# Patent

## Title
Antiviral vectors

## Abstract

A viral vector production system is provided which system comprises:

    (i) a viral genome comprising at least one first nucleotide sequence encoding a gene product capable of binding to and effecting the cleavage, directly or indirectly, of a second nucleotide sequence, or transcription product thereof, encoding a viral polypeptide required for the assembly of viral particles;
    (ii) a third nucleotide sequence encoding said viral polypeptide required for the assembly of the viral genome into viral particles, which third nucleotide sequence has a different nucleotide sequence to the second nucleotide sequence such that said third nucleotide sequence, or transcription product thereof, is resistant to cleavage directed by said gene product.


The viral vector production system may be used to produce viral particles for use in treating or preventing viral infection.

## Background
RELATED APPLICATIONS
This application is a divisional of U.S. application Ser. No. 09/552,950, filed on Apr. 20, 2000, now U.S. Pat. No. 6,541,248, which is a continuation-in-part of PCT/GB99/00325, filed Feb. 17, 1999, designating the U.S., published as WO 99/41397 on Aug. 19, 1999, and claiming priority from U.K. (GB) application No. 9803351.7, filed Feb. 17, 1998. Each of the above-referenced applications, and each document cited in each of the above-referenced applications (“application cited documents”), and each document cited or referenced in each of the application cited documents, as well as all documents cited herein (in the following text, i.e., “herein cited documents”) and all documents cited or referenced in herein cited documents, are hereby incorporated herein by reference.


FIELD OF THE INVENTION
The present invention relates to novel viral vectors capable of delivering anti-viral inhibitory RNA molecules to target cells.
BACKGROUND TO THE INVENTION
The application of gene therapy to the treatment of AIDS and HIV infection has been discussed widely (14). The types of therapeutic gene proposed usually fall into one of two broad categories. In the first the gene encodes protein products that inhibit the virus in a number of possible ways. One example of such a protein is the RevM10 derivative of the HIV Rev protein (16). The RevM10 protein acts as a transdominant negative mutant and so competitively inhibits Rev function in the virus. Like many of the protein-based strategies, the RevM10 protein is a derivative of a native HIV protein. While this provides the basis for the anti-HIV effect, it also has serious disadvantages. In particular, this type of strategy demands that in the absence of the virus there is little or no expression of the gene. Otherwise, healthy cells harbouring the gene become a target for the host cytotoxic T lymphocyte (CTL) system, which recognises the foreign protein (17, 25). The second broad category of therapeutic gene circumvents these CTL problems. The therapeutic gene encodes inhibitory RNA molecules; RNA is not a target for CTL recognition. The RNA molecules may be anti-sense RNA (15, 31), ribozymes (5) or competitive decoys (1).
Ribozymes are enzymatic RNA molecules which catalyse sequence-specific RNA processing. The design and structure of ribozymes has been described extensively in the literature in recent years (3, 7, 31). Amongst the most powerful systems are those that deliver multitarget ribozymes that cleave RNA of the target virus at multiple sites (5, 21).
In recent years a number of laboratories have developed retroviral vector systems based on HIV (2, 4, 18, 19, 22-24, 27, 32, 35, 39, 43). In the context of anti-HIV gene therapy these vectors have a number of advantages over the more conventional murine based vectors such as murine leukaemia virus (MLV) vectors. Firstly, HIV vectors would target precisely those cells that are susceptible to HIV infection (22, 23). Secondly, the HIV-based vector would transduce cells such as macrophages that are normally refractory to transduction by murine vectors (19, 20). Thirdly, the anti-HIV vector genome would be propagated through the CD4+ cell population by any virus (HIV) that escaped the therapeutic strategy (7). This is because the vector genome has the packaging signal that will be recognised by the viral particle packaging system. These various attributes make HIV-vectors a powerful tool in the field of anti-HIV gene therapy.
A combination of the multitarget ribozyme and an HIV-based vector would be attractive as a therapeutic strategy. However, until now this has not been possible. Vector particle production takes place in producer cells which express the packaging components of the particles and package the vector genome. The ribozymes that are designed to destroy the viral RNA would therefore also interrupt the expression of the components of the HIV-based vector system during vector production. The present invention aims to overcome this problem.
SUMMARY OF THE INVENTION
It is therefore an object of the invention to-provide a system and method for producing viral particles, in particular HIV particles, which carry nucleotide constructs encoding inhibitory RNA molecules such as ribozymes and/or antisense RNAs directed against a corresponding virus, such as HIV, within a target cell, that overcomes the above-mentioned problems. The system includes both a viral genome encoding the inhibitory RNA molecules and nucleotide constructs encoding the components required for packaging the viral genome in a producer cell. However, in contrast to the prior art, although the packaging components have substantially the same amino acid sequence as the corresponding components of the target virus, the inhibitory RNA molecules do not affect production of the viral particles in the producer cells because the nucleotide sequence of the packaging components used in the viral system have been modified to prevent the inhibitory RNA molecules from effecting cleavage or degradation of the RNA transcripts produced from the constructs. Such a viral particle may be used to treat viral infections, in particular HIV infections.
Accordingly the present invention provides a viral vector system comprising:

    (i) a first nucleotide sequence encoding a gene product capable of binding to and effecting the cleavage, directly or indirectly, of a second nucleotide sequence, or transcription product thereof, encoding a viral polypeptide required for the assembly of viral particles; and
    (ii) a third nucleotide sequence encoding said viral polypeptide required for the assembly of viral particles, which third nucleotide sequence has a different nucleotide sequence to the second nucleotide sequence such that the third nucleotide sequence, or transcription product thereof, is resistant to cleavage directed by said gene product.


In another aspect, the present invention provides a viral vector production system comprising:

    (i) a viral genome comprising at least one first nucleotide sequence encoding a gene product capable of binding to and effecting the cleavage, directly or indirectly, of a second nucleotide sequence, or transcription product thereof, encoding a viral polypeptide required for the assembly of viral particles;
    (ii) a third nucleotide sequence encoding said viral polypeptide required for the assembly of the viral genome into viral particles, which third nucleotide sequence has a different nucleotide sequence to the second nucleotide sequence such that said third nucleotide sequence, or transcription product thereof, is resistant to cleavage directed by said gene product.


The gene product is typically an RNA inhibitory sequence selected from a ribozyme and an anti-sense ribonucleic acid, preferably a ribozyme.
Preferably, the viral vector is a retroviral vector, more preferably a lentiviral vector, such as an HIV vector. The second nucleotide sequence and the third nucleotide sequences are typically from the same viral species, more preferably from the same viral strain. Generally, the viral genome is also from the same viral species, more preferably from the same viral strain.
In the case of retroviral vectors, the polypeptide required for the assembly of viral particles is selected from gag, pol and env proteins. Preferably at least the gag and pol sequences are lentiviral sequences, more preferably HIV sequences. Alternatively, or in addition, the env sequence is a lentiviral sequence, more preferably an HIV sequence.
In a preferred embodiment, the third nucleotide sequence is resistant to cleavage directed by the gene product as a result of one or more conservative alterations in the nucleotide sequence which remove cleavage sites recognised by the at least one gene product and/or binding sites for the at least one gene product. For example, where the gene product is a ribozyme, the third nucleotide sequence is adapted to be resistant to cleavage by the ribozyme.
Preferably the third nucleotide sequence is codon optimised for expression in host cells. The host cells, which term includes producer cells and packaging cells, are typically mammalian cells.
In a particularly preferred embodiment, (i) the viral genome is an HIV genome comprising nucleotide sequences encoding anti-HIV ribozymes and/or anti-HIV antisense sequences directed against HIV packaging component sequences (such as gag-pol) in a target HIV and (ii) the viral system for producing packaged HIV particles further comprises nucleotide constructs encoding the same packaging components (such as gag-pol proteins) as in the target HIV wherein the sequence of the nucleotide constructs is different from that found in the target HIV so that the anti-HIV ribozyme and/or antisense HIV sequences cannot effect cleavage or degradation of the gag-pol transcripts during production of the HIV particles in producer cells.
The present invention also provides a viral particle comprising a viral vector according to the present invention and one or more polypeptides encoded by the third nucleotide sequences according to the present invention. For example the present invention provides a viral particle produced using the viral vector production system of the invention.
In another aspect, the present invention provides a method for producing a viral particle which method comprises introducing into a host cell (i) a viral genome vector according to the present invention; (ii) one or more third nucleotide sequences according to the present invention; and (iii) nucleotide sequences encoding the other essential viral packaging components not encoded by the one or more third nucleotide sequences.
The present invention further provides a viral particle produced using by the method of the invention.
The present invention also provides a pharmaceutical composition comprising a viral particle according to the present invention together with a pharmaceutically acceptable carrier or diluent.
The viral system of the invention or viral particles of the invention may be used to treat viral infections, particularly retroviral infections such as lentiviral infections including HIV infections. Thus the present invention provides a method of treating a viral infection which method comprises administering to a human or animal patient suffering from the viral infection an effective amount of a viral 9 system, viral particle or pharmaceutical composition of the present invention.
The invention relates in particular to HIV-based vectors carrying anti-HIV ribozymes. However, the invention can be applied to any other virus, in particular any other lentivirus, for which treatment by gene therapy may be desirable. The invention is illustrated herein for HIV, but this is not considered to limit the scope of the invention to HIV-based anti-HIV vectors.
It is a further object of the invention to provide a system for producing viral particles, in particular HIV particles, which do not require Rev/RRE for the production thereof. This system involves codon-optimising the gag-pol gene. Titre remains good and the system has the advantage that accessory proteins in the producer cell, and hence in the transduced cell, may be eliminated.
The HIV genome is AU-rich and this imparts a codon bias that is quite different from the one used by human genes. The codon usage is particularly marked in the case of the gag, pol and env genes. Interestingly, the expression of these genes is dependent on the presence of the Rev/RRE regulatory system, even in contexts other than the HIV genome. The Rev dependency has been explained in part by the presence of RNA instability sequences (INS) residing in these coding regions. The requirement for Rev also places a limitation on the development of HIV based vectors, because of the requirement to provide an accessory factor. We have now synthesised a complete codon optimised HIV-1 gag-pol gene. We show that expression levels are high and expression is Rev independent. This effect is due to an increase in the amount of gag-pol mRNA. Provision of the RRE in cis did not lower protein or RNA levels or stimulate a Rev response. Furthermore we have used this synthetic gag-pol gene to produce HIV vectors that now lack all of the accessory proteins.
Accordingly the present invention provides a nucleotide sequence coding for retroviral gag and pol proteins wherein the nucleotide sequence is codon optimised for expression in producer cells.
Preferably, the gag and pol proteins are lentiviral proteins, more preferably, they are HIV proteins. Typically, the producer cells are mammalian cells.
In a preferred embodiment, the nucleotide sequence is derived from a wild type sequence which has been codon optimised using the codon usage table of FIG. 4a. Preferably, the nucleotide sequence has the sequence as shown in SEQ. ID. No. 2 or the sequence from about nucleotide 1108 to about nucleotide 5414 as shown in SEQ. ID. No. 5.
In another aspect, the present invention provides a viral vector system comprising a nucleotide sequence of interest (NOI) and a nucleotide sequence according to the present invention encoding a viral polypeptide required for the assembly of viral particles.
In a further aspect, the present invention provides a viral production system comprising a viral genome comprising at least one nucleotide sequence of interest and a nucleotide sequence according to the present invention encoding a viral polypeptide required for the assembly of the viral genome into viral particles.
Preferably, the viral vector is a retroviral vector, more preferably, a lentiviral vector, such as a vector substantially derived from HIV-1.
In a preferred embodiment, the peptide required for assembly of viral particles also includes an envelope protein. Preferably, said envelope protein is encoded by a codon optimised env gene.
Typically, the NOI is selected from a therapeutic gene, a marker gene and a selection gene.
Preferably, the system according to the present invention is devoid of any functional accessory genes and may be used in a method of producing viral particles.
In another aspect, the present invention provides a method for producing a viral particle which method comprises introducing into a producer cell a viral genome according to the present invention, one or more nucleotide sequences according to the present invention, and nucleotide sequences encoding other essential viral packaging components not encoded by one or more of the above nucleotide sequences.
In another aspect, the invention provides a viral particle produced by a production system according to the invention, or by a method according to the invention.
In a further aspect, the present invention provides the use of a viral system according to the invention, or of a viral particle according to the invention, in treating a viral infection.
In another aspect, the present invention provides a pharmaceutical composition comprising a viral system or viral particle according to the invention, together with a pharmaceutically acceptable carrier or diluent.
DETAILED DESCRIPTION OF THE INVENTION
The term “viral vector” refers to a nucleotide construct comprising a viral genome capable of being transcribed in a host cell, which genome comprises sufficient viral genetic information to allow packaging of the viral RNA genome, in the presence of packaging components, into a viral particle capable of infecting a target cell. Infection of the target cell includes reverse transcription and integration into the target cell genome, where appropriate for particular viruses. The viral vector in use typically carries heterologous coding sequences (nucleotides of interest) which are to be delivered by the vector to the target cell, for example a first nucleotide sequence encoding a ribozyme. A viral vector is incapable of independent replication to produce infectious viral particles within the final target cell.
The term “viral vector system” is intended to mean a kit of parts which can be used when combined with other necessary components for viral particle production to produce viral particles in host cells. For example, the first nucleotide sequence may typically be present in a plasmid vector construct suitable for cloning the first nucleotide sequence into a viral genome vector construct. When combined in a kit with a third nucleotide sequence, which will also typically be present in a separate plasmid vector construct, the resulting combination of plasmid containing the first nucleotide sequence and plasmid containing the third nucleotide sequence comprises the essential elements of the invention. Such a kit may then be used by the skilled person in the production of suitable viral vector genome constructs which when transfected into a host cell together with the plasmid containing the third nucleotide sequence, and optionally nucleic acid constructs encoding other components required for viral assembly, will lead to the production of infectious viral particles.
Alternatively, the third nucleotide sequence may be stably present within a packaging cell line that is included in the kit.
The kit may include the other components needed to produce viral particles, such as host cells and other plasmids encoding essential viral polypeptides required for viral assembly. By way of example, the kit may contain (i) a plasmid containing a first nucleotide sequence encoding an anti-HIV ribozyme and (ii) a plasmid containing a third nucleotide sequence encoding a modified HIV gag-pol construct which cannot be cleaved by the anti-HIV ribozyme. Optional components would then be (a) an HIV viral genome construct with suitable restriction enzyme recognition sites for cloning the first nucleotide sequence into the viral genome; (b) a plasmid encoding a VSV-G env protein. Alternatively, nucleotide sequence encoding viral polypeptides required for assembly of viral particles may be provided in the kit as packaging cell lines comprising the nucleotide sequences, for example a VSV-G expressing cell line.
The term “viral vector production system” refers to the viral vector system described above wherein the first nucleotide sequence has already been inserted into a suitable viral vector genome.
Viral vectors are typically retroviral vectors, in particular lentiviral vectors such as HIV vectors. The retroviral vector of the present invention may be derived from or may be derivable from any suitable retrovirus. A large number of different retroviruses have been identified. Examples include: murine leukemia virus (MLV), human immunodeficiency virus (HIV), simian immunodeficiency virus, human T-cell leukemia virus (HTLV). equine infectious anaemia virus (EIAV), mouse mammary tumour virus (MMTV), Rous sarcoma virus (RSV), Fujinami sarcoma virus (FuSV), Moloney murine leukemia virus (Mo-MLV), FBR murine osteosarcoma virus (FBR MSV), Moloney murine sarcoma virus (Mo-MSV), Abelson murine leukemia virus (A-MLV), Avian myelocytomatosis virus-29 (MC29), and Avian erythroblastosis virus (AEV). A detailed list of retroviruses may be found in Coffin et al., 1997, “Retroviruses”, Cold Spring Harbour Laboratory Press Eds: J M Coffin, S M Hughes, H E Varmus pp 758-763.
Details on the genomic structure of some retroviruses may be found in the art. By way of example, details on HIV and Mo-MLV may be found from the NCBI Genbank (Genome Accession Nos. AF033819 and AF033811, respectively).
The lentivirus group can be split even further into “primate” and “non-primate”. Examples of primate lentiviruses include human immunodeficiency virus (HIV), the causative agent of human auto-immunodeficiency syndrome (AIDS), and simian immunodeficiency virus (SIV). The non-primate lentiviral group includes the prototype “slow virus” visna/maedi virus (VMV), as well as the related caprine arthritis-encephalitis virus (CAEV), equine infectious anaemia virus (EIAV) and the more recently described feline immunodeficiency virus (FIV) and bovine immunodeficiency virus (BIV).
The basic structure of a retrovirus genome is a 5′ LTR and a 3′ LTR, between or within which are located a packaging signal to enable the genome to be packaged, a primer binding site, integration sites to enable integration into a host cell genome and gag, pol and env genes encoding the packaging components—these are polypeptides required for the assembly of viral particles. More complex retroviruses have additional features, such as rev and RRE sequences in HIV, which enable the efficient export of RNA transcripts of the integrated provirus from the nucleus to the cytoplasm of an infected target cell.
In the provirus, these genes are flanked at both ends by regions called long terminal repeats (LTRs). The LTRs are responsible for proviral integration, and transcription. LTRs also serve as enhancer-promoter sequences and can control the expression of the viral genes. Encapsidation of the retroviral RNAs occurs by virtue of a psi sequence located at the 5′ end of the viral genome.
The LTRs themselves are identical sequences that can be divided into three elements, which are called U3, R and U5. U3 is derived from the sequence unique to the 3′ end of the RNA. R is derived from a sequence repeated at both ends of the RNA and U5 is derived from the sequence unique to the 5′ end of the RNA. The sizes of the three elements can vary considerably among different retroviruses.
In a defective retroviral vector genome gag, pol and env may be absent or not functional. The R regions at both ends of the RNA are repeated sequences. U5 and U3 represent unique sequences at the 5′ and 3′ ends of the RNA genome respectively.
In a typical retroviral vector for use in gene therapy, at least part of one or more of the gag, pol and env protein coding regions essential for replication may be removed from the virus. This makes the retroviral vector replication-defective. The removed portions may even be replaced by a nucleotide sequence of interest (NOT), such as a first nucleotide sequence of the invention, to generate a virus capable of integrating its genome into a host genome but wherein the modified viral genome is unable to propagate itself due to a lack of structural proteins. When integrated in the host genome, expression of the NOI occurs—resulting in, for example, a therapeutic and/or a diagnostic effect. Thus, the transfer of an NOI into a site of interest is typically achieved by: integrating the NOI into the recombinant viral vector; packaging the modified viral vector into a virion coat; and allowing transduction of a site of interest—such as a targeted cell or a targeted cell population.
A minimal retroviral genome for use in the present invention will therefore comprise (5′)R—U5—one or more first nucleotide sequences—U3-R (3′). However, the plasmid vector used to produce the retroviral genome within a host cell/packaging cell will also include transcriptional regulatory control sequences operably linked to the retroviral genome to direct transcription of the genome in a host cell/packaging cell. These regulatory sequences may be the natural sequences associated with the transcribed retroviral sequence, i.e. the 5′ U3 region, or they may be a heterologous promoter such as another viral promoter, for example the CMV promoter.
Some retroviral genomes require additional sequences for efficient virus production. For example, in the case of HIV, rev and RRE sequence are preferably included. However the requirement for rev and RRE can be reduced or eliminated by codon optimisation.
Once the retroviral vector genome is integrated into the genome of its target cell as proviral DNA, the ribozyme sequences need to be expressed. In a retrovirus, the promoter is located in the 5′ LTR U3 region of the provirus. In retroviral vectors, the promoter driving expression of a therapeutic gene may be the native retroviral promoter in the 5′ U3 region, or an alternative promoter engineered into the vector. The alternative promoter may physically replace the 5′ U3 promoter native to the retrovirus, or it may be incorporated at a different place within the vector genome such as between the LTRs.
Thus, the first nucleotide sequence will also be operably linked to a transcriptional regulatory control sequence to allow transcription of the first nucleotide sequence to occur in the target cell. The control sequence will typically be active in mammalian cells. The control sequence may, for example, be a viral promoter such as the natural viral promoter or a CMV promoter or it may be a mammalian promoter. It is particularly preferred to use a promoter that is preferentially active in a particular cell type or tissue type in which the virus to be treated primarily infects. Thus, in one embodiment, a tissue-specific regulatory sequences may be used. The regulatory control sequences driving expression of the one or more first nucleotide sequences may be constitutive or regulated promoters.
Replication-defective retroviral vectors are typically propagated, for example to prepare suitable titres of the retroviral vector for subsequent transduction, by using a combination of a packaging or helper cell line and the recombinant vector. That is to say, that the three packaging proteins can be provided in trans.
A “packaging cell line” contains one or more of the retroviral gag, pol and env genes. The packaging cell line produces the proteins required for packaging retroviral DNA but it cannot bring about encapsidation due to the lack of a psi region. However, when a recombinant vector carrying an NOI and a psi region is introduced into the packaging cell line, the helper proteins can package the psi-positive recombinant vector to produce the recombinant virus stock. This virus stock can be used to transduce cells to introduce the NOI into the genome of the target cells. It is preferred to use a psi packaging signal, called psi plus, that contains additional sequences spanning from upstream of the splice donor to downstream of the gag start codon (Bender et al. (46)) since this has been shown to increase viral titres.
The recombinant virus whose genome lacks all genes required to make viral proteins can transduce only once and cannot propagate. These viral vectors which are only capable of a single round of transduction of target cells are known as replication defective vectors. Hence, the NOI is introduced into the host/target cell genome without the generation of potentially harmful retrovirus. A summary of the available packaging lines is presented in Coffin et al., 1997 (ibid).
Retroviral packaging cell lines in which the gag, pol and env viral coding regions are carried on separate expression plasmids that are independently transfected into a packaging cell line are preferably used. This strategy, sometimes referred to as the three plasmid transfection method (Soneoka et al. (33)), reduces the potential for production of a replication-competent virus since three recombinant events are required for wild type viral production. As recombination is greatly facilitated by homology, reducing or eliminating homology between the genomes of the vector and the helper can also be used to reduce the problem of replication-competent helper virus production.
An alternative to stably transfected packaging cell lines is to use transiently transfected cell lines. Transient transfections may advantageously be used to measure levels of vector production when vectors are being developed. In this regard, transient transfection avoids the longer time required to generate stable vector-producing cell lines and may also be used if the vector or retroviral packaging components are toxic to cells. Components typically used to generate retroviral vectors include a plasmid encoding the gag and pol proteins, a plasmid encoding the env protein and a plasmid containing an NOI. Vector production involves transient transfection of one or more of these components into cells containing the other required components. If the vector encodes toxic genes or genes that interfere with the replication of the host cell, such as inhibitors of the cell cycle or genes that induce apoptosis, it may be difficult to generate stable vector-producing cell lines, but transient transfection can be used to produce the vector before the cells die. Also, cell lines have been developed using transient transfection that produce vector titre levels that are comparable to the levels obtained from stable vector-producing cell lines (Pear et al. (47)).
Producer cells/packaging cells can be of any suitable cell type. Most commonly, mammalian producer cells are used but other cells, such as insect cells are not excluded. Clearly, the producer cells will need to be capable of efficiently translating the env and gag, pol mRNA. Many suitable producer/packaging cell lines are known in the art. The skilled person is also capable of making suitable packaging cell lines by, for example stably introducing a nucleotide construct encoding a packaging component into a cell line.
As will be discussed below, where the retroviral genome encodes an inhibitory RNA molecule capable of effecting the cleavage of gag, pol and/or env RNA transcripts, the nucleotide sequences present in the packaging cell line, either integrated or carried on plasmids, or in the transiently transfected producer cell line, which encode gag, pol and or env proteins will be modified so as to reduce or prevent binding of the inhibitory RNA molecule(s). In this way, the inhibitory RNA molecule(s) will not prevent expression of components in packaging cell lines that are essential for packaging of viral particles.
It is highly desirable to use high-titre virus preparations in both experimental and practical applications. Techniques for increasing viral titre include using a psi plus packaging signal as discussed above and concentration of viral stocks. In addition, the use of different envelope proteins, such as the G protein from vesicular-stomatitis virus has improved titres following concentration to 109 per ml (Cosset et al. (48)). However, typically the envelope protein will be chosen such that the viral particle will preferentially infect cells that are infected with the virus which it desired to treat. For example where an HIV vector is being used to treat HIV infection, the env protein used will be the HIV env protein.
Suitable first nucleotide sequences for use according to the present invention encode gene products that result in the cleavage and/or enzymatic degradation of a target nucleotide sequence, which will generally be a ribonucleotide. As particular examples, ribozymes, and antisense sequences may be mentioned.
Ribozymes are RNA enzymes which cleave RNA at specific sites. Ribozymes can be engineered so as to be specific for any chosen sequence containing a ribozyme cleavage site. Thus, ribozymes can be engineered which have chosen recognition sites in transcribed viral sequences. By way of an example, ribozymes encoded by the first nucleotide sequence recognise and cleave essential elements of viral genomes required for the production of viral particles, such as packaging components. Thus, for retroviral genomes, such essential elements include the gag, pol and env gene products. A suitable ribozyme capable of recognising at least one of the gag, pol and env gene sequences, or more typically, the RNA sequences transcribed from these genes, is able to bind to and cleave such a sequence. This will reduce or prevent production of the gal, pol or env protein as appropriate and thus reduce or prevent the production of retroviral particles.
Ribozymes come in several forms, including hammerhead, hairpin and hepatitis delta antigenomic ribozymes. Preferred for use herein are hammerhead ribozymes, in part because of their relatively small size, because the sequence requirements for their target cleavage site are minimal and because they have been well characterised. The ribozymes most commonly used in research at present are hammerhead and hairpin ribozymes.
Each individual ribozyme has a motif which recognises and binds to a recognition site in the target RNA. This motif takes the form of one or more “binding arms”, generally two binding arms. The binding arms in hammerhead ribozymes are the flanking sequences Helix I and Helix III, which flank Helix II. These can be of variable length, usually between 6 to 10 nucleotides each, but can be shorter or longer. The length of the flanking sequences can affect the rate of cleavage. For example, it has been found that reducing the total number of nucleotides in the flanking sequences from 20 to 12 can increase the turnover rate of the ribozyme cleaving a HIV sequence, by 10-fold (44). A catalytic motif in the ribozyme Helix II in hammerhead ribozymes cleaves the target RNA at a site which is referred to as the cleavage site. Whether or not a ribozyme will cleave any given RNA is determined by the presence or absence of a recognition site for the ribozyme containing an appropriate cleavage site.
Each type of ribozyme recognises its own cleavage site. The hammerhead ribozyme cleavage site has the nucleotide base, triplet GUX directly upstream where G is guanine, U is uracil and X is any nucleotide base. Hairpin ribozymes have a cleavage site of BCUGNYR, where B is any nucleotide base other than adenine, N is any nucleotide, Y is cytosine or thymine and R is guanine or adenine. Cleavage by hairpin ribozymes takes places between the G and the N in the cleavage site.
The nucleic acid sequences encoding the packaging components (the “third nucleotide sequences”) may be resistant to the ribozyme or ribozymes because they lack any cleavage sites for the ribozyme or ribozymes. This prohibits enzymatic activity by the ribozyme or ribozymes and therefore there is no effective recognition site for the ribozyme or ribozymes. Alternatively or additionally, the potential recognition sites may be altered in the flanking sequences which form the part of the recognition site to which the ribozyme binds. This either eliminates binding of the ribozyme motif to the recognition site, or reduces binding capability enough to destabilise any ribozyme-target complex and thus reduce the specificity and catalytic activity of the ribozyme. Where the flanking sequences only are altered, they are preferably altered such that catalytic activity of the ribozyme at the altered target sequence is negligible and is effectively eliminated.
Preferably, a series of several anti-HIV ribozymes is employed in the invention (5, 7, 10, 13, 21, 36, 38, 40). These can be any anti-HIV ribozymes but must include one or more which cleave the RNA that is required for the expression of gag, pol or env. Preferably, a plurality of ribozymes is employed, together capable of cleaving gag, pol and env RNA of the native retrovirus at a plurality of sites. Since HIV exists as a population of quasispecies, not all of the target sequences for the ribozymes will be included in all HIV variants. The problem presented by this variability can be overcome by using multiple ribozymes. Multiple ribozymes can be included in series in a single vector and can function independently when expressed as a single RNA sequence. A single RNA containing two or more ribozymes having different target recognition sites may be referred to as a multitarget ribozyme. The placement of ribozymes in series has been demonstrated to enhance cleavage. The use of a plurality of ribozymes is not limited to treating HIV infection but may be used in relation to other viruses, retroviruses or otherwise.
Antisense technology is well known on the art. There are various mechanisms by which antisense sequences are believed to inhibit gene expression. One mechanism by which antisense sequences are believed to function is the recruitment of the cellular protein RNAseH to the target sequence/antisense construct heteroduplex which results in cleavage and degradation of the heteroduplex. Thus the antisense construct, by contrast to ribozymes, can be said to lead indirectly to cleavage/degradation of the target sequence. Thus according to the present invention, a first nucleotide sequence may encode an antisense RNA that binds to either a gene encoding an essential/packaging component or the RNA transcribed from said gene such that expression of the gene is inhibited, for example as a result of RNAseH degradation of a resulting heteroduplex. It is not necessary for the antisense construct to encode the entire complementary sequence of the gene encoding an essential/packaging component—a portion may suffice. The skilled person will easily be able to determine how to design a suitable antisense construct.
By contrast, the nucleic acid sequences encoding the essential/packaging components of the viral particles required for the assembly of viral particles in the host cells/producer cells/packaging cells (the third nucleotide sequences) are resistant to the inhibitory RNA molecules encoded by the first nucleotide sequence. For example in the case of ribozymes, resistance is typically by virtue of alterations in the sequences which eliminate the ribozyme recognition sites. At the same time, the amino acid coding sequence for the essential/packaging components is retained so that the viral components encoded by the sequences remain the same, or at least sufficiently similar that the function of the essential/packaging components is not compromised.
The term “viral polypeptide required for the assembly of viral particles” means a polypeptide normally encoded by the viral genome to be packaged into viral particles, in the absence of which the viral genome cannot be packaged. For example, in the context of retroviruses such polypeptides would include gag, pol and env. The terms “packaging component” and “essential component” are also included within this definition.
In the case of antisense sequences, the third nucleotide sequence differs from the second nucleotide sequence encoding the target viral packaging component antisense sequence to the extent that although the antisense sequence can bind to the second nucleotide sequence, or transcript thereof, the antisense sequence can not bind effectively to the third nucleotide sequence or RNA transcribed from therefrom. The changes between the second and third nucleotide sequences will typically be conservative changes, although a small number of amino acid changes may be tolerated provided that, as described above, the function of the essential/packaging components is not significantly impaired.
Preferably, in addition to eliminating the ribozyme recognition sites, the alterations to the coding sequences for the viral components improve the sequences for codon usage in the mammalian cells or other cells which are to act as the producer cells for retroviral vector particle production. This improvement in codon usage is referred to as “codon optimisation”. Many viruses, including HIV and other lentiviruses, use a large number of rare codons and by changing these to correspond to commonly used mammalian codons, increased expression of the packaging components in mammalian producer cells can be achieved. Codon usage tables are known in the art for mammalian cells, as well as for a variety of other organisms.
Thus preferably, the sequences encoding the packaging components are codon optimised. More preferably, the sequences are codon optimised in their entirety. Following codon optimisation, it is found that there are numerous sites in the wild type gag, pol and env sequences which can serve as ribozyme recognition sites and which are no longer present in the sequences encoding the packaging components. In an alternative but less practical strategy, the sequences encoding the packaging components can be altered by targeted conservative alterations so as to render them resistant to selected ribozymes capable of cleaving the wild type sequences.
An additional advantage of codon optimising HIV packaging components is that this can increase gene expression. In particular, it can render gag-pol expression Rev independent. In order to enable the use of anti-rev or RRE factors in the retroviral vector, however, it would be necessary to render the viral vector generation system totally Rev/RRE independent (58). Thus, the genome also needs to be modified. This is achieved by optimising the HIV-1 based vector genome components in addition to gag-pol. Advantageously, these modifications also lead to the production of a safer system absent of all accessory proteins both in the producer and in the transduced cell.
The gag-pol gene comprises two overlapping reading frames encoding gag and pol proteins respectively. The expression of both proteins depends on a frameshift during translation. This frameshift occurs as a result of ribosome “slippage” during translation. This slippage is thought to be caused at least in part by ribosome-stalling RNA secondary structures. Such secondary structures exist downstream of the frameshift site in the gag-pol gene. The region of overlap extends from nucleotide 1222 downstream of the beginning of gag (wherein nucleotide 1 is the A of the gag ATG) to the end of gag (nt 1503). Consequently, a 281 bp fragment spanning the frameshift site and the overlapping region of the two reading frames is preferably not codon optimised. Retaining this fragment will enable more efficient expression of the gag-pol polyprotein.
As described above, the packaging components for a retroviral vector include expression products of gag, pol and env genes. In addition, efficient packaging depends on a short sequence of 4 stem loops followed by a partial sequence from gag and env (the “packaging signal”). Thus, inclusion of a deleted gag sequence in the retroviral vector genome (in addition to the full gag sequence on the packaging construct) will optimise vector titre. To date efficient packaging has been reported to require from 255 to 360 nucleotides of gag in vectors that still retain env sequences, or about 40 nucleotides of gag in a particular combination of splice donor mutation, gag and env deletions. We have surprisingly found that a deletion of up to 360 nucleotides in gag leads to an increase in vector titre. Further deletions resulted in lower titres. Additional mutations at the major splice donor site upstream of gag were found to disrupt packaging signal secondary structure and therefore lead to decreased vector titre. Thus, preferably, the retroviral vector genome includes a gag sequence from which up to 360 nucleotides have been removed.
In accordance with the present invention, gag and pol employed in the packaging system are derived from the target retrovirus on which the vector genome is based. Thus, in the RNA transcript form, gag and pol would normally be cleavable by the ribozymes present in the vector genome. The env gene employed in the packaging system may be derived from a different virus, including other retroviruses such as MLV and non-retroviruses such as VSV (a Rhabdovirus), in which case it may not need any sequence alteration to render it resistant to ribozyme cleavage. Alternatively, env may be derived from the same retrovirus as gag and pol, in which case any recognition sites for the ribozymes will need to be eliminated by sequence alteration.
The process of producing a retroviral vector in which the envelope protein is not the native envelope of the retrovirus is known as “pseudotyping”. Certain envelope proteins, such as MLV envelope protein and vesicular stomatitis virus G (VSV-G) protein, pseudotype retroviruses very well. Pseudotyping can be useful for altering the target cell range of the retrovirus. Alternatively, to maintain target cell specificity for target cells infected with the particular virus it is desired to treat, the envelope protein may be the same as that of the target virus, for example HIV.
Other therapeutic coding sequences may be present along with the first nucleotide sequence or sequences. Other therapeutic coding sequences include, but are not limited to, sequences encoding cytokines, hormones, antibodies, immunoglobulin fusion proteins, enzymes, immune co-stimulatory molecules, anti-sense RNA, a transdominant negative mutant of a target protein, a toxin, a conditional toxin, an antigen, a single chain antibody, tumour suppresser protein and growth factors. When included, such coding sequences are operatively linked to a suitable promoter, which may be the promoter driving expression of the first nucleotide sequence or a different promoter or promoters.
Thus the invention comprises two components. The first is a genome construction that will be packaged by viral packaging components and which carries a series of anti-viral inhibitory RNA molecules such as anti-HIV ribozymes (5, 7, 10, 13, 21, 36, 38, 40). These could be any anti-HIV ribozymes but the key issue for this invention is that some of them cleave RNA that is required for the expression of native or wild type HIV gag, pol or env coding sequences. The second component is the packaging system which comprises a cassette for the expression of HIV gag, pol and a cassette either for HIV env or an envelope gene encoding a pseudotyping envelope protein—the packaging system being resistant to the inhibitory RNA molecules.
The viral particles of the present invention, and the viral vector system and methods used to produce may thus be used to treat or prevent viral infections, preferably retroviral infections, in particular lentiviral, especially HIV, infections. Specifically, the viral particles of the invention, typically produced using the viral vector system of the present invention may be used to deliver inhibitory RNA molecules to a human or animal in need of treatment for a viral infection.
Alternatively, or in addition, the viral production system may be used to transfect cells obtained from a patient ex vivo and then returned to the patient. Patient cells transfected ex vivo may be formulated as a pharmaceutical composition (see below) prior to readminstration to the patient.
Preferably the viral particles are combined with a pharmaceutically acceptable carrier or diluent to produce a pharmaceutical composition. Thus, the present invention also provides a pharmaceutical composition for treating an individual, wherein the composition comprises a therapeutically effective amount of the viral particle of the present invention, together with a pharmaceutically acceptable carrier, diluent, excipient or adjuvant. The pharmaceutical composition may be for human or animal usage.
The choice of pharmaceutical carrier, excipient or diluent can be selected with regard to the intended route of administration and standard pharmaceutical practice. Suitable carriers and diluents include isotonic saline solutions, for example phosphate-buffered saline. The pharmaceutical compositions may comprise as—or in addition to—the carrier, excipient or diluent any suitable binder(s), lubricant(s), suspending agent(s), coating agent(s), solubilising agent(s), and other carrier agents that may aid or increase the viral entry into the target site (such as for example a lipid delivery system).
The pharmaceutical composition may be formulated for parenteral, intramuscular, intravenous, intracranial, subcutaneous, intraocular or transdermal administration.
Where appropriate, the pharmaceutical compositions can be administered by any one or more of: inhalation, in the form of a suppository or pessary, topically in the form of a lotion, solution, cream, ointment or dusting powder, by use of a skin patch, orally in the form of tablets containing excipients such as starch or lactose, or in capsules or ovules either alone or in admixture with excipients, or in the form of elixirs, solutions or suspensions containing flavouring or colouring agents, or they can be injected parenterally, for example intracavernosally, intravenously, intramuscularly or subcutaneously. For parenteral administration, the compositions may be best used in the form of a sterile aqueous solution which may contain other substances, for example enough salts or monosaccharides to make the solution isotonic with blood. For buccal or sublingual administration the compositions may be administered in the form of tablets or lozenges which can be formulated in a conventional manner.
The amount of virus administered is typically in the range of from 103 to 1010 pfu, preferably from 105 to 108 pfu, more preferably from 106 to 107 pfu. When injected, typically 1-10 μl of virus in a pharmaceutically acceptable suitable carrier or diluent is administered.
When the polynucleotide/vector is administered as a naked nucleic acid, the amount of nucleic acid administered is typically in the range of from 1 μg to 10 mg, preferably from 100 μg to 1 mg.
Where the first nucleotide sequence (or other therapeutic sequence) is under the control of an inducible regulatory sequence, it may only be necessary to induce gene expression for the duration of the treatment. Once the condition has been treated, the inducer is removed and expression of the NOI is stopped. This will clearly have clinical advantages. Such a system may, for example, involve administering the antibiotic tetracycline, to activate gene expression via its effect on the tet repressor/VP16 fusion protein.



The invention will now be further described by way of Examples, which are meant to serve to assist one of ordinary skill in the art in carrying out the invention and are not intended in any way to limit the scope of the invention. The Examples refer to the Figures. In the Figures
FIG. 1 shows schematically ribozymes inserted into four different HIV vectors;
FIG. 2 shows schematically how to create a suitable 3′ LTR by PCR;
FIG. 3 shows the codon usage table for wild type HIV gag-pol of strain HXB2 (accession number: K03455).
FIG. 4 shows the codon usage table of the codon optimised sequence designated gagpol-SYNgp. FIG. 4a shows a comparative codon usage table.
FIG. 5 shows the codon usage table of the wild type HIV env called env-mn.
FIG. 6 shows the codon usage table of the codon optimised sequence of HIV env designated SYNgp160 mn.
FIG. 7 shows three plasmid constructs for use in the invention.
FIG. 8 shows the principle behind two systems for producing retroviral vector particles.
FIGS. 9A-9D show a sequence comparison between the wild type HIV gag-pol sequence (pGP-RRE3; SEQ ID NO:1) and the codon optimized gag-pol sequence (pSYNGP; SEQ ID NO:5).
FIG. 10 shows Rev independence of protein expression particle formation.
FIG. 11 shows translation rates of WT and codon optimised gag-pol.
FIG. 12 shows gag-pol mRNA levels in total and cytoplasmic fractions.
FIG. 13 shows the effect of insertion of WT gag downstream of the codon optimised gene on RNA and protein levels.
FIG. 14 shows the plasmids used to study the effect of HIV-1 gag on the codon optimised gene.
FIG. 15 shows the effect on cytoplasmic RNA of insertion of HIV-1 gag upstream of the codon optimised gene.
FIG. 16 shows the effect of LMB on protein production.
FIG. 17 shows the cytoplasmic RNA levels of the vector genomes.
FIG. 18 shows transduction efficiency at MOI 1.
FIG. 19 shows a schematic representation of pGP-RRE3.
FIG. 20 shows a schematic representation of pSYNGP.
FIG. 21 shows vector titres generated with different gag-pol constructs.
FIG. 22 shows vector titres from the Rev/RRE (−) and (+) genomes.
FIG. 23 shows vector titres from the pHS series of vector genomes.
FIG. 24 shows vector titres for the pHS series of vector genomes in the presence or absence of Rev/RRE.



In more detail, FIG. 9 shows a sequence comparison between the wild-type HIV gag-pol sequence (pGP-RRE3; SEQ ID NO:1) and the codon optimized gag-pol sequence (pSYNGP; SEQ ID NO:5) wherein the upper sequence represents pSYNGP and the lower sequence represents pGP-RRE3.
FIG. 10 shows Rev independence of protein expression particle formation. 5 μg of the gag-pol expression plasmids were transfected into 293T cells in the presence or absence of Rev (pCMV-Rev, 1 μg) and protein levels were determined 48 hours post transfection in culture supernatants (A) and cell lysates (B). HIV-1 positive human serum was used to detect the gag-pol proteins. The blots were re-probed with an anti-actin antibody, as an internal control (C). The protein marker (New England Biolabs) sizes (in kDa) are shown on the side of the gel. Lanes: 1. Mock transfected 293T cells, 2. pGP-RRE3, 3. pGP-RRE3+pCMV-Rev, 4. pSYNGP, 5. pSYNGP+pCMV-Rev, 6. pSYNGP-RRE, 7. pSYNGP-RRE+pCMV-Rev, 8. pSYNGP-ERR, 9. pSYNGP-ERR+pCMV-Rev.
FIG. 11 shows translation rates of WT and codon optimised gag-pol. 293T cells were transfected with 2 μg pGP-RRE3 (+/−1 μg pCMV-Rev) or 2 μg pSYNGP. Protein samples from culture supernatants (A) and cell extracts (B) were analysed by Western blotting 12, 25, 37 and 48 hours post-transfection. HIV-1 positive human serum was used to detect gag-pol proteins (A, B) and an anti-actin antibody was used as an internal control (C). The protein marker sizes are shown on the side of the gel (in kD). A Phosphorimager was used for quantification of the results. Lanes: 1. pGP-RRE3 12 h, 2. pGP-RRE3 25 h, 3. pGP-RRE3 37 h, 4. pGP-RRE3 48 h, 5. pGP-RRE3+pCMV-Rev 12 h, 6. pGP-RRE3+pCMV-Rev 25 h, 7. pGP-RRE3+pCMV-Rev 37 h, 8. pGP-RRE3+pCMV-Rev 48 h, 9. pSYNGP 12 h, 10. pSYNGP 25 h, 11. pSYNGP 37 h, 12. pSYNGP 48 h, 13. Mock transfected 293T cells.
FIG. 12 shows gag-pol mRNA levels in total and cytoplasmic fractions. Total and cytoplasmic RNA was extracted from 293T cells 36 hours after transfection with 5 μg of the gag-pol expression plasmid (+/−1 μg pCMV-Rev) and mRNA levels were estimated by Northern blot analysis. A probe complementary to nt 1222-1503 of both the wild type and codon optimised gene was used. Panel A shows the band corresponding to the HIV-1 gag-pol. The sizes of the mRNAs are 4.4 kb for the codon optimised and 6 kb for the wild type gene. Panel B shows the band corresponding to human ubiquitin (internal control for normalisation of results). Quantification was performed using a Phosphorimager. Lane numbering: c indicates cytoplasmic fraction and t indicates total RNA fraction. Lanes: 1. pGP-RRE3 , 2. pGP-RRE3+pCMV-Rev, 3. pSYNGP, 4. pSYNGP+pCMV-Rev, 5. pSYNGP-RRE, 6. pSYNGP-RRE+pCMV-Rev, 7. Mock transfected 293T cells, 8. pGP-RRE3+pCMV-Rev, 19. Mock transfected 293T cells, 10. pSYNGP.
FIG. 13 shows the effect of insertion of WT gag downstream of the codon optimised gene on RNA and protein levels. The wt gag sequence was inserted downstream of the codon optimised gene in both orientations (NotI site), resulting in plasmids pSYN6 (correct orientation, see FIG. 6) and pSYN7 (reverse orientation, see FIG. 6). The gene encoding for β-galactosidase (LacZ) was also inserted in the same site and the correct orientation (plasmid pSYN8, see FIG. 6). 293T cells were transfected with 5 μg of each plasmid and 48 hours post transfection mRNA and protein levels were determined as previously described by means of Northern and Western blot analysis respectively.

    A. Northern blot analysis in cytoplasmic RNA fractions. The blot was probed with a probe complementary to nt 1510-2290 of the codon optimised gene (I) and was re-probed with a probe specific for human ubiquitin (II). Lanes: 1. pSYNGP, 2. pSYN8, 3. pSYN7, 4. pSYN6
    B. Western blot analysis: HIV-1 positive human serum was used to detect the gag-pol proteins (I) and an anti-actin antibody was used as an internal control (II). Lanes: Cell lysates: 1. Mock transfected 293T cells, 2. pGP-RRE3+pCMV-Rev, 3. pSYNGP, 4. pSYN6, 5. pSYN7, 6. pSYN8. Supernatants: 7. Mock transfected 293T cells, 8. pGP-RRE3+pCMV-Rev, 9. pSYNGP, 10. pSYN6, 11. pSYN7, 12. pSYN8. The protein marker (New England Biolabs) sizes are shown on the side of the gel.


FIG. 14 shows the plasmids used to study the effect of HIV-1 gag on the codon optimised gene. The backbone for all constructs was pCI-Neo. Syn gp: The codon optimised HIV-1 gag-pol gene. HXB2 gag: The wild type HIV-1 gag gene. HXB2 gag,r: The wild type HIV-1 gag gene in the reverse orientation. HXB2 gagΔATG: The wild type HIV-1 gag gene without the gag ATG. HXB2 gag-fr.sh.: The wild type HIV-1 gag gene with a frameshift mutation. HXB2 gag 625-1503: Nucleotides 625-1503 of the wild type HIV-1gag gene. HXB2 gag 1-625: Nucleotides 1-625 of the wild type HIV-1 gag gene.
FIG. 15 shows the effect on cytoplasmic RNA of insertion of HIV-1 gag upstream of the codon optimised gene. Cytoplasmic RNA was extracted 48 hours post transfection of 293T cells (5 μg of each pSYN plasmid was used and 1 μg of pCMV-Rev was co-transfected in some cases). The probe that was used was designed to be complementary to nt 1510-2290 of the codon optimised gene (I). A probe specific for human ubiquitin was used as an internal control (II).

    A. Lanes: 1. pSYNGP, 2. pSYN9, 3. pSYN10, 4. pSYN10+pCMV-Rev, 5. pSYN11, 6. pSYN11+pCMV-Rev, 7. pCMV-Rev.
    B. Lanes: 1. pSYNGP, 2. pSYNGP-RRE, 3. pSYNGP-RRE+pCMV-Rev, 4. pSYN12, 5. pSYN14, 6. pSYN14+pCMV-Rev, 7. pSYN13, 8. pSYN15, 9. pSYN17, 10. pGP-RRE3, 11. pSYN6, 12. pSYN9, 13. pCMV-Rev.


FIG. 16 shows the effect of LMB on protein production. 293T cells were transfected with 1 μg pCMV-Rev and 3 μg of pGP-RRE3/pSYNGP/pSYNGP-RRE (+/−1 μg pCMV-Rev). Transfections were done in duplicate. 5 hours post transfection the medium was replaced with fresh medium in the first set and with fresh medium containing 7.5 nM LMB in the second. 20 hours later the cells were lysed and protein production was estimated by Western blot analysis. HIV-1 positive human serum was used to detect the gag-pol proteins (A) and an anti-actin antibody was used as an internal control (B). Lanes: 1. pGP-RRE3, 2. pGP-RRE3+LMB, 3. pGP-RRE3+pCMV-Rev, 4. pGP-RRE3+pCMV-Rev+LMB, 5. pSYNGP, 6. pSYNGP+LMB, 7. pSYNGP+pCMV-Rev, 8. pSYNGP+pCMV-Rev+LMB, 9. pSYNGP-RRE, 10. pSYNGP-RRE+LMB, 11. pSYNGP-RRE+pCMV-Rev, 12. pSYNGP-RRE+pCMV-Rev+LMB.
FIG. 17 shows the cytoplasmic RNA levels of the vector genomes. 293T cells were transfected with 10 μg of each vector genome. Cytoplasmic RNA was extracted 48 hours post transfection. 20 μg of RNA were used from each sample for Northern blot analysis. The 700 bp probe was designed to hybridise to all vector genome RNAs (see Materials and Methods). Lanes: 1. pH6nZ, 2. pH6nZ+pCMV-Rev, 3. pH6.1nZ, 4. pH6.1nZ+pCMV-Rev, 5. pHS1nZ, 6. pHS2nZ, 7. pHS3nZ, 8. pHS4nZ, 9. pHS5nZ, 10. pHS6nZ, 11. pHS7nZ, 12. pHS8nZ, 13. pCMV-Rev.
FIG. 18 shows transduction efficiency at MOI 1. Viral stocks were generated by co-transfection of each gag-pol expression plasmid (5 or 0.5 μg), 15 μg pH6nZ or pHS3nZ (vector genome plasmid) and 5 μg pHCMVG (VSV envelope expression plasmid) on 293T cells. Virus was concentrated as previously described (45) and transduction efficiency was determined at m.o.i.'s 0.01-1 on HT1080 cells. There was a linear correlation of transduction efficiency and m.o.i. in all cases. An indicative picture at m.o.i. 1 is shown here. Transduction efficiency was >80% with either genome, either gag-pol and either high or low amounts of pSYNGP. Titres before concentration (I.U./ml): on 293T cells: A. 6.6×105, B. 7.6×105, C. 9.2×105, D. 1.5×105, on HT1080 cells: A. 6.0×104, B. 9.9×104, C. 8.0×104, D. 2.9×104. Titres after concentration (I.U./ml) on HT1080 cells: A. 6.0×105, B. 2.0×106, C. 1.4×106, D. 2.0×105.
FIG. 21 shows vector titers obtained with differed gag-pol constructs. Viral stocks were generated by co-transfection of each gag-pol expression plasmid, pH6nZ (vector genome plasmid) and pHCMVG (VSV envelope expression plasmid, 2.5 μg for each transfection) on 293T cells. Titres (I.U./ml of virs stock) were measured on 293T cells by counting the number of blue colonies following X-Gal staining 48 hours after transduction. Experiments were performed at least twice and the variation between experiments was less than 15%.
FIG. 22 shows vector titres from the Rev/RRE (−) and (+) genomes. The retroviral vectors were generated as described in the Examples. Titres (I.U./ml of viral stock+SD) were determined in 293T cells.
FIG. 23 shows vector titres from the pHS series of vector genomes. The retroviral vector was generated as described in the Examples. Titres (I.U./ml of viral stock+SD) were determined in 293T cells. Rev is provided from pCMV-Rev. Note that pH6nZ expresses Rev and contains the RRE. None of the other genomes express Rev or contain the RRE. Expression from pSYNGP is Rev independent, whereas it is Rev dependent for pGP-RRE3.
FIG. 24 shows vector titres for the pHS series of vector genomes in the presence or absence of Rev/RRE. The retroviral vector was generated as described in the Examples. 5 μg of vector genome, 5 μg of pSYNGP and 2.5 μg of pHCMVG were used and titres (I.U./ml) were determined in 293T cells. Experiments were performed at least twice and the variation between experiments was less than 15%. Rev is provided from pCMV-Rev (1 μg). Note that pH6nZ expresses Rev and contains the RRE. None of the pHS genomes expresses Rev and only pHS1nZR, pHS3nZR, pHS7nZR and pH6.1nZR contain the RRE. gag-pol expression from pSYNGP is Rev independent.
We show that codon optimisation of the HIV-1 gag-pol gene results in a 10-fold increase in steady state levels of cognate RNA with an equivalent 10-fold increase in protein production. Furthermore, unlike the wild type gag-pol gene, expression occurs independently of the Rev/RRE system. We further demonstrate that, consistent with Rev indepedence, Leptomycin B has no effect on expression, implying that the exporting (CRM1) nuclear export pathway is not involved.
Although Rev independent expression of HIV-1 genes has been previously shown (11, 28), in previous studies increased protein production upon codon optimisation has been attributed to more efficient translation (11). Without wishing to be bound by any theory, it is believed that elimination of INS sequences residing within the coding sequence (82, 29, 99) is one possible explanation for this result. Another possibility is that inefficient translation can lead to increased probability of mRNA degradation and this has been obviated by the change in codon bias. For example, it has been shown that mRNAs that contain premature termination codons are easily degraded (54), reviewed in (74), or that sequences involved in rapid mRNA turnover can be active only when they are part of the translation ORF (e.g. in c-myc, (109). However, the increased levels of protein paralleled rather than exceeded the increase in RNA levels. It is possible that gag is autoregulating its expression to allow viral RNA packaging as it has been proposed for RSV (101). This is further supported by the fact that HIV-1 gag interacts with translation factors and inhibits translation in vitro (60, 107) and it could also explain why codon optimisation for HIV-1 env results in a significant augmentation in protein levels and equal RNA levels (11) and not for the gag-pol.
We also demonstrate that HIV-1 gag INS sequences can act in a position dependent manner, irrespective of translation and their effects are INS size dependent. Without wishing to be bound by any theory, the INS elements may induce mRNA deadenylation and rapid degradation in the cytoplasm. This is the favoured scenario for AU-rich elements found in the 3′ UTR of cellular labile mRNAs (111). Alternatively, they may exert their effects prior to the exit of the mRNA from the nucleus (87). The results obtained here are in agreement with the second hypothesis, as the observed effect seemed to be translation independent, and indicate that HIV-1 gag INS elements may also act by retaining the mRNA in the nucleus (90) and possibly directing it towards a nuclear degradation pathway (83, 87). This is further supported by previous reports showing that HIV-1 pol INS elements interact with several cellular factors, one of which has been identified as hnRNP C, a component of the splicing machinery (90). However, a translational effect cannot be ruled out.
With our codon optimised gene we achieved higher vector particle production compared to the wild type gene, but this did not convert into higher vector titres, indicating that gag-pol is not limiting. As expected however, in plasmid ratios where the gag-pol is limiting, i.e. 1 gag-pol: 50 genomes, then a 10-fold increase in titres was observed with the codon optimised gene.
The codon optimised gene may be of particular use for the production of simpler and safer HIV vectors. To date these still require the provision of Rev to facilitate gag-pol expression (64, 12) and this requirement is now removed by using the codon optimised gene. We have now demonstrated the feasibility of making a filly Rev independent vector system without a significant compromise in titre. Our results indicate that the vector genome is also Rev dependent when large portions of gag or gag and env are present, but also that retention of more than 260 bases of gag is required for efficient infectious vector production. Further manipulations, such as inclusion of a CTE in the vector genome may be used to overcome these limitations and fully restore titres.
There are other advantages of employing a codon optimised gag-pol, for example therapeutic ribozymes can now be targeted against gag and pol and yet still be delivered by HIV vectors that will be resistant to their effects during production.
In conclusion, we have shown that codon optimisation of the HIV-1 gag-pol gene leads to higher expression without the requirement for Rev/RRE. Furthermore, based on this codon optimised gene, we have constructed an HIV-1 based vector system that now lacks all the accessory proteins, retains only minimal HIV-1 sequences (required for packaging and reverse transcription) in the vector genome construct.
EXAMPLES
Cell Lines
293T cells (63) and HeLa cells (71) were maintained in Dubecco's modified Eagle's medium containing 10% (v/v) fetal calf serum and supplemented with L-glutamine and antibiotics (penicillin-streptomycin). 293T cells were obtained from D. Baltimore (Rockefeller University).
HIV-1 Proviral Clones
Proviral clones pWI3 (77) and pNL4-3 (49) were used.
Construction of a Genome
The HIV gag-pol sequence was codon optimised (FIG. 4; SEQ I.D. No. 2 and SEQ I.D. 5) and synthesised using overlapping oligos of around 40 nucleotides. This has three advantages. Firstly it allows an HIV based vector to carry ribozymes and other therapeutic factors. Secondly the codon optimisation generates a higher vector titre due to a higher level of gene expression. Thirdly gag-pol expression becomes rev independent which allows the use of anti-rev or RRE factors.
Conserved sequences within gag-pol were identified by reference to the HIV Sequence database at Los Alamos National Laboratory and used to design ribozymes. Because of the variability between subtypes of HIV-1, the ribozymes were designed to cleave the predominant subtype within North America, Latin America and the Caribbean, Europe, Japan and Australia; that is, subtype B. The sites chosen were cross-referenced with the synthetic gag-pot sequence to ensure that there was a low possibility of cutting the codon optimised gag-pol mRNA. The ribozymes were designed with XhoI and SalI sites at the 5′ and 3′ end respectively. This allows the construction of separate and tandem ribozymes.
The ribozymes are hammerhead (25) structures of the following general structure:










Helix I
Helix II
Helix III



5′-NNNNNNNN~
CUGAUGAGGCCGAAAGGCCGAA
~NNNNNNNN~



(SEQ ID NO:6)






The catalytic domain of the ribozyme (Helix II). can tolerate some changes without reducing catalytic turnover.
The cleavage sites, targeting gag and pol, with the essential GUX triplet (where X is any nucleotide base) are as follows:











GAG 1
5′ UAGUAAGAAUGUAUAGCCCUAC





(SEQ ID NO:7)



 



GAG 2
5′ AACCCAGAUUGUAAGACUAUUU




(SEQ ID NO:8)



 



GAG 3
5′ UGUUUCAAUUGUGGCAAAGAAG




(SEQ ID NO:9)



 



GAG 4
5′ AAAAAGGGCUGUUGGAAAUGUG




(SEQ ID NO:10)



 



POL 1
5′ ACGACCCCUCGUCACAAUAAAG




(SEQ ID NO:11)



 



POL 2
5′ GGAAUUGGAGGUUUUAUCAAAG




(SEQ ID NO:12)



 



POL 3
5′ AUAUUUUUCAGUUCCCUUAGAU




(SEQ ID NO:13)



 



POL 4
5′ UGGAUGAUUUGUAUGUAGGAUC




(SEQ ID NO:14)



 



POL 5
5′ CUUUGGAUGGGUUAUGAACUCC




(SEQ ID NO:15)



 



POL 6
5′ CAGCUGGACUGUCAAUGACAUA




(SEQ ID NO:16)



 



POL 7
5′ AACUUUCUAUGUAGAUGGGGCA




(SEQ ID NO:17)



 



POL 8
5′ AAGGCCGCCUGUUGGUGGGCAG




(SEQ ID NO:18)



 



POL 9
5′ UAAGACAGCAGUACAAAUGGCA




(SEQ ID NO:19)






The ribozymes are inserted into four different HIV vectors (pH4 (10), pH6, pH4.1, or pH6.1) (FIG. 1). In pH4 and pH6, transcription of the ribozymes is driven by an internal HCMV promoter (9). From pH4.1 and pH6.1, the ribozymes are expressed fro the 5′ LTR. The major different between pH4 and pH6 (and pH4.1 and pH6.1) resides in the 3′ LTR in the production plasmid. pH4 and pH4.1 have the HIV U3 in the 3′ LTR. pH6 and pH6.1 have HCMV in the 3′ LTR. The HCMV promoter replaces most of the U3 and will drive expression at high constitutive levels while the HIV-1 U3 will support a high level of expression only in the presence of Tat.
The HCMV/HIV-1 hybrid 3′ LTR is created by recombinant PCR with three PCR primers. (FIG. 2). The first round of PCR is performed with RIB1 and RIB2 using pH4 (12) as the template to amplify the HIV-1 HXB2 sequence 8900-9123. The second round of PCR makes the junction between the 5′ end of the HIV-1 U3 and the HCMV promoter by amplifying the hybrid 5′ LTR from pH4. The PCR product from the first PCR reaction and RIB3 serves as the 5′ primer an 3′ primer respectively.









RIB1:
5′-CAGCTGCTCGAGCAGCTGAAGCTTGCATGC-3′




(SEQ ID NO:20)


 


RIB2:
5′-GTAAGTTATGTAACGGACGATATCTTGTCTTCTT-3′



(SEQ ID NO:21)


 


RIB3:
5′-CGCATAGTCGACGGGCCCGCCACTGCTAGAGATTTTC-3′



(SEQ ID NO:22)






The PCR product is then cut with SphI and SalI and inserted into pH4 thereby replacing the 3′ LTR. The resulting plasmid is designated pH6. To construct pH4.1 and pH6.1, the internal HCMV promoter (SpeI-XhoI) in pH4 and pH6 is replaced with the polycloning site of pBluescript II KS+ (Stratagene) (SpeI-XhoI).
The ribozymes are inserted into the XhoI sites in the genome vector backbones. Any ribozymes in any configuration could be used in a similar way.
Construction of a Packaging System
The packaging system can take various forms. In a first form of packaging system, the HIV gag, pol components are co-expressed with the HIV env coding sequence. In this case, both the gag, pol and the env coding sequences are altered such that they are resistant to the anti-HIV ribozymes that are built into the genome. At the same time as altering the codon usage to achieve resistance, the codons can be chosen to match the usage pattern of the most highly expressed mammalian genes. This dramatically increases expression levels (28, 29) and so increases titre. A codon optimised IV env coding sequence has been described by Haas et al (9). In the present example, a modified codon optimised HIV env sequence is used (SEQ I.D. No. 3). The corresponding env expression plasmid is designated pSYNgp160mn. The modified sequence contains extra motifs not used by Haas et al. The extra sequences were taken from the HIV env sequence of strain MN and codon optimised. Any similar modification of the nucleic acid sequence would function similarly as long as it used codons corresponding to abundant tRNAs (42) and lead to resistance to the ribozymes in the genome.
SYNgp
In one example of a gag, pol coding sequence with optimised codon usage, overlapping oligonucleotides are synthesised and then ligated together to produce the synthetic coding sequence. The sequence of a wild-type gag-pol sequence (Genbank accession no. K03455) is shown in SEQ I.D. No 1 and two possible sequences of a synthetic optimised gag-pol sequence (gagpol-SYNgp and pSYNGP) are shown in SEQ I.D. Nos 2 and 5 respectively. Their codon usage is shown in FIGS. 3 and 4, respectively. The sequence of a wild type env coding sequence (Genbank Accession No. M17449) is given in SEQ I.D. No 3, the sequence of a synthetic codon optimised sequence is given in SEQ. I.D. No. 4 and their codon usage tables are given in FIGS. 5 and 6, respectively. As with the env coding sequence any gag, pol sequence that achieves resistance to the ribozymes could be used. The synthetic sequence designated gagpol-SYNgp has an EcoRI site at the 5′ end and a NotI site at the 3′ end. It is inserted into pClneo (Promega) to produce plasmid pSYNgp. Vector particles can be produced either from a transient three-plasmid transfection system similar to that described by Soneoka et al. (33) or from producer cell lines similar to those used for other retroviral vectors (20, 35, 39). These principles are illustrated in FIGS. 7 and 8. For example, by using pH6Rz, pSYNgp or pSYNGP and pRV67 (VSV-G expression plasmid) in a three plasmid transfection of 293T cells (FIG. 8), as described by Soneoka et al (33), vector particles designated H6Rz-VSV are produced. These transduce the H6Rz genome to CD4+ cells such as C1866 or Jurkat and produce the multitarget ribozymes. HIV replication in these cells is now severely restricted.
pSYNGP
The codon optimised gag-pol gene was constructed by annealing a series of short overlapping oligonucleotides (approximately 30-40 mers with 25% overlap, i.e. approximately 9 nucleotides). Oligonucleotides were purchased from R&D SYSTEMS (R&D Systems Europe Ltd, 4-10 The Quadrant, Barton Lane, Abingdon, OX14 3YS, UK). Codon optimisation was performed using the sequence of HXB-2 strain (AC: K03455) (67). The Kozak consensus sequence for optimal translation initiation (78) was also included. A fragment from base 1222 from the beginning of gag until the end of gag (1503) was not optimised in order to maintain the frameshift site and the overlap between the gag and pol reading frames. This was from clone pNL4-3. The −1 ribosomal frameshift (occuring at the sequence TTTTTTA, 1296 bases downstream of the gag ATG) brings the overlapping out-of-phase gag and pol genes into translational phase (76, 108), thus allowing expression of the gag-pol polyprotein. Sequences downstream of the frameshift site that form secondary structures also play a role in facilitating the event (by stalling the ribosomes and allowing the ‘slippage’ to occur) (57, 92). Consequently, a 281 bp fragment spanning the frameshift site and the overlapping region of the two reading frames (gag and gag-pol) was retained. (When referring to base numbers within the gag-pol gene base 1 is the A of the gag ATG, which corresponds to base 790 from the beginning of the HXB2 sequence. When referring to sequences outside the gag-pol then the numbers refer to bases from the beginning of the HXB2 sequence, where base 1 corresponds to the beginning of the 5′ LTR). Some deviations from optimisation were made in order to introduce convenient restriction sites. The final codon usage is shown in Table 4a, which now resembles that of highly expressed human genes and is quite different from that of the wild type HIV-1 gag-pol. The gene was cloned into the mammalian expression vector pCIneo (Promega) in the EcoRI-NotI sites. The resulting plasmid was named pSYNGP. Sequencing of the gene in both strands verified the absence of any mistakes. A sequence comparison between the codon optimised and wild type HIV gag-pol sequence is shown in FIG. 9.
Rev/RRE Constructs
The HIV-1 RRE sequence (bases 7769-8021 of the HXB2 sequence) was amplified by PCR from pWI3 proviral clone with primers bearing the NotI restriction site and was subsequently cloned into the NotI site of pSYNGP. The resulting plasmids were named pSYNGP-RRE (RRE in the correct orientation) and pSYNGP-ERR (RRE in the reverse orientation).
Pseudotyped Viral Particles
In a second form of the packaging system a synthetic gag, pol cassette is coexpressed with a non-HIV envelope coding sequence that produces a surface protein that pseudotypes HIV. This could be for example VSV-G (20, 41), amphotropic MLV env (6, 34) or any other protein that would be incorporated into the HIV particle (37). This includes molecules capable of targeting the vector to specific tissues. Coding sequences for non-HIV envelope proteins not cleaved by the ribozymes and so no sequence modification is required (although some sequence modification may be desirable for other reasons such as optimisation for codon usage in mammalian cells).
Vector Genome Constructs
pH6nZ is derived from pH4Z (12) by the addition of a single nucleotide to place an extra guanine residue that was missing from pH4Z at the 5′ end of the vector genome transcript to optimise reverse transcription. In addition the gene coding for β-galactosidase (LacZ) was replaced by a gene encoding for a nuclear localising β-galactosidase. (We are grateful to Enca Martin-Rendon and Said Ismail for providing pH6nZ). In order to construct Rev(−) genome constructs the following modifications were made: a) A 1.8 kb PstI-PstI fragment was removed from pH6nZ, resulting in plasmid pH6.1nZ and b) an EcoNI (filled)-SphI fragment was substituted with a SpeI (filled)-SphI fragment from the same plasmid (pH6nZ), resulting in plasmid pH6.2nZ. In both cases sequences within gag (nt 1-625) were retained, as they have been shown to play a role in packaging (93). Rev, RRE and any other residual env sequences were removed. pH6.2nZ further contains the env splice acceptor, whereas pH6.1nZ does not.
A series of vectors encompassing further gag deletions plus or minus a mutant major splice donor (SD) (GT to CA mutation) were also derived from pH6Z. These were made by PCR with primers bearing a NarI (5′ primers) and an SpeI (3′ primers) site. The PCR products were inserted into pH6Z at the NarI-SpeI sites. The resulting vectors were named pHS1nZ (containing HIV-1 sequences up to gag 40), pHS2nZ (containing HIV-1 sequences up to gag 260), pHS3nZ (containing HIV-1 sequences up to gag 360), pHS4nZ (containing HIV-1 sequences up to gag 625), pHS5nZ (same as pHS1nZ but with a mutant SD), pHS6nZ (same as pHS2nZ but with a mutant SD), pHS7nZ (same as pHS3nZ but with a mutant SD) and pHS8nZ (same as pHS4nZ but with a mutant SD).
In addition, the RRE sequence (nt 7769-8021 of the HB2 sequence) was inserted in the SpeI (filled), site of pH6.1nZ, pHS1nZ, pHS3nZ and pHS7nZ resulting in plasmids pH6.1nZR, pHS1nZR, pHS3nZR and pHS7nZR respectively.
Transient Transfections, Transductions and Determination of Viral Titres
These were performed as previously described (12, 33). Briefly, 293T cells were seeded on 6 cm dishes and 24 hours later they were transiently transfected by overnight calcium phosphate treatment. The medium was replaced 12 hours post-transfection and unless otherwise stated supernatants were harvested 48 hours post-transfection, filtered (through 0.22 or 0.45 μm filters) and titered by transduction of 293T cells. For this reason supernatant at appropriate dilutions of the original stock was added to 293T cells (plated onto 6 or 12 well plates 24 hours prior to transduction). 8 μg/ml Polybrene (Sigma) was added to each well and 48 hours post transduction viral titres were determined by X-gal staining.
Luminescent β-galactosidase (β-gal) Assays
These were performed on total cell extracts using a luminescent β-gal reporter system (CLONTECH). Untransfected 293T cells were used as negative control and 293T cells transfected with pCMV-βgal (CLONTECH) were used as positive control.
RNA Analysis
Total or cytoplasmic RNA was extracted from 293T cells by using the RNeasy mini kit (QUIAGEN) 36-48 hours post-transfection. 5-10 μg of RNA was subjected to Northern blot analysis as previously described (98). Correct fractionation was verified by staining of the agarose gel. A probe complementary to bases 1222-1503 of the gag-pol gene was amplified by PCR from HIV-1 pNL4-3 proviral clone and was used to detect both the codon optimised and wild type gag-pol mRNAs. A second probe, complementary to nt 1510-2290 of the codon optimised gene was also amplified by PCR from plasmid pSYNGP and was used to detect the codon optimised genes only. A 732 bp fragment complementary to all vector genomes used in this study was prepared by an SpeI-AvrII digestion of pH6nZ. A probe specific for ubiquitin (CLONTECH) was used to normalise the results. All probes were labelled by random labelling (STRATAGENE) with α-32P dCTP (Amersham). The results were quantitated by using a Storm PhosphorImager (Molecular Dynamics) and shown in FIG. 12. In the total cellular fractions the 47S rRNA precursor could be clearly seen, whereas it was absent from the cytoplasmic fractions. As expected (84), Rev stimulates the cytoplasmic accumulation of wild type gag-pol mRNA (lanes 1c and 2c). RNA levels were 10-20 fold higher for the codon optimised gene compared to the wild type one, both in total and cytoplasmic fractions (compare lanes 3t-2t, 3c-2c, 10c-8c). The RRE sequence did not significantly destabilise the codon optimised RNAs since RNA levels were similar for codon optimised RNAs whether or not they contained the RRE sequence (compare lanes 3 and 5). Rev did not markedly enhance cytoplasmic accumulation of the codon optimised gag-pol mRNAs, even when they contained the RRE sequence (differences in RNA levels were less than 2-fold, compare lanes 3-4 or 5-6).
It appeared from a comparison of FIGS. 10 and 12 that all of the increase in protein expression from syngp could be accounted for by the increase in RNA levels. In order to investigate whether this was due to saturating levels of RNA in the cell, we transfected 0.1, 1 and 10 μg of the wild type or codon optimised expression vectors into 293T cells and compared protein production. In all cases protein production was 10-fold higher for the codon optimised gene for the same amount of transfected DNA, while increase in protein levels was proportional to the amount of transfected DNA for each individual gene. It seems likely therefore that the enhanced expression of the codon optimised gene can be mainly attributed to the enhanced RNA levels present in the cytoplasm and not to increased translation.
Protein Analysis
Total cell lysates were prepared from 293T cells 48 hours post-transfection (unless otherwise stated) with an alkaline lysis buffer. For extraction of proteins from cell supernatants the supernatant was first passed through a 0.22 μm filter and the vector particles were collected by centrifugation of 1 ml of supernatant at 21,000 g for 30 minutes. Pellets were washed with PBS and then re-suspended in a small volume (2-10 μl) of lysis buffer. Equal protein amounts were separated on a SDS 10-12% (v/v) polyacrylamide gel. Proteins were transferred to nitrocellulose membranes which were probed sequentially with a 1:500 dilution of HIV-1 positive human serum (AIDS Reagent Project, ADP50S, Panel E) and a 1:1000 dilution of horseradish peroxidase labelled anti-human IgG (Sigma, A0176). Proteins were visualised using the ECL or ECL-plus western blotting detection reagent (Amersham). To verify equal protein loading, membranes were stripped and re-probed with a 1:1000 dilution of anti-actin antibody (Sigma, A2066), followed by a 1:2000 dilution of horseradish peroxidase labelled anti-rabbit IgG (Vector Laboratories, PI-1000).
Expression of gag-pol Gene Products and Vector Particle Production
The wild type gag-pol (pGP-RRE3) (12), and codon optimised expression vectors (pSYNGP, pSYNGP-RRE and pSYNGP-ERR) were transiently transfected into 293T cells. Transfections were performed in the presence or absence of a Rev expression vector, pCMV-Rev (66), in order to assess Rev-dependence for expression. Western blot analysis was performed on cell lysates and supernatants to assess protein production. The results are shown in FIG. 10. As expected (72), expression of the wild type gene is observed only when Rev is provided in trans (lanes 2 and 3). In contrast, when the codon optimised gag-pol was used, there was high level expression in both the presence and absence of Rev (lanes 4 and 5), indicating that in this system there was no requirement for Rev. Protein levels were higher for the codon optimised gene than for the wild type gag-pol (compare lanes 4-9 with lane 3). The difference was more evident in the cell supernatants (approximately 10-fold higher protein levels for the codon optimised gene compared to the wild type one, quantitated by using a PhosphorImager) than in the cell lysates.
In previous studies where the RRE has been included in gag-pol expression vectors that had been engineered to remove INS sequences, inclusion of the RRE lead to a decrease in protein levels, that was restored by providing Rev in trans (28). In our hands, the presence of the RRE in the fully codon optimised gag-pol mRNA did not affect protein levels and provision of Rev in trans did not further enhance expression (lanes 6 and 7).
In order to compare translation rates between the wild type and codon optimised gene, protein production from the wild type and codon optimised expression vector was determined at several time intervals post transfection into 293T cells. Protein production and particle formation was determined by Western blot analysis and the results are shown in FIG. 11. Protein production and particle formation was 10-fold higher for the codon optimised gag-pol at all time points.
To further determine whether this enhanced expression that was observed with the codon optimised gene was due to better translation or due to effects on the RNA, RNA analysis was carried out.
The Efficiency of Vector Production Using the Codon Optimised gag-pol Gene
To determine the effects of the codon optimised gag-pol on vector production, we used an HIV vector genome, pH6nZ and the VSV-G envelope expression plasmid pHCMVG (113), in combination with either pSYNGP, pSYNGP-RRE, pSYNGP-ERR or pGP-RRE3 as a source for the gag-pol in a plasmid ratio of 2:1:2 in a 3 plasmid co-transfection of 293T cells (12). Whole cell extracts and culture supernatants were evaluated by Western blot analysis for the presence of the gag and gag-pol gene products. Particle production was, as expected (FIG. 10), 5-10 fold higher for the codon optimised genes when compared to the wild type.
To determine the effects of the codon optimised gag-pol gene on vector titres, several ratios of the vector components were used. The results are shown in FIG. 21. Where the gag-pol was the limiting component in the system (as determined by the drop in titres observed with the wild type gene), titres were 10-fold higher for the codon optimised vectors. This is in agreement with the higher protein production observed for these vectors, but suggests that under normal conditions of vector production gag-pol is saturating and the codon optimisation gives no maximum yield advantage.
The Effect of HIV-1 gag INS Sequences on the Codon Optimised Gene is Position Dependent
It has previously been demonstrated that insertion of wild type HIV-1 gag sequences downstream of other RNAs, e.g. HIV-1 tat (99), HIV-1 gag (28) or CAT (82) can lead to a dramatic decrease in steady state mRNA levels, presumably as a result of the INS sequences. In other cases, e.g. for β-globin (87), it was shown that the effect was splice site dependent. Cellular AREs (AU-rich elements) that are found in the 3′ UTR of labile mRNAs may confer mRNA destabilisation by inducing cytoplasmic deadenylation of the transcripts (111). To test whether HIV-1 gag INS sequences would destabilise the codon optimised RNA, the wild-type HIV-1 gag sequence, or parts of it (nt 1-625 or nt 625-1503), were amplified by PCR from the proviral clone pWI3. All fragments were blunt ended and were inserted into pSYNGP or pSYNGP-RRE at either a blunted EcoRI or NotI site (upstream or downstream of the codon optimised gag-pol gene repectively). As controls the wt HIV-1 gag in the reverse orientation (as INS sequences have been shown to act in an orientation dependent manner, (82) (pSYN7) and lacZ, excised from plasmid pCMV-βGal (CLONTECH) (in the correct orientation) (pSYN8) were also inserted in the same site. Contrary to our expectation, as shown in FIG. 13, the wild type HIV-1 gag sequence did not appear to significantly affect RNA or protein levels of the codon optimised gene. We further constructed another series of plasmids (by PCR and from the same plasmids) where the wild type HIV-1 gag in the sense or reverse orientation, subfragments of gag (nt 1-625 or nt 625-1503), the wild type HIV-1 gag without the ATG or with a frameshift mutation 25 bases downstream of the ATG, or nt 72-1093 of LacZ (excised from plasmid pH6Z), or the first 1093 bases of lacZ with or without the ATG were inserted upstream of the codon optimised HIV-1 gag-pol gene in pSYNGP and/or pSYNGP-RRE (pSYN9-pSYN22, FIG. 14). Northern blot analysis showed that insertion of the wild type HIV-1 gag gene upstream of the codon optimised HIV-1 gag-pol (pSYN9, pSYN10) lead to diminished RNA levels in the presence or absence of Rev/RRE (FIG. 15A, lanes 1-4 and FIG. 15B, lanes 1+12). The effect was not dependent on translation as insertion of a wild type HIV-1 gag lacking the ATG or with a frameshift mutation (pSYN12, pSYN13 and pSYN14) also diminished RNA levels (FIG. 15B, lanes 1-7). Western blot analysis verified that there was no HIV-1 gag translation product for pSYN12-14. However, it is possible that, as the wt HIV-1 gag exhibits such an adverse codon usage, it may act as a non-translatable long 5′ leader for syngp, and if this is the case, then the ATG mutation should not have any effects.
Insertion of smaller parts of the wild type HIV-1 gag gene (pSYN15 and pSYN17) also lead to a decrease in RNA levels (FIG. 15B, lanes 1-3 and 8-9), but not to levels as low as when the whole gag sequence was used (lanes 1-3, 4-7 and 8-9 in FIG. 15B). This indicates that the effect of INS sequences is dependent on their size. Insertion of the wild type HIV-1 gag in the reverse orientation (pSYN11) had no effect on RNA levels (FIG. 15A, lanes 1 and 5-6). However a splicing event seemed to take place in that case, as indicated by the size of the RNA (equal to the size of the codon optimised gag-pol RNA) and by the translation product (gag-pol, in equal amounts compared to pSYNGP, as verified by Western blot analysis).
These data indicate therefore that wild type HIV-1 gag instability sequences act in a position and size dependent manner, probably irrespective of translation. It should also be noted that the RRE was unable to rescue the destabilised RNAs through interaction with Rev.
Construction of an HIV-1 Based Vector System that Lacks all the Accessory Proteins
Until now several HIV-1 based vector systems have been reported that lack all accessory proteins but Rev (12, 88). We wished to investigate whether the codon optimised gene would permit the construction of an HIV-1 based vector system that lacks all accessory proteins. We initially deleted rev/RRE and any residual env sequences, but kept the first 625 nucleotides of gag, as they have been shown to play a role in efficient packaging (93). Two vector genome constructs were made, pH6.1nZ (retaining only HIV sequences up to nt 625 of gag) and pH6.2nZ (same as pH6.1nZ, but also retaining the env splice acceptor). These were derived from a conventional HIV vector genome that contains RRE and expresses Rev (pH6nZ). Our 3-plasmid vector system now expressed only HIV-1 gag-pol and the VSV-G envelope proteins. Vector particle titres were determined as described in the previous section. A ratio of 2:2:1 of vector genome (pH6Z or pH6.1nZ or pH6.2nZ): gag-pol expression vector (pGP-RRE3 or pSYNGP): pHCMV-G was used. Transfections were performed in the presence or absence of pCMV-Rev, as gag-pol expression was still Rev dependent for the wild type gene. The results are summarised in FIG. 22 and indicate that an HIV vector could be produced in the total absence of Rev, but that maximum titres were compromised at 20-fold lower than could be achieved in the presence of Rev. As gag-pol expression should be the same for pSYNGP with pH6nZ or pH6.1nZ or pH6.2nZ (since it is Rev independent), as well as for pGP-RRE3 when Rev is provided in trans, we suspected that the vector genome retained a requirement for Rev and was therefore limiting the titres. To confirm this, Northern blot analysis was performed on cytoplasmic RNA prepared from cells transfected with pH6nZ or pH6.1nZ in the presence or absence of pCMV-Rev. As can be seen in FIG. 17, lanes 1-4, the levels of cytoplasmic RNA derived from pH6nZ were 5-10 fold higher than those obtained with pH6.1nZ (compare lanes 1-2 to lanes 3-4). These data support the notion that RNA produced from the vector genome requires the Rev/RRE system to ensure high cytoplasmic levels. This may be due to inefficient nuclear export of the RNA, as INS sequences residing within gag were still present.
Further deletions in the gag sequences of the vector genome might therefore be necessary to restore titres. To date efficient packaging has been reported to require 360 (64) or 255 (61) nucleotides of gag in vectors that still retain env sequences, or about 40 nucleotides of gag in a particular combination of splice donor mutation, gag and env deletions (59, 61). In an attempt to remove the requirement for Rev/RRE in our vector genome without compromising efficient packaging we constructed a series of vectors derived from pH6nZ containing progressively larger deletions of HIV-1 sequences (only sequences upstream and within gag were retained) plus and minus a mutant major splice donor (SD) (GT to CA mutation). Vector particle titres were determined as before and the results are summarised in FIG. 23. As can be seen, deletion of up to nt 360 in gag (vector pHS3nZ) resulted in an increase in titres (compared to pH6.1nZ or pH6.2nZ) and only a 5-fold decrease (titres were 1.3-1.7×105) compared to pH6nZ. Further deletions resulted in titres lower than pHS3nZ and similar to pH6.1nZ. In addition, the SD mutation did not have a positive effect on vector titres and in the case of pHS3nZ it resulted in a 10-fold decrease in titres (compare titres for pHS3nZ and pHS7nZ in FIG. 23). Northern blot analysis on cytoplasmic RNA (FIG. 17, lanes 1 and 5-12) showed that RNA levels were indeed higher for pH6nZ, which could account for the maximum titres observed with this vector. RNA levels were equal for pHS1nZ (lane 5), pHS2nZ (lane 6) and pHS3nZ (lane 7) whereas titres were 5-8 fold higher for pHS3nZ. It is possible that further deletions (than that found in pHS3nZ) in gag might result in less efficient packaging (as for HIV-1 the packaging signal extends in gag) and therefore even though all 3 vectors produce similar amounts of RNA only pHS3nZ retains maximum packaging efficiency. It is also interesting to note that the SD mutation resulted in increased RNA levels in the cytoplasm (compare lanes 6 and 10, 7 and 11 or 8 and 12 in FIG. 17) but equal or decreased titres (FIG. 23). The GT dinucleotide that was mutated is in the stem of SL2 of the packaging signal (73). It has been reported that SL2 might not be very important for HIV-1 RNA encapsidation (73, 86), whereas SL3 is of great importance (81). Folding of the wild type and SD-mutant vector sequences with the RNAdraw software program revealed that the mutation alters significantly the secondary structure of the RNA and not only of SL2. It is likely therefore that although the SD mutation enhances cytoplasmic RNA levels it does not increase titres as it alters the secondary structure of the packaging signal.
To investigate whether the titre differences that were observed with the Rev minus vectors were indeed due to Rev dependence of the genomes, the RRE sequence (nt 7769-8021 of the HXB2 sequence) was inserted in the SpeI site (downstream of the gag sequence and just upstream of the internal CMV promoter) of pH6.1nZ, pHS1nZ, pHS3nZ and pHS7nZ, resulting in plasmids pH6.1nZR, pHS1nZR, pHS3nZR and pHS7nZR respectively. Vector particle titres were determined with pSYNGP and pHCMVG in the presence or absence of Rev (pCMV-Rev) as before and the results are summarised in FIG. 24. In the absence of Rev titres were further compromised for pH6.1nZR (7-fold compared to pH6.1nZ), pHS3nZR (6-fold compared to pHS3nZ) and pHS7nZR (2.5-fold compared to pHS7nz). This was expected, as the RRE also acts as an instability sequence (56) and so it would be expected to confer Rev-dependence. In the presence of Rev titres were restored to the maximum titres observed for pH6nZ in the case of pHS3nZR (5×105) and pH6.1nZR (2×105). Titres were not restored for pHS7nZR in the presence of Rev. This supports the hypothesis that the SD mutation in pHS7nZ affects the structure of the packaging signal and thus the packaging ability of this vector genome, as in this case Rev may be able to stimulate vector genome RNA levels, as for pHS3nZR and pH6.1nZR, but it can not affect the secondary structure of the packaging signal. For vector pHS1nZ inclusion of the RRE did not lead to a decrease in titres. This could be due to the fact that pHS1nZ contains only 40 nucleotides of gag sequences and therefore even with the RRE the size of instability sequences is not higher than for pHS2nZ that gives equal titres to pHS1nZ. Rev was able to partially restore titres for pHS1nZR (10-fold increase when compared to pHS1nZ and 8-fold lower than pH6nZ) but not fully as in the case of pHS3nZ. This is also in agreement with the hypothesis that 40 nucleotides of HIV-1 gag sequences might not be sufficient for efficient vector RNA packaging and this could account for the partial and not complete restoration in titres observed with pHS1nZR in the presence of Rev.
In addition, end-point titres were determined for pHS3nZ and pH6nZ with pSYNGP in HeLa and HT1180 human cell lines. In both cases titres followed the pattern observed in 293T cells, with titres being 2-3 fold lower for pHS3nZ than for pH6nZ (See FIG. 10). Finally, transduction efficiency of vector produced with pHS3nZ or pH6nZ and different amounts of pSYNGP or pGP-RRE3 at different m.o.i.'s (and as high as 1) was determined in HT1080 cells. This experiment was performed as the high level gag-pol expression from pSYNGP may result in interference by genome-empty particles at high vector concentrations. As expected for VSVG pseudotyped retroviral particles (52) transduction efficiencies correlated with the m.o.i.'s, whether high or low amounts of pSYNGP were used and with pH6nZ or pHS3nZ. For m.o.i. 1 transduction efficiency was approximately 50-60% in all cases (FIG. 18). The above data indicate that no interference due to genome-empty particles is observed in this experimental system;
The Codon Optimised gag-pol Gene does not use the Exportin-1 Nuclear Export Pathway
Rev mediates the export of unspliced and singly spliced HIV-1 mRNAs via the nuclear export receptor exportin-1 (CRM1) (68, 69, 94, 102, 103). Leptomycin B (LMB) has been shown to inhibit leucine-rich NES mediated nuclear export by disrupting the formation of the exportin-1/NES/RanGTP complex (91, 94). In particular, LMB inhibits nucleo-cytoplasmic translocation of Rev and Rev-dependent HIV mRNAs (110). To investigate whether exportin-1 mediates the export of the codon optimized gag-pol constructs, the effect of LMB on protein production was tested. Western blot analysis was performed on cell lysates from cells transfected with the gag-pol constructs (+/−pCMV-Rev) and treated or not with LMB (7.5 nM, for 20 hours, beginning treatment 5 hours post-transfection). To confirm that LMB had no global effects on transport, the expression of β-gal from the control plasmid pCMV-βGal was also measured. An actin internal control was used to account for protein variations between samples. The results are shown in FIG. 16. As expected (110), the wild type gag-pol was not expressed in the presence of LMB (compare lanes 3 and 4), whereas LMB had no effect on protein production from the codon optimized gag-pol, irrespective of the presence of the RRE in the transcript and the provision of Rev in trans (compare lanes 5 and 6, 7 and 8, 9 and 10, 11 and 12, 5-6 and 11-12). The resistance of the expression of the codon optimized gag-pol to inhibition by LMB indicates that the exportin-1 pathway is not used and therefore an alternative export pathway must be used. This offers a possible explanation for the Rev independent expression. The fact that the presence of a nonfunctional Rev/RRE interaction did not affect expression implies that the RRE does not necessarily act as an inhibitory (e.g. nuclear retention) signal per se, which is in agreement with previous observations (58, 87). In conclusion, this is the first report of an HIV-1 based vector system, composed of pSYNGP, pHS3nZ and pHCMVG, where significant vector production can be achieved in the absence of all accessory proteins. These data indicate that in order to achieve maximum titres the HIV vector genome must be configured to retain efficient packaging and that this requires the retention of gag sequences and a splice donor. By reducing the gag sequence to 360 nt in pHS3nZ and combining this with pSYNGP it is possible to achieve titre of at least 105 I.U./ml that is only 5-fold lower than the maximum levels achieved in the presence of Rev.
All publications mentioned in the above specification are herein incorporated by reference. Various modifications and variations of the described methods and system of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. Although the invention has been described in connection with specific preferred embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the invention which are obvious to those skilled in molecular biology or related fields are intended to be within the scope of the following claims.
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## Claims

1. A nucleotide sequence comprising overlapping reading frames coding for lentiviral gag and pol proteins wherein the reading frames encoding lentiviral gag and pol proteins are codon optimised for expression in mammalian producer cells.

2. The nucleotide sequence according to claim 1, wherein the gag and pol proteins are HIV proteins.

3. The nucleotide sequence according to claim 1, derived from codon optimisation of a wild type nucleotide sequence using the codon usage of FIG. 4a.

4. The nucleotide sequence according to claim 1, comprising the sequence as shown in SEQ. ID. No. 2, or comprising the sequence from nucleotide 1108 to-nucleotide 5414 as shown in SEQ. ID. No. 5.

5. A lentiviral vector system comprising:
(i) a nucleotide sequence of interest; and
(ii) a nucleotide sequence coding for lentiviral gag and pol proteins wherein the nucleotide sequence is codon optimised for expression in mammalian producer cells;
wherein the lentiviral vector system is capable of producing a lentiviral particle.

6. The system according to claim 5, wherein the nucleotide sequence of (ii) is derived from codon optimisation of a wild type nucleotide sequence using the codon usage of FIG. 4a.

7. The system according to claim 5, wherein the nucleotide sequence of (ii) comprises the sequence as shown in SEQ. ID. No. 2; or comprises the sequence from nucleotide 1108 to nucleotide 5414 as shown in SEQ. ID. No. 5.

8. The system according to claim 5, wherein the lentiviral vector is substantially derived from HIV-1.

9. The system according to claim 5, wherein the system further comprises a nucleotide sequence encoding an envelope protein.

10. The system according to claim 9, wherein the nucleotide sequence encoding the envelope protein is codon optimised.

11. The system according to claim 5, wherein the nucleotide sequence of interest is selected from a therapeutic gene, a marker gene and a selection gene.

12. The system according to claim 5, wherein the system is lacking any functional lentiviral accessory genes.

13. A pharmaceutical composition comprising the lentiviral system of claim 5, together with a pharmaceutically acceptable carrier or diluent.

14. A lentiviral production system comprising:
(i) a lentiviral genome comprising at least one nucleotide sequence of interest; and
(ii) a nucleotide sequence coding for lentiviral gag and pol proteins wherein the nucleotide sequence is codon optimised for expression in mammalian producer cells;
wherein the lentiviral vector system is capable of producing a lentiviral particle.

15. The lentviral production system according to claim 14, wherein the nucleotide sequence of (ii) is derived from codon optimisation of a wild type nucleotide sequence using the codon usage of FIG. 4a.

16. The lentiviral production system according to claim 14, wherein the nucleotide sequence of (ii) comprises the sequence as shown in SEQ. ID. No. 2; or comprises the sequence from nucleotide 1108 to nucleotide 5414 as shown in SEQ. ID. No. 5.

17. The lentiviral production system according to claim 14, wherein the lentiviral production system is from HIV-1.

18. The lentiviral production system according to claim 14, wherein the system further comprises a nucleotide sequence encoding an envelope protein.

19. The lentiviral production system according to claim 18, wherein the nucleotide sequence encoding the envelope protein is codon optimised.

20. The lentiviral production system according to claim 14, wherein the nucleotide sequence of interest is selected from a therapeutic gene, a marker gene and a selection gene.

21. The lentiviral production system according to claim 14, wherein the system is lacking any functional lentiviral accessory genes.

22. A pharmaceutical composition comprising the lentiviral system of claim 14, together with a pharmaceutically acceptable carrier or diluent.

23. A method for producing a lentiviral particle comprising introducing into a mammalian producer cell:
(i) a lentiviral genome comprising at least one nucleotide sequence of interest,
(ii) one or more nucleotide sequences coding for lentiviral gag and pol proteins wherein the nucleotide sequence is codon optimised for expression in a mammalian producer cell and,
(iii) nucleotide sequences encoding other essential lentiviral packaging components not encoded by one or more of the nucleotide sequences of (ii);
whereby a lentiviral particle is produced.

24. The method according to claim 23, wherein the lentiviral gag and pol proteins are HIV proteins.

25. The method according to claim 23, wherein the nucleotide sequence of (ii) is derived from codon optimisation of a wild type nucleotide sequence using the codon usage of FIG. 4a.

26. The method according to claim 23, wherein the nucleotide of (ii) comprises the sequence as shown in SEQ. ID. No. 2; or comprises the sequence from nucleotide 1108 to nucleotide 5414 as shown in SEQ. ID. No. 5.

27. A lentiviral rev-independent packaging vector comprising codon optimized nucleotide sequences encoding lentiviral gag and pol proteins.

28. The lentiviral rev-independent packaging vector of claim 27, that is an HIV rev-independent packaging vector.

29. A mammalian packaging cell line comprising the lentiviral rev-independent packaging vector of claim 27.

30. The packaging cell line of claim 29, wherein the lentiviral rev-independent packaging vector is an HIV rev-independent packaging vector.

31. The lentiviral production system according to claim 14, wherein the nucleotide sequence of interest is an inhibitory RNA.

32. The mammalian packaging cell line of claim 29, wherein the packaging vector is lacking any functional accessory genes.

33. The mammalian packaging cell line of claim 32, further comprising a nucleotide sequence encoding envelope protein.

34. The mammalian packaging cell line of claim 32, further comprising a nucleotide sequence of interest.

35. The mammalian packaging cell line of claim 33, further comprising a nucleotide sequence of interest.

36. The mammalian packaging cell line of claim 33, wherein the lentiviral rev-independent packaging vector is an HIV rev-independent packaging vector.

37. The mammalian packaging cell line of claim 34, wherein the lentiviral rev-independent packaging vector is an HIV rev-independent packaging vector.

38. The mammalian packaging cell line of claim 35, wherein the lentiviral rev-independent packaging vector is an HIV rev-independent packaging vector.

39. The method of claim 23, wherein lentiviral particle production is lacking any functional lentiviral accessory genes.

40. The method of claim 39, wherein lentiviral particle production is rev-independent.

41. The method of claim 40, further comprising introducing into the mammalian producer cell a nucleotide sequence encoding envelope protein.

42. The nucleotide sequence of claim 1, wherein the overlapping reading frames comprise a frameshift site that is not codon optimised.