Patent Application
20210052598
Whether glucose is predominantly metabolized via oxidative-phosphorylation or glycolysis differs between quiescent versus proliferating cells, including tumor cells. Given the high demand for biomacromolecules, including lipid, nucleotides and amino acids, to prepare for DNA replication and subsequent cell division, high rates of glycolysis and low rates of TCA cycle enable more flux of intermediates into the biomass synthesis pathways. Indeed, several lines of evidence advocate a bi-directional interplay between the cell cycle and metabolic machineries. On one hand, key metabolic enzymes are directly regulated in a cell cycle-dependent manner, such as PFKFB3 (6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase-3) by SCFGRR1, SCFβ-TRIP and APCCdh1, HK2 (hexokinase 2) by cyclin D1, PFKP and PKM2 by CDK6/cyclin D3, and GLS1 by APCCdh1. On the other hand, disturbing metabolism also could compromise cell cycle progress. Improved methods for disrupting pathways critical for tumor metabolism.
As described below, the present invention generally features compositions and methods of treating a cancer in a subject by administering to the subject a Skp2 inhibitor and an inhibitor of glycolytic metabolism (e.g., PKM2 inhibitor).
In one aspect, the invention provides a method of reducing neoplastic cell proliferation or survival involving contacting the cell with a Skp2 inhibitor and a Pyruvate kinase M2 (PKM2) inhibitor, thereby reducing neoplastic cell proliferation or survival.
In another aspect, the invention provides a method of reducing tumor growth involving contacting the tumor with a Skp2 inhibitor and a Pyruvate kinase M2 (PKM2) inhibitor, thereby reducing tumor growth.
In another aspect, the invention provides a method of treating cancer in a subject involving administering to the subject a Skp2 inhibitor and a Pyruvate kinase M2 (PKM2) inhibitor thereby treating cancer in the subject.
In another aspect, the invention provides a therapeutic combination for cancer therapy comprising a Skp2 inhibitor and a PKM2 inhibitor.
In another aspect, the invention provides a method of treating a selected subject having cancer involving administering a Skp2 inhibitor and an inhibitor of a glycolysis pathway enzyme to a selected subject, wherein the subject is selected by detecting an increased level of Skp2 and a decreased level of IDH1 and/or IDH2 in a biological sample of the subject, thereby treating the subject.
In various embodiments of any aspect delineated herein, the neoplastic cell or tumor displays one or more of increased glycolytic metabolism; reduced Tricarboxylic Acid (TCA) metabolism; increased lactate production; and/or reduced oxidative phosphorylation. In various embodiments of any aspect delineated herein, the neoplastic cell or tumor is characterized as Skp2high and IDH1low. In various embodiments, the neoplastic cell is a breast cancer, glioblastoma, or prostate cancer cell. In various embodiments, the tumor is breast cancer, glioblastoma, or prostate cancer.
In various embodiments of any aspect delineated herein, the subject has breast cancer, glioblastoma, or prostate cancer. In various embodiments, the subject's cancer displays one or more of increased glycolytic metabolism; reduced Tricarboxylic Acid (TCA) metabolism; increased lactate production; and/or reduced oxidative phosphorylation.
In various embodiments of any aspect delineated herein, the method involves detecting Skp2, p27, p21, Cyclin A, Cyclin E, IDH1, and/or IDH2 expression by immunoassay.
In various embodiments of any aspect delineated herein, the Skp2 inhibitor is one or more of a SKPin C1 and an inhibitory nucleic acid that targets Skp2 mRNA (e.g., for degradation). In various embodiments of any aspect delineated herein, the PKM2 inhibitor is one or more of 2 inhibitor compound 3k, DASA-58, and an inhibitory nucleic acid that targets PKM2 mRNA (e.g., for degradation). In various embodiments of any aspect delineated herein, the Skp2 inhibitor and PKM2 inhibitor are formulated together or separately Compositions and articles defined by the invention were isolated or otherwise manufactured in connection with the examples provided below. Other features and advantages of the invention will be apparent from the detailed description, and from the claims.
Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person skilled in the art to which this invention belongs. The following references provide one of skill with a general definition of many of the terms used in this invention: Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge Dictionary of Science and Technology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R. Rieger et al. (eds.), Springer Verlag (1991); and Hale & Marham, The Harper Collins Dictionary of Biology (1991). As used herein, the following terms have the meanings ascribed to them below, unless specified otherwise.
By “S-phase kinase-associated protein 2 (Skp2) polypeptide” is meant a polypeptide or fragment thereof having at least about 85%, or greater, amino acid identity to NCBI Accession No. NP_005974 (below) and having binding activity to cyclin A/E-CDK2, ubiquitin substrate recognizing activity, and/or oncogenic activity.
By “Skp2 nucleic acid molecule” is meant a polynucleotide encoding a Skp2 polypeptide. An exemplary Skp2 nucleic acid molecule sequence is provided at NCBI Accession No. NM_005983 (below):
By “Skp2 Inhibitor” is meant an agent that inhibits Skp2 expression, function or activity. Exemplary Skp2 inhibitors are known in the art and described, for example, by Wu et al., Chem Biol. 2012 Dec. 21; 19(12): 1515-1524. Skp2 inhibitors include, but are not limited to, SKPin C1 (Tocris; also CAS 432001-69-9, Millipore Sigma) and Skp2 inhibitory nucleic acids.
By “Isocitrate dehydrogenase 1 (Idh1) polypeptide” is meant a polypeptide or fragment thereof having at least about 85%, or greater, amino acid identity to NCBI Accession No. NP_001269315 (below) and having isocitrate dehydrogenase activity (oxidative decarboxylation of isocitrate to α-ketoglutarate); nicotinamide adenine dinucleotide phosphate (NADP+) reducing activity (catalyzing NADP+ to NADPH); and/or the ability to homodimerize.
By “Idh1 nucleic acid molecule” is meant a polynucleotide encoding an Idh1 polypeptide. An exemplary Idh1 nucleic acid molecule sequence is provided at NCBI Accession No. NM_005896 (below):
By “Isocitrate dehydrogenase 2 (Idh2) polypeptide” is meant a polypeptide or fragment thereof having at least about 85%, or greater, amino acid identity to NCBI Accession No. NP_002159 (below) and having isocitrate dehydrogenase activity (oxidative decarboxylation of isocitrate to α-ketoglutarate); nicotinamide adenine dinucleotide phosphate (NADP+) reducing activity (catalyzing NADP+ to NADPH); and/or the ability to homodimerize.
By “Idh2 nucleic acid molecule” is meant a polynucleotide encoding an Idh2 polypeptide. An exemplary Idh2 nucleic acid molecule sequence is provided at NCBI Accession No. NM_002168 (below):
By “Pyruvate kinase M2 (PKM2), polypeptide” is meant a polypeptide or fragment thereof having at least about 85%, or greater, amino acid identity to NCBI Accession No. NP_872271 (below) and having dephosphorylation activity (catalyzing dephosphorylation of phosphoenolpyruvate to pyruvate) and/or the ability to dimerize or tetramerize.
By “PKM2 nucleic acid molecule” is meant a polynucleotide encoding a PKM2 polypeptide. An exemplary PKM2 nucleic acid molecule sequence is provided at NCBI Accession No. NM_182471 (below):
By “PKM2 Inhibitor” is meant an agent that inhibits PKM2 expression, function or activity. Exemplary PKM2 inhibitors are known in the art and described, for example, by Heiden et al., Biochem Pharmacol. 2010 Apr. 15; 79(8): 1118-1124 and Dong et al., Oncol Lett. 2016 March; 11(3): 1980-1986. PKM2 inhibitors include, but are not limited to, PKM2 inhibitor compound 3k (Selleckchem), DASA-58 (Selleckchem), and PKM2 inhibitory nucleic acids.
By “agent” is meant any small molecule chemical compound, antibody, nucleic acid molecule, or polypeptide, or fragments thereof.
By “ameliorate” is meant decrease, suppress, attenuate, diminish, arrest, or stabilize the development or progression of a disease, such as cancer.
By “alteration” is meant a change (increase or decrease) in the expression levels or activity of a gene or polypeptide as detected by standard art known methods such as those described herein. As used herein, an alteration includes a 10% change in expression or activity levels, preferably a 25% change, more preferably a 40% change, and most preferably a 50% or greater change in expression levels. In one embodiment, an increase in Skp2, IDH1, or IDH2 expression is at least 5, 10, 15, 20, 25% or more relative to a reference cell at a corresponding stage of the cell cycle.
By “analog” is meant a molecule that is not identical, but has analogous functional or structural features. For example, a polypeptide analog retains the biological activity of a corresponding naturally-occurring polypeptide, while having certain biochemical modifications that enhance the analog's function relative to a naturally occurring polypeptide. Such biochemical modifications could increase the analog's protease resistance, membrane permeability, or half-life, without altering, for example, ligand binding. An analog may include an unnatural amino acid.
In this disclosure, “comprises,” “comprising,” “containing,” and “having” and the like can have the meaning ascribed to them in U.S. patent law, and can mean “includes,” “including,” and the like; “consisting essentially of” or “consists essentially” likewise has the meaning ascribed in U.S. patent law and the term is open-ended, allowing for the presence of more than that which is recited so long as basic or novel characteristics of that which is recited is not changed by the presence of more than that which is recited, but excludes prior art embodiments.
“Detect” refers to identifying the presence, absence or amount of the analyte to be detected.
By “disease” is meant any condition or disorder that damages or interferes with the normal function of a cell, tissue, or organ. In a disease, such as cancer (e.g., breast cancer, prostate cancer, glioblastoma).
By “effective amount” is meant the amount of a required to ameliorate the symptoms of a disease relative to an untreated patient. The effective amount of active compound(s) used to practice the present invention for therapeutic treatment of a disease varies depending upon the manner of administration, the age, body weight, and general health of the subject. Ultimately, the attending physician or veterinarian will decide the appropriate amount and dosage regimen. Such amount is referred to as an “effective” amount. In one embodiment, an effective amount of an agent defined herein is sufficient to reduce or stabilize the proliferation of a cancer cell. In another embodiment, an effective amount of an agent defined herein is sufficient to kill a cancer cell.
The invention provides a number of targets that are useful for the development of highly specific drugs to treat a disorder characterized by the methods delineated herein. In addition, the methods of the invention provide a facile means to identify therapies that are safe for use in subjects. In addition, the methods of the invention provide a route for analyzing virtually any number of compounds for effects on a disease described herein with high-volume throughput, high sensitivity, and low complexity.
By “fragment” is meant a portion of a polypeptide or nucleic acid molecule. This portion contains, preferably, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of the entire length of the reference nucleic acid molecule or polypeptide. A fragment may contain 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 nucleotides or amino acids.
By “inhibitory nucleic acid” is meant a double-stranded RNA, siRNA, shRNA, or antisense RNA, or a portion thereof, or a mimetic thereof, that when administered to a mammalian cell results in a decrease (e.g., by 10%, 25%, 50%, 75%, or even 90-100%) in the expression of a target gene. Typically, a nucleic acid inhibitor comprises at least a portion of a target nucleic acid molecule, or an ortholog thereof, or comprises at least a portion of the complementary strand of a target nucleic acid molecule. For example, an inhibitory nucleic acid molecule comprises at least a portion of any or all of the nucleic acids delineated herein.
The terms “isolated,” “purified,” or “biologically pure” refer to material that is free to varying degrees from components which normally accompany it as found in its native state. “Isolate” denotes a degree of separation from original source or surroundings. “Purify” denotes a degree of separation that is higher than isolation. A “purified” or “biologically pure” protein is sufficiently free of other materials such that any impurities do not materially affect the biological properties of the protein or cause other adverse consequences. That is, a nucleic acid or peptide of this invention is purified if it is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized. Purity and homogeneity are typically determined using analytical chemistry techniques, for example, polyacrylamide gel electrophoresis or high-performance liquid chromatography. The term “purified” can denote that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel. For a protein that can be subjected to modifications, for example, phosphorylation or glycosylation, different modifications may give rise to different isolated proteins, which can be separately purified.
By “isolated polynucleotide” is meant a nucleic acid (e.g., a DNA) that is free of the genes which, in the naturally-occurring genome of the organism from which the nucleic acid molecule of the invention is derived, flank the gene. The term therefore includes, for example, a recombinant DNA that is incorporated into a vector; into an autonomously replicating plasmid or virus; or into the genomic DNA of a prokaryote or eukaryote; or that exists as a separate molecule (for example, a cDNA or a genomic or cDNA fragment produced by PCR or restriction endonuclease digestion) independent of other sequences. In addition, the term includes an RNA molecule that is transcribed from a DNA molecule, as well as a recombinant DNA that is part of a hybrid gene encoding additional polypeptide sequence.
By an “isolated polypeptide” is meant a polypeptide of the invention that has been separated from components that naturally accompany it. Typically, the polypeptide is isolated when it is at least 60%, by weight, free from the proteins and naturally-occurring organic molecules with which it is naturally associated. Preferably, the preparation is at least 75%, more preferably at least 90%, and most preferably at least 99%, by weight, a polypeptide of the invention. An isolated polypeptide of the invention may be obtained, for example, by extraction from a natural source, by expression of a recombinant nucleic acid encoding such a polypeptide; or by chemically synthesizing the protein. Purity can be measured by any appropriate method, for example, column chromatography, polyacrylamide gel electrophoresis, or by HPLC analysis.
By “marker” is meant any protein or polynucleotide having an alteration in expression level or activity that is associated with a disease or disorder. Exemplary markers include Skp2, p27, p21, Cyclin A, Cyclin E, IDH1, IDH2, glycolysis, TCA cycle, lactate levels, oxidative phosphorylation levels.
As used herein, “obtaining” as in “obtaining an agent” includes synthesizing, purchasing, or otherwise acquiring the agent.
By “reduces” is meant a negative alteration of at least 10%, 25%, 50%, 75%, or 100%.
By “reference” is meant a standard or control condition.
By “substantially identical” is meant a polypeptide or nucleic acid molecule exhibiting at least 50% identity to a reference amino acid sequence (for example, any one of the amino acid sequences described herein) or nucleic acid sequence (for example, any one of the nucleic acid sequences described herein). Preferably, such a sequence is at least 60%, more preferably 80% or 85%, and more preferably 90%, 95% or even 99% identical at the amino acid level or nucleic acid to the sequence used for comparison.
Sequence identity is typically measured using sequence analysis software (for example, Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705, BLAST, BESTFIT, GAP, or PILEUP/PRETTYBOX programs). Such software matches identical or similar sequences by assigning degrees of homology to various substitutions, deletions, and/or other modifications. Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine. In an exemplary approach to determining the degree of identity, a BLAST program may be used, with a probability score between e−3 and e−100 indicating a closely related sequence.
By “subject” is meant a mammal, including, but not limited to, a human or non-human mammal, such as a bovine, equine, canine, ovine, or feline.
Ranges provided herein are understood to be shorthand for all of the values within the range. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50.
As used herein, the terms “treat,” treating,” “treatment,” and the like refer to reducing or ameliorating a disorder and/or symptoms associated therewith. It will be appreciated that, although not precluded, treating a disorder or condition does not require that the disorder, condition or symptoms associated therewith be completely eliminated.
Unless specifically stated or obvious from context, as used herein, the term “or” is understood to be inclusive. Unless specifically stated or obvious from context, as used herein, the terms “a”, “an”, and “the” are understood to be singular or plural.
Unless specifically stated or obvious from context, as used herein, the term “about” is understood as within a range of normal tolerance in the art, for example within 2 standard deviations of the mean. About can be understood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value. Unless otherwise clear from context, all numerical values provided herein are modified by the term about.
The recitation of a listing of chemical groups in any definition of a variable herein includes definitions of that variable as any single group or combination of listed groups. The recitation of an embodiment for a variable or aspect herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.
Any compositions or methods provided herein can be combined with one or more of any of the other compositions and methods provided herein.
The present disclosure features compositions and methods of treating a cancer in a subject by administering to the subject a Skp2 inhibitor and an inhibitor of glycolytic metabolism (e.g., PKM2 inhibitor).
The invention is based, at least in part, on the discovery of a cell cycle-dependent metabolic cycle in mammalian cells through SCFSkp2-mediated IDH1 degradation. Specifically, mammalian cells predominantly utilized the TCA cycle in G1 phase, but preferred glycolysis in S phase. Mechanistically, coupling cell cycle with metabolism was largely achieved by timely destruction of IDH1/2, which are key TCA cycle enzymes, in a Skp2-dependent manner. As such, depleting SKP2 abolished cell cycle-dependent fluctuation of IDH1/2 expression, leading to reduced glycolysis in S phase. Thus, SCFSkp2 controls IDH1/2 stability to ensure timely shift from TCA cycle to glycolysis during G1 to S cell cycle transition.
Whether glucose is predominantly metabolized via oxidative-phosphorylation or glycolysis differs between quiescent versus proliferating cells, including tumor cells. Given the high demand of biomacromolecules, including lipid, nucleotides and amino acids, to prepare for DNA replication and subsequent cell division, high rates of glycolysis and low rates of TCA cycle enable more flux of intermediates into the biomass synthesis pathways. Indeed, several lines of evidence advocate a bi-directional interplay between the cell cycle and metabolic machineries. On one hand, key metabolic enzymes are directly regulated in a cell cycle-dependent manner, such as PFKFB3 (6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase-3) by SCFGRR1, SCFβ-TRIP and APCCdh1, HK2 (hexokinase 2) by cyclin D1, PFKP and PKM2 by CDK6/cyclin D3, and GLS1 by APCCdh1. On the other hand, disturbing metabolism also could compromise cell cycle progress.
The present study therefore reveals a novel oncogenic role of Skp2 independent of its other biological substrate p27 in cell cycle regulation, by promoting the metabolic switch from utilization of TCA cycle to glycolysis. In one example, elevated Skp2 abundance in prostate cancer cells destabilized IDH1 to favor glycolysis and subsequent tumorigenesis. Based on these results, targeting Skp2 has the potential to provide a novel anti-cancer therapy in part by suppressing cancer metabolism.
The invention provides compositions comprising a therapeutic combination comprising a Skp2 inhibitor and an inhibitor of glycolytic metabolism (e.g., PKM2 inhibitor) and methods of using such compositions for the treatment of cancer (e.g., prostate cancer, breast cancer and glioblastoma).
The methods and compositions provided herein can be used to treat or prevent progression of a cancer (e.g., breast cancer, prostate cancer, glioblastoma) using a Skp2 inhibitor and an inhibitor of glycolytic metabolism (e.g., PKM2 inhibitor).
Compositions of the invention are administered to subjects, particularly humans, suffering from, having, susceptible to, or at risk of developing cancer (e.g., breast cancer, prostate cancer, glioblastoma). Determination of those subjects “at risk” can be made by any objective or subjective determination by a diagnostic test or opinion of a subject or health care provider (e.g., genetic test, enzyme or protein marker, family history, and the like). Identifying a subject in need of such treatment can be in the judgment of a subject or a health care professional and can be subjective (e.g. opinion) or objective (e.g., measurable by a test or diagnostic method).
In one embodiment, a therapeutic combination of the invention comprises an effective amount of a Skp2 inhibitor and an effective amount of a PKM2 inhibitor. If desired, such therapeutic combinations are administered in combination with standard chemotherapeutics. Methods for administering combination therapies (e.g., concurrently or otherwise) are known to the skilled artisan and are described for example in Remington's Pharmaceutical Sciences by E. W. Martin.
Pharmaceutical compositions of the invention contain a Skp2 inhibitor and an inhibitor of glycolytic metabolism (e.g., PKM2 inhibitor). Typically, such compositions comprise an effective amount of an agent that inhibits the expression or activity in a physiologically acceptable carrier. Therapeutic combinations of the invention are typically formulated and administered separately, but may also be combined and administered in a single formulation.
Typically, the carrier or excipient for the composition provided herein is a pharmaceutically acceptable carrier or excipient, such as sterile water, aqueous saline solution, aqueous buffered saline solutions, aqueous dextrose solutions, aqueous glycerol solutions, ethanol, or combinations thereof. The preparation of such solutions ensuring sterility, pH, isotonicity, and stability is effected according to protocols established in the art. Generally, a carrier or excipient is selected to minimize allergic and other undesirable effects, and to suit the particular route of administration, e.g., subcutaneous, intramuscular, intranasal, and the like.
The administration may be by any suitable means that results in a concentration of the therapeutic that, combined with other components, is effective in ameliorating, reducing, or stabilizing the disease symptoms in a subject. The composition may be administered systemically, for example, formulated in a pharmaceutically-acceptable buffer such as physiological saline. Preferable routes of administration include, for example, subcutaneous, intravenous, intraperitoneally, intramuscular, intrathecal, or intradermal injections that provide continuous, sustained levels of the agent in the patient. The amount of the therapeutic agent to be administered varies depending upon the manner of administration, the age and body weight of the patient, and with the clinical symptoms of the cancer. Generally, amounts will be in the range of those used for other agents used in the treatment of cancer, although in certain instances lower amounts will be needed because of the increased specificity of the agent. A composition is administered at a dosage that ameliorates or decreases effects of the cancer as determined by a method known to one skilled in the art.
The therapeutic or prophylactic composition may be contained in any appropriate amount in any suitable carrier substance, and is generally present in an amount of 1-95% by weight of the total weight of the composition. The composition may be provided in a dosage form that is suitable for parenteral (e.g., subcutaneously, intravenously, intramuscularly, intrathecally, or intraperitoneally) administration route. The pharmaceutical compositions may be formulated according to conventional pharmaceutical practice (see, e.g., Remington: The Science and Practice of Pharmacy (20th ed.), ed. A. R. Gennaro, Lippincott Williams & Wilkins, 2000 and Encyclopedia of Pharmaceutical Technology, eds. J. Swarbrick and J. C. Boylan, 1988-1999, Marcel Dekker, New York).
Pharmaceutical compositions according to the invention may be formulated to release the active agent substantially immediately upon administration or at any predetermined time or time period after administration. The latter types of compositions are generally known as controlled release formulations, which include (i) formulations that create a substantially constant concentration of the drug within the body over an extended period of time; (ii) formulations that after a predetermined lag time create a substantially constant concentration of the drug within the body over an extended period of time; (iii) formulations that sustain action during a predetermined time period by maintaining a relatively, constant, effective level in the body with concomitant minimization of undesirable side effects associated with fluctuations in the plasma level of the active substance (sawtooth kinetic pattern); (iv) formulations that localize action by, e.g., spatial placement of a controlled release composition adjacent to or in contact with an organ, such as the heart; (v) formulations that allow for convenient dosing, such that doses are administered, for example, once every one or two weeks; and (vi) formulations that target a disease using carriers or chemical derivatives to deliver the therapeutic agent to a particular cell type. For some applications, controlled release formulations obviate the need for frequent dosing during the day to sustain the plasma level at a therapeutic level.
Any of a number of strategies can be pursued in order to obtain controlled release in which the rate of release outweighs the rate of metabolism of the agent in question. In one example, controlled release is obtained by appropriate selection of various formulation parameters and ingredients, including, e.g., various types of controlled release compositions and coatings. Thus, the therapeutic agent is formulated with appropriate excipients into a pharmaceutical composition that, upon administration, releases the therapeutic agent in a controlled manner. Examples include single or multiple unit tablet or capsule compositions, oil solutions, suspensions, emulsions, microcapsules, microspheres, molecular complexes, nanoparticles, patches, and liposomes.
The pharmaceutical composition may be administered parenterally by injection, infusion or implantation (subcutaneous, intravenous, intramuscular, intraperitoneal, intrathecal, or the like) in dosage forms, formulations, or via suitable delivery devices or implants containing conventional, non-toxic pharmaceutically acceptable carriers and adjuvants. The formulation and preparation of such compositions are well known to those skilled in the art of pharmaceutical formulation. Formulations can be found in Remington: The Science and Practice of Pharmacy, supra.
Compositions for parenteral use may be provided in unit dosage forms (e.g., in single-dose ampoules), or in vials containing several doses and in which a suitable preservative may be added (see below). The composition may be in the form of a solution, a suspension, an emulsion, an infusion device, or a delivery device for implantation, or it may be presented as a dry powder to be reconstituted with water or another suitable vehicle before use. Apart from the active agent that reduces or ameliorates a cardiac dysfunction or disease, the composition may include suitable parenterally acceptable carriers and/or excipients. The active therapeutic agent(s), including a a Skp2 inhibitor and an inhibitor of glycolytic metabolism (e.g., PKM2 inhibitor) may be incorporated into microspheres, microcapsules, nanoparticles, liposomes, or the like for controlled release. Furthermore, the composition may include suspending, solubilizing, stabilizing, pH-adjusting agents, tonicity adjusting agents, and/or dispersing, agents.
In some embodiments, the composition comprising the active therapeutic agent is formulated for intravenous delivery. As indicated above, the pharmaceutical compositions according to the invention may be in the form suitable for sterile injection. To prepare such a composition, the suitable therapeutic(s) are dissolved or suspended in a parenterally acceptable liquid vehicle. Among acceptable vehicles and solvents that may be employed are water, water adjusted to a suitable pH by addition of an appropriate amount of hydrochloric acid, sodium hydroxide or a suitable buffer, 1,3-butanediol, Ringer's solution, and isotonic sodium chloride solution and dextrose solution. The aqueous formulation may also contain one or more preservatives (e.g., methyl, ethyl or n-propyl p-hydroxybenzoate). In cases where one of the agents is only sparingly or slightly soluble in water, a dissolution enhancing or solubilizing agent can be added, or the solvent may include 10-60% w/w of propylene glycol or the like.
Inhibitory nucleic acid molecules that inhibit the expression or activity of Skp2 or PKM2 are useful for the treatment of cancer in the methods of the invention. Such oligonucleotides include single and double stranded nucleic acid molecules (e.g., DNA, RNA, and analogs thereof) that bind a nucleic acid molecule that encodes a Skp2 or PKM2 polypeptide (e.g., antisense molecules, siRNA, shRNA), as well as nucleic acid molecules that bind directly to the polypeptide to modulate its biological activity (e.g., aptamers). Inhibitory nucleic acid molecules described herein are useful for the treatment of cancer (e.g., breast cancer, glioblastoma, prostate cancer).
siRNA
Short twenty-one to twenty-five nucleotide double-stranded RNAs are effective at down-regulating gene expression (Zamore et al., Cell 101: 25-33; Elbashir et al., Nature 411: 494-498, 2001, hereby incorporated by reference). The therapeutic effectiveness of an siRNA approach in mammals was demonstrated in vivo by McCaffrey et al. (Nature 418: 38-39.2002).
Given the sequence of a target gene, siRNAs may be designed to inactivate that gene. Such siRNAs, for example, could be administered directly to an affected tissue, or administered systemically. The nucleic acid sequence of a gene can be used to design small interfering RNAs (siRNAs). The 21 to 25 nucleotide siRNAs may be used, for example, as therapeutics to treat cancer.
The inhibitory nucleic acid molecules of the present invention may be employed as double-stranded RNAs for RNA interference (RNAi)-mediated knock-down of expression. In one embodiment, expression of Skp2 polypeptide and/or PKM2 polypeptide is reduced in a subject having cancer. RNAi is a method for decreasing the cellular expression of specific proteins of interest (reviewed in Tuschl, Chembiochem 2:239-245, 2001; Sharp, Genes & Devel. 15:485-490, 2000; Hutvagner and Zamore, Curr. Opin. Genet. Devel. 12:225-232, 2002; and Hannon, Nature 418:244-251, 2002). The introduction of siRNAs into cells either by transfection of dsRNAs or through expression of siRNAs using a plasmid-based expression system is increasingly being used to create loss-of-function phenotypes in mammalian cells.
In one embodiment of the invention, a double-stranded RNA (dsRNA) molecule is made that includes between eight and nineteen consecutive nucleobases of a nucleobase oligomer of the invention. The dsRNA can be two distinct strands of RNA that have duplexed, or a single RNA strand that has self-duplexed (small hairpin (sh)RNA). Typically, dsRNAs are about 21 or 22 base pairs, but may be shorter or longer (up to about 29 nucleobases) if desired. dsRNA can be made using standard techniques (e.g., chemical synthesis or in vitro transcription). Kits are available, for example, from Ambion (Austin, Tex.) and Epicentre (Madison, Wis.). Methods for expressing dsRNA in mammalian cells are described in Brummelkamp et al. Science 296:550-553, 2002; Paddison et al. Genes & Devel. 16:948-958, 2002. Paul et al. Nature Biotechnol. 20:505-508, 2002; Sui et al. Proc. Natl. Acad. Sci. USA 99:5515-5520, 2002; Yu et al. Proc. Natl. Acad. Sci. USA 99:6047-6052, 2002; Miyagishi et al. Nature Biotechnol. 20:497-500, 2002; and Lee et al. Nature Biotechnol. 20:500-505 2002, each of which is hereby incorporated by reference.
Small hairpin RNAs (shRNAs) comprise an RNA sequence having a stem-loop structure. A “stem-loop structure” refers to a nucleic acid having a secondary structure that includes a region of nucleotides which are known or predicted to form a double strand or duplex (stem portion) that is linked on one side by a region of predominantly single-stranded nucleotides (loop portion). The term “hairpin” is also used herein to refer to stem-loop structures. Such structures are well known in the art and the term is used consistently with its known meaning in the art. As is known in the art, the secondary structure does not require exact base-pairing. Thus, the stem can include one or more base mismatches or bulges. Alternatively, the base-pairing can be exact, i.e. not include any mismatches. The multiple stem-loop structures can be linked to one another through a linker, such as, for example, a nucleic acid linker, a miRNA flanking sequence, other molecule, or some combination thereof.
As used herein, the term “small hairpin RNA” includes a conventional stem-loop shRNA, which forms a precursor miRNA (pre-miRNA). While there may be some variation in range, a conventional stem-loop shRNA can comprise a stem ranging from 19 to 29 bp, and a loop ranging from 4 to 30 bp. “shRNA” also includes micro-RNA embedded shRNAs (miRNA-based shRNAs), wherein the guide strand and the passenger strand of the miRNA duplex are incorporated into an existing (or natural) miRNA or into a modified or synthetic (designed) miRNA. In some instances, the precursor miRNA molecule can include more than one stem-loop structure. MicroRNAs are endogenously encoded RNA molecules that are about 22-nucleotides long and generally expressed in a highly tissue- or developmental-stage-specific fashion and that post-transcriptionally regulate target genes. More than 200 distinct miRNAs have been identified in plants and animals. These small regulatory RNAs are believed to serve important biological functions by two prevailing modes of action: (1) by repressing the translation of target mRNAs, and (2) through RNA interference (RNAi), that is, cleavage and degradation of mRNAs. In the latter case, miRNAs function analogously to small interfering RNAs (siRNAs). Thus, one can design and express artificial miRNAs based on the features of existing miRNA genes.
shRNAs can be expressed from DNA vectors to provide sustained silencing and high yield delivery into almost any cell type. In some embodiments, the vector is a viral vector. Exemplary viral vectors include retroviral, including lentiviral, adenoviral, baculoviral and avian viral vectors, and including such vectors allowing for stable, single-copy genomic integrations. Retroviruses from which the retroviral plasmid vectors can be derived include, but are not limited to, Moloney Murine Leukemia Virus, spleen necrosis virus, Rous sarcoma Virus, Harvey Sarcoma Virus, avian leukosis virus, gibbon ape leukemia virus, human immunodeficiency virus, Myeloproliferative Sarcoma Virus, and mammary tumor virus. A retroviral plasmid vector can be employed to transduce packaging cell lines to form producer cell lines. Examples of packaging cells which can be transfected include, but are not limited to, the PE501, PA317, R-2, R-AM, PA12, T19-14x, VT-19-17-H2, RCRE, RCRIP, GP+E-86, GP+envAm12, and DAN cell lines as described in Miller, Human Gene Therapy 1:5-14 (1990), which is incorporated herein by reference in its entirety. The vector can transduce the packaging cells through any means known in the art. A producer cell line generates infectious retroviral vector particles which include polynucleotide encoding a DNA replication protein. Such retroviral vector particles then can be employed, to transduce eukaryotic cells, either in vitro or in vivo. The transduced eukaryotic cells will express a DNA replication protein.
Catalytic RNA molecules or ribozymes that include an antisense sequence of the present invention can be used to inhibit expression of a nucleic acid molecule in vivo (e.g., a nucleic acid encoding Skp2 or PKM2). The inclusion of ribozyme sequences within antisense RNAs confers RNA-cleaving activity upon them, thereby increasing the activity of the constructs. The design and use of target RNA-specific ribozymes is described in Haseloff et al., Nature 334:585-591. 1988, and U.S. Patent Application Publication No. 2003/0003469 A1, each of which is incorporated by reference.
Accordingly, the invention also features a catalytic RNA molecule that includes, in the binding arm, an antisense RNA having between eight and nineteen consecutive nucleobases. In preferred embodiments of this invention, the catalytic nucleic acid molecule is formed in a hammerhead or hairpin motif. Examples of such hammerhead motifs are described by Rossi et al., Aids Research and Human Retroviruses, 8:183, 1992. Example of hairpin motifs are described by Hampel et al., “RNA Catalyst for Cleaving Specific RNA Sequences,” filed Sep. 20, 1989, which is a continuation-in-part of U.S. Ser. No. 07/247,100 filed Sep. 20, 1988, Hampel and Tritz, Biochemistry, 28:4929, 1989, and Hampel et al., Nucleic Acids Research, 18: 299, 1990. These specific motifs are not limiting in the invention and those skilled in the art will recognize that all that is important in an enzymatic nucleic acid molecule of this invention is that it has a specific substrate binding site which is complementary to one or more of the target gene RNA regions, and that it have nucleotide sequences within or surrounding that substrate binding site which impart an RNA cleaving activity to the molecule.
Alternatively, expression of Skp2, PKM2, or both, may be inhibited, or silenced by introducing vectors encoding Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 nuclease engineered to target Skp2, PKM2, or both.
Essentially any method for introducing a nucleic acid construct into cells can be employed. Physical methods of introducing nucleic acids include injection of a solution containing the construct, bombardment by particles covered by the construct, soaking a cell, tissue sample or organism in a solution of the nucleic acid, or electroporation of cell membranes in the presence of the construct. A viral construct packaged into a viral particle can be used to accomplish both efficient introduction of an expression construct into the cell and transcription of the encoded shRNA. Other methods known in the art for introducing nucleic acids to cells can be used, such as lipid-mediated carrier transport, chemical mediated transport, such as calcium phosphate, and the like. Thus, the shRNA-encoding nucleic acid construct can be introduced along with components that perform one or more of the following activities: enhance RNA uptake by the cell, promote annealing of the duplex strands, stabilize the annealed strands, or otherwise increase inhibition of the target gene.
For expression within cells, DNA vectors, for example plasmid vectors comprising either an RNA polymerase II or RNA polymerase III promoter can be employed. Expression of endogenous miRNAs is controlled by RNA polymerase II (Pol II) promoters and in some cases, shRNAs are most efficiently driven by Pol II promoters, as compared to RNA polymerase III promoters (Dickins et al., 2005, Nat. Genet. 39: 914-921). In some embodiments, expression of the shRNA can be controlled by an inducible promoter or a conditional expression system, including, without limitation, RNA polymerase type II promoters. Examples of useful promoters in the context of the invention are tetracycline-inducible promoters (including TRE-tight), IPTG-inducible promoters, tetracycline transactivator systems, and reverse tetracycline transactivator (rtTA) systems. Constitutive promoters can also be used, as can cell- or tissue-specific promoters. Many promoters will be ubiquitous, such that they are expressed in all cell and tissue types. A certain embodiment uses tetracycline-responsive promoters, one of the most effective conditional gene expression systems in in vitro and in vivo studies. See International Patent Application PCT/US2003/030901 (Publication No. WO 2004-029219 A2) and Fewell et al., 2006, Drug Discovery Today 11: 975-982, for a description of inducible shRNA.
Naked polynucleotides, or analogs thereof, are capable of entering mammalian cells and inhibiting expression of a gene of interest (e.g., a SKP2 or PKM2 polynucleotide). Nonetheless, it may be desirable to utilize a formulation that aids in the delivery of oligonucleotides or other nucleobase oligomers to cells (see, e.g., U.S. Pat. Nos. 5,656,611, 5,753,613, 5,785,992, 6,120,798, 6,221,959, 6,346,613, and 6,353,055, each of which is hereby incorporated by reference).
The present invention features assays for the detection of Skp2, IDH1, and/or IDH2 protein levels or activity. In other embodiments, the invention features assays for characterizing metabolism (e.g., glycolysis, TCA activity). Levels Skp2, IDH1, and/or IDH2 are measured in a subject sample (e.g., tumor biopsy) and used to select patient therapies (e.g., treatment with Skp2 and/or PKM2 inhibitors). Standard methods may be used to measure levels of Skp2, IDH1, and/or IDH2 in any biological sample. Such methods include immunoassay, ELISA, western blotting and radioimmunoassay.
The diagnostic methods described herein can be used individually or in combination with any other diagnostic method known in the art.
The invention provides kits for the treatment or prevention of cancer. In some embodiments, the kit includes a therapeutic composition containing a Skp2 inhibitor and an inhibitor of glycolytic metabolism (e.g., PKM2 inhibitor) in unit dosage form. In other embodiments, the Skp2 inhibitor and inhibitor of glycolytic metabolism (e.g., PKM2 inhibitor) are provided in a sterile container. Such containers can be boxes, ampoules, bottles, vials, tubes, bags, pouches, blister-packs, or other suitable container forms known in the art. Such containers can be made of plastic, glass, laminated paper, metal foil, or other materials suitable for holding medicaments.
If desired a pharmaceutical composition of the invention is provided together with instructions for administering the pharmaceutical composition to a subject having or at risk of contracting or developing cancer. The instructions will generally include information about the use of the composition for the treatment or prevention of cancer. In other embodiments, the instructions include at least one of the following: description of the therapeutic/prophylactic agent; dosage schedule and administration for treatment or prevention of cancer or symptoms thereof; precautions; warnings; indications; counter-indications; over dosage information; adverse reactions; animal pharmacology; clinical studies; and/or references. The instructions may be printed directly on the container (when present), or as a label applied to the container, or as a separate sheet, pamphlet, card, or folder supplied in or with the container.
The practice of the present invention employs, unless otherwise indicated, conventional techniques of molecular biology (including recombinant techniques), microbiology, cell biology, biochemistry and immunology, which are well within the purview of the skilled artisan. Such techniques are explained fully in the literature, such as, “Molecular Cloning: A Laboratory Manual”, second edition (Sambrook, 1989); “Oligonucleotide Synthesis” (Gait, 1984); “Animal Cell Culture” (Freshney, 1987); “Methods in Enzymology” “Handbook of Experimental Immunology” (Weir, 1996); “Gene Transfer Vectors for Mammalian Cells” (Miller and Calos, 1987); “Current Protocols in Molecular Biology” (Ausubel, 1987); “PCR: The Polymerase Chain Reaction”, (Mullis, 1994); “Current Protocols in Immunology” (Coligan, 1991). These techniques are applicable to the production of the polynucleotides and polypeptides of the invention, and, as such, may be considered in making and practicing the invention. Particularly useful techniques for particular embodiments will be discussed in the sections that follow.
The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the assay, screening, and therapeutic methods of the invention, and are not intended to limit the scope of what the inventors regard as their invention.
Actively proliferating cancer cells are addicted to glycolysis despite the presence of oxygen, whereas normal differentiated cells largely rely on oxidative phosphorylation (OXPHOS) (Warburg, Science 123, 309 (1956)). For cancer cells, this phenotype is termed the “Warburg Effect”, which has been shown to benefit cancer cell growth and tumorigenesis (Warburg, Science 123, 309 (1956)). Clinically, increased glycolysis in cancer cells is accompanied by robust glucose uptake, which underlies the usage of fluorodeoxyglucose positron emission tomography (FDG-PET) for tumor diagnosis and response to cancer therapy (Boellaard et al., European journal of nuclear medicine and molecular imaging 42, 328 (2015)). Mechanistic investigations reveal that unlike non-proliferating cells, actively dividing cells, including tumor cells, incorporate intermediates of glycolysis into the macromolecules (e.g. non-essential amino acids, fatty acids and nucleotides) to facilitate cell growth and division, a process tightly controlled by many oncogenic signaling pathways, involving PKM2, HIF, Akt, Ras and Myc as important regulatory components (Vander Heiden et al., Science 324, 1029 (2009); Christofk et al., Nature 452, 230 (2008); Manning et al., Cell 129, 1261 (2007); Gordan et al., Cancer cell 12, 108 (2007); Dang et al., Trends in biochemical sciences 24, 68 (1999); Bensaad et al., Cell 126, 107 (2006); Kaelin et al., Molecular cell 30, 393 (2008); Shi et al., Mot Cancer 8, 32 (Jun. 5, 2009)). However, the molecular underpinnings responsible for the distinct metabolic dependence between proliferating and non-proliferating cells remain largely unknown.
Intriguingly, a metabolic cycle has been reported in yeasts that is coupled with cell cycle events (Tu et al., Science 310, 1152 (2005)). A shift from the tricarboxylic acid (TCA) cycle to glycolysis in S phase in yeast was found to minimize intracellular reactive oxygen species (ROS) production, possibly to avoid damage to newly duplicated DNA (Chen et al., Science 316, 1916 (2007)). Although a previous study indicates crosstalk between cell cycle regulators and glycolysis (Tudzarova et al., P Natl Acad Sci USA 108, 5278 (Mar. 29, 2011)), the exact molecular mechanism that governs a similar coupling of metabolism to the cell-cycle in mammalian cells remains elusive.
To understand the molecular mechanisms that govern coupling of metabolism to the cell-cycle in mammalian cells, rates of glycolysis (indicated by extracellular acidification rate, ECAR) and TCA cycle activity (indicated by oxygen consumption rate, OCR) were measured at different cell cycle phases (
To further explore this cell cycle-dependent metabolic shift between glycolysis and TCA cycle, cells were synchronized and released into either G1 or S phase (
The rate of TCA cycle is primarily governed by a cohort of essential enzymes (
To understand the importance of fluctuations of IDH1 and IDH2 during the cell cycle, IDH1 and IDH2 knockout haploid HAP1 cells were generated by CRISPR/Cas-9. IDH2 knockout cells, and with a similar trend, the IDH1 knockout cells, displayed increased glycolysis and compromised mitochondrial respiration (
To identify the E3 ubiquitin ligase(s) responsible for S-phase specific degradation of IDH1/2, IDH1 and IDH2 protein levels were determined. Endogenous IDH1 and IDH2 protein abundance were elevated in cells treated with either the proteosome inhibitor MG132 or the Cullin neddylation inhibitor, MLN4924 (
Consistent with this notion, it was found that Skp2, but not Fbw4 was capable of promoting IDH1 ubiquitination in cells (
SCFSkp2 typically binds and ubiquitinates its downstream substrates in a phosphorylation-dependent manner (Wang et al., Nature reviews Cancer 14, 233 (2014)). Therefore, a panel of modifying kinase(s) potentially involved in Skp2-mediated degradation of IDH1/2 in cells was examined. Notably, cyclin E/CDK2, and to a lesser extent, cyclin A/CDK2, promoted Skp2-mediated degradation of IDH1 and IDH2 in cells (
Importantly, the phosphorylation on T157 of exogenous IDH1 can be detected using mass spectroscopy (
Previous studies revealed that numerous cyclin E substrates contain an RXL cyclin A/E-binding motif (Adams et al., Molecular and Cellular Biology 16, 6623 (1996)). Such an RXL motif was identified in both IDH1 and IDH2 (
Skp2 plays an important role in prostate tumorigenesis (Lin et al., Nature 464, 374 (2010)). In keeping with an oncogenic role for Skp2, an inverse correlation between Skp2 and IDH1 expression was observed in a panel of prostate cancer (PrCa) cell lines (
In keeping with this notion, treating 22-Rv1 and LNCaP cells with the Skp2 inhibitor, SKPin C1, which was developed as a selective inhibitor to block an interaction between Skp2 and p27 (Wu et al., Chemistry & biology 19, 1515 (2012)), significantly stabilized both IDH1 and IDH2 (
The present study defined a cell cycle-dependent metabolic cycle in mammalian cells, in part through SCFSkp2-mediated IDH1 degradation (
The results described herein above, were obtained using the following methods and materials.
Plasmids and shRNAs
Skp2 cDNA was subcloned into CMV-GST, pcDNA3-HA and Lenti-puro-HA vectors via BamHI and XhoI sites. IDH1-WT cDNA were subcloned into pET28a-His, pGEX-GST, Flag-CMV and Lenti-hygro-HA vectors via BamHI and XhoI sites. Site directed mutagenesis to generate various IDH1 degron mutants were performed using the QuikChange XL Site-Directed Mutagenesis Kit (Stratagene) according to the manufacturer's instructions. HA-cyclin A, HA-cyclin E, HA-CDK2, HA-ERK1, HA-GSK3β and HA-Rbx1 were generated by cloning the corresponding cDNAs into pcDNA3-HA vector via BamHI and XhoI sites. CMV-GST-Fbl3a, CMV-GST-Fbl13, CMV-GST-Fbl18, CMV-GST-Fbo16, CMV-GST-β-TRCP1, CMV-GST-Fbw4, CMV-GST-Fbw6, CMV-GST-Fbw7 and CMV-GST-Skp2 were a kind gift of Dr. Wade Harper (Harvard Medical School). Myc-cullin 1, Myc-cullin 2, Myc-cullin 3, Myc-cullin 4A, Myc-cullin 4B and Myc-cullin 5 were a kind gift of Dr. James DeCaprio (Dana-Farber Cancer Institute). The lentiviral vectors containing Skp2 and p27 shRNAs were described before (Koff et al., Science 257, 1689 (1992)). The lentiviral vectors containing cullin 1, cullin 3 and Fbw4 shRNAs were purchased from Open biosystem.
Anti-IDH1 (3997, 8137), anti-IDH2 (12652), anti-cullin 1(4995), anti-cullin 3 (2759), anti-cullin 4A (2699), anti-PTEN (9188), anti-Akt (pan) (2920), anti-pS473-Akt (4070), anti-pT308-Akt (8205), Anti-cyclin A2 (4656), anti-cyclin D1 (2978), anti-cyclin D2 (3741), anti-cyclin D3 (2936), anti-cyclin E1 (4129), anti-cyclin E2 (4132), anti-GST (2625), anti-p27 Kip (3698), anti-citrate synthase (14309), anti-aconitase (6922), anti-OGDH (13407), anti-succinyl-CoA synthetase (8071), anti-SDHA (11998), anti-fumarase (4567), anti-MDH2 (11908), anti-Myc-tag (2276, 2278) and anti-Histon H3 (4499) antibodies were purchased from Cell Signaling Technology. Anti-Skp2 (A-2, H435), anti-Plk1 (F-8), anti-Cdc20 (E-7), and polyclonal anti-HA (Y-11) antibodies were purchased from Santa Cruz. Anti-Tubulin (T-5168) and anti-Vinculin (V-4505) antibodies were purchased from Bethyl Labs. Polyclonal anti-Flag antibody (F-2425), monoclonal anti-Flag (F-3165) antibody, anti-Flag agarose beads (A-2220), anti-HA agarose beads (A-2095) as well as peroxidase-conjugated anti-mouse secondary antibody (A-4416) and peroxidase-conjugated anti-rabbit secondary antibody (A-4914) were purchased from Sigma. Monoclonal anti-HA antibody (MMS-101P) was purchased from Covance. Anti-GFP antibody (632380) and polyclonal anti-Cdh1 antibody (34-2000) were purchased from Invitrogen. Anti-Fbw4 antibody (60116) was purchased from Abcam.
Human embryonic kidney 293 (HEK293) cells, HEK293FT, HeLa, DLD1, HCT116, U205, T98G, A375, VCaP, HAP1 cells and mouse embryonic fibroblasts (MEFs) were maintained in Dulbecco's Modified Eagle's Medium (DMEM) containing 10% fetal bovine serum (FBS), 100 Units of penicillin and 100 mg/ml streptomycin. PC3, DU145, 22Rv1, LNCaP and C4-2 cells were cultured in RPMI1640 containing 10% fetal bovine serum (FBS), 100 Units of penicillin and 100 mg/ml streptomycin. RWPE cells were maintained in keratinocyte serum free medium (K-SFM, Invitrogen, 44019). Skp2+/+ and Skp2−/− MEFs were described previously (Inuzuka et al., Cell 150, 179-193 (2012)). Cyclin A2f/f, cyclin E1−/−E2−/−, cyclin E1−/−, cyclin E2−/−, cyclin D1−/−, cyclin D2−/− and cyclin D3−/− MEFs were a kind gift of Dr. Piotr Sicinski (Dana Farber Cancer Institute). HAP1-IDH1−/− (HZGHC003323c006) and HAP1-IDH2−/− (HZGHC000919c010) cells were purchased from Horizon Discovery. HAP1 is a near-haploid human cell line, which was derived from KBM-7, a chronic myelogenous leukemia (CML) cell line (Carette et al., Science 326, 1231-1235). HeLa-IDH1−/− cells were generated using CRISPR/Cas 9 with a guide sequence of 5′-TACGAAATATTCTGGGTGGC-3′ (Sanjana et al., Nature methods 11, 783-784 (2014)). Cell culture transfection, lentiviral virus packaging and subsequent infection of various cell lines were performed according to the protocol described previously (Boehm et al., Molecular and cellular biology 25, 6464-6474 (2005)). To determine the proliferation ability of HAP1 after depletion of IDH1 or IDH2, cells were cultured in H-DMEM, then transferred into DMEM media without glucose (Thermo Fisher, 11966025) after adding either 25 mM of D-glucose (Sigma, G8270) or D-galactose (Sigma, G0750).
HeLa and HCT116 cells were used for synchronization. HeLa cells, which have low endogenous Skp2 activity, were used for ectopic expression-based degradation assays. HEK293 cell line was used for ubiquitination assays and co-IP assays to define the interaction between two ectopically expressed proteins, which is the most frequently used cell line for this type of experiment. Human prostate cancer cells, DU145, PC3, LNCaP, VCaP, 22Rv1 and C4-2 were used for compared endogenous Skp2 and IDH1 levels, as well as Skp2 knockdown and Skp2 overexpression. HAP1, LNCaP, and 22Rv1 cells were also used for treating with Skp2 inhibitor, SKPin C1 (MCE, HY-16661).
Cell synchronization with nocodazole arrest was described previously (Wan et al., Developmental cell 29, 377-391 (2014); Wei et al., Nature 428, 194-198 (2004)). Briefly, HeLa cells or HCT116 cells were incubated with 10 μg/mL for 20 hours, followed by knocking the dish on a hard surface to dislodge mitotic cells, and washing with PBS for 3 times. The cells were released at the indicated times before harvest.
Oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) were measured using Seahorse XF24 analyzer (Boston, Mass., USA). OCR assays used Seahorse XF basal media containing 25 mM glucose, 1 mM sodium pyruvate, and 2 mM glutamine, while ECAR assays used Seahorse XF basal media containing no glucose, no pyruvate, and 2 mM glutamine. For OCR assays, the final concentrations of oligomycin, FCCP, and antimycin A were 1, 0.3, and 1 μM, unless indicated otherwise. For ECAR assays, the final concentrations of glucose, oligomycin, and 2-DG were 10 mM, 1 μM, and 50 mM, unless indicated otherwise.
Cells were lysed in EBC buffer (50 mM Tris pH 7.5, 120 mM NaCl, 0.5% NP-40) 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 protein assay reagent on a Beckman Coulter DU-800 spectrophotometer. The lysates were then resolved by SDS-PAGE and immunoblotted with indicated antibodies. For immunoprecipitation, 1 mg lysates were incubated with the appropriate sepharose beads for 4 hours at 4° C. Immuno-complexes were washed four 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 indicated antibodies.
IDH1 in vitro kinase assays were performed as previous reported (Liu et al., Nature 508, 541-545 (2014)). Briefly, His-IDH1 was expressed in BL21 E. coli and purified using Ni-NTA (Ni-nitrilotriacetic acid) agarose (Thermo Fisher Scientific) according to the manufacturer's instructions. One microgram of His-IDH1 WT or mutant protein was incubated in the absence or presence of Cyclin E/Cdk2 kinase in kinase assay buffer (10 mM HEPES, pH 8.0, 10 mM MgCl2, 1 mM dithiothreitol, 0.1 mM ATP). The reaction was initiated by the addition of 10× kinase assay buffer in a volume of 30 μl for 45 min at 30° C. followed by the addition of SDS-PAGE sample buffer to stop the reaction before resolved by SDS-PAGE.
His-Skp2 and GST-IDH1 were expressed in BL21 E. coli and purified using Ni-NTA agarose or Glutathione Sepharose 4B (GE Healthcare Life Sciences) according to the manufacturer's instructions. The GST-IDH1 proteins (2 μg) were eluted using elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM reduced glutathione) and incubated with or without cyclin E/Cdk2 in kinase assay buffer for 1 hour. Then, the reaction solution was added with His-Skp2 beads (1 μg) and incubated at 4° C. for 3 hours followed by the addition of SDS-PAGE sample buffer to stop the reaction before resolved by SDS-PAGE.
Denatured in vivo ubiquitination assays were performed as previous described (Wei et al., Nature 428, 194-198 (2004)). Briefly, HEK293 cells were transfected with Flag-IDH1, His-ubiquitin and HA-Skp2. 48 hours after transfection, 30 μM MG132 was added to block proteasome degradation for 6 hours and cells were harvested in denatured buffer (6 M guanidine-HCl, pH 8.0, 0.1 M Na2HPO4/NaH2PO4, 10 mM imidazole). After sonication, the ubiquitinated proteins were purified by incubation with Ni-NTA matrices for 3 hours at room temperature. The pull-down products were washed sequentially twice in buffer A, twice in buffer ANTI mixture (buffer A: buffer TI=1:3) and once in buffer TI (25 mM Tris-HCl, pH 6.8, 20 mM imidazole). The poly-ubiquitinated proteins were separated by SDS-PAGE for immunoblot analysis.
Cells synchronized with nocodazole-arrest and release were collected at the indicated time points and stained with propidium iodide (Roche) according to the manufacturer's instructions. Stained cells were sorted with a Dako-Cytomation MoFlo sorter (Dako) at the Dana-Farber Cancer Institute FACS core facility.
The IDH1 peptides with/without phosphorylation modification were synthesized by LifeTein, LLC (Somerset, N.J.). Each peptide contained an N-terminal biotin and free C-terminus. The peptides were diluted into 1 mg/ml for further biochemical assays. The sequences are listed below:
Peptides (2 μg) were incubated with 10 μg of recombinant SKP2 proteins for 4 hours at 4° C., 10 μl Streptavidin agarose (GE Healthcare Life Sciences) was added in the sample for another 1 hour. The agarose was washed four times with NETN buffer. Bound proteins were added in 2×SDS loading buffer and resolved by SDS-PAGE for immunoblot analysis.
The procedures of mass spectrometry analysis were performed as described previously with minor modifications (Liu et al., Nature 508, 541-545 (2014)). Briefly, anti-Flag-IDH1 immunoprecipitations were performed with the whole cell lysates derived from three 10 cm dishes of HEK293 cells co-transfected with Flag-IDH1, HA-cyclin E and HA-CDK2. The immunoprecipitations proteins were resolved by SDS-PAGE, and stained by Gelgold staining buffer. The band containing IDH1 was reduced with 10 mM DTT for 30 min, alkylated with 55 mM iodoacetamide for 45 min, and in-gel-digested with trypsin enzymes. The resulting peptides were extracted from the gel and analyzed by microcapillary reversed-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS) using a high resolution Orbitrap Elite (Thermo Fisher Scientific) in positive ion DDA mode via CID, as previously described. MS/MS data were searched against the human protein database using Mascot (Matrix Science) and data analysis was performed using the Scaffold 4 software (Proteome Software).
Cells were cultured in 10% FBS containing DMEM or RPMI-1640 media before plating into 6-well plate at 10,000 cells (3,000 cells for HeLa) per well. Ten days later, cells were fixed with 10% acetic acid/10% methanol for 10 min, stained with 0.4% crystal violet/20% ethanol, followed by counting the colony numbers. For soft agar assays, cells were seeded in 0.4% low-melting-point agarose in DMEM or RPMI-1640 with 10% FBS at 100,000 per well (30,000 cells for HeLa), layered onto 0.8% agarose in DMEM or RPMI-1640 with 10% FBS. The plates were kept in the cell culture incubator for 3-4 weeks after which the cells were stained with iodonitrotetrazolium chloride and colonies were counted.
U-13C6-glucose-labeled DMEM medium was prepared with non-glucose, non-glutamine and non-pyruvate DMEM media by adding 10 mM of U-13C6 D-glucose (Cambridge Isotope Laboratories), 1 mM sodium pyruvate and 2 mM glutamine. U-13C5-glutamine-labeled DMEM medium was prepared with non-glucose, non-glutamine and non-pyruvate DMEM media by adding 2 mM of U-13C5 glutamine (Cambridge Isotope Laboratories), 1 mM sodium pyruvate and 25 mM glucose.
Unlabeled and 13C-labeled flux assays were performed according as previously reported (Wan et al., Developmental cell 29, 377-391 (2014)). Briefly, media was refreshed one hour before harvesting cells to remove accumulated metabolic wastes. For metabolites labeling, before harvesting sample, media were changed to U-13C6-glucose-labeled media for labeling for 30, 60 and 120 seconds or U-13C5-glutamine-labeled media for labeling for 1, 2 and 3 hours. Then the media was aspirated completely and 4 ml of dry ice-cold 80% MeOH was added, followed by placing the plates at −80° C. for 30 minutes. Then the metabolites were extracted as previously described and normalized by protein amount. All metabolites were analyzed as previously described (Yuan et al., Nature protocols 7, 872-881 (2012)).
The uptakes of glucose and glutamine for HeLa cells in either G1 phase or S phase were measured using Glucose Uptake Cell-Based Assay Kit (600470, Cayman Chemical) and Glutamate Assay kit (ab83389, Abcam) according to the manufacturer's protocol. For glucose uptake, cells were stained with 2-NBDG followed by flow cytometry analysis (excitation/emission=485/538 nm). For glutamine uptake, cells were harvested and analyzed at OD450.
Cells were harvested and subjected to fractionation of cytoplasm (C), mitochondria (M), and nuclei (N) using Cell Fractionation kit (ab109719, Abcam). All fractions and the whole cell lysate (WCL) were subjected to immunoblot analysis for the indicated proteins, with tubulin, citrate synthase, and Histone H3 as markers of cytoplasm, mitochondria, and nucleus, respectively.
The quantitative data from multiple repeat experiments were analyzed by a two-tailed unpaired Student's t test or one-way ANOVA, and presented as mean±s.e.m. When P<0.05, the data were considered as statistically significant.
From the foregoing description, it will be apparent that variations and modifications may be made to the invention described herein to adopt it to various usages and conditions. Such embodiments are also within the scope of the following claims.
The recitation of a listing of elements in any definition of a variable herein includes definitions of that variable as any single element or combination (or subcombination) of listed elements. The recitation of an embodiment herein includes that embodiment as any single embodiment or in combination with any other embodiments or portions thereof.
All patents and publications mentioned in this specification are herein incorporated by reference to the same extent as if each independent patent and publication was specifically and individually indicated to be incorporated by reference.
This application claims the benefit of the following U.S. Provisional Application No. 62/639,561, filed Mar. 7, 2018, the entire contents of which are incorporated herein by reference.
This invention was made with government support under Grant Nos. GM094777 and CA200573 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US19/20924 | 3/6/2019 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 62639561 | Mar 2018 | US |
