Patent Grant
7342111
1.1 Field of the Invention
The present invention relates generally to the fields of genetics, molecular and cellular biology and medicine. More particularly, it concerns identification of novel genes involved in a variety of cellular processes, including retinal degeneration, cancer, memory and learning, and identification of the function of a variety of genes and gene fragments of unknown function. The genes thus identified, as well as the compositions used in the identification methods, are also disclosed.
1.2 Description of the Related Art
Recent advances in human genome research, assisted by the advent of automated DNA sequencing, have yielded a wealth of knowledge about human genes and proteins. Advances in gene sequencing and gene isolation, combined with computer-based bioinformation systems and analysis, offer the potential for many new treatments.
Advances in genomics and combinatorial chemistry have revolutionized the way drugs are discovered. With sequencing and characterization of the 100,000 human genes only a few years away, random compound screening is being replaced by identifying disease-associated genes, followed by rational drug design to specifically target gene products that are involved in the disease pathway. However, the sheer volume of genetic information being produced means that the problem of finding a new genetic target is being replaced by the problem of determining which of the many new targets are the best.
Through the efforts of the Human Genome Project, academic centers and the biopharmaceutical industry, there is now a significant amount of gene sequence information available to researchers. However, while this information is accessible, knowing a gene sequence alone, without an understanding of its biological function, is not usually enough to enable effective drug development. What is needed, and is presently lacking in the art, are methods of identifying the particular gene or genes involved in selected biological and physiological processes. This lack of adequate technologies to accomplish in vivo target validation currently represents a major roadblock in the translation of gene sequence information emerging from the Human Genome Project into new therapeutic targets.
The present invention overcomes these and other deficiencies in the art by providing methods for the identification of novel genes that are involved, either directly or indirectly, in a variety of cellular, biological and physiological processes. Additionally, the present invention overcomes other shortcomings of the art by providing methods for identifying the function of previously identified genes or gene fragments, such as expressed sequence tags (ESTs), which heretofore has been both difficult and extremely time consuming and labor intensive. The present invention provides methods to “knock-out”, or inactivate, genes of unknown function in any cell, or more importantly somatic tissue, and obtain evidence of the function of the genes based on the resulting “knock-out” phenotype. These methods are also useful in testing genes of known or suspected function for their disease-causing potential, thereby identifying new disease-causing genes. The present invention provides significant advantages over traditional gene disruptions in embryonic stem cells, as genes that are critical to development and lead to embryonic lethality can be “knocked-out” in adult animals and studied using the methods provided herein. Thus, the present invention also overcomes further deficiencies in the art by providing animal models of a variety of different physiological conditions, including certain inborn errors, and diseases.
The present invention provides methods of identifying one or more genes having a selected function, comprising contacting a plurality of genes suspected of comprising the gene with a plurality or library of ribozymes, and identifying one or more ribozymes from the plurality or library that alter the selected function of the one or more genes, thereby identifying one or more genes having the selected function.
In preferred aspects of the invention, the gene or genes to be identified are involved in one or more cellular, biological and/or physiological process. The processes can be life threatening, for example acquired or in-born diseases such as cancer, degenerative, such retinal degeneration, impaired learning or long or short-term memory loss, or any other normal or abnormal process of interest.
In various embodiments the plurality of genes are comprised within an animal, for example a mammal or a human subject. However, this is not essential, and thus in other embodiments the plurality of genes are provided in an ex vivo setting, for example in tissue culture or cell culture, or in an in vitro setting, using crude, partially isolated or purified nucleic acids.
The library of ribozymes comprises a plurality of ribozymes that comprise degenerate bases within the region of the ribozyme involved in target recognition and binding of the ribozyme to its target nucleic acid. In certain aspects of the present invention the ribozymes are completely degenerate at these recognition and binding positions, having the sequence shown in SEQ ID NO:1, while in other aspects of the invention the ribozymes have completely or partially (only two or three of the possible four ribonucleotide bases) degenerate bases at one, two, three four, five, six, seven, eight, nine or ten positions or so. All types of ribozymes, including hammerhead, hairpin, a hepatitis δ virus, group I intron or RNaseP RNA (in association with an RNA guide sequence) or Neurospora VS RNA motifs are contemplated for use in the present invention, although in certain preferred aspects the ribozymes are hammerhead ribozymes. In various aspects of the invention, the ribozymes are chemically synthesized or transcribed either in vitro or in vivo.
The ribozymes can be delivered by a variety of different method, as described herein below, but in preferred aspects of the invention, the ribozymes or library of ribozymes are cloned into an adeno-associated viral expression vector, and comprised within a plurality of adeno-associated virus particles.
In preferred aspects of the present invention, the one or more ribozymes and/or the one or more genes identified by the present methods are isolated, and in certain aspects of the invention, the nucleotide sequence of all or a portion of the ribozymes and/or genes is obtained.
Thus, the present invention provides a method of identifying at least a first gene involved in retinal degeneration, comprising contacting a plurality of genes suspected of comprising the at least a first gene with a library of ribozymes, and identifying at least a first ribozyme from the library that alters retinal degeneration, thereby identifying the at least a first gene involved in retinal degeneration. One ribozyme contemplated for use in identifying genes involved in retinal degeneration has the nucleotide sequence of SEQ ID NO:29. Among the genes that can be thus identified are rhodopsin genes and genes encoding the β-subunit of cGMP phosphodiesterase.
The present invention also provides a method of identifying at least a first tumor suppressor gene, comprising contacting a plurality of genes suspected of comprising the at least a first tumor suppressor gene with a library of ribozymes, and identifying at least a first ribozyme from the library that alters tumor suppression, thereby identifying the at least a first tumor suppressor gene. Ribozymes contemplated for use in identifying tumor suppressor genes include, but are not limited to, those having the nucleotide sequence of SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7 and SEQ ID NO:9. Examples of genes that can be identified using these methods include, but are not limited to, a p53 gene, a p16 gene, a retinoblastoma gene and a p19ARF gene.
The present invention also provides a method of identifying at least a first gene involved in amyotrophic lateral sclerosis disease, comprising contacting a plurality of genes suspected of comprising the at least a first gene with a library of ribozymes, and identifying at least a first ribozyme from the library that is involved amyotrophic lateral sclerosis disease, thereby identifying the at least a first gene involved in causing such a disorder in a mammal. Ribozymes contemplated for use in identifying genes involved in ALS include, but are not limited to, those having a nucleotide sequence comprising all or a portion of a gene encoding superoxide dismutase or a manganese superoxide dismutase.
The present invention also provides a method of identifying at least a first gene involved in amyotrophic lateral sclerosis disease, comprising contacting a plurality of genes suspected of comprising the at least a first gene with a library of ribozymes, and identifying at least a first ribozyme from the library that is involved amyotrophic lateral sclerosis disease, thereby identifying the at least a first gene involved in causing such a disorder in a mammal. Ribozymes contemplated for use in identifying genes involved in ALS include, but are not limited to, those having a nucleotide sequence comprising all or a portion of a gene encoding superoxide dismutase or a manganese superoxide dismutase.
The present invention also provides the isolated genes and ribozymes identified by the methods provided herein. Thus, genes and ribozymes that are involved in or alter retinal degeneration, retinal disease, memory, learning, ALS, and tumor suppressor genes, identified by these methods, are provided by the present invention.
In certain aspects of the present invention, a ribozyme is designed based upon a small fragment of a gene, for example an EST, where the function of the gene from which the EST is derived is either known or unknown, and where the full length gene has not yet been cloned. The present invention provides a method of identifying an essentially full-length gene having a selected function, comprising contacting a plurality of genes suspected of comprising the essentially full-length gene with at least a first ribozyme that cleaves the ribonucleic acid of the essentially full-length gene, thereby identifying the essentially full-length gene having the selected function.
Since certain ribozymes provided by the present invention have been designed to target specific or particular genes, the present invention provides a method of identifying these specific or particular genes, comprising contacting a plurality of genes suspected of comprising the specific gene with at least a first ribozyme that cleaves the ribonucleic acid of the specific gene, thereby identifying the specific or particular gene. Thus, the present invention provides methods for identifying a rhodopsin gene, a gene encoding the γ- or the β-subunit of cGMP phosphodiesterase, a p53 gene, a p16 gene, a retinoblastoma gene, a p19ARF gene, a gene encoding a subunit of NADH dehydrogenase, a superoxide dismutase- or a manganese superoxide dismutase-encoding gene, and/or a CREB gene.
Additionally, the present invention provides a method of identifying a function of a selected gene, comprising contacting a plurality of genes suspected of comprising the selected gene with a ribozyme that cleaves the ribonucleic acid of the selected gene, and identifying the effect of the ribozyme, thereby identifying the function of the selected gene.
The present invention also provides a method of inducing a selected physiologically abnormal condition in an animal, comprising administering to the animal at least a first ribozyme that cleaves the ribonucleic acid of at least a first gene involved in preventing the selected physiologically abnormal condition, thereby inducing the selected physiologically abnormal condition in the animal. In certain methods, the physiologically abnormal condition is retinal degeneration, cancer, memory loss or impaired learning. Thus, the present invention also provides an animal in which any particular gene of interest has been inactivated, thereby providing animal models for a variety of different abnormal conditions and diseases. Likewise, the present invention provides a method of inducing a selected physiologically abnormal condition in an animal, comprising administering to the animal at least a first ribozyme that cleaves the ribonucleic acid of at least a first gene involved in causing the selected physiologically abnormal condition, thereby inducing the selected physiologically abnormal condition in the animal. Thus, the present invention also provides methods for creating non-human animal models in which any particular gene of interest has been inactivated, thereby providing tools for the study of a variety of different abnormal conditions and diseases.
The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings in combination with the detailed description of specific embodiments presented herein:
Illustrative embodiments of the invention are described below. In the interest of clarity, not all features of an actual implementation are described in this specification. It will of course be appreciated that in the development of any such actual embodiment, numerous implementation-specific decisions must be made to achieve the developers' specific goals, such as compliance with system-related and business-related constraints, which will vary from one implementation to another. Moreover, it will be appreciated that such a development effort might be complex and time-consuming, but would nevertheless be a routine undertaking for those of ordinary skill in the art having the benefit of this disclosure.
The present invention provides methods for the identification of novel genes that are involved, either directly or indirectly, in a variety of cellular, biological and physiological processes, as well as methods for identifying the function of previously identified genes or gene fragments, such as expressed sequence tags (ESTs). The present invention provides methods to “knock-out” genes of unknown function in any somatic tissue and obtain evidence of the function of the genes based on the resulting “knock-out” phenotype. The invention also provides methods for testing genes of known or suspected function for their disease-causing potential, thereby identifying new disease-causing genes. The present invention also provides animal models of a variety of different physiological conditions, including certain inborn errors, and diseases.
The present methods involve the use of ribozymes, either designed to target a specific gene or gene fragment, or libraries of ribozymes that, through degeneracy in the bases involved in target recognition and binding, target random genes. Additionally, the invention provides methods of delivering or providing the ribozyme constructs to cells or animals using adeno-associated viral vectors and virus particles.
4.1 Adeno-Associated Virus Delivery of Ribozymes
For the vast amounts of data produced by the Human Genome Project to be useful, the function of identified genes must be deduced and their roles in human disease, if any, established. However, to date, only about 6,000 of the 50,000-100,000 human genes have been associated with a phenotype. Thus, documenting the full spectrum of disease-causing genes and creating animal models to understand pathogenic mechanisms and develop therapies are the next major challenges of human genetics. The present invention combines tools of virus-vectored gene therapy and promoter-regulated ribozymes to functionally identify such genes and create animal models of genetic disease. Ribozymes are RNA enzymes that have the potential to block the expression of specific genes. Adeno-associated virus (AAV) has been successfully used to deliver ribozymes as therapy in animal models of dominant genetic disease. The present invention extends the approach to create disease in experimental animals, and therefore to establish animal models for disease. The AAV-ribozyme approach permits the generation of somatic gene knockouts, avoiding the problem of embryonic lethality and the limitation to small animals typical of current gene-disruption strategies.
Over 100 genetic loci have been linked to retinal disease in man. Of these, some are well documented to be associated genes for retinal proteins, but most are simply intervals on the human genetic map. In addition, the genetic etiology of some major retinal diseases, including age-related macular degeneration, is obscure. Age related macular degeneration affects one in three individuals over the age of 70. Differential-display and expressed sequence tag libraries are available that contain clones of genes expressed highly in specific retinal cells, including photoreceptor cells and the retinal pigment epithelium. To identify which among these highly expressed genes may be required for retinal function, hammerhead and hairpin ribozymes have been designed to cleave the messenger RNA molecules that they encode. These are then delivered to experimental animals using AAV to determine which lead to retinal degeneration.
Mutations in two major genetic pathways, characterized by the P53 and by the Rb genes respectively, have been demonstrated to lead to unregulated cell division associated with cancer. Other genes associated with, and perhaps independent of these pathways, may also be involved in controlling the replication and spread of tumor cells. A library of ribozymes containing partially randomized targeting domains have been delivered to specific tissues in order to create animals prone to tumors due to deficits in the expression of previously unidentified tumor suppressor genes. Sequence tags based on these ribozymes are then used to identify and clone potential tumor suppressor genes.
4.2 Ribozymes
Although proteins traditionally have been used for catalysis of nucleic acids, another class of macromolecules has emerged as useful in this endeavor. Ribozymes are RNA-protein complexes that cleave nucleic acids in a site-specific fashion. Ribozymes have specific catalytic domains that possess endonuclease activity (Kim and Cech, 1987; Gerlach et al., 1987; Forster and Symons, 1987). For example, a large number of ribozymes accelerate phosphoester transfer reactions with a high degree of specificity, often cleaving only one of several phosphoesters in an oligonucleotide substrate (Cech et al., 1981; Michel and Westhof, 1990; Reinhold-Hurek and Shub, 1992). This specificity has been attributed to the requirement that the substrate bind via specific base-pairing interactions to the internal guide sequence (“IGS”) of the ribozyme prior to chemical reaction.
Ribozyme catalysis has primarily been observed as part of sequence-specific cleavage/ligation reactions involving nucleic acids (Joyce, 1989; Cech et al., 1981). For example, U.S. Pat. No. 5,354,855 (specifically incorporated herein by reference) reports that certain ribozymes can act as endonucleases with a sequence specificity greater than that of known ribonucleases and approaching that of the DNA restriction enzymes. Thus, sequence-specific ribozyme-mediated inhibition of gene expression may be particularly suited to therapeutic applications (Scanlon et al., 1991; Sarver et al., 1990). Recently, it was reported that ribozymes elicited genetic changes in some cells lines to which they were applied; the altered genes included the oncogenes H-ras, c-fos and genes of HIV. Most of this work involved the modification of a target mRNA, based on a specific mutant codon that is cleaved by a specific ribozyme.
Six basic varieties of naturally occurring enzymatic RNAs are known presently. Each can catalyze the hydrolysis of RNA phosphodiester bonds in trans (and thus can cleave other RNA molecules) under physiological conditions. In general, enzymatic nucleic acids act by first binding to a target RNA. Such binding occurs through the target binding portion of a enzymatic nucleic acid which is held in close proximity to an enzymatic portion of the molecule that acts to cleave the target RNA. Thus, the enzymatic nucleic acid first recognizes and then binds a target RNA through complementary base pairing, and once bound to the correct site, acts enzymatically to cut the target RNA. Strategic cleavage of such a target RNA will destroy its ability to direct synthesis of an encoded protein. After an enzymatic nucleic acid has bound and cleaved its RNA target, it is released from that RNA to search for another target and can repeatedly bind and cleave new targets.
The enzymatic nature of a ribozyme is advantageous over many technologies, such as antisense technology (where a nucleic acid molecule simply binds to a nucleic acid target to block its translation) since the concentration of ribozyme necessary to affect a therapeutic treatment is lower than that of an antisense oligonucleotide. This advantage reflects the ability of the ribozyme to act enzymatically. Thus, a single ribozyme molecule is able to cleave many molecules of target RNA. In addition, the ribozyme is a highly specific inhibitor, with the specificity of inhibition depending not only on the base pairing mechanism of binding to the target RNA, but also on the mechanism of target RNA cleavage. Single mismatches, or base-substitutions, near the site of cleavage can completely eliminate catalytic activity of a ribozyme. Similar mismatches in antisense molecules do not prevent their action (Woolf et al., 1992). Thus, the specificity of action of a ribozyme is greater than that of an antisense oligonucleotide binding the same RNA site.
The enzymatic nucleic acid molecule may be formed in a hammerhead, hairpin, a hepatitis δ virus, group I intron or RNaseP RNA (in association with an RNA guide sequence) or Neurospora VS RNA motif. Examples of hammerhead motifs are described by Rossi et al. (1992). Examples of hairpin motifs are described by Hampel et al. (Eur. Pat. Appl. Publ. No. EP 0360257), Hampel and Tritz (1989), Hampel et al. (1990) and U.S. Pat. No. 5,631,359 (specifically incorporated herein by reference). An example of the hepatitis δ virus motif is described by Perrotta and Been (1992); an example of the RNaseP motif is described by Guerrier-Takada et al. (1983); Neurospora VS RNA ribozyme motif is described by Collins (Saville and Collins, 1990; Saville and Collins, 1991; Collins and Olive, 1993); and an example of the Group I intron is described in U.S. Pat. No. 4,987,071 (specifically incorporated herein by reference). All that is important in an enzymatic nucleic acid molecule of this invention is that it has a specific substrate binding site which is complementary to one or more of the target gene RNA regions, and that it have nucleotide sequences within or surrounding that substrate binding site which impart an RNA cleaving activity to the molecule. Thus the ribozyme constructs need not be limited to specific motifs mentioned herein.
In certain embodiments, it may be important to produce enzymatic cleaving agents that exhibit a high degree of specificity for the RNA of a desired target, such as one of the sequences disclosed herein. The enzymatic nucleic acid molecule is preferably targeted to a highly conserved sequence region of a target mRNA. Such enzymatic nucleic acid molecules can be delivered exogenously to specific cells as required, although in preferred embodiments the ribozymes are expressed from DNA or RNA vectors that are delivered to specific cells.
Small enzymatic nucleic acid motifs (e.g., of the hammerhead or the hairpin structure) may also be used for exogenous delivery. The simple structure of these molecules increases the ability of the enzymatic nucleic acid to invade targeted regions of the mRNA structure. Alternatively, catalytic RNA molecules can be expressed within cells from eukaryotic promoters (e.g., Scanlon et al., 1991; Kashani-Sabet et al., 1992; Dropulic et al., 1992; Weerasinghe et al., 1991; Ojwang et al., 1992; Chen et al., 1992; Sarver et al., 1990). Those skilled in the art realize that any ribozyme can be expressed in eukaryotic cells from the appropriate DNA vector. The activity of such ribozymes can be augmented by their release from the primary transcript by a second ribozyme (Int. Pat. Appl. Publ. No. WO 93/23569, and Int. Pat. Appl. Publ. No. WO 94/02595, both hereby incorporated by reference; Ohkawa et al., 1992; Taira et al., 1991; and Ventura et al., 1993).
Ribozymes may be added directly, or can be complexed with cationic lipids, lipid complexes, packaged within liposomes, or otherwise delivered to target cells. The RNA or RNA complexes can be locally administered to relevant tissues ex vivo, or in vivo through injection, aerosol inhalation, infusion pump or stent, with or without their incorporation in biopolymers.
Ribozymes may be designed as described in int. Pat. Appl. Publ. No. WO 93/23569 and Int. Pat. Appl. Publ. No. WO 94/02595 (each specifically incorporated herein by reference) and synthesized to be tested in vitro and in vivo, as described. Such ribozymes can also be optimized for delivery. While specific examples are provided, those in the art will recognize that equivalent RNA targets in other species can be utilized when necessary.
Hammerhead or hairpin ribozymes may be individually analyzed by computer folding (Jaeger et al., 1989) to assess whether the ribozyme sequences fold into the appropriate secondary structure, as described herein. Those ribozymes with unfavorable intramolecular interactions between the binding arms and the catalytic core are eliminated from consideration. Varying binding arm lengths can be chosen to optimize activity. Generally, at least 5 or so bases on each arm are able to bind to, or otherwise interact with, the target RNA.
Ribozymes of the hammerhead or hairpin motif may be designed to anneal to various sites in the mRNA message, and can be chemically synthesized. The method of synthesis used follows the procedure for normal RNA synthesis as described in Usman et al. (1987) and in Scaringe et al. (1990) and makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5′-end, and phosphoramidites at the 3′-end. Average stepwise coupling yields are typically >98%. Hairpin ribozymes may be synthesized in two parts and annealed to reconstruct an active ribozyme (Chowrira and Burke, 1992). Ribozymes may be modified extensively to enhance stability by modification with nuclease resistant groups, for example, 2′-amino, 2′-C-allyl, 2′-flouro, 2′-o-methyl, 2′-H (for a review see e.g., Usman and Cedergren, 1992). Ribozymes may be purified by gel electrophoresis using general methods or by high-pressure liquid chromatography and resuspended in water.
Ribozyme activity can be optimized by altering the length of the ribozyme binding arms, or chemically synthesizing ribozymes with modifications that prevent their degradation by serum ribonucleases (see e.g., Int. Pat. Appl. Publ. No. WO 92/07065; Perrault et al, 1990; Pieken et al., 1991; Usman and Cedergren, 1992; Int. Pat. Appl. Publ. No. WO 93/15187; Int. Pat. Appl. Publ. No. WO 91/03162; Eur. Pat. Appl. Publ. No. 92110298.4; U.S. Pat. No. 5,334,711; and Int. Pat. Appl. Publ. No. WO 94/13688, which describe various chemical modifications that can be made to the sugar moieties of enzymatic RNA molecules), modifications which enhance their efficacy in cells, and removal of stem II bases to shorten RNA synthesis times and reduce chemical requirements.
A preferred means of accumulating high concentrations of a ribozyme(s) within cells is to incorporate the ribozyme-encoding sequences into a DNA expression vector. Transcription of the ribozyme sequences are driven from a promoter for eukaryotic RNA polymerase I (pol I), RNA polymerase II (pol II), or RNA polymerase III (pol III). Transcripts from pol II or pol III promoters will be expressed at high levels in all cells; the levels of a given pol II promoter in a given cell type will depend on the nature of the gene regulatory sequences (enhancers, silencers, etc.) present nearby. Prokaryotic RNA polymerase promoters may also be used, providing that the prokaryotic RNA polymerase enzyme is expressed in the appropriate cells (Elroy-Stein and Moss, 1990; Gao and Huang, 1993; Lieber et al., 1993; Zhou et al, 1990). Ribozymes expressed from such promoters can function in mammalian cells (Kashani-Sabet et al, 1992; Ojwang et al, 1992; Chen et at, 1992; Yu et al., 1993; L'Huillier et al., 1992; Lisziewicz et al, 1993). Although incorporation of the present ribozyme constructs into adeno-associated viral vectors is preferred, such transcription units can be incorporated into a variety of vectors for introduction into mammalian cells, including but not restricted to, plasmid DNA vectors, other viral DNA vectors (such as adenovirus vectors), or viral RNA vectors (such as retroviral, semliki forest virus, sindbis virus vectors).
Sullivan et al. (Int. Pat. Appl. Publ. No. WO 94/02595) describes general methods for delivery of enzymatic RNA molecules. Ribozymes may be administered to cells by a variety of methods known to those familiar to the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as hydrogels, cyclodextrins, biodegradable nanocapsules, and bioadhesive microspheres. For some indications, ribozymes may be directly delivered ex vivo to cells or tissues with or without the aforementioned vehicles. Alternatively, the RNA/vehicle combination may be locally delivered by direct inhalation, by direct injection or by use of a catheter, infusion pump or stent. Other routes of delivery include, but are not limited to, intravascular, intramuscular, subcutaneous or joint injection, aerosol inhalation, oral (tablet or pill form), topical, systemic, ocular, intraperitoneal and/or intrathecal delivery. More detailed descriptions of ribozyme delivery and administration are provided in Int. Pat. Appl. Publ. No. WO 94/02595 and Int. Pat. Appl. Publ. No. WO 93/23569, each specifically incorporated herein by reference.
Ribozymes of this invention may be used to inhibit gene expression and define the role (essentially) of specified gene products in the progression of disease. In this manner, other genetic targets may be defined as important mediators of the disease. These studies lead to better treatment of the disease progression by affording the possibility of combination therapies (e.g., multiple ribozymes targeted to different genes, ribozymes coupled with known small molecule inhibitors, or intermittent treatment with combinations of ribozymes and/or other chemical or biological molecules).
4.3 Promoters and Enhancers
Recombinant vectors form important aspects of the present invention. The term “expression vector or construct” means any type of genetic construct containing a nucleic acid in which part or all of the nucleic acid encoding sequence is capable of being transcribed. In preferred embodiments, expression only includes transcription of the nucleic acid, for example, to generate ribozyme constructs.
Particularly useful vectors are contemplated to be those vectors in which the nucleic acid segment to be transcribed is positioned under the transcriptional control of a promoter. A “promoter” refers to a DNA sequence recognized by the synthetic machinery of the cell, or introduced synthetic machinery, required to initiate the specific transcription of a gene. The phrases “operatively positioned,” “under control” or “under transcriptional control” means that the promoter is in the correct location and orientation in relation to the nucleic acid to control RNA polymerase initiation and expression of the gene.
In preferred embodiments, it is contemplated that certain advantages will be gained by positioning the coding DNA segment under the control of a recombinant, or heterologous, promoter. As used herein, a recombinant or heterologous promoter is intended to refer to a promoter that is not normally associated with a ribozyme construct in its natural environment. Such promoters may include promoters normally associated with other genes, and/or promoters isolated from any other bacterial, viral, eukaryotic, or mammalian cell.
Naturally, it will be important to employ a promoter that effectively directs the expression of the DNA segment in the cell type, organism, or even animal, chosen for expression. The use of promoter and cell type combinations for protein expression is generally known to those of skill in the art of molecular biology; for example, see Sambrook et al. (1989), incorporated herein by reference. The promoters employed may be constitutive, or inducible, and can be used under the appropriate conditions to direct high-level expression of the introduced DNA segment.
At least one module in a promoter functions to position the start site for RNA synthesis. The best-known example of this is the TATA box, but in some promoters lacking a TATA box, such as the promoter for the mammalian terminal deoxynucleotidyl transferase gene and the promoter for the SV40 late genes, a discrete element overlying the start site itself helps to fix the place of initiation.
Additional promoter elements regulate the frequency of transcriptional initiation. Typically, these are located in the region 30-110 bp upstream of the start site, although a number of promoters have been shown to contain functional elements downstream of the start site as well. The spacing between promoter elements frequently is flexible, so that promoter function is preserved when elements are inverted or moved relative to one another. In the tk promoter, the spacing between promoter elements can be increased to 50 bp apart before activity begins to decline. Depending on the promoter, it appears that individual elements can function either co-operatively or independently to activate transcription.
The particular promoter that is employed to control the expression of a nucleic acid is not believed to be critical, so long as it is capable of expressing the nucleic acid in the targeted cell. Thus, where a human cell is targeted, it is preferable to position the nucleic acid coding region adjacent to and under the control of a promoter that is capable of being expressed in a human cell. Generally speaking, such a promoter might include either a human or viral promoter, such as a CMV or an HSV promoter. In certain aspects of the invention, tetracycline controlled promoters are contemplated.
In various other embodiments, the human cytomegalovirus (CMV) immediate early gene promoter, the SV40 early promoter and the Rous sarcoma virus long terminal repeat can be used to obtain high-level expression of transgenes. The use of other viral or mammalian cellular or bacterial phage promoters that are well known in the art to achieve expression of a transgene is contemplated as well, provided that the levels of expression are sufficient for a given purpose. Tables 1 and 2 below list several elements/promoters that may be employed, in the context of the present invention, to regulate the expression of the present ribozyme constructs. This list is not intended to be exhaustive of all the possible elements involved in the promotion of transgene expression but, merely, to be exemplary thereof.
Enhancers were originally detected as genetic elements that increased transcription from a promoter located at a distant position on the same molecule of DNA. This ability to act over a large distance had little precedent in classic studies of prokaryotic transcriptional regulation. Subsequent work showed that regions of DNA with enhancer activity are organized much like promoters. That is, they are composed of many individual elements, each of which binds to one or more transcriptional proteins.
The basic distinction between enhancers and promoters is operational. An enhancer region as a whole must be able to stimulate transcription at a distance; this need not be true of a promoter region or its component elements. On the other hand, a promoter must have one or more elements that direct initiation of RNA synthesis at a particular site and in a particular orientation, whereas enhancers lack these specificities. Promoters and enhancers are often overlapping and contiguous, often seeming to have a very similar modular organization.
Additionally any promoter/enhancer combination (as per the Eukaryotic Promoter Data Base EPDB) could also be used to drive expression. Use of a T3, T7 or SP6 cytoplasmic expression system is another possible embodiment. Eukaryotic cells can support cytoplasmic transcription from certain bacterial promoters if the appropriate bacterial polymerase is provided, either as part of the delivery complex or as an additional genetic expression construct.
As used herein, the terms “engineered” and “recombinant” cells are intended to refer to a cell into which an exogenous DNA segment, such as DNA segment that leads to the transcription of a ribozyme, has been introduced. Therefore, engineered cells are distinguishable from naturally occurring cells, which do not contain a recombinantly introduced exogenous DNA segment. Engineered cells are thus cells having DNA segment introduced through the hand of man.
To express a ribozyme in accordance with the present invention one would prepare an expression vector that comprises a ribozyme-encoding nucleic acid under the control of one or more promoters. To bring a sequence “under the control of” a promoter, one positions the 5′ end of the transcription initiation site of the transcriptional reading frame generally between about 1 and about 50 nucleotides “downstream” of (i.e., 3′ of) the chosen promoter. The “upstream” promoter stimulates transcription of the DNA and promotes expression of the encoded ribozyme. This is the meaning of “recombinant expression” in this context.
4.4 Adeno-Associated Virus (AAV)
Adeno-associated virus (AAV) is particularly attractive for gene transfer because it does not induce any pathogenic response and can integrate into the host cellular chromosome (Kotin et al., 1990). The AAV terminal repeats (TRs) are the only essential cis-components for the chromosomal integration (Muzyczka and McLaughin, 1988). These TRs are reported to have promoter activity (Flotte et al., 1993). They may promote efficient gene transfer from the cytoplasm to the nucleus or increase the stability of plasmid DNA and enable longer-lasting gene expression (Bartlett et al., 1996). Studies using recombinant plasmid DNAs containing AAV TRs have attracted considerable interest. AAV-based plasmids have been shown to drive higher and longer transgene expression than the identical plasmids lacking the TRs of AAV in most cell types (Philip et al., 1994; Shafron et al., 1998; Wang et al., 1999).
AAV (Ridgeway, 1988; Hermonat and Muzyczka, 1984) is a parvovirus, discovered as a contamination of adenoviral stocks. It is a ubiquitous virus (antibodies are present in 85% of the US human population) that has not been linked to any disease. It is also classified as a dependovirus, because its replication is dependent on the presence of a helper virus, such as adenovirus. Five serotypes have been isolated, of which AAV-2 is the best characterized. AAV has a single-stranded linear DNA that is encapsidated into capsid proteins VP1, VP2 and VP3 to form an icosahedral virion of 20 to 24 nm in diameter (Muzyczka and McLaughlin, 1988).
The AAV DNA is approximately 4.7 kilobases long. It contains two open reading frames and is flanked by two ITRs. There are two major genes in the AAV genome: rep and cap. The rep gene encodes a protein responsible for viral replications, whereas the cap gene encodes the capsid protein VP1-3. Each ITR forms a T-shaped hairpin structure. These terminal repeats are the only essential cis components of the AAV for chromosomal integration. Therefore, the AAV can be used as a vector with all viral coding sequences removed and replaced by the cassette of genes for delivery. Three viral promoters have been identified and named p5, p19, and p40, according to their map position. Transcription from p5 and p19 results in production of rep proteins, and transcription from p40 produces the capsid proteins (Hermonat and Muzyczka, 1984).
There are several factors that prompted researchers to study the possibility of using rAAV as an expression vector. One is that the requirements for delivering a gene to integrate into the host chromosome are surprisingly few. It is necessary to have the 145-bp ITRs, which are only 6% of the AAV genome. This leaves room in the vector to assemble a 4.5-kb DNA insertion. While this carrying capacity may prevent the AAV from delivering large genes, it is amply suited for delivering the antisense constructs of the present invention.
AAV is also a good choice of delivery vehicles due to its safety. There is a relatively complicated rescue mechanism: not only wild type adenovirus but also AAV genes are required to mobilize rAAV. Likewise, AAV is not pathogenic and not associated with any disease. The removal of viral coding sequences minimizes immune reactions to viral gene expression, and therefore, rAAV does not evoke an inflammatory response. AAV therefore, represents an ideal candidate for delivery of the present hammerhead ribozyme constructs.
4.5 Pharmaceutical Compositions and Kits
Pharmaceutical compositions of the present invention will generally comprise an effective amount of at least a first ribozyme or ribozyme library, incorporated into an adeno-associated viral vector, or adeno-associated viral particles containing at least a first ribozyme or ribozyme library, dissolved or dispersed in a pharmaceutically acceptable carrier or aqueous medium.
The phrases “pharmaceutically or pharmacologically acceptable” refer to molecular entities and compositions that do not produce an adverse, allergic or other untoward reaction when administered to an animal, or a human, as appropriate. As used herein, “pharmaceutically acceptable carrier” includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.
4.5.1 Parenteral Formulations
The agents of the present invention will often be formulated for parenteral administration, e.g., formulated for injection via the intravenous, intramuscular, sub-cutaneous or other such routes. The preparation of an aqueous composition that contains one or more agents, such as a ribozyme, ribozyme library or adeno-associated virus containing a ribozyme or ribozyme library, will be known to those of skill in the art in light of the present disclosure. Typically, such compositions can be prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for using to prepare solutions or suspensions upon the addition of a liquid prior to injection can also be prepared; and the preparations can also be emulsified.
Solutions of the active compounds as freebase or pharmacologically acceptable salts can be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms.
The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions; formulations including sesame oil, peanut oil or aqueous propylene glycol; and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. In all cases the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi.
Compositions comprising the agents of the present invention can be formulated into a composition in a neutral or salt form. Pharmaceutically acceptable salts include the acid addition salts and those formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like.
The carrier can also be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), dimethylsulfoxide (DMSO), suitable mixtures thereof, and vegetable oils. The proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying techniques, which yield a powder of the active ingredient, plus any additional desired ingredient from a previously sterile-filtered solution thereof.
Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is biologically or therapeutically effective. Formulations are easily administered in a variety of dosage forms, such as the type of injectable solutions described above, but drug release capsules and the like can also be employed.
Suitable pharmaceutical compositions in accordance with the invention will generally include an amount of one or more of the agents of the present invention admixed with an acceptable pharmaceutical diluent or excipient, such as a sterile aqueous solution, to give a range of final concentrations, depending on the intended use. The techniques of preparation is generally well known in the art as exemplified by Remington's Pharmaceutical Sciences, 16th Ed. Mack Publishing Company, 1980, incorporated herein by reference. It should be appreciated that endotoxin contamination should be kept minimally at a safe level, for example, less that 0.5 ng/mg protein. Moreover, for human administration, preparations should meet sterility, pyrogenicity, general safety and purity standards as required by FDA Office of Biological Standards.
In addition to the compounds formulated for parenteral administration, such as intravenous or intramuscular injection, other pharmaceutically acceptable forms are also contemplated, e.g., tablets or other solids for oral administration, time release capsules, liposomal forms and the like. Other pharmaceutical formulations may also be used, dependent on the condition to be treated. Of course, methods for the determination of optimal dosages for conditions such as these would be evident to those of skill in the art in light of the instant specification, and the knowledge of the skilled artisan.
It is contemplated that certain benefits will result from the manipulation of the agents of the present invention to provide them with a longer in vivo half-life. Slow release formulations are generally designed to give a constant drug level over an extended period. Increasing the half-life of a drug, such as agents of the present invention, is intended to result in high intracellular levels upon administration, which levels are maintained for a longer time, but which levels generally decay depending on the pharmacokinetics of the construct.
4.5.2 Therapeutic Kits
The present invention also provides therapeutic kits comprising the agents of the present invention described herein. Such kits will generally contain, in suitable container, a pharmaceutically acceptable formulation of at least a first ribozyme, ribozyme library or adeno-associated virus particles comprising at least a first ribozyme or ribozyme library, in accordance with the invention. The kits may also contain other pharmaceutically acceptable formulations.
The kits may have a single container that contains the agent, with or without any additional components, or they may have distinct container means for each desired agent. In such kits, the components may be pre-complexed, either in a molar equivalent combination, or with one component in excess of the other; or each of the components of the kit may be maintained separately within distinct containers prior to administration to a patient.
When the components of the kit are provided in one or more liquid solutions, the liquid solution is an aqueous solution, with a sterile aqueous solution being particularly preferred. However, the components of the kit may be provided as dried powder(s). When reagents or components are provided as a dry powder, the powder can be reconstituted by the addition of a suitable solvent. It is envisioned that the solvent may also be provided in another container means. One of the components of the kit may be provided in capsules for oral administration.
The container means of the kit will generally include at least one vial, test tube, flask, bottle, syringe or other container means, into which a ribozyme, ribozyme library or adeno-associated viral particles comprising a ribozyme or ribozyme library, and any other desired agent, may be placed and, preferably, suitably aliquoted. Where additional components are included, the kit will also generally contain a second vial or other container into which these are placed, enabling the administration of separated designed doses. The kits may also comprise a second/third container means for containing a sterile, pharmaceutically acceptable buffer or other diluent.
The kits may also contain a means by which to administer the ribozyme, ribozyme library or adeno-associated viral particles comprising a ribozyme or ribozyme library to an animal or patient, e.g., one or more needles or syringes, or even an eye dropper, pipette, or other such like apparatus, from which the formulation may be injected into the animal or applied to a diseased area of the body. The kits of the present invention will also typically include a means for containing the vials, or such like, and other component, in close confinement for commercial sale, such as, e.g., injection or blow-molded plastic containers into which the desired vials and other apparatus are placed and retained.
4.6 Mutagenesis
Site-specific mutagenesis is a technique useful in the preparation and testing of sequence variants by introducing one or more nucleotide sequence changes into the DNA. Site-specific mutagenesis allows the production of mutants through the use of specific oligonucleotide sequences which encode the DNA sequence of the desired mutation, as well as a sufficient number of adjacent nucleotides, to provide a primer sequence of sufficient size and sequence complexity to form a stable duplex on both sides of the deletion junction being traversed. Typically, a primer of about 17 to 25 nucleotides in length is preferred, with about 5 to 10 residues on both sides of the junction of the sequence being altered.
In general, the technique of site-specific mutagenesis is well known in the art. As will be appreciated, the technique typically employs a bacteriophage vector that exists in both a single stranded and double stranded form. Typical vectors useful in site-directed mutagenesis include vectors such as the M13 phage. These phage vectors are commercially available and their use is generally well known to those skilled in the art. Double stranded plasmids are also routinely employed in site directed mutagenesis, which eliminates the step of transferring the gene of interest from a phage to a plasmid.
In general, site-directed mutagenesis is performed by first obtaining a single-stranded vector, or melting of two strands of a double stranded vector that includes within its sequence a DNA sequence encoding the desired ribozyme or other nucleic acid construct. An oligonucleotide primer bearing the desired mutated sequence is synthetically prepared. This primer is then annealed with the single-stranded DNA preparation, and subjected to DNA polymerizing enzymes such as E. coli polymerase I Klenow fragment, in order to complete the synthesis of the mutation-bearing strand. Thus, a heteroduplex is formed wherein one strand encodes the original non-mutated sequence and the second strand bears the desired mutation. This heteroduplex vector is then used to transform appropriate cells, such as E. coli cells, and clones are selected that include recombinant vectors bearing the mutated sequence arrangement.
The preparation of sequence variants of the selected ribozyme using site-directed mutagenesis is provided as a means of producing potentially useful species and is not meant to be limiting, as there are other ways in which sequence variants may be obtained. For example, recombinant vectors encoding the desired gene may be treated with mutagenic agents, such as hydroxylamine, to obtain sequence variants.
4.7 Nucleic Acid Amplification
Nucleic acid, used as a template for amplification, may be isolated from cells contained in the biological sample according to standard methodologies (Sambrook et al., 1989). The nucleic acid may be genomic DNA or fractionated or whole cell RNA. Where RNA is used, it may be desired to convert the RNA to a complementary DNA. In one embodiment, the RNA is whole cell RNA and is used directly as the template for amplification.
Pairs of primers that selectively hybridize to nucleic acids corresponding to the ribozymes or conserved flanking regions are contacted with the isolated nucleic acid under conditions that permit selective hybridization. The term “primer”, as defined herein, is meant to encompass any nucleic acid that is capable of priming the synthesis of a nascent nucleic acid in a template-dependent process. Typically, primers are oligonucleotides from ten to twenty base pairs in length, but longer sequences can be employed. Primers may be provided in double-stranded or single-stranded form, although the single-stranded form is preferred.
Once hybridized, the nucleic acid:primer complex is contacted with one or more enzymes that facilitate template-dependent nucleic acid synthesis. Multiple rounds of amplification, also referred to as “cycles,” are conducted until a sufficient amount of amplification product is produced.
Next, the amplification product is detected. In certain applications, the detection may be performed by visual means. Alternatively, the detection may involve indirect identification of the product via chemiluminescence, radioactive scintigraphy of incorporated radiolabel or fluorescent label or even via a system using electrical or thermal impulse signals (Affymax technology).
A number of template dependent processes are available to amplify the marker sequences present in a given template sample. One of the best-known amplification methods is the polymerase chain reaction (referred to as PCR™), which is described in detail in U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,800,159 (each of which is incorporated herein by reference in its entirety).
Briefly, in PCR™, two primer sequences are prepared that are complementary to regions on opposite complementary strands of the marker sequence. An excess of deoxynucleoside triphosphates is added to a reaction mixture along with a DNA polymerase, e.g., Taq polymerase. If the marker sequence is present in a sample, the primers will bind to the marker and the polymerase will cause the primers to be extended along the marker sequence by adding on nucleotides. By raising and lowering the temperature of the reaction mixture, the extended primers will dissociate from the marker to form reaction products, excess primers will bind to the marker and to the reaction products and the process is repeated.
A reverse transcriptase PCR™ amplification procedure may be performed in order to quantify the amount of mRNA amplified. Methods of reverse transcribing RNA into cDNA are well known and described in Sambrook et al. (1989). Alternative methods for reverse transcription utilize thermostable, RNA-dependent DNA polymerases. These methods are described in Int. Pat. Appl. Publ. No. WO 90/07641 (specifically incorporated herein by reference). Polymerase chain reaction methodologies are well known in the art.
Another method for amplification is the ligase chain reaction (“LCR”), disclosed in EPA No. 320 308, incorporated herein by reference in its entirety. In LCR, two complementary probe pairs are prepared, and in the presence of the target sequence, each pair will bind to opposite complementary strands of the target such that they abut. In the presence of a ligase, the two probe pairs will link to form a single unit. By temperature cycling, as in PCR™, bound ligated units dissociate from the target and then serve as “target sequences” for ligation of excess probe pairs. U.S. Pat. No. 4,883,750 describes a method similar to LCR for binding probe pairs to a target sequence.
Qβ Replicase (QβR), described in Int. Pat. Appl. No. PCT/US87/00880, incorporated herein by reference, may also be used as still another amplification method in the present invention. In this method, a replicative sequence of RNA that has a region complementary to that of a target is added to a sample in the presence of an RNA polymerase. The polymerase will copy the replicative sequence that can then be detected.
An isothermal amplification method, in which restriction endonucleases and ligases are used to achieve the amplification of target molecules that contain nucleotide 5′-[α-thio]-triphosphates in one strand of a restriction site may also be useful in the amplification of nucleic acids in the present invention.
Strand Displacement Amplification (SDA), described in U.S. Pat. Nos. 5,455,166, 5,648,211, 5,712,124 and 5,744,311, each incorporated herein by reference, is another method of carrying out isothermal amplification of nucleic acids which involves multiple rounds of strand displacement and synthesis, i.e., nick translation. A similar method, called Repair Chain Reaction (RCR), involves annealing several probes throughout a region targeted for amplification, followed by a repair reaction in which only two of the four bases are present. The other two bases can be added as biotinylated derivatives for easy detection. A similar approach is used in SDA. Target specific sequences can also be detected using a cyclic probe reaction (CPR). In CPR, a probe having 3′ and 5′ sequences of non-specific DNA and a middle sequence of specific RNA is hybridized to DNA that is present in a sample. Upon hybridization, the reaction is treated with RNase H, and the products of the probe identified as distinctive products that are released after digestion. The original template is annealed to another cycling probe and the reaction is repeated.
Still another amplification methods described in GB Application No. 2 202 328, and in Int. Pat. Appl. No. PCT/US89/01025, each of which is incorporated herein by reference in its entirety, may be used in accordance with the present invention. In the former application, “modified” primers are used in a PCR™-like, template- and enzyme-dependent synthesis. The primers may be modified by labeling with a capture moiety (e.g., biotin) and/or a detector moiety (e.g., enzyme). In the latter application, an excess of labeled probes is added to a sample. In the presence of the target sequence, the probe binds and is cleaved catalytically. After cleavage, the target sequence is released intact to be bound by excess probe. Cleavage of the labeled probe signals the presence of the target sequence.
Other nucleic acid amplification procedures include transcription-based amplification systems (TAS), including nucleic acid sequence based amplification (NASBA) and 3SR Gingeras et al., Int. Pat. Appl. Publ. No. WO 88/10315, incorporated herein by reference. In NASBA, the denaturation of a clinical sample, treatment with lysis buffer and minispin columns for isolation of DNA and RNA or guanidinium chloride extraction of RNA. These amplification techniques involve annealing a primer that has target specific sequences. Following polymerization, DNA/RNA hybrids are digested with RNase H while double stranded DNA molecules are heat denatured again. In either case the single stranded DNA is made fully double stranded by addition of second target specific primer, followed by polymerization. The double-stranded DNA molecules are then multiply transcribed by an RNA polymerase such as T7 or SP6. In an isothermal cyclic reaction, the RNA's are reverse transcribed into single stranded DNA, which is then converted to double stranded DNA, and then transcribed once again with an RNA polymerase such as T7 or SP6. The resulting products, whether truncated or complete, indicate target specific sequences.
Davey et al, EPA No. 329 822 (incorporated herein by reference in its entirety) disclose a nucleic acid amplification process involving cyclically synthesizing single-stranded RNA (“ssRNA”), ssDNA, and double-stranded DNA (dsDNA), which may be used in accordance with the present invention. The ssRNA is a template for a first primer oligonucleotide, which is elongated by reverse transcriptase (RNA-dependent DNA polymerase). The RNA is then removed from the resulting DNA:RNA duplex by the action of ribonuclease H(RNase H, an RNase specific for RNA in duplex with either DNA or RNA). The resultant ssDNA is a template for a second primer, which also includes the sequences of an RNA polymerase promoter (exemplified by T7 RNA polymerase) 5′ to its homology to the template. This primer is then extended by DNA polymerase (exemplified by the large “Klenow” fragment of E. coli DNA polymerase I), resulting in a double-stranded DNA (“dsDNA”) molecule, having a sequence identical to that of the original RNA between the primers and having additionally, at one end, a promoter sequence. This promoter sequence can be used by the appropriate RNA polymerase to make many RNA copies of the DNA. These copies can then re-enter the cycle leading to very swift amplification. With proper choice of enzymes, this amplification can be done isothermally without addition of enzymes at each cycle. Because of the cyclical nature of this process, the starting sequence can be chosen to be in the form of either DNA or RNA.
Miller et al., Int. Pat. Appl. Publ. No. WO 89/06700 (incorporated herein by reference in its entirety) disclose a nucleic acid sequence amplification scheme based on the hybridization of a promoter/primer sequence to a target single-stranded DNA (“ssDNA”) followed by transcription of many RNA copies of the sequence. This scheme is not cyclic, i.e., new templates are not produced from the resultant RNA transcripts. Other amplification methods include “RACE” and “one-sided PCR™” (Frohman, 1990, specifically incorporated herein by reference).
Methods based on ligation of two (or more) oligonucleotides in the presence of nucleic acid having the sequence of the resulting “di-oligonucleotide,” thereby amplifying the di-oligonucleotide, may also be used in the amplification step of the present invention.
Following any amplification, it may be desirable to separate the amplification product from the template and the excess primer for the purpose of determining whether specific amplification has occurred. In one embodiment, amplification products are separated by agarose, agarose-acrylamide or polyacrylamide gel electrophoresis using standard methods (see e.g., Sambrook et al., 1989).
Alternatively, chromatographic techniques may be employed to effect separation. There are many kinds of chromatography which may be used in the present invention: adsorption, partition, ion-exchange and molecular sieve, and many specialized techniques for using them including column, paper, thin-layer and gas chromatography.
Amplification products must be visualized in order to confirm amplification of the marker sequences. One typical visualization method involves staining of a gel with ethidium bromide and visualization under UV light. Alternatively, if the amplification products are integrally labeled with radio- or fluorometrically-labeled nucleotides, the amplification products can then be exposed to x-ray film or visualized under the appropriate stimulating spectra, following separation.
In one embodiment, visualization is achieved indirectly. Following separation of amplification products, a labeled, nucleic acid probe is brought into contact with the amplified marker sequence. The probe preferably is conjugated to a chromophore but may be radiolabeled. In another embodiment, the probe is conjugated to a binding partner, such as an antibody or biotin, and the other member of the binding pair carries a detectable moiety.
In one embodiment, detection is by Southern blotting and hybridization with a labeled probe. The techniques involved in Southern blotting are well known to those of skill in the art and can be found in many standard books on molecular protocols. See Sambrook et al., 1989. Briefly, amplification products are separated by gel electrophoresis. The gel is then contacted with a membrane, such as nitrocellulose, permitting transfer of the nucleic acid and non-covalent binding. Subsequently, the membrane is incubated with a chromophore-conjugated probe that is capable of hybridizing with a target amplification product. Detection is by exposure of the membrane to x-ray film or ion-emitting detection devices.
One example of the foregoing is described in U.S. Pat. No. 5,279,721, incorporated by reference herein, which discloses an apparatus and method for the automated electrophoresis and transfer of nucleic acids. The apparatus permits electrophoresis and blotting without external manipulation of the gel and is ideally suited to carrying out methods according to the present invention.
The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventors to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.
Preparation of Ribozyme and Selection of Ribozyme Targets
Targets for ribozymes are chosen from complete cDNA sequences or 100-300 nt expressed sequence tags from among genes that are highly expressed in photoreceptor cells or the retinal pigment epithelium. Targets consist of 4 nucleotides 5′ and 6 nucleotides 3′ of the nucleotide triplets GUC, CUC, UUC or AUC. Analysis of possible secondary structure of the 25 nt sequence containing the target sites is made using the MFOLD algorithm (http://mfold2.wustl.edu/rna/form.cgi, Genetics Computer Group, Madison, Wis.), and targets likely to be embedded in local stem structures are avoided. Ribozyme-accessible sites may also be detected by treatment with single-strand RNA-specific modifying reagents (Shaw and Lewin, 1995).
Hammerhead ribozymes of the general structure shown in
Target sequences of 14 nucleotides and cognate ribozymes are chemically synthesized and obtained from a commercial vendor (Dharmacon, Inc. Boulder, Colo.). Protecting groups are removed from the 2′ positions of RNA oligonucleotides according to the manufacturer's instructions, and oligonucleotides are labeled with polynucleotide kinase and [γ-32P]ATP at 37° C. for 30 minutes and then is diluted to 100 μl with sterile water and extracted with phenol:chloroform:isoamyl alcohol (50:50:1) to inactivate the enzyme. Unincorporated nucleotides are removed by passing the aqueous phase over a G-25 Sephadex spin column. Ribozymes or larger targets (>30 nucleotides) are purified on 8% acrylamide, 8M urea sequencing gels run in TBE buffer (89 mM Tris borate, pH 8.3, 20 mM EDTA). Labeled molecules are visualized by autoradiography, excised with a sterile scalpel, and eluted from the gel in 1 M NH4OAc, 50 mM Tris HCl, pH 7.5, 20 mM EDTA, 0.5% SDS at 37° C. for 1-4 hours. In embodiments where the gel purification is omitted, the transcript is treated with RNase-free DNase I to remove DNA sequences that may anneal to the target or to the ribozyme.
Specific radioactivity of each molecule is used to calculate the concentration of target and ribozyme molecules. Analyses to determine multiple turnover kinetic constants are typically carried out in 20 mM MgCl2, 40 mM Tris-HCl, pH 7.5, at 37° C. for short intervals. The appropriate interval is determined by a time-course experiment under multiple turnover conditions (i.e. substrate excess). Cleavage products for target RNAs produced by in vitro transcription are analyzed by electrophoresis on 8 or 10% acrylamide 8 M urea sequencing gels run in TBE. Initial rates are measured when the amount of cleavage is linear with time and when no more than 10% of substrate has been converted to product. Rates are measured at several intervals (e.g., 5, 10 and 20 min) to insure linearity. Samples are pre-incubated at 37° C. prior to initiation of cleavage and contain 1-10 nM ribozyme and increasing concentrations of substrate RNA, holding ribozyme concentration constant. Substrate concentrations greatly exceed ribozyme concentration, the lowest being in 5-fold excess. Kinetic parameters are obtained by double reciprocal plots of velocity versus substrate concentration (Lineweaver-Burke plots) or by plots of reaction velocity versus the ratio of velocity to substrate concentration (Eadie-Hofstee plots). Ribozymes with a kcat of less than 0.5 min or a KM>5 μM are discarded.
DNA oligonucleotides encoding kinetically competent ribozymes are cloned in a derivative of AAV vector pTR-GS-HP (
5.1.1 Construction of the Vector Backbone
AAV vectors are packaged using a 2-plasmid transfection system and EK 293 cells as follows. To produce rAAV, a triple co-transfection procedure is used to introduce a rAAV vector plasmid together with pACG2 AAV helper plasmid and pXX6 Ad helper plasmid (Xiao et al., 1998) at a 1:1:1 molar ratio. Alternatively, rAAV vector plasmid is co-transfected with the helper plasmid pDG carrying the AAV rep and cap genes, as well as Ad helper genes required for rAAV replication and packaging (Grimm et al., 1998). Plasmid DNA used in the transfection is purified by a conventional alkaline lysis/CsCl gradient protocol. The transfection is carried out as follows: 293 cells are split 1:2 the day prior to the experiment, so that, when transfected, the cell confluence is about 75-80%. Ten 15-cm plates are transfected as one batch. To make CaPO4 precipitate, 180 μg of pACG2 is mixed with 180 μg of rAAV vector plasmid and 540 μg of pXX6 in a total volume of 12.5 ml of 0.25 M CaCl2. Alternatively, 0.7 mg of pDG and 180 μg of rAAV vector plasmid are mixed in the same volume. The old media is removed from the cells and the formation of the CaPO4-precipitate is initiated by adding 12.5 ml of 2×HBS pH 7.05 (pre-warmed at 37° C. to the DNA-CaCl2 solution. The DNA is incubated for 1 min; and transferring the mixture into pre-warmed 200 ml of DMEM-10% FBS stops the formation of the precipitate. Twenty-two ml of the media is immediately dispensed into each plate and cells are incubated at 37° C. for 48 hrs. The CaPO4-precipitate is allowed to stay on the cells during the whole incubation period without compromising cell viability. Forty-eight hr post-transfection cells are harvested by centrifugation at 1,140×g for 10 min; the media is discarded. Cells are then lysed in 15 ml of 0.15 M NaCl, 50 mM Tris HCl pH 8.5 by 3 freeze/thaw cycles in dry ice-ethanol and 37° C. baths. Benzonase™ (Nycomed Pharma A/S, pure grade, Benzon Pharma A/S, Roskilde, Denmark) is added to the mixture (50 U/ml, final concentration) and the lysate is incubated for 30 min at 37° C. The lysate is clarified by centrifugation at 3,700×g for 20 min and the virus-containing supernatant is considered the crude lysate, from which a high titer stock can be prepared using standard protocols. No helper adenovirus is used in this preparation. Infectious titers are routinely 1010-1011 virus per milliliter.
5.1.2 Assay of Ribozyme Activity
To test for the function of target genes, 2 μl of AAV-expressing ribozymes are injected subretinally in the right eyes of 15-day-old mice, under general and local anesthetic. This leads to a local retinal detachment that resolves within minutes. Groups of 8 mice are used for each ribozyme construct, and the left eyes of these animals are untreated and serve as controls. Animals which develop cataracts as a result of the injection or which show signs of injury or inflammation are removed from the study and euthanized.
At 6 weeks of age (4 weeks post injection) animals are assayed for retinal function by electroretinography (ERG) and for retinal thickness by optical coherence tomography (OCT) (Ripandelli et al., 1998; Jacobson et al., 1998). For ERG, mice are dark adapted overnight, and then in dim red light anesthetized with intramuscular injections of xylazine (13 mg/kg) and ketamine (87 mg/kg). Full-field scotopic ERGs are elicited with 10-μsec flashes of white light and responses are recorded using a UTAS-E 2000 Visual Electrodiagnostic System (LKC Technologies, Inc., Gaithersburg, Md.). The corneas of the mice are anesthetized with a drop of 0.5% proparacaine hydrochloride, and the pupils are dilated with 1% atropine and 2.5% phenylephrine hydrochloride. Small contact lenses with gold wire loops are placed on both corneas with a drop of 2.5% methylcellulose to maintain corneal hydration. A silver wire reference electrode is placed subcutaneously between the eyes and a ground electrode is placed subcutaneously in the hind leg. Stimuli are presented at intensities of −1.1, 0.9 and 1.9 log cd m−2 at 10-second, 30-second and 1-minute intervals, respectively. Responses are amplified at a gain of 4,000, filtered between 0.3 to 500 Hz and digitized at a rate of 2,000 Hz on 2 channels. Three responses are averaged for each intensity. The a-waves are measured from the baseline to the peak in the cornea-negative direction, and b-waves are measured from the cornea-negative peak to the major cornea-positive peak. For quantitative comparison of differences between the two eyes of mice, the values from all the stimulus intensities are averaged for a given animal.
This analysis is repeated at 16 weeks of age, at which time all animals are euthanized. Left and right eyes of the animals showing evidence of retinal degeneration (by either ERG or OCT) are fixed in a mixture of mixed aldehydes (2% formaldehyde and 2.5% glutaraldehyde). Eyes are embedded in epoxy resin, and 1-μm thick histological sections are made along the vertical meridian. Tissue sections are aligned so that the ROS and Müller cell processes crossing the inner plexiform layer are continuous throughout the plane of section to assure that the sections are not oblique, and the thickness of the ONL and lengths of RIS and ROS are measured (Faktorovich et al., 1990). RPE and choroidal layers are examined for evidence of neovascularization, RPE cell death or abnormal deposits.
AAV-ribozymes that lead to retinal degeneration are tested a second time in a similar protocol to confirm the result. EST clones are identified as containing ribozyme targets the cleavage of which leads to retinal dystrophy in animals. Clamped PCR™ methods (5′ and 3′ RACE) are used to sequence the entire cDNAs for ESTs containing those targets. Searches of GenBank and other sequence databases are made to identify known genes or similarity to genes of known function. The tissue distribution of gene expression of ESTs of interest is determined by Northern hybridization of RNA extracted from a variety of mouse tissues.
5.1.3 Identification of Candidate Genes
In situ hybridization analysis is used to map the general genomic location of previously unknown genes. This is followed by mapping of the gene by hybridization to YAC, BAC and cosmid clones of the mouse genome. Based on the synteny between the human and mouse genomes, this information is used to map genes of interest in intervals of the human genome. In these way regions containing candidate genes for inherited retinal disease are identified. Of particular interest are loci mapped on the human genome that contain unknown genes responsible for retinal degeneration (Daiger et al., 1998).
Similar analysis is performed for all three retinal-specific promoters. Because these promoters function in a retinal specific manner in a variety of mammals, similar analysis is conducted using other animal models. For example, AAV-ribozymes are tested in the cone-rich retina of pigs and in the macular retina of rhesus macaques.
The 7-kb vector pTR-GS-HP (
In pTR-UF33-HP (
Candidate Genes for Retinal Degeneration
5.2.1 β-Subunit of Mouse cGMP Phosphodiesterase
Using the rod opsin promoters that are well characterized in vivo a retinitis pigmentosa (RP)-like rod degeneration was created in rd/+mice (Bowes et al., 1990; Bennett et al., 1998). These mice have one rd allele and one wild-type allele of the gene for the β-subunit of cGMP phosphodiesterase (βPDE; GenBank Accession No. X55968), and have an apparently normal retina at all ages. In the homozygous condition, the rd/rd mouse is a classical animal model for recessive RP, losing all rods within a month or two after birth.
A ribozyme was designed (
5.2.2 γ-Subunit of Mouse cGMP Phosphodiesterase
Two novel ribozymes have been generated that target the gamma subunit of the cyclic GMP phosphodiesterase. These are termed HHRZ35 and HHRZ42 (
Candidate Tumor Suppressor Genes
The analysis of DNA isolated from malignant tumors has identified two major groups of genes that are involved in tumorigenesis, oncogenes and tumor suppressor genes (Knudson 1993). The former is a group of genes that are overactive or constitutively active due to certain mutations and lead to uncontrolled cell growth. These genes often are transcription factors, such as the ras-family, or genes that drive the cell cycle into G1 and S phase (Collins et al., 1997). The latter group, tumor suppressor genes, inhibits progression of the cell cycle. The major role of tumor suppressor genes such as p53, p16, Smad4 (DPC4) or Rb in tumorigenesis is widely recognized. They also play an important role in determining the biological behavior of (metastasis, growth dynamics, invasion) of malignant tumors (Vogelstein and Kinzler, 1993). Although roughly 20 tumor suppressor genes are known, an estimated 100 exist. Currently, the search and discovery of new potential tumor suppressor genes is a long and laborious process.
A library of hammerhead ribozymes is delivered by recombinant AAV to several tissues (liver, skeletal muscle, epithelium of the small and large intestine, retina). Recombinant AAV has been shown to stably express a transgene at high levels in various tissues (brain, liver, skeletal muscle, retina, intestinal epithelium) for up to 18 months (Klein et al., 1998; Song et al., 1998; Flannery et al., 1997; Herzog et al., 1997; During et al., 1998; Fisher et al., 1997). Ribozymes contained in the library that target a tumor suppressor gene cause a tumor to arise from that particular cell. The tumor growth itself is an amplification step that makes the isolation of that individual ribozyme more straightforward. Using the specific recognition sequence of these ribozymes, new potential tumor suppressor genes are discovered.
In order to facilitate the induction of malignant tumors, ribozymes against known tumor suppressor genes (p53, p16, p19ARF and Retinoblastoma (Rb); “positive control” ribozymes) are injected in combination with the library. The probability of infecting a single cell with two recombinant AAV vectors at the same time (e.g., in the liver) is approximately 5-10%. As a “positive control” ribozymes that target known tumor suppressor genes, e.g., are included. They are injected individually or in combination to induce tumor development in mice.
Tumorigenesis is a multi-step process that involves a series of genetic alterations and mutations (Vogelstein and Kinzler, 1993). The two major groups of genes that are involved in this process are oncogenes and tumor suppressor genes (Knudson, 1993). Mutations in the two tumor-suppressor genes encoding p53 and the retinoblastoma protein (Rb), which function as important regulators of the cell cycle, lead to transformation of the cell and ultimately autonomous tumor growth (Collins et al., 1997). The causative role of tumor suppressor genes in the development of malignant tumors has further been validated by the generation of knockout mice for these genes. p53 knock-out or p16 knock-out mice are highly susceptible to spontaneous tumor development (Jacks et al., 1994; Serrano et al., 1996). Moreover, if two tumor suppressor genes, such as p53 and Rb, are inactivated at the same time the mice become even more susceptible to cancer (Harvey et al., 1995). Tumor suppressor genes also play an important role in determining the biological behavior (growth dynamics, invasion, metastasis) of malignant tumors (Vogelstein and Kinzler, 1993).
Although a number of genes and pathways that are involved in the regulation of the cell cycle and cell replication have been identified as tumor suppressor genes other, so far unknown genes associated with, or perhaps independent of these pathways certainly play a role in controlling this process. Estimates of the total numbers of tumor suppressor genes run in the hundreds.
5.3.1 Methods
A library of ribozymes packaged into recombinant AAV are delivered to various tissues in mice. If one (or more) of the ribozymes contained in the library targets a tumor suppressor gene, cells producing this ribozyme may give rise to a tumor. The growth of the tumor constitutes an amplification of that particular ribozyme against the background of the library, making the isolation of that ribozyme possible. The specific target sequence are then determined and used as a probe for the identification of novel tumor suppressor genes.
For this purpose, a degenerate hammerhead ribozyme (library) was designed (
After packaging, recombinant virus are delivered to various tissues in mice (skeletal muscle, liver, neuronal tissue, mammary glands). Protocols for packaging and purification of rAAV routinely provide titers of 1012 infectious units per milliliter, meaning that tissues will be infected at high multiplicity. Recombinant AAV has been shown to stably express marker genes at high levels in these tissues for up to 24 months (Klein et al., 1998; Song et al., 1998; Herzog et al., 1997). In order to facilitate the induction of tumors in vivo, the packaged ribozyme library are injected as a mixture with virus carrying ribozyme against known tumor suppressor genes. Hammerhead ribozymes that target Rb (
Once a tumor has developed in injected mice, it is analyzed by standard histology techniques, and a cell-line will be established if possible. The ribozyme itself can be amplified by RT-PCR from tumor RNA. Alternatively, the portion of the vector containing the ribozyme may be amplified by standard PCR from DNA. An rAAV expressing this ribozyme may be generated to confirm that this virus alone can induce tumors in specific tissues. Sequencing can identify the 14 base pair recognition sequence of that ribozyme, and this sequence-tag will be used to screen DNA databases (e.g., GenBank). If the sequence matches a known gene involved in cell growth regulation or, in fact, a known tumor-suppressor gene, this result serves as an internal positive control and validates the overall method.
In some cases a tumor may develop because more than one tumor suppressor gene has been inactivated. One of the potential strengths of this approach is the fact that several ribozymes within the library are delivered simultaneously to the same cell and act in a combinatorial fashion. The initial tumors that are screened will, therefore, result in the isolation of an enriched subpopulation of ribozymes. To identify the ribozymes that were responsible for tumor induction, the enriched subpopulation is then re-cloned in AAV vectors and re-injected into animals. In this manner, the minimum ribozyme (i.e. tumor suppressor) combination necessary for tumor induction is identified for each target tissue.
5.3.2 Construction/Cloning of the Hammerhead Ribozyme Library
The degenerate hammerhead ribozyme (library ribozyme) has the structure shown in
Two DNA-oligonucleotides (oligos) are designed with the respective nucleotides being degenerate. The sense and antisense oligos overlap 12 base pairs. The oligos are annealed in buffer containing 50 mM NaCl, 10 mM Tris-HCl, 10 mM MgCl2, 1 mM dithiothreitol (pH 7.9). The overhanging ends are filled in with DNA polymerase Klenow fragment in the presence of 0.1 mM dNTP. They are digested sequentially with the two enzymes HindIII and NsiI. The double stranded library ribozyme oligo is purified on a 12% non-denaturing poly acrylamide gel.
The backbone vectors are sequentially cut with HindIII and NsiI and purified on an agarose gel. 300 ng of the vector is used per ligation reaction. The optimal amount of insert (library ribozyme) oligo is determined by a set of test ligations with a titration of the insert. Once the optimal vector:insert ratio is found, a sufficient number of ligation reactions are set up.
The ligation is transformed into Supercompetent Surecells (Epicuran Coli® SURE® Electroporation Competent Cells, Stratagene, La Jolla, Calif.). With the optimal vector:insert ratio approximately 2.0-2.5×106 colonies per transformation are achieved.
A sufficient multiple of the complexity of the library is obtained when performing 20 transformations. The transformations are pooled and plated out on LB-agar containing 50 μg/ml ampicillin and grown overnight at 37° C. The colonies are counted on a set of dilutions to obtain the exact number of colonies. The colonies are washed off the plate in a total of 100 ml of LB media. Aliquots of 2 ml are frozen down as a glycerol stock.
Plasmid DNA is isolated on a CsCl gradient by standard techniques (Sambrook et al., 1989) in sufficient quantities.
5.3.3 Packaging of AAV-Vectors
AAV vectors are packaged as described in Example 1 above.
5.3.4 Injection of Recombinant AAV into Animals
Each animal is injected with 1010 infectious units. For each procedure the mice are lightly anesthetized with an inhalant anesthetic methoxyfluorane (Metofane™, The Dow Chemical Company, Midland, Mich.; Johnson & Johnson, New Brunswick, N.J.). The application sites are skeletal muscle, intravenous (tail vein), peroral application and peranal application.
For skeletal muscle injection, recombinant AAV in a volume of 50 μl is injected into the hamstring muscle group of both hind legs. A 1-ml syringe with a 28-Gauge needle is used. For better visualization the coat over the injection site is removed with a razor. For tail vein injection, each mouse is restrained in a Plexiglas™ (Rohm & Haas Company, Philadelphia, Pa.) box by holding the mouse by its tail for the duration of the injection. The AAV suspension in a total volume of 100 μl is slowly injected into one of the tail veins. For peroral application, an orogastric tube is carefully inserted. The AAV suspension is administered through this tube in a total volume of 100 μl. Mice are then allowed to recover and returned to ad libitum access to water and standard mouse diet. For peranal application, 100 μl of recombinant AAV are instilled by an enema. A total of 50 animals are injected for each route of application.
The injected mice are monitored on a regular basis (twice weekly) by weighing them and by “clinical assessment.” If any signs of an obvious tumor are discovered or if a mouse loses more than 20% of its bodyweight the mouse is sacrificed and an autopsy is performed. All relevant organs (brain, heart, lung, liver, kidneys, spleen, injected skeletal muscle, stomach, large and small bowel) are harvested and a blood sample is taken. The injected sites are carefully examined for any tumors. Tumors are divided into three pieces and analyzed as described in the flow sheet shown in
5.3.5 Tumor Analysis
Tumors are fixed in 4% paraformaldehyde in PBS, pH 7.5 for 2 days followed by equilibration in 30% sucrose in PBS pH 7.5 until equilibrated. The samples are frozen at −20° C. and cryosectioned on cryostat. GFP expression is analyzed under fluorescent light microscope.
For primary tissue culture, the tumor tissue is mechanically dissociated and placed in RPMI 1640 media, 15% FCS. The cells are split as necessary. If necessary tumor cells are separated from fibroblasts by selectively trypsinizing. GFP expression is analyzed under the fluorescent light microscope or by FACScan™ (Becton Dickinson and Company, Franklin Lakes, N.J.) analysis.
The isolation of genomic RNA and total DNA is carried out according to standard procedures (Sambrook et al., 1989). DNA analysis (Southern Blot) and RNA analysis (Northern Blot) is carried out according to standard procedures (Sambrook et al., 1989).
For RT-PCR™, cDNA is synthesized with reverse transcriptase (Gibco BRL) according to the manufacturer's instructions. The PCR™ is carried out with a Perkin-Elmer PCR™ Kit according to the manufacturer's instructions. For PCR™ of genomic DNA, a Perkin-Elmer PCR™ Kit with pfu-polymerase is used. The manufacturer's instructions are followed. The following primers are used: sense 5′-GGACTGTCAGATATCG-3′ (SEQ ID NO:27); antisense 5′-ACTGAGTGGGTGGAGACTGA-3′ (SEQ ID NO:28).
The PCR™-fragments are subcloned into pT7/T3-19 at the restriction sites HindIII and NsiI by standard techniques for sequence analysis. A standard T7 sequencing primer is used. For sequencing a Big Dye Sequencing Kit is used. A cDNA library screen is carried out by standard procedures (Sambrook et al., 1989).
Alternatively, Balb C 3T3 fibroblasts may be used to select sub-libriaries of potentially oncogenic ribozymes, which are then re-tested in mice by the method described above.
Candidate Genes Involved in Memory and Learning
The formation of long-term memories involves the expression of genes; disruption of mRNA and protein synthesis affects memory formation (Rosenzweig, 1996). For the last two decades scientists have been looking for candidate genes involved in this process using pharmacological and genetic techniques. The hippocampus has been shown to be the locus for memory, since lesions in this region result in impaired acquisition of spatial memory (Morris et al., 1990). CREB, a ubiquitous transcription factor that binds the cAMP responsive element (Gonzalez et al., 1989), has been shown to play a role in the switch from short term to long-term memory in Aplysia, drosophila, mice and rats (Silva et al., 1998). CREB deficient knockout mice, and antisense CREB injected rats present memory abnormalities (Silva et al., 1998; Guzowski et al., 1997). Because virus-targeted ribozymes are well suited for studying learning and memory where temporal and spatial specificity are critical, ribozymes directed to CREB mRNA are chosen to knock out CREB expression. This approach is also used to alter the expression of a number of downstream targets of CREB, as well as novel genes. The ability to disrupt these neuronal functions is important in the development of animal models for neurological disorders.
In brief, appropriate ribozymes that target CREB mRNA are designed and cloned, and these ribozymes are shown to cleave their target RNA substrate both in vitro and in vivo. Then, the levels of hippocampal CREB protein are analyzed to detect the decrease in CREB ribozyme injected animals. Loss of function of Long Term Memory (LTM) in rats is studied using the Morris water maze-learning paradigm (Morris, 1981). Differential display methods are used to identify other candidate genes involved in learning and memory, and the process outlined above is repeated for these newly identified genes.
A number of CREB isoforms have been characterized (Blendy et al., 1996). Three ribozymes were designed and termed CREB230 (
Rat hippocampi are injected with AAV-expressing ribozymes using standard stereotactical procedures (Klein et al., 1998). The decrease in levels of CREB mRNA in the injected brains is determined by in situ hybridization (Simmons et al., 1989). Brains are also analyzed for a decrease in protein levels by immunocytochemistry using an anti-CREB antibody. The Morris water maze paradigm (Rozenzweig, 1996) is used to look for phenotypic differences in learning and memory between control and ribozyme injected animals.
The differential display method is used to identify novel genes involved in the consolidation of memory formation (Liang and Pardee, 1997). Normal and memory deficient animals (CREBhh) are subjected to the training paradigm. mRNA is isolated from the hippocampi of these animals at different times after training, and PCR™ amplified using a series of primer sets and run on sequencing gels to display the differential pattern of expression of mRNAs in CREBhh versus normal rats. Differentially expressed mRNAs are cloned and characterized. Searching the GenBank database identifies known genes. The differential pattern of expression is confirmed by dot blot analysis and the presence of these messages in the hippocampus is determined by RNase protection assay (Gilman et al., 1987), or by in situ hybridization (Simmons et al., 1989). Candidate genes are further evaluated for their role in learning and memory by designing candidate gene-specific ribozymes and testing them as described above for CREB.
Candidate Genes for Retinal Disease
This example describes methods for delivering ribozymes against specific wild type (wt) alleles in a somatic retinal tissue to reduce the corresponding mRNA level sufficiently to create a “somatic knockdown” and lead to photoreceptor (PR) cell loss and a retinal disease-like phenotype. This approach permits the functional screening in animals of candidate photoreceptor-restricted ESTs (expressed sequence tags, i.e. mRNA sequences) from retina-specific libraries to identify all of the genes associated with retinal disease.
Recombinant AAV (rAAV) has been demonstrated as an efficient and nontoxic way to deliver and express genes in photoreceptor cells of the rodent retina. Proximal rod opsin promoters regulating reporter genes in rAAV were found to target expression efficiently and specifically to rod photoreceptors without pathology (Flannery et al., 1997). The duration of expression was long-term and undiminished for the life of the rat (>30 months). Additionally the number of photoreceptors expressing the transgene and the fraction of the retina transduced suggested alteration of retinal phenotypes might be possible. Indeed, rAAV delivered ribozymes against a mutant P23H rod opsin gene (Drenser et al., 1998) in transgenic rats (an animal model for autosomal dominant Retinitis Pigmentosa) preserved 30-80% of the photoreceptors that would have been lost at 8 and 3 months respectively (Lewin et al., 1998). Rescue was confirmed functionally by electroretinographic (ERG) analysis, cellularly by preservation of photoreceptor morphology and molecularly by specific reduction in mutant mRNA levels. Thus rAAV delivered ribozymes can rescue a disease phenotype in vivo.
To test whether ribozymes targeted against wild type alleles might also create photoreceptor dysfunction, Retinitis Pigmentosa (RP)-like rod degeneration was produced in rd/+mice (Bowes et al., 1990). These mice have one mutant rd allele and one wt allele of the βPDE gene and have an apparently normal retina at all ages. In the homozygous condition, the rd/rd mouse is a classical model for recessive RP, losing all rods within 1-2 months. Ribozymes designed against the wt allele were first tested in vitro and seen to digest normal βPDE mRNA well but not rd mRNA. This ribozyme was then packaged into rAAV downstream of a proximal rod opsin promoter and injected into one eye of a series of rd/+mice. At 4 months post-injection, 50%-80% fewer rod photoreceptors were found in ribozyme treated eyes relative to PBS treated contralateral control eyes. Control eyes exhibited a normal number of photoreceptors. ERG analysis in which the inventors simultaneously measured the light evoked electrical response in ribozyme treated and PBS control eyes in each animal, confirmed that a profound functional vision deficit had been created that paralleled the loss of rod cells in the treated eye. To validate this approach further, a second heterozygous mouse with a recessive mutation in a different gene (γPDE) that also exhibits an RP-like PR dysfunction in the homozygous condition was tested using rAAV-delivered ribozymes against the wt γPDE gene (
In vivo screening for candidate genes of unknown retinal disease significance is accomplished through the development of a differential hybridization screening strategy to identify both PR-specific genes and genes that are abundantly expressed both in PRs and in a few other tissues. The retinal cDNA library array used encompasses 40,000 cDNA clones of a normalized directionally cloned human retinal cDNA library, available for screening on high-density filters. This array is predicted to contain the majority of genes expressed in the retina at more than a few copies/cell. It has been demonstrated that the arrayed library has been effectively normalized, contains cDNAs of known retinal genes expressed over a wide range of levels, and that the cDNA inserts are long and often full-length. The array was probed with total retinal cDNA first from normal mice and then from 5-week-old rd/rd mice that lack all PRs. Retinal cDNAs detected by the wild-type probe and not by the rd/rd probe are putatively PR-specific within the retina. Of 1596 cDNAs that were screened, 144 putative PR-specific cDNAs have been identified. To date, 130 of these have been sequenced and 28 (21%) are entirely novel, 62 (46%) are known as ESTs only (including 18 previously known retina-specific ESTs), and 40 (30%) correspond to known genes. Importantly, two of the known cDNAs are rhodopsin and arrestin, well-studied photoreceptor-specific RP-causing genes, demonstrating that the strategy indeed selects genes associated with retinal disease. Eight of these human ESTs (3 expressed in the retina only, 3 of restricted expression, 2 housekeeping genes) with predicted open reading frames are associated with human retinal disease loci and have mouse EST homologues.
These sequences were the targets for validation of the results in mice. Ribozymes against each gene were designed and tested in vitro and those showing acceptable activity and specificity are then tested in vivo as outlined above. Animals may be tested at monthly intervals for impaired visual function (by ERG) and for impaired retinal morphology by optical coherence tomography (OCT) and microscopic analysis of tissue.
5.5.1 Injection of Animals
For the following animal studies pTR-UF33-HP constructs were used.
Newborn BalbC mice were injected within 24 hours of birth. The recombinant virus was administered intravenously through the temporal vein. Five groups of animals were injected according to the following groups:
A: Control (pTR-UF5)
B: rAAV carrying ribozymes against p53, p19, p16, and Rb (the retinoblastoma gene)
C: rAAV carrying the ribozyme library
D: rAAV carrying the ribozyme library+virus carrying ribozyme against p53
E: rAAV carrying the ribozyme library+virus carrying ribozymes against p19, p16, and Rb.
Each group consisted of 5 animals. A total 5×109 infectious units (IU) of each virus was injected per mouse. The mice were individually marked and followed by regular weight measurements (weekly). In addition they were checked upon at least twice a week for tumors or tumor-like lesions.
Likewise, in a second set of studies adult mice were injected intramuscularly into the hamstring muscles of the hindleg. The groups were the same as described above for newborn mice, except for group C that was not performed. As in the newborn mouse study, 5×109 IU of each virus was injected. These animals were followed the same way as the mice that were injected as newborns.
5.5.2 In Vitro Transformation Assay
In vitro transformation of cultured cells has long been used to identify genetic changes required for the formation of tumors. Several growth indicators are accepted as signs of malignant transformation. One of those signs is the loss of contact inhibition, which leads to the formation of so-called foci. Normal cells are inhibited by contact with neighboring cells, which means cultured cells growing on a petri dish stop dividing once they cover the plate with a single layer of cells (grow to 100% confluency). If, in that monolayer, a cell becomes transformed and loses contact inhibition, it will grow and form a small “pile” of cells (focus). Those foci can be detected with the naked eye. This phenomenon/sign has been employed herein for the screening of the ribozyme library in vitro.
BalbC 3T3 cells are mouse fibroblasts that are not transformed. BalbC 3T3 cells were infected at an MOI (multiplicity of infection) of 1000 with the ribozyme library in the pTR-UF21-HP virus. The cells were kept in 15-cm dishes and the medium was changed twice a week. After 4-6 weeks, the formation of foci was observed. Compared to a control plate which was infected with pTR-UF5 (an AAV construct expressing only GFP) 8-10 fold more foci in the plates treated with AAV-ribozymes than in plates treated with the control virus (spontaneous transformation, which occurs at a low rate, will give rise to foci even in the control plate).
A total of 36 foci were picked and expanded (re-grown in fresh culture medium). Genomic DNA was isolated from each focus that was grown up. The foci were screened by PCR™ the presence of a library ribozyme. Out of 28 foci that have been screened so far 8 had a clearly positive PCR™ signal. The PCR™ fragments of 3 out of the 8 PCR™ positive foci were subcloned into an E. coli plasmid (pT7T3-19). Eight or nine individual clones from each subcloned PCR product were sequenced. The results are shown in the following table:
None of the sequences matched any known tumor suppressor genes (which would serve as an internal positive control). But these sequences may identify novel genes whose function is to control cell growth or division. These genes would fall under the heading of tumor suppressor genes.
Once the screening of the foci, and the subcloning and sequencing of all the PCR™ positive foci is completed, the isolated library ribozyme may then be recloned into pTR-UF21-HP and packaged into virus. This represents an enriched sub-library that is then used in a second in vitro transformation assay. Once the libraries and sub-libraries are narrowed down to 4-6 different ribozymes, these sequences are then used to screen cDNA libraries. The ribozyme library and sub-library are then coninfected with rAAV vectors carrying the ribozymes against the known tumor suppressor genes of mice (Rb, p53, p19arf, p16ink4a).
5.5.3 Construction of Retinal Disease Animal Models
Once candidate disease genes have been identified through the array expression analysis methods described herein, a study may be performed to confirm retinal disease association in large animals with more human-like eyes (pigs and monkeys). AAV-vectored ribozymes will permit the preparation of new, more relevant models of retinal disease for development of appropriate therapies. In an illustrative example, analysis of the ABCR gene has been conducted. A defect in this gene is the cause of Stargardt's Disease, a central retinal defect in humans. This is currently the best-understood genetic disease of the cone-rich central retina, the macula. Macular disease is the major cause of age-related and heritable blindness in the United States, afflicting 2-5 million people. In addition to Stargardt's Disease, the principal macular diseases are Age-Related Macular Degeneration (currently the leading cause of legal blindness in the West) and the end stages of RP when macular cones degenerate after loss of most rod cells. There is currently no cure or long-term therapy. No animal model of macular disease is currently available, primarily because any such model necessarily must affect the macula, a retinal structure present only in primates.
ABCR specific ribozymes have been constructed and tested in vitro. These ribozymes and their target sequences are shown in
Ribozymes Targeted to Huntingtin
Due to the apparent gain of toxic function that occurs when CAG repeats are abnormally expanded in the affected gene in Huntington's disease, reduction of expression of the resultant mutant protein specifically in the neostriatum may be beneficial in this disorder. The present example describes the creation and testing of an rAAV vector to deliver an RNA cleaving molecule that will reduce the striatal expression of huntingtin. Because reduced expression of normal huntingtin is not toxic to the host, and reduced expression of mutant huntingtin is beneficial, the method provides means for treating and/or preventing accumulation of the mutant protein in an animal, and serves as a first approach to treating the disease that results from such excess.
The relatively recent establishment of transgenic animal models and cellular models utilizing human huntingtin (htt) genes with expanded CAG repeats have suggested that mutant htt induces neuropathology through a gain of abnormal function rather than a loss of normal function of the protein. The possibility that some new function of mutant htt with expanded polyglutamine (polyQ) tracts induces cellular pathology over time raises the possibility that the reduction of the transcription of mutant htt might also reduce ongoing pathological processes. Indeed, recent data showed that using an inducible system to drive expression of mutant htt, a reversal of mutant htt expression could also lead to reversal of the motor phenotype.
Recently, viral vectors that have been conclusively demonstrated to transduce large numbers of striatal neurons for long periods of time have been described. A large percentage of striatal neurons can be transduced in a dopamine deficient transgenic mouse striatum and this can rescue the phenotype for well over one year using recombinant adeno-associated viral vectors (rAAV) to deliver L-dopa. Moreover, AAV has been demonstrated to successfully deliver both ribozymes and antisense to neural tissue in order to reduce gene expression. Therefore, the possibility currently exists to try to reverse the HD-like phenotype in R6/2 transgenic mice by reducing mutant htt expression specifically in striatum via an rAAV delivered ribozyme.
5.6.1 Experimental Methods
5.6.1.1 Construction and Testing of Functional Ribozymes
Using hammerhead ribozymes, the strategy developed was to select a region in the RNA containing the triplet GUC or, in general, NUX, where N stands for any nucleotide and X is any nucleotide except guanosine (The human Huntington's disease gene has 15 GUC sites). One then creates two stretches of antisense nucleotides 6 to 8 nucleotides long and puts the 21-nucleotide sequence forming the catalytic hammerhead ribozyme between them. The principle is the same for hairpin ribozymes, except that the catalytic core is larger (34 nucleotides) and this type of ribozyme requires more specificity in the target site. Hairpins recognize the sequence NNNBNGUCNNNNNN (SEQ ID NO:67), where N is any nucleotide and B is any nucleotide but adenosine. Four functional ribozymes were tested and then packaged in an rAAV vector to test the activity of the construct in vivo. These ribozymes (shown in
5.6.1.2 In Vitro Testing on Synthetic Targets
To be effective for gene therapy, ribozymes must pass several tests in vitro. First, ribozymes are tested under standard buffer conditions (10 mM MgCl2, 40 mM Tris HCl, pH 7.4) on oligonucleotide targets (13-15 nucleotides) to be sure that they are highly active and specific. Such ribonucleotide targets may be purchased from a variety of sources, including Dharmacon, Inc. (Boulder, Colo.) and deprotected according to the manufacturer's instructions. To quantify cleavage reactions, the target oligonucleotides are labeled using polynucleotide kinase and γ-32P-ATP. At this stage, ribozymes are rejected or redesigned if they exhibit a turnover number significantly less than naturally occurring hairpin or hammerhead ribozymes (1 min−1). Since the rate-limiting step for ribozyme reactions is the release of products, these tests are performed under target-excess, multi-turnover conditions. Ribozymes are also rejected if they cleave imperfectly matched targets (i.e. oligonucleotides with mismatches at or near the cleavage site).
To determine if a ribozyme with good kinetic properties and adequate substrate specificity is likely to cleave full-length mRNA, ribozymes are tested on transcripts of 50-80 nucleotides in length derived from the huntingtin mRNA. These sequences are cloned by PCR from a cDNA clone of huntingtin mRNA, with the target RNA molecules being generated and labeled with 32P in vitro using T7 RNA polymerase. Targets are purified by electrophoresis on acrylamide-urea gels, and renatured by heating and gradual cooling in the presence of magnesium. If the rate of cleavage of the long target appears to be significantly less (reduced by 10 fold or more) than the rate for the oligonucleotide target, then target site may not be accessible, and the candidate ribozyme may be abandoned in favor of a ribozyme recognizing an alternative target site.
Active selective ribozymes are then tested on full-length RNA transcripts derived from cloned cDNA to be certain that the target site is accessible within the folded structure of the 9.3 kb huntingtin mRNA. Ribozymes may be excluded at this stage if a significant fraction of the huntingtin RNA remains intact. Cleavage of full-length mRNA can also be detected in tissue culture, by transfecting cells that express huntingtin with plasmid vectors that encode the ribozymes to be tested driven an appropriate promoter. For this purpose, a hybrid promoter containing the enhancer elements for the immediate early promoter of cytomegalovirus (CMV) and the proximal promoter elements of the chicken gene for β-actin may be used. Reduction in the mRNA for huntingtin will be detected by RT-PCR analysis. Ribozymes that are kinetically competent and are able to cut the full-length RNA are generally useful tools for gene therapy in suppression of gene expression is desired.
5.6.1.3 Production of rAAV-Ribo-htt
To generate recombinant virus, human 293 cells are cotransfected with ribozyme-encoding rAAV plasmids and helper plasmid pDG. This plasmid contains both the AAV rep and cap genes and the adenoviral genes needed for AAV propagation. No replication competent adenovirus is detected using this method. Large-scale DNA preparations are made using Iodixanol density gradient centrifugation and affinity chromatography on heparin-agarose columns. Routine yields of virus are currently 1010-1011 infectious particles per ml and are free of contaminating wild-type AAV.
5.6.1.4 In Vivo Testing of rAAV-ribo-htt Function
rAAV-ribo-htt is injected into the right striatum in 2 locations (2 μl each site) in 24 normal 6-8 week old CBA mice. These mice are killed 4 weeks, 8 weeks and 26 weeks after vector injections (n=6 per time period). They are decapitated and their striata rapidly dissected on dry-ice. Quantitative northern blot analysis of homogenized striatum may be used to determine if there is significant reduction of htt mRNA compared to the levels measured in non-injected striatum. If the northern blot method is not sufficiently sensitive rt-PCR normalized against mouse β-actin mRNA levels may be used to determine ribozyme-induced reduction of striatal htt mRNA levels. Samples are also saved for observing reduced htt protein levels via immunoblotting. The time-points were chosen to correspond to intervals important for the behavioral studies described herein.
5.6.1.5 Testing Long-Term Intrastriatal Ribo-htt Function
Two parallel studies may be performed to characterize the effects of an anti-htt ribozyme in normal mice. Eight, 6-week-old normal CBA mice are injected intrastriatally with rAAV-ribo-htt in 2 locations in the right striatum as above. An additional 8 mice are injected identically with an rAAV-GFP control vector. These unilateral animals are tested for asymmetric rotational behavior using a series of dopamine agonists weekly beginning 4 weeks after the vector injection. Destruction of striatal function should create an asymmetry between the 2 hemispheres, which may allow detection of ribozyme-induced dysfunction in the rotational paradigm. The second study is identical to the first except that the mice receive bilateral vector injections. These mice are then tested weekly beginning 4 weeks after the vector injections on a series of tests (e.g., beam walking, rotorod, pre-pulse inhibition of the acoustic startle response, and gait analysis of foot prints). In both studies, ⅝ of the mice are killed at the end of the experiment and processed to assess htt mRNA levels as above. The remaining 3 mice/group are perfused with 4% paraformaldehyde and processed for GFP immunohistochemistry to access transgene expression.
Ribozymes Targeted to Superoxide Dismutase
Amyotrophic lateral sclerosis (ALS) is a degenerative disease of motor neurons in the spinal cord, brainstem and cortex. (Brown, 1997) In most cases, its cause is unknown but ALS is uniformly fatal, usually within 5 years of diagnosis. About 10% of ALS cases are inherited as an autosomal dominant trait, and are collectively described as familial ALS, or FALS. Approximately 20% of FALS cases are linked to mutations in the SOD1 gene, which encodes the cytosolic enzyme Cu/Zn superoxide dismutase (Rosen et al., 1993). This 153-amino acid protein converts the toxic superoxide anion to hydrogen peroxide and molecular oxygen. More than 26 mis-sense mutations in SOD1 have been identified as leading to FALS. Three major hypotheses have been proposed for how SOD1 mutations lead to neurodegeneration (Cleveland, 1999): (i) mutant enzyme has an altered substrate affinity that leads to an accumulation of toxic products; (ii) reduced SOD activity may permit increased oxidative stress leading to damage of particularly sensitive cells; (iii) poorly or unstably folded mutant SOD protein form aggregates that are toxic specifically to motor neurons. Several animal models exist expressing mutant forms of the human SOD1 gene (Buijn et al., 1998; Shefner et al., 1999; Azzouz et al., 1997; Browne et al., 1998; Morrison et al., 1996; Ratovitski et al., 1999; Ripps et al., 1995). These do completely discriminate between the aforementioned models but suggest that accumulation of aggregates contributes to neuropathogenesis. Furthermore, at least some of the mis-sense mutants retain catalytic function, suggesting that reduced activity is not the cause of cell death. Mice devoid of SOD1 do not develop ALS, but high expression of mutant SOD1 transgenes leads to an ALS-like disease.
Several ribozymes have been designed and tested that cleave the mRNA for human SOD1 present in the mouse models of ALS (
A ribozyme (SEQ ID NO:49) has been generated and tested that cleaves a sequence region (SEQ ID NO:50) of the mRNA for mouse manganese superoxide dismutase (MnSOD) (
Ribozymes Targeted to NADH-Dehydrogenase Subunits
A ribozyme to the MWFE subunit of the mouse mitochondrial enzyme NADH-dehydrogenase has been constructed and tested (
The following references, to the extent that they provide exemplary procedural or other details supplementary to those set forth herein, are specifically incorporated herein by reference, each in their entirety:
All of the compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents that are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. While the invention is susceptible to various modifications and alternative forms, specific embodiments thereof have been shown by way of example in the drawings and are herein described in detail. It should be understood, however, that the description herein of specific embodiments is not intended to limit the invention to the particular forms disclosed, but on the contrary, the intention is to cover all modifications, equivalents, and alternatives falling within the spirit and scope of the invention as defined by the appended claims.
The present application is a divisional of currently pending application Ser. No. 09/561,498, filed Apr. 28, 2000, which claims the benefit of provisional patent application Ser. No. 60/131,942 filed Apr. 30, 1999, the entire contents of which is specifically incorporated herein by reference in its entirety.
The United States government has certain rights in the present invention pursuant to Grant Numbers EY11596 from the National Institutes of Health.
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