveness of the tumor can be predicted by determining the integrity of the six major DNA repair pathways in a cancer cell (
Accordingly, the invention provides methods of determining the responsiveness, e.g., sensitivity or resistance, of a cancer cell to a therapeutic agent by determining which DNA repair pathway is altered. These methods are also useful for monitoring subjects undergoing treatments and therapies for cancer or other cell proliferative disorders, and for selecting therapies and treatments that would be efficacious in subjects having cancer or other cell proliferative disorders, wherein selection and use of such treatments and therapies slow the progression of cancer or other cell proliferative disorders. The present invention further relates to biomarkers which are useful in detecting alterations in a DNA repair pathway.
There are six major DNA repair pathways distinguishable by several criteria which can be divided into three groups those that repair single strand damage and those that repair double stand damage. Single stranded damage repair pathways include Base-Excision Repair (BER); Nucleotide Excision Repair (NER); Mismatch Repair (MMR); Homologous Recombination/Fanconi Anemia pathway (HR/FA); Non-Homologous Endjoining (NHEJ), and Translesion DNA Synthesis repair (TLS).
BER, NER and MMR repair single strand DNA damage. When only one of the two strands of a double helix has a defect, the other strand can be used as a template to guide the correction of the damaged strand. In order to repair damage to one of the two paired molecules of DNA, there exist a number of excision repair mechanisms that remove the damaged nucleotide and replace it with an undamaged nucleotide complementary to that found in the undamaged DNA strand. BER repairs damage due to a single nucleotide caused by oxidation, alkylation, hydrolysis, or deamination. NER repairs damage affecting longer strands of 2-30 bases. This process recognizes bulky, helix-distorting changes such as thymine dimers as well as single-strand breaks (repaired with enzymes such UvrABC endonuclease). A specialized form of NER known as Transcription-Coupled Repair (TCR) deploys high-priority NER repair enzymes to genes that are being actively transcribed. MMR corrects errors of DNA replication and recombination that result in mispaired nucleotides following DNA replication.
NEHJ and HR repair double stranded DNA damage. Double stranded damage is particularly hazardous to dividing cells. The NHEJ pathway operates when the cell has not yet replicated the region of DNA on which the lesion has occurred. The process directly joins the two ends of the broken DNA strands without a template, losing sequence information in the process. Thus, this repair mechanism is necessarily mutagenic. However, if the cell is not dividing and has not replicated its DNA, the NHEJ pathway is the cell's only option. NHEJ relies on chance pairings, or microhomologies, between the single-stranded tails of the two DNA fragments to be joined. There are multiple independent “failsafe” pathways for NHEJ in higher eukaryotes. Recombinational repair requires the presence of an identical or nearly identical sequence to be used as a template for repair of the break. The enzymatic machinery responsible for this repair process is nearly identical to the machinery responsible for chromosomal crossover during meiosis. This pathway allows a damaged chromosome to be repaired using the newly created sister chromatid as a template, i.e. an identical copy that is also linked to the damaged region via the centromere. Double-stranded breaks repaired by this mechanism are usually caused by the replication machinery attempting to synthesize across a single-strand break or unrepaired lesion, both of which result in collapse of the replication fork.
Translesion synthesis Translesion synthesis is an error-prone (almost error-guaranteeing) last-resort method of repairing a DNA lesion that has not been repaired by any other mechanism. The DNA replication machinery cannot continue replicating past a site of DNA damage, so the advancing replication fork will stall on encountering a damaged base. The translesion synthesis pathway is mediated by specific DNA polymerases that insert extra bases at the site of damage and thus allow replication to bypass the damaged base to continue with chromosome duplication. The bases inserted by the translesion synthesis machinery are template-independent, but not arbitrary; for example, one human polymerase inserts adenine bases when synthesizing past a thymine dimmer.
Cancer cells, like normal human cells, can arrest their growth in response to DNA damage. Cell cycle arrest is accomplished, at least in part, by a complex array of intracellular checkpoint kinases. Checkpoint kinases, such as Chk1 (CHEK1), Chk2 (CHEK2), and MapKapKinase2 (MK2, Chk3), once activated, terminate cell growth by arresting the cell cycle in discrete stages, say, at the G1/S, G2/M, or mitotic spindle stage. Cell cycle arrest provides an opportunity to repair DNA damage, before resuming growth.
Cells activate the Chk1 kinase in response to DNA damage. Chk1 phosphorylates multiple protein substrates (effector proteins), which subsequently contribute to the checkpoint response. For instance, Chk1 phosphorylates the protein, Cdc25c, leading to a block in the transition from G2 to M phase of the cell cycle. This checkpoint allows cells (both normal cells and cancer cells) to repair their DNA before entering mitosis (M).
Cancer cells accumulate high levels of DNA damage. This damage may result from their heightened proliferative activity or from exposure to chemotherapy or ionizing radiation. Cancer cells are often hyperdependent on the Chk1-kinase-mediated G2/M cell cycle checkpoint. Increased reliance on Chk1 also results from the tumor cell's loss of another important checkpoint mediator, the p53 protein. Inhibition of Chk1 therefore knocks out a vital checkpoint of tumor cells. Without this checkpoint, tumor cells progress into mitosis, despite the persistence of un-repaired DNA damage, leading to a “mitotic catastrophe” and cell death. Based on this principle, Chk1 inhibitors have been developed. 7-hydroxy-staurosporine (UCN01) is furthest along with clinical development, as it is in phase II clinical trials. However, UCN01 has a clinical problem because of its prolonged half-life that may manifest in unwanted toxicities. Therefore, identifying the patients that are most appropriately treatable with inhibitors is an important clinical problem. In the case of Chk1 inhibitors broadly, it would be critical to identify the patient responders as a subgroup, so that these patients could be better directed to the therapy that is likely to work. Similarly, patients could also be identified where there would be no apparent benefit to Chk1 inhibitor treatments, and thus these patients may be able to avoid Chk1 inhibitor-associated toxicities. As demonstrated herein, in response to DNA damage, Chk1 directly phosphorylates the FANCE subunit of the FA core complex on two conserved sites (Threonine 346 and Serine 374). Phosphorylated FANCE assembles in nuclear foci and colocalizes with FANCD2. A nonphosphorylated mutant form of FANCE (FANCE-T346A/S374A), when expressed in a FANCE-deficient cell line, allows FANCD2 monoubiquitination, FANCD2 foci assembly, and normal S phase progression. However, the mutant FANCE protein fails to complement the mitomycin C hypersensitivity of the transfected cells. Taken together, these results elucidate a novel role of Chk1 in the regulation of the FA/BRCA pathway and in DNA crosslink repair. Chk1-mediated phosphorylation of FANCE is required for a function independent of FANCD2 monoubiquitination.
DNA Repair and DNA Damage Response Markers
Patients have varying degrees of responsiveness to therapy and methods are needed to distinguish the capability of the treatment in a dynamic manner. Identification of changes (e.g., active, hyperactive, repressed, downmodulated, or inactive) to the cellular DNA repair pathways are useful in monitoring and predicting the response to a therapeutic compound. Accordingly, included in the invention are biomarkers associated with DNA repair and DNA damage response. The invention features methods for identifying subjects who either are or are pre-disposed to developing resistance or are sensitive to a therapeutic compound, e.g., a chemotherapeutic drug by detection of the biomarkers disclosed herein. These biomarkers are also useful for monitoring subjects undergoing treatments and therapies for cancer and cell proliferative disorders, and for selecting therapies and treatments that would be efficacious in subjects having cancer and cell proliferative disorders.
The term “biomarker” in the context of the present invention encompasses, without limitation, proteins, nucleic acids, polymorphisms of proteins and nucleic acids, elements, metabolites, and other analytes. Biomarkers can also include mutated proteins or mutated nucleic acids. The term “analyte” as used herein can mean any substance to be measured and can encompass electrolytes and elements, such as calcium.
Proteins, nucleic acids, polymorphisms, and metabolites whose levels are changed in subjects who have resistance or sensitivity to therapeutic compound, or are predisposed to developing resistance or sensitivity to therapeutic compound are summarized in Table 1 and are collectively referred to herein as, inter alia, “DNA Repair and DNA damage response proteins or DNARMARKER”.
Expression of the DNARMARKERS is determined at the protein or nucleic acid level using any method known in the art. For example, at the nucleic acid level Northern hybridization analysis using probes which specifically recognize one or more of these sequences can be used to determine gene expression. Alternatively, expression is measured using reverse-transcription-based PCR assays, e.g., using primers specific for the differentially expressed sequence of genes. Expression is also determined at the protein level, i.e., by measuring the levels of peptides encoded by the gene products described herein, or activities thereof. Such methods are well known in the art and include, e.g., immunoassays based on antibodies to proteins encoded by the genes, aptamers or molecular imprints. Any biological material can be used for the detection/quantification of the protein or its activity. Alternatively, a suitable method can be selected to determine the activity of proteins encoded by the marker genes according to the activity of each protein analyzed.
The DNARMARKER proteins are detected in any suitable manner, but is typically detected by contacting a sample from the patient with an antibody which binds the DNARMARKER protein and then detecting the presence or absence of a reaction product. The antibody may be monoclonal, polyclonal, chimeric, or a fragment of the foregoing, as discussed in detail above, and the step of detecting the reaction product may be carried out with any suitable immunoassay. The sample from the subject is typically a biological fluid as described above, and may be the same sample of biological fluid used to conduct the method described above. The sample may also be in the form of a tissue specimen from a patient where the specimen is suitable for immunohistochemistry in a variety of formats such as paraffin-embedded tissue, frozen sections of tissue, and freshly isolated tissue. The immunodetection methods are antibody-based but there are numerous additional techniques that allow for highly sensitive determinations of binding to an antibody in the context of a tissue. Those skilled in the art will be familiar with various immunohistochemistry strategies.
Immunoassays carried out in accordance with the present invention may be homogeneous assays or heterogeneous assays. In a homogeneous assay the immunological reaction usually involves the specific antibody (e.g., anti-DNARMARKER protein antibody), a labeled analyte, and the sample of interest. The signal arising from the label is modified, directly or indirectly, upon the binding of the antibody to the labeled analyte. Both the immunological reaction and detection of the extent thereof are carried out in a homogeneous solution. Immunochemical labels which may be employed include free radicals, radioisotopes, fluorescent dyes, enzymes, bacteriophages, or coenzymes.
In a heterogeneous assay approach, the reagents are usually the sample, the antibody, and means for producing a detectable signal. Samples as described above may be used. The antibody is generally immobilized on a support, such as a bead, plate or slide, and contacted with the specimen suspected of containing the antigen in a liquid phase. The support is then separated from the liquid phase and either the support phase or the liquid phase is examined for a detectable signal employing means for producing such signal. The signal is related to the presence of the analyte in the sample. Means for producing a detectable signal include the use of radioactive labels, fluorescent labels, or enzyme labels. For example, if the antigen to be detected contains a second binding site, an antibody which binds to that site can be conjugated to a detectable group and added to the liquid phase reaction solution before the separation step. The presence of the detectable group on the solid support indicates the presence of the antigen in the test sample. Examples of suitable immunoassays are radioimmunoassays, immunofluorescence methods, chemilumenescence methods, electrochemilumenescence or enzyme-linked immunoassays.
Those skilled in the art will be familiar with numerous specific immunoassay formats and variations thereof which may be useful for carrying out the method disclosed herein. See generally E. Maggio, Enzyme-Immunoassay, (1980) (CRC Press, Inc., Boca Raton, Fla.); see also U.S. Pat. No. 4,727,022 to Skold et al. titled “Methods for Modulating Ligand-Receptor Interactions and their Application,” U.S. Pat. No. 4,659,678 to Forrest et al. titled “Immunoassay of Antigens,” U.S. Pat. No. 4,376,110 to David et al., titled “Immunometric Assays Using Monoclonal Antibodies,” U.S. Pat. No. 4,275,149 to Litman et al., titled “Macromolecular Environment Control in Specific Receptor Assays,” U.S. Pat. No. 4,233,402 to Maggio et al., titled “Reagents and Method Employing Channeling,” and U.S. Pat. No. 4,230,767 to Boguslaski et al., titled “Heterogenous Specific Binding Assay Employing a Coenzyme as Label.”
Antibodies are conjugated to a solid support suitable for a diagnostic assay (e.g., beads, plates, slides or wells formed from materials such as latex or polystyrene) in accordance with known techniques, such as passive binding. Antibodies as described herein may likewise be conjugated to detectable groups such as radiolabels (e.g., 35 S, 125 I, 131 I), enzyme labels (e.g., horseradish peroxidase, alkaline phosphatase), and fluorescent labels (e.g., fluorescein) in accordance with known techniques.
The skilled artisan can routinely make antibodies, nucleic acid probes, e.g., oligonucleotides, aptamers, siRNAs against any of the DNARMARKERS in Table 1.
The invention also includes a DNARMARKER-detection reagent, e.g., nucleic acids that specifically identify one or more DNARMARKER nucleic acids by having homologous nucleic acid sequences, such as oligonucleotide sequences, complementary to a portion of the DNARMARKER nucleic acids or antibodies to proteins encoded by the DNARMARKER nucleic acids packaged together in the form of a kit. The oligonucleotides are fragments of the DNARMARKER genes. For example the olignucleotides are 200, 150, 100, 50, 25, 10 or less nucleotides in length. The kit may contain in separate containers a nucleic acid or antibody (either already bound to a solid matrix or packaged separately with reagents for binding them to the matrix), control formulations (positive and/or negative), and/or a detectable label. Instructions (e.g., written, tape, VCR, CD-ROM, etc.) for carrying out the assay may be included in the kit. The assay may for example be in the form of a Northern hybridization or a sandwich ELISA as known in the art.
For example, DNARMARKER detection reagent, is immobilized on a solid matrix such as a porous strip to form at least one DNARMARKER detection site. The measurement or detection region of the porous strip may include a plurality of sites containing a nucleic acid. A test strip may also contain sites for negative and/or positive controls. Alternatively, control sites are located on a separate strip from the test strip. Optionally, the different detection sites may contain different amounts of immobilized nucleic acids, i.e., a higher amount in the first detection site and lesser amounts in subsequent sites. Upon the addition of test sample, the number of sites displaying a detectable signal provides a quantitative indication of the amount of DNARMARKER present in the sample. The detection sites may be configured in any suitably detectable shape and are typically in the shape of a bar or dot spanning the width of a test strip.
Alternatively, the kit contains a nucleic acid substrate array comprising one or more nucleic acid sequences. The nucleic acids on the array specifically identify one or more nucleic acid sequences represented by DNARMARKER 1-259. In various embodiments, the expression of 2, 3,4, 5, 6, 7,8, 9, 10, 15, 20, 25, 40 or 50 or more of the sequences represented by DNARMARKER 1-259. are identified by virtue of binding to the array. The substrate array can be on, e.g., a solid substrate, e.g., a “chip” as described in U.S. Pat. No. 5,744,305. Alternatively the substrate array can be a solution array, e.g., Luminex, Cyvera, Vitra and Quantum Dots' Mosaic.
Preferably, the kit contains antibodies for the detection of DNARMARKERS.
Therapeutic Methods
Responsiveness (e.g., resistance or sensitivity) of a cell to an agent is determined by identifying a deficiency in a DNA repair pathway in the cell. The cell is for example a cancer cell. The DNA repair pathway is Base Excision Repair, Nucleotide Excision Repair, Mismatch Repair, Homologous Recombination/Fanconi Anemia (FA) pathway, Non-Homologous Endjoining, or Translesion DNA Synthesis repair (
The presence of a deficiency in a particular DNA repair pathway indicates that the cell is resistant to agents that are specific for that DNA pathway. Whereas, the absence of a deficiency indicates that the cell is sensitive to agents that are specific for that DNA pathway.
By resistance is meant that the failure if a cell to respond to an agent. For example, resistance to a chemotherapeutic drug means the drug is not damaged or killed by the drug. By sensitivity is meant that that the cell responds to an agent. For example, sensitivity to a chemotherapeutic drug means the drug is damaged or killed by the drug.
For example, responsiveness of a cell to a DNA crosslinking agent or ionizing radiation is identified by identifying a deficiency in the Homologous Recombination/FA pathway. The presence of a deficiency in Homologous Recombination/FA pathway indicates that the cell is sensitive to a DNA crosslinking agent or ionizing radiation. Whereas, the absence of a deficiency indicates that the cell is resistant to DNA crosslinking agent or ionizing radiation. Cross linking reagent include for example cisplatin. Responsiveness of a cancer cell to a Homologous Recombination/FA pathway inhibitor is identified by identifying a deficiency in the mismatch repair DNA pathway. The presence of a deficiency in the mismatch repair DNA pathway indicates that the cell is sensitive to a Homologous Recombination/FA pathway inhibitor. Whereas, the absence of a deficiency indicates that the cell is resistant to a Homologous Recombination/FA pathway inhibitor. Homologous Recombination/FA pathway inhibitors include for example curcumin, velcade or alsterpaulone.
Sensitivity of a cancer cell to a therapeutic drug is increased by inhibiting or reducing the activity one or more DNA repair pathway protein or gene. By increasing the number of inoperative DNA repair pathways, the number of mechanisms by which mechanisms by which the cancer cell can repair DNA damages decreases, which makes the cell more sensitive to the affects of a therapeutic drug. For example, the sensitivity of a cancer cell to DNA cross linking agents or ionizing radiation by contacting the cancer cell with an inhibitor of the Homologous Recombination/FA pathway. Suitable inhibitors include MAP2KAP2 inhibitors.
Therapeutic agents capable of inducing cell death or damage for a particular cell by determining a deficiency in a DNA repair pathway in the cell. Suitable therapeutic agents for that cell would specifically target a DNA pathway other that the deficient pathway. The pathway that is targeted is a pathway that repairs a different type of DNA damage. For example, if the pathway that is deficient is repairs single stranded breaks then the pathway that is targeted repairs double stranded breaks. Likewise if the if the pathway that is deficient is repairs double stranded breaks then the pathway that is targeted repairs single stranded breaks.
Alternatively, the pathway that is targeted is a redundant pathway of the deficient pathway. By redundant pathway it is meant that the pathway repairs similar DNA damage. For example, BER, NER, and MMR all repair single stranded breaks, and therefore are redundant pathways. Thus, if the BER pathway is the deficient pathway it is advantageous to target the NER or MMR pathway. Likewise if the NER pathway is the deficient pathway it is advantageous to target the BER or MMR pathway. If the MMR pathway is the deficient pathway it is advantageous to target the NER or BER pathway Likewise, if the NHEJ pathway is the deficient pathway it is advantageous to target the HR/FA pathway. Similarly, HR/FA and NHEJ both repair double stranded breaks and therefore are redundant pathways. Thus, if the HR/FA pathway is the deficient pathway it is advantageous to target the NHEJ pathway. Likewise, if the NHEJ pathway is the deficient pathway it is advantageous to target the HR/FA pathway.
Drugs that target specific DNA repair pathways are known in the art and include for example the drugs listed on Table 2.
Temozolomide is an alkylating that causes the formation of a critical toxic lesion, O-6 methyl guanine (O-6MG). Inactivation of a DNA repair protein that repairs this lesion, MGMT, was shown to be associated with longer survival in brain cancer patients (Hegi M E, et al. Clin Cancer Res 2004; 10:1871-4). Additional studies in inoperable glioblastoma have also indicated that response to temozolomide is associated with MGMT (Paz M F, et al. Clin Cancer Res 2004; 10:4933-8).
PARP1 inhibitors are now one of the most widely investigated drug classes for oncology indications. Several companies are progressing PARP1 inhibitors of distinctive chemotypes into clinical trials (reviewed in Ratnam and Low, 2007). It was shown that deficiency in BRCA1 or BRCA2, such as occurs with genetically typed women as a prognostic factor for breast and ovarian cancer, and these being two key factors in the HR pathway, allows tumor cells hypersensitive to PARP1 inhibitors (Bryant et al., 2005; Farmer et al., 2005). These studies have been followed up with the use of PARP1 inhibitors in clinical trials (Brody, L. C. (2005) Treating cancer by targeting a weakness. N. Engl.J. Med. 353, 949-950; Turner, N. et al. (2005) Targeting the DNA repair defect of BRCA tumours. Curr. Opin. Pharmacol. 5, 388-393) raising the possibility of selective cancer therapy against a DNA repair component that targets this tumor weakness. Identifying the spectrum of deficiencies in HR presumably extends beyond BRCA1 and BRCA2, and is likely to involve any of the HR DNA repair proteins and FA DNA repair proteins.
The ATM serine threonine kinase has several known substrates in homologous recombination pathway. Inhibition of this enzyme has been demonstrated to target an inactivation of Homologous recombination (an example paper is Hickson, I. et al. (2004) Identification and characterization of a novel and specific inhibitor of the ataxia-telangiectasia mutated kinase ATM. Cancer Res. 64, 9152-9159).
The DNAPK enzyme is a serine threonine kinase in the Non-homologous endjoining DNA repair pathway. The kinase activity of DNAPK supplies an essential step in this pathway. Inhibition of DNAPK by loss of activity of the enzyme, or by drug treatment, leads to a sensitivity of treated cells to radiation and other forms of DNA damage that are strand breakers.
Compounds that target ubiquitin and sumo ligases are also thought to be relevant to inhibition of DNA repair because target enzymes for these agents are known to modify other DNA repair proteins. Ubiquitin and SUMO ligases are important components of homologous recombination, translesion synthesis, nucleotide excision repair, and base excision repair steps. Therefore, inhibitory agents against this class of enzymes will interrupt the designated DNA repair pathways.
The methods are useful to treat, alleviate the symptoms of, monitor the progression of or delay the onset of cancer or a cell proliferative disease in a subject. Cancers and cell proliferative disorders are treated for example by determining if the cancer cell is deficient in a DNA repair pathway and administering a DNA damaging agent or inhibitor specific for at least one different DNA repair pathway. Optionally, a DNA repair pathway protein or gene that is upregulated is identified in the cell and administering a DNA damaging agent or inhibitor specific for a the DNA repair pathway in which the protein or gene is upregulated.
Expression of an effective amount of DNARMARKER proteins, nucleic acids or metabolites also allows for the course of treatment of cancer or a cell proliferative disorder to be monitored. In this method, a biological sample is provided from a subject undergoing treatment, e.g., chemotherapeutic treatment, for cancer or a cell proliferative disorder. If desired, biological samples are obtained from the subject at various time points before, during, or after treatment. Expression of an effective amount of DNARMARKER proteins, nucleic acids or metabolites is then determined and compared to a reference, e.g. a control individual or population whose cancer or a cell proliferative disorder state is known or an index value. The reference sample or index value may be taken or derived from one or more individuals who have been exposed to the treatment. Alternatively, the reference sample or index value may be taken or derived from one or more individuals who have not been exposed to the treatment. For example, samples may be collected from subjects who have received initial treatment for cancer or a cell proliferative disorder and subsequent treatment for diabetes to monitor the progress of the treatment.
Differences in the genetic makeup of individuals can result in differences in their relative abilities to metabolize various drugs. Accordingly, the DNARMARKER disclosed herein allow for a putative therapeutic or prophylactic to be tested from a selected subject in order to determine if the agent is a suitable for treating or preventing cancer or a cell proliferative disorder in the subject.
To identify therapeutic that is appropriate for a specific subject a the expression of one or more of DNARMARKER proteins, nucleic acids or metabolites is in a test sample form the subject is determined.
The pattern of DNARMARKER expression in the test sample is measured and compared to a reference profile, e.g., a therapeutic compound reference expression profile. Comparison can be performed on test and reference samples measured concurrently or at temporally distinct times. An example of the latter is the use of compiled expression information, e.g., a sequence database, which assembles information about expression levels of DNARMARKERS.
If the reference sample, e.g., a control sample is from cells that are sensitive to a therapeutic compound then a similarity in the amount of the DNARMARKER proteins in the test sample and the reference sample indicates that treatment with that therapeutic compound will be efficacious. However, a change in the amount of the DNARMARKER in the test sample and the reference sample indicates treatment with that compound will result in a less favorable clinical outcome or prognosis. In contrast, if the reference sample, e.g., a control sample is from cells that are resistant to a therapeutic compound then a similarity in the amount of the DNARMARKER proteins in the test sample and the reference sample indicates that the treatment with that compound will result in a less favorable clinical outcome or prognosis. However, a change in the amount of the DNARMARKER in the test sample and the reference sample indicates that treatment with that therapeutic compound will be efficacious.
By “efficacious” is meant that the treatment leads to an decrease in the amount of a DNARMARKER protein, or a decrease in size, prevalence, or metastatic potential of cancer in a subject. When treatment is applied prophylactically, “efficacious” means that the treatment retards or prevents cancer or a cell proliferative disorder from forming. Assessment of cancer and cell proliferative disorders is made using standard clinical protocols.
Cancer includes solid tumors such as breast, ovarian, prostate, lung, kidney, gastric, colon, testicular, head and neck, pancreas, brain, melanoma, and other tumors of tissue organs and cancers of the blood cells, such as lymphomas and leukemias, including acute myelogenous leukemia, chronic lymphocytic leukemia, T cell lymphocytic leukemia, and B cell lymphomas.
A “cellular proliferative disorder” includes those disorders that affect cell proliferation, activation, adhesion, growth, differentiation, or migration processes. As used herein, a “cellular proliferation, activation, adhesion, growth, differentiation, or migration process” is a process by which a cell increases in number, size, activation state, or content, by which a cell develops a specialized set of characteristics which differ from that of other cells, or by which a cell moves closer to or further from a particular location or stimulus. Disorders characterized by aberrantly regulated growth, activation, adhesion, differentiation, or migration. cell proliferative disorders” include autoimmune diseases and inflammation. for example, an inflammatory or immune system disorder, and/or a cellular proliferative disorder.
The subject is preferably a mammal. The mammal is, e.g., a human, non-human primate, mouse, rat, dog, cat, horse, or cow. The subject has been previously diagnosed as having cancer or a cell proliferative disorder, and possibly has already undergone treatment for the cancer or a cell proliferative disorder.
The subject is suffering from or at risk of developing cancer or a cell proliferative disorder. Subjects suffering from or at risk of developing cancer or a cell proliferative disorder are identified by methods known in the art.
By agents that are specific for a particular DNA repair pathway is meant the agent induces the type of DNA damage that the particular DNA repair pathway corrects.
By deficiency is meant that that cell has a reduced or abrogated ability to repair DNA damage through that pathway. Activity may be determined relative to normal (i.e. non-cancer) cells, preferably from the same tissue. A deficiency in a pathway is determined by methods known in the art. For example, activity of the HR repair pathway may be determined by measuring the formation of foci containing Rad51 in the nucleus in response to DNA damaging agents. Cells deficient in the HR repair pathway lack the ability to produce such foci. The presence of Rad51 foci may be determined using standard immunofluorescent techniques. Alternatively, the deficiency is determined by measuring the expression (e.g. increase or decrease relative to a control), detecting a sequence variation or posttranslational modification of one or more DNARMARKERS described herein.
Posttranslational modification include for example, phosphorylation, ubiquitination, sumo-ylation, acetylation, alkylation, methylation, glycylation, glycosylation, isoprenylation, lipoylation, phosphopantetheinylation, sulfation, selenation and C-terminal amidation. For example, a deficiency in the Homologous Recombination/FA pathway is determined by detecting the monoubiquitination of FANCD2. Similarly, responsiveness of cancer cell to a MAP2KAP2 inhibitor is determined by detecting phosphorylation of a MAP2KAP2 protein. Phosphorylation indicates the cell is sensitive to a MAP2KAP2 inhibitor. In contrast the absence of phosphorylation indicates the cell is resistant to a MAP2KAP2 inhibitor.
Sequence variations such as mutations and polymorphisms may include a deletion, insertion or substitution of one or more nucleotides, relative to the wild-type nucleotide sequence. The one or more variations may be in a coding or non-coding region of the nucleic acid sequence and, may reduce or abolish the expression or function of the DNA repair pathway component polypeptide. In other words, the variant nucleic acid may encode a variant polypeptide which has reduced or abolished activity or may encode a wild-type polypeptide which has little or no expression within the cell, for example through the altered activity of a regulatory element. A variant nucleic acid may have one, two, three, four or more mutations or polymorphisms relative to the wild-type sequence.
The presence of one or more variations in a nucleic acid which encodes a component of a DNA repair pathway, is determined for example by detecting, in one or more cells of a test sample, the presence of an encoding nucleic acid sequence which comprises the one or more mutations or polymorphisms, or by detecting the presence of the variant component polypeptide which is encoded by the nucleic acid sequence.
Various methods are available for determining the presence or absence in a sample obtained from an individual of a particular nucleic acid sequence, for example a nucleic acid sequence which has a mutation or polymorphism that reduces or abrogates the expression or activity of a DNA repair pathway component. Furthermore, having sequenced nucleic acid of an individual or sample, the sequence information can be retained and subsequently searched without recourse to the original nucleic acid itself. Thus, for example, scanning a database of sequence information using sequence analysis software may identify a sequence alteration or mutation.
Methods according to some aspects of the present invention may comprise determining the binding of an oligonucleotide probe to nucleic acid obtained from the sample, for example, genomic DNA, RNA or cDNA. The probe may comprise a nucleotide sequence which binds specifically to a nucleic acid sequence which contains one or more mutations or polymorphisms and does not bind specifically to the nucleic acid sequence which does not contain the one or more mutations or polymorphisms, or vice versa. The oligonucleotide probe may comprise a label and binding of the probe may be determined by detecting the presence of the label.
A method may include hybridization of one or more (e.g. two) oligonucleotide probes or primers to target nucleic acid. Where the nucleic acid is double-stranded DNA, hybridization will generally be preceded by denaturation to produce single-stranded DNA. The hybridization 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 hybridization.
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 labeled. Other methods not employing labeling of probe include examination of restriction fragment length polymorphisms, amplification using PCR, RN'ase cleavage and allele specific oligonucleotide probing. Probing may employ the standard Southern blotting 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 nitrocellulose filter. Labeled probe may be hybridized to the DNA fragments on the filter and binding determined.
Those skilled in the art are well able to employ suitable conditions of the desired stringency for selective hybridization, taking into account factors such as oligonucleotide length and base composition, temperature and so on. Suitable selective hybridization conditions for oligonucleotides of 17 to 30 bases include hybridization overnight at 42° C. in 6×SSC and washing in 6.x SSC at a series of increasing temperatures from 42° C. to 65° C. Other suitable conditions and protocols are described in Molecular Cloning: a Laboratory Manual: 3rd edition, Sambrook & Russell (2001) Cold Spring Harbor Laboratory Press NY and Current Protocols in Molecular Biology, Ausubel et al. eds. John Wiley & Sons (1992).
Nucleic acid, which may be genomic DNA, RNA or cDNA, or an amplified region thereof, may be sequenced to identify or determine the presence of polymorphism or mutation therein. A polymorphism or mutation may be identified by comparing the sequence obtained with the database sequence of the component, as set out above. In particular, the presence of one or more polymorphisms or mutations that cause abrogation or loss of function of the polypeptide component, and thus the DNA repair pathway as a whole, may be determined.
Sequencing may be performed using any one of a range of standard techniques. Sequencing of an amplified product may, for example, involve precipitation with isopropanol, resuspension and sequencing using a TaqFS+Dye terminator sequencing kit. Extension products may be electrophoresed on an ABI 377 DNA sequencer and data analyzed using Sequence Navigator software.
A specific amplification reaction such as PCR using one or more pairs of primers may conveniently be employed to amplify the region of interest within the nucleic acid sequence, for example, the portion of the sequence suspected of containing mutations or polymorphisms. 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 mutation or polymorphism which reduces or abrogates the expression or activity of the DNA repair pathway component. Suitable amplification reactions include the polymerase chain reaction (PCR) (reviewed for instance in “PCR protocols; A Guide to Methods and Applications”, Eds. Innis et al, 1990, Academic Press, New York, Mullis et al, Cold Spring Harbor Symp. Quant. Biol., 51:263, (1987), Ehrlich (ed), PCR technology, Stockton Press, N Y, 1989, and Ehrlich et al, Science, 252:1643-1650, (1991)).
Mutations and polymorphisms associated with cancer may also be detected at the protein level by detecting the presence of a variant (i.e. a mutant or allelic variant) polypeptide.
A method of identifying a cancer cell in a sample from an individual as deficient in DNA repair may include contacting a sample with a specific binding member directed against a variant (e.g. a mutant) polypeptide component of the pathway, and determining binding of the specific binding member to the sample. Binding of the specific binding member to the sample may be indicative of the presence of the variant polypeptide component of the DNA repair pathway in a cell within the sample. Preferred specific binding molecules for use in aspects of the present invention include antibodies and fragments or derivatives thereof (‘ antibody molecules’).
The reactivities of a binding member such as an antibody on normal and test samples may be determined by any 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 bond or non-covalently. Linkage via a peptide bond may be as a result of recombinant expression of a gene fusion encoding binding molecule (e.g. antibody) and reporter molecule.
Examples are provided below to further illustrate different features of the present invention. The examples also illustrate useful methodology for practicing the invention. These examples do not limit the claimed invention.
EXAMPLES Example 1. Identification of siRNA Targets Selectively Toxic to FA Pathway Deficient CellsThe EUFA 326 cell line is a patient derived FA-G fibroblast line. This cell line was previously corrected with a FANCG expressing construct to make the isogenic EUFA326G cell line (Garcia-Higuera et al., Blood 96(9): 3224-3230, 2000). These cell lines were selected for screening purposes as they grow at comparable rates and were found to demonstrate equal levels of gene knockdown with siRNA oligonucleotides.
The Qiagen DNA repair siRNA library that contains siRNA oligonucleotides targeting 356 DNA damage response genes was used for the screening assays. A feature of this library is the inclusion of two individual siRNA oligonucleotides targeting each individual gene in order to reduce the risk of off target effects.
After siRNA transfection, the relative survival between the EUFA326 and the EUFA326G cell line was calculated for each oligonucleotide. The assay was repeated twice and the mean relative survival in the EUFA326 versus the EUFA326G cell line was calculated for each gene target. The mean relative survival between the EUFA326 and EUFA326E cell line along with the standard error of the mean (SEM) for each gene target was calculated from 4 individual measurements. The 4 survival values for each siRNA target represent duplicate results from the two oligonucleotides targeting each gene. Table 3 shows that the top ten siRNA oligonucleotide targets that are selectively toxic to FA pathway deficient EUFA326 cells when compared to the corrected EUFA326G cell line. In
Importantly, it was found that knockdown of either of the base excision repair genes PARP1 or NEIL1 was selectively toxic to FA pathway deficient cells, with a relative survival of 64% for PARP1 knockdown and 74% for NEIL1 knockdown compared to the corrected cell line. This is in keeping with a recent study reporting that FA pathway deficient MEF cells are selectively sensitive to disruption of BER by PARP inhibitors (McCabe et al., Cancer Res 66(16): 8109-8115, 2006) and indicated that the screening assay is a valid approach for identifying novel targets and associations between DNA repair pathways. In addition, depletion of other proteins in DNA repair pathways also leads to reduction in cell survival in the above experiments. For example, the ratio of EUFA326/EUFA326G viability was also changed for siRNA knockdown of other DNA repair and DNA damage response genes (Table 3).
Therefore inhibitors of PARP1 and other BER enzymes, such as NEIL1, other Uracil Deglycosylases, DNA polymerase beta, and inhibitors of BER acting by disruption of protein:protein associations may have utility in the clinic by implementing a biomarker strategy that involves surveying the activity/depletion of DNA repair and DNA damage response pathways as described in this invention. DNAR biomarkers that identify DNA repair and DNA damage signaling modulation and/or protein levels are particularly relevant to drugs and classes of drugs that inhibit one or more target protein member of one of the DNA repair and/or DNA damage signaling pathways.
Shown in this example, one type of a PARP1 inhibitor (siRNA for PARP1) is used to define an hypersensitivity of cells that are depleted in a FA gene. In addition to siRNA experiments, it would be assumed that selective inhibitors of PARP1 (such as small molecules, peptides, therapeutic antibodies and other biotherapeutics) would have a similar outcome. A PARP1 inhibitor may have select utility when applied to clinical specimens being evaluated for treatment decisions in oncology, be it as monotherapies or as combination therapies with other chemotherapeutic agents or radiation. Patients with cancers that have been defined by the DNAR biomarkers for the Fanconi Anemia pathway would be expected to identify the patient subset particularly sensitive or resistant to PARP1 inhibitors. Understanding the DNA repair status of one or more of the DNA repair and damage pathways is an important determinant of responsiveness versus resistance of the drug class.
Monitoring DNA repair deficiency as shown here is a means to evaluate the responsiveness of a tumor to target-directed therapies in addition to chemotherapies. To further evaluate the connection between identifying a DNA repair change by molecular monitoring of a DNA repair pathway (FA deficiency) and change to the other pathways, an incubation with an inhibitor of the second DNA repair or DNA damage protein was used. If cells of known changed DNA repair status are hypersensitive to inhibition of a protein in the other identified pathway, then the implication is that the cells become hyper-dependant on that second protein and pathway.
Therefore, the identification of a connection between FA-deficiency and PARP1 was also tested by examining the hypersensitivity of these cells to PARP1 inhibitors. FANCA-deficient cells were compared with FANCA-deficient cells that were complemented with the FANCA gene introduced by retroviral transduction. In the experiment shown in
Interestingly, knockdown of TP53BP1 or ATM was selectively toxic to FA pathway deficient EUFA326 cells, with a relative survival of 60% and 70% respectively when compared to the EUFA326G cell line (Table 3 and
In order to confirm that FA pathway deficient cells required ATM function, the EUFA326 and EUFA326G cell lines were transfected with an alternative ATM siRNA oligonucleotide.
Consistent with the screen results, the EUFA326 cell line was more sensitive to ATM knockdown (viability 54.9% of GFPsi control) than the EUFA326G cell line (viability 75.5% of GFPsi control), (
Since FA pathway deficient cells did not tolerate loss of ATM expression, it was asked if the converse was true, namely, if ATM deficient cells were sensitive to loss of the FA pathway. ATM deficient AT22 cells and an isogenic ATM corrected cell line were transfected with siRNA targeting FANCG and cellular viability was measured at 72 hours (
The validity of targeting DNA response pathways in cancer treatment has recently been demonstrated by two groups. In these preclinical studies, inhibition of PARP1, a component of base excision repair, resulted in specific toxicity to BRCA1 and BRCA2 deficient (and therefore homologous recombination defective) cells while having little effect on cells competent for DNA repair (Bryant et al., Nature 434(7035): 913-917, 2005; Farmer et al., Nature 434(7035): 917-921, 2005).
Loss of the FA pathway has been reported in a number of different tumor types, therefore it was asked if inhibition of alternative DNA damage response pathways could be selectively toxic to cells that have lost FA pathway function. An siRNA screening approach identified the ATM DNA damage response kinase as being required for the survival of FA pathway deficient cells. Moreover, ATM deficient cells were sensitive to loss of FANCG indicating that the combined loss of both ATM and FA pathway function is toxic to cells. Interestingly FA pathway deficient cells were found to have constitutive activation of ATM and this was predominantly during the S phase of the cell cycle. Although ATM was active in FA pathway deficient cells, the level of activation was relatively low when compared to irradiated cells. These data indicate that the endogenous DNA damage resulting in ATM activation is at a relatively low level, and occurs mostly during DNA synthesis. This is in keeping with recent studies that have demonstrated that xenopus egg cells immunodepleted for FANCA or FANCD2 have a higher level of spontaneous DS DNA breaks during DNA replication when compared to normal cells (Sobeck et al., Mol Cell Biol 26(2): 425-437, 2006). It is predicted that the low level of ATM activation observed in human FA cell lines is in response to these spontaneous S phase DNA breaks. The observation that inhibition of ATM by siRNA resulted in selective cell death in FA pathway deficient cells, indicates that this S phase activation of ATM, although relatively low, is critical for cell survival.
Therefore inhibitors of Atm kinase and other DNA damage signaling steps may have increased utility in the clinic by implementing a biomarker strategy that involves surveying the activity/depletion of DNA repair and DNA damage response pathways as described in this invention. DNAR biomarkers that identify DNA repair and DNA damage signaling modulation and/or protein levels are particularly relevant to drugs and classes of drugs that inhibit one or more target protein member of one of the DNA repair and/or DNA damage signaling pathways.
Shown in Examples 2-7, it would be assumed that selective inhibitors of Atm (such as small molecules, peptides, therapeutic antibodies and other biotherapeutics) would have a similar outcome. A Atm inhibitor may have select utility when applied to clinical specimens being evaluated for treatment decisions in oncology, be it as monotherapies or as combination therapies with other chemotherapeutic agents or radiation. Patients with cancers that have been defined by the DNAR biomarkers for the Fanconi Anemia pathway would be expected to identify the patient subset particularly sensitive or resistant to Atm inhibitors. Understanding the DNA repair status of one or more of the DNA repair and damage pathways is an important determinant of responsiveness versus resistance of the drug class.
Example 3. Double Knockout of Murine Fancg and Atm Results in Embryonic LethalityThe ATM pathway is known to converge with the FA pathway, following ionizing radiation treatment, through the ATM-mediated phosphorylation of FANCD2 (Taniguchi et al., Cell 109(4): 459-472, 2002). Therefore, the FA and ATM pathway was investigated though the interbreeding of Fancg+/− Atm+/− mice. A consistent observation has been the preimplantation lethality of Atm−/− Fancg−/− offspring (
The mechanism underlying the sensitivity of FA pathway deficient cells to loss of ATM function was also investigated. The protein from isogenic pairs of FA pathway functional and deficient cells was extracted and auto-phosphorylation of ATM was measured by Western blotting.
In each case the FA deficient cell lines EUFA326 (FANCG deficient), EUFA426 (FANCC deficient), EUFA6914 (FANCA deficient) lines demonstrated constitutive activation of ATM (
To further confirm constitutive activation of ATM in FA cells, an in vitro kinase assay was performed for ATM activity in lysates taken from EUFA326 and EUFA326G cell lines. In keeping with the Western blot data, ATM immunoprecipitated from the FANCG mutant EUFA326 cell line demonstrated increased ATM-mediated phosphorylation of recombinant p53 (
Next it was asked if the observed ATM activation in FA pathway deficient cells was due to dysregulation of ATM function. ATM is strongly activated by ionizing radiation; therefore the EUFA326 and EUFA326G cells were irradiated with 10Gys of ionizing radiation and measured ATM auto-phosphorylation by Western blotting (
ATM is involved in the response to double strand breaks (DSBs) in DNA. Therefore, it was asked if constitutive ATM activation in FA pathway deficient cells may be required for the repair of spontaneous DNA breaks. To address this question the FANCG deficient EUFA326 and the corrected EUFA326G cell lines were treated with siRNA targeting ATM or a control GFP sequence and performed single cell electrophoresis (Comet assay) on each cell line after 72 hours. The mean length of the Comet tail from each cell line is a measure of the mean number of DNA breaks per cell. With control siRNA the EUFA326 cell line demonstrated a two fold greater number of DNA breaks when compared to the corrected EUFA326G cell line. This is consistent with other studies that have reported that FA pathway deficient cells have a greater amount of spontaneous DNA breakage when compared to FA pathway functional cells. Following treatment with siRNA targeting ATM, the EUFA326 cell line demonstrated a 92.0% increase in DNA breaks compared to the EUFA326G cell line which had a 57.6% increase in DNA breaks. These data indicate that constitutive ATM activation in FA pathway deficient cells is necessary to prevent the accumulation of DNA breaks following endogenous DNA damage.
Example 5. FA Pathway Deficient Cells are Sensitive to the ATM Inhibitor KU55933The compound KU55933 has recently been reported to be a highly specific, competitive ATP binding site inhibitor of ATM (Hickson et al., Cancer Res 64(24): 9152-9159, 2004). In the light of the siRNA data, it was reasoned that FA pathway deficient cells should be selectively sensitive to treatment with this inhibitor. To test this hypothesis, the dose viability curves of isogenic pairs of FA pathway deficient and corrected cell lines treated with increasing doses of KU55933 was compared.
To ensure that the observed sensitivity to KU55933 in the FA pathway deficient cells was not assay dependent, colony counts were performed using the FANCC mutant and corrected EUFA426 cell line. This cell line was chosen as it forms distinct colonies when seeded at low density. Each cell line was treated with KU55933 10 μM for 24 hrs and then cells were seeded for colony count assays. After 14 days the FANCC mutant cell line demonstrated an approximately 50% reduction in colonies when compared to the FA pathway proficient EUFA426C cell line (
At the same time as EUFA426 and EUFA426C cells were seeded for the colony count assay a proportion were collected for analysis of ATM and FANCD2 activity by Western blotting. Following treatment with KU55933, ATM phosphorylation was no longer observed in the EUFA426 cell line, consistent with complete inhibition (
Until recently, pharmacological inhibition of ATM was relatively non-specific with drugs such as Wortmanin which also targeted ATR and DNA-PK. Recently, the specific ATM inhibitor KU55933 has been developed and has been reported not to demonstrate these off target effects at effective concentrations (Hickson et al., 2004). It was asked if this drug could be selectively toxic to FA pathway defective cells, thereby offering a possible treatment strategy for FA pathway deficient tumors. In the FA cell lines tested, loss of FA pathway function specifically sensitized the cells to KU55933 suggesting that this compound may have a therapeutic role.
Treatment of FA pathway deficient cells with KU55933 resulted in marked chromosomal breakage when compared to the corrected cell line. These chromosomal breaks most likely represent the persistence of DS DNA breaks that have not been repaired during S phase. Interestingly, there was no evidence of chromosomal breaks in the FA pathway proficient cell line suggesting that either the FA pathway repaired the forks efficiently without DS DNA breakage thereby negating the requirement for ATM or the FA pathway was able to repair DS DNA breaks independent of ATM. In support of the second hypothesis, increased activity of the FA pathway was observed in FA pathway competent cells following KU55933 treatment, as measured by increased FANCD2 monoubiquitination.
Together these data demonstrate the specificity of KU55933-mediated cytotoxicity to cells deficient in the FA pathway. As regards to cancer therapy, this is encouraging as it displays a potential therapeutic window between normal cells and cancer cells for ATM inhibitors. Moreover, the identification of loss of FANCD2 monoubiquitination or the presence of constitutive ATM activation in tumor tissue may represent useful biomarkers to select patients for this type of treatment.
Example 6. KU55933 Treatment Results in Chromosomal Breakage and Cell Death in FA Pathway Deficient CellsSince ATM primarily responds to double strand DNA breaks and the aforementioned data indicated a requirement in FA pathway deficient cells, it was hypothesized that these cells may demonstrate chromosomal breakage following treatment with KU55933. To test this, the FANCE mutant (EUFA1179) and corrected (EUFA1179E) lymphoblast cell lines were used. The FANCE corrected cell line EUFA1179 demonstrates complete correction of mitomycin C induced chromosomal breakage when compared to the FANCE mutant EUFA1179 cell line indicating a complete correction of the FA pathway. Therefore, these cell lines were ideal to measure the effect of FA pathway status on genomic stability following KU55933 treatment.
Each cell line was treated with 20 μM KU55933 for 24 and 48 hrs and chromosomal breakage was assessed by microscopy on metaphase spreads (
Next, it was asked if KU55933 could be exerting its selective toxicity in FA pathway deficient cells through cell cycle effects. The EUFA130 and EUFA130E cell lines are useful for cell cycle analysis as they have comparable profiles at baseline (
The ATM-mediated pathway may be less efficient in the absence of the FA pathway, accounting for the sporadic chromosomal breaks seen in FA cells, but is sufficient to allow the majority of cells to survive. However the addition of KU55933 to FA pathway deficient cells (
Several genetic experiments were carried out following the generation of Fancd2/Pkrdc, Fancd2/Rad52, Fancd2/Mlh1 knockout mice. Both male and female Fancd2-−/− mice were infertile and displayed the onset of epithelial tumors at 15-18 months. Slightly decreased birth rate was also observed on some strain backgrounds. Fancd2/Pkrdc mice were not embryonic lethal, showed normal Mendellsian ratios at birth and displayed no striking adult phenotypes.
To further support our findings, double mutant mice were irradiated with 420 rads of ionizing radiation. While only 3 of 11 scid mice died at the same dose, 3 of 3 double mutant mice died very quickly following administration of IR indicating that Fancd2 operates in a pathway distinct from NHEJ in the repair of IR induced DNA damage (
To investigate the role of Fancd2 in repair of DSBs, we crossed Fancd2 knockout mice to scid mice. Scid mice have a defect in NHEJ due to a nonsense mutation in the gene encoding the catalytic subunit of DNA-PK, a protein required for NHEJ. Wildtype, Double mutant cells, scid cells, and singly mutant Fancd2 cells were compared in a cell growth assay following increasing doses of IR. While Fancd2 and wt cells are not particularly sensitive to increasing doses of IR scid cells are sensitive (
The identical genotypes were exposed to increasing doses of photoactivated psoralen. Scid cells are no more sensitive than wt cells and double mutant cells are equally sensitive as scid cells (
The results in
Fancd2/Mlh1 mice were not embryonic lethal, showed normal Mendellian ratios at birth and developed tumors (e.g., intestinal, leukemia) later in life. Fancd2/Mlh1 crossed mice are predicted to yield 1/16 double mutants. However, no double mutants were obtained. Specifically, 73 embryos were harvested and cultured at ED15 with an expected double mutant yield of 6. No double mutants were observed. 40 embryos were harvested and cultured at ED12 and no double mutants were observed.
Inducible knockdown of Mlh1 was carried out in human FA-A fibroblasts and DOX induced expression of shRNA (shMlh1 A and shMlh1 B or combinations thereof) was examined. The immunoblot results in
The results in
To examine the role of Chk1 in the FA/BRCA pathway, the primary amino acid sequence of the eleven FA proteins were scanned (A, B, C, D1, D2, E, F, G, L, M, J) for the Chk1 phosphorylation consensus sequence (-7(Leu/Arg)-6(Xaa)-(Leu/hydrophobic/Arg)-4(basic/Val)-3(Arg/Lys)-2(Tyr/Xaa)-1(Xaa) Ser+1(Phe/Met/hydrophobic). Two highly conserved phosphorylation sites were identified in the carboxy terminal region of the FANCE protein, Thr346 and Ser374 (
The ability of the FANCE mutant proteins to restore FANCD2 monoubiquitination was examined (
The assembly of FANCD2 nuclear foci in the FA-E cells expressing the double mutant FANCE (FLAG-TS/AA) (
To demonstrate whether Chk1 directly phosphorylates FANCE, phosphorylation of the two highly conserved threonine and serine residues by Chk1 in vitro was examined. Glutathione S-transferase (GST) peptide fusion proteins containing different regions of FANCE (
To further study the phosphorylation of FANCE on T346 and S374 by Chk1, rabbit polyclonal antisera were produced against FANCE peptides containing the putative phosphorylated residues, SDLGLLRLCpT(346)WL (anti-pT346) or against LFLGRILpS (374) LTSS (anti-pS374). Purified recombinant wild-type (rFANCEwt) or the double mutant (rTS/AA) of FANCE proteins were incubated with Chk1 or with the two related checkpoint kinases, Chk2 and MAPKAP2 (MK2) in vitro (
It was then determined whether FANCE is phosphorylated in vivo following DNA damage (
Immunofluorescence was used to demonstrate the in vivo phosphorylation of FANCE by Chk1. The anti-pT346 antiserum detected activated FANCE protein in corrected FA-E lymphoblasts (EUFA130+FLAG-FANCE) after cellular exposure to DNA damage, but not in FA-E cells stably expressing vector and the double mutant (TS/AA) (
The effect of siRNA knockdown of Chk1 on FANCD2 monoubiquitination and FANCD2 foci formation after DNA damage was examined (
The assembly of phospho-T346-FANCE foci and FANCD2 foci following DNA damage was examined (
Recent studies indicate that the FA core complex has additional replication and checkpoint activities which are discrete from FANCD2 monoubiquitination. To address whether phosphorylation of FANCE by Chk1 is required for normal S phase progression, we compared the ability of FANCE wild-type (FLAG-FANCEwt) or the double mutant (FLAG-TS/AA) to restore DNA replication and S phase progression (
It was tested whether the double mutant of FANCE could prevent MMC-mediated cell death when expressed in the FA-E cell line. Cell death results in nuclear fragmentation (the sub G1 population), and this was assessed by flow cytometry following MMC treatment. As shown in
The disappearance of phospho-FANCE-T346 foci after DNA damage (
HeLa cells were synchronized at the G1-S boundary with double-thymidine block and released the cells into S phase for 1 hour before DNA damage treatment. The level of FANCE protein was significantly decreased when a genotoxic stress (UV, HU, MMC or cisplatin) was delivered to cells undergoing DNA replication (
It was tested whether Chk1-dependent phosphorylation regulates FANCE stability (
The role of the ubiquitin-proteasome pathway in the degradation of FANCE (
The activity of the Fanconi Anemia pathway can be monitored by evaluating FANCD2 monoubiquitination on the molecular level. Human HeLa cells were previously shown to have a viable FA-HR pathway by many criteria. The effect of a Chk1 inhibitor on HeLa cells by treating these cells with the inhibitor, G06976 was examined. Following treatment, HeLa lysates were examined by immunoblotting with the FANCD2 antibody (
EUFA426 human cells are FANCC-deficient cells isolated from a Fanconi Anemia patient. Previous experiments have demonstrated that these cells are deficient in the FANCC protein on the molecular level, and fail to activate downstream steps in the Fanconi Anemia-Homologous Recombination (FA-HR) DNA repair pathway, including a block of FANCD2 monoubiquitination following various DNA damage stresses by genotoxic agents and irradiation. EUFA426 levels complemented with a FANCC gene retrovirus were observed to restore FANCC levels, and to complement the hypersensitivity of these cells to genotoxic stresses and irradiation.
EUFA426 and EUFA426+C cells were transfected with siRNAs for the Chk1 kinase according to standard protocols in previous experiments For controls, the same cells were also transfected with a control LacZ si RNA. Cell viability was scored for the cells that were not transfected (control) compared with LacZ and Chk1 siRNAs. It was found that EUFA426 cells had reduced viability after transfection with the Chk1 siRNA (
The sensitivity of Fanconi Anemia deficient cells was also examined by testing with a known Chk1 kinase inhibitor, G06976. In the experiment, EUFA326 cells that are isolated from a Fanconi Anemia patient known to be deficient in the FANCG complementation group gene, were evaluated. In addition, EUFA326 cells that have been complemented with FANCG by retroviral transduction, were compared. Previous experiments have demonstrated that these cells are deficient in the FANCG protein by immunoblotting, and fail to activate downstream steps in the Fanconi Anemia-Homologous Recombination (FA-HR) DNA repair pathway, including a block of FANCD2 monoubiquitination following various DNA damage stresses by genotoxic agents and irradiation. EUFA326 levels complemented with a FANCG gene retrovirus were observed to restore FANCG levels, and to complement the hypersensitivity of these cells to genotoxic stresses and irradiation (
The EUFA326 (FANCG-deficient) and EUFA326+G (FANCG-complemented) cells were tested for sensitivity to the Chk1 inhibitor. In cell viability determinations, EUFA326 cells were hypersensitive to the Chk1 inhibitor G06976 relative to the EUFA326+G cells at all doses.
Example 18. Treatment of FA-HR Deficient Cells with a Chk1 Inhibitor Leads to Extensive Chromosome Damage and BreakageThe FANCE-deficient human fibroblast cell line, EUFA130, and EUFA130 complemented with a stably reintroduced FANCE expression from a retrovirus, were compared in several tests for genome stability and cell cycle control. EUFA130+E cells were shown to have restored FANCE levels by immunoblotting.
EUFA130 and EUFA130+E cells were plated at low density, and subsequently treated with 1 uM of the Chk1 inhibitor G06976 and then tested for the distribution of cells at different cell cycle phases. It was found that the Chk1 inhibitor caused an increased fraction of cells in G1 and the subG1 cell population by propidium iodide staining. SubG1 cells are indicative of cells entering apoptosis.
In addition, the level of chromosome breaks was scored for EUFA130 and EUFA130+E cells treated with the Chk1 inhibitor. EUFA130 cells have a low level of chromosome breakage (
These experiments indicate the selective vulnerability of the FA-deficient cells to chromosome damage in the presence of a Chk1 inhibitor. The two parts of the experiment combined would indicate that the Chk1 inhibitor preferentially drives FA-deficient cells into cell death.
Example 19. Human Tumor Cell Lines are Sensitive to Inhibition of Chk1 Kinase or Atm KinaseHuman cancers show many genomic alterations including the chromosomal rearrangement, deletion, amplification, mutation and/or epigenetic silencing or overexpression of many genes. In the cases of DNA repair and DNA damage response pathway genes, there is significant evidence of modification of these genes in human cancers. For the Fanconi Anemia-Homologous Recombination pathway there is ample evidence to suggest that changed expression or mutation is often observed in tumors (
The human ovarian tumor cell line, 2008, is known to be deficient in the FA-HR pathway because these cells have epigenetic silencing of the FANCF gene from the hypermethylation of the FANCF promoter. Hypermethylation of the FANCF promoter leads to reduction in FANCF transcription and consequently FANCF protein levels of the cells are significantly lower. Epigenetic silencing of FANCF is a frequently observed event in human tumors. The 2008 cell line was transfected with the FANCF gene, expressed separably, and these derivative cells (2008+F) shown to express elevated levels of FANCF.
The ovarian 2008 cells and 2008+F cells were then compared for cell survival following treatments with the Chk1 kinase inhibitor G06976, or the Atm kinase inhibitor KU55933 and cell viability and proliferation tested in a clonogenic assay. Cell colonies were stained by standard procedures and visualized (
Collectively, the experiments demonstrate that the biomarker identification of FA deficiency identifies a subgroup of cells where there would be a utility for the application of Chk1 inhibitors. The selective use of a Chk1 inhibitor can be defined by evaluating tumor specimens for FA-deficiency as is illustrated here with FANCE-deficient cells (
This discovery has important ramifications in oncology clinical settings as it points to the therapeutic utility of Chk1 kinase inhibitors in circumstances where the status of the DNA repair pathways is understood. In the examples shown here, it is clear that the status of the Fanconi Anemia-Homologous Recombination pathway is an important component of prediction for the hypersensitivity of tumors to Chk1 inhibitors. The status of the pathways is likely to be identifiable by multiple biomarker components reflecting different nodal points of the activity of the overall pathway. This invention discloses the means to evaluate DNA repair biomarkers from one or more than one pathway in conjunction.
The DNA repair biomarkers are particularly applicable in several settings. Biomarkers of this type will be useful for preclinical development, for the subsetting of patients, as pharmacodynamic biomarkers in the course of clinical trials, and for directing therapeutic decision-making in the oncology clinics.
Example 20: Evidence for DNA Repair Protein Changes in Human CancersDNA repair pathway proteins were monitored by immunohistochemistry (IHC) using pathway-, protein-, or post-translational epitope-specific changes as biomarkers of the pathway activity.
Human cancers may be surveyed by analysis of formalin-fixed paraffin-embedded (FFPE) specimens where multiple sections of whole specimens or tumor micro arrays (TMAs) may be evaluated. For TMAs, human cancers were arrayed in a format to display three sections of tumor and three sections of pathologically normal surrounding tissues for each patient with a designated cancer diagnosis. Alternatively, TMAs of identified tumor zones from patients are compared to one another.
To illustrate the dynamic nature of DNA repair biomarker expression patterns in human cancers, TMAs of the same cancer type [head and neck squamous cell carcinomas] were analyzed extensively.
The images are also viewable based on single patient tumor cores as shown in
Another example of DNA repair biomarker analysis is shown for human prostate cancer specimens. In
A further example of DNA repair biomarker analysis is demonstrated for human Non-small cell lung cancer (NSCLC) specimens. In
Whole sections of human tumors are evaluated by inspection of serial sections. The Region of Interest (ROI) within the tumor is identified by a pathology team of investigators by considering the Hematoxylin and Eosin staining pattern and by the collective staining patterns of the groups of biomarkers. The image file is manipulated and annotated to overlay the same zone of the tumors. The ROIs are designated in this example by boxes in
Patients with head and neck cancer were evaluated using a group of DNA repair biomarkers as noted in the following figures. Patients were treated with chemoadjuvant (induction) therapies containing docetaxel, cisplatin, 5-FU, and received radiation therapies. However, the distinction of an ability to respond or fail to respond to this chemoradiation therapy regimen is not understood with regard to molecular markers. Tumor biopsies were received prior to the therapy, at which point tumor specimens were formalin-fixed and paraffin-embedded. The four markers (A=FANCD2, B=MLH1, C=XPF, and D=PT334 MAPKAPKINASE2) were co-analyzed with 6 patient tumor specimens, and the results are shown in
Pathology scoring of DNA repair biomarkers can be conducted by routine pathology scoring. For example, specimens are examined for the integrity of the staining pattern. Quality analysis with these biomarkers at higher power than is shown in the example indicates that the staining is entirely nuclear for the biomarkers FANCD2, XPF, MLH1, and Ki67 shown below. In addition, the biomarker PT334 MAPKAPKinase2 has nuclear and cytoplasmic staining depending on the context of the tumor. For example, ovarian tumors show a combination of nuclear and cytoplasmic staining whereas head and neck cancers show principally nuclear staining. An alternative strategy is to use machine-driven collection of IHC signals and algorithms to interpret the staining pattern. For DNA repair proteins, generally the IHC pattern is nuclear. Positive pixels are seen either in a nuclear or subnuclear distribution, such as with nuclear foci. Shown in the
In this study, all patients had stage 3 or 4 ovarian or primary peritoneal carcinoma, and were treated with surgery followed by platinum-based chemotherapy. The ovarian cancer patients were evaluated using a group of DNA repair biomarkers as noted in
Pathology scoring is used to differentiate the trends in expression changes with each of the biomarkers. Four pathologists established a scoring system where the intensity (I) and quantity (Q) measurements were made from each tumor specimen. I scores ranged from values 1, 2, and 3 with increasing intensity where 1 is weak, 2 is moderate, and 3 is strong. Q scores were determined to be 1 (1-9%), 2 (10-39%), 3 (40-69%), OR 4(70-100%) based on the fraction of nuclei that were positive with the marker. A combined score of I×Q yields a scoring in the range of 1-12.
Head and neck cancer specimens were evaluated by the above criteria and the scores for each patient per biomarker plotted against each other (
Tumor specimens from a patient with ovarian cancer were evaluated in the primary biopsy (surgical resection of the tumor) and in follow-up when the ovarian cancer had a recurrence following chemotherapy with cisplatin. The patient had an ovarian serous carcinoma, FIGO grade 3, FIGO stage 3c. Four biomarkers of DNA repair and DNA damage signaling were co-investigated: FANCD2, MLH1, XPF, and PT334 MAPKAPKinase2. In
It has been demonstrated that the Fanconi Anemia proteins are important determinants of cisplatin-sensitivity of cells (Chimomas and DAndrea, 2006). The identification of a biomarker such as FANCD2 that increases in intensity in ovarian cancer specimen that is from a recurrence is indicative of an association between increased FANCD2 and platin-resistance during therapy. Likewise, the observation that PT334 Mapkapkinase2 biomarker, which is indicative of hyperactivation of the Mapkapkinase2 enzyme and signaling pathway, would be a second indicator of the adaptive response to platin-based therapies in human cancers.
Example 25: General MethodsCell Culture
HeLa cells, U2OS cells, GM6914 (FA-A), PD326 (FA-G), PD426 (FA-C), PD20 (FA-D2), and EUFA423 (FA-D1) were grown in DMEM supplemented with 15% heat-inactivated fetal calf serum (FCS) in a humidified 5% CO2 incubator at 37° C. DF1179 (FA-E) fibroblasts derived from another FA-E patient were cultured in Chang medium (Irivine Scientific) (generously provided by Akiko Shimamura, Children's Hospital, Harvard Medical School, Boston, Mass.). Epstein-Barr virus EBV-transformed lymphoblasts EUFA130 (FA-E) were maintained in RPMI 1640 with 15% FCS.
Generation of DNA Damage
Cells were UV irradiated with a Stratalinker (Stratagene) at 50%-70% confluency without any medium after washing with PBS once in 100 mm dish without the lid. After UV irradiation, the fresh medium was added and cells were continuously cultured for the indicated time before lysis. Gamma irradiation was delivered using a Gammacell 40 apparatus (MDS Nordion). For MMC (Sigma) treatment, cells were continuously exposed to the drug for the indicated time before lysis. MMC sensitivity assays of human fibroblasts, and lymphoblasts was performed essentially as described with modifications as below (5, 7). Human fibroblasts and lymphoblasts were seeded in duplicate in 96-well microplates at a density of 1000 cells/well in appropriate medium. MMC was added at a final concentration of 0-200 μM. Cells were then incubated at 37° C. in 5% CO2 incubator for 5 days, and cell survival was then determined by staining nucleic acids with a proprietary dye (CyQUANT; Molecular Probes) and subsequently analyzed by a Fluorescence microplate reader according to manufacturer's protocol.
Plasmids and Purification of Recombinant Proteins
Human FANCE cDNA (generously provided by J. deWinter and H. Joenj e, Free University Medical Center, Amsterdam, The Netherlands) was subcloned into the retroviral vector pMMP-puro by adding the FLAG tag at the amino terminus of FANCE to generate pMMP-puro-FLAG-FANCE. Specific single, double mutations (pMMP-FLAG-T346A, pMMP-FLAG-S374A, pMMP-FLAG-T346A/S374A (TS/AA)) were introduced by using the QuikChange™ site-directed mutagenesis kit (Stratagene) according to the manufacturer's protocol. For construction of pGEX-FANCE (332-365), pGEX-FANCE (349-382) and pGEX-FANCE (332-382), PCR products of corresponding fragments were ligated to the EcoRI/NotI sites of the plasmid pGEX4T-1 (Pharmacia). The cDNAs of T346A, S374A and the double mutant of FANCE (T346A/S374A-TS/AA) were produced with the QuikChange™ site-directed mutagenesis kit (Stratagene). Recombinant FANCE (149-536) wild-type (rFANCEwt) construct was cloned to the EcoRI/Hind III sites of pET32a-PPS vector (Novagen). For recombinant double mutant FANCE (rTS/AA), the fragment of 149-536 with T346A and S374A was produced by PCR using pMMP-FLAG-TS/AA as a template, the product was cloned to the EcoRI/Hind III sites of pET32a-PPS vector. All constructs and mutants were confirmed by DNA sequencing.
GST-FANCE constructs spanning FANCE sequence (332-382) were expressed in E. coli BL21 cells. A GST-Cdc25C (200-256) construct (generously provided by Michael Yaffe, Massachusetts Institute of Technology, Boston, Mass.) was used as a positive control for in vitro kinase assay. The GST fusion proteins were then purified on glutathione S-Sepharose beads and used as substrates in the in vitro kinase reaction. Recombinant FANCE wild-type (rFANCEwt) and double mutants (rTS/AA) were expressed and induced in E. coli BL21(DE3)RP cells and then were purified by metal affinity chromatography using polyhistidine (His) binding HiTrap chelating HP columns (Pharmacia). After recombinant proteins were eluted from the column by incubation with precision protease to cleave its N-terminal His-tag sequence, further purification by HiTrapQFF anion exchange columns (Pharmacia) and S-200 gel filtration columns were performed.
Retroviral Infection
Production of pMMP retroviral supernatants and infection of fibroblasts or lymphoblasts were performed as previously described.
Generation of Anti-FANCE, Anti-FANCE-Phosphothreonine-T346, Anti-FANCE-Phosphoserine-S374 Antibodies
A rabbit polyclonal antibody against FANCE was generated by Invitrogen (Zymed) using a C-terminal peptide 521-536 of FANCE as an antigen source. For generation of phosphospecific antibodies (anti-pT346-FANCE and anti-pS374-FANCE), rabbits were immunized with a KLH (Keyhole limpet hemocyanin)-conjugated FANCE phosphopeptide (SDLGLLRLC (pT) WL) (SEQ ID NO: 1), or phosphopeptide (LFLGRIL(pS)LTSS) (SEQ ID NO: 2), derived from amino acids 337-348 or 367-378 of FANCE, respectively. Antibodies were affinity purified using the corresponding phosphorylated and nonophosphorylated peptide-conjugated gels.
Immunoblotting
Cells were lysed, and whole cell extracts were subjected to SDS-PAGE, transferred to nitrocellulose membranes, and subjected to Western blot analysis (5). The following antibodies were used: anti-FANCD2 (FI-17) (Santa Cruz Biotech.), anti-HA (HA. 11, Babcock), anti-FLAG (M2) (Sigma), anti-β-Tubulin (Santa Cruz Biotech.), anti-ATR (N-19) (Santa Cruz Biotech.), anti-phopsho-317-Chk1 (Cell Signaling technology), anti-Chk1(G-4) (Santa Cruz Biotech.).
In Vitro Kinase Assay
The GST-fusion proteins of FANCE (2 μg) were incubated with purified recombinant Chk1 (100 ng) (Upstate Technology) in 30 μl of kinase buffer (20 mM Tris HCL, 10 mM MgCl2, 10 mM MnCl2, 1 mm DTT, 10 μM ATP) containing 10 μCi of [γ32P]-ATP. Kinase reactions were incubated for 30 min at 30° C., stopped by addition of SDS sample buffer, and boiled for 5 min, then analyzed by SDS-PAGE and X-ray film autoradiography. In vitro kinase assays were performed using GST-Cdc25C (200-256) and GST for positive and negative controls. Assay conditions were the same as described above. Recombinant FANCE proteins (rFANCEwt and rTS/AA) (3 μg) were incubated without or with 100 ng of purified recombinant Chk1, Chk2, MAPKAP K2 (MK2) (Upstate Technology) or GST in 30 μl of kinase buffer (20 mM Tris HCL, 10 mM MgCl2, 10 mM MnCl2, 1 mm DTT, 1 mM ATP) for 30 min at 30° C., the kinase reaction was stopped by addition of SDS sample buffer, and boiled for 5 min, then analyzed by SDS-PAGE, followed by Western blot with anti-pT346-FANCE, anti-pS374-FANCE antibodies.
Immunoprecipitation
Immunoprecipitation was performed as previously described.
SiRNA and Transfection
Expression of targeted genes was knocked down by transient expression of siRNA directed against GFP (5′-AACACTTGTCACTACTTTCTC-3′) (SEQ ID NO: 3), Chk1 (5′-AAGAAGCAGTCGCAGTGAAGA-3′) (SEQ ID NO: 4), ATR (5′-CAGGCACTAATTGTTCTTCAA-3′) (SEQ ID NO: 5). Transfection of siRNAs was performed using Hiperfect (Qiagen) according to the manufacturer's protocol. At 72 hr of transfection, cells were treated with DNA damage.
Immunofluorescence Microscopy
Preparation of cells for immunofluorescence microscopy was performed as described. Lymphoblasts cell lines were grown on culture slide coated with poly-D-lysine (BD Bioscience) to promote adhesion for 36 hours before treatment. Images were acquired using a Axioplan 2 imaging microscope (Carl Zeiss) equipped with a digital camera and processed using Openlab software.
FACS Analysis
G2/M checkpoint analysis and DNA replication were performed as described previously (30). To detect of sub G1 population, cells were harvested at 0, 24, 48 and 72 hr after MMC (160 ng/ml) treatment, washed with PBS, fixed in 70% ethanol (106 cells per ml) for at least 1 hour at 4° C. and permeabilized in 0.25% Triton X-100/PBS at 4° C. for 15 min. Following washing with PBS, cells were resuspended in PBS containing 25/ml μg of propidium iodide (PI) (Sigma) and 0.1 mg/ml of RNase A (Sigma) prior to FACS analysis using a Becton Dickinson FACSCalibur flow cytometer. Cell death was measured as the sub G1 (less than 2N DNA content) population.
Mutation Analysis
The mutations were analyzed by RT-PCR amplification of total RNA purified from DF1179 cells (FA-E) and U2OS cells (control) using the specific primer pairs, then cDNA of both cell lines were analyzed by DNA sequencing using different primers spanning from exon 1 to exon 10 of FANCE.
OTHER EMBODIMENTSWhile the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.
Claims
1.-43. (canceled)
44. A method of treating cancer in a human subject, comprising:
- a) determining whether a cell of the cancer is deficient in TRF2, FANCD1, FANCJ, hHef1, FANCI, USP1, or FANCN as compared to a wild type control; and
- b) when the cell is deficient in TRF2, FANCD1, FANCJ, hHef1, FANCI, USP1, or FANCN, administering to the human subject an ATM inhibitor.
45. The method of claim 44, further comprising step c) administering a chemotherapeutic agent or radiation therapy to the human subject.
46. The method of claim 45, wherein the chemotherapeutic agent is selected from the group consisting of a crosslinking agent, a strand break agent, an alkylating agent, an anti-metabolite agent, a microtubule disruptor, a radiomimetic agent, a radiosensitizer, an intercalator, a DNA replication inhibitor, an anthracycline, an etoposide, and a topoisomerase II inhibitor.
47. The method of claim 44, further comprising step c) administering a Chk1 or an Mlh1 inhibitor to the human subject.
48. The method of claim 44, further comprising step c) administering a Chk1 inhibitor and an Mlh1 inhibitor to the human subject.
49. A method of treating cancer in a human subject, comprising:
- a) determining whether a cell of the cancer is deficient in TRF2, FANCD1, FANCJ, hHef1, FANCI, USP1, or FANCN as compared to a wild type control; and
- b) when the cell is deficient in TRF2, FANCD1, FANCJ, hHef1, FANCI, USP1, or FANCN, administering to the subject an Mlh1 and/or a Chk1 inhibitor.
50. The method of claim 49, wherein the human subject is not administered an ATM inhibitor.
51. A method of treating colon cancer in a human subject, comprising:
- a) determining whether a cell of the colon cancer is deficient in Mlh1 as compared to a wild type control; and
- b) when the cell is deficient in Mlh1, administering to the human subject an inhibitor specific for the Fanconi Anemia (FA) pathway.
52. The method of claim 51, wherein the inhibitor specific for the FA pathway is a MAP2KAP2 inhibitor.
53. The method of claim 51, wherein step (a) further comprises determining whether the cell is deficient in TRF2, FANCD1, FANCA, FANCB, FANCC, FANCD2, FANCE, FANCF, FANCG, FANCJ, FANCL, FANCM, hHef1, FANCI, USP1, or FANCN as compared to a wild type control at a first period of time.
Type: Application
Filed: Aug 12, 2019
Publication Date: May 7, 2020
Inventors: Alan D. D'ANDREA (Winchester, MA), David T. WEAVER (Newton, MA), Markus GROMPE (Portland, OR), Richard KENNEDY (Belfast)
Application Number: 16/537,899
