Patent Application
20110105593
The present invention relates to the field of gene expression, and more specifically to nucleic acid-based technologies for inhibiting expression of target genes. The invention encompasses vectors for mediating RNA interference via the microRNA pathway and methods for using the same to inhibit both endogenous and pathogen gene expression in mammals and mammalian cells.
RNA interference (RNAi) is an endogenous cell process that can suppress gene expression in a highly specific manner and it is providing new approaches for the development of therapies for viral infections and other diseases [20]. RNAi-based anti-viral strategies are particularly attractive since infection produces a unique set of viral transcripts that can serve as therapeutic targets. As an example, certain aspects of hepatitis B virus (HBV) biology and pathology make it a good candidate for RNAi-based therapies [1, 5]. The virus replicates through an RNA intermediate, so interfering RNAs can directly down-regulate viral replication and the production of infectious viral particles. In addition, a significant element in immune response-mediated HBV pathogenesis and persistence is the large excess of viral antigens, relative to infectious particles, produced in hepatocytes from either episomal or integrated forms of the viral genome [6]. The ability to reduce viral antigen production by silencing viral mRNAs is an important feature of RNAi-based strategies that is not shared by nucleoside analog inhibitors of the HBV polymerase [5].
The potential value of RNAi-based approaches in treating HBV infection has been demonstrated in many studies that have used interfering RNAs to down-regulate viral transcripts in both cell culture and animal models of infection (reviewed in [7]). Interfering RNAs that target HBV can be transfected into cultured hepatocytes either as pre-formed, synthetic short interfering RNAs (siRNAs) [8], or as plasmids that express short hairpin RNAs (shRNAs) [5, 9-12]. In a variety of mouse models of infection, HBV-targeted interfering RNAs have reduced viral antigen, transcript, or DNA production when delivered as siRNAs or as shRNAs expressed from plasmid or viral vectors [5, 13-17]. While many methods have been successful in laboratory studies, it remains a challenge to deliver RNAi agents to hepatocytes in a manner that will be clinically relevant in human patients.
Therapeutic interfering RNA can be directly introduced into cells as exogenously produced small interfering RNA (siRNA), or can be expressed within cells from vector-based systems, as eiRNA (expressed interfering RNA). Silencing mediated by synthetic siRNAs has been shown to be highly effective [21, 22], although it can be short-lived in in vivo applications [13]. Recent progress in chemical modification of siRNAs has improved both the longevity and specificity of these agents [23-25]. Nevertheless, plasmid or virus based vectors designed for cellular expression of interfering RNAs still provide the longest lasting effects and may therefore be most appropriate for the treatment of chronic diseases.
In early work on vector-based RNAi, pol III promoters were chosen to drive the expression of shRNAs that can be processed by intracellular enzymes into mature interfering RNAs [26-29]. The strong and ubiquitously active pol III promoters, with defined start and stop sequences, are well-suited for transcription of these short RNAs. Since then, however, as an understanding of the organization, expression, and processing of microRNAs (miRNAs) has grown (see
In previous work, a therapeutic silencing vector for HBV with four different pol III driven sh-eiRNAs showed efficacy in cell culture and animals models of infection [5]. See PCT/US2005/029976, which is herein incorporated by reference in its entirety. In the second generation vector system described here, we have incorporated several aspects of miRNA expression to take advantage of its potential for polycistronic and tissue-specific expression. The miRNA formatted multitarget expression constructs described herein are ideal for treating viral infections characterized by a high rate of mutation, as multiple viral-targeted miRNAs within a single construct significantly decrease the chance of viral escape mutants and broaden the range of viral genetic variants that can be targeted.
In recent years, other groups have developed multitarget miRNA-based vector constructs for use in mammalian cells [42, 43, 48, 49]. However, no one to the present inventor's knowledge has yet to demonstrate inhibition of target gene expression in a mammal, and more specifically tissue-specific inhibition of viral gene expression in a mammal, using a miRNA-formatted multitarget expression construct. In fact, Zhou et al. recently reported that expressing two tandem copies of a miR-30-based synthetic miRNA in a single transcription unit was less effective for RNAi than a single copy of the same miRNA, suggesting that multitarget miRNA based constructs might not provide any benefit over single targeting constructs [50]. The vector constructs described in the present invention overcome the deficiencies of the prior art vectors, and are shown to be surprisingly effective in mammalian cells when expressed in a tissue-specific manner.
The present invention provides nucleic acid vectors encoding multiple expressed microRNA (miRNA)-formatted interfering RNAs specific for one or more target genes, and methods of using the same to inhibit gene expression and treat a variety of diseases and infections in mammals. In one embodiment, among others, the invention provides a vector encoding at least two miRNA-formatted interfering RNAs specific for one or more target genes. In certain embodiments, the nucleic acid encoding the two or more miRNA-formatted interfering RNAs is operably linked to a single tissue-specific pol II promoter. In contrast to other miRNA-based constructs reported in the literature, the constructs of the present invention decrease or inhibit expression of the target gene(s) in a mammalian cell at least as effectively or more effectively than a vector expressing either of said miRNA-formatted interfering RNAs alone.
The vectors are conveniently designed so that single miRNA regions may be easily and sequentially inserted to construct vectors containing at least about two, three, four, five, six, seven, eight, nine, ten, etc. or more miRNA-formatted regions. The vector backbone, containing the miRNA 5′ and 3′ arms prior to the cloning of the stem-loop regions, is also included in the present invention. The vector backbone may be designed with restriction cloning sites between the 5′ and 3′ miRNA arm regions, particularly restriction cloning sites that enable successive cloning of individual miRNA units.
Also included in the invention are methods of inhibiting or decreasing expression of at least one target gene in a mammalian cell in vitro or in vivo comprising delivering to said cell a nucleic acid vector of the invention such that the nucleic acid encoding at least two microRNA (miRNA)-formatted interfering RNAs is expressed and expression of said at least one target gene is inhibited or decreased. The methods of the invention may be used to inhibit either endogenous mammalian genes, for instance genes involved in cancer or autoimmunity, or genes of mammalian pathogens including viruses.
The vectors described herein will help to maximize the efficacy of expressed interfering RNAs (eiRNAs) by increasing their potency and range of targets by allowing multiple eiRNAs to be produced from a single therapeutic vector. At the same time, the use of RNA pol II promoters can help in directing the therapeutic activity of these agents to specific cell types in an organism, even in the absence of precisely targeted delivery. Since the miR-eiRNA expression cassette described herein is built into non-protein coding RNA, co-expression of a protein product is not necessary, and this is a desirable feature for therapeutic vectors. While we have designed our vector to target HBV as an example, the general format of the disclosed miR-eiRNA vectors should be useable for silencing the expression of additional cellular or disease related genes.
The present invention provides nucleic acid vectors encoding multiple expressed miRNA-formatted interfering RNAs specific for one or more target genes. The phrase “miRNA-formatted interfering RNA” refers to an RNA having a secondary structure comprising a double stranded, target-specific stem-loop region flanked by miRNA arm regions, wherein the miRNA arm regions have sequences taken from a naturally occurring miRNA, or sequences that are predicted to form a secondary structure that models the structure of a naturally occurring miRNA. Depending on the naturally occurring miRNA, the first 9 to 13 bases of the arm regions typically have some potential for secondary structure, and the rest of the arm sequence is relatively unstructured. A consensus sequence or format for the microRNA arm regions has been reported. See Han, J., et al. (2006), Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125: 887-901, which is herein incorporated by reference in its entirety.
The double stranded stem region is designed to be specific for the target gene. This means that the double stranded stem region of the expressed miRNA contains one strand that is at least substantially complementary to a sequence in the target gene, and the other strand is at least substantially identical to the complementary sequence in the target gene, substituting uracil for any thymidine residues. “Substantially” means at least about 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99%, or sufficiently complementary or identical to the target gene to modulate expression of the target gene in a target-specific manner. In some embodiments, the double stranded stem region is completely complementary and identical to a sequence of the target gene. In some embodiments, expression of the miRNA-formatted interfering RNAs results in degradation of the target mRNA via the RNA interference pathway. In other embodiments, expression of the miRNA-formatted interfering RNAs may lead to translational arrest of the target mRNA or a mixture of translational arrest and degradation.
In one embodiment, the double stranded stem region is about 22 base pairs, but may range in length from about 19 to about 29, about 21 to about 27 or about 20 to about 25 base pairs, i.e., 19, 20, 21, 22, 23, 25, 25, 26, 27, 28, 29, or longer. The two portions of the stem region can be completely complementary. The two portions of the stem region may also be partially complementary, i.e., at least about 50%, 60%, 70%, 80%, 90%, 95% or 99% complementary. When completely complementary, the two portions of the stem are encoded by a DNA construct containing an inverted repeat of the sequences in the stem region, separated by the “loop” region, such that transcription of the DNA construct produces a RNA that forms a stem-loop structure.
The loop region is approximately 19 ribonucleotides, but may range in length from about 4 to about 30 ribonucleotides. The loop region is between and connects the two arms of the stem region such that complementary base pairing of the stem region forces the intervening region to “loop” out. In contrast to the miRNA arms, the loop region between the two portions of the stem has minimal potential for base pairing.
In some embodiments, among others, the miRNA arm regions are about 20 to 45 nucleotides. In other embodiments, the miRNA arms are about 25 to about 40 nucleotides. The length of the miRNA arms may vary depending on the microRNA species used to make or model the constructs. For instance, the present inventor has determined that for constructs encoding multiple miR-30-formatted interfering RNAs, about 36 nucleotides is sufficient for the 5′ miRNA arm, and about 28 nucleotides for the 3′ miRNA arm. However, depending on the miRNA, other lengths for the 5′ and 3′ arm regions could also be suitable, including 5′ and/or 3′ arm regions of about 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39 or 40 nucleotides.
MiR-30 is a naturally occurring miRNA encoded in the third intron of an mRNA-like non-coding RNA found on human chromosome 6 [53]. This region naturally encodes a single miRNA, not a cluster of multiple miRNAs, although the present inventor has demonstrated that miR-30 sequences can form the basis of multi-miRNA expression constructs. However, other miRNAs may be used in the constructs of the present invention, including but not limited to miRNAs naturally encoded either singly or in clusters, those encoded in exons of mRNAs, exons of non-coding RNAs, introns of mRNAs, or introns of non-coding RNAs. Particular miRNAs that could be used in the methods of the invention include, but are not limited to, miR-1 through miR-34; miR-2-1; miR-92 through miR-101; miR-103 through miR-107; miR-109 through miR-114; miR-116; miR-119; miR-122; miR-125; miR-126; miR-127; miR-129; miR-130; miR-132; miR-133; miR-134; miR-136; miR-138; miR-140; miR-141; miR-144 through miR-151; miR-153; miR-154; miR-157; miR-158; miR-160; miR-162; miR-164; miR-172 through miR-180; miR-182 through miR-189; miR-191; miR-192; miR-193; miR-195; miR-196; miR-197; miR-199; miR-201; miR-203; miR-205; miR-224. Any suitable miRNA sequence may be used in the methods of the invention, such as any of those listed in the miRBase database, which is a database housed at the Wellcome Trust Sanger Institute that lists all miRNA sequences (and other associated information). See http:/microrna.sanger.ac.uk.
As noted above, the present invention includes vectors providing multiple miRNA-formatted interfering RNAs specific for one or more target genes. A “vector” is a composition of matter which can be used to deliver a nucleic acid of interest to the interior of a cell. Numerous vectors are known in the art including, but not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses. Thus, the term “vector” includes an autonomously replicating plasmid or a virus. Examples of viral vectors include, but are not limited to, adenoviral vectors, adeno-associated virus vectors, retroviral vectors, and the like. An expression construct can be replicated in a living cell, or it can be made synthetically. For purposes of this application, the terms “expression construct,” “expression vector,” and “vector,” are used interchangeably to demonstrate the application of the invention in a general, illustrative sense, and are not intended to limit the invention.
In one embodiment, among others, the invention provides a nucleic acid vector comprising a nucleic acid encoding at least two microRNA (miRNA)-formatted interfering RNAs specific for at least one target gene, wherein said nucleic acid encoding said at least two (miRNA)-formatted interfering RNAs is operably linked to a single pol II promoter. The phrase “under transcriptional control” or “operably linked” as used herein means that the promoter is in the correct location and orientation in relation to a polynucleotide to control the initiation of transcription by RNA polymerase and expression of the polynucleotide. Preferably, the nucleic acid vectors of the invention decrease expression of said at least one target gene in a mammalian cell at least as effectively or more effectively than a vector expressing either of said microRNA (miRNA)-formatted interfering RNAs alone. Such expression levels may be measured and/or quantified using any suitable method, for instance by detecting degradation of the target mRNA transcript, by quantifying or measuring a decrease in functional activity of the protein encoded by the target gene, or, in methods of treating infection, by measuring a decrease in the amount of target pathogen detectable in the mammal.
In addition to the attributes described above for the encoded miRNA-formatted interfering RNAs, the nucleic acid regions encoding each miRNA-formatted interfering RNA may be operably linked with a nucleic acid linker region. The intervening linker region may range from about 1 to about 5 to about 15 to about 20 nucleotides in length or longer. In some embodiments, the linker regions are not more than about 6 to 10 nucleotides. The linker regions may contain one or more restriction cloning sites for sequential cloning of multiple miRNA unit constructs. Any suitable restriction cloning site may be used. Particularly preferred are cloning sites that enable sequential cloning by creating overhangs that are compatible with other restriction enzymes, such as the XbaI/SpeI sites used in the Examples of the present invention. Other suitable, compatible restriction enzyme pairs are known in the art, i.e. SalI/XhoI; NdeI/AseI; BclI/BamHI/BglII/MboI; and AvaI/XmaI, to name a few. See also, for example, the chain reaction cloning methods taught in U.S. Pat. No. 6,143,527, incorporated herein by reference.
In some embodiments of the invention, the nucleic acid encoding said at least two (miRNA)-formatted interfering RNAs is not operably linked to a separate protein coding sequence. It is particularly surprising that the pol II expression constructs of the present invention are so effective in the absence of a linked, co-expressed protein coding sequence, since many researchers have reported that pol II expression constructs are not as effective in the absence of a separate protein coding region encoded on the same transcript as the miRNA [41].
In some embodiments, among others, the nucleic acid encoding said at least two miRNA-formatted interfering RNAs is located in a nucleic acid encoding an intron or in a nucleic acid encoding an untranslated region of an mRNA or in a non-coding RNA. In one embodiment, the nucleic acid encoding said at least two miRNA-formatted interfering RNAs is located in a nucleic acid encoding a functional intron, wherein the expression construct contains at least one other intron 5′ and/or 3′ to the intron containing the at least two miRNA-formatted interfering RNAs. In other embodiments, the expression construct encodes a single transcript with multiple functional intron regions, each encompassing one or more miRNA-formatted interfering RNAs. By “functional intron” is meant a sequence flanked by splice junctions or other sequences that facilitate functional splicing. In some embodiments, a nucleic acid encoding one or more miRNA-formatted interfering RNAs is located in an exon sequence. In other embodiments, said exon sequence containing one or more miRNA-formatted interfering RNAs is located between nucleic acid sequences encoding functional introns. The expression construct may encode a single transcript containing multiple intron regions separated by one or more exon regions, wherein miRNA-formatted interfering RNAs may be located in one or more of the intron and/or exon regions.
As described above, the miRNA-formatted interfering RNAs encoded by the expression vectors of the invention are specific for at least one target gene. In one embodiment, the target gene is an endogenous gene of a mammalian cell. In another embodiment, the target gene is a gene of a pathogen that infects a mammalian cell, including viruses and intracellular parasites. The multiple (two or more) miRNA-formatted interfering RNAs on a single expression construct may be the same miRNA repeated in succession. Alternatively, the multiple miRNAs may be different miRNAs that are specific for the same target gene. Alternatively, the multiple miRNAs may be different miRNAs that are specific for two or more target genes of the same cell or pathogen. Alternatively, the multiple miRNAs may be different miRNAs that are specific for target genes of different pathogens or pathogen variants, for instance target genes of different viruses or viral variants.
Viruses that may be targeted by the vectors of the present invention include but are not limited to Retroviridae (e.g. human immunodeficiency viruses, such as HIV-1 (also referred to as HTLV-III, LAV or HTLV-III/LAV, or HIV-III; and other isolates, such as HIV-LP)); Picornaviridae (e.g. polio viruses, hepatitis A virus; enteroviruses, human coxsackie viruses, rhinoviruses, echoviruses); Calciviridae (e.g. strains that cause gastroenteritis); Togaviridae (e.g. equine encephalitis viruses, rubella viruses); Flaviviridae (e.g. dengue viruses, encephalitis viruses, yellow fever viruses); Coronaviridae (e.g. coronaviruses); Rhabdoviridae (e.g. vesicular stomatitis viruses, rabies viruses); Filoviridae (e.g. ebola viruses); Paramyxoviridae (e.g. parainfluenza viruses, mumps virus, measles virus, respiratory syncytial virus); Orthomyxoviridae (e.g. influenza viruses); Bungaviridae (e.g. Hantaan viruses, bunga viruses, phleboviruses and Nairo viruses); Arena viridae (hemorrhagic fever viruses); Reoviridae (e.g. reoviruses, orbiviruses and rotaviruses); Birnaviridae; Hepadnaviridae (Hepatitis B virus); Parvovirida (parvoviruses); Papovaviridae (papilloma viruses, polyoma viruses); Adenoviridae (most adenoviruses); Herpesviridae (herpes simplex virus (HSV) 1 and 2, varicella zoster virus, cytomegalovirus (CMV), herpes virus); Poxviridae (variola viruses, vaccinia viruses, pox viruses); and Iridoviridae (e.g. African swine fever virus); and unclassified viruses (e.g. the etiological agents of Spongiform encephalopathies, the agent of delta hepatitis (thought to be a defective satellite of hepatitis B virus), the agents of non-A, non-B hepatitis (class 1=internally transmitted; class 2=parenterally transmitted (i.e. Hepatitis C); Norwalk and related viruses, and astroviruses).
The miRNA formatted multitarget expression constructs described herein are particularly useful for treating viral infections characterized by a high rate of mutation, such as HIV and influenza, since multiple viral-targeted miRNAs within a single construct significantly decrease the chance of viral escape mutants and broaden the range of genetic viral variants that can be treated. Ideal target sequences that are conserved across different influenza viruses, including human, bird and swine viruses, have been identified, and may be used in the miRNA constructs of the present invention. See U.S. Provisional Application No. 60/907,650 entitled “Influenza Sirna Molecules, Expression Constructs, Compositions, And Methods Of Use”, filed Apr. 12, 2007, which is herein incorporated by reference in its entirety.
In one embodiment, the vectors of the present invention are designed to express one, two, three, four, five, or more HBV-specific miRNA-formatted interfering RNAs, for instance in a liver cell or in the liver of a mammal. Specific sequences in HBV that may be targeted are disclosed in the examples reported herein. Other target sequences are also known, and are disclosed in PCT/US2004/019229 and PCT/US2005/0046162, each of which is herein incorporated by reference in its entirety.
Endogenous genes that may be targeted by the methods of the present invention include genes involved in autoimmunity and/or cancer. The miRNA formatted multitarget expression constructs described herein are ideal for treating such diseases, which are typically characterized by the involvement of multiple genes.
The term “autoimmune disease” as used herein is defined as a disorder that results from an autoimmune response. An autoimmune disease is the result of an inappropriate and excessive response to a self-antigen. Examples of autoimmune diseases, include but are not limited to, Addision's disease, alopecia greata, ankylosing spondylitis, autoimmune hepatitis, autoimmune parotitis, Crohn's disease, diabetes (Type I), dystrophic epidermolysis bullosa, epididymitis, glomerulonephritis, Graves' disease, Guillain-Barr syndrome, Hashimoto's disease, hemolytic anemia, systemic lupus erythematosus, multiple sclerosis, myasthenia gravis, pemphigus vulgaris, psoriasis, rheumatic fever, rheumatoid arthritis, sarcoidosis, scleroderma, Sjogren's syndrome, spondyloarthropathies, thyroiditis, vasculitis, vitiligo, myxedema, pernicious anemia, ulcerative colitis, among others.
The term “cancer” as used herein is defined as disease characterized by the rapid and uncontrolled growth of aberrant cells. Cancer cells can spread locally or through the bloodstream and lymphatic system to other parts of the body. Examples of various cancers include but are not limited to, breast cancer, prostate cancer, ovarian cancer, cervical cancer, skin cancer, pancreatic cancer, colorectal cancer, renal cancer, liver cancer, brain cancer, lymphoma, leukemia, lung cancer and the like.
In one embodiment of the invention, the multiple miRNA-formatted interfering RNAs are expressed on a single transcript from a pol II promoter. However, in other embodiments, promoters other than pol II might be used so long as the promoter facilitates expression of the multiple miRNA-formatted interfering RNAs and inhibition of target gene expression at least as effectively or more effectively than a vector expressing either of said microRNA (miRNA)-formatted interfering RNAs alone. Where a pol II promoter is used, the expression construct typically terminates with a polyadenylation signal. Examples of additional promoters are RNA polymerase I and III promoters.
As used herein, the term “promoter/regulatory sequence” means a nucleic acid sequence which is required for expression of a gene product operably linked to the promoter/regulatory sequence. In some instances, this sequence may be the core promoter sequence and in other instances, this sequence may also include an enhancer sequence and other regulatory elements which are required for expression of the gene product.
The promoters employed in the vector constructs of the invention may be constitutive or inducible. A “constitutive” promoter is a nucleotide sequence which, when operably linked with a polynucleotide which encodes or specifies a gene product, causes the gene product to be produced in a cell under most or all physiological conditions of the cell. An “inducible” or “regulatable” promoter is a nucleotide sequence which, when operably linked with a polynucleotide which encodes or specifies a gene product, causes the gene product to be produced in a cell substantially only when an inducer which corresponds to the promoter is present in the cell.
The promoters employed in the vector constructs of the invention may be tissue-specific or ubiquitous. A ubiquitous promoter is expressed in a broad range of cell types, and may include certain viral promoters, for instance, the CMV promoter. A “tissue-specific” promoter is one that is not universally expressed in all cells, and that substantially enhances expression of a gene in one or more particular tissues as compared with other tissues. The choice of tissue-specific pol II promoter will depend on the cell or tissue targeted for expression, or where a pathogen is targeted, on the cell or tissue infected by the pathogen. Suitable tissue-specific promoters are known in the art, and include but are not limited to the alpha fetoprotein enhancer/albumin promoter for liver-specific expression, the secretoglobin family 1A, member 1 promoter for expression in the bronchial epithelium, surfactant, pulmonary-associated proteins A, B, or C promoters for lung parenchymal expression, to name just a few. Liver-specific promoters are particularly useful for the HBV targeting constructs described herein. Such liver-specific promoters include but are not limited to the human alpha-1 antitrypsin (hAAT) promoter, the lecithin-cholesterol acyl transferase (LCAT) promoter, the apolipoprotein H (ApoH) promoter, and the prealbumin promoter, to name a few, alone or in combination with liver-specific enhancer regions such as that of the alpha fetoprotein or the enhancer of the gene for ApoE.
The expression vectors of the present invention include the backbone vectors for building the constructs described herein. For example, the present invention includes a nucleic acid vector for expressing one or more miRNA-formatted interfering RNAs comprising a tissue-specific pol II promoter operably linked to at least first and second intron sequences and a polyadenylation signal, wherein said second intron comprises 5′ and 3′ miRNA-formatted arm regions of no more than about 20 to about 45 consecutive nucleotides each flanking one or more cloning sites for recombinantly inserting a nucleic acid encoding a target-specific stem-loop construct having the attributes described above. The 5′ and 3′ arm regions are derived from a naturally occurring miRNA, or have a secondary structure modeled after a naturally occurring miRNA, as described above. In some embodiments, the vector further comprises one or more cloning restriction sites 5′ and/or 3′ of said miRNA-formatted arm regions for sequential cloning of multiple miRNA units as also described above.
The vector constructs of the present invention are useful in methods of inhibiting or decreasing expression of at least one target gene in a cell in vitro or in vivo. In the context of the present invention, “in vitro” means that an expression vector of the invention is expressed in a cell in culture. “In vivo” means that an expression vector of the invention is expressed in a cell in a mammal or other multicellular animal. The vector constructs of the invention may also be expressed in a test tube in the presence of cell extracts containing the necessary transcriptional machinery or proteins to generate the primary miRNA transcript (pri-miRNA), and contacted with the isolated Microprocessor complex containing the double-stranded RNA binding protein Pasha (also called DGCR8) and the RNase III enzyme Drosha in order to process the pri-miRNA transcript into pre-miRNAs, and RISC (RNA induced silencing complex) components for further processing into individual miRNAs [51,52]. The individual miRNAs may then be delivered to the target cell or tissue.
In one embodiment, the present invention includes a method comprising transfecting a cell containing the target gene or delivering to the cell the expression vector of the invention such that the nucleic acid encoding the two or more miRNA-formatted interfering RNAs is expressed in the cell and expression of said at least one target gene is inhibited or decreased. Preferably, expression of the target gene(s) is decreased at least as effectively or more effectively than with a vector expressing any of said microRNA (miRNA)-formatted interfering RNAs alone. The methods of the present invention are useful in methods of treating a patient infected with a target pathogen, or a patient in which target endogenous genes are aberrantly expressed. In one embodiment, the methods of the present invention include delivering to the patient a nucleic acid vector according to the present invention such that at least two miRNA-formatted interfering RNAs are expressed and expression of at least one target gene is inhibited or decreased.
Depending on the cell or tissue targeted by the methods of the invention, there will be multiple means of delivering the expression vector of the invention to the target tissue. For example, the vector can be readily introduced into a host cell, e.g., mammalian, bacterial, yeast or insect cell using any method in the art. For example, the expression vector can be transferred into a host cell by physical, chemical or biological means. Physical methods for introducing a polynucleotide into a host cell include calcium phosphate precipitation, lipofection, particle bombardment, microinjection, electroporation, and the like. Methods for producing cells comprising vectors and/or exogenous nucleic acids are well-known in the art. See, for example, Sambrook et al. (2001, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York), and in Ausubel et al. (1997, Current Protocols in Molecular Biology, John Wiley & Sons, New York).
Biological methods for introducing a polynucleotide of interest into a host cell include the use of DNA and RNA vectors. Viral vectors, and especially retroviral vectors, have become the most widely used method for inserting genes into mammalian, e.g., human cells. Other viral vectors can be derived from lentivirus, poxviruses, herpes simplex virus I, adenoviruses and adeno-associated viruses, and the like. See, for example, U.S. Pat. Nos. 5,350,674 and 5,585,362.
Chemical means for introducing a polynucleotide into a host cell include colloidal dispersion systems, such as macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. A preferred colloidal system for use as a delivery vehicle in vitro and in vivo is a liposome (i.e., an artificial membrane vesicle). The preparation and use of such systems is well known in the art. Exemplary formulations are also disclosed in U.S. Pat. No. 5,981,505; U.S. Pat. Nos. 6,217,900; 6,383,512; U.S. Pat. No. 5,783,565; the Boutin patent family, U.S. Pat. No. 7,202,227; U.S. Pat. No. 6,379,965; U.S. Pat. No. 6,127,170; and U.S. Pat. No. 5,837,533; and WO03/093449, which are herein incorporated by reference in their entireties.
The invention also encompasses the use of pharmaceutical compositions of the appropriate vector to practice the methods of the invention. The pharmaceutical compositions useful for practicing the invention may be administered to deliver a dose of between 1 ng/kg/day and 100 mg/kg/day.
As used herein, the term “physiologically acceptable” ester or salt means an ester or salt form of the active ingredient which is compatible with any other ingredients of the pharmaceutical composition, which is not deleterious to the subject to which the composition is to be administered. The formulations of the pharmaceutical compositions described herein may be prepared by any method known or hereafter developed in the art of pharmacology. In general, such preparatory methods include the step of bringing the active ingredient into association with a carrier or one or more other accessory ingredients, and then, if necessary or desirable, shaping or packaging the product into a desired single- or multi-dose unit. Suitable carriers include, but are not limited to, saline, buffered saline, dextrose, water, glycerol, ethanol, and combinations thereof. The composition can be adapted for the mode of administration and can be in the form of, for example, a pill, tablet, capsule, spray, powder, or liquid.
Although the description of pharmaceutical compositions provided herein are principally directed to pharmaceutical compositions which are suitable for ethical administration to humans, it will be understood by the skilled artisan that such compositions are generally suitable for administration to animals of all sorts. Modification of pharmaceutical compositions suitable for administration to humans in order to render the compositions suitable for administration to various animals is well understood, and the ordinarily skilled veterinary pharmacologist can design and perform such modification with merely ordinary, if any, experimentation. Subjects to which administration of the pharmaceutical compositions of the invention is contemplated include, but are not limited to, humans and other primates, mammals including commercially relevant mammals such as non-human primates, cattle, pigs, horses, sheep, cats, and dogs.
As used herein, “parenteral administration” of a pharmaceutical composition includes any route of administration characterized by physical breaching of a tissue of a subject and administration of the pharmaceutical composition through the breach in the tissue. Parenteral administration thus includes, but is not limited to, administration of a pharmaceutical composition by injection of the composition, by application of the composition through a surgical incision, by application of the composition through a tissue-penetrating non-surgical wound, and the like. In particular, parenteral administration is contemplated to include, but is not limited to, subcutaneous, intraperitoneal, intramuscular, intrasternal injection, intravenous (IV), intra-arterial, intradermal, intrathecal, intramuscular (IM) and kidney dialytic infusion techniques. The compositions of the invention may also be administered, without limitation, topically, orally, and by mucosal routes of delivery such as intranasal, inhalation, rectal, vaginal, buccal, and sublingual.
The present invention may, in certain embodiments, employ the methods disclosed in the U.S. Provisional Application No. 60/907,014, filed Mar. 16, 2007 entitled “Methods and Compositions For Directing RNAi-Mediated Gene Silencing In Distal Organs Upon Intramuscular Administration Of DNA Expression Vectors,” which is hereby incorporated by reference in its entirety. Specifically, intramuscular injection or electroporation of expression constructs encoding dsRNA(s) results in targeted inhibition of gene expression in other organs and tissues of the body. Without being bound by any theory, the inventors thereof hypothesize that delivery of dsRNA to distal tissues such as respiratory epithelial cells, for example, may be mediated by extracellular vesicles (exovesicles) containing expressed dsRNA or injected siRNA or shRNA that bud from the surface of transfected muscle cells. In particular, it has been shown that dsRNA expressed in muscle cells is delivered in vivo to the liver. Targeting to other cells and tissues may be accomplished by coexpressing cell surface ligands that are incorporated into exovesicles and target such dsRNA containing exovesicles to the target cell or tissue. Such cell surface ligands may be coexpressed from the same vector as the multiple miRNA constructs, or from a separate expression vector. In this embodiment, the target gene is in a different cell than the transfected cell that expresses the vector encoding the multiple miRNAs.
It is known that some dsRNA sequences, possibly in certain cell types and through certain delivery methods, may result in an interferon response. The methods of the invention may be performed so as not to trigger an interferon/PKR response, by expressing the multiple miRNA-formatted interfering RNA molecules intracellularly from an expression vector. See US Published Application 20040152117, which is herein incorporated by reference. However, in embodiments where the miRNA constructs are not expressed intracellularly, the interferon/PKR response may also be inhibited by other means. For instance, interferon and PKR responses may be silenced in the transfected and target cells using a dsRNA species directed against the mRNAs that encode proteins involved in the response. Alternatively, interferon response promoters are silenced using dsRNA, or the expression of proteins or transcription factors that bind interferon response element (IRE) sequences is abolished using dsRNA or other known techniques.
By “under conditions that inhibit or prevent an interferon response or a dsRNA stress response” is meant conditions that prevent or inhibit one or more interferon responses or cellular RNA stress responses involving cell toxicity, cell death, an anti-proliferative response, or a decreased ability of a dsRNA to carry out a PTGS event. These responses include, but are not limited to, interferon induction (both Type 1 and Type II), induction of one or more interferon stimulated genes, PKR activation, 2′5′-OAS activation, and any downstream cellular and/or organismal sequelae that result from the activation/induction of one or more of these responses. By “organismal sequelae” is meant any effect(s) in a whole animal, organ, or more locally (e.g., at a site of injection) caused by the stress response. Exemplary manifestations include elevated cytokine production, local inflammation, and necrosis. Desirably the conditions that inhibit these responses are such that not more than 95%, 90%, 80%, 75%, 60%, 40%, or 25%, and most desirably not more than 10% of the cells undergo cell toxicity, cell death, or a decreased ability to carry out a PTGS event, compared to a cell not exposed to such interferon response inhibiting conditions, all other conditions being equal (e.g., same cell type, same transformation with the same dsRNA).
Apoptosis, interferon induction, 2′5′ OAS activation/induction, PKR induction/activation, anti-proliferative responses, and cytopathic effects are all indicators for the RNA stress response pathway. Exemplary assays that can be used to measure the induction of an RNA stress response as described herein include a TUNEL assay to detect apoptotic cells, ELISA assays to detect the induction of alpha, beta and gamma interferon, ribosomal RNA fragmentation analysis to detect activation of 2′5′ OAS, measurement of phosphorylated eIF2a as an indicator of PKR (protein kinase RNA inducible) activation, proliferation assays to detect changes in cellular proliferation, and microscopic analysis of cells to identify cellular cytopathic effects. See, e.g., US Published Application 20040152117, which is herein incorporated by reference.
The following examples are provided to describe and illustrate the present invention. As such, they should not be construed to limit the scope of the invention. Those in the art will well appreciate that many other embodiments also fall within the scope of the invention, as it is described hereinabove and in the claims.
For therapeutic applications, interfering RNAs can be introduced into cells in several different ways. For example, synthetic short double-stranded RNAs (approximately 21 nucleotides) can be directly transfected into cells, where a single strand is incorporated into active RISC. Longer lasting silencing can be achieved by expressing interfering RNAs from viral or plasmid vectors. Typically, these expressed interfering RNAs (eiRNAs) are processed from short hairpin RNAs (shRNAs) transcribed by RNA polymerase III using U6, H1, or 7SK promoters. These promoters are strong, active in virtually all cell types, and well-adapted for transcription of short RNAs. See
Previous work has identified regions in the HBV genome that are well-conserved among HBV serotypes and susceptible to silencing by expressed interfering RNAs (eiRNAs) [5]. These regions are found throughout the 3.2 kb genome and, because of the highly overlapping pattern of transcription, can include sequences that are simultaneously present on the 3.5 kb pregenomic RNA and one or more of the mRNAs that encode viral proteins, as depicted in
Vectors that express multiple shRNAs from a single plasmid were developed to maximize the efficacy of a clinical vector against a broad range of viral genotypes. This vector strategy is useful in minimizing the potential for selection of escape mutants, which is a serious limitation of some current HBV therapies based on nucleoside analog inhibitors of the viral polymerase. Such a vector was designed to express each shRNA from its own RNA polymerase III promoter (7SK or U6). See PCT/US2005/029976, which is herein incorporated by reference in its entirety. See
Current HBV anti-viral agents reduce the burden of infectious virus, but are considerably less effective in decreasing viral antigenemia. High titers of subviral particles, consisting primarily of the viral surface antigen (HBsAg), are found in the serum of chronically infected patients. This is thought to contribute to viral persistence and to liver pathology. The ability of RNAi-based therapeutics to target the viral RNA pregenome as well as mRNAs encoding viral proteins offers a significant improvement over existing therapies. Reductions are seen in both RNA and protein products of viral replication, as well as in viral DNA replicative intermediates.
It has been observed that viral RNAs, DNA replicative intermediates, and surface antigen proteins are coordinately reduced in an infected cell (e.g. HepG2 cells transfected with pHBV2) when shRNAs were expressed from a vector containing the Pol III promoter (See
While shRNA expression plasmids can be highly effective suppressors of viral antigen production and infectious particle formation after transfection into cultured cells, in vivo delivery of these agents to hepatocytes remains a difficult challenge. The following experiments were designed to test the therapeutic effects of the RNAi-based silencing in an animal model. The shRNA expression plasmid was formulated with molecules that allowed transport to the liver and uptake by hepatocytes. Numerous formulations have been tested for delivery of shRNA expression plasmids to the liver in mouse models of HBV infection. See, e.g., U.S. Pat. No. 5,783,565; U.S. Pat. No. 7,202,227; U.S. Pat. No. 6,379,965; U.S. Pat. No. 6,127,170; U.S. Pat. No. 5,837,533, and US 2006/0084617, which are herein incorporated by reference in their entireties. Results obtained with a single dose using a cholesterol-spermine formulation are depicted in
In the design of a second generation of vectors described here, we have used an miRNA format in order to capture the advantages of driving expression from a tissue specific RNA pol II promoter and processing multiple interfering RNAs from a single transcript that does not co-express any protein product.
Initially, we tested HBV-targeted interfering RNAs expressed from pol III promoters, but formatted as miRNAs instead of shRNAs. We based our constructs on the expression cassette found in Expression Arrest™ plasmids that use a U6 promoter to drive expression of interfering RNAs built into the context of human miR-30 [18]. To generate the pUC-U6-30/XX series of plasmids, we moved the expression cassette out of the pSM2 vector backbone and into the plasmid pUC19. The stem-loop region was then replaced with sequence targeting HBV RNAs in conserved regions near position 1737 or 1907 in the HBV genome.
The 1907 and 1737 regions of the HBV genome correspond approximately to D (1907) and E (1737) in
The efficacy of these plasmids was tested by assaying hepatitis S antigen (HBsAg) secretion from Huh7 cells after co-transfection with a constant amount of the infectious plasmid pHBV/2 and increasing amounts of silencing plasmid. A SEAP reporter plasmid, pM1-SEAP, was included to control for transfection efficiency. We found that direct transfer of sequence based on our shRNA plasmids [5] was not effective in the miRNA format. Results for the miRNA-formatted 1737 shRNA are shown in
HBV genome target sequence (GenBank V01460). Targeted region is shown in bold, underlined print.
Sequence of regions encoding HBV-targeted miRNAs (XbaI/SpeI restriction fragments):
RNA Pol II Driven miR-eiRNAs
Several groups have reported successful silencing with plasmid or viral vectors that express miR-formatted interfering RNAs (miR-eiRNAs) from RNA pol II promoters. In general, however, the miR-eiRNAs were processed from a longer transcript that co-expresses a protein product. While this may have advantages in some research applications, it is undesirable for therapeutic eiRNAs where the co-expressed protein could be antigenic or toxic.
In our first attempts to introduce a pol II promoter into the pUC-U6-30/XX plasmids, we exchanged the U6 promoter for a liver specific promoter derived from the plasmid pLIVE. In addition we inserted a BGH 3′UTR downstream of the miR-30 3′ flanking sequence to prevent transcriptional readthrough into plasmid sequence. These constructs were inactive in silencing (data not shown). In order to correct this, we generated plasmids of the pLV-30s/XX series, where the eiRNA stem-loops are inserted into non-protein coding sequence, more closely mimicking natural miRNAs. For these plasmids, we moved the silencing stem-loop of pUC-U6-30/XX plasmids into the second intron of the pLIVE vector so that it would be processed from a transcript that consists primarily of two introns and contains no open reading frame for the production of a protein (see
Silencing activity of these pol II driven miR-eiRNAs was tested in Huh7 cells co-transfected with the silencing plasmid and a dual luciferase reporter plasmid. HBV target sequence was inserted into the 3′UTR of the Renilla luciferase gene cassette in the vector psiCHECK-2, while expression of firefly luciferase from the same plasmid serves as a transfection efficiency control. Results shown in
Silencing Activity and Processing of Individual miR-eiRNAS Expressed from a Bicistronic Plasmid
While the inclusion of a second miR-eiRNA stem-loop improved silencing of HBV targets, we sought direct evidence that each of the stem-loops in our bicistronic plasmid is active. Two dual luciferase reporter plasmids were constructed that contain HBV target sequence for either the 1737 or 1907 miR-eiRNAs, individually. As shown in
Additionally, we have examined the expression and processing of eiRNAs from the bicistronic plasmid in northern blots. Huh7 cells were transfected either with the monocistronic plasmids pLV-30s/1737B, pLV-30s/1907A, or pLV-30s/EGFP, or with the bicistronic plasmid pLV-30s/1737B/1097A. RNA isolated from these cells was analyzed by northern blotting, with sequential detection on the same blot using oligonucleotide probes for the anti-sense (guide) strand of each of the miRNAs. It is evident from the results shown in
The efficiency of processing of the miR-eiRNAs may help to account for their potency, despite their being expressed from pol II promoters that are generally less strong than pol III promoters. Results in
In using a pol II promoter, we expect to be able to select promoters that will enhance the relative expression of miR-eiRNAs in targeted tissues. For HBV therapeutic eiRNAs it will be advantageous to maximize expression in hepatocytes and minimize expression in other tissues, thereby reducing concerns about potentially deleterious effects in non-targeted tissues. The liver specific promoter from pLIVE, used in our pLV-30s/XX plasmids, combines a mouse alpha-fetoprotein enhancer and minimal albumin promoter. To test the tissue specificity of silencing with this promoter, we compared silencing in HeLa cells transfected with plasmids carrying the liver-specific promoter (pLV-30s/1737B/1907A) to that with the broadly active CMV promoter (pCMV-30s/1737B/1907A).
The expression of interfering RNAs in cells, whether formatted as sh- or mi-RNAs, leads to the production of highly structured RNAs that have the potential to induce an interferon response. To test whether the miR-eiRNAs produced from our bicistronic plasmid trigger an interferon response, we transfected cells and assayed several mRNAs that serve a markers for this response. In these experiments, we used HeLa cells since they are capable of a more robust interferon response than Huh7 cells. The plasmid pCMV-30s/1737B/1907A was transfected into cells in an amount higher than required for >85% reduction in HBV reporter activity (see
As shown in
The indicated silencing plasmids (
As can be seen in graphs A and B of
To examine whether inclusion of additional miR-eiRNA stem-loop structures would enhance the suppression of target gene expression, we constructed a plasmid expressing four different miR-eiRNAs under the control of a liver-specific promoter so that four distinct regions of the HBV genome were targeted. In addition to the pLVD construct expressing 1737B and 1907A HBV miR-eiRNAs, we added two additional miR-eiRNAs targeting the 799B (SEQ ID NO: 12) and 2791A (SEQ ID NO: 15) regions of the HBV genome (pLVQ construct, see
miR-eiRNAs Expressed from Exons are as Effective as miR-eiRNAs Expressed from Introns
Four miR-eiRNAs targeting the 1737B, 1907A, 799B, and 2791A regions of the HBV genome were placed either into the second intron (pLVQ-Int2,
To ensure that no loss of function occurred when individual miR-eiRNAs were expressed from a multi-cistronic plasmid as compared to a monocistronic plasmid, a dual luciferase reporter construct containing a HBV target sequence for 1737, 1907, 799, or 2791 (as indicated along the X axis in
All publications, patents and patent applications discussed and cited herein are incorporated herein by reference. While in the foregoing specification this invention has been described in relation to certain preferred embodiments thereof, and many details have been set forth for purposes of illustration, it will be apparent to those skilled in the art that the invention is susceptible to additional embodiments and that certain of the details described herein may be varied considerably without departing from the basic principles of the invention.
This is continuation of U.S. patent application Ser. No. 12/445,388 filed Apr. 13, 2009 which is a National Stage application of PCT International Application No. PCT/US2007/081103, filed Oct. 11, 2007, which in turn claims the benefit pursuant to 35 U.S.C. §119(e) of U.S. Provisional Application No. 60/907,651, filed on Apr. 12, 2007 and U.S. Provisional Application No. 60/850,906, filed on Oct. 11, 2006, all of which are hereby incorporated by reference in their entirety herein.
This invention was made with government support from the National Institute of Health, grant number AI053988. The government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 60907651 | Apr 2007 | US | |
| 60850906 | Oct 2006 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 12445388 | US | |
| Child | 12793248 | US |
