Patent Grant
10137180
A Sequence Listing is being submitted with this application in the form of a text file, created 4 Sep. 2013 named “0915110572seq.txt” (26,749 bytes), the contents of which are incorporated herein by reference in their entirety.
Methods and compositions for the rapid and reversible destabilizing of specific proteins in vivo using cell-permeable, synthetic molecules are described.
Techniques that target gene function at the level of DNA and mRNA provide powerful methods for modulating the expression of proteins encoded by specific genes. For example, the tet/dox and Cre/lox systems have been widely used to target gene expression at the transcriptional level (Ryding, A. D. S. et al. (2001) J. Endocrinol. 171:1-14) and RNA interference is rapidly being adopted as a method to achieve post-transcriptional gene silencing (Fire, A. at al. (1998) Nature 391:806-811; Medema, R. H. (2004) Biochem. J. 380:593-603; Raab, R. M. and Stephanopoulos, G. (2004) Biotechnology & Bioengineering 88:121-132).
However, methods for regulating protein function directly are limited, especially in mammalian cells. Inhibitors or activators of particular proteins have been identified, and often take the form of cell-permeable small molecules. Many of these molecules have found widespread use as biological probes, often because the speed, dosage-dependence, and reversibility of their activities, which complement methods for genetically modulating gene expression (Schreiber, S. L. (2003) Chem. & Eng. News 81:51-61). However these inhibitors or activators are often promiscuous, affecting several proteins rather than a specific protein (Davies, S. P. et al. (2000) Biochem. J. 351:95-105; Bain, J. et al. (2003) Biochem. J. 371:199-204; Godl, K. et al. (2003) Proc. Natl. Acad. Sci. U.S.A. 100:15434-15439; Tan, D. S. (2005) Nat. Chem. Biol. 1:74-84; Mayer, T. U. et al., (1999) Science, 286:971-974).
Shokat and coworkers have developed a method by which specific kinases can be inhibited using a small-molecule modulator (Shah et al., 1997; Bishop, A. C. et al. (1998) Current Biology 8:257-266). This method involves mutating the protein of interest, typically replacing a large conserved residue in the active site with a smaller residue, such as glycine or alanine. Specificity is achieved by chemically modifying a promiscuous inhibitor to include a bulky side-chain substituent (e.g., R-group), which fills the corresponding cavity in the binding site of the modified protein of interest, while preventing productive interactions with other kinases. While this so-called “bump-hole” approach has been successful both in cultured cells and in mice (Bishop, A. C. et al. (2000) Nature 407:395-401; Wang, H. et al. (2003) Proc. Natl. Acad. Sci. U.S.A. 100:4287-4292, Chen, X. et al. (2005) Neuron 46:13-21), it appears to be limited to ATPases and GTPases. Additional methods are required to probe the function of a wider variety of proteins.
Other investigators have devised alternative strategies to perturb protein function by exploiting existing cellular processes (Banaszynski, L. A. et al. (2006) Chem. Biol. 13:11-21). For example, Varshaysky and coworkers developed methods for controlling protein function based on the importance of certain N-terminal residues for protein stability (Bachmair, A. et al. (1986). Science 234:179-186). Szostak and coworkers showed that a small peptide sequence could be fused to the N-terminus of a protein of interest to modulate protein stability (Park, E-C. et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89:1249-1252). Varshaysky and coworkers have further isolated a temperature-sensitive peptide sequence that greatly reduced the half-life or dihydrofolate reductase (DHFR) at the non-permissive temperatures (Dohmen, R. J. et al. (1994) Science 263:1273-1276). This approach has been used to study proteins in yeast (Labib, K. et al. (2000) Science 288:1643-1646; Kanemaki, M. et al. (2003) Nature 423:720-724). More recently, several researchers have engineered systems in which dimeric small molecules are used to conditionally target fusion proteins for degradation via E3 ligase or the proteasome, itself (Schneekloth et al., 2004; Janse, D. M. et al. (2004) J. Biol. Chem. 279:21415-21420). However, these systems require either a prior knowledge of the high-affinity ligands that modulate the activity of a protein of interest or they are restricted to genetically engineered yeast strains.
An alternative approach for controlling protein function directly is to interfere with subcellular localization. Several methods are available to regulate protein localization using small-molecule by taking advantage of the FKBP-rapamycin-FRB ternary complex (Kohler, J. J. and Bertozzi, C. R. (2003) Chem. Biol. 10:1303-1331 and Inoue, T. et al., (2005) Nature Methods 2:415-418). Rapamycin and FK506 are potent, commercially available immunosuppressive agents, which are ligands of the FK506-binding protein (FKBP12, FKBP). Rapamycin also binds to FKBP-rapamycin-associated protein (FRAP). FRAP is also called the mammalian target of rapamycin (mTOR), rapamycin and FKBP target 1 (RAFT1), and FRB. Rapamycin binds to and inhibits mTOR by interacting with its FKBP-rapamycin-binding (FRB) domain to inhibit/delay G1 cell cycle progression in mammalian cells (see, e.g., Choi, J. et al. (1996) Science 273:239-42 and Vilella-Bach, M. et al. (1999) J. Biol. Chem. 274:4266-72. The FKBP-rapamycin-binding domain is required for FKBP-rapamycin-associated protein kinase activity and G1 progression. Fusions of proteins of interest can be made to either FKBP or to the FRP domain of FRAP/mTOR. Colocalization of the protein of interest is induced upon addition of rapamycin.
Because rapamycin has inherent biological activity, researchers have developed a “bump-hole” strategy (similar to that employed by Shokat and coworkers), wherein rapamycin derivatives possessing large substituents at the FRB binding interface bind poorly to wild-type FRB and in turn the biologically relevant target FRAP/mTOR, with binding restored upon introduction of compensatory cavity-forming mutations in FRB. Specifically, a C20-methallyl-rapamycin derivative (MaRap) binds to a triple-mutated variant of FRB called FRB* (Liberles, S. D. et al. (1997) Proc. Natl. Acad. Sci. U.S.A. 94:7825-7830).
While these methods for regulating protein function directly are noteworthy, there has yet to be described a convenient, general method for regulating protein function, particularly a method that does not require the interaction of multiple proteins. Improved methods for regulating protein function directly, particularly in mammalian cells and in animals, are needed.
Compositions, systems, and methods for modulating the stability of proteins in vitro and in vivo using cell-permeable small molecules are described. Proteins of interest are fused to a stability-affecting protein capable of interacting with a small-molecule ligand, the presence, absence, or amount of which is used to modulate the stability of the fusion protein.
In one aspect, an in vivo conditional protein stability system is provided comprising a nucleic acid sequence encoding a fusion protein that comprises a protein of interest fused to a single-polypeptide chain, ligand-dependent, stability-affecting protein derived from a naturally-occurring ligand binding protein, and a ligand that binds to the stability-affecting protein to modulate stability of the stability-affecting protein, wherein upon introduction of the nucleic acid sequence to a eukaryotic cell the fusion protein is expressed and the stability of the fusion protein can be modulated by administering the ligand to the eukaryotic cell.
In one embodiment, the single-polypeptide chain, ligand-dependent, stability-affecting protein is a FKBP variant protein. In another embodiment the naturally-occurring ligand binding protein is a naturally occurring or wildtype FKBP protein.
In some embodiments, the protein of interest is a reporter protein. In some embodiments, the protein of interest is a therapeutic protein.
In one embodiment, the protein of interest is a cytokine. In yet another embodiment, the protein of interest is TNF-α or IL-2.
In one embodiment, the ligand is Shield1.
In one embodiment, the stability-affecting protein destabilizes the protein of interest or fusion protein in the absence of a ligand. In another embodiment, the stability-affecting protein does not destabilize the protein of interest in the presence of ligand. In yet another embodiment, the stability-affecting protein destabilizes the protein of interest or fusion protein in the absence of the ligand to a greater degree or extent than it destabilizes the protein of interest in the presence of the ligand.
In one embodiment, the stability-affecting protein destabilizes the protein of interest or fusion protein in the presence of a ligand. In yet another embodiment, the stability-affecting protein does not destabilize the protein of interest or fusion protein in the absence of ligand. In yet another embodiment, the stability-affecting protein destabilizes the protein of interest or fusion protein in the presence of the ligand to a greater degree or extent than it destabilizes the protein of interest or fusion protein in the absence of the ligand.
In some embodiments, the stability-affecting protein destabilizes the protein of interest by causing an increase in the degradation or destruction of the protein of interest or the fusion protein when not bound to the ligand as compared to the level of degradation of the protein of interest or the fusion protein when the stability-affecting protein is bound to the ligand.
In one embodiment, the ligand binds preferably to the single-polypeptide chain, ligand-dependent, stability-affecting protein as compared to the naturally-occurring ligand binding protein.
In one embodiment, the eukaryotic cells are transformed with the nucleic acid. In another embodiment, the eukaryotic cells are transformed with the nucleic acid to produce stably transformed eukaryotic cells. In another embodiment, the transformed eukaryotic cells are implanted into an animal. In yet another embodiment, the transformed eukaryotic cells are implanted into immunodeficient mice as xenografts.
In one embodiment, the nucleic acid sequence is in a viral vector. In another embodiment, the viral vector is a pox virus. In yet another embodiment, the viral vector is a vaccinia virus. In yet another embodiment, the viral vector is a vvDD.
In one embodiment, the ligand is administered to the eukaryotic cells in culture. In another embodiment, the ligand is administered to the cells by injecting the ligand into the animal intraperitoneally or intravenously.
In another aspect, a method for modulating stability of a protein of interest in vivo comprising introducing into a eukaryotic cell a nucleic acid comprising a polynucleotide which encodes a fusion protein wherein the fusion protein comprises a protein of interest and a single-polypeptide chain, ligand-dependent, stability-affecting protein derived from a naturally-occurring ligand binding protein, and administering a ligand to the eukaryotic cell is provided wherein the ligand binds to the single-polypeptide chain, ligand-dependent, stability-affecting protein to modulate stability of the fusion protein.
In one embodiment the single-polypeptide chain, ligand-dependent, stability-affecting protein is a FKBP variant protein. In another embodiment the naturally-occurring ligand binding protein is a naturally occurring or wildtype FKBP protein.
In some embodiments, the protein of interest is a reporter protein. In some embodiments, the protein of interest is a therapeutic protein.
In one embodiment, the protein of interest is a cytokine. In yet another embodiment, the protein of interest is TNF-α or IL-2.
In one embodiment, the ligand is Shield1.
In one embodiment, the stability-affecting protein destabilizes the protein of interest or fusion protein in the absence of a ligand. In another embodiment, the stability-affecting protein does not destabilize the protein of interest or fusion protein in the presence of ligand. In yet another embodiment, the stability-affecting protein destabilizes the protein of interest or fusion protein in the absence of the ligand to a greater degree or extent than it destabilizes the protein of interest or fusion protein in the presence of the ligand.
In yet another embodiment, the stability-affecting protein destabilizes the protein of interest or fusion protein in the presence of a ligand. In yet another embodiment, the stability-affecting protein does not destabilize the protein of interest or fusion protein in the absence of ligand. In yet another embodiment, the stability-affecting protein destabilizes the protein of interest or fusion protein in the presence of the ligand to a greater degree or extent than it destabilizes the protein of interest or fusion protein in the absence of the ligand.
In one embodiment, the ligand binds preferably to the single-polypeptide chain, ligand-dependent, stability-affecting protein as compared to the naturally-occurring ligand binding protein.
In one embodiment, the nucleic acid sequence is introduced into the eukaryotic cell by transforming the eukaryotic cell in culture with a plasmid comprising the nucleic acid to produce stably transformed eukaryotic cells. In another embodiment, the stably transformed eukaryotic cells are administered to an animal. In yet another embodiment, the stably transformed eukaryotic cells are transplanted into a mouse. In yet another embodiment, the stably transformed eukaryotic cells are transplanted as a xenograft into an immunodeficient mouse.
In one embodiment, the nucleic acid sequence is introduced into the eukaryotic cell by transforming the eukaryotic cell in culture with a viral vector which comprises the nucleic acid sequence. In another embodiment, the nucleic acid is introduced into the eukaryotic cell by administering to an animal a viral vector which comprises the nucleic acid sequence. In yet another embodiment, the animal has tumor cells.
In another aspect, a method for modulating cellular proliferation in an animal, comprising administering to the animal a nucleic acid comprising a polynucleotide which encodes a fusion protein wherein the fusion protein comprises a protein of interest and a single-polypeptide chain, ligand-dependent, stability-affecting protein derived from a naturally-occurring ligand binding protein, and administering a ligand which binds preferably to the single-polypeptide chain, ligand-dependent, stability-affecting protein as compared to the naturally-occurring ligand binding protein is provided.
In one embodiment the single-polypeptide chain, ligand-dependent, stability-affecting protein is a FKBP variant protein. In another embodiment the naturally-occurring ligand binding protein is a naturally occurring or wildtype FKBP protein.
In some embodiments, the protein of interest is a reporter protein. In some embodiments, the protein of interest is a therapeutic protein.
In one embodiment, the protein of interest is a cytokine. In yet another embodiment, the protein of interest is TNF-α or IL-2.
In one embodiment, the ligand is Shield1.
In one embodiment, the stability-affecting protein destabilizes the protein of interest in the absence of a ligand. In another embodiment, the stability-affecting protein does not destabilize the protein of interest in the presence of ligand. In yet another embodiment, the stability-affecting protein destabilizes the protein of interest or fusion protein in the absence of the ligand to a greater degree or extent than it destabilizes the protein of interest or fusion protein in the presence of the ligand.
In yet another embodiment, the stability-affecting protein destabilizes the protein of interest in the presence of a ligand. In yet another embodiment, the stability-affecting protein does not destabilize the protein of interest in the absence of ligand. In yet another embodiment, the stability-affecting protein destabilizes the protein of interest or fusion protein in the presence of the ligand to a greater degree or extent than it destabilizes the protein of interest or fusion protein in the absence of the ligand.
In one embodiment, the ligand binds preferably to the single-polypeptide chain, ligand-dependent, stability-affecting protein as compared to the naturally-occurring ligand binding protein.
In one embodiment, the method of administering the nucleic acid to the animal comprises transforming a eukaryotic cell with the nucleic acid to produce a stably transformed eukaryotic cell and implanting the stably transformed eukaryotic cell into the animal.
In one embodiment, the eukaryotic cells are tumor cells and administering the ligand to the animal modulates establishment, progression, and/or growth of the tumor. In another embodiment, administering the ligand to the animal inhibits tumor growth. In another embodiment, administering the ligand improves survival of the animal.
In one embodiment, the animal has tumor cells and administering the nucleic acid to the animal comprises administering a viral vector or virus to the animal, wherein the viral vector or virus harbors the nucleic acid. In another embodiment, the viral vector or virus is a pox virus. In yet another embodiment, the viral vector or virus is a vaccinia virus. In yet another embodiment, the viral vector or virus is a vvDD virus.
In another aspect, a method for modulating tumor establishment, tumor progression and/or tumor growth in an animal is provided, comprising introducing into cells of the animal a nucleic acid sequence encoding a fusion protein comprising a therapeutic protein and a single-polypeptide chain, ligand-dependent, stability-affecting protein, and controlling expression of the therapeutic protein by administering a preselected amount of the ligand, is provided wherein the ligand binds to the stability-affecting protein to modulate the stability of the therapeutic protein and the therapeutic protein modulate tumor progression or development.
In some embodiments, the nucleic acid sequence is in a plasmid. In some embodiments, the nucleic acid sequence is in a viral vector.
In some embodiments, the stability-affecting protein destabilizes the protein of interest in the absence of the ligand. In another embodiment, the stability-affecting protein does not destabilize the protein in the presence of the ligand.
In some embodiments, the ligand preferentially binds to the stability-affecting protein compared to the corresponding naturally-occurring ligand-binding protein.
In some embodiments, the stability-affecting protein is a variant FKBP protein and the fusion protein is stabilized in the presence of a FKBP ligand. In particular embodiments, the FKBP ligand is Shield1.
In some embodiments, the therapeutic protein is a cytokine. In particular embodiments, the therapeutic protein is interleukin-2.
In one embodiment, the ligand is administered by intraperitoneal or intravenous injection of the ligand into animal.
In some embodiments, the therapeutic protein modulates tumor establishment. In some embodiments, the therapeutic protein modulates tumor progression. In some embodiments, the therapeutic protein prevents tumor establishment or progression. In some embodiments, the therapeutic protein prevents or inhibits tumor growth.
In one aspect, an in vivo conditional protein stability system is provided, comprising a nucleic acid sequence encoding a fusion protein that includes a protein of interest fused in-frame to a single-polypeptide chain, ligand-dependent, stability-affecting protein derived from a naturally-occurring ligand binding protein, and a ligand that binds to the stability-affecting protein to modulate its stability, wherein upon introduction of the nucleic acid sequence to cells of an organism the fusion protein is expressed and the stability of the fusion protein can be modulated by amount of ligand present in the cells of the organism.
In some embodiments, the stability-affecting protein destabilizes the protein of interest in the absence of the ligand and does not destabilize the protein in the presence of the ligand. In some embodiments, the stability-affect protein destabilizes the protein of interest in the absence of the ligand to a greater degree or extent than in the presence of the ligand.
In some embodiments, the stability-affecting protein does not destabilize the protein of interest in the absence of the ligand and destabilizes the protein in the presence of the ligand. In some embodiments, the stability-affect protein destabilizes the protein of interest in the presence of the ligand to a greater degree or extent than in the absence of the ligand.
In some embodiments, the ligand preferentially binds to the stability-affecting protein compared to the naturally-occurring ligand-binding protein.
In some embodiments, the stability-affecting protein is a variant FKBP protein and the fusion protein is stabilized in the presence of a FKBP ligand. In particular embodiments, the FKBP ligand is Shield1.
In some embodiments, the protein of interest is a reporter protein. In some embodiments, the protein of interest is a therapeutic protein.
In a related aspect, a method of using the described in vivo conditional protein stability system for controlling the expression of protein is provided. In some embodiments, the protein of interest is a reporter protein or a therapeutic protein.
In another aspect, a method for modulating tumor establishment or progression in an animal is provided, comprising introducing into cells of the animal a nucleic acid sequence encoding a fusion protein that includes a therapeutic protein fused in-frame to a single-polypeptide chain, ligand-dependent, stability-affecting protein, and controlling expression of the therapeutic protein by administering a preselected amount of the ligand, wherein the ligand binds to the stability-affecting protein to modulate the stability of the therapeutic protein and the therapeutic protein modulate tumor progression or development.
In some embodiments, the nucleic acid sequence is in a plasmid. In some embodiments, the nucleic acid sequence is in a viral vector.
In some embodiments, the stability-affecting protein destabilizes the protein of interest in the absence of the ligand and stabilizes the protein in the presence of the ligand.
In some embodiments, the ligand preferentially binds to the stability-affecting protein compared to the corresponding naturally-occurring ligand-binding protein.
In some embodiments, the stability-affecting protein is a variant FKBP protein and the fusion protein is stabilized in the presence of a FKBP ligand. In particular embodiments, the FKBP ligand is Shield1.
In some embodiments, the therapeutic protein is a cytokine. In particular embodiments, the therapeutic protein is interleukin-2.
In some embodiments, the therapeutic protein modulates tumor establishment. In some embodiments, the therapeutic protein modulates tumor progression. In some embodiments, the therapeutic protein prevents tumor establishment or progression.
In addition to the exemplary aspects and embodiments described above, further aspects and embodiments will become apparent by reference to the drawings and by study of the following descriptions.
Any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the teachings herein. All publications mentioned herein are incorporated herein by reference in their entirety for the purpose of describing and disclosing the methodologies which are reported in the publications which might be used in connection with the teachings herein.
It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural reference unless the context clearly dictates otherwise.
As used herein, a “protein of interest” or “POI” is any protein, or functional fragment or derivative, thereof, that one skilled in the art wishes to study.
As used herein, “preferentially binds” means to bind with greater efficiency to a subject molecule (such as a particular amino acid sequence) than another molecule. The difference in binding efficiency may be 5-fold, 10-fold, 50-fold, 100-fold, 500-fold, 1.000-fold, 10,000 fold, or more.
As used herein, “introduction of nucleic to cells” means transfection, transduction (infection), or transformation of nucleic acids (e.g., DNA) into cells, such that the nucleic acids may be used by the cell to express a protein of interest.
As used herein, “degradation” or “destruction” of a protein means its hydrolysis into smaller proteins or amino acids, such as by the cellular proteosome.
“Rapamycin” is a naturally-occurring, small molecule immunosuppressant that is a ligand for FKBP.
“FKBP12” or “FKBP” is a 12 kDa protein that binds to the small-molecules rapamycin and FK506. The rapamycin-FKBP complexes can bind to the FRB domain of FRAP.
“FRAP,” “mTOR,” or “FRAP/mTOR” is a protein that binds, via its FRB domain, to rapamycin, or the FKBP-rapamycin complex.
A “FKBP variant” refers to a protein wherein one or more amino acid residues, e.g., at positions 15, 24, 25, 36, 60, 100, and 106, are substituted for an amino acid other than the amino acid in the FKBP F36V protein (SEQ ID NO: 1). Other amino acid positions that can be substituted are indicated in the Tables and Figures.
“FRB*” is a FRB variant with three point mutations, i.e., K2095P/T2098L/W2101F (using mTOR numbering), designed to bind rapamycin analogs such as MaRAP. Amino acid substitutions, or point mutations, are denoted herein, and in accord with conventional practice, as the old (original) residue in single-letter code, followed by its codon location, followed by the substitute (mutant) amino acid in single-letter code. For example, the F36V mutant of FKBP has Val in place of Phe at position 36 of the FKBP protein.
“MaRAP” is C20-methallylrapamycin, a synthetic rapamycin derivative that binds FRB* but not FRB.
“Shield1” is a synthetic small molecule that binds to wild-type FKBP, a FKBP variant having a F36V mutation/substitution, and likely other FKBP variants. Binding is about 1.000-fold tighter to the F36V variant compared to wild-type FKBP (Clackson, T. et al. (1998) Proc. Natl. Acad. Sci. U.S.A. 95:10437-10442).
As used herein, a “single-protein, ligand-dependent destabilization protein,” “single-polypeptide chain, ligand-dependent, stability-affecting protein”, “single protein, stability-affecting protein,” or “stability-affecting protein” is a single polypeptide that functions as a ligand-dependent destabilization protein, as described herein. Such a destabilizing protein does not require the formation of a ternary complex, as is the case with the FKBP-rapamycin-FRB complex. A particular species is a “single-domain,” ligand-dependent destabilization protein, wherein the single polypeptide comprises only a single domain (i.e., folded structure or functional unit as determined by X-ray crystallography, protease digestion, computer modeling, etc.
As used herein, “fused” means arranged in-frame as part of the same contiguous sequence of amino acids in a polypeptide. Fusion can be direct such there are no additional amino acid residues or via a linker to improve performance or add functionality.
As used herein, “conservative amino acid substitutions” are substitutions that do not result in a significant change in the activity or tertiary structure of a selected polypeptide or protein. Such substitutions typically involve replacing a selected amino acid residue with a different residue having similar physico-chemical properties. For example, substitution of Glu for Asp is considered a conservative substitution since both are similarly-sized negatively-charged amino acids. Groupings of amino acids by physico-chemical properties are known to those of skill in the art.
As used herein, the terms “domain” and “region” are used interchangeably herein and refer to a contiguous sequence of amino acids within a POI or destabilizing domain, typically characterized by being either conserved or variable and having a defined function, such as ligand binding, conferring stability or instability, enzymatic function, etc.
As used herein, the terms “protein” and “polypeptide” are used interchangeably and without distinction to refer to a compound made up of a chain of amino acid residues linked by peptide bonds. Unless otherwise indicated, the sequence for peptides is given in the order from the “N” (or amino) terminus to the “C” (or carboxyl) terminus. It is understood that polypeptides include a contiguous sequence of amino acid residues.
A peptide or peptide fragment is “derived from” a parent peptide or polypeptide if it has an amino acid sequence that is homologous to, but not identical to, the parent peptide or polypeptide, or of a conserved fragment from the parent peptide or polypeptide.
Two amino acid sequences or two nucleotide sequences are considered “homologous” if they have an alignment score of >5 (in standard deviation units) using the program ALIGN with the mutation gap matrix and a gap penalty of 6 or greater (Dayhoff, M. O., in Atlas of Protein Sequence and Structure (1972) Vol. 5, National Biomedical Research Foundation, pp. 101-110, and Supplement 2 to this volume, pp. 1-10.) The two sequences (or parts thereof) are more preferably homologous if their amino acids are greater than or equal to 50%, 70%, 80%, 90%, 95%, or even 98% identical when optimally aligned using the ALIGN program mentioned above.
“Modulate” intends a lessening, an increase, or some other measurable change, e.g., in the stability or biological function of a protein.
A “small molecule ligand” is a discrete small-molecule, well known in the pharmaceutical and material sciences, which is to be distinguished from, e.g., a polypeptide or nucleic acid, which is a polymer consisting of monomeric subunits. Small molecule ligands may be naturally-occurring or synthetic as exemplified by pharmaceutical products, laboratory reagents, and the like.
“ddVV” refers to a Vaccinia virus having a double-deletion as described in Thorne et al. (2006) Science, 311:1780-1784; McCart et al. (2001) Cancer Res. 61:8751-8757.
As used herein, a “variant” protein is a protein having an amino acid sequence that does not occur in nature, as exemplified by sequences in GenBank.
As used herein, a “mutant” is a mutated protein designed or engineered to alter properties or functions relating to protein stabilization and/or ligand binding.
The present composition, system, and method (generally, “system”) relate to the conditional stabilization of a protein of interest (POI) fused to a single-polypeptide chain, ligand-dependent, stability-affecting protein in vivo. The stability-affecting protein, also referred to as a ligand-binding domain, can be preselected to confer either stability or instability to the entire fusion protein, depending on the presence or absence of the ligand.
A feature of the conditional protein stability system is that the stability-affecting protein is of a “single ligand-single domain” type, which minimizes the number of components in the system. The system is illustrated using two different ligand-binding domains, namely, the FK506-binding protein (FKBP) and dihydrofolate reductase (DHFR), binding domains, in combination with appropriate ligands. Experiments performed in support of the systems are described below, along with embodiments and examples of the system.
Rapamycin and FK506 are commercially available, cell-membrane permeable, FDA-approved immunosuppressive agents, which are ligands of the FK506-binding protein (FKBP12 or FKBP). The FKBP-rapamycin complex binds to the FKBP-rapamycin-binding (FRB) domain of the FKBP-rapamycin-associated protein (FRAP). FRAP is also known as the mammalian target of rapamycin (mTOR), rapamycin and FKBP target 1 (RAFT1), and sometimes FRB. Rapamycin complexed with FKBP binds to and inhibits FRAP/mTOR at its FRB domain, which eventually inhibits/delays cell cycle progression through G1 (see, e.g., Choi, J. et al. (1996) Science 273:239-42 and Vilella-Bach, M. et al. (1999) J. Biol. Chem. 274:4266-72. Fusion polypeptides may be made between a proteins of interest (POI) and either FKBP and/or the FRB domain of FRAP/mTOR. Colocalization of the protein(s) of interest is induced upon addition of rapamycin.
Because rapamycin has inherent biological activity, researchers developed a “bump-hole” strategy (similar to that employed by Shokat and coworkers), wherein rapamycin derivatives with bulky side-chain substituents would bind poorly to the FRB domain of a wild-type/naturally-occurring FRAP/mTOR. Binding was restored by introducing compensatory hole/cavity-forming mutations in the FRB domain. In particular, the bulky side chain of a C20-methallyl-rapamycin derivative (MaRap) is accommodated by a triple-substituted variant of FRB called FRB* (Liberles, S. D. et al. (1997) Proc. Natl. Acad. Sci. U.S.A. 94:7825-7830).
In fusing the FRB and FRB* domains to a kinase GSK-3β it was discovered that the levels of the GSK-3β-FRB* fusion protein were substantially decreased compared to an otherwise identical GSK-3β-FRB fusion protein. The levels of the FRB* fusion protein were rescued (i.e., increased to levels similar to those of the FRB fusion protein) upon the addition of MaRap (Stankunas, K. et al. (2003) Mol. Cell. 12:1615-1624). FRB* appeared to confer conditional instability to multiple different proteins in the absence of MaRap, with stabilization being dependent on the interaction of two proteins (i.e., FKBP and FRB) via a small molecule (MaRap) that is expensive, difficult to synthesize and formulate, and exhibits poor pharmacokinetic properties in vivo.
The 107-residue FK506 and rapamycin-binding protein (FKBP) was selected for use as a destabilizing domain in a “drug-ON” system. FKBP has been widely studied, often in the context of fusion proteins, and numerous high-affinity ligands for FKBP have been developed (Pollock and Clackson, T. et al. (1998) Proc. Natl. Acad. Sci. U.S.A. 95:10437-10442). In one study, ligands that possess a synthetic “bump” in the FKBP-binding domain were shown to bind more tightly to a mutated FKBP having a cavity formed by the removal of an aromatic side chain (i.e., harboring the substitution, F36V). Such engineered ligands bind preferentially to the mutated FKBP12 compared to the wild-type/naturally-occurring protein by almost three orders of magnitude (Clackson, T. et al. (1998) Proc. Natl. Acad. Sci. U.S.A. 95:10437-10442). Moreover, this family of ligands does not elicit undesired responses when administered to cultured cells or animals, including humans (Iuliucci, J. D. et al. (2001) J. Clin. Pharmacol. 41:870-879).
To identify FKBP variants (i.e., mutants) with a high affinity for the synthetic FKBP ligand, SLF* (
Five variants (F15S, V24A, H25R, E60G, and L106P) were selected for further analysis. These variant FKBP-derived, ligand-responsive destabilizing domains were separately transduced into NIH3T3 cells and assayed for stability in the presence and absence of a ligand called Shield1, which was a derivative of SLF* in which the carboxylic acid was replaced with a morpholine group at a position unlikely to interfere with FKBP binding (Example 8,
All five variants showed decreased levels of fluorescence with respect to a positive control, indicating that the variants obtained from the library screen were destabilizing (
Upon withdrawal of Shield1, distinct differences in fluorescence decay profiles were observed among the FKBP-derived, destabilizing domain variants (
These results were confirmed by immunoblot analysis using antibodies specific for either FKBP (
To compare the present methods with those known in art for regulating gene expression, the rate of degradation of a protein of interest achieved using the FKBP-derived, destabilizing domain variants, was compared to RNAi-mediated silencing of another endogenous gene, Lamin A/C, a non-essential cytoskeletal protein commonly used as a control in RNAi experiments. Previous studies have shown more than 90% reduction in lamin A/C expression in HeLa cells 40 to 45 hours following transfection of the cells with a cognate siRNA duplex (Elbashir, S. M. et al. (2001) Nature 411:494-498). In line with published results, HeLa cells transfected with siRNA against lamin A/C showed a decrease in lamin A/C levels after 24 hours, with a significant reduction in lamin A/C observed by 48 hours (
Further experiments demonstrated that NIH3T3 cells stably expressing the L106P-YFP variant produced YFP fluorescence in a dosage-dependent manner with respect to the amount of ligand present (Example 9). The results obtained using N-terminal destabilizing domains are shown in
FKBP variants were efficient in destabilizing proteins other than YFP, e.g., the kinases GSK-3β and CDK1, the cell cycle regulatory proteins securin and p21, and three small GTPases, Rac1, RhoA and Cdc42 (
FKBP variants were also efficient in destabilizing proteins other than YFP, e.g., the transcription factor CREB, or the small GTPases Arf6 or Arf7, when the FKBP mutant is fused at the C-terminus of the protein of interest (
Moreover, cell morphology could be manipulated by the presence or absence of Shield1 (Example 13). Shield1-treated cells displayed the predicted morphologies, a, expression of RhoA induced the formation of stress fibers, expression of Cdc42 resulted in filopodia formation, and expression of Ar17 induced the shrunken cell phenotype (Heo, W. D. and Meyer, T. (2003) Cell 113:315-328), while mock-treatment with Shield1 produced cells with fibroblast-like morphologies. These GTPase-dependent morphology changes were reversible, as treatment with Shield1 followed by removal of Shield1 also produced cells with fibroblast-like morphologies. The penetrance of the observed phenotype was high, with a large percentage of cells (>90%) exposed to a given experimental condition displaying the predicted behavior (data not shown).
The FKBP-derived destabilizing domains can be stabilized using Shield1 as well as the commercially available ligand, FK506 (
The above-described FKBP-derived conditional protein stability system uses a variant of FKBP to stabilize a POI in the presence of an appropriate ligand, and destabilize the POI in the absence of the ligand, representing a “drug-ON” system. In a related embodiment of the system, a variant FKBP polypeptide sequence was used to destabilize a POI in the presence of an appropriate ligand, and stabilize the POI in the absence of the ligand, representing a “drug-OFF” system.
Variant FKBP polypeptide sequences having the desired properties were identified by preparing a library of sequences encoding FKBP (F36V) with a short, 20-amino acid diversity element (i.e., population of sequences encoding different amino acids) fused at the C-terminus of FKBP. The FKBP-diversity element sequences were fused to the C-terminus of YFP, as before, and the sequences encoding the YFP-FKBP-diversity element were introduced into NIH3T3 cells for screening. Five different clones were identified in which YFP could be detected by FACS analysis in the absence of the ligand (Shield1) but was nearly undetectable in the presence of the ligand (i.e., a 5 to 6-fold decrease in the presence of ligand;
The “drug-OFF” system offers some advantages over the “drug-ON” system. In particular, the “drug-OFF” system requires the presence of the ligand only to destabilize the POI. Thus, where the POI is essential for viability, the absence of the ligand allows the protein to function normally. In contrast, in a “drug-ON” system, the ligand must be present at all times, except where the effect of removing the POI is being studied. Since the cost of maintaining cells or animals in the presence of ligand over a prolonged period of time can be considerable, the “drug-OFF” system can be more economical.
While the FKBP system was first characterized in mammalian cells, further experiments have demonstrated that the system works in eukaryote parasites, particularly Toxoplasma and Plasmodium.
In another illustration of use of the system in eukaryotic parasites,
HCT116 cancer cells were transfected with nucleic acids encoding the reporter gene luciferase fused to an FKBP-derived stability-affecting protein (F36V/L106P) mutant. Stable transformants were selected and used to challenge SCID mice. SCID were challenged with tumor cells expressing luciferase fused to-derived FKBP F36V/L106P-derived stability-affecting protein and treated with the indicated amounts of ligand (Shield1), or untreated (control), and bioluminescent signals were imaged over time as described (Lin, A. H., et al. (2005) J. Immunol. 175:547-54; Luo, J., et al. (2006) Proc. Nat'l. Acad. Sci. USA 103:18326-31; n=4-10 mice per treatment group).
The graph in
In a related experiment, polynucleotide sequences encoding the FKBP L106P stability-affecting protein were fused to polynucleotides corresponding to the N-terminus of a thermostable luciferase to obtain the chimeric gene L106P-tsLuc, which was stably integrated into HCT116 colon cancer cells. HCT116 cells expressing the resulting fusion protein were tested for conditional regulation of luciferase activity in vitro using the ligand, Shield1 (not shown) and then implanted as xenografts onto immunodeficient mice. Shield1 (or vehicle only as a control) was delivered intraperitoneally (ip) at a dose of 10 mg/kg and luciferase activity was measured by in vivo bioluminescence imaging as shown in
Animals treated with Shield1 (10 mg/kg) periodically, i.e., once every 48 hours, were also found to maintain increased bioluminescence levels over the course of several weeks compared to animals not treated with Shield1 (
Periodic administration of ligand is advantageous in terms of reducing reagent cost and reducing the handling of animals; however, the administration of Shield1 did not appear to affect feeding behavior, body weight, or overall activity (not shown), indicating that the ligand is substantially non-toxic to animals even when delivered frequently. These observations are consistent with microarray analysis of mRNA levels in cells treated with Shield1, which demonstrated no appreciable cellular response to treatment.
The experiments described above relate to the conditional stability of a reporter protein in tumors cells. Further experiments demonstrated that conditional stabilization of a protein could actually affect tumor burden.
Interleukin-2 (IL-2) is a cytokine that is instrumental in immune response, inducing the differentiation and proliferation of a variety of lymphocyte populations (Gaffen, S. L. and Liu, K. D. (2004) Cytokine 28:109-23). Recombinant IL-2 is approved for clinical treatment of renal cancers and is used in a variety of other cancer therapies.
Polynucleotides encoding the L106P stability-affecting protein were inserted between polynucleotides of the IL-2 gene that encode the signal peptide and the remainder of the IL-2 protein to produce the chimeric gene, L-L106P-IL-2, which was stably introduced into HCT116 cells. The levels of IL-2 secreted by the transfected HCT116 cells increased in a dose-dependent manner depending on the concentration of Shield1 in the media, with a dynamic range of approximately 25-fold (
Cells harboring the L-L106P-IL-2 chimeric gene, were implanted as a xenog raft onto mice (as above), and the ability of the cells to establish tumors and proliferate in the presence and absence of ligand (Shield1) was monitored (
Tumors in the untreated control animals continued to increase in size over the course of the experiment. Tumors failed to establish in mice that received HCT116 L-L106P-IL-2 cells and had been pretreated with Shield1 and continued to be treated with Shield1 (10 mg/kg) every 48 hours following implantation of the xenograft. Mice that were not pretreated with Shield1 prior to tumor implantation but were treated with Shield1 (i.p. at either 5 or 10 mg/kg every 48 hours) five days following tumor establishment showed tumor regression, with the size of the tumor eventually being reduced to that observed in the pretreated animals. By day 16, all Shield1-treated groups displayed significantly reduced tumor burden relative to untreated animals (p<0.05).
These results demonstrated that stabilization of IL-2 following implantation resulted in tumor regression, whereas stabilization of IL-2 prior to and following implantation prevented tumor establishment.
Analysis of IL-2 levels within the tumors of treated and untreated mice confirmed dose-dependent production of IL-2 at the tumor site in mice treated at 5 or 10 mg/kg Shield1 (
A viral gene delivery system for the systemic treatment of cancer based on a replication-selective (oncolytic) strain of vaccinia virus (hereafter vvDD) has been described (Thorne, S. H. et al. (2006) Science 311:1780-84). The deletion of the vira thymidine kinase genes and growth factor genes restrict the replication of this virus to cancer cells (McCart, J. A. et al. (2001) Cancer Res. 61:8751-7). Intravenous delivery of vvDD results in the initial infection of tumor and other cells, followed by rapid replication and spread of the virus in tumor cells and clearance in other cells. vvDD can deliver transgenes to tumor cells following systemic delivery, allowing the system to be used to study conditionally stabilized proteins.
Preliminary experiments established that infection of cultured cells with vvDD did not affect the kinetics or dynamic range of L106P-regulated protein stability, and that the ligand, Shield1, did not affect the replication of the virus (data not shown). Strains of vvDD were then constructed to express either L106P-tsLuc or L106P-ref fluorescent protein (RFP) fusion proteins and ligand (Shield1)-dependent protein activity (i.a, fluorescence) was measured in cultured cells (
To test the ability of a virally-delivered condition protein stabilization system to regulate physiologically relevant or therapeutic proteins, vvDD was used to deliver a conditionally stable cytokine TNF-α protein. While proven to exert cytotoxic effects against primary tumors, the systemic toxicity of TNF-α has limited its clinical use to local applications (e.g., isolated limb or organ perfusion; Lucas, R. et al. (2005) Curr. Cancer Drug Targets 5:381-392). In addition, TNF-α possesses antiviral effects to which the vaccinia strain Western Reserve (the basis for vvDD) is susceptible (Alcami, A. et al. (1999) J. Gen. Virol. 80:949-59).
An L-L106P-TNF-α chimeric gene was inserted into a strain of vvDD constitutively expressing luciferase, and dose-dependent stabilization of secreted TNF-α from cultured cells was verified (not shown). Mice bearing large (150-250 mm3) subcutaneous HCT116 tumors were treated with a single intravenous injection of this virus or a PBS control. Ligand (Shield1; 10 mg/kg) was delivered i.p. to the mice every 48 hours, starting either 1 day prior to vvDD treatment or 3 days post-treatment vvDD.
When Shield1 dosing began prior to virus delivery (causing all virus-infected cells to secrete stable TNF-α, only modest levels of virus were observed in the tumor (
When Shield1 administration was delayed until 3 days following virus treatment, the initial delivery and persistence of viral infection (as measured by luciferase expression within the tumor) were equivalent to those observed in animals treated with virus alone (
In a subsequent experiment, vvDD was used to deliver a conditionally stable interleukin-2 (IL-2) protein. An L-L106P-IL-2 chimeric gene was inserted into a strain of vvDD constitutively expressing luciferase. Mice bearing large (150-250 mm3) subcutaneous HCT116 tumors were treated with a single intravenous injection of this virus or a PBS control. Ligand (Shield1; 10 ring/kg) was delivered intraperitoneally (i.p.) to the mice every 48 hours, starting either 1 day prior to vvDD treatment or 3 days post-treatment with vvDD (72 hours after administration of the virus).
As was observed in studies with the L-L106P-TNF-α vvDD studies described above, and as shown in
However, when measuring effects on mouse survival, constitutive IL-2 expression was again more beneficial than no IL-2 expression.
It was also observed that by delaying clearance of the virus, and thus prolonging infection of the virus, an increase in Treg infiltration was observed (see
NK-92 is a highly cytotoxic NK cell line which has been shown to exhibit substantial antitumor activity against a wide range of malignancies in vitro as well as in xenografted SCID mice. This therapeutic activity is enhanced by systemic administration of IL-2. Many immune cell therapies require administration of cytokines to enhance their benefits in vivo. Use of systemic delivery of recombinant cytokines is often toxic, and is expensive. Studies were done to determine the effects of treating tumor-bearing mice with NK-92 cells pre-infected with the vvDD-L-L106P-12 virus. As a control, mice were also treated with the vvDD control virus (not containing the L-L106P-IL2 fusion construct) and co-administered recombinant IL-2.
SCID mice bearing HCT116 tumors were treated with NK-92 cell therapy. Subcutaneous tumors were formed by injecting 5×106 HeLa cells subcutaneously into athymic nu−/nu− mice. Once formed (after 7 days), mice were treated with a single intravenous injection of (i) PBS; (ii) 1×107 NK-92 cells pre-infected (a 2-hour infection step) with 1×107 PFU vaccinia with thymidine kinase deletion or (iii) 1×107 NK-92 cells pre-infected (after 2 h infection step) with 1×107 PFU vaccinia with thymidine kinase deletion and expressing L106P-IL2 (n=8 mice per group; NK-92 cells from ATCC). Group (ii) mice were treated every 48 hours with intraperitoneal injections of 1×107 IU rhIL2 (international units recombinant human IL-2), and group (iii) were treated every 48 h with 10 mg/kg Shield1. Tumor burden was followed by caliper measurement.
Dihydrofolate reductase (DHFR) is a ubiquitous enzyme involved in the regeneration of tetrahydrofolate from dihydrofolate, using NADPH. The goal was to use E. coli DHFR as a destabilizing domain (DD) when fused at either the N or the C-terminus of a protein of interest (POI). Since DHFR is an enzyme present in mammalian cells, mutants of DHFR having reduced catalytic ability were used to minimize perturbations to the intracellular environment caused by the introduction of an exogenous DHFR. Two of these mutations, Y100I (SEQ ID NO: 14) and G121V (SEQ ID NO: 15), in addition to reducing enzymatic activity, also destabilized DHFR relative to the wild-type sequence (SEQ ID NO: 13).
These DHFR mutants acted as destabilizing domains when fused to yellow fluorescent protein (YFP) at either the N- or the C-terminus of the YFP reporter (
To further improve the ligand-dependent stabilization characteristics of the DHFR-derived destabilizing domains for use at the C-termini of POIs, error-prone PCR was used to generate a library of additional mutants of DHFR, similar to manner in which mutants of FKBP were generated. The YFP-DHFR fusion protein library (i.e., the library of C-terminal DHFR mutants) was introduced into NIH3T3 fibroblasts using a retroviral expression system, as before, and the transduced cells were subjected to four rounds of sorting using flow cytometry. The cells were cultured in the absence of ligand in the first round of sorting. Low YFP-expressing cells were collected, cultured in the presence of 10 μM TMP for 24 hours (i.e., the second round of sorting), and then again cultured in the presence of 1 μM TMP (i.e., the third round of sorting) to isolate YFP-expressing cells with increased ligand-dependent stabilization.
Cells that displayed fluorescence were cultured in the presence of TMP, washed free of TMP, and sorted about four hours later to isolate mutants with fast kinetics of degradation in the fourth round of sorting. Low YFP-expressing cells (i.e., cell in which YFP was most degraded following the removal of the TMP from the cell medium), were collected, and the genomic DNA was isolated for sequence analysis. In this manner, two additional DHFR-derived destabilizing domains, having increased ligand-dependent stabilization, were isolated from the library screen, i.e., one double-mutant (N18T/A19V; SEQ ID NO: 17) and one single-mutant (F103L; SEQ ID NO: 16).
When fused to the C-terminus of YFP, these mutants destabilized YFP in the absence of TMP and stabilized YFP in the presence of TMP. As shown in
The kinetics of YFP-fusion protein decay following withdrawal of ligand is shown in
To further improve the ligand-dependent stabilization characteristics of the DHFR-derived, stability-affecting proteins for use at the N-termini of POIs, error-prone PCR was used to generate a library of additional mutants of DHFR, similar to manner in which mutants of FKBP were generated. Using the wild-type sequence as well as the Y100I and G121V mutant sequences as the basis of the library, five double mutants were identified from the screen, namely H12Y/Y100I (SEQ ID NO: 19), H12L/Y100I (SEQ ID NO: 20), R98H/F103S (SEQ ID NO: 21) M42T/H114R (SEQ ID NO: 22), and 161F/T68S (SEQ ID NO: 23).
The kinetics of decay and stabilization of the N-terminal fusion proteins harboring the H12YN100I, H12L/Y100I, and R98H/F103S mutants is shown in
These results demonstrate that the DHFR-derived stability-affecting proteins can function as in the context of either an N-terminal fusion or a C-terminal fusion with a POI.
Ideal techniques for conditionally stabilizing biological macromolecules are specific, fast, reversible, and tunable. Cell-permeable small molecules often deliver the latter three features but, apart from a few well-known exceptions, cell-permeable small molecules are typically not specific for a single biological target. The ideal conditional stabilization technology combines the specificity of reverse genetics (i.e., well-defined DNA changes in a large genomic background) with the conditionality of cell-permeable small molecules.
Using small libraries of FKBP and DHFR variants (20,000 to 30,000 members) in combination with a convenient cell-based screening assay, several ligand stabilized destruction domains were identified, which conferred ligand-dependent stability to a POI. A list of proteins that have to date been stabilized using the methods and compositions described herein is provided in Example 12. The FKBP-derived destabilizing domains conferred ligand-dependent stability to cytoplasmic, nuclear, and a transmembrane protein, indicating that the present methods and compositions are generally applicable to the study of protein function. Stability, and therefore function, of the fusion proteins was greatly increased upon addition of a cell-permeable high-affinity ligand. For example, when the most destabilizing FKBP variants from the screen, i.e., FKBP L106P, was fused to YFP, the fusion protein is expressed at only ˜1-2% of its maximum level in the absence of the stabilizing ligand. This fusion protein is fully stabilized upon the addition of 1 μM Shield1.
Variant and mutant FKBP proteins are exemplified by FKBP F36V (SEQ ID NO: 1) and the variants described in the text, Table 1 (N-terminal fusion proteins), and Table 2 (C-terminal fusion proteins). Exemplary variants have the substitutions F15S (SEQ ID NO: 2), V24A (SEQ ID NO: 3), H25R (SEQ ID NO: 4), E60G (SEQ ID NO: 5), L106P (SEQ ID NO: 6), D100G (SEQ ID NO: 7), M66T (SEQ ID NO: 8), R71G (SEQ ID NO: 9), D100N (SEQ ID NO: 10), E102G (SEQ ID NO: 11), and K105I (SEQ ID NO: 12). As tested, these variants included the F36V mutation (SEQ ID NO: 1); however, a similar mutation that accommodates a bulky side chain of a cell-permeable ligand is expected to produce similar results. Moreover, the methods allow for the screening of additional mutations that yield efficient single-ligand stabilized destruction domains.
A further mutant FKBP included additional amino acid sequence that altered the behavior of the protein such that is stabilized a POI in the absence of ligand and caused degradation of the POI in the presence of ligand. Thus the system can be used in a “drug-OFF” or “drug-ON” configuration. Such “drug-OFF” configurations may utilize a FKBP binding domain fused to a sequence substantially identical to that of SEQ ID NO:18.
The results obtained using DHFR variants suggests that Y100I (SEQ ID NO: 14) G121V (SEQ ID NO: 15) variants, particularly with the N18T/A19V (SEQ ID NO: 17) or F103L (SEQ ID NO: 16), H12Y/Y100I (SEQ ID NO: 19), H12L/Y100I (SEQ ID NO: 20), and R98H/F103S (SEQ ID NO: 21) substitutions, are well-suited for use as single-ligand stabilized destruction domain. However, the methods allow for the screening of additional mutations, including those for operation in a “drug-ON” configuration, as well as in the exemplified “drug-OFF” configuration.
The abundance of variants obtained in the screens, as well as the ability to use different ligand-binding domains, suggests that further refinements in screening may lead to additional stability-affecting proteins selected for various properties (e.g., rate of degradation, potency of stabilization, subcellular localization, and the like). Moreover, the stability-affecting proteins work when fused to either the N- or the C-terminus of a POI, illustrating the modularity of the components of the system.
The present systems work in different cell types, and work in cell culture and in animals. The system provides heretofore unprecedented control of the levels of preselected protein in cells, with excellent dose and temporal control. While the present methods have been described with reference to the FKBP and DHFR-derived destabilizing domains, other domains may be used. Preferred stability-affecting proteins modulate the degradation of a fusion protein, as determined, for example, using the kinetic and immunological assays described herein. In some embodiments, the level or extent of destabilization of the destabilization domain fusion protein is dependent upon the amount of ligand administered to the cell or to the animal expressing the destabilization domain fusion protein.
Preferred stability-affecting proteins produce a 5, 10, 20, 30, 40, 50, 60, or more-fold difference in the levels of a preselected protein that can be detected in cells or animals in the absence or presence of ligand. In some embodiments, the gene or allele encoding the naturally-occurring POI (i.e., the native protein, not a fusion protein) is deleted or disrupted in the genome of the cells or animal in which the conditional protein stability system is used or replaced by a DNA encoding the fusion protein. In this manner, the only source of the POI is the conditionally stabilized fusion protein, allowing its function to be studies in the absence of the interfering wild-type/naturally-occurring protein.
The conditional protein stability system can be used not only in vitro, but also in vivo to control the expression of a reporter gene or therapeutic gene of interest. An exemplary therapeutic gene is IL-2 but the present methods can be used control the expression of a wide variety of genes involved in tumor suppression, metabolic regulation, cell signaling, transcription, replication, apoptosis, and the like.
In some embodiments of the method, the strategy is “drug-ON,” in that the stabilizing ligand must be present for stabilization of the fusion protein. However, if the POI exhibits a dominant negative phenotype, the system may be “drug-OFF,” in that addition of the ligand stabilizes the dominant negative fusion protein, which in turn inhibits the function of its cellular target protein.
The stability-affecting proteins may encompass amino acid substitutions that do not substantially affect stability, including conservative and non-conservative substitutions Preferably, the amino acid sequences of the peptide inhibitors encompassed in the invention have at least about 60% identity, further at least about 70% identity, preferably at least about 75% or 80% identity, more preferably at least about 85% or 90% identity, and further preferably at least about 95% identity, to the amino acid sequences set forth herein. Percent identity may be determined, for example, by comparing sequence information using the advanced BLAST computer program, including version 2.2.9, available from the National Institutes of Health. The BLAST program is based on the alignment method of Karlin and Altschul ((1990) Proc. Natl. Acad. Sci. U.S.A. 87:2264-68) and as discussed in Altschul et al. ((1990) J. Mol. Biol. 215:403-10; Karlin and Altschul (1993) Proc. Natl. Acad. Sci. U.S.A. 90:5873-77; and Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402).
Conservative amino acid substitutions may be made in the amino acid sequences described herein to obtain derivatives of the peptides that may advantageously be utilized in the present invention. Conservative amino acid substitutions, as known in the art and as referred to herein, involve substituting amino acids in a protein with amino acids having similar side chains in terms of, for example, structure, size and/or chemical properties. For example, the amino acids within each of the following groups may be interchanged with other amino acids in the same group: amino acids having aliphatic side chains, including glycine, alanine, valine, leucine and isoleucine; amino acids having non-aromatic, hydroxyl-containing side chains, such as serine and threonine; amino acids having acidic side chains, such as aspartic acid and glutamic acid; amino acids having amide side chains, including glutamine and asparagine; basic amino acids, including lysine, arginine and histidine; amino acids having aromatic ring side chains, including phenylalanine, tyrosine and tryptophan; and amino acids having sulfur-containing side chains, including cysteine and methionine. Additionally, amino acids having acidic side chains, such as aspartic acid and glutamic acid, can often be substituted with amino acids having amide side chains, such as asparagine and glutamine.
The stability-affecting proteins may be fragments of the above-described destabilizing domains, including fragments containing variant amino acid sequences. Such fragments are readily identified using the assays described herein. Preferred fragments retain the ability to bind to a stabilizing ligand with similar efficiency to the destabilizing domains described herein or with at least 90% efficiency, at least 80% efficiency, at least 70% efficiency, or even at least 50% efficiency with respect to the described stability-affecting proteins.
Stabilizing ligands for use according to the methods described herein are exemplified by SLF* (i.e., 1-[2-(3,4,5-trimethoxy-phenyl)-butyryl]-piperazine-2-carboxylic acid 1-(3-carboxymethoxy-phenyl)-3-(3,4-dimethoxy-phenyl)-propyl ester) and Shield1 (i.e., 1-[2-(3,4,5-trimethoxy-phenyl)-butyryl]-piperazine-2-carboxylic acid 3-(3,4-dimethoxy-phenyl)-1-[3-(2-morpholin-4-yl-ethoxy)-phenyl]-propyl ester), both shown in
Other stabilizing ligands may be used according to the present methods. Such ligands include rapamycin-derived ligands containing other bulky side-chains at positions of the molecule known to mediate binding to FKBP. As illustrated by the exemplary stabilizing ligands, the particular side-chain is not critical, with both aliphatic and aromatic side-chains producing acceptable results. Numerous other bulky R-groups are expected to give similar results, including but not limited to alkyl, substituted alkyl, alkenyl, substituted alkenyl, cycloalkyl, substituted cycloalkyl, cycloalkenyl, substituted cycloalkenyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic and substituted heterocyclic groups. The R-groups may contain a hydroxyl, alkoxy, substituted alkoxy, alkenoxy, substituted alkenoxy, cycloalkoxy, substituted cycloalkoxy, cycloalkenoxy, substituted cycloalkenoxy, aryloxy, substituted aryloxy, heteroaryloxy, substituted heteroaryloxy, heterocyclyloxy, substituted heterocyclyloxy and secondary or tertiary amine, (i.e., —NR′R″ where each R′ or R″ is independently selected from hydrogen, alkyl, substituted alkyl, alkenyl, substituted alkenyl, cycloalkyl, substituted cycloalkyl, aryl, substituted aryl, heteroaryl, substituted heteroaryl, heterocyclic, substituted heterocyclic, etc.
A related aspect of the methods and compositions are cells transfected with nucleic acids encoding a fusion protein comprising a protein of interest fused in frame to a stability-affecting protein. Expression of the fusion protein may be driven by the endogenous promoter, ideally reproducing the spatial and temporal expression patterns of the unmodified gene. The cells may be transfected, e.g., using an expression vector, or transduced (i.e., infected) using a viral vector, including but not limited to a vector derived from a retrovirus (e.g., a lentivirus), herpesvirus, pox virus, adenovirus, adenoassociated virus, or an RNA virus, such as poliovirus, flavivirus, alphavirus, or the like. The exemplary viral vector was based on a retrovirus.
The system was shown to be effective eukaryotic cells, including mammalian cells and protozoan parasites; therefore, the system can be expected to work in various eukaryotic cells, including those of humans, primates, rodents, dogs, cats, horses, cows, sheep, insects, amphibians, and apicomplexan parasites. The cells may be in culture or in a living organism. As noted above, the wild-type or naturally-occurring gene or allele encoding the POI may be deleted to facilitate study of the conditionally stabilized POI.
The present methods and compositions also allow the creation of transgenic animals harboring engineered alleles that direct the expression of a ligand-stabilized POI. Expression of the fusion protein may be driven by the endogenous promoter, ideally reproducing the spatial and temporal expression patterns of the unmodified gene. The ligand may be administered regularly from an early age (including in utero) to stabilize the fusion protein until the mice achieve a specified age, at which time withdrawal of the ligand results in a the rapid degradation of the fusion protein. Unlike Cre-mediated gene disruption (see Background section), this method is reversible, simply by reinitiating the administration of the ligand, allowing the rapid, reversible, and conditional control of protein function in a complex system.
The ability to specifically and conditionally stabilize a POI in a cell will enable the study of many proteins to determine their biological function and importance in a cell. The present methods and composition represent a significant improvement over current methods of conditional protein regulation.
The methods and compositions described herein may be packaged together with instructions for use, as in a kit of parts. Preferred kits of parts include nucleic acids encoding stability-affecting proteins, one or more ligands, and instructions for use. The instructions may contain information relating the inserting (i.e., “cloning”) a POI into a plasmid, in-frame with a stability-affecting protein. The instructions may also include dosing recommendations and hardware, such as syringes, to deliver the fusion protein to an organism or to cells.
The following examples are illustrative in nature and are in no way intended to be limiting. Examples relating to generating and screening stability-affecting proteins apply generally to FKBP, DHFR, and other polypeptides that can be used as stability-affecting proteins.
Diversity in the FKBP sequence was generated using a combination of error-prone PCR and nucleotide analog mutagenesis. Primers for mutagenic PCR were designed to anneal upstream of the 5′ restriction site to be used for cloning the mutagenesis products into the pBMN iHcRed-tandem retroviral expression vector and downstream of the 3′ restriction site. Three independent condition sets were used to generate diversity. Condition set “A” utilized 4 ng template, 0.5 μM of each oligonucleotide primer, 5 units Taq polymerase, 5 mM MgCl2, 0.2 mM MnCl2, 0.4 mM dNTPs in equal ratio and an excess of 0.2 mM dATP and dCTP. Condition set “B” was identical to A except that dGTP and dTTP were present in excess. Condition set C utilized the non-natural nucleotides 8-oxo-dGTP and dPTP to encourage nucleotide misincorporation (Zaccolo, M. et al. (1996) J. Mol. Biol. 255:589-603). The FKBP libraries were pooled and ligated into the pBMN iHcRed-t retroviral expression vector, affording a library containing ˜3×104 members.
SLF* and Shield1 were synthesized essentially as described (Holt et al., 1993; Yang et al., 2000).
The NIH3T3 cell line was cultured in DMEM supplemented with 10% heat-inactivated donor bovine serum (Invitrogen), 2 mM glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin. All other cell lines were cultured with 10% heat-inactivated fetal bovine serum (Invitrogen), 2 mM glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin.
The ΦNX ecotropic packaging cell line was transfected using standard Lipofectamine 2000 protocols. Viral supernatants were harvested 48 hrs post-transfection, filtered and concentrated 10-fold using an Amicon Ultra centrifugal filter device (Millipore, 100-kDa cut-off). NIH3T3 cells were incubated with the concentrated retroviral supernatants supplemented with 4 μg/ml polybrene for 4 hrs at 37° C. Cells were washed once with PBS and cultured in growth media for 24-36 hrs to allow for viral integration, then assayed as described.
HeLa cells were plated at 7×104 cells per well of a 24-well plate 12 hours prior to transfection. Cells were transfected with either 200 ng Silencer® Lamin A/C siRNA (Ambion) or a negative control siRNA using the GeneSilencer protocol. Cell lysates were immunoblotted with an anti-lamin A/C antibody (Clone 14, BD Transduction Laboratories).
Twenty-four hours prior to analysis, transduced NIH3T3 cells were plated at 1×105 cells per well of a 12-well plate and treated as described. Cells were removed from the plate using PBS+2 mM EDTA, washed once with PBS, and resuspended in 2004 PBS. Cells were analyzed at the Stanford Shared FACS Facility using FlasherII with 10,000 events represented.
Proteins tested as fusions to destabilizing domains were of the following origin, and the following antibodies were used for immunoblotting: Arf6 Q67L (human, 3A-1, Santa Cruz Biotechnology); Ar17 Q72L (human, BC001051, Protein Tech Group, Inc.); Cdc42 Q61L (human, P1, Santa Cruz Biotechnology); CD8α (mouse, 5H10, Caltag Laboratories); CDK1 (human, H-297, Santa Cruz Biotechnology); CREB (mouse, 86B10, Cell Signaling Technology); FKBP (human, 2C1-97, BD PharMingen); GSK-3β (mouse, 0011-A, Santa Cruz Biotechnology); Hsp90 (mouse, 68, BD Transduction Laboratories); p21 (human, H-164, Santa Cruz Biotechnology); Rac1 Q61L (human, C-11, Santa Cruz Biotechnology); RhoA Q63L (human, 26C4, Santa Cruz Biotechnology); Securin (human, Z23.YU, Zymed Laboratories); YFP, Aequorea victoria (JL-8, Clontech).
NIH3T3 cells stably expressing constitutively active GTPases fused to destabilizing domains were treated with 1 μM Shield1 for 24 hr. At this time, cells were washed once with PBS, plated at 8×103 cells in 4-well LabTek Chambered coverglass (NUNC) coated with 1 mg/ml poly-D-lysine (Sigma), along with mock-treated transduced cells and transduced cells treated with 1 μM Shield1. Cells were cultured for 24 hr in 10% DBS, then cultured in serum-free media for 12 hr. Cells were then washed with PBS, fixed in 4% paraformaldehyde for 15 min, permeabilized in 0.2% Triton X-100 for 5 min, stained with 1 μg/ml Alexa Fluor 488-conjugated phalloidin (Invitrogen; A12379) in PBS for 20 min, and washed with PBS. Fixed cells were imaged using a Bio-Rad Radiance 2100 confocal microscope.
To identify FKBP variants (i.e., mutants) with a high affinity for the synthetic FKBP ligand SLF* (
A Moloney murine leukemia retroviral expression system was used to stably integrate this library of DNAs encoding FKBP-YFP fusion proteins into NIH3T3 fibroblasts. The transduced cells were subjected to three rounds of sorting using flow cytometry. In the first round, cells were treated with the FKBP ligand SLF* (5 μM,
The variant FKBP-derived, ligand-responsive destabilizing domains were assayed for stability in the presence and absence of a derivative of SLF* in which the carboxylic acid is replaced with a morpholine group (
Each variant FKBP-derived, ligand-responsive destabilizing domain was separately transduced into NIH3T3 cells, and YFP fluorescence levels were measured in the absence of Shield1 (
In a kinetic study of NIH3T3 cells stably expressing each of the five FKBP-derived, ligand-responsive destabilizing domain variants, YFP fluorescence increased at approximately the same rate upon addition of Shield1, with maximum fluorescence achieved at 24 hours and stably maintained for at least an additional 48 hours without further addition of Shield1 (
Upon withdrawal of Shield1, distinct differences in fluorescence decay profiles were observed among the FKBP-derived, ligand-responsive destabilizing domain variants (
To correlate YFP fluorescence with intracellular protein levels and to look for evidence of partial proteolysis, cells stably expressing each destabilizing domain fused to YFP were either mock-treated or treated with Shield1. Cell lysates were prepared and used for immunoblot analysis along with antibodies specific for either FKBP (
The mechanism of degradation was examined for the F15S and L106P variants. Since the ubiquitin-proteasome system is a major mediator of intracellular protein degradation (Pickart, C.M. (2004) Cell 116:181-190; Bence, N. F. et al. (2001); Hicke, L. and Dunn, R. (2003) Annu. Rev. Cell Dev. Biol. 19:141-172). Science 292:1552-1555), the cells expressing either the FKBP-derived, ligand-responsive destabilizing domain variants F15S or L106P were incubated with MG132 (
RNAi has become a widely used tool for reducing intracellular levels of a protein of interest. The rate of RNAi-mediated silencing of an endogenous gene was compared to the rate of degradation achieved through the fusion of a protein of interest to the above-described destabilizing domain. Lamin A/C is a non-essential cytoskeletal protein commonly used as a control in RNAi experiments. Previous studies have shown more than 90% reduction in lamin A/C expression in HeLa cells assayed 40 to 45 hours after transfection of the cells with a cognate siRNA duplex (Elbashir, S. M. et al. (2001) Nature 411:494-498), which suggests that the half-life of the lamin A/C proteins is about 10-12 hours. This half-life is significantly shorter than that of YFB, which is 26 hrs (Corish, P. and Tyler-Smith, C. (1999) Protein Eng. 12:1035-1040 and Tyler-Smith, 1999). HeLa cells transfected with siRNA against lamin NC showed a decrease in protein levels after 24 hours, with a significant reduction in lamin A/C observed by 48 hours (
To determine the ability of the variant FKBP fusion proteins, in combination with Shield1, to modulate the levels of YFP in a dose-dependent manner, NIH3T3 cells stably expressing the L106P-YFP variant were exposed to different concentrations of Shield 1 over the course of one week (
A screen of a YFP-FKBP library (reversed compared to the previous orientation of FKBP and YFP) was performed to identify candidate C-terminal destabilizing domains (Table 2). Six FKBP variants (M66T, R71G, D100G, D100N, E102G, and K105I) were selected for further analysis. Overall, destabilizing domains fused to the C-terminus of YFP are less destabilizing than their N-terminal counterparts (Table 1). For example, when the L106P mutant is fused to the N-terminus of YFP (L106P-YFP), fluorescence is only ˜1-2% of that observed in the presence of Shield1. However, when the orientation is reversed (YFP-L106P), fluorescence in the absence of Shield1 is ˜10% of that observed in its presence.
Nonetheless, C-terminal destabilizing domains respond to Shield1 in a dose-dependent manner comparable to N-terminal destabilizing domains, with EC50 values ranging from 10 nM to 100 nM (
Destabilizing domains fused to either the N- or C-terminus of YFP were also transfected into several different cells lines, i.e., NIH3T3, HEK 293T, HeLa, and COS-1 cells, to assess the behavior of the FKBP-derived, ligand-responsive destabilizing domain variants in different cells. Shield1-dependent fluorescence was observed in all cell lines (Table 3), demonstrating that ligand-dependent stability is not restricted to one cell type. The FKBP-derived destabilizing domains can be stabilized using Shield1 as well as the commercially available ligand, FK506 (
To show that FKBP variants are efficient in destabilizing proteins other than YFP, the F15S and L106P variants were fused at the N-termini, to the kinases GSK-3β and CDK1, the cell cycle regulatory proteins securin and p21, and three small GTPases, Rac1, RhoA and Cdc42 (
Expression of constitutively active small GTPases causes well-characterized changes in cellular morphology (Heo, W. D. and Meyer, T. (2003) Cell 13:315-328). To determine if FKBP-derived destabilizing domains, in combination with Shield1, could affect cell morphology by modulating GTPases levels, several small GTPases RhoA, Cdc42, or Ar17) were fused to the destabilizing domains (
Thermostable luciferase or the human IL-2 gene were cloned into pBMN L106P iBlasticidin and used to generate amphotropic retrovirus (Banaszynski, L. A. et al. (2006) Cell. 126:995-1004). HCT116 cells were incubated with retrovirus and polybrene (6 μg/mL) for 4 hrs at 37° C. and then selected with Blasticidin (5 μg/mL). Cells grown in 96-well plates (2×104 cells/well) were treated with Shield1 as indicated and either bioluminescence measured using an IVIS 50 (Xenogen Product from Caliper Life Sciences) following luciferin addition (300 μg/mL), or media collected for ELISA.
SCID or CD1 nu−/nu− mice (Charles River Co.) received subcutaneous dorsal injections of ˜1×107 cells, and tumors were allowed to establish as indicated. Animals were given an intraperitoneal injection of luciferin (225 mg/kg), anesthetized (2% isoflurane), and placed on the warmed stage (3TC) of an IVIS 100 or IVIS 200 (Xenogen Product from Caliper Life Sciences) for imaging. Light produced was measured as photons/sec for designated regions of interest as described. Tumor volumes were also determined by caliper measurement, and mice were sacrificed when tumors reached 1.44 cm3 for survival assays. In some experiments, serum samples were collected by retino-orbital bleedings and tumors collected post-mortem and homogenized for ELISA assay of cytokines. All experiments were run with institutional IACUC approval.
CV1 cells were transfected with pSC-65 p7.5 L106P-tsLuc or pSC-65 p7.5 L106P-TNF-α pSE/L Luc and simultaneously infected with viral growth factor deleted Western Reserve Vaccinia (VSC20). Cassettes were integrated into the viral thymidine kinase gene by homologous recombination and selected by resistance to bromodeoxyuridine on 143B TK− cells. Single viral plaques were purified in 143B TK− cells. The same method was used to generate vaccinia virus having the L-L106P-IL-2 construct.
HCT116 cells in a 96-well plate (2×104 cells/well) were incubated with vvDD carrying an L106P fusion (MOI>1) for 1 hr at 3TC. Virus was removed and cells were treated with Shield1. For luminescence assays, cells were incubated with luciferin (300 μg/mL) and imaged using an IVIS 50 (Xenogen product from Caliper Life Sciences). TNF-α in cell culture media was detected by ELISA.
Two-tailed, unpaired Student's T-tests were used, except for comparison of survival curves, when Gehan-Breslow-Wilcoxon test was used. Results were considered significant when p<0.05.
While a number of exemplary aspects and embodiments have been discussed above, those of skill in the art will recognize certain modifications, permutations, additions and sub-combinations thereof. It is therefore intended that the following appended claims and claims hereafter introduced are interpreted to include all such modifications, permutations, additions and sub-combinations as are within their true spirit and scope.
This application is a Divisional of U.S. patent application Ser. No. 12/437,279 filed May 7, 2009, granted as U.S. Pat. No. 8,530,636, which claims the benefit of U.S. Provisional Application No. 61/051,303 filed May 7, 2008, each of which is incorporated by reference herein in its entirety.
This invention was made with Government support under contracts GM068589 and GM073046 awarded by the National Institutes of Health. The Government has certain rights in this invention.
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| Number | Date | Country | |
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| 20140010791 A1 | Jan 2014 | US |
| Number | Date | Country | |
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| 61051303 | May 2008 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 12437279 | May 2009 | US |
| Child | 14020768 | US |
