# Patent

## Title
Ligand-regulable transactivation systems, methods of use thereof, methods of detecting estrogen receptor ligands, and methods of differentiating estrogen receptor ligand agonists and antagonists

## Abstract

Briefly described, embodiments of this disclosure include ligand-regulable transactivation systems, methods of producing ligand-regulable transactivation systems, methods of using ligand-regulable transactivation systems, reporter polynucleotides, method of producing reporter polynucleotides, activator fusion proteins, methods of producing activator fusion proteins, methods of regulating gene expression in vitro and in vivo for gene therapy, methods of screening estrogen receptor modulators with therapeutic treatments (e.g., anticancer, antiosteoporosis, and hormone replacement treatments), method of screening compounds (e.g., drugs and environmental pollutants) for the estrogenic effect, methods of evaluating the estrogen receptor pathway under different pathological conditions are provided, and the like.

## Background
CROSS-REFERENCE TO RELATED APPLICATION
This application is a divisional application of U.S. Utility Application entitled “LIGAND-REGULABLE TRANSACTIVATION SYSTEMS, METHODS OF USE THEREOF, METHODS OF DETECTING ESTROGEN RECEPTOR LIGANDS, AND METHODS OF DIFFERENTIATING ESTROGEN RECEPTOR LIGAND AGONISTS AND ANTAGONISTS” having Ser. No. 11/890,114, filed Aug. 3, 2007, now issued as U.S. Pat. No. 7,709,253, which claims priority to U.S. provisional application entitled, “LIGAND-REGULABLE TRANSACTIVATION SYSTEMS, METHODS OF USE THEREOF, METHODS OF DETECTING ESTROGEN RECEPTOR LIGANDS, AND METHODS OF DIFFERENTIATING ESTROGEN RECEPTOR LIGAND AGONISTS AND ANTAGONISTS,” having Ser. No. 60/835,674, filed on Aug. 4, 2006, which is entirely incorporated herein by reference.


STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
This invention was made with Government support under contracts CA082214 and CA114747 awarded by the National Institutes of Health. The Government has certain rights in this invention.


BACKGROUND
Gene therapies hold the potential application in treating many genetic disorders. The success of gene therapies mainly depends on many different factors; one among them is the availability of regulable gene expression systems. The use of regulable gene expression systems is not only restricted to gene therapy applications; they are also useful for different functional genomic studies and clinical applications in mammals. As gene therapy research continuously progresses, the need for regulable gene expression systems becomes more apparent. An efficient regulable gene expression system should have the quality in controlling the level of expressed transgenes in a dose dependent manner in response to externally administered pharmacological agents. In addition, the regulable gene expression system should also have the ability in producing low level of background signal before administering the activators/regulators.
So far, several regulable gene expression systems have been developed and used for different applications. The very early systems include the naturally occurring physical and chemical stimuli responsive promoters such as heat shock, electric, light and heavy metal inducible promoters. Even though these natural promoters have the potential in controlling the level of transgene expression, adopting them for mammalian gene therapy application is difficult because of hazardous effects associated with the inducers. To overcome these issues, later combination elements derived from prokaryotic and eukaryotic systems were used for developing controlled gene expression systems. These systems are efficient for utilization in mammalian cells in vitro and in vivo. Most of these systems utilize either one or a combination of the following elements that includes DNA binding domains, ligand binding domains and transactivation domains. The systems developed by using these elements include tetracycline regulated system, mifepristone (RU486) regulated system, ecdysone regulated system, rapamycin regulated system, tamoxifen regulated system and ligand activated site specific recombination system (Cre-ER). Even though all these systems showed significant levels of transgene expression in response to externally administered pharmacological agents, many of them produced significant levels of background signal before administering the activators.
Estrogens are responsible for the growth, development and maintenance of many reproductive cells. The physiological effects of these hormones are mediated by a ligand-inducible nuclear transcription factor, the estrogen receptor (ER). In the classical pathway of steroid hormone action, 17β-estradiol binds to the ligand binding domain (LBD) of an estrogen receptor and induces homodimerization, which then binds to a specific regulatory sequence of promoters of ER target genes, the estrogen response elements (ERE). The binding of hormones and a variety of other chemicals to the LBD of ER leads to a series of molecular events. This includes the activation or repression of many downstream target genes through direct interaction with the transcription machinery.
Abnormal levels of estrogen have been linked with many disorders including cancer. The deficiency in the level of estrogen in post menopausal women can lead to reduced bone densities. Similarly, the presence of excess hormones has been reported to induce the development of different types of cancers including breast cancer. Most of these cancers respond to hormonal therapy (anti-estrogens) via the estrogen receptor. Hence, estrogen receptors are a major cellular therapeutic target.
The ER-LBD is folded into a three-layered, anti-parallel, α-helical sandwich composed of a central core layer of three helices that includes H5/6, H9, and H10. This is in turn sandwiched between two additional layers of helices (H1-4 and H7, H8, H11). This helical arrangement creates a “wedge shaped” molecular scaffold that maintains a sizeable ligand binding property at the narrower end of the domain. The remaining secondary structural elements, a small two-stranded, anti-parallel β-sheet (S1 and S2) and an α-helical H12, are located at this ligand binding portion of the molecule and flank the three-layered motif. The helix 12 (H12) is mainly located in the pocket of the ligand binding region. Therefore, it is a key element of the receptor in developing conformational modifications in response to various ligands. The crystal structures of the LBD complexed with 17β-estradiol and Raloxifene show that although both ligands bind at the same site within the core of the LBD, each of these ligands induces a different conformational change on H12. In addition, the binding of ligands to the ligand-binding domain of ERα causes a conformational shift of helix 12 into an adjacent co-activator site that either prevents or enhances ERα from binding to a co-activator (NR box peptide), which would then activate a specific DNA sequence, the estrogen response element (ERE). This process controls many genes that are responsible for cell growth. Hence, helix 12 is one of the major portions of ER that plays a critical role in the ligand induced proliferative effect of cells, and it is therefore important to develop an assay based on the movement of helix 12 in response to different ligands.
SUMMARY
Briefly described, embodiments of this disclosure include ligand-regulable transactivation systems, methods of producing ligand-regulable transactivation systems, methods of using ligand-regulable transactivation systems, reporter polynucleotides, methods of producing reporter polynucleotides, activator fusion proteins, method of producing activator fusion proteins, methods of regulating gene expression in vitro and in vivo for gene therapy, methods of screening estrogen receptor modulators with therapeutic treatments (e.g., anticancer, antiosteoporosis, and hormone replacement treatments), methods of screening compounds (e.g., drugs and environmental pollutants) for the estrogenic effect, methods of evaluating the estrogen receptor pathway under different pathological conditions, and the like.
One exemplary ligand-regulable transactivation system, among others, includes: a reporter polynucleotide that includes a binding sequence, a promoter sequence, and a reporter sequence, wherein the binding sequence is connected with the promoter sequence and the promoter sequence is connected with the reporter sequence; and an activator fusion protein that includes a DNA binding domain, an estrogen receptor folding domain, and a transactivation domain, wherein the DNA binding domain is connected to the estrogen receptor folding domain, and the estrogen receptor folding domain is connected with the transactivation domain.
In an embodiment, the ER folding domain has a characteristic of changing from a first conformational position to an interacting conformational position or an non-interacting conformational position upon interaction with a compound; wherein the interacting conformational position positions the DNA binding domain and the transactivation domain so that both interact with the binding sequence and the promoter sequence of the reporter polynucleotide, which causes the reporter sequence to generate a bioluminescent protein that is detectable; wherein the non-interacting conformational position does not position the DNA binding domain and the transactivation domain so that both interact with the binding sequence and the promoter sequence of the reporter polynucleotide.
In an embodiment, the interacting conformation position corresponds to one of two states including substantially interacting and partially interacting, wherein substantially interacting means that the DNA binding domain and the transactivation domain interact with the binding sequence and the promoter sequence of the reporter polynucleotide to a greater degree than partially interacting and non-interacting, and wherein partially interacting means that the DNA binding domain and the transactivation domain interact with the binding sequence and the promoter sequence of the reporter polynucleotide to a greater degree than non-interacting.
One exemplary method of detecting a ligand, among others, includes: providing an ligand-regulable transactivation system of described herein; introducing a ligand to the system; and detecting a bioluminescent signal in the presence of a bioluminescence initiating compound if the ligand causes the ER folding domain to change from a first conformational position to an interacting conformational position.
One exemplary cell, among others, includes: a ligand-regulable transactivation system having: a reporter polynucleotide that includes a binding sequence, a promoter sequence, and a reporter sequence, wherein the binding sequence is connected with the promoter sequence and the promoter sequence is connected with the reporter sequence; and an activator fusion protein that includes a DNA binding domain, an estrogen receptor folding domain, and a transactivation domain, wherein the DNA binding domain is connected to the estrogen receptor folding domain, and the estrogen receptor folding domain is connected with the transactivation domain.
One exemplary transgenic animal, among others, includes: a ligand-regulable transactivation system having: a reporter polynucleotide that includes a binding sequence, a promoter sequence, and a reporter sequence, wherein the binding sequence is connected with the promoter sequence and the promoter sequence is connected with the reporter sequence; and an activator fusion protein that includes a DNA binding domain, an estrogen receptor folding domain, and a transactivation domain, wherein the DNA binding domain is connected to the estrogen receptor folding domain, and the estrogen receptor folding domain is connected with the transactivation domain.
One exemplary fusion protein, among others, includes: a ligand-regulable transactivation system having: a reporter polynucleotide that includes a binding sequence, a promoter sequence, and a reporter sequence, wherein the binding sequence is connected with the promoter sequence and the promoter sequence is connected with the reporter sequence; and an activator fusion protein that includes a DNA binding domain, an estrogen receptor folding domain, and a transactivation domain, wherein the DNA binding domain is connected to the estrogen receptor folding domain, and the estrogen receptor folding domain is connected with the transactivation domain.



BRIEF DESCRIPTION OF THE DRAWINGS
Many aspects of the disclosure can be better understood with reference to the following drawings. The components in the drawings are not necessarily to scale, emphasis instead being placed upon clearly illustrating the principles of the present disclosure. Moreover, in the drawings, like reference numerals designate corresponding parts throughout the several views.
FIG. 1 is a schematic of the ligand induced transactivation system developed. In this system ER ligand binding domain is expressed in between the GAL4 DNA binding domain and the VP16 transactivation domain as a fusion protein. The GAL4 DNA binding domain from the expressed fusion protein binds to its specific binding DNA sequence present in the co-delivered reporter vector. The ER (LBD) in the fusion protein is in a different conformation when it is in a ligand free form and it keeps the VP16 transactivation domain away from the minimal promoter. When the ligand is available the ER (LBD) binds with the ligand and leads to a conformational change that brings VP16 portion of the fusion protein near the promoter minimal E4 and leads to the activation of gene transcription.
FIG. 2 is a graph of a comparison of ligand induced transactivation system with the constitutive transactivation system. To compare the ER-ligand induced transactivation system with the constitutive transactivation system, 293T cells co-transfected with the reporter plasmid with either activator expressing fusion protein containing GAL4, ER and VP16 or expressing GAL4 and VP16 alone were assayed for luciferase activity before and after exposure to 1 μM concentration ligand 17-β estradiol. The ligand induced transactivation system showed significant level of activity only when receiving the ligands (p<0.001).
FIG. 3 is a graph of a comparison ligand induced transactivation system with adenoviral early and late minimal promoters. The 293T cells transiently co-transfected with reporter plasmid contain GAL4 DNA binding sequence followed by adenoviral early and late minimal promoters driving firefly luciferase and plasmid expressing GAL4-ER-VP16 under CMV promoter. The cells were assayed for luciferase activity with and without exposure to ligand 17-β estradiol. Co-transfecting with 10 ng of plasmid expressing Renilla luciferase normalized the transfections. The SEM of triplicate reading was used.
FIG. 4 illustrates a graph of the concentration dependent transactivation of reporter gene expression by the system. Ligand concentration dependent transactivation of reporter gene expression was studied in 293T and CHO cells co-transfected with the reporter plasmid and the activator plasmid expressing GAL4-ER (LBD)-VP16 fusion protein. The cells were assayed for luciferase activity after exposed to 10 different concentrations of ligand 178-estradiol. The results were normalized by co-transfecting 10 ng of Renilla luciferase plasmid. The error bars are the SEM of triplicate determinations.
FIG. 5A is a graph that illustrates the system's utility in controlling with different ER-ligands. The 293T cells co-transfected with the reporter plasmid and the activator plasmid expressing fusion protein GAL4-ER (LBD)-VP16 were induced with different ER-ligands, indlucing agonists, antagonists, partial agonists and partial antagonists. As negative control, a non-ER binding anticancer drug cisplatinum was used. The results were normalized by co-transfecting 10 ng of Renilla luciferase plasmid. The error bars are the SEM of triplicate determinations.
FIG. 5B is a Western blot analysis of the corresponding samples that were analyzed with ER-antibody and Firefly luciferase antibody to confirm the ligand-induced transactivation of the system.
FIG. 6A is a graph that illustrates the efficiency of ER ligand mediated transactivation system in controlling two different genes expressing from a single bi-directional vector in two different orientations studied by exposing the transiently co-transfected cells with reporter and the plasmid expressing GAL4-ER-VP16 fusion protein with 12 different concentrations of ligand 178-estradiol.
FIG. 6B is a graph that illustrates that the results showed significant correlation (R2=0.9936) with concentration of ligand and the expression level of two reporter proteins Renilla and firefly luciferases. The error bars are the SEM of triplicate determinations.
FIG. 7 is a graph illustrating the application of a ligand induced transactivation system developed for differentiating ER-ligands. The 293T cells co-transfected with the reporter plasmid and the activator plasmid expressing ER-ligand binding domain of amino acids 281-549 were used for differentiating ER-ligands. The cells were assayed for luciferase activity after exposure to 1 μM concentration of different ligands. The system showed ligand dependent activation for different ligands used for the study. The results were normalized by co-transfecting with 10 ng of Renilla luciferase plasmid. The error bars are the SEM of triplicate determinations.
FIG. 8 is a graph illustrating the application of ligand induced transactivation system developed with the mutant form of ER-LBD. To extend the systems utility in living animals we developed ER-ligand regulated transactivation system with a mutant form of ER-LBD (G521T) identified from our previous study that specifically had very low affinity for the endogenous estrogen 17-β estradiol. The 293T cells co-transfected with reporter and the activator plasmid expressing GAL4-ER-VP16 with mutant form of estrogen receptor showed low affinity specifically for estradiol only with the transactivation system also. The results were normalized by co-transfecting with 10 ng of Renilla luciferase plasmid. The error bars are the SEM of triplicate determinations.
FIG. 9A illustrates images to show the efficiency of ER ligand regulated transactivation system in controlling the reporter gene expressions studied in living animals by non-invasive optical CCD camera imaging. To study that, the nude mice of six weeks old (5 each for ligand induced and solvent control) were implanted with 5 million 293T cells transiently co-transfected with reporter plasmid and the plasmid expressing GAL4-ER-VP16. They were imaged immediately and once every 24 hours before and after inducing with ER ligand antagonist Raloxifene (20 mg/kg body weight). The result showed significant levels of reporter gene expression only from the animals that received ligand Raloxifene.
FIG. 9B illustrates the quantitative analysis of the results from different time points studied. The error bars are the SEM of triplicate determinations.



DETAILED DESCRIPTION
Embodiments of the present disclosure will employ, unless otherwise indicated, techniques of synthetic organic chemistry, biochemistry, molecular biology, and the like, which are within the skill of the art. Such techniques are explained fully in the literature.
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 perform the methods and use the compositions and compounds disclosed and claimed herein. Efforts have been made to ensure accuracy with respect to numbers (e.g., amounts, temperature, etc.), but some errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, temperature is in ° C., and pressure is at or near atmospheric. Standard temperature and pressure are defined as 20° C. and 1 atmosphere.
Before the embodiments of the present disclosure are described in detail, it is to be understood that, unless otherwise indicated, the present disclosure is not limited to particular materials, reagents, reaction materials, manufacturing processes, or the like, as such can vary. It is also to be understood that the terminology used herein is for purposes of describing particular embodiments only, and is not intended to be limiting. It is also possible in the present disclosure that steps can be executed in different sequence where this is logically possible.
It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a support” includes a plurality of supports. In this specification and in the claims that follow, reference will be made to a number of terms that shall be defined to have the following meanings unless a contrary intention is apparent.
DEFINITIONS
In describing and claiming the disclosed subject matter, the following terminology will be used in accordance with the definitions set forth below.
A “bioluminescent initiator molecule” is a molecule that can react with a bioluminescent protein to generate bioluminescence.
The term “polypeptides” includes proteins and fragments thereof. Polypeptides are disclosed herein as amino acid residue sequences. Those sequences are written left to right in the direction from the amino to the carboxy terminus. In accordance with standard nomenclature, amino acid residue sequences are denominated by either a three letter or a single letter code as indicated as follows: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic Acid (Asp, D), Cysteine (Cys, C), Glutamine (Gln, Q), Glutamic Acid (Glu, E), Glycine (Gly, G), Histidine (His, H), Isoleucine (Ile, I), Leucine (Leu, L), Lysine (Lys, K), Methionine (Met, M), Phenylalanine (Phe, F), Proline (Pro, P), Serine (Ser, S), Threonine (Thr, T), Tryptophan (Trp, W), Tyrosine (Tyr, Y), and Valine (Val, V).
“Variant” refers to a polypeptide or polynucleotide that differs from a reference polypeptide or polynucleotide, but retains essential properties. A typical variant of a polypeptide differs in amino acid sequence from another, reference polypeptide. Generally, differences are limited so that the sequences of the reference polypeptide and the variant are closely similar overall (homologous) and, in many regions, identical. A variant and reference polypeptide may differ in amino acid sequence by one or more modifications (e.g., substitutions, additions, and/or deletions). A substituted or inserted amino acid residue may or may not be one encoded by the genetic code. A variant of a polypeptide may be naturally occurring such as an allelic variant, or it may be a variant that is not known to occur naturally.
Modifications and changes can be made in the structure of the polypeptides of this disclosure and still result in a molecule having similar characteristics as the polypeptide (e.g., a conservative amino acid substitution). For example, certain amino acids can be substituted for other amino acids in a sequence without appreciable loss of activity. Because it is the interactive capacity and nature of a polypeptide that defines that polypeptide's biological functional activity, certain amino acid sequence substitutions can be made in a polypeptide sequence and nevertheless obtain a polypeptide with like properties.
In making such changes, the hydropathic index of amino acids can be considered. The importance of the hydropathic amino acid index in conferring interactive biologic function on a polypeptide is generally understood in the art. It is known that certain amino acids can be substituted for other amino acids having a similar hydropathic index or score and still result in a polypeptide with similar biological activity. Each amino acid has been assigned a hydropathic index on the basis of its hydrophobicity and charge characteristics. Those indices are: isoleucine (+4.5); valine (+4.2); leucine (+3.8); phenylalanine (+2.8); cysteine/cysteine (+2.5); methionine (+1.9); alanine (+1.8); glycine (−0.4); threonine (−0.7); serine (−0.8); tryptophan (−0.9); tyrosine (−1.3); proline (−1.6); histidine (−3.2); glutamate (−3.5); glutamine (−3.5); aspartate (−3.5); asparagine (−3.5); lysine (−3.9); and arginine (−4.5).
It is believed that the relative hydropathic character of the amino acid determines the secondary structure of the resultant polypeptide, which in turn defines the interaction of the polypeptide with other molecules, such as enzymes, substrates, receptors, antibodies, antigens, and the like. It is known in the art that an amino acid can be substituted by another amino acid having a similar hydropathic index and still obtain a functionally equivalent polypeptide. In such changes, the substitution of amino acids whose hydropathic indices are within ±2 is preferred, those within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred.
Substitution of like amino acids can also be made on the basis of hydrophilicity, particularly where the biologically functional equivalent polypeptide or peptide thereby created is intended for use in immunological embodiments. The following hydrophilicity values have been assigned to amino acid residues: arginine (+3.0); lysine (+3.0); aspartate (+3.0±1); glutamate (+3.0±1); serine (+0.3); asparagine (+0.2); glutamine (+0.2); glycine (0); proline (−0.5±1); threonine (−0.4); alanine (−0.5); histidine (−0.5); cysteine (−1.0); methionine (−1.3); valine (−1.5); leucine (−1.8); isoleucine (−1.8); tyrosine (−2.3); phenylalanine (−2.5); tryptophan (−3.4). It is understood that an amino acid can be substituted for another having a similar hydrophilicity value and still obtain a biologically equivalent, and in particular, an immunologically equivalent polypeptide. In such changes, the substitution of amino acids whose hydrophilicity values are within ±2 is preferred, those within ±1 are particularly preferred, and those within ±0.5 are even more particularly preferred.
As outlined above, amino acid substitutions are generally based on the relative similarity of the amino acid side-chain substituents, for example, their hydrophobicity, hydrophilicity, charge, size, and the like. Exemplary substitutions that take one or more of the foregoing characteristics into consideration are well known to those of skill in the art and include, but are not limited to (original residue: exemplary substitution): (Ala: Gly, Ser), (Arg: Lys), (Asn: Gln, H is), (Asp: Glu, Cys, Ser), (Gln: Asn), (Glu: Asp), (Gly: Ala), (His: Asn, Gln), (Ile: Leu, Val), (Leu: Ile, Val), (Lys: Arg), (Met: Leu, Tyr), (Ser: Thr), (Thr: Ser), (Tip: Tyr), (Tyr: Trp, Phe), and (Val: Ile, Leu). Embodiments of this disclosure thus contemplate functional or biological equivalents of a polypeptide as set forth above. In particular, embodiments of the polypeptides can include variants having about 50%, 60%, 70%, 80%, 90%, and 95% sequence identity to the polypeptide of interest.
“Identity,” as known in the art, is a relationship between two or more polypeptide sequences, as determined by comparing the sequences. In the art, “identity” also refers to the degree of sequence relatedness between polypeptides as determined by the match between strings of such sequences. “Identity” and “similarity” can be readily calculated by known methods, including, but not limited to, those described in Computational Molecular Biology, Lesk, A. M., Ed., Oxford University Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., Ed., Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griffin, A. M., and Griffin, H. G., Eds., Humana Press, New Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov, M. and Devereux, J., Eds., M Stockton Press, New York, 1991; and Carillo, H., and Lipman, D., SIAM J Applied Math., 48: 1073, (1988).
Preferred methods to determine identity are designed to give the largest match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. The percent identity between two sequences can be determined by using analysis software (i.e., Sequence Analysis Software Package of the Genetics Computer Group, Madison Wis.) that incorporates the Needelman and Wunsch, (J. Mol. Biol., 48: 443-453, 1970) algorithm (e.g., NBLAST, and XBLAST). The default parameters are used to determine the identity for the polypeptides of the present invention.
By way of example, a polypeptide sequence may be identical to the reference sequence, that is be 100% identical, or it may include up to a certain integer number of amino acid alterations as compared to the reference sequence such that the % identity is less than 100%. Such alterations are selected from: at least one amino acid deletion, substitution (including conservative and non-conservative substitution), or insertion, and wherein said alterations may occur at the amino- or carboxy-terminus positions of the reference polypeptide sequence or anywhere between those terminal positions, interspersed either individually among the amino acids in the reference sequence, or in one or more contiguous groups within the reference sequence. The number of amino acid alterations for a given % identity is determined by multiplying the total number of amino acids in the reference polypeptide by the numerical percent of the respective percent identity (divided by 100) and then subtracting that product from said total number of amino acids in the reference polypeptide.
Conservative amino acid variants can also comprise non-naturally occurring amino acid residues. Non-naturally occurring amino acids include, without limitation, trans-3-methylproline, 2,4-methanoproline, cis-4-hydroxyproline, trans-4-hydroxyproline, N-methyl-glycine, allo-threonine, methylthreonine, hydroxy-ethylcysteine, hydroxyethylhomocysteine, nitro-glutamine, homoglutamine, pipecolic acid, thiazolidine carboxylic acid, dehydroproline, 3- and 4-methylproline, 3,3-dimethylproline, tert-leucine, norvaline, 2-azaphenyl-alanine, 3-azaphenylalanine, 4-azaphenylalanine, and 4-fluorophenylalanine. Several methods are known in the art for incorporating non-naturally occurring amino acid residues into proteins. For example, an in vitro system can be employed wherein nonsense mutations are suppressed using chemically aminoacylated suppressor tRNAs. Methods for synthesizing amino acids and aminoacylating tRNA are known in the art. Transcription and translation of plasmids containing nonsense mutations is carried out in a cell-free system comprising an E. coli S30 extract and commercially available enzymes and other reagents. Proteins are purified by chromatography. (Robertson, et al., J. Am. Chem. Soc., 113: 2722, 1991; Ellman, et al., Methods Enzymol., 202: 301, 1991; Chung, et al., Science, 259: 806-9, 1993; and Chung, et al., Proc. Natl. Acad. Sci. USA, 90: 10145-9, 1993). In a second method, translation is carried out in Xenopus oocytes by microinjection of mutated mRNA and chemically aminoacylated suppressor tRNAs (Turcatti, et al., J. Biol. Chem., 271: 19991-8, 1996). Within a third method, E. coli cells are cultured in the absence of a natural amino acid that is to be replaced (e.g., phenylalanine) and in the presence of the desired non-naturally occurring amino acid(s) (e.g., 2-azaphenylalanine, 3-azaphenylalanine, 4-azaphenylalanine, or 4-fluorophenylalanine). The non-naturally occurring amino acid is incorporated into the protein in place of its natural counterpart. (Koide, et al., Biochem., 33: 7470-6, 1994). Naturally occurring amino acid residues can be converted to non-naturally occurring species by in vitro chemical modification. Chemical modification can be combined with site-directed mutagenesis to further expand the range of substitutions (Wynn, et al., Protein Sci., 2: 395-403, 1993).
As used herein, the term “polynucleotide” generally refers to any polyribonucleotide or polydeoxyribonucleotide, which may be unmodified RNA or DNA or modified RNA or DNA. Thus, for instance, polynucleotides as used herein refers to, among others, single- and double-stranded DNA, DNA that is a mixture of single- and double-stranded regions, single- and double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid molecules comprising DNA and RNA that may be single-stranded or, more typically, double-stranded or a mixture of single- and double-stranded regions. The terms “nucleic acid,” “nucleic acid sequence,” or “oligonucleotide” also encompass a polynucleotide as defined above.
In addition, “polynucleotide” as used herein refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The strands in such regions may be from the same molecule or from different molecules. The regions may include all of one or more of the molecules, but more typically involve only a region of some of the molecules. One of the molecules of a triple-helical region often is an oligonucleotide.
As used herein, the term polynucleotide includes DNAs or RNAs as described above that contain one or more modified bases. Thus, DNAs or RNAs with backbones modified for stability or for other reasons are “polynucleotides” as that term is intended herein. Moreover, DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritylated bases, to name just two examples, are polynucleotides as the term is used herein.
It will be appreciated that a great variety of modifications have been made to DNA and RNA that serve many useful purposes known to those of skill in the art. The term polynucleotide as it is employed herein embraces such chemically, enzymatically, or metabolically modified forms of polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including simple and complex cells, inter alia.
By way of example, a polynucleotide sequence of the present disclosure may be identical to the reference sequence, that is be 100% identical, or it may include up to a certain integer number of nucleotide alterations as compared to the reference sequence. Such alterations are selected from the group including at least one nucleotide deletion, substitution, including transition and transversion, or insertion, and wherein said alterations may occur at the 5′ or 3′ terminus positions of the reference nucleotide sequence or anywhere between those terminus positions, interspersed either individually among the nucleotides in the reference sequence or in one or more contiguous groups within the reference sequence. The number of nucleotide alterations is determined by multiplying the total number of nucleotides in the reference nucleotide by the numerical percent of the respective percent identity (divided by 100) and subtracting that product from said total number of nucleotides in the reference nucleotide. Alterations of a polynucleotide sequence encoding the polypeptide may alter the polypeptide encoded by the polynucleotide following such alterations.
The term “codon” means a specific triplet of mononucleotides in the DNA chain or mRNA that make up an amino acid or termination signal.
The term “degenerate nucleotide sequence” denotes a sequence of nucleotides that includes one or more degenerate codons (as compared to a reference polynucleotide molecule that encodes a polypeptide). Degenerate codons contain different triplets of nucleotides, but encode the same amino acid residue (e.g., GAU and GAC triplets each encode Asp).
“Operably linked” refers to a juxtaposition wherein the components are configured so as to perform their usual function. For example, control sequences or promoters operably linked to a coding sequence are capable of effecting the expression of the coding sequence, and an organelle localization sequence operably linked to protein will direct the linked protein to be localized at the specific organelle.
As used herein, the term “exogenous DNA” or “exogenous nucleic acid sequence” or “exogenous polynucleotide” refers to a nucleic acid sequence that was introduced into a cell or organelle from an external source. Typically the introduced exogenous sequence is a recombinant sequence.
As used herein, the term “transfection” refers to the introduction of a nucleic acid sequence into the interior of a membrane enclosed space of a living cell, including introduction of the nucleic acid sequence into the cytosol of a cell as well as the interior space of a mitochondria, nucleus or chloroplast. The nucleic acid may be in the form of naked DNA or RNA, associated with various proteins, or the nucleic acid may be incorporated into a vector.
As used herein, the term “vector” or “expression vector” is used to denote a DNA molecule, linear or circular, which includes a segment encoding a polypeptide of interest operably linked to additional segments that provide for its transcription and translation upon introduction into a host cell or host cell organelles. Such additional segments include promoter and terminator sequences, and may also include one or more origins of replication, one or more selectable markers, an enhancer, a polyadenylation signal, etc. Expression vectors are generally derived from yeast or bacterial genome or plasmid DNA, animal virus genome, or viral DNA, or may contain elements of both.
“DNA regulatory sequences”, as used herein, are transcriptional and translational control sequences, such as promoters, enhancers, polyadenylation signals, termination signals, and the like, that provide for and/or regulate expression of a coding sequence in a host cell.
A “promoter sequence” is a DNA regulatory region in an operon capable of binding RNA polymerase in a cell and initiating transcription of a downstream (3′ direction) coding sequence. For purposes of defining the present invention, the promoter sequence is bound at its 3′ terminus by the transcription initiation site and extends upstream (5′ direction) to include the minimum number of bases or elements necessary to initiate transcription at levels detectable above background. Within the promoter sequence will be found a transcription initiation site, as well as protein binding domains responsible for the binding of RNA polymerase. Eukaryotic promoters will often, but not always, contain “TATA” boxes and “CAT” boxes. Various promoters, including inducible promoters, may be used to drive the various vectors of the present disclosure.
The terms “chimeric”, “fusion” and “composite” are used to denote a protein, peptide domain or nucleotide sequence or molecule containing at least two component portions that are mutually heterologous in the sense that they are not, otherwise, found directly (covalently) linked in nature. More specifically, the component portions are not found in the same continuous polypeptide or gene in nature, at least not in the same order or orientation or with the same spacing present in the chimeric protein or composite domain. Such materials contain components derived from at least two different proteins or genes or from at least two non-adjacent portions of the same protein or gene. Composite proteins, and DNA sequences that encode them, are recombinant in the sense that they contain at least two constituent portions that are not otherwise found directly linked (covalently) together in nature.
The term “domain” in this context is not intended to be limited to a single discrete folding domain.
A “reporter polynucleotide” includes any gene that expresses a detectable gene product, which may be RNA or a reporter polypeptide. Reporter genes include coding sequences for which the transcriptional and/or translational product are readily detectable or selectable.
As used herein, the term “hybridization” refers to the process of association of two nucleic acid strands to form an antiparallel duplex stabilized by means of hydrogen bonding between residues of the opposite nucleic acid strands.
“Hybridizing” and “binding”, with respect to polynucleotides, are used interchangeably. The terms “hybridizing specifically to” and “specific hybridization” and “selectively hybridize to,” as used herein refer to the binding, duplexing, or hybridizing of a nucleic acid molecule preferentially to a particular nucleotide sequence under stringent conditions.
The term “stringent assay conditions” as used herein refers to conditions that are compatible to produce binding pairs of nucleic acids, e.g., surface bound and solution phase nucleic acids, of sufficient complementarity to provide for the desired level of specificity in the assay while being less compatible to the formation of binding pairs between binding members of insufficient complementarity to provide for the desired specificity. Stringent assay conditions are the summation or combination (totality) of both hybridization and wash conditions.
“Stringent hybridization conditions” and “stringent hybridization wash conditions” in the context of nucleic acid hybridization (e.g., as in array, Southern or Northern hybridizations) are sequence dependent, and are different under different experimental parameters. Stringent hybridization conditions that can be used to identify nucleic acids within the scope of the disclosure can include, e.g., hybridization in a buffer comprising 50% formamide, 5×SSC, and 1% SDS at 42° C., or hybridization in a buffer comprising 5×SSC and 1% SDS at 65° C., both with a wash of 0.2×SSC and 0.1% SDS at 65° C. Exemplary stringent hybridization conditions can also include a hybridization in a buffer of 40% formamide, 1 M NaCl, and 1% SDS at 37° C., and a wash in 1×SSC at 45° C. Alternatively, hybridization to filter-bound DNA in 0.5 M NaHPO4, 7% sodium dodecyl sulfate (SDS), 1 mM EDTA at 65° C., and washing in 0.1×SSC/0.1% SDS at 68° C. can be employed. Yet additional stringent hybridization conditions include hybridization at 60° C. or higher and 3×SSC (450 mM sodium chloride/45 mM sodium citrate) or incubation at 42° C. in a solution containing 30% formamide, 1M NaCl, 0.5% sodium sarcosine, 50 mM MES, pH 6.5. Those of ordinary skill will readily recognize that alternative but comparable hybridization and wash conditions can be utilized to provide conditions of similar stringency.
In certain embodiments, the stringency of the wash conditions sets forth the conditions that determine whether a nucleic acid will specifically hybridized to a surface bound nucleic acid. Wash conditions used to identify nucleic acids may include, e.g.: a salt concentration of about 0.02 molar at pH 7 and a temperature of at least about 50° C. or about 55° C. to about 60° C.; or, a salt concentration of about 0.15 M NaCl at 72° C. for about 15 minutes; or, a salt concentration of about 0.2×SSC at a temperature of at least about 50° C. or about 55° C. to about 60° C. for about 15 to about 20 minutes; or, the hybridization complex is washed twice with a solution with a salt concentration of about 2×SSC containing 0.1% SDS at room temperature for 15 minutes and then washed twice by 0.1×SSC containing 0.1% SDS at 68° C. for 15 minutes; or, substantially similar conditions. Stringent conditions for washing can also be, e.g., 0.2×SSC/0.1% SDS at 42° C.
A specific example of stringent assay conditions is a rotating hybridization at 65° C. in a salt based hybridization buffer with a total monovalent cation concentration of 1.5 M (e.g., as described in U.S. patent application Ser. No. 09/655,482 filed on Sep. 5, 2000, the disclosure of which is herein incorporated by reference) followed by washes of 0.5×SSC and 0.1×SSC at room temperature.
Stringent assay conditions are hybridization conditions that are at least as stringent as the above representative conditions, where a given set of conditions are considered to be “at least as stringent” if substantially no additional binding complexes that lack sufficient complementarity to provide for the desired specificity are produced in the given set of conditions as compared to the above specific conditions, where by “substantially no more” is meant less than about 5-fold more, typically less than about 3-fold more.
By “administration” is meant introducing a sensor of the present disclosure into a subject. The preferred route of administration of the sensor is intravenous. However, any route of administration, such as oral, topical, subcutaneous, peritoneal, intraarterial, inhalation, vaginal, rectal, nasal, introduction into the cerebrospinal fluid, or instillation into body compartments can be used.
In accordance with the present disclosure, “a detectably effective amount” of the sensor of the present disclosure is defined as an amount sufficient to yield an acceptable image using equipment that is available for clinical use. A detectably effective amount of the sensor of the present disclosure may be administered in more than one injection. The detectably effective amount of the sensor of the present disclosure can vary according to factors such as the degree of susceptibility of the individual, the age, sex, and weight of the individual, idiosyncratic responses of the individual, the dosimetry, and the like. Detectably effective amounts of the sensor of the present disclosure can also vary according to instrument and film-related factors. Optimization of such factors is well within the level of skill in the art.
As used herein the term “isolated” is meant to describe a polynucleotide, a polypeptide, an antibody, or a host cell that is in an environment different from that in which the polynucleotide, the polypeptide, the antibody, or the host cell naturally occurs.
As used herein, the term “organelle” refers to cellular membrane-bound structures such as the chloroplast, mitochondrion, and nucleus. The term “organelle” includes natural and synthetic organelles.
As used herein, the term “non-nuclear organelle” refers to any cellular membrane bound structure present in a cell, except the nucleus.
As used herein, the term “host” or “organism” includes humans, mammals (e.g., cats, dogs, horses, etc.), living cells, and other living organisms. A living organism can be as simple as, for example, a single eukaryotic cell or as complex as a mammal. Typical hosts to which embodiments of the present disclosure may be administered will be mammals, particularly primates, especially humans. For veterinary applications, a wide variety of subjects will be suitable, e.g., livestock such as cattle, sheep, goats, cows, swine, and the like; poultry such as chickens, ducks, geese, turkeys, and the like; and domesticated animals particularly pets such as dogs and cats. For diagnostic or research applications, a wide variety of mammals will be suitable subjects, including rodents (e.g., mice, rats, hamsters), rabbits, primates, and swine such as inbred pigs and the like. Additionally, for in vitro applications, such as in vitro diagnostic and research applications, body fluids and cell samples of the above subjects will be suitable for use, such as mammalian (particularly primate such as human) blood, urine, or tissue samples, or blood, urine, or tissue samples of the animals mentioned for veterinary applications.
General Discussion
Embodiments of the present disclosure include: ligand-regulable transactivation systems, methods of producing ligand-regulable transactivation systems, methods of using ligand-regulable transactivation systems, reporter polynucleotides, methods of producing reporter polynucleotides, activator fusion proteins, methods of producing activator fusion proteins, methods of regulating gene expression in vitro and in vivo for gene therapy, methods of screening estrogen receptor modulators with therapeutic treatments (e.g., anticancer, antiosteoporosis, and hormone replacement treatments), methods of screening compounds (e.g., drugs and environmental pollutants) for the estrogenic effect, and methods of evaluating the estrogen receptor pathway under different pathological conditions.
The ligand-regulable transactivation system includes a reporter polynucleotide and an activator fusion protein. The reporter polynucleotide includes, but is not limited to, a binding sequence, a promoter sequence, and a reporter sequence. The binding sequence is connected (e.g., directly or indirectly with a linker) with the promoter sequence, and the promoter sequence is connected (e.g., directly or indirectly with a linker) with the reporter sequence. The activator fusion protein includes, but is not limited to, a DNA binding domain, an estrogen receptor folding domain, and a transactivation domain. The DNA binding domain is connected (e.g., directly or indirectly with a linker) to the estrogen receptor folding domain, and the estrogen receptor folding domain is connected (e.g., directly or indirectly with a linker) with the transactivation domain. An illustrative embodiment of the ligand-regulable transactivation system is discussed in reference to Example 1 and depicted in FIG. 1.
Embodiments of the present disclosure can be used in cell cultures and in living animals by customizing the reporter sequence (polynucleotide), while not changing the activator fusion protein. In an embodiment, if the aim of the study is for a therapeutic approach for cancer therapy it is possible to introduce thymidine kinase (suicidal therapeutic gene) in the place of luciferase. In another embodiment, if the aim is to correct some naturally defective gene, it is possible to introduce that particular gene in active form in the place of luciferase.
Embodiments of the present disclosure can be used to screen a library of compounds for their estrogen receptor (ER) binding properties. In addition, embodiments of the present disclosure can be designed to distinguish between ER ligands and non-ER ligands and between/among ER agonists, partial ER agonists, ER antagonists, partial ER antagonists, and/or Selective Estrogen Receptor Modulators (SERMs) by exposing the compound to a cell line or host transfected with the reporter polynucleotide and the activator fusion protein vector or with a transgenic animal incorporating the ligand-regulable transactivation system.
Illustrative embodiments of the agonists can include, but are not limited to, estradiol, diethylstilbestrol, diarylpropionitrile, genistein and tetrahydrocannabinol. Illustrative embodiments of the antagonists can include, but are not limited to, methylpiperidinopyrazole and ICI 182780. Illustrative embodiments of the SERM can include, but are not limited to, hydroxytamoxifen, raloxifene, and tamoxifen. It should be noted that SERMs tend to have a mixed action (agonist and antagonist), but tend to be more similar to how an antagonist affects embodiments of the present disclosure. Distinguishing a SERM from an agonist and/or an antagonist can be conducted in a similar manner as described below for an agonist and an antagonist.
As mentioned above, the activator fusion protein includes the DNA binding domain, the ER folding domain, and the transactivation domain. The ER folding domain can be designed in such a way that it can distinguish between different types of compounds and be used in different systems. For example, the ER folding domain can be designed to distinguish between ER ligands and non-ER ligands and between/among ER agonists, partial ER agonists, ER antagonists, partial ER antagonists, and/or SERMs. In another example, the ER folding domain can be designed to reduce interaction between the ER ligand binding domain and endogenous ER ligands (e.g., 17β-estradiol). Reducing the interaction with the endogenous ER ligands enhances the ligand-regulable transactivation system's ability to be used in living hosts.
In an embodiment, the ER folding domain has a folding arrangement in a three-dimensional space. The ER folding domain can undergo a conformation change into one or more folding arrangements under the inducement of a compound (e.g., ER ligands, and ER agonists, partial ER agonists, ER antagonists, partial ER antagonists, and SERMs).
In an embodiment, the interaction of the ER folding domain with a first compound (or first type or class of compound) (e.g., antagonist, See Example 1) alters the activator fusion protein to a first conformational position (e.g., a three-dimensional folding arrangement). In the first conformational position, the transactivation domain of the fusion protein bound with the binding sequence can substantially interact with the promoter sequence and activates the promoter to transcribe the reporter polynucleotide, which causes the reporter sequence to generate a bioluminescent protein (or in another embodiment a fluorescent protein or enzyme). The bioluminescent protein can interact with a first amount of a bioluminescence initiating compound (or compound appropriate for the fluorescent protein or enzyme) to produce an emission that can be detected and measured. Thus, embodiments of the present disclosure can be used to detect, measure, quantitate, image, and the like, interactions of compounds with the ER folding domain of the activator fusion protein.
In an embodiment, the interaction of the ER folding domain with a second compound (or second type or class of compound) (e.g., agonist, See Example 1) alters the activator fusion protein to a second conformational position. The second conformational position positions the DNA binding domain and the transactivation domain so that both can interact with the binding sequence and partially activate the promoter sequence of the reporter polynucleotide, which causes the reporter sequence to generate a second amount of a bioluminescent protein. The bioluminescent protein can interact with a bioluminescence initiating compound to produce an emission that can be detected and measured. Thus, embodiments of the present disclosure can be used to detect, measure, quantitate, image, and the like, interactions of compounds with the ER folding domain of the activator fusion protein.
In an embodiment, the interaction of the ER folding domain with a third compound (or third type or class of compound) (e.g., control, See Example 1) alters the activator fusion protein to a third conformational position. The third conformational position positions the DNA binding domain and the transactivation domain so that both do not interact with the binding sequence and activate to a negligible degree (less than about 1% of the first confirmation) of the promoter sequence of the reporter polynucleotide, and the reporter sequence does not generate a bioluminescent protein. Thus, embodiments of the present disclosure can be used to detect, measure, quantitate, image, and the like, interactions of compounds with the ER folding domain of the activator fusion protein.
The first amount of bioluminescent protein is greater than the second amount of bioluminescent protein. Thus, the amount of bioluminescent energy generated by the first compound (e.g., antagonist) is greater than and distinguishable from the amount of bioluminescent energy generated by the second compound (e.g., agonist). It should be noted that a plurality of second compounds could be distinguished among one another based on relatively different amounts of partial interaction. Therefore, an antagonist, partial antagonist, an agonist, and a partial agonist are distinguishable using embodiments of the present disclosure.
The term “substantially interact” means that the first conformational position of the DNA binding domain and the transactivation domain interact with the binding sequence and the promoter sequence of the reporter polynucleotide to a greater degree than when the ER folding domain is in the second conformational position.
The term “partially interact” means that the second conformational position of the DNA binding domain and the transactivation domain interact with the binding sequence and the promoter sequence of the reporter polynucleotide to a greater degree than when the ER folding domain is in the third conformational position. As mentioned above, the term “partially interact” can correspond to a plurality of second conformational positions, and each partial interaction could be distinguishable from other partial interactions.
In other words, there can be a measurable and statistically significant difference (e.g., a statistically significant difference is enough of a difference to distinguish among the different states, such as about 0.1%, 1%, 3%, 5%, 10%, 15%, 20%, 25%, 30%, or 40% or more difference between the amount of energy emitted in each state, where the statistically significant difference is determined, at least in part, by the components of the ligand-regulable transactivation system as well as the detection system) between “substantially interact” and “partially interact”, between “partially interact” and “does not interact”, and between two degrees of “partially interact” for two different ligands that partially interact with the ER folding domain. The measurable difference can be used to distinguish between instances where a particular ligand substantially interacts, partially interact(s), or does not interact. Standards can be used to determine the relative amount of energy that is emitted. Additional details are described in the Example.
Embodiments of the present disclosure can be used to detect, study, monitor, evaluate, and/or screen, biological events in vivo and/or in vitro, such as, but not limited to, ER related interactions with ER ligands and non-ER-ligands. In addition, embodiments of the present disclosure can be used to screen molecules (e.g., drugs) related to the ER interactions with ER ligands and non-ER-ligands using methods described herein are methods similar to those described herein.
Embodiments of the present disclosure can be used to detect (and visualize) and/or quantitate ER related interactions events in in vitro as well as in in vivo studies, which can decrease time and expense since the same system can be used for cells and living organisms. Embodiments of the present disclosure can be used to test an event occurrence in a large number of samples, and has the capacity to transition from single cells to living animals without changing or substantially changing the ligand-regulable transactivation system. In an embodiment, the ER folding domain is the only portion of the ligand-regulable transactivation system that is changed.
In an embodiment, the ligand-regulable transactivation system can be used in methods of detecting an ER agonist and an ER antagonist using a ligand-regulable transactivation system having a ER folding domain designed to distinguish between ER agonists and ER antagonists (See Example 1). The ligand-regulable transactivation system or components thereof are expressed in, introduced to, and/or are part of a cell or a host. A ligand is introduced to the cell or host. The ER ligand (e.g., agonist, antagonist, or SERMs) may interact with the ER folding domain and may cause a conformational change as described above. Upon interaction of the activator fusion protein with the reporter polynucleotide, a bioluminescent protein is generated. A bioluminescence initiating compound is introduced to the system (prior to and/or after the agonist or antagonist). If a bioluminescent signal is detected, a conformational change occurred. If no bioluminescent signal is detected, a conformational change did not occur. The intensity and/or strength of the bioluminescent signal can be used to determine if the ligand is an agonist (or partial agonist), antagonist (or partial antagonist), or SERM. Standards could be used to assist in determining the relative strength between energy admitted as a result of an agonist and an antagonist. Additional details are described in the Example.
It should be noted that the same or similar methods and the same or similar ligand-regulable transactivation systems (e.g., one could modify the ER folding domain in accordance with the compounds and/or conditions being tested) could be used for distinguishing among ER agonists, partial ER agonists, ER antagonists, partial ER antagonists, and/or SERMs by changing the length of ER-ligand binding domain of amino acids 281-549 instead of 281-595 in the activator fusion protein.
In addition, the same or similar methods and the same or similar ligand-regulable transactivation systems can be used in methods of screening estrogen receptor modulators with therapeutic treatments (e.g., anticancer, antiosteoporosis, and hormone replacement therapies).
Further, the same or similar methods and the same or similar ligand-regulable transactivation systems can be used in methods of screening compounds (e.g., drugs and environmental pollutants) for the estrogenic effect.
Furthermore, the same or similar methods and the same or similar ligand-regulable transactivation systems can be used in methods of evaluating the estrogen receptor pathway under different pathological conditions by using the activator fusion protein containing the ER-ligand binding domain of both the lengths (amino acids 281-549 and 281-595).
Note that for each ligand-regulable transactivation system, protein, fusion protein, protein fragment, and nucleotide, one skilled in the art would be able to determine the corresponding nucleotide sequence or protein sequence, respectively, and be able to introduce or express each into a system of interest.
In general, ligand-regulable transactivation system can be used in vivo and/or in vitro. In an embodiment, the ligand-regulable transactivation system or components thereof can be introduced into a system (e.g., inside a cell or outside a cell and/or a to host), the ligand-regulable transactivation system or components thereof can be expressed (e.g., using a vector) in the system, and/or the ligand-regulable transactivation system or components thereof can be included in a transgenic animal or plant. In an embodiment, the ligand-regulable transactivation system or components thereof can be introduced into a host or organism in vivo.
The methods of the present disclosure can be conducted in vitro or in vivo. The ligand-regulable transactivation system or components thereof can be introduced, incorporated into, or expressed in a part of a cell or a host. The host can include a transgenic animal or transgenic plant.
In another embodiment, the ER folding domain can be designed to reduce interaction between the ER folding domain and endogenous ER ligands. This mutation enhances the ability to use the ER intramolecular folding system in living hosts. In this regard, the ER folding domain is designed to reduce the interaction between the ER folding domain and 17β-estradiol. In an embodiment, the sequence of the ER folding domain can be modified by changing the amino acid at a position 521 from glycine to threonine (SEQ. ID No. 3), which reduced interaction of the ER folding domain with 17β-estradiol by about 95%, while only reducing the interaction of the ER folding domain with other ER ligands by about 10-20%. The change from glycine to threonine (SEQ. ID Nos. 3, 23, and 24) was conducted by creating a mutation at 521 with all 20 amino acids and screening with more than 10 ER-ligands. It should also be noted that in other embodiments the amino acid at position 521 could be changed from glycine to any one of the other amino acids (e.g., the other 19 amino acids (e.g., SEQ ID Nos. 23, 24, 25, and 26), which is described in more detail in the Example.
Activator Fusion Protein
As mentioned above, the activator fusion protein includes, but is not limited to, a DNA binding domain, an estrogen receptor folding domain, and a transactivation domain. Linking polypeptides (described below) can be included in the activator fusion protein to connect one or more of the DNA binding domain, the estrogen receptor folding domain, and the transactivation domain. The activator polynucleotide can encode the activator fusion protein. The activator polynucleotide sequence can be included in an expression system (e.g., a vector) and expressed in a cell line or in a host organism (e.g., prokaryotes or eukaryotes) to produce the activator fusion protein. Methods of producing vectors, other expression systems, (e.g., viral and non-viral) and polynucleotides are well known in the art. It should be noted that the activator fusion protein can be expressed using other expression systems and the vector is merely an illustrative embodiment. Additional details regarding the reporter polynucleotide are discussed in Example 1.
DNA Binding Domain
As used herein, the term “DNA-binding domain” encompasses a small (about 150 amino acids) peptide sequence of a DNA-binding protein, up to the entire length of a DNA-binding protein, so long as the DNA-binding domain functions to associate with a particular response element (e.g., has a specific DNA binding activity towards a DNA sequence). The DNA binding domain refers to the portion of the fusion protein that interacts with the corresponding binding sequence on the reporter polynucleotide. The DNA binding domain can be from Yeast or from another organism that can include, but is not limited to, a bacteria, a human, a mouse, a rat, and the like. The DNA binding domain can include, but is not limited to, GAL4 DNA binding domain (e.g., the transcription factor of yeast) (SEQ. ID. No: 13 (polynucleotide) and 14 (polypeptide)), and the like. The DNA binding domain of the yeast GAL4 protein includes at least the first 74 amino terminal amino acids thereof (SEQ. ID. No: 14) or the GAL4 protein described in the example below (see, for example, Keegan et al., Science 231:699 704 (1986) which is incorporated herein by reference). Preferably, the first 90 or more amino terminal amino acids of the GAL4 protein (SEQ. ID. No: 14) will be used, with the 147 amino terminal amino acid residues of yeast GAL4 (SEQ. ID. No: 14) being presently most preferred.
The DNA binding domain and the binding sequence on the reporter polynucleotide are selected so that they interact in an appropriate manner for the ligand-regulable transactivation system. The selection depends, in part, on one or more of the following: the DNA binding domain, the binding sequence, the ER folding domain, the transactivation domain, the promoter sequence, and the reporter sequence.
Estrogen Receptor Folding Domain
The ER folding domain has already been discussed in detail elsewhere in this disclosure. The ER folding domain can have a sequence selected from: SEQ. ID No. 1 (human estrogen receptor, alpha, amino acids 281-549), SEQ. ID No. 2 (human estrogen receptor, alpha, amino acids 281-595), SEQ. ID No. 3 (human estrogen receptor, alpha, amino acids 1-595), SEQ. ID No. 4 (mouse estrogen receptor, alpha, amino acids 281-549), SEQ. ID No.5 (mouse estrogen receptor, alpha, amino acids 281-599), SEQ. ID No. 6 (mouse estrogen receptor amino acids 1-599) and SEQ. ID No. 27 (estrogen receptor beta).
In an embodiment, the ER folding domain is designed to reduce the interaction between the ER folding domain and 17β-estradiol. In an embodiment, the sequence of the ER folding domain can be modified by changing the amino acid at position 521 from glycine to threonine (SEQ ID Nos. 3, 23 and 24), which reduced interaction of the ER folding domain with 17β-estradiol by about 95%, while only reducing the interaction of the ER folding domain with other ER ligands slightly. Additional details are described in the Example. It should also be noted that the amino acid at position 521 could be changed from glycine to any one of the other amino acids (e.g., the other 19 amino acids (e.g., SEQ ID Nos. 23, 24, 25, and 26)).
Transactivation Domain
A transactivation domain refers to a polypeptide, which acts to activate transcription of a target nucleotide (e.g., gene). The transactivation domain refers to the portion of the fusion protein that interacts with the corresponding promoter sequence on the reporter polynucleotide. The transactivation domain can include, but is not limited to, VP16 transactivation domain (SEQ. ID No: 15 (polynucleotide) and 16 (polypeptide)) and the like.
The transactivation domain and the promoter sequence on the reporter polynucleotide are selected so that they interact in an appropriate manner for the ligand-regulable transactivation system. The selection depends, in part, on one or more of the following: the DNA binding domain, the binding sequence, the ER folding domain, the transactivation domain, the promoter sequence, and the reporter sequence.
Reporter Polynucleotide
In general, a “reporter polynucleotide” includes a polynucleotide that expresses a reporter polypeptide. Reporter polynucleotides include coding sequences for which the transcriptional and/or translational product are readily detectable or selectable (e.g., a bioluminescent protein). As mentioned above, the reporter polynucleotide includes, but is not limited to, a binding sequence, a promoter sequence, and a reporter sequence. The reporter polynucleotide can be included in an expression system (e.g., a vector) and expressed in a cell line or in a host. Methods of producing vectors, other expression systems, (e.g., viral and non-viral) and polynucleotides are well known in the art. It should be noted that the reporter polynucleotide can be incorporated in other expression systems and the vector is merely an illustrative embodiment. Additional details regarding the reporter polynucleotide are discussed in Example 1.
Binding Sequence
A binding sequence is a segment of DNA that is necessary and sufficient to specifically interact with a given polypeptide (e.g., the DNA binding domain). The binding sequence may include the repetition of the same polynucleotide sequence to enhance the activation of downstream protein expression by attracting more DNA binding domains (e.g., provide more than one location for binding). Each of these DNA binding domains can provide more strength for the transcription machinery. The binding sequence can include, but is not limited to, a GAL4 binding sequence (SEQ. ID No: 17) and the like. In an embodiment, since the GAL4 DNA binding domain is from Yeast, a eukaryotic organism, it will have more suitable conditions folding and binding efficiencies when used in these systems in activating genes for gene therapy applications in animals and animal cells.
Promoter Sequence
The promoter sequence is a sequence that enables the reporter polynucleotide to transcribe and generate the bioluminescent protein through processes known in the art such as providing the space for the RNA polymerase to bind and initiate mRNA synthesis. The promoter sequence can include, but is not limited to, an E4 promoter (SEQ. ID No: 36), an E4 minimal promoter (SEQ. ID No: 18), minimal promoter thymidine kinase (tk-promoter) (SEQ. ID No: 37), adenoviral late promoter (SEQ. ID No: 38), and the like. The E4 minimal report may generate a low leaky signal before the system is getting transactivated by transactivation domain.
Reporter Polynucleotides and Polypeptides
The reporter polynucleotide encodes a bioluminescent protein, fluorescent protein, or enzyme that has a detectable substrate either through calorimetric or by other mode that can be quantified. In an embodiment of the present disclosure, the reporter polypeptide can include, but is not limited to, Luciferases or photoproteins. In an embodiment, the reporter polypeptide can include, but is not limited to, Renilla Luciferase (the nucleotide sequence is SEQ ID: 7) and the amino acid sequence is SEQ ID: No 8), portions thereof, mutants thereof, variants thereof; Coleoptera Luciferase (the nucleotide sequence is SEQ ID: No 9, and the amino acid sequence is SEQ ID: No 10), portions thereof, mutants thereof, variants thereof; Firefly Luciferase (the nucleotide sequence is SEQ ID: No 11 and the amino acid sequence is SEQ ID: No 12), portions thereof, mutants thereof, variants thereof; Gaussia Luciferase (the nucleotide sequence is SEQ ID: No 28 and the amino acid sequence is SEQ ID: No 29), portions thereof, mutants thereof, variants thereof; aqeuorin photoproteinm Luciferase (the nucleotide sequence is SEQ ID: No 30, and the amino acid sequence is SEQ ID: No 31), portions thereof, mutants thereof, variants thereof; and bacterial luciferase (the nucleotide sequence is SEQ ID: No 32, and the amino acid sequence is SEQ ID: No 33), portions thereof, mutants thereof, variants thereof; green fluorescent protein (GFP) (SEQ ID No: 19), portions thereof, mutants thereof, variants thereof, and conservatively modified variants; red fluorescent protein (RFP) (SEQ ID No: 20), portions thereof, mutants thereof, variants thereof, and conservatively modified variants; β-galactosidase (SEQ ID No: 21), portions thereof, mutants thereof, variants thereof, and conservatively modified variants; and β-lactamase (SEQ ID No: 22) portions thereof, mutants thereof, variants thereof, and conservatively modified variants; and the like.
The reporter polynucleotide sequence corresponds to the reporter polypeptide. One skilled in the art can determine the reporter polynucleotide sequence based on the reporter polypeptide sequence or vice versa. The reporter polynucleotide sequence can be included in an expression system (e.g., a vector) and expressed in a cell line or in a host.
The term “mutant” is employed broadly to refer to a protein that differs in some way from a reference wild-type protein, where the protein may retain biological properties of the reference wild-type (e.g., naturally occurring) protein, or may have biological properties that differ from the reference wild-type protein. The term “biological property” of the subject proteins includes, but is not limited to, spectral properties, such as emission maximum, quantum yield, and brightness, the ability to catalyze the conversion of a coelenterazine substrate into a luminescent product in the presence of molecular oxygen, and the like; in vivo and/or in vitro stability (e.g., half-life); and the like. Mutants can include single amino acid changes (point mutations), deletions of one or more amino acids (point-deletions), N-terminal truncations, C-terminal truncations, insertions, and the like. Mutants can be generated using standard techniques of molecular biology.
Expression of the Reporter Sequence
As discussed above, the expression of the reporter sequence produces a bioluminescent protein. The bioluminescent protein can interact with a bioluminescence initiating compound to produce (e.g., emission from the bioluminescent protein) a bioluminescent energy.
Bioluminescence Initiating Compound
As mentioned above, the bioluminescent protein is used in conjunction with a bioluminescence initiating compound to produce a radiation emission. The bioluminescence initiating compound can include, but is not limited to, coelenterazine, analogs, and functional derivatives thereof, and D-luciferin analogs, and functional derivatives thereof. Derivatives of coelenterazine include, but are not limited to, coelenterazine 400a, coelenterazine cp, coelenterazine f, coelenterazine fcp, coelenterazine h, coelenterazine hcp; coelenterazine ip, coelenterazine n, coelenterazine O, coelenterazine c, coelenterazine c, coelenterazine i, coelenterazine icp, coelenterazine 2-methyl, and deep blue coelenterazine (DBC) (described in more detail in U.S. Pat. Nos. 6,020,192; 5,968,750 and 5,874,304). In an embodiment, the bioluminescence initiating compound can be D-luciferin when the bioluminescence compound is Firefly Luciferase.
In general, coelenterazines are known to luminesce when acted upon by a wide variety of bioluminescent proteins, specifically luciferases. Useful, but non-limiting, coelenterazines are disclosed in U.S. patent application Ser. No. 10/053,482, filed Nov. 2, 2001, the disclosure which is hereby incorporated by reference in its entirety. Coelenterazines are available from Promega Corporation, Madison, Wis. and from Molecular Probes, Inc., Eugene, Oreg. Coelenterazines may also be synthesized as described for example in Shimomura et al., Biochem. J. 261: 913-20, 1989; Inouye et al., Biochem. Biophys. Res. Comm. 233: 349-53, 1997; and Teranishi et al., Anal. Biochem. 249: 37-43, 1997.
Linkers
It should be noted that peptide linkers could be positioned between one or more of the components of the reporter polynucleotide (e.g., a binding sequence, a promoter sequence, and a reporter sequence) and the activator fusion protein (e.g., a DNA binding domain, an estrogen receptor folding domain, and a transactivation domain). In an embodiment, the GGGGSGGGGS (SEQ. ID No. 34) and/or the GGGGSGGGGSGGGGS peptide linker (SEQ. ID No. 35) can be used between one or more of the components of the reporter polynucleotide and the activator fusion protein.
Additional Methods of Use
In an embodiment, the ligand-regulable transactivation systems and methods described herein can be used to monitor and assess biological interactions by modifying vector constructs (e.g., ER interactions) in a transgenic animal or a transgenic plant.
In another embodiment, a cell line or transgenic animal is marked with vector sets described herein that are developed utilizing coding regions of sequences for the ligand-regulable transactivation system, for example, followed by optical imaging to image and/or quantitate ER related events in the presence and absence of molecules (e.g., pharmaceuticals) designed to modulate the interaction. As will be appreciated by the skilled practitioner, this technique will significantly accelerate drug validation by allowing testing in vivo.
In this regard, the present disclosure also includes transgenic animals comprising exogenous DNA incorporated into the animal's cells to effect a permanent or transient genetic change, preferably a permanent genetic change. Permanent genetic change is generally achieved by introduction of the DNA into the genome of the cell. Vectors for stable integration include plasmids, retroviruses and other animal viruses, YACS, and the like. Generally, transgenic animals are mammals, most typically mice.
The exogenous nucleic acid sequence may be present as an extrachromosomal element or stably integrated in all or a portion of the animal's cells, especially in germ cells.
Unless otherwise indicated, a transgenic animal includes stable changes to the GERMLINE sequence. During the initial construction of the animal, chimeric animals (chimeras) are generated, in which a subset of cells has the altered genome. Chimeras may then be bred to generate offspring heterozygous for the transgene. Male and female heterozygotes may then be bred to generate homozygous transgenic animals.
Typically, transgenic animals are generated using transgenes from a different species or transgenes with an altered nucleic acid sequence. For example, a human gene may be introduced as a transgene into the genome of a mouse or other animal. The introduced gene may be a wild-type gene, naturally occurring polymorphism, or a genetically manipulated sequence, for example having deletions, substitutions or insertions in the coding or non-coding regions.
For example, an introduced transgene may include genes corresponding to the ER folding system, which may become functional via complementation or reconstitution when exposed to appropriate test proteins or, alternatively, which may become non-functional when exposed to a particular test protein that blocks phosphorylation. Such a transgene, when introduced into a transgenic animal or cells in culture, is useful for testing potential therapeutic agents known or believed to interact with a particular target protein implicated in a disease or disorder. Where the introduced gene is a coding sequence, it is usually operably linked to a promoter, which may be constitutive or inducible, and other regulatory sequences required for expression in the host animal.
Transgenic animals can be produced by any suitable method known in the art, such as manipulation of embryos, embryonic stem cells, etc. Transgenic animals may be made through homologous recombination, where the endogenous locus is altered. Alternatively, a nucleic acid construct is randomly integrated into the genome. Vectors for stable integration include plasmids, retroviruses and other animal viruses, YACS, and the like.
Numerous methods for preparing transgenic animals are now known and others will likely be developed. See, e.g., U.S. Pats. Nos. 6,252,131, 6,455,757, 6,028,245, and 5,766,879, all incorporated herein by reference. Any method that produces a transgenic animal expressing a reporter gene following complementation or reconstitution is suitable for use in the practice of the present invention. The microinjection technique is particularly useful for incorporating transgenes into the genome without the accompanying removal of other genes.
Kits
This disclosure encompasses kits that include, but are not limited to, a ligand-regulable transactivation system or vectors thereof; a bioluminescence initiating compound; and directions (written instructions for their use). The components listed above can be tailored to the particular biological event (e.g., ER related events) to be monitored as described herein. The kit can further include appropriate buffers and reagents known in the art for administering various combinations of the components listed above to the host cell or host organism. The components of the present disclosure and carrier may be provided in solution or in lyophilized form. When the components of the kit are in lyophilized form, the kit may optionally contain a sterile and physiologically acceptable reconstitution medium such as water, saline, buffered saline, and the like.
It should be noted that ratios, concentrations, amounts, and other numerical data may be expressed herein in a range format. It is to be understood that such a range format is used for convenience and brevity, and thus, should be interpreted in a flexible manner to include not only the numerical values explicitly recited as the limits of the range, but also to include all the individual numerical values or sub-ranges encompassed within that range as if each numerical value and sub-range is explicitly recited. To illustrate, a concentration range of “about 0.1% to 5%” should be interpreted to include not only the explicitly recited concentration of about 0.1 wt % to about 5 wt %, but also include individual concentrations (e.g., 1%, 2%, 3%, and 4%) and the sub-ranges (e.g., 0.5%, 1.1%, 2.2%, 3.3%, and 4.4%) within the indicated range. The term “about” can include ±1%, ±2%, ±3%, ±4%, ±5%, ±6%, ±7%, ±8%, ±9%, or ±10%, or more of the numerical value(s) being modified. In addition, the phrase “about ‘x’ to ‘y’” includes “about ‘x’ to about ‘y’”.
The above discussion is meant to be illustrative of the principles and various embodiments of the present disclosure. Numerous variations and modifications will become apparent to those skilled in the art once the above disclosure is fully appreciated. It is intended that the following claims be interpreted to embrace all such variations and modifications.
Example
Now having described the embodiments of the disclosure, in general, the example describes some additional embodiments. While embodiments of present disclosure are described in connection with the example and the corresponding text and figures, there is no intent to limit embodiments of the disclosure to these descriptions. On the contrary, the intent is to cover all alternatives, modifications, and equivalents included within the spirit and scope of embodiments of the present disclosure.
Introduction
In this Example the property of estrogen receptor that usually changes its conformation in response to its ligand bindings, that specifically brings the N- and C-termini of the protein near by each other, is used in combination with the HSV1-VP16 transactivator and the Yeast DNA binding domain, to develop the current ligand-regulable transactivation system. This Example illustrates the use of the ligand binding domain of estrogen receptor as used in a fusion protein with the GAL4 binding domain and VP16 transactivation domain on either side (FIG. 1). The system was studied in cells and cell implants in living animals by non-invasive imaging. It was also shown that this system can be activated by different ER-ligands and the mutant form developed is independent of binding with the endogenous ligand. In addition, by controlling the length of ER-ligand binding domain, a system that can differentiate ER-ligands as agonist and antagonist was developed. Further, a mutant form of ER was used form a system that specifically showed low affinity for endogenous ER-ligand 17β-estradiol for the extension of this system in living animals.
Results
Development of ER-ligand induced transactivation system. To develop an ER-ligand induced transactivation system, a series of vectors were constructed that constitutively express fusion proteins containing a Yeast GAL4-DNA binding domain and a transactivator peptide of human herpes simplex virus type 1 (HSV1-VP16) with ER-ligand binding domains of different lengths. These vectors were used in combination with the reporter vector flanking five times repeats of a Yeast GAL4-DNA binding sequence, an E4 minimal promoter and the reporter gene of choice, for different co-transfection experiments. As a positive control, a vector constitutively expressing fusion protein containing a Yeast DNA binding domain directly fused to a HSV1-VP16-transactivator peptide (hereinafter, this will be stated as constitutive transactivation system) was used. Both of these systems were studied in different cell lines and cell implants in living animals (FIG. 1).
Comparison of ER-ligand induced transactivation system with the constitutive transactivation system in transiently transfected 293T cells. To study the efficiency of ER-ligand induced transactivation system, the system was compared with the constitutive transactivation system in transiently transfected 293T cells before and after exposed to 1 μM concentration of ER-ligand 17β-estradiol. The result shows significant level of luciferase signal from the cells transfected with the constitutively active system both before and after exposed to ligand 17β-estradiol (p<0.001). At the same time the cells transfected with the activatable system shows luciferase signal only from the cells exposed to 17β-estradiol (p<0.001). The cells transfected with the activatable system exposed to carrier control (DMSO) shows signal that is slightly above the mock-transfected cells (FIG. 2).
Comparison of estrogen receptor ligand induced transactivation system with adenoviral early and late minimal promoters. To compare the efficiency of adenoviral early and late minimal promoters in ligand induced transactivation system, the 293T cells co-transfected with the system containing these promoters were analyzed for luciferase activity before and after exposed to 1 μM concentration of ligand 17β-estradiol. The result shows significant level of activity from both the systems only after exposed to ligand 17β-estradiol (p<0.0001). The system containing the adenoviral late promoter shows luciferase activity that is significantly greater than with the system containing the early promoter (p<0.01: 10±3 fold). When the cells are exposed to ligand 17β-estradiol, the signal increased 3,000±200 fold more than the cells not exposed to 17β-estradiol (1.8±0.4×108 RLU/μg Protein Vs 6.0±1.8×104) (FIG. 3).
Ligand concentration dependent activation of reporter gene expression in transiently transfected 293T and CHO cells. To check the system dose dependent response to different concentrations of ligand, 293T and CHO cells transiently co-transfected with the activator and the reporter plasmids were activated with several concentrations of 17β-estradiol ranged from 0 to 1 μM. The result shows concentration dependent increase in the level of reporter gene expression in both the cell lines used for the study. It shows significant correlation between the concentration of ligand used and the luciferase signal produced (CHO: R2=0.9063; 293T: R2=0.9581) (FIG. 4).
Transactivation of reporter gene expression by different ER-ligands. In addition to the ligand concentration dependent activation of reporter gene expression by 17β-estradiol, this system has advantage in the availability of several ligands. Hence, to study the utility of other ligands in activating the system, 293T cells transiently co-transfected with the activator and the reporter plasmids were exposed to 1 μM concentration of 7 different ER-ligands including a non-ligand anticancer drug. The system shows significant levels of transactivation by all of the different ER-ligands used for the study (p<0.001). At the same time the non-ligand anticancer drug shows signal that is not significantly different from the cells exposed to carrier control. Even though all the ER-ligands showed significant levels of activation upon the system, the level of induction was different for each ligand. The fold luciferase signal produced by different ER-ligands in comparison to carrier control are; Raloxifene: 2800±400, Tamoxifen: 2000±300, 4-hydroxy tamoxifen: 3000±500, Genistein: 600±100, Diethylstilbestrol: 2200±300, 173-estradiol: 2400±100 and ICI: 300±80 (FIG. 5a). To confirm the ligand induced increase in the level of reporter protein is due to the ER-folding mediated transactivation, 293T cells co-transfected with the reporter and activator plasmids were Western blot analyzed after inducing with various ligands for 18 h for both the reporter protein and the activator fusion chimera. The result shows the increase in the level of reporter protein expression is not due to the increase in the activator protein level. It is due to the change in the ligand induced folding in ER and the following activation in response to ligands (FIG. 5b).
Efficiency of ligand induced transactivation system in activating the reporter gene expression in a bi-directional vector. To check the utility of ligand induced transactivation system in regulating two reporter genes expressing in two different directions, the plasmid vector expressing the activator fusion protein chimera containing ER was used along with the bi-directional vector developed and evaluated previously (Ray, S. et al. A Novel Bi-Directional Vector Strategy for Amplification of Therapeutic and Reporter Gene Expression. Human Gene Therapy (2004), which is incorporated herein by reference). Co-transfection of these two vectors in 293T cells were assayed for both firefly and renilla luciferases after exposed to different concentrations of ligand 178-estradiol for 18 h. The result shows ligand concentration dependent increase by both the reporters. The analysis of the expression levels of two reporters in response to different concentrations of ligand shows highly significant correlation (R2=0.9936) (FIGS. 6A and 6B).
Ligand induced transactivation system to differentiate ER-ligands. As the estrogen receptor was used to develop the current ligand induced transactivation system for the controlled expression of transgenes, this study was extended for adopting the systems utility in screening new ER-ligands and also modified the system to differentiate ER-ligands as agonists and antagonists. From our previous study it was learned that by adjusting the length of ER-ligand binding domain; it will be possible to change the folding pattern of ER in response to different ligands and its associated reporter fragment complementation (under communication). The same strategy was used in this system and achieved similar result. An activator plasmid expressing the fusion protein chimera was constructed and contained the ER of amino acids from 281 to 549. The system was studied in transiently co-transfected 293T cells by exposing to different ER-ligands (agonist, antagonist, partial agonists and partial antagonists) (FIG. 7).
Ligand induced transactivation system with mutant form of ER-ligand binding domains. To extend this system utilization in living animals, the problem of endogenous estrogen that usually interferes was considered. A mutant form of estrogen receptor hERG521T was identified with specifically low affinity to 17β-estradiol. The system with the mutant form of ER showed significant level of activity without loosing any activity for other ligands (FIG. 8).
Imaging ligand induced transactivation system in living animals. To image ligand induced transactivation system in living animals, the 293T cells transiently co-transfected with the reporter and the activator plasmids expressing fusion chimera containing the mutant form of ER (G521T/amino acids 281-599) were implanted subcutaneously in living mice (site B). The 293T cells co-transfected with the reporter and the constitutive active activator were used as control (site A). The animals (n=3 each for control and experiment group) were imaged in 24 h intervals by alternate injection of ligand Raloxifene for the experiment group. The results show no luciferase signal immediately after implanting the cells. After 24 h the animal received drug Raloxifene and produced signal that is significantly greater than the control group (p<0.001). The cells implanted with the constitutive active system showed signal that is significant both before and after injecting ligand Raloxifene in experimental group and also in control group. The system showed efficient ligand regulable gene expression in mice implanted with 293T cells transiently transfected with the reporter and the activator plasmids. The level of signal achieved before induced with the ligand was not significantly above the background. When induced with 0.5 mg of Raloxifene the reporter luciferase gene expression reached 15±5 fold more. The system showed efficient on/off mechanism in response to ligand Raloxifene (FIG. 9).
Materials and Methods
Chemicals, Enzymes and Reagents. Restriction and modification enzymes and ligase were from New England Biolabs (Beverly, Mass.). TripleMaster Taq DNA polymerase from Brinkmann Eppendorf (Hamburg, Germany) was used for the PCR amplification of different fragments used for constructing different vectors used in this study. PCR was used for the amplification of genes of different reporters and the estrogen receptor alpha of human (hERα/HE0). Different estrogen receptor antagonists and agonists include Tamoxifen, 4-hydroxytamoxifen, Raloxifene, Diethylstilbestrol, 17β-estradiol, Genistein, anticancer drugs cisplatinum and Green Tea, and antibiotics for bacterial cultures were from Sigma (St. Louis, Mo.). Lipofectamine transfection reagent was from Invitrogen (Carlsbad, Calif.). The plasmid extraction kit and DNA gel extraction kit were purchased from Qiagen (Valencia, Calif.). Coelenterazine was from Nanolight (Pinetop, Ariz.). Bacterial culture media were from BD Diagnostic Systems (Sparks, Md.). All cell culture media, fetal bovine serum, the antibiotics streptomycin, and penicillin, were from Invitrogen (Carlsbad, Calif.). The plasmids for Tet-on system were from Clontech (Valencia, Calif.). The custom oligo-nucleotides synthesized from Stanford Protein and Nucleic acid (PAN) facility were used as primers for the amplification different fragments of genes, reporters and for making different amino acid linkers. The Stratagene (La Jolla, Calif.) site directed mutagenesis kit was used for constructing the mutant ligand-binding domain of estrogen receptor. DAN sequencing were from PAN facility, Stanford and Sequetech (Mountain view, Calif.).
Construction of Plasmids. The unidirectional and bi-directional reporter vector containing five GAL4 DNA binding sites and the adenovirus early minimal promoter E4 were from our previous studies (Ray, S. et al. Novel bidirectional vector strategy for amplification of therapeutic and reporter gene expression. Hum Gene Ther 15, 681-690 (2004); Iyer, M. et al. Two-step transcriptional amplification as a method for imaging reporter gene expression using weak promoters. Proc Natl Acad Sci USA 98, 14595-14600 (2001), both of which are incorporated herein by reference). The reporter plasmid containing five GAL4 DNA binding site and the major late promoter of adenovirus from Promega (Madison, Wis.) was used for the comparison. The vector construct expressing the fusion protein contain GAL4 DNA binding domain, ER of different lengths and the transactivator VP16 was constructed by inserting PCR amplified fragments of ER to the Eco RI and Bam HI digested activator plasmid from the previous study. The mutant forms of ER were constructed by using the site directed mutagenesis kit of Stratagene (FIG. 1).
Cell Culture. Human 293T embryonic kidney cancer cells (ATCC, Manassas, Va.) were grown in MEM supplemented with 10% FBS and 1% penicillin/streptomycin solution. The estrogen receptor positive human breast cancer cells MCF7 and the estrogen receptor negative cells MDA-MB231 were grown in RPMI 1640 and DMEM high glucose respectively supplemented with 10% FBS and 1% penicillin/streptomycin. CHO cells were grown in Ham F12K medium supplemented with 10% FBS and 1% penicillin/streptomycin. The cells used for transactivation using ER ligands were grown in activated charcoal treated serum from HyClone (Logan, Utah).
Cell Transfection and Luciferase Assay. Transfections were performed in 80% confluent 24 h old cultures of 293T and CHO cells. For transfections, unless specified, 200 ng/well DNA were used in 12 well culture plates. Volumes of Lipofectamine were as recommended by the manufacturer. For induction, different ER ligands dissolved in DMSO or doxycycline dissolved in water to concentrations of 1 μM and 1 μg/ml respectively were used. Drugs were added immediately after transfection. The cells were assayed after 24 h incubation at 37° C. and in 5% CO2. The luminometry assay for Renilla luciferase activity was performed as per protocol published previously (Bhaumik, S. & Gambhir, S. S. Optical imaging of Renilla luciferase reporter gene expression in living mice. Proc Natl Acad Sci USA 99, 377-382 (2002), which is incorporated herein by reference). For firefly luciferase assay 20 μl of samples lysed in passive lysis buffer were mixed with 100 μl luciferase assay reagent II (LAR II) from Promega and counted for 10 sec in the luminometer (Turner 20/20, Sunnyvale, Calif.). Measuring the protein concentration in the cell lysates normalized the readings. Activities of FLUC and RLUC were represented as relative light units (RLU) per microgram of protein.
Studying the ER ligand induced transactivation in transiently transfected 293T cells. To study the ER ligand induced transactivation of reporter gene expression, the 293T cells co-transfected with 200 ng/well each of the reporter plasmid (pGL-G5-E4-Fluc) and the activator plasmid expressing GAL4-ER-VP16 were used. The cells were assayed for luciferase activity 24 h after exposure to 1 μM concentration of ligand 17β-estradiol (E2). The transfection efficiency was normalized by co-transfecting with 10 ng of Renilla luciferase expressing under CMV promoter in all the required experiments.
Studying the ligand concentration dependent transactivation of reporter gene expression in transiently transfected 293T and CHO cells. To study the ligand induced transactivation in a concentration dependent manner, the 293T cells were co-transfected with different reporter and activator ratio (1:1 to 1:0.1) and assayed for luciferase activity after exposure to different concentrations of 17β-estradiol (0 to 1.5 μM).
Studying different ER agonists and antagonists induced transactivation of reporter gene expression in transiently transfected 293T human embryonic kidney cancer cells and ER negative MDA-MB231 breast cancer cells. To study the impact of different ER ligands in the transactivation of reporter gene expression, the 293T and MDA-MB231 cells transiently co-transfected with the reporter (200 ng/well in 12 well culture plate) and activator (20 ng/well in 12 well culture plate) plasmids were assayed for luciferase activity 24 hours after exposure to 1 μM each separately by 17β-estradiol, 4-hydroxytamoxifen, Tamoxifen, Raloxifene, Genistein, Diethylstilbestrol, and solvent DMSO and anticancer drug Cisplatinum controls.
Comparing the efficiency of ER-ligand induced transactivation system with the constitutive active GAL4-VP16 system in transiently transfected 293T cells. To compare the efficiency of the ER ligand induced transactivation system with the previously used constitutive GAL4-VP16 system, the 293T cells co-transfected with reporter-pGL-G5-E4-Fluc and activator-pGAL4-VP16, or co-transfected with the reporter-pGL-G5-E4-Fluc and activator-pGAL4-ER-VP16 after inducing with ligand 17β-estradiol were assayed 24 hours after incubation for luciferase activity.
Ligand regulated transactivation system in the expression of reporter gene in a bi-directional vector in two different orientations. To study the efficiency of controlling the two reporter genes expressed in two different orientations in a single plasmid, the 293T cells transiently co-transfected with the reporter plasmid (pGL-G5-E4-Fluc-Rluc) and activator plasmid (pGL-GAL4-ER-VP16) in 1:0.1 ratio were exposed to different concentrations of 17β-estradiol (0, 0.006, 0.012, 0.0235, 0.047, 0.094, 0.1875, 0.375, 0.75 and 1.5 μM) and assayed for Fluc and Rluc activities. Estimating the R2 value assessed the correlation between the two enzymes level.
Ligand induced transactivation system to differentiate ER-ligands. To make the ligand induced transactivation system that can differentiate ER-ligands, the ER-LBD of different length (281-549) identified from our previous study (under communication) was used to replace the ER of 281-595. The system was studied in transiently co-transfected 293T cells by exposing to 1 μM concentrations of different ligands. The cells were lysed and assayed for luciferase activity after 24 h.
Imaging ligand induced transactivation system in living animals. All animals handling was performed in accordance with Stanford University Animal Research Committee guidelines. For imaging in living nude mice (nu/nu), 293T cells transiently co-transfected with reporter plasmid and the activator plasmid expressing GAL4-VP16 fusion protein for constitutive active system, and reporter plasmid with the activator plasmid expressing fusion protein GAL4-ER-VP16 for activatable system were used. Animals implanted with 10 million cells of each system on the back of living mice were imaged by injecting 3 mg of substrate D-luciferin. For activatable system animals were imaged periodically before and after injecting ligand Raloxifene.
Discussion
This Example provides an efficient ligand regulable transcriptional amplification system that has multiple applications. This system showed greater efficiency in controlling the expression level of transgenes both in cells and xenografts in living animals. This system can also be used to screen new ER-ligands with therapeutic potential from both natural and synthetic sources. The system can be used to distinguish and differentiate ER-ligands as agonist, antagonist, partial antagonist, and partial agonist.
From our previous study it was learned that ER can lead to intramolecular folding and following split luciferase complementations when it binds with its ligands (communicated). This was extended to develop the current ligand mediated transactivation system. In addition we also learned from our earlier study that the orientation and the distance between the N- and C-terminus of ER is differentially positioned when it binds with its ligands. Extending the length of C-terminus of the protein by adding more amino acids either from the remaining portion of the protein or by choice can also change this. So this property of the receptor in modifying the system for differentiating ER-ligands was studied.
There are several systems available for regulating transgene expression in cells and also in living animals. In contrast to the present system, most of the strategy suffers due to greater level of background or due to the toxic nature of the chemicals used for inducing the system.
There are several drugs in the market that can work as agonists or antagonists in the modulation of the estrogen receptor and other steroid receptors super family. In particular, the agonist and antagonist of estrogen receptors bind in the same ligand-binding domain with a different binding mode. But each of these ligands induces a specific conformation in the transactivation domain and leads to different downstream gene activation. As discussed in the previous section, the helix H12 is an important portion of the estrogen receptor that has different conformational changes in response to different ligands. The controls of gene transcription of many cellular genes are the indications of cell growth and development and malignant transformations. The effects of these steroid hormones including estrogens, testosterones, thyroid hormones, retinoids, ecdysone, prostaglandins and oxygenated cholesterols are mediated through specific receptors proteins termed as steroid/nuclear receptor, which are still not completely studied. The uniqueness of ER among these different steroid receptor super family receptors is in sensing many of the structurally non-steroidal compounds. There is currently no system available that can easily distinguish between agonists and antagonists based on its ligand bindings and associated conformational changes. It is also important to screen more number of Selective Estrogen Receptor Modulators (SERM) as anticancer drugs.
The extreme abundance of localized temporary, or more stable protein homodimers attests to their many functions in the cell and the important role they play in many biological processes. The ability to detect, locate, and quantify protein homodimerization in the setting of a whole living animal model has important implications for a wide variety of biological research endeavors, drug discovery, and molecular medicine. In particular, the visual representation, characterization, and quantification of these biological processes in living subjects now creates unprecedented opportunities to complement available in vitro or cell culture methodologies, in order: (i) to characterize more fully known homodimeric protein-protein interactions in the context of whole-body physiologically-authentic environments, and (ii) to accelerate the evaluation in living animal models of novel drugs that promote or inhibit active homodimeric protein assembly.
The ligand-induced conformation of a nuclear receptor ligand-binding domain is a principal factor leading to transcriptional activity and determining the pharmacological response. Even though many studies have dealt with the transcriptional activation of target genes in response to ligands, only a few have attempted in distinguishing the conformational difference in response to agonists and antagonists. The study using fluorescent labeling of specific amino acids (417 and 435) in the ligand-binding domain has been studied. The system developed from this study is not only useful for regulating transgenes expression it will also be useful in studying more about the mystery behind the biology of ER.

## Claims

1. A method of detecting a ligand in vitro, comprising:
providing a ligand-regulable transactivation system comprising:
a reporter polynucleotide that comprises a binding sequence, a promoter sequence, and a reporter sequence encoding a detectable bioluminescent protein, wherein the binding sequence is connected with the promoter sequence and the promoter sequence is connected with the reporter sequence; and
an activator fusion protein that comprises:
a DNA binding domain capable of interacting with the binding sequence of the reporter polynucleotide, an estrogen receptor folding domain (ER folding domain) capable of binding a ligand, wherein the ER folding domain is selected from: a sequence consisting of SEQ ID NO:1 (human estrogen receptor, alpha, amino acids 281-549), a sequence consisting of SEQ ID NO:2 (human estrogen receptor, alpha, amino acids 281-595), a sequence consisting of SEQ ID NO:4 (mouse estrogen receptor, alpha, amino acids 281-549), a sequence consisting of SEQ ID NO:5 (mouse estrogen receptor, alpha, amino acids 281-599), SEQ ID NO:23 and SEQ ID NO:24, and
a transactivation domain capable of interacting with the promoter sequence of the reporter polynucleotide,

wherein the DNA binding domain is connected to the estrogen receptor folding domain, and the estrogen receptor folding domain is connected with the transactivation domain, and wherein interaction of the DNA binding domain and the transactivation domain of the activator fusion protein with the binding sequence and promoter sequence of the reporter polynucleotide regulates expression of the detectable bioluminescent protein;

introducing a ligand to the system; and
detecting a bioluminescent signal in the presence of a bioluminescence initiating compound if the ligand causes the ER folding domain to change from a non-interacting conformational position to an interacting conformational position, wherein the interacting conformational position positions the DNA binding domain and the transactivation domain of the activator fusion protein so that both interact with the binding sequence and the promoter sequence of the reporter polynucleotide, which causes expression of the detectable bioluminescent protein encoded by the reporter sequence.

2. The method of claim 1, wherein the ligand is selected from: ER ligands, ER agonists, partial ER agonists, ER antagonists, partial ER antagonists, and selective estrogen receptor modulators.

3. The method of claim 1, wherein the interacting conformation position corresponds to one of two states including substantially interacting and partially interacting, wherein substantially interacting means that the DNA binding domain and the transactivation domain interact with the binding sequence and the promoter sequence of the reporter polynucleotide to generate a first amount of bioluminescent protein, and wherein partially interacting means that the DNA binding domain and the transactivation domain interact with the binding sequence and the promoter sequence of the reporter polynucleotide to generate a second amount of bioluminescent protein, wherein the first amount of bioluminescent protein is greater than the second amount of bioluminescent protein.

4. The method of claim 1, wherein the reporter sequence is selected from polynucleotide sequences encoding one of the following: a luciferase and a photoprotein.

5. The method of claim 1, wherein the reporter sequence is selected from polynucleotide sequences encoding one of the following: a Renilla Luciferase; a Coleoptera Luciferase; a Firefly Luciferase; a Gaussia Luciferase; and an aequorin photoprotein Luciferase.

6. The method of claim 1, wherein the promoter sequence is selected from: an E4 promoter (SEQ ID NO:36), an E4 minimal promoter (SEQ ID NO:18), minimal promoter thymidine kinase (tk-promoter) (SEQ ID NO:18), and an adenoviral late promoter (SEQ ID NO:38).

7. The method of claim 1, wherein the binding sequence is a GAL4 binding sequence (SEQ ID NO:17).

8. The method of claim 1, wherein the DNA binding domain is GAL4 DNA binding domain (SEQ ID NO:14).

9. The method of claim 1, wherein the transactivation domain is VP16 transactivation domain (SEQ ID No: 16).

10. The method of claim 1, wherein the ligand-regulable transactivation system is expressed in an isolated living cell or culture of cells.

11. A method of detecting a ligand in vivo, comprising:
implanting cells into a nude mouse, wherein the cells comprise exogenous polynucleotides expressing a ligand-regulable transactivation system comprising:
a reporter polynucleotide that comprises a GAL 4 binding sequence, a promoter sequence, and a reporter sequence encoding a detectable bioluminescent protein, wherein the binding sequence is connected with the promoter sequence and the promoter sequence is connected with the reporter sequence; and
an activator fusion protein that comprises:
a DNA binding domain capable of interacting with the binding sequence of the reporter polynucleotide,
an estrogen receptor folding domain (ER folding domain) capable of binding a ligand, wherein the ER folding domain is selected from: SEQ ID NO:23 and SEQ ID NO:24, and
a VP16 transactivation domain capable of interacting with the promoter sequence of the reporter polynucleotide,

wherein the DNA binding domain is connected to the estrogen receptor folding domain, and the estrogen receptor folding domain is connected with the transactivation domain, and wherein interaction of the DNA binding domain and the transactivation domain of the activator fusion protein with the binding sequence and promoter sequence of the reporter polynucleotide regulates expression of the detectable bioluminescent protein;

introducing a ligand to the animal, wherein the ligand is not an endogenous ligand in the mouse; and
detecting a bioluminescent signal in the presence of a bioluminescence initiating compound if the ligand causes the ER folding domain to change from a non-interacting conformational position to an interacting conformational position, wherein the interacting conformational position positions the DNA binding domain and the transactivation domain of the activator fusion protein so that both interact with the binding sequence and the promoter sequence of the reporter polynucleotide, which causes expression of the detectable bioluminescent protein encoded by the reporter sequence.

12. The method of claim 11, wherein the ligand is selected from: ER ligands, ER agonists, partial ER agonists, ER antagonists, partial ER antagonists, and selective estrogen receptor modulators.

13. The method of claim 11, wherein the interacting conformation position corresponds to one of two states including substantially interacting and partially interacting, wherein substantially interacting means that the DNA binding domain and the transactivation domain interact with the binding sequence and the promoter sequence of the reporter polynucleotide to generate a first amount of bioluminescent protein, and wherein partially interacting means that the DNA binding domain and the transactivation domain interact with the binding sequence and the promoter sequence of the reporter polynucleotide to generate a second amount of bioluminescent protein, wherein the first amount of bioluminescent protein is greater than the second amount of bioluminescent protein.

14. The method of claim 11, wherein the reporter sequence is selected from polynucleotide sequences encoding one of the following: a luciferase and a photoprotein.

15. The method of claim 11, wherein the reporter sequence is selected from polynucleotide sequences encoding one of the following: a Renilla Luciferase; a Coleoptera Luciferase; a Firefly Luciferase; a Gaussia Luciferase; and an aequorin photoprotein Luciferase.

16. The method of claim 11, wherein the promoter sequence is selected from: an E4 promoter (SEQ ID NO:36), an E4 minimal promoter (SEQ ID NO:18), minimal promoter thymidine kinase (tk-promoter) (SEQ ID NO:18), and an adenoviral late promoter (SEQ ID NO:38).

17. The method of claim 11, wherein the VP16 transactivation domain has the sequence of SEQ ID NO:16.

18. A method of detecting a ligand in vitro, comprising:
providing a ligand-regulable transactivation system comprising:
a reporter polynucleotide that comprises a GAL4 binding sequence of SEQ ID NO:17, a promoter sequence, and a reporter sequence encoding a detectable bioluminescent protein, wherein the binding sequence is connected with the promoter sequence and the promoter sequence is connected with the reporter sequence; and
an activator fusion protein that comprises:
a DNA binding domain capable of interacting with the GAL4 binding sequence of the reporter polynucleotide,
an estrogen receptor folding domain (ER folding domain) capable of binding a ligand, and
a transactivation domain capable of interacting with the promoter sequence of the reporter polynucleotide,

wherein the DNA binding domain is connected to the estrogen receptor folding domain, and the estrogen receptor folding domain is connected with the transactivation domain, and wherein interaction of the DNA binding domain and the transactivation domain of the activator fusion protein with the binding sequence and promoter sequence of the reporter polynucleotide regulates expression of the detectable bioluminescent protein;

introducing a ligand to the system; and
detecting a bioluminescent signal in the presence of a bioluminescence initiating compound if the ligand causes the ER folding domain to change from a non-interacting conformational position to an interacting conformational position, wherein the interacting conformational position positions the DNA binding domain and the transactivation domain of the activator fusion protein so that both interact with the binding sequence and the promoter sequence of the reporter polynucleotide, which causes expression of the detectable bioluminescent protein encoded by the reporter sequence.

19. The method of claim 18, wherein the estrogen receptor folding domain is selected from: SEQ ID NO:1 (human estrogen receptor, alpha, amino acids 281-549), SEQ ID NO:2 (human estrogen receptor, alpha, amino acids 281-595), SEQ ID NO:3 (human estrogen receptor, alpha, amino acids 1-595), SEQ ID NO:4 (mouse estrogen receptor, alpha, amino acids 281-549), SEQ ID NO:5 (mouse estrogen receptor, alpha, amino acids 281-599), SEQ ID NO:6 (mouse estrogen receptor amino acids 1-599), SEQ ID NO:23 and SEQ ID NO:24.