Patent Grant
8129510
The subject matter described herein relates to expression cassettes. More particularly, liver-specific expression cassettes are described.
Recombinant gene therapy techniques have been developed and evaluated in preclinical and clinical tests over the last fifteen years. Gene therapy techniques are particularly promising for treating diseases or deficiencies that are caused by a deficiency or abnormality in the expression of a particular gene in specific cell or tissue types because a gene of interest can be placed under the control of a cell-specific or tissue-specific promoter to achieve location-specific expression of that gene. In particular, there has been significant interest in developing gene therapy techniques to treat liver-specific diseases or deficiencies.
Multiple recombinant gene transfer vectors based on different types of viruses have been developed and tested in clinical trials in recent years. Gene transfer vectors based on adeno-associated virus (AAV) have become favored vectors because of characteristics such as an ability to (i) transduce different types of dividing and non-dividing cells of different tissues, and (ii) establish stable, long-term transgene expression. While vectors based on other viruses, such as adenoviruses and retroviruses, also posses such desirable characteristics, the use of other vectors has been associated with toxicity of some human diseases. These side effects have not been detected with gene transfer vectors based on AAV. Additionally, the technology to produce and purify AAV-based vectors without undue effort has been developed.
AAV-based vectors have provided encouraging results for providing a method of liver-specific gene expression. For example, clinical trials showed that a recombinant AAV vector containing a factor IX (FIX) sequence was able to produce a therapeutic circulating level of FIX protein from hepatocytes in hemophilia B patients. A deficiency of FIX, which is a coagulation factor normally produced by the liver, is the cause of hemophilia B. Hemophilia B is an ideal disease target for gene therapy because it is due to a single gene mutation and because a small increase in the circulating levels of FIX is sufficient to measurably reduce the symptoms of hemophilia B. However, it was observed in the clinical trials described above that the circulating level of FIX protein dropped below therapeutic levels after several weeks (Wang, L. et al., Curr. Gene Ther. 5:349-360 (2005); High, K. A., Semin. Thromb. Hemost., 30:257-267 (2004)). It is believed that the high doses of the recombinant AAV vector that were used triggered an immune response against the transduced hepatocytes.
Thus, there remains a need for providing liver-specific expression of a gene. In particular, there is a need for liver-specific expression constructs that provide robust expression levels from viral vectors that do not trigger an inactivating immune response.
The foregoing examples of the related art and limitations related therewith are intended to be illustrative and not exclusive. Other limitations of the related art will become apparent to those of skill in the art upon a reading of the specification and a study of the drawings.
In one aspect, compositions for expressing a gene or nucleotide sequence of interest in the liver are provided. The compositions are comprised of an expression cassette comprising a synthetic enhancer, a transthyretin promoter, and a nucleotide sequence operably under the control of the synthetic enhancer, and the transthyretin promoter.
In one embodiment, the synthetic enhancer and the transthyretin promoter have a sequence selected from the group consisting of sequences having at least about 80% sequence identity to SEQ ID NO:3 and SEQ ID NO: 3.
In another embodiment, the synthetic enhancer and the transthyretin promoter have a sequence selected from the group consisting of sequences having at least about 80% sequence identity to SEQ ID NO:7 and SEQ ID NO:7.
In another embodiment, the nucleotide sequence that is operably under the control of the synthetic enhancer and the transthyretin promoter is a factor IX sequence.
In another aspect, vectors comprising a composition as described above are provided.
In various embodiments, the vector is an AAV vector, such as a self-complementary AAV vector.
In another embodiment, the vector is comprised of three plasmids: a first plasmid comprising an expression cassette comprising a synthetic enhancer, a transthyretin promoter, and a nucleotide sequence operably under the control of the synthetic enhancer and the transthyretin promoter; a second plasmid comprising adenoviral helper genes; and a third plasmid comprising AAV replication and capsid genes.
In one embodiment, the synthetic enhancer and the transthyretin promoter have a sequence selected from the group consisting of sequences having at least about 80% sequence identity to SEQ ID NO:3 and SEQ ID NO: 3, the nucleotide sequence that is operably under the control of the synthetic enhancer and the transthyretin promoter is a factor IX sequence, and the capsid gene is an AAV-2 or an AAV-8 capsid gene.
In another embodiment, the synthetic enhancer and the transthyretin promoter have a sequence selected from the group consisting of sequences having at least about 80% sequence identity to SEQ ID NO:7 and SEQ ID NO: 7, the nucleotide sequence that is operably under the control of the synthetic enhancer and the transthyretin promoter is a factor IX sequence, and the capsid gene is an AAV-2 or an AAV-8 capsid gene.
In another aspect, methods of expressing a nucleotide of interest in a mammalian liver by delivering to the liver an expression cassette comprising a synthetic enhancer, a transthyretin promoter, and the nucleotide sequence operably under the control of the synthetic enhancer and the transthyretin promoter.
In one embodiment, expression of a nucleotide of interest is for use in a treating a disease or disorder by expressing a protein encoded by the nucleotide of interest in a therapeutically effective amount.
In one embodiment, the method comprises delivery of a vector for expression of factor IX (FIX) for treatment of hemophilia B.
In addition to the exemplary aspects and embodiments described above, further aspects and embodiments will become apparent by reference to the drawings and by study of the following descriptions.
SEQ ID NO:1 is a nucleotide sequence of a synthetic enhancer.
SEQ ID NO:2 is a nucleotide sequence of a transthyretin promoter.
SEQ ID NO:3 is an example of a sequence including a synthetic enhancer (SynEnh) sequence followed by a transthyretin sequence with several nucleotides between the two sequences.
SEQ ID NO:4 is a nucleotide sequence of a portion of the human FIX gene with a 0.3 kb mini-intron and a synthetic polyadenylation signal of about 70 bp.
SEQ ID NO:5 is a nucleotide sequence that includes a portion of the canine FIX gene with a 0.3 kb mini-intron (which was reduced from the 1.4 kb intron A in the canine FIX gene) and a synthetic polyadenylation signal of about 70 bp.
SEQ ID NO:6 is the nucleotide sequence of an expression cassette as depicted in
SEQ ID NO:8 is an intron sequence associated with the expression cassette of SEQ ID NO:6, and more particularly with the FIX gene of SEQ ID NO:9.
The practice of the subject matter described herein will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, cell biology and recombinant DNA, which are within the skill of the art. See, e.g., Sambrook, Fritsch, and Maniatis, MOLECULAR CLONING: A LABORATORY MANUAL, 2nd edition (1989); CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, (F. M. Ausubel et al. eds., 1987); the series METHODS IN ENZYMOLOGY (Academic Press, Inc.); PCR 2: A PRACTICAL APPROACH (M. J. McPherson, B. D. Hames and G. R. Taylor eds., 1995) and ANIMAL CELL CULTURE (R. I. Freshney. Ed., 1987).
As used in this specification and the appended claims, the singular forms “a,” “an” and “the” include plural references unless the content clearly dictates otherwise.
A polynucleotide is typically composed of a specific sequence of four nucleotide bases: adenine (A); cytosine (C); guanine (G); and thymine (T) (uracil (U) for thymine (T) when the polynucleotide is RNA). Thus, the term polynucleotide sequence is the alphabetical representation of a polynucleotide molecule. This alphabetical representation can be input into databases in a computer having a central processing unit and used for bioinformatics applications such as functional genomics and homology searching.
An “isolated polynucleotide” molecule is a nucleic acid molecule separate and discrete from the whole organism with which the molecule is found in nature; or a nucleic acid molecule devoid, in whole or part, of sequences normally associated with it in nature; or a sequence, as it exists in nature, but having heterologous sequences in association therewith.
Techniques for determining nucleic acid and amino acid “sequence identity” also are known in the art. Typically, such techniques include determining the nucleotide sequence of the mRNA for a gene and/or determining the amino acid sequence encoded thereby, and comparing these sequences to a second nucleotide or amino acid sequence. In general, “identity” refers to an exact nucleotide-to-nucleotide or amino acid-to-amino acid correspondence of two polynucleotides or polypeptide sequences, respectively. Two or more sequences (polynucleotide or amino acid) can be compared by determining their “percent identity.” The percent identity of two sequences, whether nucleic acid or amino acid sequences, is the number of exact matches between two aligned sequences divided by the length of the shorter sequences and multiplied by 100. Percent identity may also be determined, for example, by comparing sequence information using the advanced BLAST computer program, including version 2.2.9, available from the National Institutes of Health. The BLAST program is based on the alignment method of Karlin and Altschul. Proc. Natl. Acad. Sci. USA 87:2264-2268 (1990) and as discussed in Altschul, et al., J. Mol. Biol. 215:403-410 (1990); Karlin And Altschul, Proc. Natl. Acad. Sci. USA 90:5873-5877 (1993); and Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997). Briefly, the BLAST program defines identity as the number of identical aligned symbols (i.e., nucleotides or amino acids), divided by the total number of symbols in the shorter of the two sequences. The program may be used to determine percent identity over the entire length of the proteins being compared. Default parameters are provided to optimize searches with short query sequences in, for example, blastp with the program. The program also allows use of an SEG filter to mask-off segments of the query sequences as determined by the SEG program of Wootton and Federhen, Computers and Chemistry 17:149-163 (1993). Ranges of desired degrees of sequence identity are approximately 80% to 100% and integer values therebetween. Typically, the percent identities between a disclosed sequence and a claimed sequences are at least 80%, at least 85%, at least 90%, at least 95%, or at least 98%.
Alternatively, the degree of sequence similarity between polynucleotides can be determined by hybridization of polynucleotides under conditions that form stable duplexes between homologous regions, followed by digestion with single-stranded-specific nuclease(s), and size determination of the digested fragments. Two DNA, or two polypeptide sequences are “substantially homologous” to each other when the sequences exhibit at least about 80-85%, preferably 85-90%, more preferably 90-95%, and most preferably 98-100% sequence identity to the reference sequence over a defined length of the molecules, as determined using the methods above. As used herein, substantially homologous also refers to sequences showing complete identity to the specified DNA or polypeptide sequence. DNA sequences that are substantially homologous can be identified in a Southern hybridization experiment under, for example, stringent conditions, as defined for that particular system. Defining appropriate hybridization conditions is within the skill of the art. See, e.g., Sambrook et al., supra; DNA Cloning, supra; Nucleic Acid Hybridization, supra.
In a first aspect, an expression cassette comprising a gene or nucleotide sequence of interest is provided. In another aspect, vectors comprising the expression cassette, for expressing the gene or nucleotide sequence of interest in a tissue, and in particular in the liver, and particularly in mammalian livers, are provided. The expression cassettes and exemplary vectors will now be described.
In one embodiment, the expression cassette comprises a synthetic enhancer (SynEnh), a transthyretin promoter (TTR), and a nucleotide sequence operably under the control of the synthetic enhancer and the transthyretin promoter. Exemplary constructs are shown in
A synthetic enhancer sequence that may be used is shown in SEQ ID NO: 1, and it is contemplated that enhancer sequences that hybridize to SEQ ID NO:1 under stringent conditions are also suitable for use in the expression cassette. Other suitable synthetic enhancer sequences are known in the art, and include but are not limited to those disclosed by Szymanski, P. et al., J. Gene Med., 8(4):514 (2006); Gehrke, S. et al., Gene, 322:137 (2003); and McLellan, A. S., et al., Am. J. Physiol. Cell Physiol., 291(2):C300 (2006)).
The full length TTR promoter normally controls expression of the serum thyroxine-binding protein, which is made by hepatocytes and by the choroid plexus epithelium in adults. In one embodiment, a preferred TTR promoter is a TTR promoter in which the region which controls choroids plexus expression is deleted. The preferred TTR promoter described herein retains the regions which drive liver-specific expression. With continuing reference to
The SynEnh and TTR sequences in the expression cassette may be directly adjacent or separated by a short region of nucleotides. The short region of nucleotides may include one or more restriction enzyme sites. An example of a sequence including a SynEnh sequence followed by a TTR sequence with several nucleotides between the two sequences is shown in SEQ ID NO: 3.
As noted above, a nucleotide sequence is operably linked to the SynEnh-TTR sequence. A gene is “operably linked” to another nucleotide sequence when it is placed in a functional relationship with another nucleotide sequence. For example, if a coding sequence is operably linked to a promoter sequence, this generally means that the promoter may promote transcription of the coding sequence. Operably linked means that the DNA sequences being linked are typically contiguous and, where necessary to join two protein coding regions, contiguous and in reading frame. However, since enhancers may function when separated from the promoter by several kilobases and intronic sequences may be of variable length, some nucleotide sequences may be operably linked but not contiguous. Additionally, as defined herein, a nucleotide sequence is intended to refer to a natural or synthetic linear and sequential array of nucleotides and/or nucleosides, and derivatives thereof. The terms “encoding” and “coding” refer to the process by which a nucleotide sequence, through the mechanisms of transcription and translation, provides the information to a cell from which a series of amino acids can be assembled into a specific amino acid sequence to produce a polypeptide.
The nucleotide sequence that is operably under the control of the synthetic enhancer and the transthyretin promoter may encode a gene or at least a part of a gene of interest. The gene may be an endogenous or viral gene, and may be associated with a disease or pathology.
In one aspect, the nucleotide sequence that is operably under the control of the synthetic enhancer and the transthyretin promoter encodes a gene or a part of a gene whose expression is desired in the liver. The gene's expression in the liver may be desired in order to produce a protein encoded by the gene that is either missing or abnormal in the subject liver. The gene may be a gene that is normally expressed in the liver or a gene that is not normally expressed in the liver.
In one embodiment, the nucleotide sequence that is operably under the control of the synthetic enhancer and the transthyretin promoter is a factor IX (FIX) sequence. The FIX sequence may be a human sequence or a non-human sequence, e.g., a non-human mammalian sequence. In one embodiment, the FIX sequence is SEQ ID NO: 4, which is a sequence that includes a portion of the human FIX gene with a 0.3 kb mini-intron and a synthetic polyadenylation signal of about 70 bp (Xia, H. et al., Nat Biotechnol., 20:1006 (2002)).
In another embodiment, the FIX sequence is SEQ ID NO: 5, which is a sequence that includes a portion of the canine FIX gene with a 0.3 kb mini-intron (which was reduced from the 1.4 kb intron A in the canine FIX gene) and a synthetic polyadenylation signal of about 70 bp.
In another embodiment, the FIX sequence is SEQ ID NO:9, wherein the intron sequence has been shortened by about 200 bp. The shortened intron is identified herein as SEQ ID NO:8.
While preferred sequences are described for the synthetic enhancer, transthyretin promoter, and nucleotide sequence that is operably under the control of the synthetic enhancer and the transthyretin promoter are provided above, it is recognized that the sequences may be varied yet retain similar function. In particular, sequences that hybridize under stringent conditions to any of the nucleotide sequences described herein are contemplated for use in the expression cassettes, vectors, and methods of use.
A study was conducted to evaluate the activity and specificity of an expression cassette comprising the sequence of SEQ ID NO: 3, which comprises SynEnh and TTR sequences. As described in Example 1, a first plasmid was constructed in which the Renilla luciferase gene was placed under the control of the synthetic enhancer and the transthyretin promoter. A second plasmid was constructed in which the Renilla luciferase gene was placed under the control of a wildtype TTR promoter. Huh-7 and HEK293 cells were transiently transfected with the plasmids, along with a control vector expressing the firefly luciferase gene. Following incubation at standard tissue culture conditions for 36 hours, the levels of Renilla and firefly luciferase were measured. Results are shown in Table 1.
1Relative luciferase levels were normalized to the TTR expression in HEK293 cells. Standard deviations are indicated in parentheses.
As shown in Table 1, the plasmid with the SynEnh-TTR expression cassette produced a 42 fold higher level of liver specific luciferase expression than the plasmid with the wildtype TTR promoter.
In another study, described in Example 2, the activity of an expression cassette comprising the SynEnh-TTR construct was evaluated in vivo. Plasmids containing an expression cassette with the human or canine FIX (SEQ ID NO: 4 and SEQ ID NO: 5, respectively) under the control of SynEnh-TTR (SEQ ID NO: 3) were prepared. In addition, plasmids containing the human or canine FIX sequences (SEQ ID NO: 4 and SEQ ID NO: 5, respectively) under the control of the apolipoprotein E hepatic control region (ApoE-HCR) and the human α1-antitrypsin promoter (hAAT) were prepared. The four plasmids were injected into mice and circulating FIX levels were measured three days post-injection. The results are shown in
As seen in
An example of a scAAV vector is diagramed in
The construct shown in
The construct shown in
The scAAV vector plasmid described above is preferably used in combination with a second plasmid comprising adenoviral helper genes and a third plasmid comprising AAV replication (rep) and capsid (cap) genes to triple transfect HEK293 cells, as previously described (Nakai, et al., Journal of Virology, 79:214-24 (2005); Thomas et al., Journal of Virology, 78:3110-22 (2004)). The AAV rep and cap genes are the two AAV genes that encode AAV replication and capsid proteins, respectively. As defined herein, the scAAV vector plasmid in combination with a plasmid providing adenoviral helper genes and a plasmid comprising AAV rep and cap genes is an AAV vector, more specifically, a scAAV vector, that can be used to provide recombinant AAV in cells that are triple transfected with the three plasmids. Also, plasmids encoding scAAV vector genomes including either the human or canine FIX expression cassettes provided herein can be injected into mice by hydrodynamic tail vein injection to observe the FIX protein levels obtained from the vectors.
Preferably, the AAV cap genes provide an AAV-2 or AAV-8 capsid, more preferably, an AAV-8 capsid. It has been observed previously that AAV-8 vectors are more efficient at gene transfer in vivo than AAV-2 vectors. AAV-8 vectors appear to be equally efficient at liver transduction if administered by peripheral IV or hepatic vessel infusion. Also, as AAV-8 has a non-human origin, it is unlikely that pre-existing anti-AAV-8 antibodies will limit transduction in human patients treated with AAV-8 vectors.
The expression cassettes and vectors described herein provide several advantages over prior expression cassettes and vectors. For example, the synthetic enhancer and transthyretin promoter provide a short control sequence that is able to drive robust, liver-specific expression of a gene. The shortness of the synthetic enhancer and transthyretin promoter allows for the use of longer genes or gene fragments in a vector including the synthetic enhancer and transthyretin promoter, as well as the use of the expression cassettes in double stranded AAV vectors, such as self-complementary AAV vectors, that have been observed to be from 20 to 50 times more efficient than single-stranded vectors, but typically can only accept 2.3 to 2.4 kb of exogenous nucleotide sequence. Also, a lower vector dosage is required to achieve a therapeutic result because of the efficiency of the expression cassette itself in combination with the efficiency of self complementary AAV vectors. The use of lower vector dosage reduces the probability of transduced cells being recognized and destroyed by an immune response, such as a cytotoxic T lymphocyte (CTL) response that has been observed in other clinical trials.
A scAAV expression cassette as depicted in
In another aspect, methods of expressing a gene or nucleotide of interest are provided. In a preferred embodiment, a nucleotide sequence of interest is expressed in a selected tissue for treatment of a genetic disorder. For example, hemophilia B is a genetic disorder caused by a deficiency in coagulation factor IX (FIX) normally produced in the liver, and manifests as unpredictable, recurrent, and spontaneous bleeding in soft tissues and/or major joints. This recurrent bleeding can lead to crippling joint abnormalities in the most severely affected individuals.
Accordingly, in one embodiment, a vector containing an expression cassette a synthetic enhancer, a transthyretin promoter, and a nucleotide sequence operably under the control of the synthetic enhancer and the transthyretin promoter, wherein the synthetic enhancer and the transthyretin promoter comprise the sequence of SEQ ID NO: 3.
In another embodiment, a self-complementary AAV vector containing an expression cassette that is flanked by AAV inverted terminal repeats (ITR) of serotype 2 and 4 (˜50% sequence identity), where the trs of the right AAV4 ITR is deleted (ITR-4).
For treatment of hemophilia B, the vector contains a nucleotide sequence encoding for a factor IX protein. Expression of the protein after introduction of the vector to the subject is effective to increase the circulating levels of the protein in the blood.
The vector is introduced to the mammal, typically by injection, intravenously, subcutaneously, parenterally, or the like, in an amount to provide a therapeutically effective amount of the protein.
In a supporting study, a canine equivalent of the expression cassette of SEQ ID NO:6, and as shown in
In another study, in vivo expression of human FIX for the enhancer/promoter combinations described herein were determined, and compared to the hFIX expression of an ApoE(HCR) enhancer-hAAT promoter and a deltaApoE(HCR)-deltahAAT promoter (Nathwani, A. C. et al., Blood, 107(7):2653 (2005)). Following hydrodynamic tail vein injection of 20 μg of each plasmid into 3-5 mice per group, serum samples from each mouse were assayed for circulating FIX levels by ELISA experiments. As seen in
The following examples are illustrative in nature and are in no way intended to be limiting.
The expression profile of the SynEnh-TTR promoter was evaluated as follows. Two different plasmids were constructed. The first plasmid was comprised of the TTR promoter alone, which controlled expression of the Renilla luciferase gene. The second plasmid was comprised of combined SynEnh-TTR promoter (SEQ ID NO:3) controlling the expression of the Renilla luciferase gene.
The plasmids were transiently transfected into HUH-7 (liver hepatoma) and HEK293 (embryonic kidney) cell lines in triplicate. As a transfection and expression control, pGL3-Control vector (Promega) was cotransfected along with the plasmids. The pGL3-control vector contains the Firefly luciferase gene under the control of a ubiquitous SV40 promoter and enhancer.
Following incubation at standard tissue culture conditions for 36 hours, the quantities of Renilla and Firefly luciferases were measured. Results are shown in Table 1.
Plasmids (pNEB 193 derivatives) containing a 2.3 kb expression cassette with the human or canine FIX (SEQ ID NO: 4 and SEQ ID NO: 5, respectively) under the control of SynEnh-TTR (SEQ ID NO: 3) were prepared.
In addition, plasmids containing the human or canine FIX sequences (SEQ ID NO: 4 and SEQ ID NO: 5, respectively) under the control of the apolipoprotein E hepatic control region (ApoE-HCR) and the human α1-antitrypsin promoter (hAAT) were prepared.
Forty micrograms of each plasmid containing an expression cassette was introduced into C57/B6 mice via hydrodynamic tail vein injection (Nakai et al., Molecular Therapy, 7:101-111 (2003)), and serum samples from each mouse were assayed post-injection for circulating FIX levels by ELISA. About 30% of the mouse liver hepatocytes were transfected with the plasmids. Circulating FIX levels (micrograms/millileter) were measured three days post-injection and the results are shown in
A canine equivalent of the expression cassette of SEQ ID NO:6, and as shown in
A single canine suffering from hemophilia B was injected by IV infusion with a single dose of 2.0×1012 μg/kg. Whole blood clotting time (WBCT) and circulating FIX levels were measured at several time points post injection. Results are shown in
While a number of exemplary aspects and embodiments have been discussed above, those of skill in the art will recognize certain modifications, permutations, additions and sub-combinations thereof. It is therefore intended that the following appended claims and claims hereafter introduced are interpreted to include all such modifications, permutations, additions and sub-combinations as are within their true spirit and scope.
This application claims the benefit of U.S. Provisional Application No. 60/787,459, filed Mar. 30, 2006, incorporated herein by reference in its entirety.
This invention was made with Government support under contracts HL064274 & HL066948 awarded by the National Institutes of Health. The Government has certain rights in this invention. This work was supported in part by the National Institutes of Health (NIH) Grant number HL 64274. Accordingly, the United States government may have certain rights.
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| 20070243168 A1 | Oct 2007 | US |
| Number | Date | Country | |
|---|---|---|---|
| 60787459 | Mar 2006 | US |
