MCL-1 AS A THERAPEUTIC TARGET IN SCFFBW7 DEFICIENT NEOPLASM
Some embodiments are based on the discovery that proliferative diseases (e.g., neoplastic diseases, for example, tumors or cancers) having an FBW7 mutation or other FBW7 deficiency are sensitive to Mcl1 inhibiting agents, but resistant to pro-apoptotic drugs that do not inhibit Mcl1. Some embodiments provide methods of treating a proliferative disease based on an assessment of FBW7 expression level or mutation status. Some embodiments provide methods of classifying a hyperproliferative cell or cell population, for example, a malignant cell or cell population based on an assessment of FBW7 expression level or mutation status. Some embodiments provide methods of selecting a treatment regimen for treating a proliferative disease, for example, a malignant disorder, based on an assessment of FBW7 expression level or mutation status.
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This application claims the benefit under 35 U.S.C. §119(e) of U.S. provisional application 61/448,648, filed Mar. 2, 2011, and entitled “SCFFbw7 Regulates Cellular Apoptosis By Targeting Mcl-1 for Ubiquitination and Destruction,” the entire contents of which are incorporated herein by reference.
GOVERNMENT SUPPORTThis invention is based on research that was funded, at least in part, by grant GM089763 awarded by the National Institutes of Health. The Government has certain rights in this invention.
BACKGROUND OF THE INVENTIONLoss of the FBW7 tumor suppressor gene has previously been reported to be associated with various types of human cancers, including breast cancer, colon cancer, and T-cell acute lymphoblastic leukemia. The molecular mechanism by which FBW7 functions as a tumor suppressor has not been elucidated, however.
SUMMARY OF THE INVENTIONSome embodiments are based on the surprising discovery that that the tumor suppressor FBW7 (also commonly referred to as FBXW7 or hCDC4, or, in some species as Sel-10 (worm) or Ago), is a regulator of the pro-survival Bcl2 family member Mcl-1, an oncogene that is associated with some forms of cancer, for example, with leukemia. Some aspects of this invention are based on the surprising discovery that FBW7 promotes the degradation of Mcl-1.
Some embodiments are based on the recognition that Mcl-1 protein levels in a cell, for example, in a malignant cell, can be considered an arbiter of whether the cell will evade apoptosis, and thus, be prone to a cancerous phenotype. Measuring Mcl-1 protein levels is difficult, however, because it is extremely unstable relative to its other Bcl2 family members. Some aspects of this invention relate to the recognition that determining the level of FBW7 or detecting a mutation in the FBW7 gene is predictive of Mcl-1 protein levels and, thus, useful as a diagnostic marker in human cancer. In some embodiments, this invention provides a genetic FBW7-based biomarker for cancer diagnosis and classification. In some embodiments, for example, in some clinical settings, the assessment of a genomic biomarker, as provided by some aspects of this invention, is preferred over an assessment of a protein biomarker, since it is generally more reliable and easier to apply a diagnostic test that assesses genetic mutation status rather than to measure protein levels in a cell.
Some embodiments are based on the recognition that, if a cell, for example, a malignant cell, is FBW7 deficient, then it cannot degrade Mcl-1, creating a condition of ‘oncogene addiction’. In some embodiments, a cell that bears a mutation in the FBW7 gene, for example, a missense, nonsense, or frameshift mutation, or a deletion of some or all of the coding region, or of all or some of the promoter region, or a splice site mutation, or any mutation that leads to a failure of the cell to express the full-length FBW7 protein, is considered to be FBW7 deficient. According to some aspects of this invention, FBW7(−) patients, e.g., patients carrying a cell, for example, a malignant cell, that is FBW deficient, therefore, are predicted, or indicated, to be responsive to drugs that inhibit Mcl-1. Mcl-1 inhibitors are well known to those of skill in the art and include, for example, multikinase inhibitors, e.g., sorafenib (aka BAY 43-90060R Nexavar) and other drugs that are known as inhibitors of Mcl-1 expression/activity, for example, Ceflatonin (e.g., Homoharringtonine (8CI), Omacetaxine Mepesuccinate), Seliciclib (CYC202), AT-101, CND0103, and Obatoclax. Other drugs that inhibit Mcl-1, including siRNAs and RNAi nucleic acids targeting Mcl-1, will be apparent to those of skill in the art and the invention is not limited in this respect. Some aspects of this invention relate to the recognition that FBW7-deficiency in a cell, for example, a malignant cell, is an indicator for the cell being resistant to pro-apoptotic drugs, for example, to Bcl2 inhibitors (e.g., ABT-737 (CAS No.: 852808-04-9), ABT-263 (Navitoclax, CAS No.: 923564-51-6)) or any other Bcl2-antagonists described herein. Accordingly, malignant cells that are FBW7-deficient will not respond to treatment with pro-apoptotic drugs, particularly to treatment with pro-apoptotic drugs that do not inactivate Mcl-1, for example, to ABT-737 or ABT-263 treatment. According to some aspects of this invention, FBW7(−) patients, e.g., patients carrying a cell, for example, a malignant cell, that is FBW7 deficient, therefore, are predicted, or indicated, to be resistant to pro-apoptotic drugs. Pro-apoptotic drugs are well known to those of skill in the art and include, for example, Bcl2 antagonists or inhibitors (e.g., ABT-737, ABT-263). Other pro-apoptotic drugs, including siRNA and RNAi nucleic acids targeting anti-apoptotic gene products, e.g., Bcl2, will be apparent to those of skill in the art and the invention is not limited in this respect.
Some embodiments are based on the recognition that, if a cell, for example, a malignant cell, is not FBW7 deficient, for example, a cell that does not comprise an FBW7 mutation, or that expresses FBW7 at a level similar to that of a normal, healthy cell of the same tissue-of-origin, then Mcl-1 can be degraded by the FBW7-dependent SCWFBW7 complex. A subject carrying a neoplastic or malignant cell that is not FBW7 deficient, for example, a subject with unmutated FBW7, accordingly, is indicated to not be sensitive to a Mcl-1 inhibitor (e.g., sorafenib), but instead will be sensitive to other cancer drugs that otherwise fail to inactivate Mcl-1 like ABT-737 (or congeners).
In some embodiments, an FBW7-based biomarker for cancer diagnosis and classification is provided. In some embodiments, the biomarker is a genomic FBW7 biomarker. In some embodiments, a mutation in the FBW7 gene of a diseased cell, is indicative of the cell being FBW7-deficient. In some embodiments, a mutation in the FBW7 gene of a diseased cell, for example, a neoplastic cell or a malignant cell, is indicative of the cell's susceptibility to a drug that inhibits Mcl-1, for example, to a multikinase inhibitor (e.g. sorafenib). In some embodiments, a mutation in the FBW7 gene of a diseased cell, for example, a neoplastic cell or a malignant cell, is indicative of the cell's resistance to a pro-apoptotic drug, for example, a drug that inhibits Bcl2. In some embodiments, the absence of a mutation in the FBW7 gene of a diseased cell, for example, a neoplastic cell or a malignant cell, is indicative of the cell's susceptibility to a pro-apoptotic drug, for example, a drug that inhibits Bcl2. In some embodiments.
The term “mutation” as used herein, refers to any alteration in a wild-type nucleic acid sequence, coding or non-coding, that affects the expression of a gene. In some embodiments, “expression of a gene” refers to expression of a functional gene product, for example, to expression of a functional protein (e.g., a wild-type protein or a protein comprising a mutation as compared to the wild-type protein that might leads to compromised function of the mutant protein). In the case of the FBW7 gene, a mutation, accordingly, is an alteration in the wild-type FBW7 genomic sequence that alters the expression of the FBW7 protein, including, but not limited to, a deletion, totally or partially, of an FBW7 coding sequence, or of an FBW7 promoter sequence, a deletion or alteration of an FBW7 splice site (a splice site mutation) leading to aberrant splicing of the FBW7 transcript, a partial or complete deletion of the FBW7 gene, a partial or complete deletion of the FBW7 coding region, a nonsense mutation, a missense mutation, a frameshift mutation, a mutation causing a truncation of the FBW7 protein, or a splice site mutation, or a point mutation resulting in an amino acid substitution. Amino acid substitutions associated with FBW deficiency, as provided by aspects of this invention, are well known to those of skill in the art, and include, for example, a G423 mutation, a R456 mutation, mutation, a R479 mutation, a R479 mutation, a R505 mutation, a D527 mutation, or a S668 mutation, for example, a G423V mutation, a R456c mutation, a R456H mutation, a R479L mutation, a R479Q mutation, a R505c mutation, a D527G mutation, an Exon 8 splice site mutation, or a S668 frameshift mutation.G423V. Additional mutations associated with FBW7 deficiency are well known to those of skill in the art, for example, as described in
Methods for the detection of mutations, for example, of FBW7 mutations as provided herein are well known to those of skill in the art and include, but are not limited to, isolation and sequencing of genomic DNA, FBW7-encoding mRNA, or cDNA derived therefrom, mRNA profiling (e.g. to detect underabundance of mRNA or to detect truncated mRNA, gene-chip (e.g., to detect an underabundance of FBW7 sequences in the genome), massive parallel sequencing technologies, PCR, RT-PCR, and hybridization-based methods, for example, SNP arrays, or southern or northern blot. Any of these methods can be used to detect an FBW7 mutation as described herein and other methods useful to detect an FBW7 mutation in embodiments of this invention will be apparent to those of skill in the art, as the invention is not limited in this respect.
In some embodiments, a method for cancer diagnosis is based on an assessment of FBW7, for examples, in a tumor of a subject diagnosed with a cancer. In some embodiments, the method comprises obtaining a sample, for example, a sample comprising a diseased cell, for example, a malignant cell, from a subject diagnosed with a proliferative disease, for example, with a cancer. In some embodiments, the method further comprises assessing the FBW7 gene for a mutation or a plurality of mutations in the sample or cell. For example, in some embodiments, the method comprises isolating genomic DNA from the cell and sequencing the FBW7 genomic locus or a part thereof or hybridizing the genomic DNA, or complementary DNA to a SNP array. In some embodiments, if a mutation of the FBW7 locus is detected, the cell is identified as FBW7-deficient. In some embodiments, a cell comprising an FBW7 mutation is defined as FBW7-deficient only if the mutation is a mutation described herein, for example, a deletion, totally or partially, of an FBW7 coding sequence, or of an FBW7 promoter sequence, a deletion or alteration of an FBW7 splice site (a splice site mutation) leading to aberrant splicing of the FBW7 transcript, a partial or complete deletion of the FBW7 gene, a partial or complete deletion of the FBW7 coding region, a nonsense mutation, a missense mutation, a frameshift mutation, a mutation causing a truncation of the FBW7 protein, or a splice site mutation, or a point mutation resulting in an amino acid substitution. Amino acid substitutions associated with FBW deficiency, as provided by aspects of this invention, are well known to those of skill in the art, and include, for example, a G423 mutation, a R456 mutation, a R479 mutation, a R479 mutation, a R505 mutation, a D527 mutation, or a S668 mutation, a G423V mutation, a R456c mutation, a R456H mutation, a R479L mutation, a R479Q mutation, a R505c mutation, a D527G mutation, an Exon 8 splice site mutation, or a S668 frameshift mutation. In some embodiments, the cell is obtained from the subject by biopsy, for example, by biopsy from a tumor, or by obtaining a blood sample comprising the cell, for example, a leukemia cell. In some embodiments, the cell is a diseased cell, e.g., a malignant cell, and the method further comprises selecting a treatment appropriate for the disease, e.g., a tumor or cancer, based on the FBW7 mutation status. In some embodiments, if the cell is identified as FBW7 deficient, the subject is indicated to be a candidate for treatment with a drug inhibiting Mcl-1. In some embodiments, the method comprises selecting and/or administering to the subject an Mcl-1 inhibitor based on the cell being identified as FBW7-deficient. In some embodiments, if the cell is identified to not be FBW7 deficient, e.g., a cell that does not carry an FBW7 mutation as described herein, the subject is not indicated to be a candidate for treatment with a drug inhibiting Mcl-1. In some embodiments, if the cell is identified to not be FBW7 deficient, e.g., a cell that does not carry an FBW7 mutation as described herein, the subject is indicated to not be a candidate for treatment with a drug inhibiting Mcl-1. In some embodiments, if the cell is identified to not be FBW7 deficient, e.g., a cell that does not carry an FBW7 mutation as described herein, the subject is indicated to be a candidate for treatment with a pro-apoptotic drug. Several suitable Mcl-1 inhibitors are described herein and are well known to those of skill in the art and include multikinase inhibitors, e.g. sorafenib (e.g., BAY 43-9006 or Nexavar), Ceflatonin (e.g., Homoharringtonine (8CI), Omacetaxine Mepesuccinate), R-roscovitine (e.g., Seliciclib or CYC202), AT-101 (e.g., CAS No: 90141-22-3), apogossypol (e.g., CNDO103), Sabutoclax (e.g., BI-97C1), or Obatoclax (e.g., CAS No: 803712-67-6, 803712-79-0). Similarly, pro-apoptotic drugs are well known to those of skill in the art and include Bcl2-inhibitors, e.g., ABT-737. Additional suitable Mcl-1 inhibitors and pro-apoptotic drugs will be apparent to those of skill in the art, and the invention is not limited in this respect.
In some embodiments, the cells assessed for FBW7 mutation status and/or expression level by the methods provided herein are diseased cells, e.g., cells that are causing a disease or are symptomatic for a disease. In some embodiments, the cells are aberrantly proliferating cells and the disease is a proliferative disease. In some embodiments, the cells are neoplastic cells and the disease is a neoplastic disease. In some embodiments, the cells are malignant cells and the disease is a malignant disease. In some embodiments, the cells are part of a tumor, for example, of a solid tumor or of a liquid tumor. In some embodiments, the tumor is the manifestation of a cancer, for example, lung cancer, breast cancer, colon cancer, blood cancer (e.g., leukemia such as T-ALL), lymphoma, melanoma, pancreatic cancer, or skin cancer. In some embodiments, the proliferative disease is a neoplastic disease.
In some embodiments, a method for cancer classification is based on an assessment of FBW7, for example, in a tumor of a subject diagnosed with a cancer. In some embodiments, the method comprises obtaining a cancer cell, for example, a cell of a solid or a liquid tumor from a subject diagnosed with a cancer. In some embodiments, the method comprises assessing the cell for a mutation of the FBW7 gene. In some embodiments, this assessment comprises isolating the genomic DNA of the cell and obtaining sequence information of the FBW7 gene locus, for example, by sequencing all or part of the locus, or by performing a SNP analysis, or by any other method described herein or known to those of skill in the art to be useful to obtain sequence information. In some embodiments, the method comprises identifying the cell as FBW7-deficient if a mutation is detected, or FBW7-normal, if a mutation is not detected. In some embodiments, the method further comprises classifying the cancer as FBW7-deficient or FBW7-normal, based on whether the cell is identified as FBW7-deficient or FBW7-normal. In some embodiments, the method further comprises indicating that the cancer is sensitive to treatment with a drug inhibiting Mcl-1 based on the cell being identified as FBW7-deficient. the method further comprises indicating that the cancer is resistant to treatment with a drug inhibiting Mcl-1 based on the cell being identified as FBW7-deficient. the method further comprises indicating that the cancer is sensitive to treatment with a pro-apoptotic drug based on the cell being identified as FBW7-normal. In some embodiments, the method further comprises selecting an appropriate drug for treatment of the cancer based on FBW7 mutation status of the cell. For example, in some embodiments, the method comprises selecting an Mcl-1 inhibitor for the treatment of a cancer that is identified to be FBW7 deficient. In some embodiments, the method comprises selecting a pro-apoptotic drug for the treatment of a cancer that is identified to be FBW7-normal. In some embodiments, the method further comprises administering the selected drug to the subject, for example, administering a multikinase inhibitor targeting Mcl-1 (e.g., sorafenib or seliciclib) to a subject having a cancer identified to be FBW7-deficient or administering a pro-apoptotic drug (e.g. a Bcl2-antagonist such as ABT737, ABT-263) to a subject having a cancer that is identified to be FBW7-normal.
In some embodiments, a method for cancer therapy is based on an assessment of FBW7, for example, in a tumor of a subject diagnosed with a cancer. In some embodiments, the method comprises administering a multi-kinase inhibitor to a subject having a tumor based on the tumor exhibiting a decreased level of FBW7 expression and/or a mutation in the SFBW7 gene in the tumor. In some embodiments, the method further comprises determining that the tumor exhibits a decreased level of FBW7 expression and/or a mutation in the FBW7 gene. In some embodiments, the multikinase inhibitor is a multikinase inhibitor described herein, for example, sorafenib, or seliciclib (CYC202).
In some embodiments, a method is provided that comprises administering a pro-apoptotic drug to a subject having a tumor based on the tumor exhibiting a normal or increased level of FBW7 expression and/or no mutation in the FBW7 gene in the tumor. In some embodiments, the method further comprises determining that the tumor does not exhibit a decreased level of FBW7 expression and/or a mutation in the FBW7 gene, for example, via a method described herein or otherwise known to those of skill in the art. In some embodiments, the pro-apoptotic drug is a Bcl2-inhibitor. In some embodiments, the Bcl2-inhibitor is ABT-737, ABT-737, Ceflatonin (e.g., Homoharringtonine (8CI), Omacetaxine Mepesuccinate), Obatoclax, CND0103, or AT-101.
Some embodiments are based on the discovery that proliferative diseases (e.g., neoplastic diseases, for example, tumors or cancers) having a FBW7 mutation or other deficiency are sensitive to Mcl1 inhibiting agents, but resistant to pro-apoptotic drugs that do not inhibit Men. Accordingly, subjects having a proliferative disease associated with an FBW7 deficiency should be treated with an Mcl1 inhibitor, alone or in combination with one or more additional therapeutic agents. It should be appreciated, that an Mcl1 inhibitor may be useful to prevent unwanted proliferation or may be used to help prevent unwanted proliferation by rendering diseased cells or tissue more sensitive to other agents.
For example, some embodiments are based on the recognition that if a subject having a proliferative disease presents with FBW7 deficiency, the disease will not be responsive to therapy with Bcl-2 inhibitors (e.g., ABT-737 and functional pro-apoptotic congeners, like ABT-263, RG7433, AT-101, EU-517, ABT-199, CND0103, CND0113, CND0123, CND0133). Some embodiments are based on the recognition that such subjects should not be treated with Bcl-2 inhibitors, but should be treated with a drug that inhibits Mcl-1, e.g., by decreasing Mcl-1 expression, function, or bioavailability.
Similarly, some embodiments are based on the recognition that if a subject having a proliferative disease presents with wild-type, or normal, levels of FBW7, the disease will be responsive to therapy with Bcl-2 inhibitors (e.g., ABT-737 and functional pro-apoptotic congeners, like Navitoclax (e.g., ABT-263, RG7433), AT-101, EU-517, BH-3 mimetics, ABT-199, CND0103, CND0113, CND0123, CND0133). Some embodiments are based on the recognition that such subjects should be treated with Bcl-2 inhibitors.
The term “Mcl1” refers to induced myeloid leukemia cell differentiation protein MeI-1. The term can refer to a protein and/or encoding nucleic acid sequence. Mcl1 sequences are well known to those of skill in the art and Mcl1 protein sequences include, for example, the following human sequences:
Additional Mcl1 sequences, for example, Mcl1 encoding sequences, such as DNA and mRNA sequences and additional protein sequences, for example, Mcl1 sequences from other species will be readily apparent to those of skill based on the instant disclosure.
The term “FBW7,” interchangeably used herein with the term “SCFFBW7” refers to F-box/WD repeat-containing protein 7. The term can refer to a protein and/or encoding nucleic acid sequence. FBW7 sequences are well known to those of skill in the art and FBW7 protein sequences include, for example, the following human sequences:
Additional FBW7 sequences, for example, FBW7 encoding sequences, such as DNA and mRNA sequences and additional protein sequences, for example, FBW7 sequences from other species will be readily apparent to those of skill based on the instant disclosure.
Some embodiments involve a drug inhibiting Mcl-1, also referred to as an Mcl-1 inhibitor. In some embodiments, a drug inhibiting Mcl-1 inhibits a biological activity of Mcl-1. For example, in some embodiments, a drug inhibiting Mcl-1 diminishes a pro-survival, or anti-apoptotic function of Mcl-1. Some drugs inhibiting Mcl-1 bind Mcl-1 directly, some modulate the expression or biological activity of Mcl-1, and some bind or modulate the expression or biological activity of MeI-1-interacting proteins or upstream regulators or downstream effectors of Mcl-1 activity. For example, some drugs inhibiting Mcl-1 bind or modulate the expression or biological activity of a kinase or phosphatase targeting Mcl-1, or stabilize an Mcl-1 antagonist, or de-stabilize an Mcl-1 agonist. Mcl-1 agonists and antagonists as well as drugs targeting them are well known to those of skill in the art. Some drugs inhibiting Mcl-1 bind or modulate the expression or biological activity of an Mcl-1-interacting protein. MeI-1-interacting proteins are known to those of skill in the art and include, for example, BAK1, Noxa, BCL2Ll1, Bcl-2-associated death promoter, PCNA, DAD1, TNKS, and/or BH3 interacting domain death agonist. Drugs targeting, binding, and/or modulating the biological activity of Mcl-1 interacting proteins are well known to those of skill in the art. Accordingly, the term “inhibiting Mcl-1,” in some embodiments, refers to direct inhibition of a biological function of Mcl-1, and in some embodiments, it refers to indirect inhibition of Mcl-1, for example, by modulation of an upstream regulator or a downstream effector of Mcl-1 signaling activity. For example, the kinase inhibitor sorafenib is a drug inhibiting Mcl-1, even though it does not directly bind to Mcl-1, but acts upstream or otherwise indirectly to inhibit Mcl-1 activity and/or expression level.
The term “proliferative disease” is a term of art and is used herein interchangeably with the term neoplastic disease. In some embodiments, the term refers to a disease or disorder associated with a neoplastic cell population (also referred to as a neoplasm). Neoplasia refers to an abnormal proliferation of cells. The growth of neoplastic cells exceeds and is typically not coordinated with that of the normal tissues around it. A neoplasm can take the form of a tumor, e.g., a benign or a malign tumor.
The methods provided herein are useful to classify, select a course of treatment for, and/or treat any neoplastic disorder in which FBW7 deficiency can be detected or that are associated with FBW7 deficiency. For example, the methods provided herein are useful to classify neoplastic diseases including, but not limited to, breast cancer, colon cancer, gastric cancer, prostate cancer, pancreatic cancer, lung cancer, hepatic cancer, brain cancer, kidney cancer, hematologic proliferative disorders, blood cancer (e.g., leukemia, such as acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), hairy cell leukemia, T-cell prolymphocytic leukemia, juvenile myelomonocytic ALL, or T-cell acute lymphoblastic leukemia (T-ALL). Other neoplastic diseases or disorders in which loss of FBW7 can be detected or which are associated with loss of FBW7 are known to those of skill in the art and this disclosure is not limited in this respect.
The term “tumor” as used herein, refers to a neoplastic cell growth, including benign, malignant, pre-cancerous and/or cancerous cell neoplasms. A tumor may be a liquid tumor, for example, a leukemic tumor, or a solid tumor, for example, an ovarian epithelial tumor, a breast tumor, a colon tumor, a gastric tumor, a prostate tumor, a pancreatic tumor, a lung tumor, a liver tumor, a brain tumor, or a kidney tumor. In some embodiments, the tumor is an epithelial tumor. In some embodiments, the tumor is a tumor harboring a cell with a defect in homologous recombination. In some embodiments, the tumor may be the manifestation of a cancer, for example, blood cancer, ovarian epithelial cancer, breast cancer, colon cancer, gastric cancer, prostate cancer, pancreatic cancer, lung cancer, liver cancer, brain cancer, or kidney cancer. The term tumor also refers to cancers of other organs or tissues as aspects of the invention are not limited in this respect.
In some embodiments, the tumor being classified according to methods provided herein is a primary tumor. In some embodiments, the tumor being classified according to methods provided herein is a secondary, metastatic, or recurrent tumor.
The term “subject”, as used herein, refers to an individual that may be, but is not limited to, a human, or a non-human mammal, for example, a mouse, rat, cow, sheep, cat, dog, or goat.
In some embodiments, a method for the diagnostic classification of a cancer tumor as chemoresistant or chemosensitive is provided. In some embodiments, the method includes obtaining information about the presence or absence of one or more gene mutations, and/or an increase or decrease in expression levels as described herein. A positive result (e.g., the detection of) one or more gene mutations, and/or an increase or decrease in expression levels as described herein can be obtained from a cell or a tissue from a tumor, for example, from a tumor biopsy, or from any other biological sample that includes tumor material (e.g., intact tumor cells and/or cellular debris derived from tumor cells). It should be appreciated that a sample also can contain normal cells or material (e.g., non-tumor cells or debris). However, in some embodiments, the relative amount of tumor cells or material is sufficient to determine whether an FBW7 deficiency is present in a tumor or not.
The term “expression level”, as used herein, refers to information about the level of one or more gene products (e.g., an mRNA, a protein, or a combination thereof) in a cell or tissue. In some embodiments, the detection of one or more gene mutations, and/or an increase or decrease in expression levels as described herein may be based on one or more measurements or assays, for example, a quantitative or semi-quantitative value of expression of a single gene, for example, reflective of the signal obtained from a quantitative or semi-quantitative assay detecting the abundance of a gene product (e.g., a protein or a nucleic acid transcript). Suitable assays for the detection of gene expression products are well known to those of skill in the art and include, for example, western blots, ELISA, RT-PCR (e.g., end-point RT-PCR, real-time PCR, or qPCR), protein or nucleic acid microarray, and massive parallel sequencing assays. However, any suitable assay may be used based on hybridization, specific binding (e.g., antibody binding), or any other technique, as aspects of the invention are not limited in this respect. In some embodiments, the presence of one or more gene mutations, and/or an increase or decrease in expression levels as described herein may involve a plurality of data points, for example, quantitative or semi-quantitative values of expression and/or one or sequence or mutation data points. In some embodiments, the presence of one or more gene mutations, and/or an increase or decrease in expression levels as described herein may be evaluated in a disease tissue sample (e.g., a biopsy sample) or in any suitable patient sample. Methods for the detection or for the generation of data for one or more gene mutations, and/or an increase or decrease in expression levels as described herein are well known to those in the art and include, for example, southern blot, western blot, ELISA, northern blot, reverse northern blot, RT-PCR (e.g. endpoint, real time, or qPCR), microarray (for either protein or transcript detection), SNP analysis, PCR, hybridization assays, sequencing assays, etc., or any combination thereof (for exemplary detection methods, see, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, Third Edition (3 Volume Set), Cold Spring Harbor Laboratory Press; 3rd edition (Jan. 15, 2001), ISBN-10: 0879695773; Robert Grützmann (Editor), Christian Pilarsky (Editor), Cancer Gene Profiling: Methods and Protocols (Methods in Molecular Biology), Humana Press; 1st edition (Nov. 6, 2009), ISBN-10: 1934115762, both incorporated herein by reference for disclosure of gene product detection and expression profiling methods).
Further, methods to generate comprehensive transcript levels for one or more genes (e.g., wild type alleles and/or mutations) from a given cell or tissue are well known in the art.
In some embodiments, a quantitative expression value is a value reflecting the abundance of a gene transcript in the starting sample, for example, a tumor cell or tissue sample. In some embodiments, a semi-quantitative expression value is a value reflecting the abundance of a gene transcript in the starting sample in relation to a control or reference quantity. In some embodiments, a semi-quantitative value may be a non-numeric indication of gene regulation (e.g., “up”, “down”, “+”, “++”, “+++”, “−”, “−−”, or “−−−”). In some embodiments, a semi-quantitative expression value may give a numeric dimension of gene regulation (e.g., “1.5-fold upregulated”, “2.456”, “0.32” or “−1.5”). Methods of calculating semi-quantitative expression values are well known to those in the art. Appropriate control or reference quantities for the generation of semi-quantitative expression values are well known to those in the art and include, for example, expression values of housekeeping genes (e.g., beta-actin or GAPDH), external controls (e.g., spiked in RNA or DNA controls not usually expressed in the cell to be analyzed), overall expression values (e.g., all expression values obtained from a cell added together), or historic or empiric values.
In some embodiments, an expression level of FBW7 (e.g., RNA and/or protein) that is determined for a sample is compared to a reference FBW7 expression level. In some embodiments, the reference is a standard that is indicative of a normal FBW7 expression level. In some embodiments, the reference is a standard that is indicative of a deficient FBW7 expression level (and any test levels that are at or below the reference would be indicative of an FBW7 deficiency). In some embodiments, a reference level is obtained by determining the expression level of FBW7 in a sample of normal or healthy tissue. In some embodiments, the reference level is determined by assaying FBW7 in a reference sample (e.g., a sample containing no malignant cells) obtained from the same subject from which a test sample (e.g., a sample containing or suspected of containing tumor cells or cellular material). The reference sample may be obtained from a different region of the same tissue or from a different region of the subject's body as the test sample.
It should be appreciated that expression levels of interest may be evaluated or determined in any suitable biological sample. In some embodiments, a biopsy of a tumor may be obtained and one or more gene mutations, and/or an increase or decrease in expression levels as described herein may be obtained from a biopsy cell or tissue. In some embodiments, one or more circulating cells (e.g., one or more circulating tumor cells) may be obtained and one or more gene mutations, and/or an increase or decrease in expression levels as described herein may be obtained from the cell or cells. In some embodiments, one or more tumor cells may be obtained from ascites fluid, peripheral blood, or from cerebrospinal fluid of a subject.
In some embodiments, a subject, or a biopsy or other biological sample obtained from a subject, is evaluated to determine whether a FBW deficiency, also referred to as FBW loss of function, is present, for example, detected as a genetic defect (e.g., deletion, loss of function, frameshift, inversion, or other mutation) or as a decreased level of FBW7 expression. It should be appreciated that any of the genetic and/or expression information described herein may be used alone or in combination, with or without additional patient information to assist in a prognosis, therapeutic recommendation, or other diagnostic or predictive evaluation of the health, outcome, and/or treatment for the patient.
In some embodiments, aspects of the invention relate to identifying patients that are candidates for one or more therapeutic treatments (e.g., one or more treatments such as small molecules, antibodies, antisense, hnRNA, siRNA, aptamer) that inhibit Mcl-1 gene products (e.g., transcripts or proteins), e.g., treatment with a multikinase inhibitor, such as sorafenib, or with Mcl-1 siRNAs. In some embodiments, aspects of the invention relate to identifying patients that should not be treated with one or more Mcl-1 inhibitory therapeutics agents described herein.
The terms “therapy”, “therapeutic”, “treat” or “treatment” refer to, but are not limited to, one or more clinical interventions with an intent to prevent, ameliorate, or cure a condition or symptoms of the condition in a subject, for example, a cancer or tumor, e.g., an FBW7-deficient or an FBW7-normal cancer or tumor.
In some embodiments, a treatment as provided by some aspects of this invention is aimed to eliminate a tumor, to induce a decrease in the size of a tumor, to induce a decrease in the number of tumor cells, or to inhibit or halt the growth of a tumor in a subject. Apparent to those skilled in the relevant medical arts, this can be accomplished by various approaches including, but not limited to, chemotherapeutic interventions. Suitable chemotherapeutic methods and administration schedules of chemotherapeutic compounds, alone or in combination with other therapeutics, will be apparent to those of skill in the relevant medical art.
Some methods for killing or inhibiting the proliferation of tumor cells, according to some embodiments of this invention, feature contacting such cells with a chemotherapeutic agent (e.g., in addition to one or more of the Mcl-1 inhibitory drugs or the pro-apoptotic drugs described herein), for example, a cytotoxic or cytostatic agent. In some embodiments, the cells are contacted with a chemotherapeutic agent, for example, a cytotoxic or cytostatic agent, that selectively targets tumor cells. By “selectively targeting” is meant that the agent or combination of agents selectively recognizes, binds, or acts upon tumor cells. In some embodiments, the agent or combination of agents can effectively kill tumor cells by one or more of several mechanisms, such as by induction of apoptosis, or by attracting other cells such as cytotoxic T lymphocytes or macrophages that can kill or inhibit proliferation of the targeted cells. By “cytotoxic or cytostatic agent” is meant an agent (for example a molecule) that kills or reduces proliferation of cells. Some examples of cytotoxic agents include, but are not limited to, cytotoxic radionuclides, chemical toxins, and protein toxins.
In some embodiments, the chemotherapeutic agent is a cytotoxic radionuclide or radiotherapeutic isotope, for example, an alpha-emitting isotope such as 225Ac, 211At, 212Bi, 213Bi, 212Pb, 224Ra or 223Ra. Alternatively, the cytotoxic radionuclide may a beta-emitting isotope such as 186Rh, 188Rh, 177Lu, 90Y, 131I, 67Cu, 64Cu, 153Sm or 166Ho. Further, the cytotoxic radionuclide may emit Auger and low energy electrons and may be one of the isotopes 125I, 123I or 77Br.
Chemotherapeutic compounds that can be used in combination with the Mcl-1 inhibitors or the pro-apoptotic drugs described herein are well known in the art, and non-limiting examples of suitable chemotherapeutic agents include, but are not limited to, alkylating agents, for example platinum compounds (e.g., carboplatin, cisplatin and oxaliplatin), mechlorethamine, cyclophosphamide, chlorambucil, and ifosfamide. PARP inhibitors are well known in the art, and non-limiting examples of PARP inhibitors include BSI201, AZD2281, ABT888, AG014699, MK4827, INO-1001, NU1025.
Other chemotherapeutic compounds are also well known to those of skill in the art, and non-limiting examples of such compounds include members of the enediyne family of molecules, such as calicheamicin and esperamicin. Chemical toxins can also be taken from the group consisting of methotrexate, doxorubicin, melphalan, chlorambucil, ARA-C, vindesine, mitomycin C, cis-platinum, etoposide, bleomycin and 5-fluorouracil. Examples of antineoplastic agents include, but are not limited to, dolastatins (U.S. Pat. Nos. 6,034,065 and 6,239,104) and derivatives thereof, for example, dolastatin 10 (dolavaline-valine-dolaisoleuine-dolaproine-dolaphenine) and the derivatives auristatin PHE (dolavaline-valine-dolaisoleuine-dolaproine-phenylalanine-methyl ester) (Pettit, G. R. et al., Anticancer Drug Des. 13(4):243-277, 1998; Woyke, T. et al., Antimicrob. Agents Chemother. 45(12):3580-3584, 2001), and aurastatin E and the like. Other chemotherapeutic agents are known to those skilled in the art.
However, it should be appreciated that other chemotherapeutic compounds, and/or combinations of compounds (e.g., two or more compounds described herein alone or with other compounds) may be used as aspects of the invention are not limited in this respect.
Therapeutic compositions of the present invention may be administered in pharmaceutically acceptable preparations. Such preparations may contain pharmaceutically acceptable concentrations of salt, buffering agents, preservatives, compatible carriers, supplementary immune potentiating agents such as adjuvants and cytokines, and optionally other therapeutic agents.
As used herein, the term “pharmaceutically acceptable” means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredients. The term “physiologically acceptable” refers to a non-toxic material that is compatible with a biological system such as a cell, cell culture, tissue, or organism. The characteristics of the carrier will depend on the route of administration. Examples of physiologically and pharmaceutically acceptable carriers include, without being limited to, diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials which are well known in the art. The term “carrier” denotes an organic or inorganic ingredient, natural or synthetic, with which the active ingredient is combined to facilitate the application. The components of the pharmaceutical compositions also are capable of being co-mingled with the molecules of the present invention, and with each other, in a manner such that there is no interaction which would substantially impair the desired pharmaceutical efficacy.
Therapeutics according to some embodiments of the invention can be administered by any conventional route, for example injection or gradual infusion over time. The administration may, for example, be oral, intravenous, intratumoral, intraperitoneal, intramuscular, intracavity, subcutaneous, or transdermal, or by pulmonary aerosol.
The compositions of some embodiments of the invention are administered in effective amounts. An “effective amount” is that amount of a composition that alone, or together with further doses, produces the desired clinical response. In some cases of treating a particular disease or condition, for example, a cancer manifested in a tumor, the desired response is inhibiting the progression of the disease, for example, the growth of the tumor or the spread of a primary tumor to secondary sites via metastasis. This may involve slowing the progression of the disease temporarily, although more preferably, it involves halting the progression of the disease permanently. In some cases, the desired response to treatment is a permanent eradication of tumor cells. In some cases, the desired response to treatment can be delaying or preventing the manifestation of clinical symptoms, for example, of recurrent tumors.
The effect of treatment can be monitored by routine methods or can be monitored according to diagnostic methods of the invention discussed herein.
The effective amount of a therapeutic compound or a combination of such compounds will depend, of course, on the particular tumor being treated, the severity of the condition, the individual patient parameters including age, physical condition, size and weight, the duration of the treatment, the nature of concurrent therapy (if any), the specific route of administration and like factors within the knowledge and expertise of the health practitioner. These factors are well known to those of ordinary skill in the art and can be addressed with no more than routine experimentation. It is generally preferred that a maximum dose of the individual components or combinations thereof be used, that is, the highest safe dose according to sound medical judgment. It will be understood by those of ordinary skill in the art, however, that a patient may insist upon a lower dose or tolerable dose for medical reasons, psychological reasons or for virtually any other reasons.
In some embodiments, a kit is provided, comprising reagents useful for determining an expression level and/or the presence of a mutation of interest. A reagent useful for determining an expression level of a gene may, in some embodiments, be a detectable agent that binds to an expression product of the gene. Detectable agents, their generation and/or purification and their use are well known to those of skill in the art and non-limiting, exemplary detection agents include detectable binding agents, for example antibodies, antibody fragments, nucleic acids complementary to a sequence comprised in a transcript of the informative gene, aptamers, and adnectins. In some embodiments, a kit may comprise a plurality of different nucleic acid molecules that correspond to different informative gene transcripts. In some embodiments, the plurality of nucleic acid molecules is attached to a solid support. In some embodiments, a kit is provided that includes a focused microarray for the detection of informative expression levels or mutations as described herein, for example, an FBW7 expression level or an Mcl1 exression level, a deletion, totally or partially, of an FBW7 coding sequence, or of an FBW7 promoter sequence, a deletion or alteration of an FBW7 splice site (a splice site mutation) leading to aberrant splicing of the FBW7 transcript, a partial or complete deletion of the FBW7 gene, a partial or complete deletion of the FBW7 coding region, a nonsense mutation, a missense mutation, a frameshift mutation, a mutation causing a truncation of the FBW7 protein, or a splice site mutation, or a point mutation resulting in an amino acid substitution. Amino acid substitutions associated with FBW deficiency, as provided by aspects of this invention, are well known to those of skill in the art, and include, for example, a G423 mutation, a R456 mutation, mutation, a R479 mutation, a R479 mutation, a R505 mutation, a D527 mutation, or a S668 mutation, for example, a G423V mutation, a R456c mutation, a R456H mutation, a R479L mutation, a R479Q mutation, a R505c mutation, a D527G mutation, an Exon 8 splice site mutation, or a S668 frameshift mutation. In some embodiments, a plurality of primer pairs is provided for determining an expression level and/or one or more mutations of interest.
These and other aspects of the invention are illustrated by the following non-limiting examples.
EXAMPLES Example 1The effective use of targeted therapy is highly dependent upon the identification of responder patient populations. Loss of the Fbw7 tumor suppressor is frequently found in various types of human cancers including breast cancer, colon cancer1 and T-cell acute lymphoblastic leukemia (T-ALL)2. In line with these genomic data, engineered deletion of Fbw7 in mouse T cells results in T-ALL3-5, validating Fbw7 as a T-ALL tumor suppressor. The precise molecular mechanisms by which Fbw7 exerts anti-tumor activity remain areas of intensive investigation and are thought to relate in part to Fbw7-mediated destruction of key cancer relevant proteins including c-Jun6, c-Myc7, Cyclin E8 and Notch-19, all of which possess oncogenic activity and are overexpressed in various human cancers including leukemia. Besides accelerating cell growth10, overexpression of either c-Jun, c-Myc or Notch-1 can also provoke programmed cell death11. Thus, considerable uncertainty surrounded how Fbw7-deficient cells evade cell death in the setting of upregulated c-Jun, c-Myc and/or Notch-1. Here it is shown that SCFFbw7 governs cellular apoptosis by targeting the pro-survival Bcl-2 family member, Mcl-1, for ubiquitination and destruction in a GSK3 phosphorylation-dependent manner. Human T-ALL cell lines showed a close relationship between Fbw7 loss and Mcl-1 overexpression. Correspondingly, T-ALL cell lines with defective Fbw7 are particularly sensitive to the multi-kinase inhibitor, sorafenib, but resistant to the Bcl-2 antagonist, ABT-737. On the genetic level, Fbw7 reconstitution or Mcl-1 depletion restores ABT-737 sensitivity, establishing Mcl-1 as a therapeutically relevant bypass survival mechanism for Fbw7-deficient cells to evade apoptosis. Therefore, this work provides novel molecular insight into Fbw7-direct tumor suppression with direct implications for the targeted treatment of Fbw7-deficient T-ALL patients.
Mcl-1 is frequently overexpressed in various leukemias via mechanisms that are not fully understood12. Mcl-1 is distinct from other Bcl-2 family members in its extremely unstable nature13, which provides a mechanism for cells to switch into either survival or apoptotic mode in response to various stresses14. While GSK3 phosphorylation regulates Mcl-1 stability13, little is known about the identity of the E3 ubiquitin ligase that targets phosphorylated Mcl-1 for destruction.
Upon examination of the GSK3 sites on Mcl-1, it was surmised that they resemble a possible degron sequence that can be recognized by Fbw7 (
Depletion of Fbw7 (
Consistent with a post-translational mode of regulation, no changes in Mcl-1 mRNA levels were observed after depletion of Fbw7 in DLD1 cells (
As proper substrate phosphorylation events are required for Fbw7 to recognize and target its substrates for ubiquitination16, next it was investigated which phosphorylation events that trigger Mcl-1 destruction by Fbw7. Mass spectrometry analysis revealed that Mcl-1 is phosphorylated at multiple sites in vivo (
Consistent with this Fbw7-Mcl-1 regulatory axis, Mcl-1 specifically interacts with Fbw7 (
Next, the mechanism by which Fbw7 alters Mcl-1 stability was explored. Overexpression of Fbw7 and GSK3 significantly decreased Mcl-1 abundance (
Next, how Fbw7 affects the cellular apoptotic response by modulating Mcl-1 abundance was explored. The results are shown in
These results imply that inhibition of Mcl-1 could be used to restore ABT-737 sensitivity in Fbw7-deficient T-ALL cells. Given that the clinical application of siRNA- or shRNA-mediated target extinction is not yet mature due to delivery challenges, instead small molecule strategies were exploited to reduce Mcl-1 expression, specifically with the use of sorafenib (
These studies provide experimental evidence for a role of Fbw7 in governing the apoptotic pathway by controlling Mcl-1 destruction. Mcl-1 plays a key role in regulating the cellular apoptosis of T cells14, but not other tissue types such as liver cells. Therefore, these studies also provide a possible mechanism for why loss of Fbw7 is frequently seen in T-ALL patients. Although other E3 ubiquitin ligases including c-Mule25 and b-TRCP17 have been implicated in Mcl-1 stability control, c-Mule activity was not implicated in GSK3-dependent regulation of Mcl-1 (
Altogether, without wishing to be bound by theory, these data support the hypothesis that Fbw7 is a physiological E3 ubiquitin ligase for Mcl-1 with USP9X as the nominated deubiquitinase26, and loss of Fbw7 contributes to T-ALL development via Mcl-1 upregulation. More importantly, these studies suggest that there is a correlation between Fbw7 genetic status and ABT-737 sensitivity and further provide insight into the usage of Mcl-1 inhibitors as a practical method to specifically kill Fbw7-deficient T-ALL cells. This work provides a basis for the rational treatment of FBW7 deficient neoplasm, for example, FBW7 deficient leukemias (e.g., in FBW7 deficient T-ALL patients) with Mcl-1 antagonists, or agents that significantly reduce Mcl-1 expression or activity, e.g., sorefanib, obatoclax, the MCL-1 BH3 helix SAHB, or any other Mcl-1 inhibitor described herein or known to those of skill in the art.
Materials and Methods Methods SummaryExpression plasmid constructs, proteins, antibodies and cell lines are described in the Methods. The sequences of various siRNA oligos used in this study are also listed in the Methods section. Mcl-1 in vivo phosphorylation was detected by mass spectrometry analysis, and the identified major GSK3 phosphorylation sites were examined by in vitro kinase assays. All mutants were generated using PCR and the sequences were verified. Fbw7-mediated Mcl-1 destruction and ubiquitination were examined by cell-based ubiquitination and degradation assays. Cell viability assays were used to detect the response of various T-ALL cell lines to sorafenib and ABT-737. Annexin V/7-AAD double staining was used to detect the percentage of cellular apoptosis. A detailed description of the experimental procedures is provided in the Methods section.
Plasmids:
HA-Fbw7 and HA-GSK3 constructs were described previously6. Fbw7 cDNA was subcloned using the Pfu polymerase (Stratagene) into the pBabe-Puro-HA retrovirus vector. Myc-Mcl-1 WT, Myc-Mcl-1 3A, and GST-Mcl-1 WT constructs were kind gifts from Dr. Mien-Chie Hung. Fbw7 and Mcl-1 mutants were generated with the QuikChange XL Site-Directed Mutagenesis Kit (Stratagene) according to the manufacturer's instructions. HA-ERK1, shERK1 and shERK2 constructs were kind gifts from Dr. John Blenis. Flag-β-TRCP1, Flag-Ubiquitin, shTRCP1 and shTRCP1+2 retroviral constructs were kind gifts from Dr. Wade Harper. shFbw7 retroviral vector was purchased from Addgene, which has been validated and described previously27. To generate the lentiviral shFbw7 and sh-c-Mule vectors, DNA oligos for shRNA against Fbw7 and c-Mule were annealed and subcloned into AgeI and EcoRI sites of the pLKO lentiviral plasmid. The following are DNA oligo sequences for the Fbw7 shRNA (sense; 5′-CCGGAACCTTCTCTGGAGAGAGAAACTCGAGTTTCTCTCTCCAGAGAAGGTTTTT TTG-3′ (SEQ ID NO: 30), anti-sense; 5′-AATTCAAAAAAACCTTCTCTGGAGAGAGAAACTCGAGTTTCTCTCTCCAGAGAAG GTT-3′ (SEQ ID NO: 31)), and for c-Mule shRNA (sense; 5′-CCGGAATTGCTATGTCTCTGGGACACTCGAGTGTCCCAGAGACATAGCAATTTTT TTG-3′ (SEQ ID NO: 32), antisense; 5′-AATTCAAAAAAATTGCTATGTCTCTGGGACACTCGAGTGTCCCAGAGACATAGCA ATT-3′ (SEQ ID NO: 33)). Lentiviral shRNA constructs against GFP and Mcl-1 were obtained from Dr. William Hahn. WT-Mcl-1 and 3A-Mcl-1 cDNAs were amplified with PCR and subcloned into the BamH I and Sal I sites of the pLenti-GFP-Puro construct (Addgene, Cat. No.: 658-5).
Antibodies and Reagents:
Anti-c-Myc antibody (sc-40), polyclonal anti-HA antibody (SC-805), anti-Cyclin A antibody (SC-751), anti-Plk1 antibody (SC-17783), anti-Cullin-1 antibody (sc-70895), anti-Rictor antibody (sc-81538), anti-p27 antibody (sc-528), anti-Skp1 antibody (sc-7163), anti-Mcl-1 antibody (sc-819) and anti-Cyclin E antibody (SC-247) were purchased from Santa Cruz. Anti-tubulin antibody (T-5168), polyclonal anti-FLAG antibody (F2425), monoclonal anti-FLAG antibody (F-3165), anti-1-Catenin antibody (C7207), anti-Vinculin antibody (V9131), peroxidase-conjugated anti-mouse secondary antibody (A4416) and peroxidase-conjugated anti-rabbit secondary antibody (A4914) were purchased from Sigma. Anti Mcl-1 antibody (4572), anti-Bcl-2 antibody (2872), anti-COX IV antibody (4850), anti-cleaved Caspase-3 (Asp175) antibody (9661), anti-cleaved PARP (Asp214) antibody (9541), anti-ERK1/2 antibody (4695), anti-c-Jun antibody (9162), anti-phospho-GSK3b (Ser-9) antibody (9336) and anti-Bim antibody (4582) were purchased from Cell Signaling. Anti-c-Mule antibody (A300-486A) was purchased from Bethyl. Monoclonal anti-HA antibody (MMS-101P) was purchased from Convace. Anti-Rbx1 antibody (RB-069P1) was purchased from Neomarker. Anti-Mcl-1 antibody (559027) was purchased from BD Pharmingen. Anti-GFP antibody (632380) and anti-Cullin-1 antibody (32-2400) were purchased from Invitrogen. Anti-Cdh1 antibody (CC43) was purchased from Oncogene. Oligofectamine, Lipofectamine and Plus reagents were purchased from Invitrogen. GSK3b inhibitor VIII was purchased from Calbiochem.
siRNAs:
Human siRNA oligos against Fbw7, Skp2, Cdh1 and Cullin-1 have been described previously6,28,29. A human siRNA oligo which can deplete both 13-TRCP1 and (3-TRCP2 (sense, 5′-AAGUGGAAUUUGUGGAACAUC-3′ (SEQ ID NO: 34)) was purchased from Dharmacon. Human siRNA oligos against c-Mule (sense, 5′-CAUGCCGCAAUCCAGACAUAU-3′ (SEQ ID NO: 35))25 and (sense, 5′-AAUUGCUAUGUCUCUGGGACA-3′ (SEQ ID NO: 36))30 have been validated previously and were purchased from Dharmacon. Luciferase GL2 siRNA oligo was purchased from Dharmacon. siRNA oligos to deplete endogenous Rbx1 (AACUGUGCCAUCUGCAGGAACAA (SEQ ID NO: 37)), Cullin1 (GGUCGCUUCAUAAACAACAUU (SEQ ID NO: 38)), and Rictor (AAACUUGUGAAGAAUCGUAUCUU (SEQ ID NO: 39)) were synthesized by Dharmacon. Cocktailed siRNAs targeting Skp1 were purchased from Invitrogen (1299003). A GSK3a siRNA oligo (6312) and a GSK3a/b siRNA oligo (6301) were purchased from Cell Signaling. The GSK3b siRNA oligo (51012) was purchased from Ambion. As described previously, siRNA oligos were transfected into subconfluent cells with Oligofectamine or Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions6.
Cell Culture:
Cell culture including synchronization and transfection has been described6,28. Wild type and Fbw7−/− DLD1 cell lines were kind gifts from Dr. Bert Vogelstein. Murine T-ALL cell lines derived from Tall transgenic mice were kind gifts from Dr. Michele A. Kelliher. Human T-ALL cell lines were previously described2. Loucy and CMLT1 T-ALL cell lines were obtained from Jon Aster. For various assays described below, T-ALL cells were cultured in either 0.5% FBS or 10% FBS-containing medium for sorafenib (Alexis Biochemicals) or ABT-737 (Symansis) treatment. In the case of combined treatment with both sorafenib and ABT-737, T-ALL cells were maintained in 10% FBS-containing medium. Lentiviral shRNA virus packaging, retrovirus packaging, and subsequent infections were performed as described previously28. For cell viability assays, cells were plated at 10,000 per well in 96-well plates, and incubated with the appropriate medium containing sorafenib, ABT-737 or DMSO for 48 h. Assays were performed with CellTiter-Glo Luminescent Cell Viability Assay kit according to the manufacturer's instructions (Promega). For detection of apoptosis, cells treated with various drugs were stained with propidium iodide (Roche), or co-stained with Annexin V-PE and 7-amino-actinomycin D (Annexin V-PE Apoptosis Detection Kit I, BD Bioscience) according to the manufacturer's instructions. Stained cells were sorted with Dako-Cytomation MoFlos sorter (Dako) at the Dana-Farber Cancer Institute FACS core facility.
Immunoblots and Immunoprecipitation:
Cells were lysed in EBC (50 mM Tris pH 8.0, 120 mM NaCl, 0.5% NP-40) buffer supplemented with protease inhibitors (Complete Mini, Roche) and phosphatase inhibitors (phosphatase inhibitor cocktail set I and II, Calbiochem). The protein concentrations of the lysates were measured using the Bio-Rad Bradford protein assay reagent on a Beckman Coulter DU-800 spectrophotometer. The lysates were then resolved by SDS-PAGE and immunoblotted with the indicated antibodies. For immunoprecipitation, 800 μg lysates were incubated with the appropriate antibody (1-2 μg) for 3-4 h at 4° C. followed by one-hour incubation with Protein-A Sepharose beads (GE Healthcare). Immuno-complexes were washed five times with NETN buffer (20 mM Tris, pH 8.0, 100 mM NaCl, 1 mM EDTA and 0.5% NP-40) before being resolved by SDS-PAGE and immunoblotted with the indicated antibodies. Quantification of the immunoblot band intensity was performed with Image J software.
Detection of Mcl-1 Phosphorylation Sites In Vivo:
To map Mcl-1 phosphorylation status in vivo, 293T cells were transfected with HA-Mcl-1 using the calcium phosphate method. Thirty hours post-transfection, 293T cells were treated with 10 mM MG132 for 16 hours to block the 26S proteasome pathway prior to collecting the whole cell lysates for HA-immunoprecipitation. After extensive washing with NETN buffer, the HA-immunoprecipitates were separated by SDS-PAGE and visualized by colloidal Coomassie Blue. The band containing Mcl-1 was excised and treated with DTT to reduce disulfide bonds and iodoacetamide to derivatize cysteine residues. In-gel digestion of the protein was done using trypsin or chymotrypsin. The resulting peptides were extracted from the gel and analyzed by nanoscale-microcapillary reversed phase liquid chromatography tandem mass spectrometry (LC-MS/MS). Peptides were separated across a 37-min gradient ranging from 4% to 27% (v/v) acetonitrile in 0.1% (v/v) formic acid in a microcapillary (125 μm×18 cm) column packed with C18 reverse-phase material (Magic C18AQ, 5 μm particles, 200 Å pore size, Michrom Bioresources) and on-line analyzed on The LTQ Orbitrap XL™ hybrid FTMS (Thermo Scientific, Bremen, Germany). For each cycle, one full MS scan acquired on the Orbitrap at high mass resolution was followed by ten MS/MS spectra on the linear ion trap XL from the ten most abundant ions. MS/MS spectra were searched using the SEQUEST algorithm against a database created on the basis of a protein sequence database containing the sequence for Mcl-1, for common contaminants, such as human keratins protein with static modification of cysteine carboxymethylation, dynamic modification of methionine oxidation and serine, threonine and tyrosine phosphorylation. All peptide matches were filtered based on mass deviation, tryptic state, XCorr and dCn and confirmed by manual validation. The reliability of site-localization of phosphorylation events was evaluated using the Ascore algorithm.
Real-Time RT-PCR Analysis:
RNA was extracted using the Qiagen RNeasy mini kit, and the reverse transcription reaction was performed using the ABI Taqman Reverse Transcriptional Reagents (N8O8-0234). After mixing the resulting template with Mcl-1 (Hs00172036_ml) or GAPDH (Hs99999905_ml) primers and ABI Taqman Fast Universal PCR Master Mix (4352042), the real-time RT-PCR was performed with the ABI-7500 Fast Real-time PCR system. Fbw7 (Hs00217794_ml), Skp2 (Hs00180634_ml), b-TRCP1 (Hs00182707_ml), Mcl-1 (Hs00172036_ml) and GAPDH (Hs99999905_ml) primers were purchased from ABI.
Protein Degradation Analysis:
Cells were transfected with Myc-Mcl-1 along with HA-Fbw7, or Flag-β-TRCP1, and GFP as a negative control, in the presence or absence of HA-GSK3 and/or HA-ERK1. For half-life studies, cycloheximide (20 μg/ml, Sigma) was added to the media 40 h post-transfection. At various time points thereafter, cells were lysed and protein abundances were measured by immunoblot analysis.
In vivo Ubiquitination Assay:
Cells were transfected with a plasmid encoding Flag-Ubiquitin along with Myc-Mcl-1 and HA-Fbw7 in the presence or absence of HA-GSK3. Thirty-six hours after transfection, cells were treated with the proteasome inhibitor MG132 (30 mM, Calbiochem) for 6 hours, and then harvested. Anti-Myc immunoprecipitates were recovered and immunoblotted with the anti-Flag antibody. Alternatively, cells were transfected with His-Ubiquitin along with Myc-Mcl-1 and HA-Fbw7 in the presence or absence of HA-GSK3. Thirty-six hours after transfection, cells were harvested, and the lysates were incubated with Ni-NTA matrices (Qiagen) at 4° C. for 12 h in the presence of 8 M Urea pH 7.5. Immobilized proteins were washed five times with 8 M Urea pH 6.3 before being resolved by SDS-PAGE and immunoblotted with the anti-Myc antibody.
In vitro Ubiquitination Assay:
The in vitro ubiquitination assays were performed as described previously8. To purify the SCFFbw7 E3 ligase complex, 293T cells were transfected with vectors encoding GST-Fbw7, HA-Cullin-1, Myc-Skp1 and Flag-Rbx1. The SCFFbw7 E3 complexes were purified from the whole cell lysates using GST-agarose beads. Purified, recombinant GST-Mcl-1 proteins were incubated with purified SCFFbw7 complexes in the presence of purified, recombinant active E1, E2 (UbcH5a and UbCH3), ATP and ubiquitin. The reactions were stopped by the addition of 2×SDS-PAGE sample buffer and the reaction products were resolved by SDS-PAGE gel and probed with the indicated antibodies.
In Vitro Kinase Assay:
GSK-3 was purchased from New England Biolabs. The in vitro kinase reaction was performed according to the manufacturer's instructions. Briefly, 5 μg of the indicated GST fusion proteins were incubated with purified active GSK3 in the presence of 5 μCi [γ-32] ATP and 20 μM cold ATP in the kinase reaction buffer for 20 min. The reaction was stopped by the addition of SDS-containing lysis buffer, resolved on SDS-PAGE, and detected by autoradiography.
Mcl-1 Binding Assays:
Binding to immobilized GST proteins was performed as described previously28. Where indicated, the GST-Mcl-1 proteins were incubated with GSK3 in the presence of ATP for 1 h prior to the binding assays.
Subcellular Fractionation:
Mitochondrial and cytosolic (S 100) fractions were prepared by resuspending HeLa cells in 0.8 ml ice-cold buffer A (250 mM sucrose, 20 mM HEPES [pH 7.4], 10 mM KCl, 1.5 mM MgCl2, 1 mM EDTA, 1 mM EGTA, 1 mM DTT, 17 mg/ml phenylmethylsulfonyl fluoride, 8 mg/ml aprotinin, 2 mg/ml leupeptin). Cells were then passed through an ice-cold cylinder cell homogenizer. Unlysed cells and nuclei were pelleted through a 10 min, 750 g spin. The recovered supernatant was spun at 10,000 g for 25 min. This pellet was resuspended in buffer A and represents the mitochondrial fraction. The supernatant was spun at 100,000 g for 1 hr. The supernatant from this final centrifugation represents the S100 (cytosolic) fraction.
Mice:
Generation of conditional Fbw7 knockout mice (Lck-Cre/Fbw7fl/fl and Mx1-Cre/Fbw7fl/fl) was described previously3,4.
In Vivo Imaging:
CMLT1 cells were infected with lentiviral vectors encoding a shRNA against Mcl-1 (shMcl-1) or an irrelevant control (shGFP). After selection in puromycin 1 μg/ml, cells were engineered for in vivo imaging by transduction with a retrovirus encoding a fusion of firefly luciferase fused to neomycin phosphotransferase, and then selected with G418 at 0.5 mg/ml. After selection, the luciferase activity of each engineered cell line was measured and found to have similar reading. Subsequently, equal numbers of viable cells (0.5−1×107 cells) were injected into NSG mice via the lateral tail vein. Tumor burden was determined using bioluminescence imaging (IVIS Spectrum, Caliper Life Sciences) after intraperitoneal injection of D-Luciferin 75 mg/kg. Total body luminescence was quantified using the Living Images software package (Caliper Life Sciences), and are expressed as photons/second/standardized region of interest (ph/s/ROI) encompassing the entire mouse. Data represented as mean±SEM with statistical significance determined by Student's t-test.
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All references listed above are incorporated in their entirety by reference herein, as if each and every reference was individually incorporated by reference.
Various aspects of the present invention may be used alone, in combination, or in a variety of arrangements not specifically discussed in the embodiments described in the foregoing and is therefore not limited in its application to the details and arrangement of components set forth in the foregoing description or illustrated in the drawings. For example, aspects described in one embodiment may be combined in any manner with aspects described in other embodiments.
Also, the invention may be embodied as a method, of which an example has been provided. The acts performed as part of the method may be ordered in any suitable way. Accordingly, embodiments may be constructed in which acts are performed in an order different than illustrated, which may include performing some acts simultaneously, even though shown as sequential acts in illustrative embodiments.
Use of ordinal terms such as “first,” “second,” “third,” etc., in the claims to modify a claim element does not by itself connote any priority, precedence, or order of one claim element over another or the temporal order in which acts of a method are performed, but are used merely as labels to distinguish one claim element having a certain name from another element having a same name (but for use of the ordinal term) to distinguish the claim elements.
Also, the phraseology and terminology used herein is for the purpose of description and should not be regarded as limiting. The use of “including,” “comprising,” or “having,” “containing,” “involving,” and variations thereof herein, is meant to encompass the items listed thereafter and equivalents thereof as well as additional items.
Having described several embodiments of the invention in detail, various modifications and improvements will readily occur to those skilled in the art. Such modifications and improvements are intended to be within the spirit and scope of the invention. Accordingly, the foregoing description is by way of example only, and is not intended as limiting. The invention is limited only as defined by the following claims and the equivalents thereto.
Claims
1. A method for treating a proliferative disease comprising
- (a) obtaining a cell from a subject diagnosed with a proliferative disease
- (b) determining whether the cell is FBW7 deficient; wherein if the cell is FBW7 deficient, the subject is indicated to be a candidate for treatment with a drug inhibiting Mcl-1; and/or if the cell is not FBW7 deficient, the subject is not indicated to be a candidate for treatment with a drug inhibiting Mcl-1 and/or the subject is indicated to be a candidate for treatment with a pro-apoptotic drug.
2. The method of claim 1, wherein the proliferative disease is a neoplastic disease.
3. The method of claim 1, wherein the proliferative disease is a malignant disease.
4. The method of claim 1, wherein the proliferative disease is a cancer.
5. The method of claim 1, wherein the proliferative disease is a leukemia.
6. The method of claim 1, wherein the proliferative disease is T-ALL.
7. The method of claim 1, wherein the determining whether the cell is FBW7 is deficient comprises assessing the mutation status of the FBW7 gene in the cell; wherein
- if the cell does not comprise a mutation of the FBW7 gene, then the cell is not FBW7 deficient; and/or
- if the cell comprises a mutation of the FBW7 gene, then the cell is FBW7 deficient.
8. The method of claim 1, wherein the mutation causes a decrease in expression or a loss of function of FBW7 in the cell.
9. The method of claim 1, wherein the mutation is a partial or complete deletion of the FBW7 gene, a partial or complete deletion of the FBW7 coding region, a nonsense mutation, a missense mutation, a frameshift mutation, a mutation causing a truncation of the FBW7 protein, or a splice site mutation.
10. The method of claim 1, wherein the mutation is a G423 mutation, a R456 mutation, a R479 mutation, a R505 mutation, a D527 mutation, or a S668 mutation.
11. (canceled)
12. The method of claim 1, wherein the drug inhibiting Mcl-1 is a multikinase inhibitor.
13. (canceled)
14. The method of claim 1, wherein the pro-apoptotic drug is a Bcl2-inhibitor.
15. (canceled)
16. A method of assisting in the evaluation of a subject having a tumor for treatment, the method comprising
- (a) determining the expression level and/or the mutation status of the FBW7 gene in a tumor sample obtained from a subject; and
- (b) if the expression level is decreased or if the FBW7 gene exhibits a mutation, indicating the subject to be a candidate for treatment with a multikinase inhibitor; or
- if the expression level is not decreased or if the FBW7 gene does not exhibit a mutation, indicating the subject to be a candidate for treatment with a pro-apoptotic drug.
17. The method of claim 16, further comprising
- (c) administering a multikinase inhibitor to the subject if the FBW7 expression level is decreased or if the FBW7 gene exhibits a mutation; or administering a multikinase inhibitor to the subject based on the FBW7 expression level being decreased or the FBW7 gene exhibiting a mutation; or
- (d) administering a pro-apoptotic drug to the subject if the FBW7 expression level is not decreased or if the FBW7 gene does not exhibit a mutation, then the subject is indicated to be a candidate for treatment with a Bcl-2 inhibitor.
18-20. (canceled)
21. The method of claim 16, wherein the mutation is a nonsense mutation, a missense mutation, a frameshift mutation, a splice site mutation, or a partial or complete deletion of the coding region.
22. The method of claim 16, wherein the mutation is a G423 mutation, a R456 mutation, a R479 mutation, a R505 mutation, a D527 mutation, or a S668 mutation.
23. (canceled)
24. A method, comprising
- (a) administering a multi-kinase inhibitor to a subject having a tumor, based on the tumor exhibiting a decreased level of FBW7 expression and/or a mutation in the FBW7 gene in the tumor; or
- (b) administering a pro-apoptotic drug to a subject having a tumor, based on the tumor exhibiting a normal or increased level of FBW7 expression and/or no mutation in the FBW7 gene in the tumor.
25. The method of claim 24, further comprising determining that the tumor exhibits a decreased level of FBW7 expression and/or a mutation in the FBW7 gene, and/or determining that the tumor does not exhibit a decreased level of FBW7 expression and/or a mutation in the FBW7 gene.
26. (canceled)
27. The method of claim 24, wherein the mutation is a nonsense mutation, a missense mutation, a frameshift mutation, a splice site mutation, or a partial or complete deletion of the coding region.
28. The method of claim 24, wherein the mutation is a G423 mutation, a R456 mutation, a R479 mutation, a R505 mutation, a D527 mutation, or a S668 mutation.
29-41. (canceled)
Type: Application
Filed: Mar 2, 2012
Publication Date: Jan 1, 2015
Patent Grant number: 10006089
Applicant: Beth Israel Deaconess Medical Center, Inc. (Boston, MA)
Inventor: Wenyi Wei (Brookline, MA)
Application Number: 14/001,970
International Classification: C12Q 1/68 (20060101); G01N 33/574 (20060101); A61K 31/495 (20060101); A61K 31/44 (20060101);
